Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 15 of 290
Found at i:5224299 original size:16 final size:16
Alignment explanation
Indices: 5224275--5224305 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5224265 GCTCCTCCCC
*
5224275 CTCTCTCTCTATCTCG
1 CTCTATCTCTATCTCG
5224291 CTCTATCTCTATCTC
1 CTCTATCTCTATCTC
5224306 TGTTGAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (16 bp):
CTCTATCTCTATCTCG
Found at i:5239121 original size:6 final size:6
Alignment explanation
Indices: 5239099--5239132 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5239089 GATTAATACT
* *
5239099 AAATCA AATTTA AAATCA AAATCA AAATCA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
5239133 TGATTTTACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (6 bp):
AAATCA
Found at i:5241502 original size:103 final size:103
Alignment explanation
Indices: 5241323--5241532 Score: 393
Period size: 103 Copynumber: 2.0 Consensus size: 103
5241313 GAGGCATATC
*
5241323 TTTGACATAGCTATGTATTTTTCTAAGTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
1 TTTGAAATAGCTATGTATTTTTCTAAGTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
5241388 TCTCTGACTCCAATATGTTGCGTATAAACCCGTTTGAG
66 TCTCTGACTCCAATATGTTGCGTATAAACCCGTTTGAG
*
5241426 TTTGAAATAGCTATGTATTTTTCTAATTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
1 TTTGAAATAGCTATGTATTTTTCTAAGTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
*
5241491 TCTCTGACTCCAATATGTTGCGTATAAACTCGTTTGAG
66 TCTCTGACTCCAATATGTTGCGTATAAACCCGTTTGAG
5241529 TTTG
1 TTTG
5241533 TTTATCACTT
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.41
Consensus pattern (103 bp):
TTTGAAATAGCTATGTATTTTTCTAAGTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
TCTCTGACTCCAATATGTTGCGTATAAACCCGTTTGAG
Found at i:5241917 original size:21 final size:21
Alignment explanation
Indices: 5241891--5241959 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
5241881 ACAATATTAT
5241891 AATAAAAAATAGTTAGTTCAA
1 AATAAAAAATAGTTAGTTCAA
* * *
5241912 AATAAACCTAAACA-ATA-TT-AT
1 AATAAA---AAATAGTTAGTTCAA
5241933 AATAAAAAATAGTTAGTTCAA
1 AATAAAAAATAGTTAGTTCAA
5241954 AATAAA
1 AATAAA
5241960 CCTAAAGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 4 0.11
19 2 0.06
20 2 0.06
21 20 0.56
22 2 0.06
23 2 0.06
24 4 0.11
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (21 bp):
AATAAAAAATAGTTAGTTCAA
Found at i:5241933 original size:42 final size:42
Alignment explanation
Indices: 5241881--5241965 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
5241871 TAAAATATAT
5241881 ACAATATTATAATAAAAAATAGTTAGTTCAAAATAAACCTAA
1 ACAATATTATAATAAAAAATAGTTAGTTCAAAATAAACCTAA
5241923 ACAATATTATAATAAAAAATAGTTAGTTCAAAATAAACCTAA
1 ACAATATTATAATAAAAAATAGTTAGTTCAAAATAAACCTAA
5241965 A
1 A
5241966 GTTTTACATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.28
Consensus pattern (42 bp):
ACAATATTATAATAAAAAATAGTTAGTTCAAAATAAACCTAA
Found at i:5242735 original size:22 final size:22
Alignment explanation
Indices: 5242710--5242753 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5242700 ATTTTTTAAA
*
5242710 ATTTTTTAGAATAATAAATTAT
1 ATTTATTAGAATAATAAATTAT
* * *
5242732 ATTTATTATATTAATAATTTAT
1 ATTTATTAGAATAATAAATTAT
5242754 TATATGACTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTATTAGAATAATAAATTAT
Found at i:5247688 original size:22 final size:22
Alignment explanation
Indices: 5247633--5247698 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
5247623 TTGATCAAGG
* *
5247633 AAGTCTTGAGACAATCTAACTT
1 AAGTCTCGAGACAATGTAACTT
*
5247655 AAGTCTCAAGACAATGTAACTT
1 AAGTCTCGAGACAATGTAACTT
** * *
5247677 TTGTTTCGAGACAATGTCACTT
1 AAGTCTCGAGACAATGTAACTT
5247699 CGAAGCTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (22 bp):
AAGTCTCGAGACAATGTAACTT
Found at i:5248510 original size:11 final size:11
Alignment explanation
Indices: 5248463--5248510 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
5248453 TTTTTTTCAC
5248463 TATTTTGCTAT
1 TATTTTGCTAT
* *
5248474 CATTTTACTAT
1 TATTTTGCTAT
* *
5248485 TATGTTGCTAC
1 TATTTTGCTAT
*
5248496 TATTTTGCTGT
1 TATTTTGCTAT
5248507 TATT
1 TATT
5248511 ATTTGGATAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.58
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:5249648 original size:22 final size:21
Alignment explanation
Indices: 5249595--5249650 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
5249585 TGAAGTTACG
* *
5249595 AAAATAAAATGTATGATACAT
1 AAAAGAAAATGTTTGATACAT
*
5249616 AAAAGAGAATGTTTGTATACAT
1 AAAAGAAAATGTTTG-ATACAT
* *
5249638 ATATGAAAATGTT
1 AAAAGAAAATGTT
5249651 AAGAAACTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (21 bp):
AAAAGAAAATGTTTGATACAT
Found at i:5251636 original size:26 final size:24
Alignment explanation
Indices: 5251607--5251655 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
5251597 TTAAATAAAA
* *
5251607 ATTTTAAAATATAATAAATCAAATAC
1 ATTTAAAAACATAA-AAA-CAAATAC
5251633 ATTTAAAAACATAAAAACAAATA
1 ATTTAAAAACATAAAAACAAATA
5251656 TTAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAC
Found at i:5251774 original size:23 final size:23
Alignment explanation
Indices: 5251748--5251794 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
5251738 ATTAAAATTG
*
5251748 AAAAT-AAAATATAAATATGATTT
1 AAAATAAAAATAAAAATAT-ATTT
5251771 AAAATAAAAATAAAAATATATTT
1 AAAATAAAAATAAAAATATATTT
5251794 A
1 A
5251795 GTATATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
AAAATAAAAATAAAAATATATTT
Found at i:5265020 original size:20 final size:20
Alignment explanation
Indices: 5264987--5265064 Score: 65
Period size: 19 Copynumber: 4.0 Consensus size: 20
5264977 TTAAATTTAT
* * *
5264987 TAAAAATTAGAAAAAATCTA
1 TAAAAATCATAAAAAATATA
5265007 TAAAAATCAT-AAAAATATA
1 TAAAAATCATAAAAAATATA
* *
5265026 TTAAAAA--ATATAAAATTTTA
1 -TAAAAATCATA-AAAAATATA
5265046 TAAAAATCAT-AAAAATATA
1 TAAAAATCATAAAAAATATA
5265065 AAATGCATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
18 2 0.04
19 21 0.46
20 21 0.46
21 2 0.04
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (20 bp):
TAAAAATCATAAAAAATATA
Found at i:5265064 original size:17 final size:18
Alignment explanation
Indices: 5264999--5265076 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 18
5264989 AAAATTAGAA
*
5264999 AAAATCTATAAAAATCAT
1 AAAATATATAAAAATCAT
5265017 AAAAATATATTAAAAAAT-AT
1 -AAAATATA-T-AAAAATCAT
*
5265037 AAAATTTTATAAAAATCAT
1 AAAA-TATATAAAAATCAT
5265056 AAAA-ATAT-AAAATGCAT
1 AAAATATATAAAAAT-CAT
5265073 AAAA
1 AAAA
5265077 AGAACTTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
16 5 0.10
17 10 0.20
18 6 0.12
19 18 0.35
20 6 0.12
21 6 0.12
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.28
Consensus pattern (18 bp):
AAAATATATAAAAATCAT
Found at i:5265291 original size:8 final size:9
Alignment explanation
Indices: 5265277--5265450 Score: 54
Period size: 9 Copynumber: 18.6 Consensus size: 9
5265267 TTTTTTACGA
5265277 ATTTTATAT
1 ATTTTATAT
5265286 -TTTTATAT
1 ATTTTATAT
5265294 ATTTT-TAT
1 ATTTTATAT
* *
5265302 AATTTTCTTACG
1 -ATTTT-ATA-T
* *
5265314 ACTTTATAAA
1 ATTTTAT-AT
5265324 ATTTTATATT
1 ATTTTATA-T
* *
5265334 TTTTTCTAT
1 ATTTTATAT
5265343 ATTTTATACT
1 ATTTTATA-T
*
5265353 -TTTTTTAT
1 ATTTTATAT
5265361 AATTTT-TAT
1 -ATTTTATAT
* *
5265370 ATTTTTTTT
1 ATTTTATAT
*
5265379 AATTTTTAGTAA
1 -A-TTTTA-TAT
*
5265391 ATTTTAAAT
1 ATTTTATAT
5265400 ATTTT-TAT
1 ATTTTATAT
*
5265408 ATTTTTATTAA
1 A-TTTTA-TAT
*
5265419 AATTTA-AT
1 ATTTTATAT
*
5265427 AATTTTATAA
1 -ATTTTATAT
*
5265437 ATTTTATAA
1 ATTTTATAT
5265446 ATTTT
1 ATTTT
5265451 TAAATGTGAT
Statistics
Matches: 123, Mismatches: 23, Indels: 38
0.67 0.12 0.21
Matches are distributed among these distances:
8 21 0.17
9 57 0.46
10 29 0.24
11 15 0.12
12 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (9 bp):
ATTTTATAT
Found at i:5265294 original size:10 final size:10
Alignment explanation
Indices: 5265281--5265413 Score: 77
Period size: 10 Copynumber: 13.8 Consensus size: 10
5265271 TTACGAATTT
5265281 TATATTTTTA
1 TATATTTTTA
5265291 TATATTTTTA
1 TATATTTTTA
5265301 TA-ATTTTCT-
1 TATATTTT-TA
* *
5265310 TACGA-CTTTA
1 TA-TATTTTTA
* *
5265320 TAAAATTTTA
1 TATATTTTTA
* *
5265330 TATTTTTTTC
1 TATATTTTTA
5265340 TATA-TTTTA
1 TATATTTTTA
*
5265349 TACTTTTTTTA
1 TA-TATTTTTA
5265360 TA-ATTTTTA
1 TATATTTTTA
*
5265369 TAT-TTTTTT
1 TATATTTTTA
5265378 TA-ATTTTTA
1 TATATTTTTA
*
5265387 GTA-AATTTTA
1 -TATATTTTTA
*
5265397 AATATTTTTA
1 TATATTTTTA
5265407 TAT-TTTT
1 TATATTTT
5265414 ATTAAAATTT
Statistics
Matches: 95, Mismatches: 17, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
9 40 0.42
10 47 0.49
11 8 0.08
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (10 bp):
TATATTTTTA
Found at i:5265298 original size:39 final size:39
Alignment explanation
Indices: 5265255--5265415 Score: 127
Period size: 39 Copynumber: 4.2 Consensus size: 39
5265245 TGGTACAATA
*
5265255 ATTTTTATAATTTTTTTTACGAATTTTATATTTTTATAT
