Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 2 of 17
Found at i:189152 original size:17 final size:17
Alignment explanation
Indices: 189130--189162 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
189120 TATATAAATA
189130 TTAATATAAAAATAATT
1 TTAATATAAAAATAATT
*
189147 TTAATATATAAATAAT
1 TTAATATAAAAATAAT
189163 AAATTAAAAT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAATATAAAAATAATT
Found at i:189245 original size:17 final size:17
Alignment explanation
Indices: 189220--189256 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
189210 TTTTTAAATA
*
189220 ATAATTAAATATAATTT
1 ATAAATAAATATAATTT
*
189237 ATAAATAAATCTAATTT
1 ATAAATAAATATAATTT
189254 ATA
1 ATA
189257 CTAAAACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAAATAAATATAATTT
Found at i:189438 original size:1 final size:1
Alignment explanation
Indices: 189432--189456 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
189422 TATTTACCAG
189432 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
189457 CCTTCAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:194078 original size:14 final size:14
Alignment explanation
Indices: 194055--194086 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
194045 ATAACCAGCA
194055 TTCT-TCATTAATG
1 TTCTATCATTAATG
194068 TTCTATCATTAATG
1 TTCTATCATTAATG
194082 TTCTA
1 TTCTA
194087 CACCAAAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (14 bp):
TTCTATCATTAATG
Found at i:197742 original size:22 final size:20
Alignment explanation
Indices: 197699--197743 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
197689 ATTAAATTTG
* *
197699 TATAAATAATATAAATATAA
1 TATAAAAAATATAAATAAAA
197719 TATAAAAAATATACGAATAAAA
1 TATAAAAAATATA--AATAAAA
197741 TAT
1 TAT
197744 GAATATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
22 9 0.43
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
TATAAAAAATATAAATAAAA
Found at i:198902 original size:23 final size:23
Alignment explanation
Indices: 198873--198931 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
198863 ATAATTTTAA
*
198873 TTATATTCAAATAAATATTTTTCTT
1 TTAT-TTCAAATAAA-ATTTTACTT
*
198898 TTATTTTAAATAAAATTTTAC-T
1 TTATTTCAAATAAAATTTTACTT
*
198920 TTATTTTAAATA
1 TTATTTCAAATA
198932 TTGATTTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 13 0.41
23 6 0.19
24 9 0.28
25 4 0.12
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATTTCAAATAAAATTTTACTT
Found at i:198922 original size:22 final size:24
Alignment explanation
Indices: 198881--198931 Score: 79
Period size: 22 Copynumber: 2.2 Consensus size: 24
198871 AATTATATTC
*
198881 AAATAAATATTTTTCTTTTATTTT
1 AAATAAATATTTTACTTTTATTTT
198905 AAATAAA-ATTTTAC-TTTATTTT
1 AAATAAATATTTTACTTTTATTTT
198927 AAATA
1 AAATA
198932 TTGATTTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 13 0.50
23 6 0.23
24 7 0.27
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
AAATAAATATTTTACTTTTATTTT
Found at i:199436 original size:26 final size:27
Alignment explanation
Indices: 199372--199438 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 27
199362 GAAAATAATA
* * *
199372 AAAAATTAT-TAATTATTATATTTAAT
1 AAAAATTATATAAATAATATATTGAAT
* *
199398 ATAATATTTTATAAATAATATA-TGAAT
1 A-AAAATTATATAAATAATATATTGAAT
199425 AAAAATTATATAAA
1 AAAAATTATATAAA
199439 ATATCTTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
26 12 0.38
27 11 0.34
28 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
AAAAATTATATAAATAATATATTGAAT
Found at i:202647 original size:12 final size:12
Alignment explanation
Indices: 202618--202650 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
202608 TTTTATTTTT
*
202618 TAATATTTTTAA
1 TAATATTTATAA
202630 -AATATTTATAA
1 TAATATTTATAA
202641 TAATATTTAT
1 TAATATTTAT
202651 GTTAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATATTTATAA
Found at i:214828 original size:2 final size:2
Alignment explanation
Indices: 214823--214861 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
214813 TGTGTGTGTG
214823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
214862 TCCATTAGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:216440 original size:2 final size:2
Alignment explanation
Indices: 216435--216461 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
216425 TCGTTTTTGT
216435 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
216462 GTCTTAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:217384 original size:2 final size:2
Alignment explanation
Indices: 217379--217405 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
217369 ACACACACAC
217379 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 A
217406 ATAAGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:219311 original size:18 final size:17
Alignment explanation
Indices: 219285--219342 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 17
219275 CACTTAATAA
*
219285 TTAAAAATTTTGATATAT
1 TTAATAATTTT-ATATAT
219303 TTAATAATTTTTATTATAT
1 TTAATAA-TTTTA-TATAT
*
219322 TTTAT-A-TTTATATAT
1 TTAATAATTTTATATAT
219337 TTAATA
1 TTAATA
219343 TAAAATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 9 0.26
16 4 0.12
18 8 0.24
19 13 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTAATAATTTTATATAT
Found at i:219320 original size:19 final size:18
Alignment explanation
Indices: 219285--219342 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
219275 CACTTAATAA
* *
219285 TTAAAAATTTTGATATAT
1 TTAATAATTTTTATATAT
219303 TTAATAATTTTTATTATAT
1 TTAATAATTTTTA-TATAT
*
219322 TT--T-ATATTTATATAT
1 TTAATAATTTTTATATAT
219337 TTAATA
1 TTAATA
219343 TAAAATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 7 0.21
16 6 0.18
17 2 0.06
18 11 0.33
19 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTAATAATTTTTATATAT
Found at i:227650 original size:3 final size:3
Alignment explanation
Indices: 227642--227682 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
227632 TACAGAAGCT
227642 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
227683 TTAAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:231324 original size:131 final size:131
Alignment explanation
Indices: 230934--231333 Score: 310
Period size: 131 Copynumber: 3.0 Consensus size: 131
230924 CCTTCCTGCT
* *
230934 TCTTTATGAAATTGATAGTTAAAATCATCGTCCATGACTAAAAGCACTCTCTCTCATATTTATGT
1 TCTTTATGAAATTGATAGTTAAGATCATCGTCCATGACTAAAAGCACTCTCTCTCATATGTATGT
* *
230999 TAGGATCAAACTCAAATGATTCACATCAAGCAACCACGGCTTCTTCAATGCGATGAAGTTCAACT
66 TAGGATCAAACTCGAATGATTCACATCAAGCAATCACGGCTTCTTCAATGCGATGAAGTTCAACT
231064 C
131 C
* * * ***** *
231065 TCTTTCTATGATATTTCA-AGTT-AG--CA-C-TCCATG--TGAAAG-A-GAGAAC-AAT-TGT-
1 TC-TT-TATGA-AATTGATAGTTAAGATCATCGTCCATGACTAAAAGCACTCTCTCTCATATGTA
** * * * * *
231117 TAGTTAAGATGATCTTTA-T-GAAATGATTCAC-TCGATGCGATGAAGTTCGACTCTCTTTCTAT
