Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold481
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: 370912
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
File 3 of 3
Found at i:264388 original size:2 final size:2
Alignment explanation
Indices: 264381--264427 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
264371 ATTAAATCTT
264381 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
264423 TA TA T
1 TA TA T
264428 CAATTTGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:264836 original size:14 final size:15
Alignment explanation
Indices: 264819--264853 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
264809 TAATTTTTAA
264819 TATATTA-ATAAATT
1 TATATTATATAAATT
264833 TATATTATATAAATT
1 TATATTATATAAATT
264848 TGATAT
1 T-ATAT
264854 ATTTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 8 0.42
16 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:264841 original size:19 final size:20
Alignment explanation
Indices: 264798--264842 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
264788 ATAAGATATT
* *
264798 ATATATTTATATAATTTTTA
1 ATATATTAATATAATTTATA
264818 ATATATTAATA-AATTTATA
1 ATATATTAATATAATTTATA
*
264837 TTATAT
1 ATATAT
264843 AAATTTGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATATTAATATAATTTATA
Found at i:266568 original size:2 final size:2
Alignment explanation
Indices: 266561--266591 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
266551 ATTTTAGATT
266561 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 T
266592 TTGAAGAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:267898 original size:17 final size:16
Alignment explanation
Indices: 267876--267917 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
267866 AAGAATAAAA
267876 AAATATTTATTAATACT
1 AAATATTTATTAATA-T
*
267893 AAATATTTGTTAATAT
1 AAATATTTATTAATAT
*
267909 TAATATTTA
1 AAATATTTA
267918 AATTTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (16 bp):
AAATATTTATTAATAT
Found at i:270173 original size:2 final size:2
Alignment explanation
Indices: 270166--270202 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
270156 TGATGTTATG
270166 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
270203 GTATTAGGGT
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:271475 original size:16 final size:16
Alignment explanation
Indices: 271464--271531 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
271454 TTAAATAACT
271464 TAAATTTAAAATAATA
1 TAAATTTAAAATAATA
*
271480 TAAACTTAAAATAATA
1 TAAATTTAAAATAATA
* *
271496 TAAATTTAAAATCATC
1 TAAATTTAAAATAATA
*
271512 TATATTTAAAATAATA
1 TAAATTTAAAATAATA
271528 TAAA
1 TAAA
271532 AATTTCAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATTTAAAATAATA
Found at i:271475 original size:21 final size:21
Alignment explanation
Indices: 271433--271489 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
271423 CGATCCACAC
*
271433 TTAAATAACATAAATATTAAA
1 TTAAATAACTTAAATATTAAA
271454 TTAAATAACTTAAAT-TTAAA
1 TTAAATAACTTAAATATTAAA
*
271474 ATAATATAAACTTAAA
1 TTAA-AT-AACTTAAA
271490 ATAATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 8 0.25
21 16 0.50
22 8 0.25
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TTAAATAACTTAAATATTAAA
Found at i:271500 original size:32 final size:32
Alignment explanation
Indices: 271456--271531 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
271446 ATATTAAATT
271456 AAATAACT-TAAATTTAAAATAATATAAACTTA
1 AAATAA-TATAAATTTAAAATAATATAAACTTA
* * * *
271488 AAATAATATAAATTTAAAATCATCTATATTTA
1 AAATAATATAAATTTAAAATAATATAAACTTA
271520 AAATAATATAAA
1 AAATAATATAAA
271532 AATTTCAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (32 bp):
AAATAATATAAATTTAAAATAATATAAACTTA
Found at i:275069 original size:15 final size:16
Alignment explanation
Indices: 275049--275080 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
275039 TCGAATACTT
275049 AAAATTAA-TGATAAA
1 AAAATTAATTGATAAA
275064 AAAATTAATTGATAAA
1 AAAATTAATTGATAAA
275080 A
1 A
275081 GATACAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAATTAATTGATAAA
Found at i:276405 original size:19 final size:20
Alignment explanation
Indices: 276350--276411 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 20
276340 ATGATGAAAA
*
276350 ATAATTAAA-ATATAAATTGAT
1 ATAAATAAATATATAAA-T-AT
276371 ATAAA-AAATAATATAAATAT
1 ATAAATAAAT-ATATAAATAT
276391 A-AAATAAATATATAAATAT
1 ATAAATAAATATATAAATAT
276410 AT
1 AT
276412 TAAAATTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 14 0.39
20 10 0.28
21 5 0.14
22 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
ATAAATAAATATATAAATAT
Found at i:276471 original size:10 final size:10
Alignment explanation
Indices: 276388--276471 Score: 59
Period size: 10 Copynumber: 8.4 Consensus size: 10
276378 ATAATATAAA
*
276388 TATAAAATAAA
1 TATAAAAT-AT
276399 TATATAAATA-
1 TATA-AAATAT
276409 TATTAAAAT-T
1 TA-TAAAATAT
* *
276419 TATATATTAT
1 TATAAAATAT
*
276429 T-TTAAATAT
1 TATAAAATAT
276438 TATAATAATA-
1 TATAA-AATAT
*
276448 TATAAAATAA
1 TATAAAATAT
276458 TATAAAATAT
1 TATAAAATAT
276468 TATA
1 TATA
276472 TGAATATATT
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
9 14 0.24
10 30 0.51
11 11 0.19
12 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATAAAATAT
Found at i:276471 original size:20 final size:19
Alignment explanation
Indices: 276358--276467 Score: 73
Period size: 20 Copynumber: 5.6 Consensus size: 19
276348 AAATAATTAA
*
276358 AATATAAATTGATATAAAA-
1 AATATAAAAT-ATATAAAAT
*
276377 AATAATATAA-ATATAAAAT
1 AAT-ATAAAATATATAAAAT
276396 AAATATATAAATATATTAAAAT
1 -AATATA-AAATATA-TAAAAT
* * * * *
276418 -TTATATATTATTTTAAAT
1 AATATAAAATATATAAAAT
*
276436 ATTATAATAATATATAAAAT
1 AATATAA-AATATATAAAAT
276456 AATATAAAATAT
1 AATATAAAATAT
276468 TATATGAATA
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
18 13 0.19
19 20 0.29
20 28 0.40
21 3 0.04
22 6 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (19 bp):
AATATAAAATATATAAAAT
Found at i:276666 original size:41 final size:43
Alignment explanation
