Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004900.1 Hibiscus syriacus cultivar Beakdansim tig00011027_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: 106888
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:742 original size:18 final size:19
Alignment explanation
Indices: 721--760 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
711 GGATATTATA
721 ATAAAATAA-ATTAAAAAT
1 ATAAAATAAGATTAAAAAT
*
739 ATAAACTAAGGATTAAAAAT
1 ATAAAATAA-GATTAAAAAT
759 AT
1 AT
761 TATTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (19 bp):
ATAAAATAAGATTAAAAAT
Found at i:1460 original size:21 final size:19
Alignment explanation
Indices: 1435--1475 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1425 CTTTCTTCGG
1435 TTCTGTCTCTCTCTTTTTTTT
1 TTCTGTCTCT-T-TTTTTTTT
*
1456 TTCTGTCTGTTTTTTTTTT
1 TTCTGTCTCTTTTTTTTTT
1475 T
1 T
1476 CAGGTTGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 1 0.05
21 9 0.47
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (19 bp):
TTCTGTCTCTTTTTTTTTT
Found at i:1905 original size:14 final size:13
Alignment explanation
Indices: 1882--1911 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1872 CTGTAATTAT
1882 TTATTTATATATA
1 TTATTTATATATA
1895 TTATTTAATATATA
1 TTATTT-ATATATA
1909 TTA
1 TTA
1912 ATAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTTATATATA
Found at i:1916 original size:3 final size:3
Alignment explanation
Indices: 1900--1954 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
1890 ATATATTATT
* *
1900 TAA TATA TAT TAA TAA TAA TAA TAA TGA TAA TAA TAAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
1947 TAA TAA TA
1 TAA TAA TA
1955 TGGATAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4383 original size:25 final size:25
Alignment explanation
Indices: 4337--4386 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4327 CTCGTATAAA
* *
4337 TTGCACCGAAGTGCCGCTTAGAAAT
1 TTGCACCGAAGTGCCACATAGAAAT
4362 TTGCACCGAAAG-GCCACATAGAAAT
1 TTGCACCG-AAGTGCCACATAGAAAT
4387 GTTCCGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (25 bp):
TTGCACCGAAGTGCCACATAGAAAT
Found at i:4401 original size:23 final size:23
Alignment explanation
Indices: 4371--4468 Score: 81
Period size: 23 Copynumber: 4.3 Consensus size: 23
4361 TTTGCACCGA
*
4371 AAGG-CCACATAGAAATGTTCCG
1 AAGGACCACATAGAAATGTCCCG
* * *
4393 AAGGACCACACAGTATTGTCCCG
1 AAGGACCACATAGAAATGTCCCG
* * *
4416 AAGGATCGCATAGAAATGTCCCA
1 AAGGACCACATAGAAATGTCCCG
* * ** *
4439 AAGGAACACGTAGATTTGTCCCA
1 AAGGACCACATAGAAATGTCCCG
4462 AAGGACC
1 AAGGACC
4469 TCGTAGAACC
Statistics
Matches: 59, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
22 4 0.07
23 55 0.93
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.17
Consensus pattern (23 bp):
AAGGACCACATAGAAATGTCCCG
Found at i:4473 original size:23 final size:23
Alignment explanation
Indices: 4432--4475 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4422 CGCATAGAAA
4432 TGTCCCAAAGGAACACGTAGATT
1 TGTCCCAAAGGAACACGTAGATT
* *
4455 TGTCCCAAAGGACCTCGTAGA
1 TGTCCCAAAGGAACACGTAGA
4476 ACCTCGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (23 bp):
TGTCCCAAAGGAACACGTAGATT
Found at i:4599 original size:15 final size:16
Alignment explanation
Indices: 4564--4602 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
4554 ACAGAGGTTA
4564 TCACATAGACATGTAT
1 TCACATAGACATGTAT
4580 TCACATAGATCAT-T-T
1 TCACATAGA-CATGTAT
4595 TCACATAG
1 TCACATAG
4603 CTTATATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 10 0.45
17 3 0.14
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (16 bp):
TCACATAGACATGTAT
Found at i:4647 original size:16 final size:16
Alignment explanation
Indices: 4626--4675 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 16
4616 CTCATATATC
4626 CACATAGATCATGTAA
1 CACATAGATCATGTAA
4642 CACATAGGATGACATGTAA
1 CACATA-GAT--CATGTAA
*
4661 CACATAGCTCATGTA
1 CACATAGATCATGTA
4676 TAACAGTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 12 0.40
17 3 0.10
18 2 0.07
19 13 0.43
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (16 bp):
CACATAGATCATGTAA
Found at i:6028 original size:116 final size:116
Alignment explanation
Indices: 5823--6052 Score: 388
Period size: 116 Copynumber: 2.0 Consensus size: 116
5813 TGATAAATTG
* *
5823 ACTAAGTTAACACACTTCATTCCCATTCGAACTAATAATTCTATGGATAAGTATGTTGAGTCATA
1 ACTAAGTTAACACACTTCATTCCCATTCAAACCAATAATTCTATGGATAAGTATGTTGAGTCATA
* * *
5888 TATTCGATAGATAGTTTGACTTCATGGGATACTAGAATCGATTGTGTGTTA
66 TATTCGAAAAATAGTTCGACTTCATGGGATACTAGAATCGATTGTGTGTTA
