Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 12 of 20
Found at i:1933162 original size:44 final size:42
Alignment explanation
Indices: 1933100--1933240 Score: 155
Period size: 44 Copynumber: 3.3 Consensus size: 42
1933090 CTAAACTTAT
1933100 TCAG-TTCTTTTTTCAAGTAGAAACAAACTTTTCCTGACCAAAA
1 TCAGTTTCTTTTTT-AAGTA-AAACAAACTTTTCCTGACCAAAA
* *
1933143 TCAGTTTCTTTTTCTAAGTATAAACAGACTTTTCCTGAGCAAAA
1 TCAGTTTCTTTTT-TAAGTA-AAACAAACTTTTCCTGACCAAAA
* * * *
1933187 TCGGTGTCTTCTTTTAAGT---ACAAACATTTCCCGACCAAAA
1 TCAGTTTCTT-TTTTAAGTAAAACAAACTTTTCCTGACCAAAA
1933227 TCAGTTTCTTTTTT
1 TCAGTTTCTTTTTT
1933241 CAACTGAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
39 4 0.05
40 25 0.30
43 4 0.05
44 47 0.56
45 4 0.05
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.39
Consensus pattern (42 bp):
TCAGTTTCTTTTTTAAGTAAAACAAACTTTTCCTGACCAAAA
Found at i:1933387 original size:16 final size:15
Alignment explanation
Indices: 1933368--1933438 Score: 69
Period size: 16 Copynumber: 4.8 Consensus size: 15
1933358 ATAGTAGAGT
1933368 TTAATAAATAATTTAA
1 TTAATAAA-AATTTAA
1933384 TTAATAAATATATTTAA
1 TTAATAAA-A-ATTTAA
*
1933401 -TAATAAAATTTTAA
1 TTAATAAAAATTTAA
*
1933415 TAAAT-AAAATTTAA
1 TTAATAAAAATTTAA
1933429 TT--TAAAAATT
1 TTAATAAAAATT
1933439 ATAAAAATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
12 1 0.02
13 6 0.12
14 14 0.29
15 4 0.08
16 17 0.35
17 6 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAATAAAAATTTAA
Found at i:1933411 original size:13 final size:13
Alignment explanation
Indices: 1933367--1933429 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 13
1933357 AATAGTAGAG
*
1933367 TTTAATAA-ATAA
1 TTTAATAATAAAA
1933379 TTTAATTAATAAATATA
1 TTTAA-TAAT-AA-A-A
1933396 TTTAATAATAAAA
1 TTTAATAATAAAA
1933409 TTTTAATAAATAAAA
1 -TTTAAT-AATAAAA
1933424 TTTAAT
1 TTTAAT
1933430 TTAAAAATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
12 5 0.12
13 4 0.09
14 13 0.30
15 10 0.23
16 5 0.12
17 6 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTAATAATAAAA
Found at i:1933427 original size:14 final size:14
Alignment explanation
Indices: 1933384--1933429 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1933374 AATAATTTAA
*
1933384 TTAATAAAT-ATAT
1 TTAATAAATAAAAT
1933397 TTAAT-AATAAAATT
1 TTAATAAATAAAA-T
1933411 TTAATAAATAAAAT
1 TTAATAAATAAAAT
1933425 TTAAT
1 TTAAT
1933430 TTAAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 3 0.10
13 7 0.24
14 12 0.41
15 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATAAATAAAAT
Found at i:1933907 original size:25 final size:24
Alignment explanation
Indices: 1933879--1933930 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
1933869 AATAAATAAT
* *
1933879 TATAAGGTAAAAATTTATAGTTAAA
1 TATAAGATAAAAATTTATA-TAAAA
* *
1933904 TATATGATAAATATTTATATAAAA
1 TATAAGATAAAAATTTATATAAAA
1933928 TAT
1 TAT
1933931 TTTGAATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (24 bp):
TATAAGATAAAAATTTATATAAAA
Found at i:1934073 original size:14 final size:14
Alignment explanation
Indices: 1934054--1934086 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1934044 TAAAAATAAA
1934054 TTTTAATATATTAT
1 TTTTAATATATTAT
1934068 TTTTAATATATTAT
1 TTTTAATATATTAT
1934082 TTTTA
1 TTTTA
1934087 TTTTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTAATATATTAT
Found at i:1934125 original size:18 final size:17
Alignment explanation
Indices: 1934062--1934127 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 17
1934052 AATTTTAATA
1934062 TATTATTTTTAATATATTAT
1 TATTATTTTT-AT-TA-TAT
* *
1934082 TTTTATTTTTTATTATAA
1 TATTA-TTTTTATTATAT
1934100 T-TTA-TTTTATTATCAT
1 TATTATTTTTATTAT-AT
1934116 TATTATTTTTAT
1 TATTATTTTTAT
1934128 ATTTATAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
15 9 0.23
16 2 0.05
17 6 0.15
18 9 0.23
19 2 0.05
20 6 0.15
21 5 0.13
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTATTTTTATTATAT
Found at i:1934716 original size:8 final size:8
Alignment explanation
Indices: 1934705--1934736 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
1934695 AAATATATTT
1934705 ATTTTTTA
1 ATTTTTTA
1934713 ATTTTTTA
1 ATTTTTTA
1934721 ATTTTTTA
1 ATTTTTTA
1934729 ATTTTTTA
1 ATTTTTTA
1934737 TATAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTTTA
Found at i:1938129 original size:23 final size:24
Alignment explanation
Indices: 1938085--1938128 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1938075 TTTACTATTA
1938085 ATAAATATAATTGATAAATTTTGT
1 ATAAATATAATTGATAAATTTTGT
*
1938109 ATAAATA-AATTTA-AAATTTT
1 ATAAATATAATTGATAAATTTT
1938129 TAAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 5 0.26
24 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (24 bp):
ATAAATATAATTGATAAATTTTGT
Found at i:1939223 original size:19 final size:20
Alignment explanation
Indices: 1939199--1939237 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1939189 ATTAAAATTA
1939199 AATAT-AAATATATATTTTT
1 AATATAAAATATATATTTTT
*
1939218 AATATAAAATATTTATTTTT
1 AATATAAAATATATATTTTT
1939238 TAAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATAAAATATATATTTTT
Found at i:1940905 original size:17 final size:18
Alignment explanation
Indices: 1940883--1940917 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1940873 TGGAGATTAA
1940883 TTTAAAAAAATA-ATTTT
1 TTTAAAAAAATATATTTT
1940900 TTTAAAAAAATATATTTT
1 TTTAAAAAAATATATTTT
1940918 AATAGACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAAAAATATATTTT
Found at i:1941231 original size:5 final size:5
Alignment explanation
Indices: 1941218--1941248 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1941208 ATGAAGCACT
*
1941218 AGGAA AGGAG AGGAG AGGAG AGGAG AGGAG A
1 AGGAG AGGAG AGGAG AGGAG AGGAG AGGAG A
1941249 TTATTAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (5 bp):
AGGAG
Found at i:1941461 original size:4 final size:4
Alignment explanation
Indices: 1941452--1941481 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1941442 GTGGTGCACT
1941452 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
1941482 GTTGGGTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:1942031 original size:16 final size:17
Alignment explanation
Indices: 1942007--1942063 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
1941997 TTACTTATAA
*
1942007 TATAATATAAAA-TATT
1 TATATTATAAAATTATT
1942023 TATATTATAATAACTTATT
1 TATATTATAA-AA-TTATT
*
1942042 TAT-TTATAAAATTATA
1 TATATTATAAAATTATT
1942058 TATATT
1 TATATT
1942064 GAACATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 16 0.46
17 6 0.17
18 6 0.17
19 7 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATTATAAAATTATT
Found at i:1942375 original size:16 final size:15
Alignment explanation
Indices: 1942351--1942389 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1942341 ATAAATCTTA
1942351 TTAATAATTAAAAATAT
1 TTAA-AATTAAAAA-AT
1942368 TTAAAATTAAAAAAT
1 TTAAAATTAAAAAAT
*
1942383 TAAAAAT
1 TTAAAAT
1942390 ATAATTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 9 0.43
17 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAATTAAAAAAT
Found at i:1942813 original size:14 final size:15
Alignment explanation
Indices: 1942772--1942814 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
1942762 TTATAAATAG
1942772 TTTTAACATAATTTC
1 TTTTAACATAATTTC
* *
1942787 TTTAAAGATAATTT-
1 TTTTAACATAATTTC
1942801 TTTTAACATAATTT
1 TTTTAACATAATTT
