Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 161 of 199
Found at i:47748536 original size:74 final size:73
Alignment explanation
Indices: 47748398--47748539 Score: 196
Period size: 74 Copynumber: 1.9 Consensus size: 73
47748388 CTCGGATTTC
* * * **
47748398 AAAAATGGATCATGCCTAGTAAGTTAGGACACGATCTTTTTTTAATTCCCGAGATCGTTTAAAAC
1 AAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTCTAATAATTCCCGAGATC-TTTAAAAC
47748463 TTGAGAAAA
65 TTGAGAAAA
*
47748472 AAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTCTAATAATTTCCGAGAT-TTCTAAAAA
1 AAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTCTAATAATTCCCGAGATCTT-T-AAAA
47748536 CTTG
64 CTTG
47748540 TTTGAAAATA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
72 2 0.03
73 1 0.02
74 57 0.95
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (73 bp):
AAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTCTAATAATTCCCGAGATCTTTAAAACT
TGAGAAAA
Found at i:47748929 original size:20 final size:21
Alignment explanation
Indices: 47748891--47748930 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
47748881 AAAGAAATAA
47748891 ATAAAGAAAAAGAATAAGATT
1 ATAAAGAAAAAGAATAAGATT
47748912 ATAAA-AAAAAGTAA-AAGAT
1 ATAAAGAAAAAG-AATAAGAT
47748931 ATATGTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (21 bp):
ATAAAGAAAAAGAATAAGATT
Found at i:47748980 original size:18 final size:17
Alignment explanation
Indices: 47748946--47748997 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
47748936 TATGTACATA
*
47748946 AATATATAAATTATAAGAT
1 AATATATATA-TATAAG-T
47748965 AATATATATATATAAGT
1 AATATATATATATAAGT
*
47748982 ATGTATATATATATAA
1 A-ATATATATATATAA
47748998 ATTATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 19 0.63
19 9 0.30
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (17 bp):
AATATATATATATAAGT
Found at i:47750543 original size:2 final size:2
Alignment explanation
Indices: 47750530--47750567 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
47750520 TTTATTTAAA
* *
47750530 AT AT AC AT AT AT AT AT A- AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47750568 AAGAAGTACC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:47750552 original size:13 final size:13
Alignment explanation
Indices: 47750530--47750559 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
47750520 TTTATTTAAA
47750530 ATAT-ACATATAT
1 ATATAACATATAT
47750542 ATATAACATATAT
1 ATATAACATATAT
47750555 ATATA
1 ATATA
47750560 TATATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAACATATAT
Found at i:47751261 original size:11 final size:11
Alignment explanation
Indices: 47751244--47751273 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
47751234 TCTTATTTTT
47751244 TAATTTTAAAA
1 TAATTTTAAAA
*
47751255 TACTTTTAAAA
1 TAATTTTAAAA
47751266 TAATTTTA
1 TAATTTTA
47751274 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:47751281 original size:41 final size:43
Alignment explanation
Indices: 47751219--47751303 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
47751209 CCGAATATAA
* *
47751219 TAAATATATTTTTATTCTTA-TTTTTTAATTTTAAAATACTTT
1 TAAATATAATTTTATTCTTATTTTTTTAATTTTAAAATAATTT
* *
47751261 TAAA-ATAATTTTATTTTTATTTTTTTATTTTTAAAATAATTT
1 TAAATATAATTTTATTCTTATTTTTTTAATTTTAAAATAATTT
47751303 T
1 T
47751304 TTAATGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 13 0.34
42 25 0.66
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (43 bp):
TAAATATAATTTTATTCTTATTTTTTTAATTTTAAAATAATTT
Found at i:47751755 original size:16 final size:16
Alignment explanation
Indices: 47751734--47751770 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
47751724 ATTATTATCC
*
47751734 TTATTATTACTAATTT
1 TTATTATCACTAATTT
*
47751750 TTATTATCATTAATTT
1 TTATTATCACTAATTT
47751766 TTATT
1 TTATT
47751771 TGCTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATCACTAATTT
Found at i:47751945 original size:18 final size:18
Alignment explanation
Indices: 47751922--47751966 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
47751912 TTCAAAAATC
* *
47751922 TTATTATTATTATTTCTA
1 TTATTATTAATATTACTA
47751940 TTATTATTAATATTACTA
1 TTATTATTAATATTACTA
*
47751958 GTATTATTA
1 TTATTATTA
47751967 CACTTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATTATTAATATTACTA
Found at i:47752409 original size:71 final size:71
Alignment explanation
Indices: 47752293--47752434 Score: 248
Period size: 71 Copynumber: 2.0 Consensus size: 71
47752283 TCTTTTCAAA
* * * *
47752293 CTCAAGTTTTAAACGATTTCGGGAATTAAGAAGAGATTGTGTCCTAACTTACTGGGCATGATCCT
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
47752358 TTTTTT
66 TTTTTT
47752364 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
47752429 TTTTTT
66 TTTTTT
47752435 AAATCCGAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (71 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
TTTTTT
Found at i:47753625 original size:9 final size:9
Alignment explanation
Indices: 47753607--47753664 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
47753597 TTTGGTTAAA
*
47753607 AATTACCCG
1 AATTAACCG
47753616 AATTAACCG
1 AATTAACCG
*
47753625 AATTAACTG
1 AATTAACCG
* *
47753634 AATTACCCA
1 AATTAACCG
*
47753643 AATTAACTG
1 AATTAACCG
47753652 AATTAACCG
1 AATTAACCG
47753661 AATT
1 AATT
47753665 GAATCACTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:47753636 original size:18 final size:18
Alignment explanation
Indices: 47753615--47753664 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
47753605 AAAATTACCC
47753615 GAATTAACCGAATTAACT
1 GAATTAACCGAATTAACT
* *
47753633 GAATTACCCAAATTAACT
1 GAATTAACCGAATTAACT
47753651 GAATTAACCGAATT
1 GAATTAACCGAATT
47753665 GAATCACTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (18 bp):
GAATTAACCGAATTAACT
Found at i:47753640 original size:27 final size:27
Alignment explanation
Indices: 47753607--47753664 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
47753597 TTTGGTTAAA
* *
47753607 AATTACCCGAATTAACCGAATTAACTG
1 AATTACCCAAATTAACCGAATTAACCG
*
47753634 AATTACCCAAATTAACTGAATTAACCG
1 AATTACCCAAATTAACCGAATTAACCG
47753661 AATT
1 AATT
47753665 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTACCCAAATTAACCGAATTAACCG
Found at i:47753720 original size:19 final size:20
Alignment explanation
Indices: 47753684--47753731 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
47753674 CATAATTAAA
*
47753684 TTAATTTTAGACTTTTAGACT
1 TTAATTTTAGA-TTTTAGAAT
47753705 TTAATTTTAG-TTTTAGAAT
1 TTAATTTTAGATTTTAGAAT
*
47753724 TTTATTTT
1 TTAATTTT
47753732 TTATTCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.60
21 10 0.40
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (20 bp):
TTAATTTTAGATTTTAGAAT
Found at i:47760246 original size:41 final size:41
Alignment explanation
Indices: 47760179--47760341 Score: 226
Period size: 40 Copynumber: 4.0 Consensus size: 41
47760169 CTTCCCTCTT
*
47760179 CTTCTTCTTTCTTTCTTTTTTCTCTTCTCCTTTCGTTTTCTTTC
1 CTTCTT-TTTCTTTC-TTTTT-TCTTCTCCTTTCCTTTTCTTTC
* *
47760223 CTTCTTTTTCTTTCTTTTTTCTTCTCCTCTCCTTTTCTTTA
1 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
47760264 C-TCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
* *
47760304 CTTCTTTTTC--T-TTATTTCCTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
47760342 TTTCCCTCTC
Statistics
Matches: 111, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
38 25 0.23
39 1 0.01
40 38 0.34
41 28 0.25
42 5 0.05
43 8 0.07
44 6 0.05
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.68
Consensus pattern (41 bp):
CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
Found at i:47760286 original size:81 final size:81
Alignment explanation
Indices: 47760181--47760340 Score: 236
Period size: 81 Copynumber: 2.0 Consensus size: 81
47760171 TCCCTCTTCT
* * *
47760181 TCTTCTTTCTTTCTTTTTTCTCTTCTCCTTTCGTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCTT
1 TCTTCTTTCTTTCTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTC--T-TTATTTCCT
47760246 CTCCTCTCCTTTTCTTTAC
63 CTCCTCTCCTTTTCTTTAC
47760265 TCTT-TTTCTTTC-TTTTT-TCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTATTTCCTCTC
1 TCTTCTTTCTTTCTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTATTTCCTCTC
*
47760327 CTTTCCTTTTCTTT
66 CTCTCCTTTTCTTT
47760341 CTTTCCCTCT
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
78 23 0.32
79 1 0.01
81 31 0.43
82 5 0.07
83 8 0.11
84 4 0.06
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (81 bp):
TCTTCTTTCTTTCTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTATTTCCTCTC
CTCTCCTTTTCTTTAC
Found at i:47760340 original size:10 final size:10
Alignment explanation
Indices: 47760208--47760341 Score: 52
Period size: 10 Copynumber: 13.5 Consensus size: 10
47760198 TTCTCTTCTC
*
47760208 CTTTCGTTTT
1 CTTTCCTTTT
47760218 CTTTCCTTCTT
1 CTTTCCTT-TT
47760229 -TTT-CTTTCT
1 CTTTCCTTT-T
* * *
47760238 TTTTTCTTCTC
1 CTTTCCTT-TT
*
47760249 CTCTCCTTTT
1 CTTTCCTTTT
47760259 CTTTACTCTTTTT
1 CTTT-C-C-TTTT
47760272 CTTT-C-TTT
1 CTTTCCTTTT
*
47760280 -TTT-CTTCTC
1 CTTTCCTT-TT
47760289 CTTTCCTTTT
1 CTTTCCTTTT
47760299 CTTTCCTTCTT
1 CTTTCCTT-TT
47760310 -TTT-C-TTT
1 CTTTCCTTTT
* * *
47760317 ATTTCCTCTC
1 CTTTCCTTTT
47760327 CTTTCCTTTT
1 CTTTCCTTTT
47760337 CTTTC
1 CTTTC
47760342 TTTCCCTCTC
Statistics
Matches: 94, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
7 6 0.06
8 9 0.10
9 7 0.07
10 46 0.49
11 16 0.17
12 2 0.02
13 8 0.09
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.68
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:47760429 original size:27 final size:27
Alignment explanation
Indices: 47760391--47760457 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
47760381 TTATAAGACT
* *
47760391 GGTGCCGCCAATGACTTTGGCACCATC
1 GGTGCCGCCAATCACATTGGCACCATC
* *
47760418 GGTGCCGCCAATCACATTGGCACCTTT
1 GGTGCCGCCAATCACATTGGCACCATC
47760445 GGTGCCGCCAATC
1 GGTGCCGCCAATC
47760458 TCTTTCCCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.18, C:0.34, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTGCCGCCAATCACATTGGCACCATC
Found at i:47761688 original size:156 final size:155
Alignment explanation
Indices: 47761499--47761945 Score: 644
Period size: 156 Copynumber: 2.9 Consensus size: 155
47761489 AAAAATATAC
* * *
47761499 TATTTTCTAATTTTACATTATTTTAGTTCATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTT
1 TATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTG-TTTTT
47761564 TAAATAAATTTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTTCCGAG-TTTTATT
65 TAAATAAA-TTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTTCCGAGATTTTATT
47761628 ACTTTCAATAAAAATATATTATTTT-T
129 ACTTTCAATAAAAATATATTATTTTCT
* * * * *
47761654 GTATTTTATTATTTTACATTTTTTTAGTACATTATGTTTGAAATGTATTAATTAATTTTGTTTTT
1 -TATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTT
* * *
47761719 TAAATAAATTTAGTAAAAAATCCTTATTTCGGCCATTTGTTCGTATTTTTTTCTCTG-GATTTTA
65 TAAATAAATTTA--AAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTT-TCCGAGATTTTA
