Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003085.1 Hibiscus syriacus cultivar Beakdansim tig00006439_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: 82678
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1620 original size:22 final size:22
Alignment explanation
Indices: 1593--1646 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1583 TACCATAGCA
* *
1593 TAGTATCGGTACCATTGTATGG
1 TAGTATCGATACCATGGTATGG
1615 TAGTATCGATACCATGGTATGG
1 TAGTATCGATACCATGGTATGG
1637 --GTATCGATAC
1 TAGTATCGATAC
1647 TGAGGAGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.33
22 20 0.67
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (22 bp):
TAGTATCGATACCATGGTATGG
Found at i:2118 original size:55 final size:55
Alignment explanation
Indices: 1953--2230 Score: 309
Period size: 55 Copynumber: 5.1 Consensus size: 55
1943 ATTACCAAAT
* * * *
1953 AGGCATTATGTGTGCAAATCCATGAAATTCATCATGAGTTTATGAATAACCT-TAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAA-CTGTAC
* ** * *
2008 ACGCTTTATATGTGCAAATCCACGGAA-TCATCATGAATTGATGAATAACCT-TAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAA-CTGTAC
* *
2062 AGGCACTATGTGTGTAAATCCACGGAATTCATTATGAGTTGATGAATAACTGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
* * * *
2117 AGTCCCTATGTGTGCAAATCCACGGAATTTATCATGAGTTGATGAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
* * * * *
2172 AGGCA-TATGTATG--AA-CCACGGAATTCATCATGAGTAGATGAATTACCGTAT
1 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
2223 AGGCACTA
1 AGGCACTA
2231 CTCATGCATT
Statistics
Matches: 193, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
51 37 0.19
52 4 0.02
54 56 0.29
55 96 0.50
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (55 bp):
AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
Found at i:2144 original size:109 final size:108
Alignment explanation
Indices: 1953--2214 Score: 327
Period size: 109 Copynumber: 2.4 Consensus size: 108
1943 ATTACCAAAT
* * * **
1953 AGGCATTATGTGTGCAAATCCATGAAATTCATCATGAGTTTATGAATAACCTTACACGCTTTATA
1 AGGCA-TATGTGTG-AAATCCACGGAATTCATCATGAGTTGATGAATAACCTTACACGCCCTATA
*
2018 TGTGCAAATCCACGGAA-TCATCATGAATTGATGAATAACCTTAC
64 TGTGCAAATCCACGGAATTCATCATGAATTGATGAATAACCGTAC
*
2062 AGGCACTATGTGTGTAAATCCACGGAATTCATTATGAGTTGATGAATAA-CTGTACA-GTCCCTA
1 AGGCA-TATGTGTG-AAATCCACGGAATTCATCATGAGTTGATGAATAACCT-TACACG-CCCTA
* * *
2125 TGTGTGCAAATCCACGGAATTTATCATGAGTTGATGAATAACCGTAC
62 TATGTGCAAATCCACGGAATTCATCATGAATTGATGAATAACCGTAC
* *
2172 AGGCATATGTATG-AA-CCACGGAATTCATCATGAGTAGATGAAT
1 AGGCATATGTGTGAAATCCACGGAATTCATCATGAGTTGATGAAT
2215 TACCGTATAG
Statistics
Matches: 135, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
106 26 0.19
107 2 0.01
108 3 0.02
109 75 0.56
110 29 0.21
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (108 bp):
AGGCATATGTGTGAAATCCACGGAATTCATCATGAGTTGATGAATAACCTTACACGCCCTATATG
TGCAAATCCACGGAATTCATCATGAATTGATGAATAACCGTAC
Found at i:2919 original size:22 final size:21
Alignment explanation
Indices: 2885--2998 Score: 68
Period size: 23 Copynumber: 5.0 Consensus size: 21
2875 CAAAAAACAT
*
2885 AAAAAGATTGAAAG-AGAAAATGA
1 AAAAAGA-AGAAAGAAGAAAA--A
2908 AAAAAGAAGAAAAGAAGAAAAA
1 AAAAAGAAG-AAAGAAGAAAAA
2930 AAAAAGAAGAAAAAGAGAGAAAAA
1 AAAAAGAAG--AAAGA-AGAAAAA
* * * *
2954 GAAAAGAAAAAATAAACAAAAGA
1 AAAAAGAAGAAA-GAAGAAAA-A
* *
2977 AAAAAAAAGAGAAAAAGAAAAA
1 AAAAAGAAGA-AAGAAGAAAAA
2999 TAGACAAATC
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
22 20 0.27
23 33 0.44
24 22 0.29
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.04
Consensus pattern (21 bp):
AAAAAGAAGAAAGAAGAAAAA
Found at i:2920 original size:8 final size:8
Alignment explanation
Indices: 2895--2997 Score: 71
Period size: 8 Copynumber: 13.4 Consensus size: 8
2885 AAAAAGATTG
2895 AAAG-AGA
1 AAAGAAGA
2902 AAATGAA-A
