Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001005.1 Hibiscus syriacus cultivar Beakdansim tig00002007_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: 142537
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2403 original size:18 final size:18
Alignment explanation
Indices: 2380--2484 Score: 156
Period size: 18 Copynumber: 5.8 Consensus size: 18
2370 ATTCTTAAGG
*
2380 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
*
2398 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAT
*
2416 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
2434 AGTGGTCCTTCGTGACAT
1 AGTGGTCCTTCGGGACAT
* *
2452 AGTGGTCCTTCGGGATAA
1 AGTGGTCCTTCGGGACAT
2470 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
2485 TAAGTGTTAA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 78 1.00
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2444 original size:54 final size:54
Alignment explanation
Indices: 2380--2484 Score: 176
Period size: 54 Copynumber: 1.9 Consensus size: 54
2370 ATTCTTAAGG
*
2380 AGTGGTCCTTCAG-GACATAGTGGTCCTTCGGGACAAAGTGGTCTTTCGGGACAT
1 AGTGGTCCTTC-GTGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGACAT
*
2434 AGTGGTCCTTCGTGACATAGTGGTCCTTCGGGATAAAGTGGTCCTTCGGGA
1 AGTGGTCCTTCGTGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGA
2485 TAAGTGTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 1 0.02
54 47 0.98
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.29
Consensus pattern (54 bp):
AGTGGTCCTTCGTGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGACAT
Found at i:9149 original size:21 final size:21
Alignment explanation
Indices: 9125--9164 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9115 GAGAAATTGT
9125 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
*
9146 TTTTGAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
9165 AAAGAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:10490 original size:18 final size:18
Alignment explanation
Indices: 10467--10504 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
10457 TTTACTGAGT
10467 TTTGTAATTCTAATGGTA
1 TTTGTAATTCTAATGGTA
10485 TTTGTAATTCTAATGGTA
1 TTTGTAATTCTAATGGTA
10503 TT
1 TT
10505 AGCCATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (18 bp):
TTTGTAATTCTAATGGTA
Found at i:15014 original size:25 final size:25
Alignment explanation
Indices: 14986--15043 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
14976 TTTTAATGCT
*
14986 TTTGGATTGTTTTATTTTGAGTTTG
1 TTTGGATTGTTTTACTTTGAGTTTG
15011 TTTGGATTGTTTTACTTTGAGTTTG
1 TTTGGATTGTTTTACTTTGAGTTTG
15036 TTTGGATT
1 TTTGGATT
15044 TTGGATGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.12, C:0.02, G:0.24, T:0.62
Consensus pattern (25 bp):
TTTGGATTGTTTTACTTTGAGTTTG
Found at i:15379 original size:28 final size:28
Alignment explanation
Indices: 15346--15401 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
15336 AAAGGGTGAG
15346 AAGTGTTAAAGTGTTTTAAAGGGGAGAA
1 AAGTGTTAAAGTGTTTTAAAGGGGAGAA
15374 AAGTGTTAAAGTGTTTTAAAGGGGAGAA
1 AAGTGTTAAAGTGTTTTAAAGGGGAGAA
15402 GTGTTAGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (28 bp):
AAGTGTTAAAGTGTTTTAAAGGGGAGAA
Found at i:15893 original size:20 final size:19
Alignment explanation
Indices: 15827--15900 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 19
15817 GAATGCTCGA
*
15827 ATGGTACCGATACCCCC-T
1 ATGGTACCGATACCCCCAG
*
15845 ATAGGTATCGATACCCCCATG
1 AT-GGTACCGATACCCCCA-G
*
15866 CAATGGTATCGATACCCCTCAG
1 --ATGGTACCGATACCCC-CAG
15888 ATGGTACCGATAC
1 ATGGTACCGATAC
15901 TCTAAGGCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 2 0.04
19 14 0.30
20 12 0.26
22 15 0.32
23 4 0.09
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (19 bp):
ATGGTACCGATACCCCCAG
Found at i:15975 original size:21 final size:21
Alignment explanation
Indices: 15951--15998 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
15941 ACAGGTACCG
15951 ATACCCTATAAAGGAGTACTA
1 ATACCCTATAAAGGAGTACTA
* *
15972 ATACCCTATAAAGGGGTACTG
1 ATACCCTATAAAGGAGTACTA
15993 ATACCC
1 ATACCC
15999 CCCCACGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (21 bp):
ATACCCTATAAAGGAGTACTA
Found at i:18428 original size:35 final size:35
Alignment explanation
Indices: 18389--18459 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
18379 ATGCGGTTCT
*
18389 TCGGGACACATATTTGGTCCTTTGGAATATATATG
1 TCGGGACACATATTTGGCCCTTTGGAATATATATG
18424 TCGGGACACATATTTGGCCCTTTGGAATATATATG
1 TCGGGACACATATTTGGCCCTTTGGAATATATATG
18459 T
1 T
18460 GATTCTTAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (35 bp):
TCGGGACACATATTTGGCCCTTTGGAATATATATG
Found at i:18498 original size:18 final size:18
Alignment explanation
Indices: 18475--18568 Score: 143
Period size: 18 Copynumber: 5.2 Consensus size: 18
