Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009567.1 Hibiscus syriacus cultivar Beakdansim tig00116926_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 158088
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:4191 original size:21 final size:21
Alignment explanation
Indices: 4173--4258 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
4163 ATGAAGCAAG
*
4173 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
4194 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
4215 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
4236 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
4257 GG
1 GG
4259 CAGAACAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.37, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:4259 original size:21 final size:21
Alignment explanation
Indices: 4181--4269 Score: 90
Period size: 21 Copynumber: 4.2 Consensus size: 21
4171 AGGGAAACAG
* *
4181 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * * *
4203 -TAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
4223 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
4244 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
4265 AGAGA
1 AGAGA
4270 AAGTAATATA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.38, C:0.20, G:0.40, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:4770 original size:43 final size:44
Alignment explanation
Indices: 4625--4832 Score: 166
Period size: 43 Copynumber: 4.9 Consensus size: 44
4615 TTTTTGATAA
* * * * *
4625 AAACGCCGCAAAATCTCAATACATATTCGCAGCGTTTGTAA-GA-
1 AAACGCCGCTAAATATCAACACCTATT-GCGGCGTTTGTAATGAC
* * * *
4668 AAACGCCG-TAAAAAT-AAAATCTACTGCGGCGTTTTTGT-A-GA-
1 AAACGCCGCTAAATATCAACACCTATTGCGGCG--TTTGTAATGAC
* *
4709 AAACGCCGCTAAACATCAACGA-CTATTGCGGCGTTTGT-ATGCC
1 AAACGCCGCTAAATATCAAC-ACCTATTGCGGCGTTTGTAATGAC
* * *
4752 AAATGCCGTTAAATATCAACACCTATTGCGGCGTTT-TAATGAT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTAATGAC
* *
4795 AAACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT
4833 TGAACTATCG
Statistics
Matches: 134, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
40 5 0.04
41 23 0.17
42 18 0.13
43 86 0.64
44 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (44 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTAATGAC
Found at i:4940 original size:15 final size:13
Alignment explanation
Indices: 4896--4938 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
4886 CGCCGCAAAC
4896 TTTAGCGGCGCTATT
1 TTTAGCGGCG-T-TT
*
4911 TTTAGCGGCG-CT
1 TTTAGCGGCGTTT
4923 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
4936 TTT
1 TTT
4939 TTTTACGCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 11 0.44
13 4 0.16
15 10 0.40
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (13 bp):
TTTAGCGGCGTTT
Found at i:5812 original size:17 final size:17
Alignment explanation
Indices: 5790--5822 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5780 TATTATATAT
5790 ATATTT-ATGAATATAAA
1 ATATTTAAT-AATATAAA
5807 ATATTTAATAATATAA
1 ATATTTAATAATATAA
5823 TAAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
ATATTTAATAATATAAA
Found at i:7239 original size:3 final size:3
Alignment explanation
Indices: 7231--7286 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
7221 AATATATATT
*
7231 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7279 TAA TAA TA
1 TAA TAA TA
7287 TGGGTAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:7626 original size:116 final size:116
Alignment explanation
Indices: 7422--8270 Score: 1328
Period size: 116 Copynumber: 7.4 Consensus size: 116
7412 ATTGAATAAA
* * ** * *
7422 TTCTTC-TCTTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTCT-GCTGGGGATGATGATC
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC--TCTACCTGGCAAAGATAATC
7482 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* *
7535 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
7600 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* *
7651 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
7716 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* *
7767 TTCTTCTTCCTTCTTCAGATGGCGAGTTCTTCTCATTATGAACTCTTCCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
7832 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
7883 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
*
7948 TCAAATGATGAATTCAAGAAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
7999 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
* * * *
8064 TCAACTTGATGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 TCAA-ATGATGAATTCAAG-CAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* * *
8116 TTCTTCTTCCTTCTTCAGAT-A--AGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGACTGATC
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGA-TAATC
* ** * *
8177 CATCAAATGATGGATTCGGGTAAAAGATTGAACAAATTCTTCTCATTATGAAC
64 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
8230 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACT
8271 TTCTCTGGAA
Statistics
Matches: 701, Mismatches: 24, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
113 8 0.01
114 121 0.17
115 14 0.02
116 477 0.68
117 81 0.12
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (116 bp):
TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
Found at i:9172 original size:83 final size:83
Alignment explanation
Indices: 9033--9508 Score: 812
Period size: 83 Copynumber: 5.7 Consensus size: 83
9023 GTAGTTCTTA
*
9033 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
9098 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
9116 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
9181 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
9199 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
9264 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
9282 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
9347 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
** * * *
9365 GTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
9430 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
9448 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTT
9509 TCATTTAATG
Statistics
Matches: 369, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
83 368 1.00
84 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:10554 original size:8 final size:8
Alignment explanation
Indices: 10541--10612 Score: 87
Period size: 8 Copynumber: 9.4 Consensus size: 8
10531 CTTGACCCCC
10541 TTTTTCTT
1 TTTTTCTT
*
10549 TTTTTCCT
1 TTTTTCTT
*
10557 CTTTTCTT
1 TTTTTCTT
10565 TTTTTCTT
1 TTTTTCTT
10573 TTTTTC-T
1 TTTTTCTT
*
10580 TTTCTCTT
1 TTTTTCTT
10588 TTTTTC-T
1 TTTTTCTT
10595 TTTTT-TT
1 TTTTTCTT
*
10602 TCTTTCTT
1 TTTTTCTT
10610 TTT
1 TTT
10613 CTTCAAGCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
7 17 0.32
8 36 0.68
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:10568 original size:24 final size:23
Alignment explanation
Indices: 10541--10612 Score: 103
Period size: 23 Copynumber: 3.1 Consensus size: 23
10531 CTTGACCCCC
10541 TTTTTCTTTTTTTCCTCTTTTCTT
1 TTTTTCTTTTTTT-CTCTTTTCTT
10565 TTTTTCTTTTTTTCT-TTTCTCTT
1 TTTTTCTTTTTTTCTCTTT-TCTT
*
10588 TTTTTCTTTTTTTTTC-TTTCTT
1 TTTTTCTTTTTTTCTCTTTTCTT
10610 TTT
1 TTT
10613 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
22 10 0.22
23 22 0.49
24 13 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTTCTTTTTTTCTCTTTTCTT
Found at i:10576 original size:10 final size:10
Alignment explanation
Indices: 10558--10615 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
10548 TTTTTTCCTC
10558 TTTTCTTTTT
1 TTTTCTTTTT
10568 TTCTT-TTTTT
1 TT-TTCTTTTT
*
10578 CTTTTCTCTTT
1 -TTTTCTTTTT
10589 TTTTCTTTTT
1 TTTTCTTTTT
*
10599 TTTTCTTTCT
1 TTTTCTTTTT
10609 TTTTCTT
1 TTTTCTT
10616 CAAGCATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 34 0.81
11 8 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:23403 original size:3 final size:3
Alignment explanation
Indices: 23385--23445 Score: 95
Period size: 3 Copynumber: 19.7 Consensus size: 3
23375 TATATATGTT
*
23385 TAA TATA TAT TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
23432 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
23446 TGGGTAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:29792 original size:30 final size:30
Alignment explanation
Indices: 29708--29830 Score: 124
Period size: 30 Copynumber: 4.1 Consensus size: 30
29698 TCAAGGTAAG
* * * *
29708 TCCGTCACCGCACCTGCGGTTCAGAGAAGA
1 TCCGTCACTGCACCGGCGGTTCAGGGAAGT
*
29738 TCCGTCA-TCGCACCTGCGGTTCAGGGAAGT
1 TCCGTCACT-GCACCGGCGGTTCAGGGAAGT
* *
29768 TCCGTCACTGCACCGGCGGTTCAGGTAGGT
1 TCCGTCACTGCACCGGCGGTTCAGGGAAGT
* * *
29798 TCCATCACTGCACCAGG-GATTCAGGGAAAT
1 TCCGTCACTGCACC-GGCGGTTCAGGGAAGT
29828 TCC
1 TCC
29831 TCCACTGTGC
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
30 76 0.96
31 3 0.04
ACGTcount: A:0.20, C:0.31, G:0.28, T:0.21
Consensus pattern (30 bp):
TCCGTCACTGCACCGGCGGTTCAGGGAAGT
Found at i:29811 original size:60 final size:60
Alignment explanation
Indices: 29693--29830 Score: 138
Period size: 60 Copynumber: 2.3 Consensus size: 60
29683 CTATGTACGT
* * * * * *
29693 GGGATTCAAGGTAAGTCCGTCACCGCACCTGCGGTTCAGAGAAGATCCGTCATCGCACCT
1 GGGATTCAGGGAAATTCCGTCACCGCACCGGCGGTTCAGAGAAGATCCATCATCGCACCA
* * * *
