Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015341.1 Kokia drynarioides strain JFW-HI SEQ_130388, 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: 327941
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 190 characters in sequence are not A, C, G, or T
Found at i:68 original size:22 final size:22
Alignment explanation
Indices: 28--69 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18 TTATCATTTT
* **
28 TATATATTTTTAATTTTTTGAA
1 TATATATTTATAAAATTTTGAA
50 TATATATTTATAAAATTTTG
1 TATATATTTATAAAATTTTG
70 GAAAAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TATATATTTATAAAATTTTGAA
Found at i:115 original size:31 final size:31
Alignment explanation
Indices: 73--138 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
63 AATTTTGGAA
*
73 AAAAAAATATTTTATAAATA-TTCTATTTTTT
1 AAAAAAATATTTTA-AAATATTTATATTTTTT
* *
104 AAAAAATTATTTTAAATTATTTATATTTTTT
1 AAAAAAATATTTTAAAATATTTATATTTTTT
135 AAAA
1 AAAA
139 GGATCAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
AAAAAAATATTTTAAAATATTTATATTTTTT
Found at i:421 original size:25 final size:25
Alignment explanation
Indices: 373--421 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
363 GAGATCAAGA
* *
373 TGAATAGATAAATATTATTCTTTTT
1 TGAAAAGATAAATATTATTATTTTT
*
398 TGAAAAGATAAATATTGTTATTTT
1 TGAAAAGATAAATATTATTATTTT
422 CCAGAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (25 bp):
TGAAAAGATAAATATTATTATTTTT
Found at i:3518 original size:24 final size:24
Alignment explanation
Indices: 3490--3572 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 24
3480 TAGACTAATA
*
3490 AGAGTTTAACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* **
3514 AGAGTTTAATTGAAGTAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* * *
3538 AAAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
3562 AGAATTTAACT
1 AGAGTTTAACT
3573 AAAAGATTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.28
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:7547 original size:23 final size:24
Alignment explanation
Indices: 7508--7558 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
7498 TAATAAGGAT
7508 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACTATCAC
* *
7531 TTTCAA-TTCCAATTTCACTTTCAC
1 TTTCAATTTACAA-TTCACTATCAC
7555 TTTC
1 TTTC
7559 GTTTTCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 10 0.42
24 9 0.38
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTCAATTTACAATTCACTATCAC
Found at i:9723 original size:14 final size:14
Alignment explanation
Indices: 9704--9737 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
9694 CGAGAAGGAT
9704 ATTTGATTATCTCG
1 ATTTGATTATCTCG
*
9718 ATTTGATTATCTTG
1 ATTTGATTATCTCG
9732 ATTTGA
1 ATTTGA
9738 AGAAAGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (14 bp):
ATTTGATTATCTCG
Found at i:9872 original size:96 final size:96
Alignment explanation
Indices: 9722--9902 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 96
9712 ATCTCGATTT
** * * *
9722 GATTATCTTGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCGGAATCGAAGA
1 GATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCGGAACCCAAAA
9787 TAAGAA-AACATTGCCTCGATTAAGGGTATTC
66 TAA-AAGAACATTGCCTCGATTAAGGGTATTC
* *
9818 GATTA-CTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGGAACCCAA
1 GATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTCGGAACCCAA
*
9881 AATAAAAGAATATTGCCTCGAT
64 AATAAAAGAACATTGCCTCGAT
9903 ATTAAAAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 6 0.08
96 68 0.92
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.28
Consensus pattern (96 bp):
GATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCGGAACCCAAAA
TAAAAGAACATTGCCTCGATTAAGGGTATTC
Found at i:10201 original size:30 final size:29
Alignment explanation
Indices: 10169--10478 Score: 264
Period size: 30 Copynumber: 10.5 Consensus size: 29
10159 AAAATAGGAT
10169 TTTTTGGAAGTTCGAGGGTAAAATGGTAA
1 TTTTTGGAAGTTCGAGGGTAAAATGGTAA
* *
10198 TTTTTAGAAGATTCGA-GGTCAAAAATGG-GA
1 TTTTTGGAAG-TTCGAGGGT--AAAATGGTAA
*
10228 TTTTTGGAAGTTCGGGGGTAAAATGGTAA
1 TTTTTGGAAGTTCGAGGGTAAAATGGTAA
10257 TTTTTGGAACGTTC-AGGGTCAAAAAT-G-AGA
1 TTTTTGGAA-GTTCGAGGGT--AAAATGGTA-A
* *
10287 TTTTTGGAAGTTTG-GGGATAAAATAGTAA
1 TTTTTGGAAGTTCGAGGG-TAAAATGGTAA
* * *
10316 TTTTTAGAAGGTTTG-GGGTCAAAAATGG-GA
1 TTTTTGGAA-GTTCGAGGGT--AAAATGGTAA
* * *
10346 TTTTTGGAATTTTGAGGGTAAAATGATAA
1 TTTTTGGAAGTTCGAGGGTAAAATGGTAA
* *
10375 TTTTTGGAAGGTTTG-GGGTTAAAAATGG-GA
1 TTTTTGGAA-GTTCGAGGG-T-AAAATGGTAA
*
10405 TTTTTGGAAGTTCAAGGGTAAAATGGTAA
1 TTTTTGGAAGTTCGAGGGTAAAATGGTAA
*
10434 TTTTTGGAAAGTTCGGGGGTAAAATGGTAA
1 TTTTTGG-AAGTTCGAGGGTAAAATGGTAA
10464 -TTTTGGAAAGTTCGA
1 TTTTTGG-AAGTTCGA
10479 CCCCCGGGGT
Statistics
Matches: 234, Mismatches: 23, Indels: 48
0.77 0.08 0.16
Matches are distributed among these distances:
28 25 0.11
29 91 0.39
30 94 0.40
31 24 0.10
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
TTTTTGGAAGTTCGAGGGTAAAATGGTAA
Found at i:10232 original size:59 final size:59
Alignment explanation
Indices: 10156--10478 Score: 366
Period size: 59 Copynumber: 5.5 Consensus size: 59
10146 ATGTTCGGAA
* *
10156 TCAAAAATAGGATTTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGATTCGAGG
1 TCAAAAATGGGA-TTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
* * *
10216 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAACGTTC-AGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGA-GG
* * * * *
10275 TCAAAAATGAGATTTTTGGAAGTTTG-GGGATAAAATAGTAATTTTTAGAAGGTTTGGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAAATGGTAATTTTTAGAAGGTTCGAGG
* * * * * *
10334 TCAAAAATGGGATTTTTGGAATTTTGAGGGTAAAATGATAATTTTTGGAAGGTTTGGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
* * * * *
10393 TTAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAGTTCGGGGG
1 TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTC-GAGG
* *
10453 T--AAAATGGTAATTTTGGAAAGTTCGA
1 TCAAAAATGGGATTTTTGG-AAGTTCGA
10479 CCCCCGGGGT
Statistics
Matches: 230, Mismatches: 27, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
58 18 0.08
59 193 0.84
60 19 0.08
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (59 bp):
TCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAGAAGGTTCGAGG
Found at i:12258 original size:15 final size:15
Alignment explanation
Indices: 12240--12319 Score: 79
Period size: 15 Copynumber: 5.3 Consensus size: 15
12230 TTTTGGGTAG
12240 TTTGTAATTGGACCA
1 TTTGTAATTGGACCA
* *
12255 TTTGTATTTGGGCCA
1 TTTGTAATTGGACCA
* * * *
12270 TCTATAACTGGACTA
1 TTTGTAATTGGACCA
* *
12285 TTTGTTATTGGGCCA
1 TTTGTAATTGGACCA
*
12300 TTTGTAACTGGACCA
1 TTTGTAATTGGACCA
12315 TTTGT
1 TTTGT
12320 TCTGGATTTT
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (15 bp):
TTTGTAATTGGACCA
Found at i:12282 original size:30 final size:30
Alignment explanation
Indices: 12248--12320 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
12238 AGTTTGTAAT
12248 TGGACCATTTG-TATTTGGGCCATCTATAAC
