Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007005.1 Hibiscus syriacus cultivar Beakdansim tig00018082_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: 71803
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:5154 original size:31 final size:31
Alignment explanation
Indices: 5116--5178 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
5106 GATGTCTCGT
5116 TGATGTTATGAATTGAACTTTAATTCTAAAC
1 TGATGTTATGAATTGAACTTTAATTCTAAAC
*
5147 TGATGTTATGAATTGAACTTTAATTTTAAAC
1 TGATGTTATGAATTGAACTTTAATTCTAAAC
5178 T
1 T
5179 AAGATAAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (31 bp):
TGATGTTATGAATTGAACTTTAATTCTAAAC
Found at i:15440 original size:16 final size:16
Alignment explanation
Indices: 15419--15458 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
15409 ATTTCAGCGA
*
15419 AACCAAAATCAACTAG
1 AACCAAAATCAACCAG
* *
15435 AACCAAAATTAACCCG
1 AACCAAAATCAACCAG
15451 AACCAAAA
1 AACCAAAA
15459 CCGAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.28, G:0.05, T:0.10
Consensus pattern (16 bp):
AACCAAAATCAACCAG
Found at i:15580 original size:21 final size:20
Alignment explanation
Indices: 15556--15595 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
15546 ATTTTTAATA
*
15556 ATAATTAATTTAAATAAATTG
1 ATAATTAA-TTAAAAAAATTG
*
15577 ATAATTTATTAAAAAAATT
1 ATAATTAATTAAAAAAATT
15596 ATATATATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
ATAATTAATTAAAAAAATTG
Found at i:15856 original size:18 final size:18
Alignment explanation
Indices: 15833--15887 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
15823 TTATTTTTTA
15833 AAATTTAATAAAAATATT
1 AAATTTAATAAAAATATT
* *
15851 AAATTT-ATAATGAATATA
1 AAATTTAATAA-AAATATT
15869 AAATTTTAATAAAAA-ATT
1 AAA-TTTAATAAAAATATT
15887 A
1 A
15888 TTTCTTTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 4 0.13
18 17 0.57
19 5 0.17
20 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATTTAATAAAAATATT
Found at i:22117 original size:15 final size:16
Alignment explanation
Indices: 22087--22119 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
22077 TTTTTTTTAG
*
22087 TATTTTAGTTTTGGAA
1 TATTTTAGTTTCGGAA
22103 TATTTTA-TTTCGGAA
1 TATTTTAGTTTCGGAA
22118 TA
1 TA
22120 AAATATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.27, C:0.03, G:0.15, T:0.55
Consensus pattern (16 bp):
TATTTTAGTTTCGGAA
Found at i:25054 original size:23 final size:23
Alignment explanation
Indices: 24994--25048 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
24984 CAGCTCATAT
24994 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCTAAGTGCCACGTAG
* *
25017 AATTGCACCTGAGTGCCGCGTAG
1 AATTGCACCTAAGTGCCACGTAG
25040 AATTGCACC
1 AATTGCACC
25049 GTAGTGTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
AATTGCACCTAAGTGCCACGTAG
Found at i:25189 original size:103 final size:103
Alignment explanation
Indices: 25073--25290 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
25063 TAATGTCCAT
25073 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
25138 GACCTCACACATGTTTCAAAGAATATATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
25176 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
25241 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
25279 AATGACCACATA
1 AAGGACCACATA
25291 GACCCTATAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:31730 original size:23 final size:23
Alignment explanation
Indices: 31704--31767 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
31694 CAGCTCATAT
31704 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCTAAGTGCCACGTAG
* *
31727 AATTGCACCTAAGTACCGCGTAG
1 AATTGCACCTAAGTGCCACGTAG
31750 AATTGCACCGT-AGTGCCA
1 AATTGCACC-TAAGTGCCA
