Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 90 of 128
Found at i:29440486 original size:60 final size:61
Alignment explanation
Indices: 29440397--29440535 Score: 158
Period size: 61 Copynumber: 2.3 Consensus size: 61
29440387 ATTTATCTTT
* * * * *
29440397 AATAAAAAAAAAACAAAGGATAAATAAAT-AAAAAAGCTGAGAAA-GTAAATAAAGAAAAACA
1 AATAAAAAAAGAA-AAAGGACAAACAAATAAAAAAAGATGAAAAAGGTAAA-AAAGAAAAACA
* * *
29440458 AATAAAAAACGAAAAAGGACAAACAAATAAAAAAATATGAAAAAGGTAAAAATGAAAAACA
1 AATAAAAAAAGAAAAAGGACAAACAAATAAAAAAAGATGAAAAAGGTAAAAAAGAAAAACA
*
29440519 AA-AAAAAAGGAAAAAGG
1 AATAAAAAAAGAAAAAGG
29440536 TGTTGGAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
60 27 0.40
61 35 0.52
62 5 0.07
ACGTcount: A:0.73, C:0.05, G:0.13, T:0.09
Consensus pattern (61 bp):
AATAAAAAAAGAAAAAGGACAAACAAATAAAAAAAGATGAAAAAGGTAAAAAAGAAAAACA
Found at i:29440491 original size:36 final size:35
Alignment explanation
Indices: 29440451--29440526 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
29440441 GTAAATAAAG
* *
29440451 AAAAACAAATAAAAAACG-AAAAAGGACAAACAAA
1 AAAAAAAAATAAAAAACGTAAAAAGGAAAAACAAA
* * * *
29440485 TAAAAAAATATGAAAAAGGTAAAAATGAAAAACAAA
1 -AAAAAAAAATAAAAAACGTAAAAAGGAAAAACAAA
29440521 AAAAAA
1 AAAAAA
29440527 GGAAAAAGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 20 0.59
36 14 0.41
ACGTcount: A:0.76, C:0.07, G:0.09, T:0.08
Consensus pattern (35 bp):
AAAAAAAAATAAAAAACGTAAAAAGGAAAAACAAA
Found at i:29440737 original size:17 final size:17
Alignment explanation
Indices: 29440711--29440743 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29440701 TGATGTGGCA
*
29440711 TATTGGTGGCGCCAAAG
1 TATTGATGGCGCCAAAG
29440728 TATTGATGGCGCCAAA
1 TATTGATGGCGCCAAA
29440744 CATTTTGGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (17 bp):
TATTGATGGCGCCAAAG
Found at i:29443492 original size:14 final size:15
Alignment explanation
Indices: 29443467--29443496 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29443457 TTTTTGTACT
29443467 TTTTATATTTTAAAA
1 TTTTATATTTTAAAA
29443482 TTTTA-ATTTTAAAA
1 TTTTATATTTTAAAA
29443496 T
1 T
29443497 AAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTATATTTTAAAA
Found at i:29451437 original size:6 final size:6
Alignment explanation
Indices: 29451381--29451426 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
29451371 TTTGATAATG
*
29451381 AATACT AATACT AATACT AATACT AATACT AATACT AATAAT AATA
1 AATACT AATACT AATACT AATACT AATACT AATACT AATACT AATA
29451427 AATAATAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (6 bp):
AATACT
Found at i:29453232 original size:132 final size:132
Alignment explanation
Indices: 29453091--29453477 Score: 569
Period size: 132 Copynumber: 2.9 Consensus size: 132
29453081 CAGCCTACTT
* * * * * * * * * *
29453091 CACTGCTGCTCAGGGAGACATGGTTTGCAATCTTCAACCTACTTCACTGCTGCTCAGAGAGATAT
1 CACTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
* * * * *
29453156 GACTGGTGGCCTAAATTTGCTTCCCTACTACCTTGAGAAGATAAGATTCGTCGTCTTCGATCTGC
66 GACTGGTGGCTTAAATCTACTTCCCTACTTCCTTGAGAAGATAAGATTCGCCGTCTTCGATCTGC
29453221 TC
131 TC
29453223 CACTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
1 CACTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
* * * * *
29453288 GACTGGTGGCTTAAATCTACTTCCCTACTTCTTTGGGAAGATAAAAGTCGCCGTCTTCGATTTGC
66 GACTGGTGGCTTAAATCTACTTCCCTACTTCCTTGAGAAGATAAGATTCGCCGTCTTCGATCTGC
29453353 TC
131 TC
*
29453355 CACTACTGCTTAGGGAGACAAGATCTACAATTTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
1 CACTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
29453420 GACTGGTGGCTTAAATCTACTTCCCTACTTCCTT-AGGAAGATAAGATTCGCCGTCTTC
66 GACTGGTGGCTTAAATCTACTTCCCTACTTCCTTGA-GAAGATAAGATTCGCCGTCTTC
29453478 TTCAATCCAC
Statistics
Matches: 229, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
132 229 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
CACTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGATAG
GACTGGTGGCTTAAATCTACTTCCCTACTTCCTTGAGAAGATAAGATTCGCCGTCTTCGATCTGC
TC
Found at i:29453246 original size:44 final size:44
Alignment explanation
Indices: 29453198--29453378 Score: 100
Period size: 44 Copynumber: 4.1 Consensus size: 44
29453188 TTGAGAAGAT
* *
29453198 AAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGAC
1 AAGATTCGTCGTCTTCAATCTACTCCACTACTGCTTAGGGAGAC
* * ** * *
29453242 AAGA-TC-TACAATCTTCAACCTACTCCACTGTTGCTCAGGGAGAT
1 AAGATTCGT-C-GTCTTCAATCTACTCCACTACTGCTTAGGGAGAC
* * * * * * * *
29453286 AGGACTGGT-GGCTTAAATCTACTTCC-CTACTTCTTTGGGAAGAT
1 AAGATTCGTCGTCTTCAATCTAC-TCCACTACTGCTTAGGG-AGAC
* * * * * *
29453330 AAAAGTCGCCGTCTTCGATTTGCTCCACTACTGCTTAGGGAGAC
1 AAGATTCGTCGTCTTCAATCTACTCCACTACTGCTTAGGGAGAC
29453374 AAGAT
1 AAGAT
29453379 CTACAATTTT
Statistics
Matches: 95, Mismatches: 34, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
42 1 0.01
43 20 0.21
44 53 0.56
45 20 0.21
46 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (44 bp):
AAGATTCGTCGTCTTCAATCTACTCCACTACTGCTTAGGGAGAC
Found at i:29465599 original size:15 final size:14
Alignment explanation
Indices: 29465580--29465637 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 14
29465570 ATGTGATGAA
29465580 AATAATAAATAAAT
1 AATAATAAATAAAT
*
29465594 AAATAA-AAGAGAAAT
1 -AATAATAA-ATAAAT
29465609 AATAAT-AAT-AAT
1 AATAATAAATAAAT
29465621 AATAAT-AAT-AAT
1 AATAATAAATAAAT
29465633 AATAA
1 AATAA
29465638 ACAACTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 20 0.51
13 1 0.03
14 8 0.21
15 10 0.26
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AATAATAAATAAAT
Found at i:29465614 original size:3 final size:3
Alignment explanation
Indices: 29465606--29465637 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29465596 ATAAAAGAGA
29465606 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29465638 ACAACTAATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29467827 original size:9 final size:9
Alignment explanation
Indices: 29467809--29467847 Score: 69
Period size: 9 Copynumber: 4.3 Consensus size: 9
29467799 TGAATTTTGC
*
29467809 AATTCGAAT
1 AATTCAAAT
29467818 AATTCAAAT
1 AATTCAAAT
29467827 AATTCAAAT
1 AATTCAAAT
29467836 AATTCAAAT
1 AATTCAAAT
29467845 AAT
1 AAT
29467848 AGATTGGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (9 bp):
AATTCAAAT
Found at i:29482217 original size:43 final size:43
Alignment explanation
Indices: 29482150--29482244 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 43
29482140 AGGTTAATAC
*
29482150 GCTACTAGATGGTTGTGAATACACAACATAAATGTAGATGAGA
1 GCTACCAGATGGTTGTGAATACACAACATAAATGTAGATGAGA
* *
29482193 GCTATCAGATGGTTGTGAATACACAAGATAAATGTAGATGAGA
1 GCTACCAGATGGTTGTGAATACACAACATAAATGTAGATGAGA
29482236 GCTACCAGA
1 GCTACCAGA
29482245 AAGTATGTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (43 bp):
GCTACCAGATGGTTGTGAATACACAACATAAATGTAGATGAGA
Found at i:29484411 original size:21 final size:21
Alignment explanation
Indices: 29484374--29484426 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
29484364 GGAGAAGAGA
*
29484374 AATGG-GTTATGTAATATGTTT
1 AATGGAGTTTTGTAATAT-TTT
29484395 AATGGAGTTTTGT-ATATTTT
1 AATGGAGTTTTGTAATATTTT
*
29484415 -CTGGAGTTTTGT
1 AATGGAGTTTTGT
29484427 TATTAGAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 9 0.31
22 6 0.21
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.51
Consensus pattern (21 bp):
AATGGAGTTTTGTAATATTTT
Found at i:29488696 original size:13 final size:13
Alignment explanation
Indices: 29488662--29488697 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
29488652 TTTAGCATAA
29488662 CTTTTGAAAAATG
1 CTTTTGAAAAATG
* *
29488675 CTGTGGAAAAATG
1 CTTTTGAAAAATG
29488688 CTTTTGAAAA
1 CTTTTGAAAA
29488698 GTCCGGTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.33
Consensus pattern (13 bp):
CTTTTGAAAAATG
Found at i:29502216 original size:79 final size:79
Alignment explanation
Indices: 29502111--29502269 Score: 284
Period size: 79 Copynumber: 2.0 Consensus size: 79
29502101 ATTTTTTAGA
*
29502111 CTTTGTTCTATTATTAGAGATTGTATTTTTAGTTGTTTTATTTAAATATTTTATACAAAAATAGT
1 CTTTGTTCTAATATTA-AGATTGTATTTTTAGTTGTTTTATTTAAATATTTTATACAAAAATAGT
29502176 AAAAGATGATAATAT
65 AAAAGATGATAATAT
29502191 CTTTGTTCTAAATATT-AGATTGTATTTTTAGTTGTTTTATTTAAATATTTTATACAAAAATAGT
1 CTTTGTTCT-AATATTAAGATTGTATTTTTAGTTGTTTTATTTAAATATTTTATACAAAAATAGT
29502255 AAAAGATGATAATAT
65 AAAAGATGATAATAT
29502270 AATTATATTA
Statistics
Matches: 77, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
79 63 0.82
80 9 0.12
81 5 0.06
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (79 bp):
CTTTGTTCTAATATTAAGATTGTATTTTTAGTTGTTTTATTTAAATATTTTATACAAAAATAGTA
AAAGATGATAATAT
Found at i:29506902 original size:19 final size:19
Alignment explanation
Indices: 29506861--29506902 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
29506851 AGATTTGTTT
*
29506861 TTTATTTTTGAATTATAGT
1 TTTATTTTTGAATTATAGA
29506880 TTTATTTTATGAATT-TAGA
1 TTTATTTT-TGAATTATAGA
29506899 TTTA
1 TTTA
29506903 AAAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (19 bp):
TTTATTTTTGAATTATAGA
Found at i:29512892 original size:28 final size:27
Alignment explanation
Indices: 29512836--29512897 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
29512826 GTATGCTTTA
**
29512836 ATAAAAAAAATTAAGTACTTAATTGGG
1 ATAAAAAAAATTAAGTACTTAATCAGG
*
29512863 ATAAAAAAATTTTAAGTA-TTAAATCAGG
1 ATAAAAAAA-ATTAAGTACTT-AATCAGG
29512891 ATAAAAA
1 ATAAAAA
29512898 TTTCTCAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.29
Consensus pattern (27 bp):
ATAAAAAAAATTAAGTACTTAATCAGG
Found at i:29513320 original size:25 final size:27
Alignment explanation
Indices: 29513292--29513349 Score: 93
