Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 136 of 343
Found at i:45605592 original size:28 final size:29
Alignment explanation
Indices: 45605544--45605638 Score: 104
Period size: 29 Copynumber: 3.3 Consensus size: 29
45605534 AAGTCTACAT
* * * *
45605544 ACATGCATATGGTCCACTAGGCTC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
45605572 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
45605601 ACATTCATATGGCCCA-TCGGCCCCCAATC
1 ACATTCATATGGCCCATTAGG-CCCAAATC
45605630 ACATTCATA
1 ACATTCATA
45605639 GTCATGCAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
28 22 0.39
29 35 0.61
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:45605878 original size:16 final size:16
Alignment explanation
Indices: 45605857--45605889 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45605847 CAAACTTCCA
*
45605857 ACTTTTCGGCATTTCG
1 ACTTTTCAGCATTTCG
45605873 ACTTTTCAGCATTTCG
1 ACTTTTCAGCATTTCG
45605889 A
1 A
45605890 GATTTGCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.42
Consensus pattern (16 bp):
ACTTTTCAGCATTTCG
Found at i:45616378 original size:18 final size:18
Alignment explanation
Indices: 45616336--45616378 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
45616326 ATGGTAGCTT
*
45616336 GGCTACATGATTTCCACA
1 GGCTACTTGATTTCCACA
*
45616354 GGCTACTTGATTTCCGCA
1 GGCTACTTGATTTCCACA
45616372 GGCTACT
1 GGCTACT
45616379 GAGTTTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (18 bp):
GGCTACTTGATTTCCACA
Found at i:45616942 original size:28 final size:28
Alignment explanation
Indices: 45616902--45616957 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
45616892 GGAAATGTTT
45616902 GAGAATGATTAGCTATTGCAGTGGCTAA
1 GAGAATGATTAGCTATTGCAGTGGCTAA
**
45616930 GAGAATGATTAGCTATTGGTGTGGCTAA
1 GAGAATGATTAGCTATTGCAGTGGCTAA
45616958 TCAAGATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (28 bp):
GAGAATGATTAGCTATTGCAGTGGCTAA
Found at i:45620557 original size:6 final size:6
Alignment explanation
Indices: 45620539--45620651 Score: 97
Period size: 6 Copynumber: 18.3 Consensus size: 6
45620529 TAAGAACATT
* *
45620539 ATCAGA A-CTAGA ATCAGA ATCAAA ATCAGA ATCAGGTA A-CAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
* * *
45620588 ATCAGA ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGA TAGCAGA
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA -ATCAGA
*
45620638 ATCAAA ATCAGA AT
1 ATCAGA ATCAGA AT
45620652 GTGAATGCAA
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
5 5 0.06
6 65 0.76
7 12 0.14
8 4 0.05
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:45620583 original size:13 final size:13
Alignment explanation
Indices: 45620565--45620610 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
45620555 GAATCAAAAT
45620565 CAGAATCAGGTAA
1 CAGAATCAGGTAA
*
45620578 CAGAATCA--AAA
1 CAGAATCAGGTAA
45620589 TCAGAATCAGGTAA
1 -CAGAATCAGGTAA
45620603 CAGAATCA
1 CAGAATCA
45620611 AAATCAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 2 0.07
12 8 0.29
13 16 0.57
14 2 0.07
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.15
Consensus pattern (13 bp):
CAGAATCAGGTAA
Found at i:45620641 original size:25 final size:25
Alignment explanation
Indices: 45620553--45620623 Score: 142
Period size: 25 Copynumber: 2.8 Consensus size: 25
45620543 GAACTAGAAT
45620553 CAGAATCAAAATCAGAATCAGGTAA
1 CAGAATCAAAATCAGAATCAGGTAA
45620578 CAGAATCAAAATCAGAATCAGGTAA
1 CAGAATCAAAATCAGAATCAGGTAA
45620603 CAGAATCAAAATCAGAATCAG
1 CAGAATCAAAATCAGAATCAG
45620624 TATCAGATAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.15
Consensus pattern (25 bp):
CAGAATCAAAATCAGAATCAGGTAA
Found at i:45620648 original size:31 final size:29
Alignment explanation
Indices: 45620539--45620651 Score: 119
Period size: 31 Copynumber: 3.9 Consensus size: 29
45620529 TAAGAACATT
* *
45620539 ATCAG-AACTAGAATCAGAATCAAAATCAG
1 ATCAGTAAC-AGAATCAAAATCAGAATCAG
45620568 AATCAGGTAACAGAATCAAAATCAGAATCAG
1 -ATCA-GTAACAGAATCAAAATCAGAATCAG
45620599 ----GTAACAGAATCAAAATCAGAATCAG
1 ATCAGTAACAGAATCAAAATCAGAATCAG
*
45620624 TATCAGATAGCAGAATCAAAATCAGAAT
1 -ATCAG-TAACAGAATCAAAATCAGAAT
45620652 GTGAATGCAA
Statistics
Matches: 72, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
25 25 0.35
30 5 0.07
31 39 0.54
32 3 0.04
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.18
Consensus pattern (29 bp):
ATCAGTAACAGAATCAAAATCAGAATCAG
Found at i:45621084 original size:27 final size:26
Alignment explanation
Indices: 45621054--45621464 Score: 340
Period size: 27 Copynumber: 15.3 Consensus size: 26
45621044 GGGGAAAAAT
* * * *
45621054 GGTAATTTTACCCCATAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTAT-TC
45621081 GGTAATTCTACCCTACAGGGGTATTAC
1 GGTAATTCTACCCTACAGGGGTATT-C
45621108 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTA-TTC
* *
45621135 AGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTA-TTC
* *
45621162 GGTAATTCTACCTTACAGGGATATTTC
1 GGTAATTCTACCCTACAGGGGTA-TTC
* *
45621189 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTA-TTC
* * *
45621216 AGTAATTCTACCATATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTA-TTC
** *
45621243 AATAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTA-TTC
* * *
45621270 AGTAATTTTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTA-TTC
*
45621297 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTA-TTC
* * *
45621324 AGTAATTCTACTCTACAGGGGCATTC
1 GGTAATTCTACCCTACAGGGGTATTC
* * *
45621350 AGTAATTCTACCTTACTA-GGGTATTTT
1 GGTAATTCTACCCTAC-AGGGGTA-TTC
* * * *
45621377 AGTAATTCTACCCTGCAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTA-TTC
* *
45621404 GGTAATTCTACCTTACTA-GGGTATTTT
1 GGTAATTCTACCCTAC-AGGGGTA-TTC
* * * *
45621431 AGTAATTGTACCTTACAGGGGTGTTTC
1 GGTAATTCTACCCTACAGGGGT-ATTC
45621458 GGTAATT
1 GGTAATT
45621465 TTATAAATCA
Statistics
Matches: 328, Mismatches: 48, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
26 24 0.07
27 301 0.92
28 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (26 bp):
GGTAATTCTACCCTACAGGGGTATTC
Found at i:45621101 original size:54 final size:54
Alignment explanation
Indices: 45621053--45621464 Score: 402
Period size: 54 Copynumber: 7.6 Consensus size: 54
45621043 AGGGGAAAAA
* * * *
45621053 TGGTAATTTTACCCCATAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTA
1 TGGTAATTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
* * * *
45621107 CGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
*
45621161 TGGTAATTCTA-CCT-TACAGGGATATTTCGATAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTATA-AGGG-TATTTCGGTAATTCTACCCTACAGGGGTATTT
* * * ** *
45621215 TAGTAATTCTACCATATAGGGGTATTTCAATAATTCTACCTTACAGGGGTATTT
1 TGGTAATTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
** * * *
45621269 CAGTAATTTTACCCTACAAGGGTATTTCGGTAATTCTACCTTACAGGGGTATTT
1 TGGTAATTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
** * * * * * *
45621323 CAGTAATTCTACTCTACAGGGGCA-TTCAGTAATTCTACCTTACTA-GGGTATTT
1 TGGTAATTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTAC-AGGGGTATTT
* ** * *
45621376 TAGTAATTCTACCCTGCAAGGGTATTTTGGTAATTCTACCTTACTA-GGGTATTT
1 TGGTAATTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTAC-AGGGGTATTT
* * * * * *
45621430 TAGTAATTGTACCTTACAGGGGTGTTTCGGTAATT
1 TGGTAATTCTACCCTATAAGGGTATTTCGGTAATT
45621465 TTATAAATCA
Statistics
Matches: 309, Mismatches: 43, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
52 1 0.00
53 51 0.17
54 250 0.81
55 5 0.02
56 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (54 bp):
TGGTAATTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
Found at i:45621179 original size:81 final size:81
Alignment explanation
Indices: 45621072--45621464 Score: 472
Period size: 81 Copynumber: 4.9 Consensus size: 81
45621062 TACCCCATAA
* * * *
45621072 GGGTATCTCGGTAATTCTACCCTACAGGGGTATTACGGTAATTCTACCCTACAGGGGTATTTCAG
1 GGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAG
45621137 TAATTCTACCCTACAG
66 TAATTCTACCCTACAG
* * *
45621153 GGGTATTTTGGTAATTCTACCTTACAGGGATATTTC-GATAATTCTACCCTACAGGGGTATTTTA
1 GGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCAG-TAATTCTACCCTACAGGGGTATTTCA
* *
45621217 GTAATTCTACCATATAG
65 GTAATTCTACCCTACAG
** * * *
45621234 GGGTATTTCAATAATTCTACCTTACAGGGGTATTTCAGTAATTTTACCCTACAAGGGTATTTCGG
1 GGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAG
*
45621299 TAATTCTACCTTACAG
66 TAATTCTACCCTACAG
* * * *
45621315 GGGTATTTCAGTAATTCTA-CTCTACAGGGGCA-TTCAGTAATTCTACCTTACTA-GGGTATTTT
1 GGGTATTTCGGTAATTCTACCT-TACAGGGGTATTTCAGTAATTCTACCCTAC-AGGGGTATTTC
* *
45621377 AGTAATTCTACCCTGCAA
64 AGTAATTCTACCCTACAG
