Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 10 of 45
Found at i:1937808 original size:18 final size:18
Alignment explanation
Indices: 1937787--1937822 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1937777 GAAATGGAAG
1937787 GAAAAAAAAAATTTAAAT
1 GAAAAAAAAAATTTAAAT
*
1937805 GAAATAAAAAATTTAAAT
1 GAAAAAAAAAATTTAAAT
1937823 TTATTTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (18 bp):
GAAAAAAAAAATTTAAAT
Found at i:1938661 original size:23 final size:23
Alignment explanation
Indices: 1938618--1938663 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1938608 TATCATATTA
*
1938618 ATAGTCTATATATTATTATTTTT
1 ATAGTCTATATATAATTATTTTT
1938641 ATAGTCTATAT-TAATTGATTTTT
1 ATAGTCTATATATAATT-ATTTTT
1938664 CGAGCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (23 bp):
ATAGTCTATATATAATTATTTTT
Found at i:1942258 original size:9 final size:9
Alignment explanation
Indices: 1942244--1942281 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
1942234 AACTTCTTAA
1942244 TAAAAAAAT
1 TAAAAAAAT
*
1942253 TAAAAAATAA
1 TAAAAAA-AT
1942263 TAAAAAAAT
1 TAAAAAAAT
1942272 TAAAAAAAT
1 TAAAAAAAT
1942281 T
1 T
1942282 TATTGTAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:1942265 original size:19 final size:19
Alignment explanation
Indices: 1942241--1942278 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1942231 CTTAACTTCT
1942241 TAATAAAAAAATTAAAAAA
1 TAATAAAAAAATTAAAAAA
1942260 TAATAAAAAAATTAAAAAA
1 TAATAAAAAAATTAAAAAA
1942279 ATTTATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
TAATAAAAAAATTAAAAAA
Found at i:1943463 original size:17 final size:16
Alignment explanation
Indices: 1943436--1943474 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1943426 ATTTCATACG
*
1943436 TTTAGATATAAATATAT
1 TTTA-ATATAAAAATAT
1943453 ATTTAATATAAAAATAT
1 -TTTAATATAAAAATAT
1943470 TTTAA
1 TTTAA
1943475 AATTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 11 0.55
18 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TTTAATATAAAAATAT
Found at i:1948159 original size:9 final size:9
Alignment explanation
Indices: 1948145--1948176 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1948135 CTTGTTTGTA
1948145 AAAAAAATG
1 AAAAAAATG
1948154 AAAAAAATG
1 AAAAAAATG
1948163 AAAAAAAT-
1 AAAAAAATG
1948171 AAAAAA
1 AAAAAA
1948177 TCAAAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.09
Consensus pattern (9 bp):
AAAAAAATG
Found at i:1949811 original size:21 final size:20
Alignment explanation
Indices: 1949771--1949814 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
1949761 AAAATCTCAA
1949771 TATTTATTATATATATTTTT
1 TATTTATTATATATATTTTT
1949791 TATTT-TTATATTATGATTTTT
1 TATTTATTATA-TAT-ATTTTT
1949812 TAT
1 TAT
1949815 ATAAAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.23
20 8 0.36
21 9 0.41
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TATTTATTATATATATTTTT
Found at i:1952672 original size:5 final size:5
Alignment explanation
Indices: 1952662--1952687 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1952652 AACAAATAAT
1952662 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
1952688 GTGGACCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1956208 original size:3 final size:3
Alignment explanation
Indices: 1956202--1956239 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1956192 AACAACATAC
1956202 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1956240 GCATGAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1956417 original size:21 final size:20
Alignment explanation
Indices: 1956380--1956418 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1956370 ATAAATAAAT
* *
1956380 AAAAAAAAGAGAGAGAAAAA
1 AAAAAAAAAAGAAAGAAAAA
1956400 AAAAAAAACAAGAAAGAAA
1 AAAAAAAA-AAGAAAGAAA
1956419 GATGCGGTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAGAAAGAAAAA
Found at i:1956663 original size:30 final size:30
Alignment explanation
Indices: 1956616--1956673 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1956606 GGTTGATTCA
* * *
1956616 TTATCTATATTATATTTATATTATTTTTAT
1 TTATCTATATTAAATTTAAAATATTTTTAT
1956646 TTAT-TATAATTAAATTTAAAATATTTTT
1 TTATCTAT-ATTAAATTTAAAATATTTTT
1956674 TTAATTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TTATCTATATTAAATTTAAAATATTTTTAT
Found at i:1957549 original size:28 final size:25
Alignment explanation
Indices: 1957520--1957570 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1957510 ATAATATATA
1957520 AAAAGTTTTAATTAATAAATAATTTTT
1 AAAA-TTTTAA-TAATAAATAATTTTT
1957547 AAAATTTTAATAA-AAATATATTTT
1 AAAATTTTAATAATAAATA-ATTTT
1957571 AAATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 8 0.35
26 6 0.26
27 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
AAAATTTTAATAATAAATAATTTTT
Found at i:1957781 original size:3 final size:3
Alignment explanation
Indices: 1957775--1957799 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1957765 CTGCAAAAAA
1957775 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
1957800 GGGAATGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1960731 original size:2 final size:2
Alignment explanation
Indices: 1960724--1960764 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1960714 CCGTAATTGC
1960724 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1960765 ACAGCTCCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1961269 original size:2 final size:2
Alignment explanation
Indices: 1961262--1961301 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1961252 TGTCCCGTCC
1961262 CT CT CT CT CT CT CT 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 CT CT CT CT CT CT CT
1961302 ATATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1961306 original size:2 final size:2
Alignment explanation
Indices: 1961301--1961327 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1961291 TCTCTCTCTC
1961301 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1961328 CCCCATGAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1963975 original size:24 final size:22
Alignment explanation
Indices: 1963937--1963980 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
1963927 AATTATATAA
*
1963937 ATATAATAAAATATTTATATTT
1 ATATAATAAAATATTAATATTT
1963959 ATATAATATAAATTATTAATAT
1 ATATAATA-AAA-TATTAATAT
1963981 ATTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATAATAAAATATTAATATTT
Found at i:1963980 original size:18 final size:18
Alignment explanation
Indices: 1963954--1964003 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1963944 AAAATATTTA
*
1963954 TATTTATATAATATAAAT
1 TATTAATATAATATAAAT
*
1963972 TATTAATATATTA-AAAT
1 TATTAATATAATATAAAT
1963989 T-TATATATATAATAT
1 TAT-TA-ATATAATAT
1964004 TTTAATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 1 0.04
17 7 0.27
18 18 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTAATATAATATAAAT
Found at i:1963980 original size:40 final size:39
Alignment explanation
