Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 66 of 93
Found at i:25142198 original size:22 final size:19
Alignment explanation
Indices: 25142173--25142229 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 19
25142163 GAATTAATCA
25142173 TATTAAAATTTAAATAACAATT
1 TATTAAAATTTAAAT-A-AA-T
* *
25142195 TATTAATATTTTTAATAAAT
1 TATTAA-AATTTAAATAAAT
25142215 TATTAAAATATTAAA
1 TATTAAAAT-TTAAA
25142230 AATTTTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 2 0.07
20 11 0.38
21 2 0.07
22 7 0.24
23 7 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTAAAATTTAAATAAAT
Found at i:25142250 original size:21 final size:22
Alignment explanation
Indices: 25142217--25142269 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
25142207 TAATAAATTA
*
25142217 TTAAAATATTAAAAATTTTAAT
1 TTAAAATATTAAAAATTATAAT
*
25142239 TTAAAA-ATTAAATATTATAAT
1 TTAAAATATTAAAAATTATAAT
**
25142260 AAAAAATATT
1 TTAAAATATT
25142270 TTTTTCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAATATTAAAAATTATAAT
Found at i:25143029 original size:17 final size:17
Alignment explanation
Indices: 25142999--25143031 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25142989 TTCTTGATAA
25142999 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
25143016 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
25143032 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:25143228 original size:28 final size:28
Alignment explanation
Indices: 25143196--25143347 Score: 130
Period size: 28 Copynumber: 5.3 Consensus size: 28
25143186 TAAGACAAAA
*
25143196 AAATAT-TTTATCTTGTATAAATTGAGAC
1 AAATATGTTT-TCTTGTATAAATTAAGAC
25143224 AAATATGTTTTCTTG-ACTAAATTAAGAC
1 AAATATGTTTTCTTGTA-TAAATTAAGAC
* * *
25143252 AAAAAATAT-TTTTCATGTCTTAAATTAAGGC
1 ---AAATATGTTTTCTTGT-ATAAATTAAGAC
* * *
25143283 AAACATATTTTCTTGTCTAAATTAAGACC
1 AAATATGTTTTCTTGTATAAATTAAGA-C
* *
25143312 AAACATGTTTTCTTGTCTAAATTAAGAC
1 AAATATGTTTTCTTGTATAAATTAAGAC
*
25143340 AAACATGT
1 AAATATGT
25143348 CAAAGCTGCC
Statistics
Matches: 106, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
27 1 0.01
28 44 0.42
29 38 0.36
30 7 0.07
31 16 0.15
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (28 bp):
AAATATGTTTTCTTGTATAAATTAAGAC
Found at i:25143276 original size:59 final size:58
Alignment explanation
Indices: 25143183--25143347 Score: 206
Period size: 59 Copynumber: 2.8 Consensus size: 58
25143173 TCTTGTCTGT
* * *
25143183 AATTAAGACAAAAAAATATTTTATCTTGTATAAATTGAGACAAATATGTTTTCTTGACTA
1 AATTAAGAC-AAAAAATATTTT-TCTTGTCTAAATTAAGACAAACATGTTTTCTTGACTA
* * * *
25143243 AATTAAGACAAAAAATATTTTTCATGTCTTAAATTAAGGCAAACATATTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTTTTCTTGACTA
* * *
25143302 AATTAAGACCAAACAT-GTTTTCTTGTCTAAATTAAGACAAACATGT
1 AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGT
25143348 CAAAGCTGCC
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
57 17 0.19
58 14 0.15
59 51 0.56
60 9 0.10
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (58 bp):
AATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGACTA
Found at i:25143299 original size:29 final size:28
Alignment explanation
Indices: 25143173--25143345 Score: 166
Period size: 29 Copynumber: 5.9 Consensus size: 28
25143163 TTAAGACAAC
* *
25143173 TCTTGTCTGTAATTAAGACAAAAAAATATTTT
1 TCTTGTCT-AAATTAAGAC--AAACATA-TTT
* * * *
25143205 ATCTTGTATAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAACATATTT
* *
25143234 TCTTGACTAAATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGAC-AAACATA-TTT
* *
25143264 TCATGTCTTAAATTAAGGCAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATATTT
*
25143293 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
25143322 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
25143346 GTCAAAGCTG
Statistics
Matches: 119, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
28 31 0.26
29 44 0.37
30 19 0.16
31 10 0.08
32 8 0.07
33 7 0.06
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:25148762 original size:38 final size:38
Alignment explanation
Indices: 25148719--25148791 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
25148709 ATTGTCTTTC
*
25148719 ATAATCATCATAAACTGGCTGTAATTCCTCATCTTCAT
1 ATAATCATCATAAACTGACTGTAATTCCTCATCTTCAT
* * * *
25148757 ATAATCATCATATATTGATTGTAATTCCTCCTCTT
1 ATAATCATCATAAACTGACTGTAATTCCTCATCTT
25148792 GCCTTCTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (38 bp):
ATAATCATCATAAACTGACTGTAATTCCTCATCTTCAT
Found at i:25156899 original size:13 final size:14
Alignment explanation
Indices: 25156881--25156910 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
25156871 GGCTTGAGAG
25156881 TTTTCACTTTC-AC
1 TTTTCACTTTCAAC
25156894 TTTTCACTTTCAAC
1 TTTTCACTTTCAAC
25156908 TTT
1 TTT
25156911 CACACGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTCACTTTCAAC
Found at i:25164340 original size:20 final size:18
Alignment explanation
Indices: 25164315--25164351 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
25164305 GATTTATTAA
25164315 TTTTTAAAATAGATATTTTG
1 TTTTTAAAA-A-ATATTTTG
25164335 TTTTTAAAAAATATTTT
1 TTTTTAAAAAATATTTT
25164352 TTACTAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTTTAAAAAATATTTTG
Found at i:25164637 original size:21 final size:20
Alignment explanation
Indices: 25164603--25164651 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
25164593 ATGTTTTTAT
* *
25164603 TTTTTAAAATATAATAATAA
1 TTTTTAAAATATAAAAAGAA
*
25164623 TTTTTAAATTAATAAAAAGAA
1 TTTTTAAAAT-ATAAAAAGAA
25164644 TATTTTAA
1 T-TTTTAA
25164652 TTTTTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.38
21 9 0.38
22 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TTTTTAAAATATAAAAAGAA
Found at i:25169577 original size:4 final size:4
Alignment explanation
Indices: 25169525--25169559 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
25169515 AGAATTGATA
*
25169525 TATG TATA TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
25169560 ACGTGTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:25174667 original size:30 final size:28
Alignment explanation
Indices: 25174617--25174683 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
25174607 AGTAATTTTT
* *
25174617 AAAATTTACACTTTTACCCCCGTAAAAGTC
1 AAAAATTACACTTTTACCCCC--AAAACTC
* * *
25174647 AAAAATTACATTTTTGCCCCCAAAACTG
1 AAAAATTACACTTTTACCCCCAAAACTC
25174675 AAAAATTAC
1 AAAAATTAC
25174684 CCATAGACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 14 0.44
30 18 0.56
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (28 bp):
AAAAATTACACTTTTACCCCCAAAACTC
Found at i:25177251 original size:35 final size:35
Alignment explanation
Indices: 25177212--25177321 Score: 115
Period size: 35 Copynumber: 3.2 Consensus size: 35
25177202 CCAAGCTTAG
25177212 CCAAAACCTTTCACAATGGTTTTT-ACCGGGATCAA
1 CCAAAACCTTTCACAATGGTTTTTCA-CGGGATCAA
** *
25177247 CCAAAACC---CA-AAGTGGTTTTTCAAAGGCTCAA
1 CCAAAACCTTTCACAA-TGGTTTTTCACGGGATCAA
*
25177279 -CAACAACCTTTCACAATGGTTTTTCACGGAATCAA
1 CCAA-AACCTTTCACAATGGTTTTTCACGGGATCAA
25177314 CCAAAACC
1 CCAAAACC
25177322 CAACAACTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
31 5 0.08
32 20 0.33
33 1 0.02
35 29 0.48
36 5 0.08
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (35 bp):
CCAAAACCTTTCACAATGGTTTTTCACGGGATCAA
Found at i:25177883 original size:73 final size:73
Alignment explanation
Indices: 25177702--25177883 Score: 194
Period size: 73 Copynumber: 2.5 Consensus size: 73
25177692 AACAGAATGA
* * *
25177702 TCTTAGTCGACTAA-TTGCGCTCTTAGTCGACTAAGTTGTCTTTCTCTTCTGAATCTAGTTTTTG
1 TCTTAGTCGACTAACTTAC-TTCTTGGTCGACTAAGTTGTCTTTCTCTTCTGAATCTAGTTTTTG
*
25177766 GCAGTGAGC
65 GCAATGAGC
* * * * *
25177775 TCTTAGTCTACTAACTTCCTTCTTGGTC-ATTTAAGTTGTTTTTGTC-T-TGAAGTCTAGATTTT
1 TCTTAGTCGACTAACTTACTTCTTGGTCGA-CTAAGTTGTCTTTCTCTTCTGAA-TCTAG-TTTT
25177837 TGGCAAT-AGGC
63 TGGCAATGA-GC
*
25177848 TTTTAGTCGACTAACTTACTTCTTGGTCGACTAAGT
1 TCTTAGTCGACTAACTTACTTCTTGGTCGACTAAGT
25177884 CTTCTCTGTC
Statistics
Matches: 91, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
71 4 0.04
72 8 0.09
73 75 0.82
74 4 0.04
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (73 bp):
TCTTAGTCGACTAACTTACTTCTTGGTCGACTAAGTTGTCTTTCTCTTCTGAATCTAGTTTTTGG
CAATGAGC
Found at i:25183596 original size:20 final size:20
Alignment explanation
Indices: 25183568--25183620 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
25183558 AAAATCTAAT
*
25183568 TTTCTAGCAACTTCTTCAAA
1 TTTCCAGCAACTTCTTCAAA
*
25183588 TTTCCAGCAGA-TTCTTCAAG
1 TTTCCAGCA-ACTTCTTCAAA
*
25183608 CTTCCAGCAACTT
1 TTTCCAGCAACTT
25183621 TTTCTTCCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.36
Consensus pattern (20 bp):
TTTCCAGCAACTTCTTCAAA
Found at i:25187029 original size:36 final size:36
Alignment explanation
Indices: 25186894--25187014 Score: 179
Period size: 36 Copynumber: 3.4 Consensus size: 36
25186884 TAAAAAATTA
* * * *
25186894 AGGGTTATCGCTTGATCCCATTAAAAAGCCATTGTG
1 AGGGTTATCACTTGATCTCGTGAAAAAGCCATTGTG
* * *
25186930 AAGGTTATCACTTGATCTCGTGAAATAGCCGTTGTG
1 AGGGTTATCACTTGATCTCGTGAAAAAGCCATTGTG
25186966 AGGGTTATCACTTGATCTCGTGAAAAAGCCATTGTG
1 AGGGTTATCACTTGATCTCGTGAAAAAGCCATTGTG
25187002 AGGGTTATCACTT
1 AGGGTTATCACTT
25187015 CACCTTGTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 75 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (36 bp):
AGGGTTATCACTTGATCTCGTGAAAAAGCCATTGTG
Found at i:25191558 original size:20 final size:19
Alignment explanation
