Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 87 of 318
Found at i:29552935 original size:21 final size:21
Alignment explanation
Indices: 29552911--29552958 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
29552901 TTCTGTTCTG
* *
29552911 CTCCGCCTCCCTCGCTACTGC
1 CTCCGCCTCCCGCACTACTGC
*
29552932 CTCCGCCTCCCGCACTGCTGC
1 CTCCGCCTCCCGCACTACTGC
29552953 CTCCGC
1 CTCCGC
29552959 TCTAAGTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.58, G:0.17, T:0.21
Consensus pattern (21 bp):
CTCCGCCTCCCGCACTACTGC
Found at i:29558516 original size:9 final size:9
Alignment explanation
Indices: 29558502--29558611 Score: 96
Period size: 9 Copynumber: 11.6 Consensus size: 9
29558492 ATGTATTAGT
29558502 TAAGTTATG
1 TAAGTTATG
29558511 TAAGTTGTTATG
1 TAA---GTTATG
29558523 TACA-TTATG
1 TA-AGTTATG
29558532 TAAGTTATG
1 TAAGTTATG
*
29558541 TGAGTTATG
1 TAAGTTATG
29558550 TAAGTTGTTATG
1 TAA---GTTATG
*
29558562 TAAATTATG
1 TAAGTTATG
*
29558571 TAAGTTATA
1 TAAGTTATG
*
29558580 TGAGTTATG
1 TAAGTTATG
29558589 TAAGTTATG
1 TAAGTTATG
* *
29558598 TAATTTATT
1 TAAGTTATG
29558607 TAAGT
1 TAAGT
29558612 AATGATTAAT
Statistics
Matches: 82, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
8 1 0.01
9 63 0.77
12 17 0.21
13 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:29558536 original size:30 final size:28
Alignment explanation
Indices: 29558502--29558600 Score: 101
Period size: 30 Copynumber: 3.4 Consensus size: 28
29558492 ATGTATTAGT
*
29558502 TAAGTTATGTAAGTTGTTATGTACATTATG
1 TAAGTTATGTAAGTT-TTATGTA-GTTATG
* * *
29558532 TAAGTTATGTGAGTTATGTAAGTTGTTATG
1 TAAGTTATGTAAGTT-T-TATGTAGTTATG
* *
29558562 TAAATTATGTAAGTTATATG-AGTTATG
1 TAAGTTATGTAAGTTTTATGTAGTTATG
29558589 TAAGTTATGTAA
1 TAAGTTATGTAA
29558601 TTTATTTAAG
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
27 17 0.30
28 3 0.05
30 33 0.58
31 4 0.07
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.45
Consensus pattern (28 bp):
TAAGTTATGTAAGTTTTATGTAGTTATG
Found at i:29558547 original size:39 final size:39
Alignment explanation
Indices: 29558504--29558594 Score: 164
Period size: 39 Copynumber: 2.3 Consensus size: 39
29558494 GTATTAGTTA
* *
29558504 AGTTATGTAAGTTGTTATGTACATTATGTAAGTTATGTG
1 AGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATG
29558543 AGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATG
1 AGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATG
29558582 AGTTATGTAAGTT
1 AGTTATGTAAGTT
29558595 ATGTAATTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (39 bp):
AGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATG
Found at i:29559314 original size:10 final size:10
Alignment explanation
Indices: 29559299--29559327 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
29559289 AATAAAATTA
29559299 ATTCATACTT
1 ATTCATACTT
29559309 ATTCATACTT
1 ATTCATACTT
29559319 ATTCATACT
1 ATTCATACT
29559328 CCACTCTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTCATACTT
Found at i:29559823 original size:183 final size:182
Alignment explanation
Indices: 29559516--29559846 Score: 599
Period size: 183 Copynumber: 1.8 Consensus size: 182
29559506 CCTAGAACAG
29559516 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAACAAATATAAAACTTTATCTATA
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAACAAATATAAAACTTTATCTATA
*
29559581 TCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGGA
66 TCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAATTGAACCAATAGTTGCAGGAGGA
29559646 GCAAGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
131 GCAAGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
* *
29559698 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATTTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAACAAATAT-AAAACTTTATCTAT
* *
29559763 ATCAGTATCAAATATTAATTCGAAGATTAAATGGCAGCTTCAATTGAACTAATAGTTGCAGGAGG
65 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAATTGAACCAATAGTTGCAGGAGG
*
29559828 AGCAGGAAGCAGTAACTGA
130 AGCAAGAAGCAGTAACTGA
29559847 TGCTGAATCT
Statistics
Matches: 142, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
182 49 0.35
183 93 0.65
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAACAAATATAAAACTTTATCTATA
TCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAATTGAACCAATAGTTGCAGGAGGA
GCAAGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
Found at i:29561145 original size:148 final size:146
Alignment explanation
Indices: 29560855--29561149 Score: 554
Period size: 148 Copynumber: 2.0 Consensus size: 146
29560845 CCTTAATCAT
29560855 AAGCTTGTGGAAGTTTAAAGTAGCTTATTCCAAACATAGCAGCAACTAGCTGTTATCGACTTAAA
1 AAGCTTGTGGAAGTTTAAAGTAGCTTATTCCAAACATAGCAGCAACTAGCTGTTATCGACTTAAA
*
29560920 GGATATGCCAAAAGCTGCAATTAGATACTAATATTTTACCCTTGAGTGCATATAAATCTCCTTTT
66 GGATATGCCAAAAGCTGCAATTAGATACTAATATTTTACCCTTGAATGCATATAAATCTCCTTTT
29560985 TACAATTTATTGCATA
131 TACAATTTATTGCATA
29561001 AAGCTTGTGGAAGTTTAAAGTAGCTTATTCCAAACATAGCAGCAACTAGCTGTTATCGACTTAAA
1 AAGCTTGTGGAAGTTTAAAGTAGCTTATTCCAAACATAGCAGCAACTAGCTGTTATCGACTT-AA
*
29561066 AGGATATGCCAAAAAGCTGCAATTAGATACTAATATTTTACCCTTGAATGTATATAAATCTCCTT
65 AGGATATGCC-AAAAGCTGCAATTAGATACTAATATTTTACCCTTGAATGCATATAAATCTCCTT
29561131 TTTACAATTTATTGCATA
129 TTTACAATTTATTGCATA
29561149 A
1 A
29561150 CATTTCTGAG
Statistics
Matches: 145, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
146 62 0.43
147 12 0.08
148 71 0.49
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (146 bp):
AAGCTTGTGGAAGTTTAAAGTAGCTTATTCCAAACATAGCAGCAACTAGCTGTTATCGACTTAAA
GGATATGCCAAAAGCTGCAATTAGATACTAATATTTTACCCTTGAATGCATATAAATCTCCTTTT
TACAATTTATTGCATA
Found at i:29571958 original size:21 final size:21
Alignment explanation
Indices: 29571898--29571970 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
29571888 AAAAATATTT
*
29571898 TTTAAA-ATACTAATTACAAATA
1 TTTAAATATTCTAATT--AAATA
* *
29571920 TTT-AATAGTTATATTTAAATA
1 TTTAAATA-TTCTAATTAAATA
*
29571941 TTTAAATATTCTAATTAAATT
1 TTTAAATATTCTAATTAAATA
29571962 TTATAAATA
1 TT-TAAATA
29571971 ATTAATATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
21 22 0.54
22 14 0.34
23 5 0.12
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (21 bp):
TTTAAATATTCTAATTAAATA
Found at i:29571976 original size:21 final size:21
Alignment explanation
Indices: 29571934--29571976 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
29571924 ATAGTTATAT
*
29571934 TTAAATATTTAAATATTCTAA
1 TTAAATATTTAAATAATCTAA
*
29571955 TTAAATTTTATAAATAAT-TAA
1 TTAAATATT-TAAATAATCTAA
29571976 T
1 T
29571977 ATTTATTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAATATTTAAATAATCTAA
Found at i:29572706 original size:26 final size:25
Alignment explanation
Indices: 29572666--29572723 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
29572656 AATTTCTACA
* *
29572666 CTTTTTAAAATTAAATATGTATCAT
1 CTTTTTAAAATTAAAAATCTATCAT
*
29572691 CTTATTTAAGAA-TAAAAATCTCTCAT
1 CTT-TTTAA-AATTAAAAATCTATCAT
29572717 CTTTTTA
1 CTTTTTA
29572724 TTATGTATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.25
26 19 0.68
27 2 0.07
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (25 bp):
CTTTTTAAAATTAAAAATCTATCAT
Found at i:29575434 original size:12 final size:12
Alignment explanation
Indices: 29575417--29575446 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29575407 ATCAGGTACG
29575417 ACGCCAATGCCA
1 ACGCCAATGCCA
*
29575429 ACGCCAATGCCG
1 ACGCCAATGCCA
29575441 ACGCCA
1 ACGCCA
29575447 TATTTCCCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.43, G:0.20, T:0.07
Consensus pattern (12 bp):
ACGCCAATGCCA
Found at i:29579344 original size:14 final size:14
Alignment explanation
Indices: 29579325--29579355 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29579315 TAAAAATTAT
29579325 AAATAATAATAGTA
1 AAATAATAATAGTA
*
29579339 AAATAATAGTAGTA
1 AAATAATAATAGTA
29579353 AAA
1 AAA
29579356 GGTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (14 bp):
AAATAATAATAGTA
Found at i:29579407 original size:14 final size:14
Alignment explanation
Indices: 29579360--29579399 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
29579350 GTAAAAGGTA
*
29579360 AAAAAATAATAAAT
1 AAAATATAATAAAT
*
29579374 AAAATATGATAAAT
1 AAAATATAATAAAT
29579388 AAAATATAATAA
1 AAAATATAATAA
29579400 GTATAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (14 bp):
AAAATATAATAAAT
Found at i:29579460 original size:32 final size:30
Alignment explanation
Indices: 29579403--29579461 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
29579393 ATAATAAGTA
* **
29579403 TAATAAACTATATTTAAAATTATTAACTTT
1 TAATAAAATATATTTAAAAAAATTAACTTT
29579433 TAATAAAATATATATATAAAAAAATTAAC
1 TAATAAAATATAT-T-TAAAAAAATTAAC
29579462 ATAAATAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.50
31 1 0.04
32 11 0.46
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (30 bp):
TAATAAAATATATTTAAAAAAATTAACTTT
Found at i:29579708 original size:16 final size:16
Alignment explanation
Indices: 29579687--29579736 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 16
29579677 TGAAAATGAT
29579687 ATAATAAGTATAATAA
1 ATAATAAGTATAATAA
*
29579703 ATAAT-AGTGTAA-AA
1 ATAATAAGTATAATAA
29579717 A-AATAA-TATAATAA
1 ATAATAAGTATAATAA
29579731 ATAATA
1 ATAATA
29579737 GGAAAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 7 0.24
14 7 0.24
15 10 0.34
16 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
ATAATAAGTATAATAA
Found at i:29581195 original size:135 final size:134
Alignment explanation
Indices: 29580962--29581450 Score: 714
Period size: 135 Copynumber: 3.6 Consensus size: 134
29580952 GATCTGCTGT
* * ** **
29580962 AATTTAATCTGCTTTACTCCTGCTCAGTAAAGATAAGATCTGGTACGTTTAGCCTGCTCCACTCC
1 AATTTGATCTGCTTCACTCCTGCTCAGCGAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCC
* ** *