18465 TTAAGGAGTA
*
18475 GTCCTTCAGGACATAGTG
1 GTCCTTCGGGACATAGTG
18493 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
*
18511 GTCCTTCGGGACATAATG
1 GTCCTTCGGGACATAGTG
18529 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
* *
18547 GTCCTTCAGGGAAAAAGTG
1 GTCCTTC-GGGACATAGTG
18566 GTC
1 GTC
18569 ATTTGGGATA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
18 58 0.83
19 12 0.17
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:26718 original size:26 final size:25
Alignment explanation
Indices: 26673--26723 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
26663 TTGTATTTAT
* *
26673 ATATATATATATAATCATATTCAAAA
1 ATATATATAAAAAATCATATT-AAAA
*
26699 ATATATATAAAAAATTATATTAAAA
1 ATATATATAAAAAATCATATTAAAA
26724 TTGTTCATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATATATAAAAAATCATATTAAAA
Found at i:33883 original size:15 final size:15
Alignment explanation
Indices: 33859--33897 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
33849 CGAACAAAAC
*
33859 TGGGGCCATTCTGTA
1 TGGGGCCATTCTATA
*
33874 TGGGGTCATTCTATA
1 TGGGGCCATTCTATA
*
33889 TGGTGCCAT
1 TGGGGCCAT
33898 GACGATAGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.15, C:0.18, G:0.31, T:0.36
Consensus pattern (15 bp):
TGGGGCCATTCTATA
Found at i:36441 original size:18 final size:18
Alignment explanation
Indices: 36418--36452 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36408 ACTGAATATT
*
36418 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
36436 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
36453 GAAAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:39046 original size:15 final size:13
Alignment explanation
Indices: 39025--39065 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
39015 TTTTACCAGA
39025 TAAAAAACCGGTT
1 TAAAAAACCGGTT
39038 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
39052 TAAAAAACCGGTT
1 TAAAAAACCGGTT
39065 T
1 T
39066 TTATCCGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:41385 original size:21 final size:21
Alignment explanation
Indices: 41361--41400 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41351 TTTATTTTAT
41361 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
41382 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
41401 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:41448 original size:33 final size:33
Alignment explanation
Indices: 41395--41493 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
41385 TTTGTTTCAA
41395 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
41427 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
41460 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
41493 T
1 T
41494 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:41522 original size:13 final size:13
Alignment explanation
Indices: 41479--41533 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
41469 TTGGAAGTAT
41479 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
41492 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
41506 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
41519 TTAAGTATTTGAA
1 TTAAGTATTTCAA
41532 TT
1 TT
41534 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:41755 original size:21 final size:21
Alignment explanation
Indices: 41729--41785 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
41719 TGGAGCGTGG
*
41729 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
41750 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
41771 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
41786 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:41982 original size:15 final size:15
Alignment explanation
Indices: 41962--42007 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
41952 TAAAATCGAT
*
41962 TTTTTTTATAACCGG
1 TTTTTTTAAAACCGG
*
41977 TTTTTTAAAAAAACCGG
1 TTTTTT--TAAAACCGG
41994 TTTTTTTAAAACCG
1 TTTTTTTAAAACCG
42008 AAACTGGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.50
17 13 0.50
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (15 bp):
TTTTTTTAAAACCGG
Found at i:41991 original size:17 final size:18
Alignment explanation
Indices: 41971--42004 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41961 TTTTTTTTAT
41971 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
41988 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
42005 CCGAAACTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:42124 original size:15 final size:17
Alignment explanation
Indices: 42098--42129 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
42088 TTCTATGGGA
42098 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
42114 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
