Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 148 of 335
Found at i:43443824 original size:43 final size:42
Alignment explanation
Indices: 43443613--43443824 Score: 167
Period size: 43 Copynumber: 5.0 Consensus size: 42
43443603 CACATAAGCT
* * * * * *
43443613 CATACAATGCC-ATATCCCGGATATGGTCTTACATGTTATCA
1 CATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCG
* * * * * * *
43443654 CATATCGATGCCACTGTCCTAAACAGGGTCTTACACGAAATCA
1 CATA-CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCG
* * * * * *
43443697 TATAACGATGCCAATGTCCCAAATATGGTCTTACACATAATAG
1 CAT-ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCG
* *
43443740 CATA-ATGATGCCAATGCCCCAGACATGGTCTTACACATAATCG
1 CATACA--ATGCCAATGTCCCAGACATGGTCTTACACGTAATCG
*
43443783 CAATACAATGCCAATGTCCCAGACATGGTCTTACATGTAATC
1 C-ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATC
43443825 TCATCTTGGT
Statistics
Matches: 135, Mismatches: 29, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
41 4 0.03
42 7 0.05
43 119 0.88
44 4 0.03
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (42 bp):
CATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCG
Found at i:43448976 original size:2 final size:2
Alignment explanation
Indices: 43448969--43448993 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43448959 TTTATTTTAT
43448969 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
43448994 TAATCTATGC
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
Found at i:43449572 original size:21 final size:21
Alignment explanation
Indices: 43449548--43449592 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43449538 ATAATGTGAC
*
43449548 AATTAACATATACTTCATAAA
1 AATTAACAAATACTTCATAAA
* *
43449569 AATTCAGAAATACTTCATAAA
1 AATTAACAAATACTTCATAAA
43449590 AAT
1 AAT
43449593 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.31
Consensus pattern (21 bp):
AATTAACAAATACTTCATAAA
Found at i:43454334 original size:2 final size:2
Alignment explanation
Indices: 43454329--43454385 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
43454319 CTTATATATA
*
43454329 TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
43454371 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
43454386 TTGATTATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:43455105 original size:2 final size:2
Alignment explanation
Indices: 43455098--43455146 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
43455088 AATTCATGTT
43455098 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
43455140 AC AC AC A
1 AC AC AC A
43455147 TATATATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:43466918 original size:77 final size:77
Alignment explanation
Indices: 43466821--43466974 Score: 211
Period size: 77 Copynumber: 2.0 Consensus size: 77
43466811 ACCTTTCATT
* ** * *
43466821 TTTTTTAAGTCTTTTTAATTTTTTGTCTTTTTGATCCATACATTTATATTATTTGTTAAATTACT
1 TTTTTTAAATCTTTTTAATTTTTCATCTTTTTAATCCATACATTTATATTATTTGTTAAATCACT
*
43466886 TGAAATGAATGA
66 CGAAATGAATGA
* * *
43466898 TTTTTTAAAT-TTTTTAAATTTTTCATCTTTTTAATCTATATATTTGTATTATTTGTTAAATCAC
1 TTTTTTAAATCTTTTT-AATTTTTCATCTTTTTAATCCATACATTTATATTATTTGTTAAATCAC
43466962 TCGAAATGAATGA
65 TCGAAATGAATGA
43466975 AAAAATTAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
76 5 0.07
77 62 0.93
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (77 bp):
TTTTTTAAATCTTTTTAATTTTTCATCTTTTTAATCCATACATTTATATTATTTGTTAAATCACT
CGAAATGAATGA
Found at i:43466991 original size:77 final size:77
Alignment explanation
Indices: 43466837--43466992 Score: 170
Period size: 77 Copynumber: 2.0 Consensus size: 77
43466827 AAGTCTTTTT
** * * * ****
43466837 AATTTTTTGTCTTTTTGATCCATACATTTATATTATTTGTTAAATTACTTGAAATGAATGATTTT
1 AATTTTTCATCTTTTTAATCCATACATTTATATTATTTGTTAAATCACTCGAAATGAATGAAAAA
**
43466902 TTAAATTTTTTA
66 TTAAATAATTTA
* * *
43466914 AATTTTTCATCTTTTTAATCTATATATTTGTATTATTTGTTAAATCACTCGAAATGAATGAAAAA
1 AATTTTTCATCTTTTTAATCCATACATTTATATTATTTGTTAAATCACTCGAAATGAATG-AAAA
43466979 ATT-AATAATTTA
65 ATTAAATAATTTA
43466991 AA
1 AA
43466993 AATAAATAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
77 61 0.95
78 3 0.05
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (77 bp):
AATTTTTCATCTTTTTAATCCATACATTTATATTATTTGTTAAATCACTCGAAATGAATGAAAAA
TTAAATAATTTA
Found at i:43481017 original size:19 final size:19
Alignment explanation
Indices: 43480993--43481032 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
43480983 TATTTTGGTC
43480993 TTTTCCCATTTAGATTGCT
1 TTTTCCCATTTAGATTGCT
43481012 TTTTCCCATTTAGATTGCT
1 TTTTCCCATTTAGATTGCT
43481031 TT
1 TT
43481033 CTAACTCTAA
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:0.15, C:0.20, G:0.10, T:0.55
Consensus pattern (19 bp):
TTTTCCCATTTAGATTGCT
Found at i:43491108 original size:12 final size:12
Alignment explanation
Indices: 43491075--43491108 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
43491065 TAGAAATTAC
43491075 TTAACTT-GTAA
1 TTAACTTGGTAA
43491086 TTAAC-TGGTAA
1 TTAACTTGGTAA
43491097 TTAACTTGGTAA
1 TTAACTTGGTAA
43491109 ACATAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (12 bp):
TTAACTTGGTAA
Found at i:43501107 original size:15 final size:15
Alignment explanation
Indices: 43501064--43501098 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
43501054 AGGTGAGAGA
*
43501064 AGAAGAAAGAGGAGG
1 AGAAGAAAGAGAAGG
43501079 AGAAGAAAGAGAAGG
1 AGAAGAAAGAGAAGG
43501094 AGAAG
1 AGAAG
43501099 GAGAAGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (15 bp):
AGAAGAAAGAGAAGG
Found at i:43503067 original size:19 final size:20
Alignment explanation
Indices: 43503043--43503087 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
43503033 AGGAAAATGG
43503043 AGAAAAA-AAAATAGAA-AAA
1 AGAAAAAGAAAA-AGAAGAAA
*
43503062 AGAAAAAGAAGAAGAAGAAA
1 AGAAAAAGAAAAAGAAGAAA
43503082 AGAAAA
1 AGAAAA
43503088 GCTAATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (20 bp):
AGAAAAAGAAAAAGAAGAAA
Found at i:43505201 original size:101 final size:99
Alignment explanation
Indices: 43505018--43505201 Score: 242
Period size: 101 Copynumber: 1.8 Consensus size: 99
43505008 CTAGTACGCA
* * * *
43505018 TAGTAGCCTGTACATAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCTTGCACTTA
1 TAGTAGCCTGCACATAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
* *
43505083 GTACTACAGACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACCTAACCATCTGATACACG
* * * * *
43505117 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACATAGTACTACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACT
*
43505182 TAGTACTACACATGCGACCT
64 TAGTACTACACACGCGACCT
43505202 CACAATAGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 27 0.38
100 3 0.04
101 41 0.58
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACATAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTAACCATCTGATACACG
Found at i:43511121 original size:51 final size:51
Alignment explanation
Indices: 43511066--43511170 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
43511056 AAAAGGCATG
*
43511066 TTTTCATTGCCACATCAGTGAAAACACGCCCTATAAGATGCGTTTTTTTTC
1 TTTTCATTGCCACATCAATGAAAACACGCCCTATAAGATGCGTTTTTTTTC
43511117 TTTTCATTGCCACATCAATGAAAACACGCCCTATAAGATGCGTTTTTTTTC
1 TTTTCATTGCCACATCAATGAAAACACGCCCTATAAGATGCGTTTTTTTTC
43511168 TTT
1 TTT
43511171 CTCCTAAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (51 bp):
TTTTCATTGCCACATCAATGAAAACACGCCCTATAAGATGCGTTTTTTTTC
Found at i:43513377 original size:17 final size:18
Alignment explanation
Indices: 43513347--43513384 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
43513337 AATTAAAATA
*
43513347 AATTTAATTGATTTTCTT
1 AATTAAATTGATTTTCTT
43513365 AATTAAATT-ATTTTCTT
1 AATTAAATTGATTTTCTT
43513382 AAT
1 AAT
43513385 CCATTTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (18 bp):
AATTAAATTGATTTTCTT
Found at i:43513892 original size:18 final size:19
Alignment explanation
Indices: 43513859--43513897 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
43513849 AATTTGAAAC
*
43513859 AAAACAGAAAATTTTTTAA
1 AAAACAGAAAATTTTTGAA
*
43513878 AAAACCGAAAA-TTTTGAA
1 AAAACAGAAAATTTTTGAA
43513896 AA
1 AA
43513898 CAAGGGTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.26
Consensus pattern (19 bp):
AAAACAGAAAATTTTTGAA
Found at i:43517074 original size:33 final size:33
Alignment explanation
Indices: 43516997--43517074 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
43516987 ATATGTATAC
* *
43516997 GTGTAAGACCATAGCTGGGCTATGCCATCCTGA
1 GTGTAAGACCATAACTGGGCTATGCCATCATGA
* * * *
43517030 -TGATAAAACCATAACTGGGTTATGGCATTATGA
1 GTG-TAAGACCATAACTGGGCTATGCCATCATGA
43517063 GTGTAAGACCAT
1 GTGTAAGACCAT
43517075 GGCAGGGCCA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
32 2 0.06
33 32 0.89
34 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (33 bp):
GTGTAAGACCATAACTGGGCTATGCCATCATGA
Found at i:43518949 original size:17 final size:17
Alignment explanation
Indices: 43518923--43518968 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
43518913 ATGCTAAAAC
*
43518923 AATTATAAAAACATAAA
1 AATTACAAAAACATAAA
43518940 AATTACAAAAACATAAA
1 AATTACAAAAACATAAA
*
43518957 ACTTACTAAAAA
1 AATTAC-AAAAA
43518969 ACGGAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (17 bp):
AATTACAAAAACATAAA
Found at i:43523144 original size:2 final size:2
Alignment explanation
Indices: 43523095--43523131 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
43523085 ATTGCATAAT
* *
43523095 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43523132 CTTGTGTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43536194 original size:163 final size:158
Alignment explanation
Indices: 43535826--43536849 Score: 840
Period size: 163 Copynumber: 6.3 Consensus size: 158
43535816 TTTTTGTATA
*
43535826 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
* * *** * *
