Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 135 of 206
Found at i:41270648 original size:26 final size:26
Alignment explanation
Indices: 41270619--41270676 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
41270609 TTATCAATGT
* * *
41270619 TAAAATTGTCAAACTTTTGCTAAGGG
1 TAAAATCGTCAAAATTTTACTAAGGG
* *
41270645 TAAAATCGTCAAAATTTTATTTAGGG
1 TAAAATCGTCAAAATTTTACTAAGGG
41270671 TAAAAT
1 TAAAAT
41270677 AGGGATAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (26 bp):
TAAAATCGTCAAAATTTTACTAAGGG
Found at i:41272018 original size:16 final size:16
Alignment explanation
Indices: 41271997--41272030 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41271987 ATCTTTGAGC
41271997 TTGTGTTAGACTATGT
1 TTGTGTTAGACTATGT
41272013 TTGTGTTAGACTATGT
1 TTGTGTTAGACTATGT
41272029 TT
1 TT
41272031 TTCAATTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.24, T:0.53
Consensus pattern (16 bp):
TTGTGTTAGACTATGT
Found at i:41273305 original size:16 final size:16
Alignment explanation
Indices: 41273281--41273312 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41273271 TAACTGTTAT
*
41273281 AAATTACATAATACAA
1 AAATAACATAATACAA
41273297 AAATAACATAATACAA
1 AAATAACATAATACAA
41273313 TATATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (16 bp):
AAATAACATAATACAA
Found at i:41274659 original size:9 final size:9
Alignment explanation
Indices: 41274645--41274681 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41274635 TATAGTTTAA
41274645 TATTCGAAT
1 TATTCGAAT
41274654 TATTCGAAT
1 TATTCGAAT
*
41274663 TATTCGAGT
1 TATTCGAAT
41274672 TATTCGAAT
1 TATTCGAAT
41274681 T
1 T
41274682 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41277035 original size:13 final size:13
Alignment explanation
Indices: 41277017--41277082 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
41277007 AAATTTTTTT
*
41277017 CTAAATATTATCC
1 CTAAATATTATCA
*
41277030 CTAAATA--A-CC
1 CTAAATATTATCA
*
41277040 CTAAATATTATTA
1 CTAAATATTATCA
*
41277053 CTAAATACT-T--
1 CTAAATATTATCA
41277063 CTAAATATTATCA
1 CTAAATATTATCA
41277076 CTAAATA
1 CTAAATA
41277083 ATTTAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 17 0.40
11 2 0.05
12 2 0.05
13 22 0.51
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:41277043 original size:23 final size:24
Alignment explanation
Indices: 41277017--41277083 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
41277007 AAATTTTTTT
*
41277017 CTAAATATTATCCCTAAATAAC-C
1 CTAAATATTATCACTAAATAACTC
* *
41277040 CTAAATATTATTACTAAAT-ACTT
1 CTAAATATTATCACTAAATAACTC
41277063 CTAAATATTATCACTAAATAA
1 CTAAATATTATCACTAAATAA
41277084 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 2 0.05
23 35 0.92
24 1 0.03
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (24 bp):
CTAAATATTATCACTAAATAACTC
Found at i:41287087 original size:4 final size:4
Alignment explanation
Indices: 41287078--41287108 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
41287068 TTAAATATTA
41287078 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
41287109 ATGTGGGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:41290953 original size:23 final size:23
Alignment explanation
Indices: 41290927--41290987 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
41290917 TTAGATTTTT
* *
41290927 CCTAAATATTATCTCTAAATAAC
1 CCTAAATATTATCACTAAAGAAC
*
41290950 CCTAAATATTATCACTAAAGAAT
1 CCTAAATATTATCACTAAAGAAC
*
41290973 TCTAAATATTATCAC
1 CCTAAATATTATCAC
41290988 AACCATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (23 bp):
CCTAAATATTATCACTAAAGAAC
Found at i:41292118 original size:9 final size:9
Alignment explanation
Indices: 41292101--41292146 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
41292091 TGAGTTTTCA
41292101 AATTCGAAT
1 AATTCGAAT
*
41292110 AACTCGAAT
1 AATTCGAAT
41292119 AATTCGAAT
1 AATTCGAAT
*
41292128 AATTTGAAT
1 AATTCGAAT
41292137 AATTCGAAT
1 AATTCGAAT
41292146 A
1 A
41292147 TCAAAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41292991 original size:5 final size:5
Alignment explanation
Indices: 41292981--41293006 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
41292971 CTCGAAAATT
41292981 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
41293007 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:41301381 original size:20 final size:20
Alignment explanation
Indices: 41301356--41301411 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
41301346 CCTTAAGTGA
41301356 CAACTAAACATCAATTACAT
1 CAACTAAACATCAATTACAT
*
41301376 CAACTAAACATTAATTACAT
1 CAACTAAACATCAATTACAT
41301396 CAACTAAACATCAATT
1 CAACTAAACATCAATT
41301412 TGCAAGTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (20 bp):
CAACTAAACATCAATTACAT
Found at i:41301408 original size:11 final size:11
Alignment explanation
Indices: 41301356--41301409 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
41301346 CCTTAAGTGA
41301356 CAACTAAACAT
1 CAACTAAACAT
*
41301367 CAA-T-TACAT
1 CAACTAAACAT
41301376 CAACTAAACAT
1 CAACTAAACAT
* *
41301387 TAA-T-TACAT
1 CAACTAAACAT
41301396 CAACTAAACAT
1 CAACTAAACAT
41301407 CAA
1 CAA
41301410 TTTGCAAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 13 0.39
10 4 0.12
11 16 0.48
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (11 bp):
CAACTAAACAT
Found at i:41316240 original size:30 final size:32
Alignment explanation
Indices: 41316204--41316263 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
41316194 ATCATAAATT
*
41316204 CAAAAAAAAAAATCAT-AAAATCC-AAAAAGA
1 CAAAAAAAAAAAGCATAAAAATCCTAAAAAGA
*
41316234 CAAAAAAAAAAAGCTTAAAAATCCTAAAAA
1 CAAAAAAAAAAAGCATAAAAATCCTAAAAA
41316264 CTAAAGATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 14 0.54
31 7 0.27
32 5 0.19
ACGTcount: A:0.72, C:0.13, G:0.03, T:0.12
Consensus pattern (32 bp):
CAAAAAAAAAAAGCATAAAAATCCTAAAAAGA
Found at i:41318529 original size:34 final size:39
Alignment explanation
Indices: 41318461--41318537 Score: 110
Period size: 40 Copynumber: 2.1 Consensus size: 39
41318451 GAGAACGGGC
41318461 TTTGTTGCCACGTAGGCAAAGCGCGCCCTCGGGGACGCGT
1 TTTGTTGCCACGTAGGC-AAGCGCGCCCTCGGGGACGCGT
41318501 TTTGTTGCCACGTA-GC-A-CGC-CCCT-GGGGACGCGT
1 TTTGTTGCCACGTAGGCAAGCGCGCCCTCGGGGACGCGT
41318535 TTT
1 TTT
41318538 CCCCGCGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
34 13 0.35
35 4 0.11
36 3 0.08
37 1 0.03
39 2 0.05
40 14 0.38
ACGTcount: A:0.13, C:0.30, G:0.32, T:0.25
Consensus pattern (39 bp):
TTTGTTGCCACGTAGGCAAGCGCGCCCTCGGGGACGCGT
Found at i:41318677 original size:11 final size:11
Alignment explanation
Indices: 41318661--41318705 Score: 81
Period size: 11 Copynumber: 4.1 Consensus size: 11
41318651 TCAATTATTT
41318661 TCTCAATTTCC
1 TCTCAATTTCC
41318672 TCTCAATTTCC
1 TCTCAATTTCC
*
41318683 TCTCAATTTGC
1 TCTCAATTTCC
41318694 TCTCAATTTCC
1 TCTCAATTTCC
41318705 T
1 T
41318706 TCCAAATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.18, C:0.33, G:0.02, T:0.47
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:41318689 original size:22 final size:21
Alignment explanation
Indices: 41318647--41318721 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 21
41318637 AAACTAATAC
**
41318647 TCTCTCAATTATTTTCTCAATT
1 TCTCTCAATT-TCCTCTCAATT
41318669 TCCTCTCAATTTCCTCTCAATT
1 T-CTCTCAATTTCCTCTCAATT
41318691 TGCTCTCAATTTCCT-TCCAAATT
1 T-CTCTCAATTTCCTCT-C-AATT
41318714 TCTCTCAA
1 TCTCTCAA
41318722 ATCCCTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
21 1 0.02
22 32 0.68
23 14 0.30
ACGTcount: A:0.21, C:0.31, G:0.01, T:0.47
Consensus pattern (21 bp):
TCTCTCAATTTCCTCTCAATT
Found at i:41321079 original size:125 final size:125
Alignment explanation
Indices: 41320781--41321213 Score: 679
Period size: 127 Copynumber: 3.5 Consensus size: 125
41320771 CATGCTACTA
* * * * *
41320781 TAGCAAAAGAGCATCCACGAGGGCGCGATTTCATAAATTCTTCTGATAAAGCATCCTACTTGAAG
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
* *
41320846 CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTT-AGGACCTATTG
66 CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTG
* *
41320905 TAGCAAAAGCGCGTCCACGTGGGCGCAATTTCAGAAATTCTTCTAATAAAGCATCCTGCTTGAAG
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
* * *
41320970 CGTTTTTTATACTGTTCGCTCAGAAACGTCAACTCGAAATTATTTTTTCAAGACCAACTG
66 CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTG
* *
41321030 TAGCAAAAGCGCGTCCACGTGGGCGGGATTTTAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
* *
41321095 CGTTTTTTTTATACTATTTTCTCAAAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTG
66 CG--TTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTG
* *
41321157 TAGCAAAAACGCGTCCACGTGGGTGCGATTTCAGAAATTCTTCTGATAAAGCATCCT
1 TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCT
41321214 AAACCATAAA
Statistics
Matches: 281, Mismatches: 25, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
124 104 0.37
125 71 0.25
127 106 0.38
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (125 bp):
TAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGCTTGAAG
CGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCAACTG
Found at i:41321285 original size:16 final size:15
Alignment explanation
Indices: 41321264--41321293 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
41321254 TTTTTCTCTA
41321264 AAACCTTAAAACCCTT
1 AAACCTT-AAACCCTT
41321280 AAACCTTAAACCCT
1 AAACCTTAAACCCT
41321294 AACCCTAAAA
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:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (15 bp):
AAACCTTAAACCCTT
Found at i:41332465 original size:83 final size:84
Alignment explanation
Indices: 41332315--41332479 Score: 296
Period size: 83 Copynumber: 2.0 Consensus size: 84
41332305 TTTATGCTTA
* *
41332315 ATGTGACAATTGCCCACTATAATTTAGGTTAAAGTTCAATTTGCCACTATACTTTATCTTCTTTT
1 ATGTGACAATTGCCCACTATAATTTAGGTTAAAGTTCAATTTACCACTATACTTTATCTTCCTTT
41332380 ATATTTGTCATTATAATAT
66 ATATTTGTCATTATAATAT
*
41332399 ATGTGTCAATTGCCCACTATAATTTAGGTTAAA-TTCAATTTACCACTATACTTTATCTTCCTTT
1 ATGTGACAATTGCCCACTATAATTTAGGTTAAAGTTCAATTTACCACTATACTTTATCTTCCTTT
41332463 ATATTTGTCATTATAAT
66 ATATTTGTCATTATAAT
41332480 TTTGAGTTGA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 46 0.59
84 32 0.41
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.45
Consensus pattern (84 bp):
ATGTGACAATTGCCCACTATAATTTAGGTTAAAGTTCAATTTACCACTATACTTTATCTTCCTTT
ATATTTGTCATTATAATAT
Found at i:41333074 original size:40 final size:39
Alignment explanation
Indices: 41333030--41333113 Score: 91
Period size: 40 Copynumber: 2.1 Consensus size: 39
41333020 ACTCGGCCTG
41333030 AATATATAATAAATATA-TTTTTTTAATTTTTTAATTT-TAA
1 AATAT-TAATAAA-ATACTTTTTTTAATTTTTT-ATTTGTAA
** *
41333070 AATATTTTTAAAATACTTTTTTTTTATTTTTTATTTGTAA
1 AATATTAATAAAATAC-TTTTTTTAATTTTTTATTTGTAA
41333110 AATA
1 AATA
41333114 AATTTTTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
38 3 0.08
39 9 0.24
40 26 0.68
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (39 bp):
AATATTAATAAAATACTTTTTTTAATTTTTTATTTGTAA
Found at i:41338959 original size:23 final size:23
Alignment explanation
Indices: 41338933--41338984 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
41338923 GGCACACGAG
41338933 GTGCCTAAAATACGACACATAAA
1 GTGCCTAAAATACGACACATAAA
* *
41338956 GTGCCCAATATACGACACATAAA
1 GTGCCTAAAATACGACACATAAA
41338979 GTGCCT
1 GTGCCT
41338985 GATCGGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.19
Consensus pattern (23 bp):
GTGCCTAAAATACGACACATAAA
Found at i:41348456 original size:406 final size:405
Alignment explanation
Indices: 41347669--41348480 Score: 1306
Period size: 406 Copynumber: 2.0 Consensus size: 405
41347659 CTTCAGTAGT
*
41347669 TTTGACATGTACACATTTGTCACACTCATTAATCTTAAAGTCATTTATCATCATGAAATTATCAA
1 TTTGACATGTACACATTTGTCACACTCATTAATCTTAAAGTCATTTATAATCATGAAATTATCAA
* * *
41347734 AATTTTCATACGTTGCTTTGGTACTTGCTTAAGTCCATACAAATACTTTACCAATTTTCAAACTT
66 AATTTTCATACATTGCTTTGGTACTTGCTTAAGTCCATACAAAGACTTTACCAATTTACAAACTT
* *
41347799 TCATTTCTTGTCTTGGAACTATATTACCCTCAAGTTGTTCCTTGTAAATTTCTTCATCAATCTTC
131 TCA--T-TTGTCCTGGAACTATATTACCCTCAAGTTGTTCCATGTAAATTTCTTCATCAATCTTC
* * *
41347864 ATTTAGGAAAGCTATTTTAACGTCCATTTGATGTACTTCTAAATTTTCGAAAGGCGGCAATCGCA
193 ATTTAGGAAAGCTATTTTAACATCCATTTGATGTAATTCTAAA-TTTCCAAAGGCGGCAATCGCA
* * *
41347929 AGTATCATCCTTATCGAAGTTATCCTGGATACTAGAGAACAAGTGTCAAAATAGTCAAGACCTTC
257 AGTATCATCCTTATCGAAGTTATCCTGGATAATAGAGAACAAGTATCAAAATAGTCAAAACCTTC
* *
41347994 CTTTTGTCTATAACCTTTTATAACCAACCTAGCCTTGTACTTGTCAATAGTTCCATTTGCTTTCA
322 CTTTTATCTATAACCTTTTATAACCAACCTAGCCTTGTACTTGTCAATAGTTCCATTTGATTTCA
*
41348059 TTTTCTGTTTGAAAATTCA
387 TTTTCTATTTGAAAATTCA
* **
41348078 TTTGACATGTACACATTTGTCATACTCATTAATCTTAAAGTCATTTATAATCATGGCATTATCAA
1 TTTGACATGTACACATTTGTCACACTCATTAATCTTAAAGTCATTTATAATCATGAAATTATCAA
*
41348143 AATTTTCATACATTGCTTTGGTGCTTGCTTAAGTCCATACAAAGACTTTACCAATTTACAAACTT
66 AATTTTCATACATTGCTTTGGTACTTGCTTAAGTCCATACAAAGACTTTACCAATTTACAAACTT
* *
41348208 TCA-TTGTCCTGGAACTATATTACCCTCATGTTGTTCCATGTAAATTTCTTTATCAAGATC-TCT
131 TCATTTGTCCTGGAACTATATTACCCTCAAGTTGTTCCATGTAAATTTCTTCATC-A-ATCTTC-
*
41348271 ATTTAGGAAAGCTATTTTAACATCCATTTGATGTAATTCTAAA-TTCCACAAGGCGTCAATCGCA
193 ATTTAGGAAAGCTATTTTAACATCCATTTGATGTAATTCTAAATTTCCA-AAGGCGGCAATCGCA
41348335 AGTATCATCCTTATCGAAGTTATCCTGGATAATAGAGAACAAGTATCAAAATAGTCAAAACCTTC
257 AGTATCATCCTTATCGAAGTTATCCTGGATAATAGAGAACAAGTATCAAAATAGTCAAAACCTTC
* * *
41348400 CTTTTATCTATAACCTTTTATAACCAATCTGGCCTTGTACTTGTCAATGGTTCCATTTGATTTCA
322 CTTTTATCTATAACCTTTTATAACCAACCTAGCCTTGTACTTGTCAATAGTTCCATTTGATTTCA
41348465 TTTTCTATTTGAAAAT
387 TTTTCTATTTGAAAAT
41348481 CCACTTAGAA
Statistics
Matches: 374, Mismatches: 25, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
405 51 0.14
406 154 0.41
407 44 0.12
409 125 0.33
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (405 bp):
TTTGACATGTACACATTTGTCACACTCATTAATCTTAAAGTCATTTATAATCATGAAATTATCAA
AATTTTCATACATTGCTTTGGTACTTGCTTAAGTCCATACAAAGACTTTACCAATTTACAAACTT
TCATTTGTCCTGGAACTATATTACCCTCAAGTTGTTCCATGTAAATTTCTTCATCAATCTTCATT
TAGGAAAGCTATTTTAACATCCATTTGATGTAATTCTAAATTTCCAAAGGCGGCAATCGCAAGTA
TCATCCTTATCGAAGTTATCCTGGATAATAGAGAACAAGTATCAAAATAGTCAAAACCTTCCTTT
TATCTATAACCTTTTATAACCAACCTAGCCTTGTACTTGTCAATAGTTCCATTTGATTTCATTTT
CTATTTGAAAATTCA
Found at i:41348937 original size:40 final size:41
Alignment explanation
Indices: 41348882--41348976 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 41
41348872 AAAATGCCGC
*
41348882 AATGCAGCAAAAGGTAAGAAATAGTGGCGTTTGTCG-TAA-A
1 AATGCCGCAAAAGGTAAGAAATAGTGGCGTTTGT-GTTAACA
* *
41348922 AATGCCGCAAAAGGTAAGCAATAGTGGTGTTTGTGTTAACA
1 AATGCCGCAAAAGGTAAGAAATAGTGGCGTTTGTGTTAACA
*
41348963 AA-GCCGTAAAAGGT
1 AATGCCGCAAAAGGT
41348977 TTTTTACTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
39 1 0.02
40 45 0.92
41 3 0.06
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (41 bp):
AATGCCGCAAAAGGTAAGAAATAGTGGCGTTTGTGTTAACA
Found at i:41349177 original size:49 final size:48
Alignment explanation
Indices: 41349058--41349184 Score: 125
Period size: 47 Copynumber: 2.6 Consensus size: 48
41349048 TACTTAAAAA
* * *
41349058 GAAAACCCCAAAAATCAT-TTCCCTTTTCTTTCCCAGACTTTCTTTGCTT
1 GAAAACCCC-AAAATC-TCATCCCTTTTCTTTCCCAGACTTTCGTTGCTG
* * *
41349107 G-AAACCCTAAAATCCCATCCCTTTTCTTTCTCA-ATCTTTTCGTTGCTG
1 GAAAACCCCAAAATCTCATCCCTTTTCTTTCCCAGA-C-TTTCGTTGCTG
*
41349155 GAAAACCCCAAAATCTCGTCCCTTGTTCTT
1 GAAAACCCCAAAATCTCATCCCTT-TTCTT
41349185 CTATTTCAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
46 1 0.02
47 22 0.34
48 16 0.25
49 20 0.31
50 5 0.08
ACGTcount: A:0.24, C:0.31, G:0.08, T:0.37
Consensus pattern (48 bp):
GAAAACCCCAAAATCTCATCCCTTTTCTTTCCCAGACTTTCGTTGCTG
Found at i:41350221 original size:2 final size:2
Alignment explanation
Indices: 41350216--41350244 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41350206 TACATGCATA
41350216 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
41350245 CCCTTCTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:41350484 original size:12 final size:12
Alignment explanation
Indices: 41350469--41350494 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41350459 CATTATGATC
41350469 TTATTTATTTGT
1 TTATTTATTTGT
41350481 TTATTTATTTGT
1 TTATTTATTTGT
41350493 TT
1 TT
41350495 TCAGTGGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTATTTATTTGT
Found at i:41354011 original size:16 final size:16
Alignment explanation
Indices: 41353990--41354028 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
41353980 TGGTCCCGAA
41353990 ACCACTACTTTTCGAC
1 ACCACTACTTTTCGAC
*
41354006 ACCACTATTTTTCGAC
1 ACCACTACTTTTCGAC
41354022 ACCACTA
1 ACCACTA
41354029 AAAAACGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.31
Consensus pattern (16 bp):
ACCACTACTTTTCGAC
Found at i:41365562 original size:20 final size:19
Alignment explanation
Indices: 41365534--41365574 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
41365524 ATCAACTGTC
41365534 TCTTAAATTTACTCAAAAAA
1 TCTTAAA-TTACTCAAAAAA
* *
41365554 TCTTCAATTACTCCAAAAA
1 TCTTAAATTACTCAAAAAA
41365573 TC
1 TC
41365575 AGCACAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (19 bp):
TCTTAAATTACTCAAAAAA
Found at i:41367862 original size:39 final size:40
Alignment explanation
Indices: 41367785--41367874 Score: 130
Period size: 39 Copynumber: 2.3 Consensus size: 40
41367775 TCCACGTAAG
* *
41367785 CGCGATTTGCTTCCACGTCAGCAAATCGCGCTTACGTGGA
1 CGCGATTTGCTTCCACGTAAGCAAATCGCGCTGACGTGGA
*
41367825 CGCGATTTG-TTGCCACGTAAG-TAATCGCGCTGACGTGGA
1 CGCGATTTGCTT-CCACGTAAGCAAATCGCGCTGACGTGGA
41367864 CGCGATTTGCT
1 CGCGATTTGCT
41367875 GACACATCCC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 27 0.60
40 18 0.40
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.27
Consensus pattern (40 bp):
CGCGATTTGCTTCCACGTAAGCAAATCGCGCTGACGTGGA
Found at i:41369939 original size:21 final size:21
Alignment explanation
Indices: 41369913--41369953 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41369903 TTAAGAGATA
* *
41369913 TTACTTAAATAGTTGTATCTC
1 TTACTTAAATAATTGCATCTC
*
41369934 TTACTTTAATAATTGCATCT
1 TTACTTAAATAATTGCATCT
41369954 ATTTAAGAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (21 bp):
