Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004209.1 Hibiscus syriacus cultivar Beakdansim tig00009217_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: 120020
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5116 original size:17 final size:18
Alignment explanation
Indices: 5083--5116 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5073 TCAATTCTGT
*
5083 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
5101 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
5117 GACCTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:10475 original size:17 final size:18
Alignment explanation
Indices: 10442--10475 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10432 TCAATTCTGT
*
10442 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
10460 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
10476 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:30076 original size:3 final size:3
Alignment explanation
Indices: 30068--30098 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30058 CGATTTGTGC
30068 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
30099 TATTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:31650 original size:81 final size:81
Alignment explanation
Indices: 31515--31699 Score: 273
Period size: 81 Copynumber: 2.3 Consensus size: 81
31505 AACCTTTCGT
* * * *
31515 TTTTACTCAACAG-AGTTTAACCGTTCATCTAACTGGTATAATTGACATTTTTCTACCAATTGCA
1 TTTTACTCAACGGTA-TTTAACCATTCATCTAACTGGCATAATTGACATCTTTCTACCAATTGCA
31579 CAGTTAGACCATTATTA
65 CAGTTAGACCATTATTA
* *
31596 TTTTACTCAACGGTATTTAACTATTCATCTAACTGGCATAATTGGCATCTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACATCTTTCTACCAATTGCAC
* *
31661 AGTTAGGCCATTATTT
66 AGTTAGACCATTATTA
*
31677 TTTTACTCAACGGTATTTCACCA
1 TTTTACTCAACGGTATTTAACCA
31700 CATTTTTACC
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
81 92 0.99
82 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (81 bp):
TTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACATCTTTCTACCAATTGCAC
AGTTAGACCATTATTA
Found at i:31822 original size:137 final size:139
Alignment explanation
Indices: 31563--31831 Score: 452
Period size: 137 Copynumber: 1.9 Consensus size: 139
31553 TAATTGACAT
*
31563 TTTTCTACCAATTGCACAGTTAGACCATTATTATTTTACTCAACGGTATTTAACTATTCATCTAA
1 TTTTCTACCAATTGCACAATTAGACCATTATTATTTTACTCAACGGTATTTAACTATTCATCTAA
* * *
31628 CTGGCATAATTGGCATCTTTCTACCAATTGCACAGTTAGGCCATTATTTTTTTACTCAACGGTAT
66 CTGGCATAATTGGCACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGATAT
31693 TTCACCACA
131 TTCACCACA
* * * *
31702 TTTT-TACCAATTGCATAATTAGGCCATTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAA
1 TTTTCTACCAATTGCACAATTAGACCATTATTATTTTACTCAACGGTATTTAACTATTCATCTAA
31766 CT-GCATAATTGGCACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGATAT
66 CTGGCATAATTGGCACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGATAT
31830 TT
131 TT
31832 AATCATTCAT
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
137 61 0.50
138 57 0.47
139 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.40
Consensus pattern (139 bp):
TTTTCTACCAATTGCACAATTAGACCATTATTATTTTACTCAACGGTATTTAACTATTCATCTAA
CTGGCATAATTGGCACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGATAT
TTCACCACA
Found at i:31841 original size:80 final size:80
Alignment explanation
Indices: 31706--31968 Score: 377
Period size: 81 Copynumber: 3.3 Consensus size: 80
31696 ACCACATTTT
* * *
31706 TACCAATTGCATAATTAGGCCATTATTCTTTTACTCAACGGTATTTAA-CTGTTCATCTAACTGC
1 TACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAATC-GTTCATCTAACTGA
31770 ATAATTGGCACCTTTC
65 ATAATTGGCACCTTTC
* *
31786 TACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGATATTTAATCATTCATCTAACTGAT
1 TACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGA-
* ** *
31851 ATAATTGACATATTTA
65 ATAATTGGCACCTTTC
*
31867 TACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAATCGTTCATTTAACTGGA
1 TACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAATCGTTCATCTAACT-GA
*
31932 ATAATTGGCACCTCTC
65 ATAATTGGCACCTTTC
31948 TACCAATTGCAC-GATTAGGCC
1 TACCAATTGCACAG-TTAGGCC
31969 TCAAAGGCAC
Statistics
Matches: 162, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
80 58 0.36
81 102 0.63
82 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (80 bp):
TACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGAA
TAATTGGCACCTTTC
Found at i:31901 original size:218 final size:219
Alignment explanation
Indices: 31515--31912 Score: 622
Period size: 218 Copynumber: 1.8 Consensus size: 219
31505 AACCTTTCGT
* **
31515 TTTTACTCAACAGAGTTTAACCGTTCATCTAACTGGTATAATTGACATTTTTCTACCAATTGCAC
1 TTTTACTCAACAGAGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGCAC
* * * *
31580 AGTTAGACCATTATTATTTTACTCAACGGTATTTAACTATTCATCTAACTGGCATAATTGGCATC
66 AGTTAGACCATTATTATTTTACTCAACGATATTTAACTATTCATCTAACTGACATAATTGACATA
* *
31645 TTTCTACCAATTGCACAGTTAGGCCATTATTTTTTTACTCAACGGTATTTCACCACATTTTTACC
131 TTTATACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTCACCACATTTTTACC
31710 AATTGCATAATTAGGCCATTATTC
196 AATTGCATAATTAGGCCATTATTC
* * *
31734 TTTTACTCAACGGTA-TTTAACTGTTCATCTAACT-GCATAATTGGCACCTTTCTACCAATTGCA
1 TTTTACTCAACAG-AGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGCA
* * *
31797 CAGTTAGGCCATTATTCTTTTACTCAACGATATTTAA-TCATTCATCTAACTGATATAATTGACA
65 CAGTTAGACCATTATTATTTTACTCAACGATATTTAACT-ATTCATCTAACTGACATAATTGACA
31861 TATTTATACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTT
129 TATTTATACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTT
31913 AATCGTTCAT
Statistics
Matches: 162, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
217 1 0.01
218 130 0.80
219 30 0.19
220 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (219 bp):
TTTTACTCAACAGAGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAATTGCAC
AGTTAGACCATTATTATTTTACTCAACGATATTTAACTATTCATCTAACTGACATAATTGACATA
TTTATACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTCACCACATTTTTACC
AATTGCATAATTAGGCCATTATTC
Found at i:32052 original size:68 final size:68
