Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 54 of 167
Found at i:16660692 original size:24 final size:24
Alignment explanation
Indices: 16660665--16660712 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
16660655 TATTTTGAAA
16660665 GACATATCTATATTAGTAAATTTT
1 GACATATCTATATTAGTAAATTTT
16660689 GACATATCTATATTAGTAAATTTT
1 GACATATCTATATTAGTAAATTTT
16660713 ACTTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (24 bp):
GACATATCTATATTAGTAAATTTT
Found at i:16661133 original size:149 final size:149
Alignment explanation
Indices: 16660863--16661159 Score: 576
Period size: 149 Copynumber: 2.0 Consensus size: 149
16660853 GGGAAACAAT
16660863 ACCTCACGAGTGCCATGTTCAACGACCCAATTTCTTCATCTAGCCAAGAATAATAGTCGCTACCA
1 ACCTCACGAGTGCCATGTTCAACGACCCAATTTCTTCATCTAGCCAAGAATAATAGTCGCTACCA
* *
16660928 CTTTCCCTGAACACTCCATCCTCAGAATCAAGCTCCACATCCATATAACGGGGAGTTTCACCTCC
66 CTTTCCCCGAACACTCCATCCTCAGAATCAAGCTCCACATCCATATAACAGGGAGTTTCACCTCC
16660993 TTTCCTCTTATGATTTTCC
131 TTTCCTCTTATGATTTTCC
16661012 ACCTCACGAGTGCCATGTTCAACGACCCAATTTCTTCATCTAGCCAAGAATAATAGTCGCTACCA
1 ACCTCACGAGTGCCATGTTCAACGACCCAATTTCTTCATCTAGCCAAGAATAATAGTCGCTACCA
16661077 CTTTCCCCGAACACTCCATCCTCAGAATCAAGCTCCACATCCATATAACAGGGAGTTTCACCTCC
66 CTTTCCCCGAACACTCCATCCTCAGAATCAAGCTCCACATCCATATAACAGGGAGTTTCACCTCC
16661142 TTTCCTCTTATGATTTTC
131 TTTCCTCTTATGATTTTC
16661160 TTTATTTTGA
Statistics
Matches: 146, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 146 1.00
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.29
Consensus pattern (149 bp):
ACCTCACGAGTGCCATGTTCAACGACCCAATTTCTTCATCTAGCCAAGAATAATAGTCGCTACCA
CTTTCCCCGAACACTCCATCCTCAGAATCAAGCTCCACATCCATATAACAGGGAGTTTCACCTCC
TTTCCTCTTATGATTTTCC
Found at i:16663666 original size:13 final size:13
Alignment explanation
Indices: 16663650--16663682 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16663640 TTTAATTAAA
*
16663650 TTAGTTAATTAGT
1 TTAGATAATTAGT
16663663 TTAGATAATTAGT
1 TTAGATAATTAGT
16663676 TTA-ATAA
1 TTAGATAA
16663683 ACAAATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:16674968 original size:8 final size:8
Alignment explanation
Indices: 16674920--16674979 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
16674910 AGCCGGCAGC
16674920 AAAGAAGAA
1 AAAG-AGAA
16674929 AAAGA-AA
1 AAAGAGAA
16674936 ATAAGAGAA
1 A-AAGAGAA
* *
16674945 GAAG-GAT
1 AAAGAGAA
*
16674952 AAAGCGAA
1 AAAGAGAA
16674960 AAAGAGAA
1 AAAGAGAA
16674968 AAAG-GAA
1 AAAGAGAA
16674975 AAAGA
1 AAAGA
16674980 AAGAAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
7 15 0.36
8 21 0.50
9 6 0.14
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAGAGAA
Found at i:16674977 original size:15 final size:16
Alignment explanation
Indices: 16674920--16674979 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 16
16674910 AGCCGGCAGC
16674920 AAAGAAGAAAAAGA-AA
1 AAAG-AGAAAAAGAGAA
* *
16674936 ATAAGAGAAGAAG-GAT
1 A-AAGAGAAAAAGAGAA
*
16674952 AAAGCGAAAAAGAGAA
1 AAAGAGAAAAAGAGAA
16674968 AAAG-GAAAAAGA
1 AAAGAGAAAAAGA
16674980 AAGAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 17 0.47
16 16 0.44
17 3 0.08
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.03
Consensus pattern (16 bp):
AAAGAGAAAAAGAGAA
Found at i:16679404 original size:28 final size:27
Alignment explanation
Indices: 16679372--16679439 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 27
16679362 TTCACCACAG
*
16679372 GCTATTCTTTTCAAAGTTTGCCACAAA
1 GCTATTCTTTTCAAAGTTCGCCACAAA
*
16679399 TGCTATTCTTTTCATAGTTCGCCACAAA
1 -GCTATTCTTTTCAAAGTTCGCCACAAA
16679427 GACTATTCTTTTC
1 G-CTATTCTTTTC
16679440 TGTCGTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.41
Consensus pattern (27 bp):
GCTATTCTTTTCAAAGTTCGCCACAAA
Found at i:16681408 original size:19 final size:19
Alignment explanation
Indices: 16681384--16681422 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
16681374 AGAAGCTAAG
16681384 AGATAACTTTTCGAACGCT
1 AGATAACTTTTCGAACGCT
16681403 AGATAACTTTTCGAACGCT
1 AGATAACTTTTCGAACGCT
16681422 A
1 A
16681423 TGAAGACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (19 bp):
AGATAACTTTTCGAACGCT
Found at i:16685759 original size:13 final size:13
Alignment explanation
Indices: 16685741--16685767 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16685731 TTTTAAAATA
16685741 TGAAAAATAAAAG
1 TGAAAAATAAAAG
16685754 TGAAAAATAAAAG
1 TGAAAAATAAAAG
16685767 T
1 T
16685768 ATAAGGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.19
Consensus pattern (13 bp):
TGAAAAATAAAAG
Found at i:16693055 original size:10 final size:11
Alignment explanation
Indices: 16693036--16693068 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
16693026 TTATTTAGTT
16693036 TAATTATAATA
1 TAATTATAATA
16693047 TAA-TATAATA
1 TAATTATAATA
16693057 TAATTATAATA
1 TAATTATAATA
16693068 T
1 T
16693069 TTTCTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TAATTATAATA
Found at i:16704292 original size:19 final size:20
Alignment explanation
Indices: 16704255--16704291 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
16704245 TGGTAATGTT
16704255 AATGTTTTAATTGAATTTTG
1 AATGTTTTAATTGAATTTTG
16704275 AATG-TTTAATTG-ATTTT
1 AATGTTTTAATTGAATTTT
16704292 TATGTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (20 bp):
AATGTTTTAATTGAATTTTG
Found at i:16711220 original size:4 final size:4
Alignment explanation
Indices: 16711204--16711255 Score: 50
Period size: 4 Copynumber: 13.0 Consensus size: 4
16711194 AATAAAAGAT
* * * * * *
16711204 CATA CAAA CATA CATA CATA CATG CATG CATG CATG CATA CATA CACA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
16711252 CATA
1 CATA
16711256 TATCTGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.44, C:0.27, G:0.08, T:0.21
Consensus pattern (4 bp):
CATA
Found at i:16712473 original size:20 final size:18
Alignment explanation
Indices: 16712426--16712474 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
16712416 TTCAATTATG
16712426 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
16712443 ATTAAGA-TAATTACTTTAAT
1 ATTAA-ATTAA-TA-TTTAAT
16712463 ATTAAATTAATA
1 ATTAAATTAATA
16712475 ATGTAACACC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 4 0.15
20 14 0.52
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:16721108 original size:56 final size:56
Alignment explanation
Indices: 16721005--16721111 Score: 169
Period size: 56 Copynumber: 1.9 Consensus size: 56
16720995 TTACATGTAA
* * *
16721005 TCACATATCGATGCCACTGTCCCAGACAGTGTCTTACTTACATACATATATTGGAG
1 TCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTCACACACATATATTGGAG
* *
16721061 TCACATATCGATGCCACTGTCCCTGACAGGGTCTTACTCGCACACATATAT
1 TCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTCACACACATATAT
16721112 CTATGCCATG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (56 bp):
TCACATATCGATGCCACTGTCCCAGACAGGGTCTTACTCACACACATATATTGGAG
Found at i:16723219 original size:19 final size:20
Alignment explanation
Indices: 16723195--16723236 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
16723185 TTCGACCAGT
*
16723195 TTTTGGG-TCTTGGTCTCAA
1 TTTTGGGCTCTTGGCCTCAA
16723214 TTTTGGGCTCTTGGCCTCAA
1 TTTTGGGCTCTTGGCCTCAA
16723234 TTT
1 TTT
16723237 AAGATCTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.48
Consensus pattern (20 bp):
TTTTGGGCTCTTGGCCTCAA
Found at i:16724478 original size:36 final size:36
Alignment explanation
Indices: 16724431--16724502 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
16724421 TCTTCAGTTT
* * *
16724431 GAACTTAGGCAATCTATGAGCTAATATTTGCTTGTC
1 GAACTTAGGCAATCAATAACCTAATATTTGCTTGTC
16724467 GAACTTAGGCAATCAATAACCTAATATTTGCTTGTC
1 GAACTTAGGCAATCAATAACCTAATATTTGCTTGTC
16724503 ACAATTTCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (36 bp):
GAACTTAGGCAATCAATAACCTAATATTTGCTTGTC
Found at i:16725146 original size:21 final size:21
Alignment explanation
Indices: 16725117--16725174 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
16725107 ATTTTTAGAC
*
16725117 TTTAGTTTTTAGGATTTTATT
1 TTTAATTTTTAGGATTTTATT
* ** **
16725138 TTTATTTTTTATTACATTATT
1 TTTAATTTTTAGGATTTTATT
16725159 TTTAATTTTTAGGATT
1 TTTAATTTTTAGGATT
16725175 GGGTTGGATT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (21 bp):
TTTAATTTTTAGGATTTTATT
Found at i:16726358 original size:39 final size:40
Alignment explanation
Indices: 16726301--16726387 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 40
16726291 TATTTGGCTA
* *
16726301 AATAAATTTATTTGTTAAA-AAATTTATCATACAT-ATAAAT
1 AATAATTTTAATTGTTAAATAAATTTAT-ATA-ATAATAAAT
*
16726341 AATAATTTTAATT-TTAAATGAATTTATATAATAATAAAT
1 AATAATTTTAATTGTTAAATAAATTTATATAATAATAAAT
*
16726380 AAAAATTT
1 AATAATTT
16726388 AAAATTTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.05
39 21 0.51
40 18 0.44
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (40 bp):
AATAATTTTAATTGTTAAATAAATTTATATAATAATAAAT
Found at i:16737164 original size:55 final size:55
Alignment explanation
Indices: 16737087--16737199 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
16737077 TTATTAAAGA
16737087 GAATGTTTCTTAGGGTTAATATAGGATATCGCAGGGAGCCCAGCCTACTTAAAAT
1 GAATGTTTCTTAGGGTTAATATAGGATATCGCAGGGAGCCCAGCCTACTTAAAAT
