Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 51
Found at i:4568331 original size:19 final size:20
Alignment explanation
Indices: 4568307--4568356 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
4568297 GATAAATTTA
*
4568307 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
4568326 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
4568347 TT-ATAATTTT
1 TTAATAATTTT
4568357 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:4568359 original size:31 final size:30
Alignment explanation
Indices: 4568274--4568360 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
4568264 TTCGATAATA
* *
4568274 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
4568305 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
4568336 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
4568361 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:4582315 original size:17 final size:17
Alignment explanation
Indices: 4582293--4582332 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
4582283 TCATATTAGA
4582293 TGCAATGTCAATAATTT
1 TGCAATGTCAATAATTT
4582310 TGCAATGTCAATAATTT
1 TGCAATGTCAATAATTT
4582327 TGCAAT
1 TGCAAT
4582333 CATTATACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (17 bp):
TGCAATGTCAATAATTT
Found at i:4587753 original size:13 final size:13
Alignment explanation
Indices: 4587735--4587764 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4587725 AATGACACGC
*
4587735 AATGTAAGTCGTA
1 AATGTAAGTCATA
4587748 AATGTAAGTCATA
1 AATGTAAGTCATA
4587761 AATG
1 AATG
4587765 CGTTTCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (13 bp):
AATGTAAGTCATA
Found at i:4593771 original size:43 final size:43
Alignment explanation
Indices: 4593723--4593808 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
4593713 TAAAGAATGT
*
4593723 TTTTAATATGTAAATTTGTTGTATTTAT-AGATTGTTACTTTGG
1 TTTTAATATGTAAATTTGATGTATTTATGA-ATTGTTACTTTGG
* * *
4593766 TTTTAATATGTTAGTTTGATGTATTTATGAATTGTTATTTTGG
1 TTTTAATATGTAAATTTGATGTATTTATGAATTGTTACTTTGG
4593809 AGTTTAGAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.24, C:0.01, G:0.17, T:0.57
Consensus pattern (43 bp):
TTTTAATATGTAAATTTGATGTATTTATGAATTGTTACTTTGG
Found at i:4596519 original size:168 final size:168
Alignment explanation
Indices: 4596234--4596570 Score: 656
Period size: 168 Copynumber: 2.0 Consensus size: 168
4596224 TATCATAATT
4596234 AGGATAAACATGAGAGCACATGGAATTTAAGTTGTGATCAAAAGTGGGTGATAATATGTGTATTT
1 AGGATAAACATGAGAGCACATGGAATTTAAGTTGTGATCAAAAGTGGGTGATAATATGTGTATTT
*
4596299 CTATCATTTAAGTCAACGATTGGTTTGAGGTTTTATTAGTACTTGTCGCCATCTGTGCAGCCTTA
66 CTATCATTTAAGTCAACGATTGGTTTGAGGTTTTATTAGTAATTGTCGCCATCTGTGCAGCCTTA
4596364 CTCGATAAAACTTGACTCGAACAGCTAAGTCAGACTGC
131 CTCGATAAAACTTGACTCGAACAGCTAAGTCAGACTGC
*
4596402 AGGATATACATGAGAGCACATGGAATTTAAGTTGTGATCAAAAGTGGGTGATAATATGTGTATTT
1 AGGATAAACATGAGAGCACATGGAATTTAAGTTGTGATCAAAAGTGGGTGATAATATGTGTATTT
4596467 CTATCATTTAAGTCAACGATTGGTTTGAGGTTTTATTAGTAATTGTCGCCATCTGTGCAGCCTTA
66 CTATCATTTAAGTCAACGATTGGTTTGAGGTTTTATTAGTAATTGTCGCCATCTGTGCAGCCTTA
4596532 CTCGATAAAACTTGACTCGAACAGCTAAGTCAGACTGC
131 CTCGATAAAACTTGACTCGAACAGCTAAGTCAGACTGC
4596570 A
1 A
4596571 AAACAAAGAG
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 167 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (168 bp):
AGGATAAACATGAGAGCACATGGAATTTAAGTTGTGATCAAAAGTGGGTGATAATATGTGTATTT
CTATCATTTAAGTCAACGATTGGTTTGAGGTTTTATTAGTAATTGTCGCCATCTGTGCAGCCTTA
CTCGATAAAACTTGACTCGAACAGCTAAGTCAGACTGC
Found at i:4601771 original size:44 final size:44
Alignment explanation
Indices: 4601689--4601781 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
4601679 GAGTGACATA
* * * * *
4601689 TAGAATTTTCCCGAATGTCCACATATATGTCCCGAAAGA-CTGCG
1 TAGAATTTTCCCAAAGGACCACATATATATCCCAAAAGACCT-CG
*
4601733 TAGAATTTTCCCAAAGGACCACATATATATCCTAAAAGACCTCG
1 TAGAATTTTCCCAAAGGACCACATATATATCCCAAAAGACCTCG
4601777 TAGAA
1 TAGAA
4601782 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (44 bp):
TAGAATTTTCCCAAAGGACCACATATATATCCCAAAAGACCTCG
Found at i:4604879 original size:20 final size:20
Alignment explanation
Indices: 4604854--4604920 Score: 98
Period size: 20 Copynumber: 3.2 Consensus size: 20
4604844 TTTGAGTATT
4604854 GATACCCTATGGATAATATC
1 GATACCCTATGGATAATATC
4604874 GATACCCTATGGATAATATC
1 GATACCCTATGGATAATATC
* *
4604894 GATACCTCTTTGAATAAGTATC
1 GATACC-CTATGGATAA-TATC
4604916 GATAC
1 GATAC
4604921 TTTCAGCTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 26 0.60
21 8 0.19
22 9 0.21
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
GATACCCTATGGATAATATC
Found at i:4607258 original size:19 final size:19
Alignment explanation
Indices: 4607234--4607273 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4607224 CTCTCTCTCG
*
4607234 TTCTTCACTTTCATCACAT
1 TTCTTCACTTTCATCAAAT
*
4607253 TTCTTCATTTTCATCAAAT
1 TTCTTCACTTTCATCAAAT
4607272 TT
1 TT
4607274 ATTCCTCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.53
Consensus pattern (19 bp):
TTCTTCACTTTCATCAAAT
Found at i:4610449 original size:104 final size:104
Alignment explanation
Indices: 4610259--4610449 Score: 226
Period size: 104 Copynumber: 1.8 Consensus size: 104
4610249 CCCCATAGGG
* * * * *
4610259 GTATCGATACTTAGGTATTTTCCAAAACATCAAAAATAATTTTGGTATCGGTACTCGAGGGAGTA
1 GTATCGATACTGAGATAATTTCCAAAACATCAAAAATAATTTTGGTACCGATACTCGAGGGAGTA
* *
4610324 CTGATATCCAAGAGGAGGAGTATTTATGCTCTTAGGGAA
66 CTGATACCCAAAAGGAGGAGTATTTATGCTCTTAGGGAA
* * ** *
4610363 GTATCGGTACTGAGATAATTTCCAAAACATCGAATGTATTTTTGGTACCGATACTC-AGGGAAGT
1 GTATCGATACTGAGATAATTTCCAAAACATCAAAAATAATTTTGGTACCGATACTCGAGGG-AGT
4610427 A-TCGATACCGCAAAAGGA-GAGTA
65 ACT-GATACC-CAAAAGGAGGAGTA
4610450 CCAATACCCA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
103 5 0.07
104 60 0.83
105 7 0.10
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (104 bp):
GTATCGATACTGAGATAATTTCCAAAACATCAAAAATAATTTTGGTACCGATACTCGAGGGAGTA
CTGATACCCAAAAGGAGGAGTATTTATGCTCTTAGGGAA
Found at i:4615476 original size:21 final size:21
Alignment explanation
Indices: 4615446--4615521 Score: 143
Period size: 21 Copynumber: 3.6 Consensus size: 21
4615436 TAATGTAGGC
*
4615446 AGTACTGATACTCCAAGCCTG
1 AGTACCGATACTCCAAGCCTG
4615467 AGTACCGATACTCCAAGCCTG
1 AGTACCGATACTCCAAGCCTG
4615488 AGTACCGATACTCCAAGCCTG
1 AGTACCGATACTCCAAGCCTG
4615509 AGTACCGATACTC
1 AGTACCGATACTC
4615522 AAGGCGTTTG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (21 bp):
AGTACCGATACTCCAAGCCTG
Found at i:4628985 original size:35 final size:35
Alignment explanation
Indices: 4628912--4628986 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
4628902 CGTCACTAAC
**
4628912 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
4628947 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
4628982 AGTAA
1 AGTAA
4628987 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:4629092 original size:24 final size:24
Alignment explanation
Indices: 4629065--4629139 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
4629055 CATAATTCAA
*
4629065 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
4629089 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
4629113 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
4629136 GTCA
1 GTCA
4629140 GGATCATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:4629145 original size:23 final size:23
Alignment explanation
Indices: 4629069--4629145 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
4629059 ATTCAAGTCA
*
4629069 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
4629092 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
4629116 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
4629139 AGGATCA
1 AGTATCA
4629146 TAATAGAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:4629172 original size:47 final size:47
Alignment explanation
Indices: 4629048--4629161 Score: 124
Period size: 47 Copynumber: 2.4 Consensus size: 47
4629038 TATATCAAAA
* * * * *
4629048 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAAATCAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
4629096 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
*
4629142 ATCATAAT-AGAATTCAAGTC
1 ATCA-AATCAGAATCCAAGTC
4629162 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 15 0.27
47 23 0.42
48 17 0.31
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:4630320 original size:18 final size:18
Alignment explanation
Indices: 4630299--4630334 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4630289 CTTCCATCCG
*
4630299 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
4630317 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
4630335 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:4631642 original size:7 final size:7
Alignment explanation
Indices: 4631630--4631661 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
4631620 TGGTCAACTC
4631630 CGGTCAA
1 CGGTCAA
4631637 CGGTCAA
1 CGGTCAA
4631644 CGGTCAA
1 CGGTCAA
4631651 CGGGTCAA
1 C-GGTCAA
4631659 CGG
1 CGG
