Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 97 of 198
Found at i:31063700 original size:12 final size:12
Alignment explanation
Indices: 31063685--31063717 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
31063675 ATCACCACCA
31063685 TCATCATCATCG
1 TCATCATCATCG
*
31063697 TCATCGTCATCG
1 TCATCATCATCG
31063709 TCATCATCA
1 TCATCATCA
31063718 GAGTAGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.33
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:31072477 original size:8 final size:8
Alignment explanation
Indices: 31072460--31072490 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
31072450 AGGGTTCTTT
*
31072460 GTTTTTGA
1 GTTTTCGA
31072468 GTTTTCGA
1 GTTTTCGA
31072476 GTTTTCGA
1 GTTTTCGA
31072484 GTTTTCG
1 GTTTTCG
31072491 GGGTTTTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.10, G:0.26, T:0.55
Consensus pattern (8 bp):
GTTTTCGA
Found at i:31072780 original size:11 final size:11
Alignment explanation
Indices: 31072764--31072798 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
31072754 TTATATTACA
31072764 AAAAATCAAAT
1 AAAAATCAAAT
31072775 AAAAATCAAAT
1 AAAAATCAAAT
31072786 AAAAATCAAAT
1 AAAAATCAAAT
31072797 AA
1 AA
31072799 TCTAATTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATCAAAT
Found at i:31074580 original size:50 final size:50
Alignment explanation
Indices: 31074456--31074847 Score: 439
Period size: 50 Copynumber: 7.7 Consensus size: 50
31074446 GATAATAACA
* * ** * * *
31074456 TGCCAAAGCCATGTCCCAGACATGATCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * ** *
31074505 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
31074555 TGCCCATGCCATGTCCCAAACATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATATCGG
* * *
31074605 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
31074655 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTATTATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
31074705 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
31074755 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
31074811 TGCCAATTCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
31074848 TCTCATTCCC
Statistics
Matches: 296, Mismatches: 37, Indels: 13
0.86 0.11 0.04
Matches are distributed among these distances:
49 39 0.13
50 219 0.74
51 1 0.00
53 2 0.01
56 35 0.12
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:31075504 original size:31 final size:31
Alignment explanation
Indices: 31075469--31075535 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
31075459 AAATAAACAC
31075469 ATTTCATA-AAAATCAAAAGTTGTTTAACATA
1 ATTTCA-ACAAAATCAAAAGTTGTTTAACATA
***
31075500 ATTTCAAGCTTCATCAAAAGTTGTTTAACATA
1 ATTTCAA-CAAAATCAAAAGTTGTTTAACATA
31075532 ATTT
1 ATTT
31075536 TAAGCTTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 6 0.19
32 24 0.77
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (31 bp):
ATTTCAACAAAATCAAAAGTTGTTTAACATA
Found at i:31075517 original size:32 final size:32
Alignment explanation
Indices: 31075480--31075545 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
31075470 TTTCATAAAA
31075480 ATCAAAAGTTGTTTAACATAATTTCAAGCTTC
1 ATCAAAAGTTGTTTAACATAATTTCAAGCTTC
*
31075512 ATCAAAAGTTGTTTAACATAATTTTAAGCTTC
1 ATCAAAAGTTGTTTAACATAATTTCAAGCTTC
31075544 AT
1 AT
31075546 ACTCTACCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (32 bp):
ATCAAAAGTTGTTTAACATAATTTCAAGCTTC
Found at i:31077943 original size:219 final size:219
Alignment explanation
Indices: 31077564--31078003 Score: 799
Period size: 219 Copynumber: 2.0 Consensus size: 219
31077554 TGGCTTGCAA
*
31077564 AATAGCCCTTGAAGATTCCTTCAAATTTCATCCAAACCCTTCTACTATTTATGCCTTTATAGATT
1 AATAGCCCTTGAAGATTCCTTCAAATTTCATCCAAACCCGTCTACTATTTATGCCTTTATAGATT
31077629 TGCCCCTACCTTAAAATAGCAAGTTTGAAACCTTCAAACTTGCCACATGTGTGGCCAGTCATGGG
66 TGCCCCTACCTTAAAATAGCAAGTTTGAAACCTTCAAACTTGCCACATGTGTGGCCAGTCATGGG
31077694 GGGACTCCATGGCTGCTGATTTCTGCTAATTTTGGCGACCATCTCAACCTATAAATACCCCCAAT
131 GGGACTCCATGGCTGCTGATTTCTGCTAATTTTGGCGACCATCTCAACCTATAAATACCCCCAAT
*
31077759 GGCTGCTCACTTTAAACCCATCTC
196 GGCTGCTCACTTCAAACCCATCTC
* * *
31077783 AATAGCCTTTGAAGATTCCTTCAAATTTCATTCAAACCCGTCTACTATTTATGCCTTTCTAGATT
1 AATAGCCCTTGAAGATTCCTTCAAATTTCATCCAAACCCGTCTACTATTTATGCCTTTATAGATT
31077848 TGCCCCTACCTTAAAATAGCAAGTTTGAAACCTTCAAACTTGCCACATGTGTGGCCAGTCATGGG
66 TGCCCCTACCTTAAAATAGCAAGTTTGAAACCTTCAAACTTGCCACATGTGTGGCCAGTCATGGG
* * * *
31077913 GGGACTCTATGGCTGCTGATTTTTGCTAATTTTGGTGACCATCTCAACCTATAAATACCCCGAAT
131 GGGACTCCATGGCTGCTGATTTCTGCTAATTTTGGCGACCATCTCAACCTATAAATACCCCCAAT
31077978 GGCTGCTCACTTCAAACCCATCTC
196 GGCTGCTCACTTCAAACCCATCTC
31078002 AA
1 AA
31078004 CTCTTTTCAT
Statistics
Matches: 212, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
219 212 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (219 bp):
AATAGCCCTTGAAGATTCCTTCAAATTTCATCCAAACCCGTCTACTATTTATGCCTTTATAGATT
TGCCCCTACCTTAAAATAGCAAGTTTGAAACCTTCAAACTTGCCACATGTGTGGCCAGTCATGGG
GGGACTCCATGGCTGCTGATTTCTGCTAATTTTGGCGACCATCTCAACCTATAAATACCCCCAAT
GGCTGCTCACTTCAAACCCATCTC
Found at i:31085915 original size:25 final size:23
Alignment explanation
Indices: 31085882--31085941 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 23
31085872 AAATTTTCTC
* *
31085882 TTAAATTTTAATTTTATTTAATTA
1 TTAATTTTTAA-TTTATTGAATTA
31085906 TTTAATTTTTCAATTTATTGAATTA
1 -TTAATTTTT-AATTTATTGAATTA
31085931 TTAATATTTTA
1 TTAAT-TTTTA
31085942 TACTAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 6 0.19
25 23 0.74
26 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TTAATTTTTAATTTATTGAATTA
Found at i:31087704 original size:27 final size:28
Alignment explanation
Indices: 31087636--31087711 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
31087626 ATTTACTCTT
* *
31087636 AGGGGCATTACGGTCATTTTACCCTATA
1 AGGGGTATTATGGTCATTTTACCCTATA
* * * *
31087664 AGGGGTTTTTTGGTCATTTTAGCCTA-C
1 AGGGGTATTATGGTCATTTTACCCTATA
*
31087691 AGGGGTATTATGGTTATTTTA
1 AGGGGTATTATGGTCATTTTA
31087712 TAAATATTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.41
Consensus pattern (28 bp):
AGGGGTATTATGGTCATTTTACCCTATA
Found at i:31092114 original size:10 final size:10
Alignment explanation
Indices: 31092099--31092145 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
31092089 TAACATGCTG
31092099 AATTTTAATT
1 AATTTTAATT
31092109 AATTTTATAATT
1 AA-TTT-TAATT
*
31092121 AATTTTTATT
1 AATTTTAATT
*
31092131 AATTTTGATT
1 AATTTTAATT
31092141 AATTT
1 AATTT
31092146 CGACATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 20 0.61
11 6 0.18
12 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
AATTTTAATT
Found at i:31092121 original size:12 final size:11
Alignment explanation
Indices: 31092101--31092145 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 11
31092091 ACATGCTGAA
31092101 TTTTAATTAAT
1 TTTTAATTAAT
31092112 TTTATAATTAAT
1 TTT-TAATTAAT
31092124 TTTT-ATTAA-
1 TTTTAATTAAT
*
31092133 TTTTGATTAAT
1 TTTTAATTAAT
31092144 TT
1 TT
31092146 CGACATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.13
10 10 0.32
11 6 0.19
12 11 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TTTTAATTAAT
Found at i:31099719 original size:18 final size:17
Alignment explanation
Indices: 31099698--31099740 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
31099688 AAATCAAAAT
*
31099698 AAAATAGAAAATTTTAGA
1 AAAATAGAAAATTTT-CA
*
31099716 AAAACATGAAAATTTTCA
1 AAAATA-GAAAATTTTCA
31099734 AAAATAG
1 AAAATAG
31099741 GGGTTACACG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 11 0.52
19 9 0.43
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAATAGAAAATTTTCA
Found at i:31101554 original size:25 final size:25
Alignment explanation
Indices: 31101501--31101554 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
31101491 TACCGATGTC
* * *
31101501 AGCTCGTATGAGCTTATCGATACTC
1 AGCTCGCATGAGCTTACCGATACTA
* *
31101526 AGCTCGCATGAGCTTACCGTTATTA
1 AGCTCGCATGAGCTTACCGATACTA
31101551 AGCT
1 AGCT
31101555 TAGAGGAGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (25 bp):
AGCTCGCATGAGCTTACCGATACTA
Found at i:31104381 original size:20 final size:20
Alignment explanation
Indices: 31104277--31104382 Score: 74
Period size: 20 Copynumber: 5.3 Consensus size: 20
31104267 GTAGATGCGT
*
31104277 AACAGAGGCACCAAAGTG-A
1 AACAGAGGCATCAAAGTGTA
* * **
31104296 AGATAGAGGCATGATTGTGTA
1 A-ACAGAGGCATCAAAGTGTA
* * * *
31104317 ATA-AGAAGCATCGAACTGCA
1 A-ACAGAGGCATCAAAGTGTA
* *
31104337 AACAGAGACACCAAAGTGT-
1 AACAGAGGCATCAAAGTGTA
31104356 AACAGAGGCATCAAAGTGTA
1 AACAGAGGCATCAAAGTGTA
31104376 AACAGAG
1 AACAGAG
31104383 ACACTCAAGT
Statistics
Matches: 62, Mismatches: 21, Indels: 7
0.69 0.23 0.08
Matches are distributed among these distances:
19 19 0.31
20 40 0.65
21 3 0.05
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.14
Consensus pattern (20 bp):
AACAGAGGCATCAAAGTGTA
Found at i:31104393 original size:20 final size:21
Alignment explanation
Indices: 31104336--31104390 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
31104326 ATCGAACTGC
31104336 AAACAGAGACAC-CAAAGTGT
1 AAACAGAGACACTCAAAGTGT
*
31104356 -AACAGAGGCA-TCAAAGTGT
1 AAACAGAGACACTCAAAGTGT
31104375 AAACAGAGACACTCAA
1 AAACAGAGACACTCAA
31104391 GTGGAATCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 17 0.57
20 9 0.30
21 4 0.13
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (21 bp):
AAACAGAGACACTCAAAGTGT
Found at i:31107052 original size:13 final size:13
Alignment explanation
Indices: 31107034--31107058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31107024 TAATTTATAT
31107034 GTGTGAAAATTTC
1 GTGTGAAAATTTC
31107047 GTGTGAAAATTT
1 GTGTGAAAATTT
31107059 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:31108205 original size:42 final size:43