63 T-GTT-AG--GATC-AAACTCG-AATGATTCACATC-AAGCAAT-CA---CGGCT-TC-TTCAAT
** *
231179 GATATTTCAAGTTCAACTC
115 GCGA--TGAAGTTCAACTC
231198 TCTTTATGAAATTGATAGTTAAGATCATCGTCCATGACTAAAAGCACTCTCTCTCATATGTATGT
1 TCTTTATGAAATTGATAGTTAAGATCATCGTCCATGACTAAAAGCACTCTCTCTCATATGTATGT
*
231263 TAGGATCAAACTCGAATGATTCACATCAAGCAATCACGGCTTCTTCGATGCGATGAAGTTCAACT
66 TAGGATCAAACTCGAATGATTCACATCAAGCAATCACGGCTTCTTCAATGCGATGAAGTTCAACT
231328 C
131 C
231329 TCTTT
1 TCTTT
231334 CTATGATATT
Statistics
Matches: 193, Mismatches: 42, Indels: 68
0.64 0.14 0.22
Matches are distributed among these distances:
121 1 0.01
122 5 0.03
123 4 0.02
124 3 0.02
125 20 0.10
126 7 0.04
128 6 0.03
129 5 0.03
130 8 0.04
131 35 0.18
132 7 0.04
133 30 0.16
134 8 0.04
135 5 0.03
136 6 0.03
138 7 0.04
139 21 0.11
140 4 0.02
141 4 0.02
142 6 0.03
143 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (131 bp):
TCTTTATGAAATTGATAGTTAAGATCATCGTCCATGACTAAAAGCACTCTCTCTCATATGTATGT
TAGGATCAAACTCGAATGATTCACATCAAGCAATCACGGCTTCTTCAATGCGATGAAGTTCAACT
C
Found at i:236513 original size:86 final size:86
Alignment explanation
Indices: 236408--236579 Score: 344
Period size: 86 Copynumber: 2.0 Consensus size: 86
236398 AATAGTTGAG
236408 ATATGGAATTAAATTTTATGCTCAGGCATGCCAAACCCTTTCTGTAATGATGTTCAATCAGCAAG
1 ATATGGAATTAAATTTTATGCTCAGGCATGCCAAACCCTTTCTGTAATGATGTTCAATCAGCAAG
236473 TAACTAAATAGATAGCAGCTA
66 TAACTAAATAGATAGCAGCTA
236494 ATATGGAATTAAATTTTATGCTCAGGCATGCCAAACCCTTTCTGTAATGATGTTCAATCAGCAAG
1 ATATGGAATTAAATTTTATGCTCAGGCATGCCAAACCCTTTCTGTAATGATGTTCAATCAGCAAG
236559 TAACTAAATAGATAGCAGCTA
66 TAACTAAATAGATAGCAGCTA
236580 CCCCACAGCT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (86 bp):
ATATGGAATTAAATTTTATGCTCAGGCATGCCAAACCCTTTCTGTAATGATGTTCAATCAGCAAG
TAACTAAATAGATAGCAGCTA
Found at i:237867 original size:18 final size:19
Alignment explanation
Indices: 237842--237881 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
237832 TTTAATTATA
237842 TGTGTGTGAAAAAAAAAAAT
1 TGTGTGT-AAAAAAAAAAAT
*
237862 TGTGTGTGAAAAAAAAAAT
1 TGTGTGTAAAAAAAAAAAT
237881 T
1 T
237882 CTAATTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.28
Consensus pattern (19 bp):
TGTGTGTAAAAAAAAAAAT
Found at i:237867 original size:20 final size:20
Alignment explanation
Indices: 237842--237879 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
237832 TTTAATTATA
237842 TGTGTGTGAAAAAAAAAAAT
1 TGTGTGTGAAAAAAAAAAAT
237862 TGTGTGTGAAAAAAAAAA
1 TGTGTGTGAAAAAAAAAA
237880 TTCTAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (20 bp):
TGTGTGTGAAAAAAAAAAAT
Found at i:239942 original size:15 final size:15
Alignment explanation
Indices: 239924--239953 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
239914 AAATTTTGCC
239924 AAAACAAAAGAAAAA
1 AAAACAAAAGAAAAA
*
239939 AAAAGAAAAGAAAAA
1 AAAACAAAAGAAAAA
239954 GCACAAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAACAAAAGAAAAA
Found at i:247752 original size:61 final size:61
Alignment explanation
Indices: 247633--247752 Score: 186
Period size: 61 Copynumber: 2.0 Consensus size: 61
247623 TTTTTTTAAA
* *
247633 TAACTTTTTACCACAGTTATTGAATGATTTTACCATTAATTAGTTAAGTATGGTTTTTTTT
1 TAACTTTTTACCACAATTATTGAATGATTTTACCATTAATTAGTTAAGTATAGTTTTTTTT
* * *
247694 TAACTTTTTACCACAATTATTGGATTATTTTACTATTAATTAGTTAAGTATTAGTTTTT
1 TAACTTTTTACCACAATTATTGAATGATTTTACCATTAATTAGTTAAGTA-TAGTTTTT
247753 GGAGTATAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
61 46 0.87
62 7 0.13
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.52
Consensus pattern (61 bp):
TAACTTTTTACCACAATTATTGAATGATTTTACCATTAATTAGTTAAGTATAGTTTTTTTT
Found at i:248894 original size:25 final size:25
Alignment explanation
Indices: 248821--248907 Score: 88
Period size: 27 Copynumber: 3.4 Consensus size: 25
248811 ATATATTTTT
* * * *
248821 AATAATTAAATATTAAATAAATTAA
1 AATATTTAAATAATACATAAATTCA
248846 TAATATTATAAATAATACATAAATT-A
1 -AATATT-TAAATAATACATAAATTCA
248872 AAT-TTTAAATTAATTACATAAATTCA
1 AATATTTAAA-TAA-TACATAAATTCA
248898 AATATTTAAA
1 AATATTTAAA
248908 AAATTATTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
23 4 0.08
24 5 0.09
25 13 0.25
26 10 0.19
27 21 0.40
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATTTAAATAATACATAAATTCA
Found at i:252801 original size:26 final size:24
Alignment explanation
Indices: 252755--252811 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
252745 ATAAATATCT
*
252755 TTAATTTTACATTTGACTCAATAA
1 TTAATTTTACATTTGACTCAAAAA
* *
252779 TTAATATTTACGTTTGAAGTCAAAAA
1 TTAAT-TTTACATTTG-ACTCAAAAA
*
252805 TTTATTT
1 TTAATTT
252812 GTTTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 5 0.19
25 11 0.41
26 11 0.41
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (24 bp):
TTAATTTTACATTTGACTCAAAAA
Found at i:254525 original size:2 final size:2
Alignment explanation
Indices: 254518--254549 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
254508 TAACGTTAGG
254518 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
254550 AACATTTTGG
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:257880 original size:3 final size:3
Alignment explanation
Indices: 257872--257897 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
257862 ATTTCATTGT
257872 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
257898 GAAGGAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:260256 original size:2 final size:2
Alignment explanation
Indices: 260251--260311 Score: 76
Period size: 2 Copynumber: 32.5 Consensus size: 2
260241 TTAAAAAAAT
* *
260251 TA TA TA TA AA TA TA TA T- TA T- TA -A TA CA TA -A 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
260289 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
260312 TGAAAGAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
1 4 0.08
2 47 0.92
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:261204 original size:2 final size:2
Alignment explanation
Indices: 261197--261223 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
261187 ATAATAAAAT
261197 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
261224 TGCTAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:262492 original size:2 final size:2
Alignment explanation
Indices: 262472--262517 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
262462 TAACCAGCGT
* *
262472 TA TA T- TA TA TA CA TT 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
262513 TA TA T
1 TA TA T
262518 CGTAAAGTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:262846 original size:3 final size:3
Alignment explanation
Indices: 262840--262865 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
262830 GAAACAAAAA
262840 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
262866 ATAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:263054 original size:17 final size:17
Alignment explanation
