Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 34 of 34
Found at i:5390426 original size:35 final size:36
Alignment explanation
Indices: 5390387--5390488 Score: 120
Period size: 35 Copynumber: 2.9 Consensus size: 36
5390377 ATTCTCAAGG
5390387 GAGGCTTTAAAA-TCTTAGTTGAAATATCCTCGAA-A
1 GAGGCTTTAAAAGT-TTAGTTGAAATATCCTCGAATA
* * **
5390422 GAGGCTTCAAAAGTTTTAGATGAAATAT-CTTTAATA
1 GAGGCTTTAAAAG-TTTAGTTGAAATATCCTCGAATA
*
5390458 GAGGCTTTAAAAGTTTGGTTGAAATATCCTC
1 GAGGCTTTAAAAGTTTAGTTGAAATATCCTC
5390489 AAGAAAGGCT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
35 27 0.49
36 27 0.49
37 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (36 bp):
GAGGCTTTAAAAGTTTAGTTGAAATATCCTCGAATA
Found at i:5390448 original size:71 final size:71
Alignment explanation
Indices: 5390373--5390536 Score: 181
Period size: 71 Copynumber: 2.3 Consensus size: 71
5390363 GCTTTTGCCA
* * *
5390373 AAATATTCTCAAGGGAGGCTTTAAAA-TCTTAGTTGAAATATCCTCGAA-AGAGGCTTCAAAAGT
1 AAATATTCTCAAGAGAGGCTTTAAAAGT-TTAGTTGAAATATCCTC-AAGAAAGGCTTCAAAAGA
5390436 TTTAGATG
64 TTTAGATG
* * * * *
5390444 AAATA-TCTTTAATAGAGGCTTTAAAAGTTTGGTTGAAATATCCTCAAGAAAGGCTTCAGATGAT
1 AAATATTC-TCAAGAGAGGCTTTAAAAGTTTAGTTGAAATATCCTCAAGAAAGGCTTCAAAAGAT
*
5390508 TTGGATG
65 TTAGATG
* *
5390515 AAATATCCTCCAGAGAGGCTTT
1 AAATATTCTCAAGAGAGGCTTT
5390537 GAAGTGTTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
70 4 0.05
71 70 0.92
72 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (71 bp):
AAATATTCTCAAGAGAGGCTTTAAAAGTTTAGTTGAAATATCCTCAAGAAAGGCTTCAAAAGATT
TAGATG
Found at i:5390498 original size:35 final size:34
Alignment explanation
Indices: 5390157--5390536 Score: 175
Period size: 36 Copynumber: 10.9 Consensus size: 34
5390147 TGCGGAAGTC
* * *
5390157 TTTGCTGAAATATCCTCAAGAAAGGCTTT-AAAT
1 TTTGTTGAAATATCCTCAAGAGAGGCTTTAAAAG
* * * *
5390190 TTTGGTTTAAATATCCTCGAGAGATGCTTTAAAACT
1 TTT-GTTGAAATATCCTCAAGAGAGGCTTTAAAA-G
* * * * *
5390226 TTTAGATAAAATATCCTTAA-AAAGGCTTTAGAAG
1 TTT-GTTGAAATATCCTCAAGAGAGGCTTTAAAAG
* * * * ** *
5390260 TCT-TTAATAATCATCATCAATAGAGGCTTTGGAGG
1 TTTGTTGA-AAT-ATCCTCAAGAGAGGCTTTAAAAG
* *
5390295 TTT-TTGAAAAATCCTCAA-AGAAGGCTTTGAAAG
1 TTTGTTGAAATATCCTCAAGAG-AGGCTTTAAAAG
* * *
5390328 TTTTTAATGAAATATGCCT-AAGAGAGGCTTTGAATG
1 TTTGT--TGAAATAT-CCTCAAGAGAGGCTTTAAAAG
* * *
5390364 CTT-TTGCCAAAATATTCTCAAGGGAGGCTTTAAAA-
1 TTTGTTG---AAATATCCTCAAGAGAGGCTTTAAAAG
*
5390399 TCTTAGTTGAAATATCCTCGAA-AGAGGCTTCAAAAG
1 T-TT-GTTGAAATATCCTC-AAGAGAGGCTTTAAAAG
* * * *
5390435 TTTTAGATGAAATATCTTTAATAGAGGCTTTAAAAG
1 -TTT-GTTGAAATATCCTCAAGAGAGGCTTTAAAAG
* * * *
5390471 TTTGGTTGAAATATCCTCAAGAAAGGCTTCAGATG
1 TTT-GTTGAAATATCCTCAAGAGAGGCTTTAAAAG
* *
5390506 ATTTGGATGAAATATCCTCCAGAGAGGCTTT
1 -TTT-GTTGAAATATCCTCAAGAGAGGCTTT
5390537 GAAGTGTTTA
Statistics
Matches: 268, Mismatches: 55, Indels: 45
0.73 0.15 0.12
Matches are distributed among these distances:
32 5 0.02
33 28 0.10
34 32 0.12
35 80 0.30
36 114 0.43
37 6 0.02
38 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (34 bp):
TTTGTTGAAATATCCTCAAGAGAGGCTTTAAAAG
Found at i:5391869 original size:153 final size:153
Alignment explanation
Indices: 5391695--5392322 Score: 738
Period size: 153 Copynumber: 4.1 Consensus size: 153
5391685 CCATAGAATT
* *
5391695 AGTTTTGA-AAATTTTAATTTATTTTATGAGTTTTAAAATTTTTCTTACTATCAAAATACGAAGT
1 AGTTTTGACAAA-TTCAATTTATTTTATGAGTTTTAAAATTTTTCTTATTATCAAAATACGAAGT
*
5391759 TTTATACTCCATCAATTTTTTGTTAGGATTTTTCT-AAGTTTATAATTTTTAAAATTCTTCAAAT
65 TTTATACTCCATAAATTTTTTG-TAGGATTTTTCTAAAGTTTATAATTTTTAAAATTCTTCAAAT
*
5391823 TTTATTGTTTAATTGATATTAAATC
129 ATTATTGTTTAATTGATATTAAATC
* * *
5391848 AGTTTTGACAAATTCAATTTATTTTATGAGTTTTAGAATTTTTCTTATTATGAAAATACGGAGTT
1 AGTTTTGACAAATTCAATTTATTTTATGAGTTTTAAAATTTTTCTTATTATCAAAATACGAAGTT
* * * *
5391913 TTCTACTTCGT-AATTTTTTAGTAAGATTTTT-TGAAAGTTTAT-ATTTTTCAAAATTCATT-AA
66 TTATACTCCATAAATTTTTT-GTAGGATTTTTCT-AAAGTTTATAATTTTT-AAAATTC-TTCAA
*
5391974 ATATTATTATTTAATTGATATTAAATC
127 ATATTATTGTTTAATTGATATTAAATC
* ** * * * *
5392001 ATTTTTGACAAATTCAATTTATTTTACAAGTTTT-TAATTTTTTTTGTTATCGAAATAC-AGAGT
1 AGTTTTGACAAATTCAATTTATTTTATGAGTTTTAAAATTTTTCTTATTATCAAAATACGA-AGT
* * *
5392064 TTTCA-ACTCCGTAAATTTTTTGGTAGGATTTTTCTAAAGTTTATAAATTTTAAAATTCTCCAAA
65 TTT-ATACTCCATAAATTTTTT-GTAGGATTTTTCTAAAGTTTATAATTTTTAAAATTCTTCAAA
* *
5392128 TATTATTGTTTAATTAATATTAAATA
128 TATTATTGTTTAATTGATATTAAATC
* * * *
5392154 ATTTTTGAAAAATTTAATTTATTTTATGAGTTTTAAAATTTTT-TCTATTATCGAAATACGAAGT
1 AGTTTTGACAAATTCAATTTATTTTATGAGTTTTAAAATTTTTCT-TATTATCAAAATACGAAGT
* * * * * *
5392218 TTTCTACTCCAAAAATTTTTCAGTAGGATTTTT-TTAAGTTTATAATTTTCAAAATTCTTAAAAT
65 TTTATACTCCATAAATTTTT-TGTAGGATTTTTCTAAAGTTTATAATTTTTAAAATTCTTCAAAT
* *
5392282 ATTATTTTTTTAATTCATATTAAATC
129 ATTA-TTGTTTAATTGATATTAAATC
5392308 AGTTTTGAACAAATT
1 AGTTTTG-ACAAATT
5392323 TTTCTTTAAT
Statistics
Matches: 407, Mismatches: 49, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
151 1 0.00
152 55 0.14
153 259 0.64
154 85 0.21
155 7 0.02
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (153 bp):
AGTTTTGACAAATTCAATTTATTTTATGAGTTTTAAAATTTTTCTTATTATCAAAATACGAAGTT
TTATACTCCATAAATTTTTTGTAGGATTTTTCTAAAGTTTATAATTTTTAAAATTCTTCAAATAT
TATTGTTTAATTGATATTAAATC
Found at i:5392150 original size:306 final size:307
Alignment explanation
Indices: 5391695--5392322 Score: 833
Period size: 306 Copynumber: 2.0 Consensus size: 307
5391685 CCATAGAATT
* **
5391695 AGTTTTGA-AAATTTTAATTTATTTTATGAGTTTTAAAATTTTTCTTACTATCAAAATACGAAGT
1 AGTTTTGACAAA-TTCAATTTATTTTACAAGTTTTAAAATTTTTCTTACTATCAAAATACGAAGT
* * * * *
5391759 TTTATACTCCATCAATTTTTTGTTAGGATTTTTCTAAGTTTATAATTTTTAAAATTCTTCAAATT
65 TTTATACTCCATAAATTTTTTGGTAGGATTTTTCTAAGTTTATAAATTTTAAAATTCTCCAAATA
* * * *
5391824 TTATTGTTTAATTGATATTAAATCAGTTTTGACAAATTCAATTTATTTTATGAGTTTTAGAA-TT
130 TTATTGTTTAATTAATATTAAATAAGTTTTGAAAAATTCAATTTATTTTATGAGTTTTAAAATTT
* * ** *
5391888 TTTCTTATTAT-GAAAATACGGAGTTTTCTACTTC-GTAATTTTTTAGTAAGATTTTTTGAAAGT
195 TTTC-TATTATCG-AAATACGAAGTTTTCTACTCCAAAAATTTTTCAGTAAGATTTTTT-AAAGT
* *
5391951 TTATATTTTTCAAAATTCATT-AAATATTA-TTATTTAATTGATATTAAATC
257 TTATAATTTTCAAAATTC-TTAAAATATTATTTATTTAATTCATATTAAATC
* * * ** *
5392001 ATTTTTGACAAATTCAATTTATTTTACAAGTTTT-TAATTTTTTTTGTTATCGAAATAC-AGAGT
1 AGTTTTGACAAATTCAATTTATTTTACAAGTTTTAAAATTTTTCTTACTATCAAAATACGA-AGT
*
5392064 TTTCA-ACTCCGTAAATTTTTTGGTAGGATTTTTCTAAAGTTTATAAATTTTAAAATTCTCCAAA
65 TTT-ATACTCCATAAATTTTTTGGTAGGATTTTTCT-AAGTTTATAAATTTTAAAATTCTCCAAA
* *
5392128 TATTATTGTTTAATTAATATTAAATAATTTTTGAAAAATTTAATTTATTTTATGAGTTTTAAAAT
128 TATTATTGTTTAATTAATATTAAATAAGTTTTGAAAAATTCAATTTATTTTATGAGTTTTAAAAT
* *
5392193 TTTTTCTATTATCGAAATACGAAGTTTTCTACTCCAAAAATTTTTCAGTAGGATTTTTTTAAGTT
193 TTTTTCTATTATCGAAATACGAAGTTTTCTACTCCAAAAATTTTTCAGTAAGATTTTTTAAAGTT
*
5392258 TATAATTTTCAAAATTCTTAAAATATTATTTTTTTAATTCATATTAAATC
258 TATAATTTTCAAAATTCTTAAAATATTATTTATTTAATTCATATTAAATC
5392308 AGTTTTGAACAAATT
1 AGTTTTG-ACAAATT
5392323 TTTCTTTAAT
Statistics
Matches: 280, Mismatches: 32, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
304 1 0.00
305 54 0.19
306 164 0.59
307 54 0.19
308 7 0.03
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (307 bp):
AGTTTTGACAAATTCAATTTATTTTACAAGTTTTAAAATTTTTCTTACTATCAAAATACGAAGTT
TTATACTCCATAAATTTTTTGGTAGGATTTTTCTAAGTTTATAAATTTTAAAATTCTCCAAATAT
TATTGTTTAATTAATATTAAATAAGTTTTGAAAAATTCAATTTATTTTATGAGTTTTAAAATTTT
TTCTATTATCGAAATACGAAGTTTTCTACTCCAAAAATTTTTCAGTAAGATTTTTTAAAGTTTAT
AATTTTCAAAATTCTTAAAATATTATTTATTTAATTCATATTAAATC
Found at i:5392519 original size:16 final size:17
Alignment explanation
Indices: 5392492--5392548 Score: 91
Period size: 16 Copynumber: 3.5 Consensus size: 17
5392482 CATTGCTGAG
*
5392492 AATTGATTTTAATTTTA
1 AATTTATTTTAATTTTA
5392509 AATTT-TTTTAATTTTA
1 AATTTATTTTAATTTTA
5392525 AATTTATTTT-ATTTTA
1 AATTTATTTTAATTTTA
5392541 AATTTATT
1 AATTTATT
5392549 AGGTAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
16 30 0.79
17 8 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
AATTTATTTTAATTTTA
Found at i:5397848 original size:20 final size:20
Alignment explanation
Indices: 5397823--5397876 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
5397813 CTACCACTGT
*
5397823 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
