Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001533.1 Kokia drynarioides strain JFW-HI SEQ_113102, 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: 116383
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 123 characters in sequence are not A, C, G, or T
Found at i:2496 original size:29 final size:29
Alignment explanation
Indices: 2462--2595 Score: 121
Period size: 30 Copynumber: 4.5 Consensus size: 29
2452 GTAAAAGGGT
* *
2462 ATTTTTTGAAAGTTTTGGGGTCAAAATGAA
1 ATTTTTGGAAAG-TTTGGGGTCAAAATAAA
* *
2492 ATTTTTGGAAACTTTGAGGGTAAAAATAAA
1 ATTTTTGGAAAGTTTG-GGGTCAAAATAAA
*
2522 ATTTTTGGAAAGTTTGGGGTCAAAAATATA
1 ATTTTTGGAAAGTTTGGGGTC-AAAATAAA
* * *
2552 A-TTTTGGAGAA-TTCGAGGGTTAAAATATA
1 ATTTTTGGA-AAGTTTG-GGGTCAAAATAAA
2581 ATTTTT-GAACAGTTT
1 ATTTTTGGAA-AGTTT
2596 AGGAGCCTCC
Statistics
Matches: 87, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
28 1 0.01
29 30 0.34
30 56 0.64
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.38
Consensus pattern (29 bp):
ATTTTTGGAAAGTTTGGGGTCAAAATAAA
Found at i:2527 original size:59 final size:59
Alignment explanation
Indices: 2464--2595 Score: 164
Period size: 59 Copynumber: 2.2 Consensus size: 59
2454 AAAAGGGTAT
*
2464 TTTTTGAAAGTTTTGGGGTC-AAAATGA-AATTTTTGGA-AACTTTGAGGGTAAAAATAAAA
1 TTTTTGAAAGTTTTGGGGTCAAAAAT-ATAA-TTTTGGAGAA-TTCGAGGGTAAAAATAAAA
* *
2523 TTTTTGGAAAG-TTTGGGGTCAAAAATATAATTTTGGAGAATTCGAGGGTTAAAATATAA
1 TTTTT-GAAAGTTTTGGGGTCAAAAATATAATTTTGGAGAATTCGAGGGTAAAAATAAAA
2582 TTTTTGAACAGTTT
1 TTTTTGAA-AGTTT
2596 AGGAGCCTCC
Statistics
Matches: 64, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
58 3 0.05
59 45 0.70
60 16 0.25
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (59 bp):
TTTTTGAAAGTTTTGGGGTCAAAAATATAATTTTGGAGAATTCGAGGGTAAAAATAAAA
Found at i:3855 original size:206 final size:205
Alignment explanation
Indices: 3487--4182 Score: 914
Period size: 206 Copynumber: 3.4 Consensus size: 205
3477 TCTGGTTTCA
* * * * ** * ** *
3487 TTGACTTGGCCTTTTTCTCAGTATCTCATCAGGAAGGTGACCGCATCACTTATTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* * * * *
3552 CTCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCCA-TATCTCATC-AGAAAGCTAATC
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT-CAGTATCTCATCAAG-AAGCTAACC
* * * * *
3615 ACTTTATTGCTTTGACCTGCTCCTCAGTATCTCATCCAGAAGCAAGGGTTCGAAGATTTGCTCAC
129 ATTTTATTGCTTCGACCCGCTTCTCAGTATCTCAT-CAGAAGCAAGGATTCGAAGATTTGCTCAC
3680 ATCGAGCGTGGGT
193 ATCGAGCGTGGGT
** *
3693 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGGGTCGTTTGTTTCAATCCGTTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* *
3758 CTCTGTATCACATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
*
3823 TTTATTGCTTCGACCCGCTTCTAAGTATCTCATCAGAAAG-ATAGGATTCGAAGATTTGCTCACA
131 TTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAG-AAGCA-AGGATTCGAAGATTTGCTCACA
*
3887 TCGAGCGTTGGT
194 TCGAGCGTGGGT
* *
3899 TTGATTTAGTCTTCTTCTCAGTATC-CTATCAGGAAGATGACCGCATCGTTTGTTTCAATCTGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTC-ATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCT
* * * *
3963 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTTATCAGGAAGCTAACTA
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCA
* * * *
4028 TTTTATTGCTTCGAACCGCTTCTCAGTATCTCATCAGGAAGCTATGATTCGAAGATTTACTCACA
130 TTTTATTGCTTCGACCCGCTTCTCAGTATCTCATCA-GAAGCAAGGATTCGAAGATTTGCTCACA
* *
4093 TTGAGCATGGGT
194 TCGAGCGTGGGT
* * *
4105 TTGATTTGGTCTTTTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
*
4170 CTCAGTATCTCAT
66 CTCTGTATCTCAT
4183 GAAGAAGCTA
Statistics
Matches: 430, Mismatches: 52, Indels: 16
0.86 0.10 0.03
Matches are distributed among these distances:
205 7 0.02
206 419 0.97
207 4 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (205 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
TTTATTGCTTCGACCCGCTTCTCAGTATCTCATCAGAAGCAAGGATTCGAAGATTTGCTCACATC
GAGCGTGGGT
Found at i:4388 original size:39 final size:39
Alignment explanation
Indices: 4345--4562 Score: 154
Period size: 39 Copynumber: 5.6 Consensus size: 39
4335 CTCCATGATT
* *
4345 GGGGTAGGAGTTTGGTTGACGATGATCTGCCTCAAGCTC
1 GGGGTAAGAGATTGGTTGACGATGATCTGCCTCAAGCTC
* ** * * **
4384 GGGGTAAGAGATCGAATGGCTG-TAATCTGCCTCTGGCTC
1 GGGGTAAGAGATTGGTTGAC-GATGATCTGCCTCAAGCTC
* *
4423 GAGGTAAGAGATTGGTTGATGATGATCTGCCTCAAGCTC
1 GGGGTAAGAGATTGGTTGACGATGATCTGCCTCAAGCTC
* **** * * * *
4462 GGGGTAAAAGATCAAATGGC-TTCAATCTGCC-CTAGGCTC
1 GGGGTAAGAGATTGGTTGACGAT-GATCTGCCTC-AAGCTC
* * * *
4501 GGGTTAAGAGACTGGTTGATGATGATCTGCCCCAAGCTC