* * * * * *
45621395 GGGTATTTTGGTAATTCTACCTTACTA-GGGTATTTTAGTAATTGTACCTTACAGGGGTGTTTCG
1 GGGTATTTCGGTAATTCTACCTTAC-AGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCA
45621459 GTAATT
65 GTAATT
45621465 TTATAAATCA
Statistics
Matches: 269, Mismatches: 35, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
80 67 0.25
81 201 0.75
82 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (81 bp):
GGGTATTTCGGTAATTCTACCTTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAG
TAATTCTACCCTACAG
Found at i:45638861 original size:64 final size:64
Alignment explanation
Indices: 45638781--45638964 Score: 201
Period size: 67 Copynumber: 2.8 Consensus size: 64
45638771 AGACATTATG
* * * *
45638781 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGATCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
45638845 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
45638910 AA
63 AA
* * * *
45638912 AT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
45638965 CGAACTATAT
Statistics
Matches: 98, Mismatches: 18, Indels: 9
0.78 0.14 0.07
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.26
66 22 0.22
67 31 0.32
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:45642363 original size:27 final size:26
Alignment explanation
Indices: 45642317--45642368 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
45642307 GCGAGGCTGC
45642317 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGTCACCAGAA
* *
45642343 CAGATATATGTGGCGAGGTCACCAGA
1 CAGATAT-TGTGACGAAGTCACCAGA
45642369 TTGCAGCGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGACGAAGTCACCAGAA
Found at i:45645117 original size:19 final size:19
Alignment explanation
Indices: 45645093--45645129 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
45645083 CCATGCATTA
45645093 AACTAAGACAAATTAAATG
1 AACTAAGACAAATTAAATG
*
45645112 AACTAAGACAACTTAAAT
1 AACTAAGACAAATTAAAT
45645130 AGCTGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.14, G:0.08, T:0.22
Consensus pattern (19 bp):
AACTAAGACAAATTAAATG
Found at i:45647965 original size:11 final size:11
Alignment explanation
Indices: 45647943--45647980 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
45647933 CTTATTCTTC
45647943 TTTTTTCATGAA
1 TTTTTTC-TGAA
45647955 TTTTTTCTGAA
1 TTTTTTCTGAA
45647966 -TTTTT-TGAA
1 TTTTTTCTGAA
45647975 TTTTTT
1 TTTTTT
45647981 GATTTCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 4 0.16
12 7 0.28
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTTCTGAA
Found at i:45649363 original size:19 final size:18
Alignment explanation
Indices: 45649341--45649403 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
45649331 AAGAAAGTGA
*
45649341 GAAAAATAAAAACGAAATT
1 GAAAAAGAAAAA-GAAATT
45649360 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATT
**
45649378 GATCAAG-AAAAGAAAATT
1 GAAAAAGAAAAAG-AAATT
45649396 GAAAAAGA
1 GAAAAAGA
45649404 GAGTGAGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 5 0.14
18 21 0.57
19 11 0.30
ACGTcount: A:0.68, C:0.03, G:0.16, T:0.13
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:45650042 original size:30 final size:30
Alignment explanation
Indices: 45650008--45650104 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
45649998 AGCTCACTCC
*
45650008 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
45650038 TAGCTCAACTTTAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
45650068 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
45650098 TAGCTCA
1 TAGCTCA
45650105 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:45653330 original size:20 final size:20
Alignment explanation
Indices: 45653284--45653321 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
45653274 AGCTCGTTTC
*
45653284 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
*
45653304 CAACTCACTCAAGCTCAA
1 CAGCTCACTCAAGCTCAA
45653322 TTTAGCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.37, G:0.13, T:0.18
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:45656037 original size:48 final size:47
Alignment explanation
Indices: 45655958--45656063 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
45655948 GAGTGTCATG
*
45655958 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
45656006 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
45656054 GAAAAAGAAA
1 GAAAAAGAAA
45656064 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:45657780 original size:20 final size:20
Alignment explanation
Indices: 45657734--45657780 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
45657724 AGCTCGTTTC
*
45657734 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
45657754 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
45657774 CAGCTCA
1 CAGCTCA
45657781 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:45662799 original size:533 final size:533
Alignment explanation
Indices: 45661793--45662860 Score: 2136
Period size: 533 Copynumber: 2.0 Consensus size: 533
45661783 ACCAATAATA
45661793 CGGGAATAGCACAGGGACTTAGGCTCTCGCGAATGTAGCCTTTTTCCATCAGTTCATTGACTTGT
1 CGGGAATAGCACAGGGACTTAGGCTCTCGCGAATGTAGCCTTTTTCCATCAGTTCATTGACTTGT
45661858 CTTTGCAACTCCTTGGTCTCCTCCGGATTGGCTCAGTAAGCAGGTCAATTTGGAATAACCGCTCT
66 CTTTGCAACTCCTTGGTCTCCTCCGGATTGGCTCAGTAAGCAGGTCAATTTGGAATAACCGCTCT
45661923 CGGCACAAAATCAATTTGATGCTCGATTCCACGAACTGGTGGAAGACCACTCGGGTTTCTTCCAG
131 CGGCACAAAATCAATTTGATGCTCGATTCCACGAACTGGTGGAAGACCACTCGGGTTTCTTCCAG
45661988 AAAAACGTCTTGGAAATCCTGTGACAAAGACAAAATAGGAGGGGGCGGGGTATCGGGTAAATCGT
196 AAAAACGTCTTGGAAATCCTGTGACAAAGACAAAATAGGAGGGGGCGGGGTATCGGGTAAATCGT
45662053 TAGTAGAAATTAATGCTTCCTTGTACAAAAGTACAAGAACAGTTCGGTTCATCACCAAAGCCTTC
261 TAGTAGAAATTAATGCTTCCTTGTACAAAAGTACAAGAACAGTTCGGTTCATCACCAAAGCCTTC
45662118 CTCACATCATTAACTCTTGCAAAAACACTCATTTTCTCGATTTTCTTTTCATTCTCTTTTTCAAT
326 CTCACATCATTAACTCTTGCAAAAACACTCATTTTCTCGATTTTCTTTTCATTCTCTTTTTCAAT
45662183 CTCATTTTCTTTTTCTTTTTCTTTTTGCTTTTCAAAGGCTTTTTCAAGTTCTCGCAAGATTCGCT
391 CTCATTTTCTTTTTCTTTTTCTTTTTGCTTTTCAAAGGCTTTTTCAAGTTCTCGCAAGATTCGCT
45662248 CATTTTTGGTATGTGATCCAGCTCGGGATGATGAGTCAAATTCACTTAGTTGCCCGATCGTCGTT
456 CATTTTTGGTATGTGATCCAGCTCGGGATGATGAGTCAAATTCACTTAGTTGCCCGATCGTCGTT
45662313 CGAGAGAGTCGTT
521 CGAGAGAGTCGTT
45662326 CGGGAATAGCACAGGGACTTAGGCTCTCGCGAATGTAGCCTTTTTCCATCAGTTCATTGACTTGT
1 CGGGAATAGCACAGGGACTTAGGCTCTCGCGAATGTAGCCTTTTTCCATCAGTTCATTGACTTGT
45662391 CTTTGCAACTCCTTGGTCTCCTCCGGATTGGCTCAGTAAGCAGGTCAATTTGGAATAACCGCTCT
66 CTTTGCAACTCCTTGGTCTCCTCCGGATTGGCTCAGTAAGCAGGTCAATTTGGAATAACCGCTCT
45662456 CGGCACAAAATCAATTTGATGCTCGATTCCACGAACTGGTGGAAGACCACTCGGGTTTCTTCCAG
131 CGGCACAAAATCAATTTGATGCTCGATTCCACGAACTGGTGGAAGACCACTCGGGTTTCTTCCAG
45662521 AAAAACGTCTTGGAAATCCTGTGACAAAGACAAAATAGGAGGGGGCGGGGTATCGGGTAAATCGT
196 AAAAACGTCTTGGAAATCCTGTGACAAAGACAAAATAGGAGGGGGCGGGGTATCGGGTAAATCGT
45662586 TAGTAGAAATTAATGCTTCCTTGTACAAAAGTACAAGAACAGTTCGGTTCATCACCAAAGCCTTC
261 TAGTAGAAATTAATGCTTCCTTGTACAAAAGTACAAGAACAGTTCGGTTCATCACCAAAGCCTTC
45662651 CTCACATCATTAACTCTTGCAAAAACACTCATTTTCTCGATTTTCTTTTCATTCTCTTTTTCAAT
326 CTCACATCATTAACTCTTGCAAAAACACTCATTTTCTCGATTTTCTTTTCATTCTCTTTTTCAAT
45662716 CTCATTTTCTTTTTCTTTTTCTTTTTGCTTTTCAAAGGCTTTTTCAAGTTCTCGCAAGATTCGCT
391 CTCATTTTCTTTTTCTTTTTCTTTTTGCTTTTCAAAGGCTTTTTCAAGTTCTCGCAAGATTCGCT
45662781 CATTTTTGGTATGTGATCCAGCTCGGGATGATGAGTCAAATTCACTTAGTTGCCCGATCGTCGTT
456 CATTTTTGGTATGTGATCCAGCTCGGGATGATGAGTCAAATTCACTTAGTTGCCCGATCGTCGTT
45662846 CGAGAGAGTCGTT
521 CGAGAGAGTCGTT
45662859 CG
1 CG
45662861 TGCCAAGTAT
Statistics
Matches: 535, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
533 535 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (533 bp):
CGGGAATAGCACAGGGACTTAGGCTCTCGCGAATGTAGCCTTTTTCCATCAGTTCATTGACTTGT
CTTTGCAACTCCTTGGTCTCCTCCGGATTGGCTCAGTAAGCAGGTCAATTTGGAATAACCGCTCT
CGGCACAAAATCAATTTGATGCTCGATTCCACGAACTGGTGGAAGACCACTCGGGTTTCTTCCAG
AAAAACGTCTTGGAAATCCTGTGACAAAGACAAAATAGGAGGGGGCGGGGTATCGGGTAAATCGT
TAGTAGAAATTAATGCTTCCTTGTACAAAAGTACAAGAACAGTTCGGTTCATCACCAAAGCCTTC
CTCACATCATTAACTCTTGCAAAAACACTCATTTTCTCGATTTTCTTTTCATTCTCTTTTTCAAT
CTCATTTTCTTTTTCTTTTTCTTTTTGCTTTTCAAAGGCTTTTTCAAGTTCTCGCAAGATTCGCT
CATTTTTGGTATGTGATCCAGCTCGGGATGATGAGTCAAATTCACTTAGTTGCCCGATCGTCGTT
CGAGAGAGTCGTT
Found at i:45669145 original size:20 final size:19
Alignment explanation
Indices: 45669122--45669186 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
45669112 AAGCTCAAAC
45669122 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
45669142 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
45669162 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
45669182 GAGCT
1 GAGCT