43535891 TTTCTATCCTTCAAAAAAAAATATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACGCGC
66 TTT-AATGCTT---TTCAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
* *
43535956 TGAGGTATTTTCAATTGATGTTTTTTCAATTTAC-GCT
126 TGAGGTATTTTCAA--AAT-TTTTTTCAAATT-CTG-T
** *
43535993 TTTCAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTCGGGGA-ACGCTGAGGTATTTTCA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCA
* * * **
43536057 A-TTAATGCTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAACCTCGGGTCACATGCCA
65 ATTTAATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCTG
43536121 AGGTATTTTCAAAATTTATTTTGCAAATTCTGT
128 AGGTATTTTCAAAATTT-TTTT-CAAATTCTGT
*
43536154 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
* * * *
43536219 AATTT-CTGCTTGTC-AAAATCAGCTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGA
64 AATTTAATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGA
*
43536282 GGTATTGTT---AA--TTTTT--AA-TATG-
129 GGTATT-TTCAAAATTTTTTTCAAATTCTGT
** *
43536304 TTTCAAAAATCAACTCATATT-CGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGGTATTGTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
*
43536368 TTTTTATATG--TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
66 --TTTA-ATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTG
* * *
43536431 AGGTATTTTC--AATTTCTGTC--CTTC---
128 AGGTATTTTCAAAATTTTTTTCAAATTCTGT
**** * * *
43536455 AAAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTTAGGACGCGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC-A
* *
43536520 TTGATGTTTTTTCAATTTACGCTTTTCAAAAATTAACTCATATTACGAGAGGTGAGTTGAGCCTC
65 ---A-----TTT-AA--T--GCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * *
43536585 GGGGA-ACACTGAGGTATTTTCAATTAATGTTTTTTCAATTTATGCT
117 -GGGACACGCTGAGGTATTTTCAA--AAT-TTTTTTCAAATTCTG-T
* * * *
43536631 TTTTAAAAATTAACTCATATTACGAGAGGTGAGTTGAGTCTCAGGACACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
*
43536696 TTT-CTGTTTTTCAATTTCTGTCCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
66 TTTAATG-----C---TT-T-T-C-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* * * * *
43536760 TCAGGACACGCTGAGGTATTTTCAATTGATGTTTTTTCAATTTATGC
115 TCGGGACACGCTGAGGTATTTTCAA--AAT-TTTTTTCAAATTCTGT
43536807 TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
43536850 TCACGTGTTG
Statistics
Matches: 708, Mismatches: 82, Indels: 123
0.78 0.09 0.13
Matches are distributed among these distances:
147 39 0.06
148 17 0.02
149 8 0.01
150 58 0.08
151 22 0.03
152 42 0.06
153 2 0.00
155 4 0.01
156 2 0.00
158 2 0.00
159 6 0.01
160 15 0.02
161 50 0.07
162 49 0.07
163 78 0.11
164 2 0.00
165 60 0.08
166 6 0.01
167 60 0.08
168 3 0.00
169 5 0.01
170 6 0.01
171 1 0.00
172 4 0.01
175 1 0.00
176 59 0.08
177 73 0.10
178 34 0.05
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (158 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
TTTAATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGG
TATTTTCAAAATTTTTTTCAAATTCTGT
Found at i:43536341 original size:75 final size:73
Alignment explanation
Indices: 43536160--43536521 Score: 437
Period size: 75 Copynumber: 4.8 Consensus size: 73
43536150 CTGTTTTCAA
43536160 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTCAATTT-
**
43536225 TGCTTG--TC
64 TTATTGTTTC
* * * *
43536233 -AAAATCAGCTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTTAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT-TCAATTTT
43536297 TAATATGTTTC
65 T-AT-TGTTTC
**
43536308 AAAAATCAACTCATATT-CGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGGTATTGTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT-TCAATTTT
43536372 TATATGTTTC
65 TAT-TGTTTC
*
43536382 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-TTTCAATTTT
* **
43536447 T-GTCCTTC
65 TATTGTTTC
* * *
43536455 AAAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTTAGGACGCGCTGAGGTATTTTCAA
1 ----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-TTTCAA
43536520 TT
61 TT
43536522 GATGTTTTTT
Statistics
Matches: 258, Mismatches: 19, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
71 4 0.02
72 56 0.22
73 6 0.02
74 26 0.10
75 89 0.34
76 17 0.07
77 60 0.23
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCAATTTTT
ATTGTTTC
Found at i:43536621 original size:15 final size:16
Alignment explanation
Indices: 43536601--43536634 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
43536591 CACTGAGGTA
43536601 TTTTCAATTAATG-TT
1 TTTTCAATTAATGCTT
*
43536616 TTTTCAATTTATGCTT
1 TTTTCAATTAATGCTT
43536632 TTT
1 TTT
43536635 AAAAATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTTCAATTAATGCTT
Found at i:43536708 original size:14 final size:14
Alignment explanation
Indices: 43536689--43536716 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43536679 CGCTGAGGTA
43536689 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
43536703 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
43536717 CCTAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:43536756 original size:89 final size:89
Alignment explanation
Indices: 43536436--43536849 Score: 523
Period size: 88 Copynumber: 4.6 Consensus size: 89
43536426 CGCTGAGGTA
* *
43536436 TTTTCAATTTCTGTCCTTCAAAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTTAGGA
1 TTTTCAATTTCTG-CCTT--AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
*
43536501 CGCGCTGAGGTATTTTCAATTGATGTT
63 CACGCTGAGGTATTTTCAATTGATGTT
*** * * *
43536528 TTTTCAATTTAC-G-CTTTTCAAAAATTAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGA-
1 TTTTCAATTT-CTGCCTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGAC
* *
43536590 ACACTGAGGTATTTTCAATTAATGTT
64 ACGCTGAGGTATTTTCAATTGATGTT
* *** * * *
43536616 TTTTCAATTTATG-CTTTTTAAAAATTAACTCATATTACGAGAGGTGAGTTGAGTCTCAGGACAC
1 TTTTCAATTTCTGCCTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
**
43536680 GCTGAGGTATTTTCAATTTCTG-T
66 GCTGAGGTATTTTCAATTGATGTT
*
43536703 TTTTCAATTTCTGTCCTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTG-CCTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
43536768 CGCTGAGGTATTTTCAATTGATGTT
65 CGCTGAGGTATTTTCAATTGATGTT
* * *
43536793 TTTTCAATTTATGCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTTCAATTTCTGCCTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
43536850 TCACGTGTTG
Statistics
Matches: 283, Mismatches: 32, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
87 16 0.06
88 131 0.46
89 108 0.38
90 16 0.06
92 11 0.04
93 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (89 bp):
TTTTCAATTTCTGCCTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTATTTTCAATTGATGTT
Found at i:43537055 original size:13 final size:14
Alignment explanation
Indices: 43537022--43537052 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43537012 TGCTGAGGTA
*
43537022 TTTTCAATTTTTGT
1 TTTTCAATTTATGT
43537036 TTTTCAATTTATGT
1 TTTTCAATTTATGT
43537050 TTT
1 TTT
43537053 CAAAAATCAA
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:0.16, C:0.06, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTTCAATTTATGT
Found at i:43537090 original size:159 final size:156
Alignment explanation
Indices: 43536813--43537113 Score: 376
Period size: 159 Copynumber: 1.9 Consensus size: 156
43536803 ATGCTTTCAA
* * * * *
43536813 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCACGTGTTGAGTCACTTTCACTTTCTG
1 AAAAATCAACTCATACTGCGAGAGGAGAGTTGAGCCTTCACATGCTGAGTCACTTTCAATTTCTG
*** * * *
43536878 TTTTTATGTTTGTTTTTTTAAATCAACTCATATTGCGGGAGGCGAGTTGAGCCTCGG-GGCGCGC
66 TTTTTATGTTTGTTTTCAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCGGCCGCACGC
43536942 TGAGGTATTTTCAATTGCTGTTTGTC
131 TGAGGTATTTTCAATTGCTGTTTGTC
*
43536968 AAAAATCAACTCATACTGCGAGAGGAGAGTTGAGCC-TCAGGACATGCTGAGGT-ATTTTCAATT
1 AAAAATCAACTCATACTGCGAGAGGAGAGTTGAGCCTTC---ACATGCTGA-GTCACTTTCAATT
* *
43537031 TTTGTTTTTCAAT-TTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC
62 TCTGTTTTT--ATGTT-TGTTTTCAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCGGC
43537095 TCGCACGCTGAGGTATTTT
124 -CGCACGCTGAGGTATTTT
43537114 TATTTTTTAT
Statistics
Matches: 123, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
154 2 0.02
155 34 0.28
157 23 0.19
158 4 0.03
159 44 0.36
161 16 0.13
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (156 bp):
AAAAATCAACTCATACTGCGAGAGGAGAGTTGAGCCTTCACATGCTGAGTCACTTTCAATTTCTG
TTTTTATGTTTGTTTTCAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCGGCCGCACGC
TGAGGTATTTTCAATTGCTGTTTGTC
Found at i:43538320 original size:37 final size:36
Alignment explanation
Indices: 43538269--43538368 Score: 154
Period size: 34 Copynumber: 2.8 Consensus size: 36
43538259 TAAGCCCCCC
43538269 AAAA-AAAAA-CTAACCCAAAAAAATAAAAAGAAGAA
1 AAAAGAAAAACCTAACCCAAAAAAA-AAAAAGAAGAA
43538304 AAAAGAAAAACCTAACCC--AAAAAAAAAAGAAGAA
1 AAAAGAAAAACCTAACCCAAAAAAAAAAAAGAAGAA
43538338 AAAAGAAAAACCTAACCCCAAAAAAAAAAAA
1 AAAAGAAAAACCTAA-CCCAAAAAAAAAAAA
43538369 ACTAAAAAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
34 26 0.43
35 12 0.20
36 5 0.08
37 17 0.28
ACGTcount: A:0.75, C:0.15, G:0.06, T:0.04
Consensus pattern (36 bp):
AAAAGAAAAACCTAACCCAAAAAAAAAAAAGAAGAA
Found at i:43538377 original size:37 final size:34
Alignment explanation
Indices: 43538306--43538378 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
43538296 AAGAAGAAAA
* *
43538306 AAGAAAAACCTAACCCAAAAAAAAAAGAAGAAAA
1 AAGAAAAACCTAACCCAAAAAAAAAAAAAAAAAA
43538340 AAGAAAAACCTAACCCCAAAAAAAAAAAAACTAAAAA
1 AAGAAAAACCTAA-CCCAAAAAAAAAAAAA--AAAAA
43538377 AA
1 AA
43538379 CCTAGCCACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 13 0.38
35 15 0.44
37 6 0.18
ACGTcount: A:0.74, C:0.16, G:0.05, T:0.04
Consensus pattern (34 bp):
AAGAAAAACCTAACCCAAAAAAAAAAAAAAAAAA
Found at i:43541068 original size:10 final size:10
Alignment explanation
Indices: 43541053--43541098 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
43541043 ATTGCATAAT
*
43541053 TATATATATA
