Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009214.1 Hibiscus syriacus cultivar Beakdansim tig00112801_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 549473
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 3
Found at i:237173 original size:105 final size:103
Alignment explanation
Indices: 236993--237194 Score: 386
Period size: 105 Copynumber: 1.9 Consensus size: 103
236983 TTCTGGTGCT
236993 CCGTGTAGAAGGAGCTGATGGTGGAGAGGGATCGTGTGGTGCGGCAGAAGCATGGAGTGGTAATC
1 CCGTGTAGAAGGAGCTGATGGTGGAGAGGGATCGTGTGGTGCGGCAGAAGCATGGAGTGGTAATC
237058 CCGCAGGAGAGAAGGAGGAACGTTGCCTATCGAGAACG
66 CCGCAGGAGAGAAGGAGGAACGTTGCCTATCGAGAACG
237096 CCGTGTAGAAGGAGCTGATGGTGGAGAGAGGGATCGTGTGGTGCGGCAGAAGCATGGAGTGGTAA
1 CCGTGTAGAAGGAGCTGATGGT-G-GAGAGGGATCGTGTGGTGCGGCAGAAGCATGGAGTGGTAA
237161 TCCCGCAGGAGAGAAGGAGGAACGTTGCCTATCG
64 TCCCGCAGGAGAGAAGGAGGAACGTTGCCTATCG
237195 GAAGAACGGC
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
103 22 0.23
104 1 0.01
105 74 0.76
ACGTcount: A:0.26, C:0.15, G:0.42, T:0.17
Consensus pattern (103 bp):
CCGTGTAGAAGGAGCTGATGGTGGAGAGGGATCGTGTGGTGCGGCAGAAGCATGGAGTGGTAATC
CCGCAGGAGAGAAGGAGGAACGTTGCCTATCGAGAACG
Found at i:243560 original size:18 final size:18
Alignment explanation
Indices: 243548--243586 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
243538 ACGTTGACTT
243548 TGACT-TGACCGTTGACA
1 TGACTCTGACCGTTGACA
* *
243565 TGTCTCTGACCGTTGACC
1 TGACTCTGACCGTTGACA
243583 TGAC
1 TGAC
243587 CGTTTACCGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (18 bp):
TGACTCTGACCGTTGACA
Found at i:246374 original size:2 final size:2
Alignment explanation
Indices: 246369--246406 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
246359 TTTTAAAATA
*
246369 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
246407 TTGTGGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:259737 original size:29 final size:30
Alignment explanation
Indices: 259691--259758 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
259681 TTTTATCATT
* * *
259691 TATTTTTTTATACGTATA-TTTCTATT-TTC
1 TATTTTTTAATAAGTATACTTT-TATTATAC
*
259720 TATTTTTTAATAATTATACTTTTATTATAC
1 TATTTTTTAATAAGTATACTTTTATTATAC
259750 T-TTTTTTAA
1 TATTTTTTAA
259759 GTTTTTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.65
Consensus pattern (30 bp):
TATTTTTTAATAAGTATACTTTTATTATAC
Found at i:279081 original size:48 final size:48
Alignment explanation
Indices: 279004--279096 Score: 152
Period size: 48 Copynumber: 1.9 Consensus size: 48
278994 ATAAATGATC
279004 TAATTTTGATTTTTAAGTATACTTTACTTTCTTCTCAACACTACAAGG
1 TAATTTTGATTTTTAAGTATACTTTACTTTCTTCTCAACACTACAAGG
* *
279052 TAATTTTGATTTTTAAGTATA-TTTCACTTTCTTCTTAACAGTACA
1 TAATTTTGATTTTTAAGTATACTTT-ACTTTCTTCTCAACACTACA
279097 TAATCCTAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 3 0.07
48 39 0.93
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (48 bp):
TAATTTTGATTTTTAAGTATACTTTACTTTCTTCTCAACACTACAAGG
Found at i:279395 original size:5 final size:5
Alignment explanation
Indices: 279385--279421 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
279375 AGAGCTGATT
279385 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
279422 GTAAATGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:279460 original size:5 final size:5
Alignment explanation
Indices: 279450--279517 Score: 66
Period size: 5 Copynumber: 13.8 Consensus size: 5
279440 GGGTCAGATT
* * * * *
279450 TTTTA TTTTA TTTTA TATAA TTTTA TTTTA TTTTA TATAA TTGTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* *
279500 TTCTA TCTT- TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT
279518 GTTGCGGAAA
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
4 3 0.06
5 45 0.94
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:279475 original size:20 final size:20
Alignment explanation
Indices: 279450--279501 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
279440 GGGTCAGATT
279450 TTTTATTTTATTTTATATAA
1 TTTTATTTTATTTTATATAA
279470 TTTTATTTTATTTTATATAA
1 TTTTATTTTATTTTATATAA
*
279490 TTGTATTTTATT
1 TTTTATTTTATT
279502 CTATCTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTATTTTATTTTATATAA
Found at i:280647 original size:13 final size:13
Alignment explanation
Indices: 280631--280655 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
280621 AAAAAAGACC
280631 TTAATAAAAAATT
1 TTAATAAAAAATT
280644 TTAATAAAAAAT
1 TTAATAAAAAAT
280656 AAAAAGACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAATAAAAAATT
Found at i:282069 original size:22 final size:23
Alignment explanation
Indices: 282038--282081 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
282028 ATTATTTATT
282038 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
282061 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
282082 TAAAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:282078 original size:31 final size:33
Alignment explanation
Indices: 282025--282110 Score: 101
Period size: 31 Copynumber: 2.7 Consensus size: 33
282015 TTTTCATCAA
*
282025 AATATTATT-TATTTATTAATATT-TATAATAAT
1 AATAATATTATATTTATTAATATTATATAA-AAT
282057 -ATAATATTATATTT-TTAATATTATATAAAAT
1 AATAATATTATATTTATTAATATTATATAAAAT
*
282088 AATAA-ATTATATTATAATAATAT
1 AATAATATTATATT-TATTAATAT
282111 AAGATATTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
31 26 0.55
32 15 0.32
33 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
AATAATATTATATTTATTAATATTATATAAAAT
Found at i:282101 original size:59 final size:59
Alignment explanation
Indices: 282038--282186 Score: 136
Period size: 54 Copynumber: 2.6 Consensus size: 59
282028 ATTATTTATT
**
282038 TATTAATATTTATAATAATATA-ATATTATATTTTTAATATTATATAA-A-ATAATAAATTA
1 TATTAATATTTATAATAATA-AGATATTATATTTTT-ATATTA-ATAATATATAATAAAAAA
*
282097 TATT-ATA---ATAAT-ATAAGATATTATATTTTTATTTTAATAATATATAATAAAAAA
1 TATTAATATTTATAATAATAAGATATTATATTTTTATATTAATAATATATAATAAAAAA
*
282151 T-TTATATATTTAATAATGAATAATATATTTATATTT
1 TATTA-ATATTT-ATAAT-AATAAGATA-TTATATTT
282187 AAATAATATT
Statistics
Matches: 74, Mismatches: 4, Indels: 21
0.75 0.04 0.21
Matches are distributed among these distances:
52 4 0.05
53 9 0.12
54 26 0.35
55 8 0.11
58 3 0.04
59 9 0.12
61 7 0.09
62 8 0.11
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (59 bp):
TATTAATATTTATAATAATAAGATATTATATTTTTATATTAATAATATATAATAAAAAA
Found at i:282112 original size:23 final size:22
Alignment explanation
Indices: 282074--282123 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
282064 TATATTTTTA
*
282074 ATATTATATAAAATAATAAATT
1 ATATTATATAAAATAAGAAATT
* *
282096 ATATTATAATAATATAAGATATT
1 ATATTAT-ATAAAATAAGAAATT
282119 ATATT
1 ATATT
282124 TTTATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATTATATAAAATAAGAAATT
Found at i:282144 original size:54 final size:53
Alignment explanation
Indices: 282042--282219 Score: 149
Period size: 56 Copynumber: 3.4 Consensus size: 53
282032 TTTATTTATT
*
282042 AATAT-TTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATA
1 AATATATTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATA
282092 AATTATATTATAATAATATAAGATATTATATTTTTATTTTAATAATATATAATA
1 AA-TATATTATAATAATATAAGATATTATATTTTTATTTTAATAATATATAATA
* * * * * *
282146 AA-AAATTTATATATTTAATA-ATGAATAATATATTTATATTTAAATAATATTTTAATA
1 AATATA-TTATA-A--TAATATAAG-ATATTATATTTTTATTTTAATAATA-TATAATA
282203 AATATATT-TAA-AATATA
1 AATATATTATAATAATATA
282220 CTAATTAATA
Statistics
Matches: 106, Mismatches: 8, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
50 2 0.02
51 3 0.03
52 22 0.21
53 13 0.12
54 22 0.21
55 3 0.03
56 29 0.27
57 10 0.09
58 2 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (53 bp):
AATATATTATAATAATATAAGATATTATATTTTTATTTTAATAATATATAATA
Found at i:282166 original size:23 final size:25
Alignment explanation
Indices: 282135--282194 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
282125 TTATTTTAAT
* * *
282135 AATATATAATAAAAAATTTATATATTT
1 AATA-ATAATAATATATTTATAT-TTA
282162 AATAATGAATAATATATTTATATTTA
1 AATAAT-AATAATATATTTATATTTA
282188 AATAATA
1 AATAATA
282195 TTTTAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.03
26 10 0.34
27 18 0.62
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AATAATAATAATATATTTATATTTA
Found at i:282178 original size:19 final size:19
Alignment explanation
Indices: 282132--282203 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
282122 TTTTTATTTT
*
282132 AATAATATA--TAATAAAA
1 AATAATATATTTAATAATA
* *
282149 AATTTATATATTTAATAATG
1 AA-TAATATATTTAATAATA
*
282169 AATAATATATTT-ATATTTA
1 AATAATATATTTAATA-ATA
282188 AATAATAT-TTTAATAA
1 AATAATATATTTAATAA
282204 ATATATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.05
18 12 0.28
19 21 0.49
20 8 0.19
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (19 bp):
AATAATATATTTAATAATA
Found at i:282217 original size:23 final size:23
Alignment explanation
Indices: 282180--282242 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
282170 ATAATATATT
**
282180 TATATTTAAATAATATTTTAATAAA
1 TATATTT-AA-AATATACTAATAAA
*
282205 TATATTTAAAATATACTAATTAA
1 TATATTTAAAATATACTAATAAA
*
282228 TATTTTTAAAATATA
1 TATATTTAAAATATA
282243 ATATAACACT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 25 0.74
24 2 0.06
25 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATTTAAAATATACTAATAAA
Found at i:282590 original size:15 final size:15
Alignment explanation
Indices: 282542--282581 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
282532 CATTTTTCAG
282542 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
282557 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
282572 AATTCAAATT
1 AATTCAAATT
282582 TCAATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:313736 original size:17 final size:17
Alignment explanation
Indices: 313714--313751 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
313704 TAGGTTTATG
313714 CTTCTCTATT-TTCTTTC
1 CTTCTC-ATTATTCTTTC
*
313731 CTTCTCATTATTCTTTG
1 CTTCTCATTATTCTTTC
313748 CTTC
1 CTTC
313752 GACCTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.08, C:0.29, G:0.03, T:0.61
Consensus pattern (17 bp):
CTTCTCATTATTCTTTC
Found at i:325697 original size:55 final size:55
Alignment explanation
Indices: 325631--325741 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
325621 CTTTCATGAT
325631 TACCTGATGTCCAAAAACAACAGAGGCGGTTTGAAGTACGAAATGTAAGAAATTA
1 TACCTGATGTCCAAAAACAACAGAGGCGGTTTGAAGTACGAAATGTAAGAAATTA
** * *
325686 TACCTGATGTCCAAAAACAAGGGGGGCTGTTTGAAGTACGAAATGTAAGAAATTA
1 TACCTGATGTCCAAAAACAACAGAGGCGGTTTGAAGTACGAAATGTAAGAAATTA
325741 T
1 T
325742 CTGCTCTTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (55 bp):
TACCTGATGTCCAAAAACAACAGAGGCGGTTTGAAGTACGAAATGTAAGAAATTA
