Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 60 of 150
Found at i:17923217 original size:49 final size:50
Alignment explanation
Indices: 17923158--17923260 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 50
17923148 ATAGTTCTTT
* *
17923158 TATTTTACATTAATTAGAATAAGGTTTTTCAACCT-TACT-ACACTTCATC
1 TATTTGACATTAATTAGAACAAGGTTTTTCAACCTAT-CTGACACTTCATC
* *
17923207 TATTTGACATTAATTAGAACAAGGTTTTTCAATCTATTTGACACTTCATC
1 TATTTGACATTAATTAGAACAAGGTTTTTCAACCTATCTGACACTTCATC
17923257 TATT
1 TATT
17923261 CATATTGTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
49 33 0.69
50 15 0.31
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.44
Consensus pattern (50 bp):
TATTTGACATTAATTAGAACAAGGTTTTTCAACCTATCTGACACTTCATC
Found at i:17925436 original size:25 final size:25
Alignment explanation
Indices: 17925407--17925523 Score: 146
Period size: 25 Copynumber: 4.7 Consensus size: 25
17925397 TCCAACCCAC
* *
17925407 AGCTCGTGTAAGCATACCGATTTAT
1 AGCTCGTGTGAGCATACCGATTCAT
* * *
17925432 AGCTCGTGAGAGAATACCGA-TCTAC
1 AGCTCGTGTGAGCATACCGATTC-AT
*
17925457 AGCTCGAGTGAGCATACCGATTCAT
1 AGCTCGTGTGAGCATACCGATTCAT
*
17925482 AGCTCGTATGAGCATACCGATTCAT
1 AGCTCGTGTGAGCATACCGATTCAT
*
17925507 AGCTCGTATGAGCATAC
1 AGCTCGTGTGAGCATAC
17925524 ATGTACATGA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
24 1 0.01
25 76 0.96
26 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (25 bp):
AGCTCGTGTGAGCATACCGATTCAT
Found at i:17932025 original size:3 final size:3
Alignment explanation
Indices: 17932017--17932087 Score: 61
Period size: 3 Copynumber: 22.7 Consensus size: 3
17932007 ATGTAGAAAC
* * ** * *
17932017 AAT AAT AAT AAT AAT AAC ATT AAT AAT AAT AGC AAT AAA AAC AAT GAACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AA-T
17932067 AAAT AAT AAT AAT AAT AAT AA
1 -AAT AAT AAT AAT AAT AAT AA
17932088 AGGGACTAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
3 48 0.89
4 3 0.06
5 3 0.06
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:17933651 original size:96 final size:94
Alignment explanation
Indices: 17933394--17934135 Score: 402
Period size: 99 Copynumber: 7.5 Consensus size: 94
17933384 AGTCCCGTTG
* * * *
17933394 AGGAAATAAGATTCGCCGTTGCGGCTTCAATCTTCTAGACTGCAATGTTGGGGAAGCGAGATTCG
1 AGGAAATAAGATTCGCCGTTGTGGCTTCAATCTT-TA-ATTGCAA---TGGGGAAGTGAGACTCG
* * *
17933459 CCATCGTAGCTTCAATCTGTTCCACTACACCGCA
61 CCGTTGTAGCTTCAATCTATTCCACTACACCGCA
* *
17933493 AGGAAATGAGATTCGCCGTTGTGGCTTCGATC--T-ATTGCAATGGGGAAGTGAGACTCGCCGTT
1 AGGAAATAAGATTCGCCGTTGTGGCTTCAATCTTTAATTGCAATGGGGAAGTGAGACTCGCCGTT
* * * *
17933555 GTAGCTTCAATCTATTCCGCTGCATCGCC
66 GTAGCTTCAATCTATTCCACTACACCGCA
* * * *
17933584 TGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCG
1 AGGAAATAAGATTCGCCGTTGTGGCTTCAATC-TTT-AATTGCAATGGGGAAGTGAGACTCGCCG
* * *
17933649 TTGTAGTTTCAATCGTTGTAGCTTCAATCTATTCCACTGCA
64 TTGTAGCTTCAATC----TA--TTCCA-CTA---CACCGCA
* * *
17933690 ATGCCAGAAGGTAAGATTCACCGTTGTGGCTTCGATCTTTTAAATTGCAATGTCGGGGAAGTGAG
1 A-G---GAA-ATAAGATTCGCCGTTGTGGCTTCAATC-TTT-AATTGCAA--T-GGGGAAGTGAG
* * * * * **
17933755 ATTCACTGTTGTAGCTTCAATCTGTTCCACTGCAATGC-
56 ACTCGCCGTTGTAGCTTCAATCTATTCCACTACACCGCA
* * * *
17933793 A-GAAGGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGTAATGTCGGGGAAGTGAGATTC
1 AGGAA-ATAAGATTCGCCGTTGTGGCTTCAATC-TTT-AATTGCAA--T-GGGGAAGTGAGACTC
* * * * *
17933857 GCTGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCA
60 GCCGTTGTAGCTTCAATCTATTCCACTACACCG-CA
* * * ** *
17933893 GAGG--GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTC
1 -AGGAAATAAGATTCGCCGTTGTGGCTTCAATC-TTT-AATTGCAA--T-GGGGAAGTGAGACTC
* * * * * *
17933956 GCTGTTGTAGCTTCAATTTGTTCCGCTGCACCTGCTT
60 GCCGTTGTAGCTTCAATCTATTCCACTACACC-GC-A
* * *
17933993 AGG-AATAAGATTTGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGGAAGTGAGATTCGC
1 AGGAAATAAGATTCGCCGTTGTGGCTTCAATC-TTTAATTGCAATG---GGGAAGTGAGACTCGC
* * * * ** *
17934057 CATTGTAGCTTCAATCTGTTCCGCTGCATTGCT
62 CGTTGTAGCTTCAATCTATTCCACTACACCGCA
* * * * *
17934090 TGGAAGTAAGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAAT
1 AGGAAATAAGATTCGCCGTTGTGGCTTCAATC-TTT-AATTGCAAT
17934136 CTATGGTTAA
Statistics
Matches: 539, Mismatches: 69, Indels: 70
0.79 0.10 0.10
Matches are distributed among these distances:
91 68 0.13
94 7 0.01
96 42 0.08
97 4 0.01
98 120 0.22
99 173 0.32
100 29 0.05
101 1 0.00
102 4 0.01
103 3 0.01
104 5 0.01
106 4 0.01
107 3 0.01
108 4 0.01
110 4 0.01
111 38 0.07
113 1 0.00
114 29 0.05
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (94 bp):
AGGAAATAAGATTCGCCGTTGTGGCTTCAATCTTTAATTGCAATGGGGAAGTGAGACTCGCCGTT
GTAGCTTCAATCTATTCCACTACACCGCA
Found at i:17933660 original size:47 final size:47
Alignment explanation
Indices: 17933526--17933662 Score: 132
Period size: 49 Copynumber: 2.9 Consensus size: 47
17933516 GCTTCGATCT
**
17933526 ATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTATTCC
1 ATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTATTAA
** * * * * * * *
17933573 GCTGC-ATCGCCTGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTAA
1 ATTGCAAT-G--GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTATTAA
*
17933622 ATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGTTTCAATC
1 ATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATC
17933663 GTTGTAGCTT
Statistics
Matches: 66, Mismatches: 20, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
46 2 0.03
47 29 0.44
49 33 0.50
50 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (47 bp):
ATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTATTAA
Found at i:17933667 original size:15 final size:15
Alignment explanation
Indices: 17933647--17933677 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17933637 TGAGACTCGC
*
17933647 CGTTGTAGTTTCAAT
1 CGTTGTAGCTTCAAT
17933662 CGTTGTAGCTTCAAT
1 CGTTGTAGCTTCAAT
17933677 C
1 C
17933678 TATTCCACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (15 bp):
CGTTGTAGCTTCAAT
Found at i:17933766 original size:50 final size:50
Alignment explanation
Indices: 17933700--17934135 Score: 273
Period size: 50 Copynumber: 8.8 Consensus size: 50
17933690 ATGCCAGAAG
* * * *
17933700 GTAAGATTCACCGTTGTGGCTTCGATCTTTTAAATTGCAATGTCGGGGAA
1 GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAA
* * * ** * *
17933750 GTGAGATTCACTGTTGTAGCTTCAATCTGTTCCACTGCAATG-C--AGAA
1 GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAA
* * * *
17933797 GGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGTAATGTCGGGGAA
1 -GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAA
* * **** * *
17933848 GTGAGATTCGCTGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCAGAGG--
1 GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAAT-GTC-GGGGAA
17933897 GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAA
1 GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAA
* **** * **
17933947 GCAAGATTCGCTGTTGTAGCTTCAAT-TTGTTCCGCTGCACCTG-CTTAGGAA
1 GTAAGATTCGCTGTTGTAGCTTCAATCTT-TTAAATTGCA-ATGTC-GGGGAA
* * * * *
17933998 -TAAGATTTGCCGTTGTGGCCTCAATCTTTT-AATTGCAATGTCAGGGAA
1 GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAA
* ** * **** * **
17934046 GTGAGATTCGCCATTGTAGCTTCAATCTGTTCCGCTGCATTG-CTTGGAA
1 GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAA
* * * * *
17934095 GTAAGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAAT
1 GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAAT
17934136 CTATGGTTAA
Statistics
Matches: 287, Mismatches: 83, Indels: 33
0.71 0.21 0.08
Matches are distributed among these distances:
47 3 0.01
48 41 0.14
49 103 0.36
50 126 0.44
51 14 0.05
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (50 bp):
GTAAGATTCGCTGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAA
Found at i:17933833 original size:98 final size:98
Alignment explanation
Indices: 17933663--17934135 Score: 605
Period size: 99 Copynumber: 4.8 Consensus size: 98
17933653 AGTTTCAATC
* * * *
17933663 GTTGTAGCTTCAATCTATTCCACTGCAATGCCAGAAGGTAAGATTCACCGTTGTGGCTTCGATCT
1 GTTGTAGCTTCAATCTGTTCCGCTGCAATG-CAGAAGGTAAGATTCGCCGTTGTGGCTTCAATCT
*
17933728 TTTAAATTGCAATGTCGGGGAAGTGAGATTCACT
65 TTTAAATTGCAATGTCGGGGAAGTGAGATTCGCT
* *
17933762 GTTGTAGCTTCAATCTGTTCCACTGCAATGCAGAAGGTAAGATTCGCCGTTGTGGCTTCGATCTT
1 GTTGTAGCTTCAATCTGTTCCGCTGCAATGCAGAAGGTAAGATTCGCCGTTGTGGCTTCAATCTT
*
17933827 TTAAATTGTAATGTCGGGGAAGTGAGATTCGCT
66 TTAAATTGCAATGTCGGGGAAGTGAGATTCGCT
* * *
17933860 GTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCAGAGGGTAAGATTCGCTGTTGTAGCTTCAATC
1 GTTGTAGCTTCAATCTGTTCCGCTGCAAT-G-CAGAAGGTAAGATTCGCCGTTGTGGCTTCAATC
**
17933924 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCT
64 TTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCT
* * * *
17933959 GTTGTAGCTTCAATTTGTTCCGCTGCACCTGCTTAGGAA--TAAGATTTGCCGTTGTGGCCTCAA
1 GTTGTAGCTTCAATCTGTTCCGCTGCA-ATGC--A-GAAGGTAAGATTCGCCGTTGTGGCTTCAA
* *
17934022 TCTTTT-AATTGCAATGTCAGGGAAGTGAGATTCGCC
62 TCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCT
* * * * * *
17934058 ATTGTAGCTTCAATCTGTTCCGCTGCATTGCTTGGAA-GTAAGATCCGCCGTCGTGGCCTCAATC
1 GTTGTAGCTTCAATCTGTTCCGCTGCAATGC--AGAAGGTAAGATTCGCCGTTGTGGCTTCAATC
17934122 TTTTAAATTGCAAT
64 TTTTAAATTGCAAT
17934136 CTATGGTTAA
Statistics
Matches: 335, Mismatches: 30, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
97 5 0.01
98 123 0.37
99 176 0.53
100 27 0.08
101 2 0.01
102 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (98 bp):
GTTGTAGCTTCAATCTGTTCCGCTGCAATGCAGAAGGTAAGATTCGCCGTTGTGGCTTCAATCTT
TTAAATTGCAATGTCGGGGAAGTGAGATTCGCT
Found at i:17933927 original size:197 final size:196
Alignment explanation
Indices: 17933662--17934135 Score: 614
Period size: 197 Copynumber: 2.4 Consensus size: 196
17933652 TAGTTTCAAT
* * * * *
17933662 CGTTGTAGCTTCAATCTATTCCACTGCAATGCCAGAAGGTAAGATTCACCGTTGTGGCTTCGATC
1 CGTTGTAGCTTCAATCTGTTCCGCTGC-ATGCCAGAGGGTAAGATTCGCCGTTGTGGCTTCAATC
**
17933727 TTTTAAATTGCAATGTCGGGGAAGTGAGATTCACTGTTGTAGCTTCAATCTGTTCCACTGCA-AT
65 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCCACTGCACAT
* * * *
17933791 GC-A-GAAGGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGTAATGTCGGGGAAGTGAGA
130 GCTAGGAA--TAAGATTCGCCGTTGTGGCCTCAATCTTTT-AATTGCAATGTCAGGGAAGTGAGA
17933854 TTCGC
192 TTCGC
* * *
17933859 TGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCAGAGGGTAAGATTCGCTGTTGTAGCTTCAATC
1 CGTTGTAGCTTCAATCTGTTCCGCTGCAT-GCCAGAGGGTAAGATTCGCCGTTGTGGCTTCAATC
* * * *
17933924 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATTTGTTCCGCTGCACCT
65 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCCACTGCACAT
*
17933989 GCTTAGGAATAAGATTTGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGGAAGTGAGATT
130 GC-TAGGAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGGAAGTGAGATT
17934054 CGC
194 CGC
* ** * * * *
17934057 CATTGTAGCTTCAATCTGTTCCGCTGCATTGCTTG-GAAGTAAGATCCGCCGTCGTGGCCTCAAT
1 CGTTGTAGCTTCAATCTGTTCCGCTGCA-TGCCAGAG-GGTAAGATTCGCCGTTGTGGCTTCAAT
17934121 CTTTTAAATTGCAAT
64 CTTTTAAATTGCAAT
17934136 CTATGGTTAA
Statistics
Matches: 241, Mismatches: 29, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
196 2 0.01
197 112 0.46
198 95 0.39
199 28 0.12
200 1 0.00
201 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (196 bp):
CGTTGTAGCTTCAATCTGTTCCGCTGCATGCCAGAGGGTAAGATTCGCCGTTGTGGCTTCAATCT
TTTAAATTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGTTCCACTGCACATG
CTAGGAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCAGGGAAGTGAGATTCG
C
Found at i:17934489 original size:44 final size:44
Alignment explanation
Indices: 17934439--17934527 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
17934429 TTGCCCCTAC
17934439 TGTAAACCTCCAAGTTCAATCCACTGGATGCAAAATTTAAACCA
1 TGTAAACCTCCAAGTTCAATCCACTGGATGCAAAATTTAAACCA
* *
17934483 TGTAAACCTCTAAGTTCAATCCACTGGATGCAAAATTTGAACCA
1 TGTAAACCTCCAAGTTCAATCCACTGGATGCAAAATTTAAACCA
17934527 T
1 T
17934528 CTTTCTCCCG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (44 bp):
TGTAAACCTCCAAGTTCAATCCACTGGATGCAAAATTTAAACCA
Found at i:17937007 original size:13 final size:13
Alignment explanation
Indices: 17936989--17937016 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17936979 GCGGACTAAC
17936989 TTCGGGTCTCTTG
1 TTCGGGTCTCTTG
17937002 TTCGGGTCTCTTG
1 TTCGGGTCTCTTG
17937015 TT
1 TT
17937017 TCCCATTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.29, T:0.50
Consensus pattern (13 bp):
TTCGGGTCTCTTG
Found at i:17952183 original size:16 final size:16
Alignment explanation
Indices: 17952159--17952196 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
17952149 TTTGGTTCGC
*
17952159 TGTATTGGAATAGAGG
1 TGTAATGGAATAGAGG
17952175 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
17952191 CGTAAT
1 TGTAAT
17952197 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:17952582 original size:15 final size:17
Alignment explanation
Indices: 17952548--17952581 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17952538 AATTATTATT
*
17952548 AATATATTTTAATTAAA
1 AATATAATTTAATTAAA
17952565 AATATAATTTAA-TAAA
1 AATATAATTTAATTAAA
17952581 A
1 A
17952582 TTCTTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATAATTTAATTAAA
Found at i:17960223 original size:27 final size:26
Alignment explanation
Indices: 17960182--17960234 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
17960172 AATGTGAAAG
*
17960182 GGGGTTGCTATGTGCTGATTCCTCCGA
1 GGGGTTGCTAAGTGCTGATTCC-CCGA
17960209 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
17960235 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.13, C:0.23, G:0.34, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:17960326 original size:27 final size:26
Alignment explanation
Indices: 17960285--17960337 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
17960275 AAATAAAAAG
*
17960285 GGGGTTGCTATGTGCTGATTCCTCCGA
1 GGGGTTGCTAAGTGCTGATTCC-CCGA
17960312 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
17960338 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.13, C:0.23, G:0.34, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:17960332 original size:103 final size:104
Alignment explanation
Indices: 17960104--17960369 Score: 446
Period size: 103 Copynumber: 2.6 Consensus size: 104
17960094 TGTATATAAA
** * * *
17960104 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
**
17960168 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCTCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCTCCG
17960208 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
17960273 TGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCTCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCTCCG
17960311 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
17960370 ATAACGGCTA
Statistics
Matches: 154, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
103 89 0.58
104 64 0.42
105 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCTCCG
Found at i:17966084 original size:59 final size:59
Alignment explanation
Indices: 17966002--17966236 Score: 391
Period size: 59 Copynumber: 4.0 Consensus size: 59
17965992 ACATCGAAAT
* * *
17966002 AACTCCTAATTTATTAAATGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAG
1 AACTTCTATTTTATTAAATGAAACAATATAAAAATAAATTGTACAAAAATATTCAAAAG
* *
17966061 AACTAT-TATTTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAG
1 AACT-TCTATTTTATTAAATGAAACAATATAAAAATAAATTGTACAAAAATATTCAAAAG
*
17966120 AACTTCTATTTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAAG
1 AACTTCTATTTTATTAAATGAAACAATATAAAAATAAATTGTACAAAAATATTCAAAAG
*
17966179 AACTTCTATTTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAA
1 AACTTCTATTTTATTAAATGAAACAATATAAAAATAAATTGTACAAAAATATTCAAAA
17966237 ATAAATCAAT
Statistics
Matches: 168, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
58 1 0.01
59 167 0.99
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.32
Consensus pattern (59 bp):
AACTTCTATTTTATTAAATGAAACAATATAAAAATAAATTGTACAAAAATATTCAAAAG
Found at i:17968048 original size:41 final size:41
Alignment explanation
Indices: 17968027--17968212 Score: 309
Period size: 41 Copynumber: 4.5 Consensus size: 41
17968017 GACTTTAAGT
*
17968027 CTAGCAGGCTAAGTGCCGGTGAGCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
17968068 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATATAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
17968109 CTAGCAAGCTGAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * *
17968150 CTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
17968191 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
17968213 ATAGTGTTAA
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 134 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:17969522 original size:10 final size:10
Alignment explanation
Indices: 17969480--17969536 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
17969470 GAAATTATAA
17969480 AAAAAATATT
1 AAAAAATATT
**
17969490 AATTAA-ATT
1 AAAAAATATT
17969499 ACAAAAATGA--
1 A-AAAAAT-ATT
17969509 AAAAAATATT
1 AAAAAATATT
17969519 AAAAAATATT
1 AAAAAATATT
17969529 AAAAAATA
1 AAAAAATA
17969537 AAATTAACCG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
8 1 0.03
9 10 0.26
10 26 0.68
12 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (10 bp):
AAAAAATATT
Found at i:17969533 original size:29 final size:28
Alignment explanation
Indices: 17969479--17969539 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
17969469 AGAAATTATA
**
17969479 AAAAAAATATTAATTAAATTACAAAAAT
1 AAAAAAATATTAAAAAAATTACAAAAAT
17969507 GAAAAAAATATTAAAAAATATTA-AAAAAT
1 -AAAAAAATATTAAAAAA-ATTACAAAAAT
17969536 AAAA
1 AAAA
17969540 TTAACCGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 21 0.72
30 4 0.14
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (28 bp):
AAAAAAATATTAAAAAAATTACAAAAAT
Found at i:17970339 original size:26 final size:25
Alignment explanation
Indices: 17970267--17970347 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 25
17970257 TTTACACGAA
* *
17970267 ATATT-TTGTTAATTATGTATTTA-AA
1 ATATTATTTTTAATTA--TATTTATAG
*
17970292 ATATTATTTTT-ATTATAATTATAG
1 ATATTATTTTTAATTATATTTATAG
17970316 ATATTATTTCTTAATTATATTTATAG
1 ATATTATTT-TTAATTATATTTATAG
17970342 ATATTA
1 ATATTA
17970348 AAATCTTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 5 0.10
24 10 0.21
25 11 0.23
26 22 0.46
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (25 bp):
ATATTATTTTTAATTATATTTATAG
Found at i:17970358 original size:26 final size:25
Alignment explanation
Indices: 17970301--17970364 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
17970291 AATATTATTT
* **
17970301 TTATTATAATTATAGATATTATTTC
1 TTATTATATTTATAGATATTAAATC
17970326 TTAATTATATTTATAGATATTAAAATC
1 TT-ATTATATTTATAGATATT-AAATC
17970353 TTATTAT-TTTAT
1 TTATTATATTTAT
17970365 TTTGAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.21
26 22 0.65
27 5 0.15
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (25 bp):
TTATTATATTTATAGATATTAAATC
Found at i:17972690 original size:31 final size:31
Alignment explanation
Indices: 17972652--17972715 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
17972642 GTAAGGGTTA
*
17972652 ATTTCA-TTTTTTAATATTATTTAATATTTTT
1 ATTTCATTTTTTTAAT-TTAATTAATATTTTT
17972683 ATTTCATTTTTTTAATTTAATTAATATTTTT
1 ATTTCATTTTTTTAATTTAATTAATATTTTT
17972714 AT
1 AT
17972716 AAATTTCTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (31 bp):
ATTTCATTTTTTTAATTTAATTAATATTTTT
Found at i:17972712 original size:18 final size:18
Alignment explanation
Indices: 17972659--17972714 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
17972649 TTAATTTCAT
*
17972659 TTTTTAATATTATTTAATA
1 TTTTTAAT-TTAATTAATA
*
17972678 TTTTT-ATTTCA-T--T-
1 TTTTTAATTTAATTAATA
17972691 TTTTTAATTTAATTAATA
1 TTTTTAATTTAATTAATA
17972709 TTTTTA
1 TTTTTA
17972715 TAAATTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 11
0.67 0.07 0.26
Matches are distributed among these distances:
13 5 0.17
14 6 0.21
15 1 0.03
16 1 0.03
17 3 0.10
18 8 0.28
19 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTAATTTAATTAATA
Found at i:17974720 original size:59 final size:59
Alignment explanation
Indices: 17974628--17974748 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 59
17974618 ATTGATTTAT
*
17974628 TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAAATAGAATTTC
1 TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
* *
17974687 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATTAAATAGAAGTTC
1 TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
17974746 TTT
1 TTT
17974749 ATAACTCGTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.55
Consensus pattern (59 bp):
TTTTGAATATTTTTGTAAAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
Found at i:17982840 original size:20 final size:21
Alignment explanation
Indices: 17982815--17982854 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
17982805 AAGGAATAGG
17982815 GGAAGAAAATGAAGA-ACAAT
1 GGAAGAAAATGAAGAGACAAT
* *
17982835 GGAAGAGAATTAAGAGACAA
1 GGAAGAAAATGAAGAGACAA
17982855 AAGTGAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.57, C:0.05, G:0.28, T:0.10
Consensus pattern (21 bp):
GGAAGAAAATGAAGAGACAAT
Found at i:17983274 original size:21 final size:22
Alignment explanation
Indices: 17983249--17983293 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
17983239 TATTTAACCC
17983249 AAAATAAATTGA-ATTA-AAATT
1 AAAATAAATT-ATATTATAAATT
*
17983270 AAAATTAATTATATTATAAATT
1 AAAATAAATTATATTATAAATT
17983292 AA
1 AA
17983294 TATTCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 13 0.62
22 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATAAATTATATTATAAATT
Found at i:17983279 original size:16 final size:16
Alignment explanation
Indices: 17983252--17983294 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
17983242 TTAACCCAAA
17983252 ATAAATTGAATTAAAATT
1 ATAAATT-AATT-AAATT
*
17983270 A-AAATTAATTATATT
1 ATAAATTAATTAAATT
17983285 ATAAATTAAT
1 ATAAATTAAT
17983295 ATTCATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
16 12 0.52
17 5 0.22
18 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATAAATTAATTAAATT
Found at i:17986413 original size:25 final size:24
Alignment explanation
Indices: 17986385--17986529 Score: 134
Period size: 25 Copynumber: 5.9 Consensus size: 24
17986375 ATGAGCTATG
* *
17986385 AATCGGTATGCTC-TCATGAGCTAGA
1 AATCGGTAAGCTCAT-ACGAGCT-GA
* *
17986410 AATCAGTAAGCGCATACGAGCTGA
1 AATCGGTAAGCTCATACGAGCTGA
17986434 GAATCGGTAAGCTC-TCACGAGCTGA
1 -AATCGGTAAGCTCAT-ACGAGCTGA
*
17986459 AATCGGTAAGCTCATACGAGCTTA
1 AATCGGTAAGCTCATACGAGCTGA
* *
17986483 GAATCGATAAGCT-TTCACGAGCTGA
1 -AATCGGTAAGCTCAT-ACGAGCTGA
* *
17986508 AATCGATAAGGTCATACGAGCT
1 AATCGGTAAGCTCATACGAGCT
17986530 ATGGTGTGCC
Statistics
Matches: 101, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