5939 ACTAAGTTAACACACTTCATTCCCATTCAAACCAATAATTCTATGGATAAGTATGTTGAGTCATA
1 ACTAAGTTAACACACTTCATTCCCATTCAAACCAATAATTCTATGGATAAGTATGTTGAGTCATA
* * *
6004 TATTCGAAAAATAGTTCGATTTCATGGGATACTATAATTGATTGTGTGT
66 TATTCGAAAAATAGTTCGACTTCATGGGATACTAGAATCGATTGTGTGT
6053 GATAGAGATA
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 106 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (116 bp):
ACTAAGTTAACACACTTCATTCCCATTCAAACCAATAATTCTATGGATAAGTATGTTGAGTCATA
TATTCGAAAAATAGTTCGACTTCATGGGATACTAGAATCGATTGTGTGTTA
Found at i:10527 original size:15 final size:15
Alignment explanation
Indices: 10507--10537 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10497 TACTCCCCAA
10507 TAGGGGTATCGATAC
1 TAGGGGTATCGATAC
10522 TAGGGGTATCGATAC
1 TAGGGGTATCGATAC
10537 T
1 T
10538 TATATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.29
Consensus pattern (15 bp):
TAGGGGTATCGATAC
Found at i:10698 original size:20 final size:20
Alignment explanation
Indices: 10673--10724 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
10663 AATAAGTCAA
* *
10673 TAGTATTGATACCTATAGGT
1 TAGTATCGATACCTAAAGGT
10693 TAGTATCGATACCTAAAGGT
1 TAGTATCGATACCTAAAGGT
*
10713 TAGTACCGATAC
1 TAGTATCGATAC
10725 TGAAGTGTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (20 bp):
TAGTATCGATACCTAAAGGT
Found at i:10803 original size:37 final size:37
Alignment explanation
Indices: 10751--10854 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
10741 ATTTTCGTCC
*
10751 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTA
* * *
10788 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTA
* * * *
10825 TACTAAGATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
10855 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTA
Found at i:11248 original size:18 final size:17
Alignment explanation
Indices: 11209--11251 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
11199 ATTATATGGA
*
11209 TATT-TTATTCATTTAT
1 TATTATTATTCATCTAT
*
11225 TTTTATTATTCATGCTAT
1 TATTATTATTCAT-CTAT
11243 TATTATTAT
1 TATTATTAT
11252 ATGTGTGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTATTATTCATCTAT
Found at i:16138 original size:183 final size:183
Alignment explanation
Indices: 15830--16183 Score: 620
Period size: 183 Copynumber: 1.9 Consensus size: 183
15820 ATTAAATCCG
15830 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* **
15895 ATATATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
15960 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* *
16013 TAAAGCTGAGCTATTCCACTAAGGCAATTGTTTATAGAGGAAACTCGAAAGCTCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
16078 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTACATTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* *
16142 TTTGTTAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
16184 TAAACCTGAT
Statistics
Matches: 162, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
182 1 0.01
183 161 0.99
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:17362 original size:36 final size:36
Alignment explanation
Indices: 17322--17438 Score: 146
Period size: 36 Copynumber: 3.2 Consensus size: 36
17312 CACTCAAATT
*
17322 TGTTTTTCTTAAAACATACTTTGTCTCAATTGAGAC
1 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
* * * * ** *
17358 TGTTTTTCTCGAAAAAATA-TTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAAACATACTTTGTCTCACTTGAGAC
17394 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
17430 TGTTTTTCT
1 TGTTTTTCT
17439 CGAAAAAGAT
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
35 7 0.11
36 50 0.78
37 7 0.11
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.47
Consensus pattern (36 bp):
TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
Found at i:17471 original size:35 final size:35
Alignment explanation
Indices: 17358--17473 Score: 126
Period size: 36 Copynumber: 3.3 Consensus size: 35
17348 CAATTGAGAC
17358 TGTTTTTCTCGAAAAAATATTTATTTCACTCAAGAT
1 TGTTTTTCTCG-AAAAATATTTATTTCACTCAAGAT
* * * ** *
17394 TGTTTTTCT-TAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTCGAAAA-ATA-TTTATTTCACTCAAGAT
*
17430 TGTTTTTCTCGAAAAAGATTTATTTCACTCAAGAT
1 TGTTTTTCTCGAAAAATATTTATTTCACTCAAGAT
*
17465 TATTTTTCT
1 TGTTTTTCT
17474 TAAAACAAGA
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
34 4 0.06
35 23 0.37
36 32 0.51
37 4 0.06
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (35 bp):
TGTTTTTCTCGAAAAATATTTATTTCACTCAAGAT
Found at i:17488 original size:71 final size:71
Alignment explanation
Indices: 17306--17537 Score: 306