Indices: 1963917--1964003 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
1963907 TTATACCATC
1963917 TTATATAA-A-AAATTATATAAATATAATAAAATATTTATA
1 TTATATAATATAAATTATATAAATAT-ATAAAA-ATTTATA
*
1963956 TTTATATAATATAAATTAT-T-AATATATTAAAATTTATA
1 -TTATATAATATAAATTATATAAATATATAAAAATTTATA
1963994 -TATATAATAT
1 TTATATAATAT
1964004 TTTAATAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
36 10 0.23
38 7 0.16
39 5 0.11
40 13 0.30
41 2 0.05
42 7 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (39 bp):
TTATATAATATAAATTATATAAATATATAAAAATTTATA
Found at i:1964015 original size:23 final size:23
Alignment explanation
Indices: 1963970--1964023 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
1963960 TATAATATAA
1963970 ATTATTAATATATTAAAATTTA-T
1 ATTA-TAATATATTAAAATTTATT
*
1963993 ATATATAATATTTTAATAA-TTATT
1 AT-TATAATATATTAA-AATTTATT
1964017 ATTATAA
1 ATTATAA
1964024 AAAAATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATAATATATTAAAATTTATT
Found at i:1965345 original size:23 final size:24
Alignment explanation
Indices: 1965323--1965397 Score: 66
Period size: 26 Copynumber: 3.1 Consensus size: 24
1965313 TTTTTATTTA
*
1965323 AATT-AATTTAATT-TAAATTTTT
1 AATTAAATATAATTATAAATTTTT
* *
1965345 AATTAAATATAATTATAAATATTA
1 AATTAAATATAATTATAAATTTTT
*
1965369 ATATTAAAATAATAATTA-ATATTTTT
1 A-ATT-AAAT-ATAATTATAAATTTTT
1965395 AAT
1 AAT
1965398 AATAAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
22 4 0.10
23 8 0.19
24 8 0.19
25 5 0.12
26 10 0.24
27 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTAAATATAATTATAAATTTTT
Found at i:1965380 original size:18 final size:19
Alignment explanation
Indices: 1965350--1965454 Score: 67
Period size: 18 Copynumber: 5.3 Consensus size: 19
1965340 TTTTTAATTA
*
1965350 AATA-TAATTATAAATATT
1 AATATTAATAATAAATATT
1965368 AATATTAA-AAT-AATAATT
1 AATATTAATAATAAAT-ATT
1965386 AATATTTTTAATAATAAAATATT
1 AATA---TTAATAAT-AAATATT
* *
1965409 ATTAAATATAATTATAAATATT
1 A--ATAT-TAATAATAAATATT
1965431 AATATTAA-AAT-AATAATT
1 AATATTAATAATAAAT-ATT
1965449 AATATT
1 AATATT
1965455 TTTAATAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
17 6 0.09
18 24 0.34
19 6 0.09
20 3 0.04
21 4 0.06
22 12 0.17
23 10 0.14
24 3 0.04
25 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATTAATAATAAATATT
Found at i:1965384 original size:14 final size:15
Alignment explanation
Indices: 1965356--1965447 Score: 57
Period size: 17 Copynumber: 6.0 Consensus size: 15
1965346 ATTAAATATA
*
1965356 ATTATAAATATTAAT
1 ATTATAAATAATAAT
*
1965371 ATTAAAATAATAATTAAT
1 ATT-ATA-AATAA-TAAT
* *
1965389 ATTTTTAATAATAAAAT
1 ATTATAAATAAT--AAT
1965406 ATTATTAAAT-AT-A-
1 ATTA-TAAATAATAAT
*
1965419 ATTATAAATATTAAT
1 ATTATAAATAATAAT
1965434 ATTA-AAATAATAAT
1 ATTATAAATAATAAT
1965448 TAATATTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
12 5 0.08
13 5 0.08
14 11 0.19
15 8 0.14
16 7 0.12
17 12 0.20
18 11 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTATAAATAATAAT
Found at i:1965396 original size:27 final size:27
Alignment explanation
Indices: 1965366--1965494 Score: 77
Period size: 27 Copynumber: 4.5 Consensus size: 27
1965356 ATTATAAATA
*
1965366 TTAATATTAAAATAATAATTAATATTT
1 TTAATAATAAAATAATAATTAATATTT
*
1965393 TTAATAATAAAAT-ATTATTAAATATAATT
1 TTAATAATAAAATAATAATT-AATAT--TT
* * *
1965422 ATAAATATTAATATTAA-AATAATAATTAATATT
1 -TTAATAATAA-AATAATAAT--TAA-T-AT-TT
*
1965455 TTTAATAATAAAAT-AT-ATTAATATTT
1 TTAA-TAATAAAATAATAATTAATATTT
1965481 TTAATAATAAAATA
1 TTAATAATAAAATA
1965495 TTTTTTTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 27
0.67 0.09 0.23
Matches are distributed among these distances:
25 9 0.12
26 10 0.13
27 19 0.24
28 1 0.01
29 5 0.06
30 8 0.10
31 7 0.09
32 7 0.09
33 10 0.13
34 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTAATAATAAAATAATAATTAATATTT
Found at i:1965413 original size:63 final size:62
Alignment explanation
Indices: 1965346--1965475 Score: 251
Period size: 63 Copynumber: 2.1 Consensus size: 62
1965336 TAAATTTTTA
1965346 ATTAAATATAATTATAAATATTAATATTAAAATAATAATTAATATTTTTAATAATAAAATATT
1 ATTAAATATAATTATAAATATTAATATTAAAATAATAATTAATATTTTTAATAATAAAATA-T
1965409 ATTAAATATAATTATAAATATTAATATTAAAATAATAATTAATATTTTTAATAATAAAATAT
1 ATTAAATATAATTATAAATATTAATATTAAAATAATAATTAATATTTTTAATAATAAAATAT
1965471 ATTAA
1 ATTAA
1965476 TATTTTTAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
62 6 0.09
63 61 0.91
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (62 bp):
ATTAAATATAATTATAAATATTAATATTAAAATAATAATTAATATTTTTAATAATAAAATAT
Found at i:1965480 original size:25 final size:26
Alignment explanation
Indices: 1965412--1965495 Score: 109
Period size: 25 Copynumber: 3.2 Consensus size: 26
1965402 AAATATTATT
* * *
1965412 AAATATAATT-ATAAATATTAATATTA
1 AAATATAATTAAT-ATTTTTAATAATA
1965438 AAATAATAATTAATATTTTTAATAATA
1 AAAT-ATAATTAATATTTTTAATAATA
1965465 AAATAT-ATTAATATTTTTAATAATA
1 AAATATAATTAATATTTTTAATAATA
1965490 AAATAT
1 AAATAT
1965496 TTTTTTTTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
25 25 0.47
26 6 0.11
27 20 0.38
28 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATATAATTAATATTTTTAATAATA
Found at i:1965486 original size:17 final size:17
Alignment explanation
Indices: 1965376--1965470 Score: 55
Period size: 19 Copynumber: 4.8 Consensus size: 17
1965366 TTAATATTAA
1965376 AATAATAATTAATATTTTT
1 AATAATAA--AATATTTTT
*
1965395 AATAATAAAATATTATTAA
1 AATAATAAAATATT-TT-T
1965414 ATATAATTATAAATATTAATATT
1 A-ATAA-TA-AAATATT--T-TT
1965437 AAAATAATAATTAATATTTTT
1 --AATAATAA--AATATTTTT
1965458 AATAATAAAATAT
1 AATAATAAAATAT
1965471 ATTAATATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 24
0.71 0.02 0.27
Matches are distributed among these distances:
17 11 0.17
18 2 0.03
19 17 0.27
20 4 0.06
21 4 0.06
22 9 0.14
23 4 0.06
24 11 0.17
25 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAATAAAATATTTTT
Found at i:1965638 original size:14 final size:14
Alignment explanation
Indices: 1965619--1965645 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1965609 AATTAAAAGG
1965619 TTTATTTTTATTTA
1 TTTATTTTTATTTA
1965633 TTTATTTTTATTT
1 TTTATTTTTATTT
1965646 TATCATTCAT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:1968248 original size:18 final size:19
Alignment explanation
Indices: 1968211--1968249 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1968201 AAATATTAAT
* *
1968211 AATTTTTTTTAAATATATA
1 AATTTATTTTAAATAAATA
1968230 AATTTATTTTAAA-AAATA
1 AATTTATTTTAAATAAATA
1968248 AA
1 AA
1968250 CATATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTTATTTTAAATAAATA
Found at i:1970686 original size:96 final size:96
Alignment explanation
Indices: 1970484--1970674 Score: 330
Period size: 96 Copynumber: 2.0 Consensus size: 96
1970474 GAAACAAAAA
1970484 ACAACAATGGGGATTGTTATGTTGCAGAGACAATAAACAAAATGCATTAAAGACGTTAGTTTTTC
1 ACAACAATGGGGATTGTTATGTTGCAGAGACAATAAACAAAATGCATTAAAGACGTTAGTTTTTC
1970549 TGGAATTTCTTTTGTTTTTTCTCTTAGTTTT
66 TGGAATTTCTTTTGTTTTTTCTCTTAGTTTT
* * *
