Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 37 of 235
Found at i:12030258 original size:27 final size:26
Alignment explanation
Indices: 12030210--12030261 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
12030200 GCGAGGCTGC
*
12030210 CAGATAATGTGACGAAGTCACCAGAA
1 CAGATAATGTGACGAAGCCACCAGAA
* *
12030236 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATA-ATGTGACGAAGCCACCAGA
12030262 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.37, C:0.21, G:0.27, T:0.15
Consensus pattern (26 bp):
CAGATAATGTGACGAAGCCACCAGAA
Found at i:12035441 original size:61 final size:62
Alignment explanation
Indices: 12035344--12035490 Score: 215
Period size: 61 Copynumber: 2.4 Consensus size: 62
12035334 CCATGTGACC
*
12035344 CTAATTCTAAAATAGTGAGTTACACAGCCTGGACACACGCTCGTGTCCCTAGCCCCTATGCCT
1 CTAATTCT-AAATAGTGAGTTACACAGCCTGGACACACGCCCGTGTCCCTAGCCCCTATGCCT
* * * * *
12035407 CTAATTCTAACT-GTGAGTTACACAGCCTGGACACACGCCCGTGTCCTTCGCCCGTGTGCCT
1 CTAATTCTAAATAGTGAGTTACACAGCCTGGACACACGCCCGTGTCCCTAGCCCCTATGCCT
*
12035468 CTAATTTTAAATAGTGAGTTACA
1 CTAATTCTAAATAGTGAGTTACA
12035491 TAACCTGTCA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
61 54 0.72
62 13 0.17
63 8 0.11
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (62 bp):
CTAATTCTAAATAGTGAGTTACACAGCCTGGACACACGCCCGTGTCCCTAGCCCCTATGCCT
Found at i:12039811 original size:16 final size:17
Alignment explanation
Indices: 12039788--12039825 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
12039778 AATAAACAAT
12039788 TAAA-TAAATT-GGAAA
1 TAAATTAAATTGGGAAA
12039803 TAAATTAAATTGGGAAA
1 TAAATTAAATTGGGAAA
12039820 TAAATT
1 TAAATT
12039826 CGGACTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (17 bp):
TAAATTAAATTGGGAAA
Found at i:12047128 original size:40 final size:40
Alignment explanation
Indices: 12047073--12047247 Score: 246
Period size: 40 Copynumber: 4.4 Consensus size: 40
12047063 CGTTTGACAA
*
12047073 GGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATACCC
1 GGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATATCC
* * *
12047113 GGGCTAAGTCTCGAAGGCATTTGTGCTAGCGACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATATCC
12047153 GGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATATCC
* * * *
12047193 GGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CGATATCC
1 GGGCTAAGTCCCGAAGGCATTTATGCTAG-TGACTATATCC
*
12047233 -GGCTAAATCCCGAAG
1 GGGCTAAGTCCCGAAG
12047248 ATACTTGGGT
Statistics
Matches: 121, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
39 13 0.11
40 106 0.88
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTATGCTAGTGACTATATCC
Found at i:12052697 original size:49 final size:49
Alignment explanation
Indices: 12052640--12052737 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
12052630 GAAGAGATAT
*
12052640 TGAGTATCAGGTGGGAGACAAAGTATTTCTTAAGGTGACACCTTGGAAA
1 TGAGTATCAGGTGGGAGACAAAGTATTTCTTAAAGTGACACCTTGGAAA
* **
12052689 TGAGTATCAGGTGGGAGACAAAGTGTTTCTTAAAGTTTCACCTTGGAAA
1 TGAGTATCAGGTGGGAGACAAAGTATTTCTTAAAGTGACACCTTGGAAA
12052738 AAGATACTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.29
Consensus pattern (49 bp):
TGAGTATCAGGTGGGAGACAAAGTATTTCTTAAAGTGACACCTTGGAAA
Found at i:12054612 original size:40 final size:40
Alignment explanation
Indices: 12054564--12054739 Score: 264
Period size: 40 Copynumber: 4.4 Consensus size: 40
12054554 GGACTAAGAT
** *
12054564 CCGAAGGCATTTGTGAGATTTG-CTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGTC
* *
12054604 CCGAAGGCATTTATGCTAGTGACTATACCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
12054644 TCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
12054684 CCGAAGGCATTTATGCTAGTGACTATATCCGGGCTAAGAC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
12054724 CCGAAGGCATTTGTGC
1 CCGAAGGCATTTGTGC
12054740 GAGTTGCGAT
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
39 2 0.02
40 121 0.98
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:12054690 original size:80 final size:79
Alignment explanation
Indices: 12054552--12054768 Score: 287
Period size: 80 Copynumber: 2.7 Consensus size: 79
12054542 CAGATGATAA
* * *
12054552 CCGGACTAAGATCCGAAGGCATTTGTGAGATTTGCTATATCCGGGCTAAGTCCCGAAGGCATTTA
1 CCGGGCTAAG-TCCGAAGGCATTTGTGCGATGTGCTATATCCGGGCTAAGTCCCGAAGGCATTTA
12054617 TGCTAGTGACTATAC
65 TGCTAGTGACTATAC
*
12054632 CCGGGCTAAGTCTCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTC-CGAAGGCATTTGTGCGATGTG-CTATATCCGGGCTAAGTCCCGAAGGCATTT
*
12054696 ATGCTAGTGACTATAT
64 ATGCTAGTGACTATAC
* * * *
12054712 CCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTTGCGATAT-CTGGCTAAATCCCGAAG
1 CCGGGCTAAG-TCCGAAGGCATTTGTGCGATG-TGCTATATCCGGGCTAAGTCCCGAAG
12054769 ATACTTGGGT
Statistics
Matches: 123, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
79 19 0.15
80 101 0.82
81 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCGAAGGCATTTGTGCGATGTGCTATATCCGGGCTAAGTCCCGAAGGCATTTAT
GCTAGTGACTATAC
Found at i:12056967 original size:5 final size:5
Alignment explanation
Indices: 12056957--12056984 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12056947 AACCTAGCTG
12056957 CTCCT CTCCT CTCCT CTCCT CTCCT CTC
1 CTCCT CTCCT CTCCT CTCCT CTCCT CTC
12056985 TCATTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CTCCT
Found at i:12060706 original size:38 final size:38
Alignment explanation
Indices: 12060664--12060737 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
12060654 GAAATAGTAG
12060664 TGACTAGATAGAATATTGCTTGATGGGCTCATCTATAA
1 TGACTAGATAGAATATTGCTTGATGGGCTCATCTATAA
12060702 TGACTAGATAGAATATTGCTTGATGGGCTCATCTAT
1 TGACTAGATAGAATATTGCTTGATGGGCTCATCTAT
12060738 GTTACTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (38 bp):
TGACTAGATAGAATATTGCTTGATGGGCTCATCTATAA
Found at i:12060844 original size:35 final size:35
Alignment explanation
Indices: 12060798--12060868 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
12060788 TACGTGCTTA
12060798 GGCAAATTTAACCAAATGGATGGAAACATAATATT
1 GGCAAATTTAACCAAATGGATGGAAACATAATATT
*
12060833 GGCAAATTTAACCAAATGGATGGAAACATGATATT
1 GGCAAATTTAACCAAATGGATGGAAACATAATATT
12060868 G
1 G
12060869 TATGTTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (35 bp):
GGCAAATTTAACCAAATGGATGGAAACATAATATT
Found at i:12086534 original size:146 final size:142
Alignment explanation
Indices: 12086337--12086623 Score: 520
Period size: 146 Copynumber: 2.0 Consensus size: 142
12086327 ATGAGATGTT
12086337 TAAATTTTTGTAAAACAGGTCCAGAGCGAGGGATCCCCTGTTCAAACTTTGGAAATTCACCATAA
1 TAAATTTTTGTAAAACAGGTCCAGAGCGAGGGATCCCCTGTTCAAACTTTGGAAATTCACCATAA
12086402 ATTGTTCAAAGATAATTATAAGTCATGATTTATATTTACAGATTCCTTATTGAGTCTAATTTTAT
66 ATTGTTCAAAGATAATTATAAGTCATGATTTATATTTACAGATTCCTTATTGAGTCTAATTTTAT
12086467 TAGAAACAAACA
131 TAGAAACAAACA
*
12086479 TAAATTTTTGTGAAACAGGTCCAGAGCGATTTCGGGATCCCCTGTTCAAACTTTGGAAATTCACC
1 TAAATTTTTGTAAAACAGGTCCAGAGCGA----GGGATCCCCTGTTCAAACTTTGGAAATTCACC
12086544 ATAAATTGTTCAAAGATAATTATAAGTCATGATTTATATTTACAGATTCCTTATTGAGTCTAATT
62 ATAAATTGTTCAAAGATAATTATAAGTCATGATTTATATTTACAGATTCCTTATTGAGTCTAATT
*
12086609 TTATTATAAACAAAC
127 TTATTAGAAACAAAC
12086624 GAAATAGTCA
Statistics
Matches: 139, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
142 28 0.20
146 111 0.80
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (142 bp):
TAAATTTTTGTAAAACAGGTCCAGAGCGAGGGATCCCCTGTTCAAACTTTGGAAATTCACCATAA
ATTGTTCAAAGATAATTATAAGTCATGATTTATATTTACAGATTCCTTATTGAGTCTAATTTTAT
TAGAAACAAACA
Found at i:12102030 original size:15 final size:15
Alignment explanation
Indices: 12102010--12102038 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12102000 ATAGTCGAAT
12102010 CCTTCTACCACTCTA
1 CCTTCTACCACTCTA
12102025 CCTTCTACCACTCT
1 CCTTCTACCACTCT
12102039 TCCCTAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.34
Consensus pattern (15 bp):
CCTTCTACCACTCTA
Found at i:12113504 original size:6 final size:6
Alignment explanation
Indices: 12113488--12113521 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
12113478 AGCTTTCTCC
*
12113488 AAAATG GAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
12113522 ATAAGAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:12117629 original size:16 final size:17
Alignment explanation
Indices: 12117600--12117631 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12117590 ATTTAATATA
12117600 ATTTACTGTATATAATT
1 ATTTACTGTATATAATT
12117617 ATTTACT-TATATAAT
1 ATTTACTGTATATAAT
12117632 AAGTAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTACTGTATATAATT
Found at i:12125394 original size:93 final size:93
Alignment explanation
Indices: 12125282--12125453 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
12125272 GCCCATAAGT
* *
12125282 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
12125347 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
12125375 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
12125440 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
12125454 CAAACATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:12125449 original size:46 final size:46
Alignment explanation
Indices: 12125274--12125449 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
12125264 TGTAACCCGC
* *
12125274 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
12125320 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
12125366 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
12125413 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
12125450 TGCCCAAACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:12127885 original size:30 final size:30
Alignment explanation
Indices: 12127841--12127929 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
12127831 CAAAGATAAC
