Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000483.1 Hibiscus syriacus cultivar Beakdansim tig00000920_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: 65171
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2206 original size:13 final size:12
Alignment explanation
Indices: 2178--2220 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
2168 CAATCAGAAC
*
2178 AAAAAAAAATAG
1 AAAAAAAAAAAG
**
2190 AAAAAAGCAAAG
1 AAAAAAAAAAAG
2202 AAAAATAAAAAAG
1 AAAAA-AAAAAAG
2215 AAAAAA
1 AAAAAA
2221 GAAGACAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.05
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:2400 original size:69 final size:69
Alignment explanation
Indices: 2281--2418 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
2271 GATTTAAACT
2281 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
2346 TCAA
66 TCAA
* * * * *
2350 ATGAGATTGATCAAGCACAATCATTTCTGAATTACTGTATCAC-TCTACTCGAAGATCATGGAGC
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTC-ACTCGAAGATCATAGAGC
2414 ATCAA
65 ATCAA
2419 GAGAGAAACA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 2 0.03
69 61 0.97
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
TCAA
Found at i:3412 original size:32 final size:32
Alignment explanation
Indices: 3345--3457 Score: 111
Period size: 32 Copynumber: 3.5 Consensus size: 32
3335 TGAGGGCATC
** *
3345 TTTGAAGATTCAACATCAAATGTTGGGACATTT
1 TTTG-AGATTCAACATCAAATGTTGGGGTAGTT
* *
3378 TTTTAGATTTAACATCAAATGTTGGGGTAGTT
1 TTTGAGATTCAACATCAAATGTTGGGGTAGTT
* * * *
3410 TTTGATATTCAACATCGAATATTGGGGTA-TC
1 TTTGAGATTCAACATCAAATGTTGGGGTAGTT
*
3441 TTTGGGAATTCAACATC
1 TTTGAG-ATTCAACATC
3458 CTGATGCAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
31 5 0.08
32 58 0.88
33 3 0.05
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATGTTGGGGTAGTT
Found at i:4241 original size:105 final size:105
Alignment explanation
Indices: 4078--4299 Score: 266
Period size: 105 Copynumber: 2.1 Consensus size: 105
4068 CGTGCCACTT
** * **
4078 GAGACAACACAAGTTCAACTTCACAACAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTT
1 GAGACAACACAAACTCAACTTCACAACAAGGGACGACTGGCTGTCAACAAACAATTTCCCAATCC
4143 CAGAGCCAATTTCAACTTCACAGC-GAAGATATTGGACTC
66 CAGAGCCAATTTCAACTTCACAGCGGAAGATATTGGACTC
* * * * * * *
4182 GAGACAGCACAAACTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAATAATTTCCTAGTC
1 GAGACAACACAAACTCAACTTCACAAC-AAGGGACGACTGGCTGTCAACAAACAATTTCCCAATC
* ** *
4247 CCAGAGCCAATTTTAACTTCATGGCGGAGGATATTGGACTC
65 CCAGAGCCAATTTCAACTTCACAGCGGAAGATATTGGACTC
* *
4288 GAAACAATACAA
1 GAGACAACACAA
4300 CTTACTTGGA
Statistics
Matches: 97, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
104 23 0.24
105 51 0.53
106 23 0.24
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (105 bp):
GAGACAACACAAACTCAACTTCACAACAAGGGACGACTGGCTGTCAACAAACAATTTCCCAATCC
CAGAGCCAATTTCAACTTCACAGCGGAAGATATTGGACTC
Found at i:4609 original size:36 final size:37
Alignment explanation
Indices: 4569--4654 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
4559 ATTGAAAACA
* * *
4569 TTTCCCTTGAAATG-AATTTTATCTCGATTGAGATAG
1 TTTCCCTTGAAACGAAATTTTATCTCCATTGAGACAG
* *
4605 TTTCCCTTGAAACGAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACGAAATTTTATCTCCATTGAGACAG
*
4642 TTTCTCTTGAAAC
1 TTTCCCTTGAAAC
4655 ATAAATATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACGAAATTTTATCTCCATTGAGACAG
Found at i:4765 original size:100 final size:102
Alignment explanation
Indices: 4517--4884 Score: 578
Period size: 102 Copynumber: 3.6 Consensus size: 102
4507 TTTTGGAACT
4517 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* *
4582 GAATTTTATCTCGATTGAGATAGTTTCCCTTGAAACG
66 GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
* * * *
4619 AAATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* *
4684 AAATTTTATCTCGCTTG-GGTAGTTTCCCTTGAAAC-
66 GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
* *
4719 AAATTTTGTCTCCCTTAAGATATTTTCTCTTGAAACATAAACATTGAAAACATTTCCTTTGAAAT
1 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* *
4784 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
