Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 133 of 433
Found at i:40946739 original size:30 final size:30
Alignment explanation
Indices: 40946705--40946767 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
40946695 ACTTAACAAG
40946705 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
40946735 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
40946765 CAA
1 CAA
40946768 CAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:40948504 original size:24 final size:24
Alignment explanation
Indices: 40948457--40948519 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
40948447 GCCAAACTTA
*
40948457 GGTGTCAAATTGGAAAAAAAACTCG
1 GGTGCCAAATT-GAAAAAAAACTCG
*
40948482 GGTGCCAAATTGAGAAAAAACTCG
1 GGTGCCAAATTGAAAAAAAACTCG
* *
40948506 CGTACCAAATTGAA
1 GGTGCCAAATTGAA
40948520 CATTATAACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 23 0.70
25 10 0.30
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (24 bp):
GGTGCCAAATTGAAAAAAAACTCG
Found at i:40949339 original size:16 final size:16
Alignment explanation
Indices: 40949320--40949365 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
40949310 GTTATTTTTT
40949320 GTTTAAATTATTTTGA
1 GTTTAAATTATTTTGA
* *
40949336 GTTTTAAGTATTTTGA
1 GTTTAAATTATTTTGA
* *
40949352 GTTCAAATTGTTTT
1 GTTTAAATTATTTT
40949366 TTTTAGGATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (16 bp):
GTTTAAATTATTTTGA
Found at i:40949578 original size:49 final size:50
Alignment explanation
Indices: 40949518--40949619 Score: 179
Period size: 50 Copynumber: 2.1 Consensus size: 50
40949508 ATTATTAGAA
40949518 AAATATTTA-TTTTTTACTGAATACCATTTAAAATTTTAATTAAGATATT
1 AAATATTTATTTTTTTACTGAATACCATTTAAAATTTTAATTAAGATATT
* *
40949567 AAATATTTATTTTTTTATTGAATACCATTTAAATTTTTAATTAAGATATT
1 AAATATTTATTTTTTTACTGAATACCATTTAAAATTTTAATTAAGATATT
40949617 AAA
1 AAA
40949620 CTCCACAAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 9 0.18
50 41 0.82
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (50 bp):
AAATATTTATTTTTTTACTGAATACCATTTAAAATTTTAATTAAGATATT
Found at i:40952416 original size:2 final size:2
Alignment explanation
Indices: 40952409--40952453 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
40952399 TTAATTTACT
40952409 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
40952451 TA T
1 TA T
40952454 GAGGATGAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40952665 original size:85 final size:85
Alignment explanation
Indices: 40952502--40952665 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 85
40952492 TTAATTATAA
* * * * *
40952502 ATTTTAAGAGAATTAAAGTATAATTTTATCACTGTATTAACTTATTATTTTAAAATTTTTAAAAG
1 ATTTTAAGAGAATTAAAGTATAAATTTATCACTATATTAACTTATTAATTTAAAATTTTAAAAAA
* * *
40952567 AGATTAAACTAAAAGTTATT
66 AAACTAAAATAAAAGTTATT
* * *
40952587 ATTTTAAGAGAATTAAAGTATAAATTTATCATTATATTAATTTA-TAATTTATAATTCTTAAAAA
1 ATTTTAAGAGAATTAAAGTATAAATTTATCACTATATTAACTTATTAATTTAAAATT-TTAAAAA
40952651 AAAACTAAAATAAAA
65 AAAACTAAAATAAAA
40952666 ATGGGTTGCT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 10 0.15
85 57 0.85
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.41
Consensus pattern (85 bp):
ATTTTAAGAGAATTAAAGTATAAATTTATCACTATATTAACTTATTAATTTAAAATTTTAAAAAA
AAACTAAAATAAAAGTTATT
Found at i:40953735 original size:21 final size:20
Alignment explanation
Indices: 40953711--40953754 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
40953701 AATATTTTAT
40953711 TAAAAATTAG-AAAATAAATTA
1 TAAAAATT-GTAAAA-AAATTA
40953732 TAAAAATTGTAAAAAAATTA
1 TAAAAATTGTAAAAAAATTA
40953752 TAA
1 TAA
40953755 TTTTTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
TAAAAATTGTAAAAAAATTA
Found at i:40953980 original size:19 final size:18
Alignment explanation
Indices: 40953948--40953997 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 18
40953938 GTACGATAAT
40953948 TTTTATATTTTTTTTACAAA
1 TTTTATA-TTTTTTTAC-AA
*
40953968 TTTTATATTTTTTTACAT
1 TTTTATATTTTTTTACAA
40953986 TTTTATAATTTT
1 TTTTAT-ATTTT
40953998 CTTATGACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 7 0.25
19 14 0.50
20 7 0.25
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATATTTTTTTACAA
Found at i:40954094 original size:20 final size:21
Alignment explanation
Indices: 40954071--40954109 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
40954061 TTTTTATAAA
40954071 AATTTACAAT-TTTTTATTGT
1 AATTTACAATATTTTTATTGT
**
40954091 AATTTTTAATATTTTTATT
1 AATTTACAATATTTTTATT
40954110 TTTTATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (21 bp):
AATTTACAATATTTTTATTGT
Found at i:40954462 original size:61 final size:61
Alignment explanation
Indices: 40954334--40954459 Score: 227
Period size: 61 Copynumber: 2.1 Consensus size: 61
40954324 TTTTTGATGC
*
40954334 ATTTTAAAAGTTCAAGTACCTAATTGAATGCCAAAAAAAAGTAGGGGCTTAATTGTTTTTT
1 ATTTTAAAAGTTCAAGTACCTAATTGAATGCCAAAAAAAAGTAAGGGCTTAATTGTTTTTT
40954395 ATTTTAAAAGTTCAAGTACCTAATTGAATGCC-AAAAAAAGTAAGGGCTTAATTGTTTTTT
1 ATTTTAAAAGTTCAAGTACCTAATTGAATGCCAAAAAAAAGTAAGGGCTTAATTGTTTTTT
*
40954455 TTTTT
1 ATTTT
40954460 TAAGTTTAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 31 0.49
61 32 0.51
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (61 bp):
ATTTTAAAAGTTCAAGTACCTAATTGAATGCCAAAAAAAAGTAAGGGCTTAATTGTTTTTT
Found at i:40965310 original size:42 final size:42
Alignment explanation
Indices: 40965263--40965348 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
40965253 TGTACAAACT
* *
40965263 ATCAATATAATTACCCATCTTTATATTTATGGGTTAAAAAGA
1 ATCAATATAATAACCCATCTTTATATTTATGAGTTAAAAAGA
40965305 ATCAATATAATAACCCATCTTTATATTTATGAGTTAAAAAGA
1 ATCAATATAATAACCCATCTTTATATTTATGAGTTAAAAAGA
40965347 AT
1 AT
40965349 TATGAGTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (42 bp):
ATCAATATAATAACCCATCTTTATATTTATGAGTTAAAAAGA
Found at i:40975759 original size:35 final size:38
Alignment explanation
Indices: 40975690--40975760 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
40975680 TAAATATAAA
* * *
40975690 AATAATTATATTAAGAATGTTATTAAGTTATATTTAAT
1 AATAATTATATTAAGAATATGATTAAGATATATTTAAT
40975728 AATAATTATATTAA-AATATGATTAA-AT-TATTTA
1 AATAATTATATTAAGAATATGATTAAGATATATTTA
40975761 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 6 0.20
36 1 0.03
37 9 0.30
38 14 0.47
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (38 bp):
AATAATTATATTAAGAATATGATTAAGATATATTTAAT
Found at i:40980453 original size:25 final size:25
Alignment explanation
Indices: 40980425--40980487 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
40980415 ATAAATATAA
40980425 ATTAAATAAAAAAATCATCTCAC-AT
1 ATTAAATAAAAAAATCATC-CACAAT
* * *
40980450 ATTAAACAATAAAGTCATCCACAAT
1 ATTAAATAAAAAAATCATCCACAAT
**
40980475 ATTATTTAAAAAA
1 ATTAAATAAAAAA
40980488 TCTACATCCC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
24 3 0.10
25 27 0.90
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.29
Consensus pattern (25 bp):
ATTAAATAAAAAAATCATCCACAAT
Found at i:40989181 original size:17 final size:18
Alignment explanation
Indices: 40989159--40989192 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40989149 CTCTCCTCGA
40989159 TAATGGGT-ACTTGTTCT
1 TAATGGGTAACTTGTTCT
*
40989176 TAATGGTTAACTTGTTC
1 TAATGGGTAACTTGTTC
40989193 AGTTACTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (18 bp):
TAATGGGTAACTTGTTCT
Found at i:40990888 original size:13 final size:13
Alignment explanation
Indices: 40990870--40990896 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40990860 ATGACTCCTG
40990870 ATTCTTTCTGGAT
1 ATTCTTTCTGGAT
40990883 ATTCTTTCTGGAT
1 ATTCTTTCTGGAT
40990896 A
1 A
40990897 ATTTTAGTAA
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:0.19, C:0.15, G:0.15, T:0.52
Consensus pattern (13 bp):
ATTCTTTCTGGAT
Found at i:40991899 original size:40 final size:39
Alignment explanation
Indices: 40991854--40991983 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
40991844 CGGAATACAA
40991854 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* *
40991894 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * *
40991934 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
40991974 CCGGATATAA
1 CCGGATATAA
40991984 TTTCCAGCAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:40999844 original size:40 final size:40
Alignment explanation
Indices: 40999799--40999966 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
40999789 CGGAATACAA
40999799 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
40999839 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
40999879 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
*** * ** * *
40999919 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
40999959 CCGGATAT
1 CCGGATAT
40999967 CATTCAATTG
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
39 3 0.03
40 102 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:41001597 original size:16 final size:16
Alignment explanation
Indices: 41001576--41001608 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41001566 ACCACATTCC
41001576 GACTAGGGTCAATTTT
1 GACTAGGGTCAATTTT
41001592 GACTAGGGTCAATTTT
1 GACTAGGGTCAATTTT
41001608 G
1 G
41001609 GGCTGTCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.36
Consensus pattern (16 bp):
GACTAGGGTCAATTTT
Found at i:41003203 original size:48 final size:48
Alignment explanation
Indices: 41003151--41003382 Score: 181