Period size: 25 Copynumber: 2.2 Consensus size: 27
29513282 TTAAAAATCT
*
29513292 TTTTCATAAATA-TTTCAAAA-AAAAG
1 TTTTCATAAATATTTTAAAAAGAAAAG
29513317 TTTTCATAAATATTTTAAAAAGAAAAG
1 TTTTCATAAATATTTTAAAAAGAAAAG
29513344 TTTTCA
1 TTTTCA
29513350 AGTAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 12 0.40
26 7 0.23
27 11 0.37
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (27 bp):
TTTTCATAAATATTTTAAAAAGAAAAG
Found at i:29517552 original size:14 final size:14
Alignment explanation
Indices: 29517533--29517559 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29517523 CAGTGCTTAT
29517533 AAAATTTAGTACTA
1 AAAATTTAGTACTA
29517547 AAAATTTAGTACT
1 AAAATTTAGTACT
29517560 TAATTTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
AAAATTTAGTACTA
Found at i:29518209 original size:113 final size:111
Alignment explanation
Indices: 29518010--29518234 Score: 387
Period size: 113 Copynumber: 2.0 Consensus size: 111
29518000 TTTTGTATGA
*
29518010 TGATGGCCACACATATATCTCAACCTAAAGTAAGAAGATTTAAGCAATTCCTATGTATTTACCTT
1 TGATGGCCACACATATATCTCAACCTAAAGTAAGAAGATTTAAGCAATTCCTATGTATTGACCTT
29518075 TAACTACTATTTAACGGAAGCTCATCTACATTAGATAAATTATTGT
66 TAACTACTATTTAACGGAAGCTCATCTACATTAGATAAATTATTGT
*
29518121 TGATGGCCACACATATATATCTCAAGCTAAAGTAAGAAGATTTAAGCAATTCCTATGTATTGACC
1 TGATGGCCACAC--ATATATCTCAACCTAAAGTAAGAAGATTTAAGCAATTCCTATGTATTGACC
* * *
29518186 TTTAACTAGTATTTAATGTAAGCTCATCTACATTAGATAAATTATTGT
64 TTTAACTACTATTTAACGGAAGCTCATCTACATTAGATAAATTATTGT
29518234 T
1 T
29518235 TATAATATTT
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
111 12 0.11
113 95 0.89
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (111 bp):
TGATGGCCACACATATATCTCAACCTAAAGTAAGAAGATTTAAGCAATTCCTATGTATTGACCTT
TAACTACTATTTAACGGAAGCTCATCTACATTAGATAAATTATTGT
Found at i:29522029 original size:2 final size:2
Alignment explanation
Indices: 29522022--29522050 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
29522012 ATTTACTTAG
29522022 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29522051 TAAAGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29531275 original size:18 final size:18
Alignment explanation
Indices: 29531249--29531291 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
29531239 GTTTATGTTA
29531249 AAGTGTCATATATTGGAT
1 AAGTGTCATATATTGGAT
* *
29531267 AAGTTTCATATATTGTAT
1 AAGTGTCATATATTGGAT
29531285 AAGTGTC
1 AAGTGTC
29531292 TTTCTCTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (18 bp):
AAGTGTCATATATTGGAT
Found at i:29535755 original size:49 final size:50
Alignment explanation
Indices: 29535687--29535784 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
29535677 TCTTATAAAG
* * * *
29535687 AACATATGGAAAGCATT-AAACACGTTATGTTCTTTCCAAAAAGAATTAT
1 AACATATGGAAAACATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
*
29535736 AACATATGGAAAACATTAAAAAACATTATATTTTTTCCAAAAAGAATTA
1 AACATATGGAAAACATTAAAAAACATTATATTCTTTCCAAAAAGAATTA
29535785 AAACTACCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 16 0.37
50 27 0.63
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (50 bp):
AACATATGGAAAACATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
Found at i:29538122 original size:9 final size:9
Alignment explanation
Indices: 29538108--29538135 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29538098 TGAGTTTTCG
29538108 AATTCGAAT
1 AATTCGAAT
29538117 AATTCGAAT
1 AATTCGAAT
29538126 AATTCGAAT
1 AATTCGAAT
29538135 A
1 A
29538136 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:29538210 original size:17 final size:17
Alignment explanation
Indices: 29538188--29538228 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
29538178 CATTTTACTT
29538188 TTCCTTCAAAACTTTTA
1 TTCCTTCAAAACTTTTA
29538205 TTCCTTCAAAACTTTTA
1 TTCCTTCAAAACTTTTA
*
29538222 CTCCTTC
1 TTCCTTC
29538229 CTACTTTCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.46
Consensus pattern (17 bp):
TTCCTTCAAAACTTTTA
Found at i:29541740 original size:11 final size:11
Alignment explanation
Indices: 29541724--29541773 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
29541714 TACAAAATTA
29541724 TTTAAAATGTT
1 TTTAAAATGTT
*
29541735 TTTAAATTGTAAT
1 TTTAAAATGT--T
29541748 TTTAAAAATGTT
1 TTT-AAAATGTT
*
29541760 TTTAAAATATT
1 TTTAAAATGTT
29541771 TTT
1 TTT
29541774 GAATAATACT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 19 0.58
12 4 0.12
13 4 0.12
14 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (11 bp):
TTTAAAATGTT
Found at i:29546734 original size:11 final size:11
Alignment explanation
Indices: 29546718--29546793 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
29546708 GATAATCACT
29546718 TTAATATTAAA
1 TTAATATTAAA
29546729 TTAATA--AAA
1 TTAATATTAAA
29546738 -TAATATTAAA
1 TTAATATTAAA
*
29546748 ATAAGTATTAAA
1 TTAA-TATTAAA
29546760 TTTAAT-TTAATA
1 -TTAATATTAA-A
29546772 TTAAATTATTAAA
1 TT-AA-TATTAAA
*
29546785 ATAATATTA
1 TTAATATTA
29546794 TTTTTGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
8 5 0.09
9 3 0.06
10 3 0.06
11 20 0.37
12 13 0.24
13 6 0.11
14 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:29567569 original size:311 final size:312
Alignment explanation
Indices: 29566996--29567619 Score: 1241
Period size: 311 Copynumber: 2.0 Consensus size: 312
29566986 TAAATATACT
29566996 AAAAACATTAAAATAAATTTTTCACAGCAAATTGAAAATACATTAAAAATATTTATACTTAAATA
1 AAAAACATTAAAATAAATTTTTCACAGCAAATTGAAAATACATTAAAAATATTTATACTTAAATA
29567061 ACATTAAGATAGTTAAAATTTAGCAAGAAAAATGATAGGAAAACAACAGCAAAAAAAAAAAAGCA
66 ACATTAAGATAGTTAAAATTTAGCAAGAAAAATGATAGGAAAACAACAGCAAAAAAAAAAAAGCA
29567126 AATTTGGGCTGGCCTAAACAAAAAAATCTTACTCAAGGTTCGACCCTTTTAGAACATAAGCCTTG
131 AATTTGGGCTGGCCTAAACAAAAAAATCTTACTCAAGGTTCGACCCTTTTAGAACATAAGCCTTG
29567191 TTTTTTTGTCAAAACTTATTTTTCGAGCCTATATTTTTTGTCCAAATCCTCTCACTTTTTGGATG
196 TTTTTTTGTCAAAACTTATTTTTCGAGCCTATATTTTTTGTCCAAATCCTCTCACTTTTTGGATG
29567256 GGCCTTCGGGTGTAAGACACATAACCCAACCCATGATCAGGTCTAATTGAGA
261 GGCCTTCGGGTGTAAGACACATAACCCAACCCATGATCAGGTCTAATTGAGA
29567308 AAAAACATT-AAATAAATTTTTCACAGCAAATTGAAAATACATTAAAAATATTTATACTTAAATA
1 AAAAACATTAAAATAAATTTTTCACAGCAAATTGAAAATACATTAAAAATATTTATACTTAAATA
29567372 ACATTAAGATAGTTAAAATTTAGCAAGAAAAATGATAGGAAAACAACAGCAAAAAAAAAAAAGCA
66 ACATTAAGATAGTTAAAATTTAGCAAGAAAAATGATAGGAAAACAACAGCAAAAAAAAAAAAGCA
29567437 AATTTGGGCTGGCCTAAACAAAAAAATCTTACTCAAGGTTCGACCCTTTTAGAACATAAGCCTTG
131 AATTTGGGCTGGCCTAAACAAAAAAATCTTACTCAAGGTTCGACCCTTTTAGAACATAAGCCTTG
29567502 TTTTTTTGTCAAAACTTATTTTTCGAGCCTATATTTTTTGTCCAAATCCTCTCACTTTTTGGATG
196 TTTTTTTGTCAAAACTTATTTTTCGAGCCTATATTTTTTGTCCAAATCCTCTCACTTTTTGGATG
29567567 GGCCTTCGGGTGTAAGACACATAACCCAACCCATGATCAGGTCTAATTGAGA
261 GGCCTTCGGGTGTAAGACACATAACCCAACCCATGATCAGGTCTAATTGAGA
29567619 A
1 A
29567620 CCATATTAGT
Statistics
Matches: 312, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
311 303 0.97
312 9 0.03
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (312 bp):
AAAAACATTAAAATAAATTTTTCACAGCAAATTGAAAATACATTAAAAATATTTATACTTAAATA
ACATTAAGATAGTTAAAATTTAGCAAGAAAAATGATAGGAAAACAACAGCAAAAAAAAAAAAGCA
AATTTGGGCTGGCCTAAACAAAAAAATCTTACTCAAGGTTCGACCCTTTTAGAACATAAGCCTTG
TTTTTTTGTCAAAACTTATTTTTCGAGCCTATATTTTTTGTCCAAATCCTCTCACTTTTTGGATG
GGCCTTCGGGTGTAAGACACATAACCCAACCCATGATCAGGTCTAATTGAGA
Found at i:29571580 original size:179 final size:179
Alignment explanation
Indices: 29571280--29571637 Score: 562
Period size: 179 Copynumber: 2.0 Consensus size: 179
29571270 AATTATTCTA
* *
29571280 GGGACCCCACAATAAATAACCCAATTTAATTTAAACAAAATATAAAAATTAAATATAAAAAGGGC
1 GGGACCCCACAATAAATAACCCAAATTAATTTAAACAAAATATAAAAAATAAATATAAAAAGGGC
*
29571345 TAAATTACGGAATAAAGCCCTTTTTTTCAAATTTACGAAAATAGGCCAGTTTTTTTTAAATGACA
66 TAAATTACGGAATAAAGCCCTTTTTTTCAAAATTACGAAAATAGGCCAGTTTTTTTTAAATGACA
* * * *
29571410 TAAATGGGCCGATTTTTCTAAAACGCATCTAACTAGTGTTGTTTTTATG
131 GAAATGGGCCGATTTTGCTAAAACGCATCCAACTAGTGTCGTTTTTATG
29571459 GGGACCCCACAATAAATAACCCAAATTAATTTAAACAAAATA-AAAAAATAAATAT-AAAA-GGC
1 GGGACCCCACAATAAATAACCCAAATTAATTTAAACAAAATATAAAAAATAAATATAAAAAGGGC
*
29571521 TAAATTACGGAATAAAGCCCATTTTTTTCAAAATTAC-AGAAATAGGCTAGTTTTTTTTTTAAAT
66 TAAATTACGGAATAAAGCCC-TTTTTTTCAAAATTACGA-AAATAGGCCAG--TTTTTTTTAAAT
**
29571585 GACAGAAATGGGCCGATTTTGCTAAAACGTGTCCAACTAGTGTCGTTTTTATG
127 GACAGAAATGGGCCGATTTTGCTAAAACGCATCCAACTAGTGTCGTTTTTATG
29571638 AGAAAATCAA
Statistics
Matches: 165, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
176 24 0.15
177 29 0.18
178 12 0.07
179 100 0.61
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (179 bp):
GGGACCCCACAATAAATAACCCAAATTAATTTAAACAAAATATAAAAAATAAATATAAAAAGGGC
TAAATTACGGAATAAAGCCCTTTTTTTCAAAATTACGAAAATAGGCCAGTTTTTTTTAAATGACA
GAAATGGGCCGATTTTGCTAAAACGCATCCAACTAGTGTCGTTTTTATG
Found at i:29571867 original size:11 final size:12
Alignment explanation
Indices: 29571853--29571881 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
29571843 ACCCAAATTC
29571853 TATTTTTATT-A
1 TATTTTTATTAA
29571864 TATTTTTATTAA
1 TATTTTTATTAA
29571876 TATTTT
1 TATTTT
29571882 CAAGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTTTATTAA
Found at i:29572042 original size:20 final size:22
Alignment explanation
Indices: 29571996--29572042 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
29571986 CCACTTTTCA
*
29571996 TTTTTATTACTTCTAAAATGTT
1 TTTTTATTACTTCTAAAATATT
* *
29572018 ATTTTATT-C-TCTCAAATATT
1 TTTTTATTACTTCTAAAATATT
29572038 TTTTT
1 TTTTT
29572043 TGTTTAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 13 0.62
21 1 0.05
22 7 0.33
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTATTACTTCTAAAATATT
Found at i:29572646 original size:2 final size:2
Alignment explanation