Indices: 276599--276683 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 43
276589 TTTTTATTTA
*
276599 AATTTATTTACTTATTTATTATTATT-AA-TT-AATAAAAATAT
1 AATTTATTTA-TTATTTAATATTATTAAATTTAAATAAAAATAT
276640 AATTTATTT-TTATATTAATATATATTAAATTTAAATAAAAATAT
1 AATTTATTTATTAT-TTAATAT-TATTAAATTTAAATAAAAATAT
276684 TTTTAATCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
39 4 0.11
40 6 0.16
41 13 0.34
42 2 0.05
43 2 0.05
44 11 0.29
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (43 bp):
AATTTATTTATTATTTAATATTATTAAATTTAAATAAAAATAT
Found at i:278101 original size:39 final size:39
Alignment explanation
Indices: 278047--278125 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
278037 GGGAGTAAGT
278047 CACTATCTCCCTCACTTTCTCTCTATATGCTAATATTTA
1 CACTATCTCCCTCACTTTCTCTCTATATGCTAATATTTA
278086 CACTATCTCCCTCACTTTCTCTCTATATGCTAATATTTA
1 CACTATCTCCCTCACTTTCTCTCTATATGCTAATATTTA
278125 C
1 C
278126 CCGGATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.32, G:0.03, T:0.43
Consensus pattern (39 bp):
CACTATCTCCCTCACTTTCTCTCTATATGCTAATATTTA
Found at i:279642 original size:14 final size:15
Alignment explanation
Indices: 279623--279654 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
279613 ATTCAACAAA
279623 TTTAATA-TTATAAT
1 TTTAATATTTATAAT
279637 TTTAATATTTATAAT
1 TTTAATATTTATAAT
279652 TTT
1 TTT
279655 TTATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATATTTATAAT
Found at i:279930 original size:22 final size:21
Alignment explanation
Indices: 279903--279947 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
279893 CATCATAATA
279903 ATTTTTTTATATAAAAAAAATC
1 ATTTTTTTATAT-AAAAAAATC
*
279925 ATTTTTTTGTATAAAAAAATC
1 ATTTTTTTATATAAAAAAATC
279946 AT
1 AT
279948 AACTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTTTTTATATAAAAAAATC
Found at i:280495 original size:13 final size:14
Alignment explanation
Indices: 280465--280499 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
280455 GTATGTTAGT
*
280465 TATATTTTTTTAAG
1 TATATATTTTTAAG
280479 TATATATTTTTAA-
1 TATATATTTTTAAG
280492 TATATATT
1 TATATATT
280500 AAAATACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TATATATTTTTAAG
Found at i:284945 original size:3 final size:3
Alignment explanation
Indices: 284937--284983 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
284927 GCCAAGTATC
284937 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
284984 TTATGTATGC
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:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:287957 original size:12 final size:12
Alignment explanation
Indices: 287942--287984 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
287932 TGTAAATTTG
287942 TGTTAAAATGAA
1 TGTTAAAATGAA
** *
287954 TGTTAACTTAAA
1 TGTTAAAATGAA
287966 TAGTTAAAATGAA
1 T-GTTAAAATGAA
287979 TGTTAA
1 TGTTAA
287985 TTTAAATATG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (12 bp):
TGTTAAAATGAA
Found at i:287971 original size:25 final size:25
Alignment explanation
Indices: 287943--287992 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
287933 GTAAATTTGT
287943 GTTAAAATGAATGTTAACTTAAATA
1 GTTAAAATGAATGTTAACTTAAATA
*
287968 GTTAAAATGAATGTTAATTTAAATA
1 GTTAAAATGAATGTTAACTTAAATA
287993 TGTATAAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (25 bp):
GTTAAAATGAATGTTAACTTAAATA
Found at i:289257 original size:18 final size:18
Alignment explanation
Indices: 289231--289322 Score: 96
Period size: 18 Copynumber: 5.2 Consensus size: 18
289221 CAATCACGGA
* *
289231 TTTTAGGAATTATAAATT
1 TTTTAGGAATCACAAATT
*
289249 TTCTAGGAATCACAAATT
1 TTTTAGGAATCACAAATT
*
289267 TTTTAAGAATCACAAATT
1 TTTTAGGAATCACAAATT
* * *
289285 TTTTAAGAATCATAGA-T
1 TTTTAGGAATCACAAATT
* *
289302 TTTTAGGAATTACAGATT
1 TTTTAGGAATCACAAATT
289320 TTT
1 TTT
289323 GTAATTACAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 14 0.22
18 49 0.78
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTTAGGAATCACAAATT
Found at i:289321 original size:16 final size:16
Alignment explanation
Indices: 289230--289337 Score: 54
Period size: 18 Copynumber: 6.3 Consensus size: 16
289220 TCAATCACGG
*
289230 ATTTTAGGAATTATAA
1 ATTTTAGGAATTACAA
*
289246 ATTTTCTAGGAATCACAA
1 A-TTT-TAGGAATTACAA
* *
289264 ATTTTTTAAGAATCACAA
1 A--TTTTAGGAATTACAA
* * *
289282 ATTTTTTAAGAATCATAGA
1 A--TTTTAGGAATTACA-A
* *
289301 TTTTTAGGAATTACAG
1 ATTTTAGGAATTACAA
* *
289317 ATTTTTGTAATTACAA
1 ATTTTAGGAATTACAA
289333 ATTTT
1 ATTTT
289338 CAACCCCAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
16 18 0.24
17 14 0.19
18 38 0.51
19 5 0.07
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (16 bp):
ATTTTAGGAATTACAA
Found at i:290924 original size:18 final size:18
Alignment explanation
Indices: 290901--290935 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
290891 ACATGATAAC
*
290901 AAAGAGCCCGTATTTGAT
1 AAAGAGCCAGTATTTGAT
290919 AAAGAGCCAGTATTTGA
1 AAAGAGCCAGTATTTGA
290936 CAAAAAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (18 bp):
AAAGAGCCAGTATTTGAT
Found at i:292402 original size:17 final size:17
Alignment explanation
Indices: 292380--292434 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
292370 CAATTACAAA
292380 TTTTAGGAATCACAGAT
1 TTTTAGGAATCACAGAT
* *
292397 TTTTAGGAATTACAAAT
1 TTTTAGGAATCACAGAT
* * *
292414 TTCTA-TAATCATAGAT
1 TTTTAGGAATCACAGAT
292430 TTTTA
1 TTTTA
292435 ACCCATCATA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
16 11 0.37
17 19 0.63
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (17 bp):
TTTTAGGAATCACAGAT
Found at i:292413 original size:33 final size:33
Alignment explanation
Indices: 292371--292434 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
292361 GATCAACATC
292371 AATTACAAATTT-TAGGAATCACAGATTTTTAGG
1 AATTACAAATTTCTA-GAATCACAGATTTTTAGG
* *
292404 AATTACAAATTTCTATAATCATAGATTTTTA
1 AATTACAAATTTCTAGAATCACAGATTTTTA
292435 ACCCATCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (33 bp):
AATTACAAATTTCTAGAATCACAGATTTTTAGG
Found at i:292444 original size:18 final size:18
Alignment explanation
