Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 18 of 132
Found at i:5223837 original size:17 final size:19
Alignment explanation
Indices: 5223798--5223837 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5223788 AATTATTCAA
*
5223798 AAAACAGAAAATTTTTGTG
1 AAAACAGAAAATTTATGTG
5223817 AAAA-AGAAAATTTAT-TG
1 AAAACAGAAAATTTATGTG
5223834 AAAA
1 AAAA
5223838 GACAACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 10 0.50
19 4 0.20
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (19 bp):
AAAACAGAAAATTTATGTG
Found at i:5225053 original size:43 final size:44
Alignment explanation
Indices: 5224971--5225074 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 44
5224961 TAAAAGATAG
5224971 AGAAAGTTACATGAAAAAAACCACATTCAAGAAACGACAAAGAA
1 AGAAAGTTACATGAAAAAAACCACATTCAAGAAACGACAAAGAA
* * * * * *
5225015 AGAAA-TTACGTGTAAAAAATCACTTTCATGAAATGACAAAG-A
1 AGAAAGTTACATGAAAAAAACCACATTCAAGAAACGACAAAGAA
* * *
5225057 CGAAAGCTACGTGAAAAA
1 AGAAAGTTACATGAAAAA
5225075 TATCCACTAC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
42 5 0.10
43 40 0.80
44 5 0.10
ACGTcount: A:0.54, C:0.14, G:0.15, T:0.16
Consensus pattern (44 bp):
AGAAAGTTACATGAAAAAAACCACATTCAAGAAACGACAAAGAA
Found at i:5225507 original size:20 final size:20
Alignment explanation
Indices: 5225484--5225554 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
5225474 CTTATAAAAT
*
5225484 TTTATCAATATATTTAACG-A
1 TTTATCAAAATATTTAA-GTA
* * *
5225504 TTTATTAACATTTTTAAGTA
1 TTTATCAAAATATTTAAGTA
5225524 TTTATCAAAATATTTAATGGT-
1 TTTATCAAAATATTTAA--GTA
5225545 TTTATCAAAA
1 TTTATCAAAA
5225555 ATATATCTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 1 0.02
20 29 0.69
21 10 0.24
22 2 0.05
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTATCAAAATATTTAAGTA
Found at i:5225707 original size:18 final size:18
Alignment explanation
Indices: 5225684--5225723 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
5225674 TTTATGAGAC
5225684 TTTACCA-ATTTCTAATAT
1 TTTACCAGATTTCTAA-AT
5225702 TTTACCAGTATTTCTAAAT
1 TTTACCAG-ATTTCTAAAT
5225721 TTT
1 TTT
5225724 CTAAACCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 8 0.40
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTACCAGATTTCTAAAT
Found at i:5227133 original size:43 final size:43
Alignment explanation
Indices: 5227069--5227176 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 43
5227059 CCTAAAAGAT
*
5227069 AAAAA-AAAGTTACATGAAAAAAGCCACATTCAAAAAATGACA
1 AAAAAGAAAGTTACATGTAAAAAGCCACATTCAAAAAATGACA
* * **
5227111 AAAAAGAAAGTTACATGTAAAAAACCACTTTCATGAAATGACA
1 AAAAAGAAAGTTACATGTAAAAAGCCACATTCAAAAAATGACA
* * *
5227154 AAGATGAAAGCT--ATGTAAAAAGC
1 AAAAAGAAAGTTACATGTAAAAAGC
5227177 ATCAACTACT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
41 10 0.18
42 5 0.09
43 41 0.73
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.18
Consensus pattern (43 bp):
AAAAAGAAAGTTACATGTAAAAAGCCACATTCAAAAAATGACA
Found at i:5246254 original size:20 final size:20
Alignment explanation
Indices: 5246231--5246287 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
5246221 TTTATATTAT
5246231 TTTATCAATATATTTAA-CGA
1 TTTATCAATATATTTAAGC-A
* * *
5246251 TTTATTAAAATTTTTAAGCA
1 TTTATCAATATATTTAAGCA
5246271 TTTATCAATATATTTAA
1 TTTATCAATATATTTAA
5246288 TGGCCTTATC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTATCAATATATTTAAGCA
Found at i:5249344 original size:20 final size:19
Alignment explanation
Indices: 5249306--5249348 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5249296 CTTCAGAATT
* *
5249306 TTTTTTTAAAATTTTTATAA
1 TTTTTTTAAAATGTATAT-A
5249326 TTTTTTTAAAATGTATATA
1 TTTTTTTAAAATGTATATA
5249345 TTTT
1 TTTT
5249349 GGAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTTTTAAAATGTATATA
Found at i:5254938 original size:21 final size:21
Alignment explanation
Indices: 5254896--5254939 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5254886 TGATTTACCC
* *
5254896 TTTTGAAAAGAGTAAATCATT
1 TTTTGAAAAAACTAAATCATT
* *
5254917 TTTTGAAAAAACTAGATGATT
1 TTTTGAAAAAACTAAATCATT
5254938 TT
1 TT
5254940 ATTTTTATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
TTTTGAAAAAACTAAATCATT
Found at i:5255166 original size:19 final size:19
Alignment explanation
Indices: 5255144--5255182 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5255134 ATATTTCAGT
*
5255144 TTTATTTTAATAATAAATA
1 TTTATTATAATAATAAATA
*
5255163 TTTATTATAATTATAAATA
1 TTTATTATAATAATAAATA
5255182 T
1 T
5255183 ATTAATAATA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATTATAATAATAAATA
Found at i:5259224 original size:15 final size:16
Alignment explanation
Indices: 5259191--5259224 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5259181 ATATCACAAG
5259191 ATATTTCATATTCTAA
1 ATATTTCATATTCTAA
*
5259207 ATATTTCA-ATTGTAA
1 ATATTTCATATTCTAA
5259222 ATA
1 ATA
5259225 CTAACTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (16 bp):
ATATTTCATATTCTAA
Found at i:5262013 original size:22 final size:22
Alignment explanation
Indices: 5261988--5262034 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
5261978 TTTAAAATTC
5261988 AAATCTGATT-GT-TGACATTGTT
1 AAAT-TGATTGGTGTGACATT-TT
*
5262010 AAATTTATTGGTGTGACATTTT
1 AAATTGATTGGTGTGACATTTT
5262032 AAA
1 AAA
5262035 ATAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.18
22 11 0.50
23 7 0.32
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (22 bp):
AAATTGATTGGTGTGACATTTT
Found at i:5268442 original size:21 final size:21
Alignment explanation
Indices: 5268418--5268457 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5268408 CAATATACCA
5268418 AATACTT-ACTCATTTTATATT
1 AATACTTAACT-ATTTTATATT
*
5268439 AATATTTAACTATTTTATA
1 AATACTTAACTATTTTATA
5268458 ATTATTTTTT
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:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
AATACTTAACTATTTTATATT
Found at i:5268888 original size:11 final size:11
Alignment explanation
Indices: 5268869--5268912 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
5268859 CGTTGATCAG
5268869 TTAAAAATTTAT
1 TTAAAAA-TTAT
5268881 TT-AAAATTAT
1 TTAAAAATTAT
**
5268891 AAAAAAATTAT
1 TTAAAAATTAT
5268902 TTAAAAATTAT
1 TTAAAAATTAT
5268913 AAAACTTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 4 0.15
11 21 0.78
12 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAAAAATTAT
Found at i:5268901 original size:21 final size:22
Alignment explanation
Indices: 5268871--5268916 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5268861 TTGATCAGTT
*
5268871 AAAAATTTATTT-AAAATTATA
1 AAAAAATTATTTAAAAATTATA
5268892 AAAAAATTATTTAAAAATTATA
1 AAAAAATTATTTAAAAATTATA
5268914 AAA
1 AAA
5268917 CTTGCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAAATTATTTAAAAATTATA
Found at i:5268966 original size:9 final size:9
Alignment explanation
Indices: 5268922--5268993 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
5268912 TAAAACTTGC
*
5268922 AAAAATTAT
1 AAAAAATAT
5268931 AAATAAATTAT
1 AAA-AAA-TAT
* *
5268942 AAAATATTT
1 AAAAAATAT
*
5268951 TAAAAATAT
1 AAAAAATAT
5268960 AAAAAATAT
1 AAAAAATAT
*
5268969 AAAAACTATT
1 AAAAAATA-T
*
5268979 TAAAAATATT
1 AAAAAATA-T
5268989 AAAAA
1 AAAAA
5268994 GTTGTAAAAG
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
9 26 0.53
10 17 0.35
11 6 0.12
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAAATAT
Found at i:5269001 original size:19 final size:19
Alignment explanation
Indices: 5268961--5269002 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5268951 TAAAAATATA
*
5268961 AAAAATATAAAAACTATTT
1 AAAAATATAAAAACTATGT
*
5268980 AAAAATATTAAAAAGT-TGT
1 AAAAATA-TAAAAACTATGT
5268999 AAAA
1 AAAA
5269003 GTTCTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAAATATAAAAACTATGT
Found at i:5269295 original size:19 final size:21
