Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold283
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: 2945114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 15
Found at i:2163499 original size:40 final size:41
Alignment explanation
Indices: 2163449--2163535 Score: 149
Period size: 40 Copynumber: 2.1 Consensus size: 41
2163439 TTCCAGATCT
2163449 AGAAAACAATGATAAAGAAAATTTT-GAAGAGAAAATAGAA
1 AGAAAACAATGATAAAGAAAATTTTCGAAGAGAAAATAGAA
* *
2163489 AGAAATCAATGATAAAGAAACTTTTCGAAGAGAAAATAGAA
1 AGAAAACAATGATAAAGAAAATTTTCGAAGAGAAAATAGAA
2163530 AGAAAA
1 AGAAAA
2163536 TACTGCATGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
40 23 0.53
41 20 0.47
ACGTcount: A:0.61, C:0.05, G:0.17, T:0.17
Consensus pattern (41 bp):
AGAAAACAATGATAAAGAAAATTTTCGAAGAGAAAATAGAA
Found at i:2165328 original size:26 final size:28
Alignment explanation
Indices: 2165294--2165346 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
2165284 TATATTTTTT
*
2165294 ATATATTTTTTATGTATATA-AAAAATC
1 ATATATTTTATATGTATATATAAAAATC
* *
2165321 ATAT-TTTTATATTTATTTATAAAAAT
1 ATATATTTTATATGTATATATAAAAAT
2165347 TATCTGATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
ATATATTTTATATGTATATATAAAAATC
Found at i:2169961 original size:22 final size:22
Alignment explanation
Indices: 2169916--2169961 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2169906 TACTTAATAA
* *
2169916 AAAATTATTTAAATTTAATTAT
1 AAAATTATATAAATTTAATCAT
2169938 AAAATTATATAAATATTAA-CAT
1 AAAATTATATAAAT-TTAATCAT
2169960 AA
1 AA
2169962 TAATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTATATAAATTTAATCAT
Found at i:2170032 original size:22 final size:21
Alignment explanation
Indices: 2169991--2170032 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2169981 TAATTAATAA
**
2169991 AATAAAATTTTAAACTTTAAC
1 AATAAAATTTTAAAAATTAAC
2170012 AATAAAATTTATAAAAATTAA
1 AATAAAATTT-TAAAAATTAA
2170033 ATCACAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AATAAAATTTTAAAAATTAAC
Found at i:2171629 original size:47 final size:43
Alignment explanation
Indices: 2171527--2171639 Score: 120
Period size: 46 Copynumber: 2.6 Consensus size: 43
2171517 AGTTGTGAAT
* *
2171527 ATTATTTATA-TTTATTTAAATTTGATTTGATTTAAAATATAA
1 ATTATTTATATTTTATTTATATTTGATTTGATTCAAAATATAA
* * *
2171569 ATTTTTTAAATTTTATTTATATTTATATTATGAATTCAAAATATAA
1 ATTATTTATATTTTATTTATATTT-GATT-TG-ATTCAAAATATAA
* *
2171615 GTTATTCTATATTTTATATATATTT
1 ATTATT-TATATTTTATTTATATTT
2171640 TAAGATCCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
42 8 0.14
43 12 0.21
44 3 0.05
45 2 0.04
46 16 0.28
47 16 0.28
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (43 bp):
ATTATTTATATTTTATTTATATTTGATTTGATTCAAAATATAA
Found at i:2174401 original size:22 final size:22
Alignment explanation
Indices: 2174360--2174401 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2174350 CCAATAGAGA
* * *
2174360 TGATTTAATTTTATATATTATT
1 TGATTTAATTTAAAAAATTATT
2174382 TGATTTAATTTAAAAAATTA
1 TGATTTAATTTAAAAAATTA
2174402 AATTATATTA
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:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TGATTTAATTTAAAAAATTATT
Found at i:2175139 original size:2 final size:2
Alignment explanation
Indices: 2175132--2175178 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
2175122 TTAAATTTAA
* * *
2175132 AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2175174 AT AT A
1 AT AT A
2175179 GTGAGAGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2179976 original size:18 final size:18
Alignment explanation
Indices: 2179950--2179985 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2179940 ATACATTTAT
*
2179950 CATTTAAAATAACATTAA
1 CATTAAAAATAACATTAA
2179968 CATTAAAAATAACATTAA
1 CATTAAAAATAACATTAA
2179986 GGAATTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (18 bp):
CATTAAAAATAACATTAA
Found at i:2180540 original size:20 final size:21
Alignment explanation
Indices: 2180501--2180542 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2180491 GAACTGTTGC
*
2180501 TGGGAGCTCGTTGGCAACATG
1 TGGGAGCTCATTGGCAACATG
*
2180522 TGGGAG-TCATTGGCTACATG
1 TGGGAGCTCATTGGCAACATG
2180542 T
1 T
2180543 TCGAAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.19, C:0.17, G:0.36, T:0.29
Consensus pattern (21 bp):
TGGGAGCTCATTGGCAACATG
Found at i:2188244 original size:3 final size:3
Alignment explanation
Indices: 2188238--2188267 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2188228 AAAGCAAAAA
2188238 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2188268 TCCATAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2188356 original size:11 final size:11
Alignment explanation
Indices: 2188330--2188372 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
2188320 CACTTAAAAT
2188330 AATTTTTAT-A
1 AATTTTTATAA
*
2188340 ATTTTTTATAA
1 AATTTTTATAA
*
2188351 AATTTTTAAAA
1 AATTTTTATAA
*
2188362 AATTATTATAA
1 AATTTTTATAA
2188373 TATATTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTTTATAA
Found at i:2188521 original size:9 final size:8
Alignment explanation
Indices: 2188498--2188560 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 8
2188488 AAAATTAAAT
2188498 TATTTTATA
1 TATTTT-TA
*
2188507 TGTTTTTA
1 TATTTTTA
2188515 TAATTTTTA
1 T-ATTTTTA
2188524 TATTATTTA
1 TATT-TTTA
2188533 TATTTATT-
1 TATTT-TTA
*
2188541 TA-ATTT-
1 TATTTTTA
2188547 TATTTTTA
1 TATTTTTA
2188555 TATTTT
1 TATTTT
2188561 ATTATTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
6 4 0.09
7 4 0.09
8 15 0.33
9 22 0.49
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
TATTTTTA
Found at i:2188527 original size:26 final size:24
Alignment explanation
Indices: 2188498--2188565 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 24
2188488 AAAATTAAAT
2188498 TATTTTATATGTTTTTATAATTTTTA
1 TATTTTATAT-TTTTTATAA-TTTTA
*
2188524 TATTATTTATATTTATT-TAATTTTA
1 TA-T-TTTATATTTTTTATAATTTTA
2188549 T-TTTTATATTTTATTAT
1 TATTTTATATTTT-TTAT
2188566 TTATTTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
22 9 0.25
23 3 0.08
24 1 0.03
25 6 0.17
26 5 0.14
27 5 0.14
28 7 0.19
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (24 bp):
TATTTTATATTTTTTATAATTTTA
Found at i:2188539 original size:10 final size:10
Alignment explanation
Indices: 2188501--2188575 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
2188491 ATTAAATTAT
2188501 TTTATATGTT-
1 TTTATAT-TTA
*
2188511 TTTATAATT-
1 TTTATATTTA
2188520 TTTATA-TTA
1 TTTATATTTA
2188529 TTTATATTTA
1 TTTATATTTA
2188539 TTTA-ATTTTA
1 TTTATA-TTTA
* *
2188549 TTTTTATAT-
1 TTTATATTTA