1 TATATATGTA
43541063 TATATATGTA
1 TATATATGTA
43541073 TATATATGTA
1 TATATATGTA
*
43541083 TATCTCATGTA
1 TATAT-ATGTA
43541094 TATAT
1 TATAT
43541099 TTTAATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (10 bp):
TATATATGTA
Found at i:43543199 original size:6 final size:6
Alignment explanation
Indices: 43543190--43543224 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
43543180 TTAAAATCTT
43543190 TAAATC TAAATC TAAATC TAAATC TAAATC TAAAT
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAAT
43543225 GCAAATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
TAAATC
Found at i:43543695 original size:26 final size:26
Alignment explanation
Indices: 43543666--43543717 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
43543656 TATAATATAA
*
43543666 GATTGAGCCTTAATTTGATTAGTATC
1 GATTGAACCTTAATTTGATTAGTATC
43543692 GATTGAACCTTAATTTGATTAGTATC
1 GATTGAACCTTAATTTGATTAGTATC
43543718 TTTTCTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (26 bp):
GATTGAACCTTAATTTGATTAGTATC
Found at i:43546420 original size:38 final size:38
Alignment explanation
Indices: 43546377--43546450 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
43546367 AGTGACTAAA
*
43546377 AGTTAATATTACATAGTAC-CAACAAAACATGATCATAG
1 AGTTAATATT-CATAGTACGCAAAAAAACATGATCATAG
* *
43546415 AGTTAATATTCATAGTGCGGAAAAAAACATGATCAT
1 AGTTAATATTCATAGTACGCAAAAAAACATGATCAT
43546451 TTGTCATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 7 0.22
38 25 0.78
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (38 bp):
AGTTAATATTCATAGTACGCAAAAAAACATGATCATAG
Found at i:43551796 original size:19 final size:20
Alignment explanation
Indices: 43551769--43551813 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
43551759 TTTTTAAGCC
*
43551769 AATGTTAAATATT-ATTTAT
1 AATGATAAATATTAATTTAT
*
43551788 AATGATAAATTTTAATTTAT
1 AATGATAAATATTAATTTAT
43551808 ATATGA
1 A-ATGA
43551814 ATGTAGCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 7 0.32
21 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
AATGATAAATATTAATTTAT
Found at i:43552909 original size:31 final size:31
Alignment explanation
Indices: 43552867--43552933 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
43552857 TTAAATCTCA
*
43552867 AATACTATTATTTTGATAAATAAATAGGATT
1 AATACTATTATTTTGATAAACAAATAGGATT
*
43552898 AATATTATTATTTTGATAAACAAATAGGATT
1 AATACTATTATTTTGATAAACAAATAGGATT
43552929 AATAC
1 AATAC
43552934 AGAGAGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.40
Consensus pattern (31 bp):
AATACTATTATTTTGATAAACAAATAGGATT
Found at i:43554498 original size:3 final size:3
Alignment explanation
Indices: 43554477--43554528 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
43554467 CTATTGTTTG
* *
43554477 TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43554525 TAT T
1 TAT T
43554529 TTTAAACCGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:43555564 original size:13 final size:13
Alignment explanation
Indices: 43555532--43555571 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
43555522 GAAGATATCG
*
43555532 CACACGAGCGTGT
1 CACACGGGCGTGT
43555545 CACACGGGCGTGT
1 CACACGGGCGTGT
*
43555558 CACACGGACGTGT
1 CACACGGGCGTGT
43555571 C
1 C
43555572 CCTGCTGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:43559171 original size:39 final size:39
Alignment explanation
Indices: 43559088--43559254 Score: 271
Period size: 39 Copynumber: 4.3 Consensus size: 39
43559078 CCAGTTGTGG
* * *
43559088 AACTCGCACAAATGCCTTCGGGACTTAACCCGGGTATCAC
1 AACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATCAC
*
43559128 AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAT
1 AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
*
43559167 AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAT
1 AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
43559206 AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
*
43559245 AATTCGCACA
1 AACTCGCACA
43559255 TTCATACACA
Statistics
Matches: 121, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
39 100 0.83
40 21 0.17
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
Found at i:43567209 original size:39 final size:39
Alignment explanation
Indices: 43567126--43567245 Score: 177
Period size: 39 Copynumber: 3.1 Consensus size: 39
43567116 CCGGTTGTGG
* * *
43567126 AACTCGCACAAATGCCTTCGGGACTTAACCCGGGTATCAC
1 AACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATCAC
*
43567166 AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAT
1 AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
* *
43567205 AACTCGCACAATTGCCTTCGGGCTTAGGCTGGATATCAC
1 AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
43567244 AA
1 AA
43567246 TTCCCACATC
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 52 0.71
40 21 0.29
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (39 bp):
AACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
Found at i:43571192 original size:5 final size:5
Alignment explanation
Indices: 43571191--43571234 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
43571181 CTTTTTTATT
43571191 TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA TTTTTAA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTT-A TTTTA TTT
43571235 CTTTTGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.11
5 23 0.64
6 8 0.22
7 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:43571206 original size:10 final size:10
Alignment explanation
Indices: 43571191--43571234 Score: 63
Period size: 9 Copynumber: 4.3 Consensus size: 10
43571181 CTTTTTTATT
43571191 TTTTATTTTA
1 TTTTATTTTA
43571201 TTTTA-TTTA
1 TTTTATTTTA
43571210 TTTTATTTTA
1 TTTTATTTTA
43571220 TTTTTAATTTTA
1 -TTTT-ATTTTA
43571232 TTT
1 TTT
43571235 CTTTTGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.29
10 9 0.29
11 7 0.23
12 6 0.19
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:43571206 original size:26 final size:26
Alignment explanation
Indices: 43571185--43571239 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
43571175 GATTATCTTT
*
43571185 TTTATTTT-TTATTTTATTTTATTTAT
1 TTTATTTTATT-TTTAATTTTATTTAT
*
43571211 TTTATTTTATTTTTAATTTTATTTCT
1 TTTATTTTATTTTTAATTTTATTTAT
43571237 TTT
1 TTT
43571240 GAAAACTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTATTTTATTTTTAATTTTATTTAT
Found at i:43573140 original size:13 final size:13
Alignment explanation
Indices: 43573122--43573148 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43573112 GAAGATATCG
43573122 CACACGGGCGTGT
1 CACACGGGCGTGT
43573135 CACACGGGCGTGT
1 CACACGGGCGTGT
43573148 C
1 C
43573149 CCTGCTGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:43581024 original size:25 final size:25
Alignment explanation
Indices: 43580990--43581039 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
43580980 AATTGCATCA
43580990 AGGGTCATAATCCAGAAACCTGTAG
1 AGGGTCATAATCCAGAAACCTGTAG
*
43581015 AGGGTCATAATCTAGAAACCTGTAG
1 AGGGTCATAATCCAGAAACCTGTAG
43581040 CCTTTCCCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (25 bp):
AGGGTCATAATCCAGAAACCTGTAG
Found at i:43582830 original size:46 final size:44
Alignment explanation
Indices: 43582726--43582833 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
43582716 TGTCTTTGAC
** * * *
43582726 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
43582770 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
43582816 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
43582834 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:43588889 original size:46 final size:44
Alignment explanation
Indices: 43588785--43588892 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
43588775 TGTCTTTGAC
** * * *
43588785 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
43588829 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
43588875 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
43588893 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:43595945 original size:44 final size:45
Alignment explanation
Indices: 43595711--43596495 Score: 278
Period size: 44 Copynumber: 17.5 Consensus size: 45
43595701 TTATCATGGA
* * * * * **
43595711 AAATTTTATCTCCCTAAAGTTGCAGTAGAGCAGATT-AAAGCCAC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTAC
* * * * * * * *
43595755 AAACCTTATTTCCCTGAAATTACAGTGAAGTAGGTTAAAAATAAAC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGT-TAC
* *
43595801 AAATCTT-TCTCCCTGATGTTATAGTGGAGTAGATTGAAGATGGGTTAC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAA-A---GTTAC
* * * * **
43595849 GAATCTTATCTCCCCGAAGTTGCAATGGAGTAGATT-AAAGCCAC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTAC
* *
43595893 AAACCTTATCTCCCTGAAGTTACAGTGGAGTAGGTTGAAA-TTAC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTAC
* ** * *
43595937 AAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTG-AA-TATAGC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGT-TA-C
* ** * * * * *
43595982 AAATATTATCTCTTTGAAGTTGCAGTAGAGCAGATT-AAAGCTAT
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTAC
* * * * ** * ** * **
43596026 AAATCATATTTCCCTAAATTTGTAGAGGAACAAATT-AAAGCCAC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTAC
* * * * * * * *
43596070 AAGTTTTATCTCCCTGAATTTGCAGTGGAGCAGACTG-AAGATAGA
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTA-C
** * * * * *
43596115 AAATCTTATCTCTTTGAAGTTGCACTAGAGCAGATT-AAAGTTAT
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTAC
* * * * *
43596159 AAACCTTATCTCCCTGAAGTTTCAGTAGAGCAGATT-AAAGCTAC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTAC
* * * *
43596203 AAGTCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTG-AAGTAAC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTAC
* * * *
43596247 AAGTCCTATAC-CCCTGAAGTTGCAGTGG-GTCAGATT-AAATCTATCATGGC
1 AAATCTTAT-CTCCCTGAAGTTACAGTGGAGT-AGATTGAAA-GT-T-A---C
* * ** * * * * **