Period size: 72 Copynumber: 3.2 Consensus size: 71
17296 ATGCAAATGA
* *
17306 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATACTTTGTCTCAATTGAGACTGTTTTTCTCGA
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACATACTTTGTCTCACTTGAGACTGTTTTTCTCG-
*
17370 AAAAATAT
64 AAAAAGAT
17378 TTATTTCACTCAAGATTGTTTTTCTTAAAACATACTTTGTCTCACTTGAGACTGTTTTTCTCGAA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACATACTTTGTCTCACTTGAGACTGTTTTTCTCGAA
17443 AAAGAT
66 AAAGAT
* * * * *
17449 TTATTTCACTCAAGATTATTTTTCTTAAAACA-AGATTTGTCTCGCTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCG
17513 AAAGAAGGCATT
64 AAA-AA-G-A-T
17525 TTATTTCACTCAA
1 TTATTTCACTCAA
17538 AGCTTTTTTT
Statistics
Matches: 145, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
70 1 0.01
71 59 0.41
72 66 0.46
73 3 0.02
74 1 0.01
75 1 0.01
76 14 0.10
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (71 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACATACTTTGTCTCACTTGAGACTGTTTTTCTCGAA
AAAGAT
Found at i:17612 original size:39 final size:39
Alignment explanation
Indices: 17569--17720 Score: 110
Period size: 39 Copynumber: 3.6 Consensus size: 39
17559 TTTTATCTTG
*
17569 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * *
17608 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
*
17660 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCT-C
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* *
17697 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCCCTCGAAACA
17721 TAAACATTGA
Statistics
Matches: 88, Mismatches: 11, Indels: 29
0.69 0.09 0.23
Matches are distributed among these distances:
37 2 0.02
38 19 0.22
39 25 0.28
40 5 0.06
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 5 0.06
51 24 0.27
52 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:17836 original size:105 final size:104
Alignment explanation
Indices: 17624--17941 Score: 509
Period size: 104 Copynumber: 3.1 Consensus size: 104
17614 ACAGTTTCTC
* *
17624 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
17689 TTTGTCT-CCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
17727 TTGAAAACATTTCCCTTAAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
17792 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
17832 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
17894 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
17933 TTGAAAACA
1 TTGAAAACA
17942 ATTTAACGAA
Statistics
Matches: 201, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
101 48 0.24
103 23 0.11
104 76 0.38
105 54 0.27
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:17888 original size:36 final size:36
Alignment explanation
Indices: 17841--17916 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
17831 ATTGAAAACA
* * *
17841 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
17877 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
17913 TTTC
1 TTTC
17917 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:18311 original size:105 final size:105
Alignment explanation
Indices: 18116--18746 Score: 905
Period size: 105 Copynumber: 6.0 Consensus size: 105
18106 ATATCGTGAC
* * ** * * * * *
18116 ACTCGAGACAACACAAGTTCAACTTCATAATGAAGGTACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
*
18181 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
18222 ACTCCAGACAACGCAAGTTCAACTTTACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
18287 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
18327 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
18392 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
18432 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
18497 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
18537 ACTCCATACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
18598 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
18637 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTAG-TTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT-GCTTGTCAAC-AACAACTTCC
** * * *
18701 CGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
18743 ACTC
1 ACTC
18747 GGAACAATGC
Statistics
Matches: 483, Mismatches: 35, Indels: 14
0.91 0.07 0.03
Matches are distributed among these distances:
100 79 0.16
101 4 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 308 0.64
106 82 0.17
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:19342 original size:37 final size:37
Alignment explanation
Indices: 19289--19393 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
