Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, 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: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 3 of 14
Found at i:941941 original size:55 final size:56
Alignment explanation
Indices: 941875--942147 Score: 218
Period size: 55 Copynumber: 4.8 Consensus size: 56
941865 AAATATTAAA
*
941875 AATTTATAATTAAAATTTTAATTTAA-TTTTAAAATTTAATATATTAATTTTTTAT
1 AATTTATAATTAAAATTTTAATTTAAGTTTTAAAATTTAAAATATTAATTTTTTAT
* * * *
941930 TATTTATAATTAAAATTTTAATATAATTTTTAGTTGAATTTTTAAAATTAAAATGTTAATTTTTT
1 AATTTATAATTAAAATTTTAATTTAAGTTTTA----AA-ATTTAAAA-T---A--TTAATTTTTT
941995 AT
55 AT
* * * * *
941997 AATTTATAAGTAGAATTTTAATTTAATTTTTAAAA-TTAAAATGTTAATATTTTAT
1 AATTTATAATTAAAATTTTAATTTAAGTTTTAAAATTTAAAATATTAATTTTTTAT
* * **
942052 AATTTATAACTAGAAA-TTTAATTTAA-TTTTTAAATTTAAAATATTAA-TTTACAT
1 AATTTATAATTA-AAATTTTAATTTAAGTTTTAAAATTTAAAATATTAATTTTTTAT
* * * *
942106 TATTTAT-ATTCATATTTTAATTTAAGGTTTT-AAATTCAAAAT
1 AATTTATAATTAAAATTTTAATTTAA-GTTTTAAAATTTAAAAT
942148 GTTTTTATAA
Statistics
Matches: 178, Mismatches: 23, Indels: 35
0.75 0.10 0.15
Matches are distributed among these distances:
52 2 0.01
53 12 0.07
54 27 0.15
55 71 0.40
56 7 0.04
60 3 0.02
61 12 0.07
62 1 0.01
63 2 0.01
65 1 0.01
67 40 0.22
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (56 bp):
AATTTATAATTAAAATTTTAATTTAAGTTTTAAAATTTAAAATATTAATTTTTTAT
Found at i:941961 original size:67 final size:66
Alignment explanation
Indices: 941873--942029 Score: 188
Period size: 67 Copynumber: 2.3 Consensus size: 66
941863 TAAAATATTA
* * * * * *
941873 AAAATTTATAATTAAAATTTTAATTTAATTTTAAAATTTAATATATTAATTTTTTATTATTTATA
1 AAAATTT-TAATT-AATTTTTAATTGAATTTTTAAAATTAAAATATTAATTTTTTATAATTTATA
*
941938 ATT
64 AGT
* *
941941 AAAATTTTAATATAATTTTTAGTTGAATTTTTAAAATTAAAATGTTAATTTTTTATAATTTATAA
1 AAAATTTTAAT-TAATTTTTAATTGAATTTTTAAAATTAAAATATTAATTTTTTATAATTTATAA
942006 GT
65 GT
*
942008 AGAATTTTAATTTAATTTTTAA
1 AAAATTTTAA-TTAATTTTTAA
942030 AATTAAAATG
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
67 67 0.88
68 9 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (66 bp):
AAAATTTTAATTAATTTTTAATTGAATTTTTAAAATTAAAATATTAATTTTTTATAATTTATAAG
T
Found at i:942013 original size:23 final size:23
Alignment explanation
Indices: 941920--942015 Score: 65
Period size: 23 Copynumber: 4.3 Consensus size: 23
941910 TTAATATATT
* * *
941920 AATTTTTTATTATTTATAATTAA
1 AATTTTTTATAATTTATAAGTAG
* * *
941943 AATTTTAATATAATTT-TTAGTTG
1 AATTTT-TTATAATTTATAAGTAG
* * *
941966 AA-TTTTTA-AAATTAAAATGT-T
1 AATTTTTTATAATTTATAA-GTAG
941987 AATTTTTTATAATTTATAAGTAG
1 AATTTTTTATAATTTATAAGTAG
942010 AATTTT
1 AATTTT
942016 AATTTAATTT
Statistics
Matches: 53, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
20 4 0.08
21 5 0.09
22 13 0.25
23 24 0.45
24 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
AATTTTTTATAATTTATAAGTAG
Found at i:942028 original size:26 final size:26
Alignment explanation
Indices: 941999--942083 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
941989 TTTTTTATAA
*
941999 TTTATAAGTAGAATTTTAATTTAATT
1 TTTATAACTAGAATTTTAATTTAATT
* * * * * *
942025 TTTAAAATTAAAATGTTAATATTTTATAA
1 TTTATAACTAGAAT-TTTA-ATTTAAT-T
*
942054 TTTATAACTAGAAATTTAATTTAATT
1 TTTATAACTAGAATTTTAATTTAATT
942080 TTTA
1 TTTA
942084 AATTTAAAAT
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
26 15 0.35
27 9 0.21
28 9 0.21
29 10 0.23
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (26 bp):
TTTATAACTAGAATTTTAATTTAATT
Found at i:942175 original size:21 final size:21
Alignment explanation
Indices: 942151--942196 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
942141 TCAAAATGTT
942151 TTTATAA-TTTTTATTTCAAAA
1 TTTATAATTTTTTATTT-AAAA
*
942172 TTTA-AATTTTTTATTTTAAA
1 TTTATAATTTTTTATTTAAAA
942192 TTTAT
1 TTTAT
942197 TTTATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATAATTTTTTATTTAAAA
Found at i:942189 original size:14 final size:16
Alignment explanation
Indices: 942172--942204 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
942162 TATTTCAAAA
942172 TTTAAA-TT-TTTTAT
1 TTTAAATTTATTTTAT
942186 TTTAAATTTATTTTAT
1 TTTAAATTTATTTTAT
942202 TTT
1 TTT
942205 TTTTCTTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 2 0.12
16 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTAAATTTATTTTAT
Found at i:942920 original size:16 final size:16
Alignment explanation
Indices: 942899--942933 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
942889 CAATAACTTT
*
942899 AAAATAAAAAAAATAA
1 AAAATAAAAAAAACAA
942915 AAAATAAAAAAAACAA
1 AAAATAAAAAAAACAA
942931 AAA
1 AAA
942934 TACCCTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.89, C:0.03, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAATAAAAAAAACAA
Found at i:943034 original size:22 final size:23
Alignment explanation
Indices: 942999--943097 Score: 66
Period size: 22 Copynumber: 4.5 Consensus size: 23
942989 TTTATAATTT
942999 AATTAAAATATTAATAATTTATA
1 AATTAAAATATTAATAATTTATA
*
943022 AATT-AAATGTTAAT-ATTT-T-
1 AATTAAAATATTAATAATTTATA
* * * *
943041 ATTTATAAT-TTAATAATTAACA
1 AATTAAAATATTAATAATTTATA
** *
943063 TGTTAAAATATTAAT-ATTTATTT
1 AATTAAAATATTAATAATTTA-TA
*
943086 AATTTAAATATT
1 AATTAAAATATT
943098 TTTATGATTA
Statistics
Matches: 56, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
19 8 0.14
20 7 0.12
21 4 0.07
22 19 0.34
23 18 0.32
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (23 bp):
AATTAAAATATTAATAATTTATA
Found at i:943118 original size:152 final size:152
Alignment explanation
Indices: 942953--943320 Score: 505
Period size: 152 Copynumber: 2.4 Consensus size: 152
942943 TTGTATATAC
* *
942953 GATT-ATTTATTTTATTTTATTTTTAAATACTAATAATTTATAATTTAATTAAAATATTAATAAT
1 GATTAATTTATTTTATTTTATTTTTAAATACTAATAATTGATAATTTATTTAAAATATTAATAAT
** *
943017 TTATAAATTAAATGTTAATATTTTATTTATAATTTAATAATTAACAT-GTTAAAATATTAATA-T
66 TTATAAATTAAAAATTAATATTTTATTTATAATTTAATAATTAACATAG-TAAAATATTAAAATT
*
943080 TTATTTAATTTAAATATTTTTAT
130 TTATTTAATTTAAATATTATTAT
* *
943103 GATTAATTTATTTTTATTTTATTTTTAAATATTAAAAATTGATAATTTATTTTAAAAT-TTAATA
1 GATTAATTTA-TTTTATTTTATTTTTAAATACTAATAATTGATAATTTA-TTTAAAATATTAATA
* * * * * *
943167 ATTGATCATTTAAAAATTAATATTTTATTTATAATTTAATCATTAATATAGTATAATATTAAAAT
64 ATTTATAAATTAAAAATTAATATTTTATTTATAATTTAATAATTAACATAGTAAAATATTAAAAT
943232 TTTATTTAATTTAAATATTATTAT
129 TTTATTTAATTTAAATATTATTAT
** * *
943256 GACCAA-TTATTTTATTTTATTTTTAAATAGTAATAATTGATAATTTATTTATAATATTAA-AAT
1 GATTAATTTATTTTATTTTATTTTTAAATACTAATAATTGATAATTTATTTAAAATATTAATAAT
943319 TT
66 TT
943321 TATCATTTAA
Statistics
Matches: 192, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
150 15 0.08
151 45 0.23
152 97 0.51
153 35 0.18
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (152 bp):
GATTAATTTATTTTATTTTATTTTTAAATACTAATAATTGATAATTTATTTAAAATATTAATAAT
TTATAAATTAAAAATTAATATTTTATTTATAATTTAATAATTAACATAGTAAAATATTAAAATTT
TATTTAATTTAAATATTATTAT
Found at i:943164 original size:27 final size:28
Alignment explanation
Indices: 943120--943178 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
943110 TTATTTTTAT
*
943120 TTTATTTTTAAATATTAAAAATTGATAA
1 TTTATTTTAAAATATTAAAAATTGATAA
* *
943148 TTTATTTTAAAAT-TTAATAATTGATCA
1 TTTATTTTAAAATATTAAAAATTGATAA
943175 TTTA
1 TTTA
943179 AAAATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (28 bp):
TTTATTTTAAAATATTAAAAATTGATAA
Found at i:943444 original size:22 final size:22
Alignment explanation
Indices: 943419--943496 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 22
943409 TTTATTTTTT
943419 TATTTTAT-TTGTTAAATATTAA
1 TATTTTATATT-TTAAATATTAA
943441 TATTTTATAATTATTTATAATATTAA
1 TATTTTAT-A-T-TTTA-AATATTAA
*
943467 TAATTTATCA-TTTAAATATTAA
1 TATTTTAT-ATTTTAAATATTAA
943489 TATTTTAT
1 TATTTTAT
943497 TTATAATTNN
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
22 23 0.48
23 4 0.08
25 4 0.08
26 17 0.35
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (22 bp):
TATTTTATATTTTAAATATTAA
Found at i:943468 original size:26 final size:24
Alignment explanation
Indices: 943430--943496 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 24
943420 ATTTTATTTG
*
943430 TTAAATATTAATATTTTATAATTAT
1 TTAAATATTAATATTTTAT-ATCAT
*
943455 TTATAATATTAATA-ATT-TATCAT
1 TTA-AATATTAATATTTTATATCAT
943478 TTAAATATTAATATTTTAT
1 TTAAATATTAATATTTTAT
943497 TTATAATTNN
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 10 0.28
23 9 0.25
24 2 0.06
25 5 0.14
26 10 0.28
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAAATATTAATATTTTATATCAT
Found at i:943471 original size:19 final size:19
Alignment explanation
