Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 11 of 22
Found at i:1421817 original size:105 final size:105
Alignment explanation
Indices: 1421655--1421875 Score: 415
Period size: 105 Copynumber: 2.1 Consensus size: 105
1421645 GAACATTAAA
*
1421655 TTCAAGATCTTTGTTCTGTTTTGCCAGTTCCTCATATGATTTTTCTATTTGCTTCTCTTTCAATT
1 TTCAAGATCTTTGTTCTGTTTTGCCAGTTCCTCATACGATTTTTCTATTTGCTTCTCTTTCAATT
*
1421720 TGATTTCTCTCAAGCATTCTTCATAATGCTCCTGTTTTGC
66 TGATTTCTCTAAAGCATTCTTCATAATGCTCCTGTTTTGC
1421760 TTCAAGATCTTTGTTCTGTTTTGCCAGTTCCTCATACGATTTTTCTATTTGCTTCTCTTTCAATT
1 TTCAAGATCTTTGTTCTGTTTTGCCAGTTCCTCATACGATTTTTCTATTTGCTTCTCTTTCAATT
*
1421825 TGATTTCTCTAAAGCATTCTTCATAATGCTTCTGTTTTGC
66 TGATTTCTCTAAAGCATTCTTCATAATGCTCCTGTTTTGC
1421865 TTCAAGATCTT
1 TTCAAGATCTT
1421876 GATGACCTCT
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 113 1.00
ACGTcount: A:0.17, C:0.21, G:0.11, T:0.50
Consensus pattern (105 bp):
TTCAAGATCTTTGTTCTGTTTTGCCAGTTCCTCATACGATTTTTCTATTTGCTTCTCTTTCAATT
TGATTTCTCTAAAGCATTCTTCATAATGCTCCTGTTTTGC
Found at i:1423422 original size:23 final size:22
Alignment explanation
Indices: 1423380--1423447 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
1423370 TAAATTTTTT
1423380 TAAAATTATTTATATATATTAA
1 TAAAATTATTTATATATATTAA
**
1423402 TAAAATTAAATTT-TATATATTTT
1 TAAAATT--ATTTATATATATTAA
*
1423425 TATAA-T-TTTATATATAATTAA
1 TAAAATTATTTATATAT-ATTAA
1423446 TA
1 TA
1423448 TATTAATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
19 3 0.08
20 5 0.14
21 5 0.14
22 8 0.22
23 12 0.32
24 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAAATTATTTATATATATTAA
Found at i:1423685 original size:21 final size:22
Alignment explanation
Indices: 1423631--1423691 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
1423621 TATAATTTAT
*
1423631 ATAAATAACTAATAAAATATAAACA
1 ATAAATAA--AAT-AAATATAAAAA
*
1423656 TTAAATAAAATAAATATAAAAA
1 ATAAATAAAATAAATATAAAAA
1423678 AT-AATAAAATAAAT
1 ATAAATAAAATAAAT
1423692 TTAATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 12 0.36
22 11 0.33
23 3 0.09
25 7 0.21
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAAATAAAATAAATATAAAAA
Found at i:1423705 original size:21 final size:20
Alignment explanation
Indices: 1423681--1423738 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
1423671 ATAAAAAATA
1423681 ATAAAATAAATTTAATTTTAT
1 ATAAAATAAATTTAATTTT-T
* *
1423702 ATAAATATAAAATAAATTTTT
1 ATAAA-ATAAATTTAATTTTT
*
1423723 ATTAAA-AAATTGTAAT
1 ATAAAATAAATT-TAAT
1423739 GTAGGCGTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 10 0.33
22 12 0.40
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAAAATAAATTTAATTTTT
Found at i:1424074 original size:31 final size:33
Alignment explanation
Indices: 1424028--1424103 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
1424018 ATATATTTTT
*
1424028 TAAATTATTAATTTAATAAAA-ATTTATAAAA-ATA
1 TAAATTATT--TTAAATAAAATA-TTATAAAATATA
*
1424062 TAAATTATTTTAAATATAATATTATAAAATATA
1 TAAATTATTTTAAATAAAATATTATAAAATATA
1424095 TAAA-TATTT
1 TAAATTATTT
1424104 AATGAATACA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 21 0.55
33 8 0.21
34 9 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
TAAATTATTTTAAATAAAATATTATAAAATATA
Found at i:1438190 original size:2 final size:2
Alignment explanation
Indices: 1438183--1438220 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1438173 GGTGAAAATA
* *
1438183 AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1438221 GAGTCCTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1440204 original size:32 final size:32
Alignment explanation
Indices: 1440168--1440271 Score: 93
Period size: 32 Copynumber: 3.2 Consensus size: 32
1440158 AATAAGCTTG
* *
1440168 AACTCGAAAAAGTCCAAACCTGAAGGAGCTCA
1 AACTCGAAAAAGTCCGAACCTGAATGAGCTCA
* ** * * * *
1440200 AACTCTAACGAGCCCGAACTTGAATAAACTCA
1 AACTCGAAAAAGTCCGAACCTGAATGAGCTCA
* *
1440232 AACTC-AAATAAGTCTGAATCTGAATGAGCTCA
1 AACTCGAAA-AAGTCCGAACCTGAATGAGCTCA
1440264 AACTCGAA
1 AACTCGAA
1440272 CTTGCCCAAA
Statistics
Matches: 53, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
31 2 0.04
32 49 0.92
33 2 0.04
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.18
Consensus pattern (32 bp):
AACTCGAAAAAGTCCGAACCTGAATGAGCTCA
Found at i:1440717 original size:48 final size:46
Alignment explanation
Indices: 1440627--1440739 Score: 124
Period size: 48 Copynumber: 2.4 Consensus size: 46
1440617 AGTGTCCATG
* *
1440627 AATTAAATAAAA-TTATAATTTAAAATTTTTATATTTTTATTTA-A
1 AATTAAATAAAATTTAAAATTTAAAAGTTTTATATTTTTATTTATA
*
1440671 ATTTAAATAAAATTTAAAATATTGCAAAAGTTTTA-ATTTATTATTTATA
1 AATTAAATAAAATTTAAAAT-TT--AAAAGTTTTATATTT-TTATTTATA
*
1440720 AATTAATAAAAAATTTAAAA
1 AATTAA-ATAAAATTTAAAA
1440740 ATTATTTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
44 11 0.19
45 6 0.11
46 2 0.04
47 4 0.07
48 16 0.28
49 6 0.11
50 12 0.21
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (46 bp):
AATTAAATAAAATTTAAAATTTAAAAGTTTTATATTTTTATTTATA
Found at i:1440770 original size:20 final size:19
Alignment explanation
Indices: 1440745--1440785 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
1440735 TAAAAATTAT
1440745 TTTTAT-ATTAATATTAATAA
1 TTTTATAATTAA-ATTAA-AA
1440765 TTTTATAATTAAATTAAAA
1 TTTTATAATTAAATTAAAA
1440784 TT
1 TT
1440786 AAATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTATAATTAAATTAAAA
Found at i:1440802 original size:27 final size:27
Alignment explanation
Indices: 1440741--1440818 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 27
1440731 AATTTAAAAA
* * * *
1440741 TTATTTTTATATTAATATT-AATAATT
1 TTATTATTAAATTAAAATTAAATTATT
*
1440767 TTATAATTAAATTAAAATTAAATTATT
1 TTATTATTAAATTAAAATTAAATTATT
1440794 TTATTATTAAA-TAATAATTTAAATT
1 TTATTATTAAATTAA-AA-TTAAATT
1440819 TATAATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
26 18 0.42
27 18 0.42
28 7 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTATTATTAAATTAAAATTAAATTATT
Found at i:1441944 original size:16 final size:16
Alignment explanation
Indices: 1441920--1441951 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1441910 TATTATATTT
1441920 TTTAATATTTAAATAA
1 TTTAATATTTAAATAA
*
1441936 TTTATTATTTAAATAA
1 TTTAATATTTAAATAA
1441952 AACATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATATTTAAATAA
Found at i:1442293 original size:22 final size:22
Alignment explanation
Indices: 1442239--1442317 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
1442229 GATCAAATAA
* *
1442239 TTATATTAAATAATAAAAAATTATT
1 TTATATT-AA-AATTAAATATT-TT
*
1442264 TTATATTAATAATTATATATTTT
1 TTATATTAA-AATTAAATATTTT
*
1442287 TTA-ATTAAATTTAAATA-TTT
1 TTATATTAAAATTAAATATTTT
1442307 TTATTATTAAA
1 TTA-TATTAAA
1442318 TAATAATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
20 6 0.13
21 7 0.15
22 11 0.23
23 5 0.11
24 11 0.23
25 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATATTAAAATTAAATATTTT
Found at i:1442307 original size:20 final size:19
Alignment explanation
Indices: 1442260--1442364 Score: 74
Period size: 21 Copynumber: 5.4 Consensus size: 19
1442250 AATAAAAAAT
* *
1442260 TATTTTATATTAATAATTATA
1 TATTTTAAATT-A-AATTAAA
*
1442281 TATTTTTTAATTAAATTTAAA
1 TA-TTTTAAATTAAA-TTAAA
*
1442302 TATTTTTATTATTAAA-T-AA
1 TA-TTTTA-AATTAAATTAAA
*
1442321 TAATTTAAATTAAATTAAA
1 TATTTTAAATTAAATTAAA
1442340 TTATTTTAAATT-AA-TAAA
1 -TATTTTAAATTAAATTAAA
1442358 TATTTTA
1 TATTTTA
1442365 TCTAAAACTC
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
17 13 0.19
18 9 0.13
19 8 0.11
20 13 0.19
21 14 0.20
22 13 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTAAATTAAATTAAA
Found at i:1442318 original size:22 final size:22
Alignment explanation