29753 GCGG-TTCAGGGAAGTTCCGTCACTGCACCGGCGGTTCAG-GTAGGTTCCATCA-CTGCACCA
1 G-GGATTCAGGGAAATTCCGTCACCGCACCGGCGGTTCAGAG-AAGATCCATCATC-GCACCA
29813 GGGATTCAGGGAAATTCC
1 GGGATTCAGGGAAATTCC
29831 TCCACTGTGC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
59 4 0.06
60 57 0.90
61 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.21
Consensus pattern (60 bp):
GGGATTCAGGGAAATTCCGTCACCGCACCGGCGGTTCAGAGAAGATCCATCATCGCACCA
Found at i:31041 original size:30 final size:30
Alignment explanation
Indices: 31005--31127 Score: 149
Period size: 30 Copynumber: 4.1 Consensus size: 30
30995 TTCAAGGACA
**
31005 TTCCGTCACCACACCTCCGGTTCAGGGAAG
1 TTCCGTCACTGCACCTCCGGTTCAGGGAAG
31035 TTCCGTCACTGCACCTCCGGTTCAGGGAAG
1 TTCCGTCACTGCACCTCCGGTTCAGGGAAG
* ** *
31065 CTCCGTCACTGCACCGGCGGTTCAGGGAGG
1 TTCCGTCACTGCACCTCCGGTTCAGGGAAG
** *
31095 TTCCAG-CACTGCACCTGGGGTTCTGGGAAG
1 TTCC-GTCACTGCACCTCCGGTTCAGGGAAG
31125 TTC
1 TTC
31128 TTCCACCGCA
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 80 0.99
31 1 0.01
ACGTcount: A:0.16, C:0.33, G:0.29, T:0.22
Consensus pattern (30 bp):
TTCCGTCACTGCACCTCCGGTTCAGGGAAG
Found at i:32142 original size:35 final size:35
Alignment explanation
Indices: 32049--32144 Score: 131
Period size: 35 Copynumber: 2.7 Consensus size: 35
32039 AATACAATCA
* *
32049 TCAATTATATTCTAAACCCTAAATTCCAAAATGCT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATACT
* *
32084 TTAATTATATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATACT
*
32119 TCAATTATATGTC-CAACCCCAAATTC
1 TCAATTATAT-TCTAAACCCCAAATTC
32145 ATAATCTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
35 51 0.96
36 2 0.04
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (35 bp):
TCAATTATATTCTAAACCCCAAATTCCAAAATACT
Found at i:32889 original size:148 final size:149
Alignment explanation
Indices: 32628--32919 Score: 460
Period size: 148 Copynumber: 2.0 Consensus size: 149
32618 AAACTATTTA
* * * *
32628 AATTAGAATCAAATAGTATTATAGTATTATAAATATTTATAATTAAATTTAAACATAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
32693 AAATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAAC
66 AAATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAAC
32758 TATTTTATAAACTGGACTG
131 TATTTTATAAACTGGACTG
* *
32777 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAACTC-GA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* * **** *
32841 AAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTTAAATCGAAATTTTTTTGAGTCAAC
66 AAATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAAC
32906 TATTTTATAAACTG
131 TATTTTATAAACTG
32920 AATTGAATAT
Statistics
Matches: 130, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
148 73 0.56
149 57 0.44
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (149 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AAATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAAC
TATTTTATAAACTGGACTG
Found at i:33520 original size:20 final size:20
Alignment explanation
Indices: 33495--33533 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
33485 ACAGTTTCCA
*
33495 GAATTCGCAACGCGAATTTG
1 GAATTCGCAACACGAATTTG
33515 GAATTCGCAACACGAATTT
1 GAATTCGCAACACGAATTT
33534 CTCAAATTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
GAATTCGCAACACGAATTTG
Found at i:33621 original size:88 final size:86
Alignment explanation
Indices: 33516--33743 Score: 273
Period size: 86 Copynumber: 2.6 Consensus size: 86
33506 GCGAATTTGG
**
33516 AATTCGCAACACGAATTTCTCAAATTCGCAACTCGAATTCGCCAATTTCTTAACTAAATTACCGA
1 AATTCGCAACACGAATTTCTCAAATTCGCAACTCGAATTCG-CAATTTCGCAACTAAATTACCGA
*
33581 TATATGTAAACACGGTAGAAAA
65 TATAGGTAAACACGGTAGAAAA
* * * * *
33603 AATTTCGCAACACGAATTTCCCAAATTTGCAA-TGCGAATTCG-GATTTCGCAACTCAATTCCCG
1 AA-TTCGCAACACGAATTTCTCAAATTCGCAACT-CGAATTCGCAATTTCGCAACTAAATTACCG
*
33666 ATATAGGTACACACGGTAGAAAA
64 ATATAGGTAAACACGGTAGAAAA
* ** *
33689 AATCCGCAACTTGAA-TTCGTCAATTTCGCAACTCGAATTCGTCAATTTCGCAACT
1 AATTCGCAACACGAATTTC-TCAAATTCGCAACTCGAATTCG-CAATTTCGCAACT
33744 CGAATTCCGA
Statistics
Matches: 119, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
84 3 0.03
85 27 0.23
86 40 0.34
87 14 0.12
88 35 0.29
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (86 bp):
AATTCGCAACACGAATTTCTCAAATTCGCAACTCGAATTCGCAATTTCGCAACTAAATTACCGAT
ATAGGTAAACACGGTAGAAAA
Found at i:33721 original size:22 final size:22
Alignment explanation
Indices: 33693--33750 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
33683 AGAAAAAATC
*
33693 CGCAACTTGAATTCGTCAATTT
1 CGCAACTCGAATTCGTCAATTT
33715 CGCAACTCGAATTCGTCAATTT
1 CGCAACTCGAATTCGTCAATTT
33737 CGCAACTCGAATTC
1 CGCAACTCGAATTC
33751 CGAATTCGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (22 bp):
CGCAACTCGAATTCGTCAATTT
Found at i:33843 original size:20 final size:19
Alignment explanation
Indices: 33796--33851 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
33786 TGAATTCCAA
*
33796 ATTCGGGTTGCGAAATTGG
1 ATTCGTGTTGCGAAATTGG
**
33815 AAACTGTGTTGCGAAATTGG
1 ATTC-GTGTTGCGAAATTGG
33835 AGTTCGTGTTGC-AAATT
1 A-TTCGTGTTGCGAAATT
33852 TGAAATCGCG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 7 0.23
20 22 0.73
21 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (19 bp):
ATTCGTGTTGCGAAATTGG
Found at i:39592 original size:29 final size:30
Alignment explanation
Indices: 39528--39598 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
39518 AACCGTTTTG
* *
39528 TATGATATGGTTTATTTTATTAATATATGAT
1 TATGATAT-GTATATTTTATTAATATATAAT
* *
39559 AATGATATGTAT-TTTTATTAATATTTAAT
1 TATGATATGTATATTTTATTAATATATAAT
*
39588 TATGATGTGTA
1 TATGATATGTA
39599 ATAATTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 24 0.71
30 3 0.09
31 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (30 bp):
TATGATATGTATATTTTATTAATATATAAT
Found at i:41087 original size:21 final size:21
Alignment explanation
Indices: 41061--41110 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
41051 TTAAAAAACG
41061 GATCGGATATCCGAATTTTCA
1 GATCGGATATCCGAATTTTCA
* *
41082 GATCGGATATCCGAGTTTTTA
1 GATCGGATATCCGAATTTTCA
41103 GATCGGAT
1 GATCGGAT
41111 CAATGGATCA
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:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (21 bp):
GATCGGATATCCGAATTTTCA
Found at i:42030 original size:113 final size:113
Alignment explanation
Indices: 41652--42049 Score: 645
Period size: 113 Copynumber: 3.5 Consensus size: 113
41642 GGGAAAAGTA
*
41652 ATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTTCTCTGGAAAAGCTGAT
1 ATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGAT
41717 CCATCGAGTGATGGATTTGAGTAAAAGGTTGAACAAGCTCTTCTCATT
66 CCATCGAGTGATGGATTTGAGTAAAAGGTTGAACAAGCTCTTCTCATT
*
41765 ATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGA
1 ATGAACTTAT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGA
* * * * * * * * * *
41829 TCCATCAAATTATGAATTTAAGCGAAAAGTTTGAACAAGTTTTTCTAATT
65 TCCATCGAGTGATGGATTTGAG-TAAAAGGTTGAACAAGCTCTTCTCATT
*
41879 ATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTTAT
1 ATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGAT
41944 CCATCGAGTGATGGATTTGAGTAAAAGGTTGAACAAGCTCTTCTCATT
66 CCATCGAGTGATGGATTTGAGTAAAAGGTTGAACAAGCTCTTCTCATT
*
41992 ATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1 ATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
42050 TGTTTTAAAA
Statistics
Matches: 257, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
112 1 0.00
113 156 0.61
114 99 0.39
115 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (113 bp):
ATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGAT
CCATCGAGTGATGGATTTGAGTAAAAGGTTGAACAAGCTCTTCTCATT
Found at i:42194 original size:76 final size:76
Alignment explanation
Indices: 42060--42241 Score: 267
Period size: 76 Copynumber: 2.4 Consensus size: 76
42050 TGTTTTAAAA
* * * * *
42060 AAACATTC-TGCACTGTAGGGCTTACAGCTGACTCGAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACA-TCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCA
42124 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
42136 AAATATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCAA
42201 AGGCTTTTTGG
66 AGGCTTTTTGG
*
42212 AAACATCATGCACAGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
42242 TGGGAAATAG
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 2 0.02
76 92 0.98
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCAA
AGGCTTTTTGG
Found at i:42950 original size:21 final size:22
Alignment explanation
Indices: 42921--42970 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
42911 AAGCTTTCAA
*
42921 CTTTGAAAAGAGAATCTATCAT
1 CTTTGAAAAGAGAACCTATCAT
42943 CTTT-AAAAGAGAACCTATCAT
1 CTTTGAAAAGAGAACCTATCAT
42964 CTTTGAA
1 CTTTGAA
42971 GAATGTAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (22 bp):
CTTTGAAAAGAGAACCTATCAT
Found at i:43425 original size:57 final size:54
Alignment explanation
Indices: 43337--43444 Score: 171
Period size: 57 Copynumber: 1.9 Consensus size: 54
43327 AGAATAATTG
43337 GTTCGTAAAACATTTGACAACACATGCATCATCCTTTTCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATGCATCA---TTTTCTGTGGCTTCTGCTCAGAT
* *
43394 GTTCGTAAAGCATTTGACAACACATTCATCATTTTCTGTGGCTTCTGCTCA
1 GTTCGTAAAACATTTGACAACACATGCATCATTTTCTGTGGCTTCTGCTCA
43445 AATTTATCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
54 20 0.41