16737142 GAATGTTTCTTAGGGTTAATATAGGATATCGCAGGGAGCCCAGCCTACTTAAAAT
1 GAATGTTTCTTAGGGTTAATATAGGATATCGCAGGGAGCCCAGCCTACTTAAAAT
16737197 GAA
1 GAA
16737200 AAAAATTTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (55 bp):
GAATGTTTCTTAGGGTTAATATAGGATATCGCAGGGAGCCCAGCCTACTTAAAAT
Found at i:16737822 original size:17 final size:17
Alignment explanation
Indices: 16737800--16737832 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16737790 CATTCAAAAG
*
16737800 ATGTAGTAAAAAATGTT
1 ATGTAGCAAAAAATGTT
16737817 ATGTAGCAAAAAATGT
1 ATGTAGCAAAAAATGT
16737833 CAATTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.30
Consensus pattern (17 bp):
ATGTAGCAAAAAATGTT
Found at i:16738259 original size:97 final size:97
Alignment explanation
Indices: 16738150--16738347 Score: 267
Period size: 97 Copynumber: 2.0 Consensus size: 97
16738140 TTAATTCATC
* *
16738150 TTTTTAATTAAT-AACTCTTTTATTTATATAAATAAAGTAA-AGA-AATTTAATTATATAATAAA
1 TTTTTAATTAATAAATTC-TTTATTTATATAAATAAAGTAATA-ATAATATAATTATATAATAAA
16738212 ATATAATTTATATATATATCATTATGTTAAAAATA
64 A-ATAATTTATATATATATCATTATGTTAAAAATA
* * *
16738247 TTTTTAATTAATAAATTCTTTATTTATGTAAATAAATTAATAATTATATAATTATATAATAAAAA
1 TTTTTAATTAATAAATTCTTTATTTATATAAATAAAGTAATAATAATATAATTATATAATAAAAA
* * * *
16738312 TATTTTTTATATTTATCATTATGTTGAAAATA
66 TAATTTATATATATATCATTATGTTAAAAATA
16738344 TTTT
1 TTTT
16738348 ATTTCTTAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
97 66 0.74
98 23 0.26
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (97 bp):
TTTTTAATTAATAAATTCTTTATTTATATAAATAAAGTAATAATAATATAATTATATAATAAAAA
TAATTTATATATATATCATTATGTTAAAAATA
Found at i:16744085 original size:163 final size:163
Alignment explanation
Indices: 16743906--16744231 Score: 652
Period size: 163 Copynumber: 2.0 Consensus size: 163
16743896 ATAACTATTT
16743906 CAATAAACATGTATCCCAAGTTTTTATGCAAATTTGTCAACTTATATATATATATATTGTATGAT
1 CAATAAACATGTATCCCAAGTTTTTATGCAAATTTGTCAACTTATATATATATATATTGTATGAT
16743971 CATTAATTCATCATTATGTTGAAAATGTCTTATATTGATTTCTAATTCCATTTTGTTTCATACAT
66 CATTAATTCATCATTATGTTGAAAATGTCTTATATTGATTTCTAATTCCATTTTGTTTCATACAT
16744036 TTTTTTGTGCATCATTTTATTTTGTGTCATGTA
131 TTTTTTGTGCATCATTTTATTTTGTGTCATGTA
16744069 CAATAAACATGTATCCCAAGTTTTTATGCAAATTTGTCAACTTATATATATATATATTGTATGAT
1 CAATAAACATGTATCCCAAGTTTTTATGCAAATTTGTCAACTTATATATATATATATTGTATGAT
16744134 CATTAATTCATCATTATGTTGAAAATGTCTTATATTGATTTCTAATTCCATTTTGTTTCATACAT
66 CATTAATTCATCATTATGTTGAAAATGTCTTATATTGATTTCTAATTCCATTTTGTTTCATACAT
16744199 TTTTTTGTGCATCATTTTATTTTGTGTCATGTA
131 TTTTTTGTGCATCATTTTATTTTGTGTCATGTA
16744232 AATTATCGTG
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 163 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.48
Consensus pattern (163 bp):
CAATAAACATGTATCCCAAGTTTTTATGCAAATTTGTCAACTTATATATATATATATTGTATGAT
CATTAATTCATCATTATGTTGAAAATGTCTTATATTGATTTCTAATTCCATTTTGTTTCATACAT
TTTTTTGTGCATCATTTTATTTTGTGTCATGTA
Found at i:16748887 original size:3 final size:3
Alignment explanation
Indices: 16748872--16748946 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
16748862 AATACTAACG
* ** * *
16748872 ATA ATA GTA ATA ATA ATA ACC ATA ATA ATA ATA GTA A-A CTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
16748919 ATA TTTA A-A ATA ATA ATA ATA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
16748947 CATAAAATTG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.05
3 52 0.91
4 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16749003 original size:29 final size:29
Alignment explanation
Indices: 16748958--16749045 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
16748948 ATAAAATTGC
16748958 TAAAATAT-GGGCTAAATCGAAATAAAACA
1 TAAAATATAGGGCTAAATCGAAATAAAA-A
* * *
16748987 -AAAATATAGGGCGAAATTGAAAGAAAAA
1 TAAAATATAGGGCTAAATCGAAATAAAAA
* *
16749015 TAAAATAAAAGGGACTAAATCAAAATAAAAA
1 TAAAAT-ATAGGG-CTAAATCGAAATAAAAA
16749046 AAGAAACTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 8 0.17
29 21 0.45
30 5 0.11
31 13 0.28
ACGTcount: A:0.61, C:0.07, G:0.15, T:0.17
Consensus pattern (29 bp):
TAAAATATAGGGCTAAATCGAAATAAAAA
Found at i:16749761 original size:10 final size:10
Alignment explanation
Indices: 16749748--16749786 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
16749738 AAAAACAACA
*
16749748 AAAATAAAAT
1 AAAATAAAAG
16749758 AAAATAAAAGG
1 AAAATAAAA-G
16749769 AAAAT-AAAG
1 AAAATAAAAG
16749778 AAAATAAAA
1 AAAATAAAA
16749787 ACGCAAGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 6 0.23
10 15 0.58
11 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (10 bp):
AAAATAAAAG
Found at i:16749787 original size:21 final size:21
Alignment explanation
Indices: 16749748--16749786 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16749738 AAAAACAACA
*
16749748 AAAATAAAATAAAATAAAAGG
1 AAAATAAAAGAAAATAAAAGG
16749769 AAAAT-AAAGAAAATAAAA
1 AAAATAAAAGAAAATAAAA
16749787 ACGCAAGAAC
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:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (21 bp):
AAAATAAAAGAAAATAAAAGG
Found at i:16751159 original size:17 final size:17
Alignment explanation
Indices: 16751139--16751193 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
16751129 AAAAATCAAA
16751139 AAAAATTAAAAATAATT
1 AAAAATTAAAAATAATT
*
16751156 AAAAATAAAAAAGTAA-T
1 AAAAATTAAAAA-TAATT
*
16751173 AGAAA-T-AAAAT-ATT
1 AAAAATTAAAAATAATT
16751187 AAAAATT
1 AAAAATT
16751194 TATTTAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 1 0.03
14 6 0.19
15 5 0.16
17 16 0.52
18 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (17 bp):
AAAAATTAAAAATAATT
Found at i:16751221 original size:9 final size:9
Alignment explanation
Indices: 16751207--16751334 Score: 87
Period size: 10 Copynumber: 13.2 Consensus size: 9
16751197 TTAAACCTAC
16751207 AAAAATTAT
1 AAAAATTAT
16751216 AAAAATTCAT
1 AAAAATT-AT
16751226 AAAAACTTAT
1 AAAAA-TTAT
* *
16751236 AAATATTTT
1 AAAAATTAT
*
16751245 ATAAATTAT
1 AAAAATTAT
16751254 AAAAATAATTAT
1 --AAA-AATTAT
*
16751266 AAAAAATA-
1 AAAAATTAT
*
16751274 AAACATATTAA
1 AAA-A-ATTAT
16751285 AAATAATTAT
1 AAA-AATTAT
16751295 AAAAATTAT
1 AAAAATTAT
* *
16751304 AATAAGTTCT
1 AA-AAATTAT
16751314 AATAAATTAT
1 AA-AAATTAT
*
16751324 ATAAATTAT
1 AAAAATTAT
16751333 AA
1 AA
16751335 TTTTTAATAA
Statistics
Matches: 94, Mismatches: 16, Indels: 18
0.73 0.12 0.14
Matches are distributed among these distances:
8 3 0.03
9 37 0.39
10 40 0.43
11 8 0.09
12 6 0.06
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:16751231 original size:29 final size:28
Alignment explanation
Indices: 16751199--16751258 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
16751189 AAATTTATTT
16751199 AAACCTACAAAAATTATAAAAATTCATAA
1 AAACCTACAAAAATTATAAAAATT-ATAA
* * * * *
16751228 AAACTTATAAATATTTTATAAATTATAA
1 AAACCTACAAAAATTATAAAAATTATAA
16751256 AAA
1 AAA
16751259 TAATTATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (28 bp):
AAACCTACAAAAATTATAAAAATTATAA
Found at i:16751253 original size:18 final size:19
Alignment explanation
Indices: 16751207--16751334 Score: 68
Period size: 19 Copynumber: 6.6 Consensus size: 19
16751197 TTAAACCTAC
16751207 AAAAATTATAAAAATTCAT
1 AAAAATTATAAAAATTCAT
* *
16751226 AAAAACTTATAAATATT-TT
1 AAAAA-TTATAAAAATTCAT
* *
16751245 ATAAATTATAAAAATAATTAT
1 AAAAATTATAAAAAT--TCAT
* *
16751266 AAAAA--ATAAAACATATTAA
1 AAAAATTATAAAA-AT-TCAT
16751285 AAATAATTATAAAAATT-AT
1 AAA-AATTATAAAAATTCAT
* *
16751304 AATAAGTTCTAATAAATT-AT
1 AA-AAATTATAA-AAATTCAT
*
16751324 ATAAATTATAA
1 AAAAATTATAA
16751335 TTTTTAATAA
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
18 9 0.10
19 39 0.45
20 25 0.29
21 7 0.08
22 6 0.07
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (19 bp):
AAAAATTATAAAAATTCAT
Found at i:16751265 original size:12 final size:12
Alignment explanation
Indices: 16751248--16751300 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 12
16751238 ATATTTTATA
16751248 AATTATAAAAAT
1 AATTATAAAAAT
16751260 AATTATAAAAAAT
1 AATTAT-AAAAAT
*
16751273 AAAACATATTAAAAAT
1 --AA-TTA-TAAAAAT
16751289 AATTATAAAAAT
1 AATTATAAAAAT
16751301 TATAATAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
12 13 0.38
13 8 0.24
14 2 0.06
15 2 0.06
16 8 0.24
17 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
AATTATAAAAAT
Found at i:16751342 original size:26 final size:27
Alignment explanation
Indices: 16751289--16751356 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
16751279 TATTAAAAAT
16751289 AATTATAAAAATTATAATAAGTTCTAATA
1 AATTATAAAAATTATAAT-A-TTCTAATA
* *
16751318 AATTATATAAATTATAAT-TTTTAATAA
1 AATTATAAAAATTATAATATTCTAAT-A
*
16751345 AATTAAAAAAAT
1 AATTATAAAAAT
16751357 ATGTAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 6 0.18
27 11 0.32
29 17 0.50
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (27 bp):
AATTATAAAAATTATAATATTCTAATA
Found at i:16752838 original size:21 final size:21
Alignment explanation
Indices: 16752817--16752855 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16752807 TTTTATGTTA
*
16752817 AATAA-GGTTATAATAATATT
1 AATAATGGTTAAAATAATATT
16752837 AATAATGGTTAAAATAATA
1 AATAATGGTTAAAATAATA
16752856 AAACATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (21 bp):
AATAATGGTTAAAATAATATT
