Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 58 of 190
Found at i:16516046 original size:21 final size:21
Alignment explanation
Indices: 16516020--16516068 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
16516010 GTTTCTAATA
*
16516020 TCACCGTTACAGT-ATCCAATC
1 TCACCGCTACAGTAAT-CAATC
*
16516041 TCACCGCTACAGTAATTAATC
1 TCACCGCTACAGTAATCAATC
16516062 TCACCGC
1 TCACCGC
16516069 CACCGCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.35, G:0.10, T:0.27
Consensus pattern (21 bp):
TCACCGCTACAGTAATCAATC
Found at i:16517244 original size:30 final size:30
Alignment explanation
Indices: 16517208--16517267 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
16517198 AGTCTGGTGT
16517208 TAGTTTTTATTTGTATTGGGTAGTTTGACA
1 TAGTTTTTATTTGTATTGGGTAGTTTGACA
16517238 TAGTTTTTATTTGTATTGGGTAGTTTGACA
1 TAGTTTTTATTTGTATTGGGTAGTTTGACA
16517268 GTGGTTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.53
Consensus pattern (30 bp):
TAGTTTTTATTTGTATTGGGTAGTTTGACA
Found at i:16520552 original size:44 final size:44
Alignment explanation
Indices: 16520501--16520601 Score: 127
Period size: 43 Copynumber: 2.3 Consensus size: 44
16520491 AGCAGCGTTT
*
16520501 GTCGCTAAAAGTCAAT-TTTTTATAGTGGCGTTTGTGGTAGAAGC
1 GTCGCTAAAAGTCAATGATTTT-TAGTGGCGTTTGTGGTAGAAGC
* *
16520545 GTCGCTAAATGTC-ATGATTTTTAGTGGCGTTTGTGGTATAAGC
1 GTCGCTAAAAGTCAATGATTTTTAGTGGCGTTTGTGGTAGAAGC
*
16520588 G-CTGCTAAAGGTCA
1 GTC-GCTAAAAGTCA
16520602 TCATCTTTAG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.02
43 33 0.66
44 16 0.32
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.36
Consensus pattern (44 bp):
GTCGCTAAAAGTCAATGATTTTTAGTGGCGTTTGTGGTAGAAGC
Found at i:16520619 original size:43 final size:43
Alignment explanation
Indices: 16520529--16520619 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
16520519 TTTATAGTGG
* * * * *
16520529 CGTTTGTGGTAGAAGCGTCGCTAAATGTCATGATTTTTAGTGG
1 CGTTTGTGGTAGAAGCGTCGCTAAAGGTCATCATCTTTAGCGA
*
16520572 CGTTTGTGGTATAAGCG-CTGCTAAAGGTCATCATCTTTAGCGA
1 CGTTTGTGGTAGAAGCGTC-GCTAAAGGTCATCATCTTTAGCGA
16520615 CGTTT
1 CGTTT
16520620 TTTTCACATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 40 0.98
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.36
Consensus pattern (43 bp):
CGTTTGTGGTAGAAGCGTCGCTAAAGGTCATCATCTTTAGCGA
Found at i:16520707 original size:22 final size:22
Alignment explanation
Indices: 16520682--16520723 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
16520672 GGTGCTTGTT
16520682 AAAGCGCCGCTAAAAGTCTAAA
1 AAAGCGCCGCTAAAAGTCTAAA
16520704 AAAGCGCCGCTAAAAGTCTA
1 AAAGCGCCGCTAAAAGTCTA
16520724 TTTTCCTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.14
Consensus pattern (22 bp):
AAAGCGCCGCTAAAAGTCTAAA
Found at i:16524075 original size:7 final size:7
Alignment explanation
Indices: 16524063--16524088 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16524053 AAAGTAAGTC
16524063 ATTTTCA
1 ATTTTCA
16524070 ATTTTCA
1 ATTTTCA
16524077 ATTTTCA
1 ATTTTCA
16524084 ATTTT
1 ATTTT
16524089 GAAACATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTCA
Found at i:16533928 original size:20 final size:21
Alignment explanation
Indices: 16533897--16533935 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16533887 TAATTGAATA
*
16533897 AATAATAATACATGATAAAGG
1 AATAATAATACATAATAAAGG
16533918 AATAA-AATACATAATAAA
1 AATAATAATACATAATAAA
16533936 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (21 bp):
AATAATAATACATAATAAAGG
Found at i:16535660 original size:44 final size:44
Alignment explanation
Indices: 16535559--16535679 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 44
16535549 ACTTGATACT
* * * *
16535559 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCTACTACAAATTCAGAGAGATAAGATCTATTAATTCA
* *
16535603 AT-TCGCTCCACTACAAATTCAGAGAGATAGGAT-TATTGAATTCA
1 ATCT-GCTCTACTACAAATTCAGAGAGATAAGATCTATT-AATTCA
**
16535647 ATCTGCTCTACTACAACGTCA-AGGAGATAAGAT
1 ATCTGCTCTACTACAAATTCAGA-GAGATAAGAT
16535680 TCGCTTCTTC
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.10
44 56 0.89
45 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (44 bp):
ATCTGCTCTACTACAAATTCAGAGAGATAAGATCTATTAATTCA
Found at i:16536012 original size:128 final size:128
Alignment explanation
Indices: 16535866--16536123 Score: 358
Period size: 128 Copynumber: 2.0 Consensus size: 128
16535856 TTCTTCTGTT
* * **
16535866 TGCTCCACTACTGCTTAGGGAGATAAGA-CTTGTAATTTCCAACCTATTCCACTGCTGGTCAAGG
1 TGCTCCACTACTGCTTAGGGAGACAAGATC-TGCAATTTCCAACCTATTCCACTGCTGACCAAGG
* * ** *
16535930 ACATAGGACTTGTGGCTTGAATCTA-TTTCTCTACTCCTGGGGATAAGATTTGCCATCTTCGATC
65 ACATAGGACTTGTGGCTTGAATCTACTTCCT-TACACCTGAAGATAAGATTCGCCATCTTCGATC
* *
16535994 TGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGACCAGGGA
1 TGCTCCACTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGACCAAGGA
* * *
16536059 TATAGGACTTGTGGCTTGAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTTCGATC
66 CATAGGACTTGTGGCTTGAATCTACTTCCTTACACCTGAAGATAAGATTCGCCATCTTCGATC
16536122 TG
1 TG
16536124 TTTCACTGTC
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
128 109 0.96
129 5 0.04
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (128 bp):
TGCTCCACTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGACCAAGGA
CATAGGACTTGTGGCTTGAATCTACTTCCTTACACCTGAAGATAAGATTCGCCATCTTCGATC
Found at i:16536322 original size:87 final size:88
Alignment explanation
Indices: 16536119--16536338 Score: 289
Period size: 87 Copynumber: 2.5 Consensus size: 88
16536109 GCCATCTTCG
* * * * *
16536119 ATCTGTTTCACTGTCGATGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCAGCTGCAACCA
1 ATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCAGCTACAACCA
* *
16536184 ATGGAGGCAAGGCTTTGTTTTCG
66 ATGGAGGCAAGGATTTGTTTTCA
* * * **
16536207 ATGTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCA-CTACAACTG
1 ATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCAGCTACAACCA
16536271 ATGGAGGCAAGGATTTGTTTTCA
66 ATGGAGGCAAGGATTTGTTTTCA
* * * *
16536294 ATCTGCTTCGCTGTCAATGCGGGAAGGCAAGGTCTGCTATTTTCA
1 ATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCA
16536339 CTGATCTGTT
Statistics
Matches: 113, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
87 65 0.58
88 48 0.42
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.29
Consensus pattern (88 bp):
ATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCAGCTACAACCA
ATGGAGGCAAGGATTTGTTTTCA
Found at i:16537363 original size:20 final size:21
Alignment explanation
Indices: 16537332--16537370 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16537322 TAATTGATTA
*
16537332 AATAATAATACATGATAAAGG
1 AATAATAATACATAATAAAGG
16537353 AATAA-AATACATAATAAA
1 AATAATAATACATAATAAA
16537371 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (21 bp):
AATAATAATACATAATAAAGG
Found at i:16537435 original size:12 final size:12
Alignment explanation
Indices: 16537420--16537457 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
16537410 ATAACATCTA
16537420 TAATAATAGTAG
1 TAATAATAGTAG
*
16537432 TAATAATAGTAA
1 TAATAATAGTAG
*
16537444 TAATAATAATAG
1 TAATAATAGTAG
16537456 TA
1 TA
16537458 TTATAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (12 bp):
TAATAATAGTAG
Found at i:16537472 original size:24 final size:26
Alignment explanation
Indices: 16537419--16537478 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 26
16537409 AATAACATCT
*
16537419 ATAATAATAGTAGTAATAATAGTAATA
1 ATAATAATAGTAGTAATAATA-TAAAA
*
16537446 ATAATAATAGTA-TTATAAT-TAAAA
1 ATAATAATAGTAGTAATAATATAAAA
*
16537470 ATAAGAATA
1 ATAATAATA
16537479 AAAAACAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.40
26 6 0.20
27 12 0.40
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (26 bp):
ATAATAATAGTAGTAATAATATAAAA
Found at i:16540679 original size:50 final size:50
Alignment explanation
Indices: 16540618--16541254 Score: 382
Period size: 50 Copynumber: 12.7 Consensus size: 50
16540608 CGCAACTTTT
* * * *
16540618 GGGAAGTAAGATTCGCCATTGTAGCTTCAATCTTTTTAACTGCACCGCCA
1 GGGAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAACGCCG
* * * * ** *
16540668 GGGAAGTAAGATTCGCCTTTATGGCAGCTTTAATCCTTTTAGCTAAAATGCCG
1 GGGAAGTAAGATTCGCCATTGT-G--GCTTTAATCTTTTTAACTGCAACGCCG
** * * ** *
16540721 GGGAAGCGAGATTCACCGA-TGTGGCTTTAATCTGTTCCACTGC-ACTGCCA
1 GGGAAGTAAGATTCGCC-ATTGTGGCTTTAATCTTTTTAACTGCAAC-GCCG
** * * **
16540771 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTCTTTAACTGCAACGTTG
1 GGGAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAACGCCG
* * * * ** * *
16540821 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATCGCCT
1 GGGAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAACGCCG
* * * ** * * **
16540871 GAGAGGTAAGATTCACTGTTGTAGCTTTAATCTTTTTGAACTGCAATGTTG
1 GGGAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTT-AACTGCAACGCCG
* * * ** ** * *
16540922 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGCTCCACTGCATCGCCT
1 GGGAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAACGCCG
* ** * * * * *
16540972 GGGAGGTAAGATTCGCTGTTGTAGCTTTAATCTCTTTAACTGTAATGTCG
1 GGGAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAACGCCG
* ** * ** * *
16541022 GGGAAGCAAGATTCAGGGA-TGTGGCTTTAATCTGTTCCACTGCATCGCCA
1 GGGAAGTAAGATTC-GCCATTGTGGCTTTAATCTTTTTAACTGCAACGCCG
* * * * * *
16541072 GGGAAGTAACACTCGCCGTTGTGGCTTTAGTCTTTTTAACTGCAATGTCG
1 GGGAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAACGCCG
* * * *** *
16541122 GGGAAGCAAGATTCACCATTGTGGCTTTAATCTATTCCGCTGCATCGCC-
1 GGGAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAACGCCG
* ** * * * *
16541171 TGGAATGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGTAATGTCG
1 GGGAA-GTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAACGCCG
* *
16541222 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
1 GGGAAGTAAGATTCGCCATTGTGGCTTTAATCT
16541255 ATTCCACTAC
Statistics
Matches: 419, Mismatches: 156, Indels: 24
0.70 0.26 0.04
Matches are distributed among these distances:
49 6 0.01
50 336 0.80
51 41 0.10
52 1 0.00
53 35 0.08
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTTAACTGCAACGCCG
Found at i:16540843 original size:100 final size:100
Alignment explanation
Indices: 16540618--16541262 Score: 774
Period size: 100 Copynumber: 6.4 Consensus size: 100
16540608 CGCAACTTTT
* * * * * * ** *
16540618 GGGAAGTAAGATTCGCCATTGTAGCTTCAATCTTTTTAACTGCACCGCCAGGGAAGTAAGATTCG
1 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATCGCCAGGGAAGTAAGATTCG
* * * ** *
16540683 CCTTTATGGCAGCTTTAATC-CTTTTAGCTAAAATGCCG
66 -CTGT-T-GTAGCTTTAATCTC-TTTAACTGCAATGTCG
* *
16540721 GGGAAGCGAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCA-CTGCCAGGGAAGTAAGATTC
1 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATC-GCCAGGGAAGTAAGATTC
* *
16540785 GCTGTTGTAGCTTTAATCTCTTTAACTGCAACGTTG
65 GCTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
* * * *
16540821 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATCGCCTGAGAGGTAAGATTCA
1 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATCGCCAGGGAAGTAAGATTCG
* *
16540886 CTGTTGTAGCTTTAATCTTTTTGAACTGCAATGTTG
66 CTGTTGTAGCTTTAATCTCTTT-AACTGCAATGTCG
* * *
16540922 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGCTCCACTGCATCGCCTGGGAGGTAAGATTCG
1 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATCGCCAGGGAAGTAAGATTCG
*
16540987 CTGTTGTAGCTTTAATCTCTTTAACTGTAATGTCG
66 CTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
*** * *
16541022 GGGAAGCAAGATTCAGGGATGTGGCTTTAATCTGTTCCACTGCATCGCCAGGGAAGTAACACTCG
1 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATCGCCAGGGAAGTAAGATTCG
* * * *
16541087 CCGTTGTGGCTTTAGTCTTTTTAACTGCAATGTCG
66 CTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
* * * *
16541122 GGGAAGCAAGATTCACCATTGTGGCTTTAATCTATTCCGCTGCATCGCC-TGGAATGTAAGATTC
1 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATCGCCAGGGAA-GTAAGATTC
* *
16541186 GCTGTTGTAGCTTTAATCTTTTTAACTGTAATGTCG
65 GCTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
* ** *
16541222 GGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTATTCCACT
1 GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACT
16541263 ACACCGCTTG
Statistics
Matches: 476, Mismatches: 61, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
99 4 0.01
100 317 0.67
101 98 0.21
102 4 0.01
103 53 0.11
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (100 bp):
GGGAAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATCGCCAGGGAAGTAAGATTCG
CTGTTGTAGCTTTAATCTCTTTAACTGCAATGTCG
Found at i:16541359 original size:44 final size:44
Alignment explanation
Indices: 16541309--16541560 Score: 179
Period size: 44 Copynumber: 5.5 Consensus size: 44
16541299 CTATTCCACC
*
16541309 GTAATCTCAGGGAAATAAGATTACTGGCTTCAATCTGCTCCGCT
1 GTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGCTCCGCT
* * *
16541353 GTAATCTCAGGGAGATAAGATTTCTGGCTTTAATCTGATGCGATCTACTCTGTT
1 GTAATCTCAGGGAGATAAGATTACTGGCTTCAATC---T--G--CT-C-C-GCT
** * *** * *
16541407 GTAA-CTTCAAAGAGATAAGA-TCCTTTATTTTAAT-TCGCTCCACT
1 GTAATC-TCAGGGAGATAAGATTAC-TGGCTTCAATCT-GCTCCGCT
* * * *
16541451 GTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGTT
1 GTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGCTCCGCT
* * *
16541495 GTAAACTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACT
1 GTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGCTCCGCT
16541539 GTAA-CATCAGGGAGATAAGATT
1 GTAATC-TCAGGGAGATAAGATT
16541561 CACCTTTTCC
Statistics
Matches: 162, Mismatches: 30, Indels: 32
0.72 0.13 0.14
Matches are distributed among these distances:
43 1 0.01
44 116 0.72
45 5 0.03
46 1 0.01
47 3 0.02
49 3 0.02
50 1 0.01
51 2 0.01
52 1 0.01
53 4 0.02
54 25 0.15
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (44 bp):
GTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGCTCCGCT
Found at i:16543907 original size:8 final size:8
Alignment explanation
Indices: 16543889--16543923 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
16543879 TCATCTAGAT
16543889 TTTTCTT-
1 TTTTCTTC
16543896 TTTTCTTC
1 TTTTCTTC
16543904 TTTTCTTC
1 TTTTCTTC
16543912 TTTTCTTC
1 TTTTCTTC
16543920 TTTT
1 TTTT
16543924 TCTCTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTCTTC
Found at i:16544050 original size:13 final size:13
Alignment explanation
Indices: 16544032--16544060 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16544022 CGTTATCCCT
16544032 TTTAAGAATCTTC
1 TTTAAGAATCTTC
16544045 TTTAAGAATCTTC
1 TTTAAGAATCTTC
16544058 TTT
1 TTT
16544061 GATATCGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (13 bp):
TTTAAGAATCTTC
Found at i:16550185 original size:26 final size:26
Alignment explanation
Indices: 16550149--16550201 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
16550139 GGGTGAGTTT
*
16550149 TCTCTTTGATTTCAATAAAGAAACTG
1 TCTCTTTGATTTCAACAAAGAAACTG
16550175 TCTCTTTGATTTCAACAAAGAAACTG
1 TCTCTTTGATTTCAACAAAGAAACTG
16550201 T
1 T
16550202 GATTTTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (26 bp):
TCTCTTTGATTTCAACAAAGAAACTG
Found at i:16551578 original size:18 final size:17
Alignment explanation
Indices: 16551555--16551589 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16551545 TTTATATTAG
*
16551555 CAATTCATATCATCATTT
1 CAATTCAAAT-ATCATTT
16551573 CAATTCAAATATCATTT
1 CAATTCAAATATCATTT
16551590 ATCCAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (17 bp):
CAATTCAAATATCATTT
Found at i:16564955 original size:21 final size:21
Alignment explanation
Indices: 16564929--16564982 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
16564919 ACTATAGGGT
* *
16564929 GTGTCACGACTTCGAACTCTA
1 GTGTCACGACATCGAACCCTA
*
16564950 GTGTCATGACATCGAACCCTA
1 GTGTCACGACATCGAACCCTA
16564971 GTGTCACGACAT
1 GTGTCACGACAT
16564983 AAGCAATCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (21 bp):
GTGTCACGACATCGAACCCTA
Found at i:16567819 original size:23 final size:24
Alignment explanation
Indices: 16567775--16567819 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
16567765 AAAATCATAC
*
16567775 CCATCCAGCCTCTACACACCATCT
1 CCATCCAACCTCTACACACCATCT
*
16567799 CCATCCAACC-CTACACTCCAT
1 CCATCCAACCTCTACACACCAT
16567820 GTGGAGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.27, C:0.51, G:0.02, T:0.20
Consensus pattern (24 bp):
CCATCCAACCTCTACACACCATCT
Found at i:16575349 original size:38 final size:38
Alignment explanation
Indices: 16575307--16575389 Score: 145
Period size: 35 Copynumber: 2.3 Consensus size: 38
16575297 TTGGGATCTT
16575307 TTTCCTTTTATTAATAACCTATAATAAAAAGGAAATAA
1 TTTCCTTTTATTAATAACCTATAATAAAAAGGAAATAA
16575345 TTTCC--TT-TTAATAACCTATAATAAAAAGGAAATAA
1 TTTCCTTTTATTAATAACCTATAATAAAAAGGAAATAA
16575380 TTTCCTTTTA
1 TTTCCTTTTA
16575390 CTTTTTTGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
35 33 0.79
36 2 0.05
37 2 0.05
38 5 0.12
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (38 bp):
TTTCCTTTTATTAATAACCTATAATAAAAAGGAAATAA
Found at i:16575361 original size:35 final size:35
Alignment explanation
Indices: 16575317--16575389 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
16575307 TTTCCTTTTA
16575317 TTAATAACCTATAATAAAAAGGAAATAATTTCCTT
1 TTAATAACCTATAATAAAAAGGAAATAATTTCCTT
16575352 TTAATAACCTATAATAAAAAGGAAATAATTTCCTT
1 TTAATAACCTATAATAAAAAGGAAATAATTTCCTT
16575387 TTA
1 TTA
16575390 CTTTTTTGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (35 bp):
TTAATAACCTATAATAAAAAGGAAATAATTTCCTT
Found at i:16575543 original size:17 final size:17
Alignment explanation
Indices: 16575500--16575543 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
16575490 ATCCGCAAGG
*
16575500 CAATACTATTCGCCAAA
1 CAATACTGTTCGCCAAA
* *
16575517 CGATACTGTTCGCCAAC
1 CAATACTGTTCGCCAAA
*
16575534 CAATATTGTT
1 CAATACTGTT
16575544 TCCCAAGTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (17 bp):
CAATACTGTTCGCCAAA
Found at i:16580597 original size:27 final size:27
Alignment explanation
Indices: 16580566--16580622 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
16580556 GACGGATTCA
16580566 AAAGATATTTTCAAATCTATTTTAACT
1 AAAGATATTTTCAAATCTATTTTAACT
* *
16580593 AAAGATATTTTCGAATCTATTTTAATT
1 AAAGATATTTTCAAATCTATTTTAACT
16580620 AAA
1 AAA
16580623 TGTTTTTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (27 bp):
AAAGATATTTTCAAATCTATTTTAACT
Found at i:16582512 original size:29 final size:29
Alignment explanation
Indices: 16582453--16582512 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
16582443 TACGATTTAA
* *
16582453 TGTGTAATTATATATATAAATTTTAATTT
1 TGTGTAATTATATAAATAAATTTTAAGTT
*
16582482 TGTGTAATTTTATAAATAAAATTTT-AGTT
1 TGTGTAATTATATAAAT-AAATTTTAAGTT
16582511 TG
1 TG
16582513 ATCAAATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (29 bp):
TGTGTAATTATATAAATAAATTTTAAGTT
Found at i:16594678 original size:134 final size:133
Alignment explanation
Indices: 16594519--16594799 Score: 348
Period size: 134 Copynumber: 2.1 Consensus size: 133
16594509 ATATCAGTGA
* * *** * *
16594519 TGATAGTAAATCAATGAATTGTTTGAATTGAGTTGTGATCGTAAATC-GACTAACTTAGAATAAA
1 TGATAGTAAATCAATGAATTATTTGAATGGAGTTACAATCATAAATCAG-CTAACTCAGAATAAA
* * * *
16594583 TTGTTCATGATTGTAAATCCATGAACTTAGGTTGTAATCATAAATAAACAAGCCTTAATAATACC
65 TTATTCATGATCGTAAATCAATGAAATTAGGTTGT-ATCATAAATAAACAAGCCTTAATAATACC
16594648 AGTCG
129 AGTCG
* * * *
16594653 TGATTGTAAATCAGTGAATTATTTGAATGGAGTTACAATCATAAATCAGCTAACTCATATTAAAT
1 TGATAGTAAATCAATGAATTATTTGAATGGAGTTACAATCATAAATCAGCTAACTCAGAATAAAT
* ***
16594718 TATTCATGATCGTAAATCAATGAAATTAGGTTGTATCGTAAATCTGCAAGCCTTAATAATACCAG
66 TATTCATGATCGTAAATCAATGAAATTAGGTTGTATCATAAATAAACAAGCCTTAATAATACCAG
16594783 TCG
131 TCG
* *
16594786 TGATCGTGAATCAA
1 TGATAGTAAATCAA
16594800 CGAACTGTTT
Statistics
Matches: 124, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
133 41 0.33
134 82 0.66
135 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (133 bp):
TGATAGTAAATCAATGAATTATTTGAATGGAGTTACAATCATAAATCAGCTAACTCAGAATAAAT
TATTCATGATCGTAAATCAATGAAATTAGGTTGTATCATAAATAAACAAGCCTTAATAATACCAG
TCG
Found at i:16604772 original size:51 final size:50
Alignment explanation
Indices: 16604712--16604850 Score: 172
Period size: 50 Copynumber: 2.8 Consensus size: 50