Found at i:334878 original size:2 final size:2
Alignment explanation
Indices: 334871--334899 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
334861 TGTAAGGTAA
334871 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
334900 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:340371 original size:60 final size:60
Alignment explanation
Indices: 340261--340375 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
340251 AAATTGGTCC
* * * *
340261 TTAAACTTTTATATATTTTAATTTCATCCCTAAACTATGTCACCCATTCTAAATTAATAA
1 TTAAACTTTTAAACATTCTAATTTCATCCCTAAACTATGACACCCATTCTAAATTAATAA
* * * *
340321 TTAACCTTTTAAACATTCTAATTTTATCCCTGAACTATGAC-CCTCTTTCTAAATT
1 TTAAACTTTTAAACATTCTAATTTCATCCCTAAACTATGACACC-CATTCTAAATT
340376 GGTCCCCAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.04
60 44 0.96
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (60 bp):
TTAAACTTTTAAACATTCTAATTTCATCCCTAAACTATGACACCCATTCTAAATTAATAA
Found at i:341222 original size:21 final size:21
Alignment explanation
Indices: 341105--341242 Score: 59
Period size: 21 Copynumber: 6.7 Consensus size: 21
341095 ACGCGAAATA
**
341105 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
341125 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
341145 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* * ** *
341166 AAAATCGCGATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* * **
341187 ATATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
341208 ATAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
341228 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
341243 ACACATAAAT
Statistics
Matches: 85, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.45
21 44 0.52
22 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:341304 original size:20 final size:20
Alignment explanation
Indices: 341210--341578 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
341200 GATTTTCCAT
* ** *
341210 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
341230 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
341250 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
341270 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
341290 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
341310 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
341330 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
341350 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
341370 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
341390 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
341410 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
341430 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
341450 AATCACAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
341470 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
341490 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
341510 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
341530 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
341550 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
341570 AATCACAAC
1 AATCGCAAC
341579 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:342300 original size:24 final size:24
Alignment explanation
Indices: 342261--342307 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
342251 AAATTTGGTC
342261 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
342285 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
342308 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:342498 original size:12 final size:12
Alignment explanation
Indices: 342481--342505 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
342471 ATATAATCCT
342481 GAAGAAGAAAAA
1 GAAGAAGAAAAA
342493 GAAGAAGAAAAA
1 GAAGAAGAAAAA
342505 G
1 G
342506 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:344801 original size:19 final size:19
Alignment explanation
Indices: 344779--345083 Score: 349
Period size: 19 Copynumber: 17.4 Consensus size: 19
344769 CGGAAAATAC
*
344779 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
344798 AATCCCAA--C---ATG-A
1 AATCGCAATGCGAAATGAA
344811 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
344831 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
344845 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
344864 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
344883 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
344897 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
344916 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
344935 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
344949 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
344968 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
344987 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
345006 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
345025 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
345039 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
345057 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
345076 AATCGCAA
1 AATCGCAA
345084 CGAGATAATC
Statistics
Matches: 247, Mismatches: 12, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
13 8 0.03
14 38 0.15
15 3 0.01
16 15 0.06
17 14 0.06
18 20 0.08
19 140 0.57
20 9 0.04
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:344830 original size:33 final size:33
Alignment explanation
Indices: 344779--345105 Score: 170
Period size: 33 Copynumber: 9.5 Consensus size: 33
344769 CGGAAAATAC
*
344779 AATCGCAACGCGAAATGAAAATCCCAAC-ATGA-
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAG
*
344811 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCCCAACGAGAG
* * * *
344845 AATTGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAG
* * * * *
344877 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCCCAA--CG--A-GAG
* *
344916 AATCGCAATGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAG
* * *
344949 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAG
* *
344987 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAG
* *
345025 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATG
1 AATCGCAATGCGAAATGAAAATCCCAA--CGAGA-G
* *
345056 AAATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 -AATCGCAATGCGAAATGAAAATCCCAACGAGAG
345090 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
345106 TATAAACGCA
Statistics
Matches: 246, Mismatches: 23, Indels: 51
0.77 0.07 0.16
Matches are distributed among these distances:
30 1 0.00
31 8 0.03
32 25 0.10
33 100 0.41
34 17 0.07
35 9 0.04
36 7 0.03
37 9 0.04
38 56 0.23
39 7 0.03
40 7 0.03
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAG
Found at i:344838 original size:52 final size:51
Alignment explanation
Indices: 344779--345083 Score: 320
Period size: 52 Copynumber: 5.8 Consensus size: 51
344769 CGGAAAATAC
* * *
344779 AATCGCAACGCGA-AATGAAAATCCCAACATG-AAATCGCAATGCGGAAATGAA
1 AATCGCAACGCGAGAATG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAA
*
344831 AATCGCAACGAGAGAATTGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAGAA-TGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
344883 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAGAAT-GCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
344935 AATCGCAACGAC-AGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAACG-CGAGAAT-GCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
344987 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--
1 AATCGCAACGCG--A-G--AAT-GCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
345039 AATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAACGCG--A-G-AAT-GCAATGCGAAATGAAAATCGCAA
345084 CGAGATAATC
Statistics
Matches: 234, Mismatches: 8, Indels: 23
0.88 0.03 0.09
Matches are distributed among these distances:
51 30 0.13
52 148 0.63
53 20 0.09
54 4 0.02
55 6 0.03
57 26 0.11
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (51 bp):
AATCGCAACGCGAGAATGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:344933 original size:71 final size:71
Alignment explanation
Indices: 344849--345083 Score: 356
Period size: 71 Copynumber: 3.3 Consensus size: 71
344839 CGAGAGAATT
*
344849 GCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
1 GCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG
344914 AAAATC
66 AAAATC
* *
344920 GCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCG
1 GCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAATGCG
344980 AAATGAAAATC
61 AAATGAAAATC
344991 GCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG
1 GCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG
345056 -AAATC
66 AAAATC
345061 GCAATGCGAAATGAAAATCGCAA
1 GCAATGCGAAATGAAAATCGCAA
345084 CGAGATAATC
Statistics
Matches: 149, Mismatches: 5, Indels: 21
0.85 0.03 0.12
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
70 28 0.19
71 88 0.59
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (71 bp):
GCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG
AAAATC
Found at i:345221 original size:19 final size:19
Alignment explanation
Indices: 345112--345213 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
345102 AAATTATAAA
345112 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
345131 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
345151 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
345167 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
345184 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
345203 CGCATTGCGAT
1 CGCATTGCGAT
345214 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:345338 original size:14 final size:14
Alignment explanation
Indices: 345319--345355 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
345309 CATCAATTAC
345319 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
345333 ACAAATCATCTTTT
1 ACAAATCAACTTTT
345347 ACAAATCAA
1 ACAAATCAA
345356 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:347354 original size:14 final size:14
Alignment explanation
Indices: 347335--347390 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
347325 GCGAAATTAA
*
347335 AATCGCAACGACAG
1 AATCGCAACGAAAG
347349 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
347366 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
347381 AATCGCAACG
1 AATCGCAACG
347391 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 1 0.03
16 9 0.24
17 1 0.03
18 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:347362 original size:33 final size:33
Alignment explanation
Indices: 347279--347407 Score: 143
Period size: 32 Copynumber: 3.8 Consensus size: 33
347269 TAGTTTACTT
* *