Found at i:16770643 original size:18 final size:18
Alignment explanation
Indices: 16770620--16770654 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16770610 TACGCCCGCT
16770620 ACTCCCAAGGCGGAGACC
1 ACTCCCAAGGCGGAGACC
*
16770638 ACTCCCACGGCGGAGAC
1 ACTCCCAAGGCGGAGAC
16770655 GGTAAGCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.40, G:0.29, T:0.06
Consensus pattern (18 bp):
ACTCCCAAGGCGGAGACC
Found at i:16777629 original size:18 final size:18
Alignment explanation
Indices: 16777606--16777640 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16777596 ATGCAAATAT
*
16777606 ATAAAAACAATAAATAAC
1 ATAAAAACAACAAATAAC
*
16777624 ATAAAAATAACAAATAA
1 ATAAAAACAACAAATAA
16777641 TTTATGAGAT
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:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAAAACAACAAATAAC
Found at i:16778018 original size:14 final size:14
Alignment explanation
Indices: 16777999--16778040 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
16777989 ATTTTAAAAT
16777999 TATACATAATATAA
1 TATACATAATATAA
*
16778013 TATAC--AATAAAA
1 TATACATAATATAA
*
16778025 TATAAATAATATAA
1 TATACATAATATAA
16778039 TA
1 TA
16778041 GATAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
TATACATAATATAA
Found at i:16778047 original size:26 final size:27
Alignment explanation
Indices: 16777993--16778047 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
16777983 TTACAGATTT
* *
16777993 TAAAATTATACATAATATAATATACAA
1 TAAAATTATAAATAATATAATAGACAA
*
16778020 TAAAA-TATAAATAATATAATAGATAA
1 TAAAATTATAAATAATATAATAGACAA
16778046 TA
1 TA
16778048 CAAAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAAATTATAAATAATATAATAGACAA
Found at i:16778788 original size:19 final size:18
Alignment explanation
Indices: 16778751--16778794 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
16778741 ATACATACAG
16778751 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
16778768 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
16778787 TACTAATT
1 TAATAATT
16778795 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:16780805 original size:51 final size:51
Alignment explanation
Indices: 16780728--16780977 Score: 392
Period size: 51 Copynumber: 4.9 Consensus size: 51
16780718 TGGATACACG
* *
16780728 GTGGCCTTCACATAGTACCACCCTTGTATCCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* * *
16780779 ATGGCCTTCACATAGTGCCACACTTGTGTCCAAATCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* *
16780830 GTGACCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* * **
16780881 GTGGCCTTCACATAGTACCACATTTGTGTCCAAAGCTATTATATTCATGAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
*
16780932 GTGGCCTTCACATAGTACCACACTTTTGTCCAAAGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
16780978 CTAAGGTTCA
Statistics
Matches: 182, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 182 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
Found at i:16781038 original size:28 final size:28
Alignment explanation
Indices: 16781003--16781092 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 28
16780993 GAAATTTCTT
16781003 ACTTAGCACGA-TGCCATAGACTTATTTC
1 ACTTAGCAC-ATTGCCATAGACTTATTTC
16781031 ACTTAGCACATTGCCATAGACTTATTTC
1 ACTTAGCACATTGCCATAGACTTATTTC
* * *
16781059 ACTTAG---A-TACCATGGTCTTATTTC
1 ACTTAGCACATTGCCATAGACTTATTTC
16781083 ACTTAGCACA
1 ACTTAGCACA
16781093 ATGTCATATC
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
24 20 0.36
25 1 0.02
27 2 0.04
28 32 0.58
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (28 bp):
ACTTAGCACATTGCCATAGACTTATTTC
Found at i:16782415 original size:14 final size:14
Alignment explanation
Indices: 16782396--16782437 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
16782386 ATTTTAAAAT
16782396 TATACATAATATAA
1 TATACATAATATAA
*
16782410 TATAC--AATAAAA
1 TATACATAATATAA
*
16782422 TATAAATAATATAA
1 TATACATAATATAA
16782436 TA
1 TA
16782438 GATAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
TATACATAATATAA
Found at i:16782444 original size:26 final size:27
Alignment explanation
Indices: 16782390--16782444 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
16782380 TTACAAATTT
* *
16782390 TAAAATTATACATAATATAATATACAA
1 TAAAATTATAAATAATATAATAGACAA
*
16782417 TAAAA-TATAAATAATATAATAGATAA
1 TAAAATTATAAATAATATAATAGACAA
16782443 TA
1 TA
16782445 CAAAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAAATTATAAATAATATAATAGACAA
Found at i:16782454 original size:26 final size:26
Alignment explanation
Indices: 16782401--16782455 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
16782391 AAAATTATAC
* *
16782401 ATAATATAATATACAATAAAATATAA
1 ATAATATAATAGACAATAAAATAAAA
*
16782427 ATAATATAATAGATAATACAAA-AAAA
1 ATAATATAATAGACAATA-AAATAAAA
16782453 ATA
1 ATA
16782456 TTTTTACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (26 bp):
ATAATATAATAGACAATAAAATAAAA
Found at i:16782510 original size:25 final size:26
Alignment explanation
Indices: 16782482--16782531 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
16782472 AAGTTTAAAG
16782482 TAAAATAAAT-AA-TATACAAAATATT
1 TAAAATAAATAAATTATA-AAAATATT
16782507 TAAAATAAATAAATTATAAAAATAT
1 TAAAATAAATAAATTATAAAAATAT
16782532 GTATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.43
26 9 0.39
27 4 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (26 bp):
TAAAATAAATAAATTATAAAAATATT
Found at i:16784173 original size:90 final size:90
Alignment explanation
Indices: 16784020--16784516 Score: 737
Period size: 90 Copynumber: 5.5 Consensus size: 90
16784010 TAATATCATT
* * *
16784020 GATCTGCTCCTCGTCAAATACAGAGACTCCAAATCTG-CTATCTTCGATCTGCTTCGATGTAAAC
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTC-ATCTTCGATCTGCTTCGATGTAAAC
*
16784084 ACATGAATGTCAGATCTGCTATCTTC
65 ACACGAATGTCAGATCTGCTATCTTC
* ** *
16784110 GATCTGCTCCCTGTCTAATACAGAGACGCCAAATCTACCATCTTTGATCTGCTTCGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
*
16784175 CACGAATGTCAAATCTGCTATCTTC
66 CACGAATGTCAGATCTGCTATCTTC
* *
16784200 GATCTGCTCCCCATCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTACTTCGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
*
16784265 CACGAATGTCAGATCTGCTATATTC
66 CACGAATGTCAGATCTGCTATCTTC
* * * *
16784290 GATCTGCTCCTCGTCTAATACGGAGACACCAAATCTGTCATCTTCGATCTACTTCGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
16784355 CACGAATGTCAGATCTGCTATCTTC
66 CACGAATGTCAGATCTGCTATCTTC
* * *
16784380 GATTTGCTCCCCGTCTAATACGGAGACGCTAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
* *
16784445 TACGAATGTCAGATCTGTTATCTTC
66 CACGAATGTCAGATCTGCTATCTTC
* * * * *
16784470 GATCTGCTCCCCGTTTAATACAAAGATGCCAAATTTG-CTTCTTCGAT
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGAT
16784517 TTGTTCCTTG
Statistics
Matches: 370, Mismatches: 36, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
89 9 0.02
90 360 0.97
91 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (90 bp):
GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
CACGAATGTCAGATCTGCTATCTTC
Found at i:16797150 original size:30 final size:30
Alignment explanation
Indices: 16797116--16797178 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
16797106 AAAGATATTA
*
16797116 ATATATATCAAACAATTTTCATATAACTGT
1 ATATATATCAAACAATTTTCATATAACCGT
*
16797146 ATATATATCAAACAATTTTCATTTAACCGT
1 ATATATATCAAACAATTTTCATATAACCGT
16797176 ATA
1 ATA
16797179 AATGTTGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (30 bp):
ATATATATCAAACAATTTTCATATAACCGT
Found at i:16797829 original size:18 final size:18
Alignment explanation
Indices: 16797806--16797842 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16797796 GGCGGACGGT
16797806 AGTGGTCCGACGACCGGA
1 AGTGGTCCGACGACCGGA
16797824 AGTGGTCCGACGACCGGA
1 AGTGGTCCGACGACCGGA
16797842 A
1 A
16797843 TCCGGCCGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.38, T:0.11
Consensus pattern (18 bp):
AGTGGTCCGACGACCGGA
Found at i:16798532 original size:3 final size:3
Alignment explanation
Indices: 16798526--16798649 Score: 96
Period size: 3 Copynumber: 42.0 Consensus size: 3
16798516 CTTTTGTTTC
* * * *
16798526 TTA TTA TTA TTA TT- TTC TTA CTA TTA TTA TTTA TTA TCA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * *
16798571 TTA TTA TCA TTG CTA TT- TT- TTA TT- TGTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* *
16798614 TT- TTA CTA GTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
16798650 CTGTTATTTT
Statistics
Matches: 96, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
2 9 0.09
3 80 0.83
4 7 0.07
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:16810059 original size:18 final size:18
Alignment explanation
Indices: 16810011--16810087 Score: 111
Period size: 18 Copynumber: 4.3 Consensus size: 18
16810001 ATAATCTTCA
*
16810011 ATGATATGCAACCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
16810030 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
16810047 ATAATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
16810065 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
16810083 ATGAT
1 ATGAT
16810088 ATATAATCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
17 14 0.27
18 34 0.65
19 4 0.08