16604702 GATACCAGTT
*
16604712 CACATAGTAGCCTGCACATAGTACTACACATGTGATCGAAGC-TATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCAAGCAT-TCCGGTA
* * * * * *
16604763 CGCATAGTAGCCTGCACATAGTACTACATATGCGACCTATCATTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCAAGCATTCCGGTA
* *
16604813 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCA
16604851 TCACTTTCAC
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
50 41 0.55
51 33 0.45
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCAAGCATTCCGGTA
Found at i:16608077 original size:49 final size:49
Alignment explanation
Indices: 16608024--16608118 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
16608014 TTTGAAGCAA
*
16608024 ACATAAAATAAAAAAATAAAACACATAAATTAAAATTTCTATGTACGCC
1 ACATAAAATAAAAAAACAAAACACATAAATTAAAATTTCTATGTACGCC
16608073 ACATAAAATAAAAAAACAAAACACATAAATTAAAATTTCTATGTAC
1 ACATAAAATAAAAAAACAAAACACATAAATTAAAATTTCTATGTAC
16608119 ACCCCCTACA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (49 bp):
ACATAAAATAAAAAAACAAAACACATAAATTAAAATTTCTATGTACGCC
Found at i:16611822 original size:25 final size:25
Alignment explanation
Indices: 16611794--16611843 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
16611784 CAGGTAAGGC
*
16611794 TCCTTCTCCTTCTTTCATTCTTCAT
1 TCCTTCTCCTTCTTCCATTCTTCAT
* *
16611819 TCCTTTTCCTTCTTCCCTTCTTCAT
1 TCCTTCTCCTTCTTCCATTCTTCAT
16611844 CTTCTCTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCATTCTTCAT
Found at i:16614482 original size:19 final size:20
Alignment explanation
Indices: 16614458--16614499 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
16614448 CAAACACCAA
16614458 AAAAGTAAATCA-TTTCCAG
1 AAAAGTAAATCATTTTCCAG
*
16614477 AAAAGTAAATTATTTTCCAG
1 AAAAGTAAATCATTTTCCAG
16614497 AAA
1 AAA
16614500 TCATTTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (20 bp):
AAAAGTAAATCATTTTCCAG
Found at i:16614505 original size:14 final size:14
Alignment explanation
Indices: 16614483--16614513 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16614473 CCAGAAAAGT
*
16614483 AAATTATTTTCCAG
1 AAATCATTTTCCAG
16614497 AAATCATTTTCCAG
1 AAATCATTTTCCAG
16614511 AAA
1 AAA
16614514 ATATTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:16614519 original size:14 final size:13
Alignment explanation
Indices: 16614487--16614520 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
16614477 AAAAGTAAAT
16614487 TATTTTCCAGAAA
1 TATTTTCCAGAAA
16614500 TCATTTTCCAGAAAA
1 T-ATTTTCCAG-AAA
16614515 TATTTT
1 TATTTT
16614521 ACTGGCAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 14 0.74
15 4 0.21
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (13 bp):
TATTTTCCAGAAA
Found at i:16614658 original size:45 final size:45
Alignment explanation
Indices: 16614593--16614689 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 45
16614583 TATATATGGA
*
16614593 ATCATGAATCAAACGAGTAAGACCATAGCTGAAAGACGCTATAGC
1 ATCATGAATCAAACGAGTAAGACCATAGCTGAAAGACACTATAGC
* * * * *
16614638 ATCATGATTCAAACGTGTAAGATCATAGTTGAAAGACACTATGGC
1 ATCATGAATCAAACGAGTAAGACCATAGCTGAAAGACACTATAGC
*
16614683 AACATGA
1 ATCATGA
16614690 CGGAAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (45 bp):
ATCATGAATCAAACGAGTAAGACCATAGCTGAAAGACACTATAGC
Found at i:16614714 original size:46 final size:45
Alignment explanation
Indices: 16614655--16614752 Score: 133
Period size: 46 Copynumber: 2.2 Consensus size: 45
16614645 TTCAAACGTG
* * *
16614655 TAAGATCATAGTTGAAAGACACTATGGCAACATGACGGAAAATAAA
1 TAAGACCATAGTTGAAACACACTATGGCAACAGGACGG-AAATAAA
* * *
16614701 TAAGACCATAGTTGAAACACACTATGGCACCAGGTCGGGAATAAA
1 TAAGACCATAGTTGAAACACACTATGGCAACAGGACGGAAATAAA
16614746 TAAGACC
1 TAAGACC
16614753 GTGGCTGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 13 0.28
46 33 0.72
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.18
Consensus pattern (45 bp):
TAAGACCATAGTTGAAACACACTATGGCAACAGGACGGAAATAAA
Found at i:16619679 original size:24 final size:24
Alignment explanation
Indices: 16619651--16619698 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
16619641 TGCCATTCGA
16619651 ATTAACAAACAAACCAGCAACATT
1 ATTAACAAACAAACCAGCAACATT
*
16619675 ATTAACAAACACACCAGCAACATT
1 ATTAACAAACAAACCAGCAACATT
16619699 CATGGATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.27, G:0.04, T:0.17
Consensus pattern (24 bp):
ATTAACAAACAAACCAGCAACATT
Found at i:16620478 original size:54 final size:54
Alignment explanation
Indices: 16620406--16620513 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
16620396 TTAAAATACC
*
16620406 TCCTAACTCAGAAAGAACTTAATTTAAGGAAAAGGAGATGGATCAAGCTACTCA
1 TCCTAACTCAAAAAGAACTTAATTTAAGGAAAAGGAGATGGATCAAGCTACTCA
*
16620460 TCCTAACTCAAAAAGAACTTAATTTAAGGAAAATGAGATGGATCAAGCTACTCA
1 TCCTAACTCAAAAAGAACTTAATTTAAGGAAAAGGAGATGGATCAAGCTACTCA
16620514 AAGACTACAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (54 bp):
TCCTAACTCAAAAAGAACTTAATTTAAGGAAAAGGAGATGGATCAAGCTACTCA
Found at i:16622413 original size:13 final size:13
Alignment explanation
Indices: 16622395--16622428 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
16622385 ACCTCCTTGG
16622395 ATTAAATTATTAA
1 ATTAAATTATTAA
16622408 ATTAAAATTATTAA
1 ATT-AAATTATTAA
16622422 A-TAAATT
1 ATTAAATT
16622429 GAAATTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 4 0.20
14 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATTATTAA
Found at i:16622491 original size:23 final size:23
Alignment explanation
Indices: 16622465--16622509 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
16622455 GGGTTAGTAA
16622465 AAAAAAGGTATGTTAATTAATCC
1 AAAAAAGGTATGTTAATTAATCC
16622488 AAAAAAGGTATGTTAATTAATC
1 AAAAAAGGTATGTTAATTAATC
16622510 AAAGGTCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (23 bp):
AAAAAAGGTATGTTAATTAATCC
Found at i:16626130 original size:21 final size:21
Alignment explanation
Indices: 16626096--16626136 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16626086 AAAATACAAG
*
16626096 TGAAAAAGAAGAAAATGAAAA
1 TGAAAAAGAAGAAAAGGAAAA
**
16626117 TGAAAAAGGCGAAAAGGAAA
1 TGAAAAAGAAGAAAAGGAAA
16626137 GCGAGAGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.02, G:0.24, T:0.07
Consensus pattern (21 bp):
TGAAAAAGAAGAAAAGGAAAA
Found at i:16632152 original size:2 final size:2
Alignment explanation
Indices: 16632140--16632177 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
16632130 GATTAAATGT
16632140 TA TA CTA 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 TA TA T
16632178 TACTTGTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16633035 original size:14 final size:15
Alignment explanation
Indices: 16633013--16633089 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
16633003 CAATCAAACA
16633013 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
16633027 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
16633042 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
16633062 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
16633076 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
16633090 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:16633054 original size:20 final size:20
Alignment explanation
Indices: 16633029--16633068 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16633019 AATATTTTCC
*
16633029 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
16633049 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
16633069 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:16633074 original size:34 final size:35
Alignment explanation
Indices: 16633017--16633083 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
16633007 CAAACACCAG
*
16633017 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
16633052 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
16633084 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:16634179 original size:22 final size:22
Alignment explanation
Indices: 16634136--16634179 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
16634126 AACAAAATAG
* **
16634136 AAAAAATAGAAATTATTTTGTA
1 AAAAAATAGAAAATATAGTGTA
*
16634158 AAAAAATATAAAATATAGTGTA
1 AAAAAATAGAAAATATAGTGTA
16634180 GTTTTTAATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (22 bp):
AAAAAATAGAAAATATAGTGTA
Found at i:16635249 original size:12 final size:12
Alignment explanation
Indices: 16635213--16635250 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16635203 TTGATAATGA
16635213 AAATTTATTAAT
1 AAATTTATTAAT
* *
16635225 AAAATAATT-AT
1 AAATTTATTAAT
16635236 AAATTTATTAAT
1 AAATTTATTAAT
16635248 AAA
1 AAA
16635251 ATAATAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATTTATTAAT
Found at i:16635503 original size:46 final size:45
Alignment explanation
Indices: 16635453--16635550 Score: 103
Period size: 45 Copynumber: 2.1 Consensus size: 45
16635443 ATGAAAAAAA
* *
16635453 TAAATTTTTACTATTTTTAATATATCTAAT-TATATTA-AATGATTTT-
1 TAAATATTTA-TAATTTTAATA-AT-TAATATATATTATAAT-ATTTTC
*
16635499 TAAATATTTATAATTTTATTAATTAATAATATATTATAATATTTTC
1 TAAATATTTATAATTTTAATAATTAAT-ATATATTATAATATTTTC
16635545 TAAATA
1 TAAATA
16635551 AAATTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
43 4 0.09
44 2 0.04
45 21 0.47
46 18 0.40
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (45 bp):
TAAATATTTATAATTTTAATAATTAATATATATTATAATATTTTC
Found at i:16640665 original size:22 final size:22
Alignment explanation
Indices: 16640637--16640678 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16640627 ATTGACTTAG
*
16640637 TGCAATTCAATAGCTTTATTAA
1 TGCAATTCAATAGCTCTATTAA
*
16640659 TGCAATTCAATGGCTCTATT
1 TGCAATTCAATAGCTCTATT
16640679 TTAGGTGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (22 bp):
TGCAATTCAATAGCTCTATTAA
Found at i:16640961 original size:69 final size:67
Alignment explanation
Indices: 16640872--16641330 Score: 276
Period size: 69 Copynumber: 6.7 Consensus size: 67
16640862 ATTTTAACTG
* * * *
16640872 GGAACGTAGGTTCGCTAGCTATTTTGGAGGTTGCGATCTTAAACCAACAAACCTTTATGACATCA
1 GGAACGTAGGTCCACTAGCT-TTTTAGAGGTTGCGATCATAAACCAACAAACCTTTA-GACATCA
*
16640937 GCTG
64 GCTA