43596297 AAATCTTATGTCCTTGAAGTTGTACTAGAGCAGACTG-AAGATGGC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAG-TTAC
* * * * * **
43596342 GAATCTTATCTCTCTGAAGTTGCAATGGAGCAGATT-ACAA-CCAC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGA-AAGTTAC
* * * * * *
43596386 TAACCTTATCTCCCTAAAGTTACAATGGAGTAGGTTG-AAGTTAG
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTAC
* * * * **
43596430 AAGTCTTATCTCCTTGAAGTTACAGTGGAGCAGACT-AAAGATGGC
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAG-TTAC
* *
43596475 TAACCTTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAAGTT
43596496 GTAGGGGAGC
Statistics
Matches: 546, Mismatches: 160, Indels: 69
0.70 0.21 0.09
Matches are distributed among these distances:
43 7 0.01
44 317 0.58
45 146 0.27
46 11 0.02
47 2 0.00
48 10 0.02
49 24 0.04
50 28 0.05
51 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (45 bp):
AAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAAGTTAC
Found at i:43596040 original size:133 final size:133
Alignment explanation
Indices: 43595727--43596242 Score: 487
Period size: 133 Copynumber: 3.8 Consensus size: 133
43595717 TATCTCCCTA
* * * * *
43595727 AAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTATTTCCCTGAAATTACAGTGAAGTAGGTTA
1 AAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGATTA
** * * ** * * * *
43595792 AAAATAAACAAATCTT-TCTCCCTGATGTTATAGTGGAGTAGATTGAAGATGGGTTACGAATCTT
66 AAGCT--ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AG---CAAATCTT
***
43595856 ATCTCCCCG
125 ATCTCTTTG
* * * * *
43595865 AAGTTGCAATGGAGTAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAGTGGAGTAGGTTG
1 AAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-
* * * *
43595930 AAA-TTACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAATATAGCAAATATTATCTC
65 AAAGCTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTC
43595994 TTTG
130 TTTG
* * * * * * * ** * * *
43595998 AAGTTGCAGTAGAGCAGATTAAAGCTATAAATCATATTTCCCTAAATTTGTAGAGGAACAAATTA
1 AAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGATTA
* * * *
43596063 AAGCCACAAGTTTTATCTCCCTGAATTTGCAGTGGAGCAGACTGAAGATAGAAAATCTTATCTCT
66 AAGCTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCT
43596128 TTG
131 TTG
* ** * * *
43596131 AAGTTGCACTAGAGCAGATTAAAGTTATAAACCTTATCTCCCTGAAGTTTCAGTAGAGCAGATTA
1 AAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGATTA
* * *
43596196 AAGCTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAG
66 AAGCTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
43596243 TAACAAGTCC
Statistics
Matches: 312, Mismatches: 63, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
132 3 0.01
133 209 0.67
136 9 0.03
137 29 0.09
138 59 0.19
139 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (133 bp):
AAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGATTA
AAGCTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCT
TTG
Found at i:43598218 original size:3 final size:3
Alignment explanation
Indices: 43598210--43598235 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43598200 ATTTAGCATC
43598210 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
43598236 ATATATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:43598369 original size:3 final size:3
Alignment explanation
Indices: 43598347--43598401 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
43598337 TTAGGTATTC
* * *
43598347 TAT TAT T-T GTAT TAT CAT TAT TAA TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43598392 TAT TAT TAT T
1 TAT TAT TAT T
43598402 TTTAAATTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 1 0.02
3 42 0.95
4 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:43600162 original size:24 final size:22
Alignment explanation
Indices: 43600135--43600187 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
43600125 CTCTGATGTC
43600135 CTTTTTTCTCTTTTCTTCTCGTC-T
1 CTTTTTT-TC-TTTCTT-TCGTCGT
*
43600159 CTTTCTTTTCTTTCTTTCTTCGT
1 CTTT-TTTTCTTTCTTTCGTCGT
43600182 CTTTTT
1 CTTTTT
43600188 GGTGTTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 6 0.23
23 11 0.42
24 6 0.23
25 3 0.12
ACGTcount: A:0.00, C:0.26, G:0.04, T:0.70
Consensus pattern (22 bp):
CTTTTTTTCTTTCTTTCGTCGT
Found at i:43602166 original size:25 final size:25
Alignment explanation
Indices: 43602138--43602186 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
43602128 TTATATTTGA
*
43602138 TAGTATATCTTGAAACTGCTATAGG
1 TAGTATATCTTGAAACTACTATAGG
*
43602163 TAGTATATGTTGAAACTACTATAG
1 TAGTATATCTTGAAACTACTATAG
43602187 ATAGACTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (25 bp):
TAGTATATCTTGAAACTACTATAGG
Found at i:43609696 original size:45 final size:46
Alignment explanation
Indices: 43609640--43609732 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 46
43609630 GACCTGACTT
* * *
43609640 TACAGAATTAAATTCCTAATTTGAAGTTTTAGAAAAATACAAACAC
1 TACAGAATTAAATTCCTAATATAAAATTTTAGAAAAATACAAACAC
* * *
43609686 TACAG-ATTAAATTCCTACTATAAAATTTTCGAAAAATACAATCAC
1 TACAGAATTAAATTCCTAATATAAAATTTTAGAAAAATACAAACAC
43609731 TA
1 TA
43609733 TAGACATATT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
45 36 0.88
46 5 0.12
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.31
Consensus pattern (46 bp):
TACAGAATTAAATTCCTAATATAAAATTTTAGAAAAATACAAACAC
Found at i:43610328 original size:3 final size:3
Alignment explanation
Indices: 43610320--43610348 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
43610310 TTTTACTTTC
43610320 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
43610349 GACTACTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:43617966 original size:30 final size:31
Alignment explanation
Indices: 43617930--43617996 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
43617920 TTAACAACTT
43617930 AATGACTTAAAT-AAAACTTTTGAATAATTC
1 AATGACTTAAATGAAAACTTTTGAATAATTC
*
43617960 AATGACTTAAATGAAAACTTTTGAATAGTTC
1 AATGACTTAAATGAAAACTTTTGAATAATTC
*
43617991 ATTGAC
1 AATGAC
43617997 CATTTTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (31 bp):
AATGACTTAAATGAAAACTTTTGAATAATTC
Found at i:43621938 original size:13 final size:13
Alignment explanation
Indices: 43621920--43621945 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43621910 AGGTTTTTCT
43621920 AAAAATAGACTAA
1 AAAAATAGACTAA
43621933 AAAAATAGACTAA
1 AAAAATAGACTAA
43621946 GTTTTCTTCT
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:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAATAGACTAA
Found at i:43622175 original size:19 final size:20
Alignment explanation
Indices: 43622151--43622194 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
43622141 TTAAGATATA
* *
43622151 TATTTTTTAT-TTTTTATTT
1 TATTTTATATATTTTCATTT
43622170 TATTTTATATATTTTCATTT
1 TATTTTATATATTTTCATTT
43622190 T-TTTT
1 TATTTT
43622195 CATTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (20 bp):
TATTTTATATATTTTCATTT
Found at i:43622178 original size:28 final size:28
Alignment explanation
Indices: 43622147--43622210 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
43622137 CAAATTAAGA
43622147 TATATATTTT-TTATTTTTT-ATTTTATTT
1 TATATATTTTATT-TTTTTTCATTTT-TTT
43622175 TATATATTTTCATTTTTTTTCATTTTTTT
1 TATATATTTT-ATTTTTTTTCATTTTTTT
*
43622204 TAAATAT
1 TATATAT
43622211 AATCTAACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 10 0.31
29 15 0.47
30 7 0.22
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (28 bp):
TATATATTTTATTTTTTTTCATTTTTTT
Found at i:43625346 original size:45 final size:45
Alignment explanation
Indices: 43625297--43625390 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
43625287 GTCAGTGAAG
* *
43625297 ATAAAAGCTT-CTAATATGATATGGATAAACCACTAAATGGTGCAA
1 ATAAAAG-TTGCTAATACGATATGGATAAACCAATAAATGGTGCAA
* * * *
43625342 ATAAAAGTTGTTAATACGGTGTGGATAAACCAATAAATGGTGCAT
1 ATAAAAGTTGCTAATACGATATGGATAAACCAATAAATGGTGCAA
43625387 ATAA
1 ATAA
43625391 GCTACTAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 2 0.05
45 40 0.95
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.28
Consensus pattern (45 bp):
ATAAAAGTTGCTAATACGATATGGATAAACCAATAAATGGTGCAA
Found at i:43625539 original size:34 final size:34
Alignment explanation
Indices: 43625475--43625541 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
43625465 GGTAGCAACC
* * *
43625475 AATATGCTTATAACAATTAAATACAGTAGCAAAT
1 AATATGCTTATAAAAATCAAATACAATAGCAAAT
*
43625509 AATATGCTTATAAAAGATCAACT-CAATAGCAAA
1 AATATGCTTATAAAA-ATCAAATACAATAGCAAA
43625542 GGTCTTGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 23 0.82
35 5 0.18
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (34 bp):
AATATGCTTATAAAAATCAAATACAATAGCAAAT
Found at i:43629166 original size:16 final size:16
Alignment explanation
Indices: 43629145--43629183 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
43629135 TTTTGCCATG
*
43629145 TATTTTTCGTATCATA
1 TATTTTTAGTATCATA
*
43629161 TATTTTTTATTATCATA
1 TA-TTTTTAGTATCATA
43629178 TATTTT
1 TATTTT
43629184 GTTAACTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.64
Consensus pattern (16 bp):
TATTTTTAGTATCATA
Found at i:43630214 original size:132 final size:131
Alignment explanation
Indices: 43629695--43630227 Score: 433
Period size: 132 Copynumber: 4.0 Consensus size: 131
43629685 ATTACTCATT
* * * * * *
43629695 TAAAAATTCTTTAAAACGAAGGCGATATTCGATATTTGACAATTCGTGGAATCGTGCCCTAACGT
1 TAAAAACTCTTTAAAACGAAGGCAATATTCGATGTTTGACAATT-GGGGAATAGTGCCCTATCGT
* * * * ** * * *
43629760 GTTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCAAATAACCCTTCAAAATTTCACTCGTGTCT
65 GCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCGGAATTTCACTCATATTT
43629825 TC
130 TC
* * * *
43629827 TAAAAA-TCCTTTAAAACGAAGGCAATACTCGGTGTTTGACGATTAGGGAATCA-TGCCCTATCG
1 TAAAAACT-CTTTAAAACGAAGGCAATATTCGATGTTTGACAATTGGGGAAT-AGTGCCCTATCG
** * * * * *
43629890 TGCTGGGTTGTGATTTCTCGTTTGGTCAAAACAATCAAATATTCCTTTAGG-TTTTCACTCATGT
