Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold179
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: 2991183
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.31
Warning! 65816 characters in sequence are not A, C, G, or T
File 16 of 18
Found at i:2419710 original size:28 final size:28
Alignment explanation
Indices: 2419641--2419881 Score: 247
Period size: 28 Copynumber: 8.5 Consensus size: 28
2419631 CACTAACTTG
*
2419641 TGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTGAAAAGAG--GCCACTGACT
*
2419671 CGTGTGGGCTTTGAAAAGAGGCCACCGACT
1 --TGTGGGCTTTGAAAAGAGGCCACTGACT
* * *
2419701 TGTGGGCTTTGAAAGGATGCCCCTGACT
1 TGTGGGCTTTGAAAAGAGGCCACTGACT
* * *
2419729 TATGGGCTTTG-AAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAAGAG-GCCACTGACT
* *
2419757 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGAGGCCACTGACT
2419785 TGTGGGCTTTG-AAAG-GGTACCACTGACT
1 TGTGGGCTTTGAAAAGAGG--CCACTGACT
* * * *
2419813 TATGGGCTTTGAAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAAGAGGCCACTGACT
*
2419841 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAG-GCCACTGACT
2419869 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
2419882 GAGATGAACG
Statistics
Matches: 175, Mismatches: 26, Indels: 19
0.80 0.12 0.09
Matches are distributed among these distances:
26 1 0.01
27 9 0.05
28 129 0.74
29 7 0.04
30 11 0.06
32 18 0.10
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGAGGCCACTGACT
Found at i:2419757 original size:56 final size:56
Alignment explanation
Indices: 2419641--2419881 Score: 340
Period size: 56 Copynumber: 4.2 Consensus size: 56
2419631 CACTAACTTG
* * * *
2419641 TGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAG-GCCACCGACT
1 TGTGGGCTTTG-AAAG-GATGCCACTGACT--TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
2419701 TGTGGGCTTTGAAAGGATGCCCCTGACTTATGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
*
2419757 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* *
2419813 TATGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
2419869 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
2419882 GAGATGAACG
Statistics
Matches: 165, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
55 5 0.03
56 135 0.82
58 10 0.06
59 4 0.02
60 11 0.07
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:2419769 original size:84 final size:84
Alignment explanation
Indices: 2419673--2419881 Score: 330
Period size: 84 Copynumber: 2.5 Consensus size: 84
2419663 CACCGACTCG
* * *
2419673 TGTGGGCTTTGAAAAGAGGCCACCGACTTGTGGGCTTTGAAAGGATGCCCCTGACTTATGGGCTT
1 TGTGGGCTTTGAAAAGAGGCCACTGACTTGTGGGCTTTGAAAGGATACCACTGACTTATGGGCTT
*
2419738 TGAAAGGGTGCCATTGACT
66 TGAAAGGATGCCATTGACT
* * *
2419757 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTACCACTGACTTATGGGCTT
1 TGTGGGCTTTGAAAAGAGGCCACTGACTTGTGGGCTTTGAAAGGATACCACTGACTTATGGGCTT
2419822 TGAAAGGATGCCATTGACT
66 TGAAAGGATGCCATTGACT
*
2419841 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAA
1 TGTGGGCTTTGAAAAGAG-GCCACTGACTTGTGGGCTTTGAA
2419882 GAGATGAACG
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
83 3 0.03
84 111 0.97
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (84 bp):
TGTGGGCTTTGAAAAGAGGCCACTGACTTGTGGGCTTTGAAAGGATACCACTGACTTATGGGCTT
TGAAAGGATGCCATTGACT
Found at i:2435074 original size:20 final size:19
Alignment explanation
Indices: 2435051--2435120 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
2435041 TATAGAACGC
*
2435051 ATCGATACATTGAAGAATAT
1 ATCGATACATTGAA-AATGT
* *
2435071 ATCGATACATTCATACATGT
1 ATCGATACATTGA-AAATGT
2435091 ATCGATACATTGAAAAATGT
1 ATCGATACATTG-AAAATGT
2435111 ATCGATACAT
1 ATCGATACAT
2435121 CTAGGTACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (19 bp):
ATCGATACATTGAAAATGT
Found at i:2446512 original size:49 final size:49
Alignment explanation
Indices: 2446459--2446553 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
2446449 ATGGAACATG
* *
2446459 GCATGAAATTCACAAACATGGGCTGCTAAGATGGTGAAGATGAAACCTA
1 GCATGAAATGCACAAACATGGGCTACTAAGATGGTGAAGATGAAACCTA
* *
2446508 GCATGAAATGCACAAATATGGGCTACTAAGATGGTGGAGATGAAAC
1 GCATGAAATGCACAAACATGGGCTACTAAGATGGTGAAGATGAAAC
2446554 ATGGCATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (49 bp):
GCATGAAATGCACAAACATGGGCTACTAAGATGGTGAAGATGAAACCTA
Found at i:2449216 original size:25 final size:25
Alignment explanation
Indices: 2449188--2449238 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2449178 AAAAGTGCTA
2449188 ATGACAGAAGACTTAAAGGAACATC
1 ATGACAGAAGACTTAAAGGAACATC
2449213 ATGACAGAAGACTTAAAGGAACATC
1 ATGACAGAAGACTTAAAGGAACATC
2449238 A
1 A
2449239 AATTAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.16
Consensus pattern (25 bp):
ATGACAGAAGACTTAAAGGAACATC
Found at i:2449770 original size:45 final size:43
Alignment explanation
Indices: 2449696--2449847 Score: 139
Period size: 45 Copynumber: 3.5 Consensus size: 43
2449686 CATTACTTCA
* * *
2449696 TTTCACATACATTAC-CTATTTACTGATATTTGCATTTGCATTG
1 TTTCACATGCATTACACCATTTACT-ATATTTGTATTTGCATTG
* *
2449739 TTTCACATGCATCTACACCATTTAACTATATTGGTATTTACATTG
1 TTTCACATGCAT-TACACCATTT-ACTATATTTGTATTTGCATTG
** * * **
2449784 TTTCACATGCATT-TGCCTTTTA-TATACTTGTATTTGCATCA
1 TTTCACATGCATTACACCATTTACTATATTTGTATTTGCATTG
*
2449825 TTTCACGTGCATCTACACCATTT
1 TTTCACATGCAT-TACACCATTT
2449848 GATTTCATTA
Statistics
Matches: 87, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
41 25 0.29
42 2 0.02
43 21 0.24
44 4 0.05
45 32 0.37
46 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.09, T:0.45
Consensus pattern (43 bp):
TTTCACATGCATTACACCATTTACTATATTTGTATTTGCATTG
Found at i:2450688 original size:77 final size:77
Alignment explanation
Indices: 2450550--2450731 Score: 197
Period size: 77 Copynumber: 2.4 Consensus size: 77
2450540 TCTTTAGTGA
* *
2450550 AAAGTCTAATTTAGTTGGTTAGGTAGAAAACTAGCGATGTAGGCACCTAGGAAAAAAGTTAAACC
1 AAAGTCCAATTTAGTTGGTTAGGTAGAAAACTAGCAATGTAGGCACCTAGGAAAAAAGTT-AACC
*
2450615 CA-ATAAATATGG
65 CATATAAATATAG
* * * *** * *
2450627 AAAGTCCAATTTAGTTGGTTAGGTAGAAAGCTGGCAATGTTGGCACCT-GGTAGGGAGGTTAAGC
1 AAAGTCCAATTTAGTTGGTTAGGTAGAAAACTAGCAATGTAGGCACCTAGG-AAAAAAGTTAACC
* *
2450691 CATATAGATGTAG
65 CATATAAATATAG
* *
2450704 AAAGTCCAATTTAATTGGTTAAGTAGAA
1 AAAGTCCAATTTAGTTGGTTAGGTAGAA
2450732 GACCAATGAG
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
76 7 0.08
77 81 0.92
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (77 bp):
AAAGTCCAATTTAGTTGGTTAGGTAGAAAACTAGCAATGTAGGCACCTAGGAAAAAAGTTAACCC
ATATAAATATAG
Found at i:2450755 original size:77 final size:76
Alignment explanation
Indices: 2450626--2451078 Score: 328
Period size: 77 Copynumber: 6.0 Consensus size: 76
2450616 AATAAATATG
* *** * * *
2450626 GAAAGTCCAATTTAGTTGGTTAGGTAGAA-AGCTGGCAATGTTGGCACCTGGTAGGGAGGTTAAG
1 GAAAGTCCAATTTAGTTGGTTAAGTAGAAGA-CCAACAAGGTTGACACTTGGTA-GGAGGTTAAG
*
2450690 CCATATAGATGTA
64 CCCTATAGATGTA
* ** *
2450703 GAAAGTCCAATTTAATTGGTTAAGTAGAAGACCAATGAGGTTGACACTTGGTAAGAAGGTTAAGC
1 GAAAGTCCAATTTAGTTGGTTAAGTAGAAGACCAACAAGGTTGACACTTGGT-AGGAGGTTAAGC
**
2450768 GTTATAGATGTA
65 CCTATAGATGTA
* ** * * * * * * * *
2450780 CAAAGTTTAATTTAGTTGGTTAGGTTGAAAACCAACAATGTTGGCACCTAGTA-GA---AAAGCC
1 GAAAGTCCAATTTAGTTGGTTAAGTAGAAGACCAACAAGGTTGACACTTGGTAGGAGGTTAAGCC
*
2450841 CTATAGATATA
66 CTATAGATGTA
* * * * * * **
2450852 GAGAGTCCAATTTAGTTGTTTGAGTAGAAGACTAACAATGTTGGA-ACTT-ATAAAATGGTTAAG
1 GAAAGTCCAATTTAGTTGGTTAAGTAGAAGACCAACAAGGTT-GACACTTGGTAGGA-GGTTAAG
*
2450915 GCCTATAGATGTA
64 CCCTATAGATGTA
* * * * **
2450928 GAAAATCCCATTTAGTTGGTTAAGTAAAAGACCAGCGGGGTTAGA-ACTTGGTATGGAGGTTAAG
1 GAAAGTCCAATTTAGTTGGTTAAGTAGAAGACCAACAAGGTT-GACACTTGGTA-GGAGGTTAAG
* *
2450992 CCCTATAGGTATA
64 CCCTATAGATGTA
* * * * * * *
2451005 GAAAGTCCCATTTAGTTGGTTAAATAAAAGACTAGCAAGGTTGCCACTTGGTAGTGAAGTTAAGC
1 GAAAGTCCAATTTAGTTGGTTAAGTAGAAGACCAACAAGGTTGACACTTGGTAG-GAGGTTAAGC
2451070 CCTATAGAT
65 CCTATAGAT
2451079 AGAGAGAAAG
Statistics
Matches: 290, Mismatches: 74, Indels: 24
0.75 0.19 0.06
Matches are distributed among these distances:
71 2 0.01
72 49 0.17
73 1 0.00
75 1 0.00
76 54 0.19
77 180 0.62
78 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (76 bp):
GAAAGTCCAATTTAGTTGGTTAAGTAGAAGACCAACAAGGTTGACACTTGGTAGGAGGTTAAGCC
CTATAGATGTA
Found at i:2453418 original size:21 final size:21
Alignment explanation
Indices: 2453398--2453440 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2453388 TGAGCCATTA
*
2453398 AGAGTA-GTTTGTGTGTGATT
1 AGAGTATGTATGTGTGTGATT
* *
2453418 AGTGTATGTATGTGTGTGTTT
1 AGAGTATGTATGTGTGTGATT
2453439 AG
1 AG
2453441 GCCCCATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.47
Consensus pattern (21 bp):
AGAGTATGTATGTGTGTGATT
Found at i:2453939 original size:18 final size:18
Alignment explanation
Indices: 2453913--2453949 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2453903 GAGGTGTTTG
2453913 GATTACTCTATATCAACA
1 GATTACTCTATATCAACA
* *
2453931 GATTGCTCTATATCGACA
1 GATTACTCTATATCAACA
2453949 G
1 G
2453950 TTATGTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (18 bp):
GATTACTCTATATCAACA
Found at i:2455155 original size:78 final size:78
Alignment explanation
Indices: 2455060--2455217 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
2455050 TAGTTATTTT
2455060 GTCTTTTTCATAAAATAGTTTGAAAAGGTCCATTTTTTACATAATTGAATTGATACCTATTTTGG
1 GTCTTTTTCATAAAATAGTTTGAAAAGGTCCATTTTTTACATAATTGAATTGATACCTATTTTGG
2455125 AATTCTTATTGGA
66 AATTCTTATTGGA
2455138 GTCTTTTTCATAAAATAGTTTGAAAAGGTCCATTTTTTACATAATTGAATTGATACCTATTTTGG
1 GTCTTTTTCATAAAATAGTTTGAAAAGGTCCATTTTTTACATAATTGAATTGATACCTATTTTGG
2455203 AATTCTTATTGGA
66 AATTCTTATTGGA
2455216 GT
1 GT
2455218 TTACTATCTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (78 bp):
GTCTTTTTCATAAAATAGTTTGAAAAGGTCCATTTTTTACATAATTGAATTGATACCTATTTTGG
AATTCTTATTGGA
Found at i:2459607 original size:19 final size:19
Alignment explanation
Indices: 2459583--2459621 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2459573 TATCTATCTT
2459583 TTATATAAT-ATAATAAAAA
1 TTATATAATAAT-ATAAAAA
2459602 TTATATAATAATATAAAAA
1 TTATATAATAATATAAAAA
2459621 T
1 T
2459622 AATACACGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTATATAATAATATAAAAA
Found at i:2463570 original size:6 final size:6
Alignment explanation
Indices: 2463559--2463585 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2463549 ACCAGCACAA
2463559 CCCCTC CCCCTC CCCCTC CCCCTC CCC
1 CCCCTC CCCCTC CCCCTC CCCCTC CCC
2463586 AACAATGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCCTC
Found at i:2466410 original size:6 final size:6
Alignment explanation
Indices: 2466399--2466432 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2466389 AAAAAAATTA