** * * * * * * **
16640941 GGAGTGTTGGTCCACTAGCTATATTAGAGGCTACGATCATAAACCGATAAACCTTTAGAGTTCAG
1 GGAACGTAGGTCCACTAGCT-TTTTAGAGGTTGCGATCATAAACCAACAAACCTTTAGACATCAG
*
16641006 TTA
65 CTA
* * * * * ** **
16641009 GGAACATAGGTCCCCTAGTTGTTTTAGAGGTTACGATCTTAAATCGGA-AAATATTTATGACATC
1 GGAACGTAGGTCCACTAGCT-TTTTAGAGGTTGCGATCATAAA-CCAACAAACCTTTA-GACATC
*
16641073 AGTTA
63 AGCTA
* * * * * *
16641078 GGAGCGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACCAGCAAGCCTTTAGAGTATCA
1 GGAACGTAGGTCCACTAGCTTT-TTAGAGGTTGCGATCATAAACCAACAAACCTTTAGA-CATCA
16641143 GCTA
64 GCTA
* * * * * *
16641147 GGAACGTTGGTCCACTAGCTTTGTTAGAGGTTGCGATCATAAACTAGCGAGCCTTTAGAGTATCA
1 GGAACGTAGGTCCACTAGCTTT-TTAGAGGTTGCGATCATAAACCAACAAACCTTTAGA-CATCA
16641212 GCTA
64 GCTA
* * * * *** **
16641216 GGAACATAGGT-TAGCTAGCTATTTTAGAGGTTACGATCTTAAATTGATGAACCTTTATGACATC
1 GGAACGTAGGTCCA-CTAGCT-TTTTAGAGGTTGCGATCATAAACCAACAAACCTTTA-GACATC
* *
16641280 AGTTG
63 AGCTA
* ** * *
16641285 GGAGCGTAGGTCTGCTAG-TTGTGTTGGAGGCTGCGATCATAAACCA
1 GGAACGTAGGTCCACTAGCTT-T-TTAGAGGTTGCGATCATAAACCA
16641331 TTGAGCCTTT
Statistics
Matches: 303, Mismatches: 76, Indels: 22
0.76 0.19 0.05
Matches are distributed among these distances:
67 1 0.00
68 55 0.18
69 242 0.80
70 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (67 bp):
GGAACGTAGGTCCACTAGCTTTTTAGAGGTTGCGATCATAAACCAACAAACCTTTAGACATCAGC
TA
Found at i:16641118 original size:137 final size:138
Alignment explanation
Indices: 16640925--16641189 Score: 338
Period size: 137 Copynumber: 1.9 Consensus size: 138
16640915 CCAACAAACC
* * * *
16640925 TTTATGACATCAGCTGGGAGTGTTGGTCCACTAGCTATATTAGAGGCTACGATCATAAACC-GAT
1 TTTATGACATCAGCTAGGAGCGTAGGTCCACTAGCTATATTAGAGGCTACGATCATAAACCAG-C
* * * *
16640989 AAACCTTTAGAGT-TCAGTTAGGAACATAGGTCCCCTAG-TTGTTTTAGAGGTTACGATCTTAAA
65 AAACCTTTAGAGTATCAGCTAGGAACATAGGTCCACTAGCTT-TGTTAGAGGTTACGATCATAAA
16641052 TCGGAAAATA
129 TCGGAAAATA
* * * * *
16641062 TTTATGACATCAGTTAGGAGCGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACCAGCA
1 TTTATGACATCAGCTAGGAGCGTAGGTCCACTAGCTATATTAGAGGCTACGATCATAAACCAGCA
* * * *
16641127 AGCCTTTAGAGTATCAGCTAGGAACGTTGGTCCACTAGCTTTGTTAGAGGTTGCGATCATAAA
66 AACCTTTAGAGTATCAGCTAGGAACATAGGTCCACTAGCTTTGTTAGAGGTTACGATCATAAA
16641190 CTAGCGAGCC
Statistics
Matches: 108, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
137 65 0.60
138 41 0.38
139 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (138 bp):
TTTATGACATCAGCTAGGAGCGTAGGTCCACTAGCTATATTAGAGGCTACGATCATAAACCAGCA
AACCTTTAGAGTATCAGCTAGGAACATAGGTCCACTAGCTTTGTTAGAGGTTACGATCATAAATC
GGAAAATA
Found at i:16641313 original size:207 final size:206
Alignment explanation
Indices: 16640876--16641349 Score: 544
Period size: 207 Copynumber: 2.3 Consensus size: 206
16640866 TAACTGGGAA
* * * * * *
16640876 CGTAGGTTCGCTAGCTATT-TTGGAGGTTGCGATCTTAAACCAACAAACCTTTATGA-CATCAGC
1 CGTAGGTCCACTAGCT-TTGTTGGAGGCTGCGATCATAAACCAACAAGCCTTTA-GAGTATCAGC
* ** * *
16640939 TGGGAGTGTTGGTCCACTAGCTATATTAGAGGCTACGATCATAAACCGATAAACCTTTAGAGTTC
64 TAGGAACGTTGGTCCACTAGCTATATTAGAGGCTACGATCATAAACAGACAAACCTTTAGAGTTC
* * * * *
16641004 AGTTAGGAACATAGGTCCCCTAGTTGTTTTAGAGGTTACGATCTTAAATCGGAAAATATTTATGA
129 AGCTAGGAACATAGGTCACCTAGCTATTTTAGAGGTTACGATCTTAAATCGGAAAACATTTATGA
16641069 CATCAGTTAGGAG
194 CATCAGTTAGGAG
*
16641082 CGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACCAGCAAGCCTTTAGAGTATCAGCTA
1 CGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACCAACAAGCCTTTAGAGTATCAGCTA
* * * * * *
16641147 GGAACGTTGGTCCACTAGCTTTGTTAGAGGTTGCGATCATAAACTAG-CGAGCCTTTAGAGTATC
66 GGAACGTTGGTCCACTAGCTATATTAGAGGCTACGATCATAAAC-AGACAAACCTTTAGAGT-TC
* * * * *
16641211 AGCTAGGAACATAGGTTAGCTAGCTATTTTAGAGGTTACGATCTTAAAT-TGATGAACCTTTATG
129 AGCTAGGAACATAGGTCACCTAGCTATTTTAGAGGTTACGATCTTAAATCGGA-AAACATTTATG
*
16641275 ACATCAGTTGGGAG
193 ACATCAGTTAGGAG
** *** *
16641289 CGTAGGTCTGCTAG-TTGTGTTGGAGGCTGCGATCATAAACCATTGAGCCTTTAAAGTATCA
1 CGTAGGTCCACTAGCTT-TGTTGGAGGCTGCGATCATAAACCAACAAGCCTTTAGAGTATCA
16641350 TTTGGGAAGG
Statistics
Matches: 227, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
205 4 0.02
206 104 0.46
207 119 0.52
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (206 bp):
CGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACCAACAAGCCTTTAGAGTATCAGCTA
GGAACGTTGGTCCACTAGCTATATTAGAGGCTACGATCATAAACAGACAAACCTTTAGAGTTCAG
CTAGGAACATAGGTCACCTAGCTATTTTAGAGGTTACGATCTTAAATCGGAAAACATTTATGACA
TCAGTTAGGAG
Found at i:16641364 original size:138 final size:138
Alignment explanation
Indices: 16641141--16641465 Score: 334
Period size: 138 Copynumber: 2.4 Consensus size: 138
16641131 TTTAGAGTAT
* * * * * * *
16641141 CAGCTAGGAA-CGTTGGTCCACTAGCTTTGTTAGAGGTTGCGATCATAAACTAGCGAGCCTTTAG
1 CAGCT-GGAAGCGTAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAAACCAGCGAGCCTTTAA
* * * * * *
16641205 AGTATCAGCTAGGAACATAGGTTAGCTAGCTATTTTAGAGGTTACGATCTTAAA-TTG-ATGAAC
65 AGTATCAGCTAGGAACATAGGTCAGCTAGCTAATTTAGAGGTGACAACCTTAAACCTGCA--AAC
*
16641268 CTTTATGACAT
128 CTTTATGACAC
* * * * **
16641279 CAGTTGGGAGCGTAGGTCTGCTAGTTGTGTTGGAGGCTGCGATCATAAACCATTGAGCCTTTAAA
1 CAGCTGGAAGCGTAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAAACCAGCGAGCCTTTAAA
** * ** * * *
16641344 GTATCATTTGGGAAGGTAGGTCCGTTAGCTAATTTGGAGGTGACAACCTTAAACCTGCAAACCTT
66 GTATCAGCTAGGAACATAGGTCAGCTAGCTAATTTAGAGGTGACAACCTTAAACCTGCAAACCTT
16641409 TATGACAC
131 TATGACAC
16641417 CAGCTGGAAGCGTAGGTCCGCTAGCTGTGTTGGAGGCTGC-AGTCATAAA
1 CAGCTGGAAGCGTAGGTCCGCTAGCTGTGTTGGAGGCTGCGA-TCATAAA
16641466 TCGACAAGCC
Statistics
Matches: 151, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
137 4 0.03
138 144 0.95
139 2 0.01
140 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (138 bp):
CAGCTGGAAGCGTAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAAACCAGCGAGCCTTTAAA
GTATCAGCTAGGAACATAGGTCAGCTAGCTAATTTAGAGGTGACAACCTTAAACCTGCAAACCTT
TATGACAC
Found at i:16641442 original size:207 final size:207
Alignment explanation
Indices: 16640876--16641442 Score: 472
Period size: 207 Copynumber: 2.7 Consensus size: 207
16640866 TAACTGGGAA
* * * * * * * *
16640876 CGTAGGTTCGCTAGCTATT-TTGGAGGTTGCGATCTTAAACCAACAAACCTTT-ATGACATCAGC
1 CGTAGGTCCACTAGCT-TTGTTGGAGGCTGCGATCATAAACCAGCAAGCCTTTAAAG-TATCAGC
* ** * * * * * * * * *
16640939 TGGGAGTGTTGGTCCACTAGCTATATTAGAGGCTACGATCATAAAC-CGATAAACCTTTAGAG-T
64 TAGGAACGTAGGTCCACTAGCTATGTTAGAGGTTGCAACCATAAACTAG-CAAACCTTTAGAGCA
* * * * * *
16641002 TCAGTTAGGAACATAGGTCCCCTAGTTGTTTTAGAGGTTACGATCTTAAATCGGAAAATATTTAT
128 CCAGCTAGGAACATAGGTCCGCTAGCTATTTTAGAGGTTACGATCTTAAATCGGAAAACATTTAT
16641067 GACATCAGTTAGGAG
193 GACATCAGTTAGGAG
*
16641082 CGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACCAGCAAGCCTTTAGAGTATCAGCTA
1 CGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACCAGCAAGCCTTTAAAGTATCAGCTA
* * * * * * * *
16641147 GGAACGTTGGTCCACTAGCTTTGTTAGAGGTTGCGATCATAAACTAGCGAGCCTTTAGAGTATCA
66 GGAACGTAGGTCCACTAGCTATGTTAGAGGTTGCAACCATAAACTAGCAAACCTTTAGAGCACCA
** * * *
16641212 GCTAGGAACATAGGTTAGCTAGCTATTTTAGAGGTTACGATCTTAAAT-TGATGAACCTTTATGA
131 GCTAGGAACATAGGTCCGCTAGCTATTTTAGAGGTTACGATCTTAAATCGGA-AAACATTTATGA
*
16641276 CATCAGTTGGGAG
195 CATCAGTTAGGAG
** *** **
16641289 CGTAGGTCTGCTAG-TTGTGTTGGAGGCTGCGATCATAAACCATTGAGCCTTTAAAGTATCATTT
1 CGTAGGTCCACTAGCTT-TGTTGGAGGCTGCGATCATAAACCAGCAAGCCTTTAAAGTATCAGCT
* * ** * *
16641353 GGGAAGGTAGGTCCGTTAGCTAAT-TTGGAGG-TGACAACCTTAAACCT-GCAAACCTTTATGA-
65 AGGAACGTAGGTCCACTAGCT-ATGTTAGAGGTTG-CAACCATAAA-CTAGCAAACCTTTA-GAG
*
16641414 CACCAGCT-GGAAGCGTAGGTCCGCTAGCT
126 CACCAGCTAGGAA-CATAGGTCCGCTAGCT
16641443 GTGTTGGAGG
Statistics
Matches: 293, Mismatches: 57, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
205 2 0.01
206 108 0.37
207 178 0.61
208 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (207 bp):
CGTAGGTCCACTAGCTTTGTTGGAGGCTGCGATCATAAACCAGCAAGCCTTTAAAGTATCAGCTA
GGAACGTAGGTCCACTAGCTATGTTAGAGGTTGCAACCATAAACTAGCAAACCTTTAGAGCACCA
GCTAGGAACATAGGTCCGCTAGCTATTTTAGAGGTTACGATCTTAAATCGGAAAACATTTATGAC
ATCAGTTAGGAG
Found at i:16641548 original size:138 final size:138
Alignment explanation
Indices: 16641141--16641519 Score: 331
Period size: 138 Copynumber: 2.7 Consensus size: 138
16641131 TTTAGAGTAT
* * * * * * * * *
16641141 CAGCTAGGAA-CGTTGGTCCACTAGCTTTGTTAGAGGTTGCGATCATAAACTAGCGAGCCTTTAG
1 CAGCT-GGAAGCGTAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAAACCATCAAGCCTTTAA
* ** ** * * * *
16641205 AGTATCAGCTAGGAACATAGGTTAGCTAGCTATTTTAGAGGTTACGATC-TTAAA-TTG-ATGAA
65 AGTATCAGCTGGGAAGGTAGGTCCGCTAGCTAATTTAGAGGTGAC-AACATTAAACCTGCA--AA
*
16641267 CCTTTATGACAT
127 CCTTTATGACAC
* * * * **
16641279 CAGTTGGGAGCGTAGGTCTGCTAGTTGTGTTGGAGGCTGCGATCATAAACCATTGAGCCTTTAAA
1 CAGCTGGAAGCGTAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAAACCATCAAGCCTTTAAA
** * * *
16641344 GTATCATTTGGGAAGGTAGGTCCGTTAGCTAATTTGGAGGTGACAACCTTAAACCTGCAAACCTT
66 GTATCAGCTGGGAAGGTAGGTCCGCTAGCTAATTTAGAGGTGACAACATTAAACCTGCAAACCTT
16641409 TATGACAC
131 TATGACAC
*
16641417 CAGCTGGAAGCGTAGGTCCGCTAGCTGTGTTGGAGGCTGC-AGTCATAAATCGA-CAAGCCTTTA
1 CAGCTGGAAGCGTAGGTCCGCTAGCTGTGTTGGAGGCTGCGA-TCATAAA-CCATCAAGCCTTTA
* * * *
16641480 GAGTGA-CAGCTGGGAATGTATGTCCGCTAGCTATTTTAGA
64 AAGT-ATCAGCTGGGAAGGTAGGTCCGCTAGCTAATTTAGA
16641520 TGTTGCGATA
Statistics
Matches: 192, Mismatches: 42, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
137 6 0.03
138 180 0.94
139 5 0.03
140 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (138 bp):
CAGCTGGAAGCGTAGGTCCGCTAGCTGTGTTGGAGGCTGCGATCATAAACCATCAAGCCTTTAAA
GTATCAGCTGGGAAGGTAGGTCCGCTAGCTAATTTAGAGGTGACAACATTAAACCTGCAAACCTT
TATGACAC
Found at i:16643855 original size:20 final size:20
Alignment explanation
Indices: 16643827--16643890 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
16643817 GCTGAAAGAA
* *
16643827 AGCTAAATTGAGCTCGAATG
1 AGCTGAATTGAGCTCAAATG
16643847 AGCTGAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
* *
16643867 AGCTG-ATTGGAGCTGAAACG
1 AGCTGAATT-GAGCTCAAATG
16643887 AGCT
1 AGCT
16643891 AAAGGAGCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (20 bp):
AGCTGAATTGAGCTCAAATG