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:16810062 original size:35 final size:36
Alignment explanation
Indices: 16810017--16810084 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
16810007 TTCAATGATA
16810017 TGCAACCTTAGATATGA-TACAATCTTAGATATAAT
1 TGCAACCTTAGATATGATTACAATCTTAGATATAAT
* *
16810052 TGCAATCTTAGATATGATTGCAATCTTAGATAT
1 TGCAACCTTAGATATGATTACAATCTTAGATAT
16810085 GATATATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (36 bp):
TGCAACCTTAGATATGATTACAATCTTAGATATAAT
Found at i:16810631 original size:15 final size:15
Alignment explanation
Indices: 16810592--16810647 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 15
16810582 ATATTTTAAT
16810592 TTTTTTATATAATTA
1 TTTTTTATATAATTA
16810607 TTATTCTTATA-AATATA
1 TT-TT-TTATATAAT-TA
16810624 TTTTTTATTATATATTA
1 TTTTTTA-TATA-ATTA
*
16810641 TATTTTA
1 TTTTTTA
16810648 AATTTATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 5 0.15
16 9 0.26
17 18 0.53
18 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTTATATAATTA
Found at i:16810671 original size:26 final size:26
Alignment explanation
Indices: 16810623--16810672 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
16810613 TTATAAATAT
* * * *
16810623 ATTTTTTATTATATATTATATTTTAA
1 ATTTATTATTAAATATCACATTTTAA
16810649 ATTTATTATTAAATATCACATTTT
1 ATTTATTATTAAATATCACATTTT
16810673 TTTATATGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTATTATTAAATATCACATTTTAA
Found at i:16814260 original size:172 final size:172
Alignment explanation
Indices: 16814056--16814388 Score: 657
Period size: 172 Copynumber: 1.9 Consensus size: 172
16814046 CTGAGTGAAA
*
16814056 AAGTTGAATGGGAATTAATGACGTTCCCTTACATATTCCCGACTTTTGTGTCAGGAGGGATAGCT
1 AAGTTGAATGGGAATTAACGACGTTCCCTTACATATTCCCGACTTTTGTGTCAGGAGGGATAGCT
16814121 TACCCGGAGAAGGGGGTGTTTGGAAATAAAAATCATCCCATCAATGTCACACATGAGGAAGGGAC
66 TACCCGGAGAAGGGGGTGTTTGGAAATAAAAATCATCCCATCAATGTCACACATGAGGAAGGGAC
16814186 TGAACCAAGAAACCTTGAGGGCATTCGCCCTGAGTGAAAAAG
131 TGAACCAAGAAACCTTGAGGGCATTCGCCCTGAGTGAAAAAG
16814228 AAGTTGAATGGGAATTAACGACGTTCCCTTACATATTCCCGACTTTTGTGTCAGGAGGGATAGCT
1 AAGTTGAATGGGAATTAACGACGTTCCCTTACATATTCCCGACTTTTGTGTCAGGAGGGATAGCT
16814293 TACCCGGAGAAGGGGGTGTTTGGAAATAAAAATCATCCCATCAATGTCACACATGAGGAAGGGAC
66 TACCCGGAGAAGGGGGTGTTTGGAAATAAAAATCATCCCATCAATGTCACACATGAGGAAGGGAC
16814358 TGAACCAAGAAACCTTGAGGGCATTCGCCCT
131 TGAACCAAGAAACCTTGAGGGCATTCGCCCT
16814389 TACGAACCAG
Statistics
Matches: 160, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 160 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (172 bp):
AAGTTGAATGGGAATTAACGACGTTCCCTTACATATTCCCGACTTTTGTGTCAGGAGGGATAGCT
TACCCGGAGAAGGGGGTGTTTGGAAATAAAAATCATCCCATCAATGTCACACATGAGGAAGGGAC
TGAACCAAGAAACCTTGAGGGCATTCGCCCTGAGTGAAAAAG
Found at i:16816419 original size:6 final size:6
Alignment explanation
Indices: 16816410--16816479 Score: 65
Period size: 6 Copynumber: 11.8 Consensus size: 6
16816400 AAAAAAAGAA
* * * *
16816410 AAAAAG AAAAAG GAAAA- AAAAGG AAAAAG --AAAG AAAAGG AAAAGG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
16816455 AAAAAG AAAAAAAG AAAAAG AAAAA
1 AAAAAG --AAAAAG AAAAAG AAAAA
16816480 TGGAGAGGCG
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
4 4 0.08
5 3 0.06
6 40 0.75
8 6 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:16816427 original size:16 final size:15
Alignment explanation
Indices: 16816398--16816473 Score: 77
Period size: 16 Copynumber: 5.1 Consensus size: 15
16816388 CTTCTATTTT
16816398 AAAA-AAAAAG-AAA
1 AAAAGAAAAAGAAAA
16816411 AAAAGAAAAAGGAAAA
1 AAAAGAAAAA-GAAAA
16816427 AAAAGGAAAAAGAAAGA
1 AAAA-GAAAAAGAAA-A
* *
16816444 AAAGGAAAAGGAAAA
1 AAAAGAAAAAGAAAA
*
16816459 AGAA-AAAAAGAAAA
1 AAAAGAAAAAGAAAA
16816473 A
1 A
16816474 GAAAAATGGA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
13 4 0.08
14 15 0.28
15 4 0.08
16 20 0.38
17 10 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Found at i:16816437 original size:26 final size:25
Alignment explanation
Indices: 16816398--16816479 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 25
16816388 CTTCTATTTT
16816398 AAAAAAAAAGAAAAAAAGAAAAAGG
1 AAAAAAAAAGAAAAAAAGAAAAAGG
*
16816423 AAAAAAAAGGAAAAAGAA-AGAAAAGG
1 AAAAAAAAAGAAAAA-AAGA-AAAAGG
16816449 AAAAGGAAAAAGAAAAAAAGAAAAA-G
1 AAAA--AAAAAGAAAAAAAGAAAAAGG
16816475 AAAAA
1 AAAAA
16816480 TGGAGAGGCG
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
24 1 0.02
25 15 0.30
26 17 0.34
27 6 0.12
28 11 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAGAAAAAAAGAAAAAGG
Found at i:16817440 original size:44 final size:44
Alignment explanation
Indices: 16817392--16817571 Score: 195
Period size: 44 Copynumber: 4.1 Consensus size: 44
16817382 CAAAGAAACA
16817392 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* ** * * * * **
16817436 AGATTTGACATTTCTGTGCTTACAGCGAAGCAGATTGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
* * *
16817481 AGCA--TGGCATCCCTATGTTCATAGGGAAC-GAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
*
16817524 AGATTTGGCATCCCTGTATTTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
16817568 AGAT
1 AGAT
16817572 CTAACCTTTA
Statistics
Matches: 107, Mismatches: 23, Indels: 12
0.75 0.16 0.08
Matches are distributed among these distances:
42 3 0.03
43 12 0.11
44 75 0.70
45 16 0.15
46 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
Found at i:16817821 original size:83 final size:83
Alignment explanation
Indices: 16817682--16818024 Score: 562
Period size: 83 Copynumber: 4.1 Consensus size: 83
16817672 GTTCTTAGAC
*
16817682 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATCCTTGTGCTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGATTTGGCATCCTTGTGCTT
16817747 ACAAGGAACAAATCGAGG
66 ACAAGGAACAAATCGAGG
*
16817765 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATCCTTGTGCTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGATTTGGCATCCTTGTGCTT
*
16817830 ACTAGGAACAAATCGAGG
66 ACAAGGAACAAATCGAGG
* * * * *
16817848 ACATAGCAGATTTGACTCTCAGATGTTCTTAAACAGACTCAAGATGATTTGGTATTCTTGTGTTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGATTTGGCATCCTTGTGCTT
**
16817913 ACAAAAAACAAATCGAGG
66 ACAAGGAACAAATCGAGG
* *
16817931 ACATAGCAGATTTGACTCTCAGATGTTCTCAAACAGACTTAAGATGATTTGGCATCCTTGTGCTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGATTTGGCATCCTTGTGCTT
16817996 ACAAGGAACAAATCGA-G
66 ACAAGGAACAAATCGAGG
*
16818013 ACATAGCTGATT
1 ACATAGCAGATT
16818025 TGGCTTTCAC
Statistics
Matches: 242, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
82 12 0.05
83 230 0.95
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (83 bp):
ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGATTTGGCATCCTTGTGCTT
ACAAGGAACAAATCGAGG
Found at i:16821117 original size:3 final size:3
Alignment explanation
Indices: 16821109--16821138 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16821099 CACCCAGTTC
16821109 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
16821139 GGTAAATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:16825361 original size:28 final size:28
Alignment explanation
Indices: 16825321--16825380 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
16825311 ACTCTTAAGC
16825321 TTAAACATATATTAGCTTGTTTAGAGAA
1 TTAAACATATATTAGCTTGTTTAGAGAA
16825349 TTAAACATATATTAGCTTGTTTAGAGAA
1 TTAAACATATATTAGCTTGTTTAGAGAA
16825377 TTAA
1 TTAA
16825381 GTTCTTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (28 bp):
TTAAACATATATTAGCTTGTTTAGAGAA
Found at i:16826447 original size:32 final size:32
Alignment explanation
Indices: 16826406--16826470 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
16826396 TTACTTTCGT
16826406 ACAATGACGACGTAACTCAAATTCACCTTATA
1 ACAATGACGACGTAACTCAAATTCACCTTATA
16826438 ACAATGACGACGTAACTCAAATTCACCTTATA
1 ACAATGACGACGTAACTCAAATTCACCTTATA
16826470 A
1 A
16826471 AAAGTATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (32 bp):
ACAATGACGACGTAACTCAAATTCACCTTATA
Found at i:16827947 original size:118 final size:118
Alignment explanation
Indices: 16827744--16827961 Score: 305
Period size: 118 Copynumber: 1.8 Consensus size: 118
16827734 ATTATATAAT
* * *
16827744 ATATTAATAATTTATATATATGCATCGTTGATTAAACATTATAATATCATATAATATTATATCTT
1 ATATTAATAATTTATATATATGCATCATTGACTAAACATTATAATATCATATAATACTATATCTT
*
16827809 TTATTATAATCTATATTATAATAATAGTTATATATGTATTAATATTTTTAGTA
66 TTATTATAACCTATATTATAATAATAGTTATATATGTATTAATATTTTTAGTA
* * * * * * *
16827862 ATATTAATAGTTTATATATGTGTATCAATT-ACTAAACATTATAATCTTATGTAATACTGTATCT
1 ATATTAATAATTTATATATATGCATC-ATTGACTAAACATTATAATATCATATAATACTATATCT
16827926 TTTATTATAACCTAT-TGTATAATAATAGTTATATAT
65 TTTATTATAACCTATAT-TATAATAATAGTTATATAT
16827962 TATAGTAGTA
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
117 1 0.01
118 84 0.97
119 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (118 bp):
ATATTAATAATTTATATATATGCATCATTGACTAAACATTATAATATCATATAATACTATATCTT
TTATTATAACCTATATTATAATAATAGTTATATATGTATTAATATTTTTAGTA
Found at i:16827995 original size:17 final size:17
Alignment explanation
Indices: 16827973--16828009 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
16827963 ATAGTAGTAC
16827973 ATTATATATTA-CATATT
1 ATTATATATTATC-TATT
16827990 ATTATATATTATCTATT
