Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 2 of 186
Found at i:472306 original size:10 final size:10
Alignment explanation
Indices: 472291--472316 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
472281 CGGCTAGTAA
472291 CAAACTTATT
1 CAAACTTATT
472301 CAAACTTATT
1 CAAACTTATT
472311 CAAACT
1 CAAACT
472317 CTTGGTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (10 bp):
CAAACTTATT
Found at i:475528 original size:21 final size:21
Alignment explanation
Indices: 475504--475575 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 21
475494 TATGAGTACG
475504 AAATGAACGTGTTGAATGGAA
1 AAATGAACGTGTTGAATGGAA
* * * *
475525 AAATAAAGGTGTGATAATATGAGTACG
1 AAATGAACGTGT--TGA-ATG-G-A-A
475552 AAATGAACGTGTTGAATGGAA
1 AAATGAACGTGTTGAATGGAA
475573 AAA
1 AAA
475576 CAAAGGTGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
21 13 0.35
22 1 0.03
23 3 0.08
24 6 0.16
25 3 0.08
26 1 0.03
27 10 0.27
ACGTcount: A:0.46, C:0.04, G:0.26, T:0.24
Consensus pattern (21 bp):
AAATGAACGTGTTGAATGGAA
Found at i:475563 original size:48 final size:48
Alignment explanation
Indices: 475492--475587 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
475482 TGAATAAAAA
*
475492 AATATGAGTACGAAATGAACGTGTTGAATGGAAAAATAAAGGTGTGAT
1 AATATGAGTACGAAATGAACGTGTTGAATGGAAAAACAAAGGTGTGAT
475540 AATATGAGTACGAAATGAACGTGTTGAATGGAAAAACAAAGGTGTGAT
1 AATATGAGTACGAAATGAACGTGTTGAATGGAAAAACAAAGGTGTGAT
475588 TCAATATGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.44, C:0.05, G:0.27, T:0.24
Consensus pattern (48 bp):
AATATGAGTACGAAATGAACGTGTTGAATGGAAAAACAAAGGTGTGAT
Found at i:476494 original size:140 final size:141
Alignment explanation
Indices: 476229--476514 Score: 412
Period size: 140 Copynumber: 2.0 Consensus size: 141
476219 ATACAAACTA
* *
476229 AATGAATAACTTAAAACTTTGAAGAGACTTTATCACCATATGGTTTGATGGAGCTATTAAAATCA
1 AATGAATAACTTAAAACTTTGAAGAGACTTTATCACCATACGGTCTGATGGAGCTATTAAAATCA
* * * * * * * *
476294 ACATAGGTTCCACTTCGGCTGTAGGAGTTTTGAGAGACTAAAATGGTGAATAGATCATTGGGTTC
66 ACACAAGTGCCACTTCAGCGGGAGGAGTTTTGAGAGACCAAAATGGTGAACAGATCATTGGGTTC
*
476359 AATTGTAAAAT
131 AATTGCAAAAT
* *
476370 AATGAATAACTT-AAACTTTGAAGAGACTTTATCACCATACGGTCTGATGGAGCTGTTAAGATCA
1 AATGAATAACTTAAAACTTTGAAGAGACTTTATCACCATACGGTCTGATGGAGCTATTAAAATCA
* * * *
476434 ACACAAGTGCCGCTTCAGCGGGAGGAGTTTTGATAGACCAAAATGGTGAACGGATCATTGGTTTC
66 ACACAAGTGCCACTTCAGCGGGAGGAGTTTTGAGAGACCAAAATGGTGAACAGATCATTGGGTTC
476499 AATTGCAAAAT
131 AATTGCAAAAT
476510 AATGA
1 AATGA
476515 TATGTTATGT
Statistics
Matches: 128, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
140 116 0.91
141 12 0.09
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (141 bp):
AATGAATAACTTAAAACTTTGAAGAGACTTTATCACCATACGGTCTGATGGAGCTATTAAAATCA
ACACAAGTGCCACTTCAGCGGGAGGAGTTTTGAGAGACCAAAATGGTGAACAGATCATTGGGTTC
AATTGCAAAAT
Found at i:479738 original size:22 final size:22
Alignment explanation
Indices: 479710--479755 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
479700 AGAGTCTTGG
479710 CCTAGGATAACATATACTTTGA
1 CCTAGGATAACATATACTTTGA
479732 CCTAGGATAACATATACTTTGA
1 CCTAGGATAACATATACTTTGA
479754 CC
1 CC
479756 ATCATATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (22 bp):
CCTAGGATAACATATACTTTGA
Found at i:480548 original size:54 final size:54
Alignment explanation
Indices: 480484--480594 Score: 222
Period size: 54 Copynumber: 2.1 Consensus size: 54
480474 CATTTTAATT
480484 ATTTTATACTTGTGTATGTTTCTATTCTTAATGCTCAAGTTTGGAACATAAGAA
1 ATTTTATACTTGTGTATGTTTCTATTCTTAATGCTCAAGTTTGGAACATAAGAA
480538 ATTTTATACTTGTGTATGTTTCTATTCTTAATGCTCAAGTTTGGAACATAAGAA
1 ATTTTATACTTGTGTATGTTTCTATTCTTAATGCTCAAGTTTGGAACATAAGAA
480592 ATT
1 ATT
480595 CTAGGGTTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (54 bp):
ATTTTATACTTGTGTATGTTTCTATTCTTAATGCTCAAGTTTGGAACATAAGAA
Found at i:481707 original size:25 final size:26
Alignment explanation
Indices: 481664--481715 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
481654 AACTTATTTA
*
481664 TACTAGACTTTTCCTGCAAGTAAAGT
1 TACTAGACTTTTCCTGCAAATAAAGT
* *
481690 TACTAGGC-TTTCTTGCAAATAAAGT
1 TACTAGACTTTTCCTGCAAATAAAGT
481715 T
1 T
481716 TTATTCCTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (26 bp):
TACTAGACTTTTCCTGCAAATAAAGT
Found at i:486603 original size:23 final size:22
Alignment explanation
Indices: 486577--486644 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 22
486567 GTACTTCTTT
486577 TTTTCTTTTTCTTTTTTCTTTCC
1 TTTT-TTTTTCTTTTTTCTTTCC
*
486600 TTTTTTTTCCCTTATTTTC-TTCC
1 TTTTTTTT-TCTT-TTTTCTTTCC
*
486623 TTTTTTATTCTTATTTTTCTTT
1 TTTTTTTTTC-T-TTTTTCTTT
486645 TTCTTTCCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 5 0.14
23 24 0.65
24 8 0.22
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTTTTTCTTTTTTCTTTCC
Found at i:486617 original size:24 final size:24
Alignment explanation
Indices: 486589--486644 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
486579 TTCTTTTTCT
486589 TTTTTCTTTCCTTTTTT-TTCCCTTA
1 TTTTTCTTTCCTTTTTTATT--CTTA
486614 -TTTTC-TTCCTTTTTTATTCTTA
1 TTTTTCTTTCCTTTTTTATTCTTA
486636 TTTTTCTTT
1 TTTTTCTTT
486645 TTCTTTCCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
22 4 0.14
23 15 0.54
24 9 0.32
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTCTTTCCTTTTTTATTCTTA
Found at i:487136 original size:60 final size:60
Alignment explanation
Indices: 487008--487133 Score: 209
Period size: 60 Copynumber: 2.1 Consensus size: 60
486998 ATCTCTTAAA
* *
487008 CCCCTCTCGTTTTTCTCCCCATTTTCCAACCACCATCAACCAACCTCCACCACTTCCCCT
1 CCCCTTTCATTTTTCTCCCCATTTTCCAACCACCATCAACCAACCTCCACCACTTCCCCT
*
487068 CCCCTTTCATTTTTCTCCCCATTTTCCAACCACCATCAACCAACCTCCGCC-CTTCCCCT
1 CCCCTTTCATTTTTCTCCCCATTTTCCAACCACCATCAACCAACCTCCACCACTTCCCCT
*
487127 TCCCTTT
1 CCCCTTT
487134 TCAACCTAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 14 0.23
60 48 0.77
ACGTcount: A:0.17, C:0.51, G:0.02, T:0.31
Consensus pattern (60 bp):
CCCCTTTCATTTTTCTCCCCATTTTCCAACCACCATCAACCAACCTCCACCACTTCCCCT
Found at i:487153 original size:49 final size:49
Alignment explanation
Indices: 487094--487192 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
487084 CCCCATTTTC
487094 CAACCACCATCAACCAACCTCCGCCCTTCCCCTTCCCTTTTCAACCTAA
1 CAACCACCATCAACCAACCTCCGCCCTTCCCCTTCCCTTTTCAACCTAA
*
487143 CAACCGCCATCAACCAACCTCCGCCCTTCCCCTTCCCTTTTCAACCTAA
1 CAACCACCATCAACCAACCTCCGCCCTTCCCCTTCCCTTTTCAACCTAA
487192 C
1 C
487193 CCACAAAGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.23, C:0.52, G:0.03, T:0.22
Consensus pattern (49 bp):
CAACCACCATCAACCAACCTCCGCCCTTCCCCTTCCCTTTTCAACCTAA
Found at i:487442 original size:41 final size:41
Alignment explanation
Indices: 487397--487485 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 41
487387 TTAATTTTTC
487397 ATTAAATTATTTATTAATCAAAATAATAAAACCAAAAGAAA
1 ATTAAATTATTTATTAATCAAAATAATAAAACCAAAAGAAA
*
487438 ATTAAATTATTTATTAATCAAAATGATAAAACCAAAAGAAA
1 ATTAAATTATTTATTAATCAAAATAATAAAACCAAAAGAAA
*
487479 ATAAAAT
1 ATTAAAT
487486 AAAAATTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.29
Consensus pattern (41 bp):
ATTAAATTATTTATTAATCAAAATAATAAAACCAAAAGAAA
Found at i:488374 original size:15 final size:15
Alignment explanation
Indices: 488354--488385 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
488344 TAAGTTCAAG
488354 TACCAATTTTATATT
1 TACCAATTTTATATT
488369 TACCAATTTTATATT
1 TACCAATTTTATATT
488384 TA
1 TA
488386 ACTCTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (15 bp):
TACCAATTTTATATT
Found at i:497358 original size:28 final size:28
Alignment explanation
Indices: 497318--497379 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
497308 AGTGCTCGGA
*
497318 GTGTGGATTAACTCCAGTCTCCTATCAG
1 GTGTGTATTAACTCCAGTCTCCTATCAG
497346 GTGTGTATTAACTCCAGTCTCCTATCAG
1 GTGTGTATTAACTCCAGTCTCCTATCAG
497374 GTGTGT
1 GTGTGT
497380 GTTTCTTGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (28 bp):
GTGTGTATTAACTCCAGTCTCCTATCAG
Found at i:497685 original size:27 final size:27
Alignment explanation
Indices: 497655--497852 Score: 252
Period size: 27 Copynumber: 7.3 Consensus size: 27
497645 TACTGAAATG
* * *
497655 CCCTCGATTTGTAGAATTATCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* * * *
497682 CCCTCGATTTATAGAATTATCGTTTCA
1 CCCTCGATTTATAAAATTACCATTTTA
* * *
497709 CCCTTGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* *
497736 CCCTCAATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
*
497763 CCCTCGATTTATAAAATTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
*
497790 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* *
497817 CCCTCAATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
497844 CCCTCGATT
1 CCCTCGATT
497853 GTGAAATTAC
Statistics
Matches: 151, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 151 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAAAATTACCATTTTA
Found at i:497770 original size:81 final size:81
Alignment explanation
Indices: 497655--497852 Score: 306
Period size: 81 Copynumber: 2.4 Consensus size: 81
497645 TACTGAAATG
* * * * * *
497655 CCCTCGATTTGTAGAATTATCATTTTACCCTCGATTTATAGAATTATCGTTTCACCCTTGATTTA
1 CCCTCAATTTATAGAATTACCATTTTACCCTCGATTTATAAAATTACCGTTTCACCCTCGATTTA
*
497720 CAAAATTACCGTTTTA
66 CAAAATTACCATTTTA
*
497736 CCCTCAATTTATAGAATTACCATTTTACCCTCGATTTATAAAATTACCGTTTTACCCTCGATTTA
1 CCCTCAATTTATAGAATTACCATTTTACCCTCGATTTATAAAATTACCGTTTCACCCTCGATTTA
497801 CAAAATTACCATTTTA
66 CAAAATTACCATTTTA
* *
497817 CCCTCAATTTACAAAATTACCATTTTACCCTCGATT
1 CCCTCAATTTATAGAATTACCATTTTACCCTCGATT
497853 GTGAAATTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 107 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.40
Consensus pattern (81 bp):
CCCTCAATTTATAGAATTACCATTTTACCCTCGATTTATAAAATTACCGTTTCACCCTCGATTTA
CAAAATTACCATTTTA
Found at i:497874 original size:27 final size:27
Alignment explanation
Indices: 497844--498034 Score: 142
Period size: 27 Copynumber: 7.1 Consensus size: 27
497834 TACCATTTTA
* * *
497844 CCCTCGATTGTGAAATTACTAAAATAC
1 CCCTAGATTGTAAAATTACCAAAATAC
* *
497871 CCCT-G-TAGGATAGAATTACCAAAATAC
1 CCCTAGAT-TG-TAAAATTACCAAAATAC
*
497898 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCTAGATTGTAAAATTACCAAAATAC
* * *
497925 CCCTAGTTTGTAAAATTATCGAAATAC
1 CCCTAGATTGTAAAATTACCAAAATAC
* ** * *
497952 CACTATTTTGTGAAATTACCGAAATA-
1 CCCTAGATTGTAAAATTACCAAAATAC
*
497978 CCTTCA-ATTTGTAAAATTACCAAAATAC
1 CCCT-AGA-TTGTAAAATTACCAAAATAC
*
498006 CCCT-GATT-TACAAAATTACAAAAATAC
1 CCCTAGATTGT--AAAATTACCAAAATAC
498033 CC
1 CC
498035 TTGACTTTCT
Statistics
Matches: 135, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
25 2 0.01
26 6 0.04
27 121 0.90
28 5 0.04
29 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
CCCTAGATTGTAAAATTACCAAAATAC
Found at i:498022 original size:54 final size:54