24 43 0.43
25 57 0.56
26 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (24 bp):
AATCGGTAAGCTCATACGAGCTGA
Found at i:17986480 original size:49 final size:48
Alignment explanation
Indices: 17986369--17986530 Score: 207
Period size: 49 Copynumber: 3.3 Consensus size: 48
17986359 GTACATGTAT
* * * *
17986369 GCTCATATGAGCTATGAATCGGTATGCTCTCATGAGCTAGAAATCAGTAA
1 GCTCATACGAGCTA-GAATCGGTAAGCTCTCACGAGCT-GAAATCGGTAA
*
17986419 GCGCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTGAAATCGGTAA
1 GCTCATACGAGCT-AGAATCGGTAAGCTCTCACGAGCTGAAATCGGTAA
* * *
17986468 GCTCATACGAGCTTAGAATCGATAAGCTTTCACGAGCTGAAATCGATAA
1 GCTCATACGAGC-TAGAATCGGTAAGCTCTCACGAGCTGAAATCGGTAA
*
17986517 GGTCATACGAGCTA
1 GCTCATACGAGCTA
17986531 TGGTGTGCCC
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
48 2 0.02
49 64 0.64
50 33 0.33
51 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (48 bp):
GCTCATACGAGCTAGAATCGGTAAGCTCTCACGAGCTGAAATCGGTAA
Found at i:17986526 original size:24 final size:25
Alignment explanation
Indices: 17986416--17986529 Score: 128
Period size: 24 Copynumber: 4.6 Consensus size: 25
17986406 TAGAAATCAG
* *
17986416 TAAGCGCATACGAGCTGAGAATCGG
1 TAAGCTCATACGAGCTGAGAATCGA
*
17986441 TAAGCTC-TCACGAGCTGA-AATCGG
1 TAAGCTCAT-ACGAGCTGAGAATCGA
*
17986465 TAAGCTCATACGAGCTTAGAATCGA
1 TAAGCTCATACGAGCTGAGAATCGA
*
17986490 TAAGCT-TTCACGAGCTGA-AATCGA
1 TAAGCTCAT-ACGAGCTGAGAATCGA
*
17986514 TAAGGTCATACGAGCT
1 TAAGCTCATACGAGCT
17986530 ATGGTGTGCC
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
24 41 0.53
25 36 0.47
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (25 bp):
TAAGCTCATACGAGCTGAGAATCGA
Found at i:17988191 original size:20 final size:21
Alignment explanation
Indices: 17988168--17988206 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17988158 CGATGTTAAA
17988168 GCCT-AGGTATTGACACCTAG
1 GCCTAAGGTATTGACACCTAG
*
17988188 GCCTAAGGTATTGATACCT
1 GCCTAAGGTATTGACACCT
17988207 TCATCAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
GCCTAAGGTATTGACACCTAG
Found at i:17992041 original size:28 final size:28
Alignment explanation
Indices: 17991993--17992049 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
17991983 TGTAATTTAA
*
17991993 ATTAAGTTTTAATTAAGCATT-ATTTATT
1 ATTAAGTTTTAAATAAGCATTGA-TTATT
*
17992021 ATTAAGTTTATAAATGA-CATTGATTATT
1 ATTAAGTTT-TAAATAAGCATTGATTATT
17992049 A
1 A
17992050 CAAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (28 bp):
ATTAAGTTTTAAATAAGCATTGATTATT
Found at i:17993464 original size:42 final size:42
Alignment explanation
Indices: 17993417--17993498 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
17993407 TATTATATGC
*
17993417 CACACGGCCT-GGACACACGCCCATGTCCTTGCTCGTGTGGCT
1 CACACGGCCTAGG-CACACGCCCATGTCCTTGCCCGTGTGGCT
*
17993459 CACACGGCCTAGGCACATGCCCATGTCCTTGCCCGTGTGG
1 CACACGGCCTAGGCACACGCCCATGTCCTTGCCCGTGTGG
17993499 TCCTAAGTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.15, C:0.38, G:0.27, T:0.21
Consensus pattern (42 bp):
CACACGGCCTAGGCACACGCCCATGTCCTTGCCCGTGTGGCT
Found at i:17996943 original size:3 final size:3
Alignment explanation
Indices: 17996935--17996972 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
17996925 AATATGTTTT
17996935 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
17996973 TAGCTTAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17997515 original size:18 final size:18
Alignment explanation
Indices: 17997492--17997528 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
17997482 CAGTTTGTGT
17997492 TAACTGACTTCTAACTGC
1 TAACTGACTTCTAACTGC
17997510 TAACTGACTTCTAACTGC
1 TAACTGACTTCTAACTGC
17997528 T
1 T
17997529 CTTATTACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (18 bp):
TAACTGACTTCTAACTGC
Found at i:18003296 original size:21 final size:21
Alignment explanation
Indices: 18003272--18003321 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
18003262 TTATTAAGTT
18003272 CAAGTGGTAAAACCTTAAGAA
1 CAAGTGGTAAAACCTTAAGAA
* *
18003293 CAAGTGGTAAGACCTTAAGAG
1 CAAGTGGTAAAACCTTAAGAA
18003314 CAAGTGGT
1 CAAGTGGT
18003322 TTTAGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.20
Consensus pattern (21 bp):
CAAGTGGTAAAACCTTAAGAA
Found at i:18004700 original size:25 final size:25
Alignment explanation
Indices: 18004666--18004714 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
18004656 CAAGCCCATT
* *
18004666 TTCATAGCTCGTGTGAGCATACTTA
1 TTCACAGCTCGTGTGAGCACACTTA
18004691 TTCACAGCTCGTGTGAGCACACTT
1 TTCACAGCTCGTGTGAGCACACTT
18004715 GGTGTGAGCT
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:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCACACTTA
Found at i:18006014 original size:30 final size:27
Alignment explanation
Indices: 18005974--18006053 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 27
18005964 TTTTAATAGT
18005974 TGGACTTAAATTTTGAAATTTGAAAA-ATAA
1 TGGAC-TAAATTTT-AAATTT-AAAACAT-A
*
18006004 TGGGACTAAATTCTTAAAATTAAAAGCATA
1 T-GGACTAAATT-TTAAATTTAAAA-CATA
18006034 TGGACTAAATTTTAAATTTA
1 TGGACTAAATTTTAAATTTA
18006054 TGAAGAGTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
28 8 0.18
29 14 0.32
30 14 0.32
31 8 0.18
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (27 bp):
TGGACTAAATTTTAAATTTAAAACATA
Found at i:18011672 original size:47 final size:47
Alignment explanation
Indices: 18011540--18011861 Score: 405
Period size: 47 Copynumber: 7.0 Consensus size: 47
18011530 CAACCCTGTT
* * * * * *
18011540 TTGGATAGCAATTATTCATCAAATTGGACAGCAAT-AATATGCTCTAAA
1 TTGGACAGC-ATTATACATTAAAATGGACAGC-ATCAATATACTCAAAA
* * * * *
18011588 -TGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
* *
18011634 TTGGACAGCATTATACATTAAAATGGGCAGCATCAATATACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
18011681 TTGGACAGCATTATACATTAAAATGGACAGCATC---A-A-T----A
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
*
18011719 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
*
18011766 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
*
18011813 TTGGACAACATTATACATTAAAATGGACAGCATCAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
18011860 TT
1 TT
18011862 TATAACACAA
Statistics
Matches: 247, Mismatches: 16, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
38 35 0.14
41 1 0.00
42 2 0.01
43 2 0.01
44 1 0.00
45 1 0.00
46 31 0.13
47 174 0.70
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (47 bp):
TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
Found at i:18011689 original size:25 final size:24
Alignment explanation
Indices: 18011560--18011719 Score: 124
Period size: 22 Copynumber: 6.8 Consensus size: 24
18011550 ATTATTCATC
*
18011560 AAATTGGACAGCAATAATATGCTCT-
1 AAATTGGACAGC-ATAATATACT-TA
* *
18011585 AAA-TGGACAGCAT--TATACATC
1 AAATTGGACAGCATAATATACTTA
* * *
18011606 AAATTAGACAGCTTAAATATACTCA
1 AAATTGGACAGCAT-AATATACTTA
18011631 AAATTGGACAGCAT--TATACATTA
1 AAATTGGACAGCATAATATAC-TTA
*
18011654 AAA-TGGGCAGCATCAATATACTTA
1 AAATTGGACAGCAT-AATATACTTA
18011678 AAATTGGACAGCAT--TATACATTA
1 AAATTGGACAGCATAATATAC-TTA
18011701 AAA-TGGACAGCATCAATAT
1 AAATTGGACAGCAT-AATAT
18011720 TGGACAGCAT
Statistics
Matches: 109, Mismatches: 12, Indels: 28
0.73 0.08 0.19
Matches are distributed among these distances:
20 1 0.01
21 7 0.06
22 37 0.34
23 13 0.12
24 14 0.13
25 37 0.34
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (24 bp):
AAATTGGACAGCATAATATACTTA
Found at i:18011776 original size:85 final size:85
Alignment explanation
Indices: 18011628--18011861 Score: 351
Period size: 85 Copynumber: 2.6 Consensus size: 85
18011618 TTAAATATAC
* *
18011628 TCAAAATTGGACAGCATTATACATTAAAATGGGCAGCATCAATATACTTAAAATTGGACAGCATT
1 TCAATATTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAATTGGACAGCATT
18011693 ATACATTAAAATGGACAGCA
66 ATACATTAAAATGGACAGCA
18011713 TCAATATTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAATTGGACAGCATT
1 TCAATATTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAATTGGACAGCATT
18011778 ATACATTAAAATGGACAGCA
66 ATACATTAAAATGGACAGCA
* *
18011798 TCAATATACTTAAAATTGGACAACATTATACATTAAAATGGACAGCATCAATATACTCAAAATT
1 TC---A-A--T---ATTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAATT
18011862 TATAACACAA
Statistics
Matches: 136, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
85 85 0.62
88 1 0.01
89 1 0.01
91 1 0.01
94 48 0.35
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.27
Consensus pattern (85 bp):
TCAATATTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAATTGGACAGCATT
ATACATTAAAATGGACAGCA
Found at i:18011797 original size:132 final size:132
Alignment explanation
Indices: 18011588--18011851 Score: 456
Period size: 132 Copynumber: 2.0 Consensus size: 132
18011578 ATGCTCTAAA
* *
18011588 TGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAATTGGACAGCATTATACATT
1 TGGACAGCATTATACATCAAAATAGACAGCATAAATATACTCAAAATTGGACAGCATTATACATT
* *
18011653 AAAATGGGCAGCATCAATATACTTAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAAT
66 AAAATGGACAGCATCAATATACTTAAAATTGGACAACATTATACATTAAAATGGACAGCATCAAT
18011718 AT
131 AT
* * * *
18011720 TGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAATTGGACAGCATTATACATT
1 TGGACAGCATTATACATCAAAATAGACAGCATAAATATACTCAAAATTGGACAGCATTATACATT
18011785 AAAATGGACAGCATCAATATACTTAAAATTGGACAACATTATACATTAAAATGGACAGCATCAAT
66 AAAATGGACAGCATCAATATACTTAAAATTGGACAACATTATACATTAAAATGGACAGCATCAAT
18011850 AT
131 AT
18011852 ACTCAAAATT
Statistics
Matches: 124, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 124 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (132 bp):
TGGACAGCATTATACATCAAAATAGACAGCATAAATATACTCAAAATTGGACAGCATTATACATT
AAAATGGACAGCATCAATATACTTAAAATTGGACAACATTATACATTAAAATGGACAGCATCAAT
AT
Found at i:18012852 original size:28 final size:27
Alignment explanation
Indices: 18012796--18012893 Score: 92
Period size: 28 Copynumber: 3.6 Consensus size: 27
18012786 TTAATAAGTA
*
18012796 CGCACACTTAGTGCTTAAT-AATCAAACT
1 CGCACACTTAGTGCTT--TCAATTAAACT
** *
18012824 CGCACACTTAGTGCTTTACCCTTATACT
1 CGCACACTTAGTGCTTT-CAATTAAACT
*
18012852 CACACACTT-GTGCATTTCAATTAAACT
1 CGCACACTTAGTGC-TTTCAATTAAACT
*
18012879 CGCGCACTTAGTGCT
1 CGCACACTTAGTGCT
18012894 AATCTCATTA
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
26 1 0.02
27 19 0.34
28 36 0.64
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.32
Consensus pattern (27 bp):
CGCACACTTAGTGCTTTCAATTAAACT
Found at i:18016171 original size:21 final size:22
Alignment explanation
Indices: 18016146--18016199 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
18016136 TTTACGTATA
18016146 TTTTATAGTTTTTTTTTAAAT-
1 TTTTATAGTTTTTTTTTAAATC
** *
18016167 TTTTAT-GAATTTTTTTATATC
1 TTTTATAGTTTTTTTTTAAATC
18016188 TTTTATAGTTTT
1 TTTTATAGTTTT
18016200 GACGAATCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 11 0.42
21 12 0.46
22 3 0.12
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (22 bp):
TTTTATAGTTTTTTTTTAAATC
Found at i:18019607 original size:21 final size:21
Alignment explanation
Indices: 18019583--18019628 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
18019573 GCCTAGTTCC
18019583 AAAGGAGACTTAGGTGAAGTT
1 AAAGGAGACTTAGGTGAAGTT
* *
18019604 AAAGGATACTTAGGTTAAGTT
1 AAAGGAGACTTAGGTGAAGTT
18019625 AAAG
1 AAAG
18019629 AAGGGTTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.28, T:0.26
Consensus pattern (21 bp):
AAAGGAGACTTAGGTGAAGTT