64 TGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCAAATA-TCCCTTCGGAATTTCACTCAT-A
*
43629954 TTTTT
127 TTTTC
* * ** * * * * * * *
43629959 TAAGAAAACACATTAAAACGAAGGTGATGTTCAATGTTTGGCAATTTGAGAATCGTGTCCTATCG
1 T-A-AAAACTCTTTAAAACGAAGGCAATATTCGATGTTTGACAATTGGGGAATAGTGCCCTATCG
* * * * ** * * *
43630024 TGCTGGGTTGCACTTTTTCATTGGTTCAAAACAATTGAAGATCCCTTCGGAAATTCACTCACATT
64 TGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCGGAATTTCACTCATATT
43630089 TTC
129 TTC
* * * * *
43630092 TAAAAACTCTTAAAAACGAAAGAAATGTTCGATGTTTGGCAATTCGGGGAATAGTGCCCTATCGT
1 TAAAAACTCTTTAAAACGAAGGCAATATTCGATGTTTGACAATT-GGGGAATAGTGCCCTATCGT
* * * * * * * *
43630157 GCTAGGTTGCAATCTCCCGTTTGTTCAAAATAATCGAATATCTCTTTGGAATTTCACTCGTATTT
65 GCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCGGAATTTCACTCATATTT
43630222 TC
130 TC
43630224 TAAA
1 TAAA
43630228 GTTAAGGCAA
Statistics
Matches: 310, Mismatches: 81, Indels: 20
0.75 0.20 0.05
Matches are distributed among these distances:
131 95 0.31
132 118 0.38
133 13 0.04
134 84 0.27
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (131 bp):
TAAAAACTCTTTAAAACGAAGGCAATATTCGATGTTTGACAATTGGGGAATAGTGCCCTATCGTG
CTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCAAATATCCCTTCGGAATTTCACTCATATTTT
C
Found at i:43633772 original size:48 final size:48
Alignment explanation
Indices: 43633709--43634088 Score: 325
Period size: 48 Copynumber: 7.6 Consensus size: 48
43633699 CAAGATAAAT
** **
43633709 ATATATATGTGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
*
43633757 ATATGTATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATATATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
* * * * * * **
43633805 ATATATATATGAGAT-ATG--TATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATG
1 ATATATATACGTGGTAAAGCCGA-ATG-GCT-AA--C--AT-G--AA-AT-ATGTATG-A-G
* *
43633864 AGATATGTATAAGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATA--TATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
* * * *
43633914 ACATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATATATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
* * * *
43633962 ACATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATATATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
* * * * *
43634010 ACATGTATATGTGGTAAATCCGAATGGCTAATATGAAATATGTATGAG
1 ATATATATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
* *
43634058 ATATGTATATGTGGTAAAGCCGAATGGCTAA
1 ATATATATACGTGGTAAAGCCGAATGGCTAA
43634089 TGAGCAATAT
Statistics
Matches: 283, Mismatches: 30, Indels: 38
0.81 0.09 0.11
Matches are distributed among these distances:
45 1 0.00
46 3 0.01
47 4 0.01
48 221 0.78
50 5 0.02
51 1 0.00
52 7 0.02
53 3 0.01
54 2 0.01
55 2 0.01
56 3 0.01
57 7 0.02
58 1 0.00
59 6 0.02
61 9 0.03
62 4 0.01
63 3 0.01
64 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (48 bp):
ATATATATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
Found at i:43633815 original size:13 final size:13
Alignment explanation
Indices: 43633794--43633828 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
43633784 CTAACATGAA
*
43633794 ATATGTATGAGAT
1 ATATATATGAGAT
43633807 ATATATATGAGAT
1 ATATATATGAGAT
*
43633820 ATGTATATG
1 ATATATATG
43633829 TGGTAAAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (13 bp):
ATATATATGAGAT
Found at i:43633821 original size:61 final size:61
Alignment explanation
Indices: 43633746--43633874 Score: 231
Period size: 61 Copynumber: 2.1 Consensus size: 61
43633736 CTAATGTGAA
*
43633746 ATATGTATGAGATATGTATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAGAT
1 ATATATATGAGATATGTATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAGAT
*
43633807 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAGAT
1 ATATATATGAGATATGTATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAGAT
*
43633868 ATGTATA
1 ATATATA
43633875 AGTGGTAAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (61 bp):
ATATATATGAGATATGTATACGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAGAT
Found at i:43634089 original size:48 final size:48
Alignment explanation
Indices: 43633807--43634107 Score: 496
Period size: 48 Copynumber: 6.3 Consensus size: 48
43633797 TGTATGAGAT
* *
43633807 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAACATGAA
1 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAA
* *
43633855 ATATGTATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAACATGAA
1 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAA
*
43633903 ATATGTATGAGACATGTATATGTGGTAAAGCCGAATGGCTAATATGAA
1 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAA
*
43633951 ATATGTATGAGACATGTATATGTGGTAAAGCCGAATGGCTAATATGAA
1 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAA
* *
43633999 ATATGTATGAGACATGTATATGTGGTAAATCCGAATGGCTAATATGAA
1 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAA
*
43634047 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGA-GCA
1 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAAT-ATGAA
*
43634095 ATATGTAGGAGAT
1 ATATGTATGAGAT
43634108 GTGTGTATAT
Statistics
Matches: 242, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
48 241 1.00
49 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (48 bp):
ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAA
Found at i:43634298 original size:37 final size:37
Alignment explanation
Indices: 43634248--43634318 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
43634238 GAAAATATAT
*
43634248 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
*
43634285 TCCGGGTAAGACCCGATAACTACGTGTGGGGATT
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATT
43634319 ATTCGAGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
Found at i:43635589 original size:40 final size:40
Alignment explanation
Indices: 43635534--43635808 Score: 428
Period size: 40 Copynumber: 6.9 Consensus size: 40
43635524 TGAGAGTTAT
43635534 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
43635574 ATATATCCGGGCTAAGTCCCGAAGGGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* * *
43635614 ATATATCCGGGCTAAGTCCCAAAGAGCATTCGTGTTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
43635654 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTCCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
43635694 ACATATCCAGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
43635734 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
43635774 ACATATCCGGGCTAA-ACCTCGAAG-GCATTCGTGCT
1 ATATATCCGGGCTAAGTCC-CGAAGAGCATTCGTGCT
43635809 GAAATTATAA
Statistics
Matches: 217, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 13 0.06
40 204 0.94
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
Found at i:43635730 original size:23 final size:23
Alignment explanation
Indices: 43635704--43635769 Score: 54
Period size: 23 Copynumber: 3.1 Consensus size: 23
43635694 ACATATCCAG
43635704 GCTAAGTCCCGAAGAGCATTCGT
1 GCTAAGTCCCGAAGAGCATTCGT
* * * *
43635727 GCT-AGT---G-ATA-TATCCGG
1 GCTAAGTCCCGAAGAGCATTCGT
43635744 GCTAAGTCCCGAAGAGCATTCGT
1 GCTAAGTCCCGAAGAGCATTCGT
43635767 GCT
1 GCT
43635770 GGTGACATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 12
0.59 0.16 0.24
Matches are distributed among these distances:
17 7 0.24
18 5 0.17
19 1 0.03
21 1 0.03
22 5 0.17
23 10 0.34
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
GCTAAGTCCCGAAGAGCATTCGT
Found at i:43639451 original size:48 final size:48
Alignment explanation
Indices: 43639387--43639772 Score: 664
Period size: 48 Copynumber: 8.0 Consensus size: 48
43639377 CAAGATAAAT
* *
43639387 ATATATATGTGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
**
43639435 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
43639483 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
43639531 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
43639579 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
43639627 ATATGTATATGTGGTAAATCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
43639675 ATATCTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
43639723 ATATGTATATGTGGTAAAGCCGAATGGCTAATGAGCAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
43639771 AT
1 AT
43639773 GTGTGTATAT
Statistics
Matches: 321, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 321 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:43639972 original size:37 final size:37
Alignment explanation
Indices: 43639913--43639983 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
43639903 GGAAATATAT
*
43639913 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
* *
43639950 TCCGGGTAAGACCGGATAACTACGTGTGGGGATT
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATT
43639984 ATTCGAGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
Found at i:43640833 original size:50 final size:50
Alignment explanation
Indices: 43640737--43640847 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 50
43640727 GGGTGTTACA
** * *
43640737 GCCCACACGGGTATGGCCAAGTTAGACGTATAGGCCATACAGGCGAGTGG
1 GCCCACACGGGTATAACCAAGTTAGACGTATAGGCCACACAAGCGAGTGG
* * * * *
43640787 GCCCACACGGGTATAACCAAGTTGGGCGTTTGGGCTACACAAGCGAGTGG
1 GCCCACACGGGTATAACCAAGTTAGACGTATAGGCCACACAAGCGAGTGG
43640837 GCCCACACGGG
1 GCCCACACGGG
43640848 CATGTCACAT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.24, C:0.26, G:0.34, T:0.15
Consensus pattern (50 bp):
GCCCACACGGGTATAACCAAGTTAGACGTATAGGCCACACAAGCGAGTGG
Found at i:43650197 original size:17 final size:17
Alignment explanation
Indices: 43650177--43650210 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43650167 GAATTTGATG
43650177 AGAGAATAATCAGACAA
1 AGAGAATAATCAGACAA
43650194 AGAGAATAATCAGACAA
1 AGAGAATAATCAGACAA
43650211 CAGCAGCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.12
Consensus pattern (17 bp):
AGAGAATAATCAGACAA
Found at i:43655943 original size:48 final size:49
Alignment explanation
Indices: 43655889--43655989 Score: 186