1970580 ACAACAATGGGGATTGTTATGTTGCAGAGATAATGAACAAAATGCATTGAAGACGTTAGTTTTTC
1 ACAACAATGGGGATTGTTATGTTGCAGAGACAATAAACAAAATGCATTAAAGACGTTAGTTTTTC
* *
1970645 TTGAATTTCTTTTG-TTTTTGTCTTAGTTTT
66 TGGAATTTCTTTTGTTTTTTCTCTTAGTTTT
1970675 TTGAGTGATG
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
95 15 0.17
96 75 0.83
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.42
Consensus pattern (96 bp):
ACAACAATGGGGATTGTTATGTTGCAGAGACAATAAACAAAATGCATTAAAGACGTTAGTTTTTC
TGGAATTTCTTTTGTTTTTTCTCTTAGTTTT
Found at i:1972723 original size:72 final size:71
Alignment explanation
Indices: 1972592--1972734 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 71
1972582 AAGTGTCGAC
* * **
1972592 CACCTAAAATACAATTCTACTTAGACTTTCTTGCCTGAATATTGTAGACTTCTCTTTTTGGCATA
1 CACCTAAAATACAATTCTACCTAGACTTTCTTGCCTGAATATTGTAAACTTCTAGTTTTGGCATA
1972657 AATGTT
66 AATGTT
* *
1972663 CACCTAAAAATACAATTCTACCTAGACTTTCTTGCCTGAATATTGTAAACTTTTAGTTTTGGTAT
1 CACCT-AAAATACAATTCTACCTAGACTTTCTTGCCTGAATATTGTAAACTTCTAGTTTTGGCAT
*
1972728 ACATGTT
65 AAATGTT
1972735 TTTTGAGACT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 5 0.08
72 59 0.92
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (71 bp):
CACCTAAAATACAATTCTACCTAGACTTTCTTGCCTGAATATTGTAAACTTCTAGTTTTGGCATA
AATGTT
Found at i:1973447 original size:12 final size:14
Alignment explanation
Indices: 1973419--1973460 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1973409 TTAAATTGTA
1973419 AAATATTTGTTAA-T
1 AAATATTT-TTAATT
1973433 AAAT-TTTTT-ATT
1 AAATATTTTTAATT
1973445 AAATATTTTTAATT
1 AAATATTTTTAATT
1973459 AA
1 AA
1973461 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.04
12 7 0.28
13 8 0.32
14 9 0.36
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
AAATATTTTTAATT
Found at i:1974054 original size:15 final size:17
Alignment explanation
Indices: 1974022--1974060 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
1974012 GCAAGAGAAA
1974022 TTTAATATTTTAATAAT
1 TTTAATATTTTAATAAT
1974039 TTTAAT-TTTTAA-AAT
1 TTTAATATTTTAATAAT
*
1974054 TATAATA
1 TTTAATA
1974061 AATAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.40
16 6 0.30
17 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAATATTTTAATAAT
Found at i:1974265 original size:7 final size:7
Alignment explanation
Indices: 1974255--1974304 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
1974245 ATTATAATTT
1974255 TAAAATA
1 TAAAATA
1974262 TAAAAT-
1 TAAAATA
1974268 TAAAATA
1 TAAAATA
*
1974275 TAAAATT
1 TAAAATA
1974282 TAATAATA
1 TAA-AATA
1974290 TAAAA-A
1 TAAAATA
1974296 TTAAAATA
1 -TAAAATA
1974304 T
1 T
1974305 TTTTTTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 7 0.19
7 23 0.62
8 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (7 bp):
TAAAATA
Found at i:1974268 original size:15 final size:14
Alignment explanation
Indices: 1974253--1974304 Score: 79
Period size: 13 Copynumber: 3.7 Consensus size: 14
1974243 TTATTATAAT
1974253 TTTAAAATATAAAA
1 TTTAAAATATAAAA
1974267 -TTAAAATATAAAA
1 TTTAAAATATAAAA
1974280 TTTAATAATATAAAA
1 TTTAA-AATATAAAA
*
1974295 ATTAAAATAT
1 TTTAAAATAT
1974305 TTTTTTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
13 13 0.37
14 9 0.26
15 13 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTAAAATATAAAA
Found at i:1974313 original size:28 final size:28
Alignment explanation
Indices: 1974250--1974304 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
1974240 TATTTATTAT
1974250 AATTTTAA-AATATAAAATTAAAATATA
1 AATTTTAATAATATAAAATTAAAATATA
*
1974277 AAATTTAATAATATAAAAATTAAAATAT
1 AATTTTAATAATAT-AAAATTAAAATAT
1974305 TTTTTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.28
28 5 0.20
29 13 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AATTTTAATAATATAAAATTAAAATATA
Found at i:1974402 original size:3 final size:3
Alignment explanation
Indices: 1974394--1974460 Score: 52
Period size: 3 Copynumber: 22.7 Consensus size: 3
1974384 AGATTGATTT
* * *
1974394 TAA TAA TAA TAA TAA TAA TAG TAA -AA TTAA TTA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
1974439 -AA TTAA -AA TTAA TAA TAA -AA TA
1 TAA -TAA TAA -TAA TAA TAA TAA TA
1974461 TATATTTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
2 8 0.15
3 39 0.74
4 6 0.11
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1974432 original size:27 final size:27
Alignment explanation
Indices: 1974393--1974460 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
1974383 GAGATTGATT
*
1974393 TTAATAATAATAATAATAATAGTAAAA
1 TTAATAATAATAATAATAAAAGTAAAA
* * *
1974420 TTAATTATTATAATAATAAAATTAAAA
1 TTAATAATAATAATAATAAAAGTAAAA
1974447 TTAATAATAA-AATA
1 TTAATAATAATAATA
1974461 TATATTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
26 4 0.11
27 31 0.89
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (27 bp):
TTAATAATAATAATAATAAAAGTAAAA
Found at i:1974453 original size:21 final size:22
Alignment explanation
Indices: 1974400--1974456 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
1974390 ATTTTAATAA
*
1974400 TAATAA-TAATAATAGTAAAAT
1 TAATAATTAATAATAATAAAAT
*
1974421 TAATTATT-ATAATAATAAAAT
1 TAATAATTAATAATAATAAAAT
1974442 TAA-AATTAATAATAA
1 TAATAATTAATAATAA
1974457 AATATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 3 0.10
21 27 0.87
22 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TAATAATTAATAATAATAAAAT
Found at i:1974943 original size:29 final size:28
Alignment explanation
Indices: 1974904--1974988 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 28
1974894 ATTTTATATT
1974904 AAATAATTTTAAATATAATACAAAATAAA
1 AAAT-ATTTTAAATATAATACAAAATAAA
*
1974933 AAATATGTTTAATATATTAATA-AACAT-AA
1 AAATAT-TTTAA-ATA-TAATACAAAATAAA
*
1974962 AAATATTATAGAA-ATAATATCAAAATA
1 AAATATTTTA-AATATAATA-CAAAATA
1974989 TTTAAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
26 5 0.11
27 1 0.02
28 10 0.22
29 18 0.39
30 7 0.15
31 5 0.11
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (28 bp):
AAATATTTTAAATATAATACAAAATAAA
Found at i:1981750 original size:2 final size:2
Alignment explanation
Indices: 1981743--1981770 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1981733 GATATACGTC
1981743 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1981771 CCTATTACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1982052 original size:34 final size:34
Alignment explanation
Indices: 1981987--1982050 Score: 98
Period size: 32 Copynumber: 1.9 Consensus size: 34
1981977 AATACGTAAA
1981987 AAAAATTATATGAATAATTTAAAATTTATATAAT
1 AAAAATTATATGAATAATTTAAAATTTATATAAT
1982021 AAAAATTAT-T-AAT-ATATTAAAATTTATATA
1 AAAAATTATATGAATAAT-TTAAAATTTATATA
1982051 TATATGAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 2 0.07
32 17 0.59
33 1 0.03
34 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (34 bp):
AAAAATTATATGAATAATTTAAAATTTATATAAT
Found at i:1982053 original size:18 final size:18
Alignment explanation
Indices: 1982005--1982055 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