1 AAA-GAAGA
2910 AAAGAAGA
1 AAAGAAGA
2918 AAAGAAGA
1 AAAGAAGA
2926 AAA-AA-A
1 AAAGAAGA
2932 AAAGAAGA
1 AAAGAAGA
2940 AAA-AGAGA
1 AAAGA-AGA
2948 GAAA-AAGA
1 -AAAGAAGA
2956 AAAGAA-A
1 AAAGAAGA
* *
2963 AAATAAACA
1 AAA-GAAGA
2972 AAAGAA-A
1 AAAGAAGA
*
2979 AAAAAAGA
1 AAAGAAGA
2987 GAAA-AAGA
1 -AAAGAAGA
2995 AAA
1 AAA
2998 ATAGACAAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 24
0.75 0.03 0.22
Matches are distributed among these distances:
6 4 0.05
7 27 0.33
8 38 0.47
9 12 0.15
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAGAAGA
Found at i:2930 original size:10 final size:10
Alignment explanation
Indices: 2906--2992 Score: 72
Period size: 9 Copynumber: 8.6 Consensus size: 10
2896 AAGAGAAAAT
2906 GAAAAAAGAA
1 GAAAAAAGAA
2916 GAAAAGAAGAAA
1 GAAAA-AAG-AA
*
2928 AAAAAAAGAA
1 GAAAAAAGAA
2938 G-AAAAAGAGA
1 GAAAAAAGA-A
*
2948 GAAAAAGAAAA
1 GAAAAA-AGAA
*
2959 GAAAAAATAA
1 GAAAAAAGAA
*
2969 -ACAAAAGAA
1 GAAAAAAGAA
*
2978 AAAAAAAG-A
1 GAAAAAAGAA
2987 GAAAAA
1 GAAAAA
2993 GAAAAATAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
9 20 0.32
10 18 0.29
11 17 0.27
12 8 0.13
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (10 bp):
GAAAAAAGAA
Found at i:2931 original size:11 final size:11
Alignment explanation
Indices: 2907--2995 Score: 74
Period size: 11 Copynumber: 7.8 Consensus size: 11
2897 AGAGAAAATG
2907 AAAAAAGAAGA
1 AAAAAAGAAGA
* *
2918 AAAGAAGAAAA
1 AAAAAAGAAGA
2929 AAAAAAGAAGA
1 AAAAAAGAAGA
2940 AAAAGAGAGAA-A
1 AAAA-A-AGAAGA
*
2952 AAGAAAAGAAAA
1 AA-AAAAGAAGA
*
2964 AATAAACAAAAGA
1 AA-AAA-AGAAGA
2977 AAAAAA-AAGA
1 AAAAAAGAAGA
*
2987 GAAAAAGAA
1 AAAAAAGAA
2996 AAATAGACAA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
10 9 0.14
11 29 0.45
12 14 0.22
13 12 0.19
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (11 bp):
AAAAAAGAAGA
Found at i:2993 original size:39 final size:38
Alignment explanation
Indices: 2914--2997 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 38
2904 ATGAAAAAAG
* *
2914 AAGAAAAGAAGAAAAAAAAAAGAAGAAAAAGAGAGAAA
1 AAGAAAAGAAAAAAAAAAAAAGAAGAAAAAAAGAGAAA
2952 AAGAAAAGAAAAAATAAACAAAAGAA-AAAAAAAGAGAAA
1 AAGAAAAGAAAAAA-AAA-AAAAGAAGAAAAAAAGAGAAA
2991 AAGAAAA
1 AAGAAAA
2998 ATAGACAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
38 13 0.31
39 22 0.52
40 7 0.17
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (38 bp):
AAGAAAAGAAAAAAAAAAAAAGAAGAAAAAAAGAGAAA
Found at i:5276 original size:41 final size:40
Alignment explanation
Indices: 5165--5276 Score: 100
Period size: 41 Copynumber: 2.7 Consensus size: 40
5155 AGTGTTTCTT
* *
5165 GATGAGTAAGTCCTTCT-GGCCATCAGTAAGTCTTTCGAGCAT
1 GATGA-TAAGT-CTTTTGGGCCATCA-TAAGTCTTTCGAGCAA
** * * * *
5207 GATTCTTAAATCATTTGGGTCATTATAAGTCTTTCGAGCAA
1 GA-TGATAAGTCTTTTGGGCCATCATAAGTCTTTCGAGCAA
5248 GATGATAAGTCTTTTGGGCCATCCATAAG
1 GATGATAAGTCTTTTGGGCCAT-CATAAG
5277 ACCTTCGGGC
Statistics
Matches: 53, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
40 15 0.28
41 25 0.47
42 12 0.23
43 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (40 bp):
GATGATAAGTCTTTTGGGCCATCATAAGTCTTTCGAGCAA
Found at i:5513 original size:273 final size:270
Alignment explanation
Indices: 5012--5677 Score: 845
Period size: 273 Copynumber: 2.4 Consensus size: 270
5002 GGGGTTTCTT
* * * * * * **
5012 GATGTTTTCAAATGAGTTTTTAAAAACTAATCCTGATTTTCAAGGGTTTCTTGATAATAATTTTT
1 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTAC
* * * * *
5077 AATGATTTTTTTTAAAAAAAGCTATCCTAATTTTTAGGGGTTCCTTGATGACAGCTAAGAAAGTA
66 AAAGA---ATTTTAAAAGAAGCTATCCTAA-TTTTAGGGGTTCC-T--TGACAACTAAGAAACTA
* *
5142 AGCTTGATTTTCAAGTGTTTCTTGATGAGTAAGTCCTTCTGGCCATCAGTAAGTCTTTCGAGCAT
124 AGCTTGATTTTCAAGAGTTTCTTGATGAGTAAGTCCTTCTGGCAATCAGTAAGTCTTTCGAGCAT
** * * *
5207 GATTCTTAAATCATTTGGGTCATTATAAGTCTTTCGAGCAAGATGATAAGTCTTTTGGGCCATCC
189 GATGATTAAATCATTCGGGTCATTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
**
5272 ATAAGACCTTCGGGCCG
254 ATAAGACCTTCGGGAAG
*
5289 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGATTCTTGATGATTATCTAC
1 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTAC
*
5354 AAAGAGGTTTTAAAAGGAAGCTAATCCTAATTTTAGGGGTTCCTTGACAACTAAGAAACTAAGCT
66 AAAGA-ATTTTAAAA-GAAGCT-ATCCTAATTTTAGGGGTTCCTTGACAACTAAGAAACTAAGCT
* *
5419 TGATTTTCAAGAGTTTCTTGATGAGTAAGTCCTTC-GGACAAT-AGTAAGTCTTTTGATCATGAT
128 TGATTTTCAAGAGTTTCTTGATGAGTAAGTCCTTCTGG-CAATCAGTAAGTCTTTCGAGCATGAT
*
5482 GATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
192 GATTAAATCATTCGGGTCAT-TATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCAT
* *
5547 AAGACCTTTGGGAAT
256 AAGACCTTCGGGAAG
* *
5562 GTTGTTTTCAAAAT-A-TTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTC
1 GATGTTTTC-AAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTA
* * * * *
5625 CAAAGAATTTTTAAAGAATGCTATAACTAATTTTACGGGTTTCTTGATAACTA
65 CAAAGAATTTTAAAAGAA-GCTAT-CCTAATTTTAGGGGTTCCTTGACAACTA
5678 TAAACGAATC
Statistics
Matches: 344, Mismatches: 38, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
270 5 0.01
271 34 0.10
272 89 0.26
273 118 0.34
274 4 0.01
275 9 0.03
276 18 0.05
277 67 0.19
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (270 bp):
GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTAC
AAAGAATTTTAAAAGAAGCTATCCTAATTTTAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGA
TTTTCAAGAGTTTCTTGATGAGTAAGTCCTTCTGGCAATCAGTAAGTCTTTCGAGCATGATGATT
AAATCATTCGGGTCATTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGAC
CTTCGGGAAG
Found at i:5534 original size:41 final size:42
Alignment explanation
Indices: 5438--5549 Score: 113
Period size: 41 Copynumber: 2.7 Consensus size: 42
5428 AGAGTTTCTT
* * * *
5438 GATGAGTAAGTCCTTC-GGACA-ATAGTAAGTCTTTTGATCAT
1 GATGAGTAAGTCCTTCGGGACATCTA-TAAGTCTTTCGAGCAA
* * *
5479 GATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAA
1 GATGAGTAAGTCCTTCGGGACATCTATAAGTCTTTCGAGCAA
* *
5521 GATGA-TAAGTCCTTCGGGCCATCCATAAG
1 GATGAGTAAGTCCTTCGGGACATCTATAAG
5550 ACCTTTGGGA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 35 0.59
42 22 0.37
43 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (42 bp):
GATGAGTAAGTCCTTCGGGACATCTATAAGTCTTTCGAGCAA
Found at i:6574 original size:91 final size:92
Alignment explanation
Indices: 6419--6660 Score: 362
Period size: 91 Copynumber: 2.7 Consensus size: 92
6409 ATTTTAAATA
*
6419 GAGAGTTCATAATGAGAAGAACTCATCCAACGATGGAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
6484 TCAATCTTGCATCAACATTTCTAG-TG
66 TCAACCTTGCATCAACATTTCCAGCAG
* *
6510 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTTATAATTAGAAGAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
*
6575 TCAACCTTGTATCAACATTTCCAGCAG
66 TCAACCTTGCATCAACATTTCCAGCAG
* * ** *
6602 G-GAGATCATAATGAGAAGAACTCATCCGACGAGTAAGAATAAGTTCATAATGAGAAGAA
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAA
6661 TTCATCCGAC
Statistics
Matches: 136, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
91 134 0.99
92 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (92 bp):
GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTGCATCAACATTTCCAGCAG
Found at i:6649 original size:23 final size:23
Alignment explanation
Indices: 6623--6688 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
6613 TGAGAAGAAC
*
6623 TCATCCGACGAGTAAGAATAAGT
1 TCATCCGACGAGTGAGAATAAGT
*
6646 TCAT---A--A-TGAGAAGAA-T
1 TCATCCGACGAGTGAGAATAAGT
6662 TCATCCGACGAGTGAGAATAAGT
1 TCATCCGACGAGTGAGAATAAGT
6685 TCAT
1 TCAT
6689 AATGAGAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 14
0.66 0.06 0.28
Matches are distributed among these distances:
16 5 0.15
17 7 0.21
18 1 0.03
19 1 0.03
20 1 0.03
21 1 0.03
22 8 0.24
23 9 0.27