Indices: 29572639--29572665 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29572629 TCTAAACAAT
29572639 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
29572666 TTATCTTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29573889 original size:30 final size:28
Alignment explanation
Indices: 29573853--29573972 Score: 67
Period size: 30 Copynumber: 4.2 Consensus size: 28
29573843 TATTCTAAAT
29573853 TAAATAAGGTAAATAAAATTTTATATTCCA
1 TAAATAA-GTAAATAAAATTTTATATT-CA
* *
29573883 TAAATAATTGAAATAAAATTATT-T-TTTA
1 TAAATAAGT-AAATAAAATT-TTATATTCA
* *
29573911 -AAATAA--AAATAAACGTATTCTA-AAT--
1 TAAATAAGTAAATAAA---ATTTTATATTCA
29573936 TAAATAAGGTAAATAAAATTTTATATTCCA
1 TAAATAA-GTAAATAAAATTTTATATT-CA
29573966 TAAATAA
1 TAAATAA
29573973 TTTATGTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 30
0.66 0.06 0.29
Matches are distributed among these distances:
24 7 0.10
26 12 0.17
27 12 0.17
28 1 0.01
29 10 0.14
30 25 0.36
31 2 0.03
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (28 bp):
TAAATAAGTAAATAAAATTTTATATTCA
Found at i:29573916 original size:83 final size:84
Alignment explanation
Indices: 29573803--29573974 Score: 337
Period size: 83 Copynumber: 2.1 Consensus size: 84
29573793 TATTTTATAT
29573803 TAATTGAAATAAAATTTATTTTTTAAAATAAAAATAAACGTATTCTAAATTAAATAAGGTAAATA
1 TAATTGAAATAAAATTTATTTTTTAAAATAAAAATAAACGTATTCTAAATTAAATAAGGTAAATA
29573868 AAATTTTATATTCCATAAA
66 AAATTTTATATTCCATAAA
29573887 TAATTGAAATAAAA-TTATTTTTTAAAATAAAAATAAACGTATTCTAAATTAAATAAGGTAAATA
1 TAATTGAAATAAAATTTATTTTTTAAAATAAAAATAAACGTATTCTAAATTAAATAAGGTAAATA
29573951 AAATTTTATATTCCATAAA
66 AAATTTTATATTCCATAAA
29573970 TAATT
1 TAATT
29573975 TATGTTTTAC
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 74 0.84
84 14 0.16
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (84 bp):
TAATTGAAATAAAATTTATTTTTTAAAATAAAAATAAACGTATTCTAAATTAAATAAGGTAAATA
AAATTTTATATTCCATAAA
Found at i:29575448 original size:24 final size:24
Alignment explanation
Indices: 29575413--29575463 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
29575403 ACAAAGTTAC
* *
29575413 TTGTTAATGTGTCATAATGTTCTA
1 TTGTTAACGTGTCATAATATTCTA
29575437 TTGTTAACGTGTCATAATATTCTA
1 TTGTTAACGTGTCATAATATTCTA
29575461 TTG
1 TTG
29575464 ATGCTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (24 bp):
TTGTTAACGTGTCATAATATTCTA
Found at i:29580557 original size:31 final size:29
Alignment explanation
Indices: 29580519--29580588 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
29580509 AATACCAAAA
* *
29580519 TAGTCACTTTTGTTTACCTCAGGTTACATTT
1 TAGTCACTTATGTTT-CC-AAGGTTACATTT
* *
29580550 TAGTCACTTATGTTTGCAATGTTACATTT
1 TAGTCACTTATGTTTCCAAGGTTACATTT
29580579 TAGTCACTTA
1 TAGTCACTTA
29580589 CATTATCGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 20 0.57
30 1 0.03
31 14 0.40
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTCCAAGGTTACATTT
Found at i:29590009 original size:21 final size:19
Alignment explanation
Indices: 29589966--29590014 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
29589956 TGATTGAACC
29589966 AATTTTTTTATTTTTAAAT
1 AATTTTTTTATTTTTAAAT
*
29589985 -ATTTTTTTATGATTTTTAAT
1 AATTTTTTTAT--TTTTAAAT
*
29590005 AATTTATTTA
1 AATTTTTTTA
29590015 ATAGAACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 10 0.40
20 7 0.28
21 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
AATTTTTTTATTTTTAAAT
Found at i:29591168 original size:19 final size:18
Alignment explanation
Indices: 29591144--29591183 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29591134 GAAATTTTGG
29591144 AATGGAAAAGAAGAGAGAA
1 AATGG-AAAGAAGAGAGAA
* *
29591163 AATGGAGAGAAGAGAGGA
1 AATGGAAAGAAGAGAGAA
29591181 AAT
1 AAT
29591184 ATGTGAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.07
Consensus pattern (18 bp):
AATGGAAAGAAGAGAGAA
Found at i:29593577 original size:10 final size:10
Alignment explanation
Indices: 29593564--29593594 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
29593554 ATATATATAT
29593564 ATATATCACA
1 ATATATCACA
29593574 ATATATCACA
1 ATATATCACA
*
29593584 CTATATCACA
1 ATATATCACA
29593594 A
1 A
29593595 GACTTGTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (10 bp):
ATATATCACA
Found at i:29596534 original size:24 final size:24
Alignment explanation
Indices: 29596506--29596552 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
29596496 GAGATAAAAA
29596506 ATGG-TTTGAAAAAAAATAAATGAG
1 ATGGTTTTG-AAAAAAATAAATGAG
29596530 ATGGTTTTGAAAAAAATAAATGA
1 ATGGTTTTGAAAAAAATAAATGA
29596553 TCAACTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (24 bp):
ATGGTTTTGAAAAAAATAAATGAG
Found at i:29598744 original size:45 final size:46
Alignment explanation
Indices: 29598695--29598791 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 46
29598685 TTGTAATTGA
* *
29598695 AATTTTCAAGTTTGT-ATTAATTTAATTATAACAACTATTTGGCTT
1 AATTTTCAAGTTTGTAATTAATTTAATTATAACAAATATTTGACTT
* *
29598740 AATTTTCAAGTTTGTAATTAATTTAATTATAGCAAATGTTTGACTT
1 AATTTTCAAGTTTGTAATTAATTTAATTATAACAAATATTTGACTT
29598786 AATTTT
1 AATTTT
29598792 ATTTGAAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 15 0.32
46 32 0.68
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.49
Consensus pattern (46 bp):
AATTTTCAAGTTTGTAATTAATTTAATTATAACAAATATTTGACTT
Found at i:29609878 original size:23 final size:25
Alignment explanation
Indices: 29609850--29609901 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
29609840 ATTAATTGGA
*
29609850 TAAATTCTGAATAT-T-AAAAGTAT
1 TAAATTCTAAATATCTAAAAAGTAT
*
29609873 TAAATTTTAAATATCTAAAAAGTAT
1 TAAATTCTAAATATCTAAAAAGTAT
29609898 TAAA
1 TAAA
29609902 GATGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.48
24 1 0.04
25 12 0.48
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (25 bp):
TAAATTCTAAATATCTAAAAAGTAT
Found at i:29626336 original size:21 final size:20
Alignment explanation
Indices: 29626310--29626348 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29626300 TAAGGTAGTT
29626310 TTGAAATGGAAAAGTATTGAA
1 TTGAAAT-GAAAAGTATTGAA
*
29626331 TTGAAATGTAAAGTATTG
1 TTGAAATGAAAAGTATTG
29626349 CATGGAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGAAATGAAAAGTATTGAA
Found at i:29628235 original size:18 final size:18
Alignment explanation
Indices: 29628212--29628272 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 18
29628202 ACTCCCCCTA
*
29628212 TTTACTTTCCCTCAAACT
1 TTTACTTTCCCTAAAACT
29628230 TTTAC--TCCCTAAAACTT
1 TTTACTTTCCCTAAAAC-T
* *
29628247 TTTATCTTCCCCTTAAACT
1 TTTA-CTTTCCCTAAAACT
29628266 TTTACTT
1 TTTACTT
29628273 CTCACCCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 9 0.25
17 5 0.14
18 9 0.25
19 5 0.14
20 8 0.22
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTACTTTCCCTAAAACT
Found at i:29629000 original size:20 final size:20
Alignment explanation
Indices: 29628958--29628998 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
29628948 TACAACACAA
*
29628958 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
29628978 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
29628997 TT
1 TT
29628999 TCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:29630385 original size:12 final size:12
Alignment explanation
Indices: 29630360--29630398 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29630350 ACTCGCTTCT
* *
29630360 TTACTTACTCAC
1 TTACTTGCTTAC
*
29630372 TTACTTGTTTAC
1 TTACTTGCTTAC
29630384 TTACTTGCTTAC
1 TTACTTGCTTAC
29630396 TTA
1 TTA
29630399 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:29630741 original size:50 final size:50
Alignment explanation
Indices: 29630648--29630840 Score: 176
Period size: 50 Copynumber: 3.7 Consensus size: 50
29630638 TTTTCTGTAC
* * * * *
29630648 TGCCAATGCCATATCCCAGATATGGTCTCTTACATGGG--TTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGG--TCTTACAGGGGACCTCTCATATCGA
* *
29630698 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGG-ACCTCTCATATCGA
* * *
29630748 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT-A--TC---GA
* *
29630804 TGCTAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA
29630841 TCCCATTCCT
Statistics
Matches: 118, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
47 3 0.03
48 6 0.05
50 68 0.58
51 3 0.03
53 2 0.02
56 36 0.31
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATATCGA
Found at i:29633914 original size:15 final size:15
Alignment explanation
Indices: 29633894--29633929 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29633884 TTATACTGTT
*
29633894 ACATTCTTGGTAATC
1 ACATTCTTGGCAATC
29633909 ACATTCTTGGCAATC
1 ACATTCTTGGCAATC
*
29633924 ATATTC
1 ACATTC
29633930 CCTTGGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (15 bp):
ACATTCTTGGCAATC
Found at i:29634715 original size:9 final size:9
Alignment explanation
Indices: 29634701--29634725 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29634691 CAAATCAAAG
29634701 AAAAGAGAA
1 AAAAGAGAA
29634710 AAAAGAGAA
1 AAAAGAGAA
29634719 AAAAGAG
1 AAAAGAG
29634726 GGATTCGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAGAGAA
Found at i:29635129 original size:11 final size:11
Alignment explanation
Indices: 29635113--29635141 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
29635103 GAGCTCTCTG
29635113 TTTTTTTTTCT
1 TTTTTTTTTCT
29635124 TTTTTTTTTCT
1 TTTTTTTTTCT
29635135 TTTTTTT
1 TTTTTTT
29635142 CGTTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:29645610 original size:15 final size:15
Alignment explanation
Indices: 29645583--29645615 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
29645573 ATATTTGGTA
29645583 ATTATGCATTGAATTG
1 ATTATGCATTGAA-TG
29645599 ATTATG-ATTGAATG