31768 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (23 bp):
AATTGCACCTAAGTGCCACGTAG
Found at i:31908 original size:103 final size:103
Alignment explanation
Indices: 31775--32000 Score: 400
Period size: 103 Copynumber: 2.2 Consensus size: 103
31765 CCATATAATA
* *
31775 ATGTCCAT-AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGT
1 ATGTCC-TGAAGGACCACATATCATTCCTTAAGAATCACATACATATGCCAAGGATCAAGTATGT
31839 GTCTCACCAGACCTCACACATATTCCAAAGAATACATAT
65 GTCTCACCAGACCTCACACATATTCCAAAGAATACATAT
31878 ATGTCCTGAAGGACCACATATCATTCCTTAAGAATCACATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCTGAAGGACCACATATCATTCCTTAAGAATCACATACATATGCCAAGGATCAAGTATGTG
*
31943 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACCTCACACATATTCCAAAGAATACATAT
*
31981 ATGTCCCGAAGGACCACATA
1 ATGTCCTGAAGGACCACATA
32001 GACCCTCTAC
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
102 1 0.01
103 117 0.99
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
ATGTCCTGAAGGACCACATATCATTCCTTAAGAATCACATACATATGCCAAGGATCAAGTATGTG
TCTCACCAGACCTCACACATATTCCAAAGAATACATAT
Found at i:31916 original size:21 final size:21
Alignment explanation
Indices: 31866--31918 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
31856 ACATATTCCA
31866 AAGAAT-ACATATATGTCCTG
1 AAGAATCACATATATGTCCTG
* * *
31886 AAGGACCACATATCAT-TCCTT
1 AAGAATCACATAT-ATGTCCTG
31907 AAGAATCACATA
1 AAGAATCACATA
31919 CATATGCCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.15
21 20 0.77
22 2 0.08
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (21 bp):
AAGAATCACATATATGTCCTG
Found at i:32559 original size:64 final size:64
Alignment explanation
Indices: 32449--32621 Score: 208
Period size: 64 Copynumber: 2.6 Consensus size: 64
32439 ATTTTCATCT
*
32449 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTT
1 TTTAAT-GAGG-ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTT
*
32513 GTA
62 CTA
*
32516 TTTAATGAGGATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTT
1 TTTAATGAGGATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTA
* * *
32581 TTTAAATTA--ATGCATCGATGCACTGCATGTGCATCGATGCA
1 TTT-AATGAGGATGCATCGATGCACT-CCTATGCATCGATGCA
32622 CCTTAAACAA
Statistics
Matches: 96, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
63 1 0.01
64 58 0.60
65 23 0.24
66 8 0.08
67 6 0.06
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (64 bp):
TTTAATGAGGATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTA
Found at i:33697 original size:2 final size:2
Alignment explanation
Indices: 33690--33755 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
33680 AGAGTGAAAC
33690 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
33732 GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
33756 AGAACACAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41039 original size:16 final size:16
Alignment explanation
Indices: 41016--41063 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
41006 ATTTTTCAGT
*
41016 GAGCTTAATGAGCAAC
1 GAGCTTAAAGAGCAAC
* *
41032 GGGCTTAACGAGCAAC
1 GAGCTTAAAGAGCAAC
41048 GAGCTTAAAGAGCAAC
1 GAGCTTAAAGAGCAAC
41064 AGTCGAGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.38, C:0.21, G:0.27, T:0.15
Consensus pattern (16 bp):
GAGCTTAAAGAGCAAC
Found at i:43651 original size:50 final size:50
Alignment explanation
Indices: 43597--43693 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
43587 ATTGTTGGGC
*
43597 TAAATAAACATAAATTTCTGGCTGTTGGTCTTAAATTCGAATGAATTCAA
1 TAAATAAACATAAATTTCTGGCTGTTGGGCTTAAATTCGAATGAATTCAA
43647 TAAATAAACATAAATTTCTGGCTGTTGGGCTTAAATTCGAATGAATT
1 TAAATAAACATAAATTTCTGGCTGTTGGGCTTAAATTCGAATGAATT
