Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007892.1 Hibiscus syriacus cultivar Beakdansim tig00110274_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: 177259
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:665 original size:33 final size:33
Alignment explanation
Indices: 621--689 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
611 CATCACCATA
*
621 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
654 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
687 TTC
1 TTC
690 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:6334 original size:33 final size:33
Alignment explanation
Indices: 6255--6358 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
6245 ATACAATCTG
* *
6255 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
6291 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
6324 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
6357 TC
1 TC
6359 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:7309 original size:24 final size:25
Alignment explanation
Indices: 7263--7311 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
7253 ATTTTGTTAA
7263 GGCATCAGAAGAGCCTTACATCAAGT
1 GGCATCAGAAGA-CCTTACATCAAGT
7289 GGCATCAGAAGA-CTTACATCAAG
1 GGCATCAGAAGACCTTACATCAAG
7312 CGGTAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.48
26 12 0.52
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.18
Consensus pattern (25 bp):
GGCATCAGAAGACCTTACATCAAGT
Found at i:7462 original size:27 final size:28
Alignment explanation
Indices: 7420--7482 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
7410 AGAAAATCAG
*
7420 AAAAGAAATTGAAGCACTCCAAAAGAAA
1 AAAAGAAATTGAAGCACTCAAAAAGAAA
* * *
7448 AAAAGAAATT-CAGCATTCAAAAAGAAG
1 AAAAGAAATTGAAGCACTCAAAAAGAAA
7475 AAAAGAAA
1 AAAAGAAA
7483 AGAAAAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.63, C:0.11, G:0.14, T:0.11
Consensus pattern (28 bp):
AAAAGAAATTGAAGCACTCAAAAAGAAA
Found at i:11733 original size:26 final size:26
Alignment explanation
Indices: 11679--11728 Score: 86
Period size: 24 Copynumber: 2.0 Consensus size: 26
11669 AATTTGTTAA
11679 GGCATCAGAAGAGCCTTACATCAAGT
1 GGCATCAGAAGAGCCTTACATCAAGT
11705 GGCATCAG-A-AGCCTTACATCAAGT
1 GGCATCAGAAGAGCCTTACATCAAGT
11729 TTGGCTGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 15 0.62
25 1 0.04
26 8 0.33
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (26 bp):
GGCATCAGAAGAGCCTTACATCAAGT
Found at i:17685 original size:413 final size:413
Alignment explanation
Indices: 16918--17748 Score: 1653
Period size: 413 Copynumber: 2.0 Consensus size: 413
16908 TCCATCTTTC
16918 GAATGGATTACGGACAGCAAAGGAGGAATCCATTTCATACTCGTTTTCATGTGAATGATAAAGTA
1 GAATGGATTACGGACAGCAAAGGAGGAATCCATTTCATACTCGTTTTCATGTGAATGATAAAGTA
*
16983 TGCCTTGTAGCCATTGATGGTGGTAGTTGTGCAAATCTTGCAAGCACATACATGGTTGAGAAGTT
66 TGCCTTGTAGCCATTGATGATGGTAGTTGTGCAAATCTTGCAAGCACATACATGGTTGAGAAGTT
17048 GGGGCTTATAACATTCAAACATCCCAGTCCATATGTTTTGCAAGGATTAAATGAAGATGAAGAGT
131 GGGGCTTATAACATTCAAACATCCCAGTCCATATGTTTTGCAAGGATTAAATGAAGATGAAGAGT
17113 TAGAAGTCATGGAGCAAGTACGTGTGTCATTTTCAATTGGGGGATATAAAGATGAAGTTTTGTGT
196 TAGAAGTCATGGAGCAAGTACGTGTGTCATTTTCAATTGGGGGATATAAAGATGAAGTTTTGTGT
17178 GATGTTGTTTCTATGAATTCAAGCCATCTACTCCTTGGACGTCATTGGCAGTTCGATAAACGAGC
261 GATGTTGTTTCTATGAATTCAAGCCATCTACTCCTTGGACGTCATTGGCAGTTCGATAAACGAGC
17243 ATTCTATGATGGGTTCTCCAACAAATATTCATTCAAACACCAAGGGAGAAAGATCGTGTTGGTTC
326 ATTCTATGATGGGTTCTCCAACAAATATTCATTCAAACACCAAGGGAGAAAGATCGTGTTGGTTC
17308 CAATGTGCCCAAATCAAGTCCAT
391 CAATGTGCCCAAATCAAGTCCAT
17331 GAATGGATTACGGACAGCAAAGGAGGAATCCATTTCATACTCGTTTTCATGTGAATGATAAAGTA
1 GAATGGATTACGGACAGCAAAGGAGGAATCCATTTCATACTCGTTTTCATGTGAATGATAAAGTA
17396 TGCCTTGTAGCCATTGATGATGGTAGTTGTGCAAATCTTGCAAGCACATACATGGTTGAGAAGTT
66 TGCCTTGTAGCCATTGATGATGGTAGTTGTGCAAATCTTGCAAGCACATACATGGTTGAGAAGTT
17461 GGGGCTTATAACATTCAAACATCCCAGTCCATATGTTTTGCAAGGATTAAATGAAGATGAAGAGT
131 GGGGCTTATAACATTCAAACATCCCAGTCCATATGTTTTGCAAGGATTAAATGAAGATGAAGAGT
17526 TAGAAGTCATGGAGCAAGTACGTGTGTCATTTTCAATTGGGGGATATAAAGATGAAGTTTTGTGT
196 TAGAAGTCATGGAGCAAGTACGTGTGTCATTTTCAATTGGGGGATATAAAGATGAAGTTTTGTGT
17591 GATGTTGTTTCTATGAATTCAAGCCATCTACTCCTTGGACGTCATTGGCAGTTCGATAAACGAGC
261 GATGTTGTTTCTATGAATTCAAGCCATCTACTCCTTGGACGTCATTGGCAGTTCGATAAACGAGC
17656 ATTCTATGATGGGTTCTCCAACAAATATTCATTCAAACACCAAGGGAGAAAGATCGTGTTGGTTC
326 ATTCTATGATGGGTTCTCCAACAAATATTCATTCAAACACCAAGGGAGAAAGATCGTGTTGGTTC
17721 CAATGTGCCCAAATCAAGTCCAT
391 CAATGTGCCCAAATCAAGTCCAT
17744 GAATG
1 GAATG
17749 CCAAGTTATC
Statistics
Matches: 417, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