12127841 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
12127870 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
12127900 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
12127930 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:12127889 original size:15 final size:15
Alignment explanation
Indices: 12127841--12127920 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
12127831 CAAAGATAAC
*
12127841 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
12127855 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
12127870 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
12127885 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
12127900 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
12127915 AAGAAA
1 AAGAAA
12127921 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:12127929 original size:15 final size:15
Alignment explanation
Indices: 12127852--12127929 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
12127842 AGAAAACCGA
12127852 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
12127867 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
12127881 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
12127896 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
12127912 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
12127927 ATA
1 ATA
12127930 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:12143450 original size:43 final size:43
Alignment explanation
Indices: 12143402--12143521 Score: 186
Period size: 43 Copynumber: 2.8 Consensus size: 43
12143392 TGTAGCATCT
*
12143402 GAGCTCGTTGAGAGGTTCGAGTTCATTATGGATGCGAGCACCC
1 GAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGAGCACCC
* *
12143445 GAGCTCATCGAGAGGTCCGAGTTCATTATGGATGCGAGCACCC
1 GAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGAGCACCC
* * *
12143488 GAGCTCGATAAGAGGTCCGAGTTCATAATGGATG
1 GAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
12143522 TGATTCATGT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (43 bp):
GAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGAGCACCC
Found at i:12144949 original size:18 final size:19
Alignment explanation
Indices: 12144914--12144950 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12144904 AGAATTGGCC
12144914 AAATGGGCCGGTATGGGCT
1 AAATGGGCCGGTATGGGCT
*
12144933 AAATGGGCCTG-ATGGGCT
1 AAATGGGCCGGTATGGGCT
12144951 GTTGGGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.22
Consensus pattern (19 bp):
AAATGGGCCGGTATGGGCT
Found at i:12145088 original size:29 final size:29
Alignment explanation
Indices: 12145023--12145131 Score: 89
Period size: 29 Copynumber: 3.8 Consensus size: 29
12145013 GCATGAGTAT
* *
12145023 AATATGATTTGGGCCTAATGGGCCATATG
1 AATATGAATTGGGCCTAATGGGCCATAAG
* *
12145052 AA-AGTGAATTGGGCGTAGTGGGCCATAAG
1 AATA-TGAATTGGGCCTAATGGGCCATAAG
* * **
12145081 AATATGAACTGGGCC-AGATGGACCATTTG
1 AATATGAATTGGGCCTA-ATGGGCCATAAG
* *
12145110 AATA-AAATTGGGCCTAGTGGGC
1 AATATGAATTGGGCCTAATGGGC
12145132 TATATGCATG
Statistics
Matches: 62, Mismatches: 14, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
28 14 0.23
29 47 0.76
30 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (29 bp):
AATATGAATTGGGCCTAATGGGCCATAAG
Found at i:12150791 original size:49 final size:49
Alignment explanation
Indices: 12150719--12150816 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
12150709 ATGAAAAGAG
12150719 ATATATCCAAATTTGTATCGAGATGCTTGATTTGCCAACAAGTAAAGGC
1 ATATATCCAAATTTGTATCGAGATGCTTGATTTGCCAACAAGTAAAGGC
*
12150768 ATATATCCAAATTTGTATCGAGATGCTTGATTTGCCAATAAGTAAAGGC
1 ATATATCCAAATTTGTATCGAGATGCTTGATTTGCCAACAAGTAAAGGC
12150817 TGAACACCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (49 bp):
ATATATCCAAATTTGTATCGAGATGCTTGATTTGCCAACAAGTAAAGGC
Found at i:12153338 original size:43 final size:43
Alignment explanation
Indices: 12153285--12153366 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
12153275 TAAGATATGT
*
12153285 AGCATTCGAGCTCGTTGAGAGGT-TCGAGTTCATTATGGATGAG
1 AGCATCCGAGCTCGTTGAGAGGTCT-GAGTTCATTATGGATGAG
12153328 AGCATCCGAGCTCGTTGAGAGGTCTGAGTTCATTATGGA
1 AGCATCCGAGCTCGTTGAGAGGTCTGAGTTCATTATGGA
12153367 CGTGTTACAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (43 bp):
AGCATCCGAGCTCGTTGAGAGGTCTGAGTTCATTATGGATGAG
Found at i:12163413 original size:79 final size:82
Alignment explanation
Indices: 12163302--12163486 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
12163292 GCTACTCGTT
* *
12163302 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
12163365 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
12163382 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
12163445 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
12163462 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12163487 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:12163486 original size:40 final size:40
Alignment explanation
Indices: 12163283--12163486 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
12163273 CGGAATTTAA
** *
12163283 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12163323 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
12163363 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12163402 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
12163442 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
12163482 CCGGA
1 CCGGA
12163487 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12171354 original size:79 final size:78
Alignment explanation
Indices: 12171252--12171474 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
12171242 GCTCCTCGTT
* *
12171252 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
12171317 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
12171332 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
12171396 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
12171410 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
12171473 GA
63 GA
12171475 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
78 45 0.36
79 60 0.48
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:12171369 original size:39 final size:40
Alignment explanation
Indices: 12171252--12171474 Score: 280
Period size: 39 Copynumber: 5.7 Consensus size: 40
12171242 GCTCCTCGTT
* *
12171252 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
12171292 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
12171332 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
12171371 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
12171410 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
12171451 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12171475 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 67 0.40
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:12186577 original size:35 final size:35
Alignment explanation
Indices: 12186528--12186598 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
12186518 AATAAGTTAG
*
12186528 TCTCAAGAATGATTCTTTCATAAATCATTAAAACC
1 TCTCAAGAACGATTCTTTCATAAATCATTAAAACC
12186563 TCTCAAGAACGATTCTTTCATAAATCATTAAAACC
1 TCTCAAGAACGATTCTTTCATAAATCATTAAAACC
12186598 T
1 T
12186599 GTCACGAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (35 bp):
TCTCAAGAACGATTCTTTCATAAATCATTAAAACC
Found at i:12197570 original size:60 final size:61
Alignment explanation
Indices: 12197506--12197644 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 61
12197496 CCAACTGTGT
* * *
12197506 TGATATGGGC-AAGGCCCAATATA-TCTCGA-CCTGTAATAGGGCTACGGCCCAGATTGATAC
1 TGATATGGGCTAAGGCCCAATATACTCT-GATACTGTAA-AGGGCTACGCCCCAGATTAATAC
* * *
12197566 TGATATGGGCTAA-GCCCAATATACTCTGATACTGTAAGGGGCTATGCCCCAGATTAATAT
1 TGATATGGGCTAAGGCCCAATATACTCTGATACTGTAAAGGGCTACGCCCCAGATTAATAC
*
12197626 TGGTATGGGCTAAGGCCCA
1 TGATATGGGCTAAGGCCCA
12197645 GTTAACACTA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
60 52 0.76
61 16 0.24
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (61 bp):
TGATATGGGCTAAGGCCCAATATACTCTGATACTGTAAAGGGCTACGCCCCAGATTAATAC
Found at i:12199993 original size:10 final size:10
Alignment explanation
Indices: 12199975--12200017 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
12199965 TTAGGATTTT
12199975 TTTATTTATC
1 TTTATTTATC
*
12199985 TTTAATTATC
1 TTTATTTATC
12199995 TTTATTTAT-
1 TTTATTTATC
12200004 TTGTATTTATC
1 TT-TATTTATC
12200015 TTT
1 TTT
12200018 TAGAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.07
10 25 0.86
11 2 0.07
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTATTTATC
Found at i:12201159 original size:14 final size:15
Alignment explanation
Indices: 12201125--12201160 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
12201115 AGCTAATCGC
12201125 AAGGAAACAAAGCTA
1 AAGGAAACAAAGCTA
12201140 AAGGAAACAAAGCT-
1 AAGGAAACAAAGCTA
12201154 AAGGAAA
1 AAGGAAA
12201161 AAGCAATCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.61, C:0.11, G:0.22, T:0.06
Consensus pattern (15 bp):
AAGGAAACAAAGCTA
Found at i:12212218 original size:5 final size:5
Alignment explanation
Indices: 12212208--12212288 Score: 82
Period size: 5 Copynumber: 16.4 Consensus size: 5
12212198 GCAACCCAAT
12212208 TTTTA TTTTA TTTTA TTTTA TTTTA --TTA TTTTA TTTTA --TTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
*
12212254 TTATT- TATTTA TTCATTA CTTTA TTTTA TTTTA TT
1 TT-TTA T-TTTA TT--TTA TTTTA TTTTA TTTTA TT
12212289 ATTTATTACT
Statistics
Matches: 65, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
3 6 0.09
5 51 0.78
6 4 0.06
7 4 0.06
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:12212238 original size:8 final size:8
Alignment explanation
Indices: 12212210--12212303 Score: 69
Period size: 8 Copynumber: 12.2 Consensus size: 8
12212200 AACCCAATTT
12212210 TTATTTTA
