Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 141 of 226
Found at i:47036258 original size:70 final size:71
Alignment explanation
Indices: 47036123--47036260 Score: 163
Period size: 70 Copynumber: 2.0 Consensus size: 71
47036113 AAATTACAAT
* * * * ** * **
47036123 ATTACAATATTCATGCAAAAAAATTGCAATATTCATATAAAATGATAATATTACAATATTCATAC
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACGATAATACCAAAATATAAATAC
47036188 AAAAAA
66 AAAAAA
*
47036194 ATTACAATATTCATAC-AAAAAATTACAATATTCATACAAAACGCTAAT-CCAAAACTATAAATA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACGATAATACCAAAA-TATAAATA
47036257 CAAA
65 CAAA
47036261 TTTAATTATA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
69 3 0.05
70 38 0.68
71 15 0.27
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.28
Consensus pattern (71 bp):
ATTACAATATTCATACAAAAAAATTACAATATTCATACAAAACGATAATACCAAAATATAAATAC
AAAAAA
Found at i:47036299 original size:19 final size:19
Alignment explanation
Indices: 47036268--47036337 Score: 104
Period size: 19 Copynumber: 3.5 Consensus size: 19
47036258 AAATTTAATT
47036268 ATAAAATAATTACAATATTC
1 ATAAAA-AATTACAATATTC
47036288 ATAAAAAATTACAATATTC
1 ATAAAAAATTACAATATTC
47036307 ATACAAAAAATTACAATATTC
1 AT--AAAAAATTACAATATTC
*
47036328 ATACAAAATT
1 ATAAAAAATT
47036338 CTAATCCAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
19 22 0.47
20 6 0.13
21 19 0.40
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAAAATTACAATATTC
Found at i:47036314 original size:21 final size:21
Alignment explanation
Indices: 47036270--47036335 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
47036260 ATTTAATTAT
47036270 AAAATAATTACAATATTCAT--
1 AAAA-AATTACAATATTCATAC
47036290 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
47036311 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
47036332 AAAA
1 AAAA
47036336 TTCTAATCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.34
20 4 0.09
21 25 0.57
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:47036380 original size:101 final size:102
Alignment explanation
Indices: 47036172--47036371 Score: 305
Period size: 101 Copynumber: 1.9 Consensus size: 102
47036162 AAATGATAAT
47036172 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACG
1 ATTACAATATTCAT--AAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACG
* * *
47036237 CTAATCCAAAACTATAAATACAAATTTAATTATAAAATA
64 CTAATCCAAAACTATAAACACAAATATAATAATAAAATA
**
47036276 ATTACAATATTCAT-AAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATTCT
1 ATTACAATATTCATAAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACGCT
47036340 AATCC-AAACTATAAACACTAAATATAGATAAT
66 AATCCAAAACTATAAACAC-AAATATA-ATAAT
47036372 TTATAATTAA
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
100 12 0.13
101 59 0.66
102 4 0.04
104 14 0.16
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.29
Consensus pattern (102 bp):
ATTACAATATTCATAAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACGCT
AATCCAAAACTATAAACACAAATATAATAATAAAATA
Found at i:47036418 original size:101 final size:101
Alignment explanation
Indices: 47036189--47036408 Score: 282
Period size: 101 Copynumber: 2.1 Consensus size: 101
47036179 TATTCATACA
47036189 AAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACGCTAATCCAAAACTATAA
1 AAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACGCTAATCCAAAACTATAA
* * * * * *
47036254 ATACAAATTTAATTATAAAATAATTACAATATTCAT
66 ACACAAATATAATAATAAAATAATTACAATAATAAC
**
47036290 AAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATTCTAATCC-AAACTATAA
1 AAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACGCTAATCCAAAACTATAA
** *
47036354 ACACTAAATATAGATAAT-TTATAATTAATAATTAATAAC
66 ACAC-AAATATA-ATAATAAAATAATT-ACAA-TAATAAC
47036393 AAAAAATTCACAATAT
1 AAAAAATT-ACAATAT
47036409 CTTCTAAAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
100 12 0.12
101 65 0.63
102 7 0.07
103 12 0.12
104 7 0.07
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (101 bp):
AAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACGCTAATCCAAAACTATAA
ACACAAATATAATAATAAAATAATTACAATAATAAC
Found at i:47036501 original size:3 final size:3
Alignment explanation
Indices: 47036495--47036532 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
47036485 TTTTCTTTCT
*
47036495 TTC TTC TTC TTC TTC -TC TTC TTC TCC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
47036533 CCTTTCTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:47036513 original size:14 final size:13
Alignment explanation
Indices: 47036491--47036555 Score: 69
Period size: 14 Copynumber: 4.8 Consensus size: 13
47036481 TTTTTTTTCT
47036491 TTCTTTCTTCTTC
1 TTCTTTCTTCTTC
47036504 TTCTTCTCTTCTTC
1 TTCTT-TCTTCTTC
*
47036518 TCCTTCTCTTCTTC
1 TTCTT-TCTTCTTC
*
47036532 TCCTTTCTCTCTT-
1 TTCTTTCT-TCTTC
*
47036545 TTCTTTTTTCT
1 TTCTTTCTTCT
47036556 CTACCGTGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
12 3 0.06
13 14 0.30
14 30 0.64
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (13 bp):
TTCTTTCTTCTTC
Found at i:47036730 original size:5 final size:5
Alignment explanation
Indices: 47036720--47036749 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
47036710 GATAGGCGCC
47036720 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG
47036750 TTGACCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:47038408 original size:18 final size:18
Alignment explanation
Indices: 47038350--47038411 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
47038340 AGAATTTTTT
47038350 TATAAAAATCGTAAAAAA
1 TATAAAAATCGTAAAAAA
* **
47038368 -ATTAAAAATTGTAAAATTT
1 TA-TAAAAATCGTAAAA-AA
*
47038387 TATAAAAATCATAAAAAA
1 TATAAAAATCGTAAAAAA
47038405 TATAAAA
1 TATAAAA
47038412 TGTATCAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 1 0.03
18 20 0.59
19 12 0.35
20 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
TATAAAAATCGTAAAAAA
Found at i:47038649 original size:18 final size:20
Alignment explanation
Indices: 47038628--47038667 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
47038618 CTTTATAAAA
47038628 TTTTAT-ATTTCTAT-ATAT
1 TTTTATAATTTCTATGATAT
*
47038646 TTTTATAATTTTTATGATAT
1 TTTTATAATTTCTATGATAT
47038666 TT
1 TT
47038668 ATAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 7 0.37
20 6 0.32
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTATAATTTCTATGATAT
Found at i:47038658 original size:9 final size:9
Alignment explanation
Indices: 47038628--47038797 Score: 55
Period size: 9 Copynumber: 18.4 Consensus size: 9
47038618 CTTTATAAAA
47038628 TTTTAT-AT
1 TTTTATAAT
*
47038636 TTCTATATAT
1 TTTTATA-AT
47038646 TTTTATAAT
1 TTTTATAAT
*
47038655 TTTTATGAT
1 TTTTATAAT
* *
47038664 ATTTATAAAA
1 TTTTAT-AAT
*
47038674 TTTTACAATT
1 TTTTATAA-T
*
47038684 TTTTTTATAT
1 TTTTATA-AT
**
47038694 TTTTACGAT
1 TTTTATAAT
*
47038703 TTTTATATTTT
1 TTTTATA--AT
*
47038714 TTTTCTAA-
1 TTTTATAAT
47038722 TTTT-TAAT
1 TTTTATAAT
*
47038730 ATTTA-AATT
1 TTTTATAA-T
*
47038739 TTTTATTAAAA
1 TTTTA-T-AAT
*
47038750 TTTAATAAT
1 TTTTATAAT
* *
47038759 ATTTATAGT
1 TTTTATAAT
*
47038768 TTTTATTGA-
1 TTTTA-TAAT
*
47038777 TTTTA-ATT
1 TTTTATAAT
47038785 TTTTATAAT
1 TTTTATAAT
47038794 TTTT
1 TTTT
47038798 TTTCTAATTT
Statistics
Matches: 113, Mismatches: 33, Indels: 31
0.64 0.19 0.18
Matches are distributed among these distances:
7 3 0.03
8 19 0.17
9 52 0.46
10 25 0.22
11 12 0.11
12 2 0.02
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:47038667 original size:20 final size:19
Alignment explanation
Indices: 47038631--47038733 Score: 66
Period size: 20 Copynumber: 5.4 Consensus size: 19
47038621 TATAAAATTT
*
47038631 TATATTTCTATATATTTTTA
1 TATATTTTTATA-ATTTTTA
* *
47038651 TA-ATTTTTATGATATTTA
1 TATATTTTTATAATTTTTA
* * * *
47038669 TAAAATTTTACAATTTTTTT
1 TATATTTTTATAA-TTTTTA
**
47038689 TATATTTTTACGATTTTTA
1 TATATTTTTATAATTTTTA
* *
47038708 TATTTTTTTTCTAATTTTTA
1 TA-TATTTTTATAATTTTTA
47038728 -ATATTT
1 TATATTT
47038734 AAATTTTTTA
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
18 12 0.19
19 22 0.35
20 29 0.46
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TATATTTTTATAATTTTTA
Found at i:47038670 original size:28 final size:28
Alignment explanation
Indices: 47038639--47038715 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
47038629 TTTATATTTC
*
47038639 TATATATTTTTATAATTTTTATGATATT
1 TATAAATTTTTATAATTTTTATGATATT
* * * *
47038667 TATAAAATTTTACAATTTTTTTTATATT
1 TATAAATTTTTATAATTTTTATGATATT
* * *
47038695 TTTACGATTTTTATATTTTTT
1 TATA-AATTTTTATAATTTTT
47038716 TTCTAATTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
28 26 0.68
29 12 0.32
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (28 bp):
TATAAATTTTTATAATTTTTATGATATT
Found at i:47038706 original size:29 final size:27
Alignment explanation
Indices: 47038674--47038812 Score: 95
Period size: 29 Copynumber: 5.0 Consensus size: 27
47038664 ATTTATAAAA
47038674 TTTTACAATTTTTTTTAT-ATTTTTACGAT
1 TTTTA-AATTTTTTTTATAATTTTTA--AT
* *
47038703 TTTTATATTTTTTTTCTAATTTTTAAT
1 TTTTAAATTTTTTTTATAATTTTTAAT
* * *
47038730 ATTTAAATTTTTTATTAAAATTTAATAAT
1 TTTTAAATTTTTT-TTATAATTT-TTAAT
* * * * *
47038759 ATTTATAGTTTTTAT-TGA-TTTTAATT
1 TTTTAAATTTTTTTTATAATTTTTAA-T
*
47038785 TTTTATAATTTTTTTTCTAATTTTTAAT
1 TTTTA-AATTTTTTTTATAATTTTTAAT
47038813 AAAAGCAGGG
Statistics
Matches: 85, Mismatches: 18, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
25 3 0.04
26 7 0.08
27 21 0.25
28 21 0.25
29 33 0.39
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTTAAATTTTTTTTATAATTTTTAAT
Found at i:47038938 original size:86 final size:87
Alignment explanation
Indices: 47038827--47039034 Score: 269
Period size: 86 Copynumber: 2.4 Consensus size: 87
47038817 GCAGGGGCTT
* * * * *
47038827 AATTATTTTTTTTGAAAAAAATTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTACCCAATT
1 AATTACTTTTTTTGAAAAAATTTGAGGGACTTTTTGATGCATTTTAAAAGTTTAAGTACCCAAAT
* *
47038892 GGGAG-AAAAAAATAGGGACTG
66 GAGAGTAAAAAAAAAGGGACTG
* * *
47038913 AATTGA-TTTTTTTGAAAAGATTTGAGAGCCTTTTTGATGCATTTTAAAAGTTTAAGTACCCAAA
1 AATT-ACTTTTTTTGAAAAAATTTGAGGGACTTTTTGATGCATTTTAAAAGTTTAAGTACCCAAA
* *
47038977 TGAGTGTAAAAAAAAAGGGACTT
65 TGAGAGTAAAAAAAAAGGGACTG
*
47039000 AATTACTTTTTCTGAAAAAATTTGA-GGACTTTTTG
1 AATTACTTTTTTTGAAAAAATTTGAGGGACTTTTTG
47039035 CACAATTAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
86 69 0.66
87 36 0.34
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (87 bp):
AATTACTTTTTTTGAAAAAATTTGAGGGACTTTTTGATGCATTTTAAAAGTTTAAGTACCCAAAT
GAGAGTAAAAAAAAAGGGACTG
Found at i:47057740 original size:15 final size:15
Alignment explanation
Indices: 47057720--47057752 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
47057710 AATCATTGGG
47057720 TTGAGCCTGAAAAGT
1 TTGAGCCTGAAAAGT
*
47057735 TTGAGCCTGAAAGGT
1 TTGAGCCTGAAAAGT
47057750 TTG
1 TTG
47057753 TCAACAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (15 bp):
TTGAGCCTGAAAAGT
Found at i:47059557 original size:20 final size:20
Alignment explanation
Indices: 47059497--47059568 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
47059487 TTTCATTTTC
*
47059497 TTTATTTATTTTATTAAATA
1 TTTATTTATTTTTTTAAATA
*
47059517 GTTT-TTTATTCTTTTT-CATA
1 -TTTATTTATT-TTTTTAAATA
*
47059537 TTTAATTATTTTTTTAAATA
1 TTTATTTATTTTTTTAAATA
* *
47059557 TATATATATTTT
1 TTTATTTATTTT
47059569 ACATACGTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
19 8 0.20
20 26 0.63
21 7 0.17
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (20 bp):
TTTATTTATTTTTTTAAATA
Found at i:47060058 original size:12 final size:13
Alignment explanation
Indices: 47060022--47060071 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
47060012 CATGTCATGG
47060022 ATTA-TTGTTT-T
1 ATTATTTGTTTAT
*
47060033 TTTATTTCGTTTAT
1 ATTATTT-GTTTAT
47060047 A-TATTTGTTTAT
1 ATTATTTGTTTAT
*
47060059 ATTATTTTTTTAT
1 ATTATTTGTTTAT
47060072 GCCATTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 3 0.09
12 9 0.28
13 19 0.59
14 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (13 bp):
ATTATTTGTTTAT
Found at i:47060098 original size:15 final size:15
Alignment explanation
Indices: 47060075--47060107 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
47060065 TTTTTATGCC
47060075 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
47060090 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
47060105 ATT
1 ATT
47060108 ATAGCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:47067048 original size:44 final size:44
Alignment explanation
Indices: 47066866--47067695 Score: 156
Period size: 44 Copynumber: 18.8 Consensus size: 44
47066856 AAGATTGTAG
**
47066866 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAA
* * * * *
47066910 ATCTTATCTTTCC-AAG-A-TAGTGGGAAACATATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGA-CAA
** * * * ** * * * * ** * *
47066954 GCCTTGTCTTCCTGAGCAGCGGCGGAGTAGGTTAAAAATTATAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAA
*
47066998 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAA
* * *
47067042 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGA-CAA
** * * * * * * * * * *
47067086 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGA-CGACAA
* * ** *
47067130 ATATTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAA
* * * *
47067174 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGTAGATTTAAG-CCATCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGA-CAA
** * * * * * * *
47067218 GCCTTGTCTCCCTGAGCAGCAGCGGAGTCAG-TTGAAA-ATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAG-CAGATT-AAAGA-CGACAA
* *
47067262 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAA
* * *
47067306 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGA-CAA
** * * * * * * * * *
47067350 GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAA-ATTG-TAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATT-AAAGA-CGACAA
** *
47067394 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAA
* * * * *
47067438 ATCTTATCTTTCC-AAG-A-TAGTGGGAAACAAATTTAAG-CCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGA-CAA
** * * * * * * * *
47067482 GCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAAGATTG-TAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGA-CGACAA
** * *
47067526 ATCTTATCTCCCTAAATAGTAGTGGAGCAGATCAAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAA
* * *
47067570 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACTAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGACGAC-AA
** * * * * * * * *
47067614 GCCTTATCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAA
** * *
47067658 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAG
1 ATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATTAAAG
47067696 TTGATAATCC
Statistics
Matches: 531, Mismatches: 192, Indels: 125
0.63 0.23 0.15
Matches are distributed among these distances:
42 24 0.05
43 58 0.11
44 376 0.71
45 62 0.12
46 11 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAA
Found at i:47067710 original size:132 final size:132
Alignment explanation
Indices: 47066816--47067670 Score: 1381
Period size: 132 Copynumber: 6.5 Consensus size: 132
47066806 ACCGGTGAAA
* *
47066816 CACCAAGCCTTGTC-CCCTTGAGCAGCAGCGGAGAAGGTTAAAGATTGTAGATCTTATCTCCCTA
1 CACCAAGCCTTGTCTCCC-TGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTA
* * * *
47066880 AGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAACATATTTA
65 AGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
47066945 AGC
130 AGC
* * * * *
47066948 CACCAAGCCTTGTCTTCCTGAGCAGCGGCGGAGTAGGTTAAAAATTATAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
*
47067013 GCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
47067078 GC
131 GC
* *
47067080 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATTGTAGATATTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * *
47067145 GCAGTAGTGGAGTAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGTAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
47067210 GC
131 GC
* *
47067212 CATCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTCA-GTTGAAAATTGTAGATCTTATCTCCCTA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGT-AGGTTGAAGATTGTAGATCTTATCTCCCTA
47067276 AGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
65 AGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTA
47067341 AGC
130 AGC
*
47067344 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAAATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
* * *
47067409 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAACAAATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
47067474 GC
131 GC
* * *
47067476 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTAAAGATTGTAAATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
**
47067541 ATAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
47067606 GC
131 GC
* * * * *
47067608 CACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATGGCAAATCTTATCTCCCT
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCT
47067671 GAAGTTGCAG
Statistics
Matches: 675, Mismatches: 45, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 671 0.99
133 3 0.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:47068185 original size:13 final size:13
Alignment explanation
Indices: 47068167--47068191 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47068157 CAAAACAAAC
47068167 AGAGGCCCAAGAT
1 AGAGGCCCAAGAT
47068180 AGAGGCCCAAGA
1 AGAGGCCCAAGA
47068192 CAGATGATGA
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:0.24, G:0.32, T:0.04
Consensus pattern (13 bp):
AGAGGCCCAAGAT
Found at i:47069268 original size:27 final size:28
Alignment explanation
Indices: 47069232--47069290 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
47069222 TCCTTTTTCA
*
47069232 TTTTCTTTATTTTT-TTA-TTAATTAGTT
1 TTTTCTTTATTTTTCATATTTAATTA-TT
*
47069259 TTTTTTTTATTTTTCATATTTAATTATT
1 TTTTCTTTATTTTTCATATTTAATTATT
47069287 TTTT
1 TTTT
47069291 AAAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 13 0.46
28 8 0.29
29 7 0.25
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (28 bp):
TTTTCTTTATTTTTCATATTTAATTATT
Found at i:47069465 original size:4 final size:4
Alignment explanation
Indices: 47069458--47069500 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
47069448 AAAAAACAAA
*
47069458 TATT TATT TATT TATAT ATATG TATT TATT TATT TA-T TATT TA
1 TATT TATT TATT TAT-T -TATT TATT TATT TATT TATT TATT TA
47069501 GTTTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 3 0.09
4 27 0.79
5 1 0.03
6 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:47069981 original size:18 final size:18
Alignment explanation
Indices: 47069958--47070019 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
47069948 TGTCAAAATT
47069958 TATTTTCTTTTCATTATA
1 TATTTTCTTTTCATTATA
* *
47069976 TATTTTAGTATTTTC-TTTTA
1 TA-TTT--TCTTTTCATTATA
47069996 TATTTTCTTTTCATTATA
1 TATTTTCTTTTCATTATA
47070014 TATTTT
1 TATTTT
47070020 AGTATTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
17 6 0.17
18 12 0.33
19 6 0.17
20 6 0.17
21 6 0.17
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (18 bp):
TATTTTCTTTTCATTATA
Found at i:47070000 original size:38 final size:38
Alignment explanation
Indices: 47069958--47070034 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
47069948 TGTCAAAATT
47069958 TATTTTCTTTTCATTATATATTTTAGTATTTTCTTTTA
1 TATTTTCTTTTCATTATATATTTTAGTATTTTCTTTTA
47069996 TATTTTCTTTTCATTATATATTTTAGTATTTTCTTTTA
1 TATTTTCTTTTCATTATATATTTTAGTATTTTCTTTTA
47070034 T
1 T
47070035 CTTTCCATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (38 bp):
TATTTTCTTTTCATTATATATTTTAGTATTTTCTTTTA
Found at i:47070001 original size:12 final size:12
Alignment explanation
