Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold114
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: 3219552
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 36736 characters in sequence are not A, C, G, or T
File 2 of 13
Found at i:289567 original size:2 final size:2
Alignment explanation
Indices: 289560--289609 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
289550 GATATTAATG
289560 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
289602 CT CT CT CT
1 CT CT CT CT
289610 TTGACTTCAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:292634 original size:26 final size:25
Alignment explanation
Indices: 292604--292654 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
292594 TATTTAAATA
* *
292604 TAATAAATTACTTTAATTTTTTTTTT
1 TAATAAATTA-ATCAATTTTTTTTTT
*
292630 TAATATATTAATCAATTTTTTTTTT
1 TAATAAATTAATCAATTTTTTTTTT
292655 ACTTATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (25 bp):
TAATAAATTAATCAATTTTTTTTTT
Found at i:298700 original size:80 final size:80
Alignment explanation
Indices: 298591--298744 Score: 281
Period size: 80 Copynumber: 1.9 Consensus size: 80
298581 TGGTGGGTCA
*
298591 ACAGCATTGGATCACAACCACCACTTTGATTTGAATGCTAGCAATAATTAAGCTAGCCCCACTCC
1 ACAGCATTGGATCACAACCACCACTTTGATTTGAATACTAGCAATAATTAAGCTAGCCCCACTCC
298656 GTTCTAGCAACCACC
66 GTTCTAGCAACCACC
**
298671 ACAGCATTGGATCACAACCACCACTTTGATTTGAATACTAGCAATAATTAAGCTAGCCCCTGTCC
1 ACAGCATTGGATCACAACCACCACTTTGATTTGAATACTAGCAATAATTAAGCTAGCCCCACTCC
298736 GTTCTAGCA
66 GTTCTAGCA
298745 TAATAGGCTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.25
Consensus pattern (80 bp):
ACAGCATTGGATCACAACCACCACTTTGATTTGAATACTAGCAATAATTAAGCTAGCCCCACTCC
GTTCTAGCAACCACC
Found at i:304727 original size:11 final size:11
Alignment explanation
Indices: 304707--304747 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
304697 AATTTCTAGA
304707 TTTA-TATATT
1 TTTATTATATT
304717 TTTATTATATT
1 TTTATTATATT
* *
304728 TATATTATTTT
1 TTTATTATATT
304739 TTTATTATA
1 TTTATTATA
304748 ATTATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 4 0.15
11 22 0.85
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATTATATT
Found at i:304730 original size:19 final size:19
Alignment explanation
Indices: 304706--304756 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
304696 AAATTTCTAG
304706 ATTTATA-TATTTTTATTAT
1 ATTTATATTATTTTT-TTAT
304725 ATTTATATTATTTTTTTAT
1 ATTTATATTATTTTTTTAT
*
304744 -TATA-ATTATTTTT
1 ATTTATATTATTTTT
304757 AAGACGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 9 0.30
18 3 0.10
19 11 0.37
20 7 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTATATTATTTTTTTAT
Found at i:304744 original size:17 final size:18
Alignment explanation
Indices: 304706--304756 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
304696 AAATTTCTAG
304706 ATTTATA-TATTTTTATTAT
1 ATTTATATTA-TTTT-TTAT
304725 ATTTATATTATTTTTT-T
1 ATTTATATTATTTTTTAT
304742 A-TTATAATTATTTTT
1 ATTTAT-ATTATTTTT
304757 AAGACGTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.13
17 11 0.37
18 2 0.07
19 11 0.37
20 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATATTATTTTTTAT
Found at i:304848 original size:28 final size:29
Alignment explanation
Indices: 304803--304867 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
304793 TAATATAATA
**
304803 ATTTAT-TCATATTTTA-TTTATATTATTT
1 ATTTATATCATATCATATTTTA-ATTATTT
304831 -TTTATATCATATCATATTTTAATTATTT
1 ATTTATATCATATCATATTTTAATTATTT
304859 ATTTATATC
1 ATTTATATC
304868 TCATTTGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 5 0.16
28 15 0.47
29 12 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (29 bp):
ATTTATATCATATCATATTTTAATTATTT
Found at i:305865 original size:2 final size:2
Alignment explanation
Indices: 305860--305898 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
305850 AAAAATTATC
*
305860 AT AT AT AT CAT AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
305899 TGCTGGGAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:308221 original size:15 final size:16
Alignment explanation
Indices: 308187--308224 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
308177 AATTTACCTA
*
308187 TTTATATTATTTTATAT
1 TTTA-ATTATTTAATAT
308204 TTTAATTATTTAAT-T
1 TTTAATTATTTAATAT
308219 TTTAAT
1 TTTAAT
308225 ATCAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 9 0.45
17 4 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTAATTATTTAATAT
Found at i:308704 original size:2 final size:2
Alignment explanation
Indices: 308697--308727 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
308687 AAAGAAGACG
308697 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 G
308728 GCGGCAAAGT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:311047 original size:21 final size:21
Alignment explanation
Indices: 311021--311088 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
311011 AAATACTTCA
*
311021 TAAAATAAAATTTATAAAATT
1 TAAAATAAAATTAATAAAATT
* **
311042 TAAAAT-TAATTAATAATTTT
1 TAAAATAAAATTAATAAAATT
*
311062 TTAAATAAAA-TAATATAAATT
1 TAAAATAAAATTAATA-AAATT
311083 TAAAAT
1 TAAAAT
311089 TAACCCATTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAATAAAATTAATAAAATT
Found at i:317799 original size:18 final size:18
Alignment explanation
Indices: 317778--317815 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
317768 AAATTTATAC
317778 AATTTTAATTACTTATTA
1 AATTTTAATTACTTATTA
317796 AATTTTAATTACTTATTA
1 AATTTTAATTACTTATTA
317814 AA
1 AA
317816 ACCACCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTTAATTACTTATTA
Found at i:324282 original size:2 final size:2
Alignment explanation
Indices: 324275--324307 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
324265 AGAAAGTAAC
324275 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
324308 ACGACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:326543 original size:13 final size:13
Alignment explanation
Indices: 326522--326563 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
326512 TAAATATATT
*
326522 ATTTTATTTTATA
1 ATTTAATTTTATA
*
326535 ATTTAATTTTTTTA
1 ATTTAA-TTTTATA
326549 A-TTAATTTTATA
1 ATTTAATTTTATA
326561 ATT
1 ATT
326564 ATGTTGGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 7 0.29
13 10 0.42
14 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTAATTTTATA
Found at i:327821 original size:3 final size:3
Alignment explanation
Indices: 327813--327847 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
327803 TATATGGCAG
327813 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
327848 ACACTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:327993 original size:2 final size:2
Alignment explanation
Indices: 327986--328021 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
327976 ATTCAATCAT
327986 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
328022 AGCCATGAAT
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):
TA
Found at i:328214 original size:2 final size:2
Alignment explanation
Indices: 328207--328234 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
328197 GCAAAACTTA
328207 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
328235 ATATATATAT