Indices: 25191533--25191574 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
25191523 AATAATAAAC
25191533 AAATTAAAAGAAATAACATA
1 AAATTAAAAGAAATAAC-TA
* *
25191553 AAATTAAAATAACTAACTA
1 AAATTAAAAGAAATAACTA
25191572 AAA
1 AAA
25191575 GTAACCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.21
Consensus pattern (19 bp):
AAATTAAAAGAAATAACTA
Found at i:25195692 original size:54 final size:54
Alignment explanation
Indices: 25195610--25195727 Score: 227
Period size: 54 Copynumber: 2.2 Consensus size: 54
25195600 GCTTGGTTGA
*
25195610 TAATGCTTGATGATGCTTAATGACTATGCTTGATAAAATTTGAAGAATAGTTAT
1 TAATGCTTGATGATGCTTAATGACTATGCTTGATAAAATTTGAAGAATACTTAT
25195664 TAATGCTTGATGATGCTTAATGACTATGCTTGATAAAATTTGAAGAATACTTAT
1 TAATGCTTGATGATGCTTAATGACTATGCTTGATAAAATTTGAAGAATACTTAT
25195718 TAATGCTTGA
1 TAATGCTTGA
25195728 AAATGATTAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (54 bp):
TAATGCTTGATGATGCTTAATGACTATGCTTGATAAAATTTGAAGAATACTTAT
Found at i:25195750 original size:54 final size:54
Alignment explanation
Indices: 25195610--25195751 Score: 151
Period size: 54 Copynumber: 2.6 Consensus size: 54
25195600 GCTTGGTTGA
** * ** * *
25195610 TAATGCTTGATGATGCTTAATGACTATGCTTGATAAAATTTGAAGAATAGTTAT
1 TAATGCTTGAAAATGATTAATGAAGATACTTGATAAAATTTGAAGAATACTTAT
** * ** *
25195664 TAATGCTTGATGATGCTTAATGACTATGCTTGATAAAATTTGAAGAATACTTAT
1 TAATGCTTGAAAATGATTAATGAAGATACTTGATAAAATTTGAAGAATACTTAT
25195718 TAATGCTTGAAAATGATTAA-GAAAGATACTTGAT
1 TAATGCTTGAAAATGATTAATG-AAGATACTTGAT
25195752 GACAATTGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 1 0.01
54 79 0.99
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (54 bp):
TAATGCTTGAAAATGATTAATGAAGATACTTGATAAAATTTGAAGAATACTTAT
Found at i:25196614 original size:2 final size:2
Alignment explanation
Indices: 25196609--25196641 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25196599 TATATATATA
25196609 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
25196642 CAATATGTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:25199799 original size:5 final size:5
Alignment explanation
Indices: 25199779--25199842 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
25199769 ATGTTATAAT
* * *
25199779 TAAAA TAAAA -ATAA TAAAA TAAAA T-ATA TAATA TAAGAA TTAGAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA -TA-AAA
25199825 TTAAAA TAAAA TAAAA TA
1 -TAAAA TAAAA TAAAA TA
25199843 TAAGAAGTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
4 6 0.12
5 32 0.64
6 4 0.08
7 7 0.14
8 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (5 bp):
TAAAA
Found at i:25199846 original size:31 final size:33
Alignment explanation
Indices: 25199793--25199857 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 33
25199783 ATAAAAATAA
25199793 TAAAATAAAATATATAATATAAGAA-TTAGAAAT
1 TAAAATAAAATATATAATATAAGAAGTTA-AAAT
25199826 TAAAATAAAATA-A-AATATAAGAAGTTAAAAT
1 TAAAATAAAATATATAATATAAGAAGTTAAAAT
25199857 T
1 T
25199858 TATATAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 15 0.48
32 4 0.13
33 12 0.39
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (33 bp):
TAAAATAAAATATATAATATAAGAAGTTAAAAT
Found at i:25199869 original size:55 final size:52
Alignment explanation
Indices: 25199779--25199886 Score: 137
Period size: 55 Copynumber: 2.0 Consensus size: 52
25199769 ATGTTATAAT
* *
25199779 TAAAATAAAAATAATAAAATAAAATATATAATATAAG-AATTAGAAATTAAAA
1 TAAAATAAAAATAAGAAAATAAAATATATAATATAAGTAA-AAGAAATTAAAA
**
25199831 TAAAATAAAATATAAGAAGTTAAAATTTATATAATATAAGTAAAAGAAATTAAAA
1 TAAAATAAAA-ATAAGAAAATAAAA--TATATAATATAAGTAAAAGAAATTAAAA
25199886 T
1 T
25199887 TTATATAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
52 10 0.21
53 11 0.23
55 25 0.52
56 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (52 bp):
TAAAATAAAAATAAGAAAATAAAATATATAATATAAGTAAAAGAAATTAAAA
Found at i:25199884 original size:30 final size:30
Alignment explanation
Indices: 25199803--25199916 Score: 141
Period size: 30 Copynumber: 4.0 Consensus size: 30
25199793 TAAAATAAAA
*
25199803 TATATAATATAAG-AATTAGAAATTAAAA--
1 TATATAATATAAGTAA-AAGAAATTAAAATT
* * *
25199831 TA-A-AATA-AAATATAAGAAGTTAAAATT
1 TATATAATATAAGTAAAAGAAATTAAAATT
25199858 TATATAATATAAGTAAAAGAAATTAAAATT
1 TATATAATATAAGTAAAAGAAATTAAAATT
25199888 TATATAATATAAGTAAAAGAAATTAAAAT
1 TATATAATATAAGTAAAAGAAATTAAAAT
25199917 AAAATATATA
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
25 12 0.16
26 5 0.07
27 3 0.04
28 3 0.04
29 4 0.05
30 46 0.63
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (30 bp):
TATATAATATAAGTAAAAGAAATTAAAATT
Found at i:25199898 original size:35 final size:33
Alignment explanation
Indices: 25199858--25199932 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 33
25199848 AGTTAAAATT
** *
25199858 TATATAATATAAGTAAAAGAAATTAAAAT---T
1 TATATAATATAAGTAAAAGAAAAGAAAATAAAA
**
25199888 TATATAATATAAGTAAAAGAAATTAAAATAAAA
1 TATATAATATAAGTAAAAGAAAAGAAAATAAAA
25199921 TATATAATATAA
1 TATATAATATAA
25199933 AAAATTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 29 0.71
33 12 0.29
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (33 bp):
TATATAATATAAGTAAAAGAAAAGAAAATAAAA
Found at i:25199987 original size:33 final size:34
Alignment explanation
Indices: 25199913--25200006 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 34
25199903 AAAGAAATTA
* *
25199913 AAAT-AAAATATATAATATAAAAAATTATATTAAAG
1 AAATGAAAATA-A-AATATATAAAATTATAATAAAG
* *
25199948 AAATGAAAATAAGATATATAAGATTATAAT-AAG
1 AAATGAAAATAAAATATATAAAATTATAATAAAG
*
25199981 AAATGAAAATAAAATATATAACATTA
1 AAATGAAAATAAAATATATAAAATTA
25200007 AAAATATATT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
33 27 0.52
34 14 0.27
35 5 0.10
36 6 0.12
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (34 bp):
AAATGAAAATAAAATATATAAAATTATAATAAAG
Found at i:25200232 original size:82 final size:82
Alignment explanation
Indices: 25200132--25200295 Score: 310
Period size: 82 Copynumber: 2.0 Consensus size: 82
25200122 CAAAGTACTT
25200132 GTAAACCAAATGTTGTAATGTTATCTTCCCTACATTTTAATCATTATTTTGCTTGTTTACCAAGC
1 GTAAACCAAATGTTGTAATGTTATCTTCCCTACATTTTAATCATTATTTTGCTTGTTTACCAAGC
*
25200197 ATTATAATATTATTTTC
66 ACTATAATATTATTTTC
25200214 GTAAACCAAATGTTGTAATGTTATCTTCCCTACATTTTAATCATTATTTTGCTTGTTTACCAAGC
1 GTAAACCAAATGTTGTAATGTTATCTTCCCTACATTTTAATCATTATTTTGCTTGTTTACCAAGC
*
25200279 ACTGTAATATTATTTTC
66 ACTATAATATTATTTTC
25200296 CCTGTAATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (82 bp):
GTAAACCAAATGTTGTAATGTTATCTTCCCTACATTTTAATCATTATTTTGCTTGTTTACCAAGC
ACTATAATATTATTTTC
Found at i:25214274 original size:44 final size:44
Alignment explanation
Indices: 25214177--25214609 Score: 446
Period size: 44 Copynumber: 9.9 Consensus size: 44
25214167 TTCAAAGAAA
** * *
25214177 AAGCTCTTCATTTATAATGAAGCTACATAACTTT-AAAATGAAT
1 AAGCTCTTCATTTGGAATGAGGCTACGTAACTTTAAAAATGAAT
* * *
25214220 AAGCTCTTCATTTGAAATAAGGCTACATAACTTTAAAAATGAAT
1 AAGCTCTTCATTTGGAATGAGGCTACGTAACTTTAAAAATGAAT
* * * * *
25214264 AAGCTTTTCATCTTGG-ATGAGCCTATGTAACTTT-TAAATAAAT
1 AAGCTCTTCAT-TTGGAATGAGGCTACGTAACTTTAAAAATGAAT
* * * *
25214307 AAGCTCTTCATCTGGAATGAAGCTGCGTAACTTTAAAAATAAAT
1 AAGCTCTTCATTTGGAATGAGGCTACGTAACTTTAAAAATGAAT
* * *
25214351 AAACTCCTCATTTGGAATGAGGCTACGTAACTTTAAAAATAAAT
1 AAGCTCTTCATTTGGAATGAGGCTACGTAACTTTAAAAATGAAT
* * *
25214395 AAACTCCTCATTTGGAATGAGGCTACGTAACTTTAAAAATAAAT
1 AAGCTCTTCATTTGGAATGAGGCTACGTAACTTTAAAAATGAAT
* ** *
25214439 AA-CT-TTCAAATTTAGAATGAGGCTATATAACTTTAAAAAGGAAT
1 AAGCTCTTC--ATTTGGAATGAGGCTACGTAACTTTAAAAATGAAT
* * * * *
25214483 GAGCTTTTCATTTGGAATGAGGTTATGTAACTTTAAATATGAAT
1 AAGCTCTTCATTTGGAATGAGGCTACGTAACTTTAAAAATGAAT
* *
25214527 AAGCTCCTT-ATCTGGAATGAGGCTACGTAACTTTAAAAAGGAAT
1 AAGCT-CTTCATTTGGAATGAGGCTACGTAACTTTAAAAATGAAT
* * * **
25214571 AAGCTCTTCATCTAGAATGAGACTAAATAACTTTAAAAA
1 AAGCTCTTCATTTGGAATGAGGCTACGTAACTTTAAAAA
25214610 AATAAACAAA
Statistics
Matches: 333, Mismatches: 47, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
42 5 0.02
43 66 0.20
44 252 0.76
45 7 0.02
46 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (44 bp):
AAGCTCTTCATTTGGAATGAGGCTACGTAACTTTAAAAATGAAT
Found at i:25214499 original size:132 final size:132
Alignment explanation
Indices: 25214177--25214609 Score: 500
Period size: 132 Copynumber: 3.3 Consensus size: 132
25214167 TTCAAAGAAA
* * * *
25214177 AAGCTCTTCATTTATAATGAAGCTACATAACTTT-AAAATGAATAAGCTCTTCATTTGAAATAAG
1 AAGCTCTTCATCTAGAATGAAGCTACATAACTTTAAAAATGAATAAGCTCTTCATTTGGAATGAG
* ** * * *
25214241 GCTACATAACTTTAAAAATGAATAAGCTTTTCATCTTGG-ATGAGCCTATGTAACTTT-TAAATA
66 GCTACGTAACTTTAAAAATGAATAAGCTCCTCAT-TTGGAATGAGGCTACGTAACTTTAAAAATA
25214304 AAT
130 AAT
* * * * * *
25214307 AAGCTCTTCATCTGGAATGAAGCTGCGTAACTTTAAAAATAAATAAACTCCTCATTTGGAATGAG
1 AAGCTCTTCATCTAGAATGAAGCTACATAACTTTAAAAATGAATAAGCTCTTCATTTGGAATGAG
* *
25214372 GCTACGTAACTTTAAAAATAAATAAACTCCTCATTTGGAATGAGGCTACGTAACTTTAAAAATAA
66 GCTACGTAACTTTAAAAATGAATAAGCTCCTCATTTGGAATGAGGCTACGTAACTTTAAAAATAA
25214437 AT
131 AT
* * * * * *
25214439 AA-CT-TTCAAATTTAGAATGAGGCTATATAACTTTAAAAAGGAATGAGCTTTTCATTTGGAATG
1 AAGCTCTTC--ATCTAGAATGAAGCTACATAACTTTAAAAATGAATAAGCTCTTCATTTGGAATG
* * * * * *
25214502 AGGTTATGTAACTTTAAATATGAATAAGCTCCTTATCTGGAATGAGGCTACGTAACTTTAAAAAG
64 AGGCTACGTAACTTTAAAAATGAATAAGCTCCTCATTTGGAATGAGGCTACGTAACTTTAAAAAT
*
25214567 GAAT
129 AAAT
*
25214571 AAGCTCTTCATCTAGAATG-AGACTAAATAACTTTAAAAA
1 AAGCTCTTCATCTAGAATGAAG-CTACATAACTTTAAAAA
25214610 AATAAACAAA
Statistics
Matches: 253, Mismatches: 42, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
