Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004628.1 Hibiscus syriacus cultivar Beakdansim tig00010360_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: 121621
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2958 original size:13 final size:13
Alignment explanation
Indices: 2940--2964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2930 TATTCCATGT
2940 TTCCTTTCAACTA
1 TTCCTTTCAACTA
2953 TTCCTTTCAACT
1 TTCCTTTCAACT
2965 CCCATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCCTTTCAACTA
Found at i:4394 original size:2 final size:2
Alignment explanation
Indices: 4387--4411 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4377 TCAATCTACA
4387 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4412 ATTTACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4590 original size:85 final size:85
Alignment explanation
Indices: 4439--4596 Score: 212
Period size: 85 Copynumber: 1.9 Consensus size: 85
4429 ATGAAACACG
* * * *
4439 AATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGTAAGTCATACATGCGTG
1 AATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCATAAATGCGTG
4504 TCATAAATTTATGACACATA
66 TCATAAATTTATGACACATA
* * * *
4524 AATGTGTGTCATCTTCATTT-ATGACGGGGGCTTCAATGACGCTCAATG-CAGCTCATAAATGTG
1 AATGTGTGTCATCTT-ATTTAATGACGGGGGCTTCAATGACACGCAATGTAAG-TCATAAATGCG
4587 TGTCATAAAT
64 TGTCATAAAT
4597 GTGCGCCATA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 2 0.03
85 58 0.92
86 3 0.05
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (85 bp):
AATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCATAAATGCGTG
TCATAAATTTATGACACATA
Found at i:4592 original size:13 final size:13
Alignment explanation
Indices: 4576--4610 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4566 TCAATGCAGC
*
4576 TCATAAATGTGTG
1 TCATAAATGTGCG
4589 TCATAAATGTGCG
1 TCATAAATGTGCG
*
4602 CCATAAATG
1 TCATAAATG
4611 CACGTCATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (13 bp):
TCATAAATGTGCG
Found at i:13240 original size:64 final size:64
Alignment explanation
Indices: 13139--13262 Score: 248
Period size: 64 Copynumber: 1.9 Consensus size: 64
13129 AGTTTTCCTT
13139 AATTTTGTGTGTCATGCATTGAAGGTAAACTGCAAATATATTCCCATCTCAAATGAAATAAGGA
1 AATTTTGTGTGTCATGCATTGAAGGTAAACTGCAAATATATTCCCATCTCAAATGAAATAAGGA
13203 AATTTTGTGTGTCATGCATTGAAGGTAAACTGCAAATATATTCCCATCTCAAATGAAATA
1 AATTTTGTGTGTCATGCATTGAAGGTAAACTGCAAATATATTCCCATCTCAAATGAAATA
13263 TAGGCTGTTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (64 bp):
AATTTTGTGTGTCATGCATTGAAGGTAAACTGCAAATATATTCCCATCTCAAATGAAATAAGGA
Found at i:13380 original size:22 final size:23
Alignment explanation
Indices: 13352--13395 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
13342 TATGTGTTTC
13352 GTACCTAAACTATC-ATTTTTTA
1 GTACCTAAACTATCAATTTTTTA
*
13374 GTACCTAAACTTTCAATTTTTT
1 GTACCTAAACTATCAATTTTTT
13396 CAAAACCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.48
Consensus pattern (23 bp):
GTACCTAAACTATCAATTTTTTA
Found at i:16512 original size:9 final size:9
Alignment explanation
Indices: 16500--16525 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
16490 ATAAATGTAA
16500 TAATATTTT
1 TAATATTTT
16509 TAATATTTT
1 TAATATTTT
16518 TAATATTT
1 TAATATTT
16526 AAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TAATATTTT
Found at i:17585 original size:21 final size:22
Alignment explanation
Indices: 17561--17602 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
17551 TAACGATCGA
17561 AAACGTGCCA-AAAGACATAGG
1 AAACGTGCCATAAAGACATAGG
* *
17582 AAACGTGTCATAAAGGCATAG
1 AAACGTGCCATAAAGACATAG
17603 TTATTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (22 bp):
AAACGTGCCATAAAGACATAGG
Found at i:18021 original size:23 final size:23
Alignment explanation
Indices: 17987--18031 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
17977 TATCAATTAA
*
17987 AATTTGATTTAATATATAATAAT
1 AATTTGAGTTAATATATAATAAT
18010 AATTTGAGTTAATATATAATAA
1 AATTTGAGTTAATATATAATAA
18032 AATAGGATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (23 bp):
AATTTGAGTTAATATATAATAAT
Found at i:25451 original size:112 final size:111
Alignment explanation
Indices: 25250--25479 Score: 334
Period size: 112 Copynumber: 2.1 Consensus size: 111
25240 GTTATAGGTG
** * * *
25250 CATTTCAACATACTTTGTGTATGATAGTATCGATCGATTTTGTTTAATGCATAACGGTGCATTTT
1 CATTTCAACATACTTCATGTATGAAAGTATCGATCAATTTTGCTTAATGCATAACGGTGCATTTT
** * *
25315 TGGCATAAAAGGTGCCACCCATGGTATTCTTAATAAGGTGAATTAC
66 CAGCATAAAAGGTGCCACCAATGGTATTCATAATAAGGTGAATTAC
* **
25361 CATTTCGACATACTTCATGTATGAAAGTTATCGATCAATTTTGCTTAATGCATAATTGTGCATTT
1 CATTTCAACATACTTCATGTATGAAAG-TATCGATCAATTTTGCTTAATGCATAACGGTGCATTT
*
25426 TCAGCATAAAAGGTGCCACCAATGGTATTCATAATGAGGTGAATTAC
65 TCAGCATAAAAGGTGCCACCAATGGTATTCATAATAAGGTGAATTAC
25473 CATTTCA
1 CATTTCA