Indices: 47069978--47070034 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 12
47069968 TCATTATATA
47069978 TTTTAGTATTTTC
1 TTTTA-TATTTTC
47069991 TTTTATATTTTC
1 TTTTATATTTTC
* *
47070003 TTTTCAT-TATATA
1 TTTT-ATAT-TTTC
47070016 TTTTAGTATTTTC
1 TTTTA-TATTTTC
47070029 TTTTAT
1 TTTTAT
47070035 CTTTCCATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
12 14 0.39
13 21 0.58
14 1 0.03
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.70
Consensus pattern (12 bp):
TTTTATATTTTC
Found at i:47092646 original size:2 final size:2
Alignment explanation
Indices: 47092639--47092670 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47092629 TGCTAACAGA
47092639 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
47092671 TTATTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47093426 original size:20 final size:24
Alignment explanation
Indices: 47093382--47093427 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
47093372 CTCTTATTCC
47093382 CTTTCTCTATAATATTTCCTATCA
1 CTTTCTCTATAATATTTCCTATCA
47093406 CTTTCTCT-T-AT-TTTCCT-TCA
1 CTTTCTCTATAATATTTCCTATCA
47093426 CT
1 CT
47093428 AATATATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.23
21 6 0.27
22 2 0.09
23 1 0.05
24 8 0.36
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.54
Consensus pattern (24 bp):
CTTTCTCTATAATATTTCCTATCA
Found at i:47095137 original size:29 final size:31
Alignment explanation
Indices: 47095095--47095155 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 31
47095085 GTATTTTAAA
* *
47095095 TTTTAAATATAAATTA-T-TCTATTTATATT
1 TTTTAAATAAAAATAATTGTCTATTTATATT
* *
47095124 TTTTATATAAAAATAATTGTTTATTTATATT
1 TTTTAAATAAAAATAATTGTCTATTTATATT
47095155 T
1 T
47095156 ATATATTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 13 0.50
30 1 0.04
31 12 0.46
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (31 bp):
TTTTAAATAAAAATAATTGTCTATTTATATT
Found at i:47096082 original size:29 final size:25
Alignment explanation
Indices: 47096039--47096096 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
47096029 CTCATCTCTT
47096039 CTCTGCTGGTGCT--TTCTTTGTTC
1 CTCTGCTGGTGCTGGTTCTTTGTTC
47096062 CTCTGCTGGTGCTGGTTCTTTGTTC
1 CTCTGCTGGTGCTGGTTCTTTGTTC
47096087 CTCTGCTGGT
1 CTCTGCTGGT
47096097 TCTTTGTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 13 0.39
25 20 0.61
ACGTcount: A:0.00, C:0.26, G:0.26, T:0.48
Consensus pattern (25 bp):
CTCTGCTGGTGCTGGTTCTTTGTTC
Found at i:47097403 original size:2 final size:2
Alignment explanation
Indices: 47097396--47097423 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47097386 TAAATTTTGT
47097396 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47097424 CACATACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47097610 original size:2 final size:2
Alignment explanation
Indices: 47097574--47097600 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47097564 TTCTATTTTC
47097574 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 A
47097601 CTTTTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47098205 original size:109 final size:106
Alignment explanation
Indices: 47098013--47098241 Score: 334
Period size: 109 Copynumber: 2.1 Consensus size: 106
47098003 TACGCATATT
* *
47098013 AATATCCTTTTAAAAAAATTCAAAATAAAGCAATGTTTTGCGTTTGGAAATTTGAGAACACGTAC
1 AATATCCTTTTAAAAAAATTCAAAATAAAGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTAC
47098078 CCCAATGTGCTAGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 CCCAATGTGCTAGGTTTCGA---TT-TCGTTCGACCAAATAGCCA
* * *
47098123 AATATCCTTTTAAAAAATTTCAAAA-AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGC
1 AATATCCTTTTAAAAAAATTCAAAATAAAGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTAC
* * *
47098187 CCTAATGTGCTAGGTTTCGATTTCGTTTGACCAAATAGCGA
66 CCCAATGTGCTAGGTTTCGATTTCGTTCGACCAAATAGCCA
*
47098228 AATATCCTCTTAAA
1 AATATCCTTTTAAA
47098242 TTTTAATCCA
Statistics
Matches: 110, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
105 30 0.27
106 2 0.02
109 54 0.49
110 24 0.22
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (106 bp):
AATATCCTTTTAAAAAAATTCAAAATAAAGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTAC
CCCAATGTGCTAGGTTTCGATTTCGTTCGACCAAATAGCCA
Found at i:47099256 original size:114 final size:114
Alignment explanation
Indices: 47099078--47099526 Score: 594
Period size: 114 Copynumber: 4.0 Consensus size: 114
47099068 AAAATAAGCA
* ** * *
47099078 TTAGCGGCGCTTTCCAGAAAGCGCCGC-AAAATACCTAAGCCCAACGGCGCCGTTTTCGGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
47099142 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
** * * * * * *
47099191 TTAGCATCATTTTTGAGAAAGCGCCACAAAAAAATCTAAGCCTAACGACGCCGTCTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
47099256 TCGGGGATTTAGTGGCGTTTTTAGGTAAGCGCCACTAATGCTCAGGTCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* *
47099305 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTATGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
47099370 TCGGGGATTTAGTGACGTTTTTAAGT---------TGATGCTCAGGGCT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
*
47099410 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
47099475 TCAGGGATTTAGTGGCATTTTTAAGTAAGCGCCGCTAATGCTCAGGGAT
66 TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
47099524 TTA
1 TTA
47099527 AAATAATTTA
Statistics
Matches: 288, Mismatches: 38, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
105 99 0.34
113 20 0.07
114 169 0.59
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
Found at i:47099475 original size:105 final size:105
Alignment explanation
Indices: 47099177--47099500 Score: 423
Period size: 105 Copynumber: 3.0 Consensus size: 105
47099167 AAAGCGCCGC
** * * * * * *
47099177 TAATGCTCAGGGCTTTAGCATCATTTTTGAGAAAGCGCCACAAAAAAATCTAAGCCTAACGACGC
1 TAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGC
* *
47099242 CGTCTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAGGTAAGCGCCAC
66 CGTTTTCTGAGCTTTCGGGGATTTAGTGGCG-TTTT---TAA--G---T
* *
47099291 TAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTATGCCCAACGACGC
1 TAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGC
*
47099356 CGTTTTCTGAGCTTTCGGGGATTTAGTGACGTTTTTAAGT
66 CGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGT
*
47099396 TGATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGC
1 TAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGC
* *
47099461 CGTTTTCTGAGCTTTCAGGGATTTAGTGGCATTTTTAAGT
66 CGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGT
47099501 AAGCGCCGCT
Statistics
Matches: 191, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
105 99 0.52
108 1 0.01
110 3 0.02
113 4 0.02
114 84 0.44
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (105 bp):
TAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAAGCCCAACGACGC
CGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGT
Found at i:47099476 original size:219 final size:220
Alignment explanation
Indices: 47099094--47099520 Score: 588
Period size: 219 Copynumber: 1.9 Consensus size: 220
47099084 GCGCTTTCCA
* *
47099094 GAAAGCGCCGCAAAATACCTAAGCCCAACGGCGCCGTTTTCGGAGCTTTCGGGGATTTAGCGGCG
1 GAAAGCGCCGCAAAATACCTAAGCCCAACGACGCCGTTTTCGGAGCTTTCGGGGATTTAGCGACG
*
47099159 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCATCATTTTTGAGAAAGCGCCACAAAAAA
66 TTTTT---AAA----CGCTAATGCTCAGGGCTTTAGCAGCATTTTTGAGAAAGCGCCACAAAAAA
* * * * *
47099224 ATCTAAGCCTAACGACGCCGTCTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAGGTAAGCGCC
124 ACCTAAGCCCAACGACGCCGTCTTCTGAGCTTTCAGGGATTTAGTGGCATTTTTAAGTAAGCGCC
47099289 ACTAATGCTCAGGTCTTTAGCGGCGTTTTTGG
189 ACTAATGCTCAGGTCTTTAGCGGCGTTTTTGG
* * *
47099321 GAAAGCGCCGCAAAAATACCTATGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGAC
1 GAAAGCGCCGC-AAAATACCTAAGCCCAACGACGCCGTTTTCGGAGCTTTCGGGGATTTAGCGAC
* * * * * * *
47099386 GTTTTT-AA-GTTGATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACCTAA
65 GTTTTTAAACGCTAATGCTCAGGGCTTTAGCAGCATTTTTGAGAAAGCGCCACAAAAAAACCTAA
* *
47099449 GCCCAACGACGCCGTTTTCTGAGCTTTCAGGGATTTAGTGGCATTTTTAAGTAAGCGCCGCTAAT
130 GCCCAACGACGCCGTCTTCTGAGCTTTCAGGGATTTAGTGGCATTTTTAAGTAAGCGCCACTAAT
47099514 GCTCAGG
195 GCTCAGG
47099521 GATTTAAAAT
Statistics
Matches: 179, Mismatches: 20, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
219 112 0.63
224 2 0.01
227 11 0.06
228 54 0.30
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (220 bp):
GAAAGCGCCGCAAAATACCTAAGCCCAACGACGCCGTTTTCGGAGCTTTCGGGGATTTAGCGACG
TTTTTAAACGCTAATGCTCAGGGCTTTAGCAGCATTTTTGAGAAAGCGCCACAAAAAAACCTAAG
CCCAACGACGCCGTCTTCTGAGCTTTCAGGGATTTAGTGGCATTTTTAAGTAAGCGCCACTAATG
CTCAGGTCTTTAGCGGCGTTTTTGG
Found at i:47100106 original size:14 final size:14
Alignment explanation
Indices: 47100084--47100149 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
47100074 AGATTATAGA
*
47100084 ATTAGGGATTATGG
1 ATTAAGGATTATGG
47100098 ATTAAGGATTATGG
1 ATTAAGGATTATGG
* *
47100112 TTTAAGGGTTAATGTG
1 ATTAAGGATT-ATG-G
*
47100128 ATTTAAGGTTTATGG
1 A-TTAAGGATTATGG
*
47100143 GTTAAGG
1 ATTAAGG
47100150 GTTAGGGGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 27 0.63
15 4 0.09
16 4 0.09
17 8 0.19
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (14 bp):
ATTAAGGATTATGG
Found at i:47100158 original size:14 final size:14
Alignment explanation
Indices: 47100130--47100186 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
47100120 TTAATGTGAT
* *
47100130 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
47100144 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
47100158 TTAGGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
47100172 TT-A-GGTTAGGTG
1 TTAAGGGTTAGGGG
47100184 TTA
1 TTA
47100187 GATGTTAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.27
14 27 0.73
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.37
