Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009124.1 Hibiscus syriacus cultivar Beakdansim tig00112614_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 858217
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:253093 original size:22 final size:23
Alignment explanation
Indices: 253068--253111 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
253058 GATTATTTTA
253068 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
253090 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
253112 AATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:253125 original size:52 final size:50
Alignment explanation
Indices: 253025--253128 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 50
253015 TATATTAAAA
* ** * *
253025 TAAAAATATATCTTATATTATTATAATATAATTGATTATTTTATATAATAT
1 TAAAAATATATATTATATTATTATAATATAATAAATTA-TATAAATAATAT
253076 TAAAAATATAATATTATATTATTATAAATATTAATAAATTA-ATAAATAATAT
1 TAAAAATAT-ATATTATATTATTAT-AATA-TAATAAATTATATAAATAATAT
253128 T
1 T
253129 TTGATGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
51 9 0.20
52 24 0.53
53 4 0.09
54 8 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (50 bp):
TAAAAATATATATTATATTATTATAATATAATAAATTATATAAATAATAT
Found at i:253356 original size:42 final size:42
Alignment explanation
Indices: 253297--253412 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 42
253287 ATTACATTCA
* * *
253297 GGAAAACCAATTACGTGAAACAAACATTGGAAAATATTTTCC
1 GGAAAACGAATTACGTGAAACAAACATCGGAAAACATTTTCC
253339 GGAAAACGAATTACGTGAAACAAACA-CGAGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAACAAACATCG-GAAAACATTTTCC
* *
253381 GAAAAACGAATTACGTGAAACAAACATGGGAA
1 GGAAAACGAATTACGTGAAACAAACATCGGAA
253413 TTCGAAGAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.01
42 65 0.97
43 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.18
Consensus pattern (42 bp):
GGAAAACGAATTACGTGAAACAAACATCGGAAAACATTTTCC
Found at i:253760 original size:16 final size:13
Alignment explanation
Indices: 253725--253759 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
253715 AATGACCAAT
253725 CCACCACCAGCGG
1 CCACCACCAGCGG
253738 CCACCACCAGCGG
1 CCACCACCAGCGG
253751 CCACCACCA
1 CCACCACCA
253760 CGAGCTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.57, G:0.17, T:0.00
Consensus pattern (13 bp):
CCACCACCAGCGG
Found at i:254335 original size:86 final size:86
Alignment explanation
Indices: 254163--254335 Score: 328
Period size: 86 Copynumber: 2.0 Consensus size: 86
254153 CATGTTATCA
254163 TTAAAAATTATCACGTTAACAGTTATGTTAATTTTTTAACAATGAGTGATCGAAATAAACTAAAA
1 TTAAAAATTATCACGTTAACAGTTATGTTAATTTTTTAACAATGAGTGATCGAAATAAACTAAAA
*
254228 TGTAACTTTAGATATGTTTTT
66 TGTAACGTTAGATATGTTTTT
254249 TTAAAAATTATCACGTTAACAGTTATGTTAATTTTTTAACAATGAGTGATCGAAATAAAACTAAA
1 TTAAAAATTATCACGTTAACAGTTATGTTAATTTTTTAACAATGAGTGATCGAAAT-AAACTAAA
254314 ATGTAACGTTAGATATGTTTTT
65 ATGTAACGTTAGATATGTTTTT
254336 GAAAAAAATC
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 56 0.66
87 29 0.34
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (86 bp):
TTAAAAATTATCACGTTAACAGTTATGTTAATTTTTTAACAATGAGTGATCGAAATAAACTAAAA
TGTAACGTTAGATATGTTTTT
Found at i:257763 original size:31 final size:31
Alignment explanation
Indices: 257694--257767 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
257684 AACTCGGGGT
* * *
257694 GACCACATCTTAATTAAATAAAAATGTAAAT
1 GACCATATCTTAATTAAATAAAAATGAAAAC
257725 GACCATATCTTAATTAAATAAAAAT-AAAAGC
1 GACCATATCTTAATTAAATAAAAATGAAAA-C
*
257756 GATCATATCTTA
1 GACCATATCTTA
257768 TATTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 3 0.08
31 35 0.92
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.30
Consensus pattern (31 bp):
GACCATATCTTAATTAAATAAAAATGAAAAC
Found at i:268193 original size:17 final size:19
Alignment explanation
Indices: 268152--268195 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
268142 TATATTCAAT
* *
268152 TTTAATTTAATCGTGAATT
1 TTTAATTTAATCGTAAATA
268171 TTTAATTTAA-C-TAAATA
1 TTTAATTTAATCGTAAATA
268188 TTTAATTT
1 TTTAATTT
268196 TTATTATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 1 0.04
19 10 0.43
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTAATTTAATCGTAAATA
Found at i:269477 original size:13 final size:14
Alignment explanation
Indices: 269459--269489 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
269449 GTATCATATT
269459 TCACATA-TTCATA
1 TCACATAGTTCATA
269472 TCACATAGTTCATA
1 TCACATAGTTCATA
269486 TCAC
1 TCAC
269490 TTGCATGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (14 bp):
TCACATAGTTCATA
Found at i:270091 original size:64 final size:64
Alignment explanation
Indices: 270004--270166 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 64
269994 TCTTTAACAT
* * *
270004 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCA-TTTTAAGGG
1 GTGCATCGATGCACT-CCTTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGGG
* * * *
270067 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTTGATGTTTCCATTTTTAAGGG
1 G-TGCATCGATGCACTCCTTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGGG
* *
270132 GTGCATCGATGCACTTCTTTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTTATGCATCGATACACA
270167 TTGAACAATT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 3 0.04
64 56 0.66
65 26 0.31
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGGG
Found at i:273051 original size:27 final size:27
Alignment explanation
Indices: 273013--273076 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
273003 GTGCCTTTGG
273013 TCTCGACAACCATGACATGGACAAGTT
1 TCTCGACAACCATGACATGGACAAGTT
273040 TCTCGACAACCATGACATGGACAAGTT
1 TCTCGACAACCATGACATGGACAAGTT
273067 TCTCGACAAC
1 TCTCGACAAC
273077 TTGTGATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (27 bp):
TCTCGACAACCATGACATGGACAAGTT
Found at i:286317 original size:19 final size:19
Alignment explanation
Indices: 286302--286341 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
286292 TTCAATGTAG
286302 AACATACAAATGAATGTGA
1 AACATACAAATGAATGTGA
286321 AACATACAAATGAATGTGA
1 AACATACAAATGAATGTGA
286340 AA
1 AA
286342 TTCAATGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.15, T:0.20
Consensus pattern (19 bp):
AACATACAAATGAATGTGA
Found at i:290230 original size:10 final size:10
Alignment explanation
Indices: 290215--290245 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
290205 TTGATTCTGC
290215 CTCCCTCTCT
1 CTCCCTCTCT
290225 CTCCCTCTCT
1 CTCCCTCTCT
290235 CTCCCTCTCT
1 CTCCCTCTCT
290245 C
1 C
290246 CTTATCTCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (10 bp):
CTCCCTCTCT
Found at i:292167 original size:20 final size:20
Alignment explanation
Indices: 292142--292185 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
292132 CTTCGAAGAG
292142 GCGGTGATGTCATGGCTACA
1 GCGGTGATGTCATGGCTACA
292162 GCGGTGATGTCATGGCTACA
1 GCGGTGATGTCATGGCTACA
292182 GCGG
1 GCGG
292186 GGTGGAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.20, G:0.39, T:0.23
Consensus pattern (20 bp):
GCGGTGATGTCATGGCTACA
Found at i:292501 original size:3 final size:3
Alignment explanation
Indices: 292495--292563 Score: 79
Period size: 3 Copynumber: 23.0 Consensus size: 3
292485 AATAATTATT
* *
292495 TAA TAA TAA T-A TAC TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
292540 TAA -ATT TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA
292564 ATTTAAATGG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
2 3 0.05
3 50 0.89
4 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:292524 original size:27 final size:25
Alignment explanation
Indices: 292484--292563 Score: 126
Period size: 24 Copynumber: 3.1 Consensus size: 25
292474 TTTGGGCTTG
292484 TAATAATTATTTAATAATAATATACTAA
1 TAATAA-TATTTAATAATAATA-A-TAA
292512 TAATAATATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
292537 TAATAA-ATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
292561 TAA
1 TAA
292564 ATTTAAATGG
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
24 21 0.40
25 9 0.17
26 1 0.02
27 15 0.29
28 6 0.12
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATAATATTTAATAATAATAATAA
Found at i:292819 original size:56 final size:57
Alignment explanation
Indices: 292728--292844 Score: 218
Period size: 56 Copynumber: 2.1 Consensus size: 57
292718 CAGATGACCC
*
292728 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACT
1 GAAGACTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACT
292784 GAAGACTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACT
1 GAAGACTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACT
292841 GAAG
1 GAAG
292845 GGCTTACAGA
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 34 0.58
57 25 0.42
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (57 bp):
GAAGACTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACT
Found at i:293341 original size:307 final size:307
Alignment explanation
Indices: 292784--293623 Score: 1578
Period size: 307 Copynumber: 2.7 Consensus size: 307
292774 ATCATGCACT
* *
292784 GAAGACTTTGAAAACATCAAAAAGCTCCCGAAGGC--TTTTTTGGAAACATCATGCACTGAAGGG
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAACATCATGCACTGAAGGA
*
292847 CTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCAT
66 CTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
292912 GCACTGAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
131 GCACTGAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
292976 TGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCC
195 TGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCC
293041 CGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
260 CGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
293089 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAACATCATGCACTGAAGGA
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAACATCATGCACTGAAGGA
293154 CTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