1 ATTATATATTATCTATT
16828007 ATT
1 ATT
16828010 GTTTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATATATTATCTATT
Found at i:16830375 original size:43 final size:43
Alignment explanation
Indices: 16830325--16830475 Score: 191
Period size: 43 Copynumber: 3.5 Consensus size: 43
16830315 TATCCCAGAT
* * *
16830325 ATGGTCTTACATTTTATCACATATCGATGCCACTGTCCTAGAC
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCTAGAC
* * *
16830368 AGGGTCTTACACGTAATCGA-TTAAT-GATGCCAATGTCCTAGAC
1 ATGGTCTTACATGTAATC-ACAT-ATCGATGCCAATGTCCTAGAC
*
16830411 ATGGTCTTACATGTAATCACA-ATACAATGCCAATGTCCTAGAC
1 ATGGTCTTACATGTAATCACATAT-CGATGCCAATGTCCTAGAC
16830454 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
16830476 CTCAGTAACC
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 86 0.93
44 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCTAGAC
Found at i:16836449 original size:17 final size:17
Alignment explanation
Indices: 16836427--16836459 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16836417 TGTGTATGTG
16836427 AATGAATGTTAATTGAT
1 AATGAATGTTAATTGAT
*
16836444 AATGAATGTTTATTGA
1 AATGAATGTTAATTGA
16836460 GTTGTGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (17 bp):
AATGAATGTTAATTGAT
Found at i:16843049 original size:56 final size:56
Alignment explanation
Indices: 16842981--16843092 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
16842971 TTATGTTTAT
16842981 TTACTTTTTGTTATTAATTTAATATTATAACTAATATATATTTCAATTAAAAATCC
1 TTACTTTTTGTTATTAATTTAATATTATAACTAATATATATTTCAATTAAAAATCC
16843037 TTACTTTTTGTTATTAATTTAATATTATAACTAATATATATTTCAATTAAAAATCC
1 TTACTTTTTGTTATTAATTTAATATTATAACTAATATATATTTCAATTAAAAATCC
16843093 CCCACTAACT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (56 bp):
TTACTTTTTGTTATTAATTTAATATTATAACTAATATATATTTCAATTAAAAATCC
Found at i:16844049 original size:19 final size:19
Alignment explanation
Indices: 16844025--16844088 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
16844015 CAAATTTTAT
16844025 AATTTTTATAAA-TATTTTG
1 AATTTTTA-AAATTATTTTG
* *
16844044 AATTTTAAAAATTATTTTT
1 AATTTTTAAAATTATTTTG
*
16844063 TATTTTTGAAAATTATTTTG
1 AATTTTT-AAAATTATTTTG
16844083 -ATTTTT
1 AATTTTT
16844089 TTTTTAGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
18 3 0.08
19 24 0.63
20 11 0.29
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTG
Found at i:16844088 original size:20 final size:20
Alignment explanation
Indices: 16844027--16844089 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
16844017 AATTTTATAA
*
16844027 TTTTTATAAA-TATTTTGA-
1 TTTTTAAAAATTATTTTGAT
* *
16844045 ATTTTAAAAATTATTTT-TT
1 TTTTTAAAAATTATTTTGAT
*
16844064 ATTTTTGAAAATTATTTTGAT
1 -TTTTTAAAAATTATTTTGAT
16844085 TTTTT
1 TTTTT
16844090 TTTTAGAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
20 20 0.57
21 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAT
Found at i:16847480 original size:40 final size:40
Alignment explanation
Indices: 16847436--16847659 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
16847426 AAGTGAATAT
* * * * **
16847436 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTGTTAA
16847476 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
16847516 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
16847556 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * **
16847596 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * *
16847635 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
16847660 TGAACGAGGA
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.20
40 136 0.80
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
Found at i:16847534 original size:80 final size:80
Alignment explanation
Indices: 16847397--16847659 Score: 318
Period size: 80 Copynumber: 3.3 Consensus size: 80
16847387 TTGAATGCTG
* * * * *
16847397 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAATATATCCGGATTAAGAT-CCGAAGGCC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCC
*
16847459 TTTGTGCGAGATACTAAA
63 TTTGTGCGAGTTACTAAA
* * *
16847477 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
**
16847542 GTGCGAGTTGTTAAA
66 GTGCGAGTTACTAAA
* * *
16847557 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGG-CATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
*
16847621 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* *
16847636 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
16847660 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
79 35 0.22
80 116 0.73
81 8 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:16847611 original size:120 final size:120
Alignment explanation
Indices: 16847397--16847659 Score: 318
Period size: 120 Copynumber: 2.2 Consensus size: 120
16847387 TTGAATGCTG
* * *
16847397 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
* **
16847461 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * *
16847517 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAG-TGAATAAATCCGGATTAAGAT-CCGAAGGCA
* ** * *
16847579 TTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
64 TTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
16847636 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
16847660 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 34 0.28
120 80 0.66
121 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:16854816 original size:22 final size:22
Alignment explanation
Indices: 16854789--16854834 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
16854779 TTGAATATTG
16854789 TTGTATCAGTGAATGCTTATGC
1 TTGTATCAGTGAATGCTTATGC
16854811 TTGTATCAGTGAATGCTTATGC
1 TTGTATCAGTGAATGCTTATGC
16854833 TT
1 TT
16854835 ATGTATGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (22 bp):
TTGTATCAGTGAATGCTTATGC
Found at i:16856562 original size:23 final size:23
Alignment explanation
Indices: 16856532--16856581 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
16856522 AACATTAATC
*
16856532 AAATGTATGAATTGCAGGCCATT
1 AAATGTATGAATTGCAGCCCATT
*
16856555 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCATT
16856578 AAAT
1 AAAT
16856582 AAACTTGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCATT
Found at i:16857409 original size:9 final size:9
Alignment explanation
Indices: 16857386--16857513 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
16857376 ATTGATCATT
*
16857386 ACTTAAATA
1 ACTTACATA
*
16857395 AATTACATA
1 ACTTACATA
16857404 ACTTACATA
1 ACTTACATA
* *
16857413 ACTCATATA
1 ACTTACATA
16857422 ACTTACATA
1 ACTTACATA
*
16857431 ATTTACATAACA
1 ACTTACAT---A
16857443 ACTTACATA
1 ACTTACATA
*
16857452 ACTCACATA
1 ACTTACATA
16857461 ACTTACATA
1 ACTTACATA
*
16857470 ATTTACATA
1 ACTTACATA
*
16857479 ACTCACATA
1 ACTTACATA
*
16857488 ACGTACATAACA
1 ACTTACAT---A
16857500 ACTTACATA
1 ACTTACATA
16857509 ACTTA
1 ACTTA
16857514 ACTAATACAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 80 0.83
12 16 0.17
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:16857455 original size:39 final size:39
Alignment explanation
Indices: 16857403--16857480 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
16857393 TAAATTACAT
*
16857403 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
16857442 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
16857481 TCACATAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:16857480 original size:57 final size:57
Alignment explanation
Indices: 16857399--16857511 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
16857389 TAAATAAATT
* * **
16857399 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* *
16857456 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
16857512 TAACTAATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:16879670 original size:46 final size:46
Alignment explanation
Indices: 16879603--16879735 Score: 178
Period size: 46 Copynumber: 2.9 Consensus size: 46
16879593 TGTAACCCGC
* * * *
16879603 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTG-TTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-AT
* *
16879649 CCATAGGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGAT
* *
16879695 ACATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
16879736 CAAACATCCT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 75 0.97
47 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGAT
Found at i:16879750 original size:46 final size:45
Alignment explanation
Indices: 16879608--16879750 Score: 139
Period size: 46 Copynumber: 3.1 Consensus size: 45
16879598 CCCGCCCATA
* * ** *
16879608 AGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACATCC-T
* *
16879653 AGGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT--A
1 A-GTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---ACATCCT
*
16879700 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AACATCCT
16879746 AGTGA
1 AGTGA
16879751 CATGTCACTT
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
44 4 0.05
45 1 0.01
46 70 0.88
47 2 0.03
50 3 0.04
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACATCCT
Found at i:16882167 original size:30 final size:30
Alignment explanation
Indices: 16882123--16882211 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
16882113 CAAAGATAAC
