Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 17 of 279
Found at i:5531052 original size:16 final size:16
Alignment explanation
Indices: 5531012--5531053 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5531002 AAAAACAAAA
5531012 AAAAATAAAATCACAT
1 AAAAATAAAATCACAT
* *
5531028 AAAGATAAATTCA-AT
1 AAAAATAAAATCACAT
5531043 AAAAATTAAAA
1 AAAAA-TAAAA
5531054 ATTTTTGACC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.21
Consensus pattern (16 bp):
AAAAATAAAATCACAT
Found at i:5533502 original size:29 final size:28
Alignment explanation
Indices: 5533412--5533491 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 28
5533402 CTGATGGCTA
* * *
5533412 TGCCATAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGGCAC
*
5533440 TGCCAC-ATATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGGCAC
5533467 TGCCACAAAATATCTGTATCTGGTG
1 TGCCACAAAATATCTGT-TCTGGTG
5533492 ACTCTGTCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 24 0.53
28 14 0.31
29 7 0.16
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGGCAC
Found at i:5533510 original size:55 final size:56
Alignment explanation
Indices: 5533412--5533516 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 56
5533402 CTGATGGCTA
* * *
5533412 TGCCATAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-TCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTATCTGGTGGCAC
* * *
5533467 TGCCACAAAATATCTGTATCTGGTGACTCTGTCACATGT-TCTGTATCTGG
1 TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTATCTGG
5533517 CAGCCATGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
55 20 0.48
56 22 0.52
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (56 bp):
TGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTATCTGGTGGCAC
Found at i:5540364 original size:47 final size:47
Alignment explanation
Indices: 5540306--5540398 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
5540296 CGTTTTACCA
*
5540306 TTCTAAGAACAAGTTGCAAAAAGCCGAAAACCCCACATTGAAAGTGT
1 TTCTAAAAACAAGTTGCAAAAAGCCGAAAACCCCACATTGAAAGTGT
5540353 TTCTAAAAACAAGTTGCAAAAAGCCGAAAACCCCACATTGAAAGTG
1 TTCTAAAAACAAGTTGCAAAAAGCCGAAAACCCCACATTGAAAGTG
5540399 ACTTGGCTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (47 bp):
TTCTAAAAACAAGTTGCAAAAAGCCGAAAACCCCACATTGAAAGTGT
Found at i:5541421 original size:29 final size:28
Alignment explanation
Indices: 5541331--5541410 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 28
5541321 CTGATGGCTA
* * *
5541331 TGCCATAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGGCAC
*
5541359 TGCCAC-ATATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGGCAC
5541386 TGCCACAAAATATCTGTATCTGGTG
1 TGCCACAAAATATCTGT-TCTGGTG
5541411 ACTCTGTCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 24 0.53
28 14 0.31
29 7 0.16
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGGCAC
Found at i:5541429 original size:55 final size:56
Alignment explanation
Indices: 5541331--5541435 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 56
5541321 CTGATGGCTA
* * *
5541331 TGCCATAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-TCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTATCTGGTGGCAC
* * *
5541386 TGCCACAAAATATCTGTATCTGGTGACTCTGTCACATGT-TCTGTATCTGG
1 TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTATCTGG
5541436 CAGCCATGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
55 20 0.48
56 22 0.52
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (56 bp):
TGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTATCTGGTGGCAC
Found at i:5542339 original size:48 final size:48
Alignment explanation
Indices: 5542283--5542374 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
5542273 AGTAATACGG
*
5542283 AATGTTTTGTACGCATCAATGTGGCACACCGGATCCGGTCATAACGTA
1 AATGTTTTGTACGCATCAATATGGCACACCGGATCCGGTCATAACGTA
*
5542331 AATGTTTTGTACGCATCAATATGGCGCACCGGATCCGGTCATAA
1 AATGTTTTGTACGCATCAATATGGCACACCGGATCCGGTCATAA
5542375 TGTCTAGGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (48 bp):
AATGTTTTGTACGCATCAATATGGCACACCGGATCCGGTCATAACGTA
Found at i:5548474 original size:48 final size:48
Alignment explanation
Indices: 5548415--5548731 Score: 320
Period size: 48 Copynumber: 6.6 Consensus size: 48
5548405 TATGTGTGCT
* * * *
5548415 AGTGTAAGACCATGTCTGGGACATGGCATCGACCACG-ATATGAGAGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTA-ATGAGAGCC
* * * * *
5548463 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAATGTAACGAGTGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTAATGAGAGCC
* * * * * *
5548511 ACTGTAAAACCATGTTTGGAACATGGCATTGGCAATGTAACGAGAACC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTAATGAGAGCC
*
5548559 AATGTAAGACCATGTTTGGAACATGGCATCGACAATGTAATGAGAGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTAATGAGAGCC
* * *
5548607 AGTGTAAGACCATGTTTGGAACATGACATCGGC-AT-TAA-GACAAGAGCT
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTAATG---AGAGCC
* * * *** *
5548655 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCCCG-ACATGTGAGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTA-ATGAGAGCC
5548703 AGTGTAAGACCATGTTTGGAACATGGCAT
1 AGTGTAAGACCATGTTTGGAACATGGCAT
5548732 TGGCAATTCA
Statistics
Matches: 230, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
45 1 0.00
46 3 0.01
47 2 0.01
48 220 0.96
49 2 0.01
50 1 0.00
51 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGAACATGGCATCGACAATGTAATGAGAGCC
Found at i:5548583 original size:96 final size:97
Alignment explanation
Indices: 5548456--5548739 Score: 369
Period size: 96 Copynumber: 2.9 Consensus size: 97
5548446 ACCACGATAT
* * * *
5548456 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAATGTAACGAGTGCCACTGTAAAAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAATGTAATGAGAGCCAGTGTAAGAC
5548521 CATGTTTGGAACATGGCATTGGCAATGT-A-AC
66 CATGTTTGGAACATGGCATTGGCAAT-TAAGAC
* * * * *
5548552 GAGAACCAATGTAAGACCATGTTTGGAACATGGCATCGACAATGTAATGAGAGCCAGTGTAAGAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAATGTAATGAGAGCCAGTGTAAGAC
* *
5548617 CATGTTTGGAACATGACATCGGC-ATTAAGAC
66 CATGTTTGGAACATGGCATTGGCAATTAAGAC
* * *** *
5548648 AAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCCCG-ACATGTGAGCCAGTGTAAGA
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAATGTA-ATGAGAGCCAGTGTAAGA
5548712 CCATGTTTGGAACATGGCATTGGCAATT
65 CCATGTTTGGAACATGGCATTGGCAATT
5548740 CACCCTCTTG
Statistics
Matches: 160, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
94 1 0.01
95 4 0.03
96 152 0.95
97 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.22
Consensus pattern (97 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAATGTAATGAGAGCCAGTGTAAGAC
CATGTTTGGAACATGGCATTGGCAATTAAGAC
Found at i:5548679 original size:144 final size:144
Alignment explanation
Indices: 5548417--5548731 Score: 368
Period size: 144 Copynumber: 2.2 Consensus size: 144
5548407 TGTGTGCTAG
* * *
5548417 TGTAAGACCATGTCTGGGACATGGCATCGACCACGATATGAGAGCCAGTGTAAGACCATGTCTGG
1 TGTAAGACCATGTTTGGAACATGGCATCGACAACGATATGAGAGCCAGTGTAAGACCATGTCTGG
* * * * * * *
5548482 GACATGGCATCGGCAATGTAACGAGTGCCACTGTAAAACCATGTTTGGAACATGGCATTGGCAAT
66 AACATGACATCGGCAATGTAACAAGAGCCACTGTAAAACCATGTCTGGAACATGGCATCGGCAAC
5548547 GTA-ACGAGAACCAA
131 G-ACACGAGAACCAA
* *
5548561 TGTAAGACCATGTTTGGAACATGGCATCGACAATG-TAATGAGAGCCAGTGTAAGACCATGTTTG
1 TGTAAGACCATGTTTGGAACATGGCATCGACAACGAT-ATGAGAGCCAGTGTAAGACCATGTCTG
* * * *
5548625 GAACATGACATCGGC-AT-TAAGACAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
65 GAACATGACATCGGCAATGT-A-ACAAGAGCCACTGTAAAACCATGTCTGGAACATGGCATCGGC
** * * * *
5548688 CCCGACATGTGAGCCAG
128 AACGACACGAGAACCAA
5548705 TGTAAGACCATGTTTGGAACATGGCAT
1 TGTAAGACCATGTTTGGAACATGGCAT
5548732 TGGCAATTCA
Statistics
Matches: 145, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
142 1 0.01
143 5 0.03
144 139 0.96
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (144 bp):
TGTAAGACCATGTTTGGAACATGGCATCGACAACGATATGAGAGCCAGTGTAAGACCATGTCTGG
AACATGACATCGGCAATGTAACAAGAGCCACTGTAAAACCATGTCTGGAACATGGCATCGGCAAC
GACACGAGAACCAA
Found at i:5550597 original size:40 final size:39
Alignment explanation
Indices: 5550536--5550628 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 39
5550526 TCTCGGTATT
* *
5550536 ACACACTTAGTGCCTCATATAGCCAAAGCTATTCCAATTT
1 ACACACTTAGTG-CTCATATAGCCAAAGCTATTCCAAATC
* *
5550576 TCACACTTAGTGCT-ATTTATAGCCAAAGCTATTTCAAATC
1 ACACACTTAGTGCTCA--TATAGCCAAAGCTATTCCAAATC
5550616 ACACACTTAGTGC
1 ACACACTTAGTGC
5550629 CGAACATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 1 0.02
39 2 0.04
40 43 0.93
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (39 bp):
ACACACTTAGTGCTCATATAGCCAAAGCTATTCCAAATC
Found at i:5552967 original size:30 final size:30
Alignment explanation
Indices: 5552921--5552981 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
5552911 ATTCCCGAGC
*
5552921 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGCGCAAAAGTGTAAATATGCAAAAGTT
* * *
5552951 TAGGCGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGCGCAAAAGTGTAAATATGCAAAAGTT
5552981 T
1 T
5552982 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGCGCAAAAGTGTAAATATGCAAAAGTT
Found at i:5553594 original size:64 final size:64
Alignment explanation
Indices: 5553514--5553697 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
5553504 AGACATTATG
* * * *
5553514 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACAACATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
5553578 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
5553643 AA
63 AA
* * *
5553645 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
5553698 CAAAATTATG
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.26
66 21 0.21
67 30 0.31
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:5557645 original size:30 final size:30
Alignment explanation
Indices: 5557611--5557671 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5557601 TTCCCAAGCC
*
5557611 TAGGGGGAAAAGTGTAAATATGAAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGAAAAAGTT
* * * *
5557641 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGAAAAAGTT
5557671 T
1 T
5557672 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGAAAAAGTT
Found at i:5559411 original size:16 final size:15
Alignment explanation
Indices: 5559385--5559416 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
5559375 GCTAGATCGG
5559385 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
5559400 CAAAATGCCGAAAAGC
1 CAAAA-GCCGAAAAGC
5559416 C
1 C
5559417 GGTATTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.28, G:0.19, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:5559864 original size:27 final size:27
Alignment explanation
Indices: 5559806--5559895 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
5559796 AGGAAGCGTC
5559806 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
5559834 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
5559861 CTGGTGGCACTGCCACAAAATATCTGCAT
1 CTGGTGGCACTGCCAC-AAATATCTG-TT
5559890 CTGGTG
1 CTGGTG
5559896 ACTCTGTCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 23 0.43
28 24 0.44
29 7 0.13
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:5559914 original size:55 final size:56
Alignment explanation
Indices: 5559806--5559920 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 56
