Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005307.1 Hibiscus syriacus cultivar Beakdansim tig00012010_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: 104310
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3727 original size:182 final size:182
Alignment explanation
Indices: 3324--3855 Score: 885
Period size: 182 Copynumber: 2.9 Consensus size: 182
3314 ATTAAATCCG
* *
3324 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTTGAAAACCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAAGCCTGGCTTTATGA
* * *
3389 ATAGATTATGTTCAAACTATGACACTGCTTGGACACTTGGCAATTGGTGTTTTCT-CACT-TTTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTGGTGTTTGCTCCACTGCTTT
3452 TGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* *
3504 TAAAGCTAAACTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAAGCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAAGCCTGGCTTTATGA
3569 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCA-TGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATT-GGTGTTTGCTCCACTGCTT
* *
3633 TTGTCATGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
130 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
3686 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCG-AAAGCCCTGGCTTTATG
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAAG-CCTGGCTTTATG
** *
3750 AATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTGGTGTTTGCTCCACTGCT
65 AATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTGGTGTTTGCTCCACTGCT
*
3814 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
129 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
3856 TAAACCTGAT
Statistics
Matches: 329, Mismatches: 17, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
180 105 0.32
181 28 0.09
182 196 0.60
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (182 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAAGCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTGGTGTTTGCTCCACTGCTTT
TGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:5085 original size:35 final size:35
Alignment explanation
Indices: 4978--5086 Score: 96
Period size: 35 Copynumber: 3.1 Consensus size: 35
4968 TAATGCAGAT
4978 GATTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA
1 GATTATCTCACTCAAGA-TTGTTTTTCTTAAAACA-A
** * ** * ** *
5014 CTTTGTCTCACTTGAGACTG-TTTTCTCGAAAGAA
1 GATTATCTCACTCAAGATTGTTTTTCTTAAAACAA
*
5048 GATTATTTCACTCAAGATTGTTTTTCTTAAAACAA
1 GATTATCTCACTCAAGATTGTTTTTCTTAAAACAA
5083 GATT
1 GATT
5087 TGTCTCTTGA
Statistics
Matches: 52, Mismatches: 19, Indels: 5
0.68 0.25 0.07
Matches are distributed among these distances:
34 14 0.27
35 25 0.48
36 12 0.23
37 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (35 bp):
GATTATCTCACTCAAGATTGTTTTTCTTAAAACAA
Found at i:5112 original size:70 final size:71
Alignment explanation
Indices: 4978--5137 Score: 186
Period size: 70 Copynumber: 2.2 Consensus size: 71
4968 TAATGCAGAT
* * *
4978 GATTATCTCACTCAA-ATTTGTTTTTCTTAAAACATACTTTGTCTCACTTGAGACTGTTTTCTCG
1 GATTATTTCACTCAAGATTTGTTTTTCTTAAAACATAATTTGTCT-ACTTGAGACCGTTTTCTCG
5042 AAAGAA-
65 AAAGAAG
5048 GATTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCT-CTTGAGACCGTTTTCACT
1 GATTATTTCACTCAAGATTTGTTTTTCTTAAAACATA-ATTTGTCTACTTGAGACCGTTTT--CT
*
5110 CGAAATAAG
63 CGAAAGAAG
5119 GCATTTCATTTCACTCAAG
1 G-A-TT-ATTTCACTCAAG
5138 GCTTTTTTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
68 13 0.17
69 1 0.01
70 47 0.60
71 2 0.03
72 1 0.01
73 2 0.03
74 12 0.15
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (71 bp):
GATTATTTCACTCAAGATTTGTTTTTCTTAAAACATAATTTGTCTACTTGAGACCGTTTTCTCGA
AAGAAG
Found at i:5299 original size:39 final size:39
Alignment explanation
Indices: 5242--5316 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
5232 CCTTGAAATT
*
5242 AATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
1 AATTTTGTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
* *
5281 AATTTTGTCTC-CCTTGAGATAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCC-TGAGATAGTTTCCCTCGAAACA
5317 TAAACATTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.06
39 30 0.94
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (39 bp):
AATTTTGTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
Found at i:5402 original size:106 final size:105
Alignment explanation
Indices: 5219--5536 Score: 488
Period size: 106 Copynumber: 3.1 Consensus size: 105
5209 ACAGTTTCTC
* *
5219 TTGAAAACATTTCCCTTGAAATTA-ATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
*
5283 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACA
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
5323 TTGAAAACATTTCCCTTGAAATGATTTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
1 TTGAAAACATTTCCCTTGAAATGA-TATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
5388 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * *
5429 TTGAAAACATTTTCCTTGAAATGA-ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC----AA
1 TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
**
5489 TTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAAC-
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
5528 TTGAAAACA
1 TTGAAAACA
5537 ATTTAACGAA
Statistics
Matches: 201, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
99 9 0.04
100 39 0.19
104 53 0.26
106 100 0.50
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (105 bp):
TTGAAAACATTTCCCTTGAAATGATATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:5491 original size:35 final size:36
Alignment explanation
Indices: 5442--5512 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
5432 AAAACATTTT
* * *
5442 CCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTC
1 CCTTGAAATCAATTTTATCTCCCTTGAGACAGTTTC
*
5478 CCTTGAAA-CAATTTTGTCTCCCTTGAGACAGTTTC
