Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 2 of 20
Found at i:228040 original size:2 final size:2
Alignment explanation
Indices: 228035--228064 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
228025 TCATATTCTA
228035 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
228065 TGTTGCTTCT
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:228939 original size:42 final size:42
Alignment explanation
Indices: 228857--228939 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
228847 TCTTTTAGAT
* *
228857 TATAGTGTTATTGAAGTAACTAAATTTGTTATGGTAAGAAAA
1 TATAGTGTGATTGAAGTAACTAAATTTGTTATGCTAAGAAAA
** *
228899 TATAGTGTGATTGAAGTGGC-ATAATTTGTTATGCTGAGAAA
1 TATAGTGTGATTGAAGTAACTA-AATTTGTTATGCTAAGAAA
228940 TATTTGTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (42 bp):
TATAGTGTGATTGAAGTAACTAAATTTGTTATGCTAAGAAAA
Found at i:242717 original size:2 final size:2
Alignment explanation
Indices: 242710--242735 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
242700 TTCTTTTTCA
242710 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
242736 CCTTTTTTAG
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):
TC
Found at i:244737 original size:2 final size:2
Alignment explanation
Indices: 244730--244770 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
244720 GCAACTACTA
244730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
244771 CAGAGAGAGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:246814 original size:24 final size:26
Alignment explanation
Indices: 246756--246814 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 26
246746 CATTTTAAGT
* *
246756 TTTTTAATTTTTTTAATAAAATATAC
1 TTTTTAATATTTATAATAAAATATAC
* *
246782 ATTTT-ATATTTAT-ATATAATATA-
1 TTTTTAATATTTATAATAAAATATAC
246805 TTTTTAATAT
1 TTTTTAATAT
246815 GAATATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 6 0.22
26 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTTAATATTTATAATAAAATATAC
Found at i:246850 original size:18 final size:17
Alignment explanation
Indices: 246829--246882 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
246819 ATAAAAATAT
246829 AATATCTTAAAAAAATTA
1 AATAT-TTAAAAAAATTA
* *
246847 AATATATAAAAAATTTA
1 AATATTTAAAAAAATTA
246864 AA-ATTT--AAAAATTA
1 AATATTTAAAAAAATTA
246878 AATAT
1 AATAT
246883 ATATTTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 9 0.29
15 2 0.06
16 3 0.10
17 12 0.39
18 5 0.16
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AATATTTAAAAAAATTA
Found at i:246856 original size:17 final size:17
Alignment explanation
Indices: 246836--246885 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
246826 TATAATATCT
246836 TAAAAAAATTAAATATA
1 TAAAAAAATTAAATATA
*
246853 TAAAAAATTTAAA-AT-
1 TAAAAAAATTAAATATA
*
246868 T-TAAAAATTAAATATA
1 TAAAAAAATTAAATATA
246884 TA
1 TA
246886 TTTATATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 9 0.33
15 3 0.11
16 3 0.11
17 12 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAAAATTAAATATA
Found at i:246857 original size:16 final size:16
Alignment explanation
Indices: 246838--246885 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
246828 TAATATCTTA
246838 AAAAAATTAAATATAT
1 AAAAAATTAAATATAT
246854 AAAAAATTTAAA-AT-T
1 AAAAAA-TTAAATATAT
*
246869 TAAAAATTAAATATAT
1 AAAAAATTAAATATAT
246885 A
1 A
246886 TTTATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 9 0.33
17 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAATTAAATATAT
Found at i:246858 original size:33 final size:30
Alignment explanation
Indices: 246817--246885 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
246807 TTTAATATGA
*
246817 ATATAAAAATATAATATCTTAAAAAAATTAAAT
1 ATATAAAAATATAAAAT-TT--AAAAATTAAAT
*
246850 ATATAAAAAATTTAAAATTTAAAAATTAAAT
1 ATAT-AAAAATATAAAATTTAAAAATTAAAT
246881 ATATA
1 ATATA
246886 TTTATATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 15 0.45
33 6 0.18
34 11 0.33
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (30 bp):
ATATAAAAATATAAAATTTAAAAATTAAAT
Found at i:247361 original size:20 final size:21
Alignment explanation
Indices: 247335--247385 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
247325 TTTAAATATT
247335 AATATATAACATAATTTTTTAA
1 AATATATAA-ATAATTTTTTAA
*
247357 AATATATAAATAATTTTAT-A
1 AATATATAAATAATTTTTTAA
247377 AATAT-TAAA
1 AATATATAAA
247386 CATATTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 6 0.21
21 9 0.32
22 9 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATATAAATAATTTTTTAA
Found at i:247736 original size:4 final size:4
Alignment explanation
Indices: 247727--247764 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
247717 CAAGAACAAA
*
247727 TATG TATG TATG TATG TATG TATG TATG TACG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
247765 AACTTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:252181 original size:16 final size:16
Alignment explanation
Indices: 252162--252224 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
252152 AGTTTGTATC
252162 ATTTCGAATTCGGATT
1 ATTTCGAATTCGGATT
* *
252178 ATTT-TAGATTCAGG-TC
1 ATTTCGA-ATTC-GGATT
*
252194 ATTTCGGATTCGGATT
1 ATTTCGAATTCGGATT
*
252210 ATTTCGAGTTCGGAT
1 ATTTCGAATTCGGAT
252225 CAATCAGGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
15 3 0.08
16 31 0.86
17 2 0.06
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (16 bp):
ATTTCGAATTCGGATT
Found at i:253297 original size:16 final size:16
Alignment explanation
Indices: 253269--253414 Score: 122
Period size: 16 Copynumber: 9.2 Consensus size: 16
253259 CGAATTAATT
*
253269 ATTCGAGTCATTTCGA
1 ATTCGAATCATTTCGA
** *
253285 ATTAAAATCATTTCAA
1 ATTCGAATCATTTCGA
*
253301 ATTCGAATCATTTTGA
1 ATTCGAATCATTTCGA
* *
253317 GTTCGAATCGTTTCGA
1 ATTCGAATCATTTCGA
*
253333 ATTCGAGTCATTTCGA
1 ATTCGAATCATTTCGA
*
253349 ATTC-AGATCA-TTCTAA
1 ATTCGA-ATCATTTC-GA
*
253365 ATTCG-ATCATTTTGA
1 ATTCGAATCATTTCGA
253380 ATTCGAATCATTTC-A
1 ATTCGAATCATTTCGA
*
253395 CATTC-AAGTCAGTTCGA
1 -ATTCGAA-TCATTTCGA
253412 ATT
1 ATT
253415 TGAGTTATCA
Statistics
Matches: 102, Mismatches: 20, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
15 17 0.17
16 84 0.82
17 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (16 bp):
ATTCGAATCATTTCGA
Found at i:253305 original size:32 final size:32
Alignment explanation
Indices: 253269--253414 Score: 152
Period size: 32 Copynumber: 4.6 Consensus size: 32
253259 CGAATTAATT
*
253269 ATTCGAGTCATTTCGAATTAAAATCATTTCAA
1 ATTCGAGTCATTTCGAATTCAAATCATTTCAA
* * * * * *
253301 ATTCGAATCATTTTGAGTTCGAATCGTTTCGA
1 ATTCGAGTCATTTCGAATTCAAATCATTTCAA
*
253333 ATTCGAGTCATTTCGAATTCAGATCA-TTCTAA
1 ATTCGAGTCATTTCGAATTCAAATCATTTC-AA
* * *
253365 ATTCGA-TCATTTTGAATTCGAATCATTTCAC
1 ATTCGAGTCATTTCGAATTCAAATCATTTCAA
* *
253396 ATTCAAGTCAGTTCGAATT
1 ATTCGAGTCATTTCGAATT
253415 TGAGTTATCA
Statistics
Matches: 90, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
31 25 0.28
32 65 0.72
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (32 bp):
ATTCGAGTCATTTCGAATTCAAATCATTTCAA
Found at i:253374 original size:15 final size:15
Alignment explanation
Indices: 253348--253391 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
253338 AGTCATTTCG
253348 AATTCAGATCATTCTA
1 AATTC-GATCATTCTA
* *
253364 AATTCGATCATTTTG
1 AATTCGATCATTCTA
253379 AATTCGAATCATT
1 AATTCG-ATCATT
253392 TCACATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (15 bp):
AATTCGATCATTCTA
Found at i:263090 original size:18 final size:19
Alignment explanation
Indices: 263069--263104 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
263059 GTTAAAATTA
*
263069 TATTAC-ATGTTATAAAAC
1 TATTACAATATTATAAAAC
263087 TATTACAATATTATAAAA
1 TATTACAATATTATAAAA
263105 AAAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (19 bp):
TATTACAATATTATAAAAC