1 GGGGTAAGAGATTGGTTGACGATGATCTGCCTCAAGCTC
* *
4540 GGGATAAGAGATTGGTTAACGAT
1 GGGGTAAGAGATTGGTTGACGAT
4563 ATAGCTTCAC
Statistics
Matches: 128, Mismatches: 45, Indels: 12
0.69 0.24 0.06
Matches are distributed among these distances:
38 3 0.02
39 122 0.95
40 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (39 bp):
GGGGTAAGAGATTGGTTGACGATGATCTGCCTCAAGCTC
Found at i:4456 original size:78 final size:77
Alignment explanation
Indices: 4346--4551 Score: 290
Period size: 78 Copynumber: 2.6 Consensus size: 77
4336 TCCATGATTG
* * * *
4346 GGGTAGGAGTTTGGTTGACGATGATCTGCCTCAAGCTCGGGGTAAGAGATCGAATGGCTGT-AAT
1 GGGTAAGAGATTGGTTGATGATGATCTGCCTCAAGCTCGGGGTAAGAGATCAAATGGCT-TCAAT
4410 CTGCCTCT-GGCTC
65 CTGCC-CTAGGCTC
*
4423 GAGGTAAGAGATTGGTTGATGATGATCTGCCTCAAGCTCGGGGTAAAAGATCAAATGGCTTCAAT
1 G-GGTAAGAGATTGGTTGATGATGATCTGCCTCAAGCTCGGGGTAAGAGATCAAATGGCTTCAAT
4488 CTGCCCTAGGCTC
65 CTGCCCTAGGCTC
* * *
4501 GGGTTAAGAGACTGGTTGATGATGATCTGCCCCAAGCTCGGGATAAGAGAT
1 GGG-TAAGAGATTGGTTGATGATGATCTGCCTCAAGCTCGGGGTAAGAGAT
4552 TGGTTAACGA
Statistics
Matches: 116, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
77 6 0.05
78 110 0.95
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (77 bp):
GGGTAAGAGATTGGTTGATGATGATCTGCCTCAAGCTCGGGGTAAGAGATCAAATGGCTTCAATC
TGCCCTAGGCTC
Found at i:5131 original size:49 final size:48
Alignment explanation
Indices: 5078--5281 Score: 130
Period size: 49 Copynumber: 4.2 Consensus size: 48
5068 GGTTTAGATA
* *
5078 TTTCCCTTTATGTCTCTGAGGTACAAGG-TCTGCCGTTACTACTTAAATC
1 TTTCCCTTTATGTCT-TGAGGTAC-AGGATCCGCCGTTACGACTTAAATC
* * * * *
5127 TTTCCC-TTGTGTCTTCATGGTACTGGATCCGCCGTTGCGACTTAGATC
1 TTTCCCTTTATGTCTTGA-GGTACAGGATCCGCCGTTACGACTTAAATC
* * * * * *
5175 TTTCCCTTCATGTCTTCGCGGCACTGGATCCGTCGTTAC-AGCTTAGATC
1 TTTCCCTTTATGTCTT-GAGGTACAGGATCCGCCGTTACGA-CTTAAATC
* * * * *
5224 TTT-CCTGTCATGTCTCTGAGGTATAAGG-TCTGCCGTTGCGACTTAAACC
1 TTTCCCT-TTATGTCT-TGAGGTA-CAGGATCCGCCGTTACGACTTAAATC
*
5273 CTTCCCTTT
1 TTTCCCTTT
5282 CGTATCTTTA
Statistics
Matches: 120, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
47 4 0.03
48 39 0.32
49 70 0.58
50 7 0.06
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (48 bp):
TTTCCCTTTATGTCTTGAGGTACAGGATCCGCCGTTACGACTTAAATC
Found at i:5161 original size:48 final size:48
Alignment explanation
Indices: 5109--5238 Score: 147
Period size: 49 Copynumber: 2.7 Consensus size: 48
5099 TACAAGGTCT
* * * *
5109 GCCGTTACTACTTAAATCTTTCCCTT-GTGTCTTCATGGTACTGGATCC
1 GCCGTTAC-ACTTAGATCTTTCCCTTCATGTCTTCACGGCACTGGATCC
* *
5157 GCCGTTGCGACTTAGATCTTTCCCTTCATGTCTTCGCGGCACTGGATCC
1 GCCGTTAC-ACTTAGATCTTTCCCTTCATGTCTTCACGGCACTGGATCC
*
5206 GTCGTTACAGCTTAGATCTTT-CCTGTCATGTCT
1 GCCGTTACA-CTTAGATCTTTCCCT-TCATGTCT
5239 CTGAGGTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
48 27 0.39
49 43 0.61
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.38
Consensus pattern (48 bp):
GCCGTTACACTTAGATCTTTCCCTTCATGTCTTCACGGCACTGGATCC
Found at i:5188 original size:97 final size:98
Alignment explanation
Indices: 4942--5189 Score: 250
Period size: 97 Copynumber: 2.5 Consensus size: 98
4932 CCCTTCAAAA
* * * * * *
4942 CTTCATGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCTTTCTTATCTTCTGAGGTTCAAGG
1 CTTCATGGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTC-TCTGAGGTACAAGG
* *
5007 TAAACCGTTGTGACTTAAACATTTCCTTTTTGTAT
65 TAAACCGTTCTGACTTAAACATTTCC-TCTTGTAT
** * * * * *
5042 CTTTGTGGTACTGGATTCACCGTTACGGTTTAGATATTTCCCTTTATGTCTCTGAGGTACAAGGT
1 CTTCATGGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGT
*** *
5107 CTGCCGTTACT-ACTTAAATC-TTTCC-CTTGTGT
66 AAACCGTT-CTGACTTAAA-CATTTCCTCTTGTAT
* *
5139 CTTCATGGTACTGGATCCGCCGTTGCGACTTAGATCTTTCCCTTCATGTCT
1 CTTCATGGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCT
5190 TCGCGGCACT
Statistics
Matches: 118, Mismatches: 28, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
97 47 0.40
99 31 0.26
100 40 0.34
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (98 bp):
CTTCATGGTACTGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGT
AAACCGTTCTGACTTAAACATTTCCTCTTGTAT
Found at i:5406 original size:100 final size:99
Alignment explanation
Indices: 5196--5436 Score: 288
Period size: 100 Copynumber: 2.4 Consensus size: 99
5186 GTCTTCGCGG
* * *
5196 CACTGGATCCGTCGTTACAG-CTTAGATCTTTCCTGTCATGTCTCTGAGGTATAAGGTCTGCCGT
1 CACTAGATCCGCCATTACAGTCTTAGATCTTTCC-GTCATGTCTCTGAGGTATAAGGTCTGCCGT
*
5260 TGCGACTTAAACCCTTCCCTTTCGTATCTTTACGA
65 TGCGACTTAAACCCTTCCATTTCGTATCTTTACGA
* * * *
