Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010681.1 Kokia drynarioides strain JFW-HI SEQ_125627, 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: 65821
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:3004 original size:44 final size:44
Alignment explanation
Indices: 2943--3030 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
2933 ATATTTAAAT
*
2943 ATATAGAAAGTATAAAAGAAATAAAACTCTAATTCTGATGACAA
1 ATATAGAAAGTATAAAAGAAATAAAACTATAATTCTGATGACAA
*
2987 ATATAGGAAGTATAAAAGAAATAAAACTATAATTCTGATGACAA
1 ATATAGAAAGTATAAAAGAAATAAAACTATAATTCTGATGACAA
3031 GTAGAATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (44 bp):
ATATAGAAAGTATAAAAGAAATAAAACTATAATTCTGATGACAA
Found at i:4291 original size:29 final size:30
Alignment explanation
Indices: 4259--4321 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
4249 TTCGAGGTGA
4259 AAAATTG-AA-TTTTGGAAAA-TCTAGGGGTC
1 AAAATTGTAATTTTTGGAAAACTC-A-GGGTC
*
4288 AAAA-TGTAATTTTTTGAAAACTCAGGGTC
1 AAAATTGTAATTTTTGGAAAACTCAGGGTC
4317 AAAAT
1 AAAAT
4322 CAAAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
28 2 0.07
29 15 0.52
30 10 0.34
31 2 0.07
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (30 bp):
AAAATTGTAATTTTTGGAAAACTCAGGGTC
Found at i:4330 original size:29 final size:30
Alignment explanation
Indices: 4266--4330 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
4256 TGAAAAATTG
**
4266 AATTTTGGAAAATCTAGGGGTCAAAATGTA
1 AATTTTGGAAAATCTAGGGGTCAAAATCAA
* *
4296 ATTTTTTGAAAA-CTCA-GGGTCAAAATCAA
1 AATTTTGGAAAATCT-AGGGGTCAAAATCAA
4325 AATTTT
1 AATTTT
4331 AAACAAAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (30 bp):
AATTTTGGAAAATCTAGGGGTCAAAATCAA
Found at i:5630 original size:19 final size:19
Alignment explanation
Indices: 5593--5630 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5583 TTTTGGTTTA
*
5593 TTTTGTTTATTTTTTTTGG
1 TTTTGTTTATTTTTGTTGG
5612 TTTTGTTT-TTTTTAGTTGG
1 TTTTGTTTATTTTT-GTTGG
5631 GCTCGGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.05, C:0.00, G:0.18, T:0.76
Consensus pattern (19 bp):
TTTTGTTTATTTTTGTTGG
Found at i:6065 original size:96 final size:96
Alignment explanation
Indices: 5947--6532 Score: 489
Period size: 96 Copynumber: 5.9 Consensus size: 96
5937 GATTCGCTAT
* * *
5947 TTATTTTGACCCACTTCTCTGTACTTCACCGGGAAGATAAGATTTGAAGTCTCACTCCACTCCAC
1 TTATTTTGACCCACTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACTCCAC
*
6012 TGTATCCTTAGGGACGTTGAGCTCAGTTTCG
66 TGTATCCTTAGGGACGTTGAGCTCAGCTTCG
* * * * *
6043 TTATTTTAACCTACTTCTCTGTACCTCACCAGAAAGATAGGATTTGAAGTATCACTCCACTCTAC
1 TTATTTTGACCCACTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACTCCAC
* * *
6108 TGTAACCTTAGGGACGTTGAGCTCTGCTTCA
66 TGTATCCTTAGGGACGTTGAGCTCAGCTTCG
* *
6139 TTATTTTGACCCACTTCTCTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCAC
1 TTATTTTGACCCACTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACTCCAC
* * * * *
6204 TTTATCCTCAAGGACGTTTAGCTCGGCTTCG
66 TGTATCCTTAGGGACGTTGAGCTCAGCTTCG
* * * * * * **
6235 TTGTTTTGATTCAACACACTAT-TTTG-ACC-CACTTCTCTGTACCTTACCA-AGAAGATG-AGA
1 TTATTTTGA--C--C-CACT-TCTCTGTACCTCA---C-CAGGA----A-GATAGGATTTGAAG-
* * * * * * * ** **
6295 TTTAAAGTCTTACTCCACTCCATTGTATCCTCATGGACGTTAAGCTTTGCTTTA
50 TCT-CACTC-CACTCCA---C--TGTATCCTTAGGGACGTTGAGCTCAGCTTCG
* *
6349 TTATTTTGACCCACTTTTCTGTACCTCACCAAGAAGATAGGATTTGAAGTCTCACTCCACTCCAC
1 TTATTTTGACCCACTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACTCCAC
* * *
6414 TGTAACCTTAGGGACGTTGAGCTCTGCTTCA
66 TGTATCCTTAGGGACGTTGAGCTCAGCTTCG
* * *
6445 TTATTTTGACCCACTTCTCTATACCTCACCAGGAAGATAGGATTTGAAGTCTTACTCCATTCCAC
1 TTATTTTGACCCACTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACTCCAC
* * *
6510 TATAACCTCAGGGACGTTGAGCT