1 ATTATGCATTGAATG
29645613 ATT
1 ATT
29645616 CATTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.45
Consensus pattern (15 bp):
ATTATGCATTGAATG
Found at i:29647972 original size:5 final size:5
Alignment explanation
Indices: 29647945--29648002 Score: 79
Period size: 5 Copynumber: 12.4 Consensus size: 5
29647935 TTTTTATGTT
*
29647945 TTATA -TATA TTAT- TT-TA TTATA TAATA -TATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
29647991 TTATA TTATA TT
1 TTATA TTATA TT
29648003 CTTTNNNNNN
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
3 1 0.02
4 11 0.23
5 35 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:29647972 original size:22 final size:24
Alignment explanation
Indices: 29647947--29648002 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 24
29647937 TTTATGTTTT
29647947 ATATATATTAT-TT-TATTATATA
1 ATATATATTATATTATATTATATA
*
29647969 ATATATATTATATTATATTATATT
1 ATATATATTATATTATATTATATA
29647993 ATATTATATT
1 ATA-TATATT
29648003 CTTTNNNNNN
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 11 0.37
23 2 0.07
24 11 0.37
25 6 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATATATATTATATTATATTATATA
Found at i:29651938 original size:40 final size:41
Alignment explanation
Indices: 29651847--29651954 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 41
29651837 AGCGGCACTT
*
29651847 TTAGCGGCGTTTGGAGCAAAAACGCTGCTAAAAATCGAGAA
1 TTAGCGGCGTTTGGAGCAAAAACGCCGCTAAAAATCGAGAA
* * * * * *
29651888 ATAGCAGCGTTT-TAGGAAAAGCGCCGCTAAAAAGT-GAGCA
1 TTAGCGGCGTTTGGAGCAAAAACGCCGCTAAAAA-TCGAGAA
* *
29651928 TTAGCGGCGTTTAGA-AAAAAACGCCGC
1 TTAGCGGCGTTTGGAGCAAAAACGCCGC
29651955 AAATAATACA
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
40 41 0.77
41 12 0.23
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGTTTGGAGCAAAAACGCCGCTAAAAATCGAGAA
Found at i:29659294 original size:13 final size:13
Alignment explanation
Indices: 29659276--29659317 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
29659266 NNNNNNNNNN
*
29659276 TTAAATTTATTAC
1 TTAAATATATTAC
*
29659289 TTAAATATGTTAC
1 TTAAATATATTAC
*
29659302 TTAAATACATTAC
1 TTAAATATATTAC
29659315 TTA
1 TTA
29659318 CTAAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (13 bp):
TTAAATATATTAC
Found at i:29659656 original size:9 final size:9
Alignment explanation
Indices: 29659638--29659986 Score: 247
Period size: 9 Copynumber: 40.2 Consensus size: 9
29659628 CTTGTGGTTA
*
29659638 AACTTGCAT
1 AACTTACAT
29659647 AACTTACAT
1 AACTTACAT
*
29659656 AA-TAACAT
1 AACTTACAT
29659664 AACAACTTACAT
1 ---AACTTACAT
29659676 AA--TACAT
1 AACTTACAT
*
29659683 AACATACAT
1 AACTTACAT
29659692 AACTTACAT
1 AACTTACAT
*
29659701 AACTTATAT
1 AACTTACAT
*
29659710 AA--TACAA
1 AACTTACAT
29659717 AACTTACAT
1 AACTTACAT
*
29659726 AACTTAAAT
1 AACTTACAT
* *
29659735 ATCTTACAC
1 AACTTACAT
29659744 AACTTACAT
1 AACTTACAT
*
29659753 AACCTACAT
1 AACTTACAT
29659762 AA--TACAT
1 AACTTACAT
29659769 AACTTACAT
1 AACTTACAT
*
29659778 AATACATA-AT
1 -A-ACTTACAT
29659788 AACTTAC--
1 AACTTACAT
29659795 AACTTACAT
1 AACTTACAT
*
29659804 AACATACAT
1 AACTTACAT
* **
29659813 TACTTTGAT
1 AACTTACAT
29659822 AACTTACAT
1 AACTTACAT
*
29659831 AAGTTACAT
1 AACTTACAT
29659840 AA--TACAT
1 AACTTACAT
29659847 AACTTACAT
1 AACTTACAT
*
29659856 AATACATA-AT
1 -A-ACTTACAT
29659866 AACTTAC--
1 AACTTACAT
29659873 AACTTACAT
1 AACTTACAT
*
29659882 AACATACAT
1 AACTTACAT
* **
29659891 TACTTTGAT
1 AACTTACAT
29659900 AACTTACAT
1 AACTTACAT
*
29659909 AAGTTACAT
1 AACTTACAT
29659918 AA-TATAC--
1 AACT-TACAT
29659925 AACTTACAT
1 AACTTACAT
* *
29659934 AGCTTACTT
1 AACTTACAT
29659943 AA--TACAT
1 AACTTACAT
29659950 AACTTACAT
1 AACTTACAT
29659959 AACTT--AT
1 AACTTACAT
*
29659966 ACACGTACAT
1 A-ACTTACAT
29659976 AACTTACAT
1 AACTTACAT
29659985 AA
1 AA
29659987 TTTANNNNNN
Statistics
Matches: 266, Mismatches: 43, Indels: 62
0.72 0.12 0.17
Matches are distributed among these distances:
7 54 0.20
8 18 0.07
9 170 0.64
10 9 0.03
11 10 0.04
12 5 0.02
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:29659692 original size:16 final size:16
Alignment explanation
Indices: 29659644--29659960 Score: 175
Period size: 16 Copynumber: 18.9 Consensus size: 16
29659634 GTTAAACTTG
29659644 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
29659661 CATAACAACTTACATAATA
1 CAT---AACTTACATAATA
*
29659680 CATAACATACATAACTTA
1 CATAACTTACATAA--TA
*
29659698 CATAACTTATATAATA
1 CATAACTTACATAATA
*
29659714 CAAAACTTACATAACTTA
1 CATAACTTACATAA--TA
* * *
29659732 AATATCTTACACAACTTA
1 CATAACTTACATAA--TA
*
29659750 CATAACCTACATAATA
1 CATAACTTACATAATA
29659766 CATAACTTACATAATA
1 CATAACTTACATAATA
*
29659782 CATAA-TAAC-T--TA
1 CATAACTTACATAATA
29659794 C--AACTTACATAACATA
1 CATAACTTACAT-A-ATA
* **
29659810 CATTACTTTGATAACTTA
1 CATAACTTACATAA--TA
*
29659828 CATAAGTTACATAATA
1 CATAACTTACATAATA
29659844 CATAACTTACATAATA
1 CATAACTTACATAATA
*
29659860 CATAATAACTTACA-ACTTA
1 C---ATAACTTACATA-ATA
* * *
29659879 CATAACATACATTACTTT
1 CATAACTTACA-TA-ATA
*
29659897 GATAACTTACATAAGTTA
1 CATAACTTACATAA--TA
*
29659915 CATAA-TATACA-ACTTA
1 CATAACT-TACATA-ATA
* *
29659931 CATAGCTTACTTAATA
1 CATAACTTACATAATA
29659947 CATAACTTACATAA
1 CATAACTTACATAA
29659961 CTTATACACG
Statistics
Matches: 233, Mismatches: 38, Indels: 59
0.71 0.12 0.18
Matches are distributed among these distances:
10 2 0.01
11 3 0.01
12 4 0.02
14 1 0.00
15 3 0.01
16 100 0.43
17 10 0.04
18 81 0.35
19 17 0.07
20 12 0.05
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:29659831 original size:78 final size:78
Alignment explanation
Indices: 29659667--29659934 Score: 350
Period size: 78 Copynumber: 3.4 Consensus size: 78
29659657 ATAACATAAC
* *
29659667 AACTTACATAA--TACATAACATACATAACTTACATAACTTATATAAT-AC--AAAACTTACATA
1 AACTTACATAAGTTACAT-A-ATACATAACTTACATAA--TACATAATAACTTACAACTTACATA
* * ** *
29659727 ACTTA-AATATCTTACAC
62 ACATACATTA-CTTTGAT
**
29659744 AACTTACATAACCTACATAATACATAACTTACATAATACATAATAACTTACAACTTACATAACAT
1 AACTTACATAAGTTACATAATACATAACTTACATAATACATAATAACTTACAACTTACATAACAT
29659809 ACATTACTTTGAT
66 ACATTACTTTGAT
29659822 AACTTACATAAGTTACATAATACATAACTTACATAATACATAATAACTTACAACTTACATAACAT
1 AACTTACATAAGTTACATAATACATAACTTACATAATACATAATAACTTACAACTTACATAACAT
29659887 ACATTACTTTGAT
66 ACATTACTTTGAT
* *
29659900 AACTTACATAAGTTACATAATATACAACTTACATA
1 AACTTACATAAGTTACATAATACATAACTTACATA
29659935 GCTTACTTAA
Statistics
Matches: 174, Mismatches: 11, Indels: 11
0.89 0.06 0.06
Matches are distributed among these distances:
75 7 0.04
76 2 0.01
77 28 0.16
78 129 0.74
79 8 0.05
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.32
Consensus pattern (78 bp):
AACTTACATAAGTTACATAATACATAACTTACATAATACATAATAACTTACAACTTACATAACAT
ACATTACTTTGAT
Found at i:29667311 original size:21 final size:21
Alignment explanation
Indices: 29667285--29667332 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
29667275 CAACAACTTA
*
29667285 AAGCAGAGGC-GACAGCGAGGG
1 AAGCAGAGGCTG-CAGCGAGAG
29667306 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
29667327 AAGCAG
1 AAGCAG
29667333 CGAGAGAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.44, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:29667334 original size:12 final size:12
Alignment explanation
Indices: 29667317--29667344 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29667307 AGCAGAGGCT
29667317 GCAGCGAGAGAA
1 GCAGCGAGAGAA
29667329 GCAGCGAGAGAA
1 GCAGCGAGAGAA
29667341 GCAG
1 GCAG
29667345 AGGTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:29669039 original size:9 final size:9
Alignment explanation
Indices: 29669025--29669055 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29669015 GTTAAACGAA
29669025 TCGAGTTAT
1 TCGAGTTAT
*
29669034 TCGAGTTAA
1 TCGAGTTAT
29669043 TCGAGTTAT
1 TCGAGTTAT
29669052 TCGA
1 TCGA
29669056 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:29669786 original size:5 final size:5
Alignment explanation
Indices: 29669776--29669806 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
29669766 GAACAAATAT
29669776 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
29669807 ATTCCATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:29675777 original size:26 final size:26
Alignment explanation
Indices: 29675748--29675797 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
29675738 AAAATATATA
*
29675748 TTTATATT-TAATTATTTTATATATTT
1 TTTAT-TTATAATGATTTTATATATTT
*
29675774 TTTATTTATTATGATTTTATATAT
1 TTTATTTATAATGATTTTATATAT
29675798 AGTCATTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTATTTATAATGATTTTATATATTT
Found at i:29681586 original size:41 final size:42
Alignment explanation
Indices: 29681503--29681607 Score: 149
Period size: 41 Copynumber: 2.5 Consensus size: 42
29681493 TGCGGCGTTT
* *
29681503 TTATAGAACATGACCTTTAGCAGTGCTTTTCCCACAAACACCG
1 TTATAAAACATGACCTTTAGCAAT-CTTTTCCCACAAACACCG
*
29681546 TTATAAAACATGACCTTTAGGAAT-TTTTCCCACAAACACCG
1 TTATAAAACATGACCTTTAGCAATCTTTTCCCACAAACACCG
* *
29681587 CTATAAAATATGACCTTTAGC
1 TTATAAAACATGACCTTTAGC
29681608 GAAAATAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 35 0.62
43 21 0.38
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (42 bp):
TTATAAAACATGACCTTTAGCAATCTTTTCCCACAAACACCG
Found at i:29682669 original size:14 final size:14
Alignment explanation
Indices: 29682636--29682675 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
29682626 AAAAATAGGC
*
29682636 ATTGGGGGTAACTGA
1 ATTGGGGG-AAATGA
*
29682651 TTTGGGGGAAATGA
1 ATTGGGGGAAATGA
29682665 ATTGGGGGAAA
1 ATTGGGGGAAA
29682676 AAGGGGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.30, C:0.03, G:0.42, T:0.25