Alignment explanation
Indices: 31962--32173 Score: 327
Period size: 68 Copynumber: 3.1 Consensus size: 68
31952 AATTGCACGA
* *
31962 TTAGGCCTCAAAGGCACTTAGCCTTTCAACTAATTGGCATAAATGACACCTTTCTGTCATAAGCA
1 TTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCA
32027 CAG
66 CAG
* * * *
32030 TTAGGCCTCAAAGGCACCTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTATCATAAGCA
1 TTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCA
32095 C-G
66 CAG
* *
32097 ATTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACATCTTTCTGTCAAAAGC
1 -TTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGC
*
32162 ATAG
65 ACAG
32166 TTAGGCCT
1 TTAGGCCT
32174 ATTAATCTTT
Statistics
Matches: 129, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
67 1 0.01
68 127 0.98
69 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (68 bp):
TTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCA
CAG
Found at i:32500 original size:55 final size:54
Alignment explanation
Indices: 32397--32532 Score: 173
Period size: 55 Copynumber: 2.5 Consensus size: 54
32387 CCATATAAAC
* * * *
32397 ATTCATACACTTGGTAAGAATTTCTTAGTTCGCACACATAGTGCCCATACGGAA
1 ATTCATACACTTAGTATGAATTTCTTAGTTCGCACACAAAGTGCCCATACAGAA
* * * * *
32451 CTTCATACACTCAGTATGAATTTCCTTATTTTGCACACAAAGTGCCCATACATAA
1 ATTCATACACTTAGTATGAATTT-CTTAGTTCGCACACAAAGTGCCCATACAGAA
*
32506 ATTCATACACTTAGTATGAATATCTTA
1 ATTCATACACTTAGTATGAATTTCTTA
32533 CAATTTTTGC
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
54 23 0.33
55 46 0.67
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (54 bp):
ATTCATACACTTAGTATGAATTTCTTAGTTCGCACACAAAGTGCCCATACAGAA
Found at i:33038 original size:95 final size:95
Alignment explanation
Indices: 32911--33098 Score: 236
Period size: 95 Copynumber: 2.0 Consensus size: 95
32901 CGATACTTCT
* * *
32911 ATACTATAGTATAGATACCCCCTTCTGGTATCGATACT-GATTTTAGGTTCGATGTTACCTAGTA
1 ATACTATAGTATAGATACCCCCTTATGATATCGATA-TAGATTTTAGATTCGATGTTACCTAGTA
* *
32975 TTGATACTCTTACCATGGTATCAATACTAGC
65 TCGATACCCTTACCATGGTATCAATACTAGC
* * * * *
33006 ATACTATGGTACT-GATACCCCCTTATGATATCGATATAGGTTTTTGATTCGATGTTACTTGGTA
1 ATACTATAGTA-TAGATACCCCCTTATGATATCGATATAGATTTTAGATTCGATGTTACCTAGTA
* *
33070 TCGATACCCTTATCATGGTATCGATACTA
65 TCGATACCCTTACCATGGTATCAATACTA
33099 CCTCTTCGGT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
94 1 0.01
95 77 0.97
96 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (95 bp):
ATACTATAGTATAGATACCCCCTTATGATATCGATATAGATTTTAGATTCGATGTTACCTAGTAT
CGATACCCTTACCATGGTATCAATACTAGC
Found at i:34211 original size:87 final size:87
Alignment explanation
Indices: 34065--34296 Score: 336
Period size: 81 Copynumber: 2.7 Consensus size: 87
34055 AACCTTTTGT
* * *
34065 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCAACCAATTGCAA
1 TTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAA
*
34130 TTGCACATTTATG-CCATTATTC
66 TTGCACAGTTA-GACCATTATTC
34152 TTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTA-C-----CAA
1 TTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAA
34211 TTGCACAGTTAGACCATTATTC
66 TTGCACAGTTAGACCATTATTC
* *
34233 TTTTACTC-ATCGGTATTTAATCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCA
1 TTTTACTCAAT-GGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCA
34297 TGGTTAGGCC
Statistics
Matches: 131, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
80 3 0.02
81 72 0.55
82 1 0.01
86 1 0.01
87 54 0.41
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (87 bp):
TTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCAA
TTGCACAGTTAGACCATTATTC
Found at i:34452 original size:68 final size:68
Alignment explanation
Indices: 34368--34494 Score: 227
Period size: 68 Copynumber: 1.9 Consensus size: 68
34358 ATAGGCACGG
*
34368 TTAGGCTTTCATCTAACTGGCATAAATGACACCTTTCTGCCATAAGCATAGTTAAGCCTCAAAGG
1 TTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGCCATAAGCATAGTTAAGCCTCAAAGG
34433 CAC
66 CAC
* *
34436 TTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATAAGCATAGTTAGGCCT
1 TTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGCCATAAGCATAGTTAAGCCT
34495 ATTAATATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (68 bp):
TTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGCCATAAGCATAGTTAAGCCTCAAAGG
CAC
Found at i:34467 original size:119 final size:119
Alignment explanation
Indices: 34256--34479 Score: 342
Period size: 119 Copynumber: 1.9 Consensus size: 119
34246 TATTTAATCG
* ** * * *
34256 TTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCATGGTTAGGCCTAAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTACCAATAGCATAGTTAAGCCTAAAAGGCACTTAG
34321 CCTTTCATCTAACTAGCATAAATGACACATTTCTGTCATAGGCACGGTTAGGCT
66 CCTTTCATCTAACTAGCATAAATGACACATTTCTGTCATAGGCACGGTTAGGCT
* *
34375 TTCATCTAACTGGCATAAATGACACCTTTCTGCC-ATAAGCATAGTTAAGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTACCAAT-AGCATAGTTAAGCCTAAAAGGCACTTA
* *
34439 GCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATA
65 GCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCATA
34480 AGCATAGTTA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 2 0.02
119 92 0.98
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (119 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTACCAATAGCATAGTTAAGCCTAAAAGGCACTTAG
CCTTTCATCTAACTAGCATAAATGACACATTTCTGTCATAGGCACGGTTAGGCT
Found at i:34842 original size:56 final size:54
Alignment explanation
Indices: 34719--34855 Score: 177
Period size: 56 Copynumber: 2.5 Consensus size: 54
34709 CCATAAAAAC
* *
34719 ATTCATACACTTAGTAAGAATTTCTTAGTTCGTACACATAGTGCCCATACGGAA
1 ATTCATACACTTAGTATGAATTTCTTAGTTCGTACACATAGTGCCCATACAGAA
** * *
34773 ATTCATACACTTAGTATGAATTTCCTTA-TTTTTGCACATAAAGTGCCCATATAGAA
1 ATTCATACACTTAGTATGAATTT-CTTAGTTCGTACACAT--AGTGCCCATACAGAA
*
34829 ATTCATACACTTAGTATGAATATCTTA
1 ATTCATACACTTAGTATGAATTTCTTA
34856 CAATCTTTTC
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
54 30 0.41
55 8 0.11
56 35 0.48
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (54 bp):