2466399 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
2466433 ATTAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:2466445 original size:15 final size:16
Alignment explanation
Indices: 2466424--2466469 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
2466414 ATTTTTATTT
2466424 TTATTTTTAATTAAAA
1 TTATTTTTAATTAAAA
2466440 -TATTTTTAAATATAAAA
1 TTATTTTT-AAT-TAAAA
2466457 TTATTTTTAATTA
1 TTATTTTTAATTA
2466470 CTATTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.26
16 5 0.19
17 8 0.30
18 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATTTTTAATTAAAA
Found at i:2466463 original size:18 final size:17
Alignment explanation
Indices: 2466424--2466466 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
2466414 ATTTTTATTT
2466424 TTATTTTT-AATTAAAA
1 TTATTTTTAAATTAAAA
2466440 -TATTTTTAAATATAAAA
1 TTATTTTTAAAT-TAAAA
2466457 TTATTTTTAA
1 TTATTTTTAA
2466467 TTACTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.29
16 3 0.12
17 5 0.21
18 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTTTTAAATTAAAA
Found at i:2466481 original size:16 final size:16
Alignment explanation
Indices: 2466462--2466495 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2466452 TAAAATTATT
2466462 TTTAATTACT-ATTAAA
1 TTTAATTA-TAATTAAA
2466478 TTTAATTATAATTAAA
1 TTTAATTATAATTAAA
2466494 TT
1 TT
2466496 ATATTTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATTATAATTAAA
Found at i:2466523 original size:19 final size:20
Alignment explanation
Indices: 2466488--2466526 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2466478 TTTAATTATA
2466488 ATTAAATTATATTTCAAGAT
1 ATTAAATTATATTTCAAGAT
*
2466508 ATTAAA-TATTTTTCAAGAT
1 ATTAAATTATATTTCAAGAT
2466527 TTGAGTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTAAATTATATTTCAAGAT
Found at i:2470528 original size:20 final size:22
Alignment explanation
Indices: 2470486--2470529 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2470476 TCACTAAATT
*
2470486 TTTAAATAATAATAATTAATTAA
1 TTTAAATAAAAATAATT-ATTAA
2470509 TTTAAATAAAAAT-ATT-TTAA
1 TTTAAATAAAAATAATTATTAA
2470529 T
1 T
2470530 AAATTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAATAAAAATAATTATTAA
Found at i:2470976 original size:2 final size:2
Alignment explanation
Indices: 2470969--2470993 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2470959 TTTCTTTTTA
2470969 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 A
2470994 ACATACACAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2471117 original size:17 final size:17
Alignment explanation
Indices: 2471095--2471131 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2471085 CAATTAATTT
*
2471095 TAATCTTACCATTATAA
1 TAATCTTACCATGATAA
*
2471112 TAATCTTACTATGATAA
1 TAATCTTACCATGATAA
2471129 TAA
1 TAA
2471132 CCAATCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.41
Consensus pattern (17 bp):
TAATCTTACCATGATAA
Found at i:2471377 original size:11 final size:11
Alignment explanation
Indices: 2471361--2471402 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
2471351 AAAGGCTTAA
2471361 TTATTTTAATT
1 TTATTTTAATT
2471372 TTATTTTAATAT
1 TTATTTTAAT-T
2471384 TATAATTTTAATT
1 T-T-ATTTTAATT
2471397 TT-TTTT
1 TTATTTT
2471403 GTATATAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.14
11 10 0.36
12 3 0.11
13 3 0.11
14 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTAATT
Found at i:2471389 original size:19 final size:21
Alignment explanation
Indices: 2471357--2471398 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
2471347 ATTAAAAGGC
*
2471357 TTAATTATTTTAATTTT-ATT
1 TTAATTATTATAATTTTAATT
2471377 TTAA-TATTATAATTTTAATT
1 TTAATTATTATAATTTTAATT
2471397 TT
1 TT
2471399 TTTTGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTAATTATTATAATTTTAATT
Found at i:2471898 original size:15 final size:15
Alignment explanation
Indices: 2471875--2471904 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2471865 TTTATTTTCA
*
2471875 AAATTAAAAATAAAT
1 AAATAAAAAATAAAT
2471890 AAATAAAAAATAAAT
1 AAATAAAAAATAAAT
2471905 TGTAATAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAAATAAAT
Found at i:2472256 original size:26 final size:27
Alignment explanation
Indices: 2472227--2472280 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 27
2472217 ATATATTTTT
*
2472227 ATTTATTTATATTTT-AT-TTTAAATTA
1 ATTT-TTTATATTTTAATAATTAAATTA
2472253 A-TTTTTATATTTTAATAATTAAATTA
1 ATTTTTTATATTTTAATAATTAAATTA
2472279 AT
1 AT
2472281 ATCTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
24 10 0.42
25 4 0.17
26 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTTTTTATATTTTAATAATTAAATTA
Found at i:2472271 original size:17 final size:16
Alignment explanation
Indices: 2472208--2472272 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 16
2472198 AAAAATTAAA
2472208 TTATTTTTAATATATTT
1 TTATTTTTAATA-ATTT
*
2472225 TTATTTATTTAT-A-TT
1 TTATTT-TTAATAATTT
*
2472240 TTATTTTAAATTAATTT
1 TTATTTTTAA-TAATTT
2472257 TTATATTTTAATAATT
1 TTAT-TTTTAATAATT
2472273 AAATTAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 2 0.05
15 9 0.23
16 2 0.05
17 17 0.44
18 9 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTTAATAATTT
Found at i:2472780 original size:3 final size:3
Alignment explanation
Indices: 2472766--2472812 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
2472756 ACAAAATCAA
*
2472766 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2472813 AAGAAATAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2473239 original size:24 final size:24
Alignment explanation
Indices: 2473205--2473276 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
2473195 ATATTAATAT
2473205 AAATATT-AAATTATTAATTATTA
1 AAATATTAAAATTATTAATTATTA
* **
2473228 AAATATTAAAATAATTTGTTATTAAA
1 AAATATTAAAATTATTAATTATT--A
*
2473254 AAATATTAATA-TATTAA-TATTA
1 AAATATTAAAATTATTAATTATTA
2473276 A
1 A
2473277 TGCTAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 16 0.41
25 3 0.08
26 11 0.28
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
AAATATTAAAATTATTAATTATTA
Found at i:2473243 original size:27 final size:27
Alignment explanation
Indices: 2473213--2473336 Score: 65
Period size: 27 Copynumber: 4.9 Consensus size: 27
2473203 ATAAATATTA
2473213 AATTATTAATTATTAAAATATTAAAAT
1 AATTATTAATTATTAAAATATTAAAAT
* *
2473240 AATT-TGTTATTA-AAAAATATT--AAT
1 AATTAT-TAATTATTAAAATATTAAAAT
**
2473264 -A-TATTAA-TATT--AATGCTAAAAT
1 AATTATTAATTATTAAAATATTAAAAT
*
2473286 ATTATATTAA-TATT-AAATATTTAAAAT
1 AAT-TATTAATTATTAAAATA-TTAAAAT
* *
2473313 ATACTATTTATTATTAAAA-ATTAA
1 A-ATTATTAATTATTAAAATATTAA
2473337 TTATATCAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
20 4 0.06
21 2 0.03
22 6 0.08
23 2 0.03
24 3 0.04
25 10 0.14
26 12 0.17
27 25 0.35
28 5 0.07
29 3 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
AATTATTAATTATTAAAATATTAAAAT
Found at i:2473654 original size:23 final size:23
Alignment explanation
Indices: 2473625--2473673 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
2473615 ATTTATTTTT
2473625 ATTAAT-ATTTCTAGTATT-AAAAC
1 ATTAATAATTT-TA-TATTAAAAAC
2473648 ATTAATAATTTTATATTAAAAAC
1 ATTAATAATTTTATATTAAAAAC
2473671 ATT
1 ATT
2473674 TATCATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.17
23 16 0.67
24 4 0.17
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAATAATTTTATATTAAAAAC
Found at i:2473837 original size:14 final size:15
Alignment explanation
Indices: 2473813--2473855 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
2473803 AGTTAAAATA
2473813 ATAA-ATTATATTA-
1 ATAATATTATATTAG
*
2473826 ATAATTTTATATTAAG
1 ATAATATTATATT-AG
2473842 ATAATATTATATTA
1 ATAATATTATATTA
2473856 TTAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 4 0.16
14 7 0.28
15 2 0.08
16 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATAATATTATATTAG
Found at i:2474497 original size:9 final size:9
Alignment explanation
Indices: 2474485--2474515 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
2474475 TAATCAAATT
2474485 AATATTTAA
1 AATATTTAA
2474494 AATATTTAA
1 AATATTTAA
2474503 AATATTTAA
1 AATATTTAA
2474512 AATA
1 AATA
2474516 ATTTTAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATATTTAA
Found at i:2474524 original size:18 final size:17
Alignment explanation
Indices: 2474483--2474524 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2474473 AATAATCAAA
2474483 TTAATATTTAAAATATT
1 TTAATATTTAAAATATT
*
2474500 TAAAATATTTAAAATAATT
1 T-TAATATTTAAAAT-ATT
2474519 TTAATA
1 TTAATA
2474525 GAATATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 16 0.76
19 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATATTTAAAATATT
Found at i:2474547 original size:14 final size:14
Alignment explanation
Indices: 2474530--2474581 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
2474520 TAATAGAATA
2474530 TAAATATATTTAAT
1 TAAATATATTTAAT
2474544 TAAATATATTT-A-
1 TAAATATATTTAAT
*
2474556 -AAATTTATTTAAT
1 TAAATATATTTAAT
*
2474569 AAAATATATTTAA
1 TAAATATATTTAA
2474582 AATCGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 9 0.27
12 1 0.03
13 1 0.03
14 22 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAATATATTTAAT
Found at i:2474559 original size:25 final size:25
Alignment explanation
Indices: 2474531--2474584 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
2474521 AATAGAATAT
*
2474531 AAATATATTTAATTAAATATATTTA
1 AAATATATTTAATAAAATATATTTA
*
2474556 AAATTTATTTAATAAAATATATTTA
1 AAATATATTTAATAAAATATATTTA
2474581 AAAT
1 AAAT
2474585 CGAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATATATTTAATAAAATATATTTA
Found at i:2474564 original size:11 final size:11
Alignment explanation
Indices: 2474486--2474584 Score: 50
Period size: 9 Copynumber: 9.0 Consensus size: 11
2474476 AATCAAATTA
2474486 ATATTT-AAA-
1 ATATTTAAAAT
2474495 ATATTT-AAA-
1 ATATTTAAAAT
2474504 ATATTTAAAAT
1 ATATTTAAAAT
*
2474515 A-ATTT-TAAT
1 ATATTTAAAAT
* *
2474524 AGA-ATATAAAT
1 ATATTTA-AAAT
2474535 ATATTTAATTAAAT
1 ATATTT-A--AAAT
2474549 ATATTTAAAAT
1 ATATTTAAAAT
*
2474560 TTATTTAATAAAAT
1 ATA-TT--TAAAAT
2474574 ATATTTAAAAT
1 ATATTTAAAAT
2474585 CGAAAAAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
9 20 0.28
10 8 0.11
11 18 0.25
12 3 0.04
13 4 0.06
14 19 0.26
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (11 bp):
ATATTTAAAAT
Found at i:2474694 original size:21 final size:21
Alignment explanation
Indices: 2474669--2474714 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2474659 TTGATCAATT
* *
2474669 TTAATATTAAATTTAATTAAA
1 TTAATATTAAATTAAAATAAA
* *
2474690 TTAATTTTTAATTAAAATAAA
1 TTAATATTAAATTAAAATAAA