TTACTTAAATAATTGCATCTC
Found at i:41377637 original size:6 final size:6
Alignment explanation
Indices: 41377628--41377664 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
41377618 GAGCGAGATA
41377628 GAGACC GAGACC GAGACC GAGACC GAGACC GAGACC G
1 GAGACC GAGACC GAGACC GAGACC GAGACC GAGACC G
41377665 GAGCAGGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.32, G:0.35, T:0.00
Consensus pattern (6 bp):
GAGACC
Found at i:41379407 original size:23 final size:23
Alignment explanation
Indices: 41379364--41379407 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
41379354 AAGTAAACAA
* *
41379364 AAATAATCAATACAAATTAAATC
1 AAATAAACAATACAAAGTAAATC
41379387 AAATAAACAAT-CAATAGTAAA
1 AAATAAACAATACAA-AGTAAA
41379408 ATCTTAGGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.23
Consensus pattern (23 bp):
AAATAAACAATACAAAGTAAATC
Found at i:41382789 original size:51 final size:50
Alignment explanation
Indices: 41382706--41382831 Score: 139
Period size: 51 Copynumber: 2.5 Consensus size: 50
41382696 CAAATAAACA
* *
41382706 AAAATGATGAAATGGAGAAATAGGAAACATTTGAAAATGATTAAGGTTTTCTCT
1 AAAATGA--AAATGGAGAAAT--GAAACATTTGAAAATGAATAAGGTTTTCTCC
* **
41382760 AAAATGAAAATGGAGAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCC
1 AAAATGAAAATGGAGAAATGAAA-CATTTGAAAATGAATAAGGTTTTCTCC
*
41382811 AAATTGAAAAT-GA-AAATGAAA
1 AAAATGAAAATGGAGAAATGAAA
41382832 ATGAAAAATG
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
49 8 0.12
50 6 0.09
51 32 0.49
52 12 0.18
54 7 0.11
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.28
Consensus pattern (50 bp):
AAAATGAAAATGGAGAAATGAAACATTTGAAAATGAATAAGGTTTTCTCC
Found at i:41382826 original size:6 final size:6
Alignment explanation
Indices: 41382815--41382855 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
41382805 TTCTCCAAAT
41382815 TGAAAA TGAAAA TGAAAA TGAAAAA TGAAAAA TGAAAA TGA
1 TGAAAA TGAAAA TGAAAA TG-AAAA TG-AAAA TGAAAA TGA
41382856 CTTGAGGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 21 0.62
7 13 0.38
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
TGAAAA
Found at i:41382839 original size:7 final size:7
Alignment explanation
Indices: 41382817--41382852 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
41382807 CTCCAAATTG
41382817 AAAATG-
1 AAAATGA
41382823 AAAATG-
1 AAAATGA
41382829 AAAATGA
1 AAAATGA
41382836 AAAATGA
1 AAAATGA
41382843 AAAATGA
1 AAAATGA
41382850 AAA
1 AAA
41382853 TGACTTGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAATGA
Found at i:41382839 original size:13 final size:13
Alignment explanation
Indices: 41382817--41382855 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
41382807 CTCCAAATTG
41382817 AAAATGAAAATG-
1 AAAATGAAAATGA
41382829 AAAATGAAAAATGA
1 AAAATG-AAAATGA
41382843 AAAATGAAAATGA
1 AAAATGAAAATGA
41382856 CTTGAGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.24
13 13 0.52
14 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATGAAAATGA
Found at i:41387138 original size:21 final size:21
Alignment explanation
Indices: 41387113--41387179 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
41387103 TTCTTGGTAG
*
41387113 GTGGATATCGTGATACCCACA
1 GTGGATATCATGATACCCACA
41387134 GTGGATATCATGATACCCACA
1 GTGGATATCATGATACCCACA
*
41387155 GTGGATATCATGATACCCAAA
1 GTGGATATCATGATACCCACA
41387176 GTGG
1 GTGG
41387180 CCTCCATTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (21 bp):
GTGGATATCATGATACCCACA
Found at i:41387252 original size:5 final size:5
Alignment explanation
Indices: 41387242--41387309 Score: 61
Period size: 5 Copynumber: 13.4 Consensus size: 5
41387232 ACCCCAAAGT
* *
41387242 AAATA AAATA AAATA AAA-A AGATA ATAT- AAAT- AAATAA TAAATA AAATAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT-A -AAATA AAAT-A
41387292 TAAATA AAATA AAATA AA
1 -AAATA AAATA AAATA AA
41387310 TTGAATTGCC
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
4 10 0.19
5 33 0.61
6 3 0.06
7 8 0.15
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:41387266 original size:9 final size:10
Alignment explanation
Indices: 41387242--41387309 Score: 61
Period size: 12 Copynumber: 6.7 Consensus size: 10
41387232 ACCCCAAAGT
41387242 AAATAAAATA
1 AAATAAAATA
41387252 AAATAAAA-A
1 AAATAAAATA
* *
41387261 AGATAATAT-
1 AAATAAAATA
41387270 AAAT-AAATAA
1 AAATAAAAT-A
41387280 TAAATAAAATAA
1 -AAATAAAAT-A
41387292 TAAATAAAATA
1 -AAATAAAATA
41387303 AAATAAA
1 AAATAAA
41387310 TTGAATTGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
8 3 0.06
9 10 0.20
10 15 0.31
11 5 0.10
12 16 0.33
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.22
Consensus pattern (10 bp):
AAATAAAATA
Found at i:41387277 original size:4 final size:4
Alignment explanation
Indices: 41387241--41387310 Score: 54
Period size: 4 Copynumber: 16.2 Consensus size: 4
41387231 AACCCCAAAG
*
41387241 TAAA TAAAA TAAAA TAAA AAAGA TAATA TAAA TAAA T-AA TAAA TAAA
1 TAAA T-AAA T-AAA TAAA TAA-A TAA-A TAAA TAAA TAAA TAAA TAAA
41387288 -ATAA TAAA TAAAA TAAAA TAAA T
1 TA-AA TAAA T-AAA T-AAA TAAA T
41387311 TGAATTGCCA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
3 4 0.07
4 27 0.47
5 26 0.46
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:41387714 original size:111 final size:110
Alignment explanation
Indices: 41387416--41387720 Score: 308
Period size: 115 Copynumber: 2.7 Consensus size: 110
41387406 CACTAGAAAT
* * * * *
41387416 AGATTTCATTCCAATAGAAAACTTAGTAAATTTTCTGCCTAGTTTCACTCCAAAAGAAACAA-AT
1 AGATTCCATTCCAAAAGAAAACTTAGTAAACTCTCTGCCTAGTTTCACTCC-AATGAAA-AAGAT
* ** * * * *
41387480 TTCGCTCCAACAGATAACTAGAAAACTAATTTCACTCCAATAGAAAT
64 TTTGCTCCAATGGAAAACTAGAAAACTAATTTCACTCCAACAAAAAC
* * * *
41387527 AGATTCCATTCCAAAAAAAAAAAAACTTAGCAAACTCTCTACCTAGTTTCACTCCAATAGAAACA
1 AGATTCCATTCC----AAAAGAAAACTTAGTAAACTCTCTGCCTAGTTTCACTCCAAT-GAAAAA
* * * *
41387592 GGTTATGCTCCAATGGAAAACTAGCAAACTAAGTTT-GCTCCAACAAAAAC
61 GATTTTGCTCCAATGGAAAACTAGAAAACTAA-TTTCACTCCAACAAAAAC
* **
41387642 AGATTCCATTCCAACAGAAAACTTAGTAAACTCTCTGCCTAGTTTCGGTCCAATGAAAATAGATT
1 AGATTCCATTCCAAAAGAAAACTTAGTAAACTCTCTGCCTAGTTTCACTCCAATGAAAA-AGATT
41387707 TTGCTCCAATGGAA
65 TTGCTCCAATGGAA
41387721 TGAGTCTATA
Statistics
Matches: 157, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
110 4 0.03
111 64 0.41
114 3 0.02
115 83 0.53
116 3 0.02
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (110 bp):
AGATTCCATTCCAAAAGAAAACTTAGTAAACTCTCTGCCTAGTTTCACTCCAATGAAAAAGATTT
TGCTCCAATGGAAAACTAGAAAACTAATTTCACTCCAACAAAAAC
Found at i:41387836 original size:17 final size:17
Alignment explanation
Indices: 41387814--41387846 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41387804 AAAAACAAAC
41387814 TAAAAA-AAAGATAAAAG
1 TAAAAATAAA-ATAAAAG
41387831 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
41387847 TTTTTAGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
TAAAAATAAAATAAAAG
Found at i:41394481 original size:27 final size:27
Alignment explanation
Indices: 41394449--41394669 Score: 163
Period size: 27 Copynumber: 8.2 Consensus size: 27
41394439 TATAATGATC
41394449 ATTTTACCCTATAGGGGTATTTCGA-TA
1 ATTTTACCC-ATAGGGGTATTTCGAGTA
* * *
41394476 ACTTTACCCATCAAGGGTATTTC-AGTC
1 ATTTTACCCAT-AGGGGTATTTCGAGTA
** * *
41394503 ATTTTACCTTTTGGGGGTATTT-TAGTA
1 ATTTTACC-CATAGGGGTATTTCGAGTA
41394530 ATTTTACCCAT-GGATGGTATTTCG-GTA
1 ATTTTACCCATAGG--GGTATTTCGAGTA
41394557 ATTTTACCCATCAGGGGTATTTC-AGTA
1 ATTTTACCCAT-AGGGGTATTTCGAGTA
* * *
41394584 ATTTTACCTATTTGGGGTATTTTG-GTA
1 ATTTTACCCA-TAGGGGTATTTCGAGTA
* *
41394611 ATTTTACCCATCGAGGGTATTTC-AGTC
1 ATTTTACCCATAG-GGGTATTTCGAGTA
* * *
41394638 ATTCTACCCTATAGAGGTATTTCG-GTT
1 ATTTTACCC-ATAGGGGTATTTCGAGTA
41394665 ATTTT
1 ATTTT
41394670 TTCTAGTTTG
Statistics
Matches: 154, Mismatches: 24, Indels: 32
0.73 0.11 0.15
Matches are distributed among these distances:
25 2 0.01
26 6 0.04
27 139 0.90
28 5 0.03
29 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.43
Consensus pattern (27 bp):
ATTTTACCCATAGGGGTATTTCGAGTA
Found at i:41394552 original size:81 final size:81
Alignment explanation
Indices: 41394449--41394633 Score: 266
Period size: 81 Copynumber: 2.3 Consensus size: 81
41394439 TATAATGATC
* *
41394449 ATTTTACCCTATAG-GGGTATTTCGATAACTTTACCCATCAAGGGTATTTCAGTCATTTTACCT-
1 ATTTTACCC-ATCGAGGGTATTTCGATAACTTTACCCATCAAGGGTATTTCAGTAATTTTACCTA
41394512 TTTGGGGGTATTTTAGTA
65 TTT-GGGGTATTTTAGTA
* * * * *
41394530 ATTTTACCCATGGATGGTATTTCGGTAATTTTACCCATCAGGGGTATTTCAGTAATTTTACCTAT
1 ATTTTACCCATCGAGGGTATTTCGATAACTTTACCCATCAAGGGTATTTCAGTAATTTTACCTAT
*
41394595 TTGGGGTATTTTGGTA
66 TTGGGGTATTTTAGTA
41394611 ATTTTACCCATCGAGGGTATTTC
1 ATTTTACCCATCGAGGGTATTTC
41394634 AGTCATTCTA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
80 3 0.03
81 87 0.94
82 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (81 bp):
ATTTTACCCATCGAGGGTATTTCGATAACTTTACCCATCAAGGGTATTTCAGTAATTTTACCTAT
TTGGGGTATTTTAGTA
Found at i:41394603 original size:54 final size:53
Alignment explanation
Indices: 41394449--41394669 Score: 198
Period size: 54 Copynumber: 4.1 Consensus size: 53