347279 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-TTAAAATCGCAA--CG-AA--AGAA
*
347318 TCGCAACGCGAAATTAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATTAAAATCGCAACGAAAGAA
* *
347351 TCGCAATGCGAAA-TGAAATCGCAACGAAAGAA
1 TCGCAACGCGAAATTAAAATCGCAACGAAAGAA
*
347383 TCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAATTAAAATCGCAA
347408 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
32 29 0.36
33 24 0.30
35 1 0.01
36 2 0.03
38 12 0.15
39 12 0.15
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.12
Consensus pattern (33 bp):
TCGCAACGCGAAATTAAAATCGCAACGAAAGAA
Found at i:347405 original size:19 final size:19
Alignment explanation
Indices: 347279--347412 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
347269 TAGTTTACTT
* *
347279 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
347299 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
347318 TCGCAACGCGAAATTAAAA
1 TCGCAACGCGAAATGAAAA
*
347337 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
347351 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
347369 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
347383 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
347402 TCGCAATGCGA
1 TCGCAACGCGA
347413 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 19
0.77 0.07 0.15
Matches are distributed among these distances:
14 16 0.17
15 1 0.01
16 14 0.15
17 6 0.06
18 8 0.08
19 39 0.41
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:347430 original size:19 final size:19
Alignment explanation
Indices: 347408--347535 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
347398 AAAATCGCAA
347408 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
347427 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
347441 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
347459 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
347473 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
347492 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
347511 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
347531 TGCGA
1 TGCGA
347536 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 2 0.02
14 20 0.23
16 3 0.03
17 1 0.01
18 10 0.11
19 39 0.44
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:347493 original size:33 final size:34
Alignment explanation
Indices: 347408--347498 Score: 143
Period size: 32 Copynumber: 2.8 Consensus size: 34
347398 AAAATCGCAA
347408 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
347441 TGCGA-TTTGGTTTCGCGTTGCGATTC-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
**
347473 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
347499 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (34 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTGTCGT
Found at i:347962 original size:92 final size:93
Alignment explanation
Indices: 347579--348143 Score: 1107
Period size: 93 Copynumber: 6.1 Consensus size: 93
347569 TTGAATGGAT
347579 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
347644 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
347672 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
347737 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
347765 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
347830 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
347858 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
347922 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
347950 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
348014 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
348042 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
348107 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
348135 AAATTTACT
1 AAATTTACT
348144 AAGCAATCTA
Statistics
Matches: 470, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 184 0.39
93 286 0.61
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:348088 original size:185 final size:186
Alignment explanation
Indices: 347579--348143 Score: 1107
Period size: 185 Copynumber: 3.0 Consensus size: 186
347569 TTGAATGGAT
347579 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
347644 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
347709 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
347765 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
347830 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
347895 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
347950 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
348014 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
348079 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
348135 AAATTTACT
1 AAATTTACT
348144 AAGCAATCTA
Statistics
Matches: 377, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 92 0.24
185 153 0.41
186 132 0.35
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:349822 original size:14 final size:14
Alignment explanation
Indices: 349803--349892 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
349793 TTGAAATGAA
349803 AATCGCAACGAGAG
1 AATCGCAACGAGAG
349817 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
349834 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
349850 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
349869 AATCGCAACGAGAG
1 AATCGCAACGAGAG
349883 AATCGCAACG
1 AATCGCAACG
349893 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:349840 original size:33 final size:33
Alignment explanation
Indices: 349795--349909 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
349785 TCTTTTGGTT
349795 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
349828 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
349861 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
349894 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
349910 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:349841 original size:19 final size:18
Alignment explanation
Indices: 349802--349914 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
349792 GTTGAAATGA
349802 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
349817 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
349834 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
349850 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
349867 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
349883 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
349900 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
349915 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:350012 original size:20 final size:19
Alignment explanation
Indices: 349933--350026 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 19
349923 TCGCGTTGCG
349933 ATTCTCTCGTTGCGATTTC
1 ATTCTCTCGTTGCGATTTC
* *
349952 ATT-TCGCGTTCGCG-TTGC
1 ATTCTCTCGTT-GCGATTTC
**
349970 GATTCTCTCGTTGCGACAGTC
1 -ATTCTCTCGTTGCGA-TTTC
349991 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGA-TTTC
*
350011 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
350027 CTCTTCTGCA
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
18 9 0.15
19 12 0.20
20 24 0.41
21 14 0.24
ACGTcount: A:0.12, C:0.26, G:0.20, T:0.43
Consensus pattern (19 bp):
ATTCTCTCGTTGCGATTTC
Found at i:350148 original size:33 final size:33
Alignment explanation
Indices: 350106--350176 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
350096 AATACTAACT
*
350106 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
350139 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
350172 TGAAA
1 TGAAA
350177 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:350410 original size:22 final size:22
Alignment explanation
Indices: 350358--350412 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
350348 TGGTTGTGAG
**
350358 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
350380 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
350402 GGATTTCTTCG
1 GGATTTCTTCG
350413 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:350581 original size:20 final size:20
Alignment explanation
Indices: 350556--350748 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
350546 CTTTAAATAT
350556 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
350576 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
350598 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
350617 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* * **
350637 TGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
350657 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
350677 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
350697 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
350717 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
350737 CGCGTTGCGATT
1 CGCGTTGCGATT
350749 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:350743 original size:60 final size:60
Alignment explanation
Indices: 350556--350748 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
350546 CTTTAAATAT
**
350556 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * * *** *
350617 CGCGTTGCGATATACGGATATGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
350677 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
350737 CGCGTTGCGATT
1 CGCGTTGCGATT
350749 ATGGAAAATC
Statistics
Matches: 109, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 82 0.75
61 27 0.25
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:350874 original size:19 final size:20
Alignment explanation
Indices: 350845--350882 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
350835 GGGATTTGCG
350845 ATTTGCGCGTTGCGATTTTT
1 ATTTGCGCGTTGCGATTTTT
350865 ATTT-CGCGTTGCGATTTT
1 ATTTGCGCGTTGCGATTTT
350883 GTTGGTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.50
Consensus pattern (20 bp):
ATTTGCGCGTTGCGATTTTT
Found at i:351674 original size:21 final size:20
Alignment explanation
Indices: 351647--351745 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
351637 AATCAGTTTC
351647 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
351668 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
351689 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
351709 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
351730 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
351746 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:351738 original size:20 final size:20
Alignment explanation
Indices: 351713--351885 Score: 215
Period size: 20 Copynumber: 8.6 Consensus size: 20
351703 GATTTTCCAG
* ** *
351713 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
351733 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