Indices: 1442262--1442318 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1442252 TAAAAAATTA
* *
1442262 TTTTA-TATTAATAATTATATAT
1 TTTTATTATTAA-ATTTAAATAT
*
1442284 TTTT-TAATTAAATTTAAATAT
1 TTTTATTATTAAATTTAAATAT
1442305 TTTTATTATTAAAT
1 TTTTATTATTAAAT
1442319 AATAATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATTATTAAATTTAAATAT
Found at i:1442427 original size:20 final size:20
Alignment explanation
Indices: 1442402--1442441 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1442392 TAAGCATGGA
*
1442402 CCTTGTCTATGACTTAGTGT
1 CCTTGTCTATGACCTAGTGT
1442422 CCTTGTCTATGACCTAGTGT
1 CCTTGTCTATGACCTAGTGT
1442442 TTATTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (20 bp):
CCTTGTCTATGACCTAGTGT
Found at i:1442560 original size:21 final size:22
Alignment explanation
Indices: 1442530--1442588 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
1442520 TAATAAAAAA
1442530 AAAT-TTTTAT-ATTATTATTT
1 AAATATTTTATAATTATTATTT
* *
1442550 ATATATTTTATAATTA-CATTT
1 AAATATTTTATAATTATTATTT
1442571 AAATATTTT-TAATTATTA
1 AAATATTTTATAATTATTA
1442589 AATAATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.28
21 19 0.59
22 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
AAATATTTTATAATTATTATTT
Found at i:1444023 original size:2 final size:2
Alignment explanation
Indices: 1444016--1444055 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1444006 AAGCATATGA
*
1444016 AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
1444056 CAATGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1448413 original size:20 final size:19
Alignment explanation
Indices: 1448384--1448422 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1448374 ATAAATAAAA
1448384 ATAAATATTAATAAATTTT
1 ATAAATATTAATAAATTTT
1448403 ATAAATCATTAATAAATTTT
1 ATAAAT-ATTAATAAATTTT
1448423 TTACTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAAATATTAATAAATTTT
Found at i:1449386 original size:17 final size:17
Alignment explanation
Indices: 1449360--1449401 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1449350 ATTAAATCAT
*
1449360 TATT-AAATATTATTTA
1 TATTAAAATATAATTTA
1449376 TATTAAAATATAATTTA
1 TATTAAAATATAATTTA
*
1449393 -ATAAAAATA
1 TATTAAAATA
1449402 AATAAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTAAAATATAATTTA
Found at i:1452361 original size:3 final size:3
Alignment explanation
Indices: 1452353--1452396 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
1452343 GCATATCTTC
1452353 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AACT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA
1452397 ATGCTAGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1452381 original size:20 final size:21
Alignment explanation
Indices: 1452356--1452397 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
1452346 TATCTTCAAT
1452356 AATAATAATAATAA-TAATAA
1 AATAATAATAATAACTAATAA
1452376 AATAATAATAATAACTAATAA
1 AATAATAATAATAACTAATAA
1452397 A
1 A
1452398 TGCTAGTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAATAATAATAACTAATAA
Found at i:1453298 original size:21 final size:21
Alignment explanation
Indices: 1453273--1453313 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1453263 AATTAAATTA
1453273 TTTA-TATAATTTTATTAATAT
1 TTTATTATAATTTTA-TAATAT
*
1453294 TTTATTTTAATTTTATAATA
1 TTTATTATAATTTTATAATA
1453314 GTATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATTATAATTTTATAATAT
Found at i:1453407 original size:49 final size:49
Alignment explanation
Indices: 1453341--1453442 Score: 113
Period size: 49 Copynumber: 2.1 Consensus size: 49
1453331 ATTTTAAAAT
1453341 TTTATATTAATAAAAATTATATAATTATAAAT-T-TTAATATATTTATT-TA
1 TTTATATTAATAAAAATTAT-T-ATTATAAATATATT-ATATATTTATTATA
* * *
1453390 TTTATATTGAAT-TAAATTATTATTTTAAATATATTTTATATTTATTATA
1 TTTATATT-AATAAAAATTATTATTATAAATATATTATATATTTATTATA
1453439 TTTA
1 TTTA
1453443 AGTAATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
47 8 0.17
48 12 0.26
49 23 0.50
50 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (49 bp):
TTTATATTAATAAAAATTATTATTATAAATATATTATATATTTATTATA
Found at i:1453434 original size:25 final size:27
Alignment explanation
Indices: 1453406--1453457 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1453396 TTGAATTAAA
1453406 TTATTAT-TTTAAAT-ATATTTTATAT
1 TTATTATATTTAAATAATATTTTATAT
* *
1453431 TTATTATATTTAAGTAATTTTTTATAT
1 TTATTATATTTAAATAATATTTTATAT
1453458 AAAATTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 6 0.26
27 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TTATTATATTTAAATAATATTTTATAT
Found at i:1453438 original size:16 final size:16
Alignment explanation
Indices: 1453378--1453441 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
1453368 TAAATTTTAA
1453378 TATATTTATT-TA-TT
1 TATATTTATTATATTT
* *
1453392 TATATTGAATTAAATTAT
1 TATATT-TATTATATT-T
*
1453410 TAT-TTTAAATATATTT
1 TATATTT-ATTATATTT
1453426 TATATTTATTATATTT
1 TATATTTATTATATTT
1453442 AAGTAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 13 0.34
17 12 0.32
18 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATATTTATTATATTT
Found at i:1455354 original size:38 final size:39
Alignment explanation
Indices: 1455311--1455427 Score: 202
Period size: 38 Copynumber: 3.1 Consensus size: 39
1455301 GAGAAAACAA
*
1455311 AGATTAGCTTGAAGCCTTAACGACATAAT-AATTTTCTT
1 AGATTAGCTTGGAGCCTTAACGACATAATAAATTTTCTT
*
1455349 AGATTAGCTTGGAGACTTAACGACATAATAAATTTT-TT
1 AGATTAGCTTGGAGCCTTAACGACATAATAAATTTTCTT
1455387 AGATTAGCTTGGAGCCTTAACGACATAATAAATTTTCTT
1 AGATTAGCTTGGAGCCTTAACGACATAATAAATTTTCTT
1455426 AG
1 AG
1455428 TAGTAAAAAG
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
38 64 0.86
39 10 0.14
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (39 bp):
AGATTAGCTTGGAGCCTTAACGACATAATAAATTTTCTT
Found at i:1463241 original size:21 final size:22
Alignment explanation
Indices: 1463216--1463270 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
1463206 CTATAAAGTG
1463216 AATTAAATTTAAAT-ATTTA-A
1 AATTAAATTTAAATAATTTATA
1463236 ATATT-AATTTAAATAATTTATA
1 A-ATTAAATTTAAATAATTTATA
1463258 AATTAAA-TTAAAT
1 AATTAAATTTAAAT
1463271 TATTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 10 0.32
21 17 0.55
22 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTAAATTTAAATAATTTATA
Found at i:1463354 original size:14 final size:14
Alignment explanation
Indices: 1463335--1463373 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1463325 AATTTATCTT
1463335 AAATTAAATAAATA
1 AAATTAAATAAATA
1463349 AAATT-AATCAAATA
1 AAATTAAAT-AAATA
*
1463363 AATTTAAATAA
1 AAATTAAATAA
1463374 TTTAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 16 0.73
15 3 0.14
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATTAAATAAATA
Found at i:1469019 original size:19 final size:17
Alignment explanation
Indices: 1468971--1469013 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
1468961 TATGCAAAAG
1468971 TATTAATAATTAATTTTA
1 TATTAAT-ATTAATTTTA
1468989 TATTAATATTAATATTTA
1 TATTAATATTAAT-TTTA
1469007 TAATTAA
1 T-ATTAA
1469014 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTAATATTAATTTTA
Found at i:1470871 original size:13 final size:13
Alignment explanation
Indices: 1470853--1470877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1470843 TTTTAAAATT
1470853 AAATATAAATATC
1 AAATATAAATATC
1470866 AAATATAAATAT
1 AAATATAAATAT
1470878 TTTTATATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAAATATC
Found at i:1475450 original size:19 final size:21
Alignment explanation
Indices: 1475412--1475450 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1475402 ACATCCATAC
1475412 TAATATAAATCTTGAATCAAG
1 TAATATAAATCTTGAATCAAG
*
1475433 TAATATTAAT-TT-AATCAA
1 TAATATAAATCTTGAATCAA