41394439 TATAATGATC
* * * *
41394449 ATTTTACCCTAT-AGGGGTATTTC-GATAACTTTACCCATCAAGGGTATTTCAGTC
1 ATTTTACCC-ATCAGGGGTATTTCAG-TAATTTTACCCAT-AGGGGTATTTCGGTA
** ** *
41394503 ATTTTACCTTTTGGGGGTATTTTAGTAATTTTACCCAT-GGATGGTATTTCGGTA
1 ATTTTACCCATCAGGGGTATTTCAGTAATTTTACCCATAGG--GGTATTTCGGTA
* * *
41394557 ATTTTACCCATCAGGGGTATTTCAGTAATTTTACCTATTTGGGGTATTTTGGTA
1 ATTTTACCCATCAGGGGTATTTCAGTAATTTTACCCA-TAGGGGTATTTCGGTA
* * * *
41394611 ATTTTACCCATC-GAGGGTATTTCAGTCATTCTACCCTATAGAGGTATTTCGGTT
1 ATTTTACCCATCAG-GGGTATTTCAGTAATTTTACCC-ATAGGGGTATTTCGGTA
41394665 ATTTT
1 ATTTT
41394670 TTCTAGTTTG
Statistics
Matches: 137, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
52 1 0.01
53 2 0.01
54 129 0.94
55 3 0.02
56 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.43
Consensus pattern (53 bp):
ATTTTACCCATCAGGGGTATTTCAGTAATTTTACCCATAGGGGTATTTCGGTA
Found at i:41394646 original size:81 final size:81
Alignment explanation
Indices: 41394449--41394683 Score: 255
Period size: 81 Copynumber: 2.9 Consensus size: 81
41394439 TATAATGATC
* * *
41394449 ATTTTACCCTATAG-GGGTATTTC-GATAACTT-TACCCATCAAGGGTATTTCAGTCATTTTACC
1 ATTTTACCC-ATCGAGGGTATTTCAG-TAA-TTCTACCCATCAGGGGTATTTCAGTAATTTTACC
41394511 T-TTTGGGGGTATTTTAGTA
63 TATTT-GGGGTATTTTAGTA
* * * *
41394530 ATTTTACCCATGGATGGTATTTCGGTAATTTTACCCATCAGGGGTATTTCAGTAATTTTACCTAT
1 ATTTTACCCATCGAGGGTATTTCAGTAATTCTACCCATCAGGGGTATTTCAGTAATTTTACCTAT
*
41394595 TTGGGGTATTTTGGTA
66 TTGGGGTATTTTAGTA
* * * * **
41394611 ATTTTACCCATCGAGGGTATTTCAGTCATTCTACCCTAT-AGAGGTATTTCGGTTATTTTTTCTA
1 ATTTTACCCATCGAGGGTATTTCAGTAATTCTACCC-ATCAGGGGTATTTCAGTAATTTTACCTA
41394675 GTTTGGGGT
65 -TTTGGGGT
41394684 CTTGGTGTAG
Statistics
Matches: 133, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
80 5 0.04
81 114 0.86
82 14 0.11
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (81 bp):
ATTTTACCCATCGAGGGTATTTCAGTAATTCTACCCATCAGGGGTATTTCAGTAATTTTACCTAT
TTGGGGTATTTTAGTA
Found at i:41396150 original size:18 final size:18
Alignment explanation
Indices: 41396127--41396162 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41396117 ACAGAGTTTG
41396127 AAACCACCTCAAACTCCT
1 AAACCACCTCAAACTCCT
41396145 AAACCACCTCAAACTCCT
1 AAACCACCTCAAACTCCT
41396163 GCCACCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.44, G:0.00, T:0.17
Consensus pattern (18 bp):
AAACCACCTCAAACTCCT
Found at i:41405851 original size:12 final size:12
Alignment explanation
Indices: 41405834--41405874 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
41405824 AAAATAAAAC
*
41405834 ATGTTAAATTTT
1 ATGTTAAATTAT
41405846 ATGTTAAATTAT
1 ATGTTAAATTAT
41405858 AT-TTAAA--AT
1 ATGTTAAATTAT
41405867 ATGTTAAA
1 ATGTTAAA
41405875 ACATTAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 5 0.19
12 13 0.48
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (12 bp):
ATGTTAAATTAT
Found at i:41411203 original size:36 final size:35
Alignment explanation
Indices: 41411134--41411227 Score: 91
Period size: 36 Copynumber: 2.6 Consensus size: 35
41411124 GTCAGTTCAA
* ** * *
41411134 CCAAAACACACCGGATGCTCACCCGAGCCAATCCCT
1 CCAAAACACA-CAGATGCTCATACGAACAAATCCCT
*
41411170 CCAAAACACACTAGATGCTCATACGAACAAATCCTT
1 CCAAAACACAC-AGATGCTCATACGAACAAATCCCT
*
41411206 CCGAAACACA-ACGATGCTCATA
1 CCAAAACACACA-GATGCTCATA
41411228 AGAGCTAGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
34 1 0.02
35 11 0.22
36 37 0.76
ACGTcount: A:0.37, C:0.36, G:0.12, T:0.15
Consensus pattern (35 bp):
CCAAAACACACAGATGCTCATACGAACAAATCCCT
Found at i:41420892 original size:18 final size:18
Alignment explanation
Indices: 41420862--41420910 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
41420852 AAAAAAAAGG
*
41420862 TTTTGAAATTGAATAATGA
1 TTTTGAAAATGAATAAT-A
*
41420881 -TTTGTAAATGAATAATA
1 TTTTGAAAATGAATAATA
41420898 TTTTGAAAATGAA
1 TTTTGAAAATGAA
41420911 AGACACGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (18 bp):
TTTTGAAAATGAATAATA
Found at i:41421492 original size:13 final size:13
Alignment explanation
Indices: 41421474--41421516 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
41421464 AATTTTAAAT
41421474 TATTTAGTGATAA
1 TATTTAGTGATAA
*
41421487 TATTTA--GA-AT
1 TATTTAGTGATAA
41421497 TATTTAGTGATAA
1 TATTTAGTGATAA
41421510 TATTTAG
1 TATTTAG
41421517 GAAAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:41421515 original size:23 final size:23
Alignment explanation
Indices: 41421467--41421516 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
41421457 ATTTTTAAAT
41421467 TTTA-AATTATTTAGTGATAATA
1 TTTAGAATTATTTAGTGATAATA
41421489 TTTAGAATTATTTAGTGATAATA
1 TTTAGAATTATTTAGTGATAATA
41421512 TTTAG
1 TTTAG
41421517 GAAAAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (23 bp):
TTTAGAATTATTTAGTGATAATA
Found at i:41422410 original size:23 final size:23
Alignment explanation
Indices: 41422356--41422414 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
41422346 TTATTTATCC
*
41422356 ATTTATTTTATTTTCTTAAATTT
1 ATTTATTTTATTTTCTGAAATTT
*
41422379 ATTTTTTTTATTTT-TGAATATATT
1 ATTTATTTTATTTTCTGAA-AT-TT
41422403 -TTTATTTTATTT
1 ATTTATTTTATTT
41422415 ATTTTTCGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 3 0.10
23 26 0.84
24 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (23 bp):
ATTTATTTTATTTTCTGAAATTT
Found at i:41428154 original size:27 final size:27
Alignment explanation
Indices: 41427990--41428145 Score: 204
Period size: 27 Copynumber: 5.8 Consensus size: 27
41427980 CTGCACCGAG
*
41427990 ACCCCCATAGGGTAAAATGACCAAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
* *
41428017 ACCTCTATAGGGTAAAATGACCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
41428044 ACCCCCATAGGGTAAAATGACCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
* * * * *
41428071 AGCCTCATAAGGCAAAATGATCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
* * * *
41428098 ATCCTCATAGGATAAAATGACTGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
41428125 ACCCCCATAGGGTAAAATGAC
1 ACCCCCATAGGGTAAAATGAC
41428146 TGTTATACCT
Statistics
Matches: 110, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 110 1.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
ACCCCCATAGGGTAAAATGACCGAAAT
Found at i:41432557 original size:23 final size:23
Alignment explanation
Indices: 41432531--41432581 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
41432521 TGATTTTTAA
* *
41432531 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTAATAAT
41432554 ATTTAGAATTATTTAGTAATAAT
1 ATTTAGAATTATTTAGTAATAAT
41432577 ATTTA
1 ATTTA
41432582 CTGATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTAATAAT
Found at i:41432558 original size:13 final size:13
Alignment explanation
Indices: 41432540--41432618 Score: 71
Period size: 13 Copynumber: 6.5 Consensus size: 13
41432530 AATTTTGAAT
41432540 TATTTAGTGATAA
1 TATTTAGTGATAA
*
41432553 TATTTA--GA-AT
1 TATTTAGTGATAA
*
41432563 TATTTAGTAATAA
1 TATTTAGTGATAA
*
41432576 TATTTACTGATAA
1 TATTTAGTGATAA
*
41432589 TATTTA--GA-AT
1 TATTTAGTGATAA
*
41432599 TATTTAGTGATAG
1 TATTTAGTGATAA
41432612 TATTTAG
1 TATTTAG
41432619 GAAAAATCTA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
10 14 0.26
11 4 0.08
12 3 0.06
13 32 0.60
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:41432587 original size:36 final size:36
Alignment explanation
Indices: 41432540--41432617 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
41432530 AATTTTGAAT
*
41432540 TATTTAGTGATAATATTTAGAATTATTTAGTAATAA
1 TATTTACTGATAATATTTAGAATTATTTAGTAATAA
* *
41432576 TATTTACTGATAATATTTAGAATTATTTAGTGATAG
1 TATTTACTGATAATATTTAGAATTATTTAGTAATAA
41432612 TATTTA
1 TATTTA
41432618 GGAAAAATCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.38, C:0.01, G:0.12, T:0.49
Consensus pattern (36 bp):
TATTTACTGATAATATTTAGAATTATTTAGTAATAA
Found at i:41432679 original size:34 final size:34
Alignment explanation
Indices: 41432640--41432707 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
41432630 CTAAATTTTA
41432640 GCAATAAAAATGTGTATAAATATCTAGTGGCTAC
1 GCAATAAAAATGTGTATAAATATCTAGTGGCTAC
41432674 GCAATAAAAATGTGTATAAATATCTAGTGGCTAC
1 GCAATAAAAATGTGTATAAATATCTAGTGGCTAC
41432708 ACCTAGTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (34 bp):
GCAATAAAAATGTGTATAAATATCTAGTGGCTAC
Found at i:41433559 original size:26 final size:26
Alignment explanation
Indices: 41433530--41433579 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
41433520 GTTTTTGTAT
41433530 TTTTGAATATATTT-TTATTTTATTTA
1 TTTTGAATAT-TTTCTTATTTTATTTA
**
41433556 TTTTTCATATTTTCTTATTTTATT
1 TTTTGAATATTTTCTTATTTTATT
41433580 AACTTAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTGAATATTTTCTTATTTTATTTA
Found at i:41438991 original size:43 final size:43
Alignment explanation
Indices: 41438930--41439015 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
41438920 TTGTAATCAC
41438930 TACGAGTAATGTAGTGACTATTACATAATAATCCAAGAAACAT
1 TACGAGTAATGTAGTGACTATTACATAATAATCCAAGAAACAT
* *
41438973 TACGAGTAATGTTGTGACTTTTACATAATAATCCAAGAAACAT
1 TACGAGTAATGTAGTGACTATTACATAATAATCCAAGAAACAT