Indices: 292421--292457 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
292411 AATTTCTATA
292421 ATCATAGATTTTTAACCC
1 ATCATAGATTTTTAACCC
292439 ATCATAGATTTTTAACCC
1 ATCATAGATTTTTAACCC
292457 A
1 A
292458 ATAATGAATT
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:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (18 bp):
ATCATAGATTTTTAACCC
Found at i:293208 original size:2 final size:2
Alignment explanation
Indices: 293201--293234 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
293191 ACTTCCATTA
293201 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
293235 GAGCTCATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:295110 original size:24 final size:24
Alignment explanation
Indices: 295065--295112 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
295055 ATATAATATC
*
295065 TTAATTTTAAATTATCTCACTTAT
1 TTAATTTTAAATTATATCACTTAT
*
295089 TTAA-TTTAAATATATATTACTTAT
1 TTAATTTTAAAT-TATATCACTTAT
295113 AAATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATTTTAAATTATATCACTTAT
Found at i:297016 original size:15 final size:15
Alignment explanation
Indices: 296996--297036 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
296986 TGAATTCACC
296996 CAAGAAGAAGCCACT
1 CAAGAAGAAGCCACT
*
297011 CAAGAAGAAGCCATT
1 CAAGAAGAAGCCACT
*
297026 CAAGAATAAGC
1 CAAGAAGAAGC
297037 ACCAGTGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.10
Consensus pattern (15 bp):
CAAGAAGAAGCCACT
Found at i:297457 original size:89 final size:89
Alignment explanation
Indices: 297337--297689 Score: 438
Period size: 89 Copynumber: 4.0 Consensus size: 89
297327 GTTCTAATAA
* * * *
297337 AATAAAATTCTTGAAACCCGAAAGATATGACAGATGCATGTGAGTATCAGATTCTTTTTAACATG
1 AATAAATTTCTTGAAACCCGAAAGATGTGACAGATGCATGTGAGTATCAGATTCCTTCTAACATG
*
297402 ACGAAAAATATTTGACTAATGCCT
66 ACAAAAAATATTTGACTAATGCCT
* * * * * * * * *
297426 GATAAATTTCTTGGAACCCAAAAGTTGTGACAGATGCATGTGGGTATTAGATTCTTTCTGATATG
1 AATAAATTTCTTGAAACCCGAAAGATGTGACAGATGCATGTGAGTATCAGATTCCTTCTAACATG
*
297491 ACAGAAAATATTTGACTAATGCCT
66 ACAAAAAATATTTGACTAATGCCT
* * * * * *
297515 AATAAGTTTCTTGGAACCCGAAAGATTTGACAGATGCATATGGGTATCAGATTCCTTCTAACACG
1 AATAAATTTCTTGAAACCCGAAAGATGTGACAGATGCATGTGAGTATCAGATTCCTTCTAACATG
*
297580 ATAAAAAATATTTGACTAATGCCT
66 ACAAAAAATATTTGACTAATGCCT
* * * *
297604 AATAAATTTCTTGAAATCCGAAAGATGTGACAGATGTATG-CAGGTATCAGATTCCTTCTGACAT
1 AATAAATTTCTTGAAACCCGAAAGATGTGACAGATGCATGTGA-GTATCAGATTCCTTCTAACAT
* *
297668 GATAAAAAATATTTAACTAATG
65 GACAAAAAATATTTGACTAATG
297690 ATATGACAGA
Statistics
Matches: 226, Mismatches: 37, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
89 226 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (89 bp):
AATAAATTTCTTGAAACCCGAAAGATGTGACAGATGCATGTGAGTATCAGATTCCTTCTAACATG
ACAAAAAATATTTGACTAATGCCT
Found at i:297679 original size:178 final size:178
Alignment explanation
Indices: 297344--297689 Score: 485
Period size: 178 Copynumber: 1.9 Consensus size: 178
297334 TAAAATAAAA
* * * * *
297344 TTCTTGAAACCCGAAAGATATGACAGATGCATGTGAGTATCAGATTCTTTTTAACATGACGAAAA
1 TTCTTGAAACCCGAAAGATATGACAGATGCATATGAGTATCAGATTCCTTCTAACACGACAAAAA
* * * ** *
297409 ATATTTGACTAATGCCTGATAAATTTCTTGGAACCCAAAAGTTGTGACAGATGCATGTGGGTATT
66 ATATTTGACTAATGCCTAATAAATTTCTTGAAACCCAAAAGATGTGACAGATGCATGCAGGTATC
* * * *
297474 AGATTCTTTCTGATATGACAGAAAATATTTGACTAATGCCTAATAAGT
131 AGATTCCTTCTGACATGACAAAAAATATTTAACTAATGCCTAATAAGT
* * * *
297522 TTCTTGGAACCCGAAAGATTTGACAGATGCATATGGGTATCAGATTCCTTCTAACACGATAAAAA
1 TTCTTGAAACCCGAAAGATATGACAGATGCATATGAGTATCAGATTCCTTCTAACACGACAAAAA
* * *
297587 ATATTTGACTAATGCCTAATAAATTTCTTGAAATCCGAAAGATGTGACAGATGTATGCAGGTATC
66 ATATTTGACTAATGCCTAATAAATTTCTTGAAACCCAAAAGATGTGACAGATGCATGCAGGTATC
*
297652 AGATTCCTTCTGACATGATAAAAAATATTTAACTAATG
131 AGATTCCTTCTGACATGACAAAAAATATTTAACTAATG
297690 ATATGACAGA
Statistics
Matches: 145, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
178 145 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (178 bp):
TTCTTGAAACCCGAAAGATATGACAGATGCATATGAGTATCAGATTCCTTCTAACACGACAAAAA
ATATTTGACTAATGCCTAATAAATTTCTTGAAACCCAAAAGATGTGACAGATGCATGCAGGTATC
AGATTCCTTCTGACATGACAAAAAATATTTAACTAATGCCTAATAAGT
Found at i:301094 original size:20 final size:20
Alignment explanation
Indices: 301049--301096 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
301039 AAAGACTTAA
*
301049 CGAAAAAAATAATGCAAAAC
1 CGAAAAAAATAAAGCAAAAC
** *
301069 TAAAAAAAATAAAGTAAAAC
1 CGAAAAAAATAAAGCAAAAC
301089 CGAAAAAA
1 CGAAAAAA
301097 TTACAAGATC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.71, C:0.10, G:0.08, T:0.10
Consensus pattern (20 bp):
CGAAAAAAATAAAGCAAAAC
Found at i:301204 original size:24 final size:24
Alignment explanation
Indices: 301177--301227 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
301167 AATAAAGTCC
*
301177 AAAAAAAT-TAATAATATAACTTAA
1 AAAAAAATATAAAAATAT-ACTTAA
**
301201 AAAAACCTATAAAAATATACTTAA
1 AAAAAAATATAAAAATATACTTAA
301225 AAA
1 AAA
301228 TTAAAAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAAAATATAAAAATATACTTAA
Found at i:301277 original size:29 final size:29
Alignment explanation
Indices: 301230--301292 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
301220 CTTAAAAATT
* * *
301230 AAAAAACTAAAAACTATAAAATAATTATAA
1 AAAAAACTAAAAACAATAAAAAAATGA-AA
301260 AAAAAACTAAAAA-AATAAAAAAATGAAA
1 AAAAAACTAAAAACAATAAAAAAATGAAA
301288 AAAAA
1 AAAAA
301293 TCGATACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 7 0.23
29 10 0.33
30 13 0.43
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.16
Consensus pattern (29 bp):
AAAAAACTAAAAACAATAAAAAAATGAAA
Found at i:307666 original size:2 final size:2
Alignment explanation
Indices: 307659--307694 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
307649 TACATGGAAG
307659 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
307695 ACAGTTTCAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:315127 original size:20 final size:19
Alignment explanation
Indices: 315093--315133 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
315083 ACTTATATAT
*
315093 ATATATATATCTTAGATTA