5397843 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
5397863 TTGTATCGATACAT
1 TTGTATCGATACAT
5397877 TGCTTGCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:5404067 original size:13 final size:13
Alignment explanation
Indices: 5404049--5404075 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5404039 ACAACATTCC
5404049 TTGTATCGATACA
1 TTGTATCGATACA
5404062 TTGTATCGATACA
1 TTGTATCGATACA
5404075 T
1 T
5404076 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5406515 original size:13 final size:13
Alignment explanation
Indices: 5406497--5406523 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5406487 ACATTATGCT
5406497 TTGTATCGATACA
1 TTGTATCGATACA
5406510 TTGTATCGATACA
1 TTGTATCGATACA
5406523 T
1 T
5406524 GCAACTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5406587 original size:13 final size:13
Alignment explanation
Indices: 5406569--5406601 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5406559 CGAGACATGG
5406569 TACATTGTATCGA
1 TACATTGTATCGA
*
5406582 TACATTGTATTGA
1 TACATTGTATCGA
5406595 TACATTG
1 TACATTG
5406602 CTTGTAACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:5412327 original size:62 final size:62
Alignment explanation
Indices: 5412272--5412425 Score: 218
Period size: 69 Copynumber: 2.4 Consensus size: 62
5412262 TCTGTATTTT
5412272 TGACCCAAATGTATCGATACATTTTTCATTGTATTGTTACATATTAATACATTCTGGGTTTC
1 TGACCCAAATGTATCGATACATTTTTCATTGTATTGTTACATATTAATACATTCTGGGTTTC
* * *
5412334 TAACCCAAATGTATTATGTATCAATACATTTTTCATTGTATTGTTACATATCAATACATTCTGGG
1 TGACCC--A---A--ATGTATCGATACATTTTTCATTGTATTGTTACATATTAATACATTCTGGG
5412399 TTTC
59 TTTC
5412403 TGACCCAAATGTATCGATACATT
1 TGACCCAAATGTATCGATACATT
5412426 CTTTAATATA
Statistics
Matches: 80, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
62 19 0.24
64 2 0.03
67 2 0.03
69 57 0.71
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (62 bp):
TGACCCAAATGTATCGATACATTTTTCATTGTATTGTTACATATTAATACATTCTGGGTTTC
Found at i:5412391 original size:69 final size:69
Alignment explanation
Indices: 5412280--5412416 Score: 247
Period size: 69 Copynumber: 2.0 Consensus size: 69
5412270 TTTGACCCAA
* *
5412280 ATGTATCGATACATTTTTCATTGTATTGTTACATATTAATACATTCTGGGTTTCTAACCCAAATG
1 ATGTATCAATACATTTTTCATTGTATTGTTACATATCAATACATTCTGGGTTTCTAACCCAAATG
5412345 TATT
66 TATT
*
5412349 ATGTATCAATACATTTTTCATTGTATTGTTACATATCAATACATTCTGGGTTTCTGACCCAAATG
1 ATGTATCAATACATTTTTCATTGTATTGTTACATATCAATACATTCTGGGTTTCTAACCCAAATG
5412414 TAT
66 TAT
5412417 CGATACATTC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (69 bp):
ATGTATCAATACATTTTTCATTGTATTGTTACATATCAATACATTCTGGGTTTCTAACCCAAATG
TATT
Found at i:5417252 original size:117 final size:118
Alignment explanation
Indices: 5417068--5417297 Score: 340
Period size: 117 Copynumber: 2.0 Consensus size: 118
5417058 ATTAAATTAA
*
5417068 TTCTAAAAAATTAATTCATTTTCAGGAGTTTTGAATTTTTTTCTTTGAAATTCCTCTTTCCCTAA
1 TTCTAAAAAATTAATTCATTTTCAGGAGTTTTGAATGTTTTTCTTTGAAATTCCTCTTTCCCT-A
*
5417133 AAAACCGAGTTT-CTACTCTGTAAATATTTTCGAGAGGA-TTTTCTTAGATCAG
65 AAAACCGAGTTTCCTACTCCGTAAATATTTTCGAGAGGATTTTTCTTAGATCAG
* * * * *
5417185 TTCTGAAAAATTAATTCATTTTTATGAGTTTTGAA-GTTTTTCTTTGAAATTTCTCTTTCCTTGA
1 TTCTAAAAAATTAATTCATTTTCAGGAGTTTTGAATGTTTTTCTTTGAAATTCCTCTTTCCCT-A
* *
5417249 AAAACCGAGTTTCCTACTCCGTAAATATTTTTGGGAGGATTTTTCTTAG
65 AAAACCGAGTTTCCTACTCCGTAAATATTTTCGAGAGGATTTTTCTTAG
5417298 TTTATAATTT
Statistics
Matches: 101, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
116 37 0.37
117 55 0.54
118 9 0.09
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (118 bp):
TTCTAAAAAATTAATTCATTTTCAGGAGTTTTGAATGTTTTTCTTTGAAATTCCTCTTTCCCTAA
AAACCGAGTTTCCTACTCCGTAAATATTTTCGAGAGGATTTTTCTTAGATCAG
Found at i:5417426 original size:165 final size:165
Alignment explanation
Indices: 5417180--5417731 Score: 777
Period size: 165 Copynumber: 3.4 Consensus size: 165
5417170 ATTTTCTTAG
* * *
5417180 ATCAGTTCTGAAAAATTAATTCATTTTTATGAGTTTTGAAGTTTTTCTTTGAAATTTCTC-TTTC
1 ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTCTTTGAAATTTCTCTTTTC
* *
5417244 CTTGAAAAACCGAGTTTCCTACTCCGTAAATATTTTTGGGAGGATTTTTCTTAGTTTATAATTTT
66 C-TGAAAAACTGAGTTTCCTA-TCCGTAAATATTTTTGGGAGGATTTTTCTTACTTTATAATTTT
*
5417309 TAAAATTTATTAAATATCATCATTTAATTCATATTAA
129 TAAAATTTATCAAATATCATCATTTAATTCATATTAA
* * *
5417346 ATCCGTTCAGTAAAATTAATTCATTTTCATGAGTTTTGAA-TTTTTCTTTCAAATTTCTCTTTTC
1 ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTCTTTGAAATTTCTCTTTTC
*
5417410 CTGAAAAACTGAGTTTCCTATTCCGTAAATATTTTTAGGAGGATTTGTT-TTACTTTATAATTTT
66 CTGAAAAACTGAGTTTCCTA-TCCGTAAATATTTTTGGGAGGATTT-TTCTTACTTTATAATTTT
*
5417474 TAAAATTCATCAAATATCATCATTTAATTCATATTAA
129 TAAAATTTATCAAATATCATCATTTAATTCATATTAA
* * * * * *
5417511 ATTAGTTTTGTAAAATTATTTCATTTTCATGAGTTTTAAATTTTTTCTTTGAAATTTCCCTTTCC
1 ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTCTTTGAAATTTCTCTTTTC
* *
5417576 CCGAAAAA-TCGAG-TT--T-T-C-T--ATCTTTTTGGGAGGATTTTTCTTACTTTATAATTTTT
66 CTGAAAAACT-GAGTTTCCTATCCGTAAATATTTTTGGGAGGATTTTTCTTACTTTATAATTTTT
*
5417632 AAAACTTATCAAATATCATCATTTAATTCATATTAA
130 AAAATTTATCAAATATCATCATTTAATTCATATTAA
*
5417668 ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTTCTTTGAAATTCCTCTTT
1 ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAA-TTTTTTCTTTGAAATTTCTCTTT
5417732 CTCCAAAAAA
Statistics
Matches: 349, Mismatches: 31, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
156 2 0.01
157 102 0.29
158 21 0.06
159 1 0.00
160 1 0.00
161 1 0.00
163 1 0.00
165 146 0.42
166 74 0.21
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (165 bp):
ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTCTTTGAAATTTCTCTTTTC
CTGAAAAACTGAGTTTCCTATCCGTAAATATTTTTGGGAGGATTTTTCTTACTTTATAATTTTTA
AAATTTATCAAATATCATCATTTAATTCATATTAA
Found at i:5417768 original size:157 final size:156
Alignment explanation
Indices: 5417180--5417804 Score: 690
Period size: 157 Copynumber: 3.9 Consensus size: 156
5417170 ATTTTCTTAG
* * * *
5417180 ATCAGTTCTGAAAAATTAATTCATTTTTATGAGTTTTGAAGTTTTTCTTTGAAATTTCTCTTTC-
1 ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTCTTTGAAATTCCTCTTTCT
* * * *
5417244 CTTGAAAAACCGAGTTTCCTACTCCGTAAATATTTTTGGGAGGATTTTTCTTAGTTTATAATTTT
66 C-CGAAAAATCGAG-TT--T--T-C-T--ATATTTTTAGGAGGATTTTTCTTACTTTATAATTTT
*
5417309 TAAAATTTATTAAATATCATCATTTAATTCATATTAA
121 TAAAA-TTATCAAATATCATCATTTAATTCATATTAA
* * * *
5417346 ATCCGTTCAGTAAAATTAATTCATTTTCATGAGTTTTGAA-TTTTTCTTTCAAATTTCTCTTT-T
1 ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTCTTTGAAATTCCTCTTTCT
5417409 CCTGAAAAA-CTGAGTTTCCTATTCCGTAAATATTTTTAGGAGGATTTGTT-TTACTTTATAATT
66 CC-GAAAAATC-GAG--T--T-TT-C-T--ATATTTTTAGGAGGATTT-TTCTTACTTTATAATT
5417472 TTTAAAATTCATCAAATATCATCATTTAATTCATATTAA
119 TTTAAAATT-ATCAAATATCATCATTTAATTCATATTAA
* * * *
5417511 ATTAGTTTTGTAAAATTATTTCATTTTCATGAGTTTTAAATTTTTTCTTTGAAATTTCC-CTTTC
1 ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTCTTTGAAA-TTCCTCTTTC
* * *
5417575 CCCGAAAAATCGAGTTTTCTATCTTTTTGGGAGGATTTTTCTTACTTTATAATTTTTAAAACTTA
65 TCCGAAAAATCGAGTTTTCTATATTTTTAGGAGGATTTTTCTTACTTTATAATTTTTAAAA-TTA
5417640 TCAAATATCATCATTTAATTCATATTAA
129 TCAAATATCATCATTTAATTCATATTAA
5417668 ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTTCTTTGAAATTCCTCTTTC
1 ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAA-TTTTTTCTTTGAAATTCCTCTTTC
* ** * * *
5417733 TCCAAAAAATCGAGTTTTCTATGGTTTTAAG-GGATTTTTCTCGA-TTTAAAATTTTTAAAATTC
65 TCCGAAAAATCGAGTTTTCTATATTTTTAGGAGGATTTTTCT-TACTTTATAATTTTTAAAATT-
*
5417796 ATCTAATAT
128 ATCAAATAT
5417805 TTTTATTAAA
Statistics
Matches: 407, Mismatches: 34, Indels: 45
0.84 0.07 0.09
Matches are distributed among these distances:
156 4 0.01
157 138 0.34
158 47 0.12
159 1 0.00
160 1 0.00
161 2 0.00
162 1 0.00
164 4 0.01
165 136 0.33
166 65 0.16
167 7 0.02
168 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (156 bp):
ATCAGTTCTGTAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTCTTTGAAATTCCTCTTTCT
CCGAAAAATCGAGTTTTCTATATTTTTAGGAGGATTTTTCTTACTTTATAATTTTTAAAATTATC
AAATATCATCATTTAATTCATATTAA
Found at i:5421888 original size:156 final size:155
Alignment explanation
Indices: 5421723--5422023 Score: 376
Period size: 155 Copynumber: 1.9 Consensus size: 155