57 29 0.59
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATGCATCATTTTCTGTGGCTTCTGCTCAGAT
Found at i:44645 original size:35 final size:35
Alignment explanation
Indices: 44586--44652 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
44576 CTTGTCGAGA
44586 TGAGCCTTCAAGAATGCCCAAATATTCATATTTTTG
1 TGAGCCTTCAAGAATGCCCAAATATTC-TATTTTTG
44622 TGAGCCTTCAA-AATGCCTC-AATATTCTATTT
1 TGAGCCTTCAAGAATGCC-CAAATATTCTATTT
44653 CTGGTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
35 13 0.43
36 12 0.40
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (35 bp):
TGAGCCTTCAAGAATGCCCAAATATTCTATTTTTG
Found at i:45769 original size:114 final size:114
Alignment explanation
Indices: 45567--45905 Score: 545
Period size: 114 Copynumber: 3.0 Consensus size: 114
45557 GATCATGCAG
*
45567 TTCATCTTTTAAATCCAATGATTGGTTTTGAGAGGTTTCTATCGAACCAAATCATATAACTCAAA
1 TTCATCTTTTAAATCTAATGATTGGTTTT--GAGGTTTCTATCGAACCAAATCATATAACTCAAA
*
45632 GAACACTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
64 GAACACTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAA
*
45683 TTCATCTTTCAAATCTAATGATTGGTTTTGAGGTTTCTATCGAACCAAATCATATAACTCAAAGA
1 TTCATCTTTTAAATCTAATGATTGGTTTTGAGGTTTCTATCGAACCAAATCATATAACTCAAAGA
*
45748 ACACTTCTAGAATATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAA
66 ACACTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAA
* * * * *
45797 TTCATCTTTTAAATCTAATGATTGGTTTTG-GGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTTAAATCTAATGATTGGTTTTGAGGTTTC-TATCGAACCAAATCATATAACTCAAAG
* *
45861 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGA
65 AACACTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGA
45906 TAACGTGGTG
Statistics
Matches: 209, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
113 5 0.02
114 177 0.85
116 27 0.13
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (114 bp):
TTCATCTTTTAAATCTAATGATTGGTTTTGAGGTTTCTATCGAACCAAATCATATAACTCAAAGA
ACACTTCTAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAA
Found at i:48397 original size:2 final size:2
Alignment explanation
Indices: 48390--48439 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
48380 ACAATAAAGG
48390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48432 AT AT AT AT
1 AT AT AT AT
48440 TAAAGGATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50105 original size:12 final size:12
Alignment explanation
Indices: 50090--50117 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
50080 CAAACCTAAA
50090 AAATGCAAATGT
1 AAATGCAAATGT
50102 AAATGCAAATGT
1 AAATGCAAATGT
50114 AAAT
1 AAAT
50118 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:50116 original size:27 final size:27
Alignment explanation
Indices: 50057--50116 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
50047 AAATGTAATT
50057 ATGT-AAAAATGAAAATGTAAATACAA
1 ATGTAAAAAATGAAAATGTAAATACAA
** * *
50083 ACCTAAAAAATGCAAATGTAAATGCAA
1 ATGTAAAAAATGAAAATGTAAATACAA
50110 ATGTAAA
1 ATGTAAA
50117 TATGTGAATG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.22
Consensus pattern (27 bp):
ATGTAAAAAATGAAAATGTAAATACAA
Found at i:52361 original size:28 final size:26
Alignment explanation
Indices: 52306--52363 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
52296 AAGCATTAAT
*
52306 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
52332 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
52360 AAAA
1 AAAA
52364 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:54165 original size:303 final size:307
Alignment explanation
Indices: 53617--54229 Score: 1189
Period size: 303 Copynumber: 2.0 Consensus size: 307
53607 AATTCGGGTT
53617 AAAATATAAATTATGAAAACATAAGGGACTAATATAGTATTTACCCTAAATATATATAAACACTT
1 AAAATATAAATTATGAAAACATAAGGGACTAATATAGTATTTACCCTAAATATATATAAACACTT
53682 GAAAGGACTAAAACATAATAAAATAATATTGGAAGACAAAATTAAAATATCCAGAAAAATAATTC
66 GAAAGGACTAAAACATAATAAAATAATATTGGAAGACAAAATTAAAATATCCAGAAAAATAATTC
53747 TAGTGACTAAATTGAAAAGATTACAAACTTGGATGGCTGCGGAAAGGGTTTGGCCATGCGCAAAA
131 TAGTGACTAAATTGAAAAGATTACAAACTTGGATGGCTGCGGAAAGGGTTTGGCCATGCGCAAAA
53812 TTACAAATATACCCCTCCCAAAACGGCGTCGTTTGGGAAGGGGTATAAATGCCCCAAACGGCTGG
196 TTACAAATATACCCCTCCCAAAACGGCGTCGTTTGGGAAGGGGTATAAATGCCCCAAACGGCTGG
53877 CCCGAAGGGCCAA-ATCTTATTTCTCTCA-TT-TCTTCTCTCTCTCA
261 CCCGAAGGGCCAACATCTTATTTCTCTCATTTCTCTTCTCTCTCTCA
53921 AAAATATAAATTATGAAAACATAAGGGACTAATATAGTATTTACCCT-AATATATATAAACACTT
1 AAAATATAAATTATGAAAACATAAGGGACTAATATAGTATTTACCCTAAATATATATAAACACTT
53985 GAAAGGACTAAAACATAATAAAATAATATTGGAAGACAAAATTAAAATATCCAGAAAAATAATTC
66 GAAAGGACTAAAACATAATAAAATAATATTGGAAGACAAAATTAAAATATCCAGAAAAATAATTC
54050 TAGTGACTAAATTGAAAAGATTACAAACTTGGATGGCTGCGGAAAGGGTTTGGCCATGCGCAAAA
131 TAGTGACTAAATTGAAAAGATTACAAACTTGGATGGCTGCGGAAAGGGTTTGGCCATGCGCAAAA
54115 TTACAAATATACCCCTCCCAAAACGGCGTCGTTTGGGAAGGGGTATAAATGCCCCAAACGGCTGG
196 TTACAAATATACCCCTCCCAAAACGGCGTCGTTTGGGAAGGGGTATAAATGCCCCAAACGGCTGG
54180 CCCGAAGGGCCAACTATCTTATTTCTCTCATTTCTCTTCTCTCTCTCA
261 CCCGAAGGGCCAAC-ATCTTATTTCTCTCATTTCTCTTCTCTCTCTCA
54228 AA
1 AA
54230 TGAGAGAACC
Statistics
Matches: 305, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
303 225 0.74
304 47 0.15
305 15 0.05
306 2 0.01
307 16 0.05
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (307 bp):
AAAATATAAATTATGAAAACATAAGGGACTAATATAGTATTTACCCTAAATATATATAAACACTT
GAAAGGACTAAAACATAATAAAATAATATTGGAAGACAAAATTAAAATATCCAGAAAAATAATTC
TAGTGACTAAATTGAAAAGATTACAAACTTGGATGGCTGCGGAAAGGGTTTGGCCATGCGCAAAA
TTACAAATATACCCCTCCCAAAACGGCGTCGTTTGGGAAGGGGTATAAATGCCCCAAACGGCTGG
CCCGAAGGGCCAACATCTTATTTCTCTCATTTCTCTTCTCTCTCTCA
Found at i:54933 original size:3 final size:3
Alignment explanation
Indices: 54927--54976 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
54917 AATTATTTAT
* *
54927 TAA TAA TAA TAA -CA TAA T-A TAA TAA TAA TAA -AA CAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54971 TAA TAA
1 TAA TAA
54977 ATAAAACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 7 0.17
3 34 0.83
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:54951 original size:19 final size:18
Alignment explanation
Indices: 54927--54982 Score: 76
Period size: 19 Copynumber: 3.0 Consensus size: 18
54917 AATTATTTAT
*
54927 TAATAATAATAACATAATA
1 TAATAATAATAA-ATAAAA
*
54946 TAATAATAATAAAACAAAA
1 TAATAATAAT-AAATAAAA
54965 TAATAATAATAAATAAAA
1 TAATAATAATAAATAAAA
54983 CAAATGAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.21
19 24 0.73
20 2 0.06
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.27
Consensus pattern (18 bp):
TAATAATAATAAATAAAA
Found at i:54987 original size:22 final size:21
Alignment explanation
Indices: 54927--54987 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 21
54917 AATTATTTAT
54927 TAAT-AATAATAACATAATATAA
1 TAATAAATAA-AACA-AATATAA
54949 TAAT-AATAAAACAAAATAATAA
1 TAATAAATAAAAC-AAAT-ATAA
54971 TAATAAATAAAACAAAT
1 TAATAAATAAAACAAAT
54988 GAAATAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.17
22 22 0.61
23 8 0.22
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
TAATAAATAAAACAAATATAA
Found at i:58144 original size:29 final size:29
Alignment explanation
Indices: 58102--58161 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
58092 TCAATTATTA
58102 CTCAATAGTTAAAAATTTATTTGCCATGT
1 CTCAATAGTTAAAAATTTATTTGCCATGT
* *
58131 CTCAATGGTTAAAAATTTATTTGTCATGT
1 CTCAATAGTTAAAAATTTATTTGCCATGT
58160 CT
1 CT
58162 AAATTAGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (29 bp):
CTCAATAGTTAAAAATTTATTTGCCATGT
Found at i:60778 original size:43 final size:44
Alignment explanation
Indices: 60730--60812 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
60720 AAAAAATTTC
60730 TAATTTGCTAATAGATAA-TAAAAATGA-TAAATTACTAATCTAT
1 TAATTTGCTAATAGATAATTAAAAAT-ATTAAATTACTAATCTAT
** *
60773 TAATTTTTTAATAGATAATTAAATATATTAAATTACTAAT
1 TAATTTGCTAATAGATAATTAAAAATATTAAATTACTAAT
60813 TGTTTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 17 0.49
44 18 0.51
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (44 bp):
TAATTTGCTAATAGATAATTAAAAATATTAAATTACTAATCTAT
Found at i:61453 original size:34 final size:34
Alignment explanation
Indices: 61422--61493 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
61412 TTTTTATATT
61422 TTTAATTTTGTAAA-AAAATTATAAATATTATAAA
1 TTTAATTTTGTAAAGAAAA-TATAAATATTATAAA
* * *
61456 TTTAATTTTTTAAAGGAAATATAAATATTTTACAA
1 TTTAATTTTGTAAAGAAAATATAAATATTATA-AA
61491 TTT
1 TTT
61494 GTAATATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 25 0.76
35 8 0.24
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (34 bp):
TTTAATTTTGTAAAGAAAATATAAATATTATAAA
Found at i:61672 original size:20 final size:20
Alignment explanation
Indices: 61636--61673 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
61626 ATCCTATTCC
**
61636 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
61656 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
61674 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:63612 original size:2 final size:2
Alignment explanation
Indices: 63605--63641 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
63595 ATAGTTTGTT
63605 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63642 GGAACGAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:68330 original size:3 final size:3
Alignment explanation