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:329400 original size:3 final size:3
Alignment explanation
Indices: 329392--329426 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
329382 CTTTGTTCCA
329392 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
329427 AAGCGTACTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:332016 original size:15 final size:15
Alignment explanation
Indices: 331980--332027 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
331970 TGTATATATC
* *
331980 TATAAATTAATTTTA
1 TATAAATTAATATAA
*
331995 TAAAAATTAATATAA
1 TATAAATTAATATAA
*
332010 TATAAA-TAAAATAA
1 TATAAATTAATATAA
332024 TATA
1 TATA
332028 TTTATAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATAAATTAATATAA
Found at i:332036 original size:19 final size:19
Alignment explanation
Indices: 331991--332037 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
331981 ATAAATTAAT
*
331991 TTTATAA-AAATTAATATA
1 TTTATAATAAAATAATATA
*
332009 -ATATAAATAAAATAATATA
1 TTTAT-AATAAAATAATATA
332028 TTTATAATAA
1 TTTATAATAA
332038 TATTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
17 3 0.13
18 2 0.09
19 15 0.65
20 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTATAATAAAATAATATA
Found at i:332982 original size:21 final size:20
Alignment explanation
Indices: 332944--332989 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
332934 TTTTTCTTTG
*
332944 TAAAATTTTTTATATAAATA
1 TAAAATTTTTTATATAAAAA
* *
332964 TAAATTTTATTTATTTAAAAA
1 TAAAATTT-TTTATATAAAAA
332985 TAAAA
1 TAAAA
332990 AAATAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAATTTTTTATATAAAAA
Found at i:337281 original size:22 final size:20
Alignment explanation
Indices: 337247--337302 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
337237 TTAAAATTTT
337247 TTTATATATAAA-TAAATATA
1 TTTATATATAAATTAAA-ATA
337267 TTTATATAATAAAATTAAAATA
1 TTTATAT-AT-AAATTAAAATA
* *
337289 -TGATACATAAATTA
1 TTTATATATAAATTA
337303 TAAAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 6 0.19
20 9 0.29
21 6 0.19
22 6 0.19
23 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
TTTATATATAAATTAAAATA
Found at i:338607 original size:17 final size:19
Alignment explanation
Indices: 338585--338620 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
338575 TCATAACATC
338585 ATATAAA-TA-TAAATATA
1 ATATAAATTATTAAATATA
338602 ATATAAATTATTAAATATA
1 ATATAAATTATTAAATATA
338621 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAATTATTAAATATA
Found at i:338635 original size:18 final size:18
Alignment explanation
Indices: 338589--338637 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
338579 AACATCATAT
* *
338589 AAATATAAATATAATATA
1 AAATTTAAATATAATAAA
* *
338607 AATTATTAAATATATTAAA
1 AAAT-TTAAATATAATAAA
338626 AAATTTAAATAT
1 AAATTTAAATAT
338638 TTATTATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTTAAATATAATAAA
Found at i:338657 original size:15 final size:14
Alignment explanation
Indices: 338634--338707 Score: 53
Period size: 15 Copynumber: 5.1 Consensus size: 14
338624 AAAAATTTAA
*
338634 ATATTTATTATATAT
1 ATATATATTATAT-T
*
338649 ATATATATTAAATGT
1 ATATATATTATAT-T
* *
338664 ATCTATCTTAT-TT
1 ATATATATTATATT
*
338677 AT-TATATTATTTTT
1 ATATATATTA-TATT
338691 ATATATATTATAATT
1 ATATATATTAT-ATT
338706 AT
1 AT
338708 CTTGTCCTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
12 6 0.13
13 4 0.09
14 6 0.13
15 31 0.66
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (14 bp):
ATATATATTATATT
Found at i:339388 original size:11 final size:11
Alignment explanation
Indices: 339374--339467 Score: 56
Period size: 11 Copynumber: 8.8 Consensus size: 11
339364 ACATAATATG
339374 ATAATA-AAACT
1 ATAATATAAA-T
339385 ATAATATAAAT
1 ATAATATAAAT
*
339396 ATAATATGAAT
1 ATAATATAAAT
*
339407 ATAATA-ATAT
1 ATAATATAAAT
**
339417 ATTAATATTTAT
1 A-TAATATAAAT
*
339429 ATAAAATAAAT
1 ATAATATAAAT
*
339440 -T-ATTTAAA-
1 ATAATATAAAT
*
339448 ATTTATATAAAT
1 A-TAATATAAAT
339460 AT-ATATAA
1 ATAATATAA
339468 TATCTTAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
9 5 0.08
10 11 0.17
11 42 0.64
12 8 0.12
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:339409 original size:22 final size:23
Alignment explanation
Indices: 339384--339439 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
339374 ATAATAAAAC
339384 TATAATATAAATA-TAATATGAA
1 TATAATATAAATATTAATATGAA
* **
339406 TATAATA-ATATATTAATATTTA
1 TATAATATAAATATTAATATGAA
*
339428 TATAAAATAAAT
1 TATAATATAAAT
339440 TATTTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 4 0.15
22 20 0.74
23 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TATAATATAAATATTAATATGAA
Found at i:343428 original size:17 final size:17
Alignment explanation
Indices: 343386--343436 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
343376 TTTATCAATT
*
343386 TATTTAGATAAATTTT-
1 TATTTAAATAAATTTTA
**
343402 TAAATAAATAAATTTTA
1 TATTTAAATAAATTTTA
343419 TATTTAAATAAAATTTTA
1 TATTTAAAT-AAATTTTA
343437 ACTATTAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 13 0.46
17 7 0.25
18 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TATTTAAATAAATTTTA
Found at i:343473 original size:29 final size:29
Alignment explanation
Indices: 343415--343487 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
343405 ATAAATAAAT
343415 TTTATATTTAAATAAAATTTTAACTATTAA
1 TTTATATTTAAAT-AAATTTTAACTATTAA
* * *
343445 TTTATTTTTAAATAAATTATTTA-TTTTAA
1 TTTATATTTAAATAAATT-TTAACTATTAA
*
343474 TTTATATTCAAATA
1 TTTATATTTAAATA
343488 TCAACTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTATATTTAAATAAATTTTAACTATTAA
Found at i:345553 original size:3 final size:3
Alignment explanation
Indices: 345545--345576 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
345535 CGTTAACTAT
*
345545 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
345577 TAAATCTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:355429 original size:14 final size:14
Alignment explanation
Indices: 355410--355440 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
355400 CTTCAAAACT
*
355410 TTTATTCTTTTATA
1 TTTATTATTTTATA
355424 TTTATTATTTTATA
1 TTTATTATTTTATA
355438 TTT
1 TTT
355441 TAACAACCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTATTTTATA
Found at i:355905 original size:25 final size:23
Alignment explanation
Indices: 355853--355920 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 23
355843 TGATTTGCTA
355853 AAAAAAAT-TAGA-TTAAAAAAAT
1 AAAAAAATAT-GATTTAAAAAAAT
*
355875 AAAAAAA-GTGTATTTAAAAAGAAT
1 AAAAAAATATG-ATTTAAAAA-AAT
*
355899 ATTAAAAATATGATTTAAAAAA
1 A-AAAAAATATGATTTAAAAAA
355921 TTTTAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 1 0.03
22 9 0.24
23 7 0.18
24 5 0.13
25 14 0.37
26 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAAAAATATGATTTAAAAAAAT
Found at i:359892 original size:15 final size:15
Alignment explanation
Indices: 359864--359908 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
359854 TTTTGTTTTG
359864 AAAATAATAG-TATTT
1 AAAA-AATAGATATTT
359879 AAAAAATAGATATTT
1 AAAAAATAGATATTT
359894 AAAAAATAGATATTT
1 AAAAAATAGATATTT
359909 TTACACTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (15 bp):
AAAAAATAGATATTT
Found at i:360465 original size:3 final size:3