ATTCATACACTTAGTATGAATTTCTTAGTTCGTACACATAGTGCCCATACAGAA
Found at i:36894 original size:23 final size:23
Alignment explanation
Indices: 36868--36928 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
36858 CTCGTATAAA
36868 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
*
36891 TGCACCAAAGTGCCGCGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
* **
36914 TACACCGTAGTGCCA
1 TGCACCAAAGTGCCA
36929 TATAAGATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.18
Consensus pattern (23 bp):
TGCACCAAAGTGCCACGTAGAAT
Found at i:43850 original size:23 final size:22
Alignment explanation
Indices: 43817--43877 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
43807 CTCGTGTAAA
*
43817 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCA-GTAGAAT
43840 TGCACCGAAGTGCCGAGTAGAAT
1 TGCACCGAAGTGCC-AGTAGAAT
* *
43863 TACACCGTAGTGCCA
1 TGCACCGAAGTGCCA
43878 TATAAGATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCAGTAGAAT
Found at i:48473 original size:18 final size:18
Alignment explanation
Indices: 48450--48484 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48440 ATATATTTGT
48450 TATTTTAATTAAAATTAA
1 TATTTTAATTAAAATTAA
*
48468 TATTTTTATTAAAATTA
1 TATTTTAATTAAAATTA
48485 CAAATACGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTTAATTAAAATTAA
Found at i:48483 original size:24 final size:26
Alignment explanation
Indices: 48442--48489 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
48432 CATAAACCAT
**
48442 ATATTTGTTATTTTAATTA-AAATTA
1 ATATTTGTTATTAAAATTACAAATTA
48467 ATATTT-TTATTAAAATTACAAAT
1 ATATTTGTTATTAAAATTACAAAT
48490 ACGTTTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATATTTGTTATTAAAATTACAAATTA
Found at i:50802 original size:424 final size:424
Alignment explanation
Indices: 50006--50847 Score: 1420
Period size: 424 Copynumber: 2.0 Consensus size: 424
49996 TGACTATTTG
* *
50006 GTTTAATGAAACCTTCTTGTCTAAATGAAGGTTGTTCTATGGTGGTCACTTATGGAACTAACACC
1 GTTTAATGAAACCTTCTTCTCTAAATGAAGGTTGTTCTATGGTGGTCACTTATAGAACTAACACC
* *
50071 TTTTGCATTTGCATTTTGCATCTACATTTGCATTCGCACTGCTTTAATTTAAGCATTTTACATGC
66 TTTTGCATTTGCATTTTGCATCTACATTTGCATTCGCACTACTTTAATTTAAGCATTTTACATGA
* * *
50136 ATTAATCATGAAAATCTGGGAATAACTCACGGAGAATCTTGTGATAGAAGTTTTTTGAGGTAAAT
131 ATCAATCATGAAAATCTGGGAATAACTCACAGAGAATCTTGTGATAGAAGTTTCTTGAGGTAAAT
50201 TGAAGTTACCTCATTCATACATAAAAAGGATTGAGATCTATAGACACGATGTTAGCACTGTCTGA
196 TGAAGTTACCTCATTCATACATAAAAAGGATTGAGATCTATAGACACGATGTTAGCACTGTCTGA
* * * *
50266 AGTTTGAGGCACATCATTGAGATTTGTGGTGCACCGAAGAGTAAGATTTAAATTTTTTTTCAACC
261 AGTTCGAGGCACATCATTGAGATCTGTGGGGCACCGAAGAGTAAGATTCAAATTTTTTTTCAACC
*
50331 CAGAGGCAATAACCTTTAACGTGTAATGAGACATTCCAGTGCCAATCAACAAAAAGTTCTTCCAT
326 CAGAGGCAATAACCTTTAACGTGTAATGAGACATTCCAGTACCAATCAACAAAAAGTTCTTCCAT
*
50396 CCACTGTGAAACC-TATTGCACTTGCTTCATGAA
391 CCACTGTGAAACCATATTGCACTAGCTTCATGAA
* *
50429 GTTTAATGAAACCTTGTTCTCTAAATGAAGGTTGTTCTATGGTGGTCACTTATAGAATTAACACC
1 GTTTAATGAAACCTTCTTCTCTAAATGAAGGTTGTTCTATGGTGGTCACTTATAGAACTAACACC
*
50494 TTTTGCATTTGCATTTTGCATCTACATTTGCATTCGTACTACTTTAATTTAAGCATTTTTACATG
66 TTTTGCATTTGCATTTTGCATCTACATTTGCATTCGCACTACTTTAATTTAAGCA-TTTTACATG
* *
50559 AATCAATCATGAAAATCTGGGAGTAACTCACAGAGAATCTTGTTATAGAAGTTTCTTGAGGTAAA
130 AATCAATCATGAAAATCTGGGAATAACTCACAGAGAATCTTGTGATAGAAGTTTCTTGAGGTAAA
* **
50624 TTGAAGTTACCTCATTCGTACATAAAAAGGATTGAGATCTATAGACGTGATGTTAGCACTGTCTG
195 TTGAAGTTACCTCATTCATACATAAAAAGGATTGAGATCTATAGACACGATGTTAGCACTGTCTG
*
50689 AAGTTCGAGGCACATCATTGAGATCTGTGGGGCACCGAAGA-TCAAGATTCGAATTTTTTTTCAA
260 AAGTTCGAGGCACATCATTGAGATCTGTGGGGCACCGAAGAGT-AAGATTCAAATTTTTTTTCAA
* *
50753 CCCAGAGGCATTAACCTTTAACGTGTAATGAGACATTCC-GATACCAATCAAGAAAAAGTTCTTC
324 CCCAGAGGCAATAACCTTTAACGTGTAATGAGACATTCCAG-TACCAATCAACAAAAAGTTCTTC
50817 CATCCACTGTGAAACCATATTGCACTAGCTT
388 CATCCACTGTGAAACCATATTGCACTAGCTT
50848 TGTCCTGTTT
Statistics
Matches: 391, Mismatches: 24, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
423 116 0.30
424 262 0.67
425 13 0.03
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (424 bp):
GTTTAATGAAACCTTCTTCTCTAAATGAAGGTTGTTCTATGGTGGTCACTTATAGAACTAACACC
TTTTGCATTTGCATTTTGCATCTACATTTGCATTCGCACTACTTTAATTTAAGCATTTTACATGA
ATCAATCATGAAAATCTGGGAATAACTCACAGAGAATCTTGTGATAGAAGTTTCTTGAGGTAAAT
TGAAGTTACCTCATTCATACATAAAAAGGATTGAGATCTATAGACACGATGTTAGCACTGTCTGA
AGTTCGAGGCACATCATTGAGATCTGTGGGGCACCGAAGAGTAAGATTCAAATTTTTTTTCAACC
CAGAGGCAATAACCTTTAACGTGTAATGAGACATTCCAGTACCAATCAACAAAAAGTTCTTCCAT
CCACTGTGAAACCATATTGCACTAGCTTCATGAA
Found at i:52077 original size:21 final size:21
Alignment explanation
Indices: 52033--52098 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
52023 AAATTTTATG
**
52033 AATAGTATCGATACTGTGTGAAC
1 AATAGTATCGATAC--CATGAAC
**
52056 AATAGTATTTATACCATGAAC
1 AATAGTATCGATACCATGAAC
*
52077 AGTAGTATCGATACCATGAAC
1 AATAGTATCGATACCATGAAC
52098 A
1 A
52099 GTACTGATGC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 24 0.67
23 12 0.33
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (21 bp):
AATAGTATCGATACCATGAAC
Found at i:52099 original size:21 final size:21
Alignment explanation
Indices: 52051--52101 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
52041 CGATACTGTG
* **
52051 TGAACAATAGTATTTATACCA
1 TGAACAGTAGTATCGATACCA
52072 TGAACAGTAGTATCGATACCA
1 TGAACAGTAGTATCGATACCA
52093 TGAACAGTA
1 TGAACAGTA
52102 CTGATGCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (21 bp):
TGAACAGTAGTATCGATACCA
Found at i:52173 original size:21 final size:21
Alignment explanation
Indices: 52134--52204 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
52124 TACAAAAATG
*
52134 GTATCGATA-C-TGTACAGTA
1 GTATCGATACCATGAACAGTA
* *
52153 GTATTGATATCATGAACAGTA
1 GTATCGATACCATGAACAGTA
* *
52174 GTATCGATACCGTGAACAGTT
1 GTATCGATACCATGAACAGTA
52195 GTATCGATAC
1 GTATCGATAC
52205 TATCAAGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.18
20 1 0.02
21 35 0.80
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (21 bp):
GTATCGATACCATGAACAGTA
Found at i:52616 original size:33 final size:33
Alignment explanation