Indices: 68318--68349 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
68308 AAACATAAAC
68318 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
68350 ATATATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:68359 original size:8 final size:7
Alignment explanation
Indices: 68318--68362 Score: 60
Period size: 6 Copynumber: 6.7 Consensus size: 7
68308 AAACATAAAC
68318 ATAATAA
1 ATAATAA
68325 ATAAT-A
1 ATAATAA
68331 ATAAT-A
1 ATAATAA
68337 ATAAT-A
1 ATAATAA
68343 ATAATAA
1 ATAATAA
68350 ATATATAA
1 ATA-ATAA
68358 ATAAT
1 ATAAT
68363 GATAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.50
7 11 0.31
8 7 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
ATAATAA
Found at i:68360 original size:15 final size:15
Alignment explanation
Indices: 68294--68362 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
68284 AAAATTTTGT
* *
68294 AATATGTAATTAATA
1 AATATATAAATAATA
*
68309 AACATA-AACATAATA
1 AATATATAA-ATAATA
68324 AATA-AT-AATAAT-
1 AATATATAAATAATA
68336 AATA-AT-AATAATA
1 AATATATAAATAATA
68349 AATATATAAATAAT
1 AATATATAAATAAT
68363 GATAAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
12 12 0.27
13 9 0.20
14 6 0.13
15 18 0.40
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (15 bp):
AATATATAAATAATA
Found at i:68811 original size:130 final size:133
Alignment explanation
Indices: 68563--68889 Score: 450
Period size: 130 Copynumber: 2.5 Consensus size: 133
68553 CGTCTAAAGG
* * * * *
68563 TGACAAGGTTCCTACATGATGAGGAAATCT-AGTC-GAGGGATGACACTGCTCATACATGATGAA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGA-TCTG-GGGATGACACGGCTCATACATGATGAA
* *
68626 GAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGGGGACGACTGGTTAT
64 GAGTTCTTGGCCATC-TTA-GAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTAT
68691 CTATGGT
127 CTATGGT
*
68698 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGG-ATGACACGGCTCATACATGATGAAG
*
68763 AGTTC-TGGCCATC-TA-AA-GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
65 AGTTCTTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTA
68824 TGGT
130 TGGT
* * * *
68828 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGTGATGACACGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACATGATGA
68890 GGATGGCTGG
Statistics
Matches: 175, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
129 20 0.11
130 82 0.47
131 2 0.01
133 2 0.01
135 39 0.22
136 30 0.17
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (133 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACATGATGAAGA
GTTCTTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAT
GGT
Found at i:68845 original size:43 final size:43
Alignment explanation
Indices: 68664--68860 Score: 188
Period size: 43 Copynumber: 4.6 Consensus size: 43
68654 ATAACTCGGT
*
68664 TCCTACGTGATGGGGACGA-CTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATCTGGTTATCTATGGTTGACACGGC
** *
68707 TCCTACGTGATGAGGAGATCT-G--ATCTGGGGAATGACACGGC
1 TCCTACGTGATGAGGAGATCTGGTTATCTATGG-TTGACACGGC
* * * ** * * *
68748 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGT
1 TCCTACGTGATGAGGAGATCTGGTTATCT-ATGGT--TGACACGGC
*
68794 TCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATCTGGTTATCTATGGTTGACACGGC
68837 TCCTACGTGATGAGGAGATCTGGT
1 TCCTACGTGATGAGGAGATCTGGT
68861 CTGGTGATGA
Statistics
Matches: 123, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
40 6 0.05
41 27 0.22
42 5 0.04
43 45 0.37
44 4 0.03
45 6 0.05
46 29 0.24
47 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.26
Consensus pattern (43 bp):
TCCTACGTGATGAGGAGATCTGGTTATCTATGGTTGACACGGC
Found at i:68890 original size:83 final size:85
Alignment explanation
Indices: 68739--68899 Score: 218
Period size: 83 Copynumber: 1.9 Consensus size: 85
68729 ATCTGGGGAA
* *
68739 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG-C-TCT--AGGTGATAACACGGTTCCTACATGA
68804 TGAGGACGGCTGGTTATCTATGGT
62 TGAGGACGGCTGGTTATCTATGGT
* * *
68828 TGACACGGCTCCTACGTGATGAGGAGATCTGG-TCT-GGTGATGACACGGTTCCTACATGATGAG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCTCTAGGTGATAACACGGTTCCTACATGATGAG
*
68891 GATGGCTGG
66 GACGGCTGG
68900 CCATCTTTAG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
83 34 0.52
86 3 0.05
89 29 0.44
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (85 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCTCTAGGTGATAACACGGTTCCTACATGATGAG
GACGGCTGGTTATCTATGGT
Found at i:68999 original size:28 final size:28
Alignment explanation
Indices: 68938--68999 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
68928 AAACCAAATT
68938 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* * *
68966 AGAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
68994 AAAGAT
1 AAAGAT
69000 GATATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:69527 original size:15 final size:15
Alignment explanation
Indices: 69503--69546 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
69493 AAGATGATCT
*
69503 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
69518 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
69533 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
69547 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:69599 original size:31 final size:30
Alignment explanation
Indices: 69535--69609 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
69525 AGAGAAAATG
*
69535 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
69566 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
69597 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
69610 TGCCTCAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:69702 original size:40 final size:40
Alignment explanation
Indices: 69642--69721 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
69632 GTTTTAATAA
69642 AAACAATCTCAAAGGTGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGTA-TTTTCAAAAGAAATTGTCT
* * *
69682 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
69722 CGAGAGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:69776 original size:63 final size:64
Alignment explanation
Indices: 69703--69827 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 64
69693 AATGTGGGTA
* * *
69703 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* * *
69766 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
69828 GGATCCCATC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 17 0.31
64 38 0.69
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:69940 original size:120 final size:119
Alignment explanation
Indices: 69725--69948 Score: 276
Period size: 120 Copynumber: 1.9 Consensus size: 119
69715 GTTGTCTCGA
* *
69725 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
*
69790 AGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCCCATCTTAAGT
66 AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCCCATCTTAAGT
* * * **
69844 GAGACCAAA-TTTGTTTCAAATGAAACAATCTCAAA-AGTTAGTTTTTCATTAGAAACTGTC-TC
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TT--TTTTTCAAAAGAAACTGTCTTC
** *
69906 AAGAGAGACAACA-TTTGTTTTTAAAGAAATAGACTCAAAGATG
63 AAGAGAGA-AA-ATTTTGTTTCAAAAGAAACAGACTCAAAGATG
69949 ATTTTGTTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
117 1 0.01
118 26 0.29
119 16 0.18
120 45 0.51
121 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (119 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCCCATCTTAAGT
Found at i:70116 original size:37 final size:37
Alignment explanation
Indices: 70060--70186 Score: 108
Period size: 37 Copynumber: 3.6 Consensus size: 37
70050 GAAACAGATT
*
70060 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
* * * *
70097 CAAAATTTTGTTTCCAAAGAAACAAAC-TCA-A-AG-
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
* * *
70130 ---ATTTTTATTTTAAAAGAAACTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
*
70164 CAAAATTTTGTTTCCAAAGAAAC
1 CAAAATTTTGTTTCAAAAGAAAC
70187 AAACTCAAAG
Statistics
Matches: 66, Mismatches: 16, Indels: 16
0.67 0.16 0.16
Matches are distributed among these distances:
30 18 0.27
31 2 0.03
32 1 0.02
33 2 0.03
34 2 0.03
35 1 0.02
36 7 0.11
37 33 0.50
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
Found at i:70161 original size:65 final size:65
Alignment explanation
Indices: 69995--70219 Score: 285
Period size: 67 Copynumber: 3.4 Consensus size: 65
69985 ATGAACATAT
** * * * * * *
69995 TCAAAGATTTAATTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT--AAGAGAAACAG
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCCAA-AGAAACAA
*
70057 AT
64 AC
*
70059 TCAAAGATTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
*
70124 TCAAAGATTTTTATTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
70189 AC
64 AC
*
70191 TCAAAGATTTTTTTCAAAAGAAACAATCT
1 TCAAAGATTTTTTTCAAAAGAAACTATCT
70220 CAAAGATTTT
Statistics
Matches: 142, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
63 1 0.01
64 41 0.29
65 31 0.22
66 10 0.07
67 59 0.42
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (65 bp):
TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
Found at i:70211 original size:95 final size:94
Alignment explanation
Indices: 70097--70271 Score: 244
Period size: 95 Copynumber: 1.9 Consensus size: 94
70087 TTAAGAGAGA
* *
70097 CAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTATTTTAAAAGAAACTATCTTAAGAGA