Alignment explanation
Indices: 360457--360501 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
360447 AAATCTCCAT
360457 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
360502 TTGCTATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:360996 original size:22 final size:21
Alignment explanation
Indices: 360971--361012 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
360961 ATTTTAAAAA
360971 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
360991 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
361012 A
1 A
361013 AATTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:361315 original size:36 final size:36
Alignment explanation
Indices: 361273--361347 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
361263 AAATGAAAAG
*
361273 TATAAATATTTAATATACAATCTAATTATTTTTTAT
1 TATAAATATTTAACATACAATCTAATTATTTTTTAT
361309 TATAAATATTTAACATACAATCTAATTATTTTTTAT
1 TATAAATATTTAACATACAATCTAATTATTTTTTAT
361345 TAT
1 TAT
361348 TTTGTTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (36 bp):
TATAAATATTTAACATACAATCTAATTATTTTTTAT
Found at i:361738 original size:18 final size:19
Alignment explanation
Indices: 361717--361762 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
361707 CAATAACTTG
*
361717 AAAATATTTG-AATATTTT
1 AAAATATATGTAATATTTT
*
361735 AAAATATATGTAGTATTTT
1 AAAATATATGTAATATTTT
361754 AAAATATAT
1 AAAATATAT
361763 ATATAATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (19 bp):
AAAATATATGTAATATTTT
Found at i:363478 original size:2 final size:2
Alignment explanation
Indices: 363471--363509 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
363461 ATCCCTTTCT
363471 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
363510 CTCAAGGATT
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:368011 original size:6 final size:6
Alignment explanation
Indices: 368000--368040 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
367990 CTGTTGCAGT
*
368000 GGCTGA GGCTGA GGCTGA GGCTGA GGCTGA GGCTGT GGCTG
1 GGCTGA GGCTGA GGCTGA GGCTGA GGCTGA GGCTGA GGCTG
368041 CTGCTGCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.12, C:0.17, G:0.51, T:0.20
Consensus pattern (6 bp):
GGCTGA
Found at i:368969 original size:28 final size:28
Alignment explanation
Indices: 368924--368980 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
368914 AAGCTAACTG
*
368924 ATATGTAAGCCCCAGTAGAGGAAGATTT
1 ATATGTAAACCCCAGTAGAGGAAGATTT
*
368952 ATATGTAAACCCTC-GTAGAGGAGGATTT
1 ATATGTAAACCC-CAGTAGAGGAAGATTT
368980 A
1 A
368981 GGCAGCCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (28 bp):
ATATGTAAACCCCAGTAGAGGAAGATTT
Found at i:372881 original size:11 final size:11
Alignment explanation
Indices: 372862--372900 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
372852 ACCAGAGAGA
372862 CAAAGCCAAAG
1 CAAAGCCAAAG
*
372873 CAAAACCAAAG
1 CAAAGCCAAAG
* *
372884 CCAAGCAAAAG
1 CAAAGCCAAAG
372895 CAAAGC
1 CAAAGC
372901 AAAAAACAGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.56, C:0.28, G:0.15, T:0.00
Consensus pattern (11 bp):
CAAAGCCAAAG
Found at i:372891 original size:16 final size:17
Alignment explanation
Indices: 372862--372900 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
372852 ACCAGAGAGA
372862 CAAAGCCAAAGCAAAAC
1 CAAAGCCAAAGCAAAAC
*
372879 CAAAGCC-AAGCAAAAG
1 CAAAGCCAAAGCAAAAC
372895 CAAAGC
1 CAAAGC
372901 AAAAAACAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.56, C:0.28, G:0.15, T:0.00
Consensus pattern (17 bp):
CAAAGCCAAAGCAAAAC
Found at i:375444 original size:16 final size:17
Alignment explanation
Indices: 375414--375447 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
375404 TAAAAGTTTA
*
375414 ATAAAAATATATTAAAT
1 ATAAAAAAATATTAAAT
375431 ATAAAAAAAT-TTAAAT
1 ATAAAAAAATATTAAAT
375447 A
1 A
375448 GTTATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAAATATTAAAT
Found at i:376638 original size:80 final size:76
Alignment explanation
Indices: 376479--376643 Score: 188
Period size: 80 Copynumber: 2.1 Consensus size: 76
376469 CTTAATTTTT
* *
376479 TATTATATTTTATATATAATATAAATCAAATATATTCATATAATAATTTAAAATTATATAATACA
1 TATTATATATTAGATATAATATAAATCAAATATATTCATATAATAATTTAAAATTATATAATACA
** **
376544 TTTATTGTTCA
66 TAAATCATTCA
* * *
376555 TATTATATATTAGATATTATATAATATACAAATATATATTTATATAATAATTTAAAATTATGTAA
1 TATTATATATTAGATATAATATAA-AT-C-AA-ATATATTCATATAATAATTTAAAATTATATAA
*
376620 TATC-TAAATCATTTA
62 TA-CATAAATCATTCA
376635 TATTATATA
1 TATTATATA
376644 ATATATAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
76 21 0.28
77 2 0.03
78 1 0.01
79 2 0.03
80 47 0.64
81 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (76 bp):
TATTATATATTAGATATAATATAAATCAAATATATTCATATAATAATTTAAAATTATATAATACA
TAAATCATTCA
Found at i:376750 original size:24 final size:25
Alignment explanation
Indices: 376723--376774 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
376713 AAACTTTATT
376723 AAATTAATCAAAATA-TTTAATTTA
1 AAATTAATCAAAATATTTTAATTTA
** *
376747 AAATTAATTTAATTATTTTAATTTA
1 AAATTAATCAAAATATTTTAATTTA
376772 AAA
1 AAA
376775 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATTAATCAAAATATTTTAATTTA
Found at i:377694 original size:36 final size:38
Alignment explanation
Indices: 377612--377694 Score: 86
Period size: 36 Copynumber: 2.3 Consensus size: 38
377602 AAAATATTGG
*
377612 TATTTAATATTTATATTAATATATATTAAAATATTAAAA
1 TATTT-ATATTTATATTAAAATATATTAAAATATTAAAA
* *
377651 TA--AATATTTGTATTAAAATA-ATTAAAA-A-TAAATA
1 TATTTATATTTATATTAAAATATATTAAAATATTAAA-A
377685 TATTTATATT
1 TATTTATATT
377695 AAGTAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
33 4 0.11
34 4 0.11
35 7 0.19
36 20 0.54
39 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (38 bp):
TATTTATATTTATATTAAAATATATTAAAATATTAAAA
Found at i:377922 original size:2 final size:2
Alignment explanation
Indices: 377915--377951 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
377905 TACCAAATAG
377915 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
377952 GTAAAGTACA
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:382073 original size:2 final size:2
Alignment explanation
Indices: 382066--382096 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
382056 AAAGGAAATG
*
382066 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
382097 CATGTAGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:382364 original size:20 final size:21
Alignment explanation
Indices: 382341--382383 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
382331 TTAACTCCTT
*
382341 AAAAATAATAT-TAAAAAATA
1 AAAAATAATATAAAAAAAATA
* *
382361 AAAATTAATCTAAAAAAAATA
1 AAAAATAATATAAAAAAAATA
382382 AA
1 AA
382384 TTCATATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAATAATATAAAAAAAATA
Found at i:385677 original size:21 final size:22
Alignment explanation
Indices: 385637--385677 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
385627 AATTTTTAAT
*
385637 TTTATTTATAAAATTAAAAAAA
1 TTTATTGATAAAATTAAAAAAA
*
385659 TTTATTGATAATA-TAAAAA
1 TTTATTGATAAAATTAAAAA
385678 TTTAAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTATTGATAAAATTAAAAAAA
Found at i:395198 original size:3 final size:3
Alignment explanation