Indices: 52568--52631 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
52558 AAGGGGTTTA
* * *
52568 GGTTCTAGCTGAGCCTGTTAAAAGCTAGGGATT
1 GGTTCTAGCTGAGCCTATGAAAAACTAGGGATT
* *
52601 GGTTCTAGTTTAGCCTATGAAAAACTAGGGA
1 GGTTCTAGCTGAGCCTATGAAAAACTAGGGA
52632 GTTTGTAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (33 bp):
GGTTCTAGCTGAGCCTATGAAAAACTAGGGATT
Found at i:55454 original size:20 final size:20
Alignment explanation
Indices: 55401--55454 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
55391 AAATTTTTTG
*
55401 TGAATAGTATTG-TACTATA
1 TGAATAGTATCGATACTATA
*
55420 TGAGTAGTA-CTGATACTATA
1 TGAATAGTATC-GATACTATA
55440 TGAATAGTATCGATA
1 TGAATAGTATCGATA
55455 TTGTGTGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.31
20 19 0.66
21 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (20 bp):
TGAATAGTATCGATACTATA
Found at i:55585 original size:21 final size:21
Alignment explanation
Indices: 55557--55604 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
55547 CGATATTGCT
*
55557 ACAGTAGTATCGATACCATGA
1 ACAGTAGTATCGAAACCATGA
*
55578 ATAGTAGTATCGAAACCATGA
1 ACAGTAGTATCGAAACCATGA
55599 ACAGTA
1 ACAGTA
55605 CATATGGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23
Consensus pattern (21 bp):
ACAGTAGTATCGAAACCATGA
Found at i:55616 original size:94 final size:94
Alignment explanation
Indices: 55469--55698 Score: 325
Period size: 94 Copynumber: 2.4 Consensus size: 94
55459 GTGAACTGTC
** * *
55469 GTATCGATACCATGAACAGTAGTATTAAAACCATAAACAGTACAGATGCTCAAAAATTCCAGAAT
1 GTATCGATACCATGAACAGTAGTATCGAAACCATGAACAGTACAGATGCTCAAAAATTACAGAAT
* *
55534 GTAAAAATGGTATCGATATTGCTACAGTA
66 ATAAAAATGGTATCGATACTGCTACAGTA
* * * *
55563 GTATCGATACCATGAATAGTAGTATCGAAACCATGAACAGTACATATGGTCAAAAATTACATAAT
1 GTATCGATACCATGAACAGTAGTATCGAAACCATGAACAGTACAGATGCTCAAAAATTACAGAAT
*
55628 ATAAGAATGGTATCGATACTGCTACAGTA
66 ATAAAAATGGTATCGATACTGCTACAGTA
* * * *
55657 TTATCGATACCATGAACAGTAATATCGATACCGTGAACAGTA
1 GTATCGATACCATGAACAGTAGTATCGAAACCATGAACAGTA
55699 GTATCGATAC
Statistics
Matches: 120, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 120 1.00
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (94 bp):
GTATCGATACCATGAACAGTAGTATCGAAACCATGAACAGTACAGATGCTCAAAAATTACAGAAT
ATAAAAATGGTATCGATACTGCTACAGTA
Found at i:55677 original size:21 final size:21
Alignment explanation
Indices: 55651--55708 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
55641 CGATACTGCT
*
55651 ACAGTATTATCGATACCATGA
1 ACAGTAATATCGATACCATGA
*
55672 ACAGTAATATCGATACCGTGA
1 ACAGTAATATCGATACCATGA
*
55693 ACAGTAGTATCGATAC
1 ACAGTAATATCGATAC
55709 TATCAAGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (21 bp):
ACAGTAATATCGATACCATGA
Found at i:56112 original size:33 final size:33
Alignment explanation
Indices: 56070--56168 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
56060 TAAAGGGGTT
* *
56070 TTGGTTCTAGCTGAGCCTGTTAAAAGCTAGGGA
1 TTGGTTCTAGTTTAGCCTGTTAAAAGCTAGGGA
56103 TTGGTTCTAGTTTAGCCTGTTAAAAGCTAGGGA
1 TTGGTTCTAGTTTAGCCTGTTAAAAGCTAGGGA
* * *
56136 TTGGTTCTAGTTTAGCCCGTGAAAAACTAGGGA
1 TTGGTTCTAGTTTAGCCTGTTAAAAGCTAGGGA
56169 GTTTGTAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.32
Consensus pattern (33 bp):
TTGGTTCTAGTTTAGCCTGTTAAAAGCTAGGGA
Found at i:58325 original size:42 final size:41
Alignment explanation
Indices: 58249--58330 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 41
58239 TAGTAAGTCC
* *
58249 TTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAATCA
1 TTCGGGCCATTAGTAAGACTTTCGAGAATGATGA-TAAATCA
*
58291 TTCGGGTCATCTA-TAAGACTTTCGAGAAAT-ATGATAAATC
1 TTCGGGCCAT-TAGTAAGACTTTCGAG-AATGATGATAAATC
58331 CTTCCGACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 6 0.17
42 25 0.71
43 4 0.11
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (41 bp):
TTCGGGCCATTAGTAAGACTTTCGAGAATGATGATAAATCA
Found at i:58778 original size:261 final size:259
Alignment explanation
Indices: 58238--58987 Score: 1044
Period size: 261 Copynumber: 2.9 Consensus size: 259
58228 GGTTTCTTAC
*
58238 TTAGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCT
1 TTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCT
* * * *
58303 ATAAGACTTTCGAGA-AATATGATAAATCCTTCCGACCATCCATAAGGCCTTCGAGCAGGATATT
66 ATAAGCCTTTCGA-ACAATATGATAAGTCCTTCAG-CCATCCATAAGGCCTTCGGGCA-GATATT
* * *
58367 TTCACATATTTTTCGAAAAATGAGAAAACGA-TTTCCATAGTTTCTCATTTAAATCTTTTCTGAA
128 TTCACATGTTTTTTGAAAAATGAGAAAACGATTTTCCAAAGTTTCTCATTTAAATCTTTTCTGAA
* *
58431 AATTAAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCGA
193 AATTGAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAA
*
58496 AC
258 AA
* *
58498 TTAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATAT
1 TTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCT
* * *
58563 ATAAGCCTTTCGAACAAGATGATAAGTCCATCAAGCCATCCATAAGGCCTTCGGGCATGATGTTT
66 ATAAGCCTTTCGAACAATATGATAAGTCCTTC-AGCCATCCATAAGGCCTTCGGGCA-GATATTT
* *
58628 TCACTTGTTTTTTGAAAAATGAGAAAATGATTTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAA
129 TCACATGTTTTTTGAAAAATGAGAAAACGATTTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAA
58693 ATTGAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAA
194 ATTGAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAA
58758 A
259 A
* * * *
58759 TTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCTTGATGATTAAATCCTTTGGGTCATCT
1 TTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCT
* * * *
58824 ATAAGCCTTTC-AAGCAATATGAAAAGTCCTTCGAGCCATTCAAAAGGCCTTCGGGTAGAATATT
66 ATAAGCCTTTCGAA-CAATATGATAAGTCCTTC-AGCCATCCATAAGGCCTTCGGGCAG-ATATT
* *
58888 TTCACATGATTTCTGAAAAATGAGAAAACGATTTT-CAAAG-------TTT-AA--TTTTCTGAA
128 TTCACATGTTTTTTGAAAAATGAGAAAACGATTTTCCAAAGTTTCTCATTTAAATCTTTTCTGAA
* * *
58942 AA-TGAAATTTTTTAAAAGTAAGTAAATTATTTCCAAAGTTTCTTAC
193 AATTGAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTAC
58988 TTATTAAGTC
Statistics
Matches: 445, Mismatches: 40, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
249 41 0.09
250 11 0.02
252 2 0.00
253 3 0.01
259 1 0.00
