Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000914.1 Hibiscus syriacus cultivar Beakdansim tig00001825_pilon, 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: 1342319
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 5 of 6
Found at i:940955 original size:21 final size:21
Alignment explanation
Indices: 940929--940972 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
940919 TTTTTTATAG
940929 AATAGGGAGACCTCATTAAAA
1 AATAGGGAGACCTCATTAAAA
940950 AATAGGGAGACCTCATTAAAA
1 AATAGGGAGACCTCATTAAAA
940971 AA
1 AA
940973 CCCCTTCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (21 bp):
AATAGGGAGACCTCATTAAAA
Found at i:941063 original size:21 final size:21
Alignment explanation
Indices: 941039--941083 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
941029 AGTGTCTCAT
941039 AAATAGGGAGACCTCATTAAA
1 AAATAGGGAGACCTCATTAAA
941060 AAATAGGGAGACCTCATTAAA
1 AAATAGGGAGACCTCATTAAA
941081 AAA
1 AAA
941084 CCCCTTCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (21 bp):
AAATAGGGAGACCTCATTAAA
Found at i:941063 original size:111 final size:111
Alignment explanation
Indices: 940929--941151 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
940919 TTTTTTATAG
940929 AATAGGGAGACCTCATTAAAAAATAGGGAGACCTCATTAAAAAACCCCTTCGTACTCAACGAAAT
1 AATAGGGAGACCTCATTAAAAAATAGGGAGACCTCATTAAAAAACCCCTTCGTACTCAACGAAAT
940994 ATGAAAGTTTCGTCGAGCATTGGAAGGAGGAAATGAGTGTCTCATA
66 ATGAAAGTTTCGTCGAGCATTGGAAGGAGGAAATGAGTGTCTCATA
941040 AATAGGGAGACCTCATTAAAAAATAGGGAGACCTCATTAAAAAACCCCTTCGTACTCAACGAAAT
1 AATAGGGAGACCTCATTAAAAAATAGGGAGACCTCATTAAAAAACCCCTTCGTACTCAACGAAAT
941105 ATGAAAGTTTCGTCGAGCATTGGAAGGAGGAAATGAGTGTCTCATA
66 ATGAAAGTTTCGTCGAGCATTGGAAGGAGGAAATGAGTGTCTCATA
941151 A
1 A
941152 TATTAAACCA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (111 bp):
AATAGGGAGACCTCATTAAAAAATAGGGAGACCTCATTAAAAAACCCCTTCGTACTCAACGAAAT
ATGAAAGTTTCGTCGAGCATTGGAAGGAGGAAATGAGTGTCTCATA
Found at i:943602 original size:15 final size:15
Alignment explanation
Indices: 943582--943612 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
943572 CCTTGATAAG
943582 CAAAGAGTAGTCAAC
1 CAAAGAGTAGTCAAC
943597 CAAAGAGTAGTCAAC
1 CAAAGAGTAGTCAAC
943612 C
1 C
943613 GAATCATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (15 bp):
CAAAGAGTAGTCAAC
Found at i:944871 original size:19 final size:20
Alignment explanation
Indices: 944839--944884 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
944829 ACTCGACCCG
944839 AAATAATATATTTATT-AAT
1 AAATAATATATTTATTCAAT
* *
944858 AAATATTATTTTTATTCAAT
1 AAATAATATATTTATTCAAT
944878 AAA-AATA
1 AAATAATA
944885 GGGATTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATAATATATTTATTCAAT
Found at i:950260 original size:11 final size:11
Alignment explanation
Indices: 950244--950275 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
950234 TCTTTTAACG
950244 AAATTATTAAA
1 AAATTATTAAA
950255 AAATTATTAAA
1 AAATTATTAAA
*
950266 AAAATATTAA
1 AAATTATTAA
950276 TGGGTTGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATTATTAAA
Found at i:956528 original size:95 final size:96
Alignment explanation
Indices: 956361--956554 Score: 336
Period size: 95 Copynumber: 2.0 Consensus size: 96
956351 TGACAGGTAA
*
956361 GATGGTTTGAGGAAACATATAGTACATGTAAGTTACTTATTTGTAAAATTTCACCAGGAATATGA
1 GATGGTTTGAGGAAACATATAGTACATGTAAG-T--TTATTTGTAAAATTTCACCAGAAATATGA
956426 CAGATGAGAGTGGCTTTAGACAAATTAAGATACT
63 CAGATGAGAGTGGCTTTAGACAAATTAAGATACT
*
956460 GATGGTTTGAGGAAACATATAGTACATGTAAG-TTATTTGTAAAATTTCACCAGAAATATGACCG
1 GATGGTTTGAGGAAACATATAGTACATGTAAGTTTATTTGTAAAATTTCACCAGAAATATGACAG
956524 ATGAGAGTGGCTTTAGACAAATTAAGATACT
66 ATGAGAGTGGCTTTAGACAAATTAAGATACT
956555 CTAAATCCAT
Statistics
Matches: 93, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
95 61 0.66
99 32 0.34
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (96 bp):
GATGGTTTGAGGAAACATATAGTACATGTAAGTTTATTTGTAAAATTTCACCAGAAATATGACAG
ATGAGAGTGGCTTTAGACAAATTAAGATACT
Found at i:960484 original size:20 final size:20
Alignment explanation
Indices: 960459--960498 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
960449 TTTGGTTCAC
960459 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
960479 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
960499 AATAAGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:960506 original size:16 final size:18
Alignment explanation
Indices: 960459--960509 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
960449 TTTGGTTCAC
960459 GGAATGTAAGATTACCAGT
1 GGAA-GTAAGATTACCAGT
960478 GGGAATGTAAGATTACCAGT
1 -GGAA-GTAAGATTACCAGT
960498 -GAA-TAAGATTAC
1 GGAAGTAAGATTAC
960510 TGGGAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.29
18 3 0.10
20 19 0.61
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGT
Found at i:962768 original size:46 final size:45
Alignment explanation
Indices: 962683--962772 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 45
962673 TAAAATATTA
* *
962683 ATTAATAATTTAATATTTTTTTATTATTTATTAAAAAATTAATAG
1 ATTAATAATTTAATATTTTTCTATTATCTATTAAAAAATTAATAG
**
962728 ATTAATAATTT-ATCATATTTTCTATTATCTATTAGTAAATTAATA
1 ATTAATAATTTAAT-AT-TTTTCTATTATCTATTAAAAAATTAATA
962773 TTTTTTAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
44 2 0.05
45 13 0.33
46 24 0.62
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (45 bp):
ATTAATAATTTAATATTTTTCTATTATCTATTAAAAAATTAATAG
Found at i:971974 original size:37 final size:36
Alignment explanation
Indices: 971899--971974 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
971889 TTTTTATATT
*
971899 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
971935 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
971972 TTT
1 TTT
971975 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:972136 original size:18 final size:18
Alignment explanation
Indices: 972113--972158 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
972103 CCCAGTAATC
*
972113 TTATTCCCTGGTAGTCTT
1 TTATTCCCTGGTAATCTT
972131 TTATTCTCACTGGTAATCTT
1 TTATTC-C-CTGGTAATCTT
972151 TTATTCCC
1 TTATTCCC
972159 ACTGATAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
19 2 0.08
20 16 0.64
ACGTcount: A:0.15, C:0.24, G:0.11, T:0.50
Consensus pattern (18 bp):
TTATTCCCTGGTAATCTT
Found at i:972145 original size:20 final size:20
Alignment explanation
Indices: 972120--972170 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
972110 ATCTTATTCC
* *
972120 CTGGTAGTCTTTTATTCTCA
1 CTGGTAATCTTTTATTCCCA
972140 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
*
972160 CTGATAATCTT
1 CTGGTAATCTT
972171 ACATTCCGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.47
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:972176 original size:20 final size:20
Alignment explanation
Indices: 972133--972177 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
972123 GTAGTCTTTT
* * **
972133 ATTCTCACTGGTAATCTTTT
1 ATTCCCACTGATAATCTTAC
972153 ATTCCCACTGATAATCTTAC
1 ATTCCCACTGATAATCTTAC
972173 ATTCC
1 ATTCC
972178 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.07, T:0.42
Consensus pattern (20 bp):
ATTCCCACTGATAATCTTAC
Found at i:973351 original size:20 final size:20
Alignment explanation
Indices: 973303--973352 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
973293 AAAATTTTAC
*
973303 TTAATTTGATTCAATCAATG
1 TTAATTTTATTCAATCAATG
* *
973323 TTAAATTTATTCAAT-ACTG
1 TTAATTTTATTCAATCAATG
973342 TTTAATTTTAT
1 -TTAATTTTAT
973353 ATTTCTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (20 bp):
TTAATTTTATTCAATCAATG
Found at i:978248 original size:16 final size:18
Alignment explanation
Indices: 978216--978250 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
978206 TTTAATTTAT
978216 TTTATAGAAATTATAGTG
1 TTTATAGAAATTATAGTG
978234 TTTATA-AAA-TATAGTG
1 TTTATAGAAATTATAGTG
978250 T
1 T
978251 AGAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (18 bp):
TTTATAGAAATTATAGTG
Found at i:979952 original size:12 final size:12
Alignment explanation
Indices: 979937--979968 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
979927 TGGGTGACAT
979937 AGGAGGTGAGTC
1 AGGAGGTGAGTC
979949 AGGAGGTGAGTC
1 AGGAGGTGAGTC
*
979961 AGAAGGTG
1 AGGAGGTG
979969 GGGATAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.06, G:0.50, T:0.16
Consensus pattern (12 bp):
AGGAGGTGAGTC
Found at i:980872 original size:31 final size:33
Alignment explanation
Indices: 980825--980886 Score: 101
Period size: 31 Copynumber: 1.9 Consensus size: 33
980815 ATTTTTGGTT
980825 TTTTTTATGATTTGAATGTTGAGGATTTTTTGA
1 TTTTTTATGATTTGAATGTTGAGGATTTTTTGA
*
980858 TTTTTT-T-ATTTGAATGTTGATGATTTTTT
1 TTTTTTATGATTTGAATGTTGAGGATTTTTT
980887 TATTCTGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 21 0.75
32 1 0.04
33 6 0.21
ACGTcount: A:0.19, C:0.00, G:0.18, T:0.63
Consensus pattern (33 bp):
TTTTTTATGATTTGAATGTTGAGGATTTTTTGA
Found at i:980901 original size:31 final size:31
Alignment explanation
Indices: 980834--980903 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
980824 TTTTTTTATG
**
980834 ATTTGAATGTTGAGGATTTTTTGATTTTTTT
1 ATTTGAATGTTGAGGATTTTTTGATTTGATT
* *
980865 ATTTGAATGTTGATGATTTTTTTATTCTGATT
1 ATTTGAATGTTGAGGATTTTTTGATT-TGATT
980897 -TTTGAAT
1 ATTTGAAT
980904 TTTTTCCTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.21, C:0.01, G:0.17, T:0.60
Consensus pattern (31 bp):
ATTTGAATGTTGAGGATTTTTTGATTTGATT
Found at i:980947 original size:48 final size:44
Alignment explanation
Indices: 980850--980959 Score: 121
Period size: 48 Copynumber: 2.4 Consensus size: 44
980840 ATGTTGAGGA
* *
980850 TTTTTTGATTTTTTTATTTGAATGTTGATGATTTTTTTATTCTG
1 TTTTTTGATTTTTTTATTTGAATATTGAGGATTTTTTTATTCTG
* * *
980894 ATTTTTGAATTTTTTCCTGATTTTAATATTGAGGATTTTTTTCTTCTG
1 TTTTTTG-ATTTTTT--T-ATTTGAATATTGAGGATTTTTTTATTCTG
**
980942 TTTTTTGGGTTTTTTATT
1 TTTTTTGATTTTTTTATT
980960 ATATGTAGAG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
44 9 0.17
45 8 0.15
47 6 0.11
48 31 0.57
ACGTcount: A:0.15, C:0.05, G:0.14, T:0.66
Consensus pattern (44 bp):
TTTTTTGATTTTTTTATTTGAATATTGAGGATTTTTTTATTCTG
Found at i:981997 original size:16 final size:17
Alignment explanation
Indices: 981961--981997 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
981951 TTGATAAATT
981961 TTTAAAAGTAAATGTAA
1 TTTAAAAGTAAATGTAA
*
981978 -TTAAAATTAAA-GTAA
1 TTTAAAAGTAAATGTAA
981993 TTTAA
1 TTTAA
981998 TCACATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
TTTAAAAGTAAATGTAA
Found at i:988692 original size:21 final size:21
Alignment explanation
