Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 16 of 28
Found at i:2458845 original size:15 final size:16
Alignment explanation
Indices: 2458812--2458846 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2458802 CTACGACAAG
*
2458812 TATTAAATATAATATA
1 TATTAAATATAAAATA
2458828 TATTAAATA-AAAATA
1 TATTAAATATAAAATA
2458843 TATT
1 TATT
2458847 TAGTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAAATATAAAATA
Found at i:2461908 original size:35 final size:35
Alignment explanation
Indices: 2461835--2461911 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
2461825 TACCATTAGG
* * *
2461835 ATTTTACATCCCAGGATGATACAAGCAGTAGTACT
1 ATTTTACATCCCAGGATGATACAAGCACTACTAAT
* *
2461870 ATTTTACATCCCAGG-TGAATATAGGCACTACTAAT
1 ATTTTACATCCCAGGATG-ATACAAGCACTACTAAT
2461905 ATTTTAC
1 ATTTTAC
2461912 GTTCTAGTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 34 0.94
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32
Consensus pattern (35 bp):
ATTTTACATCCCAGGATGATACAAGCACTACTAAT
Found at i:2462083 original size:35 final size:35
Alignment explanation
Indices: 2462044--2462119 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
2462034 CAGTGCTATT
* *
2462044 TTACATTCTAGGAGAATACAAGCACAAGTAGTATC
1 TTACATTCTAGGACAATACAAGAACAAGTAGTATC
* * *
2462079 TTACAGTCTAGGACAATACAAGAACTAGTAGTATT
1 TTACATTCTAGGACAATACAAGAACAAGTAGTATC
2462114 TTACAT
1 TTACAT
2462120 CCCGTGGGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (35 bp):
TTACATTCTAGGACAATACAAGAACAAGTAGTATC
Found at i:2463810 original size:2 final size:2
Alignment explanation
Indices: 2463803--2463830 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2463793 CCATCCCAAC
2463803 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
2463831 TTACCTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2470203 original size:22 final size:23
Alignment explanation
Indices: 2470176--2470231 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
2470166 TGTTTTTTGT
2470176 TAATATCAATAATTTAT-TATTAA
1 TAATATCAATAATTTATAT-TTAA
*
2470199 -AATATAGAAT-ATTTATATTTAA
1 TAATAT-CAATAATTTATATTTAA
2470221 TAATATCAATA
1 TAATATCAATA
2470232 CATATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATATCAATAATTTATATTTAA
Found at i:2470239 original size:48 final size:50
Alignment explanation
Indices: 2470122--2470239 Score: 111
Period size: 48 Copynumber: 2.4 Consensus size: 50
2470112 AATATTCAAA
** * * *
2470122 TAATAATATTTATAAATATTTATTATTTAAATAATAAAATATATTGTTTTT
1 TAATAATATCAAT-AATATTTATTATTAAAATAATAAAATATATTGATATT
** *
2470173 TGTTAATATCAAT-A-ATTTATTATTAAAAT-ATAGAATAT-TT-ATATT
1 TAATAATATCAATAATATTTATTATTAAAATAATAAAATATATTGATATT
2470218 TAATAATATCAATACATATTTA
1 TAATAATATCAATA-ATATTTA
2470240 AAATTAAATA
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
45 14 0.26
46 2 0.04
47 9 0.17
48 19 0.35
49 1 0.02
51 9 0.17
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (50 bp):
TAATAATATCAATAATATTTATTATTAAAATAATAAAATATATTGATATT
Found at i:2470269 original size:8 final size:8
Alignment explanation
Indices: 2470256--2470289 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2470246 AATATTAAGT
2470256 ATTTTTTA
1 ATTTTTTA
2470264 ATTTTTTA
1 ATTTTTTA
*
2470272 A-TTTTAA
1 ATTTTTTA
2470279 ATTTTTTA
1 ATTTTTTA
2470287 ATT
1 ATT
2470290 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
ATTTTTTA
Found at i:2470281 original size:15 final size:15
Alignment explanation
Indices: 2470258--2470289 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2470248 TATTAAGTAT
*
2470258 TTTTTAATTTTTTAA
1 TTTTAAATTTTTTAA
2470273 TTTTAAATTTTTTAA
1 TTTTAAATTTTTTAA
2470288 TT
1 TT
2470290 AAAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAAATTTTTTAA
Found at i:2470294 original size:14 final size:15
Alignment explanation
Indices: 2470263--2470295 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2470253 AGTATTTTTT
*
2470263 AATTTTTTAATTTTA
1 AATTTTTTAATTTAA
2470278 AATTTTTTAA-TTAA
1 AATTTTTTAATTTAA
2470292 AATT
1 AATT
2470296 AAATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
AATTTTTTAATTTAA
Found at i:2474475 original size:21 final size:22
Alignment explanation
Indices: 2474446--2474491 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2474436 TGTTCAGACA
** *
2474446 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2474468 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2474489 AGT
1 AGT
2474492 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2476458 original size:28 final size:28
Alignment explanation
Indices: 2476394--2476448 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
2476384 CAAATGCCAC
2476394 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
2476422 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
2476449 ATTTTTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:2476489 original size:24 final size:24
Alignment explanation
Indices: 2476430--2476498 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
2476420 TTCCTTTGTA
* * *
2476430 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
* *
2476456 TATGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
2476480 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
2476499 AATTTTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 21 0.60
26 14 0.40
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:2479440 original size:2 final size:2
Alignment explanation
Indices: 2479435--2479472 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2479425 CTCTCCCCCC
2479435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2479473 TCTTCGAAAT
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):
AT
Found at i:2479772 original size:12 final size:12
Alignment explanation
Indices: 2479752--2479785 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2479742 TACATAAATT
2479752 TATAATTATTTA
1 TATAATTATTTA
2479764 -ATAAATTATTTA
1 TAT-AATTATTTA
2479776 TATAATTATT
1 TATAATTATT
2479786 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.10
12 16 0.80
13 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATAATTATTTA
Found at i:2480352 original size:3 final size:3
Alignment explanation
Indices: 2480346--2480385 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2480336 ACTACTACTT
2480346 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2480386 AAATGATTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2480789 original size:42 final size:42
Alignment explanation
Indices: 2480695--2480789 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
2480685 GAAAGCACAT
*
2480695 TTATTATTTTA-TTATAATATAATTAATAATATTAATATTTTTA
1 TTATT-TTTTATTTATAATATAATTAAAAATATT-ATATTTTTA
*
2480738 TT-TTATTTATTTATAATATAATTAAAAATATT-TATGTTTTA
1 TTATTTTTTATTTATAATATAATTAAAAATATTATAT-TTTTA
2480779 TTATTTTTTAT
1 TTATTTTTTAT
2480790 CCATAACTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
40 3 0.07
41 11 0.24
42 30 0.65
43 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (42 bp):
TTATTTTTTATTTATAATATAATTAAAAATATTATATTTTTA
Found at i:2481277 original size:2 final size:2
Alignment explanation
Indices: 2481270--2481308 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2481260 TATGATTGGT