Period size: 48 Copynumber: 4.9 Consensus size: 48
41003141 AGGCAGTGAC
*
41003151 ATGTGATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCATTGTT
1 ATGTGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATTGTT
* * ** *
41003199 ATGTGATCCCATATAAGACCATGTCTGGGACATGGCATTGGCATAATA
1 ATGTGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATTGTT
** * * * *
41003247 ATAAGA-CATCGTGTAAGACCATAGT-TGGG-CTATCGGCTTT-GAAATG--
1 ATGTGATC-CCATGTAAGACCAT-GTCTGGGAC-AT-GGCTTTGGCATTGTT
* * * *
41003293 -TGTGATCCCATGTAAGACCATGTCTAGGATATGGCATTGGCATCGTT
1 ATGTGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATTGTT
* ** * * *
41003340 ATGTGGTCATATGTAAGACCATATCTGAGATATGGCTTTGGCA
1 ATGTGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
41003383 CCCTACCTTC
Statistics
Matches: 140, Mismatches: 33, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
44 7 0.05
45 23 0.16
46 1 0.01
47 2 0.01
48 100 0.71
49 7 0.05
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (48 bp):
ATGTGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATTGTT
Found at i:41010996 original size:48 final size:48
Alignment explanation
Indices: 41010925--41011191 Score: 167
Period size: 48 Copynumber: 5.6 Consensus size: 48
41010915 AGCTCCCGTA
* * **
41010925 TAAGACCATATTTGGGTTATGGCTTTGGCAGT-GACATGTGATCCCATG
1 TAAGACCATGTCTGGGACATGGCTTTGGCA-TCGACATGTGATCCCATG
**
41010973 TAAGACCATGTCTGGGACATGGCTTTGGCATCGTTATGTGATCCCATG
1 TAAGACCATGTCTGGGACATGGCTTTGGCATCGACATGTGATCCCATG
* * * * * ** * *
41011021 TAAGACCATGTCTAGGACGTGGCATTAGCATC-ATAATAAGA-CATCGTG
1 TAAGACCATGTCTGGGACATGGCTTTGGCATCGA-CATGTGATC-CCATG
* **
41011069 TAAGACCATAG-CTGGG-CTATCGGCTTCGAAAT-G---TGTGATCCCATG
1 TAAGACCAT-GTCTGGGAC-AT-GGCTTTGGCATCGACATGTGATCCCATG
* * * *
41011114 TAAGACCATGTCTGGGACATGGCATTGGCATC-ATTATGTGGTCCTATG
1 TAAGACCATGTCTGGGACATGGCTTTGGCATCGA-CATGTGATCCCATG
* * * *
41011162 TAAGGCCATATCTGGGATATGGCATTGGCA
1 TAAGACCATGTCTGGGACATGGCTTTGGCA
41011192 CCCTACCTTG
Statistics
Matches: 168, Mismatches: 36, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
44 8 0.05
45 22 0.13
46 2 0.01
47 3 0.02
48 126 0.75
49 7 0.04
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCTTTGGCATCGACATGTGATCCCATG
Found at i:41013331 original size:48 final size:48
Alignment explanation
Indices: 41013260--41013588 Score: 372
Period size: 48 Copynumber: 6.9 Consensus size: 48
41013250 GGGTAAGAGA
* * * *
41013260 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATG
1 CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACATAACAAGG
* * ***
41013308 CCGATGCCATGTTCCAAACATGGTCTTACACTGGTTCACATATTGAGG
1 CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACATAACAAGG
* * * * **
41013356 CCGATGCCAT-TTCCCAGACATAGTCTTACACTAGCTCTCAAAACAATA
1 CCGATGCCATGTT-CCAGACATGGTCTTACACTGGCTCACATAACAAGG
* ***
41013404 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATTGAGG
1 CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACATAACAAGG
* * * *
41013452 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATG
1 CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACATAACAAGG
* ** ****
41013500 CCGATGCCATGTTCCAAACACAGTCTTACACTGGCTCACATTTTGAGG
1 CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACATAACAAGG
41013548 CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACAT
1 CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACAT
41013589 GTATCATAAC
Statistics
Matches: 227, Mismatches: 52, Indels: 4
0.80 0.18 0.01
Matches are distributed among these distances:
47 2 0.01
48 223 0.98
49 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (48 bp):
CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTCACATAACAAGG
Found at i:41013424 original size:96 final size:96
Alignment explanation
Indices: 41013260--41013584 Score: 560
Period size: 96 Copynumber: 3.4 Consensus size: 96
41013250 GGGTAAGAGA
41013260 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCCGATGCCATGTTCCAA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCCGATGCCATGTTCCAA
*
41013325 ACATGGTCTTACACTGGTTCACATATTGAGG
66 ACATGGTCTTACACTGGCTCACATATTGAGG
* * * *
41013356 CCGATGCCATTTCCCAGACATAGTCTTACACTAGCTCTCAAAACAATACCGATGCCATGTTCCAA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCCGATGCCATGTTCCAA
41013421 ACATGGTCTTACACTGGCTCACATATTGAGG
66 ACATGGTCTTACACTGGCTCACATATTGAGG
41013452 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCCGATGCCATGTTCCAA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCCGATGCCATGTTCCAA
** *
41013517 ACACAGTCTTACACTGGCTCACATTTTGAGG
66 ACATGGTCTTACACTGGCTCACATATTGAGG
* *
41013548 CCGATGCCATGTTCCAGACATGGTCTTACACTGGCTC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC
41013585 ACATGTATCA
Statistics
Matches: 215, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 215 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (96 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCCGATGCCATGTTCCAA
ACATGGTCTTACACTGGCTCACATATTGAGG
Found at i:41015520 original size:30 final size:29
Alignment explanation
Indices: 41015477--41015540 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
41015467 CAAGTAGCCG
* *
41015477 AAGCTAGTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTAAATCGAACACTTACTGCCA
41015506 AAGCTAGTTTAAATCGAACACTTACTGCCA
1 AAGCTAG-TTAAATCGAACACTTACTGCCA
41015536 AAGCT
1 AAGCT
41015541 TCCAATTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (29 bp):
AAGCTAGTTAAATCGAACACTTACTGCCA
Found at i:41017907 original size:41 final size:41
Alignment explanation
Indices: 41017841--41017920 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
41017831 TACACAGGTT
41017841 TTCACATGGCCTGGTACACGCCCGTGTGCCT-GACCCGTGTCC
1 TTCACATGGCCTGGTACACGCCCGTGT-CCTAG-CCCGTGTCC
41017883 TTCACATGGCCAT-G-ACACGCCCGTGTCCTAGCCCGTGT
1 TTCACATGGCC-TGGTACACGCCCGTGTCCTAGCCCGTGT
41017921 GCAAAAACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
40 10 0.28
41 13 0.36
42 12 0.33
43 1 0.03
ACGTcount: A:0.14, C:0.38, G:0.25, T:0.24
Consensus pattern (41 bp):
TTCACATGGCCTGGTACACGCCCGTGTCCTAGCCCGTGTCC
Found at i:41018934 original size:47 final size:48
Alignment explanation
Indices: 41018860--41019131 Score: 251
Period size: 47 Copynumber: 5.8 Consensus size: 48
41018850 GGGGTGAGGT
* * *
41018860 GTCGATGCCATGTCCTATACATAGTCTTACACTGGCTCAT-ATCTC-AA
1 GTCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCATCATCTCGAA
*
41018907 GTCGATGCCATGTCCCAGACATGGTCTTACACT-GACT-ATCATCTCGTA
1 GTCGATGCCATGTCCCAGACAT-GTCTTACACTAG-CTCATCATCTCGAA
* * *
41018955 GTCGATG-CATGTCCCAGACATGTCTTACACTAGCTTA-CGTTTCGAA
1 GTCGATGCCATGTCCCAGACATGTCTTACACTAGCTCATCATCTCGAA
* * * * *
41019001 GTCAATG-CATGTTCCAGACATGTCTTACACTAGCAC-TCGTCTCGAT
1 GTCGATGCCATGTCCCAGACATGTCTTACACTAGCTCATCATCTCGAA
* * * **
41019047 GCCGATGCCATGTCCCAGACATGGTCTAACACTAGCTC-TCATAAT-GTG
1 GTCGATGCCATGTCCCAGACAT-GTCTTACACTAGCTCATCAT-CTCGAA
* *
41019095 GCCAATG-CATGTCCCAGACATGTCTTACACTAGCTCA
1 GTCGATGCCATGTCCCAGACATGTCTTACACTAGCTCA
41019132 CATTAACCCA
Statistics
Matches: 191, Mismatches: 24, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
46 79 0.41
47 80 0.42
48 31 0.16
49 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (48 bp):
GTCGATGCCATGTCCCAGACATGTCTTACACTAGCTCATCATCTCGAA
Found at i:41026501 original size:46 final size:46
Alignment explanation
Indices: 41026413--41026530 Score: 141
Period size: 46 Copynumber: 2.5 Consensus size: 46
41026403 ATCTCAAGTT
* *
41026413 GATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTTGTAGCC
1 GATG-CATGTCCAAGACAT-GTCTTACACTGACTATCATCTTGAAGCC
* *
41026461 GATGCATGTCCAAGACATGTCTTACACTGGCT-TACGTCTTGAAGCC
1 GATGCATGTCCAAGACATGTCTTACACTGACTAT-CATCTTGAAGCC
*
41026507 GATGCATATCCCAA-ACATGTCTTA
1 GATGCATGT-CCAAGACATGTCTTA
41026531 TACTAGCACT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
45 1 0.02
46 41 0.65
47 17 0.27
48 4 0.06
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (46 bp):
GATGCATGTCCAAGACATGTCTTACACTGACTATCATCTTGAAGCC
Found at i:41028629 original size:15 final size:15
Alignment explanation
Indices: 41028601--41028646 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
41028591 GAAGATTCCC
*
41028601 AAAAATCAAA-AAAT
1 AAAAATAAAATAAAT
41028615 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
41028630 AAAAATAAAACTAAAT
1 AAAAATAAAA-TAAAT
41028646 A
1 A
41028647 CTTATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 9 0.31
15 14 0.48
16 6 0.21
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:41032393 original size:30 final size:30
Alignment explanation
Indices: 41032359--41032419 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41032349 TCCTTAACTC
41032359 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
41032389 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
41032419 A
1 A
41032420 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:41036493 original size:16 final size:16
Alignment explanation
Indices: 41036454--41036486 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41036444 TTATATTTAA
41036454 TAATATAATTTATTAT
1 TAATATAATTTATTAT
41036470 TAATATAATTTATTAT
1 TAATATAATTTATTAT
41036486 T
1 T
41036487 TTAATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATATAATTTATTAT
Found at i:41036498 original size:16 final size:17
Alignment explanation
Indices: 41036436--41036501 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 17