43694 AAATCTTATC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (50 bp):
TAAATAAACATAAATTTCTGGCTGTTGGGCTTAAATTCGAATGAATTCAA
Found at i:47525 original size:13 final size:12
Alignment explanation
Indices: 47507--47554 Score: 57
Period size: 11 Copynumber: 4.1 Consensus size: 12
47497 ATTAAAATAT
47507 TAAAATATGATTA
1 TAAAATAT-ATTA
47520 TAAAATATA-TA
1 TAAAATATATTA
47531 -AAAATAATATT-
1 TAAAAT-ATATTA
47542 TAAAATATATTA
1 TAAAATATATTA
47554 T
1 T
47555 GATTTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
10 5 0.16
11 10 0.32
12 8 0.26
13 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
TAAAATATATTA
Found at i:47545 original size:22 final size:21
Alignment explanation
Indices: 47493--47551 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
47483 TTTAATATTT
47493 TAATA-TTAAAATAT-TAAAA
1 TAATATTTAAAATATATAAAA
47512 T-ATGATTATAAAATATATAAAAA
1 TAAT-ATT-TAAAATATAT-AAAA
47535 TAATATTTAAAATATAT
1 TAATATTTAAAATATAT
47552 TATGATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 1 0.03
21 8 0.24
22 11 0.32
23 8 0.24
24 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAATATTTAAAATATATAAAA
Found at i:48392 original size:20 final size:20
Alignment explanation
Indices: 48367--48404 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
48357 ATCCTATTCT
48367 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
48387 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
48405 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:49992 original size:29 final size:29
Alignment explanation
Indices: 49946--50029 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
49936 TGTTGGCCGG
49946 AGGTCGTCATGC-CTTCCGGGCGACCTTAT
1 AGGTCGTCATGCAC-TCCGGGCGACCTTAT
* *
49975 AGGTCGCCATGCACTCCGGGCGACCTTGT
1 AGGTCGTCATGCACTCCGGGCGACCTTAT
* *
50004 AGGTCGTCATACACTCTGGGCGACCT
1 AGGTCGTCATGCACTCCGGGCGACCT
50030 ACCCTTGCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 48 0.98
30 1 0.02
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.24
Consensus pattern (29 bp):
AGGTCGTCATGCACTCCGGGCGACCTTAT
Found at i:50185 original size:33 final size:33
Alignment explanation
Indices: 50136--50210 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
50126 GCGACCTACC
* * *
50136 CTCGCTCGGCTGCCCTCAGATTCCCTTGCATAA
1 CTCGCTCGGCTACCCTCAGATGCCCTCGCATAA
* * *
50169 CTCGCTCGGTTACCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGCTACCCTCAGATGCCCTCGCATAA
*
50202 CTCGTTCGG
1 CTCGCTCGG
50211 ATGGCCTCGG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.12, C:0.39, G:0.23, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGCTACCCTCAGATGCCCTCGCATAA
Found at i:50250 original size:34 final size:33
Alignment explanation
Indices: 50182--50254 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
50172 GCTCGGTTAC
* *
50182 CCTCGGATGCCCTCGCATAGCTCGTTCGGATGG
1 CCTCGGATGCCCTCGAATAGCTCGGTCGGATGG
* *
50215 CCTCGGATGCTCTCGAATGGCATCGGTCGGATGG
1 CCTCGGATGCCCTCGAATAGC-TCGGTCGGATGG
50249 CCTCGG
1 CCTCGG
50255 TCGGATGGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
33 18 0.51
34 17 0.49
ACGTcount: A:0.12, C:0.32, G:0.33, T:0.23
Consensus pattern (33 bp):
CCTCGGATGCCCTCGAATAGCTCGGTCGGATGG
Found at i:50254 original size:14 final size:14
Alignment explanation
Indices: 50231--50268 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
50221 ATGCTCTCGA
*
50231 ATGGCATCGGTCGG
1 ATGGCCTCGGTCGG
50245 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGG
50259 ATGGCCTCGG
1 ATGGCCTCGG
50269 ATGCCCAGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.11, C:0.26, G:0.42, T:0.21
Consensus pattern (14 bp):
ATGGCCTCGGTCGG
Found at i:51348 original size:2 final size:2
