Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001532.1 Kokia drynarioides strain JFW-HI SEQ_113101, 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: 132675
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:424 original size:12 final size:12
Alignment explanation
Indices: 403--445 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
393 CAATTAAGAA
*
403 AATAAATATAAT
1 AATAATTATAAT
* *
415 TATAATTATAAA
1 AATAATTATAAT
*
427 AATAATAATAAT
1 AATAATTATAAT
439 AATAATT
1 AATAATT
446 GGGTTGCCTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AATAATTATAAT
Found at i:425 original size:18 final size:18
Alignment explanation
Indices: 403--443 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
393 CAATTAAGAA
* *
403 AATAAATATAATTATAAT
1 AATAAAAATAATAATAAT
*
421 TATAAAAATAATAATAAT
1 AATAAAAATAATAATAAT
439 AATAA
1 AATAA
444 TTGGGTTGCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAAAAATAATAATAAT
Found at i:5294 original size:9 final size:9
Alignment explanation
Indices: 5282--5307 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5272 AATTCGGTTT
5282 ATTCGAATA
1 ATTCGAATA
5291 ATTCGAATA
1 ATTCGAATA
5300 ATTCGAAT
1 ATTCGAAT
5308 TCGAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (9 bp):
ATTCGAATA
Found at i:5395 original size:23 final size:23
Alignment explanation
Indices: 5352--5396 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5342 AAAAAAATTC
**
5352 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
5375 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
5397 ATTTGAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:8625 original size:21 final size:21
Alignment explanation
Indices: 8603--8656 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
8593 ATACCTCAGT
8603 TTTG-TTTTGAAAATCCACAG
1 TTTGCTTTTGAAAATCCACAG
* *
8623 TTTGCTTTTGAAAATCTATAG
1 TTTGCTTTTGAAAATCCACAG
* *
8644 ATTGCTGTTGAAA
1 TTTGCTTTTGAAA
8657 TTCAAAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (21 bp):
TTTGCTTTTGAAAATCCACAG
Found at i:9861 original size:16 final size:16
Alignment explanation
Indices: 9837--9871 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9827 GATCTGGGAA
*
9837 AAAATAAAAATAAAAG
1 AAAACAAAAATAAAAG
*
9853 AAAACAAAATTAAAAG
1 AAAACAAAAATAAAAG
9869 AAA
1 AAA
9872 TAGAAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAACAAAAATAAAAG
Found at i:10752 original size:5 final size:5
Alignment explanation
Indices: 10742--10766 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10732 ATATATATTT
10742 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
10767 CCAAGTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:13047 original size:5 final size:5
Alignment explanation
Indices: 13037--13062 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13027 ATTAATTAGC
13037 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
13063 TGAAACAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:17475 original size:16 final size:17
Alignment explanation
Indices: 17447--17502 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
17437 ATTTGCCACG
*
17447 TATTT-TATATTTTATA
1 TATTTCTATTTTTTATA
*
17463 TATTTC-ATTTTTTATT
1 TATTTCTATTTTTTATA
* *
17479 TATTTACTATTCTCTATA
1 TATTT-CTATTTTTTATA
17497 TATTTC
1 TATTTC
17503 CCATCAACCC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 18 0.56
17 2 0.06
18 12 0.38
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTCTATTTTTTATA
Found at i:17910 original size:23 final size:23
Alignment explanation
Indices: 17884--17929 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
17874 CTTAACTATC
17884 CTTAATTTTTTTTTCAATTAAAG
1 CTTAATTTTTTTTTCAATTAAAG
17907 CTTAATTTTTTTTTCAATTAAAG
1 CTTAATTTTTTTTTCAATTAAAG
17930 TCATCTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (23 bp):
CTTAATTTTTTTTTCAATTAAAG
Found at i:18040 original size:18 final size:19
Alignment explanation