Indices: 395190--395252 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
395180 ATCCAAACCC
*
395190 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TT- TT- TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* *
395234 TTA TTA TTA CTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA T
395253 ATAAACTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 4 0.08
3 45 0.87
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:395621 original size:35 final size:34
Alignment explanation
Indices: 395578--395674 Score: 124
Period size: 35 Copynumber: 2.8 Consensus size: 34
395568 ATGGTAAATA
395578 AAAATTATTAAAAATATTTAAAATATAATATAAT
1 AAAATTATTAAAAATATTTAAAATATAATATAAT
*
395612 AAAATTTATTAAAAATATTTTAAAAT-TTATATAAT
1 AAAA-TTATTAAAAATA-TTTAAAATATAATATAAT
* * *
395647 ATAAATTATTTAAAATAATTATAATATA
1 A-AAATTATTAAAAATATTTAAAATATA
395675 TAAGGTGCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
34 10 0.19
35 33 0.61
36 11 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
AAAATTATTAAAAATATTTAAAATATAATATAAT
Found at i:396689 original size:5 final size:5
Alignment explanation
Indices: 396676--396719 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
396666 TCAATCTGGT
*
396676 TTTTT TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
396720 TTAGCTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:396838 original size:2 final size:2
Alignment explanation
Indices: 396833--396857 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
396823 GCATTTTTTA
396833 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
396858 TTTATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:402675 original size:2 final size:2
Alignment explanation
Indices: 402618--402657 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
402608 ACAAAATTCC
402618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
402658 GTGATCTGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:406065 original size:2 final size:2
Alignment explanation
Indices: 406058--406088 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
406048 TTCATTTTTG
406058 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
406089 TTTTTTTTTT
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:406271 original size:19 final size:19
Alignment explanation
Indices: 406237--406285 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
406227 TTTTTTTAAT
* *
406237 TTAAATATCAACTATTACA
1 TTAAATATAAAATATTACA
**
406256 TTAAATATAAAATATTATT
1 TTAAATATAAAATATTACA
406275 TTAAATA-AAAA
1 TTAAATATAAAA
406286 ACTTAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATATAAAATATTACA
Found at i:406493 original size:22 final size:22
Alignment explanation
Indices: 406462--406513 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
406452 ATTAATTTTT
406462 ATTT-AATTATT-ATTGAATCAA
1 ATTTAAATTATTAATTGAAT-AA
*
406483 ATTTAAATTATTAATTTAATAA
1 ATTTAAATTATTAATTGAATAA
406505 ATTATAAAT
1 ATT-TAAAT
406514 ATTTTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 4 0.15
22 12 0.44
23 11 0.41
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTAAATTATTAATTGAATAA
Found at i:408178 original size:33 final size:30
Alignment explanation
Indices: 408120--408188 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
408110 TTTTGAGATT
*
408120 TAATTTTTTATATTTTACATAAATTAAAAA
1 TAATTTTTTATATTTAACATAAATTAAAAA
*
408150 TAATTATTTTATATATTAACAATGAATTAAAAA
1 TAATT-TTTTATAT-TTAAC-ATAAATTAAAAA
408183 -AATTTT
1 TAATTTT
408189 ACTAACGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 5 0.15
31 10 0.29
32 8 0.24
33 11 0.32
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATTTTTTATATTTAACATAAATTAAAAA
Found at i:410311 original size:17 final size:17
Alignment explanation
Indices: 410289--410326 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
410279 TACAAATATA
410289 ATTACAT-ATTTATAAAT
1 ATTACATAATTTAT-AAT
410306 ATTACATAAATTTATAAT
1 ATTACAT-AATTTATAAT
410324 ATT
1 ATT
410327 TTAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTACATAATTTATAAT
Found at i:410469 original size:24 final size:24
Alignment explanation
Indices: 410401--410470 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 24
410391 AAATATACAT
410401 AAAATAAAATAAATTATTAATATGTCA
1 AAAATAAAA-AAA-TA-TAATATGTCA
* *
410428 AAAATATACAAAAATATAATATTTTA
1 AAAATA-A-AAAAATATAATATGTCA
410454 AAAATAAAAAAATATAA
1 AAAATAAAAAAATATAA
410471 ATACAAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 14 0.36
27 8 0.21
28 4 0.10
29 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (24 bp):
AAAATAAAAAAATATAATATGTCA
Found at i:410514 original size:4 final size:4
Alignment explanation
Indices: 410503--410537 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
410493 ATAATTTTTT
*
410503 TTTC -TTC TTTC TTTC TTTT TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
410538 CAACTACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:410521 original size:16 final size:16
Alignment explanation
Indices: 410502--410536 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
410492 AATAATTTTT
410502 TTTTCTTCTTTCTTTC
1 TTTTCTTCTTTCTTTC
*
410518 TTTTTTTCTTTCTTTC
1 TTTTCTTCTTTCTTTC
410534 TTT
1 TTT
410537 CCAACTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTCTTTCTTTC
Found at i:410677 original size:11 final size:11
Alignment explanation
Indices: 410633--410666 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
410623 ATATTATCAT
410633 TATAATAAAAA
1 TATAATAAAAA
*
410644 -ATAATTAAAA
1 TATAATAAAAA
410654 TATAATAAAAA
1 TATAATAAAAA
410665 TA
1 TA
410667 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:410750 original size:60 final size:58
Alignment explanation
Indices: 410645--410774 Score: 137
Period size: 58 Copynumber: 2.3 Consensus size: 58
410635 TAATAAAAAA
* *
410645 TAATTAAAATATAATAAAAATAAAAATATAATATTAAATACTTTAAAATTTATATAATAT
1 TAATTAAAATATAATAAAAATAAAAATATAATATAAAATACTTT-AAATAT-TATAATAT
* *
410705 TAATTATAAATAT-AT-AAAA-AAATATATAAATATAATAATATTTTAAATATTATAATAT
1 TAATTA-AAATATAATAAAAATAAAAATAT-AATATAA-AATACTTTAAATATTATAATAT
410763 T--TT-AAATATAAT
1 TAATTAAAATATAAT
410775 TATAATTTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
54 6 0.10
55 2 0.03
56 2 0.03
58 16 0.26
59 15 0.24
60 15 0.24
61 6 0.10
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (58 bp):
TAATTAAAATATAATAAAAATAAAAATATAATATAAAATACTTTAAATATTATAATAT
Found at i:410779 original size:58 final size:57
Alignment explanation
Indices: 410651--410779 Score: 124
Period size: 59 Copynumber: 2.2 Consensus size: 57
410641 AAAATAATTA
*
410651 AAATATAA-TA-AAAATAAAAATATAATATTAAATACTTTAAAATTTATATAATATT
1 AAATATAATTATAAAATAAAAATATAATATAAAATACTTTAAAATTTATATAATATT
* * * *
410706 AATTATAAATATATAAAA-AAATATATAAATATAATAATA-TTTTAAATATTATA-ATATTTT
1 AAATAT-AAT-TATAAAATAAAAATAT-AATATAA-AATACTTTAAAAT-TTATATA-ATATT
410766 AAATATAATTATAA
1 AAATATAATTATAA
410780 TTTGATAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
55 5 0.08
56 2 0.03
58 14 0.23
59 21 0.35
60 18 0.30
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (57 bp):
AAATATAATTATAAAATAAAAATATAATATAAAATACTTTAAAATTTATATAATATT
Found at i:410790 original size:20 final size:17
Alignment explanation