Alignment explanation
Indices: 51341--51371 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51331 GGCATAGTTC
51341 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51372 TTGTAGTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51676 original size:24 final size:24
Alignment explanation
Indices: 51649--51699 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
51639 AATTATCATG
*
51649 TTAAAACCCAACATTAAAATGCTT
1 TTAAAACCCAACATTAAAATGATT
**
51673 TT-AAGTCCAACATTAAAATGATT
1 TTAAAACCCAACATTAAAATGATT
51696 TTAA
1 TTAA
51700 GTCCAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (24 bp):
TTAAAACCCAACATTAAAATGATT
Found at i:51682 original size:23 final size:23
Alignment explanation
Indices: 51656--51711 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
51646 ATGTTAAAAC
*
51656 CCAACATTAAAATGCTTTTAAGT
1 CCAACATTAAAATGATTTTAAGT
51679 CCAACATTAAAATGATTTTAAGT
1 CCAACATTAAAATGATTTTAAGT
51702 CCAAACATTA
1 CC-AACATTA
51712 CAAACATATC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 24 0.77
24 7 0.23
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (23 bp):
CCAACATTAAAATGATTTTAAGT
Found at i:52555 original size:32 final size:32
Alignment explanation
Indices: 52509--52594 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
52499 CAAGTATTGC
*
52509 TGAGGTCGACTCTACTCGAAAATTCTGAAATA
1 TGAGTTCGACTCTACTCGAAAATTCTGAAATA
52541 TGAGTTCGACTCTACTCGAAAATTCTGAAATA
1 TGAGTTCGACTCTACTCGAAAATTCTGAAATA
* *
52573 TGAGTTCAACTCGACTCGAAAA
1 TGAGTTCGACTCTACTCGAAAA
52595 CTCGCAAGCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (32 bp):
TGAGTTCGACTCTACTCGAAAATTCTGAAATA
Found at i:54858 original size:35 final size:35
Alignment explanation
Indices: 54818--54962 Score: 206
Period size: 35 Copynumber: 4.2 Consensus size: 35
54808 ATCTATGTCC
54818 GATAACTATAAAA-CATCTGATATCTGTAAATATCT
1 GATAACTA-AAAATCATCTGATATCTGTAAATATCT
* **
54853 AATAACT-GTAATCATCTGATATCTGTAAATATCT
1 GATAACTAAAAATCATCTGATATCTGTAAATATCT
* *
54887 GATAACTAAAAATCATCTAATAACTGTAAATATCT
1 GATAACTAAAAATCATCTGATATCTGTAAATATCT
54922 GATAACTAAAAATCATCTGATAAT-TGTAAATATCT
1 GATAACTAAAAATCATCTGAT-ATCTGTAAATATCT
54957 GATAAC
1 GATAAC
54963 GGTGAAATGT
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
33 2 0.02
34 28 0.29
35 66 0.68
36 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (35 bp):
GATAACTAAAAATCATCTGATATCTGTAAATATCT
Found at i:54861 original size:17 final size:17
Alignment explanation
Indices: 54818--54986 Score: 160
Period size: 17 Copynumber: 9.7 Consensus size: 17
54808 ATCTATGTCC
* *
54818 GATAACTATAAAACATCT
1 GATAACTGT-AAATATCT
*
54836 GATATCTGTAAATATCT
1 GATAACTGTAAATATCT
*
54853 AATAACTGT-AATCATCT
1 GATAACTGTAAAT-ATCT
*
54870 GATATCTGTAAATATCT
1 GATAACTGTAAATATCT
**
54887 GATAACTAAAAATCATCT
1 GATAACTGTAAAT-ATCT
*
54905 AATAACTGTAAATATCT
1 GATAACTGTAAATATCT
**
54922 GATAACTAAAAATCATCT
1 GATAACTGTAAAT-ATCT
*
54940 GATAATTGTAAATATCT
1 GATAACTGTAAATATCT
* * *
54957 GATAACGGTGAAATGTAT
1 GATAACTGT-AAATATCT
54975 GATAACTGTAAA
1 GATAACTGTAAA
54987 CATTTAGAAT
Statistics
Matches: 122, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
16 3 0.02
17 67 0.55
18 52 0.43
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (17 bp):
GATAACTGTAAATATCT
Found at i:54908 original size:52 final size:52
Alignment explanation
Indices: 54818--54981 Score: 154
Period size: 52 Copynumber: 3.1 Consensus size: 52
54808 ATCTATGTCC
* **
54818 GATAACTATAAAA-CATCTGATATCTGTAAATATCTAATAACTGT-AATCATCT
1 GATAACTA-AAAATCATCTGATAACTAAAAATATCTAATAACTGTAAAT-ATCT
* **
54870 GATATCTGTAAAT-ATCTGATAACTAAAAATCATCTAATAACTGTAAATATCT
1 GATAACTAAAAATCATCTGATAACTAAAAAT-ATCTAATAACTGTAAATATCT