1 CCTTGAAATCAATTTTATCTCCCTTGAGACAGTTTC
5513 TCTCCAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 23 0.74
36 8 0.26
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (36 bp):
CCTTGAAATCAATTTTATCTCCCTTGAGACAGTTTC
Found at i:5522 original size:35 final size:35
Alignment explanation
Indices: 5452--5522 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
5442 CCTTGAAATG
* * **
5452 AATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC
1 AATTTTATCTCCCTTGAGACAGTTTCCCTCCAAAC
* *
5487 AATTTTGTCTCCCTTGAGACAGTTTCTCTCCAAAC
1 AATTTTATCTCCCTTGAGACAGTTTCCCTCCAAAC
5522 A
1 A
5523 TAAACTTGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (35 bp):
AATTTTATCTCCCTTGAGACAGTTTCCCTCCAAAC
Found at i:5891 original size:103 final size:104
Alignment explanation
Indices: 5708--6331 Score: 838
Period size: 103 Copynumber: 6.0 Consensus size: 104
5698 ATATCGTGAC
* * * * * * *
5708 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTTTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC-A-AAACAACTTCTC
* *
5773 AATTTCAGAGCCAATTTCAACTTCACGACGAATGATATTGG
64 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
5814 ACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAA-AACTTCTCAA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAACAACTTCTCAA
5878 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
5917 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-AACAACTTCTCA
* *
5982 ATCTCAGAGCCAATTTCAACTTCACAACGAATGATATTGG
65 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
6022 ACTCC--ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC-AAAACAACTTCTCA
*
6085 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
6125 ACTCCAGACAATGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA--T-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-AACAACTTCTCA
*
6185 A-TTCAGAGTCAATTTCAACTTCACAGA-GAAGGATATTGG
65 ATTTCAGAGCCAATTTCAACTTCACA-ACGAAGGATATTGG
* * * * * * *
6224 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAAAACAATTTC-CG
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC-AAAACAACTTCTCA
* * * *
6288 GTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
6328 ACTC
1 ACTC
6332 GGAACAATGC
Statistics
Matches: 469, Mismatches: 34, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
99 79 0.17
100 6 0.01
101 1 0.00
102 3 0.01
103 197 0.42
104 47 0.10
105 94 0.20
106 42 0.09
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (104 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAACAACTTCTCAA
TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:6004 original size:208 final size:206
Alignment explanation
Indices: 5708--6331 Score: 859
Period size: 208 Copynumber: 3.0 Consensus size: 206
5698 ATATCGTGAC
* * * * * * *
5708 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTTTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTC-C
*
5773 AATTTCAGAGCCAATTTCAACTTCACGACGAATGATATTGGACTCCAGACAACGCATGTTCAACT
64 AA-TTCAGAGCCAATTTCAACTTCACGACGAATGATATTGGACTCCAGACAACGCAAGTTCAACT
5838 TCACGACGAAGGGACCGCTGCTTGTCAAAAAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
128 TCACGACGAAGGGACCGCTGCTTGTCAAAAAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
5903 ACGAAGGATATTGG
193 ACGAAGGATATTGG
*
5917 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-CCA
*
5982 ATCTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCC--ACAACGCAAGTTCAACTT
65 AT-TCAGAGCCAATTTCAACTTCACGACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
6045 CACGACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCAC
129 CACGACGAAGGGACCGCTGCTTGTC-AAAA-AACTTCTCAATTTCAGAGCCAATTTCAACTTCAC
6110 AACGAAGGATATTGG
192 AACGAAGGATATTGG
* *
6125 ACTCCAGACAATGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-C-A
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAA
* * * *
6186 TTCAGAGTCAATTTCAACTTCACAGA-GAAGGATATTGGACTCGAGACAACACAAGTTCAACTTC
66 TTCAGAGCCAATTTCAACTTCAC-GACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTC
* * * * ** * *
6250 ACAACGAAGGGACGGCTGGTTGTCAAAAACAATT-TCCGGTTCCAGAGCCAATTTCAACTTCACG
130 ACGACGAAGGGACCGCTGCTTGTCAAAAA-ACTTCT-CAATTTCAGAGCCAATTTCAACTTCACA
*
6314 ACGGAGGATATTGG
193 ACGAAGGATATTGG
6328 ACTC
1 ACTC
6332 GGAACAATGC
Statistics
Matches: 375, Mismatches: 31, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
202 37 0.10
203 50 0.13
204 40 0.11
206 44 0.12
207 7 0.02
208 151 0.40
209 46 0.12
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (206 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAA
TTCAGAGCCAATTTCAACTTCACGACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGCTTGTCAAAAAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGG
Found at i:6924 original size:37 final size:37
Alignment explanation
Indices: 6871--6975 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
6861 CATTTTCGTC
6871 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
6908 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
6945 CTACTAAGATTTAAATTCCTAAATATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
6976 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:7372 original size:48 final size:45
Alignment explanation
Indices: 7316--7445 Score: 138
Period size: 48 Copynumber: 2.8 Consensus size: 45
7306 AGTCCCTTAT
* *
7316 TTATTATATGGATATTTTATTCA-TTATTTTTATATCATGTTATATTA
1 TTATTATATAGATATATTATTCATTTATTTTTATAT-AT-TTAT-TTA
*
7363 TTATGTATATATATATATTATTCATTTATTTTTATATATTTATTTA
1 TTAT-TATATAGATATATTATTCATTTATTTTTATATATTTATTTA
*
7409 TTATTATTATATATATATATATTTC-TTTATATTTTAT
1 TTATTA-TATAGATATAT-TA-TTCATTTAT-TTTTAT
7446 TATAAGTCTA
Statistics
Matches: 74, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
45 2 0.03
46 18 0.24
47 15 0.20
48 27 0.36
49 12 0.16