1 TTATTTTA
12212218 TT-TTATT-
1 TTATT-TTA
12212225 TTATTTTA
1 TTATTTTA
12212233 TTA--TT-
1 TTATTTTA
12212238 TTATTTTA
1 TTATTTTA
12212246 TTATTTTA
1 TTATTTTA
12212254 TTA-TTTA
1 TTATTTTA
*
12212261 TT-TATTCA
1 TTAT-TTTA
*
12212269 TTACTTTATT
1 TTA-TTT-TA
12212279 TTATTTTA
1 TTATTTTA
12212287 TTA-TTTA
1 TTATTTTA
*
12212294 TTACTTTA
1 TTATTTTA
12212302 TT
1 TT
12212304 TTGTTTGGGT
Statistics
Matches: 70, Mismatches: 4, Indels: 24
0.71 0.04 0.24
Matches are distributed among these distances:
5 3 0.04
6 2 0.03
7 21 0.30
8 35 0.50
9 5 0.07
10 4 0.06
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (8 bp):
TTATTTTA
Found at i:12212252 original size:36 final size:39
Alignment explanation
Indices: 12212210--12212304 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 39
12212200 AACCCAATTT
12212210 TTATTTTA-T-TTTATTTTATT-TTA-TTATTTTATTTTA
1 TTATTTTATTATTTA-TTTATTATTACTTATTTTATTTTA
12212246 TTATTTTATTATTTATTTATTCATTACTTTATTTTATTTTA
1 TTATTTTATTATTTATTTATT-ATTAC-TTATTTTATTTTA
12212287 TTA-TTTATTACTTTATTT
1 TTATTTTATTA-TTTATTT
12212305 TGTTTGGGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
36 8 0.15
37 7 0.13
38 4 0.08
39 3 0.06
40 7 0.13
41 23 0.44
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (39 bp):
TTATTTTATTATTTATTTATTATTACTTATTTTATTTTA
Found at i:12214135 original size:10 final size:10
Alignment explanation
Indices: 12214120--12214163 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
12214110 TAAATTTAGG
12214120 ATTTATTTTT
1 ATTTATTTTT
*
12214130 ATTTATCTTT
1 ATTTATTTTT
* *
12214140 AATTATATTT
1 ATTTATTTTT
*
12214150 ATTTATTTGT
1 ATTTATTTTT
12214160 ATTT
1 ATTT
12214164 CTCTTTTAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:12222709 original size:8 final size:8
Alignment explanation
Indices: 12222698--12222723 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12222688 GTCATATTTA
12222698 CATAAGTT
1 CATAAGTT
12222706 CATAAGTT
1 CATAAGTT
12222714 CATAAGTT
1 CATAAGTT
12222722 CA
1 CA
12222724 AAATACTAAT
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:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (8 bp):
CATAAGTT
Found at i:12227495 original size:42 final size:42
Alignment explanation
Indices: 12227405--12227539 Score: 134
Period size: 44 Copynumber: 3.1 Consensus size: 42
12227395 AACGTCCCTC
* *
12227405 CTTACATGT-AATCAAATATCGATGCCACTGTCCCAAACA-GGAT
1 CTTACACGTAAATCAAATA-CGATGCGA-TGTCCCAAACATGG-T
*
12227448 CTTACACG-AAATCAAATACGATGTCGATGTCCCAGACATGGT
1 CTTACACGTAAATCAAATACGATG-CGATGTCCCAAACATGGT
* *
12227490 TTTACACGTAAATCTCAAAT-CGATGCCGATGTCCCAAACATTGT
1 CTTACACGTAAA--TCAAATACGATG-CGATGTCCCAAACATGGT
12227534 CTTACA
1 CTTACA
12227540 TATGTTTTCT
Statistics
Matches: 78, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
42 23 0.29
43 23 0.29
44 26 0.33
45 6 0.08
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (42 bp):
CTTACACGTAAATCAAATACGATGCGATGTCCCAAACATGGT
Found at i:12228160 original size:20 final size:20
Alignment explanation
Indices: 12228135--12228175 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12228125 TTCATAAAAC
12228135 CCATATTATCAACAATGACA
1 CCATATTATCAACAATGACA
12228155 CCATATTATCAACAATGACA
1 CCATATTATCAACAATGACA
12228175 C
1 C
12228176 ATCTTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (20 bp):
CCATATTATCAACAATGACA
Found at i:12230663 original size:90 final size:91
Alignment explanation
Indices: 12230491--12230664 Score: 316
Period size: 92 Copynumber: 1.9 Consensus size: 91
12230481 GTCCCCCAGT
12230491 TGTTTATATCAATCGGGAGCTAAAACCTTGAAATAATATATATATGATATACATCCAAAAGCCTA
1 TGTTTATATCAATCGGGAGCTAAAACCTTGAAATAATATATATA-GATATACATCCAAAAGCCTA
12230556 TGATTAGAACTAACCATTAAATTAGAG
65 TGATTAGAACTAACCATTAAATTAGAG
12230583 TGTTTATATCAATCGGGAGCTAAAACCTTGAAATAATATATATCA-A-ATACATCCAAAAGCCTA
1 TGTTTATATCAATCGGGAGCTAAAACCTTGAAATAATATATAT-AGATATACATCCAAAAGCCTA
12230646 TGATTAGAACTAACCATTA
65 TGATTAGAACTAACCATTA
12230665 CAAAACACGA
Statistics
Matches: 81, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
90 36 0.44
91 1 0.01
92 43 0.53
93 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.30
Consensus pattern (91 bp):
TGTTTATATCAATCGGGAGCTAAAACCTTGAAATAATATATATAGATATACATCCAAAAGCCTAT
GATTAGAACTAACCATTAAATTAGAG
Found at i:12238751 original size:29 final size:30
Alignment explanation
Indices: 12238718--12238774 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
12238708 TGGTTTAATA
*
12238718 TGCAATTGTATATATGA-ACTTTGATTTTG
1 TGCAATTGTATACATGAGACTTTGATTTTG
* *
12238747 TGCAATTTTATACATGAGATTTTGATTT
1 TGCAATTGTATACATGAGACTTTGATTT
12238775 GATCAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (30 bp):
TGCAATTGTATACATGAGACTTTGATTTTG
Found at i:12238973 original size:31 final size:31
Alignment explanation
Indices: 12238899--12238973 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
12238889 ATTTATCTAA
* * *
12238899 ATGTTTATGATTAAATAAAAATTAAAGTTTC
1 ATGTTTATAATTAAACAAAAATTAAAATTTC
* * * *
12238930 AAGTATACAATTAAACAATAATTAAAATTTC
1 ATGTTTATAATTAAACAAAAATTAAAATTTC
12238961 ATGTTTATAATTA
1 ATGTTTATAATTA
12238974 CATCAAATTA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (31 bp):
ATGTTTATAATTAAACAAAAATTAAAATTTC
Found at i:12240710 original size:20 final size:19
Alignment explanation
Indices: 12240685--12240722 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
12240675 TTACATTAAA
*
12240685 TATTATTTATATATTATTTG
1 TATTATCTATA-ATTATTTG
12240705 TATTATCTATAATTATTT
1 TATTATCTATAATTATTT
12240723 TTAATTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (19 bp):
TATTATCTATAATTATTTG
Found at i:12241440 original size:33 final size:33
Alignment explanation
Indices: 12241379--12241442 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
12241369 TATATTAATG
* *
12241379 TTTCTATTTTATTCAATAATTTATCTTTATTTT
1 TTTCTATTTTATTAAATAATTTACCTTTATTTT
* *
12241412 TTTCTATTTTATTAAATATTTTCCCTTTATT
1 TTTCTATTTTATTAAATAATTTACCTTTATT
12241443 CTTTGAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (33 bp):
TTTCTATTTTATTAAATAATTTACCTTTATTTT
Found at i:12241587 original size:17 final size:17
Alignment explanation
Indices: 12241567--12241599 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12241557 CTTTTTGAAA
12241567 TTTAAAATATTGATTTT
1 TTTAAAATATTGATTTT
*
12241584 TTTAATATATTGATTT
1 TTTAAAATATTGATTT
12241600 GTTGATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTAAAATATTGATTTT
Found at i:12244868 original size:13 final size:13
Alignment explanation
Indices: 12244852--12244891 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
12244842 CAATCTCATA
12244852 TCTCAATTTCAAT
1 TCTCAATTTCAAT
12244865 TCTCAA-TTCAATT
1 TCTCAATTTCAA-T
12244878 TCTC-ATTTC-AT
1 TCTCAATTTCAAT
12244889 TCT
1 TCT
12244892 AATAGCTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.16
12 7 0.28
13 14 0.56
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (13 bp):
TCTCAATTTCAAT
Found at i:12244877 original size:18 final size:19
Alignment explanation
Indices: 12244839--12244879 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
12244829 TGGTTCATGT
12244839 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
12244858 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
12244876 TTTC
1 TTTC
12244880 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:12245540 original size:15 final size:15
Alignment explanation
Indices: 12245516--12245568 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
12245506 ATATATATAT
*
12245516 TATAATTTCAATCAA
1 TATAAATTCAATCAA
12245531 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* * *
12245546 AATGATTTCAATCAA
1 TATAAATTCAATCAA
12245561 TATAAATT
1 TATAAATT
12245569 TGATAAATTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:12247021 original size:686 final size:688
Alignment explanation
Indices: 12245709--12247081 Score: 2615
Period size: 686 Copynumber: 2.0 Consensus size: 688
12245699 GTATTTTTCG
12245709 AGCTTTTCCAAGCTTTTCCTCGTCGACTTTGCTATTTCCTTACTTAGCCGAAACTTCTCGAGACA
1 AGCTTTTCCAAGCTTTTCCTCGTCGACTTTGCTATTTCCTTACTTAGCCGAAACTTCTCGAGACA
12245774 ACGTTAGCTACGGAAATTAAAACAATTCATATTCATTAATTCACTACTAATTTATATCTAATTAA
66 ACGTTAGCTACGGAAATTAAAACAATTCATATTCATTAATTCACTACTAATTTATATCTAATTAA
12245839 TTGAATTTTCTATTCAATTTTCTACTTTAATTTCAATTTAATCTTAACTAATTTTCACTTACGTT
131 TTGAATTTTCTATTCAATTTTCTACTTTAATTTCAATTTAATCTTAACTAATTTTCACTTACGTT
*
12245904 TCTAATTCAATTCACATTCTATTTCTATTCAATTTTCATCCATACTCTCATTTAAATATTAAATT
196 TCTAATTCAATTCACATTCTATTTCTATTCAAATTTCATCCATACTCTCATTTAAATATTAAATT
*
12245969 TCCAGCATATTTTTCTAATTTCAAAATTTCATCAATTTAGTCCCTACAACATAAAACTTATAACT
261 TCCAGCATATTTTCCTAATTTCAAAATTTCATCAATTTAGTCCCTACAACATAAAACTTATAACT
*
12246034 TACTTTACAATTTGATCCTATTATCAATTCTAGCTTGAAATTCACTCAATTAAACCCTTAATTCA
326 TACTTTACAATTTGATCCTATTATCAATTCTAACTTGAAATTCACTCAATTAAACCCTTAATTCA
*
12246099 CTATTTTATTCAACATGAACTATACTTGAAAATCTATAAACTCTCAAAATATCAACTTAATTTTA
391 CTATTTTATTCAACATGAACTATACTTGAAAATCTATAAACTCTCAAAATATCAACTTAATTTCA
12246164 ATAAAACCTTGTTTTAAAGCTTCTAAAACATCAAATTTAAGAGGAAATGACTTAATTGACTTACC
456 ATAAAACCTTGTTTTAAAGCTTCTAAAACATCAAATTTAAGAGGAAATGACTTAATTGACTTACC
* *
12246229 AAATTAAACTTCAAGCTTCAAACCTTAAATTTTTCCTTTTTTTCTTTCTTTTCTTTCTTTCCTTC
521 AAATTAAACTTCAAGCTTCAAACCTTAAATTTTCCCCTTTTTTCTTTCTTTTCTTTCTTTCCTTC
*
12246294 CTTCCCTCTCTGTTTTGTTTCTACTATTATGTTTCTT-CC-CTTCTACTTTTTTTTCTTTTGTTT
586 CTTCCCTCTCTGTTTCGTTTCTACTATTATGTTTCTTCCCTCTTCTACTTTTTTTTCTTTTGTTT
12246357 TATATACATATATATATAATATTATTTATACTTAAAAA
651 TATATACATATATATATAATATTATTTATACTTAAAAA
*
12246395 AGCTTTTCCAAGCTTTTCCTCGTCGACTTTGCTATTTCCTTAGTTAGCCGAAACTTCTCGAGACA
1 AGCTTTTCCAAGCTTTTCCTCGTCGACTTTGCTATTTCCTTACTTAGCCGAAACTTCTCGAGACA
12246460 ACGTTAGCTACGGAAATTAAAACAATTCATATTCATTAATTCACTACTAATTTATATCTAATTAA