Alignment explanation
Indices: 31108103--31108261 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
31108093 AATGTGATAT
* * * *
31108103 CGTGTAAGACCAC-GTTTGGGACGTTGCCATCGATT-TAAGATTTA
1 CGTGTAAGACC-CTGTCTGGGACATTGGCATCG-TTATATGA-TTA
* *
31108147 CGTGTAAGACCATGTCTGGGACATTGGCGTCG-TATATGATTA
1 CGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGATTA
* * *
31108189 CGTGTAAGACCCTGTCTGGGACAGTGGCATTGTTATTTGATTA
1 CGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGATTA
* * *
31108232 CATGTAAGATCAC-GTCTGGGACGTTGGCAT
1 CGTGTAAGA-CCCTGTCTGGGACATTGGCAT
31108262 TGTATGAGTT
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
42 32 0.33
43 36 0.38
44 28 0.29
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGATTA
Found at i:31116195 original size:39 final size:39
Alignment explanation
Indices: 31116152--31116229 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
31116142 CTATTACATG
* *
31116152 TATAATCACCGAACACTCAAGCATATATCATAATACTCA
1 TATAATCACAGAACACTCAAGCATATATCACAATACTCA
* * *
31116191 TATAATCACATAACATTTAAGCATATATCACAATACTCA
1 TATAATCACAGAACACTCAAGCATATATCACAATACTCA
31116230 AAAACATCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.45, C:0.23, G:0.04, T:0.28
Consensus pattern (39 bp):
TATAATCACAGAACACTCAAGCATATATCACAATACTCA
Found at i:31116859 original size:28 final size:29
Alignment explanation
Indices: 31116760--31116862 Score: 120
Period size: 30 Copynumber: 3.5 Consensus size: 29
31116750 AGAATTAGTC
* * * *
31116760 TGGGCCTGAGCCCTATACTGTAGCAGTGTG
1 TGGGCCTGAGCCCAATACAGTAACAG-ATG
31116790 TGGGCCAT-AGCCCAATACAGTAACAGAGTG
1 TGGGCC-TGAGCCCAATACAGTAACAGA-TG
*
31116820 TGGGCCTTAGCCCAATACAGTAACA-ATG
1 TGGGCCTGAGCCCAATACAGTAACAGATG
31116848 TGGGCCTGAGCCCAA
1 TGGGCCTGAGCCCAA
31116863 AACAATATTC
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
28 16 0.25
29 2 0.03
30 46 0.71
31 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.20
Consensus pattern (29 bp):
TGGGCCTGAGCCCAATACAGTAACAGATG
Found at i:31117047 original size:26 final size:26
Alignment explanation
Indices: 31116987--31117050 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
31116977 AATATAGCAG
* *
31116987 CAAAGCTGCCAGTAATAATAACACAG
1 CAAAGCTGCTAGTAATAATAACACAA
*
31117013 CAAAACTGCTAGTAATAATAACACAA
1 CAAAGCTGCTAGTAATAATAACACAA
*
31117039 CAGAGCTGCTAG
1 CAAAGCTGCTAG
31117051 AATCAGTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17
Consensus pattern (26 bp):
CAAAGCTGCTAGTAATAATAACACAA
Found at i:31117489 original size:27 final size:27
Alignment explanation
Indices: 31117245--31117492 Score: 205
Period size: 27 Copynumber: 9.2 Consensus size: 27
31117235 TATAACAGTC
*
31117245 ATTTTACCCTAT--AGGTGTATTTCGGTC
1 ATTTTACCCT-TCGAGG-GTATTTCGGTA
* * ** *
31117272 ATTTTACCCTTAGGGGGTATTTTAGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
31117299 ATTTTACCCTTCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* * * *
31117326 ATTGTACCTTTTGAGGGTAATTT-AGTA
1 ATTTTACCCTTCGAGGGT-ATTTCGGTA
* ** **
31117353 AATTTACCCTTCGAAAGTATTTTAGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
31117380 ATTTTTCCCTTCGAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* **
31117407 ATTTTACCCTTCGTGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* * *
31117434 ATTTAACCCTTCAAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
31117461 ATTTTACCCTTTGAGGGTATCTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
31117488 ATTTT
1 ATTTT
31117493 CTCAGGAATC
Statistics
Matches: 178, Mismatches: 39, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
26 5 0.03
27 167 0.94
28 6 0.03
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGGTA
Found at i:31119559 original size:28 final size:29
Alignment explanation
Indices: 31119458--31119578 Score: 109
Period size: 30 Copynumber: 4.1 Consensus size: 29
31119448 CATGCAGAAT
* * * *
31119458 CAGTCTGGGCCTGATCCCTATACAGTAGTA
1 CAGTGTGGGCCTTAGCCCAATACAGTA-TA
** * *
31119488 GTGTGTGGGCCATAGCCTAATACAGTAATA
1 CAGTGTGGGCCTTAGCCCAATACAGT-ATA
* *
31119518 GAGTGTAGGCCTTAGCCCAATACAGTA-A
1 CAGTGTGGGCCTTAGCCCAATACAGTATA
* *
31119546 CAGTGTGGGCCTTAGCCCAAAACAGTATT
1 CAGTGTGGGCCTTAGCCCAATACAGTATA
31119575 CAGT
1 CAGT
31119579 ACAAATGCAG
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
28 25 0.34
29 5 0.07
30 42 0.58
31 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (29 bp):
CAGTGTGGGCCTTAGCCCAATACAGTATA
Found at i:31119786 original size:26 final size:26
Alignment explanation
Indices: 31119688--31119787 Score: 121
Period size: 26 Copynumber: 3.8 Consensus size: 26
31119678 CCAATATCGT
* *
31119688 AGCAAAGCTGCCAGTAATAATAACGC
1 AGCAAAGCTGCCAGTAACAGTAACGC
*
31119714 AGCAAAGCTGCCAGTAACAGTAACAC
1 AGCAAAGCTGCCAGTAACAGTAACGC
* *
31119740 AGCAGAGCTGCCA-AAATCAGTAACGC
1 AGCAAAGCTGCCAGTAA-CAGTAACGC
* *
31119766 AGCAAAGCTACTAGTAACAGTA
1 AGCAAAGCTGCCAGTAACAGTA
31119788 TTTGTGGCAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
25 2 0.03
26 58 0.94
27 2 0.03
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (26 bp):
AGCAAAGCTGCCAGTAACAGTAACGC
Found at i:31120114 original size:27 final size:27
Alignment explanation
Indices: 31119958--31120200 Score: 271
Period size: 27 Copynumber: 9.0 Consensus size: 27
31119948 AGGGGTATAA
31119958 CAGTCATTTTACCCTAT-G-GGAGTATTT
1 CAGTCATTTTACCCT-TCGAGG-GTATTT
31119985 CTA-TCATTTTACCCTTCG-GAGGTATTT
1 C-AGTCATTTTACCCTTCGAG-GGTATTT
31120012 CAGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
31120039 CAGTCATTTTACCTTTCAAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
31120066 CGGTCATTTTACCCGTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
31120093 CAATCATTTTACCCTTCAAGGGTATGTT
1 CAGTCATTTTACCCTTCGAGGGTAT-TT
* *
31120121 -AGTAATTTTACCCTTCAAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* * * *
31120147 CGGTAATTTTACCTTTTGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* * *
31120174 TAGTAATTTTACCCTTCGAGGATATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
31120201 TGGTAATTTA
Statistics
Matches: 188, Mismatches: 21, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.02
27 179 0.95
28 5 0.03
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (27 bp):
CAGTCATTTTACCCTTCGAGGGTATTT
Found at i:31139110 original size:27 final size:27
Alignment explanation
Indices: 31139076--31139360 Score: 381
Period size: 27 Copynumber: 10.6 Consensus size: 27
31139066 AGACCCCAAA
* *
31139076 ATAGGGTAAAATGACTGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
31139103 ATAAGGTAAAATGACCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
31139130 ATAGGGCAAAATAACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * *
31139157 ATAGGCTAGAATGACCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
31139184 ATAGGGTAAAATGAGCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
31139211 ATAGGATAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * * *
31139238 ATAGGGTAAAATGTCTGGAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCC
*
31139265 ATAGGGTAAAATGACCGAAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCC
* **
31139292 ATAGGGTAAAATGACCAAAATACCCTT
1 ATAGGGTAAAATGACCGAAATACCCCC
31139319 ATAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
31139346 ATAAGGTAAAATGAC
1 ATAGGGTAAAATGAC
31139361 ATGTATGATA
Statistics
Matches: 226, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 226 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.19
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCCC
Found at i:31152405 original size:17 final size:17
Alignment explanation
Indices: 31152379--31152414 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
31152369 GGAAATGGAT
*
31152379 TTCCAGTTCTAAAATAG
1 TTCCACTTCTAAAATAG
31152396 TTCCACTTCTAAAATAG
1 TTCCACTTCTAAAATAG
31152413 TT
1 TT
31152415 TGCAAGGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.39
Consensus pattern (17 bp):
TTCCACTTCTAAAATAG
Found at i:31157295 original size:25 final size:25
Alignment explanation
Indices: 31157260--31157318 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
31157250 TTTTAGAATT
*
31157260 AAATCAAATCTAACAAAAT-ACCAT
1 AAATCAAATCTAACAAAATAACCAC
31157284 ACAATCAAATCTAACAAAATAACCAC
1 A-AATCAAATCTAACAAAATAACCAC
31157310 AAATCAAAT
1 AAATCAAAT
31157319 GAAACAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 1 0.03
25 26 0.81
26 5 0.16
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (25 bp):
AAATCAAATCTAACAAAATAACCAC
Found at i:31160535 original size:147 final size:148
Alignment explanation
Indices: 31160161--31160557 Score: 523
Period size: 147 Copynumber: 2.6 Consensus size: 148
31160151 TTTTGGTTTT
*
31160161 TTTTAAAAGGAGAAAGTTTAAATTTTTAAAACAAAGTTTTGATTTTTTTGTCAACTATTTCGAAA
1 TTTTAAAA-GA-AAAGTTTAAAATTTTAAAACAAAGTTTTGA-TTTTTT-TCAACTATTTC-AAA
* * * *
31160226 TAAAAGTTTTGATCTTTAAGAAAAATAGTAATTTTTTAAAAGAAAAAAAGAGAAAGTTTAGATTT
61 AAAAAGATTTGATCTTTAAGAAAAATAGTGA---TTT--AAGAAAAAAACAGAAAGTTTAGATTT
* *
31160291 TTAAAAATAACAATTTGTTTTTTTGTCA
121 TTAAAAATAAAAATATGTTTTTTTGTCA
* ** *
31160319 TTTT-AAAGAAAAGTTT-AAATTTTAAAACAAATTTTTGATTTTTTTCAACTATTTTGAAATAAA
1 TTTTAAAAGAAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAAAAAA
*
31160382 GCTTTGATCTTTAAGAAAAATAGTGATTT-A-AAAAAAACAGAAAGTTTAGATTTTTAAAAATAA
66 GATTTGATCTTTAAGAAAAATAGTGATTTAAGAAAAAAACAGAAAGTTTAGATTTTTAAAAATAA
31160445 AAATATGTTTTTTTAGTCA
131 AAATATGTTTTTTT-GTCA
*
31160464 TTTTAAAAGAAAAGTTTAAAATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAAAAAA
1 TTTTAAAAGAAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAAAAAA
* * *
31160529 GATTTGATTTTTAAGAAAAGTAATGATTT
66 GATTTGATCTTTAAGAAAAATAGTGATTT
31160558 TTTTAAAAGA
Statistics