2481270 TA 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 TA T
2481309 TAACAACTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2483463 original size:12 final size:11
Alignment explanation
Indices: 2483433--2483475 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
2483423 GAAATACCTT
*
2483433 AAATATAATTA
1 AAATATAATAA
*
2483444 TAATATAATAA
1 AAATATAATAA
2483455 AATATATAAATAA
1 AA-ATAT-AATAA
2483468 AAATATAA
1 AAATATAA
2483476 CACGAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 12 0.44
12 8 0.30
13 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATATAATAA
Found at i:2486007 original size:12 final size:13
Alignment explanation
Indices: 2485990--2486020 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2485980 TAAAAGATAA
2485990 AAAATTA-TCTCT
1 AAAATTATTCTCT
2486002 AAAATTATTCTCT
1 AAAATTATTCTCT
2486015 AAAATT
1 AAAATT
2486021 GAAAAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAATTATTCTCT
Found at i:2488124 original size:16 final size:17
Alignment explanation
Indices: 2488085--2488129 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2488075 TTTATAGTAA
*
2488085 ATTAAGTATAAAAAATT
1 ATTAAATATAAAAAATT
*
2488102 ATATAAATATAAAATATT
1 AT-TAAATATAAAAAATT
2488120 -TTAAATATAA
1 ATTAAATATAA
2488130 TTATGACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.36
17 3 0.12
18 13 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTAAATATAAAAAATT
Found at i:2488157 original size:23 final size:25
Alignment explanation
Indices: 2488124--2488174 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
2488114 AATATTTTAA
*
2488124 ATATAATTATG-ACATAACA-AAAT
1 ATATAAATATGAACATAACATAAAT
*
2488147 ATATAAATATGAACATAATATAAAT
1 ATATAAATATGAACATAACATAAAT
2488172 ATA
1 ATA
2488175 AGAATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.42
24 7 0.29
25 7 0.29
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (25 bp):
ATATAAATATGAACATAACATAAAT
Found at i:2490320 original size:3 final size:3
Alignment explanation
Indices: 2490312--2490345 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2490302 AACAAAAATC
2490312 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2490346 GTATTTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2490381 original size:2 final size:2
Alignment explanation
Indices: 2490374--2490405 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2490364 ACTTGAGTTA
2490374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2490406 GCAGAGGTAG
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):
AT
Found at i:2491357 original size:22 final size:20
Alignment explanation
Indices: 2491320--2491362 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
2491310 ACTCAAACTA
*
2491320 ATTTAAATTAAAAAAATTAT
1 ATTTAAATTAAAAAAAATAT
*
2491340 ATTTAAAACTTAATAAAAATAT
1 ATTT-AAA-TTAAAAAAAATAT
2491362 A
1 A
2491363 CTAAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 3 0.16
22 12 0.63
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTTAAATTAAAAAAAATAT
Found at i:2492352 original size:16 final size:16
Alignment explanation
Indices: 2492333--2492375 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2492323 AATATTTTAT
2492333 ATTTATATAAAAATTA
1 ATTTATATAAAAATTA
* *
2492349 ATTTAT-TAATAATTT
1 ATTTATATAAAAATTA
2492364 ATATTATATAAA
1 AT-TTATATAAA
2492376 TTTAATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 9 0.41
16 10 0.45
17 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTATATAAAAATTA
Found at i:2492396 original size:18 final size:18
Alignment explanation
Indices: 2492314--2492417 Score: 70
Period size: 18 Copynumber: 5.4 Consensus size: 18
2492304 TTTATCATAT
2492314 TATATTTAA-AATATTT-
1 TATATTTAATAATATTTA
* *
2492330 TATATTTATATAAAAATTA
1 TATATTTA-ATAATATTTA
*
2492349 -ATTTATTAATAATTTATATTA
1 TATAT-TTAATAA--TAT-TTA
2492370 TATAAATTTAATAATATTTA
1 TAT--ATTTAATAATATTTA
2492390 TATATTTAATATCATATTTA
1 TATATTTAATA--ATATTTA
2492410 TATTATTT
1 TA-TATTT
2492418 TTTATATTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
16 8 0.12
17 1 0.01
18 20 0.29
19 3 0.04
20 16 0.23
21 11 0.16
22 2 0.03
23 7 0.10
24 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATTTAATAATATTTA
Found at i:2492424 original size:18 final size:18
Alignment explanation
Indices: 2492403--2492454 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2492393 ATTTAATATC
2492403 ATATTTATATTATTTTTT
1 ATATTTATATTATTTTTT
*
2492421 ATATTTA-ATTAATTATTT
1 ATATTTATATT-ATTTTTT
2492439 ATA-TTATATATATTTT
1 ATATTTATAT-TATTTT
2492455 ATAATCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 6 0.21
18 22 0.76
19 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTTATATTATTTTTT
Found at i:2492424 original size:30 final size:28
Alignment explanation
Indices: 2492387--2492474 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 28
2492377 TTAATAATAT
2492387 TTATATATTTAATATCATATTTATATTA
1 TTATATATTTAATATCATATTTATATTA
* *
2492415 TTTTTTATATTTAAT-TAATTATTTATATTA
1 --TTATATATTTAATATCA-TATTTATATTA
*
2492445 -TATATATTTTATAATCATATTTAATATTA
1 TTATATATTTAAT-ATCATATTT-ATATTA
2492474 T
1 T
2492475 CGTATCTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
27 10 0.21
28 5 0.10
29 10 0.21
30 23 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TTATATATTTAATATCATATTTATATTA
Found at i:2494012 original size:2 final size:2
Alignment explanation
Indices: 2494005--2494038 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2493995 CCAAGGCAAA
2494005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2494039 CATGCACCCA
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):
AT
Found at i:2495186 original size:12 final size:12
Alignment explanation
Indices: 2495151--2495192 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
2495141 ATTTTATACG
2495151 ATAAAA-ATAAT
1 ATAAAATATAAT
*
2495162 -TAAAATATTAT
1 ATAAAATATAAT
*
2495173 ATAAATTATAAT
1 ATAAAATATAAT
2495185 ATAAAATA
1 ATAAAATA
2495193 AAAAATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 5 0.20
11 4 0.16
12 16 0.64
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:2495249 original size:32 final size:32
Alignment explanation
Indices: 2495203--2495288 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 32
2495193 AAAAATTATA
* * *
2495203 TTAACATAAAATAAATATTTAATATTTTAATAT
1 TTAA-ATAATATAAATATTTAATATATTAAAAT
2495236 TTAAATAATATAAAT-TATTAATATATTAAAAT
1 TTAAATAATATAAATAT-TTAATATATTAAAAT
*
2495268 TTATATAAATATAATATATTT
1 TTAAAT-AATATAA-ATATTT
2495289 TAAAATATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
31 1 0.02
32 28 0.62
33 11 0.24
34 4 0.09
35 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
TTAAATAATATAAATATTTAATATATTAAAAT
Found at i:2495286 original size:27 final size:27
Alignment explanation
Indices: 2495232--2495320 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
2495222 TAATATTTTA
* *
2495232 ATATTTAAATA-ATATAAAT-TATTAAT
1 ATATTAAAATATATATAAATATAAT-AT
*
2495258 ATATTAAAATTTATATAAATATAATAT
1 ATATTAAAATATATATAAATATAATAT
* *
2495285 ATTTTAAAATATA-ATAAAGTAT-ATTT
1 ATATTAAAATATATATAAA-TATAATAT
2495311 ATA-TAAAATA
1 ATATTAAAATA
2495321 AATTAAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
