Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 42 of 199
Found at i:12126023 original size:21 final size:21
Alignment explanation
Indices: 12125994--12126077 Score: 123
Period size: 21 Copynumber: 4.0 Consensus size: 21
12125984 CGAACATGCC
* *
12125994 AACAAAAGCTCATAAGAGCTG
1 AACAGAAGCTCAAAAGAGCTG
12126015 AACAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCAAAAGAGCTG
* * *
12126036 AATAGAAGCTCATAAGAGCTT
1 AACAGAAGCTCAAAAGAGCTG
12126057 AACAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCAAAAGAGCTG
12126078 GTCCACCCGA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (21 bp):
AACAGAAGCTCAAAAGAGCTG
Found at i:12128344 original size:13 final size:13
Alignment explanation
Indices: 12128326--12128353 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12128316 GGTAGAGAGT
12128326 ATGGTGATTTTAA
1 ATGGTGATTTTAA
12128339 ATGGTGATTTTAA
1 ATGGTGATTTTAA
12128352 AT
1 AT
12128354 AAATAGAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.46
Consensus pattern (13 bp):
ATGGTGATTTTAA
Found at i:12130824 original size:9 final size:9
Alignment explanation
Indices: 12130812--12130841 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
12130802 GAATTAAATA
12130812 ATTTAAGTT
1 ATTTAAGTT
12130821 ATTTAAGTT
1 ATTTAAGTT
*
12130830 AATTAAGTT
1 ATTTAAGTT
12130839 ATT
1 ATT
12130842 CAGATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (9 bp):
ATTTAAGTT
Found at i:12135793 original size:16 final size:18
Alignment explanation
Indices: 12135767--12135807 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12135757 TGTGCATTGG
12135767 AATTTTT-TTACTT-TTT
1 AATTTTTATTACTTATTT
12135783 -ATTTTTATTACTTATTT
1 AATTTTTATTACTTATTT
12135800 AATTTTTA
1 AATTTTTA
12135808 GTTTTTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 6 0.27
17 3 0.14
18 7 0.32
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
AATTTTTATTACTTATTT
Found at i:12140986 original size:34 final size:35
Alignment explanation
Indices: 12140942--12141009 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
12140932 GCACAGTTGA
* **
12140942 ACAGTCTTGGG-CTTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTT-AGCCCATCACAGTATCAGTG
12140977 ACAGT-TTGGGCCTTAGCCCATCACAGTATCAGT
1 ACAGTCTTGGGCCTTAGCCCATCACAGTATCAGT
12141010 AGCAGTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (35 bp):
ACAGTCTTGGGCCTTAGCCCATCACAGTATCAGTG
Found at i:12150785 original size:26 final size:26
Alignment explanation
Indices: 12150749--12150810 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
12150739 CCTGTAAGTG
12150749 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATACATGCTATGATA
* *
12150775 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTGATACATGCTATGATA
12150801 TTCTGAAACT
1 TTCTGAAACT
12150811 ACTGTAGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGATA
Found at i:12159333 original size:42 final size:42
Alignment explanation
Indices: 12159208--12159339 Score: 201
Period size: 42 Copynumber: 3.1 Consensus size: 42
12159198 CGACATGGTA
* *
12159208 ATGTGACCCACACAGCCTAGACACACGGATGTGTCCTTGGCA
1 ATGTGACCCACACAGCCTAGACACACGGGTGTGTCCTTGGCC
*
12159250 ATGTGACCCACACAGCCTAGACACACTGGTGTGTCCTTGGCC
1 ATGTGACCCACACAGCCTAGACACACGGGTGTGTCCTTGGCC
* * *
12159292 ATGTGACCCATACGGCCTACACACACGGGTGTGTCCTTGGCC
1 ATGTGACCCACACAGCCTAGACACACGGGTGTGTCCTTGGCC
*
12159334 GTGTGA
1 ATGTGA
12159340 GTTTTGGACT
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.22, C:0.31, G:0.26, T:0.21
Consensus pattern (42 bp):
ATGTGACCCACACAGCCTAGACACACGGGTGTGTCCTTGGCC
Found at i:12161310 original size:9 final size:9
Alignment explanation
Indices: 12161296--12161351 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
12161286 TGCCATCGAG
12161296 CAAACAAAA
1 CAAACAAAA
12161305 CAAACAAAA
1 CAAACAAAA
*
12161314 CAAACGAAA
1 CAAACAAAA
* *
12161323 TAACCCAAAA
1 CAA-ACAAAA
12161333 -AAACAAAAA
1 CAAAC-AAAA
12161342 CAAACTAAAA
1 CAAAC-AAAA
12161352 ACAAGAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 1 0.03
9 25 0.66
10 12 0.32
ACGTcount: A:0.73, C:0.21, G:0.02, T:0.04
Consensus pattern (9 bp):
CAAACAAAA
Found at i:12176417 original size:14 final size:13
Alignment explanation
Indices: 12176394--12176547 Score: 88
Period size: 14 Copynumber: 11.6 Consensus size: 13
12176384 TTTTTAAAAC
*
12176394 TTTT-AAAAATTA
1 TTTTAAAAAAATA
*
12176406 ATTTAAAAAAATA
1 TTTTAAAAAAATA
12176419 TTTTTAAAAAAATA
1 -TTTTAAAAAAATA
*
12176433 TTTTTAAAAAATTA
1 -TTTTAAAAAAATA
*
12176447 TTTTTAAATTTAAAAAA
1 -TTTTAAA---AAAATA
12176464 TTTT-AAAAAATA
1 TTTTAAAAAAATA
12176476 TTTT--AAAAATA
1 TTTTAAAAAAATA
**
12176487 TTTTAAAATTAT-
1 TTTTAAAAAAATA
*
12176499 TTTTAAATTAAAAAAA
1 TTTT-AA--AAAAATA
**
12176515 TTAAAAAAAAAGTA
1 TTTTAAAAAAA-TA
12176529 TTTT--AAAAATA
1 TTTTAAAAAAATA
12176540 TTTTAAAA
1 TTTTAAAA
12176548 TTAAAAAAAG
Statistics
Matches: 111, Mismatches: 17, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
11 17 0.15
12 21 0.19
13 20 0.18
14 36 0.32
15 7 0.06
16 6 0.05
17 4 0.04
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (13 bp):
TTTTAAAAAAATA
Found at i:12176427 original size:11 final size:11
Alignment explanation
Indices: 12176413--12176505 Score: 50
Period size: 12 Copynumber: 8.3 Consensus size: 11
12176403 TTAATTTAAA
12176413 AAAATATTTTT
1 AAAATATTTTT
12176424 AAAAAAATATTTTT
1 ---AAAATATTTTT
*
12176438 AAAAAATTATTT
1 AAAATATT-TTT
**
12176450 TTAA-A-T-TT
1 AAAATATTTTT
* *
12176458 AAAAAATTTTAA
1 AAAATATTTT-T
*
12176470 AAAATATTTTA
1 AAAATATTTTT
12176481 AAAATA-TTTT
1 AAAATATTTTT
12176491 AAAATTATTTTT
1 AAAA-TATTTTT
12176503 AAA
1 AAA
12176506 TTAAAAAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
8 4 0.06
9 1 0.02
10 9 0.14
11 18 0.28
12 21 0.33
14 11 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:12176502 original size:12 final size:11
Alignment explanation
Indices: 12176455--12176578 Score: 77
Period size: 11 Copynumber: 11.6 Consensus size: 11
12176445 TATTTTTAAA
12176455 TTTAAAAA-AT
1 TTTAAAAATAT
12176465 TTTAAAAAATAT
1 TTT-AAAAATAT
12176477 TTTAAAAATAT
1 TTTAAAAATAT
*
12176488 TTTAAAATTAT
1 TTTAAAAATAT
*
12176499 TTT--TAA-A-
1 TTTAAAAATAT
*
12176506 -TTAAAAAAAT
1 TTTAAAAATAT
**
12176516 TAAAAAAAAAGTAT
1 T--TTAAAAA-TAT
12176530 TTTAAAAATAT
1 TTTAAAAATAT
12176541 TTT--AAA-AT
1 TTTAAAAATAT
**
12176549 TAAAAAAAGTAT
1 TTTAAAAA-TAT
12176561 TTTAAAAATAT
1 TTTAAAAATAT
12176572 TTTAAAA
1 TTTAAAA
12176579 TTAAAAAAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 27
0.69 0.10 0.21
Matches are distributed among these distances:
6 2 0.02
8 6 0.07
9 5 0.06
10 6 0.07
11 42 0.48
12 18 0.21
13 5 0.06
14 3 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TTTAAAAATAT
Found at i:12176507 original size:42 final size:40
Alignment explanation
Indices: 12176425--12176619 Score: 139
Period size: 39 Copynumber: 4.7 Consensus size: 40
12176415 AATATTTTTA
* ***
12176425 AAAAAATATTTTTAAAAAATTATTTTTAAATT-TAAAAAATTTT
1 AAAAAATA-TTTT-AAAAA-TATTTTAAAATTATTTTAAA-TTT
12176468 AAAAAATATTTTAAAAATATTTTAAAATTATTTTTAAA-TT
1 AAAAAATATTTTAAAAATATTTTAAAATTA-TTTTAAATTT
** * *
12176508 AAAAAA-ATTAAAAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAAATATT--TTAAAAA-TATTTTAAAATTATTTT-AAATTT
** *
12176551 AAAAAAGTATTTTAAAAATATTTTAAAATTA--AAAAAATT
1 AAAAAA-TATTTTAAAAATATTTTAAAATTATTTTAAATTT
* *
12176590 AAAAAAGTATGTAAAAAATATTTTAAAATT
1 AAAAAA-TATTTTAAAAATATTTTAAAATT
12176620 TAAAAAATAA
Statistics
Matches: 126, Mismatches: 17, Indels: 22
0.76 0.10 0.13
Matches are distributed among these distances:
39 35 0.28
40 19 0.15
41 14 0.11
42 35 0.28
43 20 0.16
45 3 0.02
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (40 bp):
AAAAAATATTTTAAAAATATTTTAAAATTATTTTAAATTT
Found at i:12176554 original size:31 final size:31
Alignment explanation
Indices: 12176519--12176587 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
12176509 AAAAAATTAA
12176519 AAAAAAAGTATTTTAAAAATATTTTAAAATT
1 AAAAAAAGTATTTTAAAAATATTTTAAAATT
12176550 AAAAAAAGTATTTTAAAAATATTTTAAAATT
1 AAAAAAAGTATTTTAAAAATATTTTAAAATT
12176581 AAAAAAA
1 AAAAAAA
12176588 TTAAAAAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (31 bp):
AAAAAAAGTATTTTAAAAATATTTTAAAATT
Found at i:12183065 original size:16 final size:16
Alignment explanation
Indices: 12183041--12183071 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12183031 GTGATTAAAT
12183041 TGACAAAAAAATAGAG
1 TGACAAAAAAATAGAG
*
12183057 TGACCAAAAAATAGA
1 TGACAAAAAAATAGA
12183072 TTTTGTATTT
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:0.61, C:0.10, G:0.16, T:0.13
Consensus pattern (16 bp):
TGACAAAAAAATAGAG
Found at i:12184449 original size:23 final size:23
Alignment explanation
Indices: 12184383--12184879 Score: 469
Period size: 23 Copynumber: 21.2 Consensus size: 23
12184373 TCTACCATGT
12184383 TTGGACAGC-TCTTATACATCAAAA
1 TTGGACAGCAT-TTATACA-CAAAA
*
12184407 TT-GAGCAGCATATATATATATACAAAA
1 TTGGA-CAGC--AT-T-TATACACAAAA
12184434 TTGGACAGCATTTATACACCAAAA
1 TTGGACAGCATTTATACA-CAAAA
* * *
12184458 TTTGACAGCATATATATACAAAA
1 TTGGACAGCATTTATACACAAAA
*
12184481 TTGGACAGCATTTATACCCTAAAA
1 TTGGACAGCATTTATACAC-AAAA
* * * * *
12184505 TTGGGCAGCATATATATACCAAT
1 TTGGACAGCATTTATACACAAAA
* *
12184528 TTGGACAACACTTATACACAAAA
1 TTGGACAGCATTTATACACAAAA
* * *
12184551 TTTGACAGCATGTATATACAAAA
1 TTGGACAGCATTTATACACAAAA
* *
12184574 TTGGACAGCACTTATATACAAAA
1 TTGGACAGCATTTATACACAAAA
*
12184597 TTGGACAGCACTTATACACAAAA
1 TTGGACAGCATTTATACACAAAA
*
12184620 TTGGACAGCACTTATACACAAAA
1 TTGGACAGCATTTATACACAAAA
* * *
12184643 TTTGACAGCATGTATATACAAAA
1 TTGGACAGCATTTATACACAAAA
*
12184666 TTTGACAGCATTTATACACTAAAA
1 TTGGACAGCATTTATACAC-AAAA
* * * * * *
12184690 TTGGGCAGCGTATATATACCAAT
1 TTGGACAGCATTTATACACAAAA
*
12184713 TTGGACAGCACTTATACACAAAA
1 TTGGACAGCATTTATACACAAAA
* * *
12184736 TTTGACAGCATGTATATACAAAA
1 TTGGACAGCATTTATACACAAAA
12184759 TTGGACAGCATTTATACACTAAAA
1 TTGGACAGCATTTATACAC-AAAA
* * * *
12184783 TTGGGA-AGCATATATATACCAAT
1 TT-GGACAGCATTTATACACAAAA
*
12184806 TTGGACAGCACTTATACACAAAA
1 TTGGACAGCATTTATACACAAAA
** * * *
12184829 TTTAACAGTATATATATACAAAA
1 TTGGACAGCATTTATACACAAAA
12184852 TTGGACAGCATTTATACACCAAAA
1 TTGGACAGCATTTATACA-CAAAA
12184876 TTGG
1 TTGG
12184880 GTAGCATATA
Statistics
Matches: 381, Mismatches: 79, Indels: 26
0.78 0.16 0.05
Matches are distributed among these distances:
22 3 0.01
23 263 0.69
24 90 0.24
25 5 0.01
27 13 0.03
28 7 0.02
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (23 bp):
TTGGACAGCATTTATACACAAAA
Found at i:12184568 original size:46 final size:46
Alignment explanation
Indices: 12184383--12184877 Score: 591
Period size: 46 Copynumber: 10.5 Consensus size: 46
12184373 TCTACCATGT
*
12184383 TTGGACAGCTCTTATACATCAAAA-TTGAGCAGCATATATATATATACAAAA
1 TTGGACAGCACTTATACA-CAAAATTTGA-CAGC----ATATATATACAAAA
*
12184434 TTGGACAGCATTTATACACCAAAATTTGACAGCATATATATACAAAA
1 TTGGACAGCACTTATACA-CAAAATTTGACAGCATATATATACAAAA
* * * * * *
12184481 TTGGACAGCATTTATACCCTAAAATTGGGCAGCATATATATACCAAT
1 TTGGACAGCACTTATACAC-AAAATTTGACAGCATATATATACAAAA
* *
12184528 TTGGACAACACTTATACACAAAATTTGACAGCATGTATATACAAAA
1 TTGGACAGCACTTATACACAAAATTTGACAGCATATATATACAAAA
* * *
12184574 TTGGACAGCACTTATATACAAAATTGGACAGCACT-TATACACAAAA
1 TTGGACAGCACTTATACACAAAATTTGACAGCA-TATATATACAAAA
*
12184620 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAA
1 TTGGACAGCACTTATACACAAAATTTGACAGCATATATATACAAAA
* * * * * * *
12184666 TTTGACAGCATTTATACACTAAAATTGGGCAGCGTATATATACCAAT
1 TTGGACAGCACTTATACAC-AAAATTTGACAGCATATATATACAAAA
*
12184713 TTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAA
1 TTGGACAGCACTTATACACAAAATTTGACAGCATATATATACAAAA
* * * *
12184759 TTGGACAGCATTTATACACTAAAATTGGGA-AGCATATATATACCAAT
