Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold283
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2945114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 15
Found at i:1229144 original size:19 final size:19
Alignment explanation
Indices: 1229120--1229158 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1229110 TATTGCAGCA
1229120 TATTTGTAATTAAAAATAT
1 TATTTGTAATTAAAAATAT
1229139 TATTTGTAATTAAAAATAT
1 TATTTGTAATTAAAAATAT
1229158 T
1 T
1229159 CTGTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
TATTTGTAATTAAAAATAT
Found at i:1232311 original size:7 final size:7
Alignment explanation
Indices: 1232299--1232327 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1232289 ATTATAAATA
1232299 TTATAAT
1 TTATAAT
1232306 TTATAAT
1 TTATAAT
1232313 TTATAAT
1 TTATAAT
1232320 TTATAAT
1 TTATAAT
1232327 T
1 T
1232328 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTATAAT
Found at i:1240798 original size:12 final size:12
Alignment explanation
Indices: 1240781--1240809 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1240771 CGCACCTAAT
1240781 AAATTCAATGAC
1 AAATTCAATGAC
1240793 AAATTCAATGAC
1 AAATTCAATGAC
1240805 AAATT
1 AAATT
1240810 TATTTAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (12 bp):
AAATTCAATGAC
Found at i:1246251 original size:44 final size:43
Alignment explanation
Indices: 1246169--1246251 Score: 121
Period size: 44 Copynumber: 1.9 Consensus size: 43
1246159 TAATTAGATT
* *
1246169 TTTTTAATAATATTAAATATAATACAATATACATATATAAATA
1 TTTTTAATAATATTAAATATAATAAAATATACAAATATAAATA
* *
1246212 TTTTTAATATTATTATAATATAATAAAATATATAAATATA
1 TTTTTAATAATATTA-AATATAATAAAATATACAAATATA
1246252 TTTAAGTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 14 0.40
44 21 0.60
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (43 bp):
TTTTTAATAATATTAAATATAATAAAATATACAAATATAAATA
Found at i:1248767 original size:13 final size:13
Alignment explanation
Indices: 1248749--1248773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1248739 AATTGCTGGG
1248749 TGTTTTTTTTATT
1 TGTTTTTTTTATT
1248762 TGTTTTTTTTAT
1 TGTTTTTTTTAT
1248774 GAATTTTATG
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
TGTTTTTTTTATT
Found at i:1252128 original size:2 final size:2
Alignment explanation
Indices: 1252121--1252150 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1252111 ATCGATGGAA
1252121 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
1252151 TTGCCTGCCT
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:1257277 original size:112 final size:112
Alignment explanation
Indices: 1257080--1257302 Score: 401
Period size: 112 Copynumber: 2.0 Consensus size: 112
1257070 TTCTAAAGCA
* * *
1257080 TGCTTCTTATCTTACTCATTCTTCATTAATGATTAAATAAAGGCATAATTCACTTCCCAACATTT
1 TGCTTCTTATCTTACTCATTCTTCATTAATGATTAAACAAAGACATAATCCACTTCCCAACATTT
1257145 AGAAGAATTTTGTCTTATTAAATATTCTGATAACATATATGTTTTTG
66 AGAAGAATTTTGTCTTATTAAATATTCTGATAACATATATGTTTTTG
*
1257192 TGCTTTTTATCTTACTCATTCTTCATTAATGATTAAACAAAGACATAATCCACTTCCCAACATTT
1 TGCTTCTTATCTTACTCATTCTTCATTAATGATTAAACAAAGACATAATCCACTTCCCAACATTT
*
1257257 TGAAGAATTTTGTCTTATTAAATATTCTGATAACATATATGTTTTT
66 AGAAGAATTTTGTCTTATTAAATATTCTGATAACATATATGTTTTT
1257303 ATGGATATCC
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (112 bp):
TGCTTCTTATCTTACTCATTCTTCATTAATGATTAAACAAAGACATAATCCACTTCCCAACATTT
AGAAGAATTTTGTCTTATTAAATATTCTGATAACATATATGTTTTTG
Found at i:1260975 original size:7 final size:7
Alignment explanation
Indices: 1260965--1260994 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1260955 AATATTTAAT
1260965 AAATTTA
1 AAATTTA
1260972 AAATTTA
1 AAATTTA
1260979 AAATTTA
1 AAATTTA
*
1260986 ATATTTA
1 AAATTTA
1260993 AA
1 AA
1260995 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATTTA
Found at i:1260995 original size:13 final size:13
Alignment explanation
Indices: 1260964--1260997 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1260954 TAATATTTAA
1260964 TAAATTTAAAATT
1 TAAATTTAAAATT
*
1260977 TAAAATTTAATATT
1 T-AAATTTAAAATT
1260991 TAAATTT
1 TAAATTT
1260998 TTTTTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:1261818 original size:2 final size:2
Alignment explanation
Indices: 1261811--1261852 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1261801 GTGCGTCTAC
1261811 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
1261853 GGTAGTGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1262327 original size:20 final size:18
Alignment explanation
Indices: 1262304--1262368 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 18
1262294 ATTTAAAATA
1262304 TTATATATTTATATAATTTT
1 TTATATA-TTATATAA-TTT
*
1262324 TTATATATCA-ATAATTT
1 TTATATATTATATAATTT
1262341 TTAT-TA-TATA-AATTT
1 TTATATATTATATAATTT
*
1262356 TAATATATT-TATA
1 TTATATATTATATA
1262369 TCATGTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
15 9 0.24
16 7 0.18
17 9 0.24
18 4 0.11
19 2 0.05
20 7 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATATTATATAATTT
Found at i:1262368 original size:18 final size:17
Alignment explanation
Indices: 1262291--1262368 Score: 56
Period size: 18 Copynumber: 4.6 Consensus size: 17
1262281 ATATTATAAT
*
1262291 TATATTTA-AAATATTA
1 TATATTTATAAATTTTA
*
1262307 TATATTTATATAATTTTT
1 TATATTTATA-AATTTTA
*
1262325 TATATATCA-ATAATTTT-
1 TATAT-TTATA-AATTTTA
*
1262342 TAT-TATATAAATTTTAA
1 TATATTTATAAATTTT-A
1262359 TATATTTATA
1 TATATTTATA
1262369 TCATGTTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
15 7 0.14
16 10 0.20
17 7 0.14
18 23 0.47
19 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTTATAAATTTTA
Found at i:1262406 original size:19 final size:20
Alignment explanation
Indices: 1262300--1262407 Score: 70
Period size: 19 Copynumber: 5.7 Consensus size: 20
1262290 TTATATTTAA
* *
1262300 AATATTATATAT-TTATA-T
1 AATATTTTATATATCATATT
*
1262318 AATTTTTTATATATCA-A-T
1 AATATTTTATATATCATATT
* *
1262336 AAT-TTTTATTATATAAATTTT
1 AATATTTTA-TATAT-CATATT
* *
1262357 AATATATT-TATATCATGTT
1 AATATTTTATATATCATATT
*
1262376 AAAATTTT-TATATCATATT
1 AATATTTTATATATCATATT
1262395 -ATATTTTATATAT
1 AATATTTTATATAT
1262408 AAAATTAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
17 5 0.07
18 26 0.37
19 28 0.39
20 5 0.07
21 4 0.06
22 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (20 bp):
AATATTTTATATATCATATT
Found at i:1262921 original size:2 final size:2
Alignment explanation
Indices: 1262914--1262943 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1262904 TCTCTATAAG
1262914 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
1262944 CAAACATATG
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:1263473 original size:2 final size:2
Alignment explanation
Indices: 1263466--1263496 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1263456 TATATCACTG
1263466 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1263497 GTGCCTTCAT
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1268681 original size:39 final size:39
Alignment explanation
Indices: 1268622--1268731 Score: 177
Period size: 39 Copynumber: 2.8 Consensus size: 39
1268612 GGGGTTCACA
* *
1268622 ATCAATCTAGCACCAATGAACAAGATGATGAGATTCAAC
1 ATCAACCTAGCACCATTGAACAAGATGATGAGATTCAAC
*
1268661 ATCAACCTAGCACCATTGAACAAGAAT-TTGAGATTCAAC
1 ATCAACCTAGCACCATTGAACAAG-ATGATGAGATTCAAC
1268700 ATCAACCTAGCACCATTGAACAAGATGATGAG
1 ATCAACCTAGCACCATTGAACAAGATGATGAG
1268732 TATTGGAATT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
38 2 0.03
39 61 0.94
40 2 0.03
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (39 bp):
ATCAACCTAGCACCATTGAACAAGATGATGAGATTCAAC