2188558 TTTATTATTTA
1 TTTA-TATTTA
2188569 TTTATAT
1 TTTATAT
2188576 AAATTATATA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
8 2 0.04
9 18 0.33
10 29 0.54
11 5 0.09
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (10 bp):
TTTATATTTA
Found at i:2188551 original size:20 final size:20
Alignment explanation
Indices: 2188498--2188576 Score: 69
Period size: 20 Copynumber: 4.1 Consensus size: 20
2188488 AAAATTAAAT
2188498 TATTTT-ATATGTT-TTTATA
1 TATTTTAATAT-TTATTTATA
*
2188517 -ATTTTTATA-TTATTTATA
1 TATTTTAATATTTATTTATA
* *
2188535 TTTATTTAAT-TTTATTTTTA
1 TAT-TTTAATATTTATTTATA
*
2188555 TATTTTATTATTTATTTATA
1 TATTTTAATATTTATTTATA
2188575 TA
1 TA
2188577 AATTATATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
17 2 0.04
18 11 0.23
19 9 0.19
20 26 0.54
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (20 bp):
TATTTTAATATTTATTTATA
Found at i:2188559 original size:13 final size:14
Alignment explanation
Indices: 2188536--2188569 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2188526 TTATTTATAT
2188536 TTATTTA-ATTTTA
1 TTATTTATATTTTA
2188549 TT-TTTATATTTTA
1 TTATTTATATTTTA
2188562 TTATTTAT
1 TTATTTAT
2188570 TTATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 10 0.53
14 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTATATTTTA
Found at i:2196461 original size:7 final size:6
Alignment explanation
Indices: 2196411--2196529 Score: 70
Period size: 6 Copynumber: 20.2 Consensus size: 6
2196401 GTTAGAATAT
* * * *
2196411 TTTATT TTTATA TTTA-C TTTATT TTTCATA -TTATA ATTATA TTTAATA
1 TTTATA TTTATA TTTATA TTTATA TTT-ATA TTTATA TTTATA TTT-ATA
* *
2196459 TTTTATT TTTATA TTTAT- TTTATA -TT-TA TTTAT- TTTTTA TGTTATA
1 -TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T-TTATA
* * * *
2196505 ATTATA TTTAAA ATTATA TATATA T
1 TTTATA TTTATA TTTATA TTTATA T
2196530 ACATTTTAAT
Statistics
Matches: 87, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
4 2 0.02
5 20 0.23
6 51 0.59
7 11 0.13
8 3 0.03
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.66
Consensus pattern (6 bp):
TTTATA
Found at i:2196481 original size:11 final size:11
Alignment explanation
Indices: 2196411--2196489 Score: 68
Period size: 11 Copynumber: 6.6 Consensus size: 11
2196401 GTTAGAATAT
2196411 TTTATTTTTATA
1 TTTA-TTTTATA
* *
2196423 TTTACTTTATT
1 TTTATTTTATA
*
2196434 TTTCATATTATAA
1 TTT-ATTTTAT-A
*
2196447 TTATATTTAATA
1 TT-TATTTTATA
2196459 TTTTATTTTTATA
1 -TTTA-TTTTATA
2196472 TTTATTTTATA
1 TTTATTTTATA
2196483 TTTATTT
1 TTTATTT
2196490 ATTTTTTATG
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
11 22 0.41
12 16 0.30
13 15 0.28
14 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTATTTTATA
Found at i:2196493 original size:32 final size:33
Alignment explanation
Indices: 2196421--2196514 Score: 94
Period size: 32 Copynumber: 3.1 Consensus size: 33
2196411 TTTATTTTTA
*
2196421 TATTTACTTTATTTTTCATATTATAATTATATT
1 TATTTATTTTATTTTTCATATTATAATTATATT
* *
2196454 TA-ATATTTTATTTTT-ATATT-T-ATT-T-TA
1 TATTTATTTTATTTTTCATATTATAATTATATT
* *
2196481 TATTTA-TTTATTTTTTATGTTATAATTATATT
1 TATTTATTTTATTTTTCATATTATAATTATATT
2196513 TA
1 TA
2196515 AAATTATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
27 12 0.24
28 7 0.14
29 4 0.08
30 4 0.08
31 6 0.12
32 14 0.29
33 2 0.04
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (33 bp):
TATTTATTTTATTTTTCATATTATAATTATATT
Found at i:2196592 original size:12 final size:12
Alignment explanation
Indices: 2196575--2196600 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2196565 ACCGATAAGG
2196575 CATCAGTCATCA
1 CATCAGTCATCA
2196587 CATCAGTCATCA
1 CATCAGTCATCA
2196599 CA
1 CA
2196601 GCTTAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.08, T:0.23
Consensus pattern (12 bp):
CATCAGTCATCA
Found at i:2198062 original size:12 final size:12
Alignment explanation
Indices: 2198045--2198070 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2198035 CTATGAGGTG
2198045 ATTTTTTTTAAT
1 ATTTTTTTTAAT
2198057 ATTTTTTTTAAT
1 ATTTTTTTTAAT
2198069 AT
1 AT
2198071 GTTGCAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
ATTTTTTTTAAT
Found at i:2206208 original size:23 final size:24
Alignment explanation
Indices: 2206177--2206230 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
2206167 CATAATCTGA
2206177 AAATATTT-AAATATTATAAA-TATT
1 AAATATTTAAAAT-TTA-AAATTATT
2206201 AAAT-TTTAAAATTTAAAATTATT
1 AAATATTTAAAATTTAAAATTATT
2206224 AAATATT
1 AAATATT
2206231 ATTTTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.11
23 14 0.52
24 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATATTTAAAATTTAAAATTATT
Found at i:2206216 original size:14 final size:15
Alignment explanation
Indices: 2206181--2206227 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
2206171 ATCTGAAAAT
2206181 ATTTAAATATTATAA
1 ATTTAAATATTATAA
*
2206196 ATATTAAATTTTA-AA
1 AT-TTAAATATTATAA
2206211 ATTTAAA-ATTATTAA
1 ATTTAAATATTA-TAA
2206226 AT
1 AT
2206228 ATTATTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 5 0.19
15 10 0.37
16 9 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTAAATATTATAA
Found at i:2206557 original size:2 final size:2
Alignment explanation
Indices: 2206550--2206574 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2206540 GGTTCTTAAC
2206550 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
2206575 GAGAGAGAGA
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:2206579 original size:2 final size:2
Alignment explanation
Indices: 2206574--2206616 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2206564 ATATATATAT
2206574 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2206616 A
1 A
2206617 CAAGGCAAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2211070 original size:2 final size:2
Alignment explanation
Indices: 2211063--2211100 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2211053 TCAAGAACAT
2211063 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
2211101 ACACAAGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2214112 original size:27 final size:26
Alignment explanation
Indices: 2214065--2214116 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2214055 CTTAAATTTG
* * *
2214065 ATAATATATTTATATTTTTTTATATC
1 ATAATATATTTAAAATATTTTATATC
2214091 ATAATTATATTTAAAATATTTTATAT
1 ATAA-TATATTTAAAATATTTTATAT
2214117 TTATATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
ATAATATATTTAAAATATTTTATATC
Found at i:2214169 original size:14 final size:14
Alignment explanation
Indices: 2214118--2214169 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