1 ATATATATATCTTAGAGTA
*
315112 ATATTTATAGTCTTAGAGTA
1 ATATATATA-TCTTAGAGTA
315132 AT
1 AT
315134 TATCACTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (19 bp):
ATATATATATCTTAGAGTA
Found at i:316634 original size:11 final size:11
Alignment explanation
Indices: 316618--316642 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
316608 ATTCATATTC
316618 AAAAATATTTT
1 AAAAATATTTT
316629 AAAAATATTTT
1 AAAAATATTTT
316640 AAA
1 AAA
316643 GATGAGTATG
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:320329 original size:3 final size:3
Alignment explanation
Indices: 320321--320345 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
320311 TCTCACTATT
320321 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
320346 ATCTTCAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:320437 original size:16 final size:17
Alignment explanation
Indices: 320396--320437 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
320386 TTAAATATTT
*
320396 AATTTTAT-TTTTTATT
1 AATTTTATATTTTTATA
*
320412 AATTTGATATTTTT-TA
1 AATTTTATATTTTTATA
320428 AATTTTATAT
1 AATTTTATAT
320438 ATTAATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
AATTTTATATTTTTATA
Found at i:320762 original size:12 final size:12
Alignment explanation
Indices: 320747--320781 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
320737 CAATTTTTCA
320747 TTTATTTTATTT
1 TTTATTTTATTT
* *
320759 TTTAGTTTGTTT
1 TTTATTTTATTT
320771 TTTATTTTATT
1 TTTATTTTATT
320782 AATAATTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:320914 original size:16 final size:16
Alignment explanation
Indices: 320890--320931 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
320880 TCCTACTTTT
*
320890 TTTTCTTTTTCATTTAC
1 TTTTCTTTTTAATTT-C
320907 TTTT-TTTTTAATTTC
1 TTTTCTTTTTAATTTC
*
320922 TTTTGTTTTT
1 TTTTCTTTTT
320932 TAGGAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 14 0.61
17 4 0.17
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTCTTTTTAATTTC
Found at i:323886 original size:23 final size:23
Alignment explanation
Indices: 323860--323903 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
323850 TTGATGTAAA
323860 TTTAAATATTATATATTTATAAT
1 TTTAAATATTATATATTTATAAT
* *
323883 TTTAAATTTTATATTTTTATA
1 TTTAAATATTATATATTTATA
323904 TAAACAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTAAATATTATATATTTATAAT
Found at i:324607 original size:33 final size:33
Alignment explanation
Indices: 324570--324653 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
324560 GTTACGTTTG
324570 TATATTTTTATATGTTATAAAATTTTAAAATAT
1 TATATTTTTATATGTTATAAAATTTTAAAATAT
** * * *
324603 TATATTTTTATAAATT-TAATATTTTAATATTT
1 TATATTTTTATATGTTATAAAATTTTAAAATAT
324635 TAATATTTTTATATGTTAT
1 T-ATATTTTTATATGTTAT
324654 GAATTTATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 14 0.33
33 27 0.64
34 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (33 bp):
TATATTTTTATATGTTATAAAATTTTAAAATAT
Found at i:324648 original size:8 final size:8
Alignment explanation
Indices: 324570--324648 Score: 50
Period size: 8 Copynumber: 9.6 Consensus size: 8
324560 GTTACGTTTG
324570 TATATTTT
1 TATATTTT
*
324578 TATATGTTA
1 TATAT-TTT
* *
324587 TAAAATTT
1 TATATTTT
* * *
324595 TAAAATAT
1 TATATTTT
324603 TATATTTT
1 TATATTTT
*
324611 TATAAATTT
1 TAT-ATTTT
*
324620 AATATTTT
1 TATATTTT
*
324628 AATATTTT
1 TATATTTT
*
324636 AATATTTT
1 TATATTTT
324644 TATAT
1 TATAT
324649 GTTATGAATT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
8 46 0.81
9 11 0.19
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (8 bp):
TATATTTT
Found at i:324648 original size:16 final size:16
Alignment explanation
Indices: 324571--324648 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
324561 TTACGTTTGT
324571 ATATTTTTATATGTTATA
1 ATATTTTTATAT-TT-TA
* * * *
324589 AAATTTTAAAATATT-
1 ATATTTTTATATTTTA
*
324604 ATATTTTTATAAATTTA
1 ATATTTTTAT-ATTTTA
*
324621 ATATTTTAATATTTTA
1 ATATTTTTATATTTTA
324637 ATATTTTTATAT
1 ATATTTTTATAT
324649 GTTATGAATT
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
15 7 0.15
16 20 0.43
17 10 0.22
18 9 0.20
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
ATATTTTTATATTTTA
Found at i:324719 original size:20 final size:21
Alignment explanation
Indices: 324690--324731 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
324680 AATTTGACTC
* *
324690 AAAATAATATTTTTTAATTAA
1 AAAATAATATATTTAAATTAA
324711 AAAAT-ATATATTTAAATTAA
1 AAAATAATATATTTAAATTAA
324731 A
1 A
324732 TTATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATAATATATTTAAATTAA
Found at i:325247 original size:23 final size:23
Alignment explanation
Indices: 325204--325274 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
325194 AATATTTAAA
* *
325204 TAATAAAAAAATTTATTTAAAT-T
1 TAATATAAAAA-TTATATAAATAT
* *
325227 TAGTTATTAAAATTATATAAATAT
1 TA-ATATAAAAATTATATAAATAT
* *
325251 TAATATAAAAATTATTTTAATAT
1 TAATATAAAAATTATATAAATAT
325274 T
1 T
325275 TTAATATATT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
23 29 0.76
24 9 0.24
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
TAATATAAAAATTATATAAATAT
Found at i:325316 original size:24 final size:24
Alignment explanation
Indices: 325284--325335 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
325274 TTTAATATAT
*
325284 TTTAAATAATAATAAATT-TTTAAA
1 TTTAAATAAAAAT-AATTATTTAAA
*
325308 TTTAAATAAAAATATTTATTTAAA
1 TTTAAATAAAAATAATTATTTAAA
325332 TTTA
1 TTTA
325336 GTTTCAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTAAATAAAAATAATTATTTAAA
Found at i:327027 original size:17 final size:17
Alignment explanation
Indices: 327007--327042 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
326997 GGCGTTTTGG
327007 TTTTTGTTTTCTTTTCT
1 TTTTTGTTTTCTTTTCT
* *
327024 TTTTTTTTTTTTTTTCT
1 TTTTTGTTTTCTTTTCT
327041 TT
1 TT
327043 CTCCTTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (17 bp):
TTTTTGTTTTCTTTTCT
Found at i:328414 original size:17 final size:17
Alignment explanation
Indices: 328392--328430 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
328382 AGACTTTTTT
*