5421713 TGCCACTATA
* * * *
5421723 AGATACTTTCAAC-TTAGAAGT-GCCTGATACCCCTAAAGGA-TATAAAAAGGATTATAGATGGG
1 AGATACTTTCAACGTGA-AAGTAGCCCGATAACCCTAAAAGACT-T-AAAAGG-TTATAGATGGG
* * * * *
5421785 ATGGACCTATCCTAAATGCCCATTTTCGGCATAAAAGCAAA-CTCGGTGACAACTTAGGACTCAG
62 ATGAACCTATCCTAAATACCCACTTTCAGCATAAAAGCAAACCT-GATGACAACTTAGGACTCAG
*
5421849 TTCTAGAAAATTATGAAAATAGTCCTATGG
126 TTCTAAAAAATTATGAAAATAGTCCTATGG
* * * *
5421879 AGATACTTTCGACGTGAAAGTATCCCGATAACCCTAAAAGACTTAAAAGGTTATAGTTGGGGTGA
1 AGATACTTTCAACGTGAAAGTAGCCCGATAACCCTAAAAGACTTAAAAGGTTATAGATGGGATGA
** *
5421944 ACCTATCCTAAATACCCACTTTCAGCATAAAAGCGGACCTGATGACAACTTAGGACTCGGTTCTA
66 ACCTATCCTAAATACCCACTTTCAGCATAAAAGCAAACCTGATGACAACTTAGGACTCAGTTCTA
5422009 AAAAATTATGAAAAT
131 AAAAATTATGAAAAT
5422024 GCCTCTAAAG
Statistics
Matches: 124, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
155 81 0.65
156 24 0.19
157 18 0.15
158 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (155 bp):
AGATACTTTCAACGTGAAAGTAGCCCGATAACCCTAAAAGACTTAAAAGGTTATAGATGGGATGA
ACCTATCCTAAATACCCACTTTCAGCATAAAAGCAAACCTGATGACAACTTAGGACTCAGTTCTA
AAAAATTATGAAAATAGTCCTATGG
Found at i:5422129 original size:117 final size:116
Alignment explanation
Indices: 5421912--5422133 Score: 286
Period size: 117 Copynumber: 1.9 Consensus size: 116
5421902 CCCGATAACC
* * *
5421912 CTAAAAGACTTAAAAGGTTATAGTTGGGGTGAACCTATCCTAAATACCCACTTTCAGCATAAAAG
1 CTAAAAGACTTAAAAGGTTATAGATGCGGTGAACCTATCCTAAATACCCACTTTCAGCATAAAAA
* * * *
5421977 CGGACCTGATGACAACTTAGGACTCGGTTCTAAAAAATTATGAAAATGCCT
66 CAGACCTGATGACAACCTAAGACTCAGTTCTAAAAAATTATGAAAATGCCT
* * *
5422028 CTAAAGGACTTAAAAAGGTTATAGATGCGGTGAACCTATCCTAGATACCCACCTTT-GGCATAAA
1 CTAAAAGACTT-AAAAGGTTATAGATGCGGTGAACCTATCCTAAATACCCA-CTTTCAGCATAAA
* * *
5422092 AATAGACCTTG-TGACAACCTAAGACTTAGTTTTAAAAAATTA
64 AACAGACC-TGATGACAACCTAAGACTCAGTTCTAAAAAATTA
5422134 CAAAAATACC
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
116 10 0.11
117 74 0.82
118 6 0.07
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (116 bp):
CTAAAAGACTTAAAAGGTTATAGATGCGGTGAACCTATCCTAAATACCCACTTTCAGCATAAAAA
CAGACCTGATGACAACCTAAGACTCAGTTCTAAAAAATTATGAAAATGCCT
Found at i:5427946 original size:33 final size:33
Alignment explanation
Indices: 5427904--5427968 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
5427894 CAACGATTTG
5427904 TATCGATACATAAAGTGTTGTATCGATACAATA
1 TATCGATACATAAAGTGTTGTATCGATACAATA
*** *
5427937 TATCGATACATATTTTTTTGTATCGATACAAT
1 TATCGATACATAAAGTGTTGTATCGATACAAT
5427969 TTAAGCTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (33 bp):
TATCGATACATAAAGTGTTGTATCGATACAATA
Found at i:5428027 original size:13 final size:13
Alignment explanation
Indices: 5428009--5428033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5427999 ATCACTTAAA
5428009 TGTATCGATACAT
1 TGTATCGATACAT
5428022 TGTATCGATACA
1 TGTATCGATACA
5428034 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5428086 original size:52 final size:51
Alignment explanation
Indices: 5428022--5428170 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 51
5428012 ATCGATACAT
**
5428022 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
5428074 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
5428126 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
5428171 TCATATTTCG
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:5441996 original size:1 final size:1
Alignment explanation
Indices: 5441990--5442056 Score: 71
Period size: 1 Copynumber: 67.0 Consensus size: 1
5441980 CGTCCTCCAC
* * * * * * *
5441990 AAAAAAAAAAACAAAAAAAAACAAAAAAAAACAAAAAAAACAAAACAAAAAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5442055 AA
1 AA
5442057 GGGGTCTGGA
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5442007 original size:10 final size:10
Alignment explanation
Indices: 5441992--5442056 Score: 98
Period size: 10 Copynumber: 6.7 Consensus size: 10
5441982 TCCTCCACAA
5441992 AAAAAAAAAC
1 AAAAAAAAAC
5442002 AAAAAAAAAC
1 AAAAAAAAAC
5442012 AAAAAAAAAC
1 AAAAAAAAAC
5442022 -AAAAAAAAC
1 AAAAAAAAAC
*
5442031 AAAACAAAA-
1 AAAAAAAAAC
*
5442040 AAACAAAAAC
1 AAAAAAAAAC
5442050 AAAAAAA
1 AAAAAAA
5442057 GGGGTCTGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.33
10 33 0.67
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:5442009 original size:14 final size:14
Alignment explanation
Indices: 5441992--5442056 Score: 85
Period size: 14 Copynumber: 4.5 Consensus size: 14
5441982 TCCTCCACAA
*
5441992 AAAAAAAAACAAAAA
1 AAAAAAAAA-AAAAC
5442007 AAAACAAAAAAAAAC
1 AAAA-AAAAAAAAAC
*
5442022 AAAAAAAACAAAAC
1 AAAAAAAAAAAAAC
*
5442036 AAAAAAACAAAAAC
1 AAAAAAAAAAAAAC
5442050 AAAAAAA
1 AAAAAAA
5442057 GGGGTCTGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
14 28 0.62
15 12 0.27
16 5 0.11
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:5442013 original size:22 final size:22
Alignment explanation
Indices: 5441988--5442056 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 22
5441978 GGCGTCCTCC
5441988 ACAAAAAAAAAAACAAAAAAAA
1 ACAAAAAAAAAAACAAAAAAAA
*
5442010 ACAAAAAAAAACAAAAAAAACAAA
1 ACAAAAAAAAA-AACAAAAA-AAA
5442034 ACAAAAAAACAAAAACAAAAAAA
1 AC-AAAAAA-AAAAACAAAAAAA
5442057 GGGGTCTGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.27
23 7 0.17
24 7 0.17
25 13 0.32
26 3 0.07
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (22 bp):
ACAAAAAAAAAAACAAAAAAAA
Found at i:5442015 original size:19 final size:19
Alignment explanation
Indices: 5441992--5442056 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
5441982 TCCTCCACAA
5441992 AAAAAAAAACAAAAAAAAAC
1 AAAAAAAAAC-AAAAAAAAC
5442012 AAAAAAAAACAAAAAAAAC
1 AAAAAAAAACAAAAAAAAC
*
5442031 AAAACAAAAA-AACAAAAAC
1 AAAA-AAAAACAAAAAAAAC
5442050 AAAAAAA
1 AAAAAAA
5442057 GGGGTCTGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
18 3 0.07
19 25 0.58
20 15 0.35
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAAAC
Found at i:5442029 original size:32 final size:33
Alignment explanation
Indices: 5441988--5442053 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 33
5441978 GGCGTCCTCC
5441988 ACAAAAAAAA-AAACAAAAAAAAACAAAAA-AAA
1 ACAAAAAAAACAAA-AAAAAAAAACAAAAACAAA
*
5442020 ACAAAAAAAACAAAACAAAAAAACAAAAACAAA
1 ACAAAAAAAACAAAAAAAAAAAACAAAAACAAA
5442053 A
1 A
5442054 AAAGGGGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 24 0.77
33 7 0.23
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (33 bp):
ACAAAAAAAACAAAAAAAAAAAACAAAAACAAA
Found at i:5443546 original size:30 final size:30
Alignment explanation
Indices: 5443493--5443584 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 30
5443483 TTCCTCACCC
* * ** *
5443493 TTCAAAGCCCATAAATCAATGGCACCCTTT
1 TTCAAAGCCCACAACTCCGTGGCACTCTTT
* * *
5443523 TTCGAAGCCCACAAGTCGGTGGCA-TCTTT
1 TTCAAAGCCCACAACTCCGTGGCACTCTTT
* *
5443552 TCCAAAGTCCACAACTCCGTGGCACTCTTT
1 TTCAAAGCCCACAACTCCGTGGCACTCTTT
5443582 TTC
1 TTC
5443585 TTTTGTAAGC
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 23 0.47
30 26 0.53
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (30 bp):
TTCAAAGCCCACAACTCCGTGGCACTCTTT
Found at i:5443601 original size:35 final size:34
Alignment explanation
Indices: 5443560--5443634 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
5443550 TTTCCAAAGT
* * *
5443560 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCATAGCACTCTTTTTCCTTT-TAAGC
* *
5443595 TCACAACTCTATAGCACTCTTTTTCCTTTTAAGC
1 CCACAACTCCATAGCACTCTTTTTCCTTTTAAGC
5443629 CCACAA
1 CCACAA
5443635 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (34 bp):
CCACAACTCCATAGCACTCTTTTTCCTTTTAAGC
Found at i:5443651 original size:34 final size:34
Alignment explanation
Indices: 5443570--5443682 Score: 101
Period size: 30 Copynumber: 3.4 Consensus size: 34
5443560 CCACAACTCC
* * *
5443570 GTGGCACTCTTTTTCTTTTGTAAGCTCACAACTCTA
1 GTGGCACTCTTTTTCCTTT-TAAGCCCACAAGT-TA
*
5443606 -TAGCACTCTTTTTCCTTTTAAGCCCACAAGTTA
1 GTGGCACTCTTTTTCCTTTTAAGCCCACAAGTTA
* **
5443639 GTGGCAC-CCTTTT-C--AAAAGCCCACAAGTTA
1 GTGGCACTCTTTTTCCTTTTAAGCCCACAAGTTA
5443669 GTGGCATCTCTTTT
1 GTGGCA-CTCTTTT
5443683 CAAAAGCCCA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
30 20 0.31
31 1 0.02
32 5 0.08
33 7 0.11
34 16 0.25
35 16 0.25