1 TTGGACAGCACTTATACAC-AAAATT-TGACAGCATATATATACAAAA
* *
12184806 TTGGACAGCACTTATACACAAAATTTAACAGTATATATATACAAAA
1 TTGGACAGCACTTATACACAAAATTTGACAGCATATATATACAAAA
*
12184852 TTGGACAGCATTTATACACCAAAATT
1 TTGGACAGCACTTATACA-CAAAATT
12184878 GGGTAGCATA
Statistics
Matches: 384, Mismatches: 51, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
45 2 0.01
46 197 0.51
47 154 0.40
48 2 0.01
51 25 0.07
52 4 0.01
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (46 bp):
TTGGACAGCACTTATACACAAAATTTGACAGCATATATATACAAAA
Found at i:12184582 original size:93 final size:93
Alignment explanation
Indices: 12184420--12184890 Score: 730
Period size: 93 Copynumber: 5.1 Consensus size: 93
12184410 AGCAGCATAT
* * * *
12184420 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGG
1 ATATATATACCAATTTGGACAGCACTTATACA-CAAAATTTGACAGCATGTATATACAAAATTGG
*
12184485 ACAGCATTTATACCCTAAAATTGGGCAGC
65 ACAGCATTTATACACTAAAATTGGGCAGC
*
12184514 ATATATATACCAATTTGGACAACACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
1 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
* * *
12184579 CAGCACTTATATAC-AAAATTGGACAGC
66 CAGCATTTATACACTAAAATTGGGCAGC
* * * *
12184606 ACT-TATACACAAAATTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTTG
1 A-TATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGG
12184670 ACAGCATTTATACACTAAAATTGGGCAGC
65 ACAGCATTTATACACTAAAATTGGGCAGC
*
12184699 GTATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
1 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
*
12184764 CAGCATTTATACACTAAAATTGGGAAGC
66 CAGCATTTATACACTAAAATTGGGCAGC
* * *
12184792 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTAACAGTATATATATACAAAATTGGA
1 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
* *
12184857 CAGCATTTATACACCAAAATTGGGTAGC
66 CAGCATTTATACACTAAAATTGGGCAGC
12184885 ATATAT
1 ATATAT
12184891 TCGATTTTTG
Statistics
Matches: 345, Mismatches: 29, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
92 83 0.24
93 234 0.68
94 28 0.08
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (93 bp):
ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
CAGCATTTATACACTAAAATTGGGCAGC
Found at i:12185239 original size:2 final size:2
Alignment explanation
Indices: 12185232--12185256 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12185222 CACCATGCAC
12185232 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12185257 CATTACCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12185267 original size:16 final size:15
Alignment explanation
Indices: 12185248--12185295 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
12185238 ATATATATAT
*
12185248 ATATATATACATTACC
1 ATATATATAC-TAACC
*
12185264 ATATAAATACTAACC
1 ATATATATACTAACC
12185279 ATA-ATATACTAATCC
1 ATATATATACTAA-CC
12185294 AT
1 AT
12185296 GATCTTAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.29
15 11 0.39
16 9 0.32
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (15 bp):
ATATATATACTAACC
Found at i:12185894 original size:43 final size:43
Alignment explanation
Indices: 12185799--12185911 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 43
12185789 TCGTACAATG
* * * *
12185799 CCAACGTCCCAGAC-GTGGTCCTACATGTAATCACATATAGATG
1 CCAACGTCCCAGACAG-GGTCTTACACGTAAACACATATAGATA
*
12185842 CC-ACTGTCCCAGACAGGGTCTTACACGTAAACACA-AGTCGATA
1 CCAAC-GTCCCAGACAGGGTCTTACACGTAAACACATA-TAGATA
*
12185885 CCAACGTCCCAGACATGGTCTTACACG
1 CCAACGTCCCAGACAGGGTCTTACACG
12185912 ATAGTACATA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
42 3 0.05
43 54 0.90
44 3 0.05
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (43 bp):
CCAACGTCCCAGACAGGGTCTTACACGTAAACACATATAGATA
Found at i:12191873 original size:28 final size:28
Alignment explanation
Indices: 12191841--12191911 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
12191831 TGACTTTCGA
*
12191841 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAATTTAATTATAAAG
* * **
12191869 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAATTTAATTATAAAG
12191897 CACTAAGTGTGCGAA
1 CACTAAGTGTGCGAA
12191912 CTTATTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (28 bp):
CACTAAGTGTGCGAATTTAATTATAAAG
Found at i:12193984 original size:28 final size:28
Alignment explanation
Indices: 12193952--12194078 Score: 164
Period size: 28 Copynumber: 4.5 Consensus size: 28
12193942 TGACTTTCGA
** *
12193952 CACTAAGTGTGTTAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
12193980 CACTAAGTGTGCGAGTTTAACTTGTAAAG
1 CACTAAGTGTGCGAGTTTAA-TTGTAAAG
*
12194009 CACTAAGTGTGCGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * * **
12194037 CACTAAGTGTGTGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
12194065 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
12194079 ACTTATTAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
28 59 0.68
29 28 0.32
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:12194040 original size:57 final size:56
Alignment explanation
Indices: 12193952--12194079 Score: 166
Period size: 57 Copynumber: 2.3 Consensus size: 56
12193942 TGACTTTCGA
** * *
12193952 CACTAAGTGTGTTAATTTAATTGTAAAGCACTAAGTGTGCGAGTTTAACTTGTAAAG
1 CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAA-TTATAAAG
* * * **
12194009 CACTAAGTGTGCGAGTTTAATGGTAAAGCACTAAGTGTGTGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTATAAAG
12194065 CACTAAGTGTGCGAA
1 CACTAAGTGTGCGAA
12194080 CTTATTAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
56 19 0.31
57 42 0.69
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (56 bp):
CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTATAAAG
Found at i:12194954 original size:23 final size:23
Alignment explanation
Indices: 12194919--12195151 Score: 122
Period size: 23 Copynumber: 10.0 Consensus size: 23
12194909 TGGTGAATCA
*
12194919 ATGCTGTCCAATTTTGTATATAC
1 ATGCTGTCAAATTTTGTATATAC
* *
12194942 ATGCTGTTAAATTTTGTGTATA-
1 ATGCTGTCAAATTTTGTATATAC
* **
12194964 AGTGCTGTCCAAA-TTGGTATATGT
1 A-TGCTGT-CAAATTTTGTATATAC
* * *
12194988 ATGCTGCCTAATTTTTGGGGA-AT-C
1 ATGCTGTC-AAATTTT--GTATATAC
*
12195012 AATGCTGTCCAATTTTGTATATAC
1 -ATGCTGTCAAATTTTGTATATAC
* *
12195036 ATGCTGTTAAATTTTGTGTATA-
1 ATGCTGTCAAATTTTGTATATAC
* **
12195058 AGTGCTGTCCAAA-TTGGTATATGT
1 A-TGCTGT-CAAATTTTGTATATAC
*
12195082 ATGCTGTCTAATTTTTGGTGA-AT-C
1 ATGCTGTC-AAATTTT-GT-ATATAC
* *
12195106 AATGCTGTCCAATTTTGTATACAC
1 -ATGCTGTCAAATTTTGTATATAC
* *
12195130 ATGCTGTTAAATTTTGTGTATA
1 ATGCTGTCAAATTTTGTATATA
12195152 AGTGTTGTCC
Statistics
Matches: 157, Mismatches: 33, Indels: 40
0.68 0.14 0.17
Matches are distributed among these distances:
22 7 0.04
23 102 0.65
24 24 0.15
25 21 0.13
26 3 0.02
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (23 bp):
ATGCTGTCAAATTTTGTATATAC
Found at i:12194984 original size:46 final size:46
Alignment explanation
Indices: 12194920--12195169 Score: 270
Period size: 46 Copynumber: 5.3 Consensus size: 46
12194910 GGTGAATCAA
* *
12194920 TGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAG
1 TGCTGTCCAAATTGGTATATACATGCTGTTAAATTTTGTGTATAAG
** * * * *
12194966 TGCTGTCCAAATTGGTATATGTATGCTGCCTAATTTTTGGGGAATCAA-
1 TGCTGTCCAAATTGGTATATACATGCTG-TTAAATTTT-GTGTAT-AAG
* *
12195014 TGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAG
1 TGCTGTCCAAATTGGTATATACATGCTGTTAAATTTTGTGTATAAG
** * *
12195060 TGCTGTCCAAATTGGTATATGTATGCTGTCTAATTTTTGGTGAATCAA-
1 TGCTGTCCAAATTGGTATATACATGCTGT-TAAATTTT-GTGTAT-AAG
* * *
12195108 TGCTGTCCAATTTTGTATACACATGCTGTTAAATTTTGTGTATAAG
1 TGCTGTCCAAATTGGTATATACATGCTGTTAAATTTTGTGTATAAG
*
12195154 TGTTGTCCAAATTGGT
1 TGCTGTCCAAATTGGT
12195170 GTATGTATGC
Statistics
Matches: 164, Mismatches: 32, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
45 4 0.02
46 71 0.43
47 28 0.17
48 57 0.35
49 4 0.02
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (46 bp):
TGCTGTCCAAATTGGTATATACATGCTGTTAAATTTTGTGTATAAG
Found at i:12195051 original size:94 final size:94
Alignment explanation
Indices: 12194890--12195262 Score: 575
Period size: 94 Copynumber: 3.9 Consensus size: 94
12194880 NNNNNNNNNN
*
12194890 ATGTATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATT
1 ATGTATGCTGCCTAATTTTTGGGGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATT
12194955 TTGTGTATAAGTGCTGTCCAAATTGGTAT
66 TTGTGTATAAGTGCTGTCCAAATTGGTAT
12194984 ATGTATGCTGCCTAATTTTTGGGGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATT
1 ATGTATGCTGCCTAATTTTTGGGGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATT
12195049 TTGTGTATAAGTGCTGTCCAAATTGGTAT
66 TTGTGTATAAGTGCTGTCCAAATTGGTAT
* * *
12195078 ATGTATGCTGTCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATACACATGCTGTTAAATT
1 ATGTATGCTGCCTAATTTTTGGGGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATT
* *
12195143 TTGTGTATAAGTGTTGTCCAAATTGGTGT
66 TTGTGTATAAGTGCTGTCCAAATTGGTAT
* ** * * * *
12195172 ATGTATGCTGCCTAATTTTTGGTGAAAAAAAATGCTTTCCAATTTTATATATATATGCTGCTCAA
1 ATGTATGCTGCCTAATTTTTGG-G-GAATCAATGCTGTCCAATTTTGTATATACATGCTG-TTAA
* *
12195237 TTTTTGATGTATAAGAGCTGTCCAAA
63 ATTTTG-TGTATAAGTGCTGTCCAAA
12195263 CAGGGTAGAT
Statistics
Matches: 256, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
94 203 0.79
96 28 0.11
97 8 0.03
98 17 0.07
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.42
Consensus pattern (94 bp):
ATGTATGCTGCCTAATTTTTGGGGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATT
TTGTGTATAAGTGCTGTCCAAATTGGTAT
Found at i:12200795 original size:94 final size:94
Alignment explanation
Indices: 12200649--12201462 Score: 1376
Period size: 94 Copynumber: 8.6 Consensus size: 94
12200639 TTGATGTAAA
*
12200649 AATGCTGTCCAATTTTGTATACACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
1 AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
12200714 TATGTATGCTGCCTAATTTTTGGTGAATC
66 TATGTATGCTGCCTAATTTTTGGTGAATC
* * *
12200743 AATGCTGTCCAATTTTGTATATACATGCTATTAAATTTTGTGTATAAGTGCTGTCAAAATTGGTA
1 AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
12200808 TATGTATGCTGCCTAATTTTTGGTGAATC
66 TATGTATGCTGCCTAATTTTTGGTGAATC
* *
12200837 AATGCTGTCTAATTTTGTATACACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
1 AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
12200902 TATGTATGCTGCCTAATTTTTGGTGAATC
66 TATGTATGCTGCCTAATTTTTGGTGAATC
12200931 AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
1 AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
* *
12200996 TATATATGCTGCCGAATTTTTGGTGAATC
66 TATGTATGCTGCCTAATTTTTGGTGAATC
* *
12201025 AATGCTGTCCAATTTCGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTTGTG
1 AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
*
12201090 TATGTATGCTTCCTAATTTTTGGTGAATC
66 TATGTATGCTGCCTAATTTTTGGTGAATC
*
12201119 AATGGTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
1 AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
12201184 TATGTATGCTGCCTAATTTTTGGTGAATC
66 TATGTATGCTGCCTAATTTTTGGTGAATC
*
12201213 AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTA
1 AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
*
12201278 TATGTATGTTGCCTAATTTTTGGTGAATC
66 TATGTATGCTGCCTAATTTTTGGTGAATC
* * * *
12201307 AATGCTGTCCAATTTTATATACACATGCTGTTAAATTTTGTGTATAAGTGTTGTCCAAATTGGTA
1 AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
**
12201372 TATGTATGCTGCCTAATTTTTGGTGAAAAA
66 TATGTATGCTGCCTAATTTTTGGTG-AATC
* * * * *
12201402 AATGCTGTCCAATTTTATATATATATGCTGCTCAATTTTTGATGTATAAGAGCTGTCCAAA
1 AATGCTGTCCAATTTTGTATATACATGCTG-TTAAATTTTG-TGTATAAGTGCTGTCCAAA
12201463 CAGGGTAGAT
Statistics
Matches: 680, Mismatches: 37, Indels: 3
0.94 0.05 0.00
Matches are distributed among these distances:
94 625 0.92
95 30 0.04
96 8 0.01
97 17 0.03