413 417 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (413 bp):
GAATGGATTACGGACAGCAAAGGAGGAATCCATTTCATACTCGTTTTCATGTGAATGATAAAGTA
TGCCTTGTAGCCATTGATGATGGTAGTTGTGCAAATCTTGCAAGCACATACATGGTTGAGAAGTT
GGGGCTTATAACATTCAAACATCCCAGTCCATATGTTTTGCAAGGATTAAATGAAGATGAAGAGT
TAGAAGTCATGGAGCAAGTACGTGTGTCATTTTCAATTGGGGGATATAAAGATGAAGTTTTGTGT
GATGTTGTTTCTATGAATTCAAGCCATCTACTCCTTGGACGTCATTGGCAGTTCGATAAACGAGC
ATTCTATGATGGGTTCTCCAACAAATATTCATTCAAACACCAAGGGAGAAAGATCGTGTTGGTTC
CAATGTGCCCAAATCAAGTCCAT
Found at i:20655 original size:21 final size:20
Alignment explanation
Indices: 20627--20676 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
20617 TTTGATAACA
20627 TTCC-TTTCCATTT-CTATTCT
1 TTCCATTTCCATTTACT-TT-T
20647 TTCCATTTCCATTTACTTTT
1 TTCCATTTCCATTTACTTTT
20667 TTCTCATTTC
1 TTC-CATTTC
20677 TTAATTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.30
21 17 0.63
22 2 0.07
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (20 bp):
TTCCATTTCCATTTACTTTT
Found at i:21112 original size:65 final size:65
Alignment explanation
Indices: 20982--21105 Score: 212
Period size: 65 Copynumber: 1.9 Consensus size: 65
20972 TGACCAGCCC
*
20982 CCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCTCTCCCTATTCGACCAAG
1 CCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGCTCTCTCCCTATTCGACCAAG
* * *
21047 CCATGTGCCTTGCATGTGGTTTATTTAGGTGCCAAGATGAAGAGCTCTCTCCCTATTCG
1 CCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGCTCTCTCCCTATTCG
21106 GGCAAGCATC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (65 bp):
CCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGCTCTCTCCCTATTCGACCAAG
Found at i:21960 original size:14 final size:14
Alignment explanation
Indices: 21941--21976 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
21931 CTCAAAGAGC
21941 AAGAAAA-AAAAGAA
1 AAGAAAAGAAAAG-A
21955 AAGAAAAGAAAAGA
1 AAGAAAAGAAAAGA
21969 AAGAAAAG
1 AAGAAAAG
21977 TTGGAAGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAAGA
Found at i:21973 original size:4 final size:5
Alignment explanation
Indices: 21941--21976 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
21931 CTCAAAGAGC
21941 AAGAA AA-AA AAGAA AAGAA AAGAA AAG-A AAGAA AAG
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAG
21977 TTGGAAGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:24626 original size:11 final size:13
Alignment explanation
Indices: 24594--24623 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
24584 TGGCCAAAGA
24594 TGAAAAGGTATGT
1 TGAAAAGGTATGT
24607 TGAAAAGGTATG-
1 TGAAAAGGTATGT
24619 TGAAA
1 TGAAA
24624 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:28251 original size:60 final size:60
Alignment explanation
Indices: 28141--28253 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
28131 TGGACCATAC
* ** * *
28141 CACACGTTGGGATAGTTTGGTGGAGCATTTTGAAGACATATACAGGTCACAAACAGATGA
1 CACACGTTGGGACAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAACAGATGA
* **
28201 CACACGTTGGGACAACTTGGTGGAGCATTTGGGAGACATATATTGCTCACAAA
1 CACACGTTGGGACAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAA
28254 TAGCTCACAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.25
Consensus pattern (60 bp):
CACACGTTGGGACAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAACAGATGA
Found at i:35732 original size:8 final size:8
Alignment explanation
Indices: 35719--35749 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
35709 CTTTGAATGT
35719 ACTTTGCA
1 ACTTTGCA
35727 ACTTTGCA
1 ACTTTGCA
35735 ACTTTGCA
1 ACTTTGCA
35743 ACTTTGC
1 ACTTTGC
35750 TTCACTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39
Consensus pattern (8 bp):
ACTTTGCA
Found at i:35846 original size:12 final size:12
Alignment explanation
Indices: 35820--35853 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 12
35810 TGTAGGAGTC
35820 TTTCTCTTTCTT
1 TTTCTCTTTCTT
35832 TTTCTTCTTTCTT
1 TTTC-TCTTTCTT
35845 TTTCTCTTT
1 TTTCTCTTT
35854 TGTTGCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTCTTTCTT
Found at i:46447 original size:15 final size:17
Alignment explanation
Indices: 46424--46457 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
46414 TTAAGATATG
46424 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
46440 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
46456 TT
1 TT
46458 AGGACCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:51415 original size:30 final size:31
Alignment explanation
Indices: 51381--51440 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
51371 CTTAGCCTTA
**
51381 TATTATGCTTACATATGTTTTAGAT-TCATT