1 ATTTTTATAATTTTTTTTACGAATTTTAAATTTTTATAT
* * *
5265294 ATTTTTATAA-TTTTCTTACGACTTTATAAAATTTTATAT
1 ATTTTTATAATTTTTTTTACGAATTT-TAAATTTTTATAT
* * * * ***
5265333 TTTTTTCT-ATATTTTATACTTTTTTTATAATTTTTATAT
1 ATTTTTATAATTTTTTTTACGAATTTTA-AATTTTTATAT
* **
5265372 -TTTTTTTAATTTTTAGTA--AATTTTAAATATTTT-TAT
1 ATTTTTATAATTTTTTTTACGAATTTTAAAT-TTTTATAT
5265408 ATTTTTAT
1 ATTTTTAT
5265416 TAAAATTTAA
Statistics
Matches: 96, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
36 6 0.06
37 15 0.16
38 22 0.23
39 53 0.55
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (39 bp):
ATTTTTATAATTTTTTTTACGAATTTTAAATTTTTATAT
Found at i:5265357 original size:20 final size:18
Alignment explanation
Indices: 5265323--5265444 Score: 86
Period size: 19 Copynumber: 6.5 Consensus size: 18
5265313 GACTTTATAA
*
5265323 AATTTTATATTTTTTTCT
1 AATTTTATATTTTTTTAT
5265341 ATATTTTATACTTTTTTTAT
1 A-ATTTTATA-TTTTTTTAT
5265361 AATTTTTATATTTTTTT-T
1 AA-TTTTATATTTTTTTAT
* **
5265379 AATTTTTAGTAAATTTTAAAT
1 AA-TTTTA-T-ATTTTTTTAT
* *
5265400 ATTTTTATATTTTTATTAA
1 AATTTTATATTTTT-TTAT
* * *
5265419 AATTTAATAATTTTATA-
1 AATTTTATATTTTTTTAT
5265436 AATTTTATA
1 AATTTTATA
5265445 AATTTTTAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
17 8 0.10
18 17 0.20
19 30 0.36
20 26 0.31
21 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (18 bp):
AATTTTATATTTTTTTAT
Found at i:5265358 original size:11 final size:10
Alignment explanation
Indices: 5265325--5265377 Score: 56
Period size: 9 Copynumber: 5.4 Consensus size: 10
5265315 CTTTATAAAA
5265325 TTTTATATTT
1 TTTTATATTT
* *
5265335 TTTTCTA-TA
1 TTTTATATTT
5265344 TTTTATACTTT
1 TTTTATA-TTT
*
5265355 TTTTATA-AT
1 TTTTATATTT
5265364 TTTTATATTT
1 TTTTATATTT
5265374 TTTT
1 TTTT
5265378 TAATTTTTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 15 0.44
10 11 0.32
11 8 0.24
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTATATTT
Found at i:5265414 original size:18 final size:19
Alignment explanation
Indices: 5265316--5265452 Score: 79
Period size: 19 Copynumber: 7.2 Consensus size: 19
5265306 TTCTTACGAC
*
5265316 TTTATA-AAATTTTATATT
1 TTTATATAATTTTTATATT
* *
5265334 TTTTTCT-ATATTTTATACTT
1 TTTATATAAT-TTTTATA-TT
*
5265354 TTTTTATAATTTTTATATT
1 TTTATATAATTTTTATATT
* *
5265373 TTT-TTTAATTTTTAGTAAAT
1 TTTATATAATTTTTA-T-ATT
*
5265393 TTTAAAT-ATTTTTATATT
1 TTTATATAATTTTTATATT
* * *
5265411 TTTAT-TAAAATTTAATAAT
1 TTTATAT-AATTTTTATATT
*
5265430 TTTATA-AATTTTATAAATT
1 TTTATATAATTTT-TATATT
5265449 TTTA
1 TTTA
5265453 AATGTGATTG
Statistics
Matches: 91, Mismatches: 17, Indels: 21
0.71 0.13 0.16
Matches are distributed among these distances:
17 1 0.01
18 26 0.29
19 34 0.37
20 27 0.30
21 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTATATAATTTTTATATT
Found at i:5265427 original size:27 final size:28
Alignment explanation
Indices: 5265374--5265435 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
5265364 TTTTATATTT
*
5265374 TTTTTA-ATTTTTAGTAAATTTTAAATA
1 TTTTTATATTTTTAGTAAAATTTAAATA
*
5265401 TTTTTATATTTTTATTAAAATTT-AATA
1 TTTTTATATTTTTAGTAAAATTTAAATA
*
5265428 ATTTTATA
1 TTTTTATA
5265436 AATTTTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 17 0.55
28 14 0.45
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTTATATTTTTAGTAAAATTTAAATA
Found at i:5265440 original size:17 final size:17
Alignment explanation
Indices: 5265418--5265455 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5265408 ATTTTTATTA
5265418 AAATTTAAT-AATTTTAT
1 AAATTTAATAAATTTT-T
*
5265435 AAATTTTATAAATTTTT
1 AAATTTAATAAATTTTT
5265452 AAAT
1 AAAT
5265456 GTGATTGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATTTAATAAATTTTT
Found at i:5265446 original size:27 final size:29
Alignment explanation
Indices: 5265373--5265455 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 29
5265363 TTTTTATATT
* * *
5265373 TTTTTTAATTTTTAGTAAATTTTAAATAT
1 TTTTATAATTTTTAGTAAAATTTAAATAA
*
5265402 TTTTAT-ATTTTTATTAAAATTT-AATAA
1 TTTTATAATTTTTAGTAAAATTTAAATAA
* *
5265429 TTTTATAAATTTTA-TAAATTTTTAAAT
1 TTTTATAATTTTTAGTAAA-ATTTAAAT
5265456 GTGATTGTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
27 14 0.31
28 23 0.51
29 8 0.18
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TTTTATAATTTTTAGTAAAATTTAAATAA
Found at i:5265450 original size:38 final size:38
Alignment explanation
Indices: 5265355--5265452 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 38
5265345 TTTATACTTT
* ** *
5265355 TTTTAT-AATTTTTATATTTTTTTTAATTTTTAGTAAA
1 TTTTATAAATTTTTATATTTTTATTAAAATTTAATAAA
5265392 TTTTA-AATATTTTTATATTTTTATTAAAATTTAAT-AA
1 TTTTATAA-ATTTTTATATTTTTATTAAAATTTAATAAA
*
5265429 TTTTATAAATTTTATAAATTTTTA
1 TTTTATAAATTTT-TATATTTTTA
5265453 AATGTGATTG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
37 18 0.35
38 34 0.65
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (38 bp):
TTTTATAAATTTTTATATTTTTATTAAAATTTAATAAA
Found at i:5265454 original size:8 final size:9
Alignment explanation
Indices: 5265355--5265455 Score: 66
Period size: 9 Copynumber: 11.1 Consensus size: 9
5265345 TTTATACTTT
*
5265355 TTTTATAAT
1 TTTTATAAA
**
5265364 TTTTATATT
1 TTTTATAAA
* *
5265373 TTTTTTAAT
1 TTTTATAAA
5265382 TTTTAGTAAA
1 TTTTA-TAAA
5265392 TTTTA-AATA
1 TTTTATAA-A
*
5265401 TTTT-TATAT
1 TTTTATA-AA
5265410 TTTTATTAAA
1 TTTTA-TAAA
*
5265420 ATTTA-ATAA
1 TTTTATA-AA
5265429 TTTTATAAA
1 TTTTATAAA
5265438 TTTTATAAA
1 TTTTATAAA
5265447 TTTT-TAAA
1 TTTTATAAA
5265455 T
1 T
5265456 GTGATTGTGG
Statistics
Matches: 75, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
8 8 0.11
9 50 0.67
10 15 0.20
11 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTATAAA
Found at i:5269148 original size:23 final size:23
Alignment explanation
Indices: 5269105--5269148 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5269095 AAAAAATATC
* *
5269105 TATTTATATTATTTTTAATTTAA
1 TATTTATATGATTTATAATTTAA
5269128 TATTTA-ATGATTTATATATTT
1 TATTTATATGATTTATA-ATTT
5269149 TTTTATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTTATATGATTTATAATTTAA
Found at i:5274731 original size:11 final size:11
Alignment explanation
Indices: 5274715--5274770 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
5274705 AAGAAAAAAA
5274715 TTATTGTTTTC
1 TTATTGTTTTC
5274726 TTATTGTTTTC
1 TTATTGTTTTC
** *
5274737 CCATTATTTTAC
1 TTATTGTTTT-C
*
5274749 -TATTGTTTTT
1 TTATTGTTTTC
*
5274759 TTGTTGTTTTC
1 TTATTGTTTTC
5274770 T
1 T
5274771 CACTATTTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 34 0.97
12 1 0.03
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.70
Consensus pattern (11 bp):
TTATTGTTTTC
Found at i:5274766 original size:33 final size:33
Alignment explanation
Indices: 5274716--5274779 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
5274706 AGAAAAAAAT
*
5274716 TATTGTTTTCTTATTGTTTTCCCATTATTTTAC
1 TATTGTTTTCTTATTGTTTTCCCACTATTTTAC
* * *
5274749 TATTGTTTTTTTGTTGTTTTCTCACTATTTT
1 TATTGTTTTCTTATTGTTTTCCCACTATTTT
5274780 GTTACCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.12, C:0.12, G:0.08, T:0.67
Consensus pattern (33 bp):
TATTGTTTTCTTATTGTTTTCCCACTATTTTAC
Found at i:5277740 original size:2 final size:2
Alignment explanation
Indices: 5277733--5277758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5277723 TGAGCACTCC
5277733 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
5277759 ATACACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5288131 original size:40 final size:44
Alignment explanation
Indices: 5288087--5288173 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
5288077 AATAATATTT
*
5288087 AAATTAGT-TAA-TATTATT-ATATTTTAATA-AGAATATAAAA
1 AAATTAGTATAACTATTATTAATATTTTAATATAGAAAATAAAA
* *
5288127 AAATTATTATAACTTATTATTAATATTTTAATATATAAAATAAAA
1 AAATTAGTATAAC-TATTATTAATATTTTAATATAGAAAATAAAA
5288172 AA
1 AA
5288174 TTTAAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
40 7 0.18
41 3 0.08
43 7 0.18
44 11 0.28
45 11 0.28
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (44 bp):
AAATTAGTATAACTATTATTAATATTTTAATATAGAAAATAAAA
Found at i:5288267 original size:33 final size:31
Alignment explanation
Indices: 5288191--5288271 Score: 80
Period size: 33 Copynumber: 2.6 Consensus size: 31
5288181 ATTTTTAAGT
*
5288191 AATA-AATATT-AATTATTTATAAA-ATTTA
1 AATATAATATTAAATTATTTTTAAATATTTA
* *
5288219 ATTAGAATATATAAATTATATTTTAAATATTTA
1 AATATAATAT-TAAATTAT-TTTTAAATATTTA
5288252 AATATAACTATTAAA-TATTT
1 AATATAA-TATTAAATTATTT
5288272 GTAATTAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 3 0.07
29 5 0.12
30 1 0.02
31 8 0.19
32 9 0.21
33 14 0.33
34 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (31 bp):
AATATAATATTAAATTATTTTTAAATATTTA
Found at i:5293275 original size:16 final size:16
Alignment explanation
Indices: 5293254--5293285 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5293244 TCTTTCATGA
*
5293254 TTCCCAGTGGAATAGC
1 TTCCCAATGGAATAGC
5293270 TTCCCAATGGAATAGC
1 TTCCCAATGGAATAGC
