Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013545.1 Kokia drynarioides strain JFW-HI SEQ_128571, 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: 227783
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 54 characters in sequence are not A, C, G, or T
Found at i:10759 original size:158 final size:158
Alignment explanation
Indices: 10563--10903 Score: 540
Period size: 158 Copynumber: 2.2 Consensus size: 158
10553 ATAAAAGGTT
* *
10563 AGCTTCTTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGA
1 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGA
* *
10628 ATTGAAACAAACGACGC-GATCATCTTCCTAATGAGATACTGAGAAGAAGATCAAATCAAACCCC
66 ATTGAAACAAACGACGCAG-TCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCA
* * *
10692 CGCTCGATGTGAGAAAATCTTTAAATCCC
130 CACTCGATGTGAGAAAATCTTCAAACCCC
* * *
10721 ATCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGA
1 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGA
*
10786 ATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
66 ATTGAAACAAACGACGCAGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
* *
10851 ACTCGATGTGAGCAAATCTTCGAACCCC
131 ACTCGATGTGAGAAAATCTTCAAACCCC
*
10879 AGCTTCCTGATAAGATACTGAGAAG
1 AGCTTCCTGATGAGATACTGAGAAG
10904 CAAGTCAAAG
Statistics
Matches: 167, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
158 166 0.99
159 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (158 bp):
AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGA
ATTGAAACAAACGACGCAGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
ACTCGATGTGAGAAAATCTTCAAACCCC
Found at i:11380 original size:6 final size:6
Alignment explanation
Indices: 11366--11434 Score: 74
Period size: 6 Copynumber: 11.8 Consensus size: 6
11356 TTTAATTTAT
* *
11366 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA -TTTAAA
11413 TTT-AA TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAA
11435 TTCCAAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
4 2 0.04
5 10 0.19
6 33 0.62
7 7 0.13
8 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:11382 original size:17 final size:17
Alignment explanation
Indices: 11359--11433 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
11349 CCCCCTTTTT
11359 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
11376 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
11393 AATTAATCTTAAATTTTA
1 AATTTATTTTAAA-TTTA
*
11411 AATTTAATTTAAATTTA
1 AATTTATTTTAAATTTA
11428 AATTTA
1 AATTTA
11434 ATTCCAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
17 36 0.72
18 14 0.28
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:11436 original size:11 final size:11
Alignment explanation
Indices: 11356--11434 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
11346 GGGCCCCCTT
*
11356 TTTAATTT-AT
1 TTTAATTTAAA
*
11366 TTTAAATTTAGA
1 TTT-AATTTAAA
*
11378 TTTATTTTAAA
1 TTTAATTTAAA
*
11389 TTTAAATT-AA
1 TTTAATTTAAA
11399 TCTTAAATTTTAAA
1 T-TT-AA-TTTAAA
11413 TTTAATTTAAA
1 TTTAATTTAAA
11424 TTTAAATTTAA
1 TTT-AATTTAA
11435 TTCCAAAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
10 6 0.11
11 28 0.51
12 14 0.25
13 4 0.07
14 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:12142 original size:3 final size:3
Alignment explanation
Indices: 12136--12214 Score: 63
Period size: 3 Copynumber: 26.3 Consensus size: 3
12126 ATTATTATGG
* * * * *
12136 TAA TAA TAA TAA TAA TAT TAC TAA T-A TCAT TAA TAA TAT TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* *
12181 CAA TAA TAA CAA TAA TAA TAA TAA -AA TTAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA T
12215 GGCATTAATT
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
2 4 0.07
3 52 0.88
4 3 0.05
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12169 original size:27 final size:27
Alignment explanation
Indices: 12139--12223 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
12129 ATTATGGTAA
* *
12139 TAATAATAATAATATTACTAATATCAT
1 TAATAATAATAATATTAATAATAACAT
* * *
12166 TAATAATATTAATGA-CAATAATAACAA
1 TAATAATAATAAT-ATTAATAATAACAT
* **
12193 TAATAATAATAAAATTAATAATGGCAT
1 TAATAATAATAATATTAATAATAACAT
12220 TAAT
1 TAAT
12224 TAAAAAAGGA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
26 1 0.02
27 43 0.96
28 1 0.02
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (27 bp):
TAATAATAATAATATTAATAATAACAT
Found at i:13334 original size:59 final size:57
Alignment explanation
Indices: 13228--13482 Score: 234
Period size: 59 Copynumber: 4.4 Consensus size: 57
13218 GAGGTCCTCG
* * *
13228 AACTGTCCAAAAATTCCATTTT-ACTCCGAACTTCCAAAAATCTCATTTTTGACCCCGA
1 AACT-TCCAAAAATTCCATTTTGCCTCGGAACTTCCAAAAATCCCATTTTT-ACCCCGA
* *
13286 AACTTCCAAAAATTCCATTTTGGCCTTGGAACTTCCAAAAATCCCATTTTTTACCTCGA
1 AACTTCCAAAAATTCCATTTT-GCCTCGGAACTTCCAAAAATCCCA-TTTTTACCCCGA
* *
13345 AACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTC-A
1 AACTTCCAAAAATTCCA-TTTTG-CCTCGGAACTTCCAAAAATCCCATTTTTACCC-CGA
* * * * **
13404 AACCTCC-AAAATCTCCATTTTCAACCTCGAAAC-TCTAAAAATTACATTTTTACCCCCG-
1 AACTTCCAAAAAT-TCCATTTT--GCCTCGGAACTTCCAAAAATCCCATTTTTA-CCCCGA
*
13462 AA-TGTCTAAAAATTCCATTTT
1 AACT-TCCAAAAATTCCATTTT
13483 TTAAACCCTA
Statistics
Matches: 169, Mismatches: 15, Indels: 26
0.80 0.07 0.12
Matches are distributed among these distances:
57 17 0.10
58 43 0.25
59 79 0.47
60 30 0.18
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (57 bp):
AACTTCCAAAAATTCCATTTTGCCTCGGAACTTCCAAAAATCCCATTTTTACCCCGA
Found at i:13381 original size:89 final size:89
Alignment explanation
Indices: 13223--13482 Score: 279
Period size: 89 Copynumber: 3.0 Consensus size: 89
13213 CCTTGGAGGT
*
13223 CCTCGAACTGTCCAAAAATTCCA--TTTTA-CTCCG-AACTTCCAAAAA-TCTCATTTTTGACCC