Indices: 410731--410774 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
410721 AAAAAATATA
410731 TAAATATAATAATATTT
1 TAAATATAATAATATTT
*
410748 TAAATATTATAATATTT
1 TAAATATAATAATATTT
410765 TAAATATAAT
1 TAAATATAAT
410775 TATAATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATATAATAATATTT
Found at i:412246 original size:21 final size:20
Alignment explanation
Indices: 412220--412271 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 20
412210 TATTTAAAAA
412220 TATAATATAAAAATAAATACG
1 TATAATATAAAAAT-AATACG
412241 TATAATAT--AAAT-ATACG
1 TATAATATAAAAATAATACG
412258 TAT-ATATAAAAATA
1 TATAATATAAAAATA
412272 TATATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.14
17 8 0.29
18 4 0.14
19 4 0.14
21 8 0.29
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (20 bp):
TATAATATAAAAATAATACG
Found at i:412256 original size:17 final size:18
Alignment explanation
Indices: 412224--412273 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
412214 TAAAAATATA
412224 ATATAAAAATAAATACGTAT
1 ATATAAAAAT--ATACGTAT
*
412244 A-ATATAAATATACGTAT
1 ATATAAAAATATACGTAT
412261 ATATAAAAATATA
1 ATATAAAAATATA
412274 TATTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 9 0.33
18 10 0.37
19 7 0.26
20 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (18 bp):
ATATAAAAATATACGTAT
Found at i:412389 original size:8 final size:7
Alignment explanation
Indices: 412370--412435 Score: 60
Period size: 8 Copynumber: 8.7 Consensus size: 7
412360 AATTTTTCTC
*
412370 TCTTCTT
1 TCTTTTT
412377 TCTTTTAT
1 TCTTTT-T
412385 TCTTTTT
1 TCTTTTT
412392 TCTTCTTT
1 TCTT-TTT
412400 TCTCTTTT
1 TCT-TTTT
**
412408 CTCTCCTT
1 -TCTTTTT
412416 TCTTTTT
1 TCTTTTT
412423 TCTTTCTT
1 TCTTT-TT
412431 TCTTT
1 TCTTT
412436 GTCAGCTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
7 20 0.41
8 25 0.51
9 4 0.08
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (7 bp):
TCTTTTT
Found at i:412393 original size:15 final size:14
Alignment explanation
Indices: 412370--412435 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 14
412360 AATTTTTCTC
*
412370 TCTTCTTTCTTTTAT
1 TCTTTTTTCTTTT-T
412385 TCTTTTTTCTTCTTT
1 TCTTTTTTCTT-TTT
**
412400 TCTCTTTTCTCTCCTT
1 TCT-TTTT-TCTTTTT
412416 TCTTTTTTCTTTCTT
1 TCTTTTTTCTTT-TT
412431 TCTTT
1 TCTTT
412436 GTCAGCTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 3 0.07
15 25 0.60
16 11 0.26
17 3 0.07
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (14 bp):
TCTTTTTTCTTTTT
Found at i:412417 original size:16 final size:15
Alignment explanation
Indices: 412384--412435 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
412374 CTTTCTTTTA
*
412384 TTCTTTTTTCTTCTT
1 TTCTTTTTTCTTCCT
*
412399 TTCTCTTTTCTCTCCT
1 TTCTTTTTTCT-TCCT
*
412415 TTCTTTTTTCTTTCT
1 TTCTTTTTTCTTCCT
412430 TTCTTT
1 TTCTTT
412436 GTCAGCTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TTCTTTTTTCTTCCT
Found at i:421786 original size:16 final size:16
Alignment explanation
Indices: 421765--421807 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
421755 CGTAATTAAT
421765 TATTTTTAAAATATTA
1 TATTTTTAAAATATTA
*
421781 TATTTTTATTAA-ATTA
1 TATTTTTA-AAATATTA
421797 T-TTTTTAAAAT
1 TATTTTTAAAAT
421808 TTAAAATGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 2 0.09
15 6 0.26
16 13 0.57
17 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTTAAAATATTA
Found at i:422010 original size:15 final size:15
Alignment explanation
Indices: 421971--422010 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
421961 TTTATGAAAT
*
421971 TAAAAAATAATTATAA
1 TAAAAAAT-ATTAAAA
421987 -AAAAAATATTAAAA
1 TAAAAAATATTAAAA
422001 TAAAAAATAT
1 TAAAAAATAT
422011 AGATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAAAAATATTAAAA
Found at i:422088 original size:21 final size:22
Alignment explanation
Indices: 422047--422091 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
422037 AAAATATATA
422047 AAAATTATTAATAATTTAAAAT
1 AAAATTATTAATAATTTAAAAT
*
422069 AAAATATATT-ATAATTAAAAAT
1 AAAAT-TATTAATAATTTAAAAT
422091 A
1 A
422092 TTGATAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATTATTAATAATTTAAAAT
Found at i:422337 original size:24 final size:24
Alignment explanation
Indices: 422309--422392 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 24
422299 AATTTTTTTT
422309 AATTTTATTATTTTATTTAATTAA
1 AATTTTATTATTTTATTTAATTAA
*
422333 AATTTTA-TATTTTTATTATATTTAAA
1 AATTTTATTA-TTTTATT-TAATT-AA
* * *
422359 TAAATTAATAATTTTAATTTATATTAA
1 -AATTTTATTATTTT-ATTTA-ATTAA
422386 AATTTTA
1 AATTTTA
422393 ATTTATATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
23 2 0.04
24 14 0.30
25 4 0.09
26 7 0.15
27 13 0.28
28 6 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTTTATTATTTTATTTAATTAA
Found at i:422355 original size:34 final size:34
Alignment explanation
Indices: 422317--422418 Score: 89
Period size: 34 Copynumber: 2.9 Consensus size: 34
422307 TTAATTTTAT
422317 TATTTTATTTAATTAAAATTTTATATTTTTATT-A
1 TATTTTATTTAATTAAAATTTTA-ATTTTTATTAA
* * * *
422351 TATTTAAATAAATTAATAATTTTAATTTATATTAA
1 TATTTTATTTAATTAA-AATTTTAATTTTTATTAA
* **
422386 AATTTTAATTTATATTAATTTTTTAAATTTTTA
1 TATTTT-ATTTA-ATTAAAATTTT-AATTTTTA
422419 ATTTGTATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
34 21 0.40
35 12 0.23
36 7 0.13
37 12 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATTTTATTTAATTAAAATTTTAATTTTTATTAA
Found at i:422411 original size:18 final size:18
Alignment explanation
Indices: 422318--422403 Score: 83
Period size: 18 Copynumber: 4.9 Consensus size: 18
422308 TAATTTTATT
422318 ATTTT-ATTTA-ATTAAA
1 ATTTTAATTTATATTAAA
* *
422334 ATTTTATATTTTTATT-AT
1 ATTTTA-ATTTATATTAAA
* *
422352 A-TTTAA-ATAAATTAATA
1 ATTTTAATTTATATTAA-A
422369 ATTTTAATTTATATTAAA
1 ATTTTAATTTATATTAAA
422387 ATTTTAATTTATATTAA
1 ATTTTAATTTATATTAA
422404 TTTTTTAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 4 0.07
16 7 0.13
17 5 0.09
18 29 0.53
19 10 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATTTATATTAAA
Found at i:422417 original size:26 final size:26
Alignment explanation
Indices: 422372--422453 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
422362 ATTAATAATT
*
422372 TTAATTTATATTAAAATTTTAATTTATA
1 TTAATTT-T-TTAAATTTTTAATTTATA
*
422400 TTAATTTTTTAAATTTTTAATTTGTA
1 TTAATTTTTTAAATTTTTAATTTATA
* *
422426 TTTAA-GTTTTCAATTTTTAATTTATA
1 -TTAATTTTTTAAATTTTTAATTTATA
422452 TT
1 TT
422454 TAATATAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
25 2 0.04
26 34 0.71
27 5 0.10
28 7 0.15
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (26 bp):
TTAATTTTTTAAATTTTTAATTTATA
Found at i:422454 original size:26 final size:27
Alignment explanation
Indices: 422382--422457 Score: 102
Period size: 26 Copynumber: 2.9 Consensus size: 27
422372 TTAATTTATA
* *
422382 TTAAAATTTTAATTTATA-TTAATTTT
1 TTAAATTTTTAATTTATATTTAATGTT
*
422408 TTAAATTTTTAATTTGTATTTAA-GTT
1 TTAAATTTTTAATTTATATTTAATGTT
*
422434 TTCAATTTTTAATTTATATTTAAT
1 TTAAATTTTTAATTTATATTTAAT
422458 ATAAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 39 0.91
27 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (27 bp):
TTAAATTTTTAATTTATATTTAATGTT
Found at i:422495 original size:23 final size:23
Alignment explanation