1 TGGACCATTTGTTA-TTGGGCCATCTATAAC
* * *
12278 TGGACTATTTGTTATTGGGCCATTTGTAAC
1 TGGACCATTTGTTATTGGGCCATCTATAAC
12308 TGGACCATTTGTT
1 TGGACCATTTGTT
12321 CTGGATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 36 0.95
31 2 0.05
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (30 bp):
TGGACCATTTGTTATTGGGCCATCTATAAC
Found at i:16031 original size:11 final size:11
Alignment explanation
Indices: 15981--16033 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
15971 TATTTACGAT
*
15981 TAATATAAAAA
1 TAATATAACAA
15992 TAATAATAACAA
1 TAAT-ATAACAA
* *
16004 TAAAATTA-AA
1 TAATATAACAA
16014 TAATATAACAA
1 TAATATAACAA
*
16025 TACTATAAC
1 TAATATAAC
16034 GTGAAATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 8 0.24
11 17 0.50
12 9 0.26
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATATAACAA
Found at i:16760 original size:17 final size:18
Alignment explanation
Indices: 16728--16761 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16718 GAGATTTATC
*
16728 TATTTTCTAAATTAAAAA
1 TATTTTCTAAAGTAAAAA
16746 TATTTT-TAAAGTAAAA
1 TATTTTCTAAAGTAAAA
16762 TCTAAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
TATTTTCTAAAGTAAAAA
Found at i:20436 original size:174 final size:171
Alignment explanation
Indices: 20145--20475 Score: 407
Period size: 174 Copynumber: 1.9 Consensus size: 171
20135 TTCTGACTCA
* * * * *
20145 TGAGGTGGAAAAGGTAGAGAGAGGGCAATGCAGGAGCAAGGAAAGGAGTGAAAATGTTTATTCTG
1 TGAGGTGGAAAAGGTAGAAAGAGGGCAATGCAGGAGCAACGAAAGGACTGAAAAGGTTTACTCTG
* * * * *
20210 GTAGAGTCACTAGATCACGAAGTTCAATCCATCCTTCCATGTCTGAGAGTGGGCCTTCAGGTACA
66 GTAGAGTCACAAGATCAAGAAGTTCAATCCAACCTTCAAAGTCTGAGAGTGGGCCTTCAGGTACA
* *
20275 GGCAACGACTCCTTTGTTGCAAAGCAGGATAATGTTGTCAGTAG
131 GGAAAC-ACT--TCTGTTGCAAAGCAGGATAATGTTGTCAGTAG
*
20319 TGAGGTGGAAAAAGG-AGAAAGAGTGG-AATGCAGGAGTAACGAAAGGACTGAAAAGGTTTACTC
1 TGAGGTGG-AAAAGGTAGAAAGAG-GGCAATGCAGGAGCAACGAAAGGACTGAAAAGGTTTACTC
* * * * *
20382 TGGTCGAGTCACAAGATCAAGAGGTTCAGTTCAACCTTCAAAGTCT-ATGAGTGGGCTTTCAGGT
64 TGGTAGAGTCACAAGATCAAGAAGTTCAATCCAACCTTCAAAGTCTGA-GAGTGGGCCTTCAGGT
* *
20446 GCAGGAAACACTTCTGTTGCTAAGCAGGAT
128 ACAGGAAACACTTCTGTTGCAAAGCAGGAT
20476 GGTGTGGTAC
Statistics
Matches: 134, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
171 16 0.12
173 4 0.03
174 106 0.79
175 8 0.06
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (171 bp):
TGAGGTGGAAAAGGTAGAAAGAGGGCAATGCAGGAGCAACGAAAGGACTGAAAAGGTTTACTCTG
GTAGAGTCACAAGATCAAGAAGTTCAATCCAACCTTCAAAGTCTGAGAGTGGGCCTTCAGGTACA
GGAAACACTTCTGTTGCAAAGCAGGATAATGTTGTCAGTAG
Found at i:40060 original size:18 final size:19
Alignment explanation
Indices: 40037--40072 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40027 TTTTTTTTCA
40037 AATTTT-AAAAAATAAATT
1 AATTTTGAAAAAATAAATT
*
40055 AATTTTGAAAAGATAAAT
1 AATTTTGAAAAAATAAAT
40073 AGAAAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (19 bp):
AATTTTGAAAAAATAAATT
Found at i:40307 original size:2 final size:2
Alignment explanation
Indices: 40295--40323 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
40285 TAACATAACA
40295 AT AT AT A- 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
40324 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42245 original size:7 final size:7
Alignment explanation
Indices: 42235--42259 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42225 AACAAAAAAC
42235 AAATGGT
1 AAATGGT
42242 AAATGGT
1 AAATGGT
42249 AAATGGT
1 AAATGGT
42256 AAAT
1 AAAT
42260 AGATGCTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (7 bp):
AAATGGT
Found at i:43704 original size:65 final size:64
Alignment explanation
Indices: 43557--43748 Score: 248
Period size: 62 Copynumber: 3.0 Consensus size: 64
43547 AGAAAAAGAG
* * *
43557 ATTATTTCTCTAAAAATCTCTGGAGTTTTTGTTTCTCAAAAGAAGGAATCGAAGAAGAAG--AG
1 ATTATTTCTCTAAAAATCTCTAGAGTTTTTGTTTCTCAAAAGAAAGAATCGAAGAAGAAGAAAA
* *
43619 ATTATTTCTCTAAAAATCTCTTGAGTTTTTTGTCTT-TC-AAAGAAAGAATCAAAGAAGAAGAAA
1 ATTATTTCTCTAAAAATCTCTAGAG-TTTTTGT-TTCTCAAAAGAAAGAATCGAAGAAGAAGAAA
43682 CA
64 -A
* * * *
43684 ATTATTTCTCTAAAGATCTCTAGAATTTTTGTTTCTCAAAAGAGAGAATCGAAGAAGATGAAAA
1 ATTATTTCTCTAAAAATCTCTAGAGTTTTTGTTTCTCAAAAGAAAGAATCGAAGAAGAAGAAAA
43748 A
1 A
43749 AAGAAGAAGG
Statistics
Matches: 113, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
62 44 0.39
63 11 0.10
64 14 0.12
65 44 0.39
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (64 bp):
ATTATTTCTCTAAAAATCTCTAGAGTTTTTGTTTCTCAAAAGAAAGAATCGAAGAAGAAGAAAA
Found at i:53057 original size:20 final size:21
Alignment explanation
Indices: 53032--53075 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
53022 AAAAATTATA
53032 TTTTTATG-TTTTTATAAGTT
1 TTTTTATGATTTTTATAAGTT
*
53052 TTTTTATGATTTTTATACGTT
1 TTTTTATGATTTTTATAAGTT
53073 TTT
1 TTT
53076 ATAGAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.70
Consensus pattern (21 bp):
TTTTTATGATTTTTATAAGTT
Found at i:53660 original size:19 final size:17
Alignment explanation
Indices: 53631--53701 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 17
53621 AAAATTTTAT
53631 AAAATTAATAAAAATCCATA
1 AAAATT-ATAAAAAT--ATA
*
53651 AAAATTATAAATAATATG
1 AAAATTATAAA-AATATA
*
53669 AAAATTAAAAAATATATA
1 AAAATTATAAAA-ATATA
53687 ATAAATTTATAAAAA
1 A-AAA-TTATAAAAA
53702 AAATTTTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 1 0.02
18 17 0.40
19 9 0.21
20 16 0.37
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (17 bp):
AAAATTATAAAAATATA
Found at i:66589 original size:21 final size:21
Alignment explanation
Indices: 66563--66603 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
66553 GAATAGGGCA
* *
66563 GATGATGATATGGCTGATGAG
1 GATGATGACATGGCGGATGAG
66584 GATGATGACATGGCGGATGA
1 GATGATGACATGGCGGATGA
66604 TGGAGAGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.39, T:0.24
Consensus pattern (21 bp):
GATGATGACATGGCGGATGAG
Found at i:74556 original size:12 final size:12
Alignment explanation
Indices: 74531--74563 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
74521 GCCTCAACTG
74531 AAATATTCTAAAA
1 AAATATT-TAAAA
74544 AAATATTTAAAA
1 AAATATTTAAAA
74556 AAATATTT
1 AAATATTT
74564 TCCGCGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATATTTAAAA
Found at i:79280 original size:2 final size:2
Alignment explanation
Indices: 79273--79315 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
79263 ACATAAATAG
* *
79273 GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA GG GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
79315 G
1 G
79316 TGTAACTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (2 bp):
GA
Found at i:79296 original size:14 final size:14
Alignment explanation
Indices: 79273--79315 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
79263 ACATAAATAG
*
79273 GAGAGAGAGAGAGA
1 GAGAGGGAGAGAGA
79287 GAGAGGGAGAGAGA
1 GAGAGGGAGAGAGA
79301 GAGAGGGAGAGAGA
1 GAGAGGGAGAGAGA
79315 G
1 G
79316 TGTAACTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (14 bp):