Alignment explanation
Indices: 5269267--5269305 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5269257 TATATTTGAA
*
5269267 TTCAATGTTT-GTTT-TTTAG
1 TTCAAAGTTTAGTTTATTTAG
5269286 TTCAAAGTTTAGTTTATTTA
1 TTCAAAGTTTAGTTTATTTA
5269306 CCAAAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.23, C:0.05, G:0.13, T:0.59
Consensus pattern (21 bp):
TTCAAAGTTTAGTTTATTTAG
Found at i:5269510 original size:21 final size:21
Alignment explanation
Indices: 5269485--5269555 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
5269475 ATTTCTTAAT
5269485 AATTTTTATAGAATTTTAAAC
1 AATTTTTATAGAATTTTAAAC
*
5269506 AATTTTTTTAGGAAATTTT--AC
1 AATTTTTATA-G-AATTTTAAAC
* * *
5269527 AACTTTTTA-ATATTTTTAAAT
1 AA-TTTTTATAGAATTTTAAAC
5269548 AATTTTTA
1 AATTTTTA
5269556 CATGTTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
19 5 0.12
20 6 0.15
21 17 0.43
22 6 0.15
23 6 0.15
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (21 bp):
AATTTTTATAGAATTTTAAAC
Found at i:5269563 original size:21 final size:19
Alignment explanation
Indices: 5269530--5269576 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
5269520 ATTTTACAAC
5269530 TTTTTAATATTTTTAAATAA
1 TTTTTAATATTTTTAAAT-A
* *
5269550 TTTTTACATGTTTTTATATA
1 TTTTTA-ATATTTTTAAATA
5269570 TTTTTAA
1 TTTTTAA
5269577 ATAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 13 0.54
21 10 0.42
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTAATATTTTTAAATA
Found at i:5269671 original size:20 final size:20
Alignment explanation
Indices: 5269646--5269698 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
5269636 TTTTTTTATT
5269646 GATCAACATGTCACATCATC
1 GATCAACATGTCACATCATC
* *
5269666 GATCAACACGTCACATCATT
1 GATCAACATGTCACATCATC
*
5269686 GATCAACCTGTCA
1 GATCAACATGTCA
5269699 TGCCATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (20 bp):
GATCAACATGTCACATCATC
Found at i:5270030 original size:2 final size:2
Alignment explanation
Indices: 5269990--5270014 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5269980 ATCAATAGGT
5269990 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
5270015 GTGTGTATCG
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:5271647 original size:21 final size:19
Alignment explanation
Indices: 5271623--5271664 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
5271613 TCGAATTCCA
5271623 TTCTTCATTTGAATGTATATT
1 TTCTTCA-TT-AATGTATATT
*
5271644 TTCTTGATTAATGTATATT
1 TTCTTCATTAATGTATATT
5271663 TT
1 TT
5271665 TCATGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.60
Consensus pattern (19 bp):
TTCTTCATTAATGTATATT
Found at i:5281314 original size:28 final size:28
Alignment explanation
Indices: 5281270--5281323 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
5281260 ACCAAACCAC
* *
5281270 ACAAGTTCTCCAGCAAATATAGATCAAT
1 ACAAGTTATCCAACAAATATAGATCAAT
5281298 ACAAGTTATCCAACAAATATAGATCA
1 ACAAGTTATCCAACAAATATAGATCA
5281324 GCATTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.24
Consensus pattern (28 bp):
ACAAGTTATCCAACAAATATAGATCAAT
Found at i:5283274 original size:32 final size:32
Alignment explanation
Indices: 5283214--5283276 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
5283204 ATTAATAGGT
*
5283214 ATGAATTATCAAATTAAATTAATTAATTTATC
1 ATGAATTATCAAATTAAATTAATAAATTTATC
* *
5283246 ATGAGTTATTAAATTCAAA-TAATAAATTTAT
1 ATGAATTATCAAATT-AAATTAATAAATTTAT
5283277 AATTTTACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (32 bp):
ATGAATTATCAAATTAAATTAATAAATTTATC
Found at i:5284702 original size:18 final size:18
Alignment explanation
Indices: 5284681--5284740 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
5284671 TGTATTGAAT
5284681 AAATATTATAATAAGTAA
1 AAATATTATAATAAGTAA
* *
5284699 AAATATGTAGTGCATTAA-TAT
1 AAATAT-TA-T--AATAAGTAA
*
5284720 AAACATTATAATAAGTAA
1 AAATATTATAATAAGTAA
5284738 AAA
1 AAA
5284741 AAGGTTGAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
17 4 0.12
18 11 0.34
19 3 0.09
20 3 0.09
21 7 0.22
22 4 0.12
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (18 bp):
AAATATTATAATAAGTAA
Found at i:5284928 original size:42 final size:42
Alignment explanation
Indices: 5284862--5284944 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
5284852 CCAAGGTGTA
* * *
5284862 AATTTCTAGTTTTGGCCTGTCAAATTTGATAGATAATAATTT
1 AATTTCTAGCTTTGGCCAGACAAATTTGATAGATAATAATTT
*
5284904 AATTTCTAGCTTTGGCCAGACAAATTTGGTAGATAATAATT
1 AATTTCTAGCTTTGGCCAGACAAATTTGATAGATAATAATT
5284945 GGGATAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (42 bp):
AATTTCTAGCTTTGGCCAGACAAATTTGATAGATAATAATTT
Found at i:5285024 original size:29 final size:30
Alignment explanation
Indices: 5284962--5285041 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
5284952 ATACCAAAAC
* * *
5284962 TATACATGAACTATGGTTTAATGTGTAATTG
1 TATACATGAACTTTGATTT-ATGTGCAATTG
5284993 TATACATGAACTTTGATTT-TGTGCAATTG
1 TATACATGAACTTTGATTTATGTGCAATTG
*
5285022 TATACATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
5285042 GATTCAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 17 0.39
30 10 0.23
31 17 0.39
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.45
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTG
Found at i:5285297 original size:29 final size:27
Alignment explanation
Indices: 5285231--5285297 Score: 62
Period size: 31 Copynumber: 2.3 Consensus size: 27
5285221 GAGTTTCACG
* *
5285231 TGTATAATTGCACCAAATTAAAATTCA
1 TGTATAATTGCACCAAATCAAAATTAA
* *
5285258 TGTATACAATTGCACATTAAATCAAAGTTAA
1 TGTAT--AATTGCAC--CAAATCAAAATTAA
5285289 TGTATAATT
1 TGTATAATT
5285298 TTAAGATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.16
29 12 0.38
31 15 0.47
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAATTAA
Found at i:5285388 original size:26 final size:27
Alignment explanation
Indices: 5285359--5285423 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
5285349 GATAGATCAT
5285359 AATTTAAATTAAATT-AGAATAATT-AG
1 AATTTAAATTAAATTAAG-ATAATTAAG
* * * *
5285385 AATTTTAATTTATTTAAGATAATTAAT
1 AATTTAAATTAAATTAAGATAATTAAG
5285412 AATTTAAATTAA
1 AATTTAAATTAA
5285424 TATGTTAGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.45
Consensus pattern (27 bp):
AATTTAAATTAAATTAAGATAATTAAG
Found at i:5285515 original size:26 final size:24
Alignment explanation
Indices: 5285463--5285518 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 24
5285453 TACATATTAA
*
5285463 TTATTTATTTTGTATTTTTTAAAT
1 TTATTTATTTTGTATATTTTAAAT
*
5285487 TTATTTATGTTATGTGTATTTTAAAT
1 TTATTTAT-TT-TGTATATTTTAAAT
5285513 TTATTT
1 TTATTT
5285519 TGTAAGTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 8 0.29
25 2 0.07
26 18 0.64
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (24 bp):
TTATTTATTTTGTATATTTTAAAT
Found at i:5285603 original size:17 final size:17
Alignment explanation
Indices: 5285581--5285636 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
5285571 AAGTTTTTAA
*
5285581 TAAAATGAAAAAATATT
1 TAAAATTAAAAAATATT
***
5285598 TAAAATTTTGAAATA-T
1 TAAAATTAAAAAATATT
5285614 TAAAATTAAAATAATATT
1 TAAAATTAAAA-AATATT
5285632 TAAAA
1 TAAAA
5285637 AATTCAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 9 0.30
17 15 0.50
18 6 0.20
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (17 bp):
TAAAATTAAAAAATATT
Found at i:5296442 original size:4 final size:4
Alignment explanation
Indices: 5296433--5296457 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5296423 CGCCCTAAGG
5296433 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
5296458 TGTATATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:5302396 original size:9 final size:9
Alignment explanation
Indices: 5302382--5302428 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
5302372 ATTATTAAAT
5302382 AAAATTATA
1 AAAATTATA
*
5302391 AAAATTATT
