Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold425
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: 711097
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 3 of 5
Found at i:361181 original size:16 final size:16
Alignment explanation
Indices: 361139--361289 Score: 96
Period size: 16 Copynumber: 9.6 Consensus size: 16
361129 CTGCTTTTGT
361139 ATTT-AATTATTTTAA
1 ATTTAAATTATTTTAA
* *
361154 GTTTGAATTTATTTTAA
1 ATTT-AAATTATTTTAA
*
361171 ATTTAAATTATATTAA
1 ATTTAAATTATTTTAA
**
361187 ATTTAAA-TATTTTTT
1 ATTTAAATTATTTTAA
* *
361202 ATTTAAATT-TTTGAG
1 ATTTAAATTATTTTAA
*
361217 ATTTGAATTATATTT-A
1 ATTTAAATTAT-TTTAA
* * **
361233 ATTTATATCATTTTGG
1 ATTTAAATTATTTTAA
* *
361249 ATATAAAAT-TTTTAA
1 ATTTAAATTATTTTAA
* *
361264 TTTTTAATTATTTTAA
1 ATTTAAATTATTTTAA
*
361280 ATTTAGATTA
1 ATTTAAATTA
361290 ATTTGAGTTT
Statistics
Matches: 98, Mismatches: 31, Indels: 13
0.69 0.22 0.09
Matches are distributed among these distances:
15 38 0.39
16 45 0.46
17 15 0.15
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:361181 original size:33 final size:31
Alignment explanation
Indices: 361138--361246 Score: 82
Period size: 33 Copynumber: 3.5 Consensus size: 31
361128 GCTGCTTTTG
361138 TATTT-AATTATTTTAAGTTTGAATTTATTT
1 TATTTAAATTATTTTAAGTTTGAATTTATTT
* * *
361168 TAAATTTAAATTATATTAAATTTAAATATT-TTT
1 T--ATTTAAATTATTTTAAGTTTGAAT-TTATTT
*
361201 TATTTAAA-T-TTTTGAGATTTGAATTATATTT
1 TATTTAAATTATTTTAAG-TTTGAATT-TATTT
* * *
361232 AATTTATATCATTTT
1 TATTTAAATTATTTT
361247 GGATATAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
29 5 0.08
30 9 0.15
31 16 0.27
32 4 0.07
33 24 0.40
34 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.59
Consensus pattern (31 bp):
TATTTAAATTATTTTAAGTTTGAATTTATTT
Found at i:361283 original size:47 final size:44
Alignment explanation
Indices: 361164--361284 Score: 109
Period size: 47 Copynumber: 2.6 Consensus size: 44
361154 GTTTGAATTT
* * ** *
361164 ATTTTAAATTTAAATTATATTAAATTTAAATATTTTTTATTTAA
1 ATTTTTAATTTAAATTATTTTAAATTTAAATATTTTGGATTAAA
* *
361208 ATTTTTGAGATTTGAATTATATTT-AATTTATATCATTTTGGATATAAA
1 ATTTTT-A-ATTTAAATTAT-TTTAAATTTAAAT-ATTTTGGAT-TAAA
*
361256 ATTTTTAATTTTTAATTATTTTAAATTTA
1 ATTTTTAA-TTTAAATTATTTTAAATTTA
361285 GATTAATTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
44 5 0.08
45 1 0.02
46 22 0.35
47 25 0.40
48 9 0.15
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (44 bp):
ATTTTTAATTTAAATTATTTTAAATTTAAATATTTTGGATTAAA
Found at i:362079 original size:21 final size:22
Alignment explanation
Indices: 362043--362085 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
362033 ATTAGATTTT
362043 TTTTTAAGTCTTTGTATTATAAA
1 TTTTTAAG-CTTTGTATTATAAA
362066 TTTTTAAG-TTTGTATTATAA
1 TTTTTAAGCTTTGTATTATAA
362086 TTTGATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
23 8 0.40
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (22 bp):
TTTTTAAGCTTTGTATTATAAA
Found at i:363066 original size:16 final size:16
Alignment explanation
Indices: 363027--363098 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
363017 AGATTTTAGG
363027 TTTTTTTTCAATTTTGAA
1 TTTTTTTT-AATTTT-AA
*
363045 -TTTTTTTAAATTTAA
1 TTTTTTTTAATTTTAA
363060 TTTTTTTTAATTTTATA
1 TTTTTTTTAATTTTA-A
* * * *
363077 CTTATTTGAATTTAAA
1 TTTTTTTTAATTTTAA
363093 TTTTTT
1 TTTTTT
363099 AAATTCATAC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
15 2 0.05
16 23 0.52
17 19 0.43
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTTTTAATTTTAA
Found at i:363089 original size:32 final size:32
Alignment explanation
Indices: 363027--363112 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 32
363017 AGATTTTAGG
* *
363027 TTTTTTTTCAATTTTGA-ATTTTTTTAAATTTAA
1 TTTTTTTT-AATTTT-ATACTTATTTAAATTTAA
*
363060 TTTTTTTTAATTTTATACTTATTTGAATTTAA
1 TTTTTTTTAATTTTATACTTATTTAAATTTAA
* * *
363092 -ATTTTTTAAATTCATACTTAT
1 TTTTTTTTAATTTTATACTTAT
363113 AATTTTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 19 0.41
32 19 0.41
33 8 0.17
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (32 bp):
TTTTTTTTAATTTTATACTTATTTAAATTTAA
Found at i:363095 original size:33 final size:33
Alignment explanation
Indices: 363027--363098 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
363017 AGATTTTAGG
* *
363027 TTTTTTTTCAATTTTGAATTTTTTTAAATTTAA
1 TTTTTTTTCAATTTTGAACTTATTTAAATTTAA
*
363060 TTTTTTTT-AATTTT-ATACTTATTTGAATTTAA
1 TTTTTTTTCAATTTTGA-ACTTATTTAAATTTAA
*
363092 ATTTTTT
1 TTTTTTT
363099 AAATTCATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.03
32 25 0.74
33 8 0.24
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (33 bp):
TTTTTTTTCAATTTTGAACTTATTTAAATTTAA
Found at i:364036 original size:25 final size:23
Alignment explanation
Indices: 363987--364047 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
363977 ATTTAAGTTA
363987 TTATTTAATTAATAAAAAATATT
1 TTATTTAATTAATAAAAAATATT
*
364010 TTATTTAAATTTAATTATAAAAT-TT
1 TTATTT-AA-TTAA-TAAAAAATATT
*
364035 TTAATT-ATTAATA
1 TTATTTAATTAATA
364048 TAAGATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
21 2 0.06
22 4 0.12
23 7 0.21
24 2 0.06
25 11 0.33
26 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTTAATTAATAAAAAATATT
Found at i:364058 original size:25 final size:27
Alignment explanation
Indices: 364030--364088 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
364020 TTAATTATAA
364030 AATTTTTAAT-TATT-AATA-TAAGATT
1 AATTTTTAATATATTAAATAGTAA-ATT
*
364055 AATTTTTAATATTTTAAATAGTAAATT
1 AATTTTTAATATATTAAATAGTAAATT
364082 AATTTTT
1 AATTTTT
364089 TTTTAAGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 10 0.33
26 3 0.10
27 14 0.47
28 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
AATTTTTAATATATTAAATAGTAAATT
Found at i:367303 original size:28 final size:29
Alignment explanation
Indices: 367270--367324 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
367260 TAAAATTTTT
* *
367270 AATAATAGTATAAATA-TATTAAAAATAA
1 AATAATAATATAAATATTATAAAAAATAA
367298 AATAATAATATAAATATTATAAAAAAT
1 AATAATAATATAAATATTATAAAAAAT
367325 TTTGATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
AATAATAATATAAATATTATAAAAAATAA
Found at i:367392 original size:31 final size:31
Alignment explanation
Indices: 367351--367410 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
367341 TTAAATATTA
*
367351 AAAT-ATTTAAATTTAAATTATT-TAATAATTT
1 AAATAATTAAAATTT-AA-TATTCTAATAATTT
367382 AAATAATTAAAATTTAATATTCTAATAAT
1 AAATAATTAAAATTTAATATTCTAATAAT
367411 AATAATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 13 0.50
32 9 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
AAATAATTAAAATTTAATATTCTAATAATTT
Found at i:368308 original size:10 final size:10
Alignment explanation
Indices: 368295--368358 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
368285 ATATAAATTA
368295 AAAATAATAT
1 AAAATAATAT
368305 AAAATAATAT
1 AAAATAATAT
*
368315 AAATATGATAT
1 AAA-ATAATAT
368326 -AAAT-ATAT
1 AAAATAATAT
*
368334 AAACA-CATA-
1 AAA-ATAATAT
368343 AAAAT-ATAT
1 AAAATAATAT
368352 AAAATAA
1 AAAATAA
368359 ATTATTAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
8 8 0.17
9 12 0.26
10 20 0.43
11 6 0.13
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAATAATAT
Found at i:368329 original size:11 final size:11
Alignment explanation
Indices: 368293--368332 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
368283 TTATATAAAT
*
368293 TAAAAATAATA
1 TAAATATAATA
368304 TAAA-ATAATA
1 TAAATATAATA
*
368314 TAAATATGATA
1 TAAATATAATA
368325 TAAATATA
1 TAAATATA
368333 TAAACACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
TAAATATAATA
Found at i:368374 original size:20 final size:19
Alignment explanation
Indices: 368264--368398 Score: 59
Period size: 18 Copynumber: 7.1 Consensus size: 19
368254 AGTAAAACTA
*
368264 ATTAT-TAATATATAAAA-
1 ATTATATAATTTATAAAAT
*
368281 ATTTATATAAATTA-AAAAT
1 A-TTATATAATTTATAAAAT
* * *
368300 AATATA-AAATAATATAAAT
1 ATTATATAATTTATA-AAAT
* * *
368319 ATGATATAAATATATAAACAC
1 ATTATAT-AATTTATAAA-AT
* *
368340 A-TA-AAAATATATAAAAT
1 ATTATATAATTTATAAAAT