41439016 ACTCATAGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (43 bp):
TACGAGTAATGTAGTGACTATTACATAATAATCCAAGAAACAT
Found at i:41442096 original size:7 final size:7
Alignment explanation
Indices: 41442086--41442129 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
41442076 TATGTATGCC
41442086 ATATGAT
1 ATATGAT
41442093 ATATGAT
1 ATATGAT
41442100 ATATGTAT
1 ATATG-AT
*
41442108 GTATGAT
1 ATATGAT
41442115 ATATGAT
1 ATATGAT
41442122 -TATGAT
1 ATATGAT
41442128 AT
1 AT
41442130 GCATGTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 6 0.18
7 21 0.64
8 6 0.18
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (7 bp):
ATATGAT
Found at i:41442106 original size:29 final size:28
Alignment explanation
Indices: 41442074--41442129 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
41442064 AAAGTACATG
*
41442074 TGTATGTATGCCATATGATATATGATATA
1 TGTATGTATGACATATGAT-TATGATATA
*
41442103 TGTATGTATGATATATGATTATGATAT
1 TGTATGTATGACATATGATTATGATAT
41442130 GCATGTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.45
Consensus pattern (28 bp):
TGTATGTATGACATATGATTATGATATA
Found at i:41442115 original size:22 final size:22
Alignment explanation
Indices: 41442087--41442130 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41442077 ATGTATGCCA
41442087 TATGATATATGATATATG-TATG
1 TATGATATATGAT-TATGATATG
41442109 TATGATATATGATTATGATATG
1 TATGATATATGATTATGATATG
41442131 CATGTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (22 bp):
TATGATATATGATTATGATATG
Found at i:41442364 original size:5 final size:5
Alignment explanation
Indices: 41442354--41442424 Score: 88
Period size: 5 Copynumber: 14.2 Consensus size: 5
41442344 GGGGTAGGAC
* * *
41442354 ATGAT ATGAT ATGTT ATGTT ATGAT ATGAT ATGAT ATGAT ATGAT ATGTT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT
* * *
41442404 ATGAT ACGTT ATGAA ATGAT A
1 ATGAT ATGAT ATGAT ATGAT A
41442425 AAATATACTT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (5 bp):
ATGAT
Found at i:41446963 original size:23 final size:23
Alignment explanation
Indices: 41446930--41446973 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
41446920 GTAATTATAA
41446930 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
41446953 ATACATTTGTAATTAATATAT
1 ATACATGTGTAATAAATATAT
41446974 ATACATACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:41448388 original size:23 final size:23
Alignment explanation
Indices: 41448361--41448411 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
41448351 CTGCCGATCT
41448361 GGCACTTTATGTGTCATATATCA
1 GGCACTTTATGTGTCATATATCA
* *
41448384 GGCACTTTATGTGTCGTATTTCA
1 GGCACTTTATGTGTCATATATCA
41448407 GGCAC
1 GGCAC
41448412 CTCGTGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (23 bp):
GGCACTTTATGTGTCATATATCA
Found at i:41450378 original size:32 final size:32
Alignment explanation
Indices: 41450336--41450396 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
41450326 TTTTTTGAAA
41450336 AATAATTATAACTATTTAAAT-AAT-ATTATTTG
1 AATAATTATAA-TA-TTAAATGAATAATTATTTG
*
41450368 AATAGTTATAATATTAAATGAATAATTAT
1 AATAATTATAATATTAAATGAATAATTAT
41450397 GTGTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 5 0.19
32 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (32 bp):
AATAATTATAATATTAAATGAATAATTATTTG
Found at i:41450389 original size:20 final size:20
Alignment explanation
Indices: 41450355--41450396 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41450345 AACTATTTAA
** *
41450355 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
41450375 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
41450395 AT
1 AT
41450397 GTGTTTATTT
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:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:41455471 original size:32 final size:32
Alignment explanation
Indices: 41455429--41455489 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
41455419 TTTTTTGAAA
41455429 AATAATTATAACTATTTAAAT-AAT-ATTATTTG
1 AATAATTATAA-TA-TTAAATGAATAATTATTTG
*
41455461 AATAGTTATAATATTAAATGAATAATTAT
1 AATAATTATAATATTAAATGAATAATTAT
41455490 GTGTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 5 0.19
32 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (32 bp):
AATAATTATAATATTAAATGAATAATTATTTG
Found at i:41455482 original size:20 final size:20
Alignment explanation
Indices: 41455448--41455489 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41455438 AACTATTTAA
** *
41455448 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
41455468 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
41455488 AT
1 AT
41455490 GTGTTTATTT
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:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:41458349 original size:34 final size:35
Alignment explanation
Indices: 41458269--41458349 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 35
41458259 CTCAAGGTTT
*
41458269 AGGGTTTGGGTTCGAGATTTAAGATTTAAGGTTCA
1 AGGGTTTGGGTTCGAGATTCAAGATTTAAGGTTCA
* *
41458304 A-AGTTTAGGGTTC-ATGATTCAA-ATTTAGGGTTCA
1 AGGGTTT-GGGTTCGA-GATTCAAGATTTAAGGTTCA
41458338 AGGGTTTGGGTT
1 AGGGTTTGGGTT
41458350 TGGGGTTCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
34 22 0.56
35 17 0.44
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (35 bp):
AGGGTTTGGGTTCGAGATTCAAGATTTAAGGTTCA
Found at i:41458672 original size:17 final size:16
Alignment explanation
Indices: 41458644--41458675 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41458634 TATTTATAAA
41458644 TTAAATTATAATTATT
1 TTAAATTATAATTATT
41458660 TTAAATATATAATTAT
1 TTAAAT-TATAATTAT
41458676 CTCAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATTATAATTATT
Found at i:41458673 original size:23 final size:23
Alignment explanation
Indices: 41458634--41458701 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 23
41458624 TTTTAGCTAA
41458634 TATTTATAAATTA-AATTAT-AAT
1 TATTT-TAAATTATAATTATCAAT
41458656 TATTTTAAATATATAATTATCTCAAT
1 TATTTTAAAT-TATAATTA--TCAAT
*
41458682 TTTTATTAAATTATAATTAT
1 TATT-TTAAATTATAATTAT
41458702 TTTTAAAGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
21 5 0.13
22 7 0.18
23 5 0.13
24 1 0.03
25 1 0.03
26 14 0.36
27 6 0.15
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTTTAAATTATAATTATCAAT
Found at i:41458703 original size:20 final size:20
Alignment explanation
Indices: 41458643--41458706 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
41458633 ATATTTATAA
*
41458643 ATTAAATTATAATTATTTTAA
1 ATTAAATTATAATTATTTT-T
* *
41458664 ATATATAATTAT-CTCAATTTTT
1 AT-TA-AATTATAAT-TATTTTT
41458686 ATTAAATTATAATTATTTTT
1 ATTAAATTATAATTATTTTT
41458706 A
1 A
41458707 AAGGTATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
20 13 0.38
21 5 0.15
22 5 0.15
23 11 0.32
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTAAATTATAATTATTTTT
Found at i:41460463 original size:18 final size:19
Alignment explanation
Indices: 41460440--41460476 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41460430 GCAGGTGCAT
*
41460440 CTGGTGGTGGT-GGAGGGG
1 CTGGTGGTCGTGGGAGGGG
41460458 CTGGTGGTCGTGGGAGGGG
1 CTGGTGGTCGTGGGAGGGG
41460477 TCGTGGTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.05, C:0.08, G:0.65, T:0.22
Consensus pattern (19 bp):
CTGGTGGTCGTGGGAGGGG
Found at i:41461717 original size:3 final size:3
Alignment explanation
Indices: 41461709--41461740 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41461699 AAACTATTCT
41461709 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
41461741 ATTTCACTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:41462678 original size:185 final size:185
Alignment explanation
Indices: 41462361--41462739 Score: 704
Period size: 185 Copynumber: 2.0 Consensus size: 185
41462351 ATTATCAGAG
* * *
41462361 CATTGGCTTCATTTCCTCTTCTATGTTCTTTTCTTTAATTGTATTCACATCCCATTTTTTTTACT
1 CATTTGCTTCATTTCCTCTTCTATGTTATTTTCTTTAATTGTATTCACATCCCATTTTTTTGACT
*
41462426 CATTTAATATGCTTTTACTAGATGGAGTGAAATGCTAGTTTGCTTTTGTCATTTTACTACAGTAT
66 CATTTAATATGCTTTTACTAGATGGAGTGAAATGCTAGTTTGCTTTTGTCATTTTACTAAAGTAT
41462491 TACTGAGCTTTCACTCCTACCCTTCGATTTTTACTGCTATGTGCAAAGCATCTTA
131 TACTGAGCTTTCACTCCTACCCTTCGATTTTTACTGCTATGTGCAAAGCATCTTA
41462546 CATTTGCTTCATTTCCTCTTCTATGTTATTTTCTTTAATTGTATTCACATCCCATTTTTTTGACT
1 CATTTGCTTCATTTCCTCTTCTATGTTATTTTCTTTAATTGTATTCACATCCCATTTTTTTGACT
*
41462611 CATTTAATATGCTTTTACTAGATGGAGTGAAATGCTAGTTTGTTTTTGTCATTTTACTAAAGTAT
66 CATTTAATATGCTTTTACTAGATGGAGTGAAATGCTAGTTTGCTTTTGTCATTTTACTAAAGTAT
41462676 TACTGAGCTTTCACTCCTACCCTTCGATTTTTACTGCTATGTGCAAAGCATCTTA
131 TACTGAGCTTTCACTCCTACCCTTCGATTTTTACTGCTATGTGCAAAGCATCTTA
*
41462731 CGTTTGCTT
1 CATTTGCTT
41462740 TAAACCTGTG
Statistics
Matches: 188, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 188 1.00
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.47
Consensus pattern (185 bp):
CATTTGCTTCATTTCCTCTTCTATGTTATTTTCTTTAATTGTATTCACATCCCATTTTTTTGACT
CATTTAATATGCTTTTACTAGATGGAGTGAAATGCTAGTTTGCTTTTGTCATTTTACTAAAGTAT
TACTGAGCTTTCACTCCTACCCTTCGATTTTTACTGCTATGTGCAAAGCATCTTA
Found at i:41467581 original size:2 final size:2