47761783 TTACTTT--A-AAAAATATATTATTTTCT
127 TTACTTTCAATAAAAATATATTATTTTCT
* *
47761809 AATTTTATTATTTTACATTATTTTAATACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTT
1 TATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTT
*
47761874 AAATAAA-TT-AAAAAACCCTTATTTCGGCCCTTTGTTCGTA--TTTTTTCCCAGATTTTATTAC
66 AAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTTCCGAGATTTTATTAC
47761935 TTTCAATAAAA
131 TTTCAATAAAA
47761946 CACACACTAA
Statistics
Matches: 260, Mismatches: 22, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
147 2 0.01
148 19 0.07
150 30 0.12
151 4 0.02
153 2 0.01
154 85 0.33
155 15 0.06
156 88 0.34
157 15 0.06
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (155 bp):
TATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTT
AAATAAATTTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTTCCGAGATTTTATTAC
TTTCAATAAAAATATATTATTTTCT
Found at i:47763013 original size:39 final size:37
Alignment explanation
Indices: 47762969--47763135 Score: 97
Period size: 39 Copynumber: 4.3 Consensus size: 37
47762959 TTTCAGATTT
47762969 TATTATTTTATATTATTTTAGTACATAATGTTTGAAATG
1 TATTATTTTATATT-TTTTAGTACATAAT-TTTGAAATG
**
47763008 TATTATTTTAGTATTTTTTA-TACA-AATTTAGTGAAAAC
1 TATTATTTTA-TATTTTTTAGTACATAATTT--TGAAATG
** ** ** * * * *
47763046 CCTTATTTTGGCCATTTGTTT-GTATTTTTATTTTCGGATTT
1 TATTATTTT--ATATTT-TTTAGTA-CATAATTTT-GAAATG
47763087 TATTATTTTATATTATTTTAGTACATAATGTTTGAAATG
1 TATTATTTTATATT-TTTTAGTACATAAT-TTTGAAATG
47763126 TATTATTTTA
1 TATTATTTTA
47763136 GTGTATTTTT
Statistics
Matches: 92, Mismatches: 23, Indels: 26
0.65 0.16 0.18
Matches are distributed among these distances:
36 2 0.02
37 3 0.03
38 16 0.17
39 41 0.45
40 17 0.18
41 9 0.10
42 4 0.04
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (37 bp):
TATTATTTTATATTTTTTAGTACATAATTTTGAAATG
Found at i:47763112 original size:118 final size:120
Alignment explanation
Indices: 47762883--47763197 Score: 454
Period size: 118 Copynumber: 2.6 Consensus size: 120
47762873 TGTCCCCTTA
* * * * * *
47762883 TATTAATTTAGTGTGTTTTTTTTTATAAATTTAGTAAAAAATCCTTATTTTGGCCATTTGTTCGT
1 TATTATTTTAG-GTATTTTTTTATACAAATTTAGT-GAAAACCCTTATTTTGGCCATTTGTTCGT
47762948 ATTTTTCTTATTTTCAGATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATG
64 A--TTT-TTATTTTCAGATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATG
*
47763008 TATTATTTTA-GTA-TTTTTTATACAAATTTAGTGAAAACCCTTATTTTGGCCATTTGTTTGTAT
1 TATTATTTTAGGTATTTTTTTATACAAATTTAGTGAAAACCCTTATTTTGGCCATTTGTTCGTAT
*
47763071 TTTTATTTTCGGATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATG
66 TTTTATTTTCAGATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATG
* *
47763126 TATTATTTTAGTGTATTTTTTTTATAGAAATTTAGTGAAAAACCCTTATTTTGGCCCTTTGTTCG
1 TATTATTTTAG-GTA-TTTTTTTATACAAATTTAGTG-AAAACCCTTATTTTGGCCATTTGTTCG
47763191 TATTTTT
63 TATTTTT
47763198 TCAGATTTTA
Statistics
Matches: 174, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
118 62 0.36
119 3 0.02
120 3 0.02
121 27 0.16
122 36 0.21
123 34 0.20
125 9 0.05
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.55
Consensus pattern (120 bp):
TATTATTTTAGGTATTTTTTTATACAAATTTAGTGAAAACCCTTATTTTGGCCATTTGTTCGTAT
TTTTATTTTCAGATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATG
Found at i:47763428 original size:58 final size:54
Alignment explanation
Indices: 47763366--47763484 Score: 143
Period size: 53 Copynumber: 2.1 Consensus size: 54
47763356 ATATCTAATC
*
47763366 AACATAAAACACACTTATAAAATAAATTAAATAAAATAATAAAACATA-TAATGTACAT
1 AACATAAAACA-A-TAATAAAATAAA-T-AATAAAATAATAAAACATAGT-ATGTACAT
* * *
47763424 AACAT-AAATAATAATAACATAAATAATAAAATAATAAGACATAGTATGTACAT
1 AACATAAAACAATAATAAAATAAATAATAAAATAATAAAACATAGTATGTACAT
47763477 AACATAAA
1 AACATAAA
47763485 TAATTAAACA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
53 31 0.56
54 4 0.07
55 10 0.18
56 1 0.02
57 4 0.07
58 5 0.09
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.25
Consensus pattern (54 bp):
AACATAAAACAATAATAAAATAAATAATAAAATAATAAAACATAGTATGTACAT
Found at i:47763435 original size:30 final size:30
Alignment explanation
Indices: 47763399--47763522 Score: 124
Period size: 30 Copynumber: 4.4 Consensus size: 30
47763389 AAATTAAATA
47763399 AAATAATAAAACATATAATGTACATAACAT
1 AAATAATAAAACATATAATGTACATAACAT
47763429 AAATAATAATAACATA-AA--TA-AT---A-
1 AAATAATAA-AACATATAATGTACATAACAT
*
47763452 AAATAATAAGACATAGT-ATGTACATAACAT
1 AAATAATAAAACATA-TAATGTACATAACAT
* *
47763482 AAATAATTAAACATAGAATGTACATAACAT
1 AAATAATAAAACATATAATGTACATAACAT
47763512 AAA-AATTAAAA
1 AAATAA-TAAAA
47763523 TCAAAACCAA
Statistics
Matches: 77, Mismatches: 5, Indels: 24
0.73 0.05 0.23
Matches are distributed among these distances:
22 5 0.06
23 10 0.13
24 1 0.01
25 2 0.03
26 2 0.03
27 2 0.03
28 2 0.03
29 3 0.04
30 44 0.57
31 6 0.08
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (30 bp):
AAATAATAAAACATATAATGTACATAACAT
Found at i:47763442 original size:15 final size:15
Alignment explanation
Indices: 47763399--47763452 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
47763389 AAATTAAATA
47763399 AAATAATAA-AACAT
1 AAATAATAATAACAT
*
47763413 ATAAT-GTACATAACAT
1 A-AATAATA-ATAACAT
47763429 AAATAATAATAACAT
1 AAATAATAATAACAT
47763444 AAATAATAA
1 AAATAATAA
47763453 AATAATAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 3 0.09
15 23 0.68
16 8 0.24
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (15 bp):
AAATAATAATAACAT
Found at i:47763445 original size:20 final size:20
Alignment explanation
Indices: 47763420--47763460 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
47763410 CATATAATGT
*
47763420 ACATAACATAA-ATAATAATA
1 ACATAA-ATAATAAAATAATA
47763440 ACATAAATAATAAAATAATA
1 ACATAAATAATAAAATAATA
47763460 A
1 A
47763461 GACATAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (20 bp):
ACATAAATAATAAAATAATA
Found at i:47763457 original size:53 final size:52
Alignment explanation
Indices: 47763395--47763496 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 52
47763385 AAATAAATTA
47763395 AATAAAATAATAAAACATA-TAATGTACATAACATAAATAATAATAACATAAAT
1 AATAAAATAATAAAACATAGT-ATGTACATAACATAAATAATAA-AACATAAAT
* *
47763448 AATAAAATAATAAGACATAGTATGTACATAACATAAATAATTAAACATA
1 AATAAAATAATAAAACATAGTATGTACATAACATAAATAATAAAACATA
47763497 GAATGTACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
52 6 0.13
53 39 0.85
54 1 0.02
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (52 bp):
AATAAAATAATAAAACATAGTATGTACATAACATAAATAATAAAACATAAAT
Found at i:47763576 original size:17 final size:17
Alignment explanation
Indices: 47763556--47763588 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47763546 ATAACAACAA
*
47763556 AAATAAAATACGAAAAG
1 AAATAAAAAACGAAAAG
47763573 AAATAAAAAACGAAAA
1 AAATAAAAAACGAAAA
47763589 TAGTATATTT
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:0.76, C:0.06, G:0.09, T:0.09
Consensus pattern (17 bp):
AAATAAAAAACGAAAAG
Found at i:47767688 original size:20 final size:18
Alignment explanation
Indices: 47767646--47767688 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
47767636 AATTTGGAAT
*
47767646 TTTTTATAAATATTTTAA
1 TTTTTAAAAATATTTTAA
*
47767664 ATTTTAAAAATTACTTTTAA
1 TTTTTAAAAA-TA-TTTTAA
47767684 TTTTT
1 TTTTT
47767689 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 8 0.40
19 2 0.10
20 10 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTAAAAATATTTTAA
Found at i:47768581 original size:10 final size:10
Alignment explanation
Indices: 47768566--47768597 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
47768556 TAAAAATTAG
*
47768566 AAAATAAATT
1 AAAATAAATA
47768576 AAAATAAATA
1 AAAATAAATA
47768586 AAAATAAATA
1 AAAATAAATA
47768596 AA
1 AA
47768598 TTTTAGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAATAAATA
Found at i:47768609 original size:19 final size:18
Alignment explanation
Indices: 47768587--47768639 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
47768577 AAATAAATAA
47768587 AAATAAATAAATTTTAGAT
1 AAATAAATAAATTTTA-AT
* *
47768606 AAATTATTAAATTTTAAT
1 AAATAAATAAATTTTAAT
47768624 AAA-AATATAAAATTTT
1 AAATAA-AT-AAATTTT
47768640 CAAATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 6 0.21
19 21 0.75
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
AAATAAATAAATTTTAAT
Found at i:47768636 original size:27 final size:27
Alignment explanation
Indices: 47768606--47768718 Score: 88
Period size: 27 Copynumber: 4.1 Consensus size: 27
47768596 AATTTTAGAT
*
47768606 AAATTATTAAATTTTAATAAAAATATA
1 AAATTATAAAATTTTAATAAAAATATA
* * *
47768633 AAATTTTCAAA-TTTATTAAAAATTATA
1 AAATTATAAAATTTTAATAAAAA-TATA
** * *
47768660 ATTTTTTATAAAAATTGTAA-AAAATTATA
1 A--AATTAT-AAAATTTTAATAAAAATATA
47768689 AAATTATAAAATTTT-ATAAAAATCATA
1 AAATTATAAAATTTTAATAAAAAT-ATA
47768716 AAA
1 AAA
47768719 AAATTATAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
25 1 0.02
26 22 0.34
27 24 0.37
29 8 0.12
30 7 0.11
31 3 0.05
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (27 bp):
AAATTATAAAATTTTAATAAAAATATA
Found at i:47768671 original size:19 final size:19
Alignment explanation
Indices: 47768644--47768718 Score: 80
Period size: 19 Copynumber: 3.9 Consensus size: 19
47768634 AATTTTCAAA
**
47768644 TTTATTAAAAATTATAATTT
1 TTTA-TAAAAATTATAAAAT
* *
47768664 TTTATAAAAATTGTAAAAA
1 TTTATAAAAATTATAAAAT
*
47768683 ATTAT-AAAATTATAAAAT
1 TTTATAAAAATTATAAAAT
*
47768701 TTTATAAAAATCATAAAA
1 TTTATAAAAATTATAAAA
47768719 AAATTATAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
18 15 0.33
19 26 0.58
20 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (19 bp):
TTTATAAAAATTATAAAAT
Found at i:47768691 original size:9 final size:9
Alignment explanation
Indices: 47768665--47768731 Score: 64
Period size: 10 Copynumber: 7.1 Consensus size: 9
47768655 TTATAATTTT
47768665 TTATAAAAA
1 TTATAAAAA
*
47768674 TTGTAAAAAA
1 TTAT-AAAAA
47768684 TTAT-AAAA
1 TTATAAAAA
*
47768692 TTATAAAATT
1 TTATAAAA-A
47768702 TTATAAAAA
1 TTATAAAAA
*
47768711 TCATAAAAAAA
1 T--TATAAAAA
47768722 TTATAAAAA
1 TTATAAAAA
47768731 T
1 T
47768732 GCATCAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
8 8 0.17
9 15 0.32
10 16 0.34
11 8 0.17
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:47768692 original size:37 final size:38
Alignment explanation
Indices: 47768647--47768729 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 38
47768637 TTTCAAATTT
** **
47768647 ATTA-AAAATTATAATTTTTTATAAAAATTGT-AAAAA
1 ATTATAAAATTATAAAATTTTATAAAAATCATAAAAAA
47768683 ATTATAAAATTATAAAATTTTATAAAAATCATAAAAAA
1 ATTATAAAATTATAAAATTTTATAAAAATCATAAAAAA
47768721 ATTATAAAA
1 ATTATAAAA
47768730 ATGCATCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 4 0.10
37 23 0.56
38 14 0.34
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (38 bp):
ATTATAAAATTATAAAATTTTATAAAAATCATAAAAAA
Found at i:47768730 original size:21 final size:22
Alignment explanation