* ** * * * *
54922 GATAACTAAAAATCATCTGATAATTGTAAATATCTGATAACGGTGAAATGTAT
1 GATAACTAAAAATCATCTGATAACTAAAAATATCTAATAACTGT-AAATATCT
54975 GATAACT
1 GATAACT
54982 GTAAACATTT
Statistics
Matches: 91, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
51 17 0.19
52 44 0.48
53 30 0.33
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (52 bp):
GATAACTAAAAATCATCTGATAACTAAAAATATCTAATAACTGTAAATATCT
Found at i:54986 original size:70 final size:69
Alignment explanation
Indices: 54818--54962 Score: 186
Period size: 69 Copynumber: 2.1 Consensus size: 69
54808 ATCTATGTCC
* * **
54818 GATAACTATAAAA-CATCTGATATCTGTAAATATCTAATAACTGTAATCATCTGATATCTGTAAA
1 GATAACTA-AAAATCATATGATAACTGTAAATATCTAATAACTAAAATCATCTGATATCTGTAAA
54882 TATCT
65 TATCT
* * *
54887 GATAACTAAAAATCATCTAATAACTGTAAATATCTGATAACTAAAAATCATCTGATAAT-TGTAA
1 GATAACTAAAAATCATATGATAACTGTAAATATCTAATAACT-AAAATCATCTGAT-ATCTGTAA
54951 ATATCT
64 ATATCT
54957 GATAAC
1 GATAAC
54963 GGTGAAATGT
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
68 4 0.06
69 34 0.50
70 28 0.41
71 2 0.03
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (69 bp):
GATAACTAAAAATCATATGATAACTGTAAATATCTAATAACTAAAATCATCTGATATCTGTAAAT
ATCT
Found at i:55751 original size:15 final size:16
Alignment explanation
Indices: 55719--55751 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55709 AATTTAAATT
*
55719 TAAATATAAAATTCGA
1 TAAAAATAAAATTCGA
55735 TAAAAATAAAA-TCGA
1 TAAAAATAAAATTCGA
55750 TA
1 TA
55752 CTTAAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (16 bp):
TAAAAATAAAATTCGA
Found at i:59422 original size:20 final size:20
Alignment explanation
Indices: 59397--59436 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
59387 CTGTCCAGTG
59397 CCAGCTGTCCTTATGCAGAA
1 CCAGCTGTCCTTATGCAGAA
59417 CCAGCTGTCCTTATGCAGAA
1 CCAGCTGTCCTTATGCAGAA
59437 ATATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (20 bp):
CCAGCTGTCCTTATGCAGAA
Found at i:65033 original size:14 final size:15
Alignment explanation
Indices: 65014--65076 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 15
65004 AATTTTCTGA
65014 AAAAT-AATTTACGT
1 AAAATAAATTTACGT
* *
65028 AAAATAAATTATATGA
1 AAAATAAATT-TACGT
*
65044 AAAAT-ATTTTACGT
1 AAAATAAATTTACGT
* *
65058 AAAATGAA-TTACCT
1 AAAATAAATTTACGT
65072 AAAAT
1 AAAAT
65077 TGTTTTACAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
14 23 0.59
15 8 0.21
16 8 0.21
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.33
Consensus pattern (15 bp):
AAAATAAATTTACGT
Found at i:65047 original size:30 final size:30
Alignment explanation
Indices: 65011--65068 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
65001 ATTAATTTTC
65011 TGAAAAATAATTTACGTAAAATAAATTATA
1 TGAAAAATAATTTACGTAAAATAAATTATA
* *
65041 TGAAAAATATTTTACGTAAAATGAATTA
1 TGAAAAATAATTTACGTAAAATAAATTA
65069 CCTAAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.34
Consensus pattern (30 bp):
TGAAAAATAATTTACGTAAAATAAATTATA
Found at i:65429 original size:41 final size:41
Alignment explanation
Indices: 65383--65461 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
65373 TTATTATATG
* * *
65383 ATATTA-AATATAAATTAATATTACTCATTAATAATTTAATA
1 ATATTATAATATAAATAAATATAAAT-ATTAATAATTTAATA
*
65424 ATATTATATTATAAATAAATATAAATATTAATAATTTA
1 ATATTATAATATAAATAAATATAAATATTAATAATTTA
65462 TTTAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 18 0.55
42 15 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (41 bp):
ATATTATAATATAAATAAATATAAATATTAATAATTTAATA
Found at i:65534 original size:30 final size:30
Alignment explanation
Indices: 65413--65563 Score: 80
Period size: 30 Copynumber: 4.7 Consensus size: 30