41036426 AAATACATGC
41036436 TAAATTATTTATATTTAA
1 TAAATTATTTAT-TTTAA
*
41036454 TAATATAATTTATTATTAA
1 TAA-ATTATTTATT-TTAA
41036473 TATAATT-TATTATTTTAA
1 TA-AATTAT-TTATTTTAA
41036491 TAAATTATTTA
1 TAAATTATTTA
41036502 ATATTAAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 7 0.17
18 12 0.29
19 21 0.51
20 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATTATTTATTTTAA
Found at i:41036563 original size:23 final size:23
Alignment explanation
Indices: 41036520--41036563 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
41036510 GTTTTATTTT
* *
41036520 AATTATAAATTTTAGAAAATAAA
1 AATTATAAAATTTAAAAAATAAA
41036543 AATT-TAAAATTTAAAATAATA
1 AATTATAAAATTTAAAA-AATA
41036564 TTCTTAGTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AATTATAAAATTTAAAAAATAAA
Found at i:41038111 original size:28 final size:28
Alignment explanation
Indices: 41038079--41038137 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
41038069 TTCATCCTAA
41038079 ATGGATTTATTCACTTGTGACATTCATG
1 ATGGATTTATTCACTTGTGACATTCATG
*
41038107 ATGGATTTATTCGCTTGTGACATTCATG
1 ATGGATTTATTCACTTGTGACATTCATG
41038135 ATG
1 ATG
41038138 TGACTTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (28 bp):
ATGGATTTATTCACTTGTGACATTCATG
Found at i:41054999 original size:7 final size:7
Alignment explanation
Indices: 41054976--41055010 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
41054966 AAACATTTAA
41054976 TTATTATT
1 TTATT-TT
41054984 TTATGTTT
1 TTAT-TTT
41054992 TTATTTT
1 TTATTTT
41054999 TTATTTT
1 TTATTTT
41055006 TTATT
1 TTATT
41055011 AAAATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.58
8 10 0.38
9 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (7 bp):
TTATTTT
Found at i:41055040 original size:24 final size:24
Alignment explanation
Indices: 41054995--41055054 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
41054985 TATGTTTTTA
*
41054995 TTTTTTATT-TTTTATTAAAATTAT
1 TTTTTTATTATATTATTAAAATT-T
*
41055019 TTTTTTATTATATT-TTAGAATTT
1 TTTTTTATTATATTATTAAAATTT
41055042 TATTTTTAATTAT
1 T-TTTTT-ATTAT
41055055 CAATTTCGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 2 0.06
24 21 0.68
25 8 0.26
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTTTATTATATTATTAAAATTT
Found at i:41059934 original size:27 final size:26
Alignment explanation
Indices: 41059889--41060002 Score: 104
Period size: 27 Copynumber: 4.2 Consensus size: 26
41059879 CCCTGTTTAG
* *
41059889 AATACTTTAGTTTACTAAAATTACCGA
1 AATACCTTAGTTT-GTAAAATTACCGA
* *
41059916 AATACCCTTAGTTTGTAAAAATACTGA
1 AATA-CCTTAGTTTGTAAAATTACCGA
* *
41059943 AATACCTTCGATTTGTAAAATTACTGA
1 AATACCTTAG-TTTGTAAAATTACCGA
**
41059970 AATACCTTCAACTTGTAAAATTACC-A
1 AATACCTT-AGTTTGTAAAATTACCGA
41059996 AAGTACC
1 AA-TACC
41060003 CCCGATTTAC
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
26 8 0.11
27 57 0.78
28 8 0.11
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (26 bp):
AATACCTTAGTTTGTAAAATTACCGA
Found at i:41060018 original size:27 final size:27
Alignment explanation
Indices: 41059999--41060209 Score: 251
Period size: 27 Copynumber: 7.8 Consensus size: 27
41059989 ATTACCAAAG
*
41059999 TACCCCCGATTTACAGAATTATCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
*
41060026 TACCCCCGATTTACATAATTACCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
* * *
41060053 TACCCCCGATTTACATAATTATCATTT
1 TACCCCCGATTTACAGAATTACCGTTT
* *
41060080 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
*
41060107 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
* * * *
41060134 TACCCTCAATTTATAGAATTACTGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
*** * *
41060161 TACCCTTAATTTATAGAATTACTGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
* *
41060188 TACCCTCGATTTACAAAATTAC
1 TACCCCCGATTTACAGAATTAC
41060210 TAAAATACCC
Statistics
Matches: 166, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 166 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (27 bp):
TACCCCCGATTTACAGAATTACCGTTT
Found at i:41060219 original size:54 final size:54
Alignment explanation
Indices: 41060115--41060221 Score: 133
Period size: 54 Copynumber: 2.0 Consensus size: 54
41060105 TTTACCCTCG
* * ****
41060115 ATTTACAGAATTACCGTTTTACCCTCAATTTATAGAATTACTGTTTTACCCTTA
1 ATTTACAGAATTACCGTTTTACCCTCAATTTACAAAATTACTAAAATACCCTTA
* * *
41060169 ATTTATAGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTT
1 ATTTACAGAATTACCGTTTTACCCTCAATTTACAAAATTACTAAAATACCCTT
41060222 GGTTTGTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.41
Consensus pattern (54 bp):
ATTTACAGAATTACCGTTTTACCCTCAATTTACAAAATTACTAAAATACCCTTA
Found at i:41060311 original size:54 final size:53
Alignment explanation
Indices: 41060188--41060326 Score: 190
Period size: 54 Copynumber: 2.6 Consensus size: 53
41060178 ATTACTGTTT
* ** *
41060188 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTTGGTTTGTAAATTACCAAAA
* * *
41060241 TACCC-CTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTGAAATTATCGAAA
1 TACCCTC-AATTTGTAAAATTACCAAAATACCCTTGGTTTGT-AAATTACCAAAA
41060295 TACCCTCAATTTGTAAAATTACCAAAATACCC
1 TACCCTCAATTTGTAAAATTACCAAAATACCC
41060327 CTGATTTACA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
52 1 0.01
53 34 0.45
54 39 0.52
55 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.32
Consensus pattern (53 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCCTTGGTTTGTAAATTACCAAAA
Found at i:41060426 original size:27 final size:27
Alignment explanation
Indices: 41060202--41060439 Score: 203
Period size: 27 Copynumber: 8.8 Consensus size: 27
41060192 CTCGATTTAC
*
41060202 AAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41060229 -AAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
41060255 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * * ***
41060282 GAAATTATCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * **
41060309 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
41060336 AAAGTTA-CAGAAATACCCTTGACTTTCT
1 AAAATTACCA-AAATACCCTTG-GTTTGT
* * **
41060364 AAAAATTA-TAGAAATACCATTGGTTTAC
1 -AAAATTACCA-AAATACCCTTGGTTTGT
*
41060392 AAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
41060419 AGATTTACCAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
41060440 TAGGATGAAA
Statistics
Matches: 169, Mismatches: 37, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
26 25 0.15
27 118 0.70
28 8 0.05
29 18 0.11
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGGTTTGT
Found at i:41060527 original size:27 final size:27
Alignment explanation
Indices: 41060457--41060530 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
41060447 AAATGACTAA
41060457 AATACCCCTATTAGGTAAAAAGACCGT
1 AATACCCCTATTAGGTAAAAAGACCGT
* **
41060484 AA-AGCCCCT-GTAGGGTAAAGTGACCGT
1 AATA-CCCCTATTA-GGTAAAAAGACCGT
*
41060511 AATACCCCTATTTGGTAAAA
1 AATACCCCTATTAGGTAAAA
41060531 TGATGAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
26 3 0.08
27 32 0.86
28 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (27 bp):
AATACCCCTATTAGGTAAAAAGACCGT
Found at i:41061434 original size:25 final size:26
Alignment explanation
Indices: 41061337--41061434 Score: 189
Period size: 26 Copynumber: 3.8 Consensus size: 26
41061327 GAGGAAGTGC
41061337 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
41061363 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
41061389 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
41061415 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
41061435 ATTAAAGAGG
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
25 10 0.14
26 62 0.86
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:41063083 original size:40 final size:40
Alignment explanation
Indices: 41062941--41063105 Score: 138
Period size: 40 Copynumber: 4.2 Consensus size: 40
41062931 GAATATAACT
* ** * *
41062941 GGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCC
1 GGATATAACCACCAGCACAATTGTCTTCGGGTCTTAGCCC
* ** *
41062981 GGATAGAATAACTC-GCACGAA-TGCCTTCGGGTCTTAGCCC
1 GGATATAACCAC-CAGCAC-AATTGTCTTCGGGTCTTAGCCC
* * *
41063021 GGATATAGCCACTAGCACAATTGTCTTCGGGTCTTAACCC
1 GGATATAACCACCAGCACAATTGTCTTCGGGTCTTAGCCC
*** * *
41063061 GGATATAATTTCCAGCATAATTGTCTTCAGG-CTTAGCCC
1 GGATATAACCACCAGCACAATTGTCTTCGGGTCTTAGCCC
41063100 GGATAT
1 GGATAT
41063106 CATATCAATT
Statistics
Matches: 103, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
39 15 0.15
40 86 0.83
41 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (40 bp):
GGATATAACCACCAGCACAATTGTCTTCGGGTCTTAGCCC
Found at i:41070535 original size:40 final size:40
Alignment explanation
Indices: 41070490--41070656 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
41070480 CGGAATATAA
41070490 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41070530 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41070570 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41070610 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41070649 CCGGATAT
1 CCGGATAT
41070657 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41072419 original size:42 final size:44
Alignment explanation
Indices: 41072360--41072454 Score: 131
Period size: 42 Copynumber: 2.2 Consensus size: 44
41072350 TAGCCTCCCC
* ** *
41072360 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATA-T-TG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATACTATG
41072402 AAATGGGCTTGCATACATCCATTGACATTACATGTGATACTACTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATACTA-TG
41072447 AAATGGGC
1 AAATGGGC
41072455 CTATGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
42 35 0.76
43 1 0.02
45 10 0.22
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (44 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATACTATG
Found at i:41072513 original size:31 final size:31
Alignment explanation
Indices: 41072478--41072585 Score: 143
Period size: 31 Copynumber: 3.5 Consensus size: 31
41072468 CGTTTACAGT
41072478 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
* *
41072509 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
*
41072540 AAAGGCTTCGGCCCAGT--AATCG-TTAAATG-
1 AAAGGCTTCGGCCCAGTGAAAT-GATT-TATGA
41072569 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
41072586 ATATGTCAAG
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
29 21 0.30
30 4 0.06
31 45 0.64
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTTATGA
Found at i:41073543 original size:40 final size:40
Alignment explanation
Indices: 41073482--41073584 Score: 102
Period size: 40 Copynumber: 2.6 Consensus size: 40
41073472 ATTCATTTCT
** *
41073482 ATCCGTATAAACTGTAATTCATTCA-T-ATAACCAGTAGTTC
1 ATCCGTATAAACAATAATTCA-TCAGTAATAA-CAGTAATTC
*
41073522 ATCCGTATAAACAATAGTTCATCAGTAATAACAGTAATTC
1 ATCCGTATAAACAATAATTCATCAGTAATAACAGTAATTC
* * * *
41073562 AACCGTATTAATAGTAATTCATC
1 ATCCGTATAAACAATAATTCATC
41073585 CATTAATACT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.06
40 45 0.87
41 4 0.08
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (40 bp):
ATCCGTATAAACAATAATTCATCAGTAATAACAGTAATTC
Found at i:41073562 original size:20 final size:19
Alignment explanation
Indices: 41073495--41073584 Score: 65
Period size: 20 Copynumber: 4.5 Consensus size: 19
41073485 CGTATAAACT
41073495 GTAATTCATTCA-TATAACCA
1 GTAATTCA-TCAGTATAA-CA
* *
41073515 GTAGTTCATCCGTATAAACA
1 GTAATTCATCAGTAT-AACA
* *
41073535 ATAGTTCATCAGTAATAACA
1 GTAATTCATCAGT-ATAACA
* * *
41073555 GTAATTCAACCGTATTAATA
1 GTAATTCATCAGTA-TAACA
41073575 GTAATTCATC
1 GTAATTCATC
41073585 CATTAATACT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
19 3 0.05
20 49 0.88
21 4 0.07
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (19 bp):
GTAATTCATCAGTATAACA
Found at i:41073591 original size:18 final size:19
Alignment explanation
Indices: 41073554--41073592 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
41073544 CAGTAATAAC
41073554 AGTAATTCAACCGTATTAAT
1 AGTAATTCAACCG-ATTAAT
*
41073574 AGTAATTCATCC-ATTAAT
1 AGTAATTCAACCGATTAAT
41073592 A
1 A
41073593 CTATACCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (19 bp):
AGTAATTCAACCGATTAAT
Found at i:41074090 original size:36 final size:36
Alignment explanation
Indices: 41074043--41074116 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
41074033 AGGGCTCGAT
41074043 AACATATACATTATATCAATAAAGCATTCATACTTC
1 AACATATACATTATATCAATAAAGCATTCATACTTC
41074079 AACATATACATTATATCAATAAAGCATTCATACTTC
1 AACATATACATTATATCAATAAAGCATTCATACTTC
41074115 AA
1 AA
41074117 GTATTTCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (36 bp):
AACATATACATTATATCAATAAAGCATTCATACTTC
Found at i:41080133 original size:20 final size:20
Alignment explanation
Indices: 41080110--41080155 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
41080100 TAAACTGTAA
* * *
41080110 TTCATTCATATAACCAGTAG
1 TTCATCCATATAAACAATAG
*
41080130 TTCATCCGTATAAACAATAG
1 TTCATCCATATAAACAATAG
41080150 TTCATC
1 TTCATC
41080156 AATAATAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (20 bp):
TTCATCCATATAAACAATAG
Found at i:41080457 original size:23 final size:23
Alignment explanation
Indices: 41080414--41080493 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
41080404 TGAGCTGATG
*
41080414 AACAGTAAGCTCTATTAAGCTAA
1 AACAGTAAGCTCTATCAAGCTAA
* * *
41080437 AACAGTAAGCTTTATCGAGCT-G
1 AACAGTAAGCTCTATCAAGCTAA
* * *
41080459 ATCAGTAAGCTC-ATAAGAGCTGA
1 AACAGTAAGCTCTATCA-AGCTAA
*
41080482 AACGGTAAGCTC
1 AACAGTAAGCTC
41080494 CATTGAGTTG
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
21 2 0.05
22 14 0.32
23 28 0.64
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24
Consensus pattern (23 bp):
AACAGTAAGCTCTATCAAGCTAA
Found at i:41082643 original size:18 final size:18
Alignment explanation
Indices: 41082600--41082634 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41082590 AAATCAAAAT
41082600 ATTGTGAGAGTTAAAAGC
1 ATTGTGAGAGTTAAAAGC
* *
41082618 ATGGTGAGTGTTAAAAG
1 ATTGTGAGAGTTAAAAG
41082635 TTTTGTGAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.31, T:0.29
Consensus pattern (18 bp):
ATTGTGAGAGTTAAAAGC
Found at i:41088850 original size:5 final size:5
Alignment explanation
Indices: 41088835--41088876 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
41088825 AGTGGAAAAG
* *
41088835 TGAATT TGAAT TGAAT TGAAT TGAAT TGAAT GGAAT GGAAT T
1 TGAA-T TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT T
41088877 ATGATTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (5 bp):
TGAAT
Found at i:41089347 original size:45 final size:45
Alignment explanation
Indices: 41089283--41089420 Score: 204
Period size: 45 Copynumber: 3.1 Consensus size: 45
41089273 CTGTTACCGC
* *
41089283 TACTGCTAATGTTACCGATTTGGCACTTTGTGTGTCGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
41089328 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGC
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * * * *
41089373 TACTGTTACCGTTACTGATTCAGCACTTTGTGTGTTGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
41089418 TAC
1 TAC
41089421 CGTTACTATT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:41089433 original size:45 final size:45
Alignment explanation
Indices: 41089305--41089434 Score: 188
Period size: 45 Copynumber: 2.9 Consensus size: 45
41089295 TACCGATTTG
* * *
41089305 GCACTTTGTGTGTCGAATATTGTTACTGCTACTGTTACCGATTCG
1 GCACTTTGTGTGTCGAATATTGTTACTGTTACTGTTACTGATTCA
* *
41089350 GCACTTTGTGTGTCGAATATTGCTACTGTTACCGTTACTGATTCA
1 GCACTTTGTGTGTCGAATATTGTTACTGTTACTGTTACTGATTCA
* * *
41089395 GCACTTTGTGTGTTGAATATTGTTACCGTTACTATTACTG
1 GCACTTTGTGTGTCGAATATTGTTACTGTTACTGTTACTG
41089435 TTACTGCTAC
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (45 bp):
GCACTTTGTGTGTCGAATATTGTTACTGTTACTGTTACTGATTCA
Found at i:41089438 original size:18 final size:18
Alignment explanation
Indices: 41089415--41089452 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41089405 TGTTGAATAT
*
41089415 TGTTACCGTTACTATTAC
1 TGTTACCGCTACTATTAC
*
41089433 TGTTACTGCTACTATTAC
1 TGTTACCGCTACTATTAC
41089451 TG
1 TG
41089453 ATTATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (18 bp):
TGTTACCGCTACTATTAC
Found at i:41090980 original size:29 final size:30
Alignment explanation
Indices: 41090935--41091002 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
41090925 TGGCCCAAGA
* *
41090935 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATA-TCAAAATTTGAAGGACTAATAGT
*
41090965 GTAAATATGAAAATTTGAAGGACTAATAGT
1 GTAAATATCAAAATTTGAAGGACTAATAGT
*
41090995 GCAAATAT
1 GTAAATAT
41091003 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (30 bp):
GTAAATATCAAAATTTGAAGGACTAATAGT
Found at i:41092981 original size:46 final size:46
Alignment explanation
Indices: 41092928--41093103 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
41092918 TATTTGGGCA
41092928 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
41092974 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
41093021 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
41093067 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41093104 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:41093083 original size:93 final size:93
Alignment explanation
Indices: 41092924--41093095 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
41092914 GGGATATTTG
* *
41092924 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
41092989 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
41093017 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
41093082 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
41093096 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:41096073 original size:15 final size:15
Alignment explanation
Indices: 41096053--41096121 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
41096043 GTATCTTGGG
41096053 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
41096068 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
41096083 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
41096098 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
41096113 TTTCTTTAT
1 TTTCTTTAT
41096122 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:41096122 original size:30 final size:30
Alignment explanation
Indices: 41096044--41096131 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
41096034 CATAGTATCG
* * * *
41096044 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
41096074 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
41096104 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
41096132 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:41098563 original size:46 final size:46
Alignment explanation
Indices: 41098513--41098688 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
41098503 TATTTGGGCA