Alignment explanation
Indices: 497884--498088 Score: 146
Period size: 54 Copynumber: 3.8 Consensus size: 54
497874 TGTAGGATAG
* ** * *
497884 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACC-CCTAGTTTGTAA
1 AATTACCAAAATACCACTAGTTTACAAAATTACCAAAATACCTTC-AATTTGTAA
* * * *** *
497938 AATTATCGAAATACCACTATTTTGTGAAATTACCGAAATACCTTCAATTTGTAA
1 AATTACCAAAATACCACTAGTTTACAAAATTACCAAAATACCTTCAATTTGTAA
* * * * *
497992 AATTACCAAAATACCCCT-GATTTACAAAATTACAAAAATACCCTTGACTTTCTAA
1 AATTACCAAAATACCACTAG-TTTACAAAATTACCAAAATA-CCTTCAATTTGTAA
* * * * **
498047 AATTTA-TAGAATACCATTGGTTTACAAAATTACTGAAATACC
1 AA-TTACCAAAATACCACTAGTTTACAAAATTACCAAAATACC
498089 CTTGGTTTGT
Statistics
Matches: 120, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
54 76 0.63
55 40 0.33
56 4 0.03
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (54 bp):
AATTACCAAAATACCACTAGTTTACAAAATTACCAAAATACCTTCAATTTGTAA
Found at i:498180 original size:27 final size:27
Alignment explanation
Indices: 498137--498210 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
498127 AAATGACTAA
*
498137 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
498164 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
498191 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
498211 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:498214 original size:27 final size:27
Alignment explanation
Indices: 498150--498214 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
498140 ACCCCTAATA
*
498150 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
498177 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
498204 GGTAAAATGAC
1 GGTAAAATGAC
498215 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:498586 original size:19 final size:19
Alignment explanation
Indices: 498540--498587 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
498530 AGTTGGGCCT
** *
498540 CAATGGGCAGGAATTGGGC
1 CAATGGGCTTGAATTGGAC
498559 CAATGGGCTTGAATTGGAC
1 CAATGGGCTTGAATTGGAC
498578 CAATGGGCTT
1 CAATGGGCTT
498588 TTGGGCCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (19 bp):
CAATGGGCTTGAATTGGAC
Found at i:499076 original size:25 final size:24
Alignment explanation
Indices: 499042--499111 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 24
499032 AGGAAGTGCT
499042 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTCTGCCCCAGTTTACC
*
499066 GAAAAGGGCTCTGCCCCAGTTTATC
1 -AAAAGGGCTCTGCCCCAGTTTACC
*
499091 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTCTGCCCCAGTT
499112 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (24 bp):
AAAAGGGCTCTGCCCCAGTTTACC
Found at i:499124 original size:24 final size:24
Alignment explanation
Indices: 499041--499124 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
499031 GAGGAAGTGC
*
499041 TAAAAGGGCTCTGCCCCAGTTTACC
1 TAAAAGGGCTCTGCCCCAGTTTA-T
*
499066 GAAAAGGGCTCTGCCCCAGTTTAT
1 TAAAAGGGCTCTGCCCCAGTTTAT
* *
499090 CAGAAAGGGCTTTGCCCCAG-TTAT
1 TA-AAAGGGCTCTGCCCCAGTTTAT
499114 TAAAAGAGGCT
1 TAAAAG-GGCT
499125 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (24 bp):
TAAAAGGGCTCTGCCCCAGTTTAT
Found at i:499306 original size:42 final size:42
Alignment explanation
Indices: 499259--499350 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
499249 TAGTCACCCC
*
499259 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTA
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
*
499301 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
499343 AAATGGGC
1 AAATGGGC
499351 CTAAGGGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
Found at i:499409 original size:31 final size:31
Alignment explanation
Indices: 499381--499457 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
499371 AGTAAAGGTG
499381 TCGGCCCAGTGATATGATTTATGAAAAGGCT
1 TCGGCCCAGTGATATGATTTATGAAAAGGCT
*
499412 TCGGCCCAGTGATATGATTTATGGAAAGGCT
1 TCGGCCCAGTGATATGATTTATGAAAAGGCT
*
499443 TCGGCACAGT-ATATG
1 TCGGCCCAGTGATATG
499458 TCAAGACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 5 0.11
31 39 0.89
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (31 bp):
TCGGCCCAGTGATATGATTTATGAAAAGGCT
Found at i:503413 original size:66 final size:66
Alignment explanation
Indices: 503307--503440 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
503297 TGACTATTGT
*
503307 AAACTGAAAAACATATAGGATTTTTCCTATATAATTCATCACATTTTTACTTAAATTTGTTGTTA
1 AAACTGAAAAACATATAGGATTTTTCCTATATAATTCATCACATTTTTACTTAAATTTGTTGCTA
503372 A
66 A
* *
503373 AAACTGAAAAATATATAGGATTTTTCCTATATAATTCATCACCTTTTTACTTAAATTTGTTGCTA
1 AAACTGAAAAACATATAGGATTTTTCCTATATAATTCATCACATTTTTACTTAAATTTGTTGCTA
503438 A
66 A
503439 AA
1 AA
503441 CCAAGTAATT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (66 bp):
AAACTGAAAAACATATAGGATTTTTCCTATATAATTCATCACATTTTTACTTAAATTTGTTGCTA
A
Found at i:507292 original size:23 final size:23
Alignment explanation
Indices: 507266--507312 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
507256 AGTTTGAGAC
507266 TAAGCATACTCATATTAGTATAG
1 TAAGCATACTCATATTAGTATAG
507289 TAAGCATACTCATATTAGTATAG
1 TAAGCATACTCATATTAGTATAG
507312 T
1 T
507313 TCGGTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (23 bp):
TAAGCATACTCATATTAGTATAG
Found at i:515948 original size:15 final size:16
Alignment explanation
Indices: 515913--515960 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
515903 TAACGCTCTA
515913 AAAAATCCTGAAATCC
1 AAAAATCCTGAAATCC
*
515929 AAAAATCTTGAAATCC
1 AAAAATCCTGAAATCC
* *
515945 AAAAAGCCCGAAATCC
1 AAAAATCCTGAAATCC
515961 TGAATTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.08, T:0.17
Consensus pattern (16 bp):
AAAAATCCTGAAATCC
Found at i:517086 original size:8 final size:8
Alignment explanation
Indices: 517061--517103 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
517051 ATGTATCGGC
517061 AAAAGCCG
1 AAAAGCCG
517069 AAATA-CCG
1 AAA-AGCCG
*
517077 AAAAGTCG
1 AAAAGCCG
*
517085 AAATGCCG
1 AAAAGCCG
517093 AAAAGCCG
1 AAAAGCCG
517101 AAA
1 AAA
517104 GTTTGGCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 1 0.03
8 27 0.93
9 1 0.03
ACGTcount: A:0.51, C:0.21, G:0.21, T:0.07
Consensus pattern (8 bp):
AAAAGCCG
Found at i:517086 original size:16 final size:16
Alignment explanation
Indices: 517061--517103 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
517051 ATGTATCGGC
517061 AAAAGCCGAAATACCG
1 AAAAGCCGAAATACCG
* *
517077 AAAAGTCGAAATGCCG
1 AAAAGCCGAAATACCG
517093 AAAAGCCGAAA
1 AAAAGCCGAAA
517104 GTTTGGCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.51, C:0.21, G:0.21, T:0.07
Consensus pattern (16 bp):
AAAAGCCGAAATACCG
Found at i:517368 original size:29 final size:29
Alignment explanation
Indices: 517313--517412 Score: 121
Period size: 29 Copynumber: 3.5 Consensus size: 29
517303 GTGAGCATGA
* *
517313 ATATGAATGTGA-TTGGGCCTAACGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
*
517341 ATATAAATGTGATTTGGGCCTAATGGGCT
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* * *
517370 ATATACAGGTGATTTGGGCCTAATAGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* *
517399 ATATGAATATGATT
1 ATATAAATGTGATT
517413 AAGCTTAATG
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
28 11 0.18
29 49 0.82
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATGGGCC
Found at i:521009 original size:27 final size:27
Alignment explanation
Indices: 520978--521033 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
520968 TATTTATTTG
520978 ATTCATGCTTATAATGTTTGTGCCTCT
1 ATTCATGCTTATAATGTTTGTGCCTCT
521005 ATTCATGCTTATAATGTTTGTGCCTCT
1 ATTCATGCTTATAATGTTTGTGCCTCT
521032 AT
1 AT
521034 CGATCATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (27 bp):
ATTCATGCTTATAATGTTTGTGCCTCT
Found at i:523944 original size:93 final size:93
Alignment explanation
Indices: 523835--524006 Score: 265
Period size: 93 Copynumber: 1.8 Consensus size: 93
523825 GCCCATAAGT
* * * * *
523835 GAACTCGGACTCAACTCAAGGAGCTCAGG-CGTTCGCATCCATAAGTGAACTTGGACTCAACTTA
1 GAACTCAGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
523899 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
*
523928 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
523993 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
524007 CAAACATCCT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:524002 original size:46 final size:45
Alignment explanation
Indices: 523827--524001 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
523817 TGTAACCCGC
* *
523827 CCATAAGTGAACTCGGACTCAACTCAAGGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
* * *
523873 CCATAAGTGAACTTGGACTCAACTTAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** * *
523919 ACATCTCTCGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
*
523966 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
524002 ATGCCCAAAC
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 63 0.61
47 29 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:526441 original size:30 final size:30
Alignment explanation
Indices: 526406--526465 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
526396 CAAGAAAATC
*
526406 GAATAAAGAAATCCA-AGATAGAGAAACCCA
1 GAATAAAGAAATCCAGA-ATAAAGAAACCCA
526436 GAATAAAGAAATCCAGAATAAAGAAACCCA
1 GAATAAAGAAATCCAGAATAAAGAAACCCA
526466 AGATACGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.58, C:0.17, G:0.15, T:0.10
Consensus pattern (30 bp):
GAATAAAGAAATCCAGAATAAAGAAACCCA
Found at i:526445 original size:15 final size:15
Alignment explanation
Indices: 526406--526465 Score: 77
Period size: 15 Copynumber: 4.0 Consensus size: 15
526396 CAAGAAAATC
*
526406 GAATAAAGAAATCCA
1 GAATAAAGAAACCCA
*
526421 -AGATAGAGAAACCCA
1 GA-ATAAAGAAACCCA
*
526436 GAATAAAGAAATCCA
1 GAATAAAGAAACCCA
526451 GAATAAAGAAACCCA
1 GAATAAAGAAACCCA
526466 AGATACGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
14 1 0.03
15 36 0.95
16 1 0.03
ACGTcount: A:0.58, C:0.17, G:0.15, T:0.10
Consensus pattern (15 bp):
GAATAAAGAAACCCA
Found at i:540562 original size:47 final size:45
Alignment explanation
Indices: 540493--540715 Score: 195
Period size: 46 Copynumber: 4.8 Consensus size: 45
540483 AGGGTATAAT
* *
540493 GTCGATGCCATATCCCAGACATGGTCTTACGCTGGCTCATCCATCAA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-C-TCAA
* * **
540540 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTTGTA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-TCAA
* * *
540586 GTCGATG-CATGTCCTAGACAT-GTCTTACATTGGCTTACATCTCGA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CATCTCAA
* * *
540631 GCCCGATG-CATGTCCCAGACAT-ATCTTACACTGGCTCTCGTCTCAA
1 G-TCGATGCCATGTCCCAGACATGGTCTTACACTGG--CTCATCTCAA
* *
540677 TGCCAATGCCATG-CTCCAGACATGGTCTTACACTGGCTC
1 -GTCGATGCCATGTC-CCAGACATGGTCTTACACTGGCTC
540716 TCATAATGTG
Statistics
Matches: 146, Mismatches: 21, Indels: 19