65403 TTACTCATTA
* * *
65413 ATAAT-TTAATAATATTATATTATAAATAAAT
1 ATAATATTATTAAAATTATATTAT--ATTAAT
*
65444 ATAA-A-TATTAATAATT-TATTTAAATATAAT
1 ATAATATTATTAA-AATTATA-TTATAT-TAAT
65474 ATCATATATTATT-AAATATATGAGTATATATTAAT
1 AT-A-ATATTATTAAAAT-TAT-A-T-TATATTAAT
*
65509 ATAATATTATTAAAATTATATTATATTTAT
1 ATAATATTATTAAAATTATATTATATTAAT
65539 ATTAAATATT-TTAATAATTAATATT
1 A-T-AATATTATTAA-AATT-ATATT
65564 TTAATTAAAA
Statistics
Matches: 96, Mismatches: 7, Indels: 32
0.71 0.05 0.24
Matches are distributed among these distances:
29 2 0.02
30 21 0.22
31 17 0.18
32 15 0.16
33 19 0.20
34 10 0.10
35 8 0.08
36 4 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
ATAATATTATTAAAATTATATTATATTAAT
Found at i:65563 original size:15 final size:15
Alignment explanation
Indices: 65505--65568 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 15
65495 GAGTATATAT
65505 TAATATAATATTATTAA
1 TAAT-TAATATT-TTAA
65522 -AATTATATTATATTT-A
1 TAATTA-A-TAT-TTTAA
65538 T-ATTAAATATTTTAA
1 TAATT-AATATTTTAA
65553 TAATTAATATTTTAA
1 TAATTAATATTTTAA
65568 T
1 T
65569 TAAAATGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
14 3 0.08
15 18 0.45
16 12 0.30
17 6 0.15
18 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTAATATTTTAA
Found at i:65617 original size:26 final size:26
Alignment explanation
Indices: 65531--65617 Score: 63
Period size: 27 Copynumber: 3.2 Consensus size: 26
65521 AAATTATATT
* *
65531 ATATTT-ATATTAAATATTTTAATAATTA
1 ATATTTAATATTAAAT-GTATAA-AA-TA
*
65559 ATATTTTAAT-TAAAATG-ATATAAATA
1 ATA-TTTAATATTAAATGTATA-AAATA
*
65585 TTAATTTAATATTAAATGTATAAAATA
1 AT-ATTTAATATTAAATGTATAAAATA
65612 ATATTT
1 ATATTT
65618 TTTGAGTGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
26 13 0.28
27 17 0.36
28 7 0.15
29 8 0.17
30 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
ATATTTAATATTAAATGTATAAAATA
Found at i:67758 original size:60 final size:60
Alignment explanation
Indices: 67589--67766 Score: 179
Period size: 59 Copynumber: 3.0 Consensus size: 60
67579 ACACATATAA
* * * *
67589 TTTA-GGATTAAATTGCAATATTAAAAAAGTTTAGGGACCAATTTAGAATGAAGATCATAG
1 TTTAGGGATAAAATTGAAATATT-TAAAAGTTTAAGGACCAATTTAGAATGAAGATCATAG
* * **
67649 TTT-GGGTATAAAAAT-AAA-ATGTTAAAAGTTTGAGGAGTAATTTAGAATGATA-ATCATAG
1 TTTAGGG-ATAAAATTGAAATAT-TTAAAAGTTTAAGGACCAATTTAGAATGA-AGATCATAG
* * *
67708 TTTAGGGATGAAATTGAAATATTTAAAAGTTTAAGGACCAATTTAAAATG-AGGTCATAG
1 TTTAGGGATAAAATTGAAATATTTAAAAGTTTAAGGACCAATTTAGAATGAAGATCATAG
67767 ATTGTGATGT
Statistics
Matches: 95, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
58 1 0.01
59 47 0.49
60 39 0.41
61 8 0.08
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (60 bp):
TTTAGGGATAAAATTGAAATATTTAAAAGTTTAAGGACCAATTTAGAATGAAGATCATAG
Found at i:67837 original size:24 final size:23
Alignment explanation
Indices: 67796--67840 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
67786 ATTAACTTGC
*
67796 TTTTATTTTAAAAATAATAAATA
1 TTTTATTGTAAAAATAATAAATA
*
67819 TTTTATTAGTAAAAGTAATAAA
1 TTTTATT-GTAAAAATAATAAA
67841 CAAGAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TTTTATTGTAAAAATAATAAATA
Found at i:67965 original size:39 final size:38
Alignment explanation
Indices: 67913--67990 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
67903 ATTTTTATAA
* * *
67913 ATTTAAATATATCAAAATTTTAAATGTATTTTTAAAATT
1 ATTTAAATATATCAAAATATTAAA-ATATTTATAAAATT
* *
67952 ATTTAAATTTATCAATATATTAAAATATTTATAAAATT
1 ATTTAAATATATCAAAATATTAAAATATTTATAAAATT
67990 A
1 A
67991 AATTTTATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 13 0.38
39 21 0.62
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (38 bp):
ATTTAAATATATCAAAATATTAAAATATTTATAAAATT
Done.