1 AAAATTATA
5302400 AAAA--ATA
1 AAAATTATA
*
5302407 AAAATTATT
1 AAAATTATA
5302416 AAAATTATA
1 AAAATTATA
5302425 AAAA
1 AAAA
5302429 AATATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 6 0.19
9 26 0.81
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:5302409 original size:16 final size:16
Alignment explanation
Indices: 5302388--5302419 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5302378 AAATAAAATT
5302388 ATAAAAATTATTAAAA
1 ATAAAAATTATTAAAA
5302404 ATAAAAATTATTAAAA
1 ATAAAAATTATTAAAA
5302420 TTATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAAATTATTAAAA
Found at i:5302410 original size:25 final size:24
Alignment explanation
Indices: 5302371--5302429 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
5302361 GTTAGTAATT
5302371 AATTATT--AAATAAAATTATAAA
1 AATTATTAAAAATAAAATTATAAA
*
5302393 AATTATTAAAAATAAAAATTATTAA
1 AATTATTAAAAAT-AAAATTATAAA
*
5302418 AATTATAAAAAA
1 AATTATTAAAAA
5302430 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 7 0.22
24 4 0.12
25 21 0.66
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTATTAAAAATAAAATTATAAA
Found at i:5302875 original size:22 final size:20
Alignment explanation
Indices: 5302836--5302883 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
5302826 TTAAATTTTA
* *
5302836 AAAAATCAAAATAATA-TAT
1 AAAAATTAAAAAAATATTAT
5302855 AAAAATTAAAAAAATATTAT
1 AAAAATTAAAAAAATATTAT
5302875 AAAAATTAA
1 AAAAATTAA
5302884 TATATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAATTAAAAAAATATTAT
Found at i:5302992 original size:2 final size:2
Alignment explanation
Indices: 5302985--5303032 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
5302975 TAAATTCTTT
5302985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5303027 T- TA TA T
1 TA TA TA T
5303033 TTACAATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5303063 original size:12 final size:13
Alignment explanation
Indices: 5302985--5303063 Score: 69
Period size: 12 Copynumber: 6.2 Consensus size: 13
5302975 TAAATTCTTT
5302985 TATATATATAT-A
1 TATATATATATAA
5302997 TATATATATATATA
1 TATATATATATA-A
5303011 TATATATATATATA
1 TATATATATATA-A
* *
5303025 TATTATATTTACAA
1 TA-TATATATATAA
*
5303039 T-TTTA-AT-TAA
1 TATATATATATAA
5303049 TATA-ATATATAA
1 TATATATATATAA
5303061 TAT
1 TAT
5303064 TAAAAAAACA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
10 4 0.07
11 4 0.07
12 20 0.36
14 19 0.35
15 8 0.15
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATATATATAA
Found at i:5304886 original size:6 final size:6
Alignment explanation
Indices: 5304856--5304939 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
5304846 TAATTTTGCC
* * *
5304856 TAAATTT TAATTT TAAA-- TAAGTT TAAATT T-ATTT TAAATT TAAATT
1 TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* ** * *
5304902 CATTTTT TGAATT TAAATT T-ACTT TAAATT TAAATT TA
1 TA-AATT TAAATT TAAATT TAAATT TAAATT TAAATT TA
5304940 TTTTTAATTA
Statistics
Matches: 56, Mismatches: 16, Indels: 11
0.67 0.19 0.13
Matches are distributed among these distances:
4 3 0.05
5 8 0.14
6 40 0.71
7 5 0.09
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TAAATT
Found at i:5304897 original size:17 final size:17
Alignment explanation
Indices: 5304877--5304953 Score: 91
Period size: 17 Copynumber: 4.4 Consensus size: 17
5304867 TTTAAATAAG
5304877 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
5304894 TTTAAATTCATTTTTTGAA
1 TTTAAATT--TATTTTAAA
*
5304913 TTTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
*
5304930 TTTAAATTTATTTTTAA
1 TTTAAATTTATTTTAAA
*
5304947 TTAAAAT
1 TTTAAAT
5304954 AAAATTAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
17 35 0.70
19 15 0.30
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:5308649 original size:30 final size:30
Alignment explanation
Indices: 5308615--5308671 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5308605 TTCATAATGT
*
5308615 ATTAAA-TCAAAATTTTATCATTTTTAAAAA
1 ATTAAAGTCAAAA-TTTATCATTATTAAAAA
*
5308645 ATTAAAGTGAAAATTTATCATTATTAA
1 ATTAAAGTCAAAATTTATCATTATTAA
5308672 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (30 bp):
ATTAAAGTCAAAATTTATCATTATTAAAAA
Found at i:5309740 original size:31 final size:30
Alignment explanation
Indices: 5309702--5309784 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
5309692 CCATTTGTCC
* *
5309702 AGGACTAAATATTCAA-AATTTGAAAAGTACA
1 AGGACTAAA-ATT-AACAAATTGAAAACTACA
5309733 AGGACTAAAATTAACCAAATTGAAAACTACA
1 AGGACTAAAATTAA-CAAATTGAAAACTACA
* *
5309764 AAGACTAAAATTGATCAAATT
1 AGGACTAAAATT-AACAAATT
5309785 AAAGTATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 2 0.04
30 3 0.07
31 39 0.87
32 1 0.02
ACGTcount: A:0.53, C:0.12, G:0.11, T:0.24
Consensus pattern (30 bp):
AGGACTAAAATTAACAAATTGAAAACTACA
Found at i:5314524 original size:23 final size:23
Alignment explanation
Indices: 5314469--5314525 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 23
5314459 ATTTTATCAA
5314469 ATTTGTTGAATT-TTTTTTTGAAT
1 ATTTG-TGAATTATTTTTTTGAAT
*
5314492 ATTT-T-CATTATTTTTTTGAACT
1 ATTTGTGAATTATTTTTTTGAA-T
5314514 -TTTGTGAATTAT
1 ATTTGTGAATTAT
5314526 AACTAGACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 3 0.11
21 14 0.50
22 2 0.07
23 9 0.32
ACGTcount: A:0.23, C:0.04, G:0.11, T:0.63
Consensus pattern (23 bp):
ATTTGTGAATTATTTTTTTGAAT
Found at i:5318810 original size:16 final size:16
Alignment explanation
Indices: 5318789--5318819 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5318779 CATGATCGAC
5318789 ACATCTATTGCTTATA
1 ACATCTATTGCTTATA
5318805 ACATCTATTGCTTAT
1 ACATCTATTGCTTAT
5318820 TCAATTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (16 bp):
ACATCTATTGCTTATA
Found at i:5319433 original size:21 final size:21
Alignment explanation
Indices: 5319407--5319449 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5319397 AGAAACAATA
**
5319407 TAATGATTTTTCCTTTTAACT
1 TAATGATTTTGACTTTTAACT
5319428 TAATGATTTTGACTTTTAACT
1 TAATGATTTTGACTTTTAACT
5319449 T
1 T
5319450 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.56
Consensus pattern (21 bp):
TAATGATTTTGACTTTTAACT
Found at i:5329731 original size:89 final size:89
Alignment explanation
Indices: 5329631--5329806 Score: 343
Period size: 89 Copynumber: 2.0 Consensus size: 89
5329621 ACTAACAGTG
5329631 TAATATACCCATTTAAGTATTATTATTTAAGATTTTTGAACTATTTCTAAGTTAACATTTTGGTT
1 TAATATACCCATTTAAGTATTATTATTTAAGATTTTTGAACTATTTCTAAGTTAACATTTTGGTT
5329696 ACTCAACTTCAAAAGGTTACAATA
66 ACTCAACTTCAAAAGGTTACAATA
*
5329720 TAATATACCCATTTAAGTATTATTATTTAAGATTTTTGAACTATTTCTAAGTTTACATTTTGGTT
1 TAATATACCCATTTAAGTATTATTATTTAAGATTTTTGAACTATTTCTAAGTTAACATTTTGGTT
5329785 ACTCAACTTCAAAAGGTTACAA
66 ACTCAACTTCAAAAGGTTACAA
5329807 AATGGTCATT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (89 bp):
TAATATACCCATTTAAGTATTATTATTTAAGATTTTTGAACTATTTCTAAGTTAACATTTTGGTT
ACTCAACTTCAAAAGGTTACAATA
Found at i:5329851 original size:60 final size:60
Alignment explanation
Indices: 5329771--5329899 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 60
5329761 TATTTCTAAG
* ** * * *
5329771 TTTACATTTTGGTTACTCAACTTCAAAAGGTTACAAAATGGTCATTAAACTATTTGAAAA
1 TTTACATTTTGGTCACTCAACTTCAAAAACTTACAAAATGATCACTAAACTATTCGAAAA
*
5329831 TTTACAATTTT-GTCACTCAACTTCAAAAACTTACAAAATGATCACTGAACTATTCGAAAA
1 TTTAC-ATTTTGGTCACTCAACTTCAAAAACTTACAAAATGATCACTAAACTATTCGAAAA
*
5329891 TTTTCATTT
1 TTTACATTT
5329900 AAGTCATTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 4 0.07
60 51 0.85
61 5 0.08
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (60 bp):
TTTACATTTTGGTCACTCAACTTCAAAAACTTACAAAATGATCACTAAACTATTCGAAAA
Found at i:5330498 original size:22 final size:22
Alignment explanation
Indices: 5330470--5330517 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5330460 CGATTTAAGG
5330470 AAAAATAAAAGAAAACAAAATT