Indices: 988650--988692 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
988640 TTTCTGGGCT
* *
988650 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
988671 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
988692 A
1 A
988693 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:989420 original size:23 final size:23
Alignment explanation
Indices: 989376--989420 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
989366 ATTATTATAT
*
989376 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
989399 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
989421 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:995480 original size:21 final size:21
Alignment explanation
Indices: 995438--995480 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
995428 TTTATGGGCT
* *
995438 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
995459 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
995480 A
1 A
995481 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:996045 original size:25 final size:25
Alignment explanation
Indices: 996011--996075 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
996001 GGGTAGAGGG
996011 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
*
996036 TCTACGCGGTCTTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
996061 TCTACGCGGTCCTTC
1 TCTACGCGGTCCTTC
996076 AGGATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.31
Consensus pattern (25 bp):
TCTACGCGGTCCTTCGGGACAATAT
Found at i:996238 original size:23 final size:23
Alignment explanation
Indices: 996194--996238 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
996184 ATTATTATAT
*
996194 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
996217 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
996239 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1000649 original size:21 final size:20
Alignment explanation
Indices: 1000625--1000688 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1000615 AACTTTGAAA
1000625 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
1000646 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
1000660 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
1000681 AAATGTTT
1 AAATGTTT
1000689 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:1000663 original size:35 final size:36
Alignment explanation
Indices: 1000617--1000738 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
1000607 TGACAACCAA
1000617 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
1000654 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
1000689 CTTTGAAAAATAATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGA-TTTTCAAAGTTTGGTAAATGTTT
*
1000726 -ATTGAAAAATGAT
1 CTTTGAAAAATGAT
1000739 AATGAGATAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
35 35 0.45
36 15 0.19
37 27 0.35
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:1012628 original size:31 final size:31
Alignment explanation
Indices: 1012590--1012774 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
1012580 GGGTCGAGGG
1012590 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1012621 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1012652 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1012683 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
1012714 TTACCTATGTTCTTCAGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1012745 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1012775 GTCCTTCGGG
Statistics
Matches: 149, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 148 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1013558 original size:2 final size:2
Alignment explanation
Indices: 1013551--1013591 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1013541 ATGAGTTATG
* *
1013551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT TT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1013592 GATAGATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1016843 original size:31 final size:31
Alignment explanation
Indices: 1016805--1016872 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1016795 GGGTCGAGGG
1016805 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
1016836 TTACCTATGTTCTTCGGTACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1016867 TTACCT
1 TTACCT
1016873 GTAACACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1017660 original size:18 final size:18
Alignment explanation
Indices: 1017637--1017693 Score: 114
Period size: 18 Copynumber: 3.2 Consensus size: 18
1017627 ACCGGTCACA
1017637 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1017655 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1017673 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1017691 ACC
1 ACC
1017694 GTTGACCCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1017702 original size:15 final size:15
Alignment explanation
Indices: 1017682--1017710 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1017672 GACCCGACCC
1017682 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
1017697 GACCCGTTGACCGT
1 GACCCGTTGACCGT
1017711 CGTTGACCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:1017716 original size:10 final size:8
Alignment explanation
Indices: 1017682--1017728 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
1017672 GACCCGACCC
1017682 GACCCGTT
1 GACCCGTT
1017690 GA-CCGTT
1 GACCCGTT
1017697 GACCCGTT
1 GACCCGTT
1017705 GACCGTCGTT
1 GACC--CGTT
1017715 GACCACTGTT
1 GACC-C-GTT
1017725 GACC
1 GACC
1017729 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 1 0.03
10 15 0.44
ACGTcount: A:0.15, C:0.34, G:0.26, T:0.26
Consensus pattern (8 bp):
GACCCGTT
Found at i:1019023 original size:18 final size:18
Alignment explanation
Indices: 1018997--1019031 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1018987 TCGAAAGGAC
*
1018997 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1019015 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1019032 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1022825 original size:18 final size:18
Alignment explanation
Indices: 1022802--1022872 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
1022792 ACCGGTCACA
*
1022802 ACCCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
1022820 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
1022837 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1022851 A-CCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1022868 ACCCG
1 ACCCG
1022873 TTGACCGTCG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
13 12 0.27
17 14 0.31
18 19 0.42
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1022858 original size:30 final size:31
Alignment explanation
Indices: 1022806--1022872 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
1022796 GTCACAACCC
*
1022806 GACCTGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
1022837 TACCCGACCCGTTGA-CCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
1022867 GACCCG
1 GACCCG
1022873 TTGACCGTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:1022870 original size:25 final size:26
Alignment explanation
Indices: 1022810--1022879 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 26
1022800 CAACCCGACC
1022810 TGACCCGTTGACCCGACCCGACCCGTT
1 TGACCCGTTGA-CCGACCCGACCCGTT
1022837 TACCCGACCCGTTGACCGACCCGACCCG-T
1 T----GACCCGTTGACCGACCCGACCCGTT
1022866 TGACCCGTTGACCG
1 TGACCCGTTGACCG
1022880 TCGTTGACCA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
25 13 0.33
27 1 0.03
29 2 0.05
30 13 0.33
31 10 0.26
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.17
Consensus pattern (26 bp):
TGACCCGTTGACCGACCCGACCCGTT
Found at i:1022872 original size:13 final size:13
Alignment explanation
Indices: 1022824--1022859 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1022814 CCGTTGACCC
1022824 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1022837 TACCCGACCCGTT
1 GACCCGACCCGTT
1022850 GA-CCGACCCG
1 GACCCGACCCG
1022860 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1026631 original size:31 final size:31
Alignment explanation
Indices: 1026593--1026715 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
1026583 GGGTGTTACA
1026593 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1026624 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1026655 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1026686 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1026716 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1045566 original size:18 final size:18
Alignment explanation
Indices: 1045529--1045594 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
1045519 TTTTACTATT
1045529 TTATTA-TTTCTATTATTA
1 TTATTATTTTCTATT-TTA
1045547 TTATTATTTTCT-TTTCTA
1 TTATTATTTTCTATTT-TA
1045565 TT-TTACTTTTCTATTTTA
1 TTATTA-TTTTCTATTTTA
1045583 TTTATTCATTTT
1 -TTATT-ATTTT
1045595 TACTTTCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
17 4 0.10
18 20 0.49
19 10 0.24
20 6 0.15
21 1 0.02
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTATTTTCTATTTTA
Found at i:1045842 original size:26 final size:26
Alignment explanation
Indices: 1045813--1045876 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
1045803 TTTACTTCAT
*
1045813 TCATTTTTTTTCTTTATTATTTATTA
1 TCATTTTTTTACTTTATTATTTATTA
1045839 TCATTTTTTTACTTTATTATTTATTA
1 TCATTTTTTTACTTTATTATTTATTA
1045865 TCATTTTTTTAC
1 TCATTTTTTTAC
1045877 ATATCTTTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (26 bp):
TCATTTTTTTACTTTATTATTTATTA
Found at i:1046423 original size:13 final size:13
Alignment explanation
Indices: 1046405--1046442 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1046395 TTCACTTAAG
1046405 GCTCTAAACCCGA
1 GCTCTAAACCCGA
1046418 GCTCTAAACCCGA
1 GCTCTAAACCCGA
*
1046431 GCTCCAAACCCG
1 GCTCTAAACCCG
1046443 TTTTAAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.29, C:0.42, G:0.16, T:0.13
Consensus pattern (13 bp):
GCTCTAAACCCGA
Found at i:1049794 original size:95 final size:95
Alignment explanation
Indices: 1049689--1049870 Score: 312
Period size: 95 Copynumber: 1.9 Consensus size: 95
1049679 ATATTATTTA
1049689 TATACAATAAAGCTTGAGTTGTCCCTAT-AGAGCAATTGGTTAAACACCCCGGCTTTATGGATAA
1 TATACAATAAAGCTTGAGTTGTCCCTATAAG-GCAATTGGTTAAACACCCCGGCTTTATGGATAA
* *
1049753 TATTCAGCTAGCCTGATAAAGGTGATTATAC
65 GATTCAGCTAACCTGATAAAGGTGATTATAC
* *
1049784 TATACAATAAAGCTTGAGTTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
1 TATACAATAAAGCTTGAGTTGTCCCTATAAGGCAATTGGTTAAACACCCCGGCTTTATGGATAAG
1049849 ATTCAGCTAACCTGATAAAGGT