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (94 bp):
AATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTGTGTATAAGTGCTGTCCAAATTGGTG
TATGTATGCTGCCTAATTTTTGGTGAATC
Found at i:12201018 original size:25 final size:22
Alignment explanation
Indices: 12200682--12201322 Score: 168
Period size: 23 Copynumber: 27.3 Consensus size: 22
12200672 CATGCTGTTA
12200682 AATTTT-GTGTATAAGTGCTGTCC
1 AATTTTGGTGTATAA-TGCTG-CC
* *
12200705 AA-ATTGGTGTATGTATGCTGCC
1 AATTTTGGTGTAT-AATGCTGCC
*
12200727 TAATTTTTGGTGAATCAATGCTGTCC
1 -AA-TTTTGGTGTAT-AATGCTG-CC
* ***
12200753 AATTTT-GTATATACATGCTATTA
1 AATTTTGGTGTATA-ATGCT-GCC
*
12200776 AATTTT-GTGTATAAGTGCTGTC
1 AATTTTGGTGTATAA-TGCTGCC
** * *
12200798 AAAATTGGTATATGTATGCTGCC
1 AATTTTGGTGTAT-AATGCTGCC
* *
12200821 TAATTTTTGGTGAATCAATGCTGTCT
1 -AA-TTTTGGTGTAT-AATGCTG-CC
* * **
12200847 AATTTT-GTATACACATGCTGTTA
1 AATTTTGGTGTATA-ATGCTG-CC
12200870 AATTTT-GTGTATAAGTGCTGTCC
1 AATTTTGGTGTATAA-TGCTG-CC
* *
12200893 AA-ATTGGTGTATGTATGCTGCC
1 AATTTTGGTGTAT-AATGCTGCC
*
12200915 TAATTTTTGGTGAATCAATGCTGTCC
1 -AA-TTTTGGTGTAT-AATGCTG-CC
* **
12200941 AATTTT-GTATATACATGCTGTTA
1 AATTTTGGTGTATA-ATGCTG-CC
12200964 AATTTT-GTGTATAAGTGCTGTCC
1 AATTTTGGTGTATAA-TGCTG-CC
*
12200987 AA-ATTGGTGTATATATGCTGCC
1 AATTTTGGTGTATA-ATGCTGCC
*
12201009 GAATTTTTGGTGAATCAATGCTGTCC
1 -AA-TTTTGGTGTAT-AATGCTG-CC
* * **
12201035 AA-TTTCGTATATACATGCTGTTA
1 AATTTTGGTGTATA-ATGCTG-CC
12201058 AATTTT-GTGTATAAGTGCTGTCC
1 AATTTTGGTGTATAA-TGCTG-CC
* * *
12201081 AAATTT-GTGTATGTATGCTTCC
1 AATTTTGGTGTAT-AATGCTGCC
* *
12201103 TAATTTTTGGTGAATCAATGGTGTCC
1 -AA-TTTTGGTGTAT-AATGCTG-CC
* **
12201129 AATTTT-GTATATACATGCTGTTA
1 AATTTTGGTGTATA-ATGCTG-CC
12201152 AATTTT-GTGTATAAGTGCTGTCC
1 AATTTTGGTGTATAA-TGCTG-CC
* *
12201175 AA-ATTGGTGTATGTATGCTGCC
1 AATTTTGGTGTAT-AATGCTGCC
*
12201197 TAATTTTTGGTGAATCAATGCTGTCC
1 -AA-TTTTGGTGTAT-AATGCTG-CC
* **
12201223 AATTTT-GTATATACATGCTGTTA
1 AATTTTGGTGTATA-ATGCTG-CC
12201246 AATTTT-GTGTATAAGTGCTGTCC
1 AATTTTGGTGTATAA-TGCTG-CC
* * * *
12201269 AA-ATTGGTATATGTATGTTGCC
1 AATTTTGGTGTAT-AATGCTGCC
*
12201291 TAATTTTTGGTGAATCAATGCTGTCC
1 -AA-TTTTGGTGTAT-AATGCTG-CC
12201317 AATTTT
1 AATTTT
12201323 ATATACACAT
Statistics
Matches: 464, Mismatches: 99, Indels: 109
0.69 0.15 0.16
Matches are distributed among these distances:
22 39 0.08
23 268 0.58
24 39 0.08
25 104 0.22
26 14 0.03
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (22 bp):
AATTTTGGTGTATAATGCTGCC
Found at i:12203501 original size:93 final size:93
Alignment explanation
Indices: 12203341--12203765 Score: 516
Period size: 93 Copynumber: 4.6 Consensus size: 93
12203331 ATATATATAT
* * * *
12203341 ATATATATAC-AAATTAGGGCAGCATTTATACACCAAAATTTGACAGCGTATATATACAAAATTG
1 ATATATATACAAAATT-GGACAGCATTTATACACTAAAATTGGACAGCATATATATACAAAATTG
* * * * *
12203405 GACAGGATTTATACCCTAAAATTGGGCAGC
65 GACAGCACTTATACAC-AAAATTTGACAGC
* ** *
12203435 ATATATATATC-AATTTGGACAGCGCTTATACAC-AAAAGTT-GACAGCATGTATATACAAAATT
1 ATATATATA-CAAAATTGGACAGCATTTATACACTAAAA-TTGGACAGCATATATATACAAAATT
*
12203497 GGACAGGACTTATACACAAAATTTGACAGC
64 GGACAGCACTTATACACAAAATTTGACAGC
** * * * *
12203527 ATGGATATACAAAATTGGACAGCATTTATACACTAAAATTGGGCAGCGTATATATACCAATTTGG
1 ATATATATACAAAATTGGACAGCATTTATACACTAAAATTGGACAGCATATATATACAAAATTGG
12203592 ACAGCACTTATACACAAAATTTGACAGC
66 ACAGCACTTATACACAAAATTTGACAGC
* * * *
12203620 ATGTATATACAAAATTGGACAGCATTTATACACTAAAATTGGGCAGCATATATATACCAATTTGG
1 ATATATATACAAAATTGGACAGCATTTATACACTAAAATTGGACAGCATATATATACAAAATTGG
**
12203685 ACAGCACTTATACACAAAATTTGGTAGC
66 ACAGCACTTATACACAAAATTTGACAGC
* * * *
12203713 ATATATATACAAAATTAGACAACATTTATACACCAAAATTGGGCAGCATATAT
1 ATATATATACAAAATTGGACAGCATTTATACACTAAAATTGGACAGCATATAT
12203766 TCGATTTTTG
Statistics
Matches: 297, Mismatches: 29, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
91 1 0.00
92 39 0.13
93 227 0.76
94 25 0.08
95 5 0.02
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (93 bp):
ATATATATACAAAATTGGACAGCATTTATACACTAAAATTGGACAGCATATATATACAAAATTGG
ACAGCACTTATACACAAAATTTGACAGC
Found at i:12203624 original size:139 final size:139
Alignment explanation
Indices: 12203344--12203761 Score: 552
Period size: 139 Copynumber: 3.0 Consensus size: 139
12203334 TATATATATA
* *
12203344 TATATAC-AAATTAGGGCAGCATTTATACACCAAAATTTGACAGCGTATATATACAAAATTGGAC
1 TATATACAAAATT-GGACAGCATTTATACA-CAAAATTTGACAGCATATATATACAAAATTGGAC
* * * * *
12203408 AGGATTTATACCCTAAAATTGGGCAGCATATATATATCAATTTGGACAGCGCTTATACACAAAAG
64 AGCATTTATACACTAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAAT
12203473 TTGACAGCATG
129 TTGACAGCATG
* * **
12203484 TATATACAAAATTGGACAGGACTTATACACAAAATTTGACAGCATGGATATACAAAATTGGACAG
1 TATATACAAAATTGGACAGCATTTATACACAAAATTTGACAGCATATATATACAAAATTGGACAG
*
12203549 CATTTATACACTAAAATTGGGCAGCGTATATATACCAATTTGGACAGCACTTATACACAAAATTT
66 CATTTATACACTAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTT
12203614 GACAGCATG
131 GACAGCATG
* * * *
12203623 TATATACAAAATTGGACAGCATTTATACACTAAAATTGGGCAGCATATATATACCAATTTGGACA
1 TATATACAAAATTGGACAGCATTTATACAC-AAAATTTGACAGCATATATATACAAAATTGGACA
* * * * * * * *
12203688 GCACTTATACAC-AAAATTTGGTAGCATATATATACAAAATTAGACAACATTTATACACCAAAAT
65 GCATTTATACACTAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACA-CAAAAT
* *
12203752 TGGGCAGCAT
129 TTGACAGCAT
12203762 ATATTCGATT
Statistics
Matches: 244, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
139 166 0.68
140 73 0.30
141 5 0.02
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (139 bp):
TATATACAAAATTGGACAGCATTTATACACAAAATTTGACAGCATATATATACAAAATTGGACAG
CATTTATACACTAAAATTGGGCAGCATATATATACCAATTTGGACAGCACTTATACACAAAATTT
GACAGCATG
Found at i:12203742 original size:46 final size:46
Alignment explanation
Indices: 12203341--12203765 Score: 485
Period size: 46 Copynumber: 9.1 Consensus size: 46
12203331 ATATATATAT
* *
12203341 ATATATATAC-AAATTAGGGCAGCATTTATACACCAAAATTTGACAGC
1 ATATATATACAAAATT-GGACAGCATTTATACA-CAAAATTTGGCAGC
* * * *
12203388 GTATATATACAAAATTGGACAGGATTTATACCCTAAAATTGGGCAGC
1 ATATATATACAAAATTGGACAGCATTTATACAC-AAAATTTGGCAGC
* ** * *
12203435 ATATATATATC-AATTTGGACAGCGCTTATACACAAAAGTTGACAGC
1 ATATATATA-CAAAATTGGACAGCATTTATACACAAAATTTGGCAGC
* * * *
12203481 ATGTATATACAAAATTGGACAGGACTTATACACAAAATTTGACAGC
1 ATATATATACAAAATTGGACAGCATTTATACACAAAATTTGGCAGC
** *
12203527 ATGGATATACAAAATTGGACAGCATTTATACACTAAAATTGGGCAGC
1 ATATATATACAAAATTGGACAGCATTTATACAC-AAAATTTGGCAGC
* * * * *
12203574 GTATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGC
1 ATATATATACAAAATTGGACAGCATTTATACACAAAATTTGGCAGC
* *
12203620 ATGTATATACAAAATTGGACAGCATTTATACACTAAAATTGGGCAGC
1 ATATATATACAAAATTGGACAGCATTTATACAC-AAAATTTGGCAGC
* * * *
12203667 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGGTAGC
1 ATATATATACAAAATTGGACAGCATTTATACACAAAATTTGGCAGC
* * *
12203713 ATATATATACAAAATTAGACAACATTTATACACCAAAATTGGGCAGC
1 ATATATATACAAAATTGGACAGCATTTATACA-CAAAATTTGGCAGC
12203760 ATATAT
1 ATATAT
12203766 TCGATTTTTG
Statistics
Matches: 318, Mismatches: 53, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
45 1 0.00
46 157 0.49
47 154 0.48
48 6 0.02
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (46 bp):
ATATATATACAAAATTGGACAGCATTTATACACAAAATTTGGCAGC
Found at i:12204733 original size:43 final size:43
Alignment explanation
Indices: 12204644--12204755 Score: 140
Period size: 43 Copynumber: 2.6 Consensus size: 43
12204634 AACTCGTACA
* *
12204644 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATAG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACATATAG
*
12204687 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACA-AGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACATA-TAG
*
12204730 ATGCCAACGTCCCAAACGTGGTCTTA
1 ATGCCAACGTCCCAGACGTGGTCTTA
12204756 AACGATAGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
42 4 0.07
43 53 0.88
44 3 0.05
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACATATAG
Found at i:12210647 original size:56 final size:52
Alignment explanation
Indices: 12210569--12210761 Score: 214
Period size: 50 Copynumber: 3.7 Consensus size: 52
12210559 GGGAATGAGA
*
12210569 TCCCATGTAAGATCATATCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCATC---GAGA-TATGAGAGG
* * *
12210625 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG--ATGAGAGG
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGAGATATGAGAGG
** * * **
12210675 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATC--GATATGAGAAC
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGAGATATGAGAGG
* *
12210725 TCCCATGTAAGACTATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCA
12210762 GTAAAGAAAA
Statistics
Matches: 118, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
48 1 0.01
50 79 0.67
53 3 0.03
56 35 0.30
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (52 bp):
TCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCGAGATATGAGAGG
Found at i:12210754 original size:100 final size:102
Alignment explanation
Indices: 12210575--12210761 Score: 243
Period size: 100 Copynumber: 1.8 Consensus size: 102
12210565 GAGATCCCAT
* * **
12210575 GTAAGATCATATCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTAAGACCA
1 GTAAGACCATATCTGGGACATGGCATGGGCATC----AGATTATGAGAACTCCCATGTAAGACCA
* *
12210640 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCC
62 TATCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCCC
* *
12210681 GTAAGACCATGTCTGGGACATGGCATGGGCATC-GA-TATGAGAACTCCCATGTAAGACTATATC
1 GTAAGACCATATCTGGGACATGGCATGGGCATCAGATTATGAGAACTCCCATGTAAGACCATATC
*
12210744 TGGGATATGGCATTGGCA
66 TGGGACATGGCATTGGCA
12210762 GTAAAGAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 40 0.56
101 2 0.03
106 30 0.42
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (102 bp):
GTAAGACCATATCTGGGACATGGCATGGGCATCAGATTATGAGAACTCCCATGTAAGACCATATC
TGGGACATGGCATTGGCACCGAGATGAGAGGTCCCCC
Found at i:12216476 original size:30 final size:30
Alignment explanation
Indices: 12216442--12216504 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
12216432 ACTTAACAAG
12216442 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
12216472 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
12216502 CAA
1 CAA
12216505 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:12217948 original size:43 final size:42
Alignment explanation
Indices: 12217901--12218027 Score: 155
Period size: 43 Copynumber: 3.0 Consensus size: 42
12217891 AGAACATAAC
* * *
12217901 CTTTAGCGGCGTTTTTAGGGAAAGCACCACTAAATGTCATGTT
1 CTTTAGCGGCGTTTGT-GGGAAAGCGCCGCTAAATGTCATGTT
** * **
12217944 CTTTAAAGGCGTTTGTGGGGAAAGCGCCGTTAAAAATCATGTT
1 CTTTAGCGGCGTTTGT-GGGAAAGCGCCGCTAAATGTCATGTT
12217987 CTTTAGCGGCGTTTGTGGGATAAGCGCCGCTAAATGTCATG
1 CTTTAGCGGCGTTTGTGGGA-AAGCGCCGCTAAATGTCATG
12218028 CTCTATAACA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
42 4 0.06
43 65 0.94
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (42 bp):
CTTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAATGTCATGTT
Found at i:12218043 original size:43 final size:43
Alignment explanation
Indices: 12217909--12218043 Score: 130
Period size: 43 Copynumber: 3.1 Consensus size: 43
12217899 ACCTTTAGCG
* * * *
12217909 GCGTTTTTAGGGAAAGCACCACTAAATGTCATGTTCTTTAA-A
1 GCGTTTGTGGGGAAAGCGCCGCTAAATGTCATGTTCTTTAACA
* ** * *
12217951 GGCGTTTGTGGGGAAAGCGCCGTTAAAAATCATGTTCTTTAGCG
1 -GCGTTTGTGGGGAAAGCGCCGCTAAATGTCATGTTCTTTAACA
* *
12217995 GCGTTTGT-GGGATAAGCGCCGCTAAATGTCATGCTCTATAACA
1 GCGTTTGTGGGGA-AAGCGCCGCTAAATGTCATGTTCTTTAACA
*
12218038 ACGTTT
1 GCGTTT
12218044 TTCCACATAA
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
42 4 0.05
43 69 0.95
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