1 CCTCGAACT-TCCAAAAATCCCATTTTTTACCT-CGAAACTTCCAAAAATTC-CATTTTTGACCC
*
13283 CGAAACTTCCAAAAATTCCATTTTGGC
63 CGAAACTTCCAAAAATTCCATTTTGAC
* * *
13310 CTTGGAACTTCCAAAAATCCCATTTTTTACCTCGAAACTTCCAAAAATTCCATTTTTGACCTCGA
1 CCTCGAACTTCCAAAAATCCCATTTTTTACCTCGAAACTTCCAAAAATTCCATTTTTGACCCCGA
*
13375 AACTTCCAAAAATTCCATTTTTAC
66 AACTTCCAAAAATTCCATTTTGAC
* * ** * *
13399 CCTCAAACCTCC-AAAATCTCCATTTTCAACCTCGAAAC-TCTAAAAATTACATTTTT-ACCCCC
1 CCTCGAACTTCCAAAAATC-CCATTTTTTACCTCGAAACTTCCAAAAATTCCATTTTTGA-CCCC
*
13461 G-AA-TGTCTAAAAATTCCATTTT
64 GAAACT-TCCAAAAATTCCATTTT
13483 TTAAACCCTA
Statistics
Matches: 149, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
86 13 0.09
87 26 0.17
88 33 0.22
89 75 0.50
90 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (89 bp):
CCTCGAACTTCCAAAAATCCCATTTTTTACCTCGAAACTTCCAAAAATTCCATTTTTGACCCCGA
AACTTCCAAAAATTCCATTTTGAC
Found at i:13431 original size:29 final size:30
Alignment explanation
Indices: 13223--13483 Score: 240
Period size: 30 Copynumber: 8.9 Consensus size: 30
13213 CCTTGGAGGT
13223 CCTCG-AACTGTCCAAAAATTCCA-TTTT-A
1 CCTCGAAACT-TCCAAAAATTCCATTTTTAA
*
13251 -CTCCG-AACTTCCAAAAA-TCTCATTTTTGA
1 CCT-CGAAACTTCCAAAAATTC-CATTTTTAA
* **
13280 CCCCGAAACTTCCAAAAATTCCA-TTTTGG
1 CCTCGAAACTTCCAAAAATTCCATTTTTAA
* * * *
13309 CCTTGGAACTTCCAAAAATCCCATTTTTTA
1 CCTCGAAACTTCCAAAAATTCCATTTTTAA
*
13339 CCTCGAAACTTCCAAAAATTCCATTTTTGA
1 CCTCGAAACTTCCAAAAATTCCATTTTTAA
*
13369 CCTCGAAACTTCCAAAAATTCCATTTTTAC
1 CCTCGAAACTTCCAAAAATTCCATTTTTAA
* *
13399 CCTC-AAACCTCC-AAAATCTCCATTTTCAA
1 CCTCGAAACTTCCAAAAAT-TCCATTTTTAA
* * *
13428 CCTCGAAAC-TCTAAAAATTACATTTTTAC
1 CCTCGAAACTTCCAAAAATTCCATTTTTAA
* *
13457 CCCCG-AA-TGTCTAAAAATTCCATTTTT
1 CCTCGAAACT-TCCAAAAATTCCATTTTT
13484 TAAACCCTAA
Statistics
Matches: 197, Mismatches: 23, Indels: 25
0.80 0.09 0.10
Matches are distributed among these distances:
26 2 0.01
27 12 0.06
28 17 0.09
29 78 0.40
30 86 0.44
31 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (30 bp):
CCTCGAAACTTCCAAAAATTCCATTTTTAA
Found at i:13859 original size:96 final size:97
Alignment explanation
Indices: 13754--13936 Score: 230
Period size: 96 Copynumber: 1.9 Consensus size: 97
13744 AAAACTTTAA
* *
13754 AATCGAGGCAATGTTAT-GTTAT-TTCGAGTT-TCGAAAAGTTGCACCTTAACTTACTAGGTGTA
1 AATCGAGGCAATGTT-TCCTTATCTTCGA-TTCT-GAAAAGTTGCACCTTAACTTACTAGGTGCA
* * *
13816 A-TTTTTCTTCAAATTGAAATAATCGAATACCTTT
63 ACCTTTTCCTCAAATCGAAATAATCGAATACCTTT
* * *
13850 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGATAATTTGCGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAAAGTTGCACCTTAACTTACTAGGTGCAACC
*
13915 TTTTCCTCAAATCGAGATAATC
66 TTTTCCTCAAATCGAAATAATC
13937 AAACATCCTT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
95 1 0.01
96 48 0.65
97 25 0.34
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (97 bp):
AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAAAGTTGCACCTTAACTTACTAGGTGCAACC
TTTTCCTCAAATCGAAATAATCGAATACCTTT
Found at i:17672 original size:11 final size:11
Alignment explanation
Indices: 17656--17680 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17646 CTTACTCATG
17656 ATGCTGCTACA
1 ATGCTGCTACA
17667 ATGCTGCTACA
1 ATGCTGCTACA
17678 ATG
1 ATG
17681 GGAGACAATG
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:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (11 bp):
ATGCTGCTACA
Found at i:20899 original size:19 final size:19
Alignment explanation
Indices: 20875--20911 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20865 TCTGTTAAGT
20875 TTAGTTACTGGCAGTTGAG
1 TTAGTTACTGGCAGTTGAG
* *
20894 TTAGTTATTGTCAGTTGA
1 TTAGTTACTGGCAGTTGA
20912 AGGCTGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.43
Consensus pattern (19 bp):
TTAGTTACTGGCAGTTGAG
Found at i:23397 original size:38 final size:40
Alignment explanation
Indices: 23342--23420 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
23332 TATGCACTCA
*
23342 ATGGACACCCTTTGAAGAGTCACAACCC-TTTCATATTGG
1 ATGGACACCCTTTGAAGAATCACAACCCTTTTCATATTGG
*
23381 ATGGACA-CTTTTGAAGAATCACAACCCTTTTCATATTGG
1 ATGGACACCCTTTGAAGAATCACAACCCTTTTCATATTGG
23420 A
1 A
23421 CATACCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 18 0.49
39 19 0.51
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (40 bp):
ATGGACACCCTTTGAAGAATCACAACCCTTTTCATATTGG
Found at i:23436 original size:39 final size:38
Alignment explanation
Indices: 23352--23436 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
23342 ATGGACACCC
* **
23352 TTTGAAGAGTCACAACCCTTTCATATTGGATGGACACT
1 TTTGAAGAATCACAACCCTTTCATATTGGACAGACACT
*
23390 TTTGAAGAATCACAACCCTTTTCATATTGGACATAC-CT
1 TTTGAAGAATCACAACCC-TTTCATATTGGACAGACACT
23428 TTTGGAAGA
1 TTT-GAAGA
23437 GACTTGCCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
38 22 0.54
39 19 0.46
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (38 bp):
TTTGAAGAATCACAACCCTTTCATATTGGACAGACACT
Found at i:29472 original size:20 final size:21
Alignment explanation
Indices: 29449--29487 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
29439 AATTTGACAC
29449 TTTTTATTAATTT-GTATTAT
1 TTTTTATTAATTTGGTATTAT
* *
29469 TTTTTTTTATTTTGGTATT
1 TTTTTATTAATTTGGTATT
29488 TAATTTGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (21 bp):
TTTTTATTAATTTGGTATTAT
Found at i:29765 original size:22 final size:22
Alignment explanation
Indices: 29726--29783 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
29716 CTTTATTACT
* *
29726 TTGTTATCCTTATTTTTT-TTTG
1 TTGTT-TCATTATTTTTTATTTA
29748 TTGTTTCATTATTATTTTATTTA
1 TTGTTTCATTATT-TTTTATTTA
*
29771 TT-TTTCTTTATTT
1 TTGTTTCATTATTT