66 CTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
293219 GCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT
131 GCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT
293284 GGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCC
196 GGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCC
**
293349 GAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAGGC
261 GAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
293396 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAACATCATGCACTGAAGGA
1 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAACATCATGCACTGAAGGA
* *
293461 CTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAATCATCAT
66 CTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
293526 GCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTT
131 GCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT
293591 GGAAACATCATGCACTGAAGGACTTACAGATGA
196 GGAAACATCATGCACTGAAGGACTTACAGATGA
293624 GGGAAATAGT
Statistics
Matches: 524, Mismatches: 8, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
305 34 0.06
307 489 0.93
308 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (307 bp):
GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAACATCATGCACTGAAGGA
CTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
GCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT
GGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCC
GAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC
Found at i:293625 original size:231 final size:228
Alignment explanation
Indices: 292789--293623 Score: 1512
Period size: 231 Copynumber: 3.6 Consensus size: 228
292779 GCACTGAAGA
*
292789 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAG
*
292854 ATGACCCTGAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
65 ATGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
292919 AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
130 AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
292984 TCATGCACTGAAGGACTTACAGATGACCCTGAGG
195 TCATGCACTGAAGGACTTACAGATGACCCTGAGG
293018 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
293083 TGACCC-GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAACATCATGCAC
66 TGACCCTG-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC---TTTTTGGAAACATCATGCAC
293147 TGAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGA
127 TGAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGA
293211 AACATCATGCACTGAAGGACTTACAGATGACCCTGAGG
191 AACATCATGCACTGAAGGACTTACAGATGACCCTGAGG
293249 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
293314 TGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
66 TGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
**
293379 GGACTTACAGATGAGGCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAA
131 GGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC---TTTTTGGAAA
293444 CATCATGCACTGAAGGACTTACAGATGACCCTGAGG
193 CATCATGCACTGAAGGACTTACAGATGACCCTGAGG
* *
293480 CTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAATCATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
*
293545 TGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGAA
66 TGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
293610 GGACTTACAGATGA
131 GGACTTACAGATGA
293624 GGGAAATAGT
Statistics
Matches: 589, Mismatches: 7, Indels: 18
0.96 0.01 0.03
Matches are distributed among these distances:
227 2 0.00
228 144 0.24
229 30 0.05
231 411 0.70
232 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (228 bp):
CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
TGACCCTGAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
GGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAT
CATGCACTGAAGGACTTACAGATGACCCTGAGG
Found at i:293649 original size:76 final size:76
Alignment explanation
Indices: 292789--293623 Score: 1496
Period size: 76 Copynumber: 10.9 Consensus size: 76
292779 GCACTGAAGA
*
292789 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGAAGGACTTACAG
292854 ATGACCCTGAGG
65 ATGACCCTGAGG
*
292866 CTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
292931 TGACCC-GAAGG
66 TGACCCTG-AGG
292942 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
293007 TGACCCTGAGG
66 TGACCCTGAGG
293018 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
293083 TGACCC-GAAGG
66 TGACCCTG-AGG
293094 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAACATCATGCACTGAAGGACTTAC
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGC---TTTTTGGAAACATCATGCACTGAAGGACTTAC
293159 AGATGACCCTGAGG
63 AGATGACCCTGAGG
293173 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
293238 TGACCCTGAGG
66 TGACCCTGAGG
293249 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
293314 TGACCCTGAGG
66 TGACCCTGAGG
293325 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
**
293390 TGAGGC-GAAGG
66 TGACCCTG-AGG
293401 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTTTGGAAACATCATGCACTGAAGGACTTAC
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGC---TTTTTGGAAACATCATGCACTGAAGGACTTAC
293466 AGATGACCCTGAGG
63 AGATGACCCTGAGG
* *
293480 CTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAATCATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
293545 TGACCCTGAGG
66 TGACCCTGAGG
*
293556 CTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
293621 TGA
66 TGA
293624 GGGAAATAGT
Statistics
Matches: 734, Mismatches: 12, Indels: 25
0.95 0.02 0.03
Matches are distributed among these distances:
75 3 0.00
76 554 0.75
77 30 0.04
79 145 0.20
80 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (76 bp):
CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
TGACCCTGAGG
Found at i:294742 original size:54 final size:54
Alignment explanation
Indices: 294660--294771 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
294650 CGAATAGCAG
***
294660 GTTCGTAAAACATTTAACAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* **
294714 GTTCGTAAAACATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
294768 GTTC
1 GTTC
294772 TCAATCATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:295770 original size:74 final size:76
Alignment explanation
Indices: 295638--295807 Score: 220
Period size: 74 Copynumber: 2.3 Consensus size: 76
295628 ATTGTGGGCC
* * *
295638 TTCAACATGCCCCAACA-TTGGCTAATACAAGTGTTCAAAATGCATCAACAGTTCTGATTCTGAT
1 TTCAGCATGCCCCAACATTTGGCTAATACAAGTATTCAAAATACATCAACAGTTCTGATTCTGAT
*
295702 TGAAATGGGTT
66 TGAAAAGGGTT
* * ** * *
295713 TTCAGCATGCCCCAACATTTTGCTAATA-AA-TATTCAGAATATTTCAACATTTCTGATTCTGTT
1 TTCAGCATGCCCCAACATTTGGCTAATACAAGTATTCAAAATACATCAACAGTTCTGATTCTGAT
295776 TGAAAAGGGTT
66 TGAAAAGGGTT
*
295787 TTCAGCATGCCCCAATATTTG
1 TTCAGCATGCCCCAACATTTG
295808 CTTCTTGTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
74 55 0.67
75 18 0.22
76 9 0.11
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (76 bp):
TTCAGCATGCCCCAACATTTGGCTAATACAAGTATTCAAAATACATCAACAGTTCTGATTCTGAT
TGAAAAGGGTT
Found at i:297109 original size:114 final size:114
Alignment explanation
Indices: 296909--297225 Score: 528
Period size: 114 Copynumber: 2.8 Consensus size: 114
296899 GATCATGCAG
* * * * *
296909 TTCATCTTTCAATTCCAATGATCGGTTCTGGAGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
* * * *
296974 ACACTTCCAGAAGATGATATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
297023 TTCATCTTTCAAATCCAATGATTGGTTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
297088 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
* *
297137 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAATTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
297202 ACACTTCCAGAAGATGCTA-TGAGC
66 ACACTTCCAGAAGATGCTATTGAGC
297226 ACATTTATCT
Statistics
Matches: 192, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
113 5 0.03
114 187 0.97
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
Found at i:297292 original size:93 final size:93
Alignment explanation
Indices: 297128--297405 Score: 431
Period size: 93 Copynumber: 3.0 Consensus size: 93
297118 TATTTCTACC
* * * *
297128 ATGAGCAAATTCATCTTTC-AAATCCAATGATTGATT-T-TGGAGTTCATACCAAATCAGATCAG
1 ATGAGCACATTCATC-TTCAAAATTCAATGATTGATTATGTGG-TTTCATACCAAACCAGATCAG
*
297190 ATAATTCAAAGAACACTTCCAGAAGATGCT
64 ATAACTCAAAGAACACTTCCAGAAGATGCT
*
297220 ATGAGCACATTTATCTTCAAAATTCAATGATTGATTATGTGGTTTCATACCAAACCAGATCAGAT
1 ATGAGCACATTCATCTTCAAAATTCAATGATTGATTATGTGGTTTCATACCAAACCAGATCAGAT
297285 AACTCAAAGAACACTTCCAGAAGATGCT
66 AACTCAAAGAACACTTCCAGAAGATGCT
297313 ATGAGCACATTCATCTTCAAAATTCAATGATTGATTATGTGGTTTCATACCAAACCAGATCAG--
1 ATGAGCACATTCATCTTCAAAATTCAATGATTGATTATGTGGTTTCATACCAAACCAGATCAGAT
* *
297376 AACTCAAAGAACTCTTCCAGAAGATACT
66 AACTCAAAGAACACTTCCAGAAGATGCT
297404 AT
1 AT
297406 TGGGTCTTCT
Statistics
Matches: 174, Mismatches: 9, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
91 31 0.18
92 29 0.17
93 111 0.64
94 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (93 bp):
ATGAGCACATTCATCTTCAAAATTCAATGATTGATTATGTGGTTTCATACCAAACCAGATCAGAT
AACTCAAAGAACACTTCCAGAAGATGCT
Found at i:299491 original size:6 final size:6
Alignment explanation
Indices: 299480--299529 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
299470 TTGATTTAAT
* * *
299480 TTTTTC TTTTTC TTTTT- TTTTTA ATTTTG TTTTTC -TTTTC TTCTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC
299527 TTT
1 TTT
299530 GCTGGATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 10 0.27
6 21 0.57
7 6 0.16
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:299830 original size:2 final size:2
Alignment explanation
Indices: 299823--299850 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
299813 ATAACAAATG
299823 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
299851 TAAAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:302110 original size:14 final size:14
Alignment explanation
Indices: 302093--302131 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