2474711 TTAA
1 TTAA
2474715 ATCGATCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATATTAAATTAAAATAAA
Found at i:2474712 original size:26 final size:27
Alignment explanation
Indices: 2474665--2474716 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
2474655 CAATTTGATC
* *
2474665 AATTTTAATATTAAATTTAATTAAATT
1 AATTTTAATATTAAAATAAATTAAATT
*
2474692 AATTTTTA-ATTAAAATAAATTAAAT
1 AATTTTAATATTAAAATAAATTAAAT
2474717 CGATCAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTTTAATATTAAAATAAATTAAATT
Found at i:2475008 original size:20 final size:19
Alignment explanation
Indices: 2474963--2475027 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
2474953 CTTTTATAAA
*
2474963 TTATATTTAAATAAATTATT
1 TTATATTT-ATTAAATTATT
* *
2474983 TCATATTTATTATATTATTT
1 TTATATTTATTAAATTA-TT
*
2475003 TTATATTTATTAAA-TATG
1 TTATATTTATTAAATTATT
2475021 TTATATT
1 TTATATT
2475028 AGCAAAACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 8 0.21
19 9 0.24
20 21 0.55
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATATTTATTAAATTATT
Found at i:2476614 original size:17 final size:17
Alignment explanation
Indices: 2476594--2476631 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2476584 AATAATTTAA
*
2476594 AATATTTAATATT-TTTT
1 AATA-TTAAAATTATTTT
2476611 AATATTAAAATTATTTT
1 AATATTAAAATTATTTT
2476628 AATA
1 AATA
2476632 ATATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATTAAAATTATTTT
Found at i:2476641 original size:21 final size:21
Alignment explanation
Indices: 2476610--2476651 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2476600 TAATATTTTT
*
2476610 TAATATTAAAATTAT-TTTAA
1 TAATATTAAAATCATATTTAA
2476630 TAATATTTAAAATCATATTTAA
1 TAATA-TTAAAATCATATTTAA
2476652 ATGAATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATATTAAAATCATATTTAA
Found at i:2479984 original size:78 final size:78
Alignment explanation
Indices: 2479890--2480150 Score: 312
Period size: 79 Copynumber: 3.3 Consensus size: 78
2479880 GGTGTTCCAG
* *
2479890 AAATAAAATCGGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCTGATTAT-AAA
1 AAATAAAATCAGGGTTGGAGTATCCCCTC-GAAATAACAGGGTTGGAGTATCCCTGATTGTGAAA
*
2479954 AATCGGTATTTTGA
65 AATCGATATTTTGA
* * * *
2479968 AAATGAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAA
1 AAATAAAATCAGGGTTGGAGTATCCCCTCG-AAATAACAGGGTTGGAGTATCCCTGATTGTGAAA
*
2480033 AATCGATGATTTAG-
65 AATCGAT-ATTTTGA
*** * *
2480047 AAATAAGGCCAGGGTTGAAGTATCCCCTTGGAAATAACAGGGTTGGAGTATCCCCTG-TTGTGAA
1 AAATAAAATCAGGGTTGGAGTATCCCC-TCGAAATAACAGGGTTGGAGTAT-CCCTGATTGTGAA
* *
2480111 AAATTGATGTTTTGA
64 AAATCGATATTTTGA
*
2480126 AAATAAAATCAGAGTTGGAGTATCC
1 AAATAAAATCAGGGTTGGAGTATCC
2480151 TCGATTGTGA
Statistics
Matches: 154, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
77 1 0.01
78 59 0.38
79 83 0.54
80 11 0.07
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (78 bp):
AAATAAAATCAGGGTTGGAGTATCCCCTCGAAATAACAGGGTTGGAGTATCCCTGATTGTGAAAA
ATCGATATTTTGA
Found at i:2480156 original size:130 final size:127
Alignment explanation
Indices: 2480009--2480256 Score: 336
Period size: 130 Copynumber: 1.9 Consensus size: 127
2479999 AAATAACGGG
**
2480009 GTTGGAGTATCCCCGATTGTGAAAAATCGATGA-TTTAGAAATAAGGCCAGGGTTGAAGTATCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCGAT-ATTTTAGAAATAAAACCAGGGTTGAAGTATCCC
* * *
2480073 CTTGGAAATAACAGGGTTGGAGTATCCCCTGTTGTGAAAAATTGATGTTTTGAAAATAAAATCAG
65 CTCGAAAATAACAGGGTTGGAGTATCCCC-G--ATGAAAAATTGATGTTTTGAAAATAAAATCAG
2480138 A
127 A
* * * ** *
2480139 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTAGAAATAAAACTGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAACCAGGGTTGAAGTATCCCC
* *
2480204 TCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTGGAAAT
66 TCGAAAATAACAGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTGAAAAT
2480257 GAAACCGGGA
Statistics
Matches: 104, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
127 22 0.21
129 2 0.02
130 80 0.77
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (127 bp):
GTTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAACCAGGGTTGAAGTATCCCC
TCGAAAATAACAGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTGAAAATAAAATCAGA
Found at i:2480159 original size:51 final size:51
Alignment explanation
Indices: 2480088--2480204 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
2480078 AAATAACAGG
*
2480088 GTTGGAGTATCCCCTGTTGTGAAAAATTGATGTTTT-GAAAATAAAA-TCAGA
1 GTTGGAGTATCCCCTGTTGTGAAAAATTGATATTTTAG-AAATAAAACT-AGA
* * * *
2480139 GTTGGAGTATCCTC-GATTGTGAAAAATTGGTATTTTAGAAATAAAACTGGG
1 GTTGGAGTATCCCCTG-TTGTGAAAAATTGATATTTTAGAAATAAAACTAGA
2480190 GTTGGAGTATCCCCT
1 GTTGGAGTATCCCCT
2480205 CGAAAATAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
50 1 0.02
51 53 0.95
52 2 0.04
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCTGTTGTGAAAAATTGATATTTTAGAAATAAAACTAGA
Found at i:2480311 original size:130 final size:128
Alignment explanation
Indices: 2480058--2480311 Score: 266
Period size: 130 Copynumber: 2.0 Consensus size: 128
2480048 AATAAGGCCA
* * *
2480058 GGGTTGAAGTATCCCCTTGGAAATAACAGGGTTGGAGTATCCCCTGTTGTGAAAAATTGATGTTT
1 GGGTTGAAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCTG-TATGAAAAATTGATGTTT
* * ** * *
2480123 TGAAAATAAAATCAGAGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTAGAAATAAAACTG
65 TGAAAATAAAACCAGAGTTGAAGTATCCTCGA-TGTGAAAAATTGAAATTTCAAAAATAAAACTG
* *
2480188 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC-G-ATGAAAAATTGATGTTTT
1 GGGTTGAAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCTGTATGAAAAATTGATGTTTT
* * *
2480251 GGAAATGAAACC-GGGATTGAAGTATCC-CTGA-GATGAAAAATCTAGAAATTTAACAAAAATA
66 GAAAATAAAACCAGAG-TTGAAGTATCCTC-GATG-TGAAAAAT-T-GAAATTT--CAAAAATA
2480312 CTTTTAGGTT
Statistics
Matches: 103, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
125 1 0.01
126 11 0.11
127 39 0.38
128 5 0.05
129 1 0.01
130 46 0.45
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (128 bp):
GGGTTGAAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCTGTATGAAAAATTGATGTTTT
GAAAATAAAACCAGAGTTGAAGTATCCTCGATGTGAAAAATTGAAATTTCAAAAATAAAACTG
Found at i:2482623 original size:20 final size:20
Alignment explanation
Indices: 2482576--2482698 Score: 113
Period size: 20 Copynumber: 5.8 Consensus size: 20
2482566 AAAAATGGTG
* *
2482576 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGC
2482596 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGC
* *
2482616 AATATATCGATATAATGTATCGATAC
1 AATGTATCGATACAATG-A--G---C
2482642 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGC
* *
2482662 AATGTATCGATACAAAGATC
1 AATGTATCGATACAATGAGC
*
2482682 GATGTATCGATACAATG
1 AATGTATCGATACAATG
2482699 TATCGATACA
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
19 1 0.01
20 65 0.76
21 1 0.01
23 2 0.02
25 1 0.01
26 16 0.19
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAGC
Found at i:2482638 original size:13 final size:13
Alignment explanation
Indices: 2482615--2482708 Score: 77
Period size: 13 Copynumber: 8.2 Consensus size: 13
2482605 ATACAATGAG
*
2482615 CAATATATCGATA
1 CAATGTATCGATA
*
2482628 TAATGTATCGATA
1 CAATGTATCGATA
2482641 CAATGTATCGATA
1 CAATGTATCGATA
2482654 CAATG-A--G---
1 CAATGTATCGATA
2482661 CAATGTATCGATA
1 CAATGTATCGATA
2482674 CAA---A--GAT-
1 CAATGTATCGATA
*
2482681 CGATGTATCGATA
1 CAATGTATCGATA
2482694 CAATGTATCGATA
1 CAATGTATCGATA
2482707 CA
1 CA
2482709 TTGAATAATG
Statistics
Matches: 64, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
7 7 0.11
8 4 0.06
10 4 0.06
12 4 0.06
13 45 0.70
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2482638 original size:33 final size:33
Alignment explanation
Indices: 2482596--2482728 Score: 128
Period size: 33 Copynumber: 4.0 Consensus size: 33
2482586 TACATTGTAA
* *
2482596 AATGTATCGATACAATGAGCAATATATCGATAT
1 AATGTATCGATACAATGATCAATATATCGATAC
* * *
2482629 AATGTATCGATACAATGTATCGATACAAT-GA-GC
1 AATGTATCGATACAATG-ATCAATA-TATCGATAC
* * *
2482662 AATGTATCGATACAAAGATCGATGTATCGATAC
1 AATGTATCGATACAATGATCAATATATCGATAC
* *
2482695 AATGTATCGATACATTGAAT-AATGTATCGATAC
1 AATGTATCGATACAATG-ATCAATATATCGATAC
2482728 A
1 A
2482729 TTTCCTTGGC
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
31 2 0.02
32 8 0.10
33 62 0.75
34 9 0.11
35 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (33 bp):
AATGTATCGATACAATGATCAATATATCGATAC
Found at i:2482690 original size:66 final size:66
Alignment explanation
Indices: 2482576--2482708 Score: 187
Period size: 66 Copynumber: 2.0 Consensus size: 66
2482566 AAAAATGGTG
* * *
2482576 AATGTATCGATACATTGTAAAATGTATCGATACAATGAGCAATATATCGATATAATGTATCGATA
1 AATGTATCGATACAATGTAAAATGTATCGATACAAAGAGCAATATATCGATACAATGTATCGATA
2482641 C
66 C
* * * *
2482642 AATGTATCGATACAATG-AGCAATGTATCGATACAAAGATCGATGTATCGATACAATGTATCGAT
1 AATGTATCGATACAATGTA-AAATGTATCGATACAAAGAGCAATATATCGATACAATGTATCGAT
2482706 AC
65 AC
2482708 A
1 A
2482709 TTGAATAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 58 0.98
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (66 bp):
AATGTATCGATACAATGTAAAATGTATCGATACAAAGAGCAATATATCGATACAATGTATCGATA
C
Found at i:2485184 original size:16 final size:17
Alignment explanation
Indices: 2485153--2485187 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2485143 TTATTTATGC
*
2485153 ATATTCAGAGTTCATGA
1 ATATTCAGAATTCATGA
2485170 ATATTCA-AATTCATGA
1 ATATTCAGAATTCATGA
2485186 AT
1 AT
2485188 TTATGTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
ATATTCAGAATTCATGA
Found at i:2496084 original size:13 final size:13
Alignment explanation
Indices: 2496066--2496180 Score: 77
Period size: 13 Copynumber: 7.5 Consensus size: 13
2496056 ACAAAAATGC
2496066 TGTATCGATACAA
1 TGTATCGATACAA
2496079 TGTATCGATACATAAGTA
1 TGTATCGATAC---A--A
2496097 TTGTATCGATACAA
1 -TGTATCGATACAA
2496111 TGTATCGATACATAA
1 TGTATCGATAC--AA
2496126 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2496143 TGTATCGATACATAA
1 TGTATCGATAC--AA
2496158 GTTTGTATCGATACAA
1 ---TGTATCGATACAA
2496174 TGTATCG
1 TGTATCG
2496181 CTACGAAGCT
Statistics
Matches: 85, Mismatches: 0, Indels: 34
0.71 0.00 0.29
Matches are distributed among these distances:
13 40 0.47
14 1 0.01
15 4 0.05
16 4 0.05
17 2 0.02
18 12 0.14
19 22 0.26
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2496085 original size:32 final size:32
Alignment explanation
Indices: 2496047--2496180 Score: 225
Period size: 32 Copynumber: 4.2 Consensus size: 32
2496037 TTCAATGATT
* * *
2496047 TGTATCGATACAAAAATGCTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