2214108 ATTTTATATT
2214118 TATATAAATTTTAA
1 TATATAAATTTTAA
* *
2214132 TATATTAATCATCTATAT
1 TATA-TAA--AT-TTTAA
2214150 TATATAAATTTTAA
1 TATATAAATTTTAA
2214164 TATATA
1 TATATA
2214170 TTTATATCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 13 0.43
15 5 0.17
17 5 0.17
18 7 0.23
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:2214181 original size:27 final size:27
Alignment explanation
Indices: 2214083--2214205 Score: 76
Period size: 27 Copynumber: 4.4 Consensus size: 27
2214073 TTTATATTTT
* *
2214083 TTTATATCATA-ATTATATTTAAAATAT-
1 TTTATATCATATA-AAT-TTTAATATATA
*
2214110 TTTATATTTATATAAATTTTAATATATTAA
1 TTTATA-TCATATAAATTTTAATATA-T-A
*
2214140 TCATCTATATTATATAAATTTTAATATATA
1 T--T-TATATCATATAAATTTTAATATATA
* *
2214170 TTTATATCATAT---TTTAAATATTTTA
1 TTTATATCATATAAATTTTAATA-TATA
2214195 TTTATATCATA
1 TTTATATCATA
2214206 ATTTATGTGA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
24 7 0.09
25 14 0.17
27 23 0.28
28 8 0.10
29 1 0.01
30 3 0.04
31 1 0.01
32 20 0.25
33 4 0.05
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTATATCATATAAATTTTAATATATA
Found at i:2214182 original size:32 final size:30
Alignment explanation
Indices: 2214100--2214205 Score: 93
Period size: 32 Copynumber: 3.7 Consensus size: 30
2214090 CATAATTATA
*
2214100 TTTAAAATATTT-TAT-AT-TTATATAAAT
1 TTTAATATATTTATATCATATTATATAAAT
*
2214127 TTTAATATATTAATCATCTATATTATATAAAT
1 TTTAATATATTTAT-ATC-ATATTATATAAAT
2214159 TTTAATATATATTTATATCATATT-T-TAAAT
1 TTT-A-ATATATTTATATCATATTATATAAAT
*
2214189 ATT--T-TATTTATATCATA
1 TTTAATATATTTATATCATA
2214206 ATTTATGTGA
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
25 13 0.19
26 1 0.01
27 10 0.15
28 1 0.01
29 2 0.03
30 7 0.10
31 3 0.04
32 18 0.26
33 4 0.06
34 9 0.13
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTAATATATTTATATCATATTATATAAAT
Found at i:2218164 original size:37 final size:37
Alignment explanation
Indices: 2218123--2218198 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
2218113 CAGATTAGCC
2218123 AGTGGAGAAGAAGAGATTATGAACGAACGATGATTGG
1 AGTGGAGAAGAAGAGATTATGAACGAACGATGATTGG
2218160 AGTGGAGAAGAAGAGATTATGAACGAACGATGATTGG
1 AGTGGAGAAGAAGAGATTATGAACGAACGATGATTGG
2218197 AG
1 AG
2218199 GAAGTCGCCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.41, C:0.05, G:0.36, T:0.18
Consensus pattern (37 bp):
AGTGGAGAAGAAGAGATTATGAACGAACGATGATTGG
Found at i:2218332 original size:3 final size:3
Alignment explanation
Indices: 2218324--2218349 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2218314 GGTTTTTGTA
2218324 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2218350 ATATTTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2222358 original size:32 final size:31
Alignment explanation
Indices: 2222299--2222358 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
2222289 AATATTTAAT
*
2222299 CATAATTAATTATAATAATATTCATTATACA
1 CATAATTAATTAAAATAATATTCATTATACA
*
2222330 CATAATATAATTAAAAATAA-ATTTATTAT
1 CATAAT-TAATT-AAAATAATATTCATTAT
2222359 CGTAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 6 0.24
32 13 0.52
33 6 0.24
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.42
Consensus pattern (31 bp):
CATAATTAATTAAAATAATATTCATTATACA
Found at i:2222436 original size:88 final size:88
Alignment explanation
Indices: 2222299--2222460 Score: 216
Period size: 88 Copynumber: 1.8 Consensus size: 88
2222289 AATATTTAAT
* * * * * * * *
2222299 CATAATTAATTATAATAATATTCATTATACACATAATATAATTAAAAATAAATTTATTATCGTAA
1 CATAATTAATTATAATAACATTCATTATACACATAACACAATCAAAAATAAAATCATGATCGCAA
2222364 TTTAAATATCTGATAAATTATTA
66 TTTAAATATCTGATAAATTATTA
* * * *
2222387 CATAATTAATTATATTAACATTCATTATACACGTAGCACAATCAGAAATAAAATCATGATCGCAA
1 CATAATTAATTATAATAACATTCATTATACACATAACACAATCAAAAATAAAATCATGATCGCAA
2222452 TTTAAATAT
66 TTTAAATAT
2222461 ATAATAGGTT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
88 62 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (88 bp):
CATAATTAATTATAATAACATTCATTATACACATAACACAATCAAAAATAAAATCATGATCGCAA
TTTAAATATCTGATAAATTATTA
Found at i:2223971 original size:16 final size:18
Alignment explanation
Indices: 2223945--2223979 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2223935 AATACGATTC
2223945 ATTTAATTATTTAT-TTT
1 ATTTAATTATTTATGTTT
2223962 ATTT-ATTATTTATGTTT
1 ATTTAATTATTTATGTTT
2223979 A
1 A
2223980 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTAATTATTTATGTTT
Found at i:2228824 original size:2 final size:2
Alignment explanation
Indices: 2228817--2228853 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2228807 TGCCACCTTA
2228817 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2228854 AAACATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2231316 original size:12 final size:12
Alignment explanation
Indices: 2231301--2231346 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
2231291 TGCAGCCAAT
2231301 TTTGAAATTCAA
1 TTTGAAATTCAA
*
2231313 TTTGAAATAGTAAA
1 TTTGAAAT--TCAA
2231327 TGTTGAAATTCAA
1 T-TTGAAATTCAA
2231340 TTTGAAA
1 TTTGAAA
2231347 CAGTGAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (12 bp):
TTTGAAATTCAA
Found at i:2231358 original size:27 final size:27
Alignment explanation
Indices: 2231302--2231358 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
2231292 GCAGCCAATT
* *
2231302 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
2231329 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
2231356 TTG
1 TTG
2231359 CATAGTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:2231423 original size:9 final size:9
Alignment explanation
Indices: 2231409--2231441 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2231399 AGAAGGCTCA
2231409 AGCAGAGAC
1 AGCAGAGAC
2231418 AGCAGAGAC
1 AGCAGAGAC
*
2231427 AGCAGAGAT
1 AGCAGAGAC
2231436 AGCAGA
1 AGCAGA
2231442 AAGAGAGAAA
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:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:2236094 original size:12 final size:12
Alignment explanation
Indices: 2236079--2236124 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
2236069 TGCAGCCAAT
2236079 TTTGAAATTCAA
1 TTTGAAATTCAA
*
2236091 TTTGAAATAGTAAA
1 TTTGAAAT--TCAA
2236105 TGTTGAAATTCAA
1 T-TTGAAATTCAA
2236118 TTTGAAA
1 TTTGAAA
2236125 CAGTGAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (12 bp):
TTTGAAATTCAA
Found at i:2236136 original size:27 final size:27
Alignment explanation
Indices: 2236080--2236136 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
2236070 GCAGCCAATT
* *