4631662 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:4631649 original size:14 final size:15
Alignment explanation
Indices: 4631630--4631661 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4631620 TGGTCAACTC
4631630 CGGTCAAC-GGTCAA
1 CGGTCAACGGGTCAA
4631644 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
4631659 CGG
1 CGG
4631662 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:4631658 original size:8 final size:8
Alignment explanation
Indices: 4631631--4631677 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
4631621 GGTCAACTCC
4631631 GGTCAAC-
1 GGTCAACG
4631638 GGTCAAC-
1 GGTCAACG
4631645 GGTCAACG
1 GGTCAACG
4631653 GGTCAACG
1 GGTCAACG
4631661 GGT---CG
1 GGTCAACG
4631666 GGTCAACG
1 GGTCAACG
4631674 GGTC
1 GGTC
4631678 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.14
7 14 0.39
8 17 0.47
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:4631682 original size:18 final size:18
Alignment explanation
Indices: 4631645--4631718 Score: 77
Period size: 18 Copynumber: 4.2 Consensus size: 18
4631635 AACGGTCAAC
4631645 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
4631666 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
4631684 GGTCAAC---T--GGTCG
1 GGTCAACGGGTCGGGTCG
*
4631697 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
4631715 GGTC
1 GGTC
4631719 GGGTTATGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
13 11 0.24
15 1 0.02
16 1 0.02
18 22 0.48
21 11 0.24
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:4631689 original size:31 final size:31
Alignment explanation
Indices: 4631651--4631718 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
4631641 CAACGGTCAA
*
4631651 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
4631682 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
4631713 CGGGTC
1 CGGGTC
4631719 GGGTTATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:4631699 original size:13 final size:13
Alignment explanation
Indices: 4631651--4631682 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
4631641 CAACGGTCAA
4631651 CGGGTCAACGGGT
1 CGGGTCAACGGGT
4631664 CGGGTCAACGGGT
1 CGGGTCAACGGGT
4631677 CGGGTC
1 CGGGTC
4631683 GGGTCAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:4631708 original size:13 final size:13
Alignment explanation
Indices: 4631677--4631712 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
4631667 GTCAACGGGT
*
4631677 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
4631690 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
4631703 CGGGTCGGGT
1 CGGGTCGGGT
4631713 CGGGTCGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:4633824 original size:35 final size:35
Alignment explanation
Indices: 4633751--4633825 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
4633741 CGTCACTAAC
**
4633751 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
4633786 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
4633821 AGTAA
1 AGTAA
4633826 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:4633930 original size:24 final size:24
Alignment explanation
Indices: 4633903--4633977 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
4633893 CATAATTCAA
*
4633903 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
4633927 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
4633951 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
4633974 GTCA
1 GTCA
4633978 GGATCATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:4633983 original size:23 final size:23
Alignment explanation
Indices: 4633907--4633983 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
4633897 ATTCAAGTCA
*
4633907 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
4633930 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
4633954 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
4633977 AGGATCA
1 AGTATCA
4633984 TAATAGAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:4634010 original size:47 final size:47
Alignment explanation
Indices: 4633886--4633999 Score: 124
Period size: 47 Copynumber: 2.4 Consensus size: 47
4633876 TATATCAAAA
* * * * *
4633886 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAAATCAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
4633934 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
*
4633980 ATCATAAT-AGAATTCAAGTC
1 ATCA-AATCAGAATCCAAGTC
4634000 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 15 0.27
47 23 0.42
48 17 0.31
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:4635157 original size:18 final size:18
Alignment explanation
Indices: 4635136--4635171 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4635126 CTTCCATCCG
*
4635136 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
4635154 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
4635172 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:4636478 original size:7 final size:7
Alignment explanation
Indices: 4636466--4636497 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
4636456 TGGTCAACTC
4636466 CGGTCAA
1 CGGTCAA
4636473 CGGTCAA
1 CGGTCAA
4636480 CGGTCAA
1 CGGTCAA
4636487 CGGGTCAA
1 C-GGTCAA
4636495 CGG
1 CGG
4636498 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:4636485 original size:14 final size:15
Alignment explanation
Indices: 4636466--4636497 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4636456 TGGTCAACTC
4636466 CGGTCAAC-GGTCAA
1 CGGTCAACGGGTCAA
4636480 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
4636495 CGG
1 CGG
4636498 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:4636494 original size:8 final size:8
Alignment explanation
Indices: 4636467--4636513 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
4636457 GGTCAACTCC
4636467 GGTCAAC-
1 GGTCAACG
4636474 GGTCAAC-
1 GGTCAACG
4636481 GGTCAACG
1 GGTCAACG
4636489 GGTCAACG
1 GGTCAACG
4636497 GGT---CG
1 GGTCAACG
4636502 GGTCAACG
1 GGTCAACG
4636510 GGTC
1 GGTC
4636514 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.14
7 14 0.39
8 17 0.47
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:4636505 original size:13 final size:13
Alignment explanation
Indices: 4636487--4636518 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
4636477 CAACGGTCAA
4636487 CGGGTCAACGGGT
1 CGGGTCAACGGGT
4636500 CGGGTCAACGGGT
1 CGGGTCAACGGGT
4636513 CGGGTC
1 CGGGTC
4636519 GGGTCAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:4637957 original size:35 final size:35
Alignment explanation
Indices: 4637884--4637958 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
4637874 CGTCACTAAC
**
4637884 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
4637919 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
4637954 AGTAA
1 AGTAA
4637959 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:4638046 original size:24 final size:24
Alignment explanation
Indices: 4638019--4638132 Score: 79
Period size: 24 Copynumber: 4.8 Consensus size: 24
4638009 TATATCAAAA
* *
4638019 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACAGAATCCAAGTCAAGT
* * *
4638043 ATCATATCAGAATCCAAGTCATGT
1 ATCAAAACAGAATCCAAGTCAAGT
* * *
4638067 ATCAGATCAGAATCCATGTCAA-T
1 ATCAAAACAGAATCCAAGTCAAGT
* * * *
4638090 ATCAGATCAGAATCCAGGTC-AGG
1 ATCAAAACAGAATCCAAGTCAAGT
* * *
4638113 ATCATAATAGAATTCAAGTC
1 ATCAAAACAGAATCCAAGTC
4638133 GGAAATCAGA
Statistics
Matches: 74, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
22 1 0.01
23 35 0.47
24 38 0.51
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
ATCAAAACAGAATCCAAGTCAAGT
Found at i:4638116 original size:23 final size:23
Alignment explanation
Indices: 4638033--4638116 Score: 105
Period size: 24 Copynumber: 3.6 Consensus size: 23
4638023 AAACATAATT
*
4638033 CAAGTCAAGTATCATATCAGAATC
1 CAAGTC-AGTATCAGATCAGAATC
4638057 CAAGTCATGTATCAGATCAGAATC
1 CAAGTCA-GTATCAGATCAGAATC
* *
4638081 CATGTCAATATCAGATCAGAATC
1 CAAGTCAGTATCAGATCAGAATC
* *
4638104 CAGGTCAGGATCA
1 CAAGTCAGTATCA
4638117 TAATAGAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
23 26 0.49
24 27 0.51
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (23 bp):
CAAGTCAGTATCAGATCAGAATC
Found at i:4639290 original size:18 final size:18
Alignment explanation
Indices: 4639269--4639304 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4639259 CTTCCATCCG
*
4639269 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
4639287 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
4639305 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:4640617 original size:14 final size:15
Alignment explanation
Indices: 4640598--4640629 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4640588 TGGTCAACTC
4640598 CGGTCAAC-GGTCAA
1 CGGTCAACGGGTCAA
4640612 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
4640627 CGG
1 CGG
4640630 GTCGGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:4640632 original size:8 final size:7
Alignment explanation
Indices: 4640598--4640629 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
4640588 TGGTCAACTC
4640598 CGGTCAA