1 AAAAATAAAAGAAAACAAAATT
* * *
5330492 AAAAATAAAAGTAAATAGAATT
1 AAAAATAAAAGAAAACAAAATT
5330514 AAAA
1 AAAA
5330518 GAAATAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAAAATT
Found at i:5330524 original size:15 final size:16
Alignment explanation
Indices: 5330497--5330526 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5330487 AAATTAAAAA
5330497 TAAAAGTAAATAGAAT
1 TAAAAGTAAATAGAAT
5330513 TAAAAG-AAATAGAA
1 TAAAAGTAAATAGAA
5330527 AATAAGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (16 bp):
TAAAAGTAAATAGAAT
Found at i:5331366 original size:19 final size:19
Alignment explanation
Indices: 5331342--5331384 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5331332 AAACATAAAT
5331342 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
5331361 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
5331380 TAAAT
1 TAAAT
5331385 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:5331625 original size:23 final size:24
Alignment explanation
Indices: 5331591--5331635 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
5331581 AGGATCATAC
5331591 TCTAAAAATATAT-ATATTTAATA
1 TCTAAAAATATATCATATTTAATA
*
5331614 TCTAAAATTATATCATATTTAA
1 TCTAAAAATATATCATATTTAA
5331636 GCATTATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (24 bp):
TCTAAAAATATATCATATTTAATA
Found at i:5334469 original size:29 final size:29
Alignment explanation
Indices: 5334384--5334469 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
5334374 ATCTGTCATA
* * *
5334384 AGTCCTTTTACTTTTCATAAATTTAAAATTT
1 AGTCCCTTTATTTTTCAT--ATTTCAAATTT
*
5334415 AGTCCCTATATTTTT-AT-TTTGACAAATTT
1 AGTCCCTTTATTTTTCATATTT--CAAATTT
5334444 AGTCCCTTTATTTTTCATATTTCAAA
1 AGTCCCTTTATTTTTCATATTTCAAA
5334470 ATTCAGGTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
27 3 0.07
29 24 0.52
30 4 0.09
31 15 0.33
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (29 bp):
AGTCCCTTTATTTTTCATATTTCAAATTT
Found at i:5338099 original size:3 final size:3
Alignment explanation
Indices: 5338093--5338117 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5338083 ATCATCGTCG
5338093 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
5338118 TGTGGTGGTC
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:5342385 original size:24 final size:24
Alignment explanation
Indices: 5342356--5342403 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5342346 TAAATTTGTG
5342356 TGTTCAATTTCTTAATTTCTTCCA
1 TGTTCAATTTCTTAATTTCTTCCA
5342380 TGTTCAATTTCTTAATTTCTTCCA
1 TGTTCAATTTCTTAATTTCTTCCA
5342404 CTATTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.54
Consensus pattern (24 bp):
TGTTCAATTTCTTAATTTCTTCCA
Found at i:5342834 original size:14 final size:14
Alignment explanation
Indices: 5342815--5342841 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5342805 TATTACGAAT
5342815 CCAATAAGTAATTC
1 CCAATAAGTAATTC
5342829 CCAATAAGTAATT
1 CCAATAAGTAATT
5342842 TCAATGATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (14 bp):
CCAATAAGTAATTC
Found at i:5344426 original size:19 final size:20
Alignment explanation
Indices: 5344389--5344426 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5344379 ATCTAACGTG
* *
5344389 GATCATATTTTAAATATATT
1 GATCATATTATAAAAATATT
5344409 GATCA-ATTATAAAAATAT
1 GATCATATTATAAAAATAT
5344427 GTATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
GATCATATTATAAAAATATT
Found at i:5344789 original size:15 final size:17
Alignment explanation
Indices: 5344768--5344807 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
5344758 TAATCCTTCA
5344768 AAAATTATGAAAAT-AT
1 AAAATTATGAAAATAAT
*
5344784 -AAATTATTAAAATAAT
1 AAAATTATGAAAATAAT
5344800 AAAATTAT
1 AAAATTAT
5344808 ATTTTTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAAATTATGAAAATAAT
Found at i:5350393 original size:58 final size:59
Alignment explanation
Indices: 5350321--5350441 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 59
5350311 TTAATATAAT
5350321 ATTTGGTATCTGAACTTGACATTTTTT-CTTAATTTGATATCTAAAC-TTTTTAGACTCA
1 ATTTGGTATCTGAACTTGACATTTTTTAC-TAATTTGATATCTAAACTTTTTTAGACTCA
** * * *
5350379 ATTTGGTA-CTTGAACTTGGTATTTTTTACTAATTTGGTATTTAAACTTTTTTAGATTCA
1 ATTTGGTATC-TGAACTTGACATTTTTTACTAATTTGATATCTAAACTTTTTTAGACTCA
5350438 ATTT
1 ATTT
5350442 ATTAAATATT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
57 1 0.02
58 38 0.69
59 16 0.29
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.51
Consensus pattern (59 bp):
ATTTGGTATCTGAACTTGACATTTTTTACTAATTTGATATCTAAACTTTTTTAGACTCA
Found at i:5351763 original size:12 final size:12
Alignment explanation
Indices: 5351760--5351810 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
5351750 AAATAACAGC
*
5351760 AAAACAAAAACA
1 AAAACAACAACA
*
5351772 AAAACATCAACA
1 AAAACAACAACA
* *
5351784 AAAATAACAGCA
1 AAAACAACAACA
*
5351796 AAAACAACACCA
1 AAAACAACAACA
5351808 AAA
1 AAA
5351811 CAGTAAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.73, C:0.22, G:0.02, T:0.04
Consensus pattern (12 bp):
AAAACAACAACA
Found at i:5351787 original size:24 final size:24
Alignment explanation
Indices: 5351760--5351842 Score: 57
Period size: 24 Copynumber: 3.5 Consensus size: 24
5351750 AAATAACAGC
*
5351760 AAAACAAAAACAAAAACATCAACA
1 AAAACAAAAACAAAAACAACAACA
* * * *
5351784 AAAATAACAGCAAAAACAAC-ACC
1 AAAACAAAAACAAAAACAACAACA
*
5351807 AAAACAGTAAAA-AAAACCAA-AACA
1 AAAACA--AAAACAAAAACAACAACA
*
5351831 ATAA-AAAAACAA
1 AAAACAAAAACAA
5351843 CACCAAAATA
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
21 4 0.09
22 2 0.05
23 8 0.18
24 28 0.64
25 2 0.05
ACGTcount: A:0.73, C:0.19, G:0.02, T:0.05
Consensus pattern (24 bp):
AAAACAAAAACAAAAACAACAACA
Found at i:5351818 original size:20 final size:20
Alignment explanation
Indices: 5351789--5351850 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
5351779 CAACAAAAAT
*
5351789 AACAGCAAAAACAACACCAA
1 AACAGTAAAAACAACACCAA
5351809 AACAGTAAAAA-AA-ACCAA
1 AACAGTAAAAACAACACCAA
*
5351827 AACAATAAAAAAACAACACCAA
1 AACAGT--AAAAACAACACCAA
5351849 AA
1 AA
5351851 TAACAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 10 0.28
19 2 0.06
20 15 0.42
21 2 0.06
22 7 0.19
ACGTcount: A:0.71, C:0.23, G:0.03, T:0.03
Consensus pattern (20 bp):
AACAGTAAAAACAACACCAA
Found at i:5351827 original size:18 final size:19
Alignment explanation
Indices: 5351789--5351841 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
5351779 CAACAAAAAT
*
5351789 AACAGCAAAAACAACACCAA
1 AACAGTAAAAA-AACACCAA
5351809 AACAGTAAAAAAA-ACCAA
1 AACAGTAAAAAAACACCAA
*
5351827 AACAATAAAAAAACA
1 AACAGTAAAAAAACA
5351842 ACACCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 17 0.57
19 3 0.10
20 10 0.33
ACGTcount: A:0.72, C:0.21, G:0.04, T:0.04
Consensus pattern (19 bp):
AACAGTAAAAAAACACCAA
Found at i:5361046 original size:15 final size:16
Alignment explanation
Indices: 5361019--5361049 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5361009 AATTCAATTA
5361019 TTACTTATTTATATTT
1 TTACTTATTTATATTT
5361035 TTACTT-TTTATATTT
1 TTACTTATTTATATTT
5361050 AAAGTGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TTACTTATTTATATTT
Found at i:5365185 original size:2 final size:2
Alignment explanation
Indices: 5365178--5365206 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5365168 TTTGAAACTT
5365178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5365207 TGGAAGAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5366698 original size:10 final size:10
Alignment explanation
Indices: 5366683--5366711 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5366673 ACATTAACAA
5366683 CTAACCAAAC
1 CTAACCAAAC
5366693 CTAACCAAAC
1 CTAACCAAAC
5366703 CTAACCAAA
1 CTAACCAAA
5366712 AAGACAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.38, G:0.00, T:0.10
Consensus pattern (10 bp):
