Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 13 of 19
Found at i:1496286 original size:15 final size:14
Alignment explanation
Indices: 1496251--1496308 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
1496241 AAATAATGTT
1496251 TTATAATTTTTA-A
1 TTATAATTTTTATA
*
1496264 TTTTTAATTTTTATA
1 -TTATAATTTTTATA
*
1496279 TTAATAATTTTTTTA
1 TT-ATAATTTTTATA
1496294 TTATAATTTTTATA
1 TTATAATTTTTATA
1496308 T
1 T
1496309 AAAAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATAATTTTTATA
Found at i:1499080 original size:15 final size:16
Alignment explanation
Indices: 1499047--1499087 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1499037 GATACTCAAA
1499047 TTATTAAAAATTTAATT
1 TTATTAAAAATTT-ATT
*
1499064 TTTTTAAAAATTT-TT
1 TTATTAAAAATTTATT
1499079 TTATTAAAA
1 TTATTAAAA
1499088 TTATTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 10 0.45
17 12 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTAAAAATTTATT
Found at i:1499959 original size:20 final size:19
Alignment explanation
Indices: 1499947--1499991 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1499937 ATTTATATAT
1499947 TAAATAAATAATTTTAATA
1 TAAATAAATAATTTTAATA
*
1499966 TAAATAAAT-A-TTAAATA
1 TAAATAAATAATTTTAATA
1499983 T-AATAAATA
1 TAAATAAATA
1499992 TTTAACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 1 0.04
19 9 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATAAATAATTTTAATA
Found at i:1499963 original size:30 final size:31
Alignment explanation
Indices: 1499943--1500006 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
1499933 AAAAATTTAT
1499943 ATATTAAATA-AATAATTTTAATATAAATAA
1 ATATTAAATATAATAATTTTAATATAAATAA
*
1499973 ATATTAAATATAATAAATATTTAACATAAA-AA
1 ATATTAAATATAAT-AAT-TTTAATATAAATAA
1500005 AT
1 AT
1500007 GTATTTGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 10 0.33
31 3 0.10
32 7 0.23
33 10 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
ATATTAAATATAATAATTTTAATATAAATAA
Found at i:1499971 original size:19 final size:18
Alignment explanation
Indices: 1499947--1499996 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
1499937 ATTTATATAT
*
1499947 TAAATAAATAATTTTAATA
1 TAAATAAATAA-TTAAATA
1499966 TAAATAAAT-ATTAAATA
1 TAAATAAATAATTAAATA
*
1499983 T-AATAAATATTTAA
1 TAAATAAATAATTAA
1499997 CATAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.25
17 11 0.39
18 1 0.04
19 9 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATAAATAATTAAATA
Found at i:1499987 original size:16 final size:16
Alignment explanation
Indices: 1499943--1499993 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
1499933 AAAAATTTAT
1499943 ATATTAAATA-AAT-A
1 ATATTAAATATAATAA
*
1499957 AT-TTTAATATAAATAA
1 ATATTAAATAT-AATAA
1499973 ATATTAAATATAATAA
1 ATATTAAATATAATAA
1499989 ATATT
1 ATATT
1499994 TAACATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 6 0.19
14 2 0.06
15 3 0.10
16 13 0.42
17 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTAAATATAATAA
Found at i:1500001 original size:16 final size:16
Alignment explanation
Indices: 1499949--1500006 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
1499939 TTATATATTA
1499949 AATAAATAATTTTAATAT
1 AATAAAT-A-TTTAATAT
*
1499967 AAATAAATATTAAATAT
1 -AATAAATATTTAATAT
*
1499984 AATAAATATTTAACAT
1 AATAAATATTTAATAT
*
1500000 AAAAAAT
1 AATAAAT
1500007 GTATTTGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 20 0.57
17 7 0.20
18 1 0.03
19 7 0.20
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAAATATTTAATAT
Found at i:1500902 original size:12 final size:12
Alignment explanation
Indices: 1500882--1500912 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
1500872 AAAATAAATA
1500882 AATTAATTTATAT
1 AATT-ATTTATAT
1500895 AATTATTTATAT
1 AATTATTTATAT
1500907 AATTAT
1 AATTAT
1500913 ATGTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATTATTTATAT
Found at i:1500973 original size:2 final size:2
Alignment explanation
Indices: 1500966--1500997 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1500956 AATATGATTT
1500966 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
1500998 AAGTGAGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1502415 original size:14 final size:15
Alignment explanation
Indices: 1502396--1502424 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1502386 CCCAACTAAT
1502396 AAGG-AAAAAAGAAA
1 AAGGAAAAAAAGAAA
1502410 AAGGAAAAAAAGAAA
1 AAGGAAAAAAAGAAA
1502425 GCAAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGGAAAAAAAGAAA
Found at i:1504284 original size:15 final size:15
Alignment explanation
Indices: 1504254--1504291 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1504244 TATAGCCTAG
1504254 AATGTAA-AACTTTA
1 AATGTAATAACTTTA
*
1504268 AATGTAATAATTTTA
1 AATGTAATAACTTTA
*
1504283 AATATAATA
1 AATGTAATA
1504292 TAAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (15 bp):
AATGTAATAACTTTA
Found at i:1504480 original size:15 final size:14
Alignment explanation
Indices: 1504461--1504517 Score: 73
Period size: 14 Copynumber: 4.0 Consensus size: 14
1504451 TATATAGTAA
1504461 TATTTTATAATTTT
1 TATTTTATAATTTT
1504475 TAATTTT-TAATTTT
1 T-ATTTTATAATTTT
1504489 TATATTTATAATTTT
1 TAT-TTTATAATTTT
1504504 T-TTATTATAATTTT
1 TATT-TTATAATTTT
1504518 CATATAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.08
14 23 0.59
15 13 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTTATAATTTT
Found at i:1504488 original size:6 final size:7
Alignment explanation
Indices: 1504462--1504504 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
1504452 ATATAGTAAT
1504462 ATTTTATA
1 ATTTT-TA
1504470 ATTTTTA
1 ATTTTTA
1504477 ATTTTTA
1 ATTTTTA
1504484 ATTTTTA
1 ATTTTTA
*
1504491 TATTTATA
1 -ATTTTTA
1504499 ATTTTT
1 ATTTTT
1504505 TTATTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 21 0.66
8 11 0.34
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTTTA
Found at i:1504514 original size:29 final size:28
Alignment explanation
Indices: 1504464--1504522 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 28
1504454 ATAGTAATAT
*
1504464 TTTATAATTTTTAATTTTTAATTTTTATA
1 TTTATAATTTTT-ATTTTTAATTTTCATA
1504493 TTTATAATTTTT-TTATTATAATTTTCATA
1 TTTATAATTTTTATT-TT-TAATTTTCATA
1504522 T
1 T
1504523 AAAAATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 2 0.07
28 2 0.07
29 23 0.85
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTATAATTTTTATTTTTAATTTTCATA
Found at i:1507276 original size:82 final size:83
Alignment explanation
Indices: 1507134--1507306 Score: 285
Period size: 82 Copynumber: 2.1 Consensus size: 83
1507124 TTTGTTTTTT
*
1507134 ACTTGTTTATCGTATTCAAATTCAATGAACTGTTACTGTCTCGAACCGATAATAATGGGACCGAT
1 ACTT-TTTATCGTATTCAAATTCAATGAACTGTTACTGTCACGAACCGATAATAATGGGACCGAT
*
1507199 A-TGTTAAAAAGGAGTTTA
65 AGTGTTAAAAAAGAGTTTA
*
1507217 ACTTTTTATCGTATTCAAATTCAATGAACTGTTACTGTCACGAGCCGATAATAATGGGACCGATA
1 ACTTTTTATCGTATTCAAATTCAATGAACTGTTACTGTCACGAACCGATAATAATGGGACCGATA
*
1507282 TGTGTTAAAAAAGAGTTTT
66 -GTGTTAAAAAAGAGTTTA
1507301 ACTTTT
1 ACTTTT
1507307 CATATAAAAG
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
82 59 0.70
83 4 0.05
84 21 0.25
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (83 bp):
ACTTTTTATCGTATTCAAATTCAATGAACTGTTACTGTCACGAACCGATAATAATGGGACCGATA
GTGTTAAAAAAGAGTTTA
Found at i:1508440 original size:16 final size:17
Alignment explanation
Indices: 1508421--1508452 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1508411 TTTAAATAGT
1508421 AATTTATATT-TAATAA
1 AATTTATATTCTAATAA
1508437 AATTTATATTCTAATA
1 AATTTATATTCTAATA
1508453 TTGTATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTATATTCTAATAA
Found at i:1508582 original size:181 final size:180
Alignment explanation
Indices: 1508119--1508625 Score: 675
Period size: 181 Copynumber: 2.8 Consensus size: 180
1508109 TCTTTTGACC
* * *
1508119 TTTTTAATAAGAGAAGTTGGGGTTTAAGAAAAGAAAGCATGGTTTAAAAAAATCAAATTGAAGAT
