Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007770.1 Hibiscus syriacus cultivar Beakdansim tig00110050_pilon, whole genome shotgun sequence
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: 1450453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:382253 original size:49 final size:51
Alignment explanation
Indices: 382147--382266 Score: 174
Period size: 49 Copynumber: 2.4 Consensus size: 51
382137 TACAAAACGT
*
382147 GGTACATGCTCCGCGCTATATAAAATTATGTCAAGAGTAAAGGTATGTCGC
1 GGTACCTGCTCCGCGCTATATAAAATTATGTCAAGAGTAAAGGTATGTCGC
* *
382198 GGTACCTGCCCCGCGCTATATAAAATTAT-T-AGGAGTAAAGGTATAGT-GC
1 GGTACCTGCTCCGCGCTATATAAAATTATGTCAAGAGTAAAGGTAT-GTCGC
*
382247 GGTACCTGATCCGCGCTATA
1 GGTACCTGCTCCGCGCTATA
382267 CCCACGTGGC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
49 33 0.52
50 3 0.05
51 27 0.43
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (51 bp):
GGTACCTGCTCCGCGCTATATAAAATTATGTCAAGAGTAAAGGTATGTCGC
Found at i:387294 original size:11 final size:12
Alignment explanation
Indices: 387278--387308 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
387268 ATAGACAAAT
387278 ACCTAACTC-TC
1 ACCTAACTCTTC
387289 ACCTAACTCTTC
1 ACCTAACTCTTC
387301 ACCTAACT
1 ACCTAACT
387309 AAATTGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:389190 original size:4 final size:4
Alignment explanation
Indices: 389181--389207 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
389171 AAAGCCTTCA
389181 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
389208 TGTGCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:390423 original size:2 final size:2
Alignment explanation
Indices: 390416--390440 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
390406 GCAGTTTAAC
390416 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
390441 GCCATTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:391003 original size:15 final size:15
Alignment explanation
Indices: 390985--391018 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
390975 CTGAAACAGC
* *
390985 AAAGGCTCAAGCTTT
1 AAAGGATCAAGCTGT
391000 AAAGGATCAAGCTGT
1 AAAGGATCAAGCTGT
391015 AAAG
1 AAAG
391019 CAAATAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (15 bp):
AAAGGATCAAGCTGT
Found at i:393394 original size:24 final size:24
Alignment explanation
Indices: 393349--393398 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
393339 TGGTGGTTGG
*
393349 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
393373 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
393397 TT
1 TT
393399 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:396629 original size:15 final size:15
Alignment explanation
Indices: 396605--396647 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
396595 TGAGTATTTG
396605 TTTG-TTTATTTTTA
1 TTTGTTTTATTTTTA
396619 TTTGTTTTATTTTT-
1 TTTGTTTTATTTTTA
* *
396633 TTAGTTTTAATTTTA
1 TTTGTTTTATTTTTA
396648 ATATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTGTTTTATTTTTA
Found at i:399012 original size:24 final size:24
Alignment explanation
Indices: 398967--399016 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
398957 TGGTGGTTGG
*
398967 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
398991 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
399015 TT
1 TT
399017 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:400938 original size:2 final size:2
Alignment explanation
Indices: 400931--400959 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
400921 TCTACCCAAA
400931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
400960 ACTTTGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:403379 original size:29 final size:29
Alignment explanation
Indices: 403336--403418 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
403326 CTCACCTAAC
403336 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
403366 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
403395 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
403419 ATTTAGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:408110 original size:29 final size:29
Alignment explanation
Indices: 408067--408149 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
408057 CTCACCTAAC
408067 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
* *
408097 TAAATGATGTAAGCAATGGCATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
*
408126 TAAATGATATAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
408150 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:412761 original size:17 final size:20
Alignment explanation
Indices: 412714--412752 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
412704 AAAATCTTGT
*
412714 TCTTCTCTTCTTTGTCTATC
1 TCTTCTCTTCTTCGTCTATC
412734 TCTTCTCTTCTTCGTCTAT
1 TCTTCTCTTCTTCGTCTAT
412753 TTTTCTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.31, G:0.05, T:0.59
Consensus pattern (20 bp):
TCTTCTCTTCTTCGTCTATC
Found at i:414799 original size:21 final size:21
Alignment explanation
Indices: 414773--414817 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
414763 GATTTCTGGG
* *
414773 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
414794 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
414815 CAA
1 CAA
414818 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:416567 original size:23 final size:22
Alignment explanation
Indices: 416508--416574 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
416498 TATGGACATC
*
416508 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
416530 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
416552 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
416575 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:418667 original size:17 final size:20
Alignment explanation
Indices: 418620--418658 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
418610 AAAATCTTGT
*
418620 TCTTCTCTTCTTTGTCTATC
1 TCTTCTCTTCTTCGTCTATC
418640 TCTTCTCTTCTTCGTCTAT
1 TCTTCTCTTCTTCGTCTAT
418659 TTTTCTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.31, G:0.05, T:0.59
Consensus pattern (20 bp):
TCTTCTCTTCTTCGTCTATC
Found at i:419171 original size:14 final size:13
Alignment explanation
Indices: 419137--419179 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 13
419127 ATATTTTTTT
419137 ATTTTTTAAATAAA
1 ATTTTTTAAA-AAA
419151 ATATTTTTAAAAATA
1 AT-TTTTTAAAAA-A
419166 ATTTTTTAAAAAA
1 ATTTTTTAAAAAA
419179 A
1 A
419180 CTTGAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.07
14 14 0.52
15 11 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTTTTAAAAAA
Found at i:435788 original size:17 final size:18
Alignment explanation
Indices: 435766--435799 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
435756 TTGAAAGGTC
*
435766 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
435783 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
435800 ATAGAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:436942 original size:12 final size:12
Alignment explanation
Indices: 436927--436996 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
436917 GATACATGAC
436927 CTGAATTATGTT
1 CTGAATTATGTT
* * *
436939 CTGATTTCTGAT
1 CTGAATTATGTT
* *
436951 CTGGATTCTGTT
1 CTGAATTATGTT
436963 CTG-ATATATGTT
1 CTGAAT-TATGTT
*
436975 CTGAATTCTGTT
1 CTGAATTATGTT
* *
436987 TTGATTTATG
1 CTGAATTATG
436997 ATATCTCCAT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTATGTT
Found at i:436959 original size:48 final size:49
Alignment explanation
Indices: 436890--436998 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 49
436880 AATTATTTTA
*
436890 TCTGATTTCCGA-CTTGAATTCTATTCTGATACATGACCTGAATTATGT
1 TCTGATTTCTGATCTTGAATTCTATTCTGATACATGACCTGAATTATGT
* * * ** *
436938 TCTGATTTCTGATC-TGGATTCTGTTCTGATATATGTTCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTATTCTGATACATGACCTGAATTATGT
* *
436986 TTTGATTTATGAT
1 TCTGATTTCTGAT
436999 ATCTCCATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 50 0.98
49 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTATTCTGATACATGACCTGAATTATGT
Found at i:436996 original size:24 final size:24
Alignment explanation
Indices: 436904--436998 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
436894 ATTTCCGACT
* ** *
436904 TGAATTCTATTCTGATACATGACC
1 TGAATTCTGTTCTGATTTATGATC
* *
436928 TGAATTATGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTATGATC
* * *
436952 TGGATTCTGTTCTGATATATGTTC
1 TGAATTCTGTTCTGATTTATGATC
*
436976 TGAATTCTGTTTTGATTTATGAT
1 TGAATTCTGTTCTGATTTATGAT