1 TATTATGCTTACATATCATTTAGATATCATT
* *
51411 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGCTTACATATCATTTAGATATCAT
51441 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (31 bp):
TATTATGCTTACATATCATTTAGATATCATT
Found at i:52356 original size:19 final size:20
Alignment explanation
Indices: 52330--52382 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
52320 TTCGGCCAAG
* *
52330 AGCATGTATCTTCAT-TAAA
1 AGCATGTATTTTCATCAAAA
*
52349 ATCATGTATTTTCATCAAAA
1 AGCATGTATTTTCATCAAAA
52369 AGCATGTATTTTCA
1 AGCATGTATTTTCA
52383 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (20 bp):
AGCATGTATTTTCATCAAAA
Found at i:53666 original size:89 final size:91
Alignment explanation
Indices: 53540--53720 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 91
53530 CCTAGAACAC
*
53540 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
53605 AA-AGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * *
53630 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
53694 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
53720 C
1 C
53721 ATCATTTCCC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
89 40 0.49
90 42 0.51
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:55040 original size:23 final size:26
Alignment explanation
Indices: 55014--55068 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 26
55004 AAATCCAGCA
55014 AAGAAAATT-AAAGCACTCAAA-A-G
1 AAGAAAATTGAAAGCACTCAAAGAGG
55037 AAG-AAATTGAAAGCACTCAAAGAGG
1 AAGAAAATTGAAAGCACTCAAAGAGG
55062 AAGAAAA
1 AAGAAAA
55069 AAAGAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.18
23 15 0.54
24 1 0.04
25 4 0.14
26 3 0.11
ACGTcount: A:0.60, C:0.11, G:0.18, T:0.11
Consensus pattern (26 bp):
AAGAAAATTGAAAGCACTCAAAGAGG
Found at i:55078 original size:5 final size:5
Alignment explanation
Indices: 55068--55096 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
55058 GAGGAAGAAA
55068 AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
55097 TTGGAAGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:65096 original size:19 final size:21
Alignment explanation
Indices: 65053--65104 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
65043 GAAACCCCTT
65053 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
65074 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
65093 TGAAGATACATG
1 TGAAAATACATG
65105 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:70833 original size:30 final size:31
Alignment explanation
Indices: 70798--70857 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
70788 CTTAGCTTTA
**
70798 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
70828 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
70858 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:72258 original size:19 final size:21
Alignment explanation
Indices: 72234--72285 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
72224 CGGCCAAGAG
*
72234 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
72253 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
72274 CATGTATTTTCA
1 CATGTATTTTCA
72286 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:72716 original size:15 final size:15
Alignment explanation
Indices: 72696--72726 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
72686 CAGCCATCTC
*
72696 TTTCATTTCTTTTTA
1 TTTCATTTCCTTTTA
72711 TTTCATTTCCTTTTA
1 TTTCATTTCCTTTTA
72726 T
1 T
72727 ATATATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCATTTCCTTTTA
Found at i:75534 original size:17 final size:18
Alignment explanation
Indices: 75512--75548 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
75502 ACCTATAGTT
*
75512 CACATCTTTATA-ATATG
1 CACATCATTATATATATG
75529 CACATCATTATATATATG
1 CACATCATTATATATATG
75547 CA
1 CA
75549 TTATATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (18 bp):
CACATCATTATATATATG
Found at i:76378 original size:19 final size:21
Alignment explanation
Indices: 76354--76405 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
76344 CGGCCAAGAG
*
76354 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
76373 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
*
76394 CACGTATTTTCA
1 CATGTATTTTCA
76406 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 6 0.21
21 12 0.41
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:77717 original size:18 final size:18
Alignment explanation
Indices: 77682--77727 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
77672 CGGCCAAGAG
*
77682 CATGTATCTTCATTAAAAT
1 CATGTAT-TTCATCAAAAT
77701 CATGTATTTCATCAAAAT
1 CATGTATTTCATCAAAAT