Found at i:18021726 original size:31 final size:30
Alignment explanation
Indices: 18021659--18021856 Score: 138
Period size: 30 Copynumber: 6.6 Consensus size: 30
18021649 TCGGCAATCG
* * * *
18021659 ATTATGAAAAAGGATGGTGATGACCATCGA
1 ATTATGAAAAGGGATAGTGACGACCATCAA
*
18021689 ATTATGAAAAGGGATAGTGACGACTATCAAA
1 ATTATGAAAAGGGATAGTGACGACCATC-AA
* *
18021720 ATTATGAAAAGGGAT-GCCT-TC-AGCTATCAA
1 ATTATGAAAAGGGATAG--TGACGA-CCATCAA
* * * * *
18021750 ATCATGCAAAGGGATAGCT-TCGGCTATCAA
1 ATTATGAAAAGGGATAG-TGACGACCATCAA
* * *
18021780 ATTATGTAGAGGGATGGTGACGACCATCAA
1 ATTATGAAAAGGGATAGTGACGACCATCAA
* *
18021810 CA--ATGAAAAGGGATGGTGATGACCATCAAA
1 -ATTATGAAAAGGGATAGTGACGACCATC-AA
18021840 ATTATGAAAAGGGATAG
1 ATTATGAAAAGGGATAG
18021857 CTTCAACTAT
Statistics
Matches: 137, Mismatches: 20, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
29 24 0.18
30 75 0.55
31 37 0.27
32 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (30 bp):
ATTATGAAAAGGGATAGTGACGACCATCAA
Found at i:18021824 original size:29 final size:30
Alignment explanation
Indices: 18021775--18021854 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
18021765 AGCTTCGGCT
* * *
18021775 ATCAAATTATGTAGAGGGATGGTGACGACC
1 ATCAAAATATGAAAAGGGATGGTGACGACC
* *
18021805 ATCAACA-ATGAAAAGGGATGGTGATGACC
1 ATCAAAATATGAAAAGGGATGGTGACGACC
18021834 ATCAAAATTATGAAAAGGGAT
1 ATCAAAA-TATGAAAAGGGAT
18021855 AGCTTCAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 25 0.60
30 5 0.12
31 12 0.29
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.21
Consensus pattern (30 bp):
ATCAAAATATGAAAAGGGATGGTGACGACC
Found at i:18021838 original size:120 final size:121
Alignment explanation
Indices: 18021636--18021911 Score: 342
Period size: 120 Copynumber: 2.3 Consensus size: 121
18021626 TCAACGAATG
* * * **
18021636 AAAAGGGATAGCTTCGGCAATC-GATTATGAAAAAGGATGGTGATGACCATCGAATTATGAAAAG
1 AAAAGGGATAGCTTCGGCTATCAAATTATGAAAAAGGATGGTGACGACCATCGAACAATGAAAAG
* * **
18021700 GGATAGTGACGACTATCAAAATTATGAAAAGGGAT-GCCTTCAGCTATCAAATCATG
66 GGATAGTGACGACCATCAAAATTATGAAAAGGGATAG-CTTCAACTATCAAATCACA
* * * *
18021756 CAAAGGGATAGCTTCGGCTATCAAATTATGTAGAGGGATGGTGACGACCATC-AACAATGAAAAG
1 AAAAGGGATAGCTTCGGCTATCAAATTATGAAAAAGGATGGTGACGACCATCGAACAATGAAAAG
* * *
18021820 GGATGGTGATGACCATCAAAATTATGAAAAGGGATAGCTTCAACTATCGAATCACA
66 GGATAGTGACGACCATCAAAATTATGAAAAGGGATAGCTTCAACTATCAAATCACA
* * * *
18021876 AAAAGGAATAGCTTTGGCTATCAAATCATGGAAAAG
1 AAAAGGGATAGCTTCGGCTATCAAATTATGAAAAAG
18021912 AATGTGTCAA
Statistics
Matches: 131, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
120 106 0.81
121 25 0.19
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (121 bp):
AAAAGGGATAGCTTCGGCTATCAAATTATGAAAAAGGATGGTGACGACCATCGAACAATGAAAAG
GGATAGTGACGACCATCAAAATTATGAAAAGGGATAGCTTCAACTATCAAATCACA
Found at i:18023001 original size:12 final size:12
Alignment explanation
Indices: 18022984--18023013 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18022974 TCAGGCAGTT
18022984 ACACGGCCTAGC
1 ACACGGCCTAGC
*
18022996 ACACGGCCTCGC
1 ACACGGCCTAGC
18023008 ACACGG
1 ACACGG
18023014 GCATGTAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.43, G:0.27, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:18023262 original size:86 final size:86
Alignment explanation
Indices: 18023117--18023301 Score: 289
Period size: 86 Copynumber: 2.2 Consensus size: 86
18023107 GTGGGCTGGG
*
18023117 ACACGGTCATGTGTCCCTACTTCAAATGCCCACAAGGCCTGTGACACGGACGTATATCTTGGTCG
1 ACACGGTCGTGTGTCCCTACTTCAAATGCCCACAAGGCCTGTGACACGGACGTATATCTTGGTCG
*
18023182 AGTGAGTCACACGGCTTGGCC
66 ACTGAGTCACACGGCTTGGCC
** * * *
18023203 ACACGGTCGTGTGTCCCTACTTTGAATGCCCATACGGCCTGTGACACGGACGTGTATCTTGGTCG
1 ACACGGTCGTGTGTCCCTACTTCAAATGCCCACAAGGCCTGTGACACGGACGTATATCTTGGTCG
*
18023268 ACTGAGTCACATGGCTTGGCC
66 ACTGAGTCACACGGCTTGGCC
*
18023289 ACACGATCGTGTG
1 ACACGGTCGTGTG
18023302 ACCCCTGCAG
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 90 1.00
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.25
Consensus pattern (86 bp):
ACACGGTCGTGTGTCCCTACTTCAAATGCCCACAAGGCCTGTGACACGGACGTATATCTTGGTCG
ACTGAGTCACACGGCTTGGCC
Found at i:18029246 original size:29 final size:29
Alignment explanation
Indices: 18029183--18029248 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
18029173 TCATCAACGA
*
18029183 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGAGATAGCTTCGGCTATCGAAT
* *
18029212 ACGAAAAGAGATTGCTTCGGCTATC-AATT
1 ATGAAAAGAGATAGCTTCGGCTATCGAA-T
18029241 ATGAAAAG
1 ATGAAAAG
18029249 GGATGGTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 2 0.06
29 30 0.94
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
ATGAAAAGAGATAGCTTCGGCTATCGAAT
Found at i:18029404 original size:29 final size:30
Alignment explanation
Indices: 18029240--18029433 Score: 157
Period size: 30 Copynumber: 6.4 Consensus size: 30
18029230 GGCTATCAAT
* *
18029240 TATGAAAAGGGATGGTGACGACCAAT-GAAT
1 TATGAAAAGGGATGGTGACGACC-ATCAAAA
*
18029270 TATGAAAAGGGATGGTGACAACCATCAAAA
1 TATGAAAAGGGATGGTGACGACCATCAAAA
* * *
18029300 TTATGAAAAGGGATGGCT-TC-AGCTAT-TAAA
1 -TATGAAAAGGGATGG-TGACGA-CCATCAAAA
* * *** * *
18029330 TCATGCAAAGGGATAGTTTTGACTATCAAAT
1 T-ATGAAAAGGGATGGTGACGACCATCAAAA
*
18029361 TATGTAAAA-GGATGGTGACGACCATCAAGA
1 TATG-AAAAGGGATGGTGACGACCATCAAAA
18029391 -ATGAAAAGGGATGGTGACGACCATCAAAA
1 TATGAAAAGGGATGGTGACGACCATCAAAA
18029420 TTATGAAAAGGGAT
1 -TATGAAAAGGGAT
18029434 AGCTTCAGCT
Statistics
Matches: 132, Mismatches: 20, Indels: 23
0.75 0.11 0.13
Matches are distributed among these distances:
28 4 0.03
29 27 0.20
30 62 0.47
31 38 0.29
32 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (30 bp):
TATGAAAAGGGATGGTGACGACCATCAAAA
Found at i:18029405 original size:120 final size:119
Alignment explanation
Indices: 18029183--18029463 Score: 370
Period size: 120 Copynumber: 2.4 Consensus size: 119
18029173 TCATCAACGA
* * * * * * *
18029183 ATGAAAAGGGATAGCTTCGGCTATCGAAT-ACGAAAAGAGATTGCTTCGGCTATCAATTATGAAA
1 ATGAAAAGGGATAGCTTCAGCTATCAAATCACG-AAAGGGATAGTTTTGACTATCAATTATGAAA
* **
18029247 AGGGATGGTGACGACCAATGAATTATGAAAAGGGATGGTGACAACCATCAAAATT
65 AGGGATGGTGACGACCAATCAAGAATGAAAAGGGATGGTGACAACCATCAAAATT
* * *
18029302 ATGAAAAGGGATGGCTTCAGCTATTAAATCATGCAAAGGGATAGTTTTGACTATCAAATTATGTA
1 ATGAAAAGGGATAGCTTCAGCTATCAAATCACG-AAAGGGATAGTTTTGACTATC-AATTATG-A
*
18029367 AAA-GGATGGTGACGACC-ATCAAGAATGAAAAGGGATGGTGACGACCATCAAAATT
63 AAAGGGATGGTGACGACCAATCAAGAATGAAAAGGGATGGTGACAACCATCAAAATT
*
18029422 ATGAAAAGGGATAGCTTCAGCTATCGAATCACGAAAGGGATA
1 ATGAAAAGGGATAGCTTCAGCTATCAAATCACGAAAGGGATA
18029464 ACTTTGGCTA
Statistics
Matches: 140, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
119 34 0.24
120 81 0.58
121 21 0.15
122 4 0.03
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (119 bp):
ATGAAAAGGGATAGCTTCAGCTATCAAATCACGAAAGGGATAGTTTTGACTATCAATTATGAAAA
GGGATGGTGACGACCAATCAAGAATGAAAAGGGATGGTGACAACCATCAAAATT
Found at i:18029461 original size:60 final size:58
Alignment explanation
Indices: 18029275--18029462 Score: 150
Period size: 60 Copynumber: 3.1 Consensus size: 58
18029265 TGAATTATGA
* **
18029275 AAAGGGATGGTGACAACCATCAAAATTATGAAAAGGGATGGCTTCAGCTATTAAATCATG
1 AAAGGGATGGTGACGACCATCAAAATTATGAAAAGGGAT-GCTTCAGCTATCGAATCA-G
* *** * * * * *
18029335 CAAAGGGATAGTTTTGACTATC-AAATTATGTAAAA-GGATG-GTGACGACCATCAAGAATGA-
1 -AAAGGGATGGTGACGACCATCAAAATTATG-AAAAGGGATGCTTCA-G-CTATC--GAATCAG
18029395 AAAGGGATGGTGACGACCATCAAAATTATGAAAAGGGATAGCTTCAGCTATCGAATCACG
1 AAAGGGATGGTGACGACCATCAAAATTATGAAAAGGGAT-GCTTCAGCTATCGAATCA-G
18029455 AAAGGGAT
1 AAAGGGAT
18029463 AACTTTGGCT
Statistics
Matches: 95, Mismatches: 21, Indels: 23
0.68 0.15 0.17
Matches are distributed among these distances:
58 7 0.07
59 22 0.23
60 39 0.41
61 21 0.22
62 6 0.06
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.22
Consensus pattern (58 bp):
AAAGGGATGGTGACGACCATCAAAATTATGAAAAGGGATGCTTCAGCTATCGAATCAG
Found at i:18029473 original size:29 final size:29
Alignment explanation
Indices: 18029426--18029481 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
18029416 AAAATTATGA
*
18029426 AAAGGGATAGCTTCAGCTATCGAATCACG
1 AAAGGGATAACTTCAGCTATCGAATCACG
** *
18029455 AAAGGGATAACTTTGGCTATTGAATCA
1 AAAGGGATAACTTCAGCTATCGAATCA
18029482 TGGAAAGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (29 bp):
AAAGGGATAACTTCAGCTATCGAATCACG
Found at i:18037490 original size:37 final size:39
Alignment explanation
Indices: 18037440--18037543 Score: 110
Period size: 37 Copynumber: 2.8 Consensus size: 39
18037430 CAAAAATAAT
* * *
18037440 ATTATTTTTATAGTTTTATATTAAATTTAAT-TT-AA-TG
1 ATTATCTTAATAGTATTATATT-AATTTAATATTAAAGTG
*
18037477 TTTATCTTAATAGTATTATATTAATTTAATATTAAAGTG
1 ATTATCTTAATAGTATTATATTAATTTAATATTAAAGTG
* *
18037516 ATTATCTTAATATTA-AAT-TTAATTTAAT
1 ATTATCTTAATAGTATTATATTAATTTAAT
18037544 GTTTATATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
36 8 0.14
37 30 0.53
38 4 0.07
39 15 0.26
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (39 bp):
ATTATCTTAATAGTATTATATTAATTTAATATTAAAGTG
Found at i:18037519 original size:25 final size:26
Alignment explanation
Indices: 18037483--18037531 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
18037473 AATGTTTATC
18037483 TTAATAGTATTATATTAAT-TTAATA
1 TTAATAGTATTATATTAATATTAATA
*
18037508 TTAA-AGTGATTATCTTAATATTAA
1 TTAATAGT-ATTATATTAATATTAA
18037532 ATTTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.67
26 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (26 bp):
TTAATAGTATTATATTAATATTAATA
Found at i:18037643 original size:62 final size:62
Alignment explanation
Indices: 18037522--18037639 Score: 152
Period size: 62 Copynumber: 2.0 Consensus size: 62
18037512 AGTGATTATC
* * * * * *
18037522 TTAATATTAAATTTAATTTAATGTTTATATTATAGATAAACATTTTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATACTATAGACAAAAATTATATTATTTTAATAAGAT
*
18037584 TTAATATTAAATTTAATCTAATATTTAT-CT-T-GACAAAAATTATATTAATTTAATAA
1 TTAATATTAAATTTAATCTAATATTTATACTATAGACAAAAATTATATTATTTTAATAA
18037640 TAAGTGATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 21 0.43
60 1 0.02
61 1 0.02
62 26 0.53
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (62 bp):
TTAATATTAAATTTAATCTAATATTTATACTATAGACAAAAATTATATTATTTTAATAAGAT
Found at i:18044131 original size:8 final size:8
Alignment explanation
Indices: 18044118--18044166 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
18044108 TTTGTTACTA
*
18044118 GTACTTTG
1 GTACTTTT
18044126 GTACTTTT
1 GTACTTTT
** *
18044134 GTA-AATA
1 GTACTTTT
18044141 GTACTTTT
1 GTACTTTT
18044149 GTACTTTT
1 GTACTTTT
18044157 GTACTTTT
1 GTACTTTT
18044165 GT
1 GT
18044167 TTCTAGCACT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
7 4 0.12
8 29 0.88
ACGTcount: A:0.18, C:0.10, G:0.16, T:0.55
Consensus pattern (8 bp):
GTACTTTT
Found at i:18044135 original size:23 final size:23
Alignment explanation
Indices: 18044105--18044159 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
18044095 CCAATTGATG
* *
18044105 ACTTTTGTTACTAGTACTTTGGT
1 ACTTTTGTAAATAGTACTTTGGT
*
18044128 ACTTTTGTAAATAGTACTTTTGT
1 ACTTTTGTAAATAGTACTTTGGT
18044151 ACTTTTGTA
1 ACTTTTGTA
18044160 CTTTTGTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.53
Consensus pattern (23 bp):
ACTTTTGTAAATAGTACTTTGGT
Found at i:18044217 original size:25 final size:23
Alignment explanation
Indices: 18044172--18044217 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