436999 ATCTCCATTT
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTATGATC
Found at i:438205 original size:31 final size:32
Alignment explanation
Indices: 438138--438206 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
438128 GTCAATGGTT
*
438138 CACA-TAGAATTTATTTTCTGAGTTGGAGAGA
1 CACATTAGAATTTATTTACTGAGTTGGAGAGA
* * * *
438169 TACATTAG-ATTTATTTACTGAGTTTGAGGGC
1 CACATTAGAATTTATTTACTGAGTTGGAGAGA
438200 CACATTA
1 CACATTA
438207 AGAGAAACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (32 bp):
CACATTAGAATTTATTTACTGAGTTGGAGAGA
Found at i:439900 original size:18 final size:18
Alignment explanation
Indices: 439877--439916 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
439867 ACTGAACCTG
439877 CCAGTGTCTTCGGTCATA
1 CCAGTGTCTTCGGTCATA
439895 CCAGTGTCTTCGGTCATA
1 CCAGTGTCTTCGGTCATA
439913 CCAG
1 CCAG
439917 AGTACCCCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.30
Consensus pattern (18 bp):
CCAGTGTCTTCGGTCATA
Found at i:440438 original size:20 final size:20
Alignment explanation
Indices: 440413--440452 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
440403 CAGAGGCATT
440413 TTGGTCATTAGATTCTTGGA
1 TTGGTCATTAGATTCTTGGA
440433 TTGGTCATTAGATTCTTGGA
1 TTGGTCATTAGATTCTTGGA
440453 GAATTCTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.25, T:0.45
Consensus pattern (20 bp):
TTGGTCATTAGATTCTTGGA
Found at i:442011 original size:19 final size:19
Alignment explanation
Indices: 441950--442000 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
441940 CAGTAAGACT
*
441950 GGTCAAAGGTCAACAGGTCA
1 GGTCAAA-GTCAACGGGTCA
*
441970 GGTCGAAGTCAACGGGTCA
1 GGTCAAAGTCAACGGGTCA
441989 GGTCAAAGTCAA
1 GGTCAAAGTCAA
442001 TGTGTCGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.33, C:0.20, G:0.31, T:0.16
Consensus pattern (19 bp):
GGTCAAAGTCAACGGGTCA
Found at i:444835 original size:25 final size:25
Alignment explanation
Indices: 444788--444835 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
444778 TATTTTAGTA
*
444788 ATTATTTTGAAAATGATGGTATTCT
1 ATTATTTTGAAAATGATGCTATTCT
*
444813 ATTATTTTGAAAATGGTGCTATT
1 ATTATTTTGAAAATGATGCTATT
444836 TTCGTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.48
Consensus pattern (25 bp):
ATTATTTTGAAAATGATGCTATTCT
Found at i:451999 original size:29 final size:29
Alignment explanation
Indices: 451969--452132 Score: 110
Period size: 29 Copynumber: 5.9 Consensus size: 29
451959 GATCGGGTGG
*
451969 TATTTTAGTAATTATTTTGAAAATGATGG
1 TATTTTAGTAATTATTTTGAAAATGATGA
* * *
451998 TATTCTCGTAATTATTTCGAAAAT-A-GTA
1 TATTTTAGTAATTATTTTGAAAATGATG-A
* *
452026 TTATTTTTGTAATT-TTTT-AAAA-AATGA
1 -TATTTTAGTAATTATTTTGAAAATGATGA
** ** * ** *
452053 TAAATTCCT-A--ATTTTAAAAAAAATAA
1 TATTTTAGTAATTATTTTGAAAATGATGA
*
452079 TATTTTAGTAATTATTTTGAAAATGGTGA
1 TATTTTAGTAATTATTTTGAAAATGATGA
*
452108 TATTTTGGTAATTATTTTGAAAATG
1 TATTTTAGTAATTATTTTGAAAATG
452133 GTGCAAAATG
Statistics
Matches: 103, Mismatches: 22, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
24 4 0.04
25 5 0.05
26 14 0.14
27 8 0.08
28 5 0.05
29 67 0.65
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (29 bp):
TATTTTAGTAATTATTTTGAAAATGATGA
Found at i:452109 original size:55 final size:59
Alignment explanation
Indices: 451969--452124 Score: 143
Period size: 52 Copynumber: 2.8 Consensus size: 59
451959 GATCGGGTGG
* * * * *
451969 TATTTTAGTAATTATTTTGAAAATGATGGT-ATTCTCGTAATTATTTCGAAAATAGTAT
1 TATTTTAGTAATTATTTTGAAAATGATGATAATTCTCGTAATTATTTCAAAAAAAATAA
* *
452027 TATTTTTGTAATT-TTTT-AAAA-AATGATAAATTC-C-TAA-T-TTT-AAAAAAAATAA
1 TATTTTAGTAATTATTTTGAAAATGATGAT-AATTCTCGTAATTATTTCAAAAAAAATAA
* * *
452079 TATTTTAGTAATTATTTTGAAAATGGTGAT-ATTTTGGTAATTATTT
1 TATTTTAGTAATTATTTTGAAAATGATGATAATTCTCGTAATTATTT
452125 TGAAAATGGT
Statistics
Matches: 77, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
52 19 0.25
53 10 0.13
54 5 0.06
55 14 0.18
56 6 0.08
57 11 0.14
58 12 0.16
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (59 bp):
TATTTTAGTAATTATTTTGAAAATGATGATAATTCTCGTAATTATTTCAAAAAAAATAA
Found at i:452147 original size:29 final size:29
Alignment explanation
Indices: 452086--452144 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
452076 TAATATTTTA
* * *
452086 GTAATTATTTTGAAAATGGTGATATTTTG
1 GTAATTATTTTGAAAATGGTGAAAATGTG
452115 GTAATTATTTTGAAAATGGTGCAAAATGTG
1 GTAATTATTTTGAAAATGGTG-AAAATGTG
452145 TAAAATGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.42
Consensus pattern (29 bp):
GTAATTATTTTGAAAATGGTGAAAATGTG
Found at i:452889 original size:14 final size:13
Alignment explanation
Indices: 452866--452914 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
452856 AAATGATATA
452866 TGATACTTGATTTC
1 TGATA-TTGATTTC
452880 TGAATATTGATTTCC
1 TG-ATATTGATTT-C
452895 TGATATCTGATTTC
1 TGATAT-TGATTTC
452909 T-ATATT
1 TGATATT
452915 TCGGTATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.03
13 4 0.12
14 15 0.47
15 12 0.38
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (13 bp):
TGATATTGATTTC
Found at i:454064 original size:89 final size:90
Alignment explanation
Indices: 453904--454167 Score: 293
Period size: 89 Copynumber: 2.9 Consensus size: 90
453894 CTTCATAGCG
* * * *
453904 GGTTTTAACCTAAAATTTTATTCTATCTACTTTAAAAAGTTATACAAATGATAATAATTTCGTTT
1 GGTTTTAACCTAAAATTTTACT-TGTCTACTCTAAAAAGTTATACAAATGATAATAATTTCGGTT
*
453969 ACAACCGAGAATGTTATATTGCGACA
65 ACAACCGAGAATGTTACATTGCGACA
* * *
453995 GGTTTCAACCTAAAATTTTA-TTGTCTACTCTAAAATGTTATACAATTGATAATAATATT-GGTT
1 GGTTTTAACCTAAAATTTTACTTGTCTACTCTAAAAAGTTATACAAATGATAATAAT-TTCGGTT
* *
454058 ATAACCGAGAATGTTACATTGCGACG
65 ACAACCGAGAATGTTACATTGCGACA
* ** * ** * *
454084 GGTTTTAACCTAAAATGTTACCACGTCTACTCTAAAAGGTTATGGAATTTG-TATTAATTTCGGT
1 GGTTTTAACCTAAAATTTTA-CTTGTCTACTCTAAAAAGTTATACAA-ATGATAATAATTTCGGT
454148 TACAACCGATG-ATGTTACAT
64 TACAACCGA-GAATGTTACAT
454168 GAGTTTCTTA
Statistics
Matches: 149, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
89 75 0.50
90 5 0.03
91 65 0.44
92 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (90 bp):
GGTTTTAACCTAAAATTTTACTTGTCTACTCTAAAAAGTTATACAAATGATAATAATTTCGGTTA
CAACCGAGAATGTTACATTGCGACA
Found at i:460404 original size:20 final size:20
Alignment explanation
Indices: 460358--460405 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 20
460348 CCAGATAAGA
*
460358 GTATCGATACTTATATAGGT
1 GTATCAATACTTATATAGGT
460378 G--TCAATACTT-TATAGGT
1 GTATCAATACTTATATAGGT
460395 GATATCAATAC
1 G-TATCAATAC
460406 CTTAATGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
20 8 0.33
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (20 bp):
GTATCAATACTTATATAGGT
Found at i:460863 original size:25 final size:25
Alignment explanation
Indices: 460815--460863 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
460805 GTATATATAT
* *
460815 ATATTTAATTATAAAATTATTAAAA
1 ATATTTAATTATAAAATAAGTAAAA
460840 ATATTTATATTA-AAAATAAGTAAA
1 ATATTTA-ATTATAAAATAAGTAAA
460864 TTTATAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
ATATTTAATTATAAAATAAGTAAAA
Found at i:462672 original size:20 final size:18
Alignment explanation
Indices: 462639--462681 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
462629 AGATTACTCA
462639 ATAATTATAAGTTTCACAAT
1 ATAATTATAAGTTT-A-AAT
**
462659 ATAATTATGTGTTTAAAT
1 ATAATTATAAGTTTAAAT
462677 ATAAT
1 ATAAT
462682 AAAATCCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 1 0.05
20 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (18 bp):
ATAATTATAAGTTTAAAT
Found at i:463117 original size:18 final size:18
Alignment explanation
Indices: 463081--463121 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
463071 TTAATAGTGA
463081 TTTA-TATAAAATATATT
1 TTTATTATAAAATATATT
463098 TTTATTATAATAATAT-TT
1 TTTATTATAA-AATATATT
463116 TTTATT
1 TTTATT
463122 TGTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.18
18 13 0.59
19 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTATTATAAAATATATT
Found at i:466369 original size:21 final size:22
Alignment explanation
Indices: 466313--466370 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
466303 AATAACTTTA
*
466313 TTATGACATGATTTCTATGTCT
1 TTATGACATGTTTTCTATGTCT
**
466335 TTATGACACATTTTCTATGTCT
1 TTATGACATGTTTTCTATGTCT
466357 TT-TGACATGTTTTC
1 TTATGACATGTTTTC
466371 GATTTTTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.52
Consensus pattern (22 bp):
TTATGACATGTTTTCTATGTCT
Found at i:468774 original size:20 final size:21
Alignment explanation
Indices: 468718--468774 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