41098513 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
41098559 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
41098606 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
41098652 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41098689 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:41098668 original size:93 final size:93
Alignment explanation
Indices: 41098509--41098680 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
41098499 TGGATATTTG
* *
41098509 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
41098574 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
41098602 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
41098667 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
41098681 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:41102433 original size:70 final size:70
Alignment explanation
Indices: 41102317--41102458 Score: 178
Period size: 70 Copynumber: 2.0 Consensus size: 70
41102307 GTGAGCAACT
* * ***
41102317 TGTTGCATGATTCGATCTGTTGCGATCTAGCATTTATTATGGACACAAACG-AAGCTTTTCGTGA
1 TGTTACATGATTCGATCGGTTGCGATCTAGCATTTATTACAAACACAAACGCAA-CTTTTCGTGA
41102381 GCGTCC
65 GCGTCC
* * * *
41102387 TGTTACATGATTTGATCGGTTGCGGTCTAGCATTTATTCCAAACACAAACGCAACTTTTCGTGGG
1 TGTTACATGATTCGATCGGTTGCGATCTAGCATTTATTACAAACACAAACGCAACTTTTCGTGAG
*
41102452 TGTCC
66 CGTCC
41102457 TG
1 TG
41102459 ATATAAGCTC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
70 59 0.97
71 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (70 bp):
TGTTACATGATTCGATCGGTTGCGATCTAGCATTTATTACAAACACAAACGCAACTTTTCGTGAG
CGTCC
Found at i:41102502 original size:23 final size:23
Alignment explanation
Indices: 41102476--41102524 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
41102466 CTCTTATGAG
*
41102476 CTTCTTGACATGGCTCGCTTGAA
1 CTTCCTGACATGGCTCGCTTGAA
*
41102499 CTTCCTGACATGGCTTGCTTGAA
1 CTTCCTGACATGGCTCGCTTGAA
41102522 CTT
1 CTT
41102525 TCTGTTATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (23 bp):
CTTCCTGACATGGCTCGCTTGAA
Found at i:41105168 original size:269 final size:269
Alignment explanation
Indices: 41104689--41105218 Score: 1006
Period size: 269 Copynumber: 2.0 Consensus size: 269
41104679 TTCTATGTTG
* *
41104689 CCTTATTTTCAAATTCTGAAACTTCTATGTGATGTATTCGGGGATACCTATGTGGTAGAATCTGG
1 CCTTATTTTCAAATTCTAAAACTTCTATGTGATGTATTCGGGGATACCTACGTGGTAGAATCTGG
41104754 TTATCCACCATTATGGTAGGATCTGGGTAAGTTATGAGATTTCTTCGATAGATAATTCTGTAATA
66 TTATCCACCATTATGGTAGGATCTGGGTAAGTTATGAGATTTCTTCGATAGATAATTCTGTAATA
41104819 ACGATCTGATACGTCTGAAGTTAACTTGGTTTGGTTAGTCTTGTGATGAAATCGAGTAAGTCTTA
131 ACGATCTGATACGTCTGAAGTTAACTTGGTTTGGTTAGTCTTGTGATGAAATCGAGTAAGTCTTA
41104884 AGGGATGTTTCCTGAAAGTAAGTATGTATCTATATTTCTAAAGAGCCATAGTAGTTTGCCAATAT
196 AGGGATGTTTCCTGAAAGTAAGTATGTATCTATATTTCTAAAGAGCCATAGTAGTTTGCCAATAT
41104949 ACTATATTA
261 ACTATATTA
*
41104958 CCTTATTTTCAAATTCTAAAACTTCTATGTGATGTATTCGGGGATACCTACGTGGTAGAATTTGG
1 CCTTATTTTCAAATTCTAAAACTTCTATGTGATGTATTCGGGGATACCTACGTGGTAGAATCTGG
*
41105023 TTATCCACCATTGTGGTAGGATCTGGGTAAGTTATGAGATTTCTTCGATAGATAATTCTGTAATA
66 TTATCCACCATTATGGTAGGATCTGGGTAAGTTATGAGATTTCTTCGATAGATAATTCTGTAATA
*
41105088 AGGATCTGATACGTCTGAAGTTAACTTGGTTTGGTTAGTCTTGTGATGAAATCGAGTAAGTCTTA
131 ACGATCTGATACGTCTGAAGTTAACTTGGTTTGGTTAGTCTTGTGATGAAATCGAGTAAGTCTTA
*
41105153 AGGGATGTTTCCTGAAAGTATGTATGTATCTATATTTCTAAAGAGCCATAGTAGTTTGCCAATAT
196 AGGGATGTTTCCTGAAAGTAAGTATGTATCTATATTTCTAAAGAGCCATAGTAGTTTGCCAATAT
41105218 A
261 A
41105219 AGAAATAGGT
Statistics
Matches: 255, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
269 255 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (269 bp):
CCTTATTTTCAAATTCTAAAACTTCTATGTGATGTATTCGGGGATACCTACGTGGTAGAATCTGG
TTATCCACCATTATGGTAGGATCTGGGTAAGTTATGAGATTTCTTCGATAGATAATTCTGTAATA
ACGATCTGATACGTCTGAAGTTAACTTGGTTTGGTTAGTCTTGTGATGAAATCGAGTAAGTCTTA
AGGGATGTTTCCTGAAAGTAAGTATGTATCTATATTTCTAAAGAGCCATAGTAGTTTGCCAATAT
ACTATATTA
Found at i:41107078 original size:40 final size:40
Alignment explanation
Indices: 41107031--41107164 Score: 133
Period size: 40 Copynumber: 3.4 Consensus size: 40
41107021 CAATGTCTCA
* * *
41107031 CACACTAAGTGCCGTACATAGCCGAAGCTATCTCAAATCT
1 CACACTAAGTGCCATATATAGCCGAAGCTATCTCAAATCG
* * ** * *
41107071 CACACTAAGTTCCATTTATAGTAGAAGCTATGTCGAATCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATCTCAAATCG
* * * ***
41107111 CACACTAAGTGTCATATATAGCCAAAGCTATGTTGTATCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATCTCAAATCG
41107151 CACACTAAGTGCCA
1 CACACTAAGTGCCA
41107165 CAAATAATTG
Statistics
Matches: 76, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (40 bp):
CACACTAAGTGCCATATATAGCCGAAGCTATCTCAAATCG
Found at i:41114545 original size:40 final size:40
Alignment explanation
Indices: 41114486--41114578 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 40
41114476 TCTCAAATTA
* *
41114486 CACACTAAGT-CCATATATAGCCGAAGCTATGTCGAATCT
1 CACACTAAGTGCCATATATAGCCAAAGCTATGTCGAATCG
* * * *
41114525 CACATTAAGTGCCATATATAGTCAAAGCTATGTTGTATCG
1 CACACTAAGTGCCATATATAGCCAAAGCTATGTCGAATCG
41114565 CACACTAAGTGCCA
1 CACACTAAGTGCCA
41114579 CAAATAATCG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 9 0.20
40 37 0.80
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (40 bp):
CACACTAAGTGCCATATATAGCCAAAGCTATGTCGAATCG
Found at i:41117171 original size:30 final size:30
Alignment explanation
Indices: 41117135--41117194 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41117125 GGCTTTTGCC
*
41117135 GAAACTCGTTTTCTACGCGATCAGAGTATA
1 GAAACTCGTTTTCTACACGATCAGAGTATA
* *
41117165 GAAACTCTTTTTCTACATGATCAGAGTATA
1 GAAACTCGTTTTCTACACGATCAGAGTATA
41117195 CACCTAGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (30 bp):
GAAACTCGTTTTCTACACGATCAGAGTATA
Found at i:41124706 original size:21 final size:22
Alignment explanation
Indices: 41124669--41124710 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
41124659 GCTTATAGAA
*
41124669 AAAGAAGAAAAACGAAGGGAAG
1 AAAGAAGAAAAAAGAAGGGAAG
41124691 AAAGAA-AAAAAAGAAGGGAA
1 AAAGAAGAAAAAAGAAGGGAA
41124711 TTTCGGCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (22 bp):
AAAGAAGAAAAAAGAAGGGAAG
Found at i:41126272 original size:5 final size:5
Alignment explanation
Indices: 41126262--41126332 Score: 135
Period size: 5 Copynumber: 14.4 Consensus size: 5
41126252 TTATGTTTTA
41126262 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
41126312 ATTAT A-TAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT AT
41126333 ATAAACATAA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.06
5 61 0.94
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:41127365 original size:17 final size:19
Alignment explanation
Indices: 41127323--41127366 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41127313 ATGAAATTTT
*
41127323 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
41127342 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
41127360 AA-TATTA
1 AATTATTA
41127367 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:41131603 original size:17 final size:19
Alignment explanation
Indices: 41131561--41131604 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41131551 ATGAAATTTT
*
41131561 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
41131580 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
41131598 AA-TATTA
1 AATTATTA
41131605 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:41135623 original size:13 final size:14
Alignment explanation
Indices: 41135592--41135627 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
41135582 GCTATTGGAA
41135592 TGAAA-TGAGAAAT
1 TGAAATTGAGAAAT
41135605 TG-AATTGA-AAAT
1 TGAAATTGAGAAAT
41135617 TGAAATTGAGA
1 TGAAATTGAGA
41135628 TATGAGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 8 0.40
13 11 0.55
14 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (14 bp):
TGAAATTGAGAAAT
Found at i:41135626 original size:26 final size:25
Alignment explanation
Indices: 41135592--41135641 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
41135582 GCTATTGGAA
41135592 TGAAATGAGAAATTGA-ATTGAAAAT
1 TGAAATGAGAAA-TGAGATTGAAAAT
*
41135617 TGAAATTGAGATATGAGATTGAAAA
1 TGAAA-TGAGAAATGAGATTGAAAA
41135642 CATGAACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (25 bp):
TGAAATGAGAAATGAGATTGAAAAT
Found at i:41146706 original size:41 final size:41
Alignment explanation
Indices: 41146661--41146778 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
41146651 TGAAAGATAA
41146661 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
41146702 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41146732 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41146773 ATGTAG
1 ATGTAG
41146779 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:41146717 original size:71 final size:71
Alignment explanation
Indices: 41146629--41146792 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41146619 GAGATGTATC
41146629 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41146694 AGGACA
66 AGGACA
41146700 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41146765 AGGACA
66 AGGACA
41146771 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
41146793 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:41153773 original size:41 final size:41
Alignment explanation
Indices: 41153728--41153845 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