Indices: 422445--422496 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
422435 TCAATTTTTA
422445 ATTTATATTTAATATAAATAAAAT
1 ATTTA-ATTTAATATAAATAAAAT
*
422469 -TTTAATTTAAATATAAA-AATAT
1 ATTTAATTT-AATATAAATAAAAT
422491 ATTTAA
1 ATTTAA
422497 ATAAAGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTTAATATAAATAAAAT
Found at i:426504 original size:33 final size:32
Alignment explanation
Indices: 426461--426522 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
426451 TGAAACCAGT
426461 TTTTCCCTACTAATGAAAGTGGTTCCTGTCAG
1 TTTTCCCTACTAATGAAAGTGGTTCCTGTCAG
*
426493 TTTTCCACTACTACTGAAAGTGGTTCCTGT
1 TTTTCC-CTACTAATGAAAGTGGTTCCTGT
426523 TTTTCTGCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (32 bp):
TTTTCCCTACTAATGAAAGTGGTTCCTGTCAG
Found at i:427940 original size:21 final size:21
Alignment explanation
Indices: 427915--427956 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
427905 GTAAAGCGTT
427915 TTTTAGATTTTCATGAACGTG
1 TTTTAGATTTTCATGAACGTG
427936 TTTTAGATTTTCATGAACGTG
1 TTTTAGATTTTCATGAACGTG
427957 GGCAGGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.48
Consensus pattern (21 bp):
TTTTAGATTTTCATGAACGTG
Found at i:429379 original size:15 final size:15
Alignment explanation
Indices: 429359--429389 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
429349 GCATGATTTC
429359 TGTTTATTCCCTTTG
1 TGTTTATTCCCTTTG
429374 TGTTTATTCCCTTTG
1 TGTTTATTCCCTTTG
429389 T
1 T
429390 TAATCTGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.13, T:0.61
Consensus pattern (15 bp):
TGTTTATTCCCTTTG
Found at i:433963 original size:3 final size:3
Alignment explanation
Indices: 433955--433984 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
433945 AACTTGTCTA
433955 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
433985 AAAAGGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:441307 original size:31 final size:31
Alignment explanation
Indices: 441272--441330 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
441262 ATTTTACTGG
*
441272 CTTCTGACCAATTAAGTCTGTTTATAAACGA
1 CTTCTGACCAATTAAGTCGGTTTATAAACGA
*
441303 CTTCTGATCAATTAAGTCGGTTTATAAA
1 CTTCTGACCAATTAAGTCGGTTTATAAA
441331 ATTTATCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (31 bp):
CTTCTGACCAATTAAGTCGGTTTATAAACGA
Found at i:441717 original size:16 final size:17
Alignment explanation
Indices: 441691--441734 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
441681 TAGTACTCTC
441691 TTTTCTCCTTTCA-ATTT
1 TTTTCT-CTTTCACATTT
*
441708 TTTTCTCTTTTACATTT
1 TTTTCTCTTTCACATTT
*
441725 TTTCCTCTTT
1 TTTTCTCTTT
441735 TGCTGAAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTCTCTTTCACATTT
Found at i:448335 original size:2 final size:2
Alignment explanation
Indices: 448316--448352 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
448306 ACTTGCTTTG
* *
448316 TA TA TG TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
448353 TATGTTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:451981 original size:16 final size:16
Alignment explanation
Indices: 451960--451991 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
451950 AGTATTATTT
451960 TTAATATACTTGTGAA
1 TTAATATACTTGTGAA
451976 TTAATATACTTGTGAA
1 TTAATATACTTGTGAA
451992 GCTTGAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
TTAATATACTTGTGAA
Found at i:453665 original size:28 final size:28
Alignment explanation
Indices: 453634--453726 Score: 100
Period size: 28 Copynumber: 3.3 Consensus size: 28
453624 TTATTATATG
453634 TAAATAAATTAATAATTTTAA-TTGATAT
1 TAAATAAATTAATAATTTTAATTTG-TAT
**
453662 TAAATAAATTTTTAATTTTTAATTTGTAT
1 TAAATAAATTAATAA-TTTTAATTTGTAT
***
453691 TAAATTTTTTAA-AATTTTAATTTGTAT
1 TAAATAAATTAATAATTTTAATTTGTAT
453718 TAAAATAAA
1 T-AAATAAA
453727 ATTTTTATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
27 14 0.27
28 19 0.37
29 16 0.31
30 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
TAAATAAATTAATAATTTTAATTTGTAT
Found at i:453682 original size:29 final size:29
Alignment explanation
Indices: 453613--453764 Score: 117
Period size: 29 Copynumber: 5.3 Consensus size: 29
453603 CAGAATTAAG
453613 TTTTTATATTTTT-ATT-ATATGTAAATAAA
1 TTTTTA-ATTTTTAATTGATAT-TAAATAAA
**
453642 TTAATAA-TTTTAATTGATATTAAATAAA
1 TTTTTAATTTTTAATTGATATTAAATAAA
453670 TTTTTAATTTTTAATTTG-TATTAAAT---
1 TTTTTAATTTTTAA-TTGATATTAAATAAA
*
453696 TTTTTAAAATTTTAATTTG-TATTAAAATAAAA
1 TTTTT-AATTTTTAA-TTGATATT-AAAT-AAA
*
453728 TTTTT-ATTTTTTATAT-ATATTTAAATAAA
1 TTTTTAATTTTTAAT-TGATA-TTAAATAAA
453757 TTTTTAAT
1 TTTTTAAT
453765 ATGAATAAAA
Statistics
Matches: 102, Mismatches: 7, Indels: 27
0.75 0.05 0.20
Matches are distributed among these distances:
26 5 0.05
27 20 0.20
28 21 0.21
29 31 0.30
30 18 0.18
31 2 0.02
32 5 0.05
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
TTTTTAATTTTTAATTGATATTAAATAAA
Found at i:453695 original size:57 final size:57
Alignment explanation
Indices: 453613--453758 Score: 156
Period size: 57 Copynumber: 2.5 Consensus size: 57
453603 CAGAATTAAG
453613 TTTTTATATTTTTA-TTATATGTAAATAAATTAATAATTTTAA-TTGATATT-AAAT-AAA
1 TTTTTA-ATTTTTATTTATAT-TAAATAAATTAA-AATTTTAATTTG-TATTAAAATAAAA
* ***
453670 TTTTTAATTTTTAATTTGTATTAAATTTTTTAAAATTTTAATTTGTATTAAAATAAAA
1 TTTTTAATTTTT-ATTTATATTAAATAAATTAAAATTTTAATTTGTATTAAAATAAAA
* *
453728 TTTTTATTTTTTATATATATTTAAATAAATT
1 TTTTTAATTTTTATTTATA-TTAAATAAATT
453759 TTTAATATGA
Statistics
Matches: 73, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
56 18 0.25
57 28 0.38
58 27 0.37
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (57 bp):
TTTTTAATTTTTATTTATATTAAATAAATTAAAATTTTAATTTGTATTAAAATAAAA
Found at i:453708 original size:27 final size:28
Alignment explanation
Indices: 453642--453721 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 28
453632 TGTAAATAAA
453642 TTAATAATTTTAA-TTGATATTAAATAAATTT
1 TTAA-AATTTTAATTTG-TATTAAAT--ATTT
*
453673 TT-AATTTTTAATTTGTATTAAAT-TTT
1 TTAAAATTTTAATTTGTATTAAATATTT
453699 TTAAAATTTTAATTTGTATTAAA
1 TTAAAATTTTAATTTGTATTAAA
453722 ATAAAATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
26 5 0.11
27 19 0.42
29 15 0.33
30 4 0.09
31 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
TTAAAATTTTAATTTGTATTAAATATTT
Found at i:453752 original size:58 final size:57
Alignment explanation
Indices: 453613--453758 Score: 156
Period size: 58 Copynumber: 2.5 Consensus size: 57
453603 CAGAATTAAG
*
453613 TTTTTATATTTTTAT-TATATGTAAATAAATTAATAATTTTAATTGATATTAAATAAA
1 TTTTTAT-TTTTTATATATATTTAAATAAATTAATAATTTTAATTGATATTAAATAAA
* * * ***
453670 TTTTTAATTTTTA-ATTTGTATTAAATTTTTTAA-AATTTTAATTTG-TATTAAAATAAAA
1 TTTTTATTTTTTATATATAT-TTAAATAAATTAATAATTTTAA-TTGATATT-AAAT-AAA
453728 TTTTTATTTTTTATATATATTTAAATAAATT
1 TTTTTATTTTTTATATATATTTAAATAAATT
453759 TTTAATATGA
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
56 21 0.30
57 22 0.31
58 23 0.33
59 4 0.06
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (57 bp):
TTTTTATTTTTTATATATATTTAAATAAATTAATAATTTTAATTGATATTAAATAAA
Found at i:453788 original size:17 final size:17
Alignment explanation
Indices: 453746--453791 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
453736 TTTTATATAT
*
453746 ATTTAAATAAATTTTTA
1 ATTTAAATAAAATTTTA