Alignment explanation
Indices: 41467574--41467600 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41467564 GGAATCAACA
41467574 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
41467601 AATTCAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41468341 original size:21 final size:20
Alignment explanation
Indices: 41468311--41468365 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
41468301 GGCTGTTTTT
41468311 ATAATCAAAATTATTAATTTA
1 ATAAT-AAAATTATTAATTTA
*
41468332 AGTAATAAAATGTTTTTAATTTA
1 A-TAATAAAA--TTATTAATTTA
41468355 AT-ATAAAATTA
1 ATAATAAAATTA
41468366 AATATAGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
19 2 0.07
21 11 0.38
22 5 0.17
23 11 0.38
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
ATAATAAAATTATTAATTTA
Found at i:41468773 original size:51 final size:51
Alignment explanation
Indices: 41468697--41468818 Score: 201
Period size: 51 Copynumber: 2.4 Consensus size: 51
41468687 TCTAATCCTC
41468697 TCAATTTCCT-TCCAACTTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
1 TCAATTTCCTCT-CAA-TTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
*
41468749 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
*
41468800 TCAATTTCCCCTCAATTTC
1 TCAATTTCCTCTCAATTTC
41468819 ATTTTTTAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 53 0.79
52 13 0.19
53 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
Found at i:41468846 original size:10 final size:10
Alignment explanation
Indices: 41468819--41468884 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
41468809 CCTCAATTTC
*
41468819 ATTTTTTAAA
1 ATTTTTTTAA
**
41468829 ATAATTTTAA
1 ATTTTTTTAA
*
41468839 ATTTTTTTAT
1 ATTTTTTTAA
41468849 ATTTTTTTAAA
1 ATTTTTTT-AA
**
41468860 ATAATTTTAA
1 ATTTTTTTAA
*
41468870 ATTTTTTTAT
1 ATTTTTTTAA
41468880 ATTTT
1 ATTTT
41468885 CATCAATGGC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
10 36 0.84
11 7 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:41468858 original size:31 final size:31
Alignment explanation
Indices: 41468820--41468884 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
41468810 CTCAATTTCA
41468820 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTTTAAATTTTTTTATAT
41468851 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTTTAAATTTTTTTATAT
41468882 TTT
1 TTT
41468885 CATCAATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTTTTAAAATAATTTTAAATTTTTTTATAT
Found at i:41469977 original size:7 final size:7
Alignment explanation
Indices: 41469965--41469989 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41469955 AGTATATTGA
41469965 TATTTAG
1 TATTTAG
41469972 TATTTAG
1 TATTTAG
41469979 TATTTAG
1 TATTTAG
41469986 TATT
1 TATT
41469990 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:41470667 original size:18 final size:18
Alignment explanation
Indices: 41470641--41470675 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41470631 AGGTGTGTTT
* *
41470641 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
41470659 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
41470676 TCCTTTTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:41471108 original size:25 final size:24
Alignment explanation
Indices: 41471079--41471260 Score: 89
Period size: 25 Copynumber: 7.6 Consensus size: 24
41471069 TTTAAATTTA
41471079 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAA-T
**
41471104 TTATTTGATGTAATACGCATAGAAT
1 TTATTTGATGTAATA-AAATAGAAT
* ** *
41471129 TTTTTTCGA-GT--T-ATTTTG-AT
1 TTATTT-GATGTAATAAAATAGAAT
41471149 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAA-T
**
41471175 TTATTTGATGTAATACGCATAGAAAT
1 TTATTTGATGTAATA-AAATAG-AAT
** *
41471201 TT-TTTCGA-GT--T-ATTTTG-AT
1 TTATTT-GATGTAATAAAATAGAAT
41471220 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAA-T
*
41471246 TTATTTGATATAATA
1 TTATTTGATGTAATA
41471261 GGCGTAGAAA
Statistics
Matches: 116, Mismatches: 21, Indels: 40
0.66 0.12 0.23
Matches are distributed among these distances:
19 2 0.02
20 8 0.07
21 16 0.14
23 4 0.03
24 6 0.05
25 59 0.51
26 19 0.16
27 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (24 bp):
TTATTTGATGTAATAAAATAGAAT
Found at i:41471165 original size:71 final size:71
Alignment explanation
Indices: 41471077--41471332 Score: 458
Period size: 71 Copynumber: 3.6 Consensus size: 71
41471067 TATTTAAATT
*
41471077 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAATTTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
41471142 TTTTGA
66 TTTTGA
41471148 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
41471213 TTTTGA
66 TTTTGA
* * *
41471219 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCGTAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
41471284 TTTTGA
66 TTTTGA
*
41471290 TATTATTTGATATAATAAAATAGAAGTTCTATTTGATGTAATA
1 TATTATTTGATGTAATAAAATAGAAGTT-TATTTGATGTAATA
41471333 AAAACCCTAA
Statistics
Matches: 178, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 165 0.93
72 13 0.07
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (71 bp):
TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
TTTTGA
Found at i:41471380 original size:29 final size:29
Alignment explanation
Indices: 41471338--41471580 Score: 391
Period size: 29 Copynumber: 8.3 Consensus size: 29
41471328 TAATAAAAAC
41471338 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
41471367 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
41471396 CCTAATTTAATTAAAAATCCACT-GCCCTAA
1 CCTAATTTAATTAAAAA-CC-CTAACCCTAA
41471426 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
41471455 CCTAATTTAATTAAAAACCTTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
41471485 CCTAATTTAATTAAAAA-CCTACTGCCCTAA
1 CCTAATTTAATTAAAAACCCTA--ACCCTAA
41471515 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
41471544 CCTATTTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
41471573 CCTAATTT
1 CCTAATTT
41471581 TACATAATTT
Statistics
Matches: 199, Mismatches: 8, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
28 3 0.02
29 117 0.59
30 73 0.37
31 6 0.03
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.30
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:41471436 original size:59 final size:58
Alignment explanation
Indices: 41471338--41471580 Score: 391
Period size: 59 Copynumber: 4.1 Consensus size: 58
41471328 TAATAAAAAC
41471338 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
*
41471396 CCTAATTTAATTAAAAATCCACT-GCCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAA-CC-CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
* *
41471455 CCTAATTTAATTAAAAACCTTAAACCCTAACCTAATTTAATTAAAAA-CCTACTGCCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTA--ACCCTAA
*
41471515 CCTAATTTAATTAAAAACCCTAACCCTAACCTATTTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
41471573 CCTAATTT
1 CCTAATTT
41471581 TACATAATTT
Statistics
Matches: 171, Mismatches: 7, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
57 1 0.01
58 37 0.22
59 101 0.59
60 32 0.19
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.30
Consensus pattern (58 bp):
CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:41471527 original size:89 final size:88
Alignment explanation
Indices: 41471338--41471580 Score: 443
Period size: 89 Copynumber: 2.8 Consensus size: 88
41471328 TAATAAAAAC
41471338 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
41471403 TAATTAAAAATCCACTGCCCTAA
66 TAATTAAAAATCCACTGCCCTAA
*
41471426 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCTTAAACCCTAACCTAAT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAACCTAAT
41471491 TTAATTAAAAA-CCTACTGCCCTAA
65 TTAATTAAAAATCC-ACTGCCCTAA
*
41471515 CCTAATTTAATTAAAAACCCTAACCCTAACCTATTTTAATTAAAAACCCTAACCCTAACCTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
41471580 T
66 T
41471581 TACATAATTT
Statistics
Matches: 150, Mismatches: 3, Indels: 4
0.96 0.02 0.03
Matches are distributed among these distances:
88 67 0.45
89 83 0.55
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.30
Consensus pattern (88 bp):
CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
TAATTAAAAATCCACTGCCCTAA
Found at i:41471641 original size:55 final size:55
Alignment explanation
Indices: 41471575--41471755 Score: 353
Period size: 55 Copynumber: 3.3 Consensus size: 55
41471565 AACCCTAACC
41471575 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
*
41471630 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
41471685 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
41471740 TAATTTTACATAATTT
1 TAATTTTACATAATTT
41471756 TACATAATGT
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 124 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (55 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
Found at i:41471754 original size:10 final size:10
Alignment explanation
Indices: 41471739--41471763 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41471729 TTTGGACTTA
41471739 ATAATTTTAC
1 ATAATTTTAC
41471749 ATAATTTTAC
1 ATAATTTTAC
41471759 ATAAT
1 ATAAT