66 GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
* * * *
4821 AAATTTTGTTTCCCTTGAGATAGTTTCTCTTGAAACATAAACCTTGAAAACGTTTCCCTTGAAA
1 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
4885 CACAAAATAT
Statistics
Matches: 241, Mismatches: 23, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
100 73 0.30
101 34 0.14
102 134 0.56
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (102 bp):
AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
Found at i:4838 original size:37 final size:37
Alignment explanation
Indices: 4785--4857 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
4775 CTTTGAAATG
*
4785 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
* *
4822 AATTTTGTTTCCCTTGAGATAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
4858 TAAACCTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
Found at i:4870 original size:202 final size:202
Alignment explanation
Indices: 4517--4884 Score: 628
Period size: 202 Copynumber: 1.8 Consensus size: 202
4507 TTTTGGAACT
4517 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* *
4582 GAATTTTATCTCGATTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCTTTGAGACAGTTTCT
66 GAATTTTATCTCGATTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
*
4647 CTTGAAACATAAATATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGTAGTTTCCC
131 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGTAGTTTCCC
4712 TTGAAAC
196 TTGAAAC
* *
4719 AAATTTTGTCTCCCTTAAGATATTTTCTCTTGAAACATAAACATTGAAAACATTTCCTTTGAAAT
1 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* ** * *
4784 GAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTTTCCCTTGAGATAGTTTCT
66 GAATTTTATCTCGATTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* *
4849 CTTGAAACATAAACCTTGAAAACGTTTCCCTTGAAA
131 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
4885 CACAAAATAT
Statistics
Matches: 154, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
202 154 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (202 bp):
AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
GAATTTTATCTCGATTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGTAGTTTCCC
TTGAAAC
Found at i:4972 original size:37 final size:37
Alignment explanation
Indices: 4922--5024 Score: 181
Period size: 36 Copynumber: 2.8 Consensus size: 37
4912 AAAACGAGTT
4922 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
* *
4959 TTGAGACGGTTTCCCTTGAAAC-AAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
4995 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
5025 TGAATATCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 34 0.56
37 27 0.44
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:5041 original size:102 final size:102
Alignment explanation
Indices: 4935--5121 Score: 245
Period size: 102 Copynumber: 1.8 Consensus size: 102
4925 AGACAGTTTC
* **
4935 CCTTGAAACAAAATCTT-GTCTCTCTTGAGACGGTTTCCCTTGA-AAC-AAATTTTGTCTCTCTT
1 CCTTGAAAC-AAAT-TTCGTCTCCCTTGAGACAATTT-CCTTGAGAACTAAATTTTGTCTCTCTT
4997 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
63 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
* * *
5037 CCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTAGAACTAAGTTTTGTCTCTCTTGAG
1 CCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCTTGAGAACTAAATTTTGTCTCTCTTGAG
* **
5102 GCAGTTTCTTTTGAAACAAA
66 ACAGTTTCCCTTGAAACAAA
5122 TTTTGTCCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 6 0.08
101 23 0.32
102 44 0.60
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (102 bp):
CCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCTTGAGAACTAAATTTTGTCTCTCTTGAG
ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
Found at i:5134 original size:36 final size:36
Alignment explanation
Indices: 4922--5155 Score: 159
Period size: 36 Copynumber: 6.6 Consensus size: 36
4912 AAAACGAGTT
** * *
4922 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCTTTTGAAAC-AAATTTTGTCCCTC
* ** *
4959 TTGAGACGGTTTCCCTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
** *
4995 TTGAGACAGTTTCCCTTGAAACAAA----AT--CT-