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:47100187 original size:7 final size:7
Alignment explanation
Indices: 47100141--47100176 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
47100131 TAAGGTTTAT
*
47100141 GGGTTAA
1 GGGTTAG
47100148 GGGTTAG
1 GGGTTAG
47100155 GGGTTAG
1 GGGTTAG
47100162 GGGTTAG
1 GGGTTAG
47100169 GGGTTAG
1 GGGTTAG
47100176 G
1 G
47100177 TTAGGTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.17, C:0.00, G:0.56, T:0.28
Consensus pattern (7 bp):
GGGTTAG
Found at i:47100193 original size:14 final size:12
Alignment explanation
Indices: 47100149--47100187 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
47100139 ATGGGTTAAG
47100149 GGTTAGGGGTTA
1 GGTTAGGGGTTA
47100161 GGGGTTAGGGGTTA
1 --GGTTAGGGGTTA
*
47100175 GGTTAGGTGTTA
1 GGTTAGGGGTTA
47100187 G
1 G
47100188 ATGTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.50
14 12 0.50
ACGTcount: A:0.15, C:0.00, G:0.51, T:0.33
Consensus pattern (12 bp):
GGTTAGGGGTTA
Found at i:47100193 original size:19 final size:19
Alignment explanation
Indices: 47100156--47100203 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
47100146 AAGGGTTAGG
*
47100156 GGTTAGGGGTTAGGGGTTA
1 GGTTAGGGGTTAGAGGTTA
* *
47100175 GGTTAGGTGTTAGATGTTAA
1 GGTTAGGGGTTAGAGGTT-A
47100195 GAGTTAGGG
1 G-GTTAGGG
47100204 ATTTAGGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 15 0.65
20 2 0.09
21 6 0.26
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (19 bp):
GGTTAGGGGTTAGAGGTTA
Found at i:47100193 original size:26 final size:26
Alignment explanation
Indices: 47100149--47100202 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
47100139 ATGGGTTAAG
* * *
47100149 GGTTAGGGGTTAGGGGTTAGGGGTTA
1 GGTTAGGGGTTAGAGGTTAAGAGTTA
* *
47100175 GGTTAGGTGTTAGATGTTAAGAGTTA
1 GGTTAGGGGTTAGAGGTTAAGAGTTA
47100201 GG
1 GG
47100203 GATTTAGGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.46, T:0.33
Consensus pattern (26 bp):
GGTTAGGGGTTAGAGGTTAAGAGTTA
Found at i:47100475 original size:21 final size:21
Alignment explanation
Indices: 47100422--47100475 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
47100412 TAAAGATTAC
47100422 TAATTTAAAA-TTGATATGCAA
1 TAATTTAAAATTTGATAT-CAA
*
47100443 T-ATATAATAATTTGAATAT-AA
1 TAATTTAA-AATTTG-ATATCAA
47100464 TAATTTAAAATT
1 TAATTTAAAATT
47100476 GTAAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 8 0.30
23 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTTGATATCAA
Found at i:47100493 original size:10 final size:9
Alignment explanation
Indices: 47100470--47100510 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
47100460 ATAATAATTT
47100470 AAAATTGTA
1 AAAATTGTA
47100479 AAAATTGTAA
1 AAAATTGT-A
47100489 AAAATTGTA
1 AAAATTGTA
*
47100498 AAAATTATA
1 AAAATTGTA
47100507 AAAA
1 AAAA
47100511 ATAAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (9 bp):
AAAATTGTA
Found at i:47100494 original size:19 final size:19
Alignment explanation
Indices: 47100470--47100512 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
47100460 ATAATAATTT
*
47100470 AAAATTGTAAAAATTGTAA
1 AAAATTGTAAAAATTATAA
47100489 AAAATTGTAAAAATTATAA
1 AAAATTGTAAAAATTATAA
47100508 AAAAT
1 AAAAT
47100513 AAAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
AAAATTGTAAAAATTATAA
Found at i:47100511 original size:10 final size:10
Alignment explanation
Indices: 47100478--47100528 Score: 54
Period size: 9 Copynumber: 5.4 Consensus size: 10
47100468 TTAAAATTGT
*
47100478 AAAAATTGTA
1 AAAAATTATA
*
47100488 AAAAATTGT-
1 AAAAATTATA
47100497 AAAAATTATA
1 AAAAATTATA
*
47100507 AAAAA-TAAA
1 AAAAATTATA
47100516 AAAAATTA-A
1 AAAAATTATA
47100525 AAAA
1 AAAA
47100529 TTAAAAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
9 21 0.57
10 16 0.43
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (10 bp):
AAAAATTATA
Found at i:47100517 original size:8 final size:9
Alignment explanation
Indices: 47100506--47100545 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
47100496 TAAAAATTAT
47100506 AAAAAATAA
1 AAAAAATAA
*
47100515 AAAAAATTA
1 AAAAAATAA
*
47100524 AAAAATTAA
1 AAAAAATAA
47100533 AAAGAAATAA
1 AAA-AAATAA
47100543 AAA
1 AAA
47100546 CACTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (9 bp):
AAAAAATAA
Found at i:47100519 original size:19 final size:19
Alignment explanation
Indices: 47100478--47100540 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
47100468 TTAAAATTGT
* ***
47100478 AAAAATTGTAAAAAATTGT
1 AAAAATTATAAAAAATAAA
47100497 AAAAATTATAAAAAATAAA
1 AAAAATTATAAAAAATAAA
*
47100516 AAAAATTA-AAAAATTAAA
1 AAAAATTATAAAAAATAAA
47100534 AAGAAAT
1 AA-AAAT
47100541 AAAAACACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
18 11 0.29
19 27 0.71
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAATTATAAAAAATAAA
Found at i:47101110 original size:199 final size:199
Alignment explanation
Indices: 47100770--47101210 Score: 767
Period size: 199 Copynumber: 2.2 Consensus size: 199
47100760 ACTGGGTTTT
*
47100770 GCGGCGCTAAGGTAAAAACGCCGCAAAGTTCTGTTCTCAGTTTTCGTAAAACGGTGTCGTTTTGA
1 GCGGCGCTAAGGAAAAAACGCCGCAAAGTTCTGTTCTCAGTTTTCGTAAAACGGTGTCGTTTTGA
* *
47100835 CTGGGCATTAGTGGGGCTACTAAAAAACGCCGCAAAAAATTCTTAATAATGAAGACAAAACGATG
66 CTGGGCATTAGTGGCGCTACTAAAAAACGCCGCAAAAAATTCTTAATAATGAAGACAAAACGATA
* * *
47100900 CAGTTTTTGGCTGTGAATTTAATGGGTTTTGTGGCGCTAAGGGAAAAACG-CTGCTAAAGGTGGT
131 CAGTTTTTGGCTGTAAATTTAATGGGTTTTGAGGCGCTAAGGGAAAAACGTC-ACTAAAGGTGGT
47100964 CATTA
195 CATTA
*
47100969 GCGGCGCTAAGGAAAAAACGCCGCAAAGTTCTGTTCTCAGTTTTCGTAAAACGGTGTCGTTTTGC
1 GCGGCGCTAAGGAAAAAACGCCGCAAAGTTCTGTTCTCAGTTTTCGTAAAACGGTGTCGTTTTGA
47101034 CTGGGCATTAGTGGCGCTACTAAAAAACGCCGCAAAAAATTCTTAATAATGAAGACAAAACGATA
66 CTGGGCATTAGTGGCGCTACTAAAAAACGCCGCAAAAAATTCTTAATAATGAAGACAAAACGATA
* *
47101099 CAGTTTTTGGCTGTAAATTTAATGGGTTTTGAGGTGCTAAGGGAAAAATGTCACTAAAGGTGGTC
131 CAGTTTTTGGCTGTAAATTTAATGGGTTTTGAGGCGCTAAGGGAAAAACGTCACTAAAGGTGGTC
47101164 ATTA
196 ATTA
* *
47101168 GCGGCGCTAAGGAACAAATGCCGCAAAGTTCTGTTCTCAGTTT
1 GCGGCGCTAAGGAAAAAACGCCGCAAAGTTCTGTTCTCAGTTT
47101211 ATATATCTAT
Statistics
Matches: 230, Mismatches: 11, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
199 229 1.00
200 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (199 bp):
GCGGCGCTAAGGAAAAAACGCCGCAAAGTTCTGTTCTCAGTTTTCGTAAAACGGTGTCGTTTTGA
CTGGGCATTAGTGGCGCTACTAAAAAACGCCGCAAAAAATTCTTAATAATGAAGACAAAACGATA
CAGTTTTTGGCTGTAAATTTAATGGGTTTTGAGGCGCTAAGGGAAAAACGTCACTAAAGGTGGTC
ATTA
Found at i:47101344 original size:2 final size:2
Alignment explanation
Indices: 47101339--47101363 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47101329 TTCTTCTCCA
47101339 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 T
47101364 TTTTTACTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:47104071 original size:51 final size:52
Alignment explanation
Indices: 47103987--47104084 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 52
47103977 TTCATTTCTA
47103987 TTAGGTCAGTTTCTGTTTTTAATTTGGTCGTTTAAATAAGAAATTTTTAAAG
1 TTAGGTCAGTTTCTGTTTTTAATTTGGTCGTTTAAATAAGAAATTTTTAAAG
* **
47104039 TTAGGTCAGTTTTTG-TTTTAATTTGGTCGTTTAAATTTGAAATTTT
1 TTAGGTCAGTTTCTGTTTTTAATTTGGTCGTTTAAATAAGAAATTTT
47104085 ACAATTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
51 29 0.67
52 14 0.33
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (52 bp):
TTAGGTCAGTTTCTGTTTTTAATTTGGTCGTTTAAATAAGAAATTTTTAAAG
Found at i:47104122 original size:21 final size:21
Alignment explanation
Indices: 47104079--47104125 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
47104069 TTAAATTTGA
* *
47104079 AATTTTACAATTTAATCATCT
1 AATTTTACAATATAATCAACT
* *
47104100 AATTTTACAATATCATTAACT
1 AATTTTACAATATAATCAACT
47104121 AATTT
1 AATTT
47104126 AAATAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTACAATATAATCAACT
Found at i:47104719 original size:46 final size:46
Alignment explanation
Indices: 47104666--47104823 Score: 131
Period size: 46 Copynumber: 3.3 Consensus size: 46
47104656 AAAAAATGTC
*
47104666 CAACTTAATAACTTATATAATTCACATAATAACTTACATAACTGAA
1 CAACTTAACAACTTATATAATTCACATAATAACTTACATAACTGAA
* * * * *
47104712 CAACTTAACAACTCACATAATTTACATAAT-ACATATATATA-TGTCATA
1 CAACTTAACAACTTATATAATTCACATAATAACTTACATA-ACTG--A-A
* * *
47104760 CCATATAACTTAATAACTTATATAATTCACATAATAATTTACATAACTTAA
1 -C----AACTTAACAACTTATATAATTCACATAATAACTTACATAACTGAA
*
47104811 TAACTTAACAACT
1 CAACTTAACAACT
47104824 CGCATAATTT
Statistics
Matches: 85, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
45 9 0.11
46 38 0.45
47 1 0.01
48 1 0.01
49 1 0.01
51 1 0.01
52 1 0.01
53 26 0.31
54 7 0.08
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (46 bp):
CAACTTAACAACTTATATAATTCACATAATAACTTACATAACTGAA
Found at i:47104847 original size:17 final size:17
Alignment explanation
Indices: 47104791--47104850 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
47104781 ATAATTCACA
47104791 TAATAATTTACATAACT
1 TAATAATTTACATAACT
* *
47104808 TAATAACTTA-ACAACT
1 TAATAATTTACATAACT
**
47104824 CGCATAATTTACATAACT
1 -TAATAATTTACATAACT
47104842 TAATAATTT
1 TAATAATTT
47104851 TAAAATATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 5 0.15
17 23 0.70
18 5 0.15
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (17 bp):
TAATAATTTACATAACT
Found at i:47104965 original size:17 final size:17
Alignment explanation
Indices: 47104943--47105019 Score: 59
Period size: 17 Copynumber: 4.4 Consensus size: 17
47104933 ATAACTCACA
47104943 TAATAACTTACATAACT
1 TAATAACTTACATAACT
*
47104960 TAATAACTTATATATA-T
1 TAATAACTTACATA-ACT
**
47104977 GCATAACTTA-ATAACT
1 TAATAACTTACATAACT
*
47104993 CATATTATAACTCACATAACT
1 --TA--ATAACTTACATAACT
47105014 TAATAA
1 TAATAA
47105020 GTTTTACGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 26 0.55
18 1 0.02
19 2 0.04
20 7 0.15
21 6 0.13
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (17 bp):
TAATAACTTACATAACT