Indices: 943447--943503 Score: 53
Period size: 22 Copynumber: 2.8 Consensus size: 19
943437 TTAATATTTT
943447 ATAATTATTTATAATATTA
1 ATAATTATTTATAATATTA
943466 ATAATTTATCATT-TAAATATTA
1 ATAA-TTAT--TTAT-AATATTA
*
943488 ATATTTTATTTATAAT
1 ATA-ATTATTTATAAT
943504 TNNNNNNNNN
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
19 4 0.13
20 9 0.29
21 2 0.06
22 16 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
ATAATTATTTATAATATTA
Found at i:943498 original size:26 final size:26
Alignment explanation
Indices: 943430--943500 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
943420 ATTTTATTTG
* *
943430 TTAAATATTAATATTTTA-TAATTAT
1 TTAAATATTAATATTTTATTTATCAT
943455 TTATAATATTAATA----ATTTATCAT
1 TTA-AATATTAATATTTTATTTATCAT
943478 TTAAATATTAATATTTTATTTAT
1 TTAAATATTAATATTTTATTTAT
943501 AATTNNNNNN
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
22 11 0.29
23 8 0.21
25 3 0.08
26 16 0.42
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
TTAAATATTAATATTTTATTTATCAT
Found at i:943721 original size:19 final size:19
Alignment explanation
Indices: 943694--943749 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
943684 TAGATCATTT
943694 AAATATTAATATTTTATTA
1 AAATATTAATATTTTATTA
943713 ATAAT-TTAATCATTTTA-TA
1 A-AATATTAAT-ATTTTATTA
*
943732 AAATACTAATATTTTATT
1 AAATATTAATATTTTATT
943750 TCTAGTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 9 0.28
19 14 0.44
20 9 0.28
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATATTAATATTTTATTA
Found at i:947222 original size:67 final size:68
Alignment explanation
Indices: 947097--947237 Score: 196
Period size: 67 Copynumber: 2.1 Consensus size: 68
947087 TGGTAGTGAA
* * * *
947097 TTTTAATTTAATTTTAAAATTTAATATATTAATTTTTTTATTATTTATAATTAAAATTTTAATAT
1 TTTTAATTGAATTTTAAAATTTAAAATATTAATTTTTTTATAATTTATAACTAAAATTTTAATAT
947162 AAT
66 AAT
* * *
947165 TTTTAATTGAATTTTTAAAA-TTAAAATGTTAA-TTTTTTATAATTTATAACTAGAATTTTAATT
1 TTTTAATTGAA-TTTTAAAATTTAAAATATTAATTTTTTTATAATTTATAACTAAAATTTTAATA
947228 TAAT
65 TAAT
947232 TTTTAA
1 TTTTAA
947238 AATTAAAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
67 37 0.57
68 20 0.31
69 8 0.12
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (68 bp):
TTTTAATTGAATTTTAAAATTTAAAATATTAATTTTTTTATAATTTATAACTAAAATTTTAATAT
AAT
Found at i:947225 original size:29 final size:29
Alignment explanation
Indices: 947178--947283 Score: 92
Period size: 29 Copynumber: 3.8 Consensus size: 29
947168 TAATTGAATT
* * *
947178 TTTAAAATTAAAATGTTAATTTTTTATAA
1 TTTAAAACTAGAATTTTAATTTTTTATAA
* * *
947207 TTTATAACTAGAATTTTAA--TTTAAT-T
1 TTTAAAACTAGAATTTTAATTTTTTATAA
* * ** *
947233 TTTAAAATTAAAAAGTTAATATTTTATAA
1 TTTAAAACTAGAATTTTAATTTTTTATAA
947262 TTTAAAACTAGAATTTTAATTT
1 TTTAAAACTAGAATTTTAATTT
947284 AATTTTTAAA
Statistics
Matches: 56, Mismatches: 18, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
26 14 0.25
27 5 0.09
28 5 0.09
29 32 0.57
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (29 bp):
TTTAAAACTAGAATTTTAATTTTTTATAA
Found at i:947241 original size:55 final size:55
Alignment explanation
Indices: 947165--947358 Score: 250
Period size: 55 Copynumber: 3.5 Consensus size: 55
947155 TTAATATAAT
*
947165 TTTTAATTGAATTTTTAAAATTAAAATGTTAATTTTTTATAATTTATAACTAGAA
1 TTTTAATTTAATTTTTAAAATTAAAATGTTAATTTTTTATAATTTATAACTAGAA
* * *
947220 TTTTAATTTAATTTTTAAAATTAAAAAGTTAATATTTTATAATTTAAAACTAGAA
1 TTTTAATTTAATTTTTAAAATTAAAATGTTAATTTTTTATAATTTATAACTAGAA
* * * * * * *
947275 TTTTAATTTAATTTTTAAATTTAAAATATTAA-TTTTCATTACTTAT-ATTAAAA
1 TTTTAATTTAATTTTTAAAATTAAAATGTTAATTTTTTATAATTTATAACTAGAA
947328 TTTTAATTTAAGTTTTT-AAATTCAAAATGTT
1 TTTTAATTTAA-TTTTTAAAATT-AAAATGTT
947359 TTTATAATTT
Statistics
Matches: 121, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
53 20 0.17
54 21 0.17
55 80 0.66
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (55 bp):
TTTTAATTTAATTTTTAAAATTAAAATGTTAATTTTTTATAATTTATAACTAGAA
Found at i:947266 original size:23 final size:21
Alignment explanation
Indices: 947227--947268 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
947217 GAATTTTAAT
947227 TTAATTTTTAAAATTAAAAAG
1 TTAATTTTTAAAATTAAAAAG
* *
947248 TTAATATTTTATAATTTAAAA
1 TTAAT-TTTTAAAATTAAAAA
947269 CTAGAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAATTTTTAAAATTAAAAAG
Found at i:948162 original size:34 final size:37
Alignment explanation
Indices: 948124--948201 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 37
948114 TATATATTAA
*
948124 TATTTAATTTA-ATTTAAATATT-ATTA-TGATCAAT
1 TATTTAATTTATATTTAAATATTAATAATTGATCAAT
* * *
948158 TATTTTATTTTATTTTTAAATATTAATAATTGATCATT
1 TA-TTTAATTTATATTTAAATATTAATAATTGATCAAT
948196 TATTTA
1 TATTTA
948202 TAATATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 2 0.06
35 8 0.22
36 10 0.28
37 7 0.19
38 9 0.25
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (37 bp):
TATTTAATTTATATTTAAATATTAATAATTGATCAAT
Found at i:948209 original size:27 final size:28
Alignment explanation
Indices: 948166--948224 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
948156 ATTATTTTAT
*
948166 TTTATTTTTAAATATTAATAATTGATCA
1 TTTATTTATAAATATTAATAATTGATCA
*
948194 TTTATTTAT-AATATTAATAATTTATCA
1 TTTATTTATAAATATTAATAATTGATCA
948221 TTTA
1 TTTA
948225 AATATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTATTTATAAATATTAATAATTGATCA
Found at i:948239 original size:22 final size:23
Alignment explanation
Indices: 948197--948247 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
948187 TTGATCATTT
948197 ATTTATAATATTAATAATTTATC
1 ATTTATAATATTAATAATTTATC
948220 ATTTA-AATATTAAT-ATTT-T-
1 ATTTATAATATTAATAATTTATC
948239 ATTTATAAT
1 ATTTATAAT
948248 TAAATGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
21 4 0.15
22 9 0.33
23 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTATAATATTAATAATTTATC
Found at i:948243 original size:109 final size:108
Alignment explanation
Indices: 948112--948360 Score: 281
Period size: 109 Copynumber: 2.3 Consensus size: 108
948102 AATTATTTAT
* *
948112 TTTATATATTAATATTTAATTTAATTTAAATATTATTATGATCAATTA-TTTTATTTTATTT-TT
1 TTTAAATATTAATATTTTATTTAATTTAAATATTATTATGATCAATTATTTTTATTTTATTTATT
* * * ** *
948175 AAATATTAATAAT-TG-ATCATTTATTTATAATATTAATAATTTATCA
66 --AT-TT-A-AATGTGAATAATTTATTTAAAACATTAATAATAGATAA
* * * *
948221 TTTAAATATTAATATTTTATTTATAATTAAATGTTATTATGATTATTTATTTTTATTTTATTTAT
1 TTTAAATATTAATATTTTATTTA-ATTTAAATATTATTATGATCAATTATTTTTATTTTATTTAT
*
948286 TGTTTAAATGTGAATAATTTATTTAAAACATTAATAATAGATAA
65 TATTTAAATGTGAATAATTTATTTAAAACATTAATAATAGATAA
948330 TTTAAATATTAATATTTTATTAATAATTTAA
1 TTTAAATATTAATATTTTATT--TAATTTAA
948361 TCATTTTATA
Statistics
Matches: 119, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
107 3 0.03
108 3 0.03
109 69 0.58
110 27 0.23
111 15 0.13
112 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (108 bp):
TTTAAATATTAATATTTTATTTAATTTAAATATTATTATGATCAATTATTTTTATTTTATTTATT
ATTTAAATGTGAATAATTTATTTAAAACATTAATAATAGATAA
Found at i:948360 original size:19 final size:19
Alignment explanation
Indices: 948338--948398 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
948328 AATTTAAATA
948338 TTAATATTTTATTAATAAT
1 TTAATATTTTATTAATAAT
948357 TTAATCATTTTA-TAA-AAT
1 TTAAT-ATTTTATTAATAAT
* *
948375 GCTAATATTTTATTTATAAT
1 -TTAATATTTTATTAATAAT
948395 TTAA
1 TTAA
948399 ATGTTAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 9 0.26
19 17 0.49
20 9 0.26
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (19 bp):
TTAATATTTTATTAATAAT
Found at i:948472 original size:27 final size:28
Alignment explanation
Indices: 948417--948484 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
948407 CTGATTATTT
*
948417 ATTTATATTTTATTTTTTAAATAGCAATA
1 ATTTATAATTTA-TTTTTAAATAGCAATA
**
948446 ATTTATAATTTA-TTTTAAATATTAATA
1 ATTTATAATTTATTTTTAAATAGCAATA
* *
948473 AGTAATAATTTA
1 ATTTATAATTTA
948485 AATGTTAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 23 0.68
29 11 0.32
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (28 bp):
ATTTATAATTTATTTTTAAATAGCAATA
Found at i:948481 original size:151 final size:143
Alignment explanation
Indices: 948205--948511 Score: 384
Period size: 151 Copynumber: 2.1 Consensus size: 143
948195 TTATTTATAA
* *
948205 TATTAATAATTT-ATCATTTAAATATTAATATTTTATTTATAATTAAATGTTATTATGATTATTT
1 TATTAATAATTTAATCATTTAAAAATTAATATTTTATTTATAATTAAATGTTAATATGATTATTT
* *** *
948269 ATTTTTATTTTATTTATTGTTTAAATGTGAATAATTTATTTAAAACATTAATAATAGATAATTTA
66 ATTTATATTTTATTTATTAAATAAATATGAATAATTTATTTAAAACATTAATAATAGATAATTTA
948334 AATATTAATATTT
131 AATATTAATATTT
*