77719 CATGTATTT
1 CATGTATTT
77728 TCAAAGGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (18 bp):
CATGTATTTCATCAAAAT
Found at i:78481 original size:12 final size:12
Alignment explanation
Indices: 78462--78498 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
78452 AGAAAAGACT
78462 AAAG-AAGAAAA
1 AAAGAAAGAAAA
78473 AAAGAAAGAAAAA
1 AAAGAAAG-AAAA
78486 AAAGAAAGAAAA
1 AAAGAAAGAAAA
78498 A
1 A
78499 GACAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 4 0.17
12 8 0.33
13 12 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:78490 original size:21 final size:22
Alignment explanation
Indices: 78449--78521 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 22
78439 GTGCAAAAAG
* *
78449 AAAAGAAAAGAC-TAAAGAAGA
1 AAAAAAAAAGACAAAAAGAAGA
78470 AAAAAAGAAAGA-AAAAA-AAG-
1 AAAAAA-AAAGACAAAAAGAAGA
*
78490 AAAGAAAAAGACAAAAAGAAGA
1 AAAAAAAAAGACAAAAAGAAGA
78512 ATAAAAAAAA
1 A-AAAAAAAA
78522 ATCAAAAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.12
20 10 0.24
21 11 0.26
22 9 0.21
23 7 0.17
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (22 bp):
AAAAAAAAAGACAAAAAGAAGA
Found at i:78534 original size:42 final size:40
Alignment explanation
Indices: 78443--78535 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 40
78433 ACTGGAGTGC
*
78443 AAAAAGA-AAAGAAAAGACTAAAGAAGAAAAAAAGAAAGA
1 AAAAAGAGAAAGAAAAGACAAAAGAAGAAAAAAAGAAAGA
*
78482 AAAAAAAGAAAGAAAAAGACAAAAAGAAGAATAAAAA-AAA-A
1 AAAAAGAGAAAG-AAAAGAC-AAAAGAAGAA-AAAAAGAAAGA
*
78523 TCAAAAGAGAAAG
1 -AAAAAGAGAAAG
78536 CAAGCCAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
39 6 0.13
40 4 0.09
41 8 0.18
42 22 0.49
43 5 0.11
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (40 bp):
AAAAAGAGAAAGAAAAGACAAAAGAAGAAAAAAAGAAAGA
Found at i:81028 original size:30 final size:31
Alignment explanation
Indices: 80992--81051 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
80982 CTTAGCTTTA
**
80992 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
81022 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
81052 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:81971 original size:19 final size:20
Alignment explanation
Indices: 81947--81997 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
81937 CGGCCAAGAG
* *
81947 CATGTATATTCATTAAAA-T
1 CATGTATTTTCATCAAAAGT
81966 CATGTATTTTCATCAAAAGT
1 CATGTATTTTCATCAAAAGT
81986 CATGTATTTTCA
1 CATGTATTTTCA
81998 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAGT
Found at i:85940 original size:33 final size:33
Alignment explanation
Indices: 85898--85966 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
85888 GTTGATGAAT
*
85898 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
85931 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
85964 GAA
1 GAA
85967 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:89982 original size:33 final size:33
Alignment explanation
Indices: 89940--90008 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
89930 GTTGATGAAT
*
89940 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
89973 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
90006 GAA
1 GAA
90009 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:111456 original size:32 final size:33
Alignment explanation
Indices: 111395--111461 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
111385 ACAACATTAA
* *
111395 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
111427 AAGAAAGTAAATGA-TAAGAA-AGAAAATGGATAG
1 AAGAAAG-AAATGATTAA-AATAGAAAATGGATAG
111460 AA
1 AA
111462 ATGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:111974 original size:19 final size:19
Alignment explanation
Indices: 111950--111999 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
111940 GAAACCCCTT
**
111950 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTAAA
111969 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
111988 TGAAGATACATG
1 TGAAAATACATG
112000 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:112831 original size:19 final size:21
Alignment explanation
Indices: 112788--112839 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
112778 GAAACCCCTT
*
112788 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTGTAAA
112809 TGAAAATACATGA-TTGT-AA
1 TGAAAATACATGACTTGTAAA
*
112828 TGAAGATACATG
1 TGAAAATACATG
112840 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
TGAAAATACATGACTTGTAAA
Found at i:116868 original size:19 final size:21
Alignment explanation
Indices: 116825--116876 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
116815 GAAACCCCTT
*