302083 TAAAAGTATG
302093 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
302107 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
302122 AATG-AAAATG
1 AATGCAAAATG
302132 CATGTATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:306460 original size:3 final size:3
Alignment explanation
Indices: 306454--306519 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
306444 AATAATTATT
* *
306454 TAA TAA TAA T-A TAC TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
306499 TAA -ATT TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
306520 ATTTAAATGA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 47 0.89
4 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:306483 original size:27 final size:25
Alignment explanation
Indices: 306443--306519 Score: 120
Period size: 24 Copynumber: 3.0 Consensus size: 25
306433 TTTGGGCTTG
306443 TAATAATTATTTAATAATAATATACTAA
1 TAATAA-TATTTAATAATAATA-A-TAA
306471 TAATAATATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
306496 TAATAA-ATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
306520 ATTTAAATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.37
25 9 0.18
26 1 0.02
27 15 0.31
28 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATAATATTTAATAATAATAATAA
Found at i:306854 original size:11 final size:11
Alignment explanation
Indices: 306838--306914 Score: 59
Period size: 11 Copynumber: 6.8 Consensus size: 11
306828 TTTGGGCTTG
* *
306838 TAATAATTATT
1 TAATAATAATA
306849 TAATAATAATA
1 TAATAATAATA
306860 TAATAATAATAA
1 TAATAATAAT-A
* *
306872 TATTTAATAAAAA
1 TA-ATAAT-AATA
306885 TAATAATAATA
1 TAATAATAATA
*
306896 -AAT-TTAATAA
1 TAATAATAAT-A
306906 TAATAATAA
1 TAATAATAA
306915 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
9 4 0.08
10 4 0.08
11 25 0.48
12 10 0.19
13 7 0.13
14 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAATAATAATA
Found at i:306855 original size:3 final size:3
Alignment explanation
Indices: 306849--306914 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
306839 AATAATTATT
* *
306849 TAA TAA TAA T-A TAA TAA TAA TAA TATT TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
306894 TAA -ATT TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
306915 ATTTAAATGA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 47 0.89
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:306869 original size:25 final size:26
Alignment explanation
Indices: 306838--306910 Score: 107
Period size: 25 Copynumber: 2.9 Consensus size: 26
306828 TTTGGGCTTG
306838 TAATAAT-TATTTAATAATAATATAA
1 TAATAATATATTTAATAATAATATAA
306863 TAATAATAATATTTAATAA-AA-ATAA
1 TAATAAT-ATATTTAATAATAATATAA
*
306888 TAATAATAAATTTAATAATAATA
1 TAATAATATATTTAATAATAATA
306911 ATAAATTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
24 10 0.23
25 20 0.47
26 3 0.07
27 10 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TAATAATATATTTAATAATAATATAA
Found at i:306889 original size:395 final size:395
Alignment explanation
Indices: 306154--306940 Score: 1529
Period size: 395 Copynumber: 2.0 Consensus size: 395
306144 GGGTGGAACA
306154 CCTGGAGGTGGCAGCTGAGCTCTTATGGAAACATGAGGCGGCGCTGCGCGGGGCTTCTGGAAACG
1 CCTGGAGGTGGCAGCTGAGCTCTTATGGAAACATGAGGCGGCGCTGCGCGGGGCTTCTGGAAACG
306219 GCGGATGATAACCTAGGGTTAGGAAACCCTAGGGTTTCCTTTGCTGGAACCGTCTGTGGACCGTT
66 GCGGATGATAACCTAGGGTTAGGAAACCCTAGGGTTTCCTTTGCTGGAACCGTCTGTGGACCGTT
306284 GGATCTCTCAGATCCAACGGCTGAGATCATTGGCGGCTGGCTGAGAAGAATAAAACCCTAATTGG
131 GGATCTCTCAGATCCAACGGCTGAGATCATTGGCGGCTGGCTGAGAAGAATAAAACCCTAATTGG
306349 GTTTAGGGTTTCTGTTAGGCCATTTCTGATTGGAATTGTAAACGGGCTTCGGGTTTTGGGCTTGT
196 GTTTAGGGTTTCTGTTAGGCCATTTCTGATTGGAATTGTAAACGGGCTTCGGGTTTTGGGCTTGT
*
306414 AAAATGGGTCTCCGGGTCCTTTGGGCTTGTAATAATTATTTAATAATAATATACTAATAATAATA
261 AAAATGGGTCTCCGGGTCCTTTGGGCTTGTAATAATTATTTAATAATAATATAATAATAATAATA
*
306479 TTTAATAATAATAATAATAATAAATTTAATAATAATAATAAATTTAAATGAAAAAATGATGTCTA
326 TTTAATAAAAATAATAATAATAAATTTAATAATAATAATAAATTTAAATGAAAAAATGATGTCTA
306544 CAGCT
391 CAGCT
*
306549 CCTGGAGGTGGCAGCTGAGCTCTTCTGGAAACATGAGGCGGCGCTGCGCGGGGCTTCTGGAAACG
1 CCTGGAGGTGGCAGCTGAGCTCTTATGGAAACATGAGGCGGCGCTGCGCGGGGCTTCTGGAAACG
*
306614 GCGGATGATAACCTAGGGTTAGGATACCCTAGGGTTTCCTTTGCTGGAACCGTCTGTGGACCGTT
66 GCGGATGATAACCTAGGGTTAGGAAACCCTAGGGTTTCCTTTGCTGGAACCGTCTGTGGACCGTT
*
306679 GGATCTCTCAGATCCAACGGCTGAGATCATTGGCGGCTGGCTGAGAAGAATGAAACCCTAATTGG
131 GGATCTCTCAGATCCAACGGCTGAGATCATTGGCGGCTGGCTGAGAAGAATAAAACCCTAATTGG
306744 GTTTAGGGTTTCTGTTAGGCCATTTCTGATTGGAATTGTAAACGGGCTTCGGGTTTTGGGCTTGT
196 GTTTAGGGTTTCTGTTAGGCCATTTCTGATTGGAATTGTAAACGGGCTTCGGGTTTTGGGCTTGT
306809 AAAATGGGTCTCCGGGTCCTTTGGGCTTGTAATAATTATTTAATAATAATATAATAATAATAATA
261 AAAATGGGTCTCCGGGTCCTTTGGGCTTGTAATAATTATTTAATAATAATATAATAATAATAATA
306874 TTTAATAAAAATAATAATAATAAATTTAATAATAATAATAAATTTAAATGAAAAAATGATGTCTA
326 TTTAATAAAAATAATAATAATAAATTTAATAATAATAATAAATTTAAATGAAAAAATGATGTCTA
306939 CA
391 CA
306941 CATGGCTTTC
Statistics
Matches: 387, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
395 387 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (395 bp):
CCTGGAGGTGGCAGCTGAGCTCTTATGGAAACATGAGGCGGCGCTGCGCGGGGCTTCTGGAAACG
GCGGATGATAACCTAGGGTTAGGAAACCCTAGGGTTTCCTTTGCTGGAACCGTCTGTGGACCGTT
GGATCTCTCAGATCCAACGGCTGAGATCATTGGCGGCTGGCTGAGAAGAATAAAACCCTAATTGG
GTTTAGGGTTTCTGTTAGGCCATTTCTGATTGGAATTGTAAACGGGCTTCGGGTTTTGGGCTTGT
AAAATGGGTCTCCGGGTCCTTTGGGCTTGTAATAATTATTTAATAATAATATAATAATAATAATA
TTTAATAAAAATAATAATAATAAATTTAATAATAATAATAAATTTAAATGAAAAAATGATGTCTA
CAGCT
Found at i:309420 original size:39 final size:39
Alignment explanation
Indices: 309377--309481 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
309367 TATAATTCTC
*
309377 AAATTATCTCACTCTAACATTCTAAATTCCTAATTTCAT
1 AAATTATCTCACTCTAACATTCTAAATTACTAATTTCAT
* * *
309416 AAATTTTGC-CA-TCATAACATTCTAAATTATTAATTTCTT
1 AAATTAT-CTCACTC-TAACATTCTAAATTACTAATTTCAT
* *
309455 ACATTATTTCACAT-TAACATTCTAAAT
1 AAATTATCTCAC-TCTAACATTCTAAAT
309482 CATTTTTTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
38 2 0.04
39 50 0.93
40 1 0.02
41 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.43
Consensus pattern (39 bp):
AAATTATCTCACTCTAACATTCTAAATTACTAATTTCAT
Found at i:309566 original size:19 final size:20
Alignment explanation
Indices: 309531--309575 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
309521 AATTTAATTA
*
309531 TAATTTTTGTTTTAATT-TT
1 TAATTTTTGTTTCAATTATT
309550 TAATATTTT-TTTCAATTATT
1 TAAT-TTTTGTTTCAATTATT
309570 TAATTT
1 TAATTT
309576 GATTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TAATTTTTGTTTCAATTATT
Found at i:310090 original size:21 final size:21
Alignment explanation
Indices: 310066--310117 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
310056 TTAGGGAGAT
*
310066 ATAATTTACATAATATAGTTA
1 ATAATTTACATAATATAATTA
* * *
310087 ATAATTAATATGATATAATTA
1 ATAATTTACATAATATAATTA
310108 AT-ATTT-CATA
1 ATAATTTACATA
310118 TTATTAAGTT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 19 0.79
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (21 bp):
ATAATTTACATAATATAATTA
Found at i:310129 original size:21 final size:22
Alignment explanation
Indices: 310078--310130 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
310068 AATTTACATA
310078 ATAT-AGTTAATAATTAATATG
1 ATATAAGTTAATAATTAATATG
* * *
310099 ATATAA-TTAATATTTCATATT
1 ATATAAGTTAATAATTAATATG
310120 AT-TAAGTTAAT
1 ATATAAGTTAAT
310131 TGAGAATATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.11
21 23 0.85
22 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (22 bp):
ATATAAGTTAATAATTAATATG
Found at i:312523 original size:42 final size:43
Alignment explanation
Indices: 312470--312559 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 43
312460 CGAATTGAAT
* *
312470 CGAAACAGACCCGAATTTTAGTCAAACCAAAAGTAACCCGAAC
1 CGAAACAGACCCGAATTTTAGCCAAACCAAAAGCAACCCGAAC
* * *
312513 TGAAAC-GACCCTAATTTTAGCCAAACTAAAAGCAACCCGAAC
1 CGAAACAGACCCGAATTTTAGCCAAACCAAAAGCAACCCGAAC
312555 CGAAA
1 CGAAA
312560 GTAACTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 36 0.88
43 5 0.12
ACGTcount: A:0.44, C:0.28, G:0.13, T:0.14
Consensus pattern (43 bp):
CGAAACAGACCCGAATTTTAGCCAAACCAAAAGCAACCCGAAC
Found at i:313090 original size:60 final size:59
Alignment explanation
Indices: 313018--313200 Score: 231
Period size: 60 Copynumber: 3.1 Consensus size: 59
313008 TTTGGATGAA
* * * * *
313018 TTTGGGGATGAAATTAAAATATCTAAAAGTTTAGGGACCAATTTAGAATGAAATTCATAG
1 TTTGGGGATGAAATTAGAATAT-TAAAAGTTTAAGGACTAATTTAAAATGAAAGTCATAG
* * * * *
313078 TTTGGGGATGAAATTTGAATGTTAAAAAGTTTAAGGACTAATTTATAATGAGAGTCATAT
1 TTTGGGGATGAAATTAGAATATT-AAAAGTTTAAGGACTAATTTAAAATGAAAGTCATAG
**
313138 TTTAAGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAAAATGAAAGTCATAG
1 TTTGGGGATGAAATTAGAATA-TTAAAAGTTTAAGGACTAATTTAAAATGAAAGTCATAG
313198 TTT
1 TTT
313201 AGGAACATAT
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.01
60 102 0.97
61 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (59 bp):
TTTGGGGATGAAATTAGAATATTAAAAGTTTAAGGACTAATTTAAAATGAAAGTCATAG
Found at i:313286 original size:12 final size:11
Alignment explanation
Indices: 313262--313300 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
313252 GATATAATAA
313262 TATAATATCATT
1 TATAATAT-ATT
313274 TATAAATATATT
1 TAT-AATATATT
313286 TATAATAATATT
1 TATAAT-ATATT
313298 TAT
1 TAT
313301 TTAAACATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.12
12 17 0.68
13 5 0.20
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATATATT
Found at i:313739 original size:32 final size:30
Alignment explanation
Indices: 313703--313807 Score: 97
Period size: 32 Copynumber: 3.4 Consensus size: 30
313693 TTGACCGGAT
313703 TTTGATCCGACCAAAAAAATCAATCGATTTGA
1 TTTGATCCGACC--AAAAATCAATCGATTTGA
* * *
313735 TTTGATTCGACC-TAAATCAA-CAGATCTGA
1 TTTGATCCGACCAAAAATCAATC-GATTTGA
* * *
313764 TATTGACCCAACCTAAAAATCAATCGATTCGA