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (45 bp):
TTATTATATAGATATATTATTCATTTATTTTTATATATTTATTTA
Found at i:7400 original size:21 final size:20
Alignment explanation
Indices: 7356--7432 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 20
7346 TATATCATGT
* * *
7356 TATATTATTATGTATATATA
1 TATATTATTATTTATTTTTA
7376 TATATTATTCATTTATTTTTA
1 TATATTATT-ATTTATTTTTA
*
7397 TATATTTATT-TATTATTATTA
1 TATA-TTATTAT-TTATTTTTA
7418 TATATATATATATTT
1 TATAT-TAT-TATTT
7433 CTTTATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
20 11 0.23
21 27 0.57
22 8 0.17
23 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (20 bp):
TATATTATTATTTATTTTTA
Found at i:7410 original size:29 final size:29
Alignment explanation
Indices: 7368--7449 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
7358 TATTATTATG
* * * *
7368 TATATATATATATTATTCATT-TATTTTTA
1 TATATTTATTTATTATT-ATTATATATATA
7397 TATATTTATTTATTATTATTATATATATA
1 TATATTTATTTATTATTATTATATATATA
* *
7426 TATATTTCTTTATATTTTATTATA
1 TATATTTATTTAT-TATTATTATA
7450 AGTCTAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.07
29 33 0.73
30 9 0.20
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (29 bp):
TATATTTATTTATTATTATTATATATATA
Found at i:7415 original size:18 final size:18
Alignment explanation
Indices: 7376--7420 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
7366 TGTATATATA
*
7376 TATATTATTCATTTATTTT
1 TATA-TATTCATTTATTAT
*
7395 TATATATTTATTTATTAT
1 TATATATTCATTTATTAT
7413 TATTATAT
1 TA-TATAT
7421 ATATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATATATTCATTTATTAT
Found at i:7424 original size:52 final size:48
Alignment explanation
Indices: 7327--7431 Score: 142
Period size: 49 Copynumber: 2.1 Consensus size: 48
7317 TATTATATGG
* *
7327 ATATTTTATTCATTATTTTTATATCATGTTATATTATTATGTATATAT
1 ATATATTATTCATTATTTTTATATCATGTTATATTATTATATATATAT
7375 ATATATTATTCATTTATTTTTATAT-AT-TTATTTATTATTATTATATATAT
1 ATATATTATTCA-TTATTTTTATATCATGTTA--TATTATTA-TATATATAT
7425 ATATATT
1 ATATATT
7432 TCTTTATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
47 3 0.06
48 13 0.25
49 20 0.39
50 15 0.29
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (48 bp):
ATATATTATTCATTATTTTTATATCATGTTATATTATTATATATATAT
Found at i:7441 original size:25 final size:25
Alignment explanation
Indices: 7368--7449 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
7358 TATTATTATG
7368 TATATATATATAT-TATTCATTTAT-T
1 TATATATATATATAT-TTC-TTTATAT
* *
7393 T-T-TATATATTTATTT-ATTATTAT
1 TATATATATATATATTTCTTTA-TAT
7416 TATATATATATATATTTCTTTATAT
1 TATATATATATATATTTCTTTATAT
*
7441 TTTAT-TATA
1 TATATATATA
7450 AGTCTAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
21 3 0.07
22 1 0.02
23 12 0.26
24 7 0.15
25 20 0.43
26 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TATATATATATATATTTCTTTATAT
Found at i:7922 original size:19 final size:21
Alignment explanation
Indices: 7900--7938 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
7890 TATATAATTA
*
7900 TTATTTTAC-TATTT-TTTTC
1 TTATCTTACTTATTTATTTTC
7919 TTATCTTACTTATTTATTTT
1 TTATCTTACTTATTTATTTT
7939 ATTTTTCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (21 bp):
TTATCTTACTTATTTATTTTC
Found at i:9158 original size:29 final size:29
Alignment explanation
Indices: 9095--9184 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
9085 TCAAAATATA
* * * *
9095 TAAA-TTTTAAAATTTACATTTTGGTCCC
1 TAAACTTTCAAAATTTATATTTTAGTCAC
*
9123 TAAACTTCTCAAAATTTATACTTT-GTCAC
1 TAAACTT-TCAAAATTTATATTTTAGTCAC
*
9152 TAAACTTTCAAAACTTATATTTTAGTCAC
1 TAAACTTTCAAAATTTATATTTTAGTCAC
9181 TAAA
1 TAAA
9185 AATGATGATT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
28 18 0.34
29 22 0.42
30 13 0.25
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.42
Consensus pattern (29 bp):
TAAACTTTCAAAATTTATATTTTAGTCAC
Found at i:9521 original size:47 final size:48
Alignment explanation
Indices: 9463--9553 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
9453 AGATGTATAC
*
9463 TTACATTGGTGTAAGTAT-TGTTAAGTGAAACACTTTTTATTTTTTAA
1 TTACATCGGTGTAAGTATGTGTTAAGTGAAACACTTTTTATTTTTTAA
** *
9510 TTACATCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTATTTT
1 TTACATCGGTGTAAGTATGTGTTAAGTGAAACACTTTTTATTTT
9554 ATTCACTTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 17 0.44
48 22 0.56
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.49
Consensus pattern (48 bp):
TTACATCGGTGTAAGTATGTGTTAAGTGAAACACTTTTTATTTTTTAA
Found at i:9552 original size:48 final size:49
Alignment explanation
Indices: 9463--9595 Score: 141
Period size: 47 Copynumber: 2.8 Consensus size: 49
9453 AGATGTATAC
** *
9463 TTACATTGGTGTAAGTAT-TGTTAAGTGAAACACTTTTTATTTT-TT-AA
1 TTACA-TGGTGTAAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCAA
*
9510 TTACATCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCAC
1 TTACAT-GGTGTAAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCAA
* * * *
9560 TTACA--ATGTAAGTATGTATTAAATGCTATATTTTTT
1 TTACATGGTGTAAGTATGTGTTAAGTGCTACATTTTTT
9596 GTAGTATGAA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
46 1 0.01
47 43 0.58
48 22 0.30
49 2 0.03
50 6 0.08
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (49 bp):
TTACATGGTGTAAGTATGTGTTAAGTGCTACATTTTTTATTTTATTCAA
Found at i:10880 original size:3 final size:3
Alignment explanation
Indices: 10872--10910 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
10862 TATTTGGCAT
* *
10872 ATA ATA ATA ATA CTAA ACA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT
10911 GTGAATGAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 30 0.97
4 1 0.03
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:16608 original size:3 final size:3
Alignment explanation
Indices: 16602--16703 Score: 122
Period size: 3 Copynumber: 35.3 Consensus size: 3