GCGTTTGTGGGGAAAGCGCCGCTAAATGTCATGTTCTTTAACA
Found at i:12224358 original size:20 final size:20
Alignment explanation
Indices: 12224335--12224372 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12224325 TGTTATTGGA
* *
12224335 TTATGAAATGTGATATTAAG
1 TTATGAAAAGTAATATTAAG
12224355 TTATGAAAAGTAATATTA
1 TTATGAAAAGTAATATTA
12224373 TGGACTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (20 bp):
TTATGAAAAGTAATATTAAG
Found at i:12224648 original size:75 final size:75
Alignment explanation
Indices: 12224411--12224679 Score: 306
Period size: 75 Copynumber: 3.6 Consensus size: 75
12224401 TCGATTCATT
* * * * *
12224411 CGACTAGCACTGGGTGCAACTTCTGTCAGTTTATCTGACTAGCGTTGGGCACATTATTATAATTG
1 CGACTAGCGCTGGGCGCAACTTCTATCAGTTTATCTGACTAGTGTTGGGCACATTATTATAATCG
* *
12224476 TTGTTATATC
66 TCGGTATATC
* * * ** *
12224486 CGACTGGCGATGGGCGCATCTTCTGCCAGTTTATCTTG-CTAGTGCTGGGCACATTATTATAATC
1 CGACTAGCGCTGGGCGCAACTTCTATCAGTTTATC-TGACTAGTGTTGGGCACATTATTATAATC
*
12224550 ATCGGTATATC
65 GTCGGTATATC
* * * *
12224561 CGACTAGCGCTGGGTGCAACTTCTATCAGTTTATTTGACTAATGTTGGGCACATAATTATAATCG
1 CGACTAGCGCTGGGCGCAACTTCTATCAGTTTATCTGACTAGTGTTGGGCACATTATTATAATCG
*
12224626 CCGGTATATC
66 TCGGTATATC
* * * * *
12224636 CGACTAGTGCTGGGCCCAACCTCTATTAGTTTGTCTGACTAGTG
1 CGACTAGCGCTGGGCGCAACTTCTATCAGTTTATCTGACTAGTG
12224680 CTCGGCATAC
Statistics
Matches: 160, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
74 2 0.01
75 156 0.98
76 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (75 bp):
CGACTAGCGCTGGGCGCAACTTCTATCAGTTTATCTGACTAGTGTTGGGCACATTATTATAATCG
TCGGTATATC
Found at i:12230068 original size:53 final size:51
Alignment explanation
Indices: 12230007--12230117 Score: 188
Period size: 53 Copynumber: 2.1 Consensus size: 51
12229997 GGTGTCATTA
12230007 GGTATGTTGATTCTGATTTTGCTGGAGACCTTAATAAAAGAAGATCTTTCACAT
1 GGTATGTTGATTCTGATTTTGCTGGAGACCTTAAT--AA-AAGATCTTTCACAT
12230061 GG-ATGTTGATTCTGATTTTGCTGGAGACCTTAATAAAAGATCTTTCACAT
1 GGTATGTTGATTCTGATTTTGCTGGAGACCTTAATAAAAGATCTTTCACAT
12230111 GGTATGT
1 GGTATGT
12230118 CTTTACTATT
Statistics
Matches: 56, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
50 16 0.29
51 6 0.11
53 32 0.57
54 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (51 bp):
GGTATGTTGATTCTGATTTTGCTGGAGACCTTAATAAAAGATCTTTCACAT
Found at i:12231844 original size:16 final size:16
Alignment explanation
Indices: 12231823--12231880 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
12231813 CCCTTCAAGA
12231823 ATTTTATTAATAAATG
1 ATTTTATTAATAAATG
* ***
12231839 ATTTTATTTTATTTTTTG
1 ATTTTA--TTAATAAATG
12231857 ATTTTATTAATAAATG
1 ATTTTATTAATAAATG
12231873 ATTTTATT
1 ATTTTATT
12231881 TGTATGACAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 20 0.62
18 12 0.38
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTTTATTAATAAATG
Found at i:12232248 original size:25 final size:23
Alignment explanation
Indices: 12232213--12232262 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
12232203 AAGATTGTTA
* *
12232213 AAAAAATTTATATATTTTATTTT
1 AAAAAATTTATAAATTTAATTTT
12232236 AAAAAATCATTATAAATTTAATTTT
1 AAAAAAT--TTATAAATTTAATTTT
12232261 AA
1 AA
12232263 TAATTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
25 16 0.70
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAAAATTTATAAATTTAATTTT
Found at i:12239907 original size:16 final size:17
Alignment explanation
Indices: 12239880--12239914 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12239870 TCATTATGGG
12239880 TTTGGATAATTTCAAAT
1 TTTGGATAATTTCAAAT
*
12239897 TTTGG-TAATTTTAAAT
1 TTTGGATAATTTCAAAT
12239913 TT
1 TT
12239915 AAGTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (17 bp):
TTTGGATAATTTCAAAT
Found at i:12241352 original size:14 final size:14
Alignment explanation
Indices: 12241333--12241364 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12241323 ATAGTTTGCA
12241333 TATAAAGCAAACGG
1 TATAAAGCAAACGG
*
12241347 TATAAAGCAAATGG
1 TATAAAGCAAACGG
12241361 TATA
1 TATA
12241365 GGCAAACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.22
Consensus pattern (14 bp):
TATAAAGCAAACGG
Found at i:12252187 original size:30 final size:29
Alignment explanation
Indices: 12252153--12252215 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
12252143 AATTTACAAG
*
12252153 AATTGGATC-AAATCAAAATTTTATGTATAA
1 AATTGGA-CAAAATC-AAAGTTTATGTATAA
* *
12252183 AATTGTACAAAATCAAAGTTTATGTATAC
1 AATTGGACAAAATCAAAGTTTATGTATAA
12252212 AATT
1 AATT
12252216 ACACATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.37
Consensus pattern (29 bp):
AATTGGACAAAATCAAAGTTTATGTATAA
Found at i:12254255 original size:28 final size:28
Alignment explanation
Indices: 12254215--12254340 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
12254205 TGACTTTCGA
*
12254215 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
*
12254243 CACTAAGTGTGCGAGTTTAATTGTTAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
12254271 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * *
12254299 CACTAAGTGTGCGAGTTTGATTATTGAA-
1 CACTAAGTGTGCGAGTTTAATT-GTAAAG
12254327 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
12254341 ACTTATGAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
28 85 0.98
29 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:12254290 original size:56 final size:56
Alignment explanation
Indices: 12254214--12254341 Score: 195
Period size: 56 Copynumber: 2.3 Consensus size: 56
12254204 TTGACTTTCG
* * *
12254214 ACACTAAGTGTGCGAATTTAATTGTAAAGCACTAAGTGTGCGAGTTTAATTGTT-A
1 ACACTAAGTGTGCGAATTTAATGGCAAAGCACTAAGTGTGCGAGTTTAATTATTGA
* *
12254269 AGCACTAAGTGTGCGAGTTTAATGGCAAAGCACTAAGTGTGCGAGTTTGATTATTGA
1 A-CACTAAGTGTGCGAATTTAATGGCAAAGCACTAAGTGTGCGAGTTTAATTATTGA
12254326 ACACTAAGTGTGCGAA
1 ACACTAAGTGTGCGAA
12254342 CTTATGAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
55 1 0.02
56 62 0.95
57 2 0.03
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (56 bp):
ACACTAAGTGTGCGAATTTAATGGCAAAGCACTAAGTGTGCGAGTTTAATTATTGA
Found at i:12255101 original size:23 final size:22
Alignment explanation
Indices: 12255039--12255803 Score: 602
Period size: 23 Copynumber: 33.0 Consensus size: 22
12255029 TCTAAAATTG
* *
12255039 GTATATATATGTTGCCCAATTTT
1 GTATATA-ATGCTGTCCAATTTT
12255062 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATAT-AATGCTGTCCAATTTT
*
12255086 GTATATACATGCTGTCAAATTTT
1 GTATATA-ATGCTGTCCAATTTT
12255109 GTATATACATGCTGTCCAATTTT
1 GTATATA-ATGCTGTCCAATTTT
* * *
12255132 GTGTATAAGTGCTGTCCAAATTG
1 GTATATAA-TGCTGTCCAATTTT
*
12255155 GTATATATATGCTGCCCAATTTT
1 GTATATA-ATGCTGTCCAATTTT
12255178 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATAT-AATGCTGTCCAATTTT
*
12255202 GTATATAAGTGCTGTCCAA-ATT
1 GTATATAA-TGCTGTCCAATTTT
* *
12255224 GCTACATATATGCTGCCCAATTTT
1 G-TATATA-ATGCTGTCCAATTTT
12255248 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATAT-AATGCTGTCCAATTTT
*
12255272 GTATATACATGTTGTCCAATTTT
1 GTATATA-ATGCTGTCCAATTTT
* *
12255295 GTGTATAAGTGCTGTCCAAATTGCT
1 GTATATAA-TGCTGTCC-AATT-TT
* *
12255320 GCATAT-ATGCTGCCCAATTTT
1 GTATATAATGCTGTCCAATTTT
12255341 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATAT-AATGCTGTCCAATTTT
*
12255365 GTATATACATGCTGTCAAATTTT
1 GTATATA-ATGCTGTCCAATTTT
* * *
12255388 GTGTATAAGTGCTGTCCAAATTG
1 GTATATAA-TGCTGTCCAATTTT
*
12255411 GTATATATATGCTGCCCAATTTT
1 GTATATA-ATGCTGTCCAATTTT
12255434 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATAT-AATGCTGTCCAATTTT
*
12255458 GTATATACATGCTGTCAAATTTT
1 GTATATA-ATGCTGTCCAATTTT
* * *
12255481 GTGTATAA-GTCTGTCCAAATTG
1 GTATATAATG-CTGTCCAATTTT
12255503 GTATATATATGCTG-CCAAATTTT
1 GTATATA-ATGCTGTCC-AATTTT
12255526 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATAT-AATGCTGTCCAATTTT
* *
12255550 GTATATACATGATGTCAAATTTT
1 GTATATA-ATGCTGTCCAATTTT
* * *
12255573 GTGTATAAGTGCTGTCCAAATTG
1 GTATATAA-TGCTGTCCAATTTT
*
12255596 GTATATATATGCTGCCCAATTTT
1 GTATATA-ATGCTGTCCAATTTT
*
12255619 GGTGA-ATAAATGCTATCCAATTTT
1 -GT-ATAT-AATGCTGTCCAATTTT
*
12255643 GTATATACATGCTGTCAAATTTT
1 GTATATA-ATGCTGTCCAATTTT
* * *
12255666 GTGTATAAGTGCTGTCCAAATTG
1 GTATATAA-TGCTGTCCAATTTT
*
12255689 GTATATATATGCTGCCCAATTTT
1 GTATATA-ATGCTGTCCAATTTT
12255712 GGTGA-ATAAATGCTGTCCAATTTT
1 -GT-ATAT-AATGCTGTCCAATTTT
*
12255736 GTATATACATGCTGTCAAATTTT
1 GTATATA-ATGCTGTCCAATTTT
* * *
12255759 GTGTATAAGTGCTGTCCAAATTG
1 GTATATAA-TGCTGTCCAATTTT
12255782 GTATATACATGCTG-CTCAATTT
1 GTATATA-ATGCTGTC-CAATTT
12255804 CTGATGTATA
Statistics
Matches: 603, Mismatches: 76, Indels: 125
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.00
22 52 0.09
23 378 0.63
24 149 0.25
25 22 0.04
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (22 bp):
GTATATAATGCTGTCCAATTTT
Found at i:12255218 original size:93 final size:93
Alignment explanation
Indices: 12255033--12255825 Score: 1240
Period size: 93 Copynumber: 8.5 Consensus size: 93
12255023 TAATGGTCTA
*
12255033 AAATTGGTATATATATGTTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
*
12255098 TGTCAAATTTTGTATATACA-TGCTGTCC
66 TGTCAAATTTTGTGTATA-AGTGCTGTCC
* * * * * * * *
12255126 AATTTTGTGTATA-AGTGCTGTCCAA-ATTGGT-ATATATATGCTGCCCAATTTTGGTGA-ATAA
1 AAATTGGTATATATA-TGCTGCCCAATTTTGGTGA-ATAAATGCTGTCCAATTTT-GT-ATATAC
* *
12255187 ATGCTGTCCAATTTTGTATATAAGTGCTGTCC
62 ATGCTGTCAAATTTTGTGTATAAGTGCTGTCC
* * *
12255219 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGT
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
*
12255284 TGTCCAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
* **
12255312 AAATTGCTGCATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
12255377 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
12255405 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
12255470 TGTCAAATTTTGTGTATAAGT-CTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
* *
12255497 AAATTGGTATATATATGCTGCCAAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGA
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
12255562 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
*
12255590 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTATCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
12255655 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
12255683 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
12255748 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
* * * *
12255776 AAATTGGTATATACATGCTGCTCAATTTCTGATGTATAAGA-GCTGTCCAA
1 AAATTGGTATATATATGCTGCCCAATTT-TGGTGAATAA-ATGCTGTCCAA
12255826 ACAGGGTAGA
Statistics
Matches: 650, Mismatches: 38, Indels: 23
0.91 0.05 0.03
Matches are distributed among these distances:
91 1 0.00
92 115 0.18
93 491 0.76
94 41 0.06
95 2 0.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (93 bp):
AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
TGTCAAATTTTGTGTATAAGTGCTGTCC
Found at i:12267074 original size:24 final size:24
Alignment explanation
Indices: 12267047--12267140 Score: 68
Period size: 24 Copynumber: 3.9 Consensus size: 24
12267037 AAAAAAAATA
*
12267047 AAATAATAATGCATAACAAATTTG
1 AAATAATAATACATAACAAATTTG
* **
12267071 AAATGATAATACATAATGAATTTG
1 AAATAATAATACATAACAAATTTG
* *
12267095 AAA-ACA-AATACATAATAAATCT-
1 AAATA-ATAATACATAACAAATTTG
* *
12267117 AAGCTAATAATACATGAAAAAATT
1 AA-ATAATAATACAT-AACAAATT
12267141 ATGATGCTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
22 2 0.04
23 15 0.27
24 32 0.58
25 6 0.11
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (24 bp):
AAATAATAATACATAACAAATTTG
Found at i:12269414 original size:5 final size:5
Alignment explanation
Indices: 12269404--12269429 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12269394 CTCAAAAATT