Indices: 263032--263072 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
263022 TATTTTATTT
263032 TTTAAAATCAATTTAAA
1 TTTAAAATCAATTTAAA
*
263049 TTTAAAATCAATTTAAT
1 TTTAAAATCAATTTAAA
263066 TTTAAAA
1 TTTAAAA
263073 AAATTAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAAATCAATTTAAA
Found at i:263224 original size:2 final size:2
Alignment explanation
Indices: 263211--263240 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
263201 ATTTAATTGA
*
263211 AT AT AT AC 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
263241 TCTTTGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:266449 original size:2 final size:2
Alignment explanation
Indices: 266442--266469 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
266432 TTATGAACCA
266442 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
266470 TTCATAACTC
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:270823 original size:8 final size:8
Alignment explanation
Indices: 270810--270834 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
270800 TATATAAATT
270810 TTATATTA
1 TTATATTA
270818 TTATATTA
1 TTATATTA
270826 TTATATTA
1 TTATATTA
270834 T
1 T
270835 AATTATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATATTA
Found at i:270899 original size:42 final size:43
Alignment explanation
Indices: 270802--270900 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
270792 TTTAATCGTA
* * * *
270802 TATAAATTT-TATAT-TATTATATTATTATATTATAATTATAT
1 TATAAATTTATAAATATATCATATTATTAAAATATAATTATAT
* *
270843 TA-ATATGTATTAAATATATCATATT-TTAAAATATAATTATAT
1 TATAAATTTA-TAAATATATCATATTATTAAAATATAATTATAT
270885 TATAAATTTATAAATA
1 TATAAATTTATAAATA
270901 AATTAAAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
40 4 0.09
41 2 0.04
42 27 0.59
43 13 0.28
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (43 bp):
TATAAATTTATAAATATATCATATTATTAAAATATAATTATAT
Found at i:270912 original size:24 final size:24
Alignment explanation
Indices: 270867--270912 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
270857 TATATCATAT
* *
270867 TTTAAAATATAATTATATTATAAA
1 TTTAAAATATAATTAAAATATAAA
270891 TTTATAAATA-AATTAAAATATA
1 TTTA-AAATATAATTAAAATATA
270913 TTTATTATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAAATATAATTAAAATATAAA
Found at i:271028 original size:14 final size:14
Alignment explanation
Indices: 271007--271040 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
270997 TTTAATACGT
271007 AAATATTTAAATTA
1 AAATATTTAAATTA
* *
271021 ACATATTTATATTA
1 AAATATTTAAATTA
271035 AAATAT
1 AAATAT
271041 ATTAGTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATTTAAATTA
Found at i:272330 original size:2 final size:2
Alignment explanation
Indices: 272323--272348 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
272313 GTTATAATTA
272323 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
272349 GAAATGCTCT
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:279963 original size:14 final size:15
Alignment explanation
Indices: 279915--279964 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
279905 ACAACAATAA
*
279915 TTTAATAATTTATTT
1 TTTAATAATTTACTT
**
279930 TTTAA-AAAATACTAT
1 TTTAATAATTTACT-T
279945 TTTAATAATTTA-TT
1 TTTAATAATTTACTT
279959 TTTAAT
1 TTTAAT
279965 TTAACTGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 12 0.43
15 12 0.43
16 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATAATTTACTT
Found at i:282228 original size:3 final size:3
Alignment explanation
Indices: 282222--282255 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
282212 CTCCTCCTCC
282222 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
282256 TAGCATCTAT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:282921 original size:17 final size:16
Alignment explanation
Indices: 282880--282921 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
282870 CAACCATTTA
*
282880 ATAAATATTTATATAT
1 ATAAATATATATATAT
*
282896 -TATATATATATATAT
1 ATAAATATATATATAT
282911 ATAAATA-ATAT
1 ATAAATATATAT
282922 GCTTAGCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAATATATATATAT
Found at i:283342 original size:35 final size:33
Alignment explanation
Indices: 283294--283361 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 33
283284 CTATATTTCA
* * *
283294 TAATTAAATTTAAATACAAATATATTAATAAATAT
1 TAATTAAAATTAAAT-CAAAT-TAATAAAAAATAT
283329 TAATTAAAATTAAATCAAATTAATAAAAAATAT
1 TAATTAAAATTAAATCAAATTAATAAAAAATAT
283362 ATCTAAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 11 0.37
34 5 0.17
35 14 0.47
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (33 bp):
TAATTAAAATTAAATCAAATTAATAAAAAATAT
Found at i:283660 original size:15 final size:15
Alignment explanation
Indices: 283642--283686 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
283632 ATACAAGACT
* *
283642 TCATTAAATAAGATA
1 TCATTAACTAAGAAA
283657 TCATTAACTAAGAAA
1 TCATTAACTAAGAAA
283672 T-ATTAACTAAGAAA
1 TCATTAACTAAGAAA
283686 T
1 T
283687 AACCCTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
14 14 0.50
15 14 0.50
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (15 bp):
TCATTAACTAAGAAA
Found at i:283739 original size:2 final size:2
Alignment explanation
Indices: 283732--283759 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
283722 ATTCATGTGC
283732 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
283760 TAAAGAGGAT
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:283987 original size:22 final size:20
Alignment explanation
Indices: 283959--284041 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 20
283949 TACGCATGAT
283959 TATATAAATAAATATATAAAA
1 TATATAAAT-AATATATAAAA
*
283980 TATAATAATTAA-AT-TAAATA
1 TAT-ATAAATAATATATAAA-A
* *
284000 AATATAAATAATATAAAAAA
1 TATATAAATAATATATAAAA
*
284020 TTTATAAA-AATATATAAAA
1 TATATAAATAATATATAAAA
284039 TAT
1 TAT
284042 TAATTTTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
19 23 0.46
20 14 0.28
21 8 0.16
22 5 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TATATAAATAATATATAAAA
Found at i:284001 original size:31 final size:28
Alignment explanation
Indices: 283963--284041 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 28
283953 CATGATTATA
283963 TAAATAAATATATAAAATATAATAATTAAAT
1 TAAATAAATATATAAAATATAA-AA--AAAT
*
283994 TAAATAAATATA-AATAATATAAAAAATT
1 TAAATAAATATATAA-AATATAAAAAAAT
284022 TATAA-AAATATATAAAATAT
1 TA-AATAAATATATAAAATAT
284042 TAATTTTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
28 17 0.39
29 4 0.09
30 4 0.09
31 19 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAATAAATATATAAAATATAAAAAAAT
Found at i:284110 original size:2 final size:2
Alignment explanation
Indices: 284105--284129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
284095 AAATTTTTTG
284105 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