66 ATTCAGCTAACCTGATAAAGGT
1049871 ATTTACATAT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
95 80 0.98
96 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGTTGTCCCTATAAGGCAATTGGTTAAACACCCCGGCTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGATTATAC
Found at i:1050799 original size:14 final size:14
Alignment explanation
Indices: 1050780--1050812 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1050770 CATATATAAG
1050780 AGCATCGCATCCAT
1 AGCATCGCATCCAT
1050794 AGCATCGCATCCAT
1 AGCATCGCATCCAT
1050808 AGCAT
1 AGCAT
1050813 AATTTTGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.21
Consensus pattern (14 bp):
AGCATCGCATCCAT
Found at i:1051223 original size:36 final size:36
Alignment explanation
Indices: 1051171--1051264 Score: 161
Period size: 36 Copynumber: 2.6 Consensus size: 36
1051161 TAATTTACTC
1051171 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
**
1051208 AAAACAAATTTTGTCTCTCTTGAGATTGTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
1051244 AAAACAAATTTTGTCTCTCTT
1 AAAACAAATTTTGTCTCTCTT
1051265 TAAACAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
36 47 0.85
37 8 0.15
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.44
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:1051227 original size:21 final size:21
Alignment explanation
Indices: 1051202--1051272 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 21
1051192 TGAGACAGTT
1051202 TCTCTTAAAACAAATTTTGTC
1 TCTCTTAAAACAAATTTTGTC
* * *
1051223 TCTCTT----GAGA--TTGTT
1 TCTCTTAAAACAAATTTTGTC
1051238 TCTCTTAAAACAAATTTTGTC
1 TCTCTTAAAACAAATTTTGTC
*
1051259 TCTCTTTAAACAAA
1 TCTCTTAAAACAAA
1051273 AACTTTGAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
15 10 0.27
17 2 0.05
19 2 0.05
21 23 0.62
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (21 bp):
TCTCTTAAAACAAATTTTGTC
Found at i:1051384 original size:36 final size:37
Alignment explanation
Indices: 1051298--1051463 Score: 219
Period size: 37 Copynumber: 4.5 Consensus size: 37
1051288 TTCCTTGAAA
** *
1051298 TAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAGAAC
1 TAAA-TTTTGTCTCTCTTGAGACAGTTTCTCGTAAAAC
*
1051336 TAAATTTTGTCTCTCTTGAGACATTTTCTCGTAAAAC
1 TAAATTTTGTCTCTCTTGAGACAGTTTCTCGTAAAAC
** *
1051373 -AAATTTTGTCTCTCTTGAGACAGTTTCTTTTAGAAC
1 TAAATTTTGTCTCTCTTGAGACAGTTTCTCGTAAAAC
* * *
1051409 TAAATTTTGTCTCTCTTGAGATATTTTCCCGTAAAAC
1 TAAATTTTGTCTCTCTTGAGACAGTTTCTCGTAAAAC
1051446 -AAATTTTGTCTCTCTTGA
1 TAAATTTTGTCTCTCTTGA
1051464 AACAAAATCT
Statistics
Matches: 113, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
36 50 0.44
37 59 0.52
38 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (37 bp):
TAAATTTTGTCTCTCTTGAGACAGTTTCTCGTAAAAC
Found at i:1051385 original size:73 final size:73
Alignment explanation
Indices: 1051303--1051463 Score: 304
Period size: 73 Copynumber: 2.2 Consensus size: 73
1051293 TGAAATAAAG
*
1051303 TTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGT
1 TTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCCCGT
1051368 AAAACAAA
66 AAAACAAA
*
1051376 TTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGATATTTTCCCGT
1 TTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCCCGT
1051441 AAAACAAA
66 AAAACAAA
1051449 TTTTGTCTCTCTTGA
1 TTTTGTCTCTCTTGA
1051464 AACAAAATCT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 86 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (73 bp):
TTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCCCGT
AAAACAAA
Found at i:1051532 original size:36 final size:34
Alignment explanation
Indices: 1051484--1051583 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 34
1051474 CTGAATATGT
*
1051484 TTTCCTTTAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCTTGAAACAAATTTT-TCTCTCTTGAGACAG
* * *
1051519 TTTCTCTTGAAACAAATTTTATCTTTCTTGATATAG
1 TTTC-CTTGAAACAAATTTT-TCTCTCTTGAGACAG
* *
1051555 TTTCCCTTGAAACGAAGTTTTC-CTCTTGA
1 TTT-CCTTGAAACAAATTTTTCTCTCTTGA
1051584 AGCACCAATC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
34 6 0.11
35 6 0.11
36 42 0.76
37 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (34 bp):
TTTCCTTGAAACAAATTTTTCTCTCTTGAGACAG
Found at i:1051633 original size:33 final size:34
Alignment explanation
Indices: 1051593--1051686 Score: 127
Period size: 33 Copynumber: 2.7 Consensus size: 34
1051583 AAGCACCAAT
1051593 CTTTGAAATTGTTTCTCTTGAAACAC-AAAAAAC
1 CTTTGAAATTGTTTCTCTTGAAACACAAAAAAAC
** *
1051626 CTTTGAAACAGTCTCTCTTGAAACACAAAAAAAAAC
1 CTTTGAAATTGTTTCTCTTGAAACAC--AAAAAAAC
1051662 CTTTTGAAATTGTTTCTCTTGAAAC
1 C-TTTGAAATTGTTTCTCTTGAAAC
1051687 GTTATTCTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
33 23 0.45
36 8 0.16
37 20 0.39
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (34 bp):
CTTTGAAATTGTTTCTCTTGAAACACAAAAAAAC
Found at i:1053015 original size:16 final size:16
Alignment explanation
Indices: 1052977--1053019 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1052967 CGTCATGGTC
*
1052977 ATTTTACTATTTGTTT
1 ATTTTACTATTTATTT
1052993 ATATTTA-TATTATATTT
1 AT-TTTACTATT-TATTT
1053010 ATTTTACTAT
1 ATTTTACTAT
1053020 AACTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (16 bp):
ATTTTACTATTTATTT
Found at i:1053054 original size:26 final size:26
Alignment explanation
Indices: 1052994--1053055 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
1052984 TATTTGTTTA
* *
1052994 TATTTATATTATATTTATTTTACTAT
1 TATTTTTATTATATTTATTTTAATAT
* * *
1053020 AACTATTATTAGTA-TTATTTTAATAT
1 TATTTTTATTA-TATTTATTTTAATAT
1053046 TATTTTTATT
1 TATTTTTATT
1053056 TCATATATGT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (26 bp):
TATTTTTATTATATTTATTTTAATAT
Found at i:1053128 original size:12 final size:12
Alignment explanation
Indices: 1053111--1053169 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
1053101 TTTTACTATT
1053111 TTATTATTTCTA
1 TTATTATTTCTA
1053123 TTATTATTAT-TA
1 TTATTATT-TCTA
1053135 TTATTATTTTTCTA
1 TTATTA--TTTCTA
1053149 TT-TTACTTTTCTA
1 TTATTA--TTTCTA
1053162 TT-TTATTT
1 TTATTATTT
1053170 ATTCATTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
11 3 0.07
12 16 0.38
13 17 0.40
14 6 0.14
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTATTTCTA
Found at i:1053167 original size:26 final size:26
Alignment explanation
Indices: 1053100--1053197 Score: 91
Period size: 26 Copynumber: 3.8 Consensus size: 26
1053090 TTTTTATACG
1053100 CTTTTACTATTTTATTATTTCTATTATTA
1 CTTTT-CTATTTTATT-TTTCTATT-TTA
*
1053129 -TTAT-TATTATTATTTTTCTATTTTA
1 CTTTTCTATT-TTATTTTTCTATTTTA
1053154 CTTTTCTATTTTATTTATTC-ATTTTTA
1 CTTTTCTATTTTATTT-TTCTA-TTTTA
1053181 C-TTTC--TTTTATTTTTCT
1 CTTTTCTATTTTATTTTTCT
1053198 TTTATTCTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
23 3 0.05
24 8 0.13
25 3 0.05
26 26 0.43
27 18 0.30
28 3 0.05
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.70
Consensus pattern (26 bp):
CTTTTCTATTTTATTTTTCTATTTTA
Found at i:1053238 original size:13 final size:14
Alignment explanation
Indices: 1053220--1053248 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1053210 TTCATCTCCC
1053220 TTTATTTATTT-CA
1 TTTATTTATTTGCA
1053233 TTTATTTATTTGCA
1 TTTATTTATTTGCA
1053247 TT
1 TT
1053249 ATCTTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTATTTATTTGCA
Found at i:1054493 original size:23 final size:23
Alignment explanation
Indices: 1054449--1054499 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
1054439 TTTGGCCAAT
1054449 TCAAATATTAAATTAAATAATAAA
1 TCAAATATTAAATTAAATAAT-AA
*
1054473 TCAATATATTACA-TAAA-AATAA
1 TCAA-ATATTAAATTAAATAATAA
1054495 TCAAA
1 TCAAA
1054500 CTTAAATGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 6 0.24
23 3 0.12
24 8 0.32
25 7 0.28
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (23 bp):
TCAAATATTAAATTAAATAATAA
Found at i:1055430 original size:329 final size:326
Alignment explanation
Indices: 1054963--1055606 Score: 1093
Period size: 329 Copynumber: 2.0 Consensus size: 326
1054953 ATACCGATAA
1054963 CATTGCAAATTTACCTATTACATTATATTATATTGAAAGTATCCATACTTTTTATAAAAAGGATC
1 CATTGCAAATTTACCTATTACATTATATTATATTGAAAGTATCCATACTTTTTATAAAAAGGATC
*
1055028 GATATTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTCCAC
66 GATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTCCAC
1055093 CTACAATATTTAATTTAATAA-TTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATA
131 CTACAATA-TTAATTTAATAATTTCATTTGCAC-AAAAATTATTTGATTGTTTTGATATTTTAT-
* *
1055157 AAATATTATTTA-AATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAG
193 AAATAATATTTAGAATTTTTAATTTAATAAT-A-ATATATCGTAACGAAAAAAATAAATCATTAG
*
1055221 ACGCTTATAATTACT-AATTAATATCTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTC
256 ACGCCTATAATTACTAAATTAATATCTAAAACTCACTCAAAAG--AA-CTTAAATTAATGTTTTC
1055285 CACAATGAG
318 CACAATGAG
*
1055294 CATTGC-AATTTACCTATTACATTATATTATATTG-AAGTGTCCATACTTTTTATAAAAAGGATC
1 CATTGCAAATTTACCTATTACATTATATTATATTGAAAGTATCCATACTTTTTATAAAAAGGATC
1055357 GATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCA
66 GATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATG-TTTCCA
1055421 CCTACAATATTAATTTAATAATTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATAA
130 CCTACAATATTAATTTAATAATTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATAA
*
1055486 ATAATATTTAGAATTTTTAATTTAATAATAATATATCGTAACGAAAAAAATAAATTATTAGACGC
195 ATAATATTTAGAATTTTTAATTTAATAATAATATATCGTAACGAAAAAAATAAATCATTAGACGC
* *
1055551 CTATAATTACTAAATTAATATCTTAAACTTACTCAAAAGAACTTAAATTAATGTTT
260 CTATAATTACTAAATTAATATCTAAAACTCACTCAAAAGAACTTAAATTAATGTTT
1055607 CACAGTGAAA
Statistics
Matches: 301, Mismatches: 8, Indels: 15
0.93 0.02 0.05
Matches are distributed among these distances:
324 15 0.05
325 2 0.01
326 43 0.14
327 37 0.12
328 81 0.27
329 89 0.30
330 28 0.09
331 6 0.02
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (326 bp):
CATTGCAAATTTACCTATTACATTATATTATATTGAAAGTATCCATACTTTTTATAAAAAGGATC
GATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTCCAC
CTACAATATTAATTTAATAATTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATAAA
TAATATTTAGAATTTTTAATTTAATAATAATATATCGTAACGAAAAAAATAAATCATTAGACGCC
TATAATTACTAAATTAATATCTAAAACTCACTCAAAAGAACTTAAATTAATGTTTTCCACAATGA
G
Found at i:1055696 original size:22 final size:23
Alignment explanation
Indices: 1055665--1055726 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
1055655 ATATAACCAC
1055665 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1055688 TA-CTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1055710 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1055727 GTTTACCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1055720 original size:23 final size:23