1 T-TTGATCCGACC-AAAAATCAATCGATTTGA
313796 TTTGATCCGACC
1 TTTGATCCGACC
313808 TGAATCAACA
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
28 1 0.02
29 14 0.25
30 8 0.14
31 9 0.16
32 24 0.42
33 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (30 bp):
TTTGATCCGACCAAAAATCAATCGATTTGA
Found at i:313764 original size:29 final size:29
Alignment explanation
Indices: 313719--313815 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 29
313709 CCGACCAAAA
* *
313719 AAATCAATCGATTTGATTTGATTCGACCT
1 AAATCAATCGATCTGATTTGATCCGACCT
* *
313748 AAATCAA-CAGATCTGATATTGACCCAACCT
1 AAATCAATC-GATCTGAT-TTGATCCGACCT
313778 AAAAATCAATCGAT-TCGATTTGATCCGACCT
1 --AAATCAATCGATCT-GATTTGATCCGACCT
*
313809 GAATCAA
1 AAATCAA
313816 CAGATCCAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
28 1 0.02
29 20 0.36
30 9 0.16
31 11 0.20
32 13 0.24
33 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (29 bp):
AAATCAATCGATCTGATTTGATCCGACCT
Found at i:313814 original size:61 final size:61
Alignment explanation
Indices: 313717--313833 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
313707 ATCCGACCAA
* * **
313717 AAAAATCAATCGATTTGATTTGATTCGACCTAAATCAACAGATCTGATATTGACCCAACCT
1 AAAAATCAATCGATTCGATTTGATCCGACCTAAATCAACAGATCCAATATTGACCCAACCT
*
313778 AAAAATCAATCGATTCGATTTGATCCGACCTGAATCAACAGATCCAATATTGACCC
1 AAAAATCAATCGATTCGATTTGATCCGACCTAAATCAACAGATCCAATATTGACCC
313834 GACCCAACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (61 bp):
AAAAATCAATCGATTCGATTTGATCCGACCTAAATCAACAGATCCAATATTGACCCAACCT
Found at i:313837 original size:30 final size:30
Alignment explanation
Indices: 313742--313837 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
313732 TGATTTGATT
*
313742 CGACCTAAATCAACAGATCTGATATTGACC
1 CGACCTAAATCAACAGATCCGATATTGACC
* * *
313772 CAACCTAAAAATCAATC-GATTCGAT-TTGATC
1 CGACCT--AAATCAA-CAGATCCGATATTGACC
* *
313803 CGACCTGAATCAACAGATCCAATATTGACC
1 CGACCTAAATCAACAGATCCGATATTGACC
313833 CGACC
1 CGACC
313838 CAACTTACTA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 1 0.02
29 12 0.23
30 15 0.29
31 10 0.19
32 13 0.25
33 1 0.02
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.23
Consensus pattern (30 bp):
CGACCTAAATCAACAGATCCGATATTGACC
Found at i:320637 original size:13 final size:13
Alignment explanation
Indices: 320619--320644 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
320609 TTCTGCAAGC
320619 AACAAGAAAAAAA
1 AACAAGAAAAAAA
320632 AACAAGAAAAAAA
1 AACAAGAAAAAAA
320645 TTATTAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
AACAAGAAAAAAA
Found at i:324573 original size:42 final size:43
Alignment explanation
Indices: 324455--324567 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 43
324445 AGTCATATAT
* * * * *
324455 TTTAGTGGTGCTTTTGTAATAAACATC-ACAATAGTAATGTGC
1 TTTAGTGGCGTTTTTGTAATAAATATCTACAATAATAATGTAC
* * * *
324497 TTTAGTGGCATTTTTGTAATAAAT-GCTAGAATAATCATGTAC
1 TTTAGTGGCGTTTTTGTAATAAATATCTACAATAATAATGTAC
324539 TTTAGTGGCGTTTTTGTAATAAATATCTA
1 TTTAGTGGCGTTTTTGTAATAAATATCTA
324568 TATAATTTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.02
42 54 0.93
43 3 0.05
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.42
Consensus pattern (43 bp):
TTTAGTGGCGTTTTTGTAATAAATATCTACAATAATAATGTAC
Found at i:324668 original size:80 final size:81
Alignment explanation
Indices: 324534--324688 Score: 249
Period size: 80 Copynumber: 1.9 Consensus size: 81
324524 AGAATAATCA
* * * **
324534 TGTACTTTAGTGGCGTTTTTGTAATAAATATCTATATAATTTTTTTAACCCAAAACTTTCTTCCT
1 TGTACCTTAGTGGCGTTTTTGTAATAAATATCCATATAATTTTTCTAACCCAAAACTACCTTCCT
324599 TCCAACTTTTGTTGAC
66 TCCAACTTTTGTTGAC
324615 TGTACCTTAGTGGCG-TTTTGTAATAAATATCCATATAATTTTTCTAACCCAAAACTACCTTCCT
1 TGTACCTTAGTGGCGTTTTTGTAATAAATATCCATATAATTTTTCTAACCCAAAACTACCTTCCT
*
324679 TCCAATTTTT
66 TCCAACTTTT
324689 TTAATAAATA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 54 0.79
81 14 0.21
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45
Consensus pattern (81 bp):
TGTACCTTAGTGGCGTTTTTGTAATAAATATCCATATAATTTTTCTAACCCAAAACTACCTTCCT
TCCAACTTTTGTTGAC
Found at i:326882 original size:41 final size:41
Alignment explanation
Indices: 326812--327199 Score: 267
Period size: 41 Copynumber: 9.5 Consensus size: 41
326802 CGCCACAAAA
*
326812 TAGTAACTTTAGCGGCGTTTTGTA-A-AAACGCCGCAACAGAG
1 TAGT-ACTTTAGCGGCGTTTT-TATACAAACGCCGCAATAGAG
*
326853 TAGTACTTTAGTGGCGTTTTTATACAAACGCCGCAATAG-G
1 TAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAG
** * * ** * *
326893 T--TCATCCATAGTGGCGTTTTTTAAACAAACGCCGTGACATAG
1 TAGT-A-CTTTAGCGGCG-TTTTTATACAAACGCCGCAATAGAG
* * *
326935 TAGTACTTTAGCGGCGTTTTAATAAAAACGCCGCAATAGGG
1 TAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAG
* * * * *
326976 TTCA-TA-TATTA-TGGCATTTTCA-ATAAACGCCGCAACAGAG
1 -T-AGTACT-TTAGCGGCGTTTTTATACAAACGCCGCAATAGAG
* *
327016 TAGTACTTTAGCGGCGTTTTTTATACAAACACCGCAAAAGAG
1 TAGTACTTTAGCGGCG-TTTTTATACAAACGCCGCAATAGAG
** * *
327058 TAGTACTTTAGCGGCGTTTTTATACAAAAACTGCTATAGA-
1 TAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAG
* * * * * *
327098 CACATACTTTAGTGGCGTTTTTATTCAAACGCCGCTATA-AA
1 TA-GTACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAG
* * * * *
327139 TGCGTTCTTTAGCGGCATTTTTATACAAACGCCGCTATAGAC
1 T-AGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAG
* *
327181 TCGTACTTTAGTGGCGTTT
1 TAGTACTTTAGCGGCGTTT
327200 GTGTTTACAA
Statistics
Matches: 273, Mismatches: 54, Indels: 40
0.74 0.15 0.11
Matches are distributed among these distances:
38 2 0.01
39 9 0.03
40 48 0.18
41 162 0.59
42 49 0.18
43 2 0.01
44 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (41 bp):
TAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAG
Found at i:331983 original size:84 final size:86
Alignment explanation
Indices: 331878--332158 Score: 249
Period size: 85 Copynumber: 3.3 Consensus size: 86
331868 ATAATTAGCG
* * *
331878 GCGTTTGCATCCAAAAACGCCGCTATAGATATGAAATTTTACGGCATTTATTC-CA-AAAACGCC
1 GCGTTTTC-TCCAAAAACGCCGCTATAGATATGACATTTTGCGGCATTT-TTCACAGAAAACGCC
* *
331941 GCTATAAATCT-GACTTTTTGAA
64 GCTATAAATCTCGACCTATTGAA
* * * *
331963 GCGTTTTCTCCAAAAACGCCGCTATAGATCTGACATTTTGCGGC-GTTTTCATAGAAAACGCCGT
1 GCGTTTTCTCCAAAAACGCCGCTATAGATATGACATTTTGCGGCATTTTTCACAGAAAACGCCGC
* **
332027 TATAGATCTCGACCTATTGCG
66 TATAAATCTCGACCTATTGAA
* * * *
332048 GCGTTTGT-TCCAAAAACGACGCTATAGATTTGACCTTTTGCGGCA-TTTT--C-GGAAACGCCG
1 GCGTTT-TCTCCAAAAACGCCGCTATAGATATGACATTTTGCGGCATTTTTCACAGAAAACGCCG
* * * **
332108 CTATAGAGCTCGACTTATTGCG
65 CTATAAATCTCGACCTATTGAA
*
332130 GCGTTTGT-TCCGAGAAACGCCGCTATAGA
1 GCGTTT-TCTCC-AAAAACGCCGCTATAGA
332159 GCCGACCTGT
Statistics
Matches: 168, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
82 42 0.25
83 18 0.11
84 50 0.30
85 57 0.34
86 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (86 bp):
GCGTTTTCTCCAAAAACGCCGCTATAGATATGACATTTTGCGGCATTTTTCACAGAAAACGCCGC
TATAAATCTCGACCTATTGAA
Found at i:332064 original size:43 final size:41
Alignment explanation
Indices: 331887--332201 Score: 278
Period size: 42 Copynumber: 7.5 Consensus size: 41
331877 GGCGTTTGCA
* ** * *
331887 TCCAAAAACGCCGCTATAGATATGAAATTTTACGGCATTTAT
1 TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTT-T
* * **
331929 TCCAAAAACGCCGCTATAAATCTGACTTTTTGAAGCGTTTT
1 TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTT
*
331970 CTCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCG-TTT
1 -TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTT
* * *
332011 TCATAGAAAACGCCGTTATAGATCTCGACCTATTGCGGCGTTTGT
1 TC-CA-AAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTT-T
* * *
332056 TCCAAAAACGACGCTATAGATTTGACCTTTTGCGGC-ATTT
1 TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTT
** *
332096 T-CGGAAACGCCGCTATAGAGCTCGA-CTTATTGCGGCGTTTGT
1 TCCAAAAACGCCGCTATAGATCT-GACCTT-TTGCGGCGTTT-T
* * * *
332138 TCCGAGAAACGCCGCTATAGAGCCGACCTGTTGCGGCGTTTT
1 TCC-AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTT
**
332180 CTAAAAAAACGCCGCTATAGAT
1 -TCCAAAAACGCCGCTATAGAT
332202 TTAGACCGAT
Statistics
Matches: 224, Mismatches: 35, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
39 19 0.08
40 13 0.06
41 9 0.04
42 114 0.51
43 43 0.19
44 23 0.10
45 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (41 bp):
TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTT
Found at i:332180 original size:168 final size:170
Alignment explanation
Indices: 331875--332217 Score: 401
Period size: 168 Copynumber: 2.0 Consensus size: 170
331865 ACGATAATTA
*
331875 GCGGCGTTTGCATCCAAAAACGCCGCTATAGATATGAAATTTTACGGCATTTATTCCAAAAACGC
1 GCGGCGTTTGCATCCAAAAACGACGCTATAGATATGAAATTTTACGGCATTTATTCCAAAAACGC
* * * * *
331940 CGCTATAAATCTGACTTTTTGAAGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACATTTTGCG
66 CGCTATAAAGCTGACTTATTGAAGCGTTTTCTCCAAAAACGCCGCTATAGAGCCGACATGTTGCG
* * * *
332005 GCGTTTTC-ATAGAAAACGCCGTTATAGATCTCGACCTATT
131 GCGTTTTCTA-AAAAAACGCCGCTATAGATCTAGACCGATT
* * ** * **
332045 GCGGCGTTTG-TTCCAAAAACGACGCTATAGATTTGACCTTTTGCGGCA-TT-TT-CGGAAACGC
1 GCGGCGTTTGCATCCAAAAACGACGCTATAGATATGAAATTTTACGGCATTTATTCCAAAAACGC
* ** * *
332106 CGCTATAGAGCTCGACTTATTGCGGCGTTTGT-TCCGAGAAACGCCGCTATAGAGCCGACCTGTT
66 CGCTATAAAGCT-GACTTATTGAAGCGTTT-TCTCC-AAAAACGCCGCTATAGAGCCGACATGTT
*
332170 GCGGCGTTTTCTAAAAAAACGCCGCTATAGATTTAGACCGATT
128 GCGGCGTTTTCTAAAAAAACGCCGCTATAGATCTAGACCGATT
332213 GCGGC
1 GCGGC
332218 ATTTTTTTTT
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
166 17 0.12
167 19 0.13
168 67 0.46
169 33 0.23
170 10 0.07
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (170 bp):
GCGGCGTTTGCATCCAAAAACGACGCTATAGATATGAAATTTTACGGCATTTATTCCAAAAACGC
CGCTATAAAGCTGACTTATTGAAGCGTTTTCTCCAAAAACGCCGCTATAGAGCCGACATGTTGCG
GCGTTTTCTAAAAAAACGCCGCTATAGATCTAGACCGATT
Found at i:332888 original size:16 final size:17
Alignment explanation
Indices: 332863--332894 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
332853 ACGGGATATT