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (23 bp):
TCATCCGACGAGTGAGAATAAGT
Found at i:6666 original size:39 final size:39
Alignment explanation
Indices: 6607--6701 Score: 172
Period size: 39 Copynumber: 2.4 Consensus size: 39
6597 AGCAGGGAGA
6607 TCATAATGAGAAGAACTCATCCGACGAGTAAGAATAAGT
1 TCATAATGAGAAGAACTCATCCGACGAGTAAGAATAAGT
* *
6646 TCATAATGAGAAGAATTCATCCGACGAGTGAGAATAAGT
1 TCATAATGAGAAGAACTCATCCGACGAGTAAGAATAAGT
6685 TCATAATGAGAAGAACT
1 TCATAATGAGAAGAACT
6702 TGTTCAACCT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (39 bp):
TCATAATGAGAAGAACTCATCCGACGAGTAAGAATAAGT
Found at i:6679 original size:22 final size:23
Alignment explanation
Indices: 6613--6688 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 23
6603 GAGATCATAA
*
6613 TGAGAAGAA-CTCATCCGACGAG
1 TGAGAAGAAGTTCATCCGACGAG
* *
6635 TAAGAATAAGTTCAT---A--A-
1 TGAGAAGAAGTTCATCCGACGAG
6652 TGAGAAGAA-TTCATCCGACGAG
1 TGAGAAGAAGTTCATCCGACGAG
*
6674 TGAGAATAAGTTCAT
1 TGAGAAGAAGTTCAT
6689 AATGAGAAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 15
0.66 0.10 0.25
Matches are distributed among these distances:
16 5 0.12
17 7 0.17
18 1 0.03
19 1 0.03
20 1 0.03
21 1 0.03
22 15 0.38
23 9 0.22
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (23 bp):
TGAGAAGAAGTTCATCCGACGAG
Found at i:6696 original size:17 final size:17
Alignment explanation
Indices: 6637--6696 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 17
6627 CCGACGAGTA
6637 AGAATAAGTTCATAATG
1 AGAATAAGTTCATAATG
*
6654 AGAAGAA-TTCATCCGACGAGTG
1 AGAATAAGTTCAT---A--A-TG
6676 AGAATAAGTTCATAATG
1 AGAATAAGTTCATAATG
6693 AGAA
1 AGAA
6697 GAACTTGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
16 5 0.15
17 12 0.35
18 1 0.03
19 1 0.03
20 1 0.03
21 1 0.03
22 8 0.24
23 5 0.15
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.23
Consensus pattern (17 bp):
AGAATAAGTTCATAATG
Found at i:6697 original size:130 final size:129
Alignment explanation
Indices: 6513--6791 Score: 380
Period size: 130 Copynumber: 2.2 Consensus size: 129
6503 TCTAGTGGAG
* *
6513 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTTATAATTAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
** * * *
6578 ACCTTGTATCAACATTTCCAGCAG-GGAGATCATAATGAGAAGAACTCATCCGACGAGTAAGAAT
66 ACCTTACATCAACA-TTCCAG-AGTGGAGATCATAATGAGAAGAACTCATCCAACGAGGAAGAAG
6642 A
129 A
* * * *
6643 AGTTCATAATGAGAAGAATTCATCCGACGAGTGAGAATAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * *
6708 ACCTTACATCAACATTCCAGTGTGGAGCTCTTAATGAGAAGAACTCATCCAACGAGGGATAAGA
66 ACCTTACATCAACATTCCAGAGTGGAGATCATAATGAGAAGAACTCATCCAACGAGGAAGAAGA
*
6772 AGTTCATAATGGGAAGAACT
1 AGTTCATAATGAGAAGAACT
6792 TGTTCAACCT
Statistics
Matches: 130, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
128 1 0.01
129 58 0.45
130 71 0.55
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (129 bp):
AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTACATCAACATTCCAGAGTGGAGATCATAATGAGAAGAACTCATCCAACGAGGAAGAAGA
Found at i:6869 original size:91 final size:91
Alignment explanation
Indices: 6643--7441 Score: 1057
Period size: 91 Copynumber: 8.8 Consensus size: 91
6633 AGTAAGAATA
* * * *
6643 AGTTCATAATGAGAAGAATTCATCCGACGAGTGAGAATAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
6708 ACCTTACATCAACA-TTCCAGTGTG-G
66 ACCTTACATCAACATTTCCAGTG-GAG
* * * *
6733 AGCTCTTAATGAGAAGAACTCATCCAACGAGGGATAAGAAGTTCATAATGGGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
6798 ACCTTACATCAACATTTCCAGTGGGG
66 ACCTTACATCAACATTTCCAGTGGAG
* * * *
6824 AGTTTATAATGAGAATAACTCATCCAAAGAGGGAGAAGAAATTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
6889 ACCTTGCATCAAAATTTCCAGTGGAG
66 ACCTTACATCAACATTTCCAGTGGAG
* * *
6915 AGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAATAAGTTCATAATGAGAATAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* **