Found at i:263133 original size:21 final size:19
Alignment explanation
Indices: 263103--263175 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 19
263093 AATATTATAA
*
263103 AAAAAATATTAAAGTAATTTT
1 AAAAATTATTAAA-TAA-TTT
* *
263124 AAAAATTATTAAAATTATAT
1 AAAAATTATT-AAATAATTT
263144 AAAAATTTATTAAAAATTAATTT
1 AAAAA-TTATT--AAA-TAATTT
263167 AAAAATTAT
1 AAAAATTAT
263176 GTTTATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 7 0.16
21 16 0.37
22 11 0.26
23 9 0.21
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (19 bp):
AAAAATTATTAAATAATTT
Found at i:263134 original size:43 final size:42
Alignment explanation
Indices: 263082--263175 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 42
263072 TACATGTTAT
*
263082 AAAACTATTACAATATTATA-AAAAAAATATT-AAAGTAATTTTA
1 AAAATTATTA-AA-ATTATATAAAAAAATATTAAAAGTAA-TTTA
** *
263125 AAAATTATTAAAATTATATAAAAATTTATTAAAAATTAATTTA
1 AAAATTATTAAAATTATATAAAAAAATATT-AAAAGTAATTTA
263168 AAAATTAT
1 AAAATTAT
263176 GTTTATAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
41 6 0.14
42 11 0.25
43 21 0.48
44 6 0.14
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (42 bp):
AAAATTATTAAAATTATATAAAAAAATATTAAAAGTAATTTA
Found at i:263150 original size:11 final size:11
Alignment explanation
Indices: 263123--263175 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
263113 AAAGTAATTT
263123 TAAAAATTAT-
1 TAAAAATTATA
263133 T-AAAATTATA
1 TAAAAATTATA
263143 TAAAAATT-TA
1 TAAAAATTATA
*
263153 TTAAAAATTAATT
1 -TAAAAATT-ATA
263166 TAAAAATTAT
1 TAAAAATTAT
263176 GTTTATAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
9 8 0.22
10 4 0.11
11 16 0.43
12 8 0.22
13 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:263198 original size:43 final size:42
Alignment explanation
Indices: 263104--263202 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 42
263094 ATATTATAAA
263104 AAAAATATT--AAAGTAATTTTAAAAATTATTAAAATTATAT
1 AAAAATATTAAAAAGTAATTTTAAAAATTATTAAAATTATAT
* *
263144 AAAAATTTATTAAAAATTAA-TTTAAAAATTATGTTTATAATTAT-T
1 AAAAA--TATTAAAAAGTAATTTTAAAAATTA---TTAAAATTATAT
263189 AAAAATATTAAAAA
1 AAAAATATTAAAAA
263203 AATTATCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
40 5 0.10
42 4 0.08
43 20 0.40
44 6 0.12
45 6 0.12
46 9 0.18
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (42 bp):
AAAAATATTAAAAAGTAATTTTAAAAATTATTAAAATTATAT
Found at i:263366 original size:21 final size:22
Alignment explanation
Indices: 263342--263382 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
263332 TTATATAACT
263342 TATATAAAAAATTA-TCAAAAA
1 TATATAAAAAATTATTCAAAAA
* *
263363 TATATTAAATATTATTCAAA
1 TATATAAAAAATTATTCAAA
263383 CTGTTGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
TATATAAAAAATTATTCAAAAA
Found at i:263930 original size:15 final size:16
Alignment explanation
Indices: 263883--263933 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
263873 TTTAATCAAT
*
263883 AAAATAAAATATTATAA
1 AAAAT-AAATATTTTAA
*
263900 AATATAAATATTTTAA
1 AAAATAAATATTTTAA
263916 AAAATAAAT-TTTTAA
1 AAAATAAATATTTTAA
263931 AAA
1 AAA
263934 TAATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 9 0.29
16 18 0.58
17 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAAATATTTTAA
Found at i:273327 original size:4 final size:4
Alignment explanation
Indices: 273320--273373 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
273310 TTTATGTATG
* * * * * *
273320 TATA TATA TATA TATA CATA CATA CATA TATA TACA TACA TACA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
273368 TATA TA
1 TATA TA
273374 AATCTTTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (4 bp):
TATA
Found at i:273350 original size:18 final size:18
Alignment explanation
Indices: 273327--273371 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
273317 ATGTATATAT
273327 ATATATATACATACATAC
1 ATATATATACATACATAC
273345 ATATATATACATACATAC
1 ATATATATACATACATAC
273363 ATATATATA
1 ATATATATA
273372 TAAATCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATATATACATACATAC
Found at i:273351 original size:22 final size:22
Alignment explanation
Indices: 273323--273373 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
273313 ATGTATGTAT
*
273323 ATATATATATATACATACATAC
1 ATATATATACATACATACATAC
*
273345 ATATATATACATACATACATAT
1 ATATATATACATACATACATAC
273367 ATATATA
1 ATATATA
273374 AATCTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATATATACATACATACATAC
Found at i:274302 original size:23 final size:22
Alignment explanation
Indices: 274253--274307 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
274243 TCCCTAGTTC
274253 TATTAAATATTTAAATATCATT
1 TATTAAATATTTAAATATCATT
* *
274275 AATTAAAT-TTTATATAGTTCATT
1 TATTAAATATTTAAATA--TCATT
274298 TATTAAATAT
1 TATTAAATAT
274308 CAATTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 7 0.26
22 7 0.26
23 12 0.44
24 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTAAATATTTAAATATCATT
Found at i:274583 original size:27 final size:28
Alignment explanation
Indices: 274526--274588 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
274516 TTTTTTAATT
* *
274526 ATATTATTTGATATTATATTGAACTATA
1 ATATTATTTGAGATGATATTGAACTATA
*
274554 ATATTATTT-AGATGATATTGAA-TTTGA
1 ATATTATTTGAGATGATATTGAACTAT-A
274581 ATATTATT
1 ATATTATT
274589 AAATCTATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 2 0.06
27 20 0.65
28 9 0.29
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.51
Consensus pattern (28 bp):
ATATTATTTGAGATGATATTGAACTATA
Found at i:281847 original size:2 final size:2
Alignment explanation
Indices: 281840--281884 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
281830 CTTAGGTAAA
* *
281840 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT CT 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
281882 AT A
1 AT A
281885 AAGGGGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:282693 original size:5 final size:5
Alignment explanation
Indices: 282660--282691 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
282650 AGTAATTCTT
282660 AAAAG AAAAG AAAAG AAAAG AAAA- AAAA- AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
282692 AACACTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:283035 original size:15 final size:16
Alignment explanation
Indices: 283015--283044 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
283005 ATGATATTAA
283015 TTTT-AAAAAATAAAT
1 TTTTAAAAAAATAAAT
283030 TTTTAAAAAAATAAA
1 TTTTAAAAAAATAAA
283045 ATTTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTTTAAAAAAATAAAT
Found at i:284381 original size:24 final size:24
Alignment explanation
Indices: 284354--284400 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
284344 TAACTTGATT
284354 GGTGAATAGATCTAATTATATTAC
1 GGTGAATAGATCTAATTATATTAC
284378 GGTGAATAGATCTAATTATATTA
1 GGTGAATAGATCTAATTATATTA
284401 TAATTAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (24 bp):
GGTGAATAGATCTAATTATATTAC
Found at i:285014 original size:18 final size:18
Alignment explanation
Indices: 284991--285027 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
284981 ACAATATTAC
284991 GTATTGGTATAATCCAAA
1 GTATTGGTATAATCCAAA
285009 GTATTGGTATAATCCAAA
1 GTATTGGTATAATCCAAA
285027 G
1 G
285028 AATCGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (18 bp):
GTATTGGTATAATCCAAA
Found at i:287595 original size:21 final size:21
Alignment explanation
Indices: 287551--287589 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
287541 AAAGATTTTA
*
287551 TTATTTTTAATTTTTAATAAT
1 TTATTTATAATTTTTAATAAT
287572 TTATTTATAA-TTTTAATA
1 TTATTTATAATTTTTAATA
287590 TTTTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTTATAATTTTTAATAAT
Found at i:290747 original size:16 final size:16
Alignment explanation
Indices: 290726--290762 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