45669187 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:45670994 original size:30 final size:32
Alignment explanation
Indices: 45670960--45671019 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
45670950 GATTACTCAC
45670960 TTCACTCG-TTTCTTTT--AGACTCTCTTTCTT
1 TTCACTCGATTTCTTTTCAAG-CTCTCTTTCTT
*
45670990 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
45671020 AATTTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.27
31 8 0.31
32 9 0.35
33 2 0.08
ACGTcount: A:0.12, C:0.27, G:0.07, T:0.55
Consensus pattern (32 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTT
Found at i:45671031 original size:6 final size:6
Alignment explanation
Indices: 45671022--45671136 Score: 82
Period size: 6 Copynumber: 19.3 Consensus size: 6
45671012 TCTCTTTCAA
* ** *
45671022 TTTCTT TTTCCT TTTCTT TTTC-T TTTCAA TTTCTT TTTC-- ATTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
*
45671067 TTTCTT TTCACTCTT TTTTTT TTTC-T TTTC-T TTTCTTT TTTCTT TCTT-TCT
1 TTTCTT TT---TCTT TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT T-TTCT-T
45671118 TTTC-T TTTCTT TTTCTT TT
1 TTTCTT TTTCTT TTTCTT TT
45671137 CTCCTCTCTT
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
4 3 0.03
5 20 0.23
6 50 0.57
7 9 0.10
9 6 0.07
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:45671046 original size:11 final size:11
Alignment explanation
Indices: 45671022--45671138 Score: 93
Period size: 11 Copynumber: 10.5 Consensus size: 11
45671012 TCTCTTTCAA
45671022 TTTCTTTTTCCT
1 TTTCTTTTT-CT
45671034 TTTCTTTTTCT
1 TTTCTTTTTCT
*
45671045 TTTCAATTTCTTTT
1 TTTC--TTT-TTCT
45671059 TCATTCTTTTTCT
1 T--TTCTTTTTCT
* *
45671072 TTTCACTCTT-T
1 TTTC-TTTTTCT
45671083 TTT-TTTTTCT
1 TTTCTTTTTCT
45671093 TTTC-TTTTCT
1 TTTCTTTTTCT
45671103 TTT-TTCTTTC-
1 TTTCTT-TTTCT
45671113 TTTC-TTTTCT
1 TTTCTTTTTCT
45671123 TTTCTTTTTCT
1 TTTCTTTTTCT
45671134 TTTCT
1 TTTCT
45671139 CCTCTCTTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 27
0.72 0.05 0.23
Matches are distributed among these distances:
9 7 0.08
10 22 0.26
11 28 0.33
12 12 0.14
13 7 0.08
14 7 0.08
16 3 0.03
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:45671047 original size:5 final size:5
Alignment explanation
Indices: 45671022--45671138 Score: 80
Period size: 5 Copynumber: 22.0 Consensus size: 5
45671012 TCTCTTTCAA
* *
45671022 TTTCTT TTTCCT TTTCTT TTTCT TTTCAA TTTCT TTT-T CATTCTT TTTCT
1 TTTC-T TTT-CT TTTC-T TTTCT TTTC-T TTTCT TTTCT -TTTC-T TTTCT
*
45671072 TTTCACT CTTT-T TTT-T TTTCT TTTCT TTTCT TTTTT CTTTC- TTTCT
1 TTT--CT -TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT -TTTCT TTTCT
45671118 TTTCT TTTCTT TTTCT TTTCT
1 TTTCT TTTC-T TTTCT TTTCT
45671139 CCTCTCTTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 27
0.74 0.05 0.22
Matches are distributed among these distances:
4 12 0.13
5 46 0.50
6 27 0.29
7 4 0.04
8 3 0.03
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:45672199 original size:11 final size:11
Alignment explanation
Indices: 45672173--45672218 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
45672163 TTCTTTTCTT
*
45672173 TTTTTTTCTCGA
1 TTTTTTT-TCAA
*
45672185 TTTTTTTTCAC
1 TTTTTTTTCAA
*
45672196 TTTTTTTTGAA
1 TTTTTTTTCAA
45672207 TTTTTTTTCAA
1 TTTTTTTTCAA
45672218 T
1 T
45672219 CAAATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 22 0.76
12 7 0.24
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:45672199 original size:22 final size:22
Alignment explanation
Indices: 45672174--45672251 Score: 61
Period size: 28 Copynumber: 3.3 Consensus size: 22
45672164 TCTTTTCTTT
45672174 TTTTTTCTCG-ATTTTTTTTCAC
1 TTTTTT-TCGAATTTTTTTTCAC
*
45672196 TTTTTTTTGAATTTTTTTTCAATC
1 TTTTTTTCGAATTTTTTTTC-A-C
*
45672220 AAATTTTTTTTCGAATTTTTTTTGA-
1 ----TTTTTTTCGAATTTTTTTTCAC
45672245 TTTTTTT
1 TTTTTTT
45672252 GTTACTCCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
21 9 0.20
22 16 0.35
23 1 0.02
24 1 0.02
27 1 0.02
28 18 0.39
ACGTcount: A:0.15, C:0.09, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTTTTTCGAATTTTTTTTCAC
Found at i:45674095 original size:19 final size:19
Alignment explanation
Indices: 45674068--45674154 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 19
45674058 TTATTCCAGC
*
45674068 AACTAAATTAACTATGATG
1 AACTTAATTAACTATGATG
* *
45674087 AACTTAATTAACCATCATG
1 AACTTAATTAACTATGATG
* * *
45674106 AA--TAATTTATTCT-A-G
1 AACTTAATTAACTATGATG
*
45674121 CAACTTAATTAACTAAGATG
1 -AACTTAATTAACTATGATG
*
45674141 AACTCAATTAACTA
1 AACTTAATTAACTA
45674155 ATATGAGTAA
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
15 1 0.02
16 3 0.06
17 7 0.14
18 7 0.14
19 32 0.63
20 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (19 bp):
AACTTAATTAACTATGATG
Found at i:45674131 original size:54 final size:54
Alignment explanation
Indices: 45674058--45674186 Score: 179
Period size: 54 Copynumber: 2.4 Consensus size: 54
45674048 CATCATTAAA
* * * *
45674058 TTATTCCAGCAACTAAATTAACTATGATGAACTTAATTAAC-CATCATGAATAAT
1 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAT-ATGAATAAT
* *
45674112 TTATTCTAGCAACTTAATTAACTAAGATGAACTCAATTAACTAATATGAGTAAT
1 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAATATGAATAAT
*
45674166 TTATTCCAGCAACTTACTTAA
1 TTATTCCAGCAACTTAATTAA
45674187 TTAAACTAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
54 64 0.97
55 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (54 bp):
TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAATATGAATAAT
Found at i:45674155 original size:19 final size:19
Alignment explanation
Indices: 45674122--45674160 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
45674112 TTATTCTAGC
*
45674122 AACTTAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
*
45674141 AACTCAATTAACTAATATG
1 AACTCAATTAACTAAGATG
45674160 A
1 A
45674161 GTAATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (19 bp):
AACTCAATTAACTAAGATG
Found at i:45676513 original size:20 final size:20
Alignment explanation
Indices: 45676490--45676543 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
45676480 AGTTTTTCCC
*
45676490 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
45676510 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
45676530 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
45676544 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:45676525 original size:30 final size:30
Alignment explanation
Indices: 45676490--45676563 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
45676480 AGTTTTTCCC
45676490 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
45676520 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
45676550 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
45676564 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:45676553 original size:20 final size:20
Alignment explanation
Indices: 45676490--45676554 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
45676480 AGTTTTTCCC
* * * *
45676490 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
45676510 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
45676529 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
45676550 AGCTC
1 AGCTC
45676555 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:45677435 original size:13 final size:13
Alignment explanation
Indices: 45677419--45677443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45677409 AAAAAGTTTT
45677419 AAAAAAAAAATCA
1 AAAAAAAAAATCA
45677432 AAAAAAAAAATC
1 AAAAAAAAAATC
45677444 GAGTTGTAAT
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAATCA
Found at i:45677554 original size:16 final size:14
Alignment explanation
Indices: 45677533--45677585 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 14
45677523 GAAATTCAAA
45677533 AAAAAAAAAGAAGT
1 AAAAAAAAAGAAGT
45677547 GAGCAAAAAAAA-AAGT
1 -A--AAAAAAAAGAAGT
*
45677563 AAAAAAAAAGAA-C
1 AAAAAAAAAGAAGT
45677576 AAAAAAAAAG
1 AAAAAAAAAG
45677586 TGAAAAGTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 18 0.53
14 2 0.06
15 2 0.06
16 4 0.12
17 8 0.24
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAAAAAAGAAGT
Found at i:45678650 original size:6 final size:6
Alignment explanation
Indices: 45678601--45678714 Score: 77
Period size: 6 Copynumber: 18.5 Consensus size: 6
45678591 AAAGAAATTG
* * * * *
45678601 AAAG-A AAACAA AAAGAA AACGAA AAATAA AAAGAA ATAGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
45678648 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
45678699 AAAGAA AAAGCAA AAA
1 AAAGAA AAAG-AA AAA
45678715 AAGAAATTGA
Statistics
Matches: 80, Mismatches: 24, Indels: 8
0.71 0.21 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.76