0.78 0.11 0.10
Matches are distributed among these distances:
44 11 0.08
45 16 0.11
46 57 0.39
47 50 0.34
48 12 0.08
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.28
Consensus pattern (45 bp):
GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCTCAA
Found at i:547286 original size:16 final size:16
Alignment explanation
Indices: 547239--547280 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
547229 ATTGTAACGC
*
547239 CCCAAAAATTTCGAAA
1 CCCAAAAATCTCGAAA
*
547255 TCCAAAAATCTCGAAA
1 CCCAAAAATCTCGAAA
547271 CCCAAAAATC
1 CCCAAAAATC
547281 CTGAAATCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.50, C:0.29, G:0.05, T:0.17
Consensus pattern (16 bp):
CCCAAAAATCTCGAAA
Found at i:561390 original size:47 final size:48
Alignment explanation
Indices: 561315--561645 Score: 596
Period size: 49 Copynumber: 6.9 Consensus size: 48
561305 NNNNNNNNNN
*
561315 ATATATACACTTTCACATTCTTCACATCGGCCATTAGGCCTTATCAC-
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
*
561362 ATATATACACTTTCACATTCATCGCATCGGCCATTAGGCCTTATCACA
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
561410 TATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
1 -ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
561459 TATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
1 -ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
561508 TATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-
1 -ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
561556 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
561603 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
561646 CTATCATTTC
Statistics
Matches: 279, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
47 135 0.48
49 144 0.52
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (48 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
Found at i:563835 original size:191 final size:192
Alignment explanation
Indices: 563483--563864 Score: 739
Period size: 191 Copynumber: 2.0 Consensus size: 192
563473 CTCAAGCTTC
563483 AAGTGACCGAATGCTACCCTCCTATCTTCCTCTCTACAATCGGCCAAGAAGAACAAGGTGATAAC
1 AAGTGACCGAATGCTACCCTCCTATCTTCCTCTCTACAATCGGCCAAGAAGAACAAGGTGATAAC
563548 CTCCCTCTTTCTTTTTTTTTTCTTTTAGTATCCTTAGTATTTCTTTTATTATTTCTTTTCTTTTA
66 CTCCCTCTTTCTTTTTTTTTTCTTTTAGTATCCTTAGTATTTCTTTTATTATTTCTTTTCTTTTA
*
563613 CTTAAAATAATGGCCACTTCATGGAAATTTACCACATAGTCTAATATATGCTCCATCATGGT
131 CTTAAAATAATGACCACTTCATGGAAATTTACCACATAGTCTAATATATGCTCCATCATGGT
*
563675 AAGTGACCGAATGCTACCCTCCTATCTTCCTCTCTACAATCGGCCAAGAAGAACAAGGTGATAAT
1 AAGTGACCGAATGCTACCCTCCTATCTTCCTCTCTACAATCGGCCAAGAAGAACAAGGTGATAAC
563740 CTCCCTCTTTC-TTTTTTTTTCTTTTAGTATCCTTAGTATTTCTTTTATTATTTCTTTTCTTTTA
66 CTCCCTCTTTCTTTTTTTTTTCTTTTAGTATCCTTAGTATTTCTTTTATTATTTCTTTTCTTTTA
563804 CTTAAAATAATGACCACTTCATGGAAATTTACCACATAGTCTAATATATGCTCCATCATGG
131 CTTAAAATAATGACCACTTCATGGAAATTTACCACATAGTCTAATATATGCTCCATCATGG
563865 CCGGCCACTA
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
191 113 0.60
192 75 0.40
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.41
Consensus pattern (192 bp):
AAGTGACCGAATGCTACCCTCCTATCTTCCTCTCTACAATCGGCCAAGAAGAACAAGGTGATAAC
CTCCCTCTTTCTTTTTTTTTTCTTTTAGTATCCTTAGTATTTCTTTTATTATTTCTTTTCTTTTA
CTTAAAATAATGACCACTTCATGGAAATTTACCACATAGTCTAATATATGCTCCATCATGGT
Found at i:564660 original size:24 final size:23
Alignment explanation
Indices: 564625--564677 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
564615 TATGTATCGA
564625 CAAAAG-TCGAAATGCCAAAAAGT
1 CAAAAGCT-GAAATGCCAAAAAGT
*
564648 CGAAAAGCTGAAATGCCGAAAAGT
1 C-AAAAGCTGAAATGCCAAAAAGT
564672 CAAAAG
1 CAAAAG
564678 TTTGGCTACG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 6 0.22
24 20 0.74
25 1 0.04
ACGTcount: A:0.51, C:0.17, G:0.21, T:0.11
Consensus pattern (23 bp):
CAAAAGCTGAAATGCCAAAAAGT
Found at i:564942 original size:29 final size:28
Alignment explanation
Indices: 564886--565000 Score: 113
Period size: 29 Copynumber: 4.0 Consensus size: 28
564876 GTGAGCATGA
* * *
564886 ATATGAATGTGACTGGGCCTAACGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
*
564914 ATATAAATGTGATTTGGGCCTAATAGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * * *
564943 ATATACAGGTGATTTAGGCCTAATGGACC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * *
564972 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
565000 A
1 A
565001 GATACAGGTA
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
28 25 0.36
29 45 0.64
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:565008 original size:57 final size:58
Alignment explanation
Indices: 564901--565009 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 58
564891 AATGTGACTG
* * *
564901 GGCCTAACGGGCCATATAAATGTGATTTGGGCCTAATAGGCCATATACAGGTGATTTA
1 GGCCTAACGGACCATATAAATATGATTTGGGCCTAATAGGCCAGATACAGGTGATTTA
* * * *
564959 GGCCTAATGGACCATATGAATATGA-TTGGGCTTAATGGGCCAGATACAGGT
1 GGCCTAACGGACCATATAAATATGATTTGGGCCTAATAGGCCAGATACAGGT
565010 ATGTGAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 23 0.52
58 21 0.48
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.27
Consensus pattern (58 bp):
GGCCTAACGGACCATATAAATATGATTTGGGCCTAATAGGCCAGATACAGGTGATTTA
Found at i:568692 original size:24 final size:24
Alignment explanation
Indices: 568658--568703 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
568648 ATGTATCGGC
*
568658 AAAAGCCGAAATTCCAAAAAGCCG
1 AAAAGCCGAAATGCCAAAAAGCCG
*
568682 AAAAGCTGAAATGCCAAAAAGC
1 AAAAGCCGAAATGCCAAAAAGC
568704 TAAAAGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.22, G:0.17, T:0.09
Consensus pattern (24 bp):
AAAAGCCGAAATGCCAAAAAGCCG
Found at i:571768 original size:79 final size:81
Alignment explanation
Indices: 571659--571841 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
571649 TACTCGTTCA
* *
571659 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
571722 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
571739 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
571802 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
571818 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
571842 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:571841 original size:40 final size:40
Alignment explanation
Indices: 571638--571841 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
571628 CGGAATTTAA
** *
571638 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
571678 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
571718 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
571757 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
571797 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
571837 CCGGA
1 CCGGA
571842 CATCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 95 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:589967 original size:29 final size:29
Alignment explanation
Indices: 589932--590031 Score: 121
Period size: 29 Copynumber: 3.5 Consensus size: 29
589922 AATGTGAGTA
*
589932 GGCCTAACGGGCCATATAAATGTGATTTG
1 GGCCTAATGGGCCATATAAATGTGATTTG
* * *
589961 GGCCTAATAGGCCATATACAGGTGATTTG
1 GGCCTAATGGGCCATATAAATGTGATTTG
* * *
589990 GGCCTAATGGGCCATATGAATATGA-TTA
1 GGCCTAATGGGCCATATAAATGTGATTTG
*
590018 GGCTTAATGGGCCA
1 GGCCTAATGGGCCA
590032 GATACAGGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
28 15 0.25
29 45 0.75
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (29 bp):
GGCCTAATGGGCCATATAAATGTGATTTG
Found at i:590002 original size:58 final size:57
Alignment explanation
Indices: 589932--590040 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 57
589922 AATGTGAGTA
* * *
589932 GGCCTAACGGGCCATATAAATGTGATTTGGGCCTAATAGGCCATATACAGGTGATTTG
1 GGCCTAACGGGCCATATAAATATGA-TTAGGCCTAATAGGCCAGATACAGGTGATTTG
* * * *
589990 GGCCTAATGGGCCATATGAATATGATTAGGCTTAATGGGCCAGATACAGGT
1 GGCCTAACGGGCCATATAAATATGATTAGGCCTAATAGGCCAGATACAGGT
590041 ATGTGAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 22 0.50
58 22 0.50
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (57 bp):
GGCCTAACGGGCCATATAAATATGATTAGGCCTAATAGGCCAGATACAGGTGATTTG
Found at i:590620 original size:21 final size:21
Alignment explanation
Indices: 590578--590620 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
590568 ATAAGGCTTC
*
590578 ATTATTATTATTATCTGGATT
1 ATTATTATTATTATCTGAATT
*
590599 ATTATTATTTTTAT-TGTAATT
1 ATTATTATTATTATCTG-AATT
590620 A
1 A
590621 CGAGAAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (21 bp):
ATTATTATTATTATCTGAATT
Found at i:593021 original size:43 final size:43
Alignment explanation
Indices: 592952--593034 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
592942 TATTTGGGAT
**** *
592952 ATGGCATCAATATGAGATTTTGTGTAAGACTATAGCTGGGCTA
1 ATGGCATCAATATGAGATCCCATGTAAGACCATAGCTGGGCTA
*
592995 ATGGCATCAATATGAGATCCCATGTAAGACCATATCTGGG
1 ATGGCATCAATATGAGATCCCATGTAAGACCATAGCTGGG
593035 ATATGGCGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (43 bp):
ATGGCATCAATATGAGATCCCATGTAAGACCATAGCTGGGCTA
Found at i:600286 original size:24 final size:25
Alignment explanation
Indices: 600240--600286 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
600230 ATAAGTGAGT
* **
600240 TAAAAACTAAAAATTAACTAATTAA
1 TAAAAACTAAAAAGTAAAAAATTAA
600265 TAAAAA-TAAAAAGTAAAAAATT
1 TAAAAACTAAAAAGTAAAAAATT
600287 CCAATGCACG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (25 bp):
TAAAAACTAAAAAGTAAAAAATTAA
Found at i:611429 original size:40 final size:40
Alignment explanation
Indices: 611376--611687 Score: 509
Period size: 40 Copynumber: 7.8 Consensus size: 40
611366 TATTACCACA
* * * *
611376 AGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATC-ACT
* * *
611416 CGCACGAATGCCTTCGGGTCTTAGCCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
611456 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
611496 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
611536 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
611576 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
611616 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
* * * *
611656 AGCATAAATGCCTTCGGGACTTAGCCCAGATA
1 AGCACAAATGCCTTCGGGTCTTAACCCGGATA
611688 TCATTCAAAT
Statistics
Matches: 257, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 254 0.99
41 3 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAACCCGGATAAAATCACT
Found at i:619556 original size:40 final size:40
Alignment explanation
Indices: 619512--619773 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
619502 GCTCCTCGTT
* *
619512 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
619552 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
619592 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
619631 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
619670 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