19279 CATTTTCGTC
* *
19289 CTACTAGGATTCAAACTCCTAAAAATGGGATAAAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
* * * *
19326 TTGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
* * *
19363 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
19394 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
Found at i:19776 original size:17 final size:18
Alignment explanation
Indices: 19750--19789 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
19740 ATTATATGGA
19750 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
19766 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
19784 TATTAT
1 TATTAT
19790 ATGTGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:19802 original size:2 final size:2
Alignment explanation
Indices: 19795--19821 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19785 ATTATATGTG
19795 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 T
19822 TATTATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20308 original size:2 final size:2
Alignment explanation
Indices: 20301--20344 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
20291 TAATACTTTG
20301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20343 AT
1 AT
20345 TTGTTTTCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22297 original size:18 final size:19
Alignment explanation
Indices: 22256--22299 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
22246 ATATGTTTTG
*
22256 TATTTT-TATTATATGATT
1 TATTTTATATTATATGATA
22274 TATTTTATATTAT-TGATA
1 TATTTTATATTATATGATA
*
22292 TGTTTTAT
1 TATTTTAT
22300 TTTTATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (19 bp):
TATTTTATATTATATGATA
Found at i:26090 original size:33 final size:33
Alignment explanation
Indices: 26048--26114 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
26038 GATATATTTT
26048 TAATTTGTGTACTCTAGATATTTGCTAATGAAA
1 TAATTTGTGTACTCTAGATATTTGCTAATGAAA
26081 TAATTTGTGTACTCTAGATATTTGCTAATGAAA
1 TAATTTGTGTACTCTAGATATTTGCTAATGAAA
26114 T
1 T
26115 CTCATAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (33 bp):
TAATTTGTGTACTCTAGATATTTGCTAATGAAA
Found at i:28435 original size:21 final size:21
Alignment explanation
Indices: 28411--28494 Score: 150
Period size: 21 Copynumber: 4.0 Consensus size: 21
28401 GCGTAGAATT
*
28411 TGTCCCGAATGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
28432 TGTCCTGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
28453 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
28474 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
28495 CCCTCGACTC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:29328 original size:20 final size:20
Alignment explanation
Indices: 29300--29357 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
29290 TTCCCATTGA
* *
29300 AGTGGATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
29320 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
29343 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
29358 CTACCATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
23 2 0.06
24 13 0.41
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:30680 original size:24 final size:24
Alignment explanation
Indices: 30653--30704 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
30643 CATCCCCACA
30653 TCTAAAACAAGCTCCAGAGATTAC
1 TCTAAAACAAGCTCCAGAGATTAC
*
30677 TCTAAAACAAGCTCCGGAGATTAC
1 TCTAAAACAAGCTCCAGAGATTAC
30701 TCTA
1 TCTA
30705 CATACCCCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.23
Consensus pattern (24 bp):
TCTAAAACAAGCTCCAGAGATTAC
Found at i:32624 original size:21 final size:21
Alignment explanation
Indices: 32600--32662 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
32590 GCGTAGAATT
*
32600 TGTCCCGAATGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
32621 TGTCCCAAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
32642 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
32663 CCCTCGACTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.16
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:33498 original size:20 final size:20
Alignment explanation
Indices: 33470--33527 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
33460 TTCCCATTGA
* *
33470 AGTGGATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
33490 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
33513 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
33528 CTACCATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
23 2 0.06
24 13 0.41