5295 CACTAGATCCGCCATTGCGGTCTTAAATCTTTCTCGTCATGTCTCTGAGGTATAAGGT-TCGCTG
1 CACTAGATCCGCCATTACAGTCTTAGATCTTTC-CGTCATGTCTCTGAGGTATAAGGTCT-GCCG
* *
5359 TTGCGACTTAAACCCTTCCATTTTGTATCTTTACGG
64 TTGCGACTTAAACCCTTCCATTTCGTATCTTTACGA
* * * * **
5395 TATTGGTTCCGCTGTTACAGTCTTAGATCTTTCCCGTCATGT
1 CACTAGATCCGCCATTACAGTCTTAGATCTTT-CCGTCATGT
5437 TTCATGGTGC
Statistics
Matches: 119, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
99 16 0.13
100 101 0.85
101 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (99 bp):
CACTAGATCCGCCATTACAGTCTTAGATCTTTCCGTCATGTCTCTGAGGTATAAGGTCTGCCGTT
GCGACTTAAACCCTTCCATTTCGTATCTTTACGA
Found at i:6699 original size:10 final size:10
Alignment explanation
Indices: 6637--6728 Score: 53
Period size: 10 Copynumber: 8.9 Consensus size: 10
6627 CGACCTCTCC
6637 TTTTCTTTTTCT
1 TTTTC-TTTT-T
*
6649 TTTTCTCTTT
1 TTTTCTTTTT
* *
6659 TTTT-TATTA
1 TTTTCTTTTT
* *
6668 TTTTATTATT
1 TTTTCTTTTT
* *
6678 TATTATTATTT
1 TTTTCTT-TTT
6689 TTTTCTTTTT
1 TTTTCTTTTT
6699 TTTTCTTTTT
1 TTTTCTTTTT
*
6709 CTTCTT-TTTTC
1 -TT-TTCTTTTT
6720 TTTTCTTTT
1 TTTTCTTTT
6729 ATTCATTGAA
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
9 9 0.14
10 32 0.50
11 16 0.25
12 7 0.11
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:6709 original size:16 final size:16
Alignment explanation
Indices: 6688--6728 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
6678 TATTATTATT
6688 TTTTTCTTTTTTTTTC
1 TTTTTCTTTTTTTTTC
*
6704 TTTTTCTTCTTTTTTC
1 TTTTTCTTTTTTTTTC
6720 -TTTTCTTTT
1 TTTTTCTTTT
6729 ATTCATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:12335 original size:59 final size:58
Alignment explanation
Indices: 12180--12349 Score: 150
Period size: 59 Copynumber: 2.9 Consensus size: 58
12170 TGGACTCTAG
* * * *
12180 GGGGTAAAACAGTAATTTTATGAAAGTTT-GGGGTTTAAAAATGGAA-CTTTAGACATCC
1 GGGGTAAAACGGTAATTTT-TGAAAGTTTCGGGG-TCAAAAATGGAATTTTTGGACATCC
* * * ** * * *
12238 GGGAGCAAAATGGTAACTTTTAGAAA-AATCGAGATCAAAAATAGAATTTTTGGACATCCC
1 GGG-GTAAAACGGTAA-TTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGACAT-CC
*
12298 GGGGTAAAAGGGTAATTTTTGAAAGTTTCGGGGTC-AAAATGGAATTTTTGGA
1 GGGGTAAAACGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGA
12350 AGTTCAGGGG
Statistics
Matches: 86, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
58 38 0.44
59 39 0.45
60 9 0.10
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (58 bp):
GGGGTAAAACGGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGACATCC
Found at i:12360 original size:58 final size:57
Alignment explanation
Indices: 12275--12422 Score: 147
Period size: 58 Copynumber: 2.6 Consensus size: 57
12265 ATCGAGATCA
* * * * *
12275 AAAATAGAATTTTTGGACA-TCCCGGGGTAAAAGGGTAATTTTTGAAAGTTTCGGGGTC
1 AAAATAGAATTTTTGGA-AGTTCAGGGGTAAAAGGGAAATTTTGGAAAGTTT-AGGGTC
* ** *
12333 AAAATGGAATTTTTGGAAGTTCAGGGGTAAAATTGAAATTTTGGAAAGTTTAGGGTT
1 AAAATAGAATTTTTGGAAGTTCAGGGGTAAAAGGGAAATTTTGGAAAGTTTAGGGTC
* *
12390 AAAATATAATTTTGGAGAAG-TCAGGGGTTAAAA
1 AAAATAGAATTTTTG-GAAGTTCAGGGG-TAAAA
12423 TATAATTTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
57 24 0.32
58 51 0.68
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (57 bp):
AAAATAGAATTTTTGGAAGTTCAGGGGTAAAAGGGAAATTTTGGAAAGTTTAGGGTC
Found at i:12365 original size:28 final size:28
Alignment explanation
Indices: 12275--12432 Score: 115
Period size: 29 Copynumber: 5.5 Consensus size: 28
12265 ATCGAGATCA
* *
12275 AAAATAGAATTTTTGGACA-TCCCGGGGT
1 AAAATAGAATTTTTGGA-AGTTCAGGGGT
** *
12303 AAAAGGGTAATTTTTGAAAGTTTC-GGGGT
1 AAAATAG-AATTTTTGGAAG-TTCAGGGGT
*
12332 CAAAATGGAATTTTTGGAAGTTCAGGGGT
1 -AAAATAGAATTTTTGGAAGTTCAGGGGT
* * * *
12361 AAAATTGAAATTTTGGAAAGTTTAGGGTT
1 AAAATAGAATTTTTGG-AAGTTCAGGGGT
* *
12390 AAAATATAATTTTGGAGAAG-TCAGGGGTT
1 AAAATAGAATTTTTG-GAAGTTCAGGGG-T
*
12419 AAAATATAATTTTT
1 AAAATAGAATTTTT
12433 TGACAGTTTA
Statistics
Matches: 105, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
28 28 0.27
29 68 0.65
30 9 0.09
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.34
Consensus pattern (28 bp):
AAAATAGAATTTTTGGAAGTTCAGGGGT
Found at i:13531 original size:3 final size:3
Alignment explanation
Indices: 13525--13577 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
13515 TTTTTAATAC
*
13525 TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
13571 TAA TAT T
1 TAT TAT T
13578 CATTCAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:14363 original size:17 final size:17
Alignment explanation
Indices: 14307--14399 Score: 87
Period size: 17 Copynumber: 5.4 Consensus size: 17
14297 CTTTATTTAT
* * *