116825 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTGTAAA
116846 TGAAAATACATGA-TTGT-AA
1 TGAAAATACATGACTTGTAAA
*
116865 TGAAGATACATG
1 TGAAAATACATG
116877 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
TGAAAATACATGACTTGTAAA
Found at i:126194 original size:11 final size:11
Alignment explanation
Indices: 126162--126204 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
126152 ACTTTCTTCA
126162 CTTTTCTTTTT
1 CTTTTCTTTTT
**
126173 CTTTGATTTTT
1 CTTTTCTTTTT
*
126184 TTTCTTCTTTTT
1 CTT-TTCTTTTT
126196 CTTTTCTTT
1 CTTTTCTTT
126205 CTTAGGCACT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:126258 original size:15 final size:16
Alignment explanation
Indices: 126238--126268 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
126228 AGAAGTATTC
126238 TTTTTTCTT-TTTCTT
1 TTTTTTCTTCTTTCTT
126253 TTTTTTCTTCTTTCTT
1 TTTTTTCTTCTTTCTT
126269 GTTGCTTTTG
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTTCTTTCTT
Found at i:127076 original size:19 final size:20
Alignment explanation
Indices: 127029--127079 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
127019 GAAACCCCTT
**
127029 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
127049 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
127068 TGAAGATACATG
1 TGAAAATACATG
127080 CTCTTGGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:130220 original size:28 final size:28
Alignment explanation
Indices: 130188--130322 Score: 109
Period size: 28 Copynumber: 4.9 Consensus size: 28
130178 TCGTGGGGTT
*
130188 CATAACACCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* *
130216 CATAACAGCATATTTATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* * * * ** **
130244 -TTAA-ATTCACGTGCACTCA---CATTCA
1 CATAACA-GCATGTTCA-TCATTTGTTTTG
*
130269 CATAACATCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
130297 CATAACAGCATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
130323 AGTTAATTCA
Statistics
Matches: 79, Mismatches: 21, Indels: 14
0.69 0.18 0.12
Matches are distributed among these distances:
25 5 0.06
26 11 0.14
27 8 0.10
28 55 0.70
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.42
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:130328 original size:81 final size:80
Alignment explanation
Indices: 130188--130349 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 80
130178 TCGTGGGGTT
* *
130188 CATAACACCATGTTCATCATTTGTTTTGCATAACAGCATATTTATCATTTGTTTTGTTAAATTCA
1 CATAACACCATGTTCATCATTTGTTTTGCATAACAGCATATTCATCATTTGTTTAGTT-AATTCA
*
130253 CGTGCACTCACATTCA
65 CGTGCACCCACATTCA
* *
130269 CATAACATCATGTTCATCATTTGTTTTGCATAACAGCATGTTCATCATTTGTTTAGTTAATTCAC
1 CATAACACCATGTTCATCATTTGTTTTGCATAACAGCATATTCATCATTTGTTTAGTTAATTCAC
130334 GTGCACCCACATTCA
66 GTGCACCCACATTCA
130349 C
1 C
130350 TTTACAACAT
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 22 0.29
81 54 0.71
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (80 bp):
CATAACACCATGTTCATCATTTGTTTTGCATAACAGCATATTCATCATTTGTTTAGTTAATTCAC
GTGCACCCACATTCA
Found at i:131308 original size:26 final size:26
Alignment explanation
Indices: 131269--131326 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
131259 TGAACGTCTA
*
131269 AGGTTCGGGTTTATACTCTTTAGTAT
1 AGGTTCGGGCTTATACTCTTTAGTAT
*
131295 AGGTTTGGGCTTATACTCTTTAGTAT
1 AGGTTCGGGCTTATACTCTTTAGTAT
131321 AGGTTC
1 AGGTTC
131327 TTCCTTGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (26 bp):
AGGTTCGGGCTTATACTCTTTAGTAT
Found at i:131637 original size:24 final size:24
Alignment explanation
Indices: 131588--131645 Score: 98
Period size: 25 Copynumber: 2.4 Consensus size: 24
131578 ATTCATCTTG
131588 AAAAAAAAAATTCCGAAAATTAAA
1 AAAAAAAAAATTCCGAAAATTAAA
131612 AAAAAAACAAATTCCGAAAATTAAA
1 AAAAAAA-AAATTCCGAAAATTAAA
*
131637 AAAAGAAAA
1 AAAAAAAAA
131646 GAAAAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 9 0.28
25 23 0.72
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (24 bp):
AAAAAAAAAATTCCGAAAATTAAA
Found at i:140595 original size:21 final size:22
Alignment explanation
Indices: 140571--140618 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
140561 TTTTTTGAAA
*
140571 TTTTGGCTCTTTTTTTG-TTTT
1 TTTTGCCTCTTTTTTTGCTTTT
*
140592 TTTTGCCTTTTTTTTTGCCTTTT
1 TTTTGCCTCTTTTTTTG-CTTTT
140615 TTTT
1 TTTT
140619 TTTTTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.77
Consensus pattern (22 bp):
TTTTGCCTCTTTTTTTGCTTTT
Found at i:140617 original size:11 final size:11
Alignment explanation
Indices: 140580--140618 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
140570 ATTTTGGCTC
140580 TTTTTTTG--T
1 TTTTTTTGCCT