351753 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
351773 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
351793 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
351813 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
351833 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
351854 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
351874 AATCGCAACGCG
1 AATCGCAACGCG
351886 ATTTTTAAAG
Statistics
Matches: 133, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
19 1 0.01
20 113 0.85
21 19 0.14
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:352302 original size:33 final size:33
Alignment explanation
Indices: 352263--352333 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
352253 TTCACTTAGA
352263 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
352296 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
352329 TTTCA
1 TTTCA
352334 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:352439 original size:21 final size:21
Alignment explanation
Indices: 352413--352489 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
352403 TGCAGAAGAG
352413 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
352434 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
352454 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
352476 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
352490 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:352493 original size:14 final size:14
Alignment explanation
Indices: 352474--352530 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
352464 GAAAAATGAA
352474 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
352488 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
352507 AATCGCAACGAGAG
1 AATCGCAACGAGAG
352521 AATCGCAACG
1 AATCGCAACG
352531 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:352505 original size:33 final size:33
Alignment explanation
Indices: 352467--352546 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
352457 GCAACGAGAA
352467 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
352500 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
352533 AAACCAAAATCGCA
1 AAATGAAAATCGCA
352547 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:352564 original size:19 final size:19
Alignment explanation
Indices: 352542--352648 Score: 81
Period size: 19 Copynumber: 6.1 Consensus size: 19
352532 GAAACCAAAA
*
352542 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
352561 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
352575 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
352594 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
352608 TCTCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
352627 CTCTCGTTGTGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
352647 TC
1 TC
352649 AACCAAAAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
14 19 0.27
16 6 0.09
17 6 0.09
19 22 0.31
20 17 0.24
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:352583 original size:14 final size:14
Alignment explanation
Indices: 352564--352620 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
352554 TTTCATTTCG
352564 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
352578 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
352597 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
352611 CATTGCGATT
1 CGTTGCGATT
352621 TTCATTCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:352589 original size:33 final size:33
Alignment explanation
Indices: 352545--352640 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
352535 ACCAAAATCG
352545 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
352578 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
352611 CATTGCGATTTTCATTCTCTCGTTGTGATT
1 CATTGCGATTTTCATT-TCGCGTTGCGATT
352641 TTCATTTCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 47 0.81
34 11 0.19
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:352629 original size:20 final size:20
Alignment explanation
Indices: 352604--352646 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
352594 TCGCGTTGCG
352604 ATTCTCTCATTGCGATTTTC
1 ATTCTCTCATTGCGATTTTC
* *
352624 ATTCTCTCGTTGTGATTTTC
1 ATTCTCTCATTGCGATTTTC
352644 ATT
1 ATT
352647 TCAACCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.21, G:0.12, T:0.53
Consensus pattern (20 bp):
ATTCTCTCATTGCGATTTTC
Found at i:354580 original size:14 final size:14
Alignment explanation
Indices: 354561--354617 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
354551 CGAAACTTAA
354561 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
354575 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
354594 AATCGCAACGACAG
1 AATCGCAACGAGAG
354608 AATCGCAACG
1 AATCGCAACG
354618 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:354599 original size:19 final size:18
Alignment explanation
Indices: 354575--354655 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 18
354565 GCAACGAGAG
354575 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
354594 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
354608 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
354627 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
354641 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
354656 CCAAAATTGC
Statistics
Matches: 50, Mismatches: 3, Indels: 19
0.69 0.04 0.26
Matches are distributed among these distances:
14 19 0.38
15 1 0.02
16 7 0.14
17 6 0.12
18 1 0.02
19 16 0.32
ACGTcount: A:0.47, C:0.27, G:0.19, T:0.07
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:354601 original size:33 final size:33
Alignment explanation
Indices: 354543--354662 Score: 168
Period size: 33 Copynumber: 3.6 Consensus size: 33
354533 TAGTTTACTT
* * *
354543 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAA-TCAAAATCGCAACGACAGAA
*
354577 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
* *
354610 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
*
354643 TCGCAACGCGAAACCAAAAT
1 TCGCAACGCGAAATCAAAAT
354663 TGCATTGCGA
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
33 68 0.85
34 12 0.15
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAATCAAAATCGCAACGACAGAA
Found at i:354643 original size:14 final size:14
Alignment explanation
Indices: 354592--354650 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
354582 ACGCGAAATG
354592 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
354606 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
354625 AAAATCGCAACGAC
1 AAAATCGCAACGAC
354639 AAAATCGCAACG
1 AAAATCGCAACG
354651 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:354662 original size:19 final size:18
Alignment explanation
Indices: 354575--354662 Score: 75
Period size: 19 Copynumber: 5.2 Consensus size: 18
354565 GCAACGAGAG
*
354575 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-CAA
*
354594 AATCGCAA--CG--ACAG
1 AATCGCAACGCGAAACAA
354608 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
354627 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAACAA
354641 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
354660 AAT
1 AAT
354663 TGCATTGCGA
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
14 20 0.36
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 24 0.43
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAACAA
Found at i:354689 original size:19 final size:19
Alignment explanation
Indices: 354667--354834 Score: 158
Period size: 19 Copynumber: 9.3 Consensus size: 19
354657 CAAAATTGCA
354667 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
354686 TTGCGATTCTC--TT---G
1 TTGCGATTTTCATTTCGCG
*
354700 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
354719 TTGCGA--TTC-TGT--CG
1 TTGCGATTTTCATTTCGCG
354733 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
354752 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCG
** *
354771 TTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCG
*
354790 TTGCGATTCTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
354809 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
354829 TTGCGA
1 TTGCGA
354835 AAGTAAACTA
Statistics
Matches: 122, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.15
16 7 0.06
17 7 0.06
19 78 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:354792 original size:38 final size:38
Alignment explanation
Indices: 354667--354834 Score: 167
Period size: 33 Copynumber: 4.7 Consensus size: 38
354657 CAAAATTGCA
354667 TTGCGATTTTCATTTCGCGTTGCGATTCTC--TT---G
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCGCG
* *
354700 TTGCGATTTTCATTTCGCATTGCGA-T-TC-TGT--CG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCGCG
* **
354733 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCGCG
** *
354771 TTGCGATTTTGGTTTCTCGTTGCGATTCTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCGCG
* *
354809 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
354835 AAGTAAACTA
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.02
32 2 0.02
33 49 0.44
34 1 0.01
35 1 0.01
36 2 0.02
38 44 0.39
39 11 0.10
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (38 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCGCG
Found at i:356774 original size:14 final size:14
Alignment explanation
Indices: 356755--356790 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
356745 ATTGTTTAAT
356755 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
356769 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
356783 TGATTTGT
1 TGATTTGT
356791 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:356914 original size:20 final size:19
Alignment explanation
Indices: 356897--356995 Score: 136
Period size: 19 Copynumber: 5.4 Consensus size: 19
356887 AAAAATGACT
356897 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
356917 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
356936 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
356950 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
356969 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
356989 ATCGCAA
1 ATCGCAA
356996 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 29 0.41
20 26 0.37
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:357027 original size:53 final size:53
Alignment explanation
Indices: 356897--357014 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
356887 AAAAATGACT
356897 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
356950 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
357003 ATCGCAATGCGA
1 ATCGCAATGCGA
357015 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 19 0.30
53 45 0.70