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
* *
5024 TTGA-ATA-TCTT-TTCCTTGAAACAAATTTCGTCTCC-C
1 TTGAGACAGT-TTCTT--TTGAAACAAATTTTGTC-CCTC
* * *
5060 TTGAGACAATTTCTTTT-AGAACTAAGTTTTGTCTCTC
1 TTGAGACAGTTTCTTTTGA-AAC-AAATTTTGTCCCTC
*
5097 TTGAGGCAGTTTCTTTTGAAACAAATTTTGTCCCTC
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
*
5133 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGACAGTTTCTTTTGAAACA
5156 CAAAAAAACC
Statistics
Matches: 161, Mismatches: 18, Indels: 37
0.75 0.08 0.17
Matches are distributed among these distances:
27 1 0.01
28 4 0.02
29 14 0.09
30 2 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 81 0.50
37 52 0.32
38 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAGACAGTTTCTTTTGAAACAAATTTTGTCCCTC
Found at i:5182 original size:33 final size:37
Alignment explanation
Indices: 5142--5223 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
5132 CTTGAGACAG
*
5142 TTTCTCTTGAAACACA-A-AAAAA-CC-TCGAAATTA
1 TTTCTCTTGAAACACACACAAAAACCCTTCGAAAATA
* *
5175 TTTCTCTTGAAACACACACAAAAACCCTTTGAAAATG
1 TTTCTCTTGAAACACACACAAAAACCCTTCGAAAATA
5212 TTTCTCTTGAAA
1 TTTCTCTTGAAA
5224 TACCAAACCT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 16 0.38
34 1 0.02
35 5 0.12
36 2 0.05
37 18 0.43
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.30
Consensus pattern (37 bp):
TTTCTCTTGAAACACACACAAAAACCCTTCGAAAATA
Found at i:6373 original size:21 final size:23
Alignment explanation
Indices: 6344--6389 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
6334 TATATATATT
*
6344 TTTATTATATT-T-TTTTATTTA
1 TTTACTATATTCTCTTTTATTTA
6365 TTTACTATATTCCTCTTTTATTTA
1 TTTACTATATT-CTCTTTTATTTA
6389 T
1 T
6390 ATTATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
23 1 0.05
24 10 0.48
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTACTATATTCTCTTTTATTTA
Found at i:6401 original size:16 final size:17
Alignment explanation
Indices: 6386--6462 Score: 101
Period size: 16 Copynumber: 4.8 Consensus size: 17
6376 CCTCTTTTAT
*
6386 TTATAT-TATTTAT-TA
1 TTATATATATATATATA
*
6401 TTATATATATCT-TATA
1 TTATATATATATATATA
6417 TTATATATATATATATA
1 TTATATATATATATATA
6434 -TATATATATATATATA
1 TTATATATATATATATA
6450 -TATATATATATAT
1 TTATATATATATAT
6463 TAATTTTTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
15 7 0.12
16 46 0.81
17 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATATATATATATA
Found at i:6409 original size:2 final size:2
Alignment explanation
Indices: 6402--6462 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
6392 TATTTATTAT
*
6402 TA TA TA TA TC T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6442 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
6463 TAATTTTTCT
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6591 original size:17 final size:17
Alignment explanation
Indices: 6553--6610 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
6543 TTTGCTTTTA
*
6553 TTTATTTATA-TATATAT
1 TTTATTTTTACTAT-TAT
*
6570 ATTATATTTTACT-TTAT
1 TTTAT-TTTTACTATTAT
*
6587 TTTATTTTTTCTATTAT
1 TTTATTTTTACTATTAT
6604 TTT-TTTT
1 TTTATTTT
6611 CTTAATATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 10 0.29
17 18 0.53
18 5 0.15
19 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTTTACTATTAT
Found at i:6831 original size:11 final size:11
Alignment explanation
Indices: 6815--6840 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6805 ATTTTGTTTA
6815 TTTTTATTATT
1 TTTTTATTATT
6826 TTTTTATTATT
1 TTTTTATTATT
6837 TTTT
1 TTTT
6841 ACGTGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:6838 original size:19 final size:20
Alignment explanation
Indices: 6796--6838 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
6786 ATTTTTTAAC
6796 ATTTTATTCATTTTGTTTAT
1 ATTTTATTCATTTTGTTTAT
6816 -TTTTATT-ATTTT-TTTATT
1 ATTTTATTCATTTTGTTTA-T
6834 ATTTT
1 ATTTT
6839 TTACGTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.19
18 6 0.29
19 11 0.52
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (20 bp):
ATTTTATTCATTTTGTTTAT
Found at i:6880 original size:26 final size:28
Alignment explanation