12269404 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
12269430 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:12269758 original size:81 final size:81
Alignment explanation
Indices: 12269623--12269784 Score: 315
Period size: 81 Copynumber: 2.0 Consensus size: 81
12269613 AGGTGGGCGG
*
12269623 CGATCATGTGAAATATATCCCTAAAGAAGATGTTGATGCAGGGAATTATTGTGTGTGTTATGGTG
1 CGATCATGTGAAATATACCCCTAAAGAAGATGTTGATGCAGGGAATTATTGTGTGTGTTATGGTG
12269688 CTTGTGTAAAATAAAC
66 CTTGTGTAAAATAAAC
12269704 CGATCATGTGAAATATACCCCTAAAGAAGATGTTGATGCAGGGAATTATTGTGTGTGTTATGGTG
1 CGATCATGTGAAATATACCCCTAAAGAAGATGTTGATGCAGGGAATTATTGTGTGTGTTATGGTG
12269769 CTTGTGTAAAATAAAC
66 CTTGTGTAAAATAAAC
12269785 TGGTGTTGAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (81 bp):
CGATCATGTGAAATATACCCCTAAAGAAGATGTTGATGCAGGGAATTATTGTGTGTGTTATGGTG
CTTGTGTAAAATAAAC
Found at i:12269801 original size:63 final size:63
Alignment explanation
Indices: 12269729--12269913 Score: 210
Period size: 63 Copynumber: 2.9 Consensus size: 63
12269719 TACCCCTAAA
* * * * *
12269729 GAAGATGTTGATGCAGGGAATTATTGTGTGTGTTATGGTGCTTGTGTAAAATAAACTGGTGTT
1 GAAGGTGTTGATGCAGGGAATGATTGTGTGTGTTGTGGTGCTTGTGTAAAATAAACTGGAGCT
* * ** * * *
12269792 GAATGTGTTGATGTAAAGAATGGTTGTGTGTGCTGTGGTACTTGTGTAAAATAAACTGGAGCT
1 GAAGGTGTTGATGCAGGGAATGATTGTGTGTGTTGTGGTGCTTGTGTAAAATAAACTGGAGCT
* * * *
12269855 GAAGGTGTTGATGC-GAGGAATGAGTGTGCGTGTTGTGATGCTTGTGTCAAATAAACTGG
1 GAAGGTGTTGATGCAG-GGAATGATTGTGTGTGTTGTGGTGCTTGTGTAAAATAAACTGG
12269914 GTTAGAACCA
Statistics
Matches: 98, Mismatches: 23, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
63 98 1.00
ACGTcount: A:0.25, C:0.06, G:0.34, T:0.35
Consensus pattern (63 bp):
GAAGGTGTTGATGCAGGGAATGATTGTGTGTGTTGTGGTGCTTGTGTAAAATAAACTGGAGCT
Found at i:12271926 original size:25 final size:27
Alignment explanation
Indices: 12271864--12271929 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
12271854 ACAGATAAAC
*
12271864 GAAATAATTATATGAATTGGTTATATG
1 GAAATAATTATATGAAGTGGTTATATG
*
12271891 GAAATAATTATATGACGTGGTT-TAT-
1 GAAATAATTATATGAAGTGGTTATATG
**
12271916 GAAATGCTTATATG
1 GAAATAATTATATG
12271930 GATAGATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 12 0.34
26 3 0.09
27 20 0.57
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (27 bp):
GAAATAATTATATGAAGTGGTTATATG
Found at i:12273529 original size:7 final size:7
Alignment explanation
Indices: 12273519--12273563 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
12273509 ATAATTGAGG
12273519 ATTGAAA
1 ATTGAAA
12273526 ATTGAAA
1 ATTGAAA
12273533 ATTGAAA
1 ATTGAAA
12273540 ATTGAAA
1 ATTGAAA
12273547 ATTGAAA
1 ATTGAAA
*
12273554 ATTGGAA
1 ATTGAAA
12273561 ATT
1 ATT
12273564 TAGGATAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (7 bp):
ATTGAAA
Found at i:12274965 original size:18 final size:18
Alignment explanation
Indices: 12274934--12274968 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12274924 TAAAATTATA
12274934 AAATAAAATAATTATTTC
1 AAATAAAATAATTATTTC
* *
12274952 AAATATAATTATTATTT
1 AAATAAAATAATTATTT
12274969 TTATATGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAAAATAATTATTTC
Found at i:12281609 original size:30 final size:31
Alignment explanation
Indices: 12281555--12281635 Score: 110
Period size: 30 Copynumber: 2.6 Consensus size: 31
12281545 ATTTCTTTAA
* *
12281555 ATGTGTATAATTAAATCAAAATCAAAGTTTC
1 ATGTGTATGATTGAATCAAAATCAAAGTTTC
*
12281586 ATGTGTATGATTGCATC-AAATCAAAGTTTC
1 ATGTGTATGATTGAATCAAAATCAAAGTTTC
* *
12281616 ATGTATATGATTGAACCAAA
1 ATGTGTATGATTGAATCAAA
12281636 TTAGAGTTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 27 0.63
31 16 0.37
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (31 bp):
ATGTGTATGATTGAATCAAAATCAAAGTTTC
Found at i:12285442 original size:24 final size:24
Alignment explanation
Indices: 12285405--12285455 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
12285395 ATGAGATAAG
12285405 ACTAGATGCAATCTGCTCTCTGCA
1 ACTAGATGCAATCTGCTCTCTGCA
** *
12285429 ACTAGATGTGATCTGCTCTCTGTA
1 ACTAGATGCAATCTGCTCTCTGCA
12285453 ACT
1 ACT
12285456 TCAGAGAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (24 bp):
ACTAGATGCAATCTGCTCTCTGCA
Found at i:12285633 original size:44 final size:45
Alignment explanation
Indices: 12285527--12285648 Score: 144
Period size: 44 Copynumber: 2.7 Consensus size: 45
12285517 TTGGCTTTAA
* *
12285527 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCTTCTTCAG
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGCCTTCTTCAG
*
12285572 TCTAC-CTCACTGCAACTTCA-AGAGGATAAGACTTG-CTTACTT-AG
1 TCTGCTC-CACTGCAACTTCAGAGA-GATAAGACTTGCCTT-CTTCAG
* *
12285616 TCTGCTCCACTGCAACTTTAGGGAGATAAGACT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACT
12285649 AGATGCGATC
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
44 33 0.50
45 33 0.50
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGCCTTCTTCAG
Found at i:12285766 original size:24 final size:24
Alignment explanation
Indices: 12285732--12285780 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
12285722 GAGATAAGAT
12285732 TAGATGAGATCTGCTCTCTGCAAC
1 TAGATGAGATCTGCTCTCTGCAAC
* *
12285756 TAGATGCGATCTGCTCTCTGTAAC
1 TAGATGAGATCTGCTCTCTGCAAC
12285780 T
1 T
12285781 TCAGAGAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (24 bp):
TAGATGAGATCTGCTCTCTGCAAC
Found at i:12285917 original size:45 final size:44
Alignment explanation
Indices: 12285853--12286411 Score: 325
Period size: 44 Copynumber: 12.7 Consensus size: 44
12285843 GGCTTTAATA
* * * *
12285853 TGCTCTACTGTAACTTTAGGGAGATAAGATTTGTCATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATCTTCAGTC
* * *
12285898 TGC-CTCACTGCAACTTTA-GGAGGATAAGACTTGCTTACTT-AGTT
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCAT-CTTCAGTC
* * * *
12285942 TGCTCCACTGTAACTTTAGGGAGATAAGACTAG-A--TGC-GATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCTTCAG-TC
* * ** * * * *
12285983 TGCT-CTCTGTAACTTCAAAGAGATAAGATCTAAG-GT-TTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCATCTTCAGTC
* * * * * *
12286026 CGCTCCACTGCAACTTCAGGGAGATAGGA-TTATCAGCTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCATCTTCAGTC
12286070 TGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCCATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTT-G-CATCTTCAGTC
*
12286115 TGC-CTCACTGCAACTTTA-GGAGGATAAGACTTGCCATCTTCAGTC
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTG-CATCTTCAGTC
* *
12286160 TGCTTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTT-AGTC
1 TGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCAT-CTTCAGTC
* * * * * *
12286204 TGCTCCACTGCAACTTTAAGGAGATAAGACCTAAG-GT-TTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCATCTTCAGTC
* * * * * ** * *
12286248 CGCTCCATTGCAACTACAGGGAGATATGA-TTATCGGCTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCATCTTCAGTC
* * *
12286292 TGCTCCACTGCAACTTTAGGAAGATAAGATTTGCCATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATCTTCAGTC
* *
12286337 TGC-CTCACTGCAACTTCA-GGAGGATAAAACTTGCTTACTT-AGTC
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCAT-CTTCAGTC
*
12286381 TGCTCCACTGTAACTTCAGGGAGATAAGACT
1 TGCTCCACTGCAACTTCAGGGAGATAAGACT
12286412 AGACACGATC
Statistics
Matches: 408, Mismatches: 71, Indels: 71
0.74 0.13 0.13
Matches are distributed among these distances:
40 22 0.05
41 7 0.02
42 4 0.01
43 9 0.02
44 210 0.51
45 153 0.38
46 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATCTTCAGTC
Found at i:12285968 original size:44 final size:44
Alignment explanation
Indices: 12285853--12286490 Score: 305
Period size: 44 Copynumber: 14.6 Consensus size: 44
12285843 GGCTTTAATA
* * * * *
12285853 TGCTCTACTGTAACTTTAGGGAGATAAGATTTG-TCATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA-CTT-AGTC
* *
12285898 TGC-CTCACTGCAACTTTA-GGAGGATAAGACTTGCTTACTTAGTT
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGTC
* * * * * *
12285942 TGCTCCACTGTAACTTTAGGGAGATAAGACTAG-ATGC-GA-TC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTACTTAGTC
* * ** * * *
12285983 TGCT-CTCTGTAACTTCAAAGAGATAAGATCTAAGGTT--TTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTACTTAGTC
* * * * *
12286026 CGCTCCACTGCAACTTCAGGGAGATAGGA-TT-ATCAGCTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA-C-TTAGTC
*
12286070 TGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGC-CATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTTA-CTT-AGTC
* *
12286115 TGC-CTCACTGCAACTTTA-GGAGGATAAGACTTGC-CATCTTCAGTC
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTA-CTT-AGTC
*
12286160 TGCTTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTC
1 TGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGTC
* * * * *
12286204 TGCTCCACTGCAACTTTAAGGAGATAAGACCTAAGGTT--TTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTACTTAGTC
* * * * * *
12286248 CGCTCCATTGCAACTACAGGGAGATATGATTATCGGC-T--TTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTTACTTAGTC
* * * *
12286292 TGCTCCACTGCAACTTTAGGAAGATAAGATTTGC-CATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA-CTT-AGTC
*
12286337 TGC-CTCACTGCAACTTCA-GGAGGATAAAACTTGCTTACTTAGTC
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGTC
* * *
12286381 TGCTCCACTGTAACTTCAGGGAGATAAGACTAGAC--AC-GA-TC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTACTTAGTC
* * * * *
12286422 TGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTT--TTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTACTTAGTC
* *
12286465 CGCTCCACTACAACTTCAGGGAGATA
1 TGCTCCACTGCAACTTCAGGGAGATA
12286491 GGATTATTGG
Statistics
Matches: 473, Mismatches: 75, Indels: 91
0.74 0.12 0.14
Matches are distributed among these distances:
40 42 0.09
41 17 0.04
42 9 0.02
43 18 0.04
44 230 0.49
45 148 0.31
46 9 0.02
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTACTTAGTC
Found at i:12285969 original size:324 final size:325
Alignment explanation
Indices: 12285397--12286057 Score: 1092
Period size: 324 Copynumber: 2.0 Consensus size: 325
12285387 TGACTTCAAT
* *
12285397 GAGATAAGACTAGATGCAATCTGCTCTCTGCAACTAGATGTGATCTGCTCTCTGTAACTTCAGAG
1 GAGATAAGATTAGATGCAATCTGCTCTCTGCAACTAGATGCGATCTGCTCTCTGTAACTTCAGAG
* * * *
12285462 AGATAAGATCTAAGGTTTTAATCCGCTCCATTGCAACTTTAGGGAGATAGGATTATTGGCTTTAA
66 AGATAAGATCTAAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAA
* *
12285527 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCTTCTTCAGTCTACCTCACTGCAACTTCA
131 TATGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTCA
12285592 AGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGA
196 AGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGA
* * *
12285657 TCTGCTCTTTGTAACTTCAGAGAGATAATATCTAAGGTTTTAATCCGCTCCACTACAACTTCAGG
261 TCTGCTCTCTGTAACTTCAAAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTACAACTTCAGG
12285722 GAGATAAGATTAGATG-AGATCTGCTCTCTGCAACTAGATGCGATCTGCTCTCTGTAACTTCAGA
1 GAGATAAGATTAGATGCA-ATCTGCTCTCTGCAACTAGATGCGATCTGCTCTCTGTAACTTCAGA
*
12285786 GAGATAAGATCTAA-ATTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
65 GAGATAAGATCTAAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTA
* * * * * *
12285850 ATATGCTCTACTGTAACTTTAGGGAGATAAGATTTGTCATCTTCAGTCTGCCTCACTGCAACTTT
130 ATATGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTC
* * *
12285915 AGGAGGATAAGACTTGCTTACTTAGTTTGCTCCACTGTAACTTTAGGGAGATAAGACTAGATGCG
195 AAGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAGATGCG
*
12285980 ATCTGCTCTCTGTAACTTCAAAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAG
260 ATCTGCTCTCTGTAACTTCAAAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTACAACTTCAG
12286045 G
325 G
*
12286046 GAGATAGGATTA
1 GAGATAAGATTA