468708 TAATACTTAG
* *
468718 TTTTTAATAAATTATAATAATA
1 TTTTTAA-AATTTAAAATAATA
* *
468740 GTTTTGAAATATTAAAAT-ATA
1 TTTTTAAAAT-TTAAAATAATA
468761 TTTTTAAAATTTAA
1 TTTTTAAAATTTAA
468775 TTTATTGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 4 0.14
21 13 0.46
22 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTTTAAAATTTAAAATAATA
Found at i:469000 original size:3 final size:3
Alignment explanation
Indices: 468992--469027 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
468982 ATTTACCTAG
468992 TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
469028 CAAATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:471413 original size:3 final size:3
Alignment explanation
Indices: 471405--471509 Score: 189
Period size: 3 Copynumber: 36.0 Consensus size: 3
471395 ATTCTATTAC
471405 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
471452 ATT A-T ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
471498 ATT ATT ATT ATT
1 ATT ATT ATT ATT
471510 CAGAGAACTA
Statistics
Matches: 99, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
2 6 0.06
3 93 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:473786 original size:35 final size:35
Alignment explanation
Indices: 473745--473821 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
473735 AAAATAGTCA
473745 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
* * *
473780 TCAATTTCATTTTAAACTCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
473815 TCAATTT
1 TCAATTT
473822 AAGGTTTAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.39
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:473839 original size:35 final size:35
Alignment explanation
Indices: 473765--473874 Score: 84
Period size: 35 Copynumber: 3.1 Consensus size: 35
473755 TCTAAACCCC
* * *
473765 AAATTCTAAAATAATTCAATTTCA-TTTTA-AACTCC
1 AAATTCTAAAATAATTCAATTTAAGGTTTAGAA-T-G
*
473800 AAATTCTAAAATACTTCAATTTAAGGTTTAGAATG
1 AAATTCTAAAATAATTCAATTTAAGGTTTAGAATG
** * *
473835 AAA-T-TAAATTATTTTTGAATTTAGGGTTTAGAATG
1 AAATTCTAAA--ATAATTCAATTTAAGGTTTAGAATG
473870 AAATT
1 AAATT
473875 AAGGACTATT
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
33 4 0.06
34 1 0.02
35 49 0.79
36 6 0.10
37 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (35 bp):
AAATTCTAAAATAATTCAATTTAAGGTTTAGAATG
Found at i:478278 original size:16 final size:17
Alignment explanation
Indices: 478252--478285 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
478242 CGAGATTACT
478252 ATTTACGTGAATAATAA
1 ATTTACGTGAATAATAA
*
478269 ATTT-CGTGAATAGTAA
1 ATTTACGTGAATAATAA
478285 A
1 A
478286 ACTTGGTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATAATAA
Found at i:484088 original size:24 final size:24
Alignment explanation
Indices: 484056--484116 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
484046 TGAATCGAGT
484056 TTCAATCGAGCTCGAGTCTCAAGC
1 TTCAATCGAGCTCGAGTCTCAAGC
*
484080 TTCAATCGAGCTCGAGTCTCGAGC
1 TTCAATCGAGCTCGAGTCTCAAGC
*
484104 TTTAATCGAGCTC
1 TTCAATCGAGCTC
484117 CTGAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (24 bp):
TTCAATCGAGCTCGAGTCTCAAGC
Found at i:490101 original size:19 final size:21
Alignment explanation
Indices: 490068--490106 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
490058 TGTTCTATTA
490068 TTATTTTATTTAAAA-CTTAG
1 TTATTTTATTTAAAATCTTAG
490088 TTATTTTA-TTAAAATCTTA
1 TTATTTTATTTAAAATCTTA
490107 TTAGGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (21 bp):
TTATTTTATTTAAAATCTTAG
Found at i:490300 original size:13 final size:13
Alignment explanation
Indices: 490259--490305 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
490249 CATCTACATC
*
490259 TTTCTTTCT-TTAC
1 TTTCTTT-TATTAT
*
490272 TTTCTTTCATTAT
1 TTTCTTTTATTAT
*
490285 TTTCTTTTATTGT
1 TTTCTTTTATTAT
490298 TTTCTTTT
1 TTTCTTTT
490306 CACAATGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.09, C:0.15, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTCTTTTATTAT
Found at i:490904 original size:13 final size:13
Alignment explanation
Indices: 490866--490914 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
490856 TATTTTCTCA
490866 TTATTATTATTTAT
1 TTATT-TTATTTAT
*
490880 TAAATATTTATTTAT
1 T-TAT-TTTATTTAT
*
490895 TTATTTTATTCAT
1 TTATTTTATTTAT
490908 TTATTTT
1 TTATTTT
490915 CATTAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 15 0.50
14 3 0.10
15 11 0.37
16 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:491274 original size:21 final size:21
Alignment explanation
Indices: 491248--491288 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
491238 TTTACATTTA
*
491248 ATTTATATATATAATT-TAAAT
1 ATTTATA-AGATAATTATAAAT
491269 ATTTATAAGATAATTATAAA
1 ATTTATAAGATAATTATAAA
491289 ATTACTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTTATAAGATAATTATAAAT
Found at i:492530 original size:3 final size:3
Alignment explanation
Indices: 492522--492546 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
492512 AGGGTAGGAG
492522 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
492547 AACTTTCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:495568 original size:3 final size:3
Alignment explanation
Indices: 495560--495616 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
495550 AAATTTAAAT
**
495560 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
495607 TTA TTTA TTA
1 TTA -TTA TTA
495617 AATATTACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:497200 original size:18 final size:19
Alignment explanation
Indices: 497177--497223 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
497167 TTTTACTTTC
*
497177 ATATATTTATGATTA-TAT
1 ATATATTTATCATTACTAT
497195 ATATATTTATCATTACTAT
1 ATATATTTATCATTACTAT
497214 -TACTATTTAT
1 ATA-TATTTAT
497224 TATTTATGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (19 bp):
ATATATTTATCATTACTAT
Found at i:497600 original size:11 final size:13
Alignment explanation
Indices: 497563--497602 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
497553 TGTTTAATAA
497563 AATATA-TATATT
1 AATATATTATATT
*
497575 AATATATTATCTT
1 AATATATTATATT
497588 AA-A-ATTATATT
1 AATATATTATATT
497599 AATA
1 AATA
497603 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:497901 original size:14 final size:15
Alignment explanation
Indices: 497882--497910 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
497872 TGACGACTCC
497882 CAAAAT-ATTTTTTT
1 CAAAATGATTTTTTT
497896 CAAAATGATTTTTTT
1 CAAAATGATTTTTTT
497911 ATCCACATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (15 bp):
CAAAATGATTTTTTT
Found at i:513133 original size:120 final size:117
Alignment explanation
Indices: 512994--513230 Score: 359
Period size: 117 Copynumber: 2.0 Consensus size: 117
512984 TTTGTCTGGG
*
512994 TTGTCGTTTTTTTATTATATATTATATATATTAAATAATTAAAT-ATTTTGTTTTATTTTATTTT
1 TTGTCGTTTTTTTATTATATATTATATATATTAAAT-ATTAAATAATTTTG--TTATTTTATTAT
* * * *
513058 TCAAGCCCAAATTACAAGCAAGATCAAGATTCAATCAAACCAATAGTACAGGGCCC
63 TCAAG-CAAAATTACAAGCAAGACCAAGATTCAATCAAACCAATACTACACGGCCC
*
513114 TTGTCGTTTTTTTATTATATATTATATATATTAAATATTAAATAATTTTGTTCTTTTATTATTCA
1 TTGTCGTTTTTTTATTATATATTATATATATTAAATATTAAATAATTTTGTTATTTTATTATTCA
* *
513179 TGTAAAATTACAAGCAAGACCAAGATTCAATCAAACCAATACTACACGGCCC
66 AGCAAAATTACAAGCAAGACCAAGATTCAATCAAACCAATACTACACGGCCC
513231 AAGGAACTAA
Statistics
Matches: 108, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
117 45 0.42
118 14 0.13
119 7 0.06
120 42 0.39
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.41
Consensus pattern (117 bp):
TTGTCGTTTTTTTATTATATATTATATATATTAAATATTAAATAATTTTGTTATTTTATTATTCA
AGCAAAATTACAAGCAAGACCAAGATTCAATCAAACCAATACTACACGGCCC
Found at i:515392 original size:32 final size:32
Alignment explanation
Indices: 515328--515409 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
515318 ATACTAGTAG
* *
515328 TGTTGCATTCAGATTATGCATAAAAGAGTCAA
1 TGTTGCATTCAGATAATGCACAAAAGAGTCAA
**
515360 TGTTGCATTCAGATAATGCACAGGAGTA-TCAA
1 TGTTGCATTCAGATAATGCACAAAAG-AGTCAA
* *
515392 TGTAGCATTTAGATAATG
1 TGTTGCATTCAGATAATG
515410 TGTAGCAGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 42 0.98
33 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (32 bp):
TGTTGCATTCAGATAATGCACAAAAGAGTCAA
Found at i:518206 original size:12 final size:12
Alignment explanation
Indices: 518189--518218 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
518179 TTGCACAGTC
518189 TTAAACTGGGAT
1 TTAAACTGGGAT
518201 TTAAACTGGGAT
1 TTAAACTGGGAT
518213 TTAAAC
1 TTAAAC