1 CGGTCAA
4640605 CGGTCAA
1 CGGTCAA
4640612 CGGTCAA
1 CGGTCAA
4640619 CGGGTCAA
1 C-GGTCAA
4640627 CGG
1 CGG
4640630 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:4652172 original size:20 final size:20
Alignment explanation
Indices: 4652147--4652186 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4652137 CCATTTTGTG
4652147 CATTTAGTATCGATAATGTT
1 CATTTAGTATCGATAATGTT
* *
4652167 CATTTAGTATTGATACTGTT
1 CATTTAGTATCGATAATGTT
4652187 GTTCATAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (20 bp):
CATTTAGTATCGATAATGTT
Found at i:4652211 original size:23 final size:23
Alignment explanation
Indices: 4652163--4652208 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
4652153 GTATCGATAA
*
4652163 TGTTCATTTAGTATTGATACTGT
1 TGTTCATTAAGTATTGATACTGT
*
4652186 TGTTCA-TAAGTATTGATATTGT
1 TGTTCATTAAGTATTGATACTGT
4652208 T
1 T
4652209 TGTCAAGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (23 bp):
TGTTCATTAAGTATTGATACTGT
Found at i:4652707 original size:15 final size:15
Alignment explanation
Indices: 4652687--4652717 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4652677 TTTTTACACA
4652687 AAAAAAAACAAATTT
1 AAAAAAAACAAATTT
*
4652702 AAAAAAATCAAATTT
1 AAAAAAAACAAATTT
4652717 A
1 A
4652718 TTTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAAAACAAATTT
Found at i:4652792 original size:20 final size:20
Alignment explanation
Indices: 4652754--4652792 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4652744 TTTCCTACAC
*
4652754 ATTTATACATATACATATAG
1 ATTTATACATAAACATATAG
* *
4652774 ATTTATATATAAACTTATA
1 ATTTATACATAAACATATA
4652793 TTATACACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (20 bp):
ATTTATACATAAACATATAG
Found at i:4653783 original size:181 final size:181
Alignment explanation
Indices: 4653479--4653842 Score: 728
Period size: 181 Copynumber: 2.0 Consensus size: 181
4653469 TTGCAACTTA
4653479 TTATCACTTGGTGGTTTCGACCATCCATTGGTAAATTCTCCACCCTTCGTAACGTTGATATTTGG
1 TTATCACTTGGTGGTTTCGACCATCCATTGGTAAATTCTCCACCCTTCGTAACGTTGATATTTGG
4653544 TTATTCATTGCTTTCAACATCATAAACAAATAAATTTCCCCAAATTATCTTTGGAGAGCTTGTTA
66 TTATTCATTGCTTTCAACATCATAAACAAATAAATTTCCCCAAATTATCTTTGGAGAGCTTGTTA
4653609 ATGTCATTAACAACTCCCAATCTAAGAAATTTGATACCCTTGTTTATGGTT
131 ATGTCATTAACAACTCCCAATCTAAGAAATTTGATACCCTTGTTTATGGTT
4653660 TTATCACTTGGTGGTTTCGACCATCCATTGGTAAATTCTCCACCCTTCGTAACGTTGATATTTGG
1 TTATCACTTGGTGGTTTCGACCATCCATTGGTAAATTCTCCACCCTTCGTAACGTTGATATTTGG
4653725 TTATTCATTGCTTTCAACATCATAAACAAATAAATTTCCCCAAATTATCTTTGGAGAGCTTGTTA
66 TTATTCATTGCTTTCAACATCATAAACAAATAAATTTCCCCAAATTATCTTTGGAGAGCTTGTTA
4653790 ATGTCATTAACAACTCCCAATCTAAGAAATTTGATACCCTTGTTTATGGTT
131 ATGTCATTAACAACTCCCAATCTAAGAAATTTGATACCCTTGTTTATGGTT
4653841 TT
1 TT
4653843 CTTCTTAACC
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
181 183 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (181 bp):
TTATCACTTGGTGGTTTCGACCATCCATTGGTAAATTCTCCACCCTTCGTAACGTTGATATTTGG
TTATTCATTGCTTTCAACATCATAAACAAATAAATTTCCCCAAATTATCTTTGGAGAGCTTGTTA
ATGTCATTAACAACTCCCAATCTAAGAAATTTGATACCCTTGTTTATGGTT
Found at i:4656398 original size:289 final size:289
Alignment explanation
Indices: 4655856--4656435 Score: 935
Period size: 289 Copynumber: 2.0 Consensus size: 289
4655846 TCTTACTTCT
* *
4655856 TTCAAAAGCTTCTAACAACTTTTTAATTTTCCAATTCACCCCCTCTTGGCCATTTTCCTTGATCG
1 TTCAAAAGCTTCCAACAACTTTTTAATTTTCCAATTCACCCACTCTTGGCCATTTTCCTTGATCG
* * *
4655921 ATTGATTCAACACTGTGGGTTTACACTTTGAAGTCAAAAGACCAAGTTTTTGAGGCATTTAAACA
66 ATTGAATCAACACTATGGGTATACACTTTGAAGTCAAAAGACCAAGTTTTTGAGGCATTTAAACA
* *
4655986 GTTTCAAGCATCAGTTGAAAGGGAAACATAGAAGAAATTGAAGTGGATTCATACCAGATAATGGT
131 GTTTCAAGCATCAGTTGAAAGGGAAACAGAGAAGAAATTGAAGTGGATTCATACCACATAATGGT
* *
4656051 GACGACTATACAGGGTCATTTCATGAGTATTGTCCGCGACAGGGAACCAAATATCAGACAACACC
196 GACGACTATACAGGGTCATTTCATGAGTATTGTCCGCGACAAGGAACCAAACATCAGACAACACC
*
4656116 ACCGAAGACTCCATAGTTGAATGGTTTAG
261 ACCGAAGACTCCACAGTTGAATGGTTTAG
4656145 TTCAAAAGCTTCCAACAACTTTTTAATTTTCCAATTCACCCACTCTTGGCCATTTTCCTTGATCG
1 TTCAAAAGCTTCCAACAACTTTTTAATTTTCCAATTCACCCACTCTTGGCCATTTTCCTTGATCG
* **
4656210 ATTGAATCAACAGTATGGGTATACACTTTGAAGTCAAAAGACCAAGTTTTTGAGGTGTTTAAACA
66 ATTGAATCAACACTATGGGTATACACTTTGAAGTCAAAAGACCAAGTTTTTGAGGCATTTAAACA
* * * *
4656275 GTTTCAAGCATTAGTTGAAAGGGAAACAGGGAAGAAGTTGAAGTGGATTCGTACCACATAATGGT
131 GTTTCAAGCATCAGTTGAAAGGGAAACAGAGAAGAAATTGAAGTGGATTCATACCACATAATGGT
* * * * ** * *
4656340 GACGAGTATACATGGTCATTTCATGAGTATTGTCTGGGACAAGGAATTAGACATCAGACGACACC
196 GACGACTATACAGGGTCATTTCATGAGTATTGTCCGCGACAAGGAACCAAACATCAGACAACACC
4656405 ACCGAAGACTCCACAGTTGAATGGTTTAG
261 ACCGAAGACTCCACAGTTGAATGGTTTAG
4656434 TT
1 TT
4656436 GAAAGAATGT
Statistics
Matches: 266, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
289 266 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (289 bp):
TTCAAAAGCTTCCAACAACTTTTTAATTTTCCAATTCACCCACTCTTGGCCATTTTCCTTGATCG
ATTGAATCAACACTATGGGTATACACTTTGAAGTCAAAAGACCAAGTTTTTGAGGCATTTAAACA
GTTTCAAGCATCAGTTGAAAGGGAAACAGAGAAGAAATTGAAGTGGATTCATACCACATAATGGT
GACGACTATACAGGGTCATTTCATGAGTATTGTCCGCGACAAGGAACCAAACATCAGACAACACC
ACCGAAGACTCCACAGTTGAATGGTTTAG
Found at i:4661330 original size:34 final size:34
Alignment explanation
Indices: 4661291--4661361 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
4661281 ATTTTCTACA
4661291 AGTTGGTGTAAAAAATTAATGTTTTCATGCTTGG
1 AGTTGGTGTAAAAAATTAATGTTTTCATGCTTGG
4661325 AGTTGGTGTAAAAAATTAATGTTTTCATGCTTGG
1 AGTTGGTGTAAAAAATTAATGTTTTCATGCTTGG
4661359 AGT
1 AGT
4661362 GTTGATTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.41
Consensus pattern (34 bp):
AGTTGGTGTAAAAAATTAATGTTTTCATGCTTGG
Found at i:4662750 original size:23 final size:24
Alignment explanation
Indices: 4662701--4662808 Score: 105
Period size: 24 Copynumber: 4.5 Consensus size: 24
4662691 ATAGATCTTG
*
4662701 ATTAGTGCATTCGTA-CACTCCTAT
1 ATTAGTGCATTCG-AGCACTCCTGT
*
4662725 ATTAGTGCTTTC-AGCACTCCTGT
1 ATTAGTGCATTCGAGCACTCCTGT
* *
4662748 ATTAGTGCATTCGTGCACACCTGT
1 ATTAGTGCATTCGAGCACTCCTGT
* * *
4662772 ATTAGTTCCATT-GGGTACTCCTGT
1 ATTAG-TGCATTCGAGCACTCCTGT
4662796 ATTTAGTGCATTC
1 A-TTAGTGCATTC
4662809 ATGTACTACT
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
22 1 0.01
23 19 0.28
24 40 0.58
25 9 0.13
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (24 bp):
ATTAGTGCATTCGAGCACTCCTGT
Found at i:4663381 original size:21 final size:21
Alignment explanation
Indices: 4663355--4663400 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
4663345 TAAGAATATC
*
4663355 ATATTGTGTTGCTTTTGATTT
1 ATATTGTGTTGCTTTTGACTT
4663376 ATATTGTGTTGCTTTTGACTT
1 ATATTGTGTTGCTTTTGACTT
4663397 ATAT
1 ATAT
4663401 AGTGACATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.59
Consensus pattern (21 bp):
ATATTGTGTTGCTTTTGACTT
Found at i:4665169 original size:15 final size:15
Alignment explanation
Indices: 4665149--4665181 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4665139 ATAAGTATAA
4665149 ATATTTATAAAAA-TG
1 ATATTT-TAAAAAGTG
4665164 ATATTTTAAAAAGTG
1 ATATTTTAAAAAGTG
4665179 ATA
1 ATA
4665182 AAACAAAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (15 bp):
ATATTTTAAAAAGTG
Found at i:4665554 original size:158 final size:158
Alignment explanation
Indices: 4665266--4666217 Score: 1786
Period size: 158 Copynumber: 6.0 Consensus size: 158
4665256 CATGATGTGT
4665266 ATGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCAC
1 ATGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCAC
4665331 GTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTAT
66 GTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTAT
4665396 CATATTATTGTGTTGTAATTGTGTGCTC
131 CATATTATTGTGTTGTAATTGTGTGCTC
4665424 ATGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCAC
1 ATGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCAC
* *
4665489 ATTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGATGTTTAT
66 GTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTAT
* *
4665554 CATATTATTGTGTTATAATGGTGTGCTC
131 CATATTATTGTGTTGTAATTGTGTGCTC
*
4665582 ATGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTATGTATCAC
1 ATGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCAC
4665647 GTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTAT
66 GTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTAT
*
4665712 CATTTTATTGTGTTGTAATTGTGTGCTC
131 CATATTATTGTGTTGTAATTGTGTGCTC
*
4665740 ATGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTATGTATCAC
1 ATGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCAC
4665805 GTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTAT
66 GTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTAT
4665870 CATATTATTGTGTTGTAATTGTGTGCT-
131 CATATTATTGTGTTGTAATTGTGTGCTC
4665897 ATTGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCA
1 A-TGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCA
4665962 CG-TTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTA
65 CGTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTA
*
4666026 TCATATTATTTTGTTGTAATTGTGTGCT-