619709 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
619750 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
619774 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:624026 original size:262 final size:262
Alignment explanation
Indices: 623559--624084 Score: 1016
Period size: 262 Copynumber: 2.0 Consensus size: 262
623549 TCGTTTAAAA
*
623559 AGCCCAATTTTATTAAGCCTCTTTGATCTAAAACGTTATTAATTTCAAAATCTCATTTGTAGCGA
1 AGCCCAACTTTATTAAGCCTCTTTGATCTAAAACGTTATTAATTTCAAAATCTCATTTGTAGCGA
*
623624 AAGCTTTTCAAAATAGTTGCGTACTAGCGACTACTTGTAAAACGTTATTTTCTTGTGGTAGCTCT
66 AAGCTTTTCAAAATAGTTGCGTACTAGAGACTACTTGTAAAACGTTATTTTCTTGTGGTAGCTCT
623689 TAAAATCATTTATGTATTCGTGATATTTTTGAAAACATTTGTCTTTTTGAAAACCCGCGTGTTTT
131 TAAAATCATTTATGTATTCGTGATATTTTTGAAAACATTTGTCTTTTTGAAAACCCGCGTGTTTT
* *
623754 TCCTACTACTGGCAGTATTAAAGCAAAAAAAATATATGTTCCCCCAAATTAAAAATAAAATAGAG
196 TCCAACTACTGGCAATATTAAAGCAAAAAAAATATATGTTCCCCCAAATTAAAAATAAAATAGAG
623819 AG
261 AG
623821 AGCCCAACTTTATTAAGCCTCTTTGATCTAAAACGTTATTAATTTCAAAATCTCATTTGTAGCGA
1 AGCCCAACTTTATTAAGCCTCTTTGATCTAAAACGTTATTAATTTCAAAATCTCATTTGTAGCGA
623886 AAGCTTTTCAAAATAGTTGCGTACTAGAGACTACTTGTAAAACGTTATTTTCTTGTGGTAGCTCT
66 AAGCTTTTCAAAATAGTTGCGTACTAGAGACTACTTGTAAAACGTTATTTTCTTGTGGTAGCTCT
623951 TAAAATCATTTATGTATTCGTGATATTTTTGAAAACATTTGTCTTTTTGAAAACCCGCGTGTTTT
131 TAAAATCATTTATGTATTCGTGATATTTTTGAAAACATTTGTCTTTTTGAAAACCCGCGTGTTTT
624016 TCCAACTACTGGCAATATTAAAGCAAAAAAAATATATGTTCCCCCAAATTAAAAATAAAATAGAG
196 TCCAACTACTGGCAATATTAAAGCAAAAAAAATATATGTTCCCCCAAATTAAAAATAAAATAGAG
624081 AG
261 AG
624083 AG
1 AG
624085 GCCTTATTAC
Statistics
Matches: 260, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
262 260 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (262 bp):
AGCCCAACTTTATTAAGCCTCTTTGATCTAAAACGTTATTAATTTCAAAATCTCATTTGTAGCGA
AAGCTTTTCAAAATAGTTGCGTACTAGAGACTACTTGTAAAACGTTATTTTCTTGTGGTAGCTCT
TAAAATCATTTATGTATTCGTGATATTTTTGAAAACATTTGTCTTTTTGAAAACCCGCGTGTTTT
TCCAACTACTGGCAATATTAAAGCAAAAAAAATATATGTTCCCCCAAATTAAAAATAAAATAGAG
AG
Found at i:633213 original size:40 final size:42
Alignment explanation
Indices: 633123--633228 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 42
633113 CAATATTTTT
* *
633123 AGTGTGCATGCTTAACATGCAAATCAGATTTATAATCAACAC
1 AGTGAGCATGCTTAACATGCAAATCAGAATTATAATCAACAC
* * * ***
633165 AATCAGCATGCTTAACATGCGAATC-GAATT-TAATCAGTTC
1 AGTGAGCATGCTTAACATGCAAATCAGAATTATAATCAACAC
*
633205 AGTGAGCATGCTTAAGATGCAAAT
1 AGTGAGCATGCTTAACATGCAAAT
633229 GATATCTCAA
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 27 0.52
41 4 0.08
42 21 0.40
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (42 bp):
AGTGAGCATGCTTAACATGCAAATCAGAATTATAATCAACAC
Found at i:636800 original size:27 final size:27
Alignment explanation
Indices: 636763--636831 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
636753 TAAATTGTGC
*
636763 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATAT
* *
636790 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATAT
*
636817 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
636832 GACTTAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATAT
Found at i:636842 original size:27 final size:27
Alignment explanation
Indices: 636763--636844 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
636753 TAAATTGTGC
* *
636763 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGAATATAT
* *
636790 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGAATATAT
* *
636817 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GAATTGAATATAT
636844 A
1 A
636845 TTCTTGAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
27 44 0.92
28 4 0.08
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGAATATAT
Found at i:636966 original size:44 final size:44
Alignment explanation
Indices: 636819--636966 Score: 106
Period size: 44 Copynumber: 3.3 Consensus size: 44
636809 GATTATATAG
* *
636819 CACTGAGTGTGCGGACTTAATATATATTCTTGAATCAATATGGA
1 CACTAAGTGTGCGGACTTAATATATATTCTTGAATCATTATGGA
* * ** ** * *
636863 CACTAAGTGTGC-GACACTATTGAGTCGA-TCACGGACAGCGGATT-TAG-
1 CACTAAGTGTGCGGAC-TTAAT-A-TATATTC-TTGA-ATC--ATTATGGA
*
636910 CACTGAGTGTGCGGACTTAATATATATTCTTGAATCATTATGGA
1 CACTAAGTGTGCGGACTTAATATATATTCTTGAATCATTATGGA
636954 CACTAAGTGTGCG
1 CACTAAGTGTGCG
636967 ACACTATTGA
Statistics
Matches: 73, Mismatches: 20, Indels: 22
0.63 0.17 0.19
Matches are distributed among these distances:
42 3 0.04
43 5 0.07
44 28 0.38
45 7 0.10
46 7 0.10
47 16 0.22
48 5 0.07
49 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (44 bp):
CACTAAGTGTGCGGACTTAATATATATTCTTGAATCATTATGGA
Found at i:636971 original size:91 final size:91
Alignment explanation
Indices: 636816--636996 Score: 353
Period size: 91 Copynumber: 2.0 Consensus size: 91
636806 GTTGATTATA
636816 TAGCACTGAGTGTGCGGACTTAATATATATTCTTGAATCAATATGGACACTAAGTGTGCGACACT
1 TAGCACTGAGTGTGCGGACTTAATATATATTCTTGAATCAATATGGACACTAAGTGTGCGACACT
636881 ATTGAGTCGATCACGGACAGCGGATT
66 ATTGAGTCGATCACGGACAGCGGATT
*
636907 TAGCACTGAGTGTGCGGACTTAATATATATTCTTGAATCATTATGGACACTAAGTGTGCGACACT
1 TAGCACTGAGTGTGCGGACTTAATATATATTCTTGAATCAATATGGACACTAAGTGTGCGACACT
636972 ATTGAGTCGATCACGGACAGCGGAT
66 ATTGAGTCGATCACGGACAGCGGAT
636997 CGGGTAAGTA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (91 bp):
TAGCACTGAGTGTGCGGACTTAATATATATTCTTGAATCAATATGGACACTAAGTGTGCGACACT
ATTGAGTCGATCACGGACAGCGGATT
Found at i:639021 original size:50 final size:49
Alignment explanation
Indices: 638896--639471 Score: 296
Period size: 50 Copynumber: 11.6 Consensus size: 49
638886 GCAGTGAAGT
* * * * * *
638896 AGATTAAAGCCATAACGGTGAATCTTACTTTCTCTGACATTGCGGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTAC-CTCTCAGGCGTTGCAG-TAAAA
* * * ** * *
638947 AGATTAAAGCTACATCAGCAAATCTTACCTCTCAGGCGGTTG-AGTGGAAT
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGC-GTTGCAGT-AAAA
* * * *
638997 AGATTAAAGCCACAACGGTGAATCTTACCTCTCTGACATTGCGGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAG-TAAAA
* * * * * *
639047 AGATTAAAGCTACAACAGCGAATCTTATCTCCCAAGCAG-TGCAGTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGC-GTTGCAGTAAAA
* * * * *
639096 AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGGCATTGCGATTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGC-AGTAAAA
* *** * * * * **
639146 AGATTAAAGCTACAGTAGCGAATCTTATCTCCCAGGTGGAGCAGTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAGTAAAA
* * * * *
639195 AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGGCATTGCGATTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGC-AGTAAAA
* *** * * * * **
639245 AGATTAAAGCTACAGTAGCGAATCTTATCTCCCAGGTGGAGCAGTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAGTAAAA
* * * * *
639294 AGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGC-GATCAAAA
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAG-T-AAAA
* * * * * * * * *
639344 AGATTAAAGCTACAGCAGCGAATCTTACCTCCCAAGCGATGCAGTGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAGT-AAAA
* * *** * * * *
639394 AGATTAAATCCA-AATTGGTGAATCTTGTTTCTCCGACATTACAGTTAAAA
1 AGATTAAAGCCACAA-CGGTGAATCTTACCTCTCAGGCGTTGCAG-TAAAA
* * *
639444 ATATTAAAGCCACAATGGCGAATCTTAC
1 AGATTAAAGCCACAACGGTGAATCTTAC
639472 TTTCCAAAAG
Statistics
Matches: 372, Mismatches: 139, Indels: 29
0.69 0.26 0.05
Matches are distributed among these distances:
48 1 0.00
49 111 0.30
50 230 0.62
51 30 0.08
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (49 bp):
AGATTAAAGCCACAACGGTGAATCTTACCTCTCAGGCGTTGCAGTAAAA
Found at i:639148 original size:99 final size:99
Alignment explanation
Indices: 638896--639453 Score: 685
Period size: 99 Copynumber: 5.6 Consensus size: 99
638886 GCAGTGAAGT
* * * *
638896 AGATTAAAGCCATAACGGTGAATCTTACTTTCTCTGACATTGCGGTTAAAAAGATTAAAGCTACA
1 AGATTAAAGCCACAACGGTGAATCTTGCCTT-TCTGACATTGCGATTAAAAAGATTAAAGCTACA
* * * * * *
638961 TCAGCAAATCTTACCTCTCAGGCGGTTG-AGTGGAAT
65 GCAGCGAATCTTATCTCCCAGGCGG-TGCAGT-AAAA
* * * *
638997 AGATTAAAGCCACAACGGTGAATCTTACCTCTCTGACATTGCGGTTAAAAAGATTAAAGCTACAA
1 AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGACATTGCGATTAAAAAGATTAAAGCTACAG
* *
639062 CAGCGAATCTTATCTCCCAAGCAGTGCAGTAAAA
66 CAGCGAATCTTATCTCCCAGGCGGTGCAGTAAAA
*
639096 AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGGCATTGCGATTAAAAAGATTAAAGCTACAG
1 AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGACATTGCGATTAAAAAGATTAAAGCTACAG
* * *
639161 TAGCGAATCTTATCTCCCAGGTGGAGCAGTAAAA
66 CAGCGAATCTTATCTCCCAGGCGGTGCAGTAAAA
*
639195 AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGGCATTGCGATTAAAAAGATTAAAGCTACAG
1 AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGACATTGCGATTAAAAAGATTAAAGCTACAG
* * *
639260 TAGCGAATCTTATCTCCCAGGTGGAGCAGTAAAA
66 CAGCGAATCTTATCTCCCAGGCGGTGCAGTAAAA
** *
639294 AGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACATTGCGATCAAAAAGATTAAAGCTACAG
1 AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGACATTGCGATTAAAAAGATTAAAGCTACAG
* * * * *
639359 CAGCGAATCTTACCTCCCAAGCGATGCAGTGGAAC
66 CAGCGAATCTTATCTCCCAGGCGGTGCAGT-AAAA
* * * *
639394 AGATTAAATCCA-AATTGGTGAATCTTG--TTTCTCCGACATTAC-AGTTAAAAATATTAAAGC
1 AGATTAAAGCCACAA-CGGTGAATCTTGCCTTTCT--GACATTGCGA-TTAAAAAGATTAAAGC
639454 CACAATGGCG
Statistics
Matches: 411, Mismatches: 40, Indels: 13
0.89 0.09 0.03
Matches are distributed among these distances:
98 3 0.01
99 280 0.68
100 100 0.24
101 28 0.07
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (99 bp):
AGATTAAAGCCACAACGGTGAATCTTGCCTTTCTGACATTGCGATTAAAAAGATTAAAGCTACAG
CAGCGAATCTTATCTCCCAGGCGGTGCAGTAAAA
Found at i:639815 original size:129 final size:127
Alignment explanation
Indices: 639672--640047 Score: 448
Period size: 129 Copynumber: 2.9 Consensus size: 127
639662 AGAATTTCAG
* * ** * * *
639672 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGGTTAC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACA-ATCCTATCTCCCTGAAGTTAC
* *
639737 AGTGGAGCGGATTAAAATAATAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAAAGCGCATCCA
65 AGTGAAGCGGATTAAAAT-ATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAAAGCGCATCCA
* * * *
639801 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CGAAAGAAACCTATCCTATCTCTCTGAAGTTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-AAGAAA-CAATCCTATCTCCCTGAAGTTA
* * *
639865 CAGTGAAGCGGATTAAAACTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCA
64 CAGTGAAGCGGATTAAAA-TATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAAAGCGCATCCA
* * * * * * *
639930 ATCTTATCTCCCTGAAGTTGCAATGGAGGAGATTAAAAAAATCAATCCTATCTTCCTAAAGTTGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAA-CAATCCTATCTCCCTGAAGTTAC
* * *
639995 AGTGAAGTGGATTAAAATGGTGGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
65 AGTGAAGCGGATTAAAAT-ATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