518219 CTAATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (12 bp):
TTAAACTGGGAT
Found at i:522633 original size:76 final size:76
Alignment explanation
Indices: 522409--522635 Score: 303
Period size: 77 Copynumber: 3.0 Consensus size: 76
522399 GATTGTACCT
** * *
522409 AAAAATGA-CATGGTTCACTAAGAAGCATGTTACGATTTGGAATGTTAATATTTTTATTAATAAA
1 AAAAAT-ATCATGGTTCACTAA-AAAAATGTTATGATATGGAATGTTAATATTTTTATTAATAAA
522473 ATGGGTTGCGTCC
64 ATGGGTTGCGTCC
* * * *
522486 AAAAATTTAATGGTTCACTAAAAAATAGGTTGTGATATGGAATGTTAATATTTTTATTAATAAAA
1 AAAAATATCATGGTTCACTAAAAAA-ATGTTATGATATGGAATGTTAATATTTTTATTAATAAAA
*
522551 TGGGTTGTGTCC
65 TGGGTTGCGTCC
* * *
522563 AAAAATATCATGGTTCACTAAAAAAATGTTATGATATGAAATATTAATATTTTAATTAATAAAAT
1 AAAAATATCATGGTTCACTAAAAAAATGTTATGATATGGAATGTTAATATTTTTATTAATAAAAT
*
522628 AGGTTGCG
66 GGGTTGCG
522636 ATATGGAATA
Statistics
Matches: 130, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
76 43 0.33
77 87 0.67
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (76 bp):
AAAAATATCATGGTTCACTAAAAAAATGTTATGATATGGAATGTTAATATTTTTATTAATAAAAT
GGGTTGCGTCC
Found at i:523030 original size:110 final size:116
Alignment explanation
Indices: 522835--523076 Score: 343
Period size: 110 Copynumber: 2.1 Consensus size: 116
522825 AACTATTCCA
* * *
522835 AAAGTATCGATACTTTCGAATTTAAAGAAAAACATGGAAAATGAGGACGCTGCAAAGTATAGATA
1 AAAGTATCGATACTTTCGAATTTAAAGAAAAACATGGAAAATAAGAACACTGCAAAGTATAGATA
* * *
522900 CTTTTAAATTCGAAA-TTTAAATATCA-TTTTC-T-ATT-TTTT-AATTCT
66 CTTTTAAATTAGAAAGTTAAAATATCATTTTTCATCATTATTTTAAATTCG
* * * *
522945 AAAGTATCAATACTTTCGAATTTAAAGAAAAACATGGAAAATAAGAATATTGCAAAGTATCGATA
1 AAAGTATCGATACTTTCGAATTTAAAGAAAAACATGGAAAATAAGAACACTGCAAAGTATAGATA
*
523010 CTTTTAAATTAGAAAGTTAAAATATCATTTTTCATCTTTATTTTAAATTCG
66 CTTTTAAATTAGAAAGTTAAAATATCATTTTTCATCATTATTTTAAATTCG
523061 AAAGTATCGATACTTT
1 AAAGTATCGATACTTT
523077 AAGCAAAAAT
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
110 72 0.63
111 10 0.09
112 5 0.04
113 1 0.01
114 2 0.02
115 4 0.04
116 20 0.18
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (116 bp):
AAAGTATCGATACTTTCGAATTTAAAGAAAAACATGGAAAATAAGAACACTGCAAAGTATAGATA
CTTTTAAATTAGAAAGTTAAAATATCATTTTTCATCATTATTTTAAATTCG
Found at i:523493 original size:100 final size:100
Alignment explanation
Indices: 523251--523636 Score: 368
Period size: 100 Copynumber: 3.9 Consensus size: 100
523241 AGGTAGCTCA
* * * ** *
523251 TTTTTTTTAATGTCAACTGTTTAAGTAATAAGTATGAAACCGTTTATATGCTGCAAAAGTATGAC
1 TTTTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAACCATTTATATTATGCAAAAGTAAGAC
* * * *
523316 --AACATGTTTCTCATGATAACGTAGTAGGTAAC-
66 AAAACATATTGCTCATGATAACGTACTAGATAACG
** * * * *** * *
523348 ACTTTTTT-ATATCAATCGTTTAAGTTATAAGTACGAAATTGTTTATATTATGCAAGAGAAAGAC
1 TTTTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAACCATTTATATTATGCAAAAGTAAGAC
*
523412 AAAACATACTGCTCATGATAACGTACTAGATAACG
66 AAAACATATTGCTCATGATAACGTACTAGATAACG
* * *
523447 TTTTTTTTAGTGTCAACCGTTTAAATTATAAGTATGAAACCATTTATATTATGTAAAAGTAAGAC
1 TTTTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAACCATTTATATTATGCAAAAGTAAGAC
* * * *
523512 AAAAGATGTTGCTTATGATAACGTACTAGATAGCG
66 AAAACATATTGCTCATGATAACGTACTAGATAACG
* * * * * *
523547 CATTTTTCTTAAATGTTAATCGTTTAAGTTATAAGTAT-AAATTCATTTATTTTATGTAAAAGTA
1 --TTTTT-TTTAATGTCAACCGTTTAAGTTATAAGTATGAAA-CCATTTATATTATGCAAAAGTA
* **
523611 AGACAAAATATATTTTTCATGATAAC
62 AGACAAAACATATTGCTCATGATAAC
523637 ATGATAGGTA
Statistics
Matches: 232, Mismatches: 49, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
96 44 0.19
97 6 0.03
98 27 0.12
99 6 0.03
100 75 0.32
102 8 0.03
103 66 0.28
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (100 bp):
TTTTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAACCATTTATATTATGCAAAAGTAAGAC
AAAACATATTGCTCATGATAACGTACTAGATAACG
Found at i:526395 original size:35 final size:34
Alignment explanation
Indices: 526299--526384 Score: 154
Period size: 34 Copynumber: 2.5 Consensus size: 34
526289 CCCGAACCCG
526299 AAAATATTATATATATAATTAATATAAAAAAATAT
1 AAAATATTATATATATAATTAATAT-AAAAAATAT
*
526334 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
526368 AAAATATTATATATATA
1 AAAATATTATATATATA
526385 TATATATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 25 0.50
35 25 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:528544 original size:47 final size:47
Alignment explanation
Indices: 528493--528590 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 47
528483 TATTACACAC
* *
528493 TATTAAAATAATTATGAATACAATTATAAATAGATATTATTTTGTAA
1 TATTAAAAAAATTATGAATAAAATTATAAATAGATATTATTTTGTAA
528540 TATTAAAAAAATTATGAATAAAATTATAAATAGATATTATTTTGTAA
1 TATTAAAAAAATTATGAATAAAATTATAAATAGATATTATTTTGTAA
528587 TATT
1 TATT
528591 TCGTATTAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (47 bp):
TATTAAAAAAATTATGAATAAAATTATAAATAGATATTATTTTGTAA
Found at i:539412 original size:17 final size:17
Alignment explanation
Indices: 539386--539418 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
539376 TTTTGTTTTT
539386 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
539404 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
539419 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:539420 original size:17 final size:19
Alignment explanation
Indices: 539381--539420 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
539371 TAATATTTTG
*
539381 TTTTTAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
539400 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
539416 TTTTA
1 TTTTA
539421 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:539538 original size:18 final size:19
Alignment explanation
Indices: 539515--539555 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
539505 AAAGTAACAT
539515 TTTAAAGTTTTAAT-ATAA
1 TTTAAAGTTTTAATAATAA
* *
539533 TTTAAATTTTTAGTAATAA
1 TTTAAAGTTTTAATAATAA
539552 TTTA
1 TTTA
539556 TTTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTAAAGTTTTAATAATAA
Found at i:544912 original size:96 final size:96
Alignment explanation
Indices: 544739--545023 Score: 525
Period size: 96 Copynumber: 3.0 Consensus size: 96
544729 AGTTAGAATG
*
544739 TATTTTTTAAAAGTTAATTTGAACATTTTAGTTTTGAAATTACTCGATAAAAAGTACTTTTGAGA
1 TATTTTTTAAAAGTTAATTTTAACATTTTAGTTTTGAAATTACTCGATAAAAAGTACTTTTGAGA
*
544804 AAATAAACTTTTCATTTTAGATGTGATAATT
66 AAATAAAATTTTCATTTTAGATGTGATAATT
544835 TATTTTTTAAAAGTTAATTTTAACATTTTAGTTTTGAAATTACTCGATAAAAAGTACTTTTGAGA
1 TATTTTTTAAAAGTTAATTTTAACATTTTAGTTTTGAAATTACTCGATAAAAAGTACTTTTGAGA
*
544900 AAGTAAAATTTTCATTTTAGATGTGATAATT
66 AAATAAAATTTTCATTTTAGATGTGATAATT
*
544931 TATTTTTTAAAAGTTAATTTTAACATTTTAGTTTTGAAATTGCTCGATAAAAAGTACTTTTGAGA
1 TATTTTTTAAAAGTTAATTTTAACATTTTAGTTTTGAAATTACTCGATAAAAAGTACTTTTGAGA
*
544996 AAATAAAATTTTTATTTTAGATGTGATA
66 AAATAAAATTTTCATTTTAGATGTGATA
545024 TTGTAAATAA
Statistics
Matches: 183, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 183 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.46
Consensus pattern (96 bp):
TATTTTTTAAAAGTTAATTTTAACATTTTAGTTTTGAAATTACTCGATAAAAAGTACTTTTGAGA
AAATAAAATTTTCATTTTAGATGTGATAATT
Found at i:553379 original size:51 final size:52
Alignment explanation
Indices: 553290--553403 Score: 142
Period size: 51 Copynumber: 2.2 Consensus size: 52
553280 AAGTGTAACA
** *
553290 AAAATAGAAA-AAAAATAGCTAAATCAGAAATAGGCAGTGACCAAAAT-GAAT
1 AAAATA-AAATAAAAATAGCTAAATCAGAAATAAACAGTGACCAAAATAAAAT
* ** *
553341 AAAATAAAATAACAATAGCTAAATCAGAAATAAACAGTGATTAAATTAAAAT
1 AAAATAAAATAAAAATAGCTAAATCAGAAATAAACAGTGACCAAAATAAAAT
553393 AAAATAAAATA
1 AAAATAAAATA
553404 GAACGATAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 3 0.06
51 37 0.69
52 14 0.26
ACGTcount: A:0.62, C:0.08, G:0.11, T:0.19
Consensus pattern (52 bp):
AAAATAAAATAAAAATAGCTAAATCAGAAATAAACAGTGACCAAAATAAAAT
Found at i:556028 original size:18 final size:18
Alignment explanation
Indices: 556005--556039 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
555995 GGTACAAATC
* *
556005 AGTGGTCCTTTGGGACAT
1 AGTGGTCATTCGGGACAT
556023 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
556040 AATATACAAT
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:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:560954 original size:18 final size:18
Alignment explanation
Indices: 560927--560998 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 18
560917 GTTTTTAAGG
560927 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
560945 AGTTGTCCTTCGGGATAAAT
1 AGTGGTCCTTCGGG--ACAT