1 CAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTATTTTAAAA-AAACTATCTCAAGAGA
*
70162 GACAAAATTTTGTTTCCAAAGAAACAAACT
65 GACAAAACTTTGTTTCCAAAGAAACAAACT
* * * * * *
70192 CAAAGATTTT-TTTCAAAAGAAACAATCTCAAAGATTTTTTTTTTCACAAAATTGTCTCAAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTATTTTAAAAAAACTATCTCAAGAGA
70256 GACAAAACTTTGTTTC
65 GACAAAACTTTGTTTC
70272 AGACTCAAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
94 28 0.40
95 37 0.53
96 5 0.07
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (94 bp):
CAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTATTTTAAAAAAACTATCTCAAGAGAG
ACAAAACTTTGTTTCCAAAGAAACAAACT
Found at i:70229 original size:27 final size:28
Alignment explanation
Indices: 70164--70232 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
70154 TTAAGAGAGA
*
70164 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
70192 CAAAGATTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
70220 CAAAGATTTTTTT
1 CAAAGATTTTTTT
70233 TTTCACAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:70403 original size:29 final size:28
Alignment explanation
Indices: 70335--70431 Score: 128
Period size: 29 Copynumber: 3.5 Consensus size: 28
70325 AAATAAATAG
*
70335 ACTCAAAGA--TTT-TTCAAAAGAAACA
1 ACTCAAAGATTTTTATTCAAAAGGAACA
*
70360 ACTCAAAGATATTTATTCAAAAGGAACA
1 ACTCAAAGATTTTTATTCAAAAGGAACA
*
70388 GACTCCAAGATTTTTATTCAAAAGGAACAA
1 -ACTCAAAGATTTTTATTCAAAAGGAAC-A
70418 ACTCAAAGATTTTT
1 ACTCAAAGATTTTT
70432 TCAAGAGAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
25 9 0.14
27 3 0.05
28 12 0.19
29 38 0.60
30 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.28
Consensus pattern (28 bp):
ACTCAAAGATTTTTATTCAAAAGGAACA
Found at i:70766 original size:36 final size:35
Alignment explanation
Indices: 70682--70779 Score: 117
Period size: 36 Copynumber: 2.8 Consensus size: 35
70672 GAGAAAATGA
* *
70682 TGTCTCAAGCGAGACAAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
* ** *
70716 AGTCTCAAATGAGACAAAATTTGTTTTTAGTGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAT
*
70752 TGTCTCAAGCGAGACAAAGTTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
70780 GAGGAAACGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 20 0.38
35 4 0.08
36 28 0.54
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:70794 original size:36 final size:36
Alignment explanation
Indices: 70683--70801 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
70673 AGAAAATGAT
* * * *
70683 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGTGAAATC
** *
70717 GTCTCAAATGAGACAAAATTTGTTTTTAGTGAAATT
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGTGAAATC
*
70753 GTCTCAAGCGAGACAAAGTTTGTTTTTGAG-GAAA-C
1 GTCTCAAGCGAGACAAAATTTGTTTTT-AGTGAAATC
*
70788 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
70802 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 20 0.29
35 5 0.07
36 43 0.61
37 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGTGAAATC
Found at i:70940 original size:105 final size:100
Alignment explanation
Indices: 70753--70985 Score: 272
Period size: 105 Copynumber: 2.2 Consensus size: 100
70743 TAGTGAAATT
*
70753 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGGAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACAAA-TTTG-TTTTGAAGAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
* *
70818 TGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 TGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
70855 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAAGAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGAC-AAATTTGTTTTG-AAGAAAC--G-ATCTCAA-GTGAGATCAACTTTGTTT
* * * *
70919 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 AAT-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
70960 GTCTCAAGCGAAACACAATTTGTTTT
1 GTCTCAAGCGAGACA-AATTTGTTTT
70986 AAAATTCTCA
Statistics
Matches: 113, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
101 5 0.04
102 24 0.21
103 3 0.03
104 5 0.04
105 76 0.67
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (100 bp):
GTCTCAAGCGAGACAAATTTGTTTTGAAGAAACGATCTCAAGTGAGATCAACTTTGTTTAATGTG
AAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:71470 original size:4 final size:4
Alignment explanation
Indices: 71461--71498 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
71451 TTTATGTATC
71461 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
71499 GTATACTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 30 0.94
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:71497 original size:26 final size:25
Alignment explanation
Indices: 71453--71502 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
71443 ATACAAATTT
71453 TATGTATCATGTATGTATGTGTATG
1 TATGTATCATGTATGTATGTGTATG
*
71478 TATGTATGTATGTATGTATGTGTAT
1 TATGTAT-CATGTATGTATGTGTAT
71503 ACTCTTCTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.50
Consensus pattern (25 bp):
TATGTATCATGTATGTATGTGTATG
Found at i:72703 original size:12 final size:11
Alignment explanation
Indices: 72675--72712 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
72665 CCTCTTTTTG
*
72675 TTCTTTGCTTT
1 TTCTTTGATTT
72686 TTCTTTGATTT
1 TTCTTTGATTT
72697 TTGCTTTGATTT
1 TT-CTTTGATTT
72709 TTCT
1 TTCT
72713 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:72716 original size:13 final size:12
Alignment explanation
Indices: 72670--72717 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
72660 TTTGTCCTCT
72670 TTTTGTTCTTTG-
1 TTTT-TTCTTTGA
*
72682 CTTTTTCTTTGA
1 TTTTTTCTTTGA
*
72694 TTTTTGCTTTGA
1 TTTTTTCTTTGA
72706 TTTTTCTCTTTG
1 TTTTT-TCTTTG
72718 CTCTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.23
12 18 0.60
13 5 0.17
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:73367 original size:26 final size:24
Alignment explanation
Indices: 73337--73407 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 24
73327 CAAGGTGGAA
73337 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
* *
73361 AGGGAATGTTTCAAGG--TCGAA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
73383 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
73407 A
1 A
73408 TAGAATGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
20 12 0.32
22 5 0.14
23 2 0.05
24 6 0.16
26 12 0.32
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:73392 original size:20 final size:20
Alignment explanation
Indices: 73324--73398 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
73314 AAATACAGTG
*
73324 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
73343 TTTCAAGGTCTCAAAGAGAGGGAATG
1 TTTCAAGG--TCGAA-A-A--GAATA
73369 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
73389 TTTCAAGGTC
1 TTTCAAGGTC
73399 TCAAAGAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 1 0.02
22 2 0.05
23 2 0.05
24 5 0.11
26 12 0.27
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:73412 original size:26 final size:26
Alignment explanation
Indices: 73334--73413 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
73324 TTTCAAGGTG
73334 GAAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
73360 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
73381 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
73406 GATAGAAT
1 GAAAGAAT
73414 GTCAAAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 20 0.49
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:73414 original size:46 final size:45
Alignment explanation
Indices: 73322--73415 Score: 152
Period size: 46 Copynumber: 2.1 Consensus size: 45
73312 ATAAATACAG
* *
73322 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
73367 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
73413 TGT
1 TGT
73416 CAAAAATTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 11 0.24
46 34 0.76
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:75903 original size:31 final size:32
Alignment explanation
Indices: 75847--75908 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
75837 TGACAAAATG
75847 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
75879 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
75909 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:79554 original size:3 final size:3
Alignment explanation
Indices: 79542--79576 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
79532 AAACATAAAC
79542 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
79577 ATATATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:79586 original size:8 final size:7
Alignment explanation
Indices: 79542--79589 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 7
79532 AAACATAAAC
79542 ATAATAA
1 ATAATAA
79549 ATAAT-A
1 ATAATAA
79555 ATAAT-A
1 ATAATAA
79561 ATAATAATA
1 ATAAT-A-A
79570 ATAATAA
1 ATAATAA
79577 ATATATAA
1 ATA-ATAA
79585 ATAAT
1 ATAAT
79590 GATAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 12 0.32
7 11 0.30
8 8 0.22
9 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
ATAATAA
Found at i:79587 original size:15 final size:15
Alignment explanation
Indices: 79518--79589 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
79508 AAAATGTTGT
* *
79518 AATATGTAATTAATA
1 AATATATAAATAATA
*
79533 AACATA-AACATAATA
1 AATATATAA-ATAATA
79548 AATA-AT-AATAAT-
1 AATATATAAATAATA
79560 AATA-ATAATAATAATA
1 AATATAT-A-AATAATA
79576 AATATATAAATAAT
1 AATATATAAATAAT