16592 CTAAAAAAAC
* * * * * *
16602 ATT ATT ATT ATT ATT ATT ATT ATC ATC ATC ATC ATC ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16650 A-T ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16695 ATT A-T ATT A
1 ATT ATT ATT A
16704 CATTTTTTTC
Statistics
Matches: 93, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
2 8 0.09
3 85 0.91
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:18290 original size:10 final size:10
Alignment explanation
Indices: 18276--18305 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
18266 AATCTTTTCA
18276 CTTTTATTTT
1 CTTTTATTTT
*
18286 GTTTTATTTT
1 CTTTTATTTT
18296 CTTTTATTTT
1 CTTTTATTTT
18306 ATCATTGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (10 bp):
CTTTTATTTT
Found at i:20263 original size:13 final size:12
Alignment explanation
Indices: 20245--20336 Score: 64
Period size: 13 Copynumber: 7.2 Consensus size: 12
20235 TAAAACAAAG
20245 AGAAAATAAGAAA
1 AGAAAA-AAGAAA
20258 AGAAAACAA-ACAA
1 AGAAAA-AAGA-AA
20271 AGAAAAAAG-AA
1 AGAAAAAAGAAA
20282 AGAAAAAAGAGCAA
1 AGAAAAAAGA--AA
*
20296 AGAAAAAAATAAA
1 AG-AAAAAAGAAA
*
20309 AGGAAAAGAACAAA
1 A-GAAAA-AAGAAA
*
20323 AGAAAGAA-AAA
1 AGAAAAAAGAAA
20334 AGA
1 AGA
20337 TAAGAAGCAC
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
11 17 0.25
12 5 0.07
13 27 0.40
14 11 0.16
15 7 0.10
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.02
Consensus pattern (12 bp):
AGAAAAAAGAAA
Found at i:20275 original size:18 final size:16
Alignment explanation
Indices: 20247--20332 Score: 55
Period size: 19 Copynumber: 4.8 Consensus size: 16
20237 AAACAAAGAG
*
20247 AAAATAAGAAAAGAAA
1 AAAAAAAGAAAAGAAA
20263 ACAAACAAAGAAAAAAGAAA
1 A-AAA-AAAG--AAAAGAAA
*
20283 GAAAAAAGAGCAAAGAAAA
1 -AAAAAA-AGAAAAG-AAA
20302 AAATAAAAGGAAAAGAACA
1 AAA-AAAA-GAAAAGAA-A
*
20321 AAAGAAAGAAAA
1 AAAAAAAGAAAA
20333 AAGATAAGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
16 1 0.02
17 8 0.14
18 16 0.29
19 17 0.30
20 13 0.23
21 1 0.02
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAA
Found at i:20288 original size:25 final size:25
Alignment explanation
Indices: 20245--20336 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 25
20235 TAAAACAAAG
20245 AGAAAATAAGAAAAGAAAACA-AACAA
1 AGAAAA-AAGAAAAGAAAA-AGAACAA
*
20271 AGAAAAAAG-AAAGAAAAAAGAGCAA
1 AGAAAAAAGAAAAG-AAAAAGAACAA
* *
20296 AGAAAAAAATAAAAGGAAAAGAACAAA
1 AG-AAAAAAGAAAAGAAAAAGAAC-AA
*
20323 AGAAAGAA-AAAAGA
1 AGAAAAAAGAAAAGA
20337 TAAGAAGCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
24 5 0.09
25 18 0.33
26 24 0.44
27 8 0.15
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.02
Consensus pattern (25 bp):
AGAAAAAAGAAAAGAAAAAGAACAA
Found at i:20299 original size:14 final size:13
Alignment explanation
Indices: 20236--20304 Score: 65
Period size: 14 Copynumber: 5.3 Consensus size: 13
20226 AGATTCAATT
20236 AAAA-CAAAGAGAA
1 AAAAGCAAAGA-AA
*
20249 AATAAGAAAAGAAA
1 AA-AAGCAAAGAAA
20263 ACAAA-CAAAG-AA
1 A-AAAGCAAAGAAA
20275 AAAAG-AAAGAAA
1 AAAAGCAAAGAAA
20287 AAAGAGCAAAGAAA
1 AAA-AGCAAAGAAA
20301 AAAA
1 AAAA
20305 TAAAAGGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
11 7 0.15
12 8 0.17
13 9 0.19
14 17 0.36
15 6 0.13
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.01
Consensus pattern (13 bp):
AAAAGCAAAGAAA
Found at i:21412 original size:31 final size:32
Alignment explanation
Indices: 21374--21468 Score: 147
Period size: 32 Copynumber: 3.0 Consensus size: 32
21364 TAAGAAACGA
*
21374 AGAATGATGGGACATCTTT-GAGATTCAACAT
1 AGAATGATGGGGCATCTTTAGAGATTCAACAT
*
21405 AGAATGATGGGGCATCTTTGGAGATTCAACAT
1 AGAATGATGGGGCATCTTTAGAGATTCAACAT
* *
21437 CGAATGTTGGGGCATCTTTAGAGATTCAACAT
1 AGAATGATGGGGCATCTTTAGAGATTCAACAT
21469 CCTGATGTGA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 18 0.31
32 41 0.69
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (32 bp):
AGAATGATGGGGCATCTTTAGAGATTCAACAT
Found at i:21731 original size:62 final size:65
Alignment explanation
Indices: 21629--21766 Score: 165
Period size: 62 Copynumber: 2.2 Consensus size: 65
21619 GACATAACCC
* *** * * * *
21629 ATCTTTGAGTCTGTTTCTTTGGAAATAAAATTTTGTCTC-TTGAGACAATTT-TTTTG-AGAAAA
1 ATCTTTGAGTCCGTTTCTCCAGAAACAAAATTCTGACTCTTTGAGACAATTTCTTTTGAAAAAAA
*
21691 ATCTTTGAGTCCGTTTCTCCAGAAACAAAGTTCTGACTCTTTTGAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTCCGTTTCTCCAGAAACAAAATTCTGACTC-TTTGAGACAATTTCTTTTGAAAAAA
21756 A
65 A
21757 ATCTTTGAGT
1 ATCTTTGAGT
21767 ATTTTTCTCT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
62 31 0.49
64 12 0.19
65 5 0.08
66 15 0.24
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (65 bp):
ATCTTTGAGTCCGTTTCTCCAGAAACAAAATTCTGACTCTTTGAGACAATTTCTTTTGAAAAAAA
Found at i:22122 original size:131 final size:131
Alignment explanation
Indices: 21883--22373 Score: 454
Period size: 131 Copynumber: 3.7 Consensus size: 131
21873 TGAAACCATT
* * *
21883 ATCCCTAAAGATGGCATGA-CGTTCTCATCACGTAGGAACCGTGTCATCC-CCTGACCAGACCTT
1 ATCCCTAAAGATGGCCT-ACCATTCTCATCACGTAGGAACCGTGTCATCCACC-GACCAGACCTC
* * * * * *
21946 CTCAACACGTAGGAGCTGTGTCACCCTTAGATAACTTGTCATCCTCATCACGTAGAAATCGTGTT
64 CTCATCACGTAGGAGCCGTGTCACCCCTAGATAACTAGCCATCCTCATCACGTAGAAATCATGTT
*
22011 ATT
129 ATC
* *** *
22014 ATCCCTAAAGATGGCCTACCATTCTCATCACGTATGAGTTGTGTCATCCACCGACTAGACCTCCT
1 ATCCCTAAAGATGGCCTACCATTCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCT
* * *
22079 CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTA-AGAATTATGTTA
66 CATCACGTAGGAGCCGTGTCACCCCTAGATAACTAGCCATCCTCATCACGTAGA-AATCATGTTA
22143 TC
130 TC
* * * * * * * * *
22145 ATTCCTAAAAGATAGCCTGCCATCCTCATCACGTAGGAATCATATCATCCCCCAACCAGACCTCC
1 ATCCCT-AAAGATGGCCTACCATTCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCC
* ** * * *
22210 TCATC-CTGTAGTAGCCGTGTCAATCCTAGATAACTAGCCATCCTCATCACATAGGAACCATGTT