1942815 ATCTCATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (15 bp):
TTTTAACATAATTTC
Found at i:1945779 original size:3 final size:3
Alignment explanation
Indices: 1945771--1945825 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
1945761 GAACATACTT
*
1945771 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1945819 TTA TTA T
1 TTA TTA T
1945826 CATCATCATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1948657 original size:3 final size:3
Alignment explanation
Indices: 1948649--1948683 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1948639 GAACATACTT
1948649 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1948684 TTGCTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1953145 original size:19 final size:17
Alignment explanation
Indices: 1953106--1953146 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
1953096 ATATTTTATT
*
1953106 TATATTTAAAATTTTAA
1 TATATTTAAAATTTAAA
1953123 TATATTTAATAATTTAAAA
1 TATATTTAA-AATTT-AAA
1953142 TATAT
1 TATAT
1953147 AAATACAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 5 0.24
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATTTAAAATTTAAA
Found at i:1953263 original size:20 final size:19
Alignment explanation
Indices: 1953238--1953284 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1953228 TTGATCATAT
**
1953238 TTTAAATAATTTTTTATTAA
1 TTTAAATAATTTAAT-TTAA
1953258 TTTAAATTAATTTAATTTAA
1 TTTAAA-TAATTTAATTTAA
1953278 TTTAAAT
1 TTTAAAT
1953285 TGATATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 16 0.67
21 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAAATAATTTAATTTAA
Found at i:1953303 original size:28 final size:26
Alignment explanation
Indices: 1953253--1953421 Score: 94
Period size: 28 Copynumber: 5.9 Consensus size: 26
1953243 ATAATTTTTT
1953253 ATTAATTTAAATTAATTTAATTTAATTTAA
1 ATTAATTTAAA-T-A-TT-ATTTAATTTAA
*
1953283 ATTGATATTTAAATATTATTTTATTTAA
1 ATT-A-ATTTAAATATTATTTAATTTAA
**
1953311 ATTTAATTATAAA-ATGTA-TTAATTTTTT
1 A-TTAATT-TAAATAT-TATTTAA-TTTAA
*
1953339 ATTAATTTAAGTTAATTTAATTTAATTTAA
1 ATTAATTTAA-AT-A-TT-ATTTAATTTAA
*
1953369 ATTAATATTTAAATATTATTTTATTTAA
1 ATT-A-ATTTAAATATTATTTAATTTAA
1953397 ATTTAATTATAAA-ATGTA-TTAATTT
1 A-TTAATT-TAAATAT-TATTTAATTT
1953422 TTTATTAATT
Statistics
Matches: 112, Mismatches: 10, Indels: 37
0.70 0.06 0.23
Matches are distributed among these distances:
26 3 0.03
27 25 0.22
28 40 0.36
29 10 0.09
30 13 0.12
31 8 0.07
32 13 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTAATTTAAATATTATTTAATTTAA
Found at i:1953337 original size:86 final size:86
Alignment explanation
Indices: 1953244--1953437 Score: 361
Period size: 86 Copynumber: 2.2 Consensus size: 86
1953234 ATATTTTAAA
*
1953244 TAATTTTTTATTAATTTAAATTAATTTAATTTAATTTAAATTGATATTTAAATATTATTTTATTT
1 TAATTTTTTATTAATTTAAATTAATTTAATTTAATTTAAATTAATATTTAAATATTATTTTATTT
1953309 AAATTTAATTATAAAATGTAT
66 AAATTTAATTATAAAATGTAT
*
1953330 TAATTTTTTATTAATTTAAGTTAATTTAATTTAATTTAAATTAATATTTAAATATTATTTTATTT
1 TAATTTTTTATTAATTTAAATTAATTTAATTTAATTTAAATTAATATTTAAATATTATTTTATTT
1953395 AAATTTAATTATAAAATGTAT
66 AAATTTAATTATAAAATGTAT
1953416 TAATTTTTTATTAATTTTAAAT
1 TAATTTTTTATTAA-TTTAAAT
1953438 AATAAATATA
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
86 98 0.94
87 6 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (86 bp):
TAATTTTTTATTAATTTAAATTAATTTAATTTAATTTAAATTAATATTTAAATATTATTTTATTT
AAATTTAATTATAAAATGTAT
Found at i:1953404 original size:5 final size:5
Alignment explanation
Indices: 1953254--1953374 Score: 68
Period size: 5 Copynumber: 23.0 Consensus size: 5
1953244 TAATTTTTTA
* *
1953254 TTAAT TTAAA TTAAT TTAAT TTAAT TTAAAT TGATAT TTAAAT ATT-AT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TT-AAT TTA-AT TT-AAT -TTAAT
* * ** *
1953302 TTTAT TTAAAT TTAAT TATAAAAT GT-A- TTAAT TTTTT ATTAAT TTAAG
1 TTAAT TT-AAT TTAAT T-T--AAT TTAAT TTAAT TTAAT -TTAAT TTAAT
*
1953350 TTAAT TTAAT TTAAT TTAAA TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT
1953375 ATTTAAATAT
Statistics
Matches: 89, Mismatches: 15, Indels: 24
0.70 0.12 0.19
Matches are distributed among these distances:
3 1 0.01
4 4 0.04
5 60 0.67
6 17 0.19
7 4 0.04
8 3 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
TTAAT
Found at i:1953468 original size:16 final size:16
Alignment explanation
Indices: 1953440--1953480 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1953430 TTTTAAATAA
*
1953440 TAAATATAAATTAA-T
1 TAAATAAAAATTAATT
1953455 TAAATTAAAAATTAATT
1 TAAA-TAAAAATTAATT
1953472 TAAATAAAA
1 TAAATAAAA
1953481 TGTAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 14 0.61
17 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATAAAAATTAATT
Found at i:1954438 original size:12 final size:12
Alignment explanation
Indices: 1954423--1954476 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
1954413 TATTTTTATA
1954423 TAAAT-TTAATT
1 TAAATATTAATT
1954434 GTAAATATTAATT
1 -TAAATATTAATT
* *
1954447 TAAAAATAAATT
1 TAAATATTAATT
* *
1954459 TTAATATTATTT
1 TAAATATTAATT
1954471 TAAATA
1 TAAATA
1954477 ATAAAATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 28 0.82
13 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
TAAATATTAATT
Found at i:1956947 original size:17 final size:17
Alignment explanation
Indices: 1956921--1956953 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1956911 ACGTATATAT
1956921 ATTTAAAATAA-AATAG
1 ATTTAAAATAAGAATAG
1956937 ATTTAAAAATAAGAATA
1 ATTT-AAAATAAGAATA
1956954 ATAACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
ATTTAAAATAAGAATAG
Found at i:1957903 original size:43 final size:43
Alignment explanation
Indices: 1957848--1957929 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
1957838 CATTATTCTT
* *
1957848 AATGAATCTATATATCTATATATCTATTAATTAATTTAAAGTC
1 AATGAATATATATATCTATACATCTATTAATTAATTTAAAGTC
* *
1957891 AATGAATATATATTTCTATACATCTATTGATTAATTTAA
1 AATGAATATATATATCTATACATCTATTAATTAATTTAA
1957930 TATTATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (43 bp):
AATGAATATATATATCTATACATCTATTAATTAATTTAAAGTC
Found at i:1958039 original size:43 final size:43
Alignment explanation
Indices: 1957992--1958142 Score: 121
Period size: 43 Copynumber: 3.8 Consensus size: 43
1957982 TAATACTTCG
*
1957992 TGAATCTATATATCTTTATATCTATTAATTAATTTAAAATCAA
1 TGAATCTATATATCTATATATCTATTAATTAATTTAAAATCAA
* *
1958035 TGAA--TATATATCTCTATA-C-ATCT-A-T--TCT----T-AA
1 TGAATCTATATATCTATATATCTAT-TAATTAATTTAAAATCAA
*
1958066 TGAATCTATATATCTATGTATCTATTAATTAATTTAAAATCAA
1 TGAATCTATATATCTATATATCTATTAATTAATTTAAAATCAA
* * * * *
1958109 TTAATATATATCTCTATACATCTATTGATTAATT
1 TGAATCTATATATCTATATATCTATTAATTAATT
1958143 CAATATGATA
Statistics
Matches: 83, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
31 6 0.07
32 1 0.01
33 12 0.14
34 2 0.02
35 3 0.04
36 3 0.04
38 3 0.04
39 3 0.04
40 2 0.02
41 13 0.16
42 1 0.01
43 34 0.41
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.46
Consensus pattern (43 bp):
TGAATCTATATATCTATATATCTATTAATTAATTTAAAATCAA
Found at i:1958042 original size:39 final size:38
Alignment explanation
Indices: 1957999--1958117 Score: 90
Period size: 39 Copynumber: 3.2 Consensus size: 38
1957989 TCGTGAATCT
1957999 ATATATCTTTATATCTATTAATTAATTTAAAATCAATGAA
1 ATATATCTTTATATCTATTAATTAATTTAAAATCAAT--A
* * *
1958039 TATATATCTCTATACATCTATT-CTTAA--T-GAATC--T-
1 -ATATATCT-T-TATATCTATTAATTAATTTAAAATCAATA
* *
1958073 ATATATCTATGTATCTATTAATTAATTTAAAATCAATTA