284130 GTTGATATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:284310 original size:15 final size:15
Alignment explanation
Indices: 284292--284332 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
284282 TTCTTCAATT
284292 TTTTAATTTATCTTG-
1 TTTTAATTTATC-TGA
284307 TTTT-ATTTGATCTGA
1 TTTTAATTT-ATCTGA
284322 TTTTAATTTAT
1 TTTTAATTTAT
284333 TATTTGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.26
15 13 0.57
16 4 0.17
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (15 bp):
TTTTAATTTATCTGA
Found at i:284370 original size:2 final size:2
Alignment explanation
Indices: 284363--284392 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
284353 TGAGAGGCTG
284363 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
284393 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:285776 original size:12 final size:12
Alignment explanation
Indices: 285759--285783 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
285749 CTACAACATT
285759 AGTAAGATGAGA
1 AGTAAGATGAGA
285771 AGTAAGATGAGA
1 AGTAAGATGAGA
285783 A
1 A
285784 AAAAGCTTTC
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:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
AGTAAGATGAGA
Found at i:289246 original size:30 final size:30
Alignment explanation
Indices: 289210--289271 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
289200 ACTTACATAG
289210 TTTTTACAAATAAACTTAAGAACAGAGGAA
1 TTTTTACAAATAAACTTAAGAACAGAGGAA
289240 TTTTTACAAATAAACTTAAGAACAGAGGAA
1 TTTTTACAAATAAACTTAAGAACAGAGGAA
289270 TT
1 TT
289272 GCGGAAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (30 bp):
TTTTTACAAATAAACTTAAGAACAGAGGAA
Found at i:291405 original size:2 final size:2
Alignment explanation
Indices: 291398--291427 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
291388 AAATAAACGG
291398 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
291428 TTACGTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:296714 original size:33 final size:34
Alignment explanation
Indices: 296625--296716 Score: 84
Period size: 33 Copynumber: 2.7 Consensus size: 34
296615 TTGTAATTTT
* *
296625 TTTTTTTTTTGTAT-AT-TTTAATGTTGAAGTTTTA
1 TTTTTTATTTGTATAATATTTTAT-TTGAAG-TTTA
* *
296659 TTTTTTATTTTTATAATTTTTTATTTGAAG-TTA
1 TTTTTTATTTGTATAATATTTTATTTGAAGTTTA
*
296692 -TTTTTATGTTGTATCATATTTTATT
1 TTTTTTAT-TTGTATAATATTTTATT
296717 ATTATTATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
32 7 0.14
33 17 0.35
34 12 0.24
35 8 0.16
36 5 0.10
ACGTcount: A:0.22, C:0.01, G:0.09, T:0.68
Consensus pattern (34 bp):
TTTTTTATTTGTATAATATTTTATTTGAAGTTTA
Found at i:297122 original size:23 final size:22
Alignment explanation
Indices: 297090--297145 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
297080 ATATTTTATT
297090 AATT-AATTTTATAACTTAATAA
1 AATTAAATTTTATAA-TTAATAA
* *
297112 AATTAAATTTTTTAATTAATTA
1 AATTAAATTTTATAATTAATAA
*
297134 ATTATAAATTTT
1 AAT-TAAATTTT
297146 TTAAAATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTAAATTTTATAATTAATAA
Found at i:304510 original size:18 final size:19
Alignment explanation
Indices: 304487--304529 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
304477 TTGGTAGGAG
*
304487 TCTTTGACAT-AAGGATTT
1 TCTTTGACATGAAGAATTT
*
304505 TCTTTGCCATGAAGAATTT
1 TCTTTGACATGAAGAATTT
304524 TACTTT
1 T-CTTT
304530 ACCATCTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 8 0.38
20 4 0.19
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (19 bp):
TCTTTGACATGAAGAATTT
Found at i:307218 original size:29 final size:29
Alignment explanation
Indices: 307132--307220 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
307122 AATTGATGTG
*
307132 GTTATATTCACGTCATATTTATTTTT-TAT
1 GTTATATTCATGTCATATTTATTTTTAT-T
** * * *
307161 AATATAAT-AT-TTACTATTTTTTTTATATT
1 GTTATATTCATGTCA-TATTTATTTT-TATT
307190 GTTATATTCATGTCATATTTATTTTTATT
1 GTTATATTCATGTCATATTTATTTTTATT
307219 GT
1 GT
307221 GTTTTAATTA
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
27 2 0.05
28 10 0.23
29 18 0.41
30 12 0.27
31 2 0.05
ACGTcount: A:0.27, C:0.07, G:0.06, T:0.61
Consensus pattern (29 bp):
GTTATATTCATGTCATATTTATTTTTATT
Found at i:307641 original size:16 final size:17
Alignment explanation
Indices: 307601--307644 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
307591 TATTCATGTC
*
307601 ATGTTCATGTTATTTTTT
1 ATGTT-ATGTTATTATTT
*
307619 GTGTTATGTT-TTATTT
1 ATGTTATGTTATTATTT
307635 ATGTTATGTT
1 ATGTTATGTT
307645 CATATCGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 5 0.22
18 4 0.17
ACGTcount: A:0.16, C:0.02, G:0.16, T:0.66
Consensus pattern (17 bp):
ATGTTATGTTATTATTT
Found at i:308385 original size:17 final size:18
Alignment explanation
Indices: 308363--308400 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
308353 CTTCAAATTC
*
308363 AATTACATAAAAT-TTTA
1 AATTACAAAAAATATTTA
308380 AATTACAAAAAATATTTA
1 AATTACAAAAAATATTTA
308398 AAT
1 AAT
308401 AAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTACAAAAAATATTTA
Found at i:313961 original size:22 final size:21
Alignment explanation
Indices: 313924--313976 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
313914 AAAAAAAATC
*
313924 ATATTAAA-CTTAAAATGATTT
1 ATATTAAATATTAAAAT-ATTT
313945 ATATTAAATATTAAAATATTT
1 ATATTAAATATTAAAATATTT
*
313966 AAATTTAAATA
1 ATA-TTAAATA
313977 ATTCCTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATTAAATATTAAAATATTT
Found at i:318357 original size:28 final size:29
Alignment explanation
Indices: 318319--318376 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
318309 TTATTATTTA
*
318319 AATAATAAAATATTTTATTTAA-ATTTAAT
1 AATAATAAAATAATTT-TTTAATATTTAAT
318348 AATAA-AAAATAATTTTTTAATATTTAAT
1 AATAATAAAATAATTTTTTAATATTTAAT
318376 A
1 A
318377 GATGGGTCCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 5 0.19
28 17 0.63
29 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AATAATAAAATAATTTTTTAATATTTAAT
Found at i:324222 original size:4 final size:4
Alignment explanation
Indices: 324206--324253 Score: 89
Period size: 4 Copynumber: 12.2 Consensus size: 4
324196 GAAACATACA
324206 CCAT CCA- CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT
1 CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT
324253 C
1 C
324254 TGTCCATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 3 0.07
4 40 0.93
ACGTcount: A:0.25, C:0.52, G:0.00, T:0.23
Consensus pattern (4 bp):
CCAT
Found at i:325259 original size:21 final size:21
Alignment explanation
Indices: 325233--325276 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
325223 AATAAATATG
325233 AATTATAAAAAATCGATTCAA
1 AATTATAAAAAATCGATTCAA
* *
325254 AATTATAAAAAATCTATTTAA
1 AATTATAAAAAATCGATTCAA
325275 AA
1 AA
325277 CTCAACTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (21 bp):
AATTATAAAAAATCGATTCAA