328392 TTATT-AATAATATTTAC
1 TTATTAAAT-ATATTTAA
328409 TTATTAAATATATTTAA
1 TTATTAAATATATTTAA
328426 TTATT
1 TTATT
328431 GAGTAATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTAAATATATTTAA
Found at i:331820 original size:20 final size:20
Alignment explanation
Indices: 331805--331848 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
331795 TTAATATATT
331805 ATATTTTATATAAATATAAA
1 ATATTTTATATAAATATAAA
* *
331825 ATATTTTAAATATATATAATA
1 ATATTTTATATAAATATAA-A
331846 ATA
1 ATA
331849 ATATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTTTATATAAATATAAA
Found at i:331821 original size:33 final size:31
Alignment explanation
Indices: 331739--331869 Score: 98
Period size: 32 Copynumber: 4.3 Consensus size: 31
331729 AATATAAAAA
* * * *
331739 ATTATATTAATATGATATAAATATATGAATAT
1 ATTAAATTTATATAATATAAAT-TATTAATAT
*
331771 TTTAAATTTATATAATATAAATTATTAATAT
1 ATTAAATTTATATAATATAAATTATTAATAT
*
331802 ATTATATTTTATATAAATATAAA--A-T-AT-T
1 ATTA-AATTTATAT-AATATAAATTATTAATAT
*
331830 -TTAAATATATATAATA-ATAATATATTAAT-T
1 ATTAAATTTATATAATATA-AAT-TATTAATAT
331860 ATTAAATTTA
1 ATTAAATTTA
331870 ATTTATTAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 19
0.73 0.09 0.17
Matches are distributed among these distances:
24 1 0.01
25 6 0.08
26 7 0.09
27 3 0.04
28 2 0.03
29 3 0.04
30 4 0.05
31 20 0.25
32 26 0.32
33 8 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
ATTAAATTTATATAATATAAATTATTAATAT
Found at i:331828 original size:58 final size:59
Alignment explanation
Indices: 331753--331868 Score: 166
Period size: 58 Copynumber: 2.0 Consensus size: 59
331743 TATTAATATG
* * *
331753 ATATAAATATATGAATATTTTAAATTTATATAAT-ATAA-ATTATTAATATATTATATTTT
1 ATATAAATATATAAATATTTTAAATATATATAATAATAATA-TATTAAT-TATTAAATTTT
331812 ATATAAATATA-AAATATTTTAAATATATATAATAATAATATATTAATTATTAAATTT
1 ATATAAATATATAAATATTTTAAATATATATAATAATAATATATTAATTATTAAATTT
331869 AATTTATTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
58 29 0.56
59 22 0.42
60 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (59 bp):
ATATAAATATATAAATATTTTAAATATATATAATAATAATATATTAATTATTAAATTTT
Found at i:332736 original size:21 final size:21
Alignment explanation
Indices: 332710--332753 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
332700 GTCGGCTTTT
*
332710 TGGCTTCATCCCTGATCTTCA
1 TGGCTTCACCCCTGATCTTCA
332731 TGGCTTCACCCCTGATCTTCA
1 TGGCTTCACCCCTGATCTTCA
332752 TG
1 TG
332754 TACCTTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.34, G:0.16, T:0.36
Consensus pattern (21 bp):
TGGCTTCACCCCTGATCTTCA
Found at i:334013 original size:2 final size:2
Alignment explanation
Indices: 334006--334043 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
333996 TCAAAGTTTA
334006 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
334044 ATATATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:334080 original size:2 final size:2
Alignment explanation
Indices: 334043--334070 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
334033 TCTCTCTCTC
334043 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
334071 ATTAATATAT
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):
TA
Found at i:335112 original size:15 final size:17
Alignment explanation
Indices: 335089--335121 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
335079 CTTGACATAT
335089 AAATAAATTT-AATTTA
1 AAATAAATTTAAATTTA
335105 AAAT-AATTTAAATTTA
1 AAATAAATTTAAATTTA
335121 A
1 A
335122 TAGTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATAAATTTAAATTTA
Found at i:337325 original size:3 final size:3
Alignment explanation
Indices: 337317--337363 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
337307 ACATGCAGCA
337317 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
337364 GGCAAATACT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:339026 original size:14 final size:14
Alignment explanation
Indices: 339007--339035 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
338997 TGAATTTAAA
339007 AAAAAAGAAAAATT
1 AAAAAAGAAAAATT
339021 AAAAAAGAAAAATT
1 AAAAAAGAAAAATT
339035 A
1 A
339036 CTTTTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAGAAAAATT
Found at i:339392 original size:20 final size:22
Alignment explanation
Indices: 339369--339411 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
339359 CTATATTTAA
339369 TATTTATTTAAG-A-TTAAAAT
1 TATTTATTTAAGTATTTAAAAT
*
339389 TATTTTTTTAAGTATTTAAAAT
1 TATTTATTTAAGTATTTAAAAT
339411 T
1 T
339412 TAGTTATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
TATTTATTTAAGTATTTAAAAT
Found at i:341842 original size:18 final size:20
Alignment explanation
Indices: 341797--341895 Score: 56
Period size: 17 Copynumber: 5.3 Consensus size: 20
341787 TATAATTATT
*
341797 TATTTTAAAATATATTTAAA
1 TATTTTAAAATATATTAAAA
*
341817 T-TTATAAAA-ATA-TAAAA
1 TATTTTAAAATATATTAAAA
341834 TATTTT-AAATATAATTAAGAA
1 TATTTTAAAATAT-ATTAA-AA
**
341855 -ATGATAAAATATA-T-AAA
1 TATTTTAAAATATATTAAAA
*
341872 TA-CTT-AAAT-TATTAAATA
1 TATTTTAAAATATATTAAA-A
341890 TATTTT
1 TATTTT
341896 TTTAATGTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 23
0.66 0.09 0.25
Matches are distributed among these distances:
15 2 0.03
16 5 0.08
17 13 0.22
18 13 0.22
19 11 0.18
20 8 0.13
21 8 0.13
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (20 bp):
TATTTTAAAATATATTAAAA
Found at i:342058 original size:19 final size:19
Alignment explanation
Indices: 342036--342149 Score: 74
Period size: 19 Copynumber: 5.8 Consensus size: 19
342026 AAAAATAATA
*
342036 ATATAAATATTACATAAAT
1 ATATAAATATTAAATAAAT
**
342055 ATATAAATATTTTAAA-ATTT
1 ATATAAATA--TTAAATAAAT
*
342075 ATATAATATATT-ATTAACAT
1 ATATAA-ATATTAAATAA-AT
*
342095 AT-TAAATTTTAAATAAAT
1 ATATAAATATTAAATAAAT
342113 ATA-AATATATTAAATATAAT
1 ATATAA-ATATTAAATA-AAT
*
342133 ATAAAAAATATATAAAT
1 AT-ATAAATAT-TAAAT
342150 TATTAAATTA
Statistics
Matches: 74, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
18 11 0.15
19 28 0.38
20 16 0.22
21 12 0.16
22 7 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAAATATTAAATAAAT
Found at i:342136 original size:26 final size:26