1 TTTTTAATAAGAGAAGTTGTGGTTTAAGAATAGAAAGCATGGTTT-AAAAAATCAAATTGAAGGT
* *
1508184 AAAATCGATGGGATTTTTAATTATCATTTTAATTGATTAGA-TTTTTT-AATAATAATTTATATT
65 AAAATTGATGGGATTTTTAATTATCA-TTTAATTGATTAGATTTTTTTAAATAGTAATTTATATT
* * *
1508247 TAAAAAAAATTTACATACTAATTTTGTATGTTTGTATGACCAGAATTAAAGTTA
129 T--AAAAAATTTATATACTAATATTGTATGTTTGTATGACCAGAAATAAAGTTA
* * * * *
1508301 TTTTTAATAAAAAAAAGTTGTGGTTTGAA-ACTAGAAAACATGGTTCAAAAAATCAAATTGAAGG
1 TTTTTAAT-AAGAGAAGTTGTGGTTT-AAGAATAGAAAGCATGGTTTAAAAAATCAAATTGAAGG
* *
1508365 TAAAATTGATGGGATTTTTAATTTTCGTATTAATTGATTAGATTTTTTTAAATAGTAATTTATAT
64 TAAAATTGATGGGATTTTTAATTATCAT-TTAATTGATTAGATTTTTTTAAATAGTAATTTATAT
*
1508430 TTAATAAAATTTATATTCTAATATTGTATGTTTGTATGACCAGAAATAAAGTT-
128 TTAA-AAAATTTATATACTAATATTGTATGTTTGTATGACCAGAAATAAAGTTA
* * *
1508483 TTTTTAATAAGAGAAGTTGTGGTTTAAGAATAGAAAGCATGGTTTAAAATATCAAATTGGAGGTC
1 TTTTTAATAAGAGAAGTTGTGGTTTAAGAATAGAAAGCATGGTTTAAAAAATCAAATTGAAGGTA
* * * *
1508548 AAATTGATGAGATCTTTAATTGTCATTCTAATTGATT--ATATTTTTAAATAGTAATTTATATTT
66 AAATTGATGGGATTTTTAATTATCATT-TAATTGATTAGATTTTTTTAAATAGTAATTTATATTT
1508611 AAAAAATTTTATATA
130 AAAAAA-TTTATATA
1508626 TTAAATAAGT
Statistics
Matches: 286, Mismatches: 30, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
178 4 0.01
179 34 0.12
180 3 0.01
181 78 0.27
182 72 0.25
183 77 0.27
184 18 0.06
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.41
Consensus pattern (180 bp):
TTTTTAATAAGAGAAGTTGTGGTTTAAGAATAGAAAGCATGGTTTAAAAAATCAAATTGAAGGTA
AAATTGATGGGATTTTTAATTATCATTTAATTGATTAGATTTTTTTAAATAGTAATTTATATTTA
AAAAATTTATATACTAATATTGTATGTTTGTATGACCAGAAATAAAGTTA
Found at i:1508613 original size:18 final size:18
Alignment explanation
Indices: 1508590--1508640 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 18
1508580 TGATTATATT
1508590 TTTAAATAGTAATTTATA
1 TTTAAATAGTAATTTATA
1508608 TTTAAA-A--AATTTTATA
1 TTTAAATAGTAA-TTTATA
1508624 TATTAAATAAGTAATTT
1 T-TTAAAT-AGTAATTT
1508641 TAATAATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
15 2 0.07
16 7 0.26
17 6 0.22
18 6 0.22
19 1 0.04
20 3 0.11
21 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TTTAAATAGTAATTTATA
Found at i:1509402 original size:2 final size:2
Alignment explanation
Indices: 1509395--1509424 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1509385 TATGATTTCT
1509395 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
1509425 GTGAGAGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1510882 original size:8 final size:8
Alignment explanation
Indices: 1510864--1510896 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
1510854 ACTAATAAGG
1510864 AAAAAAG-
1 AAAAAAGA
1510871 AAAAAAGA
1 AAAAAAGA
1510879 AAAAAAGA
1 AAAAAAGA
1510887 AAAAAAGA
1 AAAAAAGA
1510895 AA
1 AA
1510897 GCAAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1511607 original size:14 final size:14
Alignment explanation
Indices: 1511584--1511620 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1511574 TTGGAGAAAA
*
1511584 TGTATTATTGGATT
1 TGTATAATTGGATT
1511598 TGTATAATTGGATT
1 TGTATAATTGGATT
*
1511612 TGGATAATT
1 TGTATAATT
1511621 ACGGTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (14 bp):
TGTATAATTGGATT
Found at i:1514263 original size:19 final size:19
Alignment explanation
Indices: 1514222--1514264 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1514212 TTAATATTTT
* *
1514222 TTTTTTAAAATTTAAATTT
1 TTTTTTAAAATATAAATTA
* *
1514241 TTTTTTAAAATATCACTTA
1 TTTTTTAAAATATAAATTA
1514260 TTTTT
1 TTTTT
1514265 ATATAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTAAAATATAAATTA
Found at i:1514305 original size:15 final size:15
Alignment explanation
Indices: 1514263--1514306 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1514253 TCACTTATTT
*
1514263 TTATATAAATTTTGA
1 TTATATAAATTTTAA
1514278 -TATAATAAA-TTTAA
1 TTAT-ATAAATTTTAA
1514292 TTATATAAATTTTAA
1 TTATATAAATTTTAA
1514307 AATATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TTATATAAATTTTAA
Found at i:1514311 original size:14 final size:14
Alignment explanation
Indices: 1514264--1514311 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1514254 CACTTATTTT
*
1514264 TATATAAATTTTGA
1 TATATAAATTTTAA
1514278 TATAATAAA-TTTAA
1 TAT-ATAAATTTTAA
1514292 TTATATAAATTTTAA
1 -TATATAAATTTTAA
*
1514307 AATAT
1 TATAT
1514312 TAATATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:1516672 original size:25 final size:25
Alignment explanation
Indices: 1516643--1516705 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1516633 TCTATTTATT
1516643 AAATT-ATTCAAATTAAATTTAAATC
1 AAATTAATT-AAATTAAATTTAAATC
* * *
1516668 AAATTAATTTAATTAATTTTAAATTT
1 AAATTAATTAAATTAAATTTAAA-TC
*
1516694 AAATTAAATAAA
1 AAATTAATTAAA
1516706 CTCATTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATTAATTAAATTAAATTTAAATC
Found at i:1516678 original size:15 final size:16
Alignment explanation
Indices: 1516650--1516702 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1516640 ATTAAATTAT
1516650 TCAAATTAAATTTAAA
1 TCAAATTAAATTTAAA
1516666 TCAAATT-AATTT-AA
1 TCAAATTAAATTTAAA
* *
1516680 TTAATTTTAAATTTAAA
1 TCAA-ATTAAATTTAAA
*
1516697 TTAAAT
1 TCAAAT
1516703 AAACTCATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 13 0.42
17 6 0.19
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (16 bp):
TCAAATTAAATTTAAA
Found at i:1517399 original size:22 final size:22
Alignment explanation
Indices: 1517342--1517402 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
1517332 AAGTTGTAAA
1517342 TAAATAATA-ATAATTTTATTT
1 TAAATAATATATAATTTTATTT
1517363 TAAGATCAAT-T-TAATTTTA-TT
1 TAA-AT-AATATATAATTTTATTT
1517384 TAAATAATTATATAATTTT
1 TAAATAA-TATATAATTTT
1517403 TTAAAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 9 0.26
22 17 0.50
23 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TAAATAATATATAATTTTATTT
Found at i:1517530 original size:144 final size:143
Alignment explanation
Indices: 1517150--1517576 Score: 602
Period size: 144 Copynumber: 3.0 Consensus size: 143
1517140 TAATAAATAA
* * *
1517150 TAATGTAA-TTTTTA-TAAATATTATAATATATAAAATTAAGTTATAGATAAAAATTAAAAA-AA
1 TAATATAATTTTTTATTAAA-ATTATAATATATAAAATTAAGTTGTAAATAAAAA-TAAAAATAA
* * *
1517212 TAATTTTCTTTTGAGATTAATTTAATTTTATTTAAATAATTATATAATTTTTTAAAAGAATTTTG
64 TAATTTTATTTTAAGATCAATTTAATTTTATTTAAATAATTATATAATTTTTTAAAA-AATTTTG
**
1517277 GGGTTGGTGCCTTGCT
128 GGGTTGGACCCTTGCT
* *
1517293 TAATATATATTTTTTATAAAAATTATAATATATAAAATCAAGTTGTAAAT--AAAT---AATAAT
1 TAATATA-ATTTTTTATTAAAATTATAATATATAAAATTAAGTTGTAAATAAAAATAAAAATAAT
*
1517353 AATTTTATTTTAAGATCAATTTAATTTTATTTAAATAATTATATAATTTTTTAAAAAAATTTGGG
65 AATTTTATTTTAAGATCAATTTAATTTTATTTAAATAATTATATAATTTTTTAAAAAATTTTGGG
1517418 GTT-GACCCTTGCT
130 GTTGGACCCTTGCT
*
1517431 TAATATAATTTTTTATTAAAATTATAATATATAAAATTAAATTGTAAATAAAAAATAAAAAATAA
1 TAATATAATTTTTTATTAAAATTATAATATATAAAATTAAGTTGTAAAT-AAAAAT-AAAAATAA
* *
1517496 AAATTTTATTTTAAGATCAATTTATTTTTATTTAAATAATTATATAATTTTTTAAAAAATTTTGG
64 TAATTTTATTTTAAGATCAATTTAATTTTATTTAAATAATTATATAATTTTTTAAAAAATTTTGG
*
1517561 GGTTGGCCCCTTGCT
129 GGTTGGACCCTTGCT
1517576 T
1 T
1517577 CAATTTTGCA
Statistics
Matches: 254, Mismatches: 18, Indels: 22
0.86 0.06 0.07
Matches are distributed among these distances:
137 39 0.15
138 15 0.06
139 13 0.05
140 60 0.24
142 1 0.00
143 9 0.04
144 72 0.28
145 42 0.17
146 3 0.01
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (143 bp):
TAATATAATTTTTTATTAAAATTATAATATATAAAATTAAGTTGTAAATAAAAATAAAAATAATA
ATTTTATTTTAAGATCAATTTAATTTTATTTAAATAATTATATAATTTTTTAAAAAATTTTGGGG
TTGGACCCTTGCT
Found at i:1517546 original size:22 final size:24
Alignment explanation
Indices: 1517497--1517546 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 24
1517487 AAAAAATAAA
1517497 AATTTTATTTTAAGATCAATTTAT
1 AATTTTATTTTAAGATCAATTTAT
1517521 --TTTTA-TTTAA-AT-AATTATAT
1 AATTTTATTTTAAGATCAATT-TAT
1517541 AATTTT
1 AATTTT
1517547 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
19 4 0.17