14307 TTTAAATTTATAATAAT
1 TTTAAACTTAAAATAAA
*
14324 TTTAAATTTGAAAATAAA
1 TTTAAACTT-AAAATAAA
* *
14342 ATTAAACTTAAATTAAA
1 TTTAAACTTAAAATAAA
* *
14359 TTTAAATTTTAAAACAAA
1 TTTAAA-CTTAAAATAAA
*
14377 TTTAATCTTAAAATAAA
1 TTTAAACTTAAAATAAA
14394 TTTAAA
1 TTTAAA
14400 ATGAGTTTGG
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
17 35 0.57
18 26 0.43
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:14363 original size:35 final size:35
Alignment explanation
Indices: 14308--14399 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 35
14298 TTTATTTATT
* * * *
14308 TTAAATTTATAATAATTTTAAATTTGAAAATAAAA
1 TTAAACTTAAAATAAATTTAAATTTGAAAACAAAA
* * *
14343 TTAAACTTAAATTAAATTTAAATTTTAAAACAAAT
1 TTAAACTTAAAATAAATTTAAATTTGAAAACAAAA
*
14378 TTAATCTTAAAATAAATTTAAA
1 TTAAACTTAAAATAAATTTAAA
14400 ATGAGTTTGG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (35 bp):
TTAAACTTAAAATAAATTTAAATTTGAAAACAAAA
Found at i:23194 original size:83 final size:83
Alignment explanation
Indices: 23021--23429 Score: 630
Period size: 83 Copynumber: 5.0 Consensus size: 83
23011 ATGCGGCAAT
* * *
23021 TTGAATTCGGTTAATGTATATATTTAATTGCTTTTAATTTATTTTAAAATT-TCA-TTTTTATGA
1 TTGAATTTGGTTAATGTATATATTTAATGGCTTTTAATTTATTTT-AAATTGTTATTTTTTATGA
*
23084 ACTTATTTGGTGAACATAG
65 ACTTATTTGGTGAACATAA
* *
23103 TTGAATTTGGTTGATGTATATATTCAATGGCTTTTAATTTATTTTAAATTGTTATTTTTTATGAA
1 TTGAATTTGGTTAATGTATATATTTAATGGCTTTTAATTTATTTTAAATTGTTATTTTTTATGAA
23168 CTTATTTGGTGAACATAA
66 CTTATTTGGTGAACATAA
* *
23186 TTGAATTTGGTTAATGTATGTATTTAATGGTTTTTAATTTATTTTAAATTGTTATTTTTTATGAA
1 TTGAATTTGGTTAATGTATATATTTAATGGCTTTTAATTTATTTTAAATTGTTATTTTTTATGAA
23251 CTTATTTGGTGAACATAA
66 CTTATTTGGTGAACATAA
*
23269 TTGAATTTGGTTGATGTATATATTTAATGGCTTTTAATTTATTTTAAATTGTTATTTTTTATGAA
1 TTGAATTTGGTTAATGTATATATTTAATGGCTTTTAATTTATTTTAAATTGTTATTTTTTATGAA
23334 CTTATTTGGTGAACA-AA
66 CTTATTTGGTGAACATAA
* ** * * *
23351 TTGAATTTGGTTAATGTATGCT-TTTAATTCCTTTTAATTTATTTGAAGTTGTCATTTTTTATGA
1 TTGAATTTGGTTAATGTAT-ATATTTAATGGCTTTTAATTTATTTTAAATTGTTATTTTTTATGA
23415 ACTTATTTGG-GAACA
65 ACTTATTTGGTGAACA
23430 CTCTCATGAG
Statistics
Matches: 304, Mismatches: 20, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
81 10 0.03
82 110 0.36
83 184 0.61
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (83 bp):
TTGAATTTGGTTAATGTATATATTTAATGGCTTTTAATTTATTTTAAATTGTTATTTTTTATGAA
CTTATTTGGTGAACATAA
Found at i:23355 original size:165 final size:166
Alignment explanation
Indices: 23021--23429 Score: 675
Period size: 165 Copynumber: 2.5 Consensus size: 166
23011 ATGCGGCAAT
* *
23021 TTGAATTCGGTTAATGTATATATTTAATTGCTTTTAATTTATTTTAAAATT-TCA-TTTTTATGA
1 TTGAATTTGGTTAATGTATGTATTTAATTGCTTTTAATTTATTTT-AAATTGTCATTTTTTATGA
*
23084 ACTTATTTGGTGAACATAGTTGAATTTGGTTGATGTATATATTCAATGGCTTTTAATTTATTTTA
65 ACTTATTTGGTGAACATAATTGAATTTGGTTGATGTATATATTCAATGGCTTTTAATTTATTTTA
23149 AATTGTTATTTTTTATGAACTTATTTGGTGAACATAA
130 AATTGTTATTTTTTATGAACTTATTTGGTGAACATAA
* * *
23186 TTGAATTTGGTTAATGTATGTATTTAATGGTTTTTAATTTATTTTAAATTGTTATTTTTTATGAA
1 TTGAATTTGGTTAATGTATGTATTTAATTGCTTTTAATTTATTTTAAATTGTCATTTTTTATGAA
*
23251 CTTATTTGGTGAACATAATTGAATTTGGTTGATGTATATATTTAATGGCTTTTAATTTATTTTAA
66 CTTATTTGGTGAACATAATTGAATTTGGTTGATGTATATATTCAATGGCTTTTAATTTATTTTAA
23316 ATTGTTATTTTTTATGAACTTATTTGGTGAACA-AA
131 ATTGTTATTTTTTATGAACTTATTTGGTGAACATAA
* * *
23351 TTGAATTTGGTTAATGTATGCT-TTTAATTCCTTTTAATTTATTTGAAGTTGTCATTTTTTATGA
1 TTGAATTTGGTTAATGTATG-TATTTAATTGCTTTTAATTTATTTTAAATTGTCATTTTTTATGA
23415 ACTTATTTGG-GAACA
65 ACTTATTTGGTGAACA
23430 CTCTCATGAG
Statistics
Matches: 228, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
164 10 0.04
165 111 0.49
166 107 0.47
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (166 bp):
TTGAATTTGGTTAATGTATGTATTTAATTGCTTTTAATTTATTTTAAATTGTCATTTTTTATGAA
CTTATTTGGTGAACATAATTGAATTTGGTTGATGTATATATTCAATGGCTTTTAATTTATTTTAA
ATTGTTATTTTTTATGAACTTATTTGGTGAACATAA
Found at i:27739 original size:138 final size:137
Alignment explanation
Indices: 27487--27900 Score: 699
Period size: 138 Copynumber: 3.0 Consensus size: 137
27477 AAGCAACTAG
27487 AGAAGAAAAACTGGAAAAGACGAGGAATTGGGCCAAGAAAGATGGAGGAGGATCTGATTTGTCTG
1 AGAAGAAAAACTGGAAAAGACGAGGAATTGGGCCAAGAAAGATGGAGGAGGATC-GATTTGTCTG
*
27552 CTTCAAACTCGAGGCAGGTGAATGCTGTTAATAATAATGAAACTGATACCATTGGATATAGACAA
65 CTTCAAACTCGAGGCAGGTGAATGCTGTTAATAATAATGAAACTAATACCATTGGATATAGACAA
27617 TATGATCC
130 TATGATCC
* *
27625 AGAAGAAAAACCGGAAAAGACGAGGAATTGGGCCAAGAAAGATGGAGGAGGATCCGATAAT-TCT
1 AGAAGAAAAACTGGAAAAGACGAGGAATTGGGCCAAGAAAGATGGAGGAGGAT-CGAT-TTGTCT