948347 TATTAATAATTTAATCATTTTATAAAATGCTAATATTTTATTTATAATTTAAATGTTAATCTGAT
1 TATTAATAATTTAATCA-TTTA-AAAAT--TAATATTTTATTTATAA-TTAAATGTTAATATGAT
* ** * *
948412 TATTTATTTATATTTTATTTTTTAAATAGCAATAATTTATAATTTATTTTAAATATTAATAAGTA
61 TATTTATTTATATTTTATTTATTAAATA--AAT-ATGAATAATTTATTTAAAACATTAATAA-TA
*
948477 -ATAATTTAAATGTTAATATTT
122 GATAATTTAAATATTAATATTT
*
948498 TATTTATAATTTAA
1 TATTAATAATTTAA
948512 ATATTATTAC
Statistics
Matches: 140, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
142 12 0.09
143 4 0.03
144 4 0.03
145 4 0.03
147 17 0.12
148 38 0.27
150 3 0.02
151 56 0.40
152 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (143 bp):
TATTAATAATTTAATCATTTAAAAATTAATATTTTATTTATAATTAAATGTTAATATGATTATTT
ATTTATATTTTATTTATTAAATAAATATGAATAATTTATTTAAAACATTAATAATAGATAATTTA
AATATTAATATTT
Found at i:948601 original size:22 final size:21
Alignment explanation
Indices: 948549--948623 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 21
948539 TTATTTTTTC
* *
948549 CAAAGATTTATAATTTAT-TGA
1 CAAATATTAATAATTTATGT-A
*
948570 -AAATAATAATAATTTA-GTA
1 CAAATATTAATAATTTATGTA
* *
948589 CTTAAATATTAATATTTTATTTA
1 C--AAATATTAATAATTTATGTA
948612 CAAATATTAATA
1 CAAATATTAATA
948624 TAAGTATGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 1 0.02
20 14 0.33
21 11 0.26
22 14 0.33
23 3 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (21 bp):
CAAATATTAATAATTTATGTA
Found at i:948601 original size:108 final size:109
Alignment explanation
Indices: 948377--948611 Score: 262
Period size: 113 Copynumber: 2.1 Consensus size: 109
948367 TATAAAATGC
* *
948377 TAATATTTTATTTATAATTTAAATGTTAATCTGATTATTTATTTATATTTTATTTTTTAAATAGC
1 TAATATTTTATTTATAATTTAAATATTAATCTGATTATTTATTTATATATTATTTTTTAAATAG-
** * * *
948442 AATAATTTATAATTTATTTTAAATATTAATAAGTAATAATTTAAATGT
65 ---AATTTATAATTTATTGAAAATAATAATAAGTAATAACTTAAATAT
* * * *
948490 TAATATTTTATTTATAATTTAAATATTATTACT-ATTGTTTATTTTTATATTATTTTTTCCAA-A
1 TAATATTTTATTTATAATTTAAATATTAAT-CTGATTATTTATTTATATATTATTTTTT-AAATA
* *
948553 G-ATTTATAATTTATTGAAAATAATAATAATTTAGT-ACTTAAATAT
64 GAATTTATAATTTATTGAAAATAATAATAA-GTAATAACTTAAATAT
948598 TAATATTTTATTTA
1 TAATATTTTATTTA
948612 CAAATATTAA
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
108 47 0.44
109 3 0.03
113 52 0.49
114 4 0.04
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (109 bp):
TAATATTTTATTTATAATTTAAATATTAATCTGATTATTTATTTATATATTATTTTTTAAATAGA
ATTTATAATTTATTGAAAATAATAATAAGTAATAACTTAAATAT
Found at i:957696 original size:38 final size:39
Alignment explanation
Indices: 957642--957721 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 39
957632 TATTTCAATT
957642 ATAAAGAAGTTAAGAATAAATAAATATCAAATAATTGTG
1 ATAAAGAAGTTAAGAATAAATAAATATCAAATAATTGTG
*
957681 ATAAAGAA-TTAAGAATAAATAAATATCACATAATTGTG
1 ATAAAGAAGTTAAGAATAAATAAATATCAAATAATTGTG
957719 ATA
1 ATA
957722 TCAAATAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 32 0.80
39 8 0.20
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (39 bp):
ATAAAGAAGTTAAGAATAAATAAATATCAAATAATTGTG
Found at i:958164 original size:18 final size:18
Alignment explanation
Indices: 958124--958163 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
958114 GACACTAAAA
958124 ATTTTAATTTATCAAATT
1 ATTTTAATTTATCAAATT
*
958142 ATTTTCATTTAT-AAATT
1 ATTTTAATTTATCAAATT
*
958159 CTTTT
1 ATTTT
958164 TATAAACATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTAATTTATCAAATT
Found at i:958534 original size:29 final size:27
Alignment explanation
Indices: 958501--958568 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
958491 ATTTTAAAAA
* *
958501 ATTTAAATAAATTTTTACTTTTTTGTTAT
1 ATTTAAATAAATTCTTA-TATTTT-TTAT
*
958530 ATTTAATTAAATTCTTATATTTTTTAT
1 ATTTAAATAAATTCTTATATTTTTTAT
958557 -TTTAAATCAAAT
1 ATTTAAAT-AAAT
958569 AAACTCTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 6 0.18
27 8 0.24
28 5 0.15
29 15 0.44
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (27 bp):
ATTTAAATAAATTCTTATATTTTTTAT
Found at i:959869 original size:7 final size:8
Alignment explanation
Indices: 959851--959880 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
959841 CAACAGTCAC
959851 AAAAATTA
1 AAAAATTA
959859 AAAAATTAA
1 AAAAATT-A
959868 AAAAATTA
1 AAAAATTA
959876 AAAAA
1 AAAAA
959881 ACAAAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAAATTA
Found at i:959870 original size:9 final size:9
Alignment explanation
Indices: 959851--959881 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
959841 CAACAGTCAC
959851 AAAAATT-A
1 AAAAATTAA
959859 AAAAATTAA
1 AAAAATTAA
959868 AAAAATTAA
1 AAAAATTAA
959877 AAAAA
1 AAAAA
959882 CAAAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAATTAA
Found at i:959886 original size:17 final size:17
Alignment explanation
Indices: 959851--959904 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
959841 CAACAGTCAC
**
959851 AAAAATTAAAAAATTAA
1 AAAAATTAAAAAAACAA
959868 AAAAATTAAAAAAACAA
1 AAAAATTAAAAAAACAA
**
959885 AAAAACAAAACAAAACAA
1 AAAAATTAAA-AAAACAA
959903 AA
1 AA
959905 CATTTCGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAATTAAAAAAACAA
Found at i:982249 original size:13 final size:13
Alignment explanation
Indices: 982185--982242 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 13
982175 TTATTTATTA
982185 ATAAAAATTAAAT
1 ATAAAAATTAAAT
* *
982198 ATAAACATCCACAAATT
1 ATAAAAAT---TAAA-T
982215 ATATAAAATTAAAT
1 ATA-AAAATTAAAT
982229 ATAAAAATTAAAT
1 ATAAAAATTAAAT
982242 A
1 A
982243 ATCAAATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
13 18 0.50
14 4 0.11
15 3 0.08
16 3 0.08
17 4 0.11
18 4 0.11
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAAAAATTAAAT
Found at i:988386 original size:27 final size:27
Alignment explanation
Indices: 988350--988406 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
988340 AGTTCGAATC
988350 TCTGAGGCATTTTCCTTTCCGATCCAA
1 TCTGAGGCATTTTCCTTTCCGATCCAA
988377 TCTGAGGCATTTTCCTTTCCGATCCAA
1 TCTGAGGCATTTTCCTTTCCGATCCAA
988404 TCT
1 TCT
988407 CTCTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.39
Consensus pattern (27 bp):
TCTGAGGCATTTTCCTTTCCGATCCAA
Found at i:988415 original size:27 final size:27
Alignment explanation
Indices: 988358--988416 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
988348 TCTCTGAGGC
* * *
988358 ATTTTCCTTTCCGATCCAATCTGAGGC
1 ATTTTCCTTTCCGATCCAATCTCACGA
* *
988385 ATTTTCCTTTCCGATCCAATCTCTCTA
1 ATTTTCCTTTCCGATCCAATCTCACGA
988412 ATTTT
1 ATTTT
988417 AATTATACCG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.29, G:0.08, T:0.44
Consensus pattern (27 bp):
ATTTTCCTTTCCGATCCAATCTCACGA
Found at i:992514 original size:19 final size:19
Alignment explanation
Indices: 992490--992547 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
992480 TTCTAGTCTT
992490 TTTTTAAACAGAAAATGGA
1 TTTTTAAACAGAAAATGGA
*** *
992509 TTTTTATTGA-AAAAT-AA
1 TTTTTAAACAGAAAATGGA
992526 TATTTTAAACAGAAAATGGA
1 T-TTTTAAACAGAAAATGGA
992546 TT
1 TT
992548 GTATTGAGAA
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 2 0.07
18 11 0.39
19 13 0.46
20 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (19 bp):
TTTTTAAACAGAAAATGGA
Found at i:992532 original size:37 final size:37
Alignment explanation
Indices: 992491--992564 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
992481 TCTAGTCTTT
*
992491 TTTTAAACAGAAAATGGATTTTTATTGA-AAAATAATA
1 TTTTAAACAGAAAATGGA-TTGTATTGAGAAAATAATA
992528 TTTTAAACAGAAAATGGATTGTATTGAGAAAATAATA
1 TTTTAAACAGAAAATGGATTGTATTGAGAAAATAATA
992565 AAGTCAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 8 0.23
37 27 0.77
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.35
Consensus pattern (37 bp):
TTTTAAACAGAAAATGGATTGTATTGAGAAAATAATA
Found at i:997568 original size:16 final size:17
Alignment explanation
Indices: 997547--997579 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
997537 ATATTTATTT
997547 AATTTAA-AAATATAAA
1 AATTTAATAAATATAAA
997563 AATTTAATTAAATATAA
1 AATTTAA-TAAATATAA
997580 TAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTTAATAAATATAAA
Found at i:997573 original size:20 final size:22
Alignment explanation
Indices: 997543--997586 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
997533 AAAAATATTT
997543 ATTTAATTTAAAAAT-ATAAAA
1 ATTTAATTTAAAAATAATAAAA
*
997564 ATTTAA-TTAAATATAATAAAA
1 ATTTAATTTAAAAATAATAAAA
997585 AT
1 AT
997587 AAAGATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTTAATTTAAAAATAATAAAA
Found at i:1001129 original size:34 final size:34
Alignment explanation
Indices: 1001091--1001201 Score: 107
Period size: 34 Copynumber: 3.1 Consensus size: 34
1001081 CTTTGGGTGA