16882123 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* * *
16882152 GAGAAACCCAGAATAAAGAAAT-CTAGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
16882182 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
16882212 CGATACTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 10 0.21
30 35 0.73
31 3 0.06
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:16882171 original size:15 final size:15
Alignment explanation
Indices: 16882123--16882202 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
16882113 CAAAGATAAC
*
16882123 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
16882137 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
16882152 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
*
16882167 AAGAAATCTAGAATA
1 AAGAAATCCAGAATA
* *
16882182 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
16882197 AAGAAA
1 AAGAAA
16882203 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 9 0.17
15 43 0.81
16 1 0.02
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:16882211 original size:15 final size:15
Alignment explanation
Indices: 16882134--16882211 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
16882124 AGAAAACCGA
*
16882134 ATAAAGAAATCCAAG
1 ATAAAGAAACCCAAG
*
16882149 ATAGAGAAACCC-AG
1 ATAAAGAAACCCAAG
* *
16882163 AATAAAGAAA-TCTAG
1 -ATAAAGAAACCCAAG
* * *
16882178 AATAAAGAGATCCAGG
1 -ATAAAGAAACCCAAG
16882194 ATAAAGAAACCCAAG
1 ATAAAGAAACCCAAG
16882209 ATA
1 ATA
16882212 CGATACTATG
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.90
16 2 0.04
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.13
Consensus pattern (15 bp):
ATAAAGAAACCCAAG
Found at i:16885191 original size:46 final size:46
Alignment explanation
Indices: 16885124--16885251 Score: 184
Period size: 46 Copynumber: 2.8 Consensus size: 46
16885114 TGTAACCCGC
* * *
16885124 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
* * *
16885170 CCATAGGTGAAGTCGGACTCAACTCAACGAGCTCAGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
* *
16885216 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
16885252 ATGCTCAACC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
Found at i:16895342 original size:25 final size:24
Alignment explanation
Indices: 16895305--16895355 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
16895295 ATGTTCATGC
*
16895305 GAGCCATGTCAGGAAGCTCATAAA
1 GAGCCATATCAGGAAGCTCATAAA
*
16895329 GAGCCTATATCAGGATGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
16895354 GA
1 GA
16895356 TCTGTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:16902759 original size:26 final size:26
Alignment explanation
Indices: 16902702--16902768 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
16902692 TACATAGTTC
16902702 CTCACACGAGTTGTGAAATAGGTATG
1 CTCACACGAGTTGTGAAATAGGTATG
* * * *
16902728 CACACATGAGTTGTGAAATGGGTCTG
1 CTCACACGAGTTGTGAAATAGGTATG
*
16902754 CTCACACGAGATGTG
1 CTCACACGAGTTGTG
16902769 GGTCAAAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (26 bp):
CTCACACGAGTTGTGAAATAGGTATG
Found at i:16911497 original size:28 final size:28
Alignment explanation
Indices: 16911466--16911528 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
16911456 TGTCATCTGA
*
16911466 CCGTGTCACACACTGCTGAGACACATGC
1 CCGTGTCACACACGGCTGAGACACATGC
16911494 CCGTGTCACACACGGCTGAGACACATGC
1 CCGTGTCACACACGGCTGAGACACATGC
16911522 CCGTGTC
1 CCGTGTC
16911529 TCTACCTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.22, C:0.37, G:0.24, T:0.17
Consensus pattern (28 bp):
CCGTGTCACACACGGCTGAGACACATGC
Found at i:16924315 original size:46 final size:46
Alignment explanation
Indices: 16924248--16924422 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
16924238 TGTAACCCGC
* *
16924248 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
16924294 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * ** *
16924344 -C-TCA-CGAACTCGAACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
16924387 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
16924423 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 59 0.56
47 26 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:16924368 original size:93 final size:93
Alignment explanation
Indices: 16924255--16924426 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
16924245 CGCCCATAAG
** *
16924255 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16924320 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
16924348 CGAACTC-GAACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCAG-ACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTC
16924412 AACGAGTTCGGATGC
65 AACGAGTTCGGATGC
16924427 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 1 0.01
93 73 0.99
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:16924442 original size:46 final size:46
Alignment explanation
Indices: 16924297--16924435 Score: 126
Period size: 47 Copynumber: 3.0 Consensus size: 46
16924287 TTCGCATCCA
16924297 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * * * *
16924345 TCA-CGAACTCGAACTCAACTCAACGAGTTCGAACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG--GATGCTCAACCATC
16924390 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
16924436 CTAGTGACAT
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 26 0.37
47 28 0.39
48 2 0.03
49 4 0.06
50 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:16926161 original size:27 final size:28
Alignment explanation
Indices: 16926131--16926198 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 28
16926121 ATTAAGTCCG
16926131 CACACTCAGTGCTATATAATC-AACTCA
1 CACACTCAGTGCTATATAATCAAACTCA
*
16926158 CACAC-CTAGTGCTATATAATCAAACTCG
1 CACACTC-AGTGCTATATAATCAAACTCA
*
16926186 CACACTTAGTGCT
1 CACACTCAGTGCT
16926199 GTACAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 1 0.03
27 19 0.53
28 16 0.44
ACGTcount: A:0.34, C:0.29, G:0.10, T:0.26
Consensus pattern (28 bp):
CACACTCAGTGCTATATAATCAAACTCA
Found at i:16926195 original size:28 final size:28
Alignment explanation
Indices: 16926129--16926226 Score: 117
Period size: 28 Copynumber: 3.5 Consensus size: 28
16926119 ATATTAAGTC
*
16926129 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
16926156 CACACACCTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
16926184 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
16926213 CGCACACTTAGTGC
1 CGCACACTTAGTGC
16926227 CAATCTCATG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
27 20 0.33
28 21 0.35
29 19 0.32
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:16931480 original size:27 final size:28
Alignment explanation
Indices: 16931400--16931493 Score: 127
Period size: 27 Copynumber: 3.4 Consensus size: 28
16931390 AGATTGGCGT
* * * *
16931400 TAAGTGTGCGGGTTTAAATTGTACAGCAC
1 TAAGTGTGCGAGTTT-GATTATATAGCAC
16931429 TAAGTGTGCGAGTTTGATTATATAGCAC
1 TAAGTGTGCGAGTTTGATTATATAGCAC
16931457 TAAGTGTGCGAG-TTGATTATATAGCAC
1 TAAGTGTGCGAGTTTGATTATATAGCAC
*
16931484 TGAGTGTGCG
1 TAAGTGTGCG
16931494 GACTTAATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.40
28 22 0.37
29 14 0.23
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (28 bp):
TAAGTGTGCGAGTTTGATTATATAGCAC
Found at i:16931507 original size:29 final size:27
Alignment explanation
Indices: 16931424--16931507 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
16931414 TAAATTGTAC
* *
16931424 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
16931452 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
16931479 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
16931508 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:16939737 original size:39 final size:40
Alignment explanation
Indices: 16939632--16939839 Score: 253
Period size: 40 Copynumber: 5.2 Consensus size: 40
16939622 TATTCGAATG
* * *
16939632 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACT
*
16939673 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
*
16939713 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACT
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
16939752 AAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * **
16939792 ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
16939832 ATATCCGG
1 ATATCCGG
16939840 TTAAATTCCG
Statistics
Matches: 146, Mismatches: 15, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
39 37 0.25
40 80 0.55
41 28 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:16939772 original size:79 final size:81
Alignment explanation
Indices: 16939632--16939818 Score: 247
Period size: 79 Copynumber: 2.3 Consensus size: 81
16939622 TATTCGAATG
* * *
16939632 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGC
16939697 ATTTGTGCGAGTTACT
66 ATTTGTGCGAGTTACT
* * **
16939713 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAG
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAG
16939774 GCATTTGTGCGAGTTACT
64 GCATTTGTGCGAGTTACT
* *
16939792 ATAACCGGGCTATGTCCCGAAGGCATT
1 ATATCCGGGCTAAGTCCCGAAGGCATT
16939819 TGAACGAGTA
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
78 1 0.01
79 51 0.55
80 29 0.31
81 12 0.13
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (81 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGC
ATTTGTGCGAGTTACT
Found at i:16939842 original size:79 final size:78
Alignment explanation
Indices: 16939636--16939853 Score: 237
Period size: 79 Copynumber: 2.7 Consensus size: 78
16939626 CGAATGATAT
* * *
16939636 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAG-TCCGAAGGCATT
*
16939700 TGTGCGAGTTACTAATT
62 TGTGCGAGTTACTAATA
* *
16939717 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAGT-CCGAAGGCATTT
16939780 GTGCGAGTTACT-ATAA
63 GTGCGAGTTACTAAT-A
* ** *
16939796 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTT-AAGTCCGAAGG
16939854 TACGTGATTC
Statistics
Matches: 117, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
78 3 0.03
79 59 0.50
80 45 0.38
81 10 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGTCCGAAGGCATTTGTG
CGAGTTACTAATA
Found at i:16942624 original size:20 final size:20
Alignment explanation
Indices: 16942599--16942637 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16942589 AGGGACTAAA
* *
16942599 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTATAAAATTTG
16942619 ATGAAAAATTATAAAATTT
1 ATGAAAAATTATAAAATTT
16942638 AATGGATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTATAAAATTTG
Found at i:16943630 original size:47 final size:47
Alignment explanation
Indices: 16943541--16943640 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 47
16943531 CCAACACACC
* * * * *
16943541 AGTACGGCACTCAATGCCTCATCGGCTTTACTGAAGTAAATAGTAAT
1 AGTACGGCACTCAATACCTCATCGGATTGACTAAAGTAAATAGCAAT
* * *
16943588 AGTACGGTACTCAGTACCTCATCGGATTGGACTAAAGT-AATAGCAGT
1 AGTACGGCACTCAATACCTCATCGGATT-GACTAAAGTAAATAGCAAT
16943635 AGTACG
1 AGTACG
16943641 ACACACATGG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 37 0.84
48 7 0.16
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (47 bp):
AGTACGGCACTCAATACCTCATCGGATTGACTAAAGTAAATAGCAAT
Found at i:16944574 original size:389 final size:389
Alignment explanation
Indices: 16943855--16944634 Score: 1506
Period size: 389 Copynumber: 2.0 Consensus size: 389
16943845 ATAATTCAAT
16943855 AACATTCAATTCACTTTTCAATAACAAATGTTCCAAATTCCACATTAATCACATATTCATATTTA
1 AACATTCAATTCACTTTTCAATAACAAATGTTCCAAATTCCACATTAATCACATATTCATATTTA
16943920 TTTCGTCACATTCCCAATCAATTTAATTTTCAATTTAAAATACATTCAATATTCAATTTCCACAT
66 TTTCGTCACATTCCCAATCAATTTAATTTTCAATTTAAAATACATTCAATATTCAATTTCCACAT
16943985 CAATCATATATATCCATATAAATTCAATAAATTTATCACATACCAAATCAATCCATTTCAATTGT
131 CAATCATATATATCCATATAAATTCAATAAATTTATCACATACCAAATCAATCCATTTCAATTGT
16944050 AAAACACAATACAAATAATTCTCACCTAAATTACTTACCATAATATTTAATCAAAATATAACAAT
196 AAAACACAATACAAATAATTCTCACCTAAATTACTTACCATAATATTTAATCAAAATATAACAAT
*
16944115 TATAATTAAATTCACTTTTCAATTTCAACCAATATTCACTCCAATTCAAATAATCATCCTGATGC
261 TATAATTAAATTCACTTTTCAATTTCAACCAATATTCACTCCAATTCAAATAATCATCCTGATCC
* *
16944180 ATTTACTATACATATTAAATAATAATTTTAACAATTAAATATTAAGTTCGGATTATAGAAATAC
326 ATTTACTATACATACTAAATAATAATTTTAACAATTAAATATTAAGTGCGGATTATAGAAATAC
16944244 AACATTCAATTCACTTTTCAATAACAAATGTTCCAAATTCCACATTAATCACATATTCATATTTA
1 AACATTCAATTCACTTTTCAATAACAAATGTTCCAAATTCCACATTAATCACATATTCATATTTA
16944309 TTTCGTCACATTCCCAATCAATTTAATTTTCAATTTAAAATACATTCAATATTCAATTTCCACAT
66 TTTCGTCACATTCCCAATCAATTTAATTTTCAATTTAAAATACATTCAATATTCAATTTCCACAT
16944374 CAATCATATATATCCATATAAATTCAATAAATTTATCACATACCAAATCAATCCATTTCAATTGT
131 CAATCATATATATCCATATAAATTCAATAAATTTATCACATACCAAATCAATCCATTTCAATTGT
* *
16944439 AAAACACGATACAAATAATTCTCACCTAAATTACTTACCATAATATTTAATCAAAATATGACAAT
196 AAAACACAATACAAATAATTCTCACCTAAATTACTTACCATAATATTTAATCAAAATATAACAAT
16944504 TATAATTAAATTCACTTTTCAATTTCAACCAATATTCACTCCAATTCAAATAATCATCCTGATCC
261 TATAATTAAATTCACTTTTCAATTTCAACCAATATTCACTCCAATTCAAATAATCATCCTGATCC
*
16944569 ATTTACTCTACATACTAAATAATAATTTTAACAATTAAATATTAAGTGCGGATTATAGAAATAC
326 ATTTACTATACATACTAAATAATAATTTTAACAATTAAATATTAAGTGCGGATTATAGAAATAC
16944633 AA
1 AA
16944635 ACCGTAATTT
Statistics
Matches: 385, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
389 385 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (389 bp):
AACATTCAATTCACTTTTCAATAACAAATGTTCCAAATTCCACATTAATCACATATTCATATTTA
TTTCGTCACATTCCCAATCAATTTAATTTTCAATTTAAAATACATTCAATATTCAATTTCCACAT
CAATCATATATATCCATATAAATTCAATAAATTTATCACATACCAAATCAATCCATTTCAATTGT
AAAACACAATACAAATAATTCTCACCTAAATTACTTACCATAATATTTAATCAAAATATAACAAT
TATAATTAAATTCACTTTTCAATTTCAACCAATATTCACTCCAATTCAAATAATCATCCTGATCC
ATTTACTATACATACTAAATAATAATTTTAACAATTAAATATTAAGTGCGGATTATAGAAATAC
Found at i:16945308 original size:3 final size:3
Alignment explanation
Indices: 16945300--16945354 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
16945290 ATATATTAGT
* *
16945300 TAA TAA TAA TAT TAA TAA TAA TAA TAA TACA TTA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
16945345 T-A TAA TAA TA
1 TAA TAA TAA TA
16945355 TTTAATTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:16945338 original size:13 final size:13
Alignment explanation
Indices: 16945320--16945354 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
16945310 ATTAATAATA
*
16945320 ATAATAATACATT
1 ATAATAATACAAT
*
16945333 ATAATAATATAAT
1 ATAATAATACAAT
16945346 ATAATAATA
1 ATAATAATA
16945355 TTTAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATAATACAAT
Found at i:16945518 original size:24 final size:23
Alignment explanation
Indices: 16945468--16945520 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 23
16945458 TTGTCTTCAT
16945468 TTTAATAATTTAATATAAAACTA
1 TTTAATAATTTAATATAAAACTA
*
16945491 --TAATAATTATAATA-AATATCTA
1 TTTAATAATT-TAATATAA-AACTA
16945513 TTTAATAA
1 TTTAATAA
16945521 CAAATACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 10 0.40
22 9 0.36
24 6 0.24
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAATAATTTAATATAAAACTA
Found at i:16949217 original size:36 final size:36
Alignment explanation
Indices: 16949174--16949245 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
16949164 AAATAAAAAG
16949174 ATAGAAAATTAATGAAGCCTTATTACATAATTTAAA
1 ATAGAAAATTAATGAAGCCTTATTACATAATTTAAA
*
16949210 ATAGAAAATTAATGAGGCCTTATTACATAATTTAAA
1 ATAGAAAATTAATGAAGCCTTATTACATAATTTAAA
16949246 CCCAAAATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (36 bp):
ATAGAAAATTAATGAAGCCTTATTACATAATTTAAA
Found at i:16949643 original size:27 final size:28
Alignment explanation
Indices: 16949620--16949685 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
16949610 TGTAAAGCTG
*
16949620 CCAGTAACAGTA-TCTGTGGCAAAGCCA
1 CCAGTAACAGTATTATGTGGCAAAGCCA
*
16949647 CCAGTAATAGTATTATGTGGCAAAGCCA
1 CCAGTAACAGTATTATGTGGCAAAGCCA
16949675 CCAGT-ACAGTA
1 CCAGTAACAGTA
16949686 CACTTACTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (28 bp):
CCAGTAACAGTATTATGTGGCAAAGCCA
Found at i:16957426 original size:27 final size:27
Alignment explanation
Indices: 16957363--16957428 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
16957353 AGCAAAGCTG
* *
16957363 CCAGCAACAGTATCTGTGGCAAACCAA
1 CCAGTAACAGTATATGTGGCAAACCAA
*
16957390 CCAGTAACAGTATTATGTGGCAGAGCCAA
1 CCAGTAACAGTA-TATGTGGCA-AACCAA
16957419 -CAGT-ACAGTA
1 CCAGTAACAGTA
16957429 CACTTCCTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 17 0.50
28 12 0.35
29 5 0.15
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGGCAAACCAA
Found at i:16961398 original size:16 final size:17
Alignment explanation
Indices: 16961359--16961390 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16961349 GATATTTCTA
16961359 TTTAATTATTTATCATC
1 TTTAATTATTTATCATC
16961376 TTTAATTATTT-TCAT
1 TTTAATTATTTATCAT
16961391 TTCTAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATTATTTATCATC
Found at i:16971049 original size:50 final size:50
Alignment explanation
Indices: 16970974--16971212 Score: 258
Period size: 50 Copynumber: 4.9 Consensus size: 50
16970964 TGATGCTAGG
* * * *
16970974 GAGATATCATAGCTAGTGTAAGACCATGTCTGGGACATGGCGTTGGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
*
16971024 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGACATCGG-CT-
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
* * * *
16971072 -TGATATGTG-TC-AGTGTAAGACCATGTGTGGGACATGGCATCGGCAC-C
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTC
* * * * *
16971119 GATAGATGAGAGCCAGTGTAAGACCATGCCTGAGACATGGCATCGGCCTC
1 GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
* * *
16971169 GATATACGAGAG-TCAGTGTAAGACCATGCCTGGGACATGGCATC
1 GAGATATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATC
16971213 AACTTTGATG
Statistics
Matches: 159, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
45 30 0.19
46 1 0.01
47 8 0.05
48 5 0.03
49 4 0.03
50 111 0.70
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (50 bp):
GAGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTC
Found at i:16971128 original size:95 final size:97
Alignment explanation
Indices: 16970988--16971212 Score: 285
Period size: 95 Copynumber: 2.3 Consensus size: 97
16970978 TATCATAGCT
* * * * *
16970988 AGTGTAAGACCATGTCTGGGACATGGCGTTGGCCTCGAGATATGAGAGCTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAGATGAGAGCCAGTGTAAGACCATGC
* * *
16971053 CTGGGACATGACATCGG-CTTGATAT-GTGTC
66 CTGAGACATGACATCGGCCTCGATATAGAGTC
* *