1981995 TATGAATAAT
1982005 TTAAAATTTATATA-ATA
1 TTAAAATTTATATATATA
1982022 --AAAA-TTAT-TAATATA
1 TTAAAATTTATAT-ATATA
1982037 TTAAAATTTATATATATA
1 TTAAAATTTATATATATA
1982055 T
1 T
1982056 GAATGATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
13 1 0.04
14 5 0.18
15 7 0.25
17 4 0.14
18 10 0.36
19 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAATTTATATATATA
Found at i:1982066 original size:32 final size:32
Alignment explanation
Indices: 1982005--1982072 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1981995 TATGAATAAT
*
1982005 TTAAAATTTATATAATAAAAATTATTAATATA
1 TTAAAATTTATATAATAAAAATGATTAATATA
** *
1982037 TTAAAATTTATATATATATGAATGA-TAATATT
1 TTAAAATTTATATA-ATAAAAATGATTAATATA
1982069 TTAA
1 TTAA
1982073 TCATGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 24 0.77
33 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (32 bp):
TTAAAATTTATATAATAAAAATGATTAATATA
Found at i:1991140 original size:21 final size:22
Alignment explanation
Indices: 1991103--1991145 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1991093 TGAGATTTTC
1991103 AAATATATATATATTAA-AAAT
1 AAATATATATATATTAATAAAT
*
1991124 AAATATATTTA-ATTTAATAAAT
1 AAATATATATATA-TTAATAAAT
1991146 GGTAGCCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 14 0.74
22 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATATATATATATTAATAAAT
Found at i:1992176 original size:24 final size:25
Alignment explanation
Indices: 1992133--1992188 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
1992123 CAGACTCTAT
*
1992133 TATT-ATTATTAATTATATTAATAA
1 TATTAATTTTTAATTATATTAATAA
*
1992157 TA-TAATTTTTAATTGA-ATTAATAT
1 TATTAATTTTTAATT-ATATTAATAA
1992181 TATTAATT
1 TATTAATT
1992189 AAATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 20 0.74
25 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TATTAATTTTTAATTATATTAATAA
Found at i:1992200 original size:21 final size:21
Alignment explanation
Indices: 1992136--1992207 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 21
1992126 ACTCTATTAT
*
1992136 TATTATTAATTATATTAATAATA
1 TATTATTAATTA-AATAATAA-A
* *
1992159 TAATTTTTAATTGAAT--T-AA
1 T-ATTATTAATTAAATAATAAA
1992178 TATTATTAATTAAATAATAAA
1 TATTATTAATTAAATAATAAA
*
1992199 TATAATTAA
1 TATTATTAA
1992208 AAAAGTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 12 0.31
19 2 0.05
20 2 0.05
21 11 0.28
23 3 0.08
24 9 0.23
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TATTATTAATTAAATAATAAA
Found at i:1998501 original size:27 final size:30
Alignment explanation
Indices: 1998447--1998505 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
1998437 TTGATTTAAA
1998447 TTAATTTAATATTTAATTATTAAAAAATATTT
1 TTAATTTAATATTTAATTATT--AAAATATTT
1998479 TTAATTTAA-ATTTAATTA-TAAATATAT
1 TTAATTTAATATTTAATTATTAAA-ATAT
1998506 AAATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 3 0.12
29 4 0.15
30 1 0.04
31 9 0.35
32 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TTAATTTAATATTTAATTATTAAAATATTT
Found at i:1998515 original size:17 final size:17
Alignment explanation
Indices: 1998492--1998536 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1998482 ATTTAAATTT
*
1998492 AATTATAAATATATAAA
1 AATTATAAATAAATAAA
*
1998509 TATTATATAA-AAATAAA
1 AATTATA-AATAAATAAA
1998526 AATTATAAATA
1 AATTATAAATA
1998537 GTAAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTATAAATAAATAAA
Found at i:1998548 original size:26 final size:27
Alignment explanation
Indices: 1998485--1998550 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 27
1998475 ATTTTTAATT
* * *
1998485 TAAATTTAATTATAAATATATAAATAT
1 TAAATTTAAATAAAAATATATAAATAG
* **
1998512 TATATAAAAATAAAAAT-TATAAATAG
1 TAAATTTAAATAAAAATATATAAATAG
1998538 TAAATTTAAATAA
1 TAAATTTAAATAA
1998551 TATAGGTGGA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAATTTAAATAAAAATATATAAATAG
Found at i:1998980 original size:2 final size:2
Alignment explanation
Indices: 1998973--1999000 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1998963 ATTAAAACTC
1998973 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1999001 TGAGGCGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1999403 original size:21 final size:20
Alignment explanation
Indices: 1999378--1999500 Score: 65
Period size: 21 Copynumber: 5.9 Consensus size: 20
1999368 AGTTGAATTT
1999378 ATATATTATTAATATATTAAA
1 ATATATTATT-ATATATTAAA
*
1999399 TTATATTATT-TA-ATTAAA
1 ATATATTATTATATATTAAA
* * *
1999417 A-ATTTTAATAATAAATATAAA
1 ATATATT-ATTATATAT-TAAA
* * *
1999438 TTATTTTATT-TATAATAAA
1 ATATATTATTATATATTAAA
*
1999457 ATATCATTAATTAATTTATTAATA
1 ATAT-ATT-ATT-ATATATTAA-A
1999481 ATATATTGACTTATATATTA
1 ATATATT-A-TTATATATTA
1999501 TCCGCATATA
Statistics
Matches: 77, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
17 4 0.05
18 8 0.10
19 11 0.14
20 7 0.09
21 18 0.23
22 5 0.06
23 17 0.22
24 7 0.09
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (20 bp):
ATATATTATTATATATTAAA
Found at i:1999449 original size:26 final size:28
Alignment explanation
Indices: 1999420--1999483 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
1999410 AATTAAAAAT
*
1999420 TTTAATAATAAATAT-A-AATTATTTTA
1 TTTAATAATAAATATCATAATTAATTTA
1999446 TTT-ATAATAAAATATCATTAATTAATTTA
1 TTTAATAAT-AAATATCA-TAATTAATTTA
1999475 -TTAATAATA
1 TTTAATAATA
1999484 TATTGACTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
25 5 0.16
26 9 0.28
27 1 0.03
28 3 0.09
29 14 0.44
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAATAATAAATATCATAATTAATTTA
Found at i:1999465 original size:25 final size:26
Alignment explanation
Indices: 1999424--1999486 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
1999414 AAAAATTTTA
* *
1999424 ATAAT-AAATATAAATTATTTTATTT
1 ATAATAAAATATAAATTAATTAATTT
*
1999449 ATAATAAAATAT-CATTAATTAATTT
1 ATAATAAAATATAAATTAATTAATTT
*
1999474 ATTAATAATATAT
1 A-TAATAAAATAT
1999487 TGACTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
ATAATAAAATATAAATTAATTAATTT
Found at i:1999633 original size:2 final size:2
Alignment explanation
Indices: 1999626--1999656 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1999616 CTATTATTTC
*
1999626 AT AT AT AT AA 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 AT AT A
1999657 ACTTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2000066 original size:2 final size:2
Alignment explanation
Indices: 2000054--2000087 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
2000044 CAAAAATACC
2000054 AT AT CAT 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 AT AT AT A
2000088 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2002073 original size:15 final size:15
Alignment explanation
Indices: 2002053--2002083 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2002043 CACCATTAAT
2002053 AATTTATAGAGATGA
1 AATTTATAGAGATGA
2002068 AATTTATAGAGATGA
1 AATTTATAGAGATGA
2002083 A
1 A
2002084 GGGAATGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (15 bp):
AATTTATAGAGATGA