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:357073 original size:53 final size:52
Alignment explanation
Indices: 357010--357227 Score: 302
Period size: 53 Copynumber: 4.1 Consensus size: 52
357000 AGAATCGCAA
357010 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
357063 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
* *
357116 TGCGATTTTCATTTTGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
357174 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
357221 TGCGATT
1 TGCGATT
357228 GTAATTTCCG
Statistics
Matches: 155, Mismatches: 4, Indels: 18
0.88 0.02 0.10
Matches are distributed among these distances:
47 8 0.05
49 2 0.01
50 2 0.01
51 3 0.02
52 10 0.06
53 109 0.70
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:357091 original size:72 final size:71
Alignment explanation
Indices: 357004--357213 Score: 248
Period size: 72 Copynumber: 2.9 Consensus size: 71
356994 AACGAGAGAA
* *
357004 TCGCAATGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCA-TTGCGATTCTCT-CGTTGC
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCG-ATTTGC-ATT-T-TGCATTGC
357066 GATTTTCATT
62 GATTTTCATT
* * *
357076 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTTGCATTGCGA
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATT-T-TCATTTCCGATTTGCATTTTGCATTGCGA
357140 TTTTCATT
64 TTTTCATT
** * *
357148 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-TTCCGATTTGCATTTTGCATTGCGAT
357213 T
65 T
357214 CTCTCGTTGC
Statistics
Matches: 123, Mismatches: 8, Indels: 14
0.85 0.06 0.10
Matches are distributed among these distances:
70 2 0.02
71 2 0.02
72 93 0.76
73 16 0.13
74 8 0.07
75 2 0.02
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (71 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCGATTTGCATTTTGCATTGCGATT
TTCATT
Found at i:357235 original size:33 final size:33
Alignment explanation
Indices: 357081--357227 Score: 179
Period size: 33 Copynumber: 4.2 Consensus size: 33
357071 TCATTTCGCA
357081 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
* *
357115 TTGCGATTTTCATTTTGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
357151 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
357187 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
357220 TTGCGATT
1 TTGCGATT
357228 GTAATTTCCG
Statistics
Matches: 97, Mismatches: 8, Indels: 17
0.80 0.07 0.14
Matches are distributed among these distances:
32 1 0.01
33 31 0.32
34 29 0.30
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 9 0.09
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:359723 original size:24 final size:24
Alignment explanation
Indices: 359689--359735 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
359679 CTGAAACATC
359689 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
359713 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
359736 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:360449 original size:20 final size:20
Alignment explanation
Indices: 360421--360649 Score: 253
Period size: 20 Copynumber: 11.4 Consensus size: 20
360411 AAATTTCAGT
* * *
360421 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
360441 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
360461 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
360481 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
360501 GTTGTGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
360521 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
360541 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
360561 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
360581 GTTGTGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
360601 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
360621 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
360641 GTTGCGATT
1 GTTGCGATT
360650 CTGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:363560 original size:19 final size:20
Alignment explanation
Indices: 363525--363562 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
363515 AAAATAGGAT
*
363525 AGTTATCATCATTTTAATTC
1 AGTTATAATCATTTTAATTC
363545 AGTTATAATC-TTTTAATT
1 AGTTATAATCATTTTAATT
363563 ATCGATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (20 bp):
AGTTATAATCATTTTAATTC
Found at i:369344 original size:21 final size:20
Alignment explanation
Indices: 369310--369367 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
369300 ATATTAATAT
*
369310 AAAAATATTCATTTTAAGTAA
1 AAAAATAAT-ATTTTAAGTAA
* *
369331 CGAAATTAATATTTCT-AGTAA
1 -AAAAATAATATTT-TAAGTAA
369352 AAAAATAATATTTTAA
1 AAAAATAATATTTTAA
369368 ATAGTACTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 9 0.31
22 7 0.24
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAAATAATATTTTAAGTAA
Found at i:370236 original size:20 final size:21
Alignment explanation
Indices: 370211--370256 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
370201 ACGTGAGAGC
370211 AGAGAAAAACGAGTCACAA-G
1 AGAGAAAAACGAGTCACAAGG
*
370231 AGAGAAAAACGTGTCACAAGG
1 AGAGAAAAACGAGTCACAAGG
370252 AGAGA
1 AGAGA
370257 TTTTCTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.52, C:0.13, G:0.28, T:0.07
Consensus pattern (21 bp):
AGAGAAAAACGAGTCACAAGG
Found at i:370997 original size:21 final size:22
Alignment explanation
Indices: 370957--370997 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
370947 ATTTTGAGGG
*
370957 TTTTTTAATTATAATATTAAGT
1 TTTTTTAAATATAATATTAAGT
*
370979 TTTTTTAAATA-AATTTTAA
1 TTTTTTAAATATAATATTAA
370998 AATTTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTTTAAATATAATATTAAGT
Found at i:371695 original size:36 final size:37
Alignment explanation
Indices: 371624--371695 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
371614 CTATGTGATA
* *
371624 TTTATATATTTTCTTTAAAAAATTTAAATTCATAAAC
1 TTTATATATTTTCTTTAAAAAATTAAAAATCATAAAC
*
371661 TTTATATAATTTT-TTTACAAAATTAAAAAT-ATAAA
1 TTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
371696 AAGGTTTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 5 0.16
37 21 0.68
38 5 0.16
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (37 bp):
TTTATATATTTTCTTTAAAAAATTAAAAATCATAAAC
Found at i:372683 original size:162 final size:163
Alignment explanation
Indices: 372416--372741 Score: 645
Period size: 162 Copynumber: 2.0 Consensus size: 163
372406 CTTTATTTAT
372416 CGCTTTGACGCGATCTGTGGAATGGTATGATAATAGAAGATTGCGCCTTTAGCTGCTGTTACTGA
1 CGCTTTGACGCGATCTGTGGAATGGTATGATAATAGAAGATTGCGCCTTTAGCTGCTGTTACTGA
372481 AAAGCTGTAAATGTCTACTACTAGGATCATTCCAAGAA-TTTATTGTTTACTATATGAAACATTG
66 AAAGCTGTAAATGTCTACTACTAGGATCATTCCAAGAATTTTATTGTTTACTATATGAAACATTG
372545 AGGGTATTAAGAACATAGTTCAGTGATTTACTG
131 AGGGTATTAAGAACATAGTTCAGTGATTTACTG
372578 CGCTTTGACGCGATCTGTGGAATGGTATGATAATAGAAGATTGCGCCTTTAGCTGCTGTTACTGA
1 CGCTTTGACGCGATCTGTGGAATGGTATGATAATAGAAGATTGCGCCTTTAGCTGCTGTTACTGA
372643 AAAGCTGTAAATGTCTACTACTAGGATCATTCCAAGAATTTTATTGTTTACTATATGAAACATTG
66 AAAGCTGTAAATGTCTACTACTAGGATCATTCCAAGAATTTTATTGTTTACTATATGAAACATTG
372708 AGGGTATTAAGAACATAGTTCAGTGATTTACTG
131 AGGGTATTAAGAACATAGTTCAGTGATTTACTG
372741 C
1 C
372742 AAATTAAGCT
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 103 0.63
163 60 0.37
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (163 bp):
CGCTTTGACGCGATCTGTGGAATGGTATGATAATAGAAGATTGCGCCTTTAGCTGCTGTTACTGA
AAAGCTGTAAATGTCTACTACTAGGATCATTCCAAGAATTTTATTGTTTACTATATGAAACATTG
AGGGTATTAAGAACATAGTTCAGTGATTTACTG
Found at i:373387 original size:29 final size:29
Alignment explanation
Indices: 373343--373419 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
373333 GAGGAGCAGG
*
373343 AGGAGTGCATGACGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
373372 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
373401 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
373420 TGCTGGGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.25, C:0.27, G:0.34, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:375310 original size:36 final size:38
Alignment explanation
Indices: 375248--375320 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 38
375238 AATTTATAAA
* *
375248 TAATAAAAAATAATAAGTTAACTAAT-ATATTATTTTT
1 TAATAAAAAAGAATAAGTTAACTAATAAAATTATTTTT
* *
375285 TAATAAAAAAGATTAA-TTAATTAATAAAATTATTTT
1 TAATAAAAAAGAATAAGTTAACTAATAAAATTATTTT
375321 AGTACAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 8 0.26
37 23 0.74
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.42
Consensus pattern (38 bp):
TAATAAAAAAGAATAAGTTAACTAATAAAATTATTTTT
Found at i:375889 original size:20 final size:20
Alignment explanation
Indices: 375861--375908 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
375851 ATATATTATA
*
375861 TTTTTGAGCTGCTCACGAGC
1 TTTTCGAGCTGCTCACGAGC
375881 TTTTCGAGCTGCTCACGAGC
1 TTTTCGAGCTGCTCACGAGC
375901 TTTTCGAG
1 TTTTCGAG
375909 TCGAGTATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (20 bp):
TTTTCGAGCTGCTCACGAGC
Found at i:377760 original size:24 final size:24
Alignment explanation
Indices: 377728--377775 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
377718 CACTCTTGGG
377728 TTGACAACAGGGAAGGCGAAGGAA
1 TTGACAACAGGGAAGGCGAAGGAA
377752 TTGACAACAGGGAAGGCGAAGGAA
1 TTGACAACAGGGAAGGCGAAGGAA
377776 CATAAAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.38, T:0.08
Consensus pattern (24 bp):
TTGACAACAGGGAAGGCGAAGGAA
Found at i:381046 original size:35 final size:35
Alignment explanation
Indices: 380977--381270 Score: 147
Period size: 35 Copynumber: 8.3 Consensus size: 35
380967 ATATAGTGTG
** **
380977 AAATCATTTTGAAAATTATATAATATATGGTTTTTTT
1 AAAT-ATTTTGAAAA-TATATAATATATAATTTTTGA
381014 AAATATTTTGAAAATATATAATATATAATTTTTGA
1 AAATATTTTGAAAATATATAATATATAATTTTTGA
* ** *
381049 AAACATTTTTGAAAATGCAT-AT-TATATTGTTTTGA
1 AAATA-TTTTGAAAATATATAATATATAAT-TTTTGA
* * ** *
381084 AAACTTTTTTTAAATATATATAATATATAGCTTTTAA
1 AAA-TATTTTGAAA-ATATATAATATATAATTTTTGA
* **
381121 AAACATTTTGAAAA-ACGT-ATATATAA-TTTTGA
1 AAATATTTTGAAAATATATAATATATAATTTTTGA
* ** * *
381153 AAATTAGTTTCTAAATATATATTATAT-AGTTTTGA
1 AAA-TATTTTGAAAATATATAATATATAATTTTTGA
* * * *
381188 AAATTAGTTTTTAAAAAAAGTATATTATAT-AGTTTTGA
1 AAA-TA--TTTTGAAAATA-TATAATATATAATTTTTGA
* * *
381226 AAATTAGTTTTTAAAA-ATATATTATAT-AGTTTTGA
1 AAA-TA-TTTTGAAAATATATAATATATAATTTTTGA
381261 AAATTATTTT
1 AAA-TATTTT
381271 TTTAAAAAAC
Statistics
Matches: 208, Mismatches: 36, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
32 8 0.04
33 14 0.07
34 14 0.07
35 81 0.39
36 34 0.16
37 29 0.14
38 28 0.13
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (35 bp):
AAATATTTTGAAAATATATAATATATAATTTTTGA
Found at i:381246 original size:73 final size:72
Alignment explanation
Indices: 381067--381311 Score: 256