Found at i:47104965 original size:29 final size:28
Alignment explanation
Indices: 47104933--47105019 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
47104923 ATGTTATATC
*
47104933 ATAACTCACATAATAACTTACATAACTTA
1 ATAACTCATAT-ATAACTTACATAACTTA
* *
47104962 ATAACTTATATAT-A--TGCATAACTTA
1 ATAACTCATATATAACTTACATAACTTA
*
47104987 ATAACTCATATTATAACTCACATAACTTA
1 ATAACTCATA-TATAACTTACATAACTTA
47105016 ATAA
1 ATAA
47105020 GTTTTACGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 19 0.40
26 3 0.06
27 2 0.04
28 2 0.04
29 22 0.46
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.34
Consensus pattern (28 bp):
ATAACTCATATATAACTTACATAACTTA
Found at i:47104971 original size:50 final size:50
Alignment explanation
Indices: 47104897--47105075 Score: 205
Period size: 50 Copynumber: 3.5 Consensus size: 50
47104887 AATAATTAAC
*
47104897 AACTCACATAACTTAATAAGTTATACATGTTATATCATAACTCACATAAT
1 AACTCACATAACTTAATAACTTATACATGTTATATCATAACTCACATAAT
* * * * * * *
47104947 AACTTACATAACTTAATAACTTATATATATGCATAACTTAATAACTCATATTAT
1 AACTCACATAACTTAATAACTTATACATGT-TAT-A--TCATAACTCACATAAT
* * * *
47105001 AACTCACATAACTTAATAAGTTTTACGTGTTATATCATAACTCACCTAAT
1 AACTCACATAACTTAATAACTTATACATGTTATATCATAACTCACATAAT
*
47105051 AACTTACATAACTTAATAACTTATA
1 AACTCACATAACTTAATAACTTATA
47105076 TATATGCATA
Statistics
Matches: 103, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
50 60 0.58
51 2 0.02
52 2 0.02
53 2 0.02
54 37 0.36
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (50 bp):
AACTCACATAACTTAATAACTTATACATGTTATATCATAACTCACATAAT
Found at i:47104987 original size:25 final size:25
Alignment explanation
Indices: 47104951--47105118 Score: 112
Period size: 25 Copynumber: 6.5 Consensus size: 25
47104941 CATAATAACT
47104951 TACATAACTTAATAACTTATATATA
1 TACATAACTTAATAACTTATATATA
* *
47104976 TGCATAACTTAATAACTCATATTATAA
1 TACATAACTTAATAACTTATA-TAT-A
* * *
47105003 CTCACATAACTTAATAAGTTTTACGTGTTA
1 -T-ACATAACTTAATAACTTATA--T-ATA
* * *
47105033 TATCATAACTCACCTAA--TA-A-CT-
1 TA-CATAACTTA-ATAACTTATATATA
47105055 TACATAACTTAATAACTTATATATA
1 TACATAACTTAATAACTTATATATA
* * *
47105080 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTTATA-TATA
47105106 TACATAACTTAAT
1 TACATAACTTAAT
47105119 CATTGTAAAA
Statistics
Matches: 110, Mismatches: 19, Indels: 27
0.71 0.12 0.17
Matches are distributed among these distances:
20 3 0.03
21 8 0.07
22 4 0.04
23 2 0.02
24 1 0.01
25 38 0.35
26 18 0.16
27 2 0.02
28 3 0.03
29 25 0.23
30 5 0.05
31 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (25 bp):
TACATAACTTAATAACTTATATATA
Found at i:47105014 original size:104 final size:104
Alignment explanation
Indices: 47104897--47105104 Score: 389
Period size: 104 Copynumber: 2.0 Consensus size: 104
47104887 AATAATTAAC
47104897 AACTCACATAACTTAATAAGTTATACATGTTATATCATAACTCACATAATAACTTACATAACTTA
1 AACTCACATAACTTAATAAGTTATACATGTTATATCATAACTCACATAATAACTTACATAACTTA
47104962 ATAACTTATATATATGCATAACTTAATAACTCATATTAT
66 ATAACTTATATATATGCATAACTTAATAACTCATATTAT
* * *
47105001 AACTCACATAACTTAATAAGTTTTACGTGTTATATCATAACTCACCTAATAACTTACATAACTTA
1 AACTCACATAACTTAATAAGTTATACATGTTATATCATAACTCACATAATAACTTACATAACTTA
47105066 ATAACTTATATATATGCATAACTTAATAACTCATATTAT
66 ATAACTTATATATATGCATAACTTAATAACTCATATTAT
47105105 TTACATAACT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (104 bp):
AACTCACATAACTTAATAAGTTATACATGTTATATCATAACTCACATAATAACTTACATAACTTA
ATAACTTATATATATGCATAACTTAATAACTCATATTAT
Found at i:47105069 original size:17 final size:17
Alignment explanation
Indices: 47105047--47105118 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
47105037 ATAACTCACC
47105047 TAATAACTTACATAACT
1 TAATAACTTACATAACT
*
47105064 TAATAACTTATATATA-T
1 TAATAACTTACATA-ACT
**
47105081 GCATAACTTA-ATAACT
1 TAATAACTTACATAACT
* * *
47105097 CATATTATTTACATAACT
1 TA-ATAACTTACATAACT
47105115 TAAT
1 TAAT
47105119 CATTGTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 30 0.70
18 8 0.19
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (17 bp):
TAATAACTTACATAACT
Found at i:47105696 original size:43 final size:43
Alignment explanation
Indices: 47105624--47105763 Score: 199
Period size: 43 Copynumber: 3.3 Consensus size: 43
47105614 CACCAAACAA
** * *
47105624 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGAACATTACCTT
1 TAGCGGCGTTTGCAGGAAAAGCGCCGCTAAAGAACATGACCTT
* * * *
47105667 TAGCAGCGTTTTCAGGAAAAGCGCTGCTAAAGAACATGGCCTT
1 TAGCGGCGTTTGCAGGAAAAGCGCCGCTAAAGAACATGACCTT
*
47105710 TAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGCAGGAAAAGCGCCGCTAAAGAACATGACCTT
47105753 TAGCGGCGTTT
1 TAGCGGCGTTT
47105764 ATTTCTATAA
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTGCAGGAAAAGCGCCGCTAAAGAACATGACCTT
Found at i:47126749 original size:41 final size:41
Alignment explanation
Indices: 47126695--47126849 Score: 202
Period size: 41 Copynumber: 3.8 Consensus size: 41
47126685 TTAATTTAAA
* * * * * *
47126695 CAGATTCAACGGCACATAACCTGCTAAACTTATAGCATGATT
1 CAGA-TCACCGGCACGTAGCCTGCTAGACTTATAACCTGATT
**
47126737 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACGTAGCCTGCTAGACTTATAACCTGATT
* **
47126778 CAGATCACCGGCGCGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACGTAGCCTGCTAGACTTATAACCTGATT
47126819 CAGATCACCGGCACGTAGCCTGCTAGACTTA
1 CAGATCACCGGCACGTAGCCTGCTAGACTTA
47126850 AAGTCTGAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
41 97 0.96
42 4 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (41 bp):
CAGATCACCGGCACGTAGCCTGCTAGACTTATAACCTGATT
Found at i:47128850 original size:13 final size:13
Alignment explanation
Indices: 47128832--47128856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47128822 CAATCAAATG
47128832 CACACAAAATAAA
1 CACACAAAATAAA
47128845 CACACAAAATAA
1 CACACAAAATAA
47128857 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:47129793 original size:91 final size:91
Alignment explanation
Indices: 47129638--47129847 Score: 402
Period size: 91 Copynumber: 2.3 Consensus size: 91
47129628 AAATATGTTA
*
47129638 TTTTAAGGACTGTTGTTTGGTGTATTAATGCAGCAGAAAAATTCTTGTTTAGTCGTCAATTAATG
1 TTTTAAGGACTGTTGTTTGGTGTATTAATGCAACAGAAAAATTCTTGTTTAGTCGTCAATTAATG
47129703 TTGTCTAAGTGACTGTATTTATATTG
66 TTGTCTAAGTGACTGTATTTATATTG
47129729 TTTTAAGGACTGTTGTTTGGTGTATTAATGCAACAGAAAAATTCTTGTTTAGTCGTCAATTAATG
1 TTTTAAGGACTGTTGTTTGGTGTATTAATGCAACAGAAAAATTCTTGTTTAGTCGTCAATTAATG
47129794 TTGTCTAAGTGACTGTATTTATATTG
66 TTGTCTAAGTGACTGTATTTATATTG
*
47129820 TTTTAAGGACTATTGTTTGGTGTATTAA
1 TTTTAAGGACTGTTGTTTGGTGTATTAA
47129848 AACAGCAGTA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 117 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (91 bp):
TTTTAAGGACTGTTGTTTGGTGTATTAATGCAACAGAAAAATTCTTGTTTAGTCGTCAATTAATG
TTGTCTAAGTGACTGTATTTATATTG
Found at i:47130995 original size:41 final size:42
Alignment explanation
Indices: 47130893--47130995 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
47130883 CGATATGTGT
*
47130893 TTTCGTGTAAGACCAC-GTCTGGGACGTTGGCATCAACTTATG
1 TTTCGTGTAAGACC-CTGTCTGGGACATTGGCATCAACTTATG
* * **
47130935 TTACGTGTAAGACCATGTCTGGGACATTGGCATTGTA-TT-TG
1 TTTCGTGTAAGACCCTGTCTGGGACATTGGCA-TCAACTTATG
47130976 TTTCGTGTAAGACCCTGTCT
1 TTTCGTGTAAGACCCTGTCT
47130996 AGGAAAGCGG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
41 20 0.38
42 30 0.58
43 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (42 bp):
TTTCGTGTAAGACCCTGTCTGGGACATTGGCATCAACTTATG
Found at i:47131242 original size:36 final size:36
Alignment explanation
Indices: 47131202--47131297 Score: 149
Period size: 36 Copynumber: 2.7 Consensus size: 36
47131192 GTATATTTGA
*
47131202 ATTGATGTACTTGTGATATTATAAGTGATTCGGCCT
1 ATTGATATACTTGTGATATTATAAGTGATTCGGCCT
47131238 ATTGATATACTTGTGATATTATAAGTGATTCGGCCT
1 ATTGATATACTTGTGATATTATAAGTGATTCGGCCT
* * *
47131274 AATGATATAGTTGTGTTATT-TAAG
1 ATTGATATACTTGTGATATTATAAG
47131298 AGTGATAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
35 4 0.07
36 52 0.93
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (36 bp):
ATTGATATACTTGTGATATTATAAGTGATTCGGCCT
Found at i:47135270 original size:45 final size:49
Alignment explanation
Indices: 47135221--47135310 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
47135211 GGGGTTGAAA
47135221 TTAAATTTT-AATTTT-TAAA-AGATTAAATTAAT-ATTTT-TATTAATT
1 TTAAATTTTAAATTTTCTAAAGAGATTAAA-TAATGATTTTCTATTAATT
*
47135266 TTAAATTTTAAATTTTCTAAAGAGCTTAAATAATGATTTTCTATT
1 TTAAATTTTAAATTTTCTAAAGAGATTAAATAATGATTTTCTATT
47135311 TTAAGAAGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
45 9 0.23
46 6 0.15
47 8 0.21
48 12 0.31
49 4 0.10
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (49 bp):
TTAAATTTTAAATTTTCTAAAGAGATTAAATAATGATTTTCTATTAATT
Found at i:47144691 original size:28 final size:28
Alignment explanation
Indices: 47144659--47144719 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
47144649 AAGAAAATGT
47144659 CATATGGTGTATAAACTTAAGAAGTAAA
1 CATATGGTGTATAAACTTAAGAAGTAAA
*
47144687 TATATGGTGTATAAACTTAAGAAGTAAA
1 CATATGGTGTATAAACTTAAGAAGTAAA
47144715 CATAT
1 CATAT
47144720 AGGAAAGGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.31
Consensus pattern (28 bp):
CATATGGTGTATAAACTTAAGAAGTAAA
Found at i:47145627 original size:3 final size:3
Alignment explanation
Indices: 47145619--47145668 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
47145609 TTTAATGCAC
47145619 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
47145667 TA
1 TA
47145669 AGTTAACAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:47147141 original size:21 final size:21
Alignment explanation
Indices: 47147115--47147157 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
47147105 ACGGGTTAGT
47147115 TTGACTATAATAATTAATAAA
1 TTGACTATAATAATTAATAAA
* *
47147136 TTGACTATAATAGTTCATAAA
1 TTGACTATAATAATTAATAAA
47147157 T
1 T
47147158 AATATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