1 ATATATCTTTATATCTATTAATTAATTTAAAATCAA-TA
1958112 ATATAT
1 ATATAT
1958118 ATCTCTATAC
Statistics
Matches: 60, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
31 8 0.13
32 4 0.07
33 8 0.13
34 1 0.02
35 4 0.07
37 1 0.02
38 1 0.02
39 10 0.17
40 1 0.02
41 8 0.13
42 5 0.08
43 9 0.15
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (38 bp):
ATATATCTTTATATCTATTAATTAATTTAAAATCAATA
Found at i:1958051 original size:35 final size:34
Alignment explanation
Indices: 1958012--1958125 Score: 104
Period size: 35 Copynumber: 3.1 Consensus size: 34
1958002 TATCTTTATA
1958012 TCTATTAATTAATTTAAAATCAATGAATATATATC
1 TCTATTAATTAATTTAAAATCAAT-AATATATATC
* * * * *
1958047 TCTA-TACATCTATTCTTAATGAATCTATATATCTATGTA
1 TCTATTA-AT-TAAT-TTAA--AATCAATA-ATATATATC
1958086 TCTATTAATTAATTTAAAATCAATTAATATATATC
1 TCTATTAATTAATTTAAAATCAA-TAATATATATC
1958121 TCTAT
1 TCTAT
1958126 ACATCTATTG
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
34 2 0.03
35 22 0.36
36 5 0.08
37 8 0.13
38 4 0.07
39 18 0.30
40 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (34 bp):
TCTATTAATTAATTTAAAATCAATAATATATATC
Found at i:1958068 original size:31 final size:31
Alignment explanation
Indices: 1958033--1958091 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1958023 ATTTAAAATC
*
1958033 AATGAATATATATCTCTATACATCTATTCTT
1 AATGAATATATATATCTATACATCTATTCTT
* **
1958064 AATGAATCTATATATCTATGTATCTATT
1 AATGAATATATATATCTATACATCTATT
1958092 AATTAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.46
Consensus pattern (31 bp):
AATGAATATATATATCTATACATCTATTCTT
Found at i:1958075 original size:74 final size:74
Alignment explanation
Indices: 1957992--1958134 Score: 259
Period size: 74 Copynumber: 1.9 Consensus size: 74
1957982 TAATACTTCG
*
1957992 TGAATCTATATATCTTTATATCTATTAATTAATTTAAAATCAATGAATATATATCTCTATACATC
1 TGAATCTATATATCTATATATCTATTAATTAATTTAAAATCAATGAATATATATCTCTATACATC
1958057 TATTCTTAA
66 TATTCTTAA
* *
1958066 TGAATCTATATATCTATGTATCTATTAATTAATTTAAAATCAATTAATATATATCTCTATACATC
1 TGAATCTATATATCTATATATCTATTAATTAATTTAAAATCAATGAATATATATCTCTATACATC
1958131 TATT
66 TATT
1958135 GATTAATTCA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (74 bp):
TGAATCTATATATCTATATATCTATTAATTAATTTAAAATCAATGAATATATATCTCTATACATC
TATTCTTAA
Found at i:1958190 original size:216 final size:207
Alignment explanation
Indices: 1957816--1958260 Score: 676
Period size: 216 Copynumber: 2.1 Consensus size: 207
1957806 CCAGCATGAT
*
1957816 TCAATGAATATATATCTCTATGCATTATTCTTAATGAATCTATATATCTATATATCTATTAATTA
1 TCAATGAATATATATCTCTATACATTATTCTTAATGAATCTATATATCTATATATCTATTAATTA
* * * *
1957881 ATTTAAAGTCAATGAATATATATTTCTATACATCTATTGATTAATTTAATATTATAAAAAAATTC
66 ATTTAAAATCAATGAATATATATCTCTATACATCTATTGATTAATTCAATATGATAAAAAAATTC
* * *
1957946 ATAATAGATATTAACATTTATATCAAAAAAAATAATTAATACTTCGTGAATCTATATATCTTTAT
131 ATAATAAATATTAACATTTATATCAAAAAAAATAATTAATAC-T--T-AAT-GA-AT-T-TATAT
1958011 ATCTATTAATTAATTTAAAA
188 ATCTATTAATTAATTTAAAA
*
1958031 TCAATGAATATATATCTCTATACATCTATTCTTAATGAATCTATATATCTATGTATCTATTAATT
1 TCAATGAATATATATCTCTATACAT-TATTCTTAATGAATCTATATATCTATATATCTATTAATT
*
1958096 AATTTAAAATCAATTAATATATATCTCTATACATCTATTGATTAATTCAATATGAT-AAAAAATC
65 AATTTAAAATCAATGAATATATATCTCTATACATCTATTGATTAATTCAATATGATAAAAAAAT-
* *
1958160 TCATAATAAATATTAACATTTATGTCAAAAAAATTAATTAATACTTAATGAATTTATATATCTAT
129 TCATAATAAATATTAACATTTATATCAAAAAAAATAATTAATACTTAATGAATTTATATATCTAT
1958225 TAATTAATTTAAAA
194 TAATTAATTTAAAA
*
1958239 TTAATGAATATATATCTCTATA
1 TCAATGAATATATATCTCTATA
1958261 AAAAAACTCA
Statistics
Matches: 215, Mismatches: 13, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
208 45 0.21
209 1 0.00
210 2 0.01
211 1 0.00
212 3 0.01
213 1 0.00
215 32 0.15
216 130 0.60
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.43
Consensus pattern (207 bp):
TCAATGAATATATATCTCTATACATTATTCTTAATGAATCTATATATCTATATATCTATTAATTA
ATTTAAAATCAATGAATATATATCTCTATACATCTATTGATTAATTCAATATGATAAAAAAATTC
ATAATAAATATTAACATTTATATCAAAAAAAATAATTAATACTTAATGAATTTATATATCTATTA
ATTAATTTAAAA
Found at i:1958230 original size:35 final size:35
Alignment explanation
Indices: 1958191--1958259 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
1958181 ATGTCAAAAA
* *
1958191 AATTAA-TTAATACTTAATGAATTTATATATCTATT
1 AATTAATTTAA-AATTAATGAATATATATATCTATT
*
1958226 AATTAATTTAAAATTAATGAATATATATCTCTAT
1 AATTAATTTAAAATTAATGAATATATATATCTAT
1958260 AAAAAAACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 26 0.87
36 4 0.13
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (35 bp):
AATTAATTTAAAATTAATGAATATATATATCTATT
Found at i:1958298 original size:33 final size:32
Alignment explanation
Indices: 1958261--1958331 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
1958251 TATCTCTATA
*
1958261 AAAAAACTCATAATAAATATTAATATTTATGTT
1 AAAAAACT-ATAATAAATATTAATATTTATGTC
* *
1958294 AAAAAACTGTATTAAATATTAATATTTATGTC
1 AAAAAACTATAATAAATATTAATATTTATGTC
1958326 AAAAAA
1 AAAAAA
1958332 ATTAATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 27 0.77
33 8 0.23
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (32 bp):
AAAAAACTATAATAAATATTAATATTTATGTC
Found at i:1958339 original size:140 final size:140
Alignment explanation
Indices: 1958166--1958439 Score: 485
Period size: 140 Copynumber: 2.0 Consensus size: 140
1958156 AATCTCATAA
*
1958166 TAAATATTAACATTTATGTCAAAAAAATTAATTAATACTTAATGAATTTATATATCTATTAATTA
1 TAAATATTAACATTTATGTCAAAAAAATTAATTAATACCTAATGAATTTATATATCTATTAATTA
* * *
1958231 ATTTAAAATTAATGAATATATATCTCTATAAAAAAACTCATAATAAATATTAATATTTATGTTAA
66 ATTTAAAATTAATAAATATATACCTCTATAAAAAAACTCATAATAAATATTAATATTTATATTAA
1958296 AAAACTGTAT
131 AAAACTGTAT
*
1958306 TAAATATTAATATTTATGTCAAAAAAATTAATTAATACCTAATGAATTTATATATCTATTAATTA
1 TAAATATTAACATTTATGTCAAAAAAATTAATTAATACCTAATGAATTTATATATCTATTAATTA
* *
1958371 ATTTAAAATTAATAAATATATACCTCTCTAAAAAAACTCATATTAAATATTAATATTTATATTAA
66 ATTTAAAATTAATAAATATATACCTCTATAAAAAAACTCATAATAAATATTAATATTTATATTAA
1958436 AAAA
131 AAAA
1958440 TTATATTTTA
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.41
Consensus pattern (140 bp):
TAAATATTAACATTTATGTCAAAAAAATTAATTAATACCTAATGAATTTATATATCTATTAATTA
ATTTAAAATTAATAAATATATACCTCTATAAAAAAACTCATAATAAATATTAATATTTATATTAA
AAAACTGTAT
Found at i:1958445 original size:19 final size:20
Alignment explanation
Indices: 1958410--1958452 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1958400 AAAAAAACTC
*
1958410 ATATTAAATATTAATA-TTT
1 ATATTAAAAATTAATATTTT
1958429 ATATTAAAAAATT-ATATTTT
1 ATATT-AAAAATTAATATTTT
1958449 ATAT
1 ATAT
1958453 ATATTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTAAAAATTAATATTTT
Found at i:1958547 original size:25 final size:25
Alignment explanation
Indices: 1958519--1958576 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
1958509 AATGTATTTA
*
1958519 ATAATTTAAAATATATAAATATAAT
1 ATAACTTAAAATATATAAATATAAT
**
1958544 ATAACTTATTATATATAAATATAAT
1 ATAACTTAAAATATATAAATATAAT
1958569 ATAACTTA
1 ATAACTTA
1958577 TTAAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAACTTAAAATATATAAATATAAT
Found at i:1958577 original size:25 final size:25
Alignment explanation
Indices: 1958529--1958595 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
1958519 ATAATTTAAA
1958529 ATATATAAATATAATATAACTTATT
1 ATATATAAATATAATATAACTTATT
1958554 ATATATAAATATAATATAACTTATT
1 ATATATAAATATAATATAACTTATT
* *
1958579 AAATTTAAA-AT-ATATAA