42130 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:48032 original size:55 final size:56
Alignment explanation
Indices: 47933--48051 Score: 134
Period size: 55 Copynumber: 2.1 Consensus size: 56
47923 TTTTAGATAA
* * * * *
47933 ATTCGATTTCAAAATCTCTATTTTTATGCTTCTTAATAGCAACAATTGATAAATAT
1 ATTCGATTTCAAAATCCCTATTTTTATACTTATTAATAGCAACAACTAATAAATAT
* * *
47989 ATTCGATTTCGAGATCCCTA-TTTTATACTTATTAAT-GACAACAACTAATAGATAT
1 ATTCGATTTCAAAATCCCTATTTTTATACTTATTAATAG-CAACAACTAATAAATAT
*
48044 ATTTGATT
1 ATTCGATT
48052 CGGACCATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
54 1 0.02
55 35 0.66
56 17 0.32
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42
Consensus pattern (56 bp):
ATTCGATTTCAAAATCCCTATTTTTATACTTATTAATAGCAACAACTAATAAATAT
Found at i:48854 original size:2 final size:2
Alignment explanation
Indices: 48817--48843 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48807 AATTAACATG
48817 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
48844 TGATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55936 original size:43 final size:43
Alignment explanation
Indices: 55850--55941 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
55840 TTAATCGAAA
**
55850 AGAAAAGTAATAAGAATCTGAAAATTTGATAGATTGATTGAAT
1 AGAAAAGTAATAAGAATCTGAAAATTTGATAGATTGAGAGAAT
* * * *
55893 AGAAAAGTATTAGGAATCATG-AAATTTGATTGTTTGAGAGAAT
1 AGAAAAGTAATAAGAATC-TGAAAATTTGATAGATTGAGAGAAT
*
55936 AAAAAA
1 AGAAAA
55942 AATTAACCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 39 0.95
44 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (43 bp):
AGAAAAGTAATAAGAATCTGAAAATTTGATAGATTGAGAGAAT
Found at i:56643 original size:62 final size:61
Alignment explanation
Indices: 56540--56663 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 61
56530 CTAAAACTTT
* *
56540 CAAGCATAAACAATTTCAACTTATCGACTTCGAAGCAGTAGGCTT-TACATTCAATAATTTG
1 CAAGCATAAACAATTTCAAATCATCGACTTCGAAGCAGTAGGCTTCT-CATTCAATAATTTG
* * *
56601 CAAGCTTAAACAATTTCAAATCATTCGACTTTGAAGCAGTAGGCTTCTCATTCCATAATTTG
1 CAAGCATAAACAATTTCAAATCA-TCGACTTCGAAGCAGTAGGCTTCTCATTCAATAATTTG
56663 C
1 C
56664 TTTGAATCTT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
61 20 0.36
62 35 0.62
63 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (61 bp):
CAAGCATAAACAATTTCAAATCATCGACTTCGAAGCAGTAGGCTTCTCATTCAATAATTTG
Found at i:60767 original size:62 final size:61
Alignment explanation
Indices: 60658--60775 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 61
60648 CTTTTAAGGA
* * * *
60658 TAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTCAATAATTTGCAAGCT
1 TAAACAATTTCAAATCATTGACCTCGAAGCAGTAGGCTTTACATTCAATAATTTGCAAGCT
60719 TAAACAATTTCAAATCATTTGACACT-GAAGCAGTAGGCTTCT-CATTCAATAATTTGC
1 TAAACAATTTCAAATCA-TTGAC-CTCGAAGCAGTAGGCTT-TACATTCAATAATTTGC
60776 TTTCAATCTG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
61 16 0.32
62 32 0.64
63 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (61 bp):
TAAACAATTTCAAATCATTGACCTCGAAGCAGTAGGCTTTACATTCAATAATTTGCAAGCT
Found at i:62271 original size:37 final size:36
Alignment explanation
Indices: 62212--62331 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
62202 ATCCCATTAT
* *
62212 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
62248 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
62284 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
62319 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
62332 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:62287 original size:21 final size:21
Alignment explanation
Indices: 62263--62323 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
62253 TTCAAAGAAA
62263 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
62284 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
62298 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
62319 CATTT
1 CATTT
62324 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:62340 original size:35 final size:36
Alignment explanation
Indices: 62214--62358 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
62204 CCCATTATCA
*
62214 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
62249 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
62286 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
62322 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
62356 TTT
1 TTT
62359 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:64617 original size:13 final size:13
Alignment explanation
Indices: 64585--64619 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
64575 GTTCATGCGC
*
64585 TCTGCTACGCCAT
1 TCTGCTGCGCCAT
64598 TCTGCTGCGCCAT
1 TCTGCTGCGCCAT
64611 TCTGCTGCG
1 TCTGCTGCG
64620 GTGTCATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.37, G:0.23, T:0.31
Consensus pattern (13 bp):
TCTGCTGCGCCAT