Consensus pattern (14 bp):
ATTGGGGGAAATGA
Found at i:29689761 original size:43 final size:43
Alignment explanation
Indices: 29689698--29689825 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 43
29689688 GGATCTCTGG
* *
29689698 TATGTGTTTTCGTATAAGACCACGTCTGGGACGTTGGCATTGA
1 TATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATTGA
*
29689741 CT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA
1 -TATGTGTTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATTGA
* * * *
29689784 TATGTGATTACATGTAAGACCACGTCTAGGACGTTGGTATTG
1 TATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATTG
29689826 TACGAGCTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
42 3 0.04
43 65 0.92
44 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
TATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATTGA
Found at i:29691318 original size:2 final size:2
Alignment explanation
Indices: 29691311--29691335 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29691301 AAAATGCTCT
29691311 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
29691336 TAGTGATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29697205 original size:24 final size:24
Alignment explanation
Indices: 29697178--29697228 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
29697168 AGCCTATAAC
*
29697178 GGGTAGCTCCAAAGAGTAATTAAT
1 GGGTAGCTCCAAAGAGCAATTAAT
*
29697202 GGGTAGCTCCGAAGAGCAATTAAT
1 GGGTAGCTCCAAAGAGCAATTAAT
29697226 GGG
1 GGG
29697229 AAGTACCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (24 bp):
GGGTAGCTCCAAAGAGCAATTAAT
Found at i:29704313 original size:17 final size:17
Alignment explanation
Indices: 29704238--29704314 Score: 51
Period size: 17 Copynumber: 4.8 Consensus size: 17
29704228 TTTGAAATGT
29704238 TTAGAAATTAAA-T-AA
1 TTAGAAATTAAATTAAA
29704253 TT-GAAA-TAACA-TAAA
1 TTAGAAATTAA-ATTAAA
*
29704268 -TAAACAATTAAA-TAAA
1 TTAGA-AATTAAATTAAA
*
29704284 TTAGAAATAAAATTAAA
1 TTAGAAATTAAATTAAA
* *
29704301 TTGGGAATTAAATT
1 TTAGAAATTAAATT
29704315 CGGATTTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
13 3 0.06
14 7 0.14
15 5 0.10
16 13 0.27
17 21 0.43
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (17 bp):
TTAGAAATTAAATTAAA
Found at i:29707484 original size:341 final size:342
Alignment explanation
Indices: 29707069--29707751 Score: 1359
Period size: 341 Copynumber: 2.0 Consensus size: 342
29707059 TAATGGTTAG
29707069 AAGCAAGTCAATGAAGATTGTATCAATTTTAGGATTAAATTATAATATTATCATATACTAATTTA
1 AAGCAAGTCAATGAAGATTGTATCAATTTTAGGATTAAATTATAATATTATCATATACTAATTTA
29707134 TTTATTTTATAAAATTTATAGCACCAAACATGCCATTTTTCATGGATGGAGAAAAGTGAGATATG
66 TTTATTTTATAAAATTTATAGCACCAAACATGCCATTTTTCATGGATGGAGAAAAGTGAGATATG
29707199 GGAAGACAGTTGCAAAATTTATGGGAAGATATCCTTTTTTAAAAATATATTAATTGATAATGAAA
131 GGAAGACAGTTGCAAAATTTATGGGAAGATATCCTTTTTTAAAAATATATTAATTGATAATGAAA
29707264 TAAAAAATATTTGGATAAATTATCTAATTGGTGATCCAATTCTTTGGACGTTTTTATTTTAATTA
196 TAAAAAATATTTGGATAAATTATCTAATTGGTGATCCAATTCTTTGGACGTTTTTATTTTAATTA
29707329 CTGAAATTTAAAAAAAAAAACTTATAATTTAATCACTACCCATTAAAATTTTTCGACAAACTTTT
261 CTGAAATTTAAAAAAAAAAACTTATAATTTAATCACTACCCATTAAAATTTTTCGACAAACTTTT
29707394 CCACCAATCAAAATTCT
326 CCACCAATCAAAATTCT
29707411 AAGCAAGTC-ATGAAGATTGTATCAATTTTAGGATTAAATTATAATATTATCATATACTAATTTA
1 AAGCAAGTCAATGAAGATTGTATCAATTTTAGGATTAAATTATAATATTATCATATACTAATTTA
29707475 TTTATTTTATAAAATTTATAGCACCAAACATGCCATTTTTCATGGATGGAGAAAAGTGAGATATG
66 TTTATTTTATAAAATTTATAGCACCAAACATGCCATTTTTCATGGATGGAGAAAAGTGAGATATG
29707540 GGAAGACAGTTGCAAAATTTATGGGAAGATATCCTTTTTTAAAAATATATTAATTGATAATGAAA
131 GGAAGACAGTTGCAAAATTTATGGGAAGATATCCTTTTTTAAAAATATATTAATTGATAATGAAA
29707605 TAAAAAATATTTGGATAAATTATCTAATTGGTGATCCAATTCTTTGGACGTTTTTATTTTAATTA
196 TAAAAAATATTTGGATAAATTATCTAATTGGTGATCCAATTCTTTGGACGTTTTTATTTTAATTA
29707670 CTGAAATTTAAAAAAAAAAACTTATAATTTAATCACTACCCATTAAAATTTTTCGACAAACTTTT
261 CTGAAATTTAAAAAAAAAAACTTATAATTTAATCACTACCCATTAAAATTTTTCGACAAACTTTT
29707735 CCACCAATCAAAATTCT
326 CCACCAATCAAAATTCT
29707752 CCTTCATTCT
Statistics
Matches: 341, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
341 332 0.97
342 9 0.03
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (342 bp):
AAGCAAGTCAATGAAGATTGTATCAATTTTAGGATTAAATTATAATATTATCATATACTAATTTA
TTTATTTTATAAAATTTATAGCACCAAACATGCCATTTTTCATGGATGGAGAAAAGTGAGATATG
GGAAGACAGTTGCAAAATTTATGGGAAGATATCCTTTTTTAAAAATATATTAATTGATAATGAAA
TAAAAAATATTTGGATAAATTATCTAATTGGTGATCCAATTCTTTGGACGTTTTTATTTTAATTA
CTGAAATTTAAAAAAAAAAACTTATAATTTAATCACTACCCATTAAAATTTTTCGACAAACTTTT
CCACCAATCAAAATTCT
Found at i:29708315 original size:17 final size:17
Alignment explanation
Indices: 29708293--29708327 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29708283 AACAATTAAA
29708293 TAAATTGGAAATAAAAT
1 TAAATTGGAAATAAAAT
* *
29708310 TAAATTGGGAATTAAAT
1 TAAATTGGAAATAAAAT
29708327 T
1 T
29708328 CGGATTTTGT
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:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (17 bp):
TAAATTGGAAATAAAAT
Found at i:29714758 original size:26 final size:25
Alignment explanation
Indices: 29714729--29714779 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
29714719 AATTTTTAAT
29714729 ATAC-TTTATAATTTATATATACATAC
1 ATACATTTATAA--TATATATACATAC
29714755 ATACATTTTATAATATATATACATA
1 ATACA-TTTATAATATATATACATA
29714780 TACGTGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 16 0.70
28 7 0.30
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (25 bp):
ATACATTTATAATATATATACATAC
Found at i:29716434 original size:14 final size:14
Alignment explanation
Indices: 29716415--29716444 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29716405 ATGGATTCAA
29716415 ATCTAATGGTTGAC
1 ATCTAATGGTTGAC
29716429 ATCTAATGGTTGAC
1 ATCTAATGGTTGAC
29716443 AT
1 AT
29716445 TTTGGTAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (14 bp):
ATCTAATGGTTGAC
Found at i:29716578 original size:26 final size:27
Alignment explanation
Indices: 29716544--29716606 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
29716534 ATAAAAAATA
29716544 ACCAAAATATTATAAA-TTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
29716570 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
29716597 ACCAAAATAT
1 ACCAAAATAT
29716607 ACAAAAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 16 0.44
27 20 0.56
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:29716686 original size:27 final size:27
Alignment explanation
Indices: 29716656--29716734 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
29716646 GGCCAATCAC
*
29716656 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
29716683 ATTGGCGGCACCAATGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
*
29716710 ATTGGCAGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
29716735 GACTAAAATG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.32, C:0.23, G:0.32, T:0.14
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:29717010 original size:20 final size:20
Alignment explanation
Indices: 29716985--29717022 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29716975 ATTTTATTAT
29716985 TAAAGTAAATA-TATTTTACC
1 TAAAGTAAA-ACTATTTTACC
29717005 TAAAGTAAAACTATTTTA
1 TAAAGTAAAACTATTTTA
29717023 AAAAGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (20 bp):
TAAAGTAAAACTATTTTACC
Found at i:29717949 original size:26 final size:27
Alignment explanation
Indices: 29717920--29717979 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 27
29717910 TTTTTTTAGT
29717920 ATATTTTGATAAATAAAAAAA-TTATA
1 ATATTTTGATAAATAAAAAAATTTATA
*
29717946 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTGATAAATAAAAAAATTTATA
29717973 ATATTTT
1 ATATTTT
29717980 AGTTATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 20 0.62
27 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (27 bp):
ATATTTTGATAAATAAAAAAATTTATA
Found at i:29723629 original size:113 final size:113
Alignment explanation
Indices: 29723431--29723654 Score: 430
Period size: 113 Copynumber: 2.0 Consensus size: 113
29723421 AAAACCTGCA
29723431 AAAGATTGTTCTCGCGTATTGTGTAAAACTGATAAACATTGACAAGTCAGTTGGTACTTTAATTT
1 AAAGATTGTTCTCGCGTATTGTGTAAAACTGATAAACATTGACAAGTCAGTTGGTACTTTAATTT
29723496 CCTTGCACCACTTGGATATGACAGGCTGTTTAAACCTTGTTGAATTCG
66 CCTTGCACCACTTGGATATGACAGGCTGTTTAAACCTTGTTGAATTCG
*
29723544 AAAGATTGTTCTTGCGTATTGTGTAAAACTGATAAACATTGACAAGTCAGTTGGTACTTTAATTT
1 AAAGATTGTTCTCGCGTATTGTGTAAAACTGATAAACATTGACAAGTCAGTTGGTACTTTAATTT
*
29723609 CCTTGCGCCACTTGGATATGACAGGCTGTTTAAACCTTGTTGAATT
66 CCTTGCACCACTTGGATATGACAGGCTGTTTAAACCTTGTTGAATT
29723655 TCCAAGTGAT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (113 bp):
AAAGATTGTTCTCGCGTATTGTGTAAAACTGATAAACATTGACAAGTCAGTTGGTACTTTAATTT
CCTTGCACCACTTGGATATGACAGGCTGTTTAAACCTTGTTGAATTCG
Found at i:29728529 original size:23 final size:23
Alignment explanation
Indices: 29728503--29728548 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
29728493 AAATCACTGG
29728503 GCTGTTAAATCTTTTTTAAGCCT
1 GCTGTTAAATCTTTTTTAAGCCT
29728526 GCTGTTAAATCTTTTTTAAGCCT
1 GCTGTTAAATCTTTTTTAAGCCT
29728549 AGTCAGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (23 bp):
GCTGTTAAATCTTTTTTAAGCCT
Found at i:29736012 original size:20 final size:20
Alignment explanation
Indices: 29735971--29736014 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29735961 AAAATATTAA
*
29735971 AAAATTGTAAAAAGATCTTT
1 AAAATTGTAAAAAGATCGTT
*
29735991 AAAATTGTACAAAA-ATGGTT
1 AAAATTGTA-AAAAGATCGTT
29736011 AAAA
1 AAAA
29736015 ATGAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (20 bp):
AAAATTGTAAAAAGATCGTT
Found at i:29740646 original size:17 final size:17