1 ATATATAAATATAATATAA
1958596 ATATAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.15
24 2 0.05
25 32 0.80
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATATAAATATAATATAACTTATT
Found at i:1959718 original size:18 final size:17
Alignment explanation
Indices: 1959677--1959724 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
1959667 ATTTAACTTT
*
1959677 TATTATTTTCAAAATTG
1 TATTTTTTTCAAAATTG
* *
1959694 TATTTTTTTCAATATTT
1 TATTTTTTTCAAAATTG
*
1959711 TA-ATTTTTCAAAAT
1 TATTTTTTTCAAAAT
1959725 ACTTTTTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTTTTTCAAAATTG
Found at i:1959754 original size:24 final size:23
Alignment explanation
Indices: 1959712--1959767 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1959702 TCAATATTTT
*
1959712 AATTTTTCAAAATACTTTTTCATA
1 AATTTTT-TAAATACTTTTTCATA
*
1959736 AATTTTTTAAATACATTTTTTATA
1 AATTTTTTAAATAC-TTTTTCATA
*
1959760 ACTTTTTT
1 AATTTTTT
1959768 TAATCTAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTTTTTAAATACTTTTTCATA
Found at i:1960542 original size:5 final size:5
Alignment explanation
Indices: 1960526--1960620 Score: 50
Period size: 5 Copynumber: 18.2 Consensus size: 5
1960516 TTTGAGTTAT
* *
1960526 TTTAA TTTTAA TTTAA TTAAA TTT-A TATTAT TTTATA TTT-A TATTAA
1 TTTAA -TTTAA TTTAA TTTAA TTTAA T-TTAA TTTA-A TTTAA T-TTAA
* ** * * *
1960573 TTAAA TTTAA TATTAAA AATAA TTAAA TTTAA ATTAA TTAAA TTTAA T
1 TTTAA TTTAA T-TT-AA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
1960621 ATTCATTTTG
Statistics
Matches: 66, Mismatches: 16, Indels: 15
0.68 0.16 0.15
Matches are distributed among these distances:
4 4 0.06
5 46 0.70
6 14 0.21
7 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTTAA
Found at i:1960560 original size:31 final size:32
Alignment explanation
Indices: 1960522--1960629 Score: 96
Period size: 37 Copynumber: 3.2 Consensus size: 32
1960512 TATTTTTGAG
1960522 TTATTTTA-ATTT-TAATTTAATTAAATTT-ATA
1 TTATTTTATATTTAT-A-TTAATTAAATTTAATA
1960553 TTATTTTATATTTATATTAATTAAATTTAATA
1 TTATTTTATATTTATATTAATTAAATTTAATA
* * *
1960585 TTAAAAATAATTAAATTTAAATTAATTAAATTTAATA
1 TT----AT-TTTATATTTATATTAATTAAATTTAATA
1960622 TTCATTTT
1 TT-ATTTT
1960630 GAATTTGATT
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
31 20 0.31
32 10 0.16
33 3 0.05
34 2 0.03
36 2 0.03
37 27 0.42
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.56
Consensus pattern (32 bp):
TTATTTTATATTTATATTAATTAAATTTAATA
Found at i:1960565 original size:16 final size:16
Alignment explanation
Indices: 1960485--1960587 Score: 72
Period size: 16 Copynumber: 6.5 Consensus size: 16
1960475 TGGTAGCGGG
*
1960485 TTATATTATTTTAAAA
1 TTATATTATTTTAAAT
*
1960501 TTATATCATTTT--AT
1 TTATATTATTTTAAAT
* *
1960515 TTTTGAGTTATTTTAATT
1 TTAT-A-TTATTTTAAAT
*
1960533 TTA-ATT-TAATTAAAT
1 TTATATTAT-TTTAAAT
*
1960548 TTATATTATTTTATAT
1 TTATATTATTTTAAAT
*
1960564 TTATATTA-ATTAAAT
1 TTATATTATTTTAAAT
1960579 TTAATATTA
1 TT-ATATTA
1960588 AAAATAATTA
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
14 5 0.07
15 18 0.27
16 40 0.60
17 1 0.01
18 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (16 bp):
TTATATTATTTTAAAT
Found at i:1960580 original size:47 final size:47
Alignment explanation
Indices: 1960495--1960588 Score: 104
Period size: 47 Copynumber: 2.0 Consensus size: 47
1960485 TTATATTATT
* *
1960495 TTAAAATTATATCATTTTATTTTTGAGTTATTTTAATTTTAAT-TTAA
1 TTAAAATTATATCATTTTATTTTTGAGTTA-ATTAAATTTAATATTAA
* *
1960542 TTAAATTTATATTATTTTATATTTAT-A-TTAATTAAATTTAATATTAA
1 TTAAAATTATATCATTTTAT-TTT-TGAGTTAATTAAATTTAATATTAA
1960589 AAATAATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
46 10 0.25
47 25 0.62
48 4 0.10
49 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (47 bp):
TTAAAATTATATCATTTTATTTTTGAGTTAATTAAATTTAATATTAA
Found at i:1960588 original size:16 final size:16
Alignment explanation
Indices: 1960527--1960623 Score: 76
Period size: 15 Copynumber: 5.9 Consensus size: 16
1960517 TTGAGTTATT
*
1960527 TTAATTTTAAT-TTAA
1 TTAAATTTAATATTAA
*
1960542 TTAAATTT-ATATTATT
1 TTAAATTTAATATTA-A
*
1960558 TTATATTT-ATATTAA
1 TTAAATTTAATATTAA
1960573 TTAAATTTAATATTAAAAATAA
1 TTAAATTTAATA-T-----TAA
1960595 TTAAATTTAA-ATTAA
1 TTAAATTTAATATTAA
1960610 TTAAATTTAATATT
1 TTAAATTTAATATT
1960624 CATTTTGAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.03
15 30 0.45
16 19 0.28
17 1 0.01
20 1 0.01
21 1 0.01
22 13 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAAATTTAATATTAA
Found at i:1961102 original size:22 final size:22
Alignment explanation
Indices: 1961077--1961118 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1961067 ATGATTTTTT
*
1961077 TTAAAATAAATATTTAATTTAA
1 TTAAAATAAATAATTAATTTAA
* *
1961099 TTAAATTATATAATTAATTT
1 TTAAAATAAATAATTAATTT
1961119 TAAATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAAATAAATAATTAATTTAA
Found at i:1961543 original size:3 final size:3
Alignment explanation
Indices: 1961535--1961561 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1961525 CAAAGGAAAA
1961535 GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT
1961562 TTTTTGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:1979123 original size:2 final size:2
Alignment explanation
Indices: 1979116--1979146 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1979106 TTGCTGAGAT
1979116 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1979147 TATATTTGAT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1980139 original size:2 final size:2
Alignment explanation
Indices: 1980132--1980157 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1980122 GAAGTTGGCA
1980132 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1980158 ATTTCAAAAT
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):
TC
Found at i:1984733 original size:26 final size:26
Alignment explanation
Indices: 1984697--1984748 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1984687 TTAGTTCTTT
1984697 CTTTTGTTTTTTTTTTCTAGCCTTAA
1 CTTTTGTTTTTTTTTTCTAGCCTTAA
1984723 CTTTTGTTTTTTTTTTCTAGCCTTAA
1 CTTTTGTTTTTTTTTTCTAGCCTTAA
1984749 TTGCTGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.12, C:0.15, G:0.08, T:0.65
Consensus pattern (26 bp):
CTTTTGTTTTTTTTTTCTAGCCTTAA
Found at i:1989429 original size:20 final size:20
Alignment explanation
Indices: 1989384--1989420 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1989374 ACAATTTACA
1989384 TCTAGAAAAATCTATACAAG
1 TCTAGAAAAATCTATACAAG
*
1989404 TCTAGAAATATCT-TACA
1 TCTAGAAAAATCTATACA
1989421 CATTCTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (20 bp):
TCTAGAAAAATCTATACAAG
Found at i:1993214 original size:18 final size:19
Alignment explanation
Indices: 1993191--1993226 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1993181 TTAAAAAAAA
*
1993191 ATTT-AAAATTCTTTAAAT
1 ATTTAAAAAATCTTTAAAT
1993209 ATTTAAAAAATCTTTAAA
1 ATTTAAAAAATCTTTAAA
1993227 AAATTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTAAAAAATCTTTAAAT
Found at i:1993384 original size:32 final size:32
Alignment explanation
Indices: 1993342--1993403 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1993332 CATTATTCAT
*
1993342 TGAAGAATCAACCAGATGACATCAAACTGAAA
1 TGAAGAATCAACCAGATGAAATCAAACTGAAA
*
1993374 TGAATAATCAACCAGATGAAATCAAACTGA
1 TGAAGAATCAACCAGATGAAATCAAACTGA
1993404 CCATAACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.18
Consensus pattern (32 bp):
TGAAGAATCAACCAGATGAAATCAAACTGAAA