5559796 AGGAAGCGTC
* * *
5559806 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGATCTGGTGACCCTGCCACATATATCTGTAT
* * * *
5559861 CTGGTGGC-ACTGCCACAAAATATCTGCATCTGGTGACTCTGTCATAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTG-ATCTGGTGACCCTGCCACATATATCTGTAT
5559917 CTGG
1 CTGG
5559921 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.58
56 20 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGATCTGGTGACCCTGCCACATATATCTGTAT
Found at i:5571267 original size:31 final size:31
Alignment explanation
Indices: 5571232--5571294 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5571222 CCATGTGCTA
5571232 GGCTGTGTGGAGGACACGATTGAGACACACG
1 GGCTGTGTGGAGGACACGATTGAGACACACG
5571263 GGCTGTGTGGAGGACACGATTGAGACACACG
1 GGCTGTGTGGAGGACACGATTGAGACACACG
5571294 G
1 G
5571295 CCGTGTCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.40, T:0.16
Consensus pattern (31 bp):
GGCTGTGTGGAGGACACGATTGAGACACACG
Found at i:5575959 original size:102 final size:102
Alignment explanation
Indices: 5575783--5576695 Score: 1826
Period size: 102 Copynumber: 9.0 Consensus size: 102
5575773 AATGCTCACT
5575783 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
1 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
5575848 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
66 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
5575885 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
1 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
5575950 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
66 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
5575987 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
1 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
5576052 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
66 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
5576089 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
1 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
5576154 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
66 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
5576191 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
1 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
5576256 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
66 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
5576293 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
1 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
5576358 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
66 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
5576395 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
1 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
5576460 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
66 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
5576497 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
1 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
5576562 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
66 TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
5576599 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
1 TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
5576664 TATTCACATATGAACTTACCTTTGTAACAGCC
66 TATTCACATATGAACTTACCTTTGTAACAGCC
5576696 TGATTTTGGG
Statistics
Matches: 811, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 811 1.00
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.32
Consensus pattern (102 bp):
TATATCAACAACATAACATTTAAATTTACAAAATAACAAAGTATTATACATGATACATATTGCAT
TATTCACATATGAACTTACCTTTGTAACAGCCCAAAA
Found at i:5578012 original size:47 final size:45
Alignment explanation
Indices: 5577904--5578030 Score: 134
Period size: 47 Copynumber: 2.8 Consensus size: 45
5577894 TTGTGTGAGC
*
5577904 TAGTGTAAGACATGTCTGGGACAT-GCATCGGCCACATTTTGAGAGG
1 TAGTGTAAGACATGTCTGGGACATGGCATCGG-C-CATTATGAGAGG
* *
5577950 CAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGAGATGAGTGG
1 TAGTGTAAGA-CATGTCTGGGACATGGCATCGGCCATT---ATGAGAGG
* *
5577998 TAGTGCAAGACATGTCTGGGACAT-GCTTCGGCC
1 TAGTGTAAGACATGTCTGGGACATGGCATCGGCC
5578031 TCGAGACGTA
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
45 4 0.06
46 15 0.22
47 29 0.42
48 21 0.30
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (45 bp):
TAGTGTAAGACATGTCTGGGACATGGCATCGGCCATTATGAGAGG
Found at i:5580126 original size:13 final size:13
Alignment explanation
Indices: 5580108--5580136 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5580098 GGTTGTTTAT
5580108 TAAACTAATTAAC
1 TAAACTAATTAAC
5580121 TAAACTAATTAAC
1 TAAACTAATTAAC
5580134 TAA
1 TAA
5580137 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:5582203 original size:21 final size:20
Alignment explanation
Indices: 5582168--5582215 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
5582158 CATGTATTAG
*
5582168 ATATTAAATAGATATTTATT
1 ATATTAAAAAGATATTTATT
5582188 ATATTATAAAAGATATTTATT
1 ATATTA-AAAAGATATTTATT
5582209 A-ATTAAA
1 ATATTAAA
5582216 TAATTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 10 0.38
21 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
ATATTAAAAAGATATTTATT
Found at i:5584452 original size:46 final size:46
Alignment explanation
Indices: 5584400--5584766 Score: 522
Period size: 46 Copynumber: 8.0 Consensus size: 46
5584390 AGTGTGCTCT
5584400 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
5584446 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
5584492 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
5584538 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** *
5584584 ATGATA-GAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
5584630 GTGACATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** ** *
5584676 ATGATGGGAAAATGAATAAGAACATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
5584723 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
5584767 TCATGTCAAA
Statistics
Matches: 297, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
45 1 0.00
46 255 0.86
47 41 0.14
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:5584724 original size:24 final size:24
Alignment explanation
Indices: 5584651--5584725 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
5584641 TGTATAAGAC
5584651 CATGGTTGAAAGATACCATGGCAA
1 CATGGTTGAAAGATACCATGGCAA
* * *
5584675 CATGATGGGAAA-ATGA--ATAAG-AA
1 CATGGT-TGAAAGAT-ACCAT-GGCAA
5584698 CATGGTTGAAAGATACCATGGCAA
1 CATGGTTGAAAGATACCATGGCAA
5584722 CATG
1 CATG
5584726 ACAGAAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 5 0.13
23 12 0.32
24 16 0.42
25 5 0.13
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.20
Consensus pattern (24 bp):
CATGGTTGAAAGATACCATGGCAA
Found at i:5585073 original size:16 final size:17
Alignment explanation
Indices: 5585052--5585084 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5585042 ATGATGGAGT
5585052 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
5585068 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
5585085 TATACTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:5587366 original size:50 final size:49
Alignment explanation
Indices: 5587210--5587487 Score: 313
Period size: 49 Copynumber: 5.6 Consensus size: 49
5587200 GTACGCATAA
5587210 TAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGTTACATGTAG
1 TAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGTTACATGTAG
* **
5587259 TAGCCTACACTTAGTACTACACATGAAACCAATTATCCGTTACATGTAG
1 TAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGTTACATGTAG
* ** ** *
5587308 TAGCCTGCACTTAGTACTACACACGTGACCTAACCATTTGATACATGTAG
1 TAGCCTGCACTTAGTACTACACATGTGACC-AATTATCCGTTACATGTAG
* * * * ***
5587358 TAGTCTGCACTTAGTACTACACATGTGATCGAAGTTATCGGGTACGCATAG
1 TAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCCGTTACATGTAG
* * * * * **
5587409 TAGCCTACACTTAGTACTACACATGCGACGAATTATGCGGTACACCTAG
1 TAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGTTACATGTAG
*
5587458 TAGCCTGCACTTAGTACTACACACGTGACC
1 TAGCCTGCACTTAGTACTACACATGTGACC
5587488 TCACAATAGA
Statistics
Matches: 192, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
49 111 0.58
50 46 0.24
51 35 0.18
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (49 bp):
TAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGTTACATGTAG
Found at i:5587483 original size:150 final size:148
Alignment explanation
Indices: 5587214--5587488 Score: 415
Period size: 150 Copynumber: 1.8 Consensus size: 148
5587204 GCATAATAGC
* **
5587214 CTGCACTTAGTACTACACATGTGACCAATTATCCGTTACATGTAGTAGCCTACACTTAGTACTAC
1 CTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACATAGTAGCCTACACTTAGTACTAC
* **
5587279 ACATGAAACCAATTATCCGTTACATGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCA
66 ACATGAAACCAATTATCCGGTACACCTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCA
5587344 TTTGATACATGTAGTAGT
131 TTTGATACATGTAGTAGT
* * *
5587362 CTGCACTTAGTACTACACATGTGATCGAAGTTATCGGGTACGCATAGTAGCCTACACTTAGTACT
1 CTGCACTTAGTACTACACATGTGA-CCAA-TTATCCGGTACACATAGTAGCCTACACTTAGTACT
** * *
5587427 ACACATGCGACGAATTATGCGGTACACCTAGTAGCCTGCACTTAGTACTACACACGTGACCT
64 ACACATGAAACCAATTATCCGGTACACCTAGTAGCCTGCACTTAGTACTACACACGTGACCT
5587489 CACAATAGAT
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
148 24 0.21
149 3 0.03
150 85 0.76
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (148 bp):
CTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACATAGTAGCCTACACTTAGTACTAC
ACATGAAACCAATTATCCGGTACACCTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCA
TTTGATACATGTAGTAGT
Found at i:5587763 original size:26 final size:26
Alignment explanation
Indices: 5587734--5587785 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5587724 TCATACAACC
* *
5587734 CATGTAATAGTAATTTAACATTCAAT
1 CATGTAACAATAATTTAACATTCAAT
**
5587760 CATGTAACAATAATTTGCCATTCAAT
1 CATGTAACAATAATTTAACATTCAAT
5587786 TTCACATGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (26 bp):
CATGTAACAATAATTTAACATTCAAT
Found at i:5592728 original size:83 final size:83
Alignment explanation
Indices: 5592638--5592800 Score: 308
Period size: 83 Copynumber: 2.0 Consensus size: 83
5592628 TAATTCCTTA
*
5592638 TTTTTTTGAAATCTAATTCAACTTACACAATTTTTGGTGAAATTTCAAAGTCACGCAACTGCTGC
1 TTTTTTTGAAATCTAATTCAACTTACACAATTTTTGGTGAAATTTCAAAGTCACGCAACTGCAGC
5592703 TGTCCAACACTGTTTAAT
66 TGTCCAACACTGTTTAAT
*
5592721 TTTTTTTGAAATTTAATTCAACTTACACAATTTTTGGTGAAATTTCAAAGTCACGCAACTGCAGC
1 TTTTTTTGAAATCTAATTCAACTTACACAATTTTTGGTGAAATTTCAAAGTCACGCAACTGCAGC
5592786 TGTCCAACACTGTTT
66 TGTCCAACACTGTTT
5592801 TACTACTAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (83 bp):
TTTTTTTGAAATCTAATTCAACTTACACAATTTTTGGTGAAATTTCAAAGTCACGCAACTGCAGC
TGTCCAACACTGTTTAAT
Found at i:5593162 original size:100 final size:100
Alignment explanation
Indices: 5593031--5593223 Score: 253
Period size: 100 Copynumber: 1.9 Consensus size: 100
5593021 TAGACAAGGC
* * * *
5593031 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTA
1 TATCGGGTACGCATAGTAGCCAGCACTTAGTACTACACACGCGACC-AACCATCCGATACACGTA
* * * *
5593096 GTAG-TTGCAGTTCGTACTACACACGTGATCGAAGT
65 GTAGCCTACACTTAGTACTACACACGTGATCGAAGT
* * ** *
5593131 TATCGGGTATGCATAGTAGCCAGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAG
1 TATCGGGTACGCATAGTAGCCAGCACTTAGTACTACACACGCGACCAACCATCCGATACACGTAG