368357 AAATTAT-TAATTTATAAAAT
1 --ATTATATAATTTATAAAAT
*
368377 TTTATATAATTTATAAATAT
1 ATTATATAATTTATAAA-AT
368397 AT
1 AT
368399 AAAAAATAAT
Statistics
Matches: 87, Mismatches: 17, Indels: 25
0.67 0.13 0.19
Matches are distributed among these distances:
17 7 0.08
18 27 0.31
19 27 0.31
20 19 0.22
21 7 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (19 bp):
ATTATATAATTTATAAAAT
Found at i:368395 original size:47 final size:45
Alignment explanation
Indices: 368256--368402 Score: 136
Period size: 47 Copynumber: 3.1 Consensus size: 45
368246 AAAATTTAAG
*
368256 TAAAACTAATTATTAATATATAAAAATTTATATAAATTAAAAATAATA
1 TAAAA-TAATTATTAATTTAT-AAAATTTATATAAATTAAAAAT-ATA
* * * *
368304 TAAAATAA-TATAAATATGATATAAATATATA-AACACATAAAAATATA
1 TAAAATAATTATTAAT-TTATA-AAATTTATATAA-A-TTAAAAATATA
* *
368351 TAAAATAAATTATTAATTTATAAAATTTTATATAATTTATAAATATA
1 TAAAAT-AATTATTAATTTATAAAA-TTTATATAAATTAAAAATATA
368398 TAAAA
1 TAAAA
368403 AATAATAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
46 9 0.11
47 40 0.50
48 23 0.29
49 8 0.10
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (45 bp):
TAAAATAATTATTAATTTATAAAATTTATATAAATTAAAAATATA
Found at i:368719 original size:27 final size:29
Alignment explanation
Indices: 368688--368741 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
368678 ATTACAGGTT
*
368688 ATAAAAATATAT-TT-TAAATTTTAAAAA
1 ATAAAAATATATCTTAAAAATTTTAAAAA
*
368715 ATAAAAATTTATCTTAAAAATTTTAAA
1 ATAAAAATATATCTTAAAAATTTTAAA
368742 TTTTATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 2 0.09
29 10 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
ATAAAAATATATCTTAAAAATTTTAAAAA
Found at i:368802 original size:10 final size:11
Alignment explanation
Indices: 368775--368809 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
368765 GATAACACTT
368775 ATATTTTAAAA
1 ATATTTTAAAA
368786 TATATTTTAAAA
1 -ATATTTTAAAA
368798 A-ATTTTAAAA
1 ATATTTTAAAA
368808 AT
1 AT
368810 TAATATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 1 0.05
12 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATTTTAAAA
Found at i:369735 original size:16 final size:16
Alignment explanation
Indices: 369705--369773 Score: 79
Period size: 16 Copynumber: 4.4 Consensus size: 16
369695 GTATGATATT
*
369705 TTTAA-TTGATATTAA
1 TTTAATTTGATTTTAA
369720 TTTAATTTGATTTTAA
1 TTTAATTTGATTTTAA
*
369736 TTTGATTTGATTTTAA
1 TTTAATTTGATTTTAA
* * *
369752 -TTATTTTTATTTAAA
1 TTTAATTTGATTTTAA
369767 TTTAATT
1 TTTAATT
369774 ATAAAATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
15 16 0.36
16 29 0.64
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTAATTTGATTTTAA
Found at i:370591 original size:20 final size:21
Alignment explanation
Indices: 370566--370604 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
370556 TCAGTGAATT
*
370566 AAATAATATTATTT-TATTAA
1 AAATAAAATTATTTATATTAA
370586 AAATAAAATTATTTATATT
1 AAATAAAATTATTTATATT
370605 TTTTATTTAT
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:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAAAATTATTTATATTAA
Found at i:371146 original size:51 final size:51
Alignment explanation
Indices: 371089--371186 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
371079 TAAAATAATT
* * *
371089 TCTTATCTCTT-ATATAAAATGAGATAAACTAATCTATATCTTTTATCTTTA
1 TCTTATCTCTTAATAT-AAATGAAATAAACTAATATATATCTCTTATCTTTA
* *
371140 TCTTATCTCTTAATATAAATGAAATAAATTAATATTTATCTCTTATC
1 TCTTATCTCTTAATATAAATGAAATAAACTAATATATATCTCTTATC
371187 ATTTTTATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 37 0.90
52 4 0.10
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (51 bp):
TCTTATCTCTTAATATAAATGAAATAAACTAATATATATCTCTTATCTTTA
Found at i:372771 original size:2 final size:2
Alignment explanation
Indices: 372764--372788 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
372754 AAAAGGTTGC
372764 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
372789 GTGTCTTTAT
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:374040 original size:2 final size:2
Alignment explanation
Indices: 374035--374075 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
374025 CACAGACATT
374035 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
374076 TTTGCCTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:375810 original size:35 final size:36
Alignment explanation
Indices: 375764--375834 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
375754 CAGAACTAAG
*
375764 CAATAATAACACTTGTTACAATG-TTTGAAAAAAAA
1 CAATAATAACACTTGTTACAATGCTTGGAAAAAAAA
375799 CAATAATAACACTTGTTACAATGCTTGGAAAAAAAA
1 CAATAATAACACTTGTTACAATGCTTGGAAAAAAAA
375835 TGATAGTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 23 0.68
36 11 0.32
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.27
Consensus pattern (36 bp):
CAATAATAACACTTGTTACAATGCTTGGAAAAAAAA
Found at i:377049 original size:18 final size:19
Alignment explanation
Indices: 377026--377078 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 19
377016 TTTTTATTTG
377026 TATTATATTTATATTATT-
1 TATTATATTTATATTATTA
* *
377044 TATTATATTTAAAATATTA
1 TATTATATTTATATTATTA
377063 TATTA-ATTTATATTAT
1 TATTATATTTATATTAT
377079 ATAAAATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATATTTATATTATTA
Found at i:377083 original size:27 final size:26
Alignment explanation
Indices: 377034--377085 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
377024 TGTATTATAT
*
377034 TTATATTATTTATTATATTTAAAATA
1 TTATATTATTTATTATATATAAAATA
377060 TTATATTAATTTA-TATTATATAAAAT
1 TTATATT-ATTTATTA-TATATAAAAT
377086 TGAACACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATATTATTTATTATATATAAAATA
Found at i:378248 original size:4 final size:4
Alignment explanation
Indices: 378239--378272 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
378229 AAAAACAAGA
*
378239 TTTC TTTC TTTC TTTC TTTC TTTT TTTC -TTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
378273 TTTTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:379002 original size:69 final size:69
Alignment explanation
Indices: 378911--379114 Score: 327
Period size: 69 Copynumber: 3.0 Consensus size: 69
378901 GGGACAAAAG
* * * *
378911 AAATAGAATTGTTATTCCTAAATTTGAGGATAGATGAACATATAATGTAATATAATGCAAATTTA
1 AAATGGAATTGTTATTCTTAAATTTGAGGAAAGATGAAAATATAATGTAATATAATGCAAATTTA
*
378976 TTAG
66 TTAA
*
378980 GAATGGAATTGTTATTCTTAAATTTGAGGAAAGATGAAAATATAATGTAATATAATGCAAATTTA
1 AAATGGAATTGTTATTCTTAAATTTGAGGAAAGATGAAAATATAATGTAATATAATGCAAATTTA
379045 TTAA
66 TTAA
* * *
379049 AAATGGAATTGTTATTCTCAAATTTGAGAAAAGATGAAAATATAATGTAATATAATACAAATTTA
1 AAATGGAATTGTTATTCTTAAATTTGAGGAAAGATGAAAATATAATGTAATATAATGCAAATTTA
379114 T
66 T
379115 CGTATTAAAA
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 125 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (69 bp):
AAATGGAATTGTTATTCTTAAATTTGAGGAAAGATGAAAATATAATGTAATATAATGCAAATTTA
TTAA
Found at i:386142 original size:31 final size:31
Alignment explanation
Indices: 386107--386171 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
386097 AATTTTATGT
386107 CTAAAATAACCCTCAAATTAAATTTAATAAC
1 CTAAAATAACCCTCAAATTAAATTTAATAAC
*
386138 CTAAAATAACCCTCAAATTAAATTTAATGAC
1 CTAAAATAACCCTCAAATTAAATTTAATAAC
386169 CTA
1 CTA
386172 TTGCTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (31 bp):
CTAAAATAACCCTCAAATTAAATTTAATAAC
Found at i:388358 original size:26 final size:25
Alignment explanation
Indices: 388329--388416 Score: 92
Period size: 25 Copynumber: 3.5 Consensus size: 25
388319 AATACAATAC
*
388329 AATTATATATTTATATAATATAAAAA
1 AATTA-ATATATATATAATATAAAAA
* *
388355 AATTAA-A-ATATGATATTATATAAA
1 AATTAATATATAT-ATAATATAAAAA
388379 AATTAATATGA-ATATAATATAAAAA
1 AATTAATAT-ATATATAATATAAAAA
*
388404 AATAAATATATAT
1 AATTAATATATAT
388417 CACAATTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
23 3 0.06
24 18 0.35
25 22 0.43
26 7 0.14
27 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AATTAATATATATATAATATAAAAA
Found at i:388379 original size:24 final size:23
Alignment explanation