Indices: 17968--18040 Score: 78
Period size: 18 Copynumber: 3.8 Consensus size: 19
17958 ATATAGCAAA
* *
17968 AAAAAATTATAAAAATAG-
1 AAAATATTATAAAAATTGT
17986 AAAATATTATAAAAATTGT
1 AAAATATTATAAAAATTGT
*
18005 AAAAGTATATAGAAAAATTGT
1 AAAA-TAT-TATAAAAATTGT
*
18026 ATAAT-TTATAAAAAT
1 AAAATATTATAAAAAT
18041 CGTTGACCGT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
18 24 0.51
19 5 0.11
20 4 0.09
21 14 0.30
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.32
Consensus pattern (19 bp):
AAAATATTATAAAAATTGT
Found at i:18260 original size:29 final size:27
Alignment explanation
Indices: 18227--18307 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 27
18217 TTTGTTTACT
18227 TTTTATAATTTTCTTACAATTTTATAAAA
1 TTTTATAATTTT-TTACAATTTTAT-AAA
* * *
18256 TTTTATAATTTTTTTCTATATTCTATATA
1 TTTTATAATTTTTTAC-A-ATTTTATAAA
18285 TTTTATAATTTTTTACCAATTTT
1 TTTTATAATTTTTTA-CAATTTT
18308 TTTTTTTCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 7 0.16
29 30 0.68
30 7 0.16
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTTATAATTTTTTACAATTTTATAAA
Found at i:28050 original size:59 final size:58
Alignment explanation
Indices: 27929--28092 Score: 183
Period size: 59 Copynumber: 2.8 Consensus size: 58
27919 GTTTGGGGTT
* * * * * *
27929 AAAAACGAAA-CTTTAGACATCCGAGGTAAAACGGTAACTTTTAGGAAAAATTAGGATA
1 AAAAACGAAATTTTTGGACATCCGGGGTAAAATGGTAATTTTTA-GAAAAATGAGGATA
*
27987 AAAAACGAAATTTTTGGACATCCTGGGGTAAAATGGTAATTTTTAGAAAAATCGA-GATC
1 AAAAACGAAATTTTTGGACATCC-GGGGTAAAATGGTAATTTTTAGAAAAAT-GAGGATA
* *
28046 AAAAACGGAATTTTTGGACATTCGGGGGT-AAATGGTAATTTTT-GAAA
1 AAAAACGAAATTTTTGGACA-TCCGGGGTAAAATGGTAATTTTTAGAAA
28093 GTTTTGGGGT
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
57 4 0.04
58 24 0.26
59 44 0.47
60 21 0.23
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.27
Consensus pattern (58 bp):
AAAAACGAAATTTTTGGACATCCGGGGTAAAATGGTAATTTTTAGAAAAATGAGGATA
Found at i:28222 original size:58 final size:57
Alignment explanation
Indices: 28047--28419 Score: 305
Period size: 59 Copynumber: 6.5 Consensus size: 57
28037 ATCGAGATCA
* * * * *
28047 AAAACGGAATTTTTGGACA-TTCGGGGGT-AAATGGTAATTTTTGAAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAT-GTAATTTTTGGAAGTTTCGGGGTC
* * *
28104 AAAATGGAA-TTTTGGAAGTTCGAGGGT-AAATGGTAATTTTTGAAAGTTTCGGGTTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAT-GTAATTTTTGGAAGTTTCGGGGTC
*
28160 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTAGAAGTTTCGGGGTC
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-AAAATGTAATTTTTGGAAGTTTCGGGGTC
* **
28218 AAAATTGGAATTTTTGGAAGCTT-AAGGGTAAAAATGTAATTTTTGGAAGTTTCGAAGTC
1 AAAA-TGGAATTTTTGGAAG-TTCGAGGGT-AAAATGTAATTTTTGGAAGTTTCGGGGTC
* * * * * * *
28277 AAAAATGTATTTTTTGGGAAAATT-GAGGTTAAAATGGAATTTTGGGAAGTTT-GGAGGTA
1 -AAAATGGAATTTTT-GG-AAGTTCGAGGGTAAAATGTAATTTTTGGAAGTTTCGG-GGTC
* * * * * * *
28336 AAAATGTAATTTTTAGAAAGTTTGAGGTTAAAGTGGAA-TTTTGGAAAGTTTAGGGGT-
1 AAAATGGAATTTTT-GGAAGTTCGAGGGTAAAATGTAATTTTTGG-AAGTTTCGGGGTC
* *
28393 AAAATGTAATTTTTAGAAAGTTCGAGG
1 AAAATGGAATTTTT-GGAAGTTCGAGG
28420 ACCTTCAAGG
Statistics
Matches: 274, Mismatches: 29, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
55 1 0.00
56 51 0.19
57 61 0.22
58 62 0.23
59 83 0.30
60 14 0.05
61 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (57 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGTAATTTTTGGAAGTTTCGGGGTC
Found at i:28232 original size:30 final size:28
Alignment explanation
Indices: 28047--28406 Score: 229
Period size: 29 Copynumber: 12.5 Consensus size: 28
28037 ATCGAGATCA
*
28047 AAAACGGAATTTTTGGACA--TTCGGGGGT
1 AAAATGGAATTTTTGGA-AGTTTC-GGGGT
* *
28075 -AAATGGTAATTTTTGAAAGTTTTGGGGTT
1 AAAATGG-AATTTTTGGAAGTTTCGGGG-T
28104 AAAATGGAA-TTTTGGAAG-TTCGAGGGT
1 AAAATGGAATTTTTGGAAGTTTCG-GGGT
* *
28131 -AAATGGTAATTTTTGAAAGTTTCGGGTTT
1 AAAATGG-AATTTTTGGAAGTTTCGGG-GT
28160 AAAATGGAATTTTTGGAAG-TTCGAGGGT
1 AAAATGGAATTTTTGGAAGTTTCG-GGGT