Indices: 47768696--47768743 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
47768686 ATAAAATTAT
*
47768696 AAAATTTTATAAAAAT-CATAAA
1 AAAATTAT-TAAAAATGCATAAA
*
47768718 AAAATTA-TAAAAATGCATCAA
1 AAAATTATTAAAAATGCATAAA
47768739 AAAAT
1 AAAAT
47768744 CCCTTTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.30
21 10 0.43
22 6 0.26
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAATTATTAAAAATGCATAAA
Found at i:47768989 original size:20 final size:20
Alignment explanation
Indices: 47768964--47769045 Score: 68
Period size: 20 Copynumber: 4.3 Consensus size: 20
47768954 TTCTTTCGAC
47768964 TTTATAAAATTTTATATTTT
1 TTTATAAAATTTTATATTTT
*
47768984 TTTAT---ATTTCTATA-TAT
1 TTTATAAAATTT-TATATTTT
*
47769001 TTTAT-AAATTTT-TATGATT
1 TTTATAAAATTTTATAT-TTT
* *
47769020 TTTATAAAATTTTACAATTT
1 TTTATAAAATTTTATATTTT
47769040 TTTATA
1 TTTATA
47769046 TTTTTTACGA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
17 13 0.27
18 5 0.10
19 10 0.20
20 20 0.41
21 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTATAAAATTTTATATTTT
Found at i:47769013 original size:10 final size:10
Alignment explanation
Indices: 47768964--47769045 Score: 55
Period size: 10 Copynumber: 8.6 Consensus size: 10
47768954 TTCTTTCGAC
*
47768964 TTTATAAAAT
1 TTTATAAATT
47768974 TTTAT--ATT
1 TTTATAAATT
* *
47768982 TTTTTATATT
1 TTTATAAATT
* *
47768992 TCTATATA-T
1 TTTATAAATT
47769001 TTTATAAATT
1 TTTATAAATT
*
47769011 TTTAT-GATT
1 TTTATAAATT
*
47769020 TTTATAAAAT
1 TTTATAAATT
* *
47769030 TTTACAATTT
1 TTTATAAATT
47769040 TTTATA
1 TTTATA
47769046 TTTTTTACGA
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
8 6 0.11
9 15 0.27
10 34 0.62
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTATAAATT
Found at i:47769032 original size:19 final size:18
Alignment explanation
Indices: 47768964--47769033 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
47768954 TTCTTTCGAC
47768964 TTTATAAAATTTTATATT
1 TTTATAAAATTTTATATT
* *
47768982 TTT-TTATATTTCTATATAT
1 TTTATAAAATTT-TATAT-T
*
47769001 TTTATAAATTTTTATGATT
1 TTTATAAAATTTTAT-ATT
47769020 TTTATAAAATTTTA
1 TTTATAAAATTTTA
47769034 CAATTTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 6 0.14
18 8 0.19
19 21 0.50
20 7 0.17
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (18 bp):
TTTATAAAATTTTATATT
Found at i:47769039 original size:19 final size:19
Alignment explanation
Indices: 47769000--47769041 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
47768990 TTTCTATATA
* **
47769000 TTTTATAAATTTTTATGAT
1 TTTTATAAAATTTTACAAT
47769019 TTTTATAAAATTTTACAAT
1 TTTTATAAAATTTTACAAT
47769038 TTTT
1 TTTT
47769042 TATATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATAAAATTTTACAAT
Found at i:47769040 original size:37 final size:39
Alignment explanation
Indices: 47768964--47769064 Score: 95
Period size: 37 Copynumber: 2.7 Consensus size: 39
47768954 TTCTTTCGAC
* * * *
47768964 TTTATAAAATTTTAT-ATTTTT-TTATATTTCTATATAT
1 TTTATAAATTTTTATGATTTTTATAAAATTTCTACATAT
47769001 TTTATAAATTTTTATGATTTTTATAAAATTT-TACA-AT
1 TTTATAAATTTTTATGATTTTTATAAAATTTCTACATAT
* * *
47769038 TTTTTATATTTTTTACGA-TTTTATAAA
1 TTTATA-AATTTTTATGATTTTTATAAA
47769065 GTTGAAACGA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
37 30 0.56
38 18 0.33
39 6 0.11
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (39 bp):
TTTATAAATTTTTATGATTTTTATAAAATTTCTACATAT
Found at i:47770657 original size:22 final size:23
Alignment explanation
Indices: 47770594--47770654 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
47770584 ATAGTACGTG
47770594 ATAAAAAGAATTAAAATAATAGTAC
1 ATAAAAA-AA-TAAAATAATAGTAC
* *
47770619 GTAATAAAATAAAATAAT-GTAC
1 ATAAAAAAATAAAATAATAGTAC
47770641 ATAAAAAAGATAAA
1 ATAAAAAA-ATAAA
47770655 TAAATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 10 0.32
23 14 0.45
24 2 0.06
25 5 0.16
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.23
Consensus pattern (23 bp):
ATAAAAAAATAAAATAATAGTAC
Found at i:47772332 original size:50 final size:50
Alignment explanation
Indices: 47772228--47772345 Score: 121
Period size: 50 Copynumber: 2.4 Consensus size: 50
47772218 GCAACGCTAG
* ** ** * *
47772228 GGAAATAAGATTCGTTGTTGTAGCTTTAATCTATTTGACTGCAATGTTGA
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCTATTCCACTGCAATATAGA
* * *
47772278 GGAAGTAAGTTTCACTGTTGTAGCTTTAATCTGTTCCACTGCACTATCAG-
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCTATTCCACTGCAATAT-AGA
*
47772328 GGAAGTAAGATTCGCTGT
1 GGAAGTAAGATTCACTGT
47772346 CTTCGATCTG
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 54 0.98
51 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (50 bp):
GGAAGTAAGATTCACTGTTGTAGCTTTAATCTATTCCACTGCAATATAGA
Found at i:47772405 original size:44 final size:44
Alignment explanation
Indices: 47772370--47772826 Score: 758
Period size: 44 Copynumber: 10.4 Consensus size: 44
47772360 ACTACTGCTT
* *
47772370 AGGGAGACAGGA-TCTACAATCTTCAACCTATTCCACTGCTGTCT
1 AGGGAGATAGGACT-TACAATCTTCAACCTATTCCACTGCTGTCC
* *
47772414 AGGGAGATAGGACTTACAACCTTCAACCTATTCCACTCCTGTCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
*
47772458 AGGGAGATAGGACTTACAATCTTCGACCTATTCCA-TGCTGTCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
**
47772501 AGGGAGATAGGACTTACAATCTTTGACCTATTCCACTGCTGTCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
47772545 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
47772589 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
47772633 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
*
47772677 AGGGAGATAGGACTTACAACCTTCAACCTATTCCACTGCTGTCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
**
47772721 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTG-TAGTTT
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCT-GTCC
* **
47772765 AGGGAGATAGGACTTACAATCTTCGACCTATTCCACTATTGTCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
47772809 AGGGAGATAGGACTTACA
1 AGGGAGATAGGACTTACA
47772827 GTTTCACCAG
Statistics
Matches: 391, Mismatches: 18, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
43 42 0.11
44 347 0.89
45 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (44 bp):
AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
Found at i:47773736 original size:15 final size:16
Alignment explanation
Indices: 47773705--47773737 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
47773695 TATCTTGAAA
*
47773705 AAGAATGAAGTATTTC
1 AAGAATGAAGTAATTC
47773721 AAGAAT-AAGTAATTC
1 AAGAATGAAGTAATTC
47773736 AA
1 AA
47773738 TATAAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (16 bp):
AAGAATGAAGTAATTC
Found at i:47785340 original size:22 final size:23
Alignment explanation
Indices: 47785277--47785337 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
47785267 ATAGTACGTG
47785277 ATAAAAAGAATTAAAATAATAGTAC
1 ATAAAAA-AA-TAAAATAATAGTAC
*
47785302 ATAATAAAATAAAATAAT-GTAC
1 ATAAAAAAATAAAATAATAGTAC
47785324 ATAAAAAAGATAAA
1 ATAAAAAA-ATAAA
47785338 TAAATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 11 0.33
23 14 0.42
24 2 0.06
25 6 0.18
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (23 bp):
ATAAAAAAATAAAATAATAGTAC
Found at i:47786516 original size:12 final size:12
Alignment explanation
Indices: 47786490--47786531 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
47786480 TTAATTTTTA
47786490 TTTATTTTTGTGT
1 TTTATTTTTG-GT
47786503 TTTATTTTTGGT
1 TTTATTTTTGGT
47786515 TTT-TCTTTTGGT
1 TTTAT-TTTTGGT
47786527 GTTTA
1 -TTTA
47786532 CTGGGCTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.04
12 12 0.46
13 13 0.50
ACGTcount: A:0.07, C:0.02, G:0.17, T:0.74
Consensus pattern (12 bp):
TTTATTTTTGGT
Found at i:47794918 original size:40 final size:40
Alignment explanation
Indices: 47794874--47794987 Score: 169
Period size: 40 Copynumber: 2.9 Consensus size: 40
47794864 GTTTGGACAA
* *
47794874 AAAACGCCGCTAAAAATTGAGTATTAGCGGCGCTTTACAT
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTACAG
* *
47794914 AAAACGCCGCTAAAGATTGAGCATTAGCGGCGC-TTCCAG
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTACAG
47794953 AAAAGCGCCGCTAAAAA-TGAGCATTAGCGGCGCTT
1 AAAA-CGCCGCTAAAAATTGAGCATTAGCGGCGCTT
47794988 CTTGGAAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 24 0.36
40 43 0.64
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTACAG
Found at i:47795008 original size:39 final size:40
Alignment explanation
Indices: 47794873--47795009 Score: 163
Period size: 40 Copynumber: 3.4 Consensus size: 40
47794863 CGTTTGGACA
* *
47794873 AAAAACGCCGCTAAAAATTGAGTATTAGCGGCGC-T-TTAC
1 AAAAACGCCGCTAAAAA-TGAGCATTAGCGGCGCTTCTTAG
* *
47794912 ATAAAACGCCGCTAAAGATTGAGCATTAGCGGCGCTTC-CAG
1 A-AAAACGCCGCTAAA-AATGAGCATTAGCGGCGCTTCTTAG
* *
47794953 AAAAGCGCCGCTAAAAATGAGCATTAGCGGCGCTTCTTGG
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTCTTAG
*
47794993 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
47795010 CCTAAGCCCA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
39 21 0.25
40 58 0.70
41 4 0.05
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTCTTAG
Found at i:47795087 original size:41 final size:41
Alignment explanation
Indices: 47795025--47795237 Score: 329
Period size: 41 Copynumber: 5.2 Consensus size: 41
47795015 GCCCAACGAC
*
47795025 AGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTGTGAAAA
1 AGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAAAA
* * *
47795066 AGCGTCGCTAATGCTCAGGCTTTCAGCGGCGTTTTTAAAAA
1 AGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAAAA
47795107 AGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAAAA
1 AGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAAAA
* * * *
47795148 AGCACCGCTATTGTTCATGCTTTTAGCGGCGTTTTT-AAAGA
1 AGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAAA-A
*
47795189 AGCGCCGCTAATGCTCTGGCTTTTAGCGGCGTTTTTGAAAA
1 AGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAAAA
47795230 AGCGCCGC
1 AGCGCCGC
47795238 AAAAACATTG
Statistics
Matches: 154, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 3 0.02
41 148 0.96
42 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.30
Consensus pattern (41 bp):
AGCGCCGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAAAA
Found at i:47795535 original size:14 final size:15
Alignment explanation
Indices: 47795505--47795537 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
47795495 AAGGTTTATA
47795505 GATTATGAAATTAGG
1 GATTATGAAATTAGG
*
47795520 GATTATGGAA-TAGG
1 GATTATGAAATTAGG
47795534 GATT
1 GATT
47795538 CTGGTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (15 bp):
GATTATGAAATTAGG
Found at i:47795668 original size:21 final size:21
Alignment explanation
Indices: 47795637--47795699 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
47795627 TATTAAATAA
47795637 GGTTTAGGGGTTAGTAGTTAGG
1 GGTTT-GGGGTTAGTAGTTAGG
* **
47795659 GGTTTGGGGTTTGGGGTTAGG
1 GGTTTGGGGTTAGTAGTTAGG
* * *
47795680 GGTTAGAGGTTAATAGTTAG
1 GGTTTGGGGTTAGTAGTTAG