130 36 0.14
131 73 0.29
132 139 0.55
133 2 0.01
134 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (132 bp):
AAGCTCTTCATCTAGAATGAAGCTACATAACTTTAAAAATGAATAAGCTCTTCATTTGGAATGAG
GCTACGTAACTTTAAAAATGAATAAGCTCCTCATTTGGAATGAGGCTACGTAACTTTAAAAATAA
AT
Found at i:25217172 original size:21 final size:22
Alignment explanation
Indices: 25217143--25217183 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
25217133 CCTAGGTGGA
*
25217143 AAAACTCAAGGGAA-AAGTGTG
1 AAAACTCAAGGAAACAAGTGTG
*
25217164 AAAATTCAAGGAAACAAGTG
1 AAAACTCAAGGAAACAAGTG
25217184 AAAAAAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.51, C:0.10, G:0.24, T:0.15
Consensus pattern (22 bp):
AAAACTCAAGGAAACAAGTGTG
Found at i:25217188 original size:21 final size:20
Alignment explanation
Indices: 25217141--25217188 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
25217131 ACCCTAGGTG
*
25217141 GAAAAACTCAAGGGAAAAGT
1 GAAAAACTCAAGGAAAAAGT
* *
25217161 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAACTCAAGGAAA-AAGT
25217183 GAAAAA
1 GAAAAA
25217189 AAAGGTAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.56, C:0.08, G:0.23, T:0.12
Consensus pattern (20 bp):
GAAAAACTCAAGGAAAAAGT
Found at i:25227090 original size:21 final size:22
Alignment explanation
Indices: 25227064--25227104 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
25227054 CCCTAGGTGA
*
25227064 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
25227085 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
25227105 AAAAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:25227105 original size:20 final size:21
Alignment explanation
Indices: 25227064--25227108 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
25227054 CCCTAGGTGA
*
25227064 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
25227085 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
25227105 AAAA
1 AAAA
25227109 AAAGGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:25227109 original size:21 final size:20
Alignment explanation
Indices: 25227060--25227109 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
25227050 AAAACCCTAG
*
25227060 GTGAAAAATTCAAGGGAAAA
1 GTGAAAAATTCAAGGAAAAA
*
25227080 GTGTGAAAATTCAAGGAAACAA
1 GTG-AAAAATTCAAGGAAA-AA
25227102 GTGAAAAA
1 GTGAAAAA
25227110 AAGGTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 17 0.68
22 5 0.20
ACGTcount: A:0.54, C:0.06, G:0.24, T:0.16
Consensus pattern (20 bp):
GTGAAAAATTCAAGGAAAAA
Found at i:25228137 original size:28 final size:27
Alignment explanation
Indices: 25228093--25228147 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
25228083 CTAATTGATT
*
25228093 GGCTTATGGCAATATTGGCATGAATGG
1 GGCTTATGGCAACATTGGCATGAATGG
25228120 NGGCTTATGGCAACATTGGCATGAATGG
1 -GGCTTATGGCAACATTGGCATGAATGG
25228148 CTGAATTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.33, T:0.27
Consensus pattern (27 bp):
GGCTTATGGCAACATTGGCATGAATGG
Found at i:25236999 original size:39 final size:39
Alignment explanation
Indices: 25236945--25237033 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
25236935 TGATAATTTT
* * *
25236945 TGTCTTCCTTACCTTAGAATCACTAAACTGAATCACCAA
1 TGTCTTCTTTACCTTAGAATCACTAAACCGAATAACCAA
25236984 TGTCTTCTTTACCTTAGAATCACTAAACCGAATAACCAA
1 TGTCTTCTTTACCTTAGAATCACTAAACCGAATAACCAA
25237023 TGTCTTCTTTA
1 TGTCTTCTTTA
25237034 TGCTCCAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (39 bp):
TGTCTTCTTTACCTTAGAATCACTAAACCGAATAACCAA
Found at i:25237129 original size:9 final size:8
Alignment explanation
Indices: 25237110--25237145 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
25237100 TTCCTTTCTA
25237110 TTTTCTTC
1 TTTTCTTC
25237118 TTTTCTTTC
1 TTTTC-TTC
25237127 TTTTCTTC
1 TTTTCTTC
25237135 TTTTC-TC
1 TTTTCTTC
25237142 TTTT
1 TTTT
25237146 ACTTTGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 6 0.22
8 13 0.48
9 8 0.30
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCTTC
Found at i:25238800 original size:13 final size:13
Alignment explanation
Indices: 25238782--25238806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25238772 AATTACTGTT
25238782 TTATATATATATA
1 TTATATATATATA
25238795 TTATATATATAT
1 TTATATATATAT
25238807 TACAAAGTGT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATATATATA
Found at i:25238983 original size:30 final size:30
Alignment explanation
Indices: 25238927--25238983 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
25238917 TGCAATATGT
*
25238927 AATTATAAGTTATATATTTTAAATGATATA
1 AATTATAAGTTATATATTATAAATGATATA
* *
25238957 AATTATATGTTA-ATATTAATATATGAT
1 AATTATAAGTTATATATT-ATAAATGAT
25238984 TAATAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (30 bp):
AATTATAAGTTATATATTATAAATGATATA
Found at i:25239427 original size:9 final size:9
Alignment explanation
Indices: 25239413--25239441 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
25239403 TGTACAAATA
25239413 AAAAATAAT
1 AAAAATAAT
25239422 AAAAATAAT
1 AAAAATAAT
25239431 AAAAATAAT
1 AAAAATAAT
25239440 AA
1 AA
25239442 CTATAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:25240209 original size:22 final size:22
Alignment explanation
Indices: 25240163--25240222 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
25240153 AAATAAATTT
25240163 TTAATATTTTAATATTTAAAAATA
1 TTAATATTTT-AT-TTTAAAAATA
*
25240187 TTAATATTTTATTTTTAAAATA
1 TTAATATTTTATTTTAAAAATA
* *
25240209 TTAAAATATTATTT
1 TTAATATTTTATTT
25240223 ATGATTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 21 0.64
23 2 0.06
24 10 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAATATTTTATTTTAAAAATA
Found at i:25240234 original size:26 final size:25
Alignment explanation
Indices: 25240205--25240272 Score: 61
Period size: 25 Copynumber: 2.7 Consensus size: 25
25240195 TTATTTTTAA
25240205 AATATTAAAATATTATTTATGATTTC
1 AATATTAAAATATTATTTAT-ATTTC
* * *
25240231 AATA-TAATAAT-TTAATTAATTTTTT
1 AATATTAA-AATATT-ATTTATATTTC
25240256 AA-ATTAAAATATTATTT
1 AATATTAAAATATTATTT
25240273 TTTATAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
24 7 0.21
25 15 0.44
26 12 0.35
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (25 bp):
AATATTAAAATATTATTTATATTTC
Found at i:25240269 original size:21 final size:21
Alignment explanation
Indices: 25240245--25240307 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
25240235 TAATAATTTA
25240245 ATTAATTTTTTAAATTAAAAT
1 ATTAATTTTTTAAATTAAAAT
*
25240266 ATT-ATTTTTTATAATATATAAT
1 ATTAATTTTTTA-AAT-TAAAAT
*
25240288 ATATAATTTTTCAAACTTAA
1 AT-TAATTTTTTAAA-TTAA
25240308 TAAGGGCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 8 0.24
21 6 0.18
22 7 0.21
23 5 0.15
24 8 0.24
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAATTTTTTAAATTAAAAT
Found at i:25247124 original size:21 final size:21
Alignment explanation
Indices: 25247065--25247124 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 21
25247055 ACTTTTCAAA
25247065 TATTAATT-TTCA-TTA-TAAT
1 TATT-ATTATTCATTTATTAAT
*
25247084 TATTTTTA-TC-TTTATT-AT
1 TATTATTATTCATTTATTAAT
25247102 TATTATTATTCATTTATTAAT
1 TATTATTATTCATTTATTAAT
25247123 TA
1 TA
25247125 AAATTTGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 16 0.48
19 7 0.21
20 6 0.18
21 4 0.12
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTATTATTCATTTATTAAT
Found at i:25247433 original size:252 final size:251
Alignment explanation
Indices: 25246821--25247454 Score: 686
Period size: 257 Copynumber: 2.5 Consensus size: 251
25246811 AATTACTAAA
* * *
25246821 TTTCACTATAATTATTTTTATCCTTACTATTATTCT-TTTTTAAATTAAAATTTGTAAACTGTTA
1 TTTCACTATAATTATTTTTATCCTTATTATTATT-TATCTATAAATTAAAATTTGTAAACTGTTA
* * * ** * *
25246885 AATACTTTATACTCGAAAAAATAAATTTAAACGTTTAATTTTCA-AAAAAATTATATTTATTTGA
65 AATACTTTAAACTCGAGAATATAAATTTAAATATTTAATTTT-ATAAAAAATTATGTTTATTTAA
* * * * * * * *
25246949 TATAGTTGATTTGTTATATTAAATCTCATATGTTTAAGTCAATATTTTAACAATACTTGTTTTAC
129 GATAATTAACTTGTTACATTAAATCTCACAGGTTTAAGTCAATATTTTAACAATACTTGTTCTAC
* *
25247014 TTTTATAATTTTTACATTAATCCGTACTATTTTACATCAAAACTTTTCAAATATTAAT
194 TTTTATAATTTTTACATTAATCCGTACTAATTTACATCAAAACTTTTCAAATAGTAAT
* * * *
25247072 TTTCATTATAATTATTTTTATCTTTATTATTATTATTATTCATTTATTAATTAAAATTTGTAAAT
1 TTTCACTATAATTATTTTTATCCTTATTATTA-T-TTA-TC---TATAAATTAAAATTTGTAAAC
* *
25247137 TGTTAAATACTTTAAACTCAAGAATATAAATTTAAATATTTAATTTTATAAAAAATCATGTTTAT
60 TGTTAAATACTTTAAACTCGAGAATATAAATTTAAATATTTAATTTTATAAAAAATTATGTTTAT
* * **
25247202 TTAAGATAATTAACTTGTTACGTTAAATCTCACAGGTTTACGTCAATATTTTAACAATGGTTGTT
125 TTAAGATAATTAACTTGTTACATTAAATCTCACAGGTTTAAGTCAATATTTTAACAATACTTGTT
* * * * ** *** * * *
25247267 CTA-TGTTTATAATTTTTTTACTTTAATTCTTACTAATTTACGTTTAGGTTTTTTAATTGGT-AT
190 CTACT-TTTATAA--TTTTTACATTAATCCGTACTAATTTACATCAAAACTTTTCAAATAGTAAT
* *
25247330 TGTTCACTGTAATTA-TTTTATCCTTATTATTATTTATCTATAAATTAAAACTTGTAAACCT-TT
1 T-TTCACTATAATTATTTTTATCCTTATTATTATTTATCTATAAATTAAAATTTGTAAA-CTGTT
* *
25247393 AAATACTTTAAACTCGAGAATATAAATTTAAATTTTTAATTTTTTAAAAAATTTATGTTTAT
64 AAATACTTTAAACTCGAGAATATAAATTTAAATATTTAATTTTATAAAAAA-TTATGTTTAT
25247455 CTTTAAGCAA
Statistics
Matches: 317, Mismatches: 52, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
251 29 0.09
252 70 0.22
253 11 0.03
254 1 0.00
255 2 0.01
256 5 0.02
257 136 0.43
258 19 0.06
259 44 0.14
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (251 bp):
TTTCACTATAATTATTTTTATCCTTATTATTATTTATCTATAAATTAAAATTTGTAAACTGTTAA
ATACTTTAAACTCGAGAATATAAATTTAAATATTTAATTTTATAAAAAATTATGTTTATTTAAGA