130 TCATATTATTGTGTTGTAATTGTGTGCTC
4666054 ATTGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCA
1 A-TGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCA
4666119 CGTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTA
65 CGTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTA
4666184 TCATATTATTGTGTTGTAATTGTGTGCTC
130 TCATATTATTGTGTTGTAATTGTGTGCTC
4666213 A-GCAT
1 ATGCAT
4666218 TAATCATTGT
Statistics
Matches: 777, Mismatches: 14, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
157 161 0.21
158 615 0.79
159 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (158 bp):
ATGCATGTGAATTTTCATTCTAAGATGAATTCAAGTGAGTATGGTTTCCATAAGTTCTGTATCAC
GTTTTTTGTATTATGAAACCACGTGTATAAGTAAAATTTTCTCCACTCATTCGTGTGAGGTTTAT
CATATTATTGTGTTGTAATTGTGTGCTC
Found at i:4666546 original size:7 final size:7
Alignment explanation
Indices: 4666534--4666591 Score: 107
Period size: 7 Copynumber: 8.3 Consensus size: 7
4666524 GGGGCCCTTT
4666534 GATGTTA
1 GATGTTA
4666541 GATGTTA
1 GATGTTA
4666548 GATGTTA
1 GATGTTA
4666555 GATGTTA
1 GATGTTA
4666562 GATGTTA
1 GATGTTA
*
4666569 GACGTTA
1 GATGTTA
4666576 GATGTTA
1 GATGTTA
4666583 GATGTTA
1 GATGTTA
4666590 GA
1 GA
4666592 GGGTGTGCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.29, C:0.02, G:0.29, T:0.40
Consensus pattern (7 bp):
GATGTTA
Found at i:4668696 original size:23 final size:21
Alignment explanation
Indices: 4668660--4668711 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
4668650 TGATTCAACC
*
4668660 TAAATTTTTTTAT-TTTTTAT
1 TAAATTTTTTGATATTTTTAT
4668680 TAAATGTTTTTGATATTTTTAT
1 TAAAT-TTTTTGATATTTTTAT
*
4668702 TTAATTTTTT
1 TAAATTTTTT
4668712 AAATAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 5 0.18
21 12 0.43
22 11 0.39
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
TAAATTTTTTGATATTTTTAT
Found at i:4670422 original size:10 final size:10
Alignment explanation
Indices: 4670407--4670448 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
4670397 TTCATCACAC
4670407 CAAATTCTCT
1 CAAATTCTCT
*
4670417 CAAATTTTCT
1 CAAATTCTCT
*
4670427 CAATTTCTCT
1 CAAATTCTCT
*
4670437 CAAATACTCT
1 CAAATTCTCT
4670447 CA
1 CA
4670449 CTGTTTAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:4670526 original size:17 final size:18
Alignment explanation
Indices: 4670489--4670529 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
4670479 ATATTATGTA
*
4670489 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
4670507 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
4670524 TTTACT
1 TTTACT
4670530 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:4672776 original size:31 final size:28
Alignment explanation
Indices: 4672730--4672795 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 28
4672720 AGTTAATTTT
4672730 GTTTATTACCATTTAATATCAGTTATTGTAA
1 GTTTATTACCATTTAATA-C--TTATTGTAA
*
4672761 -TTTAGTTATCATTTAATACTTATTGTAA
1 GTTTA-TTACCATTTAATACTTATTGTAA
4672789 GTTTATT
1 GTTTATT
4672796 GTATTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
28 11 0.34
29 4 0.12
30 5 0.16
31 12 0.38
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (28 bp):
GTTTATTACCATTTAATACTTATTGTAA
Found at i:4676412 original size:95 final size:95
Alignment explanation
Indices: 4676301--4676479 Score: 313
Period size: 95 Copynumber: 1.9 Consensus size: 95
4676291 TAGCGCGGGT
* *
4676301 CAGGGACCGCGTTAAATATAATTCCGATACGGCGTATAATGTGGCCCCTGATCCGCGCTATACCC
1 CAGGGACCGCGTTAAATATAATTCCGATACGGCGTATAACGCGGCCCCTGATCCGCGCTATACCC
4676366 CTACGTGGCGTATAGCGCGATAGAGTGGAC
66 CTACGTGGCGTATAGCGCGATAGAGTGGAC
* * *
4676396 CAGGGGCCGCGTTAAATATAATTCTGATACGGCGTATAGCGCGGCCCCTGATCCGCGCTATACCC
1 CAGGGACCGCGTTAAATATAATTCCGATACGGCGTATAACGCGGCCCCTGATCCGCGCTATACCC
4676461 CTACGTGGCGTATAGCGCG
66 CTACGTGGCGTATAGCGCG
4676480 GATCAGGGGG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 79 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (95 bp):
CAGGGACCGCGTTAAATATAATTCCGATACGGCGTATAACGCGGCCCCTGATCCGCGCTATACCC
CTACGTGGCGTATAGCGCGATAGAGTGGAC
Found at i:4681538 original size:2 final size:2
Alignment explanation
Indices: 4681523--4681562 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
4681513 TATTAATGAA
4681523 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4681563 TTATTAGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4682731 original size:17 final size:16
Alignment explanation
Indices: 4682706--4682756 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
4682696 CTCTTAAGTT
4682706 TAAGTTAAGTAAAAAAA
1 TAAG-TAAGTAAAAAAA
4682723 TAAGATAAGTAAAAAAA
1 TAAG-TAAGTAAAAAAA
* *
4682740 AAAGTAGGTAAAAAAA
1 TAAGTAAGTAAAAAAA
4682756 T
1 T
4682757 TAAATTGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 11 0.37
17 19 0.63
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.20
Consensus pattern (16 bp):
TAAGTAAGTAAAAAAA
Found at i:4683341 original size:178 final size:181
Alignment explanation
Indices: 4683041--4683402 Score: 495
Period size: 178 Copynumber: 2.0 Consensus size: 181
4683031 TTTGTTGTTG
*
4683041 TATTCACTCGTCGGTCTCTACGGGCAATCGTCGTCAATGATCGCCTTCATGCATCAAAAAGTTTT
1 TATTCACTCGTCGGTCTCTACGGGCAATCGTCATCAATGATCGCCTTCATGCATCAAAAAGTTTT
4683106 CCTTTTATATTGTTTCAATTTTCCCTTTTTCTGGAATCGCCAATTTTCACTTTCACAAAAATATA
66 CCTTTTATATTGTTTCAATTTTCCCTTTTTCTGGAATCGCCAATTTTCACTTTCAC-AAAATATA
4683171 ACTTCTTTTCTTAGGATCGAAT-TTTTACAGTGGTC-AAT-ATA-TATATATA
130 ACTTCTTTTCTTAGGATC-AATATTTTACAGTGGTCAAATGATATTATATATA
* * * * * * * **
4683220 TATTCACTCGTCGGTCTCT-TGGTCCATCGTCATTAGTGATTGCCTTCATGCATTAGTAAGTTTT
1 TATTCACTCGTCGGTCTCTACGGGCAATCGTCATCAATGATCGCCTTCATGCATCAAAAAGTTTT
* *
4683284 TCTTTTATATTGTTTCAATTTT-CCTTTTTCCTTGAATTC-CCAATTTTCACTTTCACAAAATAT
66 CCTTTTATATTGTTTCAATTTTCCCTTTTT-CTGGAA-TCGCCAATTTTCACTTTCACAAAATAT
* * * *
4683347 AACTTGTTTTCTTAGGATCCATATTTTAGAGTGGTCAAATGCTATTATATATA
129 AACTTCTTTTCTTAGGATCAATATTTTACAGTGGTCAAATGATATTATATATA
4683400 TAT
1 TAT
4683403 ATATATATGC
Statistics
Matches: 161, Mismatches: 16, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
176 2 0.01
177 44 0.27
178 81 0.50
179 23 0.14
180 11 0.07
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (181 bp):
TATTCACTCGTCGGTCTCTACGGGCAATCGTCATCAATGATCGCCTTCATGCATCAAAAAGTTTT
CCTTTTATATTGTTTCAATTTTCCCTTTTTCTGGAATCGCCAATTTTCACTTTCACAAAATATAA
CTTCTTTTCTTAGGATCAATATTTTACAGTGGTCAAATGATATTATATATA
Found at i:4684811 original size:72 final size:72
Alignment explanation
Indices: 4684688--4684834 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 72
4684678 AATACGTAGT
4684688 TCTTAAGGCTAATTTTGTGGATCTTGATTAGAAGCTTCAAAAGCGAATACTCAACTTTGTTCATT
1 TCTTAAGGCTAATTTTGTGGATCTTGATTAGAAGCTTCAAAAGCGAATACTCAACTTTGTTCATT
4684753 TGTCGCC
66 TGTCGCC
**
4684760 TCTTAAGGCTAATTTTGTGGATCTTGATTAGAAGCTTCAAAAGCGGGTACTCAACTTTGTTCATT
1 TCTTAAGGCTAATTTTGTGGATCTTGATTAGAAGCTTCAAAAGCGAATACTCAACTTTGTTCATT
4684825 TGTCGCC
66 TGTCGCC
4684832 TCT
1 TCT
4684835 AAGAAAAGGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (72 bp):
TCTTAAGGCTAATTTTGTGGATCTTGATTAGAAGCTTCAAAAGCGAATACTCAACTTTGTTCATT
TGTCGCC
Found at i:4685704 original size:17 final size:17
Alignment explanation
Indices: 4685682--4685735 Score: 108
Period size: 17 Copynumber: 3.2 Consensus size: 17
4685672 ATTAAAATTA
4685682 TAGTTTGCTTAGGATTT
1 TAGTTTGCTTAGGATTT
4685699 TAGTTTGCTTAGGATTT
1 TAGTTTGCTTAGGATTT
4685716 TAGTTTGCTTAGGATTT
1 TAGTTTGCTTAGGATTT
4685733 TAG
1 TAG
4685736 CTTACTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.19, C:0.06, G:0.24, T:0.52
Consensus pattern (17 bp):
TAGTTTGCTTAGGATTT
Found at i:4686341 original size:21 final size:20
Alignment explanation
Indices: 4686317--4686355 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4686307 TAATAAGTAG
*
4686317 TAATCATTAAGTTATATTTCA
1 TAAT-ATTAAGTTAAATTTCA
*
4686338 TAATATTTAGTTAAATTT
1 TAATATTAAGTTAAATTT
4686356 AATTACATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
TAATATTAAGTTAAATTTCA
Found at i:4686867 original size:79 final size:79
Alignment explanation
Indices: 4686736--4686978 Score: 378
Period size: 79 Copynumber: 3.1 Consensus size: 79
4686726 TTATAGTATA
* * ** *
4686736 CTTTTATGTTGATAATGCACCCATATTCATTTCAACTTTGGCATCCTTTCATGCCAATAATTCAC
1 CTTTTATGTCGATAATGCACCCATATGCATTTCAACTAAGGCATCCTTTCATGCCAATAATACAC
*
4686801 CCATATGCACTATT
66 CCATATGCATTATT
* *
4686815 CTTTTATGTCGATAATGCACCCATATGCATTTCAAATAAGGCATCCTTTCATGGCAATAATACAC
1 CTTTTATGTCGATAATGCACCCATATGCATTTCAACTAAGGCATCCTTTCATGCCAATAATACAC
4686880 CCATATGCATTATT
66 CCATATGCATTATT
* * * *
4686894 ATTTTATGCCGATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCAATAATGCAC
1 CTTTTATGTCGATAATGCACCCATATGCATTTCAACTAAGGCATCCTTTCATGCCAATAATACAC
4686959 CCATATGCATTATT
66 CCATATGCATTATT
4686973 CTTTTA
1 CTTTTA
4686979 ATCATCTATT
Statistics
Matches: 149, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 149 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (79 bp):
CTTTTATGTCGATAATGCACCCATATGCATTTCAACTAAGGCATCCTTTCATGCCAATAATACAC
CCATATGCATTATT