47795700 TGATTAAAGG
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (21 bp):
GGTTTGGGGTTAGTAGTTAGG
Found at i:47795684 original size:7 final size:7
Alignment explanation
Indices: 47795640--47795691 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
47795630 TAAATAAGGT
47795640 TTAGGGG
1 TTAGGGG
**
47795647 TTAGTAG
1 TTAGGGG
47795654 TTAGGGG
1 TTAGGGG
*
47795661 TTTGGGG
1 TTAGGGG
*
47795668 TTTGGGG
1 TTAGGGG
47795675 TTAGGGG
1 TTAGGGG
*
47795682 TTAGAGG
1 TTAGGGG
47795689 TTA
1 TTA
47795692 ATAGTTAGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.37
Consensus pattern (7 bp):
TTAGGGG
Found at i:47795846 original size:7 final size:7
Alignment explanation
Indices: 47795804--47795874 Score: 70
Period size: 7 Copynumber: 10.1 Consensus size: 7
47795794 ATTGTAAAAG
47795804 AGGGGTT
1 AGGGGTT
*
47795811 AAGGGTT
1 AGGGGTT
*
47795818 AGGGGAT
1 AGGGGTT
*
47795825 AGGGGAT
1 AGGGGTT
**
47795832 AGTAGTT
1 AGGGGTT
47795839 AGGGGTT
1 AGGGGTT
47795846 AGGGGTT
1 AGGGGTT
* *
47795853 TGGGGCT
1 AGGGGTT
47795860 AGGGGTT
1 AGGGGTT
*
47795867 AGAGGTT
1 AGGGGTT
47795874 A
1 A
47795875 AGAGTTAGTG
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.21, C:0.01, G:0.51, T:0.27
Consensus pattern (7 bp):
AGGGGTT
Found at i:47795956 original size:183 final size:183
Alignment explanation
Indices: 47795641--47796012 Score: 654
Period size: 183 Copynumber: 2.0 Consensus size: 183
47795631 AAATAAGGTT
* * * *
47795641 TAGGGGTTAGTAGTTAGGGGTTTGGGGTTTGGGGTTAGGGGTTAGAGGTTAATAGTTAGTGATTA
1 TAGGGGATAGTAGTTAGGGGTTAGGGGTTTGGGGCTAGGGGTTAGAGGTTAAGAGTTAGTGATTA
*
47795706 AAGGTTTAGAGATTCGGGGTCGGGTTAGGGTTTAAGGTTTAAATTAATTAGTATTTTTTAATTTA
66 AAGGTTTAGAGATTCGGGGCCGGGTTAGGGTTTAAGGTTTAAATTAATTAGTATTTTTTAATTTA
* *
47795771 TATATTAATTAAGTTCTTATATAATTGTAAAAGAGGGGTTAAGGGTTAGGGGA
131 TATATTAATTAAGTTCTTATATAATTGTAAAAGAGGGGTTAAGGGATAGGAGA
*
47795824 TAGGGGATAGTAGTTAGGGGTTAGGGGTTTGGGGCTAGGGGTTAGAGGTTAAGAGTTAGTGATTT
1 TAGGGGATAGTAGTTAGGGGTTAGGGGTTTGGGGCTAGGGGTTAGAGGTTAAGAGTTAGTGATTA
*
47795889 AAGGTTTAGAGATTTGGGGCCGGGTTAGGGTTTAAGGTTTAAATTAATTAGTATTTTTTAATTTA
66 AAGGTTTAGAGATTCGGGGCCGGGTTAGGGTTTAAGGTTTAAATTAATTAGTATTTTTTAATTTA
*
47795954 TATATTAATTAAGTTCTTATATAATTGTAAAAGAGGGGTTAGGGGATAGGAGA
131 TATATTAATTAAGTTCTTATATAATTGTAAAAGAGGGGTTAAGGGATAGGAGA
47796007 TAGGGG
1 TAGGGG
47796013 TTTAGGGTTT
Statistics
Matches: 179, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 179 1.00
ACGTcount: A:0.28, C:0.02, G:0.33, T:0.37
Consensus pattern (183 bp):
TAGGGGATAGTAGTTAGGGGTTAGGGGTTTGGGGCTAGGGGTTAGAGGTTAAGAGTTAGTGATTA
AAGGTTTAGAGATTCGGGGCCGGGTTAGGGTTTAAGGTTTAAATTAATTAGTATTTTTTAATTTA
TATATTAATTAAGTTCTTATATAATTGTAAAAGAGGGGTTAAGGGATAGGAGA
Found at i:47796011 original size:148 final size:144
Alignment explanation
Indices: 47795839--47796132 Score: 326
Period size: 144 Copynumber: 2.0 Consensus size: 144
47795829 GATAGTAGTT
* * * *
47795839 AGGGGTTAGGGGTTTGGGGCTAGGGG-TTAGAGG-TTAAGAGTTAGTGATTTAAGGTTT-AGAGA
1 AGGGGTTAGGGGATAGGAGATAGGGGTTTAG-GGTTTAAGAGTTA-TGATTTAAGGTTTAAGAGA
* * * * * *
47795901 TTTGGGGCCGGGTTA-GGGTTTAAGGTTTAAATTAATTAGTATTTTTTAATTTATATATTAATTA
64 --T--AG--GGGTTAGGGGTGTAAGGCTTAAATTAATTAGTATTTTTAAAATTATATATTAAATA
47795965 AGTTCTTATATAATTGTAAAAG
123 AGTTCTTATATAATTGTAAAAG
* ** *
47795987 AGGGGTTAGGGGATAGGAGATAGGGGTTTAGGGTTTATGTTTTATGATTTAGGGTTTAAGAGATA
1 AGGGGTTAGGGGATAGGAGATAGGGGTTTAGGGTTTAAGAGTTATGATTTAAGGTTTAAGAGATA
* * * *
47796052 GGGGTTAGGGGTGTAGGGCTTAGATTAATTAGTGTTTTTAAAATTATATATTAAATAATTTCTTA
66 GGGGTTAGGGGTGTAAGGCTTAAATTAATTAGTATTTTTAAAATTATATATTAAATAAGTTCTTA
47796117 TATAATTGTAAAAG
131 TATAATTGTAAAAG
47796131 AG
1 AG
47796133 ATAATATTAA
Statistics
Matches: 124, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
143 6 0.05
144 64 0.52
145 1 0.01
147 1 0.01
148 36 0.29
149 16 0.13
ACGTcount: A:0.30, C:0.02, G:0.29, T:0.39
Consensus pattern (144 bp):
AGGGGTTAGGGGATAGGAGATAGGGGTTTAGGGTTTAAGAGTTATGATTTAAGGTTTAAGAGATA
GGGGTTAGGGGTGTAAGGCTTAAATTAATTAGTATTTTTAAAATTATATATTAAATAAGTTCTTA
TATAATTGTAAAAG
Found at i:47796505 original size:38 final size:39
Alignment explanation
Indices: 47796422--47796506 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
47796412 TAGTCTCCCA
47796422 CTAAAAATAAGCATTAGTGGCGCTTTTCAGAAAACGCCG
1 CTAAAAATAAGCATTAGTGGCGCTTTTCAGAAAACGCCG
* * *
47796461 CTAAAAATGAGCATTAGTGGTG-TTTTTAGAAAAGCGCCG
1 CTAAAAATAAGCATTAGTGGCGCTTTTCAGAAAA-CGCCG
*
47796500 CAAAAAA
1 CTAAAAA
47796507 CCTAGGCCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 10 0.24
39 31 0.76
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (39 bp):
CTAAAAATAAGCATTAGTGGCGCTTTTCAGAAAACGCCG
Found at i:47796627 original size:41 final size:40
Alignment explanation
Indices: 47796546--47796627 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
47796536 TTTTTGAGGC
*
47796546 TTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTCTATT
1 TTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTATATT
* * *
47796586 TTTAGTGGCGTTTTTTAGAAAGCGCCACTAATGCTAATATT
1 TTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCT-ATATT
47796627 T
1 T
47796628 ATTCTAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 32 0.86
41 5 0.14
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGCTATATT
Found at i:47797378 original size:38 final size:38
Alignment explanation
Indices: 47797298--47797379 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 38
47797288 GGTTACAAAC
* * * *
47797298 TTTATCTGTTTTTTATATGTTTATCTCACAAATTTTCT
1 TTTATCTGCTTTTTACATGTTTATCTCACAAAGTTTCG
*
47797336 TTTATCTGCTTTTTACATGTTTATCTCACAAAGTTTGG
1 TTTATCTGCTTTTTACATGTTTATCTCACAAAGTTTCG
47797374 TTTATC
1 TTTATC
47797380 AATTGTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.56
Consensus pattern (38 bp):
TTTATCTGCTTTTTACATGTTTATCTCACAAAGTTTCG
Found at i:47801760 original size:43 final size:43
Alignment explanation
Indices: 47801677--47801969 Score: 426
Period size: 43 Copynumber: 6.8 Consensus size: 43
47801667 TTTTTGCGAG
* * * * * *
47801677 AAGCGTCGCTAAAGGT-TTGTTTTTTAGTGGCGTTTATGATAA
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAA
* * *
47801719 AAGCGTCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAG
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAA
* *
47801762 AAGCGCCGTTAAAGGTCATGTTCTTTAGCGGCATTTGTGACAA
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAA
* *
47801805 AAGCGCTGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAG
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAA
* *
47801848 AAGCGCTGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAG
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAA
47801891 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAA
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAA
**
47801934 AAGCGCCGCTAAAGGTCATGGCCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTT
47801970 CCTCACATAA
Statistics
Matches: 232, Mismatches: 18, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
42 16 0.07
43 216 0.93
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAA
Found at i:47803699 original size:152 final size:152
Alignment explanation
Indices: 47803423--47803727 Score: 610
Period size: 152 Copynumber: 2.0 Consensus size: 152
47803413 GTTATCAAGA
47803423 ATTTGCAGCGGAAGTTTAAAAAACGTTTTGCTCGAAACCAAGCTCGTGTTTCCAAAAACCACTTG
1 ATTTGCAGCGGAAGTTTAAAAAACGTTTTGCTCGAAACCAAGCTCGTGTTTCCAAAAACCACTTG
47803488 TTAAAACCATTTGTTTGCGTAAAGTGTTTTTGTCAACGTTGTGGAAAAGAAAGCAAAACAAAATC
66 TTAAAACCATTTGTTTGCGTAAAGTGTTTTTGTCAACGTTGTGGAAAAGAAAGCAAAACAAAATC
47803553 CAAATCCAAAAGTTAAAACCAT
131 CAAATCCAAAAGTTAAAACCAT
47803575 ATTTGCAGCGGAAGTTTAAAAAACGTTTTGCTCGAAACCAAGCTCGTGTTTCCAAAAACCACTTG
1 ATTTGCAGCGGAAGTTTAAAAAACGTTTTGCTCGAAACCAAGCTCGTGTTTCCAAAAACCACTTG
47803640 TTAAAACCATTTGTTTGCGTAAAGTGTTTTTGTCAACGTTGTGGAAAAGAAAGCAAAACAAAATC
66 TTAAAACCATTTGTTTGCGTAAAGTGTTTTTGTCAACGTTGTGGAAAAGAAAGCAAAACAAAATC
47803705 CAAATCCAAAAGTTAAAACCAT
131 CAAATCCAAAAGTTAAAACCAT
47803727 A
1 A
47803728 CAGTCTAGAG
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 153 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (152 bp):
ATTTGCAGCGGAAGTTTAAAAAACGTTTTGCTCGAAACCAAGCTCGTGTTTCCAAAAACCACTTG
TTAAAACCATTTGTTTGCGTAAAGTGTTTTTGTCAACGTTGTGGAAAAGAAAGCAAAACAAAATC
CAAATCCAAAAGTTAAAACCAT
Found at i:47805880 original size:2 final size:2
Alignment explanation
Indices: 47805873--47805903 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
47805863 CACTATTAAC
47805873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47805904 ATTTATGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47807914 original size:24 final size:24
Alignment explanation
Indices: 47807868--47807918 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
47807858 CTAGGAAAAG
* *
47807868 AAATAACAAAGATTTTATGCTAAT
1 AAATAACAAAGATATTATACTAAT
* *
47807892 AAATAACAAATATATTCTACTAAT
1 AAATAACAAAGATATTATACTAAT
47807916 AAA
1 AAA
47807919 ATCTAAATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (24 bp):
AAATAACAAAGATATTATACTAAT
Found at i:47813161 original size:35 final size:35
Alignment explanation
Indices: 47813122--47813205 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
47813112 TACACGGTTA
* * *
47813122 ACCATTCAGCATACCAAATGCTCATAAGAGGCAGT
1 ACCATCCAGCACACCAAATGCTCATAAGAGCCAGT
**
47813157 ACCATCCAGCACACCAGTTGCTCATAAGAGCCAGT
1 ACCATCCAGCACACCAAATGCTCATAAGAGCCAGT
* *
47813192 GCCATCCAACACAC
1 ACCATCCAGCACAC
47813206 TAGATAACAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.35, C:0.33, G:0.15, T:0.17
Consensus pattern (35 bp):
ACCATCCAGCACACCAAATGCTCATAAGAGCCAGT
Found at i:47813458 original size:22 final size:22
Alignment explanation
Indices: 47813433--47813474 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
47813423 CTCGATTGTC
47813433 AAATATCAACACATTAGTCATG
1 AAATATCAACACATTAGTCATG
*
47813455 AAATATCAATACATTAGTCA
1 AAATATCAACACATTAGTCA
47813475 GCAATCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.29
Consensus pattern (22 bp):
AAATATCAACACATTAGTCATG
Found at i:47815169 original size:37 final size:37
Alignment explanation
Indices: 47815101--47815174 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
47815091 TACGCAACAA
* *
47815101 ATTAAATTTACAGATACAAGAAAATACAAACATTCTAG
1 ATTAAATTTACA-ATACAAGAAAACACAAACAGTCTAG
*
47815139 ATTAAATTTAC-ATCACAAGAAAACATAAACAGTCTA
1 ATTAAATTTACAAT-ACAAGAAAACACAAACAGTCTA
47815175 AAAAATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 2 0.06
37 19 0.59
38 11 0.34
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.26
Consensus pattern (37 bp):
ATTAAATTTACAATACAAGAAAACACAAACAGTCTAG
Found at i:47816959 original size:2 final size:2
Alignment explanation
Indices: 47816952--47816993 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
47816942 AATATAAAAG
47816952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47816994 AACAAATGCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47817045 original size:24 final size:25