TAATTAACTTGTTACATTAAATCTCACAGGTTTAAGTCAATATTTTAACAATACTTGTTCTACTT
TTATAATTTTTACATTAATCCGTACTAATTTACATCAAAACTTTTCAAATAGTAAT
Found at i:25250987 original size:253 final size:252
Alignment explanation
Indices: 25250359--25251386 Score: 1267
Period size: 252 Copynumber: 4.1 Consensus size: 252
25250349 TATAAACCTA
* * ** * * **
25250359 TAAAAAATCTTGACGTAAATTTGTAAGAATTAATGTAAAATATTATCAAAGTAAAACAAGCATTG
1 TAAAAAACCTTGACGTAAACTTGTAAGAATTAACATAAAAAATTATAAAAGTGGAACAAGCATTG
* * *
25250424 TAAAAATATTTATGTAAATATATGAGATTTAACGTAACAAGTCAATTATGTCAAATAAACATACT
66 TCAAAATATTGATGTAAATATATGAGATTTAACGTAACAAGTCAATTATGTCAAATAAACATAAT
* *
25250489 TTTTTGAAAAATTAAATATTTAAATTTATATTCTCGAGTTTAAAGTATTTAATGATTTACAAATT
131 TTTTTGAAAAATTAAATATTTAAATTTATATTCTCAAGTTTAAAGTATTTAATGATTTATAAATT
* ** * ** **
25250554 TTAATTTATAAATAAATAATAGTAACAATACAAATAATTATAGCAAAAATTAGTTGT
196 TTAATTTATAAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAGCAGT
* * * * * * *
25250611 TAAAAAACCTTGACATAAAAC-AGTAAGAATTAACGTTAAAAATTATAAAAATGGAATAGGCATT
1 TAAAAAACCTTGACGT-AAACTTGTAAGAATTAACATAAAAAATTATAAAAGTGGAACAAGCATT
* * ** *
25250675 GTTAAAATATTAATGTAAACGTATGAGATTTAACGTAACAAGTCAATTATGTCAAATAAATATAA
65 GTCAAAATATTGATGTAAATATATGAGATTTAACGTAACAAGTCAATTATGTCAAATAAACATAA
* *
25250740 TTTTTTGAAAAATTAAATATTTAAATTTATATTATCAAGTTTAAAGTATTTAATGGTTTATAAAT
130 TTTTTTGAAAAATTAAATATTTAAATTTATATTCTCAAGTTTAAAGTATTTAATGATTTATAAAT
* * *
25250805 TTTAATTTATAAATGAACAATTAGTTAGGATAAAAATAATTATAGTGAAAATTAGTAGT
195 TTTAATTTATAAATGAATAA-TAGTAAGGATAAAAATAATTATAGTGAAAATTAGCAGT
* * * *
25250864 TAAAAAACCTTGATGTAAACTTGTAAGAATTAACATAAAAAATTATAGAGGTGGAACAAGCATTA
1 TAAAAAACCTTGACGTAAACTTGTAAGAATTAACATAAAAAATTATAAAAGTGGAACAAGCATTG
* * * * * *
25250929 TCAAAAGATTGATATAAATATGTGAGGTTTAACGTAATAAGTCAATTATGTTAAATAAACATAAT
66 TCAAAATATTGATGTAAATATATGAGATTTAACGTAACAAGTCAATTATGTCAAATAAACATAAT
* * ** *
25250994 TTTTTTAAAAATTAAATATTTAAATTTCTATTCTCAAGTTTATAATGT-TGGAGTG-TTTATAAA
131 TTTTTGAAAAATTAAATATTTAAATTTATATTCTCAAGTTTA-AA-GTATTTAATGATTTATAAA
* * * *
25251057 TTTTAATCTATGAATGAATAATAGTAAGGATAAAAATAATTACAGTGAAAA-TAGCAAT
194 TTTTAATTTATAAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAGCAGT
* ** * *
25251115 TAAAAAACCTTGACGTAAACCTACAAGAATTAACATAAAAAATTATAAAGGTGGAACAAACATTG
1 TAAAAAACCTTGACGTAAACTTGTAAGAATTAACATAAAAAATTATAAAAGTGGAACAAGCATTG
* ** *
25251180 TCAAAATATTGACGTAAACGTATGAAATTTTAA-GTAACAAGTCAATTATGTCAAATAAACAT-A
66 TCAAAATATTGATGTAAATATATGAGA-TTTAACGTAACAAGTCAATTATGTCAAATAAACATAA
** * * **
25251243 TGTTTTAAAAAAAATTAAATATTTAAATTTATATTCTCGAGTTTAAATTATTTAACAATTTATAA
130 T-TTTT-TGAAAAATTAAATATTTAAATTTATATTCTCAAGTTTAAAGTATTTAATGATTTATAA
* * *
25251308 ATTTTAATTTATAAAAGAATATTAGTAAGGATAAAAATAATTATAGTGAAAATTAACAGT
193 ATTTTAATTTATAAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAGCAGT
*
25251368 TGAAAAACCTTGACGTAAA
1 TAAAAAACCTTGACGTAAA
25251387 ACTCCAATAG
Statistics
Matches: 663, Mismatches: 102, Indels: 21
0.84 0.13 0.03
Matches are distributed among these distances:
250 3 0.00
251 117 0.18
252 310 0.47
253 225 0.34
254 6 0.01
255 2 0.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (252 bp):
TAAAAAACCTTGACGTAAACTTGTAAGAATTAACATAAAAAATTATAAAAGTGGAACAAGCATTG
TCAAAATATTGATGTAAATATATGAGATTTAACGTAACAAGTCAATTATGTCAAATAAACATAAT
TTTTTGAAAAATTAAATATTTAAATTTATATTCTCAAGTTTAAAGTATTTAATGATTTATAAATT
TTAATTTATAAATGAATAATAGTAAGGATAAAAATAATTATAGTGAAAATTAGCAGT
Found at i:25251309 original size:505 final size:503
Alignment explanation
Indices: 25250048--25251386 Score: 1504
Period size: 505 Copynumber: 2.6 Consensus size: 503
25250038 AATTTTAAAT
* * * * *
25250048 GTAAGGATAAAAATAATTATATTGAAAATTAGCAATTGAAAAATCTTAACTTAAAACACTAAGAA
1 GTAAGGATAAAAATAATTATAGTGAAAATTAGCAATTAAAAAACCTTGACATAAAACAC-AAGAA
* * * * * * *
25250113 TTAACATAAAAAATTATAAATGTGGAACAAATATTGTCAAAATATTAACATAAACATGTAAAAGT
65 TTAACATAAAAAATTATAAAAGTGGAACAAACATTGTCAAAATATTAACGTAAACGTATGAAATT
* * * * *
25250178 TAACATAACATGTAAATTATGTCAAATAAATATAATTTTTTGAAAAATTGAACATTTAAATTTAT
130 TAACGTAACAAGTCAATTATGTCAAATAAATATAATTTTTTGAAAAATTAAATATTTAAATTTAT
* * * * * *
25250243 ATTCTCGAGTTTAGAGTATTTAACGGTTTACAAATTTTTATTTATAAAGGAATAA-TAATAAAGA
195 ATTCTCGAGTTTAAAGTATTTAACGGTTTATAAATTTTAATTTATAAAAGAA-AATTAGTAAGGA
* *
25250307 TAAAAATAATTATAATGAAAATCAATAGTTGAAAAACCTTGATATAAACCTATAAAAAATCTTGA
259 TAAAAATAATTATAGTGAAAAT---TAG-T-----A----G---------T-TAAAAAACCTTGA
* ** * * * *
25250372 CGTAAATTTGTAAGAATTAATGTAAAATATTATCAAAGTAAAACAAGCATTGTAAAAATATTTAT
301 CGTAAACTTGTAAGAATTAACATAAAAAATTATCAAAGTAAAACAAGCATTATAAAAAGATTGAT
* *
25250437 GTAAATATATGAGATTTAACGTAACAAGTCAATTATGTCAAATAAACATACTTTTTTGAAAAATT
366 ATAAATATATGAGATTTAACGTAACAAGTCAATTATGTCAAATAAACATAATTTTTTGAAAAATT
* ** *
25250502 AAATATTTAAATTTATATTCTCGAGTTTAAAGTATTTAATGATTTACAAATTTTAATTTATAAAT
431 AAATATTTAAATTTATATTCTCAAGTTTAAAGTATGGAATGATTTACAAATTTTAATCTATAAAT
25250567 AAATAATA
496 AAATAATA
** * ** *** *
25250575 GTAACAATACAAATAATTATAGCAAAAATTAGTTGTTAAAAAACCTTGACATAAAACAGTAAGAA
1 GTAAGGATAAAAATAATTATAGTGAAAATTAGCAATTAAAAAACCTTGACATAAAACA-CAAGAA
* * * * ** * * *
25250640 TTAACGTTAAAAATTATAAAAATGGAATAGGCATTGTTAAAATATTAATGTAAACGTATGAGATT
65 TTAACATAAAAAATTATAAAAGTGGAACAAACATTGTCAAAATATTAACGTAAACGTATGAAATT
25250705 TAACGTAACAAGTCAATTATGTCAAATAAATATAATTTTTTGAAAAATTAAATATTTAAATTTAT
130 TAACGTAACAAGTCAATTATGTCAAATAAATATAATTTTTTGAAAAATTAAATATTTAAATTTAT
* * * * *
25250770 ATTATCAAGTTTAAAGTATTTAATGGTTTATAAATTTTAATTTATAAATGAACAATTAGTTAGGA
195 ATTCTCGAGTTTAAAGTATTTAACGGTTTATAAATTTTAATTTATAAAAGAA-AATTAGTAAGGA
*
25250835 TAAAAATAATTATAGTGAAAATTAGTAGTTAAAAAACCTTGATGTAAACTTGTAAGAATTAACAT
259 TAAAAATAATTATAGTGAAAATTAGTAGTTAAAAAACCTTGACGTAAACTTGTAAGAATTAACAT
* ** * * *
25250900 AAAAAATTAT-AGAGGTGGAACAAGCATTATCAAAAGATTGATATAAATATGTGAGGTTTAACGT
324 AAAAAATTATCA-AAGTAAAACAAGCATTATAAAAAGATTGATATAAATATATGAGATTTAACGT
* * * *
25250964 AATAAGTCAATTATGTTAAATAAACATAATTTTTTTAAAAATTAAATATTTAAATTTCTATTCTC
388 AACAAGTCAATTATGTCAAATAAACATAATTTTTTGAAAAATTAAATATTTAAATTTATATTCTC
* * * *
25251029 AAGTTTATAATGT-TGGAGTG-TTTATAAATTTTAATCTATGAATGAATAATA
453 AAGTTTA-AA-GTATGGAATGATTTACAAATTTTAATCTATAAATAAATAATA
* * *
25251080 GTAAGGATAAAAATAATTACAGTGAAAA-TAGCAATTAAAAAACCTTGACGTAAACCTACAAGAA
1 GTAAGGATAAAAATAATTATAGTGAAAATTAGCAATTAAAAAACCTTGACATAAAAC-ACAAGAA
* *
25251144 TTAACATAAAAAATTATAAAGGTGGAACAAACATTGTCAAAATATTGACGTAAACGTATGAAATT
65 TTAACATAAAAAATTATAAAAGTGGAACAAACATTGTCAAAATATTAACGTAAACGTATGAAA-T
* **
25251209 TTAA-GTAACAAGTCAATTATGTCAAATAAACAT-ATGTTTTAAAAAAAATTAAATATTTAAATT
129 TTAACGTAACAAGTCAATTATGTCAAATAAATATAAT-TTTT-TGAAAAATTAAATATTTAAATT
* ** *
25251272 TATATTCTCGAGTTTAAATTATTTAACAATTTATAAATTTTAATTTATAAAAGAATATTAGTAAG
192 TATATTCTCGAGTTTAAAGTATTTAACGGTTTATAAATTTTAATTTATAAAAGAAAATTAGTAAG
** *
25251337 GATAAAAATAATTATAGTGAAAATTAACAGTTGAAAAACCTTGACGTAAA
257 GATAAAAATAATTATAGTGAAAATTAGTAGTTAAAAAACCTTGACGTAAA
25251387 ACTCCAATAG
Statistics
Matches: 688, Mismatches: 115, Indels: 41
0.82 0.14 0.05
Matches are distributed among these distances:
503 2 0.00
504 167 0.24
505 271 0.39
506 7 0.01
507 2 0.00
515 1 0.00
519 1 0.00
524 1 0.00
525 3 0.00
527 206 0.30
528 27 0.04
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (503 bp):
GTAAGGATAAAAATAATTATAGTGAAAATTAGCAATTAAAAAACCTTGACATAAAACACAAGAAT
TAACATAAAAAATTATAAAAGTGGAACAAACATTGTCAAAATATTAACGTAAACGTATGAAATTT
AACGTAACAAGTCAATTATGTCAAATAAATATAATTTTTTGAAAAATTAAATATTTAAATTTATA
TTCTCGAGTTTAAAGTATTTAACGGTTTATAAATTTTAATTTATAAAAGAAAATTAGTAAGGATA
AAAATAATTATAGTGAAAATTAGTAGTTAAAAAACCTTGACGTAAACTTGTAAGAATTAACATAA
AAAATTATCAAAGTAAAACAAGCATTATAAAAAGATTGATATAAATATATGAGATTTAACGTAAC
AAGTCAATTATGTCAAATAAACATAATTTTTTGAAAAATTAAATATTTAAATTTATATTCTCAAG
TTTAAAGTATGGAATGATTTACAAATTTTAATCTATAAATAAATAATA
Found at i:25254520 original size:42 final size:42
Alignment explanation
Indices: 25254473--25254597 Score: 178
Period size: 42 Copynumber: 3.0 Consensus size: 42
25254463 CATCTCATAT
** *
25254473 GCAACGGCTTATGCACACTCCCACTCGCACATAGCCAGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* *
25254515 GCAACGGCTTATGTGCACTCTCACTCGCACATAGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* * *
25254557 GCAATGGCTTATGTGCACTCCTACTTGCACATAGCCGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
25254598 CACATCAACA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:25254933 original size:20 final size:20
Alignment explanation
Indices: 25254908--25254949 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
25254898 TATTAATTCA
25254908 CTTACTATAAACCCTAAAAG
1 CTTACTATAAACCCTAAAAG
25254928 CTTACTATAAACCCTAAAAG
1 CTTACTATAAACCCTAAAAG
25254948 CT
1 CT
25254950 ATCTCTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.26, G:0.05, T:0.26
Consensus pattern (20 bp):
CTTACTATAAACCCTAAAAG
Found at i:25257458 original size:253 final size:256
Alignment explanation
Indices: 25256985--25257464 Score: 655
Period size: 253 Copynumber: 1.9 Consensus size: 256
25256975 AACAAAAGCA
* * * * *
25256985 GTAAGAATTAATGTAAAAAATTATACAGGTGGAACAAGTATTGCCAAAATATTGATGTAAATATG
1 GTAAGAATTAATGTAAAAAATTAGAAAGGTGGAACAAATATTACCAAAATATTGACGTAAATATG
* * * * * * * **
25257050 TGAGATTTAACGTAATAAGTCAATTATGTTAAATAAACATATATATATTTTTTTTAAATTAAACA
66 TGAAATTTAACATAATAAGTCAAATAAGTAAAATAAACATATATATACTTTGTAAAAATTAAACA
* * *
25257115 TTTAAATTTATAGTCTCGAGTTTAAAGTATTTAACGGTTTATAAATTTTAATTTATAAATGAATA
131 TTTAAATTTATAGTATCGAGCTAAAAGTATTTAACGGTTTATAAATTTTAATTTATAAATGAATA
* * * *
25257180 ATAGTAAGGATAACAATACTTATAGTGAAAATTAATAGTTGAAAAATCTTAACATAAATCT