* *
27689 GCTTCAAACTTGAGGCAGGTGAATGCTGTTAATAATAATGAAACTAATACCGTTGGATATAGACA
64 GCTTCAAACTCGAGGCAGGTGAATGCTGTTAATAATAATGAAACTAATACCATTGGATATAGACA
27754 ATATGATCC
129 ATATGATCC
* *
27763 AGAAGAAAAACTGGAAAAGATGAGGAATTGGGCCAAGAAAGATGGAGGA-TAT-GATTTGTCTGC
1 AGAAGAAAAACTGGAAAAGACGAGGAATTGGGCCAAGAAAGATGGAGGAGGATCGATTTGTCTGC
* *
27826 TTCAAACTCGAGGCAGGTGAATGCTGTTAATAATAACGAAACTAATCCCATTGGATATAGACAAT
66 TTCAAACTCGAGGCAGGTGAATGCTGTTAATAATAATGAAACTAATACCATTGGATATAGACAAT
27891 ATGATCC
131 ATGATCC
27898 AGA
1 AGA
27901 GCCTCCTACT
Statistics
Matches: 260, Mismatches: 13, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
134 1 0.00
135 79 0.30
137 2 0.01
138 176 0.68
139 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.22
Consensus pattern (137 bp):
AGAAGAAAAACTGGAAAAGACGAGGAATTGGGCCAAGAAAGATGGAGGAGGATCGATTTGTCTGC
TTCAAACTCGAGGCAGGTGAATGCTGTTAATAATAATGAAACTAATACCATTGGATATAGACAAT
ATGATCC
Found at i:31016 original size:29 final size:29
Alignment explanation
Indices: 30984--31043 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
30974 GAAAAGAAAA
30984 ATAAAATTATATAATAAAAAGTAGGCCGG
1 ATAAAATTATATAATAAAAAGTAGGCCGG
31013 ATAAAATTATATAATAAAAAGTAGGCCGG
1 ATAAAATTATATAATAAAAAGTAGGCCGG
31042 AT
1 AT
31044 CAAACTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.25
Consensus pattern (29 bp):
ATAAAATTATATAATAAAAAGTAGGCCGG
Found at i:39185 original size:31 final size:29
Alignment explanation
Indices: 39134--39193 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
39124 CATTTAATTA
*
39134 AAAAAATTAAATTTGATCACTGAAATATT
1 AAAAAATTAAATTTAATCACTGAAATATT
* *
39163 AAAAAATTCACATTTAAGTCACTGAATTATT
1 AAAAAATT-AAATTTAA-TCACTGAAATATT
39194 TAAATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 6 0.23
31 12 0.46
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (29 bp):
AAAAAATTAAATTTAATCACTGAAATATT
Found at i:39727 original size:14 final size:13
Alignment explanation
Indices: 39687--39734 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
39677 TTTAATGTGT
*
39687 AATTGTATACATG
1 AATTTTATACATG
*
39700 AATTTTATTTCATG
1 AATTTTA-TACATG
39714 CAATTTTATACATG
1 -AATTTTATACATG
39728 AAATTTT
1 -AATTTT
39735 GATTTGATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 6 0.21
14 16 0.55
15 7 0.24
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTTTATACATG
Found at i:42808 original size:28 final size:27
Alignment explanation
Indices: 42777--42838 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
42767 AAAATTTACC
*
42777 CTTTTTTATTCTGTTTTTTAAATTAAAT
1 CTTTTTTATTAT-TTTTTTAAATTAAAT
* *
42805 CTTTTATTTTTATTTTTTTAAATTCAAT
1 CTTTT-TTATTATTTTTTTAAATTAAAT
*
42833 CATTTT
1 CTTTTT
42839 ACTCCTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 1 0.03
28 23 0.79
29 5 0.17
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (27 bp):
CTTTTTTATTATTTTTTTAAATTAAAT
Found at i:47221 original size:14 final size:13
Alignment explanation
Indices: 47202--47256 Score: 74
Period size: 14 Copynumber: 4.1 Consensus size: 13
47192 AATTTCACCC
47202 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
*
47215 GAAAAAAAGAAAA
1 AAAAAAAAGAAAA
*
47228 AGAAGAAAAGAAAA
1 A-AAAAAAAGAAAA
47242 AGAAAAAAAGAAAA
1 A-AAAAAAAGAAAA
47256 A
1 A
47257 TGAGAGGTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
13 12 0.32
14 25 0.68
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:47233 original size:22 final size:22
Alignment explanation
Indices: 47202--47253 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
47192 AATTTCACCC
*
47202 AAAAAAAAGAAAAGAAAAA-AA
1 AAAAAGAAGAAAAGAAAAAGAA
47223 GAAAAAGAAGAAAAGAAAAAGAA
1 -AAAAAGAAGAAAAGAAAAAGAA
47246 AAAAAGAA
1 AAAAAGAA
47254 AAATGAGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAGAAAAGAAAAAGAA
Found at i:47256 original size:6 final size:6
Alignment explanation
Indices: 47205--47248 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
47195 TTCACCCAAA
*
47205 AAAAAG AAAAGAA AAAAAG AAAAAG AAGAAAAG AAAAAG AAAAA
1 AAAAAG AAAA-AG AAAAAG AAAAAG -A-AAAAG AAAAAG AAAAA
47249 AAGAAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 21 0.64
7 7 0.21
8 5 0.15
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:48286 original size:49 final size:49
Alignment explanation
Indices: 48230--48473 Score: 224
Period size: 49 Copynumber: 5.0 Consensus size: 49
48220 CTAGAAGACA
* * *
48230 TGAAGGGAAAGTTTGAAGCCACAATGGTGAATCTTATACCTTAAAGATG
1 TGAAGGGAAAGATTGAAGCCACAATGGCGAATCTTATACCCTAAAGATG
* * * * * * * *
