Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, whole genome shotgun sequence
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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 4 of 29
Found at i:828332 original size:81 final size:80
Alignment explanation
Indices: 828120--828324 Score: 268
Period size: 80 Copynumber: 2.5 Consensus size: 80
828110 TCAAAATACA
* * * * *
828120 GTGTCACAGATTCTCACCATGCCGTGTCACACATTGCT-ACCACGGCGTGTCATAAACTCTAAAC
1 GTGTCACATATTCTCACCATGCCGTCTCACATATT-CTCACCATGGCGTGTCACAAACTCTAAAC
*
828184 TTACTGTGTCATAGTC
65 TTACTATGTCATAGTC
* * *
828200 GTATCACATATTCTCACCATGTCGTCTCACATATTCTCACCATGGCGTGTCACAAACTTTAAACT
1 GTGTCACATATTCTCACCATGCCGTCTCACATATTCTCACCATGGCGTGTCACAAACTCTAAACT
** *
828265 TTGTCATGTCGTAGTC
66 TACT-ATGTCATAGTC
*
828281 GTGTCACATATTCTCACCATGCCATCTCACATATTCTCACCATG
1 GTGTCACATATTCTCACCATGCCGTCTCACATATTCTCACCATG
828325 ACATGTCATA
Statistics
Matches: 108, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
79 2 0.02
80 56 0.52
81 50 0.46
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (80 bp):
GTGTCACATATTCTCACCATGCCGTCTCACATATTCTCACCATGGCGTGTCACAAACTCTAAACT
TACTATGTCATAGTC
Found at i:828363 original size:44 final size:46
Alignment explanation
Indices: 828282--828408 Score: 143
Period size: 44 Copynumber: 2.8 Consensus size: 46
828272 GTCGTAGTCG
*
828282 TGTCACATATTCTCACCATGCCATCTCACATATTCTCAC-CATGACA
1 TGTCATATATTCTCACCATGCCATCTCACATATTCTCACAC-TGACA
* * * * * *
828328 TGTCATATATTCACACCATGGCATGTCA-A-ATTCTCATACTGGCG
1 TGTCATATATTCTCACCATGCCATCTCACATATTCTCACACTGACA
* *
828372 TGTCATATATTCTCACCATGTCGTCTCACATATTCTC
1 TGTCATATATTCTCACCATGCCATCTCACATATTCTC
828409 TATAAATCAT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
44 34 0.51
45 3 0.04
46 30 0.45
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.34
Consensus pattern (46 bp):
TGTCATATATTCTCACCATGCCATCTCACATATTCTCACACTGACA
Found at i:828445 original size:90 final size:89
Alignment explanation
Indices: 828280--828445 Score: 199
Period size: 90 Copynumber: 1.8 Consensus size: 89
828270 ATGTCGTAGT
** *
828280 CGTGTCACATATTCTCACCATGCCATCTCACATATTCTCACCATGACATGTCATATATTCACACC
1 CGTGTCACATATTCTCACCATGCCATCTCACATATTCTCAAAAT-ACATGTCACATATTCACACC
**
828345 ATGGCATGTCAAATTCTCATACTGG
65 ATACCATGTCAAATTCTCATACTGG
* * * *
828370 CGTGTCATATATTCTCACCATGTCGTCTCACATATTCTCTATAAAT-CATGTCACATATTCTCAC
1 CGTGTCACATATTCTCACCATGCCATCTCACATATTCTC-A-AAATACATGTCACATATTCACAC
* *
828434 CCTACCGTGTCA
64 CATACCATGTCA
828446 TTTATTCCTT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
90 60 0.95
91 1 0.02
92 2 0.03
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (89 bp):
CGTGTCACATATTCTCACCATGCCATCTCACATATTCTCAAAATACATGTCACATATTCACACCA
TACCATGTCAAATTCTCATACTGG
Found at i:829227 original size:171 final size:171
Alignment explanation
Indices: 828942--829282 Score: 601
Period size: 171 Copynumber: 2.0 Consensus size: 171
828932 ATGAAAATGT
* * *
828942 CTCATTAAGGGTATTTTTGTCCAACAATCTCTTTTTTTGACTAAAAATAGTTAAAATTATTTAAA
1 CTCATTAAGGGCATTTTTGTCCAAAAATCTCTTCTTTTGACTAAAAATAGTTAAAATTATTTAAA
****
829007 GTGTTATTTTCAAAAACACCTTGTATTTTAAGGCTAAAATTTTTTTTCCCTAAATATAAACCATG
66 GTGTTATTTTCAAAAACACCTTGTATTTTAAGGCTAAAAAAAATTTTCCCTAAATATAAACCATG
829072 ATAGTCAATTCATAGTCATCAACATAAAAGCATAAACCAGA
131 ATAGTCAATTCATAGTCATCAACATAAAAGCATAAACCAGA
* *
829113 CTCATTAAGGGCATTTTTGTCTAAAAATCTCTTCTTTTGGCTAAAAATAGTTAAAATTATTTAAA
1 CTCATTAAGGGCATTTTTGTCCAAAAATCTCTTCTTTTGACTAAAAATAGTTAAAATTATTTAAA
829178 GTGTTATTTTCAAAAACACCTTGTATTTTAAGGCTAAAAAAAATTTTCCCTAAATATAAACCATG
66 GTGTTATTTTCAAAAACACCTTGTATTTTAAGGCTAAAAAAAATTTTCCCTAAATATAAACCATG
829243 ATAGTCAATTCATAGTCATCAACATAAAAGCATAAACCAG
131 ATAGTCAATTCATAGTCATCAACATAAAAGCATAAACCAG
829283 TAGACACATT
Statistics
Matches: 161, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
171 161 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (171 bp):
CTCATTAAGGGCATTTTTGTCCAAAAATCTCTTCTTTTGACTAAAAATAGTTAAAATTATTTAAA
GTGTTATTTTCAAAAACACCTTGTATTTTAAGGCTAAAAAAAATTTTCCCTAAATATAAACCATG
ATAGTCAATTCATAGTCATCAACATAAAAGCATAAACCAGA
Found at i:832685 original size:32 final size:32
Alignment explanation
Indices: 832636--832703 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
832626 TAGTCTACTA
* *
832636 AGAGGCTACTGCCAGAAACTGGATTTAGAGAC
1 AGAGCCTACTGCCAGAAACTGGATTCAGAGAC
* * *
832668 AGAGCCTACTGCTAGAAACTGGGTTCAGAGAT
1 AGAGCCTACTGCCAGAAACTGGATTCAGAGAC
832700 AGAG
1 AGAG
832704 ACAACTTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (32 bp):
AGAGCCTACTGCCAGAAACTGGATTCAGAGAC
Found at i:837438 original size:14 final size:14
Alignment explanation
Indices: 837390--837438 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
837380 AATTATTAGT
*
837390 AAATAAATAAATAA
1 AAATAAATAAATTA
*
837404 AAATAACTAAGA-TA
1 AAATAAATAA-ATTA
837418 AAATAAATAAATTA
1 AAATAAATAAATTA
*
837432 AATTAAA
1 AAATAAA
837439 ATGCTTAGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (14 bp):
AAATAAATAAATTA
Found at i:850396 original size:2 final size:2
Alignment explanation
Indices: 850384--850415 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
850374 GTTGTTTGTG
850384 TA TA CTA 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 TA TA T
850416 GTAAAGTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:865365 original size:25 final size:25
Alignment explanation
Indices: 865275--865366 Score: 70
Period size: 25 Copynumber: 3.8 Consensus size: 25
865265 TTGAAGCCCT
* *
865275 AATCAGGCTCTCCATGGGAGCCCCA
1 AATCAGGCTCCCCAAGGGAGCCCCA
* * *
865300 AAACAAGCTCCCCAAAGGAG---C-
1 AATCAGGCTCCCCAAGGGAGCCCCA
*
865321 ACT-AGAGCT-CCCAAGAGGAGCCCCA
1 AATCAG-GCTCCCCAAG-GGAGCCCCA
865346 AATCAGGCTCCCCAAGGGAGC
1 AATCAGGCTCCCCAAGGGAGC
865367 ATCGATCGGT
Statistics
Matches: 49, Mismatches: 10, Indels: 16
0.65 0.13 0.21
Matches are distributed among these distances:
20 6 0.12
21 8 0.16
22 1 0.02
24 1 0.02
25 25 0.51
26 8 0.16
ACGTcount: A:0.32, C:0.35, G:0.24, T:0.10
Consensus pattern (25 bp):
AATCAGGCTCCCCAAGGGAGCCCCA
Found at i:866862 original size:15 final size:15
Alignment explanation
Indices: 866842--866871 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
866832 GCACTAGATC
866842 TAGTGCTTCCTTTGG
1 TAGTGCTTCCTTTGG
866857 TAGTGCTTCCTTTGG
1 TAGTGCTTCCTTTGG
866872 AACCTTGATT
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:0.07, C:0.20, G:0.27, T:0.47
Consensus pattern (15 bp):
TAGTGCTTCCTTTGG
Found at i:869865 original size:31 final size:31
Alignment explanation
Indices: 869830--869898 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
869820 AAAAAAAATT
869830 AAATTTTCCTGTAAAATATTTTACATAGAAA
1 AAATTTTCCTGTAAAATATTTTACATAGAAA
869861 AAATTTTCCTGTAAAATATTTTACATAGAAA
1 AAATTTTCCTGTAAAATATTTTACATAGAAA
*
869892 AAGTTTT
1 AAATTTT
869899 TCGTTAGCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (31 bp):
AAATTTTCCTGTAAAATATTTTACATAGAAA
Found at i:869866 original size:16 final size:16
Alignment explanation
Indices: 869842--869898 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
869832 ATTTTCCTGT
*
869842 AAAATATTTTACATAG
1 AAAAAATTTTACATAG
*
869858 AAAAAATTTT-CCT-G
1 AAAAAATTTTACATAG
*
869872 TAAAATATTTTACATAG
1 -AAAAAATTTTACATAG
*
869889 AAAAAGTTTT
1 AAAAAATTTT
869899 TCGTTAGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
14 1 0.03
15 11 0.34
16 19 0.59
17 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (16 bp):
AAAAAATTTTACATAG
Found at i:869881 original size:15 final size:15
Alignment explanation
Indices: 869832--869882 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
869822 AAAAAATTAA
869832 ATTTTCCTGTAAAAT
1 ATTTTCCTGTAAAAT
* *
869847 ATTTTACATAG-AAAAA
1 ATTTT-CCT-GTAAAAT
869863 ATTTTCCTGTAAAAT
1 ATTTTCCTGTAAAAT
869878 ATTTT
1 ATTTT
869883 ACATAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.55
16 11 0.38
17 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (15 bp):
ATTTTCCTGTAAAAT
Found at i:871164 original size:16 final size:16
Alignment explanation
Indices: 871135--871166 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
871125 CATATTTATC
*
871135 TTTTTTTTTATTTTTG
1 TTTTTTATTATTTTTG
871151 TTTTTTATTATTTTTG
1 TTTTTTATTATTTTTG
871167 AACTTCTAAA
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:0.09, C:0.00, G:0.06, T:0.84
Consensus pattern (16 bp):
TTTTTTATTATTTTTG
Found at i:871437 original size:87 final size:86
Alignment explanation
Indices: 871312--871554 Score: 251
Period size: 87 Copynumber: 2.8 Consensus size: 86
871302 CTTTATCTAA