Indices: 6821--6881 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 28
6811 TTTATTTTTA
*
6821 TTATTT-TTTTATTATTTTTTACGTGTT
1 TTATTTATTTTATCATTTTTTACGTGTT
* *
6848 TT-GTTATTTT-TCATTTTTT-CTTGTT
1 TTATTTATTTTATCATTTTTTACGTGTT
6873 TTATTTATT
1 TTATTTATT
6882 ATTCTCACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
25 7 0.25
26 15 0.54
27 6 0.21
ACGTcount: A:0.13, C:0.05, G:0.07, T:0.75
Consensus pattern (28 bp):
TTATTTATTTTATCATTTTTTACGTGTT
Found at i:10999 original size:70 final size:70
Alignment explanation
Indices: 10911--11044 Score: 241
Period size: 70 Copynumber: 1.9 Consensus size: 70
10901 TGTTCTGTGT
*
10911 GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATTCTACCATTTGAATTTTACAT
1 GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACAT
10976 GATCC
66 GATCC
* *
10981 GCTTATTTCTATATGTATATTTGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACA
1 GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACA
11045 CTGTTTTTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (70 bp):
GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACAT
GATCC
Found at i:17699 original size:21 final size:22
Alignment explanation
Indices: 17662--17702 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
17652 ACACGTTTTA
*
17662 CTCTACTATTGTGGCATGTTTC
1 CTCTACTATTATGGCATGTTTC
17684 CTCTACT-TTATGGCATGTT
1 CTCTACTATTATGGCATGTT
17703 GTTCGCCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (22 bp):
CTCTACTATTATGGCATGTTTC
Found at i:32690 original size:20 final size:20
Alignment explanation
Indices: 32651--32701 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
32641 TATTAACTCA
* *
32651 ATTTAAAAATAATTTATTTTT
1 ATTTTAAAATAATATA-TTTT
32672 ATTTTAAAA-AATATATTTT
1 ATTTTAAAATAATATATTTT
*
32691 ATGTTAAAATA
1 ATTTTAAAATA
32702 TTGTGAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 12 0.46
20 6 0.23
21 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTTAAAATAATATATTTT
Found at i:36648 original size:24 final size:24
Alignment explanation
Indices: 36621--36708 Score: 140
Period size: 24 Copynumber: 3.7 Consensus size: 24
36611 TTCTATTATA
*
36621 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
*
36645 ATACTTGACCTGGATTCTGATCGA
1 ATACTTGACCTGGATTCTGATCGG
* *
36669 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
36693 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
36709 ATGTTTTGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:41382 original size:24 final size:24
Alignment explanation
Indices: 41362--41442 Score: 126
Period size: 24 Copynumber: 3.4 Consensus size: 24
41352 ATAATACCTT
41362 ACCTGGATTCTGATCGGATACTTG
1 ACCTGGATTCTGATCGGATACTTG
* *
41386 ACTTGGATTCTGATCGAATACTTG
1 ACCTGGATTCTGATCGGATACTTG
* *
41410 ACCTGGATTTTGATCTGATACTTG
1 ACCTGGATTCTGATCGGATACTTG
41434 ACCTGGATT
1 ACCTGGATT
41443 ATGTTTTGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (24 bp):
ACCTGGATTCTGATCGGATACTTG
Found at i:41568 original size:35 final size:35
Alignment explanation
Indices: 41524--41623 Score: 182
Period size: 35 Copynumber: 2.9 Consensus size: 35
41514 ATACTTGGAA
41524 GCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACCG
1 GCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACCG
*
41559 GCTCATCGGCTGTGTGCTCAGGGCCTTACTTACCG
1 GCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACCG
*
41594 ACTCCTCGGCTGTGTGCTCAGGGCCTTACT
1 GCTCCTCGGCTGTGTGCTCAGGGCCTTACT
41624 GGACTTGACG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.10, C:0.33, G:0.28, T:0.29
Consensus pattern (35 bp):
GCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACCG
Found at i:45442 original size:23 final size:22
Alignment explanation
Indices: 45385--45444 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
45375 ATTCAAGAAG
45385 TTCTCTTCTCTT-GAAAAATATT
1 TTCTC-TCTCTTAGAAAAATATT
45407 TTCTCTCATTCTTAGAAAATATTATT
1 TTCTCTC--TCTTAGAAAA-A-TATT
45433 TTC-CTCTCTTAG
1 TTCTCTCTCTTAG
45445 TTTTTCCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
21 2 0.06
22 5 0.15
23 10 0.30
24 5 0.15
25 4 0.12
26 7 0.21