1001091 AACATCTGGTGCTAAAACTTTAGCCTTGGCATGT
1 AACATCTGGTGCTAAAACTTTAGCCTTGGCATGT
* * * *
1001125 AACATCTGGTACTAAAGCCTTAACCTTGGCATGGCATGT
1 AACATCTGGTGCTAAAACTTTAGCC-T----TGGCATGT
* *
1001164 AACATCTGATGCTAGAACTTT-GACCTTGGCATGT
1 AACATCTGGTGCTAAAACTTTAG-CCTTGGCATGT
1001198 AACA
1 AACA
1001202 ACTACTATTG
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
34 33 0.54
35 1 0.02
38 1 0.02
39 26 0.43
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (34 bp):
AACATCTGGTGCTAAAACTTTAGCCTTGGCATGT
Found at i:1001190 original size:39 final size:39
Alignment explanation
Indices: 1001117--1001196 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
1001107 ACTTTAGCCT
*
1001117 TGGCATGTAACATCTGGTACTAAAGCCTTAACCTTGGCA
1 TGGCATGTAACATCTGATACTAAAGCCTTAACCTTGGCA
* * *
1001156 TGGCATGTAACATCTGATGCTAGAA-CTTTGACCTTGGCA
1 TGGCATGTAACATCTGATACTA-AAGCCTTAACCTTGGCA
1001195 TG
1 TG
1001197 TAACAACTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
39 34 0.94
40 2 0.06
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (39 bp):
TGGCATGTAACATCTGATACTAAAGCCTTAACCTTGGCA
Found at i:1012940 original size:29 final size:29
Alignment explanation
Indices: 1012899--1012962 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1012889 ATAATAATTT
*
1012899 TTTTTTAAATATAGTGTGTAACAATAATA
1 TTTTTTAAATATAATGTGTAACAATAATA
* * *
1012928 TTTTTTCAATATAATGTGTAACAATGATT
1 TTTTTTAAATATAATGTGTAACAATAATA
1012957 TTTTTT
1 TTTTTT
1012963 TCAACGTGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (29 bp):
TTTTTTAAATATAATGTGTAACAATAATA
Found at i:1013030 original size:43 final size:42
Alignment explanation
Indices: 1012948--1013030 Score: 121
Period size: 43 Copynumber: 2.0 Consensus size: 42
1012938 ATAATGTGTA
* * **
1012948 ACAATGATTTTTTTTTCAACGTGGCATATAACATGTTTTTGT
1 ACAATAATTTTTTTTTCAACATGGCATATAACAACTTTTTGT
1012990 ACAATAATATTTTTTTTCAACATGGCATATAACAACTTTTT
1 ACAATAAT-TTTTTTTTCAACATGGCATATAACAACTTTTT
1013031 TTAATCATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 7 0.19
43 29 0.81
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (42 bp):
ACAATAATTTTTTTTTCAACATGGCATATAACAACTTTTTGT
Found at i:1013055 original size:24 final size:24
Alignment explanation
Indices: 1013028--1013073 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1013018 ATAACAACTT
1013028 TTTTTA-ATCATGATATATAACATA
1 TTTTTATA-CATGATATATAACATA
* *
1013052 TTTTTGTACATGATATGTAACA
1 TTTTTATACATGATATATAACA
1013074 ATAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (24 bp):
TTTTTATACATGATATATAACATA
Found at i:1013055 original size:26 final size:25
Alignment explanation
Indices: 1013000--1013103 Score: 88
Period size: 26 Copynumber: 4.0 Consensus size: 25
1012990 ACAATAATAT
**
1013000 TTTTTTTCAACATGGCATATAACA-A
1 TTTTTTT-AACATGATATATAACATA
1013025 CTTTTTTTAATCATGATATATAACATA
1 -TTTTTTTAA-CATGATATATAACATA
* *
1013052 TTTTTGT-ACATGATATGTAACAATAA
1 TTTTTTTAACATGATATATAAC-AT-A
*
1013078 TATTTTTTAACATGA-ATGTAACATA
1 T-TTTTTTAACATGATATATAACATA
1013103 T
1 T
1013104 GTGCACTTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
24 12 0.18
25 7 0.10
26 29 0.43
27 13 0.19
28 6 0.09
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.44
Consensus pattern (25 bp):
TTTTTTTAACATGATATATAACATA
Found at i:1013193 original size:15 final size:16
Alignment explanation
Indices: 1013173--1013222 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 16
1013163 GTTAAAATGA
1013173 TAAAAAGA-GTTATTT
1 TAAAAAGATGTTATTT
1013188 TAAAAA-ATGTTATTT
1 TAAAAAGATGTTATTT
* * *
1013203 TTAAAAGTTATT-TTT
1 TAAAAAGATGTTATTT
1013218 TAAAA
1 TAAAA
1013223 TGCCTTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.03
15 25 0.86
16 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (16 bp):
TAAAAAGATGTTATTT
Found at i:1014491 original size:16 final size:16
Alignment explanation
Indices: 1014470--1014502 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1014460 TTATTTAATA
1014470 TTTGCTTGGACAGATC
1 TTTGCTTGGACAGATC
*
1014486 TTTGCTTTGACAGATC
1 TTTGCTTGGACAGATC
1014502 T
1 T
1014503 CGTTACTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (16 bp):
TTTGCTTGGACAGATC
Found at i:1016172 original size:74 final size:74
Alignment explanation
Indices: 1016035--1016174 Score: 167
Period size: 74 Copynumber: 1.9 Consensus size: 74
1016025 TTATATAATA
* * *
1016035 TCATCTCTTAAATATAATTTGTAATGTCATATATTTTATTTTCATTTATTATTACAATCTTATAT
1 TCATCTCTTAAATATAATTTGTAATATCATATATTTTATTTTCAATTATTATTACAATATTATAT
1016100 ATTTTATTT
66 ATTTTATTT
* * * * * *
1016109 TCATTTCTTTAATATAATTTTTTATATTATATATTTTATTTT-AATTACTT-TTATCTATATTAT
1 TCATCTCTTAAATATAATTTGTAATATCATATATTTTATTTTCAATTA-TTATTA-CAATATTAT
1016172 ATA
64 ATA
1016175 AATTTTAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 7 0.13
74 48 0.87
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.59
Consensus pattern (74 bp):
TCATCTCTTAAATATAATTTGTAATATCATATATTTTATTTTCAATTATTATTACAATATTATAT
ATTTTATTT
Found at i:1016204 original size:26 final size:26
Alignment explanation
Indices: 1016123--1016237 Score: 92
Period size: 28 Copynumber: 4.2 Consensus size: 26
1016113 TTCTTTAATA
*
1016123 TAATTTTTTATATTATATATTTTATTT
1 TAATTTTTTATATTATAT-TTTAATTT
*
1016150 TAATTACTTTTAT-CTATATTATATAAATTT
1 TAATT--TTTTATATTATATT-T-T-AATTT
1016180 TAATTTTTTATATTATATTTTAATTTT
1 TAATTTTTTATATTATATTTTAA-TTT
* *
1016207 TGA-TTCTTATATCATATATTTT-ATTT
1 TAATTTTTTATAT--TATATTTTAATTT
1016233 TAATT
1 TAATT
1016238 ATAACATTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 20
0.73 0.06 0.20
Matches are distributed among these distances:
26 15 0.21
27 14 0.19
28 21 0.29
29 13 0.18
30 9 0.12
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (26 bp):
TAATTTTTTATATTATATTTTAATTT
Found at i:1016218 original size:50 final size:49
Alignment explanation
Indices: 1016120--1016224 Score: 113
Period size: 50 Copynumber: 2.1 Consensus size: 49
1016110 CATTTCTTTA
* * * * *
1016120 ATATAATTTTTTATATTATATATTTTATTTTAATTACTTTTATCTATATT
1 ATATAAATTTTAATATTATATATTATATTTTAATTA-TTTGATCTATATC
* *
1016170 ATATAAATTTTAATTTTTTATATTATATTTTAATT-TTTGATTCTTATATC
1 ATATAAATTTTAATATTATATATTATATTTTAATTATTTGA-TC-TATATC
1016220 ATATA
1 ATATA
1016225 TTTTATTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 4 0.09
49 2 0.04
50 40 0.87
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (49 bp):
ATATAAATTTTAATATTATATATTATATTTTAATTATTTGATCTATATC
Found at i:1020733 original size:2 final size:2
Alignment explanation
Indices: 1020728--1020755 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1020718 ACATACACAC
1020728 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
1020756 TCTACACATT
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:1021746 original size:16 final size:16
Alignment explanation
Indices: 1021727--1021761 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1021717 ATATATTATT
1021727 TTATAAATTTATCAAA
1 TTATAAATTTATCAAA
* *
1021743 TTATTAATTTATTAAA
1 TTATAAATTTATCAAA
1021759 TTA
1 TTA
1021762 ATCTCAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATAAATTTATCAAA
Found at i:1021798 original size:17 final size:18
Alignment explanation
Indices: 1021778--1021813 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1021768 AATCAAAATC
1021778 AATTAAAAATATT-ATTT
1 AATTAAAAATATTAATTT
*
1021795 AATTAAAAGTATTAATTT
1 AATTAAAAATATTAATTT
1021813 A
1 A
1021814 TCAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AATTAAAAATATTAATTT
Found at i:1058960 original size:42 final size:42
Alignment explanation
Indices: 1058901--1058984 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
1058891 CTATTCTAAA
* *
1058901 TTCTTGTTATCATTTTTTATCCAACACAAAATGATATGTCAT
1 TTCTTGTCATCATTTTTTATCCAACAAAAAATGATATGTCAT
1058943 TTCTTGTCATCATTTTTTATCCAACAAAAAATGATATGTCAT
1 TTCTTGTCATCATTTTTTATCCAACAAAAAATGATATGTCAT
1058985 CAAATTAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (42 bp):
TTCTTGTCATCATTTTTTATCCAACAAAAAATGATATGTCAT
Found at i:1064314 original size:24 final size:24
Alignment explanation
Indices: 1064282--1064359 Score: 120
Period size: 24 Copynumber: 3.2 Consensus size: 24
1064272 GAACCTTGCC
*
1064282 ACTTGTTCTGAGTTACTTTTACTT
1 ACTTGTTCTGAGTTACTTTCACTT
* *
1064306 ACTTTTTCTGAATTACTTTCACTT
1 ACTTGTTCTGAGTTACTTTCACTT
1064330 ACTTGTTCTGAGTTACTTTCACTT
1 ACTTGTTCTGAGTTACTTTCACTT
*
1064354 CCTTGT
1 ACTTGT
1064360 ACAAACAGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.17, C:0.21, G:0.10, T:0.53
Consensus pattern (24 bp):
ACTTGTTCTGAGTTACTTTCACTT
Found at i:1067142 original size:17 final size:17
Alignment explanation