TTGACTATAATAATTAATAAA
Found at i:47147807 original size:21 final size:20
Alignment explanation
Indices: 47147783--47147821 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
47147773 TATTTACTAA
*
47147783 TTTTTATAGATTTCTTTAATG
1 TTTTTATAGAATT-TTTAATG
47147804 TTTTTATAGAATTTTTAA
1 TTTTTATAGAATTTTTAA
47147822 AATTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTTATAGAATTTTTAATG
Found at i:47148119 original size:2 final size:2
Alignment explanation
Indices: 47148112--47148138 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47148102 AAAGCAAAAC
47148112 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 A
47148139 CTTGAGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47148248 original size:19 final size:19
Alignment explanation
Indices: 47148185--47148250 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
47148175 TTAAAATTAT
*
47148185 TATTTTAGAATATTTTTAAA
1 TATTTTAAAAT-TTTTTAAA
**
47148205 -ATTTT-AGCTTTTTTATATA
1 TATTTTAAAATTTTTTA-A-A
*
47148224 TTTTTTAAAATTTTTTAAA
1 TATTTTAAAATTTTTTAAA
47148243 TATTTTAA
1 TATTTTAA
47148251 TTTTTTTGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 9
0.69 0.14 0.18
Matches are distributed among these distances:
17 6 0.17
18 2 0.06
19 14 0.40
20 5 0.14
21 8 0.23
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (19 bp):
TATTTTAAAATTTTTTAAA
Found at i:47150747 original size:2 final size:2
Alignment explanation
Indices: 47150705--47150729 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47150695 ATTTTTTGTG
47150705 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
47150730 CATGTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47150753 original size:16 final size:17
Alignment explanation
Indices: 47150705--47150757 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
47150695 ATTTTTTGTG
* *
47150705 TATATATATATATAT-A
1 TATATATATATGTTTCA
47150721 TATATATATCATGTTTCA
1 TATATATAT-ATGTTTCA
*
47150739 TATATATAT-TTTTTCA
1 TATATATATATGTTTCA
47150755 TAT
1 TAT
47150758 TGATATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 18 0.56
17 4 0.12
18 10 0.31
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (17 bp):
TATATATATATGTTTCA
Found at i:47156522 original size:110 final size:110
Alignment explanation
Indices: 47156302--47156510 Score: 364
Period size: 110 Copynumber: 1.9 Consensus size: 110
47156292 TATCGATTAT
* *
47156302 TTTACCCCAAGTATTGATACTCATGCTATGGTATCAATATCAAATTATGATACCGACTTCCTGCA
1 TTTACCCCAAGTATTGATACTCATGCTATGATATCAATATCAAATTACGATACCGACTTCCTGCA
47156367 CTTTCAAAAATCATGGAGGTATCATTTTTAAAACCTATATATCAA
66 CTTTCAAAAATCATGGAGGTATCATTTTTAAAACCTATATATCAA
* * * *
47156412 TTTACCCCAAGTATTGATGCTCGTGCTATGATATCAATATCAAATTACGTTACTGACTTCCTGCA
1 TTTACCCCAAGTATTGATACTCATGCTATGATATCAATATCAAATTACGATACCGACTTCCTGCA
47156477 CTTTCAAAAATCATGGAGGTATCATTTTTAAAAC
66 CTTTCAAAAATCATGGAGGTATCATTTTTAAAAC
47156511 TTGAATATCA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 93 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (110 bp):
TTTACCCCAAGTATTGATACTCATGCTATGATATCAATATCAAATTACGATACCGACTTCCTGCA
CTTTCAAAAATCATGGAGGTATCATTTTTAAAACCTATATATCAA
Found at i:47164743 original size:23 final size:25
Alignment explanation
Indices: 47164713--47164758 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
47164703 TCAATAATGT
47164713 AATTA-TTTTATAT-ATATATATGC
1 AATTATTTTTATATAATATATATGC
*
47164736 AATTATTTTTTTATAATATATAT
1 AATTATTTTTATATAATATATAT
47164759 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTATTTTTATATAATATATATGC
Found at i:47164773 original size:27 final size:26
Alignment explanation
Indices: 47164718--47164774 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
47164708 AATGTAATTA
*
47164718 TTTTATATATATATATGCAATTATTT
1 TTTTATATATATATATGCAATTATAT
*
47164744 TTTTATAATATATATATG-TATATATAT
1 TTTTAT-ATATATATATGCAAT-TATAT
47164771 TTTT
1 TTTT
47164775 TGGTATATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (26 bp):
TTTTATATATATATATGCAATTATAT
Found at i:47165093 original size:5 final size:5
Alignment explanation
Indices: 47165077--47165119 Score: 61
Period size: 5 Copynumber: 8.4 Consensus size: 5
47165067 TCTTATATTC
47165077 TTTAT ATTTAT TTTAT TTTAT TTTAT TTTAT TTT-T TCTTAT TT
1 TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT TT
47165120 CCTGCACTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
4 2 0.06
5 26 0.74
6 7 0.20
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:47165197 original size:20 final size:20
Alignment explanation
Indices: 47165174--47165217 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
47165164 AGAATGTTTT
47165174 TATTTTGCCCATTTATTTAA
1 TATTTTGCCCATTTATTTAA
* *
47165194 TATTTTTCTCATTTATTTAA
1 TATTTTGCCCATTTATTTAA
47165214 TATT
1 TATT
47165218 GCATGCCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTTTGCCCATTTATTTAA
Found at i:47180038 original size:43 final size:44
Alignment explanation
Indices: 47179967--47180057 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 44
47179957 TGGAATAGGT
*
47179967 GAATCCTACCTCCCTGGTCAGCACTGGAATAGGTTGACGATTG-
1 GAATCCTACCTCCCTGGTCAGCACTGGAATAGGTTGAAGATTGC
** * *
47180010 GAATCCTATGTCCCTGGTTAGCAGTGGAATAGGTTGAAGATTGC
1 GAATCCTACCTCCCTGGTCAGCACTGGAATAGGTTGAAGATTGC
47180054 GAAT
1 GAAT
47180058 TTTACTTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 38 0.90
44 4 0.10
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (44 bp):
GAATCCTACCTCCCTGGTCAGCACTGGAATAGGTTGAAGATTGC
Found at i:47180355 original size:169 final size:168
Alignment explanation
Indices: 47180076--47180547 Score: 746
Period size: 169 Copynumber: 2.8 Consensus size: 168
47180066 CATAACGTTA
* * *
47180076 TAGCGGAGCAGATTAAAGCTAAGGGCAGCGAATCTTATCTCTCGGGAGTTAAGACTTGAAAAAGC
1 TAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCT-TGGAGTTAAGACTTGAAATAGC
*
47180141 TAAAGTGGAGCGGATTAAAGCTGTGGGTAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGA
65 TAAAGTGGAGCGGATTAAAGCTGTGGGAAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGA
47180206 TTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTG
130 TTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTG
* *
47180245 TAGCGGAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCATTGGTGTTAAGACTTGAAATAGC
1 TAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTC-TTGGAGTTAAGACTTGAAATAGC
* *
47180310 TGAAGTGGAGCGGATTAAAGCTGTGGGAAGCGAATCCTATCTCTTTGGCGTTATAGTGGAACAGA
65 TAAAGTGGAGCGGATTAAAGCTGTGGGAAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGA
*
47180375 TTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTG
130 TTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTG
* * * * *
47180414 TAGTGGGGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTCGCGTTAAGACTTGAAATAGC
1 TAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCT-CTTGGAGTTAAGACTTGAAATAGC
* * * * *
47180479 TAAAGCGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTAAAGTGGAGCAGA
65 TAAAGTGGAGCGGATTAAAGCTGTGGGAAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGA
47180544 TTAA
130 TTAA
47180548 GGCCACAATG
Statistics
Matches: 279, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
169 277 0.99
170 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (168 bp):
TAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCTTGGAGTTAAGACTTGAAATAGCT
AAAGTGGAGCGGATTAAAGCTGTGGGAAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTG
Found at i:47180412 original size:51 final size:51
Alignment explanation
Indices: 47180338--47180464 Score: 137
Period size: 51 Copynumber: 2.5 Consensus size: 51
47180328 AGCTGTGGGA
* ** * *
47180338 AGCGAATCCTATCTCTTTGGCGTTATAGTGGAACAGATTAAAGCTAAAGGT
1 AGCGAATCTTATCTCCCTAGCGTTATAGTGGAACAGATTAAAGCTAAAGGC
* * * ** * *
47180389 AGCGAATCTTGTTTCCCTAGCGTTGTAGTGGGGCAGATTAAAGCTGAGGGC
1 AGCGAATCTTATCTCCCTAGCGTTATAGTGGAACAGATTAAAGCTAAAGGC
*
47180440 AGCGAATCTTATCTCCCTCGCGTTA
1 AGCGAATCTTATCTCCCTAGCGTTA
47180465 AGACTTGAAA
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (51 bp):
AGCGAATCTTATCTCCCTAGCGTTATAGTGGAACAGATTAAAGCTAAAGGC
Found at i:47180716 original size:44 final size:44
Alignment explanation
Indices: 47180654--47180776 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 44
47180644 CTGAAGACGG
* * * *
47180654 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGTCA
1 CAAATCTTATCTCACTGAAGTTGCAGTAGAGCAGATTAAAATCA
* *
47180698 -ATAATCATATCTCACTGAAGTTGCAGTAGAGCGGATTAAAATCA
1 CA-AATCTTATCTCACTGAAGTTGCAGTAGAGCAGATTAAAATCA
* *
47180742 CAAATCTTATCTCTCTAAAGTTGCAG-AGAGCAGAT
1 CAAATCTTATCTCACTGAAGTTGCAGTAGAGCAGAT
47180777 CGTATCTAGT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
43 9 0.13
44 57 0.85
45 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCACTGAAGTTGCAGTAGAGCAGATTAAAATCA
Found at i:47183320 original size:15 final size:15
Alignment explanation
Indices: 47183300--47183330 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47183290 GTTATGTAAG
47183300 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
47183315 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
47183330 T
1 T
47183331 ATGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:47187577 original size:15 final size:15
Alignment explanation
Indices: 47187557--47187585 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47187547 TATGTAAGTA
47187557 AAAGGTCAAGAGTTG
1 AAAGGTCAAGAGTTG
47187572 AAAGGTCAAGAGTT
1 AAAGGTCAAGAGTT
47187586 ATGTTGTTTT
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:0.41, C:0.07, G:0.31, T:0.21
Consensus pattern (15 bp):
AAAGGTCAAGAGTTG
Found at i:47197159 original size:41 final size:41
Alignment explanation
Indices: 47197125--47197244 Score: 161
Period size: 41 Copynumber: 2.9 Consensus size: 41
47197115 ACCGGCAATT
* * *
47197125 AGCCTGCTAGACGTAAAG-CTCGAAACATTTCACCGGCATCG
1 AGCCTGCTAGACATAAAGTCT-GAAATATTTCACCGGCATCA