Alignment explanation
Indices: 342075--342137 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
342065 TTTAAAATTT
* *
342075 ATATAATAT-ATTATTAACATATTAA
1 ATATAATATAAATATAAACATATTAA
* *
342100 ATTTTAA-ATAAATATAAATATATTAA
1 A-TATAATATAAATATAAACATATTAA
342126 ATATAATATAAA
1 ATATAATATAAA
342138 AAATATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATAATATAAATATAAACATATTAA
Found at i:343185 original size:30 final size:29
Alignment explanation
Indices: 343117--343186 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
343107 AAAGTTTACG
343117 TAATTCAAAATTTTTATTTTATTATTTAAAA
1 TAATT-AAAATTTTTATTTTATTATTT-AAA
*
343148 TATATTAAAATATTTTATTATTATTATTT-TA
1 TA-ATTAAAAT-TTTTATT-TTATTATTTAAA
343179 TAATTAAA
1 TAATTAAA
343187 TTTAAATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
30 6 0.17
31 10 0.29
32 10 0.29
33 9 0.26
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
TAATTAAAATTTTTATTTTATTATTTAAA
Found at i:344422 original size:191 final size:191
Alignment explanation
Indices: 344093--344456 Score: 602
Period size: 191 Copynumber: 1.9 Consensus size: 191
344083 AATTTAAAAT
* *
344093 CTTTTTATTTGATTTATATTTATTTAATCTAATGATCATATTTCATCATCTACTTACATAGATCA
1 CTTTTTATTTGATTCATATTTATTTAATCTAACGATCATATTTCATCATCTACTTACATAGATCA
* *
344158 TGCACATTAAGCTTTAAGTAAATAAAAAATATCTTAGTATTTGTTTAGTGTAAAAAACCTTCAAC
66 TACACATTAAGCTTTAAGTAAATAAAAAATATCTTAGTATTTGTTTAGTGTAAAAAACCTCCAAC
*
344223 CGTTAAATATATATTGAAAACATCAGTATTTTTAATCGATATTATTGGAATGTTAAATCGC
131 CATTAAATATATATTGAAAACATCAGTATTTTTAATCGATATTATTGGAATGTTAAATCGC
* * * * *
344284 CTTTTTATTTGATTCATATTTGTTTAATCTAACGATCATATTTTATCATCTATTTACGTAGATTA
1 CTTTTTATTTGATTCATATTTATTTAATCTAACGATCATATTTCATCATCTACTTACATAGATCA
* * *
344349 TACACATTGAGCTTTAAGTAAATAAAAAATTTCTTAGTATTTGTTTGGTGTAAAAAACCTCCAAC
66 TACACATTAAGCTTTAAGTAAATAAAAAATATCTTAGTATTTGTTTAGTGTAAAAAACCTCCAAC
*
344414 CATTAAATATATATTGAAAACATCAGTATTTTTAATTGATATT
131 CATTAAATATATATTGAAAACATCAGTATTTTTAATCGATATT
344457 GGATCAATTC
Statistics
Matches: 159, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
191 159 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (191 bp):
CTTTTTATTTGATTCATATTTATTTAATCTAACGATCATATTTCATCATCTACTTACATAGATCA
TACACATTAAGCTTTAAGTAAATAAAAAATATCTTAGTATTTGTTTAGTGTAAAAAACCTCCAAC
CATTAAATATATATTGAAAACATCAGTATTTTTAATCGATATTATTGGAATGTTAAATCGC
Found at i:347201 original size:2 final size:2
Alignment explanation
Indices: 347194--347223 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
347184 GCAAAACAAC
347194 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
347224 GATGTTTCAA
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:349435 original size:382 final size:382
Alignment explanation
Indices: 348703--350227 Score: 2812
Period size: 382 Copynumber: 4.0 Consensus size: 382
348693 GTATTTTCAT
*
348703 ATATGAACTTTGAACTCAAAGTCATCTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAA
1 ATATGAACTTTGAACTCAAACTCA-CTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAA
*
348768 ATATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAATTCATGTTATTAAAAAAATA
65 ATATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATT-AAAAAATA
348833 ATATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTA
129 ATATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTA
*
348898 GTTTGC-GAGTGACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCG
194 ATTTGCAG-GTGACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCG
* *
348962 AAGGGGTTTTTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAATACTATTAAA
258 AAAGGGTTTTTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAA
*
349027 AATAGTTGTGATAGTTAAATTAATTATTTTAATAGCGAGATTGGATACTATAATAATGAG
323 AATAGTTGTGATAGTTAAATTAATTATTTTAATAACGAGATTGGATACTATAATAATGAG
* *
349087 ATATGAACTTTGAACTCAAAGTCACTTATTCAAATTTATCCATCTAAGCCTATTTATATTAAAAA
1 ATATGAACTTTGAACTCAAACTCACTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAAA
349152 TATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAAT
66 TATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAAT
349217 ATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAAT
131 ATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAAT
349282 TTGCAGGTGACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAA
196 TTGCAGGTGACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAA
349347 GGGTTTTTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAAT
261 GGGTTTTTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAAT
349412 AGTTGTGATAGTTAAATTAATTATTTTAATAACGAGATTGGATACTATAATAATGAG
326 AGTTGTGATAGTTAAATTAATTATTTTAATAACGAGATTGGATACTATAATAATGAG
349469 ATATGAACTTTGAACTCAAACTCACTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAAA
1 ATATGAACTTTGAACTCAAACTCACTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAAA
349534 TATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAAT
66 TATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAAT
*
349599 ATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAGT
131 ATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAAT
* *
349664 TTGCGGGTGACTTGATCCATAAATAGATTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAA
196 TTGCAGGTGACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAA
*
349729 GGGTTTTTATTATTATAGGATAACTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAAT
261 GGGTTTTTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAAT
*
349794 AGTTGTGATAGTTAAATTAATTATTTTAATAGCGAGATTGGATAC-----T-ATGAG
326 AGTTGTGATAGTTAAATTAATTATTTTAATAACGAGATTGGATACTATAATAATGAG
349845 ATATGAACTTTGAACTCAAACTCACTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAAA
1 ATATGAACTTTGAACTCAAACTCACTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAAA
349910 TATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAAT
66 TATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAAT
* *
349975 ATTCAAATCAAATCAAATATTTATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAAT
131 ATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAAT
*