Found at i:73422 original size:29 final size:29
Alignment explanation
Indices: 73388--73468 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
73378 ATAAAGCATA
73388 GAGAATATTTTTAATTTAATTATAATTTT
1 GAGAATATTTTTAATTTAATTATAATTTT
**
73417 GAGAATATTTTTTGTTTCAA-TAT-ATTTT
1 GAGAATATTTTTAATTT-AATTATAATTTT
*
73445 TA-AA-A-TTTTAATTTAATTAATAAT
1 GAGAATATTTTTAATTTAATT-ATAAT
73469 ATTTTAATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
24 2 0.05
25 8 0.19
26 3 0.07
27 4 0.09
28 6 0.14
29 18 0.42
30 2 0.05
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (29 bp):
GAGAATATTTTTAATTTAATTATAATTTT
Found at i:75487 original size:21 final size:23
Alignment explanation
Indices: 75463--75506 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
75453 AGTAAGAGGG
*
75463 GGAGG-GC-GAAGAGAGGGGTGA
1 GGAGGCGCTGAAGAGAGCGGTGA
75484 GGAGGCCGCTGAAGAGAGCGGTG
1 GGAGG-CGCTGAAGAGAGCGGTG
75507 GCGGAGTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.25, C:0.11, G:0.57, T:0.07
Consensus pattern (23 bp):
GGAGGCGCTGAAGAGAGCGGTGA
Found at i:75689 original size:23 final size:23
Alignment explanation
Indices: 75658--75712 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
75648 TCATTTTTTA
*
75658 TTTT-TTAATTATTAACTTAAAC
1 TTTTATTAATTATCAACTTAAAC
75680 TTTTATTAATTATCAACTTAAAC
1 TTTTATTAATTATCAACTTAAAC
75703 TTTTATTAAT
1 TTTTATTAAT
75713 GGGTTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTATTAATTATCAACTTAAAC
Found at i:76053 original size:62 final size:61
Alignment explanation
Indices: 75935--76056 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 61
75925 GCTAACCCTA
* * * * *
75935 AAGCATAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTCGATAATTTGC
1 AAGCATAAACAATCTCAAATCATTGACTTCGAAGCAGTAGGCTTTACATTCAATAATTTGC
*
75996 AAGCTTAAACAATCTCAAATCATTTGACTTCGAAGCAGTAGGCTTCT-CATTCAATAATTTG
1 AAGCATAAACAATCTCAAATCA-TTGACTTCGAAGCAGTAGGCTT-TACATTCAATAATTTG
76057 ATTTCAATCT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 19 0.36
62 33 0.62
63 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (61 bp):
AAGCATAAACAATCTCAAATCATTGACTTCGAAGCAGTAGGCTTTACATTCAATAATTTGC
Found at i:79584 original size:12 final size:12
Alignment explanation
Indices: 79567--79596 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
79557 GGCATCGGAC
79567 TAGCAAATAATA
1 TAGCAAATAATA
79579 TAGCAAATAATA
1 TAGCAAATAATA
79591 TAGCAA
1 TAGCAA
79597 GTGCTCAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (12 bp):
TAGCAAATAATA
Found at i:84209 original size:15 final size:15
Alignment explanation
Indices: 84191--84225 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
84181 CGAGGGTTCT
84191 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
84206 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
84221 GTAGT
1 GTAGT
84226 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:91066 original size:15 final size:15
Alignment explanation
Indices: 91048--91097 Score: 100
Period size: 15 Copynumber: 3.3 Consensus size: 15
91038 CGAGGGTTCT
91048 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
91063 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
91078 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
91093 GTAGT
1 GTAGT
91098 GGTCCTACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:96510 original size:15 final size:15
Alignment explanation
Indices: 96486--96524 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
96476 GTAACTCTTT
*
96486 TGGGGCCATTCTGTA
1 TGGGGCCATTCTATA
*
96501 TGGGGTCATTCTATA
1 TGGGGCCATTCTATA
*
96516 TGGTGCCAT
1 TGGGGCCAT
96525 GGAGATAGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.15, C:0.18, G:0.31, T:0.36
Consensus pattern (15 bp):
TGGGGCCATTCTATA
Found at i:99077 original size:18 final size:18
Alignment explanation
Indices: 99054--99088 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
99044 ACTGAATATT
*
99054 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
99072 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
99089 GAAAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:106200 original size:151 final size:153
Alignment explanation
Indices: 105958--106263 Score: 474
Period size: 151 Copynumber: 2.0 Consensus size: 153
105948 AACATTTTAG
* * *
105958 TGTCTAAAGAATTTTTCGTTAAAAATAGGTGTTTAATGTTTTATCGGTTATACTTTTAGGGACCT
1 TGTCTAAAGAATTTTTCGTTAAAAATA-GTGTGTAACGTTTTATCGATTATACTTTTAGGGACCT
**
106023 ACAATTTATTTTTTTGGTTTTTTAATAATAAAAATATTATTTTTAATTAAAAAAGAAAAAAGTTT
65 ACAATTTATTTTTTTAATTTTTTAATAATAAAAATATTATTTTTAATTAAAAAAGAAAAAAGTTT
106088 AATATATTTATAAAAA-AACTAAC
130 AATATATTTATAAAAAGAACTAAC
* * * *
106111 TGTCTAAATAATTTTTCGTTAAAAATA-TGTGTAACGTTTTCTTGATTATACTTTTAGGTACCTA
1 TGTCTAAAGAATTTTTCGTTAAAAATAGTGTGTAACGTTTTATCGATTATACTTTTAGGGACCTA