20 5 0.22
21 5 0.22
22 9 0.39
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
AATTTTATTTTAAGATCAATTTAT
Found at i:1517705 original size:6 final size:7
Alignment explanation
Indices: 1517673--1517772 Score: 63
Period size: 6 Copynumber: 14.9 Consensus size: 7
1517663 TGGTGGACGT
1517673 TATATTCA
1 TATATT-A
1517681 TATA-TA
1 TATATTA
1517687 TATA-TA
1 TATATTA
1517693 TATATTA
1 TATATTA
1517700 TA-ATTA
1 TATATTA
1517706 TAT-TTAA
1 TATATT-A
* *
1517713 AATATTT
1 TATATTA
1517720 TATATT-
1 TATATTA
*
1517726 TATATAA
1 TATATTA
*
1517733 T-TTTTA
1 TATATTA
1517739 TATATTA
1 TATATTA
1517746 -ATAATT-
1 TAT-ATTA
1517752 TATATTA
1 TATATTA
*
1517759 TATTATAA
1 TA-TATTA
1517767 TATATT
1 TATATT
1517773 TTATTTATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
6 33 0.45
7 28 0.38
8 12 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATTA
Found at i:1517707 original size:17 final size:17
Alignment explanation
Indices: 1517673--1517771 Score: 59
Period size: 17 Copynumber: 5.9 Consensus size: 17
1517663 TGGTGGACGT
1517673 TATATTCATATATATATATA
1 TATATT-ATA-AT-TATATA
1517693 TATATTATAATTATAT-
1 TATATTATAATTATATA
** *
1517709 T-TAAAAT-ATTTTATA
1 TATATTATAATTATATA
* *
1517724 TTTA-TATAATT-TTTA
1 TATATTATAATTATATA
1517739 TATATTAATAATT-TATA
1 TATATT-ATAATTATATA
1517756 TTATATTATAA-TATAT
1 -TATATTATAATTATAT
1517772 TTTATTTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
14 6 0.09
15 13 0.20
16 8 0.12
17 21 0.32
18 8 0.12
19 3 0.05
20 6 0.09
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAATTATATA
Found at i:1518344 original size:23 final size:23
Alignment explanation
Indices: 1518326--1518368 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1518316 TATAAAAGAG
1518326 ATAAT-AAT-TTAAAATTAAAAA
1 ATAATAAATATTAAAATTAAAAA
*
1518347 ATTATAAATATTAAAATTAAAA
1 ATAATAAATATTAAAATTAAAA
1518369 TTAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAATAAATATTAAAATTAAAAA
Found at i:1518384 original size:21 final size:21
Alignment explanation
Indices: 1518334--1518383 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 21
1518324 AGATAATAAT
1518334 TTAAAATTAAAAAATTATAAATA
1 TTAAAATT--AAAATTATAAATA
*
1518357 TTAAAATTAAAATTAAAATATA
1 TTAAAATTAAAATTATAA-ATA
1518379 TTAAA
1 TTAAA
1518384 TGTTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
22 8 0.32
23 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAAAATTAAAATTATAAATA
Found at i:1519720 original size:27 final size:26
Alignment explanation
Indices: 1519665--1519725 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
1519655 ATATTAAAAT
1519665 TTAAATA-ATATAAATTATCAATTTA
1 TTAAATATATATAAATTATCAATTTA
1519690 TTAAAATATATATAAATATAT-AATATT-
1 TT-AAATATATATAAAT-TATCAAT-TTA
1519717 TTAAATATA
1 TTAAATATA
1519726 ATTATAACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 2 0.06
26 12 0.38
27 13 0.41
28 5 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TTAAATATATATAAATTATCAATTTA
Found at i:1520832 original size:22 final size:24
Alignment explanation
Indices: 1520807--1520850 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1520797 AATATATAAA
*
1520807 TATTAA-TAT-AATATTAATTTTT
1 TATTAATTATAAATAATAATTTTT
1520829 TATTAATTATAAATAATAATTT
1 TATTAATTATAAATAATAATTT
1520851 AAATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 3 0.16
24 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTAATTATAAATAATAATTTTT
Found at i:1520872 original size:30 final size:30
Alignment explanation
Indices: 1520803--1520872 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
1520793 ATAAAATATA
*
1520803 TAAATATTAAT-ATAATATTAATTTTTTAT
1 TAAATATAAATAATAATATTAATTTTTTAT
*
1520832 TAATTATAAATAATAAT-TTAAATTTTTTATT
1 TAAATATAAATAATAATATT-AATTTTTTA-T
1520863 TAAAT-TAAAT
1 TAAATATAAAT
1520873 TTGATTTGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 11 0.31
30 19 0.54
31 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TAAATATAAATAATAATATTAATTTTTTAT
Found at i:1521173 original size:30 final size:30
Alignment explanation
Indices: 1521100--1521203 Score: 120
Period size: 30 Copynumber: 3.5 Consensus size: 30
1521090 TATATTTTTA
* *
1521100 TTATATTTAAATAAATT-TTTAATTTTGAT
1 TTATATTTAAATAAATTATTAAATTTTAAT
* ** *
1521129 TTGTATAGATATAAATTATTAAATTTTAAT
1 TTATATTTAAATAAATTATTAAATTTTAAT
* **
1521159 TTATATTTAAATAAAATATTATTTTTTAAT
1 TTATATTTAAATAAATTATTAAATTTTAAT
1521189 TTATATTTAAATAAA
1 TTATATTTAAATAAA
1521204 AATTTAATAT
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
29 13 0.21
30 48 0.79
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TTATATTTAAATAAATTATTAAATTTTAAT
Found at i:1521592 original size:29 final size:28
Alignment explanation
Indices: 1521531--1521592 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
1521521 TAGAAATACT
* **
1521531 TTTTTATCATAAAATTATTTATTTTATA
1 TTTTTATCATAAAATTATTGATTGAATA
* *
1521559 ATTTTATTATAATAATTATTGATTGAATA
1 TTTTTATCATAA-AATTATTGATTGAATA
1521588 TTTTT
1 TTTTT
1521593 GACCGATTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTTATCATAAAATTATTGATTGAATA
Found at i:1525812 original size:22 final size:22
Alignment explanation
Indices: 1525787--1525835 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1525777 AATAATTTTT
1525787 TATTTAAAT-TTAATTATAAAAA
1 TATTTAAATATTAA-TATAAAAA
*
1525809 TATTTAAATATTAATATTAAAA
1 TATTTAAATATTAATATAAAAA
1525831 TATTT
1 TATTT
1525836 TTTTAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTAAATATTAATATAAAAA
Found at i:1526214 original size:22 final size:22
Alignment explanation
Indices: 1526186--1526228 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1526176 AAAAAATTAA
1526186 TTTTAT-ATTAATATTTATATAT
1 TTTTATAATTAA-ATTTATATAT
1526208 TTTTATAATTAAATTTATATA
1 TTTTATAATTAAATTTATATA
1526229 AAAATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATAATTAAATTTATATAT
Found at i:1527486 original size:21 final size:21
Alignment explanation
Indices: 1527440--1527486 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1527430 ATAATAATTT
* *
1527440 TATTTAAATTTAATTATAATA
1 TATTTAAATTTAATAAAAATA
1527461 TATTTAAATATTAATAAAAATA
1 TATTTAAAT-TTAATAAAAATA
1527483 -ATTT
1 TATTT
1527487 TTTAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTTAAATTTAATAAAAATA
Found at i:1527531 original size:15 final size:15
Alignment explanation
Indices: 1527511--1527552 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1527501 ATATATAAAT
1527511 AATAAATTTAAATTA
1 AATAAATTTAAATTA
* *
1527526 AATAAAATTAATTTA
1 AATAAATTTAAATTA
1527541 AATCAAATTTAA
1 AAT-AAATTTAA
1527553 TTCATCTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAAATTTAAATTA
Found at i:1527554 original size:20 final size:20
Alignment explanation
Indices: 1527509--1527554 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1527499 ATATATATAA
* *
1527509 ATAATAAATTTAAATTAAAT
1 ATAATTAATTTAAATCAAAT
*
1527529 AAAATTAATTTAAATCAAAT
1 ATAATTAATTTAAATCAAAT
*
1527549 TTAATT
1 ATAATT
1527555 CATCTATCCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAATTAATTTAAATCAAAT
Found at i:1532876 original size:6 final size:6
Alignment explanation
Indices: 1532856--1532913 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
1532846 TTAATAAAAA
* * * *
1532856 TAAATT TAATTTT TATATT TAATTT TAAATT TAATTATT TATATT TAAATT
1 TAAATT TAA-ATT TAAATT TAAATT TAAATT TAA--ATT TAAATT TAAATT
1532907 TAAATT T
1 TAAATT T
1532914 TTTAATATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
6 32 0.78
7 4 0.10
8 5 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
TAAATT
Found at i:1532896 original size:26 final size:25
Alignment explanation
Indices: 1532856--1532913 Score: 98
Period size: 26 Copynumber: 2.3 Consensus size: 25
1532846 TTAATAAAAA
*
1532856 TAAATTTAATTTTTATATTTAATTT
1 TAAATTTAATTTTTATATTTAAATT
1532881 TAAATTTAATTATTTATATTTAAATT
1 TAAATTTAATT-TTTATATTTAAATT
1532907 TAAATTT
1 TAAATTT
1532914 TTTAATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 11 0.35