Found at i:16650255 original size:3 final size:3
Alignment explanation
Indices: 16650247--16650282 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
16650237 TCATGATATT
16650247 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
16650283 GATGGATGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:16659095 original size:42 final size:40
Alignment explanation
Indices: 16659037--16659264 Score: 183
Period size: 42 Copynumber: 5.4 Consensus size: 40
16659027 CATTGAATAA
* *
16659037 AAAGGGGTTGCTAAGTGCTGATTCCCCGAATTAGTGACTTT
1 AAAGGGGTTGCTAAGTGCTGATTCCCCGTATTA-TGAATTT
* *
16659078 AAAGGTGGTCGCTAAGTGCTGATTCCACCGTATCT-TTAATTGT
1 AAAGG-GGTTGCTAAGTGCTGATTCC-CCGTAT-TATGAATT-T
* *
16659121 GAAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATAT
1 -AAAGGGGTTGCTAAGTGCTGATTCCCCGTATTA-TGAATTT
* * *
16659163 AAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCCT-TGACTGTG
1 AAAGG-GGTTGCTAAGTGCTGATTCC-CCGTAT--TATGAAT-TT
* * ** *
16659207 AAAAGGGTTGCTATGTGCTGATTCTTCGTATCACTGAATTT
1 AAAGGGGTTGCTAAGTGCTGATTCCCCGTATTA-TGAATTT
16659248 -AAGGTGGTTGCTAAGTG
1 AAAGG-GGTTGCTAAGTG
16659265 ATGAATCCAC
Statistics
Matches: 149, Mismatches: 23, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
40 3 0.02
41 23 0.15
42 57 0.38
43 55 0.37
44 10 0.07
45 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
AAAGGGGTTGCTAAGTGCTGATTCCCCGTATTATGAATTT
Found at i:16659180 original size:85 final size:84
Alignment explanation
Indices: 16659037--16659274 Score: 314
Period size: 85 Copynumber: 2.8 Consensus size: 84
16659027 CATTGAATAA
* * * * * *
16659037 AAAGGGGTTGCTAAGTGCTGATTCCCCGAATTAGTGACTTTAAAGGTGGTCGCTAAGTGCTGATT
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGA-ATTAAAGGTGGTTGCTAAGTGATGATT
* *
16659102 CCACCGTATCTTTAATTGTG
65 CCACCGTATCCTTAACTGTG
*
16659122 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATATAAAGGTGGTTGCTAAGTGTTGATT
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAAT-TAAAGGTGGTTGCTAAGTGATGATT
*
16659187 CCACCGTATCCTTGACTGTG
65 CCACCGTATCCTTAACTGTG
* ** * * *
16659207 AAAAGGGTTGCTATGTGCTGATTCTTCGTATCACTGAATTTAAGGTGGTTGCTAAGTGATGAATC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGATGATTC
16659272 CAC
66 CAC
16659275 TGAGTATCGG
Statistics
Matches: 136, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
84 27 0.20
85 109 0.80
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (84 bp):
AAAGGGGTTGCTATGTGCTGATTCCCCGTATTACTGAATTAAAGGTGGTTGCTAAGTGATGATTC
CACCGTATCCTTAACTGTG
Found at i:16667518 original size:17 final size:18
Alignment explanation
Indices: 16667487--16667520 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
16667477 CATATTGTCG
16667487 GCCTGTGTGGGCCCACAT
1 GCCTGTGTGGGCCCACAT
16667505 GCCTGTGT-GGCCCACA
1 GCCTGTGTGGGCCCACA
16667521 CGGCCCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.12, C:0.35, G:0.32, T:0.21
Consensus pattern (18 bp):
GCCTGTGTGGGCCCACAT
Found at i:16668826 original size:51 final size:51
Alignment explanation
Indices: 16668706--16668888 Score: 176
Period size: 51 Copynumber: 3.6 Consensus size: 51
16668696 AGTGATAGTA
* * * * *
16668706 ACATGTGTAGTACTATGTGCATGCTACTACGTGTACTGGGAT-G--ATAGGTC
1 ACATGTGTAGTACTATGTGCAGGCTACTATGCGTAC-CGGATAGTAAT-GATC
* * *
16668756 GCATGTGTAGTACTATGTGCAGGCTATTATGCGTACCGGATAGT-TTCGATC
1 ACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAAT-GATC
* * * * * *
16668807 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGCTC
1 ACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATGATC
*
16668858 ACATGTGTAGTACTATGTGTAGGCTACTATG
1 ACATGTGTAGTACTATGTGCAGGCTACTATG
16668889 TGAACCAAAC
Statistics
Matches: 109, Mismatches: 21, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
49 4 0.04
50 32 0.29
51 72 0.66
52 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (51 bp):
ACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATGATC
Found at i:16668890 original size:26 final size:26
Alignment explanation
Indices: 16668810--16668890 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
16668800 TTCGATCACG
*
16668810 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGTAGGCTACTA
* * *
16668836 CGTGTA-T-CGGATG-GTAATGCTCAC-A
1 TGTGTAGTAC-TATGTGT-AGGCT-ACTA
16668861 TGTGTAGTACTATGTGTAGGCTACTA
1 TGTGTAGTACTATGTGTAGGCTACTA
16668887 TGTG
1 TGTG
16668891 AACCAAACAT
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 2 0.05
25 16 0.39
26 20 0.49
27 3 0.07
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGTAGGCTACTA
Found at i:16671302 original size:30 final size:31
Alignment explanation
Indices: 16671278--16671336 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
16671268 GTAAATACTC
* **
16671278 AAAATTTGAGGGATTAA-AGTGTAAATATGA
1 AAAATTTGAAGGACCAATAGTGTAAATATGA
16671308 AAAATTTGAAGGACCAATAGTGTAAATAT
1 AAAATTTGAAGGACCAATAGTGTAAATAT
16671337 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.29
Consensus pattern (31 bp):
AAAATTTGAAGGACCAATAGTGTAAATATGA
Found at i:16675238 original size:35 final size:36
Alignment explanation
Indices: 16675146--16675254 Score: 98
Period size: 35 Copynumber: 3.1 Consensus size: 36
16675136 ACCAGTGCAA
* * * *
16675146 GGCACAATTATTATCAGTTTATCCGACCAGTGCTGG
1 GGCACAATTATTGTCGGTTTATCCGACTAGTGCTAG
* ** * *
16675182 GTGTA-AAGCATTGTTGATTTATCCGACTAGTG-TAG
1 G-GCACAATTATTGTCGGTTTATCCGACTAGTGCTAG
*
16675217 GGCACAATTATTGTCGGTTTATCCGACTAGCGCT-G
1 GGCACAATTATTGTCGGTTTATCCGACTAGTGCTAG
16675252 GGC
1 GGC
16675255 GTAAAACAAC
Statistics
Matches: 55, Mismatches: 15, Indels: 7
0.71 0.19 0.09
Matches are distributed among these distances:
34 2 0.04
35 29 0.53
36 22 0.40
37 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (36 bp):
GGCACAATTATTGTCGGTTTATCCGACTAGTGCTAG
Found at i:16675274 original size:71 final size:71
Alignment explanation
Indices: 16675136--16675325 Score: 184
Period size: 71 Copynumber: 2.7 Consensus size: 71
16675126 GGTATAACCA
* * * * * * * * ** *
16675136 ACCAGTGCAAGGCACAATTATTATCAGTTTATCCGACCAGTGCTGGGTGTAAAGCATTGTTGATT
1 ACCACTGCAGGGCACAATTATTGTCGGTTTATCCGACTAGCGCTGGGCGTAAAACAACGTAGATT
*
16675201 TATCCG
66 TATCCC
* * *
16675207 ACTAGTGTAGGGCACAATTATTGTCGGTTTATCCGACTAGCGCTGGGCGTAAAACAACGTCAG-T
1 ACCACTGCAGGGCACAATTATTGTCGGTTTATCCGACTAGCGCTGGGCGTAAAACAACGT-AGAT
16675271 TTATCCC
65 TTATCCC
** * * *
16675278 ACCACTGCAGGGCACAACAATTGTCGATTTATTCAACTAGCGCTGGGC
1 ACCACTGCAGGGCACAATTATTGTCGGTTTATCCGACTAGCGCTGGGC
16675326 ACAAAAATTT
Statistics
Matches: 97, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
71 96 0.99
72 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (71 bp):
ACCACTGCAGGGCACAATTATTGTCGGTTTATCCGACTAGCGCTGGGCGTAAAACAACGTAGATT
TATCCC
Found at i:16679926 original size:15 final size:16
Alignment explanation
Indices: 16679897--16679926 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16679887 GATAGTGTTG
16679897 TAAAATGTAGAATTAA
1 TAAAATGTAGAATTAA
16679913 TAAAATGT-GAATTA
1 TAAAATGTAGAATTA
16679927 TTCTTATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (16 bp):
TAAAATGTAGAATTAA
Found at i:16685051 original size:164 final size:164
Alignment explanation
Indices: 16684780--16685112 Score: 594
Period size: 164 Copynumber: 2.0 Consensus size: 164
16684770 ATATCAAACC
*
16684780 AAGAATTAAGCACACATAATTGAGAACAAGATCTAAGCATTTATTGGGTAAAATAAAAATCAAAC
1 AAGAATTAAGCACACATAATCGAGAACAAGATCTAAGCATTTATTGGGTAAAATAAAAATCAAAC
* *
16684845 GACAAAATTCATTATAGGGTTCATCTCCCTAGGTATTTAGAAAATTAGTTCATGCTTAAAAATAA
66 GACAAAATTCATCATAAGGTTCATCTCCCTAGGTATTTAGAAAATTAGTTCATGCTTAAAAATAA
16684910 AAACATCCAATATACAGTATAATCGAAAGAAATA
131 AAACATCCAATATACAGTATAATCGAAAGAAATA
* *
16684944 AAGAATTAAGCACACATAATCGAGACCAAGATCTAAGTATTTATTGGGTAAAATAAAAATCAAAC
1 AAGAATTAAGCACACATAATCGAGAACAAGATCTAAGCATTTATTGGGTAAAATAAAAATCAAAC
* * *
16685009 GACAGAGTTCATCATAAGGTTCATCTCCTTAGGTATTTAGAAAATTAGTTCATGCTTAAAAATAA
66 GACAAAATTCATCATAAGGTTCATCTCCCTAGGTATTTAGAAAATTAGTTCATGCTTAAAAATAA
16685074 AAACATCCAATATACAGTATAATCGAAAGAAATA
131 AAACATCCAATATACAGTATAATCGAAAGAAATA
16685108 AAGAA
1 AAGAA
16685113 ACTCATGATA
Statistics
Matches: 161, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
164 161 1.00
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (164 bp):
AAGAATTAAGCACACATAATCGAGAACAAGATCTAAGCATTTATTGGGTAAAATAAAAATCAAAC
GACAAAATTCATCATAAGGTTCATCTCCCTAGGTATTTAGAAAATTAGTTCATGCTTAAAAATAA
AAACATCCAATATACAGTATAATCGAAAGAAATA
Found at i:16690528 original size:17 final size:17
Alignment explanation
Indices: 16690506--16690543 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
16690496 ATACACTCGG
16690506 CTGAATAAAACCTCTGT
1 CTGAATAAAACCTCTGT
16690523 CTGAATAAAACCTCTGT
1 CTGAATAAAACCTCTGT
16690540 CTGA
1 CTGA
16690544 CAAATCTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (17 bp):
CTGAATAAAACCTCTGT
Found at i:16694620 original size:15 final size:15
Alignment explanation
Indices: 16694600--16694636 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
16694590 GCTTCAAAAT
16694600 CGCTTCTCAGTTTTG
1 CGCTTCTCAGTTTTG
*
16694615 CGCTTCTCGGTTTTG
1 CGCTTCTCAGTTTTG
*
16694630 CACTTCT
1 CGCTTCT
16694637 AACAGTGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.30, G:0.19, T:0.46
Consensus pattern (15 bp):
CGCTTCTCAGTTTTG
Found at i:16704314 original size:13 final size:13
Alignment explanation
Indices: 16704296--16704324 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16704286 AATAATATAT
16704296 TAACAATTCAAAA
1 TAACAATTCAAAA
16704309 TAACAATTCAAAA
1 TAACAATTCAAAA
16704322 TAA
1 TAA
16704325 ATTAAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (13 bp):
TAACAATTCAAAA
Found at i:16705056 original size:16 final size:15
Alignment explanation
Indices: 16705031--16705065 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
16705021 AAAGTTGATA
*
16705031 ATAATTAATATATATT
1 ATAATAAATATA-ATT
16705047 ATAATAAATATAATT
1 ATAATAAATATAATT
16705062 ATAA
1 ATAA
16705066 ACTAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:16712860 original size:27 final size:28
Alignment explanation
Indices: 16712822--16712891 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