Found at i:1291015 original size:20 final size:20
Alignment explanation
Indices: 1290992--1291083 Score: 57
Period size: 20 Copynumber: 4.7 Consensus size: 20
1290982 ATAAAGTTCC
*
1290992 AGAACCTTCCACATTATTCT
1 AGAACCTTCCAAATTATTCT
* * *
1291012 AGAA-CATCTAGAATTTTTC-
1 AGAACCTTCCA-AATTATTCT
*
1291031 A-AAGCCTTCCACGA-TATTCT
1 AGAA-CCTTCCA-AATTATTCT
* *
1291051 AGAACATTCCAAAATATTCT
1 AGAACCTTCCAAATTATTCT
*
1291071 AGAACTTTCCAAA
1 AGAACCTTCCAAA
1291084 GTGTTCAAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
18 2 0.04
19 10 0.19
20 40 0.74
21 2 0.04
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (20 bp):
AGAACCTTCCAAATTATTCT
Found at i:1291181 original size:22 final size:23
Alignment explanation
Indices: 1291142--1291189 Score: 89
Period size: 22 Copynumber: 2.1 Consensus size: 23
1291132 GAATTCTCCA
1291142 CCAAATTGTCAAAAAATTAAAAC
1 CCAAATTGTCAAAAAATTAAAAC
1291165 CCAAATTGTC-AAAAATTAAAAC
1 CCAAATTGTCAAAAAATTAAAAC
1291187 CCA
1 CCA
1291190 TTTAACAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.54, C:0.21, G:0.04, T:0.21
Consensus pattern (23 bp):
CCAAATTGTCAAAAAATTAAAAC
Found at i:1294546 original size:74 final size:74
Alignment explanation
Indices: 1294436--1294721 Score: 292
Period size: 74 Copynumber: 3.8 Consensus size: 74
1294426 CCCGGCATAG
*
1294436 TCGCCAAAAGGACAGAATCTCGATAGCCAACACTCACTCTGGCTACCAGACTTGTGCTCGCC-CT
1 TCGCCAAAAGGACA-AATCTTGATAGCCAACACTCACTCTGGCTACCAGACTTGTGCTCGCCAC-
* *
1294500 ATAAATCTTAA
64 ATAAATCCTGA
* * * * * **
1294511 TCGCCGAAAGGACAAATCTTGATAGTCAACTCTCACTCTGACTGCCAGACAAGTGCTCGCCACAT
1 TCGCCAAAAGGACAAATCTTGATAGCCAACACTCACTCTGGCTACCAGACTTGTGCTCGCCACAT
*
1294576 AAATCCTGG
66 AAATCCTGA
* * * * * * *
1294585 TTGCCAAAAAGG-CGAATCTTGATAGCCAACTCTCACTTTGGCTGCCAGACCTGTGCTTGCCACA
1 TCGCC-AAAAGGACAAATCTTGATAGCCAACACTCACTCTGGCTACCAGACTTGTGCTCGCCACA
1294649 TAAATCCTGA
65 TAAATCCTGA
* * * *
1294659 TCGTCAGAAA-GATAAAATCTTGATAGCCAACACTCACTCTGGTTGA-CAGACTTGTACTCGCCA
1 TCGCCA-AAAGGA-CAAATCTTGATAGCCAACACTCACTCTGGCT-ACCAGACTTGTGCTCGCCA
1294722 TTTAAATCTT
Statistics
Matches: 173, Mismatches: 32, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
73 2 0.01
74 112 0.65
75 59 0.34
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.24
Consensus pattern (74 bp):
TCGCCAAAAGGACAAATCTTGATAGCCAACACTCACTCTGGCTACCAGACTTGTGCTCGCCACAT
AAATCCTGA
Found at i:1294729 original size:149 final size:150
Alignment explanation
Indices: 1294441--1294721 Score: 345
Period size: 148 Copynumber: 1.9 Consensus size: 150
1294431 CATAGTCGCC
*
1294441 AAAAGGACAGAATCTCGATAGCCAACACTCACTCTGGCTACCAGACTTGTGCTCGCCCTATAAAT
1 AAAAGGACAGAATCTCGATAGCCAACACTCACTCTGGCTACCAGACCTGTGCTCGCCCTATAAAT
* * * * * * *
1294506 CTTAATCGCCGAAAGGACAAATCTTGATAGTCAACTCTCACTCTGACTGCCAGACAAGTGCTCGC
66 CCTAATCGCAGAAAGGAAAAATCTTGATAGCCAACACTCACTCTGACTGACAGACAAGTACTCGC
1294571 CACATAAATCCTGGTTGCCA
131 CACATAAATCCTGGTTGCCA
* * * * *
1294591 AAAAGG-C-GAATCTTGATAGCCAACTCTCACTTTGGCTGCCAGACCTGTGCTTGCCAC-ATAAA
1 AAAAGGACAGAATCTCGATAGCCAACACTCACTCTGGCTACCAGACCTGTGCTCGCC-CTATAAA
* ** **
1294653 TCCTGATCGTCAGAAA-GATAAAATCTTGATAGCCAACACTCACTCTGGTTGACAGACTTGTACT
65 TCCTAATCG-CAGAAAGGA-AAAATCTTGATAGCCAACACTCACTCTGACTGACAGACAAGTACT
1294717 CGCCA
128 CGCCA
1294722 TTTAAATCTT
Statistics
Matches: 110, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
148 56 0.51
149 48 0.44
150 6 0.05
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (150 bp):
AAAAGGACAGAATCTCGATAGCCAACACTCACTCTGGCTACCAGACCTGTGCTCGCCCTATAAAT
CCTAATCGCAGAAAGGAAAAATCTTGATAGCCAACACTCACTCTGACTGACAGACAAGTACTCGC
CACATAAATCCTGGTTGCCA
Found at i:1296808 original size:2 final size:2
Alignment explanation
Indices: 1296801--1296826 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1296791 GAATTAAAGA
1296801 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
1296827 CCACCGTAAC
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:1302333 original size:16 final size:15
Alignment explanation
Indices: 1302310--1302362 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
1302300 ATTGTCCAAG
1302310 TTTTTAAATATTAAT
1 TTTTTAAATATTAAT
1302325 TTATTTAAA-ATTTAAAT
1 TT-TTTAAATA-TT-AAT
* *
1302342 TTTTTTATTATTAAT
1 TTTTTAAATATTAAT
1302357 TTTTTA
1 TTTTTA
1302363 TATGATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 11 0.35
16 14 0.45
17 6 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTAAATATTAAT
Found at i:1302417 original size:9 final size:9
Alignment explanation
Indices: 1302405--1302439 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
1302395 TCAATATCTA
1302405 AAATATATT
1 AAATATATT
1302414 AAATAT-TT
1 AAATATATT
*
1302422 AAATTTATT
1 AAATATATT
1302431 AAATATATT
1 AAATATATT
1302440 TTAAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AAATATATT
Found at i:1306901 original size:4 final size:4
Alignment explanation
Indices: 1306892--1306916 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1306882 AATCGAAGGG
1306892 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
1306917 CTTTTGGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1307555 original size:19 final size:21
Alignment explanation
Indices: 1307518--1307559 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
1307508 ATTTTTAATA
1307518 AATTTATATTATAAAACTTTT
1 AATTTATATTATAAAACTTTT
*
1307539 AATTTAT-TTAT-ATACTTTT
1 AATTTATATTATAAAACTTTT
1307558 AA
1 AA
1307560 AAAATATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTTATATTATAAAACTTTT
Found at i:1308209 original size:33 final size:30
Alignment explanation
Indices: 1308164--1308230 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
1308154 TAGTATATTA
* * *
1308164 ATATAAATATAAATATTATATTAATTTTTTAT
1 ATATAAACATAAATA-TAT-TAAAATTTTTAT
1308196 ATATACAACATAAATATATTAAAATTTTTAT
1 ATATA-AACATAAATATATTAAAATTTTTAT
1308227 ATAT
1 ATAT
1308231 TTTTACATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 14 0.45
32 8 0.26
33 9 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
ATATAAACATAAATATATTAAAATTTTTAT
Found at i:1308277 original size:13 final size:14
Alignment explanation
Indices: 1308249--1308287 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1308239 ATTTAAAATT
1308249 TTTTAAATAATTATA
1 TTTTAAAT-ATTATA
1308264 TTTTAAAT-TTATA
1 TTTTAAATATTATA
1308277 TTTT-AATATTA
1 TTTTAAATATTA
1308288 ATCAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.13
13 12 0.52
15 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTAAATATTATA
Found at i:1314268 original size:342 final size:340
Alignment explanation
Indices: 1313629--1314311 Score: 1249
Period size: 342 Copynumber: 2.0 Consensus size: 340
1313619 AGAGTTGATC
* *
1313629 AGACCGATGGTCCAGGTGGACCAGCAGGGGGTGGAAGTAGTGCTGGCGGTGATGATAGAAACTGC
1 AGACCGATGGTCCAGGTGGACCAGCAGAGGGTGGAAGTAGTGCTGGCGGCGATGATAGAAACTGC
* *
1313694 AGTAGAAAATATGGACTCTAATAGTTTGTAGAAATGTAGAGGCATGTAGCTTTCGGATGACTGGT
66 AGTAGAAAATATCGACTCTAATAGTTTGTAGAAATGTAGAGGCATGTAGATTTCGGATGACTGGT
* *
1313759 TATGCGGATGAAAAATGACAAACTCCGTAACCACCCTCCGTCTCTCTCTTTCACTCTCCCCTCCG
131 TATGCGGATGAAAAATGACAAACTCCGTAACCACCCTCCGTCTCCCTCTTTCACTCTCCCATCCG
*
1313824 GAGTCCATCACCACCCAAAATCAAGGAGAACACAAAAATTCGGAAGAGTAAAAAATGCTGGAATC
196 CAGTCCATCACCACCCAAAATCAAGGAGAACACAAAAATTCGGAAGAGTAAAAAATGCTGGAATC
1313889 GGAAAATTGAAGCATCACATAAAACTATTCTCTTTAAGGAGAGGCAATTGAAGTATTGTTCGACA
261 GGAAAATTGAAGCATCACATAAAACTATTCTCTTTAAGGAGAGGCAATTGAAGTATTGTTCGACA
1313954 GGTCTAGTTGTAACT
326 GGTCTAGTTGTAACT
*
1313969 AGACCGATGGTCCAGGTGGACCAGCAGAGGGTGGAAGTAGTGCTGGCGGCGATGATAGCAACTGC
1 AGACCGATGGTCCAGGTGGACCAGCAGAGGGTGGAAGTAGTGCTGGCGGCGATGATAGAAACTGC
*