Matches: 216, Mismatches: 20, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
144 44 0.20
145 9 0.04
146 12 0.06
147 67 0.31
148 3 0.01
151 29 0.13
152 10 0.05
153 6 0.03
154 20 0.09
155 7 0.03
156 2 0.01
157 3 0.01
158 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (148 bp):
TTTTAAAAGAAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAAAAAA
GATTTGATCTTTAAGAAAAATAGTGATTTAAGAAAAAAACAGAAAGTTTAGATTTTTAAAAATAA
AAATATGTTTTTTTGTCA
Found at i:31162651 original size:20 final size:21
Alignment explanation
Indices: 31162620--31162659 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
31162610 TGTTTGTACA
*
31162620 TATTAGATTTATTTATTTGTG
1 TATTAGATTTATTTAATTGTG
31162641 TATTA-ATTTATTTAATTGT
1 TATTAGATTTATTTAATTGT
31162660 CTAATGTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (21 bp):
TATTAGATTTATTTAATTGTG
Found at i:31164665 original size:29 final size:29
Alignment explanation
Indices: 31164610--31164665 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
31164600 TGTGTCAGTG
* **
31164610 CAATTCAAGGGAAAGAGGAAGGTCCCAAA
1 CAATTCAAGGGAAAGAGAAAGAACCCAAA
*
31164639 CAATTCAAGGGAAAGATAAAGAACCCA
1 CAATTCAAGGGAAAGAGAAAGAACCCA
31164666 GATGATGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (29 bp):
CAATTCAAGGGAAAGAGAAAGAACCCAAA
Found at i:31165573 original size:19 final size:20
Alignment explanation
Indices: 31165549--31165586 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
31165539 GTTTATTTAG
31165549 AAACATTATTT-TGAAAAAA
1 AAACATTATTTATGAAAAAA
*
31165568 AAACATTTTTTATGAAAAA
1 AAACATTATTTATGAAAAA
31165587 TCCAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
AAACATTATTTATGAAAAAA
Found at i:31169458 original size:19 final size:21
Alignment explanation
Indices: 31169427--31169469 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
31169417 TTTAAAAATC
31169427 AATAAATAATA-TTTCAGAAA
1 AATAAATAATATTTTCAGAAA
*
31169447 AATAAA-AATATTTTTAGAAA
1 AATAAATAATATTTTCAGAAA
31169467 AAT
1 AAT
31169470 TAATTGTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (21 bp):
AATAAATAATATTTTCAGAAA
Found at i:31170716 original size:20 final size:20
Alignment explanation
Indices: 31170670--31170718 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
31170660 ATCACGGTCT
31170670 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTCTTTACTTAC
* *
31170689 TCT-ATTACTTGTTTACTTAC
1 T-TGCTTACTTCTTTACTTAC
31170709 TTGCTTACTT
1 TTGCTTACTT
31170719 AAATAACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.14, C:0.22, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTCTTTACTTAC
Found at i:31171045 original size:50 final size:50
Alignment explanation
Indices: 31170921--31171162 Score: 245
Period size: 50 Copynumber: 4.7 Consensus size: 50
31170911 GATAATAACA
* ** * * *
31170921 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
31170970 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
31171020 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* **
31171070 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
31171126 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
31171163 TCTCATTCCC
Statistics
Matches: 159, Mismatches: 26, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
48 1 0.01
49 38 0.24
50 82 0.52
53 2 0.01
56 36 0.23
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:31192771 original size:136 final size:136
Alignment explanation
Indices: 31192519--31192772 Score: 332
Period size: 136 Copynumber: 1.9 Consensus size: 136
31192509 GTTTACCGTA
* * * * * *
31192519 TTTCAGGTGGTGGTCTTGAATGTCCTACTAGTGGCTGAGTTCTGACATTTGTTACGGATACTCGA
1 TTTCAAGTGCTGGTCTTGAATGTCCTACCAATGGCTGAGTTCTAACATTTCTTACGGATACTCGA
**
31192584 TAGCTTGAGGAGCAGCACCATGTAGCTACGTTCTGACCGACAGCTTGTGTGAGCAGACCCAGGTT
66 TAGCTTGAGGAGCAGCACCATGTAGCTACGTTCTGACCGACAGCTCATGTGAGCAGACCCAGGTT
31192649 ATCATG
131 ATCATG
* * *
31192655 TTTCAAGTGCTGGTCTTGAATGTCCTACCAATGGCTGAGTT-TCAACGTTTCTTTCGGATACTGG
1 TTTCAAGTGCTGGTCTTGAATGTCCTACCAATGGCTGAGTTCT-AACATTTCTTACGGATACTCG
* * * * *
31192719 ATAGCTTGTGGAGCAGCATCGTGTAGTTACGTT-TCGACCGATAGCTCATGTGAG
65 ATAGCTTGAGGAGCAGCACCATGTAGCTACGTTCT-GACCGACAGCTCATGTGAG
31192773 TAGGCTCATT
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
135 2 0.02
136 98 0.98
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (136 bp):
TTTCAAGTGCTGGTCTTGAATGTCCTACCAATGGCTGAGTTCTAACATTTCTTACGGATACTCGA
TAGCTTGAGGAGCAGCACCATGTAGCTACGTTCTGACCGACAGCTCATGTGAGCAGACCCAGGTT
ATCATG
Found at i:31196193 original size:21 final size:21
Alignment explanation
Indices: 31196169--31196209 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31196159 GAAATCCATT
* *
31196169 TCATCATCTCCTTCTTCTTCG
1 TCATCACCTCCTTCCTCTTCG
*
31196190 TCATCCCCTCCTTCCTCTTC
1 TCATCACCTCCTTCCTCTTC
31196210 ATTTTCACGG
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:0.07, C:0.46, G:0.02, T:0.44
Consensus pattern (21 bp):
TCATCACCTCCTTCCTCTTCG
Found at i:31197446 original size:23 final size:22
Alignment explanation
Indices: 31197420--31197467 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
31197410 AAATAAGGGG
31197420 ATAATATGTATTTA-GGTTAGAAA
1 ATAA-ATGTATTTATGGTTA-AAA
* *
31197443 ATAAGTGTTTTTATGGTTAAAA
1 ATAAATGTATTTATGGTTAAAA
31197465 ATA
1 ATA
31197468 GGGTAAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (22 bp):
ATAAATGTATTTATGGTTAAAA
Found at i:31214590 original size:25 final size:25
Alignment explanation
Indices: 31214562--31214620 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
31214552 GAAGCTCTAT
31214562 TTGCAATTCAAGAGGTATTTTATAG
1 TTGCAATTCAAGAGGTATTTTATAG
*
31214587 TTGCAATTCAAGAGGTTTTTTATAG
1 TTGCAATTCAAGAGGTATTTTATAG
31214612 TTGCAATTC
1 TTGCAATTC
31214621 CAGTAAATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (25 bp):
TTGCAATTCAAGAGGTATTTTATAG
Found at i:31214866 original size:32 final size:32
Alignment explanation
Indices: 31214825--31214886 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
31214815 CTTGCACTAG
*
31214825 TGTATATTCATATACAATGCATTAATTAAATA
1 TGTATATTCATATACAACGCATTAATTAAATA
31214857 TGTATATTCATATACAACGCATTAATTAAA
1 TGTATATTCATATACAACGCATTAATTAAA
31214887 AATATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (32 bp):
TGTATATTCATATACAACGCATTAATTAAATA
Found at i:31215074 original size:63 final size:64
Alignment explanation
Indices: 31215002--31215182 Score: 262
Period size: 63 Copynumber: 2.9 Consensus size: 64
31214992 AAATAAAATA
*
31215002 AAAATTGGATCATTAGATATAATCAAGTAAACAAGTTGATTAAAAAA-ATATT-TAT-AACATAT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACA-ATTAT-TGAACATAT
*
31215064 T
64 G
* * *
31215065 AAAATTGGATCATTAGATATAATCAAGTAAATAACTTGATTAAAAAACAATTATTGGATATATG
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAATTATTGAACATATG
*
31215129 AAAATTGGATCATTAGATATAATCAA-TAAACAACTTGATTAAAAAACAAATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAATTATT
31215183 CATTGTTAAT
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
63 75 0.69
64 33 0.31
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (64 bp):
AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAATTATTGAACATATG
Found at i:31216771 original size:49 final size:49
Alignment explanation
Indices: 31216714--31216817 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 49
31216704 TCATGTGTTA
* * * *
31216714 TAATTTTATACAGTGTTGA-GTTTGTGATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTT-TGATTCATGATATTAAACTCAATTT
*
31216763 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
31216812 TAATTT
1 TAATTT
31216818 CTTTTTTTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
49 46 0.94
50 3 0.06
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.49
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:31218554 original size:44 final size:44
Alignment explanation
Indices: 31218491--31218627 Score: 238
Period size: 44 Copynumber: 3.1 Consensus size: 44
31218481 TTACACCTCT
31218491 ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
31218535 ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
* *
31218579 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTTTATTCC
1 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
31218625 ATT
1 ATT
31218628 ACAGCGAACC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
44 67 0.75
45 4 0.04
46 18 0.20
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.28
Consensus pattern (44 bp):
ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
Found at i:31219210 original size:41 final size:39
Alignment explanation
Indices: 31219159--31219398 Score: 159
Period size: 41 Copynumber: 6.0 Consensus size: 39
31219149 GAAGACTATC
* * *
31219159 AGGCTCAAAGCCTGATATAACGCACCGGCATAAAGCCTACT
1 AGGCACAAAGCCTGATATAA-GCACCGGCA-GAAGCCTGCT
* * **
31219200 AGGCAGAAAGCCTGATATAATACACCAACACGAAGCCTGCT
1 AGGCACAAAGCCTGATATAA-GCACCGGCA-GAAGCCTGCT
* *
31219241 AGGAACAAAGCCTGATATAAGACATCGGCAGAAGCCTGCT
1 AGGCACAAAGCCTGATATAAG-CACCGGCAGAAGCCTGCT
* * * * *
31219281 AGGCACAGAG-CTAGA-AT-ATCACTGGCACAAAGCCAGCT
1 AGGCACAAAGCCT-GATATAAGCACCGGCA-GAAGCCTGCT
* * * *
31219319 AGGCACAAAGCCTGAT-T-ATCACTGGCACCAATCCTGCT
1 AGGCACAAAGCCTGATATAAGCACCGGCA-GAAGCCTGCT
* *
31219357 AGGCACAAAGTC-GAATATAATACACCGGCACGAAGCCTGCT
1 AGGCACAAAGCCTG-ATATAA-GCACCGGCA-GAAGCCTGCT
31219398 A
1 A
31219399 CACACAGAGC
Statistics
Matches: 159, Mismatches: 31, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
37 7 0.04
38 52 0.33
39 7 0.04
40 21 0.13
41 72 0.45
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (39 bp):
AGGCACAAAGCCTGATATAAGCACCGGCAGAAGCCTGCT
Found at i:31219323 original size:38 final size:38
Alignment explanation
Indices: 31219185--31219374 Score: 143
Period size: 38 Copynumber: 4.9 Consensus size: 38
31219175 ATAACGCACC
* * * *