16712812 TTAAAGGAAG
**
16712822 GCCTTTGTGGCGCAA-TATG-AAATGAAC
1 GCCTTTGTGGCG-AATTATGAAAAAAAAC
*
16712849 GCCTTTGTGGCGAATTATGAAAAAAAAT
1 GCCTTTGTGGCGAATTATGAAAAAAAAC
16712877 GCCTTTGTGGCGAAT
1 GCCTTTGTGGCGAAT
16712892 CAAGAAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.05
27 16 0.42
28 20 0.53
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (28 bp):
GCCTTTGTGGCGAATTATGAAAAAAAAC
Found at i:16713827 original size:34 final size:35
Alignment explanation
Indices: 16713787--16713860 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
16713777 AGCATATATT
* *
16713787 TATACTTATCAAT-TACATGTGCCGAATGC-ACATA
1 TATACTTAT-AATCCACATATGCCGAATGCAACATA
16713821 TATACTTATAATCCACATATGCCGAATGCATACATA
1 TATACTTATAATCCACATATGCCGAATGCA-ACATA
16713857 TATA
1 TATA
16713861 TATCCAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 3 0.09
34 23 0.66
36 9 0.26
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (35 bp):
TATACTTATAATCCACATATGCCGAATGCAACATA
Found at i:16714085 original size:41 final size:41
Alignment explanation
Indices: 16714040--16714150 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
16714030 ATTCATCGGT
* * *
16714040 ACTTAGCCCGTTAGGCTTAAAGCCTGATTCAGATCACCGGC
1 ACTTAGCCCGCTAGGCTTAAAGCCTGATACAGATCACCAGC
* * *
16714081 ACTTAGCCTGCTAGGCTTATAGCCTGATACATATCACCAGC
1 ACTTAGCCCGCTAGGCTTAAAGCCTGATACAGATCACCAGC
* * *
16714122 ACTTAGCCTGCTAGGTTTTAAAACCTGAT
1 ACTTAGCCCGCTAGG-CTTAAAGCCTGAT
16714151 TTAGTACACC
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 50 0.83
42 10 0.17
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (41 bp):
ACTTAGCCCGCTAGGCTTAAAGCCTGATACAGATCACCAGC
Found at i:16715004 original size:78 final size:78
Alignment explanation
Indices: 16714884--16715161 Score: 443
Period size: 78 Copynumber: 3.6 Consensus size: 78
16714874 ACATTCAACA
*
16714884 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
16714948 AACATACATACTT
66 AACATACATACTT
*
16714961 TTAACTAAATTCAAGAA-TTCATTCATGTATAAACATATATATCCGAACTTTATATATATAAATA
1 TTAACTAAATTCAAGAACTT-ATTCATGTATATACATATATATCCGAACTTTATATATATAAATA
*
16715025 TAACATACATACTG
65 TAACATACATACTT
* * *
16715039 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATTCGAGCTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
16715104 AACATACATACTT
66 AACATACATACTT
* * *
16715117 TTAACTAAATTCCAGAACTTATACATGGATATACATATATTATCC
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATA-TATCC
16715162 ACTATTAGTT
Statistics
Matches: 185, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
77 16 0.09
78 163 0.88
79 6 0.03
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (78 bp):
TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTT
Found at i:16720669 original size:78 final size:77
Alignment explanation
Indices: 16720516--16720701 Score: 182
Period size: 76 Copynumber: 2.4 Consensus size: 77
16720506 ATGTACATAT
* * * *
16720516 ATACATATTCGATTCTAACATATATGCATATATAATTTTATACTTACATTCGAAACAAGTACTTA
1 ATACATATTCGATTCTAACATATA-GCATATATAATTTCATACTTACACTCGAAACAAGCAATTA
*
16720581 TACTTGTATACAC
65 TACTTATATACAC
* * *
16720594 ATACATTTTCGAATT-TAACATATA-CATATATAATTTCATACTTATACTC-AATATAAGCAATT
1 ATACATATTCG-ATTCTAACATATAGCATATATAATTTCATACTTACACTCGAA-ACAAGCAATT
* *
16720656 ATACATATATATAC
64 ATACTTATATACAC
* * * * *
16720670 ATGCTTATTCGATCCAAACATAT-GCAAATATA
1 ATACATATTCGATTCTAACATATAGCATATATA
16720702 TTATACATAT
Statistics
Matches: 88, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
75 4 0.05
76 62 0.70
78 19 0.22
79 3 0.03
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (77 bp):
ATACATATTCGATTCTAACATATAGCATATATAATTTCATACTTACACTCGAAACAAGCAATTAT
ACTTATATACAC
Found at i:16720681 original size:76 final size:76
Alignment explanation
Indices: 16720446--16720681 Score: 203
Period size: 76 Copynumber: 3.1 Consensus size: 76
16720436 AAATTTAAAC
* * * **
16720446 ATTCGAATCTCACATATACCTATATAATTTCATAACCCAT-TTCAATACAA-AAACTTATACATG
1 ATTCGAATTTAACATATACATATATAATTTCAT-ACTTATATTCAATACAAGAAA-TTATACATG
* * *
16720509 TACATATATACAT
64 TATATACATACTT
* * * * *
16720522 ATTCG-ATTCTAACATATATGCATATATAATTTTATACTTACATTCGAA-ACAAGTACTTATACT
1 ATTCGAATT-TAACATATA--CATATATAATTTCATACTTATATTC-AATACAAGAAATTATACA
*
16720585 TGTATACACATACATT
62 TGTATATACATAC-TT
* * * *
16720601 -TTCGAATTTAACATATACATATATAATTTCATACTTATACTCAATATAAGCAATTATACATATA
1 ATTCGAATTTAACATATACATATATAATTTCATACTTATATTCAATACAAGAAATTATACATGTA
*
16720665 TATACATGCTT
66 TATACATACTT
16720676 ATTCGA
1 ATTCGA
16720682 TCCAAACATA
Statistics
Matches: 126, Mismatches: 24, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
75 6 0.05
76 61 0.48
77 3 0.02
78 49 0.39
79 7 0.06
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (76 bp):
ATTCGAATTTAACATATACATATATAATTTCATACTTATATTCAATACAAGAAATTATACATGTA
TATACATACTT
Found at i:16720926 original size:78 final size:78
Alignment explanation
Indices: 16720708--16721081 Score: 476
Period size: 78 Copynumber: 4.8 Consensus size: 78
16720698 TATATTATAC
* * * *
16720708 ATATATATATGTAACATCCATACTTTTAA-TAAAATCCAAGAATTTATACTCA--TATATACATA
1 ATATATAAATATAACATACATACTTTTAACT-AAATTCAAGAATTTAT--TCATGTATATACATA
** *
16720770 CCTATTCGAACCTCTTGT
63 TATATTCGAA-CT-TTAT
* * * * * *
16720788 A-A-ACATATATAACATTCA-AC-ATTAACTAAATTCAA-AACTTATTCATGTATATACACATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATAT
16720848 ATTCGAACTTTAT
66 ATTCGAACTTTAT
*
16720861 ATATATAAATATAACATACACACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATAT
*
16720926 ATCCGAACTTTAT
66 ATTCGAACTTTAT
16720939 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATAT
*
16721004 ATTTGAACTTTAT
66 ATTCGAACTTTAT
* * *
16721017 ATGTATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATGTATATACATATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATAT
16721082 TATCCACTAT
Statistics
Matches: 263, Mismatches: 23, Indels: 18
0.87 0.08 0.06
Matches are distributed among these distances:
73 7 0.03
74 3 0.01
75 36 0.14
76 13 0.05
77 17 0.06
78 185 0.70
79 1 0.00
80 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.38
Consensus pattern (78 bp):
ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATAT
ATTCGAACTTTAT
Found at i:16723413 original size:7 final size:7
Alignment explanation
Indices: 16723401--16723425 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16723391 TTCAAGTATT
16723401 ATTTTCA
1 ATTTTCA
16723408 ATTTTCA
1 ATTTTCA
16723415 ATTTTCA
1 ATTTTCA
16723422 ATTT
1 ATTT
16723426 GTATGTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTCA
Found at i:16729666 original size:12 final size:12
Alignment explanation
Indices: 16729649--16729673 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16729639 TCCCGTAAGT
16729649 TAGAATATGATC
1 TAGAATATGATC
16729661 TAGAATATGATC
1 TAGAATATGATC
16729673 T
1 T
16729674 TTTGTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TAGAATATGATC
Found at i:16735630 original size:2 final size:2
Alignment explanation
Indices: 16735625--16735703 Score: 77
Period size: 2 Copynumber: 39.5 Consensus size: 2
16735615 CAAAAACAAA
* * * * *
16735625 AT AT AT AT GT GT AT AT AT AT TT AT AT AT TT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
16735667 GT AT AT AT AT AT AT AA AT AT GT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16735704 AGCAAATCTA
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16735651 original size:20 final size:20
Alignment explanation
Indices: 16735625--16735703 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
16735615 CAAAAACAAA
16735625 ATATATATGTGTATATATAT
1 ATATATATGTGTATATATAT
*
16735645 -T-TATATAT-T-TATATAT
1 ATATATATGTGTATATATAT
*
16735661 A-A-ATATGTATATATATAT
1 ATATATATGTGTATATATAT
*
16735679 ATAAATATGTGTATATATAT
1 ATATATATGTGTATATATAT
16735699 ATATA
1 ATATA
16735704 AGCAAATCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
16 12 0.24
17 2 0.04
18 14 0.29
19 2 0.04
20 19 0.39
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (20 bp):
ATATATATGTGTATATATAT
Found at i:16735704 original size:22 final size:20
Alignment explanation
Indices: 16735648--16735701 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
16735638 TATATATTTA
*
16735648 TATATTTATATATAAATATG
1 TATATATATATATAAATATG
16735668 TATATATATATATAAATATG
1 TATATATATATATAAATATG
*
16735688 TGTATATATATATA
1 TATATATATATATA
16735702 TAAGCAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (20 bp):
TATATATATATATAAATATG
Found at i:16737152 original size:20 final size:20
Alignment explanation
Indices: 16737104--16737154 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
16737094 GGGCTGTATT
16737104 TTGTTTTGGG-TTTATTTGA
1 TTGTTTTGGGCTTTATTTGA
*
16737123 TCTGATTTGGGCTTTATTT-A
1 T-TGTTTTGGGCTTTATTTGA
16737143 TTGTTATTGGGC
1 TTGTT-TTGGGC
16737155 CGGACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 16 0.59
21 7 0.26
ACGTcount: A:0.12, C:0.06, G:0.25, T:0.57
Consensus pattern (20 bp):
TTGTTTTGGGCTTTATTTGA
Found at i:16740937 original size:24 final size:24
Alignment explanation
Indices: 16740910--16740955 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16740900 CACCAAAACT
* * *
16740910 AATCAAGGGCTGATATTAAAATTA
1 AATCAAAGGATGATATAAAAATTA
16740934 AATCAAAGGATGATATAAAAAT
1 AATCAAAGGATGATATAAAAAT
16740956 ATTTATGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (24 bp):
AATCAAAGGATGATATAAAAATTA
Found at i:16741410 original size:14 final size:14
Alignment explanation
Indices: 16741391--16741420 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16741381 GATGTGTTTA
*
16741391 AAACTAAATTTACT
1 AAACTAAATTAACT
16741405 AAACTAAATTAACT
1 AAACTAAATTAACT
16741419 AA
1 AA
16741421 GAACTCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (14 bp):
AAACTAAATTAACT
Found at i:16745413 original size:21 final size:21
Alignment explanation
Indices: 16745389--16745432 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
16745379 AATATTAATA
*
16745389 CTCATTCATCAATCTTAAATT
1 CTCAATCATCAATCTTAAATT
* * *
16745410 CTCAATCCTCAATTTTCAATT
1 CTCAATCATCAATCTTAAATT
16745431 CT
1 CT