* *
453763 ATATGAATAAAATTTTA
1 ATTTAAATAAAATTTTA
453780 ATTTAAATAAAA
1 ATTTAAATAAAA
453792 AATATTTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTTAAATAAAATTTTA
Found at i:453800 original size:15 final size:16
Alignment explanation
Indices: 453780--453812 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
453770 TAAAATTTTA
453780 ATTTAAATAAAA-AAT
1 ATTTAAATAAAATAAT
453795 ATTTAAATAAAATAAT
1 ATTTAAATAAAATAAT
453811 AT
1 AT
453813 AATTAAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTAAATAAAATAAT
Found at i:453807 original size:20 final size:19
Alignment explanation
Indices: 453771--453809 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
453761 TAATATGAAT
* *
453771 AAAATTTTAATTTAAATAA
1 AAAATTTTAAATAAAATAA
453790 AAAATATTTAAATAAAATAA
1 AAAAT-TTTAAATAAAATAA
453810 TATAATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTTTAAATAAAATAA
Found at i:457313 original size:17 final size:16
Alignment explanation
Indices: 457289--457330 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
457279 CTCTCTGTAG
*
457289 TATATTTTTCTTTTTTT
1 TATATTTTT-TATTTTT
*
457306 TTTATTTTTTATTTTT
1 TATATTTTTTATTTTT
457322 TATATTTTT
1 TATATTTTT
457331 GAAGGGGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.83
Consensus pattern (16 bp):
TATATTTTTTATTTTT
Found at i:502712 original size:145 final size:145
Alignment explanation
Indices: 502449--502743 Score: 572
Period size: 145 Copynumber: 2.0 Consensus size: 145
502439 CAGTTTTCCA
*
502449 ATTTTTGAGCAATATATGGGTTTGATATATACTCCATTTTTTTATGTTTGTATGTTCAGCTGTTT
1 ATTTTTGAGCAATATATGGGTTTGATATATACTCCATTTTTTAATGTTTGTATGTTCAGCTGTTT
*
502514 ATTTAATGTAAAATAGATGATATCTCTGTAGTTTTTGCTATTGACATTATTCCATTGTTTTTGTG
66 ATTTAATGTAAAATAGATGATATCTCTGTAGTTTTTGCTATTGACATTATTCCAATGTTTTTGTG
502579 TTGATTACCTTCAAT
131 TTGATTACCTTCAAT
502594 ATTTTTGAGCAATATATGGGTTTGATATATACTCCATTTTTTAATGTTTGTATGTTCAGCTGTTT
1 ATTTTTGAGCAATATATGGGTTTGATATATACTCCATTTTTTAATGTTTGTATGTTCAGCTGTTT
502659 ATTTAATGTAAAATAGATGATATCTCTGTAGTTTTTGCTATTGACATTATTCCAATGTTTTTGTG
66 ATTTAATGTAAAATAGATGATATCTCTGTAGTTTTTGCTATTGACATTATTCCAATGTTTTTGTG
502724 TTGATTACCTTCAAT
131 TTGATTACCTTCAAT
502739 ATTTT
1 ATTTT
502744 CTGAAATATT
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 148 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (145 bp):
ATTTTTGAGCAATATATGGGTTTGATATATACTCCATTTTTTAATGTTTGTATGTTCAGCTGTTT
ATTTAATGTAAAATAGATGATATCTCTGTAGTTTTTGCTATTGACATTATTCCAATGTTTTTGTG
TTGATTACCTTCAAT
Found at i:505785 original size:34 final size:34
Alignment explanation
Indices: 505742--505814 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
505732 TTTGGTGAAG
505742 TTTCTCTGCTTAAAGTGAGTCATTCTGACTAATA
1 TTTCTCTGCTTAAAGTGAGTCATTCTGACTAATA
505776 TTTCTCTGCTTAAAGTGAGTCATTCTGACTAATA
1 TTTCTCTGCTTAAAGTGAGTCATTCTGACTAATA
505810 TTTCT
1 TTTCT
505815 ATCTCAAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (34 bp):
TTTCTCTGCTTAAAGTGAGTCATTCTGACTAATA
Found at i:509338 original size:16 final size:16
Alignment explanation
Indices: 509317--509347 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
509307 TGATAGAAAG
509317 GCAAGTTTCTATCATT
1 GCAAGTTTCTATCATT
*
509333 GCAAGTTTTTATCAT
1 GCAAGTTTCTATCAT
509348 ACAATGATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (16 bp):
GCAAGTTTCTATCATT
Found at i:512236 original size:11 final size:10
Alignment explanation
Indices: 512218--512250 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
512208 AACAAGTTGA
512218 TTTTTTGTTT
1 TTTTTTGTTT
512228 TTGTTTTGTTT
1 TT-TTTTGTTT
512239 TTTTTT-TTT
1 TTTTTTGTTT
512248 TTT
1 TTT
512251 AAGTTGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 6 0.27
11 10 0.45
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:516857 original size:11 final size:10
Alignment explanation
Indices: 516827--516864 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
516817 AATCAAATTG
516827 CAAAATTTTA
1 CAAAATTTTA
516837 CAAAATTTTA
1 CAAAATTTTA
*
516847 TAAATATTTTA
1 CAAA-ATTTTA
516858 CAAAATT
1 CAAAATT
516865 GCAGTACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
CAAAATTTTA
Found at i:520027 original size:342 final size:344
Alignment explanation
Indices: 519385--520027 Score: 1033
Period size: 353 Copynumber: 1.8 Consensus size: 344
519375 GATATGCAGG
* * *
519385 TTAGACCCCATATTGCTTAGCTTTTGCCTTTTGTGTTCTTACTTGTGTGTATTTTATTTTTATAG
1 TTAGAACCCATATTACTTAGCTTTTGCCTTTTGTGTTCTGACTTGTGTGTATTTTATTTTTATAG
*
519450 AGAACTTTTTTCTTAACAACTGGGTGTCGAAGGTAGGATACCAGAATGGAAACTGGTGGAGAAGT
66 AGAACTTTTTTCTTAACAACTGGGTGTCGAAGGTAGGATACCAGAAAGGAAACTGGTGGAGAAGT
* *
519515 TTTTTGATTCCAATCTTAATCAGTTGATTTCTTGTTTTTTTTTTTTTAATTTGAAAACCCAAATT
131 TTTTCGATTCCAACCTTAATCAGTTGA---------TTTTTTTTTTTAATTTGAAAACCCAAATT
* *
519580 ATTTAGAATAAGCAGGGCTGTCGCTTGATCTGGCAATGGTGTTCTAGATTTCCTTTTTTAATTTT
187 ATTTAGAATAAGCACGGCTGTCACTTGATCTGGCAATGGTGTTCTAGATTTCCTTTTTTAATTTT
519645 GAACTGTTTTGAAACTGGTGAAAATGTTCTTTGATTGACTTACTCCCTTTCTGCTTAGACTTCCT
252 GAACTGTTTTGAAACTGGTGAAAATGTTCTTTGATTGACTTACTCCCTTTCTGCTTAGACTTCCT
519710 CATCCACTCCATTTACCGGCCGGAGATA
317 CATCCACTCCATTTACCGGCCGGAGATA
*
519738 TTAGAACCCATATTACTTAGCTTTTGGCTTTTGTGTTCTGACTTGTGTGTATTTTATTTTTATAG
1 TTAGAACCCATATTACTTAGCTTTTGCCTTTTGTGTTCTGACTTGTGTGTATTTTATTTTTATAG
* *
519803 AGAACTTTTTTCTTAACAACTGGGTGTCGAAGGTAGGATACTAGAAAGGAAACTGTTGGA-AATG
66 AGAACTTTTTTCTTAACAACTGGGTGTCGAAGGTAGGATACCAGAAAGGAAACTGGTGGAGAA-G
**
519867 TTTTTCGATTCCTCCCTTAA-CAAGTTGA-TTTTTTTTTT-ATTTGAAAACCCAAATTATTTAGA
130 TTTTTCGATTCCAACCTTAATC-AGTTGATTTTTTTTTTTAATTTGAAAACCCAAATTATTTAGA
*
519929 ATAAGCACGGCTGTCACTTGATCTGGCCATGGTGTTCTAGATTTCCTTTTTTAATTTTGAACTGT
194 ATAAGCACGGCTGTCACTTGATCTGGCAATGGTGTTCTAGATTTCCTTTTTTAATTTTGAACTGT
519994 TTTGAAACTGGTGAAAATGTTCTTTGATTGACTT
259 TTTGAAACTGGTGAAAATGTTCTTTGATTGACTT
520028 TTTCCTTTCA
Statistics
Matches: 274, Mismatches: 14, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
342 120 0.44
343 10 0.04
352 3 0.01
353 141 0.51
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (344 bp):
TTAGAACCCATATTACTTAGCTTTTGCCTTTTGTGTTCTGACTTGTGTGTATTTTATTTTTATAG
AGAACTTTTTTCTTAACAACTGGGTGTCGAAGGTAGGATACCAGAAAGGAAACTGGTGGAGAAGT
TTTTCGATTCCAACCTTAATCAGTTGATTTTTTTTTTTAATTTGAAAACCCAAATTATTTAGAAT
AAGCACGGCTGTCACTTGATCTGGCAATGGTGTTCTAGATTTCCTTTTTTAATTTTGAACTGTTT
TGAAACTGGTGAAAATGTTCTTTGATTGACTTACTCCCTTTCTGCTTAGACTTCCTCATCCACTC
CATTTACCGGCCGGAGATA
Found at i:529340 original size:65 final size:65
Alignment explanation
Indices: 529232--529363 Score: 221
Period size: 65 Copynumber: 2.0 Consensus size: 65
529222 TTTTTAAAAA
* *
529232 TTTATTTGAAATAAAGCTTAAAAAAAAAGAAACCTTTTAATCTTAACCTTTTACCAAATTAAGTT
1 TTTATTTGAAATAAAACTTAAAAAAAAAGAAACCTTTTAATCTTAACCTTTTACCAAATTAAATT
*
529297 TTTATTTGAAATAAAAC-TAAAAAAAAAGGAAACCTTTTGATCTTAACCTTTTACCAAATTAAAT
1 TTTATTTGAAATAAAACTTAAAAAAAAA-GAAACCTTTTAATCTTAACCTTTTACCAAATTAAAT
529361 T
65 T
529362 TT
1 TT
529364 CATATTTTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 10 0.16
65 53 0.84
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (65 bp):
TTTATTTGAAATAAAACTTAAAAAAAAAGAAACCTTTTAATCTTAACCTTTTACCAAATTAAATT
Found at i:529949 original size:2 final size:2
Alignment explanation