Indices: 388347--388403 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
388337 ATTTATATAA
*
388347 TATAAAAAAATTAAAATATG-ATAT
1 TATATAAAAATT--AATATGAATAT
388371 TATATAAAAATTAATATGAATAT
1 TATATAAAAATTAATATGAATAT
*
388394 AATATAAAAA
1 TATATAAAAA
388404 AATAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 6 0.20
23 13 0.43
24 11 0.37
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
TATATAAAAATTAATATGAATAT
Found at i:388404 original size:24 final size:24
Alignment explanation
Indices: 388341--388416 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
388331 TTATATATTT
388341 ATATAATATAAAAAAATTAAAATATG
1 ATATAATAT-AAAAAATT-AAATATG
*
388367 ATATTATAT-AAAAATT-AATATG
1 ATATAATATAAAAAATTAAATATG
*
388389 AATATAATATAAAAAAATAAATAT-
1 -ATATAATATAAAAAATTAAATATG
388413 ATAT
1 ATAT
388417 CACAATTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 6 0.14
23 12 0.27
24 13 0.30
25 5 0.11
26 8 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (24 bp):
ATATAATATAAAAAATTAAATATG
Found at i:388750 original size:20 final size:21
Alignment explanation
Indices: 388713--388753 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
388703 TTAATCATGG
*
388713 TTAATAAATATGATTTTATAA
1 TTAATAAATATAATTTTATAA
388734 TTAATAAATA-AATTTTATAA
1 TTAATAAATATAATTTTATAA
388754 GTGAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTAATAAATATAATTTTATAA
Found at i:389356 original size:43 final size:44
Alignment explanation
Indices: 389289--389372 Score: 161
Period size: 43 Copynumber: 1.9 Consensus size: 44
389279 TTATAATGAA
389289 AGCATTCAAACGATGACGACACCAATGTTTGATTTTTCAGTGAT
1 AGCATTCAAACGATGACGACACCAATGTTTGATTTTTCAGTGAT
389333 AGCATTCAAACG-TGACGACACCAATGTTTGATTTTTCAGT
1 AGCATTCAAACGATGACGACACCAATGTTTGATTTTTCAGT
389373 ATAAGGTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 28 0.70
44 12 0.30
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (44 bp):
AGCATTCAAACGATGACGACACCAATGTTTGATTTTTCAGTGAT
Found at i:395818 original size:2 final size:2
Alignment explanation
Indices: 395811--395844 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
395801 CATCACAAAA
395811 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
395845 CTAAGGGCTT
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):
AG
Found at i:396338 original size:3 final size:3
Alignment explanation
Indices: 396330--396363 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
396320 TCAGATGCAA
396330 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
396364 GTCTGAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:403688 original size:281 final size:279
Alignment explanation
Indices: 403158--403726 Score: 1032
Period size: 281 Copynumber: 2.0 Consensus size: 279
403148 CCTTTCCTGT
*
403158 TTGAGGTTGGATTTAGGAGTTCTCACTCTATCAATTACCATATTCACGCTGACCCTTTGCAACTT
1 TTGAGTTTGGATTTAGGAGTTCTCACTCTATCAATTACCATATTCACGCTGACCCTTTGCAACTT
*
403223 GTATATGCCTATATCATATAGATAATCAAAATAACAGTACACGCTCTTGAGATGCTCCTGCTTGA
66 GTATATACCTATATCATATAGATAATCAAAATAACAGTACACGCTCTTGAGATGCTCCTGCTTGA
*
403288 GTGAATTTTCAATTTAGAATCTTTGTGCTTCTATCCTGAGTGAATCCGCAATTATAGAATTCTTG
131 GTGAATTTTCAATTTAGAATCTTTGTGCTTCTATCCTGAGTGAATCCGCAAATATAGAATTCTTG
* *
403353 TGCATCAACTCTTGCACGCTTATCTTTCGGACCTATGGGAGGTCATGACCACCTTGTTCGTGAGC
196 TGCATCAACTCTTGCACACTTACCTTTCGGACCTATGGGAGGTCATGACCACCTTGTTCGTGAGC
403418 TTGTGCATATAATTGTTGA
261 TTGTGCATATAATTGTTGA
403437 TTGAGTTTGGATTTAGGAGTTCTCACTCTTATCAATTACCATATTCACGCTGACCCTTTGCTAA-
1 TTGAGTTTGGATTTAGGAGTTCTCACTC-TATCAATTACCATATTCACGCTGACCCTTTGC-AAC
*
403501 TTGTATAATACCTATATCATATAGATAATTAAAATAACAGTACACGCTCTTGAGATGCTCCTGCT
64 TTGTAT-ATACCTATATCATATAGATAATCAAAATAACAGTACACGCTCTTGAGATGCTCCTGCT
*
403566 TGAGTGAATTTTCAATTTAGAATCTTTGTGCTTCTATCCTGAGTGAATCTGCAAATATAGAATTC
128 TGAGTGAATTTTCAATTTAGAATCTTTGTGCTTCTATCCTGAGTGAATCCGCAAATATAGAATTC
*
403631 TTGTGCATCAACTCTTGCACACTTACCTTTCGGACCTATGGGAGGTCATGACCACCTTGTTCTTG
193 TTGTGCATCAACTCTTGCACACTTACCTTTCGGACCTATGGGAGGTCATGACCACCTTGTTCGTG
403696 AGCTTGTGCATATAATTGTTGA
258 AGCTTGTGCATATAATTGTTGA
403718 TTGAGTTTG
1 TTGAGTTTG
403727 TCCTATCAAA
Statistics
Matches: 279, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
279 27 0.10
280 38 0.14
281 214 0.77
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (279 bp):
TTGAGTTTGGATTTAGGAGTTCTCACTCTATCAATTACCATATTCACGCTGACCCTTTGCAACTT
GTATATACCTATATCATATAGATAATCAAAATAACAGTACACGCTCTTGAGATGCTCCTGCTTGA
GTGAATTTTCAATTTAGAATCTTTGTGCTTCTATCCTGAGTGAATCCGCAAATATAGAATTCTTG
TGCATCAACTCTTGCACACTTACCTTTCGGACCTATGGGAGGTCATGACCACCTTGTTCGTGAGC
TTGTGCATATAATTGTTGA
Found at i:404308 original size:52 final size:53
Alignment explanation
Indices: 404193--404316 Score: 196
Period size: 52 Copynumber: 2.4 Consensus size: 53
404183 TCATATGCAT
*
404193 CATATCCGGATATGGTTAACTCTTTATTTTTCTTGAAGTACTCGTGTTTGACA
1 CATATCCGGATATGGTTAACTCTTTATTTTTCTTGAAGTACTCGTGTCTGACA
* *
404246 TATATCCGGATATGGTTAACTCTTTATTTTT-TTTAAGTACTCGTGTCTGACA
1 CATATCCGGATATGGTTAACTCTTTATTTTTCTTGAAGTACTCGTGTCTGACA
* *
404298 CATATTCGGATATGTTTAA
1 CATATCCGGATATGGTTAA
404317 TGGTGATATG
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
52 35 0.54
53 30 0.46
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.44
Consensus pattern (53 bp):
CATATCCGGATATGGTTAACTCTTTATTTTTCTTGAAGTACTCGTGTCTGACA
Found at i:405530 original size:22 final size:21
Alignment explanation
Indices: 405486--405539 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
405476 AAATTGAATC
*
405486 ATAATAATAAATTATATAAAAT
1 ATAA-AATAAATTAGATAAAAT
*
405508 ATAAAATAAATTAAGATATAAT
1 ATAAAATAAATT-AGATAAAAT
405530 ATAAATATAA
1 ATAAA-ATAA
405540 TATAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 8 0.29
22 16 0.57
23 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAAATAAATTAGATAAAAT
Found at i:405544 original size:16 final size:17
Alignment explanation
Indices: 405499--405552 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
405489 ATAATAAATT
*
405499 ATATAAAATATAAAATAA
1 ATAT-AAATATAATATAA
405517 AT-TAAGATATAATATAA
1 ATATAA-ATATAATATAA
*
405534 ATAT-AATATAATAAAA
1 ATATAAATATAATATAA
405550 ATA
1 ATA
405553 ATTAAAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 15 0.47
17 14 0.44
18 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATATAAATATAATATAA
Found at i:405719 original size:16 final size:17
Alignment explanation
Indices: 405698--405729 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
405688 TTCACTCTTT
405698 TTTTTC-TTTTTCCTTA
1 TTTTTCTTTTTTCCTTA
405714 TTTTTCTTTTTTCCTT
1 TTTTTCTTTTTTCCTT
405730 CCTTTCCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTTTCCTTA
Found at i:405759 original size:17 final size:17
Alignment explanation
Indices: 405715--405766 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
405705 TTTTCCTTAT
*
405715 TTTTCTTTTTTCCTTCC
1 TTTTCTTTTTTCTTTCC
* **
405732 TTTCCCCTTTTCTTTCC
1 TTTTCTTTTTTCTTTCC
405749 TTTTCTTTTTTCCTTTCC
1 TTTTCTTTTTT-CTTTCC
405767 CATTTAAATT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTCC
Found at i:405874 original size:2 final size:2
Alignment explanation
Indices: 405863--405904 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
405853 CAAAACAACT
405863 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
405904 T
1 T
405905 GAAATTAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:406165 original size:24 final size:24
Alignment explanation
Indices: 406128--406173 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
406118 AATTTTAATA
406128 TATTAATAATTTATATTATATTTT
1 TATTAATAATTTATATTATATTTT
406152 TATTATATAA-TTATATTATATT
1 TATTA-ATAATTTATATTATATT
406174 AAAAAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTAATAATTTATATTATATTTT
Found at i:406170 original size:13 final size:13
Alignment explanation
Indices: 406126--406172 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
406116 TAAATTTTAA
406126 TATATTA-ATAATT
1 TATATTATATAA-T
406139 TATATTATAT--T
1 TATATTATATAAT
*
406150 TTTATTATATAAT
1 TATATTATATAAT
406163 TATATTATAT
1 TATATTATAT