Found at i:4686890 original size:45 final size:44
Alignment explanation
Indices: 4686826--4686969 Score: 155
Period size: 45 Copynumber: 3.5 Consensus size: 44
4686816 TTTTATGTCG
*
4686826 ATAATGCACCCATATGCATTTCAAATAAGGCATCCTTTCATGGCA
1 ATAATGCACCCATATGCATTTC-AATAAGGCATCCTTTCATGCCA
* * *
4686871 ATAATACACCCATATGCA-TT--AT----TAT--TTT-ATGCCG
1 ATAATGCACCCATATGCATTTCAATAAGGCATCCTTTCATGCCA
*
4686905 ATAATGCACCCATATGCATTTCAGCTAAGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCA-ATAAGGCATCCTTTCATGCCA
4686950 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
4686970 ATTCTTTTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
34 21 0.26
35 5 0.06
37 2 0.03
38 1 0.01
41 2 0.03
42 2 0.03
44 5 0.06
45 42 0.52
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (44 bp):
ATAATGCACCCATATGCATTTCAATAAGGCATCCTTTCATGCCA
Found at i:4687560 original size:75 final size:74
Alignment explanation
Indices: 4687404--4687563 Score: 171
Period size: 75 Copynumber: 2.1 Consensus size: 74
4687394 CTTCTACCCT
* * * *
4687404 GGTATCAATACTAATATTAGGTTCGATGTTTCCTGGTATCAATACTACCATACTATGGTACTGAT
1 GGTATCGATACCAATATTAGATTCAATGTTTCCTGGTATCAATAC-ACCATACTATGGTACTGAT
*
4687469 ACCCCCTTAC
65 ACCCCCTAAC
* * * *
4687479 GCTATCGATACCAATATTAGATTCAATGTTTGCTTGGTATCGATAC-CCTTACTATGGTA-TCGA
1 GGTATCGATACCAATATTAGATTCAATGTTT-CCTGGTATCAATACACCATACTATGGTACT-GA
**
4687542 TACTGCCTCAAC
64 TACCCCCT-AAC
4687554 GGTATCGATA
1 GGTATCGATA
4687564 TTGATTGAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
73 1 0.01
74 20 0.29
75 37 0.53
76 12 0.17
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (74 bp):
GGTATCGATACCAATATTAGATTCAATGTTTCCTGGTATCAATACACCATACTATGGTACTGATA
CCCCCTAAC
Found at i:4702379 original size:36 final size:37
Alignment explanation
Indices: 4702309--4702379 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
4702299 TAAAGTTGAA
*
4702309 AAAATATAATAAAATAAATAATTATAAATAAAAAAGG
1 AAAATATAATAAAATAAATAATCATAAATAAAAAAGG
* *
4702346 AAAA-ATAATAAAAT-AATAAATCATTAATTAAAAA
1 AAAATATAATAAAATAAAT-AATCATAAATAAAAAA
4702380 TAGTAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 3 0.10
36 23 0.77
37 4 0.13
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (37 bp):
AAAATATAATAAAATAAATAATCATAAATAAAAAAGG
Found at i:4703152 original size:76 final size:76
Alignment explanation
Indices: 4703054--4703263 Score: 350
Period size: 76 Copynumber: 2.8 Consensus size: 76
4703044 TCTTAAATCC
*
4703054 TAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
1 TAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
*
4703118 TATTCTAAAACT
65 TATCCTAAAACT
*
4703130 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAGACAAAGATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
4703195 ATCCTAAAACT
66 ATCCTAAAACT
* * *
4703206 TAATTAAATTATTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAA
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
4703264 TATTTAAAAT
Statistics
Matches: 126, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
75 5 0.04
76 121 0.96
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.28
Consensus pattern (76 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
ATCCTAAAACT
Found at i:4704554 original size:11 final size:11
Alignment explanation
Indices: 4704538--4704562 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4704528 AGTTCAGCAC
4704538 ACACAAGTCAA
1 ACACAAGTCAA
4704549 ACACAAGTCAA
1 ACACAAGTCAA
4704560 ACA
1 ACA
4704563 ATGAGCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.28, G:0.08, T:0.08
Consensus pattern (11 bp):
ACACAAGTCAA
Found at i:4705275 original size:9 final size:10
Alignment explanation
Indices: 4705252--4705298 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
4705242 GTTCAGAGAA
*
4705252 AAAATAAAAT
1 AAAATAAATT
4705262 AAAAT-AATT
1 AAAATAAATT
4705271 AAAATAAATT
1 AAAATAAATT
** *
4705281 AAAAGGAATG
1 AAAATAAATT
4705291 AAAATAAA
1 AAAATAAA
4705299 GTTTGCTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAAATAAATT
Found at i:4705323 original size:11 final size:11
Alignment explanation
Indices: 4705307--4705338 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4705297 AAGTTTGCTA
4705307 AAAAATAAAAC
1 AAAAATAAAAC
*
4705318 AAAAATAACAC
1 AAAAATAAAAC
4705329 AAAAATAAAA
1 AAAAATAAAA
4705339 TGAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.09
Consensus pattern (11 bp):
AAAAATAAAAC
Found at i:4705338 original size:5 final size:5
Alignment explanation
Indices: 4705308--4705358 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
4705298 AGTTTGCTAA
* *
4705308 AAAAT AAAACA AAAAT AACACA- AAAAT AAAAT GAAAT AAAAT AAAAT
1 AAAAT AAAA-T AAAAT AA-A-AT AAAAT AAAAT AAAAT AAAAT AAAAT
4705355 AAAA
1 AAAA
4705359 AATAGAACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 1 0.03
5 29 0.76
6 7 0.18
7 1 0.03
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:4705370 original size:12 final size:12
Alignment explanation
Indices: 4705306--4705370 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 12
4705296 AAAGTTTGCT
4705306 AAAAAATAAAAC
1 AAAAAATAAAAC
*
4705318 -AAAAATAACAC
1 AAAAAATAAAAC
*
4705329 -AAAAATAAAATGA
1 AAAAAATAAAA--C
*
4705342 AATAAAATAAAAT
1 AA-AAAATAAAAC
*
4705355 AAAAAATAGAAC
1 AAAAAATAAAAC
4705367 AAAA
1 AAAA
4705371 TGGGTTGCCT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 19 0.44
12 12 0.28
13 2 0.05
14 1 0.02
15 9 0.21
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAATAAAAC
Found at i:4715910 original size:18 final size:18
Alignment explanation
Indices: 4715855--4715898 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
4715845 TGTATAATAA
* *
4715855 AATAAATGATTAT-AAAT
1 AATAAATAATAATAAAAT
4715872 AA-AAATAATAATAAAAT
1 AATAAATAATAATAAAAT
4715889 AATAAATAAT
1 AATAAATAAT
4715899 GAATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AATAAATAATAATAAAAT
Found at i:4715917 original size:38 final size:39
Alignment explanation
Indices: 4715848--4715925 Score: 90
Period size: 38 Copynumber: 2.0 Consensus size: 39
4715838 TTGAAAATGT
*
4715848 ATAATAAAATAAATGATTATAAATAAAAATAATA-ATAAA
1 ATAATAAAATAAATGATTAAAAATAAAAATAA-AGATAAA
**
4715887 ATAAT-AAAT-AATGAATTAAAAATAGTAATAAAGATAAA
1 ATAATAAAATAAATG-ATTAAAAATAAAAATAAAGATAAA
4715925 A
1 A
4715926 AGGGGGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
37 5 0.15
38 24 0.71
39 5 0.15
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (39 bp):
ATAATAAAATAAATGATTAAAAATAAAAATAAAGATAAA
Found at i:4715985 original size:17 final size:17
Alignment explanation
Indices: 4715965--4715998 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4715955 AATGAGATAA
*
4715965 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
4715982 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
4715999 TAGGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:4718348 original size:457 final size:457
Alignment explanation
Indices: 4717494--4718407 Score: 1684
Period size: 457 Copynumber: 2.0 Consensus size: 457
4717484 AGTTAATTGG
* *
4717494 TTATAAATGAGTATTTATAATCAAGATGGATGCAAATAGTGATGTTTATAAGTATAAGGTATGTC
1 TTATAAATGAGTATTTATAATCAAGATGGATGCAAATAGTGATGTTTATAAATATAAGATATGTC
* *
4717559 TTGTATATAAAGTATATACTCAGAAATGAGGCATTGTTTTTGTAGAGACTTTCTCTTTGGTTTTA
66 TTGTATATAAAGTATATACTCAGAAATGAGGCATTGTTTTTGTAGAGACTTTCTCTTTGATTTCA
4717624 TTGAAAGACTATTTCATTATAATTATGATACTTGTTGCTCATATTTGATTTTGAGTTACATAAGT
131 TTGAAAGACTATTTCATTATAATTATGATACTTGTTGCTCATATTTGATTTTGAGTTACATAAGT
*
4717689 TGGATTTCGAAATTGTGTTTCTCAATAGTAACATTGATGAAATATTTTATACGGTGCAATTAGAA
196 TGGATTTCGAAATTGTGTTTCTCAATAGTAACATTGATAAAATATTTTATACGGTGCAATTAGAA
*
4717754 AATTGTATCTAATGATACAAAATTAATAATATGAAAATTATGGAAATCCATTTATAAGTTCAAAT
261 AATTGTATCTAATGATACAAAATTAATAATATGAAAATTAAGGAAATCCATTTATAAGTTCAAAT
*
4717819 ATTACTCCCGTTAATTATATAACAAACTTCAGCAAGTGATTATCTTGTTTGGTTTTGAGATGAAT
326 ATTACTCCCGTTAATTATATAACAAACTTCACCAAGTGATTATCTTGTTTGGTTTTGAGATGAAT
* *
4717884 TCGGTTGATAATTGTATATATTATAAGCTCAATGGGAGTGAACCAAATAATACCCCTTATAGAAA
391 TCGGTTGATAACTGTATATATTATAAGCTCAATGGGAATGAACCAAATAATACCCCTTATAGAAA
4717949 AA
456 AA
4717951 TTATAAATGAGTATTTATAATCAAGATGGATGCAAATAGTGATGTTTATAAATATAAGATATGTC
1 TTATAAATGAGTATTTATAATCAAGATGGATGCAAATAGTGATGTTTATAAATATAAGATATGTC
*
4718016 TTGTATATAAAGTATATACTGAGAAATGAGGCATTGTTTTTGTAGAGACTTTCTCTTTGATTTCA
66 TTGTATATAAAGTATATACTCAGAAATGAGGCATTGTTTTTGTAGAGACTTTCTCTTTGATTTCA
*
4718081 TTGAAAGACTCTTTCATTATAATTATGATACTTGTTGCTCATATTTGATTTTGAGTTACATAAGT
131 TTGAAAGACTATTTCATTATAATTATGATACTTGTTGCTCATATTTGATTTTGAGTTACATAAGT
* *
4718146 TGGATTTCGAAATTGTGTTTCTCAATGGTAACATTGATAAAATATTTTATATGGTGCAATTAGAA
196 TGGATTTCGAAATTGTGTTTCTCAATAGTAACATTGATAAAATATTTTATACGGTGCAATTAGAA
*
4718211 AATTGTATCTAATGATACAAAATTAATAATATGGAAATTAAGGAAATCCATTTATAAGTTCAAAT
261 AATTGTATCTAATGATACAAAATTAATAATATGAAAATTAAGGAAATCCATTTATAAGTTCAAAT
*
4718276 ATTACTCTCGTTAATTATATAACAAACTTCACCAAGTGATTATCTTGTTTGGTTTTGAGATGAAT
326 ATTACTCCCGTTAATTATATAACAAACTTCACCAAGTGATTATCTTGTTTGGTTTTGAGATGAAT
*
4718341 TCGGTTGATAACTGTATATATTATAAGCTCAATGGGAATGAACCAAATAATACCCCTTATTGAAA