41153718 TGAAAGATAA
41153728 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
41153769 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41153799 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
41153840 ATGTAG
1 ATGTAG
41153846 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:41153784 original size:71 final size:71
Alignment explanation
Indices: 41153696--41153859 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41153686 GAGATGTATC
41153696 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41153761 AGGACA
66 AGGACA
41153767 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41153832 AGGACA
66 AGGACA
41153838 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
41153860 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:41156386 original size:5 final size:5
Alignment explanation
Indices: 41156376--41156417 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
41156366 TTATGTTTTA
41156376 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
41156418 ATAAACATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:41158092 original size:39 final size:39
Alignment explanation
Indices: 41157982--41158116 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
41157972 GACCTCGAGT
* * * *
41157982 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
41158023 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
41158061 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
41158100 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
41158117 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:41158275 original size:25 final size:24
Alignment explanation
Indices: 41158231--41158278 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
41158221 GCTATTGGAA
41158231 TGAAATGAGAAATTGAATTGAAAT
1 TGAAATGAGAAATTGAATTGAAAT
*
41158255 TGAAATTGAGATA-TGAGATTGAAA
1 TGAAA-TGAGAAATTGA-ATTGAAA
41158279 ACATGAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (24 bp):
TGAAATGAGAAATTGAATTGAAAT
Found at i:41158277 original size:19 final size:17
Alignment explanation
Indices: 41158239--41158278 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
41158229 AATGAAATGA
41158239 GAAATTGAATTGAAATT
1 GAAATTGAATTGAAATT
*
41158256 GAAATTGAGATATGAGATT
1 GAAATTGA-AT-TGAAATT
41158275 GAAA
1 GAAA
41158279 ACATGAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 2 0.10
19 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (17 bp):
GAAATTGAATTGAAATT
Found at i:41172629 original size:40 final size:39
Alignment explanation
Indices: 41172584--41172713 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
41172574 CGGAATATAA
41172584 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
41172624 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
41172664 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
41172704 CCGGATATAA
1 CCGGATATAA
41172714 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:41172728 original size:40 final size:40
Alignment explanation
Indices: 41172600--41172751 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
41172590 ATAACCATGT
* * *
41172600 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
41172640 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
41172680 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
41172720 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
41172752 CATTCAGTTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:41172734 original size:80 final size:80
Alignment explanation
Indices: 41172600--41172749 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
41172590 ATAACCATGT
*
41172600 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
41172664 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
41172680 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
41172743 CCCGGAT
64 CCCGGAT
41172750 ATCATTCAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:41179627 original size:19 final size:19
Alignment explanation
Indices: 41179603--41179639 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41179593 TATCCAACCC
41179603 ATTGAAGAATAATACACAG
1 ATTGAAGAATAATACACAG
*
41179622 ATTGAAGCATAATACACA
1 ATTGAAGAATAATACACA
41179640 CTTTCAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.22
Consensus pattern (19 bp):
ATTGAAGAATAATACACAG
Found at i:41181817 original size:40 final size:40
Alignment explanation
Indices: 41181761--41181928 Score: 170
Period size: 40 Copynumber: 4.2 Consensus size: 40
41181751 CAATTGAATG
*
41181761 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTG-CTT
41181802 -TATCCGGGCTAAGACCCGAAGGC-ATTCGTG-TAAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCT-AG-TGCTT
* * *
41181841 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGT-CGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGC-TT
* *
41181881 ATATCCGGGTTAAGACCCGAAGGC-ATTCGTGCGT-GTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGC-TAGTGCTT
41181921 ATATCCGG
1 ATATCCGG
41181929 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 9, Indels: 23
0.77 0.06 0.17
Matches are distributed among these distances:
39 9 0.08
40 94 0.88
41 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGCTT
Found at i:41181895 original size:80 final size:79
Alignment explanation
Indices: 41181761--41181911 Score: 223
Period size: 80 Copynumber: 1.9 Consensus size: 79
41181751 CAATTGAATG
* *
41181761 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGA-TTTATCCGGGCTAAGACCCGAAGGCA
41181826 TTCGTGTAAGTTGTT
65 TTCGTGTAAGTTGTT
* * *
41181841 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GATT-TATCCGGGCTAAGACCCGAAGGC
41181905 ATTCGTG
64 ATTCGTG
41181912 CGTGTGGTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
79 2 0.03
80 61 0.95
81 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTTATCCGGGCTAAGACCCGAAGGCAT
TCGTGTAAGTTGTT
Found at i:41181922 original size:80 final size:79
Alignment explanation
Indices: 41181761--41181928 Score: 221
Period size: 80 Copynumber: 2.1 Consensus size: 79
41181751 CAATTGAATG
* *
41181761 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGA-TTTATCCGGGCTAAGACCCGAAGGCA
* *
41181826 TTCGTGTAAGTTGTT
65 TTCGTGCAAGTGGTT
* * *
41181841 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCG-TTATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT-GATT-TATCCGGGCTAAGACCCGAAGGC
**
41181905 ATTCGTGCGTGTGGTT
64 ATTCGTGCAAGTGGTT
41181921 ATATCCGG
1 ATATCCGG
41181929 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
79 2 0.03
80 74 0.96
81 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATTTATCCGGGCTAAGACCCGAAGGCAT
TCGTGCAAGTGGTT
Found at i:41188995 original size:38 final size:37
Alignment explanation
Indices: 41188911--41188996 Score: 88
Period size: 39 Copynumber: 2.3 Consensus size: 37
41188901 AATAATAAAT
* *
41188911 TAAATAA-AAATAAATAGAATACTAATATAGAATGAA
1 TAAATAAGAAATAAATACAATACAAATATAGAATGAA
*
41188947 TTAATAAAGAAATAAAATACAATA-AAATAATA-AATGAAA
1 TAAAT-AAGAAAT-AAATACAATACAAAT-ATAGAATG-AA
41188986 TAAATAAGAAA
1 TAAATAAGAAA
41188997 ATAGGGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
36 4 0.10
37 2 0.05
38 17 0.41
39 18 0.44
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (37 bp):
TAAATAAGAAATAAATACAATACAAATATAGAATGAA
Found at i:41191668 original size:38 final size:38
Alignment explanation
Indices: 41191585--41191774 Score: 218
Period size: 38 Copynumber: 4.9 Consensus size: 38
41191575 GAATCCAGTC
* * *
41191585 ACCAGCACAAAACCTGCGGGACTTTAAGCTCGAATATAAT
1 ACCAGCACAAAGCCTGCGGGA-TTTAA-CCCGGATATAAT
* *
41191625 ACCAGCACTAAGCCTACGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
* * *
41191663 ACCAGCACGAAGCCTGCCGGATTTAACCCGGATATATT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
* * *
41191701 ACTAGTACAAAGGCTGCGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
* **
41191739 ACCAGCACATAGCCTGCGAGTCTTTAAGCCCGGATA
1 ACCAGCACAAAGCCTGCG-GGATTTAA-CCCGGATA
41191775 CACATCAAAT
Statistics
Matches: 127, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
38 90 0.71
39 11 0.09
40 26 0.20
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (38 bp):
ACCAGCACAAAGCCTGCGGGATTTAACCCGGATATAAT
Found at i:41192795 original size:64 final size:64
Alignment explanation
Indices: 41192694--41192816 Score: 246
Period size: 64 Copynumber: 1.9 Consensus size: 64
41192684 ATGCATAAAA
41192694 TCCATTTATGATTAATATATAATCCATTCAGCCCTAACTACTCAACTTAACTTTCATATTCAAT
1 TCCATTTATGATTAATATATAATCCATTCAGCCCTAACTACTCAACTTAACTTTCATATTCAAT
41192758 TCCATTTATGATTAATATATAATCCATTCAGCCCTAACTACTCAACTTAACTTTCATAT
1 TCCATTTATGATTAATATATAATCCATTCAGCCCTAACTACTCAACTTAACTTTCATAT
41192817 CAACTTAACT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (64 bp):
TCCATTTATGATTAATATATAATCCATTCAGCCCTAACTACTCAACTTAACTTTCATATTCAAT
Found at i:41192821 original size:17 final size:17
Alignment explanation
Indices: 41192799--41192833 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
41192789 CCCTAACTAC
41192799 TCAACTTAACTTTCATA
1 TCAACTTAACTTTCATA
41192816 TCAACTTAACTTTCATA
1 TCAACTTAACTTTCATA
41192833 T
1 T
41192834 TCAATTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (17 bp):
TCAACTTAACTTTCATA
Found at i:41192832 original size:81 final size:81
Alignment explanation
Indices: 41192735--41192897 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
41192725 CCCTAACTAC