560965 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
560984 TGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
560999 TAAATATACA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
18 27 0.59
19 3 0.07
20 3 0.07
21 13 0.28
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:560981 original size:39 final size:39
Alignment explanation
Indices: 560927--561003 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
560917 GTTTTTAAGG
*
560927 AGTGGTCCTTCGGGACATAGTTGTCCTTCGGGATAAATC
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGATAAATC
*
560966 AGTGGTCCTTCGGGACATTGTGGTCCTTCGGGATAAAT
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGATAAAT
561004 ATACAGTGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.31
Consensus pattern (39 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGATAAATC
Found at i:561426 original size:21 final size:21
Alignment explanation
Indices: 561402--561441 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
561392 TAATTGAGGA
561402 AAAAGG-TATATAAATAAGTAT
1 AAAAGGATAT-TAAATAAGTAT
*
561423 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAAATAAGT
561442 TTTGTAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAAATAAGTAT
Found at i:562799 original size:93 final size:92
Alignment explanation
Indices: 562659--562902 Score: 301
Period size: 93 Copynumber: 2.6 Consensus size: 92
562649 ATTTCCACTG
* * * * *
562659 AAAATGTTGATCCCTCGAGTGAGGCGTTACTGATTTGAAATGCCGTGAATCGAGAAAAGGTTGAA
1 AAAATGTTGGTCCCTCGAGTGAGGCGTTGCTGATTCGAAATGACGTGAATCGAGCAAAGGTTGAA
*
562724 CAAGATCTTCATTATGAATTCTCTACTA
66 CAAGATCTTC-TCATGAATTCTCTACTA
* * *
562752 AAAATGTTGGTCCCTCGAGTGAGGCGTTGCTGATTCAAAATGACGTGAATCGAGCCAAGGTTGGA
1 AAAATGTTGGTCCCTCGAGTGAGGCGTTGCTGATTCGAAATGACGTGAATCGAGCAAAGGTTGAA
* * *
562817 TAAGTTCTTCTCATGAATTCTCTACTG
66 CAAGATCTTCTCATGAATTCTCTACTA
* * * * **
562844 GAAATGTTGGTCCCTC-ATGTGAGGCGTCGATGATTCGAAGTGTTGTGAATCGAGCAAAG
1 AAAATGTTGGTCCCTCGA-GTGAGGCGTTGCTGATTCGAAATGACGTGAATCGAGCAAAG
562903 AAAATTTTGA
Statistics
Matches: 130, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
91 1 0.01
92 64 0.49
93 65 0.50
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (92 bp):
AAAATGTTGGTCCCTCGAGTGAGGCGTTGCTGATTCGAAATGACGTGAATCGAGCAAAGGTTGAA
CAAGATCTTCTCATGAATTCTCTACTA
Found at i:562937 original size:59 final size:59
Alignment explanation
Indices: 562854--563032 Score: 232
Period size: 59 Copynumber: 3.0 Consensus size: 59
562844 GAAATGTTGG
* * * * * * **
562854 TCCCTCATGTGAGGCGTCGATGATTCGAAGTGTTGTGAATCGAGCAAAGAAAATTTTGA
1 TCCCTCAAGTGAGGCATTGATGATTCAAAGTGTTGTGAATCGAGCAAAGGAAATGTAAA
* *
562913 TCCTTCAAGTGAGGCATTGATGATTCAAAGTGTTATGAATCGAGCAAAGGAAATGTAAA
1 TCCCTCAAGTGAGGCATTGATGATTCAAAGTGTTGTGAATCGAGCAAAGGAAATGTAAA
* * * *
562972 TCCCTCAAGTGAGGCATTGCTAATTTAAAGTGTTGTGAATCGAGCAAAGGAAATGTTAA
1 TCCCTCAAGTGAGGCATTGATGATTCAAAGTGTTGTGAATCGAGCAAAGGAAATGTAAA
563031 TC
1 TC
563033 ACTAAAAAAG
Statistics
Matches: 104, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 104 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (59 bp):
TCCCTCAAGTGAGGCATTGATGATTCAAAGTGTTGTGAATCGAGCAAAGGAAATGTAAA
Found at i:563139 original size:74 final size:74
Alignment explanation
Indices: 563050--563422 Score: 335
Period size: 74 Copynumber: 5.0 Consensus size: 74
563040 AAGGCGTAGT
* * *
563050 TTATTTTAAGAAAAACAATCTCAAGTGAGATTAATCTTCTGTTTCGAGTGAAATTATCTCAAGCG
1 TTATTTTAAGAAAAACAATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
563115 AGATAAATC
66 AGATAAATC
* *
563124 TTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTGAAGCG
1 TTATTTTAAGAAAAACAATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
*
563189 AGATTAATC
66 AGATAAATC
* * * * ** * *
563198 TTGTTTTAAGAAAAATAATCTCAAGCGAGATAAATCTTAT-TTT-AAGAAAAACAATCTCAAGTG
1 TTATTTTAAGAAAAACAATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
563261 AGATAAATC
66 AGATAAATC
* * ** * * * ** * *
563270 TTCTGTTTCGAGTGAAACTATCTGAAGCGAGATTAATC-T-TGTTTTAAG-AAAAATAATCTCAA
1 TTAT-TTT-AAGAAAAACAATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACT-ATCTCAA
* *
563332 GTGAGCTAAATC
63 GCGAGATAAATC
* * ** * * *
563344 TTCTGTTTCGAGTGAAACTATCTTAAGCGAAATAAAATC-TCTGTTTCGAGTGAAACTATCTCAA
1 TTAT-TTT-AAGAAAAACAATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAA
563408 GCGAGATAAAATC
63 GCGAGAT-AAATC
563421 TT
1 TT
563423 CTGTTTCGAG
Statistics
Matches: 255, Mismatches: 35, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
72 26 0.10
73 14 0.05
74 180 0.71
75 5 0.02
76 19 0.07
77 11 0.04
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (74 bp):
TTATTTTAAGAAAAACAATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
AGATAAATC
Found at i:563282 original size:110 final size:110
Alignment explanation
Indices: 563100--563414 Score: 488
Period size: 110 Copynumber: 2.8 Consensus size: 110
563090 GTTTCGAGTG
*
563100 AAATTATCTCAAGCGAGATAAATCTTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTG
1 AAATAATCTCAAGCGAGATAAATCTTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTG
563165 TTTCGAGTGAAACTATCTGAAGCGAGATTAATCTTGTTTTAAGAA
66 TTTCGAGTGAAACTATCTGAAGCGAGATTAATCTTGTTTTAAGAA
563210 AAATAATCTCAAGCGAGATAAATCTTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTG
1 AAATAATCTCAAGCGAGATAAATCTTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTG
563275 TTTCGAGTGAAACTATCTGAAGCGAGATTAATCTTGTTTTAAGAA
66 TTTCGAGTGAAACTATCTGAAGCGAGATTAATCTTGTTTTAAGAA
* * * * ** * * * *
563320 AAATAATCTCAAGTGAGCTAAATCTTCTGTTTCGAGTGAAACTATCTTAAGCGAAATAAAATC-T
1 AAATAATCTCAAGCGAGATAAATCTTAT-TTT-AAGAAAAACAATCTCAAGTGAGAT-AAATCTT
*
563384 CTGTTTCGAGTGAAACTATCTCAAGCGAGAT
63 CTGTTTCGAGTGAAACTATCTGAAGCGAGAT
563415 AAAATCTTCT
Statistics
Matches: 190, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
110 134 0.71
111 3 0.02
112 48 0.25
113 5 0.03
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (110 bp):
AAATAATCTCAAGCGAGATAAATCTTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTG
TTTCGAGTGAAACTATCTGAAGCGAGATTAATCTTGTTTTAAGAA
Found at i:563359 original size:184 final size:187
Alignment explanation
Indices: 563050--563422 Score: 583
Period size: 184 Copynumber: 2.0 Consensus size: 187
563040 AAGGCGTAGT
* *
563050 TTATTTTAAGAAAAACAATCTCAAGTGAGATTAATCTTCTGTTTCGAGTGAAATTATCTCAAGCG
1 TTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
563115 AGATAAATCTTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTA
66 AGATAAATCTTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTA
* * *
563180 TCTGAAGCGAGAT-TAATCT-TGTTTTAAG-AAAAATAATCTCAAGCGAGAT-AAATC
131 TCTGAAGCGAAATAAAATCTCTGTTTCAAGTAAAAAT-ATCTCAAGCGAGATAAAATC
*
563234 TTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTGAAGCG
1 TTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
* * * *
563299 AGATTAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGCTAAATCTTCTGTTTCGAGTGAAACTA
66 AGATAAATCTTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTA
* * * *
563364 TCTTAAGCGAAATAAAATCTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
131 TCTGAAGCGAAATAAAATCTCTGTTTCAAGTAAAAATATCTCAAGCGAGATAAAATC
563421 TT
1 TT
563423 CTGTTTCGAG
Statistics
Matches: 171, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
184 134 0.78
185 5 0.03
186 21 0.12
187 11 0.06
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (187 bp):
TTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
AGATAAATCTTATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTA
TCTGAAGCGAAATAAAATCTCTGTTTCAAGTAAAAATATCTCAAGCGAGATAAAATC
Found at i:565267 original size:20 final size:20
Alignment explanation
Indices: 565244--565331 Score: 52
Period size: 20 Copynumber: 4.3 Consensus size: 20
565234 GTTTCCAGAT
*
565244 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTTTGACAA
*** * *
565264 TCGCGTTGCAATTTTAGAAAA
1 TCGCAACGCGATTTT-GACAA
* * *
565285 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTTTG-ACAA
* *
565305 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTTTGACAA
565325 TCGCAAC
1 TCGCAAC
565332 ACTGAATTTT
Statistics
Matches: 50, Mismatches: 15, Indels: 6
0.70 0.21 0.08
Matches are distributed among these distances:
19 1 0.02
20 35 0.70
21 14 0.28
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTTTGACAA
Found at i:566144 original size:24 final size:24
Alignment explanation
Indices: 566117--566170 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
566107 GTATTCGAAA
566117 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
566141 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