25 7 0.13
26 19 0.36
27 24 0.45
28 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
ATATTAAAATATATATAAATATAATAT
Found at i:2495290 original size:20 final size:20
Alignment explanation
Indices: 2495266--2495321 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
2495256 ATATATTAAA
2495266 ATTTATATAAATATAA-TAT
1 ATTTATATAAATATAAGTAT
*
2495285 ATTT-TAAAATATAATAAAGTAT
1 ATTTATATAA-AT-AT-AAGTAT
2495307 ATTTATATAAA-ATAA
1 ATTTATATAAATATAA
2495322 ATTAAAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
18 4 0.13
19 8 0.27
20 4 0.13
21 2 0.07
22 8 0.27
23 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTATATAAATATAAGTAT
Found at i:2495297 original size:25 final size:24
Alignment explanation
Indices: 2495232--2495320 Score: 65
Period size: 26 Copynumber: 3.5 Consensus size: 24
2495222 TAATATTTTA
* *
2495232 ATATTTAAATAATATAAATTATTAAT
1 ATATTAAAAT-ATATAAAGTA-TAAT
2495258 ATATTAAAATTTATATAAA-TATAAT
1 ATATTAAAA--TATATAAAGTATAAT
2495283 ATATTTTAAAATATAATAAAGTAT-AT
1 ATA--TTAAAATAT-ATAAAGTATAAT
*
2495309 TTATATAAAATA
1 ATAT-TAAAATA
2495321 AATTAAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
24 1 0.02
25 17 0.31
26 19 0.35
27 16 0.30
28 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
ATATTAAAATATATAAAGTATAAT
Found at i:2495322 original size:20 final size:19
Alignment explanation
Indices: 2495266--2495323 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
2495256 ATATATTAAA
2495266 ATTTATAT-AAATATAATAT
1 ATTTATATAAAATA-AATAT
* *
2495285 ATTTTAAAATATAATAAAGTAT
1 A-TTT-ATATAAAATAAA-TAT
2495307 ATTTATATAAAATAAAT
1 ATTTATATAAAATAAAT
2495324 TAAAAAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
19 2 0.06
20 13 0.42
21 8 0.26
22 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTATATAAAATAAATAT
Found at i:2495856 original size:29 final size:30
Alignment explanation
Indices: 2495810--2495884 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
2495800 TTATATATTT
**
2495810 AAATTTAAATAATCATA-TAATATTTAAA-A
1 AAATTTAAATAAAAATATTAA-ATTTAAATA
2495839 AAATTTAAATAAAAATATTAAATTTAAATA
1 AAATTTAAATAAAAATATTAAATTTAAATA
*
2495869 ATATATATAAATAAAA
1 A-A-ATTTAAATAAAA
2495885 TAAGATTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 22 0.56
30 5 0.13
31 1 0.03
32 11 0.28
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATTTAAATAAAAATATTAAATTTAAATA
Found at i:2496884 original size:33 final size:32
Alignment explanation
Indices: 2496821--2496882 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
2496811 TCTATATTAT
* *
2496821 TAATTTATTTTTTAATATAAATATAATTTTAA
1 TAATTTATTTTTTAAAATAAACATAATTTTAA
2496853 TAATTTATTTTTTTAAAATAAACA-AATTTT
1 TAATTTA-TTTTTTAAAATAAACATAATTTT
2496883 TAGTTACTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
TAATTTATTTTTTAAAATAAACATAATTTTAA
Found at i:2496943 original size:22 final size:21
Alignment explanation
Indices: 2496911--2496952 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
2496901 AATATAATTT
2496911 TATTTTTAATATAAATATAAG
1 TATTTTTAATATAAATATAAG
2496932 TATTATTTAATATAAATATAA
1 TATT-TTTAATATAAATATAA
2496953 TTTTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TATTTTTAATATAAATATAAG
Found at i:2497086 original size:21 final size:20
Alignment explanation
Indices: 2497041--2497103 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
2497031 ATTATTGATT
*
2497041 TTAATCTTATTATTACAAT--
1 TTAAT-TTATTATTATAATAA
2497060 TTAATTATATTATTATAATAA
1 TTAATT-TATTATTATAATAA
*
2497081 TTAATTTCACTATTATAATAA
1 TTAATTT-ATTATTATAATAA
2497102 TT
1 TT
2497104 TTTTAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 1 0.03
19 16 0.42
20 1 0.03
21 20 0.53
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATTTATTATTATAATAA
Found at i:2497126 original size:15 final size:15
Alignment explanation
Indices: 2497106--2497140 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2497096 TAATAATTTT
*
2497106 TTAATTTTATTGAAA
1 TTAATTTTATCGAAA
2497121 TTAATTTTATCGAAA
1 TTAATTTTATCGAAA
2497136 TTAAT
1 TTAAT
2497141 GTAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (15 bp):
TTAATTTTATCGAAA
Found at i:2497419 original size:20 final size:22
Alignment explanation
Indices: 2497367--2497420 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
2497357 TTTTACATGT
*
2497367 AATTTTAATATAAAAATTTAATT
1 AATTTTAAT-TAAAAATTTAATA
*
2497390 AA-TTTGATTAAAAA-TTAA-A
1 AATTTTAATTAAAAATTTAATA
2497409 AATTTTAATTAA
1 AATTTTAATTAA
2497421 TTAAAATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.07
20 12 0.44
21 6 0.22
22 5 0.19
23 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTTTAATTAAAAATTTAATA
Found at i:2502530 original size:16 final size:16
Alignment explanation
Indices: 2502496--2502534 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2502486 GTCAAATGTT
2502496 TATTT-TTATTTTAAG
1 TATTTATTATTTTAAG
2502511 TATTTATTATATTTAA-
1 TATTTATTAT-TTTAAG
2502527 TATTTATT
1 TATTTATT
2502535 TAATGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 12 0.55
17 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TATTTATTATTTTAAG
Found at i:2504516 original size:32 final size:31
Alignment explanation
Indices: 2504450--2504516 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
2504440 TTATTTTTTA
* *
2504450 TTTTAATTTGATTTTAAATATTAATATAATT
1 TTTTAATTTGATTTTAAATATGAATATAAGT
*
2504481 TTTTAATATT-ATTTTAAATTATGATTATAAGT
1 TTTTAAT-TTGATTTTAAA-TATGAATATAAGT
2504513 TTTT
1 TTTT
2504517 GAGTCAAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (31 bp):
TTTTAATTTGATTTTAAATATGAATATAAGT
Found at i:2504824 original size:22 final size:22
Alignment explanation
Indices: 2504799--2504914 Score: 91
Period size: 22 Copynumber: 5.2 Consensus size: 22
2504789 AGCGTATTTA
2504799 GTGAGAATGTTAGGTGTGTTAG
1 GTGAGAATGTTAGGTGTGTTAG
*
2504821 GTGATGTAT-TT-GGTGAGAATGTTAG
1 GTGA-GAATGTTAGGT--G--TGTTAG
*
2504846 GT--G--TGTTAGGTGATGTGTTTG
1 GTGAGAATGTTAGGTG---TGTTAG
*
2504867 GTGAGAATATTAGGTGTGTTAG
1 GTGAGAATGTTAGGTGTGTTAG
2504889 GTGAGAATGTTAGGTGTGTTAG
1 GTGAGAATGTTAGGTGTGTTAG
2504911 GTGA
1 GTGA
2504915 TGTATTTGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 24
0.71 0.07 0.23
Matches are distributed among these distances:
20 2 0.03
21 12 0.16
22 40 0.53
23 5 0.07
25 16 0.21
ACGTcount: A:0.22, C:0.00, G:0.40, T:0.39
Consensus pattern (22 bp):
GTGAGAATGTTAGGTGTGTTAG
Found at i:2504830 original size:34 final size:34
Alignment explanation
Indices: 2504792--2504892 Score: 175
Period size: 34 Copynumber: 3.0 Consensus size: 34
2504782 TTTGTTAAGC
*
2504792 GTATTTAGTGAGAATGTTAGGTGTGTTAGGTGAT
1 GTATTTGGTGAGAATGTTAGGTGTGTTAGGTGAT
2504826 GTATTTGGTGAGAATGTTAGGTGTGTTAGGTGAT
1 GTATTTGGTGAGAATGTTAGGTGTGTTAGGTGAT
* *
2504860 GTGTTTGGTGAGAATATTAGGTGTGTTAGGTGA
1 GTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
2504893 GAATGTTAGG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.41
Consensus pattern (34 bp):
GTATTTGGTGAGAATGTTAGGTGTGTTAGGTGAT
Found at i:2504892 original size:56 final size:56
Alignment explanation
Indices: 2504832--2504943 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
2504822 TGATGTATTT
*