1314034 AGTGGAAAATATCGACTCTAATAGTTTGTAGAAATGTAGAGGCATGTAGATTTCGGATGACTGGT
66 AGTAGAAAATATCGACTCTAATAGTTTGTAGAAATGTAGAGGCATGTAGATTTCGGATGACTGGT
1314099 TATGCGGATGAAAAATGATACAAACTCCGTAACCACCCTCCGTCTCCCTCTTTCACTCTCCCATC
131 TATGCGGATGAAAAATG--ACAAACTCCGTAACCACCCTCCGTCTCCCTCTTTCACTCTCCCATC
* *
1314164 CGCAGTCCATCACCACCCGAAATCAAGGAGAACACAAAAATTCGGAAGAGTAAACAATGCTGGAA
194 CGCAGTCCATCACCACCCAAAATCAAGGAGAACACAAAAATTCGGAAGAGTAAAAAATGCTGGAA
1314229 TCGGAAAATTGAAGCATCACATAAAACTATTCTCTTTAAGGAGAGGCAATTGAAGTATTGTTCGA
259 TCGGAAAATTGAAGCATCACATAAAACTATTCTCTTTAAGGAGAGGCAATTGAAGTATTGTTCGA
1314294 CAGGTCTAGTTGTAACT
324 CAGGTCTAGTTGTAACT
1314311 A
1 A
1314312 AAGTGGTATT
Statistics
Matches: 330, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
340 141 0.43
342 189 0.57
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (340 bp):
AGACCGATGGTCCAGGTGGACCAGCAGAGGGTGGAAGTAGTGCTGGCGGCGATGATAGAAACTGC
AGTAGAAAATATCGACTCTAATAGTTTGTAGAAATGTAGAGGCATGTAGATTTCGGATGACTGGT
TATGCGGATGAAAAATGACAAACTCCGTAACCACCCTCCGTCTCCCTCTTTCACTCTCCCATCCG
CAGTCCATCACCACCCAAAATCAAGGAGAACACAAAAATTCGGAAGAGTAAAAAATGCTGGAATC
GGAAAATTGAAGCATCACATAAAACTATTCTCTTTAAGGAGAGGCAATTGAAGTATTGTTCGACA
GGTCTAGTTGTAACT
Found at i:1315530 original size:32 final size:35
Alignment explanation
Indices: 1315491--1315574 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 35
1315481 AAAATTATTA
*
1315491 TATTATTAAAATAATTT-TAA-AAATTTTAAAAAT
1 TATTATTAAAATAATTTATAATAAATTTAAAAAAT
1315524 TA-TATT--AAT-ATTTATAATTAAATTTAAAAAAT
1 TATTATTAAAATAATTTATAA-TAAATTTAAAAAAT
*
1315556 TATTATTTAAATTAATTTA
1 TATTA-TTAAAATAATTTA
1315575 ATTTAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
29 4 0.10
30 6 0.15
32 18 0.44
33 4 0.10
34 2 0.05
36 2 0.05
37 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
TATTATTAAAATAATTTATAATAAATTTAAAAAAT
Found at i:1315592 original size:18 final size:18
Alignment explanation
Indices: 1315564--1315599 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1315554 ATTATTATTT
1315564 AAATTAATTT-AATTTAA
1 AAATTAATTTAAATTTAA
1315581 AAATTAAATTTAAATTTAA
1 AAATT-AATTTAAATTTAA
1315600 TTTAATATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTAATTTAAATTTAA
Found at i:1318569 original size:2 final size:2
Alignment explanation
Indices: 1318562--1318591 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1318552 CTGCCAAGAA
1318562 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
1318592 GTATGCACCA
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:1318775 original size:23 final size:22
Alignment explanation
Indices: 1318744--1318787 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1318734 CATCTAATTT
1318744 ATAAATAATATATTAATATATAC
1 ATAAATAATATATTAA-ATATAC
*
1318767 ATAATTAATATATTAAATATA
1 ATAAATAATATATTAAATATA
1318788 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAATAATATATTAAATATAC
Found at i:1321361 original size:15 final size:15
Alignment explanation
Indices: 1321338--1321369 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1321328 CGTTTGTTTC
*
1321338 AAACTCCTAACCATG
1 AAACCCCTAACCATG
1321353 AAACCCCTAACCATG
1 AAACCCCTAACCATG
1321368 AA
1 AA
1321370 CTAATTTCAA
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:0.44, C:0.34, G:0.06, T:0.16
Consensus pattern (15 bp):
AAACCCCTAACCATG
Found at i:1322457 original size:18 final size:19
Alignment explanation
Indices: 1322419--1322460 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1322409 GCTCATTTGC
*
1322419 AATAAAAATTCATAGTAAT
1 AATAAAAATTCATAATAAT
*
1322438 AATAAGAATT-ATAATAAT
1 AATAAAAATTCATAATAAT
1322456 AATAA
1 AATAA
1322461 TCAATACATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (19 bp):
AATAAAAATTCATAATAAT
Found at i:1329156 original size:21 final size:21
Alignment explanation
Indices: 1329118--1329157 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1329108 AATACTATAA
1329118 GATTTAAATATTAAAAAATCG
1 GATTTAAATATTAAAAAATCG
* * *
1329139 GATTTGAATCTTATAAAAT
1 GATTTAAATATTAAAAAAT
1329158 AATTTTATAT
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:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
GATTTAAATATTAAAAAATCG
Found at i:1330110 original size:2 final size:2
Alignment explanation
Indices: 1330103--1330128 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1330093 TTCGTACTCC
1330103 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
1330129 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1331273 original size:14 final size:14
Alignment explanation
Indices: 1331254--1331280 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1331244 TTTTTTATTG
1331254 TTAATTATAATAAA
1 TTAATTATAATAAA
1331268 TTAATTATAATAA
1 TTAATTATAATAA
1331281 TATTTATTTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATTATAATAAA
Found at i:1332594 original size:14 final size:14
Alignment explanation
Indices: 1332575--1332604 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1332565 GGTTTGATTG
*
1332575 TTTTTAATATTATT
1 TTTTTAATATAATT
1332589 TTTTTAATATAATT
1 TTTTTAATATAATT
1332603 TT
1 TT
1332605 AATCAACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTAATATAATT
Found at i:1336287 original size:15 final size:14
Alignment explanation
Indices: 1336262--1336310 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
1336252 GTTTATATTA
1336262 TTTTGAGTTTGAATAT
1 TTTTGA-TTTGAAT-T
*
1336278 TTTTGATTTGATTTT
1 TTTTGATTTGA-ATT
*
1336293 TTTTAATTTGAATT
1 TTTTGATTTGAATT
1336307 TTTT
1 TTTT
1336311 TTTAAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 6 0.21
15 16 0.55
16 7 0.24
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.67
Consensus pattern (14 bp):
TTTTGATTTGAATT
Found at i:1336311 original size:15 final size:15
Alignment explanation
Indices: 1336269--1336311 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1336259 TTATTTTGAG
* *
1336269 TTTGAATATTTTTGA
1 TTTGAATTTTTTTAA
*
1336284 TTTGATTTTTTTTAA
1 TTTGAATTTTTTTAA
1336299 TTTGAATTTTTTT
1 TTTGAATTTTTTT
1336312 TTAAATTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (15 bp):
TTTGAATTTTTTTAA
Found at i:1337671 original size:16 final size:16
Alignment explanation
Indices: 1337644--1337688 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1337634 TTGATTTAAT
1337644 TTAAATTATTTTAAAAA
1 TTAAA-TATTTTAAAAA
* *
1337661 TTAAATATTTTTAAAT
1 TTAAATATTTTAAAAA
1337677 TTAAA-ATTTTAA
1 TTAAATATTTTAA
1337689 CTTTTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 6 0.24
16 14 0.56
17 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAATATTTTAAAAA
Found at i:1338511 original size:6 final size:6
Alignment explanation
Indices: 1338500--1338557 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
1338490 AATAAATAAT
* *
1338500 AATTTA AATTTA AA--TA AA-TTG AA-TTA AA-TTA AATTTA TATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
1338543 AATTTAA AATTTA AA
1 AATTT-A AATTTA AA
1338558 ACTTTTTAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
4 4 0.09
5 12 0.27
6 23 0.51
7 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:1339097 original size:2 final size:2
Alignment explanation
Indices: 1339092--1339124 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1339082 ATATAAGGGC
1339092 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 T
1339125 GTACACACAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1339233 original size:14 final size:14
Alignment explanation
Indices: 1339186--1339235 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
1339176 TTTTTTATAA
1339186 ATTTTATATGATTTAT
1 ATTTTATAT--TTTAT
*
1339202 ATTATT-TAATTTAT
1 ATT-TTATATTTTAT
1339216 -TTTTATATTTTAT