196 ATAATAAAGATAAAAATAATTATAGTGAAAATTAATAGTTGAAAAATCTTAACATAAATCT
* *
25257241 GTAAGAATTAATGTAAAAAATTAGAAAGGT-GACATAAATATTATCAAAATATTGACGTAAATAT
1 GTAAGAATTAATGTAAAAAATTAGAAAGGTGGA-ACAAATATTACCAAAATATTGACGTAAATAT
*
25257305 GTGAAATTTAATATAATAAGTCAAATAAGTCAAAAT-AA-ATATA-AT-CTTTGTAAAAATTAAA
65 GTGAAATTTAACATAATAAGTCAAATAAGT-AAAATAAACATATATATACTTTGTAAAAATTAAA
* * *
25257366 CATTTAAATTTTTATTATTGAGCTAAAAGTATTTAACGGTTTATAAATTTTAATTTATAAATGAA
129 CATTTAAATTTATAGTATCGAGCTAAAAGTATTTAACGGTTTATAAATTTTAATTTATAAATGAA
*
25257431 TAATAATAAAGATAAAAATAATTATAGTTAAAAT
194 TAATAATAAAGATAAAAATAATTATAGTGAAAAT
25257465 AATTATTTAT
Statistics
Matches: 194, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
253 100 0.52
254 2 0.01
255 7 0.04
256 81 0.42
257 4 0.02
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.36
Consensus pattern (256 bp):
GTAAGAATTAATGTAAAAAATTAGAAAGGTGGAACAAATATTACCAAAATATTGACGTAAATATG
TGAAATTTAACATAATAAGTCAAATAAGTAAAATAAACATATATATACTTTGTAAAAATTAAACA
TTTAAATTTATAGTATCGAGCTAAAAGTATTTAACGGTTTATAAATTTTAATTTATAAATGAATA
ATAATAAAGATAAAAATAATTATAGTGAAAATTAATAGTTGAAAAATCTTAACATAAATCT
Found at i:25258057 original size:12 final size:12
Alignment explanation
Indices: 25258028--25258068 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
25258018 TTTTTTGTTA
25258028 TAAAAAAT-AAT
1 TAAAAAATAAAT
25258039 T--AAAATAAAT
1 TAAAAAATAAAT
25258049 TAAAAAATAAAT
1 TAAAAAATAAAT
25258061 TAAAAAAT
1 TAAAAAAT
25258069 TTTAAATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
11 1 0.04
12 17 0.63
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAAAATAAAT
Found at i:25262351 original size:12 final size:12
Alignment explanation
Indices: 25262311--25262354 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
25262301 AAATAGATAT
*
25262311 GAGAGAGAGAAA
1 GAGAGAGAGAAG
* *
25262323 GAGAAAGAGAGG
1 GAGAGAGAGAAG
25262335 GAGAGAGAGAAG
1 GAGAGAGAGAAG
25262347 GAGAGAGA
1 GAGAGAGA
25262355 TATCATTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (12 bp):
GAGAGAGAGAAG
Found at i:25263050 original size:16 final size:16
Alignment explanation
Indices: 25263029--25263060 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25263019 GCATTGAATG
25263029 AGAGGAAATTAAGTCA
1 AGAGGAAATTAAGTCA
25263045 AGAGGAAATTAAGTCA
1 AGAGGAAATTAAGTCA
25263061 GAAAAGCAAT
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:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (16 bp):
AGAGGAAATTAAGTCA
Found at i:25264660 original size:13 final size:13
Alignment explanation
Indices: 25264644--25264668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25264634 TAAGGGAAAA
25264644 TTGAAAGGGGAAT
1 TTGAAAGGGGAAT
25264657 TTGAAAGGGGAA
1 TTGAAAGGGGAA
25264669 ACAGGAAACT
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:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (13 bp):
TTGAAAGGGGAAT
Found at i:25270177 original size:64 final size:63
Alignment explanation
Indices: 25270054--25270177 Score: 167
Period size: 64 Copynumber: 2.0 Consensus size: 63
25270044 TGGTTAAGAA
* * * * * * *
25270054 TCATGGGATTTCAAAAGTACTTGAATTCTGAATCTTTGAATTGCCAATTTACATGATTTAGAC
1 TCATGAGATTTAAAAAATACTTGAATTCAGAACCTTTAAATTGCCAATTCACATGATTTAGAC
*
25270117 TCATGAGATTTAAAAAATACTTGAATTTCAGAACCTTTAAATTGTCAATTCACATGATTTA
1 TCATGAGATTTAAAAAATACTTGAA-TTCAGAACCTTTAAATTGCCAATTCACATGATTTA
25270178 AACATTATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
63 22 0.42
64 30 0.58
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (63 bp):
TCATGAGATTTAAAAAATACTTGAATTCAGAACCTTTAAATTGCCAATTCACATGATTTAGAC
Found at i:25273704 original size:29 final size:30
Alignment explanation
Indices: 25273662--25273721 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
25273652 CCACTTTTTT
25273662 TTTTAAATTTTTTTAAAATTTTTGTTT-TGAA
1 TTTTAAA-TTTTTTAAAATTTTT-TTTATGAA
25273693 TTTTAAA-TTTTTAAAATTTTTTTTATGAA
1 TTTTAAATTTTTTAAAATTTTTTTTATGAA
25273722 CTTGCACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 3 0.11
29 18 0.64
31 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTTTTAAAATTTTTTTTATGAA
Found at i:25276291 original size:2 final size:2
Alignment explanation
Indices: 25276284--25276322 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25276274 TTTCTATAAC
25276284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25276323 GTATNGCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25276426 original size:38 final size:38
Alignment explanation
Indices: 25276370--25276453 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
25276360 TATCATCATC
* * * * *
25276370 ATCATCATGTGCATTCCCTATTCTCACATTTCGATATA
1 ATCATCATGTGCACTCCCTACTCACACAATTCAATATA
*
25276408 ATCATCATGTGCACTCCCTACTCACACAATTCAATATC
1 ATCATCATGTGCACTCCCTACTCACACAATTCAATATA
25276446 ATCA-CATG
1 ATCATCATG
25276454 CACTCCTGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 4 0.10
38 36 0.90
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (38 bp):
ATCATCATGTGCACTCCCTACTCACACAATTCAATATA
Found at i:25277326 original size:3 final size:3
Alignment explanation
Indices: 25277318--25277342 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25277308 CATGAGATGG
25277318 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
25277343 CTACTGAAAA
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:25283525 original size:2 final size:2
Alignment explanation
Indices: 25283518--25283552 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
25283508 TTTCTAGAAC
*
25283518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25283553 CATACATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25283653 original size:41 final size:40
Alignment explanation
Indices: 25283590--25283706 Score: 166
Period size: 38 Copynumber: 3.0 Consensus size: 40
25283580 CACACTTAGT
* ***
25283590 TCATGTGCACTCCCTACACGCACAAGGCAATATCATCATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCAT-A
*
25283631 TCATGTGCACTCCTTACTCGCACATTTCAATATCAT--TA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCATA
25283669 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
25283707 CATGCACTCC
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
38 36 0.53
39 1 0.01
41 31 0.46
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.30
Consensus pattern (40 bp):
TCATGTGCACTCCCTACTCGCACATTTCAATATCATCATA
Found at i:25283725 original size:32 final size:37
Alignment explanation
Indices: 25283624--25283717 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 37
25283614 AGGCAATATC
*
25283624 ATCATCATCATGTGCACTCCTTACTCGCACATTTCAAT
1 ATCATCATCA-GTGCACTCCCTACTCGCACATTTCAAT
*
25283662 ATCATTATCATGTGCACTCCCTACTCGCACATTTCAAT
1 ATCATCATCA-GTGCACTCCCTACTCGCACATTTCAAT
25283700 ATCATCA-CA-TGCACTCCC
1 ATCATCATCAGTGCACTCCC
25283718 ACCCACATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
35 9 0.17
37 2 0.04
38 42 0.79
ACGTcount: A:0.27, C:0.34, G:0.07, T:0.32
Consensus pattern (37 bp):
ATCATCATCAGTGCACTCCCTACTCGCACATTTCAAT
Found at i:25284602 original size:19 final size:18
Alignment explanation
Indices: 25284578--25284623 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 18
25284568 ATGAGAGGAA
25284578 GAAAAAGAAGAAGCTGCT
1 GAAAAAGAAGAAGCTGCT
25284596 GGAAAAATGAGAAGAAGCTGCT
1 -G-AAAA--AGAAGAAGCTGCT
25284618 GAAAAA
1 GAAAAA
25284624 TGATATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 1 0.04
19 1 0.04
20 8 0.33
21 1 0.04
22 13 0.54
ACGTcount: A:0.52, C:0.09, G:0.28, T:0.11
Consensus pattern (18 bp):
GAAAAAGAAGAAGCTGCT
Found at i:25284608 original size:22 final size:21
Alignment explanation
Indices: 25284583--25284626 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 21
25284573 AGGAAGAAAA
25284583 AGAAGAAGCTGCTGGAAAAATG
1 AGAAGAAGCTGCT-GAAAAATG
25284605 AGAAGAAGCTGCTGAAAAATG
1 AGAAGAAGCTGCTGAAAAATG
25284626 A
1 A
25284627 TATTTATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.48, C:0.09, G:0.30, T:0.14
Consensus pattern (21 bp):
AGAAGAAGCTGCTGAAAAATG
Found at i:25285610 original size:21 final size:21
Alignment explanation
Indices: 25285557--25285624 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
25285547 TTGAATGGAG
* *
25285557 GCATCAGTCC-TTATCATAAAT
1 GCATCAG-CCTTTGTCATGAAT
* *
25285578 GCATCAGTCTTTGTTATGAAT
1 GCATCAGCCTTTGTCATGAAT
25285599 GCATCAGCCTTTGTCATGAATT
1 GCATCAGCCTTTGTCATGAA-T
25285621 GCAT
1 GCAT
25285625 GAACATATCC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 1 0.03
21 33 0.85
22 5 0.13
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (21 bp):
GCATCAGCCTTTGTCATGAAT
Found at i:25306627 original size:35 final size:35
Alignment explanation
Indices: 25306583--25306720 Score: 149
Period size: 35 Copynumber: 4.0 Consensus size: 35
25306573 GTTAGTTTTG
* * *
25306583 GGTTTTGGTTGTTCTTGTGAAAAACCATTGTTAAA
1 GGTTGTGGTTGATCTTGTGAAAAGCCATTGTTAAA
* * *
25306618 GGTTGTGGTTAAGCCTT-TGAAAAGCCATT-TT--G
1 GGTTGTGGTTGA-TCTTGTGAAAAGCCATTGTTAAA
* *
25306650 GGTTTTGGTTGATCTTGTGAAAAGCCATTATTAAA
1 GGTTGTGGTTGATCTTGTGAAAAGCCATTGTTAAA
* *
25306685 GGTTGTGGTTGAGCTTGTGAAAAGCCATTGTAAAA
1 GGTTGTGGTTGATCTTGTGAAAAGCCATTGTTAAA
25306720 G
1 G
25306721 CTTGGTGGAA
Statistics
Matches: 84, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
31 3 0.04
32 22 0.26
33 2 0.02
34 2 0.02
35 52 0.62
36 3 0.04
ACGTcount: A:0.26, C:0.09, G:0.27, T:0.38
Consensus pattern (35 bp):
GGTTGTGGTTGATCTTGTGAAAAGCCATTGTTAAA
Found at i:25306666 original size:67 final size:67
Alignment explanation
Indices: 25306578--25306713 Score: 220
