Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold160
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: 1852349
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 51288 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:256267 original size:18 final size:19
Alignment explanation
Indices: 256234--256269 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
256224 GGGAATTCAG
256234 AAAATAAAGAAAACAAATT
1 AAAATAAAGAAAACAAATT
*
256253 AAAATAACG-AAACAAAT
1 AAAATAAAGAAAACAAAT
256270 CAGAAGGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (19 bp):
AAAATAAAGAAAACAAATT
Found at i:263491 original size:85 final size:85
Alignment explanation
Indices: 263402--263577 Score: 334
Period size: 85 Copynumber: 2.0 Consensus size: 85
263392 TATATTAATT
263402 TATATTTATGCTTTTAAGATATTTGTATATTTCAATACATTTTAATATGTCAAATGTTTATTTTA
1 TATATTTATGC--TTAAGATATTTGTATATTTCAATACATTTTAATATGTCAAATGTTTATTTTA
263467 TGTAGATTTTAAAACGTTTATA
64 TGTAGATTTTAAAACGTTTATA
263489 TATATTTATGCTTAAGATATTTGTATATTTCAATACATTTTAATATGTCAAATGTTTATTTTATG
1 TATATTTATGCTTAAGATATTTGTATATTTCAATACATTTTAATATGTCAAATGTTTATTTTATG
263554 TAGATTTTAAAACGTTTATA
66 TAGATTTTAAAACGTTTATA
263574 TATA
1 TATA
263578 CATATATATT
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
85 78 0.88
87 11 0.12
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (85 bp):
TATATTTATGCTTAAGATATTTGTATATTTCAATACATTTTAATATGTCAAATGTTTATTTTATG
TAGATTTTAAAACGTTTATA
Found at i:264997 original size:16 final size:17
Alignment explanation
Indices: 264973--265007 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
264963 TATAAATAGT
264973 ATAAATATATAATT-TA
1 ATAAATATATAATTATA
*
264989 ATAATTATATAATTATA
1 ATAAATATATAATTATA
265006 AT
1 AT
265008 TTCTTAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAAATATATAATTATA
Found at i:264997 original size:22 final size:21
Alignment explanation
Indices: 264972--265043 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
264962 ATATAAATAG
264972 TATAAATATATAATTTAATAAT
1 TATAAAT-TATAATTTAATAAT
**
264994 TATATAATTATAATTTCTTAA-
1 TATA-AATTATAATTTAATAAT
*
265015 -AGAAATTATAATTTAATAAT
1 TATAAATTATAATTTAATAAT
265035 AATATAAAT
1 --TATAAAT
265044 ATATGTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 14 0.36
20 2 0.05
22 15 0.38
23 8 0.21
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (21 bp):
TATAAATTATAATTTAATAAT
Found at i:265052 original size:12 final size:12
Alignment explanation
Indices: 265037--265063 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
265027 TTAATAATAA
265037 TATAAATATATG
1 TATAAATATATG
265049 TATAAATATATG
1 TATAAATATATG
265061 TAT
1 TAT
265064 CTAATGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (12 bp):
TATAAATATATG
Found at i:265153 original size:44 final size:46
Alignment explanation
Indices: 265073--265160 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 46
265063 TCTAATGAAT
265073 TTTTATTTGATAAAAAAATGAAAAAAAAAGAGTTTATATGTAAAAA
1 TTTTATTTGATAAAAAAATGAAAAAAAAAGAGTTTATATGTAAAAA
* *
265119 TTTTATTTGGT-AAAAAATGAAAAAGATAA-A-TTTATATGTAAA
1 TTTTATTTGATAAAAAAATGAAAAA-AAAAGAGTTTATATGTAAA
265161 TTTATCGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 12 0.31
45 14 0.36
46 13 0.33
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.35
Consensus pattern (46 bp):
TTTTATTTGATAAAAAAATGAAAAAAAAAGAGTTTATATGTAAAAA
Found at i:271150 original size:125 final size:125
Alignment explanation
Indices: 270777--271143 Score: 603
Period size: 124 Copynumber: 2.9 Consensus size: 125
270767 GGGTTTTTAT
* *
270777 GTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGA-TCAAATAGTACAAAATCGCTTCTAGCAG
1 GTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGT-AAATAGTATAAAATCGCTTCTAGCAG
* * * * * * *
270841 AATGCTGTTTGATAAGATTTTGTGAAATCGCGCCCTCGTGGATGCGCTTTTGCTACAGTAG
65 GATGCTATTTGAGAAGAATTTGTGAAAGCGCGCCCTCATGGACGCGCTTTTGCTACAGTAG
* * *
270902 GTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTAT-AAATTGCTTCTAGCAGG
1 GTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTAGCAGG
270966 ATGCTATTTGAGAAGAATTTGTGAAAGCGCGCCCTCATGGACGCGCTTTTGCTACAGTAG
66 ATGCTATTTGAGAAGAATTTGTGAAAGCGCGCCCTCATGGACGCGCTTTTGCTACAGTAG
271026 GTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTAGCAGG
1 GTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTAGCAGG
271091 ATGCTATTTGAGAAGAATTTGTGAAAGCGCGCCCTCATGGACGCGCTTTTGCT
66 ATGCTATTTGAGAAGAATTTGTGAAAGCGCGCCCTCATGGACGCGCTTTTGCT
271144 CTAGTAGCAT
Statistics
Matches: 225, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
124 114 0.51
125 111 0.49
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (125 bp):
GTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTAGCAGG
ATGCTATTTGAGAAGAATTTGTGAAAGCGCGCCCTCATGGACGCGCTTTTGCTACAGTAG
Found at i:274247 original size:22 final size:22
Alignment explanation
Indices: 274177--274882 Score: 534
Period size: 22 Copynumber: 32.3 Consensus size: 22
274167 ATCAAATAAA
*
274177 TTTAAGTTAAGGG-TTACGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
274198 TTTAAGTTCTA--GTTTAAAGTT
1 TTTAAGTT-AAGGGTTTAGGGTT
* *
274219 TTAAAGTTAAGGGTTAAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
274241 TTTAAGTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
274262 TTTAAGTTGAGGG-TTAGCGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
274283 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
274305 TTCAA-TTAA-ATTAGTTAGGGTT
1 TTTAAGTTAAGGGT--TTAGGGTT
*
274327 TTTAAGTTTAAGGGTTTAAGGTT
1 TTTAAG-TTAAGGGTTTAGGGTT
** *
274350 TTT-A-TTAAATTAGTTTAGAGTT
1 TTTAAGTT-AA-GGGTTTAGGGTT
*
274372 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
274394 TTTAAATTTAAGGGTTTAGGGTT
1 TTT-AAGTTAAGGGTTTAGGGTT
**
274417 TTTAA-TTAAATTAGTTTAGGGTT
1 TTTAAGTT-AA-GGGTTTAGGGTT
*
274440 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
274462 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
** *
274484 TTTAA-TTAAATTAGTTTAGAGTT
1 TTTAAGTT-AA-GGGTTTAGGGTT
*
274507 TTTAAGTTAAGGGTTTAAGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
274528 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
274549 TTTAAGTTTAAGAGTTTATGG-T
1 TTTAAG-TTAAGGGTTTAGGGTT
* **
274571 TTTAGGTTTAAATTAGTTTAGGGTT
1 TTTAAG-TT-AA-GGGTTTAGGGTT
274596 TTTAAGTTAAGGG-TTAGGG--
1 TTTAAGTTAAGGGTTTAGGGTT
* * * *
274615 TTTAGGGTTTAGGATTTA-GGAT
1 TTTA-AGTTAAGGGTTTAGGGTT
*
274637 TTTAGGGTTTAA-GGTTT----TT
1 TTTA-AG-TTAAGGGTTTAGGGTT
* * *
274656 AATTAAATT---TGTTTAGGGTT
1 -TTTAAGTTAAGGGTTTAGGGTT
274676 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
274698 TTTAATTTTAAGGGTTTAGGGTT
1 TTTAA-GTTAAGGGTTTAGGGTT
*
274721 TTTAATTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
274742 TTTACGTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
274763 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
274785 TTTAATTTTAAAGGCTTAGGGTT
1 TTTAA-GTTAAGGGTTTAGGGTT
**
274808 TTTAA-TTAAATTAGTTTAGGGTT
1 TTTAAGTT-AA-GGGTTTAGGGTT
* *
274831 TTTAAGTTAAAGGTTTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
*
274853 TTTAATTTTAAGGGTTTAGGGTT
1 TTTAA-GTTAAGGGTTTAGGGTT
274876 TTTAAGT
1 TTTAAGT
274883 AATAACTCAA
Statistics
Matches: 550, Mismatches: 88, Indels: 93
0.75 0.12 0.13
Matches are distributed among these distances:
16 4 0.01
18 2 0.00
19 11 0.02
20 22 0.04
21 137 0.25
22 192 0.35
23 153 0.28
24 22 0.04
25 7 0.01
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.47
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:274389 original size:67 final size:67
Alignment explanation
Indices: 274238--274882 Score: 425
Period size: 68 Copynumber: 9.5 Consensus size: 67
274228 AGGGTTAAGG
* * * ** *
274238 GTTTTTAAGTTAA-GGGTTAAGGTTTTTAAGTTGAGGG-TTAGCGTTTTTAAGTT-AA-GGGGTT
1 GTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAA-TTAAATTAGTTT
*
274299 AGG
65 AGA
* *** *
274302 GTTTTCAA-TTAAATTAGTTAGGGTTTTTAAGTTTAAGGGTTTAAGGTTTTT-ATTAAATTAGTT
1 GTTTTTAAGTT-AAGGGGTTAGGGTTTTTAAG-TTAAGGGTTTAGGGTTTTTAATTAAATTAGTT
274365 TAGA
64 TAGA
*
274369 GTTTTTAAGTTAAGGGGTTAGGGTTTTTAAATTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTT
1 GTTTTTAAGTTAAGGGGTTAGGGTTTTT-AAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTT
*
274434 AGG
65 AGA
274437 GTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTA
1 GTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTA
274502 GA
66 GA
* * * *
274504 GTTTTTAAGTTAAGGGTTTAAGG-TTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTTAA-GAGTTT
1 GTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAA-TTAAATTAGTTT
274566 ATG-
65 A-GA
* ** *
274569 G-TTTTAGGTTTAAATTAGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTAGGGTTTAGGATTT
1 GTTTTTAAG-TT-AA-GGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGG-TT----TTTA--A-TT
* * **
274632 AGGATTTTAGGGTTTAA
55 A--A-ATTA-GTTTAGA
** * * **
274649 GGTTTTTAA-TTAAATTTGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTTAA-GGG
1 -GTTTTTAAGTT-AA-GGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAA-TTAAATTAG
*
274712 TTTAGG
62 TTTAGA
* * * **
274718 GTTTTTAATTTAA-GGGTTAGGGTTTTTACGTTAAGGG-TTAAGGTTTTTAAGTT-AA-GGGTTT
1 GTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAA-TTAAATTAGTTT
*
274779 AGG
65 AGA
* * * ** *
274782 GTTTTTAATTTTAAAGGCTTAGGGTTTTTAA-TTAAATTAGTTTAGGGTTTTTAAGTTAAA--GG
1 GTTTTTAA-GTTAAGGGGTTAGGGTTTTTAAGTT-AA-GGGTTTAGGGTTTTTAA-TTAAATTAG
274844 TTTAG-
62 TTTAGA
* *
274849 GATTTTTAATTTTAAGGGTTTAGGGTTTTTAAGT
1 G-TTTTTAA-GTTAAGGGGTTAGGGTTTTTAAGT
274883 AATAACTCAA
Statistics
Matches: 484, Mismatches: 57, Indels: 75
0.79 0.09 0.12
Matches are distributed among these distances:
63 2 0.00
64 34 0.07
65 59 0.12
66 67 0.14
67 120 0.25
68 127 0.26
69 10 0.02
72 1 0.00
73 4 0.01
74 4 0.01
75 3 0.01
76 4 0.01
77 1 0.00
79 1 0.00
80 35 0.07
81 7 0.01
82 5 0.01
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.47
Consensus pattern (67 bp):
GTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTA
GA
Found at i:274624 original size:7 final size:7
Alignment explanation
Indices: 274605--274653 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
274595 TTTTAAGTTA
274605 AGGG-TT
1 AGGGTTT
274611 AGGGTTT
1 AGGGTTT
274618 AGGGTTT
1 AGGGTTT
*
274625 AGGATTT
1 AGGGTTT
*
274632 AGGATTTT
1 AGG-GTTT
274640 AGGGTTT
1 AGGGTTT
*
274647 AAGGTTT
1 AGGGTTT
274654 TTAATTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 4 0.11
7 27 0.73
8 6 0.16
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (7 bp):
AGGGTTT
Found at i:274675 original size:23 final size:22
Alignment explanation
Indices: 274642--274882 Score: 238
Period size: 23 Copynumber: 10.8 Consensus size: 22
274632 AGGATTTTAG
*
274642 GGTTTAAGGTTTTTAA-TTAAA
1 GGTTTAGGGTTTTTAAGTTAAA
* *
274663 TTTGTTTAGGGTTTTTAAGTTAAG
1 --GGTTTAGGGTTTTTAAGTTAAA
* *
274687 GGTTTAGGGTTTTTAATTTTAAG
1 GGTTTAGGGTTTTTAA-GTTAAA
*
274710 GGTTTAGGGTTTTTAA-TTTAA
1 GGTTTAGGGTTTTTAAGTTAAA
* *
274731 GGGTTAGGGTTTTTACGTT-AA
1 GGTTTAGGGTTTTTAAGTTAAA
* * *
274752 GGGTTAAGGTTTTTAAGTTAAG
1 GGTTTAGGGTTTTTAAGTTAAA
*
274774 GGTTTAGGGTTTTTAATTTTAAA
1 GGTTTAGGGTTTTTAA-GTTAAA
*
274797 GGCTTAGGGTTTTTAA-TTAAA
1 GGTTTAGGGTTTTTAAGTTAAA
*
274818 TTAGTTTAGGGTTTTTAAGTTAAA
1 --GGTTTAGGGTTTTTAAGTTAAA
* * *
274842 GGTTTAGGATTTTTAATTTTAAG
1 GGTTTAGGGTTTTTAA-GTTAAA
274865 GGTTTAGGGTTTTTAAGT
1 GGTTTAGGGTTTTTAAGT
274883 AATAACTCAA
Statistics
Matches: 184, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
21 41 0.22
22 47 0.26
23 87 0.47
24 9 0.05
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (22 bp):
GGTTTAGGGTTTTTAAGTTAAA
Found at i:274881 original size:45 final size:44
Alignment explanation
Indices: 274216--274882 Score: 468
Period size: 45 Copynumber: 15.2 Consensus size: 44