* *
47197166 AGCCTGCTAGACATAAAGTCTGAAATATTTCAGCGACATCA
1 AGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCA
* *
47197207 AGCCTGCTAGACATAAAGTCTGAATTATTTCACTGGCA
1 AGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCA
47197245 ATAAATCTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 67 0.97
42 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCA
Found at i:47200813 original size:18 final size:19
Alignment explanation
Indices: 47200792--47200827 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
47200782 ACTTAGACGT
47200792 TTTAATTA-CTTTAGTTTA
1 TTTAATTATCTTTAGTTTA
*
47200810 TTTAATTATGTTTAGTTT
1 TTTAATTATCTTTAGTTT
47200828 CTTACAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (19 bp):
TTTAATTATCTTTAGTTTA
Found at i:47201747 original size:31 final size:31
Alignment explanation
Indices: 47201712--47201777 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
47201702 CAAGTGTGGC
47201712 TGACTTGGGTCACATGCTCGTATGTGACAAA
1 TGACTTGGGTCACATGCTCGTATGTGACAAA
*
47201743 TGACTTGGGTCACATGCTCGTGTGTGACAAA
1 TGACTTGGGTCACATGCTCGTATGTGACAAA
47201774 TGAC
1 TGAC
47201778 CGTGTGTCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (31 bp):
TGACTTGGGTCACATGCTCGTATGTGACAAA
Found at i:47202584 original size:20 final size:19
Alignment explanation
Indices: 47202555--47202594 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
47202545 TCTTTTCAAG
47202555 TTTCACATCTCATTTCATCA
1 TTTCACATCTCATTTC-TCA
*
47202575 TTTCATATCTCATTTCTCA
1 TTTCACATCTCATTTCTCA
47202594 T
1 T
47202595 AATTCAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTCACATCTCATTTCTCA
Found at i:47206518 original size:43 final size:42
Alignment explanation
Indices: 47206470--47206553 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
47206460 TGAGGGCACT
* * *
47206470 ATCACTTAAGCTTGCATAGGGAGCTTTGTTGGGACACAAGTTC
1 ATCACTTAAGCTTACAT-GGGAGCTTCGTTGAGACACAAGTTC
* *
47206513 ATCACTTAAGCTTACATGGGATCTTCGTTGATACACAAGTT
1 ATCACTTAAGCTTACATGGGAGCTTCGTTGAGACACAAGTT
47206554 ATCCATAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 20 0.56
43 16 0.44
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (42 bp):
ATCACTTAAGCTTACATGGGAGCTTCGTTGAGACACAAGTTC
Found at i:47206647 original size:78 final size:78
Alignment explanation
Indices: 47206541--47206789 Score: 295
Period size: 78 Copynumber: 3.2 Consensus size: 78
47206531 GGATCTTCGT
* * * * *
47206541 TGATACACAAGTTATCCATAAGATCACAGAGGAGCTTCCCTTATA-ACAACTTATCCTTCGCTCA
1 TGATACACAACTTATCCATAAGCTCACAG-GGAGATTCCCTGATACACAACTTATCCTTAGCTCA
* *
47206605 CGCAGGAGCTTTGG
65 CGGAGGAGCTTTGC
* * ** *
47206619 TGATACACAGCTTATTCATAAGCTCACAGGGGAGATTTTCTGATACACAACTTGTCCTTAGCTCA
1 TGATACACAACTTATCCATAAGCTCACA-GGGAGATTCCCTGATACACAACTTATCCTTAGCTCA
47206684 CGGA-GAGCTTTGC
65 CGGAGGAGCTTTGC
* * * * * * *
47206697 TGATACACAACTTATCCATAAGCTTAAAGGGAGTTTCGCTGATACACGACTTCTCCTTAGCTCAT
1 TGATACACAACTTATCCATAAGCTCACAGGGAGATTCCCTGATACACAACTTATCCTTAGCTCAC
47206762 GGAGGAGCTTTGC
66 GGAGGAGCTTTGC
47206775 TGATACACAACTTAT
1 TGATACACAACTTAT
47206790 AAAGTTATTC
Statistics
Matches: 146, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
77 34 0.23
78 91 0.62
79 21 0.14
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (78 bp):
TGATACACAACTTATCCATAAGCTCACAGGGAGATTCCCTGATACACAACTTATCCTTAGCTCAC
GGAGGAGCTTTGC
Found at i:47206777 original size:39 final size:39
Alignment explanation
Indices: 47206541--47206789 Score: 195
Period size: 39 Copynumber: 6.4 Consensus size: 39
47206531 GGATCTTCGT
* * * **
47206541 TGATACACAAGTTATCCATAAGATCACA-GAGGAGCTTCCC
1 TGATACACAACTTATCC-TTAGCTCA-AGGAGGAGCTTTGC
* * * * *
47206581 TTATA-ACAACTTATCCTTCGCTCACGCAGGAGCTTTGG
1 TGATACACAACTTATCCTTAGCTCAAGGAGGAGCTTTGC
* * * * *
47206619 TGATACACAGCTTATTCATAAGCTCACAGG-GGAGATTTTC
1 TGATACACAACTTA-TCCTTAGCTCA-AGGAGGAGCTTTGC
* *
47206659 TGATACACAACTTGTCCTTAGCTCACGGA-GAGCTTTGC
1 TGATACACAACTTATCCTTAGCTCAAGGAGGAGCTTTGC
* * *
47206697 TGATACACAACTTATCCATAAGCTTAAAG-GGAG-TTTCGC
1 TGATACACAACTTATCC-TTAGCTCAAGGAGGAGCTTT-GC
* * *
47206736 TGATACACGACTTCTCCTTAGCTCATGGAGGAGCTTTGC
1 TGATACACAACTTATCCTTAGCTCAAGGAGGAGCTTTGC
47206775 TGATACACAACTTAT
1 TGATACACAACTTAT
47206790 AAAGTTATTC
Statistics
Matches: 159, Mismatches: 40, Indels: 21
0.72 0.18 0.10
Matches are distributed among these distances:
38 52 0.33
39 72 0.45
40 34 0.21
41 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (39 bp):
TGATACACAACTTATCCTTAGCTCAAGGAGGAGCTTTGC
Found at i:47214904 original size:31 final size:31
Alignment explanation
Indices: 47214869--47214930 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
47214859 ACATGCAATT
47214869 AGAATAACAGA-AATAGTAGACATGTATTAAC
1 AGAATAAC-GATAATAGTAGACATGTATTAAC
** * *
47214900 AGAATGTCGATAATAGTAGGCATGTTTTAAC
1 AGAATAACGATAATAGTAGACATGTATTAAC
47214931 GTTACAGAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (31 bp):
AGAATAACGATAATAGTAGACATGTATTAAC
Found at i:47216083 original size:12 final size:12
Alignment explanation
Indices: 47216048--47216115 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
47216038 GGTAAGAAAC
47216048 AAAAGG-GAAGA
1 AAAAGGAGAAGA
*
47216059 AAGA-GAGAAGA
1 AAAAGGAGAAGA
* *
47216070 AAATGGAGAGGA
1 AAAAGGAGAAGA
47216082 AAAAGGAGAAGA
1 AAAAGGAGAAGA
***
47216094 GTGAGGAG-AGA
1 AAAAGGAGAAGA
47216105 AAAGAGGAGAA
1 AAA-AGGAGAA
47216116 AAGTTTGGTG
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
10 1 0.02
11 13 0.32
12 26 0.63
13 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (12 bp):
AAAAGGAGAAGA
Found at i:47216091 original size:21 final size:24
Alignment explanation
Indices: 47216074--47216119 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
47216064 AGAAGAAAAT
*
47216074 GGAGAGGAAAA-AGGAGAAGAGTGA
1 GGAGA-GAAAAGAGGAGAAAAGTGA
47216098 GGAGAGAAAAGAGGAGAAAAGT
1 GGAGAGAAAAGAGGAGAAAAGT
47216120 TTGGTGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.52, C:0.00, G:0.43, T:0.04
Consensus pattern (24 bp):
GGAGAGAAAAGAGGAGAAAAGTGA
Found at i:47218972 original size:15 final size:15
Alignment explanation
Indices: 47218952--47218984 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
47218942 AATCATTGGG
47218952 TTGAGCCTGAAAAGT
1 TTGAGCCTGAAAAGT
*
47218967 TTGAGCCTGAAAGGT
1 TTGAGCCTGAAAAGT
47218982 TTG
1 TTG
47218985 TCAGCAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (15 bp):
TTGAGCCTGAAAAGT
Found at i:47223667 original size:3 final size:3
Alignment explanation
Indices: 47223647--47223693 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
47223637 TATTTTCTTC
*
47223647 ATT ATT -TT AAT A-T ATT ATT ATCT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
47223691 ATT
1 ATT
47223694 GCTTGATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:47223862 original size:3 final size:3
Alignment explanation
Indices: 47223854--47223902 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
47223844 ACTATTCTTG
47223854 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47223902 T
1 T
47223903 ACTAGTTCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:47224289 original size:22 final size:20
Alignment explanation
Indices: 47224252--47224293 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
47224242 TTTATATTTT
47224252 TATATCTTATAATTTATGTA
1 TATATCTTATAATTTATGTA
*
47224272 TATATTTTAATAATTTTATGTA
1 TATATCTT-ATAA-TTTATGTA
47224294 CATACATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (20 bp):
TATATCTTATAATTTATGTA
Found at i:47224768 original size:109 final size:111
Alignment explanation
Indices: 47224572--47224879 Score: 464
Period size: 109 Copynumber: 2.8 Consensus size: 111
47224562 TTTTTAAAAG
* *
47224572 AGGCAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
47224637 CATTCAACCAAATGGCTAAATATCCTTTT-AAAAA-TTTCAAAATA
66 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTCAAAATA
*
47224681 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
47224746 CGTTCAACCAAATGGCTTAATATCCTTTTAAAAAATTTTCAAAATA
66 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTCAAAATA
* * * * *
47224792 AGGCAGTGTTTTGCGTTTGGAAATTCGAG-GAACGTGTCCTAATGTGCTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
** *
47224854 CGTTTGACCAAATAGCTAAATATCCT
66 CGTTCAACCAAATGGCTAAATATCCT
47224880 CTTGAACTTC
Statistics
Matches: 182, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
108 27 0.15
109 89 0.49
110 28 0.15
111 38 0.21
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (111 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATGGCTAAATATCCTTTTAAAAAATTTTCAAAATA
Found at i:47227336 original size:30 final size:31
Alignment explanation
Indices: 47227293--47227352 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
47227283 AGAGGTGAGA
* * *
47227293 TGGGAAGGGAATAAAAGTTTTTGGGGAAAAG
1 TGGGAAGGAAATAAAAATTTTGGGGGAAAAG
47227324 TGGG-AGGAAATAAAAATTTTGGGGGAAAA
1 TGGGAAGGAAATAAAAATTTTGGGGGAAAA
47227353 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.22
Consensus pattern (31 bp):
TGGGAAGGAAATAAAAATTTTGGGGGAAAAG
Found at i:47227974 original size:15 final size:15
Alignment explanation
Indices: 47227954--47227986 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
47227944 TACTTAGGAC
47227954 GACGTAAAAAAAGTT
1 GACGTAAAAAAAGTT
47227969 GACGTAAAAAAAGTT
1 GACGTAAAAAAAGTT
47227984 GAC
1 GAC
47227987 ATAGATTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.09, G:0.21, T:0.18
Consensus pattern (15 bp):
GACGTAAAAAAAGTT
Found at i:47237377 original size:15 final size:15
Alignment explanation
Indices: 47237357--47237389 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
47237347 AATCATTGGG
47237357 TTGAGCCTGAAAAGT
1 TTGAGCCTGAAAAGT
*
47237372 TTGAGCCTGAAAGGT
1 TTGAGCCTGAAAAGT
47237387 TTG
1 TTG
47237390 TCAACAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (15 bp):
TTGAGCCTGAAAAGT
Found at i:47238094 original size:12 final size:12