5593196 TAGCCTACACTTAGTACTACACACGTGA
66 TAGCCTACACTTAGTACTACACACGTGA
5593224 CCTCACAATA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 18 0.23
100 61 0.77
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (100 bp):
TATCGGGTACGCATAGTAGCCAGCACTTAGTACTACACACGCGACCAACCATCCGATACACGTAG
TAGCCTACACTTAGTACTACACACGTGATCGAAGT
Found at i:5593197 original size:49 final size:49
Alignment explanation
Indices: 5593044--5593225 Score: 170
Period size: 49 Copynumber: 3.7 Consensus size: 49
5593034 CTGGTACGCA
* ** * *
5593044 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCAGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
** * * * * ** *
5593094 TAGTAG-TTGCAGTTCGTACTACACACGTGATCGAAGTTATCGGGTATGCA
1 TAGTAGCCAGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACG
* *
5593144 TAGTAGCCAGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCAGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
5593193 TAGTAGCCTA-CACTTAGTACTACACACGTGACC
1 TAGTAGCC-AGCACTTAGTACTACACACGTGACC
5593226 TCACAATAGA
Statistics
Matches: 104, Mismatches: 24, Indels: 9
0.76 0.18 0.07
Matches are distributed among these distances:
49 62 0.60
50 24 0.23
51 18 0.17
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCAGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:5593502 original size:27 final size:27
Alignment explanation
Indices: 5593472--5593525 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5593462 TCATACAACC
* *
5593472 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
5593499 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
5593526 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:5597948 original size:40 final size:40
Alignment explanation
Indices: 5597900--5598173 Score: 485
Period size: 40 Copynumber: 6.8 Consensus size: 40
5597890 GCAAACACCT
* * *
5597900 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
5597940 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
5597980 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
5598020 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
5598060 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
5598100 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
5598140 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTC
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
5598174 ATATATATAT
Statistics
Matches: 224, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 224 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:5601272 original size:47 final size:47
Alignment explanation
Indices: 5601204--5601409 Score: 313
Period size: 47 Copynumber: 4.4 Consensus size: 47
5601194 CCCTTCGGGA
* * * * *
5601204 CTTATCACATTTATACTCTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5601251 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
5601298 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5601345 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5601392 CTTATCACATATACACAC
1 CTTATCACATATATACAC
5601410 CTTATACATC
Statistics
Matches: 143, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 143 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:5601366 original size:94 final size:94
Alignment explanation
Indices: 5601204--5601409 Score: 358
Period size: 94 Copynumber: 2.2 Consensus size: 94
5601194 CCCTTCGGGA
* * *
5601204 CTTATCACATTTATACTCTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
*
5601269 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
5601298 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACGC
1 CTTATCACATATACACACTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
5601363 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
5601392 CTTATCACATATACACAC
1 CTTATCACATATACACAC
5601410 CTTATACATC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 106 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACATATACACACTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:5606372 original size:46 final size:47
Alignment explanation
Indices: 5606216--5606581 Score: 284
Period size: 46 Copynumber: 7.8 Consensus size: 47
5606206 TCACTTGTGT
* * * * *
5606216 GAGCTAGTGCAAGACATGTCTGGGACATGCATCGGCCAC-A-TTTTGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGT-A
* * *
5606262 GAGGCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATG-A
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA
* * * * * *
5606310 GTGCTAGTATAAGACATGTTTGGGACATGCTTCGGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA
* * *
5606357 -AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-TTTTGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGT-A
* * *
5606402 GAGGCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATG-A
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA
* * * * * *
5606450 GTGCTAGTATAAGACATGTTTGGGACATGCTTCGGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA
* * *
5606497 -AGCCAGTGTAAGACATGTCTGGGACATGGCAACGGCAC-AGATATGCTA
1 GAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGGC-CTCGAGATG-TA
* *
5606545 GAACTTA-TGTAAGACTATGTCTGGGACATGCATCGGC
1 GAGC-CAGTGTAAGAC-ATGTCTGGGACATGCATCGGC
5606582 ACCTAACCCC
Statistics
Matches: 249, Mismatches: 53, Indels: 33
0.74 0.16 0.10
Matches are distributed among these distances:
44 1 0.00
45 2 0.01
46 104 0.42
47 66 0.27
48 41 0.16
49 19 0.08
50 16 0.06
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (47 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA
Found at i:5606478 original size:140 final size:140
Alignment explanation
Indices: 5606221--5606524 Score: 599
Period size: 140 Copynumber: 2.2 Consensus size: 140
5606211 TGTGTGAGCT
*
5606221 AGTGCAAGACATGTCTGGGACATGCATCGGCCACATTTTGAGAGGCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTTTGAGAGGCAGTGTAAGACCATGTCTGG
5606286 GACATGGCATCGGCATTGAGATGAGTGCTAGTATAAGACATGTTTGGGACATGCTTCGGCCTCGA
66 GACATGGCATCGGCATTGAGATGAGTGCTAGTATAAGACATGTTTGGGACATGCTTCGGCCTCGA
5606351 GACGTAAGCC
131 GACGTAAGCC
5606361 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTTTGAGAGGCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTTTGAGAGGCAGTGTAAGACCATGTCTGG
5606426 GACATGGCATCGGCATTGAGATGAGTGCTAGTATAAGACATGTTTGGGACATGCTTCGGCCTCGA
66 GACATGGCATCGGCATTGAGATGAGTGCTAGTATAAGACATGTTTGGGACATGCTTCGGCCTCGA
5606491 GACGTAAGCC
131 GACGTAAGCC
5606501 AGTGTAAGACATGTCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
5606525 GCAACGGCAC
Statistics
Matches: 163, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 163 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTTTGAGAGGCAGTGTAAGACCATGTCTGG
GACATGGCATCGGCATTGAGATGAGTGCTAGTATAAGACATGTTTGGGACATGCTTCGGCCTCGA
GACGTAAGCC
Found at i:5607739 original size:21 final size:20
Alignment explanation
Indices: 5607713--5607751 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
5607703 TCAAATTGGT
5607713 CACACGGGCGTGTTGCCCTTC
1 CACACGGGCGTGTT-CCCTTC
5607734 CACACGGGCGTGTTCCCT
1 CACACGGGCGTGTTCCCT
5607752 GTTTCAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.10, C:0.38, G:0.28, T:0.23
Consensus pattern (20 bp):
CACACGGGCGTGTTCCCTTC
Found at i:5611067 original size:50 final size:50
Alignment explanation
Indices: 5610946--5611225 Score: 206
Period size: 50 Copynumber: 5.6 Consensus size: 50
5610936 TCTCTAGTAG
* *** * * *
5610946 CATAGTAACCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACATGACTTAACCATCTGGTACA
* * * * * * *
5610996 CGTAGAAGCCTACAGTCAGTACTAAACACATGACTTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACATGACTTAACCATCTGGTACA
* * * * * ** * * **
5611046 CGTAGTAGCTTGCACTTAGTACTACATACGTGA-TCGAAGTTAACGGGTATG
1 CATAGTAGCCTGCACTTAGTACTACACACATGACT-TAA-CCATCTGGTACA
***
5611097 CATAGTAGCCTGCACTTAGTACTACACATGCGACCTATAA--ATCTGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACATGA-CT-TAACCATCTGGTACA
* ** *
5611147 CTTAGTAGCCTGCACTTAGTACTACACATGTGACTTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACATGACTTAACCATCTGGTACA
*
5611197 CATAGTAGCCTACACTTAGTACTACACAC
1 CATAGTAGCCTGCACTTAGTACTACACAC
5611226 GTGATCGAAG
Statistics
Matches: 177, Mismatches: 47, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
48 3 0.02
49 3 0.02
50 135 0.76
51 33 0.19
53 3 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACACATGACTTAACCATCTGGTACA
Found at i:5611219 original size:151 final size:151
Alignment explanation
Indices: 5610945--5611321 Score: 521
Period size: 151 Copynumber: 2.5 Consensus size: 151
5610935 CTCTCTAGTA
* * *
5610945 GCATAGTAACCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGAAGCCTACA
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGCCTGCA
* * * * * * *
5611010 GTCAGTACTAAACACATGACTTAACCATCTGATACACGTAGTAGCTTGCACTTAGTACTACATAC
66 CTTAGTACTACACACATGACTTAACCATCTGATACACATAGTAGCCTACACTTAGTACTACACAC
*
5611075 GTGATCGAAGTTAACGGGTAT
131 GTGATCGAAGTTAACGGGTAC
* *
5611096 GCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATAAATCTGGTACACTTAGTAGCCTGCA
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGCCTGCA
**
5611161 CTTAGTACTACACATGTGACTTAACCATCTGATACACATAGTAGCCTACACTTAGTACTACACAC
66 CTTAGTACTACACACATGACTTAACCATCTGATACACATAGTAGCCTACACTTAGTACTACACAC
*
5611226 GTGATCGAAGTTAATGGGTAC
131 GTGATCGAAGTTAACGGGTAC
* * * * *
5611247 GCATAGTAGCTTGCAC-----ACTACACATGTGACCTATCAATCTAGTACCCGTAGTAGCCTGAA
1 GCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGCCTGCA
*
5611307 CTTAGTACTGCACAC
66 CTTAGTACTACACAC
5611322 GTTACTCACA
Statistics
Matches: 201, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
146 51 0.25
151 150 0.75
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (151 bp):
GCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGCCTGCA
CTTAGTACTACACACATGACTTAACCATCTGATACACATAGTAGCCTACACTTAGTACTACACAC
GTGATCGAAGTTAACGGGTAC
Found at i:5611703 original size:19 final size:20
Alignment explanation
Indices: 5611675--5611721 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
5611665 AAGAACAGGT
5611675 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
5611696 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
5611715 TATATAT
1 TATATAT
5611722 ACTTAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:5614707 original size:22 final size:22
Alignment explanation
Indices: 5614682--5614740 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
5614672 ACAGCTCGTA
5614682 AGAGCTTATTGTTCAGCTCAAT
1 AGAGCTTATTGTTCAGCTCAAT
*
5614704 AGAGCTTACCATT-TTTAGCTCAAT
1 AGAGCTT---ATTGTTCAGCTCAAT
5614728 AGAGCTTATTGTT
1 AGAGCTTATTGTT
5614741 TATCAGCCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
21 3 0.09
22 9 0.28
24 17 0.53
25 3 0.09
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (22 bp):
AGAGCTTATTGTTCAGCTCAAT
Found at i:5616784 original size:29 final size:29
Alignment explanation
Indices: 5616742--5616799 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
5616732 AAATGTTTGC
*
5616742 CAATTGGGTTATGAAATATGGTCAAATAT
1 CAATTGGGTTATGAAATATCGTCAAATAT
5616771 CAATTGGGTTATGAAATATCGTCAAATAT
1 CAATTGGGTTATGAAATATCGTCAAATAT
5616800 GCTTGTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (29 bp):
CAATTGGGTTATGAAATATCGTCAAATAT
Found at i:5620112 original size:85 final size:85
Alignment explanation
Indices: 5619955--5620112 Score: 201
Period size: 85 Copynumber: 1.8 Consensus size: 85
5619945 ACTAGATATC