140589 TTTTTTTGCCTT
1 TTTTTTTGCC-T
140601 TTTTTTTGCCT
1 TTTTTTTGCCT
140612 TTTTTTT
1 TTTTTTT
140619 TTTTTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.30
11 8 0.30
12 11 0.41
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:140620 original size:13 final size:12
Alignment explanation
Indices: 140588--140619 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
140578 TCTTTTTTTG
140588 TTTTTTTTGCCT
1 TTTTTTTTGCCT
140600 TTTTTTTTGCCT
1 TTTTTTTTGCCT
140612 TTTTTTTT
1 TTTTTTTT
140620 TTTTTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTTGCCT
Found at i:140954 original size:186 final size:189
Alignment explanation
Indices: 140640--141016 Score: 708
Period size: 186 Copynumber: 2.0 Consensus size: 189
140630 AAAAATAGCA
140640 ACTAACAAGAGGATTTAAATCTAAATTAAAATTAAATAAAAAGAACCTGAAACGCTGAATCTTTT
1 ACTAACAAGAGGATTTAAATCTAAATTAAAATTAAATAAAAAGAACCTGAAACGCTGAATCTTTT
140705 GTGAACTAGCTCCGTTGGGGTACCTTGACGATTTTGTGTGCAAGAACAAGCAAAATTGCTTGCTT
66 GTGAACTAGCTCCGTTGGGGTACCTTGACGATTTTGTGTGCAAGAACAAGCAAAATTGCTTGCTT
140770 CTTTCCAAGAATCGGCCCAGCTCTGATACCAATTGATA-GGGAAGC-GT-GGCGGATTG
131 CTTTCCAAGAATCGGCCCAGCTCTGATACCAATTGATAGGGGAAGCGGTGGGCGGATTG
140826 ACTAACAAGAAGGATTTAAATCTAAATTAAAATTAAAT-AAAAGAACCTGAAACGCTGAATCTTT
1 ACTAACAAG-AGGATTTAAATCTAAATTAAAATTAAATAAAAAGAACCTGAAACGCTGAATCTTT
140890 TGTGAACTAGCTCCGTTGGGGTACCTTGACGATTTTGTGTGCAAGAACAAGCAAAATTGCTTGCT
65 TGTGAACTAGCTCCGTTGGGGTACCTTGACGATTTTGTGTGCAAGAACAAGCAAAATTGCTTGCT
140955 TCTTTCCAAGAATCGGCCCAGCTCTGATACCAATTGATAGGGGGAAGCGGTGGGCGGATTG
130 TCTTTCCAAGAATCGGCCCAGCTCTGATACCAATTGATA-GGGGAAGCGGTGGGCGGATTG
141016 A
1 A
141017 TGAACGTTGC
Statistics
Matches: 186, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
186 139 0.75
187 28 0.15
188 7 0.04
189 2 0.01
190 10 0.05
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (189 bp):
ACTAACAAGAGGATTTAAATCTAAATTAAAATTAAATAAAAAGAACCTGAAACGCTGAATCTTTT
GTGAACTAGCTCCGTTGGGGTACCTTGACGATTTTGTGTGCAAGAACAAGCAAAATTGCTTGCTT
CTTTCCAAGAATCGGCCCAGCTCTGATACCAATTGATAGGGGAAGCGGTGGGCGGATTG
Found at i:141617 original size:42 final size:48
Alignment explanation
Indices: 141570--141674 Score: 132
Period size: 50 Copynumber: 2.3 Consensus size: 48
141560 ATAACTAAAG
*
141570 AATAAAATATTAATAA-CT-AAACA-TGTTTTAA-C-CC-TAATTCCT
1 AATAAAATAATAATAACCTAAAACATTGTTTTAACCACCTTAATTCCT
*
141612 AATAAAATAATAATAACCTAAAAATATTGTTTTAACCAACCTTAATTCCT
1 AATAAAATAATAATAACCT-AAAACATTGTTTTAACC-ACCTTAATTCCT
141662 AATAAAATAATAA
1 AATAAAATAATAA
141675 ATCTGATCCT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
42 15 0.28
43 2 0.04
45 4 0.08
46 8 0.15
47 1 0.02
49 2 0.04
50 21 0.40
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.33
Consensus pattern (48 bp):
AATAAAATAATAATAACCTAAAACATTGTTTTAACCACCTTAATTCCT
Found at i:149807 original size:28 final size:28
Alignment explanation
Indices: 149774--149907 Score: 118
Period size: 28 Copynumber: 4.9 Consensus size: 28
149764 TCGTGGGGTT
149774 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* *
149802 CATAACAGCATATTTATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* * * ** **
149830 --TAA-ATTCACGTGCACTCA---CATTCA
1 CATAACA-GCATGTTCA-TCATTTGTTTTG
149854 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
*
149882 CATAACAACATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
149908 AGTTAATTCA
Statistics
Matches: 79, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
24 2 0.03
25 4 0.05
26 16 0.20
27 4 0.05
28 53 0.67
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:149874 original size:80 final size:80
Alignment explanation
Indices: 149774--149934 Score: 268
Period size: 80 Copynumber: 2.0 Consensus size: 80
149764 TCGTGGGGTT
* * *
149774 CATAACAGCATGTTCATCATTTGTTTTGCATAACAGCATATTTATCATTTGTTTTGTAAATTCAC
1 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
*
149839 GTGCACTCACATTCA
66 GTGCACCCACATTCA
* *
149854 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATGTTCATCATTTGTTTAGTTAATTCAC
1 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
149919 GTGCACCCACATTCA
66 GTGCACCCACATTCA
149934 C
1 C
149935 TTTACAACAT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.39
Consensus pattern (80 bp):
CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
GTGCACCCACATTCA
Found at i:151660 original size:19 final size:20
Alignment explanation
Indices: 151636--151687 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
151626 CGGCCAAGAG
*
151636 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
151655 CATGTATTTTCATTAAAAAAT
1 CATGTATTTTCATT-AAAAAT
151676 CATGTATTTTCA