29581027 TGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
66 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
29581092 ATCAA
131 A-CAA
**
29581097 AATTTGATCTGCTTTGCTCCTGCTCAGCGAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCC
1 AATTTGATCTGCTTCACTCCTGCTCAGCGAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCC
* * *
29581162 TGCTTAGTGAAGATAAGACTGGTGGCTGAAATCTGCTCCATTGCCAATACATGGAGATAAGATTC
66 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
29581227 ACCAA
131 A-CAA
* * *
29581232 AATTTGATCTGCTCCACTCCTGCTCAGCGAAGATAAGATTTAGTATA--TAGCCTGCTCCACTCC
1 AATTTGATCTGCTTCACTCCTGCTCAGCGAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCC
*
29581295 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCTGATACATGGAGATAAGACTT
66 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGA-TT
29581360 GC-CAA
130 -CACAA
* ** *
29581365 AATTTGATTTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCC
1 AATTTGATCTGCTTCACTCCTGCTCAGCGAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCC
29581430 TGCTCAGTGAAGATAAGGCTG
66 TGCTCAGTGAAGATAAGGCTG
29581451 ATGATATTTA
Statistics
Matches: 320, Mismatches: 30, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
133 117 0.37
134 2 0.01
135 201 0.63
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (134 bp):
AATTTGATCTGCTTCACTCCTGCTCAGCGAAGATAAGATCTGGTATATTTAGCCTGCTCCACTCC
TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGATTC
ACAA
Found at i:29584519 original size:33 final size:33
Alignment explanation
Indices: 29584482--29584568 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
29584472 TCCACCCATG
* *
29584482 TACTCAACTCCTCCAGAGC-CGTATCCACCGCCA
1 TACTCTACTCCTCCAG-GCTCATATCCACCGCCA
* * *
29584515 TACTCTACTTCTCCCGGCTCATATCCATCGCCA
1 TACTCTACTCCTCCAGGCTCATATCCACCGCCA
*
29584548 TATTCTACTCCTCTCA-GCTCA
1 TACTCTACTCCTC-CAGGCTCA
29584569 AGTTCATAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
32 2 0.05
33 41 0.93
34 1 0.02
ACGTcount: A:0.21, C:0.43, G:0.09, T:0.28
Consensus pattern (33 bp):
TACTCTACTCCTCCAGGCTCATATCCACCGCCA
Found at i:29586098 original size:18 final size:18
Alignment explanation
Indices: 29586075--29586143 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
29586065 GAACGATTAT
*
29586075 TTATTCAATAACAGTCAG
1 TTATTCAATAACAATCAG
** *
29586093 TTATTCGGTAACAATCAA
1 TTATTCAATAACAATCAG
*
29586111 TTATTCAATAATAATCAG
1 TTATTCAATAACAATCAG
* *
29586129 TTATTTAGTAACAAT
1 TTATTCAATAACAAT
29586144 TAAATTATTC
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.38
Consensus pattern (18 bp):
TTATTCAATAACAATCAG
Found at i:29586116 original size:36 final size:37
Alignment explanation
Indices: 29586075--29586163 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 37
29586065 GAACGATTAT
* *
29586075 TTATTCAATAACAGTCAGTTATTCGGTAACAA-TCAA
1 TTATTCAATAACAGTCAGTTATTCAGTAACAATTAAA
* * *
29586111 TTATTCAATAATAATCAGTTATTTAGTAACAATTAAA
1 TTATTCAATAACAGTCAGTTATTCAGTAACAATTAAA
*
29586148 TTATTCAGTAACAGTC
1 TTATTCAATAACAGTC
29586164 GATCTTTCCA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 28 0.64
37 16 0.36
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (37 bp):
TTATTCAATAACAGTCAGTTATTCAGTAACAATTAAA
Found at i:29586357 original size:47 final size:47
Alignment explanation
Indices: 29586288--29586394 Score: 160
Period size: 47 Copynumber: 2.3 Consensus size: 47
29586278 CAGTAACAGT
* * *
29586288 AACAGTAGCAATACGGTACACAGAGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
* **
29586335 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAATAAATTTGA
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
29586382 AACAGTAACAGTA
1 AACAGTAACAGTA
29586395 ACAGTAACAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:29586395 original size:53 final size:49
Alignment explanation
Indices: 29586281--29586400 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 49
29586271 GCCGAAACAG
* *
29586281 TAACAGTAACAGTAGCAATACGGTACACAGAGTACCTCATCGGAACAAA
1 TAACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAA
* * *
29586330 T--CCGGAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAATAAA
1 TAACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAA
29586377 TTTGAAACAGTAACAGTAACAGTA
1 --T--AACAGTAACAGTAACAGTA
29586401 ACAATATCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
47 41 0.71
49 2 0.03
53 15 0.26
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (49 bp):
TAACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAA
Found at i:29586613 original size:20 final size:20
Alignment explanation
Indices: 29586576--29586612 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29586566 TTTTCAGTTT
29586576 TTAATTAATTCATATTTTAA
1 TTAATTAATTCATATTTTAA
29586596 TTAATTAATT-ATATTTT
1 TTAATTAATTCATATTTT
29586613 TTTTCAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATTAATTCATATTTTAA
Found at i:29586621 original size:20 final size:20
Alignment explanation
Indices: 29586573--29586621 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
29586563 CACTTTTCAG
29586573 TTTTTAATTAATTCATATTT
1 TTTTTAATTAATTCATATTT
**
29586593 TAATTAATTAATT-ATATTT
1 TTTTTAATTAATTCATATTT
29586612 TTTTTCAATT
1 TTTTT-AATT
29586622 CAATATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTAATTAATTCATATTT
Found at i:29587168 original size:15 final size:17
Alignment explanation
Indices: 29587137--29587168 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
29587127 ATATATATAT
29587137 AATATGTTAACTTAATA
1 AATATGTTAACTTAATA
29587154 AATAT-TTAA-TTAATA
1 AATATGTTAACTTAATA
29587169 TCAAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
AATATGTTAACTTAATA
Found at i:29587679 original size:22 final size:24
Alignment explanation
Indices: 29587640--29587686 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
29587630 TGTATTACAA
29587640 ATGTATATACATTATTTATCACAC
1 ATGTATATACATTATTTATCACAC
*
29587664 ATGTATA-ATATT-TTTATCACAC
1 ATGTATATACATTATTTATCACAC
29587686 A
1 A
29587687 CTTGGCACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 4 0.18
24 7 0.32
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (24 bp):
ATGTATATACATTATTTATCACAC
Found at i:29595830 original size:241 final size:241
Alignment explanation
Indices: 29595407--29595893 Score: 884
Period size: 241 Copynumber: 2.0 Consensus size: 241
29595397 ATGAATTAAT
29595407 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
* *
29595472 ATTTTAAAAATTTTAAAGATTCAAAGTATATGGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAAAATTTTAAAGATTCAAAGTATATAGGCTGCAAACCTGACGGGTTGCCTTATATCGAG
29595537 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTACGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTACGATGAATCTTAAAAAATTC
*
29595602 AAAAAGACTTGGAAAAAGTTCTATCGATCTCATTTACTATTGAATA
196 AAAAAGACTTGGAAAAAGTTCTATCAATCTCATTTACTATTGAATA
*
29595648 TTTATTACCATGTAGCTTGCTTGTTCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
* *
29595713 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGTTGCAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAAAATTTTAAAGATTCAAAGTATATAGGCTGCAAACCTGACGGGTTGCCTTATATCGAG
* * *
29595778 CTGTAAGATATAATGGATCCTCCCTATGTGTAACAACGCTACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTACGATGAATCTTAAAAAATTC
*
29595843 AAAAAGACTTGGAAAAAGTTCTATCAATCTCATTTACTATTGAATG
196 AAAAAGACTTGGAAAAAGTTCTATCAATCTCATTTACTATTGAATA
29595889 TTTAT
1 TTTAT
29595894 ATAACCTTAA
Statistics
Matches: 236, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
241 236 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (241 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
ATTTTAAAAATTTTAAAGATTCAAAGTATATAGGCTGCAAACCTGACGGGTTGCCTTATATCGAG
CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTACGATGAATCTTAAAAAATTC
AAAAAGACTTGGAAAAAGTTCTATCAATCTCATTTACTATTGAATA
Found at i:29596097 original size:9 final size:9
Alignment explanation
Indices: 29596074--29596240 Score: 154
Period size: 9 Copynumber: 17.6 Consensus size: 9
29596064 ATTGATCATT
*
29596074 ACTTAAATA
1 ACTTACATA
*
29596083 AATTACATA
1 ACTTACATA
29596092 ACTTACATA
1 ACTTACATA
* *
29596101 ACTCATATA
1 ACTTACATA
29596110 ACTTACATA
1 ACTTACATA
*
29596119 ATTTACATAACA
1 ACTTACAT---A
29596131 ACTTACATA
1 ACTTACATA
*
29596140 ACTCACATA
1 ACTTACATA
29596149 ACTTACATA
1 ACTTACATA
*
29596158 ATTTACATAACA
1 ACTTACAT---A
29596170 ACTTACATA
1 ACTTACATA
*
29596179 ACTCACATA
1 ACTTACATA
29596188 ACTTACATA
1 ACTTACATA
*
29596197 ATTTACATA
1 ACTTACATA
*
29596206 ACTCACATA
1 ACTTACATA
*
29596215 ACGTACATAACA
1 ACTTACAT---A
29596227 ACTTACATA
1 ACTTACATA
29596236 ACTTA
1 ACTTA
29596241 ACTAATACAT
Statistics
Matches: 128, Mismatches: 21, Indels: 18
0.77 0.13 0.11
Matches are distributed among these distances:
9 104 0.81
12 24 0.19
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:29596143 original size:39 final size:39
Alignment explanation
Indices: 29596091--29596207 Score: 225
Period size: 39 Copynumber: 3.0 Consensus size: 39
29596081 TAAATTACAT
*
29596091 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
29596130 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
29596169 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
29596208 TCACATAACG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:29596164 original size:48 final size:47
Alignment explanation
Indices: 29596085--29596240 Score: 186
Period size: 48 Copynumber: 3.3 Consensus size: 47
29596075 CTTAAATAAA
* * *
29596085 TTACATAACTTACATAACTCATATAACTTACATAATTTACATAACAAC
1 TTACATAACTTACATAACTTACATAACTTACATAA-CTACATAACAAC
* * * * *
29596133 TTACATAACTCACATAACTTACATAATTTACATAACAACTTACATAAC
1 TTACATAACTTACATAACTTACATAACTTACATAACTACATA-ACAAC
* * *
29596181 TCACATAACTTACATAATTTACATAACTCACATAACGTACATAACAAC
1 TTACATAACTTACATAACTTACATAACTTACATAAC-TACATAACAAC