25480 GCACTTCGGT
Statistics
Matches: 104, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
111 23 0.22
112 81 0.78
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (111 bp):
CATTTCAACATACTTCATGTATGAAAGTATCGATCAATTTTGCTTAATGCATAACGGTGCATTTT
CAGCATAAAAGGTGCCACCAATGGTATTCATAATAAGGTGAATTAC
Found at i:29272 original size:18 final size:18
Alignment explanation
Indices: 29249--29294 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
29239 AGGCATTTGA
29249 TCCTCTGGCT-GTGCTTGT
1 TCCTCT-GCTCGTGCTTGT
29267 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
29285 TCCTCGTGCT
1 TCCTC-TGCT
29295 GTTCTGGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.00, C:0.33, G:0.24, T:0.43
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:29304 original size:18 final size:19
Alignment explanation
Indices: 29259--29309 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
29249 TCCTCTGGCT
*
29259 GTGCTTGTTCCTC-TGCTC
1 GTGCTGGTTCCTCGTGCTC
*
29277 GTGCTTGTTCCTCGTGCT-
1 GTGCTGGTTCCTCGTGCTC
* *
29295 GTTCTGGTTCATCGT
1 GTGCTGGTTCCTCGT
29310 CGGAGTCGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.45
Consensus pattern (19 bp):
GTGCTGGTTCCTCGTGCTC
Found at i:30901 original size:21 final size:21
Alignment explanation
Indices: 30867--30935 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
30857 GAACCCCAGA
* *
30867 GGGGTATCGATTCCCCTACAG
1 GGGGAATCGGTTCCCCTACAG
* *
30888 GGGGAATTGGTTCCCCTTCAAAG
1 GGGGAATCGGTTCCCC-T-ACAG
*
30911 GGGGAATCGGTTCCCCTTCAG
1 GGGGAATCGGTTCCCCTACAG
30932 GGGG
1 GGGG
30936 GGTATCGATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 19 0.49
22 2 0.05
23 18 0.46
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGAATCGGTTCCCCTACAG
Found at i:30915 original size:23 final size:23
Alignment explanation
Indices: 30886--30948 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
30876 ATTCCCCTAC
*
30886 AGGGGGAATTGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
30909 AGGGGGAATCGGTTCCCCTTCAG
1 AGGGGGAATCGGTTCCCCTTCAA
* * *
30932 GGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
30949 TCTGCACTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.17, C:0.24, G:0.35, T:0.24
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:41922 original size:111 final size:112
Alignment explanation
Indices: 41791--42018 Score: 359
Period size: 112 Copynumber: 2.0 Consensus size: 112
41781 CTTATAGGTT
* * * * * *
41791 CATTTCGACATACTTTGTGTATGATAG-TATCGATCGATTTTGTTTAATGCATAACGTTGCATTT
1 CATTTCGACATACTCTGTGTATGAAAGTTATCGATCAATTTCGCTTAATGCATAACGGTGCATTT
* * *
41855 TTGGCATAAAAGGTGCCACCCATGGTATTTATAATTAGGTGAATTAC
66 TCGGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
*
41902 CATTTCGACATACTCTGTGTATGAAAGTTATCGATCAATTTCGCTTAATGCATAATGGTGCATTT
1 CATTTCGACATACTCTGTGTATGAAAGTTATCGATCAATTTCGCTTAATGCATAACGGTGCATTT
41967 TCGGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
66 TCGGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
42014 CATTT
1 CATTT
42019 TAGCACGTTG
Statistics
Matches: 106, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
111 25 0.24
112 81 0.76
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (112 bp):
CATTTCGACATACTCTGTGTATGAAAGTTATCGATCAATTTCGCTTAATGCATAACGGTGCATTT
TCGGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
Found at i:43472 original size:14 final size:14
Alignment explanation
Indices: 43453--43501 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
43443 TTTTTATTTA
43453 TTTAATTTCAGTCC
1 TTTAATTTCAGTCC
* *
43467 TTTAATTTCATTAC
1 TTTAATTTCAGTCC
* *
43481 TTTAATTTTAGTCA
1 TTTAATTTCAGTCC
43495 TTTAATT
1 TTTAATT
43502 ATTGCGCTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.27, C:0.12, G:0.04, T:0.57
Consensus pattern (14 bp):
TTTAATTTCAGTCC
Found at i:43550 original size:2 final size:2
Alignment explanation
Indices: 43543--43608 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
43533 AGTCCCACGA
43543 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
43585 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
43609 GCATGCATGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47832 original size:19 final size:19
Alignment explanation
Indices: 47806--47850 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
47796 TTATATTTAA
47806 TTAT-TTAT-TTTATTAT-T
1 TTATCTTATCTTT-TTATCT
47823 TTATTCTTATCTTTTTATCT
1 TTA-TCTTATCTTTTTATCT
47843 TTATCTTA
1 TTATCTTA
47851 AATTATATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 13 0.54
20 7 0.29
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATCTTATCTTTTTATCT
Found at i:53376 original size:30 final size:30
Alignment explanation
Indices: 53340--53403 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
53330 AGAAATAGGT
*
53340 GCACGTTAGTATAGCCCAATCCCATGTGGC
1 GCACGTTAGCATAGCCCAATCCCATGTGGC
* * *