406173 TAAAAAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 10 0.34
13 17 0.59
14 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTATATAAT
Found at i:407695 original size:19 final size:19
Alignment explanation
Indices: 407671--407717 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
407661 AGTAAATAAA
*
407671 TTATTTAAATTTAATT-TAT
1 TTATTTAAA-TGAATTATAT
*
407690 TTATTTAAATGAGTTATAT
1 TTATTTAAATGAATTATAT
407709 TTATTTAAA
1 TTATTTAAA
407718 AATATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
TTATTTAAATGAATTATAT
Found at i:410675 original size:23 final size:22
Alignment explanation
Indices: 410618--410675 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
410608 AATCGATTTA
*
410618 TTAAAATAA-AATTTTAAATAT
1 TTAAAAAAATAATTTTAAATAT
410639 TTAAAAAAATAATTTT-AATAT
1 TTAAAAAAATAATTTTAAATAT
410660 TTAATAATAAATAATT
1 TTAA-AA-AAATAATT
410676 AATAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 17 0.52
22 8 0.24
23 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAAAAAATAATTTTAAATAT
Found at i:410699 original size:35 final size:35
Alignment explanation
Indices: 410632--410703 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
410622 AATAAAATTT
*
410632 TAAATATTTAAAAAAATAATTTTAATATTTAATAA
1 TAAATAATTAAAAAAATAATTTTAATATTTAATAA
*
410667 TAAATAATTAATAAAAATATATTTT-TTA-TTAATAA
1 TAAATAATTAA-AAAAATA-ATTTTAATATTTAATAA
410702 TA
1 TA
410704 TGATCTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 19 0.58
36 9 0.27
37 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
TAAATAATTAAAAAAATAATTTTAATATTTAATAA
Found at i:412032 original size:11 final size:11
Alignment explanation
Indices: 412004--412032 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
411994 TTTTAATAGG
412004 AAAAAAA-TGA
1 AAAAAAAGTGA
412014 AAAAAAAGTGA
1 AAAAAAAGTGA
412025 AAAAAAAG
1 AAAAAAAG
412033 GGAGAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (11 bp):
AAAAAAAGTGA
Found at i:412196 original size:21 final size:22
Alignment explanation
Indices: 412171--412216 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
412161 AGAAATGTCA
412171 AAATTCACT-TAT-TTTCTTACC
1 AAATTC-CTATATCTTTCTTACC
*
412192 AAATTCCTATTTCTTTCTTACC
1 AAATTCCTATATCTTTCTTACC
412214 AAA
1 AAA
412217 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 2 0.09
21 8 0.36
22 12 0.55
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATTCCTATATCTTTCTTACC
Found at i:412654 original size:2 final size:2
Alignment explanation
Indices: 412607--412644 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
412597 TTTCCTTTGT
412607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
412645 GCTGTATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:413875 original size:5 final size:5
Alignment explanation
Indices: 413865--413889 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
413855 AATATATTTA
413865 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
413890 TACAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:414038 original size:14 final size:14
Alignment explanation
Indices: 414019--414049 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
414009 GAAACTTTTG
414019 ATACCTCTCAATTA
1 ATACCTCTCAATTA
*
414033 ATACCTCTCGATTA
1 ATACCTCTCAATTA
414047 ATA
1 ATA
414050 TCTAGCAAAA
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:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (14 bp):
ATACCTCTCAATTA
Found at i:414756 original size:21 final size:21
Alignment explanation
Indices: 414710--414773 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
414700 TATAATTATG
414710 TATAATATCTTAGAAAACAAA
1 TATAATATCTTAGAAAACAAA
* **
414731 AATAATATCTT-GAAGATTAAA
1 TATAATATCTTAGAA-AACAAA
* * *
414752 TATAACATCTTAAAAAAAAAA
1 TATAATATCTTAGAAAACAAA
414773 T
1 T
414774 TGAAACATTG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 3 0.09
21 28 0.85
22 2 0.06
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.30
Consensus pattern (21 bp):
TATAATATCTTAGAAAACAAA
Found at i:415035 original size:14 final size:13
Alignment explanation
Indices: 415009--415076 Score: 79
Period size: 14 Copynumber: 5.2 Consensus size: 13
414999 ACATCACTCA
415009 ATAATAT-TAAAT
1 ATAATATATAAAT
415021 ATAATTATATAAAT
1 ATAA-TATATAAAT
415035 ATAATATA-AAAT
1 ATAATATATAAAT
415047 A-AATATAATATAAT
1 ATAATAT-ATA-AAT
415061 ATAAATATATAAAT
1 AT-AATATATAAAT
415075 AT
1 AT
415077 TTTAAATTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.10
12 10 0.20
13 8 0.16
14 18 0.37
15 3 0.06
16 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATATAAAT
Found at i:415035 original size:21 final size:21
Alignment explanation
Indices: 415011--415103 Score: 67
Period size: 19 Copynumber: 4.6 Consensus size: 21
415001 ATCACTCAAT
415011 AATATTAAATATAATTATATA
1 AATATTAAATATAATTATATA
415032 AATA-T-AATATAA--A-ATA
1 AATATTAAATATAATTATATA
*
415048 AATATAATATAATATAAATATATA
1 AATAT--TA-AATATAATTATATA
*
415072 AATATT--TTA-AATTTATATA
1 AATATTAAATATAA-TTATATA
*
415091 AATATAAAATATA
1 AATATTAAATATA
415104 TTTTATATTA
Statistics
Matches: 56, Mismatches: 4, Indels: 23
0.67 0.05 0.28
Matches are distributed among these distances:
16 7 0.12
17 1 0.02
18 2 0.04
19 21 0.38
20 1 0.02
21 13 0.23
22 2 0.04
23 1 0.02
24 8 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATTAAATATAATTATATA
Found at i:415042 original size:5 final size:5
Alignment explanation
Indices: 415018--415148 Score: 59
Period size: 5 Copynumber: 27.4 Consensus size: 5
415008 AATAATATTA
*
415018 AATAT AAT-T -ATAT AAATAT AATAT AAAAT AAATAT AATAT AATAT AA-AT
1 AATAT AATAT AATAT -AATAT AATAT AATAT -AATAT AATAT AATAT AATAT
* * * * ** *
415067 -ATAT AA-AT ATTTT AA-ATT TATAT AAATAT AAAAT -ATAT TTTAT ATTAT
1 AATAT AATAT AATAT AATA-T AATAT -AATAT AATAT AATAT AATAT AATAT
*
415115 AATAT AATCA- AATAT -ATA- AAAAT AATAT AA-AT AA
1 AATAT AAT-AT AATAT AATAT AATAT AATAT AATAT AA
415149 ATGATTCTTC
Statistics
Matches: 96, Mismatches: 15, Indels: 31
0.68 0.11 0.22
Matches are distributed among these distances:
3 3 0.03
4 22 0.23
5 57 0.59
6 14 0.15
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:415050 original size:16 final size:16
Alignment explanation
Indices: 415009--415150 Score: 96
Period size: 16 Copynumber: 8.7 Consensus size: 16
414999 ACATCACTCA
415009 ATAATATTAAATATAAT
1 ATAATA-TAAATATAAT
415026 -T-ATATAAATATAAT
1 ATAATATAAATATAAT
*
415040 ATAAAATAAATATAAT
1 ATAATATAAATATAAT
*
415056 ATAATATAAATATATAA
1 ATAATATAAATATA-AT
* * *
415073 ATATTTTAAAT-TTAT
1 ATAATATAAATATAAT
415088 ATAAATATAAA-ATATAT
1 AT-AATATAAATATA-AT
* *
415105 TTTATATTATAATATAAT
1 ATAATA-TA-AATATAAT
* *
415123 CAAATATATAAAAATAAT
1 -ATA-ATATAAATATAAT
415141 ATAA-ATAAAT
1 ATAATATAAAT
415151 GATTCTTCCT
Statistics
Matches: 96, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
14 10 0.10
15 12 0.12
16 38 0.40
17 17 0.18
18 11 0.11
19 5 0.05
20 3 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATATAAATATAAT
Found at i:415100 original size:7 final size:8
Alignment explanation
Indices: 415019--415104 Score: 63
Period size: 8 Copynumber: 10.5 Consensus size: 8
415009 ATAATATTAA
*
415019 ATATAATT
1 ATATAAAT
415027 ATATAAAT
1 ATATAAAT
415035 ATAATATAA-
1 AT-ATA-AAT
415044 A-ATAAAT
1 ATATAAAT
*
415051 ATA-ATAT
1 ATATAAAT
415058 AATATAAAT
1 -ATATAAAT
415067 ATATAAAT
1 ATATAAAT
*
415075 ATTTTAAATTT
1 A-TATAAA--T
415086 ATATAAAT
1 ATATAAAT
415094 ATA-AAAT
1 ATATAAAT
415101 ATAT
1 ATAT
415105 TTTATATTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
6 2 0.03
7 14 0.22
8 26 0.41
9 12 0.19
10 7 0.11
11 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:415114 original size:27 final size:27
Alignment explanation
Indices: 415011--415132 Score: 92
Period size: 27 Copynumber: 4.6 Consensus size: 27
415001 ATCACTCAAT
* *
415011 AATATTAAATATA-ATTATA-TAAATA
1 AATATAAAATATATATTATATTATATA
* * *
415036 TAATATAAAATAAATATAATATAATATA
1 -AATATAAAATATATATTATATTATATA
*
415064 AATATATAAATAT-T-TTAAATTTATATA
1 AATATA-AAATATATATTATA-TTATATA
*
415091 AATATAAAATATATTTTATATTATA-A
1 AATATAAAATATATATTATATTATATA