* * * * *
5619955 GTGTAAGACCGTGTCTGGGACACAGGCCTTGATTTGAGAATTACGTGTAAGATCATGTCTGGGGC
1 GTGTAAGACCGTGTCTGGGACACAGGCATTGATCT-AGAATTACATGTAAGACCATGTCCGGGGC
*
5620020 ATTGGCATCATATCTGATTTT
65 ATCGGCATCATATCTGATTTT
* * *
5620041 GTGTAAGACCTTGTTTGGGACAGAGGCATTGATACT-GAATTACATGTAAGACCATGTCCGGGGC
1 GTGTAAGACCGTGTCTGGGACACAGGCATTGAT-CTAGAATTACATGTAAGACCATGTCCGGGGC
*
5620105 GTCGGCAT
65 ATCGGCAT
5620113 TGTACCCAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
85 31 0.51
86 29 0.48
87 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (85 bp):
GTGTAAGACCGTGTCTGGGACACAGGCATTGATCTAGAATTACATGTAAGACCATGTCCGGGGCA
TCGGCATCATATCTGATTTT
Found at i:5623197 original size:43 final size:42
Alignment explanation
Indices: 5623149--5623318 Score: 184
Period size: 43 Copynumber: 4.0 Consensus size: 42
5623139 AGCTCATACA
* ***
5623149 ATGCCAACGTCCCAGATGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACAAAATCAAATAT-G
5623192 ATGCC-ACTGTCCCAGACAG-GGTCTTACACAAAATCAAATATG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACAAAATCAAATATG
* *
5623234 ATGCCAATGTCCTAGACGTGGTCTTACACATAAATCATAAGT-TG
1 ATGCCAACGTCCCAGACGTGGTCTTACACA-AAATCA-AA-TATG
* * *
5623278 ATGCCAACGTCCCAGACGTGGCCTTACACGAAATCACATAT
1 ATGCCAACGTCCCAGACGTGGTCTTACACAAAATCAAATAT
5623319 CAGATCCTAT
Statistics
Matches: 108, Mismatches: 11, Indels: 17
0.79 0.08 0.12
Matches are distributed among these distances:
41 2 0.02
42 29 0.27
43 45 0.42
44 31 0.29
45 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACAAAATCAAATATG
Found at i:5640626 original size:56 final size:56
Alignment explanation
Indices: 5640534--5640645 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
5640524 AGAGTCACCT
* *
5640534 TGGCCCAGTACAGAAATCAAAATGAAACCCATAGGCCCATAGTAGATACAGAACAA
1 TGGCCCAGTACAGAAATCAAAATGAAACCCACAGGCCCATAGCAGATACAGAACAA
* *
5640590 TGGCCCAGTACAGAAATCAGAATGAAATCCACAGGCCCATAGCAGATACAGAACAA
1 TGGCCCAGTACAGAAATCAAAATGAAACCCACAGGCCCATAGCAGATACAGAACAA
5640646 ATATATCATG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.44, C:0.24, G:0.19, T:0.13
Consensus pattern (56 bp):
TGGCCCAGTACAGAAATCAAAATGAAACCCACAGGCCCATAGCAGATACAGAACAA
Found at i:5651287 original size:39 final size:40
Alignment explanation
Indices: 5651230--5651330 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
5651220 TGGATGAAAA
* * *
5651230 CCGGGCTAAGTCCCGAAGGCATCTCCACTAGTGACT-AAT
1 CCGGGCTAAGTCCTGAAGGCATCTCCACGAGTGACTAAAC
*** *
5651269 CCGGGCTAAGTCCTGAAGGCATCTGTGCGAGTTACTAAAC
1 CCGGGCTAAGTCCTGAAGGCATCTCCACGAGTGACTAAAC
5651309 CCGGGCTAAGTCCTGAAGGCAT
1 CCGGGCTAAGTCCTGAAGGCAT
5651331 TTGTGTGAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 30 0.56
40 24 0.44
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.21
Consensus pattern (40 bp):
CCGGGCTAAGTCCTGAAGGCATCTCCACGAGTGACTAAAC
Found at i:5651323 original size:40 final size:40
Alignment explanation
Indices: 5651230--5651391 Score: 209
Period size: 40 Copynumber: 4.1 Consensus size: 40
5651220 TGGATGAAAA
*** * *
5651230 CCGGGCTAAGTCCCGAAGGCATCTCCACTAGTGACT-AAT
1 CCGGGCTAAGTCCCGAAGGCATCTGTGCGAGTTACTAAAT
* *
5651269 CCGGGCTAAGTCCTGAAGGCATCTGTGCGAGTTACTAAAC
1 CCGGGCTAAGTCCCGAAGGCATCTGTGCGAGTTACTAAAT
* * * *
5651309 CCGGGCTAAGTCCTGAAGGCATTTGTGTGAATTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATCTGTGCGAGTTACTAAAT
*
5651349 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATCTGTGCGAGTTACTAAAT
5651389 CCG
1 CCG
5651392 ATTTTCATAG
Statistics
Matches: 108, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 30 0.28
40 78 0.72
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATCTGTGCGAGTTACTAAAT
Found at i:5660233 original size:9 final size:9
Alignment explanation
Indices: 5660219--5660247 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
5660209 ATGGTTAGGG
5660219 TTTCCAAGC
1 TTTCCAAGC
5660228 TTTCCAAGC
1 TTTCCAAGC
5660237 TTTCCAAGC
1 TTTCCAAGC
5660246 TT
1 TT
5660248 AATAGTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.31, G:0.10, T:0.38
Consensus pattern (9 bp):
TTTCCAAGC
Found at i:5661528 original size:54 final size:55
Alignment explanation
Indices: 5661464--5661616 Score: 193
Period size: 54 Copynumber: 2.8 Consensus size: 55
5661454 TGGCATTTGG
* *
5661464 TAAGATAAGGATATCATGTAAGACCATGGCAAGGCATGGCATTGATAAGTT-CTA
1 TAAGGTAAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTACTA
* * * * *
5661518 TAAGGTAAGGAAATCATGTAAGAACATGTCAAGACATGGCATTGATGAGTTACTA
1 TAAGGTAAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTACTA
* **
5661573 TAAGGCAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTG
1 TAAGG-TAAGGATATCATGTAAGACCATGCCAAGGCATGGCATTG
5661617 GTGAGTTCAT
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
54 45 0.54
55 35 0.42
56 4 0.05
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.24
Consensus pattern (55 bp):
TAAGGTAAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTACTA
Found at i:5661594 original size:55 final size:54
Alignment explanation
Indices: 5661478--5661663 Score: 180
Period size: 55 Copynumber: 3.4 Consensus size: 54
5661468 ATAAGGATAT
* * * *
5661478 CATGTAAGACCATGGCAAGGCATGGCATTGATAAGTTCTATAAGGTAAGGAAAT
1 CATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGAAAGGAAAC
* * * **
5661532 CATGTAAGAACATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGG-TCC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATGAGTT-CTATAAGG-AAAGGAAAC
* * *
5661587 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATATA-GCAAGGATAC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATA-AGGAAAGGAAAC
* * * *
5661640 CACGTACGACCATGTCAAGACATG
1 CATGTAAGACCATGCCAAGGCATG
5661664 ACAATAGTAA
Statistics
Matches: 110, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
52 4 0.04
53 26 0.24
54 35 0.32
55 41 0.37
56 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (54 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGAAAGGAAAC
Found at i:5663587 original size:13 final size:13
Alignment explanation
Indices: 5663571--5663603 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5663561 TTTAATTAAA
*
5663571 TTAGTTAATTAGT
1 TTAGATAATTAGT
5663584 TTAGATAATTAGT
1 TTAGATAATTAGT
5663597 TTA-ATAA
1 TTAGATAA
5663604 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:5668395 original size:13 final size:13
Alignment explanation
Indices: 5668379--5668411 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5668369 TTTAATTAAA
*
5668379 TTAGTTAATTAGT
1 TTAGATAATTAGT
5668392 TTAGATAATTAGT
1 TTAGATAATTAGT
5668405 TTA-ATAA
1 TTAGATAA
5668412 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:5673703 original size:5 final size:5
Alignment explanation
Indices: 5673693--5673762 Score: 70
Period size: 5 Copynumber: 13.0 Consensus size: 5
5673683 TGAATCCTCC
5673693 TATTT TATTT TATTTT TATTT ATATTT TA-TT TATTT TATTCT TATTTT
1 TATTT TATTT TA-TTT TATTT -TATTT TATTT TATTT TATT-T TA-TTT
*
5673741 TCTTT TGATTT TATTT TCATTT
1 TATTT T-ATTT TATTT T-ATTT
5673763 CAATTTTCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
4 4 0.07
5 27 0.48
6 23 0.41
7 2 0.04
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:5673711 original size:6 final size:6
Alignment explanation
Indices: 5673695--5673762 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
5673685 AATCCTCCTA
* * * *
5673695 TTTTA- TTTTAT TTTTAT TTATAT TTTATTT ATTTTAT TCTTAT TTTTCT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT -TTTTAT TTTTAT TTTTAT
* *
5673744 TTTGA- TTTTAT TTTCAT TT
1 TTTTAT TTTTAT TTTTAT TT
5673763 CAATTTTCTT
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
5 9 0.19
6 32 0.67
7 4 0.08
8 3 0.06
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:5673711 original size:11 final size:11
Alignment explanation
Indices: 5673695--5673762 Score: 63
Period size: 11 Copynumber: 6.2 Consensus size: 11
5673685 AATCCTCCTA
5673695 TTTTATTTTAT
1 TTTTATTTTAT
5673706 TTTTA-TTTAT
1 TTTTATTTTAT
5673716 ATTTTA-TTTA-
1 -TTTTATTTTAT
5673726 TTTTATTCTTAT
1 TTTTATT-TTAT
*
5673738 TTTTCTTTTGA-
1 TTTTATTTT-AT
5673749 TTTTATTTTCAT
1 TTTTATTTT-AT
5673761 TT
1 TT
5673763 CAATTTTCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
9 5 0.10
10 6 0.12
11 28 0.58
12 9 0.19
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:5673752 original size:32 final size:31
Alignment explanation
Indices: 5673693--5673756 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 31
5673683 TGAATCCTCC
5673693 TATTTTATTTTATTTTTATTTATATTTTATT
1 TATTTTATTTTATTTTTATTTATATTTTATT
*
5673724 TATTTTATTCTTATTTTTCTTT-TGATTTTATT
1 TATTTTATT-TTATTTTTATTTAT-ATTTTATT
5673756 T
1 T
5673757 TCATTTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.77
Consensus pattern (31 bp):
TATTTTATTTTATTTTTATTTATATTTTATT
Found at i:5674479 original size:26 final size:27
Alignment explanation
Indices: 5674427--5674482 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5674417 TAAGTATACA
5674427 GGAATGACATCAAAAACCTAAATTTTT
1 GGAATGACATCAAAAACCTAAATTTTT
5674454 GGAATGACATCAAAAACCTAAATTTTT
1 GGAATGACATCAAAAACCTAAATTTTT
5674481 GG
1 GG
5674483 TTAGATTTTT
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (27 bp):
GGAATGACATCAAAAACCTAAATTTTT
Found at i:5676710 original size:13 final size:13
Alignment explanation
Indices: 5676694--5676726 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5676684 TTTAATAAAA
*
5676694 TTAGTTAATTAGT
1 TTAGATAATTAGT
5676707 TTAGATAATTAGT
1 TTAGATAATTAGT
5676720 TTA-ATAA
1 TTAGATAA
5676727 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:5699168 original size:7 final size:7
Alignment explanation
Indices: 5699151--5699180 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5699141 ACTTTCCCTA
5699151 AAAAAAT
1 AAAAAAT
5699158 -AAAAAT
1 AAAAAAT
5699164 AAAAAAT
1 AAAAAAT
5699171 AAAAAAT
1 AAAAAAT
5699178 AAA
1 AAA
5699181 CAAACAGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:5699168 original size:14 final size:15
Alignment explanation
Indices: 5699149--5699180 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
5699139 TGACTTTCCC
5699149 TAAAAAAAT-AAAAA
1 TAAAAAAATAAAAAA
5699163 T-AAAAAATAAAAAA
1 TAAAAAAATAAAAAA
5699177 TAAA
1 TAAA
5699181 CAAACAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.44
14 7 0.44
15 2 0.12
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:5699899 original size:18 final size:19
Alignment explanation
Indices: 5699859--5699900 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
5699849 CCCATATTAC
5699859 GGCCCATGTCGGCCCACAT
1 GGCCCATGTCGGCCCACAT
*
5699878 -GCCCTTGT-GGCCCACAT
1 GGCCCATGTCGGCCCACAT
5699895 GGCCCA
1 GGCCCA
5699901 AAATTGTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.14, C:0.43, G:0.26, T:0.17
Consensus pattern (19 bp):
GGCCCATGTCGGCCCACAT
Found at i:5700094 original size:43 final size:42
Alignment explanation
Indices: 5700011--5700128 Score: 107
Period size: 43 Copynumber: 2.8 Consensus size: 42
5700001 CTGAAAGCTC
** * * *
5700011 GTATAATGCCAACGTCCTAGAC-GTGGTCATACATGTAATCAA
1 GTATAATGCCATTGTCCTAGACAG-GGTCTTACACGAAATCAA
5700053 GTATCAATGCCATTGTCCTAGACAGGGTCTTACACGAAATCAA
1 GTAT-AATGCCATTGTCCTAGACAGGGTCTTACACGAAATCAA
* * * *
5700096 ATATGATGCC-TATGTCCCA-ACATGGTCTTACAC
1 GTATAATGCCAT-TGTCCTAGACAGGGTCTTACAC
5700129 ATAAATCTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 14 0.22