66 TGTATCCTTAGGGACGTTGAGCT
6533 TTGCTTTGTT
Statistics
Matches: 389, Mismatches: 73, Indels: 56
0.75 0.14 0.11
Matches are distributed among these distances:
96 280 0.72
98 2 0.01
99 2 0.01
100 4 0.01
101 13 0.03
102 6 0.02
103 10 0.03
104 2 0.01
106 2 0.01
107 9 0.02
108 6 0.02
109 13 0.03
110 4 0.01
111 2 0.01
112 2 0.01
114 32 0.08
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (96 bp):
TTATTTTGACCCACTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACTCCAC
TGTATCCTTAGGGACGTTGAGCTCAGCTTCG
Found at i:6356 original size:114 final size:114
Alignment explanation
Indices: 6140--6357 Score: 303
Period size: 114 Copynumber: 1.9 Consensus size: 114
6130 TCTGCTTCAT
* * * *
6140 TATTTTGACCCACTTCTCTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACT
1 TATTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGAGATTTAAAGTCTCACTCCACTCCACT
* * *
6205 TTATCCTCAAGGACGTTTAGCTCGGCTTCGTTGTTTTGATTCAACACAC
66 TTATCCTCAAGGACGTTAAGCTCGGCTTCATTATTTTGATTCAACACAC
* *
6254 TATTTTGACCCACTTCTCTGTACCTTACCAAGAAGATGAGATTTAAAGTCTTACTCCACTCCA-T
1 TATTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGAGATTTAAAGTCTCACTCCACTCCACT
* ** *
6318 TGTATCCTCATGGACGTTAAGCTTTGCTTTATTATTTTGA
66 T-TATCCTCAAGGACGTTAAGCTCGGCTTCATTATTTTGA
6358 CCCACTTTTC
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
113 2 0.02
114 88 0.98
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (114 bp):
TATTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGAGATTTAAAGTCTCACTCCACTCCACT
TTATCCTCAAGGACGTTAAGCTCGGCTTCATTATTTTGATTCAACACAC
Found at i:6431 original size:210 final size:210
Alignment explanation
Indices: 6044--6453 Score: 554
Period size: 210 Copynumber: 2.0 Consensus size: 210
6034 TCAGTTTCGT
* * *
6044 TATTTTAACCTACTTCTCTGTACCTCACCAGAAAGATAGGATTTGAAGTATCACTCCACTCTACT
1 TATTTTAACCCACTTCTCTGTACCTCACCAGAAAGATAGGATTTAAAGTATCACTCCACTCCACT
* * * *
6109 GTAACCTTAGGGACGTTGAGCTCTGCTTCATTATTTTGACCCACTTCTCTGTACCTCACTAGGAA
66 GTAACCTCAGGGACGTTAAGCTCTGCTTCATTATTTTGACCCACTTCTCTGTACCTCACCAAGAA
* * * * * *
6174 GATGGGATTTGAAGTCTCACTCCACTCCACTTTATCCTCAAGGACGTTTAGCTCGGCTTCGTTGT
131 GATAGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGCTCGGCTTCATTAT
6239 TTTGATTCAACACAC
196 TTTGATTCAACACAC
* * * *
6254 TATTTTGACCCACTTCTCTGTACCTTACCA-AGAAGAT-GAGATTTAAAGTCTTACTCCACTCCA
1 TATTTTAACCCACTTCTCTGTACCTCACCAGA-AAGATAG-GATTTAAAGTATCACTCCACTCCA
* * * * * *
6317 TTGTATCCTCATGGACGTTAAGCTTTGCTTTATTATTTTGACCCACTTTTCTGTACCTCACCAAG
64 CTGTAACCTCAGGGACGTTAAGCTCTGCTTCATTATTTTGACCCACTTCTCTGTACCTCACCAAG
* * *
6382 AAGATAGGATTTGAAGTCTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCTGCTTCATT
129 AAGATAGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGCTCGGCTTCATT
6447 ATTTTGA
194 ATTTTGA
6454 CCCACTTCTC
Statistics
Matches: 172, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
209 2 0.01
210 170 0.99
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (210 bp):
TATTTTAACCCACTTCTCTGTACCTCACCAGAAAGATAGGATTTAAAGTATCACTCCACTCCACT
GTAACCTCAGGGACGTTAAGCTCTGCTTCATTATTTTGACCCACTTCTCTGTACCTCACCAAGAA
GATAGGATTTGAAGTCTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGCTCGGCTTCATTAT
TTTGATTCAACACAC
Found at i:6527 original size:306 final size:306
Alignment explanation
Indices: 5948--6547 Score: 891
Period size: 306 Copynumber: 2.0 Consensus size: 306
5938 ATTCGCTATT
** *
5948 TATTTTGACCCACTTCTCTGTACTTCACCGGGAAGATAAGATTTGAAGTCTCACTCCACTCCACT
1 TATTTTGACCCACTTCTCTGTACTTCACCAAGAAGATAAGATTTAAAGTCTCACTCCACTCCACT
* * * *
6013 GTATCCTTAGGGACGTTGAGCTCAGTTTCGTTATTTTAACCTACTTCTCTGTACCTCACCAGAAA
66 GTATCCTCAGGGACGTTAAGCTCAGTTTCATTATTTTAACCCACTTCTCTGTACCTCACCAGAAA
*
6078 GATAGGATTTGAAGTATCACTCCACTCTACTGTAACCTTAGGGACGTTGAGCTCTGCTTCATTAT
131 GATAGGATTTGAAGTATCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCTGCTTCATTAT
* * * *
6143 TTTGACCCACTTCTCTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTTTA
196 TTTGACCCACTTCTCTATACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACTCCACTATA
* *
6208 TCCTCAAGGACGTTTAGCTCGGCTTCGTTGTTTTGATTCAACACAC
261 ACCTCAAGGACGTTGAGCTCGGCTTCGTTGTTTTGATTCAACACAC
* * *
6254 TATTTTGACCCACTTCTCTGTACCTT-ACCAAGAAGATGAGATTTAAAGTCTTACTCCACTCCAT
1 TATTTTGACCCACTTCTCTGTA-CTTCACCAAGAAGATAAGATTTAAAGTCTCACTCCACTCCAC
* ** * *
6318 TGTATCCTCATGGACGTTAAGCTTTGCTTT-ATTATTTTGACCCACTTTTCTGTACCTCACCA-A
65 TGTATCCTCAGGGACGTTAAGCTCAG-TTTCATTATTTTAACCCACTTCTCTGTACCTCACCAGA
*
6381 GAAGATAGGATTTGAAGTCTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCTGCTTCAT
129 -AAGATAGGATTTGAAGTATCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCTGCTTCAT
* *
6446 TATTTTGACCCACTTCTCTATACCTCACCAGGAAGATAGGATTTGAAGTCTTACTCCATTCCACT
193 TATTTTGACCCACTTCTCTATACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACTCCACT
* ** *
6511 ATAACCTCAGGGACGTTGAGCTTTGCTTTGTTGTTTT
258 ATAACCTCAAGGACGTTGAGCTCGGCTTCGTTGTTTT
6548 AATCTGCTTC
Statistics
Matches: 262, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
305 1 0.00
306 255 0.97
307 6 0.02
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (306 bp):
TATTTTGACCCACTTCTCTGTACTTCACCAAGAAGATAAGATTTAAAGTCTCACTCCACTCCACT
GTATCCTCAGGGACGTTAAGCTCAGTTTCATTATTTTAACCCACTTCTCTGTACCTCACCAGAAA
GATAGGATTTGAAGTATCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCTGCTTCATTAT
TTTGACCCACTTCTCTATACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCCACTCCACTATA
ACCTCAAGGACGTTGAGCTCGGCTTCGTTGTTTTGATTCAACACAC
Found at i:6876 original size:49 final size:49
Alignment explanation
Indices: 6803--7386 Score: 283
Period size: 49 Copynumber: 11.9 Consensus size: 49
6793 ATGTTTCTAA
* * * *
6803 GGTACTAGGTTCACTGTTGTGGCCTCAACCTTTCCCTTTATATTTCCAT
1 GGTACTAGATTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCAT
* * * * * * * *
6852 TGTACTAGATCCGCTGTTGCGGCCTTAATCC-TTCCCATCACATCTTCTGA-
1 GGTACTAGATTCGCCGTTGCGGCCTCAA-CCTTTCCCTTTATAT-TTC-CAT
* * * * * **
6902 GGGACAACG-TTTGCCGTTGCTGCCTCAACCTTTCCTTTTATATTTTTAT
1 GGTACTA-GATTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCAT
* * * ** * * * * *
6951 GGTACTAGATTAGCCGTTACGACCTCAATATTTCTCATTACATTTCTAA
1 GGTACTAGATTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCAT
* *
7000 GGTACTAGGTTCGCCGTTGCGGCCTCAACCTTTCCTTTTATATTTCCAT
1 GGTACTAGATTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCAT
* * * * * * * ** * *
7049 GGTACTAGATTCGTCGTTGCGACTTTAATCTTTCCCATCACGTTTCTAA
1 GGTACTAGATTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCAT
* * ** *
7098 GGTACCAGGTTCGCTATTGCGACCTCAACCTTTCCC-TT-TATTTCCAT
1 GGTACTAGATTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCAT
* * * * * * * * *
7145 GATACTGGATTCGCCATTGCAGCCTCAATCC-TTCCCATCACATTTTCTAA
1 GGTACTAGATTCGCCGTTGCGGCCTCAA-CCTTTCCCTTTATA-TTTCCAT
* *
7195 GGTAC-CGAGTTCGCCGTTGCGGCCTCAACCTTTCCCTTAATATCTT-CAT
1 GGTACTAGA-TTCGCCGTTGCGGCCTCAACCTTTCCCTTTATAT-TTCCAT
* * * * *
7244 GGTA-TCAGATTCGCCGTTGCGGCCTCAATCC-TTCCCATCACATTTTCTAC
1 GGTACT-AGATTCGCCGTTGCGGCCTCAA-CCTTTCCCTTTATA-TTTCCAT
* * * * * *
7294 GGTAC-CGAATTCGTCATTGCGGCCTCAACCTTTCCCTTTACATCTTCTAA
1 GGTACTAG-ATTCGCCGTTGCGGCCTCAACCTTTCCCTTTATAT-TTCCAT
* * * * * *
7344 GGTA-TCGGGTTCACCGTTGCTGTCTCAACCTTTCCCTTCATAT
1 GGTACT-AGATTCGCCGTTGCGGCCTCAACCTTTCCCTTTATAT
7387 CTTCATGTTC
Statistics
Matches: 393, Mismatches: 117, Indels: 49
0.70 0.21 0.09
Matches are distributed among these distances:
47 31 0.08
48 6 0.02
49 213 0.54
50 140 0.36
51 3 0.01
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (49 bp):
GGTACTAGATTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCAT
Found at i:7298 original size:99 final size:100
Alignment explanation
Indices: 6796--7333 Score: 569
Period size: 99 Copynumber: 5.5 Consensus size: 100
6786 TTCTATCATG
* * * * *
6796 TTTCTAAGGTA-CTAGGTTCACTGTTGTGGCCTCAACCTTTCCCTTTATATTTCCATTGTACTAG
1 TTTCTAAGGTACCGAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCATGGTACTAG
* * *
6860 ATCCGCTGTTGCGGCCTTAATCCTTCCCATCACAT
66 ATTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* * * * * * * * **
6895 CTTCTGAGGGA-CAACGTTTGCCGTTGCTGCCTCAACCTTTCCTTTTATATTTTTATGGTACTAG
1 TTTCTAAGGTACCGAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCATGGTACTAG
* * * ** * *
6959 ATTAGCCGTTACGACCTCAATATTTCTCATTACA-
66 ATTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* *
6993 TTTCTAAGGTA-CTAGGTTCGCCGTTGCGGCCTCAACCTTTCCTTTTATATTTCCATGGTACTAG
1 TTTCTAAGGTACCGAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCATGGTACTAG
* * * * * *
7057 ATTCGTCGTTGCGACTTTAATCTTTCCCATCAC-G
66 ATTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
** * * *
7091 TTTCTAAGGTACC-AGGTTCGCTATTGCGACCTCAACCTTTCCC-TT-TATTTCCATGATACTGG
1 TTTCTAAGGTACCGAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCATGGTACTAG
* *
7153 ATTCGCCATTGCAGCCTCAATCCTTCCCATCACAT
66 ATTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
*
7188 TTTCTAAGGTACCGA-GTTCGCCGTTGCGGCCTCAACCTTTCCCTTAATATCTT-CATGGTA-TC
1 TTTCTAAGGTACCGAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATAT-TTCCATGGTACT-
7250 AGATTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
64 AGATTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* * * *
7287 TTTCTACGGTACCGA-ATTCGTCATTGCGGCCTCAACCTTTCCCTTTA
1 TTTCTAAGGTACCGAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTA
7334 CATCTTCTAA
Statistics
Matches: 363, Mismatches: 68, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
96 41 0.11
97 40 0.11
98 120 0.33
99 160 0.44
100 2 0.01
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (100 bp):
TTTCTAAGGTACCGAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATATTTCCATGGTACTAG
ATTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
Found at i:8008 original size:112 final size:114
Alignment explanation
Indices: 7808--8020 Score: 290
Period size: 112 Copynumber: 1.9 Consensus size: 114
7798 ATTCCTTATA
*
7808 TCATTAGACCACTAACCTTTATTTCCAATGAAAAAAATACTTGAATCAAGGTTGTAAGGTGGATG
1 TCATTAGACCACTAACCGTTATTTCCAATGAAAAAAATACTTGAATCAAGGTTGTAAGGTGGATG
7873 AAATTGAATTTGATTAGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAT
66 AAATTGAATTTGATTAGAGGCAAA-CTCGCATGAATGAAAAGATTAAAAT
* ** * * * *
7923 TCATTAGTCCACTAACCGTTATTT-TGATG-CAAAAATGCTTGAA-CATGGTTGTGAGGTGGAT-
1 TCATTAGACCACTAACCGTTATTTCCAATGAAAAAAATACTTGAATCAAGGTTGTAAGGTGGATG
* *
7984 AAAGTTGAATTTTATTGGAGGCAAACTCGCATGAATG
66 AAA-TTGAATTTGATTAGAGGCAAACTCGCATGAATG
8021 CAAACATTGA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
111 15 0.17
112 35 0.40
113 12 0.14
114 3 0.03
115 22 0.25
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (114 bp):
TCATTAGACCACTAACCGTTATTTCCAATGAAAAAAATACTTGAATCAAGGTTGTAAGGTGGATG
AAATTGAATTTGATTAGAGGCAAACTCGCATGAATGAAAAGATTAAAAT
Found at i:8355 original size:24 final size:24
Alignment explanation
Indices: 8328--8414 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 24
8318 TTGACCTCTC
8328 CTTTTCTTTTTCCTTCTTTTTTTT
1 CTTTTCTTTTTCCTTCTTTTTTTT
8352 CTTTTCCTTTTT-CTTCTTTTTTCTTT
1 CTTTT-CTTTTTCCTTC-TTTTT-TTT
*
8378 CTTTTTTCTTTTTCTCTTCCCTTTTTTT
1 C--TTTTCTTTTTC-CTT-CTTTTTTTT
8406 -TTTT-TTTTT
1 CTTTTCTTTTT
8415 GGGATAAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
24 14 0.26
25 15 0.28
26 4 0.07
27 6 0.11
28 7 0.13
29 7 0.13
30 1 0.02