7 12 0.15
8 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:45678663 original size:18 final size:18
Alignment explanation
Indices: 45678571--45678663 Score: 75
Period size: 18 Copynumber: 5.3 Consensus size: 18
45678561 ATTGAGCGAG
* *
45678571 AAAAGTAAAAAGAGATTGA
1 AAAAG-AAAAAGAAATCGA
**
45678590 AAAAGAAATTGAAA--G-
1 AAAAGAAAAAGAAATCGA
* *
45678605 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* * *
45678623 AAAATAAAAAGAAATAGC
1 AAAAGAAAAAGAAATCGA
45678641 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
45678659 AAAAG
1 AAAAG
45678664 TGAGAGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
15 11 0.19
16 1 0.02
17 1 0.02
18 40 0.69
19 5 0.09
ACGTcount: A:0.71, C:0.04, G:0.16, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:45678688 original size:15 final size:15
Alignment explanation
Indices: 45678668--45678725 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 15
45678658 AAAAAGTGAG
45678668 AGAAAAAGAAAATGA
1 AGAAAAAGAAAATGA
45678683 AG-AAAAGAAAAT--
1 AGAAAAAGAAAATGA
* *
45678695 TGAAAAAGAAAAAGCA
1 AGAAAAAGAAAATG-A
*
45678711 A-AAAAAGAAATTGA
1 AGAAAAAGAAAATGA
45678725 A
1 A
45678726 AGAGAGCTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
12 1 0.03
13 9 0.26
14 12 0.35
15 12 0.35
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (15 bp):
AGAAAAAGAAAATGA
Found at i:45678690 original size:14 final size:13
Alignment explanation
Indices: 45678670--45678726 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
45678660 AAAGTGAGAG
45678670 AAAAAGAAAATGA
1 AAAAAGAAAATGA
45678683 AGAAAAGAAAATTG-
1 A-AAAAGAAAA-TGA
*
45678697 AAAAAGAAAAAGCAA
1 AAAAAGAAAATG--A
*
45678712 AAAAAGAAATTGA
1 AAAAAGAAAATGA
45678725 AA
1 AA
45678727 GAGAGCTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
12 1 0.03
13 13 0.36
14 10 0.28
15 12 0.33
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:45678699 original size:27 final size:27
Alignment explanation
Indices: 45678669--45678726 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
45678659 AAAAGTGAGA
* *
45678669 GAAAAAGAAAATG-AAGAAAAGAAAATT
1 GAAAAAGAAAAAGCAAAAAAAG-AAATT
45678696 GAAAAAGAAAAAGCAAAAAAAGAAATT
1 GAAAAAGAAAAAGCAAAAAAAGAAATT
45678723 GAAA
1 GAAA
45678727 GAGAGCTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (27 bp):
GAAAAAGAAAAAGCAAAAAAAGAAATT
Found at i:45678703 original size:13 final size:12
Alignment explanation
Indices: 45678577--45678706 Score: 74
Period size: 12 Copynumber: 10.8 Consensus size: 12
45678567 CGAGAAAAGT
* *
45678577 AAAAAGAGATTG
1 AAAAAGAAAATG
*
45678589 AAAAAGAAATTG
1 AAAAAGAAAATG
*
45678601 --AAAGAAAA-C
1 AAAAAGAAAATG
*
45678610 AAAAAGAAAACG
1 AAAAAGAAAATG
* *
45678622 AAAAATAAAAAG
1 AAAAAGAAAATG
*
45678634 AAATAGCAAAA-G
1 AAAAAG-AAAATG
45678646 AAAAAG-AAATCG
1 AAAAAGAAAAT-G
* *
45678658 AAAAAGTGAGA-G
1 AAAAAG-AAAATG
45678670 AAAAAGAAAATG
1 AAAAAGAAAATG
45678682 AAGAAAAGAAAATTG
1 -A-AAAAGAAAA-TG
45678697 AAAAAGAAAA
1 AAAAAGAAAA
45678707 AGCAAAAAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
10 10 0.11
11 10 0.11
12 46 0.49
13 14 0.15
14 12 0.13
15 2 0.02
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:45678760 original size:33 final size:33
Alignment explanation
Indices: 45678723--45678785 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
45678713 AAAAGAAATT
45678723 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
45678756 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
45678786 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:45680582 original size:20 final size:20
Alignment explanation
Indices: 45680559--45680612 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
45680549 AGTTTTTCCC
*
45680559 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
45680579 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
45680599 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
45680613 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:45680594 original size:30 final size:30
Alignment explanation
Indices: 45680559--45680632 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
45680549 AGTTTTTCCC
45680559 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
45680589 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
45680619 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
45680633 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:45680622 original size:20 final size:20
Alignment explanation
Indices: 45680559--45680623 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
45680549 AGTTTTTCCC
* * * *
45680559 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
45680579 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
45680598 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
45680619 AGCTC
1 AGCTC
45680624 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:45681498 original size:21 final size:20
Alignment explanation
Indices: 45681471--45681522 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
45681461 ATGGAAAAAG
*
45681471 AAATGAGCTGGAACGAAGCT-
1 AAATGAGCTGAAAC-AAGCTC
*
45681491 AAATTGAGCTCAAACAAGCTC
1 AAA-TGAGCTGAAACAAGCTC
45681512 AAATGAGCTGA
1 AAATGAGCTGA
45681523 TTGGAGCTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (20 bp):
AAATGAGCTGAAACAAGCTC
Found at i:45683436 original size:30 final size:30
Alignment explanation
Indices: 45683402--45683498 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
45683392 TAAACTAAAA
45683402 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
45683432 TGAGCTGAGGC-TAAACTCTTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
45683462 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
45683492 TGAGCTA
1 TGAGCTA
45683499 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:45686889 original size:30 final size:30
Alignment explanation
Indices: 45686818--45686900 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
45686808 CTTTTGTTTC
* *
45686818 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
45686849 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
45686878 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
45686901 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:45686900 original size:18 final size:18
Alignment explanation
Indices: 45686851--45686906 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
45686841 CACTCTCAAA
* *
45686851 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
45686868 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
45686886 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
45686905 TT
1 TT
45686907 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:45686907 original size:12 final size:12
Alignment explanation
Indices: 45686876--45686900 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45686866 TTTTTCAATC
45686876 TCATTTTCTTTT
1 TCATTTTCTTTT
45686888 TCATTTTCTTTT
1 TCATTTTCTTTT
45686900 T
1 T
45686901 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:45686979 original size:5 final size:5
Alignment explanation
Indices: 45686969--45687025 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
45686959 CTCTTGCCTC
*
45686969 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTTT TCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TC-TTT TC-TTT TCTTT
45687016 TCTTT TCTTT
1 TCTTT TCTTT
45687026 ATTTTCTCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 26 0.58
6 14 0.31
7 1 0.02
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:45689595 original size:30 final size:30
Alignment explanation
Indices: 45689561--45689659 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
45689551 TAAACTAAAA
45689561 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
45689591 TGAGCTGAGGC-TAAACTCTTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
45689621 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
45689651 TGAGCTAAG
1 TGAGCTAAG
45689660 AGTGAGCTCG
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
29 2 0.04
30 44 0.85
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:45691486 original size:18 final size:19
Alignment explanation
Indices: 45691465--45691506 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
45691455 CAATTTTCTC
*
45691465 TTCTTGATCAA-TTTCTTT
1 TTCTTGATCAATTTTATTT
**
45691483 TTCTTTTTCAATTTTATTT
1 TTCTTGATCAATTTTATTT
45691502 TTCTT
1 TTCTT
45691507 TTCTCACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.69
Consensus pattern (19 bp):
TTCTTGATCAATTTTATTT
Found at i:45691521 original size:19 final size:19
Alignment explanation
Indices: 45691472--45691522 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