350040 TTGCAGGTAACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAA
196 TTGCAGGTGACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAA
350105 GGGTTTTTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAAT
261 GGGTTTTTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAAT
* *
350170 AGTTGTGATAGTTGAATTAATTATTTTAATAATGAGATTGGATACTATAATAATGAG
326 AGTTGTGATAGTTAAATTAATTATTTTAATAACGAGATTGGATACTATAATAATGAG
350227 A
1 A
350228 CTAAAATAAG
Statistics
Matches: 1111, Mismatches: 23, Indels: 16
0.97 0.02 0.01
Matches are distributed among these distances:
376 365 0.33
377 1 0.00
381 1 0.00
382 625 0.56
383 95 0.09
384 24 0.02
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (382 bp):
ATATGAACTTTGAACTCAAACTCACTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAAA
TATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAAT
ATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAAT
TTGCAGGTGACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAA
GGGTTTTTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAAT
AGTTGTGATAGTTAAATTAATTATTTTAATAACGAGATTGGATACTATAATAATGAG
Found at i:350190 original size:758 final size:762
Alignment explanation
Indices: 348703--350227 Score: 2860
Period size: 758 Copynumber: 2.0 Consensus size: 762
348693 GTATTTTCAT
*
348703 ATATGAACTTTGAACTCAAAGTCATCTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAA
1 ATATGAACTTTGAACTCAAACTCATCTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAA
*
348768 ATATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAATTCATGTTATTAAAAAAATA
66 ATATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAAATA
348833 ATATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTA
131 ATATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTA
*
348898 GTTTGCGAGTGACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGA
196 GTTTGCGAGTGACTTGATCCATAAATAGATTTAAGATAATCATGATTAATTTAAATAGAAGTCGA
* *
348963 AGGGGTTTTTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAATACTATTAAAA
261 AAGGGTTTTTATTATTATAGGATAACTTTGGATGGATTGTGGGATTAACTCTAATACTATTAAAA
349028 ATAGTTGTGATAGTTAAATTAATTATTTTAATAGCGAGATTGGATACTATAATAATGAGATATGA
326 ATAGTTGTGATAGTTAAATTAATTATTTTAATAGCGAGATTGGATAC----ATAATGAGATATGA
*
349093 ACTTTGAACTCAAAGTCACTTATTCAAATTTATCCATCTAAGCCTATTTATATTAAAAATATTTT
387 ACTTTGAACTCAAACTCACTTATTCAAATTTATCCATCTAAGCCTATTTATATTAAAAATATTTT
349158 TATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAATATTCAA
452 TATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAATATTCAA
349223 ATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAATTTGCAG
517 ATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAATTTGCAG
*
349288 GTGACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAAGGGTTT
582 GTAACTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAAGGGTTT
349353 TTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAATAGTTGT
647 TTATTATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAATAGTTGT
349418 GATAGTTAAATTAATTATTTTAATAACGAGATTGGATACTATAATAATGAG
712 GATAGTTAAATTAATTATTTTAATAACGAGATTGGATACTATAATAATGAG
349469 ATATGAACTTTGAACTCAAACTCA-CTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAA
1 ATATGAACTTTGAACTCAAACTCATCTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAA
349533 ATATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATT-AAAAAATA
66 ATATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAAATA
349597 ATATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTA
131 ATATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTA
*
349662 GTTTGCGGGTGACTTGATCCATAAATAGATTTAAGATAATCATGATTAATTTAAATAGAAGTCGA
196 GTTTGCGAGTGACTTGATCCATAAATAGATTTAAGATAATCATGATTAATTTAAATAGAAGTCGA
*
349727 AAGGGTTTTTATTATTATAGGATAACTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAA
261 AAGGGTTTTTATTATTATAGGATAACTTTGGATGGATTGTGGGATTAACTCTAATACTATTAAAA
349792 ATAGTTGTGATAGTTAAATTAATTATTTTAATAGCGAGATTGGATAC-T-ATGAGATATGAACTT
326 ATAGTTGTGATAGTTAAATTAATTATTTTAATAGCGAGATTGGATACATAATGAGATATGAACTT
*
349855 TGAACTCAAACTCACTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAAATATTTTTATA
391 TGAACTCAAACTCACTTATTCAAATTTATCCATCTAAGCCTATTTATATTAAAAATATTTTTATA
349920 TTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAATATTCAAATCA
456 TTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAATATTCAAATCA
* *
349985 AATCAAATATTTATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAATTTGCAGGTAA
521 AATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAATTTGCAGGTAA
350050 CTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAAGGGTTTTTAT
586 CTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAAGGGTTTTTAT
350115 TATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAATAGTTGTGATA
651 TATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAATAGTTGTGATA
* *
350180 GTTGAATTAATTATTTTAATAATGAGATTGGATACTATAATAATGAG
716 GTTAAATTAATTATTTTAATAACGAGATTGGATACTATAATAATGAG
350227 A
1 A
350228 CTAAAATAAG
Statistics
Matches: 745, Mismatches: 14, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
758 381 0.51
759 1 0.00
764 245 0.33
765 95 0.13
766 23 0.03
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (762 bp):
ATATGAACTTTGAACTCAAACTCATCTTATTCAAATTTGTCCATCTAAGCCTATTTATATTAAAA
ATATTTTTATATTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAAATA
ATATTCAAATCAAATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTA
GTTTGCGAGTGACTTGATCCATAAATAGATTTAAGATAATCATGATTAATTTAAATAGAAGTCGA
AAGGGTTTTTATTATTATAGGATAACTTTGGATGGATTGTGGGATTAACTCTAATACTATTAAAA
ATAGTTGTGATAGTTAAATTAATTATTTTAATAGCGAGATTGGATACATAATGAGATATGAACTT
TGAACTCAAACTCACTTATTCAAATTTATCCATCTAAGCCTATTTATATTAAAAATATTTTTATA
TTTTACATACATTTTGAAATTAATATTAAACAAACTCATGTTATTAAAAAATAATATTCAAATCA
AATCAAACATTGATTTGAAAAATACTATTCAAAGATTAATTGAGTTGAATTTAATTTGCAGGTAA
CTTGATCCATAAATAGGTTTAAGATAATCATGATTAATTTAAATAGAAGTCGAAAGGGTTTTTAT
TATTATAGGATAATTTTGGATGGATTGTGGGATTAACTCTAGTACTATTAAAAATAGTTGTGATA
GTTAAATTAATTATTTTAATAACGAGATTGGATACTATAATAATGAG
Found at i:351109 original size:2 final size:2
Alignment explanation