Period size: 73 Copynumber: 3.4 Consensus size: 72
381057 TTGAAAATGC
* * *
381067 ATATTATATTGTTTTGAAAACTT-TTTTTAAATATATATAATATATAGCTTTT-AAAA--ACATT
1 ATATTATATAGTTTTGAAAA-TTGTTTTTAAA-A-ATATATTATATAG-TTTTGAAAATTACTTT
* *
381128 TTGAAAAACGT
62 TTAAAAAAAGT
* * *
381139 ATA-TATA-A-TTTTGAAAATTAGTTTCTAAATATATATTATATAGTTTTGAAAATTAGTTTTTA
1 ATATTATATAGTTTTGAAAATT-GTTTTTAAAAATATATTATATAGTTTTGAAAATTACTTTTTA
381201 AAAAAAGT
65 AAAAAAGT
*
381209 ATATTATATAGTTTTGAAAATTAGTTTTTAAAAATATATTATATAGTTTTGAAAATTATTTTTTT
1 ATATTATATAGTTTTGAAAATT-GTTTTTAAAAATATATTATATAGTTTTGAAAATTA-CTTTTT
381274 AAAAAACA-T
64 AAAAAA-AGT
* *
381283 ATATTGTATAGTTTT-AAAAATGTTTTTAA
1 ATATTATATAGTTTTGAAAATTGTTTTTAA
381312 TTAATTTATT
Statistics
Matches: 150, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
67 4 0.03
68 18 0.12
69 9 0.06
70 22 0.15
71 8 0.05
72 12 0.08
73 50 0.33
74 26 0.17
75 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (72 bp):
ATATTATATAGTTTTGAAAATTGTTTTTAAAAATATATTATATAGTTTTGAAAATTACTTTTTAA
AAAAAGT
Found at i:381272 original size:35 final size:35
Alignment explanation
Indices: 381019--381303 Score: 213
Period size: 35 Copynumber: 7.9 Consensus size: 35
381009 TTTTTAAATA
* * * *
381019 TTTTGAAAATATATAATATATAATTTTTGAAAA-CA-
1 TTTTTAAAA-ATATATTATAT-AGTTTTGAAAATTAT
* * *
381054 TTTTTGAAAATGCATATTATATTGTTTTGAAAACT-T
1 TTTTTAAAAAT--ATATTATATAGTTTTGAAAATTAT
* **
381090 TTTTTAAATATATATAATATATAGCTTTT-AAAAACA-
1 TTTTTAAA-A-ATATATTATATAG-TTTTGAAAATTAT
* ** * *
381126 TTTTGAAAAACGTA-TATATAATTTTGAAAATTAG
1 TTTTTAAAAATATATTATATAGTTTTGAAAATTAT
* *
381160 TTTCTAAATATATATTATATAGTTTTGAAAATTAGT
1 TTTTTAAAAATATATTATATAGTTTTGAAAATTA-T
* *
381196 TTTTAAAAAAAGTATATTATATAGTTTTGAAAATTAG
1 TTTT-TAAAAA-TATATTATATAGTTTTGAAAATTAT
381233 TTTTTAAAAATATATTATATAGTTTTGAAAATTATT
1 TTTTTAAAAATATATTATATAGTTTTGAAAATTA-T
* *
381269 TTTTTAAAAAACATATATTGTATAGTTTTAAAAAT
1 TTTTT--AAAA-ATATATTATATAGTTTTGAAAAT
381304 GTTTTTAATT
Statistics
Matches: 200, Mismatches: 32, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
32 4 0.02
33 11 0.05
34 14 0.07
35 59 0.29
36 48 0.24
37 13 0.06
38 30 0.15
39 21 0.10
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (35 bp):
TTTTTAAAAATATATTATATAGTTTTGAAAATTAT
Found at i:381339 original size:4 final size:4
Alignment explanation
Indices: 381315--381378 Score: 66
Period size: 4 Copynumber: 17.0 Consensus size: 4
381305 TTTTTAATTA
* *
381315 ATTT A-TT AGTTT ATCT ATTT ATTT ATTT ATTT A-TT ATTT -TTT -TTC
1 ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
381360 ATTT ATTT ATTT A-TT ATTT
1 ATTT ATTT ATTT ATTT ATTT
381379 GTTTCAGGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
3 14 0.27
4 34 0.67
5 3 0.06
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:381365 original size:21 final size:24
Alignment explanation
Indices: 381335--381384 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
381325 TTATCTATTT
*
381335 ATTTATTTATTTATTATTTTTTTTC
1 ATTTATTTATTTATTA-TTTGTTTC
381360 ATTTATTTATTTATTATTTGTTTC
1 ATTTATTTATTTATTATTTGTTTC
381384 A
1 A
381385 GGTCCAGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTATTTATTTATTATTTGTTTC
Found at i:381547 original size:16 final size:15
Alignment explanation
Indices: 381526--381556 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
381516 GGCCGGCCGG
381526 CATCCCGGGACTGACC
1 CATCCCGGGA-TGACC
381542 CATCCCGGGATGACC
1 CATCCCGGGATGACC
381557 GGTCATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (15 bp):
CATCCCGGGATGACC
Found at i:384275 original size:19 final size:19
Alignment explanation
Indices: 384241--384285 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
384231 ATTTAGACAT
384241 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
384259 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
384278 TTTGCATT
1 TTTGCATT
384286 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:387766 original size:81 final size:82
Alignment explanation
Indices: 387538--388420 Score: 782
Period size: 80 Copynumber: 10.9 Consensus size: 82
387528 TTTAACAACT
*
387538 ATTTACAAGCATAACTCAAGGCTAG-AGGG-TATCTGTGACCAAAGACCTTCGAGTTCGACTACG
1 ATTTAC-AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACG
* * *
387601 CTCAGCTCCAAGGCACATC
65 CTCAGCTTCGAGG-GCATC
* * * * * * * *
387620 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACC-CCGAGTTCGATTACAC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACGC
387681 TCAGCTTCGAGGGCATC
66 TCAGCTTCGAGGGCATC
*
387698 ATTTACAGCATAACTCAAGGCTAGAA-GGTTATCTGTGACCAAAAGA-CTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGATTACG
* *
387761 CTCAGCTCCCA---CATC
65 CTCAGCTTCGAGGGCATC
** * * * * * ** *
387776 ATTCGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCCCGAGTTCGATTACAC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACGC
*
387838 TCAGCTTCGAGGGAACAAAC
66 TCAGCTTCGAGGG--C-ATC
*
387858 TATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
1 -ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGATTAC
* * *
387923 GCTCAGCTCCAAGGCACATC
64 GCTCAGCTTCGAGG-GCATC
* * * * * * ** *
387943 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CCAAAGACCCCCGAGTTCGATTACAC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACGC
388005 TCAGCTTCGAGGGCA-C
66 TCAGCTTCGAGGGCATC
* *
388021 ATCATTACAGCATAACTCAAGGCTAGAAGGGGTTATCTGTGAGCAAAAGACCTTCGAGTTCGACT
1 AT--TTACAGCATAACTCAAGGCTAGAA-GGGTTATCTGTGA-CCAAAGACCTTCGAGTTCGATT
* *
388086 -CGCTCAGC-TCCAAGGCA-C
62 ACGCTCAGCTTCGAGGGCATC
* * * * * * *
388104 ATTATTGCAGCATAGCTTAA-TCGAGAAGGGCTATC--TG-CCAAAGACC-CCGAGTTCGATTAC
1 A-T-TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTAC
*
388164 ACTCAGCTTCGAGGGCACATC
64 GCTCAGCTTCGAGGG--CATC
388185 ATTTACAGCATAACTCAAGGCTA-AAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGATTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGATTACG
* * *
388249 CTCAGCTCCAAGGCACATC
65 CTCAGCTTCGAGG-GCATC
** * * * * ** *
388268 ATTCGCAGCATAGCTTAAGTCGAGAAGGGTTATC--TG-CCAAAGACCCCCGAGTTCGATTACAC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACGC
388330 TCAGCTTCGAGGGCACATC
66 TCAGCTTCGAGGG--CATC
*
388349 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGATTACG
388414 CTCAGCT
65 CTCAGCT
388421 CCAAGGCACA
Statistics
Matches: 631, Mismatches: 122, Indels: 93
0.75 0.14 0.11
Matches are distributed among these distances:
75 5 0.01
76 34 0.05
77 23 0.04
78 57 0.09
79 57 0.09
80 97 0.15
81 97 0.15
82 22 0.03
83 86 0.14
84 72 0.11
85 48 0.08
86 3 0.00
87 30 0.05
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (82 bp):
ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACGC
TCAGCTTCGAGGGCATC
Found at i:388278 original size:325 final size:330
Alignment explanation
Indices: 387534--388470 Score: 1629
Period size: 325 Copynumber: 2.9 Consensus size: 330
387524 CATTTTTAAC
*
387534 AACTATTTACAAGCATAACTCAAGGCTAGAGGG-TATCTGTGACC-AAAGACCTTCGAGTTCGAC
1 AACTATTTAC-AGCATAACTCAAGGCTAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGAC
387597 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
65 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
387662 A-CCCCGAGTTCGATTACACTCAGCTTCGAGGG--CATCATTTACAGCATAACTCAAGGCTAGAA
130 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAA
387724 -GGTTATCTGTGACCAAAAGA-CTTCGAGTTCGACTACGCTCAGCTCC----CACATCATTCGCA
195 GGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT-GCA
387783 GCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGA
259 GCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGA
387848 GGGAACA
324 GGGAACA
387855 AACTATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGAC
1 AACTATTTACAGCATAACTCAAGGCTA-AAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGAC
387920 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
65 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
387985 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCA-TTACAGCATAACTCAAGGCTAGAA
130 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAA
* *
388049 GGGGTTATCTGTGAGCAAAAGACCTTCGAGTTCGACT-CGCTCAGCTCCAAGGCACATTATTGCA
195 -GGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTGCA
388113 GCATAGCTTAA-TCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATTACACTCAGCTTCGA
259 GCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGA
*
388176 GGGCAC-
324 GGGAACA
* *
388182 ATC-ATTTACAGCATAACTCAAGGCTAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGATT
1 AACTATTTACAGCATAACTCAAGGCTAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACT
* *
388246 ACGCTCAGCTCCAAGGCACATCATTCGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
388311 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
131 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
388376 GGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
196 GGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA-TTGCAG
*
388441 TATAGCTTAAGTCGAGAAGGGCTATCTGCC
260 CATAGCTTAAGTCGAGAAGGGCTATCTGCC
388471 TACGCTCAGC
Statistics
Matches: 588, Mismatches: 11, Indels: 27
0.94 0.02 0.04
Matches are distributed among these distances:
320 17 0.03
321 14 0.02
322 11 0.02
323 85 0.14
324 31 0.05
325 198 0.34
326 73 0.12
327 47 0.08
328 66 0.11
329 24 0.04
330 14 0.02
331 8 0.01
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (330 bp):
AACTATTTACAGCATAACTCAAGGCTAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
GGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTGCAGC
ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
GAACA
Found at i:388433 original size:165 final size:165
Alignment explanation
Indices: 387538--388470 Score: 1623
Period size: 165 Copynumber: 5.7 Consensus size: 165
387528 TTTAACAACT
387538 ATTTACAAGCATAACTCAAGGCTAG-AGGG-TATCTGTGACC-AAAGACCTTCGAGTTCGACTAC
1 ATTTAC-AGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
387600 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-C
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
387664 CCCGAGTTCGATTACACTCAGCTTCGAGGG--CATC
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
387698 ATTTACAGCATAACTCAAGGCTAGAA-GGTTATCTGTGACCAAAAGA-CTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
*
387761 CTCAGCTCC----CACATCATTCGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
* *
387822 CCGAGTTCGATTACACTCAGCTTCGAGGGAACAAAC
131 CCGAGTTCGATTACACTCAGCTTCGAGGGCAC-ATC
387858 TATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
1 -ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
387923 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
387988 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
*
388024 A-TTACAGCATAACTCAAGGCTAGAAGGGGTTATCTGTGAGCAAAAGACCTTCGAGTTCGACT-C