45691462 CTCTTCTTGA
45691472 TCAA-TTTCTTTTTCTTTT
1 TCAACTTTCTTTTTCTTTT
* *
45691490 TCAATTTTATTTTTCTTTT
1 TCAACTTTCTTTTTCTTTT
45691509 CTC-ACTTTCTTTTT
1 -TCAACTTTCTTTTT
45691523 GCTCTCTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 22 0.79
20 2 0.07
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (19 bp):
TCAACTTTCTTTTTCTTTT
Found at i:45691548 original size:16 final size:16
Alignment explanation
Indices: 45691527--45691578 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
45691517 CTTTTTGCTC
45691527 TCTTTCATGCTCTTTT
1 TCTTTCATGCTCTTTT
45691543 TCTTTCATGCTCTTTTTT
1 TCTTTCATGCTC--TTTT
**
45691561 TCTTTCACACTCTTTT
1 TCTTTCATGCTCTTTT
45691577 TC
1 TC
45691579 GATTTTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
18 14 0.44
ACGTcount: A:0.08, C:0.27, G:0.04, T:0.62
Consensus pattern (16 bp):
TCTTTCATGCTCTTTT
Found at i:45691562 original size:18 final size:18
Alignment explanation
Indices: 45691527--45691577 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
45691517 CTTTTTGCTC
45691527 TCTTTCATGCTC--TTTT
1 TCTTTCATGCTCTTTTTT
45691543 TCTTTCATGCTCTTTTTT
1 TCTTTCATGCTCTTTTTT
**
45691561 TCTTTCACACTCTTTTT
1 TCTTTCATGCTCTTTTT
45691578 CGATTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.39
18 19 0.61
ACGTcount: A:0.08, C:0.25, G:0.04, T:0.63
Consensus pattern (18 bp):
TCTTTCATGCTCTTTTTT
Found at i:45715680 original size:15 final size:15
Alignment explanation
Indices: 45715648--45715681 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
45715638 GTTCAACGAA
*
45715648 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
45715663 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
45715678 GAGG
1 GAGG
45715682 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:45720796 original size:23 final size:22
Alignment explanation
Indices: 45720744--45720796 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
45720734 TCCACGTCTT
*
45720744 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
45720766 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
45720789 TTTCTTTT
1 TTTCTTTT
45720797 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:45724158 original size:22 final size:22
Alignment explanation
Indices: 45724130--45724173 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
45724120 TTTTGAACCA
45724130 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
45724152 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
45724174 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:45725790 original size:19 final size:18
Alignment explanation
Indices: 45725766--45725805 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
45725756 ATTAAAGCAG
45725766 ACATATTAAACACATTTAA
1 ACATATTAAACACA-TTAA
*
45725785 ACATATTAAACATATTAA
1 ACATATTAAACACATTAA
45725803 ACA
1 ACA
45725806 CTTAACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (18 bp):
ACATATTAAACACATTAA
Found at i:45725897 original size:19 final size:19
Alignment explanation
Indices: 45725870--45725962 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
45725860 TTATTCCAGC
*
45725870 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
* *
45725889 AACTTAATTTACTAACATG
1 AACTTAATTAACTAAGATG
* * * *
45725908 AA--TAATTTATTCCAG--C
1 AACTTAATTAACT-AAGATG
45725924 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
45725943 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
45725962 A
1 A
45725963 GTAATTTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
16 2 0.04
17 10 0.18
18 8 0.14
19 37 0.65
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:45725918 original size:54 final size:54
Alignment explanation
Indices: 45725860--45725988 Score: 213
Period size: 54 Copynumber: 2.4 Consensus size: 54
45725850 CATCATTAGA
* * *
45725860 TTATTCCAGCAACTAAATTAACTAAGATGAACTTAATTTACTAACATGAATAAT
1 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAACATGAATAAT
* *
45725914 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
1 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAACATGAATAAT
45725968 TTATTCCAGCAACTTAATTAA
1 TTATTCCAGCAACTTAATTAA
45725989 TTAAACTAAG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (54 bp):
TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAACATGAATAAT
Found at i:45729194 original size:54 final size:54
Alignment explanation
Indices: 45729112--45729265 Score: 193
Period size: 53 Copynumber: 2.9 Consensus size: 54
45729102 CATTAGGGTT
* *
45729112 TAAGGATATCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGG
1 TAAGGATATCAAGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCACAAGG
* * * *
45729166 TAAGGAAATCATGTAAGACCATGCCAAGGCATGGCAATGGTGAG-TTCATAAGG
1 TAAGGATATCAAGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCACAAGG
* * * * * *
45729219 CAAGTATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTT
1 TAAGGATATCAAGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTT
45729266 AAAAAGGAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
53 43 0.51
54 42 0.49
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (54 bp):
TAAGGATATCAAGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCACAAGG
Found at i:45730139 original size:14 final size:14
Alignment explanation
Indices: 45730120--45730164 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
45730110 AACTCATCTT
*
45730120 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
45730134 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
45730147 AATTTAATTTAATG
1 AGTTTAATTTAATG
45730161 AGTT
1 AGTT
45730165 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:45730779 original size:29 final size:29
Alignment explanation
Indices: 45730746--45730805 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
45730736 ATAACCAAAC
* *
45730746 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
45730775 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
45730804 CT
1 CT
45730806 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:45730798 original size:15 final size:15
Alignment explanation
Indices: 45730752--45730799 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
45730742 AAACCTACAA
*
45730752 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
45730767 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
45730781 AAACTTCATATCCAT
1 AAACTTCATATCCAT
45730796 AAAC
1 AAAC
45730800 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:45731640 original size:17 final size:17
Alignment explanation
Indices: 45731615--45731649 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
45731605 TGAATGTGAG
*
45731615 AAAATTAAAATTTTTTT
1 AAAAGTAAAATTTTTTT
*
45731632 AAAAGTAAATTTTTTTT
1 AAAAGTAAAATTTTTTT
45731649 A
1 A
45731650 TGCCCCGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
AAAAGTAAAATTTTTTT
Found at i:45734054 original size:28 final size:28
Alignment explanation
Indices: 45733991--45734144 Score: 265
Period size: 28 Copynumber: 5.5 Consensus size: 28
45733981 ATATTAAGTC
* *
45733991 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
45734018 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
45734046 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
45734074 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
45734102 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
45734130 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
45734145 GTACAATTTA
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 22 0.18
28 100 0.82
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:45734083 original size:56 final size:55
Alignment explanation
Indices: 45733991--45734169 Score: 268
Period size: 56 Copynumber: 3.2 Consensus size: 55
45733981 ATATTAAGTC
* *
45733991 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTATATAATCAAACT
*
45734046 CGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAA-CTCGCACACTTAGTGCTATATAATCAAACT
* * * *
45734102 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTATATAA-TCAAACT
45734159 CGCACACTTAG
1 CGCACACTTAG
45734170 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
55 23 0.20
56 72 0.64
57 18 0.16
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTATATAATCAAACT
Found at i:45746007 original size:18 final size:17
Alignment explanation
Indices: 45745986--45746030 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
45745976 TCTTTTTCTT
* *
45745986 TTTCGTTTTCTTTTTTAA
1 TTTC-TTTTCTTTCTCAA
45746004 TTTCTTTTTCTTTCTCAA
1 TTTC-TTTTCTTTCTCAA
45746022 TTTCTTTTC
1 TTTCTTTTC
45746031 AAATTCGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTCTTTTCTTTCTCAA
Found at i:45749707 original size:14 final size:14
Alignment explanation
Indices: 45749685--45749734 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
45749675 ACCTCTTGTA
*
45749685 AAAAGAAAATGA-G
1 AAAAGAAAAAGATG
45749698 AAAAGAAAAAGATG
1 AAAAGAAAAAGATG
*
45749712 AAAA-AAAAGAGATC
1 AAAAGAAAA-AGATG
45749726 AAAAGAAAA
1 AAAAGAAAA
45749735 GAGAGGCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 15 0.47
14 13 0.41
15 4 0.12
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (14 bp):
AAAAGAAAAAGATG
Found at i:45749734 original size:15 final size:15
Alignment explanation
Indices: 45749698--45749738 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
45749688 AGAAAATGAG
*
45749698 AAAAGAAAA-AGATG
1 AAAAGAAAAGAGATC
45749712 AAAA-AAAAGAGATC
1 AAAAGAAAAGAGATC
45749726 AAAAGAAAAGAGA
1 AAAAGAAAAGAGA
45749739 GGCAAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 12 0.50
15 8 0.33
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (15 bp):
AAAAGAAAAGAGATC
Found at i:45749852 original size:12 final size:12
Alignment explanation
Indices: 45749832--45749874 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
45749822 GAGAGGAAAC
*
45749832 AAAATGAGATTG
1 AAAAAGAGATTG
45749844 AAAAAGAGATTG
1 AAAAAGAGATTG
* *
45749856 AAAAAGAGAATC
1 AAAAAGAGATTG
45749868 AAAAAGA
1 AAAAAGA
45749875 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.63, C:0.02, G:0.21, T:0.14
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:45749907 original size:30 final size:31
Alignment explanation
Indices: 45749873--45749933 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
45749863 GAATCAAAAA
**
45749873 GAAAAAGAGTTTGA-ATAAAAGAAAAGAGTG
1 GAAAAAGAAATTGAGATAAAAGAAAAGAGTG
* *
45749903 GAAAAAGAAATTGAGGTAAAAGAAATGAGTG
1 GAAAAAGAAATTGAGATAAAAGAAAAGAGTG
45749934 TTTCCAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (31 bp):
GAAAAAGAAATTGAGATAAAAGAAAAGAGTG
Found at i:45752665 original size:46 final size:46
Alignment explanation
Indices: 45752598--45752820 Score: 213
Period size: 46 Copynumber: 4.8 Consensus size: 46
45752588 TGTAACCCGC
* *
45752598 CCATAAGCGAACTCGGACTCAACTCAAAGAGCTT-GGGTGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAAAGAG-TTCGGATGCTCGCAT
* * * *
45752644 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAAAGAGTTCGGATG-CTCGCAT
* * * * ** *
45752690 ACATTTCA-TGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAAAGAGTTCGGATGCTCGCAT
*
45752737 CCATAAGTGAACTCGGACTCAACTCAACA-AGTTCGGATGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAA-AGAGTTCGGATGCTCGCAT
**
45752783 CCATAAGTGAACTTAGACTCAACTCAACA-AGTTCGGAT
1 CCATAAGTGAACTCGGACTCAACTCAA-AGAGTTCGGAT
45752821 TCCCAAATAT
Statistics
Matches: 146, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
45 4 0.03
46 107 0.73
47 33 0.23
48 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAAAGAGTTCGGATGCTCGCAT
Found at i:45754502 original size:11 final size:10
Alignment explanation
Indices: 45754477--45754537 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
45754467 ACCAATAAAA
45754477 TAAA-TGAGC
1 TAAATTGAGC
*
45754486 TGAATTGTAGC
1 TAAATTG-AGC
45754497 TAAATTGAGC
1 TAAATTGAGC
**
45754507 TCGATTGAGC
1 TAAATTGAGC
45754517 TGAAA-TGAGC
1 T-AAATTGAGC
*
45754527 TCAATTGAGC
1 TAAATTGAGC
45754537 T
1 T
45754538 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:45754538 original size:20 final size:20
Alignment explanation
Indices: 45754478--45754538 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
45754468 CCAATAAAAT
*
45754478 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
45754498 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
45754519 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
45754539 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:45756623 original size:18 final size:18
Alignment explanation
Indices: 45756602--45756636 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
45756592 TTTTTCTTTT
45756602 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
45756620 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
45756637 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:45756695 original size:12 final size:12
Alignment explanation
Indices: 45756675--45756710 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
45756665 ACTATTTTGA
*
45756675 TTTCTTTTTCTT
1 TTTCGTTTTCTT
45756687 TTTCGTTTTCTT
1 TTTCGTTTTCTT
45756699 TTT-GTTTTCTT
1 TTTCGTTTTCTT
45756710 T
1 T
45756711 CAATTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTCGTTTTCTT
Found at i:45762547 original size:22 final size:22
Alignment explanation
Indices: 45762517--45762560 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
45762507 TTTGGTATTT
45762517 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
45762539 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
45762561 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:45764135 original size:11 final size:10
Alignment explanation
Indices: 45764116--45764146 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
45764106 TTTTTGTCAC
45764116 TTCTTTTTTT
1 TTCTTTTTTT
45764126 TTCTTTTTTT
1 TTCTTTTTTT
45764136 TTCTTTTTTT
1 TTCTTTTTTT
45764146 T
1 T
45764147 GAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:45764153 original size:11 final size:11
Alignment explanation
Indices: 45764139--45764163 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
45764129 TTTTTTTTTC
45764139 TTTTTTTTGAA
1 TTTTTTTTGAA
45764150 TTTTTTTTGAA
1 TTTTTTTTGAA
45764161 TTT
1 TTT
45764164 CTTCTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:45764153 original size:20 final size:20
Alignment explanation
Indices: 45764116--45764157 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
45764106 TTTTTGTCAC
***
45764116 TTCTTTTTTTTTCTTTTTTT
1 TTCTTTTTTTTGAATTTTTT
45764136 TTCTTTTTTTTGAATTTTTT
1 TTCTTTTTTTTGAATTTTTT
45764156 TT
1 TT
45764158 GAATTTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.86
Consensus pattern (20 bp):
TTCTTTTTTTTGAATTTTTT
Found at i:45764256 original size:11 final size:12
Alignment explanation
Indices: 45764240--45764269 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
45764230 CCAACTCAAA
45764240 TTTTTTTGA-TT
1 TTTTTTTGACTT
45764251 TTTTTTTGACTT
1 TTTTTTTGACTT
45764263 TTTTTTT
1 TTTTTTT
45764270 CGTTACGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTTGACTT
Found at i:45765563 original size:20 final size:20
Alignment explanation
Indices: 45765524--45765584 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
45765514 CCAATAAAAT
* *
45765524 AAATGAGCTGAATTGTAGCT-
1 AAATAAGCTCAATTG-AGCTG
*
45765544 AAATTAAGCTCGATTGAGCTG
1 AAA-TAAGCTCAATTGAGCTG
*
45765565 AAATGAGCTCAATTGAGCTG
1 AAATAAGCTCAATTGAGCTG
45765585 GTCGGAGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (20 bp):
AAATAAGCTCAATTGAGCTG
Found at i:45768066 original size:49 final size:47
Alignment explanation
Indices: 45768006--45768462 Score: 680
Period size: 47 Copynumber: 9.6 Consensus size: 47
45767996 GATAATTGTG
* *
45768006 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
45768053 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
45768100 ATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
45768149 GTGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG----TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
45768200 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
45768249 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
45768296 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
45768343 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
45768390 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
45768437 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
45768463 TCCCGAAGGG
Statistics
Matches: 384, Mismatches: 22, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 243 0.63
49 95 0.25
51 46 0.12
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:45769777 original size:20 final size:19
Alignment explanation
Indices: 45769737--45769797 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
45769727 ACCAATAAAA
45769737 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCG-ATTG-AGC
45769757 TAAATTGAGCTCGATTGAGC
1 TAAA-TGAGCTCGATTGAGC
* *
45769777 TGAAATAAGCTCAATTGAGC
1 T-AAATGAGCTCGATTGAGC
45769797 T
1 T
45769798 GGTCGGAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 22 0.61
21 13 0.36
22 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (19 bp):
TAAATGAGCTCGATTGAGC
Found at i:45769797 original size:10 final size:10
Alignment explanation