Alignment explanation
Indices: 47816977--47817046 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
47816967 ATATATATAT
47816977 ATATATATATATATATAAACAAATGCG
1 ATATATATAT-TATATAAA-AAATGCG
* **
47817004 -TGTATACTA-TATGGAAAAAATG-G
1 ATATATA-TATTATATAAAAAATGCG
47817027 ATATATATATTATATAAAAA
1 ATATATATATTATATAAAAA
47817047 CTAAGCGTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
23 3 0.09
24 18 0.53
25 6 0.18
26 5 0.15
27 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.34
Consensus pattern (25 bp):
ATATATATATTATATAAAAAATGCG
Found at i:47817737 original size:10 final size:11
Alignment explanation
Indices: 47817722--47817755 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
47817712 TTGCTATTTT
47817722 AAATG-AAATA
1 AAATGAAAATA
47817732 AAATGAAAATA
1 AAATGAAAATA
47817743 AAA-GAAAATA
1 AAATGAAAATA
47817753 AAA
1 AAA
47817756 ATATATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (11 bp):
AAATGAAAATA
Found at i:47818630 original size:44 final size:45
Alignment explanation
Indices: 47818610--47818977 Score: 429
Period size: 44 Copynumber: 8.3 Consensus size: 45
47818600 ATAAGACTTG
47818610 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGC
* * * *
47818655 TATCTTCGATCTACTTTAC-GCCAATACATGAAGACAAGATCTAC
1 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGC
* * ** * *
47818699 TTTTTTCGATCTACTTCACCACCAGTACAGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGC
* ** * * *
47818744 TATCTTTGATCTACTTCACCACCAGTATGGGAAAACAAGATCTGC
1 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGC
* * * * *
47818789 TATCTTTGATCTACTTCAC-GGCAATACATGAAGACAAGATCTAC
1 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGC
** * *
47818833 TATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGC
* *
47818878 TATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGC
* * *
47818922 TATCTTCGATCTACTTCA-TGCCAATACATGAAGACAAGATCTAC
1 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGC
*
47818966 TTTCTTCGATCT
1 TATCTTCGATCT
47818978 GCCCCACTGC
Statistics
Matches: 280, Mismatches: 40, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
44 146 0.52
45 134 0.48
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (45 bp):
TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGC
Found at i:47818822 original size:89 final size:89
Alignment explanation
Indices: 47818610--47818939 Score: 464
Period size: 89 Copynumber: 3.7 Consensus size: 89
47818600 ATAAGACTTG
* *
47818610 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTTA-C
1 TATCTTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACC
* * *** *
47818674 GCCAATACATGAAGACAAGATCTAC
65 ACCAGTATGGGAAGACAAGATCTGC
* * * * *
47818699 TTTTTTCGATCTACTTCACCACCAGTACAGGAAGACAAGATCTGCTATCTTTGATCTACTTCACC
1 TATCTTCGATCTACTTCA-CGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACC
*
47818764 ACCAGTATGGGAAAACAAGATCTGC
65 ACCAGTATGGGAAGACAAGATCTGC
* * * *
47818789 TATCTTTGATCTACTTCACGGCAATACATGAAGACAAGATCTACTATCTTCGATCTACTTCACCA
1 TATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCA
47818854 CCAGTATGGGAAGACAAGATCTGC
66 CCAGTATGGGAAGACAAGATCTGC
*
47818878 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCA
1 TATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
47818940 TGCCAATACA
Statistics
Matches: 212, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
89 177 0.83
90 35 0.17
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (89 bp):
TATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCA
CCAGTATGGGAAGACAAGATCTGC
Found at i:47818850 original size:134 final size:134
Alignment explanation
Indices: 47818610--47818977 Score: 585
Period size: 134 Copynumber: 2.8 Consensus size: 134
47818600 ATAAGACTTG
* *
47818610 TATCTTCGATCTACTTCACTGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTTACG
1 TATCTTCGATCTACTTCACCGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
*
47818675 CCAATACATGAAGACAAGATCTACTTTTTTCGATCTACTTCACCACCAGTACAGGAAGACAAGAT
66 CCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTACAGGAAGACAAGAT
47818740 CTGC
131 CTGC
* * * * * *
47818744 TATCTTTGATCTACTTCACCACCAGTATGGGAAAACAAGATCTGCTATCTTTGATCTACTTCACG
1 TATCTTCGATCTACTTCACCGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * **
47818809 GCAATACATGAAGACAAGATCTACTATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGAT
66 CCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTACAGGAAGACAAGAT
47818874 CTGC
131 CTGC
* * *
47818878 TATCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCATG
1 TATCTTCGATCTACTTCACCGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
47818942 CCAATACATGAAGACAAGATCTACTTTCTTCGATCT
66 CCAATACATGAAGACAAGATCTACTTTCTTCGATCT
47818978 GCCCCACTGC
Statistics
Matches: 210, Mismatches: 24, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
133 72 0.34
134 138 0.66
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (134 bp):
TATCTTCGATCTACTTCACCGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
CCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTACAGGAAGACAAGAT
CTGC
Found at i:47827811 original size:100 final size:100
Alignment explanation
Indices: 47827638--47827826 Score: 258
Period size: 100 Copynumber: 1.9 Consensus size: 100
47827628 CAGTGGAATG
* * *
47827638 GATTGAAGCTACAACGATGAATCTTACTTTCCTGACAGTGTAAGGGAACAGATTGAAGTCACGAC
1 GATTGAAGCCACAACGATGAATCTTACTCTCCTGACAATGTAAGGGAACAGATTGAAGTCACGAC
*
47827703 GGCGAATCTTGTTTCCCCGACATTGAAATTAAAAA
66 GGCGAATCTGGTTTCCCCGACATTGAAATTAAAAA
* * *
47827738 GATTGAAGCCACAACGGTGAATCTTAC-CTCCTTAGCAATGT-AGTGGAACAGATTGAAG-CTAG
1 GATTGAAGCCACAACGATGAATCTTACTCTCCTGA-CAATGTAAG-GGAACAGATTGAAGTC-AC
*
47827800 GATGGCGAATCTGGTTTCCCCGACATT
63 GACGGCGAATCTGGTTTCCCCGACATT
47827827 ACAGTTAAAC
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
99 8 0.10
100 70 0.90
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (100 bp):
GATTGAAGCCACAACGATGAATCTTACTCTCCTGACAATGTAAGGGAACAGATTGAAGTCACGAC
GGCGAATCTGGTTTCCCCGACATTGAAATTAAAAA
Found at i:47827990 original size:44 final size:43
Alignment explanation
Indices: 47827931--47828247 Score: 191
Period size: 44 Copynumber: 7.4 Consensus size: 43
47827921 ACACATCCAG
* *
47827931 TCTTATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGAAAATAA
1 TCTTATCTCCTTGAAGTTGCAGTAGAGCAGATT-AAGAAAATAA
* * * ** *
47827975 TCTTATCTCCTTGAAGTTGCAGTGGAGCGGATTAACATGA-GA
1 TCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTAAGAAAATAA
* * * * * *
47828017 TCTTATCT-CTCTGAAGTTGCAGAAGAGCAGA-T-CGCATACAG
1 TCTTATCTCCT-TGAAGTTGCAGTAGAGCAGATTAAGAAAATAA
* * *
47828058 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAATAA
1 TCTTATCTCCTTGAAGTTGCAGTAGAGCAGATT-AAGAAAATAA
* * * * ** *
47828102 TCATATCTCCTTGAAGTTGCAGTGGAGCGGATTAACATCA-GA
1 TCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTAAGAAAATAA
* * * * * * *
47828144 TCTTATCT-CTCTGAAGTTGTAGAAGAGCAGA-T-CGCATACAG
1 TCTTATCTCCT-TGAAGTTGCAGTAGAGCAGATTAAGAAAATAA
* ** **
47828185 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGACAGAAGAAACCAA
1 TCTTATCTCCTTGAAGTTGCAGTAGAGCAGA-TTAAGAAAATAA
* *
47828229 TCTTATCTCCCTAAAGTTG
1 TCTTATCTCCTTGAAGTTG
47828248 TAATGGACTG
Statistics
Matches: 204, Mismatches: 57, Indels: 24
0.72 0.20 0.08
Matches are distributed among these distances:
40 2 0.01
41 57 0.28
42 53 0.26
43 8 0.04
44 84 0.41
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
TCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTAAGAAAATAA
Found at i:47828102 original size:127 final size:127
Alignment explanation
Indices: 47827839--47828307 Score: 637
Period size: 127 Copynumber: 3.7 Consensus size: 127
47827829 AGTTAAACAA
* *
47827839 ATTGAAGAAAATAATC--CTCTCCCTAAAGTTGCAGTGGAGCGAATTAAAATCAGATCTTA--TC
1 ATTGAAGAAAATAATCTTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTC
* * *
47827900 TCTGAAGTTGCAGAAGAGCAGA-CACATCCAGTCTTATCTCCCTGAAGTTGCAGTAGAGTAG
66 TCTGAAGTTGCAGAAGAGCAGATCGCATACAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * *
47827961 ATTGAAGAAAATAATCTTATCTCCTTGAAGTTGCAGTGGAGCGGATTAACATGAGATCTTATCTC
1 ATTGAAGAAAATAATCTTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTC
* *
47828026 TCTGAAGTTGCAGAAGAGCAGATCGCATACAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAG
66 TCTGAAGTTGCAGAAGAGCAGATCGCATACAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAG
* * * *
47828088 ATTGAAGAAAATAATCATATCTCCTTGAAGTTGCAGTGGAGCGGATTAACATCAGATCTTATCTC
1 ATTGAAGAAAATAATCTTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTC
*
47828153 TCTGAAGTTGTAGAAGAGCAGATCGCATACAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAG
66 TCTGAAGTTGCAGAAGAGCAGATCGCATACAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAG
** ** * * *
47828215 ACAGAAGAAACCAATCTTATCTCCCTAAAGTTGTAATGGA-CTGGATTAAAAAACAGATCTTATC
1 ATTGAAGAAAATAATCTTATCTCCCTAAAGTTGCAGTGGAGC-GGATT-AAAATCAGATCTTATC
** *
47828279 TCAATGAA-TTGCAGAAGAGCAGGTCGCAT
64 TCTCTGAAGTTGCAGAAGAGCAGATCGCAT
47828308 CAACTCTCAG
Statistics
Matches: 309, Mismatches: 31, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
122 16 0.05
124 37 0.12
126 25 0.08
127 211 0.68
128 20 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (127 bp):
ATTGAAGAAAATAATCTTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTC
TCTGAAGTTGCAGAAGAGCAGATCGCATACAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAG
Found at i:47832571 original size:31 final size:30
Alignment explanation
Indices: 47832536--47832624 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
47832526 ATTTCTTATG
47832536 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TCGATACCCATATCTTTGACTTT
*
47832567 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTCGATACCCATATCTTTGACTTT
* *
47832597 ---AT-TT-GATACTCATATCTTTGACCTT
1 CCAATATTCGATACCCATATCTTTGACTTT
47832622 CCA
1 CCA
47832625 TAAATATTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
25 19 0.37
26 2 0.04
27 2 0.04
30 22 0.42
31 7 0.13
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.42
Consensus pattern (30 bp):
CCAATATTCGATACCCATATCTTTGACTTT
Found at i:47832582 original size:30 final size:29
Alignment explanation
Indices: 47832536--47832624 Score: 105
Period size: 25 Copynumber: 3.1 Consensus size: 29
47832526 ATTTCTTATG
*
47832536 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGAC-TT
47832567 CCAATATTTGATACCCATATCTTTGACTT
1 CCAATATTTGATACCCATATCTTTGACTT
*
47832596 ----TATTTGATACTCATATCTTTGACCTT
1 CCAATATTTGATACCCATATCTTTGA-CTT
47832622 CCA
1 CCA
47832625 TAAATATTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
25 21 0.40
26 3 0.06
29 2 0.04
30 19 0.37
31 7 0.13
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.42
Consensus pattern (29 bp):
CCAATATTTGATACCCATATCTTTGACTT
Found at i:47832591 original size:15 final size:15
Alignment explanation
Indices: 47832546--47832592 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