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (22 bp):
TTCTCTCTCTTAGAAAAATATT
Found at i:46748 original size:20 final size:19
Alignment explanation
Indices: 46703--46750 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
46693 GCGATCGATA
46703 ATTCGCAAATCAATCTCCG
1 ATTCGCAAATCAATCTCCG
* *
46722 GTATCGCAAATCAATTTCCAG
1 AT-TCGCAAATCAATCTCC-G
46743 ATTCGCAA
1 ATTCGCAA
46751 CGCGATTCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.88
21 2 0.08
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (19 bp):
ATTCGCAAATCAATCTCCG
Found at i:46816 original size:21 final size:21
Alignment explanation
Indices: 46766--46817 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
46756 TTCTGACTAC
46766 CGCATTGCGATTTTCCAAATT
1 CGCATTGCGATTTTCCAAATT
* *
46787 CGCGTTGCGATTTTCCTAATT
1 CGCATTGCGATTTTCCAAATT
*
46808 CGCAATGCGA
1 CGCATTGCGA
46818 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (21 bp):
CGCATTGCGATTTTCCAAATT
Found at i:46832 original size:20 final size:20
Alignment explanation
Indices: 46807--46889 Score: 105
Period size: 19 Copynumber: 4.2 Consensus size: 20
46797 TTTTCCTAAT
46807 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
46827 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
46848 TCGCAATGCGATTACGT-AA
1 TCGCAATGCGAATACGTAAA
46867 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
46887 TCG
1 TCG
46890 TATCGCAAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
19 18 0.35
20 18 0.35
21 15 0.29
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:46933 original size:60 final size:60
Alignment explanation
Indices: 46807--46919 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
46797 TTTTCCTAAT
* * *
46807 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAA
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATCTGGAAAATCGCAATGAGATTACGTAA
* * **
46867 TCGCAATGCGAATACGTAAATCGTATCGCAAATCT-GACTATCGCAATGAGATT
1 TCGCAATGCGAATACGTAAATCGCAACGCAAATCTGGAAAATCGCAATGAGATT
46920 CTGACTATCG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 15 0.33
60 31 0.67
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAACGCAAATCTGGAAAATCGCAATGAGATTACGTAA
Found at i:48046 original size:14 final size:14
Alignment explanation
Indices: 48021--48056 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
48011 GAAAAAGAAG
48021 AAGAAGAAATCCCCA
1 AAGAA-AAATCCCCA
*
48036 AAGAAAAATCCCCG
1 AAGAAAAATCCCCA
48050 AAGAAAA
1 AAGAAAA
48057 TGCCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (14 bp):
AAGAAAAATCCCCA
Found at i:50291 original size:20 final size:20
Alignment explanation
Indices: 50266--50354 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
50256 CAACGCAGAA
50266 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
50286 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
50306 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
50326 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
50346 ATCGCAACG
1 ATCGCAACG
50355 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 61 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:50365 original size:14 final size:14
Alignment explanation
Indices: 50346--50399 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
50336 GGAAATGACT
50346 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
50360 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
50379 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
50393 ATCGCAA
1 ATCGCAA
50400 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:50414 original size:34 final size:33
Alignment explanation
Indices: 50326--50421 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
50316 GGAATTGACT
* **
50326 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
50360 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
50393 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
50422 CGAATTTAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.55
34 26 0.45
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:50417 original size:20 final size:19
Alignment explanation