Alignment explanation
Indices: 29740606--29740647 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
29740596 ATAAATAAAC
*
29740606 AATT-AATTAAATTTGA
1 AATTAAATTAAATTGGA
* *
29740622 AATAAAATTAAATTGGG
1 AATTAAATTAAATTGGA
29740639 AATTAAATT
1 AATTAAATT
29740648 TGGATTTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (17 bp):
AATTAAATTAAATTGGA
Found at i:29745450 original size:15 final size:15
Alignment explanation
Indices: 29745430--29745459 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29745420 GTCATATCCC
29745430 AAAAATTGGGTTAGT
1 AAAAATTGGGTTAGT
29745445 AAAAATTGGGTTAGT
1 AAAAATTGGGTTAGT
29745460 GAATTGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (15 bp):
AAAAATTGGGTTAGT
Found at i:29771867 original size:1 final size:1
Alignment explanation
Indices: 29771861--29771886 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
29771851 CTGAGACTTC
29771861 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
29771887 CAGACTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29772757 original size:10 final size:10
Alignment explanation
Indices: 29772742--29772769 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
29772732 CTTATTAATA
29772742 CATAATTTAT
1 CATAATTTAT
29772752 CATAATTTAT
1 CATAATTTAT
29772762 CATAATTT
1 CATAATTT
29772770 TATGGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (10 bp):
CATAATTTAT
Found at i:29773813 original size:31 final size:31
Alignment explanation
Indices: 29773770--29773831 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
29773760 GCGAATCGAA
29773770 GGAGCACAAAGAGTACGAGAAAGAAAAACCC
1 GGAGCACAAAGAGTACGAGAAAGAAAAACCC
*
29773801 GGAGCACGAAGAGTACGAGAAAGAAAAACCC
1 GGAGCACAAAGAGTACGAGAAAGAAAAACCC
29773832 AATTTCCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.50, C:0.19, G:0.27, T:0.03
Consensus pattern (31 bp):
GGAGCACAAAGAGTACGAGAAAGAAAAACCC
Found at i:29774904 original size:27 final size:27
Alignment explanation
Indices: 29774759--29774911 Score: 95
Period size: 27 Copynumber: 5.8 Consensus size: 27
29774749 AAATATATTA
*
29774759 AAATT-TTAATTATACTAATTTAATTT
1 AAATTCTTAATTATCCTAATTTAATTT
* * ** *
29774785 AAATTATTAATTATCTTAACTAAAATCTA
1 AAATTCTTAATTATCCTAA-TTTAAT-TT
* *
29774814 AAATT-TTATTTAACCT-A-TTAA-TT
1 AAATTCTTAATTATCCTAATTTAATTT
* * * *
29774837 AAATTCCTAATTAT-CTTATCTAAATTA
1 AAATTCTTAATTATCCTAAT-TTAATTT
* *
29774864 AAAATC-TAAATATCCTAATTTAATTT
1 AAATTCTTAATTATCCTAATTTAATTT
*
29774890 AAATTCTTAATTATCTTAATTT
1 AAATTCTTAATTATCCTAATTT
29774912 GTAACCTCCT
Statistics
Matches: 93, Mismatches: 24, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
23 8 0.09
24 6 0.06
25 2 0.02
26 24 0.26
27 35 0.38
28 12 0.13
29 6 0.06
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (27 bp):
AAATTCTTAATTATCCTAATTTAATTT
Found at i:29778096 original size:54 final size:54
Alignment explanation
Indices: 29778033--29778141 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
29778023 AACCATATCA
*
29778033 TATACAATCATTCAAACCATGCCCAATTTTAAAAATTAACAAATCAATTAATGT
1 TATACAATCATTCAAACCATGCCCAATTTGAAAAATTAACAAATCAATTAATGT
* * * *
29778087 TATACAATCATTCATACCATGCCCAATTTGCAAAATTAACAACTCAATTCATGT
1 TATACAATCATTCAAACCATGCCCAATTTGAAAAATTAACAAATCAATTAATGT
29778141 T
1 T
29778142 CACATAATTC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (54 bp):
TATACAATCATTCAAACCATGCCCAATTTGAAAAATTAACAAATCAATTAATGT
Found at i:29782169 original size:18 final size:18
Alignment explanation
Indices: 29782148--29782185 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29782138 ATTTTTTTAG
29782148 TTTTCTATTTCTTTTATC
1 TTTTCTATTTCTTTTATC
* *
29782166 TTTTCTTTTTCTTTTTTC
1 TTTTCTATTTCTTTTATC
29782184 TT
1 TT
29782186 GTTTGTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCTATTTCTTTTATC
Found at i:29782194 original size:18 final size:18
Alignment explanation
Indices: 29782148--29782194 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
29782138 ATTTTTTTAG
*
29782148 TTTTCTATTTCTTTTATC
1 TTTTCTGTTTCTTTTATC
* *
29782166 TTTTCTTTTTCTTTTTTC
1 TTTTCTGTTTCTTTTATC
29782184 TTGTT-TGTTTC
1 TT-TTCTGTTTC
29782195 CATTAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTTCTGTTTCTTTTATC
Found at i:29784918 original size:54 final size:54
Alignment explanation
Indices: 29784855--29784963 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
29784845 AACCATATCA
*
29784855 TATACAATCATTCAAACCATGCCCAATTTTAAAAATTAACAAATCAATTAATGT
1 TATACAATCATTCAAACCATGCCCAATTTGAAAAATTAACAAATCAATTAATGT
* * * * *
29784909 TATACAATCATTCATACCATGCCTAATTTGCAAAATTAACAACTCAATTCATGT
1 TATACAATCATTCAAACCATGCCCAATTTGAAAAATTAACAAATCAATTAATGT
29784963 T
1 T
29784964 CACATAATTC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (54 bp):
TATACAATCATTCAAACCATGCCCAATTTGAAAAATTAACAAATCAATTAATGT
Found at i:29796592 original size:168 final size:168
Alignment explanation
Indices: 29796314--29796654 Score: 558
Period size: 168 Copynumber: 2.0 Consensus size: 168
29796304 CTGCAAACAG
*
29796314 CATGAAGAGTACCACGAGTCACACGAATCAAAGGAGCACAAAGAGTACGAGAAAGAAAAACCCGA
1 CATGAAGAGTACCACGAATCACACGAATCAAAGGAGCACAAAGAGTACGAGAAAGAAAAACCCGA
* *
29796379 GTTCCCCAAATGGGAAAAGCCTAAAGAGCACGAGAAACACGAAGTCGAATATCCGAAAATACCCG
66 GTTCCCCAAATGAGAAAAGCCTAAAGAGCACCAGAAACACGAAGTCGAATATCCGAAAATACCCG
* *
29796444 AGTACAAGGTAAAA-CAAGATGAGGGCAAGGAACATAAA
131 AATACAA-GAAAAAGCAAGATGAGGGCAAGGAACATAAA
* * *
29796482 CATGAAGAGTACCACGAATCACGCGAATCGAAGGAGCACGAAGAGTACGAGAAAGAAAAACCCGA
1 CATGAAGAGTACCACGAATCACACGAATCAAAGGAGCACAAAGAGTACGAGAAAGAAAAACCCGA
* * *
29796547 GTTCCCTAAATTAGAAAAGCCTAAAGAGCACCAGAAACACGAAGTCGAATATCCGGAAATACCCG
66 GTTCCCCAAATGAGAAAAGCCTAAAGAGCACCAGAAACACGAAGTCGAATATCCGAAAATACCCG
*
29796612 AATACAAGAAAAAGCAAGATGAGGGTAAGGAACATAAA
131 AATACAAGAAAAAGCAAGATGAGGGCAAGGAACATAAA
29796650 CATGA
1 CATGA
29796655 GTTCCCAAAG
Statistics
Matches: 160, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
167 5 0.03
168 155 0.97
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (168 bp):
CATGAAGAGTACCACGAATCACACGAATCAAAGGAGCACAAAGAGTACGAGAAAGAAAAACCCGA
GTTCCCCAAATGAGAAAAGCCTAAAGAGCACCAGAAACACGAAGTCGAATATCCGAAAATACCCG
AATACAAGAAAAAGCAAGATGAGGGCAAGGAACATAAA
Found at i:29797484 original size:27 final size:26
Alignment explanation
Indices: 29797454--29797602 Score: 94
Period size: 27 Copynumber: 5.6 Consensus size: 26
29797444 TATTAAAATT
29797454 TTAATTATACTAATTTAATTTAAACTC
1 TTAATTAT-CTAATTTAATTTAAACTC
* *
29797481 TTAATTATC---TTTAA-CTAAAATC
1 TTAATTATCTAATTTAATTTAAACTC
* *
29797503 TATAATTTTATTTAACCTATTAA-TTAAATTC
1 T-TAA--TTATCTAA--T-TTAATTTAAACTC
* * *
29797534 CTAATTATCTTATCTAATTTAAAACTC
1 TTAATTATCTAATTTAATTT-AAACTC
*
29797561 -TAATTATCCTAATTTAATTTAAATTC
1 TTAATTAT-CTAATTTAATTTAAACTC
29797587 TTAATTATCTTAATTT
1 TTAATTATC-TAATTT
29797603 GTAACCTCCT
Statistics
Matches: 95, Mismatches: 13, Indels: 28
0.70 0.10 0.21
Matches are distributed among these distances:
22 7 0.07
23 8 0.08
25 7 0.07
26 17 0.18
27 36 0.38
28 6 0.06
30 4 0.04
31 10 0.11
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAATTATCTAATTTAATTTAAACTC
Found at i:29797508 original size:23 final size:22
Alignment explanation
Indices: 29797474--29797518 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
29797464 TAATTTAATT
* *
29797474 TAAACTCTTAATTATCTTTAAC
1 TAAAATCTTAATTATATTTAAC
*
29797496 TAAAATCTATAATTTTATTTAAC
1 TAAAATCT-TAATTATATTTAAC
29797519 CTATTAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAATCTTAATTATATTTAAC
Found at i:29797583 original size:53 final size:54
Alignment explanation
Indices: 29797446--29797599 Score: 172
Period size: 53 Copynumber: 2.9 Consensus size: 54
29797436 TTTAAATATA
* *
29797446 TTAAAATTTTAATTATACTAATTTAATTTAAACTCTTAATTATCTTTAACTAAAAT
1 TTAAAATTTTAATTATCCTAATTTAATTTAAATTCTTAATTATC-TTAACT-AAAT
* * * * * *
29797502 CTATAATTTTATTTAACCT-A-TTAA-TTAAATTCCTAATTATCTTATCT-AAT
1 TTAAAATTTTAATTATCCTAATTTAATTTAAATTCTTAATTATCTTAACTAAAT
* *
29797552 TTAAAACTCTAATTATCCTAATTTAATTTAAATTCTTAATTATCTTAA
1 TTAAAATTTTAATTATCCTAATTTAATTTAAATTCTTAATTATCTTAA
29797600 TTTGTAACCT
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
50 16 0.20
51 1 0.01
52 9 0.11
53 34 0.43
54 4 0.05
55 1 0.01
56 14 0.18
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (54 bp):
TTAAAATTTTAATTATCCTAATTTAATTTAAATTCTTAATTATCTTAACTAAAT
Found at i:29802040 original size:27 final size:27
Alignment explanation
Indices: 29802005--29802081 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 27
29801995 CTCCATTGCC
* *
29802005 ACCAATACCATTGCCACCTCCATCTTT
1 ACCAGTACCATTGCCACCTCCATATTT
* ** *
29802032 ACTAGTACCATTGCCATTTGCATATTT
1 ACCAGTACCATTGCCACCTCCATATTT
*
29802059 ACCGGTACCATTGCCACCTCCAT
1 ACCAGTACCATTGCCACCTCCAT
29802082 TGTCACCACT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.25, C:0.35, G:0.09, T:0.31
Consensus pattern (27 bp):
ACCAGTACCATTGCCACCTCCATATTT
Found at i:29803883 original size:9 final size:9
Alignment explanation
Indices: 29803851--29803921 Score: 51
Period size: 9 Copynumber: 8.1 Consensus size: 9
29803841 CAAAATTATT
29803851 TTAT-AAAA
1 TTATAAAAA
29803859 -TATAAAAA
1 TTATAAAAA
**
29803867 TTGCAAAAA
1 TTATAAAAA
29803876 TTAT-AAAA
1 TTATAAAAA
29803884 -TATATAAAA
1 TTATA-AAAA
* *
29803893 TTACAAATA
1 TTATAAAAA
*
29803902 TATATATAAA
1 T-TATAAAAA
29803912 TTATAAAAA
1 TTATAAAAA
29803921 T
1 T
29803922 GATTATAGAC
Statistics
Matches: 47, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
7 6 0.13
8 8 0.17
9 24 0.51
10 9 0.19
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:29803907 original size:27 final size:26
Alignment explanation