Indices: 1067120--1067169 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
1067110 ATTGTTTATG
1067120 AAGATAATTATA-ATTGA
1 AAGATAATTATATATT-A
1067137 AAGATAATTATATATTA
1 AAGATAATTATATATTA
* *
1067154 AAAATAATTAAATATT
1 AAGATAATTATATATT
1067170 TTATAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 27 0.90
18 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAGATAATTATATATTA
Found at i:1089985 original size:12 final size:12
Alignment explanation
Indices: 1089968--1089993 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1089958 CGGGATCCGT
1089968 AGTCAACTTAGA
1 AGTCAACTTAGA
1089980 AGTCAACTTAGA
1 AGTCAACTTAGA
1089992 AG
1 AG
1089994 CAATCAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (12 bp):
AGTCAACTTAGA
Found at i:1092219 original size:18 final size:20
Alignment explanation
Indices: 1092188--1092224 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1092178 GTCAAGTGAC
1092188 ATTTTTTGATTTATTAATTA
1 ATTTTTTGATTTATTAATTA
1092208 ATTTTTT-A-TTATTAATT
1 ATTTTTTGATTTATTAATT
1092225 TATGTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTTTTTGATTTATTAATTA
Found at i:1092223 original size:14 final size:15
Alignment explanation
Indices: 1092197--1092225 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1092187 CATTTTTTGA
1092197 TTTATTAATTAATTT
1 TTTATTAATTAATTT
1092212 TTTATT-ATTAATTT
1 TTTATTAATTAATTT
1092226 ATGTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTAATTAATTT
Found at i:1092239 original size:5 final size:5
Alignment explanation
Indices: 1092211--1092260 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
1092201 TTAATTAATT
* *
1092211 TTTTA TTATTA ATTTA -TGTA TTTTA TTTTA TATTTA TTTTA TTTTA TTTT
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTT
1092261 TCAGCGATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
4 3 0.08
5 27 0.69
6 9 0.23
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:1092253 original size:21 final size:19
Alignment explanation
Indices: 1092211--1092260 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
1092201 TTAATTAATT
1092211 TTTTATTATTAATTTATGTA
1 TTTTATT-TTAATTTATGTA
*
1092231 TTTTATTTTATATTTATTTTA
1 TTTTATTTTA-ATTTA-TGTA
1092252 TTTTATTTT
1 TTTTATTTT
1092261 TCAGCGATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.11
20 12 0.44
21 12 0.44
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTATTTTAATTTATGTA
Found at i:1094350 original size:21 final size:22
Alignment explanation
Indices: 1094324--1094379 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1094314 GGATAAAATT
*
1094324 ATAAAATTTTAAAA-A-TTAAA
1 ATAAAATTTAAAAATATTTAAA
1094344 AGTAAAA-TTAAAAATATTTAAA
1 A-TAAAATTTAAAAATATTTAAA
*
1094366 ATAAAATTAAAAAA
1 ATAAAATTTAAAAA
1094380 AGTTATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 7 0.23
21 11 0.37
22 12 0.40
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAAAATTTAAAAATATTTAAA
Found at i:1094352 original size:12 final size:11
Alignment explanation
Indices: 1094335--1094377 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
1094325 TAAAATTTTA
1094335 AAAATTAAAAGT
1 AAAATTAAAA-T
1094347 AAAATTAAAA-
1 AAAATTAAAAT
* *
1094357 ATATTTAAAAT
1 AAAATTAAAAT
1094368 AAAATTAAAA
1 AAAATTAAAA
1094378 AAAGTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.31
11 8 0.31
12 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:1094389 original size:22 final size:20
Alignment explanation
Indices: 1094324--1094380 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1094314 GGATAAAATT
**
1094324 ATAAAATTTTAAAAATTAAA
1 ATAAAATTAAAAAAATTAAA
*
1094344 AGTAAAATTAAAAATATTTAAA
1 A-TAAAATTAAAAA-AATTAAA
1094366 ATAAAATTAAAAAAA
1 ATAAAATTAAAAAAA
1094381 GTTATAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.06
21 22 0.71
22 7 0.23
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
ATAAAATTAAAAAAATTAAA
Found at i:1106243 original size:2 final size:2
Alignment explanation
Indices: 1106236--1106266 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1106226 CATGTACGCT
*
1106236 TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1106267 ATAAATCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1109509 original size:22 final size:22
Alignment explanation
Indices: 1109457--1109510 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1109447 CATGCAATTT
* *
1109457 TTTTTATAAAAAGAATTAGTATA
1 TTTTT-TAAAAAGAATTAATAAA
* * *
1109480 CTTATTAAAAATAATTAATAAA
1 TTTTTTAAAAAGAATTAATAAA
1109502 TTTTTTAAA
1 TTTTTTAAA
1109511 TTTTTTATTA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
TTTTTTAAAAAGAATTAATAAA
Found at i:1110254 original size:22 final size:22
Alignment explanation
Indices: 1110216--1110261 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1110206 ACTAAAATGT
1110216 TATTTTTTATTAATTTAAAAAA
1 TATTTTTTATTAATTTAAAAAA
*
1110238 TATTATTTTA-TATTTTAAAAAA
1 TATT-TTTTATTAATTTAAAAAA
1110260 TA
1 TA
1110262 AAAAATGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTTTTATTAATTTAAAAAA
Found at i:1111122 original size:27 final size:27
Alignment explanation
Indices: 1111092--1111204 Score: 96
Period size: 27 Copynumber: 4.3 Consensus size: 27
1111082 ACCTTAAAAG
1111092 AAATTATAATAAAAA-AAAGATATATTA
1 AAATTATAATAAAAATAAA-ATATATTA
1111119 AAATTATAATAAAAATAAAATATA-T-
1 AAATTATAATAAAAATAAAATATATTA
** * *
1111144 -AA-TAT--TAAAAATGTATTATATAA
1 AAATTATAATAAAAATAAAATATATTA
1111167 AAATTAATAATAAAATATAAAAATATATTA
1 AAATT-ATAATAAAA-AT-AAAATATATTA
*
1111197 AATTTATA
1 AAATTATA
1111205 TTTTAATAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
21 12 0.18
23 3 0.04
24 4 0.06
25 1 0.01
26 3 0.04
27 20 0.30
28 8 0.12
29 5 0.07
30 11 0.16
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
AAATTATAATAAAAATAAAATATATTA
Found at i:1111196 original size:35 final size:37
Alignment explanation
Indices: 1111121--1111196 Score: 97
Period size: 35 Copynumber: 2.1 Consensus size: 37
1111111 ATATATTAAA
*
1111121 ATTATAATAAAAATAAAATATATAATATTAAAAATGT
1 ATTATAATAAAAATAAAATATATAATATTAAAAATAT
1111158 ATTAT-ATAAAAATTAATAATA-A-AATA-TAAAAATAT
1 ATTATAATAAAAA-TAA-AATATATAATATTAAAAATAT
1111193 ATTA
1 ATTA
1111197 AATTTATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
35 12 0.33
36 11 0.31
37 9 0.25
38 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (37 bp):
ATTATAATAAAAATAAAATATATAATATTAAAAATAT
Found at i:1124740 original size:2 final size:2
Alignment explanation
Indices: 1124733--1124767 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1124723 CCTACATTGC
* *
1124733 AT AT AT AT GT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1124768 CAATCAACCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1133970 original size:229 final size:231
Alignment explanation
Indices: 1133567--1134020 Score: 651
Period size: 229 Copynumber: 2.0 Consensus size: 231
1133557 TAAGCATTAT
** * *
1133567 TAGTCAATCACAACCATGCTGTAGTGATACTAGTTTCAAACATCAATAATTGAGCTGCGTTTGGC
1 TAGTCAATCACAACCATGCCATAGTGATACTAGTTTCAAACATCAATAATTGAGCTGCGATTGAC
* *
1133632 TGAGATTCAACAACTAAGCTCCAAGAAATTAAATCAAGGAAGAACACAAATGAGGCACTAAGCTG
66 TGAGATTCAACAACTAAGCTCCAAGAAATGAAATCAAGGAAGAACACAAATGAAGCACTAAGCTG
* * * * * **
1133697 GTAAGGAGATTCCTTAAATTTGAAGGAGGTGTTGTGTTGAAGTTATTTTGTTTTATTTGCTAACT
131 GTAAGGAGATTCCTTAAATTTGAAGAAGGTGCTATGTTGAAGTTATTCTGTTTTATTCGCTAAAG
* *
1133762 ATAATGAGCATAACACTACTGTGTGGATTAGTCAAC
196 ATAACGAGCATAACACTACTGTCTGGATTAGTCAAC
* * *
1133798 TAGTCAATCATAACTATGCCATAGTGATACTAGTTTCAAATATCAATAATTGAGCTGC-ATT-AC
1 TAGTCAATCACAACCATGCCATAGTGATACTAGTTTCAAACATCAATAATTGAGCTGCGATTGAC
* * * * * * *
1133861 TGAGATTTAAGAACTTAGCTCCAAGAAATGAAATCAGGGAAGAACAGAGATGAAGCACTGAGCTG
66 TGAGATTCAACAACTAAGCTCCAAGAAATGAAATCAAGGAAGAACACAAATGAAGCACTAAGCTG
1133926 GTAAGGAGATTCCTTAAATTTGAAGAAGGTGCTATGTTGAAGTTATTCTGTTTTATTCGCTAAAG
131 GTAAGGAGATTCCTTAAATTTGAAGAAGGTGCTATGTTGAAGTTATTCTGTTTTATTCGCTAAAG
* *
1133991 ATGACGAGCATAACACTACTTTCTGGATTA
196 ATAACGAGCATAACACTACTGTCTGGATTA
1134021 AGCTGGTCAT
Statistics
Matches: 196, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
229 141 0.72
230 2 0.01
231 53 0.27
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (231 bp):
TAGTCAATCACAACCATGCCATAGTGATACTAGTTTCAAACATCAATAATTGAGCTGCGATTGAC
TGAGATTCAACAACTAAGCTCCAAGAAATGAAATCAAGGAAGAACACAAATGAAGCACTAAGCTG
GTAAGGAGATTCCTTAAATTTGAAGAAGGTGCTATGTTGAAGTTATTCTGTTTTATTCGCTAAAG
ATAACGAGCATAACACTACTGTCTGGATTAGTCAAC
Found at i:1141015 original size:2 final size:2
Alignment explanation
Indices: 1141008--1141039 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1140998 TTCTTCTAGG