Indices: 45769741--45769797 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
45769731 ATAAAATAAA
*
45769741 TGAGCTGAAT
1 TGAGCTCAAT
*
45769751 TGTAGCTAAAT
1 TG-AGCTCAAT
*
45769762 TGAGCTCGAT
1 TGAGCTCAAT
* *
45769772 TGAGCTGAAA
1 TGAGCTCAAT
*
45769782 TAAGCTCAAT
1 TGAGCTCAAT
45769792 TGAGCT
1 TGAGCT
45769798 GGTCGGAGTT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
10 27 0.75
11 9 0.25
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (10 bp):
TGAGCTCAAT
Found at i:45775380 original size:29 final size:29
Alignment explanation
Indices: 45775290--45775368 Score: 158
Period size: 29 Copynumber: 2.7 Consensus size: 29
45775280 ATATTCATAT
45775290 GGCCCATTAGGCCCAAATCACCTGTATAG
1 GGCCCATTAGGCCCAAATCACCTGTATAG
45775319 GGCCCATTAGGCCCAAATCACCTGTATAG
1 GGCCCATTAGGCCCAAATCACCTGTATAG
45775348 GGCCCATTAGGCCCAAATCAC
1 GGCCCATTAGGCCCAAATCAC
45775369 ATTTATATGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (29 bp):
GGCCCATTAGGCCCAAATCACCTGTATAG
Found at i:45776770 original size:16 final size:16
Alignment explanation
Indices: 45776751--45776783 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
45776741 AAATAAAGAA
45776751 AATTCAGGATTTTGAG
1 AATTCAGGATTTTGAG
45776767 AATTCAGGATTTTGAG
1 AATTCAGGATTTTGAG
45776783 A
1 A
45776784 TTTTTGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (16 bp):
AATTCAGGATTTTGAG
Found at i:45776792 original size:16 final size:16
Alignment explanation
Indices: 45776757--45776807 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
45776747 AGAAAATTCA
* **
45776757 GGATTTTGAGAATTCA
1 GGATTTTGAGATTTTT
45776773 GGATTTTGAGATTTTT
1 GGATTTTGAGATTTTT
*
45776789 GGA-TTTCAGGATTTTT
1 GGATTTTGA-GATTTTT
45776805 GGA
1 GGA
45776808 GCATTACAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 4 0.13
16 26 0.87
ACGTcount: A:0.24, C:0.04, G:0.27, T:0.45
Consensus pattern (16 bp):
GGATTTTGAGATTTTT
Found at i:45789003 original size:49 final size:48
Alignment explanation
Indices: 45788931--45789117 Score: 225
Period size: 49 Copynumber: 3.8 Consensus size: 48
45788921 TGAGGTCACG
*
45788931 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTAC-TGTACCAGATAATTGGTCGCA
* * * * *
45788980 TGTGTAGTACTAAGTGCAGGCTACTA-TGCTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACTG-TACCAGATAA-T-TGGTCGCA
* *
45789030 TGTGTAGTACTAATTGCAGGCTACTACATGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTAC-TGTACCAGATAATTGGTCGCA
45789079 TGTGTAGTACTAAGTGCAGGCTACTA-TGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACT--GTACCAGATA
45789118 GCTTCGGCTA
Statistics
Matches: 117, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
47 3 0.03
48 8 0.07
49 66 0.56
50 31 0.26
51 7 0.06
52 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGCAGGCTACTACTGTACCAGATAATTGGTCGCA
Found at i:45789097 original size:99 final size:101
Alignment explanation
Indices: 45788917--45789112 Score: 333
Period size: 99 Copynumber: 2.0 Consensus size: 101
45788907 CAAATGAACT
* *
45788917 ACTGTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATG
1 ACTGTGA-GTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCGCATG
45788982 TGTAGTACTAAGTGCAGGCTACTATGC-TACCCGAAA
65 TGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAA
* *
45789018 ACTGTGA-TCACGTGTGTAGTACTAATTGCAGGCTACTACATGTACCAGATTATTGGTCGCATGT
1 ACTGTGAGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCGCATGT
45789082 GTAGTACTAAGTGCAGGCTACTATGCGTACC
66 GTAGTACTAAGTGCAGGCTACTATGCGTACC
45789113 AGATAGCTTC
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
99 79 0.88
100 4 0.04
101 7 0.08
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (101 bp):
ACTGTGAGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCGCATGT
GTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAA
Found at i:45794055 original size:30 final size:30
Alignment explanation
Indices: 45794019--45794116 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
45794009 AGCTCACTCC
45794019 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
45794049 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
45794079 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
45794109 TAGCTCAT
1 TAGCTCAT
45794117 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:45798364 original size:49 final size:49
Alignment explanation
Indices: 45798300--45798487 Score: 243
Period size: 49 Copynumber: 3.8 Consensus size: 49
45798290 ACTGGTCACG
*
45798300 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* ** * * * *
45798349 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCA-AAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGATAA-T-TGGTCGCA
*
45798400 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* *
45798449 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
45798488 GCTTCGGCTA
Statistics
Matches: 116, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 73 0.63
50 7 0.06
51 36 0.31
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:45798468 original size:100 final size:100
Alignment explanation
Indices: 45798295--45798482 Score: 349
Period size: 100 Copynumber: 1.9 Consensus size: 100
45798285 GAACTACTGG
*
45798295 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
45798360 AAGTGCAGGCTACTATGCATACCCAAAAACTGTGA
66 AAGTGCAGGCTACTATGCATACCCAAAAACTGTGA
*
45798395 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
*
45798460 AAGTGCAGGCTACTATGCGTACC
66 AAGTGCAGGCTACTATGCATACC
45798483 AGATAGCTTC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCATACCCAAAAACTGTGA
Found at i:45808647 original size:93 final size:93
Alignment explanation
Indices: 45808535--45808706 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
45808525 CGCCCATAAG
* * *
45808535 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
45808600 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
*
45808628 CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
45808693 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
45808707 TCAACCATCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:45808703 original size:46 final size:46
Alignment explanation
Indices: 45808528--45808703 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
45808518 TGTAACCCGC
* * *
45808528 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
45808574 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
45808624 --TTCA-CGAACTCGGACTCAACTCAACAAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
45808667 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
45808704 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 62 0.58
47 28 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:45814170 original size:4 final size:4
Alignment explanation
Indices: 45814151--45814187 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
45814141 GTTGTAAAGT
*
45814151 TTTA TTTT TATTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
45814188 CTTAGTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:45820202 original size:21 final size:21
Alignment explanation
Indices: 45820176--45820238 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
45820166 TTGGTATTTG
*
45820176 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
45820197 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
* *
45820218 GGTATTTGGTATGAATTGGTA
1 GG-AATTGGTATGAAATGGTA
45820239 ATGGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 22 0.58
22 16 0.42
ACGTcount: A:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (21 bp):
GGAATTGGTATGAAATGGTAT
Found at i:45820236 original size:10 final size:10
Alignment explanation
Indices: 45820177--45820238 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
45820167 TGGTATTTGG
*
45820177 GAATTGGTAC
1 GAATTGGTAT
*
45820187 GAAATGGTAT
1 GAATTGGTAT
45820197 GGAATTGGTAT
1 -GAATTGGTAT
*
45820208 GAAATGGTAT
1 GAATTGGTAT
*
45820218 GGTATTTGGTAT
1 -G-AATTGGTAT
45820230 GAATTGGTA
1 GAATTGGTA
45820239 ATGGTTCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 24 0.57
11 11 0.26
12 7 0.17
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.35
Consensus pattern (10 bp):
GAATTGGTAT
Found at i:45823253 original size:10 final size:10
Alignment explanation
Indices: 45823231--45823264 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
45823221 AAAAGAGAAG
45823231 AAATTCAAAAA
1 AAATTC-AAAA
45823242 AAATTCAAAA
1 AAATTCAAAA
*
45823252 AAAATCAAAA
1 AAATTCAAAA
45823262 AAA
1 AAA
45823265 AAAGAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:45823265 original size:10 final size:11
Alignment explanation
Indices: 45823231--45823265 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