6980 ACCTTGCATCAACATTTCCAGCAGAG
66 ACCTTACATCAACATTTCCAGTGGAG
* * *** *
7006 AGTTCATAATGAGAGGAACTTATATGACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
7071 ACCTTACATGAACATTTCCAGTGGGG
66 ACCTTACATCAACATTTCCAGTGGAG
*
7097 AGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAG--AAGAAGTTCATAATGAGAAGAACTTGTT
*
7162 CAACCTTACATCAACATTTCCAGTGGGG
64 CAACCTTACATCAACATTTCCAGTGGAG
* * * * * *
7190 AGTTCATAATGAGAAGAGCTCATCCAACGAGGGATAAGAAGTTTATAATTAGAATAACTTATTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
7255 ACCTTGGC-TCAACATTTCCAGTGGAG
66 ACCTT-ACATCAACATTTCCAGTGGAG
* * * *
7281 AGTTCTTAATGAGAAGAACTCATCCAATGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
7346 ACCTTGAC-TCAACATTTTCAATGGAG
66 ACCTT-ACATCAACATTTCCAGTGGAG
* * * * * * * *
7372 AGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTTATAATAAGAATAACGTATTCA
1 AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
7437 ACCTT
66 ACCTT
7442 TGTTTGATTC
Statistics
Matches: 625, Mismatches: 79, Indels: 9
0.88 0.11 0.01
Matches are distributed among these distances:
90 72 0.12
91 466 0.75
92 1 0.00
93 86 0.14
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (91 bp):
AGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTACATCAACATTTCCAGTGGAG
Found at i:7257 original size:366 final size:363
Alignment explanation
Indices: 6643--7441 Score: 1156
Period size: 366 Copynumber: 2.2 Consensus size: 363
6633 AGTAAGAATA
* *
6643 AGTTCATAATGAGAAGAA-TTCATCCGACGAGTGAGAATAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTT-ATCCGACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC
* * *
6707 AACCTTACATCAACATTCCAGTGTGGAGCTCTTAATGAGAAGAACTCATCCAACGAGGGATAAGA
65 AACCTTACATCAACATTCCAGTGGGGAGCTCATAATGAGAAGAACTCATCCAACGAGGGAAAAGA
* *
6772 AGTTCATAATGGGAAGAACTTGTTCAACCTTACATCAACATTTCCAGTGGGGAGTTTATAATGAG
130 AGTTCATAATGAGAAGAACTTGTTCAACCTTACATCAACATTTCCAGTGGGGAGTTCATAATGAG
* *
6837 AATAACTCATCCAAAGAGGGAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTT-GCATCAA
195 AAGAACTCATCCAAAGAGGGAGAAGAAATTCATAATGAGAAGAACTTATTCAACCTTGGC-TCAA
* * *
6901 AATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAATAAGTTCATAATGA
259 AATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGAAGAAGAAGTTCATAATGA
* *
6966 GAATAACTTGTTCAACCTTG-CATCAACATTTCCAGCAGAG
324 GAAGAACTTGTTCAACCTTGAC-TCAACATTTCCAACAGAG
* **
7006 AGTTCATAATGAGAGGAACTTATATGACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTTATCCGACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCA
* * *
7071 ACCTTACATGAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAAA
66 ACCTTACATCAACA-TTCCAGTGGGGAGCTCATAATGAGAAGAACTCATCCAACGA-GG-GAAAA
7136 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTACATCAACATTTCCAGTGGGGAGTTCATAATG
128 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTACATCAACATTTCCAGTGGGGAGTTCATAATG
* * * * * * *
7201 AGAAGAGCTCATCCAACGAGGGATAAGAAGTTTATAATTAGAATAACTTATTCAACCTTGGCTCA
193 AGAAGAACTCATCCAAAGAGGGAGAAGAAATTCATAATGAGAAGAACTTATTCAACCTTGGCTCA
* *
7266 ACATTTCCAGTGGAGAGTTCTTAATGAGAAGAACTCATCCAATGAAGAAGAAGAAGTTCATAATG
258 AAATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGAAGAAGAAGTTCATAATG
* **
7331 AGAAGAACTTGTTCAACCTTGACTCAACATTTTCAATGGAG
323 AGAAGAACTTGTTCAACCTTGACTCAACATTTCCAACAGAG
* * * * * * *
7372 AGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAA-TTTATAATAAGAATAACGTATTC
1 AGTTCATAATGAGAAGAACTTATCCGACGAGGGAGAA-AAAGTTCATAATGAGAAGAACTTGTTC
7436 AACCTT
65 AACCTT
7442 TGTTTGATTC
Statistics
Matches: 387, Mismatches: 42, Indels: 11
0.88 0.10 0.03
Matches are distributed among these distances:
363 70 0.18
364 39 0.10
365 2 0.01
366 270 0.70
367 6 0.02
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (363 bp):