1 ATTTTATATTTTAT
1339229 ATTTTAT
1 ATTTTAT
1339236 TCATTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.07
13 9 0.31
14 11 0.38
16 5 0.17
17 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
ATTTTATATTTTAT
Found at i:1339311 original size:23 final size:26
Alignment explanation
Indices: 1339270--1339316 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
1339260 TTTGAGTAAA
1339270 ATAAAAATATTTAACTATT-TATTTG
1 ATAAAAATATTTAACTATTATATTTG
*
1339295 ATAAAAA-A-TTAATTATTATATT
1 ATAAAAATATTTAACTATTATATT
1339317 ATATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 5 0.25
25 7 0.35
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
ATAAAAATATTTAACTATTATATTTG
Found at i:1340207 original size:12 final size:12
Alignment explanation
Indices: 1340166--1340205 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1340156 TCAAATGTTT
1340166 TATTTAAATTAA
1 TATTTAAATTAA
*
1340178 TATATAAATTAA
1 TATTTAAATTAA
*
1340190 TCTTTAAATT-A
1 TATTTAAATTAA
1340201 TATTT
1 TATTT
1340206 TATTTGTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 5 0.21
12 19 0.79
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTTAAATTAA
Found at i:1341834 original size:17 final size:16
Alignment explanation
Indices: 1341811--1341858 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1341801 TAAAATATAT
1341811 ATATAATAAATTTAAA
1 ATATAATAAATTTAAA
**
1341827 ATTATAATTTA-TTAAA
1 A-TATAATAAATTTAAA
1341843 ATATAATTAAATTTAA
1 ATATAA-TAAATTTAA
1341859 TTAATTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 5 0.20
16 9 0.36
17 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAATAAATTTAAA
Found at i:1341868 original size:21 final size:22
Alignment explanation
Indices: 1341814--1341868 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
1341804 AATATATATA
* *
1341814 TAATAAATTTAAAATTATAATT
1 TAATTAATTTATAATTATAATT
**
1341836 T-ATTAAAATATAATTA-AATT
1 TAATTAATTTATAATTATAATT
1341856 TAATTAATTTATA
1 TAATTAATTTATA
1341869 TAATCATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 5 0.19
21 20 0.77
22 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATTAATTTATAATTATAATT
Found at i:1344852 original size:3 final size:3
Alignment explanation
Indices: 1344844--1344869 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1344834 GACCACGATG
1344844 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1344870 GCGTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1345801 original size:16 final size:16
Alignment explanation
Indices: 1345782--1345812 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1345772 ATTATTTTTA
*
1345782 AAATTTAATATTTAAT
1 AAATTTAAAATTTAAT
1345798 AAATTTAAAATTTAA
1 AAATTTAAAATTTAA
1345813 ATATCAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTTAAAATTTAAT
Found at i:1345821 original size:23 final size:23
Alignment explanation
Indices: 1345778--1345822 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1345768 TATAATTATT
*
1345778 TTTAAAATTTAATATTTAATAAA
1 TTTAAAATTTAATATTCAATAAA
1345801 TTTAAAATTTAA-ATATCAATAA
1 TTTAAAATTTAATAT-TCAATAA
1345823 TTATTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTAAAATTTAATATTCAATAAA
Found at i:1346810 original size:50 final size:50
Alignment explanation
Indices: 1346732--1346940 Score: 274
Period size: 50 Copynumber: 4.2 Consensus size: 50
1346722 AGTTATTATT
** ** * * * *
1346732 ATTGTTGATTATTCTTCATTAATCTTTGATAATAGAGAGAGGTGATCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
* *
1346782 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAGAGAGGTGACCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
* * *
1346832 ATTGTTGATGATTCTTCACCAACCTTTGACAATAGAGAGAGGTAACCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
* * *
1346882 ATTGTTAACGATTCTTCACCAACCTTTAACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
1346932 ATTGTTGAC
1 ATTGTTGAC
1346941 TCTAAGTATA
Statistics
Matches: 139, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 139 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
Found at i:1351408 original size:50 final size:48
Alignment explanation
Indices: 1351333--1351491 Score: 237
Period size: 50 Copynumber: 3.2 Consensus size: 48
1351323 AGTTGTTGCC
* *
1351333 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGG-C-TA
1351383 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTA
*
1351431 TTATTGTTGACGATTCTTCACTAACCTTTGACAATAGAGAGAGGTGGCCATA
1 --ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGG-C-TA
1351483 ATTGTTGAC
1 ATTGTTGAC
1351492 TCTAAGTATA
Statistics
Matches: 102, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
48 2 0.02
49 1 0.01
50 96 0.94
51 1 0.01
52 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (48 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCTA
Found at i:1352285 original size:33 final size:33
Alignment explanation
Indices: 1352248--1352320 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
1352238 AAAATTCTCT
* *
1352248 TTATATTGAATTTAATAATATTAAAAACGAATG
1 TTATATTGAATATAATAAAATTAAAAACGAATG
* *
1352281 TTATATTTAATATGATAAAATTAAAAACGAATG
1 TTATATTGAATATAATAAAATTAAAAACGAATG
1352314 TTATATT
1 TTATATT
1352321 CAAAATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (33 bp):
TTATATTGAATATAATAAAATTAAAAACGAATG
Found at i:1355728 original size:2 final size:2
Alignment explanation
Indices: 1355721--1355760 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1355711 TCAGTTTTCA
1355721 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1355761 TATTTTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1356047 original size:2 final size:2
Alignment explanation
Indices: 1356040--1356064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1356030 TTATGTTGTT
1356040 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1356065 TTTCTCTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1359787 original size:19 final size:18
Alignment explanation
Indices: 1359741--1359789 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1359731 TATTTTTATG
1359741 AAATTTAATATT-TATTTA
1 AAATTTAA-ATTATATTTA
* *
1359759 ATATTAAAATTATATTTTA
1 AAATTTAAATTATA-TTTA
1359778 AAATTTAAATTA
1 AAATTTAAATTA
1359790 AATTCAAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 8 0.32
19 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATTTAAATTATATTTA
Found at i:1360816 original size:13 final size:14
Alignment explanation
Indices: 1360800--1360833 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1360790 TTATATTTTT
1360800 AAAATTTAAAT-AA
1 AAAATTTAAATAAA
1360813 AAAA-TTAAATAAA
1 AAAATTTAAATAAA
1360826 AAAATTTA
1 AAAATTTA
1360834 TTTATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 10 0.53
14 3 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTTAAATAAA
Found at i:1360957 original size:19 final size:19
Alignment explanation
Indices: 1360899--1360959 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
1360889 ATAATATAAA
*
1360899 TTTTAAAAAAA-ATCGATTAT
1 TTTTAAAAAAATAT-TATT-T
* *
1360919 TTTTAAAAATGATCACTATTT
1 TTTTAAAAA-AAT-ATTATTT
1360940 TTTTAAAAAAATATTATTT
1 TTTTAAAAAAATATTATTT
1360959 T
1 T
1360960 GTGTATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 7 0.21
20 11 0.33
21 11 0.33
22 3 0.09
23 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (19 bp):
TTTTAAAAAAATATTATTT
Found at i:1361793 original size:15 final size:15
Alignment explanation
Indices: 1361757--1361799 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
1361747 ATTTTAATAT
1361757 TTTAATTAAATTATA
1 TTTAATTAAATTATA
*
1361772 TATAATTAAATTA-A
1 TTTAATTAAATTATA
1361786 TTTGAATTATAATT