65 TCATCAC-GTAGGAGCCGTGTCACCCCTAGATAACTAGCCATCCTCATCACGTAGAAATCATGTT
22274 ATC
129 ATC
* ** * * * * * *
22277 ACCCTTCCTAAAGATGGCC-AAAACTCTTCATCACGTATGAGCTGTGTCAT-CACCCGACTAGAT
1 A---TCCCTAAAGATGGCCTACCATTC-TCATCACGTAGGAACCGTGTCATCCA-CCGACCAGAC
* *
22340 CTCCTCATCACGTAGGATCCGTGTCACCCTTAGA
61 CTCCTCATCACGTAGGAGCCGTGTCACCCCTAGA
22374 CGACCATACC
Statistics
Matches: 288, Mismatches: 60, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
130 2 0.01
131 112 0.39
132 105 0.36
133 3 0.01
134 60 0.21
135 6 0.02
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (131 bp):
ATCCCTAAAGATGGCCTACCATTCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCT
CATCACGTAGGAGCCGTGTCACCCCTAGATAACTAGCCATCCTCATCACGTAGAAATCATGTTAT
C
Found at i:22227 original size:132 final size:131
Alignment explanation
Indices: 21906--22373 Score: 449
Period size: 132 Copynumber: 3.5 Consensus size: 131
21896 GCATGACGTT
* * * * *
21906 CTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTTCTCAACACGTAGGAGCTGTGTCACC
1 CTCATCACGTAGGAATCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACC
* * * * * *
21971 CTTAGATAACTTGTCATCCTCATCACGT-AGAAATCGTGTTATTATCCCTAAAGATGGCCTACCA
66 CCTAGATAACTAGCCATCCTCATCACGTAAG-AATCATGTTATCATCCCTAAAGATAGCCTACCA
*
22035 TT
130 TC
* * * * *
22037 CTCATCACGTATGAGTTGTGTCATCCACCGACTAGACCTCCTCATCACGTAGGAGCCGTGTCACC
1 CTCATCACGTAGGAATCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACC
* * * * *
22102 CCTAGATAACCAGCCGTCCTCATCACGTAAGAATTATGTTATCATTCCTAAAAGATAGCCTGCCA
66 CCTAGATAACTAGCCATCCTCATCACGTAAGAATCATGTTATCATCCCT-AAAGATAGCCTACCA
22167 TC
130 TC
* * * * *
22169 CTCATCACGTAGGAATCATATCATCCCCCAACCAGACCTCCTCATC-CTGTAGTAGCCGTGTCAA
1 CTCATCACGTAGGAATCGTGTCATCCCCCGACCAGACCTCCTCATCAC-GTAGGAGCCGTGTCAC
* * * * * *
22233 TCCTAGATAACTAGCCATCCTCATCACATAGGAACCATGTTATCACCCTTCCTAAAGATGGCC-A
65 CCCTAGATAACTAGCCATCCTCATCACGTAAGAATCATGTTATCA---TCCCTAAAGATAGCCTA
**
22297 AAACTC
127 CCA-TC
* * * * * * *
22303 TTCATCACGTATG-AGCTGTGTCATCACCCGACTAGATCTCCTCATCACGTAGGATCCGTGTCAC
1 CTCATCACGTAGGAATC-GTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCAC
*
22367 CCTTAGA
65 CCCTAGA
22374 CGACCATACC
Statistics
Matches: 271, Mismatches: 57, Indels: 15
0.79 0.17 0.04
Matches are distributed among these distances:
131 93 0.34
132 106 0.39
133 3 0.01
134 63 0.23
135 6 0.02
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (131 bp):
CTCATCACGTAGGAATCGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACC
CCTAGATAACTAGCCATCCTCATCACGTAAGAATCATGTTATCATCCCTAAAGATAGCCTACCAT
C
Found at i:35214 original size:77 final size:78
Alignment explanation
Indices: 35098--35249 Score: 202
Period size: 77 Copynumber: 2.0 Consensus size: 78
35088 ATATAGTAAG
* * *
35098 TAAACATTAAAAGAATGTAATTCTGATTAACACTTTTTAATGAATATTTAATTCTGAA-TAATTA
1 TAAACATTAAAAGAATGTAATTCAGATTAACACTCTTTAACGAATATTTAATT-TGAATTAATTA
35162 AATAAGAGTTTAAA
65 AATAAGAGTTTAAA
* * * *
35176 TAAACATT-TAAGAGTGTAATTCAGATTAGA-AGTCTTTAACGGATATTTAATTTGAATTAATTA
1 TAAACATTAAAAGAATGTAATTCAGATTA-ACACTCTTTAACGAATATTTAATTTGAATTAATTA
35239 AATAAGAGTTT
65 AATAAGAGTTT
35250 CATTAATTCA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
76 4 0.06
77 52 0.80
78 9 0.14
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTCAGATTAACACTCTTTAACGAATATTTAATTTGAATTAATTAA
ATAAGAGTTTAAA
Found at i:37300 original size:28 final size:28
Alignment explanation
Indices: 37241--37298 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
37231 TTAAAAAATT
*
37241 AAATACTTTAAGTATCTATTTTGACTAA
1 AAATACTTTAAGTACCTATTTTGACTAA
37269 AAATACTTT-AGTTACCTATTTTGA-TAA
1 AAATACTTTAAG-TACCTATTTTGACTAA
37296 AAA
1 AAA
37299 ATGATAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (28 bp):
AAATACTTTAAGTACCTATTTTGACTAA
Found at i:37558 original size:26 final size:27
Alignment explanation
Indices: 37503--37560 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
37493 TTTTGTTCGG
* * *
37503 GTTTATTTATTTATTATATTATTATTA
1 GTTTATTTATTTAATATAGTATTAATA
*
37530 GTTTATTTTTTTAAT-TAGTATTAATA
1 GTTTATTTATTTAATATAGTATTAATA
37556 GTTTA
1 GTTTA
37561 GGGGTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (27 bp):
GTTTATTTATTTAATATAGTATTAATA
Found at i:38968 original size:86 final size:88
Alignment explanation
Indices: 38823--38996 Score: 325
Period size: 86 Copynumber: 2.0 Consensus size: 88
38813 TTCAGTTTAG
*
38823 TCCTTGTATTATTACGTATATGTATACATTTATTTTATTTCCTAAAATGTATAGTATATTAATA-
1 TCCTTGTATTATTACATATATGTATACATTTATTTTATTTCCTAAAATGTATAGTATATTAATAT
38887 TT-TGTATATATATTATATTATT
66 TTGTGTATATATATTATATTATT
38909 TCCTTGTATTATTACATATATGTATACATTTATTTTATTTCCTAAAATGTATAGTATATTAATAT
1 TCCTTGTATTATTACATATATGTATACATTTATTTTATTTCCTAAAATGTATAGTATATTAATAT
38974 TTGTGTATATATATTATATTATT
66 TTGTGTATATATATTATATTATT
38997 CAAAGCAACA
Statistics
Matches: 85, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
86 63 0.74
87 2 0.02
88 20 0.24
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (88 bp):
TCCTTGTATTATTACATATATGTATACATTTATTTTATTTCCTAAAATGTATAGTATATTAATAT
TTGTGTATATATATTATATTATT
Found at i:48535 original size:7 final size:8
Alignment explanation
Indices: 48511--48542 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
48501 TTTAGTTATT
48511 AAATTAAA
1 AAATTAAA
48519 AAATTAAA
1 AAATTAAA
48527 AAATTAAA
1 AAATTAAA
48535 AAA-TAAA
1 AAATTAAA
48542 A
1 A
48543 TAAAAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.21
8 19 0.79
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATTAAA
Found at i:49058 original size:4 final size:4
Alignment explanation
Indices: 49049--49079 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
49039 CCAGGTACTT
49049 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