66 ACGTTAGCTACGGAAATTAAAACAATTCATATTCATTAATTCACTACTAATTTATATCTAATTAA
12246525 TTGAATTTTCTATTCAATTTTCTACTTTAATTTCAATTTAATCTTAACTAATTTTCACTTACGTT
131 TTGAATTTTCTATTCAATTTTCTACTTTAATTTCAATTTAATCTTAACTAATTTTCACTTACGTT
12246590 TCTAATTCAATTCACATTCTATTTCTATTCAAATTTCATCCATACTCTCATTTAAATATTAAATT
196 TCTAATTCAATTCACATTCTATTTCTATTCAAATTTCATCCATACTCTCATTTAAATATTAAATT
*
12246655 TCCAGCATATTTTCCTAATTTCAAAATTTCATCAATTTAGTTCCTACAACATAAAACTTATAACT
261 TCCAGCATATTTTCCTAATTTCAAAATTTCATCAATTTAGTCCCTACAACATAAAACTTATAACT
12246720 TACTTTACAATTTGATCCTATTATCAATTCTAACTTGAAATTCACTCAATTAAACCCTTAATTCA
326 TACTTTACAATTTGATCCTATTATCAATTCTAACTTGAAATTCACTCAATTAAACCCTTAATTCA
12246785 CTATTTTATTCAACATGAACTATACTTGAAAATCTATAAACTCTCAAAATATCAACTTAATTTCA
391 CTATTTTATTCAACATGAACTATACTTGAAAATCTATAAACTCTCAAAATATCAACTTAATTTCA
12246850 ATAAAACCTTGTTTTAAAGCTTCTAAAACATCAAATTTAAGAGGAAATGACTTAATTGACTTACC
456 ATAAAACCTTGTTTTAAAGCTTCTAAAACATCAAATTTAAGAGGAAATGACTTAATTGACTTACC
*
12246915 AAATTAAACTTCAAGCTTCAAACCTTATATTTTCCCCTTTTTTCTTTCTTTTCTTTCTTTCCTTC
521 AAATTAAACTTCAAGCTTCAAACCTTAAATTTTCCCCTTTTTTCTTTCTTTTCTTTCTTTCCTTC
* *
12246980 CTTCCCTCTCTGTTTCGTTTCTACTATTCTGTTTCTTCCCTTCTTCTTCTTTTTTTTCTTTTGTT
586 CTTCCCTCTCTGTTTCGTTTCTACTATTATGTTTCTTCCC-TCTTCTACTTTTTTTTCTTTTGTT
12247045 TTATATACATATATATATAATATTATTTATACTTAAA
650 TTATATACATATATATATAATATTATTTATACTTAAA
12247082 TAATAAGTAA
Statistics
Matches: 672, Mismatches: 12, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
686 611 0.91
687 2 0.00
689 59 0.09
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (688 bp):
AGCTTTTCCAAGCTTTTCCTCGTCGACTTTGCTATTTCCTTACTTAGCCGAAACTTCTCGAGACA
ACGTTAGCTACGGAAATTAAAACAATTCATATTCATTAATTCACTACTAATTTATATCTAATTAA
TTGAATTTTCTATTCAATTTTCTACTTTAATTTCAATTTAATCTTAACTAATTTTCACTTACGTT
TCTAATTCAATTCACATTCTATTTCTATTCAAATTTCATCCATACTCTCATTTAAATATTAAATT
TCCAGCATATTTTCCTAATTTCAAAATTTCATCAATTTAGTCCCTACAACATAAAACTTATAACT
TACTTTACAATTTGATCCTATTATCAATTCTAACTTGAAATTCACTCAATTAAACCCTTAATTCA
CTATTTTATTCAACATGAACTATACTTGAAAATCTATAAACTCTCAAAATATCAACTTAATTTCA
ATAAAACCTTGTTTTAAAGCTTCTAAAACATCAAATTTAAGAGGAAATGACTTAATTGACTTACC
AAATTAAACTTCAAGCTTCAAACCTTAAATTTTCCCCTTTTTTCTTTCTTTTCTTTCTTTCCTTC
CTTCCCTCTCTGTTTCGTTTCTACTATTATGTTTCTTCCCTCTTCTACTTTTTTTTCTTTTGTTT
TATATACATATATATATAATATTATTTATACTTAAAAA
Found at i:12247124 original size:19 final size:19
Alignment explanation
Indices: 12247100--12247138 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12247090 AATACTTATT
*
12247100 TATTATTTATACATGTGTA
1 TATTATTAATACATGTGTA
12247119 TATTATTAATACATGTGTA
1 TATTATTAATACATGTGTA
12247138 T
1 T
12247139 CTATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TATTATTAATACATGTGTA
Found at i:12247146 original size:19 final size:19
Alignment explanation
Indices: 12247103--12247146 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
12247093 ACTTATTTAT
12247103 TATTT-ATACATGTGTATA
1 TATTTAATACATGTGTATA
*
12247121 T-TATTAATACATGTGTATC
1 TAT-TTAATACATGTGTATA
12247140 TATTTAA
1 TATTTAA
12247147 AACCACACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 1 0.05
18 3 0.14
19 17 0.77
20 1 0.05
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (19 bp):
TATTTAATACATGTGTATA
Found at i:12248911 original size:14 final size:14
Alignment explanation
Indices: 12248894--12248939 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
12248884 CAGAAATCAA
12248894 TTTCCGAAAACCAT
1 TTTCCGAAAACCAT
* *
12248908 TTTCCAAAAATCAT
1 TTTCCGAAAACCAT
*
12248922 TTTCCGATAACCAT
1 TTTCCGAAAACCAT
12248936 TTTC
1 TTTC
12248940 AGTCAAACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (14 bp):
TTTCCGAAAACCAT
Found at i:12248918 original size:28 final size:28
Alignment explanation
Indices: 12248878--12248939 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
12248868 AAAGTAAGCA
*
12248878 ATTTTCCAGAAATCAATTTCCGAAAACC
1 ATTTTCCAAAAATCAATTTCCGAAAACC
* *
12248906 ATTTTCCAAAAATCATTTTCCGATAACC
1 ATTTTCCAAAAATCAATTTCCGAAAACC
12248934 ATTTTC
1 ATTTTC
12248940 AGTCAAACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.35
Consensus pattern (28 bp):
ATTTTCCAAAAATCAATTTCCGAAAACC
Found at i:12255258 original size:40 final size:41
Alignment explanation
Indices: 12255214--12255290 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
12255204 TTTTGCAGCA
12255214 TTTTTCAAAAAAGCG-CACTAATTCTCGATCTTTAGCGGCG
1 TTTTTCAAAAAAGCGCCACTAATTCTCGATCTTTAGCGGCG
* *
12255254 TTTTTCAAAAAAGTGCCATTAATTCTCGATCTTTAGC
1 TTTTTCAAAAAAGCGCCACTAATTCTCGATCTTTAGC
12255291 ACCAATTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 14 0.41
41 20 0.59
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (41 bp):
TTTTTCAAAAAAGCGCCACTAATTCTCGATCTTTAGCGGCG
Found at i:12255299 original size:20 final size:20
Alignment explanation
Indices: 12255274--12255311 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12255264 AAGTGCCATT
12255274 AATTCTCGATCTTTAGCACC
1 AATTCTCGATCTTTAGCACC
12255294 AATTCTCGATCTTTAGCA
1 AATTCTCGATCTTTAGCA
12255312 GCGTTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (20 bp):
AATTCTCGATCTTTAGCACC
Found at i:12255584 original size:22 final size:22
Alignment explanation
Indices: 12255559--12255600 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
12255549 AAATGAAACC
12255559 AAACCCTAAACCCTAAATATTT
1 AAACCCTAAACCCTAAATATTT
12255581 AAACCCTAAACCCTAAATAT
1 AAACCCTAAACCCTAAATAT
12255601 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACCCTAAACCCTAAATATTT
Found at i:12255891 original size:22 final size:23
Alignment explanation
Indices: 12255845--12255891 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
12255835 TTAACATACT
* *
12255845 AACCACTAGACCCTAAAACATAA
1 AACCACTAAACCCTAAAACAAAA
*
12255868 AACC-CTAAACCCTAAACCAAAA
1 AACCACTAAACCCTAAAACAAAA
12255890 AA
1 AA
12255892 AATAAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.55, C:0.32, G:0.02, T:0.11
Consensus pattern (23 bp):
AACCACTAAACCCTAAAACAAAA
Found at i:12256080 original size:14 final size:14
Alignment explanation
Indices: 12256054--12256080 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12256044 GTTTTTAAAA
12256054 TTTAGGGTTTAAGC
1 TTTAGGGTTTAAGC
12256068 TTTAGGGTTTAAG
1 TTTAGGGTTTAAG
12256081 GGCTTAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTAGGGTTTAAGC
Found at i:12256285 original size:18 final size:18
Alignment explanation
Indices: 12256249--12256283 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12256239 AAAATCAGTT
*
12256249 TCAAATATCAAAATAAAA
1 TCAAATATCAAAAAAAAA
12256267 TCAAAT-TCAAAAAAAAA
1 TCAAATATCAAAAAAAAA
12256284 ATAATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (18 bp):
TCAAATATCAAAAAAAAA
Found at i:12256392 original size:41 final size:41
Alignment explanation
Indices: 12256325--12256573 Score: 318
Period size: 41 Copynumber: 6.0 Consensus size: 41
12256315 AACGAGTGTC
* * *
12256325 GGCGTTTGGACCAGAAATGCCGCTATTGCTCAGTTTTTAGC
1 GGCGTTTGGACCAAAAACGCCGCTATTGCTCAGTTTTTAGT
* ** *
12256366 AGCGTTTGGACCAAAAACGCTACTATTGCTCAGTTTTTTTGT
1 GGCGTTTGGACCAAAAACGCCGCTATTGCTCAG-TTTTTAGT
* * * *
12256408 AGCGTTTGGACCAAAAAAGCCGCTATTGTTCAATTTTTAGT
1 GGCGTTTGGACCAAAAACGCCGCTATTGCTCAGTTTTTAGT
* * *
12256449 GGCATTTGGACCAGAAACGTCGCTATTGCTCAGTTTTTAGT
1 GGCGTTTGGACCAAAAACGCCGCTATTGCTCAGTTTTTAGT
* * *
12256490 GGCGTTTGGACCAAAAACGCCGCTATTGCTCTGTTTTAAGC
1 GGCGTTTGGACCAAAAACGCCGCTATTGCTCAGTTTTTAGT
* *
12256531 GGCGTTTGGACCAGAAACACCGCTATTGCTCAGTTTTTAGT
1 GGCGTTTGGACCAAAAACGCCGCTATTGCTCAGTTTTTAGT
12256572 GG
1 GG
12256574 AATTTTCTTG
Statistics
Matches: 176, Mismatches: 31, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
41 142 0.81
42 34 0.19
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (41 bp):
GGCGTTTGGACCAAAAACGCCGCTATTGCTCAGTTTTTAGT
Found at i:12263222 original size:39 final size:40
Alignment explanation
Indices: 12263159--12263234 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
12263149 AGCTCGGATA
*
12263159 TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAAT
1 TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAAT
*
12263198 TAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
12263235 GTATCAATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 24 0.71
40 10 0.29
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAAT
Found at i:12265789 original size:27 final size:27
Alignment explanation
Indices: 12265759--12265928 Score: 195
Period size: 27 Copynumber: 6.4 Consensus size: 27
12265749 TGGATAAGTT
*
12265759 GTAGAATTACCAAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAAG
*
12265786 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAAG
**
12265813 GTAGAATTATTGAAATACCCCTGT-AG
1 GTAGAATTACCGAAATACCCCTGTAAG
12265839 GATAGAATTACCGAAATA-CCC--TAAG
1 G-TAGAATTACCGAAATACCCCTGTAAG
* * *
12265864 GTAGAAATACCGAAATTCCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAAG
* * **
12265891 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAAG
*
12265918 GTAAAATTACC
1 GTAGAATTACC
12265929 ATTTTTCCAC
Statistics
Matches: 122, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.12
25 6 0.05
26 5 0.04
27 96 0.79
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAAG
Found at i:12265909 original size:78 final size:80
Alignment explanation
Indices: 12265760--12265929 Score: 227
Period size: 78 Copynumber: 2.1 Consensus size: 80
12265750 GGATAAGTTG
* **
12265760 TAGAATTACCAAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATTG
1 TAGAATTACCAAAATACCCC-GTAAGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACCG
12265825 AAATACCCCTGTAGGA
65 AAATACCCCTGTAGGA
* *
12265841 TAGAATTACCGAAATA-CCC-TAAGGTAGAAATACCGAAATTCCCCTGTAGGGTAGAATTACCGA
1 TAGAATTACCAAAATACCCCGTAAGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACCGA
* * * *
12265904 GATACCCTTGTGGGG
66 AATACCCCTGTAGGA
*
12265919 TAAAATTACCA
1 TAGAATTACCA
12265930 TTTTTCCACT
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
78 60 0.77
80 3 0.04
81 15 0.19
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (80 bp):
TAGAATTACCAAAATACCCCGTAAGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACCGA
AATACCCCTGTAGGA
Found at i:12266627 original size:27 final size:26
Alignment explanation
Indices: 12266583--12266634 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
12266573 CTCGCTGCAA
*
12266583 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
12266610 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
12266635 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:12275418 original size:48 final size:48
Alignment explanation
Indices: 12275313--12275436 Score: 124
Period size: 48 Copynumber: 2.5 Consensus size: 48
12275303 ATAAACATTC
* * *
12275313 TATTATTTTAATAAGATTTACTATTAAATTTAATCTAATATTTAAAATAA
1 TATTATTTTAAT-AG-TTTAATACTAAATTTAATCTAATACTTAAAATAA
* * ***
12275363 TATTATTTTAATAGTTTAATAGTAAATTTAATTTAATACTTATCTTAA
1 TATTATTTTAATAGTTTAATACTAAATTTAATCTAATACTTAAAATAA
* *
12275411 T-TGTATTTTATTAATTTAATACTAAA
1 TAT-TATTTTAATAGTTTAATACTAAA
12275437 GTGATTATCT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
47 1 0.02
48 48 0.76
49 2 0.03
50 12 0.19
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (48 bp):
TATTATTTTAATAGTTTAATACTAAATTTAATCTAATACTTAAAATAA
Found at i:12275475 original size:175 final size:175
Alignment explanation
Indices: 12275181--12275521 Score: 673
Period size: 175 Copynumber: 1.9 Consensus size: 175
12275171 AATTATTCCA
12275181 AAAATAATATTATTTTAATAGTTTAATAGTAAATTTAATTTAATACTTATCTTAATTGTATTTTA
1 AAAATAATATTATTTTAATAGTTTAATAGTAAATTTAATTTAATACTTATCTTAATTGTATTTTA
12275246 TTAATTTAATACTAAAGTGATTATCTTAATATTAAATTTAATTTAATCTTTATCTTGATAAACAT
66 TTAATTTAATACTAAAGTGATTATCTTAATATTAAATTTAATTTAATCTTTATCTTGATAAACAT
12275311 TCTATTATTTTAATAAGATTTACTATTAAATTTAATCTAATATTT
131 TCTATTATTTTAATAAGATTTACTATTAAATTTAATCTAATATTT
12275356 AAAATAATATTATTTTAATAGTTTAATAGTAAATTTAATTTAATACTTATCTTAATTGTATTTTA
1 AAAATAATATTATTTTAATAGTTTAATAGTAAATTTAATTTAATACTTATCTTAATTGTATTTTA
*
12275421 TTAATTTAATACTAAAGTGATTATCTTAATATTAAATTTAATTTAATGTTTATCTTGATAAACAT
66 TTAATTTAATACTAAAGTGATTATCTTAATATTAAATTTAATTTAATCTTTATCTTGATAAACAT
12275486 TCTATTATTTTAATAAGATTTACTATTAAATTTAAT
131 TCTATTATTTTAATAAGATTTACTATTAAATTTAAT
12275522 ATTAAAGTGA
Statistics
Matches: 165, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 165 1.00
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.50
Consensus pattern (175 bp):
AAAATAATATTATTTTAATAGTTTAATAGTAAATTTAATTTAATACTTATCTTAATTGTATTTTA
TTAATTTAATACTAAAGTGATTATCTTAATATTAAATTTAATTTAATCTTTATCTTGATAAACAT
TCTATTATTTTAATAAGATTTACTATTAAATTTAATCTAATATTT
Found at i:12275682 original size:25 final size:26
Alignment explanation
Indices: 12275632--12275682 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
12275622 AGTTGTAGAG
*
12275632 AGAAAATTCTCTGAAGAGATTATTCT
1 AGAAAATTCTCTAAAGAGATTATTCT
* *
12275658 AGAAAATT-TCTAAAGATATTTTTCT
1 AGAAAATTCTCTAAAGAGATTATTCT
12275683 GATTTACGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTCT
Found at i:12277942 original size:18 final size:18
Alignment explanation
Indices: 12277913--12277961 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
12277903 AAGAATAAAG
12277913 AAGAAGAAAATAATGAAAT
1 AAGAA-AAAATAATGAAAT
* *
12277932 AATAAAAAATAATTAAAT
1 AAGAAAAAATAATGAAAT
12277950 AAGAAAAAATAA
1 AAGAAAAAATAA
12277962 AAATAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (18 bp):
AAGAAAAAATAATGAAAT
Found at i:12277968 original size:24 final size:26
Alignment explanation
Indices: 12277920--12277971 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
12277910 AAGAAGAAGA
*
12277920 AAATAATGAAATAATAAAAAATAATT
1 AAATAATGAAAAAATAAAAAATAATT
12277946 AAATAA-GAAAAAAT-AAAAATAATT
1 AAATAATGAAAAAATAAAAAATAATT
12277970 AA
1 AA
12277972 TAAACCAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 12 0.48
25 7 0.28
26 6 0.24
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (26 bp):
AAATAATGAAAAAATAAAAAATAATT
Found at i:12281241 original size:56 final size:56
Alignment explanation
Indices: 12281155--12281264 Score: 220
Period size: 56 Copynumber: 2.0 Consensus size: 56
12281145 ACATGCCAAA
12281155 ACACATGGTAAATTATAAACATCACATATATCATTTGTCAACATATAAATCAAGCC
1 ACACATGGTAAATTATAAACATCACATATATCATTTGTCAACATATAAATCAAGCC
12281211 ACACATGGTAAATTATAAACATCACATATATCATTTGTCAACATATAAATCAAG
1 ACACATGGTAAATTATAAACATCACATATATCATTTGTCAACATATAAATCAAG
12281265 GCAACTCAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.29
Consensus pattern (56 bp):
ACACATGGTAAATTATAAACATCACATATATCATTTGTCAACATATAAATCAAGCC
Found at i:12281940 original size:40 final size:40
Alignment explanation
Indices: 12281854--12281949 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
12281844 ATCTCAGTAT
* *
12281854 CGCACACTTAGTGCCACATATAGTCGAAGCTATTCCAATT
1 CGCACACTAAGTGCCACATATAGTCGAAGCTATTCCAATA
* * * *
12281894 CACACACTAAGTGCTATATATAGTCGAAGCTATCTCGAA-A
1 CGCACACTAAGTGCCACATATAGTCGAAGCTAT-TCCAATA
12281934 CGCACACTAAGTGCCA
1 CGCACACTAAGTGCCA
12281950 AACGTAGTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 43 0.91
41 4 0.09
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
CGCACACTAAGTGCCACATATAGTCGAAGCTATTCCAATA
Found at i:12283935 original size:23 final size:23
Alignment explanation
Indices: 12283907--12283964 Score: 98
Period size: 23 Copynumber: 2.4 Consensus size: 23
12283897 ATGTGTTTGT
12283907 CATCCATGTAGAGTGAATTTGAA
1 CATCCATGTAGAGTGAATTTGAA
12283930 CATCCATGTAGAGTGAATTTGAA
1 CATCCATGTAGAGTGAATTTGAA
12283953 CATGTCCATGTA
1 CA--TCCATGTA
12283965 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 25 0.76
25 8 0.24
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (23 bp):
CATCCATGTAGAGTGAATTTGAA
Found at i:12284172 original size:27 final size:26
Alignment explanation
Indices: 12284142--12284199 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
12284132 AATTCACTCA
*
12284142 ATTAGTGGTCAAATACTTGGGACTTAT
1 ATTA-TGGTCAAAAACTTGGGACTTAT
** *
12284169 ATTATTTTTAAAAACTTGGGACTTAT
1 ATTATGGTCAAAAACTTGGGACTTAT
*
12284195 TTTAT
1 ATTAT
12284200 TTTTATGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.45
Consensus pattern (26 bp):
ATTATGGTCAAAAACTTGGGACTTAT
Found at i:12284384 original size:15 final size:15
Alignment explanation
Indices: 12284377--12284414 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
12284367 ATTTAAATAA
12284377 TTAAAATTCAAAAAT
1 TTAAAATTCAAAAAT
12284392 TTAAAATTCAAAAAT
1 TTAAAATTCAAAAAT
12284407 TTAAAATT
1 TTAAAATT
12284415 TCAATCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAAATTCAAAAAT
Found at i:12291211 original size:38 final size:38
Alignment explanation
Indices: 12291168--12291245 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
12291158 GTGAGAAGTG
12291168 ATAAACTATAAATTATACATATTTTTACCCCATGTTTA
1 ATAAACTATAAATTATACATATTTTTACCCCATGTTTA
12291206 ATAAACTATAAATTATACATATTTTTACCCCATGTTTA
1 ATAAACTATAAATTATACATATTTTTACCCCATGTTTA
12291244 AT
1 AT
12291246 GCATTTTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (38 bp):
ATAAACTATAAATTATACATATTTTTACCCCATGTTTA
Found at i:12305953 original size:14 final size:15
Alignment explanation
Indices: 12305925--12305954 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12305915 CGCCCCAAAT
12305925 TTGGGCCTATAAGTA
1 TTGGGCCTATAAGTA
12305940 TTGGGCCT-TAAGTA
1 TTGGGCCTATAAGTA
12305954 T
1 T
12305955 GGGTATGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (15 bp):
TTGGGCCTATAAGTA
Found at i:12308872 original size:79 final size:78
Alignment explanation
Indices: 12308770--12308992 Score: 265
Period size: 79 Copynumber: 2.8 Consensus size: 78
12308760 GCTCCTCGTT
* *
12308770 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
12308835 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
12308850 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
12308913 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * *
12308928 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
12308991 GA
63 GA
12308993 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 47 0.38
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:12308887 original size:39 final size:40
Alignment explanation
Indices: 12308770--12308992 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
12308760 GCTCCTCGTT
* *
12308770 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
12308810 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
12308850 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
12308889 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
12308928 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
12308969 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12308993 CATCATTCAA
Statistics
Matches: 166, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:12316875 original size:79 final size:82
Alignment explanation
Indices: 12316764--12316948 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
12316754 GCTACTCGTT
* * *
12316764 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
12316827 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
12316844 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
12316907 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
12316924 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
12316949 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:12316948 original size:40 final size:40
Alignment explanation
Indices: 12316745--12316948 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