29596229 TTACATAACTTA
1 TTACATAACTTA
29596241 ACTAATACAT
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
47 4 0.04
48 81 0.91
49 4 0.04
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (47 bp):
TTACATAACTTACATAACTTACATAACTTACATAACTACATAACAAC
Found at i:29596226 original size:57 final size:57
Alignment explanation
Indices: 29596074--29596238 Score: 192
Period size: 57 Copynumber: 2.9 Consensus size: 57
29596064 ATTGATCATT
* * * *
29596074 ACTTAAATAAATTACATAACTTACATAACT-CAT-ATAACTTACATAATTTACATAACA
1 ACTTACATAAATTACATAACTTACATAACTACATAACAACTTACATAACTCACAT-A-A
* * *
29596131 ACTTACATAACTCACATAACTTACATAATTTACATAACAACTTACATAACTCACAT-A
1 ACTTACATAAATTACATAACTTACATAA-CTACATAACAACTTACATAACTCACATAA
* *
29596188 ACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACTTACATAAATTACATAACTTACATAAC-TACATAACAACTTACATAACT
29596239 TAACTAATAC
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
57 72 0.77
58 1 0.01
59 3 0.03
60 17 0.18
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.31
Consensus pattern (57 bp):
ACTTACATAAATTACATAACTTACATAACTACATAACAACTTACATAACTCACATAA
Found at i:29596236 original size:39 final size:37
Alignment explanation
Indices: 29596074--29596225 Score: 202
Period size: 39 Copynumber: 4.1 Consensus size: 37
29596064 ATTGATCATT
* * *
29596074 ACTTAAATAAATTACAT-AACTTACATAACTCATATA
1 ACTTACATAATTTACATAAACTTACATAACTCACATA
29596110 ACTTACATAATTTACATAACAACTTACATAACTCACATA
1 ACTTACATAATTTACAT-A-AACTTACATAACTCACATA
29596149 ACTTACATAATTTACATAACAACTTACATAACTCACATA
1 ACTTACATAATTTACAT-A-AACTTACATAACTCACATA
*
29596188 ACTTACATAATTTACAT-AACTCACATAACGT-ACATA
1 ACTTACATAATTTACATAAACTTACATAAC-TCACATA
29596224 AC
1 AC
29596226 AACTTACATA
Statistics
Matches: 108, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
36 33 0.31
37 1 0.01
39 74 0.69
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.31
Consensus pattern (37 bp):
ACTTACATAATTTACATAAACTTACATAACTCACATA
Found at i:29602176 original size:43 final size:43
Alignment explanation
Indices: 29602110--29602333 Score: 290
Period size: 43 Copynumber: 5.3 Consensus size: 43
29602100 ACTGGGCAAA
*
29602110 TTAGCGGCGTTTTTTAAAAAAGCGCTGCTAAAAGTCCTGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT
* * * * *
29602153 TTAGCGACGTTTTTTATATAAGCGTCGCTATAAGTCCTGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT
* * * * *
29602196 TTAGCAGCG-TTTTTAAAAAAGCACAGCTAAAAGTCCTAGTCA
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT
*
29602238 CTAGCGGCGTTTTTT-AAAAAGCGCCGCTAAAAGTCCTGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT
* * * *
29602280 TTAGCGGCGTTTTTTATATAAGCGCCGCTATAAGTCCTAGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT
29602323 TTAGCGGCGTT
1 TTAGCGGCGTT
29602334 ACATATAGCA
Statistics
Matches: 152, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
42 69 0.45
43 83 0.55
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCTGGTCT
Found at i:29602294 original size:85 final size:86
Alignment explanation
Indices: 29602110--29602333 Score: 308
Period size: 85 Copynumber: 2.6 Consensus size: 86
29602100 ACTGGGCAAA
* * * *
29602110 TTAGCGGCGTTTTTTAAAAAAGCGCTGCTAAAAGTCCTGGTCTTTAGCGACGTTTTTTATATAAG
1 TTAGCGGCGTTTTTTAAAAAAGCGCAGCTAAAAGTCCTAGTCTTTAGCGGCGTTTTTTATAAAAG
* *
29602175 CGTCGCTATAAGTCCTGGTCT
66 CGCCGCTAAAAGTCCTGGTCT
* * **
29602196 TTAGCAGCG-TTTTTAAAAAAGCACAGCTAAAAGTCCTAGTCACTAGCGGCGTTTTTTA-AAAAG
1 TTAGCGGCGTTTTTTAAAAAAGCGCAGCTAAAAGTCCTAGTCTTTAGCGGCGTTTTTTATAAAAG
29602259 CGCCGCTAAAAGTCCTGGTCT
66 CGCCGCTAAAAGTCCTGGTCT
* * * *
29602280 TTAGCGGCGTTTTTTATATAAGCGCCGCTATAAGTCCTAGTCTTTAGCGGCGTT
1 TTAGCGGCGTTTTTTAAAAAAGCGCAGCTAAAAGTCCTAGTCTTTAGCGGCGTT
29602334 ACATATAGCA
Statistics
Matches: 119, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
84 31 0.26
85 80 0.67
86 8 0.07
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (86 bp):
TTAGCGGCGTTTTTTAAAAAAGCGCAGCTAAAAGTCCTAGTCTTTAGCGGCGTTTTTTATAAAAG
CGCCGCTAAAAGTCCTGGTCT
Found at i:29603225 original size:27 final size:27
Alignment explanation
Indices: 29603195--29603251 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
29603185 CCTACCAAGA
*
29603195 AGGCACAACTAGACGTGCCTGTCAGAT
1 AGGCACAACTAGACGAGCCTGTCAGAT
* **
29603222 AGGCTCAACTAGTTGAGCCTGTCAGAT
1 AGGCACAACTAGACGAGCCTGTCAGAT
29603249 AGG
1 AGG
29603252 TGCAAAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (27 bp):
AGGCACAACTAGACGAGCCTGTCAGAT
Found at i:29611096 original size:35 final size:35
Alignment explanation
Indices: 29611005--29611171 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
29610995 CATGGCAAAG
*
29611005 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
*
29611040 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
29611075 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGT
** * * *
29611115 TAAGAAATATAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGT
**
29611150 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
29611172 TCAATGAGGA
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 81 0.71
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 28 0.25
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
Found at i:29611128 original size:75 final size:75
Alignment explanation
Indices: 29611005--29611175 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
29610995 CATGGCAAAG
** * *
29611005 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATT-TC
*
29611064 CCATACTGAGC
65 CCATACCGAGC
29611075 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATTTCC
*
29611140 CATACCGAGT
66 CATACCGAGC
**
29611150 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
29611176 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATATAGGTATGGCATTTCC
CATACCGAGC
Found at i:29615187 original size:25 final size:25
Alignment explanation
Indices: 29615159--29615217 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
29615149 CTTATCCCAG
* *
29615159 TTAAACTTTGTTTTTACTTTC-CTAC
1 TTAAACTCTATTTTTACTTTCAC-AC
*
29615184 TTAAACTCTATTTTTAGTTTCACAC
1 TTAAACTCTATTTTTACTTTCACAC
29615209 TTAAACTCT
1 TTAAACTCT
29615218 GATAAGTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 29 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.03, T:0.51
Consensus pattern (25 bp):
TTAAACTCTATTTTTACTTTCACAC
Found at i:29617605 original size:36 final size:36
Alignment explanation
Indices: 29617514--29617598 Score: 152
Period size: 36 Copynumber: 2.4 Consensus size: 36
29617504 TGGAAAATGG
29617514 ATTTAGCCCGGACGGGTAATCCGAATTAGGGTCTGA
1 ATTTAGCCCGGACGGGTAATCCGAATTAGGGTCTGA
*
29617550 ATTTAGCCCGGACGGGTAATCTGAATTAGGGTCTGA
1 ATTTAGCCCGGACGGGTAATCCGAATTAGGGTCTGA
*
29617586 ATTTAGCCTGGAC
1 ATTTAGCCCGGAC
29617599 TAGTAATTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (36 bp):
ATTTAGCCCGGACGGGTAATCCGAATTAGGGTCTGA
Found at i:29617807 original size:46 final size:46
Alignment explanation
Indices: 29617755--29618208 Score: 531
Period size: 46 Copynumber: 9.8 Consensus size: 46
29617745 AGTGTGCTCT
*
29617755 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGGAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
** *
29617801 CTGATATAAAAT-ATGTAAGACCATGGTTGAAACATACCATGGCAAC
1 CTGATATGGAATGA-GTAAGACCATGGTTGAAAGATACCATGGCAAC
*
29617847 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGGAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** *
29617893 ATGA-CGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGG--AATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
29617940 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGGAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
29617986 GTGATATGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGGAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
29618032 CTGACATGAAATGAGTAAAACCATGGCTGAAAGATACCATGGCAAC
1 CTGATATGGAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
29618078 ATGATA-GGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGG--AATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** *
29618125 ATGA-CGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGG--AATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
29618172 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-GAATGAGTAAGACCATGGTTGAAAGATAC
29618209 TATGACATCA
Statistics
Matches: 359, Mismatches: 39, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
45 2 0.01
46 232 0.65
47 124 0.35
48 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
CTGATATGGAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:29618020 original size:139 final size:138
Alignment explanation
Indices: 29617764--29618208 Score: 624
Period size: 139 Copynumber: 3.2 Consensus size: 138
29617754 TCTGATATGG
* * * * *
29617764 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATATGTAAGACCATGGTT
1 AATGAGTAAAACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTT
* * * *
29617829 GAAACATACCATGGCAACCTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
66 GAAAGATACCATGGCAACATGATATGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
*
29617894 TGACGGGAA
131 TGAC-AGAA
* * *
29617903 AATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGTGTAAGACCATGGTT
1 AATGAGTAAAACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTT
* *
29617968 GAAAGATACCATGGCAACGTGATATGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAACC
66 GAAAGATACCATGGCAACATGATATGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
29618033 TGACATG-A
131 TGACA-GAA
* * **
29618041 AATGAGTAAAACCATGGCTGAAAGATACCATGGCAACATGATAGGAAAATGAATAAGACCATGGT
1 AATGAGTAAAACCATGGTTGAAAGATACCATGGCAACATGATATG-AAATGTGTAAGACCATGGT
**
29618106 TGAAAGATACCATGGCAACATGA-CGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCA
65 TGAAAGATACCATGGCAACATGATATGG--AATGAATAAGACCATGGTTGAAAGATACCATGGCA