53370 GCACGTTAGCATAGCTCAATTCTATGTGGC
1 GCACGTTAGCATAGCCCAATCCCATGTGGC
53400 GCAC
1 GCAC
53404 ACTAGTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (30 bp):
GCACGTTAGCATAGCCCAATCCCATGTGGC
Found at i:57237 original size:21 final size:22
Alignment explanation
Indices: 57212--57264 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
57202 AGTATTTTAA
*
57212 TTAGGATTTATTTTCATTA-TT
1 TTAGGATTTATTTACATTATTT
*
57233 TTAGGATTATATTTACCTTATTT
1 TTAGGATT-TATTTACATTATTT
57256 TTAGGATTT
1 TTAGGATTT
57265 TGAAGGCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 8 0.29
22 10 0.36
23 10 0.36
ACGTcount: A:0.25, C:0.06, G:0.11, T:0.58
Consensus pattern (22 bp):
TTAGGATTTATTTACATTATTT
Found at i:60749 original size:34 final size:35
Alignment explanation
Indices: 60684--60757 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
60674 CAAAAAAGTT
* ** *
60684 AAAAAATTGTTCTTTGTTTCGAACAATAAAAGAAG
1 AAAAAAATGTTCACTGTTTCGAACAAGAAAAGAAG
60719 AAAAAAATGTTCACTGTTTCGAAC-AGAAAAGAAG
1 AAAAAAATGTTCACTGTTTCGAACAAGAAAAGAAG
*
60753 GAAAA
1 AAAAA
60758 TTGATTGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.24
Consensus pattern (35 bp):
AAAAAAATGTTCACTGTTTCGAACAAGAAAAGAAG
Found at i:61721 original size:21 final size:22
Alignment explanation
Indices: 61697--61749 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
61687 AGTATTTTAA
*
61697 TTAGGATTTATTTTCATT-ATT
1 TTAGGATTTATTTACATTGATT
* *
61718 TTAGGATTATATTTACCTTGTTT
1 TTAGGATT-TATTTACATTGATT
61741 TTAGGATTT
1 TTAGGATTT
61750 TAAAGGCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 9 0.33
23 10 0.37
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (22 bp):
TTAGGATTTATTTACATTGATT
Found at i:62653 original size:14 final size:13
Alignment explanation
Indices: 62615--62664 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
62605 ATTTTAAACA
*
62615 ATTTATATTTAATT
1 ATTT-TATTTTATT
62629 A-TTTATTTTATT
1 ATTTTATTTTATT
62641 ATTTTATTCTTATCT
1 ATTTTATT-TTAT-T
62656 -TTTTATTTT
1 ATTTTATTTT
62665 TATCTAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 9 0.28
13 10 0.31
14 12 0.38
15 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTATTTTATT
Found at i:62667 original size:14 final size:15
Alignment explanation
Indices: 62630--62670 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
62620 TATTTAATTA
62630 TTTA-TTTTAT-TAT
1 TTTATTTTTATCTAT
*
62643 TTTATTCTTATCT-T
1 TTTATTTTTATCTAT
62657 TTTATTTTTATCTA
1 TTTATTTTTATCTA
62671 AAATTCTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
14 18 0.78
15 1 0.04
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATCTAT
Found at i:64952 original size:15 final size:14
Alignment explanation
Indices: 64934--65014 Score: 62
Period size: 14 Copynumber: 5.9 Consensus size: 14
64924 ACACCTGAAG
64934 AAAAGAAGAAAAGA
1 AAAAGAAGAAAAGA
*
64948 GAAAA-AATGAGAAGA
1 -AAAAGAA-GAAAAGA
* *
64963 AAATGAAAAAAAGA
1 AAAAGAAGAAAAGA
64977 AAAAG-A-AAAAGA
1 AAAAGAAGAAAAGA
* *
64989 AAAATAAGAAAATA
1 AAAAGAAGAAAAGA
65003 AGAAA-AAGAAAA
1 A-AAAGAAGAAAA
65015 CAAACGAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
12 10 0.19
13 2 0.04
14 27 0.50
15 15 0.28
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (14 bp):
AAAAGAAGAAAAGA
Found at i:64967 original size:11 final size:11
Alignment explanation
Indices: 64937--64968 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
64927 CCTGAAGAAA
64937 AGAAGAAAA-G
1 AGAAGAAAATG
64947 AGAA-AAAATG
1 AGAAGAAAATG
64957 AGAAGAAAATG
1 AGAAGAAAATG
64968 A
1 A
64969 AAAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 4 0.20
10 9 0.45
11 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (11 bp):
AGAAGAAAATG
Found at i:64983 original size:23 final size:21
Alignment explanation
Indices: 64934--65040 Score: 78
Period size: 23 Copynumber: 4.9 Consensus size: 21
64924 ACACCTGAAG
64934 AAAAGAAGAAAAGAGAAAAAATG-
1 AAAAGAA-AAAAGA-AAAAAA-GA
* *
64957 AGAAG-AAAATGAAAAAAAGA
1 AAAAGAAAAAAGAAAAAAAGA
64977 AAAAG-AAAAAGAAAAATAAGA
1 AAAAGAAAAAAGAAAAA-AAGA
64998 AAATA-AGAAAAAGAAAACAAACGA
1 AAA-AGA-AAAAAGAAAA-AAA-GA
* *
65022 ATAATAAAAAAGAAAAAAA
1 AAAAGAAAAAAGAAAAAAA
65041 AATGAATCAA
Statistics
Matches: 71, Mismatches: 5, Indels: 17
0.76 0.05 0.18
Matches are distributed among these distances:
19 1 0.01
20 20 0.28
21 12 0.17
22 5 0.07
23 27 0.38
24 6 0.08
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.06
Consensus pattern (21 bp):
AAAAGAAAAAAGAAAAAAAGA
Found at i:64989 original size:29 final size:28
Alignment explanation
Indices: 64930--65042 Score: 83
Period size: 29 Copynumber: 4.0 Consensus size: 28
64920 AATTACACCT
* **
64930 GAAGAAAA-GAAGAAAAGAGAAAAAATGA
1 GAAGAAAATGAAAAAAAGA-AAAAAAAAA
64958 GAAGAAAATGAAAAAAAGAAAAAGAAAAA
1 GAAGAAAATGAAAAAAAGAAAAA-AAAAA
* *
64987 GAA-AAATAAGAAAATAAGAAAAAGAAAACA
1 GAAGAAA-ATGAAAAAAAGAAAAA-AAAA-A