79590 GATAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
12 6 0.13
13 5 0.11
14 4 0.09
15 24 0.52
16 5 0.11
17 2 0.04
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (15 bp):
AATATATAAATAATA
Found at i:81619 original size:39 final size:39
Alignment explanation
Indices: 81517--81626 Score: 102
Period size: 39 Copynumber: 2.8 Consensus size: 39
81507 TTTATTTTTT
* * * *
81517 ATTTCTCAAATTATTTCAC-TCCAACA-TTCAAATTCCTA
1 ATTTCTTAAATTATTTCACAT-TAACATTTTAAAATCCTA
* *
81555 ATTTCTTAAATT-TTACCACCA-TAACATTTTAAAATCTTA
1 ATTTCTTAAATTATT-TCA-CATTAACATTTTAAAATCCTA
*
81594 ATTTCTTAAATTATTTCACATTAACATTCTAAA
1 ATTTCTTAAATTATTTCACATTAACATTTTAAA
81627 TTATGTTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
37 2 0.03
38 19 0.33
39 35 0.60
40 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (39 bp):
ATTTCTTAAATTATTTCACATTAACATTTTAAAATCCTA
Found at i:105804 original size:26 final size:25
Alignment explanation
Indices: 105760--105809 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
105750 ATATATGTAT
*
105760 ATGTACATGTACATGAATTCCATAC
1 ATGTACATGAACATGAATTCCATAC
105785 ATGTACATGAAACATGAATTCCATA
1 ATGTACATG-AACATGAATTCCATA
105810 TGAACAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (25 bp):
ATGTACATGAACATGAATTCCATAC
Found at i:117515 original size:60 final size:60
Alignment explanation
Indices: 117442--117574 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 60
117432 AATTTAGGGT
* *
117442 AAAG-TACACAAATGATCCCTAAACTATA-GGA-TAAGGCTTTATTGAGTCTCTTAACTATTA
1 AAAGTTACA-AAATGATCCCTAAACTATAGGGAGT--GGCTTTATTGAGTCACTCAACTATTA
* * * *
117502 AAAGTTACAAAATGATCCTTAAACTATAGGGAGTTGCTTTGTTGAGTCACTCGACTATTA
1 AAAGTTACAAAATGATCCCTAAACTATAGGGAGTGGCTTTATTGAGTCACTCAACTATTA
117562 AAA-TTACAAAATG
1 AAAGTTACAAAATG
117575 GTCACTCTAC
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 10 0.16
60 46 0.72
61 7 0.11
62 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (60 bp):
AAAGTTACAAAATGATCCCTAAACTATAGGGAGTGGCTTTATTGAGTCACTCAACTATTA
Found at i:118733 original size:16 final size:16
Alignment explanation
Indices: 118712--118757 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
118702 TAAAGATATA
118712 TATATTTTATTATAAT
1 TATATTTTATTATAAT
**
118728 TATATTTTTATT-TTTT
1 TATA-TTTTATTATAAT
118744 TATATTTTATTATA
1 TATATTTTATTATA
118758 GTTTAAACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 7 0.28
16 11 0.44
17 7 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATATTTTATTATAAT
Found at i:119297 original size:26 final size:26
Alignment explanation
Indices: 119267--119324 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
119257 AATCGTTTCA
*
119267 TAAATACATATTTAAAAT-ATTATATC
1 TAAATACATATTTAAAATCA-CATATC
** *
119293 TAAATATTTTTTTAAAATCACATATC
1 TAAATACATATTTAAAATCACATATC
119319 TAAATA
1 TAAATA
119325 TCTAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.96
27 1 0.04
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAATACATATTTAAAATCACATATC
Found at i:122269 original size:20 final size:20
Alignment explanation
Indices: 122244--122283 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
122234 TTTTCTTACC
122244 CCTAACGGTCATTAAATATG
1 CCTAACGGTCATTAAATATG
122264 CCTAACGGTCATTAAATATG
1 CCTAACGGTCATTAAATATG
122284 TTAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (20 bp):
CCTAACGGTCATTAAATATG
Found at i:122653 original size:20 final size:20
Alignment explanation
Indices: 122630--122681 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
122620 AACGCGATCC
122630 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
122650 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
122670 CCAAAATCGCAA
1 CCAGAATCGCAA
122682 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:122762 original size:20 final size:20
Alignment explanation
Indices: 122737--122930 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
122727 GATTTTCCAT
* *
122737 AATCGCAACGCGAATA-TTAA
1 AATCGCAACGCGAACACAT-A
122757 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
122777 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
122797 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
122817 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
122837 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
122857 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
122877 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
122898 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
122918 AATCGCAACGCGA
1 AATCGCAACGCGA
122931 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 2 0.01
20 120 0.86
21 16 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:122800 original size:40 final size:39
Alignment explanation
Indices: 122756--122930 Score: 197
Period size: 40 Copynumber: 4.4 Consensus size: 39
122746 GCGAATATTA
122756 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGT
* * * **
122796 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGT
1 AAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGT
* * * *
122836 AAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGT
** *
122876 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAA-CCAT-AAATCGCAACGCGTATCCGT
122917 AAATCGCAACGCGA
1 AAATCGCAACGCGA
122931 TATTTAAAGC
Statistics
Matches: 113, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 79 0.70
41 33 0.29
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGT
Found at i:122820 original size:60 final size:60
Alignment explanation
Indices: 122756--122929 Score: 249
Period size: 60 Copynumber: 2.9 Consensus size: 60
122746 GCGAATATTA
* *
122756 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
* *** * *
122816 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
**
122876 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCG
122930 ATATTTAAAG
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 66 0.68
61 31 0.32
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:123334 original size:33 final size:33
Alignment explanation
Indices: 123295--123365 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
123285 TTCACTTAGA
*
123295 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
123328 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
123361 TTTCA
1 TTTCA
123366 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:123505 original size:14 final size:14
Alignment explanation
Indices: 123486--123540 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
123476 AGAATGACTG
123486 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
123500 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
123519 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
123533 TCGCAACG
1 TCGCAACG
123541 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:123523 original size:33 final size:33
Alignment explanation
Indices: 123486--123556 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
123476 AGAATGACTG
**
123486 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
123519 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
123552 TCGCA
1 TCGCA
123557 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:123574 original size:19 final size:19
Alignment explanation
Indices: 123552--123649 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
123542 GAAACCAAAA
*
123552 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
123571 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
123585 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
123604 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
123618 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
123637 TCGCGTTGCGATT
1 TCGCGTTGCGATT
123650 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:123593 original size:14 final size:14
Alignment explanation
Indices: 123574--123663 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
123564 TTTCATTTCG
123574 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
123588 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
123607 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
123621 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
123638 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
123654 CGTTGCGATT
1 CGTTGCGATT
123664 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:123599 original size:33 final size:33
Alignment explanation
Indices: 123557--123671 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
123547 CAAAATCGCA
123557 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
123590 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
123623 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
123656 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
123672 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:125600 original size:185 final size:186
Alignment explanation
Indices: 125369--125835 Score: 909
Period size: 185 Copynumber: 2.5 Consensus size: 186
125359 TAGATTGCTT
* *
125369 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
125434 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
125499 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
125554 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
125619 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
125684 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