Indices: 529938--529990 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
529928 GCTCAGACTG
* *
529938 TC TC TC -C TC TC TC TC TC CC TC TC TC TC GC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
529979 TC TC TC GC TC TC
1 TC TC TC TC TC TC
529991 CATACCCCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.00, C:0.53, G:0.04, T:0.43
Consensus pattern (2 bp):
TC
Found at i:539296 original size:232 final size:234
Alignment explanation
Indices: 538879--539307 Score: 675
Period size: 232 Copynumber: 1.8 Consensus size: 234
538869 AGGCATTGAC
* *
538879 AACCAGTTCTAGAAAGGAAACTGGTGAAAGAGGCTTTCGGAACGATTTGTCCATTTTTCCAAGCT
1 AACCAGTTCTAGAAAGGAAACGGGTGAAAGAGGCTTTCGGAACGATTCGTCCA-TTTTCCAAGCT
* * *
538944 GTTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGAAAGGTGATGGGTTTGGCCTTGGTGTT
65 ATTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGAAAGGTGATGGATTTGGCCTTGGTGTG
* * *
539009 CTGGATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTATTAATGTATTCTGCTTGCCTTCT
130 CCGGATTTCTTTTTTATTTTAATTTTAAAAGGTGTCTTTTTATTAATGCATTCTGCTTGCCTTCT
539074 TGTAGTTTGTTCGATAGGCCAAGTGGAAGACAATGAAGCA
195 TGTAGTTTGTTCGATAGGCCAAGTGGAAGACAATGAAGCA
* ** ** *
539114 AACCAGTTCTAGAAAGGATACGGGTGAAAGAGTTTTTTTGAATGATTCGTCCA-TTTCCAAGCTA
1 AACCAGTTCTAGAAAGGAAACGGGTGAAAGAGGCTTTCGGAACGATTCGTCCATTTTCCAAGCTA
* *
539178 TTCTTTTTATGAACCCAATTGATTTAGA-TAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTGC
66 TTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGAAAGGTGATGGATTTGGCCTTGGTGTGC
539242 CGGATTTCTTTTTTATTTTAATTTTAAAAGGTGTCTTTTT-TATAATGCATTCTGCTTGCCTTCT
131 CGGATTTCTTTTTTATTTTAATTTTAAAAGGTGTCTTTTTAT-TAATGCATTCTGCTTGCCTTCT
539306 TG
195 TG
539308 ACTTTCTTGT
Statistics
Matches: 177, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
231 1 0.01
232 93 0.53
233 38 0.21
235 45 0.25
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (234 bp):
AACCAGTTCTAGAAAGGAAACGGGTGAAAGAGGCTTTCGGAACGATTCGTCCATTTTCCAAGCTA
TTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGAAAGGTGATGGATTTGGCCTTGGTGTGC
CGGATTTCTTTTTTATTTTAATTTTAAAAGGTGTCTTTTTATTAATGCATTCTGCTTGCCTTCTT
GTAGTTTGTTCGATAGGCCAAGTGGAAGACAATGAAGCA
Found at i:540151 original size:18 final size:19
Alignment explanation
Indices: 540121--540162 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
540111 AAAATGCTTT
* *
540121 ATTTTCTTTGGTTTACTTG
1 ATTTTCTTTGGTTCACTTA
540140 ATTTTC-TTGGTTCACTTA
1 ATTTTCTTTGGTTCACTTA
540158 ATTTT
1 ATTTT
540163 TCTCAAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (19 bp):
ATTTTCTTTGGTTCACTTA
Found at i:543982 original size:18 final size:19
Alignment explanation
Indices: 543948--543983 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
543938 TGGCTTTTAA
*
543948 ATTCATATTTGTTTTCCAT
1 ATTCATATTTCTTTTCCAT
543967 ATTCATA-TTCTTTTCCA
1 ATTCATATTTCTTTTCCA
543984 GCATGTGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.22, C:0.19, G:0.03, T:0.56
Consensus pattern (19 bp):
ATTCATATTTCTTTTCCAT
Found at i:544153 original size:2 final size:2
Alignment explanation
Indices: 544146--544178 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
544136 TTATTATATG
*
544146 CA CA CA CA CA CA CA CA CA CA CA CA CG CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
544179 GTGTATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.52, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:550910 original size:21 final size:22
Alignment explanation
Indices: 550854--550899 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
550844 TATTAGAACA
*
550854 ATTATTTTATTATTAAAATTTT
1 ATTAATTTATTATTAAAATTTT
* *
550876 ATTAATTTATTATTTAATTTTT
1 ATTAATTTATTATTAAAATTTT
550898 AT
1 AT
550900 ATCTTATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTAATTTATTATTAAAATTTT
Found at i:551054 original size:2 final size:2
Alignment explanation
Indices: 551047--551081 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
551037 TTGTAATGCT
551047 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 T
551082 GCACATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:554394 original size:9 final size:9
Alignment explanation
Indices: 554363--554393 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
554353 GTCCATAAGC
554363 TTTTTCTTT
1 TTTTTCTTT
554372 TTTTTCTTT
1 TTTTTCTTT
554381 TTTTT-TTT
1 TTTTTCTTT
554389 TTTTT
1 TTTTT
554394 TAAGAAAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:561579 original size:13 final size:14
Alignment explanation
Indices: 561556--561584 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
561546 GGGATTTAGA
561556 CCTTATTTTCTTTT
1 CCTTATTTTCTTTT
561570 CCTT-TTTTCTTTT
1 CCTTATTTTCTTTT
561583 CC
1 CC
561585 CGTCTTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (14 bp):
CCTTATTTTCTTTT
Found at i:563655 original size:3 final size:3
Alignment explanation
Indices: 563647--563682 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
563637 AACTTGTTTA
563647 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
563683 AGAAGGAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:564282 original size:2 final size:2
Alignment explanation
Indices: 564277--564308 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
564267 TTTTTAACCT
*
564277 TA TA TA TA TA TA TA TG 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
564309 CTCGTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:572216 original size:21 final size:21
Alignment explanation
Indices: 572152--572218 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
572142 AATATTTTTT
*
572152 TTAATA-AAATAATTATTTAAAA
1 TTAATATAAA-AATT-TTTAATA
* *
572174 TTAAT-TATAAAATATATAAATA
1 TTAATATA-AAAAT-TTTTAATA
572196 TTAATATAAAAATTTTTAATA
1 TTAATATAAAAATTTTTAATA
572217 TT
1 TT
572219 TTTTAATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
21 8 0.22
22 23 0.64
23 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAATATAAAAATTTTTAATA
Found at i:587527 original size:19 final size:19
Alignment explanation
Indices: 587496--587543 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
587486 TATTAATATA
*
587496 AATA-TAAATATAATATTAT
1 AATATTAAATATAA-ATAAT
587515 AATATTAAA-ATAAATAAT
1 AATATTAAATATAAATAAT
587533 ATATATTAAAT
1 A-ATATTAAAT
587544 TATTCATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.20
19 16 0.64
20 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATTAAATATAAATAAT
Found at i:587527 original size:25 final size:27
Alignment explanation
Indices: 587480--587540 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 27
587470 TATATTATTT
587480 TATAT-TTATTAATATAAATATAAAT-A
1 TATATATTA-TAATATAAATATAAATAA
587506 TA-ATATTATAATATTAAA-ATAAATAA
1 TATATATTATAATA-TAAATATAAATAA
587532 TATATATTA
1 TATATATTA
587541 AATTATTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 13 0.42
26 12 0.39
27 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TATATATTATAATATAAATATAAATAA
Found at i:587866 original size:3 final size:3
Alignment explanation
Indices: 587860--587906 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
587850 ATTAAAAACC
* *
587860 AGA AGA AGA AGA AGG AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
587907 GAAGGAAGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Done.