18044162 TTTGTTTCTA
*
18044172 GCACTTTGGTGCTTCTATTATTG
1 GCACTTTGGTGATTCTATTATTG
*
18044195 GCACTTTAGTGTGATTCTGTTAT
1 GCACTTT-G-GTGATTCTATTAT
18044218 GGTTTTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 1 0.05
25 11 0.58
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (23 bp):
GCACTTTGGTGATTCTATTATTG
Found at i:18052034 original size:22 final size:22
Alignment explanation
Indices: 18052009--18052050 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18051999 TTATAGTTTT
18052009 TTTTGATAATTTTTTAAAATAG
1 TTTTGATAATTTTTTAAAATAG
* *
18052031 TTTTTATAATTTTTTGAAAT
1 TTTTGATAATTTTTTAAAAT
18052051 TTTTAAATTT
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:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTTGATAATTTTTTAAAATAG
Found at i:18053624 original size:43 final size:43
Alignment explanation
Indices: 18053563--18053647 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
18053553 TCCCCACAAG
*
18053563 ATGACGCGGGAGCTGATCAAGTGGTATGGAGGTTAAGGGTGAT
1 ATGACGCGGGAGCTGATCAAGTGGTATGGAGGTCAAGGGTGAT
18053606 ATGACGCGGGAGCTGATCAAGTGGTATGGAGGTCAAGGGTGA
1 ATGACGCGGGAGCTGATCAAGTGGTATGGAGGTCAAGGGTGA
18053648 AGCCAGAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.26, C:0.11, G:0.42, T:0.21
Consensus pattern (43 bp):
ATGACGCGGGAGCTGATCAAGTGGTATGGAGGTCAAGGGTGAT
Found at i:18059817 original size:406 final size:406
Alignment explanation
Indices: 18059023--18060242 Score: 2066
Period size: 406 Copynumber: 3.0 Consensus size: 406
18059013 AACTTATTCA
* *
18059023 TTCCATAGAGTATTTGGCTGCTTATGCTTTCCAAACCTTCGA-CATACAATACTTGAAAACTACA
1 TTCCTTAGAGTATTTGGCTGCTTATGCTTTCCAAACCTTCGACCATACAATACTTAAAAACTACA
18059087 GTATAGGTCAACTCCATGCACATTTTTGGGGTATTCACCATGTCATAAAGGGTATCGTTGTCAGG
66 GTATAGGTCAACTCCATGCACATTTTTGGGGTATTCACCATGTCATAAAGGGTATCGTTGTCAGG
* *
18059152 CTGCTGATGGAAGGGTTTATATTTCCTGTCATGTTACATTTCATGAAAATGAATTTCCATTTAAA
131 CTGCTGATGGAAGGGTCTATATTTCCCGTCATGTTACATTTCATGAAAATGAATTTCCATTTAAA
* * * * *
18059217 ACTCTCCACCCTAAGTCTGCAGCTTCCATACCTTCTATTTCGTAGTCTAGTTATAAACTTCTTGT
196 ACTCTCCGCCCCAAGTCTGCAGCTTCCATACCTTCTACTTCGCAGTCTAGTTCTAAACTTCTTGT
* * * *
18059282 TATGACATCAGTTCATACAACTCAGGGTACTCCAATAGTTAATGC-TCCAATAGTTACTAGTGTT
261 TATGACACCAGTTCATACAGCTCAGGGTACTCCAGTAGTTAAT-CTTCCAATGGTTACTAGTGTT
* *
18059346 AATTCATTGAATGAGGTTTTTGTGCTCAGTGTTGATACTCCACACAGTCCCCTTGTGTAAGTTCT
325 AATTCATTGAATGAGGTTCTTGTGCTCAGTGTTGATACTCCACACAGTCCCCTTATGTAAGTTCT
*
18059411 AATTCTAGAAGTTTTAG
390 AGTTCTAGAAGTTTTAG
18059428 TTCCTTAGAGTATTTGGCTGCTTATGCTTTCCAAACCTTCGACCATACAATACTTAAAAACTACA
1 TTCCTTAGAGTATTTGGCTGCTTATGCTTTCCAAACCTTCGACCATACAATACTTAAAAACTACA
*
18059493 GTATAGGTCAACTCCATGCACATTTTTGGGGTATTCACCATGTTATAAAGGGTATCGTTGTCAGG
66 GTATAGGTCAACTCCATGCACATTTTTGGGGTATTCACCATGTCATAAAGGGTATCGTTGTCAGG
*
18059558 CTGCTGATGGAAGGGTCTATATTTCCCGTCATGTTACATTTCATGAAAATGAATTTCCATTTAAC
131 CTGCTGATGGAAGGGTCTATATTTCCCGTCATGTTACATTTCATGAAAATGAATTTCCATTTAAA
*
18059623 ACTCTCCGCCCCAAGTCTGCAGCTTTCATACCTTCTACTTCGCAGTCTAGTTCTAAACTTCTTGT
196 ACTCTCCGCCCCAAGTCTGCAGCTTCCATACCTTCTACTTCGCAGTCTAGTTCTAAACTTCTTGT
*
18059688 TATGACACCAGTTCATACAGCTCAGGGTACTCCAGTAGTTAATCTTCCAATGGTTACTAGTATTA
261 TATGACACCAGTTCATACAGCTCAGGGTACTCCAGTAGTTAATCTTCCAATGGTTACTAGTGTTA
* *
18059753 ATTCATTGAATGAGGTTCTTGTACTCAGTGTTGATACACCACACAGTCCCCTTATGTAAGTTCTA
326 ATTCATTGAATGAGGTTCTTGTGCTCAGTGTTGATACTCCACACAGTCCCCTTATGTAAGTTCTA
*
18059818 GTTCTAGAAGTTCTAG
391 GTTCTAGAAGTTTTAG
* * *
18059834 TTCCTTAGAGTATTTGGCTGCTTATGCTTTCCGAACCTTCGACTATACAATACTTTAAAACTACA
1 TTCCTTAGAGTATTTGGCTGCTTATGCTTTCCAAACCTTCGACCATACAATACTTAAAAACTACA
* *
18059899 GTATAGGTCAACTCCATGCACATTTTTAGGGTATTCACCATGTCATAAAGGGTATCGTTGTCAAG
66 GTATAGGTCAACTCCATGCACATTTTTGGGGTATTCACCATGTCATAAAGGGTATCGTTGTCAGG
* **
18059964 CTGCTAATGGAAGGGTCTATATTTTTCGTCATGTTACATTTCATGAAAATGAATTTCCATTTAAA
131 CTGCTGATGGAAGGGTCTATATTTCCCGTCATGTTACATTTCATGAAAATGAATTTCCATTTAAA
* * *
18060029 ACTCTCCGCCCCAAGTCTGCAACTTCCATACTTTCAACTTCGCAGTCTAGTTCTAAACTTCTTGT
196 ACTCTCCGCCCCAAGTCTGCAGCTTCCATACCTTCTACTTCGCAGTCTAGTTCTAAACTTCTTGT
* *
18060094 TATGACACCAGTTCATACAGCTCAGGGTACTCCAGTAGTTAATGTTCTAATGGTTACTAGTGTTA
261 TATGACACCAGTTCATACAGCTCAGGGTACTCCAGTAGTTAATCTTCCAATGGTTACTAGTGTTA
* *
18060159 ATTCATTGAATGAGGTTCATGTGCTCAGTGTTGATACTCCACACAGTCCCCTTATGTAAGTTATA
326 ATTCATTGAATGAGGTTCTTGTGCTCAGTGTTGATACTCCACACAGTCCCCTTATGTAAGTTCTA
*
18060224 GTTCTAGAAGGTTTAG
391 GTTCTAGAAGTTTTAG
18060240 TTC
1 TTC
18060243 TGATAGGCCA
Statistics
Matches: 767, Mismatches: 46, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
405 42 0.05
406 725 0.95
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (406 bp):
TTCCTTAGAGTATTTGGCTGCTTATGCTTTCCAAACCTTCGACCATACAATACTTAAAAACTACA
GTATAGGTCAACTCCATGCACATTTTTGGGGTATTCACCATGTCATAAAGGGTATCGTTGTCAGG
CTGCTGATGGAAGGGTCTATATTTCCCGTCATGTTACATTTCATGAAAATGAATTTCCATTTAAA
ACTCTCCGCCCCAAGTCTGCAGCTTCCATACCTTCTACTTCGCAGTCTAGTTCTAAACTTCTTGT
TATGACACCAGTTCATACAGCTCAGGGTACTCCAGTAGTTAATCTTCCAATGGTTACTAGTGTTA
ATTCATTGAATGAGGTTCTTGTGCTCAGTGTTGATACTCCACACAGTCCCCTTATGTAAGTTCTA
GTTCTAGAAGTTTTAG
Found at i:18063204 original size:18 final size:18
Alignment explanation
Indices: 18063181--18063224 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
18063171 ATTTTTTTCA
*
18063181 TTGTTGTTTACTGTTGTT
1 TTGTTGTTTACTATTGTT
*
18063199 TTGTTGTTTGCTATTGTT
1 TTGTTGTTTACTATTGTT
*
18063217 TTGATGTT
1 TTGTTGTT
18063225 GTTTGCTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.07, C:0.05, G:0.23, T:0.66
Consensus pattern (18 bp):
TTGTTGTTTACTATTGTT
Found at i:18063239 original size:21 final size:21
Alignment explanation
Indices: 18063200--18063261 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
18063190 ACTGTTGTTT
* *
18063200 TGTTGTTTGCTATTGTTTTGA
1 TGTTGTTTGCTACTATTTTGA
*
18063221 TGTTGTTTGCTACTATTTTGC
1 TGTTGTTTGCTACTATTTTGA
* *
18063242 TATTATATTGCTACTATTTT
1 TGTTGT-TTGCTACTATTTT
18063262 ATTGTTATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.15, C:0.10, G:0.16, T:0.60
Consensus pattern (21 bp):
TGTTGTTTGCTACTATTTTGA
Found at i:18064124 original size:9 final size:9
Alignment explanation
Indices: 18064103--18064178 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
18064093 TAATTGATGT
*
18064103 AAAATTATT
1 AAAATTATA
18064112 AAAATTATAAA
1 AAAATTAT--A
18064123 AAAACTTATA
1 AAAA-TTATA
*
18064133 AATATTAT-
1 AAAATTATA
18064141 AAAA-TATA
1 AAAATTATA
**
18064149 ATAAATTCCA
1 A-AAATTATA
18064159 ATAAATTATA
1 A-AAATTATA
18064169 AAAA-TATA
1 AAAATTATA
18064177 AA
1 AA
18064179 TTAATAAAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
7 3 0.06
8 10 0.19
9 18 0.33
10 15 0.28
11 4 0.07
12 4 0.07
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATTATA
Found at i:18064139 original size:21 final size:20
Alignment explanation
Indices: 18064103--18064144 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
18064093 TAATTGATGT
18064103 AAAATTATTAAAATTATAAA
1 AAAATTATTAAAATTATAAA
18064123 AAAACTTA-TAAATATTATAAA
1 AAAA-TTATTAAA-ATTATAAA
18064144 A
1 A
18064145 TATAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTATTAAAATTATAAA
Found at i:18064192 original size:25 final size:26
Alignment explanation
Indices: 18064136--18064186 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
18064126 ACTTATAAAT
18064136 ATTATAAAATATAATAAATTCCAATAA
1 ATTATAAAATATAATAAATT-CAATAA
18064163 ATTATAAAA-AT-ATAAATT-AATAA
1 ATTATAAAATATAATAAATTCAATAA
18064186 A
1 A
18064187 ACTTATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 6 0.25
25 7 0.29
26 2 0.08
27 9 0.38
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (26 bp):
ATTATAAAATATAATAAATTCAATAA
Found at i:18064224 original size:32 final size:33
Alignment explanation
Indices: 18064184--18064256 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
18064174 ATAAATTAAT
18064184 AAAACTTATTTAAAA-TCTTTAAAAT-TTAAAAA
1 AAAACTTATTTAAAATTC-TTAAAATATTAAAAA
* *
18064216 AAAACTTA-TTAGAATTCTTAAAATATTATAAA
1 AAAACTTATTTAAAATTCTTAAAATATTAAAAA
*
18064248 AAAATTTAT
1 AAAACTTAT
18064257 AAAAAAAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 12 0.34
32 23 0.66
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (33 bp):
AAAACTTATTTAAAATTCTTAAAATATTAAAAA
Found at i:18064260 original size:11 final size:13
Alignment explanation
Indices: 18064235--18064273 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
18064225 TAGAATTCTT
18064235 AAAATATTATAAA
1 AAAATATTATAAA
18064248 AAAAT-TTATAAA
1 AAAATATTATAAA
18064260 AAAAGTATTA-AAA
1 AAAA-TATTATAAA
18064273 A
1 A
18064274 TATTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.46
13 10 0.42
14 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
AAAATATTATAAA
Found at i:18064291 original size:20 final size:19
Alignment explanation
Indices: 18064259--18064312 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
18064249 AAATTTATAA
*
18064259 AAAAAGTAT-TAAAAATAT
1 AAAAATTATATAAAAATAT
* **
18064277 TAAAATTGATATAAACTTAT
1 AAAAATT-ATATAAAAATAT
18064297 AAAAATTATATAAAAA
1 AAAAATTATATAAAAA
18064313 AATCATAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
18 5 0.19
19 9 0.33
20 13 0.48
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAAATTATATAAAAATAT
Found at i:18064770 original size:21 final size:22
Alignment explanation
Indices: 18064733--18064773 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18064723 TATAACTTTA
*
18064733 TATCAATTTTAATACTTTTTTT
1 TATCAAATTTAATACTTTTTTT
18064755 TATCAAATTT-ATACTTTTT
1 TATCAAATTTAATACTTTTT
18064774 AAAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (22 bp):
TATCAAATTTAATACTTTTTTT
Found at i:18064840 original size:21 final size:21
Alignment explanation
Indices: 18064801--18064840 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18064791 GATTTGTATG
* * *
18064801 GTTTTTATAGAGTTTTAATAC
1 GTTTTTATAAAATTATAATAC
18064822 GTTTTTATAAAATTATAAT
1 GTTTTTATAAAATTATAAT
18064841 TATGTTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
GTTTTTATAAAATTATAATAC
Found at i:18064886 original size:16 final size:17
Alignment explanation
Indices: 18064862--18064894 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18064852 ATATATTTTT
18064862 ATAATTTTTAATATTTA
1 ATAATTTTTAATATTTA
18064879 ATAATTTTT-ATATTTA
1 ATAATTTTTAATATTTA
18064895 TGATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTTTAATATTTA
Found at i:18065263 original size:26 final size:27
Alignment explanation
Indices: 18065231--18065288 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
18065221 GTATTTTTTA
18065231 TTTTTA-TTTTTTACTTTTAAAATATT
1 TTTTTATTTTTTTACTTTTAAAATATT
*
18065257 TTTTTATTTTTTTATTTTTAAAATATT
1 TTTTTATTTTTTTACTTTTAAAATATT
18065284 TTTTT
1 TTTTT
18065289 GTATTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTTTATTTTTTTACTTTTAAAATATT
Found at i:18066585 original size:26 final size:26
Alignment explanation
Indices: 18066552--18066604 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
18066542 TTAATTTTTT
18066552 AAAATGAAAAATATTAAAAAATTATA
1 AAAATGAAAAATATTAAAAAATTATA
*
18066578 AAAATGAAAAATATTAAAATATTATA
1 AAAATGAAAAATATTAAAAAATTATA
18066604 A
1 A
18066605 TTGATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (26 bp):
AAAATGAAAAATATTAAAAAATTATA
Found at i:18066614 original size:26 final size:23
Alignment explanation
Indices: 18066553--18066631 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 23
18066543 TAATTTTTTA