332863 AAAACGCCACTATAAAA
1 AAAACGCCACTATAAAA
332880 AAAAC-CCACTATAAA
1 AAAACGCCACTATAAA
332895 CCTATTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.59, C:0.25, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAACGCCACTATAAAA
Found at i:337666 original size:31 final size:31
Alignment explanation
Indices: 337631--337714 Score: 73
Period size: 35 Copynumber: 2.6 Consensus size: 31
337621 AAACCTTTTT
337631 ATATTTTTAATTTTGTAAAAAAAAAATATAA
1 ATATTTTTAATTTTGTAAAAAAAAAATATAA
* *
337662 ATATTATGAATTTAATTTT-TAAAGAAAATATATAA
1 ATA-T-T---TTTAATTTTGTAAAAAAAAAATATAA
*
337697 AT-TTTTTACAATTTGTAA
1 ATATTTTTA-ATTTTGTAA
337715 TATTATACAA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
29 4 0.09
30 4 0.09
31 6 0.14
32 2 0.05
33 2 0.05
35 16 0.37
36 9 0.21
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (31 bp):
ATATTTTTAATTTTGTAAAAAAAAAATATAA
Found at i:344768 original size:15 final size:16
Alignment explanation
Indices: 344730--344770 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
344720 ATAGAGTATC
344730 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
**
344746 TGAATCATTCAGTGTT
1 TGAATCATTCAGCATT
344762 T-AATCATTC
1 TGAATCATTC
344771 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:345387 original size:46 final size:47
Alignment explanation
Indices: 345290--345387 Score: 128
Period size: 45 Copynumber: 2.1 Consensus size: 47
345280 ATGATTTTTT
* * * * * *
345290 TTTATTTTTTTAATATATAAATTTTTGTAAAATTATAGTTTTTATTA
1 TTTATTTTATTAATATATAAATTTGTGTAAAAGTACAATATTTATTA
345337 -TTATTTTATTAATATAT-AATTTGTGTAAAAGTACAATATTTATTA
1 TTTATTTTATTAATATATAAATTTGTGTAAAAGTACAATATTTATTA
345382 TTTATT
1 TTTATT
345388 AATATATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 23 0.52
46 21 0.48
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (47 bp):
TTTATTTTATTAATATATAAATTTGTGTAAAAGTACAATATTTATTA
Found at i:350103 original size:2 final size:2
Alignment explanation
Indices: 350096--350130 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
350086 ATTTAAACAA
* *
350096 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
350131 AGACTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:350108 original size:129 final size:127
Alignment explanation
Indices: 349854--350106 Score: 309
Period size: 129 Copynumber: 2.0 Consensus size: 127
349844 TATTAATATA
349854 TATATAAATAAGATATTTATTTATTTATAAATATCAGAAAAGGGATTCTAGGTGCTTTAAGACAA
1 TATATAAATAAGATATTTATTTATTTATAAATATCAGAAAAGGGATTCTAGGTGCTTTAAGACAA
* ***
349919 CTCTTTTCTTAATATAAAATGAATAAATAAATATTAAAACATTTATTTAAAAATAGATATAATT
66 CCCTTTTCTTAATATAAAA-GAATAAATAAATATT-AAACATTTAAACAAAAATAGATATAATT
*
349983 TATA-AAAGTAAGATATTTATTTATTTA-AGAATATCAGAAAA-TGACTTCTAGGTGCTTTAAGA
1 TATATAAA-TAAGATATTTATTTATTTATA-AATATCAGAAAAGGGA-TTCTAGGTGCTTTAAGA
* * ** * *
350045 CAACCCATTTTCTTTGATATTAAA-AATAAATAAATATT-ATTATTTAAACAAATATATATATA
63 CAACCC-TTTTC-TTAATATAAAAGAATAAATAAATATTAAACATTTAAACAAAAATAGATATA
350107 TATATACATA
Statistics
Matches: 108, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
127 17 0.16
128 6 0.06
129 71 0.66
130 5 0.05
131 9 0.08
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (127 bp):
TATATAAATAAGATATTTATTTATTTATAAATATCAGAAAAGGGATTCTAGGTGCTTTAAGACAA
CCCTTTTCTTAATATAAAAGAATAAATAAATATTAAACATTTAAACAAAAATAGATATAATT
Found at i:350198 original size:24 final size:22
Alignment explanation
Indices: 350135--350219 Score: 81
Period size: 22 Copynumber: 3.9 Consensus size: 22
350125 TTTATAAGAC
350135 TAAAA-TAATAATAAAATA-AT
1 TAAAAGTAATAATAAAATATAT
350155 T-AAAGTAATAAATTAAAATATAT
1 TAAAAGTAAT-AA-TAAAATATAT
350178 TAAAAGTAATAAT-AAATAATAT
1 TAAAAGTAATAATAAAAT-ATAT
*
350200 TACAAA-TAAATAATGAAATA
1 TA-AAAGT-AATAATAAAATA
350220 AAATAAATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 15
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.05
20 5 0.09
21 6 0.11
22 15 0.27
23 15 0.27
24 12 0.21
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAAAGTAATAATAAAATATAT
Found at i:350220 original size:24 final size:22
Alignment explanation
Indices: 350135--350220 Score: 67
Period size: 23 Copynumber: 3.9 Consensus size: 22
350125 TTTATAAGAC
350135 TAAAA-TAATAAT-AA-AATAAT
1 TAAAAGTAATAATAAATAAT-AT
350155 T-AAAGTAATAAATTAAA-ATATAT
1 TAAAAGTAAT-AA-TAAATA-ATAT
350178 TAAAAGTAATAATAAATAATAT
1 TAAAAGTAATAATAAATAATAT
350200 TACAAA-TAAATAATGAAATAA
1 TA-AAAGT-AATAAT-AAATAA
350221 AATAAATAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.05
20 5 0.09
21 2 0.04
22 12 0.21
23 18 0.32
24 16 0.29
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (22 bp):
TAAAAGTAATAATAAATAATAT
Found at i:350443 original size:15 final size:15
Alignment explanation
Indices: 350417--350462 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
350407 TACCAATTTT
350417 AAATAAATGCAAAGAA
1 AAATAAA-GCAAAGAA
* *
350433 AATTAAAGCAAGGAA
1 AAATAAAGCAAAGAA
350448 AAATAAAGTCAAAGA
1 AAATAAAG-CAAAGA
350463 TACAAACATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.65, C:0.07, G:0.15, T:0.13
Consensus pattern (15 bp):
AAATAAAGCAAAGAA
Found at i:351689 original size:39 final size:39
Alignment explanation
Indices: 351628--351704 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
351618 ACCTGGCAGT
*
351628 GCTGGAAGCTGCTGCAACTGATGCGTGGAGGGGCTGCTC
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
* *
351667 GCTGGAAGCTGCTGGAAATGATGTGTGGAGGGGCTGCT
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCT
351705 GGATGGAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.17, C:0.18, G:0.43, T:0.22
Consensus pattern (39 bp):
GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
Found at i:352070 original size:113 final size:113
Alignment explanation
Indices: 351945--352166 Score: 372
Period size: 113 Copynumber: 2.0 Consensus size: 113
351935 GATGAAATCT
* *
351945 AGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTTTTCATTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCT
*
352010 CATTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTG
66 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
* * *
352058 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCT
* *
352123 CATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGGA
66 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGA
352167 AATTTATGTT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 101 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (113 bp):
AGCAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCT
CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
Found at i:352207 original size:37 final size:36
Alignment explanation
Indices: 352166--352359 Score: 165
Period size: 37 Copynumber: 5.3 Consensus size: 36
352156 CGAGTGATGG
*
352166 AAATTTATGTTTCGAGTGAAACTGTCTCGAGCGAGAC
1 AAATTT-TGTTTCGAGTGAAACTGTCTCGAGTGAGAC
** ** * * *
352203 AAATTTTGTTTTAAG-GAAAACAATTTCAAGTGAGAT
1 AAATTTTGTTTCGAGTG-AAACTGTCTCGAGTGAGAC
* *
352239 AAATTGTTGTTTCGAATGAAACTGTCTCGAGCGAGAC
1 AAATT-TTGTTTCGAGTGAAACTGTCTCGAGTGAGAC
** ** *** * *
352276 AAATTTTGTTTTAAGAAAAAAAATCTCAAGTGAGAT
1 AAATTTTGTTTCGAGTGAAACTGTCTCGAGTGAGAC
*
352312 AAATTGCTGTTTCGAGTGAAACTGTCTCGAGTGAGAC
1 AAATT-TTGTTTCGAGTGAAACTGTCTCGAGTGAGAC
352349 AAATTTTGTTT
1 AAATTTTGTTT
352360 TAAGAAAAAC
Statistics
Matches: 114, Mismatches: 39, Indels: 9
0.70 0.24 0.06
Matches are distributed among these distances:
35 1 0.01
36 55 0.48
37 57 0.50
38 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.34
Consensus pattern (36 bp):
AAATTTTGTTTCGAGTGAAACTGTCTCGAGTGAGAC
Found at i:352243 original size:36 final size:37
Alignment explanation
Indices: 352198--352406 Score: 176
Period size: 36 Copynumber: 5.7 Consensus size: 37
352188 TGTCTCGAGC
*
352198 GAGACAAATT-TTGTTTTAAGGAAAACAATTTCAAGT
1 GAGACAAATTGTTGTTTTAAGGAAAACAATCTCAAGT
* * * ** * *
352234 GAGATAAATTGTTGTTTCGAATG-AAACTGTCTCGAGC
1 GAGACAAATTGTTGTTT-TAAGGAAAACAATCTCAAGT
* *
352271 GAGACAAATT-TTGTTTTAAGAAAAAAAATCTCAAGT
1 GAGACAAATTGTTGTTTTAAGGAAAACAATCTCAAGT
* * ** ** *
352307 GAGATAAATTGCTGTTTCGAGTG-AAACTGTCTCGAGT
1 GAGACAAATTGTTGTTTTAAG-GAAAACAATCTCAAGT
*
352344 GAGACAAATT-TTGTTTTAAGAAAAACAATCTCAAGT
1 GAGACAAATTGTTGTTTTAAGGAAAACAATCTCAAGT
* *
352380 GAGATAAATTGTTGTTTCGAAGGAAAA
1 GAGACAAATTGTTGTTT-TAAGGAAAA
352407 TGTTTAATAA
Statistics
Matches: 128, Mismatches: 37, Indels: 14
0.72 0.21 0.08
Matches are distributed among these distances:
35 2 0.02
36 60 0.47
37 56 0.44
38 10 0.08
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (37 bp):
GAGACAAATTGTTGTTTTAAGGAAAACAATCTCAAGT
Found at i:352277 original size:73 final size:73
Alignment explanation
Indices: 352173--352405 Score: 394
Period size: 73 Copynumber: 3.2 Consensus size: 73
352163 TGGAAATTTA
* * *
352173 TGTTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGGAAAACAATTTCAAGTGAGA
1 TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
352238 TAAATTGT
66 TAAATTGT
*
352246 TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAAAAATCTCAAGTGAGA
1 TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
*
352311 TAAATTGC
66 TAAATTGT
* *
352319 TGTTTCGAGTGAAACTGTCTCGAGTGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
352384 TAAATTGT
66 TAAATTGT
*
352392 TGTTTCGAAGGAAA
1 TGTTTCGAATGAAA
352406 ATGTTTAATA
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 149 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (73 bp):
TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAATTGT
Found at i:352697 original size:166 final size:165
Alignment explanation
Indices: 352404--352725 Score: 506
Period size: 166 Copynumber: 1.9 Consensus size: 165
352394 TTTCGAAGGA
352404 AAATGTTTAATAAGTAAAAAACTAAGAAAAATAGTTTTCTTACTTTTCAACAATTTCATTTTCAG
1 AAATGTTTAATAAGTAAAAAACTAAGAAAAATAGTTTTCTTACTTTTCAACAATTTCATTTTCAG
** * * *
352469 AAAAGATTGAATGAGAAACTTTGGAAATCGTTTTCTCATTATGTTTCAAGATAACCTGTTGATTG
66 AAAAGATAAAATGAGAAACTATGGAAATCATTTTCTCATTATGTTTCAAGATAACATGTTGATTG