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:39549 original size:33 final size:33
Alignment explanation
Indices: 39502--39568 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
39492 GATATATTTT
39502 TAATTTGTGCACTCTAGATATTTGCTAATGAAA
1 TAATTTGTGCACTCTAGATATTTGCTAATGAAA
*
39535 TAATTTGTGTACTCTAGATATTTGCTAATGAAA
1 TAATTTGTGCACTCTAGATATTTGCTAATGAAA
39568 T
1 T
39569 CTCATAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (33 bp):
TAATTTGTGCACTCTAGATATTTGCTAATGAAA
Found at i:41899 original size:21 final size:21
Alignment explanation
Indices: 41875--41956 Score: 155
Period size: 21 Copynumber: 3.9 Consensus size: 21
41865 GTAGAATTTT
41875 TCCCGAAGGACCACATAGATG
1 TCCCGAAGGACCACATAGATG
*
41896 TCCCGAAAGACCACATAGATG
1 TCCCGAAGGACCACATAGATG
41917 TCCCGAAGGACCACATAGATG
1 TCCCGAAGGACCACATAGATG
41938 TCCCGAAGGACCACATAGA
1 TCCCGAAGGACCACATAGA
41957 CCCTCGACTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.13
Consensus pattern (21 bp):
TCCCGAAGGACCACATAGATG
Found at i:42792 original size:20 final size:20
Alignment explanation
Indices: 42764--42821 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
42754 TTCCCATTGA
* *
42764 AGTGGATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
42784 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
42807 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
42822 CTACCATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
23 2 0.06
24 13 0.41
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:44144 original size:24 final size:24
Alignment explanation
Indices: 44117--44168 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
44107 CATCCCCACA
44117 TCTAAAACAAGCTCCAGAGATTAC
1 TCTAAAACAAGCTCCAGAGATTAC
*
44141 TCTAAAACAAGCTCCGGAGATTAC
1 TCTAAAACAAGCTCCAGAGATTAC
44165 TCTA
1 TCTA
44169 CATACCCCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.23
Consensus pattern (24 bp):
TCTAAAACAAGCTCCAGAGATTAC
Found at i:46089 original size:21 final size:21
Alignment explanation
Indices: 46065--46148 Score: 141
Period size: 21 Copynumber: 4.0 Consensus size: 21
46055 GCGTAGAATT
*
46065 TGTCCCGAATGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
46086 TGTCCCAAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
46107 TATCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
46128 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
46149 CCCTCGACTC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.15
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:46984 original size:20 final size:20
Alignment explanation
Indices: 46956--47013 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
46946 TTCCCATTGA
* *
46956 AGTGGATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
46976 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
46999 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
47014 CTACCATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
23 2 0.06
24 13 0.41
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:56809 original size:21 final size:21
Alignment explanation
Indices: 56785--56826 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
56775 AGTTTATTTT
56785 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
56806 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
56827 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:56863 original size:33 final size:33
Alignment explanation
Indices: 56821--56924 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
56811 TTTGTTTCAA
56821 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
*
56854 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
56887 TTATCGAACTTGGAAGTATTTAAGTATTTTAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
56919 TTATCG
1 TTATCG
56925 TAAACTTTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 6 0.09
33 61 0.91
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:57349 original size:32 final size:32
Alignment explanation
Indices: 57311--57380 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
57301 TAAAGTTAAT
* *
57311 TTAGGATGAAAATTATAAATTTTAGAATAGGG
1 TTAGGATGAAAATTATAAATTTGAGAATAAGG
57343 TTAGGATGAAAATTATAAATTTGAGAATAAGG
1 TTAGGATGAAAATTATAAATTTGAGAATAAGG
57375 TTAGGA
1 TTAGGA
57381 ATTTGGTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (32 bp):
TTAGGATGAAAATTATAAATTTGAGAATAAGG
Found at i:58162 original size:43 final size:43
Alignment explanation
Indices: 58098--58192 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
58088 TAAGAACTTG
*
58098 AACATC-GAAATTAATAAACAAAACAATATCAACTACTAATCCT