29618170 ACATGACAGAA
128 ACATGACAGAA
* *
29618181 AACGAGTAAAACCATAGTTGAAAGATAC
1 AATGAGTAAAACCATGGTTGAAAGATAC
29618209 TATGACATCA
Statistics
Matches: 276, Mismatches: 25, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
138 43 0.16
139 165 0.60
140 68 0.25
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (138 bp):
AATGAGTAAAACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTT
GAAAGATACCATGGCAACATGATATGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
TGACAGAA
Found at i:29618068 original size:185 final size:185
Alignment explanation
Indices: 29617756--29618171 Score: 654
Period size: 185 Copynumber: 2.2 Consensus size: 185
29617746 GTGTGCTCTC
* *
29617756 TGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATATGTAAGA
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATATATAAGA
* * *
29617821 CCATGGTTGAAACATACCATGGCAACCTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCA
66 CCATGGTTGAAACATACCATGGCAACCTGACATGAAATGAGTAAAACCATGGCTGAAAGATACCA
* *
29617886 TGGCAACATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
131 TGGCAACATGACAGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* **
29617941 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGGAATGA-ATAAG
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT-ATATAAG
*
29618005 ACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGAGTAAAACCATGGCTGAAAGATACC
65 ACCATGGTTGAAACATACCATGGCAACCTGACATGAAATGAGTAAAACCATGGCTGAAAGATACC
*
29618070 ATGGCAACATGATAGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
130 ATGGCAACATGACAGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
*** **
29618126 TGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 TGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
29618172 ATGACAGAAA
Statistics
Matches: 212, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
185 175 0.83
186 37 0.17
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (185 bp):
TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATATATAAGA
CCATGGTTGAAACATACCATGGCAACCTGACATGAAATGAGTAAAACCATGGCTGAAAGATACCA
TGGCAACATGACAGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:29623495 original size:24 final size:23
Alignment explanation
Indices: 29623452--29623497 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
29623442 AGAAATTTTA
**
29623452 ATCAGGAAGCTCACGTAGAGCCT
1 ATCAGGAAGCTCACAAAGAGCCT
29623475 ATCAGGAATGCTCACAAAGAGCC
1 ATCAGGAA-GCTCACAAAGAGCC
29623498 ATGTAACAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (23 bp):
ATCAGGAAGCTCACAAAGAGCCT
Found at i:29624855 original size:28 final size:29
Alignment explanation
Indices: 29624824--29624901 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 29
29624814 TATTATTATT
*
29624824 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
29624852 TATATTATTAAATTAATTACATTATAAA-
1 TATATAAATAAATAAATTACATTATAAAG
*
29624880 TATTATATTAAGAAATAAATTA
1 TA-TATA--AATAAATAAATTA
29624902 AATAAAGACA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
28 17 0.45
29 11 0.29
31 10 0.26
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:29624901 original size:31 final size:28
Alignment explanation
Indices: 29624835--29624902 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
29624825 ATATAAATAT
**
29624835 ATAAATTAATTATAAAGTATATTATTAA
1 ATAAATTAATTATAAAGTATATTAAGAA
* *
29624863 ATTAATTACATTATAAATATTATATTAAGAA
1 ATAAATTA-ATTAT-AA-AGTATATTAAGAA
29624894 ATAAATTAA
1 ATAAATTAA
29624903 ATAAAGACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 5 0.16
30 3 0.09
31 17 0.53
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
ATAAATTAATTATAAAGTATATTAAGAA
Found at i:29625065 original size:20 final size:19
Alignment explanation
Indices: 29625033--29625071 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
29625023 TAAATAAAAG
*
29625033 GAAATAAAAAGAAAAGAAA
1 GAAACAAAAAGAAAAGAAA
29625052 GAAACAAAACAGAAAAGAAA
1 GAAACAAAA-AGAAAAGAAA
29625072 CAGAATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (19 bp):
GAAACAAAAAGAAAAGAAA
Found at i:29625123 original size:11 final size:11
Alignment explanation
Indices: 29625107--29625132 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29625097 AGAAAGAGAC
29625107 GAAACAGGGGA
1 GAAACAGGGGA
29625118 GAAACAGGGGA
1 GAAACAGGGGA
29625129 GAAA
1 GAAA
29625133 GAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:29625797 original size:3 final size:3
Alignment explanation
Indices: 29625789--29625820 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29625779 GTGAGGTAAG
29625789 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29625821 GTAGTAGTAG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29632341 original size:31 final size:28
Alignment explanation
Indices: 29632275--29632342 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
29632265 TTATAAATAT
**
29632275 ATAAATTAATTATAAAGTATATTATTAA
1 ATAAATTAATTATAAAGTATATTAAGAA
* *
29632303 ATTAATTACATTATAAATATTATATTAAGAA
1 ATAAATTA-ATTAT-AA-AGTATATTAAGAA
29632334 ATAAATTAA
1 ATAAATTAA
29632343 ATAAAGACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 5 0.16
30 3 0.09
31 17 0.53
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
ATAAATTAATTATAAAGTATATTAAGAA
Found at i:29632513 original size:16 final size:15
Alignment explanation
Indices: 29632468--29632514 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
29632458 GTAATTAAAT
* *
29632468 AAAAGGAAATAGAAAG
1 AAAAAGAAA-AGAAAC
29632484 AAAAAG-AAAGAAAC
1 AAAAAGAAAAGAAAC
29632498 AAAACAGAAAAGAAAC
1 AAAA-AGAAAAGAAAC
29632514 A
1 A
29632515 GAATAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 9 0.33
15 4 0.15
16 14 0.52
ACGTcount: A:0.74, C:0.06, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAGAAAC
Found at i:29632523 original size:16 final size:16
Alignment explanation
Indices: 29632473--29632514 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
29632463 TAAATAAAAG
*
29632473 GAAATAGAAAGAAAA-A
1 GAAA-AGAAACAAAACA
29632489 G-AAAGAAACAAAACA
1 GAAAAGAAACAAAACA
29632504 GAAAAGAAACA
1 GAAAAGAAACA
29632515 GAATAGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 9 0.39
15 4 0.17
16 10 0.43
ACGTcount: A:0.74, C:0.07, G:0.17, T:0.02
Consensus pattern (16 bp):
GAAAAGAAACAAAACA
Found at i:29633233 original size:3 final size:3
Alignment explanation
Indices: 29633225--29633256 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29633215 GTGAGGTAAG
29633225 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29633257 GTAGTAGTAG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29633261 original size:3 final size:3
Alignment explanation
Indices: 29633255--29633279 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29633245 TTATTATTAT
29633255 TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG T
29633280 GGGAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TAG
Found at i:29634138 original size:20 final size:20
Alignment explanation
Indices: 29634113--29634164 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
29634103 TTCAACATAA
29634113 TTTTGGTGATGTATATTTTC
1 TTTTGGTGATGTATATTTTC
29634133 TTTTGGTGATGTATATTTTC
1 TTTTGGTGATGTATATTTTC
*
29634153 TTTTGGTAATGT
1 TTTTGGTGATGT
29634165 GGCATGTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.04, G:0.21, T:0.60
Consensus pattern (20 bp):
TTTTGGTGATGTATATTTTC
Found at i:29635084 original size:8 final size:8
Alignment explanation
Indices: 29635071--29635096 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
29635061 ATACGAAAAT
29635071 AATAATAA
1 AATAATAA
29635079 AATAATAA
1 AATAATAA
29635087 AATAATAA
1 AATAATAA
29635095 AA
1 AA
29635097 AAAAACATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AATAATAA
Found at i:29636149 original size:15 final size:15
Alignment explanation
Indices: 29636107--29636150 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 15
29636097 TTTTACATGA
29636107 TATTTTAAATTAC--
1 TATTTTAAATTACTT
*
29636120 T-TTTTAAGTTA-TT
1 TATTTTAAATTACTT
29636133 TATTTTAAATTACTT
1 TATTTTAAATTACTT
29636148 TAT
1 TAT
29636151 ATATTCTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 9 0.36
13 2 0.08
14 9 0.36
15 5 0.20
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (15 bp):
TATTTTAAATTACTT
Found at i:29636300 original size:29 final size:29
Alignment explanation
Indices: 29636231--29636300 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
29636221 AAATTGTTAT
* *
29636231 TTACTGTATTTATTTTAAAACTCGTTTTTA
1 TTACT-TATTTATTTTAAAAATCGTTTTGA
29636261 TATA-TTATTTA-TTTAAAAATCGTTTTGA
1 T-TACTTATTTATTTTAAAAATCGTTTTGA
29636289 TTACTTACTTTA
1 TTACTTA-TTTA
29636301 AATTGTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 2 0.06
28 19 0.54
29 10 0.29
30 2 0.06
31 2 0.06
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.56
Consensus pattern (29 bp):
TTACTTATTTATTTTAAAAATCGTTTTGA
Found at i:29636439 original size:33 final size:32
Alignment explanation
Indices: 29636378--29636440 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
29636368 TAAGATTCTT
*
29636378 TATATTATTTATTTCACACTTTTATATATACA
1 TATATTATTTATTTAACACTTTTATATATACA
* *
29636410 TATATTATTTATTTTAATATTTTTATATATA
1 TATATTATTTA-TTTAACACTTTTATATATA
29636441 ATCCTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (32 bp):
TATATTATTTATTTAACACTTTTATATATACA
Found at i:29641538 original size:7 final size:7
Alignment explanation
Indices: 29641504--29641529 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29641494 TATTTATATT
29641504 ATTTATA
1 ATTTATA
29641511 ATTTATA
1 ATTTATA
29641518 ATTTATA
1 ATTTATA
29641525 ATTTA
1 ATTTA
29641530 ATTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTATA
Found at i:29645281 original size:15 final size:15
Alignment explanation