* *
352534 GGTAACATGTCCCAATCTCCAGATAAGGTTGTTGG
131 GGTAACATGCCCCAATCTCAAGATAAGGTTGTTGG
*
352569 AAATAGTTTAATAAGTAAAAAAACTAAG-AAAATCGTTTTCTTACTTTTCAACAATTTCATTTT-
1 AAAT-GTTTAATAAGT-AAAAAACTAAGAAAAATAGTTTTCTTACTTTTCAACAATTTCATTTTC
*
352632 AGAAAAGATAAAATGAGAAACTATGGAAATCATTTTCTCATTATGTTTTTGAA-ATAACATGTTG
64 AGAAAAGATAAAATGAGAAACTATGGAAATCATTTTCTCATTATG--TTTCAAGATAACATGTTG
352696 ATTGGGTAACATGCCCCAATCTCAAGATAA
127 ATTGGGTAACATGCCCCAATCTCAAGATAA
352726 TGCTTATTCT
Statistics
Matches: 144, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
165 45 0.31
166 83 0.58
167 16 0.11
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (165 bp):
AAATGTTTAATAAGTAAAAAACTAAGAAAAATAGTTTTCTTACTTTTCAACAATTTCATTTTCAG
AAAAGATAAAATGAGAAACTATGGAAATCATTTTCTCATTATGTTTCAAGATAACATGTTGATTG
GGTAACATGCCCCAATCTCAAGATAAGGTTGTTGG
Found at i:353263 original size:21 final size:20
Alignment explanation
Indices: 353228--353305 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 20
353218 CATAAAGTTT
353228 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTT-AAAAGA-AATCTA
* *
353250 TCATCTTTAAAAGAAATTTTG
1 TCATCTTTAAAAGAAA-TCTA
* **
353271 TCATCTCTGAAGTGAAAATCTA
1 TCATCT-TTAAAAG-AAATCTA
353293 TCATCTTTAAAAG
1 TCATCTTTAAAAG
353306 TGTAGATGTA
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
20 2 0.05
21 18 0.42
22 20 0.47
23 3 0.07
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (20 bp):
TCATCTTTAAAAGAAATCTA
Found at i:360541 original size:13 final size:14
Alignment explanation
Indices: 360493--360543 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
360483 TTGTGCAATA
* *
360493 CAAATGCAAAAATG
1 CAAATGTAAATATG
360507 CCAAATGTAAATATG
1 -CAAATGTAAATATG
360522 CAAATGTAAA-ATG
1 CAAATGTAAATATG
*
360535 TAAATGTAA
1 CAAATGTAA
360544 TTATTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 11 0.33
14 10 0.30
15 12 0.36
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:362142 original size:8 final size:8
Alignment explanation
Indices: 362129--362175 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
362119 TGAATAAAAT
362129 AAATAATA
1 AAATAATA
362137 AAATAAT-
1 AAATAATA
362144 AAATAATA
1 AAATAATA
*
362152 ATAT-AT-
1 AAATAATA
362158 AAA-AATA
1 AAATAATA
362165 AAATAATA
1 AAATAATA
362173 AAA
1 AAA
362176 AATTTGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
6 4 0.12
7 12 0.36
8 17 0.52
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAATAATA
Found at i:362144 original size:15 final size:15
Alignment explanation
Indices: 362126--362174 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
362116 TCTTGAATAA
362126 AATAAATAATAAAAT
1 AATAAATAATAAAAT
*
362141 AATAAATAATAATAT
1 AATAAATAATAAAAT
362156 -ATAAA-AATAAAAT
1 AATAAATAATAAAAT
362169 AATAAA
1 AATAAA
362175 AAATTTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 7 0.23
14 10 0.32
15 14 0.45
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAATAATAAAAT
Found at i:362188 original size:22 final size:22
Alignment explanation
Indices: 362160--362201 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
362150 TAATATATAA
*
362160 AAATAAAATAATAAAAAATTTG
1 AAATAAAAGAATAAAAAATTTG
*
362182 AAATAAAAGAATTAAAAATT
1 AAATAAAAGAATAAAAAATT
362202 AATATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (22 bp):
AAATAAAAGAATAAAAAATTTG
Found at i:362930 original size:2 final size:2
Alignment explanation
Indices: 362923--362957 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
362913 ATTTAAACAA
* *
362923 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
362958 AGACTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:362935 original size:128 final size:126
Alignment explanation
Indices: 362691--362933 Score: 296
Period size: 128 Copynumber: 1.9 Consensus size: 126
362681 TATATATATA
* *
362691 TAAGATATTTATTTATTTATAAATATCAGAAAAGGCTTCTAGGTGCTTTAAGACAACTCTTTTCT
1 TAAGATATTTATTTATTTATAAATATCAGAAAAGACTTCTAGGTGCTTTAAGACAACCCTTTTCT
***
362756 TAATATAAAATGAATAAATAAATATTAAAACATTTATTTAAAAATAGATATAATTTATAAAAG
66 TAATATAAAA-GAATAAATAAATATT-AAACATTTAAACAAAAATAGATATAATTTATAAAAG
*
362819 TAAGATATTTATTTATTTA-AGAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAGCCCATTT
1 TAAGATATTTATTTATTTATA-AATATCAGAAAA-GACTTCTAGGTGCTTTAAGACAACCC-TTT
* * ** * *
362883 TCTTTGATAT-TAA-AATAAATAAATATT-ATTATTTAAACAAATATATATATA
63 TC-TTAATATAAAAGAATAAATAAATATTAAACATTTAAACAAAAATAGATATA
362934 TATACATATA
Statistics
Matches: 99, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
126 17 0.17
127 1 0.01
128 45 0.45
129 23 0.23
130 7 0.07
131 6 0.06
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (126 bp):
TAAGATATTTATTTATTTATAAATATCAGAAAAGACTTCTAGGTGCTTTAAGACAACCCTTTTCT
TAATATAAAAGAATAAATAAATATTAAACATTTAAACAAAAATAGATATAATTTATAAAAG
Found at i:362990 original size:12 final size:12
Alignment explanation
Indices: 362965--363054 Score: 71
Period size: 12 Copynumber: 7.4 Consensus size: 12
362955 ATAAGACTAA
362965 AATAA-TAAAAT
1 AATAATTAAAAT
*
362976 AATAATTAAAGT
1 AATAATTAAAAT
362988 AATAATTAAAAT
1 AATAATTAAAAT
363000 -AT-ATTAAAAGT
1 AATAATTAAAA-T
*
363011 AATAATAAAAAT
1 AATAATTAAAAT
*
363023 ATATACA-AATAAAT
1 A-ATA-ATTA-AAAT
*
363037 AATGAAATAAAAT
1 AAT-AATTAAAAT
363050 AATAA
1 AATAA
363055 AATTAAAACT
Statistics
Matches: 66, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
10 7 0.11
11 8 0.12
12 22 0.33
13 21 0.32
14 8 0.12
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (12 bp):
AATAATTAAAAT
Found at i:363039 original size:23 final size:23
Alignment explanation
Indices: 362962--363026 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
362952 TTTATAAGAC
*
362962 TAAAA-TAATAA-AATAATA-AT
1 TAAAAGTAATAATAAAAATATAT
*
362982 T-AAAGTAATAATTAAAATATAT
1 TAAAAGTAATAATAAAAATATAT
363004 TAAAAGTAATAATAAAAATATAT
1 TAAAAGTAATAATAAAAATATAT
363027 ACAAATAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 3 0.08
20 7 0.18
21 5 0.13
22 3 0.08
23 20 0.53
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
TAAAAGTAATAATAAAAATATAT
Found at i:363267 original size:15 final size:15
Alignment explanation
Indices: 363241--363286 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
363231 TACCAATTTT
363241 AAATAAATGCAAAGAA
1 AAATAAA-GCAAAGAA
* *
363257 AATTAAAGCAAGGAA
1 AAATAAAGCAAAGAA
363272 AAATAAAGTCAAAGA
1 AAATAAAG-CAAAGA
363287 TACAAACATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.65, C:0.07, G:0.15, T:0.13
Consensus pattern (15 bp):
AAATAAAGCAAAGAA
Found at i:364513 original size:39 final size:39
Alignment explanation
Indices: 364452--364528 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
364442 ACCTGGCAGT
*
364452 GCTGGAAGCTGCTGCAACTGATGCGTGGAGGGGCTGCTC
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
* *
364491 GCTGGAAGCTGCTGGAAATGATGTGTGGAGGGGCTGCT
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCT
364529 GGATGGAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.17, C:0.18, G:0.43, T:0.22
Consensus pattern (39 bp):
GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
Found at i:365103 original size:41 final size:41
Alignment explanation
Indices: 365044--365123 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
365034 TAGTCTAGTG
* *
365044 ATTGAGCCTTGCTCTAATATTATCAACGAGGGAATAACAGT
1 ATTGAGCCTTGCTATAATATTATCAACGAGGGAAGAACAGT
365085 ATTGAGCCTTGCTATAATATTATCAACGAGGGAAGAACA
1 ATTGAGCCTTGCTATAATATTATCAACGAGGGAAGAACA
365124 ATCCTTATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (41 bp):
ATTGAGCCTTGCTATAATATTATCAACGAGGGAAGAACAGT
Found at i:369096 original size:16 final size:16
Alignment explanation
Indices: 369075--369124 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
369065 GCTCAACTGG
369075 CATCAAATAAAATAAT
1 CATCAAATAAAATAAT
369091 CATC-AAT----TAAT
1 CATCAAATAAAATAAT
369102 GCATCAAATAAAATAAT
1 -CATCAAATAAAATAAT
369119 CATCAA
1 CATCAA
369125 TTAATGCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
11 4 0.14
12 4 0.14
13 3 0.11
15 3 0.11
16 10 0.36
17 4 0.14
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (16 bp):
CATCAAATAAAATAAT
Found at i:369105 original size:28 final size:28
Alignment explanation
Indices: 369074--369146 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
369064 AGCTCAACTG
369074 GCATCAAATAAAATAATCATCAATTAAT
1 GCATCAAATAAAATAATCATCAATTAAT
369102 GCATCAAATAAAATAATCATCAATTAAT
1 GCATCAAATAAAATAATCATCAATTAAT
369130 GCATCAAATAAAATAAT
1 GCATCAAATAAAATAAT
369147 ACCTCAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (28 bp):
GCATCAAATAAAATAATCATCAATTAAT
Found at i:377903 original size:2 final size:2
Alignment explanation
Indices: 377896--377957 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
377886 ATCCTCATAA
377896 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
377938 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
377958 TACTGAAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:379893 original size:34 final size:34
Alignment explanation
Indices: 379847--379911 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
379837 ATTAATATTT
*
379847 ATTTGGGATAAGTATAAATGTAATATCTGTTCAA
1 ATTTGGGATAAGTATAAAGGTAATATCTGTTCAA
*
379881 ATTTGGGGTAAGTATAAAGGTAATATCTGTT
1 ATTTGGGATAAGTATAAAGGTAATATCTGTT
379912 AAAAGATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (34 bp):
ATTTGGGATAAGTATAAAGGTAATATCTGTTCAA
Found at i:390939 original size:2 final size:2
Alignment explanation
Indices: 390927--390959 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
390917 TGTCCATCCC
*
390927 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
390960 TCATATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 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):
TA
Found at i:391858 original size:24 final size:24
Alignment explanation
Indices: 391812--391859 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
391802 AACAAAGTTA
* * * *
391812 ACGGCCTCGACCGCGTCCCCGTCC