18066553 AAATGAAAAATATTAAAAAATTAT
1 AAATGAAAAATATT-AAAAATTAT
18066577 AAAAATGAAAAATATTAAAATATTAT
1 --AAATGAAAAATATTAAAA-ATTAT
* *
18066603 AATTGATTAAAATAATATAAAATTAT
1 AAATGA--AAAATATTA-AAAATTAT
18066629 AAA
1 AAA
18066632 ATCGATTACC
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 5 0.11
25 4 0.09
26 34 0.74
27 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATGAAAAATATTAAAAATTAT
Found at i:18072106 original size:44 final size:43
Alignment explanation
Indices: 18072009--18072298 Score: 170
Period size: 44 Copynumber: 6.7 Consensus size: 43
18071999 TTCAATCTAT
* *
18072009 TCCACTGCAACTTCAAGGA-GATAAGATTTGCCATCTTCAGTCTGGC
1 TCCACTGCAACTTC-AGGAGGATAAGACTTGCCAT-TT-AGTC-CGC
18072055 T-CACTGCAACTTCAGGAGGATAAGACTTGCCTATTTAGTCCGC
1 TCCACTGCAACTTCAGGAGGATAAGACTTGCC-ATTTAGTCCGC
* * * *
18072098 TCCACTGCAACTGCAGG-GAGATAAGACTAG--ATGT-GATCTG-
1 TCCACTGCAACTTCAGGAG-GATAAGACTTGCCATTTAG-TCCGC
*** * ** *
18072138 TTTTCTGCAACTTCA-GAGAGATAAGATCTAAG-GTTTTAATCCGC
1 TCCACTGCAACTTCAGGAG-GATAAGA-CT-TGCCATTTAGTCCGC
* * * * * *
18072182 TCCACTGCAACTTCAGGAAGATAGGATTATCGGC-TTTAATCTGC
1 TCCACTGCAACTTCAGGAGGATAAGACT-T-GCCATTTAGTCCGC
* *
18072226 TCCACTGCAACTTCAGGAAGATAAGACTTACCATCTTCAGTCCGC
1 TCCACTGCAACTTCAGGAGGATAAGACTTGCCAT-TT-AGTCCGC
*
18072271 CCCACTGCAACTTCAGG-GAGATAAGACT
1 TCCACTGCAACTTCAGGAG-GATAAGACT
18072299 AGATGCGATT
Statistics
Matches: 195, Mismatches: 31, Indels: 37
0.74 0.12 0.14
Matches are distributed among these distances:
39 1 0.01
40 21 0.11
41 8 0.04
42 3 0.02
43 13 0.07
44 88 0.45
45 58 0.30
46 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (43 bp):
TCCACTGCAACTTCAGGAGGATAAGACTTGCCATTTAGTCCGC
Found at i:18072181 original size:84 final size:84
Alignment explanation
Indices: 18072088--18072383 Score: 299
Period size: 84 Copynumber: 3.5 Consensus size: 84
18072078 GACTTGCCTA
* * *
18072088 TTTAGTCCGCTCCACTGCAACTGCAGGGAGATAAGACTAGATGTGATCTGTTTTCTGCAACTTCA
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCTGTTCTCTGCAACTTCA
18072153 GAGAGATAAGATCTAAGGT
66 GAGAGATAAGATCTAAGGT
* * * * * * * *
18072172 TTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACTA---GATGTGATCTG-TTCTCTGCAAC
***
18072237 TTCAG-GAAGATAAGA-CTTACCAT
62 TTCAGAG-AGATAAGATC-TAAGGT
* * * * * *
18072260 CTTCAGTCCGCCCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATTTGCTCTCTGCAACTTC
1 -TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCTGTTCTCTGCAACTTC
* *
18072325 AGAGAGATAAAATCTGAGGT
65 AGAGAGATAAGATCTAAGGT
* *
18072345 TTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGACTA
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACTA
18072384 TCGGCTTTAA
Statistics
Matches: 165, Mismatches: 38, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
84 68 0.41
85 22 0.13
86 8 0.05
87 10 0.06
88 24 0.15
89 33 0.20
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (84 bp):
TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCTGTTCTCTGCAACTTCA
GAGAGATAAGATCTAAGGT
Found at i:18072270 original size:173 final size:173
Alignment explanation
Indices: 18072056--18072449 Score: 589
Period size: 173 Copynumber: 2.3 Consensus size: 173
18072046 CAGTCTGGCT
*
18072056 CACTGCAACTTCAGGAGGATAAGACTTGCCTAT-TT-AGTCCGCTCCACTGCAACTGCAGGGAGA
1 CACTGCAACTTCAGGAAGATAAGACTTGCC-ATCTTCAGTCCGCTCCACTGCAACTGCAGGGAGA
* * * *
18072119 TAAGACTAGATGTGATCTGTTTTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTC
65 TAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAAATCTAAGGTTTTAATCCGCTC
* *
18072184 CACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAATCTGCTC
130 CACTGCAACTTCAGGAAGATAGGACTATCGGCTTTAATCTACTC
* * *
18072228 CACTGCAACTTCAGGAAGATAAGACTTACCATCTTCAGTCCGCCCCACTGCAACTTCAGGGAGAT
1 CACTGCAACTTCAGGAAGATAAGACTTGCCATCTTCAGTCCGCTCCACTGCAACTGCAGGGAGAT
* *
18072293 AAGACTAGATGCGATTTGCTCTCTGCAACTTCAGAGAGATAAAATCTGAGGTTTTAATCCGCTCC
66 AAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAAATCTAAGGTTTTAATCCGCTCC
* *
18072358 ACTGTAACTTCAGGGAGATAGGACTATCGGCTTTAATCTACTC
131 ACTGCAACTTCAGGAAGATAGGACTATCGGCTTTAATCTACTC
* *
18072401 CACTACAACTTCAAGG-AGATAAGACTTGCCATCTTC-GATCTGCTCCACT
1 CACTGCAACTTC-AGGAAGATAAGACTTGCCATCTTCAG-TCCGCTCCACT
18072450 ACTGCTTAGG
Statistics
Matches: 200, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
171 2 0.01
172 31 0.16
173 164 0.82
174 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (173 bp):
CACTGCAACTTCAGGAAGATAAGACTTGCCATCTTCAGTCCGCTCCACTGCAACTGCAGGGAGAT
AAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAAATCTAAGGTTTTAATCCGCTCC
ACTGCAACTTCAGGAAGATAGGACTATCGGCTTTAATCTACTC
Found at i:18072393 original size:44 final size:43
Alignment explanation
Indices: 18072056--18072426 Score: 229
Period size: 44 Copynumber: 8.6 Consensus size: 43
18072046 CAGTCTGGCT
* * *
18072056 CACTGCAACTTCA-GGAGGATAAGACT-TGCCTATTTAGTCCGCTC
1 CACTGCAACTTCAGGGA-GATAAGACTACGGC--TTTAATCCGCTC
* * * * * *
18072100 CACTGCAACTGCAGGGAGATAAGACTA--GATGTGATCTG-TT
1 CACTGCAACTTCAGGGAGATAAGACTACGGCTTTAATCCGCTC
** * * *
18072140 TTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTC
1 CACTGCAACTTCAGGGAGATAAGA-CTACGGCTTTAATCCGCTC
* * * *
18072184 CACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTA-CGGCTTTAATCCGCTC
* ** * * *
18072228 CACTGCAACTTCAGGAAGATAAGACTTACCATCTTCAGTCCGCCC
1 CACTGCAACTTCAGGGAGATAAGAC-TA-CGGCTTTAATCCGCTC
* *** **
18072273 CACTGCAACTTCAGGGAGATAAGACTA--GATGCGATTTGCT-
1 CACTGCAACTTCAGGGAGATAAGACTACGGCTTTAATCCGCTC
* * * *
18072313 CTCTGCAACTTCAGAGAGATAAAATCTGA-GGTTTTAATCCGCTC
1 CACTGCAACTTCAGGGAGATAAGA-CT-ACGGCTTTAATCCGCTC
* * **
18072357 CACTGTAACTTCAGGGAGATAGGACTATCGGCTTTAATCTACTC
1 CACTGCAACTTCAGGGAGATAAGACTA-CGGCTTTAATCCGCTC
* *
18072401 CACTACAACTTCAAGGAGATAAGACT
1 CACTGCAACTTCAGGGAGATAAGACT
18072427 TGCCATCTTC
Statistics
Matches: 248, Mismatches: 65, Indels: 28
0.73 0.19 0.08
Matches are distributed among these distances:
40 42 0.17
41 15 0.06
42 2 0.01
43 18 0.07
44 132 0.53
45 39 0.16
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (43 bp):
CACTGCAACTTCAGGGAGATAAGACTACGGCTTTAATCCGCTC
Found at i:18072463 original size:44 final size:44
Alignment explanation
Indices: 18072392--18072581 Score: 109
Period size: 44 Copynumber: 4.3 Consensus size: 44
18072382 TATCGGCTTT
* ** *
18072392 AATCTACTCCACTACAACTTCAAGGAGATAAGACTTGCCATCTTC
1 AATCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGCCATCTTC
* ** *
18072437 GATCTGCTCCACTACTGCTTAGGGAGATAAGA-TCTGTAATTTTC
1 AATCTGCTCCACTACTGCTTAGGGAGATAAGACT-TGCCATCTTC
* * * * * **** *
18072481 AACCTACTCCACTGCTGCTCAGGGAGATAAGGCTTGGTGGCTTA
1 AATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGCCATCTTC
* * *
18072525 AATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTTGCCGTCTTC
1 AATCTGC-T-CCACTACTGCTTAGG-GAGATAAGACTTGCCATCTTC
*
18072569 GATCTGCTCCACT
1 AATCTGCTCCACT
18072582 GTCGATGCAG
Statistics
Matches: 108, Mismatches: 32, Indels: 13
0.71 0.21 0.08
Matches are distributed among these distances:
42 5 0.05
43 4 0.04
44 75 0.69
45 19 0.18
46 5 0.05
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGCCATCTTC
Found at i:18077936 original size:142 final size:142
Alignment explanation
Indices: 18077764--18078047 Score: 523
Period size: 142 Copynumber: 2.0 Consensus size: 142
18077754 AAATTATCTT
*
18077764 ACTTTTCTTTCAGCATTGGAACCTCAGTTCTCCCTTGAAAATATCTCCCTAGCCCTCTTTCGGGT
1 ACTTTTCTTTCAGCATTGGAACCTCAGTTCTCCCTTGAAAATATCTCCCTAGCCCTCTTCCGGGT
*
18077829 AAAGCTCATTTTCCCACCAACAACTGTAAACCCATCTCTGTAGTTTTGGATAATTTTGGCACCAA
66 AAAGATCATTTTCCCACCAACAACTGTAAACCCATCTCTGTAGTTTTGGATAATTTTGGCACCAA
18077894 AATTTTGCTCCC
131 AATTTTGCTCCC
*
18077906 ACTTTTCTTTCAGCATTGGAACCTCAGTTCTCCCTTGAAGATATCTCCCTAGCCCTCTTCCGGGT
1 ACTTTTCTTTCAGCATTGGAACCTCAGTTCTCCCTTGAAAATATCTCCCTAGCCCTCTTCCGGGT
*
18077971 AAAGATCTTTTTCCCACCAACAACTGTAAACCCATCTCTGTAGTTTTGGATAATTTTGGCACCAA
66 AAAGATCATTTTCCCACCAACAACTGTAAACCCATCTCTGTAGTTTTGGATAATTTTGGCACCAA
*
18078036 AATTTTGTTCCC
131 AATTTTGCTCCC
18078048 TTCAGGAACA
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 137 1.00
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.35
Consensus pattern (142 bp):
ACTTTTCTTTCAGCATTGGAACCTCAGTTCTCCCTTGAAAATATCTCCCTAGCCCTCTTCCGGGT
AAAGATCATTTTCCCACCAACAACTGTAAACCCATCTCTGTAGTTTTGGATAATTTTGGCACCAA
AATTTTGCTCCC
Found at i:18087358 original size:10 final size:10
Alignment explanation
Indices: 18087333--18087382 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
18087323 TTTAATTTTT
18087333 TAAAAAATTA
1 TAAAAAATTA
* *
18087343 TTAAAAACTA
1 TAAAAAATTA
18087353 TAAAAAATTA
1 TAAAAAATTA
* *
18087363 TTAAAAATTG
1 TAAAAAATTA
*
18087373 TAAATAATTA
1 TAAAAAATTA
18087383 ACAGATCGAG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:18087621 original size:20 final size:19
Alignment explanation
Indices: 18087596--18087715 Score: 100
Period size: 20 Copynumber: 6.0 Consensus size: 19
18087586 ACTAGTTCAT
18087596 AATTTTTAAATAATTTTTAC
1 AATTTTT-AATAATTTTTAC
*
18087616 AATTTTTAATAATTATTTGC
1 AATTTTTAATAATT-TTTAC
* * *
18087636 AGTTTTTAAATAATGGTTTAT
1 AATTTTT-AATAAT-TTTTAC
18087657 AATTTTTAATAAATTTTTAC
1 AATTTTTAAT-AATTTTTAC
18087677 AA-TTTTAA-AATATTTTAAAC
1 AATTTTTAATAAT-TTTT--AC
* *
18087697 AATATTTAATATTTTTTAC
1 AATTTTTAATAATTTTTAC
18087716 TTTTCACCAT
Statistics
Matches: 81, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
17 3 0.04
18 4 0.05
19 15 0.19
20 30 0.37
21 27 0.33
22 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.53
Consensus pattern (19 bp):
AATTTTTAATAATTTTTAC
Found at i:18087643 original size:40 final size:39
Alignment explanation
Indices: 18087596--18087715 Score: 125
Period size: 41 Copynumber: 3.0 Consensus size: 39
18087586 ACTAGTTCAT
*
18087596 AATTTTTAAATAATTTTTACAATTTTTAATAATTATTTGC
1 AATTTTTAAATAATTTTTACAATTTTTAATAATT-TTTAC
* * *
18087636 AGTTTTTAAATAATGGTTTATAATTTTTAATAAATTTTTAC
1 AATTTTTAAATAAT-TTTTACAATTTTTAAT-AATTTTTAC
* * * *
18087677 AATTTTAAAAT-ATTTTAAACAATATTTAATATTTTTTAC
1 AATTTTTAAATAATTTT-TACAATTTTTAATAATTTTTAC
18087716 TTTTCACCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
39 10 0.15
40 25 0.38
41 27 0.41
42 4 0.06
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.53
Consensus pattern (39 bp):
AATTTTTAAATAATTTTTACAATTTTTAATAATTTTTAC
Found at i:18088935 original size:272 final size:273
Alignment explanation
Indices: 18088438--18088979 Score: 811
Period size: 272 Copynumber: 2.0 Consensus size: 273
18088428 AATATAGGCA
* *
18088438 TGAAAATGGGTTTGGACAAAAAAATAGGACACGTTTAAAAAACGGGCCAAGCCTTAGGTAAGATA
1 TGAAAATGGGTTTGGACAAAAAAATAAGACACGTTTAAAAAACGGGCCAAGCCTTAGGTAAGACA
* * *
18088503 TTTTTTACCCAAGCCCAGCCCGAATTCACAAAAGGACTAAAAATTGCTATTTTTGTTGTTTTAAT
66 TTTTTTACCCAAGCCCAGCCCGAATTCACAAAAGGACAAAAAACTGCTATTTTTGTTATTTTAAT
* **
18088568 ACTATTTTATTGTTGTTTTCTCCCTATTTTACTATTATATCACTATTATATTATTACTATTTTGT
131 ACTA--TTATTCTTGTTTTCTCCCTATTTTACTACCATATCACTATTATATTATTACTATTTTGT
* *
18088633 TGTTATTATTTGAATATTGTATAACACTTGTTTTATTGTTAGTTTTGTTATTATTTTAGAGGCAT
194 TGTTATTATTTGAATATTGTATAACACTTGTTTTATTGTTAATTTTATTATTATTTTAGAGGCAT
*
18088698 TTGCTTGTTATTATT
259 TTACTTGTTATTATT
* * *
18088713 TGAAAATGGGTTTTGG-C-AAAAAATAAGACCCTTTTAAAAAATGGGCCAAGCCTTAGGTAAGAC
1 TGAAAATGGG-TTTGGACAAAAAAATAAGACACGTTTAAAAAACGGGCCAAGCCTTAGGTAAGAC
** ** * *
18088776 ATTTTTTACCCGGGCCTGGCCCGAATTCATAAAAGGACAAAAAACTGGTATTTTTTGTTATTTTA
65 ATTTTTTACCCAAGCCCAGCCCGAATTCACAAAAGGACAAAAAACTGCTA-TTTTTGTTATTTTA