2236080 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
2236107 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
2236134 TTG
1 TTG
2236137 CATAGTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:2236201 original size:9 final size:9
Alignment explanation
Indices: 2236187--2236219 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2236177 AGAAGGCTCA
2236187 AGCAGAGAC
1 AGCAGAGAC
2236196 AGCAGAGAC
1 AGCAGAGAC
*
2236205 AGCAGAGAT
1 AGCAGAGAC
2236214 AGCAGA
1 AGCAGA
2236220 AAGAGAGAAA
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:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:2240872 original size:12 final size:12
Alignment explanation
Indices: 2240857--2240902 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
2240847 TGCAGCCAAT
2240857 TTTGAAATTCAA
1 TTTGAAATTCAA
*
2240869 TTTGAAATAGTAAA
1 TTTGAAAT--TCAA
2240883 TGTTGAAATTCAA
1 T-TTGAAATTCAA
2240896 TTTGAAA
1 TTTGAAA
2240903 CAGTGAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (12 bp):
TTTGAAATTCAA
Found at i:2240914 original size:27 final size:27
Alignment explanation
Indices: 2240858--2240914 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
2240848 GCAGCCAATT
* *
2240858 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
2240885 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
2240912 TTG
1 TTG
2240915 CATAGTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:2240979 original size:9 final size:9
Alignment explanation
Indices: 2240965--2240997 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2240955 AGAAGGCTCA
2240965 AGCAGAGAC
1 AGCAGAGAC
2240974 AGCAGAGAC
1 AGCAGAGAC
*
2240983 AGCAGAGAT
1 AGCAGAGAC
2240992 AGCAGA
1 AGCAGA
2240998 AAGAGAGAAA
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:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:2241869 original size:2 final size:2
Alignment explanation
Indices: 2241862--2241896 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2241852 TTAAAAAGCA
2241862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2241897 ATGGCAAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2244106 original size:6 final size:6
Alignment explanation
Indices: 2244091--2244124 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2244081 TTTAATTGTT
*
2244091 ATCACG ATCACA ATCACA ATCACA ATCACA ATCA
1 ATCACA ATCACA ATCACA ATCACA ATCACA ATCA
2244125 ATCACGATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.47, C:0.32, G:0.03, T:0.18
Consensus pattern (6 bp):
ATCACA
Found at i:2245993 original size:19 final size:21
Alignment explanation
Indices: 2245951--2245999 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
2245941 ATTATATATG
*
2245951 TAAATATGTTAAAAAATAACA
1 TAAATATATTAAAAAATAACA
*
2245972 TAAATATATT-AAAATTAA-A
1 TAAATATATTAAAAAATAACA
2245991 TAAATATAT
1 TAAATATAT
2246000 CATATGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 10 0.38
20 7 0.27
21 9 0.35
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAATATATTAAAAAATAACA
Found at i:2248986 original size:2 final size:2
Alignment explanation
Indices: 2248979--2249003 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2248969 GAAAATATTT
2248979 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 T
2249004 GCATGCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2260642 original size:2 final size:2
Alignment explanation
Indices: 2260635--2260659 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2260625 CCCTCTTATT
2260635 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2260660 GCAATAATGG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2262534 original size:2 final size:2
Alignment explanation
Indices: 2262527--2262553 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2262517 AATTATTCTG
2262527 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
2262554 GCTTTACAGT
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:2265200 original size:14 final size:14
Alignment explanation
Indices: 2265183--2265244 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
2265173 TGAATTTAAA
*
2265183 AATTTTAATTAATT
1 AATTTAAATTAATT
2265197 AATTTAAATTAA-T
1 AATTTAAATTAATT
** *
2265210 AA-AAAAATCAA-T
1 AATTTAAATTAATT
2265222 AATTTAAAATTAATT
1 AATTT-AAATTAATT
2265237 AATTTAAA
1 AATTTAAA
2265245 ATAAAAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
12 9 0.24
13 3 0.08
14 20 0.53
15 6 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTTAAATTAATT
Found at i:2265260 original size:22 final size:22
Alignment explanation
Indices: 2265227--2265269 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
2265217 TCAATAATTT
* *
2265227 AAAATTAATT-AATTTAAAATA
1 AAAAATAATTAAATTCAAAATA
2265248 AAAAATAATTTAAATTCAAAAT
1 AAAAATAA-TTAAATTCAAAAT
2265270 GACTCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAATAATTAAATTCAAAATA
Found at i:2265268 original size:17 final size:17
Alignment explanation
Indices: 2265219--2265261 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
2265209 TAAAAAAATC
*
2265219 AATAATTTAAAAT--TA
1 AATAATTTAAAATAAAA
*
2265234 ATTAATTTAAAATAAAA
1 AATAATTTAAAATAAAA
2265251 AATAATTTAAA
1 AATAATTTAAA
2265262 TTCAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 12 0.52
17 11 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATAATTTAAAATAAAA
Found at i:2266202 original size:15 final size:15
Alignment explanation
Indices: 2266184--2266223 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
2266174 AAAATTTTAA
2266184 AACTCAAAATAA-TC
1 AACTCAAAATAATTC
2266198 TAACTCAAAATAATTC
1 -AACTCAAAATAATTC
2266214 AACTCAAAAT
1 AACTCAAAAT
2266224 CAACTTATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 22 0.92
16 2 0.08
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (15 bp):
AACTCAAAATAATTC
Found at i:2270674 original size:2 final size:2
Alignment explanation
Indices: 2270667--2270700 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2270657 CGGAGAAGTG
2270667 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
2270701 GTAGGAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2273837 original size:20 final size:20
Alignment explanation
Indices: 2273799--2273848 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2273789 CTAGCTTCCA
*
2273799 AATTCAAATTTAACATAAAT
1 AATTCAAATTTAAAATAAAT
*
2273819 AATT-AAATTTAAAATTAA-
1 AATTCAAATTTAAAATAAAT
*
2273837 AATTAAAATTTA
1 AATTCAAATTTA
2273849 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 4 0.15
19 19 0.70
20 4 0.15
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTCAAATTTAAAATAAAT
Found at i:2273864 original size:27 final size:28