1475451 TAACAATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (21 bp):
TAATATAAATCTTGAATCAAG
Found at i:1480007 original size:12 final size:12
Alignment explanation
Indices: 1479990--1480040 Score: 66
Period size: 12 Copynumber: 4.1 Consensus size: 12
1479980 CTAATAAAAA
1479990 ATATTTAATTTT
1 ATATTTAATTTT
1480002 ATATTTAATTTT
1 ATATTTAATTTT
*
1480014 AAATTTAATTATTT
1 ATATTTAA-T-TTT
*
1480028 ATATTTAAATTT
1 ATATTTAATTTT
1480040 A
1 A
1480041 AATTGAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 23 0.68
13 1 0.03
14 10 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATTTAATTTT
Found at i:1480028 original size:20 final size:20
Alignment explanation
Indices: 1479990--1480041 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1479980 CTAATAAAAA
*
1479990 ATATTT-AATTTTA-TATTT
1 ATATTTAAATTTAATTATTT
1480008 A-ATTTTAAATTTAATTATTT
1 ATA-TTTAAATTTAATTATTT
1480028 ATATTTAAATTTAA
1 ATATTTAAATTTAA
1480042 ATTGAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 1 0.03
18 4 0.14
19 6 0.21
20 17 0.59
21 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTAAATTTAATTATTT
Found at i:1480041 original size:6 final size:6
Alignment explanation
Indices: 1479992--1480049 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
1479982 AATAAAAAAT
* * * *
1479992 ATTTAA TTTTAT ATTTAA TTTTAA ATTTAA TTATTTAT ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA ATTTAA
*
1480042 ATTGAA AT
1 ATTTAA AT
1480050 AATTTAATCG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
6 36 0.88
8 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (6 bp):
ATTTAA
Found at i:1480044 original size:26 final size:24
Alignment explanation
Indices: 1479992--1480044 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 24
1479982 AATAAAAAAT
*
1479992 ATTTAATTTTATATTTAATTTTAA
1 ATTTAATTTTATATTTAAATTTAA
1480016 ATTTAATTATTTATATTTAAATTTAA
1 ATTTAA-T-TTTATATTTAAATTTAA
1480042 ATT
1 ATT
1480045 GAAATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 6 0.23
25 1 0.04
26 19 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTAATTTTATATTTAAATTTAA
Found at i:1485682 original size:20 final size:19
Alignment explanation
Indices: 1485659--1485711 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1485649 TAGTTTGATT
*
1485659 TAAATTTATTTTTTAATTAA
1 TAAAATTATTTTTTAATT-A
* *
1485679 TAAAAATATTTATTTAATTT
1 TAAAATTATTT-TTTAATTA
1485699 TAAAATTATTTTT
1 TAAAATTATTTTT
1485712 ATAAGATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.07
20 19 0.68
21 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TAAAATTATTTTTTAATTA
Found at i:1485745 original size:2 final size:2
Alignment explanation
Indices: 1485738--1485770 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1485728 TTAATTTTTA
1485738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1485771 AAAGAAGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1487831 original size:27 final size:28
Alignment explanation
Indices: 1487793--1487846 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
1487783 AACATTAATT
*
1487793 TTGAAATTCAATTTGAAATAGT-AAAGG
1 TTGAAATTCAATTTGAAACAGTGAAAGG
1487820 TTGAAATTCAATTTGAAACAGTGAAAG
1 TTGAAATTCAATTTGAAACAGTGAAAG
1487847 TTGCATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (28 bp):
TTGAAATTCAATTTGAAACAGTGAAAGG
Found at i:1492523 original size:12 final size:12
Alignment explanation
Indices: 1492506--1492531 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1492496 GAAAACAAAG
1492506 GCTGCCAACTGT
1 GCTGCCAACTGT
1492518 GCTGCCAACTGT
1 GCTGCCAACTGT
1492530 GC
1 GC
1492532 CGTCAATTTT
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:0.15, C:0.35, G:0.27, T:0.23
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:1492556 original size:12 final size:12
Alignment explanation
Indices: 1492534--1492584 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
1492524 AACTGTGCCG
1492534 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
1492547 TCAATTTGAAAT
1 TCAATTTGAAAT
*
1492559 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
1492574 TCAATTTGAAA
1 TCAATTTGAAA
1492585 CAGTGAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:1493650 original size:2 final size:2
Alignment explanation
Indices: 1493643--1493669 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1493633 GTTAAAATTT
1493643 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1493670 GACTGTCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1494303 original size:44 final size:44
Alignment explanation
Indices: 1494233--1494324 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
1494223 TTACCACTAC
*
1494233 AATTAGTCATTCATATCTGCTCATCTATGTTATAAGTCAAATAT
1 AATTAGTCATTCATATCTGCTCATCTATGTTACAAGTCAAATAT
* * *
1494277 AATTTGTCATTCATATCTGTTTATCTATGTTACAAGTCAAATAT
1 AATTAGTCATTCATATCTGCTCATCTATGTTACAAGTCAAATAT
1494321 AATT
1 AATT
1494325 CGATGGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (44 bp):
AATTAGTCATTCATATCTGCTCATCTATGTTACAAGTCAAATAT
Found at i:1499201 original size:13 final size:13
Alignment explanation
Indices: 1499185--1499214 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1499175 TTTAAATTTT
*
1499185 TATTAAATATATA
1 TATTAAATATAAA
1499198 TATTAAATATAAA
1 TATTAAATATAAA
1499211 TATT
1 TATT
1499215 TAAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATTAAATATAAA
Found at i:1507504 original size:13 final size:13
Alignment explanation
Indices: 1507480--1507538 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
1507470 GTAGCCATGG
* *
1507480 AAAGAGAGAAAGG
1 AAAGAAAGAAAGA
*
1507493 AGAGAAAGAAAGA
1 AAAGAAAGAAAGA
1507506 AAAGAAAGAAA-A
1 AAAGAAAGAAAGA
*
1507518 AAATGAAA-AGAGA
1 AAA-GAAAGAAAGA
*
1507531 AAAAAAAG
1 AAAGAAAG
1507539 GGAGAATTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 9 0.24
13 28 0.76
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:1507515 original size:17 final size:17
Alignment explanation
Indices: 1507479--1507528 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1507469 AGTAGCCATG
* * *
1507479 GAAAGAGAGAAAGGAGA
1 GAAAGAAAGAAAAGAAA
1507496 GAAAGAAAGAAAAGAAA
1 GAAAGAAAGAAAAGAAA
*
1507513 GAAAAAAATGAAAAGA
1 GAAAGAAA-GAAAAGA
1507529 GAAAAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 21 0.75
18 7 0.25
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (17 bp):
GAAAGAAAGAAAAGAAA
Found at i:1507645 original size:24 final size:24
Alignment explanation
Indices: 1507614--1507665 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1507604 TTTTTTTATG
*
1507614 TTTTTATA-TTTGTATCATATTCAT
1 TTTTTATACTTTGTATCA-ATTAAT
*
1507638 TTTTTATACTTTGTTTCAATTAAT
1 TTTTTATACTTTGTATCAATTAAT
1507662 TTTT
1 TTTT
1507666 ATGTCATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.23, C:0.08, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTTATACTTTGTATCAATTAAT
Found at i:1508687 original size:16 final size:16
Alignment explanation
Indices: 1508666--1508703 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1508656 AAATAAAATA
1508666 AAATAATTAATTAATT
1 AAATAATTAATTAATT
**
1508682 AAATAATTTTTTAATT
1 AAATAATTAATTAATT
1508698 AAATAA
1 AAATAA
1508704 CTAGGACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATAATTAATTAATT
Found at i:1509025 original size:35 final size:36
Alignment explanation
Indices: 1508947--1509033 Score: 122
Period size: 35 Copynumber: 2.4 Consensus size: 36
1508937 TTATTAATGT
*
1508947 ATAAAAAATTATATAATATCTCAAATATAATTACAAT
1 ATAAAAAA-TATATAATATCTCAAATATAATTACAAC
* *
1508984 ACAAAAAA-ATATAATATCTCAAATATAATTATAAC
1 ATAAAAAATATATAATATCTCAAATATAATTACAAC
*
1509019 ATAAAAAATAAATAA
1 ATAAAAAATATATAA
1509034 GCACGGTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