274206 CTAGTTTAAA
* * * * *
274216 GTTTTAAAGTTAAGGGTTAAGGGTTTTTAAGTTAAGGG-TTAAG
1 GTTTTTAAGTTAAAGGTTTAGGGTTTTTAATTTAAGGGTTTAGG
* * * * *
274259 GTTTTTAAGTT-GAGGGTTAGCGTTTTTAAGTTAAGGGGTTAGG
1 GTTTTTAAGTTAAAGGTTTAGGGTTTTTAATTTAAGGGTTTAGG
* * *
274302 GTTTTCAA-TTAAA-TTAGTTAGGGTTTTTAAGTTTAAGGGTTTAAG
1 GTTTTTAAGTTAAAGGT--TTAGGGTTTTTAA-TTTAAGGGTTTAGG
* * * *
274347 GTTTTT-A-TTAAATTAGTTTAGAGTTTTTAAGTTAAGGGGTTAGG
1 GTTTTTAAGTTAAA--GGTTTAGGGTTTTTAATTTAAGGGTTTAGG
* * * **
274391 GTTTTTAAATTTAAGGGTTTAGGGTTTTTAATTAAATTAGTTTAGG
1 GTTTTT-AAGTTAAAGGTTTAGGGTTTTTAATTTAA-GGGTTTAGG
* * *
274437 GTTTTTAAGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTTAGG
1 GTTTTTAAGTTAAAGGTTTAGGGTTTTTAATTTAAGGGTTTAGG
* * * *
274481 GTTTTTAA-TTAAATTAGTTTAGAGTTTTTAAGTTAAGGGTTTAAG
1 GTTTTTAAGTTAAA--GGTTTAGGGTTTTTAATTTAAGGGTTTAGG
* * *
274526 G-TTTTAAGTT-AAGGGTTAGGGTTTTTAAGTTTAAGAGTTTATG
1 GTTTTTAAGTTAAAGGTTTAGGGTTTTTAA-TTTAAGGGTTTAGG
* * *
274569 G-TTTTAGGTTTAAATTAGTTTAGGGTTTTTAAGTTAAGGG-TTAGG
1 GTTTTTAAG-TTAAA--GGTTTAGGGTTTTTAATTTAAGGGTTTAGG
* * * *
274614 G--TTTAGGGTT-TAGGATTTA-GGATTTTAGGGTTTAA-GG--T---
1 GTTTTTA-AGTTAAAGG-TTTAGGGTTTTTA--ATTTAAGGGTTTAGG
* *
274652 --TTTTAA-TTAAATTTGTTTAGGGTTTTTAAGTTAAGGGTTTAGG
1 GTTTTTAAGTTAAA--GGTTTAGGGTTTTTAATTTAAGGGTTTAGG
* *
274695 GTTTTTAATTTTAAGGGTTTAGGGTTTTTAATTTAAGGG-TTAGG
1 GTTTTTAA-GTTAAAGGTTTAGGGTTTTTAATTTAAGGGTTTAGG
* * * *
274739 GTTTTTACGTT-AAGGGTTAAGGTTTTTAAGTTAAGGGTTTAGG
1 GTTTTTAAGTTAAAGGTTTAGGGTTTTTAATTTAAGGGTTTAGG
* * * **
274782 GTTTTTAATTTTAAAGGCTTAGGGTTTTTAATTAAATTAGTTTAGG
1 GTTTTTAA-GTTAAAGGTTTAGGGTTTTTAATTTAA-GGGTTTAGG
*
274828 GTTTTTAAGTTAAAGGTTTAGGATTTTTAATTTTAAGGGTTTAGG
1 GTTTTTAAGTTAAAGGTTTAGGGTTTTTAA-TTTAAGGGTTTAGG
274873 GTTTTTAAGT
1 GTTTTTAAGT
274883 AATAACTCAA
Statistics
Matches: 494, Mismatches: 86, Indels: 86
0.74 0.13 0.13
Matches are distributed among these distances:
36 2 0.00
37 5 0.01
38 10 0.02
39 8 0.02
40 1 0.00
41 9 0.02
42 64 0.13
43 63 0.13
44 80 0.16
45 191 0.39
46 38 0.08
47 23 0.05
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.47
Consensus pattern (44 bp):
GTTTTTAAGTTAAAGGTTTAGGGTTTTTAATTTAAGGGTTTAGG
Found at i:275376 original size:18 final size:18
Alignment explanation
Indices: 275350--275391 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
275340 GACTCGGAAA
* *
275350 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
275368 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
275386 AGGAAA
1 AGGAAA
275392 TGCACCTGGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.29, T:0.17
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:276260 original size:20 final size:20
Alignment explanation
Indices: 276222--276260 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
276212 CTTTTATTTT
*
276222 TAAAATCTACATAATAATTG
1 TAAAATCTACATAAAAATTG
276242 TAAAATCTA-ATATAAAATT
1 TAAAATCTACATA-AAAATT
276261 TGCCTCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAATCTACATAAAAATTG
Found at i:277049 original size:11 final size:11
Alignment explanation
Indices: 277035--277111 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
277025 TTAAATATGG
277035 ATTTGAGAGAA
1 ATTTGAGAGAA
*
277046 ATTTG-GAAGGA
1 ATTTGAG-AGAA
* *
277057 GTTTGAGAGCAG
1 ATTTGAGAG-AA
277069 A-TTGAGAGGAA
1 ATTTGAGA-GAA
277080 ATTT-AGAGGAA
1 ATTTGAGA-GAA
277091 A-TTGAGAGGAA
1 ATTTGAGA-GAA
277102 ATTTGAGAGA
1 ATTTGAGAGA
277112 GGATTAGTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
10 3 0.06
11 40 0.75
12 10 0.19
ACGTcount: A:0.40, C:0.01, G:0.34, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:277078 original size:22 final size:23
Alignment explanation
Indices: 277058--277110 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
277048 TTGGAAGGAG
*
277058 TTTGAGAGCAGATTGAGAGGAAA
1 TTTGAGAGCAAATTGAGAGGAAA
*
277081 TTT-AGAGGAAATTGAGAGGAAA
1 TTTGAGAGCAAATTGAGAGGAAA
277103 TTTGAGAG
1 TTTGAGAG
277111 AGGATTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.40, C:0.02, G:0.34, T:0.25
Consensus pattern (23 bp):
TTTGAGAGCAAATTGAGAGGAAA
Found at i:281174 original size:12 final size:13
Alignment explanation
Indices: 281144--281169 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
281134 AATAAACTAC
281144 AGAAAAATGGAAG
1 AGAAAAATGGAAG
281157 AGAAAAATGGAAG
1 AGAAAAATGGAAG
281170 TAAAAGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (13 bp):
AGAAAAATGGAAG
Found at i:283020 original size:20 final size:20
Alignment explanation
Indices: 282995--283037 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
282985 TTAACATTAT
282995 CTAGATAAAAATCAAAAGTA
1 CTAGATAAAAATCAAAAGTA
283015 CTAGATAAAAATCAAAAGTA
1 CTAGATAAAAATCAAAAGTA
283035 CTA
1 CTA
283038 TTAGTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (20 bp):
CTAGATAAAAATCAAAAGTA
Found at i:284544 original size:39 final size:39
Alignment explanation
Indices: 284490--284565 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
284480 CATTCATTAC
284490 ATAATTTACTAATTTTTCTCTTTTTATATATTTCTATGA
1 ATAATTTACTAATTTTTCTCTTTTTATATATTTCTATGA
*
284529 ATAATTTACTAATTTTTCTCTTTTTGTATATTTCTAT
1 ATAATTTACTAATTTTTCTCTTTTTATATATTTCTAT
284566 AATTTATACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.61
Consensus pattern (39 bp):
ATAATTTACTAATTTTTCTCTTTTTATATATTTCTATGA
Found at i:288144 original size:26 final size:26
Alignment explanation
Indices: 288115--288188 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 26
288105 GAATGTTCTT
*
288115 AAAATTTTACTGGCGGTAAAATCGTCA
1 AAAATTTTACTGG-GGTAAAATCATCA
* * *
288142 AAAAATTTACCAGGGGTAAAATTATC-
1 AAAATTTTA-CTGGGGTAAAATCATCA
*
288168 AAAATTTTACTAGGGTAAAAT
1 AAAATTTTACTGGGGTAAAAT
288189 TGGGCTGACA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 10 0.26
26 8 0.21
27 18 0.46
28 3 0.08
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (26 bp):
AAAATTTTACTGGGGTAAAATCATCA
Found at i:288159 original size:27 final size:25
Alignment explanation
Indices: 288129--288188 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
288119 TTTTACTGGC
*
288129 GGTAAAATCGTCAAAAAATTTACCAGG
1 GGTAAAATCATC-AAAAATTTACCA-G
* * *
288156 GGTAAAATTATCAAAATTTTACTAG
1 GGTAAAATCATCAAAAATTTACCAG
288181 GGTAAAAT
1 GGTAAAAT
288189 TGGGCTGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 9 0.31
26 10 0.34
27 10 0.34
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (25 bp):
GGTAAAATCATCAAAAATTTACCAG
Found at i:300705 original size:35 final size:34
Alignment explanation
Indices: 300625--300755 Score: 183
Period size: 35 Copynumber: 3.8 Consensus size: 34
300615 AATTTGCATC
* *
300625 TACCTAGGGTTCGCACACATATACAGTTCGCATG-
1 TACCTAGGGTTCACACACATATACAG-TCACATGT
*
300659 TACCTAGGGTTCGCACACATATACAGTCCACATGT
1 TACCTAGGGTTCACACACATATACAGT-CACATGT
*
300694 TACCTAGGGTTCATACACATATACAGGTCACATGT
1 TACCTAGGGTTCACACACATATACA-GTCACATGT
*
300729 CACCTAGGGTTCACACACATATACAGT
1 TACCTAGGGTTCACACACATATACAGT
300756 TCGCATGTAC
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
33 1 0.01
34 33 0.37
35 53 0.60
36 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (34 bp):
TACCTAGGGTTCACACACATATACAGTCACATGT
Found at i:300728 original size:69 final size:70
Alignment explanation
Indices: 300625--300755 Score: 210
Period size: 69 Copynumber: 1.9 Consensus size: 70
300615 AATTTGCATC
* * * *
300625 TACCTAGGGTTCGCACACATATACAGTTCGCATGT-ACCTAGGGTTCGCACACATATACAGTCCA
1 TACCTAGGGTTCACACACATATACAGGTCACATGTCACCTAGGGTTCACACACATATACAGTCCA
300689 CATGT
66 CATGT
*
300694 TACCTAGGGTTCATACACATATACAGGTCACATGTCACCTAGGGTTCACACACATATACAGT
1 TACCTAGGGTTCACACACATATACAGGTCACATGTCACCTAGGGTTCACACACATATACAGT
300756 TCGCATGTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
69 31 0.55
70 25 0.45
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (70 bp):
TACCTAGGGTTCACACACATATACAGGTCACATGTCACCTAGGGTTCACACACATATACAGTCCA
CATGT
Found at i:300763 original size:35 final size:34
Alignment explanation
Indices: 300581--300765 Score: 226
Period size: 34 Copynumber: 5.4 Consensus size: 34
300571 GGCTTCGCAG
* * *
300581 AGTTCACATGTACATAGGGTTCACATATATATAC
1 AGTTCACATGTACCTAGGGTTCACACACATATAC
* ** * *
300615 AATTTGCATCTACCTAGGGTTCGCACACATATAC
1 AGTTCACATGTACCTAGGGTTCACACACATATAC
* *
300649 AGTTCGCATGTACCTAGGGTTCGCACACATATAC
1 AGTTCACATGTACCTAGGGTTCACACACATATAC
* *
300683 AGTCCACATGTTACCTAGGGTTCATACACATATAC
1 AGTTCACATG-TACCTAGGGTTCACACACATATAC
*
300718 AGGTCACATGTCACCTAGGGTTCACACACATATAC
1 AGTTCACATGT-ACCTAGGGTTCACACACATATAC
*
300753 AGTTCGCATGTAC
1 AGTTCACATGTAC
300766 TTGCCATAAA
Statistics
Matches: 129, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
34 68 0.53
35 61 0.47
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (34 bp):
AGTTCACATGTACCTAGGGTTCACACACATATAC
Found at i:301543 original size:43 final size:43
Alignment explanation
Indices: 301491--301716 Score: 294
Period size: 43 Copynumber: 5.3 Consensus size: 43
301481 ATATTTTTAT
* * * *
301491 AAACGCCGCTAAAGGTCCTGTTCTTTAACGGAGCTTTTTCAAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGAGCTTTTTCCAC
* *
301534 AAACGCCGCTAAAGATCATGTTCCTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGAGCTTTTTCCAC
*
301577 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGAGCTTTTTCCAC
* *
301620 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCA-CTTCTTCCGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGG-AGCTTTTTCCAC
* * * *
301663 AAACGCCACTAAAGGTCATGTTCTTTTAGCGGCG-TTTTTACAC
1 AAACGCCGCTAAAGATCATGTTC-TTTAGCGGAGCTTTTTCCAC
*
301706 AAACGTCGCTA
1 AAACGCCGCTA
301717 TTTGTTTGGT
Statistics
Matches: 162, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
43 154 0.95
44 8 0.05
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGAGCTTTTTCCAC
Found at i:301701 original size:86 final size:86
Alignment explanation
Indices: 301491--301716 Score: 328
Period size: 86 Copynumber: 2.6 Consensus size: 86
301481 ATATTTTTAT
* * * *
301491 AAACGCCGCTAAAGGTCCTGTTCTTTAACGGAGCTTTTTCAACAAACGCCGCTAAAGATCATGTT
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGTT
* *
301556 CCTTAGCGGCGCTTTTTCCAC
66 CCTTAGCGGCACTTCTTCCAC
*
301577 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGTT
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGTT
* *
301642 CTTTAGCGGCACTTCTTCCGC
66 CCTTAGCGGCACTTCTTCCAC
* * *
301663 AAACGCCACTAAAGGTCATGTTCTTTTAGCGGCG-TTTTTACACAAACGTCGCTA
1 AAACGCCGCTAAAGGTCATGTTC-TTTAGCGGCGCTTTTTCCACAAACGCCGCTA
301717 TTTGTTTGGT
Statistics
Matches: 126, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
86 116 0.92
87 10 0.08
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (86 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGATCATGTT
CCTTAGCGGCACTTCTTCCAC
Found at i:302092 original size:21 final size:21
Alignment explanation
Indices: 302066--302114 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
302056 TTTGCTCTAC
* *
302066 TCTGCTTCCCTCGCTGCAGCG
1 TCTGCTTCCCTCGATGCAGCA
* *
302087 TCTGCTTCTCTCGATGCCGCA
1 TCTGCTTCCCTCGATGCAGCA
302108 TCTGCTT
1 TCTGCTT
302115 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.06, C:0.39, G:0.20, T:0.35
Consensus pattern (21 bp):
TCTGCTTCCCTCGATGCAGCA
Found at i:307634 original size:25 final size:25
Alignment explanation
Indices: 307587--308454 Score: 1610
Period size: 25 Copynumber: 34.5 Consensus size: 25
307577 ATATATTTAT
* *
307587 GTAAGTTATGTAAGTTATATATTAA
1 GTAAATTATGTAAGTTATGTATTAA
*
307612 TTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307637 GTAAATTATGTAAGTTATAAGTTATATTTAA
1 GTAAATTATGTAAGTTAT--G---TA-TTAA
*
307668 TTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307693 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
*