41192735 TCAACTTAACTTTCATATTCAATTCCATTTATGATTAATATATAATCCATTCAGCCCTAACTACT
1 TCAACTTAACTTTCATATTCAATTCCATTTATGATTAATATATAATCCATTCAGCCCTAACTACT
41192800 CAACTTAACTTTCATA
66 CAACTTAACTTTCATA
41192816 TCAACTTAACTTTCATATTCAATTCCATTTATGATTAATATATAATCCATTCAGCCCTAACTACT
1 TCAACTTAACTTTCATATTCAATTCCATTTATGATTAATATATAATCCATTCAGCCCTAACTACT
41192881 CAACTTAACTTTCATA
66 CAACTTAACTTTCATA
41192897 T
1 T
41192898 TCAATTCCAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.40
Consensus pattern (81 bp):
TCAACTTAACTTTCATATTCAATTCCATTTATGATTAATATATAATCCATTCAGCCCTAACTACT
CAACTTAACTTTCATA
Found at i:41197391 original size:49 final size:49
Alignment explanation
Indices: 41197323--41197416 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
41197313 ATCAAATGGT
41197323 AAAGCATCAAATCGGCTGGAAAACAGGAACCTCAGATTATCAGGGGGTA
1 AAAGCATCAAATCGGCTGGAAAACAGGAACCTCAGATTATCAGGGGGTA
* *
41197372 AAAGTATCAAATCGGCTGGAAAACAGGAACCTCGGATTATCAGGG
1 AAAGCATCAAATCGGCTGGAAAACAGGAACCTCAGATTATCAGGG
41197417 AGCATTTCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (49 bp):
AAAGCATCAAATCGGCTGGAAAACAGGAACCTCAGATTATCAGGGGGTA
Found at i:41199986 original size:38 final size:38
Alignment explanation
Indices: 41199895--41200046 Score: 178
Period size: 38 Copynumber: 3.9 Consensus size: 38
41199885 GAATCCAGTC
* * * *
41199895 ACCAGCACAAAACCTGCGGGACTTTAAGCTCGAATATAAT
1 ACCAGCACAAAGCTTGCGGGA-TTTAA-CCCGGATATAAT
* *
41199935 ACCAGCACTAAGCTTGCGGGATTTAACCCGGAGATAAT
1 ACCAGCACAAAGCTTGCGGGATTTAACCCGGATATAAT
41199973 ACCAGCACAAAGCTTGCGGGATTTAACCCGGATATAAT
1 ACCAGCACAAAGCTTGCGGGATTTAACCCGGATATAAT
* * * *
41200011 ACCAGCACATATCCTGCGGGTCTTTAAGCCCGGATA
1 ACCAGCACAAAGCTTGCGGG-ATTTAA-CCCGGATA
41200047 CACATCAAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
38 62 0.63
39 10 0.10
40 26 0.27
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (38 bp):
ACCAGCACAAAGCTTGCGGGATTTAACCCGGATATAAT
Found at i:41202822 original size:36 final size:35
Alignment explanation
Indices: 41202782--41202853 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 35
41202772 TTAAATAGGT
41202782 AAATTGGTTATTAAAGGTTAATTAAATAAAATGAAA
1 AAATTGGTTATTAAAGGTTAATTAAATAAAAT-AAA
41202818 AAATTGGTTATTAAAGGTTAATTAAATAAAATAAA
1 AAATTGGTTATTAAAGGTTAATTAAATAAAATAAA
41202853 A
1 A
41202854 CATTTTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 4 0.11
36 32 0.89
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (35 bp):
AAATTGGTTATTAAAGGTTAATTAAATAAAATAAA
Found at i:41209512 original size:47 final size:47
Alignment explanation
Indices: 41209405--41209806 Score: 247
Period size: 47 Copynumber: 8.6 Consensus size: 47
41209395 GATATGTGTC
* * * *
41209405 CTAGTGTAAGACATGTTTGGGACATGCATC-GACCAC-A-TTATGAGAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCAG-CCTCGAGATAT-AAAG
* *
41209451 CCAGTGTAAGACATGTCTGGGATATGCATCAGCCTCGAGATATAAAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATAAAG
* * * * *
41209498 CTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAT-GAGAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATAAAG
* *
41209544 CTAGTGTAAGACATGTCTAGGACATGCATCAGCCTGGAGATATAAAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATAAAG
* * * * * * **
41209591 CTAGTGTAAGACCTGTCTAGGACATGGCGTCAG-CTTGTTG-TGT--TT
1 CTAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCG-AGATATAAAG
* ** * *
41209636 C-AGTGTAAGACCTGTCTGGGACATGGCATC-GACAACAGTAGAT-GAGAG
1 CTAGTGTAAGACATGTCTGGGACAT-GCATCAG-CCTC-G-AGATATAAAG
* * * *
41209684 CCAGTGTAAGACCTGTTTGGGACATGGCATCAGCCTCGATATATGAAAG
1 CTAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGAGATAT-AAAG
* * ** * **
41209733 -TCAGTGTAAGACCTGTCTGGGACATGGCATC-GACT-TTGATGTGCTAG
1 CT-AGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGAGATAT-AAAG
41209780 CTAGTGTAAGACTATGTCTGGGACATG
1 CTAGTGTAAGAC-ATGTCTGGGACATG
41209807 GTGTCGGCAT
Statistics
Matches: 286, Mismatches: 51, Indels: 37
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.00
44 27 0.09
45 1 0.00
46 73 0.26
47 94 0.33
48 28 0.10
49 61 0.21
50 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (47 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATAAAG
Found at i:41209571 original size:93 final size:91
Alignment explanation
Indices: 41209405--41209616 Score: 300
Period size: 93 Copynumber: 2.3 Consensus size: 91
41209395 GATATGTGTC
* *
41209405 CTAGTGTAAGACATGTTTGGGACATGCATCGACCACATTATGAGAGCCAGTGTAAGACATGTCTG
1 CTAGTGTAAGACATGTCTGGGACATGCATCG--CACATTATGAGAGCCAGTGTAAGACATGTCTA
*
41209470 GGATATGCATCAGCCTCGAGATATAAAG
64 GGACATGCATCAGCCTCGAGATATAAAG
* *
41209498 CTAGTGTAAGACATGTCTGGGACATGCATCG-GCATTGAGATGAGAGCTAGTGTAAGACATGTCT
1 CTAGTGTAAGACATGTCTGGGACATGCATCGCACATT---ATGAGAGCCAGTGTAAGACATGTCT
*
41209562 AGGACATGCATCAGCCTGGAGATATAAAG
63 AGGACATGCATCAGCCTCGAGATATAAAG
* *
41209591 CTAGTGTAAGACCTGTCTAGGACATG
1 CTAGTGTAAGACATGTCTGGGACATG
41209617 GCGTCAGCTT
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
90 4 0.04
93 104 0.96
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (91 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGCACATTATGAGAGCCAGTGTAAGACATGTCTAGG
ACATGCATCAGCCTCGAGATATAAAG
Found at i:41209696 original size:49 final size:47
Alignment explanation
Indices: 41209407--41209766 Score: 204
Period size: 49 Copynumber: 7.7 Consensus size: 47
41209397 TATGTGTCCT
* * *
41209407 AGTGTAAGACATGTTTGGGACATGCATCGACCACAT-TATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCACGTAGATGAGAGCC
* * * * *
41209453 AGTGTAAGACATGTCTGGGATATGCATC-AGCCTCG-AGATATAAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGA-CCACGTAGAT-GAGAGCC
* * *
41209500 AGTGTAAGACATGTCTGGGACATGCATCG-GCA-TTGAGATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGACCACGT-AGATGAGAGCC
* * * * * *
41209546 AGTGTAAGACATGTCTAGGACATGCATC-AGCC-TGGAGATATAAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGA-CCACGTAGAT-GAGAGCC
* * * * * * * ***
41209593 AGTGTAAGACCTGTCTAGGACATG--GCG-TCA-GCTTGTTGTGTTTC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCACG-TAGATGAGAGCC
* *
41209637 AGTGTAAGACCTGTCTGGGACATGGCATCGACAACAGTAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGACCAC-GTAGATGAGAGCC
* * * * * *
41209686 AGTGTAAGACCTGTTTGGGACATGGCATC-AGCCTCGATATATGAAAGTC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGA-CCACG-TAGATGAGAGCC
*
41209735 AGTGTAAGACCTGTCTGGGACATGGCATCGAC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGAC
41209767 TTTGATGTGC
Statistics
Matches: 242, Mismatches: 50, Indels: 41
0.73 0.15 0.12
Matches are distributed among these distances:
44 24 0.10
45 5 0.02
46 68 0.28
47 66 0.27
48 3 0.01
49 74 0.31
50 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACCACGTAGATGAGAGCC
Found at i:41224297 original size:46 final size:46
Alignment explanation
Indices: 41224244--41224413 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 46
41224234 TATGTGTGCT
41224244 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCC
* * *
41224290 AGTGTAAGACATGTCTAGGACATGCATCGGCC-TCGAGATAT-ACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAT--A-TTATGA-GAGCC
* * * *
41224338 AGTGTAAGACATGTTTGGGACATGCATCAG--A-ATTGAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATT---ATGAGAGCC
41224384 AGTGTAAGACATGTCTGGGACATGCATCGG
1 AGTGTAAGACATGTCTGGGACATGCATCGG
41224414 TCTGGAGATA
Statistics
Matches: 103, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
43 1 0.01
44 1 0.01
45 1 0.01
46 63 0.61
47 3 0.03
48 34 0.33
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCC
Found at i:41224351 original size:48 final size:46
Alignment explanation
Indices: 41224244--41224642 Score: 222
Period size: 47 Copynumber: 8.5 Consensus size: 46
41224234 TATGTGTGCT
* *
41224244 AGTGTAAGACATGTCTGGGACATGCATCGGCCAT-A-TTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC-TGAGATAT-AAAGCC
*
41224290 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-GAGATATA-AAGCC
* *** ** * *
41224338 AGTGTAAGACATGTTTGGGACATGCATCAGAATTGAGA-CGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCCTGAGATATAAAGCC
* * *
41224384 AGTGTAAGACATGTCTGGGACATGCATCGGTCTGGAGATACAAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-GAGATATAAAGCC
* ** * * * *
41224431 AGTGTAAGACCTGTCTGGGACATGGCATCAACTTGTTG-TGT---GTC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTG-AGATATAAAGCC
* * * * * *
41224475 AGTGTAAGACCTGTCTGGGACATGGAATCGACACCGAGAT-GAGAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGC-CTGAGATATAAAGCC
* * * * * * *
41224522 AATGTAAGACCTGTCTGGGACACGGTATCAGCCTCGATATATGAAAGTC
1 AGTGTAAGACATGTCTGGGACA-TGCATCGGCCT-GAGATAT-AAAGCC
* * ** **
41224571 AGTGTAAGACCTGTCTGGGACATGGCATC-GACTTTGATATGCTAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTGAGATAT-AAAGCC
*
41224618 AGTGTAAGACCATGTCTAGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
41224643 GCGTCGGCAT
Statistics
Matches: 275, Mismatches: 58, Indels: 39
0.74 0.16 0.10
Matches are distributed among these distances:
44 32 0.12
45 5 0.02
46 66 0.24
47 82 0.30
48 59 0.21
49 31 0.11
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTGAGATATAAAGCC
Found at i:41224393 original size:94 final size:92
Alignment explanation
Indices: 41224244--41224460 Score: 276
Period size: 94 Copynumber: 2.3 Consensus size: 92
41224234 TATGTGTGCT
* *
41224244 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCCAGTGTAAGACATGTCTAGG
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CATATTACGAGAGCCAGTGTAAGACATGTCTAGG
*
41224309 ACATGCATCGGCCTCGAGATATACAAGCC
65 ACATGCATCGGCCTCGAGATACA-AAGCC
* * *
41224338 AGTGTAAGACATGTTTGGGACATGCATCAG-A-ATTGAGACGAGAGCTAGTGTAAGACATGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCATATT---ACGAGAGCCAGTGTAAGACATGTCTA
* * *
41224401 GGACATGCATCGGTCTGGAGATACAAAGCT
63 GGACATGCATCGGCCTCGAGATACAAAGCC
*
41224431 AGTGTAAGACCTGTCTGGGACATGGCATCA
1 AGTGTAAGACATGTCTGGGACAT-GCATCA
41224461 ACTTGTTGTG
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
91 3 0.03
92 1 0.01
93 25 0.23
94 79 0.73
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCATATTACGAGAGCCAGTGTAAGACATGTCTAGGA
CATGCATCGGCCTCGAGATACAAAGCC
Found at i:41226459 original size:13 final size:13
Alignment explanation
Indices: 41226441--41226465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41226431 ACACACGGGT
41226441 GTGTGGCTCGATC
1 GTGTGGCTCGATC
41226454 GTGTGGCTCGAT
1 GTGTGGCTCGAT
41226466 TTGTATGTAG
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:0.08, C:0.20, G:0.40, T:0.32
Consensus pattern (13 bp):
GTGTGGCTCGATC
Found at i:41234540 original size:25 final size:26
Alignment explanation
Indices: 41234492--41234543 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
41234482 GGATTTTGGC
*
41234492 ATATTTGCTATCTGAATCTAAAACTG
1 ATATTTGCAATCTGAATCTAAAACTG
* *
41234518 ATATTTG-AATCTGAGTCTGAAACTG
1 ATATTTGCAATCTGAATCTAAAACTG
41234543 A
1 A
41234544 GTCTATATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (26 bp):
ATATTTGCAATCTGAATCTAAAACTG
Found at i:41238523 original size:13 final size:13
Alignment explanation
Indices: 41238505--41238539 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
41238495 AAAAGGACTT
*
41238505 AATTAAGCTTACC
1 AATTAAACTTACC
41238518 AATTAAACTTACC
1 AATTAAACTTACC
41238531 AATTAAACT
1 AATTAAACT
41238540 CCAAACTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (13 bp):
AATTAAACTTACC
Found at i:41239215 original size:3 final size:3
Alignment explanation
Indices: 41239207--41239300 Score: 131
Period size: 3 Copynumber: 31.7 Consensus size: 3
41239197 TTTATTTCAA
41239207 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
41239255 AAT AAT AAT AAT AAT -AT AATT CAAT -TT AAT AAC AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AA-T -AAT AAT AAT AAT AAT AAT AAT AAT
41239299 AA
1 AA
41239301 GATATGCTAA
Statistics
Matches: 82, Mismatches: 4, Indels: 10
0.85 0.04 0.10
Matches are distributed among these distances:
2 5 0.06
3 73 0.89
4 2 0.02
5 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:41245871 original size:13 final size:12
Alignment explanation
Indices: 41245838--41245871 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41245828 AAAATTAAAA
*
41245838 TAATTATACCAT
1 TAATTATAACAT
41245850 TAATTATAACAT
1 TAATTATAACAT
41245862 TAATTTATAA
1 TAA-TTATAA
41245872 TAATAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATTATAACAT
Found at i:41246456 original size:24 final size:25
Alignment explanation
Indices: 41246424--41246488 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 25
41246414 TGTTTTATTT
*
41246424 ATTTTATTAACTTAATATAT-TATA
1 ATTTAATTAACTTAATATATCTATA
*
41246448 ATTTAATT-ACTATAA-ATATCTATC
1 ATTTAATTAACT-TAATATATCTATA
*
41246472 ATATAATTAA--TAATATA
1 ATTTAATTAACTTAATATA
41246489 ATAGAAATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
22 3 0.09
23 10 0.29
24 20 0.59
25 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTTAATTAACTTAATATATCTATA
Found at i:41252168 original size:6 final size:6
Alignment explanation
Indices: 41252157--41252200 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
41252147 CATATTTGCC
41252157 ATCTGA ATCTGAA AT-TGA TATCTGA ATCTGA ATCTGA ATCTGA A
1 ATCTGA ATCTG-A ATCTGA -ATCTGA ATCTGA ATCTGA ATCTGA A
41252201 AATGAGTCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 1 0.03
6 28 0.80
7 6 0.17
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (6 bp):
ATCTGA
Found at i:41260286 original size:4 final size:4
Alignment explanation
Indices: 41260277--41260305 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
41260267 AAAATATTTG
41260277 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
41260306 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:41263046 original size:6 final size:6
Alignment explanation
Indices: 41263037--41263061 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41263027 CCTTAATCAT
41263037 AATTAC AATTAC AATTAC AATTAC A
1 AATTAC AATTAC AATTAC AATTAC A
41263062 TAACCATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAC
Found at i:41271299 original size:43 final size:43
Alignment explanation
Indices: 41271252--41271365 Score: 174
Period size: 43 Copynumber: 2.7 Consensus size: 43
41271242 TGTGACTACA
* *
41271252 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGATTAGG
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTATGATTACG
* *
41271295 TGTAAGACCATGTCTGGGACATTAGCATTGTATTATGATTTCG
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTATGATTACG
* *
41271338 TGTAAGACCCTGTCTGGGACAATGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
41271366 CAATATGTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATTGTATTATGATTACG
Found at i:41273512 original size:46 final size:45
Alignment explanation
Indices: 41273457--41273631 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
41273447 TGGTTGAGCA
*
41273457 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGACGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * * *
41273503 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G
*
41273548 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * * *
41273596 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACCTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGG
41273632 GGCGGGTTAC
Statistics
Matches: 106, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 5 0.05
46 58 0.55
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATG
Found at i:41273613 original size:93 final size:93
Alignment explanation
Indices: 41273454--41273624 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
41273444 GGATGGTTGA
* ** *
41273454 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGACGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGACGCGAACGCCCGAACTCATTGAGT
41273519 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
41273547 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGACGCGAACGCCCGAACTCATTGAGT
41273612 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41273625 ACCTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGACGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41278752 original size:46 final size:46
Alignment explanation
Indices: 41278685--41278862 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
41278675 TGTAACCCGC
* *
41278685 CCATAAGCGAACTCGGACTCAACTCAACGAGATCGGGTGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCAT
* * * *
41278731 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATG-TTCGCAT
* * **
41278777 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCAT
* *
41278824 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGATG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATG
41278863 CTCAACCATC
Statistics
Matches: 107, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
45 2 0.02
46 69 0.64
47 34 0.32
48 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCAT
Found at i:41278804 original size:93 final size:93
Alignment explanation
Indices: 41278692--41278863 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
41278682 CGCCCATAAG
***
41278692 CGAACTCGGACTCAACTCAACGAGATCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
41278757 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACAAGTTCGGATGCCTAGTTACATTTCA
*
41278785 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41278850 ACAAGTTCGGATGC
66 ACAAGTTCGGATGC
41278864 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGTTCGGATGCCTAGTTACATTTCA
Found at i:41287878 original size:39 final size:39
Alignment explanation
Indices: 41287833--41288031 Score: 326
Period size: 39 Copynumber: 5.1 Consensus size: 39
41287823 AAGCAAGACA
41287833 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
**
41287872 CTGGAAATGTATCCTAGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
*
41287911 CTGGAAATGTATCCGGGCTAAAGACTCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* *
41287950 CTGGAAAGGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* * *
41287989 CTGGAAATGTATCCGAGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
41288028 CTGG
1 CTGG
41288032 TAATATAATT
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 149 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
Found at i:41298576 original size:34 final size:34
Alignment explanation
Indices: 41298502--41298576 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
41298492 CAGTATTATT
*
41298502 TGGTGTGCTGGATGGTTTAGCTCATACGAGCAAT
1 TGGTGTGCTGGATGGTTTAGCTCATACGAGCAAC
* * *
41298536 TCGTGTGCTGGATGGTTTAGCTTATATGAG-AACC
1 TGGTGTGCTGGATGGTTTAGCTCATACGAGCAA-C
41298570 TGGTGTG
1 TGGTGTG
41298577 TGCTAGACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 2 0.06
34 33 0.94
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.35
Consensus pattern (34 bp):
TGGTGTGCTGGATGGTTTAGCTCATACGAGCAAC
Done.