1 ACGGCCACGACCACGACCACGTCC
391836 ACGGCCACGACCACGACCACGTCC
1 ACGGCCACGACCACGACCACGTCC
391860 CAAAGGCTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.52, G:0.23, T:0.08
Consensus pattern (24 bp):
ACGGCCACGACCACGACCACGTCC
Found at i:402766 original size:33 final size:33
Alignment explanation
Indices: 402720--402788 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
402710 GATCATCGGA
*
402720 CGAATGGTTCAAAGCTGATGACAAGGACCTAAT
1 CGAATGGTACAAAGCTGATGACAAGGACCTAAT
*
402753 CGAATGGTACAAAGCTGATGACAAGGAGCTAAT
1 CGAATGGTACAAAGCTGATGACAAGGACCTAAT
402786 CGA
1 CGA
402789 TGAAGAGTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (33 bp):
CGAATGGTACAAAGCTGATGACAAGGACCTAAT
Found at i:421432 original size:36 final size:36
Alignment explanation
Indices: 421294--421434 Score: 185
Period size: 36 Copynumber: 3.9 Consensus size: 36
421284 CCATAGAACG
* * * *
421294 AGATTCAACATCTTTTATTCGCCTACTACAAGAAT-G
1 AGATTCAACATCCTTTATTCACCTACTACATG-ATCA
* *
421330 AGATTCAACATCCTTCATTCACCTACCACATGATCA
1 AGATTCAACATCCTTTATTCACCTACTACATGATCA
*
421366 AGATTCAACATCCTTTATTCGCCTACTACATGATCA
1 AGATTCAACATCCTTTATTCACCTACTACATGATCA
* *
421402 AGGTTCAACATCTTTTATTCACCTACTACATGA
1 AGATTCAACATCCTTTATTCACCTACTACATGA
421435 AATCAAAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
35 2 0.02
36 90 0.98
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.33
Consensus pattern (36 bp):
AGATTCAACATCCTTTATTCACCTACTACATGATCA
Found at i:422321 original size:28 final size:30
Alignment explanation
Indices: 422290--422347 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
422280 TAAATTAATA
*
422290 TTTTAATATCATTTTAATA-ATAT-TATAT
1 TTTTAATATCATATTAATATATATATATAT
*
422318 TTTTAATATTATATTAATATATATATATAT
1 TTTTAATATCATATTAATATATATATATAT
422348 ATACTCAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 17 0.65
29 4 0.15
30 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTTAATATCATATTAATATATATATATAT
Found at i:422336 original size:11 final size:11
Alignment explanation
Indices: 422273--422343 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 11
422263 TTTTATACAT
*
422273 TTAATATTAAA
1 TTAATATTATA
422284 TTAATA-T-T-
1 TTAATATTATA
* *
422292 TTAATATCATT
1 TTAATATTATA
422303 TTAATA--ATA
1 TTAATATTATA
422312 TT-ATATT-T-
1 TTAATATTATA
422320 TTAATATTATA
1 TTAATATTATA
422331 TTAATATATATA
1 TTAATAT-TATA
422343 T
1 T
422344 ATATATACTC
Statistics
Matches: 48, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
8 11 0.23
9 10 0.21
10 3 0.06
11 19 0.40
12 5 0.10
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (11 bp):
TTAATATTATA
Found at i:422821 original size:29 final size:29
Alignment explanation
Indices: 422779--422860 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 29
422769 TAGAAAATGT
*
422779 AATTCATTTTACGTAAAACAGTTTTAGGC
1 AATTCATGTTACGTAAAACAGTTTTAGGC
* * * *
422808 AATTTATGTTACGTAAAACAG-TTCATGT
1 AATTCATGTTACGTAAAACAGTTTTAGGC
*
422836 AATTCATTTTACGTAAAACAGTTTT
1 AATTCATGTTACGTAAAACAGTTTT
422861 CAAGTAATCC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 23 0.52
29 21 0.48
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (29 bp):
AATTCATGTTACGTAAAACAGTTTTAGGC
Found at i:422892 original size:30 final size:30
Alignment explanation
Indices: 422777--422882 Score: 119
Period size: 30 Copynumber: 3.6 Consensus size: 30
422767 CTTAGAAAAT
* *
422777 GTAATTCATTTTACGTAAAACAGTTTT-AG
1 GTAATCCATTTTACGTAAAACAGTTTTCAA
* ** * *
422806 GCAATTTATGTTACGTAAAACAG--TTCAT
1 GTAATCCATTTTACGTAAAACAGTTTTCAA
*
422834 GTAATTCATTTTACGTAAAACAGTTTTCAA
1 GTAATCCATTTTACGTAAAACAGTTTTCAA
422864 GTAATCCATTTTACGTAAA
1 GTAATCCATTTTACGTAAA
422883 TTATTTTTCA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
27 2 0.03
28 21 0.32
29 20 0.31
30 22 0.34
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (30 bp):
GTAATCCATTTTACGTAAAACAGTTTTCAA
Found at i:422986 original size:12 final size:13
Alignment explanation
Indices: 422964--423023 Score: 65
Period size: 12 Copynumber: 4.9 Consensus size: 13
422954 TGTTCACGAA
422964 CAAACTCATTTAT
1 CAAACTCATTTAT
422977 CAAA-TCATTTAT
1 CAAACTCATTTAT
422989 -AAACTCATTTAT
1 CAAACTCATTTAT
** *
423001 -TGACTCGTTTAT
1 CAAACTCATTTAT
423013 -AAACTCATTTA
1 CAAACTCATTTA
423024 CGCGGATCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
11 3 0.08
12 33 0.82
13 4 0.10
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (13 bp):
CAAACTCATTTAT
Found at i:422994 original size:24 final size:24
Alignment explanation
Indices: 422965--423023 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
422955 GTTCACGAAC
422965 AAACTCATTTATCAAATCATTTAT
1 AAACTCATTTATCAAATCATTTAT
** * *
422989 AAACTCATTTATTGACTCGTTTAT
1 AAACTCATTTATCAAATCATTTAT
423013 AAACTCATTTA
1 AAACTCATTTA
423024 CGCGGATCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.42
Consensus pattern (24 bp):
AAACTCATTTATCAAATCATTTAT
Found at i:424433 original size:64 final size:64
Alignment explanation
Indices: 424365--424529 Score: 206
Period size: 64 Copynumber: 2.6 Consensus size: 64
424355 TGTTTGAATG
* * *
424365 TGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAAAAGAAGAACATCGAATGCCTTTGA
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CTTTTAAAAGAAGAACATCGAATGCATTTAA
* * * * *
424429 TGCATCGATGCATAGATAATGCATCGATGCATCCTTTTGAAATAATAACATCGAATGCATTTAA
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTAA
* * * *
424493 TGCACCGATGCACAAGTAGTGCATCGATGCATACTTT
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCTTT
424530 CATTAAAAGA
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 85 0.99
65 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTAA
Found at i:424949 original size:15 final size:16
Alignment explanation
Indices: 424929--424958 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
424919 GATCTACGTG
424929 AATACATGT-ATATGT
1 AATACATGTGATATGT
424944 AATACATGTGATATG
1 AATACATGTGATATG
424959 ATATGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (16 bp):
AATACATGTGATATGT
Found at i:426214 original size:101 final size:102
Alignment explanation
Indices: 426080--426266 Score: 263
Period size: 101 Copynumber: 1.8 Consensus size: 102
426070 ACAAATTCAT
** * * *
426080 TGTCAAAACAGATTGCACCGAGTCACTCTACCTCGTGTATCACTAAGGTACACCGAGTCAGAGCA
1 TGTCAAAACAGATTGCACCGAACCACTCTACCTCGTGCACCACTAAGGTACACCGAGTCAAAGCA
426145 CGAGTGACCCATCTTGGTGCCACATCATATATGTATAG
66 CGAGTGACCCAT-TTGGTGCCACATCATATATGTATAG
* *
426183 TGTC-AAACA-ATTGCACCGAACCACT-TCACCTCGTGCACCATTAAGGTACGCCGAGTCAAAGC
1 TGTCAAAACAGATTGCACCGAACCACTCT-ACCTCGTGCACCACTAAGGTACACCGAGTCAAAGC
*
426245 ACGAGTGATCCATTTGGTGCCA
65 ACGAGTGACCCATTTGGTGCCA
426267 GATCTGAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
100 10 0.13
101 56 0.75
102 5 0.07
103 4 0.05
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (102 bp):
TGTCAAAACAGATTGCACCGAACCACTCTACCTCGTGCACCACTAAGGTACACCGAGTCAAAGCA
CGAGTGACCCATTTGGTGCCACATCATATATGTATAG
Found at i:428545 original size:26 final size:26
Alignment explanation
Indices: 428516--428566 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
428506 AAGATGAACA
*
428516 AAATATAAACACTTTTAAGAATAAAC
1 AAATATAAACACTTTTAAAAATAAAC
428542 AAATATAAACACTTTTAAAAATAAA
1 AAATATAAACACTTTTAAAAATAAA
428567 TAAACAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (26 bp):
AAATATAAACACTTTTAAAAATAAAC
Found at i:435217 original size:14 final size:14
Alignment explanation
Indices: 435198--435235 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
435188 ATTTAAAGCT
435198 GAAACCCAGAATTC
1 GAAACCCAGAATTC
435212 GAAACCCAGAATTC
1 GAAACCCAGAATTC
* *
435226 AAAATCCAGA
1 GAAACCCAGA
435236 TTAGGATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.26, G:0.13, T:0.13
Consensus pattern (14 bp):
GAAACCCAGAATTC
Found at i:442473 original size:16 final size:15
Alignment explanation
Indices: 442452--442485 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
442442 ATTAGATATC
*
442452 AAAATTCAATTTAACT
1 AAAATTCAAGTTAA-T
442468 AAAATTCAAGTTAAT
1 AAAATTCAAGTTAAT
442483 AAA
1 AAA
442486 GATTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (15 bp):
AAAATTCAAGTTAAT
Found at i:445622 original size:33 final size:33
Alignment explanation
Indices: 445576--445641 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
445566 AAAGAAATGA
* * *
445576 GAAATCACGATTTTAGTCCTCTGACGTGGAAAC
1 GAAATCACAATTTTAGTCATATGACGTGGAAAC
445609 GAAATCACAATTTTAGTCATATGACGTGGAAAC
1 GAAATCACAATTTTAGTCATATGACGTGGAAAC
445642 AGTTGGCGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (33 bp):
GAAATCACAATTTTAGTCATATGACGTGGAAAC
Found at i:450771 original size:21 final size:21
Alignment explanation
Indices: 450745--450784 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
450735 CAGAACCCCA
*
450745 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
450766 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
450785 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:450813 original size:20 final size:21
Alignment explanation
Indices: 450767--450827 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
450757 TTCCCCTGTG
450767 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
450790 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
450810 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
450828 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:456028 original size:16 final size:17
Alignment explanation
Indices: 455997--456028 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
455987 TTCTCTATGA
455997 TTTCTTATTGCTTGATG
1 TTTCTTATTGCTTGATG
456014 TTTCTTATT-CTTGAT
1 TTTCTTATTGCTTGAT
456029 CAATGGCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTCTTATTGCTTGATG
Found at i:456761 original size:3 final size:3
Alignment explanation
Indices: 456753--456800 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
456743 CAAGTATATT
456753 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