* * *
871312 AATGAGGCTATGTAAC-TCAAA-AAGAAATAAGCTCCTCATCTGAAATAAGGCTATGTAACTTTA
1 AATGAGGCTACGTAACTTTAAATAAG-AAGAAGCTCCTCATCT-AAATAAGGCTATGTAACTTTA
** *
871375 AAATG-AATAAGTTCCTTACCTGG
64 AAA-GAAATAAACTCCTCACCTGG
* * *
871398 AATGAGGCTACGTAACTTTAAATAAGAGGAAGCTCCTCATCTAGAATAAGGCTACGTAATTTTAA
1 AATGAGGCTACGTAACTTTAAATAAGAAGAAGCTCCTCATCTA-AATAAGGCTATGTAACTTTAA
*
871463 AAGAAATAAACTCCTCATCTGG
65 AAGAAATAAACTCCTCACCTGG
* * * * * * * *
871485 AGTGAGGTTACGTAACTTTAAATAGGAATAAACTCCTTATCTTAAATGAGACTATGTAACTTT-A
1 AATGAGGCTACGTAACTTTAAATAAGAAGAAGCTCCTCATC-TAAATAAGGCTATGTAACTTTAA
871549 AAGAAA
65 AAGAAA
871555 GCATATGTTC
Statistics
Matches: 131, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
86 24 0.18
87 102 0.78
88 5 0.04
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (86 bp):
AATGAGGCTACGTAACTTTAAATAAGAAGAAGCTCCTCATCTAAATAAGGCTATGTAACTTTAAA
AGAAATAAACTCCTCACCTGG
Found at i:871456 original size:44 final size:43
Alignment explanation
Indices: 871316--871550 Score: 195
Period size: 43 Copynumber: 5.4 Consensus size: 43
871306 ATCTAAAATG
* * *
871316 AGGCTATGTAAC-TCAAAAAGAAATAAGCTCCTCATCTGAAATA
1 AGGCTACGTAACTTTAAAAAG-AATAAGCTCCTCATCTGGAATA
* * * * * *
871359 AGGCTATGTAACTTTAAAATGAATAAGTTCCTTACCTGGAATG
1 AGGCTACGTAACTTTAAAAAGAATAAGCTCCTCATCTGGAATA
** *
871402 AGGCTACGTAACTTTAAATAAGAGGAAGCTCCTCATCTAGAATA
1 AGGCTACGTAACTTTAAA-AAGAATAAGCTCCTCATCTGGAATA
* * * *
871446 AGGCTACGTAA-TTTTAAAAGAAATAAACTCCTCATCTGGAGTG
1 AGGCTACGTAACTTTAAAAAG-AATAAGCTCCTCATCTGGAATA
* * * * ** *
871489 AGGTTACGTAACTTTAAATAGGAATAAACTCCTTATCTTAAATG
1 AGGCTACGTAACTTTAAA-AAGAATAAGCTCCTCATCTGGAATA
* *
871533 AGACTATGTAACTTTAAA
1 AGGCTACGTAACTTTAAA
871551 GAAAGCATAT
Statistics
Matches: 154, Mismatches: 33, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
42 3 0.02
43 77 0.50
44 72 0.47
45 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (43 bp):
AGGCTACGTAACTTTAAAAAGAATAAGCTCCTCATCTGGAATA
Found at i:873793 original size:21 final size:22
Alignment explanation
Indices: 873758--873801 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
873748 CTCTTAAAGT
873758 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
873780 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
873801 A
1 A
873802 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:881263 original size:7 final size:7
Alignment explanation
Indices: 881251--881277 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
881241 TTGTTGTTGG
881251 TTCAAAC
1 TTCAAAC
881258 TTCAAAC
1 TTCAAAC
881265 TTCAAAC
1 TTCAAAC
881272 TTCAAA
1 TTCAAA
881278 AGTAACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (7 bp):
TTCAAAC
Found at i:903879 original size:11 final size:11
Alignment explanation
Indices: 903863--903935 Score: 56
Period size: 11 Copynumber: 6.6 Consensus size: 11
903853 TTAAACCTAT
*
903863 CAAAATTTGCA
1 CAAAATTTACA
903874 CAAAATTTACA
1 CAAAATTTACA
* *
903885 CAAAAGTCACA
1 CAAAATTTACA
* * *
903896 CAAAAGTCATA
1 CAAAATTTACA
*
903907 CAAAATTTGCA
1 CAAAATTTACA
* **
903918 TAAAATTTGTA
1 CAAAATTTACA
903929 CAAAATT
1 CAAAATT
903936 CACTAAATGT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 51 1.00
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (11 bp):
CAAAATTTACA
Found at i:923463 original size:18 final size:18
Alignment explanation
Indices: 923437--923476 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
923427 TTAAAGTAAA
* *
923437 ACTATACATGCATAAAGC
1 ACTAAACATGCATAAAAC
*
923455 ACTAAACATGCTTAAAAC
1 ACTAAACATGCATAAAAC
923473 ACTA
1 ACTA
923477 TGTGAGTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (18 bp):
ACTAAACATGCATAAAAC
Found at i:923553 original size:21 final size:21
Alignment explanation
Indices: 923528--923570 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
923518 CATGTTGCAA
923528 AAATATTTATCATACTCCACC
1 AAATATTTATCATACTCCACC
923549 AAATATTTATCATACTCCACC
1 AAATATTTATCATACTCCACC
923570 A
1 A
923571 CACCTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATTTATCATACTCCACC
Found at i:928045 original size:2 final size:2
Alignment explanation
Indices: 928004--928031 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
927994 TGTCTTGATC
928004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
928032 GCACAAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:928470 original size:25 final size:25
Alignment explanation
Indices: 928428--928477 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
928418 CCATGGTCTG
*
928428 TGATATACGTGGCAAGGCCATAAGT
1 TGATATACGTGGCAAGGCCACAAGT
* **
928453 TGATATATGTGGTTAGGCCACAAGT
1 TGATATACGTGGCAAGGCCACAAGT
928478 AATATACACG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (25 bp):
TGATATACGTGGCAAGGCCACAAGT
Found at i:940029 original size:48 final size:49
Alignment explanation
Indices: 939930--940042 Score: 210
Period size: 49 Copynumber: 2.3 Consensus size: 49
939920 TCTTAGCGAA
939930 TTTTTAAGTAATACCAATTCACATTCAAAAACTTAAAAAAGAATATATT
1 TTTTTAAGTAATACCAATTCACATTCAAAAACTTAAAAAAGAATATATT
*
939979 TTTTTAAGTTATACCAATTCACATTCAAAAACTTAAAAAAGAATAT-TT
1 TTTTTAAGTAATACCAATTCACATTCAAAAACTTAAAAAAGAATATATT
940027 TTTTTAAGTAATACCA
1 TTTTTAAGTAATACCA
940043 TTAGATTTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
48 17 0.27
49 45 0.73
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.37
Consensus pattern (49 bp):
TTTTTAAGTAATACCAATTCACATTCAAAAACTTAAAAAAGAATATATT
Found at i:941472 original size:18 final size:18
Alignment explanation
Indices: 941451--941486 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
941441 TAAAAGAAAA
*
941451 ATATAATAAAAAATGAAT
1 ATATAATAAAAAAAGAAT
*
941469 ATATATTAAAAAAAGAAT
1 ATATAATAAAAAAAGAAT
941487 GAGAAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (18 bp):
ATATAATAAAAAAAGAAT
Found at i:943103 original size:27 final size:28
Alignment explanation
Indices: 943059--943112 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
943049 GATTGAAGAA
*
943059 AGATATAACTTAAATTTT-AAAAAAAAT
1 AGATATAACATAAATTTTCAAAAAAAAT
*
943086 AGATATAACATAACTTTTCAAAAAAAA
1 AGATATAACATAAATTTTCAAAAAAAA
943113 AAAGATGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (28 bp):
AGATATAACATAAATTTTCAAAAAAAAT
Found at i:944547 original size:20 final size:20
Alignment explanation
Indices: 944524--944563 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
944514 ATATACATTA
944524 ATTA-AAAATATAAAAAAATC
1 ATTAGAAAATA-AAAAAAATC
*
944544 ATTAGAAAATAAGAAAAATC
1 ATTAGAAAATAAAAAAAATC
944564 TATTTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (20 bp):
ATTAGAAAATAAAAAAAATC
Found at i:948957 original size:15 final size:15
Alignment explanation
Indices: 948934--948972 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
948924 TTTATTTTTG
948934 TTTTT-TTTTAAATT
1 TTTTTATTTTAAATT
**
948948 TTTTTATTTTCCATT
1 TTTTTATTTTAAATT
948963 TTTTTATTTT
1 TTTTTATTTT
948973 CTAATTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTATTTTAAATT
Found at i:948973 original size:15 final size:15
Alignment explanation
Indices: 948945--948973 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
948935 TTTTTTTTAA
948945 ATTTTTTTATTTTCC
1 ATTTTTTTATTTTCC
948960 ATTTTTTTATTTTC
1 ATTTTTTTATTTTC
948974 TAATTCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTTTATTTTCC
Found at i:953431 original size:27 final size:27
Alignment explanation
Indices: 953391--953446 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
953381 TTGAGCAATC
* *
953391 ATTTTAGTTTAATGAAAATGTGACAGG
1 ATTTTAGGTCAATGAAAATGTGACAGG
953418 ATTTTAGGTCAATGAAAATGTGACAGG
1 ATTTTAGGTCAATGAAAATGTGACAGG
953445 AT
1 AT
953447 GAGACTGGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (27 bp):
ATTTTAGGTCAATGAAAATGTGACAGG
Found at i:954849 original size:2 final size:2
Alignment explanation
Indices: 954842--954870 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
954832 GATGGAACAC
954842 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
954871 CTGGTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:958543 original size:15 final size:15
Alignment explanation
Indices: 958502--958543 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
958492 CCTTCAATAG
*
958502 TTTTT-AAAATTAAA
1 TTTTTAAAAATTTAA
*
958516 TTATTAAAAATTTAA
1 TTTTTAAAAATTTAA
958531 TTTTTAAAAATTT
1 TTTTTAAAAATTT
958544 GAAAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTTAAAAATTTAA
Found at i:982741 original size:22 final size:23
Alignment explanation
Indices: 982716--982758 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