391 TCGGTTGATAACTGTATATATTATAAGCTCAATGGGAATGAACCAAATAATACCCCTTATAGAAA
4718406 AA
456 AA
4718408 GGAACGAAGT
Statistics
Matches: 441, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
457 441 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (457 bp):
TTATAAATGAGTATTTATAATCAAGATGGATGCAAATAGTGATGTTTATAAATATAAGATATGTC
TTGTATATAAAGTATATACTCAGAAATGAGGCATTGTTTTTGTAGAGACTTTCTCTTTGATTTCA
TTGAAAGACTATTTCATTATAATTATGATACTTGTTGCTCATATTTGATTTTGAGTTACATAAGT
TGGATTTCGAAATTGTGTTTCTCAATAGTAACATTGATAAAATATTTTATACGGTGCAATTAGAA
AATTGTATCTAATGATACAAAATTAATAATATGAAAATTAAGGAAATCCATTTATAAGTTCAAAT
ATTACTCCCGTTAATTATATAACAAACTTCACCAAGTGATTATCTTGTTTGGTTTTGAGATGAAT
TCGGTTGATAACTGTATATATTATAAGCTCAATGGGAATGAACCAAATAATACCCCTTATAGAAA
AA
Found at i:4721346 original size:17 final size:17
Alignment explanation
Indices: 4721321--4721353 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4721311 CTTTTAAGTT
*
4721321 TAAGTTAAGTAAAAAAG
1 TAAGATAAGTAAAAAAG
4721338 TAAGATAAGTAAAAAA
1 TAAGATAAGTAAAAAA
4721354 AAGTAGGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (17 bp):
TAAGATAAGTAAAAAAG
Found at i:4723419 original size:20 final size:19
Alignment explanation
Indices: 4723396--4723456 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 19
4723386 ATCATAAAAC
4723396 TTAATATTATTTTTTAAATA
1 TTAATATTATTTTTT-AATA
* * *
4723416 TTAAAATAATTTATTTATTA
1 TTAATATTATTT-TTTAATA
4723436 TTAAAATATTATTTTTATAAT
1 TT--AATATTATTTTT-TAAT
4723457 TTTATTTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
20 15 0.48
21 5 0.16
22 11 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATATTATTTTTTAATA
Found at i:4723799 original size:22 final size:23
Alignment explanation
Indices: 4723771--4723817 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
4723761 TTGATTATTT
4723771 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
4723793 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
4723816 TA
1 TA
4723818 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:4723822 original size:22 final size:22
Alignment explanation
Indices: 4723778--4723834 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
4723768 TTTTATTATA
* *
4723778 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
4723799 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
4723821 ATATTTTAAATATT
1 ATATTATAAATATT
4723835 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:4724721 original size:7 final size:7
Alignment explanation
Indices: 4724711--4724735 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4724701 TTGCTATTAT
4724711 TTATTTA
1 TTATTTA
4724718 TTATTTA
1 TTATTTA
4724725 TTATTTA
1 TTATTTA
4724732 TTAT
1 TTAT
4724736 GAGTTTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:4727099 original size:22 final size:22
Alignment explanation
Indices: 4727074--4727115 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4727064 ATATTTACTA
4727074 ATATTTATAATAATATAATATT
1 ATATTTATAATAATATAATATT
* *
4727096 ATATTTTTAATATTATAATA
1 ATATTTATAATAATATAATA
4727116 AAATAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTTATAATAATATAATATT
Found at i:4727718 original size:29 final size:29
Alignment explanation
Indices: 4727685--4727769 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
4727675 TTCCAGAAAT
* *
4727685 GTAATTCGTTTTCCAGAATTTAATTTCCA
1 GTAATTCATTTTCCAGAATTCAATTTCCA
4727714 GTAATTCATTTTCCAGAATTCAATTTCCA
1 GTAATTCATTTTCCAGAATTCAATTTCCA
*
4727743 GTAATTCAATTTCCAGAATTCAATTTC
1 GTAATTCATTTTCCAGAATTCAATTTC
4727770 TAGAAAACCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAATTTCCA
Found at i:4727726 original size:15 final size:14
Alignment explanation
Indices: 4727694--4727774 Score: 117
Period size: 14 Copynumber: 5.6 Consensus size: 14
4727684 TGTAATTCGT
*
4727694 TTTCCAGAATTTAA
1 TTTCCAGAATTCAA
*
4727708 TTTCCAGTAATTCAT
1 TTTCCAG-AATTCAA
4727723 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
4727737 TTTCCAGTAATTCAA
1 TTTCCAG-AATTCAA
4727752 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
*
4727766 TTTCTAGAA
1 TTTCCAGAA
4727775 AACCAATTAC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
14 35 0.57
15 26 0.43
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (14 bp):
TTTCCAGAATTCAA
Found at i:4730760 original size:7 final size:6
Alignment explanation
Indices: 4730725--4730804 Score: 67
Period size: 6 Copynumber: 13.0 Consensus size: 6
4730715 TTTGGCATGC
* *
4730725 ATAAAA AT-AAA ATAAAG ATAAAG ATAAAA TATAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA -ATAAAA ATAAAA ATAAAA
*
4730773 A-AATAG ATAAATA A-ATAAA ATAGAAA ATAAAA
1 ATAA-AA ATAAA-A ATA-AAA ATA-AAA ATAAAA
4730805 GAACTGGGCG
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
5 7 0.11
6 37 0.60
7 18 0.29
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:4730764 original size:19 final size:19
Alignment explanation
Indices: 4730725--4730772 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
4730715 TTTGGCATGC
*
4730725 ATAAAAAT-AAA-ATAAAG
1 ATAAAAATAAAATATAAAA
*
4730742 ATAAAGATAAAATATAAAA
1 ATAAAAATAAAATATAAAA
4730761 ATAAAAATAAAA
1 ATAAAAATAAAA
4730773 AAATAGATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 7 0.27
18 3 0.12
19 16 0.62
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (19 bp):
ATAAAAATAAAATATAAAA
Found at i:4730770 original size:12 final size:12
Alignment explanation
Indices: 4730725--4730804 Score: 67
Period size: 13 Copynumber: 6.5 Consensus size: 12
4730715 TTTGGCATGC
4730725 ATAAAAAT-AAA
1 ATAAAAATAAAA
* *
4730736 ATAAAGATAAAG
1 ATAAAAATAAAA
4730748 ATAAAATATAAAA
1 ATAAAA-ATAAAA
4730761 ATAAAAATAAAA
1 ATAAAAATAAAA
*
4730773 A-AATAGATAAATA
1 ATAA-AAATAAA-A
4730786 A-ATAAAATAGAAA
1 ATA-AAAATA-AAA
4730799 ATAAAA
1 ATAAAA
4730805 GAACTGGGCG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
11 9 0.16
12 20 0.36
13 23 0.41
14 4 0.07
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:4730771 original size:31 final size:30
Alignment explanation
Indices: 4730725--4730804 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
4730715 TTTGGCATGC
*
4730725 ATAAAAAT-AAAATAAAGATAA-AGATAAAAT
1 ATAAAAATAAAAATAAA-AAAATAGAT-AAAT
4730755 ATAAAAATAAAAATAAAAAAATAGATAAAT
1 ATAAAAATAAAAATAAAAAAATAGATAAAT
*
4730785 AAATAAAATAGAAAATAAAA
1 ATA-AAAATA-AAAATAAAA
4730805 GAACTGGGCG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
30 17 0.39
31 18 0.41
32 9 0.20
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (30 bp):
ATAAAAATAAAAATAAAAAAATAGATAAAT
Found at i:4731649 original size:18 final size:18
Alignment explanation
Indices: 4731626--4731671 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
4731616 ACCGGTCATA
4731626 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
4731644 ACCCGACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
4731662 ACCCGACCCG
1 ACCCGACCCG
4731672 TTTACCGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.50, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:4733003 original size:18 final size:18
Alignment explanation
Indices: 4732977--4733011 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4732967 TCGAAAGGAC
*
4732977 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
4732995 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
4733012 CCGGATGGCA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:4734329 original size:24 final size:24
Alignment explanation
Indices: 4734207--4734322 Score: 171
Period size: 24 Copynumber: 4.8 Consensus size: 24
4734197 TTCGATTTGA
4734207 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
4734231 ATTCTGATCTGATATTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
4734255 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
4734279 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
4734302 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
4734323 CTGATTTATG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
23 2 0.02
24 82 0.98
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:4738667 original size:33 final size:32
Alignment explanation
Indices: 4738628--4738745 Score: 155
Period size: 33 Copynumber: 3.6 Consensus size: 32
4738618 ATGATGTCAT
*
4738628 ATTTTTGTAAGTAAACTTAACATGTTGTTGCC
1 ATTTTTGTAAGTAAACTTAACATGTTGTTGTC
* * *
4738660 ATCTTTTGTATGTAAACTTAACTTGTTGATGTC
1 AT-TTTTGTAAGTAAACTTAACATGTTGTTGTC
**
4738693 ATATTTTTGTAAGTAAACTTAACATGCAGTTGTC
1 --ATTTTTGTAAGTAAACTTAACATGTTGTTGTC
4738727 ATTTTTGTAAGTAAACTTA
1 ATTTTTGTAAGTAAACTTA
4738746 CTCATGATAC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 21 0.28
33 26 0.35
34 25 0.34
35 2 0.03
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (32 bp):
ATTTTTGTAAGTAAACTTAACATGTTGTTGTC
Found at i:4738692 original size:67 final size:66
Alignment explanation
Indices: 4738619--4738745 Score: 209
Period size: 67 Copynumber: 1.9 Consensus size: 66
4738609 AACATAGACA
** *
4738619 TGATGTCATATTTTTGTAAGTAAACTTAACATGTTGTTGCCATCTTTTGTATGTAAACTTAACTT