Found at i:2007617 original size:2 final size:2
Alignment explanation
Indices: 2007610--2007636 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2007600 TTTCTCTTTG
2007610 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2007637 TTGTATTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2008791 original size:18 final size:19
Alignment explanation
Indices: 2008758--2008793 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2008748 TCCGTAGTTC
2008758 ATATATTTTGATTATATTT
1 ATATATTTTGATTATATTT
2008777 ATATATTTT-ATTATATT
1 ATATATTTTGATTATATT
2008794 ATAATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
ATATATTTTGATTATATTT
Found at i:2008850 original size:33 final size:34
Alignment explanation
Indices: 2008811--2008884 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 34
2008801 TATTTAAAAT
* *
2008811 ATTTATATTTAAATAAATT-TTGATATATTAATA-
1 ATTTATATTTAAAT-AATTATTAAAATATTAATAC
2008844 ATTTATA-TTAAATAATTATTAAAATATTAATAC
1 ATTTATATTTAAATAATTATTAAAATATTAATAC
2008877 ATTTATAT
1 ATTTATAT
2008885 CTTTTTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 4 0.11
32 18 0.50
33 14 0.39
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (34 bp):
ATTTATATTTAAATAATTATTAAAATATTAATAC
Found at i:2008927 original size:22 final size:23
Alignment explanation
Indices: 2008897--2008946 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
2008887 TTTTTAATAT
*
2008897 GTTT-ATTATTTAT-GTATTATA
1 GTTTAATTATTTATAATATTATA
*
2008918 GTTTAATTATTTTTAATATTATA
1 GTTTAATTATTTATAATATTATA
2008941 -TTTAAT
1 GTTTAAT
2008947 ATTACTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 14 0.56
23 7 0.28
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (23 bp):
GTTTAATTATTTATAATATTATA
Found at i:2011842 original size:18 final size:18
Alignment explanation
Indices: 2011819--2011856 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2011809 ATTTTTTATT
*
2011819 TTTAAAAATAATTATTTA
1 TTTAAAAATAATTAATTA
*
2011837 TTTAAAATTAATTAATTA
1 TTTAAAAATAATTAATTA
2011855 TT
1 TT
2011857 GTTAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAAAATAATTAATTA
Found at i:2014960 original size:22 final size:21
Alignment explanation
Indices: 2014931--2014979 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
2014921 ATGTCTCAGT
*
2014931 TTTCTTTTGGCAAATCTTACG
1 TTTCTTTTTGCAAATCTTACG
2014952 TTTCTTTTTGCAAATCTTACG
1 TTTCTTTTTGCAAATCTTACG
2014973 TTTCTTT
1 TTTCTTT
2014980 GGTTAGCTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.18, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTCTTTTTGCAAATCTTACG
Found at i:2016363 original size:2 final size:2
Alignment explanation
Indices: 2016356--2016388 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2016346 ATGTGAATAC
2016356 AT AT AT 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 AT AT AT A
2016389 ATAGGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2022515 original size:2 final size:2
Alignment explanation
Indices: 2022508--2022538 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2022498 TGCAAAATAC
2022508 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2022539 GCATATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2022886 original size:4 final size:4
Alignment explanation
Indices: 2022877--2022908 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
2022867 CCGTTTCCCT
2022877 CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
2022909 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:2022926 original size:2 final size:2
Alignment explanation
Indices: 2022921--2022946 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2022911 TATATATACG
2022921 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
2022947 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2023396 original size:2 final size:2
Alignment explanation
Indices: 2023353--2023379 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2023343 TCTTCAAATA
2023353 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
2023380 AATTATGTCA
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:2024737 original size:15 final size:16
Alignment explanation
Indices: 2024701--2024745 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
2024691 GAAAGAAGAG
*
2024701 AAGAAAGATG-GGGAC
1 AAGAAAGACGAGGGAC
*
2024716 AAAAAAGACGAGGGA-
1 AAGAAAGACGAGGGAC
2024731 AAGAAAGACGAGGGA
1 AAGAAAGACGAGGGA
2024746 GGCAAGAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.53, C:0.07, G:0.38, T:0.02
Consensus pattern (16 bp):
AAGAAAGACGAGGGAC
Found at i:2025617 original size:55 final size:55
Alignment explanation
Indices: 2025550--2025659 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
2025540 TAAACGCCAG
* * *
2025550 TTGGAAAGTGTAGTTTGATGACTTTTGAAACTCGGTATGGACATTTGGCATTTGA
1 TTGGAAAGTGTAGTTTGATGACTTCTGAAACTCGATATGGACATTTGACATTTGA
* *
2025605 TTGGAAATTGTAGTTTGATGACTTCTGAAAGTCGATATGGACATTTGACATTTGA
1 TTGGAAAGTGTAGTTTGATGACTTCTGAAACTCGATATGGACATTTGACATTTGA
2025660 GGTTTCAGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.38
Consensus pattern (55 bp):
TTGGAAAGTGTAGTTTGATGACTTCTGAAACTCGATATGGACATTTGACATTTGA
Found at i:2027340 original size:16 final size:16
Alignment explanation
Indices: 2027319--2027351 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2027309 GTAATTATAT
2027319 AAATTAACTAAGTTAA
1 AAATTAACTAAGTTAA
*
2027335 AAATTAACTGAGTTAA
1 AAATTAACTAAGTTAA
2027351 A
1 A
2027352 GTTTGAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (16 bp):
AAATTAACTAAGTTAA
Found at i:2031344 original size:18 final size:18
Alignment explanation
Indices: 2031321--2031398 Score: 52
Period size: 18 Copynumber: 4.2 Consensus size: 18
2031311 TATATTAATA
2031321 AATTAAATAATTTTATTT
1 AATTAAATAATTTTATTT
**
2031339 AATTAAA-AATGTTTA-GA
1 AATTAAATAAT-TTTATTT
*
2031356 AATATATATAATTTTATTTTT
1 AAT-TAAATAATTTTA--TTT
* * *
2031377 AATAAAATGATATTATTT
1 AATTAAATAATTTTATTT
2031395 AATT
1 AATT
2031399 TATTAATGAT
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
17 6 0.14
18 24 0.55
19 3 0.07
20 8 0.18
21 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
AATTAAATAATTTTATTT
Found at i:2036804 original size:45 final size:45
Alignment explanation
Indices: 2036743--2036833 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
2036733 CCATCTAAGC
* * *
2036743 AAAGGTCAGATTACATTTAGAAGTTTCATACTCGTTTATTTTTCT
1 AAAGGCCAGATTACATTGAGAAGTTTCATACTCGTTTAATTTTCT
*
2036788 AAAGGCCAGATTACATTGAGAAGTTTCATAGTCGTTTAATTTTCT
1 AAAGGCCAGATTACATTGAGAAGTTTCATACTCGTTTAATTTTCT
2036833 A
1 A
2036834 TGATTTTAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (45 bp):
AAAGGCCAGATTACATTGAGAAGTTTCATACTCGTTTAATTTTCT
Found at i:2037299 original size:130 final size:129
Alignment explanation
Indices: 2037080--2037341 Score: 391
Period size: 130 Copynumber: 2.0 Consensus size: 129
2037070 TCCACAACAC
* * * *
2037080 AATGAAGCAGCACATCTCCTGCAACATATTAATCCCTATATCGTTAGAATGAAAAGCAAATTATG
1 AATGAAGCAGCAAATCTCCTGCAACATATTAATCCCTACATAGTTAGAATCAAAAGCAAATTATG