290716 GCCGTTGAAG
290726 AAAGTATCTTAATTAA
1 AAAGTATCTTAATTAA
290742 AAAGTATCTTAATTAA
1 AAAGTATCTTAATTAA
290758 AAAGT
1 AAAGT
290763 TATTAATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (16 bp):
AAAGTATCTTAATTAA
Found at i:290768 original size:15 final size:16
Alignment explanation
Indices: 290726--290769 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
290716 GCCGTTGAAG
*
290726 AAAGTATCTTAATTAA
1 AAAGTATATTAATTAA
*
290742 AAAGTATCTTAATTAA
1 AAAGTATATTAATTAA
290758 AAAGT-TATTAAT
1 AAAGTATATTAAT
290770 AAGTATGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (16 bp):
AAAGTATATTAATTAA
Found at i:293952 original size:14 final size:15
Alignment explanation
Indices: 293927--293955 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
293917 CTTTAATCAA
293927 TTTTATTAAATTATT
1 TTTTATTAAATTATT
293942 TTTTATT-AATTATT
1 TTTTATTAAATTATT
293956 ACATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATTAAATTATT
Found at i:294076 original size:8 final size:8
Alignment explanation
Indices: 294063--294090 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
294053 TAATAAATTA
294063 AAAAAAAC
1 AAAAAAAC
294071 AAAAAAAC
1 AAAAAAAC
294079 AAAAAAAC
1 AAAAAAAC
294087 AAAA
1 AAAA
294091 GATAGGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:294411 original size:17 final size:17
Alignment explanation
Indices: 294389--294421 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
294379 CATTAATTTT
*
294389 TTAATTTTATAAAATAA
1 TTAATTATATAAAATAA
294406 TTAATTATATAAAATA
1 TTAATTATATAAAATA
294422 TATCTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATTATATAAAATAA
Found at i:294662 original size:19 final size:19
Alignment explanation
Indices: 294630--294673 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
294620 ATTAAATTTA
* *
294630 AATAAA-AATTATTTTATT
1 AATAAATAATAATTTAATT
294648 AATAAATAATAATTTAATT
1 AATAAATAATAATTTAATT
*
294667 AAAAAAT
1 AATAAAT
294674 CTGTATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAAATAATAATTTAATT
Found at i:296815 original size:26 final size:23
Alignment explanation
Indices: 296777--296846 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 23
296767 TAAATTTTAC
*
296777 AAAA-AAATTAATATATAAAATA
1 AAAATAAATAAATATATAAAATA
*
296799 AAATTTAATATAAA-ATAATAAAAATA
1 AAA-ATAA-ATAAATAT-AT-AAAATA
296825 AAAATAAATAAATAT-TAAAATA
1 AAAATAAATAAATATATAAAATA
296847 TATTAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
22 9 0.23
23 1 0.03
24 9 0.23
25 11 0.28
26 9 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAATAAATAAATATATAAAATA
Found at i:296834 original size:16 final size:16
Alignment explanation
Indices: 296805--296856 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
296795 AATAAAATTT
296805 AATATAAAAT-AATAAA
1 AATA-AAAATAAATAAA
296821 AATAAAAATAAATAAA
1 AATAAAAATAAATAAA
* * * *
296837 TATTAAAATATATTAA
1 AATAAAAATAAATAAA
296853 AATA
1 AATA
296857 TTAACATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 5 0.17
16 24 0.83
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAAAATAAATAAA
Found at i:296857 original size:18 final size:18
Alignment explanation
Indices: 296834--296920 Score: 56
Period size: 16 Copynumber: 4.8 Consensus size: 18
296824 AAAAATAAAT
296834 AAATATTAAAATATATTA
1 AAATATTAAAATATATTA
*
296852 AAATATT--AACATATTA
1 AAATATTAAAATATATTA
* *
296868 ATATTTATATAAATATA-TA
1 AAATAT-TA-AAATATATTA
* *
296887 ATAT-TTTAAATATAATTA
1 AAATATTAAAATAT-ATTA
*
296905 TAATATATAAAATATA
1 AAATAT-TAAAATATA
296921 AACTATCAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
16 18 0.34
17 3 0.06
18 12 0.23
19 8 0.15
20 12 0.23
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATTAAAATATATTA
Found at i:296894 original size:20 final size:21
Alignment explanation
Indices: 296829--296921 Score: 68
Period size: 20 Copynumber: 4.4 Consensus size: 21
296819 AAAATAAAAA
*
296829 TAAATA-AATATTAAAATATATT
1 TAAATATAATA-TATAATAT-TT
* *
296851 AAAATATTAACATATTAATA-TT
1 TAAATA-TAATATA-TAATATTT
*
296873 TATATA-AATATATAATATTT
1 TAAATATAATATATAATATTT
*
296893 TAAATATAAT-TATAATATAT
1 TAAATATAATATATAATATTT
*
296913 AAAATATAA
1 TAAATATAA
296922 ACTATCAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
19 5 0.09
20 29 0.51
21 3 0.05
22 11 0.19
23 2 0.04
24 7 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATAATATATAATATTT
Found at i:296908 original size:6 final size:7
Alignment explanation
Indices: 296785--296921 Score: 53
Period size: 6 Copynumber: 20.4 Consensus size: 7
296775 ACAAAAAAAT
296785 TAATATA
1 TAATATA
296792 TAA-A-A
1 TAATATA
* *
296797 TAAAATT
1 TAATATA
296804 TAATATA
1 TAATATA
*
296811 AAATA-A
1 TAATATA
*
296817 TAA-AAA
1 TAATATA
*
296823 TAA-AAA
1 TAATATA
296829 TAA-ATA
1 TAATATA
296835 -AATATTA
1 TAATA-TA
*
296842 AAATATA
1 TAATATA
*
296849 TTAAAATA
1 -TAATATA
*
296857 TTAACATA
1 -TAATATA
296865 TTAATAT-
1 -TAATATA
*
296872 TTATATA
1 TAATATA
296879 -AATATA
1 TAATATA
*
296885 TAATATTT
1 TAATA-TA
296893 TAA-ATA
1 TAATATA
296899 TAAT-TA
1 TAATATA
296905 TAATATA
1 TAATATA
*
296912 TAAAATA
1 TAATATA
296919 TAA
1 TAA
296922 ACTATCAAAT
Statistics
Matches: 103, Mismatches: 15, Indels: 24
0.73 0.11 0.17
Matches are distributed among these distances:
5 7 0.07
6 38 0.37
7 32 0.31
8 26 0.25
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (7 bp):
TAATATA
Found at i:296918 original size:36 final size:38
Alignment explanation
Indices: 296831--296920 Score: 95
Period size: 36 Copynumber: 2.5 Consensus size: 38
296821 AATAAAAATA
296831 AATA-AATAT-TAAAATATATTAAAATATTAACATATT
1 AATATAATATATAAAATATATTAAAATATTAACATATT
* * *
296867 AATAT-TTATAT-AAATATA-TAATATTTTAA-ATA-T
1 AATATAATATATAAAATATATTAAAATATTAACATATT
296900 AATTATAATATATAAAATATA
1 AA-TATAATATATAAAATATA
296921 AACTATCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
33 3 0.07
34 6 0.13
35 14 0.31
36 21 0.47
37 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (38 bp):
AATATAATATATAAAATATATTAAAATATTAACATATT
Found at i:301372 original size:19 final size:18
Alignment explanation
Indices: 301348--301405 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
301338 ATATGATTTG
301348 ATATAAAATAATATATATA
1 ATATAAAAT-ATATATATA
*
301367 ATAT-AAATATATAAAT-
1 ATATAAAATATATATATA
301383 ATATCAAAAT-T-TATATA
1 ATAT-AAAATATATATATA
301400 ATATAA
1 ATATAA
301406 CTTATTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 10 0.29
17 12 0.35
18 8 0.24
19 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATAAAATATATATATA
Found at i:301383 original size:14 final size:14
Alignment explanation
Indices: 301348--301385 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
301338 ATATGATTTG
301348 ATATAAA-AT-AAT
1 ATATAAATATAAAT
301360 ATATATAATATAAAT
1 ATATA-AATATAAAT
301375 ATATAAATATA
1 ATATAAATATA
301386 TCAAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.22
13 2 0.09
14 8 0.35
15 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATAAATATAAAT
Found at i:301415 original size:33 final size:32
Alignment explanation
Indices: 301361--301423 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
301351 TAAAATAATA
301361 TATATAATATAAATATATAAATATATCAAAATT
1 TATATAATATAAATATATAAAT-TATCAAAATT
* *
301394 TATATAATATAACT-TATTAAATTATTAAAA
1 TATATAATATAAATATA-TAAATTATCAAAA
301424 ATATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (32 bp):
TATATAATATAAATATATAAATTATCAAAATT
Found at i:309815 original size:13 final size:13
Alignment explanation
Indices: 309799--309832 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
309789 TTAAATATCC
*
309799 ATATTTAATATTT
1 ATATTTAATATAT
*
309812 ATATTAAATATAT
1 ATATTTAATATAT
309825 ATATTTAA
1 ATATTTAA
309833 ACATAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATTTAATATAT
Found at i:309864 original size:18 final size:17
Alignment explanation
Indices: 309823--309865 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
309813 TATTAAATAT
309823 ATATATTTAAACATAAAA
1 ATATA-TTAAACATAAAA
* *
309841 AAATATTAAACATATTAA
1 ATATATTAAACATA-AAA
309859 ATATATT
1 ATATATT
309866 TATATCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATATTAAACATAAAA
Found at i:315614 original size:228 final size:228
Alignment explanation
Indices: 315305--316338 Score: 987
Period size: 228 Copynumber: 4.5 Consensus size: 228
315295 GATAAGCCTT
* * * * * * * *
315305 TGCTGATCTGGAGGGATTCCTTCCTTGTCCTGAATCTTTGACTTGACATTGTCAATTGTATCCGA
1 TGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATCTTTGCCTTGACGTTATCAATCGTGTCCGA
* * * * * * * *
315370 ACTTTCAACCTCCAGGGTGATAGTTTTTCCAGTCAAGGTCTTGACAAAAATCTGCATTCCTCCAC
66 ACTCTCGACCTCCAGAGTGATAGTCTTGCCGGTCAAGGTCTTGACAAAGATCTGCATGCCTCCAC
* * ** ** * * * * *
315435 GCAGCCTCAAAACAAGGTGAAGGGTCGATTCCTTTTGGATATTATAATCGGCCAAGGTCCTACCA
131 GAAGACGGAGGACAAGGTGAAGAGTTGATTCCTTTTGGATATTATAATCGGCCAAAGTACGACCA
* * *
315500 TCCTCAAGCTGCTTCCCAGCGAAGATCAAACGT
196 TCCTCAAGCTGTTTCCCAGCGAAGATGAAACGC
* * * * * *
315533 TGTTGGTCTGGTGGGATCCCTTCCTTGTCCTGAATCTTTGCCTTTACATTATCAATCGTGTCCGA
1 TGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATCTTTGCCTTGACGTTATCAATCGTGTCCGA
* * * * * *
315598 ACTCTCGACCTCCAGGGTTATAGTCTTCCCTGTCAAGGTTTTGACAAAGATTTGCATGCCTCCAC
66 ACTCTCGACCTCCAGAGTGATAGTCTTGCCGGTCAAGGTCTTGACAAAGATCTGCATGCCTCCAC
* * * * * * * * *
315663 GGAGCCTGAGGACAAGGTGGAGTGTTGACTCCTTTTGGATATTATAATCAGCCAAAGTACGGCCG
131 GAAGACGGAGGACAAGGTGAAGAGTTGATTCCTTTTGGATATTATAATCGGCCAAAGTACGACCA
** *
315728 TCCTCAAGCTGTTTCCCAGCGAAGATGAGCCGT
196 TCCTCAAGCTGTTTCCCAGCGAAGATGAAACGC
* * * * * * *
315761 TGCTGGTCTGGAGGGATACCTTCTTTGTCTTGGATCTTGGCTTTGACGTTGTCGATCGTGTCGGA
1 TGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATCTTTGCCTTGACGTTATCAATCGTGTCCGA
* * * * * * * * * *
315826 ACTTTCGACTTCGAGAGTGATGGTTTTGCCGGTTAAGGTTTTGACAAAGATTTGCATACCCCCAC
66 ACTCTCGACCTCCAGAGTGATAGTCTTGCCGGTCAAGGTCTTGACAAAGATCTGCATGCCTCCAC
* * * * * * *
315891 GAAGACGGAGCACAAGGTGAAGAGTAGATT-CTTTCTGGATGTTATAGTCGG-CAAGGGTCCGGC
131 GAAGACGGAGGACAAGGTGAAGAGTTGATTCCTTT-TGGATATTATAATCGGCCAA-AGTACGAC
* * *
315954 CATCTTCAAGCTGTTTACCAGCGAAGATGAGACGC
194 CATCCTCAAGCTGTTTCCCAGCGAAGATGAAACGC
* * * * *
315989 TGCTGGTCAGGAGGGATACCTTCCTTGTCTTGTATCTTGGCCTTAACGTTATCAATGGTGTCCGA
1 TGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATCTTTGCCTTGACGTTATCAATCGTGTCCGA
* * * * *
316054 ACTCTCGACCTCGAGAGTTATGGTCTTGCCGGTTAAGGTCTTGACAAAGATCTGCATGCCACCAC
66 ACTCTCGACCTCCAGAGTGATAGTCTTGCCGGTCAAGGTCTTGACAAAGATCTGCATGCCTCCAC
* * * * * * *
316119 GAAGACGGAGGACCAGATGGAGAGTTGATTCCTTCTGGATGTTATAATCCGCCAAAGTACGACCG
131 GAAGACGGAGGACAAGGTGAAGAGTTGATTCCTTTTGGATATTATAATCGGCCAAAGTACGACCA
* * *
316184 TCTTCGAGCTGTTTGCCAGCGAAGAT-AAGACGC
196 TCCTCAAGCTGTTTCCCAGCGAAGATGAA-ACGC
* * * * *
316217 TGCTGGTCAGGTGGGATCCCTTCCTTGTCTTGAAT-TTTAGCCTTGACGTTATCGATCGTGTCGG
1 TGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATCTTT-GCCTTGACGTTATCAATCGTGTCCG
* * * * * * *
316281 AACTCTCGACCTCGAGAGTTATGGTCTTGCCGGTCAGGGTTTTCACGAAGATCTGCAT
65 AACTCTCGACCTCCAGAGTGATAGTCTTGCCGGTCAAGGTCTTGACAAAGATCTGCAT
316339 CTTCTAAAAG
Statistics
Matches: 675, Mismatches: 125, Indels: 12
0.83 0.15 0.01
Matches are distributed among these distances:
227 10 0.01
228 659 0.98
229 6 0.01
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (228 bp):
TGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATCTTTGCCTTGACGTTATCAATCGTGTCCGA
ACTCTCGACCTCCAGAGTGATAGTCTTGCCGGTCAAGGTCTTGACAAAGATCTGCATGCCTCCAC
GAAGACGGAGGACAAGGTGAAGAGTTGATTCCTTTTGGATATTATAATCGGCCAAAGTACGACCA
TCCTCAAGCTGTTTCCCAGCGAAGATGAAACGC
Found at i:316208 original size:456 final size:455
Alignment explanation
Indices: 315284--316338 Score: 1214
Period size: 456 Copynumber: 2.3 Consensus size: 455
315274 CTCCAATTGC
* * * * * * *
315284 TTGCCGGCAAAGATAAGCCTTTGCTGATCTGGAGGGATTCCTTCCTTGTCCTGAATCTTTGACTT
1 TTGCCAGCGAAGATAAGCCGTTGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATC-TTGGCTT
* * * * * * * * * * * *
315349 GACATTGTCAATTGTATCCGAACTTTCAACCTCCAGGGTGATAGTTTTTCCAGTCAAGGTCTTGA
65 GACGTTGTCGATCGTGTCGGAACTTTCGACCTCGAGAGTGATGGTTTTGCCGGTCAAGGTTTTGA
* * * * * * * *
315414 CAAAAATCTGCATTCCTCCACGCAGCCTCAAAACAAGGTGAAGGGTCGATTCCTTTTGGATATTA
130 CAAAGATCTGCATACCCCCACGAAGACGCAAAACAAGGTGAAGAGTAGATTCCTTTTGGATATTA
* * * * *
315479 TAATCGGCCAAGGTCCTACCATCCTCAAGCTGCTTCCCAGCGAAGATCAAACGTTGTTGGTCTGG
195 TAATCGGCCAAGGTCCGACCATCCTCAAGCTGCTTACCAGCGAAGATCAAACGCTGCTGGTCAGG
* * * *
315544 TGGGATCCCTTCCTTGTCCTGAATCTTTGCCTTTACATTATCAATCGTGTCCGAACTCTCGACCT
260 AGGGATACCTTCCTTGTCCTGAATCTTGGCCTTAACATTATCAATCGTGTCCGAACTCTCGACCT
* * * * * * * *
315609 CCAGGGTTATAGTCTTCCCTGTCAAGGTTTTGACAAAGATTTGCATGCCTCCACGGAGCCTGAGG
325 CCAGAGTTATAGTCTTCCCGGTCAAGGTCTTGACAAAGATCTGCATGCCACCACGAAGACGGAGG
* * * *
315674 ACAAGGTGGAGTGTTGACTCCTTTTGGATATTATAATCAGCCAAAGTACGGCCGTCCTCAAGCTG
390 ACAAGATGGAGAGTTGACTCCTTCTGGATATTATAATCAGCCAAAGTACGACCGTCCTCAAGCTG
315739 T
455 T
* * * *
315740 TTCCCAGCGAAGATGAGCCGTTGCTGGTCTGGAGGGATACCTTCTTTGTCTTGGATCTTGGCTTT
1 TTGCCAGCGAAGATAAGCCGTTGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATCTTGGC-TT
* *
315805 GACGTTGTCGATCGTGTCGGAACTTTCGACTTCGAGAGTGATGGTTTTGCCGGTTAAGGTTTTGA
65 GACGTTGTCGATCGTGTCGGAACTTTCGACCTCGAGAGTGATGGTTTTGCCGGTCAAGGTTTTGA
* * ** *
315870 CAAAGATTTGCATACCCCCACGAAGACGGAGCACAAGGTGAAGAGTAGATT-CTTTCTGGATGTT
130 CAAAGATCTGCATACCCCCACGAAGACGCAAAACAAGGTGAAGAGTAGATTCCTTT-TGGATATT
* * * * * *
315934 ATAGTCGG-CAAGGGTCCGGCCATCTTCAAGCTGTTTACCAGCGAAGATGAGACGCTGCTGGTCA
194 ATAATCGGCCAA-GGTCCGACCATCCTCAAGCTGCTTACCAGCGAAGATCAAACGCTGCTGGTCA
* * * *
315998 GGAGGGATACCTTCCTTGTCTTGTATCTTGGCCTTAACGTTATCAATGGTGTCCGAACTCTCGAC
258 GGAGGGATACCTTCCTTGTCCTGAATCTTGGCCTTAACATTATCAATCGTGTCCGAACTCTCGAC
* * * *
316063 CTCGAGAGTTATGGTCTTGCCGGTTAAGGTCTTGACAAAGATCTGCATGCCACCACGAAGACGGA
323 CTCCAGAGTTATAGTCTTCCCGGTCAAGGTCTTGACAAAGATCTGCATGCCACCACGAAGACGGA
* * * * * *
316128 GGACCAGATGGAGAGTTGATTCCTTCTGGATGTTATAATCCGCCAAAGTACGACCGTCTTCGAGC
388 GGACAAGATGGAGAGTTGACTCCTTCTGGATATTATAATCAGCCAAAGTACGACCGTCCTCAAGC
316193 TGT
453 TGT
* * * * * * *
316196 TTGCCAGCGAAGATAAGACGCTGCTGGTCAGGTGGGATCCCTTCCTTGTCTTGAATTTTAGCCTT
1 TTGCCAGCGAAGATAAGCCGTTGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATCTT-GGCTT
* * * * * *
316261 GACGTTATCGATCGTGTCGGAACTCTCGACCTCGAGAGTTATGGTCTTGCCGGTCAGGGTTTTCA
65 GACGTTGTCGATCGTGTCGGAACTTTCGACCTCGAGAGTGATGGTTTTGCCGGTCAAGGTTTTGA
*
316326 CGAAGATCTGCAT
130 CAAAGATCTGCAT
316339 CTTCTAAAAG
Statistics
Matches: 495, Mismatches: 100, Indels: 8
0.82 0.17 0.01
Matches are distributed among these distances:
455 11 0.02
456 482 0.97
457 2 0.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (455 bp):
TTGCCAGCGAAGATAAGCCGTTGCTGGTCTGGAGGGATACCTTCCTTGTCTTGAATCTTGGCTTG
ACGTTGTCGATCGTGTCGGAACTTTCGACCTCGAGAGTGATGGTTTTGCCGGTCAAGGTTTTGAC
AAAGATCTGCATACCCCCACGAAGACGCAAAACAAGGTGAAGAGTAGATTCCTTTTGGATATTAT
AATCGGCCAAGGTCCGACCATCCTCAAGCTGCTTACCAGCGAAGATCAAACGCTGCTGGTCAGGA
GGGATACCTTCCTTGTCCTGAATCTTGGCCTTAACATTATCAATCGTGTCCGAACTCTCGACCTC
CAGAGTTATAGTCTTCCCGGTCAAGGTCTTGACAAAGATCTGCATGCCACCACGAAGACGGAGGA
CAAGATGGAGAGTTGACTCCTTCTGGATATTATAATCAGCCAAAGTACGACCGTCCTCAAGCTGT
Found at i:322337 original size:2 final size:2
Alignment explanation
Indices: 322330--322366 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
322320 TACTTACAAA
322330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
322367 ATTGTATCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:325739 original size:20 final size:20
Alignment explanation
Indices: 325653--325739 Score: 61
Period size: 20 Copynumber: 4.2 Consensus size: 20