1 TTT-AATTA-AATT
1361800 TAGTTTGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 17 0.71
16 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TTTAATTAAATTATA
Found at i:1363721 original size:2 final size:2
Alignment explanation
Indices: 1363714--1363758 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1363704 TCAAATTTAC
1363714 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1363756 AG A
1 AG A
1363759 TTATACTTCT
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1364916 original size:16 final size:17
Alignment explanation
Indices: 1364886--1364924 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1364876 ATATATATTT
* *
1364886 TAAATATAATTTAAATA
1 TAAAAATAATATAAATA
1364903 -AAAAATAATATAAATA
1 TAAAAATAATATAAATA
1364919 TAAAAA
1 TAAAAA
1364925 ATTTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAATAATATAAATA
Found at i:1375661 original size:2 final size:2
Alignment explanation
Indices: 1375654--1375687 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1375644 GGTGCGTGTG
1375654 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
1375688 AGTAGGAAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1375940 original size:3 final size:3
Alignment explanation
Indices: 1375932--1375973 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1375922 AAGTCCTAAC
* * *
1375932 TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA GAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1375974 ATGACTTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1376185 original size:2 final size:2
Alignment explanation
Indices: 1376178--1376202 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1376168 GCTGTTGCTT
1376178 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1376203 TTTTGAGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1376403 original size:20 final size:21
Alignment explanation
Indices: 1376373--1376411 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1376363 ATTAATAGTC
1376373 TTTATATTATTAAATTTAATA
1 TTTATATTATTAAATTTAATA
*
1376394 TTTA-ATTATTATATTTAA
1 TTTATATTATTAAATTTAA
1376412 AAATAATAGT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATATTATTAAATTTAATA
Found at i:1377582 original size:2 final size:2
Alignment explanation
Indices: 1377575--1377607 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1377565 TGCTCCCTCG
1377575 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
1377608 CATGTGTGTG
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:1383538 original size:14 final size:14
Alignment explanation
Indices: 1383519--1383549 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1383509 ACATCTCTTA
*
1383519 ATATGTATATATGC
1 ATATGTATATATAC
1383533 ATATGTATATATAC
1 ATATGTATATATAC
1383547 ATA
1 ATA
1383550 AGCTTATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (14 bp):
ATATGTATATATAC
Found at i:1385526 original size:2 final size:2
Alignment explanation
Indices: 1385519--1385544 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1385509 CTAAATTTCA
1385519 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
1385545 TTGATCTGTT
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:1387734 original size:6 final size:6
Alignment explanation
Indices: 1387720--1387753 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1387710 AACTTGCAGC
*
1387720 TTCATT TTCAGT TTCAGT TTCAGT TTCAGT TTCA
1 TTCAGT TTCAGT TTCAGT TTCAGT TTCAGT TTCA
1387754 AGGTGAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.53
Consensus pattern (6 bp):
TTCAGT
Found at i:1391690 original size:34 final size:33
Alignment explanation
Indices: 1391651--1391717 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
1391641 TATGTTATAA
* *
1391651 TTATATTTAAA-AATTTTATCTTCATATAAATTTT
1 TTATATATAAATAA-TTTAT-TTCAAATAAATTTT
*
1391685 TTATATATAAATAATTTATTTTAAATAAATTTT
1 TTATATATAAATAATTTATTTCAAATAAATTTT
1391718 AATTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 12 0.41
34 15 0.52
35 2 0.07
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (33 bp):
TTATATATAAATAATTTATTTCAAATAAATTTT
Found at i:1392584 original size:6 final size:6
Alignment explanation
Indices: 1392574--1392620 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
1392564 GGAAGGACAA
* *
1392574 AGACCA AGACCG AGACCG AGACCG AGACCG AGACCG AGACTG AGACC
1 AGACCG AGACCG AGACCG AGACCG AGACCG AGACCG AGACCG AGACC
1392621 AAAGACTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.36, C:0.32, G:0.30, T:0.02
Consensus pattern (6 bp):
AGACCG
Found at i:1395240 original size:2 final size:2
Alignment explanation
Indices: 1395235--1395264 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1395225 TCATTGTGTG
1395235 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1395265 CACACGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1396341 original size:2 final size:2
Alignment explanation
Indices: 1396336--1396360 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1396326 ATACACACAC
1396336 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1396361 ACTGCTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1398514 original size:3 final size:3
Alignment explanation
Indices: 1398506--1398536 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1398496 GTGATCTGTG
1398506 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1398537 CATCATCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1402372 original size:28 final size:25
Alignment explanation
Indices: 1402321--1402372 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
1402311 GTATATATTA
*
1402321 TAATAATTCTTTTTATTTAGTAAGG
1 TAATAATTCTTTTTATTTAATAAGG
*
1402346 TAATAATTTTTTGTTGATTTAAATAAG
1 TAATAATTCTTT-TT-ATTT-AATAAG
1402373 AGTTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 11 0.50
26 2 0.09
27 4 0.18
28 5 0.23
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.52
Consensus pattern (25 bp):
TAATAATTCTTTTTATTTAATAAGG
Found at i:1404403 original size:2 final size:2
Alignment explanation
Indices: 1404396--1404426 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1404386 TCCAATTTCA
1404396 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 A
1404427 GTATCATGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1404583 original size:22 final size:22
Alignment explanation
Indices: 1404540--1404584 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1404530 CCTTTCAATC
* *
1404540 TTAAATTAAATTTATTCATAGA
1 TTAAATTAAATTGAATCATAGA
*
1404562 TTAAATTAAATTGAATCTTAGA
1 TTAAATTAAATTGAATCATAGA
1404584 T
1 T
1404585 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (22 bp):
TTAAATTAAATTGAATCATAGA
Found at i:1410177 original size:12 final size:12
Alignment explanation
Indices: 1410143--1410192 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1410133 GTTATCCTAT
*
1410143 TTAAAAAAAAAA
1 TTAAAAAAAAAG
*
1410155 TT-CAAAAAAAG
1 TTAAAAAAAAAG
1410166 TTAAAAAAAAAG
1 TTAAAAAAAAAG
*
1410178 TTTAAAATAAAAG
1 -TTAAAAAAAAAG
1410191 TT
1 TT
1410193 TATTCTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 9 0.28
12 12 0.38
13 11 0.34
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (12 bp):
TTAAAAAAAAAG
Found at i:1410193 original size:13 final size:13
Alignment explanation
Indices: 1410158--1410194 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1410148 AAAAAAATTC
1410158 AAAAAAAG-TTAA
1 AAAAAAAGTTTAA
1410170 AAAAAAAGTTTAA
1 AAAAAAAGTTTAA
*
1410183 AATAAAAGTTTA
1 AAAAAAAGTTTA
1410195 TTCTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAAAAGTTTAA
Found at i:1412716 original size:21 final size:21
Alignment explanation