*
106175 CAGTTTA-TTTTTTAATTTTTGTAATAATAAAAATATTATTTTTAATTAAAAAAGAAAAAAGTTT
66 CAATTTATTTTTTTAATTTTT-TAATAATAAAAATATTATTTTTAATTAAAAAAGAAAAAAGTTT
*
106239 AATCTATTTATAAAAAGAACTAAC
130 AATATATTTATAAAAAGAACTAAC
106263 T
1 T
106264 TTTTACTGAA
Statistics
Matches: 140, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
150 11 0.08
151 95 0.68
152 8 0.06
153 26 0.19
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (153 bp):
TGTCTAAAGAATTTTTCGTTAAAAATAGTGTGTAACGTTTTATCGATTATACTTTTAGGGACCTA
CAATTTATTTTTTTAATTTTTTAATAATAAAAATATTATTTTTAATTAAAAAAGAAAAAAGTTTA
ATATATTTATAAAAAGAACTAAC
Found at i:107951 original size:2 final size:2
Alignment explanation
Indices: 107944--107982 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
107934 AAATTAACAG
*
107944 TA TA TA TA TA TA TA TA TC 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 TA TA TA TA T
107983 GATAATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:110562 original size:17 final size:17
Alignment explanation
Indices: 110542--110583 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
110532 ATGCAGCAGA
*
110542 AAACACAATGGAACGAT
1 AAACACAAAGGAACGAT
110559 AAACA-AAAGGAACGAT
1 AAACACAAAGGAACGAT
110575 AAACACAAA
1 AAACACAAA
110584 TCCACTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.62, C:0.17, G:0.14, T:0.07
Consensus pattern (17 bp):
AAACACAAAGGAACGAT
Found at i:112832 original size:62 final size:61
Alignment explanation
Indices: 112720--112837 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 61
112710 ATTTTAAGGA
* * * * *
112720 TAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTGAATAATTTGCAAGCT
1 TAAACAATTTCAAATCATTGACCTCGAAGCAGTAGGCTTTACATTCAATAATTTGCAAGCT
112781 TAAACAATTTCAAATCATTTGACACT-GAAGCAGTAGGCTTCT-CATTCAATAATTTGC
1 TAAACAATTTCAAATCA-TTGAC-CTCGAAGCAGTAGGCTT-TACATTCAATAATTTGC
112838 TTTCATCTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
61 16 0.33
62 31 0.63
63 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (61 bp):
TAAACAATTTCAAATCATTGACCTCGAAGCAGTAGGCTTTACATTCAATAATTTGCAAGCT
Found at i:113011 original size:62 final size:61
Alignment explanation
Indices: 112898--113016 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 61
112888 CAGTTGAAGG
* * * * *
112898 TTAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTGAATAATTTGCAAGC
1 TTAAACAATTTCAAATCATTGACCTCGAAGCAGTAGGCTTTACATTCAATAATTTGCAAGC
112959 TTAAACAATTTCAAATCATTTGACACT-GAAGCAGTAGGCTTCT-CATTCAATAATTTGC
1 TTAAACAATTTCAAATCA-TTGAC-CTCGAAGCAGTAGGCTT-TACATTCAATAATTTGC
113017 TTTCAATCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
61 17 0.34
62 31 0.62
63 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (61 bp):
TTAAACAATTTCAAATCATTGACCTCGAAGCAGTAGGCTTTACATTCAATAATTTGCAAGC
Found at i:113020 original size:179 final size:179
Alignment explanation
Indices: 112715--113078 Score: 703
Period size: 179 Copynumber: 2.0 Consensus size: 179
112705 ACAAAATTTT
*
112715 AAGGATAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTGAATAATTTGCAAGC
1 AAGGTTAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTGAATAATTTGCAAGC
112780 TTAAACAATTTCAAATCATTTGACACTGAAGCAGTAGGCTTCTCATTCAATAATTTGCTTTC-AT
66 TTAAACAATTTCAAATCATTTGACACTGAAGCAGTAGGCTTCTCATTCAATAATTTGCTTTCAAT
112844 CTGTTTTTATCTACCTTCTTCCTTAGTCAAGGTGAGTGCATTTTCAGTTG
131 CTG-TTTTATCTACCTTCTTCCTTAGTCAAGGTGAGTGCATTTTCAGTTG
112894 AAGGTTAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTGAATAATTTGCAAGC
1 AAGGTTAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTGAATAATTTGCAAGC
112959 TTAAACAATTTCAAATCATTTGACACTGAAGCAGTAGGCTTCTCATTCAATAATTTGCTTTCAAT
66 TTAAACAATTTCAAATCATTTGACACTGAAGCAGTAGGCTTCTCATTCAATAATTTGCTTTCAAT
113024 CTGTTTTATCTACCTTCTTCCTTAGTCAAGGTGAGTGCATTTTCAGTTG
131 CTGTTTTATCTACCTTCTTCCTTAGTCAAGGTGAGTGCATTTTCAGTTG
113073 AAGGTT
1 AAGGTT
113079 GTGTATTCAA
Statistics
Matches: 183, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
179 178 0.97
180 5 0.03
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (179 bp):
AAGGTTAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTGAATAATTTGCAAGC
TTAAACAATTTCAAATCATTTGACACTGAAGCAGTAGGCTTCTCATTCAATAATTTGCTTTCAAT
CTGTTTTATCTACCTTCTTCCTTAGTCAAGGTGAGTGCATTTTCAGTTG
Found at i:113620 original size:46 final size:46
Alignment explanation
Indices: 113553--113645 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
113543 CCCGTCGATC
113553 GCGTACTCCGGCGACATATAACCACTGAAACAAATGATCAAGCAAA
1 GCGTACTCCGGCGACATATAACCACTGAAACAAATGATCAAGCAAA
113599 GCGTACTCCGGCGACATATAACCACTGAAACAAATGATCAAGCAAA
1 GCGTACTCCGGCGACATATAACCACTGAAACAAATGATCAAGCAAA
113645 G
1 G
113646 TGTAAGCTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (46 bp):
GCGTACTCCGGCGACATATAACCACTGAAACAAATGATCAAGCAAA