29784 ATATTGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 8 0.26
22 18 0.58
23 5 0.16
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (22 bp):
TTGTTTCATTATTTTTTATTTA
Found at i:40760 original size:14 final size:13
Alignment explanation
Indices: 40738--40772 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
40728 TACTTTGAAA
40738 TAATTATAATATAT
1 TAATTATAATAT-T
*
40752 TATTTATAATATT
1 TAATTATAATATT
40765 TAATTATA
1 TAATTATA
40773 TGTGAGTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATTATAATATT
Found at i:43102 original size:31 final size:31
Alignment explanation
Indices: 43067--43133 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
43057 AATTCTTTAT
43067 ATTAAGATAGTTGCAAATAAAGTAGTAAAAA
1 ATTAAGATAGTTGCAAATAAAGTAGTAAAAA
*
43098 ATTAATATAGTTGCAAATAAAGTAGTAAAAA
1 ATTAAGATAGTTGCAAATAAAGTAGTAAAAA
43129 ATTAA
1 ATTAA
43134 CAATAAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.28
Consensus pattern (31 bp):
ATTAAGATAGTTGCAAATAAAGTAGTAAAAA
Found at i:43274 original size:32 final size:31
Alignment explanation
Indices: 43238--43363 Score: 107
Period size: 32 Copynumber: 4.1 Consensus size: 31
43228 AAATAGCAGC
*
43238 AAAAATAACAGCAAAACAACAACAAAAACAAT
1 AAAAA-AACAACAAAACAACAACAAAAACAAT
* * * *
43270 AAAAACAGCAACAAAAAAAACATCAAAAACAGT
1 AAAAA-AACAAC-AAAACAACAACAAAAACAAT
* * *
43303 AAAAAAACAACAAAACAGCAACCAAAACAGT
1 AAAAAAACAACAAAACAACAACAAAAACAAT
*
43334 GAAAAAAAC--CAAAACAATAA-AAAAA-AAT
1 -AAAAAAACAACAAAACAACAACAAAAACAAT
43362 AA
1 AA
43364 CACCAAAACA
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
27 2 0.03
28 2 0.03
29 4 0.05
30 9 0.12
31 16 0.21
32 22 0.29
33 22 0.29
ACGTcount: A:0.72, C:0.17, G:0.05, T:0.06
Consensus pattern (31 bp):
AAAAAAACAACAAAACAACAACAAAAACAAT
Found at i:43281 original size:24 final size:24
Alignment explanation
Indices: 43254--43314 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
43244 AACAGCAAAA
*
43254 CAACAACAAAAACAAT-AAAAACAG
1 CAACAAAAAAAAC-ATCAAAAACAG
43278 CAACAAAAAAAACATCAAAAACAG
1 CAACAAAAAAAACATCAAAAACAG
* *
43302 TAA-AAAAACAACA
1 CAACAAAAAAAACA
43315 AAACAGCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.33
24 22 0.67
ACGTcount: A:0.72, C:0.20, G:0.03, T:0.05
Consensus pattern (24 bp):
CAACAAAAAAAACATCAAAAACAG
Found at i:43308 original size:23 final size:23
Alignment explanation
Indices: 43254--43329 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 23
43244 AACAGCAAAA
*
43254 CAACAACAAAAACAATAAAAACAG
1 CAACAAAAAAAAC-ATAAAAACAG
43278 CAACAAAAAAAACATCAAAAACAG
1 CAACAAAAAAAACAT-AAAAACAG
* *
43302 TAA-AAAAACAAC---AAAACAG
1 CAACAAAAAAAACATAAAAACAG
*
43321 CAACCAAAA
1 CAACAAAAA
43330 CAGTGAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
19 9 0.20
20 4 0.09
23 10 0.22
24 22 0.49
ACGTcount: A:0.71, C:0.21, G:0.04, T:0.04
Consensus pattern (23 bp):
CAACAAAAAAAACATAAAAACAG
Found at i:43359 original size:18 final size:18
Alignment explanation
Indices: 43322--43359 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43312 ACAAAACAGC
* *
43322 AACCAAAACAGTGAAAAA
1 AACCAAAACAATAAAAAA
43340 AACCAAAACAATAAAAAA
1 AACCAAAACAATAAAAAA
43358 AA
1 AA
43360 ATAACACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.74, C:0.16, G:0.05, T:0.05
Consensus pattern (18 bp):
AACCAAAACAATAAAAAA
Found at i:43360 original size:20 final size:21
Alignment explanation
Indices: 43335--43394 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
43325 CAAAACAGTG
43335 AAAAAAACCAAAACAATAAAAA
1 AAAAAAACCAAAACAAT-AAAA
*
43357 AAAATAACACCAAAACAGT-AAA
1 AAAA-AA-ACCAAAACAATAAAA
* *
43379 AACAACACCAAAACAA
1 AAAAAAACCAAAACAA
43395 CAATATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 9 0.28
21 1 0.03
22 10 0.31
23 2 0.06
24 10 0.31
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.05
Consensus pattern (21 bp):
AAAAAAACCAAAACAATAAAA
Found at i:44757 original size:30 final size:30
Alignment explanation
Indices: 44700--44757 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
44690 AGAATGATTT
*
44700 TTTAACAAAAAAGATCAATTTGTCCTTTGA
1 TTTAACAAAAAAGATCAATTTGACCTTTGA
* *
44730 TTTAACATACAAAGATGAATTT-ACCTTT
1 TTTAACA-AAAAAGATCAATTTGACCTTT
44758 TTTCGAGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTAACAAAAAAGATCAATTTGACCTTTGA
Found at i:45858 original size:24 final size:24
Alignment explanation
Indices: 45811--45867 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
45801 ATCAATTTGT
*
45811 GTTTTAAATATTAATGTGTATGAG
1 GTTTTAAATATTAATGGGTATGAG
* *
45835 GTTTTAAATTTTAATGGGTTTGAG
1 GTTTTAAATATTAATGGGTATGAG
* *
45859 CTCTTAAAT
1 GTTTTAAAT
45868 GTATTAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (24 bp):
GTTTTAAATATTAATGGGTATGAG
Found at i:46266 original size:2 final size:2
Alignment explanation
Indices: 46259--46287 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46249 GTGCCGTAAA
46259 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46288 AAAGAAGATA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49718 original size:14 final size:14
Alignment explanation
Indices: 49695--49729 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
49685 ACACTTGTAA
*
49695 TTCTGCTGGCATGT
1 TTCTGTTGGCATGT
49709 TTCTGTTGGCATGT
1 TTCTGTTGGCATGT
49723 TTCTGTT
1 TTCTGTT
49730 TTGCTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.06, C:0.17, G:0.26, T:0.51
Consensus pattern (14 bp):
TTCTGTTGGCATGT
Found at i:52445 original size:14 final size:14
Alignment explanation
Indices: 52401--52447 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
52391 TATAACCACA
52401 TATTTAAATTAATT
1 TATTTAAATTAATT
*** *
52415 T-TTTCTGTTAATA
1 TATTTAAATTAATT
52428 TATTTAAATTAATT