Alignment explanation
Indices: 2273826--2273880 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2273816 AATAATTAAA
2273826 TTTAAAATT-AAAATTAAAATT-TATTT
1 TTTAAAATTAAAAATTAAAATTATATTT
*
2273852 TTTAAAATATAAAAATTAAACTTATATTT
1 TTTAAAAT-TAAAAATTAAAATTATATTT
2273881 GTACTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 1 0.04
28 11 0.44
29 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTAAAATTAAAAATTAAAATTATATTT
Found at i:2278465 original size:54 final size:54
Alignment explanation
Indices: 2278406--2278517 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
2278396 TGGCAGAGTT
2278406 TTTCTCCTCGGTTAGCTTGGAAATGAGAGACCTTGTCTGCAATTAAGAAAAAAG
1 TTTCTCCTCGGTTAGCTTGGAAATGAGAGACCTTGTCTGCAATTAAGAAAAAAG
2278460 TTTCTCCTCGGTTAGCTTGGAAATGAGAGACCTTGTCTGCAATTAAGAAAAAAG
1 TTTCTCCTCGGTTAGCTTGGAAATGAGAGACCTTGTCTGCAATTAAGAAAAAAG
2278514 TTTC
1 TTTC
2278518 AGAATAGAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (54 bp):
TTTCTCCTCGGTTAGCTTGGAAATGAGAGACCTTGTCTGCAATTAAGAAAAAAG
Found at i:2281511 original size:13 final size:13
Alignment explanation
Indices: 2281493--2281518 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2281483 CCTCATTTCA
2281493 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
2281506 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
2281519 GTTTATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:2281895 original size:2 final size:2
Alignment explanation
Indices: 2281882--2281917 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2281872 CTCTTCTCTT
* *
2281882 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2281918 CATTTTTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2288103 original size:3 final size:3
Alignment explanation
Indices: 2288090--2288126 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
2288080 ATTTAACAGT
2288090 TTC TCTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2288127 ATCAAGTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:2291101 original size:2 final size:2
Alignment explanation
Indices: 2291096--2291120 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2291086 AAAAAAAAAA
2291096 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 A
2291121 ACTTGAGAGG
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2293936 original size:3 final size:3
Alignment explanation
Indices: 2293928--2293977 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2293918 ACTCTTACAC
2293928 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2293976 AT
1 AT
2293978 CTTCAAAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2297002 original size:29 final size:29
Alignment explanation
Indices: 2296970--2297046 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
2296960 TATAATAGAA
2296970 ATAAATATAAAATTAATTTAAGATATAAT
1 ATAAATATAAAATTAATTTAAGATATAAT
* *
2296999 ATAAATATAAAATTAATTTAATATATATT
1 ATAAATATAAAATTAATTTAAGATATAAT
**
2297028 ATATTTATATAAATTAATT
1 ATAAATATA-AAATTAATT
2297047 AATATTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 34 0.79
30 9 0.21
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (29 bp):
ATAAATATAAAATTAATTTAAGATATAAT
Found at i:2297008 original size:11 final size:11
Alignment explanation
Indices: 2296960--2297023 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
2296950 AAGGCTATTG
*
2296960 TATAATAGAAA
1 TATAATATAAA
2296971 TA-AATATAAA
1 TATAATATAAA
*
2296981 -ATTAATTTAAGA
1 TA-TAATATAA-A
2296993 TATAATATAAA
1 TATAATATAAA
* *
2297004 TATAAAATTAA
1 TATAATATAAA
*
2297015 TTTAATATA
1 TATAATATA
2297024 TATTATATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
9 1 0.02
10 7 0.17
11 24 0.59
12 8 0.20
13 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
TATAATATAAA
Found at i:2297037 original size:15 final size:15
Alignment explanation
Indices: 2296973--2297051 Score: 60
Period size: 16 Copynumber: 5.3 Consensus size: 15
2296963 AATAGAAATA
2296973 AATATAAAATTAATTT
1 AATAT-AAATTAATTT
* *
2296989 AAGAT--A-TAATATA
1 AATATAAATTAAT-TT
2297002 AATATAAAATTAATTT
1 AATAT-AAATTAATTT
*
2297018 AATATATATTATATTT
1 AATATAAATTA-ATTT
2297034 -ATATAAATTAA-TT
1 AATATAAATTAATTT
2297047 AATAT
1 AATAT
2297052 TAAAAATATA
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
12 4 0.08
13 8 0.16
14 5 0.10
15 14 0.28
16 15 0.30
17 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (15 bp):
AATATAAATTAATTT
Found at i:2297395 original size:26 final size:26
Alignment explanation
Indices: 2297347--2297400 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
2297337 TTTATTTTTA
* *
2297347 AGAAAATGAATCATATATCTATATAT
1 AGAAAATGAATCATACATCTATAAAT
* *
2297373 AGAAAATGAATCATACCTTTATAAAT
1 AGAAAATGAATCATACATCTATAAAT
2297399 AG
1 AG
2297401 CCAATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (26 bp):
AGAAAATGAATCATACATCTATAAAT
Found at i:2297493 original size:2 final size:2
Alignment explanation
Indices: 2297486--2297547 Score: 72
Period size: 2 Copynumber: 30.5 Consensus size: 2
2297476 CATTTAAGTT
* * *
2297486 TA TA TA TA TT TA TA TA TA GTC TA TA T- TA CCA 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
2297529 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
2297548 TGACTACACA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 2 0.04
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2297672 original size:11 final size:11
Alignment explanation
Indices: 2297656--2297682 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2297646 AGTTGGTATG
2297656 ATTATATTTGT
1 ATTATATTTGT
2297667 ATTATATTTGT
1 ATTATATTTGT
2297678 ATTAT
1 ATTAT
2297683 CTTTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (11 bp):
ATTATATTTGT
Found at i:2298987 original size:90 final size:90
Alignment explanation
Indices: 2298834--2299039 Score: 376
Period size: 90 Copynumber: 2.3 Consensus size: 90
2298824 GATAGTTACA
* *
2298834 TTCAACTCTGCAAGCCATTTCGTCAACAAAAAAGAATAATTAGAAAATTGAAGCATTTGGGAATT
1 TTCAACTGTACAAGCCATTTCGTCAACAAAAAAGAATAATTAGAAAATTGAAGCATTTGGGAATT
2298899 TGGTAGAGAAATGAAGTTTAAATTC
66 TGGTAGAGAAATGAAGTTTAAATTC
*
2298924 TTCAATTGTACAAGCCATTTCGTCAACAAAAAAGAATAATTAGAAAATTGAAGCATTTGGGAATT
1 TTCAACTGTACAAGCCATTTCGTCAACAAAAAAGAATAATTAGAAAATTGAAGCATTTGGGAATT
2298989 TGGTAGAGAAATGAAGTTTAAATTC
66 TGGTAGAGAAATGAAGTTTAAATTC
*
2299014 TTCAACTGTGCAAGCCATTTCGTCAA
1 TTCAACTGTACAAGCCATTTCGTCAA
2299040 GGCTATAAAA
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 111 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (90 bp):
TTCAACTGTACAAGCCATTTCGTCAACAAAAAAGAATAATTAGAAAATTGAAGCATTTGGGAATT