GAGAGGGAGAGAGA
Found at i:82619 original size:35 final size:35
Alignment explanation
Indices: 82573--82644 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
82563 CACATATCCA
82573 ATCCGTCGTTTGAATCCTTAAGCTTCATCAGGAAC
1 ATCCGTCGTTTGAATCCTTAAGCTTCATCAGGAAC
* *
82608 ATCCGTCGTTTGAGTCCTTAAGCTTCATCGGGAAC
1 ATCCGTCGTTTGAATCCTTAAGCTTCATCAGGAAC
82643 AT
1 AT
82645 GAAGTTGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (35 bp):
ATCCGTCGTTTGAATCCTTAAGCTTCATCAGGAAC
Found at i:83575 original size:12 final size:12
Alignment explanation
Indices: 83536--83575 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
83526 TCAAAAAAAA
83536 TAAATTATTTTT
1 TAAATTATTTTT
*
83548 TAAAATA-TTTT
1 TAAATTATTTTT
*
83559 AAAATTATTTTT
1 TAAATTATTTTT
83571 TAAAT
1 TAAAT
83576 ATAAAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TAAATTATTTTT
Found at i:84377 original size:6 final size:6
Alignment explanation
Indices: 84357--84405 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
84347 GTAAGGCTGA
* *
84357 AAGGAG AAAGG-G AAGGGG AAGGAG AAAGAG AAGGAG AAGGAG AAGGAG
1 AAGGAG -AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG AAGGAG
84405 A
1 A
84406 GCAGAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.11
6 30 0.79
7 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
AAGGAG
Found at i:84380 original size:18 final size:18
Alignment explanation
Indices: 84357--84405 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
84347 GTAAGGCTGA
* *
84357 AAGGAGAAAGGGAAGGGG
1 AAGGAGAAAGAGAAGGAG
84375 AAGGAGAAAGAGAAGGAG
1 AAGGAGAAAGAGAAGGAG
*
84393 AAGGAGAAGGAGA
1 AAGGAGAAAGAGA
84406 GCAGAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (18 bp):
AAGGAGAAAGAGAAGGAG
Found at i:84498 original size:21 final size:23
Alignment explanation
Indices: 84453--84496 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
84443 TTTAATAATT
84453 TTATATTTAAAAATAATTTTAAA
1 TTATATTTAAAAATAATTTTAAA
84476 TTAT-TTTAAAAA-AATTATTAA
1 TTATATTTAAAAATAATT-TTAA
84497 TTTTTGCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTATATTTAAAAATAATTTTAAA
Found at i:97110 original size:18 final size:19
Alignment explanation
Indices: 97087--97128 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
97077 TTTTAAAAAA
97087 TATAAAATATTGA-ATTTT
1 TATAAAATATTGAGATTTT
*
97105 TAT-AAATATTTAGATTTT
1 TATAAAATATTGAGATTTT
97123 T-TAAAA
1 TATAAAA
97129 ATTACTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TATAAAATATTGAGATTTT
Found at i:97140 original size:20 final size:18
Alignment explanation
Indices: 97090--97144 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
97080 TAAAAAATAT
*
97090 AAAATA-TTGAATTTTTA
1 AAAATATTTGATTTTTTA
*
97107 TAAATATTTAGATTTTTTA
1 AAAATATTT-GATTTTTTA
97126 AAAATTACTTTGATTTTTT
1 AAAA-TA-TTTGATTTTTT
97145 TTTGAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 5 0.16
18 2 0.06
19 11 0.35
20 10 0.32
21 3 0.10
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (18 bp):
AAAATATTTGATTTTTTA
Found at i:106634 original size:84 final size:84
Alignment explanation
Indices: 106527--106695 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
106517 TACTAAAAGT
106527 ATTCAAGTTGTCTTTTTCTTCTTGAATTGAAGGGAGTATTCAAGCTTCAAATGAATGATTACATA
1 ATTCAAGTTGTCTTTTTCTTCTTGAATTGAAGGGAGTATTCAAGCTTCAAATGAATGATTACATA
106592 TTTGGTTACTACATCACCA
66 TTTGGTTACTACATCACCA
106611 ATTCAAGTTGTCTTTTTCTTCTTGAATTGAAGGGAGTATTCAAGCTTCAAATGAATGATTACATA
1 ATTCAAGTTGTCTTTTTCTTCTTGAATTGAAGGGAGTATTCAAGCTTCAAATGAATGATTACATA
106676 TTTGGTTACTACATCACCA
66 TTTGGTTACTACATCACCA
106695 A
1 A
106696 CTGCAGCTAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (84 bp):
ATTCAAGTTGTCTTTTTCTTCTTGAATTGAAGGGAGTATTCAAGCTTCAAATGAATGATTACATA
TTTGGTTACTACATCACCA
Found at i:106965 original size:20 final size:20
Alignment explanation
Indices: 106940--106980 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
106930 GTGTCGGCTA
106940 GTGACATGCATCACTGACAT
1 GTGACATGCATCACTGACAT
106960 GTGACATGCATCACTGACAT
1 GTGACATGCATCACTGACAT
106980 G
1 G
106981 GAAACACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (20 bp):
GTGACATGCATCACTGACAT
Found at i:107232 original size:22 final size:23
Alignment explanation
Indices: 107203--107250 Score: 82
Period size: 21 Copynumber: 2.2 Consensus size: 23
107193 ATTTTAAAAT
107203 TTTTAAAAAATTAAAAA-ATT-A
1 TTTTAAAAAATTAAAAATATTCA
107224 TTTTAAAAAATTAAAAATATTCA
1 TTTTAAAAAATTAAAAATATTCA
107247 TTTT
1 TTTT
107251 TAAACGTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.68
22 3 0.12
23 5 0.20
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTTAAAAAATTAAAAATATTCA
Found at i:107675 original size:21 final size:21
Alignment explanation
Indices: 107619--107667 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
107609 AATGTCAATC
*
107619 CCATAAATAAT-AAATCAAAT
1 CCATAAACAATAAAATCAAAT
107639 CCATAAACAATAAAATCAAAT
1 CCATAAACAATAAAATCAAAT
107660 -CATAAACA
1 CCATAAACA
107668 CTGAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.20
Consensus pattern (21 bp):
CCATAAACAATAAAATCAAAT
Found at i:108298 original size:57 final size:57
Alignment explanation
Indices: 108225--108334 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
108215 TTAATATCTA
*
108225 AAATTTTTTTAGTCCAATTTGGTACCTAAATTTGACAC-TTTTTTAAGTTGGTTCTT
1 AAATTTTTTTAGTCCAATTTGGTACCTAAACTTGACACTTTTTTTAAGTTGGTTCTT
* * *
108281 AAATTTTTTTGGTTCCAATTTGGTACCTAAACTTGACTCTTTTTTTAATTTGGT
1 AAATTTTTTTAG-TCCAATTTGGTACCTAAACTTGACACTTTTTTTAAGTTGGT
108335 ACCTAATCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 11 0.23
57 24 0.50
58 13 0.27
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.51
Consensus pattern (57 bp):
AAATTTTTTTAGTCCAATTTGGTACCTAAACTTGACACTTTTTTTAAGTTGGTTCTT
Found at i:108347 original size:58 final size:56
Alignment explanation
Indices: 108225--108349 Score: 162
Period size: 57 Copynumber: 2.2 Consensus size: 56
108215 TTAATATCTA
* * *
108225 AAATTTTTTTAGTCCAATTTGGTACCTAAATTTGACACTTTTTTAAGTTGGTTCTT
1 AAATTTTTTTAGTCCAATTTGGTACCTAAACTTGACACTTTTTTAAGTTGGTACCT
* * *
108281 AAATTTTTTTGGTTCCAATTTGGTACCTAAACTTGACTCTTTTTTTAATTTGGTACCT
1 AAATTTTTTTAG-TCCAATTTGGTACCTAAACTTGACAC-TTTTTTAAGTTGGTACCT
108339 -AATCTTTTTTA
1 AAAT-TTTTTTA
108350 ATATTAATTC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
56 11 0.19
57 27 0.46
58 21 0.36
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (56 bp):
AAATTTTTTTAGTCCAATTTGGTACCTAAACTTGACACTTTTTTAAGTTGGTACCT
Found at i:109693 original size:23 final size:21
Alignment explanation
Indices: 109667--109709 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
109657 AACTTACATT
109667 TTAAAATCCGTAAAATACAAAAA
1 TTAAAATCC-TAAAATA-AAAAA
**
109690 TTAACCTCCTAAAATAAAAA
1 TTAAAATCCTAAAATAAAAA
109710 TAAAAAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.23
Consensus pattern (21 bp):
TTAAAATCCTAAAATAAAAAA
Found at i:112533 original size:15 final size:15
Alignment explanation