* * * *
18088841 ATACTA-TCTTCTTGTTTTCTCCCTATTTTGCTACCATTTCACTATTATGTTATTACTATTTTGT
129 ATACTATTATTCTTGTTTTCTCCCTATTTTACTACCATATCACTATTATATTATTACTATTTTGT
18088905 TGTTATTATTTGAATATTGTATAACACTTGTTTTATTGTTAATTTTATTATTATTTTAGAGGCAT
194 TGTTATTATTTGAATATTGTATAACACTTGTTTTATTGTTAATTTTATTATTATTTTAGAGGCAT
18088970 TTACTTGTTA
259 TTACTTGTTA
18088980 AGTTGCATCT
Statistics
Matches: 241, Mismatches: 24, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
272 123 0.51
274 83 0.34
275 30 0.12
276 5 0.02
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (273 bp):
TGAAAATGGGTTTGGACAAAAAAATAAGACACGTTTAAAAAACGGGCCAAGCCTTAGGTAAGACA
TTTTTTACCCAAGCCCAGCCCGAATTCACAAAAGGACAAAAAACTGCTATTTTTGTTATTTTAAT
ACTATTATTCTTGTTTTCTCCCTATTTTACTACCATATCACTATTATATTATTACTATTTTGTTG
TTATTATTTGAATATTGTATAACACTTGTTTTATTGTTAATTTTATTATTATTTTAGAGGCATTT
ACTTGTTATTATT
Found at i:18089109 original size:11 final size:11
Alignment explanation
Indices: 18089095--18089125 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
18089085 TATATATATT
18089095 TAAAAATTATA
1 TAAAAATTATA
*
18089106 TAAAAATAATA
1 TAAAAATTATA
18089117 TAAAAATTA
1 TAAAAATTA
18089126 ATACAAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:18090620 original size:36 final size:36
Alignment explanation
Indices: 18090557--18090628 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
18090547 AACGCGTTTT
* *
18090557 GTAGAAAGTGTTTTCTAACATTGCAGCTGAAAACGC
1 GTAGAAAGTGTTTTCCAACATTGCAGCTAAAAACGC
*
18090593 GTAGAAAGTGTTTTCCAATA-TGTCAGCTAAAAACGC
1 GTAGAAAGTGTTTTCCAACATTG-CAGCTAAAAACGC
18090629 TTCCTGCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (36 bp):
GTAGAAAGTGTTTTCCAACATTGCAGCTAAAAACGC
Found at i:18090717 original size:23 final size:23
Alignment explanation
Indices: 18090648--18090720 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
18090638 AAAGCGTTTT
* *
18090648 CTATTTCTCTCTTCAACATCGAC
1 CTATTTCTCTCTTCAAAATTGAC
* *
18090671 CTA-TT-TCTC-T-AAATCTGTGGC
1 CTATTTCTCTCTTCAAA-AT-TGAC
18090692 CTATTTCTCTCTTCAAAATTGAC
1 CTATTTCTCTCTTCAAAATTGAC
18090715 CTATTT
1 CTATTT
18090721 TCTTCAAGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 9 0.24
22 4 0.11
23 16 0.42
24 2 0.05
25 3 0.08
ACGTcount: A:0.22, C:0.27, G:0.07, T:0.44
Consensus pattern (23 bp):
CTATTTCTCTCTTCAAAATTGAC
Found at i:18091564 original size:44 final size:44
Alignment explanation
Indices: 18091514--18091601 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
18091504 AATTTTAAAA
* *
18091514 AATAGAAGTTGTGATAATTATACATCTAAAAATAATTATAATTT
1 AATAGAAGTTGTGATAATTACACATCTAAAAATAATTAGAATTT
* *
18091558 AATAGAAGTTGTGATAATTGCACATTTAAAAATAATTAGAATTT
1 AATAGAAGTTGTGATAATTACACATCTAAAAATAATTAGAATTT
18091602 CCTTTCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.38
Consensus pattern (44 bp):
AATAGAAGTTGTGATAATTACACATCTAAAAATAATTAGAATTT
Found at i:18098738 original size:38 final size:38
Alignment explanation
Indices: 18098687--18098761 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
18098677 GATAACTCCA
* * *
18098687 CAATCCCATATTTTCCTCCTAAAGTCACTCCAACACTT
1 CAATCCCACATTTTCCTCCCAAAATCACTCCAACACTT
*
18098725 CAATCCCACATTTTCCTCCCAAAATCACTCTAACACT
1 CAATCCCACATTTTCCTCCCAAAATCACTCCAACACT
18098762 CCCCCACCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.31, C:0.39, G:0.01, T:0.29
Consensus pattern (38 bp):
CAATCCCACATTTTCCTCCCAAAATCACTCCAACACTT
Found at i:18105082 original size:82 final size:82
Alignment explanation
Indices: 18104984--18105288 Score: 432
Period size: 82 Copynumber: 3.7 Consensus size: 82
18104974 CCGGCTTTTG
* * * * * *
18104984 GCCTGCTAGACTTAAAGTCCGAAATATTTCACCGGCATCAAGCCTACTAGACGTAAAG-TCTGAA
1 GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAAGCCTGCTAGACATAAAGTTC-GAA
*
18105048 ACATTTCACTGGCATCAA
65 ATATTTCACTGGCATCAA
*
18105066 GCCTGCTAGACGTAAAGTCTGAAACATTTCTCCAGCATCAAGCCTGCTAGACATAAAGTTCGAAA
1 GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAAGCCTGCTAGACATAAAGTTCGAAA
* *
18105131 TATTTCACCGACATCAA
66 TATTTCACTGGCATCAA
*
18105148 GCCTGCTAAACGTAAAGTCTGAAACATTTCACCAGCATCAAGCCTGCTAGACATAAAGTTCGAAA
1 GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAAGCCTGCTAGACATAAAGTTCGAAA
*
18105213 TATTTCATTGGCATCAA
66 TATTTCACTGGCATCAA
* * * ** *
18105230 GCTTGCTAGATGTAAAGTCTAAAACATTTCACTTGCATCAAGCCTGCTAGACGTAAAGT
1 GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAAGCCTGCTAGACATAAAGT
18105289 CTGAGTCATC
Statistics
Matches: 200, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
82 198 0.99
83 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (82 bp):
GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAAGCCTGCTAGACATAAAGTTCGAAA
TATTTCACTGGCATCAA
Found at i:18105290 original size:41 final size:41
Alignment explanation
Indices: 18104984--18105292 Score: 381
Period size: 41 Copynumber: 7.5 Consensus size: 41
18104974 CCGGCTTTTG
* * * *
18104984 GCCTGCTAGACTTAAAGTCCGAAATATTTCACCGGCATCAA
1 GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAA
* **
18105025 GCCTACTAGACGTAAAGTCTGAAACATTTCACTGGCATCAA
1 GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAA
*
18105066 GCCTGCTAGACGTAAAGTCTGAAACATTTCTCCAGCATCAA
1 GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAA
* *
18105107 GCCTGCTAGACATAAAGT-TCGAAATATTTCACC-GACATCAA
1 GCCTGCTAGACGTAAAGTCT-GAAACATTTCACCAG-CATCAA
*
18105148 GCCTGCTAAACGTAAAGTCTGAAACATTTCACCAGCATCAA
1 GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAA
* * ***
18105189 GCCTGCTAGACATAAAGT-TCGAAATATTTCATTGGCATCAA
1 GCCTGCTAGACGTAAAGTCT-GAAACATTTCACCAGCATCAA
* * * **
18105230 GCTTGCTAGATGTAAAGTCTAAAACATTTCACTTGCATCAA
1 GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAA
18105271 GCCTGCTAGACGTAAAGTCTGA
1 GCCTGCTAGACGTAAAGTCTGA
18105293 GTCATCTTAC
Statistics
Matches: 231, Mismatches: 31, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
40 3 0.01
41 225 0.97
42 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (41 bp):
GCCTGCTAGACGTAAAGTCTGAAACATTTCACCAGCATCAA
Found at i:18105318 original size:2 final size:2
Alignment explanation
Indices: 18105311--18105351 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
18105301 ACTTTCAAAC
18105311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18105352 CAAATCCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18108127 original size:57 final size:58
Alignment explanation
Indices: 18108052--18108171 Score: 190
Period size: 57 Copynumber: 2.1 Consensus size: 58
18108042 TTCAGGTCAT
18108052 TTTCATTTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTTC-ATTTCTCCA
1 TTTCATTTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTTCTATTTCTCCA
** *
18108109 TGTTCA-TTTTCATTTTGGAGAAAACCTTAATCATTTCCAAATGTTTTCTATTTCTCCA
1 T-TTCATTTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTTCTATTTCTCCA
18108167 TTTCA
1 TTTCA
18108172 CCATTTTTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
57 44 0.76
58 14 0.24
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (58 bp):
TTTCATTTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTTCTATTTCTCCA
Found at i:18114550 original size:29 final size:29
Alignment explanation
Indices: 18114464--18114598 Score: 135
Period size: 29 Copynumber: 4.6 Consensus size: 29
18114454 ACCCTTTTAA
* * * **
18114464 AAATTTTATAGTTTTTCCACTGGTTTTTTT
1 AAATTTTACAATTTTGCCACT-GTTTTTCC
* *
18114494 AGATTTTACAATTTTGCCACTGGTTTTCC
1 AAATTTTACAATTTTGCCACTGTTTTTCC
* *
18114523 AAATTTTATAGTTTTGCCACTGTTTTTCC
1 AAATTTTACAATTTTGCCACTGTTTTTCC
** * * *
18114552 GGATTTTACAATTCTGCCACTATTTTTCA
1 AAATTTTACAATTTTGCCACTGTTTTTCC
18114581 AAATTTTACAATTTTGCC
1 AAATTTTACAATTTTGCC
18114599 CAAAATTTTC
Statistics
Matches: 84, Mismatches: 21, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
29 67 0.80
30 17 0.20
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (29 bp):
AAATTTTACAATTTTGCCACTGTTTTTCC
Found at i:18114570 original size:58 final size:59
Alignment explanation
Indices: 18114458--18114598 Score: 176
Period size: 58 Copynumber: 2.4 Consensus size: 59
18114448 TGCACCACCC
* * ** * *
18114458 TTTTAAAAATTTTATAGTTTTTCCACTGGTTTTTTTAGATTTTACAATTTTGCCACTGG
1 TTTTCAAAATTTTATAGTTTTGCCACTGGTTTTTCCAGATTTTACAATTCTGCCACTAG
* * *
18114517 TTTTCCAAATTTTATAGTTTTGCCACT-GTTTTTCCGGATTTTACAATTCTGCCACTAT
1 TTTTCAAAATTTTATAGTTTTGCCACTGGTTTTTCCAGATTTTACAATTCTGCCACTAG
* *
18114575 TTTTCAAAATTTTACAATTTTGCC
1 TTTTCAAAATTTTATAGTTTTGCC
18114599 CAAAATTTTC
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
58 46 0.66
59 24 0.34
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.50
Consensus pattern (59 bp):
TTTTCAAAATTTTATAGTTTTGCCACTGGTTTTTCCAGATTTTACAATTCTGCCACTAG
Found at i:18115690 original size:37 final size:37
Alignment explanation
Indices: 18115633--18115733 Score: 103
Period size: 37 Copynumber: 2.7 Consensus size: 37
18115623 TATTGAATTG
** *
18115633 ATTGATATGCGAAACCGTTTGTTATTATGTTAAATAA
1 ATTGATATGCGAAATTGTTTGTTATTATATTAAATAA
* * * * **
18115670 ATTGATATGCAAAATTGTTTGTCATTGTATTGAATTG
1 ATTGATATGCGAAATTGTTTGTTATTATATTAAATAA
* *
18115707 ATTGACATGTGAAATTGTTTGTTATTA
1 ATTGATATGCGAAATTGTTTGTTATTA
18115734 CTTTACATAT
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.45
Consensus pattern (37 bp):
ATTGATATGCGAAATTGTTTGTTATTATATTAAATAA
Found at i:18116373 original size:28 final size:29
Alignment explanation
Indices: 18116341--18116398 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
18116331 ATCAGTTCAA
* *
18116341 TTTTATTTTTTTGAATGT-CCCCTAAAAT
1 TTTTATTTTTTTCAATATACCCCTAAAAT
18116369 TTTTATTTTTTTCAATATAACCCCTAAAAT
1 TTTTATTTTTTTCAATAT-ACCCCTAAAAT
18116399 CGAAATAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.16, G:0.03, T:0.52
Consensus pattern (29 bp):
TTTTATTTTTTTCAATATACCCCTAAAAT
Found at i:18117316 original size:23 final size:21
Alignment explanation
Indices: 18117276--18117339 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 21
18117266 ACTTAAATCC
18117276 TTTTTCTCAAATTCTCTCATA
1 TTTTTCTCAAATTCTCTCATA
18117297 TTTTTCTCCAATATTCTCTCATA
1 TTTTTCT-CAA-ATTCTCTCATA
**
18117320 TTTCCCTCAAATTCCTCTCA
1 TTTTTCTCAAATT-CTCTCA
18117340 AATTCCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 10 0.26
22 12 0.32
23 16 0.42
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTTCTCAAATTCTCTCATA
Found at i:18117339 original size:11 final size:11
Alignment explanation
Indices: 18117280--18117353 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
18117270 AAATCCTTTT
18117280 TCTCAAATT-C
1 TCTCAAATTCC
* **
18117290 TCTCATATTTT
1 TCTCAAATTCC
18117301 TCTCCAATATT-C
1 TCT-CAA-ATTCC
*
18117313 TCTCATATTTCC
1 TCTCA-AATTCC
18117325 -CTCAAATTCC
1 TCTCAAATTCC
18117335 TCTCAAATTCC
1 TCTCAAATTCC
*
18117346 TCTTAAAT
1 TCTCAAAT
18117354 CTCTCTTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
10 13 0.25
11 28 0.55
12 7 0.14
13 3 0.06
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.45
Consensus pattern (11 bp):
TCTCAAATTCC
Found at i:18119178 original size:18 final size:18
Alignment explanation
Indices: 18119142--18119184 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
18119132 TGCCAGGTGC
* * *
18119142 GTATCCTAGCCTTTTTAT
1 GTATCCTAACCCTTATAT
18119160 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
18119178 GTTTCCT
1 GTATCCT
18119185 TTTTCTAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:18121951 original size:39 final size:39
Alignment explanation