Indices: 29645254--29645312 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
29645244 TTATTATTTT
29645254 TATATTAATATTAATA
1 TATATT-ATATTAATA
*
29645270 TATATTATATTATAATT
1 TATATTATA-T-TAATA
* *
29645287 TATATAATTTTAATA
1 TATATTATATTAATA
*
29645302 TGTATTATATT
1 TATATTATATT
29645313 TCGATATATG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 15 0.44
16 8 0.24
17 11 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TATATTATATTAATA
Found at i:29645285 original size:17 final size:17
Alignment explanation
Indices: 29645265--29645312 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
29645255 ATATTAATAT
29645265 TAATATATATTATATTA
1 TAATATATATTATATTA
* *
29645282 TAATTTATA-TA-ATTT
1 TAATATATATTATATTA
*
29645297 TAATATGTATTATATT
1 TAATATATATTATATT
29645313 TCGATATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 10 0.40
16 4 0.16
17 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TAATATATATTATATTA
Found at i:29645300 original size:32 final size:31
Alignment explanation
Indices: 29645236--29645312 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
29645226 TAATGTATAA
*
29645236 AATATTATT-TATTATTTTTATATTAATATT
1 AATATTATTATATTATATTTATATTAATATT
*
29645266 AATATATATTATATTATAATTTATA-TAATTTT
1 AATAT-TATTATATTAT-ATTTATATTAATATT
29645298 AATATGTATTATATT
1 AATAT-TATTATATT
29645313 TCGATATATG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
30 5 0.12
31 4 0.10
32 26 0.63
33 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (31 bp):
AATATTATTATATTATATTTATATTAATATT
Found at i:29646006 original size:9 final size:9
Alignment explanation
Indices: 29645994--29646081 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
29645984 ATAAAAATGC
29645994 AAAAATTAT
1 AAAAATTAT
29646003 AAAAA-TAT
1 AAAAATTAT
* * * *
29646011 TATAATGAC
1 AAAAATTAT
*
29646020 AAAATTTTAT
1 AAAA-ATTAT
*
29646030 ATAAATTAT
1 AAAAATTAT
* *
29646039 ATAATTTAT
1 AAAAATTAT
29646048 GAAAAATTAT
1 -AAAAATTAT
29646058 AAAAA-TAT
1 AAAAATTAT
*
29646066 AAGAATTAT
1 AAAAATTAT
29646075 GAAAAAT
1 -AAAAAT
29646082 ATTTTATAAT
Statistics
Matches: 58, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
8 13 0.22
9 28 0.48
10 17 0.29
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29646066 original size:27 final size:26
Alignment explanation
Indices: 29645994--29646081 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 26
29645984 ATAAAAATGC
*
29645994 AAAAATTATAAAAATAT-T-ATAATG
1 AAAAATTATAAAAATATATAATTATG
*
29646018 ACAAAATTTTATATAAATTATATAATTTATG
1 A-AAAA--TTATA-AAAATATATAA-TTATG
*
29646049 AAAAATTATAAAAATATAAGAATTATG
1 AAAAATTATAAAAATAT-ATAATTATG
29646076 AAAAAT
1 AAAAAT
29646082 ATTTTATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
24 1 0.02
25 4 0.08
27 22 0.42
28 14 0.27
29 1 0.02
30 5 0.10
31 5 0.10
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (26 bp):
AAAAATTATAAAAATATATAATTATG
Found at i:29646133 original size:25 final size:26
Alignment explanation
Indices: 29646096--29646145 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
29646086 TATAATACAG
*
29646096 AAAATTAATAAAACATTT-TAAAAAT
1 AAAATTAACAAAACATTTATAAAAAT
* *
29646121 AAAATTTACAAAATATTTATAAAAA
1 AAAATTAACAAAACATTTATAAAAA
29646146 GCACAAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAATTAACAAAACATTTATAAAAAT
Found at i:29646695 original size:18 final size:18
Alignment explanation
Indices: 29646645--29646702 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 18
29646635 TATATTGTCA
29646645 TTTATAATTTTCTATATTT
1 TTTA-AATTTTCTATATTT
* *
29646664 TTGTGCACTTTTCTATATTT
1 TT-T-AAATTTTCTATATTT
29646684 TTTAAATTTTCTAT-TTT
1 TTTAAATTTTCTATATTT
29646701 TT
1 TT
29646703 ATGATCTCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 5 0.15
18 9 0.27
19 3 0.09
20 16 0.48
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTAAATTTTCTATATTT
Found at i:29648988 original size:21 final size:21
Alignment explanation
Indices: 29648964--29649003 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29648954 TAAAACCCTA
29648964 ATTTATCCTTTCTTTCTTTCC
1 ATTTATCCTTTCTTTCTTTCC
* *
29648985 ATTTTTCTTTTCTTTCTTT
1 ATTTATCCTTTCTTTCTTT
29649004 TTCTCCCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTATCCTTTCTTTCTTTCC
Found at i:29653978 original size:29 final size:30
Alignment explanation
Indices: 29653913--29653979 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
29653903 TTTTAATTTT
* *
29653913 ATTTGATTCATTTTAATAGTATAATAACTA
1 ATTTGATCCATTTTAATAGTAGAATAACTA
** *
29653943 AAGTGATCCA-TTTAATAGTAGAATGACTA
1 ATTTGATCCATTTTAATAGTAGAATAACTA
29653972 ATTTGATC
1 ATTTGATC
29653980 AGGTCCATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (30 bp):
ATTTGATCCATTTTAATAGTAGAATAACTA
Found at i:29654828 original size:30 final size:30
Alignment explanation
Indices: 29654786--29654860 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
29654776 TATACTTTTG
*
29654786 TTATATCCAAATAAGCCCTTACTC-TTTAA
1 TTATATCCAAATAAGCCCTTAATCTTTTAA
*
29654815 TTGATATTCAAATAAGCCCTTAATCTTTTAA
1 TT-ATATCCAAATAAGCCCTTAATCTTTTAA
*
29654846 TTATATCCAATTAAG
1 TTATATCCAAATAAG
29654861 TTATTATGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.05
30 31 0.77
31 7 0.17
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (30 bp):
TTATATCCAAATAAGCCCTTAATCTTTTAA
Found at i:29656153 original size:16 final size:16
Alignment explanation
Indices: 29656134--29656165 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29656124 TATTATGATC
29656134 CCATGTTATTGAGTCA
1 CCATGTTATTGAGTCA
29656150 CCATGTTATTGAGTCA
1 CCATGTTATTGAGTCA
29656166 TTCATCCGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
CCATGTTATTGAGTCA
Found at i:29666990 original size:15 final size:15
Alignment explanation
Indices: 29666956--29666994 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
29666946 ACACAGATCA
*
29666956 AGATGATCATGAGAT
1 AGATGATGATGAGAT
*
29666971 AGATGATGATGAGTT
1 AGATGATGATGAGAT
*
29666986 TGATGATGA
1 AGATGATGA
29666995 AGTATTGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.03, G:0.31, T:0.31
Consensus pattern (15 bp):
AGATGATGATGAGAT
Found at i:29690211 original size:15 final size:15
Alignment explanation
Indices: 29690191--29690223 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29690181 CTCGAGGAGA
*
29690191 AACAGAGACTTGCTG
1 AACAGAAACTTGCTG
29690206 AACAGAAACTTGCTG
1 AACAGAAACTTGCTG
29690221 AAC
1 AAC
29690224 CTGAAATGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (15 bp):
AACAGAAACTTGCTG
Found at i:29705185 original size:13 final size:13
Alignment explanation
Indices: 29705167--29705214 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
29705157 TGCGAATCGA
29705167 TTTTCTTTCTTTT-
1 TTTTCTTT-TTTTC
29705180 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
*
29705193 TTTTCCTTTTTTC
1 TTTTCTTTTTTTC
*
29705206 TTTCCTTTT
1 TTTTCTTTT
29705215 CCTATTCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
12 4 0.13
13 27 0.87
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:29705390 original size:20 final size:19
Alignment explanation
Indices: 29705338--29705392 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
29705328 CAGACCCCCT
29705338 CTCTCCTTTC-CTCTCTTC
1 CTCTCCTTTCTCTCTCTTC
* *
29705356 CTCCTCCCTCCTCTCTCTTC
1 CT-CTCCTTTCTCTCTCTTC
29705376 CTCTCCTTTCT-TCTCTT
1 CTCTCCTTTCTCTCTCTT
29705393 TTTCTCCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 8 0.26
19 13 0.42
20 10 0.32
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (19 bp):
CTCTCCTTTCTCTCTCTTC
Found at i:29705924 original size:12 final size:12
Alignment explanation
Indices: 29705907--29705937 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29705897 TAATATTTAT
29705907 ATTATTACTATC
1 ATTATTACTATC
*
29705919 ATTATTATTATC
1 ATTATTACTATC
29705931 ATTATTA
1 ATTATTA
29705938 GTATAGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTATTACTATC
Found at i:29706092 original size:12 final size:13
Alignment explanation
Indices: 29706052--29706106 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
29706042 AATCTATGTA
*
29706052 TTATATATATGTT
1 TTATATATATATT
*
29706065 TTCA-ATATTGTATT
1 TT-ATATA-TATATT
29706079 TTATATATAT-TT
1 TTATATATATATT
*
29706091 TTATGTATATATT
1 TTATATATATATT
29706104 TTA
1 TTA
29706107 ACACTATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 11 0.32
13 13 0.38
14 10 0.29
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (13 bp):
TTATATATATATT
Found at i:29706166 original size:19 final size:19
Alignment explanation
Indices: 29706142--29706178 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29706132 TACTATTTTA
*
29706142 TATATTTCTAATATCATTG
1 TATATTTCTAACATCATTG
29706161 TATATTTCTAACATCATT
1 TATATTTCTAACATCATT
29706179 ATTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATTTCTAACATCATTG
Found at i:29706480 original size:26 final size:26
Alignment explanation
Indices: 29706447--29706502 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
29706437 ATGTATAATA
29706447 TTATTTTCA-GA-TATTATTATATTTAT
1 TTATTTTCACGAGTATTATTAT-TTT-T
*
29706473 TTATTTTCACTAGTATTATTATTTTT
1 TTATTTTCACGAGTATTATTATTTTT
29706499 TTAT
1 TTAT
29706503 CATTATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 14 0.52
27 4 0.15
28 9 0.33
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (26 bp):
TTATTTTCACGAGTATTATTATTTTT
Found at i:29706661 original size:17 final size:19
Alignment explanation
Indices: 29706626--29706665 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
29706616 TTATTTTAAA
29706626 TATTTTTATATTATGTATAT
1 TATTTTTATATTA-GTATAT
29706646 TATTTTT-TATTA-TATAT
1 TATTTTTATATTAGTATAT
29706663 TAT
1 TAT
29706666 GTACATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TATTTTTATATTAGTATAT
Found at i:29706877 original size:26 final size:25