35 32 0.73
36 5 0.11
37 7 0.16
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (36 bp):
ATAAAAAATATATAATATCTCAAATATAATTACAAC
Found at i:1510549 original size:19 final size:18
Alignment explanation
Indices: 1510515--1510550 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1510505 TTTCTGAATA
*
1510515 TTTTAAATTTATATATTC
1 TTTTAAATTTAAATATTC
1510533 TTTTAACATTTAAATATT
1 TTTTAA-ATTTAAATATT
1510551 TTCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAAATTTAAATATTC
Found at i:1511085 original size:16 final size:15
Alignment explanation
Indices: 1511018--1511088 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
1511008 AAAAATAATT
1511018 TTTTGTATTTATTATA
1 TTTT-TATTTATTATA
1511034 TTTTTATGTTATTAT-
1 TTTTTAT-TTATTATA
*
1511049 TTTTTATTT-TAAATA
1 TTTTTATTTAT-TATA
1511064 TTTTTA-TTA-TAT-
1 TTTTTATTTATTATA
*
1511076 TTTTAATTTATTA
1 TTTTTATTTATTA
1511089 ATAATAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
12 5 0.11
13 6 0.13
14 8 0.17
15 16 0.35
16 11 0.24
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTTATTTATTATA
Found at i:1511087 original size:11 final size:11
Alignment explanation
Indices: 1511025--1511080 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
1511015 ATTTTTTGTA
1511025 TTTATTATATT
1 TTTATTATATT
1511036 TTTATGT-TATT
1 TTTAT-TATATT
1511047 ATTT-TT-TA-T
1 -TTTATTATATT
*
1511056 TTTA-AATATT
1 TTTATTATATT
1511066 TTTATTATATT
1 TTTATTATATT
1511077 TTTA
1 TTTA
1511081 ATTTATTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 8 0.22
11 19 0.51
12 4 0.11
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTATTATATT
Found at i:1515221 original size:20 final size:22
Alignment explanation
Indices: 1515184--1515232 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
1515174 AGTCCAAACT
1515184 TATTT-TTTAATTAATAAAA-A
1 TATTTATTTAATTAATAAAATA
*
1515204 TATTTATTTAATT-TTAAAATTA
1 TATTTATTTAATTAATAAAA-TA
1515226 TATTTAT
1 TATTTAT
1515233 AAAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 10 0.40
21 7 0.28
22 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATTTATTTAATTAATAAAATA
Found at i:1516734 original size:25 final size:24
Alignment explanation
Indices: 1516669--1516719 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
1516659 AATGAGAGAC
* *
1516669 AGAATGGAGAGAAAAAAAAAGAAA
1 AGAATGAAAAGAAAAAAAAAGAAA
1516693 AGAATGAAAAGACAAAAAAAAGAAA
1 AGAATGAAAAGA-AAAAAAAAGAAA
1516718 AG
1 AG
1516720 GATAGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.04
Consensus pattern (24 bp):
AGAATGAAAAGAAAAAAAAAGAAA
Found at i:1518594 original size:128 final size:128
Alignment explanation
Indices: 1518361--1518612 Score: 416
Period size: 128 Copynumber: 2.0 Consensus size: 128
1518351 AGCGCAAACC
* *
1518361 TTTCATCTTCTTTAAAAATAACTGTGGAGTTCTCAATGGATTACGATCAGAGAATAACAAATGAT
1 TTTCATATTCTTTAAAAATAACTGAGGAGTTCTCAATGGATTACGATCAGAGAATAACAAATGAT
* *
1518426 GAATATTTTTAGAAGCATTTATCATTTGCTGATCTGCGATTAAACATTCTTCTTATGAATACA
66 GAATATTTTTAGAAGCATTTATCATTTGCTGATCTACGATTAAACACTCTTCTTATGAATACA
* * *
1518489 TTTCATATT-TTTCAAAAATAACTGAGGAGTTCTCAATGGATTATGATTAGAGAATAACAAATGC
1 TTTCATATTCTTT-AAAAATAACTGAGGAGTTCTCAATGGATTACGATCAGAGAATAACAAATGA
*
1518553 TGAATATTTTTAGAAGCATTTATCATTTGCTGATCTACGATTAAACACTCTTCTTGTGAA
65 TGAATATTTTTAGAAGCATTTATCATTTGCTGATCTACGATTAAACACTCTTCTTATGAA
1518613 ATATCTAGTC
Statistics
Matches: 115, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
127 3 0.03
128 112 0.97
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (128 bp):
TTTCATATTCTTTAAAAATAACTGAGGAGTTCTCAATGGATTACGATCAGAGAATAACAAATGAT
GAATATTTTTAGAAGCATTTATCATTTGCTGATCTACGATTAAACACTCTTCTTATGAATACA
Found at i:1519447 original size:15 final size:16
Alignment explanation
Indices: 1519427--1519463 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1519417 TTATTATTAT
1519427 TATCTATCTAT-AATC
1 TATCTATCTATAAATC
*
1519442 TATCTATTTATAAATC
1 TATCTATCTATAAATC
1519458 TATCTA
1 TATCTA
1519464 AAATAGACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (16 bp):
TATCTATCTATAAATC
Found at i:1519579 original size:15 final size:15
Alignment explanation
Indices: 1519555--1519591 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1519545 GAGAGAAATT
*
1519555 AAGA-AGAAAAAAAG
1 AAGAGAGAAAAAAAA
1519569 AA-AGAGAAAAAAAA
1 AAGAGAGAAAAAAAA
1519583 AAGAGAGAA
1 AAGAGAGAA
1519592 TTTTTTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 13 0.65
15 6 0.30
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGAGAGAAAAAAAA
Found at i:1522246 original size:25 final size:24
Alignment explanation
Indices: 1522174--1522246 Score: 56
Period size: 27 Copynumber: 2.8 Consensus size: 24
1522164 TGTTATCATA
* *
1522174 TTTATTTTAAATATTTTATTATATT
1 TTTATTTAAAAT-TTTTATTATAAT
* **
1522199 TTTAACTTATAAATTATAAATTATAAT
1 TTT-ATTTA-AAATT-TTTATTATAAT
1522226 TTTATTTAAAATTTTTCATTA
1 TTTATTTAAAATTTTT-ATTA
1522247 AATATATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
24 1 0.03
25 12 0.33
26 8 0.22
27 15 0.42
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTATTTAAAATTTTTATTATAAT
Found at i:1522517 original size:13 final size:13
Alignment explanation
Indices: 1522495--1522530 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1522485 TATTAAATAT
*
1522495 ATATATATATCAA
1 ATATAAATATCAA
*
1522508 ATATAAATATTAA
1 ATATAAATATCAA
1522521 ATATAAATAT
1 ATATAAATAT
1522531 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAAATATCAA
Found at i:1522517 original size:15 final size:14
Alignment explanation
Indices: 1522488--1522565 Score: 77
Period size: 15 Copynumber: 5.3 Consensus size: 14
1522478 AAATTTTTAT
1522488 TAAATATATATATATA
1 TAAATATA-A-ATATA
1522504 TCAAATATAAATAT-
1 T-AAATATAAATATA
*
1522518 TAAATATAAATATT
1 TAAATATAAATATA
*
1522532 TAAAAAATAAATATA
1 T-AAATATAAATATA
*
1522547 TTTAATATAAATATA
1 -TAAATATAAATATA
1522562 TAAA
1 TAAA
1522566 CTCCTTTAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
13 12 0.23
14 5 0.09
15 26 0.49
16 3 0.06
17 7 0.13
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATATAAATATA
Found at i:1522520 original size:30 final size:30
Alignment explanation
Indices: 1522485--1522565 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
1522475 TTCAAATTTT
* **
1522485 TATTAAATATATATATATATCAAATATAA-A
1 TATTAAATATAAATATATAAAAAATA-AATA
*
1522515 TATTAAATATAAATATTTAAAAAATAAATA
1 TATTAAATATAAATATATAAAAAATAAATA
*
1522545 TATTTAATATAAATATATAAA
1 TATTAAATATAAATATATAAA
1522566 CTCCTTTAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
29 2 0.05
30 42 0.95
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (30 bp):
TATTAAATATAAATATATAAAAAATAAATA
Found at i:1523380 original size:45 final size:45
Alignment explanation
Indices: 1523329--1523414 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
1523319 AGTTTATTTA
* * *
1523329 TAATTGATTATTTCAATCTAATTTATTTTTTCGAAAAATAAATTG
1 TAATTGATTATTACAAACTAATTTATTCTTTCGAAAAATAAATTG
*
1523374 TAATTGATTATTACAAACTAATTTATTCTTTGGAAAAATAA
1 TAATTGATTATTACAAACTAATTTATTCTTTCGAAAAATAA
1523415 TTTGATAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (45 bp):
TAATTGATTATTACAAACTAATTTATTCTTTCGAAAAATAAATTG
Found at i:1523933 original size:82 final size:81
Alignment explanation
Indices: 1523806--1523965 Score: 275
Period size: 82 Copynumber: 2.0 Consensus size: 81
1523796 TTTGTACATC
* *
1523806 CATCAAATATGTTTTTCAAAAAAAATAATAATCACGTGATAAATAATATTAAAATTAATATTTGA
1 CATCAAATATGTTTTTCAAAAAAAATAATAATAACGTGATAAATAATATTAAAATCAATATTTGA
*
1523871 TTGATTAATTTTTTTT
66 TTGACTAATTTTTTTT
*
1523887 CATCAAATATGTTTTTGAGAAAAAAATAATAATAACGTGATAAATAATATTAAAATCAATATTTG
1 CATCAAATATGTTTTTCA-AAAAAAATAATAATAACGTGATAAATAATATTAAAATCAATATTTG