2504832 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATATTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATATTAGGTGTGTTA
*
2504888 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATATTAGGTGTGTTA
2504944 ACATGTATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (56 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATATTAGGTGTGTTA
Found at i:2509657 original size:34 final size:34
Alignment explanation
Indices: 2509619--2509749 Score: 253
Period size: 34 Copynumber: 3.9 Consensus size: 34
2509609 CTTTGTTAAG
2509619 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
2509653 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
2509687 TGTGTTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
2509721 TGTATTTGGTGAGAATGTTAGGTGTGTTA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTA
2509750 ACATGTATAT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 95 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:2509672 original size:25 final size:23
Alignment explanation
Indices: 2509642--2509744 Score: 74
Period size: 25 Copynumber: 4.4 Consensus size: 23
2509632 AATGTTAGGT
2509642 GTGTTAGGTGATGTATTTGGTGA
1 GTGTTAGGTGATGTATTTGGTGA
*
2509665 GAATGTTAGGTG-TG--TTAGGTGA
1 G--TGTTAGGTGATGTATTTGGTGA
* *
2509687 TGTGTTTGGTGA-GAATGTTAGGT--
1 -GTGTTAGGTGATGTAT-TT-GGTGA
2509710 GTGTTAGGTGATGTATTTGGTGA
1 GTGTTAGGTGATGTATTTGGTGA
2509733 GAATGTTAGGTG
1 G--TGTTAGGTG
2509745 TGTTAACATG
Statistics
Matches: 62, Mismatches: 5, Indels: 24
0.68 0.05 0.26
Matches are distributed among these distances:
21 12 0.19
22 19 0.31
23 7 0.11
24 3 0.05
25 21 0.34
ACGTcount: A:0.19, C:0.00, G:0.40, T:0.41
Consensus pattern (23 bp):
GTGTTAGGTGATGTATTTGGTGA
Found at i:2511240 original size:2 final size:2
Alignment explanation
Indices: 2511233--2511260 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2511223 AACAGTTTTG
2511233 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2511261 ACAAAACAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2513619 original size:2 final size:2
Alignment explanation
Indices: 2513608--2513649 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
2513598 GGGGAAATTC
* * *
2513608 TA TA TA -A TA TA TA TG TA TG TG 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
2513649 T
1 T
2513650 TATGCTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2513818 original size:11 final size:11
Alignment explanation
Indices: 2513802--2513827 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2513792 GCAACTGACC
2513802 TTTTTTTTAAT
1 TTTTTTTTAAT
2513813 TTTTTTTTAAT
1 TTTTTTTTAAT
2513824 TTTT
1 TTTT
2513828 AAACAGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:2525097 original size:17 final size:17
Alignment explanation
Indices: 2525072--2525114 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
2525062 ATATCCTTTC
2525072 ATAAAAATAATATAATA
1 ATAAAAATAATATAATA
*
2525089 ATAATAATAATATAATTA
1 ATAAAAATAATATAA-TA
2525107 ATTAAAAA
1 A-TAAAAA
2525115 ATTAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 14 0.64
18 3 0.14
19 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAAATAATATAATA
Found at i:2526245 original size:20 final size:20
Alignment explanation
Indices: 2526212--2526250 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2526202 TTATAATTTT
* *
2526212 AATTTTATATTAACATTATA
1 AATTTTACACTAACATTATA
*
2526232 AATTTTACACTAACTTTAT
1 AATTTTACACTAACATTAT
2526251 GTAATTTGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTTACACTAACATTATA
Found at i:2528126 original size:16 final size:17
Alignment explanation
Indices: 2528092--2528126 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2528082 CTTTCGTAGT
*
2528092 TTACATTTCTGCTTTGA
1 TTACATTTCTGCCTTGA
2528109 TTACATTTCT-CCTTGA
1 TTACATTTCTGCCTTGA
2528125 TT
1 TT
2528127 CAGCTATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.17, C:0.20, G:0.09, T:0.54
Consensus pattern (17 bp):
TTACATTTCTGCCTTGA
Found at i:2535447 original size:15 final size:17
Alignment explanation
Indices: 2535427--2535464 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
2535417 AATATATTTT
2535427 TTTAATTCAAA-TA-TA
1 TTTAATTCAAATTATTA
*
2535442 TTTAATTTAAATTATTA
1 TTTAATTCAAATTATTA
2535459 TTTAAT
1 TTTAAT
2535465 AATTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 2 0.10
17 8 0.40
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTCAAATTATTA
Found at i:2535454 original size:21 final size:19
Alignment explanation
Indices: 2535416--2535454 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
2535406 ATTAAGTCTT
*
2535416 AAATATATTTTTTTAATTC
1 AAATATATTTTTTAAATTC
2535435 AAATATATTTAATTTAAATT
1 AAATATATTT--TTTAAATT
2535455 ATTATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATATATTTTTTAAATTC
Found at i:2535917 original size:5 final size:5
Alignment explanation
Indices: 2535900--2535946 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
2535890 CAAAATCTAC
* *
2535900 CTTTT CTTCT CTTTT CTTTT CTTTT CTTTT CTTTT ATTTT CTTTT CT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CT
2535947 CCCCATTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:2536328 original size:21 final size:22
Alignment explanation
Indices: 2536287--2536336 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
2536277 GAAACAATCA
2536287 AATTTAAATATAGTAATA-TTT
1 AATTTAAATATAGTAATATTTT
* *
2536308 AATTTAAATA-ATTTATAATTTT
1 AATTTAAATATAGTAAT-ATTTT
2536330 AATTTAA
1 AATTTAA
2536337 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AATTTAAATATAGTAATATTTT
Found at i:2536339 original size:18 final size:17
Alignment explanation
Indices: 2536310--2536367 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
2536300 TAATATTTAA
*
2536310 TTTAAATAATTTATAAT
1 TTTAATTAATTTATAAT
* *
2536327 TTTAATTTAATTTTTTATT
1 TTTAA-TTAA-TTTATAAT
2536346 TTTAATTAATATTATAAAT
1 TTTAATTAAT-TTAT-AAT
2536365 TTT
1 TTT
2536368 TAAATTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 6 0.19
18 10 0.31
19 16 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATTAATTTATAAT
Found at i:2536343 original size:21 final size:21
Alignment explanation
Indices: 2536300--2536380 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 21
2536290 TTAAATATAG
*
2536300 TAATATTTAATTTAAATAATTTA
1 TAAT-TTTAATTT-AATATTTTA
2536323 TAATTTTAATTTAAT-TTTT-
1 TAATTTTAATTTAATATTTTA
* *
2536342 TATTTTTAA-TTAATATTATA
1 TAATTTTAATTTAATATTTTA
*
2536362 -AATTTTTAAATTAA-ATTTT
1 TAA-TTTTAATTTAATATTTT
2536381 TATACAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.10
19 12 0.24
20 13 0.27
21 7 0.14
22 8 0.16
23 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTTAATTTAATATTTTA
Found at i:2536369 original size:39 final size:36
Alignment explanation
Indices: 2536310--2536427 Score: 102
Period size: 39 Copynumber: 3.2 Consensus size: 36
2536300 TAATATTTAA
* *
2536310 TTTAAATAATTTATAATTTTAATTTAATTTTTTATT
1 TTTAAATAATTTATAATTTTAAATTAAATTTTTATT
*
2536346 TTTAATTAATATTATAAATTTTTAAATTAAATTTTTA--
1 TTTAAATAAT-TTAT-AA-TTTTAAATTAAATTTTTATT
**
2536383 TACAAATAA-TTA-AATTTTAAATTTAAA-TTTTATT
1 TTTAAATAATTTATAATTTTAAA-TTAAATTTTTATT
2536417 ATATTAAATAA
1 -T-TTAAATAA
2536428 ATCTAAAATC
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