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (34 bp):
GTGGCACTCTTTTTCCTTTTAAGCCCACAAGTTA
Found at i:5443724 original size:28 final size:29
Alignment explanation
Indices: 5443625--5443807 Score: 214
Period size: 28 Copynumber: 6.3 Consensus size: 29
5443615 TTTTCCTTTT
* *
5443625 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTT-AA
* *
5443655 AAGCCCACAAGTTAGTGGCATCTCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAAC-CTTTT-AA
5443686 AAGCCCACAAGTCAGTGGCAACC-TTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTTAA
*
5443714 AAGCCCACAAGTCAGTGGCAATC-TTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTTAA
*
5443742 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTTAA
* *
5443770 AAGCACACAAGT-TGAT-GCAATCCTTTTAA
1 AAGCCCACAAGTCAG-TGGCAA-CCTTTTAA
5443799 AAGCCCACA
1 AAGCCCACA
5443808 CAAGTTGGTG
Statistics
Matches: 139, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.04
28 69 0.50
29 15 0.11
30 22 0.16
31 28 0.20
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.21
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTTAA
Found at i:5443907 original size:52 final size:50
Alignment explanation
Indices: 5443829--5444018 Score: 232
Period size: 52 Copynumber: 3.9 Consensus size: 50
5443819 CGTCTTCTTC
*
5443829 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGGTACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTT-GTACC-T
* * *
5443881 TAAGTCCAATGTAGCTGGCCTTGAATCAGTACATTGGCACC----T-CC-
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTACCT
* *
5443925 -AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGT-A-CCT
*
5443976 TAAGTCCTATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
5444019 CATCTTTAAC
Statistics
Matches: 117, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
43 35 0.30
46 2 0.02
47 2 0.02
50 2 0.02
52 76 0.65
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (50 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTACCT
Found at i:5443993 original size:95 final size:95
Alignment explanation
Indices: 5443830--5444017 Score: 299
Period size: 95 Copynumber: 2.0 Consensus size: 95
5443820 GTCTTCTTCT
*
5443830 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGGTACCTTTAAGTCCAATGTAG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGGTACCTTTAAGTCCAATATAG
*
5443895 CTGGCCTTGAATCAGTACATTGGCACCTCC
66 CTGGCCTTGAATCAGCACATTGGCACCTCC
* *
5443925 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTT-GTCATCC-TTAAGTCCTATAT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGGT-A-CCTTTAAGTCCAATAT
*
5443988 CGCTGGCCTTGAATCAGCACATTGGCACCT
64 AGCTGGCCTTGAATCAGCACATTGGCACCT
5444018 TCATCTTTAA
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
94 2 0.02
95 82 0.95
96 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (95 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGGTACCTTTAAGTCCAATATAG
CTGGCCTTGAATCAGCACATTGGCACCTCC
Found at i:5444927 original size:13 final size:13
Alignment explanation
Indices: 5444909--5444933 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5444899 ATCACTTAAA
5444909 TGTATCGATACAT
1 TGTATCGATACAT
5444922 TGTATCGATACA
1 TGTATCGATACA
5444934 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5449048 original size:48 final size:48
Alignment explanation
Indices: 5448931--5449062 Score: 147
Period size: 48 Copynumber: 2.8 Consensus size: 48
5448921 GTATCTGGTC
* * *
5448931 ATCATTCTTTGTTTGACTGTATTGGTGTTAGGGCCTAGTCAAACTCAA
1 ATCATCCTTCGTTTGACTATATTGGTGTTAGGGCCTAGTCAAACTCAA
* * * * **
5448979 ATCTTCCCTCATTTGAGTATATTGGTGTTAGGGCCTAGTCAAACTCTT
1 ATCATCCTTCGTTTGACTATATTGGTGTTAGGGCCTAGTCAAACTCAA
* * **
5449027 TTCATCCTTCGTTTCACTATATAAGTGTTAGGGCCT
1 ATCATCCTTCGTTTGACTATATTGGTGTTAGGGCCT
5449063 GGTTGAACTC
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (48 bp):
ATCATCCTTCGTTTGACTATATTGGTGTTAGGGCCTAGTCAAACTCAA
Found at i:5449168 original size:44 final size:43
Alignment explanation
Indices: 5449115--5450455 Score: 624
Period size: 44 Copynumber: 30.7 Consensus size: 43
5449105 CTAGTCAGAT
*
5449115 TCTTTTCATTCTGATTTGACATATGGTTACCACCCTGGTCAAA
1 TCTTTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
** * * **
5449158 TCTGCCTCATTCTTG-TCTGATGTATGGTTACCACTCC-GGTCAGTT
1 TCT-TTTCATTC-TGATTTGACGTATGGTTACCAC-CCTGGTCA-AA
* *
5449203 TCGTTTT-ATT-TCGATTTGATGTGTGGTTACCACCCTGGTCAAA
1 TC-TTTTCATTCT-GATTTGACGTATGGTTACCACCCTGGTCAAA
* * * * *
5449246 TCTATCTC-TCTCTTATTTGACGTGTGGTTACCACCCTGGTTAGAT
1 TCT-TTTCAT-TCTGATTTGACGTATGGTTACCACCCTGGTCA-AA
* *
5449291 TCCTTTT-ATTCTGATTTGACATATGGTTACCACCCTGGCCAAA
1 T-CTTTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
* * * * * *
5449334 T-TTGCTTTATTCCTG-TCTGATGTATGTTTACCACCCTGGTTAGAT
1 TCTT--TTCATT-CTGATTTGACGTATGGTTACCACCCTGGTCA-AA
* * * * *
5449379 TCTTTCCATTCTAATTTGACGTATGATTATCACCCTGATCAAA
1 TCTTTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
** * * *
5449422 TC-TGCCAGCCTTCT-ATTTGACATATGGTTACTACCCTGGTCAGA
1 TCTTTTCA---TTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
* ** * *
5449466 TTTTTTTTTGTTTCGATTTAACGTATGGTTACCACCCTGGTCAAA
1 TCTTTTCAT-TCT-GATTTGACGTATGGTTACCACCCTGGTCAAA
* * *
5449511 TC---ACATGTCTGA--T---GTATGGTTACCACCTTGGTCAGAT
1 TCTTTTCAT-TCTGATTTGACGTATGGTTACCACCCTGGTCA-AA
* * *
5449548 TCTTTTCATTCTGATTTGATGTATGGTTACCATCCTGGTCAGA
1 TCTTTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
** ** * *
5449591 TCTGCCTCCCTCTTG-TCTGATGTATGGTTACCACCCTGGTCAAA
1 TCT-TTTCATTC-TGATTTGACGTATGGTTACCACCCTGGTCAAA
* * *
5449635 TTCTTTTCATTATGATTTGACGTATGGTTACCAACCTAGTCAAA
1 -TCTTTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
** * * * * * *
5449679 TCTGCCTCCTTCTTG-TCTGACATATGGTTACCGCCCTAGTCAGAT
1 TCT-TTTCATTC-TGATTTGACGTATGGTTACCACCCTGGTCA-AA
* * *
5449724 TCTTTTCATT-TCGATTTGACATATGGTTACCACCTTGGTCGAA
1 TCTTTTCATTCT-GATTTGACGTATGGTTACCACCCTGGTCAAA
* * * * * * *
5449767 TCTGCTTCCTTCCTG-TCTGACGTATGGTTATCGCCCTAGTCAGAT
1 TCT-TTTCATT-CTGATTTGACGTATGGTTACCACCCTGGTCA-AA
* * * *
5449812 TCTTTTCATTCTTATTTGACATATGGTTACCACCGTAGTCAAA
1 TCTTTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
* * * * * ** ** *
5449855 TATGCCTCCCTTCT-ACTTGACGTATGGTTACCGTCCTAATCAGAT
1 TCT--TTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCA-AA
* * *
5449900 TCTTTTTATT-TCGATTTGACATATGGTTACCACCCTAGTCAAA
1 TCTTTTCATTCT-GATTTGACGTATGGTTACCACCCTGGTCAAA
* * * * * *
5449943 TCTGTCTCTTTCTTG-TCTGACGTATGGTTACTACCTTAGTCAAA
1 TCT-TTTCATTC-TGATTTGACGTATGGTTACCACCCTGGTCAAA
* ** *
5449987 TCCTTTTCAGTT-TGATTTGATGTATGGTTACTGCCCTGGTTAAA
1 T-CTTTTCA-TTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
* * * * * * * *
5450031 TCTGCTTTCTTTTTG-TCTAACGTATGGTTATCGCCCTAGTCAGAT
1 TCT--TTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCA-AA
* * * * *
5450076 TCTTTTCATTTTAATTTCATGTATGGTTACCACCCTAGTCAAA
1 TCTTTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
** * * ** *
5450119 TCTGCCTCATTTCTG-CTTGACGTATGGTTATCACCCTAATCAGAT
1 TCT-TTTCA-TTCTGATTTGACGTATGGTTACCACCCTGGTCA-AA
* *
5450164 TCTTTTTATTCCGATTTGACGTATGGTTACCACCCTGGTCAAA
1 TCTTTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
* * * * * * * * *
5450207 T-TTGCCTCCCTTTTG-CTTGACATATAGTTACCACCCTCGTTAGAT
1 TCTT---TTCATTCTGATTTGACGTATGGTTACCACCCTGGTCA-AA
* * **
5450252 TCTTTTCATTCCGTTTTGACGTATGGTTTTCACCCTGGTCAAA
1 TCTTTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
* * * * * *
5450295 TCTGTCTCTTTCCTG-TCTGACGTATGGTTAACACCCTAGTCAGAT
1 TCT-TTTCATT-CTGATTTGACGTATGGTTACCACCCTGGTCA-AA
*
5450340 TCTTTTCATT-TCGATTTGACGTATGGTTACCACCTTGGTCAAA
1 TCTTTTCATTCT-GATTTGACGTATGGTTACCACCCTGGTCAAA
* ** * * * *
5450383 TATACATCCTTCCT-ATCTGACGTATGGTTATCACCCTGGTCGAAT
1 TCT-TTTCATT-CTGATTTGACGTATGGTTACCACCCTGGTC-AAA
*
5450428 TCTTTTTATTCTGATTTGACGTATGGTT
1 TCTTTTCATTCTGATTTGACGTATGGTT
5450456 CCTATAGACA
Statistics
Matches: 961, Mismatches: 249, Indels: 175
0.69 0.18 0.13
Matches are distributed among these distances:
36 20 0.02
37 3 0.00
39 6 0.01
40 3 0.00
41 5 0.01
42 16 0.02
43 84 0.09
44 701 0.73
45 113 0.12
46 10 0.01
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (43 bp):
TCTTTTCATTCTGATTTGACGTATGGTTACCACCCTGGTCAAA
Found at i:5449185 original size:88 final size:88
Alignment explanation
Indices: 5449083--5450455 Score: 1250