AGTTCATAATGAGAAGAACTTATCCGACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTACATCAACATTCCAGTGGGGAGCTCATAATGAGAAGAACTCATCCAACGAGGGAAAAGAA
GTTCATAATGAGAAGAACTTGTTCAACCTTACATCAACATTTCCAGTGGGGAGTTCATAATGAGA
AGAACTCATCCAAAGAGGGAGAAGAAATTCATAATGAGAAGAACTTATTCAACCTTGGCTCAAAA
TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTGACTCAACATTTCCAACAGAG
Found at i:7573 original size:20 final size:19
Alignment explanation
Indices: 7511--7574 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
7501 TCATTGGAGA
7511 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
7530 CATCCAACAATAGAGAAGAA--
1 -GTTC-ATAAT-GAGAAGAACT
7550 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
7570 GTTCA
1 GTTCA
7575 ACCTTGGTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 2 0.06
20 7 0.21
21 4 0.12
22 8 0.24
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:9225 original size:54 final size:54
Alignment explanation
Indices: 9115--9444 Score: 425
Period size: 54 Copynumber: 6.1 Consensus size: 54
9105 TTGATGAACG
* *
9115 ATAGGCACTATGTGTGCAAACCAC--ATATTCATCATATGTTGATGAACGACCAT
1 ATAGGCACTATGTGTGCAACCCACGGA-ATTCATCATATGTTGATGAACGACCGT
* * *
9168 ATAGGAACTATGTGTGCAACCCACGGAATCCATCATATGTTAATGAAC-ACCCGT
1 ATAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGA-CCGT
* * *
9222 ATAGGAACTATGTGTGCAACCCACAGAATCCATCATATGTTGATGAACGACCGT
1 ATAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGT
* ***
9276 ATATGCACTATGTGTGCAACCCAAAAAATTCATCATATGTTGATGAAC-AGCCGT
1 ATAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGA-CCGT
* * * * *
9330 ATAGGCACTATGTGTGAAACCAATGGAGTTCATCATATGTTGATGAACGACTGT
1 ATAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGT
* *
9384 ATAGGCACTAAGTGTGCAACCCACGGAATTCATTATATGTTGATGAACGACCGT
1 ATAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGT
*
9438 ATCGGCA
1 ATAGGCA
9445 TTACGTATAC
Statistics
Matches: 243, Mismatches: 28, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
53 24 0.10
54 216 0.89
55 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (54 bp):
ATAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGT
Found at i:10169 original size:27 final size:27
Alignment explanation
Indices: 10122--10176 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
10112 ATGAAAAGAA
*
10122 TTTTTTTGATTTTTTGCTCTCCATTTT
1 TTTTTTTGATTTTTTGCTCTCCAGTTT
* *
10149 TTTTTTTGCTTTCTTT-TTCTCCAGTTT
1 TTTTTTTGATTT-TTTGCTCTCCAGTTT
10176 T
1 T
10177 ACTTTACCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.05, C:0.16, G:0.07, T:0.71
Consensus pattern (27 bp):
TTTTTTTGATTTTTTGCTCTCCAGTTT
Found at i:19419 original size:38 final size:38
Alignment explanation
Indices: 19351--19484 Score: 173
Period size: 38 Copynumber: 3.6 Consensus size: 38
19341 ATTCTAATCT
* **
19351 AATATAAATTCAT-ATTAATATATTTGTATTTTAATTG
1 AATATAAATTCATAAATAATATATTCATATTTTAATTG
*
19388 AATATAAATTCATAAATAATATATTCATATTTCAATTG
1 AATATAAATTCATAAATAATATATTCATATTTTAATTG
* *
19426 AATATAAATTCGTAAATAATATATTTGA-ATTTTAATTG
1 AATATAAATTCATAAATAATATA-TTCATATTTTAATTG
* *
19464 AATATAAATCCTTAAATAATA
1 AATATAAATTCATAAATAATA
19485 GAGCATTATC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
37 13 0.15
38 70 0.81
39 3 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (38 bp):
AATATAAATTCATAAATAATATATTCATATTTTAATTG
Found at i:24462 original size:65 final size:61
Alignment explanation
Indices: 24380--24516 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 61
24370 GTATGTTTAT
* * *
24380 ATTAGCACTAGTGTGTAAGGACACTAATTGCAGGTGGAGGGCACAACTTTATGTGTCATATCCGG
1 ATTAGCACTAGAGTGTAA--AC-CT-AGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCGG
* * * **
24445 ATTAGCCCTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTGTCATATCCGG
1 ATTAGCACTAGAGTGTAAACCTAGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCGG
24506 ATTTAGCACTA
1 A-TTAGCACTA