5293286 AAATTTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (16 bp):
TTCCCAATGGAATAGC
Found at i:5312547 original size:9 final size:9
Alignment explanation
Indices: 5312533--5312637 Score: 54
Period size: 9 Copynumber: 11.2 Consensus size: 9
5312523 ATTTTAGAAT
5312533 ATTTTTAAA
1 ATTTTTAAA
*
5312542 ATTTTTATAT
1 ATTTTTA-AA
5312552 ATTCTTTAGAA
1 ATT-TTTA-AA
*
5312563 TTTTCTTAAA
1 ATTT-TTAAA
*
5312573 ATTTTTTTATA
1 A--TTTTTAAA
5312584 ATTTTTAAA
1 ATTTTTAAA
** *
5312593 AAATAT-AA
1 ATTTTTAAA
*
5312601 ATTTTGAAA
1 ATTTTTAAA
*
5312610 ATTTTAAAA
1 ATTTTTAAA
5312619 ATATTTT-AA
1 AT-TTTTAAA
5312628 A-TTTTAAA
1 ATTTTTAAA
5312636 AT
1 AT
5312638 CTATTTTGAA
Statistics
Matches: 71, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
7 4 0.06
8 7 0.10
9 32 0.45
10 10 0.14
11 15 0.21
12 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:5312560 original size:31 final size:31
Alignment explanation
Indices: 5312525--5312583 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5312515 AAATTATTAT
5312525 TTTAGAATATTT-TTAAAATTTTTATATATTC
1 TTTAGAAT-TTTCTTAAAATTTTTATATATTC
*
5312556 TTTAGAATTTTCTTAAAATTTTTTTATA
1 TTTAGAATTTTCTTAAAATTTTTATATA
5312584 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTAGAATTTTCTTAAAATTTTTATATATTC
Found at i:5314617 original size:39 final size:40
Alignment explanation
Indices: 5314574--5314655 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 40
5314564 AAACATTATT
* *
5314574 TAATAAAATATTTATTATATTTAT--TTGTGTTTTTTAATA
1 TAATAAAACATTTATTATATTTATGGTAGTG-TTTTTAATA
*
5314613 TAATAAAGCATTTATTATATTTATGGTAGTGTTTTTAATA
1 TAATAAAACATTTATTATATTTATGGTAGTGTTTTTAATA
5314653 TAA
1 TAA
5314656 ACACTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 22 0.58
40 12 0.32
41 4 0.11
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.54
Consensus pattern (40 bp):
TAATAAAACATTTATTATATTTATGGTAGTGTTTTTAATA
Found at i:5320208 original size:9 final size:9
Alignment explanation
Indices: 5320196--5320234 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
5320186 AATTTAGCTT
*
5320196 TTTTAAAAA
1 TTTTAAATA
*
5320205 TTTTAATTA
1 TTTTAAATA
*
5320214 TTTTAAATT
1 TTTTAAATA
5320223 TTTTAAATA
1 TTTTAAATA
5320232 TTT
1 TTT
5320235 AATGACATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTAAATA
Found at i:5331588 original size:3 final size:3
Alignment explanation
Indices: 5331527--5331579 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
5331517 TTTGTTAACT
* *
5331527 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
*
5331572 TTA GTA TT
1 TTA TTA TT
5331580 GGTATTATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5331787 original size:36 final size:36
Alignment explanation
Indices: 5331708--5331787 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
5331698 AATTTGTTTA
* *
5331708 ATATATATACGTATACTCATATTTCTTTTTATATAT
1 ATATATATACATATACTCATATTTATTTTTATATAT
* *
5331744 ATCTATATACATATACAT-ATTTTTATTTTTATA-AGT
1 ATATATATACATATAC-TCATATTTATTTTTATATA-T
5331780 ATATATAT
1 ATATATAT
5331788 TTATGTATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.03
36 35 0.95
37 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (36 bp):
ATATATATACATATACTCATATTTATTTTTATATAT
Found at i:5342999 original size:1 final size:1
Alignment explanation
Indices: 5342993--5343017 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5342983 TTTGCTTCCT
5342993 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
5343018 GGGAACTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5344278 original size:46 final size:44
Alignment explanation
Indices: 5344225--5344553 Score: 222
Period size: 44 Copynumber: 7.6 Consensus size: 44
5344215 TATATACAGG
*
5344225 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA--TCAGA
* * * *
5344271 TCTTATCTCCCTGAGATTACGGCGGAGCGGATCAAAG-AT-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATCAG--A
* * * * * *
5344315 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATCAGA
* * * *
5344354 TCTTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--A-CATCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGAATCAGA
*
5344395 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA--TCAGA
* * ** * *
5344441 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-GAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-AATCAGA
* *
5344485 TCTTATCTCCCTGAGATTACAGCGGAACAGATCAAAG-A-CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATCA-GA
*
5344528 TCCTATCTCCCTGA-AGTTACAGTGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGA
5344554 GTGGATTAAA
Statistics
Matches: 223, Mismatches: 41, Indels: 41
0.73 0.13 0.13
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 23 0.10
40 1 0.00
41 28 0.13
42 6 0.03
43 25 0.11
44 68 0.30
45 1 0.00
46 68 0.30
47 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATCAGA
Found at i:5344505 original size:44 final size:43
Alignment explanation
Indices: 5344225--5344593 Score: 191
Period size: 44 Copynumber: 8.5 Consensus size: 43
5344215 TATATACAGG
* ** * *
5344225 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCA---GAGA
* * * * *
5344271 TCTTATCTCCCTGAGATTACGGCGGAGCGGATCAAAG-ATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAG--A
* * * *
5344315 TCCTATCTCCTTGAGATTACAATGGAGCGGATT-AA--AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAGA
* * * * * *
5344354 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAGCAGAGA
* ** * *
5344395 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCA---GAGA
* *
5344441 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG-CAGAGA
* * * **
5344485 TCTTATCTCCCTGAGATTACAGCGGAACAGATCAAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG-CAGAGA
* ** ** *
5344528 TCCTATCTCCCTGA-AGTTACAGTGGAGTGGATTAAAATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAGCAGA-GA
* *
5344572 TCTTATCTCTCTGAGGTTACAG
1 TCTTATCTCCCTGAGATTACAG
5344594 CAGAGTAGGT
Statistics
Matches: 247, Mismatches: 59, Indels: 36
0.72 0.17 0.11
Matches are distributed among these distances:
38 1 0.00
39 24 0.10
40 1 0.00
41 30 0.12
42 9 0.04
43 31 0.13
44 84 0.34
45 2 0.01
46 64 0.26
47 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAGA
Found at i:5344586 original size:87 final size:88
Alignment explanation
Indices: 5344395--5344594 Score: 226
Period size: 87 Copynumber: 2.3 Consensus size: 88
5344385 TCACATCAGG
* * *
5344395 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAA--TCAGATCCTATCTCCCTGAAGTTA
* **
5344460 CAGTGGAGCAGATTGAAGCCAGAGA
64 CAGTGGAGCAGATTAAAGAAAGAGA
* *
5344485 TCTTATCTCCCTGAGATTACAGCGGAACAGATCAAAG-A-CACTATCCTATCTCCCTGAAGTTAC
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCA-GATCCTATCTCCCTGAAGTTAC
** *
5344548 AGTGGAGTGGATTAAAATAAAG-GA
65 AGTGGAGCAGATT-AAAGAAAGAGA
* *
5344572 TCTTATCTCTCTGAGGTTACAGC
1 TCTTATCTCCCTGAGATTACAGC
5344595 AGAGTAGGTC
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
86 2 0.02
87 53 0.56
88 4 0.04
89 1 0.01
90 35 0.37
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCAGATCCTATCTCCCTGAAGTTACA
GTGGAGCAGATTAAAGAAAGAGA
Found at i:5346198 original size:3 final size:3
Alignment explanation
Indices: 5346137--5346189 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
5346127 TTTGTTAACT
* *
5346137 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
*
5346182 TTA GTA TT
1 TTA TTA TT
5346190 GGTATTATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5346397 original size:36 final size:36
Alignment explanation
Indices: 5346318--5346397 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
5346308 AATTTGTTTA
* *
5346318 ATATATATACGTATACTCATATTTCTTTTTATATAT
1 ATATATATACATATACTCATATTTATTTTTATATAT
* *
5346354 ATCTATATACATATACAT-ATTTTTATTTTTATA-AGT
1 ATATATATACATATAC-TCATATTTATTTTTATATA-T
5346390 ATATATAT
1 ATATATAT
5346398 TATATGTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.03
36 35 0.95
37 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (36 bp):
ATATATATACATATACTCATATTTATTTTTATATAT
Found at i:5355699 original size:12 final size:12
Alignment explanation
Indices: 5355682--5355706 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5355672 AGTTTTGTTG
5355682 TTAAACAAATAA
1 TTAAACAAATAA
5355694 TTAAACAAATAA
1 TTAAACAAATAA
5355706 T
1 T
5355707 CTCACAAACT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAACAAATAA
Found at i:5367163 original size:35 final size:35
Alignment explanation
Indices: 5367117--5367185 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
5367107 ACTTCAATAT
*
5367117 TATTAATAATTATAATATAGTATGTATTGTAGATA
1 TATTAATAATTATAAAATAGTATGTATTGTAGATA
*
5367152 TATTATTAATTATAAAATAGTATGTATTGTAGAT
1 TATTAATAATTATAAAATAGTATGTATTGTAGAT
5367186 TAATGAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (35 bp):
TATTAATAATTATAAAATAGTATGTATTGTAGATA
Found at i:5375269 original size:11 final size:11
Alignment explanation
Indices: 5375253--5375286 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5375243 CAAGGAGAGA