Period size: 88 Copynumber: 15.7 Consensus size: 88
5449073 TTCTTATTCC
** ** *
5449083 TGTCTGACAAATGGTTACCATTCTAGTCAGATTCTTTTCATTCTGATTTGACATATGGTTACCAC
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCAC
*
5449148 CCTGGTCAAATCTGCCTCATTCT
66 CCTGGTCAAATCTGCCTCCTTCT
* * * * *
5449171 TGTCTGATGTATGGTTACCACTCC-GGTCAGTTTCGTTTT-ATT-TCGATTTGATGTGTGGTTAC
1 TGTCTGACGTATGGTTACCAC-CCTAGTCAGATTC-TTTTCATTCT-GATTTGACGTATGGTTAC
**
5449233 CACCCTGGTCAAATCTATCT-CTCTCT
63 CACCCTGGTCAAATCTGCCTCCT-TCT
* * * * * *
5449259 TATTTGACGTGTGGTTACCACCCTGGTTAGATTCCTTTT-ATTCTGATTTGACATATGGTTACCA
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATT-CTTTTCATTCTGATTTGACGTATGGTTACCA
* * * ** *
5449323 CCCTGGCCAAATTTGCTTTATTCC
65 CCCTGGTCAAATCTGCCTCCTTCT
* * * * * * * *
5449347 TGTCTGATGTATGTTTACCACCCTGGTTAGATTCTTTCCATTCTAATTTGACGTATGATTATCAC
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCAC
* *
5449412 CCTGATCAAATCTGCCAGCCTTCT
66 CCTGGTCAAATCTGCC-TCCTTCT
* * * ** * *
5449436 AT-T-TGACATATGGTTACTACCCTGGTCAGATT-TTTTTTTGTTTCGATTTAACGTATGGTTAC
1 -TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCAT-TCT-GATTTGACGTATGGTTAC
* *
5449498 CACCCTGGTCAAA------T-C-ACA
63 CACCCTGGTCAAATCTGCCTCCTTCT
* * * * *
5449516 TGTCTGATGTATGGTTACCACCTTGGTCAGATTCTTTTCATTCTGATTTGATGTATGGTTACCAT
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCAC
* *
5449581 CCTGGTCAGATCTGCCTCCCTCT
66 CCTGGTCAAATCTGCCTCCTTCT
* * * * *
5449604 TGTCTGATGTATGGTTACCACCCTGGTCAAATTCTTTTCATTATGATTTGACGTATGGTTACCAA
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCAC
*
5449669 CCTAGTCAAATCTGCCTCCTTCT
66 CCTGGTCAAATCTGCCTCCTTCT
* * *
5449692 TGTCTGACATATGGTTACCGCCCTAGTCAGATTCTTTTCATT-TCGATTTGACATATGGTTACCA
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCT-GATTTGACGTATGGTTACCA
* * * *
5449756 CCTTGGTCGAATCTGCTTCCTTCC
65 CCCTGGTCAAATCTGCCTCCTTCT
* * * *
5449780 TGTCTGACGTATGGTTATCGCCCTAGTCAGATTCTTTTCATTCTTATTTGACATATGGTTACCAC
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCAC
* * *
5449845 CGTAGTCAAATATGCCTCCCTTCT
66 CCTGGTCAAATCTGCCT-CCTTCT
** ** * * *
5449869 ACT-TGACGTATGGTTACCGTCCTAATCAGATTCTTTTTATT-TCGATTTGACATATGGTTACCA
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCT-GATTTGACGTATGGTTACCA
* * *
5449932 CCCTAGTCAAATCTGTCTCTTTCT
65 CCCTGGTCAAATCTGCCTCCTTCT
* * * * * **
5449956 TGTCTGACGTATGGTTACTACCTTAGTCAAATCCTTTTCAGTT-TGATTTGATGTATGGTTACTG
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCA-TTCTGATTTGACGTATGGTTACCA
* * * *
5450020 CCCTGGTTAAATCTGCTTTCTTTT
65 CCCTGGTCAAATCTGCCTCCTTCT
* * * * * * *
5450044 TGTCTAACGTATGGTTATCGCCCTAGTCAGATTCTTTTCATTTTAATTTCATGTATGGTTACCAC
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCAC
* *
5450109 CCTAGTCAAATCTGCCTCATT-T
66 CCTGGTCAAATCTGCCTCCTTCT
* * * *
5450131 CTG-CTTGACGTATGGTTATCACCCTAATCAGATTCTTTTTATTCCGATTTGACGTATGGTTACC
1 -TGTC-TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACC
*
5450195 ACCCTGGTCAAATTTGCCTCCCTT-T
64 ACCCTGGTCAAATCTGCCT-CCTTCT
* * * * * * **
5450220 TG-CTTGACATATAGTTACCACCCTCGTTAGATTCTTTTCATTCCGTTTTGACGTATGGTTTTCA
1 TGTC-TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCA
* * *
5450284 CCCTGGTCAAATCTGTCTCTTTCC
65 CCCTGGTCAAATCTGCCTCCTTCT
*
5450308 TGTCTGACGTATGGTTAACACCCTAGTCAGATTCTTTTCATT-TCGATTTGACGTATGGTTACCA
1 TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCT-GATTTGACGTATGGTTACCA
* * * * *
5450372 CCTTGGTCAAATATACATCCTTCC
65 CCCTGGTCAAATCTGCCTCCTTCT
* * * *
5450396 TATCTGACGTATGGTTATCACCCTGGTC-GAATTCTTTTTATTCTGATTTGACGTATGGTT
1 TGTCTGACGTATGGTTACCACCCTAGTCAG-ATTCTTTTCATTCTGATTTGACGTATGGTT
5450456 CCTATAGACA
Statistics
Matches: 1047, Mismatches: 199, Indels: 78
0.79 0.15 0.06
Matches are distributed among these distances:
79 1 0.00
80 29 0.03
81 28 0.03
82 5 0.00
86 1 0.00
87 29 0.03
88 899 0.86
89 54 0.05
90 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (88 bp):
TGTCTGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTGACGTATGGTTACCAC
CCTGGTCAAATCTGCCTCCTTCT
Found at i:5450881 original size:34 final size:33
Alignment explanation
Indices: 5450836--5450903 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
5450826 GCCAAGGAAA
* *
5450836 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCAATACATTAATC-AATGTATCGATACAT
**
5450870 TGTATCAATACATTAATCTTTGTATCGATACAT
1 TGTATCAATACATTAATCAATGTATCGATACAT
5450903 T
1 T
5450904 TGGGAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 14 0.47
34 16 0.53
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (33 bp):
TGTATCAATACATTAATCAATGTATCGATACAT
Found at i:5455225 original size:13 final size:13
Alignment explanation
Indices: 5455207--5455231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5455197 CATATTACTT
5455207 TGTATCGATACAC
1 TGTATCGATACAC
5455220 TGTATCGATACA
1 TGTATCGATACA
5455232 TGATCTTGGT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:5458235 original size:168 final size:167
Alignment explanation
Indices: 5457930--5458255 Score: 444
Period size: 168 Copynumber: 1.9 Consensus size: 167
5457920 TTCGGTAATA
* * **
5457930 ATTTGAAGTGAATGTGTCTCAAAAACATAGACTCTACATTTAGACACTCAAATAACTCAAACTTA
1 ATTTGAAGTAAAGGTGTCTCAAAAACATAGACTCTACATTTAGACACTCAAATAACTCAAACCCA
* *
5457995 TCGTACAACTATAAAGAACAATCATTAGGCCTGCATCAAGCAACTGGAACTCATGTACAAAGAAC
66 TCGTACAACTATAAAGAACAATCATCAGGCCTACATCAAGCAACTGGAACTCATGTACAAAGAAC
*
5458060 CTCAAGAACA-TCAGCCCAAAGGAATGACTCAAAAAC
131 CTCAAGAACAGTCAGCCCAAAAGAATGACTCAAAAAC
5458096 ATTTGAAGTAAAGGTGTC-CTAAAAACATAGACTCTACATTTAGACACTCATACA-ATACTCAAA
1 ATTTGAAGTAAAGGTGTCTC-AAAAACATAGACTCTACATTTAGACACTCA-A-ATA-ACTCAAA
* * * * * * *
5458159 CCCATCTTAGAGCTATAGAGAACGATCATCAGGCGC-ACATCAAGCGACTGGAACTCATGTATAA
62 CCCATCGTACAACTATAAAGAACAATCATCAGGC-CTACATCAAGCAACTGGAACTCATGTACAA
*
5458223 AGAATCTCAAGAACAGTCAGCCCAAAAGAATGA
126 AGAACCTCAAGAACAGTCAGCCCAAAAGAATGA
5458256 AGAACTTTAA
Statistics
Matches: 139, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
165 1 0.01
166 46 0.33
167 2 0.01
168 73 0.53
169 17 0.12
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (167 bp):
ATTTGAAGTAAAGGTGTCTCAAAAACATAGACTCTACATTTAGACACTCAAATAACTCAAACCCA
TCGTACAACTATAAAGAACAATCATCAGGCCTACATCAAGCAACTGGAACTCATGTACAAAGAAC
CTCAAGAACAGTCAGCCCAAAAGAATGACTCAAAAAC
Found at i:5466007 original size:51 final size:51
Alignment explanation
Indices: 5465946--5466061 Score: 223
Period size: 51 Copynumber: 2.3 Consensus size: 51
5465936 CAAAAATCTT
5465946 TAAGGCTTGACCTCTATAAATAGGTGCTATCTAAAATAGGTTTTGGTTTTC
1 TAAGGCTTGACCTCTATAAATAGGTGCTATCTAAAATAGGTTTTGGTTTTC
5465997 TAAGGCTTGACCTCTATAAATAGGTGCTATCTAAAATAGGTTTTGGTTTTC
1 TAAGGCTTGACCTCTATAAATAGGTGCTATCTAAAATAGGTTTTGGTTTTC
*
5466048 TAAGGCTTAACCTC
1 TAAGGCTTGACCTC
5466062 CTTAGACAGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (51 bp):
TAAGGCTTGACCTCTATAAATAGGTGCTATCTAAAATAGGTTTTGGTTTTC
Found at i:5466073 original size:51 final size:51
Alignment explanation
Indices: 5465946--5466074 Score: 197
Period size: 51 Copynumber: 2.5 Consensus size: 51
5465936 CAAAAATCTT
* *
5465946 TAAGGCTTGACCTCTATAAATAGGTGCTATCTAAAATAGGTTTTGGTTTTC
1 TAAGGCTTAACCTCTATAAACAGGTGCTATCTAAAATAGGTTTTGGTTTTC
* *
5465997 TAAGGCTTGACCTCTATAAATAGGTGCTATCTAAAATAGGTTTTGGTTTTC
1 TAAGGCTTAACCTCTATAAACAGGTGCTATCTAAAATAGGTTTTGGTTTTC
*
5466048 TAAGGCTTAACCTCCT-TAGACAGGTGC
1 TAAGGCTTAACCT-CTATAAACAGGTGC
5466075 CAACTAATGT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
51 72 0.97
52 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (51 bp):
TAAGGCTTAACCTCTATAAACAGGTGCTATCTAAAATAGGTTTTGGTTTTC
Found at i:5466262 original size:30 final size:31
Alignment explanation
Indices: 5466195--5466309 Score: 133
Period size: 31 Copynumber: 3.7 Consensus size: 31
5466185 ACTTAGTTGT
* *
5466195 CACCAACTCGTGTGGGCTTTGACTCGGGTGC
1 CACCAACTCATGTGGGCTTTGACTAGGGTGC
** ** *
5466226 TGCCAACTTGTGTGGGCTTTGA-TTGGGTGC
1 CACCAACTCATGTGGGCTTTGACTAGGGTGC
* *
5466256 CACCAACTCATGTAGGCTTTGACTAAGGTGC
1 CACCAACTCATGTGGGCTTTGACTAGGGTGC
*
5466287 CACTAACTCATGTGGGCTTTGAC
1 CACCAACTCATGTGGGCTTTGAC
5466310 ATTCTAAGGC
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
30 24 0.34
31 46 0.66
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.30