* *
415117 TATAATCAAATATATA
1 AAT-ATAAAATATATA
415133 AAAATAATAT
Statistics
Matches: 76, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
26 23 0.30
27 40 0.53
28 13 0.17
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (27 bp):
AATATAAAATATATATTATATTATATA
Found at i:415148 original size:27 final size:25
Alignment explanation
Indices: 415008--415148 Score: 87
Period size: 27 Copynumber: 5.6 Consensus size: 25
414998 GACATCACTC
*
415008 AATAATATTAAAT-ATAATTATATAA
1 AATAATA-TAAATAATAAATATATAA
415033 ATATAATAT-AA-AAT-AA-ATATAA
1 A-ATAATATAAATAATAAATATATAA
* *
415055 TATAATATAAATATATAAATATTTTAA
1 AATAATATAAATA-ATAAATA-TATAA
* * **
415082 ATTTATATAAAT-ATAAAATATATTT
1 AATAATATAAATAAT-AAATATATAA
* *
415107 TATATTATAATATAATCAAATATATAAA
1 AATAATATAA-ATAAT-AAATATAT-AA
415135 AATAATATAAATAA
1 AATAATATAAATAA
415149 ATGATTCTTC
Statistics
Matches: 86, Mismatches: 18, Indels: 22
0.68 0.14 0.17
Matches are distributed among these distances:
21 7 0.08
22 8 0.09
23 2 0.02
24 6 0.07
25 14 0.16
26 14 0.16
27 27 0.31
28 8 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
AATAATATAAATAATAAATATATAA
Found at i:416282 original size:2 final size:2
Alignment explanation
Indices: 416275--416318 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
416265 CTCAAAACTC
416275 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
416317 AT
1 AT
416319 CTCGAATCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:417026 original size:23 final size:23
Alignment explanation
Indices: 417000--417048 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
416990 ATATGATAAA
*
417000 ATAATATGAATATATTAAAT-TTT
1 ATAATATAAAT-TATTAAATATTT
417023 ATAATATAAATTATTAAATATTT
1 ATAATATAAATTATTAAATATTT
417046 ATA
1 ATA
417049 TAAATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAATATAAATTATTAAATATTT
Found at i:417066 original size:20 final size:20
Alignment explanation
Indices: 417012--417053 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
417002 AATATGAATA
*
417012 TATTAAATTTTATAATATAAAT
1 TATTAAATATT-T-ATATAAAT
417034 TATTAAATATTTATATAAAT
1 TATTAAATATTTATATAAAT
417054 ATATAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTAAATATTTATATAAAT
Found at i:417635 original size:19 final size:19
Alignment explanation
Indices: 417607--417665 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 19
417597 TTTTTTATTT
417607 AAAT-TAAATTAAATTTAA
1 AAATATAAATTAAATTTAA
*
417625 AAATATAAATT-ATTTTGAA
1 AAATATAAATTAAATTT-AA
*
417644 TAATA-AAA-TAAATTTATA
1 AAATATAAATTAAATTTA-A
417662 AAAT
1 AAAT
417666 TAATCAAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 2 0.06
18 19 0.58
19 12 0.36
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AAATATAAATTAAATTTAA
Found at i:417964 original size:12 final size:11
Alignment explanation
Indices: 417944--418027 Score: 62
Period size: 12 Copynumber: 7.4 Consensus size: 11
417934 ATAATTTAAC
*
417944 ATATAATATAA
1 ATATGATATAA
417955 ATGATGATATAA
1 AT-ATGATATAA
417967 ATATGATATATA
1 ATATGATATA-A
* *
417979 TTATAAATATAA
1 ATAT-GATATAA
*
417991 ATA-AATATAA
1 ATATGATATAA
*
418001 ATATAATATAAA
1 ATATGATAT-AA
* *
418013 ATATGTTTTAA
1 ATATGATATAA
418024 ATAT
1 ATAT
418028 AATTAATCTA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
10 10 0.16
11 21 0.34
12 25 0.41
13 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (11 bp):
ATATGATATAA
Found at i:417974 original size:11 final size:11
Alignment explanation
Indices: 417934--418012 Score: 79
Period size: 12 Copynumber: 6.9 Consensus size: 11
417924 AGTAAATTTG
*
417934 ATAATTTAACAT
1 ATAATATAA-AT
417946 ATAATATAAAT
1 ATAATATAAAT
*
417957 GATGATATAAAT
1 -ATAATATAAAT
* *
417969 ATGATATATATT
1 ATAATATA-AAT
417981 ATAAATATAAAT
1 AT-AATATAAAT
417993 A-AATATAAAT
1 ATAATATAAAT
418003 ATAATATAAA
1 ATAATATAAA
418013 ATATGTTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
10 10 0.17
11 18 0.31
12 25 0.43
13 5 0.09
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:417989 original size:6 final size:6
Alignment explanation
Indices: 417944--418012 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
417934 ATAATTTAAC
* * *
417944 ATAT-A ATATAA ATGAT-G ATATAA ATAT-G ATATATA TTATAA ATAT-A
1 ATATAA ATATAA AT-ATAA ATATAA ATATAA ATATA-A ATATAA ATATAA
417990 A-ATAA ATATAA ATAT-A ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
418013 ATATGTTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
4 2 0.04
5 19 0.38
6 23 0.46
7 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:417996 original size:10 final size:10
Alignment explanation
Indices: 417981--418012 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
417971 GATATATATT
417981 ATAAATATAA
1 ATAAATATAA
417991 ATAAATATAA
1 ATAAATATAA
418001 ATATAATATAA
1 ATA-AATATAA
418012 A
1 A
418013 ATATGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAAATATAA
Found at i:418758 original size:20 final size:20
Alignment explanation
Indices: 418679--418750 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
418669 AATACTCAAA
418679 AAAATAAAAAATAATTATTTT
1 AAAATAAAAAATAATTA-TTT
418700 AAAAT-AAAAATAATTATTT
1 AAAATAAAAAATAATTATTT
418719 AAAATAAAAAATAATTATTT
1 AAAATAAAAAATAATTATTT
418739 AAAATAAAAAAT
1 AAAATAAAAAAT
418751 TTTAATTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.16
20 37 0.74
21 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATAAAAAATAATTATTT
Found at i:422529 original size:18 final size:18
Alignment explanation
Indices: 422508--422565 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
422498 CTTTTTTGCC
422508 TTCATTTTGCACTCTCTT
1 TTCATTTTGCACTCTCTT
** * *
422526 TTCATTTT-TTCTTTTTT
1 TTCATTTTGCACTCTCTT
*
422543 TTCATTTTGCACTCTCTG
1 TTCATTTTGCACTCTCTT
422561 TTCAT
1 TTCAT
422566 CACTCACTAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.10, C:0.22, G:0.05, T:0.62
Consensus pattern (18 bp):
TTCATTTTGCACTCTCTT
Found at i:422553 original size:35 final size:36
Alignment explanation
Indices: 422494--422565 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
422484 GTCAATAATC
*
422494 TTTTCTTTTTTGCCTTCATTTTGCACTCTCTTTTCATT
1 TTTTCTTTTTT--CTTCATTTTGCACTCTCTGTTCATT
422532 TTTTCTTTTTT-TTCATTTTGCACTCTCTGTTCAT
1 TTTTCTTTTTTCTTCATTTTGCACTCTCTGTTCAT
422566 CACTCACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 22 0.67
38 11 0.33
ACGTcount: A:0.08, C:0.22, G:0.06, T:0.64
Consensus pattern (36 bp):
TTTTCTTTTTTCTTCATTTTGCACTCTCTGTTCATT
Found at i:430681 original size:24 final size:23
Alignment explanation
Indices: 430648--430693 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
430638 CTTAATTTAA
430648 GTTCGGGTCACTTTGAATTAATT
1 GTTCGGGTCACTTTGAATTAATT
* *
430671 GTTCAGGGTCATTTTGAGTTAAT
1 GTTC-GGGTCACTTTGAATTAAT
430694 ATTATTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (23 bp):
GTTCGGGTCACTTTGAATTAATT
Found at i:430722 original size:32 final size:32
Alignment explanation
Indices: 430678--430749 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
430668 ATTGTTCAGG
* * * *
430678 GTCATTTTGAGTTAATATTATTTTGAATTTAA
1 GTCATTTCGAGTTAAGATCATTTTGAATTCAA
** *
430710 GTCATTTCGAGTTCGGATCATTTTGAGTTCAA
1 GTCATTTCGAGTTAAGATCATTTTGAATTCAA
430742 GTCATTTC
1 GTCATTTC
430750 ATATTCGAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (32 bp):
GTCATTTCGAGTTAAGATCATTTTGAATTCAA
Found at i:430746 original size:16 final size:16
Alignment explanation
Indices: 430678--430748 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
430668 ATTGTTCAGG
430678 GTCATTTTGAGTT-AA
1 GTCATTTTGAGTTCAA
* * * *
430693 TATTATTTTGAATTTAA
1 -GTCATTTTGAGTTCAA
* *
430710 GTCATTTCGAGTTC-G
1 GTCATTTTGAGTTCAA
430725 GATCATTTTGAGTTCAA
1 G-TCATTTTGAGTTCAA
430742 GTCATTT
1 GTCATTT
430749 CATATTCGAA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
15 1 0.02
16 37 0.90
17 3 0.07
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (16 bp):
GTCATTTTGAGTTCAA
Found at i:431841 original size:28 final size:25
Alignment explanation
Indices: 431804--431869 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 25