31219185 GGCATAAAGCCTACTAGGCAGAAAGCCTGATATAATACACC
1 GGCACAAAGCCTGCTAGGCACAAAGCCTGA-AT-AT-CACT
** * * **
31219226 AACACGAAGCCTGCTAGGAACAAAGCCTGATATAAGACAT
1 GGCACAAAGCCTGCTAGGCACAAAGCCTGA-ATATCAC-T
* *
31219266 CGGCA-GAAGCCTGCTAGGCACAGAG-CTAGAATATCACT
1 -GGCACAAAGCCTGCTAGGCACAAAGCCT-GAATATCACT
* *
31219304 GGCACAAAGCCAGCTAGGCACAAAGCCTGATTATCACT
1 GGCACAAAGCCTGCTAGGCACAAAGCCTGAATATCACT
* * *
31219342 GGCACCAATCCTGCTAGGCACAAAGTC-GAATAT
1 GGCACAAAGCCTGCTAGGCACAAAGCCTGAATAT
31219375 AATACACCGG
Statistics
Matches: 119, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
37 9 0.08
38 50 0.42
39 11 0.09
40 21 0.18
41 28 0.24
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (38 bp):
GGCACAAAGCCTGCTAGGCACAAAGCCTGAATATCACT
Found at i:31225989 original size:21 final size:21
Alignment explanation
Indices: 31225964--31226004 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31225954 TAGTGTACTT
*
31225964 ATCCATAACCTAGATAAATTC
1 ATCCATAACCTAAATAAATTC
*
31225985 ATCCATAACTTAAATAAATT
1 ATCCATAACCTAAATAAATT
31226005 TTGCACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (21 bp):
ATCCATAACCTAAATAAATTC
Found at i:31226504 original size:41 final size:41
Alignment explanation
Indices: 31226427--31226776 Score: 306
Period size: 41 Copynumber: 8.8 Consensus size: 41
31226417 ACTTACTTGG
** * * * *
31226427 TATAATACATTGGCACGAAGACTGCCAGGCTCAAAGCTTGA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* ** ** * *
31226468 TATAACACATTGGCATAAAGCCTGCTAGGCAGAAAGCCTAA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* * *
31226509 TATAATACACTGGCACGAA-CCTTGGTAGGCACAAAACCTGA
1 TATAATACACCGGCACGAAGCC-TGCTAGGCACAAAGCCTGA
** * * *
31226550 TATAATACACCAACACAAAGCCTACTAGGCACAAATCCTGA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
*
31226591 TATAATACACCGGCACGAAGTCTGCTAGGCACAAAGCCTGA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* * *
31226632 TATAATACACCGGCACGAAGCCTGCTAGGCATAGAGCC-CA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* * * * *
31226672 AAT-AT-CACCAGCACAAAGCCTGCTAGGCACAGAGCCCGA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* * *
31226711 -AT-AT-CACCAGCACAAAGCCTGCTAGGCACAAAGCTTGA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* *
31226749 T-T-AT-CACCGGCACAAAGCCTGTTAGGCA
1 TATAATACACCGGCACGAAGCCTGCTAGGCA
31226777 TAGAGCCCGA
Statistics
Matches: 261, Mismatches: 44, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
38 88 0.34
39 3 0.01
40 5 0.02
41 163 0.62
42 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.17
Consensus pattern (41 bp):
TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
Found at i:31226696 original size:38 final size:38
Alignment explanation
Indices: 31226553--31226789 Score: 224
Period size: 38 Copynumber: 6.1 Consensus size: 38
31226543 AACCTGATAT
* * * * *
31226553 AATA-CACCAACACAAAGCCTACTAGGCACAAATCCTG
1 AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
* * * * *
31226590 ATATAATACACCGGCACGAAGTCTGCTAGGCACAAAGCCTG
1 A-AT-AT-CACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
* * * *
31226631 ATATAATACACCGGCACGAAGCCTGCTAGGCATAGAGCCCA
1 A-AT-AT-CACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
31226672 AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
1 AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
* **
31226710 AATATCACCAGCACAAAGCCTGCTAGGCACAAAGCTTG
1 AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
* * * *
31226748 ATTATCACCGGCACAAAGCCTGTTAGGCATAGAGCCCG
1 AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
31226786 AATA
1 AATA
31226790 ACGTTACATT
Statistics
Matches: 170, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
37 1 0.01
38 100 0.59
39 3 0.02
40 2 0.01
41 64 0.38
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.15
Consensus pattern (38 bp):
AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
Found at i:31227803 original size:14 final size:14
Alignment explanation
Indices: 31227784--31227823 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31227774 TTGATTGCCA
31227784 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
31227798 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
31227812 GGAAAATGTTTT
1 GTAAAATGTTTT
31227824 ACTTTTCTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:31233623 original size:30 final size:30
Alignment explanation
Indices: 31233587--31233643 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
31233577 CACATTTAAC
* *
31233587 ATAGAACAGCCATAAAGGCTTCTACATATA
1 ATAGAACAGCCACAAAGGCTTCCACATATA
*
31233617 ATAGAACAGTCACAAAGGCTTCCACAT
1 ATAGAACAGCCACAAAGGCTTCCACAT
31233644 TTTGGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (30 bp):
ATAGAACAGCCACAAAGGCTTCCACATATA
Found at i:31239795 original size:20 final size:20
Alignment explanation
Indices: 31239772--31239811 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31239762 GTAGTGTTAT
*
31239772 ACAGAGGCACCGAATTGCAA
1 ACAGAGGCACCGAAGTGCAA
*
31239792 ACAGAGGCATCGAAGTGCAA
1 ACAGAGGCACCGAAGTGCAA
31239812 TCCTGTACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.28, T:0.10
Consensus pattern (20 bp):
ACAGAGGCACCGAAGTGCAA
Found at i:31242678 original size:14 final size:14
Alignment explanation
Indices: 31242659--31242693 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
31242649 ATAATTAAAC
*
31242659 TTTAATTAAGTTAA
1 TTTAATTAACTTAA
31242673 TTTAATTAACTTAA
1 TTTAATTAACTTAA
31242687 -TTAATTA
1 TTTAATTA
31242694 CTAACCCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (14 bp):
TTTAATTAACTTAA
Found at i:31246628 original size:16 final size:16
Alignment explanation
Indices: 31246607--31246638 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31246597 CTCTCTTTAA
31246607 CATGAAACACATATAT
1 CATGAAACACATATAT
*
31246623 CATGAATCACATATAT
1 CATGAAACACATATAT
31246639 GTACACATAT
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:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (16 bp):
CATGAAACACATATAT
Found at i:31248627 original size:19 final size:20
Alignment explanation
Indices: 31248590--31248634 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
31248580 TGTTATCTAT
*
31248590 ATCTTAATTAATATAGTTTA
1 ATCTTAAATAATATAGTTTA
31248610 ATCTTAAATAAT-TAGTTTA
1 ATCTTAAATAATATAGTTTA
31248629 ATCTTA
1 ATCTTA
31248635 GTTTAGTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (20 bp):
ATCTTAAATAATATAGTTTA
Found at i:31266796 original size:259 final size:255
Alignment explanation
Indices: 31266329--31266796 Score: 645
Period size: 259 Copynumber: 1.8 Consensus size: 255
31266319 AAAAGTATTC
* * *
31266329 TTCCGTATTTAGAATAAGTTATGTTATTAAATGGTACTTTAACTTTTTATTCTTTTTAAAAAATA
1 TTCCGTATTTAGAATAAGTTATATTATTAAACGGTACTTTAACGTTTTATTCTTTTTAAAAAATA
* * * **
31266394 AAAACTTTGCTTATTGAGATACTTGAACCCATACCATTTGCATCAATAAATTTTAACTTTACCAC
66 AAAAC-TTGCTTATTAAGATA-TTAAACCCATACCAATTGCATCAATAAACCTTAACTTTACCAC
* * *
31266459 TCAACCAAAATTTTATTTTACTATATTTTATACATTTTAATATTATTATGCATACTTTATTACCT
129 TCAAACAAAATTTTATTTTAATATATTTTATACATTTTAATATTATTATGCACACTTTATTACCT
*
31266524 CCGTCAATTGTATATCTATATTTATTTCTATTTAAACCCCTAACTAAGTTACGGAAATGTCT
194 CCATCAATTGTATATCTATATTTATTTCTATTTAAACCCCTAACTAAGTTACGGAAATGTCT
** *
31266586 TTCCGTATTTAGAATAAGTTATATTATTTGACGGTACTTTAGTCGTTTTATTCTTTTTAAAAATC
1 TTCCGTATTTAGAATAAGTTATATTATTAAACGGTACTTTA-ACGTTTTATTCTTTTT-AAAA--
* **
31266651 AATAAAAA-TTGCTTATGATAAGAT-TTAAACTCATGTCAATTGCATCAATAAAACCTTAACTTT
62 AATAAAAACTTGCTTAT--TAAGATATTAAACCCATACCAATTGCATCAAT-AAACCTTAACTTT
* *
31266714 ACCACTCAAACAAAATTTTATTTTAATAT-TTTTATACATTTTAATTTTATTGTGCACACTTTAT
124 ACCACTCAAACAAAATTTTATTTTAATATATTTTATACATTTTAATATTATTATGCACACTTTAT
*
31266778 TACCTCCATCATTTGTATA
189 TACCTCCATCAATTGTATA
31266797 CATTGATAAT
Statistics
Matches: 183, Mismatches: 21, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
257 37 0.20
258 14 0.08
259 81 0.44
260 38 0.21
261 13 0.07
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (255 bp):
TTCCGTATTTAGAATAAGTTATATTATTAAACGGTACTTTAACGTTTTATTCTTTTTAAAAAATA
AAAACTTGCTTATTAAGATATTAAACCCATACCAATTGCATCAATAAACCTTAACTTTACCACTC
AAACAAAATTTTATTTTAATATATTTTATACATTTTAATATTATTATGCACACTTTATTACCTCC
ATCAATTGTATATCTATATTTATTTCTATTTAAACCCCTAACTAAGTTACGGAAATGTCT
Found at i:31272435 original size:14 final size:14
Alignment explanation
Indices: 31272416--31272452 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
31272406 GTTTGGTTTA
31272416 GAGGAAAATTCGAG
1 GAGGAAAATTCGAG
* *
31272430 GAGGAAATTTTGAG
1 GAGGAAAATTCGAG
31272444 GAGGAAAAT
1 GAGGAAAAT
31272453 AAATAATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.03, G:0.35, T:0.19
Consensus pattern (14 bp):
GAGGAAAATTCGAG
Found at i:31273448 original size:30 final size:31
Alignment explanation
Indices: 31273409--31273468 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
31273399 AGAGGTGGGA
*
31273409 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
31273440 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
31273469 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:31274087 original size:26 final size:26
Alignment explanation
Indices: 31274043--31274096 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
31274033 GTTCACTCTA
*
31274043 TTTAAGATGAGGCACCAAATTAATTG
1 TTTAAGATGAGGCACCAAACTAATTG
* *
31274069 TTTAAGGTGAGGCGA-CAAACTGATTG
1 TTTAAGATGAGGC-ACCAAACTAATTG
31274095 TT
1 TT
31274097 CTAGTGGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (26 bp):
TTTAAGATGAGGCACCAAACTAATTG
Found at i:31274871 original size:94 final size:94
Alignment explanation
Indices: 31274670--31274983 Score: 285
Period size: 94 Copynumber: 3.4 Consensus size: 94
31274660 AATATCCATT
* * * * * * * *
31274670 TTGGGGTGTCTACTTTGTAACTTTACAAAATTAAGTTAAGTACCTTAAAAGAGTCTAGAAGTAG-