Found at i:2002350 original size:2 final size:2
Alignment explanation
Indices: 2002345--2002381 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2002335 TTCAAGTGTG
2002345 TA TA TA 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 TA TA TA T
2002382 TTTTGTGAAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2003638 original size:2 final size:2
Alignment explanation
Indices: 2003631--2003676 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2003621 GACGTTTTGC
2003631 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
2003673 TA TA
1 TA TA
2003677 ATTTTTGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2004114 original size:17 final size:18
Alignment explanation
Indices: 2004092--2004127 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2004082 ATTAATTTTT
*
2004092 TAAAA-TATTTTTAATTA
1 TAAAATTATTTGTAATTA
2004109 TAAAATTATTTGTAATTA
1 TAAAATTATTTGTAATTA
2004127 T
1 T
2004128 TATCAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TAAAATTATTTGTAATTA
Found at i:2008473 original size:2 final size:2
Alignment explanation
Indices: 2008466--2008515 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2008456 AGCCTTTTCA
2008466 AT 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 AT
2008508 AT AT AT AT
1 AT AT AT AT
2008516 TAAAAAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2011465 original size:25 final size:24
Alignment explanation
Indices: 2011437--2011510 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
2011427 TAATTATTTT
2011437 TTAAAAAAATATTATTATTTTTAAC
1 TTAAAAAAATATTA-TATTTTTAAC
* * * *
2011462 TTAAAAAATTA-TACACTTTTTTAT
1 TTAAAAAAATATTATA-TTTTTAAC
2011486 TTAAAAAAATATATAATATTTTTAA
1 TTAAAAAAATAT-T-ATATTTTTAA
2011511 TGATCATTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
23 1 0.03
24 18 0.47
25 10 0.26
26 7 0.18
27 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAAAAAAATATTATATTTTTAAC
Found at i:2012116 original size:19 final size:18
Alignment explanation
Indices: 2012092--2012151 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 18
2012082 GATTAAATAA
2012092 ATTAAATATATTATAAATT
1 ATTAAATATA-TATAAATT
*
2012111 ATTAAATATATAAAAATT
1 ATTAAATATATATAAATT
2012129 A-TAAATATATATTAAATTT
1 ATTAAATATATA-TAAA-TT
2012148 ATTA
1 ATTA
2012152 TATTAATCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
17 10 0.28
18 11 0.31
19 13 0.36
20 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAAATATATATAAATT
Found at i:2012118 original size:28 final size:25
Alignment explanation
Indices: 2012083--2012134 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2012073 TTTTTTATCG
2012083 ATTAAATAAATTAAATATATTATAAATT
1 ATTAAATAAA-TAAA-A-ATTATAAATT
*
2012111 ATTAAATATATAAAAATTATAAAT
1 ATTAAATAAATAAAAATTATAAAT
2012135 ATATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 9 0.39
26 1 0.04
27 4 0.17
28 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTAAATAAATAAAAATTATAAATT
Found at i:2012133 original size:17 final size:18
Alignment explanation
Indices: 2012092--2012139 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
2012082 GATTAAATAA
*
2012092 ATTAAATATATTATAAATT
1 ATTAAATATA-TAAAAATT
2012111 ATTAAATATATAAAAATT
1 ATTAAATATATAAAAATT
2012129 A-TAAATATATA
1 ATTAAATATATA
2012140 TTAAATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 10 0.36
18 8 0.29
19 10 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTAAATATATAAAAATT
Found at i:2012396 original size:14 final size:14
Alignment explanation
Indices: 2012377--2012415 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2012367 TTAACGTGTC
*
2012377 AAATATAATTATAT
1 AAATATAATTATAA
2012391 AAATATAA-TATAA
1 AAATATAATTATAA
2012404 ATAATATAATTA
1 A-AATATAATTA
2012416 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 15 0.68
15 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATAATTATAA
Found at i:2012412 original size:20 final size:19
Alignment explanation
Indices: 2012378--2012429 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
2012368 TAACGTGTCA
*
2012378 AATAT-AATTATATAAATAT
1 AATATAAATAATATAAAT-T
2012397 AATATAAATAATAT-AATT
1 AATATAAATAATATAAATT
* *
2012415 AAAATAAAAAATATA
1 AATATAAATAATATA
2012430 TTTTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 13 0.46
19 8 0.29
20 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AATATAAATAATATAAATT
Found at i:2012447 original size:20 final size:19
Alignment explanation
Indices: 2012424--2012472 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
2012414 TAAAATAAAA
2012424 AATATATTTTAAATTTATAT
1 AATATATTTTAAATTTAT-T
*
2012444 AATATATTATAAATTTATT
1 AATATATTTTAAATTTATT
*
2012463 AAAATATTTT
1 AATATATTTT
2012473 TAATATGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATATTTTAAATTTATT
Found at i:2013876 original size:3 final size:3
Alignment explanation
Indices: 2013868--2013902 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2013858 ATCACAACTT
2013868 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2013903 TGAAACTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2015117 original size:16 final size:16
Alignment explanation
Indices: 2015091--2015123 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2015081 ATACTTATAA
2015091 ATTTATATTTATAACTT
1 ATTTATATTTAT-ACTT
2015108 ATTT-TATTTATACTT
1 ATTTATATTTATACTT
2015123 A
1 A
2015124 AAATTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATATTTATACTT
Found at i:2015131 original size:22 final size:22
Alignment explanation
Indices: 2015091--2015132 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2015081 ATACTTATAA
* *
2015091 ATTTATATTTATAACTTATTTT
1 ATTTATACTTAAAACTTATTTT
*
2015113 ATTTATACTTAAAATTTATT
1 ATTTATACTTAAAACTTATT
2015133 ATTAAATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTATACTTAAAACTTATTTT
Found at i:2018678 original size:41 final size:42
Alignment explanation
Indices: 2018633--2018717 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 42
2018623 ATGGAGCTTC
*
2018633 AATCCTTGTAAG-TTTTTTTTTATAGGTTCTGATGATTTGAA
1 AATCCTTGTAAGTTTTTTTTTTACAGGTTCTGATGATTTGAA
2018674 AATCCTTGTAAGTTTTTTTTTTTTACAGGTTCTGATGATTTGAA
1 AATCCTTGTAAG--TTTTTTTTTTACAGGTTCTGATGATTTGAA
2018718 GAATATTGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
41 12 0.30
44 28 0.70
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (42 bp):
AATCCTTGTAAGTTTTTTTTTTACAGGTTCTGATGATTTGAA
Found at i:2019560 original size:3 final size:3
Alignment explanation
Indices: 2019552--2019579 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2019542 TATTAAACTT
2019552 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2019580 ATTTCTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2019628 original size:31 final size:31
Alignment explanation
Indices: 2019570--2019629 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2019560 ATTATTATTA
* * *
2019570 TTATTATTATATTTCTAATTTTGAAATAAAT
1 TTATTATCATATTTCTAACTTTAAAATAAAT
2019601 TTATTATCATATTT-TAAACTTTAAAATAA
1 TTATTATCATATTTCT-AACTTTAAAATAA
2019630 TTGAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (31 bp):
TTATTATCATATTTCTAACTTTAAAATAAAT
Found at i:2025326 original size:16 final size:17
Alignment explanation
Indices: 2025291--2025329 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2025281 TTATCAAAGT
*
2025291 AATTTATTTTAATTATA
1 AATTTATTTTAATTAAA
*
2025308 AATTTA-TTTACTTAAA
1 AATTTATTTTAATTAAA