431794 TATTTTGATG
* *
431804 AAATAATAAAATATAAACTTAAATAATA
1 AAATATTAAAAAATAAA-TT-AA-AATA
*
431832 AAATATTAAAAAATTAATTAAAATA
1 AAATATTAAAAAATAAATTAAAATA
431857 ATAATATTAAAAA
1 A-AATATTAAAAA
431870 TATTTCAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.15
26 13 0.38
27 2 0.06
28 14 0.41
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (25 bp):
AAATATTAAAAAATAAATTAAAATA
Found at i:431871 original size:15 final size:14
Alignment explanation
Indices: 431828--431868 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
431818 AAACTTAAAT
431828 AATAA-AATATTAA
1 AATAATAATATTAA
*
431841 AA-AATTA-ATTAA
1 AATAATAATATTAA
431853 AATAATAATATTAA
1 AATAATAATATTAA
431867 AA
1 AA
431869 ATATTTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
12 9 0.39
13 7 0.30
14 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAATAATATTAA
Found at i:439725 original size:23 final size:23
Alignment explanation
Indices: 439699--439744 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
439689 TTTTTATATT
*
439699 TATAAT-TTTTTTAATTTTTAAAA
1 TATAATATCTTTT-ATTTTTAAAA
439722 TATAATATCTTTTATTTTTAAAA
1 TATAATATCTTTTATTTTTAAAA
439745 AAATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATAATATCTTTTATTTTTAAAA
Found at i:440910 original size:13 final size:13
Alignment explanation
Indices: 440894--440956 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
440884 AATTTAATAA
440894 TTTATATTTTATT
1 TTTATATTTTATT
440907 TTTATATTTTATT
1 TTTATATTTTATT
* *
440920 ATGATATAATTATATT
1 -T-TTAT-ATTTTATT
* *
440936 TTAAATATTTTATA
1 TT-TATATTTTATT
440950 TTTATAT
1 TTTATAT
440957 AAATTTTAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
13 17 0.44
14 9 0.23
15 6 0.15
16 7 0.18
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
TTTATATTTTATT
Found at i:440915 original size:27 final size:27
Alignment explanation
Indices: 440881--441032 Score: 105
Period size: 27 Copynumber: 5.3 Consensus size: 27
440871 ATAAAGTGAA
*
440881 TTAA-ATTTAATAATTTATATTTTATT
1 TTAATATTTAATAATTTATATTATATT
* * * *
440907 TTTATATTTTATTATGATATAATTATATT
1 TTAATATTTAATAAT-TTAT-ATTATATT
* *
440936 TTAAATATTTTAT-ATTTATA-TAAATT
1 TT-AATATTTAATAATTTATATTATATT
440962 TTAATATATTAATAATTTATATTATATAAATT
1 TTAATAT-TTAATAATTTATA-T-TAT--ATT
440994 TTAAAATATTT-ATATATTTATATTATATT
1 TT--AATATTTAATA-ATTTATATTATATT
441023 TTAAGTATTT
1 TTAA-TATTT
441033 TTATGTAGTA
Statistics
Matches: 101, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
25 5 0.05
26 14 0.14
27 18 0.18
28 11 0.11
29 16 0.16
30 11 0.11
31 3 0.03
32 9 0.09
33 9 0.09
34 5 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (27 bp):
TTAATATTTAATAATTTATATTATATT
Found at i:440948 original size:16 final size:16
Alignment explanation
Indices: 440929--440984 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
440919 TATGATATAA
440929 TTATATTTTAAATATT
1 TTATATTTTAAATATT
440945 TTATATTTATATAA-ATT
1 TTATATTT-TA-AATATT
* *
440962 TTAATATATT-AATAAT
1 TT-ATATTTTAAATATT
440978 TTATATT
1 TTATATT
440985 ATATAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
15 6 0.18
16 12 0.36
17 8 0.24
18 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATATTTTAAATATT
Found at i:440971 original size:20 final size:19
Alignment explanation
Indices: 440942--441022 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 19
440932 TATTTTAAAT
440942 ATTTT-ATAT-TTATATAA
1 ATTTTAATATATTATATAA
440959 ATTTTAATATATTA-AT-A
1 ATTTTAATATATTATATAA
440976 A--TT--TATATTATATAA
1 ATTTTAATATATTATATAA
* *
440991 ATTTTAAAATATT-TATAT
1 ATTTTAATATATTATATAA
*
441009 ATTTATATTATATT
1 ATTT-TAATATATT
441023 TTAAGTATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
13 7 0.14
14 2 0.04
15 4 0.08
17 9 0.18
18 14 0.27
19 15 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTAATATATTATATAA
Found at i:441010 original size:8 final size:8
Alignment explanation
Indices: 440893--441016 Score: 61
Period size: 7 Copynumber: 16.0 Consensus size: 8
440883 AAATTTAATA
440893 ATTTATAT
1 ATTTATAT
440901 -TTTAT-T
1 ATTTATAT
440907 -TTTATAT
1 ATTTATAT
440914 -TTTAT-T
1 ATTTATAT
*
440920 A-TGATAT
1 ATTTATAT
*
440927 AATTATAT
1 ATTTATAT
*
440935 -TTTAAAT
1 ATTTATAT
440942 ATTT-TAT
1 ATTTATAT
440949 ATTTATAT
1 ATTTATAT
440957 AAATTTTAATAT
1 --A-TTT-ATAT
*
440969 ATTAATA-
1 ATTTATAT
440976 ATTTATAT
1 ATTTATAT
* *
440984 -TATATAA
1 ATTTATAT
*
440991 ATTTTAAAAT
1 A-TTT-ATAT
441001 ATTTATAT
1 ATTTATAT
441009 ATTTATAT
1 ATTTATAT
441017 TATATTTTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
6 10 0.11
7 35 0.39
8 25 0.28
9 7 0.08
10 5 0.06
11 3 0.03
12 4 0.04
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (8 bp):
ATTTATAT
Found at i:441013 original size:33 final size:33
Alignment explanation
Indices: 440939--441021 Score: 125
Period size: 32 Copynumber: 2.5 Consensus size: 33
440929 TTATATTTTA
*
440939 AATAT-TTTATATTTATATAAATTTTAATATATT
1 AATATATTTATA-TTATATAAATTTTAAAATATT
440972 AATA-ATTTATATTATATAAATTTTAAAATATT
1 AATATATTTATATTATATAAATTTTAAAATATT
*
441004 TATATATTTATATTATAT
1 AATATATTTATATTATAT
441022 TTTAAGTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 23 0.50
33 23 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
AATATATTTATATTATATAAATTTTAAAATATT
Found at i:442882 original size:18 final size:18
Alignment explanation
Indices: 442861--442902 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
442851 GGACGAATAT
442861 AATATAAAAAATAATTAA
1 AATATAAAAAATAATTAA
* * *
442879 AATATATAATATTATTAA
1 AATATAAAAAATAATTAA
442897 AA-ATAA
1 AATATAA
442903 TATAAACAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAAAAAATAATTAA
Found at i:443015 original size:21 final size:21
Alignment explanation
Indices: 442991--443051 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
442981 TATAATTTTT
*
442991 AAATATAATTATAATATATAA
1 AAATATAATTATAAAATATAA
*
443012 AAATAT-ATCAATAAAATATAA
1 AAATATAAT-TATAAAATATAA
*
443033 AATATATGAATTATCAAAT
1 AA-ATAT-AATTATAAAAT
443052 TATTCTGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.06
21 18 0.56
22 4 0.12
23 6 0.19
24 2 0.06
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATATAATTATAAAATATAA
Found at i:443051 original size:23 final size:22
Alignment explanation
Indices: 442993--443051 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 22
442983 TAATTTTTAA
442993 ATATAATTATAATATATAAAAAT
1 ATATAATTATAA-ATATAAAAAT
443016 ATATCAA-TA-AAATAT-AAAAT
1 ATAT-AATTATAAATATAAAAAT
443036 ATATGAATTATCAAAT
1 ATAT-AATTAT-AAAT
443052 TATTCTGAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 11 0.35
21 6 0.19
22 2 0.06
23 10 0.32
24 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (22 bp):
ATATAATTATAAATATAAAAAT
Found at i:444857 original size:25 final size:23
Alignment explanation
Indices: 444794--444862 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 23
444784 AATTATTATT
* *
444794 TAATAAAAAGTTATTAA-ATTAA
1 TAATAAAAATTTATAAATATTAA
*
444816 TTATAAAAATTTATAAATATTAA
1 TAATAAAAATTTATAAATATTAA
*
444839 TAATAAAATAATTTTTAAATATTA
1 TAAT-AAA-AATTTATAAATATTA
444863 TTCAAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 14 0.36
23 8 0.21
24 3 0.08
25 14 0.36
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
TAATAAAAATTTATAAATATTAA
Found at i:445077 original size:28 final size:27
Alignment explanation
Indices: 445018--445086 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
445008 CACCCATTTG
*
445018 TTTGTCAAAAATGGTGGTTATTTTATG
1 TTTGTCAAAAATGGTGGTTATTTTATA
*
445045 TTTGTCAAAAATGGTGGTT-TCCTTTGTA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
*
445073 TTTGTCAAATATGG
1 TTTGTCAAAAATGG
445087 AAGCTTGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.51
28 17 0.46
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:449625 original size:27 final size:28
Alignment explanation
Indices: 449591--449661 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
449581 GCCACCCATT
449591 TGTTTGTCAAAAATGGTGG-TTATTTTG
1 TGTTTGTCAAAAATGGTGGTTTATTTTG
*
449618 TGTTTGTCAAAAATGGTGGTTTCTTTTG