Found at i:329389 original size:20 final size:21
Alignment explanation
Indices: 329364--329417 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
329354 ATTAATAAAA
329364 AAATTATTATTTAT-TATTTT
1 AAATTATTATTTATATATTTT
*
329384 AAATTAATA-TTATATATTTT
1 AAATTATTATTTATATATTTT
*
329404 --ATTATTATTAATAT
1 AAATTATTATTTATAT
329418 TTATTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.21
19 9 0.31
20 14 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAATTATTATTTATATATTTT
Found at i:329422 original size:21 final size:20
Alignment explanation
Indices: 329366--329428 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
329356 TAATAAAAAA
329366 ATTATTATT-TA-TTATTTT
1 ATTATTATTATATTTATTTT
*
329384 AAATTAATATTATA--TATTTT
1 --ATTATTATTATATTTATTTT
*
329404 ATTATTATTAATATTTATTTA
1 ATTATTATT-ATATTTATTTT
329425 ATTA
1 ATTA
329429 AGTTAATCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 8 0.22
19 3 0.08
20 14 0.39
21 11 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATTATTATATTTATTTT
Found at i:329422 original size:28 final size:25
Alignment explanation
Indices: 329366--329422 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 25
329356 TAATAAAAAA
329366 ATTATTATTTATTATTTTAAATTAAT
1 ATTATTATTTATTATTTTAAATT-AT
329392 ATTATATATTTTATTATTATTAATATT-T
1 ATTAT-TA-TTTATTATT-TTAA-ATTAT
329420 ATT
1 ATT
329423 TAATTAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 5 0.19
27 2 0.07
28 13 0.48
29 4 0.15
30 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTATTATTTATTATTTTAAATTAT
Found at i:329631 original size:18 final size:17
Alignment explanation
Indices: 329591--329644 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
329581 AATGATAATT
329591 TTATTTATTCAAATTTAA
1 TTATTTATT-AAATTTAA
329609 TTATTTATT-AATTT-A
1 TTATTTATTAAATTTAA
329624 TATATATT-TTAAATTATAA
1 T-TAT-TTATTAAATT-TAA
329643 TT
1 TT
329645 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.06
16 10 0.32
17 6 0.19
18 11 0.35
19 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTTATTAAATTTAA
Found at i:329991 original size:19 final size:19
Alignment explanation
Indices: 329964--330000 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
329954 AAACTTTGTT
*
329964 AATTATTATTTTTTAATAC
1 AATTATTATTTGTTAATAC
*
329983 AATTTTTATTTGTTAATA
1 AATTATTATTTGTTAATA
330001 TTTTTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
AATTATTATTTGTTAATAC
Found at i:330240 original size:13 final size:13
Alignment explanation
Indices: 330222--330254 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
330212 TTTTAAATCT
330222 AATAAATTTAAAA
1 AATAAATTTAAAA
330235 AATAAA-TTAAAA
1 AATAAATTTAAAA
330247 AATTAAAT
1 AA-TAAAT
330255 ACGTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAAATTTAAAA
Found at i:330315 original size:29 final size:30
Alignment explanation
Indices: 330259--330322 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
330249 TTAAATACGT
* *
330259 AAAATTACTTGTAAAATATATGTAATATTA
1 AAAATTACATGTAAAATATATATAATATTA
330289 AAAATTACAT-TAAAATATTATATATATATATA
1 AAAATTACATGTAAAATA-TATATA-ATAT-TA
330321 AA
1 AA
330323 CACAAATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 7 0.24
30 14 0.48
31 4 0.14
32 4 0.14
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATTACATGTAAAATATATATAATATTA
Found at i:330387 original size:24 final size:25
Alignment explanation
Indices: 330345--330399 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
330335 TTTTTTAAAT
*
330345 TAATAAAGATAATTATTATTATCTA
1 TAATAAAGATAATTATTATTATCCA
*
330370 TAATAAA-ATAGTTATTATTATCCA
1 TAATAAAGATAATTATTATTATCCA
330394 TAATAA
1 TAATAA
330400 CTGTTTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (25 bp):
TAATAAAGATAATTATTATTATCCA
Found at i:332265 original size:13 final size:13
Alignment explanation
Indices: 332247--332271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
332237 AACTGTGTTT
332247 CTTTTCCTTTTTC
1 CTTTTCCTTTTTC
332260 CTTTTCCTTTTT
1 CTTTTCCTTTTT
332272 TCCACATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
CTTTTCCTTTTTC
Found at i:336933 original size:27 final size:24
Alignment explanation
Indices: 336869--336934 Score: 62
Period size: 27 Copynumber: 2.6 Consensus size: 24
336859 AAAAAGTTTT
*
336869 TTATTTTTATTATATTTGAATAAA
1 TTATTTTTATTTTATTTGAATAAA
*
336893 TTATTATATT-TTTTATTTGTATCTAAA
1 TTATT-T-TTATTTTATTTG-A-ATAAA
336920 TTAATTTTTATTTTA
1 TT-ATTTTTATTTTA
336935 AATGAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
24 5 0.15
25 9 0.26
26 5 0.15
27 12 0.35
28 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (24 bp):
TTATTTTTATTTTATTTGAATAAA
Found at i:336987 original size:30 final size:30
Alignment explanation
Indices: 336941--337018 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
336931 TTTAAATGAA
* *
336941 ATAATTTAAAATTTTATTTAGATATAAATT
1 ATAAATTAAAATTTTATTTAAATATAAATT
*
336971 ATAAATTAAAAATTTATTTAAATATAAATT
1 ATAAATTAAAATTTTATTTAAATATAAATT
*
337001 A-AAAAT-AAATTTTATTTA
1 ATAAATTAAAATTTTATTTA
337019 TCATAAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 11 0.26
29 4 0.09
30 28 0.65
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (30 bp):
ATAAATTAAAATTTTATTTAAATATAAATT
Found at i:337012 original size:23 final size:24
Alignment explanation
Indices: 336965--337012 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
336955 TATTTAGATA
**
336965 TAAATTATAAATTAAAAATTTATT
1 TAAATTATAAATTAAAAATAAATT
336989 TAAA-TATAAATTAAAAATAAATT
1 TAAATTATAAATTAAAAATAAATT
337012 T
1 T
337013 TATTTATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAATTATAAATTAAAAATAAATT
Found at i:338118 original size:2 final size:2
Alignment explanation
Indices: 338106--338144 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
338096 AAACATGCAT
*
338106 GA GA GA CA GA 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 GA GA GA GA GA G
338145 GTAATTTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:339771 original size:7 final size:7
Alignment explanation
Indices: 339761--339786 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
339751 TTACCTTTTA
339761 TTTTTCT
1 TTTTTCT
339768 TTTTTCT
1 TTTTTCT
339775 TTTTTCT
1 TTTTTCT
339782 TTTTT
1 TTTTT
339787 TTTAAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:345007 original size:37 final size:35
Alignment explanation
Indices: 344940--345012 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 35
344930 AATTTAAATT
344940 AATTTAATTTGATTTAATTTATTATTTAAATAATTAA
1 AATTTAATTTGATTTAATTTATTA-TTAAAT-ATTAA
* *
344977 AATTTATTTTTATTTAAATTTAATTA-TAAATATTAA
1 AATTTAATTTGATTT-AATTT-ATTATTAAATATTAA
345013 TATAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 5 0.16
37 18 0.56
38 5 0.16
39 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (35 bp):
AATTTAATTTGATTTAATTTATTATTAAATATTAA
Found at i:352324 original size:2 final size:2