26 20 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TAAATTTAATTTTTATATTTAAATT
Found at i:1532924 original size:21 final size:21
Alignment explanation
Indices: 1532871--1532932 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
1532861 TTAATTTTTA
*
1532871 TATTTAATTTTAAATTT-AAT
1 TATTTAATATTAAATTTAAAT
1532891 TATTT-ATATTTAAATTTAAAT
1 TATTTAATA-TTAAATTTAAAT
*
1532912 TTTTTAATATT-AATTATAAAT
1 TATTTAATATTAAATT-TAAAT
1532933 AAAAACTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 2 0.06
20 17 0.47
21 14 0.39
22 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTTAATATTAAATTTAAAT
Found at i:1536574 original size:30 final size:30
Alignment explanation
Indices: 1536504--1536571 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
1536494 CTTTTAATGC
1536504 TTTTAAAAATTATATTTATAATTTAATAAA
1 TTTTAAAAATTATATTTATAATTTAATAAA
*
1536534 TTTTAAAAATTATATTTATTATTT-ATAAA
1 TTTTAAAAATTATATTTATAATTTAATAAA
1536563 TTTTAAAAA
1 TTTTAAAAA
1536572 ATTTTAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 14 0.38
30 23 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTTAAAAATTATATTTATAATTTAATAAA
Found at i:1537040 original size:17 final size:17
Alignment explanation
Indices: 1537018--1537071 Score: 90
Period size: 17 Copynumber: 3.1 Consensus size: 17
1537008 AATTTATATA
1537018 TTCAAATTTTTAATTTT
1 TTCAAATTTTTAATTTT
1537035 TTCAAATTTTTAATTTT
1 TTCAAATTTTTAATTTT
*
1537052 TTCAAATTATTAATATTT
1 TTCAAATTTTTAAT-TTT
1537070 TT
1 TT
1537072 TTATTTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
17 30 0.86
18 5 0.14
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (17 bp):
TTCAAATTTTTAATTTT
Found at i:1540090 original size:21 final size:19
Alignment explanation
Indices: 1540057--1540107 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 19
1540047 ATGTATATAT
1540057 ATTTAAATATAAATATAAA
1 ATTTAAATATAAATATAAA
*
1540076 ATTTAAAATTATAAATATCAA
1 ATTT-AAA-TATAAATATAAA
1540097 A--TAAATATAAA
1 ATTTAAATATAAA
1540108 AATATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 3 0.10
19 5 0.17
20 3 0.10
21 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTTAAATATAAATATAAA
Found at i:1541979 original size:32 final size:31
Alignment explanation
Indices: 1541943--1542032 Score: 96
Period size: 30 Copynumber: 2.9 Consensus size: 31
1541933 TATTTAAAAA
1541943 TTTATATAAAATAAAT-TATTAATATATTAAAT
1 TTTATATAAAATAAATATATTAATATA-T-AAT
*
1541975 TTTATATAAATATAAATATTTTAA-ATATAAT
1 TTTATATAAA-ATAAATATATTAATATATAAT
* *
1542006 TATA-ATATAATAAAATATATTAATATA
1 TTTATATAAAAT-AAATATATTAATATA
1542033 GAGAGAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
29 2 0.04
30 14 0.28
31 9 0.18
32 11 0.22
33 9 0.18
34 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TTTATATAAAATAAATATATTAATATATAAT
Found at i:1545341 original size:22 final size:25
Alignment explanation
Indices: 1545295--1545344 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1545285 TAATTCAATT
1545295 ATATATATATATTAATTTTGATATTA
1 ATATATATATATTAATTTT-ATATTA
*
1545321 ATATAT-TATATTATTTTTAT-TTA
1 ATATATATATATTAATTTTATATTA
1545344 A
1 A
1545345 AAATAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 2 0.09
25 11 0.48
26 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATATATATATTAATTTTATATTA
Found at i:1545358 original size:25 final size:27
Alignment explanation
Indices: 1545320--1545373 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1545310 TTTTGATATT
* **
1545320 AATATATTATATTATTTTTA-TTTAAA
1 AATAAATTATATTATCATTATTTTAAA
1545346 AATAAATTA-ATTATCATTATTTTAAA
1 AATAAATTATATTATCATTATTTTAAA
1545372 AA
1 AA
1545374 GTTTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
AATAAATTATATTATCATTATTTTAAA
Found at i:1545978 original size:13 final size:14
Alignment explanation
Indices: 1545954--1545982 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1545944 AGAAGATGTA
1545954 TAAATATTAAAATT
1 TAAATATTAAAATT
1545968 TAAAT-TTAAAATT
1 TAAATATTAAAATT
1545981 TA
1 TA
1545983 TAAACTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATATTAAAATT
Found at i:1546707 original size:15 final size:15
Alignment explanation
Indices: 1546674--1546711 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
1546664 AATCTTTTAG
*
1546674 AATATTTTTTAAAAT
1 AATAATTTTTAAAAT
1546689 --TAATTTTTAAAAT
1 AATAATTTTTAAAAT
1546702 AATAATTTTT
1 AATAATTTTT
1546712 TTATTACGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 12 0.60
15 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATAATTTTTAAAAT
Found at i:1547271 original size:124 final size:123
Alignment explanation
Indices: 1547133--1547372 Score: 444
Period size: 124 Copynumber: 1.9 Consensus size: 123
1547123 TTTTTTTTGG
1547133 ATTTTTTTTTGTTTGAAGCTCAAATGTGACATTCTCTTATTAATCTCATGAACCCATCAACCCTA
1 ATTTTTTTTTGTTTGAAGCTCAAATGTGACATTCTCTTATTAATCTCATGAACCCATCAACCCTA
* *
1547198 TCACTAAAAAAAATATAAACATATAAAAACTTTTACATTAAATCTAAGGATGTTCTTTA
66 TCACCAAAAAAAACATAAACATAT-AAAACTTTTACATTAAATCTAAGGATGTTCTTTA
1547257 ATTTTTTTTTGTTTGAAGCTCAAATGTGACATTCTCTTATTAATCTCATGAACCCATCAACCCTA
1 ATTTTTTTTTGTTTGAAGCTCAAATGTGACATTCTCTTATTAATCTCATGAACCCATCAACCCTA
*
1547322 TCACCAAAAAAGACATAAACATATAAAACTTTTACATTAAATCTAAGGATG
66 TCACCAAAAAAAACATAAACATATAAAACTTTTACATTAAATCTAAGGATG
1547373 ATGTAAGTAA
Statistics
Matches: 113, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
123 27 0.24
124 86 0.76
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (123 bp):
ATTTTTTTTTGTTTGAAGCTCAAATGTGACATTCTCTTATTAATCTCATGAACCCATCAACCCTA
TCACCAAAAAAAACATAAACATATAAAACTTTTACATTAAATCTAAGGATGTTCTTTA
Found at i:1548178 original size:2 final size:2
Alignment explanation
Indices: 1548173--1548218 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1548163 GAATTGTTAG
1548173 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
1548215 TA TA
1 TA TA
1548219 CACACATGAG
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:1548439 original size:17 final size:18
Alignment explanation
Indices: 1548406--1548450 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1548396 TTATAAATTA
*
1548406 TAATAAATATGATATATT
1 TAATATATATGATATATT
1548424 TAATATATAT-ATATATT
1 TAATATATATGATATATT
* *
1548441 AAATTTATAT
1 TAATATATAT
1548451 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TAATATATATGATATATT
Found at i:1549950 original size:8 final size:8
Alignment explanation
Indices: 1549924--1550024 Score: 51
Period size: 8 Copynumber: 11.8 Consensus size: 8
1549914 ATTTAATAAC
1549924 TTATATAT
1 TTATATAT
*
1549932 TTATCACAT
1 TTAT-ATAT
1549941 TTATATAT
1 TTATATAT
*
1549949 TTTTATAT
1 TTATATAT
1549957 TATAATTATAT
1 T-T-A-TATAT
*
1549968 TTA-AAAT
1 TTATATAT
1549975 ATTATATATT
1 -TTATATA-T
*
1549985 TTATAAATT
1 TTATATA-T
*
1549994 TTAACATAT
1 TT-ATATAT
*
1550003 TCATATAT
1 TTATATAT
*
1550011 ATATATAT
1 TTATATAT
*
1550019 ATATAT
1 TTATAT
1550025 TAATATTAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
7 3 0.04
8 35 0.49
9 23 0.32
10 5 0.07
11 6 0.08
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (8 bp):
TTATATAT
Found at i:1550052 original size:22 final size:24
Alignment explanation
Indices: 1550027--1550092 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
1550017 ATATATATTA
1550027 ATATTA-ATTCATA-TTAA-TTTTT
1 ATATTATATT-ATATTTAATTTTTT
1550049 ATATTATATTATATTTTAATTTTTT
1 ATATTATATTATA-TTTAATTTTTT
* *
1550074 ATATCATATTTTATTTAAT
1 ATATTATATTATATTTAAT
1550093 ATTACTAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.24
23 3 0.08
24 10 0.26
25 16 0.42
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATTATATTATATTTAATTTTTT
Found at i:1550060 original size:10 final size:10
Alignment explanation
Indices: 1549951--1550063 Score: 51
Period size: 10 Copynumber: 11.2 Consensus size: 10
1549941 TTATATATTT
1549951 TTATATTATAA
1 TTATATTAT-A
1549962 TTATATT-TA
1 TTATATTATA
**
1549971 AAATATTATA
1 TTATATTATA
*
1549981 -TATTTTATAAA
1 TTATATTAT--A