65017 -AACGAATAAT--AAAAAAGAAAAAAAAA
1 GAA-GAA-AATGAAAAAAAGAAAAAAAAA
65043 TGAATCAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
28 19 0.27
29 47 0.66
30 1 0.01
31 3 0.04
32 1 0.01
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (28 bp):
GAAGAAAATGAAAAAAAGAAAAAAAAAA
Found at i:65000 original size:20 final size:20
Alignment explanation
Indices: 64939--65115 Score: 98
Period size: 20 Copynumber: 8.7 Consensus size: 20
64929 TGAAGAAAAG
* *
64939 AAGAAAAGAGAAAAAATG-AG
1 AAGAAAA-AGAAAAAAAGAAA
*
64959 AAGAAAATGAAAAAAAGAAA
1 AAGAAAAAGAAAAAAAGAAA
64979 AAGAAAAAGAAAAATAAGAAAA
1 AAGAAAAAGAAAAA-AAG-AAA
65001 TAAGAAAAAGAAAACAAACGAATA
1 -AAGAAAAAGAAAA-AAA-GAA-A
65025 ATA-AAAAAGAAAAAAA-AATGA
1 A-AGAAAAAGAAAAAAAGAA--A
** *
65046 ATCAAAAA-TAAAAAAG--A
1 AAGAAAAAGAAAAAAAGAAA
* **
65063 AAGAGAAAGAAGTAAAGAAA
1 AAGAAAAAGAAAAAAAGAAA
* *
65083 AAGACAAATGAATAAAA-AAA
1 AAGA-AAAAGAAAAAAAGAAA
*
65103 AGGAAAAAGAAAA
1 AAGAAAAAGAAAA
65116 TTGAAAGGAG
Statistics
Matches: 122, Mismatches: 20, Indels: 31
0.71 0.12 0.18
Matches are distributed among these distances:
17 6 0.05
18 5 0.04
19 15 0.12
20 40 0.33
21 18 0.15
22 6 0.05
23 28 0.23
24 4 0.03
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (20 bp):
AAGAAAAAGAAAAAAAGAAA
Found at i:65059 original size:29 final size:27
Alignment explanation
Indices: 64969--65070 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 27
64959 AAGAAAATGA
*
64969 AAAAAAGAAAAAGAAAAAGAA-AAATAAG
1 AAAAAAGAAAAAG-AAAAGAACAAA-AAT
* *
64997 AAAATAAGAAAAAGAAAACAAACGAATAAT
1 AAAA-AAGAAAAAGAAAA-GAAC-AAAAAT
65027 AAAAAAGAAAAA-AAAATGAATCAAAAAT
1 AAAAAAGAAAAAGAAAA-GAA-CAAAAAT
*
65055 AAAAAAGAAAGAGAAA
1 AAAAAAGAAAAAGAAA
65071 GAAGTAAAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
28 30 0.49
29 23 0.38
30 6 0.10
31 2 0.03
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (27 bp):
AAAAAAGAAAAAGAAAAGAACAAAAAT
Found at i:65084 original size:52 final size:52
Alignment explanation
Indices: 64972--65086 Score: 123
Period size: 52 Copynumber: 2.2 Consensus size: 52
64962 AAAATGAAAA
*
64972 AAAGAAAAAGAAAAAGAAAAATAAGAAAATAAGAAAAAGAAAACAAACGAAT
1 AAAGAAAAAGAAAAAAAAAAATAAGAAAATAAGAAAAAGAAAACAAACGAAT
* *
65024 AATA-AAAAAGAAAAAAAAATGAATCA-AAAAT-A-AAAAAGAAAGAGAAA-GAAGT
1 AA-AGAAAAAGAAAAAAAAA--AATAAGAAAATAAGAAAAAGAAA-ACAAACGAA-T
65076 AAAGAAAAAGA
1 AAAGAAAAAGA
65087 CAAATGAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
51 13 0.24
52 31 0.57
53 6 0.11
54 4 0.07
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.07
Consensus pattern (52 bp):
AAAGAAAAAGAAAAAAAAAAATAAGAAAATAAGAAAAAGAAAACAAACGAAT
Found at i:65111 original size:7 final size:6
Alignment explanation
Indices: 64970--65115 Score: 67
Period size: 6 Copynumber: 24.7 Consensus size: 6
64960 AGAAAATGAA
* * *
64970 AAAAAG AAAAAG AAAAAG AAAAAT AAGAA- AATAAG AAAAAG -AAAA-
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * * * *
65015 CAAACG AATAATA- AAAAAG AAAAA- AAAATG AATCAA- AAATA- AAAAAG
1 AAAAAG AA-AA-AG AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAAAG
* * *
65062 AAAGAG AAAGAAG -TAAAG AAAAAG ACAAATG AATAAA- AAAAAGG AAAAAG
1 AAAAAG AAA-AAG AAAAAG AAAAAG A-AAAAG AA-AAAG AAAAA-G AAAAAG
65112 AAAA
1 AAAA
65116 TTGAAAGGAG
Statistics
Matches: 106, Mismatches: 19, Indels: 30
0.68 0.12 0.19
Matches are distributed among these distances:
5 27 0.25
6 60 0.57
7 19 0.18
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.07
Consensus pattern (6 bp):
AAAAAG
Found at i:65121 original size:13 final size:12
Alignment explanation
Indices: 64959--65121 Score: 54
Period size: 12 Copynumber: 13.0 Consensus size: 12
64949 AAAAAATGAG
64959 AAGAAAATGAAAAA
1 AAGAAAATG--AAA
*
64973 AAGAAAAAGAAA
1 AAGAAAATGAAA
64985 AAGAAAAATAAGAAAA
1 AAG-AAAAT--G-AAA
*
65001 TAAGAAAAAGAAA
1 -AAGAAAATGAAA
*
65014 ACA-AACGAAT-AAT
1 A-AGAA--AATGAAA
65027 AA-AAAA-GAAA
1 AAGAAAATGAAA
*
65037 AA-AAAATGAAT
1 AAGAAAATGAAA
* *
65048 CA-AAAATAAAA
1 AAGAAAATGAAA
65059 AAGAAAGA-GAAA
1 AAGAAA-ATGAAA
*
65071 GAAGTAAA-GAAA
1 -AAGAAAATGAAA
65083 AAGACAAATGAATA
1 AAGA-AAATGAA-A
* *
65097 AAAAAAAGGAAA
1 AAGAAAATGAAA
65109 AAGAAAATTGAAA
1 AAGAAAA-TGAAA
65122 GGAGTGTTCA
Statistics
Matches: 114, Mismatches: 18, Indels: 35
0.68 0.11 0.21
Matches are distributed among these distances:
10 10 0.09
11 15 0.13
12 33 0.29
13 30 0.26
14 15 0.13
15 1 0.01
16 7 0.06
17 3 0.03
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.08
Consensus pattern (12 bp):
AAGAAAATGAAA
Found at i:66335 original size:29 final size:28
Alignment explanation
Indices: 66301--66391 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 28
66291 TCAAATTACT
66301 ATAAAATACAAATTTTTTTAGAATTTATA
1 ATAAAATA-AAATTTTTTTAGAATTTATA
* * *
66330 ATAAAAGTTTAAA-CTTTTTAGAATTTACA
1 ATAAAA--TAAAATTTTTTTAGAATTTATA