566165 TTTGAT
1 TTTGAT
566171 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:566389 original size:14 final size:14
Alignment explanation
Indices: 566360--566396 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
566350 AGAAAAAGAA
566360 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
566375 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
566389 GAAGAAAA
1 GAAGAAAA
566397 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:568432 original size:18 final size:18
Alignment explanation
Indices: 568409--568443 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
568399 AGCAAAAGGC
*
568409 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
568427 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
568444 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:568661 original size:20 final size:20
Alignment explanation
Indices: 568636--568719 Score: 116
Period size: 20 Copynumber: 4.2 Consensus size: 20
568626 TAACGCAAAA
*
568636 ATCGCAACGCAAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
568656 ATCGCAACGTGAATTTGATT
1 ATCGCAACGCGAATTTGACT
*
568676 ATCGCAACGGGAATTTGACT
1 ATCGCAACGCGAATTTGACT
568696 ATCGCAACGCGAA-TTGACT
1 ATCGCAACGCGAATTTGACT
*
568715 TTCGC
1 ATCGC
568720 GTTGCGATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 10 0.18
20 47 0.82
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:568930 original size:67 final size:64
Alignment explanation
Indices: 568818--568987 Score: 166
Period size: 71 Copynumber: 2.5 Consensus size: 64
568808 GATTGAAATC
*
568818 AACAAATCAACTTTTACATTTCAATCAATTAAACAAGCACAAATAAGAA-ATATTCACACATCAA
1 AACAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAATAAGAATATATTC-CACATCAA
568882 TTA
62 TTA
* **
568885 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATAATAATAATTCTTATTTTCCTTA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGC-AAAAATAAGAAT-A----TA--TTCCACA
568949 TCAATTA
58 TCAATTA
*
568956 AACAAATCAACTTTTA-AGAATCAATTAAACAA
1 AACAAATCAACTTTTACATAATCAATTAAACAA
568988 TAAAAAAAAG
Statistics
Matches: 89, Mismatches: 4, Indels: 16
0.82 0.04 0.15
Matches are distributed among these distances:
63 16 0.18
64 9 0.10
66 1 0.01
67 18 0.20
70 3 0.03
71 39 0.44
72 3 0.03
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAATAAGAATATATTCCACATCAATTA
Found at i:570345 original size:42 final size:42
Alignment explanation
Indices: 570286--570379 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
570276 GTGAATCGAG
*
570286 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGACAGGGGC
* ** *
570328 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
570370 CTCTTGAACG
1 CTCTTGAACG
570380 ATAGGAGAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.20, C:0.19, G:0.38, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
Found at i:570346 original size:21 final size:21
Alignment explanation
Indices: 570286--570400 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
570276 GTGAATCGAG
* *
570286 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
570307 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
570328 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
* **
570349 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
570370 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
*
570391 CTATTGAACG
1 CTCTTGAACG
570401 ATGATATGTG
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.04
21 65 0.93
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:570404 original size:42 final size:42
Alignment explanation
Indices: 570313--570406 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
570303 GGACCTCTTC
* * * * *
570313 AACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTG
1 AACGATGATAGGGGCCTCTTGAACGATAGGAGAGGACTATTG
** *
570355 AGGGATGATAGGGGCCTCTTGAACGATAGGAGAGGCCTATTG
1 AACGATGATAGGGGCCTCTTGAACGATAGGAGAGGACTATTG
570397 AACGATGATA
1 AACGATGATA
570407 TGTGAGTCGG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.27, C:0.16, G:0.37, T:0.20
Consensus pattern (42 bp):
AACGATGATAGGGGCCTCTTGAACGATAGGAGAGGACTATTG
Found at i:570909 original size:20 final size:20
Alignment explanation
Indices: 570884--570927 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
570874 AATAGTTTCT
570884 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
570904 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
570924 GAAA
1 GAAA
570928 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:570937 original size:20 final size:20
Alignment explanation
Indices: 570914--570961 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
570904 GAAACTTAAA
570914 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
570934 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
570954 ATCGCAAC
1 ATCGCAAC
570962 AAGATAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:571035 original size:20 final size:20
Alignment explanation
Indices: 571006--571043 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
570996 CGAAACTAAA
*
571006 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
571026 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATTTTCA
571044 CGTTGCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:572734 original size:25 final size:25
Alignment explanation
Indices: 572706--572760 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
572696 CAAAAACAAT
572706 AAACATACCAAGTT-AGATATACCAA
1 AAACATA-CAAGTTAAGATATACCAA
**
572731 AAAC-TACACTTTGAAGATATACCAA
1 AAACATACAAGTT-AAGATATACCAA
572756 AAACA
1 AAACA
572761 ATAATAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 4 0.16
24 2 0.08
25 19 0.76
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (25 bp):
AAACATACAAGTTAAGATATACCAA
Found at i:572994 original size:19 final size:20
Alignment explanation
Indices: 572907--573012 Score: 117
Period size: 20 Copynumber: 5.4 Consensus size: 20
572897 TCTGAAACTT
*
572907 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
572927 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
572947 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
572967 ACTATCGCAACGC-AAAATG
1 AAAATCGCAACGCGAAAATG
*
572986 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
573005 AAAATCGC
1 AAAATCGC
573013 GTTGCGATTC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
19 23 0.31
20 52 0.69
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:573590 original size:20 final size:19
Alignment explanation
Indices: 573520--573594 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
573510 GCGCTTTGAA
*
573520 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAG-CAG
* * *
573540 AATCGCGTTGCGATTTTGTAT
1 AATCGCGTTGCGA--TAGCAG
* *
573561 TATCGTGTTGCGATAGCCAG
1 AATCGCGTTGCGATAG-CAG
573581 AATCGCGTTGCGAT
1 AATCGCGTTGCGAT
573595 TTACATATTC
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 2 0.05
20 25 0.61
21 12 0.29
22 2 0.05
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.32
Consensus pattern (19 bp):
AATCGCGTTGCGATAGCAG
Found at i:573634 original size:21 final size:21
Alignment explanation
Indices: 573610--573656 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
573600 TATTCGCATT
*
573610 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
573631 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
573652 GCGAT
1 GCGAT
573657 AGTCAAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:573726 original size:19 final size:19
Alignment explanation
Indices: 573702--573738 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
573692 TGCGACACTG
*
573702 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
573721 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
573739 TGTTGTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:575204 original size:21 final size:21
Alignment explanation
Indices: 575178--575249 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
575168 GTCAGGGTTC
*
575178 TATGTGGTCCTTTGGGACAAT
1 TATGTGGTCCTTTGGGAAAAT
** * *
575199 TATGTGGAACTTCGGTGCAAAAC
1 TATGTGGTCCTTTGG-G-AAAAT
* *
575222 TATATGGTCCTTTGGGATAAT
1 TATGTGGTCCTTTGGGAAAAT
575243 TATGTGG
1 TATGTGG
575250 CACTTCGGTG
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
21 21 0.57
22 2 0.05
23 14 0.38
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (21 bp):
TATGTGGTCCTTTGGGAAAAT
Found at i:576602 original size:22 final size:20
Alignment explanation
Indices: 576560--576604 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
576550 TGTGAAAATA
**
576560 AAAATATTAAATTTATTTTT