2496079 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2496111 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2496143 TGTATCGATACATAAGT-TTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2496174 TGTATCG
1 TGTATCG
2496181 CTACGAAGCT
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
31 21 0.22
32 76 0.78
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2496103 original size:19 final size:19
Alignment explanation
Indices: 2496079--2496172 Score: 88
Period size: 13 Copynumber: 5.6 Consensus size: 19
2496069 ATCGATACAA
2496079 TGTATCGATACATAAGTAT
1 TGTATCGATACATAAGTAT
2496098 TGTATCGATAC---A--A-
1 TGTATCGATACATAAGTAT
*
2496111 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTAT
2496130 TGTATCGATAC---A--A-
1 TGTATCGATACATAAGTAT
2496143 TGTATCGATACATAAGT-T
1 TGTATCGATACATAAGTAT
2496161 TGTATCGATACA
1 TGTATCGATACA
2496173 ATGTATCGCT
Statistics
Matches: 61, Mismatches: 2, Indels: 25
0.69 0.02 0.28
Matches are distributed among these distances:
13 22 0.36
14 1 0.02
16 4 0.07
18 12 0.20
19 22 0.36
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTAT
Found at i:2496243 original size:13 final size:13
Alignment explanation
Indices: 2496225--2496249 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2496215 ATTACCTAAA
2496225 TGTATCGATACAT
1 TGTATCGATACAT
2496238 TGTATCGATACA
1 TGTATCGATACA
2496250 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2496300 original size:52 final size:52
Alignment explanation
Indices: 2496258--2496386 Score: 195
Period size: 52 Copynumber: 2.5 Consensus size: 52
2496248 CACTGATCTT
**
2496258 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
2496310 TGTATCGATACATACAGGCAAATTTGGCCAGATGTATCGATACATTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
2496362 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATACAGGCAAATTT
2496387 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2511765 original size:29 final size:29
Alignment explanation
Indices: 2511731--2511815 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 29
2511721 CACCCTTTAC
2511731 AAGCCCACAAGTCAGTGGCATCTTTTTCA
1 AAGCCCACAAGTCAGTGGCATCTTTTTCA
* * * *
2511760 AAGCCCACAAATCAGTGGCAAC-CTTTAA
1 AAGCCCACAAGTCAGTGGCATCTTTTTCA
*
2511788 AAGCCCACAAGTCCGTGGCATCTTTTTC
1 AAGCCCACAAGTCAGTGGCATCTTTTTC
2511816 CTTTTAAGCC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
28 23 0.50
29 23 0.50
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCATCTTTTTCA
Found at i:2511825 original size:33 final size:34
Alignment explanation
Indices: 2511788--2511929 Score: 182
Period size: 33 Copynumber: 4.2 Consensus size: 34
2511778 CAACCTTTAA
*
2511788 AAGCCCACAAGTCCGTGGCA-TCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
* **
2511821 AAGCCCATC-ACTTCGTGGCAC-CTTTTTTTTTTT
1 AAGCCCA-CAACTCCGTGGCACTCTTTTTCCTTTT
* *
2511854 AAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTT-T
*
2511889 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
2511923 AAGCCCA
1 AAGCCCA
2511930 TAAGTTAGTG
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
32 1 0.01
33 43 0.46
34 19 0.20
35 31 0.33
ACGTcount: A:0.18, C:0.30, G:0.13, T:0.38
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:2511849 original size:35 final size:34
Alignment explanation
Indices: 2511788--2511949 Score: 170
Period size: 33 Copynumber: 4.8 Consensus size: 34
2511778 CAACCTTTAA
* *
2511788 AAGCCCACAAGTCCGTGGCA-TCTTTTTCCTTTT
1 AAGCCCACAACTTCGTGGCACTCTTTTTCCTTTT
**
2511821 AAGCCCATC-ACTTCGTGGCAC-CTTTTTTTTTTT
1 AAGCCCA-CAACTTCGTGGCACTCTTTTTCCTTTT
* * *
2511854 AAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGT
1 AAGCCCACAACTTCGTGGCACTCTTTTTCCTTT-T
2511889 AAGCCCACAAC-TCTGTGGCACTCTTTTTCCTTTT
1 AAGCCCACAACTTC-GTGGCACTCTTTTTCCTTTT
* * * *
2511923 AAGCCCATAAGTTAGTGGCACCCTTTT
1 AAGCCCACAACTTCGTGGCACTCTTTT
2511950 CAAAAGCCCA
Statistics
Matches: 108, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
32 1 0.01
33 43 0.40
34 34 0.31
35 30 0.28
ACGTcount: A:0.19, C:0.29, G:0.14, T:0.38
Consensus pattern (34 bp):
AAGCCCACAACTTCGTGGCACTCTTTTTCCTTTT
Found at i:2511909 original size:68 final size:67
Alignment explanation
Indices: 2511792--2511925 Score: 175
Period size: 68 Copynumber: 2.0 Consensus size: 67
2511782 CTTTAAAAGC
* **
2511792 CCACAAGTCCGTGGCATCTTTTTCCTTTTAAGCCCATCACTTCGTGGCAC-CTTTTTTTTTTTAA
1 CCACAACTCCGTGGCATCTTTTTCCTTTTAAGCCCATCACTTCGTGGCACTCTTTTTCCTTTTAA
2511856 GT
66 GT
*
2511858 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCCCA-CAAC-TCTGTGGCACTCTTTTTCCTT
1 CCACAACTCCGTGGCA-TCTTTTTCCTTT-TAAGCCCATC-ACTTC-GTGGCACTCTTTTTCCTT
2511921 TTAAG
62 TTAAG
2511926 CCCATAAGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
66 15 0.25
67 14 0.24
68 17 0.29
69 13 0.22
ACGTcount: A:0.17, C:0.29, G:0.13, T:0.40
Consensus pattern (67 bp):
CCACAACTCCGTGGCATCTTTTTCCTTTTAAGCCCATCACTTCGTGGCACTCTTTTTCCTTTTAA
GT
Found at i:2512078 original size:43 final size:43
Alignment explanation
Indices: 2512009--2512277 Score: 250
Period size: 43 Copynumber: 5.9 Consensus size: 43
2511999 CGTCTTCTTC
* * *
2512009 TAAGTCCAATGTCGCTGGCCTAGAATCAGCACATTGGCACCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
*
2512052 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTTTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACC------TT
* * *
2512101 TAAGACCAATGTCGCTGGCCTTGAATCAGTACACTGGCACCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
2512144 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTCATCT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-C-C-T-T
* * *
2512191 TGAAGACCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTCATCTT
1 T-AAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
* *
2512241 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG
2512278 TGCCTTCGTC
Statistics
Matches: 185, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
43 72 0.39
44 1 0.01
45 1 0.01
46 1 0.01
47 2 0.01
48 32 0.17
49 70 0.38
50 2 0.01
51 2 0.01
52 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (43 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:2512122 original size:49 final size:49
Alignment explanation
Indices: 2512004--2512889 Score: 424
Period size: 49 Copynumber: 18.0 Consensus size: 49
2511994 GGTGACGTCT
* * *
2512004 TCTTCTAAGTCCAATGTCGCTGGCCTAGAATCAGCACATTGGCA----C-
1 TCTT-TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* **
2512049 -CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTG
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * * *
2512097 TTTTTAAGACCAATGTCGCTGGCCTTGAATCAGTACACTGGCA----C-
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * *
2512141 -CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACC-TCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * * *
2512188 TCTTGAAGACCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * **
2512237 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTCGTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC-T--TCA
* * *
2512289 TCTTTCAA-ATCAATGTCGCTGGCCTTGAATCAGCACATTGACACCTTCA
1 TCTTT-AAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * ** * * * *
2512338 TCCTTAAGTCCAAAATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * * * * ** * **
2512387 ACATTCCTAAGCCCAATGTCACCGGCATTGCCTCAGCACATTGGCA--TTTT
1 TC-TT--TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
** * * * * * * *
2512437 TCTCCAAGTCTAAATGTCGCTGGCCATGAATCAACACATTGTCATTCTTCGCA
1 TCTTTAAGAC-CAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CCTT--CA
* * * * * ** * *
2512490 TCTTCAAGCCCAATATTGCTAGCC--GCATATTGGC-TCCTT--TATCCTTTTTCTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTG-A-ATCAGCAT-ATTGGCA-CC----T-TCA
* * **
2512543 TCTTTAAAACCAATGTCGCTGGCCTTGAATTAGCATATTGGTGCCTATGTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCA
* * * * * **
2512595 CCTTTAAGTCCAATATCGCTAGCCTTGAATCATCATATTGGCACCTTTG
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
*
2512644 TC-TT-AGTACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAG-ACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
* * *
2512692 TCTTTAAGACCACTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC-T--TCA
* * * * * * * *
2512744 TCTTTAAAACCCAATGTTGTTGGCCTT-ATCTCAACACATTGG-A-ATTCT
1 TCTTTAAGA-CCAATGTCGCTGGCCTTGA-ATCAGCATATTGGCACCTTCA
* * * * * * *
2512792 TCTTCAAGTCTAACT-TCGCTGGCCATGAATCAGCACATTGTCATTCTTC-
1 TCTTTAAGACCAA-TGTCGCTGGCCTTGAATCAGCATATTGGCA-CCTTCA
* * * *
2512841 TCATCTTAAGCCCAATATCACTGGTCTTGAATCAGCATATTGGCACCTT
1 TC-T-TTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTT
2512890 TATCACTCTT
Statistics
Matches: 628, Mismatches: 158, Indels: 105
0.70 0.18 0.12
Matches are distributed among these distances:
43 70 0.11
44 3 0.00
46 1 0.00
47 27 0.04
48 112 0.18
49 156 0.25
50 23 0.04
51 34 0.05
52 134 0.21
53 60 0.10
54 5 0.01
55 3 0.00
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (49 bp):
TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
Found at i:2512171 original size:92 final size:94
Alignment explanation
Indices: 2512009--2512380 Score: 423
Period size: 92 Copynumber: 3.9 Consensus size: 94
2511999 CGTCTTCTTC
* * *
2512009 TAAGTCCAATGTCGCTGGCCTAGAATCAGCACATTGGCA-C-CTTTAAGACCAATATCGCTGGCC
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCAATATCGCTGGCC
*
2512072 TTGAATCAGCATATTGGCACCTTTGTTTT
66 TTGAATCAGCATATTGGCACCTTCGTTTT
* * *
2512101 TAAGACCAATGTCGCTGGCCTTGAATCAGTACACTGGCA-C-CTTTAAGTCCAATATTGCTGGCC
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCAATATCGCTGGCC
* *
2512164 TTGAATCAGCATATTGGCACC-TCATCTT
66 TTGAATCAGCATATTGGCACCTTCGTTTT
* * *
2512192 GAAGACCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C--C-TCTTTAAGTCCAATATCGCT
**
2512257 GGCCTTGAATCAGCATATTGGTGCCTTCGTCATCTT
62 GGCCTTGAATCAGCATATTGGCACCTTCGT--T-TT
* * * *
2512293 TCAA-ATCAATGTCGCTGGCCTTGAATCAGCACATTGACACCTTCATCCTTAAGTCCAAAATCGT
1 T-AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TC-T--TTAAGTCCAATATCGC
*
2512357 TGGCCTTGAATCAGCGTATTGGCA
61 TGGCCTTGAATCAGCATATTGGCA
2512381 TCTTTAACAT
Statistics
Matches: 236, Mismatches: 30, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
91 38 0.16
92 78 0.33
95 1 0.00
97 41 0.17
98 6 0.03
99 1 0.00
100 1 0.00
101 68 0.29
102 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (94 bp):
TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCAATATCGCTGGCC
TTGAATCAGCATATTGGCACCTTCGTTTT
Found at i:2512608 original size:52 final size:51
Alignment explanation
Indices: 2512540--2512889 Score: 231
Period size: 52 Copynumber: 7.0 Consensus size: 51
2512530 ATCCTTTTTC
** * * **
2512540 TCATCTTTAAAACCAATGTCGCTGGCCTTGAATTAGCATATTGGTGCCTATG
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-TG