260 149 0.33
261 238 0.53
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (259 bp):
TTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTCATCT
ATAAGCCTTTCGAACAATATGATAAGTCCTTCAGCCATCCATAAGGCCTTCGGGCAGATATTTTC
ACATGTTTTTTGAAAAATGAGAAAACGATTTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAAT
TGAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAA
Found at i:59504 original size:20 final size:20
Alignment explanation
Indices: 59453--59508 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
59443 TTTATTACTT
*
59453 AGTAAGTCCTTCGAGCCATC
1 AGTAAGTCTTTCGAGCCATC
59473 AGTAAGTCTTTCGAGCCATC
1 AGTAAGTCTTTCGAGCCATC
*
59493 AGTAAGTTTTTCGAGC
1 AGTAAGTCTTTCGAGC
59509 ATGATGCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (20 bp):
AGTAAGTCTTTCGAGCCATC
Found at i:59740 original size:260 final size:253
Alignment explanation
Indices: 59022--59800 Score: 663
Period size: 256 Copynumber: 3.1 Consensus size: 253
59012 TAAGTATGTT
* * * * * * * * * *
59022 TAAATCCTTTGAGTCATTTGTATGTCTTTTGAGTAATATGATGAGTCC-TTCGGGCCATCCATAA
1 TAAATCCTTTGGGTCATCTATAAGTCTTTTAAGCAAGATGATAAG-CCATTCAGGCCATACATAA
* * * *
59086 GACCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAACGATTTTCAAAGTTTCTC
65 GACCTTCAGGCAGGATGTTTTCACATGATTTAC-AAAAATGAGAAAACAATTTCCAAAGTTTCTC
* * *
59151 ATTT-AAATCTTTTCTGAAAA-TGAAATTTTTGAAAAGTAAGAAAAAGTTTTCCAAAGTTTCTTA
129 ATTTAAAAT-TTTTCT-AAAATTG--ATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTATTA
* * ** *
59214 CTTAGTAAG----T--CC-T---T---T-G---G-GCTATCAATAAGTCTTTTAAGCTTGATGC
190 CCTAGTAAGTCCTTCGCCATCAGTAAGTCGTTCGAGCCATCAATAAGTCTTTCGAGCATGATGC
* * * * * *
59260 TTAAATCCTTCGGGTCATCTTTAATTCTTTTAAGCAAGATTATAAGCCCTTCAGGCCATATATAA
1 -TAAATCCTTTGGGTCATCTATAAGTCTTTTAAGCAAGATGATAAGCCATTCAGGCCATACATAA
* *
59325 GACCTTCTGGCAGGATGTTTTCACATGATTTCCAAAAATGAGAAAACAATTTCCAAAGTTTCTCA
65 GACCTTCAGGCAGGATGTTTTCACATGATTTACAAAAATGAGAAAACAATTTCCAAAGTTTCTCA
* * *
59390 TTTAAAATTTTTCTAAATTTGATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTATTACTTAG
130 TTTAAAATTTTTCTAAAATTGATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTATTACCTAG
* * *
59455 TAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCCATCAGTAAGTTTTTCGAGCATGATGC
195 TAAGTCCTTC--GCCATCAGTAAGTCGTTCGAGCCATCAATAAGTCTTTCGAGCATGATGC
* * * * *
59516 TAAAATCCTTTGGGTTATCTATCAGTCTTTCT-AGCAAGATGATAAGTCATTCGGGCCATCCATA
1 T-AAATCCTTTGGGTCATCTATAAGTCTTT-TAAGCAAGATGATAAGCCATTCAGGCCATACATA
* ** * *
59580 AGTCCTTCAGGCAGGATGTTTTCATGTGATTTTAGAAAAATGAGAAAATAATTTCCAAAGTTTCA
64 AGACCTTCAGGCAGGATGTTTTCACATGA-TTTACAAAAATGAGAAAACAATTTCCAAAGTTTC-
* * *
59645 T-ATTT-AAATATTTTCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGCGGTTTCCAAAGTTTCT
127 TCATTTAAAAT-TTTTCT-AAAATTG--ATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTAT
* ** ** *
59708 TACCTAGTAAATTGTTTC-CCAAATTGGTAAGTCGTTCGGGCCATCAATAAGTCTTTCGAGCATG
188 TACCTAGT-AAGTCCTTCGCC--ATCAGTAAGTCGTTCGAGCCATCAATAAGTCTTTCGAGCATG
*
59772 ATACC
250 AT-GC
* * *
59777 TAAATCCTTTAGGCCATCCATAAG
1 TAAATCCTTTGGGTCATCTATAAG
59801 ACATTCGGGC
Statistics
Matches: 437, Mismatches: 68, Indels: 49
0.79 0.12 0.09
Matches are distributed among these distances:
236 45 0.10
237 3 0.01
238 43 0.10
239 82 0.19
240 1 0.00
244 2 0.00
245 1 0.00
248 1 0.00
251 1 0.00
255 2 0.00
256 101 0.23
257 42 0.10
258 9 0.02
260 96 0.22
261 8 0.02
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (253 bp):
TAAATCCTTTGGGTCATCTATAAGTCTTTTAAGCAAGATGATAAGCCATTCAGGCCATACATAAG
ACCTTCAGGCAGGATGTTTTCACATGATTTACAAAAATGAGAAAACAATTTCCAAAGTTTCTCAT
TTAAAATTTTTCTAAAATTGATTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTATTACCTAGT
AAGTCCTTCGCCATCAGTAAGTCGTTCGAGCCATCAATAAGTCTTTCGAGCATGATGC
Found at i:60344 original size:133 final size:133
Alignment explanation
Indices: 60133--60766 Score: 708
Period size: 133 Copynumber: 4.8 Consensus size: 133
60123 GCAAATCGAA
* * * * *
60133 CTCGATTTAATCTTCCCTAAAGAACAGTGGAATGAATCAACGTTTCTAGATTTGATTTACTCTGA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTACCCTGA
* * * * *
60198 AGATGCAGCAGAGCATATCCCTTTTTTTCTAGATTTGATCTTCCCTCAGGAACATTGGAA-AAAT
66 AGAAGCAGTAGAGCATATCCC-TTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAAT
*
60262 CTTC
130 CTGC
* * * * * *
60266 CTCGATTCAATCTTCCTTGAAGAATAGTGGAATGAATCAATGTTTCCATAACTGATTTACCTTGA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTACCCTGA
* * *
60331 AGAAGCAGTAGAGCAGATCCATTTTTTCCAGATTTGATCTTCCATGAGGAACAGTGGAACAAATC
66 AGAAGCAGTAGAGCATATCCCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAATC
60396 TGC
131 TGC
* ** * *
60399 CTAGATTCAAAATTCCCTGAAGAA-ATGTAGAATGAATCAACGTTTCAAGATCTGATTTACCCTG
1 CTCGATTCAATCTTCCCTGAAGAACA-GTGGAATGAATCAACGTTTCCAGATCTGATTTACCCTG
* * ** * * * * *
60463 ATGAAACAACAGAGCATATCCCTTTTTCCCATATTTGATCTTCACTGAGGAGCAGTGGAACAAGT
65 AAGAAGCAGTAGAGCATATCCCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAAT
*
60528 CTTC
130 CTGC
* * * ** * * *
60532 CTTGATTCAATCTACCCTGAA-AAGCAATGGAGCGAACCAACATTTCCAGATATGATTTACCCTG
1 CTCGATTCAATCTTCCCTGAAGAA-CAGTGGAATGAATCAACGTTTCCAGATCTGATTTACCCTG
* *
60596 AAGAAGCAGTGGAGCATATCCC-CTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAAT
65 AAGAAGCAGTAGAGCATATCCCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAAT
60660 CTGC
130 CTGC
* * * *
60664 CTCGATTCAATATTCCCTTAAGAACAGTGGAATGAATCAACGCTTCCAGATCTGATCTACCCTGA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTACCCTGA
* * * *
60729 A-AAACGGTGGAGCAGATCCC--TTTT-CAGATTTGATCTTC
66 AGAAGCAGTAGAGCATATCCCTTTTTTCCAGATTTGATCTTC
60767 AAAAATATCT
Statistics
Matches: 414, Mismatches: 82, Indels: 14
0.81 0.16 0.03
Matches are distributed among these distances:
129 14 0.03
130 4 0.01
131 16 0.04
132 127 0.31
133 252 0.61
134 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (133 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTACCCTGA
AGAAGCAGTAGAGCATATCCCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAATC
TGC
Found at i:60935 original size:3 final size:3
Alignment explanation
Indices: 60927--61018 Score: 168