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (24 bp):
CTTTTCTTTTTCCTTCTTTTTTTT
Found at i:8356 original size:18 final size:17
Alignment explanation
Indices: 8329--8410 Score: 76
Period size: 17 Copynumber: 4.6 Consensus size: 17
8319 TGACCTCTCC
*
8329 TTTTCTTTTTCCTTCTT
1 TTTTTTTTTTCCTTCTT
8346 TTTTTTCTTTTCCTT-TT
1 TTTTTT-TTTTCCTTCTT
* *
8363 TCTTCTTTTTTCTTTCTT
1 T-TTTTTTTTTCCTTCTT
*
8381 TTTTCTTTTTCTCTTCCCTT
1 TTTTTTTTTTC-CTT--CTT
8401 TTTTTTTTTT
1 TTTTTTTTTT
8411 TTTTGGGATA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
17 23 0.44
18 17 0.33
20 12 0.23
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTTCCTTCTT
Found at i:8361 original size:15 final size:15
Alignment explanation
Indices: 8343--8392 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
8333 CTTTTTCCTT
*
8343 CTTTTTTTTCTTTTC
1 CTTTTTCTTCTTTTC
8358 CTTTTTCTTCTTTT-
1 CTTTTTCTTCTTTTC
8372 -TTCTTTCTT-TTTT-
1 CTT-TTTCTTCTTTTC
8385 CTTTTTCT
1 CTTTTTCT
8393 CTTCCCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 11 0.34
14 8 0.25
15 13 0.41
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
CTTTTTCTTCTTTTC
Found at i:8371 original size:39 final size:38
Alignment explanation
Indices: 8328--8414 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
8318 TTGACCTCTC
*
8328 CTTTTCTTTTTCCTTCTTT-TTTTTCT-TTTCCTTTTTCTT
1 CTTTT-TTTTT-CTTCTTTCTTTTTCTCTTCCCTTTTT-TT
*
8367 CTTTTTTCTTTCTTTTTTCTTTTTCTCTTCCCTTTTTTT
1 CTTTTTT-TTTCTTCTTTCTTTTTCTCTTCCCTTTTTTT
8406 -TTTTTTTTT
1 CTTTTTTTTT
8415 GGGATAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
37 3 0.07
38 14 0.33
39 17 0.40
40 9 0.21
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (38 bp):
CTTTTTTTTTCTTCTTTCTTTTTCTCTTCCCTTTTTTT
Found at i:8374 original size:10 final size:10
Alignment explanation
Indices: 8331--8387 Score: 54
Period size: 10 Copynumber: 6.2 Consensus size: 10
8321 ACCTCTCCTT
*
8331 TTCTTTTTCC
1 TTCTTTTTTC
8341 TTCTTTTTT-
1 TTCTTTTTTC
8350 TTC--TTTTC
1 TTCTTTTTTC
8358 --C-TTTTTC
1 TTCTTTTTTC
8365 TTCTTTTTTC
1 TTCTTTTTTC
8375 TTTCTTTTTTC
1 -TTCTTTTTTC
8386 TT
1 TT
8388 TTTCTCTTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
6 1 0.03
7 9 0.22
9 4 0.10
10 16 0.40
11 10 0.25
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:8375 original size:7 final size:7
Alignment explanation
Indices: 8341--8395 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
8331 TTCTTTTTCC
8341 TTCTTTT
1 TTCTTTT
8348 TT-TTCTT
1 TTCTT-TT
*
8355 TTCCTTT
1 TTCTTTT
8362 TTCTTCTT
1 TTCTT-TT
*
8370 TT-TTCT
1 TTCTTTT
8376 TTCTTTT
1 TTCTTTT
8383 TTCTTTT
1 TTCTTTT
8390 TCTCTT
1 T-TCTT
8396 CCCTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
6 5 0.13
7 25 0.64
8 9 0.23
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTCTTTT
Found at i:8385 original size:11 final size:11
Alignment explanation
Indices: 8330--8388 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
8320 GACCTCTCCT
*
8330 TTTCTTTTTCC
1 TTTCTTTTTTC
*
8341 TTCTTTTTTTTC
1 TT-TCTTTTTTC
*
8353 TTTTCCTTTTTC
1 -TTTCTTTTTTC
8365 -TTCTTTTTTC
1 TTTCTTTTTTC
8375 TTTCTTTTTTC
1 TTTCTTTTTTC
8386 TTT
1 TTT
8389 TTCTCTTCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 9 0.22
11 15 0.38
12 14 0.35
13 2 0.05
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:8405 original size:33 final size:31
Alignment explanation
Indices: 8344--8414 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 31
8334 TTTTTCCTTC
**
8344 TTTTTTTTCTTTTCCTTTTTCTTCTTTTTTCT
1 TTTTTTTTCTTTTCCTTTCCCTTCTTTTTT-T
*
8376 TTCTTTTTTCTTTTTCTCTTCCCTT-TTTTTTT
1 TT-TTTTTTCTTTTCCT-TTCCCTTCTTTTTTT
8408 TTTTTTT
1 TTTTTTT
8415 GGGATAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 5 0.15
32 5 0.15
33 19 0.56