32 12 0.18
33 7 0.11
35 4 0.06
36 15 0.23
37 10 0.15
38 2 0.03
39 16 0.24
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (36 bp):
TTTAAATAATTTATAATTTTAAATTAAATTTTTATT
Found at i:2537163 original size:2 final size:2
Alignment explanation
Indices: 2537156--2537189 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2537146 AAATGAATAT
2537156 TC TC 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
2537190 CTTTTGGTGA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2537641 original size:28 final size:28
Alignment explanation
Indices: 2537610--2537671 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
2537600 TTTTTATTAC
2537610 TTTTTAAAATATA-AATAAT-TTAATATA
1 TTTTTAAAATATATAATAATATT-ATATA
* *
2537637 TTTTTAATATATATTATAATATTATATA
1 TTTTTAAAATATATAATAATATTATATA
2537665 TTATTTA
1 TT-TTTA
2537672 TATAATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 12 0.40
28 12 0.40
29 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTTTAAAATATATAATAATATTATATA
Found at i:2537674 original size:28 final size:27
Alignment explanation
Indices: 2537617--2537682 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
2537607 TACTTTTTAA
2537617 AATATAA--ATAATTTAATATATTTTT
1 AATATAATTATAATTTAATATATTTTT
2537642 AATATATATTATAATATT-ATATATTATTT
1 AATATA-ATTATAAT-TTAATATATT-TTT
2537671 -ATATAATTATAA
1 AATATAATTATAA
2537683 AACACATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
25 6 0.17
26 1 0.03
27 7 0.19
28 17 0.47
29 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATAATTATAATTTAATATATTTTT
Found at i:2539811 original size:29 final size:27
Alignment explanation
Indices: 2539755--2539817 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 27
2539745 AAATACTTTT
*
2539755 TTTAATTATAAAAATATCATATAAAAAA
1 TTTAATTATAAAAATA-CATAAAAAAAA
2539783 TTTATATTATAATAAATA-ATAAAATAAAA
1 TTTA-ATTATAA-AAATACATAAAA-AAAA
2539812 TATTAA
1 T-TTAA
2539818 AACTTTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
28 9 0.30
29 13 0.43
30 8 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
TTTAATTATAAAAATACATAAAAAAAA
Found at i:2542166 original size:24 final size:23
Alignment explanation
Indices: 2542134--2542179 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
2542124 TAAAAAATTA
*
2542134 AATATATTATTATATTTAATTATC
1 AATATATTATAATA-TTAATTATC
2542158 AATATATTATAATATTAATTAT
1 AATATATTATAATATTAATTAT
2542180 ATATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATATTATAATATTAATTATC
Found at i:2543654 original size:46 final size:47
Alignment explanation
Indices: 2543587--2543685 Score: 191
Period size: 46 Copynumber: 2.1 Consensus size: 47
2543577 CTATAGATAA
2543587 GCTATAGATAATATATGGATGATAAAGTTTT-TTTTATTAAGTTAGT
1 GCTATAGATAATATATGGATGATAAAGTTTTCTTTTATTAAGTTAGT
2543633 GCTATAGATAATATATGGATGATAAAGTTTTCTTTTATTAAGTTAGT
1 GCTATAGATAATATATGGATGATAAAGTTTTCTTTTATTAAGTTAGT
2543680 GCTATA
1 GCTATA
2543686 ATTTTTTTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 31 0.60
47 21 0.40
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.44
Consensus pattern (47 bp):
GCTATAGATAATATATGGATGATAAAGTTTTCTTTTATTAAGTTAGT
Found at i:2545587 original size:16 final size:16
Alignment explanation
Indices: 2545563--2545606 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2545553 ACATCAATAA
*
2545563 TAAAATTTTTAATTTT
1 TAAAATTTTTAATATT
* *
2545579 TAAATTTTTTTATATT
1 TAAAATTTTTAATATT
*
2545595 TAAAGTTTTTAA
1 TAAAATTTTTAA
2545607 AAATTAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TAAAATTTTTAATATT
Found at i:2546812 original size:2 final size:2
Alignment explanation
Indices: 2546805--2546834 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2546795 TCAATTCTTG
*
2546805 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
2546835 GTAAAGAAAA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2547203 original size:33 final size:33
Alignment explanation
Indices: 2547156--2547220 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
2547146 CTGAACGTTG
*
2547156 AACCTATGGAAGACTCTAAGCTGTATGAGATTC
1 AACCAATGGAAGACTCTAAGCTGTATGAGATTC
*
2547189 AACCAATGGAAGACTCTAAGCTTTATGAGATT
1 AACCAATGGAAGACTCTAAGCTGTATGAGATT
2547221 GAAATGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (33 bp):
AACCAATGGAAGACTCTAAGCTGTATGAGATTC
Found at i:2551828 original size:22 final size:22
Alignment explanation
Indices: 2551800--2551843 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2551790 GCGGAAGATT
2551800 CCCTCTCAATATATTTTTTAAA
1 CCCTCTCAATATATTTTTTAAA
2551822 CCCTCTCAATATATTTTTTAAA
1 CCCTCTCAATATATTTTTTAAA
2551844 GCACAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (22 bp):
CCCTCTCAATATATTTTTTAAA
Found at i:2562097 original size:23 final size:22
Alignment explanation
Indices: 2562074--2562143 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
2562064 TTAGATCAAT
2562074 TTTAAATTAAAATTATTATAAA
1 TTTAAATTAAAATTATTATAAA
2562096 TTTAAATT---A-T-TTA-AAA
1 TTTAAATTAAAATTATTATAAA
* *
2562112 TTTAAAATTTAAATTATTTTAAA
1 TTT-AAATTAAAATTATTATAAA
2562135 TTTAAATTA
1 TTTAAATTA
2562144 TTTTAAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
16 6 0.15
17 8 0.21
18 1 0.03
19 1 0.03
20 1 0.03
21 1 0.03
22 15 0.38
23 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAAATTAAAATTATTATAAA
Found at i:2562112 original size:10 final size:9
Alignment explanation
Indices: 2562095--2562146 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 9
2562085 ATTATTATAA
2562095 ATTTAAATT
1 ATTTAAATT
2562104 ATTTAAA--
1 ATTTAAATT
2562111 ATTTAAA--
1 ATTTAAATT
2562118 ATTTAAATT
1 ATTTAAATT
*
2562127 ATTTTAA--
1 ATTTAAATT
2562134 ATTTAAATT
1 ATTTAAATT
2562143 ATTT
1 ATTT
2562147 TAAAACTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 20 0.54
9 17 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTTAAATT
Found at i:2562119 original size:17 final size:17
Alignment explanation
Indices: 2562076--2562120 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
2562066 AGATCAATTT
2562076 TAAA-TTAAAATTATTA
1 TAAATTTAAAATTATTA
2562092 TAAATTT-AAATTATT-
1 TAAATTTAAAATTATTA
2562107 TAAAATTTAAAATT
1 T-AAATTTAAAATT
2562121 TAAATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.04
16 18 0.69
17 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTTAAAATTATTA
Found at i:2562132 original size:17 final size:17
Alignment explanation
Indices: 2562112--2562151 Score: 73
Period size: 16 Copynumber: 2.4 Consensus size: 17
2562102 TTATTTAAAA
2562112 TTTAAAATTTAAATTAT
1 TTTAAAATTTAAATTAT
2562129 TTT-AAATTTAAATTAT
1 TTTAAAATTTAAATTAT
2562145 TTTAAAA
1 TTTAAAA
2562152 CTCATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAATTTAAATTAT
Found at i:2562144 original size:39 final size:40
Alignment explanation
Indices: 2562035--2562151 Score: 134
Period size: 39 Copynumber: 3.0 Consensus size: 40
2562025 AATGTTAAGA
** *
2562035 TTAAAATATAAAATT-TTATAAATTTCAAATTA-GAT-CAAT
1 TTAAAAT-TAAAATTATTATAAATTT-AAATTATTTTAAAAT
*
2562074 TTTAAATTAAAATTATTATAAATTTAAATTA-TTTAAAAT
1 TTAAAATTAAAATTATTATAAATTTAAATTATTTTAAAAT
* *
2562113 TTAAAATTTAAATTATTTTAAATTTAAATTATTTTAAAA
1 TTAAAATTAAAATTATTATAAATTTAAATTATTTTAAAA
2562152 CTCATTAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