Consensus pattern (31 bp):
CACCAACTCATGTGGGCTTTGACTAGGGTGC
Found at i:5466402 original size:179 final size:178
Alignment explanation
Indices: 5466097--5466428 Score: 436
Period size: 179 Copynumber: 1.9 Consensus size: 178
5466087 ACTTGACTCG
* * * * * **
5466097 GACTTAGGTGCCACCAACTCGTGTGGACTTTAACATTTTAAGGCTTAACTTTCTTAAATAGTTTT
1 GACTAAGGTGCCACCAACTCATGTGGACTTTAACATTCTAAGGCTTAACTCTCTTAAATAGGTGC
* * * *
5466162 GAACTAATATGGACTTGACTCAAACTTAGTTGTCACCAACTCGTGTGGGCTTTGACTCGGGTGCT
66 CAACTAATATCGACTTGACTCAAACTTAGGTGTCACCAACTCGTGTGAGCTTTGACTCGGGTG-T
* *
5466227 GC-CAACTTGTGTGGGCTTTGATTGGGTGCCACCAACTCATGTAGGCTTT
130 -CACAACTTATGTAGGCTTTGATTGGGTGCCACCAACTCATGTAGGCTTT
* * * *
5466276 GACTAAGGTGCCACTAACTCATGTGGGCTTTGACATTCTAAGGCTTAAC-CTCTTTAGATAGGTG
1 GACTAAGGTGCCACCAACTCATGTGGACTTTAACATTCTAAGGCTTAACTCTC-TTAAATAGGTG
*
5466340 CCAACTAATGTCGACTTGACTCAAACTTAGGTG-CAACCAACTCGTGTGAGCTTTGACTCGGGTG
65 CCAACTAATATCGACTTGACTCAAACTTAGGTGTC-ACCAACTCGTGTGAGCTTTGACTCGGGTG
5466404 TCATCAACTTATGTAGGCTTTGATT
129 TCA-CAACTTATGTAGGCTTTGATT
5466429 AAGATGCCAT
Statistics
Matches: 131, Mismatches: 18, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
177 1 0.01
178 4 0.03
179 126 0.96
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (178 bp):
GACTAAGGTGCCACCAACTCATGTGGACTTTAACATTCTAAGGCTTAACTCTCTTAAATAGGTGC
CAACTAATATCGACTTGACTCAAACTTAGGTGTCACCAACTCGTGTGAGCTTTGACTCGGGTGTC
ACAACTTATGTAGGCTTTGATTGGGTGCCACCAACTCATGTAGGCTTT
Found at i:5466437 original size:149 final size:148
Alignment explanation
Indices: 5466228--5466653 Score: 543
Period size: 149 Copynumber: 2.9 Consensus size: 148
5466218 TCGGGTGCTG
* * * *
5466228 CCAACTTGTGTGGGCTTTGA-TTGGGTGCCACCAACTCATGTAGGCTTTGACTAAGGTGCCACTA
1 CCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTTATGTAGGCTTTGACTAAGGTGCCACTA
** *
5466292 ACTCATGTGGGCTTTGACATTCTAAGGCTTAACCTCTTTAGATAGGTGCCAACTAATGTCGACTT
66 ACTTGTGTGGGCTTTGACATTCTAAGGCTTAACCTCCTTAGATAGGTGCCAACTAATGT-GACTT
5466357 GACTCAAACTTAGGTGCAA
130 GACTCAAACTTAGGTGCAA
* * * *
5466376 CCAACTCGTGTGAGCTTTGACTCGGGTGTCATCAACTTATGTAGGCTTTGATTAAGATGCCA-TC
1 CCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTTATGTAGGCTTTGACTAAGGTGCCACT-
* *
5466440 AACTTGTGTGGGCTTTGACATTCTAAAGCTTAACCTCCTTAGACAGGTGCCAACTAATGTGAACT
65 AACTTGTGTGGGCTTTGACATTCTAAGGCTTAACCTCCTTAGATAGGTGCCAACTAATGTG-ACT
*
5466505 TGACTCAAACTTAGGTGCCA
129 TGACTCAAACTTAGGTGCAA
* ** ** * ** * * **
5466525 CCAACTCGTGTGGGCTTTAACTCAAGTGTTGCCAACTTGTGCGGGCTTTAACTAGGGTATCACTA
1 CCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTTATGTAGGCTTTGACTAAGGTGCCACTA
* *
5466590 ACTTGTGTGGGC-TTAACATTCTAAGGCTTAACCTCCTTAGATAGGTGGCAACTAATGTGGACTT
66 ACTTGTGTGGGCTTTGACATTCTAAGGCTTAACCTCCTTAGATAGGTGCCAACTAATGT-GACTT
5466654 TAAAGGGGAA
Statistics
Matches: 239, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
148 66 0.28
149 172 0.72
150 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (148 bp):
CCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTTATGTAGGCTTTGACTAAGGTGCCACTA
ACTTGTGTGGGCTTTGACATTCTAAGGCTTAACCTCCTTAGATAGGTGCCAACTAATGTGACTTG
ACTCAAACTTAGGTGCAA
Found at i:5466902 original size:120 final size:120
Alignment explanation
Indices: 5466697--5466916 Score: 289
Period size: 120 Copynumber: 1.8 Consensus size: 120
5466687 TTTTGAGAAC
* * **
5466697 AAAGGAAAAAGGAGAATAAAATGCGTCCTGCTCTTTGAGGACAAAGGAAAAAAAGAAATGCAATG
1 AAAGGAAAAAGGAGAACAAAATGCATCCTGCTCTTCAAGGACAAAGGAAAAAAAGAAATGCAATG
** * * *
5466762 GGTCCTGCTCCTTGAGGACAAAAGAAAAAAGGAAAACATCCTACTCCTTGAGGAT
66 CATCCTACTCCTTAAAGACAAAAGAAAAAAGGAAAACATCCTACTCCTTGAGGAT
* * *
5466817 AAAGGGAAAAGGAGAACAAAATGCATCCTGCTCTTCAAGGATAAAGGAAAAAAGGAAATG-AAGT
1 AAAGGAAAAAGGAGAACAAAATGCATCCTGCTCTTCAAGGACAAAGGAAAAAAAGAAATGCAA-T
* * *
5466881 GCATCCTACTCTTTAAAGACAAAGGAGAAAAGGAAA
65 GCATCCTACTCCTTAAAGACAAAAGAAAAAAGGAAA
5466917 TAAAGAGCAT
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
119 2 0.02
120 82 0.98
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.16
Consensus pattern (120 bp):
AAAGGAAAAAGGAGAACAAAATGCATCCTGCTCTTCAAGGACAAAGGAAAAAAAGAAATGCAATG
CATCCTACTCCTTAAAGACAAAAGAAAAAAGGAAAACATCCTACTCCTTGAGGAT
Found at i:5466942 original size:42 final size:42
Alignment explanation
Indices: 5466695--5467117 Score: 234
Period size: 42 Copynumber: 10.3 Consensus size: 42
5466685 CTTTTTGAGA
* * *
5466695 ACAAAGGA-AAAAGGAGAATAAAATGCGTCCTGCTCTTTGAGG
1 ACAAAGGAGAAAAGGA-AATAAAGTGCATCCTGCTCTTTGAAG
* * * ** * *
5466737 ACAAAGGAAAAAAAGAAATGCAA-TGGGTCCTGCTCCTTGAGG
1 ACAAAGGAGAAAAGGAAAT-AAAGTGCATCCTGCTCTTTGAAG
* * * * *
5466779 ACAAAAGAAAAAAGG--A-AAA---CATCCTACTCCTTGAGG
1 ACAAAGGAGAAAAGGAAATAAAGTGCATCCTGCTCTTTGAAG
* * * *
5466815 ATAAAGG-GAAAAGGAGAACAAAATGCATCCTGCTC-TTCAAGG
1 ACAAAGGAGAAAAGGA-AATAAAGTGCATCCTGCTCTTTGAA-G
* * * * *
5466857 ATAAAGGAAAAAAGGAAATGAAGTGCATCCTACTCTTTAAAG
1 ACAAAGGAGAAAAGGAAATAAAGTGCATCCTGCTCTTTGAAG
* *
5466899 ACAAAGGAGAAAAGGAAATAAAGAGCATCTTGCTCTTTGAAG
1 ACAAAGGAGAAAAGGAAATAAAGTGCATCCTGCTCTTTGAAG
* * * ** *
5466941 ACAACGAAGAAAAAGAAATAAAGTGTGTCCTACTCTTTGAAG
1 ACAAAGGAGAAAAGGAAATAAAGTGCATCCTGCTCTTTGAAG
* * ** * *
5466983 ACAAAGCAAAAAAGGAAAATGAAA-TGGGTCCTCCTCCTTGAAG
1 ACAAAGGAGAAAAGG-AAAT-AAAGTGCATCCTGCTCTTTGAAG
* * *
5467026 ATAAAGGAGAAAAGG----AAA-TGCATCTTGTTCTTTG-AG
1 ACAAAGGAGAAAAGGAAATAAAGTGCATCCTGCTCTTTGAAG
* * * *
5467062 AACTAAAAGGTGAAAAAGAAATAAAGTGCTTCCTGCTCTTTGAGG
1 -AC--AAAGGAGAAAAGGAAATAAAGTGCATCCTGCTCTTTGAAG
5467107 ACAAAGG-GAAA
1 ACAAAGGAGAAA
5467118 CGAATGAAAT
Statistics
Matches: 298, Mismatches: 60, Indels: 47
0.74 0.15 0.12
Matches are distributed among these distances:
35 6 0.02
36 21 0.07
37 14 0.05
38 3 0.01
39 14 0.05
40 1 0.00
41 7 0.02
42 159 0.53
43 54 0.18
44 18 0.06
45 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.19
Consensus pattern (42 bp):
ACAAAGGAGAAAAGGAAATAAAGTGCATCCTGCTCTTTGAAG
Found at i:5474612 original size:20 final size:20
Alignment explanation
Indices: 5474587--5474638 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
5474577 CATTTTAGGC
* *
5474587 ATGTATCGATACATTCATTT
1 ATGTATCGATACATTCACTA
*
5474607 ATGTATTGATACATTCACTA
1 ATGTATCGATACATTCACTA
5474627 ATTGTATCGATA
1 A-TGTATCGATA
5474639 TTAATCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:5479639 original size:73 final size:71
Alignment explanation
Indices: 5479397--5479644 Score: 239
Period size: 73 Copynumber: 3.6 Consensus size: 71
5479387 AACTTAAACA
* *
5479397 CTTTTATTTTAGTCCTCAAAGAGCAAGACACTTTT-TTTTTC-TTTT-AAAGCCCACACAAGCTG
1 CTTTTATTTTAGTCCTCAAAGAGCAAGACACTTTTCTTTTTCTTTTTCAAAG-CCATACAAGTTG
*
5479459 GTAGCAC
65 GTGGCAC
* * * *
5479466 C-TTTATTTTATTCCTCAAAGAGCAAG--A---TGCTTTTT-TTTTTCAAAATCCATGCAAGTTG
1 CTTTTATTTTAGTCCTCAAAGAGCAAGACACTTTTCTTTTTCTTTTTC-AAAGCCATACAAGTTG
*
5479524 GTGGCTC
65 GTGGCAC
* * * *
5479531 CTTTTATTTTAGTCCTCAAA-ATGTAGGACATTTTTCCTTTTTCTTTTTCAAAGCCTATATAAGT
1 CTTTTATTTTAGTCCTCAAAGA-GCAAGACACTTTT-CTTTTTCTTTTTCAAAGCC-ATACAAGT
5479595 TGGTGGCAC
63 TGGTGGCAC
* **
5479604 CTTTTATTTTAGTCCTCAAAGAGTAAGATGCTTTTCTTTTT
1 CTTTTATTTTAGTCCTCAAAGAGCAAGACACTTTTCTTTTT
5479645 TAAAGCCCAC
Statistics
Matches: 144, Mismatches: 20, Indels: 27
0.75 0.10 0.14
Matches are distributed among these distances:
63 1 0.01
64 9 0.06
65 16 0.11
66 24 0.17
68 25 0.17
69 1 0.01
71 1 0.01
72 17 0.12
73 49 0.34
74 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.43
Consensus pattern (71 bp):
CTTTTATTTTAGTCCTCAAAGAGCAAGACACTTTTCTTTTTCTTTTTCAAAGCCATACAAGTTGG
TGGCAC
Found at i:5479644 original size:139 final size:134
Alignment explanation
Indices: 5479397--5479644 Score: 336
Period size: 139 Copynumber: 1.8 Consensus size: 134
5479387 AACTTAAACA
5479397 CTTTTATTTTAGTCCTCAAAGAGCAAGACACTTTTTTTTTCTTTTAAAGCCCACACAAGCTGGTA
1 CTTTTATTTTAGTCCTCAAAGAGCAAGACACTTTTTTTTTCTTTTAAAGCCCACACAAGCTGGTA
* *
5479462 GCACCTTTATTTTATTCCTCAAAGAGCAAGATGCTTTTTTTTTTCAAAATCCATGCAAGTTGGTG
66 GCACCTTTATTTTAGTCCTCAAAGAGCAAGATGCTTTTCTTTTTCAAAATCCATGCAAGTTGGTG
5479527 GCTC
131 GCTC
* * * * * * *
5479531 CTTTTATTTTAGTCCTCAAA-ATGTAGGACATTTTTCCTTTTTCTTTTTCAAAGCCTATATAAGT
1 CTTTTATTTTAGTCCTCAAAGA-GCAAGACACTTTT--TTTTTC-TTTT-AAAGCCCACACAAGC
* *
5479595 TGGTGGCACCTTTTATTTTAGTCCTCAAAGAGTAAGATGCTTTTCTTTTT