47832536 CCAATATCTC
47832546 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
47832561 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
47832576 GATACCCATATCTTT
1 GATACCCATATCTTT
47832591 GA
1 GA
47832593 CTTTATTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:47837361 original size:47 final size:47
Alignment explanation
Indices: 47837303--47837691 Score: 537
Period size: 47 Copynumber: 8.3 Consensus size: 47
47837293 CAATTACATG
* * * * * *
47837303 CTCAAAA-TGGACAGCATTATACATCAAATTAGACAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* * * * * * *
47837349 CCCAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* * * * * * *
47837396 CTCACAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* *
47837443 CTCACAATTGGACAGCATTATATATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
47837490 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
47837537 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* *
47837584 CTCAAAATTGGACAGCATTACACATTAAAATGGACAACATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* *
47837631 CTCAAAATTGGACAGCATTACACATTAAAATGGGCAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
47837678 CTCAAAATTGGACA
1 CTCAAAATTGGACA
47837692 TCAAATTTGG
Statistics
Matches: 326, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
46 6 0.02
47 320 0.98
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (47 bp):
CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
Found at i:47838707 original size:28 final size:27
Alignment explanation
Indices: 47838675--47838773 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
47838665 TTAATAAGTA
*
47838675 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT-ATAATTAAACT
* *
47838703 CGCACACTTAGTGCTT-TACCCTTATACT
1 CGCACACTTAGTGCTTATA--ATTAAACT
47838731 CGCACACTTAGTGCATT-TCAATTAAACT
1 CGCACACTTAGTGC-TTAT-AATTAAACT
47838759 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
47838774 AATCTCATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 55 0.89
29 3 0.05
30 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATTAAACT
Found at i:47840358 original size:30 final size:31
Alignment explanation
Indices: 47840312--47840375 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
47840302 ATTTCTTATG
47840312 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTTT
*
47840343 CCAATAT-TTGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTTT
47840373 CCA
1 CCA
47840376 TAAATATTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39
Consensus pattern (31 bp):
CCAATATCTCGATACCCATATCTTTGACTTT
Found at i:47840367 original size:15 final size:15
Alignment explanation
Indices: 47840322--47840368 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
47840312 CCAATATCTC
47840322 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
47840337 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
47840352 GATACCCATATCTTT
1 GATACCCATATCTTT
47840367 GA
1 GA
47840369 CTTTCCATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:47841251 original size:2 final size:2
Alignment explanation
Indices: 47841244--47841277 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
47841234 AACTTGTGAC
47841244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47841278 TCTGACTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47842893 original size:21 final size:21
Alignment explanation
Indices: 47842863--47843065 Score: 103
Period size: 21 Copynumber: 10.0 Consensus size: 21
47842853 CAATGGGTAA
*
47842863 TTTTGAATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
47842884 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
47842905 ATTT-TAT-AATTAATTTTATATT
1 TTTTGTATGAA-T-ATTGTA-ATT
* *
47842927 TATAGTT-TTTG-AT-TAGT-A--
1 T-T--TTGTATGAATATTGTAATT
47842945 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* * *
47842966 ATTTTATAATTAATTTTGT-ATT
1 -TTTTGT-ATGAATATTGTAATT
* * * * *
47842988 TATAGTTTTGGAT-TAGT-A-T
1 TTTTG-TATGAATATTGTAATT
47843007 T-TTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
47843027 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
47843046 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
47843066 ATTGTAATTT
Statistics
Matches: 138, Mismatches: 23, Indels: 43
0.68 0.11 0.21
Matches are distributed among these distances:
15 2 0.01
16 3 0.02
17 8 0.06
18 9 0.07
19 25 0.18
20 11 0.08
21 50 0.36
22 14 0.10
23 10 0.07
24 1 0.01
25 5 0.04
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.57
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:47842979 original size:61 final size:61
Alignment explanation
Indices: 47842884--47843030 Score: 269
Period size: 61 Copynumber: 2.4 Consensus size: 61
47842874 TATTGTAATT
*
47842884 TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTGATTAGTA
1 TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTGGATTAGTA
*
47842945 TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTA
1 TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTGGATTAGTA
47843006 TTTTGTATGAATATTGTAATT-TTTT
1 TTTTGTATGAATATTGTAATTATTTT
47843031 GTATGAATAT
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
60 4 0.05
61 80 0.95
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (61 bp):
TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTGGATTAGTA
Found at i:47843051 original size:19 final size:19
Alignment explanation
Indices: 47843005--47843114 Score: 130
Period size: 19 Copynumber: 6.2 Consensus size: 19
47842995 TTGGATTAGT
47843005 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
47843024 ATTTTTTGTATGAATATTGTA
1 A--TTTTGTATGAATATTGTA
47843045 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
*
47843064 ATATTG--T--A-A-T-T-
1 ATTTTGTATGAATATTGTA
47843075 -TTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
47843093 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
47843112 ATT
1 ATT
47843115 CTTTTATAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 22
0.76 0.02 0.22
Matches are distributed among these distances:
10 4 0.05
12 2 0.03
13 1 0.01
14 2 0.03
15 2 0.03
16 1 0.01
17 2 0.03
19 45 0.58
21 19 0.24
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.55
Consensus pattern (19 bp):
ATTTTGTATGAATATTGTA
Found at i:47843067 original size:48 final size:48
Alignment explanation
Indices: 47843015--47843202 Score: 209
Period size: 48 Copynumber: 3.7 Consensus size: 48
47843005 ATTTTGTATG
47843015 AATATTGTAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTGT
1 AATATTGTAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTGT
47843063 AATATTGTAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTGT
1 AATATTGTAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTGT
* * * *
47843111 AATTCTTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATTGT
1 AA---TATTGTAATT--TTTTGTA-TGA-A--TATTG--TA--ATTTTGTATGAATATTGT
47843172 AATATTGTAA--TTTTGTATGAATATTGTAATT
1 AATATTGTAATTTTTTGTATGAATATTGTAATT
47843203 ATTTTATAAT
Statistics
Matches: 119, Mismatches: 8, Indels: 28
0.77 0.05 0.18
Matches are distributed among these distances:
46 3 0.03
48 52 0.44
50 4 0.03
51 8 0.07
52 1 0.01
53 9 0.08
54 9 0.08
55 1 0.01
57 4 0.03
58 6 0.05
59 2 0.02
61 20 0.17
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (48 bp):
AATATTGTAATTTTTTGTATGAATATTGTAATTTTGTATGAATATTGT
Found at i:47843088 original size:21 final size:20
Alignment explanation
Indices: 47843006--47843114 Score: 130
Period size: 21 Copynumber: 5.0 Consensus size: 20
47842996 TGGATTAGTA
47843006 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAA-T
47843027 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAA-T
47843048 TTGTATGAATATTGTAATATTGTAATT
1 TT-T-TG--TA-TG-AATATTGTAA-T
47843075 TTTTGTATGAATATTGTAA-
1 TTTTGTATGAATATTGTAAT
47843094 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
47843114 T
1 T
47843115 CTTTTATAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 15
0.84 0.00 0.16
Matches are distributed among these distances:
19 19 0.23
20 1 0.01
21 33 0.41
22 3 0.04
23 4 0.05
25 4 0.05
26 3 0.04
27 14 0.17
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (20 bp):
TTTTGTATGAATATTGTAAT
Found at i:47843135 original size:149 final size:143
Alignment explanation
Indices: 47842862--47843218 Score: 479
Period size: 149 Copynumber: 2.4 Consensus size: 143
47842852 CCAATGGGTA
* * *
47842862 ATTTTGAATGAATATTGTAATTTTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATT
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTATTGTATAATTAATTTAATATT
47842927 TATAGTTTTTGATTAGTATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATA
66 TATAGTTTTTGATTAGTATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATA
47842992 GTTTTGGATTAGT
131 GTTTTGGATTAGT
47843005 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATT-TTGTATGAA-T-ATTGTAATA
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTATTGTAT-AATTAATT-TAATA
* *
47843067 TTGTA-ATTTTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTCTTTTATAATTAATTT
64 TT-TATAGTTTTTG-AT---TA--GT-ATTTTGTATGAATATTGTAATTATTTTATAATTAATTT
*
47843131 TGTATTTATAGTTTTTGATTAGT
121 TGTATTTATAGTTTTGGATTAGT
*
47843154 ATTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTT
1 ATTTTGTATGAATATTGT-A-A-T-T--TTTTGTATGAATATTGTAATTATTGTATAATTAATTT
47843219 GTTAGTAATT
Statistics
Matches: 188, Mismatches: 7, Indels: 25
0.85 0.03 0.11
Matches are distributed among these distances:
141 3 0.02
142 19 0.10
143 48 0.26
146 2 0.01
148 2 0.01
149 77 0.41
150 1 0.01
151 1 0.01
152 1 0.01
153 1 0.01
155 23 0.12
156 7 0.04
157 3 0.02
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (143 bp):
ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTATTGTATAATTAATTTAATATT
TATAGTTTTTGATTAGTATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATA
GTTTTGGATTAGT
Found at i:47843260 original size:60 final size:60
Alignment explanation
Indices: 47843195--47843316 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
47843185 TGTATGAATA
* * * * *
47843195 TTGTAATTATTTTATAA-TTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
47843255 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
47843315 TT
1 TT
47843317 AGTTTAGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 6 0.11
60 50 0.89
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:47843470 original size:15 final size:16
Alignment explanation
Indices: 47843434--47843470 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
47843424 CTCATTTAAT
47843434 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
47843450 TTTTATATAATGTAA-
1 TTTTATATAATGTAAC
47843465 TTTTAT
1 TTTTAT
47843471 TTGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:47843586 original size:27 final size:27
Alignment explanation
Indices: 47843535--47843619 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
47843525 ATAAAATAAG
*
47843535 ACTATTGGCGCCTCTCA-ACATGGCACC
1 ACTATTGGCGCCTCTCAGATA-GGCACC