Period size: 48 Copynumber: 2.1 Consensus size: 49
43655879 GTATTCTTAA
*
43655889 AAATGTAAAAAAAAATTCTTATTTATATTAATAGTGTTGAAGAGAGGT-
1 AAATGTAAAAAAAAATTCTCATTTATATTAATAGTGTTGAAGAGAGGTC
43655937 AAATGTAAAAAAAAATTCTCATTTATATTAATAGTGTTGAAGAGAGGTC
1 AAATGTAAAAAAAAATTCTCATTTATATTAATAGTGTTGAAGAGAGGTC
43655986 AAAT
1 AAAT
43655990 CCTTCATGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 47 0.92
49 4 0.08
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.34
Consensus pattern (49 bp):
AAATGTAAAAAAAAATTCTCATTTATATTAATAGTGTTGAAGAGAGGTC
Found at i:43657563 original size:92 final size:92
Alignment explanation
Indices: 43657444--43657616 Score: 240
Period size: 92 Copynumber: 1.9 Consensus size: 92
43657434 ATGTAGTATG
* * * **
43657444 AACTGCCAGATCAGATAATAGTACGTAGCATAGCTAACGTCCCTATAGTATGGTGCAATGCGGTA
1 AACTGCCAGATCAGATAATAGTACGTAGCATAGCTAACGTACATACAGTAAAGTGCAATGCGGTA
43657509 ATCCGCTATACCGATAGGTCGCAATAA
66 ATCCGCTATACCGATAGGTCGCAATAA
* * * * *
43657536 AACTGCCAGTTCAG-TCAATGGTACGTAGCGTAGCTAATGTACATGCAGTAAAGTGCAATGCGGT
1 AACTGCCAGATCAGAT-AATAGTACGTAGCATAGCTAACGTACATACAGTAAAGTGCAATGCGGT
43657600 AATCCGCTATACCGATA
65 AATCCGCTATACCGATA
43657617 TGATGTCACC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
91 1 0.01
92 69 0.99
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (92 bp):
AACTGCCAGATCAGATAATAGTACGTAGCATAGCTAACGTACATACAGTAAAGTGCAATGCGGTA
ATCCGCTATACCGATAGGTCGCAATAA
Found at i:43659753 original size:92 final size:91
Alignment explanation
Indices: 43659633--43659806 Score: 233
Period size: 92 Copynumber: 1.9 Consensus size: 91
43659623 ATTAAGCTCC
* * *
43659633 TCTTTTTTTTTCACTCAATTGAGCACTTGAATTTTAAAAATGCATAAAAAAGACTATC-AAACTT
1 TCTTCTTTTTTCACTCAATTGAGCACTTGAACTTTAAAAATGCATAAAAAAGACCATCAAAACTT
43659697 CATCAAAAAAAGCAATTAAACCCTTGCT
66 -ATC-AAAAAAGCAATTAAACCCTTGCT
* * * * * *
43659725 TCTTCTTTTTTCACTCGATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAACTT
1 TCTTCTTTTTTCACTCAATTGAGCACTTGAACTTTAAAAATGCATAAAAAAGACCATCAAAACTT
*
43659790 TTCAAAAAAGCAATTAA
66 ATCAAAAAAGCAATTAA
43659807 GCCCCTACTC
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
91 14 0.20
92 51 0.72
93 6 0.08
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (91 bp):
TCTTCTTTTTTCACTCAATTGAGCACTTGAACTTTAAAAATGCATAAAAAAGACCATCAAAACTT
ATCAAAAAAGCAATTAAACCCTTGCT
Found at i:43659874 original size:39 final size:39
Alignment explanation
Indices: 43659827--43659932 Score: 110
Period size: 39 Copynumber: 2.8 Consensus size: 39
43659817 TTACTAAAAA
* *
43659827 TTAG-AAAAAATAATAAATTTTAGAAAAATTATTAAATT
1 TTAGTAAAAAATAATAAATTTTATAAAAATTAGTAAATT
* * **
43659865 TTAGTAAAAAAT-TTAAAATTTATTAAAAATTAGTATTTT
1 TTAGTAAAAAATAATAAATTTTA-TAAAAATTAGTAAATT
* *
43659904 TTA-TAAAAATTAAAAAATTTTATAAAAAT
1 TTAGTAAAAAATAATAAATTTTATAAAAAT
43659933 CATAAAAATA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
38 26 0.47
39 29 0.53
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (39 bp):
TTAGTAAAAAATAATAAATTTTATAAAAATTAGTAAATT
Found at i:43659924 original size:19 final size:19
Alignment explanation
Indices: 43659831--43659932 Score: 91
Period size: 19 Copynumber: 5.3 Consensus size: 19
43659821 TAAAAATTAG
* *
43659831 AAAAAATAATAAATTTTAG
1 AAAAATTAATAAATTTTAT
*
43659850 AAAAATTATTAAATTTTAGT
1 AAAAATTAATAAATTTTA-T
*
43659870 AAAAAATT--TAAAATTTATT
1 -AAAAATTAATAAATTTTA-T
* **
43659889 AAAAATTAGTATTTTTTAT
1 AAAAATTAATAAATTTTAT
*
43659908 AAAAATTAAAAAATTTTAT
1 AAAAATTAATAAATTTTAT
43659927 AAAAAT
1 AAAAAT
43659933 CATAAAAATA
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
18 7 0.10
19 47 0.70
20 6 0.09
21 7 0.10
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
AAAAATTAATAAATTTTAT
Found at i:43660455 original size:20 final size:20
Alignment explanation
Indices: 43660430--43660467 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43660420 GTTTATTCGC
*
43660430 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
43660450 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
43660468 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:43662110 original size:28 final size:28
Alignment explanation
Indices: 43662078--43662146 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
43662068 GCGTAGATCA
43662078 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
43662106 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
43662134 CGATA-TACCCCTA
1 CGAAATTACCCCTA
43662147 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:43666887 original size:20 final size:20
Alignment explanation
Indices: 43666862--43666899 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43666852 GTTTATTCGC
*
43666862 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
43666882 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
43666900 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:43668548 original size:28 final size:28
Alignment explanation
Indices: 43668516--43668584 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
43668506 GCGTAGATCA
43668516 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
43668544 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
43668572 CGATA-TACCCCTA
1 CGAAATTACCCCTA
43668585 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:43671007 original size:43 final size:39
Alignment explanation
Indices: 43670959--43671089 Score: 142
Period size: 38 Copynumber: 3.3 Consensus size: 39
43670949 TTTATCAAAT
*
43670959 AGTCCAACAGTACAAAAATAGTGAACATGTTTAACATGTATTC
1 AGTCCAACAGTA-AAAAATA-T--ACATGCTTAACATGTATTC
* *
43671002 AGTCCAACAGT-AGAAATATACATGCTTAACATGTATTT
1 AGTCCAACAGTAAAAAATATACATGCTTAACATGTATTC
* *
43671040 AGTTCAACAGT-AGAAATATACATGCTTAACATGTAATT-
1 AGTCCAACAGTAAAAAATATACATGCTTAACATGT-ATTC
*
43671078 AGTTCAACAGTA
1 AGTCCAACAGTA
43671090 GCAGTAGGCA
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
38 61 0.74
39 3 0.04
40 1 0.01
41 6 0.07
43 11 0.13
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (39 bp):
AGTCCAACAGTAAAAAATATACATGCTTAACATGTATTC
Found at i:43671110 original size:38 final size:38
Alignment explanation
Indices: 43670983--43671090 Score: 173
Period size: 38 Copynumber: 2.8 Consensus size: 38
43670973 AAAATAGTGA
* *
43670983 ACATGTTTAACATGT-ATTCAGTCCAACAGTAGAAATAT
1 ACATGCTTAACATGTAATT-AGTTCAACAGTAGAAATAT
*
43671021 ACATGCTTAACATGTATTTAGTTCAACAGTAGAAATAT
1 ACATGCTTAACATGTAATTAGTTCAACAGTAGAAATAT
43671059 ACATGCTTAACATGTAATTAGTTCAACAGTAG
1 ACATGCTTAACATGTAATTAGTTCAACAGTAG
43671091 CAGTAGGCAT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
38 63 0.97
39 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (38 bp):
ACATGCTTAACATGTAATTAGTTCAACAGTAGAAATAT
Found at i:43672775 original size:18 final size:18
Alignment explanation
Indices: 43672762--43672796 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43672752 TTAATTTTCT
*
43672762 AGGTTTTTGGAATTTTTG
1 AGGTTTTAGGAATTTTTG
43672780 AGGTTTTAGGAATTTTT
1 AGGTTTTAGGAATTTTT
43672797 TTGAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (18 bp):
AGGTTTTAGGAATTTTTG
Found at i:43673462 original size:17 final size:16
Alignment explanation
Indices: 43673431--43673469 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
43673421 TATAAATAAA
*
43673431 TATATATATTAAAAAT
1 TATAAATATTAAAAAT
*
43673447 TGTAAATATTATAAAAT
1 TATAAATATTA-AAAAT
43673464 TATAAA
1 TATAAA
43673470 ACAAAGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TATAAATATTAAAAAT
Found at i:43673531 original size:2 final size:2
Alignment explanation
Indices: 43673524--43673549 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43673514 TCACACGATC
43673524 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
43673550 TACGCATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43674027 original size:22 final size:22
Alignment explanation
Indices: 43673985--43674027 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
43673975 GGTTTTACAA
*
43673985 AGATTTAAATATTTTAATTTTG
1 AGATTTAAATATTCTAATTTTG
*
43674007 AGATATTAAAT-TTCTATTTTT
1 AGAT-TTAAATATTCTAATTTT
43674028 TTCATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (22 bp):
AGATTTAAATATTCTAATTTTG
Found at i:43674943 original size:3 final size:3
Alignment explanation
Indices: 43674937--43674965 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
43674927 TTATTTTTCT
43674937 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
43674966 TCTATGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:43675305 original size:21 final size:22
Alignment explanation
Indices: 43675262--43675305 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
43675252 TGAAACGTTT
* *
43675262 GTCTATTTTGGTATAAAACTTTA
1 GTCTATTTT-GTAGAAAAATTTA
43675285 GTCTATTTT-TAGAAAAATTTA
1 GTCTATTTTGTAGAAAAATTTA
43675306 CGAGTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (22 bp):
GTCTATTTTGTAGAAAAATTTA
Found at i:43677757 original size:21 final size:21
Alignment explanation
Indices: 43677733--43677775 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
43677723 TCATTTTAGA
43677733 TTAATAC-CTAATTATATTATT
1 TTAATACTCTAATTA-ATTATT
*
43677754 TTAATACTTTAATTAATTATT
1 TTAATACTCTAATTAATTATT
43677775 T
1 T
43677776 ATGATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAATACTCTAATTAATTATT
Found at i:43679413 original size:20 final size:20
Alignment explanation
Indices: 43679388--43679429 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
43679378 CAGGATATTC
43679388 TATGCATATATAT-ATATATA
1 TATGCATATATATCATA-ATA
*
43679408 TATGCATATGTATCATAATA
1 TATGCATATATATCATAATA
43679428 TA
1 TA
43679430 ATTTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (20 bp):
TATGCATATATATCATAATA
Found at i:43682162 original size:16 final size:17
Alignment explanation
Indices: 43682141--43682174 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
43682131 AAAAATTTAC
43682141 TATATTTAA-TTTAATT
1 TATATTTAATTTTAATT