Period size: 67 Copynumber: 2.0 Consensus size: 67
25306568 GAAAAGTTAG
* *
25306578 TTTTGGGTTTTGGTTGTTCTTGTGAAAAACCATTGTTAAAGGTTGTGGTTAAGCCTT-TGAAAAG
1 TTTTGGGTTTTGGTTGATCTTGTGAAAAACCATTATTAAAGGTTGTGGTTAAG-CTTGTGAAAAG
25306642 CCA
65 CCA
* *
25306645 TTTTGGGTTTTGGTTGATCTTGTGAAAAGCCATTATTAAAGGTTGTGGTTGAGCTTGTGAAAAGC
1 TTTTGGGTTTTGGTTGATCTTGTGAAAAACCATTATTAAAGGTTGTGGTTAAGCTTGTGAAAAGC
25306710 CA
66 CA
25306712 TT
1 TT
25306714 GTAAAAGCTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 3 0.05
67 61 0.95
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (67 bp):
TTTTGGGTTTTGGTTGATCTTGTGAAAAACCATTATTAAAGGTTGTGGTTAAGCTTGTGAAAAGC
CA
Found at i:25308528 original size:43 final size:43
Alignment explanation
Indices: 25308434--25308557 Score: 171
Period size: 43 Copynumber: 2.9 Consensus size: 43
25308424 TGATGACCTA
* * *
25308434 GCTATGTGCGATGT-GGGAGTGCACATGAG-CGATGATGACTTG
1 GCTATGTGCGA-GTAGGGAGTGCGCATAAGCCGATGATGACTCG
*
25308476 GCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATTATGACTCG
1 GCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGACTCG
* *
25308519 GCTATGTGCGAGTAAGGAGTACGCATAAGCCGATGATGA
1 GCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGA
25308558 TGACCCGGCT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.03
42 24 0.33
43 47 0.64
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.23
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGACTCG
Found at i:25319140 original size:20 final size:20
Alignment explanation
Indices: 25319103--25319140 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25319093 TTAACAAGCA
*
25319103 AAGAAGAAAGAGTTTTAATG
1 AAGAAGAAAGAGTCTTAATG
25319123 AAGACAGAAAG-GTCTTAA
1 AAGA-AGAAAGAGTCTTAA
25319141 CTGGTTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.21
Consensus pattern (20 bp):
AAGAAGAAAGAGTCTTAATG
Found at i:25319788 original size:35 final size:35
Alignment explanation
Indices: 25319743--25319867 Score: 141
Period size: 35 Copynumber: 3.7 Consensus size: 35
25319733 GTTAGTTCTG
*
25319743 GGTTTTGGTTGATCCCATGAAAAACCATTGTTAAA
1 GGTTGTGGTTGATCCCATGAAAAACCATTGTTAAA
* ** * *
25319778 GGTTGTGGTTGAGCCTTTGAAAAGCCATT-TT--G
1 GGTTGTGGTTGATCCCATGAAAAACCATTGTTAAA
*
25319810 GGTTTTGGTTGATCCCATGAAAAACCATTGTTAAA
1 GGTTGTGGTTGATCCCATGAAAAACCATTGTTAAA
*
25319845 GGTTGTGGCTGA-CCCTATGAAAA
1 GGTTGTGGTTGATCCC-ATGAAAA
25319868 GCTATTGTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
32 24 0.33
33 2 0.03
34 5 0.07
35 41 0.57
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (35 bp):
GGTTGTGGTTGATCCCATGAAAAACCATTGTTAAA
Found at i:25319819 original size:67 final size:67
Alignment explanation
Indices: 25319741--25319869 Score: 231
Period size: 67 Copynumber: 1.9 Consensus size: 67
25319731 AAGTTAGTTC
* * *
25319741 TGGGTTTTGGTTGATCCCATGAAAAACCATTGTTAAAGGTTGTGGTTGAGCCTTTGAAAAGCCAT
1 TGGGTTTTGGTTGATCCCATGAAAAACCATTGTTAAAGGTTGTGGCTGACCCTATGAAAAGCCAT
25319806 TT
66 TT
25319808 TGGGTTTTGGTTGATCCCATGAAAAACCATTGTTAAAGGTTGTGGCTGACCCTATGAAAAGC
1 TGGGTTTTGGTTGATCCCATGAAAAACCATTGTTAAAGGTTGTGGCTGACCCTATGAAAAGC
25319870 TATTGTAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (67 bp):
TGGGTTTTGGTTGATCCCATGAAAAACCATTGTTAAAGGTTGTGGCTGACCCTATGAAAAGCCAT
TT
Found at i:25319831 original size:32 final size:33
Alignment explanation
Indices: 25319741--25319841 Score: 123
Period size: 32 Copynumber: 3.0 Consensus size: 33
25319731 AAGTTAGTTC
25319741 TGGGTTTTGGTTGATCCCATGAAAAACCATTGT
1 TGGGTTTTGGTTGATCCCATGAAAAACCATTGT
* * * ** *
25319774 TAAAGGTTGTGGTTGAGCCTTTGAAAAGCCATT-T
1 T--GGGTTTTGGTTGATCCCATGAAAAACCATTGT
25319808 TGGGTTTTGGTTGATCCCATGAAAAACCATTGT
1 TGGGTTTTGGTTGATCCCATGAAAAACCATTGT
25319841 T
1 T
25319842 AAAGGTTGTG
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
32 24 0.45
33 3 0.06
34 2 0.04
35 24 0.45
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.37
Consensus pattern (33 bp):
TGGGTTTTGGTTGATCCCATGAAAAACCATTGT
Found at i:25338644 original size:60 final size:60
Alignment explanation
Indices: 25338529--25338645 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
25338519 TATAAAGGGG
* * * *
25338529 GACTTGAAGCCTTGAGTTATATTAGGTGGCGTGGGGAGTTCCCACGAGTAGGTAAAAGGT
1 GACTTGAAGCCCTGAGTTATATTAGATGGCGTGGGGAGTTCCCACAAGTAAGTAAAAGGT
* * * *
25338589 GACTTGAAGCCCTGATTTATATTTGATGGCGTGGGGAGTTTCCATAAGTAAGTAAAA
1 GACTTGAAGCCCTGAGTTATATTAGATGGCGTGGGGAGTTCCCACAAGTAAGTAAAA
25338646 AGGGAACTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (60 bp):
GACTTGAAGCCCTGAGTTATATTAGATGGCGTGGGGAGTTCCCACAAGTAAGTAAAAGGT
Found at i:25341134 original size:2 final size:2
Alignment explanation
Indices: 25341124--25341157 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
25341114 CATGACACAC
* *
25341124 AT AT CT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25341158 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25346440 original size:22 final size:22
Alignment explanation
Indices: 25346388--25346440 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
25346378 GCTATAAATA
*
25346388 TCATT-TTCCAGCAGCTTCTTC
1 TCATTCTTCCAGCAGCTTATTC
* *
25346409 TCATTTTTCCAGTAGCTTATTC
1 TCATTCTTCCAGCAGCTTATTC
25346431 TTC-TTCTTCC
1 -TCATTCTTCC
25346441 TCCCATCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 20 0.74
23 2 0.07
ACGTcount: A:0.13, C:0.30, G:0.08, T:0.49
Consensus pattern (22 bp):
TCATTCTTCCAGCAGCTTATTC
Found at i:25348706 original size:44 final size:44
Alignment explanation
Indices: 25348652--25348739 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
25348642 TTCATCACTA
*
25348652 AGAGTATTCCACAGACCTCACAAATCACACTTATGTCACTGTAT
1 AGAGTATTCCACAAACCTCACAAATCACACTTATGTCACTGTAT
25348696 AGAGTATTCCACAAACCTCACAAATCACACTTATGTCACTGTAT
1 AGAGTATTCCACAAACCTCACAAATCACACTTATGTCACTGTAT
25348740 CTTCATAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.27
Consensus pattern (44 bp):
AGAGTATTCCACAAACCTCACAAATCACACTTATGTCACTGTAT
Found at i:25350460 original size:37 final size:37
Alignment explanation
Indices: 25350353--25350462 Score: 103
Period size: 37 Copynumber: 3.0 Consensus size: 37
25350343 CCTCAGCTCT
* * *** * * *
25350353 TGTGCACTACCTACACGCACAAGGCAATACCACCATA
1 TGTGCACTCCCTACCCGCACACCTCAATATCATCATG
* ** *
25350390 TGTGCACTCCCTACTCGCACATTTCAATGTCATCATG
1 TGTGCACTCCCTACCCGCACACCTCAATATCATCATG
*
25350427 TGTGCACTCCCTACCCGCACACCTCATTATCATCAT
1 TGTGCACTCCCTACCCGCACACCTCAATATCATCAT
25350463 ATAACATTAT
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.26, C:0.36, G:0.12, T:0.25
Consensus pattern (37 bp):
TGTGCACTCCCTACCCGCACACCTCAATATCATCATG
Found at i:25354567 original size:39 final size:41
Alignment explanation
Indices: 25354523--25354625 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 41
25354513 ATAAGAGACC
* * * *
25354523 AAAACAGAAAGTTTTTCGCTGCAGT-GAAATTTCTACCCA-
1 AAAACAGAAAGTTTCTCGCTGCAGTCAAAATTACAACCCAG
*
25354562 AAAACAGAATGTTTCTCGCTGCA-TCAAAATTACAACCCAG
1 AAAACAGAAAGTTTCTCGCTGCAGTCAAAATTACAACCCAG
**
25354602 AAATTAGAAAGTTTCTCGCTGCAG
1 AAAACAGAAAGTTTCTCGCTGCAG
25354626 CGAGAATGCC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.02
39 32 0.60
40 20 0.38
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (41 bp):
AAAACAGAAAGTTTCTCGCTGCAGTCAAAATTACAACCCAG
Found at i:25355932 original size:19 final size:20
Alignment explanation
Indices: 25355898--25355935 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
25355888 GAGAAAGACC
25355898 AGCTGCTAGAAAATTCAAGA
1 AGCTGCTAGAAAATTCAAGA
*
25355918 AGCTGCT-GGAAATTCAAG
1 AGCTGCTAGAAAATTCAAG
25355936 GTATTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (20 bp):
AGCTGCTAGAAAATTCAAGA
Found at i:25360926 original size:37 final size:37
Alignment explanation
Indices: 25360856--25360928 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
25360846 TACCACCATA
** *
25360856 TGTGCACTCCCTACTCGCACATTTCAATGTCATCATT
1 TGTGCACTCCCTACTCGCACACCTCAATATCATCATT
* *
25360893 TGTGCACTCCTTACTCGCACACCTCATTATCATCAT
1 TGTGCACTCCCTACTCGCACACCTCAATATCATCAT
25360929 ACAACATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.22, C:0.34, G:0.10, T:0.34
Consensus pattern (37 bp):
TGTGCACTCCCTACTCGCACACCTCAATATCATCATT
Found at i:25361543 original size:2 final size:2
Alignment explanation
Indices: 25361536--25361566 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25361526 ATGTGCATAG
25361536 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25361567 AGAACGTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:25367419 original size:20 final size:19
Alignment explanation
Indices: 25367365--25367419 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
25367355 TAATAATATT
25367365 ATTAATTAATTAA-TTTAA
1 ATTAATTAATTAATTTTAA
*
25367383 ATAAATTATATTTAATTTTAA
1 ATTAATTA-A-TTAATTTTAA
*
25367404 ATTAACTAATTCAATT
1 ATTAATTAATT-AATT
25367420 CTATAGACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.23
19 3 0.10
20 9 0.30
21 11 0.37
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAATTAATTAATTTTAA
Found at i:25371325 original size:17 final size:17
Alignment explanation
Indices: 25371295--25371327 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25371285 TTCTTGATAA
25371295 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
25371312 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
25371328 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:25372568 original size:16 final size:17
Alignment explanation
Indices: 25372547--25372581 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