Alignment explanation
Indices: 29706848--29706914 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
29706838 TATTATTAGT
29706848 ATTTCTAATATATATGGTATATGT-TC
1 ATTT-TAATATATAT-GTATATGTATC
*
29706874 ATTTTTATATATTATGTATATGTATC
1 ATTTTAATATA-TATGTATATGTATC
*
29706900 TTTTTAATATTATAT
1 ATTTTAATA-TATAT
29706915 CTTTATACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 14 0.40
26 19 0.54
27 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
ATTTTAATATATATGTATATGTATC
Found at i:29706892 original size:25 final size:26
Alignment explanation
Indices: 29706855--29706912 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
29706845 AGTATTTCTA
29706855 ATATA-TATGGTATATGT-TCATTTTT
1 ATATATTATGGTATATGTATC-TTTTT
29706880 ATATATTAT-GTATATGTATCTTTTT
1 ATATATTATGGTATATGTATCTTTTT
29706905 A-ATATTAT
1 ATATATTAT
29706913 ATCTTTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 7 0.23
25 19 0.61
26 5 0.16
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (26 bp):
ATATATTATGGTATATGTATCTTTTT
Found at i:29707041 original size:24 final size:24
Alignment explanation
Indices: 29706999--29707044 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29706989 TATTTTTTAC
*
29706999 TACATTATACATGTATTTTAATGT
1 TACATTATACATATATTTTAATGT
* *
29707023 TACATTATATATATTTTTTAAT
1 TACATTATACATATATTTTAAT
29707045 ATAGGTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (24 bp):
TACATTATACATATATTTTAATGT
Found at i:29708916 original size:26 final size:26
Alignment explanation
Indices: 29708880--29708963 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
29708870 TGATACAAAT
29708880 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
29708906 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
29708932 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
29708958 TGATAA
1 TGATAA
29708964 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:29714264 original size:17 final size:17
Alignment explanation
Indices: 29714230--29714266 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29714220 CAAGGCACCG
*
29714230 CACGTCGTGCGACTCTC
1 CACGTCGTGCGACACTC
*
29714247 CACGTCGTGCGCCACTC
1 CACGTCGTGCGACACTC
29714264 CAC
1 CAC
29714267 CTCCACGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.46, G:0.22, T:0.19
Consensus pattern (17 bp):
CACGTCGTGCGACACTC
Found at i:29715954 original size:28 final size:26
Alignment explanation
Indices: 29715913--29716068 Score: 85
Period size: 28 Copynumber: 6.0 Consensus size: 26
29715903 TTATCATTGT
* *
29715913 TATTTTTTTTTATTCTTACTATTATA
1 TATTATTTATTATTCTTACTATTATA
*
29715939 TATTATTGCTATTATTCTCACTGA-TATA
1 TATTATT--TATTATTCTTACT-ATTATA
* * *
29715967 TGTTATTATCATTATTGTTACTATT-TT
1 TATTATT-T-ATTATTCTTACTATTATA
* *
29715994 TATTACTTTATTATTATTATTATT-TA
1 TATTA-TTTATTATTCTTACTATTATA
* *
29716020 TA-TA--TATTATTATTACTATTGTA
1 TATTATTTATTATTCTTACTATTATA
29716043 T-TTCACTGTTATTATT-TTACTATTAT
1 TATT-A-T-TTATTATTCTTACTATTAT
29716069 TTTTATATAC
Statistics
Matches: 103, Mismatches: 14, Indels: 25
0.73 0.10 0.18
Matches are distributed among these distances:
22 15 0.15
23 4 0.04
24 1 0.01
25 2 0.02
26 22 0.21
27 17 0.17
28 41 0.40
29 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (26 bp):
TATTATTTATTATTCTTACTATTATA
Found at i:29716009 original size:3 final size:3
Alignment explanation
Indices: 29715969--29716039 Score: 56
Period size: 3 Copynumber: 23.7 Consensus size: 3
29715959 CTGATATATG
* * * * *
29715969 TTA TTA TCA TTA TTG TTA CTA TTT TTA TTA CT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
29716016 TT- TATA TATA TTA TTA TTA CTA TT
1 TTA T-TA T-TA TTA TTA TTA TTA TT
29716040 GTATTTCACT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 46 0.87
4 5 0.09
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:29716027 original size:16 final size:16
Alignment explanation
Indices: 29715969--29716033 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 16
29715959 CTGATATATG
* *
29715969 TTATTATCATTATT-G
1 TTATTATTATTATTAT
* *
29715984 TTACTATTTTTATTACT
1 TTATTATTATTATTA-T
29716001 TTATTATTATTATTAT
1 TTATTATTATTATTAT
29716017 TTA-TATATATTATTAT
1 TTATTAT-TATTATTAT
29716033 T
1 T
29716034 ACTATTGTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
15 14 0.34
16 14 0.34
17 13 0.32
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:29718611 original size:67 final size:67
Alignment explanation
Indices: 29718493--29718621 Score: 177
Period size: 67 Copynumber: 1.9 Consensus size: 67
29718483 ATTTGAGAAA
*** * *
29718493 GAAACTATATTGCTTCGTGTAGGAATAGCAATTTTGGAATCGGAGTAATTTGCTTCATTATCAAA
1 GAAACTATATTGCTTCGTGTAGGAATAGCAATTCCAGAATCGGAATAATTTGCTTCACTATCAAA
29718558 CG
66 CG
* * * *
29718560 GAAACTATATTGCTTTGTGTAGGAATAGCAGTTCCAGAATCTGAATCATTTGCTTCACTATC
1 GAAACTATATTGCTTCGTGTAGGAATAGCAATTCCAGAATCGGAATAATTTGCTTCACTATC
29718622 TCTCTACATC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (67 bp):
GAAACTATATTGCTTCGTGTAGGAATAGCAATTCCAGAATCGGAATAATTTGCTTCACTATCAAA
CG
Found at i:29723214 original size:22 final size:21
Alignment explanation
Indices: 29723168--29723218 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
29723158 TATCTTTCTT
29723168 TTAAAATTATTTAAAATAATA
1 TTAAAATTATTTAAAATAATA
29723189 -TAAAATT-TTATAACAATAATA
1 TTAAAATTATT-TAA-AATAATA
29723210 TTAAAATTA
1 TTAAAATTA
29723219 AAATATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.08
20 10 0.38
21 7 0.27
22 7 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAATTATTTAAAATAATA
Found at i:29724680 original size:13 final size:13
Alignment explanation
Indices: 29724641--29724688 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
29724631 TATTTAAGAT
29724641 TTTAATATATTTTA
1 TTTAAT-TATTTTA
* * *
29724655 TTTTATAAATTTA
1 TTTAATTATTTTA
29724668 TTTAATTATTTTA
1 TTTAATTATTTTA
*
29724681 ATTAATTA
1 TTTAATTA
29724689 ACTAATTATA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATTATTTTA
Found at i:29726131 original size:20 final size:21
Alignment explanation
Indices: 29726103--29726149 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
29726093 TTTTTAATAT
29726103 TTAAAATTA-AAAAAAAATTA
1 TTAAAATTATAAAAAAAATTA
* *
29726123 TTAACATTATTAAAAAAA-TA
1 TTAAAATTATAAAAAAAATTA
29726143 -TAAAATT
1 TTAAAATT
29726150 TTTAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TTAAAATTATAAAAAAAATTA
Found at i:29726154 original size:19 final size:21
Alignment explanation
Indices: 29726103--29726157 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 21
29726093 TTTTTAATAT
*
29726103 TTAAAATTA-AAAAAAAATTA
1 TTAAAATTATTAAAAAAATTA
*
29726123 TTAACATTATTAAAAAAA-TA
1 TTAAAATTATTAAAAAAATTA
*
29726143 -TAAAATTTTTAAAAA
1 TTAAAATTATTAAAAA
29726158 TTTAAAGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 13 0.43
20 10 0.33
21 7 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TTAAAATTATTAAAAAAATTA
Found at i:29726719 original size:7 final size:7
Alignment explanation
Indices: 29726707--29726736 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
29726697 TGCAATACTC
29726707 AAATTTA
1 AAATTTA
29726714 AAATTTA
1 AAATTTA
29726721 AAATTTA
1 AAATTTA
29726728 AAATATTA
1 AAAT-TTA
29726736 A
1 A
29726737 TTTTTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:29729735 original size:33 final size:33
Alignment explanation
Indices: 29729708--29729870 Score: 208
Period size: 33 Copynumber: 4.9 Consensus size: 33
29729698 CTCACCCGCT
*
29729708 TTTTTAATGGATTCACCTTCTCCCTCACCTGGA
1 TTTTCAATGGATTCACCTTCTCCCTCACCTGGA
*
29729741 TTTTCAATGGTTTCACCTTCTCCCTCACCTGGA
1 TTTTCAATGGATTCACCTTCTCCCTCACCTGGA
*
29729774 TTTTCAATGGATTCACCCTTC-CCCTCACCT-GC
1 TTTTCAATGGATTCA-CCTTCTCCCTCACCTGGA
* * *
29729806 TTTTGCAGTGGATTTACGTT-TCCCCTCACCTGGA
1 TTTT-CAATGGATTCACCTTCT-CCCTCACCTGGA
29729840 TTTTCAATGGATTCACCTT-TCCCCTCACCTG
1 TTTTCAATGGATTCACCTTCT-CCCTCACCTG
29729871 CTGCTACAGG
Statistics
Matches: 114, Mismatches: 11, Indels: 10
0.84 0.08 0.07
Matches are distributed among these distances:
32 8 0.07
33 96 0.84
34 10 0.09
ACGTcount: A:0.16, C:0.33, G:0.13, T:0.38
Consensus pattern (33 bp):
TTTTCAATGGATTCACCTTCTCCCTCACCTGGA
Found at i:29737151 original size:3 final size:3
Alignment explanation
Indices: 29737136--29737167 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
29737126 TTTTACCCTG
29737136 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
29737168 ATACCAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:29738019 original size:46 final size:47
Alignment explanation
Indices: 29737957--29738275 Score: 384
Period size: 46 Copynumber: 7.0 Consensus size: 47
29737947 TTTGACATGA
* * * * * *
29737957 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
* ** * * *
29738003 TACCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*** *** *
29738049 TGCCATGGTATCTTTCAACCATGGTCTTATTTA-TTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*
29738095 TGCCATGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCAGG-
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
* *
29738140 TGCCATGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
29738186 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
29738232 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAG
29738276 AAAGCACACT
Statistics
Matches: 248, Mismatches: 21, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
45 49 0.20
46 199 0.80
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
Found at i:29738188 original size:137 final size:137
Alignment explanation
Indices: 29737952--29738275 Score: 434
Period size: 137 Copynumber: 2.4 Consensus size: 137
29737942 TTATCTTTGA
* * * * * * *
29737952 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTACCATGGTATCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCA-GGTACCATGGTATCT