* * * *
2037145 GAAAATAAAAGCAGCTAATACAACCTAGAAATACAGATTCCAGATAAATATATATTAGGGATAA
66 GAAAATAAAAGCAGATAATACAACCAAGAAATACAGATTCCAGATAAAAATATATTAGGGAAAA
*
2037209 AATGAAGCAGCAAATCTCCTGCAACATATTAATCCCTACATAGTTTAGAATCAAAATCAAATTAT
1 AATGAAGCAGCAAATCTCCTGCAACATATTAATCCCTACATAG-TTAGAATCAAAAGCAAATTAT
* **
2037274 GGAAAATTTAAA-CAGATAATACAACCAAGAAATAGGGATTCCAGATAAAAATATATTAGGGAAA
65 GGAAAA-TAAAAGCAGATAATACAACCAAGAAATACAGATTCCAGATAAAAATATATTAGGGAAA
2037338 A
129 A
2037339 AAT
1 AAT
2037342 TGTGGGGTTG
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
129 40 0.34
130 75 0.63
131 4 0.03
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.24
Consensus pattern (129 bp):
AATGAAGCAGCAAATCTCCTGCAACATATTAATCCCTACATAGTTAGAATCAAAAGCAAATTATG
GAAAATAAAAGCAGATAATACAACCAAGAAATACAGATTCCAGATAAAAATATATTAGGGAAAA
Found at i:2037644 original size:3 final size:3
Alignment explanation
Indices: 2037638--2037668 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2037628 AGAAGAAGAA
2037638 GAT GAT GAT GAT GAT GAT GAT GAT GAT -AT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
2037669 GGTTATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:2038417 original size:27 final size:27
Alignment explanation
Indices: 2038379--2038431 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2038369 TTCTGATTAT
2038379 ATGATGCTTTTTTATTATATGAGTATG
1 ATGATGCTTTTTTATTATATGAGTATG
*
2038406 ATGATGTTTTTTTATTATATGAGTAT
1 ATGATGCTTTTTTATTATATGAGTAT
2038432 AATTTGATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.55
Consensus pattern (27 bp):
ATGATGCTTTTTTATTATATGAGTATG
Found at i:2042664 original size:14 final size:13
Alignment explanation
Indices: 2042636--2042669 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2042626 AATAAATAAA
*
2042636 TAAATTTATTATT
1 TAAATTTACTATT
2042649 TAAATATTACTATT
1 TAAAT-TTACTATT
2042663 TAAATTT
1 TAAATTT
2042670 TTATTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATTTACTATT
Found at i:2051135 original size:20 final size:21
Alignment explanation
Indices: 2051112--2051151 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2051102 ATTATTAAAG
2051112 ATTA-TTAAATTAATAAAAAA
1 ATTATTTAAATTAATAAAAAA
*
2051132 ATTATTTTAATTAATAAAAA
1 ATTATTTAAATTAATAAAAA
2051152 TTAAAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATTTAAATTAATAAAAAA
Found at i:2052340 original size:15 final size:16
Alignment explanation
Indices: 2052308--2052348 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2052298 AATATAAATA
*
2052308 TAAAATATA-ATTTCT
1 TAAAATATATATATCT
2052323 TAAAATATATATAT-T
1 TAAAATATATATATCT
*
2052338 TAAAAAATATA
1 TAAAATATATA
2052349 AAAAATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATATATATATCT
Found at i:2063248 original size:25 final size:25
Alignment explanation
Indices: 2063220--2063271 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2063210 GCGTTGAATT
2063220 AATATGTAAGCTTAAATTCAATTTC
1 AATATGTAAGCTTAAATTCAATTTC
2063245 AATATGTAAGCTTAAATTCAATTTC
1 AATATGTAAGCTTAAATTCAATTTC
2063270 AA
1 AA
2063272 ATATCTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (25 bp):
AATATGTAAGCTTAAATTCAATTTC
Found at i:2064613 original size:3 final size:3
Alignment explanation
Indices: 2064605--2064641 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2064595 TCATTGATAC
*
2064605 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2064642 CCAATGGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2070720 original size:17 final size:17
Alignment explanation
Indices: 2070675--2070722 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
2070665 AAGTAATTGC
2070675 ATTTTTTATAA-AAATA
1 ATTTTTTATAATAAATA
2070691 ATTTTATT-TAATAAATA
1 ATTTT-TTATAATAAATA
*
2070708 ATTTTTTAAAATAAA
1 ATTTTTTATAATAAA
2070723 AATATTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 10 0.36
17 18 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTTTATAATAAATA
Found at i:2074344 original size:20 final size:20
Alignment explanation
Indices: 2074319--2074372 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
2074309 TTATATTTTA
*
2074319 TTTCATATCATAATTTATTT
1 TTTCATATCATAATTTACTT
*
2074339 TTTCATATTAT-ATTTACTT
1 TTTCATATCATAATTTACTT
*
2074358 TAT-ATATACATAATT
1 TTTCATAT-CATAATT
2074373 GAAATTGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.14
19 11 0.39
20 13 0.46
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTCATATCATAATTTACTT
Found at i:2077261 original size:3 final size:3
Alignment explanation
Indices: 2077253--2077288 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2077243 TAACAATCCC
2077253 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2077289 ATAAAATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2081440 original size:2 final size:2
Alignment explanation
Indices: 2081433--2081468 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2081423 TTTTATGATA
*
2081433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2081469 GTATCGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2082594 original size:3 final size:3
Alignment explanation
Indices: 2082586--2082610 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2082576 GTAAATATTT
2082586 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
2082611 CAACAACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2083165 original size:19 final size:18
Alignment explanation
Indices: 2083143--2083193 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 18
2083133 AAACTGAATA
2083143 ATTTATATATTTATATTAT
1 ATTTATATATTT-TATTAT
2083162 ATTTATATATTTTATTAT
1 ATTTATATATTTTATTAT
*
2083180 A-TCATA-ATTTTATT
1 ATTTATATATTTTATT
2083194 TAAAATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 8 0.26
17 4 0.13
18 7 0.23
19 12 0.39
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:2083331 original size:26 final size:26
Alignment explanation
Indices: 2083268--2083331 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
2083258 ATATACTCAT
*
2083268 ATTATATT--ATATCATATTTTTATA
1 ATTATATTAAATATCATATTTATATA
2083292 ATT-T-TTACATATATCATATTTATATA
1 ATTATATTA-A-ATATCATATTTATATA
2083318 ATTATATTAAATAT
1 ATTATATTAAATAT
2083332 TATCGAGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
22 2 0.06
23 1 0.03
24 3 0.09
26 22 0.67
27 2 0.06
28 3 0.09
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTATATTAAATATCATATTTATATA
Found at i:2083911 original size:22 final size:22
Alignment explanation
Indices: 2083876--2083918 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2083866 ATAAAACTTT
2083876 AAAATATAAAAAAAT-ATTTTA
1 AAAATATAAAAAAATAATTTTA
*
2083897 AAAATGATAATAAAATAATTTT
1 AAAAT-ATAAAAAAATAATTTT
2083919 TAACTAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAATATAAAAAAATAATTTTA
Found at i:2085197 original size:2 final size:2
Alignment explanation
Indices: 2085179--2085232 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
2085169 TTACACCAAG
* *