* * *
2512592 TCACCTTTAAGTCCAATATCGCTAGCCTTGAATCATCATATTGGCACCTT-
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTG
* * *
2512642 T-GTC-TT-AGTACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-
1 TCATCTTTAAGT-CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTG
* * *
2512689 TCATCTTTAAGACCACTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCG
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-G
** * * * * * * *
2512741 TCATCTTTAAAACCCAATGTTGTTGGCCTT-ATCTCAACACATTGG-A--AT-
1 TCATCTTT-AAGTCCAATATCGCTGGCCTTGA-ATCAGCATATTGGCACCTTG
* * * * * * * *
2512789 TCTTCTTCAAGTCTAACT-TCGCTGGCCATGAATCAGCACATTGTCATTCTTC
1 TCATCTTTAAGTCCAA-TATCGCTGGCCTTGAATCAGCATATTGGCA-CCTTG
* * *
2512841 TCATC-TTAAGCCCAATATCACTGGTCTTGAATCAGCATATTGGCACCTT
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
2512890 TATCACTCTT
Statistics
Matches: 227, Mismatches: 54, Indels: 36
0.72 0.17 0.11
Matches are distributed among these distances:
47 28 0.12
48 45 0.20
49 35 0.15
50 9 0.04
51 32 0.14
52 53 0.23
53 25 0.11
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.33
Consensus pattern (51 bp):
TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTG
Found at i:2512671 original size:100 final size:97
Alignment explanation
Indices: 2512009--2512738 Score: 276
Period size: 101 Copynumber: 7.4 Consensus size: 97
2511999 CGTCTTCTTC
* * * * * * *
2512009 TAAGTCCAATGTCGCTGGCCTAGAATCAGCACATTGGCACC--T-T-TAAG-ACCAATATCGCTG
1 TAAGACCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTAGTACCAATGTCGCTG
* ****
2512069 GCCTTGAATCAGCATATTGGCACCTTTGTTTT
66 GCCTTGAATCAGCACATTGGCACCTTCACCTT
* * * * * * * *
2512101 TAAGACCAATGTCGCTGGCCTTGAATCAGTACACTGGCACC--T-T-TAAGT-CCAATATTGCTG
1 TAAGACCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTAGTACCAATGTCGCTG
* *
2512161 GCCTTGAATCAGCATATTGGCACC-TCATCTT
66 GCCTTGAATCAGCACATTGGCACCTTCACCTT
* * * * ** *
2512192 GAAGACCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGT-CCAATATCGC
1 TAAGACCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTC-TT-AGTACCAATGTCGC
* ** *
2512256 TGGCCTTGAATCAGCATATTGGTGCCTTCGTCATCTT
64 TGGCCTTGAATCAGCACATTGGCACC-T--TCACCTT
* * * * * ** **
2512293 TCAA-ATCAATGTCGCTGGCCTTGAATCAGCACATTGACACCTTCATCCTTAAGT-CCAAAATCG
1 T-AAGACCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGT-CTT-AGTACCAATGTCG
* ** * * *
2512356 TTGGCCTTGAATCAGCGTATTGGCATCTTTAACATT
63 CTGGCCTTGAATCAGCACATTGGCA-CCTTCACCTT
* * * ** * ** * ** * ** *
2512392 CCTAAGCCCAATGTCACCGGCATTGCCTCAGCACATTGGCATTTTTCTCCAAGT-CTAAATGTCG
1 --TAAGACCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTAGTAC-CAATGTCG
* * * * *
2512456 CTGGCCATGAATCAACACATTGTCATTCTTCGCATCTT
63 CTGGCCTTGAATCAGCACATTGGCA-CCTT--CACCTT
* * * ** * * * **
2512494 CAAGCCCAATATTGCTAGCC--GCATATTGGC-TCCTT--TATCCTTTTTCTCATCTTTAAAACC
1 TAAGACCAATATCGCTAGCCTTG-A-ATCAGCAT-ATTGGCA-CC---TT-T-GTC-TTAGTACC
* * **
2512554 AATGTCGCTGGCCTTGAATTAGCATATTGGTGCCTATGTCACCTT
56 AATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCACCTT
* *
2512599 TAAGTCCAATATCGCTAGCCTTGAATCATCATATTGGCACCTTTGTCTTAGTACCAATGTCGCTG
1 TAAGACCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTAGTACCAATGTCGCTG
*
2512664 GCCTTGAATCAGCACATTGGCACCTTCATCTT
66 GCCTTGAATCAGCACATTGGCACCTTCACCTT
* * *
2512696 TAAGACCACTATCGCTGGCCTTGAATCAGCATATTGGCGCCTT
1 TAAGACCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTT
2512739 CGTCATCTTT
Statistics
Matches: 487, Mismatches: 112, Indels: 73
0.72 0.17 0.11
Matches are distributed among these distances:
91 40 0.08
92 78 0.16
94 1 0.00
96 1 0.00
97 80 0.16
98 3 0.01
99 8 0.02
100 84 0.17
101 114 0.23
102 10 0.02
103 3 0.01
104 3 0.01
105 53 0.11
106 6 0.01
107 3 0.01
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (97 bp):
TAAGACCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTAGTACCAATGTCGCTG
GCCTTGAATCAGCACATTGGCACCTTCACCTT
Found at i:2512834 original size:354 final size:353
Alignment explanation
Indices: 2512184--2512858 Score: 840
Period size: 354 Copynumber: 1.9 Consensus size: 353
2512174 ATATTGGCAC
* *
2512184 CTCATCTTGAAGACCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGTCCA
1 CTCATCTTGAAAACCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTCACCTTTAAGTCCA
* ** *
2512249 ATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTCGTCATCTTTCAAATCAATGTCGCTGGCCT
66 ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTC-TCATCTTTCAAACCAATGTCGCTGGCCT
* * *
2512314 TGAATCAGCACATTGACACCTTCATCCTTAAGTCCAAAATCGTTGGCCTTGAATCAGCGTATTGG
130 TGAATCAGCACATTGACACCTTCATCCTTAAGACCAAAATCGCTGGCCTTGAATCAGCATATTGG
* * * * * * *
2512379 CATCTTTAACATTCCTAAGCCCAATGTCACCGGCATTGCCTCAGCACATTGGCATTTTTCTCCAA
195 CACCTTCAACATTCCTAAACCCAATGTCACCGGCATTACCTCAACACATTGGAATTCTTCTCCAA
2512444 GTCTAAATGTCGCTGGCCATGAATCAACACATTGTCATTCTTCGCATCTTCAAGCCCAATATTGC
260 GTCTAAATGTCGCTGGCCATGAATCAACACATTGTCATTCTTCGCATCTT-AAGCCCAATATTGC
2512509 TAGCCGCATATTGGCTCCTTTATCCTTTTT
324 TAGCCGCATATTGGCTCCTTTATCCTTTTT
* * * * * **
2512539 CTCATCTTTAAAACCAATGTCGCTGGCCTTGAATTAGCATATTGGTGCCTATGTCACCTTTAAGT
1 CTCATCTTGAAAACCAATGTCGCTAGCCTTGAATCAACACATTGGCACC--T-TCACCTTTAAGT
* * *
2512604 CCAATATCGCTAGCCTTGAATCATCATATTGGCACCTT-T-GTC-TT-AGTACCAATGTCGCTGG
63 CCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCTCATCTTTCA-AACCAATGTCGCTGG
* * **
2512665 CCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCACTATCGCTGGCCTTGAATCAGCATAT
127 CCTTGAATCAGCACATTGACACCTTCATCCTTAAGACCAAAATCGCTGGCCTTGAATCAGCATAT
* ** * **** * *
2512730 TGGCGCCTTCGTCA-TCTTTAAAACCCAATGTTGTTGGCCTTATCTCAACACATTGGAATTCTTC
192 TGGCACCTTCAACATTC-CT-AAACCCAATGTCACCGGCATTACCTCAACACATTGGAATTCTTC
* * * *
2512794 TTCAAGTCTAACT-TCGCTGGCCATGAATCAGCACATTGTCATTCTTCTCATCTTAAGCCCAATA
255 TCCAAGTCTAAATGTCGCTGGCCATGAATCAACACATTGTCATTCTTCGCATCTTAAGCCCAATA
2512858 T
320 T
2512859 CACTGGTCTT
Statistics
Matches: 270, Mismatches: 44, Indels: 14
0.82 0.13 0.04
Matches are distributed among these distances:
353 14 0.05
354 122 0.45
355 87 0.32
356 1 0.00
357 1 0.00
358 45 0.17
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (353 bp):
CTCATCTTGAAAACCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTCACCTTTAAGTCCA
ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCTCATCTTTCAAACCAATGTCGCTGGCCTT
GAATCAGCACATTGACACCTTCATCCTTAAGACCAAAATCGCTGGCCTTGAATCAGCATATTGGC
ACCTTCAACATTCCTAAACCCAATGTCACCGGCATTACCTCAACACATTGGAATTCTTCTCCAAG
TCTAAATGTCGCTGGCCATGAATCAACACATTGTCATTCTTCGCATCTTAAGCCCAATATTGCTA
GCCGCATATTGGCTCCTTTATCCTTTTT
Found at i:2513588 original size:32 final size:32
Alignment explanation
Indices: 2513551--2513652 Score: 177
Period size: 32 Copynumber: 3.2 Consensus size: 32
2513541 TCAACGATTC
* * *
2513551 GTATCGATACAAAAATGTTGTATTGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
2513583 GTATCGATACATAAGTGTTGTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
2513615 GTATCGATACATAAGTGTTGTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
2513647 GTATCG
1 GTATCG
2513653 CTACGAAGCT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (32 bp):
GTATCGATACATAAGTGTTGTATCGATACAAT
Found at i:2513591 original size:13 final size:13
Alignment explanation
Indices: 2513569--2513625 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
2513559 ACAAAAATGT
*
2513569 TGTATTGATACAA
1 TGTATCGATACAA
2513582 TGTATCGATACATAA
1 TGTATCGATAC--AA
2513597 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2513614 TGTATCGATACA
1 TGTATCGATACA
2513626 TAAGTGTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2513606 original size:19 final size:19
Alignment explanation
Indices: 2513582--2513644 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
2513572 ATTGATACAA
2513582 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
2513601 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
2513614 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
2513633 TGTATCGATACA
1 TGTATCGATACA
2513645 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:2513715 original size:13 final size:13
Alignment explanation
Indices: 2513697--2513721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2513687 ATTACCTAAA
2513697 TGTATCGATACAT
1 TGTATCGATACAT
2513710 TGTATCGATACA
1 TGTATCGATACA
2513722 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2513774 original size:52 final size:52
Alignment explanation
Indices: 2513730--2513858 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 52
2513720 CACTGATCTT
2513730 TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATAAAA
* * * * * * * *
2513782 TATATCGATACATACAGGTAAATTTGCCCAGATATATTGATACATTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATAAAA
2513834 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2513859 TCATATTTCG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATAAAA
Found at i:2517203 original size:52 final size:51
Alignment explanation
Indices: 2517053--2517404 Score: 190
Period size: 52 Copynumber: 6.7 Consensus size: 51
2517043 GAAGAGTGCT
* * * * ** *
2517053 AATGTGCTGATTCTAGGTCAGCGACATTGGACATAAA-ATGATAAAGGTGCT
1 AATGTGCTGATTCAAGGCCAACGACATTGG-CTTAAAGATGATAAAAATGCC
* * * * * * *
2517104 AATATGTTGACTCATGGCCAACAACATCAGGCTTAAAGGTG-TGAAAAATGCC
1 AATGTGCTGATTCAAGGCCAACGACAT-TGGCTTAAAGATGAT-AAAAATGCC
*
2517156 AATGTGCTGATTCAAGGCCAGCGACATTAGGCTTAAAGATGATAAAAAGTGCC
1 AATGTGCTGATTCAAGGCCAACGACATT-GGCTTAAAGATGATAAAAA-TGCC
* ** * * * ***
2517209 AATATATTAATTCAAGGCCAACGATATTGGACTTAAAGA-CA-AAGTGTGCC
1 AATGTGCTGATTCAAGGCCAACGACATTGG-CTTAAAGATGATAAAAATGCC
* * * ** ***
2517259 AATGTGCTAATTCAAGGCCAACGACATTGGGTTTAAAAAAAATAATGGTGCC
1 AATGTGCTGATTCAAGGCCAACGACATT-GGCTTAAAGATGATAAAAATGCC
** * * *
2517311 AATAAGCTGATTCAAGGCCATCGATATTGGACTTAAAGAAATAAGATTTAACAAATACC
1 AATGTGCTGATTCAAGGCCAACGACATTGG-CTTAAAG--AT--GA--TAA-AAATGCC
*
2517370 AATGTGTTGATTCAAGGCCAACGACATTAGGCTTA
1 AATGTGCTGATTCAAGGCCAACGACATT-GGCTTA
2517405 GAAGGGTTAC
Statistics
Matches: 223, Mismatches: 59, Indels: 30
0.71 0.19 0.10
Matches are distributed among these distances:
50 34 0.15
51 32 0.14
52 85 0.38
53 35 0.16
54 1 0.00
56 1 0.00
58 3 0.01
59 30 0.13
60 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (51 bp):
AATGTGCTGATTCAAGGCCAACGACATTGGCTTAAAGATGATAAAAATGCC
Found at i:2517276 original size:50 final size:50
Alignment explanation
Indices: 2517152--2517351 Score: 186
Period size: 50 Copynumber: 3.9 Consensus size: 50
2517142 GTGTGAAAAA
* * * *
2517152 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGG-CTTAAAGATGATAAAAAG
1 TGCCAATATGCTAATTCAAGGCCAACGACATT-GGACTTAAAGA--A-AAAATG
** * * *
2517205 TGCCAATATATTAATTCAAGGCCAACGATATTGGACTTAAAGACAAAGTG