49080 TACTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:54859 original size:3 final size:3
Alignment explanation
Indices: 54853--54966 Score: 205
Period size: 3 Copynumber: 38.7 Consensus size: 3
54843 TTTTTATCCA
*
54853 TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54901 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54948 TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
54967 AATATATTAA
Statistics
Matches: 107, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
2 4 0.04
3 103 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:55479 original size:16 final size:17
Alignment explanation
Indices: 55458--55489 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
55448 ACAGAACCGG
55458 AGAGAAAA-AAAAAAAC
1 AGAGAAAAGAAAAAAAC
55474 AGAGAAAAGAAAAAAA
1 AGAGAAAAGAAAAAAA
55490 AACAAACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AGAGAAAAGAAAAAAAC
Found at i:67774 original size:11 final size:10
Alignment explanation
Indices: 67736--67798 Score: 56
Period size: 11 Copynumber: 6.0 Consensus size: 10
67726 TTATGCTTGA
*
67736 AAAAAAAAAA
1 AAAAAAAAAG
67746 AAAGAGAAAAAG
1 AAA-A-AAAAAG
* *
67758 -AGAAAAACG
1 AAAAAAAAAG
67767 AAAAAAAAAG
1 AAAAAAAAAG
67777 AAAAAAAAAAG
1 -AAAAAAAAAG
67788 AAAGAAAAAAG
1 AAA-AAAAAAG
67799 GGGGTCAAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 5 0.12
10 14 0.33
11 19 0.44
12 5 0.12
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:67794 original size:25 final size:27
Alignment explanation
Indices: 67736--67797 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
67726 TTATGCTTGA
67736 AAAA-AAAAAAAAAGAGAAAAAGAGAA
1 AAAAGAAAAAAAAAGAGAAAAAGAGAA
*
67762 AAACGAAAAAAAAAGA-AAAAA-A-AA
1 AAAAGAAAAAAAAAGAGAAAAAGAGAA
67786 AGAAAGAAAAAA
1 A-AAAGAAAAAA
67798 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 3 0.09
25 10 0.31
26 8 0.25
27 11 0.34
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (27 bp):
AAAAGAAAAAAAAAGAGAAAAAGAGAA
Found at i:69016 original size:50 final size:50
Alignment explanation
Indices: 68941--69042 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
68931 TGAATTTACC
68941 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAAACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAAACAG
* *
68991 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAAACAG
69041 AA
1 AA
69043 CCAATCAGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAAACAG
Found at i:69165 original size:133 final size:133
Alignment explanation
Indices: 68927--69167 Score: 464
Period size: 133 Copynumber: 1.8 Consensus size: 133
68917 CATTAAATGA
68927 AAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAAACAGA
1 AAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAAACAGA
68992 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAATT
66 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAATT
69057 TAG
131 TAG
* *
69060 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGA
1 AAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAAACAGA
69125 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
66 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
69168 GGATAGAACA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 106 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (133 bp):
AAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAAACAGA
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAACAGAACCAATCAGTGAATT
TAG
Found at i:69392 original size:52 final size:52
Alignment explanation
Indices: 69075--69391 Score: 498
Period size: 52 Copynumber: 6.1 Consensus size: 52
69065 GAATTTGCCA
* *
69075 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG-A-
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
69125 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGATAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
69177 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGATAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
69229 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
69281 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * * * *
69333 ATAGCATTTTCTGGAAGTGTTTTTTGAGATATCTGATCTGATTAGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-C
69386 A-AGCAT
1 ATAGCAT
69392 TGAGTTTAGA
Statistics
Matches: 251, Mismatches: 11, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
50 46 0.18
51 3 0.01
52 198 0.79
53 4 0.02
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:69472 original size:83 final size:83
Alignment explanation
Indices: 69333--69536 Score: 372
Period size: 83 Copynumber: 2.5 Consensus size: 83
69323 TGGACAGAAC
69333 ATAGCATTTTCTGGAAGTGTTTTTTGAGATATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
1 ATAGCATTTTCTGGAAGTGTTTTTTGAGATATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
69398 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
69416 ATAGCATTTTCTGGAAGTGTTTTTTGAGATATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
1 ATAGCATTTTCTGGAAGTGTTTTTTGAGATATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
69481 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
* * * *
69499 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATTTTCTGGAAGTGTTTTTTGAGATATCTGATC
69537 CGAAGAAGTG
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 117 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (83 bp):
ATAGCATTTTCTGGAAGTGTTTTTTGAGATATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
TAGAAGATGAATTTGCCA
Found at i:70568 original size:119 final size:116
Alignment explanation
Indices: 70094--70768 Score: 1051
Period size: 119 Copynumber: 5.8 Consensus size: 116
70084 TTGAATTCAC
*
70094 CATCAAATTGATGGATCATTGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
1 CATCAAATTGATGGATCATCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAA--C-TCATCTGAA