1523952 ATTGACTAATTTTT
65 ATTGACTAATTTTT
1523966 CATTAAATGC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 17 0.23
82 57 0.77
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (81 bp):
CATCAAATATGTTTTTCAAAAAAAATAATAATAACGTGATAAATAATATTAAAATCAATATTTGA
TTGACTAATTTTTTTT
Found at i:1525357 original size:22 final size:21
Alignment explanation
Indices: 1525331--1525387 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
1525321 AATTTTTGTA
1525331 TTTATTATATTTTT--ATATT
1 TTTATTATATTTTTAAATATT
* *
1525350 GTTATTATTTATTTTAAATATT
1 TTTATTATAT-TTTTAAATATT
1525372 TTTATTATATTTTTAA
1 TTTATTATATTTTTAA
1525388 TTTATAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 8 0.26
20 4 0.13
21 6 0.19
22 13 0.42
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTATTATATTTTTAAATATT
Found at i:1525383 original size:11 final size:11
Alignment explanation
Indices: 1525331--1525386 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
1525321 AATTTTTGTA
1525331 TTTATTATATT
1 TTTATTATATT
1525342 TTTA-TAT-TGT
1 TTTATTATAT-T
1525352 TATTATT-TA-T
1 T-TTATTATATT
*
1525362 TTTA-AATATT
1 TTTATTATATT
1525372 TTTATTATATT
1 TTTATTATATT
1525383 TTTA
1 TTTA
1525387 ATTTATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
9 6 0.17
10 12 0.33
11 17 0.47
12 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (11 bp):
TTTATTATATT
Found at i:1526331 original size:24 final size:24
Alignment explanation
Indices: 1526304--1526350 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1526294 TAAAAAAGAA
1526304 CTTGATCATCATTC-CTCTACCTTG
1 CTTGATCATCATTCGC-CTACCTTG
*
1526328 CTTGATCGTCATTCGCCTACCTT
1 CTTGATCATCATTCGCCTACCTT
1526351 TCATAACCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.15, C:0.34, G:0.11, T:0.40
Consensus pattern (24 bp):
CTTGATCATCATTCGCCTACCTTG
Found at i:1529937 original size:33 final size:33
Alignment explanation
Indices: 1529892--1529964 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 33
1529882 ATATGTAAGA
* *
1529892 TATGTTGTCATGTAATATGCC-ACATCTTTAAT
1 TATGTTGTCATGTAATATACCAACATCCTTAAT
* *
1529924 TATGTTAGTCATGTTATGTACCAGACATCCTTAAT
1 TATGTT-GTCATGTAATATACCA-ACATCCTTAAT
1529959 TATGTT
1 TATGTT
1529965 TTAAGTGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 6 0.18
33 12 0.35
35 16 0.47
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (33 bp):
TATGTTGTCATGTAATATACCAACATCCTTAAT
Found at i:1530224 original size:19 final size:20
Alignment explanation
Indices: 1530202--1530252 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
1530192 CTTTTGAATC
1530202 TAATCAAGATTT-TTATTTT
1 TAATCAAGATTTATTATTTT
**
1530221 TAATACATATTTTTATTATTTT
1 TAAT-CA-AGATTTATTATTTT
*
1530243 TAATTAAGAT
1 TAATCAAGAT
1530253 CGAAAAACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 5 0.21
22 11 0.46
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
TAATCAAGATTTATTATTTT
Found at i:1535270 original size:26 final size:28
Alignment explanation
Indices: 1535226--1535306 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 28
1535216 AGATGGTATT
*
1535226 AAAATATAATATTAAATATAATTTAATAA
1 AAAATATAATATT-AATATAATATAATAA
*
1535255 AAAATAT-ATATT-ATATAATATATTAA
1 AAAATATAATATTAATATAATATAATAA
* * *
1535281 AATAT-TAAAATTTATATAATAATAAT
1 AAAATATAATATTAATATAAT-ATAAT
1535307 CATTTATCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
25 1 0.02
26 20 0.45
27 7 0.16
28 9 0.20
29 7 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAATATAATATTAATATAATATAATAA
Found at i:1538199 original size:30 final size:29
Alignment explanation
Indices: 1538151--1538211 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
1538141 TAAGTTCAAG
* * *
1538151 TAAATTTTTAATTTTTAATTTATATTTAAA
1 TAAAATTTTAAATATTAATTTATA-TTAAA
*
1538181 TAAAATTTTAAATATTAATTTTTATTAAA
1 TAAAATTTTAAATATTAATTTATATTAAA
1538210 TA
1 TA
1538212 CTTTTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TAAAATTTTAAATATTAATTTATATTAAA
Found at i:1539398 original size:19 final size:20
Alignment explanation
Indices: 1539342--1539398 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 20
1539332 ATAATAAAAA
*
1539342 AATTATTTTAATTAATTTATAT
1 AATTA-TTT-ATTAATTTAAAT
1539364 AATTATTT-TTAA--TAAAT
1 AATTATTTATTAATTTAAAT
1539381 -ATTATTTATTAATTTAAA
1 AATTATTTATTAATTTAAA
1539399 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
16 7 0.23
17 8 0.26
19 8 0.26
21 3 0.10
22 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTATTTATTAATTTAAAT
Found at i:1539409 original size:13 final size:14
Alignment explanation
Indices: 1539391--1539419 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1539381 ATTATTTATT
1539391 AATTTAAA-ATTTA
1 AATTTAAATATTTA
1539404 AATTTAAATATTTA
1 AATTTAAATATTTA
1539418 AA
1 AA
1539420 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTTAAATATTTA
Found at i:1541711 original size:2 final size:2
Alignment explanation
Indices: 1541704--1541733 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1541694 CCCAAACAAA
1541704 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
1541734 TAAAAGGAAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1545394 original size:39 final size:39
Alignment explanation
Indices: 1545320--1545395 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
1545310 TTTACAGTCG
**
1545320 ACTCTCCCAGTCACTTCTTTAGCTGGAACTTTGATGCCA
1 ACTCTCCCAGTCACTTCTTTAGCTGGAACCGTGATGCCA
* *
1545359 ACTCTCCTAGTCACTTGTTTAGCAT-GAACCGTGATGC
1 ACTCTCCCAGTCACTTCTTTAGC-TGGAACCGTGATGC
1545396 TACTTTTGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 31 0.97
40 1 0.03
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (39 bp):
ACTCTCCCAGTCACTTCTTTAGCTGGAACCGTGATGCCA
Found at i:1552350 original size:2 final size:2
Alignment explanation
Indices: 1552343--1552368 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1552333 ACAAAAAGAA
1552343 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
1552369 CCGTATTGCG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1552798 original size:25 final size:25
Alignment explanation
Indices: 1552767--1552845 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
1552757 GATTTATTAT
1552767 TAATTTTTTAAAAAATAAAAAATAA
1 TAATTTTTTAAAAAATAAAAAATAA
* *
1552792 TAATTTTTTAAAAAATAAATATTAA
1 TAATTTTTTAAAAAATAAAAAATAA
** * *
1552817 T-ATAATTAAAAAAATTAAAAA-AA
1 TAATTTTTTAAAAAATAAAAAATAA
1552840 TAATTT
1 TAATTT
1552846 CATACTTATT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
23 3 0.07
24 16 0.37
25 24 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAATTTTTTAAAAAATAAAAAATAA
Found at i:1552990 original size:13 final size:13
Alignment explanation
Indices: 1552972--1552997 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1552962 ATTATTACAA
1552972 TTATTATTTAATT
1 TTATTATTTAATT
1552985 TTATTATTTAATT
1 TTATTATTTAATT
1552998 AATTACCAAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTATTTAATT
Found at i:1554269 original size:17 final size:17
Alignment explanation
Indices: 1554247--1554282 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1554237 TCAATCATTG
1554247 AATTTAACTATATTATT
1 AATTTAACTATATTATT
1554264 AATTTAACTATATTATT
1 AATTTAACTATATTATT
1554281 AA
1 AA
1554283 ACTTGTTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTAACTATATTATT
Found at i:1555289 original size:2 final size:2
Alignment explanation
Indices: 1555282--1555312 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1555272 CTAAAAGCAT
1555282 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 T
1555313 TTTCTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1558960 original size:4 final size:4
Alignment explanation