Alignment explanation
Indices: 1055655--1055726 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1055645 GACACTTACA
* *
1055655 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
1055678 ATATAAACGATA-CTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
1055700 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1055723 ATAT
1 ATAT
1055727 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 20 0.48
23 22 0.52
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1056164 original size:38 final size:39
Alignment explanation
Indices: 1056113--1056198 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1056103 TCAAGTTGTA
*
1056113 GATTTTGATTTCC-TTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
1056151 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1056190 GATTTTGAT
1 GATTTTGAT
1056199 GAGCATCGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 13 0.29
39 32 0.71
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:1056476 original size:18 final size:18
Alignment explanation
Indices: 1056453--1056489 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1056443 CGAAATATAT
1056453 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1056471 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1056489 A
1 A
1056490 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1057184 original size:20 final size:21
Alignment explanation
Indices: 1057146--1057185 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1057136 TTCCACAGTG
* *
1057146 AAAAAGTATGGACACTTTTAT
1 AAAAAGGATAGACACTTTTAT
1057167 AAAAAGGATAGACA-TTTTA
1 AAAAAGGATAGACACTTTTA
1057186 CAATATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
AAAAAGGATAGACACTTTTAT
Found at i:1057224 original size:23 final size:23
Alignment explanation
Indices: 1057198--1057260 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1057188 ATATAACCAC
*
1057198 TACCTATTACATTATATAAATGA
1 TACCTATTACATTATATAAAGGA
* *
1057221 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAAGGA
*
1057244 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1057261 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAAGGA
Found at i:1057301 original size:21 final size:22
Alignment explanation
Indices: 1057277--1057323 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1057267 CTATTATTTG
1057277 AAAGTG-TCCATACTTTTTATA
1 AAAGTGATCCATACTTTTTATA
* *
1057298 AAAG-GATCGATACTTTTTTTA
1 AAAGTGATCCATACTTTTTATA
1057319 AAAGT
1 AAAGT
1057324 TATGTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
AAAGTGATCCATACTTTTTATA
Found at i:1057642 original size:25 final size:25
Alignment explanation
Indices: 1057586--1057650 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
1057576 CACTCAAAAG
*
1057586 ATGTATATACCT-AATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
1057610 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
1057635 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
1057651 TTATGATAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 8 0.25
25 24 0.75
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:1060394 original size:183 final size:183
Alignment explanation
Indices: 1060082--1061114 Score: 1874
Period size: 183 Copynumber: 5.7 Consensus size: 183
1060072 TTAAAATTAC
* *
1060082 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
1060147 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
1060212 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
* * * *
1060265 CGATACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCAACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
1060330 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAATCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
1060395 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
*
1060448 CGACACTTTTTAAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
1060513 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAATCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
1060578 ATATTAC-AAATTATCTATTACATTAT-AATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
*
1060629 CGACACTTTTTAAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1060694 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
1060759 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
1060812 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1060877 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
1060942 ATATTACAAAATTATCTATTACATTAT-ATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
*
1060994 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGAAATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
1061059 TTTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTTATATT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGG-TATATT
1061115 GCAAATTTAC
Statistics
Matches: 831, Mismatches: 16, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
181 161 0.19
182 175 0.21
183 495 0.60
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
Found at i:1060753 original size:364 final size:365
Alignment explanation
Indices: 1060082--1061114 Score: 1879
Period size: 364 Copynumber: 2.8 Consensus size: 365
1060072 TTAAAATTAC
* *
1060082 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
1060147 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
1060212 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACTTTTTT
131 ATATTACAAAATTATCTATTACATTAT-AATCTGGGTTCCGATGTGTAAATGTCGACACTTTTTT
* * *
1060277 AAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCAACACAATATTAAAAAGTGT
195 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
*
1060342 CGATATAGGTTGTAGACCTATTCGCGCATAAAATCGGTATATTTATACCGGTTATATTACAAAAT
260 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
*
1060407 TATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
325 TATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
1060448 CGACACTTTTTAAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
1060513 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAATCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
1060578 ATATTAC-AAATTATCTATTACATTATAATCTGGGTTCCGATGTGTAAATGTCGACACTTTTTAA
131 ATATTACAAAATTATCTATTACATTATAATCTGGGTTCCGATGTGTAAATGTCGACACTTTTTTA
1060642 AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTC
196 AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTC
1060707 GATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATT
261 GATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATT
*
1060772 ATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
326 ATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
1060812 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1060877 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
1060942 ATATTACAAAATTATCTATTACATTATATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTA
131 ATATTACAAAATTATCTATTACATTATAATCTGGGTTCCGATGTGTAAATGTCGACACTTTTTTA
* *
1061007 AATCGTATCGACACATTTTTCTTCCAATATGGAAATAAAGTACCGACACAATTTTAAAAAGTGTC
196 AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTC
1061072 GATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTTATATT
261 GATATAGGTTGTAGACCTATTCGCGCATAAAACCGG-TATATT
1061115 GCAAATTTAC
Statistics
Matches: 644, Mismatches: 21, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
364 335 0.52
365 172 0.27
366 137 0.21
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (365 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATCTGGGTTCCGATGTGTAAATGTCGACACTTTTTTA
AATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTC
GATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATT
ATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:1062604 original size:3 final size:3
Alignment explanation
Indices: 1062596--1062674 Score: 68
Period size: 3 Copynumber: 26.3 Consensus size: 3
1062586 ACTTGTTTGG
* * * ** * *
1062596 ATC ATC ATC TTC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
1062644 ATC GTC ATC ATC ATC GTC ATC TTC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1062675 GCTTCATCTT
Statistics
Matches: 57, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:1062613 original size:12 final size:12
Alignment explanation
Indices: 1062596--1062682 Score: 93
Period size: 12 Copynumber: 7.2 Consensus size: 12
1062586 ACTTGTTTGG
1062596 ATCATCATCTTC
1 ATCATCATCTTC
*
1062608 ATCATCATCATC
1 ATCATCATCTTC
*
1062620 GTCATCATCTTC
1 ATCATCATCTTC
** *
1062632 ATCGCCAGCTTC
1 ATCATCATCTTC
* *
1062644 ATCGTCATCATC
1 ATCATCATCTTC
*
1062656 ATCGTCATCTTC
1 ATCATCATCTTC
*
1062668 ATCATCAGCTTC
1 ATCATCATCTTC
1062680 ATC
1 ATC
1062683 TTCTGCGACC
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 62 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:1062644 original size:36 final size:36
Alignment explanation
Indices: 1062604--1062682 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
1062594 GGATCATCAT
* *
1062604 CTTCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCTTCATCACCAG
* * *
1062640 CTTCATCGTCATCATCATCGTCATCTTCATCATCAG
1 CTTCATCATCATCATCATCATCATCTTCATCACCAG
1062676 CTTCATC
1 CTTCATC
1062683 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (36 bp):
CTTCATCATCATCATCATCATCATCTTCATCACCAG
Found at i:1062683 original size:18 final size:18
Alignment explanation
Indices: 1062596--1062685 Score: 92
Period size: 18 Copynumber: 5.0 Consensus size: 18
1062586 ACTTGTTTGG
* *
1062596 ATCATCATCTTCATCATC
1 ATCATCAGCTTCATCTTC
*
1062614 ATCATC-GTCATCATCTTC
1 ATCATCAG-CTTCATCTTC
** *
1062632 ATCGCCAGCTTCATCGTC
1 ATCATCAGCTTCATCTTC
* *
1062650 ATCATCATCGTCATCTTC
1 ATCATCAGCTTCATCTTC
1062668 ATCATCAGCTTCATCTTC
1 ATCATCAGCTTCATCTTC
1062686 TGCGACCGCT
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
18 55 0.98
19 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.07, T:0.37
Consensus pattern (18 bp):
ATCATCAGCTTCATCTTC
Found at i:1062685 original size:6 final size:6
Alignment explanation
Indices: 1062600--1062685 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
1062590 GTTTGGATCA
* * * * * * * *
1062600 TCATCT TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
1062648 TCATCA TCATCG TCATCT TCATCA TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
1062686 TGCGACCGCT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.21, C:0.35, G:0.07, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:1064556 original size:199 final size:197