1 TTGGGGTGTCTGCTTTATAACTTTGCAAAATAAAGCTAAGTGCC-T-GAAGAGACTAGAAGTAGT
* * *
31274734 --TTCTATTAAACATAGCGAGCAA-TTTCCTC
64 TCTTCTATTAAACTTAGCAAG-AAGTCTCCTC
* *** ** **
31274763 TTGGGGTGCCTGCTTTATAACTTTGTTGAATTTATTTAAGTGCCTGAAGAGACTAGAAGTAGTTC
1 TTGGGGTGTCTGCTTTATAACTTTGCAAAATAAAGCTAAGTGCCTGAAGAGACTAGAAGTAGTTC
* *
31274828 TTCTTTTAAACTTAGCAAGTAGTCTCCTC
66 TTCTATTAAACTTAGCAAGAAGTCTCCTC
* * * * * * * *
31274857 TTGAGGTGTTTGCTTTGTAACTTTGCAAAATAAAGCTAAGTGCCTTATGAGGCTATAAGTGGTTC
1 TTGGGGTGTCTGCTTTATAACTTTGCAAAATAAAGCTAAGTGCCTGAAGAGACTAGAAGTAGTTC
**
31274922 TTCTATTAAACTTAGTGAGAAGTCTCCTC
66 TTCTATTAAACTTAGCAAGAAGTCTCCTC
*
31274951 TCGGGGTGTCTGCTTTATAACTTTGCAAAATAA
1 TTGGGGTGTCTGCTTTATAACTTTGCAAAATAA
31274984 CATGCTATAA
Statistics
Matches: 176, Mismatches: 41, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
91 15 0.09
92 1 0.01
93 35 0.20
94 125 0.71
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (94 bp):
TTGGGGTGTCTGCTTTATAACTTTGCAAAATAAAGCTAAGTGCCTGAAGAGACTAGAAGTAGTTC
TTCTATTAAACTTAGCAAGAAGTCTCCTC
Found at i:31277332 original size:19 final size:19
Alignment explanation
Indices: 31277308--31277345 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31277298 CAATCAAGGG
31277308 TAATTAGCGACTTAATTGA
1 TAATTAGCGACTTAATTGA
* *
31277327 TAATTAGTGATTTAATTGA
1 TAATTAGCGACTTAATTGA
31277346 AAATAGGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (19 bp):
TAATTAGCGACTTAATTGA
Found at i:31277656 original size:2 final size:2
Alignment explanation
Indices: 31277651--31277677 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31277641 ACTTAATTTC
31277651 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
31277678 TTTTTTTATT
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:31280070 original size:23 final size:23
Alignment explanation
Indices: 31280039--31280087 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
31280029 ACCTACTTTC
* *
31280039 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
31280062 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
31280085 TTA
1 TTA
31280088 TACCGGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:31296135 original size:33 final size:33
Alignment explanation
Indices: 31296093--31296158 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
31296083 ATAAACAAGA
31296093 ATCGAATGAAATAGTGACTTTAATCAAAATTAT
1 ATCGAATGAAATAGTGACTTTAATCAAAATTAT
31296126 ATCGAATGAAATAGTGACTTTAATCAAAATTAT
1 ATCGAATGAAATAGTGACTTTAATCAAAATTAT
31296159 CTCATGGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (33 bp):
ATCGAATGAAATAGTGACTTTAATCAAAATTAT
Found at i:31296781 original size:14 final size:15
Alignment explanation
Indices: 31296745--31296781 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
31296735 AATGTTTCAC
*
31296745 TTCCTTCATTCTCTT
1 TTCCTTCTTTCTCTT
31296760 TTCC-TCTTTCTC-T
1 TTCCTTCTTTCTCTT
31296773 TTCCTTCTT
1 TTCCTTCTT
31296782 CTTGCCTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 11 0.55
15 4 0.20
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCCTTCTTTCTCTT
Found at i:31298501 original size:18 final size:19
Alignment explanation
Indices: 31298478--31298526 Score: 82
Period size: 18 Copynumber: 2.6 Consensus size: 19
31298468 GATGACAAAG
31298478 ATGAGAAATGG-ATATGAA
1 ATGAGAAATGGAATATGAA
31298496 ATGAGAAATGGAATATGAA
1 ATGAGAAATGGAATATGAA
31298515 ATGATGAAATGG
1 ATGA-GAAATGG
31298527 GATGAGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.38
19 11 0.38
20 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (19 bp):
ATGAGAAATGGAATATGAA
Found at i:31305919 original size:21 final size:21
Alignment explanation
Indices: 31305893--31305933 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
31305883 AAGTTATACC
31305893 TTTTTTTACCAATCGATAGCT
1 TTTTTTTACCAATCGATAGCT
31305914 TTTTTTTACCAATCGATAGC
1 TTTTTTTACCAATCGATAGC
31305934 CGAAGCTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTTTTTACCAATCGATAGCT
Found at i:31305962 original size:30 final size:30
Alignment explanation
Indices: 31305928--31306072 Score: 96
Period size: 30 Copynumber: 4.8 Consensus size: 30
31305918 TTTACCAATC
**
31305928 GATAGCCGAAGCTAACTGATTTCATAATTT
1 GATAGCCGAAGCTAACCCATTTCATAATTT
* *
31305958 GATAGCCGAAGCTATCCCTTTTCATAATTT
1 GATAGCCGAAGCTAACCCATTTCATAATTT
** * * * * *
31305988 GACGGTCG--TCTCCATCCATTTTCACAATTT
1 GATAGCCGAAGCT-AACCCA-TTTCATAATTT
* * * *
31306018 GATAGTCGAAGCTATCCCTTTTCATAATTC
1 GATAGCCGAAGCTAACCCATTTCATAATTT
* * *
31306048 GATAGCAGAAGCTATCCCTTTTCAT
1 GATAGCCGAAGCTAACCCATTTCAT
31306073 TGTTCGATGG
Statistics
Matches: 87, Mismatches: 24, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
28 2 0.02
29 2 0.02
30 79 0.91
31 2 0.02
32 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (30 bp):
GATAGCCGAAGCTAACCCATTTCATAATTT
Found at i:31306070 original size:60 final size:60
Alignment explanation
Indices: 31305947--31306071 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
31305937 AGCTAACTGA
* * * ***
31305947 TTTCATAATTTGATAGCCGAAGCTATCCCTTTTCATAATTTGACGGTCGTCTCCATCCAT
1 TTTCACAATTTGATAGCCGAAGCTATCCCTTTTCATAATTCGACAGTCGAAGCCATCCAT
* * * *
31306007 TTTCACAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATAG-CAGAAGCTATCCCT
1 TTTCACAATTTGATAGCCGAAGCTATCCCTTTTCATAATTCGACAGTC-GAAGCCATCCAT
31306067 TTTCA
1 TTTCA
31306072 TTGTTCGATG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.38
Consensus pattern (60 bp):
TTTCACAATTTGATAGCCGAAGCTATCCCTTTTCATAATTCGACAGTCGAAGCCATCCAT
Found at i:31306095 original size:30 final size:29
Alignment explanation
Indices: 31306061--31306128 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
31306051 AGCAGAAGCT
*
31306061 ATCCCTTTTCATTGTTCGATGGTCATCATC
1 ATCCCTTTTCATTGTT-GATGGTCATCACC
* *
31306091 ATCCCTTGTCATTGTTGATGGTCGTCACC
1 ATCCCTTTTCATTGTTGATGGTCATCACC
31306120 ATCCCTTTT
1 ATCCCTTTT
31306129 ATTAACTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.43
Consensus pattern (29 bp):
ATCCCTTTTCATTGTTGATGGTCATCACC
Found at i:31306154 original size:30 final size:31
Alignment explanation
Indices: 31306120--31306194 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
31306110 GGTCGTCACC
* *
31306120 ATCCCTTTT-ATTAACTTGATAGCCGAGGCT
1 ATCCCTTTTCATTAACTTGATAGCCAAAGCT
*
31306150 ATCCCTTTTCATTAATTTGATAGCCAAAGCT
1 ATCCCTTTTCATTAACTTGATAGCCAAAGCT
*
31306181 ATCCCTTTCCATTA
1 ATCCCTTTTCATTA
31306195 GTTGATAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 9 0.22
31 31 0.77
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (31 bp):
ATCCCTTTTCATTAACTTGATAGCCAAAGCT
Found at i:31312805 original size:51 final size:50
Alignment explanation
Indices: 31312720--31312919 Score: 192
Period size: 51 Copynumber: 4.0 Consensus size: 50
31312710 TTAATGATAC
* * * *
31312720 CGGTTCACATAGTAGCATGCACCTAGTACTACACATGTGACCATCACTAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
* * ** *
31312770 ACGATACACGTAGTAGCCTGTACATAGTACTACACACCTGATCGA--AGCTATT
1 -CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CTA-T
* * *
31312822 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTAT
* *
31312871 CTGGTACACGTAGTAGCCTACACATAATACTACACATGTGACCATCACT
1 C-GGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACT
31312920 TTCACTTTCA
Statistics
Matches: 119, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
49 6 0.05
50 39 0.33
51 70 0.59
52 3 0.03
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
Found at i:31328743 original size:12 final size:12
Alignment explanation
Indices: 31328726--31328750 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31328716 ATAAAAAGCA
31328726 TTTTTTCTCTCT
1 TTTTTTCTCTCT
31328738 TTTTTTCTCTCT
1 TTTTTTCTCTCT
31328750 T
1 T
31328751 CGATCCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTCTCTCT
Found at i:31330552 original size:61 final size:60
Alignment explanation
Indices: 31330445--31330601 Score: 193
Period size: 56 Copynumber: 2.6 Consensus size: 60
31330435 ATTTTCTAAT
*
31330445 ATTATATATTATTTTTATT-AATTCATATTTTAATAAT-ATTTATATTAAGA-ACGTTATTAA
1 ATTATATATTATTTTTATTAAATT-ATA-TTTAATAATAATTTATATTAA-ATACATTATTAA
* *
31330505 ATTATATATTATTGTTTTTTTAAATTATATTTAATAATAATTT-TATTAAATATATTATTAA
1 ATTATATATTA-T-TTTTATTAAATTATATTTAATAATAATTTATATTAAATACATTATTAA
31330566 A-T-TAT-TTATTTTTATTAAATTATATTTAATAATAAT
1 ATTATATATTATTTTTATTAAATTATATTTAATAATAAT
31330602 CCTATTAAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
56 26 0.30
57 1 0.01
58 3 0.03
59 3 0.03
60 13 0.15
61 25 0.28
62 13 0.15
63 4 0.05
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (60 bp):
ATTATATATTATTTTTATTAAATTATATTTAATAATAATTTATATTAAATACATTATTAA
Found at i:31330555 original size:26 final size:26
Alignment explanation
Indices: 31330519--31330610 Score: 94
Period size: 26 Copynumber: 3.4 Consensus size: 26
31330509 TATATTATTG
*
31330519 TTTTTTTAAATTATATTTAATAATAA
1 TTTTATTAAATTATATTTAATAATAA
* * *
31330545 TTTTATTAAATATATTATTAAATTATTTAT
1 TTTTATTAAAT-TA-TATTTAA-TA-ATAA
31330575 TTTTATTAAATTATATTTAATAATAA
1 TTTTATTAAATTATATTTAATAATAA
**
31330601 TCCTATTAAA
1 TTTTATTAAA
31330611 ATTTAATAAC
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
26 20 0.38
27 4 0.08
28 12 0.23
29 4 0.08
30 13 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTATTAAATTATATTTAATAATAA
Found at i:31333808 original size:70 final size:67
Alignment explanation
Indices: 31333724--31333855 Score: 165
Period size: 70 Copynumber: 1.9 Consensus size: 67
31333714 TCAGAATAAG
* * *
31333724 AAAAGACAAAACTACGCCGTTTTAATAAGCGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGACAAAACTACGCCGTTGTAATAAACGTTTA-CTTAT-T-AAGTTAAAAGTCAAAACCATT
31333789 GAGTT
63 GAGTT
* ** * *
31333794 AAAAGGCAAAACTACGTTGTTGTGATAAATGTTTACTTATTAAGTTAAAAGTCAAAACCATT