5375253 AGGGAGAGGAG
1 AGGGAGAGGAG
5375264 AGGGAGAGGGAG
1 AGGGAGA-GGAG
*
5375276 AGGCAGAGGAG
1 AGGGAGAGGAG
5375287 GTGGTGCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.35, C:0.03, G:0.62, T:0.00
Consensus pattern (11 bp):
AGGGAGAGGAG
Found at i:5379207 original size:123 final size:124
Alignment explanation
Indices: 5378888--5379375 Score: 559
Period size: 130 Copynumber: 3.8 Consensus size: 124
5378878 AGCCGAGTGA
* * * * *
5378888 AATTTTGAAGGGATATTTGATTATTTTAAAC-AAT-CGAGCAATTGCTACCCAACACGTTAGGGC
1 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGA--AATTGCAACCCAACACGTTAGGGC
* * * * * * ** * * *
5378951 ACGATCCCACAAATTGCCAAATACCGAATATCGCCTTCGTTTTAGGGATTTTAAAAGACACGAGC
64 ACGATTCCGCAAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTT-AATGA-A--TG-
5379016 G
124 G
* * * * *
5379017 AAATTTCAAAGTGATATTCGATTATTTTGAGCAAATGTGAAATTGCAACCCAACACGTTAGGGCA
1 -AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCA
5379082 CGATTCCGCAAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTT-ATGAATGG
65 CGATTCCGCAAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTAATGAATGG
*
5379141 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGTCAC
1 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCAC
* *
5379206 GATTTCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTAAAAGAAATGAATGG
66 GATTCCGCAAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTT------AATGAATGG
* *
5379271 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATACGAAATTGCAATCCAACACGTTAGGGCAC
1 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCAC
* * * *
5379336 GATTCCGCGAATTGCCGAACATCAAATTTCGTCTTCGTTT
66 GATTCCGCAAATTGCCAAACATCAAATCTCATCTTCGTTT
5379376 TGAAGAATTT
Statistics
Matches: 315, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
123 107 0.34
124 1 0.00
125 1 0.00
127 1 0.00
128 3 0.01
130 197 0.63
131 3 0.01
132 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (124 bp):
AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCAC
GATTCCGCAAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTAATGAATGG
Found at i:5379223 original size:253 final size:252
Alignment explanation
Indices: 5378888--5379375 Score: 645
Period size: 253 Copynumber: 1.9 Consensus size: 252
5378878 AGCCGAGTGA
* * *
5378888 AATTTTGAAGGGATATTTGATTATTTTAAACAATCGAGCAATTGCTACCCAACACGTTAGGGCAC
1 AATTTCGAAGGGAAATTTGATTATTTTAAACAATCGA-CAATTGCAACCCAACACGTTAGGGCAC
* * * * * *
5378953 GATCCCACAAATTGCCAAATACCGAATATCGCCTTCGTTTTAGGGATTTTAAAAGACACGAGCGA
65 GATCCCACAAATTGCCAAACACCAAATATCACCTTCGTTTAAGGGATTTTAAAAGAAACGAACGA
* * **
5379018 AATTTCAAAGTGATATTCGATTATTTTGAGCAAATGTGAAATTGCAACCCAACACGTTAGGGCAC
130 AATTTCAAAGGGAAATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCAC
5379083 GATTCCGCAAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTATGAATGG
195 GATTCCGCAAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTATGAATGG
* * *
5379141 AATTTCGAAGGGAAATTTGATTATTTTGAGCAAATGCGA-AATTGCAACCCAACACGTTAGGTCA
1 AATTTCGAAGGGAAATTTGATTATTTTAAAC-AAT-CGACAATTGCAACCCAACACGTTAGGGCA
** * * * * * * *
5379205 CGATTTCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTAAAAGAAATGAATG
64 CGATCCCACAAATTGCCAAACACCAAATATCACCTTCGTTTAAGGGATTTTAAAAGAAACGAACG
* * * *
5379270 GAATTTCGAAGGGAAATTTGATTATTTTGAGCAAATACGAAATTGCAATCCAACACGTTAGGGCA
129 AAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCA
* * * *
5379335 CGATTCCGCGAATTGCCGAACATCAAATTTCGTCTTCGTTT
194 CGATTCCGCAAATTGCCAAACATCAAATCTCATCTTCGTTT
5379376 TGAAGAATTT
Statistics
Matches: 200, Mismatches: 33, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
253 194 0.97
254 3 0.01
255 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (252 bp):
AATTTCGAAGGGAAATTTGATTATTTTAAACAATCGACAATTGCAACCCAACACGTTAGGGCACG
ATCCCACAAATTGCCAAACACCAAATATCACCTTCGTTTAAGGGATTTTAAAAGAAACGAACGAA
ATTTCAAAGGGAAATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCACG
ATTCCGCAAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATTTTATGAATGG
Found at i:5388751 original size:2 final size:2
Alignment explanation
Indices: 5388744--5388770 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5388734 TCAGTTCAAC
5388744 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5388771 AAGAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5397279 original size:60 final size:59
Alignment explanation
Indices: 5397206--5397324 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 59
5397196 CAAAAAGCAA
5397206 GACTCCTTATAGCCAAAGAAGGATATTTAATAACGATGTTTTGATTGTCCTCTTATCCTG
1 GACTCCTTATAGCCAAAGAAGGATATTTAATAACGATGTTTTG-TTGTCCTCTTATCCTG
5397266 GACTCCTTATAGCCAAAGAAGGATATTTAATAACGATGTTTTGTTGTCCTCTTATCCTG
1 GACTCCTTATAGCCAAAGAAGGATATTTAATAACGATGTTTTGTTGTCCTCTTATCCTG
5397325 AGGCCTAGAC
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 16 0.27
60 43 0.73
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (59 bp):
GACTCCTTATAGCCAAAGAAGGATATTTAATAACGATGTTTTGTTGTCCTCTTATCCTG
Found at i:5400475 original size:24 final size:24
Alignment explanation
Indices: 5400448--5400499 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5400438 TTAGTAAGTC
*
5400448 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
5400472 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
5400496 AAAT
1 AAAT
5400500 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:5402442 original size:24 final size:24
Alignment explanation
Indices: 5402415--5402466 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5402405 TTAGTAAGTC
*
5402415 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
5402439 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
5402463 AAAT
1 AAAT
5402467 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:5408491 original size:46 final size:46
Alignment explanation
Indices: 5408424--5408640 Score: 283
Period size: 46 Copynumber: 4.7 Consensus size: 46
5408414 TGGCAACCTG
*
5408424 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* * *
5408470 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTAATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* *
5408516 TGTGTAAGACCATGCTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* ** *
5408562 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAA
* ** * *
5408608 TGAGTAAGACCATATTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
5408641 TCACGTCAAA
Statistics
Matches: 152, Mismatches: 18, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 151 0.99
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.22
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
Found at i:5408618 original size:138 final size:130
Alignment explanation
Indices: 5408378--5408640 Score: 339
Period size: 138 Copynumber: 2.0 Consensus size: 130
5408368 GTGCTCTCTG
* *
5408378 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGTTGA
1 ATATGAAATGTGTAAGACCATGCTTGAAAGATACCATGGCAACCTGTGAGTAAGACCATGGTTGA
* * * * *
5408443 AAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTA
66 AAGATACCATGGCAACATGACATGAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACCTA
* *
5408508 ATATGAGATGTGTAAGACCATGCTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACC
1 ATATGAAATGTGTAAGACCATGCTTGAAAGATACCATGGCAACCTG---TG---AG--TAAGACC
* *
5408573 ATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATATTTGAAAGACACTAT
58 ATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAGTAAGACCATAGTTGAAAGACACCAT
5408637 GGCA
122 GGCA
5408641 TCACGTCAAA
Statistics
Matches: 113, Mismatches: 11, Indels: 10
0.84 0.08 0.07
Matches are distributed among these distances:
130 43 0.38
133 2 0.02
136 1 0.01
137 1 0.01
138 66 0.58
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (130 bp):
ATATGAAATGTGTAAGACCATGCTTGAAAGATACCATGGCAACCTGTGAGTAAGACCATGGTTGA
AAGATACCATGGCAACATGACATGAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACCTA
Found at i:5413252 original size:42 final size:41
Alignment explanation
Indices: 5413190--5413303 Score: 165
Period size: 42 Copynumber: 2.7 Consensus size: 41
5413180 TTCGTTTTCT
** * *
5413190 TGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
5413232 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
5413273 TCGATGCCATAGCCCAGCTATGGTCTTACAC
1 T-GATGCCATAGCCCAGCTATGGTCTTACAC
5413304 GAATCACATA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 2 0.03
42 64 0.97
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (41 bp):
TGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:5413342 original size:46 final size:47
Alignment explanation
Indices: 5413233--5413393 Score: 160
Period size: 47 Copynumber: 3.6 Consensus size: 47
5413223 TTCACATAAT
* * *
5413233 GATGCCATAGCCCAGCTATGGTCTTACAC-AT---AT-TCAT-ATATC
1 GATGCCATATCCCAGATATGGTCTTACACAATAGCATAT-ATCACATC
* * *
5413275 GATGCCATAGCCCAGCTATGGTCTTACACGAATCA-CATATCTCAC-T-
1 GATGCCATATCCCAGATATGGTCTTACAC-AAT-AGCATATATCACATC
* *
5413321 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACATC
1 GATGCCATATCCCAGATATGGTCTTACACAATAGCATATATCACATC
5413368 GATGCCATATCCCAGATATGGTCTTA
1 GATGCCATATCCCAGATATGGTCTTA
5413394 TACAGAAATC
Statistics
Matches: 102, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
42 29 0.28
44 3 0.03
45 11 0.11
46 27 0.26
47 30 0.29
48 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (47 bp):
GATGCCATATCCCAGATATGGTCTTACACAATAGCATATATCACATC
Found at i:5413377 original size:47 final size:47
Alignment explanation
Indices: 5413272--5413398 Score: 170
Period size: 47 Copynumber: 2.7 Consensus size: 47
5413262 ATATTCATAT
* * * * *
5413272 ATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 ATCGATGCCATATCCCAGATATGGTCTTATAC-AGTCACATATATCAC
5413320 -T-GATGCCATATCCCAGATATGGTCTTATACAGT-AGCATATATCAC
1 ATCGATGCCATATCCCAGATATGGTCTTATACAGTCA-CATATATCAC
5413365 ATCGATGCCATATCCCAGATATGGTCTTATACAG
1 ATCGATGCCATATCCCAGATATGGTCTTATACAG
5413399 AAATCACTTG
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
44 1 0.01
45 11 0.15
46 27 0.38
47 32 0.45
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (47 bp):
ATCGATGCCATATCCCAGATATGGTCTTATACAGTCACATATATCAC
Found at i:5413458 original size:31 final size:31
Alignment explanation
Indices: 5413415--5413532 Score: 164
Period size: 31 Copynumber: 3.8 Consensus size: 31
5413405 CTTGTCACTT
* *
5413415 GTAGTCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
5413446 GTAGCCGGAGCTACCATTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
5413477 GTAGCCGAAACTACCACTTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5413508 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
5413533 TGTCATTTGT
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:5420001 original size:17 final size:18
Alignment explanation
Indices: 5419968--5420011 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
5419958 TTAAAAAATA
5419968 TATAAAATTTGGAATTTT
1 TATAAAATTTGGAATTTT
5419986 TATAAATATTT-G-ATTTT
1 TATAAA-ATTTGGAATTTT
*
5420003 TAAAAAATT
1 TATAAAATT
5420012 ATTTTGAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 10 0.42
18 7 0.29
19 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
TATAAAATTTGGAATTTT
Found at i:5420046 original size:17 final size:18
Alignment explanation
Indices: 5420024--5420060 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5420014 TTTGAACTTT
*
5420024 TTTTGG-ATTTTTTTTTG
1 TTTTGGAATTTTTTGTTG
5420041 TTTTGGAATTTTTTGTTG
1 TTTTGGAATTTTTTGTTG
5420059 TT
1 TT
5420061 GAGAGAGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.08, C:0.00, G:0.19, T:0.73
Consensus pattern (18 bp):
TTTTGGAATTTTTTGTTG
Found at i:5420581 original size:22 final size:24
Alignment explanation
Indices: 5420556--5420599 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5420546 GATTTTAGTC
5420556 TTTA-TATTTTTA-TTTTTAAAAA
1 TTTATTATTTTTACTTTTTAAAAA
*
5420578 TTTATTTTTTTTACTTTTTAAA
1 TTTATTATTTTTACTTTTTAAA
5420600 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTATTATTTTTACTTTTTAAAAA
Found at i:5420792 original size:23 final size:23
Alignment explanation
Indices: 5420766--5420809 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5420756 GATTAAAATT
5420766 TTAAAATATAAAAAATAAAAAAA
1 TTAAAATATAAAAAATAAAAAAA
* * *
5420789 TTAAATTTTTAAAAATAAAAA
1 TTAAAATATAAAAAATAAAAA
5420810 TATGTAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TTAAAATATAAAAAATAAAAAAA
Found at i:5422917 original size:20 final size:18
Alignment explanation
Indices: 5422888--5422932 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5422878 TAATGGTTAT
*
5422888 ATTTTAATATTTAAAATATA
1 ATTTTTATA-TTAAAATA-A
*
5422908 ATTTTTATATTCAAATAA
1 ATTTTTATATTAAAATAA
5422926 ATTTTTA
1 ATTTTTA
5422933 CAAATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 7 0.30
20 8 0.35
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTTATATTAAAATAA
Found at i:5424784 original size:3 final size:3
Alignment explanation
Indices: 5424776--5424829 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
5424766 GTTCAAACCT
5424776 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5424824 TTC TTC
1 TTC TTC
5424830 ACCAACCATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:5426955 original size:27 final size:27
Alignment explanation
Indices: 5426925--5426977 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5426915 TGAACTATTC
*
5426925 TATTTATGTTCTTAATTA-TATTAATTA
1 TATTTATATT-TTAATTATTATTAATTA
*
5426952 TATTTATATTTTATTTATTATTAATT
1 TATTTATATTTTAATTATTATTAATT
5426978 TAGGGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTTATATTTTAATTATTATTAATTA
Found at i:5430056 original size:31 final size:30
Alignment explanation
Indices: 5430015--5430082 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
5430005 ATTTTTTAAA
*
5430015 TATATATTTTTT-AAAATTTTATATAACTTTT
1 TATATTTTTTTTGAAAA-TTTATATAA-TTTT
*
5430046 TATATTTTTTTTGAAAATTTATGTAATTTT
1 TATATTTTTTTTGAAAATTTATATAATTTT
5430076 TAT-TTTT
1 TATATTTT
5430083 ATATATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 4 0.12
30 7 0.21
31 19 0.56
32 4 0.12
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (30 bp):
TATATTTTTTTTGAAAATTTATATAATTTT
Found at i:5434354 original size:2 final size:2
Alignment explanation
Indices: 5434349--5434374 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5434339 AAAAAAAAAG
5434349 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
5434375 AAAGGGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5434632 original size:2 final size:2
Alignment explanation
Indices: 5434625--5434649 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5434615 TTTGCACAGG
5434625 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
5434650 GCAATGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5434861 original size:18 final size:19
Alignment explanation
Indices: 5434827--5434863 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5434817 CTATATAATT
*
5434827 AAATTTATAACTTATTTAA
1 AAATTAATAACTTATTTAA
5434846 AAATTAATAA-TTATTTAA
1 AAATTAATAACTTATTTAA
5434864 TATATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTAATAACTTATTTAA
Found at i:5445946 original size:27 final size:29
Alignment explanation
Indices: 5445890--5445958 Score: 99
Period size: 27 Copynumber: 2.4 Consensus size: 29
5445880 CATTTTATTT
*
5445890 TTTTATTTAAAAAATTAGATAAATTGATCA
1 TTTTATTTAAAAAA-TAGATAAACTGATCA
5445920 TTTTATTTAAAAAA-A-ATAAACTGATCA
1 TTTTATTTAAAAAATAGATAAACTGATCA
5445947 TTTTA-TTAAAAA
1 TTTTATTTAAAAA
5445959 TTTTATCTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
26 7 0.18
27 16 0.42
28 1 0.03
30 14 0.37
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTTATTTAAAAAATAGATAAACTGATCA
Found at i:5464321 original size:3 final size:3
Alignment explanation
Indices: 5464313--5464342 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5464303 GCCCAGATTT
5464313 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5464343 AATTCACGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:5466879 original size:3 final size:3
Alignment explanation
Indices: 5466873--5466898 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5466863 GAATAAGACA
5466873 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5466899 CAGATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5469389 original size:19 final size:19
Alignment explanation
Indices: 5469360--5469412 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
5469350 GCACATCAAT
*
5469360 AAATATTTAAAAATTTAA-A
1 AAAT-TTTAAAAATTAAATA
5469379 AAATTTCT-AAAATTAAATA
1 AAATTT-TAAAAATTAAATA
5469398 AAATTTTAAAAATTA
1 AAATTTTAAAAATTA
5469413 TTTAAAACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTTAAAAATTAAATA
Found at i:5469392 original size:18 final size:18
Alignment explanation
Indices: 5469357--5469408 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
5469347 GGCGCACATC
* *
5469357 AATAAATATTTAAAAATTT
1 AATAAA-ATTTTAAAATTA
5469376 AA-AAAATTTCTAAAATTA
1 AATAAAATTT-TAAAATTA
5469394 AATAAAATTTTAAAA
1 AATAAAATTTTAAAA
5469409 ATTATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 16 0.55
19 9 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAAATTTTAAAATTA
Found at i:5469418 original size:19 final size:19
Alignment explanation
Indices: 5469360--5469419 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
5469350 GCACATCAAT
*
5469360 AAATATTTAAAAATT-TAAA
1 AAAT-TTTAAAAATTATATA
*
5469379 AAATTTCT-AAAATTAAATA
1 AAATTT-TAAAAATTATATA
*
5469398 AAATTTTAAAAATTATTTA
1 AAATTTTAAAAATTATATA
5469417 AAA
1 AAA
5469420 CATATAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.26
19 25 0.74
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTTAAAAATTATATA
Found at i:5470143 original size:205 final size:209
Alignment explanation
Indices: 5469786--5470254 Score: 732
Period size: 205 Copynumber: 2.2 Consensus size: 209
5469776 TTTAATGTTG
* * **
5469786 CATATTTCATCCAGATAAAGTATTTATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAA
1 CATACTTCATCCGGATAAAGTATACATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAA
*
5469851 TTATAAAACAATATGTTATTTGGAAATTAACTATTATTGTAATGAGATACATGTTTTATTAGGTA
66 TTATAAAACAATATGTTATTTGGAAATTAACAATTATTGTAATGAGATACATGTTTTATTAGGTA
*
5469916 TAAGTATTTAAAATTTTATTTTTGTAATGTGATACATGC-G-TA-ATAT-ATATAATCATATTAG
131 TAAGTATTTAAAATTTTATTTTTGTAATGTGATACATGCGGATATATATAATATAATCATATTAC
* *
5469977 TGAATCTGTTAATG
196 TGAATCTGCTAATA
* **
5469991 CGTACTTCATCCGGATAAAGTACGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAA
1 CATACTTCATCCGGATAAAGTATACATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAA
*
5470056 TTATAAAATAATATGTTATTTGGGAAA-TAACAATTATTGTAATGAGATACATGTTTTATTAGGT
66 TTATAAAACAATATGTTATTT-GGAAATTAACAATTATTGTAATGAGATACATGTTTTATTAGGT
5470120 ATAAGTATTTAAAATTTTATTTTTGTAATGTGATACATGCGTGTATATATATATAAATATAATCA
130 ATAAGTATTTAAAATTTTATTTTTGTAATGTGATACATGCG-G---ATATATAT-AATATAATCA
5470185 TATTACTGAATCTGCTAATA
190 TATTACTGAATCTGCTAATA
*
5470205 CATACTTCATCCGGATAAAATATACATTATTAAAATTAAATTAAAATATT
1 CATACTTCATCCGGATAAAGTATACATTATTAAAATTAAATTAAAATATT
5470255 TTTTAAAAAC
Statistics
Matches: 239, Mismatches: 15, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
205 155 0.65
206 5 0.02
207 1 0.00
211 2 0.01
212 4 0.02
214 72 0.30
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (209 bp):
CATACTTCATCCGGATAAAGTATACATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAA
TTATAAAACAATATGTTATTTGGAAATTAACAATTATTGTAATGAGATACATGTTTTATTAGGTA
TAAGTATTTAAAATTTTATTTTTGTAATGTGATACATGCGGATATATATAATATAATCATATTAC
TGAATCTGCTAATA
Found at i:5470719 original size:31 final size:31
Alignment explanation
Indices: 5470675--5470763 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
5470665 TATTAGATTA
* *
5470675 ATTTAT-ATTTTATATATAATTATTTAGATATC
1 ATTTATCATTATAT-TA-AATTATTTAAATATC
* *
5470707 ATTTATCATTATATTAAATTATTTAAATCTT
1 ATTTATCATTATATTAAATTATTTAAATATC
* *
5470738 ATTTATTATTATATTAAAAT-TTTAAA
1 ATTTATCATTATATTAAATTATTTAAA
5470764 ATATTTTAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.12
31 30 0.60
32 8 0.16
33 6 0.12
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (31 bp):
ATTTATCATTATATTAAATTATTTAAATATC
Found at i:5474222 original size:21 final size:24
Alignment explanation
Indices: 5474185--5474231 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
5474175 ATTTGAAATG
5474185 TTTTATAATATTA-TTTTTTAAAA
1 TTTTATAATATTATTTTTTTAAAA
5474208 TTTTA-AATA-TATTTTTTTAAAA
1 TTTTATAATATTATTTTTTTAAAA
5474230 TT
1 TT
5474232 ATTTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 2 0.09
22 16 0.70
23 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTATAATATTATTTTTTTAAAA
Found at i:5474315 original size:28 final size:28
Alignment explanation
Indices: 5474249--5474319 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
5474239 AATAATATAA
5474249 AATA-TTTAAATGTATTATTAGTTTTAT
1 AATATTTTAAATGTATTATTAGTTTTAT
* ** * *
5474276 GACCTTTCAAATTTATTATTAGTTTTAT
1 AATATTTTAAATGTATTATTAGTTTTAT
5474304 AATATTTTAAATGTAT
1 AATATTTTAAATGTAT
5474320 ATTTTAGATA
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (28 bp):
AATATTTTAAATGTATTATTAGTTTTAT
Found at i:5474354 original size:14 final size:14
Alignment explanation
Indices: 5474344--5474374 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5474334 TAATTTTATA
5474344 TATAATTTTTTAAT
1 TATAATTTTTTAAT
*
5474358 TATGATTTTTTAAT
1 TATAATTTTTTAAT
5474372 TAT
1 TAT
5474375 TTTTAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TATAATTTTTTAAT
Found at i:5474378 original size:11 final size:14
Alignment explanation
Indices: 5474348--5474374 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5474338 TTTATATATA
5474348 ATTTTTTAATTATG
1 ATTTTTTAATTATG
5474362 ATTTTTTAATTAT
1 ATTTTTTAATTAT
5474375 TTTTAAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
ATTTTTTAATTATG
Found at i:5477165 original size:30 final size:30
Alignment explanation
Indices: 5477129--5477259 Score: 142
Period size: 30 Copynumber: 4.4 Consensus size: 30
5477119 GTCGTAGAGC
5477129 AGTTCATATCACCCGGACATGGGCGGTTCA
1 AGTTCATATCACCCGGACATGGGCGGTTCA
* * *
5477159 AGTTC--ATCACCCGAAAATGGGCGGCTT-G
1 AGTTCATATCACCCGGACATGGGCGG-TTCA
** *
5477187 AGTTCATATCACTTGGACATGGGCGGTTCG
1 AGTTCATATCACCCGGACATGGGCGGTTCA
* * *
5477217 AGTTCATATCACCCAGACATAGGCGATTCA
1 AGTTCATATCACCCGGACATGGGCGGTTCA
*
5477247 AGTTCATTTCACC
1 AGTTCATATCACC
5477260 GATATCAACC
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
28 22 0.27
29 4 0.05
30 57 0.69
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATGGGCGGTTCA
Found at i:5481412 original size:46 final size:46
Alignment explanation
Indices: 5481357--5481532 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 46
5481347 TATTTGGGCA
* * *
5481357 TCCGTACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATACGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
* *** * * * *
5481403 TCCGAACTCGTTGAGTTGAGTCCGAATTCGAAAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATACGA-ACG
* *
5481450 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
* * *
5481496 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5481533 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 23, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
46 70 0.67
47 34 0.33
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
Found at i:5481512 original size:93 final size:93
Alignment explanation
Indices: 5481353--5481525 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 93
5481343 AGGATATTTG
* *
5481353 GGCATCCGTACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATACGAATGTCCGAACTCGTTGAG
1 GGCATCCGTACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG
5481418 TTGAGTCCGAATTCGAAAGATGTAACTA
66 TTGAGTCCGAATTCGAAAGATGTAACTA
* * *
5481446 GGCATCCG-AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGA
1 GGCATCCGTA-CTCGTTGAGTTCAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGA
*
5481510 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAATTCG
5481526 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
92 1 0.01
93 72 0.99
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGTACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCGTTGAG
TTGAGTCCGAATTCGAAAGATGTAACTA
Found at i:5493482 original size:15 final size:15
Alignment explanation
Indices: 5493462--5493530 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
5493452 GTATCTTGGG
5493462 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
5493477 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
5493492 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
5493507 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
5493522 TTTCTTTAT
1 TTTCTTTAT
5493531 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:5493531 original size:30 final size:30
Alignment explanation
Indices: 5493453--5493540 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
5493443 CATAGTATCG
* * * *
5493453 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
5493483 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
5493513 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
5493541 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:5499087 original size:46 final size:45
Alignment explanation
Indices: 5499034--5499209 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
5499024 TATTTGGGCA
5499034 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
5499080 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
5499127 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
5499173 CCCGAGCTCGTTGAGTTGAGTTCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5499210 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.61
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:5499189 original size:93 final size:93
Alignment explanation
Indices: 5499030--5499202 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
5499020 AGGATATTTG
* *
5499030 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
5499095 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
5499123 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
5499188 TTGAGTTCGAGTTCG
66 TTGAGTCCGAGTTCG
5499203 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:5501602 original size:21 final size:21
Alignment explanation
Indices: 5501570--5501622 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
5501560 TTTTATATTA
5501570 TTAAAAAT-ATATTTAAAATT
1 TTAAAAATAATATTTAAAATT
5501590 TTAAAAATAATATTTAAAATT
1 TTAAAAATAATATTTAAAATT
5501611 TTAAAAA-AATAT
1 TTAAAAATAATAT
5501623 ATTTGAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAAATAATATTTAAAATT
Found at i:5501659 original size:23 final size:25
Alignment explanation
Indices: 5501628--5501677 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
5501618 AATATATTTG
5501628 AAAGATAAAT-AA-AAAAACTTTAAA
1 AAAGATAAATAAATAAAAAC-TTAAA
5501652 AAAG-TAAATAAATAAAAACTTAAA
1 AAAGATAAATAAATAAAAACTTAAA