25372537 TCCTTTTGTT
25372547 TTTTAATA-AAAAAATA
1 TTTTAATACAAAAAATA
25372563 TTTTAATAGCAAAAAATA
1 TTTTAATA-CAAAAAATA
25372581 T
1 T
25372582 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
TTTTAATACAAAAAATA
Found at i:25382793 original size:19 final size:20
Alignment explanation
Indices: 25382755--25382794 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25382745 CGCGATTTCC
*
25382755 CCTTTGAATTTTCTAGTTTT
1 CCTTTGAATTTTCTACTTTT
*
25382775 CCTTTGATTTTTCT-CTTTT
1 CCTTTGAATTTTCTACTTTT
25382794 C
1 C
25382795 TTCCTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.10, C:0.20, G:0.07, T:0.62
Consensus pattern (20 bp):
CCTTTGAATTTTCTACTTTT
Found at i:25387344 original size:2 final size:2
Alignment explanation
Indices: 25387337--25387373 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25387327 NNNNNNNNNN
25387337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25387374 CATGTATAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25400656 original size:21 final size:20
Alignment explanation
Indices: 25400631--25400672 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
25400621 AATTAATTAA
25400631 TTTAAATGAATCATATTCAAT
1 TTTAAATGAATCA-ATTCAAT
* *
25400652 TTTAAATTAATTAATTCAAT
1 TTTAAATGAATCAATTCAAT
25400672 T
1 T
25400673 CTATAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTAAATGAATCAATTCAAT
Found at i:25404730 original size:38 final size:40
Alignment explanation
Indices: 25404641--25404744 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 40
25404631 CACACCCGAC
* * *
25404641 TCATGTATATCCCTCCACATCGTGCACATAGCCGACACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCCAACACCA
* * **
25404681 TCATGTGCATCCCCCCACATCGTGCACA-A-TCAATGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCCAACACCA
25404719 TCATGTACATCCCCCCACATCGTGCA
1 TCATGTACATCCCCCCACATCGTGCA
25404745 AACGGGCACT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 30 0.54
39 1 0.02
40 25 0.45
ACGTcount: A:0.26, C:0.39, G:0.12, T:0.22
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCCAACACCA
Found at i:25405660 original size:5 final size:6
Alignment explanation
Indices: 25405615--25405647 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
25405605 TGTTTTGAAG
25405615 AAAT-A AAATGA AAATGA AAATGA AAAT-A AAATG
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATG
25405648 GATGATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (6 bp):
AAATGA
Found at i:25406387 original size:24 final size:25
Alignment explanation
Indices: 25406347--25406393 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
25406337 TTTGTGCAGG
25406347 AAAATTGGATAGCTTTG-TGCTGCC
1 AAAATTGGATAGCTTTGTTGCTGCC
*
25406371 AAAATTGAGA-AGTTTTGTTGCTG
1 AAAATTG-GATAGCTTTGTTGCTG
25406394 GAAATCTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.36
Consensus pattern (25 bp):
AAAATTGGATAGCTTTGTTGCTGCC
Found at i:25406597 original size:25 final size:25
Alignment explanation
Indices: 25406559--25406618 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
25406549 GACAAAGAAA
25406559 AGAAAATAAATGGGCATGACCCAAT
1 AGAAAATAAATGGGCATGACCCAAT
* *
25406584 AGAAAATAAGTGGGCATGGCCCAAT
1 AGAAAATAAATGGGCATGACCCAAT
*
25406609 AGGAAATAAA
1 AGAAAATAAA
25406619 AATAAATAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.48, C:0.13, G:0.23, T:0.15
Consensus pattern (25 bp):
AGAAAATAAATGGGCATGACCCAAT
Found at i:25422956 original size:21 final size:21
Alignment explanation
Indices: 25422930--25422979 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
25422920 TATAGCTATT
*
25422930 TATCGATAGATCCCGTGGATC
1 TATCGATAGATCCCGTAGATC
*
25422951 TATCGATAGATTCCGTAGATC
1 TATCGATAGATCCCGTAGATC
*
25422972 TATTGATA
1 TATCGATA
25422980 AATGGTTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (21 bp):
TATCGATAGATCCCGTAGATC
Found at i:25422966 original size:92 final size:92
Alignment explanation
Indices: 25422856--25423056 Score: 366
Period size: 92 Copynumber: 2.2 Consensus size: 92
25422846 CCGTTCAGCT
*
25422856 ATCTATCGATAGATTCCGTAGATCGATTGATAAATGGTTCTCAATTTGGTTTCCATTATATTCAT
1 ATCTATCGATAGATTCCGTAGATCGATTGATAAATGGTTCTCAATTTGGTTTCCATTAGATTCAT
25422921 ATAGCTATTTATCGATAGATCCCGTGG
66 ATAGCTATTTATCGATAGATCCCGTGG
*
25422948 ATCTATCGATAGATTCCGTAGATCTATTGATAAATGGTTCTCAATTTGGTTTCCATTAGATTCAT
1 ATCTATCGATAGATTCCGTAGATCGATTGATAAATGGTTCTCAATTTGGTTTCCATTAGATTCAT
25423013 ATAGCTATTTATCGATAGATCCCGTGG
66 ATAGCTATTTATCGATAGATCCCGTGG
**
25423040 ATCTATTAATAGATTCC
1 ATCTATCGATAGATTCC
25423057 ATCTAGATCA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 105 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (92 bp):
ATCTATCGATAGATTCCGTAGATCGATTGATAAATGGTTCTCAATTTGGTTTCCATTAGATTCAT
ATAGCTATTTATCGATAGATCCCGTGG
Found at i:25431022 original size:7 final size:7
Alignment explanation
Indices: 25430990--25431028 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
25430980 CGAAAATGTT
25430990 AATAAT-
1 AATAATA
25430996 AATAATA
1 AATAATA
* *
25431003 AACAATC
1 AATAATA
25431010 AATAATA
1 AATAATA
25431017 AATAATA
1 AATAATA
25431024 AATAA
1 AATAA
25431029 AAAAGGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:25431561 original size:2 final size:2
Alignment explanation
Indices: 25431510--25431545 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25431500 AAACATATCA
25431510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25431546 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25437493 original size:27 final size:28
Alignment explanation
Indices: 25437461--25437516 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
25437451 AAAAGAGTGT
*
25437461 TTAGACTGCC-TATTAGACACATAACAA
1 TTAGACTCCCTTATTAGACACATAACAA
25437488 TTAGACTCCCTTATTAGACACATAACAA
1 TTAGACTCCCTTATTAGACACATAACAA
25437516 T
1 T
25437517 AAGAAAGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (28 bp):
TTAGACTCCCTTATTAGACACATAACAA
Found at i:25438716 original size:2 final size:2
Alignment explanation
Indices: 25438709--25438749 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
25438699 GTTGAAGTCA
25438709 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25438750 GTGTTTTAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:25455806 original size:2 final size:2
Alignment explanation
Indices: 25455801--25455965 Score: 143
Period size: 2 Copynumber: 82.5 Consensus size: 2
25455791 ACACACACAC
* ** * * * * *
25455801 AT AT AT A- AT AC AT AT AT AT GG AT AT GT AT GT AT AT GT AC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
25455842 AT AT AT AT AG AT AT GT AT AT GT AC AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * **
25455884 AT AT AT AT AT AT AT AT AT AT AT AT AC CT GAA AG GN AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
25455927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25455966 CCTGAAAGGA
Statistics
Matches: 127, Mismatches: 34, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
1 1 0.01
2 126 0.99
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (2 bp):
AT
Found at i:25457101 original size:13 final size:13
Alignment explanation
Indices: 25457083--25457109 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25457073 AAAAAATTTC
25457083 TCACATTTCATTA
1 TCACATTTCATTA
25457096 TCACATTTCATTA
1 TCACATTTCATTA
25457109 T
1 T
25457110 TAGATTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (13 bp):
TCACATTTCATTA
Found at i:25463327 original size:16 final size:18
Alignment explanation
Indices: 25463306--25463343 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
25463296 AAAAATATTT
25463306 ATAACAA-AACAAA-ATA
1 ATAACAACAACAAATATA
*
25463322 ATAACAACATCAAATATA
1 ATAACAACAACAAATATA
25463340 ATAA
1 ATAA
25463344 AATTTAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 5 0.26
18 7 0.37
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.18
Consensus pattern (18 bp):
ATAACAACAACAAATATA
Found at i:25466037 original size:16 final size:16
Alignment explanation
Indices: 25466016--25466046 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25466006 TGTCATTTTC
*
25466016 AATAAATTTTAAATTG
1 AATAAATTATAAATTG
25466032 AATAAATTATAAATT
1 AATAAATTATAAATT
25466047 TATATTTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
AATAAATTATAAATTG
Found at i:25470628 original size:50 final size:50
Alignment explanation
Indices: 25470569--25470669 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 50
25470559 ACACAATTTG
*
25470569 TTTAACTATTTATAC-ATTACTATGTATTATTTTTATCATAAC-TAAATCTA
1 TTTAACTATTTAT-CGATTACTATGTATTATTTTTACCATAACAT-AATCTA
* *
25470619 TTTAACTATTTATCGATTATTGTGTATTATTTTTACCATAACATAATCTA
1 TTTAACTATTTATCGATTACTATGTATTATTTTTACCATAACATAATCTA
25470669 T
1 T
25470670 CCTTTTACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
49 1 0.02
50 44 0.96
51 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.50
Consensus pattern (50 bp):
TTTAACTATTTATCGATTACTATGTATTATTTTTACCATAACATAATCTA
Found at i:25471983 original size:15 final size:16
Alignment explanation
Indices: 25471959--25471991 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25471949 ATTTAAAATA
25471959 TAAATAATTAATAATT
1 TAAATAATTAATAATT
*
25471975 TAAAT-ATTAATATTT
1 TAAATAATTAATAATT
25471990 TA
1 TA
25471992 TTTATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAATAATTAATAATT
Found at i:25477915 original size:4 final size:4
Alignment explanation
Indices: 25477906--25478065 Score: 203
Period size: 4 Copynumber: 40.0 Consensus size: 4
25477896 ATTATCATGG
*