* *
28188 AAAAATGTAATTTTTAGAAGTTTCGGGGT
1 -AAAATGGAATTTTTGGAAGTTTCGGGGT
* **
28217 CAAAATTGGAATTTTTGGAAGCTTAAGGGT
1 -AAAA-TGGAATTTTTGGAAGTTTCGGGGT
* **
28247 AAAAATGTAATTTTTGGAAGTTTCGAAGT
1 -AAAATGGAATTTTTGGAAGTTTCGGGGT
* * ** *
28276 CAAAAATGTATTTTTTGGGAAAATT-GAGGTT
1 --AAAATGGAATTTTT-GGAAGTTTCG-GGGT
*
28307 AAAATGGAATTTTGGGAAGTTT-GGAGGT
1 AAAATGGAATTTTTGGAAGTTTCGG-GGT
* * *
28335 AAAAATGTAATTTTTAGAAAGTTT-GAGGTT
1 -AAAATGGAATTTTT-GGAAGTTTCG-GGGT
* *
28365 AAAGTGGAA-TTTTGGAAAGTTTAGGGGT
1 AAAATGGAATTTTTGG-AAGTTTCGGGGT
*
28393 AAAATGTAATTTTT
1 AAAATGGAATTTTT
28407 AGAAAGTTCG
Statistics
Matches: 261, Mismatches: 46, Indels: 49
0.73 0.13 0.14
Matches are distributed among these distances:
26 6 0.02
27 14 0.05
28 68 0.26
29 101 0.39
30 64 0.25
31 8 0.03
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGT
Found at i:28236 original size:59 final size:57
Alignment explanation
Indices: 28012--28419 Score: 300
Period size: 58 Copynumber: 7.0 Consensus size: 57
28002 GGACATCCTG
*** * * * *
28012 GGGTAAAATGGTAATTTTTAGAAAAATCGAGATCAAAAACGGAATTTTTGGACA-TTCGG
1 GGGTAAAATGGTAATTTTT-GAAGTTTCGGGGTC-AAAATGGAATTTTTGGA-AGTTCGA
* *
28071 GGGT-AAATGGTAATTTTTGAAAGTTTTGGGGTTAAAATGGAA-TTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTG-AAGTTTCGGGGTCAAAATGGAATTTTTGGAAGTTCGA
* *
28127 GGGT-AAATGGTAATTTTTGAAAGTTTCGGGTTTAAAATGGAATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTG-AAGTTTCGGGGTCAAAATGGAATTTTTGGAAGTTCGA
*
28184 GGGTAAAAAT-GTAATTTTTAGAAGTTTCGGGGTCAAAATTGGAATTTTTGGAAGCTT-AA
1 GGGT-AAAATGGTAATTTTT-GAAGTTTCGGGGTCAAAA-TGGAATTTTTGGAAG-TTCGA
** * * *
28243 GGGTAAAAAT-GTAATTTTTGGAAGTTTCGAAGTCAAAAATGTATTTTTTGGGAAAATT-GA
1 GGGT-AAAATGGTAATTTTT-GAAGTTTCGGGGTC-AAAATGGAATTTTT-GG-AAGTTCGA
* * * * * *
28303 GGTTAAAATGG-AATTTTGGGAAGTTT-GGAGGTAAAAATGTAATTTTTAGAAAGTTTGA
1 GGGTAAAATGGTAATTTT-TGAAGTTTCGG-GGTCAAAATGGAATTTTT-GGAAGTTCGA
* * * * * *
28361 GGTTAAAGTGG-AATTTTGGAAAGTTTAGGGGT-AAAATGTAATTTTTAGAAAGTTCGA
1 GGGTAAAATGGTAATTTTTG-AAGTTTCGGGGTCAAAATGGAATTTTT-GGAAGTTCGA
28418 GG
1 GG
28420 ACCTTCAAGG
Statistics
Matches: 300, Mismatches: 32, Indels: 36
0.82 0.09 0.10
Matches are distributed among these distances:
55 1 0.00
56 51 0.17
57 59 0.20
58 86 0.29
59 86 0.29
60 15 0.05
61 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTGAAGTTTCGGGGTCAAAATGGAATTTTTGGAAGTTCGA
Found at i:28259 original size:88 final size:87
Alignment explanation
Indices: 28160--28367 Score: 215
Period size: 88 Copynumber: 2.4 Consensus size: 87
28150 TTTCGGGTTT
* ** *
28160 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTT-AGAAGTTTCGGGGTCAAAATT
1 AAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAAATT-GAGGTCAAAA-T
*
28224 GGAATTTTTGGAAGCTTAAG-GGTA
64 GGAATTTTGGGAAG-TTAAGAGGTA
* * * *
28248 AAAATGTAATTTTTGGAAGTTTCGA-AGTCAAAAATGTATTTTTTGGGAAAATTGAGGTTAAAAT
1 AAAATGTAATTTTTGGAAG-TTCGAGGGT-AAAAATGTAATTTTTGAGAAAATTGAGGTCAAAAT
**
28312 GGAATTTTGGGAAGTTTGGAGGTA
64 GGAATTTTGGGAAGTTAAGAGGTA
* * *
28336 AAAATGTAATTTTTAGAAAGTTTGAGGTTAAA
1 AAAATGTAATTTTT-GGAAGTTCGAGGGTAAA
28368 GTGGAATTTT
Statistics
Matches: 99, Mismatches: 15, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
87 3 0.03
88 59 0.60
89 32 0.32
90 5 0.05
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (87 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAAATTGAGGTCAAAATGG
AATTTTGGGAAGTTAAGAGGTA
Found at i:29435 original size:3 final size:3
Alignment explanation
Indices: 29429--29496 Score: 127
Period size: 3 Copynumber: 22.3 Consensus size: 3
29419 TTATTAATGT
29429 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29477 TTA TTA TTA TTA TTA GTTA T
1 TTA TTA TTA TTA TTA -TTA T
29497 CATCAATGCC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 61 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:30183 original size:6 final size:6
Alignment explanation
Indices: 30174--30269 Score: 76