16745433 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (21 bp):
CTCAATCATCAATCTTAAATT
Found at i:16745416 original size:14 final size:14
Alignment explanation
Indices: 16745392--16745457 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
16745382 ATTAATACTC
*
16745392 ATTCATCAATCTTAA
1 ATTC-TCAATCTTCA
*
16745407 ATTCTCAATCCTCA
1 ATTCTCAATCTTCA
*
16745421 ATTTTCAATTCTT-A
1 ATTCTCAA-TCTTCA
* * *
16745435 ATTTTTAATTTTCA
1 ATTCTCAATCTTCA
16745449 ATTCTCAAT
1 ATTCTCAAT
16745458 TATTTTTTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
13 3 0.07
14 31 0.76
15 7 0.17
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTCTCAATCTTCA
Found at i:16747913 original size:25 final size:23
Alignment explanation
Indices: 16747889--16747943 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
16747879 GGTAATTGTA
16747889 AATACTTGTGTAATAAATATATGT
1 AATACTT-TGTAATAAATATATGT
* *
16747913 -ATACATTTGTAATTAATATATAT
1 AATAC-TTTGTAATAAATATATGT
16747936 ACATACTT
1 A-ATACTT
16747944 ATTAATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 18 0.69
24 4 0.15
25 4 0.15
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (23 bp):
AATACTTTGTAATAAATATATGT
Found at i:16747936 original size:21 final size:22
Alignment explanation
Indices: 16747897--16747939 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
16747887 TAAATACTTG
16747897 TGTAATAAATATATGTATACATT
1 TGTAATAAATATA-GTATACATT
*
16747920 TGTAATTAATATA-TATACAT
1 TGTAATAAATATAGTATACAT
16747940 ACTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (22 bp):
TGTAATAAATATAGTATACATT
Found at i:16748025 original size:18 final size:18
Alignment explanation
Indices: 16747992--16748030 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
16747982 TTAATTAAGC
16747992 AAAAGAAAGAAATGAAAAT
1 AAAAGAAAGAAATG-AAAT
*
16748011 AAAAGAAA-CAATGAAAT
1 AAAAGAAAGAAATGAAAT
16748028 AAA
1 AAA
16748031 GATAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAAGAAAGAAATGAAAT
Found at i:16749233 original size:22 final size:22
Alignment explanation
Indices: 16749208--16749271 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 22
16749198 GCTCTGCTGA
16749208 TCAGGCACTTATGTGTTGTATT
1 TCAGGCACTTATGTGTTGTATT
* *
16749230 TCAGGCACCT-CGTG-TGTCATT
1 TCAGGCACTTATGTGTTGT-ATT
*
16749251 TCAGGCACTTATGTGTCGTAT
1 TCAGGCACTTATGTGTTGTAT
16749272 ACTAATCAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 3 0.09
21 15 0.44
22 14 0.41
23 2 0.06
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.39
Consensus pattern (22 bp):
TCAGGCACTTATGTGTTGTATT
Found at i:16752962 original size:2 final size:2
Alignment explanation
Indices: 16752955--16752980 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16752945 ATTCAGATAA
16752955 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16752981 GTGTGGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16762163 original size:23 final size:24
Alignment explanation
Indices: 16762129--16762173 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
16762119 CATCTCAATT
16762129 CACATATTCACAA-AT-ACATAAG
1 CACATATTCACAAGATAACATAAG
16762151 CACATAGTTCACAAGATAACATA
1 CACATA-TTCACAAGATAACATA
16762174 GGTATGGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 7 0.35
24 2 0.10
25 5 0.25
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.22
Consensus pattern (24 bp):
CACATATTCACAAGATAACATAAG
Found at i:16768551 original size:36 final size:36
Alignment explanation
Indices: 16768511--16768579 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
16768501 GAATTCTTTC
16768511 TTCTTAATTTTCCAACTCCTATCCAGCAACCAAACA
1 TTCTTAATTTTCCAACTCCTATCCAGCAACCAAACA
* * ** *
16768547 TTCTTGATTTTCCAGCTTTTGTCCAGCAACCAA
1 TTCTTAATTTTCCAACTCCTATCCAGCAACCAA
16768580 GCACTTAGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (36 bp):
TTCTTAATTTTCCAACTCCTATCCAGCAACCAAACA
Found at i:16771090 original size:11 final size:11
Alignment explanation
Indices: 16771076--16771151 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
16771066 GATAATCACT
16771076 TTAATATTAAA
1 TTAATATTAAA
16771087 TTAATA--AAA
1 TTAATATTAAA
*
16771096 -TACTATTAAGA
1 TTAATATTAA-A
*
16771107 TAAATATTAAA
1 TTAATATTAAA
16771118 TTAA-ATTTAATA
1 TTAATA-TTAA-A
16771130 TTAAATTATTAAA
1 TT-AA-TATTAAA
*
16771143 ATAATATTA
1 TTAATATTA
16771152 TTTTTAGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 20 0.39
12 12 0.24
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:16771129 original size:17 final size:17
Alignment explanation
Indices: 16771044--16771137 Score: 63
Period size: 17 Copynumber: 5.5 Consensus size: 17
16771034 GTAGATAAAC
*
16771044 ATTACATTAAATTTAAT
1 ATTAAATTAAATTTAAT
16771061 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAA--A-TTTAAT
**
16771081 ATTAAATT-AATAAAAT
1 ATTAAATTAAATTTAAT
* *
16771097 ACT--ATTAAGA-TAAAT
1 ATTAAATTAA-ATTTAAT
16771112 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
16771129 ATTAAATTA
1 ATTAAATTA
16771138 TTAAAATAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 3 0.05
15 7 0.12
16 8 0.13
17 26 0.43
18 1 0.02
19 3 0.05
20 12 0.20
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTAAATTAAATTTAAT
Found at i:16776140 original size:10 final size:10
Alignment explanation
Indices: 16776125--16776153 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
16776115 AGAAATATTT
16776125 TTAAAAAATA
1 TTAAAAAATA
16776135 TT-AAAAATA
1 TTAAAAAATA
16776144 TTAAAAAATA
1 TTAAAAAATA
16776154 AAGAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:16776162 original size:37 final size:37
Alignment explanation
Indices: 16776093--16776176 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 37
16776083 TTAAATCAAT
* *
16776093 AAAATATAAAAATATTAAATAGAGAAATA-TTTTTAA
1 AAAATATAAAAATATTAAATAAAGAAAAATTTTTTAA
*
16776129 AAAATATTAAAAATATTAAA-AAATAAAGAATTTTTTAA
1 AAAATA-TAAAAATATTAAATAAAGAAA-AATTTTTTAA
16776167 AAAATTATAA
1 AAAA-TATAA
16776177 TATTTATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 11 0.27
37 14 0.34
38 14 0.34
39 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (37 bp):
AAAATATAAAAATATTAAATAAAGAAAAATTTTTTAA
Found at i:16776677 original size:43 final size:43
Alignment explanation
Indices: 16776630--16776749 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
16776620 AGATCATGTT
16776630 CTTTAGCGGCACTTTTACCACAAATGCCGCTAAAGAACTTGAC
1 CTTTAGCGGCACTTTTACCACAAATGCCGCTAAAGAACTTGAC
* * **
16776673 CTTTAGCGGCGCTTTTACCACAAACGTTGCTAAAGAACTTGAC
1 CTTTAGCGGCACTTTTACCACAAATGCCGCTAAAGAACTTGAC
* ***
16776716 CTTTAGCGGTACTTTTGTTACAAATGCCGCTAAA
1 CTTTAGCGGCACTTTTACCACAAATGCCGCTAAA
16776750 AGTACCGTTC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCACTTTTACCACAAATGCCGCTAAAGAACTTGAC
Found at i:16781619 original size:123 final size:124
Alignment explanation
Indices: 16781398--16781702 Score: 450
Period size: 123 Copynumber: 2.5 Consensus size: 124
16781388 GAAAGTAAAT
* * * *
16781398 ACATAGTTACGGCGTTTTTGGTCAAAACGCCGCTATTACTTACCTTTTGCGGCATTTTCAACAAA
1 ACATAGTTGCGGCGTTTTTGGTCCAAACGCCACTATTACTTACCTTTTGCGGCGTTTTCAACAAA
* * * * * *
16781463 AATGCCACTAAAAAATTAAATTCTTGTATTGAAACGGTGCCATTTTGAAAAATTTTAAC
66 AACGCCACTAAAAAATTAAATTCTTGCACTGAAACGGCGCCATGTTGAAAAATGTTAAC
* * *
16781522 ACATAGTTGCGGCGTTTTTGGTCCAAACGCCACTATTTCTTA-CTTTTGTGGCGTTTTCACCAAA
1 ACATAGTTGCGGCGTTTTTGGTCCAAACGCCACTATTACTTACCTTTTGCGGCGTTTTCAACAAA
*
16781586 AACGCCACTAAAAAATTAAATTCTTGCACTGAAACGGCGCCATGTTGAAAAATGTTAAT
66 AACGCCACTAAAAAATTAAATTCTTGCACTGAAACGGCGCCATGTTGAAAAATGTTAAC
* * *
16781645 ACATATTTGCGGCGTTTATGGTCCAAACGCCACTATTGCTTACCTTTTGCGGCGTTTT
1 ACATAGTTGCGGCGTTTTTGGTCCAAACGCCACTATTACTTACCTTTTGCGGCGTTTT
16781703 TCTCATAAAC
Statistics
Matches: 162, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
123 110 0.68
124 52 0.32
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (124 bp):
ACATAGTTGCGGCGTTTTTGGTCCAAACGCCACTATTACTTACCTTTTGCGGCGTTTTCAACAAA
AACGCCACTAAAAAATTAAATTCTTGCACTGAAACGGCGCCATGTTGAAAAATGTTAAC
Found at i:16781815 original size:6 final size:6
Alignment explanation
Indices: 16781804--16781829 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16781794 AAGATTTTAA
16781804 AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AA
16781830 AAATGGTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:16782772 original size:7 final size:7
Alignment explanation
Indices: 16782762--16782828 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
16782752 ATCTTAAATA
16782762 CTAAACT
1 CTAAACT
16782769 CTAAACT
1 CTAAACT
16782776 CTAAA-T
1 CTAAACT
*
16782782 CTCAAACC
1 CT-AAACT
*
16782790 CCAAACT
1 CTAAACT
16782797 CTAAAC-
1 CTAAACT
*
16782803 CAGAAAC-
1 C-TAAACT
16782810 CATAAACT
1 C-TAAACT
*
16782818 CAAAACT
1 CTAAACT
16782825 CTAA
1 CTAA
16782829 TTCGAAAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 4 0.08
7 42 0.88
8 2 0.04
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.19
Consensus pattern (7 bp):
CTAAACT
Found at i:16782788 original size:21 final size:21
Alignment explanation
Indices: 16782756--16782801 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16782746 AAAAGAATCT
* *
16782756 TAAATACTAAACTCTAAACTC
1 TAAATACTAAACCCCAAACTC
16782777 TAAAT-CTCAAACCCCAAACTC
1 TAAATACT-AAACCCCAAACTC
16782798 TAAA
1 TAAA
16782802 CCAGAAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAATACTAAACCCCAAACTC
Found at i:16783104 original size:40 final size:40
Alignment explanation
Indices: 16783006--16783104 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
16782996 CGGTGTTTTC
* *
16783006 CAAAAAGCGCCACTAATGCTTGAACTATAGCAGCGTTTAT
1 CAAAAAGCGCCGCTAATGCTCGAACTATAGCAGCGTTTAT
* * *
16783046 CAAAAAGCGTCGCTAATGCTCGATCTATTGCAGCGTTTGA-
1 CAAAAAGCGCCGCTAATGCTCGAACTATAGCAGCGTTT-AT
* *
16783086 CATAAAGCGCCGCGAATGC
1 CAAAAAGCGCCGCTAATGC
16783105 AACTAAAGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
40 49 0.98
41 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (40 bp):
CAAAAAGCGCCGCTAATGCTCGAACTATAGCAGCGTTTAT
Found at i:16783473 original size:40 final size:40
Alignment explanation
Indices: 16783361--16783485 Score: 151