Indices: 18121908--18121987 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
18121898 GTATTAAAGG
18121908 TTAGAAGTTTTCTTAGATTAGCTGGTTATTACAGACGGT
1 TTAGAAGTTTTCTTAGATTAGCTGGTTATTACAGACGGT
18121947 TTAGAAGTTTTCTTAGATTAGCTGGTTATTACAGACGGT
1 TTAGAAGTTTTCTTAGATTAGCTGGTTATTACAGACGGT
18121986 TT
1 TT
18121988 GTAAAGGGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (39 bp):
TTAGAAGTTTTCTTAGATTAGCTGGTTATTACAGACGGT
Found at i:18125293 original size:50 final size:50
Alignment explanation
Indices: 18125236--18125526 Score: 379
Period size: 50 Copynumber: 5.8 Consensus size: 50
18125226 ATTTGGGTAA
* * * *
18125236 AGAGGTCCCATGTAAGACTATGTTTGGGACATGACATTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
18125286 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
18125336 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
18125386 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
18125436 AGAATTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
18125485 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
18125527 TGTTATTATC
Statistics
Matches: 212, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
49 40 0.19
50 172 0.81
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:18129277 original size:125 final size:126
Alignment explanation
Indices: 18129032--18129317 Score: 472
Period size: 125 Copynumber: 2.3 Consensus size: 126
18129022 GCCAAATAGC
* *
18129032 AACTATTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCC
1 AACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCC
*
18129097 TTCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTCAGG
66 TTCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGACTTCTCAAAATTATTTTTTCAGG
*
18129158 AACTA-TGTAGCAAAAGAGCATCTACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCAT-C
1 AACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCC
*
18129221 TTGCTTAAAGCATTTTTGACAC-ATTTGCTCAGAAACGACTTCTCGAAATTATTTTTTCAGG
66 TT-CTTAAAGCATTTTTGACACTATTTGCTCAGAAACGACTTCTCAAAATTATTTTTTCAGG
*
18129282 AACTACTATAGCAAAAGAG-AGTCCACGTGGGAGCTT
1 AACTACTGTAGCAAAAGAGCA-TCCACGTGGGAGCTT
18129318 TTTTAAATTA
Statistics
Matches: 151, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
124 46 0.30
125 100 0.66
126 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (126 bp):
AACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCC
TTCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGACTTCTCAAAATTATTTTTTCAGG
Found at i:18129534 original size:96 final size:94
Alignment explanation
Indices: 18129360--18129677 Score: 359
Period size: 96 Copynumber: 3.2 Consensus size: 94
18129350 CCTAAACTCC
* *
18129360 AAACCCTAATTTATTTGAATTTTTTCCTTAAACTCTAAACTC-TAAACCCTAAAACCTAATTTAT
1 AAACCCTAATTTATTT-AA-TTTTTCCTT-AA----AAAC-CATAAACACTAAACCCTAA-TTAT
*
18129424 TTTCTTTAAAATTTATAATTAATTTACTCAAGTAACCCT
57 TTT-TTAAAAATTTATAATTAATTTACTCAAGTAACCCT
* * *
18129463 AAACCCTAATTTATTTTATTTTTCCTTAAAAACCCTTAACACTAAACCCTAATATGATTTTTTAA
1 AAACCCTAATTTATTTAATTTTTCCTTAAAAACCATAAACACTAAACCCTAAT-T-ATTTTTTAA
18129528 AAATTTATAATTAATTTACTCAAGTAACCCT
64 AAATTTATAATTAATTTACTCAAGTAACCCT
* * * * * *
18129559 AAACTCTAATTTAATTGATTTTTTCCTTAAAAACCATAAACACGAAACCCTAATCTAATTTTGAA
1 AAACCCTAATTT-ATTTAATTTTTCCTTAAAAACCATAAACACTAAACCCTAAT-TATTTTTTAA
* * *
18129624 AAATTTATAATTAATTTAATTAAGAAACCCT
64 AAATTTATAATTAATTTACTCAAGTAACCCT
*
18129655 AAACCCTTATTTATTTAATTTTT
1 AAACCCTAATTTATTTAATTTTT
18129678 TCTTTAAACC
Statistics
Matches: 189, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
95 11 0.06
96 109 0.58
97 41 0.22
100 2 0.01
101 9 0.05
102 1 0.01
103 16 0.08
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.41
Consensus pattern (94 bp):
AAACCCTAATTTATTTAATTTTTCCTTAAAAACCATAAACACTAAACCCTAATTATTTTTTAAAA
ATTTATAATTAATTTACTCAAGTAACCCT
Found at i:18129678 original size:96 final size:97
Alignment explanation
Indices: 18129431--18129685 Score: 361
Period size: 96 Copynumber: 2.6 Consensus size: 97
18129421 TATTTTCTTT
*
18129431 AAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTTA-TTTTTCCTTAAAAA
1 AAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCTTAAAAA
* * * * *
18129495 CCCTTAACACTAAACCCTAATATGATTTTTTA
66 CCATAAACACGAAACCCTAATATGAATTTTGA
* * *
18129527 AAAATTTATAATTAATTTACTCAAGTAACCCTAAACTCTAATTTAATTGATTTTTTCCTTAAAAA
1 AAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCTTAAAAA
*
18129592 CCATAAACACGAAACCCTAATCT-AATTTTGA
66 CCATAAACACGAAACCCTAATATGAATTTTGA
* * * * *
18129623 AAAATTTATAATTAATTTAATTAAGAAACCCTAAACCCTTATTTATTTAATTTTTTCTTTAAA
1 AAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCTTAAA
18129686 CCCCAAAACT
Statistics
Matches: 141, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
96 108 0.77
97 33 0.23
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.40
Consensus pattern (97 bp):
AAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCTTAAAAA
CCATAAACACGAAACCCTAATATGAATTTTGA
Found at i:18129699 original size:8 final size:8
Alignment explanation
Indices: 18129683--18129712 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
18129673 TTTTTTCTTT
18129683 AAACCCCA
1 AAACCCCA
*
18129691 AAACTCCA
1 AAACCCCA
18129699 AAACCCCA
1 AAACCCCA
18129707 AAACCC
1 AAACCC
18129713 TACCCCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (8 bp):
AAACCCCA
Found at i:18129739 original size:27 final size:29
Alignment explanation
Indices: 18129685--18129748 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 29
18129675 TTTTCTTTAA
*
18129685 ACCCCAAAACTCCAAAACCCCAAAACCCT
1 ACCCCTAAACTCCAAAACCCCAAAACCCT
*
18129714 ACCCCTAAAC-CCAAAA-TCCAAAACCCT
1 ACCCCTAAACTCCAAAACCCCAAAACCCT
*
18129741 AACCCTAA
1 ACCCCTAA
18129749 TGCAGGAGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 17 0.53
28 6 0.19
29 9 0.28
ACGTcount: A:0.45, C:0.45, G:0.00, T:0.09
Consensus pattern (29 bp):
ACCCCTAAACTCCAAAACCCCAAAACCCT
Found at i:18134818 original size:87 final size:85
Alignment explanation
Indices: 18134727--18134944 Score: 235
Period size: 86 Copynumber: 2.5 Consensus size: 85
18134717 TTAAAGGTGT
* * **
18134727 AAAAAGTCCTCAAACTTTTTTCAAAAAAAGCAATTAAGCCTTTTTTTTTTTGCACTCAATTGAGC
1 AAAAAGCCCTCAAACTTTTTTCAAAAAAAGCAATTAAGCC-CTGCTTTTTT-CACTCAATTGAGC
*
18134792 ACTTGAACTTTCAAAATGCATC
64 ACTTGAACTTTCAAAATGCAAC
** * * * * *
18134814 AAAAAGGCTTTCAAAC-ATTTTCAAGAAAAGCAATTACGCACCTGCTTTTTTCACTCAATTGGGT
1 AAAAA-GCCCTCAAACTTTTTTCAAAAAAAGCAATTAAGC-CCTGCTTTTTTCACTCAATTGAGC
18134878 ACTTGAACTTTCAAAATGCAAC
64 ACTTGAACTTTCAAAATGCAAC
* *
18134900 AAAAAGACCCTCAAAATTTTTT--AAAAATGCAATTAAGCCCCTGCT
1 AAAAAG-CCCTCAAACTTTTTTCAAAAAAAGCAATTAAG-CCCTGCT
18134945 CTTATTAAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
85 19 0.18
86 44 0.41
87 36 0.34
88 8 0.07
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (85 bp):
AAAAAGCCCTCAAACTTTTTTCAAAAAAAGCAATTAAGCCCTGCTTTTTTCACTCAATTGAGCAC
TTGAACTTTCAAAATGCAAC
Found at i:18135038 original size:18 final size:18
Alignment explanation
Indices: 18135017--18135060 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
18135007 AATAAAAATA
18135017 TAAAAAATTTAAATTTAT
1 TAAAAAATTTAAATTTAT
* *
18135035 T-AAAAATTTGAATTTTT
1 TAAAAAATTTAAATTTAT
18135052 TATAAAAAT
1 TA-AAAAAT
18135061 CGTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TAAAAAATTTAAATTTAT
Found at i:18135075 original size:36 final size:37
Alignment explanation
Indices: 18135035--18135108 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
18135025 TTAAATTTAT
** *
18135035 TAAAAATTTG-AATTTTTTATAAAAATCGTAAAAAAA
1 TAAAAATTTGTAAAATTTTATAAAAATAGTAAAAAAA
*
18135071 TAAAAATTTGTAAAATTTTATAAAAATATTAAAAAAA
1 TAAAAATTTGTAAAATTTTATAAAAATAGTAAAAAAA
18135108 T
1 T
18135109 TAACAACCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 10 0.30
37 23 0.70
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (37 bp):
TAAAAATTTGTAAAATTTTATAAAAATAGTAAAAAAA
Found at i:18135266 original size:20 final size:20
Alignment explanation
Indices: 18135241--18135297 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
18135231 TACGATAATT
18135241 TTTATAATTTTTTTACGAAA
1 TTTATAATTTTTTTACGAAA
* **
18135261 TTTAT-ATTTCTTTAC-ATT
1 TTTATAATTTTTTTACGAAA
*
18135279 TTGTATAATTTTATTACGA
1 TT-TATAATTTTTTTACGA
18135298 CTTAATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.10
19 12 0.41
20 13 0.45
21 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTATAATTTTTTTACGAAA
Found at i:18135331 original size:17 final size:17
Alignment explanation
Indices: 18135309--18135393 Score: 57
Period size: 16 Copynumber: 4.9 Consensus size: 17
18135299 TTAATAAAAT
18135309 TTTATAATTTTTTTATA
1 TTTATAATTTTTTTATA
* *
18135326 TTTATATATATTTTATAATT
1 TTTATA-AT-TTTT-TTATA
* * *
18135346 TTTATGATTTTTATATT
1 TTTATAATTTTTTTATA
* *
18135363 TTTCTAA-TTTTTAATA
1 TTTATAATTTTTTTATA
*
18135379 TTT-GAATTTTTTTAT
1 TTTATAATTTTTTTAT
18135394 TAAAATTTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
15 2 0.04
16 16 0.31
17 14 0.27
18 6 0.12
19 6 0.12
20 8 0.15
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTATAATTTTTTTATA
Found at i:18135339 original size:18 final size:18
Alignment explanation
Indices: 18135309--18135381 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 18
18135299 TTAATAAAAT
*
18135309 TTTATA-ATTTTTTTATA
1 TTTATATATATTTTTATA
18135326 TTTATATATA-TTTTATAA
1 TTTATATATATTTTTAT-A
18135344 TTT-T-TATGATTTTTATA
1 TTTATATAT-ATTTTTATA
* *
18135361 TTTTTCTA-ATTTTTAATA
1 TTTATATATATTTTT-ATA
18135379 TTT
1 TTT
18135382 GAATTTTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
16 3 0.06
17 24 0.50
18 19 0.40
19 2 0.04
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTATATATATTTTTATA
Found at i:18135348 original size:9 final size:9
Alignment explanation
Indices: 18135308--18135375 Score: 68
Period size: 9 Copynumber: 7.6 Consensus size: 9
18135298 CTTAATAAAA
18135308 TTTTATAAT
1 TTTTATAAT
*
18135317 TTTT-TTAT
1 TTTTATAAT
*
18135325 ATTTATATAT
1 TTTTATA-AT
18135335 ATTTTATAAT
1 -TTTTATAAT
*
18135345 TTTTATGAT
1 TTTTATAAT
18135354 TTTTAT-AT
1 TTTTATAAT
*
18135362 TTTTCTAAT
1 TTTTATAAT
18135371 TTTTA
1 TTTTA
18135376 ATATTTGAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
8 13 0.27
9 25 0.52
10 4 0.08
11 6 0.12
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (9 bp):
TTTTATAAT
Found at i:18135559 original size:94 final size:90
Alignment explanation
Indices: 18135461--18135692 Score: 242
Period size: 94 Copynumber: 2.5 Consensus size: 90
18135451 AATTTTTAAT
*
18135461 AAAAACATGGGCTTAATTGTTTTTTCTTTGAAAAAGTTTGAGAGTATTTTTGATGTATTTTGAAA
1 AAAAACA-GGGCTTAATTGTTTTTTCTTT-AAAAAGTTTGAGAGT-TTTTTGATGCATTTTGAAA
* *
18135526 GTTCAAGCATCCAATTGAGTGCAAAAAAA
63 GTTCAAGCACCCAAATGAGTGC-AAAAAA
* * * *
18135555 AAAAACCAGAGGCTTAATTGCTTTTTTC--TAAAAAGCATTGAGGGCCTTTTTCATGCATTTTGA
1 AAAAA-CAG-GGCTTAATTG-TTTTTTCTTTAAAAAG-TTTGAGAG-TTTTTTGATGCATTTTGA
* *
18135618 AAGTTGAAGTACCCAAATGAGTGCAAAAAA
61 AAGTTCAAGCACCCAAATGAGTGCAAAAAA
* *
18135648 AAAAA-AGGACTTAATTG--TTTT-TTTAAAAAGTTTGAGAATTTTTTG
1 AAAAACAGGGCTTAATTGTTTTTTCTTTAAAAAGTTTGAGAGTTTTTTG
18135693 CACCCTTAAG
Statistics
Matches: 116, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
86 5 0.04
87 9 0.08
88 7 0.06
90 9 0.08
91 2 0.02
93 17 0.15
94 48 0.41
95 12 0.10
96 7 0.06
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (90 bp):
AAAAACAGGGCTTAATTGTTTTTTCTTTAAAAAGTTTGAGAGTTTTTTGATGCATTTTGAAAGTT
CAAGCACCCAAATGAGTGCAAAAAA
Done.