1 TATTTAAATTAATT
52442 TATTTA
1 TATTTA
52448 TATAAGCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (14 bp):
TATTTAAATTAATT
Found at i:56115 original size:9 final size:9
Alignment explanation
Indices: 56096--56129 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
56086 ATCTATATCT
56096 TTTTCTTTTC
1 TTTT-TTTTC
56106 TTTTTTTTC
1 TTTTTTTTC
56115 TTTTTTTT-
1 TTTTTTTTC
56123 TTTTTTT
1 TTTTTTT
56130 ACATTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.29
9 13 0.54
10 4 0.17
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:56118 original size:20 final size:18
Alignment explanation
Indices: 56093--56129 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
56083 ATGATCTATA
56093 TCTTTTTCTTTTCTTTTTTT
1 TCTTTTT-TTTT-TTTTTTT
56113 TCTTTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTTTT
56130 ACATTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (18 bp):
TCTTTTTTTTTTTTTTTT
Found at i:56127 original size:14 final size:14
Alignment explanation
Indices: 56095--56126 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
56085 GATCTATATC
56095 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
56109 TTTTTCTTTT-TTT
1 TTTTTCTTTTCTTT
56122 TTTTT
1 TTTTT
56127 TTTACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTCTTTTCTTT
Found at i:56285 original size:32 final size:32
Alignment explanation
Indices: 56235--56334 Score: 89
Period size: 33 Copynumber: 3.1 Consensus size: 32
56225 TCTTTTGTTA
* * *
56235 AATTTAATCTTC-AACTTTTAAAAAGAAATCG
1 AATTTAATCATCTACCTTTTAAAAAGAAGTCG
* *
56266 AATTTGATCAT-TAACCTTTTTAAAAA-AGAGTCA
1 AATTTAATCATCT-ACC-TTTTAAAAAGA-AGTCG
* *
56299 AATTTAATTATCTATCTTTTAAAAAGAAGTCG
1 AATTTAATCATCTACCTTTTAAAAAGAAGTCG
56331 AATT
1 AATT
56335 GCGGTTTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
31 9 0.17
32 20 0.37
33 24 0.44
34 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (32 bp):
AATTTAATCATCTACCTTTTAAAAAGAAGTCG
Found at i:56448 original size:2 final size:2
Alignment explanation
Indices: 56441--56465 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56431 TTTTATGAAT
56441 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
56466 TGGATTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57083 original size:17 final size:17
Alignment explanation
Indices: 57061--57099 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
57051 AAAATAAGTA
57061 TAAAAAATTACCCGAAT
1 TAAAAAATTACCCGAAT
**
57078 TAAAAAATTATTCGAAT
1 TAAAAAATTACCCGAAT
57095 TAAAA
1 TAAAA
57100 TATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (17 bp):
TAAAAAATTACCCGAAT
Found at i:64617 original size:14 final size:14
Alignment explanation
Indices: 64598--64625 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
64588 GAAGAGAATG
64598 TAACATTATGTGAT
1 TAACATTATGTGAT
64612 TAACATTATGTGAT
1 TAACATTATGTGAT
64626 AAATTCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
TAACATTATGTGAT
Found at i:68277 original size:24 final size:22
Alignment explanation
Indices: 68221--68277 Score: 60
Period size: 26 Copynumber: 2.4 Consensus size: 22
68211 TTATAACATA
*
68221 AAAATTATTTTTTGTTTTTTAT
1 AAAATTATTTTTTATTTTTTAT
68243 ATAAATTTTATTTTTTCATTTTTTAT
1 A-AAA--TTATTTTTT-ATTTTTTAT
68269 GAAAATTAT
1 -AAAATTAT
68278 AAAAAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
22 1 0.03
23 3 0.10
24 4 0.14
25 9 0.31
26 11 0.38
27 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (22 bp):
AAAATTATTTTTTATTTTTTAT
Found at i:76989 original size:6 final size:6
Alignment explanation
Indices: 76978--77011 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
76968 TTTAATCCCT
76978 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTT
77012 TTATTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCC
Found at i:86959 original size:2 final size:2
Alignment explanation
Indices: 86910--86941 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
86900 CCCCACTGTG
*
86910 AT AT AT AT GT 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
86942 GCGTGTGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90772 original size:24 final size:25
Alignment explanation
Indices: 90710--90772 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
90700 TTGAAATTTT
* *
90710 TTCGAATCAAGTTGAGTGAAATGAAA
1 TTCGAGTCAAATTGAGTGAAAT-AAA
* *
90736 TTCGAGTCGAATTGAGTGAAAT-TA
1 TTCGAGTCAAATTGAGTGAAATAAA
*
90760 TTCGAGTTAAATT
1 TTCGAGTCAAATT
90773 AAAATTAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
24 12 0.39
26 19 0.61
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (25 bp):
TTCGAGTCAAATTGAGTGAAATAAA
Found at i:91032 original size:20 final size:21
Alignment explanation
Indices: 91007--91060 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
90997 TAGAATATAA
91007 ATTTTGAAATTATT-ATAAA-T
1 ATTTTGAAATTATTGA-AAATT
91027 ATTTTGAAATT-TTGAAAATT
1 ATTTTGAAATTATTGAAAATT
*
91047 ATTTTAAAATTATT
1 ATTTTGAAATTATT
91061 TTATATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.17
20 23 0.77
21 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
ATTTTGAAATTATTGAAAATT
Found at i:91057 original size:11 final size:11
Alignment explanation
Indices: 91007--91063 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
90997 TAGAATATAA
*
91007 ATTTTGAAATT
1 ATTTTAAAATT
*
91018 ATTAT-AAA-T
1 ATTTTAAAATT
*
91027 ATTTTGAAA-T
1 ATTTTAAAATT
*
91037 -TTTGAAAATT
1 ATTTTAAAATT
91047 ATTTTAAAATT
1 ATTTTAAAATT
91058 ATTTTA
1 ATTTTA
91064 TATTTTTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 11 0.29
10 8 0.21
11 19 0.50
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
ATTTTAAAATT
Found at i:92726 original size:17 final size:18