1 AACATCAG-AATTAATAAACAAAACAATATCAACTACTAATACT
* * *
58141 AACATCAGAATTAATATACAAAACAATATTAATTACTAATACT
1 AACATCAGAATTAATAAACAAAACAATATCAACTACTAATACT
*
58184 AGCATCAGA
1 AACATCAGA
58193 TTGTGATGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 45 0.98
44 1 0.02
ACGTcount: A:0.53, C:0.18, G:0.04, T:0.25
Consensus pattern (43 bp):
AACATCAGAATTAATAAACAAAACAATATCAACTACTAATACT
Found at i:58603 original size:31 final size:30
Alignment explanation
Indices: 58565--58624 Score: 111
Period size: 31 Copynumber: 2.0 Consensus size: 30
58555 AAAAATTTAA
58565 TTTTTTAAATATTTTTCTTAGTTATTGATAT
1 TTTTTTAAATATTTTT-TTAGTTATTGATAT
58596 TTTTTTAAATATTTTTTTAGTTATTGATA
1 TTTTTTAAATATTTTTTTAGTTATTGATA
58625 ATATAGACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.65
Consensus pattern (30 bp):
TTTTTTAAATATTTTTTTAGTTATTGATAT
Found at i:61050 original size:29 final size:28
Alignment explanation
Indices: 61008--61063 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
60998 ATAATTTTGA
* * *
61008 TTCTTTTCAGTTAGGTCCTGAACTTTAAT
1 TTCTCTTCAATTAGATCCTGAA-TTTAAT
*
61037 TTCTCTTCAATTAGATCCTTAATTTAA
1 TTCTCTTCAATTAGATCCTGAATTTAA
61064 AATGAATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (28 bp):
TTCTCTTCAATTAGATCCTGAATTTAAT
Found at i:72277 original size:23 final size:22
Alignment explanation
Indices: 72253--72297 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
72243 CTTCGATATT
72253 AATAAATATTAATATAATAATTTA
1 AATAAA-ATTAA-ATAATAATTTA
*
72277 AATAAAATTAAATTATAATTT
1 AATAAAATTAAATAATAATTT
72298 TTTTATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAATTAAATAATAATTTA
Found at i:72605 original size:28 final size:26
Alignment explanation
Indices: 72559--72613 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
72549 TGAAAATATT
*
72559 TAAAATTAATTACTAAATTATAATCTAA
1 TAAAATTAAATACTAAATT-TAAT-TAA
* *
72587 TAAAATTAAATATTTAATTTAATTAA
1 TAAAATTAAATACTAAATTTAATTAA
72613 T
1 T
72614 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.17
27 4 0.17
28 16 0.67
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAAATTAAATACTAAATTTAATTAA
Found at i:73184 original size:3 final size:3
Alignment explanation
Indices: 73168--73242 Score: 132
Period size: 3 Copynumber: 24.7 Consensus size: 3
73158 TTTGGGCATG
*
73168 TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
73214 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
73243 TTTAAATGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 67 0.97
4 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:73582 original size:124 final size:122
Alignment explanation
Indices: 73377--73659 Score: 369
Period size: 124 Copynumber: 2.3 Consensus size: 122
73367 GTTGAATAAA
* * * *
73377 TTCTTCTCTTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCCACTGGGGATGATGTTGACCTA
1 TTCTT-TCTTT-TTCAGATGAGTTCTTCTCATTATGAACTTTCCACTGAGGATGATGCTAACCTA
* * * *
73442 TTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC
64 TCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
* * *
73501 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTAGAAAGGTTGATGCTAATCT
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCCACT-G--AGGATGATGCTAACCT
* *
73565 ATCTGCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
63 ATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
73625 TTC-TTC---TTCAGATGAGTTCTTCTCATTATGAACTT
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTT
73660 CTTCTTCTTC
Statistics
Matches: 143, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
120 29 0.20
121 3 0.02
122 30 0.21
123 8 0.06
124 73 0.51
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (122 bp):
TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCCACTGAGGATGATGCTAACCTATC
TCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
Found at i:73646 original size:36 final size:36
Alignment explanation
Indices: 73606--73695 Score: 180
Period size: 36 Copynumber: 2.5 Consensus size: 36
73596 TTGAACAAGC
73606 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
73642 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
73678 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
73696 TCTCTGGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.48
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
Found at i:73691 original size:16 final size:16
Alignment explanation
Indices: 73636--73691 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
73626 TCTTCTTCAG
73636 ATGAGTTCTTCTCATT
1 ATGAGTTCTTCTCATT
*
73652 ATGAACTTCTTCTTC-TT