1 CATGTATTTTCA
151688 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:152253 original size:11 final size:11
Alignment explanation
Indices: 152229--152273 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
152219 TTGGTGCTGG
152229 AAACAAGATAA
1 AAACAAGATAA
* *
152240 AAATAAGATTA
1 AAACAAGATAA
152251 AAACAAGATAA
1 AAACAAGATAA
152262 AGAA-AAGATAA
1 A-AACAAGATAA
152273 A
1 A
152274 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:152257 original size:22 final size:22
Alignment explanation
Indices: 152229--152270 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
152219 TTGGTGCTGG
152229 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
152251 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
152271 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:155857 original size:11 final size:10
Alignment explanation
Indices: 155831--155856 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
155821 AAATTTTGGC
155831 TTTTTTGTTT
1 TTTTTTGTTT
155841 TTTTTTGTTT
1 TTTTTTGTTT
155851 TTTTTT
1 TTTTTT
155857 TTGCCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:156239 original size:10 final size:10
Alignment explanation
Indices: 156207--156250 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
156197 TTGATGTTGG
156207 AAACAAGATA
1 AAACAAGATA
*
156217 AAATAAGATTA
1 AAACAAGA-TA
156228 AAACAAGATA
1 AAACAAGATA
*
156238 AAGAAAAGATA
1 AA-ACAAGATA
156249 AA
1 AA
156251 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 11 0.38
11 18 0.62
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (10 bp):
AAACAAGATA
Found at i:156250 original size:21 final size:21
Alignment explanation
Indices: 156207--156247 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
156197 TTGATGTTGG
*
156207 AAACAAGATAAAATAAGATTA
1 AAACAAGATAAAAAAAGATTA
156228 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAA-AAAAGAT
156248 AAATGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (21 bp):
AAACAAGATAAAAAAAGATTA
Found at i:156775 original size:22 final size:23
Alignment explanation
Indices: 156734--156776 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
156724 CAACCTTAAT
156734 TCCTAATAAAATAATAAATCAGA
1 TCCTAATAAAATAATAAATCAGA
* *
156757 TCCTAA-AAGATAATTAATCA
1 TCCTAATAAAATAATAAATCA
156777 TCCTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (23 bp):
TCCTAATAAAATAATAAATCAGA
Found at i:159665 original size:13 final size:12
Alignment explanation
Indices: 159646--159742 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
159636 TTATTGGCGT
159646 GATATGGTGATG
1 GATATGGTGATG
159658 GAATATGGTGAT-
1 G-ATATGGTGATG
*
159670 GATATAGGCG-T-
1 GATAT-GGTGATG
159681 GATAATGGTGATG
1 GAT-ATGGTGATG
159694 GACTATGGTGAT-
1 GA-TATGGTGATG
*
159706 GATATAGGCG-T-
1 GATAT-GGTGATG
*
159717 GATAATGGAGATG
1 GAT-ATGGTGATG
159730 GATTATGGTGATG
1 GA-TATGGTGATG
159743 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:159701 original size:36 final size:36
Alignment explanation
Indices: 159631--159743 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
159621 AATGGAAGGA
* *
159631 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
159666 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
159702 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
159738 TGATGA
1 TGATGA
159744 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:164154 original size:33 final size:33
Alignment explanation
Indices: 164112--164180 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
164102 GTTGATGAAT
*
164112 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
164145 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
164178 GAA
1 GAA
164181 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:164185 original size:13 final size:12
Alignment explanation
Indices: 164166--164262 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
164156 TTATTGGCGT
164166 GATATGGTGATG
1 GATATGGTGATG
164178 GAATATGGTGAT-
1 G-ATATGGTGATG
*
164190 GATATAGGCG-T-
1 GATAT-GGTGATG
164201 GATAATGGTGATG
1 GAT-ATGGTGATG
164214 GACTATGGTGAT-
1 GA-TATGGTGATG
*
164226 GATATAGGCG-T-
1 GATAT-GGTGATG
*
164237 GATAATGGAGATG
1 GAT-ATGGTGATG
164250 GATTATGGTGATG
1 GA-TATGGTGATG
164263 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:164221 original size:36 final size:36
Alignment explanation
Indices: 164151--164263 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
164141 AATGGAAGGA
* *
164151 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
164186 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