307718 GTAAATTATGCAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307743 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307768 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307793 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307818 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307843 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307868 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307893 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307918 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307943 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307968 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
307993 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308018 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308043 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308068 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308093 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308118 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308143 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308168 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308193 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308218 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308243 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308268 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308293 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308318 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308343 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308368 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
308393 GTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAA
* *
308418 GTAAATTATGCAAGTTATGTATTAT
1 GTAAATTATGTAAGTTATGTATTAA
*
308443 GTAAGTTATGTA
1 GTAAATTATGTA
308455 TTAAGTAAAT
Statistics
Matches: 825, Mismatches: 12, Indels: 12
0.97 0.01 0.01
Matches are distributed among these distances:
25 798 0.97
26 2 0.00
27 1 0.00
29 1 0.00
30 2 0.00
31 21 0.03
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (25 bp):
GTAAATTATGTAAGTTATGTATTAA
Found at i:307649 original size:50 final size:50
Alignment explanation
Indices: 307587--308570 Score: 1700
Period size: 50 Copynumber: 19.7 Consensus size: 50
307577 ATATATTTAT
* * *
307587 GTAAGTTATGTAAGTTATATATTAATTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
*
307637 GTAAATTATGTAAGTTATAAGTTATATTTAATTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTAT--G---TA-TTAAGTAAATTATGTAAGTTATGTATTAA
*
307693 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGCAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
307743 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
307793 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
307843 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
307893 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
307943 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
307993 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308043 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308093 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308143 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308193 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308243 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308293 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308343 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
*
308393 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGCAAG---T-TA-T--
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
*
308436 GT--ATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAT
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
* * * *
308484 GTAAGTTATGTAAGTTATGTATTATG-AAACTTATGTAAGTTATGTCTTAT
1 GTAAATTATGTAAGTTATGTATTAAGTAAA-TTATGTAAGTTATGTATTAA
** * *
308534 GTATGTTATGTAAGTTATGTATTATGTAAGTTATGTA
1 GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTA
308571 TTAAGTAAAT
Statistics
Matches: 905, Mismatches: 12, Indels: 34
0.95 0.01 0.04
Matches are distributed among these distances:
41 34 0.04
43 2 0.00
44 1 0.00
45 3 0.00
46 3 0.00
47 1 0.00
48 2 0.00
49 3 0.00
50 802 0.89
51 4 0.00
54 1 0.00
55 2 0.00
56 47 0.05
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (50 bp):
GTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
Found at i:307784 original size:75 final size:75
Alignment explanation
Indices: 307654--308570 Score: 1631
Period size: 75 Copynumber: 12.4 Consensus size: 75
307644 ATGTAAGTTA
* *
307654 TAAGTTATAT-TTAATTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
307718 GTAAATTATG
66 GTAAATTATG
*
307728 CAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
307793 GTAAATTATG
66 GTAAATTATG
307803 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
307868 GTAAATTATG
66 GTAAATTATG
307878 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
307943 GTAAATTATG
66 GTAAATTATG
307953 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308018 GTAAATTATG
66 GTAAATTATG
308028 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308093 GTAAATTATG
66 GTAAATTATG
308103 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308168 GTAAATTATG
66 GTAAATTATG
308178 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308243 GTAAATTATG
66 GTAAATTATG
308253 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308318 GTAAATTATG
66 GTAAATTATG
308328 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308393 GTAAATTATG
66 GTAAATTATG
*
308403 TAAGTTATGTATTAAGTAAATTATGCAAG---T-TA-T--GT--ATTATGTAAGTTATGTATTAA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
308459 GTAAATTATG
66 GTAAATTATG
* * * *
308469 TAAGTTATGTATTATGTAAGTTATGTAAGTTATGTATTATG-AAACTTATGTAAGTTATGTCTTA
1 TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAA-TTATGTAAGTTATGTATTA
* **
308533 TGTATGTTATG
65 AGTAAATTATG
* *
308544 TAAGTTATGTATTATGTAAGTTATGTA
1 TAAGTTATGTATTAAGTAAATTATGTA
308571 TTAAGTAAAT
Statistics
Matches: 820, Mismatches: 12, Indels: 21
0.96 0.01 0.02
Matches are distributed among these distances:
66 57 0.07
68 2 0.00
69 1 0.00
70 3 0.00
71 3 0.00
72 1 0.00
73 1 0.00
74 9 0.01
75 743 0.91
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.44
Consensus pattern (75 bp):
TAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTATTAA
GTAAATTATG
Found at i:308466 original size:25 final size:25
Alignment explanation
Indices: 308438--308570 Score: 196
Period size: 25 Copynumber: 5.3 Consensus size: 25
308428 CAAGTTATGT
*
308438 ATTATGTAAGTTATGTATTAAGTAA
1 ATTATGTAAGTTATGTATTATGTAA
308463 ATTATGTAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATGTATTATGTAA
*
308488 GTTATGTAAGTTATGTATTATG-AA
1 ATTATGTAAGTTATGTATTATGTAA
* *
308512 ACTTATGTAAGTTATGTCTTATGTAT
1 A-TTATGTAAGTTATGTATTATGTAA
*
308538 GTTATGTAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATGTATTATGTAA
*
308563 GTTATGTA
1 ATTATGTA
308571 TTAAGTAAAT
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
24 2 0.02
25 95 0.97
26 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (25 bp):
ATTATGTAAGTTATGTATTATGTAA
Found at i:309171 original size:16 final size:16
Alignment explanation
Indices: 309150--309201 Score: 77
Period size: 16 Copynumber: 3.1 Consensus size: 16
309140 TATAAATTTA
309150 AATTATGTAAGTTATG
1 AATTATGTAAGTTATG
309166 AATTATGTAAGTTATG
1 AATTATGTAAGTTATG
*
309182 TAAATTACGTAAGTTATG
1 --AATTATGTAAGTTATG
309200 AA
1 AA
309202 ATTTGAACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 18 0.55
18 15 0.45
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.40
Consensus pattern (16 bp):
AATTATGTAAGTTATG
Found at i:309180 original size:9 final size:9
Alignment explanation
Indices: 309152--309199 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
309142 TAAATTTAAA
309152 TTATGTAAG
1 TTATGTAAG
309161 TTATG-AA-
1 TTATGTAAG
309168 TTATGTAAG
1 TTATGTAAG
*
309177 TTATGTAAA
1 TTATGTAAG
*
309186 TTACGTAAG
1 TTATGTAAG
309195 TTATG
1 TTATG
309200 AAATTTGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 5 0.15
8 4 0.12
9 24 0.73
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:309256 original size:35 final size:35
Alignment explanation
Indices: 309211--309304 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
309201 AATTTGAACT
**
309211 TTAAAA-AAAATTTAATATTT-AAAAATATTCGTCA
1 TTAAAATAAAATAAAATATTTAAAAAAT-TTCGTCA
* *
309245 TTCAAATAAAATAAAATATTTAAAAAATTTCGTGA
1 TTAAAATAAAATAAAATATTTAAAAAATTTCGTCA
309280 TTAAAATAAAATAAAATATTTAAAA
1 TTAAAATAAAATAAAATATTTAAAA
309305 TATAACTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
34 5 0.09
35 42 0.79
36 6 0.11
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.35
Consensus pattern (35 bp):
TTAAAATAAAATAAAATATTTAAAAAATTTCGTCA
Found at i:313015 original size:114 final size:114
Alignment explanation
Indices: 312790--313747 Score: 1104
Period size: 114 Copynumber: 8.3 Consensus size: 114
312780 AGACAAATAA
* * * * * * * *
312790 TTTTTTTGCTGAGCTTTCCCAAAAATGCCGTTAAA-TCCTAGAGAATTAGCGGCGCTGT-ATTAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCT-GAGCATTAGCGGCGCT-TCCTTAA
* * * * *
312853 AAATGCCGTTAAAGCCCCCGAAAGGTCAGAAAACGGCGTCGTTGGGCTTATG
64 AAACGCCGCTAAA-TCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
*
312905 TTTTTTTGCGGCGCTTTAC-CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAA
1 TTTTTTTGCGGCGCTTT-CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAA
*
312969 AACGCCGCTAAATCCCCGAAAGGTCAGAAAACGGCGTCGTTGGGCTTAGG
65 AACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * * * * *
313019 TTTTTTTGCGGCACTTTGTCAAAAACACCGCTAAAGCCCTGAGCATTAGCGACACTTTCTTAAAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAA
* * * *
313084 ACACCGCTAAATCCCCAAAAAGATC-GAAAACGGCGTCGTTGGGTTTAGGTTTTTTTGCTAGG
66 ACGCCGCTAAATCCCC-GAAAGCTCAGAAAACGGCGTCGTT--G----GG-----CT--TAGG
* * * *
313146 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCTGAGCATTAGCGTCACTTCCTGAAAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAA
** *
313211 ACGCCGCTAAATCCCC-AAATGCTCAGAAAACAACATCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAAA-GCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * *
313260 TTTTTTTGCGGCGCTTTCTCAAAATCGCCGCTAAAGCCCTGAGCATTAGCAGCGCTTCC-TCAAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAA
* * *
313324 ACGCCGCTAAATCCTCGAATGCTCAGAAAATGGGCGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAA-CGGCGTCGTTGGGCTTAGG
* * * * * *
313374 -TTTTTTGCGGCGCTTTCTCAGAAATGCAGCTAAAGCCCTAAGCATTAGCGACGCTTCCTCAAAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAA
* *
313438 ACGCCGCTAAATCCCCGAATGCTCAGAAAATGGCGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * * * * * *
313487 CTTTTTTGCGGCGCTTTGTCAAAAACACTGCTAAAGCCCTGAGCATTAGTGGCACTTCCTCAAAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAA
* * *
313552 ACGCTGCTAAATCCCCGAATGCTCAGAAAACAGCGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* *
313601 TTTTTTTGCGGCGCTTTCTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAA
* *
313666 ACGCCGCTAAATCCCTGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* ** *
313715 -TTTTTTGCGGTGCTTTCTGGAAAATGCCGCTAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
313748 TGCTTATTTT
Statistics
Matches: 736, Mismatches: 83, Indels: 50
0.85 0.10 0.06
Matches are distributed among these distances:
113 126 0.17
114 438 0.60
115 65 0.09
116 6 0.01
120 2 0.00
121 2 0.00
125 5 0.01
126 3 0.00
127 89 0.12
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (114 bp):
TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTTAAAA
ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
Found at i:313147 original size:13 final size:13