12286058 TCAGCTTTAA
Statistics
Matches: 312, Mismatches: 23, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
324 238 0.76
325 74 0.24
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (325 bp):
GAGATAAGATTAGATGCAATCTGCTCTCTGCAACTAGATGCGATCTGCTCTCTGTAACTTCAGAG
AGATAAGATCTAAGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAA
TATGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCAACTTCA
AGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGA
TCTGCTCTCTGTAACTTCAAAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTACAACTTCAGG
Found at i:12286128 original size:217 final size:217
Alignment explanation
Indices: 12285754--12286497 Score: 1089
Period size: 217 Copynumber: 3.4 Consensus size: 217
12285744 GCTCTCTGCA
* * * * *
12285754 ACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTAA-ATTTTAATCCGCTCTACT
1 ACTAGATACGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTAAGGTTTTAATCCGCTCCACT
* * *
12285818 GCAACTTCAGGGAGATAGGATTATCGGCTTTAATATGCTCTACTGTAACTTTAGGGAGATAAGAT
66 GCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
* *
12285883 TTGTCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACTTGCTTACTTAGTTTGCTCC
131 TTGCCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACTTGCTTACTTAGTCTGCTCC
*
12285948 ACTGTAACTTTAGGGAGATAAG
196 ACTGTAACTTCAGGGAGATAAG
* *
12285970 ACTAGATGCGATCTGCTCTCTGTAACTTCAAAGAGATAAGATCTAAGGTTTTAATCCGCTCCACT
1 ACTAGATACGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTAAGGTTTTAATCCGCTCCACT
* *
12286035 GCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
66 GCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
* *
12286100 TCGCCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACTTGC-CATCTTCAGTCTGCT
131 TTGCCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACTTGCTTA-CTT-AGTCTGCT
* *
12286164 TCACTGCAACTTCA-GGAGGATAAG
194 CCACTGTAACTTCAGGGA-GATAAG
* * * * * * *
12286188 ACTTGCTTACTTAGTCTGCTCCACTGCAACTTTAAGGAGATAAGACCTAAGGTTTTAATCCGCTC
1 ACTAG-ATAC-GA-TCTGCT-CTCTGCAACTTCAAAGAGATAAGATCTAAGGTTTTAATCCGCTC
* * * *
12286253 CATTGCAACTACAGGGAGATATGATTATCGGCTTTAATCTGCTCCACTGCAACTTTAGGAAGATA
62 CACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATA
* *
12286318 AGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAAACTTGCTTACTTAGTCTG
127 AGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACTTGCTTACTTAGTCTG
12286383 CTCCACTGTAACTTCAGGGAGATAAG
192 CTCCACTGTAACTTCAGGGAGATAAG
* *
12286409 ACTAGACACGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACT
1 ACTAGATACGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTAAGGTTTTAATCCGCTCCACT
*
12286474 ACAACTTCAGGGAGATAGGATTAT
66 GCAACTTCAGGGAGATAGGATTAT
12286498 TGGCCAACGA
Statistics
Matches: 469, Mismatches: 49, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
216 46 0.10
217 192 0.41
218 34 0.07
219 3 0.01
220 3 0.01
221 36 0.08
222 154 0.33
223 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (217 bp):
ACTAGATACGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTAAGGTTTTAATCCGCTCCACT
GCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
TTGCCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACTTGCTTACTTAGTCTGCTCC
ACTGTAACTTCAGGGAGATAAG
Found at i:12286355 original size:177 final size:178
Alignment explanation
Indices: 12286027--12286410 Score: 528
Period size: 177 Copynumber: 2.2 Consensus size: 178
12286017 GTTTTAATCC
* * * * * *
12286027 GCTCCACTGCAACTTCAGGGAGATAGGA-TTATCA-GCTTTAATCTGCTCCACTGCAACTTCAGG
1 GCTCCACTGCAACTTCAAGGAGATAAGACCTA--AGGTTTTAATCCGCTCCACTGCAACTACAGG
* *
12286090 GAGATAAGATTCGCCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACTTGCCATCTT
64 GAGATAAGATTCGCCATCTTCAATCTGCCTCACTGCAACTTTAGGAAGATAAGACTTGCCATCTT
* *
12286155 CAGTCTGCTTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCT
129 CAGTCTGCCTCACTGCAACTTCAGGAGGATAAAACTTGCTTACTTAGTCT
* *
12286205 GCTCCACTGCAACTTTAAGGAGATAAGACCTAAGGTTTTAATCCGCTCCATTGCAACTACAGGGA
1 GCTCCACTGCAACTTCAAGGAGATAAGACCTAAGGTTTTAATCCGCTCCACTGCAACTACAGGGA
* * *
12286270 GATATGATTATCGGC-T-TT-AATCTG-CTCCACTGCAACTTTAGGAAGATAAGATTTGCCATCT
66 GATAAGA-T-TCGCCATCTTCAATCTGCCT-CACTGCAACTTTAGGAAGATAAGACTTGCCATCT
12286331 TCAGTCTGCCTCACTGCAACTTCAGGAGGATAAAACTTGCTTACTTAGTCT
128 TCAGTCTGCCTCACTGCAACTTCAGGAGGATAAAACTTGCTTACTTAGTCT
* *
12286382 GCTCCACTGTAACTTCAGGGAGATAAGAC
1 GCTCCACTGCAACTTCAAGGAGATAAGAC
12286411 TAGACACGAT
Statistics
Matches: 183, Mismatches: 18, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
176 2 0.01
177 113 0.62
178 60 0.33
179 4 0.02
180 4 0.02
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (178 bp):
GCTCCACTGCAACTTCAAGGAGATAAGACCTAAGGTTTTAATCCGCTCCACTGCAACTACAGGGA
GATAAGATTCGCCATCTTCAATCTGCCTCACTGCAACTTTAGGAAGATAAGACTTGCCATCTTCA
GTCTGCCTCACTGCAACTTCAGGAGGATAAAACTTGCTTACTTAGTCT
Found at i:12297848 original size:20 final size:21
Alignment explanation
Indices: 12297825--12297867 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
12297815 AATTTTTTAC
12297825 TAGAAAAAT-TAAAATTAATT
1 TAGAAAAATATAAAATTAATT
12297845 TAGAAAAATAATAAAATTAATT
1 TAGAAAAAT-ATAAAATTAATT
12297867 T
1 T
12297868 TTAAAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
TAGAAAAATATAAAATTAATT
Found at i:12297881 original size:21 final size:21
Alignment explanation
Indices: 12297835--12297900 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
12297825 TAGAAAAATT
**
12297835 AAAATTAATTTAGAAAAAT-AA
1 AAAATTAATTT-TTAAAATGAA
12297856 TAAAATTAATTTTTAAAATGAA
1 -AAAATTAATTTTTAAAATGAA
* *
12297878 AAAATAAATTATTAAAATGAA
1 AAAATTAATTTTTAAAATGAA
12297899 AA
1 AA
12297901 CTTATTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
21 26 0.67
22 13 0.33
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
AAAATTAATTTTTAAAATGAA
Found at i:12301601 original size:11 final size:11
Alignment explanation
Indices: 12301581--12301610 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
12301571 AGAAAATTAA
12301581 AAAAAGTATTTT
1 AAAAA-TATTTT
12301593 AAAAATATTTT
1 AAAAATATTTT
12301604 AAAAATA
1 AAAAATA
12301611 AAAAAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:12301609 original size:32 final size:32
Alignment explanation
Indices: 12301568--12301648 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 32
12301558 CCAAAAAAAA
12301568 TTTAGAAAATTAAAAAAAGTATTTTAAAA-ATAT
1 TTTA-AAAATTAAAAAAAGTATTTTAAAATAT-T
* *
12301601 TTTAAAAATAAAAAAAAAGTATTTTAAATTATT
1 TTTAAAAAT-TAAAAAAAGTATTTTAAAATATT
12301634 TTTAAAAA-TAAAAAA
1 TTTAAAAATTAAAAAA
12301649 TATATATGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 6 0.14
32 5 0.12
33 30 0.70
34 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (32 bp):
TTTAAAAATTAAAAAAAGTATTTTAAAATATT
Found at i:12301616 original size:33 final size:33
Alignment explanation
Indices: 12301579--12301648 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 33
12301569 TTAGAAAATT
12301579 AAAAAAAGTATTTTAAAA-ATATTTTAAAAATAA
1 AAAAAAAGTATTTTAAAATAT-TTTTAAAAATAA
*
12301612 AAAAAAAGTATTTTAAATTATTTTTAAAAATAA
1 AAAAAAAGTATTTTAAAATATTTTTAAAAATAA
12301645 AAAA
1 AAAA
12301649 TATATATGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.94
34 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (33 bp):
AAAAAAAGTATTTTAAAATATTTTTAAAAATAA
Found at i:12301874 original size:29 final size:31
Alignment explanation
Indices: 12301832--12301908 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
12301822 TTTACCTCAG
*
12301832 GTTACATTTTAGTCACTTATGTT-T-GAAAT
1 GTTACATTTTAGTCACTTACGTTATCGAAAT
* *
12301861 GTTACATTTTAGTCACTTACGTTATCGTATT
1 GTTACATTTTAGTCACTTACGTTATCGAAAT
*
12301892 GTAACATTTTAGTCACT
1 GTTACATTTTAGTCACT
12301909 GAGCTGTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 22 0.52
30 1 0.02
31 19 0.45
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (31 bp):
GTTACATTTTAGTCACTTACGTTATCGAAAT
Found at i:12302073 original size:20 final size:20
Alignment explanation
Indices: 12302031--12302073 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12302021 TTTTGAGTAA
* ** *
12302031 TTTAATTTTTTTTTGTTTTT
1 TTTAACTTTTTTTTCCTTAT
12302051 TTTAACTTTTTTTTCCTTAT
1 TTTAACTTTTTTTTCCTTAT
12302071 TTT
1 TTT
12302074 CATTCTCTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTAACTTTTTTTTCCTTAT
Found at i:12302260 original size:21 final size:21
Alignment explanation
Indices: 12302234--12302277 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
12302224 AAAAAAAATA
12302234 TTAAAAAATCTTTATTTTGGG
1 TTAAAAAATCTTTATTTTGGG
12302255 TTAAAAAATCTTTATTTTGGG
1 TTAAAAAATCTTTATTTTGGG
12302276 TT
1 TT
12302278 TTCGTTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.50
Consensus pattern (21 bp):
TTAAAAAATCTTTATTTTGGG
Found at i:12304493 original size:39 final size:40
Alignment explanation
Indices: 12304450--12304540 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
12304440 TTGAATTTTC
* *
12304450 ATAGGAATTTGAA-TTTTTGGTTACAAAATTAAGTTTCTA
1 ATAGGAATTTGAAGTATTTGGATACAAAATTAAGTTTCTA
* * * * *
12304489 ATAGGAGTTTTAAGTATTTGGATATAAAATTGAGTTTTTA
1 ATAGGAATTTGAAGTATTTGGATACAAAATTAAGTTTCTA
*
12304529 ATAGAAATTTGA
1 ATAGGAATTTGA
12304541 GTAAAAGTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
39 11 0.27
40 30 0.73
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (40 bp):
ATAGGAATTTGAAGTATTTGGATACAAAATTAAGTTTCTA
Found at i:12304986 original size:22 final size:22
Alignment explanation
Indices: 12304935--12304980 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12304925 AAAAAAAATT
*
12304935 AAAATTAACAATAATTGTAAAA
1 AAAATTAAAAATAATTGTAAAA
12304957 AAAATTAAAAATAATTGTAAAA
1 AAAATTAAAAATAATTGTAAAA
12304979 AA
1 AA
12304981 TGTTAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAATTAAAAATAATTGTAAAA
Found at i:12305014 original size:21 final size:21
Alignment explanation
Indices: 12304984--12305034 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
12304974 TAAAAAATGT
* *
12304984 TAATTAAAAATT-ATAAAAAT
1 TAATTTAAAATTCATAAAAAA
*
12305004 TAATTGTAAAATTCTTAAAAAA
1 TAATT-TAAAATTCATAAAAAA
12305026 TAATTTAAA
1 TAATTTAAA
12305035 TTAACAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 10 0.38
22 11 0.42
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TAATTTAAAATTCATAAAAAA
Found at i:12305067 original size:23 final size:23
Alignment explanation
Indices: 12305040--12305085 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
12305030 TTAAATTAAC
*
12305040 AATTTTTACCA-TTTTTAATGAAT
1 AATTTTTACAACTTTTTAA-GAAT
12305063 AATTTTTACAACTTTTTAAGAAT
1 AATTTTTACAACTTTTTAAGAAT
12305086 TTTCATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (23 bp):
AATTTTTACAACTTTTTAAGAAT
Found at i:12305495 original size:16 final size:17
Alignment explanation
Indices: 12305474--12305512 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
12305464 TAATAATGAA
12305474 ATATT-ATAGACCCAAT
1 ATATTAATAGACCCAAT
*
12305490 ATATTAAATAGGCCCAAT
1 ATATT-AATAGACCCAAT
12305508 ATATT
1 ATATT
12305513 CTGTAAGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
18 15 0.75
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (17 bp):
ATATTAATAGACCCAAT
Found at i:12306146 original size:99 final size:99
Alignment explanation
Indices: 12305975--12306170 Score: 320
Period size: 99 Copynumber: 2.0 Consensus size: 99
12305965 TCCCTTTTGC
*
12305975 CTTTCCGAGTTACTTCCGCTTTATTTCGGTGCCTTAGAGAATTTCCCTTGAGAATTCTCACTTTC
1 CTTTCCAAGTTACTTCCGCTTTATTTCGGTGCCTTAGAGAATTTCCCTTGAGAATTCTCACTTTC
* ** *
12306040 AAGAGATAGGTTGACTTGGGCAGATTTGAAGTGT
66 AAGAGATAAGTTGACTTAAGCAGATTTAAAGTGT
* *
12306074 CTTTCCAAGTTACTTCCGTTTTATTTCGGTGGCTTAGAGAATTTCCCTTGAGAATTCTCACTTTC
1 CTTTCCAAGTTACTTCCGCTTTATTTCGGTGCCTTAGAGAATTTCCCTTGAGAATTCTCACTTTC
*