Period size: 3 Copynumber: 30.7 Consensus size: 3
60917 CTGGAGACTG
60927 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
60975 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
61019 TCTGTGGTAG
Statistics
Matches: 87, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.02
3 82 0.94
4 3 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:62881 original size:29 final size:30
Alignment explanation
Indices: 62817--62881 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
62807 CTTTTTACAT
*
62817 TATTTTATTTTTATTACTATTTGGGTTCTA
1 TATTTTATTTTTATTACTATTTGGGTTCGA
*
62847 TTTTTTA-TTTTATTA-TGATTTGGGTAT-GA
1 TATTTTATTTTTATTACT-ATTTGGGT-TCGA
62876 TATTTT
1 TATTTT
62882 CAATTTATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 22 0.73
30 7 0.23
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (30 bp):
TATTTTATTTTTATTACTATTTGGGTTCGA
Found at i:63998 original size:17 final size:17
Alignment explanation
Indices: 63967--64008 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
63957 ATTCGAGACG
*
63967 AGATCTTTTAAAAA-TA
1 AGATTTTTTAAAAATTA
63983 AGATTTTTTAAAAAATTA
1 AGATTTTTT-AAAAATTA
64001 A-ATTTTTT
1 AGATTTTTT
64009 TTTTAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 12 0.52
18 3 0.13
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (17 bp):
AGATTTTTTAAAAATTA
Found at i:64896 original size:189 final size:190
Alignment explanation
Indices: 64552--64899 Score: 556
Period size: 190 Copynumber: 1.8 Consensus size: 190
64542 AAAGATAAAT
* * *
64552 TTTAATTTGAATATTAGTAGGATAATTACTCTTTTAATAAGTAAATTTAAAAATGTATTTATTAT
1 TTTAATTTGAATATTAGTAGGATAATTACTCTTTGAATAAGTAAATTTAAAAAGGTATTTATTAC
*
64617 ATTTTTAATTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATATA
66 ATTTTTAACTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATATA
*
64682 TGTTTAAGTTTGAATAGTAAAAGGAGTTTATTTTATGACCATTGTAAATTAAATATATTA
131 TATTTAAGTTTGAATAGTAAAAGGAGTTTATTTTATGACCATTGTAAATTAAATATATTA
* * * * *
64742 TTTAATTTGAATATTAGTAGGATAATTACTCTTTGAATATGTCAGTTTAAAAAGGTGTTTGTTAC
1 TTTAATTTGAATATTAGTAGGATAATTACTCTTTGAATAAGTAAATTTAAAAAGGTATTTATTAC
* *
64807 CTTTTTAACTTTGAATATT-AAATATAATTATATACTTTTGTATATTTCAAATTAAAATAATACT
66 ATTTTTAACTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATA-T
*
64871 -TATTTAAGTTTGAATGGTAAAAGGAGTTT
130 ATATTTAAGTTTGAATAGTAAAAGGAGTTT
64900 TATCTTTTGC
Statistics
Matches: 144, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
189 69 0.48
190 75 0.52
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (190 bp):
TTTAATTTGAATATTAGTAGGATAATTACTCTTTGAATAAGTAAATTTAAAAAGGTATTTATTAC
ATTTTTAACTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATATA
TATTTAAGTTTGAATAGTAAAAGGAGTTTATTTTATGACCATTGTAAATTAAATATATTA
Found at i:68451 original size:189 final size:191
Alignment explanation
Indices: 68110--68463 Score: 543
Period size: 190 Copynumber: 1.9 Consensus size: 191
68100 AAAGATAAAT
* * * * *
68110 TTTAATTTGAATATTAGTAGGATAATTAGTCTTTTAATAAGTAAATTTAAAAATGTATTTATTAT
1 TTTAATTTAAATATTAGTAGGATAATTACTCTTTGAATAAGTAAATTTAAAAAGGTATTTATTAC
*
68175 ATTTTTAATTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATATA
66 ATTTTTAACTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATATA
*
68240 TGTTTAAGTTTGAATAGTAAAAGGAG-TTTATCTTATGACCATTGTAAATTAAATATATTA
131 TATTTAAGTTTGAATAGTAAAAGGAGTTTTATCTTATGACCATTGTAAATTAAATATATTA
* * * * *
68300 TTTAATTTAAATATTAGTAGGATAATTACTCTTTGAATATGTCAGTTTAAAAAGGTGTTTGTTAC
1 TTTAATTTAAATATTAGTAGGATAATTACTCTTTGAATAAGTAAATTTAAAAAGGTATTTATTAC
* *
68365 CTTTTTAACTTTGAATATT-AAATATAATTATATACTTTTGTATATTTCAAATTAAAATAATACT
66 ATTTTTAACTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATA-T
*
68429 -TATTTAAGTTTGAATGGTAAAAGGAGTTTTATCTT
130 ATATTTAAGTTTGAATAGTAAAAGGAGTTTTATCTT
68464 TTGCATGTTT
Statistics
Matches: 147, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
189 66 0.45
190 81 0.55
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.46
Consensus pattern (191 bp):
TTTAATTTAAATATTAGTAGGATAATTACTCTTTGAATAAGTAAATTTAAAAAGGTATTTATTAC
ATTTTTAACTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATATA
TATTTAAGTTTGAATAGTAAAAGGAGTTTTATCTTATGACCATTGTAAATTAAATATATTA
Found at i:69883 original size:52 final size:52
Alignment explanation
Indices: 69823--69931 Score: 209
Period size: 52 Copynumber: 2.1 Consensus size: 52
69813 GGAGCTATCA
69823 ATTTTAATATAATACTAAAATATTCATCCAAATTCAAGTAAGTTCACCTAAT
1 ATTTTAATATAATACTAAAATATTCATCCAAATTCAAGTAAGTTCACCTAAT
*
69875 ATTTTAATATAATACTAAAATATTCATCCAAATTCACGTAAGTTCACCTAAT
1 ATTTTAATATAATACTAAAATATTCATCCAAATTCAAGTAAGTTCACCTAAT
69927 ATTTT
1 ATTTT
69932 GGTGGATCTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.39
Consensus pattern (52 bp):
ATTTTAATATAATACTAAAATATTCATCCAAATTCAAGTAAGTTCACCTAAT
Found at i:71663 original size:46 final size:47
Alignment explanation
Indices: 71593--71699 Score: 126
Period size: 47 Copynumber: 2.3 Consensus size: 47
71583 GTGTTAACAT
* * ** *
71593 AAACATTATTTTTTTTATCAAAAATGTT-GTTATTGGGCGCTACCTA
1 AAACATTATTTTTTTTACCAAAAATGTTAATTATTAAGCACTACCTA
* *
71639 AAACATTATTTTTTTTACCGAAAATTTTAATTATTAAGCACTACCTA
1 AAACATTATTTTTTTTACCAAAAATGTTAATTATTAAGCACTACCTA
**
71686 AAATGTTATTTTTT
1 AAACATTATTTTTT
71700 CTATCGGAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
46 25 0.49
47 26 0.51
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (47 bp):
AAACATTATTTTTTTTACCAAAAATGTTAATTATTAAGCACTACCTA
Found at i:73253 original size:26 final size:29
Alignment explanation
Indices: 73223--73284 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
73213 TTAATATTCA
*
73223 AATTTAAAAGA-T-AATAAATAT-ACTTT
1 AATTTAAAAGATTAAAAAAATATGACTTT
* *
73249 AATTTAAAATATTAAAAAAATATGATTTT
1 AATTTAAAAGATTAAAAAAATATGACTTT
73278 AATTTAA
1 AATTTAA
73285 TTATTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 10 0.33
27 1 0.03
28 8 0.27
29 11 0.37
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (29 bp):
AATTTAAAAGATTAAAAAAATATGACTTT
Found at i:73289 original size:28 final size:28
Alignment explanation