640048 GATCGCGTCA
Statistics
Matches: 210, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
128 2 0.01
129 207 0.99
130 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (127 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACAATCCTATCTCCCTGAAGTTACA
GTGAAGCGGATTAAAATATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAAAGCGCATCCA
Found at i:639897 original size:44 final size:44
Alignment explanation
Indices: 639541--639967 Score: 214
Period size: 44 Copynumber: 9.8 Consensus size: 44
639531 AGAACCAAAG
* * * * * *
639541 TCTTATCCCCCTGAAGATGCAGTGGGGCAAATTGAAAA-TAAAAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAACT-ACAGA
* * * ***
639586 TCTCATCTCTCTGAAGTTACAGTAGAGCAGA-TCGCA-TACAG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACTACAGA
* * ** * *
639627 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AACTACAGA
* * * * *
639673 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACTACAGA
* * *
639717 TCTTATCTCCCTGAGGTTACAGTGGAGCGGATTAAAA-TAATAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACT-ACAGA
* * ** *** *
639761 TCTTATCTCTCTGAAGTTGCAGCAGAGCA-A--AGCGCATCCAG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAAC-TACAGA
* ** * **
639802 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-AACCTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-ACTACAGA
* * * *
639846 TCCTATCTCTCTGAAGTTACAGTGAAGCGGATTAAAACTACAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACTACAGA
* * * *** *
639890 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCA-TCCA-A
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACTACAGA
* * *
639931 TCTTATCTCCCTGAAGTTGCAATGGAGGAGATTAAAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAA
639968 AAATCAATCC
Statistics
Matches: 284, Mismatches: 83, Indels: 33
0.71 0.21 0.08
Matches are distributed among these distances:
41 81 0.29
42 11 0.04
43 8 0.03
44 126 0.44
45 28 0.10
46 30 0.11
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACTACAGA
Found at i:640008 original size:44 final size:44
Alignment explanation
Indices: 639928--640011 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
639918 AGATCGCATC
* * *
639928 CAATCTTATCTCCCTGAAGTTGCAATGGAGGAGATTAAAAAAAT
1 CAATCCTATCTCCCTAAAGTTGCAATGAAGGAGATTAAAAAAAT
* *
639972 CAATCCTATCTTCCTAAAGTTGCAGTGAAGTG-GATTAAAA
1 CAATCCTATCTCCCTAAAGTTGCAATGAAG-GAGATTAAAA
640012 TGGTGGATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 33 0.97
45 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (44 bp):
CAATCCTATCTCCCTAAAGTTGCAATGAAGGAGATTAAAAAAAT
Found at i:640116 original size:68 final size:68
Alignment explanation
Indices: 640007--640142 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
639997 TGAAGTGGAT
640007 TAAAATGGTGGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCGTCAGACTTTGTTTTTCT
1 TAAAATGGTGGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCGTCAGACTTTGTTTTTCT
640072 TAA
66 TAA
*
640075 TAAAATGGTGGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCGTCAGACTTTGTTTTTTT
1 TAAAATGGTGGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCGTCAGACTTTGTTTTTCT
640140 TAA
66 TAA
640143 AGATACAGTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (68 bp):
TAAAATGGTGGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCGTCAGACTTTGTTTTTCT
TAA
Found at i:640631 original size:75 final size:77
Alignment explanation
Indices: 640507--640655 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 77
640497 AGAAAGGCAG
*
640507 CAAGAAATCAAGATTTGGCAAGACTGGGCAAAATGGGCCTTTCTTAGTCTTTGCTCTGTTCTCGT
1 CAAGAAATCAAGATTTGGCAAGACTCGGCAAAATGGGCCTTTCTTAGTCTTTGCTCTGTTCTCGT
640572 TACA-GACACCC
66 TACACGACACCC
640583 CAAGAAATCAAGATTTGGCAAGAC-CGGCAAAATGGGCCTTTCTTAGTCTTTGCTCTGTTCTCGT
1 CAAGAAATCAAGATTTGGCAAGACTCGGCAAAATGGGCCTTTCTTAGTCTTTGCTCTGTTCTCGT
640647 TACACGACA
66 TACACGACA
640656 ACGAGCAAAG
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
75 43 0.61
76 28 0.39
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (77 bp):
CAAGAAATCAAGATTTGGCAAGACTCGGCAAAATGGGCCTTTCTTAGTCTTTGCTCTGTTCTCGT
TACACGACACCC
Found at i:641726 original size:16 final size:16
Alignment explanation
Indices: 641705--641743 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
641695 AACGTATACA
641705 TATATATACATACTTT
1 TATATATACATACTTT
*
641721 TATATATACATGCTTT
1 TATATATACATACTTT
*
641737 CATATAT
1 TATATAT
641744 CTCCATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (16 bp):
TATATATACATACTTT
Found at i:641743 original size:34 final size:34
Alignment explanation
Indices: 641703--641767 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
641693 ATAACGTATA
*
641703 CATATATATACATACTTTTATATATACATGCTTT
1 CATATATATACATAATTTTATATATACATGCTTT
* * * *
641737 CATATATCTCCATAATTTTATGTATATATGC
1 CATATATATACATAATTTTATATATACATGC
641768 ATATATATCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (34 bp):
CATATATATACATAATTTTATATATACATGCTTT
Found at i:644501 original size:39 final size:40
Alignment explanation
Indices: 644384--644567 Score: 195
Period size: 40 Copynumber: 4.7 Consensus size: 40
644374 GCTCCTCGTT
*
644384 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGT-ATCTCGCA
* *
644424 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
*
644464 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
* **
644503 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CT-TAA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGT-ATCTCGCA
644542 CACAA-GCCTTCGGGACTTAGCCCGGA
1 CA-AATGCCTTCGGGACTTAGCCCGGA
644568 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
38 2 0.02
39 53 0.42
40 65 0.52
41 5 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
Found at i:644528 original size:79 final size:80
Alignment explanation
Indices: 644384--644567 Score: 211
Period size: 79 Copynumber: 2.3 Consensus size: 80
644374 GCTCCTCGTT
* *
644384 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
*
644448 GAT-TTAGTAACTCGCA
66 GATATT-GTAACT-GAA
**
644464 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
* *
644525 CGGATATTGTCACTTAA
64 CGGATATTGTAACTGAA
644542 CACAA-GCCTTCGGGACTTAGCCCGGA
1 CA-AATGCCTTCGGGACTTAGCCCGGA
644568 CATCATTCAA
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 17 0.19
79 57 0.63
80 17 0.19
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
GATATTGTAACTGAA
Found at i:652637 original size:39 final size:40
Alignment explanation
Indices: 652520--652703 Score: 195
Period size: 40 Copynumber: 4.7 Consensus size: 40
652510 GCTCCTCGTT
*
652520 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGT-ATCTCGCA
* *
652560 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
*
652600 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
* *
652639 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGT-ATC-TCGCA
*
652680 C-AA-GCCTTTGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
652704 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
38 2 0.02
39 49 0.39
40 64 0.51
41 10 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTATCTCGCA
Found at i:652664 original size:79 final size:82
Alignment explanation
Indices: 652520--652703 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 82
652510 GCTCCTCGTT
* *
652520 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
*
652584 GAT-TTAGTAAC-TCGCA
66 GATATT-GTAACTTAGCA
**
652600 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
*
652661 CGGATATTGTCACTTAGCA
64 CGGATATTGTAACTTAGCA
*
652680 C-AA-GCCTTTGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
652704 CATCATTCAA
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 13 0.14
79 56 0.62
80 22 0.24
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
GATATTGTAACTTAGCA
Found at i:654954 original size:26 final size:26
Alignment explanation
Indices: 654925--654975 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
654915 ATAAAAATAG
*
654925 ATAATGGGTTATGTAAATGTTCCATT
1 ATAATGGGTTAGGTAAATGTTCCATT
654951 ATAATGGGTTAGGTAAATGTTCCAT
1 ATAATGGGTTAGGTAAATGTTCCAT
654976 GATGGGCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (26 bp):
ATAATGGGTTAGGTAAATGTTCCATT
Found at i:662677 original size:26 final size:26
Alignment explanation
Indices: 662641--662691 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
662631 AAAATAGATA
*
662641 ATGGGTTAGGTAAATGTTCCATGATC
1 ATGGGTTAGGTAAATATTCCATGATC
662667 ATGGGTTAGGTAAATATTCCATGAT
1 ATGGGTTAGGTAAATATTCCATGAT
662692 GGGCATTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.35
Consensus pattern (26 bp):
ATGGGTTAGGTAAATATTCCATGATC
Found at i:665713 original size:47 final size:49
Alignment explanation
Indices: 665639--665768 Score: 176
Period size: 47 Copynumber: 2.7 Consensus size: 49
665629 AGGGTATAAT
665639 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATC-C-AT-CAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCACAATCCAA
* **
665686 GCCGGTGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACA-ATCCAA
* *
665736 GCCGATGTCATGTCCTAGACATGGTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
665769 GACACTTCTC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
46 2 0.03
47 38 0.52
49 2 0.03
50 31 0.42
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.26
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACAATCCAA
Found at i:670522 original size:50 final size:50
Alignment explanation
Indices: 670447--670543 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
670437 TCGTCTAACG
* ** **
670447 TGATTGCCAGGTCGTGTTTGATCCGTCAAATTGTACACAACCGTGTGACA
1 TGATTGCCAGGCCGTGTTAAATCCGTCAAATTACACACAACCGTGTGACA
* *
670497 TGATTGCCAGGCCGTGTTAAATCCGTTAAATTACACACGACCGTGTG
1 TGATTGCCAGGCCGTGTTAAATCCGTCAAATTACACACAACCGTGTG
670544 GGTCAATGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.29
Consensus pattern (50 bp):
TGATTGCCAGGCCGTGTTAAATCCGTCAAATTACACACAACCGTGTGACA
Found at i:680118 original size:54 final size:55
Alignment explanation
Indices: 680001--680128 Score: 196
Period size: 54 Copynumber: 2.4 Consensus size: 55
679991 GGAAAATGAT
680001 GAAGAAA-AAAAA-AA--GAAA-AAAGTTCTCATGTTGTTGAACTTGGCCGAACA
1 GAAGAAAGAAAAAGAAGGGAAAGAAAGTTCTCATGTTGTTGAACTTGGCCGAACA
*
680051 GAAGAAAGAAAAAGAAGGGAAAGAAAGTTCTCATGTTG-TGAACTTGGCCGAATA
1 GAAGAAAGAAAAAGAAGGGAAAGAAAGTTCTCATGTTGTTGAACTTGGCCGAACA
*
680105 GAAGAAAGAAAAAGAGGGGAAAGA
1 GAAGAAAGAAAAAGAAGGGAAAGA
680129 GCTTGGAGAA
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
50 7 0.10
51 5 0.07
52 2 0.03
54 42 0.59
55 15 0.21
ACGTcount: A:0.49, C:0.09, G:0.27, T:0.16
Consensus pattern (55 bp):
GAAGAAAGAAAAAGAAGGGAAAGAAAGTTCTCATGTTGTTGAACTTGGCCGAACA
Found at i:681392 original size:40 final size:40
Alignment explanation
Indices: 681335--681550 Score: 312