CTAACCAAAC
Found at i:5367948 original size:16 final size:16
Alignment explanation
Indices: 5367923--5367959 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5367913 TAATGTGTTC
*
5367923 TAAATTACATAATATA
1 TAAATAACATAATATA
5367939 TAAATAACATAATATA
1 TAAATAACATAATATA
5367955 -AAATA
1 TAAATA
5367960 TTATAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAATAACATAATATA
Found at i:5369153 original size:18 final size:18
Alignment explanation
Indices: 5369114--5369175 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
5369104 AAATTACAAA
* *
5369114 AAAATTTAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
5369133 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTTAT
5369151 AAAAATTCCAAAA-A-TTAT
1 -AAAATT-CAAAATATTTAT
5369169 AGAAATT
1 A-AAATT
5369176 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.03
18 14 0.37
19 18 0.47
20 5 0.13
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:5369925 original size:21 final size:20
Alignment explanation
Indices: 5369885--5369957 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
5369875 AAATTACAAA
5369885 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
5369905 CAAAAACTT-AAAATAATTTT
1 -AAAAAATTCAAAATAATTTT
* *
5369925 -TAAAATTAAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
*
5369944 AAAAATTTCAAAAT
1 AAAAAATTCAAAAT
5369958 TTATATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 9 0.21
19 6 0.14
20 21 0.49
21 7 0.16
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:5369975 original size:17 final size:18
Alignment explanation
Indices: 5369938--5370028 Score: 82
Period size: 17 Copynumber: 5.2 Consensus size: 18
5369928 AATTAAAAAT
** *
5369938 ATTTATAAAAATTTCAAA
1 ATTTATAAATTTTTTAAA
*
5369956 ATTTAT-ATTTTTTTAAA
1 ATTTATAAATTTTTTAAA
5369973 ATTTATAAATTTTTT-AA
1 ATTTATAAATTTTTTAAA
* *
5369990 ATATATAAATTTTATACAA
1 ATTTATAAATTTTTTA-AA
*
5370009 AGTTA-AAA-TTTTTAAA
1 ATTTATAAATTTTTTAAA
5370025 ATTT
1 ATTT
5370029 CCTAAAATAA
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
16 5 0.08
17 33 0.56
18 16 0.27
19 5 0.08
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (18 bp):
ATTTATAAATTTTTTAAA
Found at i:5370169 original size:21 final size:22
Alignment explanation
Indices: 5370143--5370185 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5370133 ATACATGGTT
5370143 TGAAATT-TATATACTCTAACA
1 TGAAATTATATATACTCTAACA
* *
5370164 TGAAATTATTTATACTGTAACA
1 TGAAATTATATATACTCTAACA
5370186 AGATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (22 bp):
TGAAATTATATATACTCTAACA
Found at i:5379882 original size:139 final size:139
Alignment explanation
Indices: 5379611--5380031 Score: 772
Period size: 139 Copynumber: 3.0 Consensus size: 139
5379601 GTCATCATCC
*
5379611 ATTGCCATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
* *
5379676 T-GTTGTACAAATATTATGTTGCTTCCGATTTTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
66 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
5379740 GACCCAAAT
131 GACCCAAAT
*
5379749 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGGGGTTCAATGTGTTGC
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
5379814 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
66 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
*
5379879 GACCTAAAT
131 GACCCAAAT
* *
5379888 ATTGACATTCTATTAGAATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
5379953 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
66 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
5380018 GACCCAAAT
131 GACCCAAAT
5380027 ATTGA
1 ATTGA
5380032 GTGTTGCTTA
Statistics
Matches: 273, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
138 64 0.23
139 209 0.77
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.42
Consensus pattern (139 bp):
ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
GACCCAAAT
Found at i:5384625 original size:58 final size:58
Alignment explanation
Indices: 5384540--5384685 Score: 199
Period size: 58 Copynumber: 2.5 Consensus size: 58
5384530 ATATATTATA
* * *
5384540 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATT-ATATATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAAT-TAAT
*
5384600 A-TTTTATTAAATTTTATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
5384657 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
5384686 CTTAAAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
57 19 0.24
58 46 0.59
59 8 0.10
60 5 0.06
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
Found at i:5384666 original size:32 final size:31
Alignment explanation
Indices: 5384559--5384685 Score: 99
Period size: 32 Copynumber: 4.3 Consensus size: 31
5384549 AATTCATATT
*
5384559 TTAATAATAATTATATTAAAAATATTATTAAA
1 TTAATAATAATTATATT-AAAATATAATTAAA
* * *
5384591 TT-ATATATTATTTTATT-AAAT-T--TT-AT
1 TTAATA-ATAATTATATTAAAATATAATTAAA
5384617 TTAATAATAATTATATTAAAATATAATTAAA
1 TTAATAATAATTATATTAAAATATAATTAAA
* * * *
5384648 TTAATTAATATTTTTATTAAATTAT-ATTTAA
1 TTAA-TAATAATTATATTAAAATATAATTAAA
5384679 -TAATAAT
1 TTAATAAT
5384686 CTTAAAATTT
Statistics
Matches: 77, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
26 12 0.16
27 9 0.12
28 1 0.01
29 5 0.06
30 9 0.12
31 13 0.17
32 28 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAATAATAATTATATTAAAATATAATTAAA
Found at i:5384872 original size:46 final size:44
Alignment explanation
Indices: 5384780--5384873 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
5384770 ATTACAGCAT
* *
5384780 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
5384824 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
5384870 CATT
1 CATT
5384874 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:5384876 original size:16 final size:16
Alignment explanation
Indices: 5384855--5384910 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
5384845 TGAATTACTG
5384855 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
5384871 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTCC
*
5384887 ATTATA-CTTCTATTCC
1 ATTACAGC-TCTATTCC
5384903 ATTACAGC
1 ATTACAGC
5384911 GAACCAAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.03
16 32 0.94
17 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:5390459 original size:13 final size:14
Alignment explanation
Indices: 5390437--5390479 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 14
5390427 AAAAAATCAT
*
5390437 GGAAATTGAAGGAA
1 GGAAAATGAAGGAA
5390451 -GAAAATGAAGGAA
1 GGAAAATGAAGGAA
5390464 TGGGAAAATGAAGGAA
1 --GGAAAATGAAGGAA
5390480 AAGGAGAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 12 0.48
16 13 0.52
ACGTcount: A:0.53, C:0.00, G:0.35, T:0.12
Consensus pattern (14 bp):
GGAAAATGAAGGAA
Found at i:5396731 original size:9 final size:10
Alignment explanation
Indices: 5396686--5396731 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 10
5396676 TTTGGTGTTT
*
5396686 TTTTTTACTG
1 TTTTTTGCTG
5396696 TTTTGGTTGCTG
1 TTTT--TTGCTG
5396708 TTTTTTGCTG
1 TTTTTTGCTG
5396718 -TTTTTG-TG
1 TTTTTTGCTG
5396726 TTTTTT
1 TTTTTT
5396732 TACTGTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 2 0.06
9 11 0.34
10 10 0.31
12 9 0.28
ACGTcount: A:0.02, C:0.07, G:0.20, T:0.72
Consensus pattern (10 bp):
TTTTTTGCTG
Found at i:5396752 original size:22 final size:20
Alignment explanation
Indices: 5396673--5396743 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 20
5396663 ATTATATTGT
5396673 TGTTTTGGTGTTTTTTTTTAC
1 TGTTTTGGTG-TTTTTTTTAC
* *
5396694 TGTTTTGGTTGCTGTTTTTTGC
1 TGTTTTGG-TG-TTTTTTTTAC
*
5396716 TGTTTTTGTG-TTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
5396735 TGTTTTGGT
1 TGTTTTGGT
5396744 TGTTATTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 15 0.36
21 10 0.24
22 17 0.40
ACGTcount: A:0.03, C:0.06, G:0.23, T:0.69