Alignment explanation
Indices: 92701--92734 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
92691 ATTAATTAAG
92701 TAAAAAAAAGT-ACTAAC
1 TAAAAAAAAGTAACTAAC
*
92718 TAAATAAAAGTAACTAA
1 TAAAAAAAAGTAACTAA
92735 ACATGGTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.09, G:0.06, T:0.21
Consensus pattern (18 bp):
TAAAAAAAAGTAACTAAC
Found at i:95007 original size:18 final size:21
Alignment explanation
Indices: 94976--95027 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 21
94966 TAAATTCAGA
* *
94976 TATTTAATCGTTTTCAAT-TT
1 TATTTTATCATTTTCAATGTT
*
94996 T-TTTT-TCATTTTCCATGTT
1 TATTTTATCATTTTCAATGTT
95015 TATTTTATCATTT
1 TATTTTATCATTT
95028 CTATTCAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 9 0.35
19 6 0.23
20 5 0.19
21 6 0.23
ACGTcount: A:0.19, C:0.12, G:0.04, T:0.65
Consensus pattern (21 bp):
TATTTTATCATTTTCAATGTT
Found at i:112633 original size:13 final size:13
Alignment explanation
Indices: 112599--112643 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
112589 TCAAATCCGA
112599 AAACCAAAAAAAG
1 AAACCAAAAAAAG
112612 AAA--AAAAAAAG
1 AAACCAAAAAAAG
*
112623 AAACCAGAAAAAG
1 AAACCAAAAAAAG
112636 AAA-CAAAA
1 AAACCAAAA
112644 TATAAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 11 0.39
12 4 0.14
13 13 0.46
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (13 bp):
AAACCAAAAAAAG
Found at i:117108 original size:33 final size:33
Alignment explanation
Indices: 117066--117155 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
117056 TGTTTATGTG
117066 AAATTGAAGAGAAAGAGAAGAGAGGCAAGGATC
1 AAATTGAAGAGAAAGAGAAGAGAGGCAAGGATC
* *
117099 AAATTGAAGAGAAAAAGAAGAGAGGCAATGATC
1 AAATTGAAGAGAAAGAGAAGAGAGGCAAGGATC
*
117132 AAATTGAAGAGAAAGGAAAAGAGA
1 AAATTGAAGAGAAA-GAGAAGAGA
117156 AGAGCAAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 45 0.87
34 7 0.13
ACGTcount: A:0.56, C:0.04, G:0.30, T:0.10
Consensus pattern (33 bp):
AAATTGAAGAGAAAGAGAAGAGAGGCAAGGATC
Found at i:118080 original size:25 final size:24
Alignment explanation
Indices: 118029--118153 Score: 134
Period size: 23 Copynumber: 5.3 Consensus size: 24
118019 CACTAGCGCG
* *
118029 CTCTCTGT-TTAGCAC-GTCTCGTG
1 CTCTCTGTATTAGCACTGTGT-GTA
118052 CTCTCTGTTATTAGCACTGTGTGTA
1 CTCTCTG-TATTAGCACTGTGTGTA
* *
118077 CTCTCTG-ATTAGCACTTTGTGTG
1 CTCTCTGTATTAGCACTGTGTGTA
* *
118100 CTCTCTG-ATTAGTACTTTGTGTA
1 CTCTCTGTATTAGCACTGTGTGTA
*
118123 CTCTCTGT-TTAGCACTGTGTGTG
1 CTCTCTGTATTAGCACTGTGTGTA
118146 CTCTCTGT
1 CTCTCTGT
118154 TGCCCAGCAC
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
23 69 0.78
24 1 0.01
25 16 0.18
26 3 0.03
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (24 bp):
CTCTCTGTATTAGCACTGTGTGTA
Found at i:118128 original size:46 final size:47
Alignment explanation
Indices: 118029--118153 Score: 164
Period size: 46 Copynumber: 2.7 Consensus size: 47
118019 CACTAGCGCG
* *
118029 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTGTA
1 CTCTCTGATTAGCACTGTGT-GTGCTCTCTG-TATTAGCACTGTGTGTA
* * *
118077 CTCTCTGATTAGCACTTTGTGTGCTCTCTG-ATTAGTACTTTGTGTA
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTATTAGCACTGTGTGTA
*
118123 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGT
118154 TGCCCAGCAC
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
46 42 0.62
48 24 0.35
49 2 0.03
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (47 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGTATTAGCACTGTGTGTA
Found at i:118193 original size:69 final size:69
Alignment explanation
Indices: 118052--118201 Score: 191
Period size: 69 Copynumber: 2.1 Consensus size: 69
118042 ACGTCTCGTG
* *
118052 CTCTCTGTTATTAGCACTGTGTGTACTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTG-T-TTAGCACTGTGTGTACTCTCTGATTAGCACTTTATGTACTCTCTGATTAGTACTT
118117 TGTGTA
64 TGTGTA
*
118123 CTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTGCCCAGCAC-TTATGTACTCTCTG-TTAGTAC
1 CTCTCTGTTTAGCACTGTGTGTACTCTCTGATT----AGCACTTTATGTACTCTCTGATTAGTAC
118185 TTTG-GTA
62 TTTGTGTA
118192 CTCTCTGTTT
1 CTCTCTGTTT
118202 GTTCCGTATA
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 34 0.47
70 12 0.17
71 19 0.26
72 5 0.07
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (69 bp):
CTCTCTGTTTAGCACTGTGTGTACTCTCTGATTAGCACTTTATGTACTCTCTGATTAGTACTTTG
TGTA
Found at i:118200 original size:21 final size:23
Alignment explanation
Indices: 118052--118198 Score: 140
Period size: 23 Copynumber: 6.3 Consensus size: 23
118042 ACGTCTCGTG
*
118052 CTCTCTGTTATTAGCACTGTGTGTA
1 CTCTCTG--ATTAGCACTTTGTGTA
*
118077 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGATTAGCACTTTGTGTA
*
118100 CTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGATTAGCACTTTGTGTA
* * *
118123 CTCTCTGTTTAGCACTGTGTGTG
1 CTCTCTGATTAGCACTTTGTGTA
*
118146 CTCTCTG-TTGCCCAGCAC-TTATGTA
1 CTCTCTGATT----AGCACTTTGTGTA
*
118171 CTCTCTG-TTAGTACTTTG-GTA
1 CTCTCTGATTAGCACTTTGTGTA
118192 CTCTCTG
1 CTCTCTG
118199 TTTGTTCCGT
Statistics
Matches: 104, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
21 14 0.13
22 4 0.04
23 61 0.59
25 20 0.19
26 5 0.05
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (23 bp):
CTCTCTGATTAGCACTTTGTGTA
Found at i:119492 original size:22 final size:22
Alignment explanation
Indices: 119459--119511 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
119449 AATATAAAAA
119459 TAAA-TTGATGTATTTATTTCTT
1 TAAATTTG-TGTATTTATTTCTT
119481 TAAATTTGTGTATTTATTTCTT
1 TAAATTTGTGTATTTATTTCTT
119503 TAAATTTGT
1 TAAATTTGT
119512 ATGATTGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.60
Consensus pattern (22 bp):
TAAATTTGTGTATTTATTTCTT
Found at i:122208 original size:6 final size:6