TGGTAGAGAAATGAAGTTTAAATTC
Found at i:2307239 original size:2 final size:2
Alignment explanation
Indices: 2307232--2307275 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2307222 CGAAGATTGC
*
2307232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
2307274 AT
1 AT
2307276 GCATGGAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2311569 original size:2 final size:2
Alignment explanation
Indices: 2311553--2311585 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2311543 TAAATAGCTG
*
2311553 AT AT AA AT A- 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
2311586 GATTTGACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2315282 original size:2 final size:2
Alignment explanation
Indices: 2315270--2315300 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2315260 TGAGAAGGGG
*
2315270 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2315301 TGGGATCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2321697 original size:11 final size:11
Alignment explanation
Indices: 2321681--2321710 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2321671 GATGCATGGA
2321681 ATATAGCACAC
1 ATATAGCACAC
2321692 ATATAGCACAC
1 ATATAGCACAC
2321703 ATATAGCA
1 ATATAGCA
2321711 TGGCAGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.23, G:0.10, T:0.20
Consensus pattern (11 bp):
ATATAGCACAC
Found at i:2325438 original size:39 final size:39
Alignment explanation
Indices: 2325384--2325461 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2325374 TTGTTCTGAG
2325384 CTTTGCTTAAAAACGACGAGTGATCAGTTCTAGGGTTAA
1 CTTTGCTTAAAAACGACGAGTGATCAGTTCTAGGGTTAA
2325423 CTTTGCTTAAAAACGACGAGTGATCAGTTCTAGGGTTAA
1 CTTTGCTTAAAAACGACGAGTGATCAGTTCTAGGGTTAA
2325462 AGGTCCCGGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (39 bp):
CTTTGCTTAAAAACGACGAGTGATCAGTTCTAGGGTTAA
Found at i:2327103 original size:19 final size:17
Alignment explanation
Indices: 2327079--2327127 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
2327069 TATGTAAATA
2327079 TAAATATAATATAATTAAT
1 TAAATATAATATAATT--T
* *
2327098 TAAATATATTAAAATTT
1 TAAATATAATATAATTT
2327115 TAAATATAA-ATAA
1 TAAATATAATATAA
2327128 GATAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.12
17 9 0.35
19 14 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATATAATATAATTT
Found at i:2327154 original size:14 final size:14
Alignment explanation
Indices: 2327135--2327167 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2327125 TAAGATAAAT
2327135 ATATTAAACATATC
1 ATATTAAACATATC
*
2327149 ATATTAATCATATC
1 ATATTAAACATATC
2327163 A-ATTA
1 ATATTA
2327168 TATTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATTAAACATATC
Found at i:2333489 original size:15 final size:15
Alignment explanation
Indices: 2333469--2333499 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2333459 TTTTTAATAT
2333469 TTTTTAAAAATTTAA
1 TTTTTAAAAATTTAA
*
2333484 TTTTTAATAATTTAA
1 TTTTTAAAAATTTAA
2333499 T
1 T
2333500 ACATTTATTT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTTAAAAATTTAA
Found at i:2335507 original size:3 final size:3
Alignment explanation
Indices: 2335499--2335537 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2335489 TCTTGATAGA
*
2335499 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2335538 GGTTCATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2337920 original size:5 final size:5
Alignment explanation
Indices: 2337912--2337941 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2337902 TAATAATATA
2337912 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
2337942 TATAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:2343867 original size:5 final size:5
Alignment explanation
Indices: 2343857--2343925 Score: 50
Period size: 5 Copynumber: 13.0 Consensus size: 5
2343847 ACAATGTAAA
* * *
2343857 AATAT AATAT AAATAT AATAT -ATTT AATAATT AAAAT AATAT ATTAAT
1 AATAT AATAT -AATAT AATAT AATAT AAT-A-T AATAT AATAT AAT-AT
*
2343905 AATAT AATGTT AATAT AATAT
1 AATAT AAT-AT AATAT AATAT
2343926 TATTTACATA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
4 3 0.06
5 30 0.60
6 14 0.28
7 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:2343885 original size:25 final size:25
Alignment explanation
Indices: 2343857--2343959 Score: 83
Period size: 25 Copynumber: 4.2 Consensus size: 25
2343847 ACAATGTAAA
2343857 AATATAATATAAATATAATATATTT
1 AATATAATATAAATATAATATATTT
2343882 -A-ATAAT-TAAA-ATAATATATTAAT
1 AATATAATATAAATATAATATATT--T
* *
2343905 AATATAATGTTAATATAATATTATTT
1 AATATAATATAAATATAATA-TATTT
* *
2343931 ACATA-AA-ATTAACATAATATATTT
1 A-ATATAATATAAATATAATATATTT
*
2343955 TATAT
1 AATAT
2343960 TTTATATATA
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
21 10 0.15
22 4 0.06
23 9 0.14
24 7 0.11
25 15 0.23
26 7 0.11
27 9 0.14
28 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (25 bp):
AATATAATATAAATATAATATATTT
Found at i:2343893 original size:23 final size:20
Alignment explanation
Indices: 2343860--2343907 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 20
2343850 ATGTAAAAAT
2343860 ATAATATAAATATAATATATTTA
1 ATAAT-TAAA-ATAATATA-TTA
2343883 ATAATTAAAATAATATATTA
1 ATAATTAAAATAATATATTA
2343903 ATAAT
1 ATAAT
2343908 ATAATGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.32
21 8 0.32
22 4 0.16
23 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATTAAAATAATATATTA
Found at i:2347254 original size:15 final size:16
Alignment explanation
Indices: 2347236--2347266 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2347226 TTAGAATTTA
2347236 AATATAAAT-ATTTTT
1 AATATAAATAATTTTT
2347251 AATATAAATAATTTTT
1 AATATAAATAATTTTT
2347267 TAAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATAAATAATTTTT
Found at i:2347271 original size:27 final size:29
Alignment explanation
Indices: 2347240--2347302 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 29
2347230 AATTTAAATA
* *
2347240 TAAATATTTT-TA-ATATAAATAATTTTT
1 TAAATATTTTATATATATAAAAAAATTTT
*
2347267 TAAAT-TTTTATATATTTAAAAAAATTTT
1 TAAATATTTTATATATATAAAAAAATTTT
*
2347295 AAAATATT
1 TAAATATT
2347303 AAATTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 4 0.14
27 7 0.24
28 16 0.55
29 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TAAATATTTTATATATATAAAAAAATTTT
Found at i:2347751 original size:2 final size:2
Alignment explanation
Indices: 2347746--2347774 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2347736 TATATAAAGA
2347746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2347775 CACACAGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2348614 original size:2 final size:2