Alignment explanation
Indices: 1064143--1064891 Score: 1079
Period size: 198 Copynumber: 3.9 Consensus size: 197
1064133 TTTAAATTAG
1064143 TATCGACACAAACTATATTAGTGCGACACATTATTTAGACATATTCTCTCATAAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGCGACACATTATTTAGACATATTCTCTCAT-AAAACCGGTATA
1064208 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1064273 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTTATTCTGGAAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTGGAAAA
1064338 AAA
195 AAA
1064341 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTG-CGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1064406 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
1064471 CGACACTTTTTATATATGTATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTGG-AAA
1064536 AAAA
194 AAAA
1064540 TATCGACACAAACTATATTAGTGCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAA
1 TATCGACACAAACTATATTAGTGCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAA
1064605 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* * * *
1064670 GACAC----T-T-TATGGGT-GCACCCTGTT-T---T---CCA----TT-CATTC--T-GGAAAA
131 GACACTTTTTATATATGGATCG-ACACT-TTATGGGTGCACCATGTTTTCCATTCATTCTGGAAA
1064713 AAATA
194 AAA-A
*
1064718 TCGA-C-ACA-AACTA-TATTAGT-GT-CGACACATTATTTAGACATATTCTCTCATAAAA-CGG
1 T--ATCGACACAA--ACTA-TATTAGTGCGACACATTATTTAGACATATTCTCTCATAAAACCGG
* *
1064776 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
61 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTT
* *
1064841 GGGATTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
125 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTT
1064892 GGCCATATTG
Statistics
Matches: 506, Mismatches: 16, Indels: 63
0.86 0.03 0.11
Matches are distributed among these distances:
176 54 0.11
177 62 0.12
178 10 0.02
179 6 0.01
180 1 0.00
181 6 0.01
182 5 0.01
183 11 0.02
184 1 0.00
186 3 0.01
189 3 0.01
191 1 0.00
192 10 0.02
193 3 0.01
194 1 0.00
198 270 0.53
199 59 0.12
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (197 bp):
TATCGACACAAACTATATTAGTGCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAA
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTCCATTCATTCTGGAAAAA
AA
Found at i:1064825 original size:176 final size:178
Alignment explanation
Indices: 1064490--1064854 Score: 673
Period size: 177 Copynumber: 2.1 Consensus size: 178
1064480 TTATATATGT
1064490 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTA
1 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTA
1064555 TATTAGTGCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
66 TATTAGTGCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
1064620 TGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGG
131 TGAAAAATTACATATTACATTATACTTTTGGTGTTCGATGATTTTGGG
1064667 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGACACAAACTA
1 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTA
1064731 TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CGGTATAATTGTACCGGTTAGA
66 TATTAGTG-CGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGA
* *
1064795 TTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGG
130 TTGAAAAATTACATATTACATTATACTTTTGGTGTTCGATGATTTTGGG
*
1064844 ATTGACACTTT
1 ATCGACACTTT
1064855 TTATATATGG
Statistics
Matches: 183, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
176 84 0.46
177 99 0.54
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (178 bp):
ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTA
TATTAGTGCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
TGAAAAATTACATATTACATTATACTTTTGGTGTTCGATGATTTTGGG
Found at i:1065054 original size:19 final size:19
Alignment explanation
Indices: 1065008--1065056 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1064998 AATTATTCAC
*
1065008 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1065027 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1065046 ATACAAAATTA
1 ATACAAAATTA
1065057 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1066881 original size:33 final size:33
Alignment explanation
Indices: 1066844--1066909 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1066834 CATCTTAATA
*
1066844 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1066877 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1066910 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1066983 original size:21 final size:21
Alignment explanation
Indices: 1066943--1067007 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1066933 CCCCTTATGC
* *
1066943 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
1066964 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
1066985 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
1067006 CT
1 CT
1067008 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:1069249 original size:17 final size:18
Alignment explanation
Indices: 1069227--1069268 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
1069217 ATATATCCGG
1069227 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1069244 TATCATTTGATACCGGTTT
1 TATCATTT-ATACCGGTTT
1069263 TATCAT
1 TATCAT
1069269 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.35
19 15 0.65
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1069286 original size:20 final size:19
Alignment explanation
Indices: 1069232--1069277 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1069222 TCCGGTATCA
1069232 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
**
1069251 TGATACCGGTTTTATCATAT
1 TTTTACCGGTTTTATCAT-T
1069271 TTTTACC
1 TTTTACC
1069278 TGTTATATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1069872 original size:223 final size:226
Alignment explanation
Indices: 1069507--1069943 Score: 749
Period size: 223 Copynumber: 1.9 Consensus size: 226
1069497 TTAAAACTGC
1069507 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
1069572 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* * *
1069637 TTAGAATTTAAATTTAACAATATTAACCAAATATAAT-A-AAATGTGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
1069700 GTATGGACACTTTTATAAAATGATATATACTT
195 GTATGGACACTTTTATAAAATGATATATACTT
1069732 TTTTGAAAGTTATGTAATTTATGTTTCAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
1069796 ATTAA-TTAATAATTTCATTTACACAAAAAATTATTT-ATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
1069859 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATAA
130 TTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAA
1069924 GTATGGACACTTTTATAAAA
195 GTATGGACACTTTTATAAAA
1069944 AGGATAGATA
Statistics
Matches: 201, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
223 62 0.31
224 61 0.30
225 51 0.25
226 27 0.13
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.46
Consensus pattern (226 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
TATGGACACTTTTATAAAATGATATATACTT
Found at i:1077055 original size:82 final size:82
Alignment explanation
Indices: 1076962--1077126 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
1076952 TTCAATTTGG
*
1076962 TTATCTCGTTGATGTTGTATAGTTTAGGATATCTCCTTTGATCGCTAATTTCATTATTGTTTCTT
1 TTATCTCGTTGATGTTGTATAGTTTAGGATATCTCCTTTGATCACTAATTTCATTATTGTTTCTT
1077027 AGGTACAAAGCTGGTTC
66 AGGTACAAAGCTGGTTC
1077044 TTATCTCGTTGATGTTGTATAGTTTAGGATATCTCCTTTGATCACTAATTTCATTATTGTTTCTT
1 TTATCTCGTTGATGTTGTATAGTTTAGGATATCTCCTTTGATCACTAATTTCATTATTGTTTCTT
1077109 AGGTACAAAGCTGGTTC
66 AGGTACAAAGCTGGTTC
1077126 T
1 T
1077127 CAGCCAGACA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47
Consensus pattern (82 bp):
TTATCTCGTTGATGTTGTATAGTTTAGGATATCTCCTTTGATCACTAATTTCATTATTGTTTCTT
AGGTACAAAGCTGGTTC
Found at i:1082314 original size:18 final size:18
Alignment explanation
Indices: 1082273--1082333 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
1082263 TTTGATTCAC
*
1082273 GGAATGTAAGATTATCAGTG
1 GGAATGTAAGATTA-C-CTG
1082293 GGAATGTAAGATTACCTG
1 GGAATGTAAGATTACCTG
** *
1082311 GGAATAAAAGATTACCAG
1 GGAATGTAAGATTACCTG
1082329 GGAAT
1 GGAAT
1082334 ATGATTACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
18 22 0.59
19 1 0.03
20 14 0.38
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
GGAATGTAAGATTACCTG
Found at i:1084055 original size:2 final size:2
Alignment explanation
Indices: 1084048--1084074 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1084038 ACAAACTTTG
1084048 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 A
1084075 ATCAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1090768 original size:30 final size:30
Alignment explanation
Indices: 1090734--1090790 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1090724 TATAACTCTT
*
1090734 TAGAAGCTTATGGAAGA-GTGTGGAATCCTC
1 TAGAAGATTATGG-AGATGTGTGGAATCCTC
* *
1090764 TAGAATATTTTGGAGATGTGTGGAATC
1 TAGAAGATTATGGAGATGTGTGGAATC
1090791 TTATGGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.13
30 20 0.87
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (30 bp):
TAGAAGATTATGGAGATGTGTGGAATCCTC
Found at i:1091446 original size:2 final size:2
Alignment explanation
Indices: 1091441--1091515 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
1091431 GCCTTGTTTG
1091441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1091483 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
1091516 TTGTTTAATG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1093211 original size:2 final size:2
Alignment explanation
Indices: 1093206--1093258 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1093196 AGAAAGAGTT
*
1093206 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1093248 TA TA TA TA TA T
1 TA TA TA TA TA T
1093259 CCTAAAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1100682 original size:26 final size:27
Alignment explanation
Indices: 1100626--1100675 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
1100616 TAAGATTATT
*
1100626 ATAAAATATAAAGTGAACATAATTTAC
1 ATAAAATATAAAGTGAAAATAATTTAC
1100653 ATAAAAT-TAAA-T-AAAATAATTTA
1 ATAAAATATAAAGTGAAAATAATTTA
1100676 GACATAACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 1 0.05
26 4 0.18
27 7 0.32
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (27 bp):
ATAAAATATAAAGTGAAAATAATTTAC
Found at i:1108665 original size:20 final size:20
Alignment explanation
Indices: 1108640--1108690 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1108630 TAGAGCGTGG
1108640 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
1108660 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
1108680 GGGGAATCGGT
1 GGGGAATCGGT