2025324 AATTTA
1 AATTTA
2025330 ACAATTACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAATTAAA
Found at i:2026077 original size:19 final size:17
Alignment explanation
Indices: 2026041--2026103 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
2026031 GAATTTAATT
2026041 TTTTAATATAAA-ATATA
1 TTTTAAT-TAAATATATA
2026058 TTATTAAATTAAATATATA
1 TT-TT-AATTAAATATATA
* *
2026077 TTTTTATTATATATATA
1 TTTTAATTAAATATATA
*
2026094 TTTTATTTAA
1 TTTTAATTAA
2026104 TATTAAAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 20 0.53
18 8 0.21
19 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAATTAAATATATA
Found at i:2026088 original size:15 final size:16
Alignment explanation
Indices: 2026070--2026100 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2026060 ATTAAATTAA
2026070 ATATATAT-TTTTATT
1 ATATATATATTTTATT
2026085 ATATATATATTTTATT
1 ATATATATATTTTATT
2026101 TAATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATATATATTTTATT
Found at i:2026869 original size:16 final size:16
Alignment explanation
Indices: 2026833--2026870 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2026823 GCAGTATATC
2026833 TAAAATAAATTATTTA
1 TAAAATAAATTATTTA
*
2026849 CAAAATAAAATTATTT-
1 TAAAAT-AAATTATTTA
2026865 TAAAAT
1 TAAAAT
2026871 TATTATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATAAATTATTTA
Found at i:2030202 original size:38 final size:38
Alignment explanation
Indices: 2030160--2030236 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
2030150 TGCATATAAG
*
2030160 TAAATACCCTCTGTTCTACATCAGATGTTTTCAAGTAA
1 TAAATACCCTCTGTTCTACATCAGATGTTTCCAAGTAA
* *
2030198 TAAATACTCTCTGTTCTATATCAGATGTTTCCAAGTAA
1 TAAATACCCTCTGTTCTACATCAGATGTTTCCAAGTAA
2030236 T
1 T
2030237 GCTCTCTCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (38 bp):
TAAATACCCTCTGTTCTACATCAGATGTTTCCAAGTAA
Found at i:2031267 original size:152 final size:152
Alignment explanation
Indices: 2030991--2031296 Score: 576
Period size: 152 Copynumber: 2.0 Consensus size: 152
2030981 TTTCAGATCC
*
2030991 TGAAAGAAATTACCACTGCTTTTATCTTCTTTGTGCAGGACCGCCTGAGGTATTAATGCTTTGGT
1 TGAAAGAAATTACCACTGCTTTTACCTTCTTTGTGCAGGACCGCCTGAGGTATTAATGCTTTGGT
* *
2031056 TTTGTAATGAATATTTCTGTTTTTGGCATCAATCTTCATTTGCCTTTGAACTTGCCTATGCTGCT
66 TTTATAATGAATATTTCTGTTTTTAGCATCAATCTTCATTTGCCTTTGAACTTGCCTATGCTGCT
*
2031121 AATAGTAGGCAATGGCTGAATA
131 AATAGTAGGCAATGACTGAATA
2031143 TGAAAGAAATTACCACTGCTTTTACCTTCTTTGTGCAGGACCGCCTGAGGTATTAATGCTTTGGT
1 TGAAAGAAATTACCACTGCTTTTACCTTCTTTGTGCAGGACCGCCTGAGGTATTAATGCTTTGGT
2031208 TTTATAATGAATATTTCTGTTTTTAGCATCAATCTTCATTTGCCTTTGAACTTGCCTATGCTGCT
66 TTTATAATGAATATTTCTGTTTTTAGCATCAATCTTCATTTGCCTTTGAACTTGCCTATGCTGCT
2031273 AATAGTAGGCAATGACTGAATA
131 AATAGTAGGCAATGACTGAATA
2031295 TG
1 TG
2031297 TTCTCTGACA
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 150 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (152 bp):
TGAAAGAAATTACCACTGCTTTTACCTTCTTTGTGCAGGACCGCCTGAGGTATTAATGCTTTGGT
TTTATAATGAATATTTCTGTTTTTAGCATCAATCTTCATTTGCCTTTGAACTTGCCTATGCTGCT
AATAGTAGGCAATGACTGAATA
Found at i:2037770 original size:20 final size:20
Alignment explanation
Indices: 2037745--2037786 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2037735 TTGCCAAGAA
2037745 TTAGCTTAAACATCGTTGGC
1 TTAGCTTAAACATCGTTGGC
2037765 TTAGCTTAAACATCGTTGGC
1 TTAGCTTAAACATCGTTGGC
2037785 TT
1 TT
2037787 TCTATCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
TTAGCTTAAACATCGTTGGC
Found at i:2041686 original size:17 final size:18
Alignment explanation
Indices: 2041664--2041697 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2041654 CCAATGTTCA
2041664 AAAAAGAAAAAA-AAAAG
1 AAAAAGAAAAAAGAAAAG
2041681 AAAAAGAAAAAAGAAAA
1 AAAAAGAAAAAAGAAAA
2041698 CATAGCCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAGAAAAG
Found at i:2043093 original size:21 final size:22
Alignment explanation
Indices: 2043049--2043089 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
2043039 TTAAATTTAA
*
2043049 TTATAAAATTATATAAATAAAT
1 TTATAAAATAATATAAATAAAT
2043071 TTAT-AAATAATA-AAATAAA
1 TTATAAAATAATATAAATAAA
2043090 ATTTTTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTATAAAATAATATAAATAAAT
Found at i:2043467 original size:29 final size:29
Alignment explanation
Indices: 2043387--2043477 Score: 74
Period size: 27 Copynumber: 3.4 Consensus size: 29
2043377 ATATTTATTG
* *
2043387 TAATTATA--AAT-ATAATAAATATCATCA
1 TAATTATATTAATAATAA-AAATATTATAA
2043414 TAATTA-ATT-ATAAT-AAAATA-T-TAA
1 TAATTATATTAATAATAAAAATATTATAA
*
2043438 TTATTATATTAATAATAAAAATATTATAA
1 TAATTATATTAATAATAAAAATATTATAA
*
2043467 TCATTAT-TTAA
1 TAATTATATTAA
2043478 AATTTTAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
24 7 0.13
25 3 0.06
26 11 0.21
27 15 0.29
28 7 0.13
29 9 0.17
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
TAATTATATTAATAATAAAAATATTATAA
Found at i:2043516 original size:26 final size:26
Alignment explanation
Indices: 2043462--2043512 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
2043452 ATAAAAATAT
*
2043462 TATAATCATTATTTAAAATTTTAATA
1 TATAATCATTATTTAAAATTTTAAAA
**
2043488 TATAAT-ATTATTTAATTTTTTAAAA
1 TATAATCATTATTTAAAATTTTAAAA
2043513 ATATTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TATAATCATTATTTAAAATTTTAAAA
Found at i:2043530 original size:21 final size:21
Alignment explanation
Indices: 2043491--2043530 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2043481 TTTAATATAT
*
2043491 AATATTATTTAATTTTTTAAA
1 AATATTATTTAATTATTTAAA
2043512 AATATTTATTT-ATTATTTA
1 AATA-TTATTTAATTATTTA
2043531 TTTTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATATTATTTAATTATTTAAA
Found at i:2051480 original size:2 final size:2
Alignment explanation
Indices: 2051473--2051505 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2051463 AGGCTAGCAA
2051473 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
2051506 ATAATTGTAA
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:2052817 original size:72 final size:72
Alignment explanation
Indices: 2052741--2052885 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
2052731 AAATTGAATC
2052741 ATTATGACAAATTATACAAAATTTTCACAAATTAGGAATCATACGAACATAACATCAAACACAAA
1 ATTATGACAAATTATACAAAATTTTCACAAATTAGGAATCATACGAACATAACATCAAACACAAA
2052806 CTTTTCT
66 CTTTTCT
2052813 ATTATGACAAATTATACAAAATTTTCACAAATTAGGAATCATACGAACATAACATCAAACACAAA
1 ATTATGACAAATTATACAAAATTTTCACAAATTAGGAATCATACGAACATAACATCAAACACAAA
2052878 CTTTTCT
66 CTTTTCT
2052885 A
1 A
2052886 AATTGAATCA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.29
Consensus pattern (72 bp):
ATTATGACAAATTATACAAAATTTTCACAAATTAGGAATCATACGAACATAACATCAAACACAAA
CTTTTCT
Found at i:2053016 original size:27 final size:27
Alignment explanation
Indices: 2052986--2053039 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2052976 GACGAATAAT
2052986 AACAAATTATT-CGTATAAAATATTTAA
1 AACAAATTATTACGTATAAAAT-TTTAA
2053013 AACAAATTATTAACGTATAAAATTTTA
1 AACAAATTATT-ACGTATAAAATTTTA
2053040 TATTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 11 0.44
28 4 0.16
29 10 0.40
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (27 bp):
AACAAATTATTACGTATAAAATTTTAA
Found at i:2053075 original size:25 final size:26
Alignment explanation
Indices: 2053022--2053085 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
2053012 AAACAAATTA
* *
2053022 TTAACGTATAAAATTTTATATTATTT
1 TTAACATATAAAATTTTATAATATTT