Indices: 351102--351133 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
351092 GAAAGAGAAA
351102 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
351134 TAGCTAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351180 original size:3 final size:3
Alignment explanation
Indices: 351172--351200 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
351162 ACATGCAGCA
351172 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
351201 GGCAAATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:351828 original size:27 final size:27
Alignment explanation
Indices: 351766--351840 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
351756 AAACAACATG
*
351766 CCACCATTTTTGACAAATAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAGAAA
* * * *
351793 CTACTATTTTTTACAAACACAAAA-TAA
1 CCACCATTTTTGACAAACA-AAAAGAAA
351820 CCACCATTTTTGACAAACAAA
1 CCACCATTTTTGACAAACAAA
351841 TAACGGTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.05
27 33 0.85
28 4 0.10
ACGTcount: A:0.48, C:0.21, G:0.04, T:0.27
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGAAA
Found at i:356302 original size:27 final size:27
Alignment explanation
Indices: 356247--356347 Score: 109
Period size: 27 Copynumber: 3.9 Consensus size: 27
356237 AATAAAAATT
* *
356247 AACCACAAATTTTGACAAAC---AACA
1 AACCACAATTTTTGACAAACAAAAAGA
* * * *
356271 TACCACCATTTTTTACAAATAAAAAGA
1 AACCACAATTTTTGACAAACAAAAAGA
* *
356298 AACCACAATTTTTGACAAACACAAAGT
1 AACCACAATTTTTGACAAACAAAAAGA
356325 AACCACAATTTTTGACAAACAAA
1 AACCACAATTTTTGACAAACAAA
356348 TGGTGATTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
24 15 0.25
27 46 0.75
ACGTcount: A:0.50, C:0.22, G:0.05, T:0.23
Consensus pattern (27 bp):
AACCACAATTTTTGACAAACAAAAAGA
Found at i:359509 original size:24 final size:25
Alignment explanation
Indices: 359445--359510 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
359435 TAATAATATT
* *
359445 ATAA-ATATAATTACATATTTTAAA
1 ATAAGATATAATAAAATATTTTAAA
*
359469 ATAATATAT-ATAAAA-ATATTTAAA
1 ATAAGATATAATAAAATAT-TTTAAA
*
359493 TTAAGATATAATAAAATA
1 ATAAGATATAATAAAATA
359511 AATACCTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 2 0.06
24 21 0.62
25 10 0.29
26 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
ATAAGATATAATAAAATATTTTAAA
Found at i:360504 original size:19 final size:17
Alignment explanation
Indices: 360479--360575 Score: 84
Period size: 19 Copynumber: 5.8 Consensus size: 17
360469 ATTTCAACGA
360479 TTTGTATCGATACATTAG
1 TTTGTATCGATACA-TAG
360497 TGTTGTATCGATACA-A-
1 T-TTGTATCGATACATAG
360513 --TGTATCGATACATAAG
1 TTTGTATCGATACAT-AG
360529 TGTTGTATCGATACA-A-
1 T-TTGTATCGATACATAG
360545 --TGTATCGATACATAAG
1 TTTGTATCGATACAT-AG
360561 TTTTGTATCGATACA
1 -TTTGTATCGATACA
360576 ATGTACTACT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 24 0.36
15 2 0.03
17 2 0.03
18 1 0.02
19 37 0.56
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (17 bp):
TTTGTATCGATACATAG
Found at i:360517 original size:32 final size:32
Alignment explanation
Indices: 360481--360580 Score: 182
Period size: 32 Copynumber: 3.1 Consensus size: 32
360471 TTCAACGATT
*
360481 TGTATCGATACATTAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
360513 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
360545 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
360577 TGTA
1 TGTA
360581 CTACTACGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:360518 original size:13 final size:13
Alignment explanation
Indices: 360500--360556 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
360490 ACATTAGTGT
360500 TGTATCGATACAA
1 TGTATCGATACAA
360513 TGTATCGATACATAA
1 TGTATCGATAC--AA
360528 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
360545 TGTATCGATACA
1 TGTATCGATACA
360557 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:360704 original size:52 final size:52
Alignment explanation
Indices: 360661--360789 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
360651 CACTGATCTT
*
360661 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGGAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
360713 TGTATCAATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
360765 TGTATCGATACATGCTGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
360790 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:366348 original size:4 final size:4
Alignment explanation
Indices: 366316--366364 Score: 52
Period size: 4 Copynumber: 13.2 Consensus size: 4
366306 TAAACTTTGG
* *
366316 AGAA A-AA AGGA AGAA A-AA AGAG A-AA AGAA AGAA AGAA AGAA A-AA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
366360 AGAA A
1 AGAA A
366365 AGGCAAGTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 11 0.30
4 26 0.70
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:367959 original size:20 final size:19
Alignment explanation
Indices: 367935--367989 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
367925 AAATCAATTG
367935 TTAATATTTTAATTTTTAA
1 TTAATATTTTAATTTTTAA
* *
367954 TATAATTTTTTAA-ATTTAA
1 T-TAATATTTTAATTTTTAA
*
367973 TTAAAATTTT-ATTTTTA
1 TTAATATTTTAATTTTTA
367990 TTTTATTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 1 0.03
18 11 0.38
19 7 0.24
20 10 0.34
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATATTTTAATTTTTAA
Found at i:368013 original size:74 final size:73
Alignment explanation
Indices: 367910--368050 Score: 185
Period size: 74 Copynumber: 1.9 Consensus size: 73
367900 TATCTAAAAT
** ** * * *
367910 TTTTTATTTTATTAAAAATCAATTGTTAATATTTTAATTTTTAATA-TAATTTTTTAAATTTAAT
1 TTTTTATTTTATTAAAAATCAATAATTAATACATTAA-TTTCAACACAAATTTTTT-AATTTAAT
367974 TAAAATTTTA
64 TAAAATTTTA
*
367984 TTTTTATTTTATTAAAAATTAATAATTAATACATTAATTTCAACACAAATTTTTTAATTTAATTA
1 TTTTTATTTTATTAAAAATCAATAATTAATACATTAATTTCAACACAAATTTTTTAATTTAATTA
368049 AA
66 AA
368051 TCTTAATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
73 18 0.31
74 40 0.69
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.54
Consensus pattern (73 bp):
TTTTTATTTTATTAAAAATCAATAATTAATACATTAATTTCAACACAAATTTTTTAATTTAATTA
AAATTTTA
Done.