Indices: 1412688--1412749 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 21
1412678 AAAATTTTTT
1412688 AAAA-AAATATTAAATTTAAA
1 AAAATAAATATTAAATTTAAA
**
1412708 AAAATAAAT-TTAAATAAAAA
1 AAAATAAATATTAAATTTAAA
*
1412728 TAAAATAAA-ATT-TATTTAAA
1 -AAAATAAATATTAAATTTAAA
1412748 AA
1 AA
1412750 TAAATTAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.06
20 18 0.53
21 14 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATAAATATTAAATTTAAA
Found at i:1412733 original size:17 final size:15
Alignment explanation
Indices: 1412685--1412731 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 15
1412675 TTTAAAATTT
1412685 TTTAAAAAAATATTAAA
1 TTTAAAAAAA-A-TAAA
1412702 TTT-AAAAAAATAAA
1 TTTAAAAAAAATAAA
1412716 TTTAAATAAAAATAAA
1 TTTAAA-AAAAATAAA
1412732 ATAAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.25
15 3 0.11
16 15 0.54
17 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TTTAAAAAAAATAAA
Found at i:1412738 original size:22 final size:22
Alignment explanation
Indices: 1412691--1412762 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
1412681 ATTTTTTAAA
**
1412691 AAAATATTAAATTTAAA-AAAAT
1 AAAAT-TTAAATAAAAATAAAAT
1412713 -AAATTTAAATAAAAATAAAAT
1 AAAATTTAAATAAAAATAAAAT
** *
1412734 AAAATTTATTTAAAAATAAATT
1 AAAATTTAAATAAAAATAAAAT
*
1412756 AAGATTT
1 AAAATTT
1412763 GAGCATGTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 9 0.21
21 9 0.21
22 24 0.57
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (22 bp):
AAAATTTAAATAAAAATAAAAT
Found at i:1413544 original size:27 final size:27
Alignment explanation
Indices: 1413494--1413550 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
1413484 TATAATAATA
*
1413494 AAATAATTTTTAATTTTAATTTAATTAT
1 AAATAATTTATAATTTTAATTTAATT-T
*
1413522 AAATAATTTATATTTTTAA-TTAATTT
1 AAATAATTTATAATTTTAATTTAATTT
1413548 AAA
1 AAA
1413551 ATGATGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 4 0.15
27 6 0.22
28 17 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
AAATAATTTATAATTTTAATTTAATTT
Found at i:1413552 original size:27 final size:27
Alignment explanation
Indices: 1413492--1413596 Score: 79
Period size: 28 Copynumber: 3.7 Consensus size: 27
1413482 TATATAATAA
*
1413492 TAAAATAATTTTTAATTTTAATTTAAT
1 TAAAATAATTTATAATTTTAATTTAAT
*
1413519 TATAAATAATTTATATTTTTAA-TTAATT
1 TA-AAATAATTTATAATTTTAATTTAA-T
* *
1413547 TAAAATGATGATTTTAAAATTTTAAGTTAAAT
1 TAAAAT-A--A-TTTATAATTTTAA-TTTAAT
*
1413579 TAAATTTAATTT-TAATTT
1 TAAA-ATAATTTATAATTT
1413597 ATAAAAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
27 10 0.16
28 26 0.42
29 3 0.05
30 2 0.03
31 11 0.18
32 6 0.10
33 4 0.06
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
TAAAATAATTTATAATTTTAATTTAAT
Found at i:1415446 original size:17 final size:17
Alignment explanation
Indices: 1415424--1415456 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1415414 AAAATTTATA
1415424 AATATA-TAACATAAATC
1 AATATATTAA-ATAAATC
1415441 AATATATTAAATAAAT
1 AATATATTAAATAAAT
1415457 ATGAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATATTAAATAAATC
Found at i:1415451 original size:13 final size:12
Alignment explanation
Indices: 1415435--1415476 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1415425 ATATATAACA
1415435 TAAATCAATATAT
1 TAAAT-AATATAT
1415448 TAAATAA-ATAT
1 TAAATAATATAT
* *
1415459 GAAATAATATAA
1 TAAATAATATAT
1415471 TAAATA
1 TAAATA
1415477 TGGTATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 10 0.40
12 10 0.40
13 5 0.20
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (12 bp):
TAAATAATATAT
Found at i:1415474 original size:19 final size:19
Alignment explanation
Indices: 1415450--1415488 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1415440 CAATATATTA
1415450 AATAAATATGAAATAATAT
1 AATAAATATGAAATAATAT
**
1415469 AATAAATATGGTATAATAT
1 AATAAATATGAAATAATAT
1415488 A
1 A
1415489 TTTAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (19 bp):
AATAAATATGAAATAATAT
Found at i:1415494 original size:23 final size:20
Alignment explanation
Indices: 1415441--1415495 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 20
1415431 AACATAAATC
*
1415441 AATATATTAAATAAATATGA
1 AATATATTTAATAAATATGA
*
1415461 AATA-ATATAATAAATATGGTA
1 AATATATTTAATAAATAT-G-A
1415482 TAATATATTTAATA
1 -AATATATTTAATA
1415496 TATACTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 11 0.39
20 5 0.18
21 1 0.04
22 4 0.14
23 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AATATATTTAATAAATATGA
Found at i:1415504 original size:16 final size:15
Alignment explanation
Indices: 1415480--1415515 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1415470 ATAAATATGG
1415480 TATAATATATTTAATA
1 TATAATATATTT-ATA
*
1415496 TATACTATATTTATA
1 TATAATATATTTATA
1415511 TATAA
1 TATAA
1415516 AAATTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATATATTTATA
Found at i:1415888 original size:26 final size:26
Alignment explanation
Indices: 1415854--1415910 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
1415844 AAACATTTTA
*
1415854 TTTAAAAACCCATTTGATTTTTATAT
1 TTTAAAAACCCATTTAATTTTTATAT
* *
1415880 TTTATAAACTCATTTAATTTTTATAT
1 TTTAAAAACCCATTTAATTTTTATAT
1415906 TTTAA
1 TTTAA
1415911 TTTAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTAAAAACCCATTTAATTTTTATAT
Found at i:1416106 original size:18 final size:18
Alignment explanation
Indices: 1416082--1416120 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1416072 GTCACATTAT
*
1416082 TTTAAAAA-CAAAATAAA
1 TTTAAAAATAAAAATAAA
1416099 TTTAAAAATTAAAAATAAA
1 TTTAAAAA-TAAAAATAAA
1416118 TTT
1 TTT
1416121 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTAAAAATAAAAATAAA
Found at i:1428241 original size:25 final size:25
Alignment explanation
Indices: 1428208--1428264 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
1428198 TTAATTAATT
1428208 TTTTAATTAATTATATTA-TATTATA
1 TTTT-ATTAATTATATTATTATTATA
* * *
1428233 TTATTATTATTTTTATTATTTTTATA
1 TT-TTATTAATTATATTATTATTATA
1428259 TTTTAT
1 TTTTAT
1428265 GAAAAGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTATTAATTATATTATTATTATA
Found at i:1428249 original size:15 final size:16
Alignment explanation
Indices: 1428217--1428264 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 16
1428207 TTTTTAATTA
*
1428217 ATTA-TATTATATTAT
1 ATTATTATTATATTTT
1428232 ATTATTATTAT-TTTT
1 ATTATTATTATATTTT
*
1428247 ATTATTTTTATATTTT
1 ATTATTATTATATTTT
1428263 AT
1 AT
1428265 GAAAAGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTATTATTATATTTT
Found at i:1429739 original size:11 final size:10
Alignment explanation
Indices: 1429723--1429772 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
1429713 TCCAAATTTA
1429723 TATATTATAAT
1 TATATT-TAAT
1429734 TATATTTATAT
1 TATATTTA-AT
*
1429745 TAT-TTT-TT
1 TATATTTAAT
1429753 TATATTATAAT
1 TATATT-TAAT
1429764 TATATTTAA
1 TATATTTAA
1429773 AACATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
8 4 0.12
9 2 0.06
10 9 0.27
11 18 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATTTAAT
Found at i:1429788 original size:33 final size:30
Alignment explanation
Indices: 1429723--1429790 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
1429713 TCCAAATTTA
* *
1429723 TATATTATAATTATATTTATATTATTTTTT
1 TATATTATAATTATATTTACATTATTTATT
1429753 TATATTATAATTATATTTAAAACATTATTTATT
1 TATATTATAATTATATTT---ACATTATTTATT
1429786 TATAT
1 TATAT
1429791 AAAATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 18 0.55
33 15 0.45
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (30 bp):
TATATTATAATTATATTTACATTATTTATT
Found at i:1429832 original size:12 final size:13