Indices: 50359--50425 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
50349 GCAACGAGAG
50359 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
50378 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
50392 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
50412 AATCGCAACGCGAA
1 AATCGCAATGCGAA
50426 TTTAGGTCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
19 11 0.28
20 13 0.33
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:52027 original size:42 final size:42
Alignment explanation
Indices: 51948--52040 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
51938 CCTCTTCAAC
* * *
51948 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
51990 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
52032 GATGACAGG
1 GATGACAGG
52041 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:52543 original size:20 final size:20
Alignment explanation
Indices: 52520--52626 Score: 169
Period size: 20 Copynumber: 5.3 Consensus size: 20
52510 GAAACTTAAA
* **
52520 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
**
52540 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
52560 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
52580 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
52600 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
52620 ATCGCAA
1 ATCGCAA
52627 CGAGAGAATC
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATTTGACT
Found at i:52643 original size:34 final size:36
Alignment explanation
Indices: 52520--52645 Score: 123
Period size: 40 Copynumber: 3.3 Consensus size: 36
52510 GAAACTTAAA
* **
52520 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGAC
1 ATCGCAATGCGAATTTGACTATCGCAA-GCG--AATGAC
52559 TATCGCAATGCGAATTTGACTATCGCAATGCGAATTTGAC
1 -ATCGCAATGCGAATTTGACTATCGCAA-GCGAA--TGAC
52599 TATCGCAATGCGAATTTGACTATCGCAA-CGAGA-GA-
1 -ATCGCAATGCGAATTTGACTATCGCAAGCGA-ATGAC
52634 ATCGCAATGCGA
1 ATCGCAATGCGA
52646 TTTTCATTTC
Statistics
Matches: 80, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
34 12 0.15
36 2 0.03
38 5 0.06
39 1 0.01
40 60 0.75
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (36 bp):
ATCGCAATGCGAATTTGACTATCGCAAGCGAATGAC
Found at i:52698 original size:20 final size:20
Alignment explanation
Indices: 52673--52719 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
52663 GATTCTTTCG
52673 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
52693 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
52713 TTGCGAT
1 TTGCGAT
52720 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:52744 original size:53 final size:53
Alignment explanation
Indices: 52635--52752 Score: 132
Period size: 53 Copynumber: 2.2 Consensus size: 53
52625 AACGAGAGAA
* **
52635 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
* * ** *
52688 TCGCATTGCGATAGTCATTTTCGCGTTGCGATT-TTGTTGTTGCGATTTTC-ATT
1 TCGCATTGCGATAGTCA-TTTCGCATTGCGATTCTT-TCGTTGCGATAGTCAAAT
52741 TCGCATTGCGAT
1 TCGCATTGCGAT
52753 TCTCTCGTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 30 0.55
54 25 0.45
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.42
Consensus pattern (53 bp):
TCGCATTGCGATAGTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
Found at i:52750 original size:33 final size:34
Alignment explanation
Indices: 52693--52786 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
52683 CAAATTCGCA
* * * *
52693 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
**
52727 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
52760 TTGCGATAGTCATTTTCGCATTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
52787 AGTAAACTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.53
34 24 0.47
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:54743 original size:20 final size:20
Alignment explanation
Indices: 54685--54758 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
54675 GAAACTTTAA
* **
54685 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
54705 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
54725 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
54745 ATAGCAACGCGAAA
1 ATCGCAACGCGAAA