** * * *
66359 ATAAAGGAAAATTATTTTATAAATTATA
1 ATAAAATAAAATTTTTTTAGAATTTATA
66387 ATAAA
1 ATAAA
66392 GGACAAAATT
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
27 3 0.06
28 16 0.33
29 25 0.52
30 3 0.06
31 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (28 bp):
ATAAAATAAAATTTTTTTAGAATTTATA
Found at i:66377 original size:28 final size:27
Alignment explanation
Indices: 66314--66394 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
66304 AAATACAAAT
**
66314 TTTTTTAGAATTTATAATAAAAGTTTAAA
1 TTTTTTAGAATTTATAAT-AAAG-GAAAA
* *
66343 CTTTTTAGAATTTACAATAAAGGAAAA
1 TTTTTTAGAATTTATAATAAAGGAAAA
* *
66370 TTATTTTATAAATTATAATAAAGGA
1 TT-TTTTAGAATTTATAATAAAGGA
66395 CAAAATTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
27 4 0.09
28 23 0.53
29 16 0.37
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (27 bp):
TTTTTTAGAATTTATAATAAAGGAAAA
Found at i:66408 original size:29 final size:28
Alignment explanation
Indices: 66344--66566 Score: 196
Period size: 29 Copynumber: 7.7 Consensus size: 28
66334 AAGTTTAAAC
* * *
66344 TTTTTAGAATTTACAATAAAGGA-AAAT
1 TTTTTATAAATTACAATAAAGGACAAAA
*
66371 TATTTTATAAATTATAATAAAGGACAAAA
1 T-TTTTATAAATTACAATAAAGGACAAAA
* *
66400 TTTGTTATAAACTACAATAAAGTACAAAA
1 TTT-TTATAAATTACAATAAAGGACAAAA
* *
66429 CTATTTATAAATTACAATAAAGTACAAAA
1 -TTTTTATAAATTACAATAAAGGACAAAA
* **
66458 TAATTTATAAATTACAATAAAATACAAAA
1 T-TTTTATAAATTACAATAAAGGACAAAA
* *
66487 CTATTTATAAATTACAATAAAGGATAAAA
1 -TTTTTATAAATTACAATAAAGGACAAAA
* * * * *
66516 CCTTTCATAAATTATAATAAAAGGAGACAAT
1 -TTTTTATAAATTACAAT-AAAGGACA-AAA
*
66547 TTTTTATAAAATACAATAAA
1 TTTTTATAAATTACAATAAA
66567 TTTAGCATAA
Statistics
Matches: 165, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.01
28 22 0.13
29 117 0.71
30 23 0.14
31 2 0.01
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.33
Consensus pattern (28 bp):
TTTTTATAAATTACAATAAAGGACAAAA
Found at i:66485 original size:87 final size:85
Alignment explanation
Indices: 66340--66566 Score: 224
Period size: 87 Copynumber: 2.6 Consensus size: 85
66330 ATAAAAGTTT
* * * * *
66340 AAACTTTT-TAGAATTTACAATAAAGGAAAATTATTTTATAAATTATAATAAAGGACAAAA-TTT
1 AAACTTTTATA-AA-TTACAATAAAGGAAAAATAATTTATAAATTACAATAAAAGACAAAACTAT
*
66403 GTTATAAACTACAATAAAGTACA
64 -TTATAAACTACAATAAAGGACA
* *
66426 AAACTATTTATAAATTACAATAAAGTACAAAATAATTTATAAATTACAATAAAATACAAAACTAT
1 AAACT-TTTATAAATTACAATAAAGGA-AAAATAATTTATAAATTACAATAAAAGACAAAACTAT
* *
66491 TTATAAATTACAATAAAGGATA
64 TTATAAACTACAATAAAGGACA
* * * ** *
66513 AAACCTTTCATAAATTATAATAAAAGGAGACAATTTTTTATAAAATACAATAAA
1 AAA-CTTTTATAAATTACAAT-AAAGGA-AAAATAATTTATAAATTACAATAAA
66567 TTTAGCATAA
Statistics
Matches: 117, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
86 17 0.15
87 68 0.58
88 32 0.27
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (85 bp):
AAACTTTTATAAATTACAATAAAGGAAAAATAATTTATAAATTACAATAAAAGACAAAACTATTT
ATAAACTACAATAAAGGACA
Found at i:68534 original size:61 final size:61
Alignment explanation
Indices: 68453--68616 Score: 177
Period size: 61 Copynumber: 2.7 Consensus size: 61
68443 ATAATGACCA
* * *
68453 AAACGT-AAACACGCTGAAACAAGGAGGACATGGTACGTGATTTACCCTTAAACATGTAACT
1 AAACGTGAAACACACT-AAACAAGGAGGACTTGATACGTGATTTACCCTTAAACATGTAACT
* * * * * * *
68514 AAACGTGTAACACACTAAACAGGGAGGACTTGATGCATGATTTATCCTTTAACTTGTAACT
1 AAACGTGAAACACACTAAACAAGGAGGACTTGATACGTGATTTACCCTTAAACATGTAACT
* * * * *
68575 AATCGTGAAACATACTAGATATGGAGGACTTGATACGTGATT
1 AAACGTGAAACACACTAAACAAGGAGGACTTGATACGTGATT
68617 AGCCCAAAAC
Statistics
Matches: 84, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 77 0.92
62 7 0.08
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (61 bp):
AAACGTGAAACACACTAAACAAGGAGGACTTGATACGTGATTTACCCTTAAACATGTAACT
Found at i:72093 original size:10 final size:10
Alignment explanation
Indices: 72073--72181 Score: 53
Period size: 9 Copynumber: 11.6 Consensus size: 10
72063 ATTTGATCGG
72073 CTTTCTTTCTT
1 CTTT-TTTCTT
72084 CTTTTTTC-T
1 CTTTTTTCTT
72093 -TTTTTTC-T
1 CTTTTTTCTT
72101 C-TTTTT-TT
1 CTTTTTTCTT
72109 CTATTTTT-TT
1 CT-TTTTTCTT
72119 CCTTTTTTC-T
1 -CTTTTTTCTT
* * *
72129 CTATCTTCAT
1 CTTTTTTCTT
72139 -TTTTTTCTT
1 CTTTTTTCTT
72148 -TTTTTTC-T
1 CTTTTTTCTT
*
72156 C-TTTTACTAT
1 CTTTTTTCT-T
72166 CTCTTTTT-TT
1 CT-TTTTTCTT
72176 CTTTTT
1 CTTTTT
72182 CTTTTTTGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
8 21 0.27
9 24 0.30
10 23 0.29
11 7 0.09
12 4 0.05
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:72104 original size:28 final size:27
Alignment explanation
Indices: 72073--72181 Score: 112
Period size: 28 Copynumber: 3.9 Consensus size: 27
72063 ATTTGATCGG
72073 CTTTCTTTCTTCTTTTTTCTTTTTTTCT
1 CTTTCTTTCTT-TTTTTTCTTTTTTTCT
* *
72101 CTTTTTTTCTATTTTTTTCCTTTTTTCT
1 CTTTCTTTCT-TTTTTTTCTTTTTTTCT
* *
72129 CTATC-TTCATTTTTTTCTTTTTTTTCT