Alignment explanation
Indices: 352317--352344 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
352307 TTTCTGCGGA
352317 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
352345 GCCGGCCATT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:352793 original size:33 final size:33
Alignment explanation
Indices: 352746--352847 Score: 195
Period size: 33 Copynumber: 3.1 Consensus size: 33
352736 GTTCCTATCA
*
352746 CTTAGATTTCGGAAACTTTAATTCCACATTTAG
1 CTTAGATTTAGGAAACTTTAATTCCACATTTAG
352779 CTTAGATTTAGGAAACTTTAATTCCACATTTAG
1 CTTAGATTTAGGAAACTTTAATTCCACATTTAG
352812 CTTAGATTTAGGAAACTTTAATTCCACATTTAG
1 CTTAGATTTAGGAAACTTTAATTCCACATTTAG
352845 CTT
1 CTT
352848 TTTCCTTGTC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (33 bp):
CTTAGATTTAGGAAACTTTAATTCCACATTTAG
Found at i:359733 original size:4 final size:4
Alignment explanation
Indices: 359717--359755 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
359707 CTAAGGAACA
*
359717 ATAC ATAC GTAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
359756 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:361339 original size:17 final size:17
Alignment explanation
Indices: 361290--361340 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
361280 TATAAATTTT
361290 AATTATTATT-AATAA-A
1 AATT-TTATTAAATAATA
*
361306 AATTTAATTATAA-AATA
1 AATTTTATTA-AATAATA
361323 AATTTTATTAAATAATA
1 AATTTTATTAAATAATA
361340 A
1 A
361341 TTATATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 4 0.14
16 8 0.28
17 17 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTTATTAAATAATA
Found at i:362473 original size:15 final size:16
Alignment explanation
Indices: 362453--362482 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
362443 TTTTTAAATA
362453 AATTTTA-TTAATTAT
1 AATTTTATTTAATTAT
362468 AATTTTATTTAATTA
1 AATTTTATTTAATTA
362483 AAAAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTATTTAATTAT
Found at i:362886 original size:20 final size:18
Alignment explanation
Indices: 362861--362907 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
362851 CATATATAAA
362861 TTTTTTTCTTTCTTTCCTTT
1 TTTTTTTCTTT-TTT-CTTT
*
362881 TTTTTTCCTTTTTTCTTT
1 TTTTTTTCTTTTTTCTTT
362899 TTCTTTTTC
1 TT-TTTTTC
362908 AGCCTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.25
19 8 0.33
20 10 0.42
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTTCTTTTTTCTTT
Found at i:362898 original size:18 final size:19
Alignment explanation
Indices: 362861--362907 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
362851 CATATATAAA
362861 TTTTTTTCTTTCTTTCCTT
1 TTTTTTTCTTTCTTTCCTT
*
362880 TTTTTTTCCTTT-TTTCTTT
1 TTTTTTT-CTTTCTTTCCTT
362899 TTCTTTTTC
1 TT-TTTTTC
362908 AGCCTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTCTTTCTTTCCTT
Found at i:363017 original size:25 final size:24
Alignment explanation
Indices: 362954--363019 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
362944 TGCAAGTGTC
* *
362954 AAATATAAAAATAT-ACATGAAAT
1 AAATATAAAAATATAATATGAAAA
*
362977 AAA-AT-AAATTATTAATATGTAAAA
1 AAATATAAAAATA-TAATATG-AAAA
363001 AAATATAAAAATATAATAT
1 AAATATAAAAATATAATAT
363020 TTTAAGTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.15
22 3 0.09
23 7 0.21
24 6 0.18
25 8 0.24
26 5 0.15
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (24 bp):
AAATATAAAAATATAATATGAAAA
Found at i:363230 original size:21 final size:21
Alignment explanation
Indices: 363206--363260 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
363196 GAGACATGAT
363206 ATAAATATAACATAAAT-AAAA
1 ATAAATA-AACATAAATAAAAA
* *
363227 ATAATTAAAACA-CAATAAAAA
1 ATAAAT-AAACATAAATAAAAA
363248 ATAACATAAACAT
1 ATAA-ATAAACAT
363261 GATACGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 3 0.11
21 22 0.81
22 2 0.07
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (21 bp):
ATAAATAAACATAAATAAAAA
Found at i:363418 original size:11 final size:10
Alignment explanation
Indices: 363402--363461 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
363392 ATACAAAAAA
363402 ATAAATATGAT
1 ATAAATAT-AT
363413 AT-AA-ATAT
1 ATAAATATAT
363421 ATAAATATA-
1 ATAAATATAT
* *
363430 AAAAATATTT
1 ATAAATATAT
363440 ATAAATATTAT
1 ATAAATA-TAT
*
363451 ATAAATTTAT
1 ATAAATATAT
363461 A
1 A
363462 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
8 4 0.10
9 11 0.28
10 15 0.38
11 10 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
ATAAATATAT
Found at i:363418 original size:15 final size:14
Alignment explanation
Indices: 363400--363446 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
363390 CAATACAAAA
363400 AAATAAATATGATAT
1 AAATAAATAT-ATAT
* *
363415 AAATATATAAATAT
1 AAATAAATATATAT
*
363429 AAA-AAATATTTAT
1 AAATAAATATATAT
363442 AAATA
1 AAATA
363447 TTATATAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 10 0.38
14 8 0.31
15 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
AAATAAATATATAT
Found at i:363426 original size:19 final size:18
Alignment explanation
Indices: 363402--363497 Score: 65
Period size: 19 Copynumber: 5.3 Consensus size: 18
363392 ATACAAAAAA
363402 ATAAATATGATATAAATAT
1 ATAAATAT-ATATAAATAT
*
363421 ATAAATATA-AAAAATATTT
1 ATAAATATATATAAATA--T
*
363440 ATAAATATTATATAAATTT
1 ATAAATA-TATATAAATAT
*
363459 AT-AATAT-TTTAAATA-
1 ATAAATATATATAAATAT
* * *
363474 ATAAAAATTAAATAAAAAT
1 ATAAATA-TATATAAATAT
363493 ATAAA
1 ATAAA
363498 CCCTTAATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
15 2 0.03
16 9 0.15
17 8 0.13
18 10 0.17
19 24 0.40
20 2 0.03
21 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (18 bp):
ATAAATATATATAAATAT
Found at i:363450 original size:9 final size:9
Alignment explanation
Indices: 363402--363473 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 9
363392 ATACAAAAAA
363402 ATAAATATGAT
1 ATAAATAT--T
363413 ATAAATA-T
1 ATAAATATT
*
363421 ATAAATATA
1 ATAAATATT
*
363430 AAAAATATTT
1 ATAAATA-TT
363440 ATAAATATT
1 ATAAATATT
363449 ATATAA-ATT
1 ATA-AATATT
363458 -TATAATATT
1 ATA-AATATT
*
363467 TTAAATA
1 ATAAATA
363474 ATAAAAATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 13 0.25
9 21 0.40
10 11 0.21
11 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
ATAAATATT
Found at i:366300 original size:2 final size:2
Alignment explanation
Indices: 366295--366322 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
366285 AAACACACAA
366295 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
366323 TGAAGTGCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:371713 original size:2 final size:2
Alignment explanation
Indices: 371706--371732 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
371696 ATCTATTTGT
371706 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
371733 TAAAGGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:371886 original size:2 final size:2