Alignment explanation
Indices: 2348609--2348646 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2348599 CCTCCCCCCC
2348609 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2348647 GCTTTTCAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2349671 original size:3 final size:3
Alignment explanation
Indices: 2349663--2349694 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2349653 ATTCATAACT
*
2349663 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2349695 CATCATCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2351316 original size:2 final size:2
Alignment explanation
Indices: 2351309--2351341 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2351299 CTTCCCTTCT
2351309 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2351342 GTGTAAATTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2356662 original size:2 final size:2
Alignment explanation
Indices: 2356655--2356689 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2356645 ACATAATAGA
2356655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2356690 AAAGACAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2357142 original size:23 final size:19
Alignment explanation
Indices: 2357115--2357164 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 19
2357105 GGACTGCTAG
2357115 TAATTTTTTATATTTATTATTAA
1 TAATTTTTTA-ATTT-TTA--AA
2357138 TAATTTATTTAATTTTTAAA
1 TAATTT-TTTAATTTTTAAA
2357158 TAATTTT
1 TAATTTT
2357165 ATCAGTTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.04
20 8 0.31
22 3 0.12
23 10 0.38
24 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATTTTTTAATTTTTAAA
Found at i:2357144 original size:20 final size:20
Alignment explanation
Indices: 2357125--2357163 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2357115 TAATTTTTTA
2357125 TATTT-ATTATT-AATAATT
1 TATTTAATTATTAAATAATT
*
2357143 TATTTAATTTTTAAATAATT
1 TATTTAATTATTAAATAATT
2357163 T
1 T
2357164 TATCAGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTAATTATTAAATAATT
Found at i:2357272 original size:2 final size:2
Alignment explanation
Indices: 2357255--2357304 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
2357245 ATAACTATTT
*
2357255 TA TA TA -A TA -A TT 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
2357295 TA TA TA TA TA
1 TA TA TA TA TA
2357305 GTAGAACTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2357702 original size:39 final size:39
Alignment explanation
Indices: 2357648--2357725 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2357638 ACCTAGTAAG
2357648 CTATTAATTATTTAAAAATCAAAGATGGACACTTGGGGC
1 CTATTAATTATTTAAAAATCAAAGATGGACACTTGGGGC
2357687 CTATTAATTATTTAAAAATCAAAGATGGACACTTGGGGC
1 CTATTAATTATTTAAAAATCAAAGATGGACACTTGGGGC
2357726 ACTTGGGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (39 bp):
CTATTAATTATTTAAAAATCAAAGATGGACACTTGGGGC
Found at i:2357771 original size:17 final size:18
Alignment explanation
Indices: 2357749--2357782 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2357739 TTAAAGATGC
2357749 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
2357766 AATTATATTATTTATTT
1 AATTATATTATTTATTT
2357783 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:2357783 original size:17 final size:17
Alignment explanation
Indices: 2357749--2357800 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2357739 TTAAAGATGC
2357749 AATTATATT-TTTATTTT
1 AATTATATTATTTA-TTT
2357766 AATTATATTATTTATTT
1 AATTATATTATTTATTT
*
2357783 -ATT-TATTA-ATATTT
1 AATTATATTATTTATTT
2357797 AATT
1 AATT
2357801 CGAAATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 3 0.09
17 12 0.38
18 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTATATTATTTATTT
Found at i:2362876 original size:17 final size:18
Alignment explanation
Indices: 2362854--2362887 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2362844 TTAAAGATGC
2362854 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
2362871 AATTATATTATTTATTT
1 AATTATATTATTTATTT
2362888 ATTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:2362888 original size:17 final size:17
Alignment explanation
Indices: 2362854--2362905 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2362844 TTAAAGATGC
2362854 AATTATATT-TTTATTTT
1 AATTATATTATTTA-TTT
2362871 AATTATATTATTTATTT
1 AATTATATTATTTATTT
*
2362888 -ATT-TATTA-ATATTT
1 AATTATATTATTTATTT
2362902 AATT
1 AATT
2362906 CGAAAGACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 3 0.09
17 12 0.38
18 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTATATTATTTATTT
Found at i:2363396 original size:2 final size:2
Alignment explanation
Indices: 2363389--2363418 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2363379 CCGTGAAGAA
2363389 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
2363419 GTGAATGAAA
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):
AT
Found at i:2364131 original size:2 final size:2
Alignment explanation
Indices: 2364118--2364152 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2364108 CTTCAAACCG
2364118 TA TA TA -A T- 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
2364153 GAATATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2364605 original size:2 final size:2
Alignment explanation
Indices: 2364593--2364624 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2364583 GGATTCACAT
*
2364593 TA TA TA AA 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
2364625 AAGAACCTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2367268 original size:2 final size:2
Alignment explanation
Indices: 2367257--2367291 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2367247 TGTTTATTAA
2367257 TC TC -C TC TC 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 TC TC TC TC TC
2367292 GTTCTCGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:2376628 original size:29 final size:27
Alignment explanation
Indices: 2376596--2376655 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 27
2376586 AATTAATTTA
*
2376596 AAATATAAATTTTATTTATATTCATAAGT
1 AAATAT-AA-TTTATTTATATTCATAAAT
*
2376625 -AA-ATAATTTATTTATATTTATAAAT
1 AAATATAATTTATTTATATTCATAAAT
2376650 AAATAT
1 AAATAT
2376656 TTTAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
25 17 0.63
26 4 0.15
27 4 0.15
28 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
AAATATAATTTATTTATATTCATAAAT
Found at i:2376635 original size:25 final size:25
Alignment explanation
Indices: 2376606--2376659 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
2376596 AAATATAAAT
*