16971083 AGTGTAAGACCATGTGTGGGACATGGCATCGGCAC-CGATAGATGAGAGCCAGTGTAAGACCATG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGAGAGATGAGAGCCAGTGTAAGACCATG
*
16971147 CCTGAGACATGGCATCGGCCTCGATATACGAGAGTC
65 CCTGAGACATGACATCGGCCTCGATAT---AGAGTC
*
16971183 AGTGTAAGACCATGCCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
16971213 AACTTTGATG
Statistics
Matches: 111, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
95 71 0.64
96 8 0.07
100 32 0.29
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.22
Consensus pattern (97 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAGATGAGAGCCAGTGTAAGACCATGC
CTGAGACATGACATCGGCCTCGATATAGAGTC
Found at i:16982187 original size:79 final size:81
Alignment explanation
Indices: 16982051--16982233 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
16982041 TCGAATGATG
* *
16982051 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
16982115 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
16982130 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
16982192 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
16982210 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
16982234 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:16982249 original size:40 final size:41
Alignment explanation
Indices: 16982051--16982235 Score: 231
Period size: 40 Copynumber: 4.6 Consensus size: 41
16982041 TCGAATGATG
* * *
16982051 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
16982091 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
*
16982131 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
16982170 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
16982211 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
16982236 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 35 0.28
40 82 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:16986921 original size:30 final size:30
Alignment explanation
Indices: 16986886--16986944 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
16986876 CTTTAGCCAT
*
16986886 TTATTTTTCTTAC-AATTTAATTTAATTTTA
1 TTATTTTTATTACTAA-TTAATTTAATTTTA
*
16986916 TTATTTTTATTACTAATTAATTTACTTTT
1 TTATTTTTATTACTAATTAATTTAATTTT
16986945 TCCTTCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (30 bp):
TTATTTTTATTACTAATTAATTTAATTTTA
Found at i:16992218 original size:40 final size:40
Alignment explanation
Indices: 16992163--16992239 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
16992153 ATGATTACCT
*
16992163 ATGGATTATTTTGAGATATTATCGAT-AGAAATTATAATCA
1 ATGGATTATTTTGAGACATTATCGATAAG-AATTATAATCA
16992203 ATGGATTATTTTGAGACATTATCGATAAGAATTATAA
1 ATGGATTATTTTGAGACATTATCGATAAGAATTATAA
16992240 GTTGAGGAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 33 0.94
41 2 0.06
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (40 bp):
ATGGATTATTTTGAGACATTATCGATAAGAATTATAATCA
Found at i:16997222 original size:43 final size:43
Alignment explanation
Indices: 16997127--16997245 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
16997117 CGAGATGTGG
* *
16997127 TTACATGTAAGACCATGTCTGGGACATTAGCATTGTATTGAGA
1 TTACATGTAAGACCATGTCTGGGACATTGGCATTGTAATGAGA
* * *
16997170 TTACGTGTAAAACCATGTCTGGGACATTGGCATTGTTAAT-CGA
1 TTACATGTAAGACCATGTCTGGGACATTGGCATTG-TAATGAGA
* * *
16997213 TTTCATGTAAGACCCTGTCTGGGACAGTGGCAT
1 TTACATGTAAGACCATGTCTGGGACATTGGCAT
16997246 CGATATATGA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 62 0.95
44 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTGGGACATTGGCATTGTAATGAGA
Found at i:16997269 original size:43 final size:43
Alignment explanation
Indices: 16997127--16997269 Score: 101
Period size: 43 Copynumber: 3.3 Consensus size: 43
16997117 CGAGATGTGG
* * * * * * *
16997127 TTACATGTAAGACCATGTCTGGGACATTAGCATTG-TATTGAGA
1 TTACATATAAGACCCTGTCTGGGACAGTGGCATCGATAAT-CGA
* * * * * * *
16997170 TTACGTGTAAAACCATGTCTGGGACATTGGCATTGTTAATCGA
1 TTACATATAAGACCCTGTCTGGGACAGTGGCATCGATAATCGA
* *
16997213 TTTCATGTAAGACCCTGTCTGGGACAGTGGCATCGATATAT-GA
1 TTACATATAAGACCCTGTCTGGGACAGTGGCATCGATA-ATCGA
*
16997256 TTACATATCAGACC
1 TTACATATAAGACC
16997270 ATATTCGGGA
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
43 78 0.94
44 5 0.06
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (43 bp):
TTACATATAAGACCCTGTCTGGGACAGTGGCATCGATAATCGA
Found at i:17001183 original size:55 final size:53
Alignment explanation
Indices: 17001059--17001255 Score: 153
Period size: 55 Copynumber: 3.7 Consensus size: 53
17001049 TAGGGTTTAG
* * * * * * * * *
17001059 GATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCAAG
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGATAACTAC-ATAAGGCAAA
* * *
17001113 GAAATCATGTAAGACCATGTCAAGACATGGCACTGATAAACTACTATAAGGCAAA
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGAT-AACTAC-ATAAGGCAAA
* * * * * * * *
17001168 GATCCCATGTAAGACCATGCCAA-ATCGTGGCAATGGTGAGTTCATAAGGCAAG
1 GATACCATGTAAGACCATGTCAAGA-CATGGCAATGATAACTACATAAGGCAAA
* *
17001221 GATACCACGTAAGACCATATCAAGACATGGCAATG
1 GATACCATGTAAGACCATGTCAAGACATGGCAATG
17001256 GTAAGTTTAA
Statistics
Matches: 113, Mismatches: 27, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
53 37 0.33
54 35 0.31
55 41 0.36
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (53 bp):
GATACCATGTAAGACCATGTCAAGACATGGCAATGATAACTACATAAGGCAAA
Found at i:17001252 original size:53 final size:54
Alignment explanation
Indices: 17001057--17001262 Score: 218
Period size: 53 Copynumber: 3.8 Consensus size: 54
17001047 ATTAGGGTTT
* * * *
17001057 AGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCA
1 AGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGCA
* * * * * * *
17001111 AGGAAATCATGTAAGACCATGTCAAGACATGGCACTGATAAACTACTATAAGGCA
1 AGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTCTATAAGGCA
* * * *
17001166 AAGATCCCATGTAAGACCATGCCAA-ATCGTGGCAATGGTGAGTTC-ATAAGGCA
1 AGGATACCATGTAAGACCATGCCAAGA-CATGGCAATGGTAAGTTCTATAAGGCA
* **
17001219 AGGATACCACGTAAGACCATATCAAGACATGGCAATGGTAAGTT
1 AGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
17001263 TAAAAAGGAA
Statistics
Matches: 121, Mismatches: 28, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
53 43 0.36
54 37 0.31
55 41 0.34
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.20
Consensus pattern (54 bp):
AGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGCA
Found at i:17007011 original size:25 final size:25
Alignment explanation
Indices: 17006982--17007029 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
17006972 TTATAATATG
* * *
17006982 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
17007007 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
17007030 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:17007080 original size:9 final size:9
Alignment explanation
Indices: 17007068--17007124 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
17007058 TTTGATAAAC
17007068 ATGATATGT
1 ATGATATGT
*
17007077 ATGATATGCAC
1 ATGATATG--T
*
17007088 ATGACATGT
1 ATGATATGT
*
17007097 ATGATATGCAC
1 ATGATATG--T
17007108 ATGATATGT
1 ATGATATGT
17007117 ATGATATG
1 ATGATATG
17007125 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:17007091 original size:20 final size:20
Alignment explanation
Indices: 17007066--17007128 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
17007056 ATTTTGATAA
17007066 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
17007086 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
17007106 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
17007126 ACA
1 ACA
17007129 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:17007321 original size:25 final size:24
Alignment explanation
Indices: 17007182--17007325 Score: 222
Period size: 24 Copynumber: 6.0 Consensus size: 24
17007172 GAGGAAGTGC
17007182 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
17007206 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
17007230 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
17007254 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
17007277 AAAAAGGGGCTT-TGCCCCAGTTATT
1 -AAAA-GGGCTTATGCCCCAGTTATT
*
17007302 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
17007326 ATGATAAAGC
Statistics
Matches: 113, Mismatches: 1, Indels: 11
0.90 0.01 0.09
Matches are distributed among these distances:
23 25 0.22
24 58 0.51
25 24 0.21
26 6 0.05
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:17007554 original size:31 final size:31
Alignment explanation
Indices: 17007519--17007582 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
17007509 CGTTTACAGT
17007519 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
17007550 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
17007581 AA
1 AA
17007583 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:17008408 original size:15 final size:17
Alignment explanation
Indices: 17008378--17008409 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17008368 AAAAAGGGTA
17008378 TTTTTGAAGATGGTTTT
1 TTTTTGAAGATGGTTTT
17008395 TTTTTG-AGAT-GTTTT
1 TTTTTGAAGATGGTTTT
17008410 GCGGGGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.16, C:0.00, G:0.22, T:0.62
Consensus pattern (17 bp):
TTTTTGAAGATGGTTTT
Done.