Alignment explanation
Indices: 313129--313154 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
313119 TCGTTGGGTT
313129 TAGGTTTTTTTGC
1 TAGGTTTTTTTGC
313142 TAGGTTTTTTTGC
1 TAGGTTTTTTTGC
313155 GGCGCTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (13 bp):
TAGGTTTTTTTGC
Found at i:318198 original size:22 final size:21
Alignment explanation
Indices: 318160--318203 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
318150 AACAGCGAGG
*
318160 TTTCAAATATGTAAATTGACA
1 TTTCAAATATGTAAATTAACA
318181 TTTCAAA-ATGTGAGAATTAACA
1 TTTCAAATATGT-A-AATTAACA
318203 T
1 T
318204 GAGAAGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 8 0.40
22 8 0.40
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (21 bp):
TTTCAAATATGTAAATTAACA
Found at i:319109 original size:80 final size:81
Alignment explanation
Indices: 319008--319170 Score: 310
Period size: 80 Copynumber: 2.0 Consensus size: 81
318998 TGTGTGGACT
319008 TGAATGAGAACCATGAATATTCTGCCCTTGTGTGGTATGTGCAAATTTTGTATAAATTGTGTTTT
1 TGAATGAGAA-CATGAATATTCTGCCCTTGTGTGGTATGTGCAAATTTTGTATAAATTGTGTTTT
319073 ATACAATAGGGAGTAAA
65 ATACAATAGGGAGTAAA
319090 TGAATGAGAA-ATGAATATTCTGCCCTTGTGTGGTATGTGCAAATTTTGTATAAATTGTGTTTTA
1 TGAATGAGAACATGAATATTCTGCCCTTGTGTGGTATGTGCAAATTTTGTATAAATTGTGTTTTA
319154 TACAATAGGGAGTAAA
66 TACAATAGGGAGTAAA
319170 T
1 T
319171 TGCAAAAAGA
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
80 71 0.88
82 10 0.12
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (81 bp):
TGAATGAGAACATGAATATTCTGCCCTTGTGTGGTATGTGCAAATTTTGTATAAATTGTGTTTTA
TACAATAGGGAGTAAA
Found at i:329566 original size:20 final size:20
Alignment explanation
Indices: 329541--329588 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
329531 AAATTAATGG
329541 AAAAGAAAGAAAA-AAAAAC
1 AAAAGAAAGAAAATAAAAAC
* *
329560 AAAAAGAATGAAAATCAAAAC
1 -AAAAGAAAGAAAATAAAAAC
329581 AAAAGAAA
1 AAAAGAAA
329589 AGAATGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.79, C:0.06, G:0.10, T:0.04
Consensus pattern (20 bp):
AAAAGAAAGAAAATAAAAAC
Found at i:330807 original size:17 final size:17
Alignment explanation
Indices: 330785--330821 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
330775 ATTGAGATAA
*
330785 AAATAAATAACGAAAAT
1 AAATAAATAACAAAAAT
*
330802 AAATAAATAATAAAAAT
1 AAATAAATAACAAAAAT
330819 AAA
1 AAA
330822 CAAACGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (17 bp):
AAATAAATAACAAAAAT
Found at i:330841 original size:30 final size:30
Alignment explanation
Indices: 330781--330841 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
330771 GATAATTGAG
*
330781 ATAAAAATAAATAACGAAAATAAATAAATA
1 ATAAAAATAAAAAACGAAAATAAATAAATA
* *
330811 ATAAAAATAAACAAACGATAA-AAATTAATA
1 ATAAAAATAAA-AAACGAAAATAAATAAATA
330841 A
1 A
330842 ACTAATCAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (30 bp):
ATAAAAATAAAAAACGAAAATAAATAAATA
Found at i:330843 original size:17 final size:17
Alignment explanation
Indices: 330797--330843 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
330787 ATAAATAACG
*
330797 AAAATAAATAAATAATA
1 AAAATAAATAAACAATA
* *
330814 AAAATAAACAAACGATA
1 AAAATAAATAAACAATA
*
330831 AAAATTAATAAAC
1 AAAATAAATAAAC
330844 TAATCAGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAATAAATAAACAATA
Found at i:333423 original size:27 final size:27
Alignment explanation
Indices: 333358--333419 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
333348 GTTGAAGAAC
333358 TAAATAAATATTAATAATTTTATTTAAA
1 TAAA-AAATATTAATAATTTTATTTAAA
* *
333386 TATAAAATATTAAT-ATTTATTTTTAAA
1 TAAAAAATATTAATAATTT-TATTTAAA
333413 -AAAAAAT
1 TAAAAAAT
333420 TATTGGTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.33
27 17 0.57
28 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAAAAATATTAATAATTTTATTTAAA
Found at i:333800 original size:162 final size:163
Alignment explanation
Indices: 333615--333940 Score: 636
Period size: 162 Copynumber: 2.0 Consensus size: 163
333605 CTGTATTTTT
333615 CGTAAATTTGAAAATTATTTTTTATATTTTATATTTTTAATAATTTAGTTTTTATTTGTCAGATT
1 CGTAAATTTG-AAATTATTTTTTATATTTTATATTTTTAATAATTTAGTTTTTATTTGTCAGATT
333680 TCAAAATAAGTCTAATTATTAATACCTTTAAAATTATTTTGTTAAATTCAAGTTTATTGCAACGT
65 TCAAAATAAGTCTAATTATTAATACCTTTAAAATTATTTTGTTAAATTCAAGTTTATTGCAACGT
333745 CTGTTTTAATTACATTGTTGCCAAGTCAAGTGAG
130 CTGTTTTAATTACATTGTTGCCAAGTCAAGTGAG
333779 CGTAAATTTG-AATTATTTTTTATATTTTATATTTTTAATAATTTAGTTTTTATTTGTCAGATTT
1 CGTAAATTTGAAATTATTTTTTATATTTTATATTTTTAATAATTTAGTTTTTATTTGTCAGATTT
333843 CAAAATAAGTCTAATTATTAATACCTTTAAAATTATTTTGTTAAATTCAAGTTTATTGCAACGTC
66 CAAAATAAGTCTAATTATTAATACCTTTAAAATTATTTTGTTAAATTCAAGTTTATTGCAACGTC
333908 TGTTTTAATTACATTGTTGCCAAGTCAAGTGAG
131 TGTTTTAATTACATTGTTGCCAAGTCAAGTGAG
333941 TTTTTTTTTT
Statistics
Matches: 162, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
162 152 0.94
164 10 0.06
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (163 bp):
CGTAAATTTGAAATTATTTTTTATATTTTATATTTTTAATAATTTAGTTTTTATTTGTCAGATTT
CAAAATAAGTCTAATTATTAATACCTTTAAAATTATTTTGTTAAATTCAAGTTTATTGCAACGTC
TGTTTTAATTACATTGTTGCCAAGTCAAGTGAG
Found at i:334060 original size:29 final size:30
Alignment explanation
Indices: 334012--334078 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
334002 ATAATTGGGT
* *
334012 CTAAA-TTTTAAAATCTAAAATTA-AATGGA
1 CTAAATTTTTAAAATCTAAAAGTACAA-AGA
334041 CTAAATTTTTGAAAA-C-AAAAGTACAAAGA
1 CTAAATTTTT-AAAATCTAAAAGTACAAAGA
334070 CTAAATTTT
1 CTAAATTTT
334079 AAATTTGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 22 0.67
30 7 0.21
31 4 0.12
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (30 bp):
CTAAATTTTTAAAATCTAAAAGTACAAAGA
Found at i:345829 original size:88 final size:88
Alignment explanation
Indices: 345686--346613 Score: 1216
Period size: 88 Copynumber: 10.5 Consensus size: 88
345676 CTGCTTAGGG
* * * ** * * *
345686 AGACAAGATCTACAATTTTCAACCTAGTCCACTGCAAACTCAGAGAGGCAAGGCTGGTGT-TGTC
1 AGACAAGATCTGCTATTTTCAACCTACTCCACTGC-TGCTCAGGGAGACAAGGCTGGTATCT-TC
* *
345750 GATCTGCTTCGCTGTCAATACAGGA
64 GATCTACTTCGCTGCCAATACAGGA
** * *
345775 AGGTAATATCTGCTATCTTT-AACCTACTCCACTGCTACTCAGGGAGACAAGGCTGGTATCTTCG
1 AGACAAGATCTGCTAT-TTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTATCTTCG
*
345839 ATCTACTTCGCTGCCAATACAGAA
65 ATCTACTTCGCTGCCAATACAGGA
* * * * *
345863 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGACTGGTGTTTTTGA
1 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTATCTTCGA
*
345928 TCTACTTCCCTGCCAATACAGGA
66 TCTACTTCGCTGCCAATACAGGA
* * *
345951 AGACAAGATCTGTTATTTTTAACCTACTCCATTGCTGCTCAGGGAGACAAGGCTGGTATCTTCGA
1 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTATCTTCGA
* *
346016 TCTACTTCGCTGTCAATACAAGA
66 TCTACTTCGCTGCCAATACAGGA
* ** * * * *
346039 AGACAAGATCTACTATTTTCAACCTACTCCACTTTTGCTCAGGGAGATAAGGCTAGAATCTTCAA
1 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTATCTTCGA
*
346104 TCTACTTCGCTGCCAATACAAGA
66 TCTACTTCGCTGCCAATACAGGA
* * *
346127 AGACAAGATCTACTATTTTTAACCTACTCCACTACTGCTCAGGGAGACAAGGCTGGTATCTTCGA
1 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTATCTTCGA
*
346192 TATACTTCGCTGCCAATACAGGA
66 TCTACTTCGCTGCCAATACAGGA
* * *
346215 AGACAAGATCTGCTATTTTCAAGCTACTCCACTGCTGCTCAGGGAGATAAGGCTGAG-GTCTTCG
1 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTG-GTATCTTCG
* *
346279 ATCTTCTTCGTTGCCAATACAGGA
65 ATCTACTTCGCTGCCAATACAGGA
** * *
346303 AGACAAGATCTATTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAGGGCTGATATCTTCGA
1 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTATCTTCGA
346368 TCTACTTCGCTGCCAATACAGGA
66 TCTACTTCGCTGCCAATACAGGA
* *
346391 AGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCTCAGGGAGACAAGGCTAGTATCTTCGA
1 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTATCTTCGA
*
346456 TCTACTTCGCTACCAATACAGGA
66 TCTACTTCGCTGCCAATACAGGA
* * * * * * * * * *
346479 AAATAATATCTACTATTTTCAACCTACTCCACTACTGTTCAGGGAGATAAGGTTGAG-GTCTTCA
1 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTG-GTATCTTCG
*
346543 ATCTACTTTGCTGCCAATACAGGA
65 ATCTACTTCGCTGCCAATACAGGA
* *
346567 AGACAATATCTGCTAATTTCAACCTACTCCACTGCTGCTCAGGGAGA
1 AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
346614 TAGGACTTAT
Statistics
Matches: 735, Mismatches: 98, Indels: 13
0.87 0.12 0.02
Matches are distributed among these distances:
87 3 0.00
88 701 0.95
89 28 0.04
90 3 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (88 bp):
AGACAAGATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGTATCTTCGA
TCTACTTCGCTGCCAATACAGGA
Found at i:346177 original size:44 final size:44
Alignment explanation
Indices: 345782--346441 Score: 255
Period size: 44 Copynumber: 15.0 Consensus size: 44
345772 GGAAGGTAAT
*
345782 ATCTGCTATCTTT-AACCTACTCCACTGCTACTCAGGGAGACAAG
1 ATCTGCTAT-TTTCAACCTACTCCACTGCTGCTCAGGGAGACAAG
* * * * * * * *** **
345826 -GCTGGTATCTTCGATCTACTTCGCTGCCAATACAGAAAGACAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCT-CAGGGAGACAAG
*
345870 ATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAG
* * ** * *** *
345914 A-CTGGTGTTTTTGATCTACTTCC-CTGCCAATACAGGAAGACAAG
1 ATCTGCTATTTTCAACCTAC-TCCACTGCTGCT-CAGGGAGACAAG
* * *
345958 ATCTGTTATTTTTAACCTACTCCATTGCTGCTCAGGGAGACAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAG
* * * * * * * * *
346002 -GCTGGTATCTTCGATCTACTTCGCTG-T-CAATACAAGAAGACAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGC--T-CAGGGAGACAAG
* ** *
346046 ATCTACTATTTTCAACCTACTCCACTTTTGCTCAGGGAGATAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAG
* * * * * * *** * *
346090 -GCTAG-AATCTTCAATCTACTTCGCTGCCAATACAAGAAGACAAG
1 ATCT-GCTATTTTCAACCTACTCCACTGCTGCT-CAGGGAGACAAG
* * *
346134 ATCTACTATTTTTAACCTACTCCACTACTGCTCAGGGAGACAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAG
* * * * ** * * *** *
346178 -GCTGGTATCTTCGATATACTTCGCTGCCAATACAGGAAGACAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCT-CAGGGAGACAAG
* *
346222 ATCTGCTATTTTCAAGCTACTCCACTGCTGCTCAGGGAGATAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAG
* *** * * * * * ** *** *
346266 -GCTGAGGTCTTCGATCTTCTTCGTTGCCAATACAGGAAGACAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCT-CAGGGAGACAAG
**
346310 ATCTATTATTTTCAACCTACTCCACTGCTGCTCAGGGAGAC-AG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAG
** * * * * * * *** *
346353 GGCTGATATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCT-CAGGGAGACAAG
*
346398 ATCTGCTATTTTCAACCTACTCCACTACTGCTCAGGGAGACAAG
1 ATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAG
346442 GCTAGTATCT
Statistics
Matches: 412, Mismatches: 181, Indels: 46
0.64 0.28 0.07
Matches are distributed among these distances:
41 1 0.00
42 3 0.01
43 129 0.31
44 144 0.35
45 133 0.32
46 1 0.00
47 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
ATCTGCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAG
Found at i:347786 original size:12 final size:12
Alignment explanation
Indices: 347769--347805 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
347759 TTTTTGTTTC
347769 TTTTTGTTCTTT-
1 TTTTTGTT-TTTG
347781 TTTTTGTTTTTG
1 TTTTTGTTTTTG
347793 TTTTT-TTTTTG
1 TTTTTGTTTTTG
347804 TT
1 TT
347806 CTTATTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (12 bp):
TTTTTGTTTTTG
Found at i:347790 original size:18 final size:18
Alignment explanation
Indices: 347759--347817 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
347749 CCGGTAGAGG
*
347759 TTTTTGTTTCTTTTTGTTC
1 TTTTT-TTTGTTTTTGTTC
347778 TTTTTTTTGTTTTTGTT-
1 TTTTTTTTGTTTTTGTTC
* *
347795 TTTTTTTTGTTCTTATTC
1 TTTTTTTTGTTTTTGTTC
347813 TTTTT
1 TTTTT
347818 GTTTTGATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.42
18 16 0.44
19 5 0.14
ACGTcount: A:0.02, C:0.07, G:0.08, T:0.83