125740 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
125805 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
125836 TTCAATTTGC
Statistics
Matches: 279, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 153 0.55
186 126 0.45
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:125683 original size:93 final size:93
Alignment explanation
Indices: 125369--125835 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
125359 TAGATTGCTT
* *
125369 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
125434 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
125462 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
125526 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
125554 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
125619 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
125647 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
125712 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
125740 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
125805 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
125833 AGT
1 AGT
125836 TTCAATTTGC
Statistics
Matches: 371, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 92 0.25
93 279 0.75
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:125907 original size:19 final size:19
Alignment explanation
Indices: 125867--125995 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
125857 TAGTTTACTT
* *
125867 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
125887 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
125906 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
125925 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
125939 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
125958 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
125972 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
125991 TCGCA
1 TCGCA
125996 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:125946 original size:33 final size:32
Alignment explanation
Indices: 125903--125995 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
125893 CGCGAAACCA
**
125903 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
125935 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
125968 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
125996 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:125993 original size:52 final size:52
Alignment explanation
Indices: 125867--125995 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
125857 TAGTTTACTT
**
125867 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
125919 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
125972 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
125996 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:126013 original size:19 final size:19
Alignment explanation
Indices: 125991--126125 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
125981 GAAACCAAAA
*
125991 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
126010 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
126026 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
126043 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
126059 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
126076 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
126095 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
126115 TCGTGTTGCGA
1 TCGCGTTGCGA
126126 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:126032 original size:14 final size:14
Alignment explanation
Indices: 126013--126069 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
126003 TTTCATTTCG
126013 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
126027 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
126044 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
126060 CGTTGCGATT
1 CGTTGCGATT
126070 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:126038 original size:33 final size:33
Alignment explanation
Indices: 125996--126088 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
125986 CAAAATCGCA
*
125996 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
126029 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
126062 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
126089 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:128068 original size:14 final size:14
Alignment explanation
Indices: 128049--128084 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
128039 ATTGTTTAAT
128049 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
128063 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
128077 TGATTTGT
1 TGATTTGT
128085 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:128207 original size:19 final size:19
Alignment explanation
Indices: 128191--128292 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
128181 AAAAATGACT
128191 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
128210 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
128229 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
128243 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
128262 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
128282 ATCGCAATGCG
1 ATCGCAATGCG
128293 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:128341 original size:33 final size:36
Alignment explanation
Indices: 128299--128613 Score: 300
Period size: 33 Copynumber: 9.1 Consensus size: 36
128289 TGCGTTTATA
*
128299 ATTTCGCATTGCGA-TT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
128332 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
128368 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
128401 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
128436 ATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
128469 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
128507 ATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
128540 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
128576 -TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTT-CG-ATTGCGATTTTC
128612 AT
1 AT
128614 GTTGGGATTT
Statistics
Matches: 250, Mismatches: 8, Indels: 44
0.83 0.03 0.15
Matches are distributed among these distances:
33 136 0.54
34 10 0.04
35 27 0.11
36 33 0.13
37 1 0.00
38 43 0.17
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (36 bp):
ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
Found at i:128345 original size:19 final size:19
Alignment explanation
Indices: 128321--128641 Score: 369
Period size: 19 Copynumber: 18.4 Consensus size: 19
128311 GATTATCTCG
128321 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
128340 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
128359 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
128373 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
128392 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
128406 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
128425 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
128444 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
128458 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
128477 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
128496 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
128515 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
128529 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
128548 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
128567 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
128581 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
128601 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
128615 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
128634 TTGCGATT
1 TTGCGATT
128642 GTATTTTCCG
Statistics
Matches: 261, Mismatches: 10, Indels: 62
0.78 0.03 0.19
Matches are distributed among these distances:
14 41 0.16
16 39 0.15
17 35 0.13
18 3 0.01
19 131 0.50
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:128361 original size:52 final size:52
Alignment explanation
Indices: 128299--128613 Score: 412
Period size: 52 Copynumber: 6.0 Consensus size: 52
128289 TGCGTTTATA
*
128299 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
128351 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
128401 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
128457 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
128507 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
128559 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
128612 AT
1 AT
128614 GTTGGGATTT
Statistics
Matches: 233, Mismatches: 14, Indels: 31
0.84 0.05 0.11
Matches are distributed among these distances:
47 6 0.03
49 8 0.03
50 17 0.07
51 5 0.02
52 165 0.71
53 17 0.07
54 2 0.01
55 1 0.00
56 4 0.02
57 4 0.02
58 1 0.00
59 3 0.01
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:128378 original size:14 final size:14
Alignment explanation
Indices: 128359--128413 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
128349 TCATTTCGCA
128359 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
128373 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
128390 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
128406 TTGCGATT
1 TTGCGATT