1 CTTTCTTTCTTTTTTTTC-TTTTTTTCT
*
72156 CTTTTACTATCTCTTTTTTTCTTTTT
1 C-TTT-CTTTCT-TTTTTTTCTTTTT
72182 CTTTTTTGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
26 8 0.12
27 12 0.18
28 29 0.44
29 2 0.03
30 7 0.11
31 8 0.12
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (27 bp):
CTTTCTTTCTTTTTTTTCTTTTTTTCT
Found at i:72445 original size:2 final size:2
Alignment explanation
Indices: 72438--72485 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
72428 GGACAACAAG
72438 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
72480 AT AT AT
1 AT AT AT
72486 TCATGTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76343 original size:18 final size:20
Alignment explanation
Indices: 76304--76343 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
76294 TGGCAAAAAG
76304 AAAACAAGTTAAGACGTATAA
1 AAAACAAGTTAAGAC-TATAA
76325 AAAACAAG-TAAGA-TATAA
1 AAAACAAGTTAAGACTATAA
76343 A
1 A
76344 GCCAAATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 5 0.26
21 8 0.42
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.17
Consensus pattern (20 bp):
AAAACAAGTTAAGACTATAA
Found at i:77317 original size:11 final size:11
Alignment explanation
Indices: 77301--77329 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
77291 TAAAAGAAAA
77301 TAAATATGACT
1 TAAATATGACT
77312 TAAATATGACT
1 TAAATATGACT
77323 TAAATAT
1 TAAATAT
77330 AATCAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (11 bp):
TAAATATGACT
Found at i:79379 original size:29 final size:29
Alignment explanation
Indices: 79325--79380 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
79315 TGTAAGAAAA
* *
79325 TAAAAGTTAGTAATTAATATGCAATAAAT
1 TAAAAGTTAGTAATTAAAATGAAATAAAT
*
79354 TAAAAGTTAGTAGTTAGAAAT-AAATAA
1 TAAAAGTTAGTAATTA-AAATGAAATAA
79381 CATAGCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.32
Consensus pattern (29 bp):
TAAAAGTTAGTAATTAAAATGAAATAAAT
Found at i:81318 original size:2 final size:2
Alignment explanation
Indices: 81311--81420 Score: 220
Period size: 2 Copynumber: 55.0 Consensus size: 2
81301 AGTTTCCATA
81311 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
81353 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
81395 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
81421 TAGTATTTAG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 108 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82671 original size:19 final size:19
Alignment explanation
Indices: 82647--82689 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
82637 AACGTCACGT
82647 TTATAGTATTTTTGTGACG
1 TTATAGTATTTTTGTGACG
82666 TTATAGTATTTTTGTGACG
1 TTATAGTATTTTTGTGACG
82685 TTATA
1 TTATA
82690 CATAGTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.19, T:0.53
Consensus pattern (19 bp):
TTATAGTATTTTTGTGACG
Found at i:83226 original size:13 final size:13
Alignment explanation
Indices: 83208--83232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83198 TACAAATAAA
83208 AAAAAAGAAAGCG
1 AAAAAAGAAAGCG
83221 AAAAAAGAAAGC
1 AAAAAAGAAAGC
83233 AACACACAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAGCG
Found at i:84889 original size:27 final size:26
Alignment explanation
Indices: 84859--84914 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 26
84849 TTGAAAACTC
84859 ATTTTAGTATTTC-TAAAATTTTTATAA
1 ATTTTA-TATTTCTTAAAA-TTTTATAA
*
84886 A-TTTATTTTTCTTTAAAATTTTATAA
1 ATTTTATATTTC-TTAAAATTTTATAA
84912 ATT
1 ATT
84915 CACCATTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
25 5 0.20
26 13 0.52
27 7 0.28
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTTATATTTCTTAAAATTTTATAA
Found at i:90702 original size:59 final size:59
Alignment explanation
Indices: 90533--90706 Score: 222
Period size: 59 Copynumber: 2.9 Consensus size: 59
90523 CACATGTACT
* * * * * * *
90533 CAAACTATGATCCTCATTCGAAATTGATAACTAAAATTTTGAATATTTCAACTACATCC
1 CAAATTATGACCCTCATTCAAAATTGATACCTAAAATTTTGAATATTTCAATTTCACCC
*
90592 CAAATTATGACTCTCATTCAAAATTGATACCTAAAATTTTGAATATTTCAATTTCACCC
1 CAAATTATGACCCTCATTCAAAATTGATACCTAAAATTTTGAATATTTCAATTTCACCC
* * * * * *
90651 CAAATTATGACCCTCATTCTAAATTTATCCCCAAACTTTTGAACATTTCAATTTCA
1 CAAATTATGACCCTCATTCAAAATTGATACCTAAAATTTTGAATATTTCAATTTCA
90707 TCCAAACCTA
Statistics
Matches: 100, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 100 1.00
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (59 bp):
CAAATTATGACCCTCATTCAAAATTGATACCTAAAATTTTGAATATTTCAATTTCACCC
Found at i:90709 original size:29 final size:28
Alignment explanation
Indices: 90625--90709 Score: 75
Period size: 31 Copynumber: 2.9 Consensus size: 28
90615 TTGATACCTA
*
90625 AAATTTTGAATATTTCAATTTCA-CCCC
1 AAATTTTGAACATTTCAATTTCATCCCC
* * *
90652 AAATTATGACCCTCATTCTAAATTT-ATCCCC
1 AAATTTTGA---ACATT-TCAATTTCATCCCC
90683 AAACTTTTGAACATTTCAATTTCATCC
1 AAA-TTTTGAACATTTCAATTTCATCC