2085179 AT AT AT GT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2085221 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2085233 GAAGTGTTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2087048 original size:2 final size:2
Alignment explanation
Indices: 2087043--2087077 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2087033 CTTGGATGGA
2087043 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2087078 GAGGAGCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2088918 original size:16 final size:18
Alignment explanation
Indices: 2088887--2088922 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
2088877 TTAAACTCAA
2088887 AATTATAAATTTAAAAAT
1 AATTATAAATTTAAAAAT
2088905 AATTAT-AA-TTAAAAAT
1 AATTATAAATTTAAAAAT
2088921 AA
1 AA
2088923 AAATTCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTATAAATTTAAAAAT
Found at i:2089209 original size:2 final size:2
Alignment explanation
Indices: 2089204--2089238 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2089194 ATTCATCTTT
2089204 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2089239 CACACTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2089860 original size:10 final size:10
Alignment explanation
Indices: 2089845--2089883 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
2089835 ATATTGTCCT
2089845 TTTCCTTTCG
1 TTTCCTTTCG
*
2089855 TTTCCTTTCA
1 TTTCCTTTCG
*
2089865 TTTCTTTTCG
1 TTTCCTTTCG
2089875 TTTCCTTTC
1 TTTCCTTTC
2089884 TCTGCTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.03, C:0.28, G:0.05, T:0.64
Consensus pattern (10 bp):
TTTCCTTTCG
Found at i:2089873 original size:20 final size:20
Alignment explanation
Indices: 2089845--2089883 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2089835 ATATTGTCCT
2089845 TTTCCTTTCGTTTCCTTTCA
1 TTTCCTTTCGTTTCCTTTCA
*
2089865 TTTCTTTTCGTTTCCTTTC
1 TTTCCTTTCGTTTCCTTTC
2089884 TCTGCTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.03, C:0.28, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTCCTTTCGTTTCCTTTCA
Found at i:2089891 original size:20 final size:20
Alignment explanation
Indices: 2089850--2089892 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2089840 GTCCTTTTCC
*
2089850 TTTCGTTTCCTTTCATTTCT
1 TTTCGTTTCCTTTCATTGCT
2089870 TTTCGTTTCCTTTC-TCTGCT
1 TTTCGTTTCCTTTCAT-TGCT
2089890 TTT
1 TTT
2089893 GGAGCTGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.02, C:0.26, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTCGTTTCCTTTCATTGCT
Found at i:2098471 original size:17 final size:17
Alignment explanation
Indices: 2098438--2098470 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2098428 TGTAATTTCC
*
2098438 ATTTTTAGTTATTTTTT
1 ATTTTTAATTATTTTTT
2098455 ATTTTTAATT-TTTTTT
1 ATTTTTAATTATTTTTT
2098471 TTACTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
ATTTTTAATTATTTTTT
Found at i:2099142 original size:14 final size:14
Alignment explanation
Indices: 2099116--2099216 Score: 63
Period size: 14 Copynumber: 7.4 Consensus size: 14
2099106 ATATGATACG
*
2099116 TATATTAAATATAT
1 TATATTAATTATAT
*
2099130 TATGTTAATTATAT
1 TATATTAATTATAT
**
2099144 T-TAAAAATATTATAT
1 TAT-ATTA-ATTATAT
*
2099159 TATTTTAATTATAT
1 TATATTAATTATAT
2099173 TAT-TT--TTATAT
1 TATATTAATTATAT
*
2099184 T-TATTAAATATAAT
1 TATATTAATTAT-AT
2099198 TATATT--TTGATAT
1 TATATTAATT-ATAT
2099211 TATATT
1 TATATT
2099217 TAAAATTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
10 1 0.01
11 9 0.13
13 15 0.22
14 29 0.43
15 13 0.19
16 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TATATTAATTATAT
Found at i:2099172 original size:19 final size:20
Alignment explanation
Indices: 2099128--2099216 Score: 64
Period size: 19 Copynumber: 4.7 Consensus size: 20
2099118 TATTAAATAT
*
2099128 ATTATGTTA-ATTATATTTA
1 ATTATATTATATTATATTTA
**
2099147 AAAATATTATATTAT-TTTA
1 ATTATATTATATTATATTTA
*
2099166 ATTATATTATTTTTATATTT-
1 ATTATATTA-TATTATATTTA
*
2099186 ATTA-AATATAATTATATTT-
1 ATTATATTAT-ATTATATTTA
*
2099205 -TGATATTATATT
1 ATTATATTATATT
2099217 TAAAATTATT
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
18 6 0.11
19 32 0.58
20 14 0.25
21 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTATATTATATTATATTTA
Found at i:2099182 original size:25 final size:27
Alignment explanation
Indices: 2099153--2099220 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
2099143 TTTAAAAATA
*
2099153 TTATATTATTTTAATTAT-ATTAT-TT
1 TTATATTATTTTAAATATAATTATATT
*
2099178 TTATATT-TATTAAATATAATTATATT
1 TTATATTATTTTAAATATAATTATATT
2099204 TTGATATTATATTTAAA
1 TT-ATATTAT-TTTAAA
2099221 ATTATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 8 0.23
25 12 0.34
26 4 0.11
27 5 0.14
28 1 0.03
29 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
TTATATTATTTTAAATATAATTATATT
Found at i:2099232 original size:15 final size:16
Alignment explanation
Indices: 2099208--2099241 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2099198 TATATTTTGA
*
2099208 TATTATATTTAA-AAT
1 TATTAAATTTAATAAT
2099223 TATTAAATTTAATAAT
1 TATTAAATTTAATAAT
2099239 TAT
1 TAT
2099242 GATTAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTAAATTTAATAAT
Found at i:2100034 original size:34 final size:34
Alignment explanation
Indices: 2099988--2100172 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
2099978 GTAAAAACCA
*
2099988 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2100022 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * *
2100056 TCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2100090 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2100124 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2100157 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2100173 TTTCCCACTT
Statistics
Matches: 133, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
33 18 0.14
34 111 0.83
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2104634 original size:34 final size:34
Alignment explanation
Indices: 2104588--2104770 Score: 235
Period size: 34 Copynumber: 5.4 Consensus size: 34
2104578 GTAAAAACCA
*
2104588 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2104622 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * *
2104656 TCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2104690 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
2104724 CCATTTAGTCAATAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2104757 CCATTTAATCAACA
1 CCATTTAATCAACA
2104771 CATAATTCTA
Statistics
Matches: 129, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
33 15 0.12
34 110 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2108651 original size:2 final size:2
Alignment explanation
Indices: 2108644--2108683 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2108634 AGCACACGCC
2108644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2108684 CTCATTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2108903 original size:25 final size:25
Alignment explanation