12306139 AAGAGATAAGTTGTCTTAAGCAGATTTAAAGT
66 AAGAGATAAGTTGACTTAAGCAGATTTAAAGT
12306171 AAAGATATCT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 89 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (99 bp):
CTTTCCAAGTTACTTCCGCTTTATTTCGGTGCCTTAGAGAATTTCCCTTGAGAATTCTCACTTTC
AAGAGATAAGTTGACTTAAGCAGATTTAAAGTGT
Found at i:12306414 original size:26 final size:25
Alignment explanation
Indices: 12306369--12306418 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
12306359 TAACACTGGC
* *
12306369 TATGTTTTTAATGTAGTGTTTGTTAT
1 TATGATTTTAATGTAATG-TTGTTAT
*
12306395 TATGATTTTAATTTAATGTTGTTA
1 TATGATTTTAATGTAATGTTGTTA
12306419 GTGTTATTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (25 bp):
TATGATTTTAATGTAATGTTGTTAT
Found at i:12309216 original size:16 final size:16
Alignment explanation
Indices: 12309195--12309239 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
12309185 TTTTAAAACT
12309195 TATATTTAGATATAAA
1 TATATTTAGATATAAA
*
12309211 TATATTT--ATATGAA
1 TATATTTAGATATAAA
12309225 TATATCTTAGATATA
1 TATAT-TTAGATATA
12309240 TTTGCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 11 0.46
15 2 0.08
16 7 0.29
17 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (16 bp):
TATATTTAGATATAAA
Found at i:12309356 original size:65 final size:65
Alignment explanation
Indices: 12309285--12309412 Score: 213
Period size: 65 Copynumber: 2.0 Consensus size: 65
12309275 AACCAAAATA
* *
12309285 ATATATAATTTATGAAGAAACTAAAAATTAGATTATAAATAT-ATATGTGAAAAATATTTAAATG
1 ATATATAATTTATCAAGAAACTAAAAATTAGAGTATAAATATCATAT-TGAAAAATATTTAAATG
12309349 T
65 T
12309350 ATATATAATTTATCAAGAAACTAAAAATTAGAGTATAAATATGCATATTGAAAAATATTTAAA
1 ATATATAATTTATCAAGAAACTAAAAATTAGAGTATAAATAT-CATATTGAAAAATATTTAAA
12309413 AACAATGATA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
65 40 0.68
66 15 0.25
67 4 0.07
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (65 bp):
ATATATAATTTATCAAGAAACTAAAAATTAGAGTATAAATATCATATTGAAAAATATTTAAATGT
Found at i:12309664 original size:14 final size:14
Alignment explanation
Indices: 12309647--12309675 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12309637 GTATTTAGTT
12309647 TTGTGCTAGAACCA
1 TTGTGCTAGAACCA
12309661 TTGTGCTAGAACCA
1 TTGTGCTAGAACCA
12309675 T
1 T
12309676 AGAGATTTGT
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:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (14 bp):
TTGTGCTAGAACCA
Found at i:12312314 original size:15 final size:15
Alignment explanation
Indices: 12312275--12312315 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
12312265 CAAGAAATCC
12312275 AAAACAAACCCAAAT
1 AAAACAAACCCAAAT
* *
12312290 AGAACCAACCCAAAT
1 AAAACAAACCCAAAT
*
12312305 AAAAAAAACCC
1 AAAACAAACCC
12312316 CAAGCCCAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.63, C:0.29, G:0.02, T:0.05
Consensus pattern (15 bp):
AAAACAAACCCAAAT
Found at i:12312418 original size:16 final size:18
Alignment explanation
Indices: 12312397--12312432 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
12312387 CCAGAAAGAA
12312397 GGAAAAAGAA-AA-AAAG
1 GGAAAAAGAAGAAGAAAG
12312413 GGAAAAAGAAGAAGAAAG
1 GGAAAAAGAAGAAGAAAG
12312431 GG
1 GG
12312433 GCCCAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
GGAAAAAGAAGAAGAAAG
Found at i:12312503 original size:5 final size:5
Alignment explanation
Indices: 12312493--12312521 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12312483 CATGAAAACA
12312493 CCCAC CCCAC CCCAC CCCAC CCCAC CCCA
1 CCCAC CCCAC CCCAC CCCAC CCCAC CCCA
12312522 AATTCTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.79, G:0.00, T:0.00
Consensus pattern (5 bp):
CCCAC
Found at i:12319328 original size:30 final size:28
Alignment explanation
Indices: 12319279--12319334 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
12319269 AAAATAGATC
*
12319279 AATATAAATAAATATTTATATATAATGA
1 AATATAAATAAAAATTTATATATAATGA
*
12319307 AATATAAATAGAACAATTTATATTTAAT
1 AATATAAATA-AA-AATTTATATATAAT
12319335 TTGTGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.42
29 2 0.08
30 12 0.50
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (28 bp):
AATATAAATAAAAATTTATATATAATGA
Found at i:12323610 original size:10 final size:10
Alignment explanation
Indices: 12323593--12323634 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
12323583 AATTTAATTC
12323593 TTTTCTTTTA
1 TTTTCTTTTA
*
12323603 TGTTCTTTTAA
1 TTTTCTTTT-A
12323614 TTTTCTTTT-
1 TTTTCTTTTA
12323623 TTTTCTTTTA
1 TTTTCTTTTA
12323633 TT
1 TT
12323635 CTCCATTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 9 0.32
10 10 0.36
11 9 0.32
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:12324467 original size:21 final size:21
Alignment explanation
Indices: 12324443--12324486 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
12324433 CTTCAACGAA
12324443 AACCCAGAATAAAGATTTTTT
1 AACCCAGAATAAAGATTTTTT
*
12324464 AACCTAGAATAAAGATTTTTT
1 AACCCAGAATAAAGATTTTTT
12324485 AA
1 AA
12324487 TCTTTTTCTT
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:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (21 bp):
AACCCAGAATAAAGATTTTTT
Found at i:12328461 original size:3 final size:3
Alignment explanation
Indices: 12328390--12328450 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
12328380 AGATGGAGGA
12328390 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
12328438 AAG AAG AAG AAG A
1 AAG AAG AAG AAG A
12328451 CTTTAAGAAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12330247 original size:40 final size:40
Alignment explanation
Indices: 12330203--12330411 Score: 249
Period size: 40 Copynumber: 5.2 Consensus size: 40
12330193 GTGCTCATGA
* *
12330203 TTGTACTTCGGTACCCCTGAATGCAGATACGTGCCCCTTT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTGT
* * *
12330243 TTGTACTTCGATACCCCTGAATGCACATATGTGCCCCTGA
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTGT
* * * *
12330283 TTGTACTTCAGTA-CCCTAAATGCACATACGTGCCCTTAT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTGT
* * * * *
12330322 TTATACTTTGGTACCCTTGAATGCATATACGTGCCCCTGA
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTGT
* * * *
12330362 TTGTACTTCGGTACCCTTGAATACATATACGTGCCCCTAT
1 TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTGT
12330402 TTGTACTTCG
1 TTGTACTTCG
12330412 AAACTCCTTA
Statistics
Matches: 142, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 31 0.22
40 111 0.78
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.34
Consensus pattern (40 bp):
TTGTACTTCGGTACCCCTGAATGCACATACGTGCCCCTGT
Found at i:12345009 original size:17 final size:17
Alignment explanation
Indices: 12344987--12345023 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12344977 GATAAGTATA
*
12344987 CATTGTCATTGCATTTT
1 CATTGTCATTACATTTT
12345004 CATTGTCATTACATTTT
1 CATTGTCATTACATTTT
12345021 CAT
1 CAT
12345024 GATTAGTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.19, G:0.08, T:0.51
Consensus pattern (17 bp):
CATTGTCATTACATTTT
Found at i:12349084 original size:17 final size:18
Alignment explanation
Indices: 12349051--12349084 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12349041 ATGATGTACC
12349051 AAACTATATTCATGCTTG
1 AAACTATATTCATGCTTG
*
12349069 AAACTAT-TTGATGCTT
1 AAACTATATTCATGCTT
12349085 ACTATTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (18 bp):
AAACTATATTCATGCTTG
Found at i:12350814 original size:55 final size:55
Alignment explanation
Indices: 12350755--12350860 Score: 176
Period size: 55 Copynumber: 1.9 Consensus size: 55
12350745 GATTTTTTGG
* * *
12350755 TGAAATTGTAGTTGGGGATTAAATTGTTAAAATTATAAATCCATGGGTTTTTTAA
1 TGAAATTGTAGTTAGGGACTAAATTGTTAAAATTATAAATCCATAGGTTTTTTAA
*
12350810 TGAAATTTTAGTTAGGGACTAAATTGTTAAAATTATAAATCCATAGGTTTT
1 TGAAATTGTAGTTAGGGACTAAATTGTTAAAATTATAAATCCATAGGTTTT
12350861 ACTATGAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.42
Consensus pattern (55 bp):
TGAAATTGTAGTTAGGGACTAAATTGTTAAAATTATAAATCCATAGGTTTTTTAA
Found at i:12350868 original size:55 final size:55
Alignment explanation
Indices: 12350755--12350873 Score: 168
Period size: 55 Copynumber: 2.2 Consensus size: 55
12350745 GATTTTTTGG
* * * * *
12350755 TGAAATTGTAGTTGGGGATTAAATTGTTAAAATTATAAATCCATGGGTTTTTTAA
1 TGAAATTTTAGTTAGGGACTAAATTGTTAAAATTATAAATCCATAGGTTTTCTAA
12350810 TGAAATTTTAGTTAGGGACTAAATTGTTAAAATTATAAATCCATAGGTTTTACT-A
1 TGAAATTTTAGTTAGGGACTAAATTGTTAAAATTATAAATCCATAGGTTTT-CTAA
*
12350865 TGAATTTTT
1 TGAAATTTT
12350874 GATAATTATG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 56 0.98
56 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (55 bp):
TGAAATTTTAGTTAGGGACTAAATTGTTAAAATTATAAATCCATAGGTTTTCTAA
Found at i:12357837 original size:32 final size:32
Alignment explanation
Indices: 12357796--12357860 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
12357786 AATGAAAGCT
12357796 TTTGTTGTATGCCATTATGGTTGAGAGGTCTA
1 TTTGTTGTATGCCATTATGGTTGAGAGGTCTA
12357828 TTTGTTGTATGCCATTATGGTTGAGAGGTCTA
1 TTTGTTGTATGCCATTATGGTTGAGAGGTCTA
12357860 T
1 T
12357861 CAATGTTGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.09, G:0.28, T:0.45
Consensus pattern (32 bp):
TTTGTTGTATGCCATTATGGTTGAGAGGTCTA
Found at i:12359395 original size:3 final size:3
Alignment explanation
Indices: 12359387--12359442 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
12359377 TATTTGATTC
12359387 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
12359435 AAG AAG AA
1 AAG AAG AA
12359443 AATAAAACAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12366083 original size:37 final size:37
Alignment explanation
Indices: 12365970--12366086 Score: 100
Period size: 38 Copynumber: 3.1 Consensus size: 37
12365960 TAGATCTCTT
* *
12365970 TAAATATGGTAACTTGATCACACATAAATTCTTCAAA
1 TAAATATGTTAACTTGATCACACATAAATTCTTCATA
* *
12366007 TAAAATCAT-TGAA--TGAT-ACTCA-ACAATATCATGTCCATA
1 T-AAAT-ATGTTAACTTGATCACACATA-AAT-TC-T-T-CATA
12366046 TAAATATGTTAACTTGATCACACATAAATTCTTCATA
1 TAAATATGTTAACTTGATCACACATAAATTCTTCATA
12366083 TAAA
1 TAAA
12366087 ATCATTGAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
34 1 0.02
35 7 0.11
36 6 0.10
37 12 0.19
38 15 0.24
39 7 0.11
40 6 0.10
41 7 0.11
42 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (37 bp):
TAAATATGTTAACTTGATCACACATAAATTCTTCATA
Found at i:12366096 original size:76 final size:76
Alignment explanation
Indices: 12365970--12366124 Score: 274
Period size: 76 Copynumber: 2.0 Consensus size: 76
12365960 TAGATCTCTT
12365970 TAAATATGGTAACTTGATCACACATAAATTCTTCAAATAAAATCATTGAATGATACTCAACAATA
1 TAAATATGGTAACTTGATCACACATAAATTCTTCAAATAAAATCATTGAATGATACTCAACAATA
*
12366035 TCATGTCCATA
66 TCATATCCATA
* * *
12366046 TAAATATGTTAACTTGATCACACATAAATTCTTCATATAAAATCATTGAATGATATTCAACAATA
1 TAAATATGGTAACTTGATCACACATAAATTCTTCAAATAAAATCATTGAATGATACTCAACAATA
12366111 TCATATCCATA
66 TCATATCCATA
12366122 TAA
1 TAA
12366125 TTGTTCCTCA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (76 bp):
TAAATATGGTAACTTGATCACACATAAATTCTTCAAATAAAATCATTGAATGATACTCAACAATA
TCATATCCATA
Found at i:12375273 original size:56 final size:56
Alignment explanation
Indices: 12375187--12375300 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
12375177 ATCACACAAA
12375187 TCTTTCCTATTTCACTCTATTTTTACAAACTCCACAGTGATGTATCTACTTAACCC
1 TCTTTCCTATTTCACTCTATTTTTACAAACTCCACAGTGATGTATCTACTTAACCC
* **
12375243 TCTTTCCTATTTCACTCTATTTTTACAAACTTCGTAGTGATGTATCTACTTAACCC
1 TCTTTCCTATTTCACTCTATTTTTACAAACTCCACAGTGATGTATCTACTTAACCC
12375299 TC
1 TC
12375301 AACACGTATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.43
Consensus pattern (56 bp):
TCTTTCCTATTTCACTCTATTTTTACAAACTCCACAGTGATGTATCTACTTAACCC
Found at i:12386885 original size:29 final size:29