*
70159 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
63 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* * * * *
70213 CATC-ATTTGATGGATCAACATTGCCAGA-GAAG-GTTCATAATAAGAAGAACTCATCTGAAGAA
1 CATCAAATTGATGGATCATCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
*
70275 GGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
66 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
70326 CATCAAATTGATGGATCATTGTTTCCAGA-GAAG-GTTCATAATGAGAAGAACTCATCTGAAGAA
1 CATCAAATTGATGGATCATCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
70389 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
66 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
70440 CATCAAATTGATGGATCATTGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
1 CATCAAATTGATGGATCATCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAA--C-TCATCTGAA
70505 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
63 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
70559 CATCAAATTGATGGATCATCGTTTCCAGAGGAAGAGTTCACAATGAGAAGAACTCGTCATCTGAA
1 CATCAAATTGATGGATCATCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAA--C-TCATCTGAA
*
70624 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
63 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* * * * *
70678 CATC-ATTTGATGGATCAACATTACCAG-GTAA-AGTTCATAATGAGAAGAACTCATCTGAAGAA
1 CATCAAATTGATGGATCATCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
*
70740 GGAAGAAAAAGTTCATAATGAGAAGAACT
66 GGAAGAAGAAGTTCATAATGAGAAGAACT
70769 CATCAAGAGC
Statistics
Matches: 524, Mismatches: 26, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
113 104 0.20
114 133 0.25
115 4 0.01
116 50 0.10
117 7 0.01
118 39 0.07
119 187 0.36
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (116 bp):
CATCAAATTGATGGATCATCGTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
Found at i:71025 original size:3 final size:3
Alignment explanation
Indices: 71019--71094 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
71009 TTTTTATCCA
*
71019 TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
71067 TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
71095 AATATATTAA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:76115 original size:22 final size:22
Alignment explanation
Indices: 76074--76115 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
76064 CAACATAAAA
* *
76074 TATCAATTTTGGTATGTTTTAT
1 TATCAATTTTGCTATCTTTTAT
*
76096 TATCAATTTTTCTATCTTTT
1 TATCAATTTTGCTATCTTTT
76116 CAAAAGCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (22 bp):
TATCAATTTTGCTATCTTTTAT
Found at i:81010 original size:20 final size:21
Alignment explanation
Indices: 80971--81021 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
80961 TTAAAGTGTA
*
80971 TTATTT-TTTATTTTTATAAT
1 TTATTTATTTATTTATATAAT
80991 TTATTTATTTATTTAT-TAAT
1 TTATTTATTTATTTATATAAT
* *
81011 TGATTGATTTA
1 TTATTTATTTA
81022 AATTAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
TTATTTATTTATTTATATAAT
Found at i:81256 original size:25 final size:25
Alignment explanation
Indices: 81227--81280 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
81217 ATATGCAATT
*
81227 TAATAAATTT-AATTATTATATAATA
1 TAATAAATTTAAAAT-TTATATAATA
*
81252 TAAT--ATTTAAAATTTATATATTA
1 TAATAAATTTAAAATTTATATAATA
81275 TAATAA
1 TAATAA
81281 TAAGATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
23 17 0.71
24 3 0.12
25 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATAAATTTAAAATTTATATAATA
Found at i:82039 original size:60 final size:60
Alignment explanation
Indices: 81950--82073 Score: 149
Period size: 60 Copynumber: 2.1 Consensus size: 60
81940 TAAAGTATAT
* * * * *
81950 AAATGGTCCCTTGACTATAGGATAATGCTTTATTGTGTTTCTTAACTATTAAAAGTTACA
1 AAATGGTCCCTCGACTATAGGAGAATGCTTTATTGAGTCTCTCAACTATTAAAAGTTACA
* ** * * *
82010 AAATGGTCTCTCGACTATAGGAGGTTGCTTTATTGAGTCTCTCGATTATTAGAAGTTACA
1 AAATGGTCCCTCGACTATAGGAGAATGCTTTATTGAGTCTCTCAACTATTAAAAGTTACA
82070 AAAT
1 AAAT
82074 TATCATCTGA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (60 bp):
AAATGGTCCCTCGACTATAGGAGAATGCTTTATTGAGTCTCTCAACTATTAAAAGTTACA
Found at i:86528 original size:39 final size:39
Alignment explanation
Indices: 86485--86590 Score: 112
Period size: 39 Copynumber: 2.7 Consensus size: 39
86475 TTCATAATCC
86485 AAATTATTTCACTC-TAACATTCTATAA-TCCTAATTTCTT
1 AAATTATTTCAC-CATAACATTCTA-AATTCCTAATTTCTT
* * *
86524 AAATT-TTGACACCATAACGTTCTAAATTCTTAATTTCTT
1 AAATTATT-TCACCATAACATTCTAAATTCCTAATTTCTT
*
86563 AAATTATTTCA-CATTAACGTTCTAAATT
1 AAATTATTTCACCA-TAACATTCTAAATT
86591 ATTTTTAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
38 7 0.12
39 49 0.84
40 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (39 bp):
AAATTATTTCACCATAACATTCTAAATTCCTAATTTCTT
Found at i:86924 original size:25 final size:25
Alignment explanation
Indices: 86868--86927 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
86858 ATAGTAACTT
86868 AAAATATTTTTATATCAACTTCTTA
1 AAAATATTTTTATATCAACTTCTTA
* *
86893 AATATATTTTTAT-T-AACTTAATTTA
1 AAAATATTTTTATATCAACTT--CTTA
86918 AAAATATTTT
1 AAAATATTTT
86928 ATTTTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.17
24 1 0.03
25 24 0.80
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.52
Consensus pattern (25 bp):
AAAATATTTTTATATCAACTTCTTA
Found at i:88661 original size:23 final size:23
Alignment explanation
Indices: 88635--88692 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
88625 ATGATCATGA
88635 TAAAATTTAAAAGAAATAGATGC
1 TAAAATTTAAAAGAAATAGATGC
88658 TAAAATTTAAAAGAAATAGATGC
1 TAAAATTTAAAAGAAATAGATGC
88681 TAAAATTTAAAA
1 TAAAATTTAAAA
88693 AATTCGTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (23 bp):
TAAAATTTAAAAGAAATAGATGC
Found at i:89537 original size:26 final size:27