1141008 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1141040 GTTATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1141047 original size:2 final size:2
Alignment explanation
Indices: 1141042--1141074 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1141032 TCTCTCTCGT
1141042 TA TA TA 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 TA TA TA T
1141075 TGTGTGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1153826 original size:24 final size:24
Alignment explanation
Indices: 1153801--1153847 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1153791 ACCAATACTA
1153801 TTTAATATAAAATAATAAATAATAT
1 TTTAAT-TAAAATAATAAATAATAT
* *
1153826 TTTAATTAAATTAATAATTAAT
1 TTTAATTAAAATAATAAATAAT
1153848 TATAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAATTAAAATAATAAATAATAT
Found at i:1153900 original size:21 final size:22
Alignment explanation
Indices: 1153875--1153925 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1153865 TATTTATTTG
*
1153875 ATTTAAAATAAA-AATATAAAA
1 ATTTAAAATAAATAAAATAAAA
*
1153896 ATTT-AATTAAATAAAATAAAA
1 ATTTAAAATAAATAAAATAAAA
*
1153917 ATATAAAAT
1 ATTTAAAAT
1153926 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
ATTTAAAATAAATAAAATAAAA
Found at i:1153922 original size:70 final size:68
Alignment explanation
Indices: 1153799--1153942 Score: 159
Period size: 70 Copynumber: 2.1 Consensus size: 68
1153789 ACACCAATAC
* * * * *
1153799 TATTTAATATAAAATAATAAATAATATTTTAATTAAATTAATAATTAATTATAAAAATTTATTTA
1 TATTTAATATAAAATAAAAAATAAAAATTTAATTAAATTAATAATAAAATAT-AAAATTT-TTTA
*
1153864 ATATT
64 AAATT
* *
1153869 TATTTGATTTAAAATAAAAATATAAAAATTTAATTAAA-TAA-AATAAAAATATAAAATTTTTTA
1 TATTTAATATAAAATAAAAA-ATAAAAATTTAATTAAATTAATAAT-AAAATATAAAATTTTTTA
1153932 AAATT
64 AAATT
1153937 T-TTTAA
1 TATTTAA
1153943 AATATTATGC
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
67 4 0.06
68 9 0.14
69 10 0.16
70 25 0.40
71 15 0.24
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (68 bp):
TATTTAATATAAAATAAAAAATAAAAATTTAATTAAATTAATAATAAAATATAAAATTTTTTAAA
ATT
Found at i:1153933 original size:23 final size:25
Alignment explanation
Indices: 1153870--1153935 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 25
1153860 TTTAATATTT
1153870 ATTTGATTTAAAATAAAAATATAAAA
1 ATTT-ATTTAAAATAAAAATATAAAA
1153896 ATTTAATTAAATAAAATAAAAATAT-AAA
1 ATTT-ATT---TAAAATAAAAATATAAAA
1153924 ATTT-TTTAAAAT
1 ATTTATTTAAAAT
1153936 TTTTTAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
23 6 0.17
26 9 0.25
28 7 0.19
29 14 0.39
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTTATTTAAAATAAAAATATAAAA
Found at i:1153935 original size:10 final size:10
Alignment explanation
Indices: 1153920--1153945 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1153910 AATAAAAATA
1153920 TAAAATTTTT
1 TAAAATTTTT
1153930 TAAAATTTTT
1 TAAAATTTTT
1153940 TAAAAT
1 TAAAAT
1153946 ATTATGCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TAAAATTTTT
Found at i:1154724 original size:49 final size:51
Alignment explanation
Indices: 1154671--1154864 Score: 164
Period size: 49 Copynumber: 3.7 Consensus size: 51
1154661 TTTATTATTA
1154671 ATTTTTATATAATATCAT-ATCTTAAATATA-TTTTAATATCATATATTTT
1 ATTTTTATATAATATCATAATCTTAAATATATTTTTAATATCATATATTTT
* * * * * *
1154720 ATTTTTATTTATTATTATAATCTTTTATATTTTATTTTTATTATATTTATATTTTATTATT
1 ATTTTTATATAATATCATAATC--TTA-AATATATTTTTA--ATA-TCATA---TATT-TT
*
1154781 AATTTTTATATAATATCAT-ATCTTAAATATATTTTTAATGTCATATATTTT
1 -ATTTTTATATAATATCATAATCTTAAATATATTTTTAATATCATATATTTT
* * *
1154832 ATTTTTATTTATTATTATAATCTT--ATATATTTT
1 ATTTTTATATAATATCATAATCTTAAATATATTTT
1154865 ATTTTTATTT
Statistics
Matches: 115, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
49 24 0.21
50 18 0.16
51 7 0.06
52 7 0.06
53 4 0.03
54 5 0.04
55 4 0.03
56 5 0.04
57 4 0.03
58 10 0.09
59 3 0.03
60 4 0.03
61 5 0.04
62 15 0.13
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.62
Consensus pattern (51 bp):
ATTTTTATATAATATCATAATCTTAAATATATTTTTAATATCATATATTTT
Found at i:1154727 original size:6 final size:6
Alignment explanation
Indices: 1154716--1154789 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
1154706 ATATCATATA
* * *
1154716 TTTTAT TTTTAT TTATTAT TATAAT CTTTTAT ATTTTAT TTTTA- TTATAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT -TTTTAT -TTTTAT TTTTAT TTTTAT
* *
1154766 TTATA- TTTTAT TATTAAT TTTTAT
1 TTTTAT TTTTAT T-TTTAT TTTTAT
1154790 ATAATATCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.15
6 26 0.48
7 20 0.37
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTAT
Found at i:1154746 original size:16 final size:15
Alignment explanation
Indices: 1154714--1154789 Score: 56
Period size: 16 Copynumber: 5.2 Consensus size: 15
1154704 TAATATCATA
*
1154714 TATT-TTATTTTTATT
1 TATTATTATTATT-TT
*
1154729 TATTATTATAATCTTT
1 TATTATTATTAT-TTT
1154745 TA-TATT-TTATTTT
1 TATTATTATTATTTT
1154758 TATTA-TATTTATATTT
1 TATTATTA-TTAT-TTT
1154774 TATTATTA--ATTTT
1 TATTATTATTATTTT
1154787 TAT
1 TAT
1154790 ATAATATCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
13 12 0.24
14 7 0.14
15 12 0.24
16 17 0.33
17 3 0.06
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTATTATTATTTT
Found at i:1154780 original size:111 final size:113
Alignment explanation
Indices: 1154643--1154873 Score: 412
Period size: 112 Copynumber: 2.1 Consensus size: 113
1154633 AAAATATAAG
*
1154643 TTTAATATATTTATACTTTTTATTATTAATTTTTATATAATATCATATCTTAAATATA-TTTTAA
1 TTTATTATATTTATAC-TTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAA
*
1154707 TATCATATATTTTATTTTTATTTATTATTATAATCTTTTATATTTTATT
65 TATCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
1154756 TTTATTATATTTATA-TTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAAT
1 TTTATTATATTTATACTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAAT
*
1154820 GTCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
66 ATCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
1154868 TTTATT
1 TTTATT
1154874 TTTTAATATA
Statistics
Matches: 114, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
111 41 0.36
112 59 0.52
113 14 0.12
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (113 bp):
TTTATTATATTTATACTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAAT
ATCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
Found at i:1154792 original size:22 final size:21
Alignment explanation
Indices: 1154721--1154792 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
1154711 ATATATTTTA
1154721 TTTTTAT-TTATTATTA-TAAT
1 TTTTTATATT-TTATTATTAAT
* *
1154741 CTTTTATATTTTATT-TTTAT
1 TTTTTATATTTTATTATTAAT
1154761 TATATTTATATTTTATTATTAAT
1 T-T-TTTATATTTTATTATTAAT
1154784 TTTTATATA
1 TTTT-TATA
1154793 ATATCATATC
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 14 0.33
21 5 0.12
22 18 0.43
23 5 0.12
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTATATTTTATTATTAAT
Found at i:1154860 original size:33 final size:32
Alignment explanation
Indices: 1154823--1154907 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
1154813 TTTTAATGTC
*
1154823 ATATATTTTATTTTTATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTTATTAATAT-ATCTT
* *
1154856 ATATATTTTATTTTTATTTTTTAATATATTTT
1 ATATATTTTATTTTTATTTATTAATATATCTT
* *
1154888 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
1154908 TAATTTATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 13 0.28
33 33 0.72
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (32 bp):
ATATATTTTATTTTTATTTATTAATATATCTT
Found at i:1154885 original size:12 final size:14
Alignment explanation
Indices: 1154854--1154958 Score: 60
Period size: 14 Copynumber: 7.6 Consensus size: 14
1154844 TATTATAATC
*
1154854 TTATATATTTTAT-
1 TTATATTTTTTATA
*
1154867 TTTTATTTTTTA-A
1 TTATATTTTTTATA
1154880 -TATATTTTTTATA
1 TTATATTTTTTATA
* *
1154893 TTATATATTTTATT
1 TTATATTTTTTATA
1154907 TTA-ATTTATTT-TA
1 TTATATTT-TTTATA
* * *
1154920 CTTATATTATATAAA
1 -TTATATTTTTTATA
*
1154935 TTTTAATTTTTTATA
1 TTAT-ATTTTTTATA
1154950 GTT-TATTTT
1 -TTATATTTT
1154959 ATTTTAATTC
Statistics
Matches: 69, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
12 10 0.14
13 15 0.22
14 30 0.43
15 12 0.17
16 2 0.03
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.69
Consensus pattern (14 bp):
TTATATTTTTTATA
Found at i:1154914 original size:24 final size:23
Alignment explanation
Indices: 1154887--1155008 Score: 57
Period size: 26 Copynumber: 4.6 Consensus size: 23
1154877 TAATATATTT
1154887 TTTATATTATATATTTTATTTTAA
1 TTTAT-TTATATATTTTATTTTAA
1154911 TTTATTTTACTTATATTATATAAATTTTAA
1 TTTA-TTTA--TATATT-T-T--ATTTTAA
1154941 TTT-TTTATAGTTTATTTTATTTTAA