1 ATTTACAGCATAACTCAAGGCTAGAA-GGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
*
388087 GCTCAGCTCCAAGGCACATTA-TTGCAGCATAGCTTAA-TCGAGAAGGGCTATCTGCCAAAGA-C
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
388149 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
*
388185 ATTTACAGCATAACTCAAGGCTA-AAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGATTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
* *
388249 CTCAGCTCCAAGGCACATCATTCGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
388314 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
131 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
388349 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
*
388414 CTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
388471 TACGCTCAGC
Statistics
Matches: 736, Mismatches: 16, Indels: 37
0.93 0.02 0.05
Matches are distributed among these distances:
156 48 0.07
157 31 0.04
159 21 0.03
160 80 0.11
161 92 0.12
162 80 0.11
163 65 0.09
164 105 0.14
165 130 0.18
166 2 0.00
167 82 0.11
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (165 bp):
ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
Found at i:388483 original size:61 final size:61
Alignment explanation
Indices: 388409--388531 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
388399 TCGAGTTCGA
388409 CTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGC
1 CTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGC
388470 CTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGC
1 CTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGC
388531 C
1 C
388532 AAAGACCCTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (61 bp):
CTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGC
Found at i:388623 original size:226 final size:226
Alignment explanation
Indices: 388245--388696 Score: 762
Period size: 226 Copynumber: 2.0 Consensus size: 226
388235 CGAGTTCGAT
*
388245 TACGCTCAGCTCCAAGGCACATCATTCGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAG
1 TACGCTCAGCTCCAAGGCACATCATTCGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
** * *
388310 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAA
66 ACCCCAAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAGCATAACTCAAGGCTAGAA
*
388375 GGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCA
131 GGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATATGCA
*
388440 GTATAGCTTAAGTCGAGAAGGGCTATCTGCC
196 GCATAGCTTAAGTCGAGAAGGGCTATCTGCC
* *
388471 TACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
1 TACGCTCAGCTCCAAGGCACATCATTCGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* *
388536 ACCCTTAAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGA
66 ACCC-CAAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAGCATAACTCAAGGCTAGA
* * *
388601 AGGGTTATCTGTTAGC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATATGC
130 AGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATATGC
388665 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
195 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
388697 AAAGACTCCC
Statistics
Matches: 211, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
226 143 0.68
227 68 0.32
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (226 bp):
TACGCTCAGCTCCAAGGCACATCATTCGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
ACCCCAAAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAGCATAACTCAAGGCTAGAA
GGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATATGCA
GCATAGCTTAAGTCGAGAAGGGCTATCTGCC
Found at i:388693 original size:83 final size:81
Alignment explanation
Indices: 388470--388702 Score: 279
Period size: 82 Copynumber: 2.8 Consensus size: 81
388460 GGCTATCTGC
*
388470 CTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
1 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
388535 GACCCTTAAAGTTCGA
66 GACCCTTAAAGTTCGA
* * * * * * * * * * * *
388551 TTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAG
1 CTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---C
**
388616 CAAAGA-CCTTTGAGTTCGA
62 CAAAGACCCTTAAAGTTCGA
*
388635 CTACGCTCAGCTCCAAGGCACATCATATGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
1 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
388700 GAC
66 GAC
388703 TCCCGAGTTC
Statistics
Matches: 119, Mismatches: 28, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
80 6 0.05
81 13 0.11
82 35 0.29
83 35 0.29
84 24 0.20
85 6 0.05
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (81 bp):
CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
GACCCTTAAAGTTCGA
Found at i:389420 original size:33 final size:33
Alignment explanation
Indices: 389340--389491 Score: 121
Period size: 33 Copynumber: 4.5 Consensus size: 33
389330 TTATATAGTG
* **
389340 TGAAATCATTTTGAAAATTATATAATATATGGTTTT
1 TGAAAACATTTTGAAAA-TATAT-ATATAT-AATTT
** *
389376 TTTAAATATTTTGAAAATATATATATATAATTT
1 TGAAAACATTTTGAAAATATATATATATAATTT
*
389409 TGAAAACATTTTGAAAATGCATAT-TATAT-GTTT
1 TGAAAACATTTTGAAAAT--ATATATATATAATTT
* ** *
389442 TGAAAACTTTTTTTAAATATATATA-ATAGCTTT
1 TGAAAACATTTTGAAAATATATATATATA-ATTT
*
389475 TAAAAACATTTTGAAAA
1 TGAAAACATTTTGAAAA
389492 ACGTATATAT
Statistics
Matches: 93, Mismatches: 18, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
31 6 0.06
32 2 0.02
33 52 0.56
34 11 0.12
35 9 0.10
36 13 0.14
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (33 bp):
TGAAAACATTTTGAAAATATATATATATAATTT
Found at i:389541 original size:35 final size:35
Alignment explanation
Indices: 389501--389626 Score: 170
Period size: 33 Copynumber: 3.6 Consensus size: 35
389491 AACGTATATA
*
389501 TTTGAAAATTAG-TTTCTAAATATATATTATATAGT
1 TTTGAAAATTAGTTTTTTAAA-ATATATTATATAGT
*
389536 TTTGAAAATTAGTTTTTTAAAAAATA-TAT-TAGT
1 TTTGAAAATTAGTTTTTTAAAATATATTATATAGT
389569 TTTGAAAATTAGTTTTTTAAAATATATT-TATAGTT
1 TTTGAAAATTAGTTTTTTAAAATATATTATATAG-T
*
389604 TTTGAAAATTATTTTTTTTAAAA
1 TTTGAAAATTA-GTTTTTTAAAA
389627 AACATATATT
Statistics
Matches: 82, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
33 30 0.37
34 7 0.09
35 28 0.34
36 17 0.21
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.52
Consensus pattern (35 bp):
TTTGAAAATTAGTTTTTTAAAATATATTATATAGT
Found at i:389579 original size:68 final size:69
Alignment explanation
Indices: 389501--389633 Score: 200
Period size: 68 Copynumber: 1.9 Consensus size: 69
389491 AACGTATATA
*
389501 TTTGAAAATTAG-TTTCTAAATATATATTATATAG-TTTTGAAAATTA-GTTTTTTAAAAAATAT
1 TTTGAAAATTAGTTTTCTAAA-ATATATT-TATAGTTTTTGAAAATTATGTTTTTTAAAAAACAT
389563 ATTAGT
64 ATTAGT
* *
389569 TTTGAAAATTAGTTTTTTAAAATATATTTATAGTTTTTGAAAATTATTTTTTTTAAAAAACATAT
1 TTTGAAAATTAGTTTTCTAAAATATATTTATAGTTTTTGAAAATTATGTTTTTTAAAAAACATAT
389634 ATTGTATAGT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
67 5 0.08
68 31 0.53
69 23 0.39
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.50
Consensus pattern (69 bp):
TTTGAAAATTAGTTTTCTAAAATATATTTATAGTTTTTGAAAATTATGTTTTTTAAAAAACATAT
TAGT
Found at i:389616 original size:20 final size:21
Alignment explanation
Indices: 389578--389617 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
389568 TTTTGAAAAT
*
389578 TAGTTTTTTAAAATATATTTA
1 TAGTTTTTGAAAATATATTTA
389599 TAGTTTTTGAAAAT-TATTT
1 TAGTTTTTGAAAATATATTT
389618 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TAGTTTTTGAAAATATATTTA
Found at i:389685 original size:4 final size:4
Alignment explanation
Indices: 389656--389724 Score: 65
Period size: 4 Copynumber: 17.5 Consensus size: 4
389646 TAAAAATGTT
* *
389656 TTTA ATTA TTTA -TTA GTTTA TCTA TTTA TTTA TTTA TTT- TATTA TTT-
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA
389703 TTT- TTTCA TTTA TTTA TTTA TT
1 TTTA TTT-A TTTA TTTA TTTA TT
389725 ATTGTTCAGG
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
3 10 0.18
4 38 0.69
5 7 0.13
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:389894 original size:16 final size:15
Alignment explanation
Indices: 389873--389903 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
389863 GGCCGGCCGG
389873 CATCCCGGGACTGACC
1 CATCCCGGGA-TGACC
389889 CATCCCGGGATGACC
1 CATCCCGGGATGACC
389904 GTCATACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (15 bp):
CATCCCGGGATGACC
Found at i:391566 original size:20 final size:19
Alignment explanation
Indices: 391529--391572 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
391519 AAAGTTTTTA
391529 AAAT-AAAAAATAAGAATT
1 AAATAAAAAAATAAGAATT
*
391547 AAATAAAAAAATAATTAATT
1 AAATAAAAAAATAA-GAATT
391567 AAATAA
1 AAATAA
391573 TTTAAAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.17
19 9 0.39
20 10 0.43
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
AAATAAAAAAATAAGAATT
Found at i:393152 original size:18 final size:18
Alignment explanation
Indices: 393129--393171 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
393119 AAGAAACATA
393129 ACCTAAACACTATAATAT
1 ACCTAAACACTATAATAT
393147 ACCTAAACACTATAATAT
1 ACCTAAACACTATAATAT
*
393165 GCCTAAA
1 ACCTAAA
393172 TAAGCTAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.23, G:0.02, T:0.26
Consensus pattern (18 bp):
ACCTAAACACTATAATAT
Found at i:401577 original size:13 final size:13
Alignment explanation
Indices: 401559--401605 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
401549 AATGATAAAT
*
401559 AATAAAAAATTAC
1 AATAAAAAACTAC
* *
401572 AAT-AAAAAGTCC
1 AATAAAAAACTAC
*
401584 AATAAACAACTAC
1 AATAAAAAACTAC
401597 AATAAAAAA
1 AATAAAAAA
401606 GTACTAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.68, C:0.13, G:0.02, T:0.17
Consensus pattern (13 bp):
AATAAAAAACTAC
Found at i:401756 original size:21 final size:21
Alignment explanation
Indices: 401727--401767 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
401717 TTGTGACTCC
*
401727 TCGCTATCATCATCATCGCCA
1 TCGCCATCATCATCATCGCCA
401748 TCGCCATCATCATCATCGCC
1 TCGCCATCATCATCATCGCC
401768 GTTGTTGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.41, G:0.10, T:0.27
Consensus pattern (21 bp):
TCGCCATCATCATCATCGCCA
Found at i:402109 original size:33 final size:33
Alignment explanation
Indices: 402048--402110 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
402038 GCCTCCAGGA
* * *
402048 GGGGTCATAAAACTCTGTGACGGTGGCGGCAAC
1 GGGGTCATAAAACTCGGTGAAGGCGGCGGCAAC
402081 GGGGTCATAAAAC-CAGGTGAAGGCGGCGGC
1 GGGGTCATAAAACTC-GGTGAAGGCGGCGGC
402111 GGCGACATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.25, C:0.21, G:0.40, T:0.14
Consensus pattern (33 bp):
GGGGTCATAAAACTCGGTGAAGGCGGCGGCAAC
Found at i:403882 original size:9 final size:9
Alignment explanation
Indices: 403850--403901 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
403840 TCTGCAAAAA