90710 AAACCTATCA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
27 8 0.18
28 6 0.14
29 8 0.18
30 4 0.09
31 13 0.30
32 5 0.11
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (28 bp):
AAATTTTGAACATTTCAATTTCATCCCC
Found at i:98233 original size:21 final size:21
Alignment explanation
Indices: 98207--98246 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
98197 CCCCCTTTGA
*
98207 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
98228 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
98247 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:100523 original size:14 final size:14
Alignment explanation
Indices: 100504--100530 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
100494 GGGGGAGTAA
100504 TTTCTAATTTCAAT
1 TTTCTAATTTCAAT
100518 TTTCTAATTTCAA
1 TTTCTAATTTCAA
100531 ACTTGATTTC
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:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTCTAATTTCAAT
Found at i:104173 original size:27 final size:28
Alignment explanation
Indices: 104143--104202 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
104133 GGAATTGAAG
* *
104143 AAAATTAGG-GATCCAGTTATAAATATA
1 AAAATTAGGAGATACAATTATAAATATA
*
104170 AAAATTAGGAGCTACAATTATAAATATA
1 AAAATTAGGAGATACAATTATAAATATA
104198 AAAAT
1 AAAAT
104203 CAGAGGCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 9 0.31
28 20 0.69
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (28 bp):
AAAATTAGGAGATACAATTATAAATATA
Found at i:109133 original size:3 final size:3
Alignment explanation
Indices: 109125--109177 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
109115 TAAAATATAT
* * * *
109125 TTA TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTT TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
109170 TTA TTA TT
1 TTA TTA TT
109178 TTACAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:110092 original size:7 final size:8
Alignment explanation
Indices: 110075--110122 Score: 60
Period size: 9 Copynumber: 5.6 Consensus size: 8
110065 ATGCTTGAAG
110075 AAAAAGAA
1 AAAAAGAA
110083 AAAAAGAAA
1 AAAAAG-AA
110092 AAAAATGAA
1 AAAAA-GAA
*
110101 AAAATGAA
1 AAAAAGAA
110109 AAAAATGAA
1 AAAAA-GAA
110118 AAAAA
1 AAAAA
110123 AATGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 13 0.37
9 21 0.60
10 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.06
Consensus pattern (8 bp):
AAAAAGAA
Found at i:110095 original size:17 final size:17
Alignment explanation
Indices: 110075--110122 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
110065 ATGCTTGAAG
110075 AAAAAGAAAAAAAGAAA
1 AAAAAGAAAAAAAGAAA
*
110092 AAAAATGAAAAAATGAAA
1 AAAAA-GAAAAAAAGAAA
*
110110 AAAATGAAAAAAA
1 AAAAAGAAAAAAA
110123 AATGAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.06
Consensus pattern (17 bp):
AAAAAGAAAAAAAGAAA
Found at i:110111 original size:19 final size:20
Alignment explanation
Indices: 110099--110136 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
110089 AAAAAAAATG
110099 AAAAAATGAAAAAAATGAAA
1 AAAAAATGAAAAAAATGAAA
110119 AAAAAATG-AAAAAATGAA
1 AAAAAATGAAAAAAATGAA
110137 GAGAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAAAATGAAAAAAATGAAA
Found at i:110121 original size:28 final size:26
Alignment explanation
Indices: 110075--110136 Score: 99
Period size: 28 Copynumber: 2.3 Consensus size: 26
110065 ATGCTTGAAG
110075 AAAAA-GAAAAAAAGAAAAAAAATGA
1 AAAAATGAAAAAAAGAAAAAAAATGA
110100 AAAAATGAAAAAAATGAAAAAAAAATGA
1 AAAAATGAAAAAAA-G-AAAAAAAATGA
110128 AAAAATGAA
1 AAAAATGAA
110137 GAGAGAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.15
26 8 0.24
27 1 0.03
28 20 0.59
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (26 bp):
AAAAATGAAAAAAAGAAAAAAAATGA
Found at i:110130 original size:9 final size:9
Alignment explanation
Indices: 110070--110136 Score: 70
Period size: 8 Copynumber: 7.4 Consensus size: 9
110060 GTATTATGCT
110070 TGAAGAAAAA
1 TGAA-AAAAA
110080 -GAAAAAAA
1 TGAAAAAAA
110088 -GAAAAAAAA
1 TG-AAAAAAA
110097 TG-AAAAAA
1 TGAAAAAAA
110105 TGAAAAAAA
1 TGAAAAAAA
110114 TGAAAAAAAAA
1 TG--AAAAAAA
110125 TG-AAAAAA
1 TGAAAAAAA
110133 TGAA
1 TGAA
110137 GAGAGAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
8 22 0.43
9 19 0.37
10 1 0.02
11 9 0.18
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (9 bp):
TGAAAAAAA
Found at i:111247 original size:136 final size:135
Alignment explanation
Indices: 110998--111479 Score: 714
Period size: 136 Copynumber: 3.5 Consensus size: 135
110988 GGAGGTGAAC
* *
110998 CAACATTTCCAATGGAGATTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
* ** *
111063 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGATGCCTCGCTTG
66 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAC-GCATTTTGAATCAGTGACACCTCACTTG
111128 AGGGAT
130 AGGGAT
* * * *