*
2053048 TTAATA-ATAAAATTTTTATAATA-TT
1 TTAACATATAAAA-TTTTATAATATTT
2053073 TTAACATATAAAA
1 TTAACATATAAAA
2053086 AAAATATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 13 0.41
26 19 0.59
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAACATATAAAATTTTATAATATTT
Found at i:2058185 original size:2 final size:2
Alignment explanation
Indices: 2058172--2058213 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2058162 TAACAGATCT
*
2058172 GA GA GC GA GA GA GA GA 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 GA GA GA GA GA GA GA GA
2058214 AGAAAAAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2059193 original size:4 final size:4
Alignment explanation
Indices: 2059184--2059210 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2059174 ACCTTTAACA
2059184 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
2059211 GAGTTAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:2062317 original size:22 final size:20
Alignment explanation
Indices: 2062292--2062358 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
2062282 AAAATTATTA
2062292 AAAATAATTTTTAATTAAAAAT
1 AAAAT-ATTTTTAA-TAAAAAT
2062314 AAAAT-TTTTTATATAATAAA-
1 AAAATATTTTTA-ATAA-AAAT
*
2062334 ATTAATATTTTTTAA-AAAAAT
1 A-AAATA-TTTTTAATAAAAAT
2062355 AAAA
1 AAAA
2062359 GTTAAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
20 15 0.41
21 10 0.27
22 6 0.16
23 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATATTTTTAATAAAAAT
Found at i:2065326 original size:14 final size:14
Alignment explanation
Indices: 2065304--2065343 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
2065294 GCATGACCTG
*
2065304 TTTCCTTCTTTTTC
1 TTTCTTTCTTTTTC
2065318 TTTCTTTC-TTTTC
1 TTTCTTTCTTTTTC
*
2065331 TTTTTTTCTTTTT
1 TTTCTTTCTTTTT
2065344 TTTTAACTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTCTTTCTTTTTC
Found at i:2065347 original size:13 final size:13
Alignment explanation
Indices: 2065309--2065347 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2065299 ACCTGTTTCC
*
2065309 TTCTTTTTCTTTCT
1 TTCTTTTT-TTTTT
*
2065323 TTCTTTTCTTTTT
1 TTCTTTTTTTTTT
2065336 TTCTTTTTTTTT
1 TTCTTTTTTTTT
2065348 AACTGAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:2067512 original size:6 final size:6
Alignment explanation
Indices: 2067503--2067529 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2067493 TATATAATAA
2067503 CATTCT CATTCT CATTCT CATTCT CAT
1 CATTCT CATTCT CATTCT CATTCT CAT
2067530 AAGAAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (6 bp):
CATTCT
Found at i:2068264 original size:2 final size:2
Alignment explanation
Indices: 2068257--2068298 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2068247 CGAATATTGA
2068257 AT 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 AT
2068299 TGGCTATTCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2073510 original size:14 final size:14
Alignment explanation
Indices: 2073486--2073520 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2073476 AATAGAAAAA
2073486 AATTA-TAAATATT
1 AATTATTAAATATT
2073499 AATTATTAAATATT
1 AATTATTAAATATT
*
2073513 AAATATTA
1 AATTATTA
2073521 TATTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTATTAAATATT
Found at i:2074786 original size:20 final size:19
Alignment explanation
Indices: 2074761--2074800 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
2074751 ATGATAATTA
2074761 TATATAAAATATTATATATT
1 TATATAAAATATTAT-TATT
2074781 TATATAAAATATTATTATT
1 TATATAAAATATTATTATT
2074800 T
1 T
2074801 CATTCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATAAAATATTATTATT
Found at i:2075162 original size:15 final size:16
Alignment explanation
Indices: 2075139--2075235 Score: 65
Period size: 15 Copynumber: 5.8 Consensus size: 16
2075129 AGTACATATA
2075139 TAAAAATATA-ATTTT
1 TAAAAATATATATTTT
* *
2075154 TAAATATATATATATT
1 TAAAAATATATATTTT
2075170 TAAAAAT-TATATTTT
1 TAAAAATATATATTTT
* * *
2075185 TATAATTATGTATTATT
1 TAAAAATATATATT-TT
2075202 GTATATCAAATATA-ATTATTT
1 -TA-A--AAATATATA-T-TTT
2075223 TAAAAATATATAT
1 TAAAAATATATAT
2075236 ATAATTTCAA
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
15 21 0.34
16 15 0.24
17 10 0.16
18 3 0.05
19 1 0.02
20 3 0.05
21 8 0.13
22 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (16 bp):
TAAAAATATATATTTT
Found at i:2075335 original size:25 final size:24
Alignment explanation
Indices: 2075285--2075337 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
2075275 CAGGAAAAGG
*
2075285 AATGCATATACATATATATTATAT
1 AATGCATATACATATATATTACAT
*
2075309 AATGTATATACATAATATATTACAT
1 AATGCATATACAT-ATATATTACAT
2075334 AATG
1 AATG
2075338 GGGGGGGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (24 bp):
AATGCATATACATATATATTACAT
Found at i:2076537 original size:17 final size:17
Alignment explanation
Indices: 2076515--2076548 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2076505 CATTTTCTAC
2076515 TACCTCAACAAAGCTGT
1 TACCTCAACAAAGCTGT
2076532 TACCTCAACAAAGCTGT
1 TACCTCAACAAAGCTGT
2076549 GAAAGCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (17 bp):
TACCTCAACAAAGCTGT
Found at i:2078841 original size:21 final size:20
Alignment explanation
Indices: 2078805--2078846 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2078795 TCTAAATACT
2078805 TTTAATTTATTATTTTTAAA
1 TTTAATTTATTATTTTTAAA
*
2078825 TTTAATTT-TATATTTTTTAA
1 TTTAATTTAT-TATTTTTAAA
2078845 TT
1 TT
2078847 AAAATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTAATTTATTATTTTTAAA
Found at i:2079490 original size:13 final size:13
Alignment explanation
Indices: 2079472--2079500 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2079462 ATATTACAAA
2079472 TTAAAAAATAATT
1 TTAAAAAATAATT
2079485 TTAAAAAATAATT
1 TTAAAAAATAATT
2079498 TTA
1 TTA
2079501 TTATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAAAAATAATT
Found at i:2080551 original size:4 final size:4
Alignment explanation
Indices: 2080544--2080568 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2080534 ATATATAAAA
2080544 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2080569 GTGCTCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2081078 original size:22 final size:20
Alignment explanation
Indices: 2081053--2081109 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 20
2081043 TTGGATTATT
2081053 ATATTCTAA-ATTTTATATTAAA
1 ATATT-TAATATTTT-TA-TAAA
2081075 ATATTTAATATTTTTAT-AA
1 ATATTTAATATTTTTATAAA
2081094 A-ATTTAATATTTTTAT
1 ATATTTAATATTTTTAT
2081110 GTTTTAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.44
19 3 0.09
20 1 0.03
21 5 0.15
22 10 0.29
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTAATATTTTTATAAA
Found at i:2082634 original size:18 final size:18
Alignment explanation
Indices: 2082608--2082644 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2082598 ATCGAATAAA
*
2082608 TAAATAAAAAAATTAAGT
1 TAAAAAAAAAAATTAAGT
*
2082626 TAAAAAAAAGAATTAAGT
1 TAAAAAAAAAAATTAAGT
2082644 T
1 T
2082645 TAAAGGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (18 bp):
TAAAAAAAAAAATTAAGT
Found at i:2085176 original size:69 final size:69
Alignment explanation
Indices: 2085088--2085226 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 69
2085078 TCTTCGCTTG
* *
2085088 TGCATTATTAACCTTAGTTTTATTCAAAATCGACTCGTAGGTTTCGCCTTCTTCGTGGCCTGCCA
1 TGCATTATTAACCTTAGTTTTATTCAAAATCGACTCGTAAGTTTCGCCTTCTTCATGGCCTGCCA
2085153 GATT
66 GATT
* *