982706 ATTTAATACT
*
982716 CAATA-AAAAGTGCAGATAAATC
1 CAATATAAAAGAGCAGATAAATC
*
982738 CAATATAATAGAGCAGATAAA
1 CAATATAAAAGAGCAGATAAA
982759 CATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.56, C:0.12, G:0.14, T:0.19
Consensus pattern (23 bp):
CAATATAAAAGAGCAGATAAATC
Found at i:983693 original size:21 final size:22
Alignment explanation
Indices: 983668--983711 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
983658 AAGTGATTAA
983668 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
983689 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
983711 T
1 T
983712 ACTTTAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:992463 original size:30 final size:30
Alignment explanation
Indices: 992399--992464 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
992389 TGTTTTCAAC
* *
992399 TTCATCTTCATCTCTTTCCATGTCAATTTC
1 TTCATCTTCATCTCCTTCCATGTCAATTTA
**
992429 TTCATCTTCATCTCCTTGTATGTC-ATCTTA
1 TTCATCTTCATCTCCTTCCATGTCAAT-TTA
992459 TTCATC
1 TTCATC
992465 CTCAATCAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.17, C:0.29, G:0.05, T:0.50
Consensus pattern (30 bp):
TTCATCTTCATCTCCTTCCATGTCAATTTA
Found at i:996865 original size:6 final size:6
Alignment explanation
Indices: 996854--996879 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
996844 TGCAAAATGC
996854 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
996880 TGTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:1008451 original size:12 final size:12
Alignment explanation
Indices: 1008434--1008466 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1008424 GAATAGTTTC
1008434 TTGCTGCCTCCT
1 TTGCTGCCTCCT
1008446 TTGCTGCCT-CT
1 TTGCTGCCTCCT
*
1008457 CTGCTGCCTC
1 TTGCTGCCTC
1008467 AAAAATCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.00, C:0.42, G:0.18, T:0.39
Consensus pattern (12 bp):
TTGCTGCCTCCT
Found at i:1009144 original size:21 final size:22
Alignment explanation
Indices: 1009109--1009152 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1009099 CTCTTAAAGT
1009109 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
1009131 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
1009152 A
1 A
1009153 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:1011223 original size:30 final size:28
Alignment explanation
Indices: 1011139--1011230 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
1011129 CGTCCCCCCG
* *
1011139 CGCCGGCCCGCCGCGCC-CCTCCGGCTCGC
1 CGCCGGCCCG-CGCGCCGCCGCC-GCGCGC
*
1011168 CGCCGGCCCGCGCGCCGCCGGCGCGCGC
1 CGCCGGCCCGCGCGCCGCCGCCGCGCGC
*
1011196 GGCCGGCCCCGCGGCGCCGTCC-CCGCGCGC
1 CGCCGG-CCCGC-GCGCCG-CCGCCGCGCGC
1011226 CGCCG
1 CGCCG
1011231 CGGCGGCCTG
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
28 16 0.30
29 18 0.34
30 17 0.32
31 2 0.04
ACGTcount: A:0.00, C:0.59, G:0.38, T:0.03
Consensus pattern (28 bp):
CGCCGGCCCGCGCGCCGCCGCCGCGCGC
Found at i:1011261 original size:45 final size:43
Alignment explanation
Indices: 1011174--1011262 Score: 101
Period size: 43 Copynumber: 2.0 Consensus size: 43
1011164 TCGCCGCCGG
**
1011174 CCCGCGCGCCGCCGGCGCGCGCGGCCGGCCCCGCGGCGCCGTC
1 CCCGCGCGCCGCCGGCGCGCGCGGCCGGCCCCGCCCCGCCGTC
*
1011217 CCCGCGCGCCGCC-GCG-GCGGCCTGCTCGGCCCCGCCCCGACCGTC
1 CCCGCGCGCCGCCGGCGCGC-G-CGGC-CGGCCCCGCCCCG-CCGTC
1011262 C
1 C
1011263 GCCGGGCCCG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
41 2 0.05
42 4 0.10
43 16 0.41
44 11 0.28
45 6 0.15
ACGTcount: A:0.01, C:0.57, G:0.37, T:0.04
Consensus pattern (43 bp):
CCCGCGCGCCGCCGGCGCGCGCGGCCGGCCCCGCCCCGCCGTC
Found at i:1014841 original size:27 final size:27
Alignment explanation
Indices: 1014810--1014862 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1014800 GGGCCGCCGT
*
1014810 CTTGTCCGCCTCGCGCGCG-CGCCGGCG
1 CTTGTCCG-CGCGCGCGCGTCGCCGGCG
*
1014837 CTTGTCCGCGCGCGCGTGTCGCCGGC
1 CTTGTCCGCGCGCGCGCGTCGCCGGC
1014863 TGCCGGCCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.00, C:0.45, G:0.38, T:0.17
Consensus pattern (27 bp):
CTTGTCCGCGCGCGCGCGTCGCCGGCG
Found at i:1015517 original size:1 final size:1
Alignment explanation
Indices: 1015511--1015574 Score: 128
Period size: 1 Copynumber: 64.0 Consensus size: 1
1015501 AAGCCCACCG
1015511 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1015575 TTCAGCAACC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1022207 original size:53 final size:54
Alignment explanation
Indices: 1022150--1022285 Score: 143
Period size: 53 Copynumber: 2.5 Consensus size: 54
1022140 ATGAAAAACC
* * *
1022150 ATGAATGTCCATTCCCTGAAGTGAATATGATAAATGAGCTACTAAT-AAAAATT
1 ATGAATGTCCATTCCCTGAAGTGAATATGACAAACGAGATACTAATAAAAAATT
* * *
1022203 ATGAATGTTCATTCCAT-ATAGTGAATGTGACAAACGAGATACTAATAAAAAAATT
1 ATGAATGTCCATTCCCTGA-AGTGAATATGACAAACGAGATACTAAT-AAAAAATT
*
1022258 ATAAAT-TCATTCATTCCCTGAAGTGAAT
1 ATGAATGTC---CATTCCCTGAAGTGAAT
1022286 GCGGTATCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
52 1 0.01
53 38 0.57
54 1 0.01
55 12 0.18
57 14 0.21
58 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (54 bp):
ATGAATGTCCATTCCCTGAAGTGAATATGACAAACGAGATACTAATAAAAAATT
Found at i:1028176 original size:16 final size:14
Alignment explanation
Indices: 1028081--1028173 Score: 61
Period size: 16 Copynumber: 6.4 Consensus size: 14
1028071 NNAAATAAAA
1028081 TAAAATAATTAATCA-
1 TAAAAT-ATTAAT-AT
1028096 TAATAATATTTAA-AT
1 TAA-AATA-TTAATAT
1028111 TAAAAATATTAATATT
1 T-AAAATATTAATA-T
1028127 CTAAAATATTAATGAT
1 -TAAAATATTAAT-AT
*
1028143 TAAATTA-TAA-A-
1 TAAAATATTAATAT
1028154 TAAAATATTAATATT
1 TAAAATATTAATA-T
1028169 TAAAA
1 TAAAA
1028174 ATAAAATAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 24
0.71 0.02 0.27
Matches are distributed among these distances:
11 6 0.09
12 4 0.06
13 1 0.02
14 8 0.12
15 21 0.33
16 22 0.34
17 2 0.03
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (14 bp):
TAAAATATTAATAT
Found at i:1028180 original size:26 final size:26
Alignment explanation
Indices: 1028128--1028184 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1028118 ATTAATATTC
*
1028128 TAAAATATTAATGATTAAATTATAAA
1 TAAAATATTAATGATTAAAATATAAA
1028154 TAAAATATTAAT-ATTTAAAA-ATAAAA
1 TAAAATATTAATGA-TTAAAATAT-AAA
1028180 TAAAA
1 TAAAA
1028185 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
TAAAATATTAATGATTAAAATATAAA
Found at i:1037820 original size:18 final size:18
Alignment explanation
Indices: 1037797--1037831 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1037787 TAGATTTTAC
*
1037797 TTAATTATGTTGGGTTAG
1 TTAATTATGTTGAGTTAG
1037815 TTAATTATGTTGAGTTA
1 TTAATTATGTTGAGTTA
1037832 ATCTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (18 bp):
TTAATTATGTTGAGTTAG
Found at i:1045278 original size:17 final size:15
Alignment explanation
Indices: 1045244--1045282 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
1045234 AAATTTTATA
1045244 AAATTAAATAAAACT
1 AAATTAAATAAAACT
*
1045259 AAATTAAAGTAATCACT
1 AAATTAAA-TAA-AACT
1045276 AAATTAA
1 AAATTAA
1045283 TTAATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 3 0.14
17 10 0.48
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (15 bp):
AAATTAAATAAAACT
Found at i:1055934 original size:24 final size:24
Alignment explanation
Indices: 1055902--1055951 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1055892 CAAAATAATA
* *
1055902 TAATTTTATATAATTTTA-TATTTT
1 TAATATTATA-AATTTTAGTATGTT
1055926 TAATATTATAAATTTTAGTATGTT
1 TAATATTATAAATTTTAGTATGTT
1055950 TA
1 TA
1055952 TTTTCAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TAATATTATAAATTTTAGTATGTT
Found at i:1057018 original size:34 final size:34
Alignment explanation
Indices: 1056973--1057049 Score: 127
Period size: 34 Copynumber: 2.3 Consensus size: 34
1056963 TAATCTTTGA
*
1056973 CCATTTTAGCCCATAAATCATAGTCCAATTTAAC
1 CCATTTTAGCCCATAAATCATAGCCCAATTTAAC
* *
1057007 CTATTTTAGCCCATAAATTATAGCCCAATTTAAC
1 CCATTTTAGCCCATAAATCATAGCCCAATTTAAC
1057041 CCATTTTAG
1 CCATTTTAG
1057050 TCCAAGTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (34 bp):
CCATTTTAGCCCATAAATCATAGCCCAATTTAAC
Found at i:1062582 original size:2 final size:2
Alignment explanation
Indices: 1062575--1062604 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1062565 CATCTTAGAC
1062575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1062605 GTTAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1066804 original size:22 final size:20
Alignment explanation
Indices: 1066764--1066811 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