42 15 0.23
43 34 0.53
44 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (42 bp):
GTATAATGCCATTGTCCTAGACAGGGTCTTACACGAAATCAA
Found at i:5701989 original size:15 final size:15
Alignment explanation
Indices: 5701945--5701985 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
5701935 TATTTTAAAA
*
5701945 TTATTTTCTGTG--T
1 TTATTTTGTGTGAAT
5701958 TTATTTTGTGTGAAT
1 TTATTTTGTGTGAAT
5701973 TTATTTT-TGTGAA
1 TTATTTTGTGTGAA
5701986 ATTTTCGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 11 0.44
14 6 0.24
15 8 0.32
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.63
Consensus pattern (15 bp):
TTATTTTGTGTGAAT
Found at i:5706003 original size:23 final size:24
Alignment explanation
Indices: 5705965--5706009 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
5705955 TTTGCTCTTC
*
5705965 TAGCATGAACTTGTCTTACCTTTT
1 TAGCATGAACTCGTCTTACCTTTT
5705989 TAGCAT-AACTCGTCTTACCTT
1 TAGCATGAACTCGTCTTACCTT
5706010 ACCTTACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (24 bp):
TAGCATGAACTCGTCTTACCTTTT
Found at i:5706332 original size:55 final size:53
Alignment explanation
Indices: 5706125--5706332 Score: 188
Period size: 55 Copynumber: 3.8 Consensus size: 53
5706115 ATCCTTTTGA
* * * * *
5706125 AACTTGCCATTGCCATGTCTCGGCATGGTCTTACATGGTATCCTTGCGTTATG
1 AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATG
* * *
5706178 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTTCCTTATGG
1 AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCC-TTGCCTTAT-G
* * ** * *
5706232 TAACTTATCAATGCCATGTCTTAACATGGTCTTACATGATTTCCTTGCCTTA-G
1 -AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATG
* *
5706285 AAACCTTA-CAATTTGTCATGCCTTGGCATGGCCTTACATGGTATCCTT
1 -AA-CTTACCAA--TGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
5706333 AAACCCTAAT
Statistics
Matches: 123, Mismatches: 25, Indels: 12
0.77 0.16 0.08
Matches are distributed among these distances:
52 2 0.02
53 47 0.38
54 5 0.04
55 67 0.54
56 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (53 bp):
AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATG
Found at i:5715228 original size:40 final size:40
Alignment explanation
Indices: 5715165--5715309 Score: 186
Period size: 40 Copynumber: 3.6 Consensus size: 40
5715155 TTCTAGCACC
* * *
5715165 AGCCTGCGGGTCTCT-AGCCCGGATAGCATTCTAGCACGA-
1 AGCCTGCGGGTCTTTAAGCCCGGATAACATTCTAGCA-TAT
* *
5715204 AGCCTGCGAGTCTTTAAGCCCGGATAACATTCCAGCATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATAACATTCTAGCATAT
* * *
5715244 AGCCTGTGGGTCTTTAAGCCCGAAAAACATTCTAGCATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATAACATTCTAGCATAT
*
5715284 AACCTGCGGGTCTTTAAGCCCGGATA
1 AGCCTGCGGGTCTTTAAGCCCGGATA
5715310 CAATTCCTCA
Statistics
Matches: 90, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 14 0.16
40 76 0.84
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
AGCCTGCGGGTCTTTAAGCCCGGATAACATTCTAGCATAT
Found at i:5729505 original size:55 final size:55
Alignment explanation
Indices: 5729417--5729534 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 55
5729407 CGTGCGATAT
** * * ** *
5729417 AACCGTGGTCGAGCCTACCAAAACAACATGGGCATGAGATACGCCTGTGTGGAAG
1 AACCGTGGAAGAGCCTACCAAAACAACACGGGCATGAGACACGCCCATGTGGAAC
** *
5729472 AACCGTGGAAGAGCCTACCAAAACAGTACGGGCATGCGACACGCCCATGTGGAAC
1 AACCGTGGAAGAGCCTACCAAAACAACACGGGCATGAGACACGCCCATGTGGAAC
*
5729527 ACCCGTGG
1 AACCGTGG
5729535 TCAAACTTGT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.31, C:0.27, G:0.29, T:0.14
Consensus pattern (55 bp):
AACCGTGGAAGAGCCTACCAAAACAACACGGGCATGAGACACGCCCATGTGGAAC
Found at i:5730544 original size:45 final size:45
Alignment explanation
Indices: 5730401--5730755 Score: 522
Period size: 45 Copynumber: 8.0 Consensus size: 45
5730391 CCGAATTCGT
* * *
5730401 TCACCGGCATT-TCGCCTGCTAGGCTCGAA-GCCCG-ATA-TCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATC
* *
5730443 TCACCAGCATTATAGCCTGCTAGGCTCGAAGG-CCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* * *
5730487 TCACCGGTATTATAGCATGTTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* *
5730532 TCACCGGCATTATAGCCTGCTAGGCTCAAAAGCCCAAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
5730577 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* *
5730622 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCAGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
** * *
5730667 TCACTAGCATTATAGCATGCTAGGCTCAAAGGCCCGAATAGTATA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
5730712 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTAT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTAT
5730756 TGTACGATAT
Statistics
Matches: 284, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
42 10 0.04
43 20 0.07
44 33 0.12
45 221 0.78
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:5731669 original size:74 final size:74
Alignment explanation
Indices: 5731590--5731767 Score: 277
Period size: 74 Copynumber: 2.4 Consensus size: 74
5731580 TAATAAGGGA
* *
5731590 AAATTTAACCGGAAATATTAAGAGCAAATTTAACCGGAATTATTAAGAACAAATGTAA-CGGAAT
1 AAATTTAACCGGAATTATTAAGAGCAAATTTAACCGAAATTATTAAG-ACAAATGTAACCGGAAT
5731654 TATTAAGAAC
65 TATTAAGAAC
* *
5731664 AAATTTAACCGGAATTATTAAGAGCAAATTTAACCGAAATTATTAAGACAAGTTTAACCGGAATT
1 AAATTTAACCGGAATTATTAAGAGCAAATTTAACCGAAATTATTAAGACAAATGTAACCGGAATT
*
5731729 ATTAAGAGC
66 ATTAAGAAC
* *
5731738 AAATTTAACCGGAATTATGAAGAACAAATT
1 AAATTTAACCGGAATTATTAAGAGCAAATT
5731768 AACAAGCTTG
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
73 8 0.08
74 88 0.92
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (74 bp):
AAATTTAACCGGAATTATTAAGAGCAAATTTAACCGAAATTATTAAGACAAATGTAACCGGAATT
ATTAAGAAC
Found at i:5731765 original size:25 final size:25
Alignment explanation
Indices: 5731590--5731767 Score: 270
Period size: 25 Copynumber: 7.2 Consensus size: 25
5731580 TAATAAGGGA
* *
5731590 AAATTTAACCGGAAATATTAAGAGC
1 AAATTTAACCGGAATTATTAAGAAC
5731615 AAATTTAACCGGAATTATTAAGAAC
1 AAATTTAACCGGAATTATTAAGAAC
*
5731640 AAATGTAA-CGGAATTATTAAGAAC
1 AAATTTAACCGGAATTATTAAGAAC
*
5731664 AAATTTAACCGGAATTATTAAGAGC
1 AAATTTAACCGGAATTATTAAGAAC
*
5731689 AAATTTAACCGAAATTATTAAG-AC
1 AAATTTAACCGGAATTATTAAGAAC
* *
5731713 AAGTTTAACCGGAATTATTAAGAGC
1 AAATTTAACCGGAATTATTAAGAAC
*
5731738 AAATTTAACCGGAATTATGAAGAAC
1 AAATTTAACCGGAATTATTAAGAAC
5731763 AAATT
1 AAATT
5731768 AACAAGCTTG
Statistics
Matches: 138, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
24 44 0.32
25 94 0.68
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (25 bp):
AAATTTAACCGGAATTATTAAGAAC
Found at i:5731770 original size:49 final size:50
Alignment explanation
Indices: 5731590--5731767 Score: 279
Period size: 49 Copynumber: 3.6 Consensus size: 50
5731580 TAATAAGGGA
* * *
5731590 AAATTTAACCGGAAATATTAAGAGCAAATTTAACCGGAATTATTAAGAAC
1 AAATTTAACCGGAATTATTAAGAACAAATTTAACCGGAATTATTAAGAGC
*
5731640 AAATGTAA-CGGAATTATTAAGAACAAATTTAACCGGAATTATTAAGAGC
1 AAATTTAACCGGAATTATTAAGAACAAATTTAACCGGAATTATTAAGAGC
* *
5731689 AAATTTAACCGAAATTATTAAG-ACAAGTTTAACCGGAATTATTAAGAGC
1 AAATTTAACCGGAATTATTAAGAACAAATTTAACCGGAATTATTAAGAGC
*
5731738 AAATTTAACCGGAATTATGAAGAACAAATT
1 AAATTTAACCGGAATTATTAAGAACAAATT
5731768 AACAAGCTTG
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
49 91 0.78
50 25 0.22
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (50 bp):
AAATTTAACCGGAATTATTAAGAACAAATTTAACCGGAATTATTAAGAGC
Found at i:5742056 original size:46 final size:47
Alignment explanation
Indices: 5741911--5742134 Score: 231
Period size: 47 Copynumber: 4.8 Consensus size: 47
5741901 TGTATGTGAT
*** *
5741911 CTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCACCTTATGAGAG
1 CTAGTGTAAGACCATGTTTGGGACATGGCATCGG-CACGAGATGAAAG
* * *
5741957 CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAAAG
1 CTAGTGTAAGACCATGTTTGGGACATGGCATCGGCA-CGAGATGAAAG
*
5742005 CTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCTACGAGATGATAG
1 CTAGTGTAAGACCATGTTTGGGACATGGCATCGGC-ACGAGATGAAAG
* * ** **
5742051 TTAGTGTAAGACCATGTTTGGGACATGGCATCGACTTGAGATGTGAG
1 CTAGTGTAAGACCATGTTTGGGACATGGCATCGGCACGAGATGAAAG
* * * *
5742098 CCAGTGTAAAACCATGTCTGGGACATGGCATCAGCAC
1 CTAGTGTAAGACCATGTTTGGGACATGGCATCGGCAC
5742135 CTTACCCATG
Statistics
Matches: 147, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
46 37 0.25
47 80 0.54
48 30 0.20
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (47 bp):
CTAGTGTAAGACCATGTTTGGGACATGGCATCGGCACGAGATGAAAG
Found at i:5742073 original size:94 final size:93
Alignment explanation
Indices: 5741911--5742129 Score: 285
Period size: 94 Copynumber: 2.3 Consensus size: 93
5741901 TGTATGTGAT
**
5741911 CTAGTGTAAGACATGTTTGGGACATGCATCGGCCACCTTATGAGAGCTAGTGTAAGACCATGTCT
1 CTAGTGTAAGACATGTTTGGGACATGCATCGGCCACCAGATGAGAGCTAGTGTAAGACCATGTCT
*
5741976 GGGACATGGCATCGGCATTGAGACGAAAG
66 GGGACATGGCATCGAC-TTGAGACGAAAG
* * * * *
5742005 CTAGTGTAAGACATGTTTGGGACATGCATCGGCTACGAGATGATAGTTAGTGTAAGACCATGTTT
1 CTAGTGTAAGACATGTTTGGGACATGCATCGGCCACCAGATGAGAGCTAGTGTAAGACCATGTCT
* **
5742070 GGGACATGGCATCGACTTGAGATGTGAG
66 GGGACATGGCATCGACTTGAGACGAAAG
* * *
5742098 CCAGTGTAAAACCATGTCTGGGACATGGCATC
1 CTAGTGTAAGA-CATGTTTGGGACAT-GCATC
5742130 AGCACCTTAC
Statistics
Matches: 109, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
93 18 0.17
94 86 0.79
95 5 0.05
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (93 bp):
CTAGTGTAAGACATGTTTGGGACATGCATCGGCCACCAGATGAGAGCTAGTGTAAGACCATGTCT
GGGACATGGCATCGACTTGAGACGAAAG
Found at i:5744596 original size:27 final size:26
Alignment explanation
Indices: 5744559--5744670 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
5744549 AGCATGGCTG
** *
5744559 CCAGAACAGATAATGTGATAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
5744585 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
5744613 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
5744640 CCAGATCAGATAATTATGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
5744667 CCAG
1 CCAG
5744671 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 54 0.71
28 16 0.21
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5744650 original size:54 final size:54
Alignment explanation
Indices: 5744559--5744670 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
5744549 AGCATGGCTG
* * *
5744559 CCAGAACAGATAATGTGATAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCATGGCAGAGCCA
* * *
5744613 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTATGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATACAGATAATCATGGCAGAGCCA
5744667 CCAG
1 CCAG
5744671 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCATGGCAGAGCCA
Found at i:5744808 original size:25 final size:25
Alignment explanation
Indices: 5744774--5744822 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
5744764 CAAAAGTAAC
**
5744774 CCTAGGGGTATAATGGTAATTTTCA
1 CCTAGGGGTATAACAGTAATTTTCA
5744799 CCTAGGGGTATAACAGTAATTTTC
1 CCTAGGGGTATAACAGTAATTTTC
5744823 CATACATAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (25 bp):
CCTAGGGGTATAACAGTAATTTTCA
Found at i:5744837 original size:28 final size:25
Alignment explanation
Indices: 5744776--5744837 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
5744766 AAAGTAACCC
** *
5744776 TAGGGGTATAATGGTAATTTTCACC
1 TAGGGGTATAACAGTAATTTTCACA
5744801 TAGGGGTATAACAGTAATTTTCCATACA