1 ATG-AGTTCTTC-TCATT
73669 CAGATGAGTTCTTCTCATT
1 ---ATGAGTTCTTCTCATT
73688 ATGA
1 ATGA
73692 ACTTTCTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 7 0.22
17 9 0.28
18 4 0.12
19 9 0.28
20 3 0.09
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.46
Consensus pattern (16 bp):
ATGAGTTCTTCTCATT
Found at i:73807 original size:116 final size:116
Alignment explanation
Indices: 73641--74460 Score: 1085
Period size: 116 Copynumber: 7.1 Consensus size: 116
73631 TTCAGATGAG
*
73641 TTCTTCTCATTATGAA---CTTC-TTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTC
1 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
* * * * ** *
73698 TCTGGAAAAGCTGA-TCTATCAAGTGATGGATTTGAATAAAAGGTTGAACAAA
66 -CTGGAAATGTTGATTC-ATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
* * *
73750 TTCTTCTCATTATGAATTTCTTCTTTTTTCTTCAGATGACGAGTTCTTCTCATTATGAACT-TTC
1 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
* * * * *
73814 TCTGGAAAAGTTGATAT-ATCAAGTGATGGATT-TAGCAAAAGGTTGAACAAA
66 -CTGGAAATGTTGAT-TCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
*
73865 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
*
73930 CTGGCAATGTTGATTCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
66 CTGGAAATGTTGATTCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
* * *
73981 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAAATGACGAATTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
*
74046 CTGGCAATGTTGATTCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
66 CTGGAAATGTTGATTCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
* * *
74097 TTCTTCTCATTATGAACTTCTTCTTCCCTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
*
74162 CTGGCAATGTTGATTCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
66 CTGGAAATGTTGATTCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
* * * *
74213 TTCTTCTTATTATGAACTTCTTCTTCCCTCTTCAGATGACGAGTTCTTCTCATTATGAACT-TTC
1 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
74277 TCTGGAAATGTTGATTCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
66 -CTGGAAATGTTGATTCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
* * * *
74329 TTCTTCTCATTATGAACTTCTTCTTCCCTCTTCAGATGACGAGTTCTTCTTATTATGAACTCTAA
1 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
* * * * * * * * *
74394 CTGGTACTGCTG-TTCCA-CTGAGTGATGAATTTAAGCAAAAAGTTGAACAAG
66 CTGGAAATGTTGATT-CATC-AAATGATGAATTCAAACAAAAGGTTGAACAAA
74445 TTCTTCTCATTATGAA
1 TTCTTCTCATTATGAA
74461 TTTTTTTTTG
Statistics
Matches: 657, Mismatches: 38, Indels: 25
0.91 0.05 0.03
Matches are distributed among these distances:
109 16 0.02
112 4 0.01
113 12 0.02
114 1 0.00
115 106 0.16
116 516 0.79
117 1 0.00
118 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (116 bp):
TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
CTGGAAATGTTGATTCATCAAATGATGAATTCAAACAAAAGGTTGAACAAA
Found at i:75448 original size:93 final size:92
Alignment explanation
Indices: 75289--75765 Score: 828
Period size: 93 Copynumber: 5.1 Consensus size: 92
75279 CTTATTTCTA
* * * * *
75289 CTATGATCATATTTATCTTTCAAATCTAATGATTGGTTTTCGGGGTTCATATAAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTC-GGGTTCATATCAAACCAGATCAG
75354 ATAACTCAAAGAACACTTCCAGAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
*
75382 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTCAGGGTTCATATCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTC-GGGTTCATATCAAACCAGATCAG
75447 ATAACTCAAAGAACACTTCCAGAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
75475 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTCGAGGTTCATATCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTCG-GGTTCATATCAAACCAGATCAG
75540 ATAACTCAAAGAACACTTCCAGAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
75568 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTCGAGGTTCATATCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTCG-GGTTCATATCAAACCAGATCAG
75633 ATAACTCAAAGAACACTTCCAGAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
*
75661 CTATGAGCACATTCATCTTTTAAATCCAATGATTGGTTTTCGGGGTTCATATCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTC-GGGTTCATATCAAACCAGATCAG
*
75726 ATAACTCAAAGAACACTTCTAGAAGATG
65 ATAACTCAAAGAACACTTCCAGAAGATG
*
75754 CTATGAACACAT
1 CTATGAGCACAT
75766 GGCACTTGTT
Statistics
Matches: 371, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
92 1 0.00
93 369 0.99
94 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (92 bp):
CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTCGGGTTCATATCAAACCAGATCAGA