325643 TTTAAATTTG
325653 ATATTAATATAAAATAA-AATAA
1 ATATT-ATAT-AAATAATAA-AA
* *
325675 ATA-TAAATATAATATATTAAA
1 ATATTATATA-AATA-ATAAAA
* * *
325696 ATTTATATATAAATAATTATA
1 ATAT-TATATAAATAATAAAA
325717 ATATTATATAAATAATAAAA
1 ATATTATATAAATAATAAAA
325737 ATA
1 ATA
325740 ATTAAATTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
19 1 0.02
20 24 0.46
21 14 0.27
22 8 0.15
23 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATTATATAAATAATAAAA
Found at i:325781 original size:43 final size:43
Alignment explanation
Indices: 325734--325816 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
325724 ATAAATAATA
* *
325734 AAAATAATTAAATTT-AATTTATTATGAATTAATAAATAAAATT
1 AAAATAATTAAATTTAAAATTAAT-TGAATTAATAAATAAAATT
* *
325777 AAAATAATTTAATTTAAAATTAATTGAATTGATAAATAAA
1 AAAATAATTAAATTTAAAATTAATTGAATTAATAAATAAA
325817 GATTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 29 0.83
44 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (43 bp):
AAAATAATTAAATTTAAAATTAATTGAATTAATAAATAAAATT
Found at i:328873 original size:2 final size:2
Alignment explanation
Indices: 328868--328896 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
328858 GTGTGTGTGT
328868 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
328897 TGAGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:334918 original size:22 final size:21
Alignment explanation
Indices: 334875--334914 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
334865 AATTTTTATT
334875 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
334896 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
334915 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:335341 original size:5 final size:5
Alignment explanation
Indices: 335331--335370 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
335321 AAAATTTTGA
335331 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAGG AAAA- AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA-G AAAAG AAAAG
335371 GGTGTGTCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
6 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:336867 original size:18 final size:17
Alignment explanation
Indices: 336846--336896 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
336836 TATTTTAAAA
*
336846 ATTATATATAATAAATTT
1 ATTAAATATAA-AAATTT
*
336864 ATTAAATATCAAAATTT
1 ATTAAATATAAAAATTT
*
336881 ATATAAATAAAAAAAT
1 AT-TAAATATAAAAAT
336897 AATTTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTAAATATAAAAATTT
Found at i:336918 original size:80 final size:85
Alignment explanation
Indices: 336780--336942 Score: 198
Period size: 80 Copynumber: 2.0 Consensus size: 85
336770 GATTGAATAA
**
336780 TATTAAATATAATATAATTATATAAAATAAAAAAAATAATTAAAAATATTTATAAATATTTTAAA
1 TATTAAATATAATATAATTATATAAAATAAAAAAAATAATTAAAAATATTTATAAATATGATAAA
*
336845 A-AT-TATATATAATAAATT
66 ATATATAAATATAATAAATT
* *
336863 TATTAAATATCA-A-AATT-TATATAAAT-AAAAAAATAATT-TAAATATGATTAT-AATATGAT
1 TATTAAATATAATATAATTATATA-AAATAAAAAAAATAATTAAAAATAT--TTATAAATATGAT
336922 AAAATATATAAATATAATAAA
63 AAAATATATAAATATAATAAA
336943 AATATATAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
79 6 0.09
80 26 0.37
81 14 0.20
82 13 0.19
83 11 0.16
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (85 bp):
TATTAAATATAATATAATTATATAAAATAAAAAAAATAATTAAAAATATTTATAAATATGATAAA
ATATATAAATATAATAAATT
Found at i:337799 original size:17 final size:19
Alignment explanation
Indices: 337779--337835 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 19
337769 TGTTAATTTT
337779 TTTATTTAAA-ATAA-AAA
1 TTTATTTAAATATAATAAA
337796 TTTATTTAAATATAAATTAAA
1 TTTATTTAAATAT-AA-TAAA
337817 TTTATTTAAATATAATAAA
1 TTTATTTAAATATAATAAA
337836 AATATAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.28
18 2 0.06
19 6 0.17
20 2 0.06
21 16 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTATTTAAATATAATAAA
Found at i:338374 original size:3 final size:3
Alignment explanation
Indices: 338368--338399 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
338358 AATGATAGTA
338368 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
338400 GTTTAAAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:339186 original size:2 final size:2
Alignment explanation
Indices: 339179--339210 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
339169 CTCCCTTTAT
339179 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
339211 AATAGCATTT
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):
TA
Found at i:341234 original size:4 final size:4
Alignment explanation
Indices: 341217--341264 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
341207 TCATCGCCTG
* * * * *
341217 ATAT ATAT ACAT ATAT ATAT ATAC ATAC ATAT ATAT GTAT GTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
341265 GAGTGTGCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:341236 original size:14 final size:14
Alignment explanation
Indices: 341217--341252 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
341207 TCATCGCCTG
*
341217 ATATATATACATAT
1 ATATATATACATAC
341231 ATATATATACATAC
1 ATATATATACATAC
341245 ATATATAT
1 ATATATAT
341253 GTATGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATATACATAC
Found at i:348372 original size:2 final size:2
Alignment explanation
Indices: 348365--348408 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
348355 ATTTTAAACC
*
348365 TA TA TA TA TA T- TA T- TA TA T- TT 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
348404 TA TA T
1 TA TA T
348409 TCAAAAATAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:349370 original size:11 final size:11
Alignment explanation
Indices: 349354--349385 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
349344 ATGTAAAATT
349354 TATAAAAATAA
1 TATAAAAATAA
*
349365 TATAAATATAA
1 TATAAAAATAA
349376 TATAAAAATA
1 TATAAAAATA
349386 TGAATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:349895 original size:25 final size:25
Alignment explanation
Indices: 349850--349897 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
349840 GATAATAAAT
** *
349850 AAAAATGATAATATTTTAAATAACA
1 AAAAATGATAATAACTAAAATAACA
349875 AAAAATGATAATAACTAAAATAA
1 AAAAATGATAATAACTAAAATAA
349898 ATGGTAACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (25 bp):
AAAAATGATAATAACTAAAATAACA
Found at i:350881 original size:3 final size:3
Alignment explanation
Indices: 350867--350905 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
350857 TTCAAAATTG
*
350867 AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA AG- AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
350906 ACCTAAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:351282 original size:3 final size:3
Alignment explanation
Indices: 351276--351311 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
351266 CCTCATCATC
351276 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
351312 TTGTAGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:353406 original size:29 final size:30
Alignment explanation
Indices: 353373--353442 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
353363 TTTTCTTAAG
*
353373 TAAGCCTTTATATTTTTA-TTGTACCCAAA
1 TAAGCCTTTATACTTTTATTTGTACCCAAA
* *
353402 TAAGCCTTTATCCTTTTATTTGTACCTAAA
1 TAAGCCTTTATACTTTTATTTGTACCCAAA
*
353432 TAAGCTTTTAT
1 TAAGCCTTTAT
353443 TTCAAATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 16 0.44
30 20 0.56
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (30 bp):
TAAGCCTTTATACTTTTATTTGTACCCAAA
Found at i:353511 original size:30 final size:30
Alignment explanation
Indices: 353470--353528 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
353460 TTTATATTAA
*
353470 GAGTCTATTTTGGTATAAATTGAAGGTTAG
1 GAGTCTATTTTGGTATAAATTAAAGGTTAG
* *
353500 GAGTTTATTTTGGTATAAGTTAAAGGTTA