Found at i:114539 original size:37 final size:36
Alignment explanation
Indices: 114480--114599 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
114470 ATCCCATTAT
* *
114480 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
114516 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
114552 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
114587 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
114600 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:114555 original size:21 final size:21
Alignment explanation
Indices: 114531--114591 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
114521 TTCAAAGAAA
114531 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
114552 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
114566 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
114587 CATTT
1 CATTT
114592 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:114608 original size:35 final size:36
Alignment explanation
Indices: 114482--114626 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
114472 CCCATTATCA
*
114482 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
114517 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
114554 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
114590 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
114624 TTT
1 TTT
114627 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:116852 original size:13 final size:13
Alignment explanation
Indices: 116820--116854 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
116810 GTTCATGCGC
*
116820 TCTGCTACGCCAT
1 TCTGCTGCGCCAT
116833 TCTGCTGCGCCAT
1 TCTGCTGCGCCAT
116846 TCTGCTGCG
1 TCTGCTGCG
116855 GTGTCATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.37, G:0.23, T:0.31
Consensus pattern (13 bp):
TCTGCTGCGCCAT
Found at i:125659 original size:180 final size:179
Alignment explanation
Indices: 125293--125675 Score: 610
Period size: 180 Copynumber: 2.1 Consensus size: 179
125283 ATTAAATTTT
*
125293 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATT-AA-ATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
125358 TTTAAGATCCAACAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
64 TTTAAGATCCAACAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
* *
125423 TATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTTAATTAA
129 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAA-TAA
125475 AAATATTAAATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAACCCAATTAATAAT
1 AAATATTAAATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATAAT
* *
125539 TTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATTATCTAAAATTTT
65 TTAAGATCCAACAACTTTTAAACTTAAATCAATATTAATTAATT-AAAAAATTATATAAAATTTT
*
125604 TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTTAA-AA
129 TATTTTATAATTATATATTATTTAAATTAATTATAAAC-TGTTTTTTAATAA
* *
125655 AAATATTTAAT-TTTTATATAA
1 AAATATTAAATATTATATATAA
125676 ATTAGAAAAT
Statistics
Matches: 189, Mismatches: 9, Indels: 9
0.91 0.04 0.04
Matches are distributed among these distances:
179 11 0.06
180 106 0.56
181 56 0.30
182 16 0.08
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (179 bp):
AAATATTAAATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAATT
TAAGATCCAACAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTTTA
TTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATAA
Found at i:125820 original size:15 final size:15
Alignment explanation
Indices: 125800--125828 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
125790 AAAAAAAGTT
125800 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
125815 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
125829 CGATCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:128082 original size:29 final size:29
Alignment explanation
Indices: 128048--128128 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
128038 ATAAAGCATA
128048 GAGAATATTTTTAATTTAATTATAATTTT
1 GAGAATATTTTTAATTTAATTATAATTTT
**
128077 GAGAATATTTTTTGTTTCAA-TAT-ATTTT
1 GAGAATATTTTTAATTT-AATTATAATTTT
*
128105 TA-AA-A-TTTTAATTTAATTAATAAT
1 GAGAATATTTTTAATTTAATT-ATAAT
128129 ATTTTAATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
24 2 0.05
25 8 0.19
26 3 0.07
27 4 0.09
28 6 0.14
29 18 0.42
30 2 0.05
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (29 bp):
GAGAATATTTTTAATTTAATTATAATTTT
Found at i:130145 original size:21 final size:23
Alignment explanation
Indices: 130121--130164 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
130111 AGTAAGAGGG
*
130121 GGAGG-GC-GAAGAGAGGGGTGA
1 GGAGGCGCTGAAGAGAGCGGTGA
130142 GGAGGCCGCTGAAGAGAGCGGTG
1 GGAGG-CGCTGAAGAGAGCGGTG
130165 GCGGAGTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.25, C:0.11, G:0.57, T:0.07