Consensus pattern (18 bp):
TTTTTTTTGTTTTTGTTC
Found at i:347802 original size:29 final size:31
Alignment explanation
Indices: 347758--347822 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
347748 CCCGGTAGAG
347758 GTTTTTGTTTCTTTTTGTTC-T-TT-TTTTT
1 GTTTTTGTTTCTTTTTGTTCTTATTCTTTTT
*
347786 GTTTTTGTTTTTTTTTTGTTCTTATTCTTTTT
1 GTTTTTG-TTTCTTTTTGTTCTTATTCTTTTT
347818 GTTTT
1 GTTTT
347823 GATTGAATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.22
29 12 0.38
30 1 0.03
31 2 0.06
32 10 0.31
ACGTcount: A:0.02, C:0.06, G:0.11, T:0.82
Consensus pattern (31 bp):
GTTTTTGTTTCTTTTTGTTCTTATTCTTTTT
Found at i:347816 original size:17 final size:17
Alignment explanation
Indices: 347779--347817 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
347769 TTTTTGTTCT
* * *
347779 TTTTTTTGTTTTTGTTT
1 TTTTTTTGTTCTTATTC
347796 TTTTTTTGTTCTTATTC
1 TTTTTTTGTTCTTATTC
347813 TTTTT
1 TTTTT
347818 GTTTTGATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.85
Consensus pattern (17 bp):
TTTTTTTGTTCTTATTC
Found at i:356348 original size:3 final size:3
Alignment explanation
Indices: 356334--356374 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
356324 CATTGACCTT
* *
356334 ATC ATC ACC ATC ATC ATC ATC ATC ATC ACC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
356375 TTCCTGAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:360101 original size:11 final size:12
Alignment explanation
Indices: 360077--360101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
360067 TTAAAAGTCC
360077 AAAAAGACCAAA
1 AAAAAGACCAAA
360089 AAAAAGACCAAA
1 AAAAAGACCAAA
360101 A
1 A
360102 CATACTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAGACCAAA
Found at i:362683 original size:20 final size:20
Alignment explanation
Indices: 362658--362698 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
362648 GCATAACACA
* * *
362658 TTCTCTGCTTTGTTCTGTTC
1 TTCTCTACTCTGTTCTATTC
362678 TTCTCTACTCTGTTCTATTC
1 TTCTCTACTCTGTTCTATTC
362698 T
1 T
362699 GCTTTGCTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.27, G:0.10, T:0.59
Consensus pattern (20 bp):
TTCTCTACTCTGTTCTATTC
Found at i:389683 original size:24 final size:24
Alignment explanation
Indices: 389651--389705 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
389641 AAACATATTC
*
389651 GAACCCTATCACCTGAAGTTATGT
1 GAACCCTATCACCTGAAGGTATGT
* *
389675 GAACCCTATTACCTTAAGGTATGT
1 GAACCCTATCACCTGAAGGTATGT
*
389699 GAGCCCT
1 GAACCCT
389706 CATGTATGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (24 bp):
GAACCCTATCACCTGAAGGTATGT
Found at i:389951 original size:19 final size:19
Alignment explanation
Indices: 389929--389977 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
389919 TGTATGCGAG
389929 CCTACCACATGTAAGAACC
1 CCTACCACATGTAAGAACC
**
389948 CCTACC-CATGTGCGAACC
1 CCTACCACATGTAAGAACC
* *
389966 CATACCATATGT
1 CCTACCACATGT
389978 GAACCCATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.31, C:0.37, G:0.12, T:0.20
Consensus pattern (19 bp):
CCTACCACATGTAAGAACC
Found at i:389964 original size:18 final size:18
Alignment explanation
Indices: 389943--390005 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
389933 CCACATGTAA
*
389943 GAACCCCTACCCATGTGC
1 GAACCCATACCCATGTGC
* *
389961 GAACCCATA-CCATATGT
1 GAACCCATACCCATGTGC
*
389978 GAACCCATACTGCATGTGC
1 GAACCCATAC-CCATGTGC
*
389997 GAACTCATA
1 GAACCCATA
390006 TCATCTGTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 15 0.42
18 8 0.22
19 13 0.36
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (18 bp):
GAACCCATACCCATGTGC
Found at i:390891 original size:17 final size:18
Alignment explanation
Indices: 390852--390892 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
390842 GTGAATTGCC
* *
390852 TATTTTATGTGAACTATT
1 TATTTCATGTAAACTATT
390870 TATTTCATGTAAACTA-T
1 TATTTCATGTAAACTATT
390887 TATTTC
1 TATTTC
390893 GTACGAGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (18 bp):
TATTTCATGTAAACTATT
Found at i:397148 original size:28 final size:28
Alignment explanation
Indices: 397109--397218 Score: 118
Period size: 27 Copynumber: 3.9 Consensus size: 28
397099 AATAAGGTCC
*
397109 AAATTGTAAAAAACTAAAAAATAGGGGAA
1 AAATTGT-AAAATCTAAAAAATAGGGGAA
*
397138 AAATTGTAAAATCT-AAAAATAGGGGCA
1 AAATTGTAAAATCTAAAAAATAGGGGAA
* * *
397165 AAAGTATAAAATCTAAAAATAATA--GGTA
1 AAATTGTAAAATCT-AAAA-AATAGGGGAA
*
397193 AAATTGTAAAATCTGAAAAATAGGGG
1 AAATTGTAAAATCTAAAAAATAGGGG
397219 CACATGGTCG
Statistics
Matches: 68, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
26 4 0.06
27 27 0.40
28 23 0.34
29 10 0.15
30 4 0.06
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (28 bp):
AAATTGTAAAATCTAAAAAATAGGGGAA
Found at i:403746 original size:15 final size:15
Alignment explanation
Indices: 403726--403756 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
403716 ACAACCAGAA
*
403726 TAACACTTCAAACGG
1 TAACACCTCAAACGG
403741 TAACACCTCAAACGG
1 TAACACCTCAAACGG
403756 T
1 T
403757 GGAGTACGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.19
Consensus pattern (15 bp):
TAACACCTCAAACGG
Found at i:405431 original size:35 final size:36
Alignment explanation
Indices: 405385--405455 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
405375 CGGGCGTGGC
405385 CCGAATTCACTAAAAGACAAAAAAATAT-TTTTTTT
1 CCGAATTCACTAAAAGACAAAAAAATATGTTTTTTT
405420 CCGAATTCACTAAAAGACAAAAAAATATGTTTTTTT
1 CCGAATTCACTAAAAGACAAAAAAATATGTTTTTTT
405456 TTTGTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 28 0.80
36 7 0.20
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (36 bp):
CCGAATTCACTAAAAGACAAAAAAATATGTTTTTTT
Found at i:406819 original size:13 final size:14
Alignment explanation
Indices: 406802--406841 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
406792 TAAAATCTCA
*
406802 AAAAAAAAAAAGAG
1 AAAAAGAAAAAGAG
406816 AAAAAGAAAAA-AG
1 AAAAAGAAAAAGAG
*
406829 AAAAATAAAAAGA
1 AAAAAGAAAAAGA
406842 TAGCTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAGAG
Found at i:406827 original size:19 final size:19
Alignment explanation
Indices: 406802--406841 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
406792 TAAAATCTCA
*
406802 AAAAAAAAAAAGAGAAAAAG
1 AAAAAAGAAAA-AGAAAAAG
*
406822 AAAAAAGAAAAATAAAAAG
1 AAAAAAGAAAAAGAAAAAG
406841 A
1 A
406842 TAGCTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (19 bp):
AAAAAAGAAAAAGAAAAAG
Found at i:406885 original size:28 final size:28
Alignment explanation
Indices: 406853--406906 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
406843 AGCTTTGTTT
*
406853 TTTGGATAGGTGTCAAAAGGAAAAATTA
1 TTTGGATAGCTGTCAAAAGGAAAAATTA
*
406881 TTTGGATAGCTGTCAAAAGGAGAAAT
1 TTTGGATAGCTGTCAAAAGGAAAAAT
406907 GGTTGATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.28
Consensus pattern (28 bp):
TTTGGATAGCTGTCAAAAGGAAAAATTA
Found at i:410408 original size:15 final size:17
Alignment explanation
Indices: 410378--410410 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
410368 CTATTTTTTC
410378 TCTCGATATCAAATCAA
1 TCTCGATATCAAATCAA
410395 TCTCGA-AT-AAATCAA
1 TCTCGATATCAAATCAA
410410 T
1 T
410411 TCTCTACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (17 bp):
TCTCGATATCAAATCAA
Found at i:410958 original size:41 final size:41
Alignment explanation
Indices: 410842--410968 Score: 130
Period size: 41 Copynumber: 3.0 Consensus size: 41
410832 TTAGCTGCGG
**
410842 TTTTAGGTAAGCGCCGCTAATGCTCGGGGTTTTTAGCGGCGTT
1 TTTTA-GTAAGCGCCGCTAATGCTAAGGG-TTTTAGCGGCGTT
* * * * **
410885 TTTTATTAAGCACCACTAATGCTTAGACTTTTAGCGGCGTT
1 TTTTAGTAAGCGCCGCTAATGCTAAGGGTTTTAGCGGCGTT
* *
410926 TTTTAGTAA-CTGCCGCTAATTCTAAGGGTTTTAGTGGCGTT
1 TTTTAGTAAGC-GCCGCTAATGCTAAGGGTTTTAGCGGCGTT
410967 TT
1 TT
410969 GTTAAAGTGC
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
40 1 0.01
41 46 0.68
42 16 0.24
43 5 0.07
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.39
Consensus pattern (41 bp):
TTTTAGTAAGCGCCGCTAATGCTAAGGGTTTTAGCGGCGTT
Found at i:411860 original size:7 final size:7
Alignment explanation
Indices: 411848--411904 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
411838 TGGGATATAA
411848 GGGTTAG
1 GGGTTAG
411855 GGGTTAG
1 GGGTTAG
411862 GGGTTTAG
1 GGG-TTAG
** *
411870 GATTTAA
1 GGGTTAG
*
411877 GGGTTAC
1 GGGTTAG
411884 GGGTTAAG
1 GGGTT-AG
*
411892 GGTTTAG
1 GGGTTAG
411899 GGGTTA
1 GGGTTA
411905 ATGGGTTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
7 29 0.74
8 10 0.26
ACGTcount: A:0.19, C:0.02, G:0.46, T:0.33
Consensus pattern (7 bp):
GGGTTAG
Found at i:411869 original size:15 final size:15
Alignment explanation
Indices: 411845--411911 Score: 75
Period size: 15 Copynumber: 4.5 Consensus size: 15
411835 GTTTGGGATA
411845 TAAGGG-TTAGGGGT
1 TAAGGGTTTAGGGGT
* **
411859 TAGGGGTTTAGGATT
1 TAAGGGTTTAGGGGT
*
411874 TAAGGG-TTACGGGT
1 TAAGGGTTTAGGGGT
411888 TAAGGGTTTAGGGGT
1 TAAGGGTTTAGGGGT
411903 TAATGGGTT
1 TAA-GGGTT
411912 AATAATTTAG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
14 16 0.38
15 21 0.50
16 5 0.12
ACGTcount: A:0.21, C:0.01, G:0.43, T:0.34
Consensus pattern (15 bp):
TAAGGGTTTAGGGGT
Found at i:411872 original size:29 final size:29
Alignment explanation
Indices: 411830--411899 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
411820 GGGTATGGAT
* *
411830 TTAA-GGTTTGGGATATAAGGGTTAGGGG
1 TTAAGGGTTTAGGATATAAGGGTTACGGG
* *
411858 TTAGGGGTTTAGGATTTAAGGGTTACGGG
1 TTAAGGGTTTAGGATATAAGGGTTACGGG
411887 TTAAGGGTTTAGG
1 TTAAGGGTTTAGG
411900 GGTTAATGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 3 0.08
29 33 0.92
ACGTcount: A:0.23, C:0.01, G:0.41, T:0.34
Consensus pattern (29 bp):
TTAAGGGTTTAGGATATAAGGGTTACGGG
Found at i:411880 original size:22 final size:22
Alignment explanation
Indices: 411855--411913 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
411845 TAAGGGTTAG
* *
411855 GGGTTAGGGGTTTAGGATTTAA
1 GGGTTACGGGTTAAGGATTTAA
* *
411877 GGGTTACGGGTTAAGGGTTTAG
1 GGGTTACGGGTTAAGGATTTAA
*
411899 GGGTTAATGGGTTAA
1 GGGTT-ACGGGTTAA
411914 TAATTTAGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 23 0.74
23 8 0.26
ACGTcount: A:0.22, C:0.02, G:0.42, T:0.34
Consensus pattern (22 bp):
GGGTTACGGGTTAAGGATTTAA
Found at i:411905 original size:29 final size:29
Alignment explanation
Indices: 411845--411912 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
411835 GTTTGGGATA
* * *
411845 TAAGGGTTAGGGGTTAGGGGTTTAGGATT
1 TAAGGGTTACGGGTTAAGGGTTTAGGAGT
*
411874 TAAGGGTTACGGGTTAAGGGTTTAGGGGT
1 TAAGGGTTACGGGTTAAGGGTTTAGGAGT
411903 TAATGGGTTA
1 TAA-GGGTTA
411913 ATAATTTAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 28 0.82
30 6 0.18
ACGTcount: A:0.22, C:0.01, G:0.43, T:0.34
Consensus pattern (29 bp):
TAAGGGTTACGGGTTAAGGGTTTAGGAGT
Found at i:412773 original size:270 final size:268
Alignment explanation
Indices: 412439--413007 Score: 764
Period size: 270 Copynumber: 2.1 Consensus size: 268
412429 CGTTTCTCTC
* *
412439 CACGATTTTTAACTTATAAAAAGTTTAGAATTATTTACTTAAAACGTCACAGTTTGGCTTAAAGT
1 CACGATTTTTAACTTAGAAAAA-TTTAGAATTATTTACTTAAAACATCACAGTTTGGCTTAAAGT
** * *
412504 ACGTTAAGTATTAGTGGCGTTTTTACATAAAACGCTAGAAACAATGCAATTTGAGACTAGCAAAA
65 AAATTAAGTATTAGTGGCGTTTTTACATAAAACGCAAGAAACAATGCAATTTGAGACTAACAAAA
* * * * * * * *
412569 TGACGTCGTTTCTATTTACAACTTTAAATTTTTGTGGCGTTTTT-GGAAAAATGCCGGAA-CTTT
130 CGACATCGTTTCTATTTAAAACTTGAAATTTTAGTGGCGTTTTTAGG-AAAACGCC-GAAGATGT
* * *
412632 GGAAGCAATAGTGGCGTTTGTACAGTAAACACCACAAAAGGGTATTAAAATAGTGTCTAAACGGT
193 GGAAGCAATAGCGGCGTTTGTACAGAAAACACCACAAAA-GGTATTAAAATAATGTCTAAACGGT
412697 GCCATTTCTGTA
257 GCCATTTCTGTA
* * * *
412709 CACGATTTTTAACTTAGAAAAATTTGAGATTTATTTATTTAAAACATCACCGTTTGGGTTAAAGT
1 CACGATTTTTAACTTAGAAAAATTT-AGAATTATTTACTTAAAACATCACAGTTTGGCTTAAAGT