Indices: 1558951--1558980 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1558941 CCACTCTGTC
1558951 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1558981 GCGAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1560134 original size:17 final size:17
Alignment explanation
Indices: 1560112--1560160 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
1560102 TTTAAAATTA
1560112 ATTATTATATTATTATC
1 ATTATTATATTATTATC
* *
1560129 ATTATTATTATTTTTGTC
1 ATTATTA-TATTATTATC
1560147 ATAATATTATATTA
1 AT--TATTATATTA
1560161 AATGTGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 7 0.27
18 10 0.38
19 4 0.15
20 5 0.19
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTATTATATTATTATC
Found at i:1560137 original size:20 final size:19
Alignment explanation
Indices: 1560112--1560160 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
1560102 TTTAAAATTA
1560112 ATTATTATATTATTATCATT
1 ATTATTATATTATTATCA-T
*
1560132 ATTATTAT-TT-TTGTCAT
1 ATTATTATATTATTATCAT
*
1560149 AATATTATATTA
1 ATTATTATATTA
1560161 AATGTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 2 0.08
20 8 0.32
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTATTATATTATTATCAT
Found at i:1568623 original size:2 final size:2
Alignment explanation
Indices: 1568616--1568641 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1568606 CTAATTGTGT
1568616 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
1568642 AACAGTTAAA
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):
TA
Found at i:1568875 original size:8 final size:8
Alignment explanation
Indices: 1568862--1568973 Score: 65
Period size: 8 Copynumber: 14.0 Consensus size: 8
1568852 CTAATTAAAA
1568862 ATAAATAT
1 ATAAATAT
1568870 ATAAATAT
1 ATAAATAT
1568878 ATTAAA-AT
1 A-TAAATAT
* *
1568886 TTATATAAT
1 ATAAAT-AT
1568895 ATAAAT-T
1 ATAAATAT
*
1568902 ATTAATAT
1 ATAAATAT
1568910 ATAAA-AT
1 ATAAATAT
**
1568917 -TTTATAT
1 ATAAATAT
* *
1568924 AAAAACCTAA
1 ATAAA--TAT
1568934 ATATAAT-T
1 ATA-AATAT
1568942 ATAAATA-
1 ATAAATAT
1568949 ATAAAATAT
1 AT-AAATAT
1568958 ATAAATAT
1 ATAAATAT
1568966 ATAAATAT
1 ATAAATAT
1568974 CAAATTATCA
Statistics
Matches: 78, Mismatches: 14, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
6 2 0.03
7 18 0.23
8 39 0.50
9 13 0.17
10 4 0.05
11 2 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (8 bp):
ATAAATAT
Found at i:1568910 original size:32 final size:33
Alignment explanation
Indices: 1568862--1568925 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1568852 CTAATTAAAA
1568862 ATAAATATATAAATATATTAAAA-TTTATATAAT
1 ATAAATATATAAATATA-TAAAATTTTATATAAT
*
1568895 ATAAAT-TATTAATATATAAAATTTTATATAA
1 ATAAATATATAAATATATAAAATTTTATATAA
1568926 AAACCTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 5 0.17
32 18 0.62
33 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATAAATATATAAATATATAAAATTTTATATAAT
Found at i:1568914 original size:48 final size:49
Alignment explanation
Indices: 1568839--1568973 Score: 120
Period size: 48 Copynumber: 2.8 Consensus size: 49
1568829 CGAATTTATC
* * * *
1568839 AATATACTATAAACTAATTAA-AAATAAATATATAAATATATTAAAA-TT
1 AATATAATATAAA-TAATTAATATATAAATATATAAATATATAAAAACTA
* * *
1568887 TATATAATATAAATTATTAATATATAAA-AT-T--TTATATAAAAACCTA
1 AATATAATATAAATAATTAATATATAAATATATAAATATATAAAAA-CTA
*
1568933 AATATAATTATAAATAATAAAATATATAAATATATAAATAT
1 AATATAA-TATAAATAAT-TAATATATAAATATATAAATAT
1568974 CAAATTATCA
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
44 9 0.13
46 8 0.12
47 17 0.25
48 27 0.40
49 2 0.03
50 1 0.01
52 3 0.04
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (49 bp):
AATATAATATAAATAATTAATATATAAATATATAAATATATAAAAACTA
Found at i:1569135 original size:23 final size:23
Alignment explanation
Indices: 1569108--1569155 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1569098 TCCTAGCAGC
* **
1569108 TTCCTTGAAACTTCCTTCTCTCT
1 TTCCTGGAAACTTCAGTCTCTCT
*
1569131 TTCCTGGAAGCTTCAGTCTCTCT
1 TTCCTGGAAACTTCAGTCTCTCT
1569154 TT
1 TT
1569156 TTCTTCTGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.12, C:0.31, G:0.10, T:0.46
Consensus pattern (23 bp):
TTCCTGGAAACTTCAGTCTCTCT
Found at i:1570120 original size:2 final size:2
Alignment explanation
Indices: 1570113--1570138 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1570103 CTTTCTTAGA
1570113 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
1570139 GCATTTATCA
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:1570922 original size:24 final size:25
Alignment explanation
Indices: 1570895--1570941 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1570885 ATTATTATTT
*
1570895 AATTT-ATAA-AAATATCTTTATATA
1 AATTTAATAATAAAAAT-TTTATATA
1570919 AATTTAATAATAAAAATTTTATA
1 AATTTAATAATAAAAATTTTATA
1570942 AATATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 10 0.50
26 5 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
AATTTAATAATAAAAATTTTATATA
Found at i:1572111 original size:17 final size:18
Alignment explanation
Indices: 1572081--1572114 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1572071 AATAAAAATG
*
1572081 ATATTTTTGGATATAATC
1 ATATTTTTGAATATAATC
1572099 ATATTTTT-AATATAAT
1 ATATTTTTGAATATAAT
1572115 GAAAATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (18 bp):
ATATTTTTGAATATAATC
Found at i:1572444 original size:2 final size:2
Alignment explanation
Indices: 1572437--1572462 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1572427 ACCTCCTTCC
1572437 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
1572463 AGCTATAATT
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):
TA
Found at i:1575611 original size:2 final size:2
Alignment explanation
Indices: 1575604--1575660 Score: 59
Period size: 2 Copynumber: 30.0 Consensus size: 2
1575594 TTTTTACTTT
* *
1575604 TA TA TA TA TA TA TA TA T- TA TG TA -A TT TA TA TCA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
1575645 TA TA TA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA
1575661 GTGTTAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
1 4 0.09
2 40 0.87
3 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1575612 original size:28 final size:27
Alignment explanation
Indices: 1575563--1575618 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
1575553 CTGATCTGAT
1575563 TTATTTTTCAATTGTATAATATAGTATA
1 TTATTTTTCAATTGTATAATATA-TATA
* *
1575591 TTATTTTT-ACTTTTATATATATATATA
1 TTATTTTTCAATTGTATA-ATATATATA
1575618 T
1 T
1575619 ATTATGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (27 bp):
TTATTTTTCAATTGTATAATATATATA
Found at i:1575617 original size:27 final size:27
Alignment explanation
Indices: 1575563--1575647 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 27
1575553 CTGATCTGAT
*
1575563 TTATTTTTCAATTGTATA-ATATAGTATA
1 TTATTTTT-AATTTTATATATATA-TATA
*
1575591 TTATTTTTACTTTTATATATATATATA
1 TTATTTTTAATTTTATATATATATATA
*
1575618 -TATTATGTAATTTATATCATATATATATA
1 TTATT-TTTAATTT-TAT-ATATATATATA
1575647 T
1 T
1575648 ATATAATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
26 4 0.08
27 17 0.35
28 16 0.33
29 11 0.23
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (27 bp):
TTATTTTTAATTTTATATATATATATA
Found at i:1580891 original size:11 final size:11
Alignment explanation
Indices: 1580875--1580922 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1580865 AAATATGATT
1580875 ATATAAATATA
1 ATATAAATATA
*
1580886 ATATAAAAATA
1 ATATAAATATA
1580897 AT-TAAAATATA
1 ATAT-AAATATA
*
1580908 TTA-AAATATA
1 ATATAAATATA
1580918 ATATA
1 ATATA
1580923 TAAATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 10 0.33
11 20 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATATAAATATA
Found at i:1580905 original size:9 final size:10
Alignment explanation