1 TGTTTGTCAAAAATGGTGGTTTATTTTG
* *
449646 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
449662 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 19 0.47
28 21 0.52
ACGTcount: A:0.23, C:0.06, G:0.24, T:0.48
Consensus pattern (28 bp):
TGTTTGTCAAAAATGGTGGTTTATTTTG
Found at i:450410 original size:2 final size:2
Alignment explanation
Indices: 450403--450432 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
450393 TAACCTAGTA
450403 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
450433 TACGTTATTA
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:450896 original size:51 final size:46
Alignment explanation
Indices: 450811--450918 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 46
450801 TTATACAAAT
* *
450811 ATATAAATATATTAAAATTTATATAAAATAATTATTAATATATCAAATTTA
1 ATATAAATATATTAAAATTTA-A-ATAA-AATTATT-ATATAT-AAATATA
* *
450862 ATATAAATATA-TAATATTTTAAATATAATTATTATATATAAATATA
1 ATATAAATATATTAA-AATTTAAATAAAATTATTATATATAAATATA
450908 ATATAAATATA
1 ATATAAATATA
450919 AAAATTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
46 17 0.33
47 6 0.12
48 7 0.13
49 2 0.04
50 4 0.08
51 16 0.31
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.44
Consensus pattern (46 bp):
ATATAAATATATTAAAATTTAAATAAAATTATTATATATAAATATA
Found at i:450911 original size:11 final size:11
Alignment explanation
Indices: 450772--450919 Score: 74
Period size: 10 Copynumber: 14.2 Consensus size: 11
450762 TAACTAAAAA
450772 AATAT-AATAT
1 AATATAAATAT
450782 AATATAAA-A-
1 AATATAAATAT
450791 AATATAAATAT
1 AATATAAATAT
450802 --TATACAA-AT
1 AATATA-AATAT
450811 -ATATAAATAT
1 AATATAAATAT
*
450821 ATTA-AAAT-T
1 AATATAAATAT
*
450830 TATATAAA-AT
1 AATATAAATAT
*
450840 AATTATTAATAT
1 AA-TATAAATAT
* *
450852 -AT-CAAATTT
1 AATATAAATAT
450861 AATATAAATATAT
1 AATAT-AA-ATAT
450874 AATATTTTAAATAT
1 AATA---TAAATAT
*
450888 AAT-T-ATTAT
1 AATATAAATAT
450897 -ATATAAATAT
1 AATATAAATAT
450907 AATATAAATAT
1 AATATAAATAT
450918 AA
1 AA
450920 AAATTATTTC
Statistics
Matches: 105, Mismatches: 12, Indels: 41
0.66 0.08 0.26
Matches are distributed among these distances:
8 2 0.02
9 28 0.27
10 32 0.30
11 22 0.21
12 4 0.04
13 7 0.07
14 7 0.07
15 2 0.02
16 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATAAATAT
Found at i:450917 original size:19 final size:19
Alignment explanation
Indices: 450773--450923 Score: 92
Period size: 19 Copynumber: 7.4 Consensus size: 19
450763 AACTAAAAAA
*
450773 ATAT-AATATAATATAAAAA
1 ATATAAATATAATAT-AAAT
* *
450792 ATATAAATATTATACAAAT
1 ATATAAATATAATATAAAT
*
450811 ATATAAATATATTA-AAATTT
1 ATATAAATATAATATAAA--T
*
450831 ATATAAA-ATAATTATTAAT
1 ATATAAATATAA-TATAAAT
*
450850 ATATCAAATTTAATATAAAT
1 ATAT-AAATATAATATAAAT
*
450870 ATATAATATTTTAAATATAATTATTAT
1 ATATAA-A-TAT-AATAT-A--A--AT
450897 ATATAAATATAATATAAAT
1 ATATAAATATAATATAAAT
*
450916 ATAAAAAT
1 ATATAAAT
450924 TATTTCTTTT
Statistics
Matches: 106, Mismatches: 11, Indels: 30
0.72 0.07 0.20
Matches are distributed among these distances:
18 3 0.03
19 38 0.36
20 32 0.30
21 9 0.08
22 5 0.05
23 2 0.02
24 5 0.05
25 3 0.03
26 1 0.01
27 8 0.08
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAATATAATATAAAT
Found at i:453309 original size:17 final size:18
Alignment explanation
Indices: 453283--453316 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
453273 AATATATGAT
*
453283 AAATTTTTTAAA-ATAAA
1 AAATTATTTAAATATAAA
453300 AAATTATTTAAATATAA
1 AAATTATTTAAATATAA
453317 TTATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTATTTAAATATAAA
Found at i:453333 original size:22 final size:23
Alignment explanation
Indices: 453294--453344 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
453284 AATTTTTTAA
*
453294 AATA-AAAAATTATTTAAATA-T
1 AATATAAAAATTATATAAATATT
453315 AATTATAAAAA-TATATAAATATT
1 AA-TATAAAAATTATATAAATATT
453338 AATATAA
1 AATATAA
453345 TATAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.08
22 16 0.62
23 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATATAAAAATTATATAAATATT
Found at i:453346 original size:19 final size:18
Alignment explanation
Indices: 453324--453371 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
453314 TAATTATAAA
453324 AATATATAAATATTAATAT
1 AATATATAAATATTAAT-T
*
453343 AATATA-AAATTTTAATT
1 AATATATAAATATTAATT
*
453360 ACAAATATAAAT
1 A-ATATATAAAT
453372 TAAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 13 0.52
19 10 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATATAAATATTAATT
Found at i:453872 original size:22 final size:21
Alignment explanation
Indices: 453846--453901 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
453836 AAATAAGATT
453846 AATATATCAAATATTTATTAAA
1 AATATATCAAATATTT-TTAAA
*
453868 TATATAT--AATATTTTTAAA
1 AATATATCAAATATTTTTAAA
*
453887 AACTTTATCAAATAT
1 AA-TATATCAAATAT
453902 AATAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 6 0.21
20 11 0.39
22 11 0.39
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
AATATATCAAATATTTTTAAA
Found at i:453917 original size:21 final size:20
Alignment explanation
Indices: 453892--453933 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
453882 TTAAAAACTT
453892 TATCAAATATAA-TAATATAAA
1 TATCAAAT-TAAGTAATA-AAA
453913 TATCAAATTAAGTAATAAAA
1 TATCAAATTAAGTAATAAAA
453933 T
1 T
453934 TAAAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (20 bp):
TATCAAATTAAGTAATAAAA
Found at i:454986 original size:23 final size:23
Alignment explanation
Indices: 454955--455025 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
454945 TGTGCAAATA
*
454955 TAATTTTTAAAATTATAAATATT
1 TAATATTTAAAATTATAAATATT
*
454978 TAATATTTAAAATTTTTAAATATT
1 TAATATTTAAAA-TTATAAATATT
* ** * *
455002 AAATAAATAAATTTAAAAATATT
1 TAATATTTAAAATTATAAATATT
455025 T
1 T
455026 TTTAAAAATG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATATTTAAAATTATAAATATT
Found at i:455003 original size:16 final size:16
Alignment explanation
Indices: 454956--455004 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
454946 GTGCAAATAT
454956 AATTTTTAAA-ATTATA
1 AATTTTTAAATATTA-A
*
454972 AATATTT-AATATTTAA
1 AATTTTTAAATA-TTAA
454988 AATTTTTAAATATTAA
1 AATTTTTAAATATTAA
455004 A
1 A
455005 TAAATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 2 0.07
16 19 0.68
17 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTTTAAATATTAA
Found at i:455006 original size:24 final size:23
Alignment explanation
Indices: 454960--455024 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 23
454950 AAATATAATT
*
454960 TTTAAAATTATAAATATTTAATA
1 TTTAAAATTATAAATATTAAATA
*
454983 TTTAAAATTTTTAAATATTAAATA
1 TTTAAAA-TTATAAATATTAAATA
** * *
455007 AATAAATTTAAAAATATT
1 TTTAAAATTATAAATATT
455025 TTTTAAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 16 0.47
24 18 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAAAATTATAAATATTAAATA
Found at i:455021 original size:31 final size:32
Alignment explanation
Indices: 454956--455019 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
454946 GTGCAAATAT
**
454956 AATTTTTAAAATTATAAATATTTAATATTTAA
1 AATTTTTAAAATTATAAATAAATAATATTTAA
454988 AATTTTT-AAA-TATTAAATAAATAA-ATTTAA
1 AATTTTTAAAATTA-TAAATAAATAATATTTAA
455018 AA
1 AA
455020 ATATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 10 0.34
31 12 0.41
32 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AATTTTTAAAATTATAAATAAATAATATTTAA
Found at i:455370 original size:27 final size:27
Alignment explanation
Indices: 455340--455400 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
455330 CAGTCAGTTT
* * *
455340 AATTAATTTAGTTATATAAAATTTTAA
1 AATTAATTAAATTAAATAAAATTTTAA
* *
455367 AATTAATTAAATTAAATAAATTTTTAC
1 AATTAATTAAATTAAATAAAATTTTAA
455394 AATTAAT
1 AATTAAT
455401 CAATTATCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
AATTAATTAAATTAAATAAAATTTTAA
Found at i:455548 original size:21 final size:21
Alignment explanation
Indices: 455505--455551 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
455495 TTATTTATAT
*
455505 TATTATATAAAAATAATTGTA
1 TATTATATAAAAATAAATGTA
*