TAACTCAAAGAACACTTCCAGAAGATG
Found at i:76787 original size:22 final size:23
Alignment explanation
Indices: 76762--76826 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
76752 ATCTTGACCC
76762 CTTTTTTTCTTTTTCTT-TTTCT
1 CTTTTTTTCTTTTTCTTCTTTCT
* *
76784 CTTTTTTCCTTTTTTTTTCTTTCT
1 CTTTTTTTC-TTTTTCTTCTTTCT
76808 CTTTTCTTT-TTATTTCTTC
1 CTTTT-TTTCTT-TTTCTTC
76827 AAGCATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 8 0.23
23 9 0.26
24 16 0.46
25 2 0.06
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (23 bp):
CTTTTTTTCTTTTTCTTCTTTCT
Found at i:76795 original size:30 final size:29
Alignment explanation
Indices: 76761--76818 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
76751 CATCTTGACC
*
76761 CCTTTTTTTCTT-TTTCTTTTTCTCTTTTTT
1 CCTTTTTTT-TTCTTTCTCTTT-TCTTTTTT
76791 CCTTTTTTTTTCTTTCTCTTTTCTTTTT
1 CCTTTTTTTTTCTTTCTCTTTTCTTTTT
76819 ATTTCTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (29 bp):
CCTTTTTTTTTCTTTCTCTTTTCTTTTTT
Found at i:76823 original size:21 final size:22
Alignment explanation
Indices: 76766--76826 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
76756 TGACCCCTTT
* *
76766 TTTTCTTTTTCTTT-TTCTCTT
1 TTTTCTTTTTATTTCTTCTCTC
*
76787 TTTTCCTTTTTTTTTCTT-TCTC
1 TTTT-CTTTTTATTTCTTCTCTC
76809 TTTTCTTTTTATTTCTTC
1 TTTTCTTTTTATTTCTTC
76827 AAGCATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 16 0.47
22 16 0.47
23 2 0.06
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTCTTTTTATTTCTTCTCTC
Found at i:84188 original size:16 final size:16
Alignment explanation
Indices: 84164--84202 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
84154 TGAAATGAAT
*
84164 AATGAATGTATGCAAA
1 AATGTATGTATGCAAA
84180 AATGTATGTATGCAAA
1 AATGTATGTATGCAAA
*
84196 AAGGTAT
1 AATGTAT
84203 TGATCCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (16 bp):
AATGTATGTATGCAAA
Found at i:88284 original size:28 final size:26
Alignment explanation
Indices: 88252--88306 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
88242 TGAAAATATT
*
88252 TAAAATTAATTACTAAATTATAATCTAA
1 TAAAATTAAATACTAAATT-TAAT-TAA
*
88280 TAAAATTAAATACTTAATTTAATTAA
1 TAAAATTAAATACTAAATTTAATTAA
88306 T
1 T
88307 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 17 0.68
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAAATTAAATACTAAATTTAATTAA
Found at i:89489 original size:3 final size:3
Alignment explanation
Indices: 89483--89526 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
89473 TAATATTTAT
89483 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
89527 TTTAAATGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:92741 original size:21 final size:22
Alignment explanation
Indices: 92715--92755 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
92705 CCAGGACAGA
*
92715 GAGTATCGTTAC-TCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
92736 GAGTATCGATACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
92756 TAATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:98923 original size:31 final size:32
Alignment explanation
Indices: 98882--98953 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
98872 TATATTTAAT
* *
98882 TGATGTTGTGACATATGACT-TGTCA-CTAAAG
1 TGATGATGTGACATAT-ACTGTGTCATCCAAAG
*
98913 TGATGATGTGACATATATTGTGTCATCCAAAG
1 TGATGATGTGACATATACTGTGTCATCCAAAG
98945 TGATGATGT
1 TGATGATGT
98954 ATACATACCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.06
31 20 0.56
32 14 0.39
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (32 bp):
TGATGATGTGACATATACTGTGTCATCCAAAG
Found at i:101372 original size:24 final size:24
Alignment explanation
Indices: 101318--101380 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
101308 GGGACCTGCT
* * *
101318 AAAGAAGAAAAGAAGGACGACAAG
1 AAAGATGAAAAGAAAGACGAAAAG
101342 AAAGATGAAAAGAAAGACGAAAAG
1 AAAGATGAAAAGAAAGACGAAAAG
* *
101366 AAGGATGACAAGAAA
1 AAAGATGAAAAGAAA
101381 TGATCGTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.63, C:0.06, G:0.27, T:0.03
Consensus pattern (24 bp):
AAAGATGAAAAGAAAGACGAAAAG
Found at i:101379 original size:12 final size:12
Alignment explanation
Indices: 101318--101367 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
101308 GGGACCTGCT
*
101318 AAAGAAGAAAAG
1 AAAGACGAAAAG
* *
101330 AAGGACGACAAG
1 AAAGACGAAAAG
*
101342 AAAGATGAAAAG
1 AAAGACGAAAAG
101354 AAAGACGAAAAG
1 AAAGACGAAAAG
101366 AA
1 AA
101368 GGATGACAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.66, C:0.06, G:0.26, T:0.02
Consensus pattern (12 bp):
AAAGACGAAAAG
Done.