38 14 0.21
39 47 0.69
40 7 0.10
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (40 bp):
TTAAAATTAAAATTATTATAAATTTAAATTATTTTAAAAT
Found at i:2562682 original size:3 final size:3
Alignment explanation
Indices: 2562674--2562714 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2562664 ATCAAGTTTT
2562674 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2562715 TTATGCGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2564367 original size:92 final size:92
Alignment explanation
Indices: 2564210--2564394 Score: 361
Period size: 92 Copynumber: 2.0 Consensus size: 92
2564200 ATGTCCAAAT
2564210 ATTGTTGGACACAGGTATCAGACATGGGTACTTCAAGAAAAATGAAGAGTGGGAGCAATATAGGA
1 ATTGTTGGACACAGGTATCAGACATGGGTACTTCAAGAAAAATGAAGAGTGGGAGCAATATAGGA
2564275 ATATAAATACTTACTTTTTCTTTTTCC
66 ATATAAATACTTACTTTTTCTTTTTCC
2564302 ATTGTTGGACACAGGTATCAGACATGGGTACTTCAAGAAAAATGAAGAGTGGGAGCAATATAGGA
1 ATTGTTGGACACAGGTATCAGACATGGGTACTTCAAGAAAAATGAAGAGTGGGAGCAATATAGGA
*
2564367 ATATATATACTTACTTTTTCTTTTTCC
66 ATATAAATACTTACTTTTTCTTTTTCC
2564394 A
1 A
2564395 GATCTGATCA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (92 bp):
ATTGTTGGACACAGGTATCAGACATGGGTACTTCAAGAAAAATGAAGAGTGGGAGCAATATAGGA
ATATAAATACTTACTTTTTCTTTTTCC
Found at i:2566261 original size:2 final size:2
Alignment explanation
Indices: 2566254--2566286 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2566244 TTTTTACTTT
2566254 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2566287 ACGAAAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2567154 original size:12 final size:12
Alignment explanation
Indices: 2567135--2567167 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2567125 CAATACCAAT
2567135 TTAA-TAAAAAA
1 TTAATTAAAAAA
2567146 TTAATTAAAAAA
1 TTAATTAAAAAA
2567158 TTAAATTAAA
1 TT-AATTAAA
2567168 TTAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 9 0.45
13 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TTAATTAAAAAA
Found at i:2567161 original size:23 final size:23
Alignment explanation
Indices: 2567135--2567178 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2567125 CAATACCAAT
2567135 TTAATAAAAAATT-AATTAAAAAA
1 TTAA-AAAAAATTAAATTAAAAAA
**
2567158 TTAAATTAAATTAAATTAAAA
1 TTAAAAAAAATTAAATTAAAA
2567179 GTATTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TTAAAAAAAATTAAATTAAAAAA
Found at i:2568667 original size:3 final size:3
Alignment explanation
Indices: 2568659--2568694 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2568649 ACATGAAGAT
2568659 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2568695 TGAGATTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2569131 original size:11 final size:12
Alignment explanation
Indices: 2569109--2569160 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
2569099 AATTTAAAAC
2569109 ATAAATATATAT
1 ATAAATATATAT
2569121 ATTAAATATATTAT
1 A-TAAATATA-TAT
*
2569135 ATTAATA-ATAT
1 ATAAATATATAT
2569146 ATAAATATACTAT
1 ATAAATATA-TAT
2569159 AT
1 AT
2569161 CATATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 9 0.26
12 3 0.09
13 18 0.53
14 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
ATAAATATATAT
Found at i:2569137 original size:14 final size:14
Alignment explanation
Indices: 2569110--2569195 Score: 67
Period size: 14 Copynumber: 6.5 Consensus size: 14
2569100 ATTTAAAACA
2569110 TAAATATA-TATAT
1 TAAATATATTATAT
2569123 TAAATATATTATAT
1 TAAATATATTATAT
2569137 T-AATA-A-TATA-
1 TAAATATATTATAT
*
2569147 TAAATATACTATAT
1 TAAATATATTATAT
* * *
2569161 CATATTTATTATAT
1 TAAATATATTATAT
* *
2569175 TATATTTTATT-TAT
1 TA-AATATATTATAT
2569189 TAAATAT
1 TAAATAT
2569196 TTTGTATTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
10 1 0.02
11 8 0.14
12 2 0.03
13 19 0.33
14 22 0.38
15 6 0.10
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TAAATATATTATAT
Found at i:2569173 original size:19 final size:19
Alignment explanation
Indices: 2569151--2569190 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2569141 AATATATAAA
2569151 TATACTATATCATATTTAT
1 TATACTATATCATATTTAT
* **
2569170 TATATTATATTTTATTTAT
1 TATACTATATCATATTTAT
2569189 TA
1 TA
2569191 AATATTTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
TATACTATATCATATTTAT
Found at i:2569401 original size:12 final size:12
Alignment explanation
Indices: 2569384--2569409 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2569374 CAGCTTAGAA
2569384 TATTTTATTTTT
1 TATTTTATTTTT
2569396 TATTTTATTTTT
1 TATTTTATTTTT
2569408 TA
1 TA
2569410 ATTATTGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TATTTTATTTTT
Found at i:2569542 original size:2 final size:2
Alignment explanation
Indices: 2569535--2569564 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2569525 AGCCAAAATC
2569535 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
2569565 GATAGGTGAT
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:2569959 original size:2 final size:2
Alignment explanation
Indices: 2569952--2569983 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2569942 TCTCTATCTA
*
2569952 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2569984 GAGTATTTCA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2572311 original size:2 final size:2
Alignment explanation
Indices: 2572293--2572331 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2572283 TTTAAGAAAG
* *
2572293 TA TA TG TA TA CA 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 TA T
2572332 TTAGATGTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2572444 original size:2 final size:2
Alignment explanation
Indices: 2572437--2572490 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
2572427 TTTTGAATCT
* * * *
2572437 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2572479 TA TA TA TA TA TA
1 TA TA TA TA TA TA
2572491 GCTATTGACA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2573823 original size:14 final size:14
Alignment explanation
Indices: 2573806--2573832 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2573796 AAAAAATAAA
2573806 AAATATTAAAATTT
1 AAATATTAAAATTT
2573820 AAATATTAAAATT
1 AAATATTAAAATT
2573833 ATTTAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATTAAAATTT
Found at i:2576638 original size:21 final size:21
Alignment explanation
Indices: 2576614--2576653 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2576604 ATGAGTTGCA
*
2576614 ATTTGATTGGTTCCTTGCCAG
1 ATTTGATTGGTTCCATGCCAG
**
2576635 ATTTTCTTGGTTCCATGCC
1 ATTTGATTGGTTCCATGCC
2576654 TTCCTTGACA
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:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (21 bp):
ATTTGATTGGTTCCATGCCAG
Found at i:2580775 original size:30 final size:30
Alignment explanation
Indices: 2580741--2580797 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2580731 AAATAAAAAG
*
2580741 TTATTAAATATCATGTTAAAGGTGATTATA
1 TTATTAAATATCATGTTAAAAGTGATTATA
*
2580771 TTATTAAATATTATGTTAAAAGTGATT
1 TTATTAAATATCATGTTAAAAGTGATT
2580798 TTTATAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (30 bp):
TTATTAAATATCATGTTAAAAGTGATTATA
Found at i:2582014 original size:30 final size:31
Alignment explanation