61 TGGTAGCACC-TTTATTTTAGTCCTCAAAGAGCAAGATGCTTTTCTTTTT
5479645 TAAAGCCCAC
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
133 1 0.01
134 30 0.31
136 6 0.06
137 4 0.04
138 20 0.21
139 36 0.37
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.43
Consensus pattern (134 bp):
CTTTTATTTTAGTCCTCAAAGAGCAAGACACTTTTTTTTTCTTTTAAAGCCCACACAAGCTGGTA
GCACCTTTATTTTAGTCCTCAAAGAGCAAGATGCTTTTCTTTTTCAAAATCCATGCAAGTTGGTG
GCTC
Found at i:5479738 original size:71 final size:67
Alignment explanation
Indices: 5479432--5479743 Score: 201
Period size: 73 Copynumber: 4.6 Consensus size: 67
5479422 AGACACTTTT
* * * * * * * *
5479432 TTTTTC-TTTTAAAGCCCACACAAGCTGGTAGCA-CC-TTTATTTTATTCCTCAAAGAGCAAGAT
1 TTTTTCTTTTTAAAGCCTACATAAGTTGGTGGCATCCTTTTATTTTAGTCCTAAAAAAGTAAGAT
5479494 GC
66 GC
* * * *
5479496 TTTTT-TTTTTCAAA--ATCCATGCAAGTTGGTGGC-TCCTTTTATTTTAGTCCTCAAAATGTAG
1 TTTTTCTTTTT-AAAGCCTACAT--AAGTTGGTGGCATCCTTTTATTTTAGTCCTAAAAAAGTA-
* *
5479557 GACATTTTTCC
62 -AGA----TGC
* * *
5479568 TTTTTCTTTTTCAAAGCCTATATAAGTTGGTGGCA-CCTTTTATTTTAGTCCTCAAAGAGTAAGA
1 TTTTTCTTTTT-AAAGCCTACATAAGTTGGTGGCATCCTTTTATTTTAGTCCTAAAAAAGTAAGA
5479632 TGC
65 TGC
* * * * **
5479635 -TTTTCTTTTTTAAAGCCCACACAAGCTAGTGGCATTTTTTTAACTTTTTAGTCCTAAAAAAGTA
1 TTTTTC-TTTTTAAAGCCTACATAAGTTGGTGGCATCCTTTT-A--TTTTAGTCCTAAAAAAGTA
*
5479699 GGATGC
62 AGATGC
*
5479705 TTTTTCTTCCTTAAAGCCTACATAAGTTGGTGGCATCCT
1 TTTTTCTT-TTTAAAGCCTACATAAGTTGGTGGCATCCT
5479744 CTATCCCTTT
Statistics
Matches: 189, Mismatches: 36, Indels: 39
0.72 0.14 0.15
Matches are distributed among these distances:
63 2 0.01
64 9 0.05
65 14 0.07
66 42 0.22
67 11 0.06
68 3 0.02
70 24 0.13
71 30 0.16
72 7 0.04
73 44 0.23
75 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (67 bp):
TTTTTCTTTTTAAAGCCTACATAAGTTGGTGGCATCCTTTTATTTTAGTCCTAAAAAAGTAAGAT
GC
Found at i:5479892 original size:71 final size:70
Alignment explanation
Indices: 5479591--5479970 Score: 267
Period size: 72 Copynumber: 5.4 Consensus size: 70
5479581 AAGCCTATAT
* * * * *
5479591 AAGTTGGTGGCA-CC-TTTTA---TTTTAGTCCTCAAAGAGTAAGATGCTTTTCTTTTTTAAAGC
1 AAGTTGGTGGCACCCTTTTTATCTTTTTAGTCCTCAAAGAGCAGGAAGCATTT-TTTTTTAAAAC
*
5479651 CCACAC
65 CCATAC
* * ** * * * * *
5479657 AAGCTAGTGGCA-TTTTTTTAACTTTTTAGTCCTAAAAAAGTAGGATGC-TTTTTCTTCCTTAAA
1 AAGTTGGTGGCACCCTTTTTATCTTTTTAGTCCTCAAAGAGCAGGAAGCATTTTT-TT--TTAAA
* * * *
5479720 GCCTACAT
63 ACCCATAC
* * * ** * *
5479728 AAGTTGGTGGCATCCTCTATCCCTTTTTAATCCTCAAAGAGCAGGACA-AATTTTTTTTTTTAAA
1 AAGTTGGTGGCACCCTTTTTATCTTTTTAGTCCTCAAAGAGCAGGA-AGCA--TTTTTTTTTAAA
5479792 AGCCCATAC
63 A-CCCATAC
* * *
5479801 AAGTTGGTGGCACCCATTTTATCTTTTTAGTCCTCAAAGACCAGGAAGCCTTTTTTTTGTAAAAC
1 AAGTTGGTGGCACCCTTTTTATCTTTTTAGTCCTCAAAGAGCAGGAAGCATTTTTTTT-TAAAAC
5479866 CCATAC
65 CCATAC
* * * *
5479872 AAGTCGGTGGCACCCTTTTTATCTTTTTTAGTCCTCAAAGAGCAGGACGCATTTTTCGTTTAAAG
1 AAGTTGGTGGCACCCTTTTTATC-TTTTTAGTCCTCAAAGAGCAGGAAGCATTTTT-TTTTAAAA
* *
5479937 TCCACAC
64 CCCATAC
5479944 AAGTTGGTGGCA--CTTTATTATCTTTTT
1 AAGTTGGTGGCACCCTTT-TTATCTTTTT
5479971 TGTTTTCAAA
Statistics
Matches: 249, Mismatches: 47, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
66 10 0.04
67 5 0.02
68 2 0.01
69 5 0.02
70 31 0.12
71 62 0.25
72 83 0.33
73 44 0.18
74 2 0.01
75 5 0.02
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (70 bp):
AAGTTGGTGGCACCCTTTTTATCTTTTTAGTCCTCAAAGAGCAGGAAGCATTTTTTTTTAAAACC
CATAC
Found at i:5480547 original size:21 final size:22
Alignment explanation
Indices: 5480523--5480576 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
5480513 TTTTACAATT
5480523 TGTATCAATACAAT-AAGTGAA
1 TGTATCAATACAATAAAGTGAA
**
5480544 TGTATTGATAC-ATAAAGTGAA
1 TGTATCAATACAATAAAGTGAA
*
5480565 TGCATCAATACA
1 TGTATCAATACA
5480577 TGTCTAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (22 bp):
TGTATCAATACAATAAAGTGAA
Found at i:5481890 original size:25 final size:25
Alignment explanation
Indices: 5481861--5481920 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
5481851 TTAGTTTGTA
*
5481861 CATATTTTTTCTCCATGTTCTACAT
1 CATATTTGTTCTCCATGTTCTACAT
5481886 CATATTTGTTCTCCATGTTCTACAT
1 CATATTTGTTCTCCATGTTCTACAT
5481911 CATATTTGTT
1 CATATTTGTT
5481921 GCATTTTGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.20, C:0.22, G:0.07, T:0.52
Consensus pattern (25 bp):
CATATTTGTTCTCCATGTTCTACAT
Found at i:5483205 original size:28 final size:28
Alignment explanation
Indices: 5483173--5483233 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
5483163 GATACTCTGG
*
5483173 CCCCACCATTTTTTAGGGGATACTCCAA
1 CCCCACCATTTTTTAAGGGATACTCCAA
*
5483201 TCCCACCATTTTTTAAGGGATACTCCAA
1 CCCCACCATTTTTTAAGGGATACTCCAA
5483229 CCCCA
1 CCCCA
5483234 TTTTTACTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.28
Consensus pattern (28 bp):
CCCCACCATTTTTTAAGGGATACTCCAA
Found at i:5483340 original size:79 final size:79
Alignment explanation
Indices: 5483190--5483363 Score: 201
Period size: 79 Copynumber: 2.2 Consensus size: 79
5483180 ATTTTTTAGG
* ** *
5483190 GGATACTCCAATCCC-ACCATTTTTTAAGGGATACTCCAACCCCATTTTTACTTCTAAAACAGCA
1 GGATACTCCAA-CCCTAACATTTTCGAAGGGATACTCCAACCCCATTTTTACTTCTAAAACACCA
5483254 AAATTTTCATCTC-A
65 AAATTTTCATCTCTA
* * * *
5483268 GAGATACTCCAACCCTAACATTTTCGAAGGGATACTCCAACCTCGTTTTTA-TTTTCAAAATACC
1 G-GATACTCCAACCCTAACATTTTCGAAGGGATACTCCAACCCCATTTTTACTTCT-AAAACACC
**
5483332 AAGTTTTTCATCTCTTA
64 AAAATTTTCATCTC-TA
5483349 GGATACTCCAACCCT
1 GGATACTCCAACCCT
5483364 CGTTTTCACT
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 7 0.09
79 58 0.72
80 14 0.17
81 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (79 bp):
GGATACTCCAACCCTAACATTTTCGAAGGGATACTCCAACCCCATTTTTACTTCTAAAACACCAA
AATTTTCATCTCTA
Found at i:5483392 original size:53 final size:53
Alignment explanation
Indices: 5483295--5483415 Score: 142
Period size: 53 Copynumber: 2.3 Consensus size: 53
5483285 ACATTTTCGA
* *
5483295 AGGGATACTCCAA-CCTCGTTTTTATTTTCAAAATACCAAGTTTTTCATCTCTT
1 AGGGATACTCCAACCCTCGTTTTCATTTTAAAAATACCAAGTTTTTCATCTC-T
**
5483348 A-GGATACTCCAACCCTCGTTTTCACTTTTAAAACAT-TGAA-TTTTTCATCTCT
1 AGGGATACTCCAACCCTCGTTTTCA-TTTTAAAA-ATACCAAGTTTTTCATCTCT
*
5483400 AGGGATACTCTAACCC
1 AGGGATACTCCAACCC
5483416 CACCATTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
52 13 0.22
53 35 0.59
54 9 0.15
55 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (53 bp):
AGGGATACTCCAACCCTCGTTTTCATTTTAAAAATACCAAGTTTTTCATCTCT
Found at i:5483432 original size:133 final size:131
Alignment explanation
Indices: 5483218--5483460 Score: 342
Period size: 133 Copynumber: 1.8 Consensus size: 131
5483208 ATTTTTTAAG
*
5483218 GGATACTCCAACCCCATTTTTACTTCTAAAACAGCAAAATTTTCATCTCAGAGATACTCCAACCC
1 GGATACTCCAACCCCATTTTCACTTCTAAAACAGCAAAATTTTCATCTCAGAGATACTCCAACCC
* * * *
5483283 TAACATTTTCGAAGGGATACTCCAACCTCGTTTTTATTTTCAAAATACCAAGTTTTTCATCTCTT
66 CAACATTTTCGAAGGGATACTCCAACCTAGTTTTTACTTCCAAAATACCAAGTTTTTCATCTCTT
5483348 A
131 A
* * *** * * *
5483349 GGATACTCCAACCCTCGTTTTCACTTTTAAAACATTGAATTTTTCATCTCTAGGGATACTCTAAC
1 GGATACTCCAACCC-CATTTTCACTTCTAAAACAGCAAAATTTTCATCTC-AGAGATACTCCAAC
*
5483414 CCCACCATTTTCGAAGGGATACTCCAACCTAGTTTTTACTTCCAAAA
64 CCCAACATTTTCGAAGGGATACTCCAACCTAGTTTTTACTTCCAAAA
5483461 CATTGAATTT
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
131 14 0.15
132 28 0.29
133 54 0.56
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.34
Consensus pattern (131 bp):
GGATACTCCAACCCCATTTTCACTTCTAAAACAGCAAAATTTTCATCTCAGAGATACTCCAACCC
CAACATTTTCGAAGGGATACTCCAACCTAGTTTTTACTTCCAAAATACCAAGTTTTTCATCTCTT
A
Found at i:5483464 original size:80 final size:82
Alignment explanation
Indices: 5483349--5483504 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 82
5483339 TCATCTCTTA
* ** * *
5483349 GGATACTCCAACCCTCGTTTTCACTTTTAAAACATTGAA-TTTTTCATCTCTAGGGATACTCTAA
1 GGATACTCCAACCCTAGTTTTCACTTCCAAAACATTGAATTTTTTCATCTCAAGGGATACTCCAA
5483413 CCCCACCATTTTCGAAG
66 CCCCACCATTTTCGAAG
* *
5483430 GGATACTCCAA-CCTAGTTTTTACTTCCAAAACATTGAATTTTTTTATCTCAAGGGATACTCCAA
1 GGATACTCCAACCCTAGTTTTCACTTCCAAAACATTGAATTTTTTCATCTCAAGGGATACTCCAA
* *
5483494 TCCCATCATTT
66 CCCCACCATTT
5483505 CAGAATTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
80 23 0.35
81 42 0.65
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (82 bp):