Indices: 112513--112542 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
112503 TGGACTAGAT
112513 TATTTTATATTTTTA
1 TATTTTATATTTTTA
*
112528 TATTTTTTATTTTTA
1 TATTTTATATTTTTA
112543 GAATGTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTATATTTTTA
Found at i:115490 original size:19 final size:19
Alignment explanation
Indices: 115466--115504 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
115456 TGATATATAC
115466 ACCAGAATTATCCCAGTGG
1 ACCAGAATTATCCCAGTGG
115485 ACCAGAATTATCCCAGTGG
1 ACCAGAATTATCCCAGTGG
115504 A
1 A
115505 GTAGATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (19 bp):
ACCAGAATTATCCCAGTGG
Found at i:118070 original size:20 final size:20
Alignment explanation
Indices: 118045--118085 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
118035 ACTTAAAAGA
*
118045 AAAAGAAGTCAC-GAACAAAT
1 AAAAGAAG-CACAAAACAAAT
118065 AAAAGAAGCACAAAACAAAT
1 AAAAGAAGCACAAAACAAAT
118085 A
1 A
118086 GTGCACACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.66, C:0.15, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAAGAAGCACAAAACAAAT
Found at i:121146 original size:19 final size:19
Alignment explanation
Indices: 121108--121146 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
121098 GTAACACCCC
* * *
121108 TAAACTCGGTTTACACGTA
1 TAAACTCGGTATAAAAGTA
121127 TAAACTCGGTATAAAAGTA
1 TAAACTCGGTATAAAAGTA
121146 T
1 T
121147 TACATACAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
TAAACTCGGTATAAAAGTA
Found at i:121697 original size:27 final size:25
Alignment explanation
Indices: 121639--121710 Score: 126
Period size: 25 Copynumber: 2.8 Consensus size: 25
121629 TCAAAGTACT
121639 AACAGAGAGCACATAAGTGCTGGGA
1 AACAGAGAGCACATAAGTGCTGGGA
121664 AACAGAGAGCACATAAGTGCTGGGA
1 AACAGAGAGCACATAAGTGCTGGGA
*
121689 AACAGAGAGCACACACAGTGCT
1 AACAGAGAGCACATA-AGTGCT
121711 AAACAGAGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 39 0.87
26 6 0.13
ACGTcount: A:0.40, C:0.19, G:0.29, T:0.11
Consensus pattern (25 bp):
AACAGAGAGCACATAAGTGCTGGGA
Found at i:121714 original size:23 final size:23
Alignment explanation
Indices: 121639--121815 Score: 146
Period size: 23 Copynumber: 7.4 Consensus size: 23
121629 TCAAAGTACT
*
121639 AACAGAGAGCACATA-AGTGCTGGGA
1 AACAGAGAGCACACACAGTGCT---A
*
121664 AACAGAGAGCACATA-AGTGCTGGGA
1 AACAGAGAGCACACACAGTGCT---A
121689 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
121712 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
*
121735 ATCAGAGAGCACAC-CAAGTGCTA
1 AACAGAGAGCACACAC-AGTGCTA
* * *
121758 ATCAGAGAGCACACATAATGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
121782 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
121806 AACAGAGAGC
1 AACAGAGAGC
121816 GCGCTAGTGT
Statistics
Matches: 132, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
23 68 0.52
24 2 0.02
25 54 0.41
26 8 0.06
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:123603 original size:11 final size:11
Alignment explanation
Indices: 123583--123622 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
123573 ATTTATTAAA
*
123583 AAAAATAATTTT
1 AAAAA-AATTAT
123595 AAAAAAATTAT
1 AAAAAAATTAT
*
123606 AAAATAATTAT
1 AAAAAAATTAT
123617 AAAAAA
1 AAAAAA
123623 TAACTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 20 0.80
12 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:124463 original size:30 final size:30
Alignment explanation
Indices: 124402--124466 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
124392 AGTCTATATC
*
124402 TTTATAATTTGTAAAAGATTAAATTAAAAT
1 TTTATAATTTGTAAAAGATTAAAGTAAAAT
* * **
124432 TTTATGATTTTTAAAAGATTAAAGTGTAAT
1 TTTATAATTTGTAAAAGATTAAAGTAAAAT
124462 TTTAT
1 TTTAT
124467 TATTACTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (30 bp):
TTTATAATTTGTAAAAGATTAAAGTAAAAT
Found at i:127617 original size:31 final size:33
Alignment explanation
Indices: 127579--127657 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 33
127569 TTTGGTCCAC
*
127579 TTTGGTACTC-AATCTTGACACTTTTTT-CTAA
1 TTTGGTACTCTAAACTTGACACTTTTTTACTAA
* *
127610 TTTGGTAC-CTAAACTTGACATTTTTTTATTAA
1 TTTGGTACTCTAAACTTGACACTTTTTTACTAA
*
127642 GTTGGTACT-TAAACTT
1 TTTGGTACTCTAAACTT
127658 TCTGGGGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 23 0.56
32 17 0.41
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (33 bp):
TTTGGTACTCTAAACTTGACACTTTTTTACTAA
Found at i:127647 original size:32 final size:31
Alignment explanation
Indices: 127521--127657 Score: 88
Period size: 31 Copynumber: 4.5 Consensus size: 31
127511 AATATAATAT
* * * *
127521 TTGGTACCTGAACTTGACACGTTTTCCTAAT
1 TTGGTACCTAAACTTGACACTTTTTTCTAAG
* **
127552 TTGGTACCTAAACTT-----TTTTTGGTCCACT
1 TTGGTACCTAAACTTGACACTTTTT--TCTAAG
* *
127580 TTGGTA-CTCAATCTTGACACTTTTTTCTAAT
1 TTGGTACCT-AAACTTGACACTTTTTTCTAAG
* *
127611 TTGGTACCTAAACTTGACATTTTTTTATTAAG
1 TTGGTACCTAAACTTGACACTTTTTT-CTAAG
*
127643 TTGGTACTTAAACTT
1 TTGGTACCTAAACTT
127658 TCTGGGGTTC
Statistics
Matches: 83, Mismatches: 13, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
26 4 0.05
27 2 0.02
28 14 0.17
31 39 0.47
32 19 0.23
33 5 0.06
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.45
Consensus pattern (31 bp):
TTGGTACCTAAACTTGACACTTTTTTCTAAG
Found at i:127674 original size:91 final size:90
Alignment explanation
Indices: 127519--127712 Score: 219
Period size: 91 Copynumber: 2.1 Consensus size: 90
127509 TTAATATAAT
* * * * ** *
127519 ATTTGGTACCTGAACTTGACACGTTTTCCTAATTTGGTACCTAAACTTTTTTTGGTCCACTTTGG
1 ATTTGGTACCTAAACTTGACACGTTTTACTAAGTTGGTACCTAAACTTTCTGGGGTCCAATTTGG
* *
127584 TA-CTCAATCTTGACACTTTTTTCTA
66 TACCTAAAT-TTGACACTTTTTCCTA
** * * *
127609 ATTTGGTACCTAAACTTGACATTTTTTTATTAAGTTGGTACTTAAACTTTCTGGGGTTCAATTTG
1 ATTTGGTACCTAAACTTGACA-CGTTTTACTAAGTTGGTACCTAAACTTTCTGGGGTCCAATTTG
**
127674 GTACCTAAATTTGATTCTTTTTCCTA
65 GTACCTAAATTTGACACTTTTTCCTA
127700 ATTTGGTACCTAA
1 ATTTGGTACCTAA
127713 TCTTTTTTAA
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
90 20 0.23
91 61 0.71
92 5 0.06
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (90 bp):
ATTTGGTACCTAAACTTGACACGTTTTACTAAGTTGGTACCTAAACTTTCTGGGGTCCAATTTGG
TACCTAAATTTGACACTTTTTCCTA
Found at i:128009 original size:48 final size:49
Alignment explanation
Indices: 127919--128011 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 49
127909 GTTCAAGTAC
* * * **
127919 CAAATTGGGTCCAAAAAAAGTTTAGGTACCAATTTAGGAAAAAGTATAT
1 CAAATTGGATCCAAAAAAAGTTTAAGTACCAAATTAAAAAAAAGTATAT
*
127968 CAAATTGGAT-CAAAAAAAGTTTAAGTACTAAATTAAAAAAAAGT
1 CAAATTGGATCCAAAAAAAGTTTAAGTACCAAATTAAAAAAAAGT
128012 GTCAAGTTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
48 29 0.76
49 9 0.24
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.26
Consensus pattern (49 bp):
CAAATTGGATCCAAAAAAAGTTTAAGTACCAAATTAAAAAAAAGTATAT
Found at i:128552 original size:27 final size:27
Alignment explanation
Indices: 128521--128577 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