1 TAGGGGTATAACAGTAATTTT-C--ACA
5744829 TAGGGGTAT
1 TAGGGGTAT
5744838 TCAAGTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.61
26 1 0.03
28 11 0.35
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (25 bp):
TAGGGGTATAACAGTAATTTTCACA
Found at i:5745113 original size:8 final size:8
Alignment explanation
Indices: 5745087--5745116 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5745077 CGAAATATCA
5745087 GCTTTTCG
1 GCTTTTCG
*
5745095 GCATTTCG
1 GCTTTTCG
5745103 GCTTTTCG
1 GCTTTTCG
5745111 GCTTTT
1 GCTTTT
5745117 GCTGATCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.23, G:0.23, T:0.50
Consensus pattern (8 bp):
GCTTTTCG
Found at i:5751478 original size:46 final size:46
Alignment explanation
Indices: 5751428--5751600 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
5751418 TGGTTGAGCA
5751428 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5751474 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
5751519 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
5751567 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
5751601 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5751584 original size:93 final size:93
Alignment explanation
Indices: 5751425--5751595 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
5751415 GGATGGTTGA
* *
5751425 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5751490 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
5751518 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5751583 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
5751596 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5756717 original size:27 final size:27
Alignment explanation
Indices: 5756617--5756718 Score: 91
Period size: 27 Copynumber: 3.8 Consensus size: 27
5756607 AGCATGGTTG
* * *
5756617 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGAAAATTGTGGCAGAGCCA
* * *
5756643 CCAAACACAGACAATTGTGGCAGAGCGA
1 CCAGA-ACAGAAAATTGTGGCAGAGCCA
* *
5756671 CCAGAACA-AATATATATGGCAGAGCCA
1 CCAGAACAGAAAAT-TGTGGCAGAGCCA
*
5756698 CCAGATCAGAAAATTGTGGCA
1 CCAGAACAGAAAATTGTGGCA
5756719 TAGACACTAG
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
26 7 0.12
27 34 0.58
28 18 0.31
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.15
Consensus pattern (27 bp):
CCAGAACAGAAAATTGTGGCAGAGCCA
Found at i:5786490 original size:15 final size:16
Alignment explanation
Indices: 5786454--5786483 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5786444 ACATATCATT
5786454 TATTTCATTATACCAA
1 TATTTCATTATACCAA
5786470 TATTTCA-TATACCA
1 TATTTCATTATACCA
5786484 TAGTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTTCATTATACCAA
Found at i:5787951 original size:27 final size:27
Alignment explanation
Indices: 5787937--5788141 Score: 295
Period size: 27 Copynumber: 7.6 Consensus size: 27
5787927 TATCCCACAA
*
5787937 GGGTATCTCGATAATTCTACCCTACAG
1 GGGTATTTCGATAATTCTACCCTACAG
* *
5787964 GGGTATTAC-AGTAATTCTACCCTACAA
1 GGGTATTTCGA-TAATTCTACCCTACAG
5787991 GGGTATTTCGATAATTCTACCCTACAG
1 GGGTATTTCGATAATTCTACCCTACAG
5788018 GGGTATTTCGATAATTCTACCCTACAG
1 GGGTATTTCGATAATTCTACCCTACAG
* *
5788045 GGGTATTTCGGTAATTCTACCATACAG
1 GGGTATTTCGATAATTCTACCCTACAG
* *
5788072 GGGTATTTCAATAATTCTACCCTATAG
1 GGGTATTTCGATAATTCTACCCTACAG
* * *
5788099 GGGTATTTTGGTAATTCTACCCTACAA
1 GGGTATTTCGATAATTCTACCCTACAG
*
5788126 GGGTATTTTGATAATT
1 GGGTATTTCGATAATT
5788142 TTACAAGTCG
Statistics
Matches: 159, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
26 1 0.01
27 157 0.99
28 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (27 bp):
GGGTATTTCGATAATTCTACCCTACAG
Found at i:5787966 original size:54 final size:54
Alignment explanation
Indices: 5787908--5788130 Score: 227
Period size: 54 Copynumber: 4.1 Consensus size: 54
5787898 TTAACACCCT
* * *
5787908 AGGGGTAAAATGGTAATTTTATCCC-ACAAGGGTATCTCGATAATTCTACCCTAC
1 AGGGGTAATATGGTAATTCTA-CCCTACAAGGGTATTTCGATAATTCTACCCTAC
* **
5787962 AGGGGTATTACAGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAC
1 AGGGGTAATATGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAC
* * * * *
5788016 AGGGGT-ATTTCGATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATAC
1 AGGGGTAATAT-GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAC
* ** * * * *
5788070 AGGGGT-ATTTCAATAATTCTACCCTATAGGGGTATTTTGGTAATTCTACCCTAC
1 AGGGGTAATAT-GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAC
*
5788124 AAGGGTA
1 AGGGGTA
5788131 TTTTGATAAT
Statistics
Matches: 147, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
53 4 0.03
54 143 0.97
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (54 bp):
AGGGGTAATATGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAC
Found at i:5788133 original size:81 final size:81
Alignment explanation
Indices: 5787948--5788303 Score: 298
Period size: 81 Copynumber: 4.4 Consensus size: 81
5787938 GGTATCTCGA
* * * * *
5787948 TAATTCTACCCTACAGGGGTATTACAGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATACAGGGGTATTTCAATAATTCTACCC
* * *
5788013 TACAGGGGTATTTCGA
66 TATAGGGGTATTTTGG
5788029 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATACAGGGGTATTTCAATAATTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATACAGGGGTATTTCAATAATTCTACCC
5788094 TATAGGGGTATTTTGG
66 TATAGGGGTATTTTGG
* * * * * *
5788110 TAATTCTACCCTACAAGGGTATTTTGATAATTTTACAAGT-C-GAGGGTATTTCAGTAATT-TCA
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCA-TACAG-GGGTATTTCAATAATTCT-A
*
5788172 CAC-ATCAGGGGTATTTTGG
63 CCCTAT-AGGGGTATTTTGG
** * * * *** *
5788191 TAA-TCTTA-CAAACTAGGGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTTGGTAATTTTA
1 TAATTC-TACCCTAC-AGGGGTATTTCGGTAATTCTACCATAC-AGGGGTATTTCAATAATTCTA
**
5788253 -CAAACTAGGGGTATTTTGG
63 CCCTA-TAGGGGTATTTTGG
* ** *
5788272 TAATTTTA-CAAACTAGGGGTATTTTGGTAATT
1 TAATTCTACCCTAC-AGGGGTATTTCGGTAATT
5788304 TTACTGATCG
Statistics
Matches: 236, Mismatches: 26, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
80 11 0.05
81 220 0.93
82 5 0.02
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (81 bp):
TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCATACAGGGGTATTTCAATAATTCTACCC
TATAGGGGTATTTTGG
Found at i:5788157 original size:54 final size:53
Alignment explanation
Indices: 5787990--5788330 Score: 253
Period size: 54 Copynumber: 6.3 Consensus size: 53
5787980 CTACCCTACA
* * * * * **
5787990 AGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTAC-
1 AGGGTATTTTGGTAATTCTACCATACAGGGGTATTTTGATAATTTTACAAT-CG
* ** * * *
5788043 AGGGGTATTTCGGTAATTCTACCATACAGGGGTATTTCAATAATTCTACCCTATAG
1 A-GGGTATTTTGGTAATTCTACCATACAGGGGTATTTTGATAATTTTA--CAATCG
* *
5788099 -GGGTATTTTGGTAATTCTACCCTACAAGGGTATTTTGATAATTTTACAAGTCG
1 AGGGTATTTTGGTAATTCTACCATACAGGGGTATTTTGATAATTTTACAA-TCG
** * * * *
5788152 AGGGTATTTCAGTAATT-TCACACAT-CAGGGGTATTTTGGTAATCTTACAAACT
1 AGGGTATTTTGGTAATTCT-AC-CATACAGGGGTATTTTGATAATTTTACAATCG
* * * * *
5788205 AGGGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTTGGTAATTTTACAAACT
1 A-GGGTATTTTGGTAATTCTACCATAC-AGGGGTATTTTGATAATTTTACAATCG
* * * *
5788259 AGGGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTTGGTAATTTTACTGATCG
1 A-GGGTATTTTGGTAATTCTACCATAC-AGGGGTATTTTGATAATTTTAC-AATCG
*
5788314 AGGGTATTTTGGAAATT
1 AGGGTATTTTGGTAATT
5788331 TTGTAAACCA
Statistics
Matches: 245, Mismatches: 30, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
52 4 0.02
53 7 0.03
54 226 0.92
55 6 0.02
56 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (53 bp):
AGGGTATTTTGGTAATTCTACCATACAGGGGTATTTTGATAATTTTACAATCG
Found at i:5788319 original size:81 final size:79
Alignment explanation
Indices: 5788095--5788332 Score: 289
Period size: 81 Copynumber: 2.9 Consensus size: 79
5788085 ATTCTACCCT
* ** * *
5788095 ATAGGGGTATTTTGGTAATTCTACCCTAC-AAGGGTATTTTGATAATTTTACAAGTCGAGGGTAT
1 ATAGGGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTTGGTAATTTTACAA-TCGAGGGTAT
** * *
5788159 TTCAGTAATTTCACAC
64 TTTGGTAATTTTACAA
* * *
5788175 ATCAGGGGTATTTTGGTAATCTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAGGGGTAT
1 AT-AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAATCGA-GGGTAT
5788240 TTTGGTAATTTTACAA
64 TTTGGTAATTTTACAA
*
5788256 ACTAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACTGATCGAGGGTAT
1 A-TAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTAC-AATCGAGGGTAT
*
5788321 TTTGGAAATTTT
64 TTTGGTAATTTT
5788333 GTAAACCAAG
Statistics
Matches: 136, Mismatches: 17, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
80 7 0.05
81 125 0.92
82 4 0.03
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (79 bp):
ATAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAATCGAGGGTATTT
TGGTAATTTTACAA
Found at i:5788332 original size:27 final size:27
Alignment explanation
Indices: 5788096--5788307 Score: 268
Period size: 27 Copynumber: 7.9 Consensus size: 27
5788086 TTCTACCCTA
* **
5788096 TAGGGGTATTTTGGTAATTCTACCCTAC
1 TAGGGGTATTTTGGTAATTTTA-CAAAC
* * *
5788124 -AAGGGTATTTTGATAATTTTAC-AAG
1 TAGGGGTATTTTGGTAATTTTACAAAC
* ** * *
5788149 TCGAGGGTATTTCAGTAATTTCACACA-
1 TAG-GGGTATTTTGGTAATTTTACAAAC
*
5788176 TCAGGGGTATTTTGGTAATCTTACAAAC
1 T-AGGGGTATTTTGGTAATTTTACAAAC
5788204 TAGGGGTATTTTGGTAATTTTACAAAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
5788231 TAGGGGTATTTTGGTAATTTTACAAAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
5788258 TAGGGGTATTTTGGTAATTTTACAAAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
5788285 TAGGGGTATTTTGGTAATTTTAC
1 TAGGGGTATTTTGGTAATTTTAC
5788308 TGATCGAGGG
Statistics
Matches: 160, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.01
26 1 0.01
27 155 0.97
28 3 0.02
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (27 bp):
TAGGGGTATTTTGGTAATTTTACAAAC
Found at i:5788349 original size:54 final size:54
Alignment explanation
Indices: 5788097--5788332 Score: 264
Period size: 54 Copynumber: 4.4 Consensus size: 54
5788087 TCTACCCTAT
* ** * * *
5788097 AGGGGTATTTTGGTAATTCTACCCTAC-AAGGGTATTTTGATAATTTTACAAGTCG
1 AGGGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTTGGTAATTTTACAA-ACG
** * * * *
5788152 A-GGGTATTTCAGTAATTTCACACA-TCAGGGGTATTTTGGTAATCTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACG
*
5788205 AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACG
* *
5788259 AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACTGATCG
1 AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTAC-AAACG
*
5788314 A-GGGTATTTTGGAAATTTT
1 AGGGGTATTTTGGTAATTTT
5788333 GTAAACCAAG
Statistics
Matches: 156, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
53 4 0.03
54 147 0.94
55 5 0.03
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (54 bp):
AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACG
Found at i:5788349 original size:81 final size:81
Alignment explanation
Indices: 5788126--5788359 Score: 238
Period size: 81 Copynumber: 2.9 Consensus size: 81
5788116 TACCCTACAA
* * ** * * * * * *
5788126 GGGTATTTTGATAATTTTACAAGTCGA-GGGTATTTCAGTAATTTCACACATCAGGGGTATTTTG
1 GGGTATTTTGGTAATTTTACAA-ACGAGGGGTATTTTGGAAATTTTACAAACCAAGGATATTTTG
*
5788190 GTAATCTTACAAACTAG
65 GTAATTTTACAAACTAG
* * * * *
5788207 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAACGAGGGGTATTTTGGAAATTTTACAAACCAAGGATATTTTGG
5788272 TAATTTTACAAACTAG
66 TAATTTTACAAACTAG