455526 TATTATAT-AATATAAATGATA
1 TATTATATAAAAATAAATG-TA
455547 TATTA
1 TATTA
455552 CAAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
TATTATATAAAAATAAATGTA
Found at i:455711 original size:17 final size:17
Alignment explanation
Indices: 455691--455726 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
455681 CTAATAAAAA
*
455691 AATTAATTTTTAAAATT
1 AATTAATTTTAAAAATT
455708 AATTAATTTTAAAAATT
1 AATTAATTTTAAAAATT
455725 AA
1 AA
455727 ATAAACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAATTTTAAAAATT
Found at i:458680 original size:23 final size:23
Alignment explanation
Indices: 458654--458816 Score: 70
Period size: 23 Copynumber: 6.9 Consensus size: 23
458644 AAATCAGTAT
458654 TTATATTATTTATTATATTATAA
1 TTATATTATTTATTATATTATAA
* *
458677 TTATA-T-TTTA-AATATTATAT
1 TTATATTATTTATTATATTATAA
*
458697 TTATATAAATTT-TTACATATTAATAA
1 TTATAT-TATTTATT--ATATT-ATAA
** * *
458723 TTTATATTACATAAATTTTAATATATAT
1 -TTATATT--ATTTATTAT-AT-TATAA
* *
458751 TTATATCATATT-TTATATTATAT
1 TTATATTAT-TTATTATATTATAA
* *
458774 TTTTATTATTTTTTATATTATATAA
1 TTATATTATTTATTATATT--ATAA
458799 TTATA-TATTTA-TATATTA
1 TTATATTATTTATTATATTA
458817 GCCAACTTAT
Statistics
Matches: 104, Mismatches: 19, Indels: 36
0.65 0.12 0.23
Matches are distributed among these distances:
20 13 0.12
21 5 0.05
22 3 0.03
23 33 0.32
24 7 0.07
25 17 0.16
26 3 0.03
27 13 0.12
28 7 0.07
29 3 0.03
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATATTATTTATTATATTATAA
Found at i:458765 original size:12 final size:12
Alignment explanation
Indices: 458744--458796 Score: 72
Period size: 12 Copynumber: 4.4 Consensus size: 12
458734 TAAATTTTAA
458744 TATATATTTATAT
1 TATAT-TTTATAT
*
458757 CATATTTTATAT
1 TATATTTTATAT
458769 TATATTTT-TAT
1 TATATTTTATAT
*
458780 TATTTTTTATAT
1 TATATTTTATAT
458792 TATAT
1 TATAT
458797 AATTATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.29
12 21 0.60
13 4 0.11
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:458814 original size:8 final size:8
Alignment explanation
Indices: 458744--458815 Score: 60
Period size: 8 Copynumber: 9.0 Consensus size: 8
458734 TAAATTTTAA
458744 TATATATT
1 TATATATT
458752 TATATCATAT
1 TATAT-AT-T
*
458762 TTTATA-T
1 TATATATT
*
458769 TATATTTT
1 TATATATT
458777 TAT-TATT
1 TATATATT
*
458784 T-TTTATAT
1 TATATAT-T
*
458792 TATATAAT
1 TATATATT
458800 TATATATT
1 TATATATT
458808 TATATATT
1 TATATATT
458816 AGCCAACTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
6 1 0.02
7 12 0.24
8 27 0.53
9 6 0.12
10 5 0.10
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (8 bp):
TATATATT
Found at i:458943 original size:2 final size:2
Alignment explanation
Indices: 458936--458961 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
458926 AACTGCATAG
458936 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
458962 TAAGGATTAA
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:464139 original size:31 final size:30
Alignment explanation
Indices: 464104--464197 Score: 88
Period size: 34 Copynumber: 3.1 Consensus size: 30
464094 TCATATTTAC
464104 TTAAAAATTTATTTTATTATTTGAAATAATA
1 TTAAAAATTTATTTTATTATTT-AAATAATA
*
464135 TTAAAATTATTTTATATTATTATTTATAATTAA-A
1 TTAAAA--A-TTTATTTTATTATTTA-AA-TAATA
*
464169 TTTAAAA--T-TTTTATTATTTAAATAATA
1 TTAAAAATTTATTTTATTATTTAAATAATA
464196 TT
1 TT
464198 TAAATTATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
26 3 0.06
27 5 0.09
28 11 0.20
29 1 0.02
31 6 0.11
32 1 0.02
33 2 0.04
34 22 0.41
35 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
TTAAAAATTTATTTTATTATTTAAATAATA
Found at i:465133 original size:35 final size:36
Alignment explanation
Indices: 465054--465135 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 36
465044 TTATTTAAAA
*
465054 TTAATTATAA-AAAATTTTTTAATATTATTTTAAATT
1 TTAATTATAATAAAA-TTTTTAATACTATTTTAAATT
465090 TTAA--ATAATAAAA-TTTT-ATACTATTTTAAATT
1 TTAATTATAATAAAATTTTTAATACTATTTTAAATT
465122 TTAAATTATAATAA
1 TT-AATTATAATAA
465136 TAAAGTGGGG
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
32 16 0.39
33 6 0.15
34 4 0.10
35 11 0.27
36 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (36 bp):
TTAATTATAATAAAATTTTTAATACTATTTTAAATT
Found at i:466806 original size:2 final size:2
Alignment explanation
Indices: 466799--466830 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
466789 ACAAAAACAA
466799 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
466831 TGTTGACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:467859 original size:16 final size:17
Alignment explanation
Indices: 467826--467860 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
467816 TTAAAAAAAT
*
467826 TAAATTAATATTAATTA
1 TAAATTAATATGAATTA
467843 TAAATTAA-ATGAATTA
1 TAAATTAATATGAATTA
467859 TA
1 TA
467861 TATAATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAATTAATATGAATTA
Found at i:467953 original size:32 final size:31
Alignment explanation
Indices: 467855--467953 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 31
467845 AATTAAATGA
* *
467855 ATTATATATAATTACT-TTAAATTTGATGTAT
1 ATTATATATAATTAATCTTAAATTTGAAGT-T
* * * * **
467886 ATTAAATAGAATTATTCATAAATTTGATAAAT
1 ATTATATATAATTAATCTTAAATTTGA-AGTT
467918 ATTATATATAATTAATCTTAAATTTGACAGTT
1 ATTATATATAATTAATCTTAAATTTGA-AGTT
467950 ATTA
1 ATTA
467954 AAAGTTTCAG
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
31 13 0.25
32 39 0.75
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (31 bp):
ATTATATATAATTAATCTTAAATTTGAAGTT
Found at i:472618 original size:3 final size:3
Alignment explanation
Indices: 472610--472639 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
472600 TAACAAGTTG
472610 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
472640 TTGTGACCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:484356 original size:12 final size:12
Alignment explanation
Indices: 484304--484363 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
484294 GGTCGTCACA
484304 TTATGATTTAAATT
1 TTAT-ATTT-AATT
*
484318 TTTTATTTATATT
1 TTATATTTA-ATT
484331 TTA-ATTTAA-T
1 TTATATTTAATT
*
484341 TTATAATTAATT
1 TTATATTTAATT
484353 TTATTATTTAA
1 TTA-TATTTAA
484364 AAAAATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
10 4 0.11
11 6 0.16
12 10 0.26
13 15 0.39
14 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TTATATTTAATT
Found at i:485503 original size:14 final size:15
Alignment explanation
Indices: 485447--485507 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 15
485437 GAATTAGTAT
*
485447 TTAATAATAAAAATA
1 TTAATTATAAAAATA
* * *
485462 ATATTTTTATAAAAT-
1 TTAATTATA-AAAATA
*
485477 TTAATTATTAAAATA
1 TTAATTATAAAAATA
485492 TTAA-TATAAAAATA
1 TTAATTATAAAAATA
485506 TT
1 TT
485508 TTAATAATAT
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
14 16 0.46
15 14 0.40
16 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAATTATAAAAATA
Found at i:486442 original size:2 final size:2
Alignment explanation
Indices: 486435--486483 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
486425 TTTAATCTGA
486435 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
486477 TC TC TC T
1 TC TC TC T
486484 TTTCTGTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:486951 original size:2 final size:2
Alignment explanation
Indices: 486944--486978 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
486934 TTGATGCAAT
486944 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
486979 AGCAAATTAG
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:490359 original size:49 final size:49
Alignment explanation
Indices: 490286--490384 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
490276 AATTTTAAGT
*
490286 ATGGTTCCCTCTCAATACCTTTGAACATAAAATAATAATAATAATAAAG
1 ATGGTTCCCTCTCAATACCCTTGAACATAAAATAATAATAATAATAAAG
*
490335 ATGGTTCCCTTTCAATACCCTTGAACATAAAATAATAATAATAATAAAG
1 ATGGTTCCCTCTCAATACCCTTGAACATAAAATAATAATAATAATAAAG
490384 A
1 A
490385 AACCCAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.30
Consensus pattern (49 bp):
ATGGTTCCCTCTCAATACCCTTGAACATAAAATAATAATAATAATAAAG
Done.