12316735 CGGAATTTAA
** *
12316745 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
12316785 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
12316825 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
12316864 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
12316904 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
12316944 CCGGA
1 CCGGA
12316949 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12318796 original size:33 final size:34
Alignment explanation
Indices: 12318748--12318819 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
12318738 ATAGGCCCAC
* * * *
12318748 ACTGTTACTGCATAGGGCTTAGGCCCAGA-CTTT
1 ACTGTTAATGAATAGGGCTCAGGCCCAGACCGTT
12318781 ACTGTTAATGAATAGGGCTCAGGCCCAGACCGTT
1 ACTGTTAATGAATAGGGCTCAGGCCCAGACCGTT
12318815 ACTGT
1 ACTGT
12318820 ATGCACTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 26 0.76
34 8 0.24
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (34 bp):
ACTGTTAATGAATAGGGCTCAGGCCCAGACCGTT
Found at i:12319489 original size:27 final size:27
Alignment explanation
Indices: 12319455--12319508 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
12319445 CTATGAGTGT
*
12319455 ATAAATGTTTGCTAATGATAGTTTGTA
1 ATAAATGTTTGCTAAGGATAGTTTGTA
12319482 ATAAATGTTTGCTAAGGATAGTTTGTA
1 ATAAATGTTTGCTAAGGATAGTTTGTA
12319509 TAATTTGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (27 bp):
ATAAATGTTTGCTAAGGATAGTTTGTA
Found at i:12319491 original size:13 final size:14
Alignment explanation
Indices: 12319455--12319496 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
12319445 CTATGAGTGT
12319455 ATAAATGTTTGCTA
1 ATAAATGTTTGCTA
*
12319469 AT-GATAGTTTG-TA
1 ATAAAT-GTTTGCTA
12319482 ATAAATGTTTGCTA
1 ATAAATGTTTGCTA
12319496 A
1 A
12319497 GGATAGTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.43
Consensus pattern (14 bp):
ATAAATGTTTGCTA
Found at i:12320826 original size:28 final size:28
Alignment explanation
Indices: 12320795--12320855 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
12320785 AAGTTTTTGT
* * *
12320795 TTATGAAATGGCTTATACAAGCCTTAGG
1 TTATGAAATGGCTCACACAAGCCTTAAG
12320823 TTATGAAATGGCTCACACAAGCCTTAAG
1 TTATGAAATGGCTCACACAAGCCTTAAG
12320851 TTATG
1 TTATG
12320856 GTGACCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (28 bp):
TTATGAAATGGCTCACACAAGCCTTAAG
Found at i:12325724 original size:41 final size:43
Alignment explanation
Indices: 12325689--12325813 Score: 130
Period size: 45 Copynumber: 2.9 Consensus size: 43
12325679 CCCGAGTTCA
* *
12325689 TTCACCGGCATT-TCGCCTGTTAGGCTCGAAGCCCGACATCAT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGACATCAT
* *
12325731 TTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCTCGA-AT-AGT
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAA-GCCCGACATCA-T
* *
12325774 ATCTCACCAGCATTATAGCCTGCTAGGCTCAAAGGCCCGA
1 -T-TCACCGGCATTATAGCCTGCTAGGCTCGAA-GCCCGA
12325814 ATAATACTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
42 13 0.18
43 18 0.25
44 6 0.08
45 35 0.49
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGACATCAT
Found at i:12326340 original size:18 final size:19
Alignment explanation
Indices: 12326313--12326358 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
12326303 AAATATTTTG
* *
12326313 TTTTTCTTTT-ATTCATCT
1 TTTTTATTTTAATTAATCT
*
12326331 TTTTTATTTTAATTAATTT
1 TTTTTATTTTAATTAATCT
12326350 TTTTTATTT
1 TTTTTATTT
12326359 CATAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTAATTAATCT
Found at i:12329306 original size:47 final size:47
Alignment explanation
Indices: 12329238--12329333 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
12329228 AATTGACTTG
*
12329238 TGATGATTCAATGAAAATGTGATGATATGTGTGCTAGTATAAGACCA
1 TGATGATTAAATGAAAATGTGATGATATGTGTGCTAGTATAAGACCA
*
12329285 TGATGATTAAATGAAAATGTGATGATATGTGTTCTAGTATAAGACCA
1 TGATGATTAAATGAAAATGTGATGATATGTGTGCTAGTATAAGACCA
12329332 TG
1 TG
12329334 TCCAGGACAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.33
Consensus pattern (47 bp):
TGATGATTAAATGAAAATGTGATGATATGTGTGCTAGTATAAGACCA
Found at i:12377965 original size:20 final size:21
Alignment explanation
Indices: 12377940--12377978 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
12377930 CTCCAATGAC
*
12377940 CAAGTTGCCTTC-ACTCCAAA
1 CAAGTTGACTTCAACTCCAAA
12377960 CAAGTTGACTTCAACTCCA
1 CAAGTTGACTTCAACTCCA
12377979 TAACGGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.33, G:0.10, T:0.26
Consensus pattern (21 bp):
CAAGTTGACTTCAACTCCAAA
Found at i:12386373 original size:47 final size:48
Alignment explanation
Indices: 12386322--12386508 Score: 213
Period size: 47 Copynumber: 4.0 Consensus size: 48
12386312 AACACCCATT
** *
12386322 TTTTTCTTCTTC-CATTTTCTCTGTTTGAAACTATAATTAGCCAAAAG
1 TTTTTCTTCTTCTCATTTTCTCTGTTTGAAACTATAACCAGTCAAAAG
12386369 TTTTTC--CTGTCTCATTTTCTCTGTTTGAAACTATAACCAGTCAAAAG
1 TTTTTCTTCT-TCTCATTTTCTCTGTTTGAAACTATAACCAGTCAAAAG
* ** * *
12386416 TTTTTCCTC-TCTTGTTTTCTTTGTTTGAAACTATAACCAGACAAAAG
1 TTTTTCTTCTTCTCATTTTCTCTGTTTGAAACTATAACCAGTCAAAAG
* * * * *
12386463 TTTTCCCTC-TCTCGTTTTCTCTGTTTAAAACTATAACTAGTCAAAA
1 TTTTTCTTCTTCTCATTTTCTCTGTTTGAAACTATAACCAGTCAAAA
12386509 TTTGTTTTTT
Statistics
Matches: 123, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
45 2 0.02
46 2 0.02
47 118 0.96
49 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (48 bp):
TTTTTCTTCTTCTCATTTTCTCTGTTTGAAACTATAACCAGTCAAAAG
Found at i:12386421 original size:94 final size:94
Alignment explanation
Indices: 12386335--12386508 Score: 258
Period size: 94 Copynumber: 1.9 Consensus size: 94
12386325 TTCTTCTTCC
** * * * *
12386335 ATTTTCTCTGTTTGAAACTATAATTAGCCAAAAGTTTTTCCTGTCTCATTTTCTCTGTTTGAAAC
1 ATTTTCTCTGTTTGAAACTATAACCAGACAAAAGTTTTCCCTCTCTCATTTTCTCTGTTTAAAAC
12386400 TATAACCAGTCAAAAGTTTTTCCTCTCTT
66 TATAACCAGTCAAAAGTTTTTCCTCTCTT
* * *
12386429 GTTTTCTTTGTTTGAAACTATAACCAGACAAAAGTTTTCCCTCTCTCGTTTTCTCTGTTTAAAAC
1 ATTTTCTCTGTTTGAAACTATAACCAGACAAAAGTTTTCCCTCTCTCATTTTCTCTGTTTAAAAC
*
12386494 TATAACTAGTCAAAA
66 TATAACCAGTCAAAA
12386509 TTTGTTTTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 70 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.43
Consensus pattern (94 bp):
ATTTTCTCTGTTTGAAACTATAACCAGACAAAAGTTTTCCCTCTCTCATTTTCTCTGTTTAAAAC
TATAACCAGTCAAAAGTTTTTCCTCTCTT
Found at i:12402622 original size:11 final size:11
Alignment explanation
Indices: 12402606--12402631 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12402596 AAGAAATGCC
12402606 AAAATAAAAAG
1 AAAATAAAAAG
12402617 AAAATAAAAAG
1 AAAATAAAAAG
12402628 AAAA
1 AAAA
12402632 GCAATTTAAA
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:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAATAAAAAG
Found at i:12405053 original size:64 final size:64
Alignment explanation
Indices: 12404972--12405155 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
12404962 AGACATTATG
* * * *
12404972 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTAAACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTAAACCATGTAGACAAGAGAGCTACGAGATAA
** * * * *
12405036 ATGTAGCTAGGTCGCATGCATGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTA--A-ACCATGTAGACAAGAGAGCTACGAGAT
12405101 AA
63 AA
* **
12405103 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTAAGTGTAAACCATGTAG-ACAAGAGAGC
12405156 CAAACTATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 17 0.18
64 27 0.28
66 22 0.23
67 28 0.29
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTAAACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:12421067 original size:13 final size:13
Alignment explanation
Indices: 12421049--12421084 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
12421039 CTCGGCAGGG
12421049 ACACGCCCGTAGC
1 ACACGCCCGTAGC
12421062 ACACGCCCGTAGC
1 ACACGCCCGTAGC
12421075 ACACGCCCGT
1 ACACGCCCGT
12421085 GTTCGATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.22, C:0.47, G:0.22, T:0.08
Consensus pattern (13 bp):
ACACGCCCGTAGC
Found at i:12425043 original size:13 final size:13
Alignment explanation
Indices: 12425022--12425061 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
12425012 TGTCAGTTCA
*
12425022 CATGGCCGTGTCG
1 CATGACCGTGTCG
12425035 CATGACCGTGTGTCG
1 CATGACC--GTGTCG
12425050 CATGACCGTGTC
1 CATGACCGTGTC
12425062 TAGCTTCGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.12, C:0.30, G:0.33, T:0.25
Consensus pattern (13 bp):
CATGACCGTGTCG
Found at i:12425049 original size:15 final size:15
Alignment explanation
Indices: 12425029--12425060 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12425019 TCACATGGCC
12425029 GTGTCGCATGACCGT
1 GTGTCGCATGACCGT
12425044 GTGTCGCATGACCGT
1 GTGTCGCATGACCGT
12425059 GT
1 GT
12425061 CTAGCTTCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.25, G:0.34, T:0.28
Consensus pattern (15 bp):
GTGTCGCATGACCGT
Found at i:12442825 original size:43 final size:42
Alignment explanation
Indices: 12442739--12442864 Score: 139
Period size: 43 Copynumber: 3.0 Consensus size: 42
12442729 CGAAATCTTG
* * * * * *
12442739 TACAATTCCAACGTCCTAGACGTGGTCTTACATGTAATAAAA
1 TACAATGCCAACATCCCAGACGTGGTCTTACACGAAATCAAA
12442781 TATCAATGCC-ACTATCCCAGACAG-GGTCTTACACGAAATCAAA
1 TA-CAATGCCAAC-ATCCCAGAC-GTGGTCTTACACGAAATCAAA
*
12442824 TACGATGCCAACATCCCAGACGTGGTCTTACACGTAAATCA
1 TACAATGCCAACATCCCAGACGTGGTCTTACACG-AAATCA
12442865 TAAGTTAATG
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 30 0.42
43 39 0.55
44 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (42 bp):
TACAATGCCAACATCCCAGACGTGGTCTTACACGAAATCAAA
Found at i:12444255 original size:13 final size:13
Alignment explanation
Indices: 12444237--12444261 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12444227 TTAAACCAAT
12444237 AAAAATTAAAAAC