** * ***
29738016 TTCAACCATGGTCTTATTCATTTCATGTCACGCTGCCATGGTATCTTTCAACCATGGTCTTATTT
64 TTCAACCATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTACAC
* *
29738081 ATTTCCCGT
129 ATTTCACAT
* *
29738090 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGTGCCATGGTATCTTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTACCATGGTATCTTT
* *
29738155 CAACCATGGTCTTACACGTTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACAT
66 CAACCATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTACACAT
*
29738220 TTCATAT
131 TTCACAT
*
29738227 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
29738276 AAAGCACACT
Statistics
Matches: 163, Mismatches: 22, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
137 127 0.78
138 36 0.22
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (137 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTACCATGGTATCTTT
CAACCATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTACACAT
TTCACAT
Found at i:29740453 original size:18 final size:20
Alignment explanation
Indices: 29740438--29740474 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29740428 TAATAATAAA
*
29740438 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
29740458 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
29740475 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:29742988 original size:13 final size:13
Alignment explanation
Indices: 29742970--29742994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29742960 TATAAACACC
29742970 AAAAATATTTTTG
1 AAAAATATTTTTG
29742983 AAAAATATTTTT
1 AAAAATATTTTT
29742995 CTAACTCGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
AAAAATATTTTTG
Found at i:29743189 original size:21 final size:21
Alignment explanation
Indices: 29743164--29743211 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
29743154 GGTTTTAAGG
29743164 TTAGGGTTTTACTAAAATAAT
1 TTAGGGTTTTACTAAAATAAT
* **
29743185 TTAGGTTTTTGTTAAAATAAT
1 TTAGGGTTTTACTAAAATAAT
29743206 TTAGGG
1 TTAGGG
29743212 CTAAGAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTTACTAAAATAAT
Found at i:29743929 original size:127 final size:128
Alignment explanation
Indices: 29743745--29744064 Score: 403
Period size: 128 Copynumber: 2.5 Consensus size: 128
29743735 AACGGATAAC
* * * * **
29743745 CGAAACCCAGCACGGTAGAGCACGATTCCTCAAACTTCCAAACATTGAACATTGCCTTGTTTTAG
1 CGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATCAAACATTGCCTTGTTTTAG
* * * * *
29743810 AATTTA-AAGAATACGAATGAAATTCTAAAGGAATATTTGATTATTTTGAACAAAC-GAGAAAT
66 AATTTAGAAAAACACGAATAAAATTCTAAAGGAAGATTCGATTATTTTGAACAAACAG-GAAAT
* * *
29743872 CGAAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAGCATCAAACATCGCCTTGTTTTAG
1 CGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATCAAACATTGCCTTGTTTTAG
* * * *
29743937 AATTTAGAAAAACACGAGTAAAATTCTAAATGAAGGTTCGATTATTTTGAGCAAACAGGAAAT
66 AATTTAGAAAAACACGAATAAAATTCTAAAGGAAGATTCGATTATTTTGAACAAACAGGAAAT
* * *
29744000 CGAAACCCAGCACGGTTA-GGCACGATTTCTCGAATTTCTAAACATCAAACATTGCCTTCGTTTT
1 CGAAACCCAGCAC-GATAGGGCACGATTCCTCGAATTTCCAAACATCAAACATTGCCTT-GTTTT
29744064 A
64 A
29744065 AGGAATTTTT
Statistics
Matches: 165, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
127 62 0.38
128 93 0.56
129 10 0.06
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (128 bp):
CGAAACCCAGCACGATAGGGCACGATTCCTCGAATTTCCAAACATCAAACATTGCCTTGTTTTAG
AATTTAGAAAAACACGAATAAAATTCTAAAGGAAGATTCGATTATTTTGAACAAACAGGAAAT
Found at i:29749600 original size:14 final size:14
Alignment explanation
Indices: 29749577--29749606 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29749567 TTGAAAATAT
29749577 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
29749591 GTTGATTTGGATTG
1 GTTGAATTGGATTG
29749605 GT
1 GT
29749607 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:29750496 original size:21 final size:21
Alignment explanation
Indices: 29750458--29750502 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29750448 CTCTTAACCC
*
29750458 TAAATTATTTTAATAAAAACT
1 TAAATTATTTTAACAAAAACT
* *
29750479 TAAATTATTTTAGCAAAATCT
1 TAAATTATTTTAACAAAAACT
29750500 TAA
1 TAA
29750503 CCTTATAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAATTATTTTAACAAAAACT
Found at i:29754221 original size:91 final size:91
Alignment explanation
Indices: 29754057--29754230 Score: 260
Period size: 91 Copynumber: 1.9 Consensus size: 91
29754047 TGGGAGATGC
* **
29754057 ATGCCTAAAGCAACGTTTAAATAAGAGTTGCCTTTGTGTAGTCCTAAGACGACACTTTTGTGGTG
1 ATGCCTAAAGCAACGCTTAAATAAGAGTTGCCTTTGTGTAGTCCTAAGACGACACTTTTGTGACG
29754122 ACATTTTCCTAAGGGTTGATATATGT
66 ACATTTTCCTAAGGGTTGATATATGT
* * **
29754148 ATGCCTAAAGCAATGCTTGAATAAGAGTTGGTTTTTGTGTAGTCCTAAGACGACACTTTTGTGAC
1 ATGCCTAAAGCAACGCTTAAATAAGAGTT-GCCTTTGTGTAGTCCTAAGACGACACTTTTGTGAC
*
29754213 GACA-TTTCCTAAGTGTTG
65 GACATTTTCCTAAGGGTTG
29754231 GGATAGACTA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 39 0.53
92 35 0.47
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (91 bp):
ATGCCTAAAGCAACGCTTAAATAAGAGTTGCCTTTGTGTAGTCCTAAGACGACACTTTTGTGACG
ACATTTTCCTAAGGGTTGATATATGT
Found at i:29754409 original size:132 final size:132
Alignment explanation
Indices: 29754131--29754749 Score: 899
Period size: 132 Copynumber: 4.8 Consensus size: 132
29754121 GACATTTTCC
** * *
29754131 TAAGGGTTGATATATGTATGCCTAAAGCAATGCTTGAATAAGAGTTGGTTTTTGTGTAGTCCTAA
1 TAAGGGTTGGGATATGTATGCCTAAGGCAATGCTTGAATAAGAGTTGGCTTTTGTGTAGTCCTAA
* * *
29754196 GACGACACTTTTGTGACGACA-TTTCCTAAGTGTTGGGATAGACTATGTTTTGGCCAACTCTTTG
66 GACGACACTTTTGCGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
29754260 TA
131 TA
* * *
29754262 TAAGGGTTAGGATATGTATGCCTAAGGCAACGCTTGAATAAGAGTTGGCTTCTGTGTAGTCCTAA
1 TAAGGGTTGGGATATGTATGCCTAAGGCAATGCTTGAATAAGAGTTGGCTTTTGTGTAGTCCTAA
* * *
29754327 GAAGACACTTTTGCGGTGACACTTCCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
66 GACGACACTTTTGCGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
29754392 TA
131 TA
* *
29754394 TAAGGGTTGGGATATGTATGCCTAAGGCAATGCTTGAATAAGAGTTGGCTTTTGTGTTGTCTTAA
1 TAAGGGTTGGGATATGTATGCCTAAGGCAATGCTTGAATAAGAGTTGGCTTTTGTGTAGTCCTAA
* *
29754459 GACGACACTTTTGTGGCGACACTTTCCTAAGTGTTGGTATAGACTATGCTTTGGCCAACTCTTTG
66 GACGACACTTTTGCGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
29754524 TA
131 TA
*
29754526 TAAGGGTTGGGATATGTATGCCTAAGGCAATGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCT--
1 TAAGGGTTGGGATATGTATGCCTAAGGCAATGCTTGAATAAGAGTTGGCTTTTGTGTAGTCCTAA
* * *
29754589 ----A-A-------GGCGACACTTTTCTAAGTGTTGGGATAGACTACGTTTTGGCCAACTCTTTG
66 GACGACACTTTTGCGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
29754642 TA
131 TA
* * *
29754644 TAAGGGTTGGGATATGTATGCCTAAGACAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
1 TAAGGGTTGGGATATGTATGCCTAAGGCAATGCTTGAATAAGAGTTGGCTTTTGTGTAGTCCTAA
* *
29754709 GACGACAGTTTTGGGGCGACACTTTCCTAAGTGTTGGGATA
66 GACGACACTTTTGCGGCGACACTTTCCTAAGTGTTGGGATA
29754750 CACTTGTCAG
Statistics
Matches: 440, Mismatches: 33, Indels: 29
0.88 0.07 0.06
Matches are distributed among these distances:
118 110 0.25
124 1 0.00
125 2 0.00
126 1 0.00
131 75 0.17
132 251 0.57
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (132 bp):
TAAGGGTTGGGATATGTATGCCTAAGGCAATGCTTGAATAAGAGTTGGCTTTTGTGTAGTCCTAA
GACGACACTTTTGCGGCGACACTTTCCTAAGTGTTGGGATAGACTATGCTTTGGCCAACTCTTTG
TA
Found at i:29754681 original size:118 final size:118
Alignment explanation
Indices: 29754473--29754720 Score: 424
Period size: 118 Copynumber: 2.1 Consensus size: 118
29754463 ACACTTTTGT
* * *
29754473 GGCGACACTTTCCTAAGTGTTGGTATAGACTATGCTTTGGCCAACTCTTTGTATAAGGGTTGGGA
1 GGCGACACTTTTCTAAGTGTTGGGATAGACTACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGA
* *
29754538 TATGTATGCCTAAGGCAATGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
66 TATGTATGCCTAAGACAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
*
29754591 GGCGACACTTTTCTAAGTGTTGGGATAGACTACGTTTTGGCCAACTCTTTGTATAAGGGTTGGGA
1 GGCGACACTTTTCTAAGTGTTGGGATAGACTACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGA
29754656 TATGTATGCCTAAGACAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
66 TATGTATGCCTAAGACAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
* *
29754709 GACGACAGTTTT
1 GGCGACACTTTT
29754721 GGGGCGACAC
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 122 1.00
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (118 bp):
GGCGACACTTTTCTAAGTGTTGGGATAGACTACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGA
TATGTATGCCTAAGACAACGCTTGAATAAGAGTTGGCTTTTGTCTAGTCCTAA
Found at i:29755045 original size:21 final size:21
Alignment explanation
Indices: 29754998--29755045 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
29754988 TTAGTTTAGG
* * *
29754998 GTTTAAGGTTTAGTGCTTAAA
1 GTTTATGGTTTAGGGATTAAA
* *
29755019 GATTATGGTTTAGGGATTATA
1 GTTTATGGTTTAGGGATTAAA
29755040 GTTTAT
1 GTTTAT
29755046 ATAGTTTACG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (21 bp):
GTTTATGGTTTAGGGATTAAA
Found at i:29755075 original size:22 final size:22
Alignment explanation
Indices: 29755040--29755106 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 22
29755030 AGGGATTATA
29755040 GTTTATATAGTTTACGGTTTTAGG
1 GTTT-TAT-GTTTACGGTTTTAGG
*
29755064 GTTTTATGTTTACGGGTTT-GG
1 GTTTTATGTTTACGGTTTTAGG
* *
29755085 GGTTTATGATTTTAGGGTTTTA
1 GTTTTATG--TTTACGGTTTTA
29755107 TGATTATGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 9 0.25
22 11 0.31
23 12 0.33
24 4 0.11
ACGTcount: A:0.16, C:0.03, G:0.28, T:0.52
Consensus pattern (22 bp):
GTTTTATGTTTACGGTTTTAGG
Found at i:29755090 original size:37 final size:37
Alignment explanation
Indices: 29755049--29755126 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
29755039 AGTTTATATA
* * *
29755049 GTTTACGGTTTTAGGGTTTTATGTTTACGGGTTTGGG