34 5 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (31 bp):
TTTTTTTTCTTTTCCTTTCCCTTCTTTTTTT
Found at i:10943 original size:17 final size:18
Alignment explanation
Indices: 10899--10935 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10889 CCCATATGTT
10899 TGCACGGAA-GTGAAAACC
1 TGCAC-GAAGGTGAAAACC
10917 TGCACGAAGGTGAAAACC
1 TGCACGAAGGTGAAAACC
10935 T
1 T
10936 CATGAAGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.14
Consensus pattern (18 bp):
TGCACGAAGGTGAAAACC
Found at i:12252 original size:29 final size:30
Alignment explanation
Indices: 12220--12290 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
12210 GGCCAAACCC
12220 AAATTTTGGAAAGTTTGA-GGTAAAAAAAT
1 AAATTTTGGAAAGTTTGAGGGTAAAAAAAT
* *
12249 AAATTTTGGAAAGTTTGAGGGTTAAAACAT
1 AAATTTTGGAAAGTTTGAGGGTAAAAAAAT
*
12279 AATTTTTGGAAA
1 AAATTTTGGAAA
12291 ACTTAGGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 18 0.47
30 20 0.53
ACGTcount: A:0.44, C:0.01, G:0.21, T:0.34
Consensus pattern (30 bp):
AAATTTTGGAAAGTTTGAGGGTAAAAAAAT
Found at i:12288 original size:30 final size:30
Alignment explanation
Indices: 12220--12304 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 30
12210 GGCCAAACCC
*
12220 AAATTTTGGAAAGTTTGA-GGTAAAAAAAT
1 AAATTTTGGAAAGTTTGAGGGTTAAAAAAT
*
12249 AAATTTTGGAAAGTTTGAGGGTTAAAACAT
1 AAATTTTGGAAAGTTTGAGGGTTAAAAAAT
* **
12279 AATTTTTGGAAAACTT-AGGGTTAAAA
1 AAATTTTGGAAAGTTTGAGGGTTAAAA
12305 TCGAATTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 28 0.56
30 22 0.44
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (30 bp):
AAATTTTGGAAAGTTTGAGGGTTAAAAAAT
Found at i:12311 original size:29 final size:30
Alignment explanation
Indices: 12252--12314 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
12242 AAAAAATAAA
** *
12252 TTTTGGAAAGTTTGAGGGTTAAAACATAAT
1 TTTTGGAAAACTTGAGGGTTAAAACAGAAT
12282 TTTTGGAAAACTT-AGGGTTAAAATC-GAAT
1 TTTTGGAAAACTTGAGGGTTAAAA-CAGAAT
12311 TTTT
1 TTTT
12315 AAACAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (30 bp):
TTTTGGAAAACTTGAGGGTTAAAACAGAAT
Found at i:13194 original size:132 final size:132
Alignment explanation
Indices: 12918--13194 Score: 468
Period size: 132 Copynumber: 2.1 Consensus size: 132
12908 AAACTTTTCG
* ** *
12918 GTTTCAATTTTTTTTAAATGATAAAAATAAAAAGCACTCCTTTCTTTTCCGATTCCTAGACGATT
1 GTTTCAATTTTTTTTAAATGAAAAAAATAAAAAGCACTCCTTTCTCCTCCGATTCCTAGACGAAT
* *
12983 CAAAGGGACTTGAGTTTCACGATGATGGCGTACGGGGTTTGAAGGTAACCGTAAATCCCTCTCTT
66 CAAAGGGACTTGAGTTTCACGATGATGGCGTACAGGGTTTGAAGGTAACCATAAATCCCTCTCTT
13048 TT
131 TT
*
13050 GTTTCAAATTTTTTTAAATGAAAAAAATAAAAAGCACTCCTTTCTCCTCCGATTCCTAGACGAAT
1 GTTTCAATTTTTTTTAAATGAAAAAAATAAAAAGCACTCCTTTCTCCTCCGATTCCTAGACGAAT
*
13115 CAAAGGGACTTGAGTTTCACGATGATGGGGTACAGGGTTTGAAGGTAACCATAAATCCCTCTCTT
66 CAAAGGGACTTGAGTTTCACGATGATGGCGTACAGGGTTTGAAGGTAACCATAAATCCCTCTCTT
13180 TT
131 TT
13182 GTTTC--TTTTTTTT
1 GTTTCAATTTTTTTT
13195 GTTATTTTTC
Statistics
Matches: 136, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
130 7 0.05
132 129 0.95
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (132 bp):
GTTTCAATTTTTTTTAAATGAAAAAAATAAAAAGCACTCCTTTCTCCTCCGATTCCTAGACGAAT
CAAAGGGACTTGAGTTTCACGATGATGGCGTACAGGGTTTGAAGGTAACCATAAATCCCTCTCTT
TT
Found at i:19503 original size:22 final size:22
Alignment explanation
Indices: 19460--19513 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
19450 GTAAGCGTTA
*
19460 ATATTGAGATGAATGAAAATTT-
1 ATATTGA-ATTAATGAAAATTTG
*
19482 ATATTGAATTAATAGAATATTTG
1 ATATTGAATTAAT-GAAAATTTG
19505 A-ATTGAATT
1 ATATTGAATT
19514 TGAATGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.18
22 22 0.79
23 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (22 bp):
ATATTGAATTAATGAAAATTTG
Found at i:19554 original size:18 final size:18