* **
1549992 TTTTAACATA
1 TTATATTATA
1550002 TTCATA-TATA
1 TT-ATATTATA
1550012 TATATATATATA
1 T-TATAT-TATA
1550024 TTAATATTA-A
1 TT-ATATTATA
1550034 TTCATATTA-A
1 TT-ATATTATA
1550044 TT-T-TTATA
1 TTATATTATA
1550052 TTATATTATA
1 TTATATTATA
1550062 TT
1 TT
1550064 TTAATTTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 25
0.69 0.10 0.22
Matches are distributed among these distances:
7 3 0.04
8 4 0.05
9 13 0.16
10 32 0.41
11 14 0.18
12 13 0.16
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (10 bp):
TTATATTATA
Found at i:1551051 original size:32 final size:33
Alignment explanation
Indices: 1551015--1551085 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
1551005 GATAGTTTAT
1551015 TTATAT-AAATTTTA-ATATATTAATAATTAATA
1 TTATATAAAATTTTACATAT-TTAATAATTAATA
* * *
1551047 TTATATAAAATTTTACATATTTATTTATTTATA
1 TTATATAAAATTTTACATATTTAATAATTAATA
1551080 TTATAT
1 TTATAT
1551086 TTATATTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 6 0.18
33 24 0.71
34 4 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (33 bp):
TTATATAAAATTTTACATATTTAATAATTAATA
Found at i:1551089 original size:6 final size:6
Alignment explanation
Indices: 1551072--1551124 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
1551062 CATATTTATT
* * *
1551072 TATTTA TA-TTA TATTTA TATTAA TTTTTA TA-TTA TATTTTA TAATTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TA-TTTA TATTTA
1551119 TATTTA
1 TATTTA
1551125 ATTAATTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 10 0.26
6 23 0.61
7 5 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TATTTA
Found at i:1551097 original size:21 final size:21
Alignment explanation
Indices: 1551063--1551134 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 21
1551053 AAAATTTTAC
1551063 ATATTTAT-TT-ATTTATATT
1 ATATTTATATTAATTTATATT
1551082 ATATTTATATTAATTTTTATATT
1 ATATTTATATTAA--TTTATATT
1551105 ATATTTTATAATTATATTTA-ATT
1 ATA-TTTAT-ATTA-ATTTATATT
1551128 A-ATTTAT
1 ATATTTAT
1551135 CATATTCATT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
19 8 0.17
20 2 0.04
21 6 0.13
22 1 0.02
23 15 0.33
24 9 0.20
25 4 0.09
26 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTTATATTAATTTATATT
Found at i:1551103 original size:18 final size:18
Alignment explanation
Indices: 1551080--1551132 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1551070 TTTATTTATA
1551080 TTATATTTATATTAATTT
1 TTATATTTATATTAATTT
* **
1551098 TTATA-TTATATTTTATAA
1 TTATATTTATA-TTAATTT
1551116 TTATATTTA-ATTAATTT
1 TTATATTTATATTAATTT
1551133 ATCATATTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
17 9 0.33
18 15 0.56
19 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATATTTATATTAATTT
Found at i:1551104 original size:23 final size:23
Alignment explanation
Indices: 1551072--1551134 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
1551062 CATATTTATT
1551072 TATTTATATTATATTTAT-ATTAA
1 TATTTATATTATATTTATAATT-A
*
1551095 TTTTTATATTATATTTTATAATTA
1 TATTTATATTATA-TTTATAATTA
1551119 TATTTA-ATTA-ATTTAT
1 TATTTATATTATATTTAT
1551135 CATATTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.14
22 1 0.03
23 16 0.44
24 11 0.31
25 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTATATTATATTTATAATTA
Found at i:1552933 original size:2 final size:2
Alignment explanation
Indices: 1552928--1552973 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1552918 AATTTTTTTA
*
1552928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1552970 AT AT
1 AT AT
1552974 TCAGATTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1555014 original size:2 final size:2
Alignment explanation
Indices: 1555007--1555045 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1554997 GCTTTTCAAT
*
1555007 TA TA TA TA TA TA TA TA TG 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 TA T
1555046 TTCTTCTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1557140 original size:18 final size:17
Alignment explanation
Indices: 1557094--1557148 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
1557084 ATATCAATTT
1557094 TTTA-AAATATATTAT-
1 TTTATAAATATATTATA
*
1557109 TTTAT-ATTATTATTATA
1 TTTATAAATA-TATTATA
1557126 TTTACTAAATATATTATA
1 TTTA-TAAATATATTATA
1557144 TTTAT
1 TTTAT
1557149 TTTATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 7 0.21
16 6 0.18
17 5 0.15
18 12 0.36
19 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTATAAATATATTATA
Found at i:1557155 original size:18 final size:18
Alignment explanation
Indices: 1557100--1557155 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
1557090 ATTTTTTAAA
*
1557100 ATATATTAT-TTTATATT
1 ATATATTATATTTATTTT
* **
1557117 AT-TATTATATTTACTAA
1 ATATATTATATTTATTTT
1557134 ATATATTATATTTATTTT
1 ATATATTATATTTATTTT
1557152 ATAT
1 ATAT
1557156 TTTTTTATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 6 0.20
17 8 0.27
18 16 0.53
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATATTATATTTATTTT
Found at i:1557782 original size:19 final size:19
Alignment explanation
Indices: 1557754--1557798 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1557744 TAAGAAATTA
*
1557754 TTCTTCCTTTGTTTTTTTT
1 TTCTTTCTTTGTTTTTTTT
1557773 TTCTTTCTTTGTTTTTTTT
1 TTCTTTCTTTGTTTTTTTT
*
1557792 TTTTTTC
1 TTCTTTC
1557799 CTTTCTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.82
Consensus pattern (19 bp):
TTCTTTCTTTGTTTTTTTT
Found at i:1562092 original size:18 final size:18
Alignment explanation
Indices: 1562071--1562118 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
1562061 GTAAATATAT
* *
1562071 TTTTAATATTTTTTAAAA
1 TTTTAATATATTTAAAAA
*
1562089 TTTTTATATATTTAAAAA
1 TTTTAATATATTTAAAAA
* *
1562107 TTATATTATATT
1 TTTTAATATATT
1562119 CATATATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAATATATTTAAAAA
Found at i:1563077 original size:16 final size:17
Alignment explanation
Indices: 1563045--1563079 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1563035 ATATTCGTAT
1563045 TTAAAATTTTGATATTA
1 TTAAAATTTTGATATTA
1563062 TTAAAATTTT-ATATTA
1 TTAAAATTTTGATATTA
1563078 TT
1 TT
1563080 TTTTTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTAAAATTTTGATATTA
Found at i:1564458 original size:2 final size:2
Alignment explanation
Indices: 1564451--1564475 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1564441 TTTGATTTTC
1564451 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 A
1564476 ACAGTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1565410 original size:10 final size:10
Alignment explanation
Indices: 1565397--1565427 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1565387 ATTATTTAAA
1565397 AATATTAATT
1 AATATTAATT
1565407 AATATTAA-T
1 AATATTAATT
1565416 AATATTAATT
1 AATATTAATT
1565426 AA
1 AA
1565428 GATGATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AATATTAATT
Found at i:1565414 original size:19 final size:19
Alignment explanation
Indices: 1565366--1565427 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
1565356 TTTTAAATTA
* *
1565366 TAATATTAAAAAAATTTAT
1 TAATATTAAAAATATTAAT
*
1565385 AAATTATTTAAAAATATTAAT
1 TAA-TA-TTAAAAATATTAAT
*
1565406 TAATATTAATAATATTAAT
1 TAATATTAAAAATATTAAT
1565425 TAA
1 TAA
1565428 GATGATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 18 0.50
20 4 0.11
21 14 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATTAAAAATATTAAT
Found at i:1566124 original size:17 final size:17
Alignment explanation
Indices: 1566077--1566127 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1566067 AGAACCTAAC
1566077 AAATTTTTTA-AATT-T
1 AAATTTTTTATAATTAT
*
1566092 ATATTTTATT-TAAATTAT
1 AAATTTT-TTAT-AATTAT
1566110 AAATTTTTTATAATTAT
1 AAATTTTTTATAATTAT
1566127 A
1 A
1566128 TTAAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 6 0.21
16 2 0.07
17 13 0.45
18 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AAATTTTTTATAATTAT
Found at i:1566303 original size:19 final size:20
Alignment explanation