Indices: 29803851--29803919 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 26
29803841 CAAAATTATT
*
29803851 TTATAAAATATA-AAAATTGCAAAAA
1 TTATAAAATATATAAAATTACAAAAA
*
29803876 TTATAAAATATATAAAATTACAAATA
1 TTATAAAATATATAAAATTACAAAAA
29803902 TATATATAAAT-TATAAAA
1 T-TATA-AAATATATAAAA
29803920 ATGATTATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 12 0.31
26 12 0.31
27 11 0.28
28 4 0.10
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (26 bp):
TTATAAAATATATAAAATTACAAAAA
Found at i:29804079 original size:28 final size:28
Alignment explanation
Indices: 29804048--29804136 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
29804038 ACTAAAAAAT
*
29804048 AAAAATGGTAAAAAAATTAAAATATTTA
1 AAAAATAGTAAAAAAATTAAAATATTTA
*** *
29804076 AAAACATAG-AAAGTTATTAAAATATTTT
1 AAAA-ATAGTAAAAAAATTAAAATATTTA
* *
29804104 AAAAATACT-AAAACATATAAAATATTATA
1 AAAAATAGTAAAAAAAT-TAAAATATT-TA
29804133 AAAA
1 AAAA
29804137 GCATAAAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
27 7 0.15
28 32 0.68
29 8 0.17
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.29
Consensus pattern (28 bp):
AAAAATAGTAAAAAAATTAAAATATTTA
Found at i:29804143 original size:28 final size:27
Alignment explanation
Indices: 29804063--29804144 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 27
29804053 TGGTAAAAAA
**
29804063 ATTAAAATATTTAAAAACATAGAAAGTT
1 ATTAAAATATTTAAAAACATA-AAACAT
*
29804091 ATTAAAATATTTTAAAAATACTAAAACAT
1 ATTAAAATA-TTTAAAAACA-TAAAACAT
29804120 A-TAAAATATTATAAAAAGCATAAAA
1 ATTAAAATATT-TAAAAA-CATAAAA
29804145 TTTATAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.04
28 27 0.59
29 15 0.33
30 2 0.04
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (27 bp):
ATTAAAATATTTAAAAACATAAAACAT
Found at i:29805677 original size:14 final size:14
Alignment explanation
Indices: 29805655--29805688 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29805645 CACTTTATTT
29805655 TATTT-TTTATATA
1 TATTTATTTATATA
*
29805668 TATTTATTTATTTA
1 TATTTATTTATATA
29805682 TATTTAT
1 TATTTAT
29805689 ATATTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTATTTATATA
Found at i:29805681 original size:18 final size:17
Alignment explanation
Indices: 29805653--29805696 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
29805643 TTCACTTTAT
29805653 TTTATTTTTTATATATA
1 TTTATTTTTTATATATA
*
29805670 TTTATTTATTTATATTTA
1 TTTATTT-TTTATATATA
*
29805688 TATATTTTT
1 TTTATTTTT
29805697 GTTCACTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTTTTATATATA
Found at i:29810925 original size:12 final size:13
Alignment explanation
Indices: 29810897--29810941 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
29810887 TTTGATAATT
*
29810897 TGTTTTCAAGATA
1 TGTTTTAAAGATA
*
29810910 TGTTTT-AAGCTA
1 TGTTTTAAAGATA
29810922 TGTTTTAAAGATA
1 TGTTTTAAAGATA
29810935 TGTTTTA
1 TGTTTTA
29810942 CGTATGCTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (13 bp):
TGTTTTAAAGATA
Found at i:29811543 original size:18 final size:18
Alignment explanation
Indices: 29811520--29811554 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29811510 GGGTCTCGCA
29811520 CATTCACTGCGAACCCAG
1 CATTCACTGCGAACCCAG
29811538 CATTCACTGCGAACCCA
1 CATTCACTGCGAACCCA
29811555 ACACGCGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.40, G:0.14, T:0.17
Consensus pattern (18 bp):
CATTCACTGCGAACCCAG
Found at i:29812481 original size:196 final size:196
Alignment explanation
Indices: 29812135--29812494 Score: 567
Period size: 196 Copynumber: 1.8 Consensus size: 196
29812125 TTTTGTTTGA
* * * * *
29812135 TAAGGTTGCATGATTTACATTCTATATGTGATATTATTTCACTGTTATGCTATAACTTATCATAA
1 TAAGCTTGCATGATTTACATTATATATATGATATTATTCCACTGTTATGATATAACTTATCATAA
* * * *
29812200 CATACGTTGCAAGTAAGTGGTGTGTTGGAGGTTAGGTTGGGAGTTGATGGAGAGTCACTTCGGTG
66 CATACGTTGCAAGTAAGTGGTGTGTTAGAGGTTAGATTGGGAGTTAATGGAAAGTCACTTCGGTG
* *
29812265 GCTAATGTAACTCTCCAAATTTGGGTCGAACCTACTCAGCCGGGTTTTGGGGTGTTACATTGGTT
131 GCTAATGTAACTCGCCAAATTTAGGTCGAACCTACTCAGCCGGGTTTTGGGGTGTTACATTGGTT
29812330 T
196 T
* * * *
29812331 TAAGCTTGCATGATTTACATTATATGTATTATATTATTCCATTGTTATTATATAACTTATCATAA
1 TAAGCTTGCATGATTTACATTATATATATGATATTATTCCACTGTTATGATATAACTTATCATAA
*
29812396 TATACGTTGCAAGTAAGTGGTGTGTTAGAGGTTAGATTGGGAGTTAATGGAAAGTCACTTCGGTG
66 CATACGTTGCAAGTAAGTGGTGTGTTAGAGGTTAGATTGGGAGTTAATGGAAAGTCACTTCGGTG
*
29812461 GCTAATGTAGCTCGCCAAATTTAGGTCGAACCTA
131 GCTAATGTAACTCGCCAAATTTAGGTCGAACCTA
29812495 TTCGACTGAG
Statistics
Matches: 147, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
196 147 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (196 bp):
TAAGCTTGCATGATTTACATTATATATATGATATTATTCCACTGTTATGATATAACTTATCATAA
CATACGTTGCAAGTAAGTGGTGTGTTAGAGGTTAGATTGGGAGTTAATGGAAAGTCACTTCGGTG
GCTAATGTAACTCGCCAAATTTAGGTCGAACCTACTCAGCCGGGTTTTGGGGTGTTACATTGGTT
T
Found at i:29815281 original size:54 final size:54
Alignment explanation
Indices: 29815199--29815393 Score: 253
Period size: 54 Copynumber: 3.7 Consensus size: 54
29815189 AAGTAACTAC
* * *
29815199 TCTTCCACCATTTCCTAGAGTACCAATTCCACCACTTCCTAACCTTACCCCCAT
1 TCTTCCACCACTTCCCAGATTACCAATTCCACCACTTCCTAACCTTACCCCCAT
* *
29815253 TCTTCCACCACTTCCTAG-TGTACCAATTCCACCACTTCCTAGA--GTA---CCA-
1 TCTTCCACCACTTCCCAGAT-TACCAATTCCACCACTTCCTA-ACCTTACCCCCAT
*
29815302 -ATTCCACCACTTCCCAGATTACCAATTCCACCACTTCCTAACCTTACCCCCAT
1 TCTTCCACCACTTCCCAGATTACCAATTCCACCACTTCCTAACCTTACCCCCAT
*
29815355 TCTTCCACCACTTCCCAGCTTACCAATTCCACCACTTCC
1 TCTTCCACCACTTCCCAGATTACCAATTCCACCACTTCC
29815394 CAGCTTACCA
Statistics
Matches: 123, Mismatches: 8, Indels: 20
0.81 0.05 0.13
Matches are distributed among these distances:
47 1 0.01
48 36 0.29
49 3 0.02
50 3 0.02
52 3 0.02
53 2 0.02
54 74 0.60
55 1 0.01
ACGTcount: A:0.24, C:0.44, G:0.04, T:0.28
Consensus pattern (54 bp):
TCTTCCACCACTTCCCAGATTACCAATTCCACCACTTCCTAACCTTACCCCCAT
Found at i:29815286 original size:24 final size:23
Alignment explanation
Indices: 29815201--29815418 Score: 166
Period size: 24 Copynumber: 8.6 Consensus size: 23
29815191 GTAACTACTC
* *
29815201 TTCCACCATTTCCTAGAGTACCAA
1 TTCCACCACTTCCTAG-TTACCAA
* *
29815225 TTCCACCACTTCCTAACCTTACCCCCATTC
1 TTCCACCACTTCCT-A-GTTA---CCA--A
29815255 TTCCACCACTTCCTAGTGTACCAA
1 TTCCACCACTTCCTAGT-TACCAA
*
29815279 TTCCACCACTTCCTAGAGTACCAA
1 TTCCACCACTTCCTAG-TTACCAA
*
29815303 TTCCACCACTTCCCAGATTACCAA
1 TTCCACCACTTCCTAG-TTACCAA
* *
29815327 TTCCACCACTTCCTAACCTTACCCCCATTC
1 TTCCACCACTTCCT-A-GTTA---CCA--A
*
29815357 TTCCACCACTTCCCAGCTTACCAA
1 TTCCACCACTTCCTAG-TTACCAA
*
29815381 TTCCACCACTTCCCAGCTTACCAA
1 TTCCACCACTTCCTAG-TTACCAA
29815405 TTCCACCACTTCCT
1 TTCCACCACTTCCT
29815419 CCTATATTGC
Statistics
Matches: 161, Mismatches: 16, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
24 107 0.66
25 7 0.04
26 6 0.04
28 7 0.04
29 7 0.04
30 27 0.17
ACGTcount: A:0.24, C:0.44, G:0.04, T:0.28
Consensus pattern (23 bp):
TTCCACCACTTCCTAGTTACCAA
Found at i:29815379 original size:102 final size:102
Alignment explanation
Indices: 29815201--29815417 Score: 355
Period size: 102 Copynumber: 2.1 Consensus size: 102
29815191 GTAACTACTC
* *
29815201 TTCCACCATTTCCTAGAGTACCAATTCCACCACTTCCTAACCTTACCCCCATTCTTCCACCACTT
1 TTCCACCACTTCCCAGAGTACCAATTCCACCACTTCCTAACCTTACCCCCATTCTTCCACCACTT
* *
29815266 CCTAGTGTACCAATTCCACCACTTCCTAGAGTACCAA
66 CCCAGTGTACCAATTCCACCACTTCCCAGAGTACCAA
*
29815303 TTCCACCACTTCCCAGATTACCAATTCCACCACTTCCTAACCTTACCCCCATTCTTCCACCACTT
1 TTCCACCACTTCCCAGAGTACCAATTCCACCACTTCCTAACCTTACCCCCATTCTTCCACCACTT
**
29815368 CCCAGCT-TACCAATTCCACCACTTCCCAGCTTACCAA
66 CCCAG-TGTACCAATTCCACCACTTCCCAGAGTACCAA
29815405 TTCCACCACTTCC
1 TTCCACCACTTCC
29815418 TCCTATATTG
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 106 0.99
103 1 0.01
ACGTcount: A:0.24, C:0.44, G:0.04, T:0.28
Consensus pattern (102 bp):
TTCCACCACTTCCCAGAGTACCAATTCCACCACTTCCTAACCTTACCCCCATTCTTCCACCACTT
CCCAGTGTACCAATTCCACCACTTCCCAGAGTACCAA
Found at i:29818083 original size:74 final size:73
Alignment explanation
Indices: 29817980--29818122 Score: 232
Period size: 74 Copynumber: 1.9 Consensus size: 73
29817970 TCTTTTCAAA
* * * *
29817980 CTCAAGTTTTAAACGATCTTGAGAATTAAGAAGAGATCGTGTCCTAACTTATTGGGCATGATCCT
1 CTCAAGTTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
29818045 TTTTTTTC
66 TTTTTTTC
*
29818053 CTCAAGTTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
1 CTCAAG-TTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
29818118 CTTTT
65 CTTTT
29818123 CTAAACTCAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
73 6 0.09
74 58 0.91
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (73 bp):
CTCAAGTTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
TTTTTTTC
Found at i:29823451 original size:24 final size:24
Alignment explanation
Indices: 29823419--29823476 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
29823409 GTCCCCAGAG
* *
29823419 ATTACAGTGGATTGAACTTTGAAA
1 ATTACAGTGGATCGAACATTGAAA
* *
29823443 ATTACAGTGGATCGGACATTGAAT
1 ATTACAGTGGATCGAACATTGAAA
29823467 ATTACAGTGG
1 ATTACAGTGG
29823477 GGGCAAGCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (24 bp):
ATTACAGTGGATCGAACATTGAAA
Found at i:29823837 original size:50 final size:50
Alignment explanation
Indices: 29823784--29824456 Score: 452
Period size: 50 Copynumber: 13.3 Consensus size: 50
29823774 CCACAATGGT
* * * * **
29823784 GAATCTTACTTCCCTGGTGGTGCAGTAGAATAGATTGAAGCTACAACAAT
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
* * * * * ** * *
29823834 GAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGGC
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
* * * *
29823884 GAATCTTACTTCCCAGGCGGTGTAGTGGAACAGATTGAAGCTACAA-AGGC