1 TGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTAAAGAAAAAATG
* ** *
2517255 TGCCAATGTGCTAATTCAAGGCCAACGACATTGGGTTTAAAAAAAATAATGG
1 TGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTAAAGAAAA-AAT-G
* * * *
2517307 TGCCAATAAGCTGATTCAAGGCCATCGATATTGGACTTAAAGAAA
1 TGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTAAAGAAA
2517352 TAAGATTTAA
Statistics
Matches: 118, Mismatches: 26, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
50 42 0.36
51 2 0.02
52 40 0.34
53 34 0.29
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (50 bp):
TGCCAATATGCTAATTCAAGGCCAACGACATTGGACTTAAAGAAAAAATG
Found at i:2517346 original size:102 final size:103
Alignment explanation
Indices: 2517152--2517349 Score: 265
Period size: 102 Copynumber: 1.9 Consensus size: 103
2517142 GTGTGAAAAA
* * * ** *
2517152 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTTAAAGATGATAAAAAGTGCCAATATATT
1 TGCCAATGTGCTAATTCAAGGCCAACGACATTAGGCTTAAAAAAAATAAAAAGTGCCAATATACT
2517217 AATTCAAGGCCAACGATATTGGACTTAAAGACAAAGTG
66 AATTCAAGGCCAACGATATTGGACTTAAAGACAAAGTG
* * **
2517255 TGCCAATGTGCTAATTCAAGGCCAACGACATTGGGTTTAAAAAAAAT-AATGGTGCCAATA-AGC
1 TGCCAATGTGCTAATTCAAGGCCAACGACATTAGGCTTAAAAAAAATAAAAAGTGCCAATATA-C
* *
2517318 TGATTCAAGGCCATCGATATTGGACTTAAAGA
65 TAATTCAAGGCCAACGATATTGGACTTAAAGA
2517350 AATAAGATTT
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
101 1 0.01
102 41 0.50
103 40 0.49
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (103 bp):
TGCCAATGTGCTAATTCAAGGCCAACGACATTAGGCTTAAAAAAAATAAAAAGTGCCAATATACT
AATTCAAGGCCAACGATATTGGACTTAAAGACAAAGTG
Found at i:2517490 original size:33 final size:32
Alignment explanation
Indices: 2517402--2518053 Score: 582
Period size: 33 Copynumber: 20.2 Consensus size: 32
2517392 GACATTAGGC
* * *
2517402 TTAG-AAGGGTTACCACCGACTTGTGCGGGCT
1 TTAGAAAGGGTTGCCATCGACTTGTGTGGGCT
* *
2517433 TTAAAGAAA-GGTTG-CA-CTGACTTGTGTGGACC
1 TT--AGAAAGGGTTGCCATC-GACTTGTGTGGGCT
2517465 TTAGAAAGGGGTTGCCATCGACTTGTGTGGGCT
1 TTAGAAA-GGGTTGCCATCGACTTGTGTGGGCT
* * *
2517498 TTAGAAAAAGGGGTGCCATCGATTTCTGTGGGCT
1 TTAG--AAAGGGTTGCCATCGACTTGTGTGGGCT
* * *
2517532 TTTGAAAAGGTTGCCA-CTAACTTGTGTGGGCT
1 TTAGAAAGGGTTGCCATC-GACTTGTGTGGGCT
* * * *
2517564 TTAGAAATGGGTTGCCACCAACTTGTGTAGACT
1 TTAGAAA-GGGTTGCCATCGACTTGTGTGGGCT
* * * *
2517597 TTAG-AAGGGATGCCAACCGACTTATGTGGACT
1 TTAGAAAGGGTTGCC-ATCGACTTGTGTGGGCT
*
2517629 TTAGAAA-GGTTGCCATCGACTTGTGTCGGCT
1 TTAGAAAGGGTTGCCATCGACTTGTGTGGGCT
* * * * *
2517660 TTAG-AAGGATTGTCACCAACTTGTGTGAGCT
1 TTAGAAAGGGTTGCCATCGACTTGTGTGGGCT
2517691 TCT-GAAAGGGGTTGCCATCGACTTGTGTGGGCT
1 T-TAGAAA-GGGTTGCCATCGACTTGTGTGGGCT
*
2517724 TTAGAGAAGGGTTGCCATCGACTTATGTGGGCT
1 TTAGA-AAGGGTTGCCATCGACTTGTGTGGGCT
*
2517757 TTAG-AAGGGTTACCA-CTGACTTGTGTGGGCT
1 TTAGAAAGGGTTGCCATC-GACTTGTGTGGGCT
*
2517788 TTAGAGAAGGGTTGCCATTGACTTGTGTGGGCT
1 TTAGA-AAGGGTTGCCATCGACTTGTGTGGGCT
*
2517821 TTATAGAAGGGTTGCCA-CTGACTTGTGTGGGCT
1 TTAGA-AAGGGTTGCCATC-GACTTGTGTGGGCT
* * * * *
2517854 TTTGAGAGGGGTTGCCACCAACTTGTATGGGCT
1 TTAGA-AAGGGTTGCCATCGACTTGTGTGGGCT
* **
2517887 TTAGAAAGGTGTTGCCACCGACTTGTACGGGCT
1 TTAGAAAGG-GTTGCCATCGACTTGTGTGGGCT
* * *
2517920 TTAGAGAATGGTTGCCATCGACTTATGTGAGCT
1 TTAGA-AAGGGTTGCCATCGACTTGTGTGGGCT
* * *
2517953 TTAGAGA-GGTTGTCACCGACTTGTGTGGGCT
1 TTAGAAAGGGTTGCCATCGACTTGTGTGGGCT
*
2517984 TTAGAGAAAGGTTGCCAT-GACTTGTGTGGGCT
1 TTAGA-AAGGGTTGCCATCGACTTGTGTGGGCT
* *
2518016 TTAG-AAGGATTGCCA-CTGAGTTGTGTGGGCT
1 TTAGAAAGGGTTGCCATC-GACTTGTGTGGGCT
2518047 TTA-AAAG
1 TTAGAAAG
2518054 AGGGTGCTAC
Statistics
Matches: 515, Mismatches: 72, Indels: 68
0.79 0.11 0.10
Matches are distributed among these distances:
30 17 0.03
31 119 0.23
32 100 0.19
33 241 0.47
34 35 0.07
35 3 0.01
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (32 bp):
TTAGAAAGGGTTGCCATCGACTTGTGTGGGCT
Found at i:2517760 original size:97 final size:97
Alignment explanation
Indices: 2517404--2518049 Score: 640
Period size: 97 Copynumber: 6.7 Consensus size: 97
2517394 CATTAGGCTT
* * * * * * *
2517404 AGAAGGGTTACCACCGACTTGTGCGGGCTTTAAAGAAAGGTTG-CACTGACTTGTGTGGACCTTA
1 AGAAGGGTTGCCATCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCTTTA
* *
2517468 GAAAGGGGTTGCCATCGACTTGTGTGGGCTTTAG
66 G-AA-GGGTTGCCACCAACTTGTGTGGGCTTTAG
* * * * * * *
2517502 AAAAAGGGGTGCCATCGATTTCTGTGGGCTTTTGA-AAAGGTTGCCACTAACTTGTGTGGGCTTT
1 -AGAAGGGTTGCCATCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCTTT
* *
2517566 AGAAATGGGTTGCCACCAACTTGTGTAGACTTT--
65 AG-AA-GGGTTGCCACCAACTTGTGTGGGCTTTAG
* * * * *
2517599 AGAAGGGATGCCAACCGACTTATGTGGACTTTAGA-AA-GGTTGCCA-TCGACTTGTGTCGGCTT
1 AGAAGGGTTGCC-ATCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACT-GACTTGTGTGGGCTT
* * *
2517661 TAGAAGGATTGTCACCAACTTGTGTGAGCTTCT-G
64 TAGAAGGGTTGCCACCAACTTGTGTGGGCTT-TAG
*
2517695 A-AAGGGGTTGCCATCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCA-TCGACTTATGTGGGCTT
1 AGAA-GGGTTGCCATCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACT-GACTTGTGTGGGCTT
* **
2517758 TAGAAGGGTTACCACTGACTTGTGTGGGCTTTAG
64 TAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
* *
2517792 AGAAGGGTTGCCATTGACTTGTGTGGGCTTTATAGAAGGGTTGCCACTGACTTGTGTGGGCTTTT
1 AGAAGGGTTGCCATCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGC-TTT
* *
2517857 GAGAGGGGTTGCCACCAACTTGTATGGGCTTTAG
65 -AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
* ** * * *
2517891 A-AAGGTGTTGCCACCGACTTGTACGGGCTTTAGAGAATGGTTGCCA-TCGACTTATGTGAGCTT
1 AGAAGG-GTTGCCATCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACT-GACTTGTGTGGGCTT
* *
2517954 TAG-AGAGGTTGTCACCGACTTGTGTGGGCTTTAG
64 TAGAAG-GGTTGCCACCAACTTGTGTGGGCTTTAG
* * *
2517988 AGAAAGGTTGCCAT-GACTTGTGTGGGCTTT--AGAAGGATTGCCACTGAGTTGTGTGGGCTTTA
1 AGAAGGGTTGCCATCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCTTTA
2518050 AAAGAGGGTG
Statistics
Matches: 457, Mismatches: 72, Indels: 41
0.80 0.13 0.07
Matches are distributed among these distances:
94 46 0.10
95 26 0.06
96 60 0.13
97 156 0.34
98 25 0.05
99 144 0.32
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.31
Consensus pattern (97 bp):
AGAAGGGTTGCCATCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACTGACTTGTGTGGGCTTTA
GAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
Found at i:2518080 original size:29 final size:29
Alignment explanation
Indices: 2518049--2518140 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 29
2518039 TGTGGGCTTT
*
2518049 AAAAGAGGGTGCTACAGAGTTATGGACTTA
1 AAAAG-GGGTGCCACAGAGTTATGGACTTA
*
2518079 AAAAGGGGTGCCACAGAGTTATGGACTTT
1 AAAAGGGGTGCCACAGAGTTATGGACTTA
* * * *
2518108 GAAA-GGGTGCCACGGTGTTGTGGACTTTA
1 AAAAGGGGTGCCACAGAGTTATGGAC-TTA
2518137 AAAA
1 AAAA
2518141 AGATGCCACC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
28 18 0.34
29 30 0.57
30 5 0.09
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.24
Consensus pattern (29 bp):
AAAAGGGGTGCCACAGAGTTATGGACTTA
Found at i:2518178 original size:31 final size:31
Alignment explanation
Indices: 2518108--2518198 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 31
2518098 TATGGACTTT
* * * *
2518108 GAAAGGGTGCCACGGTGTTGTGGACTTT-AA
1 GAAAGGATGCCACCGAGTCGTGGACTTTGAA
* *
2518138 -AAAAGATGCCACCGAGTCGTGGAATTTGAA
1 GAAAGGATGCCACCGAGTCGTGGACTTTGAA
* *
2518168 GAAAGGATGCCACTGAGTCATGGACTTTGAA
1 GAAAGGATGCCACCGAGTCGTGGACTTTGAA
2518199 AAGAGACACC
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 21 0.43
30 2 0.04
31 26 0.53
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (31 bp):
GAAAGGATGCCACCGAGTCGTGGACTTTGAA
Found at i:2519164 original size:13 final size:13
Alignment explanation
Indices: 2519146--2519171 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2519136 TACAACAAGT
2519146 ATGTATCGATACA
1 ATGTATCGATACA
2519159 ATGTATCGATACA
1 ATGTATCGATACA
2519172 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2524565 original size:21 final size:21
Alignment explanation
Indices: 2524532--2524576 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2524522 TTGCAAGTTG
*
2524532 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2524554 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2524574 AAA
1 AAA
2524577 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2526400 original size:15 final size:15
Alignment explanation
Indices: 2526380--2526410 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2526370 TAAAAATGTC
*
2526380 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2526395 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2526410 C
1 C
2526411 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2528449 original size:20 final size:20
Alignment explanation
Indices: 2528424--2528502 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
2528414 AATGTCCAAA
2528424 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
*
2528444 ATGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T-G--TTTCT
* *
2528469 ATGTATCGATACATTTTTTT
1 ATGTATCGATACATGTTTCT
*
2528489 TTGTATCGATACAT
1 ATGTATCGATACAT
2528503 TGTATCGATA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
20 29 0.59
22 1 0.02
23 2 0.04
25 17 0.35
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:2528507 original size:13 final size:13
Alignment explanation
Indices: 2528489--2528525 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2528479 ACATTTTTTT
2528489 TTGTATCGATACA
1 TTGTATCGATACA
2528502 TTGTATCGATACA
1 TTGTATCGATACA
*
2528515 CTGTATCGATA
1 TTGTATCGATA
2528526 TAGGGTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2531068 original size:13 final size:13
Alignment explanation
Indices: 2531050--2531076 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2531040 TACAGCAAGT
2531050 ATGTATCGATACA
1 ATGTATCGATACA
2531063 ATGTATCGATACA
1 ATGTATCGATACA
2531076 A
1 A
2531077 AAAAAATTGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2532652 original size:13 final size:13
Alignment explanation
Indices: 2532634--2532671 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2532624 CATTTTTCTT
2532634 TGTATCGATACAA
1 TGTATCGATACAA
*
2532647 TGTATCGATACAC
1 TGTATCGATACAA
2532660 TGTATCGATACA
1 TGTATCGATACA
2532672 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2533154 original size:21 final size:20
Alignment explanation
Indices: 2533106--2533146 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2533096 CCCCTAGGCA
* * *
2533106 GCACTACCAGGTCGCGACCG
1 GCACTCCCAGGTCACAACCG
2533126 GCACTCCCAGGTCACAACCG
1 GCACTCCCAGGTCACAACCG
2533146 G
1 G
2533147 GCAGTCCCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.22, C:0.41, G:0.27, T:0.10
Consensus pattern (20 bp):
GCACTCCCAGGTCACAACCG