1066754 CGACCGCCAC
*
1066764 CGTCGGTTGTTCCGATCGGCCT
1 CGTCGGTTGATCCGATCGG--T
* *
1066786 CGTCGGTTGATCTGCTCGGT
1 CGTCGGTTGATCCGATCGGT
1066806 CGTCGG
1 CGTCGG
1066812 GAGGAACTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.04, C:0.29, G:0.35, T:0.31
Consensus pattern (20 bp):
CGTCGGTTGATCCGATCGGT
Found at i:1067203 original size:13 final size:13
Alignment explanation
Indices: 1067185--1067209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1067175 AACTATATCA
1067185 TATTTTTTAATTG
1 TATTTTTTAATTG
1067198 TATTTTTTAATT
1 TATTTTTTAATT
1067210 ACACCAAATG
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TATTTTTTAATTG
Found at i:1072527 original size:2 final size:2
Alignment explanation
Indices: 1072520--1072546 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1072510 NNNNNNNNNN
1072520 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
1072547 TAGCTAAAAA
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:1072821 original size:2 final size:2
Alignment explanation
Indices: 1072814--1072847 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1072804 TAGTTGCATA
1072814 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1072848 TATTCCTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1074621 original size:18 final size:19
Alignment explanation
Indices: 1074598--1074634 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1074588 TAAGCGGAGA
1074598 ATTTTA-GAATAAAATAAT
1 ATTTTATGAATAAAATAAT
*
1074616 ATTTTATTAATAAAATAAT
1 ATTTTATGAATAAAATAAT
1074635 CTTAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:1082892 original size:2 final size:2
Alignment explanation
Indices: 1082879--1082922 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1082869 CTTTCTGCAA
*
1082879 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1082921 AT
1 AT
1082923 TCGACAGCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1089494 original size:20 final size:20
Alignment explanation
Indices: 1089462--1089499 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1089452 ATAAAGAAAA
1089462 CATATATTTTTTTTATTTTG
1 CATATATTTTTTTTATTTTG
1089482 CATAT-TTTATTTTTATTT
1 CATATATTT-TTTTTATTT
1089500 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (20 bp):
CATATATTTTTTTTATTTTG
Found at i:1089512 original size:24 final size:23
Alignment explanation
Indices: 1089466--1089512 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1089456 AGAAAACATA
** *
1089466 TATTTTTTTTATTTTGCATATTT
1 TATTTTTTTTATTTTAAAAATTT
1089489 TATTTTTATTTATTTTAAAAATTT
1 TATTTTT-TTTATTTTAAAAATTT
1089513 CAAACAGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
TATTTTTTTTATTTTAAAAATTT
Found at i:1096524 original size:21 final size:21
Alignment explanation
Indices: 1096471--1096524 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 21
1096461 TGTCAAAATG
1096471 AATTTAAAATAA--AAATTATA
1 AATTT-AAATAATTAAATTATA
1096491 AATTATAAA-AATTAAATT-TA
1 AATT-TAAATAATTAAATTATA
1096511 AATTTAATATAATT
1 AATTTAA-ATAATT
1096525 TATGAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
19 5 0.17
20 14 0.48
21 10 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTTAAATAATTAAATTATA
Found at i:1096689 original size:23 final size:23
Alignment explanation
Indices: 1096620--1096689 Score: 54
Period size: 27 Copynumber: 3.0 Consensus size: 23
1096610 AAAATAATAA
* *
1096620 TATTAATTTTC-AATAA-TAAAT
1 TATTAATATTCTAAAAATTAAAT
* *
1096641 TATTAACATTTTGAATAAATCATAAAT
1 TATTAATATTCT-AA-AAAT--TAAAT
1096668 TATTAATATTCTAAAAATTAAA
1 TATTAATATTCTAAAAATTAAA
1096690 ATAAATAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
21 8 0.22
23 6 0.16
24 2 0.05
25 4 0.11
26 2 0.05
27 15 0.41
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (23 bp):
TATTAATATTCTAAAAATTAAAT
Found at i:1104098 original size:114 final size:114
Alignment explanation
Indices: 1103880--1104123 Score: 317
Period size: 114 Copynumber: 2.1 Consensus size: 114
1103870 GGGACATAGG
* * * * * * * *
1103880 TATCTATCGATAGATACAACTCAGGGTAACTTTCAATTGTTCCTAAGTGACAAACTATTGATAGA
1 TATCTATCAATAGATGCAACTCAAGGTAACTTTCAATTGTTCCCAAATGAAAAACTATCGATAAA
* ** *
1103945 TGCCAAGTATCTATCGATAAATCAATTTGCTACTCTTTTCTCGTATGTC
66 TGCCAAGCATCTATCGATAAATCAATTAACTACTATTTTCTCGTATGTC
*
1103994 TATCTATCAATAGATGCAACTTAAGGTAACTTTCAATTGTTCCCAAATGAAAAACTATCGATAAA
1 TATCTATCAATAGATGCAACTCAAGGTAACTTTCAATTGTTCCCAAATGAAAAACTATCGATAAA
*** * * *
1104059 TGCTGGGCATCTATCGATAGATGAATTAACTAGTATTTTCTCGTATGTC
66 TGCCAAGCATCTATCGATAAATCAATTAACTACTATTTTCTCGTATGTC
1104108 TATCTATCAATAGATG
1 TATCTATCAATAGATG
1104124 TTGAGCATCT
Statistics
Matches: 111, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (114 bp):
TATCTATCAATAGATGCAACTCAAGGTAACTTTCAATTGTTCCCAAATGAAAAACTATCGATAAA
TGCCAAGCATCTATCGATAAATCAATTAACTACTATTTTCTCGTATGTC
Found at i:1106832 original size:4 final size:4
Alignment explanation
Indices: 1106818--1106853 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
1106808 GTCTTATTCT
*
1106818 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTAA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1106854 TTTTCGCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:1110182 original size:21 final size:21
Alignment explanation
Indices: 1110156--1110195 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1110146 AATATGAAAA
1110156 TATTATGTTATT-TTTTAATGT
1 TATTAT-TTATTATTTTAATGT
1110177 TATTATTTATTATTTTAAT
1 TATTATTTATTATTTTAAT
1110196 TGTTTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TATTATTTATTATTTTAATGT
Found at i:1110432 original size:15 final size:15
Alignment explanation
Indices: 1110405--1110460 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1110395 ACATAGTTAT
*
1110405 ATTTTCAGCAATTAC
1 ATTTTCAACAATTAC
* *
1110420 ATTTTCAATAATTAT
1 ATTTTCAACAATTAC
**
1110435 ATACTCAACAATTAC
1 ATTTTCAACAATTAC
*
1110450 ATTTCCAACAA
1 ATTTTCAACAA
1110461 CATACCAAAC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.38
Consensus pattern (15 bp):
ATTTTCAACAATTAC
Found at i:1121496 original size:34 final size:34
Alignment explanation
Indices: 1121453--1121521 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1121443 TGAGCACAGA
*
1121453 TAGACTTCAATTAGATGATGCACGCTCCAATCAT
1 TAGACTTCAATTAGATGATGCACACTCCAATCAT
1121487 TAGACTTCAATTAGATGATGCACACTCCAATCAT
1 TAGACTTCAATTAGATGATGCACACTCCAATCAT
1121521 T
1 T
1121522 TTGGACAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (34 bp):
TAGACTTCAATTAGATGATGCACACTCCAATCAT
Found at i:1126255 original size:4 final size:4
Alignment explanation
Indices: 1126239--1126274 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
1126229 ACTGAGAATT
*
1126239 AAAG AAGG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1126275 TTACCAAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1126785 original size:20 final size:21
Alignment explanation
Indices: 1126760--1126801 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1126750 ACCAGTGCTG
1126760 AATATCCAATTAATTAA-GAA
1 AATATCCAATTAATTAATGAA
*
1126780 AATATCTAATTAATTAATGAA
1 AATATCCAATTAATTAATGAA
1126801 A
1 A
1126802 GAAATATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (21 bp):
AATATCCAATTAATTAATGAA
Found at i:1134925 original size:73 final size:73
Alignment explanation
Indices: 1134797--1134935 Score: 165
Period size: 73 Copynumber: 1.9 Consensus size: 73
1134787 AAGAGACAGT
* * *
1134797 GTTAGTCGACTAAAAGCTTACTGCCAGAAATCGAGTTCAAAGACAAAAACGATTTAATCGACTAA
1 GTTAGTCGACTAAAAGCTTACTGCCAGAAATAGAGTTCAAAGACAAAAACAATTTAATCAACTAA
1134862 GAAATTTC
66 GAAATTTC
* * * * * *
1134870 GTTAGTCGACTAAGAGGC-TACTGCCAGAAACTAG-GTTCAGAGATAGAGACAATTTAGTCAACT
1 GTTAGTCGACTAA-AAGCTTACTGCCAGAAA-TAGAGTTCAAAGACAAAAACAATTTAATCAACT
1134933 AAG
64 AAG
1134936 TGATAATGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 50 0.91
74 5 0.09
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (73 bp):
GTTAGTCGACTAAAAGCTTACTGCCAGAAATAGAGTTCAAAGACAAAAACAATTTAATCAACTAA
GAAATTTC
Found at i:1139028 original size:22 final size:22
Alignment explanation
Indices: 1139003--1139049 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1138993 GCTTCATATA
1139003 AACCAATCACACAATGCCTATC
1 AACCAATCACACAATGCCTATC
* ***
1139025 AACCAGTCATGTAATGCCTATC
1 AACCAATCACACAATGCCTATC
1139047 AAC
1 AAC
1139050 TAGTCACGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.32, G:0.09, T:0.21
Consensus pattern (22 bp):
AACCAATCACACAATGCCTATC
Found at i:1139054 original size:22 final size:22
Alignment explanation