Indices: 73238--73292 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
73228 AAAAGATAAT
73238 AAATATACTTTAATTTAAAATATTAAAA
1 AAATATACTTTAATTTAAAATATTAAAA
* *
73266 AAATATGATTTTAATTT-AATTATTAAA
1 AAATAT-ACTTTAATTTAAAATATTAAA
73293 TTTATCAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
AAATATACTTTAATTTAAAATATTAAAA
Found at i:76357 original size:23 final size:21
Alignment explanation
Indices: 76318--76370 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
76308 ATAGCCTTCA
76318 AAATCCTAAAAACAAGATAAAG
1 AAATCCTAAAAACAAGA-AAAG
*
76340 ATAATCCTAAAATA-AAGAAAAT
1 A-AATCCTAAAA-ACAAGAAAAG
76362 AAATCCTAA
1 AAATCCTAA
76371 TTAAAATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.29
22 5 0.18
23 14 0.50
24 1 0.04
ACGTcount: A:0.62, C:0.13, G:0.06, T:0.19
Consensus pattern (21 bp):
AAATCCTAAAAACAAGAAAAG
Found at i:86956 original size:2 final size:2
Alignment explanation
Indices: 86949--86977 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
86939 TGATGCATTC
86949 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 T
86978 GGAATAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:89978 original size:19 final size:19
Alignment explanation
Indices: 89954--90015 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
89944 AAATCGAAAC
89954 CGGTTTTTTTGGTTCGGTT
1 CGGTTTTTTTGGTTCGGTT
*
89973 CGGTTTTTTT--TAACGGTT
1 CGGTTTTTTTGGT-TCGGTT
*
89991 CGAG-TTTTTCGGTTCGGTT
1 CG-GTTTTTTTGGTTCGGTT
90010 CGGTTT
1 CGGTTT
90016 ATCGGTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
17 1 0.03
18 13 0.37
19 20 0.57
20 1 0.03
ACGTcount: A:0.05, C:0.13, G:0.29, T:0.53
Consensus pattern (19 bp):
CGGTTTTTTTGGTTCGGTT
Found at i:89981 original size:18 final size:18
Alignment explanation
Indices: 89958--90015 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
89948 CGAAACCGGT
89958 TTTTTTGGTTCGGTTCGG
1 TTTTTTGGTTCGGTTCGG
89976 TTTTTT--TTAACGGTTCGAG
1 TTTTTTGGTT--CGGTTCG-G
*
89995 TTTTTCGGTTCGGTTCGG
1 TTTTTTGGTTCGGTTCGG
90013 TTT
1 TTT
90016 ATCGGTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 2 0.06
18 17 0.50
19 13 0.38
21 2 0.06
ACGTcount: A:0.05, C:0.12, G:0.28, T:0.55
Consensus pattern (18 bp):
TTTTTTGGTTCGGTTCGG
Found at i:90020 original size:18 final size:19
Alignment explanation
Indices: 89986--90022 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
89976 TTTTTTTTAA
*
89986 CGGTTCGAGTTTTTCGGTT
1 CGGTTCGAGTTTATCGGTT
90005 CGGTTCG-GTTTATCGGTT
1 CGGTTCGAGTTTATCGGTT
90023 TTTCAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.05, C:0.16, G:0.32, T:0.46
Consensus pattern (19 bp):
CGGTTCGAGTTTATCGGTT
Found at i:93008 original size:119 final size:119
Alignment explanation
Indices: 92797--93019 Score: 329
Period size: 119 Copynumber: 1.9 Consensus size: 119
92787 TCTCTCGATT
* * * * *
92797 CCACTAGGGTTGCATGTTGTTTATCTTCTATAGGTGCCAACCAGTGGCGGCTTTACCCTGAAATC
1 CCACTAGGGCTGCATGTTGTTTATCTTCTATAGGTGCCAACCAATGGCAGCTTGACCCTAAAATC
**** *
92862 TAAATTTTTTTCGATTAGTTACTTATTTTACTGATGATGCGAAATTTTTCGTGC
66 TAAATTTAAAACGATTAGTTACTTATTTTACTAATGATGCGAAATTTTTCGTGC
*
92916 CCACTAGGGCTGCATGTTGTTTATCTTCTCTAGGTGCCAACCAATGGCAGCTTGACCCTAAAATC
1 CCACTAGGGCTGCATGTTGTTTATCTTCTATAGGTGCCAACCAATGGCAGCTTGACCCTAAAATC
* *
92981 TGAATTTAAAACGATTAGTTATTTATTTTACTAATGATG
66 TAAATTTAAAACGATTAGTTACTTATTTTACTAATGATG
93020 GCCACCCTAA
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
119 91 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (119 bp):
CCACTAGGGCTGCATGTTGTTTATCTTCTATAGGTGCCAACCAATGGCAGCTTGACCCTAAAATC
TAAATTTAAAACGATTAGTTACTTATTTTACTAATGATGCGAAATTTTTCGTGC
Found at i:93102 original size:73 final size:73
Alignment explanation
Indices: 92970--93108 Score: 188
Period size: 73 Copynumber: 1.9 Consensus size: 73
92960 TGGCAGCTTG
* * * *
92970 ACCCTAAAATCTGAATTTAAAACGATTAGTTATTTATTTTACTAATGATGGCCACCCTAAAATTT
1 ACCCTAAAATCTGAATTTAAAACAATTAGTTACTTATTTTACTAACGATGCCCACCCTAAAATTT
93035 TTGTGTCC
66 TTGTGTCC
**** * *
93043 ACCCTAAAATCTGAATTTTCTTCAATTAGTTACTTATTTTACTGACGATGCCCATCCTAAAATTT
1 ACCCTAAAATCTGAATTTAAAACAATTAGTTACTTATTTTACTAACGATGCCCACCCTAAAATTT
93108 T
66 T
93109 ATTTGTACTT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 56 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (73 bp):
ACCCTAAAATCTGAATTTAAAACAATTAGTTACTTATTTTACTAACGATGCCCACCCTAAAATTT
TTGTGTCC
Found at i:97222 original size:14 final size:14
Alignment explanation
Indices: 97203--97232 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
97193 ATATTAAAAT
*
97203 AATATATAATATTA
1 AATATATAAAATTA
97217 AATATATAAAATTA
1 AATATATAAAATTA
97231 AA
1 AA
97233 ATGTTTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATATAAAATTA
Found at i:98097 original size:9 final size:8
Alignment explanation
Indices: 98070--98094 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
98060 ATTTCGTCCT
98070 ATTTTAAA
1 ATTTTAAA
98078 ATTTTAAA
1 ATTTTAAA
98086 ATTTTAAA
1 ATTTTAAA
98094 A
1 A
98095 ATTCACTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:99105 original size:17 final size:15
Alignment explanation
Indices: 99076--99117 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
99066 TCACATGATA
99076 TAAAATAAATATTTAATT
1 TAAAAT-AATATTT--TT
99094 TAAAATAATATTTTT
1 TAAAATAATATTTTT
99109 TAAAA-AATA
1 TAAAATAATA
99118 CATTTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
17 7 0.29
18 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATAATATTTTT
Found at i:105298 original size:31 final size:31
Alignment explanation
Indices: 105249--105320 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
105239 TGATAAAGAT
* * *
105249 TAAAATTTCAATGGTATAAATGATACAACACC
1 TAAAGTTT-AATGATATAAACGATACAACACC
*
105281 TAAAGTTTAATGATATAAACGATACACCACC
1 TAAAGTTTAATGATATAAACGATACAACACC
*
105312 TATAGTTTA
1 TAAAGTTTA
105321 GTGGTAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 28 0.80
32 7 0.20
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (31 bp):
TAAAGTTTAATGATATAAACGATACAACACC
Found at i:106520 original size:131 final size:130
Alignment explanation
Indices: 106351--106714 Score: 426