Period size: 40 Copynumber: 3.1 Consensus size: 40
16783351 CGTTTTGCAG
* * * *
16783361 AAAGCGCCGCTAATGCTTGATCTATAGCGACGTTTTTTAA
1 AAAGCACCGCTAATGCTCGATCTATTGCGGCGTTTTTTAA
* * *
16783401 AAAGCACCGCTAATTCTCGAGCTATTGTGGCGTTTTTTAA
1 AAAGCACCGCTAATGCTCGATCTATTGCGGCGTTTTTTAA
* * * *
16783441 AAAGTACCGCTAATGCTCGATCTTTTGCGGCGTTTGTGAA
1 AAAGCACCGCTAATGCTCGATCTATTGCGGCGTTTTTTAA
16783481 AAAGC
1 AAAGC
16783486 CTCGCTGATG
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (40 bp):
AAAGCACCGCTAATGCTCGATCTATTGCGGCGTTTTTTAA
Found at i:16783479 original size:195 final size:193
Alignment explanation
Indices: 16783141--16783508 Score: 472
Period size: 195 Copynumber: 1.9 Consensus size: 193
16783131 GTTGTTTTGT
* * * * *
16783141 TCAACTTTTTTGTGGTGTTTTCCAAAATGCACCGCTAATGGTTGATCTATAGCGGCATTTTTTAG
1 TCAACTTTTTTATGGCGTTTTCCAAAATGCACCGCTAATGCTTGATCTATAGCGACATTTTTTAA
* * * ** * *
16783206 AAATCGCCGCTAATGCTCGATCTATTGCGGCGCTTTTTAGTAAACGCTGAGAATGCTTGGTCTTT
66 AAAGCACCGCTAATGCTCGAGCTATTGCGGCGCTTTTTAAAAAACGCT--GAATGCTCGATCTTT
16783271 TGCAGCATTTGTGAAAAAGCACT-GCTGATGCCAATAAAGCTCACTAAAAAACGGCGTCGTTTTT
129 TGCAGCATTTGTGAAAAAGC-CTCGCTGATGCCAATAAAGCTCACTAAAAAACGGCGTCGTTTTT
16783335 C
193 C
* * *
16783336 TCAACTTTTTTATGGCGTTTTGCAGAAA-GCGCCGCTAATGCTTGATCTATAGCGACGTTTTTTA
1 TCAACTTTTTTATGGCGTTTTCCA-AAATGCACCGCTAATGCTTGATCTATAGCGACATTTTTTA
* * *
16783400 AAAAGCACCGCTAATTCTCGAGCTATTGTGGCGTTTTTTAAAAAGTACCGCT-AATGCTCGATCT
65 AAAAGCACCGCTAATGCTCGAGCTATTGCGGCGCTTTTTAAAAA--A-CGCTGAATGCTCGATCT
* *
16783464 TTTGCGGCGTTTGTGAAAAAGCCTCGCTGATGCCAATAAAGCTCA
127 TTTGCAGCATTTGTGAAAAAGCCTCGCTGATGCCAATAAAGCTCA
16783509 ACGACATTGT
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
194 2 0.01
195 138 0.93
196 3 0.02
197 1 0.01
198 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (193 bp):
TCAACTTTTTTATGGCGTTTTCCAAAATGCACCGCTAATGCTTGATCTATAGCGACATTTTTTAA
AAAGCACCGCTAATGCTCGAGCTATTGCGGCGCTTTTTAAAAAACGCTGAATGCTCGATCTTTTG
CAGCATTTGTGAAAAAGCCTCGCTGATGCCAATAAAGCTCACTAAAAAACGGCGTCGTTTTTC
Found at i:16795874 original size:17 final size:18
Alignment explanation
Indices: 16795852--16795888 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16795842 AAAAATACAT
16795852 AAAAAATGCTAAATT-TAA
1 AAAAAAT-CTAAATTATAA
16795870 AAAAAATCTAAATTATAA
1 AAAAAATCTAAATTATAA
16795888 A
1 A
16795889 TTTAGTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAAAATCTAAATTATAA
Found at i:16799198 original size:12 final size:12
Alignment explanation
Indices: 16799181--16799205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16799171 AAGTGAAGAA
16799181 ATTGCGTAATTT
1 ATTGCGTAATTT
16799193 ATTGCGTAATTT
1 ATTGCGTAATTT
16799205 A
1 A
16799206 GATTGATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (12 bp):
ATTGCGTAATTT
Found at i:16802599 original size:235 final size:235
Alignment explanation
Indices: 16802180--16802634 Score: 775
Period size: 235 Copynumber: 1.9 Consensus size: 235
16802170 CTCAAGTAAA
* *
16802180 ATACACATGAATGACACCCACACTTCTACCTCCACCTAGCGTTGTCTAGCTTGGCCCTCCACTTG
1 ATACACATGAACGACACCCACACCTCTACCTCCACCTAGCGTTGTCTAGCTTGGCCCTCCACTTG
* *
16802245 ATTCTCGAGTGAAAACCTTACCCTGCAAGTAAGCAAACAATTTGTAAGTTCAAATGAACTTAGTG
66 ATTCTCAAGTGAAAACCTTACCCTGCAAGTAAGCAAACAATTTGTAAGTTCAAATGAACTTAATG
** * *
16802310 AGATTCTATGTAATGACCATATAACAAGATTCAAAACTTCAAGAAATGAAGTTTTAAATAGAGAT
131 AGATTCTACATAATGACCATATAACAAGATTCAAAACTTCAAAAAATAAAGTTTTAAATAGAGAT
*
16802375 TTCAACTCCCTGGTCATCTTTGGCCTCAAGGGAGCCCCCT
196 TTCAACTCCCTGGTCATCCTTGGCCTCAAGGGAGCCCCCT
* *
16802415 ATACACATGAACGACACCCACACCTCTACCTCCACCTAGTGTTGTCTAGCTTGGCCCTCTACTTG
1 ATACACATGAACGACACCCACACCTCTACCTCCACCTAGCGTTGTCTAGCTTGGCCCTCCACTTG
*
16802480 ATTCTCAAGTGAAAACCTTATCCTGCAAGTAAGCAAACAATTTGTAAGTTCAAATGAACTTAATG
66 ATTCTCAAGTGAAAACCTTACCCTGCAAGTAAGCAAACAATTTGTAAGTTCAAATGAACTTAATG
* * *
16802545 AGATTCTGCATAATGACCATATAACAAGATTCAAAACTTTAAAAAATAAAGTTTTAAGTAGAGAT
131 AGATTCTACATAATGACCATATAACAAGATTCAAAACTTCAAAAAATAAAGTTTTAAATAGAGAT
16802610 TTCAACTCCCTGGTCATCCTTGGCC
196 TTCAACTCCCTGGTCATCCTTGGCC
16802635 ATTCGTAGAT
Statistics
Matches: 205, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
235 205 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (235 bp):
ATACACATGAACGACACCCACACCTCTACCTCCACCTAGCGTTGTCTAGCTTGGCCCTCCACTTG
ATTCTCAAGTGAAAACCTTACCCTGCAAGTAAGCAAACAATTTGTAAGTTCAAATGAACTTAATG
AGATTCTACATAATGACCATATAACAAGATTCAAAACTTCAAAAAATAAAGTTTTAAATAGAGAT
TTCAACTCCCTGGTCATCCTTGGCCTCAAGGGAGCCCCCT
Found at i:16804264 original size:20 final size:20
Alignment explanation
Indices: 16804239--16804277 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
16804229 TTGCTTCATC
16804239 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
16804259 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
16804278 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:16804621 original size:50 final size:50
Alignment explanation
Indices: 16804549--16804673 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
16804539 TATCCTAGAT
** ** * *
16804549 ATGGTCTTACATGGGAGTTCTCATATCGGTCCCCATGCCATGTCCCAGAC
1 ATGGTCTTACGGGGGACCTCTCATATCGGTCCCAACGCCATGTCCCAGAC
* * *
16804599 ATGGTTTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACGGGGGACCTCTCATATCGGTCCCAACGCCATGTCCCAGAC
* *
16804649 ATGGTCTTATGTGGGACCTCTCATA
1 ATGGTCTTACGGGGGACCTCTCATA
16804674 ACCTCAATAA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACGGGGGACCTCTCATATCGGTCCCAACGCCATGTCCCAGAC
Found at i:16818958 original size:17 final size:18
Alignment explanation
Indices: 16818920--16818959 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
16818910 GTAGTTATCA
16818920 CAATTTTTATTAAATTAT
1 CAATTTTTATTAAATTAT
16818938 -AATTATTT-TTAAA-TAT
1 CAATT-TTTATTAAATTAT
16818954 CAATTT
1 CAATTT
16818960 AGTAATAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
16 4 0.20
17 13 0.65
18 3 0.15
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
CAATTTTTATTAAATTAT
Found at i:16821157 original size:11 final size:11
Alignment explanation
Indices: 16821135--16821208 Score: 100
Period size: 11 Copynumber: 6.9 Consensus size: 11
16821125 GGTCCATTTT
16821135 TATTTT-AAAA
1 TATTTTAAAAA
16821145 T-TTTTAAAAA
1 TATTTTAAAAA
**
16821155 -ATTAAAAAAA
1 TATTTTAAAAA
16821165 GTATTTTAAAAA
1 -TATTTTAAAAA
16821177 TATTTTAAAAA
1 TATTTTAAAAA
16821188 TATTTTAAAAA
1 TATTTTAAAAA
16821199 TATTTTAAAA
1 TATTTTAAAA
16821209 TTAAAAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
9 4 0.07
10 12 0.21
11 32 0.57
12 8 0.14
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:16821248 original size:22 final size:19
Alignment explanation
Indices: 16821172--16821259 Score: 70
Period size: 22 Copynumber: 4.4 Consensus size: 19
16821162 AAAGTATTTT
*
16821172 AAAAATATTTTAAAAATATTTT
1 AAAAATATTTT-AAAATA--TA
16821194 AAAAATATTTTAAAAT-TA
1 AAAAATATTTTAAAATATA
* **
16821212 AAAAAAATTAAAAAAGTAAGTA
1 AAAAATATTTTAAAA-T-A-TA
*
16821234 AAAAATATTTTAAAATTTA
1 AAAAATATTTTAAAATATA
16821253 AAAAATA
1 AAAAATA
16821260 AATATATTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
18 13 0.24
19 10 0.19
21 6 0.11
22 25 0.46
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAATATTTTAAAATATA
Found at i:16828285 original size:24 final size:24
Alignment explanation
Indices: 16828253--16828308 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
16828243 GTGAGCATTA
16828253 ATGTAAAGGAAAAGTTACGGTTAT
1 ATGTAAAGGAAAAGTTACGGTTAT
16828277 ATGTAAAGGAAAAGTTACGGTTAT
1 ATGTAAAGGAAAAGTTACGGTTAT
16828301 ATGTAAAG
1 ATGTAAAG
16828309 TCACACTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.43, C:0.04, G:0.25, T:0.29
Consensus pattern (24 bp):
ATGTAAAGGAAAAGTTACGGTTAT
Found at i:16828458 original size:17 final size:18
Alignment explanation
Indices: 16828427--16828460 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16828417 GTGATGTATC
*
16828427 TTATGAAATTCACTTATG
1 TTATGAAATTAACTTATG
16828445 TTAT-AAATTAACTTAT
1 TTATGAAATTAACTTAT
16828461 ATGTGATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (18 bp):
TTATGAAATTAACTTATG
Found at i:16832842 original size:13 final size:14
Alignment explanation
Indices: 16832826--16832856 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
16832816 TAAATAAAAC
16832826 TTAATTAAAATT-A
1 TTAATTAAAATTAA
16832839 TTAATTAAAATTAA
1 TTAATTAAAATTAA
16832853 TTAA
1 TTAA
16832857 AAGTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAATTAAAATTAA
Found at i:16835031 original size:41 final size:42
Alignment explanation
Indices: 16834969--16835067 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
16834959 GATCTCAGTA
* * *
16834969 TCGCACATTTAGTGCCTGTTATTC-ACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAGTT
16835010 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAGTT
1 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAGTT
16835052 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
16835068 ATTCATATAG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 22 0.41
42 32 0.59
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAGTT
Found at i:16836841 original size:43 final size:43
Alignment explanation
Indices: 16836795--16837023 Score: 230
Period size: 43 Copynumber: 5.3 Consensus size: 43
16836785 TTTCCTTAGA
* * * *
16836795 TTTATCTAATGATGCACTATTTGTGCCAATATGATTGCTTCAA
1 TTTATCTGATGATGCACTATGTGTGCCAGTATGATTGCTTCAG
* * * **
16836838 TTTATTTGATGATGCACTATGCGTGCCAGTATGAAAT-CTTTGG
1 TTTATCTGATGATGCACTATGTGTGCCAGTATG-ATTGCTTCAG
* * *
16836881 TTTATCCGATGATGCACTATGTGTGCTAGTATGATTACTTCAG
1 TTTATCTGATGATGCACTATGTGTGCCAGTATGATTGCTTCAG
* * * **
16836924 TTAATCTGATGATCCACTATGTGTGTCAGTATGATTGCTTTGG
1 TTTATCTGATGATGCACTATGTGTGCCAGTATGATTGCTTCAG
* * *
16836967 TTTATTTGATGATGCACTATGTGTG-CAGTAT-ATTTCCTTCGG
1 TTTATCTGATGATGCACTATGTGTGCCAGTATGA-TTGCTTCAG
*
16837009 TTTATTTGATGATGC
1 TTTATCTGATGATGC
16837024 TTTGCGTTGC
Statistics
Matches: 154, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 30 0.19
43 121 0.79
44 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (43 bp):
TTTATCTGATGATGCACTATGTGTGCCAGTATGATTGCTTCAG
Done.