1 GTTTACGATTTTAGGGTTTTATGATTACGGATTTGGG
* *
29755086 GTTTATGATTTTAGGGTTTTATGATTATGGATTTGGG
1 GTTTACGATTTTAGGGTTTTATGATTACGGATTTGGG
29755123 GTTT
1 GTTT
29755127 TGTGATTATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.14, C:0.03, G:0.32, T:0.51
Consensus pattern (37 bp):
GTTTACGATTTTAGGGTTTTATGATTACGGATTTGGG
Found at i:29755113 original size:22 final size:21
Alignment explanation
Indices: 29755088--29755136 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
29755078 GGTTTGGGGT
29755088 TTATGATTTTAGGGTTTTATGA
1 TTATGA-TTTAGGGTTTTATGA
* *
29755110 TTATGGATTTGGGGTTTTGTGA
1 TTAT-GATTTAGGGTTTTATGA
29755132 TTATG
1 TTATG
29755137 GGTTTGCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.88
23 2 0.08
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (21 bp):
TTATGATTTAGGGTTTTATGA
Found at i:29755137 original size:22 final size:22
Alignment explanation
Indices: 29755099--29755142 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
29755089 TATGATTTTA
29755099 GGGTTTTATGATTATGGATTTG
1 GGGTTTTATGATTATGGATTTG
* *
29755121 GGGTTTTGTGATTATGGGTTTG
1 GGGTTTTATGATTATGGATTTG
29755143 CGATTAATCT
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:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (22 bp):
GGGTTTTATGATTATGGATTTG
Found at i:29755140 original size:37 final size:37
Alignment explanation
Indices: 29755060--29755141 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
29755050 TTTACGGTTT
* * *
29755060 TAGGGTTTTATGTTTACGGGTTTGGGGTTTATGATTT
1 TAGGGTTTTATGATTACGGATTTGGGGTTTATGATTA
* *
29755097 TAGGGTTTTATGATTATGGATTTGGGGTTTTGTGATTA
1 TAGGGTTTTATGATTACGGATTTGGGG-TTTATGATTA
29755135 T-GGGTTT
1 TAGGGTTT
29755142 GCGATTAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 30 0.77
38 9 0.23
ACGTcount: A:0.15, C:0.01, G:0.33, T:0.51
Consensus pattern (37 bp):
TAGGGTTTTATGATTACGGATTTGGGGTTTATGATTA
Found at i:29755327 original size:14 final size:15
Alignment explanation
Indices: 29755295--29755327 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29755285 GGTTTAAGAT
29755295 TTTATGGTCTTGAGG
1 TTTATGGTCTTGAGG
*
29755310 TTTATGGT-TTGTGG
1 TTTATGGTCTTGAGG
29755324 TTTA
1 TTTA
29755328 AGGCTTATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.12, C:0.03, G:0.30, T:0.55
Consensus pattern (15 bp):
TTTATGGTCTTGAGG
Found at i:29755813 original size:56 final size:56
Alignment explanation
Indices: 29755747--29755859 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
29755737 TAAGAATGTA
29755747 TGCATACTTTACCCGGATAAAATATGTATTAGCAGATTCACTAATAATACATACTT
1 TGCATACTTTACCCGGATAAAATATGTATTAGCAGATTCACTAATAATACATACTT
* *
29755803 TGCATACTTTACCCGGATAAAGTATGTATTAGCAGATTCACTAATAATGCATACTT
1 TGCATACTTTACCCGGATAAAATATGTATTAGCAGATTCACTAATAATACATACTT
29755859 T
1 T
29755860 ACCCGGGTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (56 bp):
TGCATACTTTACCCGGATAAAATATGTATTAGCAGATTCACTAATAATACATACTT
Found at i:29758682 original size:7 final size:6
Alignment explanation
Indices: 29758647--29758690 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
29758637 TTCAATCTTT
*
29758647 ATTTTA ATTTTA ATTTTA ATTTTGT ATTTTAA ATTTTAA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTT-A ATTTT-A ATTTT-A ATTTT
29758691 TTTAGTTGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
6 17 0.50
7 17 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (6 bp):
ATTTTA
Found at i:29758917 original size:73 final size:73
Alignment explanation
Indices: 29758798--29759143 Score: 365
Period size: 73 Copynumber: 4.7 Consensus size: 73
29758788 TATTATACGT
* * * *
29758798 GTCTATCCCAACCTTTTTAAAGTTGCTTTAAACAGGTCTATCCCAACCTTTTTTAAAAGTTACCT
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAAACAGCTCTATCCCAACCTTTTTTAAAAGTTGCCT
29758863 TAAACATG
66 TAAACATG
* *
29758871 GTCTATCCCAACCTTTTTAAGGTTGCCTTAAACGAG-TCTATTCCAACCTTTTTTAAAGGTTGCC
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAAAC-AGCTCTATCCCAACCTTTTTTAAAAGTTGCC
*
29758935 TTAGACATG
65 TTAAACATG
* * * * * * **
29758944 GTCTATCCTAACCTGTTTAAGGTTGCCTTAGACAGCTCTATCCCAACATTTTTTTATAGGTTGTT
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAAACAGCTCTATCCCAAC-CTTTTTTAAAAGTTGCC
29759009 TTAGAGA-AT-
65 TTA-A-ACATG
* * * *
29759018 GTCGATCCCAACCTTTTTAAGGTTGCTTTAGACAGCTCTATCCCAACCGTTTTTAAAAGTTGCCT
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAAACAGCTCTATCCCAACCTTTTTTAAAAGTTGCCT
*
29759083 TAAACAAG
66 TAAACATG
** ** * * * * * *
29759091 AACTATATCGACCTTTTTAAGGTTGTCTTAGACAGGTTTATCACAACCTTTTT
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAAACAGCTCTATCCCAACCTTTTT
29759144 CAAAGATTGG
Statistics
Matches: 228, Mismatches: 38, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
71 1 0.00
72 4 0.02
73 159 0.70
74 61 0.27
75 2 0.01
76 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (73 bp):
GTCTATCCCAACCTTTTTAAGGTTGCCTTAAACAGCTCTATCCCAACCTTTTTTAAAAGTTGCCT
TAAACATG
Found at i:29759110 original size:147 final size:147
Alignment explanation
Indices: 29758875--29759143 Score: 353
Period size: 147 Copynumber: 1.8 Consensus size: 147
29758865 AACATGGTCT
* * * *
29758875 ATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATTCCAACCTTTTTTAAAGGTTGCCTTAGA
1 ATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCCAACCGTTTTTAAAAGTTGCCTTAAA
* ** *
29758940 CATGGTCTATCCTAACCTGTTTAAGGTTGCCTTAGACAGCTCTATCCCAACATTTTTTTATAGGT
66 CAAGAACTATCCTAACCTGTTTAAGGTTGCCTTAGACAGCTCTATCACAACATTTTTTTATAGGT
29759005 TGTTTTAGAGAATGTCG
131 TGTTTTAGAGAATGTCG
* *
29759022 ATCCCAACCTTTTTAAGGTTGCTTTAGAC-AGCTCTATCCCAACCGTTTTTAAAAGTTGCCTTAA
1 ATCCCAACCTTTTTAAGGTTGCCTTAAACGAG-TCTATCCCAACCGTTTTTAAAAGTTGCCTTAA
* * * * * * *
29759086 ACAAGAACTAT-ATCGACCTTTTTAAGGTTGTCTTAGACAGGTTTATCACAACCTTTTT
65 ACAAGAACTATCCT-AACCTGTTTAAGGTTGCCTTAGACAGCTCTATCACAACATTTTT
29759144 CAAAGATTGG
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
146 3 0.03
147 100 0.97
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (147 bp):
ATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCCAACCGTTTTTAAAAGTTGCCTTAAA
CAAGAACTATCCTAACCTGTTTAAGGTTGCCTTAGACAGCTCTATCACAACATTTTTTTATAGGT
TGTTTTAGAGAATGTCG
Found at i:29759180 original size:147 final size:147
Alignment explanation
Indices: 29758800--29759184 Score: 332
Period size: 147 Copynumber: 2.6 Consensus size: 147
29758790 TTATACGTGT
* * * * * * * * **
29758800 CTATCCCAACCTTTTTAAAGTTGCTTTAAACAGGTCTATCCCAAC-CTTTTTTAAA-AGTTACCT
1 CTATCCTAACCTGTTTAAGGTTGCCTTAGACAGCTCTATCACAACACTTTTTCAAAGA-TTGTCT
* * * * *
29758863 TAAACATGGTCTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATTCCAACCTTTTTTAAA
65 TAGACAAGGCCTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCCAACCGTTTTTAAA
* * * **
29758928 GGTTGCCTTAGACATGGT
130 AGTTGCCTTAAACAAGAA
* * * * * *
29758946 CTATCCTAACCTGTTTAAGGTTGCCTTAGACAGCTCTATCCCAACATTTTTTTATAGGTTGTTTT
1 CTATCCTAACCTGTTTAAGGTTGCCTTAGACAGCTCTATCACAACACTTTTTCAAAGATTGTCTT
* * * * * *
29759011 AGAGAATGTCGATCCCAACCTTTTTAAGGTTGCTTTAGAC-AGCTCTATCCCAACCGTTTTTAAA
66 AGACAAGGCCTATCCCAACCTTTTTAAGGTTGCCTTAAACGAG-TCTATCCCAACCGTTTTTAAA
29759075 AGTTGCCTTAAACAAGAA
130 AGTTGCCTTAAACAAGAA
* * * * * *
29759093 CTAT-ATCGACCTTTTTAAGGTTGTCTTAGACAGGTTTATCACAAC-CTTTTTCAAAGATTGGTC
1 CTATCCT-AACCTGTTTAAGGTTGCCTTAGACAGCTCTATCACAACACTTTTTCAAAGATT-GTC
*
29759156 TTA-ACTAGGCCTATCCCAACCCTTTTTAA
64 TTAGACAAGGCCTATCCCAA-CCTTTTTAA
29759185 AGGTCAGCAT
Statistics
Matches: 190, Mismatches: 43, Indels: 11
0.78 0.18 0.05
Matches are distributed among these distances:
146 63 0.33
147 127 0.67
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (147 bp):
CTATCCTAACCTGTTTAAGGTTGCCTTAGACAGCTCTATCACAACACTTTTTCAAAGATTGTCTT
AGACAAGGCCTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCCAACCGTTTTTAAAA
GTTGCCTTAAACAAGAA
Found at i:29763658 original size:32 final size:32
Alignment explanation
Indices: 29763622--29763683 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
29763612 TCAATGACAT
* * * *
29763622 AAATAAAAACTTTTGTATAGTTTAGTGACTTA
1 AAATAAAAAATTTCGAATAGTTCAGTGACTTA
29763654 AAATAAAAAATTTCGAATAGTTCAGTGACT
1 AAATAAAAAATTTCGAATAGTTCAGTGACT
29763684 ATTTTGTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (32 bp):
AAATAAAAAATTTCGAATAGTTCAGTGACTTA
Found at i:29764067 original size:15 final size:16
Alignment explanation
Indices: 29764040--29764081 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
29764030 TTATAATTAT
29764040 TTTTTTGAA-TTTT-AA
1 TTTTTT-AATTTTTAAA
29764055 TTTTTTAATTTTTAAA
1 TTTTTTAATTTTTAAA
29764071 TATTTTTAATT
1 T-TTTTTAATT
29764082 ATTTGTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.08
15 10 0.42
16 3 0.12
17 9 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTTTAATTTTTAAA
Found at i:29769371 original size:126 final size:126
Alignment explanation
Indices: 29769134--29769368 Score: 317
Period size: 126 Copynumber: 1.9 Consensus size: 126
29769124 CATTATCTCA
* * *
29769134 TTTTAATTTAAGAAAACATGGATGAAATTTCAAAAGGATATTCTGTATTTTAGTCGAATAAAAAA
1 TTTTAATTTAAGAAAACATAGACGAAATTTCAAAAGGATATTCTGTATTCTAGTCGAATAAAAAA
* * *
29769199 TCAAAACCTAGCATGATTGGGCACGATCTCCCAAATCCCCAAAACACAAAATATTGCCTCG
66 TCAAAACCCAGCACGATTAGGCACGATCTCCCAAATCCCCAAAACACAAAATATTGCCTCG
* * * * *
29769260 TTTTAATTTAAGAAAACATAGACGAAATTTCACAAGGATATTTTGTATTCTAGTCGATTGAGAAA
1 TTTTAATTTAAGAAAACATAGACGAAATTTCAAAAGGATATTCTGTATTCTAGTCGAATAAAAAA
* * * * *
29769325 TCGAAACCCAGCACGATTAGGTATGATCTCTCAAACCTCCCAAA
66 TCAAAACCCAGCACGATTAGGCACGATCTCCCAAATC-CCCAAA
29769369 CACGGAAGAT
Statistics
Matches: 92, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
126 86 0.93
127 6 0.07
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (126 bp):
TTTTAATTTAAGAAAACATAGACGAAATTTCAAAAGGATATTCTGTATTCTAGTCGAATAAAAAA
TCAAAACCCAGCACGATTAGGCACGATCTCCCAAATCCCCAAAACACAAAATATTGCCTCG
Done.