Alignment explanation
Indices: 12386852--12387096 Score: 368
Period size: 29 Copynumber: 8.4 Consensus size: 29
12386842 GATGGTCGAA
*
12386852 ACCATCCCTTTTCATATTCAATGGTCATC
1 ACCATCCCTTTTCATATTCGATGGTCATC
*
12386881 ACCATCCCTTTTTATATTCGATGGTCATC
1 ACCATCCCTTTTCATATTCGATGGTCATC
*
12386910 ACCATCCCTTTTTATATTCGATGGTCGA--
1 ACCATCCCTTTTCATATTCGATGGTC-ATC
* * *
12386938 AGCCATCCCTTTTCATTTTCGATGGTCGTT
1 A-CCATCCCTTTTCATATTCGATGGTCATC
*
12386968 ACCATCCCTTTTCATATTCGATGGTCGTC
1 ACCATCCCTTTTCATATTCGATGGTCATC
* *
12386997 ACCATCCCTTTTTATATTCGATGGTCGTC
1 ACCATCCCTTTTCATATTCGATGGTCATC
*
12387026 ACCATCCCTTTTCATATTCGATGGTCGTC
1 ACCATCCCTTTTCATATTCGATGGTCATC
12387055 ACCATCCCTTTTCATATTCGATGGTCATC
1 ACCATCCCTTTTCATATTCGATGGTCATC
12387084 ACCATCCCTTTTC
1 ACCATCCCTTTTC
12387097 TTTAATCGAT
Statistics
Matches: 202, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
28 1 0.00
29 199 0.99
30 2 0.01
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.40
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTCGATGGTCATC
Found at i:12386946 original size:87 final size:86
Alignment explanation
Indices: 12386841--12387095 Score: 420
Period size: 87 Copynumber: 2.9 Consensus size: 86
12386831 TTCCTTTAAC
* * *
12386841 CGATGGTCGAAACCATCCCTTTTCATATTCAATGGTCATCACCATCCCTTTTTATATTCGATGGT
1 CGATGGTCG-AACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATATTCGATGGT
12386906 CATCACCATCCCTTTTTATATT
65 CATCACCATCCCTTTTTATATT
* *
12386928 CGATGGTCGAAGCCATCCCTTTTCATTTTCGATGGTCGTTACCATCCCTTTTCATATTCGATGGT
1 CGATGGTCGAA-CCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATATTCGATGGT
*
12386993 CGTCACCATCCCTTTTTATATT
65 CATCACCATCCCTTTTTATATT
*
12387015 CGATGGTCGTCACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATATTCGATGGT
1 CGATGGTCG-AACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATATTCGATGGT
12387080 CATCACCATCCCTTTT
65 CATCACCATCCCTTTT
12387096 CTTTAATCGA
Statistics
Matches: 156, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
86 2 0.01
87 153 0.98
88 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.13, T:0.39
Consensus pattern (86 bp):
CGATGGTCGAACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATATTCGATGGTC
ATCACCATCCCTTTTTATATT
Found at i:12404539 original size:25 final size:25
Alignment explanation
Indices: 12404510--12404569 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
12404500 CTAGATTATG
12404510 CCACAAAGGCAACATACAAAGTACA
1 CCACAAAGGCAACATACAAAGTACA
* * *
12404535 CCACAAAGGTAACATACAGAGTACG
1 CCACAAAGGCAACATACAAAGTACA
12404560 CCACAAAGGC
1 CCACAAAGGC
12404570 CAAATAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (25 bp):
CCACAAAGGCAACATACAAAGTACA
Found at i:12406826 original size:21 final size:22
Alignment explanation
Indices: 12406788--12406832 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
12406778 GTCAATTTGG
*
12406788 TATGTATATGTTTTTGGA-TTT
1 TATGTATATGTTTATGGACTTT
12406809 TATGTAT-TGTTTGATGGACTTT
1 TATGTATATGTTT-ATGGACTTT
12406831 TA
1 TA
12406833 GTGCCTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.58
Consensus pattern (22 bp):
TATGTATATGTTTATGGACTTT
Found at i:12413937 original size:54 final size:54
Alignment explanation
Indices: 12413850--12413973 Score: 160
Period size: 54 Copynumber: 2.3 Consensus size: 54
12413840 GTGTATATTT
* * *
12413850 CACACGGCCTAAGACATGGCCATGTGCATCAAGTCAATGAGTTATACGGTCTAG
1 CACACGGCCTGAGACATGGCCATGTGCATCAAGTCAAAGAGTTACACGGTCTAG
* * * *
12413904 CACACGGCCTGCGACATGGTCGTGTGTCA-CAAGTCAAAGAGTTACACGGTCTGG
1 CACACGGCCTGAGACATGGCCATGTG-CATCAAGTCAAAGAGTTACACGGTCTAG
*
12413958 CACACGGCCTGTGACA
1 CACACGGCCTGAGACA
12413974 CAATCGTGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 59 0.97
55 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (54 bp):
CACACGGCCTGAGACATGGCCATGTGCATCAAGTCAAAGAGTTACACGGTCTAG
Found at i:12414004 original size:54 final size:54
Alignment explanation
Indices: 12413895--12414005 Score: 123
Period size: 54 Copynumber: 2.1 Consensus size: 54
12413885 AATGAGTTAT
*** * * *
12413895 ACGGTCTAGCACACGGCCTGCGACATGGTCGTGTGTCACAAGTCAAAGAGTTAC
1 ACGGTCTAGCACACGGCCTGCGACACAATCGTGTGACACAACTCAAAGAGATAC
* * * **
12413949 ACGGTCTGGCACACGGCCTGTGACACAATCGTGTGACCCAACTCAGTGAGATAC
1 ACGGTCTAGCACACGGCCTGCGACACAATCGTGTGACACAACTCAAAGAGATAC
12414003 ACG
1 ACG
12414006 ATTTAAGACA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.26, C:0.28, G:0.27, T:0.19
Consensus pattern (54 bp):
ACGGTCTAGCACACGGCCTGCGACACAATCGTGTGACACAACTCAAAGAGATAC
Found at i:12417904 original size:4 final size:4
Alignment explanation
Indices: 12417892--12417922 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
12417882 TAAAATTAGT
12417892 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
12417923 AAGGATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:12418321 original size:31 final size:31
Alignment explanation
Indices: 12418228--12418323 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
12418218 GGCAAATTAC
*
12418228 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
12418259 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
12418291 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
12418322 AA
1 AA
12418324 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:12423327 original size:15 final size:15
Alignment explanation
Indices: 12423307--12423358 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
12423297 TAGGCAACTT
12423307 TTTTTTTTTTTGCGC
1 TTTTTTTTTTTGCGC
*
12423322 TTTTTTGCTTTTTGC-T
1 TTTTTT--TTTTTGCGC
12423338 TCTTTTTTTTTTGCGC
1 T-TTTTTTTTTTGCGC
12423354 TTTTT
1 TTTTT
12423359 ACTCTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 17 0.55
16 2 0.06
17 12 0.39
ACGTcount: A:0.00, C:0.13, G:0.12, T:0.75
Consensus pattern (15 bp):
TTTTTTTTTTTGCGC
Found at i:12423346 original size:21 final size:21
Alignment explanation
Indices: 12423322--12423390 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 21
12423312 TTTTTTGCGC
12423322 TTTTTTGCTTTTTGCTTCTTTT
1 TTTTTTGCTTTTTGCTTC-TTT
*
12423344 TTTTTTGCGCTTTTTAC-TCTTT
1 TTTTTT--GCTTTTTGCTTCTTT
*
12423366 TTTTTGCGCTTTTTTGCTT-TTT
1 TTTTT-TGC-TTTTTGCTTCTTT
12423388 TTT
1 TTT
12423391 GTTTTTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
21 2 0.05
22 26 0.67
23 3 0.08
24 8 0.21
ACGTcount: A:0.01, C:0.14, G:0.10, T:0.74
Consensus pattern (21 bp):
TTTTTTGCTTTTTGCTTCTTT
Found at i:12423349 original size:24 final size:23
Alignment explanation
Indices: 12423328--12423379 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
12423318 GCGCTTTTTT
*
12423328 GCTTTTTGCTTCTTTTTTTTTTGC
1 GCTTTTTAC-TCTTTTTTTTTTGC
12423352 GCTTTTTACTC--TTTTTTTTGC
1 GCTTTTTACTCTTTTTTTTTTGC
12423373 GCTTTTT
1 GCTTTTT
12423380 TGCTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 17 0.63
23 2 0.07
24 8 0.30
ACGTcount: A:0.02, C:0.17, G:0.12, T:0.69
Consensus pattern (23 bp):
GCTTTTTACTCTTTTTTTTTTGC
Found at i:12423385 original size:20 final size:20
Alignment explanation
Indices: 12423342--12423391 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
12423332 TTTGCTTCTT
12423342 TTTTTTTTGCGCTTTTTACTC
1 TTTTTTTTGCGCTTTTTA-TC
12423363 TTTTTTTTGCGCTTTTT-TGC
1 TTTTTTTTGCGCTTTTTAT-C
12423383 TTTTTTTTG
1 TTTTTTTTG
12423392 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.04
20 10 0.36
21 17 0.61
ACGTcount: A:0.02, C:0.14, G:0.12, T:0.72
Consensus pattern (20 bp):
TTTTTTTTGCGCTTTTTATC
Found at i:12423399 original size:9 final size:10
Alignment explanation
Indices: 12423362--12423399 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
12423352 GCTTTTTACT
12423362 CTTTTTTTTG
1 CTTTTTTTTG
**
12423372 CGCTTTTTTG
1 CTTTTTTTTG
12423382 CTTTTTTTTG
1 CTTTTTTTTG
12423392 -TTTTTTTT
1 CTTTTTTTT
12423400 AAAGAATAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (10 bp):
CTTTTTTTTG
Found at i:12423627 original size:4 final size:4
Alignment explanation
Indices: 12423615--12423645 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
12423605 TAAAATTAGT
12423615 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
12423646 AATGATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:12428096 original size:34 final size:34
Alignment explanation
Indices: 12428053--12428125 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
12428043 AGAACAAAAC
*
12428053 CAATGATGCAAAAAGAAACCAGATATGATGTCTA
1 CAATGATGCAAAAAGAAACCAAATATGATGTCTA
*** *
12428087 CAATGATGCAATCTGAAACCAAATATGATGTTTA
1 CAATGATGCAAAAAGAAACCAAATATGATGTCTA
12428121 CAATG
1 CAATG
12428126 TTGCTTCAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (34 bp):
CAATGATGCAAAAAGAAACCAAATATGATGTCTA
Found at i:12430068 original size:23 final size:21
Alignment explanation
Indices: 12430017--12430070 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
12430007 TTATTTCACT
*
12430017 CAAATTTTCTTCCTTGCACCA
1 CAAATTTTCTTCCTTGCACAA
12430038 CAAATTTTCTTCCTTTAGCACAA
1 CAAATTTTCTTCC-TT-GCACAA
* *
12430061 GAATTTTTCT
1 CAAATTTTCT
12430071 AACAGTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 13 0.46
22 2 0.07
23 13 0.46
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (21 bp):
CAAATTTTCTTCCTTGCACAA
Found at i:12434620 original size:26 final size:27
Alignment explanation
Indices: 12434578--12434638 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
12434568 AATTTTAGAC
*
12434578 TTATTTTAA-ATATAGATTTTTTTAT-
1 TTATTATAACATATAGATTTTTTTATA
12434603 TT-TTATAACATATAAGATTTTTTTATA
1 TTATTATAACATAT-AGATTTTTTTATA
12434630 TTATTATAA
1 TTATTATAA
12434639 AAATATGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 5 0.16
25 6 0.19
26 12 0.39
27 2 0.06
28 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (27 bp):
TTATTATAACATATAGATTTTTTTATA
Found at i:12436113 original size:24 final size:24
Alignment explanation
Indices: 12436081--12436127 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12436071 CGGTGTAAAG
* *
12436081 TCACAGCCATGTGACAGTTCTTAA
1 TCACAGCCATGCGACAATTCTTAA
12436105 TCACAGCCATGCGACAATTCTTA
1 TCACAGCCATGCGACAATTCTTA
12436128 TCTGTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (24 bp):
TCACAGCCATGCGACAATTCTTAA
Found at i:12438311 original size:106 final size:106
Alignment explanation
Indices: 12438123--12438332 Score: 357
Period size: 106 Copynumber: 2.0 Consensus size: 106
12438113 AAAAGAAAAT
* *
12438123 ATTAAAAATATGAAAACATAATGTTTCTTCTCCATTTTTGTTTTGTTCTTCACCGAACCTCTATG
1 ATTAAAAATATGAAAACATAATGTTTCTTCTCCATTTTTATTTTGTTCTTCACCGAACCTCCATG
* *
12438188 GAAGTATATTCATGGTTCGGTTATGCCTAAACCCTTGCAAG
66 GAAGTATATTCAAGGTTCGGCTATGCCTAAACCCTTGCAAG
*
12438229 ATTAAAAATATGAAAACATAATGTTTCTTCTCCATTTTTATTTTGTTCTTCACTGAACCTCCATG
1 ATTAAAAATATGAAAACATAATGTTTCTTCTCCATTTTTATTTTGTTCTTCACCGAACCTCCATG
* *
12438294 GAAGTATATTCAAGGTTCGGCTATGCTTAAATCCTTGCA
66 GAAGTATATTCAAGGTTCGGCTATGCCTAAACCCTTGCA
12438333 TGGTAAGCTC
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 97 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (106 bp):
ATTAAAAATATGAAAACATAATGTTTCTTCTCCATTTTTATTTTGTTCTTCACCGAACCTCCATG
GAAGTATATTCAAGGTTCGGCTATGCCTAAACCCTTGCAAG
Found at i:12439221 original size:35 final size:35
Alignment explanation
Indices: 12439170--12439269 Score: 137
Period size: 35 Copynumber: 2.9 Consensus size: 35
12439160 TACTCTCTAT
*
12439170 TTAGCGTGTTTTGGTTGGATTAGCTCTTATGAGCA
1 TTAGCGTGTTATGGTTGGATTAGCTCTTATGAGCA
* *
12439205 TTGGCGTGTTACGGTTGGATTAGCTCTTATGAGCA
1 TTAGCGTGTTATGGTTGGATTAGCTCTTATGAGCA
* * * *
12439240 TTAGCATGTTATGGTTCGATTGGCTTTTAT
1 TTAGCGTGTTATGGTTGGATTAGCTCTTAT
12439270 AAAAATCTAG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.17, C:0.12, G:0.28, T:0.43
Consensus pattern (35 bp):
TTAGCGTGTTATGGTTGGATTAGCTCTTATGAGCA
Done.