Indices: 1139015--1139079 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
1139005 CCAATCACAC
* *
1139015 AATGCCTATCAACCAGTCATGT
1 AATGCCTATCAACTAGTCACGT
1139037 AATGCCTATCAACTAGTCACGT
1 AATGCCTATCAACTAGTCACGT
*
1139059 AAAGTCCTATCAACTAGTCAC
1 AATG-CCTATCAACTAGTCAC
1139080 ACAAAGCCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 23 0.59
23 16 0.41
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (22 bp):
AATGCCTATCAACTAGTCACGT
Found at i:1139071 original size:23 final size:22
Alignment explanation
Indices: 1139018--1139089 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
1139008 ATCACACAAT
* * *
1139018 GCCTATCAACCAGTCATGTAAT
1 GCCTATCAACTAGTCACGTAAA
1139040 GCCTATCAACTAGTCACGTAAA
1 GCCTATCAACTAGTCACGTAAA
**
1139062 GTCCTATCAACTAGTCACACAAA
1 G-CCTATCAACTAGTCACGTAAA
1139085 GCCTA
1 GCCTA
1139090 AAAAATTGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 24 0.55
23 20 0.45
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (22 bp):
GCCTATCAACTAGTCACGTAAA
Found at i:1142854 original size:22 final size:22
Alignment explanation
Indices: 1142824--1142910 Score: 70
Period size: 22 Copynumber: 3.9 Consensus size: 22
1142814 GTAGACACAC
1142824 AATGACTAAAAATCAGTCATGT
1 AATGACTAAAAATCAGTCATGT
* *
1142846 AATGCCTAAAAAT-TGATCATGT
1 AATGACTAAAAATCAG-TCATGT
* ** *
1142868 AATGCCTTACTAA-CTAGTCATGC
1 AATGAC-TAAAAATC-AGTCATGT
*
1142891 AATGACTAAAAACCAGTCAT
1 AATGACTAAAAATCAGTCAT
1142911 CAAGGCCTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
21 1 0.02
22 34 0.67
23 15 0.29
24 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (22 bp):
AATGACTAAAAATCAGTCATGT
Found at i:1143125 original size:81 final size:81
Alignment explanation
Indices: 1142923--1143117 Score: 216
Period size: 81 Copynumber: 2.4 Consensus size: 81
1142913 AGGCCTTATC
* * * ** *
1142923 AACCAGTTATGCATGCCCGATCAA-TCAGTCATGCAAACTCTAAGTCATGCAATGCCTAAACCCC
1 AACCAGTCATGCATGCCCAATCAACT-AGTCATGCAAACCCTAAGTCACACAATGCCTAAAACCC
1142987 TTAAACCCAATGCCTAA
65 TTAAACCCAATGCCTAA
* ** * *
1143004 AA-CACGTCACGCATGCCTTATCAACAATTCACT-CAAACCCTAAGTCACACAATGCCTAAAACC
1 AACCA-GTCATGCATGCCCAATCAACTAGTCA-TGCAAACCCTAAGTCACACAATGCCTAAAACC
***
1143067 CTTAAATTTAATGCCTAA
64 CTTAAACCCAATGCCTAA
1143085 AACCAGTCATGCATGCCCAATCAACTAGTCATG
1 AACCAGTCATGCATGCCCAATCAACTAGTCATG
1143118 TAGACCCTGT
Statistics
Matches: 91, Mismatches: 18, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
80 3 0.03
81 85 0.93
82 3 0.03
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.23
Consensus pattern (81 bp):
AACCAGTCATGCATGCCCAATCAACTAGTCATGCAAACCCTAAGTCACACAATGCCTAAAACCCT
TAAACCCAATGCCTAA
Found at i:1144182 original size:51 final size:51
Alignment explanation
Indices: 1144119--1144361 Score: 307
Period size: 50 Copynumber: 4.8 Consensus size: 51
1144109 AACATAAACA
*
1144119 ATTTGGACTTTGGATATTTGTTTGGCTTTGATGTTTGAACTTAATACATTTG
1 ATTTGGACTTTGGATATTTGTTTGGC-TTGATGTTTGGACTTAATACATTTG
* ** * *
1144171 ATTCGGA-TTTGGATATTTGTTCAGCTTTAGTGTTTGGACTTGATACATTTG
1 ATTTGGACTTTGGATATTTGTTTGGCTTGA-TGTTTGGACTTAATACATTTG
* *
1144222 ATTTGGATTTTGGATATTTGTTTGG-TTGATGTTTGGAATTAATACATTTG
1 ATTTGGACTTTGGATATTTGTTTGGCTTGATGTTTGGACTTAATACATTTG
* ** *
1144272 ATTTGGACTTTGGATATTTGTTTGGC-TAATGTTTGGGTTTGATACATTTGG
1 ATTTGGACTTTGGATATTTGTTTGGCTTGATGTTTGGACTTAATACATTT-G
*
1144323 A-TTGGACTTTGGATGTTTGTTTGG-TTGATGTTTGGACTT
1 ATTTGGACTTTGGATATTTGTTTGGCTTGATGTTTGGACTT
1144362 TGAGTATTCC
Statistics
Matches: 165, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
50 98 0.59
51 46 0.28
52 21 0.13
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (51 bp):
ATTTGGACTTTGGATATTTGTTTGGCTTGATGTTTGGACTTAATACATTTG
Found at i:1144776 original size:42 final size:42
Alignment explanation
Indices: 1144692--1144915 Score: 201
Period size: 42 Copynumber: 5.3 Consensus size: 42
1144682 CATGCAAATC
* * *
1144692 TTTGAAATACTTGATACT-CTT--AAAAG-AGGACATTGAGCAT
1 TTTGAAATATTTGATA-TGCTTGCAAAAGCA-GACTTTGAGAAT
1144732 TTTGAAATATTTGATATGCTTGCAAAAGCCA-ACTTTGAGAAT
1 TTTGAAATATTTGATATGCTTGCAAAAG-CAGACTTTGAGAAT
* ** *
1144774 TTTGAGATATTTGATATGCTTGCAAAAATAGACTTAGAG-AT
1 TTTGAAATATTTGATATGCTTGCAAAAGCAGACTTTGAGAAT
* ** *
1144815 CTTTGAAATATTTGATACGCTCACAAAAGCAGACTTTGAAAAT
1 -TTTGAAATATTTGATATGCTTGCAAAAGCAGACTTTGAGAAT
* * **
1144858 TTTGAGATATTTGATATGATTGCAACAAGTGGACTTTG-GAAAT
1 TTTGAAATATTTGATATGCTTGCAA-AAGCAGACTTTGAG-AAT
1144901 CTTTGAAATATTTGA
1 -TTTGAAATATTTGA
1144916 CACATTAAAA
Statistics
Matches: 149, Mismatches: 24, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
39 1 0.01
40 18 0.12
41 3 0.02
42 98 0.66
43 15 0.10
44 14 0.09
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (42 bp):
TTTGAAATATTTGATATGCTTGCAAAAGCAGACTTTGAGAAT
Found at i:1144826 original size:84 final size:86
Alignment explanation
Indices: 1144732--1144915 Score: 257
Period size: 84 Copynumber: 2.2 Consensus size: 86
1144722 CATTGAGCAT
* ** * *
1144732 TTTGAAATATTTGATATGCTTGCAAAAGCCA-ACTTTGAGAATTTTGAGATATTTGATATGCTTG
1 TTTGAAATATTTGATACGCTCACAAAAG-CAGACTTTGAAAATTTTGAGATATTTGATATGATTG
*
1144796 CAA-AAATAGAC-TTAGAGATC
65 CAACAAATAGACTTTAGAAATC
1144816 TTTGAAATATTTGATACGCTCACAAAAGCAGACTTTGAAAATTTTGAGATATTTGATATGATTGC
1 TTTGAAATATTTGATACGCTCACAAAAGCAGACTTTGAAAATTTTGAGATATTTGATATGATTGC
* * *
1144881 AACAAGTGGACTTTGGAAATC
66 AACAAATAGACTTTAGAAATC
1144902 TTTGAAATATTTGA
1 TTTGAAATATTTGA
1144916 CACATTAAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
83 2 0.02
84 59 0.67
85 6 0.07
86 21 0.24
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (86 bp):
TTTGAAATATTTGATACGCTCACAAAAGCAGACTTTGAAAATTTTGAGATATTTGATATGATTGC
AACAAATAGACTTTAGAAATC
Found at i:1150130 original size:2 final size:2
Alignment explanation
Indices: 1150118--1150156 Score: 60
Period size: 2 Copynumber: 18.5 Consensus size: 2
1150108 AGTTGTTATG
1150118 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
1150157 GTAAATGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 31 0.89
3 4 0.11
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1150580 original size:28 final size:28
Alignment explanation
Indices: 1150526--1150584 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1150516 AACTTTGTTG
* *
1150526 TTAGACATGGCTAGGCAACGGTCTGTGA
1 TTAGACATGGCTAGACAACGATCTGTGA
* *
1150554 TTAGACATGGCTAGACCACGATTTGTGA
1 TTAGACATGGCTAGACAACGATCTGTGA
1150582 TTA
1 TTA
1150585 TATGTGCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (28 bp):
TTAGACATGGCTAGACAACGATCTGTGA
Found at i:1171383 original size:22 final size:23
Alignment explanation
Indices: 1171356--1171406 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1171346 ATTTTTGATT
1171356 AATTTTAC-TATAAAATTTTA-TA
1 AATTTTACTTAT-AAATTTTACTA
**
1171378 AATTTTGGTTATAAATTTTACTA
1 AATTTTACTTATAAATTTTACTA
1171401 AATTTT
1 AATTTT
1171407 TATTATCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (23 bp):
AATTTTACTTATAAATTTTACTA
Found at i:1171412 original size:23 final size:23
Alignment explanation
Indices: 1171358--1171412 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1171348 TTTTGATTAA
*
1171358 TTTTACTATAAAATTTTATAAAT
1 TTTTATTATAAAATTTTATAAAT
**
1171381 TTTGGTTAT-AAATTTTACTAAAT
1 TTTTATTATAAAATTTTA-TAAAT
1171404 TTTTATTAT
1 TTTTATTAT
1171413 CATAATGTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTATTATAAAATTTTATAAAT
Found at i:1172183 original size:35 final size:34
Alignment explanation
Indices: 1172126--1172237 Score: 89
Period size: 34 Copynumber: 3.2 Consensus size: 34
1172116 GCTTTTTACA
* * * *
1172126 AGATCAAACAAAACTCTCACAATAGGCTTTTCATG
1 AGATCAAGCGAAACCCTTACAAT-GGCTTTTCATG
* * * * *
1172161 GGATTAAGCGAAATCCTTACAATGGTTTTTTATG
1 AGATCAAGCGAAACCCTTACAATGGCTTTTCATG
* *
1172195 AGATCAAGCGAAACCCTTCAACAATGGTTTTTCACG
1 AGATCAAGCGAAACCCTT--ACAATGGCTTTTCATG
*
1172231 AGCTCAA
1 AGATCAA
1172238 CCACAAACTC
Statistics
Matches: 60, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
34 24 0.40
35 16 0.27
36 20 0.33
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (34 bp):
AGATCAAGCGAAACCCTTACAATGGCTTTTCATG
Found at i:1173331 original size:16 final size:15
Alignment explanation
Indices: 1173310--1173339 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1173300 ATGCTCCTTA
1173310 ATTATTTTTCATTTTT
1 ATTATTTTT-ATTTTT
1173326 ATTATTTTTATTTT
1 ATTATTTTTATTTT
1173340 ATCATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTATTTTTATTTTT
Found at i:1175698 original size:12 final size:12
Alignment explanation
Indices: 1175681--1175720 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1175671 CGAACCCAAT