Indices: 1566268--1566308 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1566258 AATATGTATT
*
1566268 TTTAATTAAAAATTTTATAA
1 TTTAAATAAAAATTTTATAA
1566288 TTTAAATAAAAA-TTTATAA
1 TTTAAATAAAAATTTTATAA
1566307 TT
1 TT
1566309 ATTAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAATAAAAATTTTATAA
Found at i:1566313 original size:21 final size:21
Alignment explanation
Indices: 1566246--1566323 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 21
1566236 TCATTAAAAC
* * *
1566246 TTATTATATAAAAATATGT-A
1 TTATTAAATAAAAATTTATAA
* *
1566266 TTTTTAATTAAAAATTTTATAA
1 TTATTAAATAAAAA-TTTATAA
1566288 -T-TTAAATAAAAATTTATAA
1 TTATTAAATAAAAATTTATAA
*
1566307 TTATTAAAATTAAAATT
1 TTATT-AAATAAAAATT
1566324 AAAATATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
19 7 0.15
20 22 0.48
21 6 0.13
22 11 0.24
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (21 bp):
TTATTAAATAAAAATTTATAA
Found at i:1566321 original size:22 final size:19
Alignment explanation
Indices: 1566271--1566323 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 19
1566261 ATGTATTTTT
1566271 AATTAAAAATTTTATAATTTA
1 AATT-AAAA-TTTATAATTTA
*
1566292 AATAAAAATTTATAATTATTAA
1 AATTAAAATTTATAA-T-TT-A
1566314 AATTAAAATT
1 AATTAAAATT
1566324 AAAATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 7 0.26
20 5 0.19
21 5 0.19
22 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTAAAATTTATAATTTA
Found at i:1566777 original size:20 final size:20
Alignment explanation
Indices: 1566754--1566811 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 20
1566744 ATTATTAAAT
*
1566754 TTTATATAAATATATAATAA
1 TTTATATAAATATATAAAAA
*
1566774 TTTAAATAAAATTATAATAAAAA
1 TTTATAT-AAA-TAT-ATAAAAA
*
1566797 ATTATATAAATATAT
1 TTTATATAAATATAT
1566812 CATGAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 8 0.26
21 6 0.19
22 6 0.19
23 11 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTATATAAATATATAAAAA
Found at i:1567277 original size:27 final size:26
Alignment explanation
Indices: 1567215--1567293 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
1567205 TATAGTAGAA
* *
1567215 AAAAATTAAAAGATATTT-AAGTAATT
1 AAAAATTAAAAAATATTTAAAATAA-T
* *
1567241 GAAATATAAAAAAATATTTAAAATAAT
1 -AAAAATTAAAAAATATTTAAAATAAT
* *
1567268 AAAAATTAAATAATA-TAAAAATAAT
1 AAAAATTAAAAAATATTTAAAATAAT
1567293 A
1 A
1567294 TAATAATTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
25 10 0.23
26 12 0.28
27 16 0.37
28 5 0.12
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (26 bp):
AAAAATTAAAAAATATTTAAAATAAT
Found at i:1567280 original size:14 final size:14
Alignment explanation
Indices: 1567261--1567299 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
1567251 AAAATATTTA
*
1567261 AAATAATAAAAATT
1 AAATAATAAAAAAT
1567275 AAATAATATAAAAAT
1 AAATAATA-AAAAAT
1567290 AATATAATAA
1 AA-ATAATAA
1567300 TTTTATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 8 0.36
16 6 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAATAAAAAAT
Found at i:1567287 original size:16 final size:16
Alignment explanation
Indices: 1567266--1567298 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1567256 ATTTAAAATA
1567266 ATAAAAATTAA-ATAAT
1 ATAAAAA-TAATATAAT
1567282 ATAAAAATAATATAAT
1 ATAAAAATAATATAAT
1567298 A
1 A
1567299 ATTTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAAATAATATAAT
Found at i:1567298 original size:19 final size:19
Alignment explanation
Indices: 1567243--1567300 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1567233 AAGTAATTGA
1567243 AATATAAAAA-AATATTTAA-
1 AATATAAAAATAATA--TAAT
1567262 AATAATAAAAAT--TA-AAT
1 AAT-ATAAAAATAATATAAT
1567279 AATATAAAAATAATATAAT
1 AATATAAAAATAATATAAT
1567298 AAT
1 AAT
1567301 TTTATTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
16 10 0.30
17 3 0.09
18 2 0.06
19 11 0.33
20 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATATAAAAATAATATAAT
Found at i:1577806 original size:3 final size:3
Alignment explanation
Indices: 1577798--1577835 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1577788 CATTCTACTG
1577798 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1577836 TTGTTTTTTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1579913 original size:2 final size:2
Alignment explanation
Indices: 1579906--1579932 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1579896 AAAAATCTAG
1579906 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
1579933 TTTTTTTTTT
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:1580289 original size:139 final size:139
Alignment explanation
Indices: 1580039--1580303 Score: 467
Period size: 139 Copynumber: 1.9 Consensus size: 139
1580029 CTAAGATACT
*
1580039 TTCACCTTCTATTGGTGATCTTCAATTAGAATACAGATTAAATGATAAGACTACTACCGCAAGCC
1 TTCACCTTCTATTGGTGATCTTCAATCAGAATACAGATTAAATGATAAGACTACTACCGCAAGCC
* *
1580104 AGCTTTACTTAGGTTTGATAGATTCTGAAATAACTTCAGAACAGGAAGAATTCAGTAAAGATAGG
66 AGCTTTACTTAGGTTTGACAAATTCTGAAATAACTTCAGAACAGGAAGAATTCAGTAAAGATAGG
1580169 ACTACTACC
131 ACTACTACC
* * *
1580178 TTCACCTTCTATTGGTGATCTTCAATCAGCATACAGATTAAATGATAGGACTACTACCGCAAGCT
1 TTCACCTTCTATTGGTGATCTTCAATCAGAATACAGATTAAATGATAAGACTACTACCGCAAGCC
*
1580243 AGCTTTACTTAGGTTTGACAAATTCTGAAATAACTTCAGAATAGGAAGAATTCAGTAAAGA
66 AGCTTTACTTAGGTTTGACAAATTCTGAAATAACTTCAGAACAGGAAGAATTCAGTAAAGA
1580304 GGAGATTGGA
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
139 119 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (139 bp):
TTCACCTTCTATTGGTGATCTTCAATCAGAATACAGATTAAATGATAAGACTACTACCGCAAGCC
AGCTTTACTTAGGTTTGACAAATTCTGAAATAACTTCAGAACAGGAAGAATTCAGTAAAGATAGG
ACTACTACC
Found at i:1588402 original size:2 final size:2
Alignment explanation
Indices: 1588395--1588427 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1588385 CCTAGAGGAT
*
1588395 GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1588428 CATCTACCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1595730 original size:21 final size:20
Alignment explanation
Indices: 1595706--1595751 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
1595696 ATATATAGAA
1595706 TTTTAAATAAAAATATTGATT
1 TTTTAAA-AAAAATATTGATT
*
1595727 TTTT-AAAAAAATATTGTTT
1 TTTTAAAAAAAATATTGATT
1595746 TTTTAA
1 TTTTAA
1595752 TTTATTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 16 0.70
20 3 0.13
21 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTAAAAAAAATATTGATT
Found at i:1596335 original size:15 final size:16
Alignment explanation
Indices: 1596267--1596332 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
1596257 GTTAAGTGTG
1596267 AATTTTAAAATATTTT
1 AATTTTAAAATATTTT
1596283 -A-TTT-AAATACCTTTT
1 AATTTTAAAATA--TTTT
*
1596298 GATTATTAAAATATTTAT
1 AATT-TTAAAATATTT-T
*
1596316 AATTTTAATATATTTT
1 AATTTTAAAATATTTT
1596332 A
1 A
1596333 TTTGAGACGA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
13 5 0.12
14 3 0.07
15 5 0.12
16 3 0.07
17 14 0.34
18 6 0.15
19 5 0.12
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (16 bp):
AATTTTAAAATATTTT
Found at i:1596465 original size:16 final size:16
Alignment explanation
Indices: 1596444--1596482 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1596434 ATCAATATGT
1596444 TTATTTTTATATTTTA
1 TTATTTTTATATTTTA
*
1596460 TTATTTTTATTTTTTA
1 TTATTTTTATATTTTA
*
1596476 ATATTTT
1 TTATTTT
1596483 AATTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTTATATTTTA
Found at i:1596528 original size:15 final size:15
Alignment explanation
Indices: 1596500--1596530 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1596490 AAAAATTATG
*
1596500 TTTATTTTTTATTTT
1 TTTAATTTTTATTTT
1596515 TTTAATTTTTATTTT
1 TTTAATTTTTATTTT
1596530 T
1 T
1596531 AAAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTAATTTTTATTTT
Found at i:1603664 original size:19 final size:21
Alignment explanation
Indices: 1603640--1603731 Score: 81
Period size: 20 Copynumber: 4.6 Consensus size: 21
1603630 TTATTTATGT
*
1603640 ATTAAAAT-TTATATAA-ATA