* *
412774 AAATTAGGTATTAGTGGCGTTTTTACATAAAACGCAAGAAATAATGCAATTTGAGACTAACAAAA
65 AAATTAAGTATTAGTGGCGTTTTTACATAAAACGCAAGAAACAATGCAATTTGAGACTAACAAAA
* * *
412839 CGGCATTGTTTCTATTTAAAACTTGAACTTTTAGTGGCGTTTTTAGGAAAACGCCGAAGATGTGG
130 CGACATCGTTTCTATTTAAAACTTGAAATTTTAGTGGCGTTTTTAGGAAAACGCCGAAGATGTGG
* ** * * *
412904 AAGCAATAGCGGCGTTTTTACAGAAAATGCCGCAAAAGGTATTAAAATAATGTGTAAACGGTGTC
195 AAGCAATAGCGGCGTTTGTACAGAAAACACCACAAAAGGTATTAAAATAATGTCTAAACGGTGCC
*
412969 GTTTCTGTA
260 ATTTCTGTA
*
412978 TACGATTTTTAACTTAGAAAAATTTTAGAA
1 CACGATTTTTAACTTAGAAAAA-TTTAGAA
413008 ATTAAGTATT
Statistics
Matches: 260, Mismatches: 35, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
269 63 0.24
270 195 0.75
271 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (268 bp):
CACGATTTTTAACTTAGAAAAATTTAGAATTATTTACTTAAAACATCACAGTTTGGCTTAAAGTA
AATTAAGTATTAGTGGCGTTTTTACATAAAACGCAAGAAACAATGCAATTTGAGACTAACAAAAC
GACATCGTTTCTATTTAAAACTTGAAATTTTAGTGGCGTTTTTAGGAAAACGCCGAAGATGTGGA
AGCAATAGCGGCGTTTGTACAGAAAACACCACAAAAGGTATTAAAATAATGTCTAAACGGTGCCA
TTTCTGTA
Found at i:416396 original size:21 final size:21
Alignment explanation
Indices: 416331--416401 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
416321 CTACAACTTA
* *
416331 AAGCAGAGGCGGCAGTGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
416352 AAGTAGAGGCTGTAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
*
416373 AAGCAGAGGCTGCAGCAAGGG
1 AAGCAGAGGCTGCAGCGAGGG
416394 AAGCAGAG
1 AAGCAGAG
416402 CAGCGCAGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.34, C:0.14, G:0.45, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:416812 original size:43 final size:42
Alignment explanation
Indices: 416749--416970 Score: 286
Period size: 43 Copynumber: 5.2 Consensus size: 42
416739 AGCCAAATAA
416749 TAGCGGCGTTTGTG-GAAAAAGCGCAGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGAG-AAAAGCGC-GCTAAAGAACATGACCTT
*
416792 TAGCGGCGTTTGTGAGAAAAGTGTCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGAGAAAAGCG-CGCTAAAGAACATGACCTT
* * * *
416835 TAGCGGCGTTTG-AAGGAAAGCGACGCTAAAAAACACGACCTT
1 TAGCGGCGTTTGTGAGAAAAGCG-CGCTAAAGAACATGACCTT
* * *
416877 TAGCGGCATTTGTGGGAAAAGCACCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGAGAAAAGC-GCGCTAAAGAACATGACCTT
* *
416920 TAGCGACGTTTGTAAGAAAAGCGTCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTGAGAAAAGCG-CGCTAAAGAACATGACCTT
416963 TAGCGGCG
1 TAGCGGCG
416971 CTTCCAAAGA
Statistics
Matches: 154, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
42 35 0.23
43 117 0.76
44 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.21
Consensus pattern (42 bp):
TAGCGGCGTTTGTGAGAAAAGCGCGCTAAAGAACATGACCTT
Found at i:416882 original size:85 final size:84
Alignment explanation
Indices: 416749--416970 Score: 293
Period size: 85 Copynumber: 2.6 Consensus size: 84
416739 AGCCAAATAA
*
416749 TAGCGGCGTTTG-TGGAAAAAGCGCAGCTAAAGAACATGACCTTTAGCGGCGTTTGTGAGAAAAG
1 TAGCGGCGTTTGAAGG--AAAGCGC-GCTAAAGAACATGACCTTTAGCGGCGTTTGTGAGAAAAG
***
416813 TGTCGCTAAAGAACATGACCTT
63 CACCGCTAAAGAACATGACCTT
* * * *
416835 TAGCGGCGTTTGAAGGAAAGCGACGCTAAAAAACACGACCTTTAGCGGCATTTGTGGGAAAAGCA
1 TAGCGGCGTTTGAAGGAAAGCG-CGCTAAAGAACATGACCTTTAGCGGCGTTTGTGAGAAAAGCA
416900 CCGCTAAAGAACATGACCTT
65 CCGCTAAAGAACATGACCTT
* *
416920 TAGCGACGTTTGTAAGAAAAGCGTCGCTAAAGAACATGACCTTTAGCGGCG
1 TAGCGGCGTTTG-AAGGAAAGCG-CGCTAAAGAACATGACCTTTAGCGGCG
416971 CTTCCAAAGA
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
85 71 0.60
86 46 0.39
87 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.21
Consensus pattern (84 bp):
TAGCGGCGTTTGAAGGAAAGCGCGCTAAAGAACATGACCTTTAGCGGCGTTTGTGAGAAAAGCAC
CGCTAAAGAACATGACCTT
Found at i:416992 original size:71 final size:71
Alignment explanation
Indices: 416905--417041 Score: 222
Period size: 71 Copynumber: 1.9 Consensus size: 71
416895 AAGCACCGCT
* * *
416905 AAAGAACATGACCTTTAGC-GACGTTTGTAAGAAAAGCGTCGCTAAAGAACATGACCTTTAGCGG
1 AAAGAACATGACCTTTAACTG-CGTTTGTAAGAAAAGCGCCGCTAAAGAACATGACCTTTAGAGG
416969 CGCTTCC
65 CGCTTCC
*
416976 AAAGAACATGACCTTTAACTGCGTTTGTAGGAAAAGCGCCGCTAAAGAACATGACCTTTAGAGGC
1 AAAGAACATGACCTTTAACTGCGTTTGTAAGAAAAGCGCCGCTAAAGAACATGACCTTTAGAGGC
417041 G
66 G
417042 TTTATTTCTA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 60 0.98
72 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (71 bp):
AAAGAACATGACCTTTAACTGCGTTTGTAAGAAAAGCGCCGCTAAAGAACATGACCTTTAGAGGC
GCTTCC
Found at i:417361 original size:28 final size:27
Alignment explanation
Indices: 417329--417461 Score: 142
Period size: 28 Copynumber: 4.9 Consensus size: 27
417319 TGTTTTTCAG
* * *
417329 ATTTTACAATTTTGCCACTATTTTTTA
1 ATTTTATAGTTTTGCCCCTATTTTTTA
* **
417356 GATTTTACAGTTTTGCCTTTATTTTTTA
1 -ATTTTATAGTTTTGCCCCTATTTTTTA
*
417384 ATTTTATAGTTTTACCCCTATTTTTT-
1 ATTTTATAGTTTTGCCCCTATTTTTTA
* *
417410 ATTTTATAGTTTTGCCCATTTTTTTTAA
1 ATTTTATAGTTTTGCCCCTATTTTTT-A
* *
417438 ATTTTATAATTTTTCCCCTATTTT
1 ATTTTATAGTTTTGCCCCTATTTT
417462 GCAAAAATCA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
26 23 0.26
27 22 0.25
28 44 0.49
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (27 bp):
ATTTTATAGTTTTGCCCCTATTTTTTA
Found at i:417442 original size:54 final size:54
Alignment explanation
Indices: 417329--417461 Score: 162
Period size: 54 Copynumber: 2.4 Consensus size: 54
417319 TGTTTTTCAG
* * * *
417329 ATTTTACAATTTTGCCACTATTTTTTAGATTTTACAGTTTTGCCTTTATTTTTTA
1 ATTTTATAATTTTACCCCTATTTTTTA-ATTTTACAGTTTTGCCTTTATTTTTAA
* *
417384 ATTTTATAGTTTTACCCCTATTTTTT-ATTTTATAGTTTTGCCCATTT-TTTTTAA
1 ATTTTATAATTTTACCCCTATTTTTTAATTTTACAGTTTTG-CC-TTTATTTTTAA
*
417438 ATTTTATAATTTTTCCCCTATTTT
1 ATTTTATAATTTTACCCCTATTTT
417462 GCAAAAATCA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
53 13 0.19
54 30 0.44
55 25 0.37
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (54 bp):
ATTTTATAATTTTACCCCTATTTTTTAATTTTACAGTTTTGCCTTTATTTTTAA
Found at i:424244 original size:143 final size:143
Alignment explanation
Indices: 423976--424242 Score: 346
Period size: 143 Copynumber: 1.9 Consensus size: 143
423966 AGTTTTTTAA
* * *
423976 TTTTTAACATATTAGTTATTTAGTTAGATTGTTAGATAGTTGCAATTACATCCTTAAGTCTCGAG
1 TTTTTAACATACTAGTTATTTAGTTAGATGGTTAGATAGTTGCAATTACATCCTTAAGTCTCCAG
* * * * *
424041 TTTGATACCTCTACTCCTCATATTTATGTGTTTTTTTATTTCATGTTGTTTCAATTTTTTTAAAT
66 TTTGATACATCTACTACTCACATTTATGTGATTTTTTATTTCATGTTGCTTCAATTTTTTTAAAT
424106 TTTTAATTAATAT
131 TTTTAATTAATAT
* * *
424119 TTTTTAACATACTAGTT-TTTCCA-TTAGATGGTTAGATAGTTGTAATTATATCCTTGAGTCTCC
1 TTTTTAACATACTAGTTATTT--AGTTAGATGGTTAGATAGTTGCAATTACATCCTTAAGTCTCC
* * *
424182 AGTTTGGTTCATCTACTACTTACA-TT-TGT-ATTTTTTATTTCATGTTGCTTCAAGTTTTTTT
64 AGTTTGATACATCTACTACTCACATTTATGTGATTTTTTATTTCATGTTGCTTCAA-TTTTTTT
424243 TTTAATTATT
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
140 22 0.21
141 10 0.09
142 5 0.05
143 69 0.64
144 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (143 bp):
TTTTTAACATACTAGTTATTTAGTTAGATGGTTAGATAGTTGCAATTACATCCTTAAGTCTCCAG
TTTGATACATCTACTACTCACATTTATGTGATTTTTTATTTCATGTTGCTTCAATTTTTTTAAAT
TTTTAATTAATAT
Found at i:424339 original size:22 final size:22
Alignment explanation
Indices: 424313--424358 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
424303 TTGATTTTAT
*
424313 AAATAAAATATTTAAAAATAAA
1 AAATAAAATAATTAAAAATAAA
* *
424335 AAATACATTAATTAAAAATAAA
1 AAATAAAATAATTAAAAATAAA
424357 AA
1 AA
424359 TAATTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATAAAATAATTAAAAATAAA
Found at i:425323 original size:22 final size:23
Alignment explanation
Indices: 425277--425327 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
425267 GACGATTTAT
*
425277 TTTAATAACACGTGACACTTCTC
1 TTTAATAACACATGACACTTCTC
* *
425300 TTTAATGACACATGATA-TTCTC
1 TTTAATAACACATGACACTTCTC
425322 TTTAAT
1 TTTAAT
425328 TTTAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (23 bp):
TTTAATAACACATGACACTTCTC
Found at i:426010 original size:23 final size:24
Alignment explanation
Indices: 425975--426019 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
425965 AAATAAAATA
425975 TTATATTTATTAT-AATAATATTT
1 TTATATTTATTATAAATAATATTT
425998 TTATAATTT-TTATAAATAATAT
1 TTAT-ATTTATTATAAATAATAT
426020 ATAATGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATATTTATTATAAATAATATTT
Found at i:426034 original size:40 final size:41
Alignment explanation
Indices: 425990--426085 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 41
425980 TTTATTATAA
*
425990 TAATATTTTTATAATTTTTATAA-A-TAATATATAATGTGTT
1 TAATATTTTAAT-ATTTTTATAATATTAATATATAATGTGTT
*
426030 TAATATTTTAATATTTTTATAATTATTGATATATAATGTGTT
1 TAATATTTTAATATTTTTATAA-TATTAATATATAATGTGTT
426072 TAATATTTTAATAT
1 TAATATTTTAATAT
426086 ATATTTGGGC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 10 0.20
40 11 0.22
41 1 0.02
42 29 0.57
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (41 bp):
TAATATTTTAATATTTTTATAATATTAATATATAATGTGTT
Found at i:428322 original size:20 final size:21
Alignment explanation
Indices: 428287--428339 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
428277 AAGTTTATGC
428287 TAAGTAAAT-GAGATGGAAAG
1 TAAGTAAATGGAGATGGAAAG
*
428307 TAAGTAAATGGA-ATGGTAAG
1 TAAGTAAATGGAGATGGAAAG
* *
428327 AAAGTGAATGGAG
1 TAAGTAAATGGAG
428340 TGGTTCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (21 bp):
TAAGTAAATGGAGATGGAAAG
Found at i:436284 original size:23 final size:24
Alignment explanation
Indices: 436249--436293 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
436239 AAATAAAATA
436249 TTATATTTATTAT-AATAATATTT
1 TTATATTTATTATAAATAATATTT
436272 TTATAATTT-TTATAAATAATAT
1 TTAT-ATTTATTATAAATAATAT
436294 ATAATGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATATTTATTATAAATAATATTT
Found at i:436308 original size:40 final size:41
Alignment explanation
Indices: 436264--436359 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 41
436254 TTTATTATAA
*
436264 TAATATTTTTATAATTTTTATAA-A-TAATATATAATGTGTT
1 TAATATTTTAAT-ATTTTTATAATATTAATATATAATGTGTT
*
436304 TAATATTTTAATATTTTTATAATTATTGATATATAATGTGTT
1 TAATATTTTAATATTTTTATAA-TATTAATATATAATGTGTT
436346 TAATATTTTAATAT
1 TAATATTTTAATAT
436360 ATATTTGGGC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
39 10 0.20
40 11 0.22
41 1 0.02
42 29 0.57
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (41 bp):
TAATATTTTAATATTTTTATAATATTAATATATAATGTGTT
Found at i:438572 original size:20 final size:21
Alignment explanation
Indices: 438537--438589 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
438527 AAGTTTATGC
438537 TAAGTAAAT-GAGATGGAAAG
1 TAAGTAAATGGAGATGGAAAG
*
438557 TAAGTAAATGGA-ATGGTAAG
1 TAAGTAAATGGAGATGGAAAG
* *
438577 AAAGTGAATGGAG
1 TAAGTAAATGGAG
438590 TGGTTCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (21 bp):
TAAGTAAATGGAGATGGAAAG
Found at i:445938 original size:39 final size:39
Alignment explanation
Indices: 445893--445972 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
445883 CCTAATCTAG
445893 TTCACTTGGTCCAAGTGAAGGATGAATTCTCTAATGGAC
1 TTCACTTGGTCCAAGTGAAGGATGAATTCTCTAATGGAC
445932 TTCACTTGGTCCAAGTGAAGGATGAATTCTCTAATGGAC
1 TTCACTTGGTCCAAGTGAAGGATGAATTCTCTAATGGAC
445971 TT
1 TT
445973 TCATTGTCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (39 bp):
TTCACTTGGTCCAAGTGAAGGATGAATTCTCTAATGGAC
Found at i:449650 original size:17 final size:17
Alignment explanation
Indices: 449628--449660 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
449618 AAGAAAAATG
449628 AAAGGAGAAAA-AGAGAA
1 AAAGGA-AAAAGAGAGAA
449645 AAAGGAAAAAGAGAGA
1 AAAGGAAAAAGAGAGA
449661 GAGGGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AAAGGAAAAAGAGAGAA
Found at i:449669 original size:15 final size:15
Alignment explanation