Found at i:2534570 original size:39 final size:40
Alignment explanation
Indices: 2534515--2534595 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
2534505 TTTAATAAAA
*
2534515 GGGGAGAATGCGTGAATTTGCTAAAATTATCTT-ATTAAG
1 GGGGAGAATGCATGAATTTGCTAAAATTATCTTGATTAAG
* * *
2534554 GGGGAGAATGTATGAATTTGTTAAAATTATTTTGATTAAG
1 GGGGAGAATGCATGAATTTGCTAAAATTATCTTGATTAAG
2534594 GG
1 GG
2534596 AGAAAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (40 bp):
GGGGAGAATGCATGAATTTGCTAAAATTATCTTGATTAAG
Found at i:2535258 original size:13 final size:13
Alignment explanation
Indices: 2535240--2535265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2535230 TACACTAAGT
2535240 ATGTATCGATACA
1 ATGTATCGATACA
2535253 ATGTATCGATACA
1 ATGTATCGATACA
2535266 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2535263 original size:32 final size:33
Alignment explanation
Indices: 2535222--2535285 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2535212 TAGCCAAACT
* **
2535222 TGTATCGATACACTAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2535254 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2535286 TTAGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2537635 original size:79 final size:79
Alignment explanation
Indices: 2537499--2538003 Score: 821
Period size: 79 Copynumber: 6.4 Consensus size: 79
2537489 ATAAAATCGA
* *
2537499 GGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAGAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
* *
2537564 CTCGGAAATAACAG
66 CTCGAAAATAACGG
* *
2537578 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
2537643 CTCGGAAATAACGG
66 CTCGAAAATAACGG
* * *
2537657 GGTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
2537722 CTCGAAAATAATGG
66 CTCGAAAATAACGG
* * *
2537736 GGTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
2537801 CTCGAAAATAACGG
66 CTCGAAAATAACGG
* * *
2537815 GGTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGGTTGGATTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
2537880 CTCGAAAATAACGG
66 CTCGAAAATAACGG
* *
2537894 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTGTCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
*
2537959 CTCGGAAATAACGG
66 CTCGAAAATAACGG
*
2537973 GGTTGGAGTATCCCCGATTGTGAAAAATTGA
1 GGTTGGAGTATCCCCGATTATGAAAAATTGA
2538004 GAAACTTAAC
Statistics
Matches: 399, Mismatches: 27, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 399 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
CTCGAAAATAACGG
Found at i:2539257 original size:35 final size:35
Alignment explanation
Indices: 2539188--2539373 Score: 347
Period size: 35 Copynumber: 5.3 Consensus size: 35
2539178 CATTTGTATG
*
2539188 CATCATACCATGCCTTCATTTTT-TATTCCATGCC
1 CATCATTCCATGCCTTCATTTTTATATTCCATGCC
2539222 CATCATTCCATGCCTTCATTTTTATATTCCATGCC
1 CATCATTCCATGCCTTCATTTTTATATTCCATGCC
2539257 CATCATTCCATGCCTTCATTTTTATATTCCATGCC
1 CATCATTCCATGCCTTCATTTTTATATTCCATGCC
*
2539292 CATCATTCCATGCCTTCATTTTTTTATTCCATGCC
1 CATCATTCCATGCCTTCATTTTTATATTCCATGCC
2539327 CATCATTCCATGCCTTCATTTTTATATTCCATGCC
1 CATCATTCCATGCCTTCATTTTTATATTCCATGCC
2539362 CATCATTCCATG
1 CATCATTCCATG
2539374 TTTTTTTTAT
Statistics
Matches: 148, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
34 22 0.15
35 126 0.85
ACGTcount: A:0.20, C:0.32, G:0.06, T:0.42
Consensus pattern (35 bp):
CATCATTCCATGCCTTCATTTTTATATTCCATGCC
Found at i:2545570 original size:20 final size:20
Alignment explanation
Indices: 2545528--2545583 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2545518 AAATTTCCAG
**
2545528 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
2545548 ATGTATCGATACATTGAAT-A
1 ATGTATCGATACATTG-ATCA
*
2545568 ATGTATTGATACATTG
1 ATGTATCGATACATTG
2545584 CCTTGGCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:2547002 original size:70 final size:70
Alignment explanation
Indices: 2546914--2547053 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
2546904 GTTGACATCC
2546914 TGTCACTCTTAATCACGACATCTATCATTTCACTAGACCAAATCAATGAATTTCTTCGTGGCATT
1 TGTCACTCTTAATCACGACATCTATCATTTCACTAGACCAAATCAATGAATTTCTTCGTGGCATT
2546979 CCCTA
66 CCCTA
2546984 TGTCACTCTTAATCACGACATCTATCATTTCACTAGACCAAATCAATGAATTTCTTCGTGGCATT
1 TGTCACTCTTAATCACGACATCTATCATTTCACTAGACCAAATCAATGAATTTCTTCGTGGCATT
2547049 CCCTA
66 CCCTA
2547054 CAACTTTCTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (70 bp):
TGTCACTCTTAATCACGACATCTATCATTTCACTAGACCAAATCAATGAATTTCTTCGTGGCATT
CCCTA
Found at i:2553707 original size:13 final size:13
Alignment explanation
Indices: 2553689--2553714 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2553679 TACACAAAGT
2553689 ATGTATCGATACA
1 ATGTATCGATACA
2553702 ATGTATCGATACA
1 ATGTATCGATACA
2553715 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2553712 original size:32 final size:33
Alignment explanation
Indices: 2553671--2553734 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2553661 TAGCCAAACT
**
2553671 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2553703 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2553735 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2557195 original size:167 final size:166
Alignment explanation
Indices: 2556879--2557245 Score: 427
Period size: 167 Copynumber: 2.2 Consensus size: 166
2556869 TTCATGGGTT
*
2556879 TAAAATTTTTAAAATTTATCAAATATTATTATTTAATTTATATTAAATTATTTTTTAAAAATTAA
1 TAAAATTTTTAAAA-TTATCAAATATTATCATTTAATTTATATTAAATTATTTTTTAAAAATTAA
* * ***
2556944 TTCATTTTCATGGGTTTTTGAATTTTTTCTTTAAAATTTTCATGTTTTCAAAAAACGAAGTTTTC
65 TTCATTTTCATGAGTTTTAGAATTTTTTCTTTAAAATCCCCATGTTTTCAAAAAACGAAGTTTTC
** * *
2557009 TACTATGTAAATTTTTTTGGGGGGATTTT-TCTTAGTT
130 TACTACATAAATATTTTTGGGGGGATTTTCT-TTAGTC
** *
2557046 TTTAATTTTTAAAATTCATCAAATATTATCATTT-ATTTCATATTAAATTATTTTTTAAAAATTC
1 TAAAATTTTTAAAATT-ATCAAATATTATCATTTAATTT-ATATTAAATTATTTTTTAAAAATTA
* * * * **
2557110 ATTCATTTTCATGAGTTTTAGATTTTTTTGTTTGAAATCCCCCT-TTTCTCGAAAAATTG-AGTT
64 ATTCATTTTCATGAGTTTTAGAATTTTTTCTTTAAAATCCCCATGTTT-TC-AAAAAACGAAGTT
* * *
2557173 TTTTATTCCATAAATATTTTTGGGGGGATTTTCTTTAGTC
127 TTCTACTACATAAATATTTTTGGGGGGATTTTCTTTAGTC
* *
2557213 TAAAATTTTTAAAATGTATCTAATATTGTCATT
1 TAAAATTTTTAAAAT-TATCAAATATTATCATT
2557246 GAACTCCCAT
Statistics
Matches: 168, Mismatches: 26, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
166 9 0.05
167 151 0.90
168 8 0.05
ACGTcount: A:0.31, C:0.08, G:0.09, T:0.52
Consensus pattern (166 bp):
TAAAATTTTTAAAATTATCAAATATTATCATTTAATTTATATTAAATTATTTTTTAAAAATTAAT
TCATTTTCATGAGTTTTAGAATTTTTTCTTTAAAATCCCCATGTTTTCAAAAAACGAAGTTTTCT
ACTACATAAATATTTTTGGGGGGATTTTCTTTAGTC
Found at i:2557687 original size:31 final size:31
Alignment explanation
Indices: 2557646--2557715 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
2557636 TGGTTTTGGA
* *
2557646 AAATGAAAAAATGGAATATAAAAACAAAAAG
1 AAATGGAAAAATGGAACATAAAAACAAAAAG
*
2557677 AAATGGAAAAATGGAACATAAAAATAAAAAG
1 AAATGGAAAAATGGAACATAAAAACAAAAAG
2557708 AAATGGAA
1 AAATGGAA
2557716 TTTTTTGGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.69, C:0.03, G:0.16, T:0.13
Consensus pattern (31 bp):
AAATGGAAAAATGGAACATAAAAACAAAAAG
Found at i:2557859 original size:9 final size:9
Alignment explanation
Indices: 2557845--2557879 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
2557835 AAGAATACAA
2557845 AAAAAAAGG
1 AAAAAAAGG
2557854 AAAAAAAGG
1 AAAAAAAGG
2557863 AAGAAAAAGG
1 AA-AAAAAGG
*
2557873 GAAAAAA
1 AAAAAAA
2557880 CCGAGGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:2558791 original size:15 final size:15
Alignment explanation
Indices: 2558771--2558800 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2558761 ATGAAATTTC
2558771 AATAATAAGAAAAAA
1 AATAATAAGAAAAAA
*
2558786 AATAATAATAAAAAA
1 AATAATAAGAAAAAA
2558801 TTAATAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (15 bp):
AATAATAAGAAAAAA
Found at i:2559589 original size:155 final size:155
Alignment explanation
Indices: 2559391--2559677 Score: 400
Period size: 155 Copynumber: 1.9 Consensus size: 155
2559381 TCAAAGGTAT
* * *
2559391 CCCTTAAGGGCATTTTTGTAAATTTTTAGAACCAAGTCCTAGATTGTCATC-GAGT-CTGCTTTA
1 CCCTTAAGGGCATTTTAGTAAATTTTTAAAACCAAGTCCTAGATTGCCATCAG-GTCCT-CTTTA
* *
2559454 ATGCCGAAGGT-AGATATTTAGGATAGGTTCATCCCATTTTGTAATCCTTTTTAAGTCCTTTAGG
64 ATGCCGAAGGTGA-ATATTTAGGATAGGTTCATCCCATTTTGTAATCCTGTTTAAGTCCTTTAAG
2559518 GATATTGCGCACTTTACGTTGAAGATAA
128 GATATTGCGCACTTTACGTTGAAGATAA
* * * * * *
2559546 CCCTTAGGGGCATTTTAGTAATTTTTTAAAACTAAGTCCTAGATTGCCGTCAGGTCCTTTTTGAT
1 CCCTTAAGGGCATTTTAGTAAATTTTTAAAACCAAGTCCTAGATTGCCATCAGGTCCTCTTTAAT
* * *
2559611 GTCGAAGGTGAATATTTAGGATATGTTCATCCCATTTTGTAATTCTGTTTAAGTCCTTTAAGGAT
66 GCCGAAGGTGAATATTTAGGATAGGTTCATCCCATTTTGTAATCCTGTTTAAGTCCTTTAAGGAT
2559676 AT
131 AT
2559678 CGGGTTATCC
Statistics
Matches: 115, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
155 111 0.97
156 4 0.03
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (155 bp):
CCCTTAAGGGCATTTTAGTAAATTTTTAAAACCAAGTCCTAGATTGCCATCAGGTCCTCTTTAAT
GCCGAAGGTGAATATTTAGGATAGGTTCATCCCATTTTGTAATCCTGTTTAAGTCCTTTAAGGAT
ATTGCGCACTTTACGTTGAAGATAA
Found at i:2559864 original size:200 final size:201
Alignment explanation
Indices: 2559479--2559870 Score: 454
Period size: 201 Copynumber: 2.0 Consensus size: 201
2559469 ATTTAGGATA
*
2559479 GGTTCATCCCATTTTGTAATCCTTTTTAAGTCCTTTAGGGATATTGCGCACTTTACGTTGAAGAT
1 GGTTCATCCCATTTTGTAATCCTTTTTAAGTCCTTTAGGGATATTGCGCACTTTACGTCGAAGAT
* * **
2559544 AACCCTTAGGGGCATTTTAGTAATTTTTTAAAACTAAGTCCTAGATTGCCGTCAGGTCCTTTTTG
66 AACCCTTAGGGGCATTTTAGTAATTTTTTAAAACGAAGTCATAGATTGCCACCAGGTCCTTTTTG
* * ** * * * * *
2559609 ATGTCGAAGGTGAATATTTAGGATATGTTCATCCCATTTTGTAATTCTGTTTAAGTCCTTTAAGG
131 ATGCCAAAAATGAATATCTAGGATAGGTTCATCCCATTCTATAATACTGTTTAAGTCCTTTAAGG
2559674 ATATCG
196 ATATCG
*
2559680 GGTT-ATCCCATTTTGTAATCCTTTTTAAGTCCTTTAGGGATATTAG-GCATTTCTACGTCGAAG
1 GGTTCATCCCATTTTGTAATCCTTTTTAAGTCCTTTAGGGATATT-GCGCACTT-TACGTCGAAG
* * * * * *
2559743 ATATCTCCTTA-GGGCATTTTGGTAATTTTTTAGAACGAAGTCATAGGTTGTCACCGGGT-CTGC
64 ATAAC-CCTTAGGGGCATTTTAGTAATTTTTTAAAACGAAGTCATAGATTGCCACCAGGTCCT--
** * * * *
2559806 TTTT-ATGCCAAAAATGGGTATCTAGGGTAGGTTCATCTCA-TCTATAATACTTTTTAAGTCTTT
126 TTTTGATGCCAAAAATGAATATCTAGGATAGGTTCATCCCATTCTATAATACTGTTTAAGTCCTT
2559869 TA
191 TA
2559871 GGGGGTATCA
Statistics
Matches: 159, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
200 67 0.42
201 83 0.52
202 9 0.06
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.40
Consensus pattern (201 bp):
GGTTCATCCCATTTTGTAATCCTTTTTAAGTCCTTTAGGGATATTGCGCACTTTACGTCGAAGAT
AACCCTTAGGGGCATTTTAGTAATTTTTTAAAACGAAGTCATAGATTGCCACCAGGTCCTTTTTG
ATGCCAAAAATGAATATCTAGGATAGGTTCATCCCATTCTATAATACTGTTTAAGTCCTTTAAGG