456801 TTGTGGAGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:457278 original size:41 final size:42
Alignment explanation
Indices: 457169--457292 Score: 241
Period size: 42 Copynumber: 3.0 Consensus size: 42
457159 ATTTTATTTA
457169 AAATAAAAAGTATTTCAATTATAATAAATATTTATAATTATT
1 AAATAAAAAGTATTTCAATTATAATAAATATTTATAATTATT
457211 AAATAAAAAGTATTTCAATTATAATAAATATTTATAATTATT
1 AAATAAAAAGTATTTCAATTATAATAAATATTTATAATTATT
457253 AAATAAAAA-TATTTCAATTATAATAAATATTTATAATTAT
1 AAATAAAAAGTATTTCAATTATAATAAATATTTATAATTAT
457293 GTATTATAAG
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
41 31 0.38
42 51 0.62
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
AAATAAAAAGTATTTCAATTATAATAAATATTTATAATTATT
Found at i:465749 original size:21 final size:21
Alignment explanation
Indices: 465713--465758 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
465703 ATTAATTCGG
*
465713 TTAATTCGGTTCGGTTACCGAA
1 TTAATTCGGTTCGGTTAACG-A
465735 TTAATTCGG-TCGGTTAACGA
1 TTAATTCGGTTCGGTTAACGA
465755 TTAA
1 TTAA
465759 GAAAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 9 0.39
22 9 0.39
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (21 bp):
TTAATTCGGTTCGGTTAACGA
Found at i:466051 original size:186 final size:189
Alignment explanation
Indices: 465817--466168 Score: 631
Period size: 186 Copynumber: 1.9 Consensus size: 189
465807 ATTAAAATTT
*
465817 AAATATTAAATATATTATATATAATAACATATGGGCTTAGCCCAAACCATTTAAAACCCAATTAA
1 AAATATTAAATATATTATATATAATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAA
465882 TAATTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATAT-AAA
66 TAATTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATGAAA
465946 ATTTTTATTTTATAATTATATATTATTTAAATTAATTGTGAACTGTTTTTTTTATTTAAA
131 A-TTTTATTTTATAATTATATATTATTTAAATTAATTGTGAACTGTTTTTTTTATTTAAA
466006 AAATATTAAATATA-T-TATAT-ATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAA
1 AAATATTAAATATATTATATATAATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAA
* * *
466068 TAATTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATCTGAAA
66 TAATTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATGAAA
466133 ATTTTATTTTATAATTATATATTATTTAAATTAATT
131 ATTTTATTTTATAATTATATATTATTTAAATTAATT
466169 ATAATTTTTT
Statistics
Matches: 158, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
186 134 0.85
187 9 0.06
188 1 0.01
189 14 0.09
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (189 bp):
AAATATTAAATATATTATATATAATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAA
TAATTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATGAAA
ATTTTATTTTATAATTATATATTATTTAAATTAATTGTGAACTGTTTTTTTTATTTAAA
Found at i:475368 original size:30 final size:30
Alignment explanation
Indices: 475332--475410 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 30
475322 CGAATATAGA
475332 TCGCCAGGTGATCAT-GGCGACCAATGAAGG
1 TCGCCAGGTGATC-TGGGCGACCAATGAAGG
*
475362 TCGCCAGGTGGTCTGGGCGACCAATGAAGG
1 TCGCCAGGTGATCTGGGCGACCAATGAAGG
*
475392 TCGCCATGT-ATGCTGGGCG
1 TCGCCAGGTGAT-CTGGGCG
475411 TCATGCATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 2 0.05
30 42 0.95
ACGTcount: A:0.20, C:0.24, G:0.37, T:0.19
Consensus pattern (30 bp):
TCGCCAGGTGATCTGGGCGACCAATGAAGG
Found at i:476030 original size:49 final size:50
Alignment explanation
Indices: 475977--476093 Score: 182
Period size: 50 Copynumber: 2.4 Consensus size: 50
475967 AACGTAGAAC
* * *
475977 AAATAAAAAC-TATTGAATACAAAACAAGATATCCCAATAATCAATTTTA
1 AAATAAAAACATACTAAATACAAAACAAGATATCCCAATAATAAATTTTA
*
476026 AAATAAATACATACTAAATACAAAACAAGATATCCCAATAATAAATTTTA
1 AAATAAAAACATACTAAATACAAAACAAGATATCCCAATAATAAATTTTA
*
476076 AAATAAATACATACTAAA
1 AAATAAAAACATACTAAA
476094 ATAGGATAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 9 0.14
50 54 0.86
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.26
Consensus pattern (50 bp):
AAATAAAAACATACTAAATACAAAACAAGATATCCCAATAATAAATTTTA
Found at i:476053 original size:50 final size:50
Alignment explanation
Indices: 475992--476093 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
475982 AAAACTATTG
*
475992 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATAAATTTTAAAATAAATACATACTA
476042 AATACAAAACAAGATATCCCAATAATAAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATAAATTTTAAAATAAATACATACTA
476092 AA
1 AA
476094 ATAGGATAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (50 bp):
AATACAAAACAAGATATCCCAATAATAAATTTTAAAATAAATACATACTA
Found at i:476303 original size:30 final size:30
Alignment explanation
Indices: 476267--476338 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
476257 GGCATGGCGT
476267 CCAGACCACCTGGCGACCTTCATTGGTCGC
1 CCAGACCACCTGGCGACCTTCATTGGTCGC
*
476297 CCAGACCACCTGGCTACCTTCATTGGTCGC
1 CCAGACCACCTGGCGACCTTCATTGGTCGC
476327 CCAGACCACCTG
1 CCAGACCACCTG
476339 ACGATCTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.18, C:0.42, G:0.21, T:0.19
Consensus pattern (30 bp):
CCAGACCACCTGGCGACCTTCATTGGTCGC
Found at i:477800 original size:3 final size:3
Alignment explanation
Indices: 477792--477830 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
477782 TTCTATTTGA
477792 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
477831 TACTTTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:483002 original size:87 final size:87
Alignment explanation
Indices: 482856--483021 Score: 260
Period size: 87 Copynumber: 1.9 Consensus size: 87
482846 TCAGAACGCC
* * * * *
482856 AGCAAATTCATGCTGAGAACATAAAGTTCTATGCCTTGCTATTATTATCTTATATTGATGTCAAA
1 AGCAAATTCATGCCGAGAACATAAAGTTCTATACCTTACTACTATTATCTAATATTGATGTCAAA
482921 GACAATATTGAAATGATTATTG
66 GACAATATTGAAATGATTATTG
* *
482943 AGCAAATTCATGCCGAGTACATAAAGTTCTATATCTTACTACTATTATCTAATATTGATGTCAAA
1 AGCAAATTCATGCCGAGAACATAAAGTTCTATACCTTACTACTATTATCTAATATTGATGTCAAA
*
483008 GACAATGTTGAAAT
66 GACAATATTGAAAT
483022 CAATGAAATG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (87 bp):
AGCAAATTCATGCCGAGAACATAAAGTTCTATACCTTACTACTATTATCTAATATTGATGTCAAA
GACAATATTGAAATGATTATTG
Found at i:488114 original size:18 final size:18
Alignment explanation
Indices: 488093--488130 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
488083 AAAAAGCGAA
488093 AGGAATAGAAATCAAAAC
1 AGGAATAGAAATCAAAAC
488111 AGGAATAGAAATCAAAAC
1 AGGAATAGAAATCAAAAC
488129 AG
1 AG
488131 ACTTAACGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.61, C:0.11, G:0.18, T:0.11
Consensus pattern (18 bp):
AGGAATAGAAATCAAAAC
Found at i:489489 original size:17 final size:17
Alignment explanation
Indices: 489458--489490 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
489448 AAATATTATT
489458 TTATTATTTATTTTAAA
1 TTATTATTTATTTTAAA
489475 TTATT-TTTATATTTAA
1 TTATTATTTAT-TTTAA
489491 TAATATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTTAAA
Found at i:491074 original size:34 final size:34
Alignment explanation
Indices: 491031--491098 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
491021 GTCCGGACTT
491031 CCAAAGACGGCAATCGTTCTCGCCATTCCTAGAC
1 CCAAAGACGGCAATCGTTCTCGCCATTCCTAGAC
491065 CCAAAGACGGCAATCGTTCTCGCCATTCCTAGAC
1 CCAAAGACGGCAATCGTTCTCGCCATTCCTAGAC
491099 ACCACCATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.35, G:0.18, T:0.21
Consensus pattern (34 bp):
CCAAAGACGGCAATCGTTCTCGCCATTCCTAGAC
Found at i:495693 original size:32 final size:32
Alignment explanation
Indices: 495647--495733 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
495637 AATATTTTAT
* *
495647 TATTATTTCAGGTCGGGTCGGGTGGAGGGTATA
1 TATT-TTTCGGGTCGGGTCGGGTGGAGGATATA
495680 TATTTTTCGGGTCGGGTCGGGTGGAGGATATA
1 TATTTTTCGGGTCGGGTCGGGTGGAGGATATA
* * *
495712 AAATTTTCGGGTCGGGTTGGGT
1 TATTTTTCGGGTCGGGTCGGGT
495734 TGGCTGACAC
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 45 0.92
33 4 0.08
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.34
Consensus pattern (32 bp):
TATTTTTCGGGTCGGGTCGGGTGGAGGATATA
Found at i:499634 original size:2 final size:2
Alignment explanation
Indices: 499627--499653 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
499617 ATAATCTAGT
499627 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
499654 GAGGTGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:513610 original size:31 final size:32
Alignment explanation
Indices: 513572--513632 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
513562 TTTGAAGAAA
* *
513572 AAAATTAAAAGTTTAATTACTAAA-ACATACT
1 AAAATTAAAACTTTAAGTACTAAACACATACT
*
513603 AAAATTAATACTTTAAGTACTAAACACATA
1 AAAATTAAAACTTTAAGTACTAAACACATA
513633 ATTTATCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.31
Consensus pattern (32 bp):
AAAATTAAAACTTTAAGTACTAAACACATACT
Found at i:518393 original size:25 final size:21
Alignment explanation
Indices: 518365--518419 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 21
518355 GTTTTAAATA
518365 AAGTTAATAATAAAATATATTTAAT
1 AAGTTAATAA-AAAATAT-TTT--T
*
518390 AAGTTTATAAAAAATATTTTT
1 AAGTTAATAAAAAATATTTTT
518411 AAGTTAATA
1 AAGTTAATA
518420 TACATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.32
23 3 0.11
24 7 0.25
25 9 0.32
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
AAGTTAATAAAAAATATTTTT
Found at i:519690 original size:21 final size:20
Alignment explanation
Indices: 519662--519706 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
519652 AACCGATAAA
519662 ATTTTACCAGAAATATTATT
1 ATTTTACCAGAAATATTATT
***
519682 ATTTCTACCAGTTTTATTATT
1 ATTT-TACCAGAAATATTATT
519703 ATTT
1 ATTT
519707 GGTACTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.53
Consensus pattern (20 bp):
ATTTTACCAGAAATATTATT
Found at i:520381 original size:2 final size:2
Alignment explanation
Indices: 520374--520398 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
520364 ACTTAGTTGT
520374 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
520399 TATTTTGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.