Indices: 449634--449676 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
449624 AATGAAAGGA
* *
449634 GAAAAAGAGAAAAAG
1 GAAAAAGAGAGAGAG
449649 GAAAAAGAGAGAGAGG
1 GAAAAAGAGAGAGA-G
449665 GAAAATAGAGAG
1 GAAAA-AGAGAG
449677 TAAAGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.50
16 6 0.25
17 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (15 bp):
GAAAAAGAGAGAGAG
Found at i:463147 original size:37 final size:37
Alignment explanation
Indices: 463084--463196 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
463074 ATTGTAAAAA
*
463084 TAATATTATTTTAATAGTTTAATATTAAATTAA-ATT
1 TAATATTATCTTAATAGTTTAATATTAAATTAATATT
* *
463120 TAATACTTATCTTAATAGTATT-TTATTAATTTAATATT
1 TAATA-TTATCTTAATAGT-TTAATATTAAATTAATATT
* * * *
463158 AAAGTGATTATCTTAATA-TTAAAT-TTAATTTAATGTT
1 TAA-T-ATTATCTTAATAGTTTAATATTAAATTAATATT
463195 TA
1 TA
463197 TCTTGTAGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
36 5 0.08
37 36 0.57
38 9 0.14
39 12 0.19
40 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAAATTAATATT
Found at i:463198 original size:68 final size:68
Alignment explanation
Indices: 463101--463298 Score: 200
Period size: 62 Copynumber: 3.0 Consensus size: 68
463091 ATTTTAATAG
* * * *
463101 TTTAATATTAAATTAAATTTAATACTTATCTTAAT-AGTATTTTATTAATTTAATATTAAAGTGA
1 TTTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGA
463165 TTA
66 TTA
* * * *
463168 TCTTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATT-ATTT--TAAT-AA
1 T-TTAATATTAAATTTAATTTAATATTTATC-T-TA-ATAAATATTATATTAATTTAATATTAAA
463229 --G---A
62 GTGATTA
* *
463231 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATATTAAAGTGA
1 TTTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGA
463296 TTA
66 TTA
463299 AGTTTAATCA
Statistics
Matches: 104, Mismatches: 13, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
59 12 0.12
60 5 0.05
61 1 0.01
62 30 0.29
63 4 0.04
65 1 0.01
66 1 0.01
67 1 0.01
68 29 0.28
69 4 0.04
70 2 0.02
71 6 0.06
72 8 0.08
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (68 bp):
TTTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGA
TTA
Found at i:463997 original size:31 final size:31
Alignment explanation
Indices: 463959--464022 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
463949 TTCACATTTG
463959 TTTTTC-TTTTCCCCCTTTGTGCTTCTCTTTT
1 TTTTTCTTTTTCCCCCTTTGTGCTT-TCTTTT
* *
463990 TTTTTCTTTTTCTCCCTTTGTGGTTTCTTTT
1 TTTTTCTTTTTCCCCCTTTGTGCTTTCTTTT
464021 TT
1 TT
464023 GTTATTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (31 bp):
TTTTTCTTTTTCCCCCTTTGTGCTTTCTTTT
Found at i:469368 original size:47 final size:47
Alignment explanation
Indices: 469299--469393 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
469289 GTCCTGCGTT
469299 AGTGGCAGAGACTGAAGATAAGGTTCATTTGATTCGAGATTGACTTA
1 AGTGGCAGAGACTGAAGATAAGGTTCATTTGATTCGAGATTGACTTA
* *
469346 AGTGGCCGAGACTGAGGATAAGGTTCATTTGATTCGAGATTGACTTA
1 AGTGGCAGAGACTGAAGATAAGGTTCATTTGATTCGAGATTGACTTA
469393 A
1 A
469394 TGCCGCTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (47 bp):
AGTGGCAGAGACTGAAGATAAGGTTCATTTGATTCGAGATTGACTTA
Found at i:472361 original size:24 final size:25
Alignment explanation
Indices: 472315--472361 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
472305 ATGAATAGAG
*
472315 AATAAAAATTATTTTTTTATGATTA
1 AATAAAAATTATTTTATTATGATTA
* *
472340 AATAAATATT-TTTTATTGTGAT
1 AATAAAAATTATTTTATTATGAT
472362 AATGTATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (25 bp):
AATAAAAATTATTTTATTATGATTA
Found at i:476699 original size:120 final size:121
Alignment explanation
Indices: 476552--476793 Score: 477
Period size: 120 Copynumber: 2.0 Consensus size: 121
476542 AATTGATAAA
476552 TAAAATTTATTTATTTTTAGAGTTTTATGTTTAAAGTAAATATTAAAATTTTAATTTGTCTACTT
1 TAAAATTTATTTATTTTTAGAGTTTTATGTTTAAAGTAAATATTAAAATTTTAATTTGTCTACTT
476617 AATTTAACTTGATAATTATTTTTTAAATTAATATTTTATTTATAATAGCTTCAAGC
66 AATTTAACTTGATAATTATTTTTTAAATTAATATTTTATTTATAATAGCTTCAAGC
476673 TAAAATTTA-TTATTTTTAGAGTTTTATGTTTAAAGTAAATATTAAAATTTTAATTTGTCTACTT
1 TAAAATTTATTTATTTTTAGAGTTTTATGTTTAAAGTAAATATTAAAATTTTAATTTGTCTACTT
476737 AATTTAACTTGATAATTATTTTTTAAATTAATATTTTATTTATAATAGCTTCAAGC
66 AATTTAACTTGATAATTATTTTTTAAATTAATATTTTATTTATAATAGCTTCAAGC
476793 T
1 T
476794 TACTATAAAT
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
120 112 0.93
121 9 0.07
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (121 bp):
TAAAATTTATTTATTTTTAGAGTTTTATGTTTAAAGTAAATATTAAAATTTTAATTTGTCTACTT
AATTTAACTTGATAATTATTTTTTAAATTAATATTTTATTTATAATAGCTTCAAGC
Found at i:476906 original size:11 final size:11
Alignment explanation
Indices: 476890--476921 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
476880 CTCATCCTAC
476890 GATTTGGATCA
1 GATTTGGATCA
476901 GATTTGGATCA
1 GATTTGGATCA
*
476912 GACTTGGATC
1 GATTTGGATC
476922 TATTAGTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.34
Consensus pattern (11 bp):
GATTTGGATCA
Found at i:477928 original size:23 final size:23
Alignment explanation
Indices: 477876--477933 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 23
477866 GACGTGTGGA
*
477876 TATCACTTTGCACTGAAGTGTCAC
1 TATCAC-TTGCACTGAAGTGCCAC
*
477900 TA-CACTTGCACTGTAGTGCCAC
1 TATCACTTGCACTGAAGTGCCAC
477922 TATCACTTGCAC
1 TATCACTTGCAC
477934 GCTTAGTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 17 0.55
23 12 0.39
24 2 0.06
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (23 bp):
TATCACTTGCACTGAAGTGCCAC
Found at i:484023 original size:27 final size:27
Alignment explanation
Indices: 484002--484605 Score: 412
Period size: 27 Copynumber: 22.4 Consensus size: 27
483992 GGGTATAACA
484002 GTTATTTTACCCTATGGAGGTATTTCG
1 GTTATTTTACCCTATGGAGGTATTTCG
*
484029 GTTATTGTACCCTAT-GAGGCTATTTCG
1 GTTATTTTACCCTATGGAGG-TATTTCG
* *
484056 GTCATTTTACCCTAT-GCGGTATTTCG
1 GTTATTTTACCCTATGGAGGTATTTCG
* * * *
484082 ATCATTTTACCCTATGGGGGTATTTTG
1 GTTATTTTACCCTATGGAGGTATTTCG
* * * *
484109 GTCATTTTATCTTAT-GAGGGTATTTCA
1 GTTATTTTACCCTATGGA-GGTATTTCG
* *
484136 GTTATTTTACCCCATAGG-GGTATTTTG
1 GTTATTTTACCCTAT-GGAGGTATTTCG
* * * *
484163 GTCAATTTATCCTATGGGGGTATTTCG
1 GTTATTTTACCCTATGGAGGTATTTCG
*
484190 GTCATTTTACCCCTATTGG-GGTATTTCG
1 GTTATTTTA-CCCTA-TGGAGGTATTTCG
* * * *
484218 GTCATTCTATCCTAT-GAGGGTATTTTG
1 GTTATTTTACCCTATGGA-GGTATTTCG
* * *
484245 GTCATTCTATCCTATGG-GGATATTTCG
1 GTTATTTTACCCTATGGAGG-TATTTCG
*
484272 GTCATTTTACCCTATGGAGAGTATTTCG
1 GTTATTTTACCCTATGGAG-GTATTTCG
* * *
484300 ATCATTTTACCCTAT-AAGGATATTTCG
1 GTTATTTTACCCTATGGAGG-TATTTCG
* *
484327 GTCATTCTACCCTATAGG-GGTATTTCG
1 GTTATTTTACCCTAT-GGAGGTATTTCG
* * * *
484354 ATCATTTTACCCTATCGG-GATATTTTG
1 GTTATTTTACCCTAT-GGAGGTATTTCG
* **
484381 GTCATTTTACCCTATTGG-GGTATTTTA
1 GTTATTTTACCCTA-TGGAGGTATTTCG
*
484408 GTTATTTTACCCTATGGGGGTATTTCG
1 GTTATTTTACCCTATGGAGGTATTTCG
* * * * *
484435 ATCATTTTATCCTATGGGGGTATTTCA
1 GTTATTTTACCCTATGGAGGTATTTCG
* *
484462 GTCATTTTACCCTATAGG-GGTATTTTG
1 GTTATTTTACCCTAT-GGAGGTATTTCG
* * *
484489 ATCATTTTACCCTATGGGGGTATTTCG
1 GTTATTTTACCCTATGGAGGTATTTCG
* * *
484516 GTCATTGTATCCTATAGG-GGTATTTCG
1 GTTATTTTACCCTAT-GGAGGTATTTCG
* * * *
484543 GTCATTATACCTTA-CGAGGTATTTCG
1 GTTATTTTACCCTATGGAGGTATTTCG
* * *
484569 GTCAGTCTACCCTATAGG-GGTA-TTCG
1 GTTATTTTACCCTAT-GGAGGTATTTCG
* *
484595 GTCATTCTACC
1 GTTATTTTACC
484606 TATTTTTAGA
Statistics
Matches: 482, Mismatches: 70, Indels: 51
0.80 0.12 0.08
Matches are distributed among these distances:
25 2 0.00
26 71 0.15
27 352 0.73
28 52 0.11
29 5 0.01
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
GTTATTTTACCCTATGGAGGTATTTCG
Found at i:484156 original size:54 final size:54
Alignment explanation
Indices: 484005--484605 Score: 633
Period size: 54 Copynumber: 11.1 Consensus size: 54
483995 TATAACAGTT
* * *
484005 ATTTTACCCTATG-GAGGTATTTCGGTTATTGTACCCTAT-GAGGCTATTTCGGTC
1 ATTTTACCCTATGAG-GGTATTTCGGTCATTTTACCCTATAG-GGGTATTTCGGTC
* * * *
484059 ATTTTACCCTATG-CGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTC
* * * * * *
484112 ATTTTATCTTATGAGGGTATTTCAGTTATTTTACCCCATAGGGGTATTTTGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTC
* * * *
484166 AATTTATCCTATGGGGGTATTTCGGTCATTTTACCCCTATTGGGGTATTTCGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTCATTTTA-CCCTATAGGGGTATTTCGGTC
* * * * *
484221 ATTCTATCCTATGAGGGTATTTTGGTCATTCTATCCTAT-GGGGATATTTCGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATAGGGG-TATTTCGGTC
* * * *
484275 ATTTTACCCTATGGAGAGTATTTCGATCATTTTACCCTATAAGGATATTTCGGTC
1 ATTTTACCCTAT-GAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTC
* * * * *
484330 ATTCTACCCTAT-AGGGGTATTTCGATCATTTTACCCTATCGGGATATTTTGGTC
1 ATTTTACCCTATGA-GGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTC
** * * *
484384 ATTTTACCCTATTG-GGGTATTTTAGTTATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTA-TGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTC
* * * * *
484438 ATTTTATCCTATGGGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTTGATC
1 ATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTC
* * *
484492 ATTTTACCCTATGGGGGTATTTCGGTCATTGTATCCTATAGGGGTATTTCGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTC
* * * * *
484546 ATTATACCTTACGA-GGTATTTCGGTCAGTCTACCCTATAGGGGTA-TTCGGTC
1 ATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTC
*
484598 ATTCTACC
1 ATTTTACC
484606 TATTTTTAGA
Statistics
Matches: 467, Mismatches: 70, Indels: 22
0.84 0.13 0.04
Matches are distributed among these distances:
52 14 0.03
53 78 0.17
54 283 0.61
55 90 0.19
56 2 0.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (54 bp):
ATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTC
Found at i:484187 original size:81 final size:81
Alignment explanation
Indices: 484007--484605 Score: 624
Period size: 81 Copynumber: 7.4 Consensus size: 81
483997 TAACAGTTAT
* * * *
484007 TTTACCCTATGGAGGTATTTCGGTTATTGTACCCTATGAGGCTATTTCGGTCATTTTACCCTAT-
1 TTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATA
* * * *
484071 GCGGTATTTCGATCAT
66 GGGGTATTTTGGTCAA
* * * * * *
484087 TTTACCCTATGGGGGTATTTTGGTCATTTTATCTTATGAGGGTATTTCAGTTATTTTACCCCATA
1 TTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATA
484152 GGGGTATTTTGGTCAA
66 GGGGTATTTTGGTCAA
* * *
484168 TTTATCCTATGGGGGTATTTCGGTCATTTTACCCCTATTG-GGGTATTTCGGTCATTCTATCCTA
1 TTTACCCTATGGGGGTATTTCGGTCATTTTA-CCCTA-TGAGGGTATTTCGGTCATTTTACCCTA
484232 T-GAGGGTATTTTGGTC-A
64 TAG-GGGTATTTTGGTCAA
* * * *
484249 TTCTATCCTATGGGGATATTTCGGTCATTTTACCCTATGGAGAGTATTTCGATCATTTTACCCTA
1 TT-TACCCTATGGGGGTATTTCGGTCATTTTACCCTAT-GAGGGTATTTCGGTCATTTTACCCTA
* * *
484314 TAAGGATATTTCGGTC-A
64 TAGGGGTATTTTGGTCAA
* * * *
484331 TTCTACCCTATAGGGGTATTTCGATCATTTTACCCTATCG-GGATATTTTGGTCATTTTACCCTA
1 TT-TACCCTATGGGGGTATTTCGGTCATTTTACCCTAT-GAGGGTATTTCGGTCATTTTACCCTA
* * * *
484395 TTGGGGTATTTTAGTTAT
64 TAGGGGTATTTTGGTCAA
* * * *
484413 TTTACCCTATGGGGGTATTTCGATCATTTTATCCTATGGGGGTATTTCAGTCATTTTACCCTATA
1 TTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATA
* *
484478 GGGGTATTTTGATCAT
66 GGGGTATTTTGGTCAA
* * *
484494 TTTACCCTATGGGGGTATTTCGGTCATTGTATCCTAT-AGGGGTATTTCGGTCATTATA-CCT-T
1 TTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGA-GGGTATTTCGGTCATTTTACCCTAT
* * *
484556 ACGAGGTATTTCGGTCAG
65 A-GGGGTATTTTGGTCAA
* * *
484574 TCTACCCTATAGGGGTA-TTCGGTCATTCTACC
1 TTTACCCTATGGGGGTATTTCGGTCATTTTACC
484606 TATTTTTAGA
Statistics
Matches: 438, Mismatches: 69, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
79 15 0.03
80 86 0.20
81 201 0.46
82 134 0.31
83 2 0.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (81 bp):
TTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATA
GGGGTATTTTGGTCAA
Found at i:485839 original size:18 final size:18