1175681 TATACATACATA
1 TATACATACATA
1175693 TATACATACATA
1 TATACATACATA
* *
1175705 TATATATATATA
1 TATACATACATA
1175717 TATA
1 TATA
1175721 TATCGTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
TATACATACATA
Found at i:1175739 original size:2 final size:2
Alignment explanation
Indices: 1175690--1175723 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1175680 TTATACATAC
* *
1175690 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1175724 CGTAATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1183004 original size:15 final size:15
Alignment explanation
Indices: 1182984--1183047 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
1182974 AATCACACAT
1182984 GTTTATATATTATAA
1 GTTTATATATTATAA
* *
1182999 GTTTATATAAATAAAA
1 GTTTATAT-ATTATAA
*
1183015 GTATATATATTATAA
1 GTTTATATATTATAA
* *
1183030 -TTAATAATTTTATAA
1 GTTTAT-ATATTATAA
1183045 GTT
1 GTT
1183048 ATAATTTTCG
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 3 0.08
15 21 0.55
16 14 0.37
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
GTTTATATATTATAA
Found at i:1203810 original size:37 final size:37
Alignment explanation
Indices: 1203769--1203848 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
1203759 AGACTTACTT
* *
1203769 ATCCACTCTCACA-TTTTCTAC-AAGTGGGTTTTCTATC
1 ATCCACTCTCA-AGTATT-TACAAAGTGGGCTTTCTATC
*
1203806 ATCCATTCTCAAGTATTTACAAAGTGGGCTTTCTATC
1 ATCCACTCTCAAGTATTTACAAAGTGGGCTTTCTATC
1203843 ATCCAC
1 ATCCAC
1203849 ATTCACCCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 4 0.11
37 33 0.89
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (37 bp):
ATCCACTCTCAAGTATTTACAAAGTGGGCTTTCTATC
Found at i:1210014 original size:21 final size:22
Alignment explanation
Indices: 1209979--1210022 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1209969 AGGAGATTAA
1209979 AAAAATATGATTTT-CATAAAATT
1 AAAAATA-GATTTTCCA-AAAATT
1210002 AAAAATA-ATTTTCCAAAAATT
1 AAAAATAGATTTTCCAAAAATT
1210023 GATTACATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 11 0.55
22 2 0.10
23 7 0.35
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAAATAGATTTTCCAAAAATT
Found at i:1216624 original size:22 final size:23
Alignment explanation
Indices: 1216583--1216625 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1216573 AAATCGAATA
*
1216583 TAACAAAAATTAGTGACTACAAT
1 TAACAAAAATTAGAGACTACAAT
*
1216606 TAACAAAACTTAGAG-CTACA
1 TAACAAAAATTAGAGACTACA
1216626 GTCCCTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.23
Consensus pattern (23 bp):
TAACAAAAATTAGAGACTACAAT
Found at i:1217556 original size:11 final size:10
Alignment explanation
Indices: 1217536--1217572 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1217526 GTGACATCAT
*
1217536 AAAAGGAAAA
1 AAAAAGAAAA
*
1217546 AAAAAGCAAA
1 AAAAAGAAAA
1217556 AAAAAGAAAA
1 AAAAAGAAAA
1217566 AAAAAGA
1 AAAAAGA
1217573 GAAACTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:1229059 original size:2 final size:2
Alignment explanation
Indices: 1229052--1229080 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1229042 CAAGGCAAGA
1229052 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1229081 AATGAAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1236486 original size:20 final size:21
Alignment explanation
Indices: 1236448--1236489 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1236438 AAGTGATTAA
1236448 TTTAAGTTATTTTAGTTAAAT
1 TTTAAGTTATTTTAGTTAAAT
*
1236469 TTTAGGTTATTTTA-TTAAAT
1 TTTAAGTTATTTTAGTTAAAT
1236489 T
1 T
1236490 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (21 bp):
TTTAAGTTATTTTAGTTAAAT
Found at i:1237153 original size:12 final size:13
Alignment explanation
Indices: 1237136--1237168 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1237126 AGATTTTAGA
1237136 GCAGCAAGA-GAG
1 GCAGCAAGAGGAG
1237148 GCAGCAA-AGGAG
1 GCAGCAAGAGGAG
1237160 GCAGCAAGA
1 GCAGCAAGA
1237169 AACTATTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 17 0.89
13 1 0.05
ACGTcount: A:0.42, C:0.18, G:0.39, T:0.00
Consensus pattern (13 bp):
GCAGCAAGAGGAG
Found at i:1246427 original size:74 final size:74
Alignment explanation
Indices: 1246288--1246429 Score: 187
Period size: 74 Copynumber: 1.9 Consensus size: 74
1246278 TAGATTGTGT
* * * * * *
1246288 GACAAAGAAGACTTAATCGACTAAGAAGTATGGTTAGCCAACTAAAAGCTCTCTGTTAGAGAATT
1 GACAAAGAAGACTTAATCGACTAAAAAGAAGGGTTAGCCAACTAAAAGCTCTCTATCAGAAAATT
1246353 TGATTACAA
66 TGATTACAA
* * *
1246362 GACAGAGAAGACTTAATTGACTAAAAAGAAGGGTTAGCCAACTAAAAG-TTTACTATCAGAAAAT
1 GACAAAGAAGACTTAATCGACTAAAAAGAAGGGTTAGCCAACTAAAAGCTCT-CTATCAGAAAAT
1246426 TTGA
65 TTGA
1246430 AATTAGCACA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
73 2 0.03
74 56 0.97
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (74 bp):
GACAAAGAAGACTTAATCGACTAAAAAGAAGGGTTAGCCAACTAAAAGCTCTCTATCAGAAAATT
TGATTACAA
Found at i:1250127 original size:47 final size:46
Alignment explanation
Indices: 1250053--1250162 Score: 114
Period size: 47 Copynumber: 2.4 Consensus size: 46
1250043 TAATTTTCTT
* ***
1250053 TTTCAGTATAAATATGAGATTAAATTATAGTCAAGAGTGATTTAATC
1 TTTCGGTATAAATATTTTATTAAATTATAGTCAAGAGT-ATTTAATC
* * * *
1250100 TTTCGGTATAAATATTTTATTATATTATAGTTAAGGGTATTTTATC
1 TTTCGGTATAAATATTTTATTAAATTATAGTCAAGAGTATTTAATC
* *
1250146 TTT-GCTATAAGTATTTT
1 TTTCGGTATAAATATTTT
1250163 CATTTTTTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 12 0.23
46 10 0.19
47 31 0.58
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (46 bp):
TTTCGGTATAAATATTTTATTAAATTATAGTCAAGAGTATTTAATC
Found at i:1250161 original size:45 final size:47
Alignment explanation
Indices: 1250071--1250162 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
1250061 TAAATATGAG
*
1250071 ATTAAATTATAGTCAAGAGTGATTTAATCTTTCGGTATAAATATTTT
1 ATTAAATTATAGTCAAGAGTGATTTAATCTTTCGCTATAAATATTTT
* * * * *
1250118 ATTATATTATAGTTAAGGGT-ATTTTATCTTT-GCTATAAGTATTTT
1 ATTAAATTATAGTCAAGAGTGATTTAATCTTTCGCTATAAATATTTT
1250163 CATTTTTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 12 0.31
46 10 0.26
47 17 0.44
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (47 bp):
ATTAAATTATAGTCAAGAGTGATTTAATCTTTCGCTATAAATATTTT
Found at i:1256740 original size:44 final size:44
Alignment explanation
Indices: 1256682--1256811 Score: 251
Period size: 44 Copynumber: 3.0 Consensus size: 44
1256672 AAAATGAAAA
1256682 AATTGATTTGGAAAATGAAAATAAGAGATTGAAAATAGATTTTG
1 AATTGATTTGGAAAATGAAAATAAGAGATTGAAAATAGATTTTG
1256726 AATTGATTTGGAAAATGAAAATAAGAGATTGAAAATAGATTTTG
1 AATTGATTTGGAAAATGAAAATAAGAGATTGAAAATAGATTTTG
*
1256770 AATTGATTTGGAAAATGAAAATAAGAGATTGAAAATTGATTT
1 AATTGATTTGGAAAATGAAAATAAGAGATTGAAAATAGATTT
1256812 GGAAAATGAA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 85 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (44 bp):
AATTGATTTGGAAAATGAAAATAAGAGATTGAAAATAGATTTTG
Found at i:1256755 original size:33 final size:35
Alignment explanation
Indices: 1256718--1256823 Score: 90
Period size: 44 Copynumber: 2.8 Consensus size: 35
1256708 GATTGAAAAT
1256718 AGATTTTGAATTGATTTGGAAAATGAAAATAAGAGATTG
1 AGATTTTGAATTGATTTGGAAAATGAAAAT-A-AGA--G
1256757 AAAATAGATTTTGAATTGATTTGGAAAATGAAAAT-A-AG
1 -----AGATTTTGAATTGATTTGGAAAATGAAAATAAGAG
***
1256795 AGATTGAAAATTGATTTGGAAAATGAAAA
1 AGATTTTGAATTGATTTGGAAAATGAAAA
1256824 AATTGTTAGG
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
33 26 0.44
38 1 0.02
40 1 0.02
41 1 0.02
44 30 0.51
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (35 bp):
AGATTTTGAATTGATTTGGAAAATGAAAATAAGAG
Found at i:1256841 original size:19 final size:21
Alignment explanation
Indices: 1256801--1256842 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1256791 TAAGAGATTG
*
1256801 AAAATTGATTTGGAAAATGAA
1 AAAATTGATTAGGAAAATGAA
1256822 AAAATTG-TTAGGAAAA-GAA
1 AAAATTGATTAGGAAAATGAA
1256841 AA
1 AA
1256843 TGAAGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 8 0.40
21 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24
Consensus pattern (21 bp):
AAAATTGATTAGGAAAATGAA
Found at i:1261625 original size:32 final size:31
Alignment explanation
Indices: 1261484--1261638 Score: 141
Period size: 32 Copynumber: 4.9 Consensus size: 31
1261474 ATAACTAGTC
* * *
1261484 CACTACCTTTCCAAAAAGAAGTATAACCTTTA
1 CACTACCTTTTC-AAGAGGAGTATAACCTTTA
**
1261516 CACTACCTTTTCAAGAGGAGGTATGGCCTTTA
1 CACTACCTTTTCAAGAGGA-GTATAACCTTTA
* *
1261548 CAATACCTTTTCCAGAGGAGATATAACCTTTA
1 CACTACCTTTTCAAGAGGAG-TATAACCTTTA
* * *
1261580 CACTATCTCTTCAAGATGATGTATAACCTTTA