Period size: 6 Copynumber: 16.7 Consensus size: 6
30164 TTTGGACATT
*
30174 AATTTA AATTTA AATTTA AACTTA AATTTA TAA--TA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * * * * *
30220 TATGTA AATTTA AACTTA AA-ATA AATTTA ATTTTA AA-ATA TATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
30266 AATT
1 AATT
30270 CTGTTGGGCC
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
4 2 0.03
5 12 0.17
6 53 0.77
7 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (6 bp):
AATTTA
Found at i:30210 original size:17 final size:17
Alignment explanation
Indices: 30174--30269 Score: 102
Period size: 17 Copynumber: 5.6 Consensus size: 17
30164 TTTGGACATT
*
30174 AATTTAAATTTAAATTTA
1 AATTTAAATTTAAA-ATA
* *
30192 AACTTAAATTTATAATA
1 AATTTAAATTTAAAATA
* **
30209 AATTTAAATTTTATGTA
1 AATTTAAATTTAAAATA
*
30226 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
30243 AATTTAATTTTAAAATA
1 AATTTAAATTTAAAATA
*
30260 TATTTAAATT
1 AATTTAAATT
30270 CTGTTGGGCC
Statistics
Matches: 62, Mismatches: 16, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
17 50 0.81
18 12 0.19
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:30268 original size:40 final size:40
Alignment explanation
Indices: 30181--30269 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
30171 ATTAATTTAA
* * *
30181 ATTTAAATTTAAACTTAAATTTATAATAAATTTAAATTTT
1 ATTTAAATTTAAACTTAAATATATAATAAATTTAAAATAT
* *
30221 ATGTAAATTTAAACTTAAA-ATA-AATTTAATTTTAAAATAT
1 ATTTAAATTTAAACTTAAATATATAA--TAAATTTAAAATAT
30261 ATTTAAATT
1 ATTTAAATT
30270 CTGTTGGGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.05
39 2 0.05
40 37 0.90
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (40 bp):
ATTTAAATTTAAACTTAAATATATAATAAATTTAAAATAT
Found at i:39397 original size:3 final size:3
Alignment explanation
Indices: 39391--39418 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39381 AGATTTTTAA
39391 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
39419 AAAGTAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:42249 original size:23 final size:23
Alignment explanation
Indices: 42193--42262 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
42183 TCATTAACAT
*
42193 TGTTCGTGAACGTGTTCAATTATA
1 TGTTCGTGAACGTGTTCGATTA-A
* *
42217 TGTTCATGAACGTGTTCGTTTAA
1 TGTTCGTGAACGTGTTCGATTAA
*
42240 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACGTGTTCGATTAA
42263 GTTAAATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACGTGTTCGATTAA
Found at i:42290 original size:23 final size:23
Alignment explanation
Indices: 42246--42291 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
42236 TTAATGTTCG
* *
42246 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
42269 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
42292 CAAACAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:44221 original size:17 final size:16
Alignment explanation
Indices: 44190--44224 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
44180 TTTTAAAATT
*
44190 TAATTTTAATAATAAA
1 TAATATTAATAATAAA
44206 TAATATTAATTAATAAA
1 TAATATTAA-TAATAAA
44223 TA
1 TA
44225 CAATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATATTAATAATAAA
Found at i:44506 original size:30 final size:28
Alignment explanation
Indices: 44450--44506 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
44440 ACTAAAGAAA
44450 ATAATGAATTATTAAAAAATACATACAT
1 ATAATGAATTATTAAAAAATACATACAT
* * *
44478 ATAACTGAATTGTCTAAACAATGCATACA
1 ATAA-TGAATTAT-TAAAAAATACATACA
44507 ATTCAAGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 7 0.29
30 13 0.54
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (28 bp):
ATAATGAATTATTAAAAAATACATACAT
Found at i:48096 original size:2 final size:2
Alignment explanation
Indices: 48089--48116 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48079 AATGTTTATC
48089 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
48117 TTAAAAACGT