Alignment explanation
Indices: 89495--89550 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
89485 ATCCGAACCC
89495 GACCAAAAAATTATACACCCTCCACCT
1 GACCAAAAAATTATACACCCTCCACCT
*
89522 GACCAAAATATT-TACACCCTCCACCT
1 GACCAAAAAATTATACACCCTCCACCT
89548 GAC
1 GAC
89551 TTGAACCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.38, C:0.38, G:0.05, T:0.20
Consensus pattern (27 bp):
GACCAAAAAATTATACACCCTCCACCT
Found at i:90332 original size:14 final size:15
Alignment explanation
Indices: 90310--90347 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
90300 AATAAATATA
90310 TAAATATAAAAAAGT
1 TAAATATAAAAAAGT
*
90325 TAAA-ATAAAAGAGT
1 TAAATATAAAAAAGT
*
90339 TGAATATAA
1 TAAATATAA
90348 CAATATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (15 bp):
TAAATATAAAAAAGT
Found at i:90480 original size:20 final size:21
Alignment explanation
Indices: 90457--90498 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
90447 TAAAAATAGG
90457 AAAAATGAAA-AAA-AAATGTT
1 AAAAA-GAAAGAAATAAATGTT
90477 -AAAAGAAAGAAATAAATGTT
1 AAAAAGAAAGAAATAAATGTT
90497 AA
1 AA
90499 CAAAAATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
20 7 0.37
21 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (21 bp):
AAAAAGAAAGAAATAAATGTT
Found at i:91686 original size:21 final size:18
Alignment explanation
Indices: 91651--91708 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 18
91641 GGACCCTAAA
91651 AAAATAAAAATAAAAAAT
1 AAAATAAAAATAAAAAAT
91669 AAAATAAAGAATTAAAAAAAT
1 AAAATAAA-AA-T-AAAAAAT
* *
91690 AAAATTATAATAATAAAAT
1 AAAATAAAAATAA-AAAAT
91709 TATATGTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 10 0.29
19 8 0.24
20 3 0.09
21 13 0.38
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAATAAAAATAAAAAAT
Found at i:91799 original size:55 final size:58
Alignment explanation
Indices: 91738--91868 Score: 164
Period size: 55 Copynumber: 2.3 Consensus size: 58
91728 TTTTTAGAAA
*
91738 AAAATTATATACTATATGTTTT-AAAAAC-CATTATATACGTTTTC-AAAATGTTTT-C
1 AAAATTATATATTATATGTTTTCAAAAACACATTATATACG-TTTCAAAAATGTTTTCC
* *
91793 AAAATTATATATTATA-GTTTTCCAAAACTATATTATATACGTTTCGAAAAATGTTTTCC
1 AAAATTATATATTATATGTTTTCAAAAAC-ACATTATATACGTTTC-AAAAATGTTTTCC
*
91852 AAAACTATATATTATAT
1 AAAATTATATATTATAT
91869 ATATTTTAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
54 5 0.08
55 20 0.31
56 4 0.06
57 10 0.15
58 10 0.15
59 16 0.25
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (58 bp):
AAAATTATATATTATATGTTTTCAAAAACACATTATATACGTTTCAAAAATGTTTTCC
Found at i:91831 original size:23 final size:23
Alignment explanation
Indices: 91787--91836 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
91777 TTTTCAAAAT
*
91787 GTTTTCAAAATTATATATTATA-
1 GTTTTCAAAACTATATATTATAC
91809 GTTTTCCAAAACTATAT-TATATAC
1 GTTTT-CAAAACTATATAT-TATAC
91833 GTTT
1 GTTT
91837 CGAAAAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.25
23 14 0.58
24 4 0.17
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (23 bp):
GTTTTCAAAACTATATATTATAC
Found at i:91892 original size:37 final size:38
Alignment explanation
Indices: 91809--91911 Score: 131
Period size: 38 Copynumber: 2.7 Consensus size: 38
91799 ATATATTATA
** *
91809 GTTTTCCAAAAC--TATATTATATACGTTTCGAAAAAT
1 GTTTTCCAAAACTATATATTATATATATTTCAAAAAAT
*
91845 GTTTTCCAAAACTATATATTATATATATTTTAAAAAAT
1 GTTTTCCAAAACTATATATTATATATATTTCAAAAAAT
91883 GTTTT-CAAAACTATATTATATATATATAT
1 GTTTTCCAAAACTATA-TAT-TATATATAT
91912 ATATATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
36 12 0.20
37 10 0.17
38 28 0.47
39 9 0.15
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.44
Consensus pattern (38 bp):
GTTTTCCAAAACTATATATTATATATATTTCAAAAAAT
Found at i:91906 original size:2 final size:2
Alignment explanation
Indices: 91894--91929 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
91884 TTTTCAAAAC
91894 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
91930 CGAAAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:91950 original size:56 final size:54
Alignment explanation
Indices: 91857--91970 Score: 142
Period size: 56 Copynumber: 2.1 Consensus size: 54
91847 TTTCCAAAAC
**
91857 TATATATTATATATATTTTAAAAAATGTTTTCAAAACTATATTATATAT-ATATA
1 TATATATTATATATATTCGAAAAAATGTTTTCAAAACTATA-TATATATGATATA
* *
91911 TATATATATATATATATATCGAAAATAT-TTTTCCAAAACTATATATATATGCTATA
1 TATATAT-TATATATAT-TCGAAAAAATGTTTT-CAAAACTATATATATATGATATA
91967 TATA
1 TATA
91971 CTAAATAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
54 7 0.13
55 20 0.38
56 25 0.48
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (54 bp):
TATATATTATATATATTCGAAAAAATGTTTTCAAAACTATATATATATGATATA
Found at i:97136 original size:22 final size:21
Alignment explanation
Indices: 97111--97174 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
97101 CACACAGAAT
97111 GAAAGAAAATTAAATTCAAAAG
1 GAAAG-AAATTAAATTCAAAAG
* * * *
97133 GAAATGAAATGAAGTACAAAAT
1 GAAA-GAAATTAAATTCAAAAG
*
97155 GAAAGAAATTAAATTTAAAA
1 GAAAGAAATTAAATTCAAAA
97175 TAAAATGAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
21 12 0.36
22 20 0.61
23 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.14, T:0.20
Consensus pattern (21 bp):
GAAAGAAATTAAATTCAAAAG
Found at i:97181 original size:43 final size:44
Alignment explanation
Indices: 97108--97191 Score: 134
Period size: 43 Copynumber: 1.9 Consensus size: 44
97098 TCCCACACAG
*
97108 AATGAAAGAAAATTAAATTCAAAAGGAAATGAAATGAAGTACAA
1 AATGAAAGAAAATTAAATTCAAAAGAAAATGAAATGAAGTACAA
* *
97152 AATGAAAG-AAATTAAATTTAAAATAAAATGAAATGAAGTA
1 AATGAAAGAAAATTAAATTCAAAAGAAAATGAAATGAAGTA
97192 GGAATAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 29 0.78
44 8 0.22
ACGTcount: A:0.62, C:0.02, G:0.14, T:0.21
Consensus pattern (44 bp):
AATGAAAGAAAATTAAATTCAAAAGAAAATGAAATGAAGTACAA
Done.