1 ATTAAAATATAATATAATATA
1603659 ATTAAAATATAATATAATATA
1 ATTAAAATATAATATAATATA
* *
1603680 A-AAATAATATAA-ATATTAT-
1 ATTAA-AATATAATATAATATA
1603699 A-TAAAA-ATAATATAAGTATA
1 ATTAAAATATAATATAA-TATA
1603719 ATATAAAATATAA
1 AT-TAAAATATAA
1603732 ATATTTTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
17 4 0.07
18 5 0.08
19 14 0.24
20 16 0.27
21 11 0.19
22 5 0.08
23 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (21 bp):
ATTAAAATATAATATAATATA
Found at i:1603679 original size:27 final size:27
Alignment explanation
Indices: 1603604--1603776 Score: 103
Period size: 27 Copynumber: 6.4 Consensus size: 27
1603594 AGGATGCAGC
*
1603604 TTAAAATATATATATATATATATAAATTA
1 TTAAAATATA-ATATA-ATATATAAATAA
* ** * *
1603633 TTTATGTATTAAAAT-TTATATAAATAA
1 TTAAAATA-TAATATAATATATAAATAA
*
1603660 TTAAAATATAATATAATATAAAAATAA
1 TTAAAATATAATATAATATATAAATAA
1603687 -TATAAATAT--TAT-ATA-A-AAATAA
1 TTA-AAATATAATATAATATATAAATAA
* * *
1603709 -TATAAGTATAATATAAAATATAAATATT
1 TTA-AAATATAATATAATATATAAATA-A
*
1603737 TTAAAATTTATATATAA-ATATAAAATAA
1 TTAAAATATA-ATATAATATAT-AAATAA
*
1603765 TTTAAATATAAT
1 TTAAAATATAAT
1603777 TATTAAATCA
Statistics
Matches: 112, Mismatches: 20, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
22 14 0.12
23 1 0.01
24 6 0.05
25 5 0.04
26 8 0.07
27 38 0.34
28 17 0.15
29 21 0.19
30 2 0.02
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
TTAAAATATAATATAATATATAAATAA
Found at i:1603686 original size:16 final size:16
Alignment explanation
Indices: 1603650--1603776 Score: 71
Period size: 16 Copynumber: 8.4 Consensus size: 16
1603640 ATTAAAATTT
1603650 ATATAA-ATAATTAAA
1 ATATAATATAATTAAA
1603665 ATATAATATAATATAAA
1 ATATAATATAAT-TAAA
* **
1603682 A-ATAATATAAATATT
1 ATATAATATAATTAAA
1603697 ATATAA-A-AA-T--A
1 ATATAATATAATTAAA
1603708 ATATAAGTATAATATAAA
1 ATATAA-TATAAT-TAAA
*
1603726 ATATAA-ATATTTTAAA
1 ATATAATATA-ATTAAA
*
1603742 AT-TTATAT-A-T-AA
1 ATATAATATAATTAAA
* *
1603754 ATATAAAATAATTTAA
1 ATATAATATAATTAAA
1603770 ATATAAT
1 ATATAAT
1603777 TATTAAATCA
Statistics
Matches: 86, Mismatches: 10, Indels: 31
0.68 0.08 0.24
Matches are distributed among these distances:
11 6 0.07
12 4 0.05
13 7 0.08
14 5 0.06
15 13 0.15
16 38 0.44
17 6 0.07
18 7 0.08
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (16 bp):
ATATAATATAATTAAA
Found at i:1603694 original size:22 final size:22
Alignment explanation
Indices: 1603664--1603731 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
1603654 AAATAATTAA
1603664 AATAT-AATATAATATAAAAAT
1 AATATAAATATAATATAAAAAT
*
1603685 AATATAAATATTATATAAAAAT
1 AATATAAATATAATATAAAAAT
*
1603707 AATATAAGTATAATATAAAATAT
1 AATATAAATATAATATAAAA-AT
1603730 AA
1 AA
1603732 ATATTTTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
21 5 0.12
22 33 0.79
23 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (22 bp):
AATATAAATATAATATAAAAAT
Found at i:1603719 original size:49 final size:48
Alignment explanation
Indices: 1603642--1603763 Score: 135
Period size: 49 Copynumber: 2.6 Consensus size: 48
1603632 ATTTATGTAT
*
1603642 TAAAATT-TATATAAATAATTAAAATATAATATAATATAAAAATAATA
1 TAAAATTATATATAAATAATTAAAATATAATATAAAATAAAAATAATA
* * * * *
1603689 TAAATATTATATAAAAATAA-TATAAGTATAATATAAAATATAAATATTT
1 TAAA-ATTATATATAAATAATTA-AAATATAATATAAAATAAAAATAATA
1603738 TAAAATTTATATATAAAT-A-TAAAATA
1 TAAAA-TTATATATAAATAATTAAAATA
1603764 ATTTAAATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
47 8 0.13
48 9 0.14
49 46 0.73
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (48 bp):
TAAAATTATATATAAATAATTAAAATATAATATAAAATAAAAATAATA
Found at i:1603777 original size:11 final size:11
Alignment explanation
Indices: 1603650--1603776 Score: 91
Period size: 11 Copynumber: 11.6 Consensus size: 11
1603640 ATTAAAATTT
1603650 ATATAA-ATAA
1 ATATAATATAA
* *
1603660 TTAAAATAT-A
1 ATATAATATAA
1603670 ATATAATATAA
1 ATATAATATAA
*
1603681 AAATAATATAA
1 ATATAATATAA
*
1603692 ATATTATATAA
1 ATATAATATAA
*
1603703 AAATAATATAA
1 ATATAATATAA
*
1603714 GTATAATATAAA
1 ATATAATAT-AA
*
1603726 ATATAA-ATATT
1 ATATAATATA-A
* * * *
1603737 TTAAAATTTAT
1 ATATAATATAA
1603748 ATATAAATATAA
1 ATAT-AATATAA
*
1603760 A-ATAATTTAA
1 ATATAATATAA
1603770 ATATAAT
1 ATATAAT
1603777 TATTAAATCA
Statistics
Matches: 89, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
10 20 0.22
11 54 0.61
12 15 0.17
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1603783 original size:29 final size:29
Alignment explanation
Indices: 1603685--1603790 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 29
1603675 ATATAAAAAT
* * *
1603685 AATATAAATATTATATA-AAAATAATATA
1 AATATAATTATTAAATATAAAATAATTTA
* * *
1603713 AGTATAA-TATAAAATAT-AAATATTTTA
1 AATATAATTATTAAATATAAAATAATTTA
*
1603740 AA-AT-TTATATATAAATATAAAATAATTTA
1 AATATAAT-TAT-TAAATATAAAATAATTTA
1603769 AATATAATTATTAAATCATAAA
1 AATATAATTATTAAAT-ATAAA
1603791 GTACATAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
26 2 0.03
27 19 0.32
28 12 0.20
29 16 0.27
30 10 0.17
31 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (29 bp):
AATATAATTATTAAATATAAAATAATTTA
Found at i:1604232 original size:14 final size:15
Alignment explanation
Indices: 1604215--1604252 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1604205 TTAAATTTTA
1604215 AAATATAAT-TAATT
1 AAATATAATATAATT
*
1604229 AAATATATTATAATT
1 AAATATAATATAATT
1604244 AATATATAA
1 AA-ATATAA
1604253 ATTATTAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 8 0.40
15 7 0.35
16 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATAATATAATT
Found at i:1608198 original size:16 final size:17
Alignment explanation
Indices: 1608166--1608199 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1608156 TTACATATTG
*
1608166 TTTAATTTTAGTATATA
1 TTTAAATTTAGTATATA
1608183 TTTAAATTTA-TATATA
1 TTTAAATTTAGTATATA
1608199 T
1 T
1608200 ATATTTTACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAAATTTAGTATATA
Found at i:1608454 original size:17 final size:18
Alignment explanation
Indices: 1608416--1608455 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1608406 ATGAAAAAAT
1608416 TATTAAAATATGATGCAA
1 TATTAAAATATGATGCAA
1608434 TATTAAAATAATG-TG-AA
1 TATTAAAAT-ATGATGCAA
1608451 TATTA
1 TATTA
1608456 TACAAGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 11 0.52
19 3 0.14
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.38
Consensus pattern (18 bp):
TATTAAAATATGATGCAA
Found at i:1609433 original size:9 final size:9
Alignment explanation
Indices: 1609419--1609451 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1609409 TTTCTCTCTT
*
1609419 TCTGCTATC
1 TCTGCTGTC
1609428 TCTGCTGTC
1 TCTGCTGTC
1609437 TCTGCTGTC
1 TCTGCTGTC
1609446 TCTGCT
1 TCTGCT
1609452 TGAGCCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.03, C:0.33, G:0.18, T:0.45
Consensus pattern (9 bp):
TCTGCTGTC
Found at i:1609548 original size:27 final size:26
Alignment explanation
Indices: 1609510--1609561 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
1609500 TGCAACTTTT
1609510 ACTATTTCAAATTGAATTTCAAAATTA
1 ACTATTTCAAATTGAA-TTCAAAATTA
1609537 ACTATTTCAAATTGAATTCAAAATT
1 ACTATTTCAAATTGAATTCAAAATT
1609562 GGCTGCACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
ACTATTTCAAATTGAATTCAAAATTA
Found at i:1609562 original size:12 final size:13
Alignment explanation
Indices: 1609513--1609562 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
1609503 AACTTTTACT
1609513 ATTTC-AAATTGA
1 ATTTCAAAATTGA
*
1609525 ATTTCAAAATTAA
1 ATTTCAAAATTGA
1609538 CTATTTC-AAATTGA
1 --ATTTCAAAATTGA
1609552 A-TTCAAAATTG
1 ATTTCAAAATTG
1609563 GCTGCACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 6 0.19
14 6 0.19
15 5 0.16
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (13 bp):
ATTTCAAAATTGA
Found at i:1614210 original size:9 final size:9
Alignment explanation
Indices: 1614196--1614237 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
1614186 TTTCTCTCTT