1 AAAAGACAAAACTACGCCGTTGTAATAAACGTTTACTTATTAAGTTAAAAGTCAAAACCATT
31333856 ATATTGTGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 21 0.39
68 1 0.02
69 4 0.07
70 28 0.52
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (67 bp):
AAAAGACAAAACTACGCCGTTGTAATAAACGTTTACTTATTAAGTTAAAAGTCAAAACCATTGAG
TT
Found at i:31336371 original size:18 final size:18
Alignment explanation
Indices: 31336318--31336382 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
31336308 ATATTAAAAA
*
31336318 ATATTTTGTTATGATTTTT
1 ATATTTT-TAATGATTTTT
*
31336337 ATACTTTTTAATGATTTTA
1 ATA-TTTTTAATGATTTTT
31336356 ATATTTTTAACT-ATTTTTT
1 ATATTTTTAA-TGA-TTTTT
31336375 ATATTTTT
1 ATATTTTT
31336383 TGAATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.20
19 28 0.70
20 4 0.10
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
ATATTTTTAATGATTTTT
Found at i:31336797 original size:26 final size:26
Alignment explanation
Indices: 31336758--31336825 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 26
31336748 GAATATATAA
31336758 TAAATATATATTTTTTATTTTTTTAATTT
1 TAAA-ATA-ATTTTTTA-TTTTTTAATTT
* *
31336787 T-AAATACTTTTTTATTTTTTATTTT
1 TAAAATAATTTTTTATTTTTTAATTT
31336812 TAAAATAATTTTTT
1 TAAAATAATTTTTT
31336826 GGTGTTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 11 0.31
26 18 0.51
27 3 0.09
28 2 0.06
29 1 0.03
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (26 bp):
TAAAATAATTTTTTATTTTTTAATTT
Found at i:31340862 original size:3 final size:3
Alignment explanation
Indices: 31340854--31340903 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
31340844 GGAGACAAGA
*
31340854 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
31340902 AA
1 AA
31340904 AAGTGATAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31346094 original size:21 final size:21
Alignment explanation
Indices: 31346069--31346110 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31346059 TTCCCTCTTC
31346069 TTTTTCTTCCTTT-CTTTATTTG
1 TTTTTCTT--TTTCCTTTATTTG
31346091 TTTTTCTTTTTCCTTTATTT
1 TTTTTCTTTTTCCTTTATTT
31346111 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTCTTTTTCCTTTATTTG
Found at i:31346147 original size:13 final size:13
Alignment explanation
Indices: 31346129--31346156 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31346119 ATTTATTTTG
31346129 TTTCTTATTATTA
1 TTTCTTATTATTA
31346142 TTTCTTATTATTA
1 TTTCTTATTATTA
31346155 TT
1 TT
31346157 ATTACCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCTTATTATTA
Found at i:31346375 original size:20 final size:19
Alignment explanation
Indices: 31346310--31346369 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
31346300 GGCTTTGTTG
31346310 ATTTTTATT-TGTATTTAAT
1 ATTTTTATTATGT-TTTAAT
*
31346329 -TCTATTATTATGTTTTTAAT
1 AT-TTTTATTATG-TTTTAAT
31346349 ATTTTTATTATG-TTTAAT
1 ATTTTTATTATGTTTTAAT
31346367 ATT
1 ATT
31346370 AGTTTAGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 10 0.29
19 6 0.17
20 17 0.49
21 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (19 bp):
ATTTTTATTATGTTTTAAT
Found at i:31348848 original size:29 final size:29
Alignment explanation
Indices: 31348805--31348945 Score: 113
Period size: 29 Copynumber: 4.8 Consensus size: 29
31348795 TATCGACAAT
* * ***
31348805 CATCGACCAATGAAAAGGGATGGTTTTGAC
1 CATCGA-CTATGAAAAGGGATAGTGACGAC
* * **
31348835 CATCGATTATGAAAAAGAGATAGTTTCGAC
1 CATCGACTATG-AAAAGGGATAGTGACGAC
* * * *
31348865 TATCGACTGTGAAAAGGGATGGTGACGGC
1 CATCGACTATGAAAAGGGATAGTGACGAC
*
31348894 CATCAACTATGAAAAGGGATAGTGACGAC
1 CATCGACTATGAAAAGGGATAGTGACGAC
*
31348923 CATC-ATATATGAAAAGGGATAGT
1 CATCGA-CTATGAAAAGGGATAGT
31348946 TCACGGAGCA
Statistics
Matches: 90, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
28 1 0.01
29 60 0.67
30 29 0.32
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (29 bp):
CATCGACTATGAAAAGGGATAGTGACGAC
Found at i:31352542 original size:57 final size:57
Alignment explanation
Indices: 31352481--31352664 Score: 133
Period size: 57 Copynumber: 3.1 Consensus size: 57
31352471 TAGTGGTTTG
31352481 TGAGTATCTAGATGTGTTTCTAGAGGAGTTACCCGGGTTATGACCGATCAGAGAGGT
1 TGAGTATCTAGATGTGTTTCTAGAGGAGTTACCCGGGTTATGACCGATCAGAGAGGT
* * * * * * * *** *
31352538 TGAGTTTGCTATGTATTTGATTCT--A-GAGTT-TCTGAGTTGAAGTTAGAATCAGTTCTAGTGG
1 TGAGTAT-CTA-G-ATGTGTTTCTAGAGGAGTTACCCGGGTT-ATGACCG-ATCAG----AGAGG
31352599 TTT
57 --T
31352602 GTGAGTATCTAGATGTGTTTCTAGAGGAGTTACCCGGGTTATGACCGATCAGAGAGGT
1 -TGAGTATCTAGATGTGTTTCTAGAGGAGTTACCCGGGTTATGACCGATCAGAGAGGT
31352660 TGAGT
1 TGAGT
31352665 TTGCCATTGA
Statistics
Matches: 89, Mismatches: 22, Indels: 32
0.62 0.15 0.22
Matches are distributed among these distances:
56 5 0.06
57 19 0.21
58 10 0.11
59 1 0.01
60 12 0.13
62 12 0.13
63 1 0.01
64 10 0.11
65 14 0.16
66 5 0.06
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.35
Consensus pattern (57 bp):
TGAGTATCTAGATGTGTTTCTAGAGGAGTTACCCGGGTTATGACCGATCAGAGAGGT
Found at i:31352578 original size:122 final size:123
Alignment explanation
Indices: 31352420--31352668 Score: 491
Period size: 122 Copynumber: 2.0 Consensus size: 123
31352410 AATCCATACC
31352420 TTGCGTATGTATTTGATTCTAGAGTTTCTGAGTTGAAGTTAGAATCAGTTCTAGTGGTTTGTGAG
1 TTGCGTATGTATTTGATTCTAGAGTTTCTGAGTTGAAGTTAGAATCAGTTCTAGTGGTTTGTGAG
31352485 TATCTAGATGTGTTTCTAGAGGAGTTACCCGGGTTATGACCGATCAGAGAGGTTGAGT
66 TATCTAGATGTGTTTCTAGAGGAGTTACCCGGGTTATGACCGATCAGAGAGGTTGAGT
31352543 TTGC-TATGTATTTGATTCTAGAGTTTCTGAGTTGAAGTTAGAATCAGTTCTAGTGGTTTGTGAG
1 TTGCGTATGTATTTGATTCTAGAGTTTCTGAGTTGAAGTTAGAATCAGTTCTAGTGGTTTGTGAG
31352607 TATCTAGATGTGTTTCTAGAGGAGTTACCCGGGTTATGACCGATCAGAGAGGTTGAGT
66 TATCTAGATGTGTTTCTAGAGGAGTTACCCGGGTTATGACCGATCAGAGAGGTTGAGT
31352665 TTGC
1 TTGC
31352669 CATTGAGTTA
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 122 0.97
123 4 0.03
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (123 bp):
TTGCGTATGTATTTGATTCTAGAGTTTCTGAGTTGAAGTTAGAATCAGTTCTAGTGGTTTGTGAG
TATCTAGATGTGTTTCTAGAGGAGTTACCCGGGTTATGACCGATCAGAGAGGTTGAGT
Found at i:31363289 original size:25 final size:25
Alignment explanation
Indices: 31363258--31363356 Score: 101
Period size: 25 Copynumber: 4.0 Consensus size: 25
31363248 AGCTCTCTCT
* *
31363258 TGAGCCATATAACGGGAAGCTCATG
1 TGAGCCATATAATGGGAAGCTCATA
* * *
31363283 TGAGCCATGTAATGGGAAGCTTATT
1 TGAGCCATATAATGGGAAGCTCATA
* **
31363308 TGGGCTGTATAATGGGAAGCTCATA
1 TGAGCCATATAATGGGAAGCTCATA
* *
31363333 AGAGCCATA-ATTGGGAAGCTCATA
1 TGAGCCATATAATGGGAAGCTCATA
31363357 CTAGCCAATA
Statistics
Matches: 59, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
24 14 0.24
25 45 0.76
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.25
Consensus pattern (25 bp):
TGAGCCATATAATGGGAAGCTCATA
Found at i:31363484 original size:26 final size:26
Alignment explanation
Indices: 31363454--31363513 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
31363444 GGAGCTCTAG
* *
31363454 AGAGCCATTAATTATGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* * *
31363480 AGAGCCTTTAATCGGGAAGCTCACGA
1 AGAGCCATTAATCAGGAAGCTCACAA
31363506 AGAGCCAT
1 AGAGCCAT
31363514 ATATTAGGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:31372128 original size:29 final size:27
Alignment explanation
Indices: 31372083--31372137 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
31372073 TAATATATAA
31372083 TTTATAAATAATATAATTATATATTAAAG
1 TTTATAAATAATATAA-TA-ATATTAAAG
*
31372112 TTTATCAAATTAT-TAATAATATTAAA
1 TTTAT-AAATAATATAATAATATTAAA
31372138 AATATTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 8 0.33
30 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TTTATAAATAATATAATAATATTAAAG
Found at i:31374472 original size:51 final size:48
Alignment explanation
Indices: 31374412--31374593 Score: 204
Period size: 51 Copynumber: 3.6 Consensus size: 48
31374402 AAAGGTTGCA
31374412 TGTGTAGTACTATGTGCAGGCTACTATGCGTGCCGGATAGCTTTGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTA--CGTGCCGGATAG-TTTGATCACG
* ** *
31374463 TGTGTAGTACTATGTGCAGGCTAGTACATGTATCGGATA-TTAATGGTCACG
1 TGTGTAGTACTATGTGCAGGCTACTAC--GTGCCGGATAGTT--TGATCACG
* * *
31374514 TGTGTAGTACTATGTGCAGGCTACTACTTGAACCGGAAAGTTTGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTG--CCGGATAGTTTGATCACG
*
31374564 TGTGTAGTACTATGTGAAGGCTACTACGTG
1 TGTGTAGTACTATGTGCAGGCTACTACGTG
31374594 TATCGAATGA
Statistics
Matches: 111, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
49 4 0.04
50 34 0.31
51 71 0.64
52 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (48 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGCCGGATAGTTTGATCACG
Found at i:31374596 original size:101 final size:101
Alignment explanation
Indices: 31374412--31374598 Score: 279
Period size: 101 Copynumber: 1.8 Consensus size: 101
31374402 AAAGGTTGCA
* *
31374412 TGTGTAGTACTATGTGCAGGCTACTATGCGTGCCGGATAGCTTTGATCACGTGTGTAGTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTA-GCGTGCCGGAAAGCTTTGATCACATGTGTAGTACTATG
* *
31374477 TGCAGGCTAGTACATGTATCGGATATTAATGGTCACG
65 TGAAGGCTACTACATGTATCGGATATTAATGGTCACG
*
31374514 TGTGTAGTACTATGTGCAGGCTACTA-CTTGAACCGGAAAG-TTTGATCACATGTGTAGTACTAT
1 TGTGTAGTACTATGTGCAGGCTACTAGCGTG--CCGGAAAGCTTTGATCACATGTGTAGTACTAT
*
31374577 GTGAAGGCTACTACGTGTATCG
64 GTGAAGGCTACTACATGTATCG
31374599 AATGATAATA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
100 3 0.04
101 41 0.53
102 33 0.43
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (101 bp):
TGTGTAGTACTATGTGCAGGCTACTAGCGTGCCGGAAAGCTTTGATCACATGTGTAGTACTATGT
GAAGGCTACTACATGTATCGGATATTAATGGTCACG
Found at i:31374625 original size:101 final size:101
Alignment explanation
Indices: 31374415--31374632 Score: 262
Period size: 101 Copynumber: 2.1 Consensus size: 101
31374405 GGTTGCATGT
* * *