1 CACTACCTTTTCAAGAGGA-GTATAACCTTTA
* * *
1261612 TACCACCTTTTCAA-TGGAGGTATAACC
1 CACTACCTTTTCAAGAGGA-GTATAACC
1261639 AACAATAGTT
Statistics
Matches: 99, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
31 16 0.16
32 82 0.83
33 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (31 bp):
CACTACCTTTTCAAGAGGAGTATAACCTTTA
Found at i:1266530 original size:11 final size:11
Alignment explanation
Indices: 1266514--1266538 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1266504 TGGGGGTCAA
1266514 TCTTACAAAAT
1 TCTTACAAAAT
1266525 TCTTACAAAAT
1 TCTTACAAAAT
1266536 TCT
1 TCT
1266539 AGAAGGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTACAAAAT
Found at i:1278300 original size:20 final size:20
Alignment explanation
Indices: 1278257--1278331 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
1278247 AAGCAATATC
*
1278257 CAATATTCAACATTCAATCCA
1 CAATATTCAAAATTCAA-CCA
*
1278278 CAATATGCAAAATTCAACCA
1 CAATATTCAAAATTCAACCA
* * *
1278298 CAATGTTCAACATTCAACCG
1 CAATATTCAAAATTCAACCA
1278318 CAATATTCAAAATT
1 CAATATTCAAAATT
1278332 GCATAAGATA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.27
Consensus pattern (20 bp):
CAATATTCAAAATTCAACCA
Found at i:1281314 original size:79 final size:79
Alignment explanation
Indices: 1281178--1281339 Score: 254
Period size: 79 Copynumber: 2.1 Consensus size: 79
1281168 TTGGAGGACT
* * *
1281178 AAAGTAAACTGCACAGTAGCTAGGCAAACAAGGTAACGCAGTTGTGCCACCCCTATTCAGTAAAG
1 AAAGTAAACTGCACAGTAGCTAGGCAAACAAGGTAACGCAGTAGTGCCACCCATATTCAGCAAAG
1281243 ACTCAGCACCAACC
66 ACTCAGCACCAACC
* * *
1281257 AAAGTAAACTGCACAGTAGTTAGG-AAAGCAAGGTAATGCAGTAGTGCCACCTATATTCAGCAAA
1 AAAGTAAACTGCACAGTAGCTAGGCAAA-CAAGGTAACGCAGTAGTGCCACCCATATTCAGCAAA
1281321 GACTCAGCACCAACC
65 GACTCAGCACCAACC
1281336 AAAG
1 AAAG
1281340 AGGTCGGCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
78 3 0.04
79 73 0.96
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.17
Consensus pattern (79 bp):
AAAGTAAACTGCACAGTAGCTAGGCAAACAAGGTAACGCAGTAGTGCCACCCATATTCAGCAAAG
ACTCAGCACCAACC
Found at i:1295992 original size:15 final size:17
Alignment explanation
Indices: 1295974--1296006 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1295964 TAACATTACA
1295974 AAAATTA-TAATT-TAT
1 AAAATTATTAATTATAT
1295989 AAAATTATTAATTATAT
1 AAAATTATTAATTATAT
1296006 A
1 A
1296007 TATTCCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTATTAATTATAT
Found at i:1300731 original size:31 final size:32
Alignment explanation
Indices: 1300657--1300736 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 32
1300647 CAAAGTGTTT
* * *
1300657 GTTGATGTGTTTTAGTACAACTTTATTAGGAA
1 GTTGATGTGTTTTAATACAACTCTATTAAGAA
* * *
1300689 CTTGGTATG-TTTAATACAACTCTATTAAGAA
1 GTTGATGTGTTTTAATACAACTCTATTAAGAA
1300720 GTTGATGTGTTTTAATA
1 GTTGATGTGTTTTAATA
1300737 TGTCTATTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 25 0.66
32 13 0.34
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (32 bp):
GTTGATGTGTTTTAATACAACTCTATTAAGAA
Found at i:1306841 original size:23 final size:24
Alignment explanation
Indices: 1306792--1306841 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
1306782 GTAGTTGTTC
* * *
1306792 TTTCAAGTTATCTTTTTTTGATCT
1 TTTCAAGTTATATTTTTATAATCT
*
1306816 TTTC-AGTTATATTTTTATAATTT
1 TTTCAAGTTATATTTTTATAATCT
1306839 TTT
1 TTT
1306842 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.20, C:0.08, G:0.06, T:0.66
Consensus pattern (24 bp):
TTTCAAGTTATATTTTTATAATCT
Found at i:1330479 original size:18 final size:18
Alignment explanation
Indices: 1330452--1330509 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
1330442 ACACATTTAA
*
1330452 TTAATCGTATTATCGTAT
1 TTAATTGTATTATCGTAT
* * *
1330470 TTAATTGTATAAACGTGT
1 TTAATTGTATTATCGTAT
*
1330488 TTAATTATATTATCGTAT
1 TTAATTGTATTATCGTAT
1330506 TTAA
1 TTAA
1330510 ACGTGTATAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (18 bp):
TTAATTGTATTATCGTAT
Found at i:1334091 original size:53 final size:54
Alignment explanation
Indices: 1334008--1334131 Score: 178
Period size: 53 Copynumber: 2.3 Consensus size: 54
1333998 NNNNNNNNNA
* * *
1334008 GGAATGAACGAATTTATAATTTTTTATTAGTATCTCGTTTGTCACATTCACATCAG
1 GGAATGAAC--ATTCATAATTTTTTATTAGTAGCTCATTTGTCACATTCACATCAG
*
1334064 GGAATGAACATTCATAA-TTTTTATTAGTAGCTCATTTGTCACATTCACTTCAG
1 GGAATGAACATTCATAATTTTTTATTAGTAGCTCATTTGTCACATTCACATCAG
*
1334117 GGAATGGACATTCAT
1 GGAATGAACATTCAT
1334132 GGTTTTTCAT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
53 47 0.75
54 7 0.11
56 9 0.14
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (54 bp):
GGAATGAACATTCATAATTTTTTATTAGTAGCTCATTTGTCACATTCACATCAG
Found at i:1340110 original size:34 final size:34
Alignment explanation
Indices: 1340033--1340137 Score: 104
Period size: 34 Copynumber: 3.1 Consensus size: 34
1340023 AAAACCATGG
* ** * *
1340033 GTTATGGTTACTCTCATGAAAAACCCTTGTTAAG-
1 GTTATGGTTGCTCTTGTGAAAAGCCATTG-TAAGA
1340067 GTTATGGTTGCTCTTGTGAAAAGCCATTGTAAGA
1 GTTATGGTTGCTCTTGTGAAAAGCCATTGTAAGA
* * * * *
1340101 GTTATGGTTGATCCTGTAAAAAGCTATTGTGAGA
1 GTTATGGTTGCTCTTGTGAAAAGCCATTGTAAGA
1340135 GTT
1 GTT
1340138 TAATACTTGA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 4 0.07
34 56 0.93
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (34 bp):
GTTATGGTTGCTCTTGTGAAAAGCCATTGTAAGA
Found at i:1357064 original size:74 final size:74
Alignment explanation
Indices: 1356943--1357142 Score: 258
Period size: 74 Copynumber: 2.7 Consensus size: 74
1356933 GCAAATTGTG
* * * * * *
1356943 AGACAGAGAAGACTTAGTTGACTAAGAAGCATGGTTCGTCAACTAAGAGCACATTG-CTAGAGAC
1 AGACAGAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCACACTGTC-AAAGAA
1357007 TTCAATTACA
65 TTCAATTACA
* *
1357017 AGACAGAGAAAACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTGTCAAAGAAT
1 AGACAGAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCACACTGTCAAAGAAT
1357082 TCAATTACA
66 TCAATTACA
* * * * * *
1357091 AGACTGATAGGACTTAATCAACTAGGAAGTATGGTTAGTCAACTAAGAGCAC
1 AGACAGAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCAC
1357143 TTTGTTTGAA
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
74 108 0.99
75 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (74 bp):
AGACAGAGAAGACTTAATCGACTAAGAAGCATGGTTAGTCAACTAAGAGCACACTGTCAAAGAAT
TCAATTACA
Found at i:1361316 original size:316 final size:314
Alignment explanation
Indices: 1360708--1362742 Score: 2184
Period size: 316 Copynumber: 6.5 Consensus size: 314
1360698 CCTTTCAACA
* * * *
1360708 GAAAAAAAAAAGTCATAAAATTGGATA-TAGAGGATTATGATGAGGATTTGTCTGTTCAATAGTT
1 GAAAAAAAAAGGTCATAGAATTGGATACT-GAGGATGATGATGAGGATTTGTCTGTTCAAAAGTT
* * * *
1360772 GTTGATGAAAAAGGAAATTGAGTCAAATTCATACAAAGAGGTATCCTAAAAATTGATTAAAAAGA
65 GTTGATGAAGAAGGAAACTGAGTCAAATTCATACAAGGAGGTATCCTAAAAATTGATTAAGAAGA
* * * * *
1360837 CCTTTGACTCTAAGAGTAGTTATGTCTACTTTCAAAGCATAAGAAAAGAGTGAGAAAGAGTTGTT
130 TCTTTGAATCTAAGAGTAGTTATGTCTACTGTCAAAGCATAGGAAAAGAGTGAGAATGAGTTGTT
* * * * *
1360902 AGTTGAAATCATTGCCCAAAAAATGTTAGTTCAAGAAATTAATGATTGGCATATACAAAGGGTTG
195 GGTAGAAATCATTGCCCAACAAA-GTTAGTTCAAGAAATTAATGATTGCCATAAACAAA-GGTTG
* * *
1360967 AAAAAATCAGATGAAAAGATTTAGAGGATTAATGTTTACTTAATAAGGCTATATAAG
258 AAATAATCAGATGAAAAGATTTAGAGGATTAATGTTGAGTTAATAAGGCTATATAAG
* * * *
1361024 GAAAAAAAAAGGTCAT-GAAATTGGACATTGAGGGTGATGATGAGGAATTTGTCTATTCAAAAGT
1 GAAAAAAAAAGGTCATAG-AATTGGATACTGAGGATGATGATGAGG-ATTTGTCTGTTCAAAAGT
* * * * * * *
1361088 TGTTGATGAAGAAGGAAACTAAGTCAAATTAAAACAAGGTGGTATCTTAAACATTGATGAAGAAG
64 TGTTGATGAAGAAGGAAACTGAGTCAAATTCATACAAGGAGGTATCCTAAAAATTGATTAAGAAG
* * * * * *
1361153 ATCTTTAAATCTAAGAGCAGTTATGTCTATTGTCAAAGCATTGGAAAAAAAGTGAGAGTGACG-T
129 ATCTTTGAATCTAAGAGTAGTTATGTCTACTGTCAAAGCATAGG-AAAAGAGTGAGAATGA-GTT
* * * *
1361217 GTTGGTAGAAATCATTGCCCAAC-AAGTTAGTTCAAGAAATTATTGATTGCCGTAAACGAAGGAC
192 GTTGGTAGAAATCATTGCCCAACAAAGTTAGTTCAAGAAATTAATGATTGCCATAAACAAAGG-T
* * * * *
1361281 TGAAATAATCAGATGAAAATATTTAGATGATTAATGTTAAATTAATAAGGGTATATAAG
256 TGAAATAATCAGATGAAAAGATTTAGAGGATTAATGTTGAGTTAATAAGGCTATATAAG
* * * * * *
1361340 G--AAAGAAAGGTCATAGAATTTGATA-TGGAGGATGATGAAGACGATTTGTCTGTTCCAATGTT
1 GAAAAAAAAAGGTCATAGAATTGGATACT-GAGGATGATGATGAGGATTTGTCTGTTCAAAAGTT
* * * * ** * *
1361402 ATTGATTAATAAGGAAACTGAGTCAAATTCATATAATAAGGTATCTTAAAAATTGATTAAGAATA
65 GTTGATGAAGAAGGAAACTGAGTCAAATTCATACAAGGAGGTATCCTAAAAATTGATTAAGAAGA
* * * * ** *
1361467 TCTTTGAATCCAAGAGTAGTTCTGTTTACTATTGAAGCTTAGGAAAAGAGTGAGAATGAGTTGTT
130 TCTTTGAATCTAAGAGTAGTTATGTCTACTGTCAAAGCATAGGAAAAGAGTGAGAATGAGTTGTT
* * * * *