Alignment explanation
Indices: 47238077--47238102 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
47238067 TAATCAGACT
47238077 ATCGGTCTCTTG
1 ATCGGTCTCTTG
47238089 ATCGGTCTCTTG
1 ATCGGTCTCTTG
47238101 AT
1 AT
47238103 TGTCCTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (12 bp):
ATCGGTCTCTTG
Found at i:47245751 original size:9 final size:9
Alignment explanation
Indices: 47245737--47245761 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
47245727 ATCACAGTTG
47245737 AACTCTCTA
1 AACTCTCTA
47245746 AACTCTCTA
1 AACTCTCTA
47245755 AACTCTC
1 AACTCTC
47245762 CCTATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (9 bp):
AACTCTCTA
Found at i:47250062 original size:6 final size:6
Alignment explanation
Indices: 47250051--47250121 Score: 54
Period size: 6 Copynumber: 11.8 Consensus size: 6
47250041 CTTTTCTTCA
* ** * * * *
47250051 TTTTCT TTTTCT CTCACT TTTTCG ATTTCT TTTTCT TTTGT-A ATTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTT-TCT TTTTCT
*
47250099 TTTTCT TTTTCG TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTC
47250122 GATTTCATTA
Statistics
Matches: 47, Mismatches: 16, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
5 1 0.02
6 45 0.96
7 1 0.02
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
TTTTCT
Found at i:47250082 original size:12 final size:12
Alignment explanation
Indices: 47250067--47250127 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
47250057 TTTTCTCTCA
*
47250067 CTTTTTCGATTT
1 CTTTTTCGTTTT
47250079 CTTTTTC-TTTT
1 CTTTTTCGTTTT
* * *
47250090 GTAATTTCTTTTT
1 CT-TTTTCGTTTT
47250103 CTTTTTCGTTTT
1 CTTTTTCGTTTT
*
47250115 CTTTTTCGATTT
1 CTTTTTCGTTTT
47250127 C
1 C
47250128 ATTACAATGT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 4 0.10
12 31 0.77
13 5 0.12
ACGTcount: A:0.07, C:0.16, G:0.07, T:0.70
Consensus pattern (12 bp):
CTTTTTCGTTTT
Found at i:47250088 original size:18 final size:18
Alignment explanation
Indices: 47250067--47250121 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
47250057 TTTTCTCTCA
47250067 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
47250085 CTTTTGT-AATTTCTTTTT
1 CTTTT-TCGATTTCTTTTT
*
47250103 CTTTTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
47250121 C
1 C
47250122 GATTTCATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 1 0.03
18 30 0.94
19 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.73
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:47252911 original size:17 final size:17
Alignment explanation
Indices: 47252889--47252955 Score: 53
Period size: 17 Copynumber: 3.7 Consensus size: 17
47252879 TCCCTAACCT
47252889 CTAACCCTTAAATCCCC
1 CTAACCCTTAAATCCCC
* *
47252906 CTAACCCCTAAAGCATAACCC
1 CTAA-CCCTTAA--AT-CCCC
*
47252927 TTAACCCTTAAATCCCC
1 CTAACCCTTAAATCCCC
* *
47252944 TTAACCCCTAAA
1 CTAACCCTTAAA
47252956 GCATAACCCC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
17 18 0.45
18 8 0.20
20 8 0.20
21 6 0.15
ACGTcount: A:0.34, C:0.42, G:0.01, T:0.22
Consensus pattern (17 bp):
CTAACCCTTAAATCCCC
Found at i:47252932 original size:38 final size:38
Alignment explanation
Indices: 47252883--47252980 Score: 160
Period size: 38 Copynumber: 2.6 Consensus size: 38
47252873 CTCAAATCCC
*
47252883 TAACCTCTAACCCTTAAATCCCCCTAACCCCTAAAGCA
1 TAACCCCTAACCCTTAAATCCCCCTAACCCCTAAAGCA
* *
47252921 TAACCCTTAACCCTTAAATCCCCTTAACCCCTAAAGCA
1 TAACCCCTAACCCTTAAATCCCCCTAACCCCTAAAGCA
*
47252959 TAACCCCTAAACCTTAAATCCC
1 TAACCCCTAACCCTTAAATCCC
47252981 AAAATCTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.35, C:0.41, G:0.02, T:0.22
Consensus pattern (38 bp):
TAACCCCTAACCCTTAAATCCCCCTAACCCCTAAAGCA
Found at i:47254220 original size:8 final size:7
Alignment explanation
Indices: 47254145--47254248 Score: 59
Period size: 7 Copynumber: 14.4 Consensus size: 7
47254135 ATCTCTAAAC
47254145 CCCCTAA
1 CCCCTAA
47254152 CCCCTAA
1 CCCCTAA
** *
47254159 AGCATAA
1 CCCCTAA
47254166 -CCCTAA
1 CCCCTAA
47254172 -CCCTAAA
1 CCCCT-AA
47254179 TCCCCCTAA
1 --CCCCTAA
47254188 CCCCTAA
1 CCCCTAA
** * *
47254195 AGCATAG
1 CCCCTAA
47254202 CCCCTAA
1 CCCCTAA
47254209 CCCCTAAA
1 CCCCT-AA
47254217 CCCCCTAA
1 -CCCCTAA
47254225 CCCCTAA
1 CCCCTAA
** *
47254232 AGCATAA
1 CCCCTAA
47254239 CCCCTAA
1 CCCCTAA
47254246 CCC
1 CCC
47254249 TTAAATCTTA
Statistics
Matches: 72, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
6 8 0.11
7 49 0.68
8 4 0.06
9 7 0.10
10 4 0.06
ACGTcount: A:0.34, C:0.48, G:0.04, T:0.14
Consensus pattern (7 bp):
CCCCTAA
Found at i:47254221 original size:37 final size:36
Alignment explanation
Indices: 47254139--47254253 Score: 178
Period size: 37 Copynumber: 3.1 Consensus size: 36
47254129 CCCCAAATCT
*
47254139 CTAAACCCCCTAACCCCTAAAGCATAACCCTAA-CC
1 CTAAACCCCCTAACCCCTAAAGCATACCCCTAACCC
47254174 CTAAATCCCCCTAACCCCTAAAGCATAGCCCCTAACCC
1 CTAAA-CCCCCTAACCCCTAAAGCATA-CCCCTAACCC
47254212 CTAAACCCCCTAACCCCTAAAGCATAACCCCTAACCC
1 CTAAACCCCCTAACCCCTAAAGCAT-ACCCCTAACCC
*
47254249 TTAAA
1 CTAAA
47254254 TCTTAAATCC
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
35 5 0.07
36 21 0.28
37 40 0.54
38 8 0.11
ACGTcount: A:0.36, C:0.45, G:0.03, T:0.16
Consensus pattern (36 bp):
CTAAACCCCCTAACCCCTAAAGCATACCCCTAACCC
Found at i:47254954 original size:41 final size:41
Alignment explanation
Indices: 47254801--47255042 Score: 245
Period size: 41 Copynumber: 5.9 Consensus size: 41
47254791 TTTTATTATT
* * *
47254801 ATTAGTGGCGCTTTTTCAAAAACT-CCACTAAAGGCCCGAAC
1 ATTAGCGGCGCTTTTTCAAAAA-TGCCGCTAAAGGCCCGAGC
* ** * * * *
47254842 ATTAGTGGCGCTACTTCAAAAACGACGTTAAAGGCCCAAGC
1 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCCCGAGC
* * *
47254883 ATTAGCGGCGCTATTTCAAAAACGCAGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCCCGAGC
* *
47254924 ATTAGCGGCACTTTTTCAAAAATGCCGCTAAAGCCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCCCGAGC
* ** * *
47254965 AGTAGCAACGCTTTTTCAAAAATGCCGTTAAA-CCCCAGAGC
1 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCCC-GAGC
* * *
47255006 ATTAGCGGCGCTTTTTTAAAAATGCTGCTAAAAGCCC
1 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCCC
47255043 AAAAACTCGT
Statistics
Matches: 167, Mismatches: 31, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
40 4 0.02
41 160 0.96
42 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCCCGAGC
Found at i:47256206 original size:33 final size:31
Alignment explanation
Indices: 47256137--47256207 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 31
47256127 ATTATTCAAT
* *
47256137 TAATTTTAAAAATAATTATATTTTAATTTTA
1 TAATTATAAAAATAATTATATTTTAAATTTA
*
47256168 AAATTATAAAAA-AATTATAATTATTATAATTTA
1 TAATTATAAAAATAATTAT-ATT-TTA-AATTTA
47256201 TAATTAT
1 TAATTAT
47256208 TAGTTAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 6 0.18
31 13 0.39
32 3 0.09
33 11 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TAATTATAAAAATAATTATATTTTAAATTTA
Found at i:47263520 original size:26 final size:26
Alignment explanation
Indices: 47263484--47263547 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
47263474 AGTCGAATTG
47263484 GACTCAGATTTAATATTTTTAGTCTA
1 GACTCAGATTTAATATTTTTAGTCTA
47263510 GACTCAGATTTAATATTTTTAGTCTA
1 GACTCAGATTTAATATTTTTAGTCTA
*
47263536 GACTCAAATTTA
1 GACTCAGATTTA
47263548 GAAAAAGGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (26 bp):
GACTCAGATTTAATATTTTTAGTCTA
Found at i:47270811 original size:23 final size:23
Alignment explanation
Indices: 47270768--47270811 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
47270758 ATATTAGTTT
*
47270768 GTTAATATTATTATTGCTATTAA
1 GTTAATATTATTATTACTATTAA
* *
47270791 GTTACTATTATTATTATTATT
1 GTTAATATTATTATTACTATT
47270812 GTATTATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (23 bp):
GTTAATATTATTATTACTATTAA
Found at i:47283271 original size:50 final size:50
Alignment explanation
Indices: 47283211--47283350 Score: 210
Period size: 50 Copynumber: 2.8 Consensus size: 50
47283201 GCAATGGAAT
* * *
47283211 AGATTAAAGCCACAACGGCGAGTCTTACTTCCCTGGCATTGTAGCGGAGC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCATTGTAGCAGAGC
*
47283261 AGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCATTGTAGCAGAGC
1 AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCATTGTAGCAGAGC
* *
47283311 AGATTGAAGCCACGACGGCGAATCTTA-TCTCCCTAGCATT
1 AGATTGAAGCCACAACGGCGAATCTTACT-TCCCTGGCATT
47283351 AAGGCTTGGA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 81 0.99
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.24
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCATTGTAGCAGAGC
Found at i:47283476 original size:50 final size:50
Alignment explanation
Indices: 47283420--47283685 Score: 184
Period size: 50 Copynumber: 5.3 Consensus size: 50
47283410 TTGGCATTAC
*
47283420 AGTGGAATAGATTGAAGCCACAATGGTGAATCTTACTTCCCTGGCGATGT
1 AGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGATGT
* * * * * *
47283470 AGTGGAACAAATTGAAGTCACGACGGTGAATC-TA-TTTCCT--CGATATT
1 AGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGAT-GT
** * * *
47283517 ACAGTGGAATAGATTGAAGCCACAACGGCAAATCTTACTTCCCTAGTGGTGT
1 --AGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGATGT
* * * * ** * * *
47283569 GGTGGAACAGATTGAAGCTACGACGGTGAATC-TGGTTTCCTCGAC-ATTGC
1 AGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCT-GGCGA-TGT
* ** * * * * *
47283619 AATTAAAAAGATTGAAGCCACAACTGTGAATCTTACCTCCCTGGTGGTGT
1 AGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGATGT
47283669 AGTGGAATAGATTGAAG
1 AGTGGAATAGATTGAAG
47283686 TCATGACGGC
Statistics
Matches: 154, Mismatches: 51, Indels: 22
0.68 0.22 0.10
Matches are distributed among these distances:
46 4 0.03
47 1 0.01
48 5 0.03
49 34 0.22
50 97 0.63
51 10 0.06
52 1 0.01
53 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (50 bp):
AGTGGAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGATGT
Done.