Consensus pattern (23 bp):
GGAGGCGCTGAAGAGAGCGGTGA
Found at i:130349 original size:23 final size:23
Alignment explanation
Indices: 130319--130369 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
130309 TTTTTTATTT
*
130319 TTAATTATTAACTTAAACTTTTA
1 TTAATTATCAACTTAAACTTTTA
130342 TTAATTATCAACTTAAACTTTTA
1 TTAATTATCAACTTAAACTTTTA
130365 TTAAT
1 TTAAT
130370 GGGTTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATTATCAACTTAAACTTTTA
Found at i:130711 original size:62 final size:61
Alignment explanation
Indices: 130593--130714 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 61
130583 GCTAACCCTA
* * * * *
130593 AAGCATAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTCGATAATTTGC
1 AAGCATAAACAATCTCAAATCATTGACTTCGAAGCAGTAGGCTTTACATTCAATAATTTGC
*
130654 AAGCTTAAACAATCTCAAATCATTTGACTTCGAAGCAGTAGGCTTCT-CATTCAATAATTTG
1 AAGCATAAACAATCTCAAATCA-TTGACTTCGAAGCAGTAGGCTT-TACATTCAATAATTTG
130715 ATTTCAATCT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 19 0.36
62 33 0.62
63 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (61 bp):
AAGCATAAACAATCTCAAATCATTGACTTCGAAGCAGTAGGCTTTACATTCAATAATTTGC
Found at i:134240 original size:12 final size:12
Alignment explanation
Indices: 134223--134252 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
134213 GGCATCGGAC
134223 TAGCAAATAATA
1 TAGCAAATAATA
134235 TAGCAAATAATA
1 TAGCAAATAATA
134247 TAGCAA
1 TAGCAA
134253 GTGCTCAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (12 bp):
TAGCAAATAATA
Found at i:138631 original size:95 final size:96
Alignment explanation
Indices: 138461--138651 Score: 296
Period size: 95 Copynumber: 2.0 Consensus size: 96
138451 AGATTATAAT
* * *
138461 ATTATATCTATACAACAAAGCTTGAGTTGTCCCTCTAGAGCAATTTGTTAAACGCCTCGGCTTTA
1 ATTATATCTATACAACAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
* *
138526 TGGATAATATTCAGCTAGCCTGATAAAGGTG
66 TGGATAATATTCAGCTAACCTAATAAAGGTG
* *
138557 ATTATA-CTATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCGTCTTT
1 ATTATATCTATACAACAAAGCTTGAGCTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGGCTTT
138620 ATGGATAATATTCAGCTAACCTAATAAAGGTG
65 ATGGATAATATTCAGCTAACCTAATAAAGGTG
138652 TTTACATATT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
94 1 0.01
95 80 0.92
96 6 0.07
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (96 bp):
ATTATATCTATACAACAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
TGGATAATATTCAGCTAACCTAATAAAGGTG
Found at i:139717 original size:43 final size:43
Alignment explanation
Indices: 139669--139792 Score: 167
Period size: 43 Copynumber: 2.9 Consensus size: 43
139659 CCAAGGGGCC
* *
139669 ATCCACGATTTCAACTCCATGACGGAGGATATCGTTCCCACAA
1 ATCCACGATTTTAACTCCATGACGGAGGATATCGTGCCCACAA
* * *
139712 ATCCACGATTTTAACTCCACGAAGGAGGATATCGTGCCCACAC
1 ATCCACGATTTTAACTCCATGACGGAGGATATCGTGCCCACAA
* ** *
139755 ATCCACGATTTTAACTTCATGACTAAGGATATCATGCC
1 ATCCACGATTTTAACTCCATGACGGAGGATATCGTGCC
139793 AACTCTAGAT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (43 bp):
ATCCACGATTTTAACTCCATGACGGAGGATATCGTGCCCACAA
Found at i:140163 original size:84 final size:83
Alignment explanation
Indices: 140032--140826 Score: 773
Period size: 84 Copynumber: 9.5 Consensus size: 83
140022 GATATCGTAT
* * * * *
140032 TCATTTGCAGCATAGCTCAAAGCTAGAAGAGTTATCTGCCACAAAAAGACCTTCGAGTTCAACTA
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCAC-CAAAGACCTTCGAGTTCGACTA
* * * *
140097 CGTTCAGCTCCATGGCATA
65 CGCTCAGCTCGAGGGCACA
* * *
140116 TCATTTGTAGCATAGCTCAAGGCTAGAAGGGCTATCTACCACCAAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCACC-AAAGACCTTCGAGTTCGACTA
*
140181 CACTCAGCTTCGAGGGCACA
65 CGCTCAGC-TCGAGGGCACA
* * * * * *
140201 TCATTTGTAGCATAACTCAAGGCTAGAAGAGTTATCTGCCAACAAAGACCTTCGAGTTTGACTAC
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGACTAC
* * *
140266 GCTCAACTCAAAGGCACA
66 GCTCAGCTCGAGGGCACA
* * * * * *
140284 TCATTTGCAGCATAGCTTATGTCGAGAAGGGCTATCTGCCACCAAAAGACCTTCAAGTTCGATTA
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCACC-AAAGACCTTCGAGTTCGACTA
*
140349 CACTCAGCTTCGAGGGCACA
65 CGCTCAGC-TCGAGGGCACA
* * * * * * *
140369 TCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCAAGTTTGACTAC
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGACTAC
* * *
140434 GCTCACCTCAAAGGCACA
66 GCTCAGCTCGAGGGCACA
** * * * *
140452 TCATTTGCAGCATAGCTTGAGTCGAGAAGGGCTATCTGCCAACCAAGGACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCC-ACCAAAGACCTTCGAGTTCGACTA
* *
140517 CACTCAGCTTCGAGGGCACG
65 CGCTCAGC-TCGAGGGCACA
* ** * * * * * *
140537 TCATTTTCAATATAACTCAAGGCTAGAAGGGTTATCTACAAACAAAGACCTTCGAGTTTGACTAC
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGACTAC
* * *
140602 GCTCAGCCCAAAGGCACA
66 GCTCAGCTCGAGGGCACA
* * * * * *