1 GAGTCTATTTTGGTATAAATTAAAGGTTA
353529 ATGGCTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.25, T:0.42
Consensus pattern (30 bp):
GAGTCTATTTTGGTATAAATTAAAGGTTAG
Found at i:358073 original size:2 final size:2
Alignment explanation
Indices: 358066--358102 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
358056 TTTAATTAAG
358066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
358103 GACCAAGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:359089 original size:22 final size:22
Alignment explanation
Indices: 359038--359089 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
359028 AATATATAAG
*
359038 ATATTT-TAAAAAATTAAATAT
1 ATATTTATAAAAAATAAAATAT
* *
359059 AT-TCATATAAAATATAAAATAT
1 ATAT-TTATAAAAAATAAAATAT
359081 ATATTTATA
1 ATATTTATA
359090 TTTAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.04
21 3 0.12
22 19 0.79
23 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATTTATAAAAAATAAAATAT
Found at i:365016 original size:65 final size:65
Alignment explanation
Indices: 364935--365064 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
364925 AACCCAGTTC
* *
364935 TTTACAGTCAGACCCCATATAAAGACATCCTTAAAACTTCATAGCTGAGAATCTACGAAATCCAT
1 TTTACAGTCAGACCCCATATAAAGACAACCTTAAAACCTCATAGCTGAGAATCTACGAAATCCAT
365000 TTTACAGTCAGACCCCATATAAAGACAACCTTAAAACCTCATAGCTGAGAATCTACGAAATCCAT
1 TTTACAGTCAGACCCCATATAAAGACAACCTTAAAACCTCATAGCTGAGAATCTACGAAATCCAT
365065 ACTTAAAAGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (65 bp):
TTTACAGTCAGACCCCATATAAAGACAACCTTAAAACCTCATAGCTGAGAATCTACGAAATCCAT
Found at i:365795 original size:18 final size:18
Alignment explanation
Indices: 365774--365809 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
365764 CGCCGGCTTC
365774 CGTGCCTTCTCCGGCCAT
1 CGTGCCTTCTCCGGCCAT
365792 CGTGCCTTCTCCGGCCAT
1 CGTGCCTTCTCCGGCCAT
365810 TTACTCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.44, G:0.22, T:0.28
Consensus pattern (18 bp):
CGTGCCTTCTCCGGCCAT
Found at i:366756 original size:14 final size:13
Alignment explanation
Indices: 366739--366803 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 13
366729 ATAATTTATA
366739 TATTTATATATATT
1 TATTT-TATATATT
*
366753 TATTTTTTATGATT
1 TATTTTATAT-ATT
366767 TATTTTATA-ATTT
1 TATTTTATATA-TT
* *
366780 TATTTAAAATATT
1 TATTTTATATATT
366793 ATATATTTATA
1 -TAT-TTTATA
366804 AAAATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
12 1 0.03
13 15 0.38
14 20 0.50
15 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TATTTTATATATT
Found at i:366774 original size:12 final size:13
Alignment explanation
Indices: 366723--366784 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 13
366713 TTTTTCGAAA
366723 TATTTTATAATTT
1 TATTTTATAATTT
366736 ATATATTTATATATATT
1 -TAT-TTTATA-AT-TT
*
366753 TATTTT-TTATGATT
1 TATTTTATAAT--TT
366767 TATTTTATAATTT
1 TATTTTATAATTT
366780 TATTT
1 TATTT
366785 AAAATATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
13 9 0.22
14 13 0.32
15 12 0.29
16 5 0.12
17 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTTTATAATTT
Found at i:367998 original size:2 final size:2
Alignment explanation
Indices: 367956--367983 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
367946 CATTTTCAGC
367956 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
367984 TCTCCTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:371243 original size:3 final size:3
Alignment explanation
Indices: 371237--371283 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
371227 AGAAGTAGTT
371237 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
371284 GCTGCTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:371653 original size:17 final size:17
Alignment explanation
Indices: 371621--371654 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
371611 TTTCCTCCTC
* *
371621 TTTTGTTTTTTGTTTTT
1 TTTTGTTTTCTATTTTT
371638 TTTTGTTTTCTATTTTT
1 TTTTGTTTTCTATTTTT
371655 ACTGTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.03, G:0.09, T:0.85
Consensus pattern (17 bp):
TTTTGTTTTCTATTTTT
Found at i:375780 original size:2 final size:2
Alignment explanation
Indices: 375775--375804 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
375765 TCTACTTTCG
375775 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
375805 GGTTCATTAA
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:376732 original size:16 final size:17
Alignment explanation
Indices: 376705--376738 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
376695 TTTTTTTATC
376705 ATTATCATATTTAATAT
1 ATTATCATATTTAATAT
*
376722 ATTAT-ATATTTCATAT
1 ATTATCATATTTAATAT
376738 A
1 A
376739 AATTTTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATCATATTTAATAT
Found at i:380082 original size:15 final size:14
Alignment explanation
Indices: 380057--380104 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
380047 ATTTGATCAA
380057 AAAAGAATAAATAAAT
1 AAAA-AATAAA-AAAT
* *
380073 AAATAATAAAAATT
1 AAAAAATAAAAAAT
380087 AAAAAAATAAAAAAT
1 -AAAAAATAAAAAAT
380102 AAA
1 AAA
380105 GTTTACTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 6 0.22
15 18 0.67
16 3 0.11
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (14 bp):
AAAAAATAAAAAAT
Found at i:380104 original size:7 final size:7
Alignment explanation
Indices: 380057--380104 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
380047 ATTTGATCAA
380057 AAAAGAAT
1 AAAA-AAT
380065 AAATAAAT
1 AAA-AAAT
*
380073 AAATAAT
1 AAAAAAT
*
380080 AAAAATT
1 AAAAAAT
380087 AAAAAAAT
1 -AAAAAAT
380095 AAAAAAT
1 AAAAAAT
380102 AAA
1 AAA
380105 GTTTACTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
7 18 0.53
8 15 0.44
9 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (7 bp):
AAAAAAT
Found at i:380429 original size:13 final size:14
Alignment explanation
Indices: 380411--380448 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
380401 CAACCAGCCT
380411 CTTCTTT-TTTTTC
1 CTTCTTTCTTTTTC
380424 CTTCTTTCTTTTTTC
1 CTTCTTTC-TTTTTC
*
380439 TTTCTTTCTT
1 CTTCTTTCTT
380449 CTTTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 7 0.32
14 2 0.09
15 13 0.59
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
CTTCTTTCTTTTTC
Found at i:380437 original size:15 final size:15
Alignment explanation
Indices: 380417--380448 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
380407 GCCTCTTCTT
380417 TTTTTTCCTTCTTTC
1 TTTTTTCCTTCTTTC
*
380432 TTTTTTCTTTCTTTC
1 TTTTTTCCTTCTTTC
380447 TT
1 TT
380449 CTTTAAAATT
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:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTCCTTCTTTC
Found at i:380441 original size:11 final size:11
Alignment explanation
Indices: 380410--380452 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
380400 GCAACCAGCC
*
380410 TCTTCTTTTTTT
1 TCTTC-TTTCTT
380422 TCCTTCTTTCTT
1 T-CTTCTTTCTT
*
380434 TTTTCTTTCTT
1 TCTTCTTTCTT
380445 TCTTCTTT
1 TCTTCTTT
380453 AAAATTCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 16 0.59
12 7 0.26
13 4 0.15
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TCTTCTTTCTT
Found at i:380683 original size:73 final size:68
Alignment explanation
Indices: 380474--380665 Score: 206
Period size: 74 Copynumber: 2.6 Consensus size: 68
380464 AATTTAATAG
* *
380474 ATAATTAAATTAAAAATAAATCTTAAATTTGTGTAAATAAAATTAAATTATACCATTAAAAATTT
1 ATAATCAAA-TAAAAATAAAT-TTAAATTT-TATAAATAAAA-TAAATTATACC-TTAAAAATTT
380539 AAACTCAT
61 AAACTCAT
* * * *
380547 ATCATACCTAATAAAAA-ACACATTTAAATATTTAAAAATCAAAATAAATTATAGCTTAAAAATT
1 AT-A-ATCAAATAAAAATA-A-ATTTAAAT-TTTATAAAT-AAAATAAATTATACCTTAAAAATT
380611 TAAACTCAT
60 TAAACTCAT
380620 ATAATCAAATAAAAATAAATTTAAATTTCTATAAATAGAAATAAAT
1 ATAATCAAATAAAAATAAATTTAAATTT-TATAAATA-AAATAAAT
380666 AATATCTCTA
Statistics
Matches: 101, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