Alignment explanation
Indices: 1429792--1429840 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1429782 TATTTATATA
1429792 AAATTTTTATTA-
1 AAATTTTTATTAT
*
1429804 ATAATTTTTGTTAT
1 A-AATTTTTATTAT
1429818 AAATTTTT-TTAT
1 AAATTTTTATTAT
*
1429830 AAATATTTATT
1 AAATTTTTATT
1429841 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 12 0.38
13 19 0.59
14 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
AAATTTTTATTAT
Found at i:1429844 original size:27 final size:26
Alignment explanation
Indices: 1429778--1429844 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
1429768 TTTAAAACAT
*
1429778 TATTTATTTATATAAAATTTTTATTAA
1 TATTTATTT-TATAAAATTTTTATAAA
*
1429805 TAATTT-TTGTTATAAATTTTTTTATAAA
1 T-ATTTATT-TTATAAA-ATTTTTATAAA
1429833 TATTTATTTTAT
1 TATTTATTTTAT
1429845 TTTTATATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 17 0.50
28 17 0.50
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (26 bp):
TATTTATTTTATAAAATTTTTATAAA
Found at i:1436299 original size:16 final size:16
Alignment explanation
Indices: 1436278--1436308 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1436268 TATTTAGTAT
1436278 ATTTTAATATATATAA
1 ATTTTAATATATATAA
*
1436294 ATTTTAATTTATATA
1 ATTTTAATATATATA
1436309 TTAATATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTAATATATATAA
Found at i:1436798 original size:24 final size:23
Alignment explanation
Indices: 1436771--1436825 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
1436761 TTATCATGTC
*
1436771 AATATAAAATAAATAATAAAATGA
1 AATATAAAATAAATAA-AAAATCA
* **
1436795 AATAAAAAATTTATAAAAAATCA
1 AATATAAAATAAATAAAAAATCA
1436818 AA-ATAAAA
1 AATATAAAA
1436826 AATACTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 5 0.19
23 8 0.31
24 13 0.50
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (23 bp):
AATATAAAATAAATAAAAAATCA
Found at i:1436970 original size:22 final size:22
Alignment explanation
Indices: 1436945--1436993 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1436935 TTAAAAAAAA
1436945 AAGGAGAAGGGAGGG-GGAGGGG
1 AAGGAGAAGGG-GGGCGGAGGGG
* * *
1436967 AAGGGGGAGGGGGGCGGAGGGT
1 AAGGAGAAGGGGGGCGGAGGGG
1436989 AAGGA
1 AAGGA
1436994 AAAGACGTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.29, C:0.02, G:0.67, T:0.02
Consensus pattern (22 bp):
AAGGAGAAGGGGGGCGGAGGGG
Found at i:1447431 original size:22 final size:21
Alignment explanation
Indices: 1447382--1447436 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
1447372 ATAATAATAA
*
1447382 ATTTATAAAAAATTATAAAAT
1 ATTTAAAAAAAATTATAAAAT
**
1447403 AAATAAAAATAAATTATAAAAT
1 ATTTAAAAA-AAATTATAAAAT
*
1447425 TTTTAAAAAAAA
1 ATTTAAAAAAAA
1447437 AGCAATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTTAAAAAAAATTATAAAAT
Found at i:1448637 original size:25 final size:25
Alignment explanation
Indices: 1448575--1448638 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
1448565 ATGGATATAA
*
1448575 TAAATATTAATA-AAAAATTAATTAT
1 TAAAT-TTAATATTAAAATTAATTAT
* *
1448600 TATAATATCATATTAAAATT-ATTATT
1 TA-AATTTAATATTAAAATTAATTA-T
1448626 TAAATTTAATATT
1 TAAATTTAATATT
1448639 CATTATTAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 19 0.61
26 12 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TAAATTTAATATTAAAATTAATTAT
Found at i:1453506 original size:16 final size:16
Alignment explanation
Indices: 1453485--1453520 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
1453475 ATTGTCATAA
1453485 TACTTTTTGACACAGG
1 TACTTTTTGACACAGG
1453501 TAC--TTTGACACAGG
1 TACTTTTTGACACAGG
1453515 TACTTT
1 TACTTT
1453521 GACGCAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 14 0.78
16 4 0.22
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (16 bp):
TACTTTTTGACACAGG
Found at i:1453509 original size:14 final size:14
Alignment explanation
Indices: 1453490--1453565 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1453480 CATAATACTT
*
1453490 TTTGACACAGGTAC
1 TTTGGCACAGGTAC
*
1453504 TTTGACACAGGTAC
1 TTTGGCACAGGTAC
* * *
1453518 TTTGACGCAAGTAC
1 TTTGGCACAGGTAC
* *
1453532 -TTGGTA-AGATAC
1 TTTGGCACAGGTAC
*
1453544 TTTGGCACATGTA-
1 TTTGGCACAGGTAC
*
1453557 TTTAGCACA
1 TTTGGCACA
1453566 AATACTTAGC
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
12 4 0.08
13 16 0.33
14 29 0.59
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (14 bp):
TTTGGCACAGGTAC
Found at i:1453608 original size:36 final size:36
Alignment explanation
Indices: 1453563--1453634 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1453553 TGTATTTAGC
*
1453563 ACAAATACTTAGCTTGGTACTTCGCACAGGTACTTT
1 ACAAATACTTAGCTTGGTACTTCGCACAAGTACTTT
1453599 ACAAATACTTAGCTTGGTACTTCGCACAAGTACTTT
1 ACAAATACTTAGCTTGGTACTTCGCACAAGTACTTT
1453635 GGCACAAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (36 bp):
ACAAATACTTAGCTTGGTACTTCGCACAAGTACTTT
Found at i:1453641 original size:14 final size:14
Alignment explanation
Indices: 1453622--1453831 Score: 214
Period size: 13 Copynumber: 16.0 Consensus size: 14
1453612 TTGGTACTTC
*
1453622 GCACAAGTACTTTG
1 GCACAGGTACTTTG
* *
1453636 GCACAAGTA-TTTA
1 GCACAGGTACTTTG
1453649 GCACAGGTAC-TTG
1 GCACAGGTACTTTG
1453662 GCA-AGGTACTTTG
1 GCACAGGTACTTTG
1453675 GCACAGGTACTTTG
1 GCACAGGTACTTTG
*
1453689 GCACAAGTAC-TTG
1 GCACAGGTACTTTG
1453702 GCA-AGGTACTTTG
1 GCACAGGTACTTTG
*
1453715 GCACAGGTAC-TTA
1 GCACAGGTACTTTG
*
1453728 GCATAGGTA-TTTG
1 GCACAGGTACTTTG
1453741 GCA-AGGTAC-TTG
1 GCACAGGTACTTTG
* *
1453753 GCACAAGCACTTTG
1 GCACAGGTACTTTG
*
1453767 GTACAGGTA-TTT-
1 GCACAGGTACTTTG
1453779 GCA-AGGTACTTTG
1 GCACAGGTACTTTG
*
1453792 GTACAGGTACTTT-
1 GCACAGGTACTTTG
*
1453805 GCA-AGATACTTTG
1 GCACAGGTACTTTG
*
1453818 GCACAAGTACTTTG
1 GCACAGGTACTTTG
1453832 ACAATAATAC
Statistics
Matches: 163, Mismatches: 19, Indels: 28
0.78 0.09 0.13
Matches are distributed among these distances:
11 5 0.03
12 35 0.21
13 63 0.39
14 60 0.37
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (14 bp):
GCACAGGTACTTTG
Found at i:1456172 original size:66 final size:66
Alignment explanation
Indices: 1456079--1456592 Score: 403
Period size: 67 Copynumber: 7.7 Consensus size: 66
1456069 GTCCAATACA
* * * *
1456079 CCACTCGCGTCACTCTTTCATTTACAAGTATTCTTAATGGAGAAGTCGATCGTTGTGGTCTCCTA
1 CCACTC-CGTCACTCTCTCATTTACAAGTATTCTTAATGGAGAAGTCGACCGTTGTGGTCTCATG
1456144 CG
65 CG
* * * * *
1456146 TCACTCCGTCACTCTCTCATTTACAAGTATTCTTAATGGAGAAGTCGACTGTTGTGATCTCCTAC
1 CCACTCCGTCACTCTCTCATTTACAAGTATTCTTAATGGAGAAGTCGACCGTTGTGGTCTCATGC
1456211 G
66 G
* * * * * * *
1456212 CCACTCCATCACTCTCTCATTTACAAGTATTCTTAATGAAAAAGTTGACCGTTATGGTTTTATGC
1 CCACTCCGTCACTCTCTCATTTACAAGTATTCTTAATGGAGAAGTCGACCGTTGTGGTCTCATGC
*
1456277 A
66 G
* * * ** *
1456278 CCACTCTCGTCACTCTCTCATTTGCAAGTAGTCTTAATAGAGAAGTCGATTGTTGTGGTCTCTTG
1 CCACTC-CGTCACTCTCTCATTTACAAGTATTCTTAATGGAGAAGTCGACCGTTGTGGTCTCATG
*
1456343 CA
65 CG
* * * * * * * *
1456345 CCACTCCCGTCACTTTCTCATTTACAAATACAT-TTAATGGAGAAGTTGGCCATTATAGTCTCAT
1 CCACT-CCGTCACTCTCTCATTTACAAGTA-TTCTTAATGGAGAAGTCGACCGTTGTGGTCTCAT
1456409 GCAG
64 GC-G
* ** * ** *
1456413 -TACTCCTGTCACTCTCTCATTTACAAGTACACTTAATAGAGAAGTCGACTATTGTTGTCTCATG
1 CCACTCC-GTCACTCTCTCATTTACAAGTATTCTTAATGGAGAAGTCGACCGTTGTGGTCTCATG
*
1456477 TG
65 CG
* * * ** * *
1456479 CCACTTCTGTCACTCTCCCTATATACAAG--TTCTTCAAATGGAGAAAGTTAACCATTGTAGTC-
1 CCAC-TCCGTCACTCTCTC-ATTTACAAGTATTCTT--AATGGAG-AAGTCGACCGTTGTGGTCT
1456541 CTATGCG
61 C-ATGCG
* *
1456548 CCACTTCCGTCACTCTC-C-TTAATACAAGTATTCTTACTAGAGAAG
1 CCAC-TCCGTCACTCTCTCATT--TACAAGTATTCTTAATGGAGAAG
1456593 ACTGTTATGG
Statistics
Matches: 357, Mismatches: 73, Indels: 34
0.77 0.16 0.07