Indices: 1580886--1580981 Score: 54
Period size: 10 Copynumber: 9.4 Consensus size: 10
1580876 TATAAATATA
*
1580886 ATATAAAAAT
1 ATATTAAAAT
1580896 A-ATTAAAAT
1 ATATTAAAAT
1580905 ATATTAAAAT
1 ATATTAAAAT
1580915 ATAATATATAAAT
1 AT-AT-TA-AAAT
*
1580928 ATTTTAAAAT
1 ATATTAAAAT
* *
1580938 TTATATAATAT
1 ATAT-TAAAAT
* *
1580949 AAATTATTAAT
1 ATATTA-AAAT
*
1580960 ATAATAAAAT
1 ATATTAAAAT
*
1580970 TTA-T-AAAT
1 ATATTAAAAT
1580978 ATAT
1 ATAT
1580982 CATCAATATA
Statistics
Matches: 65, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
8 6 0.09
9 9 0.14
10 24 0.37
11 17 0.26
12 3 0.05
13 6 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATTAAAAT
Found at i:1580916 original size:32 final size:32
Alignment explanation
Indices: 1580874--1580981 Score: 96
Period size: 32 Copynumber: 3.4 Consensus size: 32
1580864 TAAATATGAT
1580874 TATAT-AAATATAATATAAAAATA-ATTAAAA
1 TATATAAAATATAATATAAAAATATATTAAAA
* *
1580904 TATATTAAAATATAATATATAAATATTTTAAAA
1 TATA-TAAAATATAATATAAAAATATATTAAAA
* * ** *
1580937 TTTATATAATATAA-ATTATTAATATAATAAAA
1 TATATAAAATATAATA-TAAAAATATATTAAAA
*
1580969 TTTATAAATATAT
1 TATATAAA-ATAT
1580982 CATCAATATA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
30 4 0.06
31 2 0.03
32 46 0.71
33 13 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
TATATAAAATATAATATAAAAATATATTAAAA
Found at i:1580948 original size:25 final size:23
Alignment explanation
Indices: 1580860--1580981 Score: 92
Period size: 23 Copynumber: 5.2 Consensus size: 23
1580850 AAATTTAATA
*
1580860 ATATT-AAATATGATTATATAAAT
1 ATATTAAAATAT-AATATATAAAT
1580883 ATAATATAAAA-ATAAT-TA-AAAT
1 AT-AT-TAAAATATAATATATAAAT
1580905 ATATTAAAATATAATATATAAAT
1 ATATTAAAATATAATATATAAAT
* *
1580928 ATTTTAAAATTTATATAATATAAAT
1 ATATTAAAATATA-AT-ATATAAAT
* *
1580953 -TATTAATATAATAAAATTTATAAAT
1 ATATT-A-A-AATATAATATATAAAT
1580978 ATAT
1 ATAT
1580982 CATCAATATA
Statistics
Matches: 80, Mismatches: 7, Indels: 21
0.74 0.06 0.19
Matches are distributed among these distances:
20 5 0.06
21 7 0.09
22 8 0.10
23 19 0.24
24 9 0.11
25 19 0.24
26 9 0.11
27 4 0.05
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
ATATTAAAATATAATATATAAAT
Found at i:1580961 original size:18 final size:18
Alignment explanation
Indices: 1580940--1580980 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1580930 TTTAAAATTT
*
1580940 ATATAATATAAA-TTATTA
1 ATATAATA-AAATTTATAA
1580958 ATATAATAAAATTTATAA
1 ATATAATAAAATTTATAA
1580976 ATATA
1 ATATA
1580981 TCATCAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATAAAATTTATAA
Found at i:1583347 original size:2 final size:2
Alignment explanation
Indices: 1583340--1583374 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1583330 GAATTCCAGG
1583340 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
1583375 ATTCTTTTTT
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:1586280 original size:15 final size:15
Alignment explanation
Indices: 1586231--1586281 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 15
1586221 TTACGTATAA
*
1586231 TTAATATATTAATTT
1 TTAATATATTTATTT
1586246 TTAATTATATTATATATTT
1 TTAA-TATA-T-T-TATTT
1586265 TTAATATATTTATTT
1 TTAATATATTTATTT
1586280 TT
1 TT
1586282 TTTACACGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 11 0.35
16 5 0.16
17 2 0.06
18 5 0.16
19 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTAATATATTTATTT
Found at i:1586285 original size:18 final size:19
Alignment explanation
Indices: 1586242--1586282 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1586232 TAATATATTA
1586242 ATTTTTAATTATATTATAT
1 ATTTTTAATTATATTATAT
1586261 ATTTTTAA-TATATT-TAT
1 ATTTTTAATTATATTATAT
1586278 -TTTTT
1 ATTTTT
1586283 TTACACGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 3 0.14
18 6 0.27
19 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTAATTATATTATAT
Found at i:1594905 original size:2 final size:2
Alignment explanation
Indices: 1594862--1594887 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1594852 GAGAATAAAA
1594862 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
1594888 TATAGTTGCA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1596726 original size:2 final size:2
Alignment explanation
Indices: 1596721--1596755 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1596711 TATGCGTGTG
1596721 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 T
1596756 CAGTAACTGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1598008 original size:218 final size:216
Alignment explanation
Indices: 1597573--1598014 Score: 582
Period size: 218 Copynumber: 2.0 Consensus size: 216
1597563 TCTTTGTTAT
* * ** * ** *
1597573 AATGTCGTGAGGTTGGGTTTAGGCGTTCAGTGGTTGTGGATGATTGGCAAAACGGCACGCGCGGT
1 AATGGCGTGAGATTGGGTTTAGAAGTTCAGTAGTTGTACATGATTGGCAAAACGGCACGCGCGGC
* * * *
1597638 GTCGTCGTGACTCTTGCGAAATCGCACGGTTTTTGTGGAGTTTAGTCAGCAATCGTGCGATGAGC
66 ATCGTCGTGACTCCTGAGAAATCGCACGGTTTTGGTGGAGTTTAGTCAGCAATCGTGCGATGAGC
* * *
1597703 GCGCGCTGCTGTGACCTTAGAAATGGTGGGACAGGCGGGTGTATTTGTGACCACTCAATCATATC
131 GCGCGCTGCTGTGACCTTAGAAATGGTGGGACAGGCGGGGGTATTTGTCACCACTCAAGCATATC
*
1597768 TAGTTTTGCTAGTTGTTTGGCAA
196 TA--TTTGCTAGTTGATTGGCAA
1597791 AATGGCGTGAGATTGGGTTTAGAAGTTCAGTAGTTGTACATGATTGGCAAAACGGCACGCGCGGC
1 AATGGCGTGAGATTGGGTTTAGAAGTTCAGTAGTTGTACATGATTGGCAAAACGGCACGCGCGGC
* * *
1597856 ATCTTCGTGACTCCTGAGGAATCGCACGGTTTTGGTGGAGTTTAGTCAGCAATCGTGCGATTAGC
66 ATCGTCGTGACTCCTGAGAAATCGCACGGTTTTGGTGGAGTTTAGTCAGCAATCGTGCGATGAG-
* * * *
1597921 TCGCGGCGCTGCTGTGGCCTT-GCAAATGGTGGGACAGGTGGGGGTATTTGTCACCAGTCAAGCG
130 -CGC-GCGCTGCTGTGACCTTAG-AAATGGTGGGACAGGCGGGGGTATTTGTCACCACTCAAGCA
* *
1597985 TGTCTA-TTGCTGGTTGATTGGCAA
192 TATCTATTTGCTAGTTGATTGGCAA
*
1598009 ATTGGC
1 AATGGC
1598015 ACGGCATCGT
Statistics
Matches: 194, Mismatches: 26, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
218 135 0.70
220 4 0.02
221 55 0.28
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (216 bp):
AATGGCGTGAGATTGGGTTTAGAAGTTCAGTAGTTGTACATGATTGGCAAAACGGCACGCGCGGC
ATCGTCGTGACTCCTGAGAAATCGCACGGTTTTGGTGGAGTTTAGTCAGCAATCGTGCGATGAGC
GCGCGCTGCTGTGACCTTAGAAATGGTGGGACAGGCGGGGGTATTTGTCACCACTCAAGCATATC
TATTTGCTAGTTGATTGGCAA
Found at i:1598892 original size:15 final size:15
Alignment explanation
Indices: 1598867--1598902 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1598857 ACTTTACAAA
1598867 AAATT-AAATTAATT
1 AAATTAAAATTAATT
*
1598881 GAATTAAAATTAATT
1 AAATTAAAATTAATT
1598896 AAATTAA
1 AAATTAA
1598903 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATTAAAATTAATT
Found at i:1599007 original size:33 final size:32
Alignment explanation
Indices: 1598943--1599012 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
1598933 TGATTATAAG
1598943 TAAATGAAATAATTAAATTATATATAGTTAAT
1 TAAATGAAATAATTAAATTATATATAGTTAAT
**
1598975 ATAAATG-AA-AATATAAATTTATATATTTTTAAT
1 -TAAATGAAATAAT-TAAA-TTATATATAGTTAAT
1599008 TAAAT
1 TAAAT
1599013 ATTAATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 3 0.09
32 11 0.33
33 19 0.58
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (32 bp):
TAAATGAAATAATTAAATTATATATAGTTAAT
Found at i:1599086 original size:13 final size:14
Alignment explanation
Indices: 1599065--1599115 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
1599055 AAGATCAATT
*
1599065 AAATAAATTT-TTA
1 AAATTAATTTATTA
1599078 AAATTAATTTATT-
1 AAATTAATTTATTA
1599091 AAATTAAATTTTATTA
1 AAATT-AA-TTTATTA
1599107 AAATTAATT
1 AAATTAATT
1599116 AAATCGAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 14 0.42
14 6 0.18
15 8 0.24
16 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTAATTTATTA
Found at i:1599115 original size:15 final size:15
Alignment explanation