69 3 0.03
70 22 0.22
71 11 0.11
72 2 0.02
73 23 0.23
74 29 0.29
75 11 0.11
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (68 bp):
ATAATCAAATAAAAATAAATTTAAATTTTATAAATAAAATAAATTATACCTTAAAAATTTAAACT
CAT
Found at i:381997 original size:16 final size:16
Alignment explanation
Indices: 381976--382010 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
381966 ACCTTTTTTT
*
381976 AAATTTTTTTAATTTA
1 AAATTTTTATAATTTA
*
381992 AAATTTTTATATTTTA
1 AAATTTTTATAATTTA
382008 AAA
1 AAA
382011 AATATAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTTTTATAATTTA
Found at i:382098 original size:24 final size:23
Alignment explanation
Indices: 382057--382119 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
382047 ATAAAGATTA
* *
382057 AATTTAATAAA-AATAAATTAAATT
1 AATTTTATAAATAA-AAA-TAAATC
382081 AATTTTATAAATAAAAATAAATC
1 AATTTTATAAATAAAAATAAATC
*
382104 ATATCTTA-AAATAAAA
1 A-ATTTTATAAATAAAA
382120 TCATTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 14 0.41
24 18 0.53
25 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (23 bp):
AATTTTATAAATAAAAATAAATC
Found at i:382446 original size:13 final size:13
Alignment explanation
Indices: 382428--382453 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
382418 GTGATCTTTT
382428 TTTATTTTTTTAA
1 TTTATTTTTTTAA
382441 TTTATTTTTTTAA
1 TTTATTTTTTTAA
382454 AAAATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTTTTTAA
Found at i:382516 original size:44 final size:43
Alignment explanation
Indices: 382427--382517 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 43
382417 TGTGATCTTT
* * * * *
382427 TTTTATTTTTTTAATTTATTTTTTTAAAAAATAATAATTAATA
1 TTTTAATTTGTTAATATAATTTTTTAAAAAATAATAAATAATA
** *
382470 TTTTAATTTGTTAATATAATTTTTTAAAATTTAATTAAATATTA
1 TTTTAATTTGTTAATATAATTTTTTAAAAAATAA-TAAATAATA
382514 TTTT
1 TTTT
382518 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (43 bp):
TTTTAATTTGTTAATATAATTTTTTAAAAAATAATAAATAATA
Found at i:382587 original size:18 final size:18
Alignment explanation
Indices: 382560--382605 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
382550 TTTCAATACA
382560 AATTTTTTAAATTTAATT
1 AATTTTTTAAATTTAATT
*
382578 AATTTCTTAAATTTAATT
1 AATTTTTTAAATTTAATT
382596 AATTTTTTAA
1 AATTTTTTAA
382606 TAATTAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTTTTAAATTTAATT
Found at i:382924 original size:42 final size:41
Alignment explanation
Indices: 382831--382979 Score: 164
Period size: 42 Copynumber: 3.7 Consensus size: 41
382821 AAGGGTGAGA
*
382831 ATGAATTAATTGCAGATTTCAGCCTTCA----TCCTGAAGT
1 ATGAATTAATTGCAGATTTCACCCTTCATTGGTCCTGAAGT
* * *
382868 ATAAATTAATTGCAGATTTCACCCTTCATTGGTAACTGCAGT
1 ATGAATTAATTGCAGATTTCACCCTTCATTGGT-CCTGAAGT
* *
382910 ATGAATTAATTGCAGATTTCATCCCTT-GTTGGTGCCTAAAGT
1 ATGAATTAATTGCAGATTTCA-CCCTTCATTGGT-CCTGAAGT
* *
382952 ATGAATTAATTGCAGATTTTATCCTTCA
1 ATGAATTAATTGCAGATTTCACCCTTCA
382980 CGATCTGTGC
Statistics
Matches: 92, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
37 26 0.28
41 5 0.05
42 56 0.61
43 5 0.05
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (41 bp):
ATGAATTAATTGCAGATTTCACCCTTCATTGGTCCTGAAGT
Found at i:383626 original size:18 final size:18
Alignment explanation
Indices: 383603--383657 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
383593 TTATTAATTT
383603 ATTTTTAATATAAATATA
1 ATTTTTAATATAAATATA
*
383621 ATTTTT-A-AT-AATTTA
1 ATTTTTAATATAAATATA
*
383636 ATTTGTAATATAAATATA
1 ATTTTTAATATAAATATA
383654 ATTT
1 ATTT
383658 AATAATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 10 0.32
16 3 0.10
17 3 0.10
18 15 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTTTAATATAAATATA
Found at i:383639 original size:15 final size:15
Alignment explanation
Indices: 383587--383645 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
383577 GTTATTTAAA
*
383587 TTAA-TTTTATTAAT
1 TTAATTTTTAATAAT
383601 TT-ATTTTTAATATAAAT
1 TTAATTTTT-A-AT-AAT
*
383618 ATAATTTTTAATAAT
1 TTAATTTTTAATAAT
*
383633 TTAATTTGTAATA
1 TTAATTTTTAATA
383646 TAAATATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
13 1 0.03
14 6 0.17
15 15 0.42
16 3 0.08
17 5 0.14
18 6 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTAATTTTTAATAAT
Found at i:383729 original size:36 final size:34
Alignment explanation
Indices: 383583--383734 Score: 129
Period size: 33 Copynumber: 4.6 Consensus size: 34
383573 GAAGGTTATT
383583 TAAAT-TAA-TTTT-ATTAA-TTTATTTTTAATA
1 TAAATATAATTTTTAATTAATTTTATTTTTAATA
* *
383613 TAAATATAATTTTTAA-TAATTTAATTTGTAATA
1 TAAATATAATTTTTAATTAATTTTATTTTTAATA
* * *
383646 TAAATATAATTTAATAATTAA--TTATGATTTAACA
1 TAAATATAATTT-TTAATTAATTTTAT-TTTTAATA
* ** *
383680 TTAATATGTTTTTTATTTATATTTTATTATTTAATA
1 TAAATATAATTTTTAATTA-ATTTTATT-TTTAATA
*
383716 CAAATATAATTTTTAATTA
1 TAAATATAATTTTTAATTA
383735 TTTATCATTA
Statistics
Matches: 92, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
30 5 0.05
31 3 0.03
32 7 0.08
33 32 0.35
34 18 0.20
35 3 0.03
36 24 0.26
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (34 bp):
TAAATATAATTTTTAATTAATTTTATTTTTAATA
Found at i:383745 original size:36 final size:36
Alignment explanation
Indices: 383601--383745 Score: 124
Period size: 36 Copynumber: 4.2 Consensus size: 36
383591 TTTTATTAAT
383601 TTATT-TTTAATATAAATATAATTTTTAATAATTTA
1 TTATTATTTAATATAAATATAATTTTTAATAATTTA
* *
383636 --ATT-TGTAATATAAATATAA--TTTAATAATTAA
1 TTATTATTTAATATAAATATAATTTTTAATAATTTA
* * * ** * *
383667 TTATGATTTAACATTAATATGTTTTTTATTTATATT-
1 TTATTATTTAATATAAATATAATTTTTAATAAT-TTA
* *
383703 TTATTATTTAATACAAATATAATTTTTAATTATTTA
1 TTATTATTTAATATAAATATAATTTTTAATAATTTA
*
383739 TCATTAT
1 TTATTAT
383746 ATATACATTT
Statistics
Matches: 84, Mismatches: 19, Indels: 13
0.72 0.16 0.11
Matches are distributed among these distances:
31 11 0.13
33 20 0.24
34 11 0.13
35 2 0.02
36 39 0.46
37 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (36 bp):
TTATTATTTAATATAAATATAATTTTTAATAATTTA
Found at i:384195 original size:24 final size:22
Alignment explanation
Indices: 384162--384226 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
384152 TAAAAAAATA
*
384162 TTTATCAAAAATTAAAGAAACATT
1 TTTAT-AAAAATTAAA-AAACAGT
* *
384186 TTTATGAAAAGTAAAAAACAGT
1 TTTATAAAAATTAAAAAACAGT
*
384208 TTTATAATAATTAATAAAA
1 TTTATAAAAATTAA-AAAA
384227 AGGATTATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.50
23 12 0.35
24 5 0.15
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (22 bp):
TTTATAAAAATTAAAAAACAGT
Found at i:384204 original size:22 final size:23
Alignment explanation
Indices: 384151--384212 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
384141 GATTGCTTAT
*
384151 GTAAAAAA-ATATTTATCAAAAA
1 GTAAAAAACATTTTTATCAAAAA
* *
384173 TTAAAGAAACATTTTTAT-GAAAA
1 GTAAA-AAACATTTTTATCAAAAA
*
384196 GTAAAAAACAGTTTTAT
1 GTAAAAAACATTTTTAT
384213 AATAATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 15 0.45
23 11 0.33
24 7 0.21
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (23 bp):
GTAAAAAACATTTTTATCAAAAA
Found at i:385843 original size:20 final size:19
Alignment explanation
Indices: 385820--385879 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
385810 ATATATTCGG
385820 TAAAAATATTATATTAAATA
1 TAAAAATATTATA-TAAATA
* *
385840 TAAAAA-ATTAAAATAATAAA
1 TAAAAATATT-ATATAA-ATA
385860 TAAATAATATT-TATAAATA
1 TAAA-AATATTATATAAATA
385879 T
1 T
385880 GAATTAATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
19 9 0.28
20 18 0.56
21 2 0.06
22 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAATATTATATAAATA
Found at i:388009 original size:15 final size:16
Alignment explanation
Indices: 387980--388010 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
387970 GATTTTTTTA
387980 ATTATAAAAATTATTT
1 ATTATAAAAATTATTT
387996 ATTATAAAAA-TATTT