54759 TGAAAATCGT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:55170 original size:22 final size:22
Alignment explanation
Indices: 55108--55173 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
55098 TGACCGTGAA
* *
55108 TGATTTCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAT
*
55130 TGATATCGTCGGAGATGGGGAT
1 TGATTTCGTCGGAGATGGGGAT
55152 TGATTTCGTCGGAGATGGGGAT
1 TGATTTCGTCGGAGATGGGGAT
55174 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.11, G:0.39, T:0.29
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAT
Found at i:55377 original size:20 final size:20
Alignment explanation
Indices: 55352--55403 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
55342 GCTATGTAAA
55352 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
55372 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
55392 TCGCATTGCGAT
1 TCGCATTGCGAT
55404 TTACGTAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:55415 original size:20 final size:20
Alignment explanation
Indices: 55392--55463 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
55382 ATAGTCAGAT
55392 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
* **
55412 TCGCATTGCGATTTTCCAAA
1 TCGCATTGCGATTTACGTAA
* *
55432 TTCGCGTTGCGATTTACGTAT
1 -TCGCATTGCGATTTACGTAA
55453 TCGCATTGCGA
1 TCGCATTGCGA
55464 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:55443 original size:41 final size:40
Alignment explanation
Indices: 55372--55463 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
55362 ATAGTCAGAT
*
55372 TCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTAA
1 TCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTAA
** * *
55412 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGTAA
55453 TCGCATTGCGA
1 TCGCATTGCGA
55464 ATTAGGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 13 0.28
41 33 0.72
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (40 bp):
TCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTAA
Found at i:55484 original size:21 final size:21
Alignment explanation
Indices: 55460--55505 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
55450 TATTCGCATT
55460 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
55481 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
55502 GCGA
1 GCGA
55506 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:57807 original size:2 final size:2
Alignment explanation
Indices: 57800--57874 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
57790 AGTTTGCACG
57800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57842 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57875 GTATTATCAA
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 69 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:58336 original size:13 final size:13
Alignment explanation
Indices: 58318--58342 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58308 ATTACAGATG
58318 TGCATATGTAGAC
1 TGCATATGTAGAC
58331 TGCATATGTAGA
1 TGCATATGTAGA
58343 TTGTTTAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (13 bp):
TGCATATGTAGAC
Found at i:58520 original size:3 final size:3
Alignment explanation
Indices: 58512--58536 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
58502 GAATAGGGTT
58512 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
58537 ATTTAAACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:59517 original size:17 final size:17
Alignment explanation
Indices: 59495--59527 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
59485 TCCATTAAAA
59495 CCTTTAACTTTTTACCC
1 CCTTTAACTTTTTACCC
59512 CCTTTAACTTTTTACC
1 CCTTTAACTTTTTACC
59528 AGTTAACCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.48
Consensus pattern (17 bp):
CCTTTAACTTTTTACCC
Found at i:62322 original size:9 final size:10
Alignment explanation
Indices: 62293--62326 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
62283 TATGTCTTTT
*
62293 ATTTTTCTTT
1 ATTTTTCTTA
62303 ATTTTTCTTA
1 ATTTTTCTTA
62313 ATTTTT-TTA
1 ATTTTTCTTA
62322 ATTTT
1 ATTTT
62327 AAATAAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTTTCTTA
Done.