164222 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
164258 TGATGA
1 TGATGA
164264 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:169390 original size:20 final size:21
Alignment explanation
Indices: 169367--169420 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
169357 TTTTTTGAAA
*
169367 TTTTGGCTTTTTTGGC-TCTT
1 TTTTGGCTTTTTTGCCTTCTT
* * *
169387 TTTTTGTTTTTTTGCCTTTTT
1 TTTTGGCTTTTTTGCCTTCTT
*
169408 TTTTGCCTTTTTT
1 TTTTGGCTTTTTT
169421 TGTTTTTTTG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.74
Consensus pattern (21 bp):
TTTTGGCTTTTTTGCCTTCTT
Found at i:169396 original size:8 final size:8
Alignment explanation
Indices: 169385--169446 Score: 61
Period size: 8 Copynumber: 7.0 Consensus size: 8
169375 TTTTTGGCTC
169385 TTTTTTTG
1 TTTTTTTG
169393 TTTTTTTG
1 TTTTTTTG
169401 CCTTTTTTTTTG
1 ----TTTTTTTG
169413 CCTTTTTTTG
1 --TTTTTTTG
169423 TTTTTTTG
1 TTTTTTTG
*
169431 TTTTTTTA
1 TTTTTTTG
169439 TTTTTTTG
1 TTTTTTTG
169447 AAAAAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 30 0.65
10 8 0.17
12 8 0.17
ACGTcount: A:0.02, C:0.06, G:0.10, T:0.82
Consensus pattern (8 bp):
TTTTTTTG
Found at i:169396 original size:19 final size:18
Alignment explanation
Indices: 169374--169409 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
169364 AAATTTTGGC
169374 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
*
169393 TTTTTTTGCCTTTTTTT
1 TTTTTTGGCCTTTTTTT
169410 TTGCCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:169408 original size:30 final size:28
Alignment explanation
Indices: 169374--169437 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 28
169364 AAATTTTGGC
169374 TTTTTTGGCTCTTTTTTTGTTTTTTTGCCTT
1 TTTTTTGGC-CTTTTTTTGTTTTTTTG--TT
*
169405 TTTTTTTGCCTTTTTTTGTTTTTTTGTT
1 TTTTTTGGCCTTTTTTTGTTTTTTTGTT
169433 TTTTT
1 TTTTT
169438 ATTTTTTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 7 0.22
30 17 0.53
31 8 0.25
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (28 bp):
TTTTTTGGCCTTTTTTTGTTTTTTTGTT
Found at i:169421 original size:11 final size:12
Alignment explanation
Indices: 169393--169421 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
169383 TCTTTTTTTG
169393 TTTTTTTGCCTT
1 TTTTTTTGCCTT
169405 TTTTTTTGCCTT
1 TTTTTTTGCCTT
169417 TTTTT
1 TTTTT
169422 GTTTTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:169426 original size:20 final size:19
Alignment explanation
Indices: 169374--169437 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
169364 AAATTTTGGC
* *
169374 TTTTTTGGCTCTTTTTTTG
1 TTTTTTTGCTTTTTTTTTG
169393 TTTTTTTGCCTTTTTTTTTG
1 TTTTTTTG-CTTTTTTTTTG
169413 CCTTTTTTTG---TTTTTTTG
1 --TTTTTTTGCTTTTTTTTTG
169431 TTTTTTT
1 TTTTTTT
169438 ATTTTTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 7 0.17
18 8 0.20
19 7 0.17
20 10 0.25
22 8 0.20
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (19 bp):
TTTTTTTGCTTTTTTTTTG
Found at i:172512 original size:1 final size:1
Alignment explanation
Indices: 172508--172554 Score: 67
Period size: 1 Copynumber: 47.0 Consensus size: 1
172498 AAATTTTGGC
* * *
172508 TTTTTTTTGTTTTTTTTTTTGTTTTTTTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
172555 GAAAAAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:172532 original size:28 final size:28
Alignment explanation
Indices: 172501--172554 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
172491 TTTTTTGAAA
172501 TTTTGGCTTTTTTTTGTTTTTTTTTTTG
1 TTTTGGCTTTTTTTTGTTTTTTTTTTTG
***
172529 TTTTTTTTTTTTTTTGTTTTTTTTTT
1 TTTTGGCTTTTTTTTGTTTTTTTTTT
172555 GAAAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (28 bp):
TTTTGGCTTTTTTTTGTTTTTTTTTTTG
Found at i:172897 original size:21 final size:21
Alignment explanation
Indices: 172871--172911 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
172861 TTGGTGCTGG
172871 AAACAAGATAAA-AATAAGATT
1 AAACAAGATAAAGAA-AAGATT
172892 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
172912 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (21 bp):
AAACAAGATAAAGAAAAGATT
Found at i:177024 original size:10 final size:10
Alignment explanation
Indices: 177011--177076 Score: 62
Period size: 10 Copynumber: 6.0 Consensus size: 10
177001 AATTTTGGTA
177011 TTTTTGTTTT
1 TTTTTGTTTT
177021 TTTTTGTTTT
1 TTTTTGTTTT
177031 TTTTTGTTTTGCCTT
1 TTTTTG--TT---TT
177046 TTTTTGCCTTTT
1 TTTTTG--TTTT
177058 TTTTT-TTTT
1 TTTTTGTTTT
177067 TTTTTGTTTT
1 TTTTTGTTTT
177077 GAAAAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
9 9 0.19
10 20 0.42
12 9 0.19
15 10 0.21
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (10 bp):
TTTTTGTTTT
Done.