24517 CGGTGCATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
61 34 0.55
62 10 0.16
63 2 0.03
65 16 0.26
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (61 bp):
ATTAGCACTAGAGTGTAAACCTAGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCGG
Found at i:25337 original size:21 final size:21
Alignment explanation
Indices: 25313--25376 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
25303 ATGGTGTTAC
25313 ATAATTAATCATAATCGTAAT
1 ATAATTAATCATAATCGTAAT
* * *
25334 ATAACTCAT-AAAATAC-T-A-
1 ATAATTAATCATAAT-CGTAAT
*
25352 ATAATTAATCCTAATCGTAAT
1 ATAATTAATCATAATCGTAAT
25373 ATAA
1 ATAA
25377 ATCACACCCT
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
18 8 0.26
19 5 0.16
20 6 0.19
21 12 0.39
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.34
Consensus pattern (21 bp):
ATAATTAATCATAATCGTAAT
Found at i:26524 original size:21 final size:20
Alignment explanation
Indices: 26498--26536 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
26488 TAAGGCATTA
26498 AACATCATAAACAAAACAAAT
1 AACATCATAAA-AAAACAAAT
*
26519 AACATCATACAAAAACAA
1 AACATCATAAAAAAACAA
26537 CCATCCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.13
Consensus pattern (20 bp):
AACATCATAAAAAAACAAAT
Found at i:27394 original size:20 final size:20
Alignment explanation
Indices: 27365--27403 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27355 TTTCCACCGC
*
27365 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
27385 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
27404 TATGGGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:28039 original size:13 final size:14
Alignment explanation
Indices: 28008--28040 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
27998 TTTATTCACA
28008 ATTTCATTTTCTTC
1 ATTTCATTTTCTTC
28022 A-TTCATTTT-TTC
1 ATTTCATTTTCTTC
28034 ATTTCAT
1 ATTTCAT
28041 GCGAGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 13 0.72
14 1 0.06
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTCATTTTCTTC
Found at i:36045 original size:39 final size:39
Alignment explanation
Indices: 36000--36078 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
35990 TACTAATAAA
* **
36000 ATAAAATACTAATAATTAATCCTATTTGTAATATAACTC
1 ATAAAATACTAATAATTAATCCTAATCATAATATAACTC
*
36039 ATAAAATACTAATAATTAATTCTAATCATAATATAACTC
1 ATAAAATACTAATAATTAATCCTAATCATAATATAACTC
36078 A
1 A
36079 CAACAACATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.37
Consensus pattern (39 bp):
ATAAAATACTAATAATTAATCCTAATCATAATATAACTC
Found at i:49468 original size:71 final size:71
Alignment explanation
Indices: 49352--49483 Score: 194
Period size: 71 Copynumber: 1.9 Consensus size: 71
49342 ATTTTAGATA
* *
49352 CGTAAGAAATTGCCAACTTGATCAGTCTGAACCTATATAAGGAATTACCAATTTGACCAAGCTGA
1 CGTAAGAAATTACCAACTTGATCAGTATGAACCTATATAAGGAATTACCAATTTGACCAAGCTGA
49417 TCCTAC
66 TCCTAC
* * * *
49423 CGTAAGAAATTACCAA-TTCTATCGGTATGAACCTATATAAGGAATTACCAGTTTGATCAAG
1 CGTAAGAAATTACCAACTT-GATCAGTATGAACCTATATAAGGAATTACCAATTTGACCAAG
49484 TTAAACCTGC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 2 0.04
71 52 0.96
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (71 bp):
CGTAAGAAATTACCAACTTGATCAGTATGAACCTATATAAGGAATTACCAATTTGACCAAGCTGA
TCCTAC
Found at i:49491 original size:35 final size:35
Alignment explanation
Indices: 49354--49491 Score: 111
Period size: 35 Copynumber: 3.9 Consensus size: 35
49344 TTTAGATACG
* * *
49354 TAAGAAATTGCCAACTTGATC-AGTCTGAACCTATA
1 TAAGGAATTACCAATTTGATCAAGT-TGAACCTATA
* * * **
49389 TAAGGAATTACCAATTTGACCAAGCTGATCCTACCG
1 TAAGGAATTACCAATTTGATCAAGTTGAACCTA-TA
* *
49425 TAAGAAATTACCAATTCT-ATC-GGTATGAACCTATA
1 TAAGGAATTACCAATT-TGATCAAGT-TGAACCTATA
* *
49460 TAAGGAATTACCAGTTTGATCAAGTTAAACCT
1 TAAGGAATTACCAATTTGATCAAGTTGAACCT
49492 GCAGATCATA
Statistics
Matches: 78, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