Period size: 40 Copynumber: 5.4 Consensus size: 40
681325 GATGATAACG
* *
681335 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
* *
681375 GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATATCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
681415 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
**
681455 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
681495 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
* *
681535 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
681551 TACTTGGTTT
Statistics
Matches: 162, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
39 16 0.10
40 145 0.90
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:689451 original size:40 final size:40
Alignment explanation
Indices: 689396--689530 Score: 270
Period size: 40 Copynumber: 3.4 Consensus size: 40
689386 GATGATAACG
689396 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
689436 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
689476 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
689516 GGGCTAAGTCCCGAA
1 GGGCTAAGTCCCGAA
689531 ATTCTGGGCT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCT
Found at i:689535 original size:20 final size:20
Alignment explanation
Indices: 689510--689550 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
689500 GCGAGTTACT
689510 AATTCTGGGCTAAGTCCCGA
1 AATTCTGGGCTAAGTCCCGA
689530 AATTCTGGGCTAAGTCCCGA
1 AATTCTGGGCTAAGTCCCGA
689550 A
1 A
689551 GGCATTTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
AATTCTGGGCTAAGTCCCGA
Found at i:689563 original size:60 final size:60
Alignment explanation
Indices: 689470--689590 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
689460 GCGAGTTACT
689470 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGA
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGA
689530 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGA
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGA
689590 A
1 A
689591 GGCATTTGTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (60 bp):
AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGA
Found at i:689603 original size:100 final size:100
Alignment explanation
Indices: 689430--689630 Score: 402
Period size: 100 Copynumber: 2.0 Consensus size: 100
689420 GCGAGTTACT
689430 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCA
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCA
689495 TTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGA
66 TTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGA
689530 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCA
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCA
689595 TTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGA
66 TTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGA
689630 A
1 A
689631 GGCATTTGTG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (100 bp):
AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGA
Found at i:689648 original size:140 final size:140
Alignment explanation
Indices: 689396--689670 Score: 550
Period size: 140 Copynumber: 2.0 Consensus size: 140
689386 GATGATAACG
689396 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTG
689461 CGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTC
66 CGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTC
689526 CCGAAATTCT
131 CCGAAATTCT
689536 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTG
689601 CGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTC
66 CGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTC
689666 CCGAA
131 CCGAA
689671 GGCATTTGTG
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (140 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTG
CGAGTTACTAATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGCTAAGTC
CCGAAATTCT
Found at i:690337 original size:40 final size:40
Alignment explanation
Indices: 689530--690325 Score: 1506
Period size: 40 Copynumber: 19.9 Consensus size: 40
689520 TAAGTCCCGA
689530 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689570 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689610 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689650 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689690 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689730 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689770 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689810 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689850 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689890 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689930 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
689970 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
690010 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
690050 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
690090 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
690130 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
690170 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
690210 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* **
690250 -ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT
1 AAT-TCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
690290 -ATATCCGGGCTAAGTCCCAAAGGCATTTGAGCGAGT
1 AAT-TCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
690326 AGCTATATCC
Statistics
Matches: 748, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
39 2 0.00
40 746 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
AATTCTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:694842 original size:14 final size:13
Alignment explanation
Indices: 694825--694864 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
694815 AACGTAATTT
694825 TAAAAATAAAAAA
1 TAAAAATAAAAAA
694838 GTAAAAATATAAAAA
1 -TAAAAATA-AAAAA
694853 TAATAAATAAAA
1 TAA-AAATAAAA
694865 GTCTTTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:727529 original size:15 final size:15
Alignment explanation
Indices: 727509--727538 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
727499 CAACACTTGT
727509 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
727524 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
727539 AATACATTAG
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:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Found at i:741788 original size:250 final size:250
Alignment explanation
Indices: 741347--741848 Score: 968
Period size: 250 Copynumber: 2.0 Consensus size: 250
741337 TTCCAGACAC
*
741347 TGCCCAGTCTGAGTACTAGTTGCTTCAAAAATCATATCTTGAGTTTCACAACTCGAAAATCAGTT
1 TGCCCAGTCTGAGTACTAGTCGCTTCAAAAATCATATCTTGAGTTTCACAACTCGAAAATCAGTT
*
741412 TTGTGATTTTTCCCTGAAACTAGACTCATGTCCCCACCTATGTATTTTTTTCTAGAATTTTTGGT
66 TTGTGATTTTTCCCTGAAACTAGACTCATGTCCCCACCTATGTATTTTTTTCTAGAATTTTTGCT
*
741477 CGGGCCAATTAGTACAGTTTATTAGTCAAAGTCTCCCATGTTACAGGGGTCGACTACACTGACCT
131 CGGGCCAATTAGTACAGTTTATTAGTCAAAGTCTCCCATGTTACAGGGGCCGACTACACTGACCT
741542 TTTCCCATTACGACTTGGATATCTCTCTACACAGAGCTTCAATACTGATGCCGTT
196 TTTCCCATTACGACTTGGATATCTCTCTACACAGAGCTTCAATACTGATGCCGTT
741597 TGCCCAGTCTGAGTACTAGTCGCTTCAAAAATCATATCTTGAGTTTCACAACTCGAAAATCAGTT
1 TGCCCAGTCTGAGTACTAGTCGCTTCAAAAATCATATCTTGAGTTTCACAACTCGAAAATCAGTT
741662 TTGTGATTTTTCCCTGAAACTAGACTCATGTCCCCACCTATGTATTTTTTTCTAGAATTTTTGCT
66 TTGTGATTTTTCCCTGAAACTAGACTCATGTCCCCACCTATGTATTTTTTTCTAGAATTTTTGCT
741727 CGGGCCAATTAGTACAGTTTATTAGTCAAAGTCTCCCATGTTACAGGGGCCGACTACACTGACCT
131 CGGGCCAATTAGTACAGTTTATTAGTCAAAGTCTCCCATGTTACAGGGGCCGACTACACTGACCT
*
741792 TTTCCCATTACGACTTGGATATCTCTCTGCACAGAGCTTCAATACTGATGCCGTT
196 TTTCCCATTACGACTTGGATATCTCTCTACACAGAGCTTCAATACTGATGCCGTT
741847 TG
1 TG
741849 TTTCTATGGA
Statistics
Matches: 248, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
250 248 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.35
Consensus pattern (250 bp):
TGCCCAGTCTGAGTACTAGTCGCTTCAAAAATCATATCTTGAGTTTCACAACTCGAAAATCAGTT
TTGTGATTTTTCCCTGAAACTAGACTCATGTCCCCACCTATGTATTTTTTTCTAGAATTTTTGCT
CGGGCCAATTAGTACAGTTTATTAGTCAAAGTCTCCCATGTTACAGGGGCCGACTACACTGACCT
TTTCCCATTACGACTTGGATATCTCTCTACACAGAGCTTCAATACTGATGCCGTT
Found at i:743019 original size:39 final size:39
Alignment explanation
Indices: 742902--743139 Score: 225
Period size: 40 Copynumber: 6.3 Consensus size: 39
742892 GCTCCTCGTT
* * *
742902 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAACCCGGAAT-TAGT-ATCTCGCA
* * *
742942 CAAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAACCCGGAATTAGTATCTCGCA
*
742982 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAACCCGGAATTAGTATCTCGCA
* *
743021 CAAATGCCTTCAGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAACCCGGAATTAGTATCTCGCA
*
743060 C-AA-----------TTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAACCCGGAATTAGTATCTCGCA
* *
743087 CAAAGGCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCA
1 CAAATGCCTTC-GGGCTTAACCCGGAATTAGTATCTCGCA
743127 CAAATGCCTTCGG
1 CAAATGCCTTCGG
743140 ATCTTAGTCC
Statistics
Matches: 169, Mismatches: 14, Indels: 31
0.79 0.07 0.14
Matches are distributed among these distances:
27 23 0.14
28 2 0.01
38 2 0.01
39 64 0.38
40 76 0.45
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAACCCGGAATTAGTATCTCGCA
Found at i:743998 original size:74 final size:74
Alignment explanation
Indices: 743877--744020 Score: 270
Period size: 74 Copynumber: 1.9 Consensus size: 74
743867 AAAGGAGGTT
* *
743877 CAAGAATCATCAAGCCATCATCACATGCATCATTAACAAGCTTCATATTTTGCATGCAATGGCAT
1 CAAGAATCATCAAGCCACCATCACATGCATCATTAACAAGCTTCATATTTAGCATGCAATGGCAT
743942 TAACACAAC
66 TAACACAAC
743951 CAAGAATCATCAAGCCACCATCACATGCATCATTAACAAGCTTCATATTTAGCATGCAATGGCAT
1 CAAGAATCATCAAGCCACCATCACATGCATCATTAACAAGCTTCATATTTAGCATGCAATGGCAT
744016 TAACA
66 TAACA
744021 TAAACTCCAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (74 bp):
CAAGAATCATCAAGCCACCATCACATGCATCATTAACAAGCTTCATATTTAGCATGCAATGGCAT
TAACACAAC
Found at i:750002 original size:42 final size:42
Alignment explanation
Indices: 749948--750062 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 42
749938 TAGGGTTATT
*
749948 TGAGATTACGTGTAAGACCATATTTGGGATA-TGACATCGATA
1 TGAGATT-CGTGTAAGACCATATCTGGGATATTGACATCGATA
* * *
749990 TGAGACTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 TGAGA-TTCGTGTAAGACCATATCTGGGATATTGACATCGATA
* *
750033 TGAGATCCCATGTAAGACCATATCTGGGAT
1 TGAGAT-TCGTGTAAGACCATATCTGGGAT
750063 TTGGCATTGG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
42 26 0.42
43 36 0.58
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (42 bp):
TGAGATTCGTGTAAGACCATATCTGGGATATTGACATCGATA
Found at i:753116 original size:18 final size:18
Alignment explanation
Indices: 753093--753127 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
753083 CAAAACTACG
*