Period size: 130 Copynumber: 2.8 Consensus size: 130
106341 TTTAAGAGAA
* * * * * *
106351 AAAATAATAATATCTAATTCTTTCAAATCGAGAATAAACGACCTCTCATACCCCTAAA-CAATCA
1 AAAATGATAATATATAATTATTTCAAATCGAGAATAAACGACATCTCATA-CCTTAAAGCAGTCA
* * * * *
106415 TTTATTACTCTAATCGAAATGAAAAAATATCATTATTCTGTCTTAAAATTCAATATCAATTCGAG
65 TTTATTACTCAAATCGAAATGAAAAGATATCAATATTCTAT-TTAAAAATCAATATCAATTCGAG
*
106480 TG
129 CG
* * * *
106482 AAAATGATAATATATAATAATTTCTAATCAAGAATAAACGACATCTCATACTTTAAAGCAGTCAT
1 AAAATGATAATATATAATTATTTCAAATCGAGAATAAACGACATCTCATACCTTAAAGCAGTCAT
* * * *
106547 TTATTGCTCAAATCGAAATGCAAAGATATCACTATTCTATTTAAAAATCAATATTAATTCGAGCG
66 TTATTACTCAAATCGAAATGAAAAGATATCAATATTCTATTTAAAAATCAATATCAATTCGAGCG
* * * * * *
106612 AAAACGGTAATATCA-AATTATTTCCAATCGAGAATAAATGATATTTCATACCTTAAAGCAGTCA
1 AAAATGATAATAT-ATAATTATTTCAAATCGAGAATAAACGACATCTCATACCTTAAAGCAGTCA
* * *
106676 TTTATTACTCCAACCGAAATGAAAAGATATTAATATTCT
65 TTTATTACTCAAATCGAAATGAAAAGATATCAATATTCT
106715 CAATATCGAT
Statistics
Matches: 197, Mismatches: 34, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
130 113 0.57
131 84 0.43
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (130 bp):
AAAATGATAATATATAATTATTTCAAATCGAGAATAAACGACATCTCATACCTTAAAGCAGTCAT
TTATTACTCAAATCGAAATGAAAAGATATCAATATTCTATTTAAAAATCAATATCAATTCGAGCG
Found at i:107774 original size:109 final size:108
Alignment explanation
Indices: 107580--107776 Score: 243
Period size: 109 Copynumber: 1.8 Consensus size: 108
107570 AAATAACCCT
* * * *
107580 AAAAATATATAGCATCCATAAAAGTGGGTAAATTACAAAAACAATCCCTACATGTGACTAACATG
1 AAAAATATATAACATCCATAAAAATGGGTAAATTACAAAAACAATCCCTACATATGACCAACATG
*
107645 CAAAAACACGCTAAAGTTAGGGGGAATAAATAACAATTAAACC
66 CAAAAACACGCTAAACTTAGGGGGAATAAATAACAATTAAACC
* * * * ** ***
107688 AAAAATATATAATATGCATAAGAAATGGGTAAATTATAAAATCGGTCCCTACATATGACCATTTT
1 AAAAATATATAACATCCATAA-AAATGGGTAAATTACAAAAACAATCCCTACATATGACCAACAT
107753 GCAAAAACACGC-ATAACTTAGGGG
65 GCAAAAACACGCTA-AACTTAGGGG
107777 ACCTAAGTAA
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
108 19 0.26
109 54 0.74
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.23
Consensus pattern (108 bp):
AAAAATATATAACATCCATAAAAATGGGTAAATTACAAAAACAATCCCTACATATGACCAACATG
CAAAAACACGCTAAACTTAGGGGGAATAAATAACAATTAAACC
Found at i:109220 original size:24 final size:24
Alignment explanation
Indices: 109187--109232 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
109177 GATATTGTTT
**
109187 ATTTAATTATTATGTAAATAAAAA
1 ATTTAATTATTAAATAAATAAAAA
*
109211 ATTTATTTATTAAATAAATAAA
1 ATTTAATTATTAAATAAATAAA
109233 TTTAAACAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTTAATTATTAAATAAATAAAAA
Found at i:109233 original size:21 final size:21
Alignment explanation
Indices: 109196--109236 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
109186 TATTTAATTA
109196 TTATGTAAATAAAAAATTTAT
1 TTATGTAAATAAAAAATTTAT
109217 TTAT-TAAATAAATAAATTTA
1 TTATGTAAATAAA-AAATTTA
109237 AACAAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTATGTAAATAAAAAATTTAT
Found at i:115110 original size:22 final size:22
Alignment explanation
Indices: 115085--115132 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
115075 AATTTCTGTT
115085 TTAACCGAATTAATCGATCGTA
1 TTAACCGAATTAATCGATCGTA
115107 TTAACCGAATTAATCGATCGTA
1 TTAACCGAATTAATCGATCGTA
115129 TTAA
1 TTAA
115133 ATATTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
TTAACCGAATTAATCGATCGTA
Found at i:116245 original size:24 final size:23
Alignment explanation
Indices: 116217--116278 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
116207 GTATTACTAC
116217 GTATCATAGTATTATATATTATTT
1 GTATCATA-TATTATATATTATTT
116241 GTATCATATTATTA-ATATTATTT
1 GTATCATA-TATTATATATTATTT
116264 -TAAT-ATATATTATAT
1 GT-ATCATATATTATAT
116279 TTTGATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 5 0.14
22 6 0.17
23 11 0.31
24 13 0.37
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (23 bp):
GTATCATATATTATATATTATTT
Found at i:116266 original size:11 final size:13
Alignment explanation
Indices: 116229--116307 Score: 60
Period size: 13 Copynumber: 6.2 Consensus size: 13
116219 ATCATAGTAT
**
116229 TATATATTATTTG
1 TATATATTATTAA
116242 TATCATATTATTAA
1 TAT-ATATTATTAA
116256 TAT-TATT-TTAA
1 TATATATTATTAA
*
116267 TATATATTA-TAT
1 TATATATTATTAA
*
116279 TTTGATATTATT-A
1 TAT-ATATTATTAA
116292 TAT-TATTATATAA
1 TATATATTAT-TAA
116305 TAT
1 TAT
116308 TAAATACATA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
11 13 0.25
12 13 0.25
13 15 0.28
14 12 0.23
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (13 bp):
TATATATTATTAA
Found at i:116292 original size:16 final size:17
Alignment explanation
Indices: 116259--116309 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 17
116249 TTATTAATAT
116259 TATTTTAATATATATTA
1 TATTTTAATATATATTA
*
116276 TATTTTGATAT-TATTA
1 TATTTTAATATATATTA
116292 TATTATT-ATATAATATTA
1 TATT-TTAATAT-ATATTA
116310 AATACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 13 0.43
17 12 0.40
18 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TATTTTAATATATATTA
Found at i:118245 original size:20 final size:21
Alignment explanation
Indices: 118196--118251 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
118186 TGCGGAGGTT
118196 TCGATACCCTTGAAGGGTGGTA
1 TCGATACCCTT-AAGGGTGGTA
*
118218 TC-AGTACCCTT-TGGGTGGTA
1 TCGA-TACCCTTAAGGGTGGTA
*
118238 TCGATACCTTTAAG
1 TCGATACCCTTAAG
118252 TATGAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 16 0.57
21 3 0.11
22 9 0.32
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (21 bp):
TCGATACCCTTAAGGGTGGTA
Found at i:118750 original size:21 final size:22
Alignment explanation
Indices: 118726--118778 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
118716 TCGAGGGTCT
118726 TATGTGGTCATTC-GGGACAAA
1 TATGTGGTCATTCTGGGACAAA
* *
118747 TATGTGGTC-CTCTGGGATAAA
1 TATGTGGTCATTCTGGGACAAA
118768 TATGTGG-CATT
1 TATGTGGTCATT
118779 TTGGTAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (22 bp):
TATGTGGTCATTCTGGGACAAA
Done.