1108691 TCCCTAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.35, T:0.20
Consensus pattern (20 bp):
GGGGAATCGGTACCCCCTAT
Found at i:1140723 original size:150 final size:149
Alignment explanation
Indices: 1140512--1140809 Score: 386
Period size: 150 Copynumber: 2.0 Consensus size: 149
1140502 TGTTTAGATA
* ** * * *
1140512 CATTATAATTTTGATTCGTCTCATTATTTTATAGATAAATTATATAAATGGTTACTAATGTTTGA
1 CATTATAATTTTAATTCGTCTCATTATTTTATAGATAAATTATATAAATAATCACAAATGTTTAA
** ** *
1140577 GT-AAATTTT-TGTTTTCCTTATTGAAGTTTCAAAAATGAA-ATATTAGTCACTAATATTATCAA
66 GTAAAATTTTAT-TTTTCC-TATT-AAAATT-AAAAAAAAACATATTAATCACTAATATTATCAA
*
1140639 TTTGTAACAAAATGATCACTCGC
127 TTTATAACAAAATGATCACTCGC
*
1140662 CATTATAATTTTAATTCTTCTCATTATTTTATAGATAAATTATATAAATAATCACAAATGTTTAA
1 CATTATAATTTTAATTCGTCTCATTATTTTATAGATAAATTATATAAATAATCACAAATGTTTAA
* *
1140727 TTAAAATTTTATTTTTCCTATTAAAATTAAAAAAAAACATATTAATCACTAATATTATTAATTTA
66 GTAAAATTTTATTTTTCCTATTAAAATTAAAAAAAAACATATTAATCACTAATATTATCAATTTA
* *
1140792 TAATAAAATGCTCACTCG
131 TAACAAAATGATCACTCG
1140810 TCGTTCGCAA
Statistics
Matches: 128, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
148 7 0.05
149 44 0.34
150 63 0.49
151 13 0.10
152 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (149 bp):
CATTATAATTTTAATTCGTCTCATTATTTTATAGATAAATTATATAAATAATCACAAATGTTTAA
GTAAAATTTTATTTTTCCTATTAAAATTAAAAAAAAACATATTAATCACTAATATTATCAATTTA
TAACAAAATGATCACTCGC
Found at i:1148134 original size:128 final size:128
Alignment explanation
Indices: 1147906--1148149 Score: 461
Period size: 128 Copynumber: 1.9 Consensus size: 128
1147896 GATACACGGA
*
1147906 CCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
1 CCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
1147971 ACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCG
66 ACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCG
*
1148034 CCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTTGGGG
1 CCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
*
1148099 ACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGTGCGTT
66 ACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTT
1148150 ATGTGAAGTT
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 113 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (128 bp):
CCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
ACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCG
Found at i:1148512 original size:34 final size:34
Alignment explanation
Indices: 1148474--1148573 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 34
1148464 AAATTTAATG
1148474 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATACTATAATTTATATTTTAAAT
* * * * *
1148508 TTAAA-TTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTTGAATACTATAATTTATATTTTAAAT
* *
1148541 TTAAATTTCGAATACTATAATTTGTATTTTAAA
1 TTAAATTTTGAATACTATAATTTATATTTTAAA
1148574 AACATTTATC
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 28 0.52
34 26 0.48
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (34 bp):
TTAAATTTTGAATACTATAATTTATATTTTAAAT
Found at i:1149181 original size:21 final size:21
Alignment explanation
Indices: 1149093--1149186 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1149083 TATGGTATAA
*
1149093 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1149114 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
1149135 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1149156 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1149177 AACCCTGCGG
1 AACCCTGCGG
1149187 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1149230 original size:21 final size:21
Alignment explanation
Indices: 1149190--1149231 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1149180 CCTGCGGAGA
*
1149190 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1149211 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
1149232 GGACATGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.38, T:0.26
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1152116 original size:97 final size:97
Alignment explanation
Indices: 1151977--1152164 Score: 340
Period size: 97 Copynumber: 1.9 Consensus size: 97
1151967 AGATTAATGA
1151977 AATAGAACTATATTGTTTCTTCACAAACACGAGTCTATTTTTCTAGCGGAATCATCAAAAACAAT
1 AATAGAACTATATTGTTTCTTCACAAACACGAGTCTATTTTTCTAGCGGAATCATCAAAAACAAT
*
1152042 TCTCAATTTTCGAACATCGTCGTACAAACAAG
66 TCTCAATTTTCGAACATCATCGTACAAACAAG
* * *
1152074 AATAGAACTATATTGTTTCTTCACAAACAGGAGTCTATTTTTCTAGTGGAATCGTCAAAAACAAT
1 AATAGAACTATATTGTTTCTTCACAAACACGAGTCTATTTTTCTAGCGGAATCATCAAAAACAAT
1152139 TCTCAATTTTCGAACATCATCGTACA
66 TCTCAATTTTCGAACATCATCGTACA
1152165 GAAACATTAA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 87 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (97 bp):
AATAGAACTATATTGTTTCTTCACAAACACGAGTCTATTTTTCTAGCGGAATCATCAAAAACAAT
TCTCAATTTTCGAACATCATCGTACAAACAAG
Found at i:1152983 original size:3 final size:3
Alignment explanation
Indices: 1152975--1153026 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1152965 CCTCTTATTG
1152975 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1153023 TAT T
1 TAT T
1153027 TATCATCTAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1158924 original size:24 final size:23
Alignment explanation
Indices: 1158880--1158934 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
1158870 ACTATACAAT
*
1158880 AATATATTAGATTTTAAAATTTTA
1 AATAT-TTAGATTTTAAAATTTGA
* *
1158904 AATATTTATATTTATACAATTTGA
1 AATATTTAGATTT-TAAAATTTGA
*
1158928 GATATTT
1 AATATTT
1158935 TGTATCCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (23 bp):
AATATTTAGATTTTAAAATTTGA
Found at i:1161961 original size:37 final size:39
Alignment explanation
Indices: 1161883--1161962 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 39
1161873 AACAAGTTGA
* * *
1161883 AAAATATTTATATATTTTCTTTAAAAAATTTACATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAATTAAAAATCAT
*
1161922 AAAAT-TTATATATATTTT-TTTACAAAATTAAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAATTAAAAATCAT
1161959 AAAA
1 AAAA
1161963 AGGTTTAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 6 0.17
38 15 0.42
39 15 0.42
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAATTAAAAATCAT
Found at i:1165544 original size:21 final size:21
Alignment explanation
Indices: 1165520--1165585 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
1165510 ACGTTGTATT
1165520 TCGCATTACGATAGTTGAAAA
1 TCGCATTACGATAGTTGAAAA
* * ** * **
1165541 TCGCGTTGCG-TTTTTGCATT
1 TCGCATTACGATAGTTGAAAA
*
1165561 TCGCATTATGATAGTTGAAAA
1 TCGCATTACGATAGTTGAAAA
1165582 TCGC
1 TCGC
1165586 GTTGCGTTTT
Statistics
Matches: 29, Mismatches: 15, Indels: 2
0.63 0.33 0.04
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGCATTACGATAGTTGAAAA
Found at i:1165562 original size:41 final size:41
Alignment explanation
Indices: 1165517--1165625 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
1165507 TTCACGTTGT
*
1165517 ATTTCGCATTACGATAGTTGAAAATCGCGTTGCGTTTTTGC
1 ATTTCGCATTACGATAGTTGAAAATCGCGTTGCGTTTTTCC
*
1165558 ATTTCGCATTATGATAGTTGAAAATCGCGTTGCGTTTTTCC
1 ATTTCGCATTACGATAGTTGAAAATCGCGTTGCGTTTTTCC
* *
1165599 ATTTCGCGTTGCGATAGTTG-AAATCGC
1 ATTTCGCATTACGATAGTTGAAAATCGC
1165626 AACGCGATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
40 7 0.11
41 56 0.89
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (41 bp):
ATTTCGCATTACGATAGTTGAAAATCGCGTTGCGTTTTTCC
Found at i:1166355 original size:19 final size:19
Alignment explanation
Indices: 1166331--1166396 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
1166321 TTAACTATCA
1166331 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
1166350 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
*
1166372 CAACGCATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
1166391 CAACGA
1 CAACGA
1166397 CAACTGTAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 18 0.53
20 1 0.03
21 2 0.06
22 13 0.38
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:1166373 original size:22 final size:22
Alignment explanation
Indices: 1166346--1166417 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
1166336 AATTTGGAAA
1166346 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
1166368 ATCGCAACG-C-A-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
1166387 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
1166409 ATCACAACG
1 ATCGCAACG
1166418 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1166382 original size:41 final size:41
Alignment explanation
Indices: 1166324--1166418 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
1166314 TTTTTTTTTA
*
1166324 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCACAACGCATTTGGAAAATCGCAACGACAACTGTAG
*
1166365 ACTATCGCAACGCATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCACAACGCATTTGGAAAATCGCAACGACAACTGTAG
1166406 ACTATCACAACGC
1 ACTATCACAACGC
1166419 GAAATGAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
ACTATCACAACGCATTTGGAAAATCGCAACGACAACTGTAG
Found at i:1166428 original size:41 final size:42
Alignment explanation
Indices: 1166340--1166472 Score: 164
Period size: 41 Copynumber: 3.2 Consensus size: 42
1166330 ACAACGAATT
**
1166340 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGC-ATT
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
*
1166381 TGGAAAATCGCAACGACAACTGTAGACTATCACAACGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
* * * * *
1166423 TGAAAAATCGTAACG-CGATTTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1166464 TGGAAAATC
1 TGGAAAATC
1166473 AAAATCGCAA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 65 0.81
42 15 0.19
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (42 bp):
TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
Found at i:1167470 original size:232 final size:235
Alignment explanation
Indices: 1166654--1168663 Score: 2948
Period size: 232 Copynumber: 8.7 Consensus size: 235
1166644 GTTATTTCTC
1166654 AAAGATTTATTGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
1 AAAGATTTATTGATCATTT-ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
1166719 TACTCTACGAAACCCTAAACCATTTTATTC-ACGTAATCGACTGGAT--TTAAACTCGAAAAAGA
65 TACTCTACGAAACCCTAAACC-TTTTATTCAACGTAATCGACTGGATGATT-AACTCGAAAAAGA
1166781 AATATACTTCGTTAGACAATTTGATAGT-AAAATATGTATCTTATCATTC-TATCATTCTCGATA
128 AATATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATA
1166844 TTTATTATTATCAGTAGATATTTATTAGTTAATATTTTTTATAGA
193 -TTATTATTATCAGTAGATATTTATTAGTT-ATATTTTTTATAGA
*
1166889 AAAGATTTATTGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATATTATTAAA
1 AAAGATTTATTGATCATTT-ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
* *
1166954 TACTCTACGGAATCCTAAACCATTTTTATTCAACGTAATCGACTGGATGATTAACTCGAAAAAG-
65 TACTCTACGAAACCCTAAACC--TTTTATTCAACGTAATCGACTGGATGATTAACTCGAAAAAGA
*
1167018 -A-ATACTTCGTTAGACAA-TTGATAGTAAAAATATGTATCTTATCATTCTTATCACTCTCGATA
128 AATATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATA
* *
1167080 -T-TT-TTATCACTAGAT-GTTATTAG-T-TATTTTTTATAGA
193 TTATTATTATCAGTAGATATTTATTAGTTATATTTTTTATAGA
*
1167117 AAAGATTTATTGATCATTTAATTAATACAATTCAAATACAATGAATTTAGTATTATAGTATTAAA
1 AAAGATTTATTGATCATTT-ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
* * * *
1167182 TACTCTACGAAACCCTAAACCATTTATTCAACAT-ATTGACTGGATGATTAAACCCGAAAAAGAA
65 TACTCTACGAAACCCTAAACCTTTTATTCAACGTAATCGACTGGATGATT-AACTCGAAAAAGAA
*
1167246 ATATACTTCGTTAGACAA-TTGATAGTAAAAATATGTATCTTATCATTCTTATCACTCTCGATAT
129 ATATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATA-
*
1167310 TTATTATTATCACTAGATATTTATTAG-T-TATTTTTTATAGA
193 TTATTATTATCAGTAGATATTTATTAGTTATATTTTTTATAGA
* *
1167351 AAAGATTTATTGATCATTTAATAATACAATTC-AATACAATGAATTTAGTATTATAGTATTAAAT
1 AAAGATTTATTGATCATTTATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAAT
* * *
1167415 ACTCTACGGAACCCTAAACCTTTTATTCAACGTAATTGACTGGATGATTAACCCGAAAAAGAAAT
66 ACTCTACGAAACCCTAAACCTTTTATTCAACGTAATCGACTGGATGATTAACTCGAAAAAGAAAT
1167480 ATACTTCGTTAGACAATTTGATAGTAAAAATATG-------T-A-TC-TATCATTCTCGATATTT
131 ATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATA-TT
1167535 ATTATTATCAGTAGATATTTATTAGTTAATATTTTTTATAG-
195 ATTATTATCAGTAGATATTTATTAGTT-ATATTTTTTATAGA
*
1167576 AAAGATTTATTGATCATTGATTAATACAATTCAAATACAATGAATTTAATA-TATAGTATTAAAT
1 AAAGATTTATTGATCATTTATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAAT
* *
1167640 ACTCTACGAAACCCTAAACCATTTTATTCAACAT-ATCGACTGGAT--TAAACTCGAAAAAGAAA
66 ACTCTACGAAACCCTAAACC-TTTTATTCAACGTAATCGACTGGATGATTAACTCGAAAAAGAAA
*
1167702 TATACTTCGTTACACAATTTGATAGTAAAAATATGTATCTTATCATT-TTATCATTCTCGATATT
130 TATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATATT
*
1167766 ATTATTATAAGTAGATATTTATTAGTTAATATTTTTTATAGA
195 ATTATTATCAGTAGATATTTATTAGTT-ATATTTTTTATAGA
1167808 AAAGATTTATTGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
1 AAAGATTTATTGATCATTT-ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
* * *
1167873 TACTCTACGAAACCCTAATCATTTTATTCAACGTAATCGACTGGATGATTAA-TCG-AAAAGTAA
65 TACTCTACGAAACCCTAAACCTTTTATTCAACGTAATCGACTGGATGATTAACTCGAAAAAGAAA
*
1167936 TATACTTTGTTAGACAA-TTGATAGTAAAAATATGTAT-TTATCATTCTTATCATTCTCGATATT
130 TATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATATT
*
1167999 ATTATTATCAGTAGATA--TATTAGTTAATATTTTTTATAAA
195 ATTATTATCAGTAGATATTTATTAGTT-ATATTTTTTATAGA
*
1168039 AAATATTTA-TGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
1 AAAGATTTATTGATCATTT-ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
* *
1168103 TACTCTACGGAACCCTAAACCATTTATTCAACGTAATCGA-TGGATGATTAAACTCG-AAAAGAA
65 TACTCTACGAAACCCTAAACCTTTTATTCAACGTAATCGACTGGATGATT-AACTCGAAAAAGAA
* * * *
1168166 AAATACTTCGTTAGACAATTTTATAGTAAAAA-ATGCATCTTATCATTCTTATCACTCTCGATAT
129 ATATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATAT
*
1168230 TATTATTATCACTAG--ATTTATTAGTTA-ATTTTTTATAGA
194 TATTATTATCAGTAGATATTTATTAGTTATATTTTTTATAGA
*
1168269 AAAGATTTATTGATCATTTAATTAATACAATTCAAATACAATGAATTTAGTATTATAGTATTAAA
1 AAAGATTTATTGATCATTT-ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
* *
1168334 TACTCTACGGAACCCTAAAACCATTTTATTCAACGTAATCGACTGCATGATTAAAC-CG-AAAAG
65 TACTCTACGAAACCCT-AAACC-TTTTATTCAACGTAATCGACTGGATGATT-AACTCGAAAAAG
*
1168397 -GA-ATACTTCGTTAGACAATTTGATAGT-AAAATA-GTATCTTATCATTCTTATCATTCTCGAT
127 AAATATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGAT
*
1168458 ATTTATTATTATCAGTAGATAATTATTAGTTAATATTTTTTTATAGA
192 A-TTATTATTATCAGTAGATATTTATTAGTT-ATA-TTTTTTATAGA
*
1168505 AAAGATTTATTGGTCATTTGA-TAATACAATTCAAATACAATGAATTTAATATTATAGTA-TAAA
1 AAAGATTTATTGATCATTT-ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
* *
1168568 TACTCTACGAAACCCTAGATCATTTTATTC-ACGTAATCGACTGGATGATTAATCTCGAAAAAGA
65 TACTCTACGAAACCCTA-AACCTTTTATTCAACGTAATCGACTGGATGATTAA-CTCGAAAAAGA
*
1168632 AATATACTTCGTTAGGCAATTTGATAGTAAAA
128 AATATACTTCGTTAGACAATTTGATAGTAAAA
1168664 TATCAACTAC
Statistics
Matches: 1636, Mismatches: 76, Indels: 124
0.89 0.04 0.07
Matches are distributed among these distances:
223 89 0.05
224 3 0.00
225 87 0.05
226 64 0.04
228 95 0.06
229 70 0.04
230 146 0.09
231 223 0.14
232 232 0.14
233 201 0.12
234 152 0.09
235 162 0.10
236 79 0.05
237 19 0.01
238 12 0.01
239 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (235 bp):
AAAGATTTATTGATCATTTATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAAT
ACTCTACGAAACCCTAAACCTTTTATTCAACGTAATCGACTGGATGATTAACTCGAAAAAGAAAT
ATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATATTA
TTATTATCAGTAGATATTTATTAGTTATATTTTTTATAGA
Found at i:1168424 original size:463 final size:475
Alignment explanation
Indices: 1166654--1168663 Score: 3068
Period size: 463 Copynumber: 4.3 Consensus size: 475
1166644 GTTATTTCTC
1166654 AAAGATTTATTGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
1 AAAGATTTATTGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
1166719 TACTCTACGAAACCCTAAACCATTTTATTC-ACGTAATCGACTGGAT--TTAAACTCGAAAAAGA
66 TACTCTACGAAACCCTAAACCATTTTATTCAACGTAATCGACTGGATGATTAAACTCGAAAAAGA
*
1166781 AATATACTTCGTTAGACAATTTGATAGT-AAAATATGTATCTTATCATTC-TATCATTCTCGATA
131 AATATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCACTCTCGATA
* *
1166844 TTTATTATTATCAGTAGATATTTATTAGTTAATATTTTTTATAGAAAAGATTTATTGATCATTTG
196 TTTATTATTATCACTAGA-ATTTATTAGTTAATATTTTTTATAGAAAAGATTTATTGATCATTTA
* *
1166909 ATTAATACAATTCAAATACAATGAATTTAATATTATATTATTAAATACTCTACGGAATCCTAAAC
260 ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAATACTCTACGGAACCCTAAAC
*
1166974 CATTTTTATTCAACGTAATCGACTGGATGATTAACTCGAAAA-AGA-ATACTTCGTTAGACAATT
325 CA-TTTTATTCAACGTAATCGACTGGATGATTAAC-CGAAAAGAAATATACTTCGTTAGACAATT
* * *
1167037 GATAGTAAAAATATGTATCTTATCATTCTTATCACTCTCGATA--T-TT-TTATCACTAGAT-GT
388 GATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATATTTATTATTATCAGTAGATAAT
*
1167097 TATTAG-T--TATTTTTTATAGA
453 TATTAGTTAATATTTTTTATAAA
* *
1167117 AAAGATTTATTGATCATTTAATTAATACAATTCAAATACAATGAATTTAGTATTATAGTATTAAA
1 AAAGATTTATTGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
* * *
1167182 TACTCTACGAAACCCTAAACCA-TTTATTCAACAT-ATTGACTGGATGATTAAACCCGAAAAAGA
66 TACTCTACGAAACCCTAAACCATTTTATTCAACGTAATCGACTGGATGATTAAACTCGAAAAAGA
1167245 AATATACTTCGTTAGACAA-TTGATAGTAAAAATATGTATCTTATCATTCTTATCACTCTCGATA
131 AATATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCACTCTCGATA
1167309 TTTATTATTATCACTAGATATTTATTAG-T--TATTTTTTATAGAAAAGATTTATTGATCATTTA
196 TTTATTATTATCACTAGA-ATTTATTAGTTAATATTTTTTATAGAAAAGATTTATTGATCATTTA
*
1167371 A-TAATACAATTC-AATACAATGAATTTAGTATTATAGTATTAAATACTCTACGGAACCCTAAAC
260 ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAATACTCTACGGAACCCTAAAC
*
1167434 C-TTTTATTCAACGTAATTGACTGGATGATTAACCCGAAAAAGAAATATACTTCGTTAGACAATT
325 CATTTTATTCAACGTAATCGACTGGATGATTAA-CCG-AAAAGAAATATACTTCGTTAGACAA-T
*
1167498 TGATAGTAAAAATATG-------T-A-TC-TATCATTCTCGATATTTATTATTATCAGTAGATAT
387 TGATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATATTTATTATTATCAGTAGATAA
*
1167553 TTATTAGTTAATATTTTTTAT-AG
452 TTATTAGTTAATATTTTTTATAAA
1167576 AAAGATTTATTGATCA-TTGATTAATACAATTCAAATACAATGAATTTAATA-TATAGTATTAAA
1 AAAGATTTATTGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
*
1167639 TACTCTACGAAACCCTAAACCATTTTATTCAACAT-ATCGACT-G--GATTAAACTCGAAAAAGA
66 TACTCTACGAAACCCTAAACCATTTTATTCAACGTAATCGACTGGATGATTAAACTCGAAAAAGA
* *
1167700 AATATACTTCGTTACACAATTTGATAGTAAAAATATGTATCTTATCATT-TTATCATTCTCGATA
131 AATATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCACTCTCGATA
* * *
1167764 -TTATTATTATAAGTAGATATTTATTAGTTAATATTTTTTATAGAAAAGATTTATTGATCATTTG
196 TTTATTATTATCACTAGA-ATTTATTAGTTAATATTTTTTATAGAAAAGATTTATTGATCATTTA
* *
1167828 ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAATACTCTACGAAACCCT-AAT
260 ATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAATACTCTACGGAACCCTAAAC
* * *
1167892 CATTTTATTCAACGTAATCGACTGGATGATTAATCGAAAAGTAATATACTTTGTTAGACAATTGA
325 CATTTTATTCAACGTAATCGACTGGATGATTAACCGAAAAGAAATATACTTCGTTAGACAATTGA
1167957 TAGTAAAAATATGTAT-TTATCATTCTTATCATTCTCGATA-TTATTATTATCAGTAGAT-A-TA
390 TAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATATTTATTATTATCAGTAGATAATTA
1168018 TTAGTTAATATTTTTTATAAA
455 TTAGTTAATATTTTTTATAAA
*
1168039 AAATATTTA-TGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
1 AAAGATTTATTGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
*
1168103 TACTCTACGGAACCCTAAACCA-TTTATTCAACGTAATCGA-TGGATGATTAAACTCG-AAAAGA
66 TACTCTACGAAACCCTAAACCATTTTATTCAACGTAATCGACTGGATGATTAAACTCGAAAAAGA
* * *
1168165 AAAATACTTCGTTAGACAATTTTATAGTAAAAA-ATGCATCTTATCATTCTTATCACTCTCGATA
131 AATATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCACTCTCGATA
1168229 -TTATTATTATCACTAG-ATTTATTAGTT-A-ATTTTTTATAGAAAAGATTTATTGATCATTTAA
196 TTTATTATTATCACTAGAATTTATTAGTTAATATTTTTTATAGAAAAGATTTATTGATCATTTAA
*
1168290 TTAATACAATTCAAATACAATGAATTTAGTATTATAGTATTAAATACTCTACGGAACCCTAAAAC
261 TTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAATACTCTACGGAACCCT-AAAC
* *
1168355 CATTTTATTCAACGTAATCGACTGCATGATTAAACCGAAAAG-GA-ATACTTCGTTAGACAATTT
325 CATTTTATTCAACGTAATCGACTGGATGATT-AACCGAAAAGAAATATACTTCGTTAGACAA-TT
1168418 GATAGT-AAAATA-GTATCTTATCATTCTTATCATTCTCGATATTTATTATTATCAGTAGATAAT
388 GATAGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATATTTATTATTATCAGTAGATAAT
*
1168481 TATTAGTTAATATTTTTTTATAGA
453 TATTAGTTAATA-TTTTTTATAAA
*
1168505 AAAGATTTATTGGTCATTTGA-TAATACAATTCAAATACAATGAATTTAATATTATAGTA-TAAA
1 AAAGATTTATTGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
* * *
1168568 TACTCTACGAAACCCTAGATCATTTTATTC-ACGTAATCGACTGGATGATTAATCTCGAAAAAGA
66 TACTCTACGAAACCCTAAACCATTTTATTCAACGTAATCGACTGGATGATTAAACTCGAAAAAGA
*
1168632 AATATACTTCGTTAGGCAATTTGATAGTAAAA
131 AATATACTTCGTTAGACAATTTGATAGTAAAA
1168664 TATCAACTAC
Statistics
Matches: 1427, Mismatches: 64, Indels: 108
0.89 0.04 0.07
Matches are distributed among these distances:
452 13 0.01
453 2 0.00
454 27 0.02
455 53 0.04
456 57 0.04
457 98 0.07
458 100 0.07
459 96 0.07
460 61 0.04
461 121 0.08
462 140 0.10
463 223 0.16
464 139 0.10
465 163 0.11
466 89 0.06
467 45 0.03
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (475 bp):
AAAGATTTATTGATCATTTGATTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAA
TACTCTACGAAACCCTAAACCATTTTATTCAACGTAATCGACTGGATGATTAAACTCGAAAAAGA
AATATACTTCGTTAGACAATTTGATAGTAAAAATATGTATCTTATCATTCTTATCACTCTCGATA
TTTATTATTATCACTAGAATTTATTAGTTAATATTTTTTATAGAAAAGATTTATTGATCATTTAA
TTAATACAATTCAAATACAATGAATTTAATATTATAGTATTAAATACTCTACGGAACCCTAAACC
ATTTTATTCAACGTAATCGACTGGATGATTAACCGAAAAGAAATATACTTCGTTAGACAATTGAT
AGTAAAAATATGTATCTTATCATTCTTATCATTCTCGATATTTATTATTATCAGTAGATAATTAT
TAGTTAATATTTTTTATAAA
Found at i:1169582 original size:20 final size:20
Alignment explanation
Indices: 1169557--1169595 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1169547 TATAAAAAAT
1169557 TATTTTTATTAAATTTTTAG
1 TATTTTTATTAAATTTTTAG
*
1169577 TATTTTTATTTAATTTTTA
1 TATTTTTATTAAATTTTTA
1169596 AATAATTATG
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:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
TATTTTTATTAAATTTTTAG
Found at i:1170689 original size:166 final size:162
Alignment explanation
Indices: 1170372--1170699 Score: 620
Period size: 166 Copynumber: 2.0 Consensus size: 162
1170362 ATAGTTTCTA
1170372 TATATATTTTCATGCATTTCGCTTCATAAAGAATATGAGAAACAGGAACCGTTTCATTAAAGACA
1 TATATATTTTCATGCATTTCGCTTCATAAAGAATATGAGAAACAGGAACCGTTTCATTAAAGACA
1170437 AAAAAATTATAAAAATGGCATGTATTATTAGTCCCATTTCAAGGGCACTGCACCTTCCGAAGGCC
66 AAAAAATTATAAAAATGGCATGTATTATTAGTCCCATTTCAAGGGCACTGCACCTTCCGAAGGCC
1170502 TACAGTCTCATTCTCACACAATGTTAATCTCC
131 TACAGTCTCATTCTCACACAATGTTAATCTCC
1170534 TATATATTTTCATGCATTTCGCTTCATAAAGAATATGAGAAACAGGAACCGTTTCATATAAAGAC
1 TATATATTTTCATGCATTTCGCTTCATAAAGAATATGAGAAACAGGAACCGTTTCAT-TAAAGAC
1170599 AAAAAAATTATAAAAAATGGCATGTTATTATTACGTCCCATTTCAAGGGCACTGCACCTTCCGAA
65 AAAAAAATTAT-AAAAATGGCATG-TATTATTA-GTCCCATTTCAAGGGCACTGCACCTTCCGAA
1170664 GGCCTACAGTCTCATTCTCACACAATGTTAATCTCC
127 GGCCTACAGTCTCATTCTCACACAATGTTAATCTCC
1170700 CGAAGAAAAC
Statistics
Matches: 162, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
162 57 0.35
163 18 0.11
164 12 0.07
165 8 0.05
166 67 0.41
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.30
Consensus pattern (162 bp):
TATATATTTTCATGCATTTCGCTTCATAAAGAATATGAGAAACAGGAACCGTTTCATTAAAGACA
AAAAAATTATAAAAATGGCATGTATTATTAGTCCCATTTCAAGGGCACTGCACCTTCCGAAGGCC
TACAGTCTCATTCTCACACAATGTTAATCTCC
Found at i:1175333 original size:263 final size:264
Alignment explanation
Indices: 1174864--1175391 Score: 1040
Period size: 263 Copynumber: 2.0 Consensus size: 264
1174854 TCTTCAAATT
1174864 GGAAATAAAACCTATAATGGTAACTGGTAAGTATATATGATGACACATTGATAAAGAAAACATAG
1 GGAAATAAAACCTATAATGGTAACTGGTAAG-ATATATGATGACACATTGATAAAGAAAACATAG
1174929 AATTCTTTGACAACAGATTGGATAAAGAAAAGAAGGGTACGGATTGCCTTGAAGCAGTGGTGCTC
65 AATTCTTTGACAACAGATTGGATAAAGAAAAGAAGGGTACGGATTGCCTTGAAGCAGTGGTGCTC
1174994 GAATGATCTCTTTGAATATTTCCAACAGAAGAAGCCGATGAAGACTTGTCATGATCAATGGCATT
130 GAATGATCTCTTTGAATATTTCCAACAGAAGAAGCCGATGAAGACTTGTCATGATCAATGGCATT
1175059 GGAAGGTGGTATATGCGTGTTGGCAAGTGCTTTGGAGAGTTCCATTGCTGACAGACTCCATGATC
195 GGAAGGTGGTATATGCGTGTTGGCAAGTGCTTTGGAGAGTTCCATTGCTGACAGACTCCATGATC
1175124 TGGCA
260 TGGCA
1175129 GGAAATAAAACCTATAATGGTAACTGGTAAG-TATATGATGACACATTGATAAAGAAAACATAGA
1 GGAAATAAAACCTATAATGGTAACTGGTAAGATATATGATGACACATTGATAAAGAAAACATAGA
1175193 ATTCTTTGACAACAGATTGGATAAAGAAAAGAAGGGTACGGATTGCCTTGAAGCAGTGGTGCTCG
66 ATTCTTTGACAACAGATTGGATAAAGAAAAGAAGGGTACGGATTGCCTTGAAGCAGTGGTGCTCG
1175258 AATGATCTCTTTGAATATTTCCAACAGAAGAAGCCGATGAAGACTTGTCATGATCAATGGCATTG
131 AATGATCTCTTTGAATATTTCCAACAGAAGAAGCCGATGAAGACTTGTCATGATCAATGGCATTG
1175323 GAAGGTGGTATATGCGTGTTGGCAAGTGCTTTGGAGAGTTCCATTGCTGACAGACTCCATGATCT
196 GAAGGTGGTATATGCGTGTTGGCAAGTGCTTTGGAGAGTTCCATTGCTGACAGACTCCATGATCT
1175388 GGCA
261 GGCA
1175392 AGATAGTCCA
Statistics
Matches: 263, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
263 232 0.88
265 31 0.12
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (264 bp):
GGAAATAAAACCTATAATGGTAACTGGTAAGATATATGATGACACATTGATAAAGAAAACATAGA
ATTCTTTGACAACAGATTGGATAAAGAAAAGAAGGGTACGGATTGCCTTGAAGCAGTGGTGCTCG
AATGATCTCTTTGAATATTTCCAACAGAAGAAGCCGATGAAGACTTGTCATGATCAATGGCATTG
GAAGGTGGTATATGCGTGTTGGCAAGTGCTTTGGAGAGTTCCATTGCTGACAGACTCCATGATCT
GGCA
Found at i:1176601 original size:21 final size:21
Alignment explanation
Indices: 1176577--1176618 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1176567 AATTAATATA
*
1176577 TTGAGTTAAACAGTGTTTGAT
1 TTGAGTTAAAAAGTGTTTGAT
* *
1176598 TTGATTTAAAAATTGTTTGAT
1 TTGAGTTAAAAAGTGTTTGAT
1176619 GTGTATTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (21 bp):
TTGAGTTAAAAAGTGTTTGAT
Found at i:1189447 original size:19 final size:19
Alignment explanation
Indices: 1189395--1189441 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1189385 TTCGAGAATG
*
1189395 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAACA
*
1189414 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACA
1189433 AAAATCGCA
1 AAAATCGCA
1189442 TTGCGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.51, C:0.26, G:0.15, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:1189507 original size:33 final size:34
Alignment explanation
Indices: 1189459--1189524 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
1189449 TTTCATTTCG
**
1189459 CGTTGCGATTTTCATTT-CGCATTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCATTGCGATTCTCT
*
1189492 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCATTGCGATTCTC
1189525 ATTATCTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 15 0.52
34 14 0.48
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.41
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCATTGCGATTCTCT
Found at i:1189526 original size:20 final size:19
Alignment explanation
Indices: 1189437--1189549 Score: 110
Period size: 19 Copynumber: 6.1 Consensus size: 19
1189427 GAAACCAAAA
*
1189437 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1189456 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1189475 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1189489 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1189508 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1189528 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1189548 TC
1 TC
1189550 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 3 0.04
19 31 0.40
20 31 0.40
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1191719 original size:21 final size:21
Alignment explanation
Indices: 1191695--1191761 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1191685 TCATTCCACG
1191695 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1191716 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1191737 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1191758 AGAG
1 AGAG
1191762 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1193278 original size:14 final size:14
Alignment explanation
Indices: 1193259--1193315 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1193249 ACGAAATGAA
1193259 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1193273 AATCGCAACTCGAAATGAA
1 AATCGCAA--CG--A-GAG
1193292 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1193306 AATCGCAACG
1 AATCGCAACG
1193316 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1193287 original size:33 final size:33
Alignment explanation
Indices: 1193241--1193331 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
1193231 AAAAAGTACT
1193241 ATCGCAA-TACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACT-CGAAATGAAAATCGCAACGAGAGA
1193274 ATCGCAACTCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACTCGAAATGAAAATCGCAACGAGAGA
* * *
1193307 ATCGCAACGCGAAATTAAATTCGCA
1 ATCGCAACTCGAAATGAAAATCGCA
1193332 TTGCGATTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.98
34 1 0.02
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.14
Consensus pattern (33 bp):
ATCGCAACTCGAAATGAAAATCGCAACGAGAGA
Found at i:1193300 original size:19 final size:18
Alignment explanation
Indices: 1193241--1193299 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
1193231 AAAAAGTACT
1193241 ATCGCAATACGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
*
1193260 ATCGCAA-CG--A-GAGA
1 ATCGCAATCGAAATGAAA
1193274 ATCGCAACTCGAAATGAAA
1 ATCGCAA-TCGAAATGAAA
1193293 ATCGCAA
1 ATCGCAA
1193300 CGAGAGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (18 bp):
ATCGCAATCGAAATGAAA
Found at i:1193363 original size:33 final size:31
Alignment explanation
Indices: 1193326--1193436 Score: 159
Period size: 33 Copynumber: 3.4 Consensus size: 31
1193316 CGAAATTAAA
1193326 TTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATT--CTCGTTGCGATTTTCAT
*
1193359 TTCGCATTGCGAAATTCGCGTTGCGATTTTCAT
1 TTCGCATTGCG--ATTCTCGTTGCGATTTTCAT
1193392 TTCGCATTGCGATTATCTCGTTGCGATTTTCAT
1 TTCGCATTGCGA-T-TCTCGTTGCGATTTTCAT
1193425 TTCGCATTGCGA
1 TTCGCATTGCGA
1193437 CAGTAATTTC
Statistics
Matches: 72, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
31 1 0.01
32 1 0.01
33 67 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.41
Consensus pattern (31 bp):
TTCGCATTGCGATTCTCGTTGCGATTTTCAT
Found at i:1193364 original size:66 final size:66
Alignment explanation
Indices: 1193294--1193430 Score: 150
Period size: 66 Copynumber: 2.1 Consensus size: 66
1193284 GAAATGAAAA
*
1193294 TCGCAACGAGAGAA-TCGCAACGCGAAATTAAATTCGCATTGCGATTCCCTCGTTGCGATTTTCA
1 TCGCAACGAGA-AATTCGCAACGCGAAATTAAATTCGCATTGCGATTACCTCGTTGCGATTTTCA
1193358 TT
65 TT
** * *** ** * * *
1193360 TCGCATTGCGAAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCAT
1 TCGCAACGAGAAATTCGCAACGCGAAATTAAATTCGCATTGCGATTACCTCGTTGCGATTTTCAT
1193425 T
66 T
1193426 TCGCA
1 TCGCA
1193431 TTGCGACAGT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
65 2 0.03
66 56 0.97
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (66 bp):
TCGCAACGAGAAATTCGCAACGCGAAATTAAATTCGCATTGCGATTACCTCGTTGCGATTTTCAT
T
Found at i:1193370 original size:19 final size:19
Alignment explanation
Indices: 1193346--1193436 Score: 85
Period size: 19 Copynumber: 5.3 Consensus size: 19
1193336 GATTCCCTCG
1193346 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1193365 TTGCGA-----AATTCGCG
1 TTGCGATTTTCATTTCGCA
1193379 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1193398 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
1193412 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1193431 TTGCGA
1 TTGCGA
1193437 CAGTAATTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
14 18 0.32
16 7 0.12
17 7 0.12
19 24 0.43
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Done.