Alignment explanation
Indices: 485816--485851 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
485806 CGCATAACAC
*
485816 AGACTCCACTACTACGCT
1 AGACTCCACCACTACGCT
485834 AGACTCCACCACTACGCT
1 AGACTCCACCACTACGCT
485852 TTCACTGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.42, G:0.11, T:0.19
Consensus pattern (18 bp):
AGACTCCACCACTACGCT
Found at i:493690 original size:90 final size:89
Alignment explanation
Indices: 493490--493693 Score: 239
Period size: 90 Copynumber: 2.3 Consensus size: 89
493480 TACCGGGTTA
* ** * * *
493490 TGGATGAACCACCAAATGTTGCAGGTTAATATGCTGCCAGATGGTTGTGAGCACACAACATAATT
1 TGGATGAACCACCAAAT-TTGCAAGTTAATACACTACCAAATGGTTGTGAACACACAACATAATT
* *
493555 ACATATAAAAGCTTCATATAATAGG
65 ACAGATAAAAGCTTCAAATAATAGG
* * *
493580 TGGGTGAACCACCTAAATTTGCAAGTTAATACACTACCAAATGGTTGTGAATACACAACTTAATT
1 TGGATGAACCACC-AAATTTGCAAGTTAATACACTACCAAATGGTTGTGAACACACAACATAATT
* *
493645 ACAGATAAAAGTTGTCAAATAATATG
65 ACAGATAAAAGCT-TCAAATAATAGG
*
493671 TGGAT-AGACCACCAGATTTGCAA
1 TGGATGA-ACCACCAAATTTGCAA
493694 ATTTATAATC
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
90 72 0.75
91 24 0.25
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (89 bp):
TGGATGAACCACCAAATTTGCAAGTTAATACACTACCAAATGGTTGTGAACACACAACATAATTA
CAGATAAAAGCTTCAAATAATAGG
Found at i:495923 original size:26 final size:26
Alignment explanation
Indices: 495852--495931 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
495842 TGGTAAGGGC
* *
495852 TTCGCTAGTCTGTTTGGCGAA-CTAAGGG
1 TTCGCTAGCCTGTTTGGC-AAGCT-A-GT
* * *
495880 TTCACTAACCTATTTGGCAAGCTAGT
1 TTCGCTAGCCTGTTTGGCAAGCTAGT
*
495906 TTCGCTAGCCTGTTTGGCTAGCTAGT
1 TTCGCTAGCCTGTTTGGCAAGCTAGT
495932 GTTTACCAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
26 23 0.55
27 3 0.07
28 16 0.38
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (26 bp):
TTCGCTAGCCTGTTTGGCAAGCTAGT
Found at i:499777 original size:27 final size:27
Alignment explanation
Indices: 499747--499999 Score: 339
Period size: 27 Copynumber: 9.4 Consensus size: 27
499737 TATAACAGTT
*
499747 ATTTTACCCTGTGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
499774 ATTTTACCTTATGGGAGTATTTCCGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
499801 ATTCTACCCTATGAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
499828 ATTTTATCCTAT-GGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
499854 ATTTTACCCTATAGGGGTATTTTGGTT
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
499881 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
499908 ATTTTACCCTATGAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
499935 ATTTTACCCTATAGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
499962 ATTTTACCTTAT-GGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
499988 ATTTTACCCTAT
1 ATTTTACCCTAT
500000 TTTAGGGTCT
Statistics
Matches: 199, Mismatches: 26, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
26 48 0.24
27 151 0.76
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:499874 original size:80 final size:78
Alignment explanation
Indices: 499747--499999 Score: 346
Period size: 80 Copynumber: 3.2 Consensus size: 78
499737 TATAACAGTT
* * *
499747 ATTTTACCCTGTGGGGGTATTTCGGTCATTTTACCTTAT-GGGAGTATTTCCGTCATTCTACCCT
1 ATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATAGGG-GTATTT-CGTCATTTTACCCT
*
499811 ATGAGGGTATTTCGGTC
63 ATG-GGGTATTTCGATC
* * * *
499828 ATTTTATCCTATGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTTGGTTATTTTACCCTAT
1 ATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATAGGGGTA-TTTCGTCATTTTACCCTAT
499893 GGGGGTATTTCGATC
65 -GGGGTATTTCGATC
*
499908 ATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCTTA
1 ATTTTACCCTATG-GGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCG-TCATTTTACCCTA
499973 TGGGGTATTTCGATC
64 TGGGGTATTTCGATC
499988 ATTTTACCCTAT
1 ATTTTACCCTAT
500000 TTTAGGGTCT
Statistics
Matches: 154, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
80 94 0.61
81 60 0.39
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.43
Consensus pattern (78 bp):
ATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGTCATTTTACCCTATG
GGGTATTTCGATC
Found at i:499885 original size:107 final size:107
Alignment explanation
Indices: 499747--499999 Score: 366
Period size: 107 Copynumber: 2.4 Consensus size: 107
499737 TATAACAGTT
* *
499747 ATTTTACCCTGTGGGGGTATTTCGGTCATTTTACCTTATGGGAGTATTTCCG-TCATTCTACCCT
1 ATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGAGTATTT-CGATCATTCTACCCT
* * *
499811 ATGAGGGTATTTCGGTCATTTTATCCTAT-GGGGTATTTTGGTC
64 ATGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGATC
* * * *
499854 ATTTTACCCTATAGGGGTATTTTGGTTATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTA
1 ATTTTACCCTAT-GGGGTATTTCGGTCATTTTACCCTATGGGAGTATTTCGATCATTCTACCCTA
499919 TGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGATC
65 TGAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGATC
* *
499962 ATTTTACCTTATGGGGTATTTCGATCATTTTACCCTAT
1 ATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTAT
500000 TTTAGGGTCT
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
106 2 0.02
107 105 0.81
108 23 0.18
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.43
Consensus pattern (107 bp):
ATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATGGGAGTATTTCGATCATTCTACCCTAT
GAGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGATC
Found at i:501862 original size:19 final size:19
Alignment explanation
Indices: 501835--501877 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
501825 TAGGATAGAA
*
501835 ATTTGACTCACAAAGGTTG
1 ATTTTACTCACAAAGGTTG
501854 ATTTTACTCACAAAGGTTG
1 ATTTTACTCACAAAGGTTG
501873 ATTTT
1 ATTTT
501878 TTTGTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (19 bp):
ATTTTACTCACAAAGGTTG
Found at i:502099 original size:14 final size:14
Alignment explanation
Indices: 502080--502112 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
502070 TATATCCTTA
502080 AAAAATATA-TTTTG
1 AAAAAT-TAGTTTTG
502094 AAAAATTAGTTTTG
1 AAAAATTAGTTTTG
502108 AAAAA
1 AAAAA
502113 AACGTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (14 bp):
AAAAATTAGTTTTG
Found at i:503395 original size:3 final size:3
Alignment explanation
Indices: 503389--503414 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
503379 GCCAGGGTGG
503389 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
503415 TTAAAGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:503905 original size:29 final size:29
Alignment explanation
Indices: 503863--503920 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
503853 ATTGATTGTG
503863 ATTGTCTTTGTGATCTTCTTTGTCATCAT
1 ATTGTCTTTGTGATCTTCTTTGTCATCAT
*
503892 ATTGTCTTTGTGATTTTCTTTGTCATCAT
1 ATTGTCTTTGTGATCTTCTTTGTCATCAT
503921 TCTCATTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (29 bp):
ATTGTCTTTGTGATCTTCTTTGTCATCAT
Found at i:506667 original size:29 final size:29
Alignment explanation
Indices: 506601--506667 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 29
506591 AATTTACAAC
* *
506601 TATT-AATTTGGGTTTGGGTTTTATTTTT
1 TATTAAATTTGGGTTTGGGTTTTAGTTTA
* * *
506629 TTTTATATTTGGG-TTGAGTTTTTAGTTTA
1 TATTAAATTTGGGTTTG-GGTTTTAGTTTA
506658 TATTAAATTT
1 TATTAAATTT
506668 TTTGGGTTGG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.19, C:0.00, G:0.18, T:0.63
Consensus pattern (29 bp):
TATTAAATTTGGGTTTGGGTTTTAGTTTA
Found at i:510120 original size:46 final size:42
Alignment explanation
Indices: 510050--510135 Score: 120
Period size: 41 Copynumber: 2.0 Consensus size: 42
510040 ATTGCAACAG
510050 GAGTTTTAGTTTTATTTATTTATTATATTAGGT-TTTATTAA
1 GAGTTTTAGTTTTATTTATTTATTATATTAGGTATTTATTAA
510091 GAGTTTTAGTTTTATTTATTTTCTCTATTATATTAGGTATTTATT
1 GAGTTTTAGTTTTATTTA---T-T-TATTATATTAGGTATTTATT
510136 TCCTTCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
41 18 0.46
44 1 0.03
45 1 0.03
46 13 0.33
47 6 0.15
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.62
Consensus pattern (42 bp):
GAGTTTTAGTTTTATTTATTTATTATATTAGGTATTTATTAA
Found at i:510963 original size:49 final size:49
Alignment explanation
Indices: 510892--511035 Score: 288
Period size: 49 Copynumber: 2.9 Consensus size: 49
510882 TTCTTCACTT
510892 TTTTCTTAAAGTTAGAATCGAAATTGTGTTTATTTTGAAGAGTTTGCTC
1 TTTTCTTAAAGTTAGAATCGAAATTGTGTTTATTTTGAAGAGTTTGCTC
510941 TTTTCTTAAAGTTAGAATCGAAATTGTGTTTATTTTGAAGAGTTTGCTC
1 TTTTCTTAAAGTTAGAATCGAAATTGTGTTTATTTTGAAGAGTTTGCTC
510990 TTTTCTTAAAGTTAGAATCGAAATTGTGTTTATTTTGAAGAGTTTG
1 TTTTCTTAAAGTTAGAATCGAAATTGTGTTTATTTTGAAGAGTTTG
511036 AGTGTGTTGA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 95 1.00
ACGTcount: A:0.27, C:0.07, G:0.19, T:0.47
Consensus pattern (49 bp):
TTTTCTTAAAGTTAGAATCGAAATTGTGTTTATTTTGAAGAGTTTGCTC
Found at i:513126 original size:8 final size:8
Alignment explanation
Indices: 513102--513193 Score: 148
Period size: 8 Copynumber: 11.5 Consensus size: 8
513092 TTTGAATTCA
*
513102 ATACATAC
1 ATACATGC
*
513110 ATGCATGC
1 ATACATGC
513118 ATACATGC
1 ATACATGC
513126 ATACATGC
1 ATACATGC
*
513134 ATACATGA
1 ATACATGC
*
513142 ATACCTGC
1 ATACATGC
513150 ATACATGC
1 ATACATGC
513158 ATACATGC
1 ATACATGC
513166 ATACATGC
1 ATACATGC
513174 ATACATGC
1 ATACATGC
513182 ATACATGC
1 ATACATGC
513190 ATAC
1 ATAC
513194 TGGTGTTGTA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 77 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (8 bp):
ATACATGC
Found at i:513788 original size:18 final size:20
Alignment explanation
Indices: 513760--513798 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
513750 TATTGTGTAA
*
513760 TATGATATGTATGAGC-TGT
1 TATGATATGTAAGAGCATGT
513779 TATG-TATGTAAGAGCATGT
1 TATGATATGTAAGAGCATGT
513798 T
1 T
513799 TAGCACTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41
Consensus pattern (20 bp):
TATGATATGTAAGAGCATGT
Found at i:522794 original size:30 final size:30
Alignment explanation
Indices: 522760--522822 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
522750 ACTAATCATA
*
522760 TTTAGTGGGAGTTAGTAGGGATATATGTGG
1 TTTAGTGGGAGTTAGTAGGGATATAGGTGG
* *
522790 TTTAGTGGGAGTTAGTGGGGATATGGGTGG
1 TTTAGTGGGAGTTAGTAGGGATATAGGTGG
522820 TTT
1 TTT
522823 TAAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.19, C:0.00, G:0.43, T:0.38
Consensus pattern (30 bp):
TTTAGTGGGAGTTAGTAGGGATATAGGTGG
Found at i:525599 original size:35 final size:35
Alignment explanation
Indices: 525548--525622 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
525538 TGAATTTTTT
* *
525548 TCTAACATATACTTTATGTAATGTTGATATTCTAA
1 TCTAGCATATACTTTATGTAATGTTGATAGTCTAA
525583 TCTAGCATATACTTTATGTAATGTTGATAGTCTAA
1 TCTAGCATATACTTTATGTAATGTTGATAGTCTAA
525618 TCTAG
1 TCTAG
525623 TAAAATAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (35 bp):
TCTAGCATATACTTTATGTAATGTTGATAGTCTAA
Found at i:527814 original size:12 final size:12
Alignment explanation
Indices: 527788--527821 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
527778 TAGTTGAAGG
*
527788 TATATTTCT-AT
1 TATATTTTTAAT
527799 TATATTTTTAAT
1 TATATTTTTAAT
527811 TATATTTTTAA
1 TATATTTTTAA
527822 AATTTTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTTTTAAT
Found at i:528066 original size:32 final size:32
Alignment explanation
Indices: 528022--528087 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
528012 TGAGAAAAAT
528022 TTGTTTTATGTAAAGTTTGCATAATATTTTAA
1 TTGTTTTATGTAAAGTTTGCATAATATTTTAA
* *
528054 TTGTTTTCTGTAAAGTTTGCATAATTTTTTAA
1 TTGTTTTATGTAAAGTTTGCATAATATTTTAA
528086 TT
1 TT
528088 ACCAAATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.27, C:0.05, G:0.12, T:0.56
Consensus pattern (32 bp):
TTGTTTTATGTAAAGTTTGCATAATATTTTAA
Done.