1 AAAAATTAAAAAC
12444250 AAAAATTAAAAA
1 AAAAATTAAAAA
12444262 TAATATAAAT
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:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATTAAAAAC
Found at i:12445058 original size:62 final size:62
Alignment explanation
Indices: 12444965--12445081 Score: 216
Period size: 62 Copynumber: 1.9 Consensus size: 62
12444955 CCATCCACTC
*
12444965 GTTAATCTCCCCTAAGGGATTCAGCCGCTCATGATATTCATTATCTCAAACTCAATCCATTT
1 GTTAATCTCCCCTAAGGGATTCAGCCACTCATGATATTCATTATCTCAAACTCAATCCATTT
*
12445027 GTTAATCTCCCCTAAGGGATTTAGCCACTCATGATATTCATTATCTCAAACTCAA
1 GTTAATCTCCCCTAAGGGATTCAGCCACTCATGATATTCATTATCTCAAACTCAA
12445082 ATGAATTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.33
Consensus pattern (62 bp):
GTTAATCTCCCCTAAGGGATTCAGCCACTCATGATATTCATTATCTCAAACTCAATCCATTT
Found at i:12446969 original size:128 final size:127
Alignment explanation
Indices: 12446722--12447012 Score: 332
Period size: 128 Copynumber: 2.3 Consensus size: 127
12446712 GCATGGTAGG
* * * ** * * * *
12446722 GCACGATTCCTCGAACTTGCAAACATTGAACATTGCTTTGTTTTAGAATTTAAAGAATACGAATG
1 GCACGATTCCCCGAATTTCCAAACATCAAACATTGCTTTGTTTCAAAATTTAAAAAACACGAATG
* * *
12446787 TAATTCTAGAGGAACATTCGATTATTTTCAATAAACGAGAAATCAAAACCCAGCACAATAGA
66 AAATTCTAAAGGAACATTCGATTATTTTCAACAAACGAGAAATCAAAACCCAGCACAATAGA
*
12446849 GCACGATTCCCCGAATTTCCAAATATCAAACATTGCTTTGTTTCAAAATTTAGAAAAACAC-AAG
1 GCACGATTCCCCGAATTTCCAAACATCAAACATTGCTTTGTTTCAAAATTTA-AAAAACACGAA-
* * * * * * * * *
12446913 TGAAATTCTAAAGGAATATTTGATTATTTTGAACAAATGGGAAATCGAAACTCAGCACGATAGG
64 TGAAATTCTAAAGGAACATTCGATTATTTTCAACAAACGAGAAATCAAAACCCAGCACAATAGA
* * *
12446977 GTACGATTCCCCGAATTTCCAAGCATCAAATATTGC
1 GCACGATTCCCCGAATTTCCAAACATCAAACATTGC
12447013 CTTCGTTTTA
Statistics
Matches: 136, Mismatches: 26, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
127 46 0.34
128 90 0.66
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (127 bp):
GCACGATTCCCCGAATTTCCAAACATCAAACATTGCTTTGTTTCAAAATTTAAAAAACACGAATG
AAATTCTAAAGGAACATTCGATTATTTTCAACAAACGAGAAATCAAAACCCAGCACAATAGA
Found at i:12449766 original size:44 final size:44
Alignment explanation
Indices: 12449721--12449946 Score: 140
Period size: 44 Copynumber: 5.2 Consensus size: 44
12449711 TCCCCTCCTG
*
12449721 CTTAGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTTACTG
1 CTTAGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTTACTA
* ** ** * * * * * *
12449765 CTTAGGAG-GTTAAGGCCCATCATCTTTGA-TCTATTCCCCTACTG
1 CTTAGG-GTGATAAGATCTGTAAT-TTTCAGCCTATTACCTTACTA
* *
12449809 CTTAGGGTGATAAGATCTGTAA-ATTCAGCCTATTACCCTACTA
1 CTTAGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTTACTA
* * ** ** * * * *
12449852 CTTAGGGGGTTAAGGGCCATCATCTTC-GATCTGTT-CCTCTACTA
1 CTTAGGGTGATAAGATCTGTAATTTTCAG-CCTATTACCT-TACTA
*
12449896 CTTAGGGTGATAAGATCTGTAATTTTCAGCCTGTTA-CTCTACTA
1 CTTAGGGTGATAAGATCTGTAATTTTCAGCCTATTACCT-TACTA
12449940 CTTAGGG
1 CTTAGGG
12449947 GGTTAAGGCC
Statistics
Matches: 132, Mismatches: 41, Indels: 18
0.69 0.21 0.09
Matches are distributed among these distances:
42 3 0.02
43 31 0.23
44 92 0.70
45 6 0.05
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (44 bp):
CTTAGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTTACTA
Found at i:12449802 original size:88 final size:88
Alignment explanation
Indices: 12449636--12450183 Score: 649
Period size: 88 Copynumber: 6.2 Consensus size: 88
12449626 ACGCCATTTC
* * * * *
12449636 AGGGAGATGAGATTTGTAATTTTCAGCCTGTTA-CTCTACTGCTTAGGGAGTTAAGG-CCAGTCA
1 AGGGTGATAAGATCTGTAATTTTCAGCCTATTACCT-TACTGCTTAGGGGGTTAAGGCCCA-TCA
*
12449699 TCTTCGATCTGTTCCCCTCCTGCTT
64 TCTTCGATCTGTTCCCCTACTGCTT
*
12449724 AGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTTACTGCTTAGGAGGTTAAGGCCCATCATC
1 AGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTTACTGCTTAGGGGGTTAAGGCCCATCATC
* *
12449789 TTTGATCTATTCCCCTACTGCTT
66 TTCGATCTGTTCCCCTACTGCTT
* * * *
12449812 AGGGTGATAAGATCTGTAA-ATTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGGCCATCATC
1 AGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTTACTGCTTAGGGGGTTAAGGCCCATCATC
* *
12449876 TTCGATCTGTTCCTCTACTACTT
66 TTCGATCTGTTCCCCTACTGCTT
* * * *
12449899 AGGGTGATAAGATCTGTAATTTTCAGCCTGTTA-CTCTACTACTTAGGGGGTTAAGGCCAATCGT
1 AGGGTGATAAGATCTGTAATTTTCAGCCTATTACCT-TACTGCTTAGGGGGTTAAGGCCCATCAT
* * * *
12449963 CTTCGATTTGCTCCACTAATGCTT
65 CTTCGATCTGTTCCCCTACTGCTT
* * * * * *
12449987 AGGGAGACAAGATCTATAATCTTCAGCCTGTTACC-TACTGCTTAGGGGGTTAAGACCCATCATC
1 AGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTTACTGCTTAGGGGGTTAAGGCCCATCATC
* *
12450051 TTCAATTTGTTCCCCTACTGCTT
66 TTCGATCTGTTCCCCTACTGCTT
* * * * *
12450074 AGGGTGATAAGATCTTGTAA-ATTCAGCCTATTACCCTACTGCTTAGGGGGTTAAGGCTCGTCGT
1 AGGGTGATAAGATC-TGTAATTTTCAGCCTATTACCTTACTGCTTAGGGGGTTAAGGCCCATCAT
* *
12450138 CTTCGATCTGCTCCACTACTGCTT
65 CTTCGATCTGTTCCCCTACTGCTT
* * *
12450162 AGGGAGACAAGATCTATAATTT
1 AGGGTGATAAGATCTGTAATTT
12450184 CCAACCCTAC
Statistics
Matches: 394, Mismatches: 58, Indels: 16
0.84 0.12 0.03
Matches are distributed among these distances:
87 152 0.39
88 236 0.60
89 6 0.02
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (88 bp):
AGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTTACTGCTTAGGGGGTTAAGGCCCATCATC
TTCGATCTGTTCCCCTACTGCTT
Found at i:12449953 original size:175 final size:175
Alignment explanation
Indices: 12449652--12450181 Score: 717
Period size: 175 Copynumber: 3.0 Consensus size: 175
12449642 ATGAGATTTG
* * *
12449652 TAATTTTCAGCCTGTTACTCTACTGCTTAGGGAGTTAA-GGCCAGTCATCTTCGATCTGTTCCCC
1 TAATATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGGCCA-TCATCTTCGATCTGTTCCCC
* *
12449716 TCCTGCTTAGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTTACTGCTTAGGAGGTTAAGGC
65 TACTGCTTAGGGTGATAAGATCTGTAATTTTCAGCCTATTACC-TACTGCTTAGGGGGTTAAGGC
* * ** * * * *
12449781 CCATCATCTTTGATCTATTCCCCTACTGCTTAGGGTGATAAGATCTG
129 CCATCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTA
* * *
12449828 TAA-ATTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGGCCATCATCTTCGATCTGTTCCTCT
1 TAATATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGGCCATCATCTTCGATCTGTTCCCCT
* * *
12449892 ACTACTTAGGGTGATAAGATCTGTAATTTTCAGCCTGTTACTCTACTACTTAGGGGGTTAAGGCC
66 ACTGCTTAGGGTGATAAGATCTGTAATTTTCAGCCTATTAC-CTACTGCTTAGGGGGTTAAGGCC
* * *
12449957 AATCGTCTTCGATTTGCTCCACTAATGCTTAGGGAGACAAGATCTA
130 CATCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTA
* ** * *
12450003 TAATCTTCAGCCTGTTA-CCTACTGCTTAGGGGGTTAAGACCCATCATCTTCAATTTGTTCCCCT
1 TAATATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGGCCATCATCTTCGATCTGTTCCCCT
*
12450067 ACTGCTTAGGGTGATAAGATCTTGTAA-ATTCAGCCTATTACCCTACTGCTTAGGGGGTTAAGGC
66 ACTGCTTAGGGTGATAAGATC-TGTAATTTTCAGCCTATTA-CCTACTGCTTAGGGGGTTAAGGC
* *
12450131 TCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTA
129 CCATCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTA
12450178 TAAT
1 TAAT
12450182 TTCCAACCCT
Statistics
Matches: 310, Mismatches: 39, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
175 284 0.92
176 26 0.08
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (175 bp):
TAATATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGGCCATCATCTTCGATCTGTTCCCCT
ACTGCTTAGGGTGATAAGATCTGTAATTTTCAGCCTATTACCTACTGCTTAGGGGGTTAAGGCCC
ATCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTA
Found at i:12450076 original size:44 final size:44
Alignment explanation
Indices: 12449844--12450077 Score: 137
Period size: 44 Copynumber: 5.3 Consensus size: 44
12449834 CAGCCTATTA
** *
12449844 CCCTACTACTTAGGGGGTTAAGGGCCATCATCTTCGATCTGTTC
1 CCCTACTACTTAGGGGGTTAAGACCCATCATCTTCAATCTGTTC
* * * * ** * * ** *
12449888 CTCTACTACTTAGGGTGATAAGATCTGTAATTTTCAGCCTGTTA
1 CCCTACTACTTAGGGGGTTAAGACCCATCATCTTCAATCTGTTC
* * * * * * *
12449932 CTCTACTACTTAGGGGGTTAAGGCCAATCGTCTTCGATTTGCTC
1 CCCTACTACTTAGGGGGTTAAGACCCATCATCTTCAATCTGTTC
* * * * ** * * * **
12449976 CACTAATGCTTAGGGAGACAAGATCTATAATCTTCAGCCTGTT-
1 CCCTACTACTTAGGGGGTTAAGACCCATCATCTTCAATCTGTTC
* * *
12450019 ACCTACTGCTTAGGGGGTTAAGACCCATCATCTTCAATTTGTTC
1 CCCTACTACTTAGGGGGTTAAGACCCATCATCTTCAATCTGTTC
*
12450063 CCCTACTGCTTAGGG
1 CCCTACTACTTAGGG
12450078 TGATAAGATC
Statistics
Matches: 132, Mismatches: 57, Indels: 2
0.69 0.30 0.01
Matches are distributed among these distances:
43 31 0.23
44 101 0.77
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (44 bp):
CCCTACTACTTAGGGGGTTAAGACCCATCATCTTCAATCTGTTC
Found at i:12450085 original size:44 final size:44
Alignment explanation
Indices: 12449696--12450085 Score: 136
Period size: 44 Copynumber: 8.9 Consensus size: 44
12449686 TTAAGGCCAG
* * * * * **
12449696 TCATCTTCGATCTGTTCCCCTCCTGCTTAGGGTGATAAGATCTG
1 TCATCTTCAATCTGTTCCCCTACTACTTAGGGGGATAAGACCCA
* * ** * * * * * * *
12449740 TAATTTTCAGCCTATTACCTTACTGCTTAGGAGGTTAAGGCCCA
1 TCATCTTCAATCTGTTCCCCTACTACTTAGGGGGATAAGACCCA
** * * * * **
12449784 TCATCTTTGATCTATTCCCCTACTGCTTAGGGTGATAAGATCTG
1 TCATCTTCAATCTGTTCCCCTACTACTTAGGGGGATAAGACCCA
** ** * * * **
12449828 T-AAATTCAGCCTATTACCCTACTACTTAGGGGGTTAAGGGCCA
1 TCATCTTCAATCTGTTCCCCTACTACTTAGGGGGATAAGACCCA
* * * * **
12449871 TCATCTTCGATCTGTTCCTCTACTACTTAGGGTGATAAGATCTG
1 TCATCTTCAATCTGTTCCCCTACTACTTAGGGGGATAAGACCCA
* * ** * * * * *
12449915 TAATTTTCAGCCTGTTACTCTACTACTTAGGGGGTTAAGGCCAA
1 TCATCTTCAATCTGTTCCCCTACTACTTAGGGGGATAAGACCCA
* * * * * * * * * * *
12449959 TCGTCTTCGATTTGCTCCACTAATGCTTAGGGAGACAAGATCTA
1 TCATCTTCAATCTGTTCCCCTACTACTTAGGGGGATAAGACCCA
* ** * * *
12450003 TAATCTTCAGCCTGTT-ACCTACTGCTTAGGGGGTTAAGACCCA
1 TCATCTTCAATCTGTTCCCCTACTACTTAGGGGGATAAGACCCA
* * *
12450046 TCATCTTCAATTTGTTCCCCTACTGCTTAGGGTGATAAGA
1 TCATCTTCAATCTGTTCCCCTACTACTTAGGGGGATAAGA
12450086 TCTTGTAAAT