1 TGATGTCATATTTTTGTAAGTAAACTTAACATGCAGTTGCCAT-TTTTGTAAGTAAACTTAACTT
4738684 GT
65 GT
*
4738686 TGATGTCATATTTTTGTAAGTAAACTTAACATGCAGTTGTCATTTTTGTAAGTAAACTTA
1 TGATGTCATATTTTTGTAAGTAAACTTAACATGCAGTTGCCATTTTTGTAAGTAAACTTA
4738746 CTCATGATAC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
66 16 0.29
67 40 0.71
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (66 bp):
TGATGTCATATTTTTGTAAGTAAACTTAACATGCAGTTGCCATTTTTGTAAGTAAACTTAACTTG
T
Found at i:4738709 original size:34 final size:34
Alignment explanation
Indices: 4738619--4738745 Score: 161
Period size: 34 Copynumber: 3.8 Consensus size: 34
4738609 AACATAGACA
4738619 TGATGTCATATTTTTGTAAGTAAACTTAACATGT
1 TGATGTCATATTTTTGTAAGTAAACTTAACATGT
* * * * *
4738653 TGTTGCCAT-CTTTTGTATGTAAACTTAACTTGT
1 TGATGTCATATTTTTGTAAGTAAACTTAACATGT
*
4738686 TGATGTCATATTTTTGTAAGTAAACTTAACATGC
1 TGATGTCATATTTTTGTAAGTAAACTTAACATGT
* *
4738720 AGTTGTC--ATTTTTGTAAGTAAACTTA
1 TGATGTCATATTTTTGTAAGTAAACTTA
4738746 CTCATGATAC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
32 19 0.24
33 28 0.35
34 32 0.41
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (34 bp):
TGATGTCATATTTTTGTAAGTAAACTTAACATGT
Found at i:4739042 original size:23 final size:23
Alignment explanation
Indices: 4739012--4739075 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
4739002 CGACCTAATA
4739012 TAATAAAAGATATTATTTTTATT
1 TAATAAAAGATATTATTTTTATT
4739035 TAATAAAAGATATTATTTTTATT
1 TAATAAAAGATATTATTTTTATT
*
4739058 CAATAAAA-ATAGTTATTT
1 TAATAAAAGATA-TTATTT
4739076 AATTGAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 3 0.08
23 36 0.92
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (23 bp):
TAATAAAAGATATTATTTTTATT
Found at i:4743175 original size:18 final size:17
Alignment explanation
Indices: 4743147--4743184 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
4743137 TTGCATTTTA
4743147 AAAGCATTTAACAAACATT
1 AAAGCATTTAA-AAA-ATT
4743166 AAAG-ATTTAAAAAATT
1 AAAGCATTTAAAAAATT
4743182 AAA
1 AAA
4743185 AAATTATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 3 0.16
18 6 0.32
19 4 0.21
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (17 bp):
AAAGCATTTAAAAAATT
Found at i:4743644 original size:21 final size:21
Alignment explanation
Indices: 4743597--4743644 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
4743587 GGTGACATAA
* * *
4743597 AACCCTGCGGGCTGGGTATGT
1 AACCCTGCGGGCTAGGAAGGT
* *
4743618 ACCCCTGTGGGCTAGGAAGGT
1 AACCCTGCGGGCTAGGAAGGT
4743639 AACCCT
1 AACCCT
4743645 ACGGTGGTGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.27, G:0.33, T:0.21
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAAGGT
Found at i:4747258 original size:18 final size:18
Alignment explanation
Indices: 4747235--4747271 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4747225 ATGTAATTTG
* *
4747235 TAATGTTTTTTAAATGTT
1 TAATGTTTGTTAAAAGTT
4747253 TAATGTTTGTTAAAAGTT
1 TAATGTTTGTTAAAAGTT
4747271 T
1 T
4747272 TTAAAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
TAATGTTTGTTAAAAGTT
Found at i:4747338 original size:18 final size:18
Alignment explanation
Indices: 4747315--4747351 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4747305 TTACATTATG
*
4747315 TAATGTTTTTTAAATGTT
1 TAATGTTTGTTAAATGTT
*
4747333 TAATGTTTGTTAATTGTT
1 TAATGTTTGTTAAATGTT
4747351 T
1 T
4747352 TTAAAATGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (18 bp):
TAATGTTTGTTAAATGTT
Found at i:4751087 original size:50 final size:51
Alignment explanation
Indices: 4751021--4751145 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 51
4751011 ATCGAACCTT
* * * *
4751021 ACCCTAAACCACTTTAACCTACATAACCCTTGACCACTCTCACCTTAA-AA
1 ACCCTAAACCACTTTAACCTAAAAAACCCTTAACCACTCTCAACTTAACAA
* * * * *
4751071 ACCCTAAACCACTTTAACTTAAAAAATCCTTAACCACTTTTAACTTAACGA
1 ACCCTAAACCACTTTAACCTAAAAAACCCTTAACCACTCTCAACTTAACAA
* *
4751122 ACCCTATATCACTTTAACCTAAAA
1 ACCCTAAACCACTTTAACCTAAAA
4751146 TCACTCCAAC
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 40 0.65
51 22 0.35
ACGTcount: A:0.39, C:0.32, G:0.02, T:0.27
Consensus pattern (51 bp):
ACCCTAAACCACTTTAACCTAAAAAACCCTTAACCACTCTCAACTTAACAA
Found at i:4751112 original size:26 final size:25
Alignment explanation
Indices: 4751021--4751145 Score: 99
Period size: 25 Copynumber: 5.0 Consensus size: 25
4751011 ATCGAACCTT
* * *
4751021 ACCCTAAACCACTTTAACCTACATA
1 ACCCTAAACCACTTTAACTTAAAAA
** * *
4751046 ACCCTTGACCACTCTCACCTT-AAAA
1 ACCCTAAACCACT-TTAACTTAAAAA
4751071 ACCCTAAACCACTTTAACTTAAAAA
1 ACCCTAAACCACTTTAACTTAAAAA
* * **
4751096 ATCCTTAACCACTTTTAACTTAACGA
1 ACCCTAAACCAC-TTTAACTTAAAAA
* * *
4751122 ACCCTATATCACTTTAACCTAAAA
1 ACCCTAAACCACTTTAACTTAAAA
4751146 TCACTCCAAC
Statistics
Matches: 75, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
24 5 0.07
25 47 0.63
26 23 0.31
ACGTcount: A:0.39, C:0.32, G:0.02, T:0.27
Consensus pattern (25 bp):
ACCCTAAACCACTTTAACTTAAAAA
Found at i:4753562 original size:140 final size:140
Alignment explanation
Indices: 4753243--4753589 Score: 396
Period size: 141 Copynumber: 2.5 Consensus size: 140
4753233 TCCCTAAACT
* * * *
4753243 TTTAATTTAGGGAGTAA-TTCGAATTGGCTCTCATATTAACTTGCCCGAGGGACCATTTCAATTA
1 TTTAATTTAGGGAGTAATTTC-AATTGGCTCTC-CATTAACATACCCGACGGACCATTTCAATTA
* *
4753307 TTCAATTAAAACATTGGTTAAAATAAATTAAGAGTAATATTAGAGCATCCACTTTAGGTTTAATT
64 TTCAATTAAAACATTGATTAAAATAAATTAAGAGTAATATTAGAGCATCCACTTTAGGTTAAATT
*
4753372 TCACTTTAGTCC
129 TCACTTTAGTAC
* * * * * *
4753384 TTTACTTTAGGGAGTAATGTGAATTGGCTCTCCAATTAACATACCTGACGGATCA-TTCTGATTA
1 TTTAATTTAGGGAGTAATTTCAATTGGCTCTCC-ATTAACATACCCGACGGACCATTTC-AATTA
** * *
4753448 TTCAATTCATTA-ATTGATTAAAATAAATTAGGATTAATATTAGAGC-TCCACTTTAGGTTAAAT
64 TTCAATT-AAAACATTGATTAAAATAAATTAAGAGTAATATTAGAGCATCCACTTTAGGTTAAAT
*
4753511 TTCACTTTATTAC
128 TTCACTTTAGTAC
* * ** * *
4753524 TTTAATTTAAGGAGTAATTTCAATTGGCTCTCGCATTAACATGCCTAAGGGACAATTTCAATTAT
1 TTTAATTTAGGGAGTAATTTCAATTGGCTCTC-CATTAACATACCCGACGGACCATTTCAATTAT
4753589 T
65 T
4753590 AGACTCAATA
Statistics
Matches: 172, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
140 80 0.47
141 89 0.52
142 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (140 bp):
TTTAATTTAGGGAGTAATTTCAATTGGCTCTCCATTAACATACCCGACGGACCATTTCAATTATT
CAATTAAAACATTGATTAAAATAAATTAAGAGTAATATTAGAGCATCCACTTTAGGTTAAATTTC
ACTTTAGTAC
Found at i:4753609 original size:140 final size:138
Alignment explanation
Indices: 4753243--4753629 Score: 419
Period size: 140 Copynumber: 2.8 Consensus size: 138
4753233 TCCCTAAACT
* * *
4753243 TTTAATTTAGGGAGTAA-TTCGAATTGGCTCTCATATTAACTTGCCCGAGGGACCATTTCAATTA
1 TTTAATTTAGGGAGTAATTTC-AATTGGCTCTC-CATTAACATGCCTGAGGGA-CATTTCAATTA
* * * * *
4753307 TTCAATTAAAACATTGGTTAAAATAAATTAAGAGTAATATTAGAGCATCCACTTTAGGTTTAATT
63 TTCAATCAATA-ATTGGTTAAAATAAATTAGGATTAATATTAGAGCATCCACTTTAGGTTAAATT
*
4753372 TCACTTTAGTCC
127 TCACTTTAGTAC
* * * * * *
4753384 TTTACTTTAGGGAGTAATGTGAATTGGCTCTCCAATTAACATACCTGACGGATCA-TTCTGATTA
1 TTTAATTTAGGGAGTAATTTCAATTGGCTCTCC-ATTAACATGCCTGAGGGA-CATTTC-AATTA
* *
4753448 TTCAATTCATTAATTGATTAAAATAAATTAGGATTAATATTAGAGC-TCCACTTTAGGTTAAATT
63 TTCAA-TCAATAATTGGTTAAAATAAATTAGGATTAATATTAGAGCATCCACTTTAGGTTAAATT
*
4753512 TCACTTTATTAC
127 TCACTTTAGTAC
* *
4753524 TTTAATTTAAGGAGTAATTTCAATTGGCTCTCGCATTAACATGCCTAAGGGACAATTTCAATTAT
1 TTTAATTTAGGGAGTAATTTCAATTGGCTCTC-CATTAACATGCCTGAGGGAC-ATTTCAATTAT
*
4753589 T-AGACTCAATAGTTGGTT-AAA-AAATTATGG-TTAATATTAGA
64 TCA-A-TCAATAATTGGTTAAAATAAATTA-GGATTAATATTAGA
4753630 ACCTCCATTG
Statistics
Matches: 206, Mismatches: 31, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
138 17 0.08
139 7 0.03
140 91 0.44
141 87 0.42
142 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (138 bp):
TTTAATTTAGGGAGTAATTTCAATTGGCTCTCCATTAACATGCCTGAGGGACATTTCAATTATTC
AATCAATAATTGGTTAAAATAAATTAGGATTAATATTAGAGCATCCACTTTAGGTTAAATTTCAC
TTTAGTAC
Found at i:4759036 original size:32 final size:31
Alignment explanation
Indices: 4758983--4759042 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
4758973 GAAAAAAATG
4758983 AAAAAAGAAGAAAAAGTAATAAATAAATGAA
1 AAAAAAGAAGAAAAAGTAATAAATAAATGAA
*
4759014 AAAAAAGAATGATAAA-TAAATAAATAAAT
1 AAAAAAGAA-GAAAAAGT-AATAAATAAAT
4759043 AATAGAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (31 bp):
AAAAAAGAAGAAAAAGTAATAAATAAATGAA
Found at i:4760360 original size:19 final size:20
Alignment explanation
Indices: 4760336--4760374 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4760326 GTAAAACTAT
4760336 TTTTAT-TAT-ATTATATTGA
1 TTTTATATATGATTAT-TTGA
4760355 TTTTATATATGATTATTTGA
1 TTTTATATATGATTATTTGA
4760375 ATAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTATATATGATTATTTGA
Found at i:4763733 original size:18 final size:17
Alignment explanation
Indices: 4763712--4763745 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4763702 AAAATGATAC
4763712 AACTAAAAAAATAAAAAG
1 AACT-AAAAAATAAAAAG
*
4763730 AACTAAATAATAAAAA
1 AACTAAAAAATAAAAA
4763746 TAATTCTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (17 bp):
AACTAAAAAATAAAAAG
Found at i:4763745 original size:26 final size:26