Matches are distributed among these distances:
66 122 0.34
67 165 0.46
68 31 0.09
69 34 0.10
70 5 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (66 bp):
CCACTCCGTCACTCTCTCATTTACAAGTATTCTTAATGGAGAAGTCGACCGTTGTGGTCTCATGC
G
Found at i:1456832 original size:2 final size:2
Alignment explanation
Indices: 1456825--1456861 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1456815 TGCTAGCCTT
1456825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1456862 TCCTTGCACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1456963 original size:28 final size:28
Alignment explanation
Indices: 1456922--1456977 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1456912 GCTCAAAAAA
* *
1456922 TAACATGTTTTTCATGTTGCATACCAAG
1 TAACATGTTCTTCATGCTGCATACCAAG
*
1456950 TAACATGTTCTTCATGCTGCATGCCAAG
1 TAACATGTTCTTCATGCTGCATACCAAG
1456978 ACTTTGTGCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (28 bp):
TAACATGTTCTTCATGCTGCATACCAAG
Found at i:1457240 original size:39 final size:39
Alignment explanation
Indices: 1457186--1457508 Score: 309
Period size: 39 Copynumber: 8.2 Consensus size: 39
1457176 ATCATAATAC
*
1457186 ACTTTGGCACAGGTACTTGGCA-AGGTACTTGGCACAAGT
1 ACTTTGGCACAGGTACTTGGCACAGGTACTTGGCA-AGGT
* * *
1457225 ACTTTGACACAGGTACTTGGCACAGATACTTGGTAAGGT
1 ACTTTGGCACAGGTACTTGGCACAGGTACTTGGCAAGGT
* *
1457264 ACTTTGGCACAGGTATTTAGCACAGGTACTTGGCAAGGT
1 ACTTTGGCACAGGTACTTGGCACAGGTACTTGGCAAGGT
* * *
1457303 A-TTTCGCACAGGTACTTTAGCACTGGTACCTTGGCAAGGT
1 ACTTTGGCACAGGTAC-TTGGCACAGGTA-CTTGGCAAGGT
* * *
1457343 AAC-TTAGCACAGGTACCTAGCACAGGTACCTT-GCAAGGT
1 -ACTTTGGCACAGGTACTTGGCACAGGTA-CTTGGCAAGGT
* * * *
1457382 ACCTTGGCACAAGTACCTGGCACAAGTACCTTGGTACAA-GT
1 ACTTTGGCACAGGTACTTGGCACAGGTA-CTTGG--CAAGGT
** * *
1457423 TTTTTGGCACAGGTACTTGGCA-AGATACTTGACACAGGT
1 ACTTTGGCACAGGTACTTGGCACAGGTACTTGGCA-AGGT
* * *
1457462 AC-TTAGCACAGGTACTTGGCACAGGTACTTTGCAAGAT
1 ACTTTGGCACAGGTACTTGGCACAGGTACTTGGCAAGGT
1457500 ACTTTGGCA
1 ACTTTGGCA
1457509 ATAATACTTC
Statistics
Matches: 236, Mismatches: 35, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
37 2 0.01
38 38 0.16
39 122 0.52
40 39 0.17
41 32 0.14
42 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (39 bp):
ACTTTGGCACAGGTACTTGGCACAGGTACTTGGCAAGGT
Found at i:1457356 original size:118 final size:116
Alignment explanation
Indices: 1457192--1457508 Score: 325
Period size: 118 Copynumber: 2.7 Consensus size: 116
1457182 ATACACTTTG
* * * * * *
1457192 GCACAGGTACTTGGCAAGGTACTTGGCACAAGTACTTTGACACAGGTACTTGGCACAGATACTTG
1 GCACAGGTACTTAGCAAGATACTTGACACAGGTACTTAG-CACAGGTACTTGGCACAGGTACTT-
* * ** *
1457257 GTAAGGTACTTTGGCACAGGTATTTAGCACAGGTA-CTTGG-CAAGGTATTTC
64 GCAAGGTACTTTGGCACAAGTACCTAGCACAAGTACCTTGGACAAGGTATTTC
* * * * *
1457308 GCACAGGTACTTTAGCACTGGTACCTTGGCA-AGGTAACTTAGCACAGGTACCTAGCACAGGTAC
1 GCACAGGTAC-TTAGCA-AGATA-CTTGACACAGGT-ACTTAGCACAGGTACTTGGCACAGGTA-
* * * * *
1457372 CTTGCAAGGTACCTTGGCACAAGTACCTGGCACAAGTACCTTGGTACAAGTTTTTTG
61 CTTGCAAGGTACTTTGGCACAAGTACCTAGCACAAGTACCTTGG-ACAAGGTATTTC
*
1457429 GCACAGGTACTTGGCAAGATACTTGACACAGGTACTTAGCACAGGTACTTGGCACAGGTACTTTG
1 GCACAGGTACTTAGCAAGATACTTGACACAGGTACTTAGCACAGGTACTTGGCACAGGTAC-TTG
*
1457494 CAAGATACTTTGGCA
65 CAAGGTACTTTGGCA
1457509 ATAATACTTC
Statistics
Matches: 166, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
116 10 0.06
117 6 0.04
118 100 0.60
119 27 0.16
120 5 0.03
121 18 0.11
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (116 bp):
GCACAGGTACTTAGCAAGATACTTGACACAGGTACTTAGCACAGGTACTTGGCACAGGTACTTGC
AAGGTACTTTGGCACAAGTACCTAGCACAAGTACCTTGGACAAGGTATTTC
Found at i:1457509 original size:13 final size:13
Alignment explanation
Indices: 1457189--1457491 Score: 269
Period size: 13 Copynumber: 23.2 Consensus size: 13
1457179 ATAATACACT
1457189 TTGGCACAGGTAC
1 TTGGCACAGGTAC
1457202 TTGGCA-AGGTAC
1 TTGGCACAGGTAC
*
1457214 TTGGCACAAGTAC
1 TTGGCACAGGTAC
*
1457227 TTTGACACAGGTAC
1 -TTGGCACAGGTAC
*
1457241 TTGGCACAGATAC
1 TTGGCACAGGTAC
*
1457254 TTGGTA-AGGTAC
1 TTGGCACAGGTAC
*
1457266 TTTGGCACAGGTAT
1 -TTGGCACAGGTAC
*
1457280 TTAGCACAGGTAC
1 TTGGCACAGGTAC
*
1457293 TTGGCA-AGGTAT
1 TTGGCACAGGTAC
*
1457305 TTCGCACAGGTAC
1 TTGGCACAGGTAC
* *
1457318 TTTAGCACTGGTACC
1 -TTGGCACAGGTA-C
1457333 TTGGCA-AGGTAAC
1 TTGGCACAGGT-AC
*
1457346 TTAGCACAGGTAC
1 TTGGCACAGGTAC
* *
1457359 CTAGCACAGGTACC
1 TTGGCACAGGTA-C
1457373 TT-GCA-AGGTACC
1 TTGGCACAGGTA-C
*
1457385 TTGGCACAAGTAC
1 TTGGCACAGGTAC
* *
1457398 CTGGCACAAGTACC
1 TTGGCACAGGTA-C
* * **
1457412 TTGGTACAAGTTTT
1 TTGGCAC-AGGTAC
1457426 TTGGCACAGGTAC
1 TTGGCACAGGTAC
*
1457439 TTGGCA-AGATAC
1 TTGGCACAGGTAC
*
1457451 TTGACACAGGTAC
1 TTGGCACAGGTAC
*
1457464 TTAGCACAGGTAC
1 TTGGCACAGGTAC
1457477 TTGGCACAGGTAC
1 TTGGCACAGGTAC
1457490 TT
1 TT
1457492 TGCAAGATAC
Statistics
Matches: 235, Mismatches: 40, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
12 46 0.20
13 132 0.56
14 54 0.23
15 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (13 bp):
TTGGCACAGGTAC
Found at i:1462018 original size:2 final size:2
Alignment explanation
Indices: 1462011--1462040 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1462001 ATGATTTTGT
1462011 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
1462041 GCTATCTTCT
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):
TC
Found at i:1464367 original size:23 final size:23
Alignment explanation
Indices: 1464321--1464371 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
1464311 AATTAAATGT
1464321 TTAAATTTAATAAAAAATTAAAA
1 TTAAATTTAATAAAAAATTAAAA
1464344 TTAAATTATAATAATAAAA-T-AAA
1 TTAAATT-TAATAA-AAAATTAAAA
1464367 TTAAA
1 TTAAA
1464372 GATATTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 15 0.58
24 7 0.27
25 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TTAAATTTAATAAAAAATTAAAA
Found at i:1464405 original size:15 final size:15
Alignment explanation
Indices: 1464387--1464424 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1464377 TTAAATTTTT
1464387 TTATTT-TAAAAATAA
1 TTATTTATAAAAA-AA
*
1464402 TTATTTATTAAAAAA
1 TTATTTATAAAAAAA
1464417 TTATTTAT
1 TTATTTAT
1464425 TTAATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATTTATAAAAAAA
Found at i:1464425 original size:15 final size:16
Alignment explanation
Indices: 1464395--1464425 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1464385 TTTTATTTTA
1464395 AAAATAATTATTTATT
1 AAAATAATTATTTATT
1464411 AAAA-AATTATTTATT
1 AAAATAATTATTTATT
1464426 TAATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAATAATTATTTATT
Found at i:1464464 original size:26 final size:26
Alignment explanation
Indices: 1464413--1464464 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1464403 TATTTATTAA
* *
1464413 AAAATTATTTATTTAATTTATAATTT
1 AAAATTATTTATTAAAATTATAATTT
1464439 AAAATTATTT-TTAAAATTATATATTT
1 AAAATTATTTATTAAAATTATA-ATTT
1464465 TTGTTCACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
AAAATTATTTATTAAAATTATAATTT
Found at i:1464985 original size:22 final size:22
Alignment explanation
Indices: 1464944--1464986 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1464934 AATTAATTAT
*
1464944 ATTTTAAATATAATATATATAG
1 ATTTTAAATATAATAAATATAG
1464966 ATTTT-AATATAATAAAATATA
1 ATTTTAAATATAAT-AAATATA
1464987 ATTAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTTTAAATATAATAAATATAG
Found at i:1465360 original size:4 final size:4
Alignment explanation
Indices: 1465351--1465375 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1465341 ACTATCCTTT
1465351 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
1465376 GCAATAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Done.