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACA-GC
* * * * **
29823934 GAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCTACAACAGC
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
* ** * * * * * *
29823984 GGATCTTACTTTTCTGGTGGTGTAGTGGAACAGATTGAAGCTACAACGGT
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
* * * * * ** *
29824034 GAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTGAAGCTACAACAAC
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
* * * * * * * * * *
29824084 GGATATTATTTTCCTGGCGGTGTAGTGGAATAGATTAAAGCCACAACGGC
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
* * * * ** *
29824134 GAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTGAAGCTACAACAGT
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
* * * * * * *
29824184 GGATTTTACTTTCCTGGCGGTACAGTGGAACAGATTGAAGCTACAACAGT
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
*** * * ** *
29824234 GAATCTTACTTCCCCAACATTGTAGTTAAAAAGATTGAAGCTACGACAGC
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
* * *
29824284 GAATCTTACCTCCCTGGCGTTGCAGTGGAACAGATTGAAGCTACAATAGC
1 GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
* * * * * *
29824334 GAATCTTACTCCCCTGACGAACCTTACTTCCA-TGGCACAGATTGAAGCTACAACGGC
1 GAATCTTACTTCCCTG--G---C---GTTGCAGTGGAAAAGATTGAAGCTACAACAGC
* * * *
29824391 TAATCTT-GTTGGCCTGGCGTTGCAGTGGAACAGATTGAAGCTACAACAGC
1 GAATCTTACTT-CCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
29824441 GAATCTTACTTCCCTG
1 GAATCTTACTTCCCTG
29824457 ACAAACCTTA
Statistics
Matches: 451, Mismatches: 159, Indels: 26
0.71 0.25 0.04
Matches are distributed among these distances:
49 4 0.01
50 403 0.89
51 3 0.01
52 2 0.00
55 2 0.00
56 1 0.00
57 32 0.07
58 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (50 bp):
GAATCTTACTTCCCTGGCGTTGCAGTGGAAAAGATTGAAGCTACAACAGC
Found at i:29823926 original size:100 final size:100
Alignment explanation
Indices: 29823753--29824459 Score: 718
Period size: 100 Copynumber: 7.0 Consensus size: 100
29823743 ACCCCTGATG
* * * ** * * * *
29823753 TTGCAATTAAAAATATTAAAGCCACAATGGTGAATCTTACTTCCCTGGTGGTGCAGTAGAATAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
*
29823818 TTGAAGCTACAACAATGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACAGTGAATCTTGCTTCCCCGACA
* * * *
29823853 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGGTGTAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* *
29823918 TTGAAGCTACAA-AGGCGAATCTTGCTTCCCTGACA
66 TTGAAGCTACAACA-GTGAATCTTGCTTCCCCGACA
* * ** * *
29823953 TTGCAATTTAAAAGATTGAAGCTACAACAGCGGATCTTACTTTTCTGGTGGTGTAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
*
29824018 TTGAAGCTACAACGGTGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACAGTGAATCTTGCTTCCCCGACA
* * * * * * * *
29824053 TTGCAATTTAAAAGATTGAAGCTACAACAACGGATATTATTTTCCTGGCGGTGTAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* * * *
29824118 TTAAAGCCACAACGGCGAATCTTGCTTCCCCGACA
66 TTGAAGCTACAACAGTGAATCTTGCTTCCCCGACA
* * * * * *
29824153 TTGCAGTTAAAAAGATTGAAGCTACAACAGTGGATTTTACTTTCCTGGCGGTACAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* *
29824218 TTGAAGCTACAACAGTGAATCTTACTTCCCCAACA
66 TTGAAGCTACAACAGTGAATCTTGCTTCCCCGACA
* * * * *
29824253 TTGTAGTTAAAAAGATTGAAGCTACGACAGCGAATCTTACCTCCCTGGCGTTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
* * *
29824318 TTGAAGCTACAATAGCGAATCTTAC-TCCCCTGACGAA
66 TTGAAGCTACAACAGTGAATCTTGCTTCCCC-GAC--A
* * *** * * * * * *
29824355 CCTTACTTCCATGGCACAGATTGAAGCTACAACGGCTAATCTT-GTTGGCCTGGCGTTGCAGTGG
1 ---T--TGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTT-CCCTGGCGGTGCAGTGG
* * *
29824419 AACAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACA
60 AACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACA
29824460 AACCTTATTT
Statistics
Matches: 520, Mismatches: 75, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
99 6 0.01
100 431 0.83
102 1 0.00
105 2 0.00
106 1 0.00
107 75 0.14
108 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGA
TTGAAGCTACAACAGTGAATCTTGCTTCCCCGACA
Found at i:29826586 original size:74 final size:73
Alignment explanation
Indices: 29826396--29826611 Score: 351
Period size: 73 Copynumber: 2.9 Consensus size: 73
29826386 TCTTTTCAAA
* *
29826396 CTCAAGTTTTAAACGATATTGGGAATTAAGAAGAGATAGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATATTGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
29826461 TTTTTTTC
66 TTTTTTTC
* * *
29826469 CTCAAGTTTTAAACGATCTTGGGAATTAAGAAAAGATCATGTCCTAACTTACCGGGCATGATCCC
1 CTCAAGTTTTAAACGATATTGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
29826534 TTTTTTTC
66 TTTTTTTC
** *
29826542 CTCAAGTTTTTAAATAATATCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
1 CTCAAG-TTTTAAACGATATTGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
29826607 CTTTT
65 CTTTT
29826612 CTAAGCTCGA
Statistics
Matches: 131, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
73 74 0.56
74 57 0.44
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (73 bp):
CTCAAGTTTTAAACGATATTGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
TTTTTTTC
Found at i:29834488 original size:21 final size:20
Alignment explanation
Indices: 29834460--29834498 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
29834450 TTTGGGATTA
29834460 AAATATGAAAATGATAATCC
1 AAATATGAAAATGATAATCC
29834480 AAATGATGAAAATGATAAT
1 AAAT-ATGAAAATGATAAT
29834499 TATTTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (20 bp):
AAATATGAAAATGATAATCC
Found at i:29836820 original size:66 final size:64
Alignment explanation
Indices: 29836750--29836948 Score: 177
Period size: 66 Copynumber: 3.2 Consensus size: 64
29836740 AAATATATTT
29836750 AATATTAATTATTTCAAATTATCTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAA
29836815 G
64 G
* * * * * **
29836816 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAG
* * *
29836870 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAA
29836935 G
64 G
*
29836936 AATATTGATTATT
1 AATATTAATTATT
29836949 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAG
Found at i:29836852 original size:61 final size:61
Alignment explanation
Indices: 29836785--29836972 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
29836775 TTATAGTATA
29836785 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
29836846 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
29836904 C
61 T
*
29836905 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
29836966 ATATATT
1 ATATATT
29836973 TTAATTATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.17
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:29836872 original size:15 final size:15
Alignment explanation
Indices: 29836837--29836888 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29836827 TTAAGAATTT
*
29836837 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29836851 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29836865 TATTTAATAATAAT-
1 TATTTAATTATAATA
29836879 TATGTTAATT
1 TAT-TTAATT
29836889 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29836914 original size:120 final size:121
Alignment explanation
Indices: 29836712--29837009 Score: 501
Period size: 120 Copynumber: 2.5 Consensus size: 121
29836702 AATTATTTTA
* * * *
29836712 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTATATTT
29836776 TATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 TATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
29836832 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTATATTT
* *
29836896 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 TATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
29836952 AATTTTATTAAATTATATATTTTAATTATAATATATTTAACAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAAT
29837010 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 162 0.97
121 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (121 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTATATTT
TATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:29839881 original size:2 final size:2
Alignment explanation
Indices: 29839832--29839872 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29839822 TGGTGATGGT
29839832 TG TG TG TG TG TG 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 TG TG TG TG TG TG T
29839873 TAATGTGTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:29843355 original size:16 final size:16
Alignment explanation
Indices: 29843334--29843385 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
29843324 TTTGGTTCGC
29843334 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
29843350 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
29843366 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
29843382 TGTA
1 TGTA
29843386 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:29843432 original size:45 final size:44
Alignment explanation
Indices: 29843366--29843460 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
29843356 GGATTAGAGG
*
29843366 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
29843411 TGTAATGGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
29843455 TGTAAT
1 TGTAAT
29843461 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:29855115 original size:16 final size:16
Alignment explanation
Indices: 29855094--29855130 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
29855084 ACGAAATTGG
29855094 TTTAACC-AATTTGAAA
1 TTTAACCAAATTT-AAA
29855110 TTTAACCAAATTTAAA
1 TTTAACCAAATTTAAA
29855126 TTTAA
1 TTTAA
29855131 ATTATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.41
Consensus pattern (16 bp):
TTTAACCAAATTTAAA
Done.