Indices: 2108857--2108925 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
2108847 AAATACTTTG
* *
2108857 ATATATTTTAAAAATATAAAAAATTTT
1 ATATA-TTTAAATA-ATAAAAAATATT
2108884 AATATATTTAAATAATAAAAAATATT
1 -ATATATTTAAATAATAAAAAATATT
2108910 AT-TATTTAAAATAATA
1 ATATATTT-AAATAATA
2108926 TTTTAATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
24 5 0.13
25 10 0.26
26 11 0.29
27 7 0.18
28 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATATTTAAATAATAAAAAATATT
Found at i:2110085 original size:8 final size:8
Alignment explanation
Indices: 2110054--2110122 Score: 52
Period size: 8 Copynumber: 8.5 Consensus size: 8
2110044 AGATTGTGAA
*
2110054 ATATTAAA
1 ATATTAAT
2110062 ATATTAAT
1 ATATTAAT
*
2110070 ATAATAAT
1 ATATTAAT
2110078 ATATTAAT
1 ATATTAAT
*
2110086 A-AATAAT
1 ATATTAAT
* *
2110093 -TTTTATT
1 ATATTAAT
2110100 ATATATAAT
1 ATAT-TAAT
2110109 AATATTTAAT
1 -ATA-TTAAT
2110119 ATAT
1 ATAT
2110123 AAAATTTTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
7 8 0.17
8 25 0.53
9 6 0.13
10 7 0.15
11 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATATTAAT
Found at i:2110090 original size:34 final size:33
Alignment explanation
Indices: 2110052--2110144 Score: 81
Period size: 34 Copynumber: 2.9 Consensus size: 33
2110042 TAAGATTGTG
2110052 AAATATTAAAATATTAATATAATAATATATTAAT
1 AAATATTAAAATATTAATATAATAATAT-TTAAT
**
2110086 AAATAATT--TTTATTATATATAATAATATTTAAT
1 AAAT-ATTAAAATATTA-ATATAATAATATTTAAT
* *
2110119 --ATA-TAAAATTTTAA-ATAATATTATTT
1 AAATATTAAAATATTAATATAATAATATTT
2110145 TACATATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
29 12 0.24
30 2 0.04
31 6 0.12
33 10 0.20
34 16 0.33
35 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
AAATATTAAAATATTAATATAATAATATTTAAT
Found at i:2110111 original size:19 final size:18
Alignment explanation
Indices: 2110063--2110130 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 18
2110053 AATATTAAAA
*
2110063 TATTAATATAATAA--TA
1 TATTAATATAATAATTTT
2110079 TATTAATA-AATAATTTT
1 TATTAATATAATAATTTT
*
2110096 TATTATATATAATAATATT
1 TATTA-ATATAATAATTTT
*
2110115 TAAT-ATATAA-AATTTT
1 TATTAATATAATAATTTT
2110131 AAATAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.11
16 13 0.30
17 12 0.27
18 3 0.07
19 11 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTAATATAATAATTTT
Found at i:2110226 original size:25 final size:25
Alignment explanation
Indices: 2110182--2110233 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2110172 AATTAACTAA
* *
2110182 TATTATATAAATTTATTAATTTATT
1 TATTATATAAATTTAATAATTAATT
2110207 TATTATATTAAA-TTAATAATTAATT
1 TATTATA-TAAATTTAATAATTAATT
2110232 TA
1 TA
2110234 AAATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATATAAATTTAATAATTAATT
Found at i:2113891 original size:1 final size:1
Alignment explanation
Indices: 2113885--2113909 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2113875 ACTGAAACGC
2113885 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2113910 CTGTGGAAGG
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:2114810 original size:2 final size:2
Alignment explanation
Indices: 2114803--2114839 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2114793 TTATGTTCCA
2114803 AT AT AT AT AT 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 AT AT AT AT AT A
2114840 CACATGCTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2117987 original size:2 final size:2
Alignment explanation
Indices: 2117980--2118008 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2117970 AAGAAACAAG
2117980 AT 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 AT A
2118009 ATAATCCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2120249 original size:25 final size:27
Alignment explanation
Indices: 2120218--2120272 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
2120208 TCTCTTCAAC
2120218 TAATATTTATTATA-AT-TAATTATAA
1 TAATATTTATTATATATGTAATTATAA
*
2120243 TAATATTTATTATATTTGTAATTATAA
1 TAATATTTATTATATATGTAATTATAA
2120270 TAA
1 TAA
2120273 ATATGACACG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 14 0.52
26 1 0.04
27 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TAATATTTATTATATATGTAATTATAA
Found at i:2123075 original size:17 final size:17
Alignment explanation
Indices: 2123042--2123095 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 17
2123032 GAGTCAAATT
*
2123042 AATTTATTTTAA-GATAA
1 AATTT-TTTTAATAATAA
2123059 AATTTTTTTAATAAT--
1 AATTTTTTTAATAATAA
* *
2123074 AATTTTTTTATTCATAA
1 AATTTTTTTAATAATAA
2123091 AATTT
1 AATTT
2123096 AAATTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 13 0.42
16 6 0.19
17 12 0.39
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTTTTTTAATAATAA
Found at i:2123077 original size:15 final size:16
Alignment explanation
Indices: 2123041--2123083 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
2123031 CGAGTCAAAT
2123041 TAATTTATTTTAAGATAA
1 TAATTT-TTTT-AGATAA
2123059 -AATTTTTTTA-ATAA
1 TAATTTTTTTAGATAA
2123073 TAATTTTTTTA
1 TAATTTTTTTA
2123084 TTCATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.17
15 11 0.46
16 4 0.17
17 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TAATTTTTTTAGATAA
Found at i:2126227 original size:25 final size:27
Alignment explanation
Indices: 2126187--2126236 Score: 86
Period size: 25 Copynumber: 1.9 Consensus size: 27
2126177 AATGTGCTGG
2126187 TCTGATTTTTTATTTTTC-TCAAGTGA
1 TCTGATTTTTTATTTTTCTTCAAGTGA
2126213 TCTGA-TTTTTATTTTTCTTCAAGT
1 TCTGATTTTTTATTTTTCTTCAAGT
2126237 ACTCACACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.18, C:0.12, G:0.10, T:0.60
Consensus pattern (27 bp):
TCTGATTTTTTATTTTTCTTCAAGTGA
Found at i:2132779 original size:2 final size:2
Alignment explanation
Indices: 2132768--2132803 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2132758 GAGGAAAAAC
*
2132768 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2132804 ATTTTATGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2133234 original size:20 final size:19
Alignment explanation
Indices: 2133207--2133248 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
2133197 ATTATTTATT
2133207 TAATAAAAATAT-TTAAATA
1 TAATAAAAATATATT-AATA
2133226 TAATAAAAAATATATTAATA
1 TAAT-AAAAATATATTAATA
2133246 TAA
1 TAA
2133249 AATTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAATAAAAATATATTAATA
Found at i:2133580 original size:14 final size:14
Alignment explanation
Indices: 2133548--2133574 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2133538 ATAATATATT
2133548 AATTAATTTTAAAA
1 AATTAATTTTAAAA
2133562 AATTAATTTTAAA
1 AATTAATTTTAAA
2133575 GCATTATTTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTAATTTTAAAA
Found at i:2134449 original size:3 final size:3
Alignment explanation
Indices: 2134443--2134467 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2134433 CACAACAAAA
2134443 CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG C
2134468 GGCGCCTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Done.