* * ** **
5788288 GGGTATTTTGGTAATTTTACTGATCGA-GGGTATTTTGGAAATTTTGTAAACCAAGGATATTTCA
1 GGGTATTTTGGTAATTTTAC-AAACGAGGGGTATTTTGGAAATTTTACAAACCAAGGATATTTTG
5788352 GTAATTTT
65 GTAATTTT
5788360 GTAAATCGAG
Statistics
Matches: 130, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
80 2 0.02
81 125 0.96
82 3 0.02
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTACAAACGAGGGGTATTTTGGAAATTTTACAAACCAAGGATATTTTGG
TAATTTTACAAACTAG
Found at i:5788383 original size:27 final size:27
Alignment explanation
Indices: 5788361--5788481 Score: 163
Period size: 27 Copynumber: 4.5 Consensus size: 27
5788351 AGTAATTTTG
5788361 TAAATCGAGGGTAAAATGATAATTCTA
1 TAAATCGAGGGTAAAATGATAATTCTA
** * *
5788388 TAAATTAAGGGTAAAACGATAATTCTG
1 TAAATCGAGGGTAAAATGATAATTCTA
*
5788415 TAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAATGATAATTCTA
* *
5788442 TAAATTGAGGGTAAAA-CAGTAATTCTA
1 TAAATCGAGGGTAAAATGA-TAATTCTA
5788469 TAAATCGAGGGTA
1 TAAATCGAGGGTA
5788482 CTTTGGTAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (27 bp):
TAAATCGAGGGTAAAATGATAATTCTA
Found at i:5788489 original size:54 final size:54
Alignment explanation
Indices: 5788350--5788506 Score: 217
Period size: 54 Copynumber: 2.9 Consensus size: 54
5788340 AAGGATATTT
* * *
5788350 CAGTAATTTTGTAAATCGAGGGTAAAATGATAATTCTATAAATTAAGGGTAAAA
1 CAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAA
5788404 C-GATAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAA
1 CAG-TAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAA
* *** * *
5788458 CAGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTACAAATTGAGGG
1 CAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGG
5788507 CACTTCAGTA
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
53 1 0.01
54 90 0.98
55 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (54 bp):
CAGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAA
Found at i:5788500 original size:27 final size:27
Alignment explanation
Indices: 5788458--5788520 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
5788448 GAGGGTAAAA
* * *
5788458 CAGTAATTCTATAAATCGAGGGTACTT
1 CAGTAATTTTACAAATCGAGGGCACTT
** *
5788485 TGGTAATTTTACAAATTGAGGGCACTT
1 CAGTAATTTTACAAATCGAGGGCACTT
5788512 CAGTAATTT
1 CAGTAATTT
5788521 CGTAAACTAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (27 bp):
CAGTAATTTTACAAATCGAGGGCACTT
Found at i:5791088 original size:30 final size:30
Alignment explanation
Indices: 5791054--5791114 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5791044 TCCTTAACTC
5791054 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
5791084 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
5791114 A
1 A
5791115 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:5800342 original size:42 final size:42
Alignment explanation
Indices: 5800290--5800414 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
5800280 GGTTACTGAT
* *
5800290 ATTACGTGTAAGACCATATCTGGGATATGGCATTGATATGAG
1 ATTACGTGTAAGACCATACCTGGGATATGGCATTGATACGAG
* * * *
5800332 ACTT-TGTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAG
1 A-TTACGTGTAAGACCATACCTGGGATA-TGGCATTGATACGAG
* * *
5800375 ATTACATGTAAGACCATACCTTGGATATGGCATTGGTACG
1 ATTACGTGTAAGACCATACCTGGGATATGGCATTGATACG
5800415 GTACTATGTG
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 34 0.50
43 34 0.50
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (42 bp):
ATTACGTGTAAGACCATACCTGGGATATGGCATTGATACGAG
Found at i:5800385 original size:43 final size:42
Alignment explanation
Indices: 5800290--5800407 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 42
5800280 GGTTACTGAT
* * *
5800290 ATTACGTGTAAGACCATATCTGGGATATGGCATTGATATGAG
1 ATTACGTGTAAGACCATAGCTGGGATATGGCATCGATACGAG
* *
5800332 ACTT-TGTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAG
1 A-TTACGTGTAAGACCATAGCTGGGATA-TGGCATCGATACGAG
* * *
5800375 ATTACATGTAAGACCATACCTTGGATATGGCAT
1 ATTACGTGTAAGACCATAGCTGGGATATGGCAT
5800408 TGGTACGGTA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
42 29 0.46
43 34 0.54
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (42 bp):
ATTACGTGTAAGACCATAGCTGGGATATGGCATCGATACGAG
Found at i:5803456 original size:35 final size:35
Alignment explanation
Indices: 5803410--5803480 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
5803400 TTTAGCAAAC
5803410 TTGTTTCTCCAAGTGAACACTTCAGAAAGTAACAA
1 TTGTTTCTCCAAGTGAACACTTCAGAAAGTAACAA
*
5803445 TTGTTTCTCCAAGTGAACACTTCGGAAAGTAACAA
1 TTGTTTCTCCAAGTGAACACTTCAGAAAGTAACAA
5803480 T
1 T
5803481 ATCCGGTGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (35 bp):
TTGTTTCTCCAAGTGAACACTTCAGAAAGTAACAA
Found at i:5803608 original size:38 final size:38
Alignment explanation
Indices: 5803565--5803721 Score: 143
Period size: 38 Copynumber: 3.9 Consensus size: 38
5803555 TTTCCAATTA
*
5803565 ACATGTATAACCGTGGCATATCCACTTAGTACCATGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCATGTT
* * * *
5803603 ACATGTTTAATCGTGGTATATCCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCATG-T--T
* * *
5803644 AAATCAATATATGTAATCGTGGCATATCCACTTAGCTCCATGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCATGTT
* *
5803688 ACATGTTTAACCGTGGTATATCCACTTAGCACCA
1 ACATGTATAACCGTGGCATATCCACTTAGCACCA
5803722 CATTAATGAA
Statistics
Matches: 95, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
38 55 0.58
39 1 0.01
40 3 0.03
41 2 0.02
42 1 0.01
43 1 0.01
44 2 0.02
45 3 0.03
46 1 0.01
47 26 0.27
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCATGTT
Found at i:5803664 original size:47 final size:47
Alignment explanation
Indices: 5803610--5803821 Score: 244
Period size: 47 Copynumber: 4.7 Consensus size: 47
5803600 GTTACATGTT
*
5803610 TAATCGTGGTATATCCACTTAGCACCACGTTAATAAATCAATATATG
1 TAATCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* * * *
5803657 TAATCGTGGCATATCCACTTAGCTCCATG-T--T--A-C-ATGT-T-
1 TAATCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* *
5803695 TAACCGTGGTATATCCACTTAGCACCACATTAATGAATCAATATATG
1 TAATCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* * * * *
5803742 TAATCGTGGCATATCCACTTGGCACCACATTACATGTATCAATATGTG
1 TAATCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
5803790 TAATCGTGGTATATCCACTTAGCACCACGTTA
1 TAATCGTGGTATATCCACTTAGCACCACGTTA
5803822 CACGTATAAC
Statistics
Matches: 137, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
38 24 0.18
39 2 0.01
40 3 0.02
41 2 0.01
42 1 0.01
43 1 0.01
44 2 0.01
45 3 0.02
46 2 0.01
47 55 0.40
48 42 0.31
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (47 bp):
TAATCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
Found at i:5803775 original size:85 final size:85
Alignment explanation
Indices: 5803576--5803778 Score: 334
Period size: 85 Copynumber: 2.4 Consensus size: 85
5803566 CATGTATAAC
* * *
5803576 CGTGGCATATCCACTTAGTACCATGTTACATGTTTAATCGTGGTATATCCACTTAGCACCACGTT
1 CGTGGCATATCCACTTAGCACCATGTTACATGTTTAACCGTGGTATATCCACTTAGCACCACATT
5803641 AATAAATCAATATATGTAAT
66 AATAAATCAATATATGTAAT
*
5803661 CGTGGCATATCCACTTAGCTCCATGTTACATGTTTAACCGTGGTATATCCACTTAGCACCACATT
1 CGTGGCATATCCACTTAGCACCATGTTACATGTTTAACCGTGGTATATCCACTTAGCACCACATT
*
5803726 AATGAATCAATATATGTAAT
66 AATAAATCAATATATGTAAT
* **
5803746 CGTGGCATATCCACTTGGCACCACATTACATGT
1 CGTGGCATATCCACTTAGCACCATGTTACATGT
5803779 ATCAATATGT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 109 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (85 bp):
CGTGGCATATCCACTTAGCACCATGTTACATGTTTAACCGTGGTATATCCACTTAGCACCACATT
AATAAATCAATATATGTAAT
Found at i:5803804 original size:48 final size:48
Alignment explanation
Indices: 5803690--5803828 Score: 199
Period size: 48 Copynumber: 2.9 Consensus size: 48
5803680 TCCATGTTAC
* * *
5803690 ATGTTTAACCGTGGTATATCCACTTAGCACCACATTA-ATGAATCAAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACATTACATGTATCAAT
* * *
5803737 ATATGTAATCGTGGCATATCCACTTGGCACCACATTACATGTATCAAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACATTACATGTATCAAT
* *
5803785 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACACGTAT
1 ATGTGTAATCGTGGTATATCCACTTAGCACCACATTACATGTAT
5803829 AACCATAGTA
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 32 0.40
48 48 0.60
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (48 bp):
ATGTGTAATCGTGGTATATCCACTTAGCACCACATTACATGTATCAAT
Found at i:5803811 original size:133 final size:132
Alignment explanation
Indices: 5803610--5803855 Score: 348
Period size: 133 Copynumber: 1.9 Consensus size: 132
5803600 GTTACATGTT
* *
5803610 TAATCGTGGTATATCCACTTAGCACCACGTTAATAAATCAATATATGTAATCGTGGCATATCCAC
1 TAATCGTGGCATATCCACTTAGCACCACATTAATAAATCAATATATGTAATCGTGGCATATCCAC
* * * * * *
5803675 TTAGCTCCATGTTACATGTTTAACCGTGGTATATCCACTTAGCACCACATTAATGAATCAATATA
66 TTAGCACCACGTTACACGTATAACCATAGTATATCCACTTAGCACCACATTAATGAATCAATATA
5803740 TG
131 TG
* ** * *
5803742 TAATCGTGGCATATCCACTTGGCACCACATTACATGTATCAATATGTGTAATCGTGGTATATCCA
1 TAATCGTGGCATATCCACTTAGCACCACATTA-ATAAATCAATATATGTAATCGTGGCATATCCA
* *
5803807 CTTAGCACCACGTTACACGTATAACCATAGTATATCCATTTAGCTCCAC
65 CTTAGCACCACGTTACACGTATAACCATAGTATATCCACTTAGCACCAC
5803856 GTTTTTTTTC
Statistics
Matches: 98, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
132 29 0.30
133 69 0.70
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (132 bp):
TAATCGTGGCATATCCACTTAGCACCACATTAATAAATCAATATATGTAATCGTGGCATATCCAC
TTAGCACCACGTTACACGTATAACCATAGTATATCCACTTAGCACCACATTAATGAATCAATATA
TG
Found at i:5805096 original size:427 final size:426
Alignment explanation
Indices: 5804302--5805157 Score: 1514
Period size: 427 Copynumber: 2.0 Consensus size: 426
5804292 TTCCGATTTA
*
5804302 AGCCCAAATCTCGATTTCCTTGATCTATAATATCACATTTAGCCTACTAATTAGTCACACTATTC
1 AGCCCAAATCTCGATTTCCTTGATCTATAATAGCACATTTAGCCTACTAATTAGTCACACTATTC
*
5804367 ATATGGGTCTAAAAATCATATTTTTACAAATTTTCATTTTGACCCCTAAACTTTTGCATATTTGC
66 ATATGGGTCTAAAAATCATATTTTTACAAATTTGCATTTTGACCCCTAAACTTTTGCATATTTGC
* * * *
5804432 ACTTTTGCCCCAAGTTTCGGAAATTAAACTTCTTCCAATTTTATTATGTTTTATGACATGCTGAT
131 ACTTTTACCCCAAGGTTCGAAAATCAAACTTCTTCCAATTTTATTATGTTTTATGACATGCTGAT
* *
5804497 CATTTTCCCCTTCCATAGCAACATCAAATTCTCACTCTAACATGTACTTATGAACATTAGGTATT
196 CATTTTCCCCTTCCATAGCAACATCAAATTCTCACTCTAACACGTACTTATGAACATCAGGTATT
5804562 TTTACCGATTATGTCGTTTTACTCGTTTTCACGTAAAATCGCTTAGCAAAAGTTGTTTAACACAA
261 TTTACCGATTATGTCGTTTTACTCGTTTTCACGTAAAATCGCTTAGCAAAAGTTGTTTAACACAA
5804627 TTTCAAGATTCATATTCTACCATTAAACATCAAAATACATGCATATCATTCATGGGTAAATTTTT
326 TTTCAAGATTCATATTCTACCATTAAACATCAAAATACATGCATATCATTCATGGGTAAATTTTT
*
5804692 AAACATAAATCCTAGCTCAAAATAATGGTAGAAATG
391 AAACATAAATCCCAGCTCAAAATAATGGTAGAAATG
* * *
5804728 AGCCCAAATCTCGATTTCCTTGATCTATAATAGCACATTTATCCTACTTATTAGTGACACTATTC
1 AGCCCAAATCTCGATTTCCTTGATCTATAATAGCACATTTAGCCTACTAATTAGTCACACTATTC
*
5804793 ATATGGGTCTAAAAATCATATTTTTTACAAATTTGCATTTTGACCCCTAAACTTTTGCATATTTT
66 ATATGGGTCTAAAAATCATA-TTTTTACAAATTTGCATTTTGACCCCTAAACTTTTGCATATTTG
* * *
5804858 TACTTTTACCCCAAGGTTCGAAAATCAAACTTCTTCCTATTTTCTTATGTTTTATGACATGCTGA
130 CACTTTTACCCCAAGGTTCGAAAATCAAACTTCTTCCAATTTTATTATGTTTTATGACATGCTGA
* * * *
5804923 TCTTTTTTCTCTTCTATAGCAACATCAAATTCTCACTCTAACACGTACTTATGAACATCAGGTAT
195 TCATTTTCCCCTTCCATAGCAACATCAAATTCTCACTCTAACACGTACTTATGAACATCAGGTAT
*
5804988 TTTTACCGATTATGTCGTTTTACTCGTTTTCACGTATAATCGCTTAGCAAAAGTTGTTTAACACA