48279 TGAAGGGAGAGATTGAAGCCGCTATGACGAATCATGTACCCTAGAGATA
1 TGAAGGGAAAGATTGAAGCCACAATGGCGAATCTTATACCCTAAAGATG
* ** * *
48328 T-AGAGGGAAAGGTTGAAGCCGTAATGACGAACCTTATACCCTAAAGATG
1 TGA-AGGGAAAGATTGAAGCCACAATGGCGAATCTTATACCCTAAAGATG
* * * * * *
48377 TGGAGGGAAAGGTTGAAG-CATAACGGCGAACCTTATACCTTAGAA-ATG
1 TGAAGGGAAAGATTGAAGCCACAATGGCGAATCTTATACCCTA-AAGATG
* * *
48425 TGAAGGGAAAAATTGAAGCCACAACGGTGAATCTTATACCCTAAAGATG
1 TGAAGGGAAAGATTGAAGCCACAATGGCGAATCTTATACCCTAAAGATG
48474 AGGAGAAGTA
Statistics
Matches: 158, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
48 41 0.26
49 117 0.74
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (49 bp):
TGAAGGGAAAGATTGAAGCCACAATGGCGAATCTTATACCCTAAAGATG
Found at i:48568 original size:21 final size:21
Alignment explanation
Indices: 48544--48596 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
48534 GCGAATCTCA
48544 AAGCTGTAAAGAATTAGATTG
1 AAGCTGTAAAGAATTAGATTG
48565 AAGCTGTAAAGAATTAGATTG
1 AAGCTGTAAAGAATTAGATTG
*
48586 AAGCTATAAAG
1 AAGCTGTAAAG
48597 GCTTACTTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (21 bp):
AAGCTGTAAAGAATTAGATTG
Found at i:49065 original size:40 final size:40
Alignment explanation
Indices: 49006--49150 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
48996 TACGTCATCA
49006 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
* * * * *
49046 CATTCAATCTTTTACCCTAACCATAGGGTAAATTGAAACAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTG-AAGAC
* * * *
49087 CATCCGATCTCTTACCCCAACCATAGGGCAGATTGAAG-C
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
* *
49126 AACCCAATCTTTTACCCTAACCAGA
1 CATCCAATCTTTTACCCTAACCAGA
49151 AGGTAGACTG
Statistics
Matches: 86, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
39 20 0.23
40 33 0.38
41 33 0.38
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (40 bp):
CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
Found at i:49102 original size:41 final size:41
Alignment explanation
Indices: 49006--49148 Score: 175
Period size: 41 Copynumber: 3.6 Consensus size: 41
48996 TACGTCATCA
* *
49006 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTG-AAGAC
1 CATCCAATCTTTTACCCTAACCATAGGGCAGATTGAAACAC
* * *
49046 CATTCAATCTTTTACCCTAACCATAGGGTAAATTGAAACAC
1 CATCCAATCTTTTACCCTAACCATAGGGCAGATTGAAACAC
* * * *
49087 CATCCGATCTCTTACCCCAACCATAGGGCAGATTGAAGCA-
1 CATCCAATCTTTTACCCTAACCATAGGGCAGATTGAAACAC
*
49127 -ACCCAATCTTTTACCCTAACCA
1 CATCCAATCTTTTACCCTAACCA
49149 GAAGGTAGAC
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
39 18 0.21
40 31 0.36
41 37 0.43
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (41 bp):
CATCCAATCTTTTACCCTAACCATAGGGCAGATTGAAACAC
Found at i:50945 original size:30 final size:28
Alignment explanation
Indices: 50882--50949 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 28
50872 TTTTATTCTA
*
50882 TTTTTTAAATTAAATCTTTTATTTTTAAT
1 TTTTTTAAATTAAATCTTTTATTTTT-AC
*
50911 TTTTTTAAATTCAATCATTTTACTCTTTT-C
1 TTTTTTAAATTAAATC-TTTTA-T-TTTTAC
50941 TTTTTTAAA
1 TTTTTTAAA
50950 AATTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 15 0.44
30 14 0.41
31 1 0.03
32 4 0.12
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTTTAAATTAAATCTTTTATTTTTAC
Found at i:52606 original size:18 final size:18
Alignment explanation
Indices: 52581--52623 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
52571 TTTTTGTTTG
52581 ATTT-TTATT-AATTTACA
1 ATTTATTATTAAATTTA-A
52598 ATTTATTATTAAATTTAA
1 ATTTATTATTAAATTTAA
52616 ATTGTATT
1 ATT-TATT
52624 TATATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTTATTATTAAATTTAA
Found at i:54058 original size:59 final size:59
Alignment explanation
Indices: 53987--54147 Score: 205
Period size: 59 Copynumber: 2.7 Consensus size: 59
53977 AATTGAATCT
* * * * **
53987 AAAAAAGCTTAGGTACCAAATTAAGAAAAAATGTCAAGTTTAGATACCAAATTTGGTCC
1 AAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAATTCAGATACCAAATTAGGTAA
* * * *
54046 AAAAAAGTTTAGGTACCAAATTAGGAAAAAATATCAAATTCAGGTACTAAATTAGGTAA
1 AAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAATTCAGATACCAAATTAGGTAA
**
54105 AAAAAATGTTTAAATACCAAATTAAGAAAAAATGTCAAATTCA
1 AAAAAA-GTTTAGGTACCAAATTAAGAAAAAATGTCAAATTCA
54148 AGTACAAAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 55 0.63
60 32 0.37
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (59 bp):
AAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAATTCAGATACCAAATTAGGTAA
Found at i:59285 original size:24 final size:24
Alignment explanation
Indices: 59257--59305 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