128511 TATCATACTA
128521 ACTTATAATTTCATAAATTTAAAAGAG
1 ACTTATAATTTCATAAATTTAAAAGAG
128548 ACTTATAATTTCATAAATTTAAAAGAG
1 ACTTATAATTTCATAAATTTAAAAGAG
128575 ACT
1 ACT
128578 AAAAAACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (27 bp):
ACTTATAATTTCATAAATTTAAAAGAG
Found at i:137645 original size:25 final size:25
Alignment explanation
Indices: 137611--137688 Score: 156
Period size: 25 Copynumber: 3.1 Consensus size: 25
137601 TGGTTGTTGG
137611 TTTAAGCATCATTTAAAATTTTGAA
1 TTTAAGCATCATTTAAAATTTTGAA
137636 TTTAAGCATCATTTAAAATTTTGAA
1 TTTAAGCATCATTTAAAATTTTGAA
137661 TTTAAGCATCATTTAAAATTTTGAA
1 TTTAAGCATCATTTAAAATTTTGAA
137686 TTT
1 TTT
137689 TCCCTGTCCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (25 bp):
TTTAAGCATCATTTAAAATTTTGAA
Found at i:147770 original size:42 final size:42
Alignment explanation
Indices: 147711--147796 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
147701 ATACAACAAA
147711 TACTGCTACCTCAGTTATAACTTTGCATTGATTGATAAGCAT
1 TACTGCTACCTCAGTTATAACTTTGCATTGATTGATAAGCAT
147753 TACTGCTACCTCAGTTATAACTTTGCATTGATTGATAAGCAT
1 TACTGCTACCTCAGTTATAACTTTGCATTGATTGATAAGCAT
147795 TA
1 TA
147797 ACAACTAGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (42 bp):
TACTGCTACCTCAGTTATAACTTTGCATTGATTGATAAGCAT
Found at i:149529 original size:16 final size:16
Alignment explanation
Indices: 149508--149540 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
149498 AATAATACTT
149508 AATTTCAAGCTCCTAA
1 AATTTCAAGCTCCTAA
*
149524 AATTTCAAGTTCCTAA
1 AATTTCAAGCTCCTAA
149540 A
1 A
149541 GTGTGAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (16 bp):
AATTTCAAGCTCCTAA
Found at i:156375 original size:33 final size:31
Alignment explanation
Indices: 156329--156412 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 31
156319 GTCACATCAG
* *
156329 TAAATAATTTAAAATTAATTTGAAATTATTTTT
1 TAAAAAATATAAAATTAA-TT-AAATTATTTTT
*
156362 TAAAAAATATAAAATT-ATTATATTATTTTT
1 TAAAAAATATAAAATTAATTAAATTATTTTT
*
156392 T--GAAATATAAAATT-ATTAAAT
1 TAAAAAATATAAAATTAATTAAAT
156413 AATTATAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 18 0.39
30 11 0.24
31 2 0.04
32 1 0.02
33 14 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
TAAAAAATATAAAATTAATTAAATTATTTTT
Found at i:156389 original size:30 final size:28
Alignment explanation
Indices: 156353--156409 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
156343 TTAATTTGAA
156353 ATTATTTTTTAAAAAATATAAAATTATTAT
1 ATTATTTTTT--AAAATATAAAATTATTAT
*
156383 ATTATTTTTTGAAATATAAAATTATTA
1 ATTATTTTTTAAAATATAAAATTATTA
156410 AATAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 16 0.62
30 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
ATTATTTTTTAAAATATAAAATTATTAT
Found at i:157258 original size:6 final size:6
Alignment explanation
Indices: 157247--157279 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
157237 TTCTTCAACA
157247 ATGAAG ATGAAG -TGAAG ATGAAG -TGAAG ATGAA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAA
157280 TGGGCTATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.18
Consensus pattern (6 bp):
ATGAAG
Found at i:157264 original size:11 final size:11
Alignment explanation
Indices: 157248--157279 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
157238 TCTTCAACAA
157248 TGAAGATGAAG
1 TGAAGATGAAG
157259 TGAAGATGAAG
1 TGAAGATGAAG
157270 TGAAGATGAA
1 TGAAGATGAA
157280 TGGGCTATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.34, T:0.19
Consensus pattern (11 bp):
TGAAGATGAAG
Found at i:159851 original size:21 final size:22
Alignment explanation
Indices: 159825--159866 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
159815 ATATAATAAC
159825 GAAACAAC-ATCAAAAA-CAGTG
1 GAAACAACTA-CAAAAAGCAGTG
159846 GAAACAACTACAAAAAGCAGT
1 GAAACAACTACAAAAAGCAGT
159867 AATTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.57, C:0.19, G:0.14, T:0.10
Consensus pattern (22 bp):
GAAACAACTACAAAAAGCAGTG
Found at i:160402 original size:28 final size:26
Alignment explanation
Indices: 160371--160423 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
160361 TTTGAAATTA
160371 AATTAGAATTT-ATTTTTCATTAATATAT
1 AATT-GAATTTAATTTTT-ATT-ATATAT
*
160399 AATTTAATTTAATTTTTATTATATA
1 AATTGAATTTAATTTTTATTATATA
160424 AAAACGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 5 0.22
27 8 0.35
28 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
AATTGAATTTAATTTTTATTATATAT
Found at i:161527 original size:20 final size:21
Alignment explanation
Indices: 161502--161540 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
161492 TAAAACGAAG
161502 TAGTTTTG-CTTTTAACTTAA
1 TAGTTTTGACTTTTAACTTAA
161522 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
161541 TAGAAAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTAA
Found at i:168265 original size:22 final size:22
Alignment explanation
Indices: 168240--168281 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
168230 AATAGCTACA
*
168240 TACTCCCTC-TCATTTATACTTC
1 TACTCCC-CATCATGTATACTTC
168262 TACTCCCCATCATGTATACT
1 TACTCCCCATCATGTATACT
168282 CCCTTTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.21, C:0.36, G:0.02, T:0.40
Consensus pattern (22 bp):
TACTCCCCATCATGTATACTTC
Found at i:185036 original size:70 final size:72
Alignment explanation
Indices: 184899--185037 Score: 192
Period size: 70 Copynumber: 2.0 Consensus size: 72
184889 ATAAGAGGAA
* * * * * *
184899 TTTAATTTTTATATATTTTAACTAGGTTTTAGATTTAGATTTTTAAGCTTAATTTTAAATAATAT
1 TTTAATTTTTAAATATTTTAACTAGATTTTAAATCTAGATTTTTAAGCTTAATTTTAAACAAAAT
184964 TTTATAT
66 TTTATAT
* *
184971 TTTAATTTTTAAAT-TTTTAGCTAGATTTTAAATCTAGA-TTTTAAGCTTAATTTTTAACAAAAT
1 TTTAATTTTTAAATATTTTAACTAGATTTTAAATCTAGATTTTTAAGCTTAATTTTAAACAAAAT
185034 TTTA
66 TTTA
185038 GATATTGGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
70 26 0.44
71 20 0.34
72 13 0.22
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (72 bp):
TTTAATTTTTAAATATTTTAACTAGATTTTAAATCTAGATTTTTAAGCTTAATTTTAAACAAAAT
TTTATAT
Found at i:187315 original size:13 final size:13
Alignment explanation
Indices: 187297--187321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187287 ATTTCATGAG
187297 GTGAAAAGAAAAC
1 GTGAAAAGAAAAC
187310 GTGAAAAGAAAA
1 GTGAAAAGAAAA
187322 AGGAGGCAAG
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:0.64, C:0.04, G:0.24, T:0.08
Consensus pattern (13 bp):
GTGAAAAGAAAAC
Found at i:195266 original size:5 final size:5
Alignment explanation
Indices: 195256--195282 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
195246 TATAACACAT
195256 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
195283 AAGTCGGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:198595 original size:17 final size:17
Alignment explanation
Indices: 198575--198607 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
198565 TGTCAACAAC
198575 AATTTA-TATGTATTTTA
1 AATTTATTAT-TATTTTA
198592 AATTTATTATTATTTT
1 AATTTATTATTATTTT