111134 CAACATTT-CAAGTGAAGAGTTCATAATGAGAAGAACTCATCCGAAAAAAGGAGAAGAAGTTCAT
1 CAACATTTCCAATTG-AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCAT
*
111198 AATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAGTATTTTGAATCAGTGACACCTCACTT
65 AATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAC-GCATTTTGAATCAGTGACACCTCACTT
111263 GAGGGAT
129 GAGGGAT
** *
111270 TGACATTTCCAATTGAGATTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
* * *
111335 ATGAGAAGAGCTTGTTTGACCTATCACTCAATTCACGACATTTTAAATCAGTGACACCTCACTTG
66 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACG-CATTTTGAATCAGTGACACCTCACTTG
111400 AGGGAT
130 AGGGAT
*** * * *
111406 TGGCATTTCCAATTGAGAGTTCTTAATGAGAAGAACTCATGCGACAGAGGGAGAAGAAGTTCACA
1 CAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
111471 ATGAGAAGA
66 ATGAGAAGA
111480 ACTTATTCAA
Statistics
Matches: 315, Mismatches: 28, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
135 5 0.02
136 305 0.97
137 5 0.02
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (135 bp):
CAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGCATTTTGAATCAGTGACACCTCACTTGA
GGGAT
Found at i:111752 original size:3 final size:3
Alignment explanation
Indices: 111744--111796 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
111734 TATATTATAT
* * * *
111744 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTA TTA TGA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
111789 TTA TTA TT
1 TTA TTA TT
111797 TTACAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:112687 original size:8 final size:8
Alignment explanation
Indices: 112688--112742 Score: 101
Period size: 8 Copynumber: 6.8 Consensus size: 8
112678 AAAAATGAAA
112688 AAAAAATG
1 AAAAAATG
112696 AAAAAAATG
1 -AAAAAATG
112705 AAAAAATG
1 AAAAAATG
112713 AAAAAATG
1 AAAAAATG
112721 AAAAAATG
1 AAAAAATG
112729 AAAAAATG
1 AAAAAATG
112737 AAAAAA
1 AAAAAA
112743 AAAAGAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
8 38 0.83
9 8 0.17
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:112753 original size:8 final size:8
Alignment explanation
Indices: 112671--112743 Score: 65
Period size: 8 Copynumber: 8.6 Consensus size: 8
112661 ATGCTTGAAG
112671 AAAAAGAA
1 AAAAAGAA
*
112679 AAAATGAAAA
1 AAAA--AGAA
112689 AAAAATGAA
1 AAAAA-GAA
112698 AAAAATGAA
1 AAAAA-GAA
*
112707 AAAATGAA
1 AAAAAGAA
*
112715 AAAATGAA
1 AAAAAGAA
*
112723 AAAATGAA
1 AAAAAGAA
*
112731 AAAATGAA
1 AAAAAGAA
112739 AAAAA
1 AAAAA
112744 AAAGAAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
8 36 0.62
9 15 0.26
10 7 0.12
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (8 bp):
AAAAAGAA
Found at i:112767 original size:27 final size:27
Alignment explanation
Indices: 112671--112742 Score: 74
Period size: 32 Copynumber: 2.5 Consensus size: 27
112661 ATGCTTGAAG
*
112671 AAAAA-GAAAAAATGAAAAAAAAATGAA
1 AAAAATGAAAAAATGAAAAAAAAAAG-A
112698 AAAAATGAAAAAATGAAAAAATGAAAAAATGA
1 AAAAATGAAAAAATG--AAAA--AAAAAA-GA
112730 AAAAATGAAAAAA
1 AAAAATGAAAAAA
112743 AAAAGAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 5 0.13
28 9 0.24
30 4 0.11
32 19 0.50
33 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (27 bp):
AAAAATGAAAAAATGAAAAAAAAAAGA
Found at i:114106 original size:136 final size:135
Alignment explanation
Indices: 113621--114113 Score: 711
Period size: 136 Copynumber: 3.6 Consensus size: 135
113611 ATGTGAACCA
*
113621 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* * * * * *
113686 GAGAAGAGCTTGTTCAACCTATCACTCGATTCACGGCATTTCGAATCAGTGATGCCTCGCTTGAG
66 GAGAAGAGCTTATTCGACCTATCACTCGATTCA-GACATTTTGAATCAGTGATACCTCACTTGAG
**
113751 GGATCA
130 GGATTG
* * *
113757 ACATTTCC-AGTGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAAGGAGAAGAAGTTCATAA
1 ACATTTCCAATTG-AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
* * * *
113821 TGAGAAGAGC-TAGTTCGACCTATTACTCGATTCACAGTATTTTGAATCAGTGACACCTCACTTG
65 TGAGAAGAGCTTA-TTCGACCTATCACTCGATTCAGA-CATTTTGAATCAGTGATACCTCACTTG
113885 AGGGATTG
128 AGGGATTG
*
113893 ACATTTCCAATTGAGAGTTCATAATTAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* *
113958 GAGAAGAGCTTATTTGACCTATCACTCGATTCATGACATTTTAAATCAGTGATACCTCACTTGAG
66 GAGAAGAGCTTATTCGACCTATCACTCGATTCA-GACATTTTGAATCAGTGATACCTCACTTGAG
114023 GGATTG
130 GGATTG
* * *
114029 ATATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATGCGACAGAGGGAGAATAAGTTCATAAT
1 ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* *
114094 GAGAAGAACTTATTCAACCT
66 GAGAAGAGCTTATTCGACCT
114114 TGGTTTCAAG
Statistics
Matches: 318, Mismatches: 33, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
135 3 0.01
136 309 0.97
137 6 0.02
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (135 bp):
ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
GAGAAGAGCTTATTCGACCTATCACTCGATTCAGACATTTTGAATCAGTGATACCTCACTTGAGG
GATTG
Done.