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:48707 original size:29 final size:30
Alignment explanation
Indices: 48650--48712 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
48640 TAAAATGGAG
48650 TTTTAAATTCTTTAAAAATTAGAGAAAAAA
1 TTTTAAATTCTTTAAAAATTAGAGAAAAAA
* * *
48680 TTTTAAATTTTTTAAAAGTTA-ATAAAAAA
1 TTTTAAATTCTTTAAAAATTAGAGAAAAAA
48709 TTTT
1 TTTT
48713 GGGCCCTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTTAAATTCTTTAAAAATTAGAGAAAAAA
Found at i:48745 original size:27 final size:28
Alignment explanation
Indices: 48691--48765 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
48681 TTTAAATTTT
** *
48691 TTAAAAGTTAATAAAAAATTTTG-GGCCC
1 TTAAAAGTTAA-AAAAAAAATTGAGCCCC
48719 TTAAAAGTTAAAAAAAAAATTGAGCCCC
1 TTAAAAGTTAAAAAAAAAATTGAGCCCC
*
48747 TTAAAACTTAAAAAAAAAA
1 TTAAAAGTTAAAAAAAAAA
48766 ATAATTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.21
28 33 0.79
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (28 bp):
TTAAAAGTTAAAAAAAAAATTGAGCCCC
Found at i:52168 original size:6 final size:6
Alignment explanation
Indices: 52159--52183 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52149 AAAAAAAACA
52159 TGTATG TGTATG TGTATG TGTATG T
1 TGTATG TGTATG TGTATG TGTATG T
52184 TTTGGATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TGTATG
Found at i:60461 original size:30 final size:30
Alignment explanation
Indices: 60421--60484 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
60411 AAACAACTCG
* *
60421 AAAAAGGC-AAAGTAACTTGAATCAAACAAA
1 AAAAAAGCAAAAG-AACTCGAATCAAACAAA
* *
60451 AAAAAAGCAAAAGAACTCGAATCGAACGAA
1 AAAAAAGCAAAAGAACTCGAATCAAACAAA
60481 AAAA
1 AAAA
60485 TCACAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.09
Consensus pattern (30 bp):
AAAAAAGCAAAAGAACTCGAATCAAACAAA
Found at i:75907 original size:35 final size:35
Alignment explanation
Indices: 75832--75921 Score: 110
Period size: 35 Copynumber: 2.6 Consensus size: 35
75822 TTTGGTTGGA
75832 GAAATGTTCTACTGGCTCTACGAAGCGGCACTATG
1 GAAATGTTCTACTGGCTCTACGAAGCGGCACTATG
* * * * * *
75867 AAAATGGTCTATTAGCTCTACGGAGTGGCA-TCATG
1 GAAATGTTCTACTGGCTCTACGAAGCGGCACT-ATG
75902 GAAATGTTCTACTGGCTCTA
1 GAAATGTTCTACTGGCTCTA
75922 TAGAGCGACA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
34 1 0.02
35 43 0.98
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (35 bp):
GAAATGTTCTACTGGCTCTACGAAGCGGCACTATG
Found at i:75942 original size:35 final size:34
Alignment explanation
Indices: 75833--75942 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 34
75823 TTGGTTGGAG
* *
75833 AAATGTTCTACTGGCTCTACGAAGCGGCACTATGA
1 AAATGTTCTACTGGCTCTAAG-AGCGGCACCATGA
* * * * * * *
75868 AAATGGTCTATTAGCTCTACGGAGTGGCATCATGG
1 AAATGTTCTACTGGCTCTA-AGAGCGGCACCATGA
* *
75903 AAATGTTCTACTGGCTCTATAGAGCGACACCATGT
1 AAATGTTCTACTGGCTCTA-AGAGCGGCACCATGA
75938 AAATG
1 AAATG
75943 GTTTATGGAC
Statistics
Matches: 57, Mismatches: 17, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
35 56 0.98
36 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (34 bp):
AAATGTTCTACTGGCTCTAAGAGCGGCACCATGA
Found at i:76506 original size:56 final size:56
Alignment explanation
Indices: 76446--76564 Score: 132
Period size: 56 Copynumber: 2.1 Consensus size: 56
76436 TGAAGGGTTG
* * *
76446 TCTTATGCGGAAAGTCCACCAAGGATCGTCTTATGCGTAAAA-TCCGTCAGGGACTA
1 TCTTATGCGGAAAGTCCACCAAGAATCATCTTATGCG-AAAAGTCCGTCACGGACTA
* * * * * * *
76502 TCTTATGTGGAATGTCCGCCAATAATTATCTTATGTGAAAAGTCTGTCACGGACTA
1 TCTTATGCGGAAAGTCCACCAAGAATCATCTTATGCGAAAAGTCCGTCACGGACTA
76558 TCTTATG
1 TCTTATG
76565 TGTAATGTCT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
55 4 0.08
56 48 0.92
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (56 bp):
TCTTATGCGGAAAGTCCACCAAGAATCATCTTATGCGAAAAGTCCGTCACGGACTA
Found at i:76519 original size:28 final size:28
Alignment explanation
Indices: 76488--76590 Score: 82
Period size: 28 Copynumber: 3.7 Consensus size: 28