Indices: 1599075--1599115 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1599065 AAATAAATTT
1599075 TTAAAATTAA-TTTA
1 TTAAAATTAATTTTA
1599089 TT-AAATTAAATTTTA
1 TTAAAATT-AATTTTA
1599104 TTAAAATTAATT
1 TTAAAATTAATT
1599116 AAATCGAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.21
14 4 0.17
15 10 0.42
16 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAAATTAATTTTA
Found at i:1599115 original size:29 final size:26
Alignment explanation
Indices: 1599062--1599115 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 26
1599052 TATAAGATCA
1599062 ATTAAATAAATTTTTAAAATTAATTT
1 ATTAAATAAATTTTTAAAATTAATTT
1599088 ATTAAATTAAATTTTATTAAAATTAATT
1 ATTAAA-TAAA-TTT-TTAAAATTAATT
1599116 AAATCGAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 6 0.24
27 4 0.16
28 3 0.12
29 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTAAATAAATTTTTAAAATTAATTT
Found at i:1599571 original size:40 final size:46
Alignment explanation
Indices: 1599527--1599646 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 46
1599517 TTAAAATATA
1599527 ATAAAATATAAATATATAAATATT-T-T-AAAA-TTT-ATATAA-T
1 ATAAAATATAAATATATAAATATTATATAAAAATTTTAATATAATT
* *
1599567 ATAAATTATTAATATATAAA-ATTTATATAAAAATTTTAATATAATT
1 ATAAAATATAAATATATAAATA-TTATATAAAAATTTTAATATAATT
* *
1599613 ATAATATAATAAAATATATAAATATAATATAAAA
1 ATAAAAT-AT-AAATATATAAATATTATATAAAA
1599647 TCACTAATTA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
39 1 0.02
40 20 0.31
41 1 0.02
42 1 0.02
43 4 0.06
44 3 0.05
45 6 0.09
46 6 0.09
47 2 0.03
48 19 0.30
49 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (46 bp):
ATAAAATATAAATATATAAATATTATATAAAAATTTTAATATAATT
Found at i:1599590 original size:31 final size:33
Alignment explanation
Indices: 1599494--1599596 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 33
1599484 TAATATTATT
* * *
1599494 ATATAAATATAATACAAATATAATTAAAATATAATAAA
1 ATATAAATAT-AT--AAATATTA-TAAAAT-TTATATA
*
1599532 ATATAAATATATAAATATTTTAAAATTTATATA
1 ATATAAATATATAAATATTATAAAATTTATATA
*
1599565 ATATAAAT-TATTAATA-TATAAAATTTATATA
1 ATATAAATATATAAATATTATAAAATTTATATA
1599596 A
1 A
1599597 AAATTTTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
31 15 0.25
32 7 0.12
33 13 0.22
34 6 0.10
35 6 0.10
37 2 0.03
38 10 0.17
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (33 bp):
ATATAAATATATAAATATTATAAAATTTATATA
Found at i:1599645 original size:11 final size:11
Alignment explanation
Indices: 1599494--1599645 Score: 68
Period size: 11 Copynumber: 13.6 Consensus size: 11
1599484 TAATATTATT
1599494 ATATAAATATA
1 ATATAAATATA
*
1599505 ATACAAATATA
1 ATATAAATATA
1599516 AT-TAAAATATA
1 ATAT-AAATATA
1599527 ATA-AAATATAA
1 ATATAAATAT-A
1599538 ATATATAA-ATA
1 ATATA-AATATA
* *
1599549 TTTTAAA-AT-
1 ATATAAATATA
*
1599558 TTATATAATATAA
1 ATATA-AATAT-A
*
1599571 ATTATTAATAT-
1 A-TATAAATATA
*
1599582 ATA-AAATTTA
1 ATATAAATATA
* *
1599592 TATAAAAATTTTA
1 -ATATAAA-TATA
*
1599605 ATATAATTATA
1 ATATAAATATA
*
1599616 ATAT-AATAAAA
1 ATATAAAT-ATA
1599627 TATATAAATATA
1 -ATATAAATATA
1599639 ATATAAA
1 ATATAAA
1599646 ATCACTAATT
Statistics
Matches: 109, Mismatches: 15, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
9 8 0.07
10 16 0.15
11 51 0.47
12 17 0.16
13 14 0.13
14 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAAATATA
Found at i:1600397 original size:2 final size:2
Alignment explanation
Indices: 1600390--1600414 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1600380 AGTTAAATCT
1600390 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
1600415 GCACGCGCAC
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:1603564 original size:20 final size:19
Alignment explanation
Indices: 1603526--1603564 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1603516 TTTATTTAGT
* *
1603526 TTTATAAATTTAATTTAAA
1 TTTATAAATATAATATAAA
1603545 TTTATAGAATATAATATAAA
1 TTTATA-AATATAATATAAA
1603565 AATTTTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TTTATAAATATAATATAAA
Found at i:1605932 original size:21 final size:21
Alignment explanation
Indices: 1605880--1605934 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1605870 TTCAATTATG
* *
1605880 TTATATAATATATTATTTTTAT
1 TTATAT-ATATATTATTGTAAT
*
1605902 TTTTATATATATTA-TGTAAT
1 TTATATATATATTATTGTAAT
1605922 TTATATCATATAT
1 TTATAT-ATATAT
1605935 ATATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 9 0.32
21 14 0.50
22 5 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATATATATATTATTGTAAT
Found at i:1606702 original size:4 final size:4
Alignment explanation
Indices: 1606695--1606737 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
1606685 GTTTTATATA
1606695 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1606738 AATATGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1613338 original size:21 final size:21
Alignment explanation
Indices: 1613276--1613330 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
1613266 GTTGAAAATT
1613276 TTAT-TTTAT-TA-TTTA-AA
1 TTATATTTATATATTTTATAA
*
1613293 TAATATTTATATATTTTATAA
1 TTATATTTATATATTTTATAA
* *
1613314 TTATATTTTTTTATTTT
1 TTATATTTATATATTTT
1613331 TTTATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 2 0.07
20 4 0.13
21 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATATTTATATATTTTATAA
Found at i:1615362 original size:221 final size:222
Alignment explanation
Indices: 1614979--1615389 Score: 567
Period size: 221 Copynumber: 1.9 Consensus size: 222
1614969 ATAATGTCAA
* ** ** * *
1614979 GAGGTTGGGTTTAGGCGTTCAGTGGCTGTAGATGATTGGCAAATGGCACGCGCGGTATTGTAGTG
1 GAGGTTGGGTTTAGACGTTCAGTGGCTGTAGACAATTGGCAAACAGCACGCGCGGCATCGTAGTG
* * *
1615044 ACCCGTGCGAAATAGCACGGTTTTGGTCGAGTTTAGTCAGCAATAGTGCGACAAGCGCTCGCCGC
66 ACCCGTGAGAAATAGCACGGTTTTGGTCGAGTTTAGTCAGCAATAGTGCAACAAGCGCGCGCCGC
1615109 GACTGTGGCCTTACAAATGGTGGGACAGGTGGGTGTATTTGTCACCACTC-AATCATATCAAAGT
131 GACTGTGGCCTTACAAATGGTGGGACAGGTGGGTGTATTTGTCACCACTCAAATCATATCAAAGT
1615173 TTCGGTGGTTGTTTGGCAAAATGGCGT
196 TTCGGTGGTTGTTTGGCAAAATGGCGT
* *
1615200 GAGGTT-GGTTTAGACGTTCAGTGGTTGTAGACAATTGGCAAAACAGCACGCGCGGCATCGTCGT
1 GAGGTTGGGTTTAGACGTTCAGTGGCTGTAGACAATTGGC-AAACAGCACGCGCGGCATCGTAGT
* * * * * ** *
1615264 GACTCGTGAGAACTCGCACGGTTTTCGG-GGAGTTTAGTCAGGAATAGTGCAATGAGCGCGCGGC
65 GACCCGTGAGAAATAGCACGGTTTT-GGTCGAGTTTAGTCAGCAATAGTGCAACAAGCGCGCGCC
* * * *
1615328 GTGAGTTTGGCCTTACAAGTGGTGGGACAGGTGGGTGTATTTGTCACCACTCAAATCATATC
129 GCGACTGTGGCCTTACAAATGGTGGGACAGGTGGGTGTATTTGTCACCACTCAAATCATATC
1615390 TAGTTTTGCT
Statistics
Matches: 163, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
220 29 0.18
221 123 0.75
222 11 0.07
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (222 bp):
GAGGTTGGGTTTAGACGTTCAGTGGCTGTAGACAATTGGCAAACAGCACGCGCGGCATCGTAGTG
ACCCGTGAGAAATAGCACGGTTTTGGTCGAGTTTAGTCAGCAATAGTGCAACAAGCGCGCGCCGC
GACTGTGGCCTTACAAATGGTGGGACAGGTGGGTGTATTTGTCACCACTCAAATCATATCAAAGT
TTCGGTGGTTGTTTGGCAAAATGGCGT
Found at i:1616946 original size:15 final size:15
Alignment explanation
Indices: 1616926--1616955 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1616916 ATAAAAAAGT
1616926 AATTAATTGAGTTGA
1 AATTAATTGAGTTGA
*
1616941 AATTAATTGATTTGA
1 AATTAATTGAGTTGA
1616956 TTAATATTAA
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:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (15 bp):
AATTAATTGAGTTGA
Found at i:1617139 original size:20 final size:21
Alignment explanation
Indices: 1617106--1617144 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1617096 AAAATAAAAA
1617106 ATTATAAATCAATTAAATTTT
1 ATTATAAATCAATTAAATTTT
*
1617127 ATTA-AAATTAATTAAATT
1 ATTATAAATCAATTAAATT
1617145 AAACTAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATAAATCAATTAAATTTT
Done.