59247 AAATAAAATA
*
59257 AAAGTAAAGTCCAAATAGAACTAG
1 AAAGTAAAGTCCAAAAAGAACTAG
59281 AAAGTAAAGTCCAAAAAGAACTAG
1 AAAGTAAAGTCCAAAAAGAACTAG
59305 A
1 A
59306 CTTTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.14
Consensus pattern (24 bp):
AAAGTAAAGTCCAAAAAGAACTAG
Found at i:63615 original size:92 final size:92
Alignment explanation
Indices: 63449--63617 Score: 203
Period size: 92 Copynumber: 1.8 Consensus size: 92
63439 AACAACGACT
* * * * * * **
63449 ATAATAAAATACATATTAATAGTTCAAGTACCACATTAGATATTTTTAAAATATATTTACCATAT
1 ATAATAAAACACATATTAATAATTCAAGCACCAAATTAAATATTTTCAAAATATAAATACCATAT
*
63514 TATACATTTTATAAAAATACAAATATC
66 TAGACATTTTATAAAAATACAAATATC
* * **
63541 ATAATAAAACACATATTAATAATTCAAGCACTAAATTAAATATTTTCAAATTATAAATATTATAT
1 ATAATAAAACACATATTAATAATTCAAGCACCAAATTAAATATTTTCAAAATATAAATACCATAT
* *
63606 TGGATATTTTAT
66 TAGACATTTTAT
63618 GAAGTTTCAG
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
92 62 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (92 bp):
ATAATAAAACACATATTAATAATTCAAGCACCAAATTAAATATTTTCAAAATATAAATACCATAT
TAGACATTTTATAAAAATACAAATATC
Found at i:66320 original size:29 final size:29
Alignment explanation
Indices: 66279--66338 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
66269 GAAGAGTCAG
*
66279 AACAACAATGGTTATAAGTGTTTTGTTTC
1 AACAACAATGGTTATAAGTGTTTTGTATC
66308 AACAACAATGGTTATAAGTGTTTTGTATC
1 AACAACAATGGTTATAAGTGTTTTGTATC
66337 AA
1 AA
66339 GTATTTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (29 bp):
AACAACAATGGTTATAAGTGTTTTGTATC
Found at i:79173 original size:10 final size:9
Alignment explanation
Indices: 79135--79164 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
79125 TTATTAATTT
79135 AAAACTTTA
1 AAAACTTTA
79144 AAAACTTTA
1 AAAACTTTA
79153 AAAACTTTA
1 AAAACTTTA
79162 AAA
1 AAA
79165 GAGTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAACTTTA
Found at i:80234 original size:14 final size:14
Alignment explanation
Indices: 80206--80243 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
80196 TTAGCCTCCG
80206 CTTTTTTTTC-ATA
1 CTTTTTTTTCTATA
*
80219 CTTTTTTTTCTTTA
1 CTTTTTTTTCTATA
*
80233 CTTTATTTTCT
1 CTTTTTTTTCT
80244 CCCATTCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74
Consensus pattern (14 bp):
CTTTTTTTTCTATA
Found at i:80858 original size:2 final size:2
Alignment explanation
Indices: 80851--80875 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
80841 GAACGAGTGT
80851 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 T
80876 GTACATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:80883 original size:6 final size:6
Alignment explanation
Indices: 80853--80907 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
80843 ACGAGTGTTA
* * * * *
80853 TATATA TATATA TATATA TATATG TACATG TATATG TATATG TACATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
80901 TATATG T
1 TATATG T
80908 CGGGCAGGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (6 bp):
TATATG
Found at i:80886 original size:18 final size:18
Alignment explanation
Indices: 80851--80905 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
80841 GAACGAGTGT
* * *
80851 TATATATATATATATATA
1 TATATATGTACATGTATA
80869 TATATATGTACATGTATA
1 TATATATGTACATGTATA
*
80887 TGTATATGTACATGTATA
1 TATATATGTACATGTATA
80905 T
1 T
80906 GTCGGGCAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (18 bp):
TATATATGTACATGTATA
Found at i:80906 original size:18 final size:18
Alignment explanation
Indices: 80865--80907 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
80855 TATATATATA
*
80865 TATATATATATGTACATG
1 TATATGTATATGTACATG
80883 TATATGTATATGTACATG
1 TATATGTATATGTACATG
80901 TATATGT
1 TATATGT
80908 CGGGCAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (18 bp):
TATATGTATATGTACATG
Found at i:88776 original size:27 final size:27
Alignment explanation
Indices: 88746--88831 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 27
88736 GACATCATGA
88746 ATAGTCCGATGGGACAATAAACACGGG
1 ATAGTCCGATGGGACAATAAACACGGG
* * *
88773 ATAGTCCAACGAGACAATAAACACGGG
1 ATAGTCCGATGGGACAATAAACACGGG
* * *
88800 ATAATCCGATGGGACATTAAACATGGG
1 ATAGTCCGATGGGACAATAAACACGGG
*
88827 GTAGT
1 ATAGT
88832 TCGGCAGGAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.17
Consensus pattern (27 bp):
ATAGTCCGATGGGACAATAAACACGGG
Found at i:90474 original size:18 final size:18
Alignment explanation
Indices: 90434--90476 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
90424 GTTCAAAGAG
90434 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