753093 GGCCCACATGCCCGTGTT
1 GGCCCACACGCCCGTGTT
753111 GGCCCACACGCCCGTGT
1 GGCCCACACGCCCGTGT
753128 GACTCGCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.43, G:0.29, T:0.17
Consensus pattern (18 bp):
GGCCCACACGCCCGTGTT
Found at i:767388 original size:29 final size:29
Alignment explanation
Indices: 767355--768139 Score: 1570
Period size: 29 Copynumber: 27.1 Consensus size: 29
767345 CATCTAAGAC
767355 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767384 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767413 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767442 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767471 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767500 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767529 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767558 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767587 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767616 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767645 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767674 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767703 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767732 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767761 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767790 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767819 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767848 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767877 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767906 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767935 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767964 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
767993 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
768022 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
768051 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
768080 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
768109 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
768138 AA
1 AA
768140 CTTGTTGATT
Statistics
Matches: 756, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 756 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (29 bp):
AAATTACTTGGTACATCATTATTATGACT
Found at i:775587 original size:29 final size:29
Alignment explanation
Indices: 775554--776338 Score: 1570
Period size: 29 Copynumber: 27.1 Consensus size: 29
775544 CATCTAAGAC
775554 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775583 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775612 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775641 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775670 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775699 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775728 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775757 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775786 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775815 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775844 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775873 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775902 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775931 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775960 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
775989 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776018 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776047 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776076 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776105 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776134 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776163 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776192 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776221 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776250 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776279 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776308 AAATTACTTGGTACATCATTATTATGACT
1 AAATTACTTGGTACATCATTATTATGACT
776337 AA
1 AA
776339 CTTGTTGATT
Statistics
Matches: 756, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 756 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (29 bp):
AAATTACTTGGTACATCATTATTATGACT
Found at i:782336 original size:43 final size:42
Alignment explanation
Indices: 782245--782349 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
782235 ATGATTTATG
* * *
782245 TGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTTCG
1 TGTAAGACCACGTCTGGGACAGTGGCATCGTATTTGATTACA
*
782287 TATAAGACC-CTGTCTGGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATCG-TATTTGATTACA
*
782330 TGTAAGACCACGTTTGGGAC
1 TGTAAGACCACGTCTGGGAC
782350 GTTGACATTG
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
41 1 0.02
42 26 0.48
43 26 0.48
44 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCGTATTTGATTACA
Found at i:783548 original size:7 final size:7
Alignment explanation
Indices: 783532--783580 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
783522 CGAATAATAA
783532 TAAAATT
1 TAAAATT
*
783539 TAATATT
1 TAAAATT
783546 T--AA-T
1 TAAAATT
783550 TAAAATT
1 TAAAATT
783557 TAAAATT
1 TAAAATT
783564 T-AAATT
1 TAAAATT
783570 TAAAATAT
1 TAAAAT-T
783578 TAA
1 TAA
783581 TACTAGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
4 2 0.06
5 1 0.03
6 8 0.23
7 20 0.57
8 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAAAATT
Found at i:783568 original size:13 final size:13
Alignment explanation
Indices: 783532--783580 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
783522 CGAATAATAA
783532 TAAAATTTAATATT
1 TAAAATTTAA-ATT
*
783546 T--AATTAAAATT
1 TAAAATTTAAATT
783557 TAAAATTTAAATT
1 TAAAATTTAAATT
783570 TAAAATATTAA
1 TAAAAT-TTAA
783581 TACTAGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 4 0.13
12 6 0.20
13 15 0.50
14 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAATTTAAATT
Found at i:788063 original size:40 final size:40
Alignment explanation
Indices: 788004--788121 Score: 209
Period size: 40 Copynumber: 3.0 Consensus size: 40
787994 TGGAAAAAAA
788004 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
*
788044 TATGACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* *
788084 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
788122 GTTACATCCG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:794399 original size:27 final size:27
Alignment explanation
Indices: 794369--794546 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
794359 ATATTGAGTC
* * * *
794369 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
794396 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
794423 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
794451 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
794478 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
794505 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
794532 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
794547 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:794508 original size:82 final size:81
Alignment explanation
Indices: 794390--794545 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
794380 TGCTATATAA
* *
794390 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
794455 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
794472 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
794536 CACTTAGTGC
65 CACTTAGTGC
794546 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:798706 original size:27 final size:27
Alignment explanation
Indices: 798675--798852 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
798665 TAAATTGTAC
798675 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
798702 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
798728 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
798756 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
798784 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
798811 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
798838 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
798853 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:798789 original size:82 final size:81
Alignment explanation
Indices: 798676--798831 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
798666 AAATTGTACA
* *
798676 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
798740 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
798757 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
798822 TGCGAGTTGA
65 TGCGAATTGA
798832 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:798843 original size:82 final size:81
Alignment explanation
Indices: 798672--798852 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
798662 GATTAAATTG
* *
798672 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
798737 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
798753 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
798817 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
798835 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
798853 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:798863 original size:27 final size:27
Alignment explanation
Indices: 798757--798863 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
798747 TGACCATGCG
* * * *
798757 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
798785 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
798812 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
798839 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
798864 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:803131 original size:15 final size:16
Alignment explanation
Indices: 803105--803160 Score: 82
Period size: 15 Copynumber: 3.7 Consensus size: 16
803095 CAAGGAAACT
803105 GAATAAAGAAATCCAA
1 GAATAAAGAAATCCAA
*
803121 G-ATAGAGAAATCC-A
1 GAATAAAGAAATCCAA
803135 GAATAAAGAAATCC-A
1 GAATAAAGAAATCCAA
803150 GAATAAAGAAA
1 GAATAAAGAAA
803161 CCTAAGATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 34 0.92
16 1 0.03
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.12
Consensus pattern (16 bp):
GAATAAAGAAATCCAA
Found at i:806250 original size:93 final size:93
Alignment explanation
Indices: 806091--806263 Score: 267
Period size: 93 Copynumber: 1.9 Consensus size: 93
806081 CGACCATAAG
* * * *
806091 CGAACTCGGACTCAACTCAATGAGCTCAGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACGCGGACTCAACTCA
806156 ACGAGTTCGCATGCCTAGTTACATCTCA
66 ACGAGTTCGCATGCCTAGTTACATCTCA
* *
806184 CGAACTCGGACTCAACTCAACGAGTTC-GGACATTTGCATCCATAAGTGAACGCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACGCGGACTCAACTC
*
806248 AACGAGTTCGGATGCC
65 AACGAGTTCGCATGCC
806264 CAAATATCCT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACGCGGACTCAACTCA
ACGAGTTCGCATGCCTAGTTACATCTCA
Found at i:806257 original size:46 final size:46
Alignment explanation
Indices: 806084--806259 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
806074 TGTAACCCGA
* * * *
806084 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTTGCAT
* * * * *
806130 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGCATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCG---GAC-ATTTGCAT
*
806180 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* *
806223 CCATAAGTGAACGCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
806260 TGCCCAAATA
Statistics
Matches: 106, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 3 0.03
46 58 0.55
47 27 0.25
48 3 0.03
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:812933 original size:65 final size:65
Alignment explanation
Indices: 812824--812955 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
812814 TTTGGAATAC
* * * *
812824 TATCAAATATTCATTAAACCTCAAACATAGGGTATGATGTCGATGCCATGTCCTAGACATGGTCT
1 TATCAAATATTCACTAAACCTCAAACATAAGGTATGATGCCGATGACATGTCCTAGACATGGTCT
*
812889 TATCAAATATTCACTAAACCTCAAACATAAGGTATGTTGCCGATGACATGTCCTAGACATGGTCT
1 TATCAAATATTCACTAAACCTCAAACATAAGGTATGATGCCGATGACATGTCCTAGACATGGTCT
812954 TA
1 TA
812956 CTCTGGCTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (65 bp):
TATCAAATATTCACTAAACCTCAAACATAAGGTATGATGCCGATGACATGTCCTAGACATGGTCT
Found at i:812996 original size:47 final size:47
Alignment explanation
Indices: 812927--813198 Score: 136
Period size: 47 Copynumber: 5.8 Consensus size: 47
812917 AAGGTATGTT
* *
812927 GCCGATGACATGTCCTAGACATGGTCTTACTCTGGCTCATGTCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACTCTGGCTCATGTCTCAA
* * * * *
812974 GCCGATGCCATGTCCGAGACATGTTCTTACAT-TGACT-ATTGTCATTGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTAC-TCTGGCTCA-TGTC--TCAA
* * *
813023 GCCGACGCCATGTCCCAGACATGGTCTTACACTGGCACA--TCTCATA
1 GCCGATGCCATGTCCCAGACATGGTCTTACTCTGGCTCATGTCTCA-A
* * * ** *
813069 GCTGATG-CATGTCCCTA-ACAT-GTCTTA-TATTGGCTTACCT-TACGAG
1 GCCGATGCCATGTCCC-AGACATGGTCTTACT-CTGGCTCATGTCT-C-AA
* * * * * * *
813115 GTCGAT-ACATGTCCTAGACA-CGTCTTACACTAGCTC-TCTTCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACTCTGGCTCAT-GTCTCAA
* *
813160 TGCCGATGCCATGTTCCAGACATGGTCTTACACTGGCTC
1 -GCCGATGCCATGTCCCAGACATGGTCTTACTCTGGCTC
813199 TCATAATGTT
Statistics
Matches: 166, Mismatches: 37, Indels: 43
0.67 0.15 0.17
Matches are distributed among these distances:
44 11 0.07
45 17 0.10
46 40 0.24
47 50 0.30
48 15 0.09
49 32 0.19
50 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACTCTGGCTCATGTCTCAA
Found at i:823681 original size:21 final size:21
Alignment explanation
Indices: 823651--823739 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
823641 CTCACAAAGA
* *
823651 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
823671 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
823692 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
823713 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
823737 AAA
1 AAA
823740 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:823732 original size:24 final size:21
Alignment explanation
Indices: 823651--823719 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
823641 CTCACAAAGA
* * *
823651 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
823671 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
823692 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
823713 AAAAAGA
1 AAAAAGA
823720 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:832725 original size:40 final size:40
Alignment explanation
Indices: 832676--832786 Score: 186
Period size: 40 Copynumber: 2.8 Consensus size: 40
832666 TGCGAGTTGG
* *
832676 TATATCCGGGCTAAGTCCCGAAAGCATTTATGCTAGTGAC
1 TATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGCGAC
* *
832716 TATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGAC
1 TATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGCGAC
832756 TATATCCGGGCTAAGTCCCGAAGGCATTTAT
1 TATATCCGGGCTAAGTCCCGAAGGCATTTAT
832787 CCAGGCTAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGCGAC
Found at i:832794 original size:26 final size:26
Alignment explanation
Indices: 832758--832810 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
832748 CTAGCGACTA
* *
832758 TATCCGGGCTAAGTCCCGAAGGCATT
1 TATCCAGGCTAAGACCCGAAGGCATT
832784 TATCCAGGCTAAGACCCGAAGGCATT
1 TATCCAGGCTAAGACCCGAAGGCATT
832810 T
1 T
832811 GTGCGAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (26 bp):
TATCCAGGCTAAGACCCGAAGGCATT
Found at i:836269 original size:42 final size:41
Alignment explanation
Indices: 836209--836362 Score: 177
Period size: 42 Copynumber: 3.7 Consensus size: 41
836199 TTAAGTTTAG
* *
836209 GTGTAAGA-CATATATGGGATATGACATC-ATGATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGAT-ATGAGA-TTC
*
836250 GTGTAAGACCATATCTGGGATATGGTATCGATATGAGATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TTC
* * * *
836292 GTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATCC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATTC
*
836334 TATGTAAGACCATATCTGGGATATGGCAT
1 -GTGTAAGACCATATCTGGGATATGGCAT
836363 TGGTGTAATA
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
41 8 0.08
42 54 0.56
43 35 0.36
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (41 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTC
Found at i:837662 original size:27 final size:26
Alignment explanation
Indices: 837621--837672 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
837611 ATCTCATATT
* *
837621 TGTAGGCTAGTATTACTAAAATACCCC
1 TGTAGGATAGAATTACT-AAATACCCC
*
837648 TGTAGGATAGAATTACTGAATACCC
1 TGTAGGATAGAATTACTAAATACCC
837673 TTGGTTTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (26 bp):
TGTAGGATAGAATTACTAAATACCCC
Found at i:837698 original size:27 final size:27
Alignment explanation
Indices: 837666--838005 Score: 219
Period size: 27 Copynumber: 12.6 Consensus size: 27
837656 AGAATTACTG
* *
837666 AATACCCTTGGTTTACAAAATTATCAA
1 AATACCCTTGATTTGCAAAATTATCAA
* * *
837693 AATACCCTCGATTAGCAAAATTACCAA
1 AATACCCTTGATTTGCAAAATTATCAA
* * *
837720 AATACCCCT-AGTTTGTAAAATTACCAA
1 AATACCCTTGA-TTTGCAAAATTATCAA
* * *** *
837747 AATACCCCTAATTTATGAAATTA-CTGA
1 AATACCCTTGATTTGCAAAATTATC-AA
** * * *
837774 AATACCCTCAAGTTGTAAAATTATCGA
1 AATACCCTTGATTTGCAAAATTATCAA
* *
837801 AATACCCTCGACTT-CTAAAATTATCAA
1 AATACCCTTGATTTGC-AAAATTATCAA
* * *
837828 AATACCCTCGATTTGTAAAATTACCAA
1 AATACCCTTGATTTGCAAAATTATCAA
* *
837855 AATACCCCTGATTTGGAAAATTATCAA
1 AATACCCTTGATTTGCAAAATTATCAA
* *
837882 AATACCCTTAATTTGGAAAATTAT-AGA
1 AATACCCTTGATTTGCAAAATTATCA-A
** *
837909 AATACCCTTGATTTATAAAATT-GCAAA
1 AATACCCTTGATTTGCAAAATTATC-AA
837936 AATACCCTTGACTTT-CAAAAATTAT-AGA
1 AATACCCTTGA-TTTGC-AAAATTATCA-A
* ** *
837964 AATACCATTGGCTTGCAAAATTA-CTGA
1 AATACCCTTGATTTGCAAAATTATC-AA
*
837991 AATACCCTTGGTTTG
1 AATACCCTTGATTTG
838006 TAGATTTACT
Statistics
Matches: 255, Mismatches: 42, Indels: 32
0.78 0.13 0.10
Matches are distributed among these distances:
26 3 0.01
27 229 0.90
28 23 0.09
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
AATACCCTTGATTTGCAAAATTATCAA
Found at i:837943 original size:108 final size:107
Alignment explanation
Indices: 837682--837943 Score: 300
Period size: 108 Copynumber: 2.4 Consensus size: 107
837672 CTTGGTTTAC
* *
837682 AAAATTATCA-AAATACCCTCGATTAGCAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACC
1 AAAATTAT-AGAAATACCCTCGATTA-TAAAATTA-CAAAATACCCTCGAGTTTGTAAAATTACC
* * *
837745 AAAATACCCCTAATTTATGAAATTACTGAAATACCCTCAAGTTGT
63 AAAATACCCCTAATTTAGGAAATTACTAAAATACCCTCAAGTTGG
* *
837790 AAAATTATCGAAATACCCTCGACTTCTAAAATTATCAAAATACCCTCGA-TTTGTAAAATTACCA
1 AAAATTATAGAAATACCCTCGA-TTATAAAATTA-CAAAATACCCTCGAGTTTGTAAAATTACCA
* * *
837854 AAATACCCCTGATTT-GGAAAATTA-TCAAAATACCCTTAATTTGG
64 AAATACCCCTAATTTAGG-AAATTACT-AAAATACCCTCAAGTTGG
* *
837898 AAAATTATAGAAATACCCTTGATTTATAAAATTGCAAAAATACCCT
1 AAAATTATAGAAATACCCTCGA-TTATAAAATTAC-AAAATACCCT
837944 TGACTTTCAA
Statistics
Matches: 132, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
107 3 0.02
108 125 0.95
109 4 0.03
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (107 bp):
AAAATTATAGAAATACCCTCGATTATAAAATTACAAAATACCCTCGAGTTTGTAAAATTACCAAA
ATACCCCTAATTTAGGAAATTACTAAAATACCCTCAAGTTGG
Found at i:837984 original size:55 final size:55
Alignment explanation
Indices: 837871--838000 Score: 138
Period size: 55 Copynumber: 2.4 Consensus size: 55
837861 CCTGATTTGG
** * * *
837871 AAAATTATC-AAAATACCCTT-AATTTGGAAAATTATAGAAATACCCTTGATTTAT
1 AAAATTA-CAAAAATACCCTTGAATTTCAAAAATTATAGAAATACCATTGACTTAC
* * * *
837925 AAAATTGCAAAAATACCCTTGACTTTCAAAAATTATAGAAATACCATTGGCTTGC
1 AAAATTACAAAAATACCCTTGAATTTCAAAAATTATAGAAATACCATTGACTTAC
**
837980 AAAATTACTGAAATACCCTTG
1 AAAATTACAAAAATACCCTTG
838001 GTTTGTAGAT
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
53 1 0.02
54 17 0.27
55 44 0.71
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (55 bp):
AAAATTACAAAAATACCCTTGAATTTCAAAAATTATAGAAATACCATTGACTTAC
Found at i:838069 original size:27 final size:27
Alignment explanation
Indices: 838013--838069 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
838003 TTGTAGATTT
* * *
838013 ACTAAAACACCCTTGTAGGGTGAAATG
1 ACTAAAACACCCCTGTAGGGTAAAAAG
*
838040 ACTAAAATACCCCTGATA-GGTAAAAAG
1 ACTAAAACACCCCTG-TAGGGTAAAAAG
838067 ACT
1 ACT
838070 GTTCTTCCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (27 bp):
ACTAAAACACCCCTGTAGGGTAAAAAG
Found at i:838299 original size:41 final size:40
Alignment explanation
Indices: 838254--838374 Score: 154
Period size: 41 Copynumber: 3.0 Consensus size: 40
838244 GGAGGAAGAA
* * *
838254 ATTGAGGATCGCATGGTTACTTCATGATCGTGGATCCACAG
1 ATTGAGGATCGCATGGTTACTTGACGAACGTGGATCCAC-G
*
838295 ATTGAGGATCGGATGGTTTA-TTGACGAACGTGGATCCATCG
1 ATTGAGGATCGCATGG-TTACTTGACGAACGTGGATCCA-CG
* *
838336 ATTAAGGATCGCATGGTTACTTGACGACCGTGGATCCAC
1 ATTGAGGATCGCATGGTTACTTGACGAACGTGGATCCAC
838375 CGGTGGCTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
40 4 0.06
41 62 0.89
42 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (40 bp):
ATTGAGGATCGCATGGTTACTTGACGAACGTGGATCCACG
Found at i:838570 original size:22 final size:22
Alignment explanation
Indices: 838518--838582 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
838508 GCCAATTATT
* *
838518 CTGATTATGGCTTTGTGCTAAC
1 CTGATTATGGCTCTGTGCCAAC
*
838540 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
838562 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
838583 ACGTATTTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Done.