41471764 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:41473403 original size:16 final size:18
Alignment explanation
Indices: 41473364--41473397 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41473354 TAAGTTTTTA
41473364 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
41473381 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
41473398 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:41482313 original size:60 final size:61
Alignment explanation
Indices: 41482219--41482347 Score: 190
Period size: 60 Copynumber: 2.1 Consensus size: 61
41482209 TGTTGTCTTT
* *
41482219 TTTTTTACATAAAAAAATAAAAATAAAATTGAAAATAGTTGCTAGT-ATTTTTTATTTTTTA
1 TTTTTTACATAAAAAAATAAAAATAAAATAGAAAATAGTTGCTAGTGA-TTTTTACTTTTTA
* * *
41482280 TTTTTTACAT-CAAAAATTAAAATAAAGTAGAAAATAGTTGCTAGTGATTTTTACTTTTTA
1 TTTTTTACATAAAAAAATAAAAATAAAATAGAAAATAGTTGCTAGTGATTTTTACTTTTTA
41482340 TTTTTTAC
1 TTTTTTAC
41482348 CAACAGATTC
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 51 0.82
61 11 0.18
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (61 bp):
TTTTTTACATAAAAAAATAAAAATAAAATAGAAAATAGTTGCTAGTGATTTTTACTTTTTA
Found at i:41483079 original size:60 final size:60
Alignment explanation
Indices: 41482986--41483106 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
41482976 CACTAGGGCA
41482986 AGTGGGAGATTGTTAGGAAATGTGATCATATTGTAGTAAACATGTAATTGTTTTCTATGT
1 AGTGGGAGATTGTTAGGAAATGTGATCATATTGTAGTAAACATGTAATTGTTTTCTATGT
41483046 AGTGGGAGATTGTTAGGAAATGTGATCATATTGTAGTAAACATGTAATTGTTTTCTATGT
1 AGTGGGAGATTGTTAGGAAATGTGATCATATTGTAGTAAACATGTAATTGTTTTCTATGT
41483106 A
1 A
41483107 TTTGAATTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.40
Consensus pattern (60 bp):
AGTGGGAGATTGTTAGGAAATGTGATCATATTGTAGTAAACATGTAATTGTTTTCTATGT
Found at i:41483505 original size:11 final size:12
Alignment explanation
Indices: 41483489--41483521 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
41483479 GACCCCAATA
41483489 TGAATTAATTT-
1 TGAATTAATTTG
*
41483500 TGAATTCATTTG
1 TGAATTAATTTG
41483512 TGAATTAATT
1 TGAATTAATT
41483522 CACTTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (12 bp):
TGAATTAATTTG
Found at i:41484728 original size:26 final size:25
Alignment explanation
Indices: 41484699--41484797 Score: 123
Period size: 26 Copynumber: 4.0 Consensus size: 25
41484689 AAAAATAATA
41484699 TTATTTTAATAGATTTAATATTAAAT
1 TTATTTTAATA-ATTTAATATTAAAT
41484725 TTATTTTAATAGATTTAATATTAAAT
1 TTATTTTAATA-ATTTAATATTAAAT
*
41484751 TTATTTTAAT-ATTT-ATCTT-AAT
1 TTATTTTAATAATTTAATATTAAAT
* *
41484773 AATATTTTATTAATTTAATATTAAA
1 -TTATTTTAATAATTTAATATTAAA
41484798 GTGATTATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
22 3 0.05
23 12 0.18
24 8 0.12
25 4 0.06
26 38 0.58
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTTTAATAATTTAATATTAAAT
Found at i:41487335 original size:16 final size:18
Alignment explanation
Indices: 41487293--41487340 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
41487283 TTACGGTAAC
*
41487293 AAAATTAGAATTAGATTGAG
1 AAAATTA-ATTTA-ATTGAG
41487313 AAAATT-ATTTAATTGAG
1 AAAATTAATTTAATTGAG
41487330 -AAATTAATTTA
1 AAAATTAATTTA
41487341 GTTAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.19
17 11 0.42
18 4 0.15
20 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (18 bp):
AAAATTAATTTAATTGAG
Found at i:41493663 original size:48 final size:48
Alignment explanation
Indices: 41493592--41493687 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
41493582 GGACAAAGTT
41493592 TCTTTCCAAGCTTTTCTTCTTACATTCAAGATCCTAATGCATTTTGTG
1 TCTTTCCAAGCTTTTCTTCTTACATTCAAGATCCTAATGCATTTTGTG
41493640 TCTTTCCAAGCTTTTCTTCTTACATTCAAGATCCTAATGCATTTTGTG
1 TCTTTCCAAGCTTTTCTTCTTACATTCAAGATCCTAATGCATTTTGTG
41493688 GTTATCTTCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (48 bp):
TCTTTCCAAGCTTTTCTTCTTACATTCAAGATCCTAATGCATTTTGTG
Found at i:41501345 original size:2 final size:2
Alignment explanation
Indices: 41501338--41501363 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41501328 GTGAAAGGTG
41501338 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
41501364 AATGAAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41501871 original size:15 final size:15
Alignment explanation
Indices: 41501851--41501879 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41501841 TAAGAGGAGG
41501851 AAATCGATTTTCATC
1 AAATCGATTTTCATC
41501866 AAATCGATTTTCAT
1 AAATCGATTTTCAT
41501880 ATCTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (15 bp):
AAATCGATTTTCATC
Found at i:41506275 original size:22 final size:21
Alignment explanation
Indices: 41506247--41506294 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
41506237 ACATTTTTCA
**
41506247 TATATATACATTGGTTTATTTT
1 TATATATACATTACTTTA-TTT
*
41506269 TATATATGCATTACTTTATTT
1 TATATATACATTACTTTATTT
41506290 TATAT
1 TATAT
41506295 GTATTATTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (21 bp):
TATATATACATTACTTTATTT
Found at i:41506595 original size:28 final size:27
Alignment explanation
Indices: 41506554--41506648 Score: 86
Period size: 29 Copynumber: 3.4 Consensus size: 27
41506544 TTATATAGAT
*
41506554 ATTTT-ATTTCTTTCAAATATTTTAAC
1 ATTTTAATTTATTTCAAATATTTTAAC
* *
41506580 ATCTTTAATTTATTTCAACTTATTTCAAC
1 AT-TTTAATTTATTTCAA-ATATTTTAAC
*
41506609 ATTGTTAATTCA-TTCAAATTTATTTTAAC
1 ATT-TTAATTTATTTCAAA--TATTTTAAC
*
41506638 TTTTTAATTTA
1 ATTTTAATTTA
41506649 CATATATTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
26 2 0.04
27 3 0.05
28 23 0.42
29 27 0.49
ACGTcount: A:0.32, C:0.12, G:0.01, T:0.56
Consensus pattern (27 bp):
ATTTTAATTTATTTCAAATATTTTAAC
Found at i:41511829 original size:24 final size:24
Alignment explanation
Indices: 41511797--41511845 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41511787 AGGTCTGTGA
41511797 TCAATTCAAAATCAGATACCATAG
1 TCAATTCAAAATCAGATACCATAG
41511821 TCAATTCAAAATCAGATACCATAG
1 TCAATTCAAAATCAGATACCATAG
41511845 T
1 T
41511846 TCATCACTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (24 bp):
TCAATTCAAAATCAGATACCATAG
Found at i:41512409 original size:7 final size:7
Alignment explanation
Indices: 41512392--41512455 Score: 87
Period size: 7 Copynumber: 9.0 Consensus size: 7
41512382 TGAGTTAGAA
41512392 AAAATATG
1 AAAA-ATG
41512400 AAAAATG
1 AAAAATG
41512407 AAAAATG
1 AAAAATG
41512414 AAAAAATG
1 -AAAAATG
41512422 -AAAATG
1 AAAAATG
41512428 AAAAATG
1 AAAAATG
41512435 AAAAATG
1 AAAAATG
41512442 AAAAA-G
1 AAAAATG
41512448 TAAAAATG
1 -AAAAATG
41512456 GAGAGGCTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
6 7 0.13
7 33 0.63
8 12 0.23
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (7 bp):
AAAAATG
Found at i:41512429 original size:28 final size:28
Alignment explanation
Indices: 41512392--41512455 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 28
41512382 TGAGTTAGAA
41512392 AAAATATGAAAAATGAAAAATGAAAAAAT
1 AAAA-ATGAAAAATGAAAAATGAAAAAAT
* *
41512421 GAAAATGAAAAATGAAAAATGAAAAAGT
1 AAAAATGAAAAATGAAAAATGAAAAAAT
41512449 AAAAATG
1 AAAAATG
41512456 GAGAGGCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (28 bp):
AAAAATGAAAAATGAAAAATGAAAAAAT
Found at i:41513761 original size:50 final size:49
Alignment explanation
Indices: 41513693--41514287 Score: 375
Period size: 50 Copynumber: 11.9 Consensus size: 49
41513683 ATCGGTGAAG
* ** * *
41513693 ACAGCAAATCTTATTTCCCTGGCGATGTAGTGGAACAGATTAAAGCCACA
1 ACAGCGAATCTTGCTTCCCTGAC-ATGCAGTGGAACAGATTAAAGCCACA
* * * * ** *
41513743 TCGGTGAATCTTGCTTCCCTGACATTCCAGTTAAAAAGATTAAAGCCACA
1 ACAGCGAATCTTGCTTCCCTGACA-TGCAGTGGAACAGATTAAAGCCACA
* ** * *
41513793 ACAGCAAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACA
1 ACAGCGAATCTTGCTTCCCTGAC-ATGCAGTGGAACAGATTAAAGCCACA
* * * * ** * * *
41513843 TCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATGAAAGCTACA
1 ACAGCGAATCTTGCTTCCCTGACA-TGCAGTGGAACAGATTAAAGCCACA
* ** * *
41513893 ACAGCGGATCTTATTTCCCTGGCAGTGCAGTGGAACAAATTAAAGCCACA
1 ACAGCGAATCTTGCTTCCCTGACA-TGCAGTGGAACAGATTAAAGCCACA
* * * * * * **
41513943 TCGGTGAATCTTGCTTCCCCGACATTGCAGT-TAAAATGATTAAAGGTACA
1 ACAGCGAATCTTGCTTCCCTGACA-TGCAGTGGAACA-GATTAAAGCCACA
* * *
41513993 ACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACA
1 ACAGCGAATCTTGCTTCCCTGAC-ATGCAGTGGAACAGATTAAAGCCACA
* * * * * ** * *
41514043 TCGGTGAATCTTGCATCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
1 ACAGCGAATCTTGCTTCCCTGACA-TGCAGTGGAACAGATTAAAGCCACA
** * * *
41514093 ACAGCGAATCTTATTTCCCTGACGGTGTAGTGGAACAGATTAACGCCACA
1 ACAGCGAATCTTGCTTCCCTGAC-ATGCAGTGGAACAGATTAAAGCCACA
* * * ** * *
41514143 ACAGTGAATCTCGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
1 ACAGCGAATCTTGCTTCCCTGACA-TGCAGTGGAACAGATTAAAGCCACA
* * * * * * * * *
41514193 ACAACAAATCTTACTTCCCAGGCGTTGTAGTGGAACAGATTGAAGCTACA
1 ACAGCGAATCTTGCTTCCCTGAC-ATGCAGTGGAACAGATTAAAGCCACA
* **
41514243 ACAGCGAATCTTGCTT-CCTCGACATCACAGTTAAACAGATTAAAG
1 ACAGCGAATCTTGCTTCCCT-GACAT-GCAGTGGAACAGATTAAAG
41514288 TTACGAGTTA
Statistics
Matches: 393, Mismatches: 140, Indels: 24
0.71 0.25 0.04
Matches are distributed among these distances:
49 7 0.02
50 383 0.97
51 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (49 bp):
ACAGCGAATCTTGCTTCCCTGACATGCAGTGGAACAGATTAAAGCCACA
Found at i:41513867 original size:100 final size:100
Alignment explanation
Indices: 41513693--41514287 Score: 866
Period size: 100 Copynumber: 6.0 Consensus size: 100
41513683 ATCGGTGAAG
* *
41513693 ACAGCAAATCTTATTTCCCTGGCGATGTAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
1 ACAGCAAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
* * *
41513758 TCCCTGACATTCCAGTTAAAAAGATTAAAGCCACA
66 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
41513793 ACAGCAAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
1 ACAGCAAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
*
41513858 TCCCCGACATTGCAGTTAAAAAGATGAAAGCTACA
66 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
** * *
41513893 ACAGCGGATCTTATTTCCCTGGCAGTGCAGTGGAACAAATTAAAGCCACATCGGTGAATCTTGCT
1 ACAGCAAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
* *
41513958 TCCCCGACATTGCAGTTAAAATGATTAAAGGTACA
66 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * *
41513993 ACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCA
1 ACAGCAAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
41514058 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
66 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * * * * * *
41514093 ACAGCGAATCTTATTTCCCTGACGGTGTAGTGGAACAGATTAACGCCACAACAGTGAATCTCGCT
1 ACAGCAAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
41514158 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
66 TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * * * * * * * * *
41514193 ACAACAAATCTTACTTCCCAGGCGTTGTAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCT
1 ACAGCAAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
* ** *
41514258 TCCTCGACATCACAGTTAAACAGATTAAAG
66 TCCCCGACATTGCAGTTAAAAAGATTAAAG
41514288 TTACGAGTTA
Statistics
Matches: 452, Mismatches: 43, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 452 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (100 bp):
ACAGCAAATCTTATTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCT
TCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
Found at i:41521435 original size:15 final size:15
Alignment explanation
Indices: 41521411--41521440 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41521401 ATAGTTATGG
*
41521411 TAACATTAATAATAA
1 TAACAATAATAATAA
41521426 TAACAATAATAATAA
1 TAACAATAATAATAA
41521441 AAATAGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
TAACAATAATAATAA
Found at i:41522587 original size:28 final size:27
Alignment explanation
Indices: 41522547--41522599 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
41522537 GACTAATGGA
*
41522547 ATTTTAATAATTTTTGTTTTTATTTTT
1 ATTTTAATAATTTTTGTGTTTATTTTT
*
41522574 ATTTTTATATATTTTTGTGTTTATTT
1 ATTTTAATA-ATTTTTGTGTTTATTT
41522600 ATTTCTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (27 bp):
ATTTTAATAATTTTTGTGTTTATTTTT
Found at i:41522667 original size:28 final size:28
Alignment explanation
Indices: 41522636--41522714 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 28
41522626 GGGTTATTAC
41522636 AATTTCTTTCAAATATTTTAACATCT-TT
1 AATTTCTTTCAAATATTTTAACAT-TGTT
* * *
41522664 AATTTATTTCAACTTATTTCAACATTGTT
1 AATTTCTTTCAA-ATATTTTAACATTGTT
*
41522693 AA-TTCATTCAAATTTATTTTAA
1 AATTTCTTTCAAA--TATTTTAA
41522715 TTTTTTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
28 19 0.47
29 21 0.52
ACGTcount: A:0.34, C:0.13, G:0.01, T:0.52
Consensus pattern (28 bp):
AATTTCTTTCAAATATTTTAACATTGTT
Found at i:41522694 original size:29 final size:28
Alignment explanation
Indices: 41522636--41522705 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
41522626 GGGTTATTAC
* *
41522636 AATTTCTTTCAAATATTTTAACATCTTT
1 AATTTATTTCAAATATTTCAACATCTTT
*
41522664 AATTTATTTCAACTTATTTCAACAT-TGTT
1 AATTTATTTCAA-ATATTTCAACATCT-TT
*
41522693 AATTCA-TTCAAAT
1 AATTTATTTCAAAT
41522706 TTATTTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 17 0.49
29 17 0.49
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.50
Consensus pattern (28 bp):
AATTTATTTCAAATATTTCAACATCTTT
Found at i:41532998 original size:27 final size:27
Alignment explanation
Indices: 41532968--41533022 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
41532958 TGTTTTAGTA
41532968 AGTTTAATTAAATTCAATAAAATGTGC
1 AGTTTAATTAAATTCAATAAAATGTGC
41532995 AGTTTAATTAAATTCAATAAAATGTGC
1 AGTTTAATTAAATTCAATAAAATGTGC
41533022 A
1 A
41533023 AATTGAGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (27 bp):
AGTTTAATTAAATTCAATAAAATGTGC
Found at i:41543201 original size:103 final size:103
Alignment explanation
Indices: 41543022--41543228 Score: 396
Period size: 103 Copynumber: 2.0 Consensus size: 103
41543012 AACGGCTCAG
*
41543022 CAACGAGTAATCTGATCTACTATCGAACCAAGCCGCAATCTATCGTGTCTCCGGCCTCTACGTAA
1 CAACGAGTAATCTGATCTACTATCGAACCAAGCCGCAATCTATCGTGACTCCGGCCTCTACGTAA
41543087 TCCACCCAGTTGACAATGAACGGAAGGAATCCCCAAAA
66 TCCACCCAGTTGACAATGAACGGAAGGAATCCCCAAAA
*
41543125 CAACGAGTAATCTGATCTACTATCGAACCAAGCCGCAATCTATCGTGACTCTGGCCTCTACGTAA
1 CAACGAGTAATCTGATCTACTATCGAACCAAGCCGCAATCTATCGTGACTCCGGCCTCTACGTAA
41543190 TCCACCCAGTTGACAATGAACGGAAGGAATCCCCAAAA
66 TCCACCCAGTTGACAATGAACGGAAGGAATCCCCAAAA
41543228 C
1 C
41543229 TGTTTTAGAA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.20
Consensus pattern (103 bp):
CAACGAGTAATCTGATCTACTATCGAACCAAGCCGCAATCTATCGTGACTCCGGCCTCTACGTAA
TCCACCCAGTTGACAATGAACGGAAGGAATCCCCAAAA
Found at i:41544821 original size:15 final size:16
Alignment explanation
Indices: 41544795--41544824 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41544785 AAAGGCACAA
41544795 CATTATACCAAAACAT
1 CATTATACCAAAACAT
41544811 CATTA-ACCAAAACA
1 CATTATACCAAAACA
41544825 AGACAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (16 bp):
CATTATACCAAAACAT
Found at i:41560653 original size:14 final size:14
Alignment explanation
Indices: 41560636--41560663 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41560626 ACACACACAC
41560636 ACCAAATTGACCAT
1 ACCAAATTGACCAT
41560650 ACCAAATTGACCAT
1 ACCAAATTGACCAT
41560664 TAACACATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (14 bp):
ACCAAATTGACCAT
Found at i:41561206 original size:26 final size:26
Alignment explanation
Indices: 41561177--41561240 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
41561167 TTTTCAATAG
* *
41561177 TGCTCACACAAGCTTTGGAATGAGCC
1 TGCTCACACAAGCTGTGAAATGAGCC
* * *
41561203 TGCTCATAGAAGCTGTGAAATGAGTC
1 TGCTCACACAAGCTGTGAAATGAGCC
41561229 TGCTCACACAAG
1 TGCTCACACAAG
41561241 TTATGGGTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (26 bp):
TGCTCACACAAGCTGTGAAATGAGCC
Found at i:41562475 original size:45 final size:45
Alignment explanation
Indices: 41562426--41562587 Score: 166
Period size: 45 Copynumber: 3.6 Consensus size: 45
41562416 CTATACACCT
* * *
41562426 AAAATGAGTATGACCATAGCTGAAAGATGTTATGGCATCAAGATA
1 AAAATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCAAGACA
* * *
41562471 AAAATGAGTAAGACCATAGTTGAAAGATGCTATGGCATCATGACG
1 AAAATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCAAGACA
* ** * * **
41562516 AAAATGAGTAAGACCAT-GCTTGAAAAACACTATGGTATCATGGTA
1 AAAATGAGTAAGACCATAGC-TGAAAGATGCTATGGCATCAAGACA
*
41562561 AATAA-GATTAAGACCATAGCTGAAAGA
1 AA-AATGAGTAAGACCATAGCTGAAAGA
41562588 CGTTTTGACA
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
44 1 0.01
45 93 0.95
46 4 0.04
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (45 bp):
AAAATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCAAGACA
Found at i:41562689 original size:27 final size:27
Alignment explanation
Indices: 41562659--41562759 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
41562649 GCTCGACGAT
* *
41562659 ACATTAAACATGGGATAGTCTGACGGG
1 ACATTAAACACGGGATAGTCTGATGGG
* * * * *
41562686 ACATGAAACACGTGATAATTTGATAGG
1 ACATTAAACACGGGATAGTCTGATGGG
* * *
41562713 ATATAAAACACGGGATAGTCCGATGGG
1 ACATTAAACACGGGATAGTCTGATGGG
41562740 ACATTAAACACGGGATAGTC
1 ACATTAAACACGGGATAGTC
41562760 AGACTGGGCC
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.22
Consensus pattern (27 bp):
ACATTAAACACGGGATAGTCTGATGGG
Found at i:41594133 original size:25 final size:26
Alignment explanation
Indices: 41594085--41594135 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
41594075 TATGAATAAT
*
41594085 TACAGGGTATGAAAATGCAAATGTGA
1 TACAGGATATGAAAATGCAAATGTGA
*
41594111 TACAGGATATG-ATATGCAAATGTGA
1 TACAGGATATGAAAATGCAAATGTGA
41594136 ATGATACAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.25
Consensus pattern (26 bp):
TACAGGATATGAAAATGCAAATGTGA
Found at i:41596279 original size:20 final size:20
Alignment explanation
Indices: 41596243--41596280 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41596233 TGGAAGCTGT
*
41596243 TGAAATGAAATTTATTTTTG
1 TGAAATGAAATTAATTTTTG
41596263 TGAAAT-AAATTGAATTTT
1 TGAAATGAAATT-AATTTT
41596281 CTAAAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (20 bp):
TGAAATGAAATTAATTTTTG
Done.