Alignment explanation
Indices: 371879--371903 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
371869 GCATTACTTT
371879 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
371904 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:375307 original size:15 final size:15
Alignment explanation
Indices: 375287--375321 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
375277 TTCTCCCTCC
*
375287 CCATCATCATCATCT
1 CCATCATCATCACCT
375302 CCATCATCATCACCT
1 CCATCATCATCACCT
375317 CCATC
1 CCATC
375322 CCGACCTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.46, G:0.00, T:0.29
Consensus pattern (15 bp):
CCATCATCATCACCT
Found at i:381828 original size:71 final size:71
Alignment explanation
Indices: 381742--381931 Score: 265
Period size: 71 Copynumber: 2.7 Consensus size: 71
381732 CACTAAGAAG
* * *
381742 AAAACAAGCCAAAACCCACAAGAATAAATATGCAAAGCCAGTGATTACAACACTAAG-AAGAAGT
1 AAAACAAGCCAAAACCCACAAGAATAAACATGCAAAGCAAGTGATTACAACACT-AGTAAGAAGC
381806 ACTAAAT
65 ACTAAAT
* * * **
381813 TAAACAAGGCAAAACCCACAAGAACAAACATGCAAAGCAAGTGACAACAACACTAGTAAGAAGCA
1 AAAACAAGCCAAAACCCACAAGAATAAACATGCAAAGCAAGTGATTACAACACTAGTAAGAAGCA
* *
381878 CTTAGT
66 CTAAAT
*
381884 AAAACAAGCCAAAACCCACAAGAATAAGCATGCAAAGCAAGTGATTAC
1 AAAACAAGCCAAAACCCACAAGAATAAACATGCAAAGCAAGTGATTAC
381932 TTGGAAAAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
70 2 0.02
71 100 0.98
ACGTcount: A:0.52, C:0.22, G:0.14, T:0.12
Consensus pattern (71 bp):
AAAACAAGCCAAAACCCACAAGAATAAACATGCAAAGCAAGTGATTACAACACTAGTAAGAAGCA
CTAAAT
Found at i:382640 original size:76 final size:79
Alignment explanation
Indices: 382517--382667 Score: 195
Period size: 76 Copynumber: 1.9 Consensus size: 79
382507 AAATTTATGT
*
382517 ATATATATATATATATATAATATTTTAAGTTTATATAATATAAATTATTAA-TTATTAAATTTTA
1 ATATATATATAAATATATAATATTTTAAGTTTATATAATATAAATTATTAATTTA-T-AATTTTA
382581 TATAAAAAATATATAA
64 TATAAAAAATATATAA
** * *
382597 ATATA-ATATAAATATATAA-A-TTTAA-TTTATATAATATTTATTATTTATTTATACTTTTATA
1 ATATATATATAAATATATAATATTTTAAGTTTATATAATATAAATTATTAATTTATAATTTTATA
*
382658 TATAAAATAT
66 TAAAAAATAT
382668 TTATTTTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
75 17 0.27
76 20 0.31
77 8 0.12
78 1 0.02
79 13 0.20
80 5 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (79 bp):
ATATATATATAAATATATAATATTTTAAGTTTATATAATATAAATTATTAATTTATAATTTTATA
TAAAAAATATATAA
Found at i:382682 original size:19 final size:20
Alignment explanation
Indices: 382651--382689 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
382641 TTATTTATAC
382651 TTTTATATATAAAATATTTA
1 TTTTATATATAAAATATTTA
*
382671 TTTTAT-TATAAAATTTTTA
1 TTTTATATATAAAATATTTA
382690 ATTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATATATAAAATATTTA
Found at i:384631 original size:2 final size:2
Alignment explanation
Indices: 384626--384661 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
384616 TTTACTTTAC
384626 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
384662 TCTTTCTCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:390368 original size:6 final size:6
Alignment explanation
Indices: 390359--390388 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
390349 AAAAATTAAA
390359 AATTTT AATTTT AATTTT AA-TTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT AATTTT A
390389 TTTATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:390376 original size:12 final size:11
Alignment explanation
Indices: 390359--390402 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
390349 AAAAATTAAA
390359 AATTTTAATTTT
1 AATTTTAA-TTT
390371 AATTTTAATTT
1 AATTTTAATTT
390382 AATTTT-ATTT
1 AATTTTAATTT
*
390392 ATATTTAAATT
1 A-ATTTTAATT
390403 ATTAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 5 0.17
11 13 0.45
12 11 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
AATTTTAATTT
Found at i:390414 original size:21 final size:19
Alignment explanation
Indices: 390390--390446 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
390380 TTAATTTTAT
390390 TTATATTTAAATTATTAAAAA
1 TTATATTT-AA-TATTAAAAA
* *
390411 TTAT-TTTTATATTAAAAT
1 TTATATTTAATATTAAAAA
*
390429 TTATATTTTATAATTAAA
1 TTATATTTAAT-ATTAAA
390447 TTTAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 12 0.38
19 7 0.22
20 9 0.28
21 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATTTAATATTAAAAA
Found at i:390425 original size:18 final size:19
Alignment explanation
Indices: 390402--390446 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
390392 ATATTTAAAT
390402 TATTAAAAATTAT-TTTTA
1 TATTAAAAATTATATTTTA
*
390420 TATTAAAATTTATATTTTA
1 TATTAAAAATTATATTTTA
390439 TAATTAAA
1 T-ATTAAA
390447 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.50
19 6 0.25
20 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTAAAAATTATATTTTA
Found at i:390439 original size:19 final size:19
Alignment explanation
Indices: 390388--390450 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
390378 ATTTAATTTT
*
390388 ATTTATATTTAAATTATTAAA
1 ATTTATATTT-TA-TATTAAA
*
390409 AATTAT-TTTTATATTAAA
1 ATTTATATTTTATATTAAA
390427 ATTTATATTTTATAATT-AA
1 ATTTATATTTTAT-ATTAAA
390446 ATTTA
1 ATTTA
390451 AATAAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 12 0.32
19 14 0.38
20 6 0.16
21 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTATATTTTATATTAAA
Found at i:391024 original size:41 final size:42
Alignment explanation
Indices: 390978--391067 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 42
390968 ATGATGCGAC
* *
390978 ATAAATTAAAATATAATTTAAA-ATATATTATTATAA-TATAA
1 ATAAATTAAAAT-TAATATAAATATATAATATTATAATTATAA
* *
391019 ATAAATTAAAATTTATATAAATATATAATATTTTAATTATAA
1 ATAAATTAAAATTAATATAAATATATAATATTATAATTATAA
*
391061 AAAAATT
1 ATAAATT
391068 TTGATGTGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 7 0.17
41 24 0.57
42 11 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (42 bp):
ATAAATTAAAATTAATATAAATATATAATATTATAATTATAA
Found at i:395551 original size:21 final size:21
Alignment explanation
Indices: 395522--395564 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
395512 AAAGTGAATA
*
395522 ATAAATAAATAATCTTTTAAT
1 ATAAATAAATAAACTTTTAAT
* *
395543 ATAAGTAAATAAAGTTTTAAT
1 ATAAATAAATAAACTTTTAAT
395564 A
1 A
395565 AATAATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (21 bp):
ATAAATAAATAAACTTTTAAT
Found at i:395576 original size:2 final size:2
Alignment explanation
Indices: 395569--395595 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
395559 TTAATAAATA
395569 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 A
395596 CACACAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:396150 original size:18 final size:16
Alignment explanation
Indices: 396119--396158 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
396109 ATTTAGATAT
396119 ATTTAATTTTTTTTAA