Alignment explanation
Indices: 4763716--4763792 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
4763706 TGATACAACT
* *
4763716 AAAAAAATAAAAAGAACTAAATAATA
1 AAAAAAATAAAAACAAATAAATAATA
* ***
4763742 AAAATAATTCTAACAAATAAATAAT-
1 AAAAAAATAAAAACAAATAAATAATA
*
4763767 AAAAAATTAAGAAACAAAATAAATAA
1 AAAAAAATAA-AAAC-AAATAAATAA
4763793 AAAGTTTATA
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
25 6 0.16
26 22 0.58
27 10 0.26
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (26 bp):
AAAAAAATAAAAACAAATAAATAATA
Found at i:4763810 original size:19 final size:19
Alignment explanation
Indices: 4763786--4763824 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
4763776 AGAAACAAAA
* *
4763786 TAAATAAAAAGTTTATAAT
1 TAAATAAAAACTTTACAAT
4763805 TAAATAAAAACTTTACAAT
1 TAAATAAAAACTTTACAAT
4763824 T
1 T
4763825 TTTGGTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (19 bp):
TAAATAAAAACTTTACAAT
Found at i:4764343 original size:21 final size:21
Alignment explanation
Indices: 4764319--4764379 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
4764309 TGAAATGGTT
4764319 GTGGTGCCATCTGAAACGGCC
1 GTGGTGCCATCTGAAACGGCC
* **
4764340 GTGGTGCCATCTGAAATGGTT
1 GTGGTGCCATCTGAAACGGCC
*
4764361 GTGGTG-CATATGAAACGGC
1 GTGGTGCCATCTGAAACGGC
4764380 TGCGAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (21 bp):
GTGGTGCCATCTGAAACGGCC
Found at i:4767262 original size:15 final size:16
Alignment explanation
Indices: 4767244--4767317 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 16
4767234 AATCCTCTAA
4767244 ATTTTAATTT-CTATT
1 ATTTTAATTTCCTATT
*
4767259 ATTTTACTTTCCTTCCATT
1 ATTTTAATTTCC-T--ATT
*
4767278 -TTTTAATTTTCTA-T
1 ATTTTAATTTCCTATT
4767292 ATTTTAATTTCCT-TT
1 ATTTTAATTTCCTATT
4767307 ATTTTTAATTT
1 A-TTTTAATTT
4767318 ATGTTCTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
14 1 0.02
15 23 0.48
16 10 0.21
17 2 0.04
18 9 0.19
19 3 0.06
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTAATTTCCTATT
Found at i:4767282 original size:33 final size:30
Alignment explanation
Indices: 4767245--4767317 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 30
4767235 ATCCTCTAAA
*
4767245 TTTTAATTTCTATTATTTTACTTTCCTTCCATT
1 TTTTAATTTCTA-TATTTTAATTTCCTT-CA-T
*
4767278 TTTTAATTTTCTATATTTTAATTTCCTTTAT
1 TTTTAA-TTTCTATATTTTAATTTCCTTCAT
4767309 TTTTAATTT
1 TTTTAATTT
4767318 ATGTTCTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.08
31 7 0.19
32 1 0.03
33 20 0.54
34 6 0.16
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTTAATTTCTATATTTTAATTTCCTTCAT
Found at i:4767811 original size:138 final size:135
Alignment explanation
Indices: 4767669--4768048 Score: 403
Period size: 132 Copynumber: 2.8 Consensus size: 135
4767659 TAGAGTCTCA
* * *
4767669 ATTTTAGGATTAATTTCACATTAGTCCTTTAATTTAGTGGAGTTTTTAATTTGATCATTGTTTTT
1 ATTTTAGGATTAATTTCACATTAGTCCTTTAATTTAG-GGAGTTTTTAATTTGGTCCTCGTTTTT
* *
4767734 GCCAGAGGTTCCATTTTGGCTATTCGATTCAATAATTAGTTAAAATTGAGCAGGTTTTAATATTT
65 GCC-GAGGTT-CATTTTGGTTATTCGATTCAATAATTAGTTAAAATTGAGCAGGTTTTAATATTA
* * *
4767799 GACCCTCT
128 CAACCTCC
** * *
4767807 ATTTTAGGATTAATTT--CATTTTTCCATTAATTTA-GGAGGCTTTTT-ATTTGGTCCTCATTTT
1 ATTTTAGGATTAATTTCACATTAGTCCTTTAATTTAGGGA-G-TTTTTAATTTGGTCCTCGTTTT
* *
4767868 TCGCCGATG-T-ATTTTGGTTAATCGATTCAATAATTAGTTAAAATTGAGCAGGTTTTAATATTA
64 T-GCCGAGGTTCATTTTGGTTATTCGATTCAATAATTAGTTAAAATTGAGCAGGTTTTAATATTA
4767931 CAACCTCC
128 CAACCTCC
* * * * * * **
4767939 ATCTTAAGTTTAATTTCACTTTAGTCCTTTTATTTAGGAGAGGTTCGAATTTGGTCCTCGTTTTT
1 ATTTTAGGATTAATTTCACATTAGTCCTTTAATTTAGG-GAGTTTTTAATTTGGTCCTCGTTTTT
** * *
4768004 GCTCGAGGTTCTATTTTAATTATTCGATTTAATAATTTGTTAAAA
65 GC-CGAGGTTC-ATTTTGGTTATTCGATTCAATAATTAGTTAAAA
4768049 ATGATTAGTG
Statistics
Matches: 198, Mismatches: 32, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
132 68 0.34
134 21 0.11
135 39 0.20
136 26 0.13
138 44 0.22
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (135 bp):
ATTTTAGGATTAATTTCACATTAGTCCTTTAATTTAGGGAGTTTTTAATTTGGTCCTCGTTTTTG
CCGAGGTTCATTTTGGTTATTCGATTCAATAATTAGTTAAAATTGAGCAGGTTTTAATATTACAA
CCTCC
Found at i:4769593 original size:17 final size:18
Alignment explanation
Indices: 4769566--4769610 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
4769556 TAAAACTATT
* * *
4769566 GACCATTGACCGTTTATC
1 GACCGTTGACCGTTGACC
4769584 G-CCGTTGACCGTTGACC
1 GACCGTTGACCGTTGACC
4769601 GACCGTTGAC
1 GACCGTTGAC
4769611 TTTGACCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (18 bp):
GACCGTTGACCGTTGACC
Found at i:4772049 original size:24 final size:24
Alignment explanation
Indices: 4772022--4772083 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
4772012 TTCTATTATA
*
4772022 ATACCTGACCTGGATTCTGATCAG
1 ATACTTGACCTGGATTCTGATCAG
* * * *
4772046 ATACTTGACTTAGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCAG
4772070 ATACTTGACCTGGA
1 ATACTTGACCTGGA
4772084 ATATGTTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCAG
Found at i:4776543 original size:24 final size:24
Alignment explanation
Indices: 4776511--4776598 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
4776501 TTCTATTATA
*
4776511 ATACCTGACCTGGATTTTGATTGG
1 ATACTTGACCTGGATTTTGATTGG
* *
4776535 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTTTGATTGG
* *
4776559 ATACTTGACCTAGATTTTGATCT-T
1 ATACTTGACCTGGATTTTGAT-TGG
*
4776583 ATACTTGACATGGATT
1 ATACTTGACCTGGATT
4776599 ATGTTTTGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
ATACTTGACCTGGATTTTGATTGG
Found at i:4780710 original size:24 final size:24
Alignment explanation
Indices: 4780678--4780765 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
4780668 TTCTATTATA
*
4780678 ATACCTGACCTGGATTTTGATTGG
1 ATACTTGACCTGGATTTTGATTGG
* *
4780702 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTTTGATTGG
* *
4780726 ATACTTGACCTAGATTTTGATAT-T
1 ATACTTGACCTGGATTTTGAT-TGG
4780750 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
4780766 ATGTTTTGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
ATACTTGACCTGGATTTTGATTGG
Found at i:4785440 original size:24 final size:24
Alignment explanation
Indices: 4785413--4785495 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
4785403 ATTATAATCC
4785413 TGACCTGGATTTTGATTGGATACT
1 TGACCTGGATTTTGATTGGATACT
*
4785437 TGACCTGGATTCTT-ATCGGATACT
1 TGACCTGGATT-TTGATTGGATACT
* *
4785461 TGACCTAGATTTTGATCT-TATACT
1 TGACCTGGATTTTGAT-TGGATACT
4785485 TGACCTGGATT
1 TGACCTGGATT
4785496 ATGTTTTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
23 2 0.04
24 47 0.92
25 2 0.04
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TGACCTGGATTTTGATTGGATACT
Found at i:4790169 original size:24 final size:23
Alignment explanation
Indices: 4790132--4790219 Score: 77
Period size: 24 Copynumber: 3.7 Consensus size: 23
4790122 TTCTATTATA
* * *
4790132 ATACCTGACATGGACTTTGATTGG
1 ATACTTGACCTGGA-TTTGATCGG
*
4790156 ATACTTTACCTGGATTCTGATCGG
1 ATACTTGACCTGGATT-TGATCGG
* **
4790180 ATACTTGACCTAGATTTTGATCTT
1 ATACTTGACCTGGA-TTTGATCGG
*
4790204 ATACTTGACTTGGATT
1 ATACTTGACCTGGATT
4790220 ATGTTTTGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
23 4 0.08
24 46 0.88
25 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (23 bp):
ATACTTGACCTGGATTTGATCGG
Found at i:4794868 original size:24 final size:24
Alignment explanation
Indices: 4794841--4794928 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 24
4794831 TTCTATTATA
* *
4794841 ATACCTGACCTGGATTCTGATTGG
1 ATACTTGACCTGGATTCTGATCGG
*
4794865 ATACTTGACCTGGAGTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* * **
4794889 ATACTTGACCTAGATTTTGATCTA
1 ATACTTGACCTGGATTCTGATCGG
*
4794913 ATACTTGACCTAGATT
1 ATACTTGACCTGGATT
4794929 ATGTTTTGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:4799670 original size:23 final size:22
Alignment explanation
Indices: 4799602--4799681 Score: 108
Period size: 23 Copynumber: 3.6 Consensus size: 22
4799592 ACATATAACA
4799602 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
* * *
4799624 GTGCATAGATACA-CCATGAAT
1 GTGCATCGATGCATCCTTGAAT
*
4799645 GTGCACCGATGCATGCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
4799668 GTGCATCGATGCAT
1 GTGCATCGATGCAT
4799682 AAGGCCATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 17 0.35
22 11 0.23
23 20 0.42
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:4799698 original size:43 final size:42
Alignment explanation
Indices: 4799601--4799703 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 42
4799591 TACATATAAC
* *
4799601 AGTGCATCGATGCATCCTTGAATGTGCATAGATACACCATGA
1 AGTGCATCGATGCATCCTTGAATGTGCATAGATACACAAGGA
* * * * *
4799643 ATGTGCACCGATGCATGCCTTGAATGTGCATCGATGCATAAGGCC
1 A-GTGCATCGATGCAT-CCTTGAATGTGCATAGATACACAAGG-A
4799688 A-TGCATCGATGCATCC
1 AGTGCATCGATGCATCC
4799704 ATCGGGTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
42 3 0.06
43 25 0.50
44 21 0.42
45 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.25
Consensus pattern (42 bp):
AGTGCATCGATGCATCCTTGAATGTGCATAGATACACAAGGA
Done.