* *
47843562 ACTAATGGCGCCTCTCAGATAGGCATC
1 ACTATTGGCGCCTCTCAGATAGGCACC
* ** * *
47843589 ACCATTAACGCCTCTAAGATAGGCGCC
1 ACTATTGGCGCCTCTCAGATAGGCACC
47843616 ACTA
1 ACTA
47843620 CTATGTATTA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
27 44 0.96
28 2 0.04
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (27 bp):
ACTATTGGCGCCTCTCAGATAGGCACC
Found at i:47844194 original size:26 final size:26
Alignment explanation
Indices: 47844143--47844194 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
47844133 ATCCGCAATC
47844143 CACTACGAAAAACCTCATTTGATGATA
1 CACTACGAAAAACCTCATTT-ATGATA
47844170 CACTAC-AAAACACTCTCATTT-TGAT
1 CACTACGAAAA-AC-CTCATTTATGAT
47844195 GGTACTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
26 8 0.35
27 8 0.35
28 7 0.30
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.29
Consensus pattern (26 bp):
CACTACGAAAAACCTCATTTATGATA
Found at i:47845035 original size:34 final size:34
Alignment explanation
Indices: 47844997--47845064 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
47844987 TATATAGTTG
** *
47844997 CATGATTTATGATTCGTCTGACTTGGTTTTTATT
1 CATGATTTACCATTCATCTGACTTGGTTTTTATT
* *
47845031 CATGATTTACCATTTATTTGACTTGGTTTTTATT
1 CATGATTTACCATTCATCTGACTTGGTTTTTATT
47845065 TTATTCGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.19, C:0.12, G:0.15, T:0.54
Consensus pattern (34 bp):
CATGATTTACCATTCATCTGACTTGGTTTTTATT
Found at i:47848976 original size:330 final size:330
Alignment explanation
Indices: 47848365--47849629 Score: 1791
Period size: 330 Copynumber: 3.8 Consensus size: 330
47848355 CAAATATATA
* * *
47848365 TTTATGCAACTAATAGTTTCATGGGGAGTTTCCAAGTGCAATTTATAAGAATCAACAAGATTCT-
1 TTTATGCAACTAATAGTTTCATGGGGAGCTTCCAAGTGCAACTTATACGAATCAACAAGATTCTG
* * * *
47848429 A-TGCAAGCGACTGTAAATTCTCTACCTGTGACTTATATTGATGAACAACAATCTTTATCTGAGA
66 AGTG--TGCGACTGCAAATTCTGTACCTGTGACTTATATTGATGAACAACAATCTTTACCTGAGA
*
47848493 CTTATACGACTCAAATGATAATTG-AAAACCCTATTGTTATTATATATGCTTACAGTCGATTAAT
129 CTTATACGACTCAAATGGTAATTGAAAAACCCTATTGTTATTATATATGCTTACAGTCGATTAAT
*
47848557 TATTATTATTATTAGAATAGTACTTTGTTTCAAATTGCTTTATCTTGAATTAGTTTTTTTAGGCT
194 TATTATTATTATTAGAATAGTACTTTGTTTCAAATTGCTTTATCTTGAATTAATTTTTTTAGGCT
* *
47848622 TGACCTTAACTAAATTATTTATTTATTACTTAATTCTTTCTTTTTAAATTAAAAAATTAATTATC
259 TGACCTTAAATAAATTATTTATTTATTACTTAATTCTTTCTTTTTAAATTAAGAAATTAATTATC
47848687 CATTGTT
324 CATTGTT
* *
47848694 TTTATGCAACTAATAGTTTCATGGGGAGCTTCCAAGTACAACTTATACGAATCAACAAGATTTTG
1 TTTATGCAACTAATAGTTTCATGGGGAGCTTCCAAGTGCAACTTATACGAATCAACAAGATTCTG
* *
47848759 AGTGTGCGACTGCAAATTCTGTACCTGTGATTTATTTTGATGAACAACAATCTTTACCTGAGACT
66 AGTGTGCGACTGCAAATTCTGTACCTGTGACTTATATTGATGAACAACAATCTTTACCTGAGACT
* *
47848824 TATACGACTCAAATGGTAATTGAAAAACCCTATTGTTATTATATATGTTTACAGTCAATTAATTA
131 TATACGACTCAAATGGTAATTGAAAAACCCTATTGTTATTATATATGCTTACAGTCGATTAATTA
47848889 TTATTATTATTAGAATAGTACTTTGTTTCAAATTGCTTTATCTTGAATTAATTTTTTTAGGCTTG
196 TTATTATTATTAGAATAGTACTTTGTTTCAAATTGCTTTATCTTGAATTAATTTTTTTAGGCTTG
*
47848954 ACCTTAAATAAATTATTTATTTATTACTTAATTATTTCTTTTTAAATTAAGAAATTAATTATCC-
261 ACCTTAAATAAATTATTTATTTATTACTTAATTCTTTCTTTTTAAATTAAGAAATTAATTATCCA
47849018 TATGTT
326 T-TGTT
47849024 TTTATGCAACTAATAGTTTCATGGGGAGCTTCCAAGTGCAACTTATACGAATCAACAAGATTCTG
1 TTTATGCAACTAATAGTTTCATGGGGAGCTTCCAAGTGCAACTTATACGAATCAACAAGATTCTG
* * * *
47849089 AGTGTGTGACTGCAAATTCTGTACTTGTGATTTATTTTGATGAACAACAATCTTTACCTGAGACT
66 AGTGTGCGACTGCAAATTCTGTACCTGTGACTTATATTGATGAACAACAATCTTTACCTGAGACT
* *
47849154 CATACGACTCAAATGGTAATTGAAAAACCCTGTTGTTATTATATATGCTTACAGTCGATTAATTA
131 TATACGACTCAAATGGTAATTGAAAAACCCTATTGTTATTATATATGCTTACAGTCGATTAATTA
47849219 TTATTATTATTAGAATAGTACTTTGTTTCAAATTGCTTTATCTTGAATTAATTTTTTTAGGCTTG
196 TTATTATTATTAGAATAGTACTTTGTTTCAAATTGCTTTATCTTGAATTAATTTTTTTAGGCTTG
* * *
47849284 ACTTTAAATAAATTATTTACTTATTACTTAATTCTTTCTTTTTAAATTAAGAAATTCATTAT--A
261 ACCTTAAATAAATTATTTATTTATTACTTAATTCTTTCTTTTTAAATTAAGAAATTAATTATCCA
*
47849347 TTAAGCT
326 TT--GTT
* * * * * * * *
47849354 TTTATGCAACTAATGGTTTCAGGGGGAGCTTACAAGTGCGACTTATATGAATCGATAATG-TTAT
1 TTTATGCAACTAATAGTTTCATGGGGAGCTTCCAAGTGCAACTTATACGAATCAACAA-GATTCT
* * * ** * * * *
47849418 ACGAGTGT--GATTTCACAGCCT-AAGCCTGTGACTTATATTGGTAAACAACAATTTTTACCTGA
65 --GAGTGTGCGACTGCAAATTCTGTA-CCTGTGACTTATATTGATGAACAACAATCTTTACCTGA
* * ** * * * *
47849480 GGCTTATACGACTCCAATGGTAATTGAAAAGTCCTGTTGTTATTATATAAGATTAGAGTCGATTA
127 GACTTATACGACTCAAATGGTAATTGAAAAACCCTATTGTTATTATATATGCTTACAGTCGATTA
* * * * * * * *
47849545 A--A-TATGATTATTAGAATAGTAATTCGATTCAAATTACTTTATTTTGAATTAAATTTTTTAAG
192 ATTATTATTATTATTAGAATAGTACTTTGTTTCAAATTGCTTTATCTTGAATTAATTTTTTTAGG
* *
47849607 TTTGACTTTAAATAAATTATTTA
257 CTTGACCTTAAATAAATTATTTA
47849630 AGTCTTTCTT
Statistics
Matches: 857, Mismatches: 68, Indels: 24
0.90 0.07 0.03
Matches are distributed among these distances:
327 74 0.09
328 2 0.00
329 138 0.16
330 634 0.74
331 3 0.00
332 6 0.01
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (330 bp):
TTTATGCAACTAATAGTTTCATGGGGAGCTTCCAAGTGCAACTTATACGAATCAACAAGATTCTG
AGTGTGCGACTGCAAATTCTGTACCTGTGACTTATATTGATGAACAACAATCTTTACCTGAGACT
TATACGACTCAAATGGTAATTGAAAAACCCTATTGTTATTATATATGCTTACAGTCGATTAATTA
TTATTATTATTAGAATAGTACTTTGTTTCAAATTGCTTTATCTTGAATTAATTTTTTTAGGCTTG
ACCTTAAATAAATTATTTATTTATTACTTAATTCTTTCTTTTTAAATTAAGAAATTAATTATCCA
TTGTT
Found at i:47849003 original size:19 final size:20
Alignment explanation
Indices: 47848957--47849003 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
47848947 AGGCTTGACC
*
47848957 TTAAATAAATTATTTATTTA
1 TTAAATTAATTATTTATTTA
* *
47848977 TT-ACTTAATTATTTCTTT-
1 TTAAATTAATTATTTATTTA
47848995 TTAAATTAA
1 TTAAATTAA
47849004 GAAATTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.09
19 18 0.82
20 2 0.09
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAAATTAATTATTTATTTA
Found at i:47849845 original size:3 final size:3
Alignment explanation
Indices: 47849830--47849860 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
47849820 CAGTTGATTA
*
47849830 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
47849861 GAATAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:47850961 original size:17 final size:16
Alignment explanation
Indices: 47850939--47850973 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
47850929 TACAACATCC
*
47850939 AAACAAGTAAAATATAA
1 AAACAAATAAAAT-TAA
47850956 AAACAAATAAAATTAA
1 AAACAAATAAAATTAA
47850972 AA
1 AA
47850974 CCTTCACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (16 bp):
AAACAAATAAAATTAA
Found at i:47851141 original size:2 final size:2
Alignment explanation
Indices: 47851134--47851180 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
47851124 ATTCACGTGA
47851134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47851176 AT AT A
1 AT AT A
47851181 CTTTGAAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47851474 original size:3 final size:3
Alignment explanation
Indices: 47851456--47851531 Score: 107
Period size: 3 Copynumber: 25.3 Consensus size: 3
47851446 AATGATAGTC
* * * **
47851456 ATA ATA GTA TTA ATA ATA ATA CTA AGG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47851504 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
47851532 CACTAAAATA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:47853144 original size:50 final size:50
Alignment explanation
Indices: 47853027--47853683 Score: 389
Period size: 50 Copynumber: 13.1 Consensus size: 50
47853017 GAGAAGTAAG
* * *
47853027 ATTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAAT-TTGCTCTG-
1 ATTGCAATGTCGAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTT--T-TGA
* * *
47853078 -CTGC-ATCGCCTG-GGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTGA
1 ATTGCAAT-GTC-GAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* * * * * ** **
47853127 ATTGCAATGTCGAGGAAGTGAGATTCGCTGCTGTAGCTTCAATCTGCTCC
1 ATTGCAATGTCGAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
** *
47853177 GCTGC-ATCGCTTG-GGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
1 ATTGCAAT-G-TCGAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* * * ** **
47853227 ATTGCAATGTCGAGGAAGTGAGATTCACTGTTGTAGCTTCAATCTGCTCC
1 ATTGCAATGTCGAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
** * *
47853277 GCTGC-ATCGCCTG-GGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTGA
1 ATTGCAAT-GTC-GAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* * * * * ** **
47853327 ATTGCAATGTCGAGGAAGTGAGATTCGCTGCTGTAGCTTCAATCTGCTCC
1 ATTGCAATGTCGAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
** **
47853377 GCTGC-ATCACCTG-GGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
1 ATTGCAAT-GTC-GAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* * * *
47853427 ATTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGCTTCG-
1 ATTGCAATGTCGAGGAAGTAAGATTCACCGTTGTGGCTTCAATCT--TTTGA
* * * * * * *
47853478 -CTGC-ATCGCCTG-GAAAGTAAGACTCACTGTTGTGGCCTCAATCTTTTAA
1 ATTGCAAT-GTC-GAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* * * * * ** **
47853527 ATTGCAATGTCGATGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCC
1 ATTGCAATGTCGAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
** *
47853577 GCTGC-A--TCGCATGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAA
1 ATTGCAATGTCG-A--GGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* * * *
47853627 ATTACAATGTCGAGGAAGTGAGATTCGCCGTTGTGGCCTCAATCTTTT-A
1 ATTGCAATGTCGAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
47853676 ATTTGCAA
1 A-TTGCAA
47853684 ACTATGGTTA
Statistics
Matches: 445, Mismatches: 127, Indels: 69
0.69 0.20 0.11
Matches are distributed among these distances:
47 3 0.01
48 5 0.01
49 20 0.04
50 391 0.88
51 19 0.04
52 4 0.01
53 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (50 bp):
ATTGCAATGTCGAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
Found at i:47853200 original size:100 final size:100
Alignment explanation
Indices: 47853027--47853671 Score: 1074
Period size: 100 Copynumber: 6.5 Consensus size: 100
47853017 GAGAAGTAAG
* * *
47853027 ATTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATTTGCTCTGCTGCATCGCCTGGG
1 ATTGCAATGTCGAGGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGG
*
47853092 AAGTAAGATTCACCGTTGTGGCTTTAATCTTTTGA
66 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* *
47853127 ATTGCAATGTCGAGGAAGTGAGATTCGCTGCTGTAGCTTCAATCTGCTCCGCTGCATCGCTTGGG
1 ATTGCAATGTCGAGGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGG
47853192 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
66 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
*
47853227 ATTGCAATGTCGAGGAAGTGAGATTCACTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGG
1 ATTGCAATGTCGAGGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGG
*
47853292 AAGTAAGATTCACCGTTGTGGCTTTAATCTTTTGA
66 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* *