76478 ATGCGTAAAA
* *
76488 TCCGTCAGGGACTATCTTATGTGGAATG
1 TCCGTCAAGGACTATCTTATGTGAAATG
* ** * *
76516 TCCGCCAATAATTATCTTATGTGAAAAG
1 TCCGTCAAGGACTATCTTATGTGAAATG
* * *
76544 TCTGTCACGGACTATCTTATGTGTAATG
1 TCCGTCAAGGACTATCTTATGTGAAATG
* * *
76572 TCTGCCAATGACTAT-TTAT
1 TCCGTCAAGGACTATCTTAT
76591 TTTGTAAAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
27 4 0.07
28 53 0.93
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (28 bp):
TCCGTCAAGGACTATCTTATGTGAAATG
Found at i:76534 original size:84 final size:84
Alignment explanation
Indices: 76380--76545 Score: 199
Period size: 84 Copynumber: 2.0 Consensus size: 84
76370 GGGAAGCCCG
* * * ** **
76380 CCAAGGATCGTCTTATGCGAAAAGTCTGCCACGGTCTATTTTATGTGGAATGTCCGTGAAGGGTT
1 CCAAGGATCGTCTTATGCGAAAAGTCCGCCACGGACTATCTTATGTGGAATGTCCGCCAAGAATT
* *
76445 GTCTTATGCGGAAAGTCCA
66 ATCTTATGCGAAAAGTCCA
* * *
76464 CCAAGGATCGTCTTATGCGTAAAA-TCCGTCAGGGACTATCTTATGTGGAATGTCCGCCAATAAT
1 CCAAGGATCGTCTTATGCG-AAAAGTCCGCCACGGACTATCTTATGTGGAATGTCCGCCAAGAAT
*
76528 TATCTTATGTGAAAAGTC
65 TATCTTATGCGAAAAGTC
76546 TGTCACGGAC
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
84 64 0.94
85 4 0.06
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (84 bp):
CCAAGGATCGTCTTATGCGAAAAGTCCGCCACGGACTATCTTATGTGGAATGTCCGCCAAGAATT
ATCTTATGCGAAAAGTCCA
Found at i:76565 original size:56 final size:56
Alignment explanation
Indices: 76474--76580 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
76464 CCAAGGATCG
*
76474 TCTTATGCGTAAAATCCGTCAGGGACTATCTTATGTGGAATGTCCGCCAATAATTA
1 TCTTATGCGTAAAATCCGTCACGGACTATCTTATGTGGAATGTCCGCCAATAATTA
* * * *
76530 TCTTATGTG-AAAAGTCTGTCACGGACTATCTTATGTGTAATGTCTGCCAAT
1 TCTTATGCGTAAAA-TCCGTCACGGACTATCTTATGTGGAATGTCCGCCAAT
76581 GACTATTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 4 0.09
56 41 0.91
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (56 bp):
TCTTATGCGTAAAATCCGTCACGGACTATCTTATGTGGAATGTCCGCCAATAATTA
Found at i:77926 original size:49 final size:49
Alignment explanation
Indices: 77873--77968 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 49
77863 TGGGCTCCCG
* *
77873 AGTTATA-TTCCAACCTGTGATCGCAAAACCACCGTCAACTAAGAGCCCT
1 AGTTATACTT-CAACCCGTGACCGCAAAACCACCGTCAACTAAGAGCCCT
* * * * *
77922 AGTTATACTTCAACCCGTGACCGTATAAGCACCGTGAACTCAGAGCC
1 AGTTATACTTCAACCCGTGACCGCAAAACCACCGTCAACTAAGAGCC
77969 TGAGTTGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
49 37 0.95
50 2 0.05
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (49 bp):
AGTTATACTTCAACCCGTGACCGCAAAACCACCGTCAACTAAGAGCCCT
Found at i:78556 original size:64 final size:64
Alignment explanation
Indices: 78477--78603 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 64
78467 ATGGTTCCAT
78477 CCTAACACAGCAATTGAAATGTGTGAGTCTCCGAGCGTTATCGCATCACCATGAACTCAAATAC
1 CCTAACACAGCAATTGAAATGTGTGAGTCTCCGAGCGTTATCGCATCACCATGAACTCAAATAC
* *
78541 CCTAACACAGCAATTGAAATGTGTGAGTCTCCGAGCGTTATTGCATCACCATTAACTCAAATA
1 CCTAACACAGCAATTGAAATGTGTGAGTCTCCGAGCGTTATCGCATCACCATGAACTCAAATA
78604 TATATTAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (64 bp):
CCTAACACAGCAATTGAAATGTGTGAGTCTCCGAGCGTTATCGCATCACCATGAACTCAAATAC
Found at i:79382 original size:24 final size:24
Alignment explanation
Indices: 79349--79428 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
79339 AACATCCAAA
* *
79349 CAACCAAAATAACAATCAAAACAG
1 CAACAAAAATAACAATAAAAACAG
* *
79373 CAGA-AAAAATAATAGA-AAAAATAG
1 CA-ACAAAAATAACA-ATAAAAACAG
*
79397 CAACAAAAATAACAATAAAAACAA
1 CAACAAAAATAACAATAAAAACAG
*
79421 CACCAAAA
1 CAACAAAA
79429 TAGTAATAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
23 2 0.05
24 40 0.91
25 2 0.05
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.09
Consensus pattern (24 bp):
CAACAAAAATAACAATAAAAACAG
Found at i:79454 original size:48 final size:48
Alignment explanation
Indices: 79346--79455 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