43682157 TATATTTAATTTTAATT
1 TATATTTAATTTTAATT
43682174 T
1 T
43682175 GTTACAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATTTAATTTTAATT
Found at i:43682577 original size:2 final size:2
Alignment explanation
Indices: 43682570--43682607 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
43682560 ATCTCTTTGC
43682570 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
43682608 TGTTGTAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43689220 original size:26 final size:26
Alignment explanation
Indices: 43689191--43689298 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
43689181 TGGTACAAAT
43689191 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
43689217 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
43689243 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
43689269 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
43689295 TGAT
1 TGAT
43689299 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:43694137 original size:17 final size:18
Alignment explanation
Indices: 43694115--43694156 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
43694105 ATTCAAGGTG
43694115 TAATTAATTTAAA-TT-TT
1 TAATTAA-TTAAATTTATT
43694132 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
43694150 TAATTAA
1 TAATTAA
43694157 AAATATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
18 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:43694152 original size:14 final size:14
Alignment explanation
Indices: 43694115--43694157 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
43694105 ATTCAAGGTG
43694115 TAATTAATTTAAATTTT
1 TAATTAA-TTAAA--TT
43694132 TAATTAATTAAATT
1 TAATTAATTAAATT
*
43694146 TATTTAATTAAA
1 TAATTAATTAAA
43694158 AATATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 13 0.52
16 5 0.20
17 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTAATTAAATT
Found at i:43696333 original size:22 final size:21
Alignment explanation
Indices: 43696298--43696373 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
43696288 AAAATGTATC
* *
43696298 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
43696319 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
43696342 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
43696361 TGC-AATCATATCT
1 TACAAATCATATCT
43696374 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:43696390 original size:35 final size:37
Alignment explanation
Indices: 43696327--43696424 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
43696317 ATTACAAAAT
43696327 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
43696363 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
43696398 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
43696425 TGAAGATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:43696432 original size:17 final size:19
Alignment explanation
Indices: 43696334--43696424 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
43696324 AATCATATCT
43696334 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
43696353 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
43696371 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
43696388 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
43696407 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
43696425 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:43696581 original size:21 final size:20
Alignment explanation
Indices: 43696544--43696582 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
43696534 TGGACTTTGA
**
43696544 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
43696564 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
43696583 TCTGGGCCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:43696837 original size:45 final size:45
Alignment explanation
Indices: 43696788--43696929 Score: 232
Period size: 45 Copynumber: 3.2 Consensus size: 45
43696778 TGCTATATTT
43696788 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTTC
1 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTTC
* *
43696833 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGCT-TCTTC
1 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTTC
* * *
43696877 AATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTT
1 GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTTC
43696922 GATCTGCT
1 GATCTGCT
43696930 TCGATGTAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 40 0.45
45 48 0.55
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (45 bp):
GATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTTC
Found at i:43698445 original size:29 final size:29
Alignment explanation
Indices: 43698411--43698571 Score: 198
Period size: 29 Copynumber: 5.6 Consensus size: 29
43698401 TACTCGATTT
** * *
43698411 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* *** * *
43698440 CGCACACATAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
43698469 CACACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
43698498 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
43698527 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
43698556 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
43698572 ATCTCGTCAC
Statistics
Matches: 114, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 112 0.98
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:43700423 original size:78 final size:78
Alignment explanation
Indices: 43700291--43700806 Score: 757
Period size: 78 Copynumber: 6.5 Consensus size: 78
43700281 GGATGTCACA
43700291 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
1 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT-C
*
43700356 A-ATCTGTTATGTC
65 AGATCTGCTATGTC
*
43700369 TTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCA
1 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCA
*
43700434 GATCTGCTGTGTC
66 GATCTGCTATGTC
*
43700447 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTTCTTCGATGTAAACAC
1 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGA---TC-T-GCT-T---CA-
43700512 ATGAAGGTCAGATCTGCTATGTC
56 ATGAAGGTCAGATCTGCTATGTC
* *
43700535 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTTCAATGAAGGTTA
1 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCA
* *
43700600 GATCTGTTGTGTC
66 GATCTGCTATGTC
* *
43700613 TTCAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTTA
1 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCA
*
43700678 GATCTGCTGTGTC
66 GATCTGCTATGTC
* *
43700691 TTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAAGTCA
1 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCA
*
43700756 AATCTGCTATGTC
66 GATCTGCTATGTC
* * *
43700769 TTCGATCTGCTCTCCGTCGAATA-TGTAGATGCCAAATC
1 TTCGATCTGCTCCCCGTCTAATACAG-AGATGCCAAATC
43700807 TGTTTCTTTG
Statistics
Matches: 402, Mismatches: 24, Indels: 24
0.89 0.05 0.05
Matches are distributed among these distances:
77 3 0.01
78 316 0.79
79 2 0.00
81 2 0.00
82 2 0.00
83 4 0.01
84 2 0.00
85 2 0.00
87 2 0.00
88 67 0.17
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (78 bp):
TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCA
GATCTGCTATGTC
Found at i:43700720 original size:244 final size:244
Alignment explanation
Indices: 43700291--43700744 Score: 820
Period size: 244 Copynumber: 1.9 Consensus size: 244
43700281 GGATGTCACA
43700291 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
1 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
**
43700356 AATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
66 AATCTGTTATGTCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
43700421 TCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCA
131 TCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCA
*
43700486 TCTTGGATCTTCTTCGATGTAAACACATGAAGGTCAGATCTGCTATGTC
196 TCTTGGATCTGCTTCGATGTAAACACATGAAGGTCAGATCTGCTATGTC
* *
43700535 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTTCAATGAAGGT-T
1 TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
*
43700599 AGATCTGTTGTGTCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGC
66 A-ATCTGTTATGTCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGC
* *
43700664 TTCAATGAAGGTTAGATCTGCTGTGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
130 TTCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
43700729 ATCTTGGATCTGCTTC
195 ATCTTGGATCTGCTTC
43700745 AATGAAAGTC
Statistics
Matches: 201, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
243 1 0.00
244 200 1.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (244 bp):
TTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
AATCTGTTATGTCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
TCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCA
TCTTGGATCTGCTTCGATGTAAACACATGAAGGTCAGATCTGCTATGTC
Found at i:43706763 original size:2 final size:2
Alignment explanation
Indices: 43706756--43706786 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
43706746 ATTGAAAGGG
43706756 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43706787 GTATTAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43712664 original size:13 final size:13
Alignment explanation
Indices: 43712646--43712670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43712636 GCAATAAGGT
43712646 AACAAACATATGC
1 AACAAACATATGC
43712659 AACAAACATATG
1 AACAAACATATG
43712671 TAAAAATAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (13 bp):
AACAAACATATGC
Found at i:43713393 original size:16 final size:17
Alignment explanation
Indices: 43713372--43713405 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43713362 GATATGATAC
*
43713372 TAAAAT-TATTAAAAAA
1 TAAAATATATAAAAAAA
43713388 TAAAATATATAAAAAAA
1 TAAAATATATAAAAAAA
43713405 T
1 T
43713406 TCAAGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATATATAAAAAAA
Found at i:43713693 original size:22 final size:21
Alignment explanation