5501676 AA
1 AA
5501678 GAAACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (25 bp):
AAAGATAAATAAATAAAAACTTAAA
Found at i:5502531 original size:152 final size:150
Alignment explanation
Indices: 5502341--5502663 Score: 540
Period size: 152 Copynumber: 2.1 Consensus size: 150
5502331 TATAAAATCT
* *
5502341 AGATTCGAAAATTTTAAAATACAAACAAATGGACAAAATTA-AGGTTATTTATTAAATTAATATA
1 AGATTCGAAAATTTTAAAATACAAACAAAGGGACAAAATTAGA-GTTATTTACTAAATTAATATA
* * *
5502405 AAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATATTGTAAAAGAATAAAATAGGA
65 AAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAA-AATAAAATAAGA
5502470 AAATAGTATATTTTAAAAAATA
129 AAATAGTATATTTTAAAAAATA
*
5502492 AGATCCGAAAATTTTAAAAATACAAACAAAGGGACAAAATTAGAGTTATTTACTAAATTAATATA
1 AGATTCGAAAATTTT-AAAATACAAACAAAGGGACAAAATTAGAGTTATTTACTAAATTAATATA
5502557 AAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATAAGAA
65 AAAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATAAGAA
5502622 AATAGTATATTTTAAAAAATA
130 AATAGTATATTTTAAAAAATA
*
5502643 AAATTCGAAAATTTTTAAAAT
1 AGATTCGAAAA-TTTTAAAAT
5502664 TTTAAAAATA
Statistics
Matches: 161, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
151 61 0.38
152 99 0.61
153 1 0.01
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.30
Consensus pattern (150 bp):
AGATTCGAAAATTTTAAAATACAAACAAAGGGACAAAATTAGAGTTATTTACTAAATTAATATAA
AAAAAACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATAAGAAA
ATAGTATATTTTAAAAAATA
Found at i:5503111 original size:25 final size:25
Alignment explanation
Indices: 5503079--5503140 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
5503069 TATTTTAGTG
5503079 CTTCTTGCTTCCCGAGTTGCTGCTT
1 CTTCTTGCTTCCCGAGTTGCTGCTT
*
5503104 CTTCTTGCTTCCCGAGTTGTTGCTT
1 CTTCTTGCTTCCCGAGTTGCTGCTT
*
5503129 CTTTTTGCTTCC
1 CTTCTTGCTTCC
5503141 AAAACTAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.03, C:0.31, G:0.18, T:0.48
Consensus pattern (25 bp):
CTTCTTGCTTCCCGAGTTGCTGCTT
Found at i:5503244 original size:17 final size:17
Alignment explanation
Indices: 5503220--5503264 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
5503210 ACACAATCCC
*
5503220 ATTTTTTTTCAATTTTTT
1 ATTTTTTTTC-ATTTTTA
5503238 ATTTTTTTTCATTTTTA
1 ATTTTTTTTCATTTTTA
*
5503255 ATTATTTTTC
1 ATTTTTTTTC
5503265 TTTAACAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTTTTCATTTTTA
Found at i:5509272 original size:20 final size:20
Alignment explanation
Indices: 5509247--5509284 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5509237 TATATATATT
* *
5509247 TATATATGCATGTATGCACC
1 TATATATACATATATGCACC
5509267 TATATATACATATATGCA
1 TATATATACATATATGCA
5509285 AAACAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
TATATATACATATATGCACC
Found at i:5527704 original size:34 final size:33
Alignment explanation
Indices: 5527665--5527733 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 33
5527655 TCAACATTTA
5527665 AAAAACAAAACATTATCACAAAAGGTGAAAAACT
1 AAAAACAAAACATTATCACAAAAGGTG-AAAACT
* *
5527699 AAAAACAGAACATTATCACAGAAGGTGAAAACT
1 AAAAACAAAACATTATCACAAAAGGTGAAAACT
5527732 AA
1 AA
5527734 TACTTACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.14
Consensus pattern (33 bp):
AAAAACAAAACATTATCACAAAAGGTGAAAACT
Found at i:5529079 original size:14 final size:15
Alignment explanation
Indices: 5529060--5529091 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
5529050 ATACGATAAA
5529060 TTAATTAAT-AATGT
1 TTAATTAATAAATGT
5529074 TTAATTAATAAATGT
1 TTAATTAATAAATGT
5529089 TTA
1 TTA
5529092 CATAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTAATTAATAAATGT
Found at i:5535634 original size:10 final size:11
Alignment explanation
Indices: 5535604--5535635 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
5535594 TAATGCATAT
5535604 TGTGTGTGT-G
1 TGTGTGTGTGG
5535614 TGTGTGTGTGG
1 TGTGTGTGTGG
5535625 TGTG-GTGTGG
1 TGTGTGTGTGG
5535635 T
1 T
5535636 TGGCATCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.00, C:0.00, G:0.53, T:0.47
Consensus pattern (11 bp):
TGTGTGTGTGG
Found at i:5540506 original size:24 final size:24
Alignment explanation
Indices: 5540479--5540527 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5540469 TGAAATTTAT
*
5540479 GATAATGAGATCGTATGAATAAAG
1 GATAATGAGATCATATGAATAAAG
5540503 GATAATGAGATCATATGAATAAAG
1 GATAATGAGATCATATGAATAAAG
5540527 G
1 G
5540528 GTTGATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.24
Consensus pattern (24 bp):
GATAATGAGATCATATGAATAAAG
Found at i:5543623 original size:19 final size:19
Alignment explanation
Indices: 5543599--5543638 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5543589 ACCATCTCAC
* *
5543599 TTAACTCCCGTGATTTTTA
1 TTAACTCCCGTAATTTCTA
5543618 TTAACTCCCGTAATTTCTA
1 TTAACTCCCGTAATTTCTA
5543637 TT
1 TT
5543639 TGGTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (19 bp):
TTAACTCCCGTAATTTCTA
Found at i:5549330 original size:26 final size:28
Alignment explanation
Indices: 5549301--5549361 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 28
5549291 ATATGAGTTA
**
5549301 ATTAAATATTAA-AA-TTTACTAAATAT
1 ATTAAATATTAATAATTTTAAAAAATAT
5549327 ATT-AAT-TTAATAATTTTAAAAAATAT
1 ATTAAATATTAATAATTTTAAAAAATAT
*
5549353 ATAAAATAT
1 ATTAAATAT
5549362 ATTATATGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 4 0.14
25 5 0.18
26 15 0.54
27 3 0.11
28 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTAAATATTAATAATTTTAAAAAATAT
Found at i:5554024 original size:28 final size:29
Alignment explanation
Indices: 5553954--5554025 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
5553944 CAATTTCTTT
5553954 AAAAA-AATCATTTTATATTATTATTTAC
1 AAAAATAATCATTTTATATTATTATTTAC
** *
5553982 TGAAATAGTCAATTTT-T-TTATTATTTACC
1 AAAAATAATC-ATTTTATATTATTATTTA-C
5554011 AAAAATAATCATTTT
1 AAAAATAATCATTTT
5554026 CCCTGAGAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
28 18 0.51
29 12 0.34
30 5 0.14
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (29 bp):
AAAAATAATCATTTTATATTATTATTTAC
Found at i:5554178 original size:20 final size:22
Alignment explanation
Indices: 5554143--5554184 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
5554133 CACAATAGTC
5554143 CTCTCACAATTCTCTCTAAATT
1 CTCTCACAATTCTCTCTAAATT
*
5554165 CTCTCA-AATT-TCTCTCAATT
1 CTCTCACAATTCTCTCTAAATT
5554185 TTTGTCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (22 bp):
CTCTCACAATTCTCTCTAAATT
Found at i:5555369 original size:7 final size:7
Alignment explanation
Indices: 5555357--5555389 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5555347 TAGTTGTTTC
5555357 GTATTTA
1 GTATTTA
5555364 GTATTTA
1 GTATTTA
*
5555371 ATATTTA
1 GTATTTA
5555378 GTATTTA
1 GTATTTA
5555385 GTATT
1 GTATT
5555390 ACCTATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:5556595 original size:108 final size:107
Alignment explanation
Indices: 5556478--5556691 Score: 367
Period size: 106 Copynumber: 2.0 Consensus size: 107
5556468 GTTTCATATA
*
5556478 ATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTTTTTTAATTTTATTAAAATAA
1 ATAAAATAAAAGTTCTTTTTAATATTTTAATTGTACTTTAC--TTTTTTAATTTTATTAAAATAA
* *
5556543 ATGTTGTTTTAAATTAGGCAATATTTTTATT-TTTTTATATTTG
64 ATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTG
*
5556586 ATAAAATAAAAGTTCTTTTTAATATTTTAATTGTATTTTACTTTTTTAATTTTATTAAAATAAAT
1 ATAAAATAAAAGTTCTTTTTAATATTTTAATTGTACTTTACTTTTTTAATTTTATTAAAATAAAT
5556651 GTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
66 GTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
5556692 ATTTTTATAT
Statistics
Matches: 101, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
106 51 0.50
107 11 0.11
108 39 0.39
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.57
Consensus pattern (107 bp):
ATAAAATAAAAGTTCTTTTTAATATTTTAATTGTACTTTACTTTTTTAATTTTATTAAAATAAAT
GTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTG
Found at i:5556631 original size:54 final size:55
Alignment explanation
Indices: 5556479--5556658 Score: 192
Period size: 54 Copynumber: 3.3 Consensus size: 55
5556469 TTTCATATAA
* * *
5556479 TAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTTTTTTAATTTTAT
1 TAAAATAAAAGTTCTTTTTAATATTTTAATTGTATTTTACTTTTTTAT-ATTTTAT
* * ** * * *
5556535 TAAAATAAATGTT-GTTTTAA-ATTAGGCAA-TAT-TTTTATTTTTTTATATTTGA-
1 TAAAATAAAAGTTCTTTTTAATATT--TTAATTGTATTTTACTTTTTTATATTTTAT
5556587 TAAAATAAAAGTTCTTTTTAATATTTTAATTGTATTTTACTTTTTTA-ATTTTAT
1 TAAAATAAAAGTTCTTTTTAATATTTTAATTGTATTTTACTTTTTTATATTTTAT
*
5556641 TAAAATAAATGTTCTTTT
1 TAAAATAAAAGTTCTTTT
5556659 AAATTAGCCA
Statistics
Matches: 100, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
52 14 0.14
53 18 0.18
54 46 0.46
55 8 0.08
56 14 0.14
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (55 bp):
TAAAATAAAAGTTCTTTTTAATATTTTAATTGTATTTTACTTTTTTATATTTTAT
Found at i:5556694 original size:53 final size:52
Alignment explanation
Indices: 5556520--5556691 Score: 188
Period size: 54 Copynumber: 3.2 Consensus size: 52