1 ATTTAATTTTTTTTAA
*
396135 ATTTAATATATTTTTTAT
1 ATTTAAT-T-TTTTTTAA
396153 ATTTAA
1 ATTTAA
396159 ATTTGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 1 0.05
18 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTAATTTTTTTTAA
Found at i:399279 original size:18 final size:18
Alignment explanation
Indices: 399252--399292 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
399242 TTTAATTTCA
* *
399252 TCTTTTTTTTTCTTTGTT
1 TCTTTCTTTTGCTTTGTT
*
399270 TCTTTCTTTTGCTTTTTT
1 TCTTTCTTTTGCTTTGTT
399288 TCTTT
1 TCTTT
399293 TATTTTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (18 bp):
TCTTTCTTTTGCTTTGTT
Found at i:399486 original size:17 final size:17
Alignment explanation
Indices: 399464--399496 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
399454 TATAAAATTG
399464 TTAAGTTTTAATTCTAT
1 TTAAGTTTTAATTCTAT
399481 TTAAGTTTTAATTCTA
1 TTAAGTTTTAATTCTA
399497 ACAGTTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
TTAAGTTTTAATTCTAT
Found at i:413671 original size:26 final size:27
Alignment explanation
Indices: 413615--413671 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
413605 CCCGAATCAT
413615 TATTTAATTAATAAAAAAATTATTTAA
1 TATTTAATTAATAAAAAAATTATTTAA
* *
413642 -ATTTAATT-ATAATATAA-TATTTTAA
1 TATTTAATTAATAAAAAAATTA-TTTAA
413667 TATTT
1 TATTT
413672 TAGATACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 2 0.08
25 12 0.46
26 12 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TATTTAATTAATAAAAAAATTATTTAA
Found at i:416525 original size:22 final size:21
Alignment explanation
Indices: 416467--416526 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
416457 ATTTCCCCAA
*
416467 TTTATTT-ATATAAATA-TAT
1 TTTATTTAATATAAAAATTAT
416486 TTATATTTAATA-ATAAAATTAAT
1 TT-TATTTAATATA-AAAATT-AT
416509 TTTATTTAATATAAAAAT
1 TTTATTTAATATAAAAAT
416527 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
19 2 0.06
20 6 0.18
21 6 0.18
22 15 0.44
23 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATTTAATATAAAAATTAT
Found at i:416559 original size:24 final size:22
Alignment explanation
Indices: 416469--416574 Score: 60
Period size: 22 Copynumber: 4.8 Consensus size: 22
416459 TTCCCCAATT
*
416469 TATTTATATAAAT-ATA-TTTA
1 TATTAATATAAATAATATTTTA
*
416489 TATTTAATAATAAA-ATTAATTTTA
1 TA-TTAAT-ATAAATAAT-ATTTTA
***
416513 T-TTAATATAAA-AATATAAAAA
1 TATTAATATAAATAATAT-TTTA
416534 TATTAATATAAAATAATATTTTAA
1 TATTAATAT-AAATAATATTTT-A
* *
416558 TAATATTATAAATAATA
1 TATTAATATAAATAATA
416575 AAATACCTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
20 4 0.06
21 13 0.20
22 18 0.28
23 12 0.18
24 18 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTAATATAAATAATATTTTA
Found at i:416571 original size:44 final size:45
Alignment explanation
Indices: 416492--416577 Score: 106
Period size: 44 Copynumber: 1.9 Consensus size: 45
416482 ATATTTATAT
* *
416492 TTAATAATAAAATTAATTTTATTTAATATAAAAAT-ATAAAAATA
1 TTAATAATAAAATAAATTTTATATAATATAAAAATAATAAAAATA
*
416536 TTAAT-ATAAAATAATATTTTA-ATAATATTATAAATAATAAAA
1 TTAATAATAAAATAA-ATTTTATATAATA-TAAAAATAATAAAA
416578 TACCTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 13 0.36
44 17 0.47
45 6 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (45 bp):
TTAATAATAAAATAAATTTTATATAATATAAAAATAATAAAAATA
Found at i:416678 original size:45 final size:45
Alignment explanation
Indices: 416582--416678 Score: 108
Period size: 45 Copynumber: 2.1 Consensus size: 45
416572 ATAAAATACC
* *
416582 TTTTAAATTTAATTTAAATTTAAATAAAAATAAAAAATTAATTTAA
1 TTTT-AATTTAATTTAAATATAAATAAAAATAAAAAATTAATATAA
* * *
416628 ATTTAATTTAATTTATAA-ATAAATCAACATACAAAAATTAA-ATAA
1 TTTTAATTTAATTTA-AATATAAATAAAAATA-AAAAATTAATATAA
416673 TTTTAA
1 TTTTAA
416679 AAAAAAATCT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
45 29 0.67
46 14 0.33
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (45 bp):
TTTTAATTTAATTTAAATATAAATAAAAATAAAAAATTAATATAA
Found at i:417013 original size:12 final size:13
Alignment explanation
Indices: 416996--417024 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
416986 ATAAAATATA
416996 AATTAATT-AATT
1 AATTAATTAAATT
417008 AATTAATTAAATT
1 AATTAATTAAATT
417021 AATT
1 AATT
417025 GTTATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTAATTAAATT
Found at i:417511 original size:9 final size:9
Alignment explanation
Indices: 417474--417552 Score: 54
Period size: 9 Copynumber: 8.7 Consensus size: 9
417464 AGATTGAATA
417474 TTATATA-T
1 TTATATATT
* *
417482 CTATAAATT
1 TTATATATT
*
417491 ATATATATTT
1 TTATATA-TT
*
417501 TTATTTATT
1 TTATATATT
*
417510 TTAAATATT
1 TTATATATT
417519 TTATAT-TT
1 TTATATATT
* *
417527 ATATAAATT
1 TTATATATT
417536 TTAATATAATT
1 TT-ATAT-ATT
417547 TTATAT
1 TTATAT
417553 TAATAATCGT
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
8 11 0.21
9 23 0.43
10 14 0.26
11 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (9 bp):
TTATATATT
Found at i:417533 original size:19 final size:19
Alignment explanation
Indices: 417488--417534 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
417478 ATATCTATAA
*
417488 ATTATATATATTTTTATTT
1 ATTATAAATATTTTTATTT
*
417507 ATTTTAAATATTTTATATTT
1 ATTATAAATATTTT-TATTT
417527 A-TATAAAT
1 ATTATAAAT
417535 TTTAATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATAAATATTTTTATTT
Found at i:418787 original size:3 final size:3
Alignment explanation
Indices: 418773--418820 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
418763 ATTCTATTCC
*
418773 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
418821 ATGAATTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:424733 original size:38 final size:37
Alignment explanation
Indices: 424676--424748 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
424666 TCGATTATGT
*
424676 TTGAAAGTTTTTCAAGTATTAAGATATTAAAATTTAA
1 TTGAAAGTTTTTCAAGTATTAAAATATTAAAATTTAA
*
424713 TTGAAAGTTTTTTTAAGTATTAAAATATTAAAATTT
1 TTGAAAG-TTTTTCAAGTATTAAAATATTAAAATTT
424749 GATAATTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 7 0.21
38 26 0.79
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (37 bp):
TTGAAAGTTTTTCAAGTATTAAAATATTAAAATTTAA
Found at i:426053 original size:10 final size:11
Alignment explanation
Indices: 426036--426062 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
426026 TTATATTTTT
426036 TTATTTTTAAA
1 TTATTTTTAAA
426047 TTATTTTTAAA
1 TTATTTTTAAA
426058 TTATT
1 TTATT
426063 ATATCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTTTTAAA
Found at i:426926 original size:11 final size:11
Alignment explanation
Indices: 426910--426934 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
426900 AATAATAATA
426910 TTTGATTTGAT
1 TTTGATTTGAT
426921 TTTGATTTGAT
1 TTTGATTTGAT
426932 TTT
1 TTT
426935 TATTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTGATTTGAT
Done.