1 AAAATATTAAATTTAAATTT
576580 AAAATATATAAATTTTAAATTT
1 AAAATAT-TAAA-TTTAAATTT
576602 AAA
1 AAA
576605 TTTTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 4 0.19
22 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATATTAAATTTAAATTT
Found at i:577940 original size:21 final size:22
Alignment explanation
Indices: 577905--577946 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
577895 ATAATATTAT
577905 TTTTATTATTAAATG-ATTAAC
1 TTTTATTATTAAATGAATTAAC
577926 TTTTATTATCT-AATGAATTAA
1 TTTTATTAT-TAAATGAATTAA
577947 AAAATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTTATTATTAAATGAATTAAC
Found at i:579910 original size:10 final size:10
Alignment explanation
Indices: 579891--579920 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
579881 TTCACCGCAC
579891 CAAATCCTCT
1 CAAATCCTCT
*
579901 CAAATTCTCT
1 CAAATCCTCT
579911 CAAATCCTCT
1 CAAATCCTCT
579921 AAAAACCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:579978 original size:17 final size:18
Alignment explanation
Indices: 579958--579991 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
579948 TTTATAAGGT
579958 ATATTTTGTTA-TATTTA
1 ATATTTTGTTAGTATTTA
579975 ATATTTTGTTAGTATTT
1 ATATTTTGTTAGTATTT
579992 TATTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
ATATTTTGTTAGTATTTA
Found at i:580013 original size:21 final size:21
Alignment explanation
Indices: 579987--580034 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
579977 ATTTTGTTAG
*
579987 TATTTTATTTAATTATTTAAT
1 TATTTTATTTAAATATTTAAT
*
580008 TATTTTATTTAAATATTTTAT
1 TATTTTATTTAAATATTTAAT
*
580029 TTTTTT
1 TATTTT
580035 GCAGTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTTATTTAAATATTTAAT
Found at i:580015 original size:13 final size:13
Alignment explanation
Indices: 579999--580030 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
579989 TTTTATTTAA
*
579999 TTATTTAATTATT
1 TTATTTAAATATT
580012 TTATTTAAATATT
1 TTATTTAAATATT
580025 TTATTT
1 TTATTT
580031 TTTTGCAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTAAATATT
Found at i:584725 original size:29 final size:29
Alignment explanation
Indices: 584692--584761 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
584682 CATATTTTGG
* *
584692 TTAGTGACCAAAATATAAATTTTG-AAAGT
1 TTAGTGACCAAAATAGAAA-TTGGAAAAGT
* * *
584721 TTAGTGGCTAAAGTAGAAATTGGAAAAGT
1 TTAGTGACCAAAATAGAAATTGGAAAAGT
*
584750 TTAGGGACCAAA
1 TTAGTGACCAAA
584762 GGGGTAATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (29 bp):
TTAGTGACCAAAATAGAAATTGGAAAAGT
Found at i:586672 original size:24 final size:24
Alignment explanation
Indices: 586571--586665 Score: 129
Period size: 24 Copynumber: 4.0 Consensus size: 24
586561 CACTGAAGTG
* * *
586571 CCACATAG-ATTTGTCTCAAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
* *
586594 ACGCGTAGAATTTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
586618 CCACGTAGAATTTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
*
586642 CCACGTAGAATTTATCCCGAAGGA
1 CCACGTAGAATTTGTCCCGAAGGA
586666 TTGCGTATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
23 5 0.08
24 58 0.92
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCGAAGGA
Found at i:591101 original size:12 final size:12
Alignment explanation
Indices: 591073--591116 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
591063 AAGTACTTAT
*
591073 TATGAATATGAAA
1 TATGAAAATG-AA
591086 TATGAAAATGAA
1 TATGAAAATGAA
**
591098 TATGTGAATGAA
1 TATGAAAATGAA
591110 TATGAAA
1 TATGAAA
591117 GTTGAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (12 bp):
TATGAAAATGAA
Found at i:592074 original size:5 final size:5
Alignment explanation
Indices: 592066--592097 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
592056 TCTTCACTTC
592066 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TT
592098 AAGGATGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:595960 original size:2 final size:2
Alignment explanation
Indices: 595953--595977 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
595943 CTAATTTTCT
595953 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
595978 TTTTATCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:596794 original size:14 final size:14
Alignment explanation
Indices: 596775--596806 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
596765 CTATAATTGG
596775 TTTTTCGAAAAATA
1 TTTTTCGAAAAATA
*
596789 TTTTTCGAAAAATG
1 TTTTTCGAAAAATA
596803 TTTT
1 TTTT
596807 CCTAATTTTC
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:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (14 bp):
TTTTTCGAAAAATA
Found at i:597025 original size:30 final size:27
Alignment explanation
Indices: 596968--597025 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
596958 CTCAAAACAT
**
596968 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATAAAAATA
596995 TATTATTTTAGTATCATTTTAATAAAAATA
1 TATTATTTTA-TAT-A-TTTAATAAAAATA
597025 T
1 T
597026 TAATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 3 0.12
29 1 0.04
30 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAATA
Found at i:597078 original size:21 final size:21
Alignment explanation
Indices: 597010--597078 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
597000 TTTTAGTATC
597010 ATTTTAATAA-A-AATATTA-
1 ATTTTAATAATATAATATTAT
* *
597028 ATTATTAA-ATTATATTTATTGAT
1 ATT-TTAATAATATA-ATATT-AT
597051 AATTTTAATAATATAATATTAT
1 -ATTTTAATAATATAATATTAT
597073 ATTTTA
1 ATTTTA
597079 TTATTTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
18 4 0.10
19 5 0.13
20 1 0.03
21 10 0.26
22 3 0.08
23 8 0.21
24 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (21 bp):
ATTTTAATAATATAATATTAT
Found at i:597430 original size:14 final size:14
Alignment explanation
Indices: 597387--597441 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
597377 AATTATAGAT
597387 ATAATATTTTAAT-A
1 ATAATA-TTTAATAA
*
597401 ATAATATTGACATAA
1 ATAATATTTA-ATAA
597416 ATAATATTTAATAA
1 ATAATATTTAATAA
*
597430 ATTATA-TTAATA
1 ATAATATTTAATA
597442 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
13 9 0.25
14 17 0.47
15 10 0.28
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
ATAATATTTAATAA
Found at i:597442 original size:20 final size:20
Alignment explanation
Indices: 597417--597478 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
597407 TTGACATAAA
597417 TAATATTTAATAAATTATAT
1 TAATATTTAATAAATTATAT
*
597437 TAATATTTTA-AAATTATTAT
1 TAATATTTAATAAATTA-TAT
* *
597457 T-ATTTGTTAATAAATAATAT
1 TAATAT-TTAATAAATTATAT
597477 TA
1 TA
597479 TTTATTGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 9 0.26
20 20 0.59
21 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATATTTAATAAATTATAT
Found at i:606666 original size:185 final size:184
Alignment explanation
Indices: 606338--606726 Score: 620
Period size: 185 Copynumber: 2.1 Consensus size: 184
606328 TTTTCTAATT
* * * *
606338 TATATAA-AAATTAAATGTTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
606402 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
66 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
* * ** *
606467 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTAGGCTTAGCCCATATGTTA
131 GAATATTAAATTATTAATTAAGTTTTAAATGGTTTAGGCTGAGCCCATATGTTA
606521 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* * *
606585 TTATAAAATAAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 TTATAAAAT-AAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* *
606650 TTGAATATTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTGAGTCCATATGTTA
129 TTGAATATTAAATTATTAATTAAGTTTTAAATGGTTTAGGCTGAGCCCATATGTTA
606706 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
606727 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
183 13 0.07
184 54 0.29
185 122 0.65
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
GAATATTAAATTATTAATTAAGTTTTAAATGGTTTAGGCTGAGCCCATATGTTA
Found at i:618215 original size:15 final size:15
Alignment explanation
Indices: 618191--618235 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
618181 GGGGAAAGTG
*
618191 GAGGAGGACGAGGAT
1 GAGGATGACGAGGAT
*
618206 GAGGATGACGAGGAG
1 GAGGATGACGAGGAT
* *
618221 GACGATGATGAGGAT
1 GAGGATGACGAGGAT
618236 TAACAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.49, T:0.11
Consensus pattern (15 bp):
GAGGATGACGAGGAT
Found at i:636689 original size:160 final size:160
Alignment explanation
Indices: 636347--636674 Score: 602
Period size: 160 Copynumber: 2.0 Consensus size: 160
636337 TATAAATTGT
* * *