1 TTTATTTATA---TATTTTATTTTAA
* *
1154966 TTCTTGATTTTTATATTATATATTTTAT
1 -T-TT-ATTTATATATT-T-TATTTTAA
*
1154994 TTTAATTATAATATT
1 TTTATTTAT-ATATT
1155009 ATAAAATTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 32
0.68 0.04 0.28
Matches are distributed among these distances:
24 7 0.09
25 12 0.16
26 20 0.26
27 6 0.08
28 13 0.17
29 9 0.12
30 10 0.13
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTATTTATATATTTTATTTTAA
Found at i:1154925 original size:33 final size:32
Alignment explanation
Indices: 1154824--1154932 Score: 98
Period size: 33 Copynumber: 3.3 Consensus size: 32
1154814 TTTAATGTCA
* * * *
1154824 TATATTTTAT-TTTTATTTATTATTATAATCTTA
1 TATATTATATATTTTATTT-TTAATAT-ATTTTT
*
1154857 TATATTTTAT-TTTTATTTTTTAATATATTTTT
1 TATATTATATATTTTA-TTTTTAATATATTTTT
*
1154889 TATATTATATATTTTA-TTTTAATTTATTTTACT
1 TATATTATATATTTTATTTTTAATATATTTT--T
1154922 TATATTATATA
1 TATATTATATA
1154933 AATTTTAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
31 13 0.19
32 13 0.19
33 38 0.57
34 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (32 bp):
TATATTATATATTTTATTTTTAATATATTTTT
Found at i:1155724 original size:20 final size:20
Alignment explanation
Indices: 1155701--1155739 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1155691 AACAGAATAA
1155701 GAAAGCAAGAAAGAGAAATG
1 GAAAGCAAGAAAGAGAAATG
*
1155721 GAAAGCAATAAAGAGAAAT
1 GAAAGCAAGAAAGAGAAAT
1155740 TAGTGGACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.26, T:0.08
Consensus pattern (20 bp):
GAAAGCAAGAAAGAGAAATG
Found at i:1164648 original size:22 final size:22
Alignment explanation
Indices: 1164605--1164648 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1164595 TTTATGTGGA
* *
1164605 AAAACACCTTTTTCTTTCTCTT
1 AAAACACCATTTTCTTTATCTT
1164627 AAAACACCAATTTT-TTTATCTT
1 AAAACACC-ATTTTCTTTATCTT
1164649 TTAAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAACACCATTTTCTTTATCTT
Found at i:1179255 original size:21 final size:21
Alignment explanation
Indices: 1179231--1179272 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1179221 ACAGTTGCCT
1179231 TAGTCTCAGCACGCACTTCAC
1 TAGTCTCAGCACGCACTTCAC
1179252 TAGTCTCAGCACGCACTTCAC
1 TAGTCTCAGCACGCACTTCAC
1179273 ACATGCCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.38, G:0.14, T:0.24
Consensus pattern (21 bp):
TAGTCTCAGCACGCACTTCAC
Found at i:1181746 original size:2 final size:2
Alignment explanation
Indices: 1181739--1181764 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1181729 CTGAAGACTG
1181739 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
1181765 TTATATCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1190479 original size:15 final size:15
Alignment explanation
Indices: 1190459--1190488 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1190449 GTTAGCAATT
*
1190459 TTCTCTTCTTGTTTC
1 TTCTCTTCTGGTTTC
1190474 TTCTCTTCTGGTTTC
1 TTCTCTTCTGGTTTC
1190489 CTCACAACAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.27, G:0.10, T:0.63
Consensus pattern (15 bp):
TTCTCTTCTGGTTTC
Found at i:1195022 original size:15 final size:13
Alignment explanation
Indices: 1194992--1195034 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1194982 ATAGCAATGA
1194992 AAATAAAAAAAAT
1 AAATAAAAAAAAT
*
1195005 AAATAATAAAAAGGT
1 AAATAA-AAAAA-AT
*
1195020 AAATAGAAAAAAT
1 AAATAAAAAAAAT
1195033 AA
1 AA
1195035 TAACCAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 9 0.36
14 10 0.40
15 6 0.24
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (13 bp):
AAATAAAAAAAAT
Found at i:1195898 original size:17 final size:20
Alignment explanation
Indices: 1195860--1195895 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
1195850 TATAATAATC
1195860 AATATTTTTATTTAAAAAAT
1 AATATTTTTATTTAAAAAAT
1195880 AATA-TTTTA-TTAAAAA
1 AATATTTTTATTTAAAAA
1195896 TAACGCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 5 0.31
20 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATATTTTTATTTAAAAAAT
Found at i:1197636 original size:20 final size:20
Alignment explanation
Indices: 1197611--1197697 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
1197601 ATGATTATAA
1197611 ATTTTAATTAATCAAAATTT
1 ATTTTAATTAATCAAAATTT
*
1197631 ATTTTATTTAA--AAGAA-TT
1 ATTTTAATTAATCAA-AATTT
* ** **
1197649 ATTTT--TTAATGATTATAA
1 ATTTTAATTAATCAAAATTT
1197667 ATTTTAATTAATCAAAATTT
1 ATTTTAATTAATCAAAATTT
*
1197687 ATTTTATTTAA
1 ATTTTAATTAA
1197698 CTTATGATTA
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
16 4 0.08
17 1 0.02
18 15 0.30
19 2 0.04
20 28 0.56
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTAATTAATCAAAATTT
Found at i:1197642 original size:56 final size:56
Alignment explanation
Indices: 1197575--1197697 Score: 210
Period size: 56 Copynumber: 2.2 Consensus size: 56
1197565 TTCATTAAAA
* * *
1197575 ATTTTACTTAAAAGATTTGTTTTTAAATGATTATAAATTTTAATTAATCAAAATTT
1 ATTTTATTTAAAAGAATTATTTTTAAATGATTATAAATTTTAATTAATCAAAATTT
*
1197631 ATTTTATTTAAAAGAATTATTTTTTAATGATTATAAATTTTAATTAATCAAAATTT
1 ATTTTATTTAAAAGAATTATTTTTAAATGATTATAAATTTTAATTAATCAAAATTT
1197687 ATTTTATTTAA
1 ATTTTATTTAA
1197698 CTTATGATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (56 bp):
ATTTTATTTAAAAGAATTATTTTTAAATGATTATAAATTTTAATTAATCAAAATTT
Found at i:1198142 original size:23 final size:23
Alignment explanation
Indices: 1198095--1198144 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1198085 AAATCTCAAT
*
1198095 AAAAATAAATAAAAATGTACATA
1 AAAAATAAATAAAAATGTAAATA
*
1198118 AAAAATAAA-ATAAAATG-AAATT
1 AAAAATAAATA-AAAATGTAAATA
1198140 AAAAA
1 AAAAA
1198145 GAAAAAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAAATAAATAAAAATGTAAATA
Found at i:1199084 original size:27 final size:27
Alignment explanation
Indices: 1199073--1199221 Score: 97
Period size: 27 Copynumber: 5.9 Consensus size: 27
1199063 TTATTTTTAA
1199073 TATTAATAATTTATAATTTAATTAAAG
1 TATTAATAATTTATAATTTAATTAAAG
1199100 TATTAATAATTTATAA--T--TTAAA-
1 TATTAATAATTTATAATTTAATTAAAG
* * * *
1199122 TATTAAT-ATTT-TAGTATAATTTAAT
1 TATTAATAATTTATAATTTAATTAAAG
* ***
1199147 TATTAATATTTTA-AATATTAA-TATTT
1 TATTAATAATTTATAAT-TTAATTAAAG
* *
1199173 TATTTATAATTTAATAATATT-ATTAAAA
1 TATTAATAATTT-ATAAT-TTAATTAAAG
1199201 TATTAATAA-TTATAA-TTAATT
1 TATTAATAATTTATAATTTAATT
1199222 TCCAAATTTA
Statistics
Matches: 96, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
20 2 0.02
21 4 0.04
22 8 0.08
23 5 0.05
24 6 0.06
25 11 0.11
26 21 0.22
27 23 0.24
28 16 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (27 bp):
TATTAATAATTTATAATTTAATTAAAG
Found at i:1199120 original size:15 final size:15
Alignment explanation
Indices: 1199065--1199217 Score: 52
Period size: 15 Copynumber: 9.7 Consensus size: 15
1199055 TTTTTATTTT
*
1199065 ATTTTTAATATTAATA
1 ATTTATAAT-TTAATA
1199081 ATTTATAATTTAATTAA
1 ATTTATAATTTAA-T-A
1199098 AGTATTAATAATTT-ATA
1 A-T-TT-ATAATTTAATA
1199115 ATTTA-AATATTAATA
1 ATTTATAAT-TTAATA
* *
1199130 TTTTAGTATAATTTAATT
1 -ATT--TATAATTTAATA
* *
1199148 ATTAATATTTTAA-A
1 ATTTATAATTTAATA
*
1199162 TATTAAT-ATTT--T-
1 -ATTTATAATTTAATA
1199174 ATTTATAATTTAATA
1 ATTTATAATTTAATA
1199189 ATATTATTAAAATATTAATA
1 AT-TTA-T--AAT-TTAATA
1199209 A-TTATAATT
1 ATTTATAATT
1199218 AATTTCCAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 46
0.66 0.06 0.29
Matches are distributed among these distances:
11 5 0.05
12 4 0.04
13 3 0.03
14 8 0.08
15 28 0.26
16 15 0.14
17 8 0.08
18 12 0.11
19 9 0.08
20 14 0.13
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATTTATAATTTAATA
Found at i:1199436 original size:22 final size:23
Alignment explanation
Indices: 1199408--1199455 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1199398 TTTTAAAAAT
1199408 TTAAAATA-TA-ATAATTTTATTA
1 TTAAAATATTATATAATTTT-TTA
1199430 TTAAAATATTATTATAATTTTTTA
1 TTAAAATATTA-TATAATTTTTTA
1199454 TT
1 TT
1199456 TTTCTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
23 2 0.09
24 5 0.22
25 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAAAATATTATATAATTTTTTA
Found at i:1199550 original size:16 final size:15
Alignment explanation
Indices: 1199529--1199558 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1199519 CAATAAATAA
1199529 AATATTAATATTTTAG
1 AATATTAAT-TTTTAG
1199545 AATATTAATTTTTA
1 AATATTAATTTTTA
1199559 ATATTTTAAT
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:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
AATATTAATTTTTAG
Found at i:1199563 original size:13 final size:15
Alignment explanation
Indices: 1199528--1199626 Score: 64
Period size: 15 Copynumber: 6.5 Consensus size: 15
1199518 GCAATAAATA