1361532 GGTAGAAGTCATTGCCTAATACAGTTAGTTCAAGAAATTAATGATTGCCACAAACCAAAGGTTGA
195 GGTAGAAATCATTGCCCAACAAAGTTAGTTCAAGAAATTAATGATTGCCATAAA-CAAAGGTTGA
* * * *
1361597 AA-AACCTAGATGAAAAGATTTAGAGGATTAATGTTTAATTAATAAGGTTATATAAG
259 AATAATC-AGATGAAAAGATTTAGAGGATTAATGTTGAGTTAATAAGGCTATATAAG
* * * *
1361653 G--AAAGAAAGGTCATAAAATTGGATA-TGTAGGATGATGATGAGGATTTATCTGTTCAAAATTT
1 GAAAAAAAAAGGTCATAGAATTGGATACTG-AGGATGATGATGAGGATTTGTCTGTTCAAAAGTT
* ** * * *
1361715 ATTGATGAAGGTGGAAATTGAGTCAAATTCATACAAGGAGATATCATAAAAATTGATTAAGAAGA
65 GTTGATGAAGAAGGAAACTGAGTCAAATTCATACAAGGAGGTATCCTAAAAATTGATTAAGAAGA
* * * * *
1361780 TCTTTGAATCTAAGAGCAGTTATGTCTACTGTTAAAGAAAAGGAAAAGAGTGAGAATGAGTTGAT
130 TCTTTGAATCTAAGAGTAGTTATGTCTACTGTCAAAGCATAGGAAAAGAGTGAGAATGAGTTGTT
* * * * ** *
1361845 GGTAAAAATCATTGCCTAACAAATTTAGTTCAAGAAATTAATGA-TGTCCATGGATGAAGGGTTG
195 GGTAGAAATCATTGCCCAACAAAGTTAGTTCAAGAAATTAATGATTG-CCAT-AAACAAAGGTTG
* * * *
1361909 AAATAATTAGATGAAAATATTTAAAGGATTAATGTTGAGTTAATAAGGATATATAAG
258 AAATAATCAGATGAAAAGATTTAGAGGATTAATGTTGAGTTAATAAGGCTATATAAG
* * * * ** *
1361966 GAAAGAAACAAGGTCATAGAATTGGATACAGAAGATTATGATGAGGATTCATC-GATTCAATAGT
1 GAAA-AAAAAAGGTCATAGAATTGGATACTGAGGATGATGATGAGGATTTGTCTG-TTCAAAAGT
* * * *
1362030 TGTTGATGAAGAAGGAAACTAAGCCAAATTTATACAATGAGGTATCCTAAAAATTGATTAAGAAG
64 TGTTGATGAAGAAGGAAACTGAGTCAAATTCATACAAGGAGGTATCCTAAAAATTGATTAAGAAG
* * * * *
1362095 ATCTTAGAATCCAAGAGTAGTT-TGGTCTATTGTCAAAGCGTAGGAAAA-ATGTGATAATGAGTT
129 ATCTTTGAATCTAAGAGTAGTTAT-GTCTACTGTCAAAGCATAGGAAAAGA-GTGAGAATGAGTT
* * * * * * *
1362158 GTTGTTAGAAATTATTACCCAACAAAGCTAGTTTAAGAAATTAATAATTGCCATATACCAAAGGT
192 GTTGGTAGAAATCATTGCCCAACAAAGTTAGTTCAAGAAATTAATGATTGCCATA-AACAAAGGT
* * *
1362223 TGAAATAATCAGATGAAAAAGACTTAAAAGATTAATGTTGAGTTAATAAGGCTATATAAG
256 TGAAATAATCAGATG-AAAAGATTTAGAGGATTAATGTTGAGTTAATAAGGCTATATAAG
* * * ** * * *
1362283 GAAAGAAAGAAGTTCACAGAATTGGATACCAAGGATTATGATGAGAATTTGTCTGTTCAATAGTT
1 GAAA-AAAAAAGGTCATAGAATTGGATACTGAGGATGATGATGAGGATTTGTCTGTTCAAAAGTT
* * * * * * *
1362348 GTTGATGAAGAAGAAAACTAAGTCAAATTCATCCAAAGAGGTATCCTAAAAATTGGTTATGTAGA
65 GTTGATGAAGAAGGAAACTGAGTCAAATTCATACAAGGAGGTATCCTAAAAATTGATTAAGAAGA
* * * **
1362413 TCTTTGAATCAAAGAGTAGTTATGTCTACTGTCAAAGCATAAGG-AAAGAGTAAGAGTGAAATGT
130 TCTTTGAATCTAAGAGTAGTTATGTCTACTGTCAAAGCAT-AGGAAAAGAGTGAGAATGAGTTGT
* * * * *
1362477 TGGTAGAAATCATTGCCCAACAAAGTTAGTTTAAGAAATTATTGATTGCCACAGACAAAGGGTGA
194 TGGTAGAAATCATTGCCCAACAAAGTTAGTTCAAGAAATTAATGATTGCCATAAACAAAGGTTGA
* * *
1362542 AAAAAGTCA-ATTGGAAAGATTTAGAGGATTAATGTTGAGTTAATAAGCCTATATAAG
259 AATAA-TCAGA-TGAAAAGATTTAGAGGATTAATGTTGAGTTAATAAGGCTATATAAG
** * * *
1362599 GAAAGAAAGTAGGTCATAGAATTGGATACTGAGGACGATGATGAGGATTTGTTTGTTCAAAGGTT
1 GAAA-AAAAAAGGTCATAGAATTGGATACTGAGGATGATGATGAGGATTTGTCTGTTCAAAAGTT
* * * * *
1362664 GTTGATGAAGGAGGAAA-TGGATTTAAATTCATACAAGGTGGTATCCTTAAAATTGATTAAG-AG
65 GTTGATGAAGAAGGAAACT-GAGTCAAATTCATACAAGGAGGTATCCTAAAAATTGATTAAGAAG
1362727 AATCTTTGAAT-TAAGA
129 -ATCTTTGAATCTAAGA
1362743 AAAAGTCCTT
Statistics
Matches: 1434, Mismatches: 251, Indels: 69
0.82 0.14 0.04
Matches are distributed among these distances:
311 1 0.00
312 41 0.03
313 438 0.31
314 40 0.03
315 14 0.01
316 498 0.35
317 361 0.25
318 40 0.03
319 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.29
Consensus pattern (314 bp):
GAAAAAAAAAGGTCATAGAATTGGATACTGAGGATGATGATGAGGATTTGTCTGTTCAAAAGTTG
TTGATGAAGAAGGAAACTGAGTCAAATTCATACAAGGAGGTATCCTAAAAATTGATTAAGAAGAT
CTTTGAATCTAAGAGTAGTTATGTCTACTGTCAAAGCATAGGAAAAGAGTGAGAATGAGTTGTTG
GTAGAAATCATTGCCCAACAAAGTTAGTTCAAGAAATTAATGATTGCCATAAACAAAGGTTGAAA
TAATCAGATGAAAAGATTTAGAGGATTAATGTTGAGTTAATAAGGCTATATAAG
Found at i:1364173 original size:30 final size:29
Alignment explanation
Indices: 1364117--1364200 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
1364107 AGTTAGAAAA
*
1364117 ATTCAAATAAGTCTTTATATTTTTATTAC
1 ATTCAAATAAGTCTTTATACTTTTATTAC
* * **
1364146 ATTCAATTAAGTCATTTGTACTTTTATTTTG
1 ATTCAAATAAGTC-TTTATACTTTTA-TTAC
*
1364177 AGTCAAATAAG-CTCTTATACTTTT
1 ATTCAAATAAGTCT-TTATACTTTT
1364201 GTTTTGAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
29 13 0.30
30 20 0.45
31 11 0.25
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (29 bp):
ATTCAAATAAGTCTTTATACTTTTATTAC
Found at i:1364225 original size:30 final size:29
Alignment explanation
Indices: 1364159--1364225 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
1364149 CAATTAAGTC
* *
1364159 ATTTGTACTTTTATTTTGAGTCAAATAAG
1 ATTTATACTTTTATTTTGAATCAAATAAG
* * *
1364188 CTCTTATACTTTTGTTTTGAATCAAATATAT
1 AT-TTATACTTTTATTTTGAATCAAATA-AG
1364219 ATTTATA
1 ATTTATA
1364226 ACTAATGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
29 1 0.03
30 27 0.90
31 2 0.07
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (29 bp):
ATTTATACTTTTATTTTGAATCAAATAAG
Found at i:1367733 original size:3 final size:3
Alignment explanation
Indices: 1367725--1367750 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1367715 TAAATATAGT
1367725 TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TA
1367751 GAGATAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:1370487 original size:4 final size:4
Alignment explanation
Indices: 1370480--1370504 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1370470 AATATATATA
1370480 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
1370505 TTGAAACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1377709 original size:25 final size:25
Alignment explanation
Indices: 1377675--1377729 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
1377665 TTCTTCAATA
1377675 TAATTTGCATAGACATATAGTAAAT
1 TAATTTGCATAGACATATAGTAAAT
*
1377700 TAATTTGCATAGGCATATAGTAAAT
1 TAATTTGCATAGACATATAGTAAAT
1377725 TAATT
1 TAATT
1377730 GGGAGAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (25 bp):
TAATTTGCATAGACATATAGTAAAT
Found at i:1379422 original size:21 final size:20
Alignment explanation
Indices: 1379391--1379458 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
1379381 GGATATGTTC
1379391 ATGCAGTTCATGACAAAGGCTG
1 ATGCA-TTCATGA-AAAGGCTG
* *
1379413 ATGCATTCATAATAAAGACTG
1 ATGCATTCATGA-AAAGGCTG
* *
1379434 ATGCATTTATGATAAGGACTG
1 ATGCATTCATGAAAAGG-CTG
1379455 ATGC
1 ATGC
1379459 TTCCATTCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 3 0.08
21 30 0.79
22 5 0.13
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (20 bp):
ATGCATTCATGAAAAGGCTG
Found at i:1382758 original size:3 final size:3
Alignment explanation
Indices: 1382739--1382776 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1382729 ACTTTACCTC
* *
1382739 TAG TGG TAG TTG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1382777 TTAACTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (3 bp):
TAG
Found at i:1383187 original size:35 final size:35
Alignment explanation
Indices: 1383141--1383216 Score: 152
Period size: 35 Copynumber: 2.2 Consensus size: 35
1383131 CAAGGTGCAG
1383141 ACTTTCACTGCACATGGCTCGGTATTTTGGCCATA
1 ACTTTCACTGCACATGGCTCGGTATTTTGGCCATA
1383176 ACTTTCACTGCACATGGCTCGGTATTTTGGCCATA
1 ACTTTCACTGCACATGGCTCGGTATTTTGGCCATA
1383211 ACTTTC
1 ACTTTC
1383217 TCTACAGAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (35 bp):
ACTTTCACTGCACATGGCTCGGTATTTTGGCCATA
Found at i:1389176 original size:22 final size:22
Alignment explanation
Indices: 1389151--1389204 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1389141 TGAAAACTAC
*
1389151 TACATAATAGGATATTTATATA
1 TACATAATAGGATATTTACATA
1389173 TACATAATAGGATATTTACATA
1 TACATAATAGGATATTTACATA
1389195 TACATAATAG
1 TACATAATAG
1389205 ATTTGAAAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
TACATAATAGGATATTTACATA
Found at i:1389993 original size:20 final size:20
Alignment explanation
Indices: 1389947--1390021 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
1389937 TTTGGTTGCT
* * *
1389947 ATCTATCAATAAATGTGGGCC
1 ATCTATCGATAAATAT-GGTC
* *
1389968 ATCTATCGATAAATCTGGTT
1 ATCTATCGATAAATATGGTC
* *
1389988 ATCTATGGATAGATATGGTC
1 ATCTATCGATAAATATGGTC
*
1390008 ATCTATCCATAAAT
1 ATCTATCGATAAAT
1390022 GTTCTTCAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
ATCTATCGATAAATATGGTC
Found at i:1395989 original size:21 final size:22
Alignment explanation
Indices: 1395960--1396003 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1395950 AAGTGATTAA
1395960 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
1395981 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1396003 T
1 T
1396004 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Done.