5556510 GTACTTTACT
* *
5556520 TTTTTTTAATTTTATTAAAATAAATGTTGTTTTAAATTAGGCAATATTTTTA
1 TTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTA
* * ** *
5556572 TTTTTTTATATTTGA-TAAAATAAAAGTTCTTTTTAATATT--TTAATTGTATTTTA
1 TTTTTTTA-ATTTTATTAAAATAAATGTTC-TTTTAA-ATTAGCCAA-TAT-TTTTA
*
5556626 CTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTA
1 TTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTA
5556678 TTATTTTTATATTT
1 TT-TTTTTA-ATTT
5556692 ATTTTTATAT
Statistics
Matches: 97, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
52 31 0.32
53 32 0.33
54 34 0.35
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.58
Consensus pattern (52 bp):
TTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTA
Found at i:5556838 original size:39 final size:38
Alignment explanation
Indices: 5556763--5556847 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 38
5556753 TTTTTTAAAA
* * *
5556763 TTTTAATACAATAAATGTTCTTTTAAATTAGTCAATAAT
1 TTTTAATAAAATAAATGTTATTTTAAATTAGACAAT-AT
* *
5556802 TTTTATTAAAATAAATGTTATTTTGAA-TATGACAATAT
1 TTTTAATAAAATAAATGTTATTTTAAATTA-GACAATAT
*
5556840 TTTAAATA
1 TTTTAATA
5556848 TTTTTTATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
38 10 0.26
39 28 0.74
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (38 bp):
TTTTAATAAAATAAATGTTATTTTAAATTAGACAATAT
Found at i:5556847 original size:127 final size:127
Alignment explanation
Indices: 5556586--5556837 Score: 323
Period size: 127 Copynumber: 2.0 Consensus size: 127
5556576 TTTATATTTG
* *
5556586 ATAAAATAAAAGTTCTTTTTAATATTTTAATTGTATTTTACTTTTTTAATTTTATTAAAATAAAT
1 ATAAAATAAAAGTTCTTTTTAATATTTTAATTGTACTTTACTTTTTTAATTTTAATAAAATAAAT
*** * * ***
5556651 GTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTATTTTTATATAGTTTTAATTA
66 GTTCTTTTAAATTAGCCAATATTTTTATTATAAATAAATTTATTTTGATATAGTGACAATTA
* *
5556713 ATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTA-TTTTTTAAAATTTTAATACAATAA
1 ATAAAATAAAAGTTCTTTTTAATATTTTAATTGTACTTTACTTTTTT--AATTTTAATAAAATAA
*
5556777 ATGTTCTTTTAAATTAGTCAATAATTTTTATTA-AAATAAATGTTATTTTGA-ATA-TGACAAT
64 ATGTTCTTTTAAATTAGCCAAT-ATTTTTATTATAAATAAAT-TTATTTTGATATAGTGACAAT
5556838 ATTTTAAATA
Statistics
Matches: 108, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
126 6 0.06
127 42 0.39
128 42 0.39
129 18 0.17
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (127 bp):
ATAAAATAAAAGTTCTTTTTAATATTTTAATTGTACTTTACTTTTTTAATTTTAATAAAATAAAT
GTTCTTTTAAATTAGCCAATATTTTTATTATAAATAAATTTATTTTGATATAGTGACAATTA
Found at i:5556961 original size:149 final size:149
Alignment explanation
Indices: 5556789--5557088 Score: 573
Period size: 149 Copynumber: 2.0 Consensus size: 149
5556779 GTTCTTTTAA
*
5556789 ATTAGTCAATAATTTTTATTAAAATAAATGTTATTTTGAATATGACAATATTTTAAATATTTTTT
1 ATTAGTCAATAATTTTTATTAAAATAAATGTTATTTTGAATACGACAATATTTTAAATATTTTTT
*
5556854 ATATTTTTAATAAAATATAAATAATGCAACATAATTTTATTACAACAACTATCAGCTATATTGAT
66 ATATTTTTAATAAAATAAAAATAATGCAACATAATTTTATTACAACAACTATCAGCTATATTGAT
5556919 TTGGACATGATTGAGTTAT
131 TTGGACATGATTGAGTTAT
5556938 ATTAGTCAATAATTTTTATTAAAATAAATGTTATTTTGAATACGACAATATTTTAAATATTTTTT
1 ATTAGTCAATAATTTTTATTAAAATAAATGTTATTTTGAATACGACAATATTTTAAATATTTTTT
5557003 ATATTTTTAATAAAATAAAAATAATGCAACATAATTTTATTACAACAACTATCAGCTATATTGAT
66 ATATTTTTAATAAAATAAAAATAATGCAACATAATTTTATTACAACAACTATCAGCTATATTGAT
*
5557068 TTGGTCATGATTGAGTTAT
131 TTGGACATGATTGAGTTAT
5557087 AT
1 AT
5557089 GGCCTAGGTT
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (149 bp):
ATTAGTCAATAATTTTTATTAAAATAAATGTTATTTTGAATACGACAATATTTTAAATATTTTTT
ATATTTTTAATAAAATAAAAATAATGCAACATAATTTTATTACAACAACTATCAGCTATATTGAT
TTGGACATGATTGAGTTAT
Found at i:5563289 original size:12 final size:12
Alignment explanation
Indices: 5563272--5563297 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5563262 TACTAGAAGT
5563272 ATTGTTGACTTC
1 ATTGTTGACTTC
5563284 ATTGTTGACTTC
1 ATTGTTGACTTC
5563296 AT
1 AT
5563298 GAAATTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (12 bp):
ATTGTTGACTTC
Found at i:5567066 original size:29 final size:30
Alignment explanation
Indices: 5567027--5567093 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
5567017 GAATTCAACC
* *
5567027 AAAATGTACAAGGACTAAAATTGA-CAATTT
1 AAAA-GTACAAGGACTAAAATTAATCAAATT
*
5567057 AAAAGTACAATGACTAAAATTAATCAAATT
1 AAAAGTACAAGGACTAAAATTAATCAAATT
5567087 AAAAGTA
1 AAAAGTA
5567094 TAGAAACTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.25
Consensus pattern (30 bp):
AAAAGTACAAGGACTAAAATTAATCAAATT
Found at i:5567973 original size:17 final size:17
Alignment explanation
Indices: 5567951--5567987 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
5567941 CTGTTCATGA
*
5567951 TCAAAAGATACAATTGT
1 TCAAAAGATACAACTGT
5567968 TCAAAAGATACAACTGT
1 TCAAAAGATACAACTGT
5567985 TCA
1 TCA
5567988 TCAAGAGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (17 bp):
TCAAAAGATACAACTGT
Found at i:5569121 original size:104 final size:106
Alignment explanation
Indices: 5568925--5569121 Score: 238
Period size: 104 Copynumber: 1.9 Consensus size: 106
5568915 TAGTATAAGG
* * * * *
5568925 ATGAAAATCTGAAATTTAACATTTATTTTTGGTAAAAATATCTCTCTAGCCTCTCTTAATTTTGA
1 ATGAAAATCAGAAAGTTAACATTTATTTTTGGTAAAAAAATCTCTCAAGCCTCTCTCAATTTTGA
* * * *** *
5568990 TATTTAGTAAATTGGTTTTTCTTAAAAACATTAGAACAACA
66 TATTGAGGAAAATGGTCCCTCTAAAAAACATTAGAACAACA
* *
5569031 ATGAAAATCAG-AAGTTGACATTTATTTTTGG-AAAAAAATCTCTCCAATCC-CTCTCAATTTTG
1 ATGAAAATCAGAAAGTTAACATTTATTTTTGGTAAAAAAATCTCT-CAAGCCTCTCTCAATTTTG
5569093 ATATTGAGGAAAATGGTCCCTCTAAAAAA
65 ATATTGAGGAAAATGGTCCCTCTAAAAAA
5569122 AATAGAGTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
104 44 0.58
105 22 0.29
106 10 0.13
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (106 bp):
ATGAAAATCAGAAAGTTAACATTTATTTTTGGTAAAAAAATCTCTCAAGCCTCTCTCAATTTTGA
TATTGAGGAAAATGGTCCCTCTAAAAAACATTAGAACAACA
Found at i:5571263 original size:29 final size:30
Alignment explanation
Indices: 5571209--5571269 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
5571199 GTAGTTTATG
* **
5571209 AAAATTATATTAAATCAAAATTTTATGCTT
1 AAAATTATATAAAATCAAAAAATTATGCTT
5571239 AAAATTATATAAAAT-AAAAAATTATGCTT
1 AAAATTATATAAAATCAAAAAATTATGCTT
5571268 AA
1 AA
5571270 TTTTGAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTATATAAAATCAAAAAATTATGCTT
Found at i:5576062 original size:20 final size:21
Alignment explanation
Indices: 5576022--5576062 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5576012 TTTTTAAAAA
* *
5576022 TAAAATATTTAATATTTTAAT
1 TAAAATATTTAACATTATAAT
5576043 TAAAA-ATTTAACATTATAAT
1 TAAAATATTTAACATTATAAT
5576063 GAAGGCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAATATTTAACATTATAAT
Found at i:5577624 original size:6 final size:6
Alignment explanation
Indices: 5577605--5577641 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
5577595 GGGTTTGTAT
*
5577605 TTTCTG TTTTTG TTTCTG TTTCTG TTTCTG TTTCTG T
1 TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG T
5577642 GGGAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.16, T:0.70
Consensus pattern (6 bp):
TTTCTG
Found at i:5581921 original size:27 final size:27
Alignment explanation
Indices: 5581856--5581925 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
5581846 CAGATTTTAG
* *
5581856 ATTGTTGGATTTTGATATATGTCTTGA
1 ATTGTTGGATATTGATATATGTCTTAA
* *
5581883 ATTGGTTAGATATTGAT-TATGTTTTAA
1 ATT-GTTGGATATTGATATATGTCTTAA
5581910 CATTGTTGGATATTGA
1 -ATTGTTGGATATTGA
5581926 ATTGATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (27 bp):
ATTGTTGGATATTGATATATGTCTTAA
Found at i:5581930 original size:32 final size:33
Alignment explanation
Indices: 5581894--5581961 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 33
5581884 TTGGTTAGAT
5581894 ATTG-ATTATGTTTTAA-CATTGTTGGATATTGA
1 ATTGTATTATGTTTTAAGC-TTGTTGGATATTGA
5581926 ATTGATTATTATGTTTTAAGCTTGTTGGATATTGA
1 ATTG--TATTATGTTTTAAGCTTGTTGGATATTGA
5581961 A
1 A
5581962 ATTATTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 4 0.12
35 27 0.84
36 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.19, T:0.50
Consensus pattern (33 bp):
ATTGTATTATGTTTTAAGCTTGTTGGATATTGA
Found at i:5583193 original size:34 final size:35
Alignment explanation
Indices: 5583127--5583193 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
5583117 CAAATACCAG
5583127 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
* *
5583162 AAAATATTTTCCAG-AATTCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAGTCATTTTACAGAAAA
5583194 CATTTTACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
Found at i:5584677 original size:20 final size:20
Alignment explanation
Indices: 5584653--5584690 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5584643 TTATAAAATT
5584653 TTTTAACATATTGTTAAAAA
1 TTTTAACATATTGTTAAAAA
* *
5584673 TTTTAATATATTTTTAAA
1 TTTTAACATATTGTTAAA
5584691 GCATTTGCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTAACATATTGTTAAAAA
Done.