45823221 AAAAGAGAAG
45823231 AAATTCAAAAA
1 AAATTCAAAAA
45823242 AAATTCAAAAA
1 AAATTCAAAAA
45823253 AAA-TCAAAAA
1 AAATTCAAAAA
45823263 AAA
1 AAA
45823266 AAGAAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:45823272 original size:21 final size:21
Alignment explanation
Indices: 45823216--45823284 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
45823206 TATTGGATTT
* *
45823216 AAAAAAAAAGAGAAGAAATTCA
1 AAAAAAAAAGA-AAAAAAATCA
***
45823238 AAAAAAATTCAAAAAAAATCA
1 AAAAAAAAAGAAAAAAAATCA
*
45823259 AAAAAAAAAGAAAAGAAA--A
1 AAAAAAAAAGAAAAAAAATCA
45823278 AAAAAAA
1 AAAAAAA
45823285 GGTGAGCAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
19 8 0.21
21 22 0.58
22 8 0.21
ACGTcount: A:0.81, C:0.04, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAAAAAAAGAAAAAAAATCA
Found at i:45824324 original size:6 final size:6
Alignment explanation
Indices: 45824315--45824434 Score: 50
Period size: 6 Copynumber: 19.0 Consensus size: 6
45824305 GAAAGAGATT
** *
45824315 GAAAAA GAAATT GAAAGAA -AAAAA -AAAAT GAAAAA GAAAAA GAAATTGCAA
1 GAAAAA GAAAAA GAAA-AA GAAAAA GAAAAA GAAAAA GAAAAA GAAA----AA
* ** * *
45824366 -AAAAA GAAATCA -AAAAA GTGAAA GAAAAA GAAAAT GAAGAAAA GAAAATT
1 GAAAAA GAAA-AA GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A
45824416 GAAAAA GAAAAA GCAAAAA
1 GAAAAA GAAAAA G-AAAAA
45824435 AGAATTTGAA
Statistics
Matches: 85, Mismatches: 16, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
5 9 0.11
6 54 0.64
7 13 0.15
8 4 0.05
9 3 0.04
10 2 0.02
ACGTcount: A:0.73, C:0.03, G:0.16, T:0.08
Consensus pattern (6 bp):
GAAAAA
Found at i:45824348 original size:7 final size:6
Alignment explanation
Indices: 45824328--45824434 Score: 56
Period size: 6 Copynumber: 16.5 Consensus size: 6
45824318 AAAGAAATTG
* *
45824328 AAAGAA AAAAAA AAATGAA AAAGAA AAAGAA ATTGCAA-AA AAAGAA ATCA-AA
1 AAAGAA AAAGAA AAA-GAA AAAGAA AAAGAA A----AAGAA AAAGAA A-AAGAA
** * *
45824380 AAAGTG AAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAGCAA
1 AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG-AA
45824432 AAA
1 AAA
45824435 AGAATTTGAA
Statistics
Matches: 77, Mismatches: 12, Indels: 23
0.69 0.11 0.21
Matches are distributed among these distances:
5 3 0.04
6 47 0.61
7 18 0.23
8 4 0.05
9 3 0.04
10 2 0.03
ACGTcount: A:0.75, C:0.03, G:0.15, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:45824408 original size:14 final size:13
Alignment explanation
Indices: 45824389--45824426 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
45824379 AAAAGTGAAA
45824389 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
45824401 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
45824416 GAAAAAGAAAA
1 GAAAAAGAAAA
45824427 AGCAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:45824427 original size:14 final size:13
Alignment explanation
Indices: 45824328--45824427 Score: 50
Period size: 13 Copynumber: 7.7 Consensus size: 13
45824318 AAAGAAATTG
*
45824328 AAAGAAAAA-AAA
1 AAAGAAAAATGAA
45824340 AAATGAAAAA-GAA
1 AAA-GAAAAATGAA
*
45824353 AAAG-AAATTGCAA
1 AAAGAAAAATG-AA
*
45824366 AAA-AAGAAATCAAA
1 AAAGAA-AAAT-GAA
**
45824380 AAAGTGAAA-GAA
1 AAAGAAAAATGAA
45824392 AAAG-AAAATGAAGA
1 AAAGAAAAATG-A-A
*
45824406 AAAGAAAATTGAA
1 AAAGAAAAATGAA
45824419 AAAGAAAAA
1 AAAGAAAAA
45824428 GCAAAAAAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 21
0.68 0.10 0.21
Matches are distributed among these distances:
11 6 0.09
12 12 0.18
13 27 0.40
14 17 0.25
15 5 0.07
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (13 bp):
AAAGAAAAATGAA
Found at i:45827871 original size:20 final size:20
Alignment explanation
Indices: 45827848--45827912 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
45827838 TAGTTTTCCC
* *
45827848 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACTTG
* **
45827868 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACTTG
* *
45827888 AGCTCAATTTAGCTTACTTT
1 AGCTCAATTTAGCTCACTTG
45827908 AGCTC
1 AGCTC
45827913 GATTGAGCTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACTTG
Found at i:45827882 original size:30 final size:30
Alignment explanation
Indices: 45827848--45827921 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
45827838 TAGTTTTCCC
45827848 AGCTCGATTTAGCTCACA-TGAGCTTAATTT
1 AGCTCGATTTAGCTCA-ATTGAGCTTAATTT
* *
45827878 AGCTCG-TTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTT-AGCTCAATTGAGCTTAATTT
*
45827908 AGCTCGATTGAGCT
1 AGCTCGATTTAGCT
45827922 TGGCTTAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 4 0.11
30 32 0.84
31 2 0.05
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTTAGCTCAATTGAGCTTAATTT
Found at i:45829503 original size:12 final size:12
Alignment explanation
Indices: 45829483--45829514 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
45829473 TTGGAGTAAC
45829483 AAAAAATTCAAA
1 AAAAAATTCAAA
*
45829495 AAGAAATTCAAA
1 AAAAAATTCAAA
45829507 AAAAAATT
1 AAAAAATT
45829515 TGATTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (12 bp):
AAAAAATTCAAA
Found at i:45829537 original size:12 final size:12
Alignment explanation
Indices: 45829521--45829554 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
45829511 AATTTGATTG
45829521 AAAAAAAAAATT
1 AAAAAAAAAATT
*
45829533 CAAAAAAAAAAGT
1 -AAAAAAAAAATT
45829546 AAAAAAAAA
1 AAAAAAAAA
45829555 TCGAGCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.09
Consensus pattern (12 bp):
AAAAAAAAAATT
Found at i:45829569 original size:31 final size:31
Alignment explanation
Indices: 45829534--45829598 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
45829524 AAAAAAATTC
45829534 AAAAAA-AAAAGTA-AAAAAAAATCGAGCAAAA
1 AAAAAAGAAAAG-AGAAAAAAAAT-GAGCAAAA
**
45829565 AAAAAAGAAAAGAGAAAAAAGGTGAGCAAAA
1 AAAAAAGAAAAGAGAAAAAAAATGAGCAAAA
45829596 AAA
1 AAA
45829599 TCAAGTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.75, C:0.05, G:0.15, T:0.05
Consensus pattern (31 bp):
AAAAAAGAAAAGAGAAAAAAAATGAGCAAAA
Found at i:45831728 original size:20 final size:20
Alignment explanation
Indices: 45831705--45831751 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
45831695 GGGTTAAGAT
*
45831705 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
45831725 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
45831745 TGAGCTG
1 TGAGCTG
45831752 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:45833468 original size:16 final size:18
Alignment explanation
Indices: 45833438--45833480 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
45833428 CTCTCTTTTG
45833438 ATTCT-TTTTCTTTTC-A
1 ATTCTCTTTTCTTTTCGA
45833454 ATTCTCTTTTC-TTTCGA
1 ATTCTCTTTTCTTTTCGA
*
45833471 TTTCTCTTTT
1 ATTCTCTTTT
45833481 TGCTTCACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTCTCTTTTCTTTTCGA
Found at i:45835336 original size:21 final size:21
Alignment explanation
Indices: 45835297--45835353 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
45835287 CAATTACCAA
*
45835297 TTCGTACCAAATACCATACTAT
1 TTCGTACC-AATTCCATACTAT
45835319 TTCGTACCAATTCCATACTAT
1 TTCGTACCAATTCCATACTAT
*
45835340 TTCGAACCAATTCC
1 TTCGTACCAATTCC
45835354 CAAATACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 25 0.76
22 8 0.24
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (21 bp):
TTCGTACCAATTCCATACTAT
Found at i:45836020 original size:20 final size:19
Alignment explanation
Indices: 45835980--45836032 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
45835970 CTTTTCACTT
*
45835980 TTTTTGTTCTTTTTT-TTAC
1 TTTTT-TTCTTTTTTGTCAC
45835999 TTTTTTTCTTTTTTGCTCAC
1 TTTTTTTCTTTTTTG-TCAC
*
45836019 TTCTTTT-TTTTTTG
1 TTTTTTTCTTTTTTG
45836033 AATTTCGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 9 0.30
19 12 0.40
20 9 0.30
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTTTTCTTTTTTGTCAC
Found at i:45837569 original size:20 final size:20
Alignment explanation
Indices: 45837546--45837592 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
45837536 GGGTTAAGAT
**
45837546 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCAAG
* *
45837566 TGAGTTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
45837586 TGAGCTG
1 TGAGCTG
45837593 GAAACGACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:45848198 original size:23 final size:22
Alignment explanation
Indices: 45848146--45848198 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
45848136 TCCACGTCTT
*
45848146 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
45848168 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
45848191 TTTCTTTT
1 TTTCTTTT
45848199 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Done.