128414 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 14 0.39
16 8 0.22
17 8 0.22
19 6 0.17
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:130937 original size:12 final size:12
Alignment explanation
Indices: 130920--130944 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
130910 TCTTCGGGGA
130920 CTTTTTCTTCTT
1 CTTTTTCTTCTT
130932 CTTTTTCTTCTT
1 CTTTTTCTTCTT
130944 C
1 C
130945 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:131152 original size:24 final size:24
Alignment explanation
Indices: 131118--131164 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
131108 CTGAAACATC
131118 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
131142 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
131165 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:131874 original size:20 final size:20
Alignment explanation
Indices: 131846--132214 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
131836 AAATTTCAGT
* * * *
131846 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
131866 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
131886 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
131906 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
131926 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
131946 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
131966 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
131986 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
132006 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
132026 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
132046 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
132066 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
132086 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
132106 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
132126 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
132146 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
132166 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
132186 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
132206 GTTGCGATT
1 GTTGCGATT
132215 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:132831 original size:16 final size:16
Alignment explanation
Indices: 132812--132847 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
132802 AATTAAATAT
132812 TAAATT-TAAAACAACA
1 TAAATTATAAAACAA-A
132828 TAAATTATAAAACAAA
1 TAAATTATAAAACAAA
132844 TAAA
1 TAAA
132848 AATATAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAATTATAAAACAAA
Found at i:132853 original size:17 final size:17
Alignment explanation
Indices: 132813--132855 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
132803 ATTAAATATT
*
132813 AAATTTAAAACAACATA
1 AAATATAAAACAACATA
*
132830 AATTATAAAACAA-ATAA
1 AAATATAAAACAACAT-A
132847 AAATATAAA
1 AAATATAAA
132856 TGAGTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATATAAAACAACATA
Found at i:134442 original size:17 final size:18
Alignment explanation
Indices: 134411--134447 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
134401 ATCTTAATTC
134411 TTATCATTATCATTT-TA
1 TTATCATTATCATTTCTA
134428 TTATCATTCAT-ATTTCTA
1 TTATCATT-ATCATTTCTA
134446 TT
1 TT
134448 CTCTTGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.27, C:0.14, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATCATTATCATTTCTA
Found at i:139204 original size:21 final size:21
Alignment explanation
Indices: 139178--139217 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
139168 CATATAGCTT
*
139178 CTTTTCATGTAATTCATATCA
1 CTTTTCATATAATTCATATCA
139199 CTTTTCATATAATTCATAT
1 CTTTTCATATAATTCATAT
139218 GTTCACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.03, T:0.50
Consensus pattern (21 bp):
CTTTTCATATAATTCATATCA
Found at i:139254 original size:30 final size:30
Alignment explanation
Indices: 139192--139256 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
139182 TCATGTAATT
* *
139192 CATATCACTTTTCATATAATTCATATGTTCA
1 CATATCACTTTTCATAT-ATTCATAGGATCA
*
139223 CATATCTCTTTTCATAT-TCTCATAGGATCA
1 CATATCACTTTTCATATAT-TCATAGGATCA
139253 CATA
1 CATA
139257 GCACATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 13 0.43
31 16 0.53
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.43
Consensus pattern (30 bp):
CATATCACTTTTCATATATTCATAGGATCA
Found at i:141995 original size:12 final size:12
Alignment explanation
Indices: 141980--142062 Score: 71
Period size: 12 Copynumber: 6.7 Consensus size: 12
141970 ATATTTGATT
141980 TTAATTTTAATA
1 TTAATTTTAATA
141992 TTAATTTTTAA-A
1 TTAA-TTTTAATA
* *
142004 -TAAATTAAATA
1 TTAATTTTAATA
*
142015 TTATTTTTTTAATA
1 TTA--ATTTTAATA
*
142029 TTATATTATATATA
1 TTA-ATTTTA-ATA
142043 TTAATTTTAATA
1 TTAATTTTAATA
142055 TTAATTTT
1 TTAATTTT
142063 TTAAATAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
10 4 0.07
11 4 0.07
12 18 0.32
13 16 0.28
14 15 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:142036 original size:26 final size:26
Alignment explanation
Indices: 141989--142057 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
141979 TTTAATTTTA
*
141989 ATATTAATTTTTAA-A-TAAATTAAAT
1 ATATTAA-TTTTAATATTATATTAAAT
* *
142014 ATTATT-TTTTTAATATTATATTATAT
1 A-TATTAATTTTAATATTATATTAAAT
142040 ATATTAATTTTAATATTA
1 ATATTAATTTTAATATTA
142058 ATTTTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
24 6 0.17
25 6 0.17
26 24 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATTAATTTTAATATTATATTAAAT
Found at i:142057 original size:63 final size:62
Alignment explanation
Indices: 141965--142090 Score: 202
Period size: 64 Copynumber: 2.0 Consensus size: 62
141955 ATTTAATTTG
*
141965 ATATTATATTTGATTTTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTATTTTTTTA
1 ATATTATATTTGATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAGTTTTTTA
142026 ATATTATATTAT-ATATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAGTTTTTTA
1 ATATTATATT-TGAT-T-TTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAGTTTTTTA
142090 A
1 A
142091 GAGAAAATAA
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
61 12 0.20
62 2 0.03
63 16 0.27
64 30 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (62 bp):
ATATTATATTTGATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAGTTTTTTA
Found at i:142281 original size:21 final size:21
Alignment explanation
Indices: 142257--142434 Score: 127
Period size: 21 Copynumber: 8.5 Consensus size: 21
142247 ATTTCGACTA
* *
142257 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
142278 TCGCGTTGCGGTAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
**
142299 TCGCGTTGCGA-A-TCTGGAAAC
1 TCGCGTTGCGATAGTC--GAAGT
**
142320 T-GATTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* * *
142340 TCGCGTTGCGATTTATTCCAACT
1 TCGCGTTGCGA--TAGTCGAAGT
* * *
142363 T--CGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA--TAGTCGAAGT
142384 T--CGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
142403 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
142424 TCGCGTTGCGA
1 TCGCGTTGCGA
142435 ATCTGGAAAC
Statistics
Matches: 128, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
19 10 0.08
20 12 0.09
21 96 0.75
22 2 0.02
23 8 0.06
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:142674 original size:19 final size:19
Alignment explanation
Indices: 142623--142675 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
142613 ATATCATACA
*
142623 AATTATTTTATATATTATT
1 AATTATTTTATTTATTATT
142642 AA-TATTTTATATTTATT-TT
1 AATTA-TTT-TATTTATTATT
142661 AATTATTTTGATTTA
1 AATTATTTT-ATTTA
142676 AGTTTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 3 0.10
19 17 0.59
20 9 0.31
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATTTTATTTATTATT
Found at i:143169 original size:31 final size:31
Alignment explanation
Indices: 143132--143191 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
143122 TAGTTGTATG
* *
143132 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
143163 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
143192 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:145194 original size:42 final size:43
Alignment explanation
Indices: 145148--145233 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 43
145138 TTAAGGATTT
*
145148 TTATTAT-TAAAATA-TATTCTTTAATTATTAAAAATATAA-AAA
1 TTATTATATAAAATATTA-T-TTTAATAATTAAAAATATAATAAA
* *
145190 TTATTATATAACATATTATTTTAATAATTTAAAATATAATAAA
1 TTATTATATAAAATATTATTTTAATAATTAAAAATATAATAAA
145233 T
1 T
145234 AAGCGTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
42 25 0.66
43 11 0.29
44 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (43 bp):
TTATTATATAAAATATTATTTTAATAATTAAAAATATAATAAA
Found at i:150889 original size:2 final size:2
Alignment explanation
Indices: 150855--150981 Score: 195
Period size: 2 Copynumber: 64.5 Consensus size: 2
150845 TTGTGTAATG
* * * * *
150855 TA TA T- TA TA CA TA TA AA TA CA TA CA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
150896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
150937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
150979 TA T
1 TA T
150982 TCCTGCTTAC
Statistics
Matches: 113, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
1 2 0.02
2 111 0.98
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Done.