Statistics
Matches: 233, Mismatches: 111, Indels: 4
0.67 0.32 0.01
Matches are distributed among these distances:
43 60 0.26
44 173 0.74
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (44 bp):
TCATCTTCAATCTGTTCCCCTACTACTTAGGGGGATAAGACCCA
Found at i:12461867 original size:128 final size:127
Alignment explanation
Indices: 12461631--12461907 Score: 333
Period size: 128 Copynumber: 2.2 Consensus size: 127
12461621 GCATGGTAGG
* * * * * * * *
12461631 GCACGATTCCTCGAACTTGCAAACATTGAACATTGCTTTGTTTTAGAATTTAAAGAATACGAATG
1 GCACGATTCCCCGAATTTCCAAACATTGAACATTGCCTTGTTTCAAAATTTAAAAAACACGAATG
* * *
12461696 TAATTCTAGAGGAATATTCGATTATTTTCAATAAACGATAAATCAAAACCCAGCACAATAGA
66 AAATTCTAGAGGAATATTCGATTATTTTCAACAAACGAGAAATCAAAACCCAGCACAATAGA
* * *
12461758 GCACGATTCCCCGAATTTCCAAATATCT-AACATTGCCTTGTTTCAAAATTTAGAAAAACGCGAG
1 GCACGATTCCCCGAATTTCCAAACAT-TGAACATTGCCTTGTTTCAAAATTTA-AAAAACACGAA
* * * * *
12461822 TGAAATTCTA-AGGGAATATTCGATTATTTTGAACAAACGGGAAATCGAAACCCAGCACGATAGG
64 TGAAATTCTAGA-GGAATATTCGATTATTTTCAACAAACGAGAAATCAAAACCCAGCACAATAGA
*
12461886 GCATGATTCCCCGAATTTCCAA
1 GCACGATTCCCCGAATTTCCAA
12461908 GCATCAAATA
Statistics
Matches: 127, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
127 44 0.35
128 83 0.65
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (127 bp):
GCACGATTCCCCGAATTTCCAAACATTGAACATTGCCTTGTTTCAAAATTTAAAAAACACGAATG
AAATTCTAGAGGAATATTCGATTATTTTCAACAAACGAGAAATCAAAACCCAGCACAATAGA
Found at i:12466250 original size:16 final size:18
Alignment explanation
Indices: 12466224--12466256 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12466214 AATTTTCACA
12466224 TATATATTAAAT-TTTTT
1 TATATATTAAATATTTTT
12466241 TATA-ATTAAATATTTT
1 TATATATTAAATATTTT
12466257 AAAATTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATATTAAATATTTTT
Found at i:12466256 original size:17 final size:17
Alignment explanation
Indices: 12466224--12466256 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12466214 AATTTTCACA
12466224 TATATATTAAATTTTTT
1 TATATATTAAATTTTTT
*
12466241 TATA-ATTAAATATTTT
1 TATATATTAAATTTTTT
12466257 AAAATTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATATTAAATTTTTT
Found at i:12488421 original size:13 final size:13
Alignment explanation
Indices: 12488403--12488448 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
12488393 ATGTATATGC
12488403 ATATAATAAAAAT
1 ATATAATAAAAAT
12488416 ATATAAT---AAT
1 ATATAATAAAAAT
*
12488426 ATATAATAATAAT
1 ATATAATAAAAAT
12488439 A-ATAATAAAA
1 ATATAATAAAA
12488449 GAAAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 10 0.34
12 8 0.28
13 11 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATATAATAAAAAT
Found at i:12488424 original size:3 final size:3
Alignment explanation
Indices: 12488405--12488446 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
12488395 GTATATGCAT
*
12488405 ATA ATA AAA ATA TATA ATA ATA TATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA A
12488447 AAGAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12488426 original size:10 final size:10
Alignment explanation
Indices: 12488403--12488445 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
12488393 ATGTATATGC
*
12488403 ATATAATAAAA
1 ATAT-ATAATA
12488414 ATATATAATA
1 ATATATAATA
12488424 ATATATAATA
1 ATATATAATA
12488434 ATA-ATAATA
1 ATATATAATA
12488443 ATA
1 ATA
12488446 AAAGAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 9 0.29
10 18 0.58
11 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATATATAATA
Found at i:12494842 original size:42 final size:41
Alignment explanation
Indices: 12494707--12494844 Score: 134
Period size: 42 Copynumber: 3.3 Consensus size: 41
12494697 CACAGAAGCA
* * * **
12494707 CATAAGTGCTAAACAGAAACCCATAAGGGTTGAACGGAAGTT
1 CATAAGAGTTAAACAGAAACCCATAAGGGTTAAAC-GAAACT
* * *
12494749 CATAAGAGTTGAAA-GGAAACCTATAAGGGTTAAACAAAAGCT
1 CATAAGAGTT-AAACAGAAACCCATAAGGGTTAAACGAAA-CT
* *
12494791 CAGAAGAGTTAAACAGAAACCCATTAGGGTTAAACTGAAACT
1 CATAAGAGTTAAACAGAAACCCATAAGGGTTAAAC-GAAACT
*
12494833 CATATGAGTTAA
1 CATAAGAGTTAA
12494845 CTGAAGCTCA
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
41 5 0.06
42 66 0.86
43 6 0.08
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.20
Consensus pattern (41 bp):
CATAAGAGTTAAACAGAAACCCATAAGGGTTAAACGAAACT
Found at i:12494843 original size:21 final size:21
Alignment explanation
Indices: 12494796--12494871 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
12494786 AAGCTCAGAA
* *
12494796 GAGTTAAACAGAAACCCAT-T
1 GAGTTAAACTGAAACTCATAT
*
12494816 AGGGTTAAACTGAAACTCATAT
1 -GAGTTAAACTGAAACTCATAT
* *
12494838 GAGTT-AACTGAAGCTCATAA
1 GAGTTAAACTGAAACTCATAT
* *
12494858 GAGCTAAACGGAAA
1 GAGTTAAACTGAAA
12494872 GCAAACAAGG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 17 0.39
21 26 0.59
22 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (21 bp):
GAGTTAAACTGAAACTCATAT
Found at i:12498290 original size:56 final size:56
Alignment explanation
Indices: 12498201--12498311 Score: 134
Period size: 56 Copynumber: 2.0 Consensus size: 56
12498191 CAACGGCAAC
** * * * * *
12498201 GTCCCAGACGTGGTCTTACATGTATCCACATATCGATGCCATATATTGATGCCATT
1 GTCCCAGACGTGGTCTTACATGTAAACAAATATCGATACCACAAATCGATGCCATT
*
12498257 GTCCCAGACAG-GGTCTTACTTGTAAACAAATATCGATACCACAAATCGATGCCAT
1 GTCCCAGAC-GTGGTCTTACATGTAAACAAATATCGATACCACAAATCGATGCCAT
12498312 GGTCTTACTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
56 45 0.98
57 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (56 bp):
GTCCCAGACGTGGTCTTACATGTAAACAAATATCGATACCACAAATCGATGCCATT
Found at i:12511694 original size:3 final size:3
Alignment explanation
Indices: 12511686--12511711 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12511676 TTACAAAAGA
12511686 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
12511712 AGGCCTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:12512394 original size:43 final size:42
Alignment explanation
Indices: 12512325--12512408 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 42
12512315 TACATGAATT
*
12512325 GCATCCATAGGAACTCGGACCACTCAACAAGCTCGGATGCTC
1 GCATCCATAGGAACTCGAACCACTCAACAAGCTCGGATGCTC
* * *
12512367 GCATCCATAATGAACTCGAACCTCTCAATAAGCTCGGATGCT
1 GCATCCAT-AGGAACTCGAACCACTCAACAAGCTCGGATGCT
12512409 ACATACCTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 8 0.22
43 29 0.78
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (42 bp):
GCATCCATAGGAACTCGAACCACTCAACAAGCTCGGATGCTC
Found at i:12518668 original size:48 final size:48
Alignment explanation
Indices: 12518605--12518701 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
12518595 CCCAGAGACG
*
12518605 AAGTATTAGGATGTTTGTTGTAAATGAAACTAGATAGTCAAAATACTA
1 AAGTATTAGGATGTTTGTTGTAAACGAAACTAGATAGTCAAAATACTA
* *
12518653 AAGTCTTAGGGTGTTTGTTGTAAACGAAACTAGATAGTCAAAATACTA
1 AAGTATTAGGATGTTTGTTGTAAACGAAACTAGATAGTCAAAATACTA
12518701 A
1 A
12518702 GTGGTCATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (48 bp):
AAGTATTAGGATGTTTGTTGTAAACGAAACTAGATAGTCAAAATACTA
Found at i:12519091 original size:13 final size:13
Alignment explanation
Indices: 12519073--12519099 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12519063 GAAGTAATCG
12519073 CACATGGGCGTGT
1 CACATGGGCGTGT
12519086 CACATGGGCGTGT
1 CACATGGGCGTGT
12519099 C
1 C
12519100 CCTACCGAGC
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:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (13 bp):
CACATGGGCGTGT
Found at i:12524150 original size:28 final size:27
Alignment explanation
Indices: 12524110--12524165 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
12524100 GCCTAAAACC
* *
12524110 TTATTTTGATGAGATTCACAGCAGGAA
1 TTATTTTGATGAGATTAACAACAGGAA
12524137 NTTATTTTGATGAGATTAACAACAGGAA
1 -TTATTTTGATGAGATTAACAACAGGAA
12524165 T
1 T
12524166 GAGGAGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (27 bp):
TTATTTTGATGAGATTAACAACAGGAA
Found at i:12524574 original size:55 final size:55
Alignment explanation
Indices: 12524445--12524581 Score: 184
Period size: 55 Copynumber: 2.5 Consensus size: 55
12524435 TGGCCGTGCA
* * *
12524445 CGAACCTGCCAAAACAACACGGGCATGTGACACGCCCGTGCCTTGAAATCGTGGC
1 CGAACCTGCCAAAACAACACCGGCATGCGACACGCCCGTGCCTTGAAACCGTGGC
* * ** * *
12524500 CAAACCTGTCAAATTAACACCGGCGTGCGACATGCCCGTGCCTTGAAACCGTGGC
1 CGAACCTGCCAAAACAACACCGGCATGCGACACGCCCGTGCCTTGAAACCGTGGC
*
12524555 CGAACCTGCCAAAACAACACAGGCATG
1 CGAACCTGCCAAAACAACACCGGCATG
12524582 GACCTTCATA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (55 bp):
CGAACCTGCCAAAACAACACCGGCATGCGACACGCCCGTGCCTTGAAACCGTGGC
Found at i:12533179 original size:156 final size:156
Alignment explanation
Indices: 12532895--12533205 Score: 622
Period size: 156 Copynumber: 2.0 Consensus size: 156
12532885 TAAATATCTT
12532895 TCTTTTAGCTCAAGAAGCTAACGTGAGTCCAAGTGATAAAGGCAAATGACATGTTTTGTAGATTG
1 TCTTTTAGCTCAAGAAGCTAACGTGAGTCCAAGTGATAAAGGCAAATGACATGTTTTGTAGATTG
12532960 TGCTAGAATTTCTGGTGTGCTCCTTTTTACTTCCATGTGTTGTAAATCTCTTTGTTATATGATTC
66 TGCTAGAATTTCTGGTGTGCTCCTTTTTACTTCCATGTGTTGTAAATCTCTTTGTTATATGATTC
12533025 GTGTAAGGTAAGTAATCTTTCTCTGA
131 GTGTAAGGTAAGTAATCTTTCTCTGA
12533051 TCTTTTAGCTCAAGAAGCTAACGTGAGTCCAAGTGATAAAGGCAAATGACATGTTTTGTAGATTG
1 TCTTTTAGCTCAAGAAGCTAACGTGAGTCCAAGTGATAAAGGCAAATGACATGTTTTGTAGATTG
12533116 TGCTAGAATTTCTGGTGTGCTCCTTTTTACTTCCATGTGTTGTAAATCTCTTTGTTATATGATTC
66 TGCTAGAATTTCTGGTGTGCTCCTTTTTACTTCCATGTGTTGTAAATCTCTTTGTTATATGATTC
12533181 GTGTAAGGTAAGTAATCTTTCTCTG
131 GTGTAAGGTAAGTAATCTTTCTCTG
12533206 TAATGGATGA
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (156 bp):
TCTTTTAGCTCAAGAAGCTAACGTGAGTCCAAGTGATAAAGGCAAATGACATGTTTTGTAGATTG
TGCTAGAATTTCTGGTGTGCTCCTTTTTACTTCCATGTGTTGTAAATCTCTTTGTTATATGATTC
GTGTAAGGTAAGTAATCTTTCTCTGA
Done.