Alignment explanation
Indices: 122191--122229 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
122181 TCACACATGA
*
122191 CACATT CGCATT CACATT CACATT CACATT CACATT CAC
1 CACATT CACATT CACATT CACATT CACATT CACATT CAC
122230 TTGTTTGAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.31
Consensus pattern (6 bp):
CACATT
Found at i:123605 original size:22 final size:22
Alignment explanation
Indices: 123580--123651 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
123570 GGCGGCAGTG
123580 CCTTGGAGCATCATTTGGCGTT
1 CCTTGGAGCATCATTTGGCGTT
** * **
123602 CCTTGGAG--TCAAGATCG-GAA
1 CCTTGGAGCATC-ATTTGGCGTT
*
123622 CCTTGGAACATCATTTGGCGTT
1 CCTTGGAGCATCATTTGGCGTT
123644 CCTTGGAG
1 CCTTGGAG
123652 TCAAGATCGG
Statistics
Matches: 34, Mismatches: 12, Indels: 8
0.63 0.22 0.15
Matches are distributed among these distances:
20 10 0.29
21 6 0.18
22 18 0.53
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (22 bp):
CCTTGGAGCATCATTTGGCGTT
Found at i:123639 original size:42 final size:42
Alignment explanation
Indices: 123580--123663 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
123570 GGCGGCAGTG
*
123580 CCTTGGAGCATCATTTGGCGTTCCTTGGAGTCAAGATCGGAA
1 CCTTGGAACATCATTTGGCGTTCCTTGGAGTCAAGATCGGAA
123622 CCTTGGAACATCATTTGGCGTTCCTTGGAGTCAAGATCGGAA
1 CCTTGGAACATCATTTGGCGTTCCTTGGAGTCAAGATCGGAA
123664 ATCGAAGTCG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (42 bp):
CCTTGGAACATCATTTGGCGTTCCTTGGAGTCAAGATCGGAA
Found at i:133252 original size:17 final size:16
Alignment explanation
Indices: 133226--133266 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
133216 GGAATTCAAA
*
133226 TATAAATTTATTATTAT
1 TATAAATTTATGATT-T
*
133243 TATTAATTTATGATTT
1 TATAAATTTATGATTT
133259 TATAAATT
1 TATAAATT
133267 ATAAAGTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TATAAATTTATGATTT
Found at i:137316 original size:40 final size:40
Alignment explanation
Indices: 137261--137341 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
137251 ACCCTCTACA
137261 GATGCTTCTTGTCTCATCTTTCTCCTTTGTTCTGGAGCCT
1 GATGCTTCTTGTCTCATCTTTCTCCTTTGTTCTGGAGCCT
137301 GATGCTTCTTGTCTCATCTTTCTCCTTTGTTCTGGAGCCT
1 GATGCTTCTTGTCTCATCTTTCTCCTTTGTTCTGGAGCCT
137341 G
1 G
137342 TAATGCATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.07, C:0.27, G:0.19, T:0.47
Consensus pattern (40 bp):
GATGCTTCTTGTCTCATCTTTCTCCTTTGTTCTGGAGCCT
Found at i:139708 original size:13 final size:13
Alignment explanation
Indices: 139692--139735 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
139682 TTATTTATTT
139692 TTATTATAATATA
1 TTATTATAATATA
139705 TTATTATAATACTA
1 TTATTATAATA-TA
*
139719 TTATTTATCATATA
1 TTA-TTATAATATA
139733 TTA
1 TTA
139736 AAACCAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 10 0.36
15 7 0.25
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATTATAATATA
Found at i:141772 original size:20 final size:20
Alignment explanation
Indices: 141747--141814 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
141737 TTAGTACTTC
141747 GTCAAAATGTGAAATTCTGA
1 GTCAAAATGTGAAATTCTGA
141767 GTCAAAATGTGAAATTCTGA
1 GTCAAAATGTGAAATTCTGA
*
141787 GTCAAAATGTGAAATTTTGA
1 GTCAAAATGTGAAATTCTGA
141807 GTCAAAAT
1 GTCAAAAT
141815 AGGCTAGTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (20 bp):
GTCAAAATGTGAAATTCTGA
Found at i:142393 original size:26 final size:27
Alignment explanation
Indices: 142356--142415 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
142346 TTTGTCTGAA
*
142356 AAAAATTGAAAT-TTAATTAATTTATTT
1 AAAAATTGAAATGCT-ATTAATTTATTT
**
142383 AAAAATT-AAATGCTATTTTTTTATTT
1 AAAAATTGAAATGCTATTAATTTATTT
142409 AAAAATT
1 AAAAATT
142416 TCAATTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
AAAAATTGAAATGCTATTAATTTATTT
Found at i:159560 original size:31 final size:31
Alignment explanation
Indices: 159510--159569 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
159500 TCCCTAAGTA
159510 TAATATAAATCAAATAAATT-AAAATTGATT
1 TAATATAAATCAAATAAATTAAAAATTGATT
159540 TAATATAAAAT-ATAATAAATTAAAAATTGA
1 TAATAT-AAATCA-AATAAATTAAAAATTGA
159570 AATATATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 7 0.26
31 12 0.44
32 8 0.30
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (31 bp):
TAATATAAATCAAATAAATTAAAAATTGATT
Found at i:160231 original size:7 final size:7
Alignment explanation
Indices: 160219--160248 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
160209 GTCTTGAATG
160219 CCTGTCC
1 CCTGTCC
160226 CCTGTCC
1 CCTGTCC
160233 CCTGTCC
1 CCTGTCC
*
160240 CCTGGCC
1 CCTGTCC
160247 CC
1 CC
160249 CTCTGCTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.60, G:0.17, T:0.23
Consensus pattern (7 bp):
CCTGTCC
Found at i:164645 original size:6 final size:6
Alignment explanation
Indices: 164634--164665 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
164624 AAAACTGCAA
164634 GAGTCT GAGTCT GAGTCT GAGTCT GAGTCT GA
1 GAGTCT GAGTCT GAGTCT GAGTCT GAGTCT GA
164666 TTACCGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (6 bp):
GAGTCT
Found at i:168615 original size:16 final size:17
Alignment explanation
Indices: 168594--168628 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
168584 CTTAAATGCT
168594 ATAAAA-CAATCTAATA
1 ATAAAACCAATCTAATA
168610 ATAAAACCAATCTAATA
1 ATAAAACCAATCTAATA
168627 AT
1 AT
168629 GAAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAACCAATCTAATA
Found at i:172715 original size:21 final size:21
Alignment explanation
Indices: 172691--172748 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
172681 TGATGCTGGG
172691 AGGATGTCATTTGATGCACCA
1 AGGATGTCATTTGATGCACCA
*
172712 AGGATGTC-TTTAGATGCAGCA