31374415 GTAGTACTATGTGCAGGCTACTATGCGTGCCGGATAGCTTTGATCACGTGTGTAGTACTATGTGC
1 GTAGTACTATGTGCAGGCTACTA-GCGTGCCGGAAAGCTTTGATCACATGTGTAGTACTATGTGA
* * * ** *
31374480 AGGCTAGTACATGTATCGGATATTAATGGTCACGTGT
65 AGGCTACTACATGTATCGAATATTAATAGTCAAATGA
*
31374517 GTAGTACTATGTGCAGGCTACTA-CTTGAACCGGAAAG-TTTGATCACATGTGTAGTACTATGTG
1 GTAGTACTATGTGCAGGCTACTAGCGTG--CCGGAAAGCTTTGATCACATGTGTAGTACTATGTG
* *
31374580 AAGGCTACTACGTGTATCGAATGA-TAATAGTTAAATGA
64 AAGGCTACTACATGTATCGAAT-ATTAATAGTCAAATGA
*
31374618 GTGGTACTATGTGCA
1 GTAGTACTATGTGCA
31374633 AACCATTGAA
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
100 3 0.03
101 66 0.66
102 31 0.31
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (101 bp):
GTAGTACTATGTGCAGGCTACTAGCGTGCCGGAAAGCTTTGATCACATGTGTAGTACTATGTGAA
GGCTACTACATGTATCGAATATTAATAGTCAAATGA
Found at i:31387397 original size:41 final size:41
Alignment explanation
Indices: 31387337--31387423 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
31387327 TACAATACAT
* * *
31387337 CGGCACGAAGACTGCTAAGCTCAAAGC-CTGATTTAAAACAC
1 CGGCACGAAGACTGATAAGCACAAAGCTC-GATATAAAACAC
* * *
31387378 CGGCACGAAGCCTGATAAGCACAGAGCTCGATATAATACAC
1 CGGCACGAAGACTGATAAGCACAAAGCTCGATATAAAACAC
31387419 CGGCA
1 CGGCA
31387424 TAACGCCTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 38 0.97
42 1 0.03
ACGTcount: A:0.36, C:0.28, G:0.22, T:0.15
Consensus pattern (41 bp):
CGGCACGAAGACTGATAAGCACAAAGCTCGATATAAAACAC
Found at i:31387475 original size:38 final size:38
Alignment explanation
Indices: 31387433--31387609 Score: 203
Period size: 38 Copynumber: 4.7 Consensus size: 38
31387423 ATAACGCCTA
* *
31387433 CTAGGCACGGGGCCTGAATATCACCGACACAAAGCTTG
1 CTAGGCACAGAGCCTGAATATCACCGACACAAAGCTTG
***
31387471 CTAGGCACAGAGCCTGAATATCACCGGTTCAAAGCCTT-
1 CTAGGCACAGAGCCTGAATATCACCGACACAAAG-CTTG
* * * * *
31387509 TTGGGAACGGAGCCCGAATATCACCGACACAAAGCTTG
1 CTAGGCACAGAGCCTGAATATCACCGACACAAAGCTTG
* * * *
31387547 TTAGGCACAGAGCCTGAATATCACCGGCATAAAGCCTG
1 CTAGGCACAGAGCCTGAATATCACCGACACAAAGCTTG
*
31387585 CTAGGCACAGAGCCCGAATATCACC
1 CTAGGCACAGAGCCTGAATATCACC
31387610 ACATTTTAAT
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
37 3 0.03
38 109 0.95
39 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.17
Consensus pattern (38 bp):
CTAGGCACAGAGCCTGAATATCACCGACACAAAGCTTG
Found at i:31387531 original size:76 final size:76
Alignment explanation
Indices: 31387412--31387609 Score: 265
Period size: 76 Copynumber: 2.6 Consensus size: 76
31387402 AGCTCGATAT
* * * * *
31387412 AATA-CACCGGCATAACGCCTACTAGGCACGGGGCCTGAATATCACCGACACAAAGCTTGCTAGG
1 AATATCACCGGCATAAAGCCTGCTAGGAACGGAGCCCGAATATCACCGACACAAAGCTTGCTAGG
31387476 CACAGAGCCTG
66 CACAGAGCCTG
* ** * *
31387487 AATATCACCGG-TTCAAAGCCTTTTGGGAACGGAGCCCGAATATCACCGACACAAAGCTTGTTAG
1 AATATCACCGGCAT-AAAGCCTGCTAGGAACGGAGCCCGAATATCACCGACACAAAGCTTGCTAG
31387551 GCACAGAGCCTG
65 GCACAGAGCCTG
* *
31387563 AATATCACCGGCATAAAGCCTGCTAGGCACAGAGCCCGAATATCACC
1 AATATCACCGGCATAAAGCCTGCTAGGAACGGAGCCCGAATATCACC
31387610 ACATTTTAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
75 5 0.05
76 99 0.94
77 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (76 bp):
AATATCACCGGCATAAAGCCTGCTAGGAACGGAGCCCGAATATCACCGACACAAAGCTTGCTAGG
CACAGAGCCTG
Found at i:31394346 original size:27 final size:27
Alignment explanation
Indices: 31394310--31394583 Score: 343
Period size: 27 Copynumber: 10.1 Consensus size: 27
31394300 AGAGGTCAAT
31394310 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
31394337 AAATGATCGAAATTCCTCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
31394364 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * *
31394391 AAATGACCAAAATGCCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
** *
31394418 AGCTGATCGAAATACCCTCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
31394445 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * * *
31394472 AAATGACCAAAATACCCCTATAGGTTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
31394499 AAATGATCGAAATACCCTCATAGGATA
1 AAATGATCGAAATACCCCCATAGGGTA
* * *
31394526 AAATTA-CTGAAATACCCTCATAGCGTA
1 AAATGATC-GAAATACCCCCATAGGGTA
* * * *
31394553 AAATGACCGAAACACCTCCACAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
31394580 AAAT
1 AAAT
31394584 TACTATTATA
Statistics
Matches: 211, Mismatches: 34, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
26 1 0.00
27 209 0.99
28 1 0.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:31394857 original size:26 final size:26
Alignment explanation
Indices: 31394749--31394855 Score: 126
Period size: 26 Copynumber: 4.1 Consensus size: 26
31394739 TAGAGGAAGT
* *
31394749 ATACTATTACTGGTAGCTTTACTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* * *
31394775 ATACTGTTATTGGTAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
*
31394801 ATACTGTTA-TGAGCAGCTTTGCTGCG
1 ATACTATTACTG-GCAGCTTTGCTGCG
* *
31394827 ATATTATTACTGGCAGTTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
31394853 ATA
1 ATA
31394856 TTGGTGTGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
25 2 0.03
26 68 0.94
27 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:31406436 original size:50 final size:50
Alignment explanation
Indices: 31406248--31406494 Score: 219
Period size: 50 Copynumber: 4.8 Consensus size: 50
31406238 GATAATAACA
* ** * * *
31406248 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * ** *
31406297 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * ***
31406347 TGCCCATGCCATGTCCTAGACATGATCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
31406397 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAACCTCAAAGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CTC---GG
* *
31406453 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31406495 TTACCCAAAT
Statistics
Matches: 158, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.25
50 76 0.48
53 3 0.02
56 39 0.25
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31420615 original size:31 final size:33
Alignment explanation
Indices: 31420580--31420669 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
31420570 AGCATGCAAG
*
31420580 CTAAATGAAGA-T-TCACT-AGGATACCACATGC
1 CTAAATTAAGAGTGTCACTAAGG-TACCACATGC
*
31420611 CTAAATTAAGAGTGTCTCTAAGGTACCACATGC
1 CTAAATTAAGAGTGTCACTAAGGTACCACATGC
*
31420644 CTAAATTAAGAGTGTCTCTAAGGTAC
1 CTAAATTAAGAGTGTCACTAAGGTAC
31420670 ATAAAAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
31 10 0.19
32 1 0.02
33 40 0.74
34 3 0.06
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (33 bp):
CTAAATTAAGAGTGTCACTAAGGTACCACATGC
Found at i:31420639 original size:33 final size:33
Alignment explanation
Indices: 31420601--31420669 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
31420591 TTCACTAGGA
31420601 TACCACATGCCTAAATTAAGAGTGTCTCTAAGG
1 TACCACATGCCTAAATTAAGAGTGTCTCTAAGG
31420634 TACCACATGCCTAAATTAAGAGTGTCTCTAAGG
1 TACCACATGCCTAAATTAAGAGTGTCTCTAAGG
31420667 TAC
1 TAC
31420670 ATAAAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (33 bp):
TACCACATGCCTAAATTAAGAGTGTCTCTAAGG
Found at i:31421908 original size:14 final size:14
Alignment explanation
Indices: 31421889--31421921 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
31421879 ATTGTCACAT
31421889 GTGTAGGCTACTAC
1 GTGTAGGCTACTAC
31421903 GTGTAGGCTACTAC
1 GTGTAGGCTACTAC
31421917 GTGTA
1 GTGTA
31421922 CTGGGTACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (14 bp):
GTGTAGGCTACTAC
Found at i:31421988 original size:45 final size:45
Alignment explanation
Indices: 31421924--31422083 Score: 241
Period size: 45 Copynumber: 3.6 Consensus size: 45
31421914 TACGTGTACT
*
31421924 GGGTACCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
1 GGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
*
31421969 GGGTATCATTGATTATAAAGGTGGTTGATGTGTGCTGATTCCACC
1 GGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
* *
31422014 GGGTA-CTATTGATTATGAAGGTGGTTGCTATGTGCTGATTCCACC
1 GGGTATC-ATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
* * *
31422059 GAGTATCATTGACTATAAGGGTGGT
1 GGGTATCATTGATTATAAAGGTGGT
31422084 GCTATGAGTT
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.01
45 102 0.98
46 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.34
Consensus pattern (45 bp):
GGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
Found at i:31435299 original size:12 final size:13
Alignment explanation
Indices: 31435275--31435303 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
31435265 GGGCTATAAC
31435275 TATTGCATTTATT
1 TATTGCATTTATT
31435288 TATTGC-TTTATT
1 TATTGCATTTATT
31435300 TATT
1 TATT
31435304 TTAGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:31444888 original size:54 final size:54
Alignment explanation
Indices: 31444757--31444934 Score: 223
Period size: 54 Copynumber: 3.3 Consensus size: 54
31444747 ACATTAAAAG
* * * * * *
31444757 TTTAATCCAGCAAC-TAAGTGAACTAAGTTGAACTTAATTAACTAAAATGAGTGAT
1 TTTATTCCAGCAACTTAA-TTAACTAAGATGAACTCAATTAACTAAGATGAGT-AA
* * *
31444812 TTTATTCCAGTAACTTAATTAACTAAGATGAACTCAAGTAACGAAGATGAGTAA
1 TTTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
* *
31444866 TTTATTCAAGCAACTTAATTAACTAAGATGAGCTCAATTAACTAAGATGAGTAA
1 TTTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
*
31444920 CTTATTCCAGCAACT
1 TTTATTCCAGCAACT
31444935 AAATACTTAT
Statistics
Matches: 106, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
54 63 0.59
55 40 0.38
56 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (54 bp):
TTTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
Found at i:31444906 original size:19 final size:19
Alignment explanation
Indices: 31444828--31444916 Score: 71
Period size: 19 Copynumber: 4.8 Consensus size: 19