*
403850 AAATTATAT
1 AAATTAAAT
*
403859 AAGTTAAAT
1 AAATTAAAT
403868 --ATTAAAT
1 AAATTAAAT
403875 AAATTAAAT
1 AAATTAAAT
*
403884 -ACTTAAAT
1 AAATTAAAT
403892 AAATTAAAT
1 AAATTAAAT
403901 A
1 A
403902 TAAAATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (9 bp):
AAATTAAAT
Found at i:403891 original size:17 final size:16
Alignment explanation
Indices: 403852--403908 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
403842 TGCAAAAAAA
* *
403852 ATTATATAAGTTAAAT
1 ATTAAATAAATTAAAT
403868 ATTAAATAAATTAAAT
1 ATTAAATAAATTAAAT
403884 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
*
403901 ATAAAATA
1 ATTAAATA
403909 TTAAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:404851 original size:20 final size:19
Alignment explanation
Indices: 404814--404874 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 19
404804 TTATCGATCC
*
404814 AAAATGAT-ATACCAGGTAA
1 AAAATGATAAAACC-GGTAA
404833 AAATATGATAAAACCGGTAA
1 AAA-ATGATAAAACCGGTAA
404853 CAAAATGATAAAACCGGTAA
1 -AAAATGATAAAACCGGTAA
404873 AA
1 AA
404875 TGTTACCGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 5 0.13
20 26 0.68
21 7 0.18
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.18
Consensus pattern (19 bp):
AAAATGATAAAACCGGTAA
Found at i:404970 original size:181 final size:182
Alignment explanation
Indices: 404616--405088 Score: 678
Period size: 181 Copynumber: 2.6 Consensus size: 182
404606 GATCCAAATT
* * * * **
404616 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * * *
404681 AAATCGGTAAAGTGCTACCGTATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAATGATACCGAATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * * *
404746 GTGAATTTAAAAGAGAAGCAGTTTTAAATCTTATAAAGTGTCGATACTTTTA
131 GGGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* * * *
404798 AAAAATTTATCGATCCAAAATGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
404863 AAACCGGTAAAATGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAATGATACCGAATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
404927 GGGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GGGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
404979 AAAAATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
405044 AAACCGGTAAAATGATACCGAATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAATGATACCGAATATATTGAAAGTGTCGATACTTT
405089 CGTAAGTTCG
Statistics
Matches: 259, Mismatches: 32, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
181 165 0.64
182 94 0.36
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAATGATACCGAATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GGGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:405057 original size:17 final size:19
Alignment explanation
Indices: 405018--405060 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
405008 ATGTAAAAAT
405018 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
405038 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
405055 ATGATA
1 ATGATA
405061 CCGAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:407309 original size:21 final size:21
Alignment explanation
Indices: 407283--407347 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
407273 AAGACAATCA
*
407283 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
407304 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
407325 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
407346 AG
1 AG
407348 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:407423 original size:33 final size:33
Alignment explanation
Indices: 407381--407446 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
407371 AAATAGATGG
*
407381 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
407414 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
407447 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:409249 original size:19 final size:19
Alignment explanation
Indices: 409225--409273 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
409215 AATGTAGGGT
409225 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
409244 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
409263 TAATTTTGTAT
1 TAATTTTGTAT
409274 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:410030 original size:201 final size:200
Alignment explanation
Indices: 409386--410327 Score: 1652
Period size: 201 Copynumber: 4.7 Consensus size: 200
409376 AATTTACAAT
*
409386 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
409451 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTGCAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* ** * *
409516 ATGAGAGAATAGGTCTAAATAATGCATCGACACTTTTTTAGTTTGTGTCGATATTTCTGGTCCAG
131 ATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
409581 AATGA
196 AATGA
* *
409586 ATGGCAAACATGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
409651 CGAAAACCAAAAGTATAATGTAATAGGTAAATTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
409716 ATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
409781 AATGA
196 AATGA
409786 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAACA-TGTCGATCCCATAAACA
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAA-AGTGTCGATCCCATAAACA
409850 TCGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
65 TCGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGG-TT
* *
409915 TTATGAGAGAATAGGTCTTACTAATGTGTCGACACTTTTGTACTTTGTGTCGATATTTTTGGTCC
129 TTATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCC
409980 AGAATGA
194 AGAATGA
* *
409987 ATGGCAAATATGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
410052 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGTTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGG-TTT
* *
410117 TATGAGAGAATAGGTCTTACTAATATGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
130 TATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
410182 GAATGA
195 GAATGA
*
410188 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
410253 CGAAAAACAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
410318 ATGAGAGAAT
131 ATGAGAGAAT
410328 TGTTATATAA
Statistics
Matches: 711, Mismatches: 28, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
200 324 0.46
201 387 0.54
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:410320 original size:401 final size:400
Alignment explanation
Indices: 409386--410327 Score: 1677
Period size: 401 Copynumber: 2.4 Consensus size: 400
409376 AATTTACAAT
* *
409386 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCATAAACAT
* * *
409451 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTGCAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
409516 ATGAGAGAATAGGTCTAAATAATGCATCGACACTTTTTTAGTTTGTGTCGATATTTCTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGCATCGACACTTTTGTACTTTGTGTCGATATTTCTGGTCCAG
409581 AATGAATGGCAAACATGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
196 AATGAATGGCAAACATGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
409646 AACATCGAAAACCAAAAGTATAATGTAATAGGTAAATTTTCAATCTAACCGGTACAAGTATACCG
261 AACATCGAAAACCAAAAGTATAATGTAATAGGTAAATTTTCAATCTAACCGGTACAAGTATACCG
*
409711 GTTTTATGAGAGAATAGGTCTTAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
326 GTTTTATGAGAGAATAGGTCTTAATAATATGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
409776 TCCAGAATGA
391 TCCAGAATGA
*
409786 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAACATGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCATAAACAT
409851 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGG-TTT
* * ** *
409916 TATGAGAGAATAGGTCTTACTAATGTGTCGACACTTTTGTACTTTGTGTCGATATTTTTGGTCCA
130 TATGAGAGAATAGGTCTAAATAATGCATCGACACTTTTGTACTTTGTGTCGATATTTCTGGTCCA
* *
409981 GAATGAATGGCAAATATGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAT
195 GAATGAATGGCAAACATGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAT
* *
410046 AAACATCGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGTTACAAGTATACC
260 AAACATCGAAAACCAAAAGTATAATGTAATAGGTAAATTTTCAATCTAACCGGTACAAGTATACC
*
410111 GGTTTTTATGAGAGAATAGGTCTTACTAATATGTCGACACTTTTGTAGTTTGTGTCGATATTTTT
325 GG-TTTTATGAGAGAATAGGTCTTAATAATATGTCGACACTTTTGTAGTTTGTGTCGATATTTTT
410176 GGTCCAGAATGA
389 GGTCCAGAATGA
410188 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCATAAACAT
* *
410253 CGAAAAACAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
410318 ATGAGAGAAT
131 ATGAGAGAAT
410328 TGTTATATAA
Statistics
Matches: 518, Mismatches: 22, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
400 120 0.23
401 203 0.39
402 195 0.38
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (400 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCATAAACAT
CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGCATCGACACTTTTGTACTTTGTGTCGATATTTCTGGTCCAG
AATGAATGGCAAACATGCTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
AACATCGAAAACCAAAAGTATAATGTAATAGGTAAATTTTCAATCTAACCGGTACAAGTATACCG
GTTTTATGAGAGAATAGGTCTTAATAATATGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
TCCAGAATGA
Found at i:411867 original size:6 final size:6
Alignment explanation
Indices: 411856--411955 Score: 101
Period size: 6 Copynumber: 16.7 Consensus size: 6
411846 CGAGCGGTCA
* * * * *
411856 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * * *
411904 ATGATG ATGAAG ATGACG ATGAAG ATGACG ATGATG ATGATG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
411952 ATGA
1 ATGA
411956 TCCAAACAAG
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.22
Consensus pattern (6 bp):
ATGAAG
Found at i:411913 original size:36 final size:36
Alignment explanation
Indices: 411873--411955 Score: 157
Period size: 36 Copynumber: 2.3 Consensus size: 36
411863 TGAAGCTGAC
411873 GATGAAGATGACGATGAAGATGACGATGATGATGAT
1 GATGAAGATGACGATGAAGATGACGATGATGATGAT
411909 GATGAAGATGACGATGAAGATGACGATGATGATGAT
1 GATGAAGATGACGATGAAGATGACGATGATGATGAT
*
411945 GATGATGATGA
1 GATGAAGATGA
411956 TCCAAACAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.39, C:0.05, G:0.34, T:0.23
Consensus pattern (36 bp):
GATGAAGATGACGATGAAGATGACGATGATGATGAT
Found at i:411956 original size:12 final size:12
Alignment explanation
Indices: 411856--411955 Score: 137
Period size: 12 Copynumber: 8.3 Consensus size: 12
411846 CGAGCGGTCA
*
411856 ATGAAGATGAAG
1 ATGACGATGAAG
*
411868 CTGACGATGAAG
1 ATGACGATGAAG
411880 ATGACGATGAAG
1 ATGACGATGAAG
*
411892 ATGACGATGATG
1 ATGACGATGAAG
*
411904 ATGATGATGAAG
1 ATGACGATGAAG
411916 ATGACGATGAAG
1 ATGACGATGAAG
*
411928 ATGACGATGATG
1 ATGACGATGAAG
* *
411940 ATGATGATGATG
1 ATGACGATGAAG
411952 ATGA
1 ATGA
411956 TCCAAACAAG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 79 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Done.