Indices: 2581980--2582043 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
2581970 TTTATACTAT
* * * *
2581980 TATAATTATTTTTTAAATATT-TTATATTTA
1 TATAATAAATTTTAAAATATTCATATATTTA
2582010 TATAATAAATTTTAAAATATTCATATATTTA
1 TATAATAAATTTTAAAATATTCATATATTTA
2582041 TAT
1 TAT
2582044 TTACATTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (31 bp):
TATAATAAATTTTAAAATATTCATATATTTA
Found at i:2582062 original size:11 final size:11
Alignment explanation
Indices: 2582043--2582084 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2582033 TATATTTATA
*
2582043 TTTACATTACT
1 TTTATATTACT
2582054 TTTATATTACAT
1 TTTATATTAC-T
*
2582066 TTTA-ATTATT
1 TTTATATTACT
2582076 TTTATATTA
1 TTTATATTA
2582085 TATTCGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 5 0.19
11 17 0.63
12 5 0.19
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTATATTACT
Found at i:2584080 original size:18 final size:18
Alignment explanation
Indices: 2584057--2584093 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2584047 ATATATAGAA
2584057 ATAGAAGCATCAAAAGAT
1 ATAGAAGCATCAAAAGAT
2584075 ATAGAAGCATCAAAAGAT
1 ATAGAAGCATCAAAAGAT
2584093 A
1 A
2584094 CCAACAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.16, T:0.16
Consensus pattern (18 bp):
ATAGAAGCATCAAAAGAT
Found at i:2586464 original size:24 final size:22
Alignment explanation
Indices: 2586425--2586468 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
2586415 TTTAAATTAG
2586425 TTATTTTTTAAAATTTAAAAAA
1 TTATTTTTTAAAATTTAAAAAA
*
2586447 TTATCTTTTTACATATTTAAAA
1 TTAT-TTTTTA-AAATTTAAAA
2586469 TTTTTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTTTTTAAAATTTAAAAAA
Found at i:2588790 original size:2 final size:2
Alignment explanation
Indices: 2588783--2588827 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2588773 AAAATTTTGA
2588783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2588825 AT A
1 AT A
2588828 ATCAGCTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2589414 original size:2 final size:2
Alignment explanation
Indices: 2589402--2589442 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2589392 TCACTTGGTC
2589402 GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2589443 CATATTATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2589703 original size:54 final size:54
Alignment explanation
Indices: 2589616--2589718 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
2589606 AAAGTTCTAA
* *
2589616 CTCCTTTTAGTCTGCTTTTGTACTTTTCTTCCATTAGGCTCATTCTTGGCTGAT
1 CTCCTTTTAGTCTGCTTATGTACTTTGCTTCCATTAGGCTCATTCTTGGCTGAT
* *
2589670 CTCCTTTTAGTCTGCTTATGTTTCTTTGC-TCCATTAGGTTCATTCTTGG
1 CTCCTTTTAGTCTGCTTATG-TACTTTGCTTCCATTAGGCTCATTCTTGG
2589719 TTGAATGTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 38 0.86
55 6 0.14
ACGTcount: A:0.11, C:0.23, G:0.16, T:0.50
Consensus pattern (54 bp):
CTCCTTTTAGTCTGCTTATGTACTTTGCTTCCATTAGGCTCATTCTTGGCTGAT
Found at i:2592396 original size:2 final size:2
Alignment explanation
Indices: 2592389--2592415 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2592379 ATTTCTTATT
2592389 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
2592416 TCAAATGCAT
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:2592605 original size:21 final size:21
Alignment explanation
Indices: 2592580--2592641 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
2592570 TAATATTAAT
2592580 ATTATTTAATGTAAAATTT-TA
1 ATTATTTAAT-TAAAATTTATA
*
2592601 ATTATTTTATTTTCAAAATTTATA
1 ATTA-TTTA-ATT-AAAATTTATA
2592625 ATTATTTAAATTAAAAT
1 ATTATTT-AATTAAAAT
2592642 ATTACCCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
21 4 0.12
22 10 0.29
23 13 0.38
24 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTATTTAATTAAAATTTATA
Found at i:2593014 original size:20 final size:20
Alignment explanation
Indices: 2592984--2593038 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2592974 ATTTAAAATT
2592984 AAATTTT-ATAATTTTTTAA
1 AAATTTTAATAATTTTTTAA
*
2593003 AAATTTTAATAATTTTTTAT
1 AAATTTTAATAATTTTTTAA
2593023 AAATTTTAAATAATTT
1 AAATTTT-AATAATTT
2593039 AATTAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 7 0.21
20 18 0.55
21 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATTTTAATAATTTTTTAA
Found at i:2593023 original size:30 final size:30
Alignment explanation
Indices: 2592987--2593047 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
2592977 TAAAATTAAA
*
2592987 TTTTATAATTTTTTAAA-AATTTTAA-TAATT
1 TTTTATAA-ATTTTAAATAA-TTTAATTAATT
2593017 TTTTATAAATTTTAAATAATTTAATTAATT
1 TTTTATAAATTTTAAATAATTTAATTAATT
2593047 T
1 T
2593048 AAAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTTATAAATTTTAAATAATTTAATTAATT
Found at i:2593035 original size:11 final size:10
Alignment explanation
Indices: 2592983--2593060 Score: 51
Period size: 10 Copynumber: 8.1 Consensus size: 10
2592973 AATTTAAAAT
2592983 TAAATTTT-A
1 TAAATTTTAA
*
2592992 TAATTTTTTAA
1 TAA-ATTTTAA
2593003 -AAATTTTAA
1 TAAATTTTAA
* *
2593012 TAATTTTTTA
1 TAAATTTTAA
2593022 TAAATTTTAA
1 TAAATTTTAA
2593032 -ATAA-TTTAA
1 TA-AATTTTAA
*
2593041 TTAA-TTTAA
1 TAAATTTTAA
2593050 -AAATATTTAA
1 TAAAT-TTTAA
2593060 T
1 T
2593061 TTAATAATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
8 2 0.04
9 22 0.42
10 28 0.53
11 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TAAATTTTAA
Found at i:2593059 original size:15 final size:15
Alignment explanation
Indices: 2593041--2593070 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2593031 AATAATTTAA
2593041 TTAATTTAAAAATAT
1 TTAATTTAAAAATAT
*
2593056 TTAATTTAATAATAT
1 TTAATTTAAAAATAT
2593071 ATATCAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATTTAAAAATAT
Found at i:2593300 original size:20 final size:20
Alignment explanation
Indices: 2593275--2593478 Score: 74
Period size: 22 Copynumber: 10.4 Consensus size: 20
2593265 AATATATAAT
2593275 TATATTTATATTATTTTTTA
1 TATATTTATATTATTTTTTA
*
2593295 TATATTTA-A--A-TTATTA
1 TATATTTATATTATTTTTTA
* *
2593311 TAAATTTATATAATTTTTTTA
1 TATATTTATATTA-TTTTTTA
* *
2593332 TATATTAATAATTTATTTTATA
1 TATATTTAT-A-TTATTTTTTA
* ** * *
2593354 TAAATTT-TA--AAATATCA
1 TATATTTATATTATTTTTTA
* * * *
2593371 AATCACTT-TA-TATTTATAA
1 TAT-ATTTATATTATTTTTTA
*
2593390 TATATTTATATTATATTTAATA
1 TATATTTATATTAT-TTT-TTA
*
2593412 TATATTTTTATTATTTTTTA
1 TATATTTATATTATTTTTTA
*
2593432 TATTAATTTATATTATATTTTA
1 TA-T-ATTTATATTATTTTTTA
* *
2593454 -AT-TTTTTA-TATTTTATA
1 TATATTTATATTATTTTTTA
2593471 TA-ATTTAT
1 TATATTTAT
2593479 TATAATAATT
Statistics
Matches: 134, Mismatches: 33, Indels: 36
0.66 0.16 0.18
Matches are distributed among these distances:
16 12 0.09
17 13 0.10
18 18 0.13
19 11 0.08
20 17 0.13
21 20 0.15
22 41 0.31
23 2 0.01
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATTTATATTATTTTTTA
Found at i:2593352 original size:69 final size:70
Alignment explanation
Indices: 2593270--2593434 Score: 164
Period size: 69 Copynumber: 2.4 Consensus size: 70
2593260 TTGAAAATAT
* * *
2593270 ATAA-TTATATTTATATTATTTTTTATATATTTAAATTA-TTATAAATTTAT-ATA-ATTT-TTT
1 ATAATTTAT-TTTATATTATTTTTTATATA-TCAAATCACTT-TAAATTTATAATATATTTATAT
2593330 TATATATTA
63 TATAT-TTA
* * * * *
2593339 ATAATTTATTTTATATAAATTTTAAAATATCAAATCACTTTATATTTATAATATATTTATATTAT