31444818 CCAGTAACTT
*
31444828 AATTAACTAAGATGAACTC
1 AATTAACTAAGATGAGCTC
* *
31444847 AAGTAACGAAGATGAG-T-
1 AATTAACTAAGATGAGCTC
* * *
31444864 AATTTATTCAAGCA--A-CTT
1 AATTAACT-AAG-ATGAGCTC
31444882 AATTAACTAAGATGAGCTC
1 AATTAACTAAGATGAGCTC
31444901 AATTAACTAAGATGAG
1 AATTAACTAAGATGAG
31444917 TAACTTATTC
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
16 1 0.02
17 9 0.17
18 11 0.21
19 32 0.60
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (19 bp):
AATTAACTAAGATGAGCTC
Found at i:31449269 original size:54 final size:54
Alignment explanation
Indices: 31449203--31449339 Score: 195
Period size: 54 Copynumber: 2.5 Consensus size: 54
31449193 ACATTAAAAT
* * * * *
31449203 TTTAATCCAGCAACTAAGTGAACTAAGTTGAACTTAATTAACTAATATGAGTAA
1 TTTATTCCAGCAACTAAGTTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
31449257 TTTATTCCAGCAACTTAA-TTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
1 TTTATTCCAGCAAC-TAAGTTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
* *
31449311 TTTATTCAAGCAACTTAGTTAACTAAGAT
1 TTTATTCCAGCAACTAAGTTAACTAAGAT
31449340 TATTAATTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
53 2 0.03
54 69 0.93
55 3 0.04
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (54 bp):
TTTATTCCAGCAACTAAGTTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
Found at i:31449295 original size:19 final size:19
Alignment explanation
Indices: 31449268--31449306 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
31449258 TTATTCCAGC
*
31449268 AACTTAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
31449287 AACTCAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
31449306 A
1 A
31449307 GTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (19 bp):
AACTCAATTAACTAAGATG
Found at i:31449333 original size:35 final size:35
Alignment explanation
Indices: 31449294--31449360 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
31449284 ATGAACTCAA
31449294 TTAACTAAGATGAGTAATTTATTCAAGCAACTTAG
1 TTAACTAAGATGAGTAATTTATTCAAGCAACTTAG
* * *
31449329 TTAACTAAGATTATTAATTTATTCCAGCAACT
1 TTAACTAAGATGAGTAATTTATTCAAGCAACT
31449361 AAATACTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (35 bp):
TTAACTAAGATGAGTAATTTATTCAAGCAACTTAG
Found at i:31452029 original size:3 final size:3
Alignment explanation
Indices: 31452021--31452045 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31452011 CTCTGTGGGA
31452021 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
31452046 TGGGATCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:31452861 original size:25 final size:25
Alignment explanation
Indices: 31452833--31452888 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
31452823 TAATTAGTAT
*
31452833 AAAATATT-AATAATTCAATAAATTG
1 AAAAT-TTAAATAATTAAATAAATTG
*
31452858 AAAATTTAAATAATTAAATAAATTT
1 AAAATTTAAATAATTAAATAAATTG
31452883 AAAATT
1 AAAATT
31452889 GAGGAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAATTTAAATAATTAAATAAATTG
Found at i:31453617 original size:16 final size:15
Alignment explanation
Indices: 31453592--31453625 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
31453582 AAAGTTGATA
*
31453592 ATAATTAATATATATT
1 ATAATAAATATA-ATT
31453608 ATAATAAATATAATT
1 ATAATAAATATAATT
31453623 ATA
1 ATA
31453626 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:31463905 original size:26 final size:26
Alignment explanation
Indices: 31463856--31463916 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
31463846 AAAGGTTTTT
* * *
31463856 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATTACCAAAATACCCTCGAA-GGCA
*
31463883 AAATTACCAAAATACCC-CTAAGGCA
1 AAATTACCAAAATACCCTCGAAGGCA
31463908 AAATTACCA
1 AAATTACCA
31463917 TTTTACCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 12 0.40
26 3 0.10
27 15 0.50
ACGTcount: A:0.46, C:0.25, G:0.13, T:0.16
Consensus pattern (26 bp):
AAATTACCAAAATACCCTCGAAGGCA
Found at i:31465645 original size:51 final size:50
Alignment explanation
Indices: 31465465--31465700 Score: 321
Period size: 50 Copynumber: 4.7 Consensus size: 50
31465455 TCATTCGATA
*
31465465 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
*
31465515 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
*
31465565 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGGTT
** * * * *** *
31465616 CATATAGTAGCCTACACTTAGTACTACACATGTGACCATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTA-CGGTT
*
31465667 CACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
31465701 TTCATCAATA
Statistics
Matches: 164, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
49 3 0.02
50 87 0.53
51 70 0.43
52 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
Found at i:31470023 original size:26 final size:27
Alignment explanation
Indices: 31469978--31470028 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
31469968 TAATTGAATG
31469978 AAATACCCTTAAAGGATAAAATTACTA
1 AAATACCCTTAAAGGATAAAATTACTA
* *
31470005 AAATA-CCTTATAGGGTAAAATTAC
1 AAATACCCTTAAAGGATAAAATTAC
31470029 CATTTTACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (27 bp):
AAATACCCTTAAAGGATAAAATTACTA
Found at i:31471500 original size:11 final size:11
Alignment explanation
Indices: 31471484--31471512 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
31471474 AGGGAATGAA
31471484 GAGAGAAAAGT
1 GAGAGAAAAGT
31471495 GAGAGAAAAGT
1 GAGAGAAAAGT
31471506 GA-AGAAA
1 GAGAGAAA
31471513 TGAATGCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (11 bp):
GAGAGAAAAGT
Found at i:31475630 original size:5 final size:5
Alignment explanation
Indices: 31475620--31475658 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
31475610 TACTGAAAAT
31475620 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
31475659 TAAAATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:31476079 original size:29 final size:30
Alignment explanation
Indices: 31476047--31476113 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
31476037 ATTGGGAAAC
31476047 ATTTTTATATTAATTA-ATAATGAGAAAAA
1 ATTTTTATATTAATTATATAATGAGAAAAA
* * * *
31476076 A-TTTTACATTAGTTATATTATGAGAAAAT
1 ATTTTTATATTAATTATATAATGAGAAAAA
*
31476105 TTTTTTATA
1 ATTTTTATA
31476114 AGGAAGTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 12 0.40
29 12 0.40
30 6 0.20
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.48
Consensus pattern (30 bp):
ATTTTTATATTAATTATATAATGAGAAAAA
Found at i:31476080 original size:28 final size:29
Alignment explanation
Indices: 31476049--31476103 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
31476039 TGGGAAACAT
*
31476049 TTTTATATTAATTA-ATAATGAGAAAAAA
1 TTTTACATTAATTATATAATGAGAAAAAA
* *
31476077 TTTTACATTAGTTATATTATGAGAAAA
1 TTTTACATTAATTATATAATGAGAAAA
31476104 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (29 bp):
TTTTACATTAATTATATAATGAGAAAAAA
Found at i:31478465 original size:29 final size:29
Alignment explanation
Indices: 31478423--31478483 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
31478413 AGGTCTACAT
31478423 CAAGATCAGAATTTAGAAACCAAGAAAAA
1 CAAGATCAGAATTTAGAAACCAAGAAAAA
*
31478452 CAAGATCAGAATTTAGAAACTAAGAAAAA
1 CAAGATCAGAATTTAGAAACCAAGAAAAA
31478481 CAA
1 CAA
31478484 TCTGGCTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (29 bp):
CAAGATCAGAATTTAGAAACCAAGAAAAA
Found at i:31483116 original size:29 final size:29
Alignment explanation
Indices: 31483034--31483124 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
31483024 TCATTAGGAT
* * *
31483034 TTATCAGGCACTATGTGCTAGAGATTACAG
1 TTATCAGGCACTTTGTGCTAGTG-TTATAG
* * *
31483064 TTATCAGGTACTTTGT-ATCCGTGTTATAG
1 TTATCAGGCACTTTGTGCT-AGTGTTATAG
*
31483093 TTATCAGGCACTTTGTGCTGGTGTTATA-
1 TTATCAGGCACTTTGTGCTAGTGTTATAG
31483121 TTAT
1 TTAT
31483125 TGGGTACTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 4 0.08
29 29 0.58
30 17 0.34
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (29 bp):
TTATCAGGCACTTTGTGCTAGTGTTATAG
Found at i:31486098 original size:28 final size:27
Alignment explanation
Indices: 31486041--31486123 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
31486031 CGAAAGCTGT
* * *
31486041 GAATAGCCTTTTTGGTGAACTCTGAAA
1 GAATAGCCTTTGTGGCGAACTATGAAA
31486068 GAATAGCCTTTGTGGCGAAACTAT-ATAA
1 GAATAGCCTTTGTGGCG-AACTATGA-AA
* ** *
31486096 GAATAACCTTTGTGATGAACTCTGAAA
1 GAATAGCCTTTGTGGCGAACTATGAAA
31486123 G
1 G
31486124 GGATGCCTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 24 0.52
28 22 0.48
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (27 bp):
GAATAGCCTTTGTGGCGAACTATGAAA
Found at i:31489583 original size:19 final size:20
Alignment explanation
Indices: 31489561--31489606 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
31489551 AAAAATGAAC
31489561 TTTTAAACATTTTTTTT-AT
1 TTTTAAACATTTTTTTTAAT
**
31489580 TTTTAAAGTTTTTTTTTCAAT
1 TTTTAAACATTTTTTTT-AAT
31489601 TTTTAA
1 TTTTAA
31489607 GAAATAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
21 8 0.35
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTAAACATTTTTTTTAAT
Found at i:31489695 original size:59 final size:62
Alignment explanation
Indices: 31489598--31489717 Score: 149
Period size: 59 Copynumber: 2.0 Consensus size: 62
31489588 TTTTTTTTTC
* * *
31489598 AATTTTTAAGAAATAAACCTAAATTGACAAAATGTGT-AACGTT-GATGG-CTAAATTTGTTG
1 AATTTTTAAGAAATAAAACTAAATTGACAAAATATGTAAACATTGGA-GGTCTAAATTTGTTG
* * *
31489658 AATTTTT-AGAATTAAAACTAAATTGATAGAATATGTAAACATTGGAGGTCTAAATTTGTT
1 AATTTTTAAGAAATAAAACTAAATTGACAAAATATGTAAACATTGGAGGTCTAAATTTGTT
31489718 ATTATGTCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
59 24 0.47
60 14 0.27
61 13 0.25
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.37
Consensus pattern (62 bp):
AATTTTTAAGAAATAAAACTAAATTGACAAAATATGTAAACATTGGAGGTCTAAATTTGTTG
Done.