2085157 TGCATTATTAACCTTAGTTTTATTTAAGATCGACTCGTAAGTTTCGCCTTCTTCATGGCCTGCCA
1 TGCATTATTAACCTTAGTTTTATTCAAAATCGACTCGTAAGTTTCGCCTTCTTCATGGCCTGCCA
2085222 GATT
66 GATT
2085226 T
1 T
2085227 CTGATCATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (69 bp):
TGCATTATTAACCTTAGTTTTATTCAAAATCGACTCGTAAGTTTCGCCTTCTTCATGGCCTGCCA
GATT
Found at i:2090322 original size:15 final size:15
Alignment explanation
Indices: 2090302--2090333 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2090292 TTCGACAACA
2090302 TGGGAGAGTTTTGTC
1 TGGGAGAGTTTTGTC
2090317 TGGGAGAGTTTTGTC
1 TGGGAGAGTTTTGTC
2090332 TG
1 TG
2090334 TCAGATGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (15 bp):
TGGGAGAGTTTTGTC
Found at i:2091748 original size:3 final size:3
Alignment explanation
Indices: 2091740--2091767 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2091730 TATTCTACAG
2091740 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2091768 GGTACCCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2092928 original size:23 final size:23
Alignment explanation
Indices: 2092893--2092940 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2092883 GATTATTTTG
2092893 AATAAGTTAAAAAAATTAAATGTT
1 AATAAGTTAAAAAAATTAAAT-TT
* *
2092917 AATAGGTT-AAAAAATTTAATTT
1 AATAAGTTAAAAAAATTAAATTT
2092939 AA
1 AA
2092941 ATATAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 11 0.50
24 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (23 bp):
AATAAGTTAAAAAAATTAAATTT
Found at i:2094311 original size:50 final size:50
Alignment explanation
Indices: 2094255--2094354 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
2094245 TAAACTAATT
2094255 CTTTAAATAATTTTAATAAAAATATTAATTCAGTATGCATACATAACTTA
1 CTTTAAATAATTTTAATAAAAATATTAATTCAGTATGCATACATAACTTA
*
2094305 CTTTAAATAATTTTAATAAAAATATTGATTCAGTATGCATACATAACTTA
1 CTTTAAATAATTTTAATAAAAATATTAATTCAGTATGCATACATAACTTA
2094355 TTTTTTAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (50 bp):
CTTTAAATAATTTTAATAAAAATATTAATTCAGTATGCATACATAACTTA
Found at i:2094949 original size:6 final size:6
Alignment explanation
Indices: 2094938--2094964 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2094928 GTAGACTTCA
2094938 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
2094965 GTAATTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:2098153 original size:18 final size:18
Alignment explanation
Indices: 2098099--2098158 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
2098089 TTATTATTAA
*
2098099 ATTTAAATAAAATATTTTT
1 ATTTAAATTAAA-ATTTTT
*
2098118 A-TTAAATT-AAA--TTA
1 ATTTAAATTAAAATTTTT
2098132 ATTTAAATTAAAATTTTT
1 ATTTAAATTAAAATTTTT
2098150 ATTTAAATT
1 ATTTAAATT
2098159 TAATTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 3 0.09
15 7 0.21
16 4 0.12
17 2 0.06
18 17 0.50
19 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTAAATTAAAATTTTT
Found at i:2098156 original size:33 final size:33
Alignment explanation
Indices: 2098098--2098173 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
2098088 TTTATTATTA
*
2098098 AATTTAAATAAAATATTTTTATTAAATTAAATT
1 AATTTAAATTAAATATTTTTATTAAATTAAATT
*
2098131 AATTTAAATTAAA-ATTTTTATTTAAATTTAATT
1 AATTTAAATTAAATATTTTTA-TTAAATTAAATT
*
2098164 AATATAAATT
1 AATTTAAATT
2098174 GAACAAGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
32 7 0.18
33 32 0.82
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
AATTTAAATTAAATATTTTTATTAAATTAAATT
Found at i:2098700 original size:16 final size:15
Alignment explanation
Indices: 2098679--2098721 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
2098669 ATCTGTATAA
2098679 TAAATTTAATTTAAAT
1 TAAA-TTAATTTAAAT
2098695 TAAATTAATTTAAAT
1 TAAATTAATTTAAAT
2098710 TGAAATTAATTT
1 T-AAATTAATTT
2098722 TTAATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TAAATTAATTTAAAT
Found at i:2098704 original size:9 final size:10
Alignment explanation
Indices: 2098679--2098743 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
2098669 ATCTGTATAA
2098679 TAAATTTAATT
1 TAAA-TTAATT
*
2098690 TAAATTAAAT
1 TAAATTAATT
*
2098700 TAATTTAAATT
1 TAAATT-AATT
*
2098711 GAAATTAATTT
1 TAAATTAA-TT
*
2098722 TTAA-TAATT
1 TAAATTAATT
*
2098731 AAAATTAATT
1 TAAATTAATT
2098741 TAA
1 TAA
2098744 TTTGAGTTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
9 4 0.10
10 22 0.54
11 15 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (10 bp):
TAAATTAATT
Found at i:2098720 original size:20 final size:20
Alignment explanation
Indices: 2098676--2098746 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
2098666 TTTATCTGTA
* *
2098676 TAATAAATTT-AATTTAAAT
1 TAATTAATTTAAATTAAAAT
*
2098695 TAAATTAATTTAAATTGAAAT
1 T-AATTAATTTAAATTAAAAT
2098716 TAATT--TTTAATAATTAAAAT
1 TAATTAATTT-A-AATTAAAAT
2098736 TAATTTAATTT
1 TAA-TTAATTT
2098747 GAGTTATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
18 3 0.07
19 2 0.05
20 23 0.55
21 11 0.26
23 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
TAATTAATTTAAATTAAAAT
Found at i:2098760 original size:35 final size:36
Alignment explanation
Indices: 2098692--2098774 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
2098682 ATTTAATTTA
2098692 AATTAAATTAATTTAAATTGAAATTAATTTTTAA-T
1 AATTAAATTAATTTAAATTGAAATTAATTTTTAAGT
* *
2098727 AATTAAAATTAATTTAATTTG-AGTT-ATTATTTAAGT
1 AATT-AAATTAATTTAAATTGAAATTAATT-TTTAAGT
2098763 AA-TAAA-TAATTT
1 AATTAAATTAATTT
2098775 TTTAACTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
33 6 0.14
34 6 0.14
35 13 0.30
36 18 0.42
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (36 bp):
AATTAAATTAATTTAAATTGAAATTAATTTTTAAGT
Found at i:2100048 original size:4 final size:4
Alignment explanation
Indices: 2100041--2100067 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2100031 AAACATGTAT
2100041 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
2100068 TCACTCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2118151 original size:10 final size:10
Alignment explanation
Indices: 2118136--2118182 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
2118126 GACTCAGACA
2118136 CACGCGCACG
1 CACGCGCACG
2118146 CACGCGCACG
1 CACGCGCACG
* *
2118156 CGCACGCA--
1 CACGCGCACG
2118164 CACGCGCACG
1 CACGCGCACG
2118174 CACGCGCAC
1 CACGCGCAC
2118183 ACACACCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 6 0.19
10 25 0.81
ACGTcount: A:0.21, C:0.51, G:0.28, T:0.00
Consensus pattern (10 bp):
CACGCGCACG
Found at i:2118153 original size:6 final size:6
Alignment explanation
Indices: 2118136--2118182 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
2118126 GACTCAGACA
*
2118136 CACGCG CA--CG CACGCG CACGCG CACGCA CACGCG CA--CG CACGCG
1 CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG CACGCG
2118180 CAC
1 CAC
2118183 ACACACCAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
4 8 0.23
6 27 0.77
ACGTcount: A:0.21, C:0.51, G:0.28, T:0.00
Consensus pattern (6 bp):
CACGCG
Found at i:2118157 original size:16 final size:16
Alignment explanation
Indices: 2118136--2118182 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
2118126 GACTCAGACA
2118136 CACGCGCACGCACGCG
1 CACGCGCACGCACGCG
2118152 CACGCGCACGCA----
1 CACGCGCACGCACGCG
2118164 CACGCGCACGCACGCG
1 CACGCGCACGCACGCG
2118180 CAC
1 CAC
2118183 ACACACCAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 12 0.44
16 15 0.56
ACGTcount: A:0.21, C:0.51, G:0.28, T:0.00
Consensus pattern (16 bp):
CACGCGCACGCACGCG
Done.