1 AGGATGTCATTT-GATGCACCA
* *
172733 AGAATGTCATGTGATG
1 AGGATGTCATTTGATG
172749 ATCCCAGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 3 0.09
21 27 0.84
22 2 0.06
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (21 bp):
AGGATGTCATTTGATGCACCA
Found at i:175043 original size:21 final size:21
Alignment explanation
Indices: 175017--175058 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
175007 AAACCCAATG
*
175017 GCCATATCACTATGATTGGAA
1 GCCATATCACTAAGATTGGAA
175038 GCCATATCACTAAGATTGGAA
1 GCCATATCACTAAGATTGGAA
175059 ACTGGCTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (21 bp):
GCCATATCACTAAGATTGGAA
Found at i:177575 original size:31 final size:30
Alignment explanation
Indices: 177540--177729 Score: 110
Period size: 31 Copynumber: 6.3 Consensus size: 30
177530 AACAGAATAA
177540 TAGGTACCAAATTAGGAAAAAGAGTCAAGTT
1 TAGGTACCAAATTAGGAAAAA-AGTCAAGTT
*
177571 TAGGTACTAAATT-GGACCCAAAAA---AA-TT
1 TAGGTACCAAATTAGGA---AAAAAGTCAAGTT
* * *
177599 TAAGTACCAACTTTA-AAAAAAAGTGTCAAGTT
1 TAGGTACCAA-ATTAGGAAAAAA--GTCAAGTT
**
177631 TAGGTACCAAATTAGGAAAACGTGTCAAGTT
1 TAGGTACCAAATTAGGAAAA-AAGTCAAGTT
* * *
177662 TAAGTATCAAATT-GGACTAAAAA--AAAGTT
1 TAGGTACCAAATTAGGA--AAAAAGTCAAGTT
* *
177691 TAGGTTCCAAATTAAGAAAAAATGTCAAGTT
1 TAGGTACCAAATTAGGAAAAAA-GTCAAGTT
*
177722 TAGATACC
1 TAGGTACC
177730 GAACATTATA
Statistics
Matches: 118, Mismatches: 22, Indels: 38
0.66 0.12 0.21
Matches are distributed among these distances:
26 5 0.04
28 15 0.13
29 20 0.17
30 8 0.07
31 47 0.40
32 19 0.16
33 4 0.03
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (30 bp):
TAGGTACCAAATTAGGAAAAAAGTCAAGTT
Found at i:177711 original size:91 final size:91
Alignment explanation
Indices: 177540--177729 Score: 249
Period size: 91 Copynumber: 2.1 Consensus size: 91
177530 AACAGAATAA
* *
177540 TAGGTACCAAATTAGGAAAAAGAGTCAAGTTTAGGTACTAAATTGGACCCAAAAAAATTTAAGTA
1 TAGGTACCAAATTAGGAAAAAGAGTCAAGTTTAAGTACTAAATTGGACCAAAAAAAATTTAAGTA
* *
177605 CCAACTTTAAAAAAAAGTGTCAAGTT
66 CCAACATTAAAAAAAAATGTCAAGTT
* * * *
177631 TAGGTACCAAATTAGGAAAACGTGTCAAGTTTAAGTA-TCAAATTGGACTAAAAAAAAGTTTAGG
1 TAGGTACCAAATTAGGAAAAAGAGTCAAGTTTAAGTACT-AAATTGGACCAAAAAAAA-TTTAAG
* *
177695 TTCCAA-ATTAAGAAAAAATGTCAAGTT
64 TACCAACATTAAAAAAAAATGTCAAGTT
*
177722 TAGATACC
1 TAGGTACC
177730 GAACATTATA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
90 1 0.01
91 75 0.87
92 10 0.12
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (91 bp):
TAGGTACCAAATTAGGAAAAAGAGTCAAGTTTAAGTACTAAATTGGACCAAAAAAAATTTAAGTA
CCAACATTAAAAAAAAATGTCAAGTT
Found at i:179281 original size:17 final size:17
Alignment explanation
Indices: 179250--179284 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
179240 AATACTAATT
179250 TAAATATAAATATATTA
1 TAAATATAAATATATTA
179267 TAAAT-TAAATAATATTA
1 TAAATATAAAT-ATATTA
179284 T
1 T
179285 TGAACCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATAAATATATTA
Found at i:181908 original size:17 final size:17
Alignment explanation
Indices: 181886--181946 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
181876 TTAGTAATAA
181886 TTTATTTGTGTTAAAAG
1 TTTATTTGTGTTAAAAG
* *
181903 TTTATTTAGTATT-AAGG
1 TTTATTT-GTGTTAAAAG
*
181920 CATGTTATTTGTGTTAGAAG
1 --T-TTATTTGTGTTAAAAG
181940 TTTATTT
1 TTTATTT
181947 AAGGTTAGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
17 16 0.47
18 5 0.15
19 5 0.15
20 8 0.24
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (17 bp):
TTTATTTGTGTTAAAAG
Found at i:183726 original size:3 final size:3
Alignment explanation
Indices: 183714--183759 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
183704 GTTTTAGTGG
*
183714 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA A-A ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
183759 A
1 A
183760 AATTATGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:183778 original size:39 final size:38
Alignment explanation
Indices: 183735--183837 Score: 109
Period size: 39 Copynumber: 2.6 Consensus size: 38
183725 TAATAATAAT
183735 AATAATAACAATAATAATAAAAT-AAAATTATGATTGCAA
1 AATAATAA-AATAA-AATAAAATAAAAATTATGATTGCAA
* * *
183774 AATAAATTAAGTGAAATAAAATAAAAATTATGATTGCAA
1 AAT-AATAAAATAAAATAAAATAAAAATTATGATTGCAA
* * *
183813 AATAAATTAAGTGAAATAAAATAAA
1 AAT-AATAAAATAAAATAAAATAAA
183838 CTGGTGATTT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
38 8 0.14
39 47 0.80
40 4 0.07
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (38 bp):
AATAATAAAATAAAATAAAATAAAAATTATGATTGCAA
Found at i:183816 original size:20 final size:19
Alignment explanation
Indices: 183753--183818 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 19
183743 CAATAATAAT
183753 AAAATAAAATTATGATTGC
1 AAAATAAAATTATGATTGC
*
183772 AAAAT-AAATTAAGTGAAAT--
1 AAAATAAAATT-A-TG-ATTGC
183791 AAAATAAAAATTATGATTGC
1 AAAAT-AAAATTATGATTGC
183811 AAAATAAA
1 AAAATAAA
183819 TTAAGTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
18 7 0.18
19 16 0.42
20 8 0.21
21 7 0.18
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (19 bp):
AAAATAAAATTATGATTGC
Found at i:190612 original size:23 final size:24
Alignment explanation
Indices: 190556--190616 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
190546 TCATTAACAT
190556 TGTTTGTGAACATGTTCAATTATA
1 TGTTTGTGAACATGTTCAATTATA
* *
190580 TGTTTATGAACATGTTC-GTT-TA
1 TGTTTGTGAACATGTTCAATTATA
190602 GTGTTTGTGAACATG
1 -TGTTTGTGAACATG
190617 CATGTTTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.06
23 15 0.45
24 16 0.48
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.46
Consensus pattern (24 bp):
TGTTTGTGAACATGTTCAATTATA
Found at i:195394 original size:23 final size:23