47853327 ATTGCAATGTCGAGGAAGTGAGATTCGCTGCTGTAGCTTCAATCTGCTCCGCTGCATCACCTGGG
1 ATTGCAATGTCGAGGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGG
47853392 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
66 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* * *
47853427 ATTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTGCTTCGCTGCATCGCCTGGA
1 ATTGCAATGTCGAGGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGG
* * * *
47853492 AAGTAAGACTCACTGTTGTGGCCTCAATCTTTTAA
66 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* *
47853527 ATTGCAATGTCGATGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCATGGG
1 ATTGCAATGTCGAGGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGG
*
47853592 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAA
66 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
* * * *
47853627 ATTACAATGTCGAGGAAGTGAGATTCGCCGTTGTGGCCTCAATCT
1 ATTGCAATGTCGAGGAAGTGAGATTCGCTGTTGTAGCTTCAATCT
47853672 TTTAATTTGC
Statistics
Matches: 509, Mismatches: 36, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 509 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (100 bp):
ATTGCAATGTCGAGGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGG
AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTGA
Found at i:47865950 original size:2 final size:2
Alignment explanation
Indices: 47865943--47865981 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
47865933 ATTCACGTGA
47865943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47865982 CTATNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47872031 original size:14 final size:14
Alignment explanation
Indices: 47872014--47872044 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47872004 AGAAAAAGAA
47872014 ATATAAATATACAT
1 ATATAAATATACAT
*
47872028 ATATAAATATATAT
1 ATATAAATATACAT
47872042 ATA
1 ATA
47872045 GAATGAGTAT
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATAAATATACAT
Found at i:47872195 original size:3 final size:3
Alignment explanation
Indices: 47872177--47872246 Score: 95
Period size: 3 Copynumber: 23.3 Consensus size: 3
47872167 AATGATAGTC
* * * **
47872177 ATA ATA GTA TTA ATA ATA ATA CTA AGG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47872225 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
47872247 CACTAAAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:47874184 original size:29 final size:29
Alignment explanation
Indices: 47874143--47874293 Score: 162
Period size: 29 Copynumber: 5.1 Consensus size: 29
47874133 ACATTTTGGG
47874143 CCCCTAAACTTTTCTAAATTACATTTCAA
1 CCCCTAAACTTTTCTAAATTACATTTCAA
*
47874172 CCCCTGAACTTTT-TGAAATTACATTTCAA
1 CCCCTAAACTTTTCT-AAATTACATTTCAA
*
47874201 CCCCTAAAC-TTTCTCAAATTTACATTTCTA
1 CCCCTAAACTTTTCT-AAA-TTACATTTCAA
* * * *
47874231 CCCCTAAACTCTTCTAAATTACGTTTTAG
1 CCCCTAAACTTTTCTAAATTACATTTCAA
* * * *
47874260 CCCCCAAATTTTTCAAAAATTACATTTTAA
1 CCCCTAAACTTTTC-TAAATTACATTTCAA
47874290 CCCC
1 CCCC
47874294 GTATTTTTGC
Statistics
Matches: 102, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.04
29 56 0.55
30 38 0.37
31 4 0.04
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (29 bp):
CCCCTAAACTTTTCTAAATTACATTTCAA
Found at i:47874225 original size:59 final size:58
Alignment explanation
Indices: 47874143--47874293 Score: 169
Period size: 59 Copynumber: 2.6 Consensus size: 58
47874133 ACATTTTGGG
* * *
47874143 CCCCTAAACTTTTCTAAATTACATTTCAACCCCTGAACT-TTTTGAAATTACATTTCAA
1 CCCCTAAACTTTTCAAAATTACATTTCAACCCCTAAACTCTTCT-AAATTACATTTCAA
* * * * *
47874201 CCCCTAAACTTTCTCAAATTTACATTTCTACCCCTAAACTCTTCTAAATTACGTTTTAG
1 CCCCTAAACTTT-TCAAAATTACATTTCAACCCCTAAACTCTTCTAAATTACATTTCAA
* * *
47874260 CCCCCAAATTTTTCAAAAATTACATTTTAACCCC
1 CCCCTAAACTTTTC-AAAATTACATTTCAACCCC
47874294 GTATTTTTGC
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 14 0.18
59 60 0.78
60 3 0.04
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (58 bp):
CCCCTAAACTTTTCAAAATTACATTTCAACCCCTAAACTCTTCTAAATTACATTTCAA
Found at i:47874309 original size:30 final size:29
Alignment explanation
Indices: 47874267--47874323 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
47874257 TAGCCCCCAA
47874267 ATTTTTCAAAAATTACA-TTTTAACCCCGT
1 ATTTTTCAAAAATTACACTTTT-ACCCCGT
*
47874296 ATTTTTGCCAAAATTACACTTTTACCCC
1 ATTTTT-CAAAAATTACACTTTTACCCC
47874324 AGAAACTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 15 0.60
31 4 0.16
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (29 bp):
ATTTTTCAAAAATTACACTTTTACCCCGT
Found at i:47874725 original size:20 final size:21
Alignment explanation
Indices: 47874697--47874740 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
47874687 AGAAAACAGC
47874697 AAGCAAAAGAAAAAAAAAGAA
1 AAGCAAAAGAAAAAAAAAGAA
* *
47874718 AAGC-AAAGAAGAAAAAGGAA
1 AAGCAAAAGAAAAAAAAAGAA
47874738 AAG
1 AAG
47874741 GGAAAAAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (21 bp):
AAGCAAAAGAAAAAAAAAGAA
Found at i:47874880 original size:32 final size:28
Alignment explanation
Indices: 47874839--47874912 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 28
47874829 GAGTGCTGCC
47874839 GAAG-GAGAAAAAAAGAAAGTTAAGAGAAGAA
1 GAAGAGAGAAAAAAAGAAA---AAGAG-AGAA
47874870 GAAGAGAGAAAAAAAAGAAAAAGAGAGAA
1 GAAGAGAG-AAAAAAAGAAAAAGAGAGAA
* *
47874899 TAAGAAAGAAAAAA
1 GAAGAGAGAAAAAA
47874913 TAAAAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 6 0.15
29 10 0.26
30 5 0.13
31 4 0.10
32 3 0.08
33 11 0.28
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (28 bp):
GAAGAGAGAAAAAAAGAAAAAGAGAGAA
Found at i:47874893 original size:19 final size:20
Alignment explanation
Indices: 47874865--47874911 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
47874855 AAGTTAAGAG
*
47874865 AAGAAGAAGAGAGAA-AAAA
1 AAGAAAAAGAGAGAATAAAA
*
47874884 AAGAAAAAGAGAGAATAAGA
1 AAGAAAAAGAGAGAATAAAA
47874904 AAGAAAAA
1 AAGAAAAA
47874912 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (20 bp):
AAGAAAAAGAGAGAATAAAA
Found at i:47874898 original size:29 final size:31
Alignment explanation
Indices: 47874839--47874921 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 31
47874829 GAGTGCTGCC
47874839 GAAG-GAG-AAAAAAAGAAAGTTAAGAGAAGAA
1 GAAGAGAGAAAAAAAAGAAA--TAAGAGAAGAA
47874870 GAAGAGAGAAAAAAAAGAAA-AAGAG-AGAA
1 GAAGAGAGAAAAAAAAGAAATAAGAGAAGAA
* *
47874899 TAAGAAAGAAAAAATAA-AAATAA
1 GAAGAGAGAAAAAA-AAGAAATAA
47874922 AAACAGCAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
29 19 0.41
30 9 0.20
31 4 0.09
32 3 0.07
33 11 0.24
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (31 bp):
GAAGAGAGAAAAAAAAGAAATAAGAGAAGAA
Found at i:47875137 original size:14 final size:14
Alignment explanation
Indices: 47875092--47875128 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
47875082 GTGCAGTAGT
47875092 CCAGCAGCTACAGC
1 CCAGCAGCTACAGC
*
47875106 CCAGCAGCTCCAGC
1 CCAGCAGCTACAGC
47875120 CCAGCAGCT
1 CCAGCAGCT
47875129 TCGGCCCAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.24, C:0.46, G:0.22, T:0.08
Consensus pattern (14 bp):
CCAGCAGCTACAGC
Found at i:47875749 original size:17 final size:17
Alignment explanation
Indices: 47875699--47875762 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
47875689 CGTGTTTCAA
* *
47875699 AAAAAATTCATGTTTTC
1 AAAAATTTCGTGTTTTC
47875716 -AAAATTTCCGTGTTTTC
1 AAAAATTT-CGTGTTTTC
47875733 AAAAATCTTCGTG-TTTC
1 AAAAAT-TTCGTGTTTTC
47875750 AAAAATTCTCGTG
1 AAAAATT-TCGTG
47875763 AATAAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 7 0.17
17 23 0.56
18 9 0.22
19 2 0.05
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:47876342 original size:15 final size:17
Alignment explanation
Indices: 47876321--47876358 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
47876311 GTTTTCAAAA
* *
47876321 AAAAAATTT-GTGTTTT
1 AAAAATTTTCGTGTTTC
47876337 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
47876354 AAAAA
1 AAAAA
47876359 GAAAATTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:47876354 original size:37 final size:39
Alignment explanation
Indices: 47876313--47876397 Score: 120
Period size: 37 Copynumber: 2.2 Consensus size: 39
47876303 AATATTATGT
* *
47876313 TTTCAAAAAAAAAATTTGTGTTT-T-AAAAATTTTCGTG
1 TTTCAAAAAAAAAATTTGTGTTTCTAAAAAAATCTCGTG
*
47876350 TTTCAAAAAGAAAATTTGTGTTTCCTAAAAAAATCTCGTG
1 TTTCAAAAAAAAAATTTGTGTTT-CTAAAAAAATCTCGTG
47876390 TTTCAAAA
1 TTTCAAAA
47876398 TTTTCGTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 22 0.52
39 1 0.02
40 19 0.45
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (39 bp):
TTTCAAAAAAAAAATTTGTGTTTCTAAAAAAATCTCGTG
Found at i:47876372 original size:20 final size:19
Alignment explanation
Indices: 47876300--47876397 Score: 69
Period size: 20 Copynumber: 5.1 Consensus size: 19
47876290 GTATTTTATC
*
47876300 AAAAATATTATGT-TTTCAAA
1 AAAAAAATT-TGTGTTTC-AA
47876320 AAAAAAATTTGTGTTT---
1 AAAAAAATTTGTGTTTCAA
* *
47876336 TAAAAATTTTCGTGTTTCAA
1 AAAAAAATTT-GTGTTTCAA
**
47876356 AAAGAAAATTTGTGTTTCCT
1 AAA-AAAATTTGTGTTTCAA
*
47876376 AAAAAAATCTCGTGTTTCAA
1 AAAAAAAT-TTGTGTTTCAA
47876396 AA
1 AA
47876398 TTTTCGTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
16 8 0.13
17 6 0.10
19 8 0.13
20 33 0.54
21 6 0.10
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (19 bp):
AAAAAAATTTGTGTTTCAA
Found at i:47877267 original size:21 final size:21
Alignment explanation
Indices: 47877243--47877295 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
47877233 AAAGCAAAAG
47877243 AAGCAGCAGCAGCAGTAGTAC
1 AAGCAGCAGCAGCAGTAGTAC
* * *
47877264 AAGCATC-GACATCAGTAGTAG
1 AAGCAGCAG-CAGCAGTAGTAC
*
47877285 TAGCAGCAGCA
1 AAGCAGCAGCA
47877296 AAACCAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.13
Consensus pattern (21 bp):
AAGCAGCAGCAGCAGTAGTAC
Found at i:47895536 original size:23 final size:23
Alignment explanation
Indices: 47895487--47895539 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
47895477 AAACATGCAT
47895487 TTAAAATGTTCAGCTAAAGACACA
1 TTAAAATGTTCAGCT-AAGACACA
* *
47895511 TTAAAATGTTGTAGCT-AGACATA
1 TTAAAATGTT-CAGCTAAGACACA
47895534 TTAAAA
1 TTAAAA
47895540 ACAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 12 0.46
24 10 0.38
25 4 0.15
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAAAATGTTCAGCTAAGACACA
Found at i:47897496 original size:12 final size:12
Alignment explanation
Indices: 47897479--47897503 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47897469 TTTCACTCAT
47897479 CTCTTTTTCAAA
1 CTCTTTTTCAAA
47897491 CTCTTTTTCAAA
1 CTCTTTTTCAAA
47897503 C
1 C
47897504 CCTCTCTTTT
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:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:47900322 original size:2 final size:2
Alignment explanation
Indices: 47900312--47900356 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
47900302 TACTTTTTTT
47900312 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47900355 TA
1 TA
47900357 ACNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Done.