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:5396764 original size:12 final size:12
Alignment explanation
Indices: 5396755--5396861 Score: 62
Period size: 12 Copynumber: 9.3 Consensus size: 12
5396745 GTTATTTTCG
5396755 TGTTGTTTTTGC
1 TGTTGTTTTTGC
* *
5396767 TGTTATTTTTGT
1 TGTTGTTTTTGC
*
5396779 TGTTGTTTTTGT
1 TGTTGTTTTTGC
* *
5396791 TGCT-ATTTT--
1 TGTTGTTTTTGC
**
5396800 TGTTGTTTTTAA
1 TGTTGTTTTTGC
5396812 TGTTG--TTTGC
1 TGTTGTTTTTGC
*
5396822 TGTTATTTTTGC
1 TGTTGTTTTTGC
* * *
5396834 TGCTGTTTTGGT
1 TGTTGTTTTTGC
* *
5396846 TGTTATTTTTGT
1 TGTTGTTTTTGC
5396858 TGTT
1 TGTT
5396862 TGGATGTTAT
Statistics
Matches: 73, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
9 3 0.04
10 11 0.15
11 4 0.05
12 55 0.75
ACGTcount: A:0.06, C:0.05, G:0.21, T:0.68
Consensus pattern (12 bp):
TGTTGTTTTTGC
Found at i:5396776 original size:24 final size:24
Alignment explanation
Indices: 5396735--5396861 Score: 112
Period size: 24 Copynumber: 5.0 Consensus size: 24
5396725 GTTTTTTTAC
* *
5396735 TGTTTTGGTTGTTATTTTCG-TGT
1 TGTTTTTGTTGTTATTTTTGTTGT
*
5396758 TGTTTTTGCTGTTATTTTTGTTGT
1 TGTTTTTGTTGTTATTTTTGTTGT
*
5396782 TGTTTTTGTTGCTATTTTTGTTGTTTTT
1 TGTTTTTGTTGTTATTTTTGTTG----T
* * *
5396810 AATGTTGTTTGCTGTTATTTTTGCTGC
1 --TGTT-TTTGTTGTTATTTTTGTTGT
*
5396837 TGTTTTGGTTGTTATTTTTGTTGT
1 TGTTTTTGTTGTTATTTTTGTTGT
5396861 T
1 T
5396862 TGGATGTTAT
Statistics
Matches: 83, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
23 17 0.20
24 41 0.49
25 4 0.05
28 1 0.01
30 4 0.05
31 16 0.19
ACGTcount: A:0.06, C:0.05, G:0.22, T:0.68
Consensus pattern (24 bp):
TGTTTTTGTTGTTATTTTTGTTGT
Found at i:5396829 original size:55 final size:54
Alignment explanation
Indices: 5396758--5396862 Score: 165
Period size: 55 Copynumber: 1.9 Consensus size: 54
5396748 ATTTTCGTGT
* * *
5396758 TGTTTTTGCTGTTATTTTTGTTGTTGTTTTTGTTGCTATTTTTGTTGTTTTTAA
1 TGTTTTTGCTGTTATTTTTGCTGCTGTTTTGGTTGCTATTTTTGTTGTTTTTAA
*
5396812 TGTTGTTTGCTGTTATTTTTGCTGCTGTTTTGGTTGTTATTTTTGTTGTTT
1 TGTT-TTTGCTGTTATTTTTGCTGCTGTTTTGGTTGCTATTTTTGTTGTTT
5396863 GGATGTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 4 0.09
55 42 0.91
ACGTcount: A:0.06, C:0.05, G:0.21, T:0.69
Consensus pattern (54 bp):
TGTTTTTGCTGTTATTTTTGCTGCTGTTTTGGTTGCTATTTTTGTTGTTTTTAA
Found at i:5396848 original size:43 final size:43
Alignment explanation
Indices: 5396774--5396875 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 43
5396764 TGCTGTTATT
* * * *
5396774 TTTGTTGTTGTTTTTGTTGCTATTTTTGTTGTT-TTTAATGTTG
1 TTTGATGTTATTTTTGCTGCTATTTTGGTTGTTATTT-ATGTTG
* * *
5396817 TTTGCTGTTATTTTTGCTGCTGTTTTGGTTGTTATTTTTGTTG
1 TTTGATGTTATTTTTGCTGCTATTTTGGTTGTTATTTATGTTG
5396860 TTTGGATGTTATTTTT
1 TTT-GATGTTATTTTT
5396876 TATGCGTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 36 0.72
44 14 0.28
ACGTcount: A:0.07, C:0.04, G:0.22, T:0.68
Consensus pattern (43 bp):
TTTGATGTTATTTTTGCTGCTATTTTGGTTGTTATTTATGTTG
Found at i:5397080 original size:49 final size:48
Alignment explanation
Indices: 5396989--5397081 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 48
5396979 TTAATATAAT
* * *
5396989 TTTTTTTAATGTATTTTAAATTTATTTATTTTTTAATGTTTGTTTTAA
1 TTTTTTTAATGTATTTGAAATTTATATATTTTTTAATATTTGTTTTAA
*
5397037 TTTTTTTAAGTGTATTTGATATATTATATATTTTTTAA-ATTTGTT
1 TTTTTTTAA-TGTATTTGAAAT-TTATATATTTTTTAATATTTGTT
5397082 GTATGTAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
48 9 0.23
49 16 0.41
50 14 0.36
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (48 bp):
TTTTTTTAATGTATTTGAAATTTATATATTTTTTAATATTTGTTTTAA
Found at i:5397767 original size:20 final size:19
Alignment explanation
Indices: 5397733--5397771 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
5397723 ATTCCTGATT
5397733 AAGTGTATGGTAATGGTAAA
1 AAGTGTATGGTAAT-GTAAA
5397753 AAGTGTATTGG-AATGTAAA
1 AAGTGTA-TGGTAATGTAAA
5397772 GAATATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 10 0.56
21 3 0.17
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (19 bp):
AAGTGTATGGTAATGTAAA
Found at i:5417378 original size:16 final size:16
Alignment explanation
Indices: 5417327--5417380 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
5417317 TCGAATCAAA
5417327 TCATTTCGAGTTTAGG
1 TCATTTCGAGTTTAGG
* * *
5417343 TCATGTT-GATTTTTGT
1 TCAT-TTCGAGTTTAGG
5417359 TCATTTCGAGTTTAGG
1 TCATTTCGAGTTTAGG
5417375 TCATTT
1 TCATTT
5417381 TTCGTTCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 26 0.87
17 2 0.07
ACGTcount: A:0.17, C:0.11, G:0.20, T:0.52
Consensus pattern (16 bp):
TCATTTCGAGTTTAGG
Found at i:5417388 original size:27 final size:29
Alignment explanation
Indices: 5417327--5417388 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 29
5417317 TCGAATCAAA
*
5417327 TCATTTCGAGTTTAGGTCATGTTGATTTTTGT
1 TCATTTCGAGTTTAGGTCA--TT-ATTTTCGT
5417359 TCATTTCGAGTTTAGGTCA-T-TTTTCGT
1 TCATTTCGAGTTTAGGTCATTATTTTCGT
5417386 TCA
1 TCA
5417389 AATTGAGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 9 0.31
29 1 0.03
32 19 0.66
ACGTcount: A:0.16, C:0.13, G:0.19, T:0.52
Consensus pattern (29 bp):
TCATTTCGAGTTTAGGTCATTATTTTCGT
Found at i:5421133 original size:27 final size:26
Alignment explanation
Indices: 5421102--5421158 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
5421092 AATATTTATA
5421102 TTATATTATTTTA-ATATTAATAAATTT
1 TTATATT-TTTTATATATTAA-AAATTT
* *
5421129 TTATATTTTTTATTTATTAAAATTTT
1 TTATATTTTTTATATATTAAAAATTT
5421155 TTAT
1 TTAT
5421159 GTAGTTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATATTTTTTATATATTAAAAATTT
Found at i:5426904 original size:15 final size:15
Alignment explanation
Indices: 5426854--5426907 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
5426844 TTTAGAATTT
*
5426854 TTAAAAAATAAAAAA
1 TTAAAAAATAGAAAA
*
5426869 TT--ATAA-AGAAAA
1 TTAAAAAATAGAAAA
5426881 TTATTAAAAATAGAAAA
1 TTA--AAAAATAGAAAA
5426898 TTAAAAAATA
1 TTAAAAAATA
5426908 ATATAAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
15 9 0.29
16 3 0.10
17 9 0.29
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (15 bp):
TTAAAAAATAGAAAA
Found at i:5427122 original size:12 final size:12
Alignment explanation
Indices: 5427077--5427130 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
5427067 TTTTTTCAAT
5427077 TAATTTAAATAA
1 TAATTTAAATAA
5427089 TAA---AAATAA
1 TAATTTAAATAA
5427098 TATTATTTCAAATAA
1 TA--ATTT-AAATAA
*
5427113 TAATTTAAATAG
1 TAATTTAAATAA
5427125 TAATTT
1 TAATTT
5427131 TAATTATTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
9 8 0.23
11 1 0.03
12 14 0.40
13 4 0.11
15 8 0.23
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (12 bp):
TAATTTAAATAA
Found at i:5433320 original size:2 final size:2
Alignment explanation
Indices: 5433313--5433348 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5433303 CTTAAAACCC
5433313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5433349 GATGTTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5440339 original size:24 final size:24
Alignment explanation
Indices: 5440307--5440353 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5440297 GAACTCGAAA
*
5440307 CCTTTAACTCTGAACATGAAATCG
1 CCTTTAACTCCGAACATGAAATCG
5440331 CCTTTAACTCCGAACATGAAATC
1 CCTTTAACTCCGAACATGAAATC
5440354 CTAAACCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.28
Consensus pattern (24 bp):
CCTTTAACTCCGAACATGAAATCG
Found at i:5450951 original size:26 final size:26
Alignment explanation
Indices: 5450892--5450959 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
5450882 TATTAATTTT
*
5450892 AAAAGTTAAAACTTTT--TTTTATAGG
1 AAAAGTT-AAACTTTTAATTTTATAAG
5450917 AAAAGTTAAACTTTTAATTCTTA-AAG
1 AAAAGTTAAACTTTTAATT-TTATAAG
*
5450943 AAAAGTTAAACATTTAA
1 AAAAGTTAAACTTTTAA
5450960 ATTACTCGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
24 8 0.21
25 7 0.18
26 20 0.53
27 3 0.08