1199528 AAATATTAATATTTT
1 AAATATTAATATTTT
1199543 AGAATATTAAT-TTTT
1 A-AATATTAATATTTT
* *
1199558 AATATTTTAATCATATT
1 AA-ATATTAAT-ATTTT
1199575 -AATATTAATAATATTT
1 AAATATTAAT-AT-TTT
* *
1199591 -AA-ATT-ATATATA
1 AAATATTAATATTTT
*
1199603 AAATATTAATATTCT
1 AAATATTAATATTTT
1199618 AAACTATTA
1 AAA-TATTA
1199627 TTTTTATAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
12 1 0.02
13 4 0.06
14 6 0.09
15 32 0.49
16 19 0.29
17 3 0.05
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.48
Consensus pattern (15 bp):
AAATATTAATATTTT
Found at i:1199590 original size:26 final size:25
Alignment explanation
Indices: 1199534--1199613 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 25
1199524 AATAAAATAT
*
1199534 TAATATTTTAGA-ATATTAAT-TT-T
1 TAATATTTTA-ATATATTAATATTAA
1199557 TAATATTTTAATCATATTAATATTAA
1 TAATATTTTAAT-ATATTAATATTAA
*
1199583 TAATATTTAAATTATATATAAAATATTAA
1 TAATATTTTAA-TATAT-T--AATATTAA
1199612 TA
1 TA
1199614 TTCTAAACTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
22 1 0.02
23 10 0.21
24 8 0.17
25 2 0.04
26 14 0.30
27 2 0.04
29 10 0.21
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (25 bp):
TAATATTTTAATATATTAATATTAA
Found at i:1199614 original size:26 final size:26
Alignment explanation
Indices: 1199556--1199620 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
1199546 ATATTAATTT
* *
1199556 TTAATATTTTAATCATATTAATATTA
1 TTAATATTTAAATCATATTAATAATA
* *
1199582 ATAATATTTAAATTATATATAA-AATA
1 TTAATATTTAAATCATAT-TAATAATA
1199608 TTAATATTCTAAA
1 TTAATATT-TAAA
1199621 CTATTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 25 0.78
27 7 0.22
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATATTTAAATCATATTAATAATA
Found at i:1208461 original size:23 final size:24
Alignment explanation
Indices: 1208435--1208479 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1208425 AAACACATTG
**
1208435 AAAATCTT-AAATCATTGAAAACT
1 AAAATCTTCAAAGAATTGAAAACT
1208458 AAAATCTTCAAAGAATTGAAAA
1 AAAATCTTCAAAGAATTGAAAA
1208480 TTTCAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (24 bp):
AAAATCTTCAAAGAATTGAAAACT
Found at i:1237307 original size:40 final size:42
Alignment explanation
Indices: 1237226--1237309 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 42
1237216 CCATTTTTAT
* * *
1237226 TTTTTTTTTAAAAAATTAATTTTTATAATTCTACTTGATAAA
1 TTTTTTATTAAAAAATTAATTTTTATAATTCTAATTCATAAA
1237268 TTTTTTATTAATAAAATT-A-TTTTATAATT-TAATTCATAAA
1 TTTTTTATTAA-AAAATTAATTTTTATAATTCTAATTCATAAA
1237308 TT
1 TT
1237310 GAATAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 11 0.29
41 10 0.26
42 11 0.29
43 6 0.16
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (42 bp):
TTTTTTATTAAAAAATTAATTTTTATAATTCTAATTCATAAA
Found at i:1248179 original size:51 final size:51
Alignment explanation
Indices: 1248119--1248218 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
1248109 CTATCTTAAG
*
1248119 GGAGAAAGAAGTGAACTCCTCTGAATCTATTAATCAATGCACCTTCTATAT
1 GGAGAAAGAAGTGAACTCCTCTGAATCCATTAATCAATGCACCTTCTATAT
*
1248170 GGAGAAAGAAGTGAACTCCTCTGAATCCATTAATCAGTGCACCTTCTAT
1 GGAGAAAGAAGTGAACTCCTCTGAATCCATTAATCAATGCACCTTCTAT
1248219 CTTCTTGTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (51 bp):
GGAGAAAGAAGTGAACTCCTCTGAATCCATTAATCAATGCACCTTCTATAT
Found at i:1255691 original size:14 final size:13
Alignment explanation
Indices: 1255654--1255693 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1255644 ATATATTATA
*
1255654 TTTTTAAATAAAT
1 TTTTTAAATAATT
*
1255667 TTTTAAAATAATT
1 TTTTTAAATAATT
1255680 TTTGTTAAATAATT
1 TTT-TTAAATAATT
1255694 AATATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
TTTTTAAATAATT
Found at i:1261480 original size:15 final size:14
Alignment explanation
Indices: 1261438--1261480 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
1261428 ATATCGTCTC
*
1261438 ATTTAATAAAT-AA
1 ATTTAAAAAATAAA
1261451 ATTTAAAAAATTAAA
1 ATTTAAAAAA-TAAA
1261466 ATTTTAAAAAATAAA
1 A-TTTAAAAAATAAA
1261481 TACTCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 9 0.35
14 1 0.04
15 7 0.27
16 9 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATTTAAAAAATAAA
Found at i:1267442 original size:21 final size:21
Alignment explanation
Indices: 1267395--1267444 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1267385 AACTTGGTTT
1267395 AATATTTAAAAGAATTTCTAA
1 AATATTTAAAAGAATTTCTAA
*
1267416 ATTATTTAAAA-AATTT-TAAGA
1 AATATTTAAAAGAATTTCT-A-A
1267437 AATATTTA
1 AATATTTA
1267445 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.04
20 6 0.24
21 18 0.72
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (21 bp):
AATATTTAAAAGAATTTCTAA
Found at i:1269908 original size:56 final size:56
Alignment explanation
Indices: 1269822--1269944 Score: 237
Period size: 56 Copynumber: 2.2 Consensus size: 56
1269812 GTAGGAATGG
1269822 GGGGTGAAGGTTCAACATATAGAAGGAAAAAGTCTATCTCTTTGGGTGGCCAGGGA
1 GGGGTGAAGGTTCAACATATAGAAGGAAAAAGTCTATCTCTTTGGGTGGCCAGGGA
*
1269878 GGGGTGAAGGTTCAACATATAGAAGGAAAAAGTCTATCTCTTTGGGTGGCCGGGGA
1 GGGGTGAAGGTTCAACATATAGAAGGAAAAAGTCTATCTCTTTGGGTGGCCAGGGA
1269934 GGGGTGAAGGT
1 GGGGTGAAGGT
1269945 GTAAATAGCC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 66 1.00
ACGTcount: A:0.28, C:0.11, G:0.37, T:0.23
Consensus pattern (56 bp):
GGGGTGAAGGTTCAACATATAGAAGGAAAAAGTCTATCTCTTTGGGTGGCCAGGGA
Found at i:1276206 original size:2 final size:2
Alignment explanation
Indices: 1276194--1276224 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1276184 TAATTGCAAC
*
1276194 TA TA TA CA 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
1276225 TCTCCAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1277153 original size:53 final size:53
Alignment explanation
Indices: 1277075--1277182 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 53
1277065 AAATATGAAG
* *
1277075 AAAAAGTACTTCAAAATCAGTTGATTAAAATGTTAACGAACA-ACCACATTTAA
1 AAAAAGTACTTAAAAATCAGTTGATTAAAATGTTAACGAA-AGACAACATTTAA
*
1277128 AAAAAGTACTTAAAAATCAGTTGATTAAAATGTTAATGAAAGACAACATTTAA
1 AAAAAGTACTTAAAAATCAGTTGATTAAAATGTTAACGAAAGACAACATTTAA
1277181 AA
1 AA
1277183 GTAAAAAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
52 1 0.02
53 50 0.98
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (53 bp):
AAAAAGTACTTAAAAATCAGTTGATTAAAATGTTAACGAAAGACAACATTTAA
Found at i:1282234 original size:31 final size:33
Alignment explanation
Indices: 1282174--1282241 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 33
1282164 TGATTATGTT
*
1282174 AATATGTCACATTATCATTCATTATGATATAAC
1 AATATGTCACATTATCATTCATTATGATATAAA
*
1282207 AATATGTCACGTTA--ATATCA-TATGATATAAA
1 AATATGTCACATTATCAT-TCATTATGATATAAA
1282238 AATA
1 AATA
1282242 ACAAGTGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 16 0.50
32 3 0.09
33 13 0.41
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (33 bp):
AATATGTCACATTATCATTCATTATGATATAAA
Found at i:1282912 original size:31 final size:30
Alignment explanation
Indices: 1282877--1282939 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1282867 ATTCATTAAT
1282877 TATAAAAACT-TATTTAACTTAAAAATAAAAA
1 TATAAAAA-TGTATTTAA-TTAAAAATAAAAA
* * *
1282908 TATAAGAATGTATTTGATTTAAAATAAAAA
1 TATAAAAATGTATTTAATTAAAAATAAAAA
1282938 TA
1 TA
1282940 CAAGGCTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (30 bp):
TATAAAAATGTATTTAATTAAAAATAAAAA
Found at i:1283829 original size:22 final size:22
Alignment explanation
Indices: 1283804--1283846 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1283794 TTATGTATGT
1283804 TATTT-ATATTAAATTTTTTTAA
1 TATTTGATATT-AATTTTTTTAA
*
1283826 TATTTGATATTATTTTTTTTA
1 TATTTGATATTAATTTTTTTA
1283847 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTTGATATTAATTTTTTTAA
Found at i:1283837 original size:23 final size:21
Alignment explanation
Indices: 1283804--1283861 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1283794 TTATGTATGT
1283804 TATTTATATTAAATTTTTTTAA
1 TATTTATATT-AATTTTTTTAA
*
1283826 TATTTGATATT-ATTTTTTTTA
1 TATTT-ATATTAATTTTTTTAA
*
1283847 TAATT-T-TTAATTTTT
1 TATTTATATTAATTTTT
1283862 AATTTGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 2 0.06
19 7 0.22
21 13 0.41
22 5 0.16
23 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTTATATTAATTTTTTTAA
Found at i:1285098 original size:22 final size:22
Alignment explanation
Indices: 1285066--1285108 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1285056 ATAAAAATCA
* *
1285066 TATTAATATTTTATTAATAAAG
1 TATTAACATTTTAATAATAAAG
1285088 TATTAACATTTTAATAATAAA
1 TATTAACATTTTAATAATAAA
1285109 TTACTAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTAACATTTTAATAATAAAG
Done.