Alignment explanation
Indices: 19531--19567 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19521 TTTGTGATCA
19531 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
19549 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
19567 A
1 A
19568 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:26860 original size:18 final size:18
Alignment explanation
Indices: 26837--26873 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
26827 TTTGTGATCA
26837 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
26855 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
26873 A
1 A
26874 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:29043 original size:21 final size:21
Alignment explanation
Indices: 29014--29071 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
29004 CAGTGCAGAC
29014 TTCTACCGATACATGTACT-AG
1 TTCTACCGATACATGTA-TAAG
* *
29035 TTTTACCGATACAAGTATAAG
1 TTCTACCGATACATGTATAAG
29056 TTCTACCGATACATGT
1 TTCTACCGATACATGT
29072 CATGCATCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (21 bp):
TTCTACCGATACATGTATAAG
Found at i:29157 original size:21 final size:21
Alignment explanation
Indices: 29131--29177 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
29121 TATCTTTTAC
*
29131 CGATATAAGCATGCAAACTAT
1 CGATATAAGCATGCAAAATAT
29152 CGATATAAGCATGCAAAATAT
1 CGATATAAGCATGCAAAATAT
29173 CGATA
1 CGATA
29178 CTTCCGTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (21 bp):
CGATATAAGCATGCAAAATAT
Found at i:29869 original size:61 final size:61
Alignment explanation
Indices: 29739--29908 Score: 227
Period size: 61 Copynumber: 2.8 Consensus size: 61
29729 TTTCACTCGT
* * * * *
29739 ATTTATTACTCACGATGACACAAAGTCATCAGACC-CTTGTT-CGCATTGGAACTCATTTC
1 ATTTAATACTCACGATGACATAAAGTCATCGGACCTCTTGTTCCGTATAGGAACTCATTTC
* * * *
29798 ATTTACTACTCATGATGACGTATAGTCATCGGACCTCTTGTTCCGTATAGGAACTCATTTC
1 ATTTAATACTCACGATGACATAAAGTCATCGGACCTCTTGTTCCGTATAGGAACTCATTTC
* *
29859 ATTTAATACTCACGATGACATACAGTCATCGGACCTCTTGTTCTGTATAG
1 ATTTAATACTCACGATGACATAAAGTCATCGGACCTCTTGTTCCGTATAG
29909 AAATTCATAT
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 29 0.30
60 6 0.06
61 61 0.64
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (61 bp):
ATTTAATACTCACGATGACATAAAGTCATCGGACCTCTTGTTCCGTATAGGAACTCATTTC
Found at i:29992 original size:51 final size:51
Alignment explanation
Indices: 29923--30052 Score: 170
Period size: 51 Copynumber: 2.5 Consensus size: 51
29913 TCATATACAT
* * * * *
29923 ACGATGTCACTAATTCATCGGACCTTTAATCCATCATGGATTCATTTACTC
1 ACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTC
* *
29974 ACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTTATTTACTC
1 ACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTC
* *
30025 ACGATGGCACTTAGTTATCGGATCCTTT
1 ACGATGACACTTAGTCATCGGA-CCTTT
30053 CGTTTATAGC
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
51 64 0.93
52 5 0.07
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (51 bp):
ACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTC
Found at i:35629 original size:3 final size:3
Alignment explanation
Indices: 35621--35667 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
35611 CGATGAAGTG
35621 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
35668 CAATGGAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:48456 original size:21 final size:22
Alignment explanation
Indices: 48430--48479 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
48420 TTTTTAATCC
* * *
48430 ATTAAATAATATATTTTTA-TA
1 ATTAAATAAAACATATTTACTA
*
48451 ATTAAAAAAAACATATTTACTA
1 ATTAAATAAAACATATTTACTA
48473 ATTAAAT
1 ATTAAAT
48480 TAGAGTTGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTAAATAAAACATATTTACTA
Found at i:52579 original size:15 final size:16
Alignment explanation
Indices: 52544--52582 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
52534 TTTTAAATAA
52544 TATAATTTATTTTTAT
1 TATAATTTATTTTTAT
52560 TATAATTT-TTTTT-T
1 TATAATTTATTTTTAT
52574 TCATAATTT
1 T-ATAATTT
52583 CTCTAACGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 12 0.55
16 8 0.36
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TATAATTTATTTTTAT
Found at i:57742 original size:40 final size:40
Alignment explanation
Indices: 57680--57785 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 40
57670 AATAGCACTA
** * *
57680 TAAACACTACATTATCATTACTGAACCAGCACTCACATTG
1 TAAACACTACAACATTACTACTGAACCAGCACTCACATTG
** * * *
57720 TAAACACTACAACATTACTACTGAACTGGTAGTGACATTG
1 TAAACACTACAACATTACTACTGAACCAGCACTCACATTG
**
57760 TAAACACTATGACATTACTACTGAAC
1 TAAACACTACAACATTACTACTGAAC
57786 TGGCAGTGAC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (40 bp):
TAAACACTACAACATTACTACTGAACCAGCACTCACATTG
Found at i:57814 original size:40 final size:40
Alignment explanation
Indices: 57714--57816 Score: 152
Period size: 40 Copynumber: 2.6 Consensus size: 40
57704 ACCAGCACTC
* *
57714 ACATTGTAAACACTACAACATTACTACTGAACTGGTAGTG
1 ACATTGTAAACACTACGACATTACTACTGAACTGGCAGTG
*
57754 ACATTGTAAACACTATGACATTACTACTGAACTGGCAGTG
1 ACATTGTAAACACTACGACATTACTACTGAACTGGCAGTG
** *
57794 ACATTGTAATTACTGCGACATTA
1 ACATTGTAAACACTACGACATTA
57817 TTATTAAACT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (40 bp):
ACATTGTAAACACTACGACATTACTACTGAACTGGCAGTG
Found at i:57827 original size:40 final size:40
Alignment explanation
Indices: 57714--57846 Score: 142
Period size: 40 Copynumber: 3.4 Consensus size: 40
57704 ACCAGCACTC
* * *
57714 ACATTGTAAACACTACAACATTACTACTGAACTGGTAGTG
1 ACATTGTAAACACTACGACATTACTACTAAACTGGCAGTG
* *
57754 ACATTGTAAACACTATGACATTACTACTGAACTGGCAGTG
1 ACATTGTAAACACTACGACATTACTACTAAACTGGCAGTG
** * * * *
57794 ACATTGTAATTACTGCGACATTATTATTAAACTGGGA-TG
1 ACATTGTAAACACTACGACATTACTACTAAACTGGCAGTG
* *
57833 ATACTGTAAACACT
1 ACATTGTAAACACT
57847 GCATTATAGT
Statistics
Matches: 78, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
39 12 0.15
40 66 0.85
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (40 bp):
ACATTGTAAACACTACGACATTACTACTAAACTGGCAGTG
Found at i:60785 original size:37 final size:40
Alignment explanation
Indices: 60744--60822 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 40
60734 TATTTTAATG
*
60744 ATTTTAATG-ATTTTT-AA-TTTTTAAAAATA-AATTATAT
1 ATTTT-ATGTATTTTTAAATTTTTTAAAAAAATAATTATAT
*
60781 ATTTTTTGTATTTTTAAATTTTTTTAAAAAAATAATTATAT
1 ATTTTATGTATTTTTAAA-TTTTTTAAAAAAATAATTATAT
60822 A
1 A
60823 AACATGTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
36 2 0.06
37 11 0.31
38 2 0.06
40 11 0.31
41 9 0.26
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (40 bp):
ATTTTATGTATTTTTAAATTTTTTAAAAAAATAATTATAT
Found at i:61412 original size:24 final size:24
Alignment explanation
Indices: 61385--61432 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
61375 TTTCCTCTGA
61385 CTTGTTCAGATCTTTTATTGACAT
1 CTTGTTCAGATCTTTTATTGACAT
61409 CTTGTTCAGATCTTTTATTGACAT
1 CTTGTTCAGATCTTTTATTGACAT
61433 AGAAGGCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (24 bp):
CTTGTTCAGATCTTTTATTGACAT
Found at i:63550 original size:24 final size:21
Alignment explanation
Indices: 63528--63569 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
63518 TCTTCTTTCG
63528 CCTTTTCTACAGCTTCTTTTTT
1 CCTTTTCT-CAGCTTCTTTTTT
*
63550 CTTTTTCTCAGCTTCTTTTT
1 CCTTTTCTCAGCTTCTTTTT
63570 ATTTCTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.07, C:0.26, G:0.05, T:0.62
Consensus pattern (21 bp):
CCTTTTCTCAGCTTCTTTTTT
Done.