GGATACTCCAACCCTAGTTTTCACTTCCAAAACATTGAATTTTTTCATCTCAAGGGATACTCCAA
CCCCACCATTTTCGAAG
Found at i:5483543 original size:81 final size:81
Alignment explanation
Indices: 5483351--5483552 Score: 205
Period size: 81 Copynumber: 2.5 Consensus size: 81
5483341 ATCTCTTAGG
* *
5483351 ATACTCCAACCCTC-GTTTTCACTTTTAAAACATTGAA-TTTTTCATCTCTAGGGATACTCTAAC
1 ATACTCCAA-CCTCGGTTTT-ACTTTTAAAACATTGAATTTTTTCATCTCAAGGGATACTCCAAC
*
5483414 CCCACCATTTTCGAAGGG
64 CCCACCATTTTCGAAGGA
* * ** * *
5483432 ATACTCCAACCTAGTTTTTACTTCCAAAACATTGAATTTTTTTATCTCAAGGGATACTCCAATCC
1 ATACTCCAACCTCGGTTTTACTTTTAAAACATTGAATTTTTTCATCTCAAGGGATACTCCAACCC
* **
5483497 CATCA-TTTCAGAATTA
66 CACCATTTTC-GAAGGA
* * *
5483513 ATACTCTAACCTCGGTTTTAATTTTTAAACACTT-AATTTT
1 ATACTCCAACCTCGGTTTTACTTTTAAAACA-TTGAATTTT
5483553 ACATCTTTGG
Statistics
Matches: 98, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
80 22 0.22
81 74 0.76
82 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (81 bp):
ATACTCCAACCTCGGTTTTACTTTTAAAACATTGAATTTTTTCATCTCAAGGGATACTCCAACCC
CACCATTTTCGAAGGA
Found at i:5485657 original size:98 final size:97
Alignment explanation
Indices: 5485472--5485701 Score: 257
Period size: 98 Copynumber: 2.4 Consensus size: 97
5485462 ATGGGGTTGG
* * * * * * *
5485472 AGTATCCCCTCGAAAGCATGGGGTTAGAGTATCTCCGATGATGATTATTTAAGCAAAAATAAGGT
1 AGTATCCCCTCAAAAGAATGGGGTTGGAGTATCCCCAATGACGATTATTTAAGCAAAAATAAGAT
*
5485537 TTAAATATTGACAACTTTAAAAAACGCGGTTAA
66 TTAAATATTGACAAC-TAAAAAAACGCGGTTAA
* *
5485570 AGTATCCCCTCAAAAGAATGGGGTTGGAGTATCCCCAATGGCGATTATTTAAGTAAAAATAAGAT
1 AGTATCCCCTCAAAAGAATGGGGTTGGAGTATCCCCAATGACGATTATTTAAGCAAAAATAAGAT
* * * **
5485635 TTAAATATTGATGAA-TAAAAAAATGGGGTTGG
66 TTAAATATTGA-CAACTAAAAAAACGCGGTTAA
***
5485667 AGTATCCCCTCGAAAA-AACCAGGTTGGAGTATCCC
1 AGTATCCCCTC-AAAAGAATGGGGTTGGAGTATCCC
5485702 AGTGAATAAA
Statistics
Matches: 112, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
97 39 0.35
98 71 0.63
99 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (97 bp):
AGTATCCCCTCAAAAGAATGGGGTTGGAGTATCCCCAATGACGATTATTTAAGCAAAAATAAGAT
TTAAATATTGACAACTAAAAAAACGCGGTTAA
Found at i:5490654 original size:97 final size:96
Alignment explanation
Indices: 5490548--5490751 Score: 302
Period size: 96 Copynumber: 2.1 Consensus size: 96
5490538 TGTCTTCGAC
* *
5490548 GATGATAATTTAAGCAAAAATAATATTTAAATCATGACAAGTTTAAAAATAGGGTTGGAGTATCT
1 GATGATAATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTTAAAAAT-GGGTTGGAGTATCC
*
5490613 CCTTGGAAGAATGGGATTAGAGTATC-CCTGAT
65 CCTCGGAAGAATGGGATTAGAGTATCGCC-GAT
* * * *
5490645 GATGATAATTTATGCAAAAATAAGATTTAAATCTTGATAAGTTTAAAAATGGTTTGGAGTATCCC
1 GATGATAATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTTAAAAATGGGTTGGAGTATCCC
* *
5490710 CTCGGAAGAATGGGGTTGGAGTATCGCCGAT
66 CTCGGAAGAATGGGATTAGAGTATCGCCGAT
5490741 GATGATAATTT
1 GATGATAATTT
5490752 TGATAATTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
96 49 0.51
97 48 0.49
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (96 bp):
GATGATAATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTTAAAAATGGGTTGGAGTATCCC
CTCGGAAGAATGGGATTAGAGTATCGCCGAT
Found at i:5493110 original size:52 final size:52
Alignment explanation
Indices: 5493053--5493191 Score: 165
Period size: 52 Copynumber: 2.7 Consensus size: 52
5493043 ATTTGCTTGC
* * *
5493053 ATGTATCCATAC-ATTAAAGAATGTATTGATACCTT-TGGGTCAAAAACCTGGA
1 ATGTATCCATACAATGAAA-AATGTATCGATACATTGT-GGTCAAAAACCTGGA
* **
5493105 ATGTATCGATACAATGAAAAATGTATCGATACATTGTGGTCAAAAACCTAAA
1 ATGTATCCATACAATGAAAAATGTATCGATACATTGTGGTCAAAAACCTGGA
* * *
5493157 ATATATCGATACAATGAAAAATGTATCAATACATT
1 ATGTATCCATACAATGAAAAATGTATCGATACATT
5493192 TTCATTCTAG
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 71 0.92
53 6 0.08
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (52 bp):
ATGTATCCATACAATGAAAAATGTATCGATACATTGTGGTCAAAAACCTGGA
Found at i:5493755 original size:93 final size:92
Alignment explanation
Indices: 5493583--5493762 Score: 243
Period size: 93 Copynumber: 1.9 Consensus size: 92
5493573 CGACATATTT
* * * * * *
5493583 TGTGAATGTATCAATATATATGGTTGGTAGTAGATAAAAAATGCTAAAACCCTTATTTTTATCCA
1 TGTGAATGTATCAATACATATAGTTGGCAGTAGATAAAAAATCCTAAAACCCTTATTTGTATCAA
*
5493648 TACAAATGAAAATGTATGGATACATTA
66 TACAAATGAAAATGTATCGATACATTA
* * *
5493675 TGTGAATGTATCGATACATCTAGTTGGCAGTAGCTAAAAAAATCCTAAAACCCTTATTTGTATCA
1 TGTGAATGTATCAATACATATAGTTGGCAGTAGAT-AAAAAATCCTAAAACCCTTATTTGTATCA
* *
5493740 ATACACATGACAATGTATCGATA
65 ATACAAATGAAAATGTATCGATA
5493763 TAATACACAA
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
92 29 0.39
93 46 0.61
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (92 bp):
TGTGAATGTATCAATACATATAGTTGGCAGTAGATAAAAAATCCTAAAACCCTTATTTGTATCAA
TACAAATGAAAATGTATCGATACATTA
Found at i:5493775 original size:92 final size:92
Alignment explanation
Indices: 5493587--5493786 Score: 222
Period size: 93 Copynumber: 2.2 Consensus size: 92
5493577 ATATTTTGTG
* * * * * * * *
5493587 AATGTATCAATATATATGGTTGGTAGTAGATAAAAAATGCTAAAACCCTTATTTTTATCCATACA
1 AATGTATCGATACATCTAGTTGGCAGTAGATAAAAAATCCTAAAACCCTTATTTGTATCAATACA
* * ***
5493652 AATGAAAATGTATGGATACATTATGTG
66 AATGAAAATGTATCGATACAATATCAC
*
5493679 AATGTATCGATACATCTAGTTGGCAGTAGCTAAAAAAATCCTAAAACCCTTATTTGTATCAATAC
1 AATGTATCGATACATCTAGTTGGCAGTAGAT-AAAAAATCCTAAAACCCTTATTTGTATCAATAC
* * *
5493744 ACATGACAATGTATCGATATAATA-CAC
65 AAATGAAAATGTATCGATACAATATCAC
*
5493771 AATGTATTGATACATC
1 AATGTATCGATACATC
5493787 CTTAAATATA
Statistics
Matches: 89, Mismatches: 18, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
92 40 0.45
93 49 0.55
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (92 bp):
AATGTATCGATACATCTAGTTGGCAGTAGATAAAAAATCCTAAAACCCTTATTTGTATCAATACA
AATGAAAATGTATCGATACAATATCAC
Found at i:5496374 original size:13 final size:13
Alignment explanation
Indices: 5496356--5496381 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5496346 TACAGCAAGT
5496356 ATGTATCGATACA
1 ATGTATCGATACA
5496369 ATGTATCGATACA
1 ATGTATCGATACA
5496382 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5498632 original size:21 final size:21
Alignment explanation
Indices: 5498599--5498643 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5498589 TTGCAAGTTG
*
5498599 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
5498621 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
5498641 AAA
1 AAA
5498644 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:5502344 original size:8 final size:8
Alignment explanation
Indices: 5502331--5502362 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
5502321 ATTTGACTAA
5502331 ATTTTGTG
1 ATTTTGTG
5502339 ATTTTGTG
1 ATTTTGTG
5502347 ATTTTGTG
1 ATTTTGTG
5502355 ATTTTGTG
1 ATTTTGTG
5502363 TTGAATGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:5502582 original size:13 final size:13
Alignment explanation
Indices: 5502564--5502602 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
5502554 ACATTTTTCT
5502564 TTGTATCGATACA
1 TTGTATCGATACA
5502577 TTGTATCGATACA
1 TTGTATCGATACA
5502590 TTGTATCGATACA
1 TTGTATCGATACA
5502603 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5505173 original size:13 final size:13
Alignment explanation
Indices: 5505155--5505180 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5505145 TACAGCAAGT
5505155 ATGTATCGATACA
1 ATGTATCGATACA
5505168 ATGTATCGATACA
1 ATGTATCGATACA
5505181 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5507586 original size:59 final size:59
Alignment explanation
Indices: 5507518--5507674 Score: 176
Period size: 59 Copynumber: 2.7 Consensus size: 59
5507508 GATTCCTAAT
* * * *
5507518 TTATGGAAAATAGCCTAAATGACCCTAGGATGTATGAAAAGTGCATAATGGATCC-CAGA
1 TTATAGAAAATAGCCTAAATGACCCTAAGATGCATGAAAAATGCATAATGGA-CCTCAGA
* * *
5507577 TTATAGAAAATAACATAAAT-AGCCCTAAGATGCATGAAAAATGCATAATGGACCTTAGA
1 TTATAGAAAATAGCCTAAATGA-CCCTAAGATGCATGAAAAATGCATAATGGACCTCAGA
* * *
5507636 TTATAAAAAATAAG-CTAAATGACCTTAAAATGCATGAAA
1 TTATAGAAAAT-AGCCTAAATGACCCTAAGATGCATGAAA
5507675 TTGGCTAAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
58 3 0.04
59 77 0.94
60 2 0.02
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (59 bp):
TTATAGAAAATAGCCTAAATGACCCTAAGATGCATGAAAAATGCATAATGGACCTCAGA
Done.