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (26 bp):
AAAAGTTAAACTTTTAATTTTATAAG
Found at i:5452659 original size:20 final size:20
Alignment explanation
Indices: 5452622--5452659 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5452612 GGGTTTAAGA
*
5452622 TTTATTTTTAGGATTTAGGG
1 TTTATTTTTAGGACTTAGGG
*
5452642 TTTATTTTTAGGGCTTAG
1 TTTATTTTTAGGACTTAG
5452660 AATTTAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.24, T:0.55
Consensus pattern (20 bp):
TTTATTTTTAGGACTTAGGG
Found at i:5452665 original size:20 final size:20
Alignment explanation
Indices: 5452621--5452665 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5452611 AGGGTTTAAG
* *
5452621 ATTTATTTTTAGGATTTAGG
1 ATTTATTTTTAGGACTTAGA
* *
5452641 GTTTATTTTTAGGGCTTAGA
1 ATTTATTTTTAGGACTTAGA
5452661 ATTTA
1 ATTTA
5452666 AGATTTAAGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.20, T:0.53
Consensus pattern (20 bp):
ATTTATTTTTAGGACTTAGA
Found at i:5453052 original size:20 final size:19
Alignment explanation
Indices: 5453018--5453067 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
5453008 TTTTTTTTAA
*
5453018 TAAAAATTGAAATAATT-T
1 TAAAAATTCAAATAATTCT
5453036 TCAAAAATTCAATATAATTCT
1 T-AAAAATTCAA-ATAATTCT
5453057 T-AAAATTCAAA
1 TAAAAATTCAAA
5453068 ATATTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.07
19 18 0.64
20 6 0.21
21 2 0.07
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAAAATTCAAATAATTCT
Found at i:5453080 original size:19 final size:19
Alignment explanation
Indices: 5453017--5453080 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
5453007 ATTTTTTTTA
*
5453017 ATAAAAATT-GAAATAATTT
1 ATAAAAATTCAAAAT-ATTT
* *
5453036 -TCAAAAATTCAATATAATT
1 AT-AAAAATTCAAAATATTT
* *
5453055 CTTAAAATTCAAAATATTT
1 ATAAAAATTCAAAATATTT
5453074 ATAAAAA
1 ATAAAAA
5453081 AAATCCAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 1 0.03
19 29 0.85
20 4 0.12
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAAAATTCAAAATATTT
Found at i:5453418 original size:7 final size:7
Alignment explanation
Indices: 5453397--5453429 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
5453387 GCATGCACTA
5453397 ATCCCAC
1 ATCCCAC
5453404 ACTCCCAC
1 A-TCCCAC
5453412 ATCCCAC
1 ATCCCAC
5453419 ATCCCAC
1 ATCCCAC
5453426 ATCC
1 ATCC
5453430 AACAACTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.27, C:0.58, G:0.00, T:0.15
Consensus pattern (7 bp):
ATCCCAC
Found at i:5455396 original size:24 final size:24
Alignment explanation
Indices: 5455352--5455397 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5455342 CGAAAATAAA
* *
5455352 ATTATGCTAATAAATGCTAAATAT
1 ATTATACTAATAAATACTAAATAT
*
5455376 ATTATACTAATAAATATTAAAT
1 ATTATACTAATAAATACTAAAT
5455398 CTTCTAGGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
ATTATACTAATAAATACTAAATAT
Found at i:5459205 original size:31 final size:30
Alignment explanation
Indices: 5459170--5459307 Score: 116
Period size: 31 Copynumber: 4.6 Consensus size: 30
5459160 TTAATATAAC
*
5459170 ATTTGGTACTTGAACTTGACACTTTTTCCTA
1 ATTTGGTACTTAAACTTGACACTTTTT-CTA
* * *** ** *
5459201 ATTTGGTACCTAAGCTT-TTTCTTGGTCAA
1 ATTTGGTACTTAAACTTGACACTTTTTCTA
* * *
5459230 ATTTGATACTCAAACTTGACATTTTTTCCTA
1 ATTTGGTACTTAAACTTGACACTTTTT-CTA
* *
5459261 ATTTGGTACCTAAACTTGACACTTTTTTTA
1 ATTTGGTACTTAAACTTGACACTTTTTCTA
*
5459291 AGTTGGTACTTAAACTT
1 ATTTGGTACTTAAACTT
5459308 TTTGGGATCC
Statistics
Matches: 78, Mismatches: 27, Indels: 5
0.71 0.25 0.05
Matches are distributed among these distances:
29 15 0.19
30 24 0.31
31 39 0.50
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (30 bp):
ATTTGGTACTTAAACTTGACACTTTTTCTA
Found at i:5459298 original size:30 final size:30
Alignment explanation
Indices: 5459241--5459307 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
5459231 TTTGATACTC
*
5459241 AAACTTGACATTTTTTCCTAATTTGGTACCT
1 AAACTTGACATTTTTT-CTAAGTTGGTACCT
*
5459272 AAACTTGACACTTTTTT-TAAGTTGGTACTT
1 AAACTTGACA-TTTTTTCTAAGTTGGTACCT
5459302 AAACTT
1 AAACTT
5459308 TTTGGGATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 17 0.52
31 10 0.30
32 6 0.18
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.45
Consensus pattern (30 bp):
AAACTTGACATTTTTTCTAAGTTGGTACCT
Found at i:5459345 original size:89 final size:91
Alignment explanation
Indices: 5459170--5459358 Score: 251
Period size: 89 Copynumber: 2.1 Consensus size: 91
5459160 TTAATATAAC
* * * * *
5459170 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAGCTTTTTCTTGGTCAAATTTG
1 ATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTCTGGGTCAAATTTG
5459235 ATACTCAAACTTGACATTTTTTCCTA
66 ATACTCAAACTTGACATTTTTTCCTA
* * *
5459261 ATTTGGTACCTAAACTTGACACTTTTT-TTAAGTTGGTACTTAAAC-TTTT-TGGGATCCAATTT
1 ATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTCTGGG-TCAAATTT
*
5459323 GATACTTAAACTTGAC-TGTTTTTCCTA
65 GATACTCAAACTTGACAT-TTTTTCCTA
5459350 ATTTGGTAC
1 ATTTGGTAC
5459359 ATAATCTTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
88 4 0.05
89 44 0.51
90 14 0.16
91 25 0.29
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (91 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTCTGGGTCAAATTTG
ATACTCAAACTTGACATTTTTTCCTA
Found at i:5459623 original size:25 final size:26
Alignment explanation
Indices: 5459530--5459624 Score: 75
Period size: 29 Copynumber: 3.4 Consensus size: 26
5459520 AATTGAATAT
* * *
5459530 AAAACAAAGCTTAGGTACCAAATTAGG
1 AAAAAAAAGTTTAGATACCAAATTA-G
5459557 AAAAAATGCCAAGTTTAGATACCAAATTAGG
1 AAAAAA----AAGTTTAGATACCAAATTA-G
*
5459588 TCCAAAAAAAGTTTAGATACCAAATTA-
1 --AAAAAAAAGTTTAGATACCAAATTAG
5459615 AAAAAAAAGT
1 AAAAAAAAGT
5459625 ATCAAGTTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
25 9 0.16
27 5 0.09
29 19 0.33
31 19 0.33
33 5 0.09
ACGTcount: A:0.53, C:0.13, G:0.14, T:0.21
Consensus pattern (26 bp):
AAAAAAAAGTTTAGATACCAAATTAG
Found at i:5459681 original size:61 final size:60
Alignment explanation
Indices: 5459529--5459703 Score: 194
Period size: 60 Copynumber: 2.9 Consensus size: 60
5459519 AAATTGAATA
* * * ** * *
5459529 TAAAACAAAGCTTAGGTACCAAATTAGGAAAAAA-TGCCAAGTTTAGATACCAAATTAGG
1 TAAAAAAAAGTTTAAGTACCAAATTAGGAAAAAAGTATCAAGTTCAGGTACCAAATTAGG
* **
5459588 TCCAAAAAAAGTTT-AGATACCAAATTAAAAAAAAAGTATCAAGTTCAGGTACCAAATTAGG
1 T-AAAAAAAAGTTTAAG-TACCAAATTAGGAAAAAAGTATCAAGTTCAGGTACCAAATTAGG
* * *
5459649 TAAAAAAAAGTTTAAGTACCGAATTAGG-AAAAAGTATCAAATTCAGGTACAAAAT
1 TAAAAAAAAGTTTAAGTACCAAATTAGGAAAAAAGTATCAAGTTCAGGTACCAAAT
5459704 GTTATATTAA
Statistics
Matches: 96, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
59 27 0.28
60 45 0.47
61 24 0.25
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (60 bp):
TAAAAAAAAGTTTAAGTACCAAATTAGGAAAAAAGTATCAAGTTCAGGTACCAAATTAGG
Found at i:5473930 original size:17 final size:17
Alignment explanation
Indices: 5473908--5473946 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5473898 CTCCACCTTG
* *
5473908 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
5473925 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
5473942 ACAAG
1 ACAAG
5473947 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:5487735 original size:22 final size:21
Alignment explanation
Indices: 5487706--5487748 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5487696 ATCATTAATG
*
5487706 ATAATTAACAACTCAATGATC
1 ATAATTAACAAATCAATGATC
*
5487727 ATAACTTAACAAATTAATGATC
1 ATAA-TTAACAAATCAATGATC
5487749 TTTGAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAATTAACAAATCAATGATC
Found at i:5499917 original size:42 final size:42
Alignment explanation
Indices: 5499870--5499953 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
5499860 AAAGGAGTTG
*
5499870 TTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGGTTTAA
1 TTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGGGTTTAA
*
5499912 TTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTAA
1 TTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAA
5499954 AAATATTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 3 0.08
42 36 0.92
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (42 bp):
TTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAA
Found at i:5504405 original size:6 final size:6
Alignment explanation
Indices: 5504394--5504421 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5504384 GGATTTGAAA
5504394 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
5504422 CAATTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.54
Consensus pattern (6 bp):
ATTTGG
Found at i:5512209 original size:12 final size:14
Alignment explanation
Indices: 5512185--5512221 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
5512175 GAAAAAAATA
5512185 AAAAATCATAAGT-T
1 AAAAAT-ATAAGTAT
5512199 AAAAA-ATAAGTAT
1 AAAAATATAAGTAT
5512212 AAAAATATAA
1 AAAAATATAA
5512222 AAATATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 6 0.29
14 9 0.43
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (14 bp):
AAAAATATAAGTAT
Found at i:5516151 original size:63 final size:63
Alignment explanation
Indices: 5516052--5516177 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
5516042 TTGAATTTGA
*
5516052 CAATTAAATTCATTTTGGTTTTTGAATTTGAATTTCATAAAAAAATTTATCATGTCATCACTT
1 CAATTAAATTCATTTTGGTCTTTGAATTTGAATTTCATAAAAAAATTTATCATGTCATCACTT
*
5516115 CAATTAAATTCATTTTGGTCTTTGAATTTGAATTTCATAAAAAATTTTATCATGTCATCACTT
1 CAATTAAATTCATTTTGGTCTTTGAATTTGAATTTCATAAAAAAATTTATCATGTCATCACTT
5516178 TAAAATTTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (63 bp):
CAATTAAATTCATTTTGGTCTTTGAATTTGAATTTCATAAAAAAATTTATCATGTCATCACTT
Found at i:5519706 original size:15 final size:15
Alignment explanation
Indices: 5519683--5519712 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5519673 CATAACTTGT
5519683 TAAAGAAATAAAATA
1 TAAAGAAATAAAATA
*
5519698 TAAATAAATAAAATA
1 TAAAGAAATAAAATA
5519713 CAGTGACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
TAAAGAAATAAAATA
Found at i:5527411 original size:150 final size:150
Alignment explanation
Indices: 5527140--5527470 Score: 626
Period size: 150 Copynumber: 2.2 Consensus size: 150
5527130 CGTCTTTTTG
**
5527140 TACGAACCCCACGATTTTTCCCATGCTCAGATTTGACACCCTTCATTTTGAATTCACTCATTGTC
1 TACGAACCGGACGATTTTTCCCATGCTCAGATTTGACACCCTTCATTTTGAATTCACTCATTGTC
5527205 CTTATCAAATCTTGATCATTGTCTCCTGCATCTCCCACATCGAGTTCTTGCATAGTGACACCTAT
66 CTTATCAAATCTTGATCATTGTCTCCTGCATCTCCCACATCGAGTTCTTGCATAGTGACACCTAT
5527270 CGAGCAATGGCATTCTTTCT
131 CGAGCAATGGCATTCTTTCT
5527290 TACGAACCGGACGATTTTTCCCATGCTCAGATTTGACACCCTTCATTTTGAATTCACTCATTGTC
1 TACGAACCGGACGATTTTTCCCATGCTCAGATTTGACACCCTTCATTTTGAATTCACTCATTGTC
* *
5527355 CTTATCAAATCTTGATCATTGTCTCCTTCATCTCCCTCATCGAGTTCTTGCATAGTGACACCTAT
66 CTTATCAAATCTTGATCATTGTCTCCTGCATCTCCCACATCGAGTTCTTGCATAGTGACACCTAT
5527420 CGAGCAATGGCATTCTTTCT
131 CGAGCAATGGCATTCTTTCT
5527440 TACGAACCGGACGATTTTTCCCATGCTCAGA
1 TACGAACCGGACGATTTTTCCCATGCTCAGA
5527471 CTCTTTGAAG
Statistics
Matches: 177, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 177 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.35
Consensus pattern (150 bp):
TACGAACCGGACGATTTTTCCCATGCTCAGATTTGACACCCTTCATTTTGAATTCACTCATTGTC
CTTATCAAATCTTGATCATTGTCTCCTGCATCTCCCACATCGAGTTCTTGCATAGTGACACCTAT
CGAGCAATGGCATTCTTTCT
Found at i:5529264 original size:31 final size:31
Alignment explanation
Indices: 5529226--5529284 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5529216 CATTTTTTAG
* * *
5529226 TTAAATTTGGCCATCAACTTTTCGAAAAGAA
1 TTAAATTTGACCATCAACCTTTCAAAAAGAA
*
5529257 TTAAATTTGACCATTAACCTTTCAAAAA
1 TTAAATTTGACCATCAACCTTTCAAAAA
5529285 AAGTTGAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (31 bp):
TTAAATTTGACCATCAACCTTTCAAAAAGAA
Found at i:5530406 original size:16 final size:18
Alignment explanation
Indices: 5530382--5530423 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
5530372 TTTTTTATAC
*
5530382 GTTTGTTTATTG-G-TAA
1 GTTTTTTTATTGAGTTAA
5530398 GTTTTTTTATTGAGTTAA
1 GTTTTTTTATTGAGTTAA
5530416 -TTTTTTTA
1 GTTTTTTTA
5530424 GAAATACGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 11 0.48
17 9 0.39
18 3 0.13
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (18 bp):
GTTTTTTTATTGAGTTAA
Found at i:5531899 original size:14 final size:16
Alignment explanation
Indices: 5531880--5531911 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
5531870 TTTGGTTTAA
5531880 ATAATATA-AA-ATTT
1 ATAATATATAACATTT
5531894 ATAATATATAACATTT
1 ATAATATATAACATTT
5531910 AT
1 AT
5531912 TAAAAAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATATATAACATTT
Found at i:5533636 original size:17 final size:18
Alignment explanation
Indices: 5533598--5533637 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
5533588 TCAACTTTTG
*
5533598 AATTTATCAAGACATTTA
1 AATTTATCAAGACATGTA
*
5533616 AATTTATCATG-CATGTA
1 AATTTATCAAGACATGTA
5533633 AATTT
1 AATTT
5533638 TTGAATCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (18 bp):
AATTTATCAAGACATGTA
Found at i:5540245 original size:30 final size:31
Alignment explanation
Indices: 5540201--5540258 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
5540191 TTTTCAAATC
* *
5540201 ATCAATATTAAGTGATAAAATTTAATTAGAA
1 ATCAAAATTAAGTGATAAAATTCAATTAGAA
5540232 ATCAAAATT-AGTGATAAAATTCAATTA
1 ATCAAAATTAAGTGATAAAATTCAATTA
5540259 TATAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (31 bp):
ATCAAAATTAAGTGATAAAATTCAATTAGAA
Found at i:5543148 original size:2 final size:2
Alignment explanation
Indices: 5543141--5543179 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5543131 CCTATTTTAA
5543141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5543180 ATAGATCAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5551956 original size:30 final size:33
Alignment explanation
Indices: 5551899--5551970 Score: 98
Period size: 30 Copynumber: 2.3 Consensus size: 33
5551889 TAATAAAGAT
*
5551899 AAAATTATATTTTAATTTATCTTAAAAATAATA
1 AAAATTATAATTTAATTTATCTTAAAAATAATA
*
5551932 AAAATT-TAATTTAA-TTAT-TTAAAAATTATA
1 AAAATTATAATTTAATTTATCTTAAAAATAATA
5551962 AAAA-TATAA
1 AAAATTATAA
5551971 ATATTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 1 0.03
30 18 0.50
31 4 0.11
32 7 0.19
33 6 0.17
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
AAAATTATAATTTAATTTATCTTAAAAATAATA
Found at i:5557965 original size:23 final size:23
Alignment explanation
Indices: 5557939--5558104 Score: 150
Period size: 23 Copynumber: 7.4 Consensus size: 23
5557929 AGTGCTGGGC
5557939 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
5557962 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
5557981 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
5558001 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
5558024 ATCGGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
5558048 TAACAGAGAGCACGAGACA-TGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
5558072 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
5558095 ATCAGAGAGC
1 AACAGAGAGC
5558105 GCGCTAGTGT
Statistics
Matches: 118, Mismatches: 14, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.08
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 4 0.03
23 77 0.65
24 2 0.02
25 14 0.12
26 4 0.03
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:5557999 original size:39 final size:39
Alignment explanation
Indices: 5557945--5558019 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
5557935 GGGCAACAGA
*
5557945 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
5557984 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
5558020 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Done.