Indices: 43713658--43713733 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
43713648 AAAAGGTATC
* *
43713658 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
43713679 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
43713702 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
43713721 TGC-AATCATATCT
1 TACAAATCATATCT
43713734 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:43713750 original size:35 final size:37
Alignment explanation
Indices: 43713687--43713784 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
43713677 ATTACAAAAT
43713687 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
43713723 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
43713758 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
43713785 TGAAGATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:43713792 original size:17 final size:19
Alignment explanation
Indices: 43713694--43713784 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
43713684 AATCATATCT
43713694 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
43713713 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
43713731 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
43713748 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
43713767 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
43713785 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:43713941 original size:21 final size:20
Alignment explanation
Indices: 43713903--43713942 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
43713893 TTGGACTTCG
**
43713903 TTTTTTTTTTGGGTTTATTA
1 TTTTTTTTTTGGACTTATTA
43713923 TTTTTGTTTTTGGACTTATT
1 TTTTT-TTTTTGGACTTATT
43713943 TCTGGGCCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTTGGACTTATTA
Found at i:43718989 original size:49 final size:49
Alignment explanation
Indices: 43718936--43719142 Score: 389
Period size: 49 Copynumber: 4.2 Consensus size: 49
43718926 TTATTCGTTG
43718936 GAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
43718985 GAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
43719034 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
43719083 GAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
43719132 G-ATATGTATAT
1 GAAAATGTATAT
43719143 GTGGTAAAGC
Statistics
Matches: 155, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
48 9 0.06
49 146 0.94
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (49 bp):
GAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
Found at i:43719264 original size:37 final size:37
Alignment explanation
Indices: 43719223--43719295 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
43719213 TTCTGGGTGA
43719223 GACCCGATGACTACATGTGGAGATTATGTCCGGGTAC
1 GACCCGATGACTACATGTGGAGATTATGTCCGGGTAC
*
43719260 GACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
1 GACCCGATGACTACATGTGGAGATTATGTCCGGGTA
43719296 AGACTTCGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (37 bp):
GACCCGATGACTACATGTGGAGATTATGTCCGGGTAC
Found at i:43721224 original size:40 final size:40
Alignment explanation
Indices: 43721180--43721490 Score: 471
Period size: 40 Copynumber: 7.8 Consensus size: 40
43721170 GAGAATTGAG
* *
43721180 AATGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AATGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
43721220 AATGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AATGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* *
43721260 AGTGATATATCCGGGCTAA-ATCCGAAGAGCATTCGTGCT
1 AATGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
43721299 AATGATATATCCGGGCTAAATTCCGAAGAGCATTCGTGCT
1 AATGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
43721339 AATGATATATCCGGGCTAAATTCCGAAGAGCATTCGTGCT
1 AATGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* *
43721379 AATGATATATCCAGGCTAAATTCCGAAGAGCATTCGTGCT
1 AATGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* * *
43721419 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AATGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* * * *
43721459 AGTGATGTATCCGGGCTAGGTCCCGAAGAGCA
1 AATGATATATCCGGGCTAAGTTCCGAAGAGCA
43721491 ATCATGCTGG
Statistics
Matches: 255, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
39 37 0.15
40 218 0.85
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (40 bp):
AATGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
Found at i:43721396 original size:119 final size:120
Alignment explanation
Indices: 43721180--43721490 Score: 516
Period size: 119 Copynumber: 2.6 Consensus size: 120
43721170 GAGAATTGAG
43721180 AATGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAATGATGTATCCGGGCTAAGTTCCG
1 AATGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAATGATGTATCCGGGCTAAGTTCCG
* *
43721245 AAGAGCATTCGTGCTAGTGATATATCCGGGCTAAA-TCCGAAGAGCATTCGTGCT
66 AAGAGCATTCGTGCTAATGATATATCCAGGCTAAATTCCGAAGAGCATTCGTGCT
* * * * *
43721299 AATGATATATCCGGGCTAAATTCCGAAGAGCATTCGTGCTAATGATATATCCGGGCTAAATTCCG
1 AATGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAATGATGTATCCGGGCTAAGTTCCG
43721364 AAGAGCATTCGTGCTAATGATATATCCAGGCTAAATTCCGAAGAGCATTCGTGCT
66 AAGAGCATTCGTGCTAATGATATATCCAGGCTAAATTCCGAAGAGCATTCGTGCT
* * * *
43721419 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAGGTCCCG
1 AATGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAATGATGTATCCGGGCTAAGTTCCG
43721484 AAGAGCA
66 AAGAGCA
43721491 ATCATGCTGG
Statistics
Matches: 175, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
119 93 0.53
120 82 0.47
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (120 bp):
AATGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAATGATGTATCCGGGCTAAGTTCCG
AAGAGCATTCGTGCTAATGATATATCCAGGCTAAATTCCGAAGAGCATTCGTGCT
Found at i:43725057 original size:49 final size:49
Alignment explanation
Indices: 43724999--43725207 Score: 366
Period size: 49 Copynumber: 4.2 Consensus size: 49
43724989 TTATTCGTTG
*
43724999 GAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
43725048 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
43725097 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
43725146 GAAAATGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 G-AAA-GTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
43725197 GATA-TGTATAT
1 GAAAGTGTATAT
43725208 GTGGTAAAGC
Statistics
Matches: 154, Mismatches: 4, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
48 6 0.04
49 98 0.64
50 5 0.03
51 45 0.29
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.32
Consensus pattern (49 bp):
GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
Found at i:43725111 original size:98 final size:99
Alignment explanation
Indices: 43725001--43725207 Score: 373
Period size: 100 Copynumber: 2.1 Consensus size: 99
43724991 ATTCGTTGGA
*
43725001 AAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAA-GTGTATATATAT
1 AAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATAT
43725064 GTGATAAGGCCTAATGGCCGATGTGATGAATGTG
66 GTGATAAGGCCTAATGGCCGATGTGATGAATGTG
43725098 AAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATA
1 AAA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATA
43725163 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
65 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
*
43725198 ATATGTATAT
1 AAATGTATAT
43725208 GTGGTAAAGC
Statistics
Matches: 105, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
97 3 0.03
98 45 0.43
99 10 0.10
100 47 0.45
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.32
Consensus pattern (99 bp):
AAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATAT
GTGATAAGGCCTAATGGCCGATGTGATGAATGTG
Found at i:43725232 original size:44 final size:42
Alignment explanation
Indices: 43725141--43725234 Score: 107
Period size: 44 Copynumber: 2.2 Consensus size: 42
43725131 CGATGTGATG
* *
43725141 AATGTGAAAATGTATATATATATGTGATAAGGCCTAATGGCC
1 AATGTGAAAATGTATATATATATGTGATAAAGCCGAATGGCC
* * * * *
43725183 GATGTGATGAATGTGATATGTATATGTGGTAAAGCCGAATGGCT
1 AATGTGA-AAATGT-ATATATATATGTGATAAAGCCGAATGGCC
43725227 AATGTGAA
1 AATGTGAA
43725235 TGTTGTAACA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
42 6 0.15
43 5 0.12
44 30 0.73
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (42 bp):
AATGTGAAAATGTATATATATATGTGATAAAGCCGAATGGCC
Found at i:43725329 original size:37 final size:36
Alignment explanation
Indices: 43725274--43725360 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 36
43725264 AACTTGGAAA
43725274 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATGTT-CGGGT-AGACCCGATGACTACGTGTGGAGAT
43725312 TATGTTCGGGTATGACCCGATGACTACGTGTGGAGAT
1 TATGTTCGGGTA-GACCCGATGACTACGTGTGGAGAT
*
43725349 TATGTCCGGGTA
1 TATGTTCGGGTA
43725361 AGACTTCGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 1 0.02
37 40 0.85
38 6 0.13
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (36 bp):
TATGTTCGGGTAGACCCGATGACTACGTGTGGAGAT
Found at i:43727821 original size:23 final size:24
Alignment explanation
Indices: 43727790--43727845 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
43727780 ACGTAACTCC
*
43727790 ATGTGATGCCTT-TGTGGCGTACT
1 ATGTAATGCCTTGTGTGGCGTACT
* *
43727813 CTGTAATG-CTTGTGTGGCGTATT
1 ATGTAATGCCTTGTGTGGCGTACT
43727836 ATGTAATGCC
1 ATGTAATGCC
43727846 CTTGAGGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.11
23 23 0.85
24 1 0.04
ACGTcount: A:0.16, C:0.16, G:0.29, T:0.39
Consensus pattern (24 bp):
ATGTAATGCCTTGTGTGGCGTACT
Found at i:43728655 original size:25 final size:25
Alignment explanation
Indices: 43728626--43728676 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
43728616 TCAAGTATGG
*
43728626 AATTATCTGCCAAGGACAGAGAAGA
1 AATTATCTGCCAAAGACAGAGAAGA
* *
43728651 AATTATTTGCCAAAGATAGAGAAGA
1 AATTATCTGCCAAAGACAGAGAAGA
43728676 A
1 A
43728677 GCCAAAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.20
Consensus pattern (25 bp):
AATTATCTGCCAAAGACAGAGAAGA
Done.