Alignment explanation
Indices: 195331--195405 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
195321 TGGAGAGTGT
* *
195331 ATTCTGGCACTACAATGCAATTC
1 ATTCTGGCACTTCAGTGCAATTC
* *
195354 ATTTTGGCACTAT-GGTGCAATTC
1 ATTCTGGCACT-TCAGTGCAATTC
*
195377 ATTCTAGCACTTCAGTGC-ATTAC
1 ATTCTGGCACTTCAGTGCAATT-C
195400 ATTCTG
1 ATTCTG
195406 TTGAGTGTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
22 4 0.10
23 37 0.90
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (23 bp):
ATTCTGGCACTTCAGTGCAATTC
Found at i:204946 original size:14 final size:14
Alignment explanation
Indices: 204929--204958 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
204919 AGGGTTTAAA
204929 AATTTTAATTAATT
1 AATTTTAATTAATT
*
204943 AATTTTATTTAATT
1 AATTTTAATTAATT
204957 AA
1 AA
204959 AGATTTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTTTAATTAATT
Found at i:208833 original size:4 final size:4
Alignment explanation
Indices: 208824--208848 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
208814 TACTTAATCC
208824 AACA AACA AACA AACA AACA AACA A
1 AACA AACA AACA AACA AACA AACA A
208849 TTGTTATTGA
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:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:208888 original size:2 final size:2
Alignment explanation
Indices: 208881--208910 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
208871 TCCACCTGTT
*
208881 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
208911 CAGCATTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:214353 original size:69 final size:69
Alignment explanation
Indices: 214267--214404 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
214257 AAGACAATTA
*
214267 AGTCTCCTACAACTTCCTCAGACACTTGATAGGCTCTTCATGTTCAGCCAATACTCTGAGGTGTA
1 AGTCTCCTACAACTTCCTCAGACACTTGATAAGCTCTTCATGTTCAGCCAATACTCTGAGGTGTA
214332 CTCT
66 CTCT
214336 AGTCTCCTACAACTTCCTCAGACACTTGATAAGCTCTTCATGTTCAGCCAATACTCTGAGGTGTA
1 AGTCTCCTACAACTTCCTCAGACACTTGATAAGCTCTTCATGTTCAGCCAATACTCTGAGGTGTA
214401 CTCT
66 CTCT
214405 TCCTTAGGCA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (69 bp):
AGTCTCCTACAACTTCCTCAGACACTTGATAAGCTCTTCATGTTCAGCCAATACTCTGAGGTGTA
CTCT
Found at i:220492 original size:25 final size:26
Alignment explanation
Indices: 220426--220494 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
220416 TATATGTCAC
* *
220426 ATAAATAAATAATTCAAAAGTTATAA
1 ATAAATAAAAAATTCAAAAGTCATAA
* *
220452 A-AAAAAAAAAAATCAAAA-TCA-AA
1 ATAAATAAAAAATTCAAAAGTCATAA
220475 ATAAATAAAAAAGTTCAAAA
1 ATAAATAAAAAA-TTCAAAA
220495 AAATTAGTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 3 0.09
24 11 0.31
25 20 0.57
26 1 0.03
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (26 bp):
ATAAATAAAAAATTCAAAAGTCATAA
Found at i:222605 original size:20 final size:21
Alignment explanation
Indices: 222557--222598 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
222547 CACATTGTGT
222557 AATTTGATCTTTTTTTTTTGC
1 AATTTGATCTTTTTTTTTTGC
*
222578 AATTTTGATTTTTTTTTTTTG
1 AA-TTTGATCTTTTTTTTTTG
222599 ACATTGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.14, C:0.05, G:0.10, T:0.71
Consensus pattern (21 bp):
AATTTGATCTTTTTTTTTTGC
Found at i:226397 original size:16 final size:17
Alignment explanation
Indices: 226365--226401 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
226355 GTTTAAAAGT
226365 TTTAATTAATTAAATTTA
1 TTTAATTAA-TAAATTTA
226383 TTTAATTAA-AAATTTA
1 TTTAATTAATAAATTTA
226399 TTT
1 TTT
226402 TCATCCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTAATAAATTTA
Found at i:226839 original size:16 final size:16
Alignment explanation
Indices: 226818--226860 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 16
226808 ATATAAAATT
226818 ATTAAATTATTTTAAA
1 ATTAAATTATTTTAAA
226834 ATTAAA-T-TTTTAAA
1 ATTAAATTATTTTAAA
226848 ATATAAAATTATT
1 AT-T-AAATTATT
226861 AAAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 9 0.39
15 2 0.09
16 9 0.39
17 1 0.04
18 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAATTATTTTAAA
Found at i:226849 original size:25 final size:25
Alignment explanation
Indices: 226786--226847 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
226776 CAAATGATTT
* *
226786 TAAAATTATTAATTTTTTTTAAATA
1 TAAAATTATTAAATTATTTTAAATA
226811 TAAAATTATTAAATTATTTTAAA-A
1 TAAAATTATTAAATTATTTTAAATA
* *
226835 TTAAATTTTTAAA
1 TAAAATTATTAAA
226848 ATATAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 12 0.36
25 21 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TAAAATTATTAAATTATTTTAAATA
Found at i:226852 original size:40 final size:43
Alignment explanation
Indices: 226777--226871 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 43
226767 CCACATTAGC
* *
226777 AAATGATTTTAAAATTATTAATTTTTTTTAAATATAAAATTATT-
1 AAATTATTTTAAAATTA-TAA-TTTTTTAAAATATAAAATTATTA
226821 AAATTATTTTAAAATTA-AA-TTTTTAAAATATAAAATTATTA
1 AAATTATTTTAAAATTATAATTTTTTAAAATATAAAATTATTA
226862 AAATTATTTT
1 AAATTATTTT
226872 TATATTTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
40 20 0.42
41 10 0.21
42 2 0.04
44 16 0.33
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (43 bp):
AAATTATTTTAAAATTATAATTTTTTAAAATATAAAATTATTA
Found at i:226862 original size:16 final size:14
Alignment explanation
Indices: 226818--226867 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 14
226808 ATATAAAATT
226818 ATTAAATTATTTTAAA
1 ATTAAATTA--TTAAA
*
226834 ATTAAATTTTTAAA
1 ATTAAATTATTAAA
226848 ATATAAAATTATTAAA
1 AT-T-AAATTATTAAA
226864 ATTA
1 ATTA
226868 TTTTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 8 0.27
15 2 0.07
16 20 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTAAATTATTAAA
Done.