ATATCG
Found at i:2563325 original size:17 final size:17
Alignment explanation
Indices: 2563294--2563328 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2563284 AATAATGAGA
2563294 ATTTGATGAGAATGATT
1 ATTTGATGAGAATGATT
2563311 ATTTAGATGAG-ATGATT
1 ATTT-GATGAGAATGATT
2563328 A
1 A
2563329 GCTTTACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (17 bp):
ATTTGATGAGAATGATT
Found at i:2565056 original size:162 final size:162
Alignment explanation
Indices: 2564873--2565170 Score: 483
Period size: 162 Copynumber: 1.8 Consensus size: 162
2564863 CGAAAGTGTT
*
2564873 AATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATAGG-AGCCCAAAAGG
1 AATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAAT-GGAAACCCAAAAGG
* ** * *
2564937 ATA-AGAAATGTTTTTGAAATCTTTTATACCTGTACAGATGCCCATAGGAATATAAAAGATTAGA
65 ATACA-AAAGGTTTTTGAAATCTTTTATACCCCTACAGATGCCCATAGAAATATAAAAGATTAAA
2565001 AAAAATAAATATTAGAATTTATCCCAAGAATACC
129 AAAAATAAATATTAGAATTTATCCCAAGAATACC
* *
2565035 AATTCAATTTAATTTTATTTATTTTCGAAAATGCCATTTCGTACCCTAATGGAAACCCGAAAGGA
1 AATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAACCCAAAAGGA
*
2565100 TACAAAAGGTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGAAATATAAAAGATTAAAAA
66 TACAAAAGGTTTTTGAAATCTTTTATACCCCTACAGATGCCCATAGAAATATAAAAGATTAAAAA
2565165 AAATAA
131 AAATAA
2565171 TAAACATGGA
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
161 2 0.02
162 122 0.98
163 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (162 bp):
AATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAACCCAAAAGGA
TACAAAAGGTTTTTGAAATCTTTTATACCCCTACAGATGCCCATAGAAATATAAAAGATTAAAAA
AAATAAATATTAGAATTTATCCCAAGAATACC
Found at i:2565977 original size:11 final size:11
Alignment explanation
Indices: 2565963--2566013 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2565953 TTTCTACCTA
2565963 TTTTCTTTCTT
1 TTTTCTTTCTT
* *
2565974 TTTTCTCTCTC
1 TTTTCTTTCTT
2565985 TTTTCTTTCTCT
1 TTTTCTTTCT-T
2565997 TTTT-TATGTCTT
1 TTTTCT-T-TCTT
2566009 TTTTC
1 TTTTC
2566014 AGCTGACCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 19 0.59
12 10 0.31
13 3 0.09
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:2566008 original size:22 final size:22
Alignment explanation
Indices: 2565951--2566010 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2565941 GTTTTTACTA
* *
2565951 TTTTTCTACCTATTTTCTTTCT
1 TTTTTCTATCTCTTTTCTTTCT
*
2565973 TTTTTCTCTCTCTTTTCTTTCT
1 TTTTTCTATCTCTTTTCTTTCT
*
2565995 CTTTTT-TATGTCTTTT
1 -TTTTTCTATCTCTTTT
2566011 TTCAGCTGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.05, C:0.22, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTTCTATCTCTTTTCTTTCT
Found at i:2573626 original size:19 final size:20
Alignment explanation
Indices: 2573602--2573654 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
2573592 CCAGATGTAA
**
2573602 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGCACAAT
2573621 TGTATCGATACATGCACAAT
1 TGTATCGATACATGCACAAT
*
2573641 TATATCGATACATG
1 TGTATCGATACATG
2573655 AAACTAGCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCACAAT
Found at i:2573648 original size:20 final size:19
Alignment explanation
Indices: 2573604--2573654 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
2573594 AGATGTAATG
** *
2573604 TATCGATACATGTTCATTG
1 TATCGATACATGCACATTA
2573623 TATCGATACATGCACAATTA
1 TATCGATACATGCAC-ATTA
2573643 TATCGATACATG
1 TATCGATACATG
2573655 AAACTAGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (19 bp):
TATCGATACATGCACATTA
Found at i:2577184 original size:14 final size:14
Alignment explanation
Indices: 2577165--2577192 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2577155 ACAAAAGATC
2577165 AATGTATCGATACA
1 AATGTATCGATACA
2577179 AATGTATCGATACA
1 AATGTATCGATACA
2577193 TTTGAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
AATGTATCGATACA
Found at i:2577269 original size:19 final size:19
Alignment explanation
Indices: 2577245--2577294 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
2577235 AGTGATACAT
2577245 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
2577264 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
2577283 TGTATCGATACA
1 TGTATCGATACA
2577295 GTTATGGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:2580657 original size:13 final size:13
Alignment explanation
Indices: 2580639--2580663 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2580629 CATAAAGTGT
2580639 TGTATCGATACAA
1 TGTATCGATACAA
2580652 TGTATCGATACA
1 TGTATCGATACA
2580664 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2580661 original size:33 final size:33
Alignment explanation
Indices: 2580619--2580685 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2580609 TTCAACGATT
2580619 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
2580652 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2580685 T
1 T
2580686 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2580815 original size:52 final size:52
Alignment explanation
Indices: 2580759--2580887 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2580749 CACTGATCTT
*
2580759 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
2580811 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2580863 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2580888 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2585034 original size:10 final size:10
Alignment explanation
Indices: 2585019--2585045 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2585009 TGCTAACTAA
2585019 GTTTTTGTTT
1 GTTTTTGTTT
2585029 GTTTTTGTTT
1 GTTTTTGTTT
2585039 GTTTTTG
1 GTTTTTG
2585046 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:2594747 original size:1 final size:1
Alignment explanation
Indices: 2594732--2594828 Score: 95
Period size: 1 Copynumber: 97.0 Consensus size: 1
2594722 GGCGTCCTCC
* * * * * * * *
2594732 AAAAAACAAACAAAAAAAAAACAAAAAAACAAAAAAAAAAACAAAAAAAAAACAAAAACAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
2594797 AAAAAAAAAAAAAACAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2594829 GGGGGTCCGG
Statistics
Matches: 74, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2594757 original size:6 final size:6
Alignment explanation
Indices: 2594739--2594826 Score: 108
Period size: 6 Copynumber: 14.5 Consensus size: 6
2594729 TCCAAAAAAC
*
2594739 AAACAA AAA-AA AAACAAAA AAACAA AAAAAA AAACAA AAA-AA AAACAA
1 AAACAA AAACAA AAAC--AA AAACAA AAACAA AAACAA AAACAA AAACAA
* *
2594787 AAACAA AAACAA AAAAAA AAAAAA CAAACAA AAACAA AAA
1 AAACAA AAACAA AAACAA AAACAA -AAACAA AAACAA AAA
2594827 AAGGGGGTCC
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
5 10 0.14
6 52 0.71
7 5 0.07
8 6 0.08
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:2594758 original size:23 final size:24
Alignment explanation
Indices: 2594732--2594828 Score: 125
Period size: 23 Copynumber: 4.2 Consensus size: 24
2594722 GGCGTCCTCC
2594732 AAAAAACAAACAAAAA-AAAAACA
1 AAAAAACAAACAAAAACAAAAACA
2594755 AAAAAAC--A-AAAAA-AAAAACA
1 AAAAAACAAACAAAAACAAAAACA
2594775 AAAAAA-AAACAAAAACAAAAACA
1 AAAAAACAAACAAAAACAAAAACA
* *
2594798 AAAAAAAAAAAAACAAACAAAAACA
1 AAAAAACAAACAA-AAACAAAAACA
2594823 AAAAAA
1 AAAAAA
2594829 GGGGGTCCGG
Statistics
Matches: 67, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
20 18 0.27
21 2 0.03
22 5 0.07
23 20 0.30
24 5 0.07
25 17 0.25
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (24 bp):
AAAAAACAAACAAAAACAAAAACA
Found at i:2594774 original size:31 final size:30
Alignment explanation
Indices: 2594732--2594828 Score: 135
Period size: 31 Copynumber: 3.2 Consensus size: 30
2594722 GGCGTCCTCC
*
2594732 AAAAAACAAACAAAAAAAAAACAAAAAAACA
1 AAAAAAAAAACAAAAAAAAAAC-AAAAAACA
2594763 AAAAAAAAAACAAAAAAAAAAC-AAAAACA
1 AAAAAAAAAACAAAAAAAAAACAAAAAACA
*
2594792 AAAACAAAAAAAAAAAAAACAAAC-AAAAACA
1 AAAA-AAAAAACAAAAAAA-AAACAAAAAACA
2594823 AAAAAA
1 AAAAAA
2594829 GGGGGTCCGG
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.18
30 15 0.24
31 36 0.58
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAACAAAAAAAAAACAAAAAACA
Found at i:2596378 original size:57 final size:56
Alignment explanation
Indices: 2596267--2596456 Score: 211
Period size: 59 Copynumber: 3.3 Consensus size: 56
2596257 CATTTATCAC
* * *** *
2596267 CCTTCAAAAGTCCACAAGTCAGTGGCATTTTTTTCAAAGCCCACAAGTCAGTGGCATT
1 CCTTTAAAAGCCCACAAGTCAGTGGCA-ACCTTTCAAAGCCCACAAGTCAGTGGCA-A
** *
2596325 TTTTTCAAAAGCCCACAAGTTAGTGGCAACC-TTCAAAGCCCACAAGTCAGTGGCAA
1 CCTTT-AAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGGCAA
*
2596381 CCTTTAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGATGCAAA
1 CCTTTAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTCAGTG--GC-AA
*
2596440 CCTCTCAAAAGCCCACA
1 CCT-TTAAAAGCCCACA
2596457 CAAGTTGGTG
Statistics
Matches: 112, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
55 24 0.21
56 23 0.21
57 24 0.21
58 4 0.04
59 25 0.22
60 12 0.11
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (56 bp):
CCTTTAAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGGCAA
Found at i:2596398 original size:28 final size:28
Alignment explanation
Indices: 2596267--2596456 Score: 202
Period size: 28 Copynumber: 6.6 Consensus size: 28
2596257 CATTTATCAC
* * *
2596267 CCTTCAAAAGTCCACAAGTCAGTGGCATT
1 CCTTTAAAAGCCCACAAGTCAGTGGCA-A
** * *
2596296 TTTTTCAAAGCCCACAAGTCAGTGGCATT
1 CCTTTAAAAGCCCACAAGTCAGTGGCA-A
** *
2596325 TTTTTCAAAAGCCCACAAGTTAGTGGCAA
1 CCTTT-AAAAGCCCACAAGTCAGTGGCAA
*
2596354 CC-TTCAAAGCCCACAAGTCAGTGGCAA
1 CCTTTAAAAGCCCACAAGTCAGTGGCAA
2596381 CCTTTAAAAGCCCACAAGTCAGTGGCAA
1 CCTTTAAAAGCCCACAAGTCAGTGGCAA
2596409 CCTTTAAAAGCCCACAAGTCAGTGATGCAAA
1 CCTTTAAAAGCCCACAAGTCAGTG--GC-AA
*
2596440 CCTCTCAAAAGCCCACA
1 CCT-TTAAAAGCCCACA
2596457 CAAGTTGGTG
Statistics
Matches: 141, Mismatches: 14, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
27 23 0.16
28 50 0.35
29 29 0.21
30 22 0.16
31 5 0.04
32 12 0.09
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (28 bp):
CCTTTAAAAGCCCACAAGTCAGTGGCAA
Found at i:2596612 original size:42 final size:42
Alignment explanation
Indices: 2596553--2596638 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
2596543 GCCTTCATAT
*
2596553 TTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCACC
1 TTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
* *
2596595 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1 TTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
2596637 TT
1 TT
2596639 TTCCATCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (42 bp):
TTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
Done.