636347 CTCTTATTATTAGAAATTAAAACTTCAAAATATATTTAATTTATAATCCTATTATTTTAAAATTA
1 CTCTT-TTATTAAAAATTAAAAATTCAAAATATATTTAATTTATAATCCTATAATTTTAAAATTA
636412 TAATTATGAAAAATATATATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATAT
65 TAATTATGAAAAATATATATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATAT
636477 CAGAAAAAGACTTCTAGGTGCCTTAAGACAG
130 CAGAAAAAGACTTCTAGGTGCCTTAAGACAG
*
636508 TTCTTTTATTAAAAATTAAAAATTCAAAATATATTTAATTTATAATCCTATAATTTTAAAATTAT
1 CTCTTTTATTAAAAATTAAAAATTCAAAATATATTTAATTTATAATCCTATAATTTTAAAATTAT
636573 AATTATGAAAAATATATATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATC
66 AATTATGAAAAATATATATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATC
*
636638 AGAAAATGACTTCTAGGTGCCTTAAGACAG
131 AGAAAAAGACTTCTAGGTGCCTTAAGACAG
636668 CTCTTTT
1 CTCTTTT
636675 TCTCGATATT
Statistics
Matches: 161, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
160 157 0.98
161 4 0.02
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (160 bp):
CTCTTTTATTAAAAATTAAAAATTCAAAATATATTTAATTTATAATCCTATAATTTTAAAATTAT
AATTATGAAAAATATATATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATC
AGAAAAAGACTTCTAGGTGCCTTAAGACAG
Found at i:638333 original size:3 final size:3
Alignment explanation
Indices: 638325--638372 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
638315 TATATATATT
* * *
638325 TAA TAA TAAA TAA TAA TAA TAA TATA TTA TAT TAA TAA TAA TTA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
638372 T
1 T
638373 TATTATTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:638349 original size:28 final size:29
Alignment explanation
Indices: 638310--638381 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
638300 ATGTAATTTG
638310 TAAT-ATATATATATT-TAATAATAAATAA
1 TAATAATATATATATTATAATAAT-AATAA
*
638338 TAATAATA-ATATATTATATTAATAATAA
1 TAATAATATATATATTATAATAATAATAA
*
638366 TTATAAT-TAT-TATTAT
1 TAATAATATATATATTAT
638382 GAAAAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 6 0.15
28 24 0.62
29 9 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAATAATATATATATTATAATAATAATAA
Found at i:638363 original size:22 final size:22
Alignment explanation
Indices: 638335--638380 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
638325 TAATAATAAA
638335 TAATAATAATAATATATTA-TAT
1 TAATAATAATAATA-ATTATTAT
*
638357 TAATAATAATTATAATTATTAT
1 TAATAATAATAATAATTATTAT
638379 TA
1 TA
638381 TGAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATAATAATAATTATTAT
Found at i:638374 original size:16 final size:16
Alignment explanation
Indices: 638319--638374 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
638309 GTAATATATA
*
638319 TATATTTAATAATAAAT
1 TATAATTAATAAT-AAT
*
638336 AATAA-TAATAATATAT
1 TATAATTAATAATA-AT
638352 TAT-ATTAATAATAAT
1 TATAATTAATAATAAT
638367 TATAATTA
1 TATAATTA
638375 TTATTATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 7 0.21
16 23 0.70
17 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATAATTAATAATAAT
Found at i:638742 original size:76 final size:76
Alignment explanation
Indices: 638500--639066 Score: 1001
Period size: 76 Copynumber: 7.5 Consensus size: 76
638490 GATGAAAATG
* * * * *
638500 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
638565 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* *
638577 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
638641 CCCAAAGGCTT
66 CCCGAAGGCTT
638652 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
638717 CCCGAAGGCTT
66 CCCGAAGGCTT
*
638728 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
638793 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
638804 TTTGGAAACATCATGCACTGCATGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
638869 CCCGAAGGCTT
66 CCCGAAGGCTT
*
638880 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGGAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
638945 CCCGAAGGCTT
66 CCCGAAGGCTT
*
638956 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
639021 CCCGAAGGCTT
66 CCCGAAGGCTT
639032 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
639067 TGGGAAATAG
Statistics
Matches: 472, Mismatches: 17, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
75 72 0.15
76 359 0.76
77 41 0.09
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:639379 original size:156 final size:152
Alignment explanation
Indices: 639092--639381 Score: 409
Period size: 156 Copynumber: 1.9 Consensus size: 152
639082 TAAGTAAGAA
* * * ** *
639092 ACTATGAAAATCGTTTTCTTACTTTTCAATAATTTCATTTTAGAAAAGATTGAATGAGAAACTAT
1 ACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAAATAAAATGACAAACTAT
* *
639157 GGAAATCATTTTCTCATTATTTTTCAAAATAACATGTTAATTGGGTAACATGCCCCAATCTCAAG
66 GAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTAATTGGGTAACATGACCCAATCTCAAG
639222 ATAAGGCTGTTGGAAATAGTTT
131 ATAAGGCTGTTGGAAATAGTTT
639244 ACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAAAAATAAAATGACAAACT
1 ACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAG--AAAAAATAAAATGACAAACT
* * * ** *
639309 ATGAAAATCGTTTTCTTATTCTGTTTTTTTAAATAACATGTTGATTGGGTAACATGACCCAATCT
64 ATGAAAATCATTTTCTCA-T-TATTTTTCAAAATAACATGTTAATTGGGTAACATGACCCAATCT
*
639374 GAAGATAA
127 CAAGATAA
639382 TGCTCATTTT
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
152 41 0.34
154 31 0.26
155 1 0.01
156 46 0.39
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (152 bp):
ACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAAATAAAATGACAAACTAT
GAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTAATTGGGTAACATGACCCAATCTCAAG
ATAAGGCTGTTGGAAATAGTTT
Found at i:640422 original size:54 final size:54
Alignment explanation
Indices: 640296--640453 Score: 184
Period size: 54 Copynumber: 3.0 Consensus size: 54
640286 ATAATCATTG
* * * *
640296 GTTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTG-TC-GA-
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCTCAGAT
* * *
640347 GAT-GTAAAACATTTGAAAACACATT-ATTCCTTTCTTGTAGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCA-TCCTTTCTTGTGGCTTCTGCTCAGAT
*
640400 GTTCGTAAAGCATTTGACAACACATTCATCCTTT-TCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCT-TGTGGCTTCTGCTCAGAT
640454 TTCTCAATTA
Statistics
Matches: 89, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
49 1 0.01
50 35 0.39
51 4 0.04
52 2 0.02
53 3 0.03
54 43 0.48
55 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCTCAGAT
Found at i:644739 original size:9 final size:8
Alignment explanation
Indices: 644724--644836 Score: 93
Period size: 8 Copynumber: 13.5 Consensus size: 8
644714 CAATTTCTCC
644724 CTTTTTTT
1 CTTTTTTT
644732 CATTTTTTTT
1 C--TTTTTTT
*
644742 CTCATTTTT
1 CT-TTTTTT
* *
644751 CCTTTTTC
1 CTTTTTTT
644759 CTTTTTTTT
1 C-TTTTTTT
644768 CTTTTTTT
1 CTTTTTTT
*
644776 CTTTTTTC
1 CTTTTTTT
*
644784 CTTTTTCT
1 CTTTTTTT
*
644792 C-ATTTTT
1 CTTTTTTT
644799 CTTTTTTCAT
1 CTTTTTT--T
*
644809 CTTTTTTC
1 CTTTTTTT
644817 CTTTTTTT
1 CTTTTTTT
*
644825 CTTTCTTT
1 CTTTTTTT
644833 CTTT
1 CTTT
644837 GCTGGATTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
7 5 0.06
8 50 0.60
9 12 0.14
10 16 0.19
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (8 bp):
CTTTTTTT
Found at i:644756 original size:7 final size:7
Alignment explanation
Indices: 644746--644822 Score: 54
Period size: 7 Copynumber: 10.7 Consensus size: 7
644736 TTTTTTCTCA
644746 TTTTTCC
1 TTTTTCC
644753 TTTTTCC
1 TTTTTCC
644760 TTTTT--
1 TTTTTCC
644765 TTTCTT--
1 TTT-TTCC
*
644771 TTTTTCT
1 TTTTTCC
644778 TTTTTCC
1 TTTTTCC
644785 TTTTTCTC
1 TTTTTC-C
*
644793 ATTTTTCT
1 -TTTTTCC
644801 TTTTTCATC
1 TTTTTC--C
644810 TTTTTTCC
1 -TTTTTCC
644818 TTTTT
1 TTTTT
644823 TTCTTTCTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 16
0.76 0.04 0.21
Matches are distributed among these distances:
5 5 0.08
6 5 0.08
7 35 0.59
8 2 0.03
9 6 0.10
10 6 0.10
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCC
Found at i:644758 original size:16 final size:16
Alignment explanation
Indices: 644737--644833 Score: 106
Period size: 16 Copynumber: 5.9 Consensus size: 16
644727 TTTTTCATTT
*
644737 TTTTTCTCATTTTTCC
1 TTTTTCTCTTTTTTCC
*
644753 TTTTTC-CTTTTTTTTC
1 TTTTTCTC-TTTTTTCC
*
644769 TTTTTTTCTTTTTTCC
1 TTTTTCTCTTTTTTCC
* *
644785 TTTTTCTCATTTTTCT
1 TTTTTCTCTTTTTTCC
644801 TTTTTCATCTTTTTTCC
1 TTTTTC-TCTTTTTTCC
*
644818 TTTTTTTCTTTCTTTC
1 TTTTTCTCTTT-TTTC
644834 TTTGCTGGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
15 1 0.01
16 48 0.72
17 18 0.27
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTCTTTTTTCC
Done.