2376606 TTTATTTATATTCATAAGTAAATAA
1 TTTATTTATATTCATAAATAAATAA
* *
2376631 TTTATTTATATTTATAAATAAATAT
1 TTTATTTATATTCATAAATAAATAA
2376656 TTTA
1 TTTA
2376660 AAATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTATTTATATTCATAAATAAATAA
Found at i:2376752 original size:28 final size:28
Alignment explanation
Indices: 2376683--2376752 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
2376673 TTAATTTATT
2376683 TTTTAAATATATTTTTATTAAAATTTTAA
1 TTTTAAATA-ATTTTTATTAAAATTTTAA
*
2376712 TAATTAAAT-ATTTTTATT-AAATTTTAGA
1 T-TTTAAATAATTTTTATTAAAATTTTA-A
2376740 TTTTAAATAATTT
1 TTTTAAATAATTT
2376753 AATATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 14 0.39
28 15 0.42
29 1 0.03
30 6 0.17
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
TTTTAAATAATTTTTATTAAAATTTTAA
Found at i:2386152 original size:12 final size:12
Alignment explanation
Indices: 2386135--2386160 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2386125 TCGTAAATGG
2386135 TGCTTTTTCTCA
1 TGCTTTTTCTCA
2386147 TGCTTTTTCTCA
1 TGCTTTTTCTCA
2386159 TG
1 TG
2386161 TAACAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.12, T:0.58
Consensus pattern (12 bp):
TGCTTTTTCTCA
Found at i:2390370 original size:2 final size:2
Alignment explanation
Indices: 2390363--2390392 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2390353 CTCATTGCTG
*
2390363 TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2390393 AATTCAGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:2400016 original size:7 final size:7
Alignment explanation
Indices: 2400004--2400044 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
2399994 TGATAAAAAT
2400004 TATATAA
1 TATATAA
2400011 TATATAA
1 TATATAA
2400018 -ATATAA
1 TATATAA
*
2400024 AAT-TAA
1 TATATAA
*
2400030 TATATAT
1 TATATAA
2400037 TATATAA
1 TATATAA
2400044 T
1 T
2400045 TAAAAAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATATAA
Found at i:2403232 original size:16 final size:17
Alignment explanation
Indices: 2403213--2403252 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2403203 AATAAAATAA
2403213 TATATAAAT-ATATTTT
1 TATATAAATAATATTTT
2403229 TATA-AAATAATATTTT
1 TATATAAATAATATTTT
*
2403245 TAAATAAA
1 TATATAAA
2403253 ATGATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 14 0.67
17 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATAAATAATATTTT
Found at i:2403270 original size:21 final size:21
Alignment explanation
Indices: 2403244--2403283 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2403234 AATAATATTT
2403244 TTAAATAAAATG-ATATATTAG
1 TTAAATAAAA-GAATATATTAG
*
2403265 TTAAATGAAAGAATATATT
1 TTAAATAAAAGAATATATT
2403284 TTTTAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTAAATAAAAGAATATATTAG
Found at i:2406519 original size:52 final size:52
Alignment explanation
Indices: 2406459--2406562 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
2406449 TGATACATTT
2406459 CCTTTATGCATAACTGTATACTTAATTATATTTTTAAATTTATAATTTAGTG
1 CCTTTATGCATAACTGTATACTTAATTATATTTTTAAATTTATAATTTAGTG
2406511 CCTTTATGCATAACTGTATACTTAATTATATTTTTAAATTTATAATTTAGTG
1 CCTTTATGCATAACTGTATACTTAATTATATTTTTAAATTTATAATTTAGTG
2406563 GGAGGTTGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.50
Consensus pattern (52 bp):
CCTTTATGCATAACTGTATACTTAATTATATTTTTAAATTTATAATTTAGTG
Found at i:2406718 original size:21 final size:21
Alignment explanation
Indices: 2406668--2406720 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
2406658 AAAAGGTATC
2406668 TTTGAATGAAATGATGCATTG
1 TTTGAATGAAATGATGCATTG
* * * *
2406689 GTTGGATGAAA-GAATGTATTT
1 TTTGAATGAAATG-ATGCATTG
2406710 TTTGAATGAAA
1 TTTGAATGAAA
2406721 AAAATACAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.38
Consensus pattern (21 bp):
TTTGAATGAAATGATGCATTG
Found at i:2408538 original size:2 final size:2
Alignment explanation
Indices: 2408531--2408569 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2408521 CAGAAGAAAA
*
2408531 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2408570 AATGACGATC
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:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2409382 original size:2 final size:2
Alignment explanation
Indices: 2409375--2409400 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2409365 AGGACAAGGA
2409375 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
2409401 GTAGTCGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2414170 original size:14 final size:13
Alignment explanation
Indices: 2414147--2414183 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2414137 ACATGTATGC
2414147 TTCCTTCTTTTTT
1 TTCCTTCTTTTTT
2414160 TTCCTT-TCTTTTT
1 TTCCTTCT-TTTTT
2414173 TT-CTTCTTTTT
1 TTCCTTCTTTTT
2414184 CTACTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCCTTCTTTTTT
Found at i:2414522 original size:2 final size:2
Alignment explanation
Indices: 2414515--2414551 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2414505 ATCTCCTCAA
2414515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2414552 AAAGCGTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2419872 original size:2 final size:2
Alignment explanation
Indices: 2419865--2419901 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2419855 TTATTCTAGT
2419865 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
2419902 GCCAAATCTA
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:2420325 original size:34 final size:34
Alignment explanation
Indices: 2420235--2420363 Score: 142
Period size: 34 Copynumber: 3.9 Consensus size: 34
2420225 TAAATAGGTA
*
2420235 ATTTAGTGGTTTGTAATTATTGATTAAATGAGTG
1 ATTTAGTGGTTTGTCATTATTGATTAAATGAGTG
* *
2420269 ATTT-GATGATTTG-C--TGTTGATTAAAT-AGGTG
1 ATTTAG-TGGTTTGTCATTATTGATTAAATGA-GTG
* *
2420300 ATTTATTGGTTTGTCATTATTGATTAAATGAGTT
1 ATTTAGTGGTTTGTCATTATTGATTAAATGAGTG
* *
2420334 ATTTAGTGGTTTGTCATTTTTGACTAAATG
1 ATTTAGTGGTTTGTCATTATTGATTAAATG
2420364 GCTAAAAAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
30 1 0.01
31 24 0.31
32 1 0.01
33 1 0.01
34 50 0.64
35 1 0.01
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.49
Consensus pattern (34 bp):
ATTTAGTGGTTTGTCATTATTGATTAAATGAGTG
Found at i:2428764 original size:2 final size:2
Alignment explanation
Indices: 2428757--2428808 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
2428747 ACATACATAC
* *
2428757 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AG 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
2428799 AT AT AT AT AT
1 AT AT AT AT AT
2428809 CAGCCTTTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Done.