25477906 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
25477954 ATAT ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT ATAT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * *
25478002 ATGT ATGT ATAT ATAT ATAT GTAT GTAT GTAT ATAT ATAT ATGT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
25478050 ATGT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT
25478066 GTATGTATGT
Statistics
Matches: 146, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 146 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:25477934 original size:22 final size:22
Alignment explanation
Indices: 25477907--25478078 Score: 208
Period size: 22 Copynumber: 8.0 Consensus size: 22
25477897 TTATCATGGA
* * *
25477907 TATATATATATATATATATATA
1 TATATATATGTATGTATGTATA
* * *
25477929 TATATATATATATATATATATA
1 TATATATATGTATGTATGTATA
* * * *
25477951 TGTATATATATATATATATATA
1 TATATATATGTATGTATGTATA
* *
25477973 TATATGTATGTATGTAT-A---
1 TATATATATGTATGTATGTATA
25477991 TATATATATGTATGTATGTATA
1 TATATATATGTATGTATGTATA
25478013 TATATATATGTATGTATGTATA
1 TATATATATGTATGTATGTATA
25478035 TATATATATGTATGTATGTATA
1 TATATATATGTATGTATGTATA
25478057 TATATATATGTATGTATGTATA
1 TATATATATGTATGTATGTATA
25478079 ACCAGGGGAG
Statistics
Matches: 138, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
18 16 0.12
22 122 0.88
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (22 bp):
TATATATATGTATGTATGTATA
Found at i:25477942 original size:26 final size:26
Alignment explanation
Indices: 25477906--25478065 Score: 221
Period size: 26 Copynumber: 6.2 Consensus size: 26
25477896 ATTATCATGG
*
25477906 ATATATATATATATATATATATATAT
1 ATATATATATATATATATATGTATAT
25477932 ATATATATATATATATATATGTATAT
1 ATATATATATATATATATATGTATAT
*
25477958 ATATATATATATATATATATGTATGT
1 ATATATATATATATATATATGTATAT
* * *
25477984 ATGTATATATATATATGTATGTATGT
1 ATATATATATATATATATATGTATAT
* *
25478010 ATATATATATATGTATGTATGTATAT
1 ATATATATATATATATATATGTATAT
* * * *
25478036 ATATATATGTATGTATGTATATATAT
1 ATATATATATATATATATATGTATAT
25478062 ATAT
1 ATAT
25478066 GTATGTATGT
Statistics
Matches: 125, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 125 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (26 bp):
ATATATATATATATATATATGTATAT
Found at i:25478070 original size:4 final size:4
Alignment explanation
Indices: 25477975--25478077 Score: 78
Period size: 4 Copynumber: 27.8 Consensus size: 4
25477965 TATATATATA
* * * *
25477975 TATG TATG TATG TA-- TATA TATA TATG TATG TATG TA-- TATA TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
25478019 TATG TATG TATG TA-- TATA TATA TATG TATG TATG TA-- TATA TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
25478063 TATG TATG TATG TAT
1 TATG TATG TATG TAT
25478078 AACCAGGGGA
Statistics
Matches: 87, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.09
4 79 0.91
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:25478073 original size:18 final size:18
Alignment explanation
Indices: 25477906--25478065 Score: 203
Period size: 18 Copynumber: 8.9 Consensus size: 18
25477896 ATTATCATGG
25477906 ATATATATATATATATAT
1 ATATATATATATATATAT
25477924 ATATATATATATATATAT
1 ATATATATATATATATAT
*
25477942 ATATATATATGTATATAT
1 ATATATATATATATATAT
25477960 ATATATATATATATATAT
1 ATATATATATATATATAT
* * *
25477978 GTATGTATGTATATATAT
1 ATATATATATATATATAT
* * *
25477996 ATATGTATGTATGTATAT
1 ATATATATATATATATAT
* * *
25478014 ATATATATGTATGTATGT
1 ATATATATATATATATAT
* *
25478032 ATATATATATATGTATGT
1 ATATATATATATATATAT
*
25478050 ATGTATATATATATAT
1 ATATATATATATATAT
25478066 GTATGTATGT
Statistics
Matches: 130, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 130 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
ATATATATATATATATAT
Found at i:25478983 original size:13 final size:13
Alignment explanation
Indices: 25478965--25478989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25478955 AGCAATTTTG
25478965 AACACGACATAAT
1 AACACGACATAAT
25478978 AACACGACATAA
1 AACACGACATAA
25478990 GAAGACATGG
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:0.56, C:0.24, G:0.08, T:0.12
Consensus pattern (13 bp):
AACACGACATAAT
Found at i:25483571 original size:22 final size:22
Alignment explanation
Indices: 25483531--25483572 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
25483521 GCACACAAGC
* *
25483531 CTCTTTCTATCTATTTTTTTCT
1 CTCTTTCTACCTATCTTTTTCT
*
25483553 CTCTTTCTACCTCTCTTTTT
1 CTCTTTCTACCTATCTTTTT
25483573 ATTTCTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (22 bp):
CTCTTTCTACCTATCTTTTTCT
Found at i:25496498 original size:20 final size:20
Alignment explanation
Indices: 25496473--25496512 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
25496463 CCTGAAGAAC
25496473 ATCTATGGATAGATGGCCAA
1 ATCTATGGATAGATGGCCAA
*
25496493 ATCTATTGATAGATGGCCAA
1 ATCTATGGATAGATGGCCAA
25496513 CAAGAAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (20 bp):
ATCTATGGATAGATGGCCAA
Found at i:25513830 original size:44 final size:44
Alignment explanation
Indices: 25513763--25513870 Score: 162
Period size: 46 Copynumber: 2.4 Consensus size: 44
25513753 AGTTTAAGTA
*
25513763 AACTAGACTCATTTAGGTATATATTTTGTTATCTATAGTTAATCTC
1 AACTAGACTCATTTAGGTATATATTTTCTTA--TATAGTTAATCTC
* *
25513809 AACTAGGCTCATTTAGGTATATATTTTCTTATATAGTTGATCTC
1 AACTAGACTCATTTAGGTATATATTTTCTTATATAGTTAATCTC
*
25513853 AACTAGACTCATATAGGT
1 AACTAGACTCATTTAGGT
25513871 TCCATATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 28 0.49
46 29 0.51
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.43
Consensus pattern (44 bp):
AACTAGACTCATTTAGGTATATATTTTCTTATATAGTTAATCTC
Found at i:25514423 original size:44 final size:44
Alignment explanation
Indices: 25514373--25514467 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
25514363 ACAAAAAACG
* * *
25514373 GTGACAATATTCTCACATTGTGACAAATACTAGTGATGGAATTA
1 GTGACAACATTATCACATTGTGACAAATACTAGTGACGGAATTA
25514417 GTGACAACATTATCACATTGTGACAAATACTAGTGACGGAATTA
1 GTGACAACATTATCACATTGTGACAAATACTAGTGACGGAATTA
25514461 GTGACAA
1 GTGACAA
25514468 AATAGATTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (44 bp):
GTGACAACATTATCACATTGTGACAAATACTAGTGACGGAATTA
Found at i:25526402 original size:5 final size:5
Alignment explanation
Indices: 25526392--25526417 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
25526382 ATGATTATAT
25526392 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
25526418 CTCTAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:25534089 original size:6 final size:6
Alignment explanation
Indices: 25534078--25534115 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
25534068 TCTCGGGGAG
* *
25534078 AAGAAA AAGAAA GAGAAA GAGAAA AAGAAA AA-AAA AAG
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG
25534116 GAGCAGCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:25534185 original size:3 final size:3
Alignment explanation
Indices: 25534177--25534241 Score: 76
Period size: 3 Copynumber: 20.3 Consensus size: 3
25534167 CGTGTCGAGG
*
25534177 AGA AGA AGA AGAA AGA AGA AAA AGA AGA AGGA AGA AGAA AGA AGAA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA A-GA AGA AG-A AGA AG-A AGA
*
25534226 AGA AAA AGA AGA AGA A
1 AGA AGA AGA AGA AGA A
25534242 AGAGAAAAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
3 42 0.78
4 12 0.22
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:25534194 original size:7 final size:7
Alignment explanation
Indices: 25534177--25534248 Score: 93
Period size: 7 Copynumber: 11.1 Consensus size: 7
25534167 CGTGTCGAGG
25534177 AGAAG-A
1 AGAAGAA
25534183 AGAAGAA
1 AGAAGAA
25534190 AGAAGAA
1 AGAAGAA
25534197 A-AAG-A
1 AGAAGAA
*
25534202 AGAAGGA
1 AGAAGAA
25534209 AGAAGAA
1 AGAAGAA
25534216 AGAAGAA
1 AGAAGAA
25534223 AGAAGAA
1 AGAAGAA
25534230 A-AAG-A
1 AGAAGAA
25534235 AGAAGAA
1 AGAAGAA
25534242 AG-AGAA
1 AGAAGAA
25534248 A
1 A
25534249 AGGAGCAGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
5 4 0.07
6 22 0.37
7 34 0.57
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:25534224 original size:33 final size:33
Alignment explanation
Indices: 25534177--25534248 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
25534167 CGTGTCGAGG
*
25534177 AGAAG-AAGAAGAAAGAAGAAAAAGAAGAAGGA
1 AGAAGAAAGAAGAAAGAAGAAAAAGAAGAAGAA
25534209 AGAAGAAAGAAGAAAGAAGAAAAAGAAGAAGAA
1 AGAAGAAAGAAGAAAGAAGAAAAAGAAGAAGAA
25534242 AG-AGAAA
1 AGAAGAAA
25534249 AGGAGCAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 10 0.26
33 28 0.74
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (33 bp):
AGAAGAAAGAAGAAAGAAGAAAAAGAAGAAGAA
Found at i:25534250 original size:26 final size:27
Alignment explanation
Indices: 25534179--25534248 Score: 110
Period size: 26 Copynumber: 2.7 Consensus size: 27
25534169 TGTCGAGGAG
25534179 AAGAAGAAGAAAGAAGAAA-AAGAAGA
1 AAGAAGAAGAAAGAAGAAAGAAGAAGA
*
25534205 AGGAAGAAGAAAGAAGAAAGAAGAA-A
1 AAGAAGAAGAAAGAAGAAAGAAGAAGA
25534231 AAGAAGAAGAAAG-AGAAA
1 AAGAAGAAGAAAGAAGAAA
25534249 AGGAGCAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.12
26 31 0.76
27 5 0.12
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (27 bp):
AAGAAGAAGAAAGAAGAAAGAAGAAGA
Found at i:25534292 original size:2 final size:2
Alignment explanation
Indices: 25534287--25534322 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
25534277 AAGGAAAAAA
* *
25534287 AT AT AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25534323 TAAGTGTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Done.