79336 AATAACATCC
* * *
79346 AAACAACCAAAATAACAATCAAAACAGCAGAAAAAATAATAGAAAAAA
1 AAACAACCAAAATAACAATAAAAACAACACAAAAAATAATAGAAAAAA
* * * *
79394 TAGCAACAAAAATAACAATAAAAACAACACCAAAATAGTAATA-AAAAAA
1 AAACAACCAAAATAACAATAAAAACAACA-CAAAA-AATAATAGAAAAAA
79443 AAAC-ACCAAAATA
1 AAACAACCAAAATA
79456 GCAACCAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
48 32 0.64
49 12 0.24
50 6 0.12
ACGTcount: A:0.70, C:0.15, G:0.05, T:0.10
Consensus pattern (48 bp):
AAACAACCAAAATAACAATAAAAACAACACAAAAAATAATAGAAAAAA
Found at i:79465 original size:25 final size:25
Alignment explanation
Indices: 79407--79465 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
79397 CAACAAAAAT
* *
79407 AACAATAAAAACAACACCAAAATAGT
1 AACAA-AAAAAAAACACCAAAATAGC
*
79433 AATAAAAAAAAAACACCAAAATAGC
1 AACAAAAAAAAAACACCAAAATAGC
*
79458 AACCAAAA
1 AACAAAAA
79466 CAATAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.69, C:0.19, G:0.03, T:0.08
Consensus pattern (25 bp):
AACAAAAAAAAAACACCAAAATAGC
Found at i:79475 original size:22 final size:21
Alignment explanation
Indices: 79450--79531 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 21
79440 AAAAAACACC
79450 AAAATAGCAACCAAAACAATAA
1 AAAATA-CAACCAAAACAATAA
*
79472 AAAA-AC-ATCAAAACAAT-A
1 AAAATACAACCAAAACAATAA
* * *
79490 AAAACACAATATCAAAACAACAA
1 AAAATAC-A-ACCAAAACAATAA
79513 AAAATAGCAACCAAAACAA
1 AAAATA-CAACCAAAACAA
79532 CAATATAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
18 5 0.10
19 12 0.24
20 1 0.02
21 1 0.02
22 23 0.46
23 7 0.14
24 1 0.02
ACGTcount: A:0.70, C:0.20, G:0.02, T:0.09
Consensus pattern (21 bp):
AAAATACAACCAAAACAATAA
Found at i:81586 original size:7 final size:7
Alignment explanation
Indices: 81574--81607 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
81564 TGATTCCTAT
81574 TGATTAA
1 TGATTAA
81581 TGATTAA
1 TGATTAA
81588 TGATTAA
1 TGATTAA
81595 TGATTAA
1 TGATTAA
81602 TGATTA
1 TGATTA
81608 CTTTGTTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (7 bp):
TGATTAA
Found at i:83385 original size:14 final size:14
Alignment explanation
Indices: 83366--83398 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
83356 TACAATATCT
83366 AAATAATAACAACA
1 AAATAATAACAACA
83380 AAATAATAACAACA
1 AAATAATAACAACA
*
83394 TAATA
1 AAATA
83399 GTGAAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:83788 original size:18 final size:18
Alignment explanation
Indices: 83751--83788 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
83741 AATTTTACCT
* *
83751 TTTAATTATATTTTTTTA
1 TTTAATTATATCTTTGTA
83769 TTTAATTATATCTTTGTA
1 TTTAATTATATCTTTGTA
83787 TT
1 TT
83789 AATATTCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTAATTATATCTTTGTA
Found at i:94375 original size:15 final size:15
Alignment explanation
Indices: 94347--94378 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
94337 GAGAGCACAT
94347 AAAATAAAATAAGAG
1 AAAATAAAATAAGAG
94362 AAAA-AAAATAA-AG
1 AAAATAAAATAAGAG
94375 AAAA
1 AAAA
94379 GATTAATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 7 0.41
15 4 0.24
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (15 bp):
AAAATAAAATAAGAG
Found at i:94773 original size:33 final size:33
Alignment explanation
Indices: 94735--94798 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
94725 CATGTGAAAA
94735 TTTTATTAGGGTTAACTAAGCAAAATTTGAATT
1 TTTTATTAGGGTTAACTAAGCAAAATTTGAATT
94768 TTTTATTAGGGTTAACTAAGCAAAATTTGAA
1 TTTTATTAGGGTTAACTAAGCAAAATTTGAA
94799 CGTGATAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (33 bp):
TTTTATTAGGGTTAACTAAGCAAAATTTGAATT
Found at i:96552 original size:20 final size:19
Alignment explanation
Indices: 96529--96579 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
96519 TTGTCCTCAT
*
96529 ATTTATTGGTATTCTTTTAG
1 ATTT-TTGGTATTCTTTCAG
*
96549 ATTTTTGGATATTCTTTCAT
1 ATTTTTGG-TATTCTTTCAG
96569 ATTTTTGGTAT
1 ATTTTTGGTAT
96580 ACCCCTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.61