1 ATAATTTATTTTATATTATTTTTTATATATCAAATCACTTTAAATTTATAATATATTTATATTAT
2593404 ATTTA
66 ATTTA
*
2593409 AT-ATATATTTT-TATTATTTTTTATAT
1 ATAATTTATTTTATATTATTTTTTATAT
2593435 TAATTTATAT
Statistics
Matches: 78, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
68 25 0.32
69 33 0.42
70 13 0.17
71 7 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (70 bp):
ATAATTTATTTTATATTATTTTTTATATATCAAATCACTTTAAATTTATAATATATTTATATTAT
ATTTA
Found at i:2593406 original size:22 final size:22
Alignment explanation
Indices: 2593378--2593465 Score: 94
Period size: 22 Copynumber: 4.1 Consensus size: 22
2593368 TCAAATCACT
2593378 TTATATTTATAATATATTTATA
1 TTATATTTATAATATATTTATA
*
2593400 TTATATTTA-ATATATATTTTTA
1 TTATATTTATA-ATATATTTATA
* *
2593422 TTATTTTTTATATTA-ATTTATA
1 TTA-TATTTATAATATATTTATA
*
2593444 TTATATTT-TAAT-TTTTTATA
1 TTATATTTATAATATATTTATA
2593464 TT
1 TT
2593466 TTATATAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
20 11 0.20
21 5 0.09
22 31 0.56
23 7 0.13
24 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATATTTATAATATATTTATA
Found at i:2593491 original size:37 final size:38
Alignment explanation
Indices: 2593417--2593496 Score: 110
Period size: 37 Copynumber: 2.1 Consensus size: 38
2593407 TAATATATAT
* * *
2593417 TTTTATTATTTTTTATATTAATTTATATTATATTTTAA
1 TTTTATTATATTTTATATTAATTTATATAATAATTTAA
2593455 TTTT-TTATATTTTATA-TAATTTATTATAATAATTTAA
1 TTTTATTATATTTTATATTAATTTA-TATAATAATTTAA
2593492 TTTTA
1 TTTTA
2593497 ATTTTAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 7 0.19
37 26 0.70
38 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (38 bp):
TTTTATTATATTTTATATTAATTTATATAATAATTTAA
Found at i:2593515 original size:49 final size:48
Alignment explanation
Indices: 2593384--2593515 Score: 141
Period size: 49 Copynumber: 2.8 Consensus size: 48
2593374 CACTTTATAT
* *
2593384 TTATAATATATTTATATTATA-TTTAA--TA-TATATTTTTATTATTTT
1 TTATAATA-ATTTATATTATATTTTAATTTATTATATTTTTATAATTTA
* *
2593429 TTATATTAATTTATATTATATTTTAATTTTTTATATTTTATATAATTTA
1 TTATAATAATTTATATTATATTTTAATTTATTATATTTT-TATAATTTA
*
2593478 TTATAATAATTTA-ATTTTAATTTTAAATTTATT-TATTT
1 TTATAATAATTTATATTAT-ATTTT-AATTTATTATATTT
2593516 AAAAAATTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
44 12 0.16
45 12 0.16
47 1 0.01
48 12 0.16
49 29 0.40
50 7 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (48 bp):
TTATAATAATTTATATTATATTTTAATTTATTATATTTTTATAATTTA
Found at i:2593578 original size:21 final size:21
Alignment explanation
Indices: 2593554--2593629 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 21
2593544 ACTAATATTC
2593554 AAAACTTTAATTTAATTTTTT
1 AAAACTTTAATTTAATTTTTT
* *
2593575 AAAAC-TTAATATATAATAAAAATATTC
1 AAAACTTTAAT-T-TAAT-----TTTTT
2593602 AAAACTTTAATTTAATTTTTT
1 AAAACTTTAATTTAATTTTTT
2593623 AAAACTT
1 AAAACTT
2593630 AATATATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
20 5 0.12
21 16 0.37
22 4 0.09
26 4 0.09
27 9 0.21
28 5 0.12
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAACTTTAATTTAATTTTTT
Found at i:2593605 original size:48 final size:48
Alignment explanation
Indices: 2593547--2593645 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
2593537 ATTATATACT
2593547 AATATTCAAAACTTTAATTTAATTTTTTAAAACTTAATATATAATAAA
1 AATATTCAAAACTTTAATTTAATTTTTTAAAACTTAATATATAATAAA
2593595 AATATTCAAAACTTTAATTTAATTTTTTAAAACTTAATATATAATAAA
1 AATATTCAAAACTTTAATTTAATTTTTTAAAACTTAATATATAATAAA
2593643 AAT
1 AAT
2593646 TTGTTTTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (48 bp):
AATATTCAAAACTTTAATTTAATTTTTTAAAACTTAATATATAATAAA
Found at i:2593747 original size:16 final size:16
Alignment explanation
Indices: 2593728--2593783 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
2593718 ATTTTAATTT
2593728 TTATTTTATTTAAAAA
1 TTATTTTATTTAAAAA
*
2593744 TTATCTT-TTTAAATAA
1 TTATTTTATTTAAA-AA
* **
2593760 TAATTTTATAAAAAAA
1 TTATTTTATTTAAAAA
2593776 TTATTTTA
1 TTATTTTA
2593784 CTTTTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 6 0.19
16 22 0.69
17 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTTTATTTAAAAA
Found at i:2594628 original size:17 final size:15
Alignment explanation
Indices: 2594579--2594629 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2594569 CATATAATTA
* *
2594579 ATTTTAA-TAATATT
1 ATTTTAATTAAAAAT
2594593 ATTTTAATTAAAAAT
1 ATTTTAATTAAAAAT
*
2594608 ATTTTAAATTTAAAAT
1 ATTTT-AATTAAAAAT
2594624 AATTTT
1 -ATTTT
2594630 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 7 0.23
15 10 0.32
16 9 0.29
17 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTAATTAAAAAT
Found at i:2595725 original size:44 final size:42
Alignment explanation
Indices: 2595647--2595739 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 42
2595637 TTAATGATAT
* *
2595647 TAAAATTTATTATTATTTTAATAAATAATATAAAAAT-TTAAA
1 TAAAATTTATTATAATATTAATAAATAATATAAAAATATT-AA
*
2595689 TAAAATTT-TTATAATATTAATAAAAATTATATTAAAAATATTAA
1 TAAAATTTATTATAATATTAAT--AAATAATA-TAAAAATATTAA
2595733 TAAAATT
1 TAAAATT
2595740 AATAAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 11 0.25
42 8 0.18
43 7 0.16
44 16 0.36
45 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (42 bp):
TAAAATTTATTATAATATTAATAAATAATATAAAAATATTAA
Found at i:2599276 original size:10 final size:10
Alignment explanation
Indices: 2599261--2599302 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
2599251 AAGAATGTAT
2599261 AAATAAATAA
1 AAATAAATAA
*
2599271 AAATAAATTA
1 AAATAAATAA
*
2599281 AAATATAATAT
1 AAATA-AATAA
2599292 AAA-AAATAA
1 AAATAAATAA
2599301 AA
1 AA
2599303 TTATTATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 6 0.22
10 15 0.56
11 6 0.22
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAATAAATAA
Found at i:2600099 original size:18 final size:19
Alignment explanation
Indices: 2600063--2600106 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2600053 TCAAATTAGT
2600063 TAAA-AAAATAATTAAAATA
1 TAAATAAAATAA-TAAAATA
2600082 TAAATAAAATAA-AAAATA
1 TAAATAAAATAATAAAATA
*
2600100 TTAATAA
1 TAAATAA
2600107 CATGTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
19 4 0.17
20 7 0.30
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAATAAAATAATAAAATA
Found at i:2600473 original size:22 final size:22
Alignment explanation
Indices: 2600448--2600503 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
2600438 TATAATAATT
* *
2600448 TTTAATTTTATTAAGTTTTA-TA
1 TTTAA-TTTATTAAATATTATTA
*
2600470 TTT-ATTTATAAAATATTATTA
1 TTTAATTTATTAAATATTATTA
2600491 TTTAATTTATTAA
1 TTTAATTTATTAA
2600504 TAATATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.39
21 6 0.21
22 11 0.39
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTAATTTATTAAATATTATTA
Found at i:2600868 original size:16 final size:16
Alignment explanation
Indices: 2600842--2600904 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
2600832 GGTAACTTCG
*
2600842 GTTTGAATTTATTTAA
1 GTTTAAATTTATTTAA
*
2600858 GTTGAAATTTATTTAA
1 GTTTAAATTTATTTAA
* * *
2600874 ATTTAAGTTTGTTTAA
1 GTTTAAATTTATTTAA
2600890 GTTTAAATTTATTTA
1 GTTTAAATTTATTTA
2600905 GATTTAAGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (16 bp):
GTTTAAATTTATTTAA
Done.