260 TTTTACCGATTATGTCGTTTTACTCGTTTTCACGTAAAATCGCTTAGCAAAAGTTGTTTAACACA
5805053 ATTTCAAGATTCATATTCTACCATTAAACATCAAAATACATGCATATCATTCATGGGTAAATTTT
325 ATTTCAAGATTCATATTCTACCATTAAACATCAAAATACATGCATATCATTCATGGGTAAATTTT
5805118 TAAACATAAATCCCAGCTCAAAATAATGGTAGAAATG
390 TAAACATAAATCCCAGCTCAAAATAATGGTAGAAATG
5805155 AGC
1 AGC
5805158 AGATCATGTT
Statistics
Matches: 408, Mismatches: 21, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
426 81 0.20
427 327 0.80
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (426 bp):
AGCCCAAATCTCGATTTCCTTGATCTATAATAGCACATTTAGCCTACTAATTAGTCACACTATTC
ATATGGGTCTAAAAATCATATTTTTACAAATTTGCATTTTGACCCCTAAACTTTTGCATATTTGC
ACTTTTACCCCAAGGTTCGAAAATCAAACTTCTTCCAATTTTATTATGTTTTATGACATGCTGAT
CATTTTCCCCTTCCATAGCAACATCAAATTCTCACTCTAACACGTACTTATGAACATCAGGTATT
TTTACCGATTATGTCGTTTTACTCGTTTTCACGTAAAATCGCTTAGCAAAAGTTGTTTAACACAA
TTTCAAGATTCATATTCTACCATTAAACATCAAAATACATGCATATCATTCATGGGTAAATTTTT
AAACATAAATCCCAGCTCAAAATAATGGTAGAAATG
Found at i:5807137 original size:98 final size:98
Alignment explanation
Indices: 5807012--5807365 Score: 665
Period size: 98 Copynumber: 3.6 Consensus size: 98
5807002 AAATTGCAGT
* *
5807012 GAGGCTACCAAATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAACAGA
1 GAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAACAGA
5807077 TATATATATGTTGTGAAGCCACCAGATTACAAC
66 TATATATATGTTGTGAAGCCACCAGATTACAAC
5807110 GAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAACAGA
1 GAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAACAGA
5807175 TATATATATGTTGTGAAGCCACCAGATTACAAC
66 TATATATATGTTGTGAAGCCACCAGATTACAAC
5807208 GAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAACAGA
1 GAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAACAGA
5807273 TATATATATGTTGTGAAGCCACCAGATTACAAC
66 TATATATATGTTGTGAAGCCACCAGATTACAAC
*
5807306 GAGGCTGCCAGATATTGTGACGAAGTCACCAGA-ACAGATATATGTGGCAAGGCCACCAGA
1 GAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATAT-TGTGGCTAGGCCACCAGA
5807366 TTACAGCGAG
Statistics
Matches: 252, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
97 8 0.03
98 244 0.97
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (98 bp):
GAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATTGTGGCTAGGCCACCAGAACAGA
TATATATATGTTGTGAAGCCACCAGATTACAAC
Found at i:5807166 original size:27 final size:26
Alignment explanation
Indices: 5807118--5807177 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
5807108 ACGAGGCTGC
*
5807118 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
5807145 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
5807171 CAGATAT
1 CAGATAT
5807178 ATATATGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:5807264 original size:27 final size:26
Alignment explanation
Indices: 5807216--5807275 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
5807206 ACGAGGCTGC
*
5807216 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
5807243 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
5807269 CAGATAT
1 CAGATAT
5807276 ATATATGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:5809884 original size:48 final size:48
Alignment explanation
Indices: 5809832--5809955 Score: 149
Period size: 48 Copynumber: 2.6 Consensus size: 48
5809822 TATCTCGGAT
**
5809832 ATGGTCTTACATGGGATCACATATTGATGCCGATGCCATGTCTTAGAC
1 ATGGTCTTACATGGGATCACATATTGATGCCGATGCCATGTCCCAGAC
* ** * * *
5809880 ATGGTCTTACAAGGGATCGTAGATTGATGCCGATGCTATGTCCCAGAG
1 ATGGTCTTACATGGGATCACATATTGATGCCGATGCCATGTCCCAGAC
* * *
5809928 ATAGTCTTACATGGTATCAGATATTGAT
1 ATGGTCTTACATGGGATCACATATTGAT
5809956 TCTGATAGCC
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (48 bp):
ATGGTCTTACATGGGATCACATATTGATGCCGATGCCATGTCCCAGAC
Found at i:5812336 original size:13 final size:13
Alignment explanation
Indices: 5812318--5812342 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5812308 GTTTATTAAA
5812318 CTAATTAACTAAC
1 CTAATTAACTAAC
5812331 CTAATTAACTAA
1 CTAATTAACTAA
5812343 TTAAAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
CTAATTAACTAAC
Found at i:5817575 original size:127 final size:127
Alignment explanation
Indices: 5817393--5817646 Score: 508
Period size: 127 Copynumber: 2.0 Consensus size: 127
5817383 GTTATTTTGA
5817393 TATCTGAAGTTATTGTTACCTATATAGTTGACTTGTTCCTCTTCAGTTGTGGGATTGAAGGATTG
1 TATCTGAAGTTATTGTTACCTATATAGTTGACTTGTTCCTCTTCAGTTGTGGGATTGAAGGATTG
5817458 ATAATCGGTATGCACACCTCCTCCACTTGAGTCACACCTCATTACTGGATGTACCTGCGTAG
66 ATAATCGGTATGCACACCTCCTCCACTTGAGTCACACCTCATTACTGGATGTACCTGCGTAG
5817520 TATCTGAAGTTATTGTTACCTATATAGTTGACTTGTTCCTCTTCAGTTGTGGGATTGAAGGATTG
1 TATCTGAAGTTATTGTTACCTATATAGTTGACTTGTTCCTCTTCAGTTGTGGGATTGAAGGATTG
5817585 ATAATCGGTATGCACACCTCCTCCACTTGAGTCACACCTCATTACTGGATGTACCTGCGTAG
66 ATAATCGGTATGCACACCTCCTCCACTTGAGTCACACCTCATTACTGGATGTACCTGCGTAG
5817647 AACTAAGAAA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 127 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.35
Consensus pattern (127 bp):
TATCTGAAGTTATTGTTACCTATATAGTTGACTTGTTCCTCTTCAGTTGTGGGATTGAAGGATTG
ATAATCGGTATGCACACCTCCTCCACTTGAGTCACACCTCATTACTGGATGTACCTGCGTAG
Found at i:5820883 original size:50 final size:50
Alignment explanation
Indices: 5820808--5820907 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
5820798 TCATCTCCAA
5820808 ATAAATGTTTTTAAAATTAATTGTATGTTTATATATGTTTCTGAATTGAG
1 ATAAATGTTTTTAAAATTAATTGTATGTTTATATATGTTTCTGAATTGAG
5820858 ATAAATGTTTTTAAAATTAATTGTATGTTTATATATGTTTCTGAATTGAG
1 ATAAATGTTTTTAAAATTAATTGTATGTTTATATATGTTTCTGAATTGAG
5820908 TTTAGCATTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (50 bp):
ATAAATGTTTTTAAAATTAATTGTATGTTTATATATGTTTCTGAATTGAG
Found at i:5822862 original size:37 final size:36
Alignment explanation
Indices: 5822804--5822880 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 36
5822794 AATAATTCAA
*
5822804 ATGATACAACATTTGTTCAGTTTGATGGTTTGCAGG
1 ATGATACAACATTTGTTCAGTTTGATGATTTGCAGG
5822840 ATGATACAACAGTTTGTTCAGTTTGATGATTTGCAGG
1 ATGATACAACA-TTTGTTCAGTTTGATGATTTGCAGG
5822877 ATGA
1 ATGA
5822881 GGATCCAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 11 0.28
37 28 0.72
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (36 bp):
ATGATACAACATTTGTTCAGTTTGATGATTTGCAGG
Found at i:5829475 original size:46 final size:46
Alignment explanation
Indices: 5829408--5829582 Score: 314
Period size: 46 Copynumber: 3.8 Consensus size: 46
5829398 TGTAACCCGC
* * * *
5829408 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
5829454 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
5829500 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
5829546 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5829583 TGCTCAACCA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:5833707 original size:85 final size:85
Alignment explanation
Indices: 5833564--5833742 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
5833554 GGCCGGCCAT
5833564 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
5833629 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
5833649 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
5833714 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
5833734 GAGCATGGG
1 GAGCATGGG
5833743 CAATAAAAAA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:5837889 original size:54 final size:54
Alignment explanation
Indices: 5837680--5837889 Score: 180
Period size: 55 Copynumber: 3.9 Consensus size: 54
5837670 TATCTTTCCT
* * * *
5837680 TTTTA-AACTTACCATTGCCAT--CTCGACATGGTCCTACGTGGTATCCTTGCC
1 TTTTATAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCC
* * * * *
5837731 --TTATGAACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTACC
1 TTTTAT-AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCC
* ** * * * * *
5837784 TTATAGTAGTTTATCAATGCCTTGTCTTGACATGGTCTTACATGATTTCCTTGCC
1 TTTTA-TAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCC
* *
5837839 TTTTATAACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 TTTTATAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
5837890 AAACCCTAAT
Statistics
Matches: 120, Mismatches: 30, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
49 3 0.03
51 15 0.12
52 2 0.02
53 21 0.17
54 37 0.31
55 39 0.32
56 3 0.03
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (54 bp):
TTTTATAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCC
Found at i:5849802 original size:40 final size:40
Alignment explanation
Indices: 5849758--5850019 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
5849748 GCTCCTCGTT
* *
5849758 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
5849798 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
5849838 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
5849877 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
5849916 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
5849955 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
5849996 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5850020 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:5877307 original size:7 final size:7
Alignment explanation
Indices: 5877297--5877350 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
5877287 AAGAATACAA
5877297 AGGGTTT
1 AGGGTTT
5877304 AGGGTTT
1 AGGGTTT
5877311 AAGGGTTTT
1 -AGGG-TTT
* *
5877320 AAGATTT
1 AGGGTTT
*
5877327 A-GGTCT
1 AGGGTTT
5877333 AGGGTTT
1 AGGGTTT
5877340 AGGGTTT
1 AGGGTTT
5877347 AGGG
1 AGGG
5877351 AAATTGAGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
6 4 0.10
7 26 0.67
8 6 0.15
9 3 0.08
ACGTcount: A:0.20, C:0.02, G:0.39, T:0.39
Consensus pattern (7 bp):
AGGGTTT
Found at i:5883901 original size:44 final size:43
Alignment explanation
Indices: 5883831--5883989 Score: 161
Period size: 43 Copynumber: 3.7 Consensus size: 43
5883821 TATGTGTTAT
* *
5883831 CGTGTAGGACCACGTCTGGGATGTTGGCATCGACTTATTATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TTATTATTTA
*
5883875 CGTGTAAGACCACGT-TCGGGACGTTGGCATCGTATT-TGATTT-
1 CGTGTAAGACCACGTCT-GGGACGTTGGCATCG-ATTATTATTTA
*
5883917 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATC-AATATT-TGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATTATTAT--TTA
*
5883960 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
5883990 TGTACGAGCT
Statistics
Matches: 98, Mismatches: 6, Indels: 23
0.77 0.05 0.18
Matches are distributed among these distances:
40 3 0.03
41 2 0.02
42 28 0.29
43 33 0.34
44 31 0.32
45 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATTATTATTTA
Found at i:5890144 original size:19 final size:19
Alignment explanation
Indices: 5890103--5890144 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5890093 AGTTGTGAGT
* * *
5890103 AAAAGATTCAGACGTTTCG
1 AAAAGATTCAGACATTCCA
5890122 AAAAGATTCAGACATTCCA
1 AAAAGATTCAGACATTCCA
5890141 AAAA
1 AAAA
5890145 CTGCATTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (19 bp):
AAAAGATTCAGACATTCCA
Found at i:5896033 original size:19 final size:19
Alignment explanation
Indices: 5896001--5896046 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5895991 ACAACATATA
* * *
5896001 ATAATGTCACATTATTTAC
1 ATAATATCAAATTATTCAC
5896020 ATAATATCAAATTATTCAC
1 ATAATATCAAATTATTCAC
5896039 ATATATAT
1 ATA-ATAT
5896047 ACTTACAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAATATCAAATTATTCAC
Done.