198608 TGAAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
AATTTATTATTATTTTA
Found at i:199389 original size:22 final size:22
Alignment explanation
Indices: 199364--199411 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
199354 TTATTTTACT
* * *
199364 ATTTTGTCGTTGTTTTGTTATC
1 ATTTTGTCATTATATTGTTATC
*
199386 ATTTTGTCATTATATTGTTATT
1 ATTTTGTCATTATATTGTTATC
199408 ATTT
1 ATTT
199412 GGTTATTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.06, G:0.12, T:0.65
Consensus pattern (22 bp):
ATTTTGTCATTATATTGTTATC
Found at i:199390 original size:11 final size:11
Alignment explanation
Indices: 199376--199418 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
199366 TTTGTCGTTG
*
199376 TTTTGTTATCA
1 TTTTGTTATTA
*
199387 TTTTGTCATTA
1 TTTTGTTATTA
*
199398 TATTGTTATTA
1 TTTTGTTATTA
*
199409 TTTGGTTATT
1 TTTTGTTATT
199419 GTTTGGATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.19, C:0.05, G:0.12, T:0.65
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:202935 original size:44 final size:45
Alignment explanation
Indices: 202873--202968 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 45
202863 TCGTATATTC
* *
202873 TTTGA-TTCAGTATTTAAACATGTAATAACTGGTG-AAGCCAATG
1 TTTGAGTTCAGTATTTAAACATGTAAGAACTGGTGAAAGCCAATA
* *
202916 TTTGAGTTCTGTATTTAAACATGTAAGAACTGGTGAAAGGCAATA
1 TTTGAGTTCAGTATTTAAACATGTAAGAACTGGTGAAAGCCAATA
202961 TTTGAGTT
1 TTTGAGTT
202969 GAGAGAGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
43 5 0.11
44 27 0.57
45 15 0.32
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (45 bp):
TTTGAGTTCAGTATTTAAACATGTAAGAACTGGTGAAAGCCAATA
Found at i:209675 original size:4 final size:4
Alignment explanation
Indices: 209666--209690 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
209656 TTATTTTATT
209666 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
209691 ATTATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:213557 original size:2 final size:2
Alignment explanation
Indices: 213550--213574 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
213540 TACCTCCATC
213550 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
213575 CATCTTTCAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:215207 original size:13 final size:13
Alignment explanation
Indices: 215189--215215 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
215179 GCTCCTGGTG
215189 TATCTGAACTATT
1 TATCTGAACTATT
215202 TATCTGAACTATT
1 TATCTGAACTATT
215215 T
1 T
215216 TTATTTAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TATCTGAACTATT
Found at i:232504 original size:41 final size:41
Alignment explanation
Indices: 232447--232528 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
232437 ACATGTCATC
232447 GAAAGAGGTACATATATGCTATATTTAGATATTTTGTTTTT
1 GAAAGAGGTACATATATGCTATATTTAGATATTTTGTTTTT
232488 GAAAGAGGTACATATATGCTATATTTAGATATTTTGTTTTT
1 GAAAGAGGTACATATATGCTATATTTAGATATTTTGTTTTT
232529 AAATCTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (41 bp):
GAAAGAGGTACATATATGCTATATTTAGATATTTTGTTTTT
Found at i:242115 original size:6 final size:6
Alignment explanation
Indices: 242104--242134 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
242094 TCCCATGGTC
242104 CATGTG CATGTG CATGTG CATGTG CATGTG C
1 CATGTG CATGTG CATGTG CATGTG CATGTG C
242135 TGTCTGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.32
Consensus pattern (6 bp):
CATGTG
Found at i:263318 original size:7 final size:7
Alignment explanation
Indices: 263306--263330 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
263296 TTTTAATATT
263306 TTTAAAA
1 TTTAAAA
263313 TTTAAAA
1 TTTAAAA
263320 TTTAAAA
1 TTTAAAA
263327 TTTA
1 TTTA
263331 TTTTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTAAAA
Found at i:269870 original size:3 final size:3
Alignment explanation
Indices: 269862--269886 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
269852 CATAGATTGG
269862 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
269887 GGTAGTGGTA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:271079 original size:15 final size:17
Alignment explanation
Indices: 271056--271098 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
271046 CAATCATAAT
271056 TAATATATTAAT-AAATA
1 TAAT-TATTAATAAAATA
271073 -AATTATTAAATAAAATA
1 TAATTATT-AATAAAATA
271090 TAATTATTA
1 TAATTATTA
271099 TAATTGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.17
16 6 0.26
17 6 0.26
18 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATTATTAATAAAATA
Found at i:275413 original size:16 final size:16
Alignment explanation
Indices: 275392--275444 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
275382 AGTTCAATTA
275392 TTTTATTATTAATTTC
1 TTTTATTATTAATTTC
* *
275408 TTTTATT-TCAA-TTA
1 TTTTATTATTAATTTC
275422 TTTTATTATTAATTTC
1 TTTTATTATTAATTTC
275438 TTTTATT
1 TTTTATT
275445 TCTACTTCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.29
15 6 0.19
16 16 0.52
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTATTATTAATTTC
Found at i:275418 original size:30 final size:30
Alignment explanation
Indices: 275384--275446 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
275374 GTTCAAAAAG
275384 TTCAATTATTTTATTATTAATTTCTTTTAT
1 TTCAATTATTTTATTATTAATTTCTTTTAT
275414 TTCAATTATTTTATTATTAATTTCTTTTAT
1 TTCAATTATTTTATTATTAATTTCTTTTAT
275444 TTC
1 TTC
275447 TACTTCTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (30 bp):
TTCAATTATTTTATTATTAATTTCTTTTAT
Found at i:280610 original size:2 final size:2
Alignment explanation
Indices: 280603--280628 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
280593 ATTATAATCA
280603 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
280629 GTATTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:286148 original size:33 final size:34
Alignment explanation
Indices: 286049--286149 Score: 141
Period size: 34 Copynumber: 3.0 Consensus size: 34
286039 ACAACTCACT
* *
286049 TTGTAAGTTTTCAAGCTCAAGAAATCAGTATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
286083 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
* * * *
286117 TTTTAATTTTTCAAACTGAAG-AATTATTATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
286150 AAAATAACAC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 11 0.18
34 50 0.82
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (34 bp):
TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
Found at i:287400 original size:24 final size:24
Alignment explanation
Indices: 287395--287730 Score: 383
Period size: 24 Copynumber: 13.4 Consensus size: 24
287385 AAGTAAACAT
*
287395 TTCCGTTCCAAGTAAACCATTCCG
1 TTCCGTTCCAAGTAAACCGTTCCG
287419 TTCCGTTCCAAGTAAACCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCG
*
287443 TTCCGTTCCAAGTACACCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCG
*
287467 TTCCGTTCCAAGTAAAACGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCG
*
287491 TTCCGTTCCAA-T---CCGAGTAAACCG
1 TTCCGTTCCAAGTAAACC--GT--TCCG
287515 TTCCGTTCCAAGTAAACCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCG
287539 TTCCGTTCCAAGTAAACCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCG
287563 TTCCGTTCCAAGTAAACTGAACCGTTCCG
1 TTCCGTTCCAAGT--A---AACCGTTCCG
*
287592 TTCCGTTCCAAGTACACCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCG
287616 TTCCGTTCCAAGTAAACCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCG
287640 TTCCGTTCCAATCCGAGTAAACCGTTCCG
1 TTCCGTTCC-A----AGTAAACCGTTCCG
* *
287669 TTCCGTTCCAATCCGAGCAAACAGTTCCG
1 TTCCGTTCC-A----AGTAAACCGTTCCG
* * *
287698 TTCCGTTCCGAGCAAACAGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCG
287722 TTCCGTTCC
1 TTCCGTTCC
287731 GAGCAAACAG
Statistics
Matches: 282, Mismatches: 12, Indels: 36
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.00
22 2 0.01
23 1 0.00
24 197 0.70
25 2 0.01
26 3 0.01
27 1 0.00
28 2 0.01
29 73 0.26
ACGTcount: A:0.21, C:0.34, G:0.17, T:0.28
Consensus pattern (24 bp):
TTCCGTTCCAAGTAAACCGTTCCG
Found at i:287404 original size:19 final size:19
Alignment explanation
Indices: 287376--287446 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
287366 GACCATTCCG
*
287376 TTCCGGTCCAAGTAAACAT
1 TTCCGTTCCAAGTAAACAT
287395 TTCCGTTCCAAGTAAACCATT
1 TTCCGTTCCAAGTAAA-CA-T
**
287416 CCGTTCCGTTCCAAGTAAACCG
1 ---TTCCGTTCCAAGTAAACAT
287438 TTCCGTTCC
1 TTCCGTTCC
287447 GTTCCAAGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
19 24 0.55
20 2 0.05
21 1 0.02
23 1 0.02
24 16 0.36
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (19 bp):
TTCCGTTCCAAGTAAACAT
Found at i:287447 original size:29 final size:29
Alignment explanation
Indices: 287414--287707 Score: 172
Period size: 29 Copynumber: 10.3 Consensus size: 29
287404 AAGTAAACCA
287414 TTCCGTTCCGTTCCAAGTAAA-----CCG
1 TTCCGTTCCGTTCCAAGTAAACCGTTCCG
*
287438 TTCCGTTCCGTTCCAAGTACACCGTT-C-
1 TTCCGTTCCGTTCCAAGTAAACCGTTCCG
*
287465 ---CGTTCCGTTCCAAGTAAAACGTTCCG
1 TTCCGTTCCGTTCCAAGTAAACCGTTCCG
** *
287491 TTCCGTTCCAATCCGAGTAAACCGTTCCG
1 TTCCGTTCCGTTCCAAGTAAACCGTTCCG
* *** *
287520 TTCCAAGTAAACCGTTCC--GTTCCGTTCCAAGTAAACCG
1 TTCC--GT--TCCGTTCCAAG-T--AAACC--GT--TCCG
* **
287558 TTCCGTTCCGTTCCAAGTAAACTGAACCG
1 TTCCGTTCCGTTCCAAGTAAACCGTTCCG
*
287587 TTCCGTTCCGTTCCAAGT--A-C--ACCG
1 TTCCGTTCCGTTCCAAGTAAACCGTTCCG
287611 TTCCGTTCCGTTCCAAGTAAACCGTTCCG
1 TTCCGTTCCGTTCCAAGTAAACCGTTCCG
** *
287640 TTCCGTTCCAATCCGAGTAAACCGTTCCG
1 TTCCGTTCCGTTCCAAGTAAACCGTTCCG
** * * *
287669 TTCCGTTCCAATCCGAGCAAACAGTTCCG
1 TTCCGTTCCGTTCCAAGTAAACCGTTCCG
287698 TTCCGTTCCG
1 TTCCGTTCCG
287708 AGCAAACAGT
Statistics
Matches: 214, Mismatches: 28, Indels: 51
0.73 0.10 0.17
Matches are distributed among these distances:
24 63 0.29
25 1 0.00
26 1 0.00
27 2 0.01
28 1 0.00
29 113 0.53
31 4 0.02
32 1 0.00
33 6 0.03
34 9 0.04
35 1 0.00
36 5 0.02
38 7 0.03
ACGTcount: A:0.20, C:0.34, G:0.17, T:0.29
Consensus pattern (29 bp):
TTCCGTTCCGTTCCAAGTAAACCGTTCCG
Found at i:287517 original size:19 final size:19
Alignment explanation
Indices: 287493--287537 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
287483 ACGTTCCGTT
*
287493 CCGTTCCAATCCGAGTAAA
1 CCGTTCCAATCCAAGTAAA
**
287512 CCGTTCCGTTCCAAGTAAA
1 CCGTTCCAATCCAAGTAAA
287531 CCGTTCC
1 CCGTTCC
287538 GTTCCGTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (19 bp):
CCGTTCCAATCCAAGTAAA
Found at i:287696 original size:53 final size:52
Alignment explanation
Indices: 287395--287739 Score: 331
Period size: 53 Copynumber: 6.8 Consensus size: 52
287385 AAGTAAACAT
*
287395 TTCCGTTCCAAGTAAACCATTCCGTTCCGTTCCAAGT----AAACCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCGTTCCGTTCCAAGTAAACAAACCGTTCCG
* ***
287443 TTCCGTTCCAAGTACACCGTTCCGTTCCGTTCCAAGTAAAACGTTCCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCGTTCCGTTCCAAGT-AAACAAACCGTTCCG
** *
287496 TTCCAATCCGAGTAAA-----CCGTTCCGTTCCAAGT----AAACCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCGTTCCGTTCCAAGTAAACAAACCGTTCCG
*
287539 TTCCGTTCCAAGTAAACCGTTCCGTTCCGTTCCAAGTAAACTGAACCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCGTTCCGTTCCAAGTAAAC-AAACCGTTCCG
* ***
287592 TTCCGTTCCAAGTACACCGTTCCGTTCCGTTCCAAGTAAACCGTTCCGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCGTTCCGTTCCAAGTAAA-CAAACCGTTCCG
** * * * *
287645 TTCCAATCCGAGTAAACCGTTCCGTTCCGTTCCAA-TCCGAGCAAACAGTTCCG
1 TTCCGTTCCAAGTAAACCGTTCCGTTCCGTTCCAAGT--AAACAAACCGTTCCG
* * * * *
287698 TTCCGTTCCGAGCAAACAGTTCCGTTCCGTTCCGAGCAAACA
1 TTCCGTTCCAAGTAAACCGTTCCGTTCCGTTCCAAGTAAACA
287740 GTTTAGAACA
Statistics
Matches: 241, Mismatches: 37, Indels: 34
0.77 0.12 0.11
Matches are distributed among these distances:
43 21 0.09
48 67 0.28
52 4 0.02
53 147 0.61
54 2 0.01
ACGTcount: A:0.22, C:0.34, G:0.17, T:0.28
Consensus pattern (52 bp):
TTCCGTTCCAAGTAAACCGTTCCGTTCCGTTCCAAGTAAACAAACCGTTCCG
Found at i:288146 original size:217 final size:212
Alignment explanation
Indices: 287742--288147 Score: 704
Period size: 216 Copynumber: 1.9 Consensus size: 212
287732 AGCAAACAGT
*
287742 TTAGAACATCAAAATGATATATTACTGAGAAAAAAAACACATACTATGATATTATTTCTCATTTC
1 TTAGAACATCAAAATGATATATTACTGAGAAAAAAAACACATACTATGATATTATTTCTCATTTA
* * *
287807 TCAGAATTCGTGATATCCAGAAAATTTGATTAAACCTATAAGCAAAATAAACGAGGAAAAATAAG
66 TCAGAATTCGTGATATCCAGAAAATTTGATTAAACCTATAAACAAAATAAAAGAGGAAAAAAAAG
*
287872 GCGGATACCTTCATAACAATACAATCCTCCAAATCACCATATTTACTCATGTATTCCCTCTACCC
131 ACGGATACCTTCATAACAATACAATCCTCCAAATCACCATATTTACTCATGTATTCCCTCTACCC
287937 GTTCCAGAAAAAAAACC
196 GTTCCAGAAAAAAAACC
*
287954 TTAGAACATCAAAATGATATATTACTGACAGAAAAAAAAAACACATACTATGATATTATTTTTCA
1 TTAGAACATCAAAATGATATATTACTG--AG--AAAAAAAACACATACTATGATATTATTTCTCA
288019 TTTATCAGAATTCGTGATATCCAGAAAATTTGATTAAACCTATAAACAAAATAAAAGAGGGAAAA
62 TTTATCAGAATTCGTGATATCCAGAAAATTTGATTAAACCTATAAACAAAATAAAAGA-GGAAAA
*
288084 AAAAGACGGATACCTTCATGACAATACAATCCTCCAAATCACCATATTTACTCATGTATTCCCT
126 AAAAGACGGATACCTTCATAACAATACAATCCTCCAAATCACCATATTTACTCATGTATTCCCT
288148 TAAACCTTCA
Statistics
Matches: 182, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
212 27 0.15
214 2 0.01
216 86 0.47
217 67 0.37
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.28
Consensus pattern (212 bp):
TTAGAACATCAAAATGATATATTACTGAGAAAAAAAACACATACTATGATATTATTTCTCATTTA
TCAGAATTCGTGATATCCAGAAAATTTGATTAAACCTATAAACAAAATAAAAGAGGAAAAAAAAG
ACGGATACCTTCATAACAATACAATCCTCCAAATCACCATATTTACTCATGTATTCCCTCTACCC
GTTCCAGAAAAAAAACC
Found at i:289797 original size:23 final size:24
Alignment explanation
Indices: 289764--289808 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
289754 TACAATGATC
* *
289764 TAATTTTTTTTTTG-TTCTATTTT
1 TAATTTATTTTTGGATTCTATTTT
289787 TAATTTATTTTTGGATTCTATT
1 TAATTTATTTTTGGATTCTATT
289809 AGATGATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.71
Consensus pattern (24 bp):
TAATTTATTTTTGGATTCTATTTT
Found at i:300192 original size:23 final size:23
Alignment explanation
Indices: 300166--300209 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