*
1614196 TCTGCTATC
1 TCTGCTGTC
1614205 TCTGCTGTC
1 TCTGCTGTC
1614214 TCTGCTGTC
1 TCTGCTGTC
1614223 TCTGCTGTC
1 TCTGCTGTC
1614232 TCTGCT
1 TCTGCT
1614238 TGAGCCTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.02, C:0.33, G:0.19, T:0.45
Consensus pattern (9 bp):
TCTGCTGTC
Found at i:1614334 original size:27 final size:26
Alignment explanation
Indices: 1614296--1614347 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
1614286 TGCAACTTTT
1614296 ACTATTTCAAATTGAATTTCAAAATTA
1 ACTATTTCAAATTGAA-TTCAAAATTA
1614323 ACTATTTCAAATTGAATTCAAAATT
1 ACTATTTCAAATTGAATTCAAAATT
1614348 GGCTGCACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
ACTATTTCAAATTGAATTCAAAATTA
Found at i:1614348 original size:12 final size:13
Alignment explanation
Indices: 1614299--1614348 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
1614289 AACTTTTACT
1614299 ATTTC-AAATTGA
1 ATTTCAAAATTGA
*
1614311 ATTTCAAAATTAA
1 ATTTCAAAATTGA
1614324 CTATTTC-AAATTGA
1 --ATTTCAAAATTGA
1614338 A-TTCAAAATTG
1 ATTTCAAAATTG
1614349 GCTGCACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 6 0.19
14 6 0.19
15 5 0.16
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (13 bp):
ATTTCAAAATTGA
Found at i:1614844 original size:21 final size:22
Alignment explanation
Indices: 1614804--1614844 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1614794 ATACCGTAAG
*
1614804 TATATGATAATTATTATATATA
1 TATATGATAATTATCATATATA
*
1614826 TATAT-ATAATTATCCTATA
1 TATATGATAATTATCATATA
1614845 CACTATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
TATATGATAATTATCATATATA
Found at i:1615497 original size:21 final size:21
Alignment explanation
Indices: 1615458--1615497 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1615448 TATTAAAAAA
** *
1615458 ATATTTTATGTTTATATTTTT
1 ATATTTTATAATTAAATTTTT
1615479 ATATTTTATAATTAAATTT
1 ATATTTTATAATTAAATTT
1615498 AAATAAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTTT
Found at i:1616425 original size:36 final size:35
Alignment explanation
Indices: 1616385--1616532 Score: 107
Period size: 34 Copynumber: 4.3 Consensus size: 35
1616375 TGGAATGGAC
1616385 ATAATA-AAAAAATTAAAATATTATATAAAGTATGAT
1 ATAATATAAAAAATTAAAATATTATATAAA-TAT-AT
1616421 ATAATATAAATAAA-T-AAATATTATCA-AAATATAT
1 ATAATATAAA-AAATTAAAATATTAT-ATAAATATAT
** *
1616455 ATAATATAAATTATTAAAA-ATAATATAAA-ATAT
1 ATAATATAAAAAATTAAAATATTATATAAATATAT
* * * * *
1616488 -TATTTTAAATATAATTATAAT-TAATAAAAATATAT
1 ATAATATAAA-A-AATTAAAATATTATATAAATATAT
1616523 A-AATATAAAA
1 ATAATATAAAA
1616533 TAAATAAACG
Statistics
Matches: 90, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
32 7 0.08
33 6 0.07
34 35 0.39
35 16 0.18
36 18 0.20
37 5 0.06
38 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (35 bp):
ATAATATAAAAAATTAAAATATTATATAAATATAT
Found at i:1616438 original size:25 final size:26
Alignment explanation
Indices: 1616407--1616465 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
1616397 TTAAAATATT
*
1616407 ATATAAAGTATGAT-ATAATATAAATA
1 ATATAAA-TATGATCAAAATATAAATA
* *
1616433 A-ATAAATATTATCAAAATATATATA
1 ATATAAATATGATCAAAATATAAATA
1616458 ATATAAAT
1 ATATAAAT
1616466 TATTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.18
25 16 0.57
26 7 0.25
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (26 bp):
ATATAAATATGATCAAAATATAAATA
Found at i:1616439 original size:8 final size:9
Alignment explanation
Indices: 1616421--1616483 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
1616411 AAAGTATGAT
1616421 ATAATATAA
1 ATAATATAA
1616430 ATAA-ATAA
1 ATAATATAA
* *
1616438 ATATTATCA
1 ATAATATAA
*
1616447 A-AATATAT
1 ATAATATAA
1616455 ATAATATAA
1 ATAATATAA
* *
1616464 ATTATTAAAA
1 A-TAATATAA
1616474 ATAATATAA
1 ATAATATAA
1616483 A
1 A
1616484 ATATTATTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
8 12 0.29
9 22 0.54
10 7 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
ATAATATAA
Found at i:1616441 original size:19 final size:19
Alignment explanation
Indices: 1616419--1616483 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
1616409 ATAAAGTATG
1616419 ATATAATATAAATAAATAA
1 ATATAATATAAATAAATAA
* *
1616438 ATAT--TAT-CA-AAATAT
1 ATATAATATAAATAAATAA
* *
1616453 ATATAATATAAATTATTAA
1 ATATAATATAAATAAATAA
*
1616472 AAATAATATAAA
1 ATATAATATAAA
1616484 ATATTATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
15 9 0.26
16 1 0.03
17 6 0.17
18 1 0.03
19 18 0.51
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAATATAAATAAATAA
Found at i:1616462 original size:34 final size:34
Alignment explanation
Indices: 1616400--1616540 Score: 109
Period size: 36 Copynumber: 4.1 Consensus size: 34
1616390 AAAAAAATTA
1616400 AAATATTATATAAAGTATGATATAATATAAATA-AAT
1 AAATATTATA-AAA-TAT-ATATAATATAAATATAAT
1616436 AAATATTATCAAAATATATATAATATAAATTATTAA-
1 AAATATTAT-AAAATATATATAATATAAA-TA-TAAT
* *
1616472 AAATAATATAAAATAT-TAT--TTTAAATATAATT
1 AAATATTATAAAATATATATAATATAAATATAA-T
*
1616504 ATAAT-TAATAAAA-ATATATAAATATAAA-ATAAAT
1 A-AATATTATAAAATATATAT-AATATAAATAT-AAT
1616538 AAA
1 AAA
1616541 CGAATTATGA
Statistics
Matches: 88, Mismatches: 5, Indels: 27
0.73 0.04 0.22
Matches are distributed among these distances:
30 3 0.03
31 4 0.05
32 15 0.17
33 5 0.06
34 19 0.22
35 19 0.22
36 20 0.23
37 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (34 bp):
AAATATTATAAAATATATATAATATAAATATAAT
Found at i:1616467 original size:24 final size:25
Alignment explanation
Indices: 1616423--1616483 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
1616413 AGTATGATAT
*
1616423 AATATAAATAAATAAATATTATCAA
1 AATATATATAAATAAATATTATCAA
1616448 AATATATATAATATAAATTATTA--AA
1 AATATATATAA-ATAAA-TATTATCAA
1616473 AATA-ATATAAA
1 AATATATATAAA
1616484 ATATTATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.03
24 6 0.18
25 16 0.48
26 5 0.15
27 5 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
AATATATATAAATAAATATTATCAA
Found at i:1616496 original size:24 final size:26
Alignment explanation
Indices: 1616421--1616487 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
1616411 AAAGTATGAT
*
1616421 ATAATATAAATAAATAAA-TATTATCAAA
1 ATAATATAAA-ATATAAATTATTA--AAA
*
1616449 AT-ATATATAATATAAATTATTAAAA
1 ATAATATAAAATATAAATTATTAAAA
1616474 ATAATATAAAATAT
1 ATAATATAAAATAT
1616488 TATTTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 5 0.15
26 16 0.47
27 11 0.32
28 2 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (26 bp):
ATAATATAAAATATAAATTATTAAAA
Found at i:1616501 original size:24 final size:24
Alignment explanation
Indices: 1616447--1616540 Score: 68
Period size: 24 Copynumber: 3.8 Consensus size: 24
1616437 AATATTATCA
*
1616447 AAATAT-ATATAATATAAATTATT
1 AAATATAATATAAAATAAATTATT
* *
1616470 AAAAATAATATAAAATATTATT-TT
1 AAATATAATATAAAATA-AATTATT
*
1616494 AAATATAATTATAATTAATAAAAATATAT
1 AAATATAA-TATAA--AAT-AAATTAT-T
*
1616523 AAATATAAAAT-AAATAAA
1 AAATATAATATAAAATAAA
1616541 CGAATTATGA
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
23 5 0.09
24 21 0.38
25 11 0.20
27 6 0.11
28 4 0.07
29 9 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATATAATATAAAATAAATTATT
Found at i:1620246 original size:11 final size:11
Alignment explanation
Indices: 1620232--1620271 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1620222 ATTAAAATAT
*
1620232 AATATTATAAA
1 AATATAATAAA
*
1620243 AATATAATATA
1 AATATAATAAA
*
1620254 AATATAATACA
1 AATATAATAAA
1620265 AATATAA
1 AATATAA
1620272 AAATATCTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
AATATAATAAA
Found at i:1620262 original size:16 final size:17
Alignment explanation
Indices: 1620225--1620257 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1620215 AAAAATAATT
*
1620225 AAAATATAATAT-TATA
1 AAAATATAATATAAATA
1620241 AAAATATAATATAAATA
1 AAAATATAATATAAATA
1620258 TAATACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 12 0.80
17 3 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATAATATAAATA
Done.