Consensus pattern (19 bp):
ATTTTTGGTATTCTTTCAG
Found at i:96895 original size:20 final size:23
Alignment explanation
Indices: 96848--96899 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
96838 CCACTCATCT
*
96848 TTTTTTGGT-TTGCCCTCTTAGA
1 TTTTTTGGTATTGCCCTCGTAGA
96870 TTTTTTGGTATT-CCCTCGT-G-
1 TTTTTTGGTATTGCCCTCGTAGA
96890 TTTTTTGGTA
1 TTTTTTGGTA
96900 ATACATCACG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.36
21 1 0.04
22 15 0.54
23 2 0.07
ACGTcount: A:0.08, C:0.15, G:0.19, T:0.58
Consensus pattern (23 bp):
TTTTTTGGTATTGCCCTCGTAGA
Found at i:100799 original size:4 final size:4
Alignment explanation
Indices: 100790--100816 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
100780 ATTTTGGGTT
100790 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
100817 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:101560 original size:15 final size:16
Alignment explanation
Indices: 101540--101572 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
101530 AGAAAAAAAA
*
101540 TATTTTTC-ATCTTTT
1 TATTTTTCTATCATTT
101555 TATTTTTCTATCATTT
1 TATTTTTCTATCATTT
101571 TA
1 TA
101573 AATGTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTTCTATCATTT
Found at i:101797 original size:6 final size:6
Alignment explanation
Indices: 101786--101812 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
101776 AAAATATCAT
101786 ATTTTC ATTTTC ATTTTC ATTTTC ATT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATT
101813 ACCAAGTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTC
Found at i:103482 original size:8 final size:8
Alignment explanation
Indices: 103455--103497 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
103445 GGATGGGAAA
103455 TTTTT-TC
1 TTTTTCTC
*
103462 TTTTCTTTC
1 TTTT-TCTC
103471 TTTTTCTC
1 TTTTTCTC
103479 TTTTTCTC
1 TTTTTCTC
*
103487 TTTCTCTC
1 TTTTTCTC
103495 TTT
1 TTT
103498 CTCCTTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 4 0.12
8 22 0.69
9 6 0.19
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCTC
Found at i:103484 original size:14 final size:14
Alignment explanation
Indices: 103456--103499 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
103446 GATGGGAAAT
*
103456 TTTTTCTTTTCTTTC
1 TTTTTCTCTT-TTTC
103471 TTTTTCTCTTTTTC
1 TTTTTCTCTTTTTC
* *
103485 TCTTTCTCTCTTTC
1 TTTTTCTCTTTTTC
103499 T
1 T
103500 CCTTATCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTCTCTTTTTC
Found at i:103500 original size:14 final size:14
Alignment explanation
Indices: 103465--103500 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
103455 TTTTTTCTTT
*
103465 TCTTTCTTTTTCTC
1 TCTTTCTCTTTCTC
*
103479 TTTTTCTCTTTCTC
1 TCTTTCTCTTTCTC
103493 TCTTTCTC
1 TCTTTCTC
103501 CTTATCGGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TCTTTCTCTTTCTC
Found at i:111213 original size:24 final size:24
Alignment explanation
Indices: 111181--111229 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
111171 CTTTTTCACT
111181 CATATTATGTTTTTTATGTAACAC
1 CATATTATGTTTTTTATGTAACAC
111205 CATATTATGTTTTTTATGTAACAC
1 CATATTATGTTTTTTATGTAACAC
111229 C
1 C
111230 TAAGCATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (24 bp):
CATATTATGTTTTTTATGTAACAC
Found at i:115617 original size:2 final size:2
Alignment explanation
Indices: 115610--115636 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
115600 NNNNNNNNNN
115610 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
115637 AAAGGTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:131049 original size:19 final size:19
Alignment explanation
Indices: 131025--131065 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
131015 TTTGGGTAAA
131025 AGATGCTCCGTCTGAAGTC
1 AGATGCTCCGTCTGAAGTC
131044 AGATGCTCCGTCTGAAGTC
1 AGATGCTCCGTCTGAAGTC
131063 AGA
1 AGA
131066 ACTGTAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (19 bp):
AGATGCTCCGTCTGAAGTC
Done.