300156 ATATGTGAAC
300166 TTTGATTTAATGTATAATTGTTT
1 TTTGATTTAATGTATAATTGTTT
* *
300189 TTTGCTTTAATGTGTAATTGT
1 TTTGATTTAATGTATAATTGT
300210 ATACATGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.02, G:0.16, T:0.59
Consensus pattern (23 bp):
TTTGATTTAATGTATAATTGTTT
Found at i:300302 original size:31 final size:31
Alignment explanation
Indices: 300204--300306 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 31
300194 TTTAATGTGT
* *
300204 AATTGTATACATG-AACTTTAATT-TGGTGT-
1 AATTATATACATGAAACTTTAATTGTGAT-TC
* * *
300233 AGTTATACACATGAAACTTTAATTGTGGTTC
1 AATTATATACATGAAACTTTAATTGTGATTC
* * * * *
300264 AAATATATACTTGAAATTTTAATTTTGATTT
1 AATTATATACATGAAACTTTAATTGTGATTC
300295 AATTATATACAT
1 AATTATATACAT
300307 TTAAAGAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
29 10 0.17
30 11 0.19
31 37 0.64
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.45
Consensus pattern (31 bp):
AATTATATACATGAAACTTTAATTGTGATTC
Found at i:300691 original size:2 final size:2
Alignment explanation
Indices: 300684--300709 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
300674 CAATTATGCC
300684 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
300710 CCTATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:301206 original size:35 final size:36
Alignment explanation
Indices: 301125--301206 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
301115 GTTATGGATG
*
301125 ATTAAAA-TTTAATTATAAAATTTTAAGGAGATTAA
1 ATTAAAATTTTAATTATAAAATTTTAAAGAGATTAA
* * *
301160 AATATAGTTTTAATT-TAAAATTTTAAA-AGAATTAA
1 ATTAAAATTTTAATTATAAAATTTTAAAGAG-ATTAA
301195 ATTAAAATTTTA
1 ATTAAAATTTTA
301207 CTATTTTGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
34 2 0.05
35 29 0.76
36 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (36 bp):
ATTAAAATTTTAATTATAAAATTTTAAAGAGATTAA
Found at i:309549 original size:16 final size:16
Alignment explanation
Indices: 309528--309579 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
309518 ATGAGCATCA
309528 CTCTTATAGCTTTCTT
1 CTCTTATAGCTTTCTT
**
309544 CTCTTA-AGCAATC-T
1 CTCTTATAGCTTTCTT
309558 CTCTTATAGCTTTCTT
1 CTCTTATAGCTTTCTT
309574 CTCTTA
1 CTCTTA
309580 AGCAATTCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 7 0.23
15 10 0.33
16 13 0.43
ACGTcount: A:0.17, C:0.27, G:0.06, T:0.50
Consensus pattern (16 bp):
CTCTTATAGCTTTCTT
Found at i:309562 original size:14 final size:15
Alignment explanation
Indices: 309540--309585 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
309530 CTTATAGCTT
309540 TCTTCTCTTAAGCAA
1 TCTTCTCTTAAGCAA
**
309555 TC-TCTCTTATAGCTT
1 TCTTCTCTTA-AGCAA
309570 TCTTCTCTTAAGCAA
1 TCTTCTCTTAAGCAA
309585 T
1 T
309586 TCCTGTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 7 0.28
15 11 0.44
16 7 0.28
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.46
Consensus pattern (15 bp):
TCTTCTCTTAAGCAA
Found at i:309562 original size:30 final size:30
Alignment explanation
Indices: 309528--309585 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
309518 ATGAGCATCA
309528 CTCTTATAGCTTTCTTCTCTTAAGCAATCT
1 CTCTTATAGCTTTCTTCTCTTAAGCAATCT
309558 CTCTTATAGCTTTCTTCTCTTAAGCAAT
1 CTCTTATAGCTTTCTTCTCTTAAGCAAT
309586 TCCTGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.21, C:0.26, G:0.07, T:0.47
Consensus pattern (30 bp):
CTCTTATAGCTTTCTTCTCTTAAGCAATCT
Found at i:314027 original size:8 final size:8
Alignment explanation
Indices: 314014--314046 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
314004 CATATTTAAA
314014 CACCACTT
1 CACCACTT
314022 CACCACTT
1 CACCACTT
314030 CACCACTT
1 CACCACTT
314038 CACCACTT
1 CACCACTT
314046 C
1 C
314047 TCTCATCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.52, G:0.00, T:0.24
Consensus pattern (8 bp):
CACCACTT
Found at i:320620 original size:5 final size:5
Alignment explanation
Indices: 320614--320647 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
320604 CTCCCCTCTC
* *
320614 CTTTC CTTTT CTTTT CTTTT CTTTT ATTTT CTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTT
320648 ATTTCTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (5 bp):
CTTTT
Found at i:322806 original size:30 final size:30
Alignment explanation
Indices: 322772--322835 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
322762 ACTTTATTTG
** *
322772 AAAATTATTTTTTGACCCTCAAATTTTTTA
1 AAAATTATAATTTGACCCTCAAATTTTTCA
* *
322802 AAAATTCTAATTTGACCCTTAAATTTTTCA
1 AAAATTATAATTTGACCCTCAAATTTTTCA
322832 AAAA
1 AAAA
322836 AATTGAATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.44
Consensus pattern (30 bp):
AAAATTATAATTTGACCCTCAAATTTTTCA
Found at i:322867 original size:32 final size:32
Alignment explanation
Indices: 322801--322891 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 32
322791 CAAATTTTTT
* * * *
322801 AAAAATTCTAATTTGACCCTTAAATTTTTCAA
1 AAAAATTCGAATTCGACCCCTAAATTTTCCAA
322833 AAAAATT-GAATTCGACCCCTAAATTTTCC-A
1 AAAAATTCGAATTCGACCCCTAAATTTTCCAA
* * * *
322863 AAAAATTCCAATTTGACCTCTAAACTTTC
1 AAAAATTCGAATTCGACCCCTAAATTTTC
322892 TAGAACTTCC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 8 0.16
31 35 0.70
32 7 0.14
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (32 bp):
AAAAATTCGAATTCGACCCCTAAATTTTCCAA
Found at i:322886 original size:31 final size:29
Alignment explanation
Indices: 322782--322941 Score: 135
Period size: 30 Copynumber: 5.3 Consensus size: 29
322772 AAAATTATTT
** *
322782 TTTGACCCTCAAATTTTTTAAAAATTCTAA
1 TTTGACCCT-AAATTTTCAAAAAATTCCAA
*
322812 TTTGACCCTTAAATTTTTCAAAAAAATT-GAA
1 TTTGACCC-TAAA-TTTTC-AAAAAATTCCAA
*
322843 TTCGACCCCTAAATTTTCCAAAAAATTCCAA
1 TTTGA-CCCTAAATTTT-CAAAAAATTCCAA
* * * *
322874 TTTGACCTCTAAACTTTCTAGAACTTCCAA
1 TTTGACC-CTAAATTTTCAAAAAATTCCAA
*
322904 TTTGATCCCTAAAATTTTC-AAAAATTCAAA
1 TTTGA-CCCT-AAATTTTCAAAAAATTCCAA
322934 TTTGACCC
1 TTTGACCC
322942 GGATTTAAAT
Statistics
Matches: 107, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
29 3 0.03
30 55 0.51
31 39 0.36
32 10 0.09
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (29 bp):
TTTGACCCTAAATTTTCAAAAAATTCCAA
Found at i:326083 original size:33 final size:33
Alignment explanation
Indices: 326046--326114 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
326036 ATAAATTTTA
326046 AAAAAATA-ATA-ATTAGAATATACAAGAAATTAG
1 AAAAAATATATATA-TA-AATATACAAGAAATTAG
* *
326079 AAAAAATATATATATATATATATAAGAAATTAG
1 AAAAAATATATATATAAATATACAAGAAATTAG
326112 AAA
1 AAA
326115 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 26 0.81
34 5 0.16
35 1 0.03
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (33 bp):
AAAAAATATATATATAAATATACAAGAAATTAG
Found at i:326226 original size:14 final size:14
Alignment explanation
Indices: 326207--326234 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
326197 NTCTAATACT
326207 AATAGAATAGAAAA
1 AATAGAATAGAAAA
326221 AATAGAATAGAAAA
1 AATAGAATAGAAAA
326235 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Done.