1 ATTATAAAAATTATTT
388011 TGTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATAAAAATTATTT
Found at i:392317 original size:34 final size:34
Alignment explanation
Indices: 392274--392351 Score: 156
Period size: 34 Copynumber: 2.3 Consensus size: 34
392264 ATTGTTAGTA
392274 AAGAAAGCTTATAAATACTCTAGACCAGGATATG
1 AAGAAAGCTTATAAATACTCTAGACCAGGATATG
392308 AAGAAAGCTTATAAATACTCTAGACCAGGATATG
1 AAGAAAGCTTATAAATACTCTAGACCAGGATATG
392342 AAGAAAGCTT
1 AAGAAAGCTT
392352 TAATAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (34 bp):
AAGAAAGCTTATAAATACTCTAGACCAGGATATG
Found at i:394688 original size:2 final size:2
Alignment explanation
Indices: 394681--394716 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
394671 CAAAACTAAG
*
394681 AT AT AT AT AT AT AT AT AT AT GT 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
394717 TAAGCAGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:399606 original size:5 final size:5
Alignment explanation
Indices: 399596--399621 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
399586 TGTTTGATAA
399596 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
399622 TAGATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:401564 original size:22 final size:24
Alignment explanation
Indices: 401539--401590 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
401529 ATAAATAAAA
*
401539 TAAAAATTAT-AAATATTAAA-TT
1 TAAAAATTATAAAATAATAAATTT
*
401561 T-AAATTTATAAAATAATAAATTT
1 TAAAAATTATAAAATAATAAATTT
401584 TAAAAAT
1 TAAAAAT
401591 AATTATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 7 0.29
22 10 0.42
23 3 0.12
24 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAAAATTATAAAATAATAAATTT
Found at i:401582 original size:16 final size:16
Alignment explanation
Indices: 401561--401593 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
401551 ATATTAAATT
401561 TAAA-TTTATAAAATAA
1 TAAATTTTA-AAAATAA
401577 TAAATTTTAAAAATAA
1 TAAATTTTAAAAATAA
401593 T
1 T
401594 TATATAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATTTTAAAAATAA
Found at i:402189 original size:23 final size:22
Alignment explanation
Indices: 402134--402209 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
402124 TAATATTAAT
*
402134 ATATATT-AAAAATA-ATTAAA
1 ATATATTAAAAAATATAATAAA
* * *
402154 ACATAATATAAAATATAATACAA
1 ATATATTAAAAAATATAATA-AA
*
402177 ATATATTAAAAAATAT-ATAAT
1 ATATATTAAAAAATATAATAAA
402198 ATAATATTAAAA
1 AT-ATATTAAAA
402210 TTTATATAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 5 0.11
21 9 0.20
22 15 0.34
23 15 0.34
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATATTAAAAAATATAATAAA
Found at i:402199 original size:30 final size:30
Alignment explanation
Indices: 402158--402228 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
402148 ATTAAAACAT
*
402158 AATATAAAATATAATA-CAAATATATTA-AAA
1 AATATATAATATAATATCAAA-AT-TTATAAA
* *
402188 AATATATAATATAATATTAAAATTTATATA
1 AATATATAATATAATATCAAAATTTATAAA
402218 AATATATAATA
1 AATATATAATA
402229 ATTTAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 30 0.83
31 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (30 bp):
AATATATAATATAATATCAAAATTTATAAA
Found at i:402204 original size:22 final size:22
Alignment explanation
Indices: 402125--402223 Score: 66
Period size: 22 Copynumber: 4.6 Consensus size: 22
402115 TTTTAGATAT
402125 AATAT-TAATAT-ATATT-AAA
1 AATATATAATATAATATTAAAA
* *
402144 AATAATTAAAACATAATA-TAAAA
1 AAT-A-TATAATATAATATTAAAA
* *
402167 TATA-ATACAAAT-ATATTAAAA
1 AATATATA-ATATAATATTAAAA
402188 AATATATAATATAATATTAAAA
1 AATATATAATATAATATTAAAA
**
402210 TTTATATAAATATA
1 AATATAT-AATATA
402224 TAATAATTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
19 3 0.05
20 6 0.10
21 15 0.25
22 23 0.38
23 14 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AATATATAATATAATATTAAAA
Found at i:402215 original size:20 final size:20
Alignment explanation
Indices: 402186--402240 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
402176 AATATATTAA
*
402186 AAAATATATAATATAATAT-T
1 AAAATTTATAATA-AATATAT
402206 AAAATTTAT-ATAAATATAT
1 AAAATTTATAATAAATATAT
*
402225 AATAATTTAAAATAAA
1 AA-AATTTATAATAAA
402241 ACATAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 5 0.17
19 6 0.20
20 14 0.47
21 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTTATAATAAATATAT
Found at i:404547 original size:12 final size:12
Alignment explanation
Indices: 404532--404556 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
404522 CACTGAGCTT
404532 ATTAATAAAAAA
1 ATTAATAAAAAA
404544 ATTAATAAAAAA
1 ATTAATAAAAAA
404556 A
1 A
404557 CTCTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATTAATAAAAAA
Found at i:407801 original size:16 final size:16
Alignment explanation
Indices: 407780--407838 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
407770 TTTTTTACAC
407780 TAAAATATTATTATTT
1 TAAAATATTATTATTT
*
407796 TAAAATA-TATTA--C
1 TAAAATATTATTATTT
407809 TAAAATATTATTATTT
1 TAAAATATTATTATTT
*
407825 TGATAAT-TTATTAT
1 T-AAAATATTATTAT
407839 ACGAAATACT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 7 0.19
14 5 0.14
15 5 0.14
16 15 0.42
17 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
TAAAATATTATTATTT
Found at i:407814 original size:13 final size:14
Alignment explanation
Indices: 407778--407821 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
407768 TTTTTTTTAC
407778 ACTAAAATATTATT
1 ACTAAAATATTATT
*
407792 ATTTTAAAATA-TATT
1 A--CTAAAATATTATT
407807 ACTAAAATATTATT
1 ACTAAAATATTATT
407821 A
1 A
407822 TTTTGATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 5 0.20
16 7 0.28
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (14 bp):
ACTAAAATATTATT
Found at i:408003 original size:13 final size:14
Alignment explanation
Indices: 407979--408015 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
407969 CCTAACATAA
407979 ATAATAATATTTTG
1 ATAATAATATTTTG
407993 ATAAT-ATATTTT-
1 ATAATAATATTTTG
*
408005 AAAATAATATT
1 ATAATAATATT
408016 ATTTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 4 0.19
13 12 0.57
14 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
ATAATAATATTTTG
Found at i:408013 original size:15 final size:16
Alignment explanation
Indices: 407993--408022 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
407983 TAATATTTTG
407993 ATAATA-TATTTTAAA
1 ATAATATTATTTTAAA
408008 ATAATATTATTTTAA
1 ATAATATTATTTTAA
408023 TAATTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATATTATTTTAAA
Found at i:408018 original size:29 final size:28
Alignment explanation
Indices: 407977--408036 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
407967 AGCCTAACAT
* *
407977 AAATAATAATATTTTGATAATATATTTTA
1 AAATAATAATATTTTAATAAT-TAATTTA
*
408006 AAATAATATTATTTTAATAATTAATTTA
1 AAATAATAATATTTTAATAATTAATTTA
408034 AAA
1 AAA
408037 CGATAGCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AAATAATAATATTTTAATAATTAATTTA
Found at i:416306 original size:37 final size:37
Alignment explanation
Indices: 416260--416336 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
416250 TTAAAAATAC
* *
416260 ATATAAAATTATTTAAATCAACCTTATTAATATTTTT
1 ATATAAAATTATTTAAACCAACCTTACTAATATTTTT
*
416297 ATATCAAATTATTTAAACCAACCTTACTAATATTTTT
1 ATATAAAATTATTTAAACCAACCTTACTAATATTTTT
416334 ATA
1 ATA
416337 CCATTTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (37 bp):
ATATAAAATTATTTAAACCAACCTTACTAATATTTTT
Found at i:417377 original size:17 final size:18
Alignment explanation
Indices: 417344--417382 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
417334 TTTTTTATTT
*
417344 TTTAAATAATATAT-AAA
1 TTTAAATAAAATATAAAA
*
417361 TTTAAATAAAATTTAAAA
1 TTTAAATAAAATATAAAA
417379 TTTA
1 TTTA
417383 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAATAAAATATAAAA
Done.