140620 TCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAATACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCC-ACCAAAGACCTTCGAGTTCGACTA
*
140685 CACTCAGCTTCGAGGGCACA
65 CGCTCAGC-TCGAGGGCACA
* * * * *
140705 TCATTTGCA-CTATAACTCAAGGCTAGAAGGGTTATCTACTAACCAAAGACATTCGAGTTCGACT
1 TCATTTGCAGC-ATAGCTCAAGGCTAGAAGGGCTATCTGC-CACCAAAGACCTTCGAGTTCGACT
* * ** *
140769 ACGCTCAGCCCCAATGTACA
64 ACGCTCAGCTCGAGGGCACA
* * *
140789 TCATTTACAGTATAGCTCAAGGCAAGAAGGGCTATCTG
1 TCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTG
140827 TCAATAAAAT
Statistics
Matches: 565, Mismatches: 135, Indels: 22
0.78 0.19 0.03
Matches are distributed among these distances:
83 120 0.21
84 253 0.45
85 192 0.34
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (83 bp):
TCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCGAGGGCACA
Found at i:140314 original size:168 final size:168
Alignment explanation
Indices: 140032--140826 Score: 1092
Period size: 168 Copynumber: 4.7 Consensus size: 168
140022 GATATCGTAT
* * * * * **
140032 TCATTTGCAGCATAGCTCAAAGCTAGAAGAGTTATCTGCCACAAAAAGACCTTCGAGTTCAACTA
1 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCA-ACAAAGACCTTCGAGTTTGACTA
* * * * * * * * *
140097 CGTTCAGCTCCATGGCATATCATTTGTAGCATAGCTCAAGGCTAGAAGGGCTATCTACC-ACCAA
65 CGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACC-A
140161 AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
129 AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
* * *
140201 TCATTTGTAGCATAACTCAAGGCTAGAAGAGTTATCTGCCAACAAAGACCTTCGAGTTTGACTAC
1 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTTGACTAC
* *
140266 GCTCAACTCAAAGGCACATCATTTGCAGCATAGCTTATGTCGAGAAGGGCTATCTGCC-ACCAAA
66 GCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACC-AA
*
140330 AGACCTTCAAGTTCGATTACACTCAGCTTCGAGGGCACA
130 AGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
* *
140369 TCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCAAGTTTGACTAC
1 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTTGACTAC
* * *
140434 GCTCACCTCAAAGGCACATCATTTGCAGCATAGCTTGAGTCGAGAAGGGCTATCTGCCAACCAAG
66 GCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAA
*
140499 GACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACG
131 GACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
* * * *
140537 TCATTTTCAATATAACTCAAGGCTAGAAGGGTTATCTACAAACAAAGACCTTCGAGTTTGACTAC
1 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTTGACTAC
* *
140602 GCTCAGCCCAAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAA
66 GCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAA
*
140667 TACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
131 GACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
* * * *
140705 TCATTTGC-ACTATAACTCAAGGCTAGAAGGGTTATCTACTAACCAAAGACATTCGAGTTCGACT
1 TCATTTGCAAC-ATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTTGACT
* * * * * * * * *
140769 ACGCTCAGCCCCAATGTACATCATTTACAGTATAGCTCAAGGCAAGAAGGGCTATCTG
64 ACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
140827 TCAATAAAAT
Statistics
Matches: 568, Mismatches: 55, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
167 1 0.00
168 458 0.81
169 109 0.19
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (168 bp):
TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTTGACTAC
GCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAA
GACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
Found at i:141493 original size:43 final size:43
Alignment explanation
Indices: 141446--141579 Score: 169
Period size: 43 Copynumber: 3.1 Consensus size: 43
141436 TATATATATA
** * **
141446 TTATTATATATACGCGTTACATATGATTTTACATTAACTTCTT
1 TTATTATATATACAAGTTACATATGAGTACACATTAACTTCTT
* * *
141489 TTATTATATATACAAGTTACATATTAGTACATATTAACTTGTT
1 TTATTATATATACAAGTTACATATGAGTACACATTAACTTCTT
* * *
141532 TTATTATATATACAAGTTACATATTAGTACATATTAACTTGTT
1 TTATTATATATACAAGTTACATATGAGTACACATTAACTTCTT
141575 TTATT
1 TTATT
141580 TGGATACATT
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (43 bp):
TTATTATATATACAAGTTACATATGAGTACACATTAACTTCTT
Found at i:141536 original size:23 final size:23
Alignment explanation
Indices: 141510--141579 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 23
141500 ACAAGTTACA
141510 TATTAGTACATATTAACTTGTTT
1 TATTAGTACATATTAACTTGTTT
* * * ***
141533 TATTA-TATATA-CAAGTT-ACA
1 TATTAGTACATATTAACTTGTTT
141553 TATTAGTACATATTAACTTGTTT
1 TATTAGTACATATTAACTTGTTT
141576 TATT
1 TATT
141580 TGGATACATT
Statistics
Matches: 32, Mismatches: 12, Indels: 6
0.64 0.24 0.12
Matches are distributed among these distances:
20 5 0.16
21 9 0.28
22 9 0.28
23 9 0.28
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (23 bp):
TATTAGTACATATTAACTTGTTT
Done.