90452 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
90470 TAATTAA
1 TAATTAA
90477 ACACTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:91828 original size:65 final size:65
Alignment explanation
Indices: 91590--91899 Score: 239
Period size: 70 Copynumber: 4.6 Consensus size: 65
91580 CCATACAGCC
* * * ** * *
91590 GATAAGATGAGATAGAAGTCCTAAGATCGACGTAAATGATCCCAT-TTCATTTGATCTAGAATAG
1 GATAAAATGAGATAAAAGTCCTAAAATCGGTGTAAATGATCCCATCTT-GTTTG-T-T--CA-AG
*
91654 AATTCC
60 AATTCT
* * * ** * *
91660 GAAAAAATGAGATAGAAGCCCTAAAATCATTGTAAATGACCCCATCTTGTTTGTTCTAGACTAGC
1 GATAAAATGAGATAAAAGTCCTAAAATCGGTGTAAATGATCCCATCTTGTTTGTTC---A--AGA
*
91725 ATCCT
61 ATTCT
*
91730 GATAAAATGAGATAGAAGTCCTAAAATCGGTGTAAATGATCCCATCTTGTTTGTTCAAGAATTCT
1 GATAAAATGAGATAAAAGTCCTAAAATCGGTGTAAATGATCCCATCTTGTTTGTTCAAGAATTCT
*** **
91795 GATAAAATGAGATAAAAGTCCTAGGCTTC-GTGTAAATGATCCCATCTCATTTGTTCAAGAATTC
1 GATAAAATGAGATAAAAGTCCTA-AAATCGGTGTAAATGATCCCATCTTGTTTGTTCAAGAATT-
91859 CT
64 CT
*** * *
91861 -ATAAAATGAGATAGGTGTTCTAAGATCGGTGTAAATGAT
1 GATAAAATGAGATAAAAGTCCTAAAATCGGTGTAAATGAT
91900 GATCCCGTCT
Statistics
Matches: 199, Mismatches: 33, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
64 2 0.01
65 89 0.45
66 4 0.02
67 1 0.01
68 1 0.01
69 2 0.01
70 98 0.49
71 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (65 bp):
GATAAAATGAGATAAAAGTCCTAAAATCGGTGTAAATGATCCCATCTTGTTTGTTCAAGAATTCT
Found at i:95751 original size:12 final size:14
Alignment explanation
Indices: 95734--95765 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
95724 TTATTTTTTG
95734 AAATTA-TAA-ATA
1 AAATTATTAATATA
95746 AAATTATTAATATA
1 AAATTATTAATATA
95760 AAATTA
1 AAATTA
95766 GTTTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 3 0.17
14 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATTATTAATATA
Found at i:97218 original size:3 final size:3
Alignment explanation
Indices: 97210--97235 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
97200 ATATTAATCC
97210 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
97236 GCTCCACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:104299 original size:2 final size:2
Alignment explanation
Indices: 104292--104319 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
104282 CTCGATATTG
104292 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
104320 TATCTTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104891 original size:2 final size:2
Alignment explanation
Indices: 104884--104919 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
104874 TTTTCCAATG
104884 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
104920 TTTACATTAA
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:105647 original size:21 final size:22
Alignment explanation
Indices: 105621--105686 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 22
105611 TTTTTCTAAT
*
105621 ATTTATGAAA-AA-ATTTGAAAA
1 ATTTATCAAATAATATTT-AAAA
105642 ATTTATCAAATAATATTTAAAA
1 ATTTATCAAATAATATTTAAAA
** *
105664 A-CCATAAAATAA-ATTTAAAA
1 ATTTATCAAATAATATTTAAAA
105684 ATT
1 ATT
105687 CAAAATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 9 0.24
21 17 0.46
22 7 0.19
23 4 0.11
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.35
Consensus pattern (22 bp):
ATTTATCAAATAATATTTAAAA
Found at i:107998 original size:2 final size:2
Alignment explanation
Indices: 107991--108030 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
107981 TAAAACATTC
107991 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
108031 TAAAAGCCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114133 original size:31 final size:29
Alignment explanation
Indices: 114098--114155 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
114088 ACTTCACTAT
*
114098 AATAATTACAGAGACCTTCTCAAAAAGAAAG
1 AATAAATACAGAG--CTTCTCAAAAAGAAAG
*
114129 AATAAATACAGAGTTTCTCAAAAAGAA
1 AATAAATACAGAGCTTCTCAAAAAGAA
114156 GAGACCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
31 12 0.48
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.21
Consensus pattern (29 bp):
AATAAATACAGAGCTTCTCAAAAAGAAAG
Found at i:115977 original size:21 final size:22
Alignment explanation
Indices: 115929--115978 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
115919 ATTATTTTTT
115929 ATTTT-TTTAAATATTTATATG
1 ATTTTATTTAAATATTTATATG
* *
115950 ATATTATTTTAATATTTA-ATG
1 ATTTTATTTAAATATTTATATG
115971 ATTTTATT
1 ATTTTATT
115979 AATTTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTTATTTAAATATTTATATG
Done.