34 1 0.01
35 48 0.62
36 28 0.36
37 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (35 bp):
TAAGGAATTACCAATTTGATCAAGTTGAACCTATA
Found at i:57004 original size:16 final size:16
Alignment explanation
Indices: 56983--57016 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
56973 ACAATATACT
56983 TTTA-TTTACTTAATTA
1 TTTATTTTACTT-ATTA
56999 TTTATTTTACTTATTA
1 TTTATTTTACTTATTA
57015 TT
1 TT
57017 CAAACTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTTACTTATTA
Found at i:60632 original size:47 final size:47
Alignment explanation
Indices: 60547--60648 Score: 114
Period size: 47 Copynumber: 2.2 Consensus size: 47
60537 CTCGAAACCA
* *** *
60547 GCTCTAGTTGTTATACATTAAAGAATTGCTAGAGGTGCCCAAAATTG
1 GCTCTAGTTGTTACACATTAAAGAAACACTAGACGTGCCCAAAATTG
* * * *
60594 GCTCTAGTTGTTACACATTCAAGAAACATTAGACGTGCCCGAAGTTG
1 GCTCTAGTTGTTACACATTAAAGAAACACTAGACGTGCCCAAAATTG
*
60641 TCTCTAGT
1 GCTCTAGT
60649 CGACTAAATT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (47 bp):
GCTCTAGTTGTTACACATTAAAGAAACACTAGACGTGCCCAAAATTG
Found at i:66885 original size:21 final size:20
Alignment explanation
Indices: 66838--66885 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
66828 AATTTAAACC
66838 TTATT-TAAAAATTAAAAAA
1 TTATTATAAAAATTAAAAAA
* *
66857 TTATTTATAAAATTTAAATTAA
1 TTA-TTATAAAAATTAAA-AAA
66879 TTATTAT
1 TTATTAT
66886 TTCCAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 14 0.58
22 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATTATAAAAATTAAAAAA
Found at i:78626 original size:24 final size:24
Alignment explanation
Indices: 78550--78658 Score: 92
Period size: 24 Copynumber: 4.5 Consensus size: 24
78540 AAACAGAGAT
* * * *
78550 ATCATAAATCAAAACAAAATTCAG
1 ATCAGAAATCAGAACAGAATCCAG
* * * *
78574 ATCATATATCAAAATAGAATCCAG
1 ATCAGAAATCAGAACAGAATCCAG
*
78598 ATCAGAAATCAGAACATAATCCAG
1 ATCAGAAATCAGAACAGAATCCAG
* ** * *
78622 GTCAGGTATCAGAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATCCAG
78646 ATCAGAAATCAGA
1 ATCAGAAATCAGA
78659 TAAAACATTC
Statistics
Matches: 67, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATCCAG
Found at i:80331 original size:20 final size:20
Alignment explanation
Indices: 80281--80337 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
80271 AAATGACCAA
80281 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGAACTC
* * * *
80301 CAATTTTGCAACTC-AATTTC
1 CAAATTCGCAACGCGAA-CTC
80321 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
80338 TATGTAAATC
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGAACTC
Found at i:80349 original size:20 final size:20
Alignment explanation
Indices: 80326--80412 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
80316 ATTTCCAAAT
*
80326 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
* * * *
80346 TCGCAACGTGCATCTATAAA
1 TCGCAACGCGAATTTGTAAA
*
80366 TCGCAATGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
* *
80386 TCGCAACGCGGATTTGTAAT
1 TCGCAACGCGAATTTGTAAA
80406 TCGCAAC
1 TCGCAAC
80413 ACAGAAGTCA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:80410 original size:40 final size:40
Alignment explanation
Indices: 80323--80412 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
80313 TCAATTTCCA
*
80323 AATTCGCAACGCGAATATGTAAATCGCAACGTGCATCTAT
1 AATTCGCAACGCGAATATGTAAATCGCAACGCGCATCTAT
* * * * * *
80363 AAATCGCAATGCGAATTTGTAAATCGCAACGCGGATTTGT
1 AATTCGCAACGCGAATATGTAAATCGCAACGCGCATCTAT
80403 AATTCGCAAC
1 AATTCGCAAC
80413 ACAGAAGTCA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (40 bp):
AATTCGCAACGCGAATATGTAAATCGCAACGCGCATCTAT
Found at i:80601 original size:22 final size:22
Alignment explanation
Indices: 80571--80623 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
80561 ACTCTCTATG
*
80571 GCGATATCCGTCCCCATCTCTA
1 GCGAAATCCGTCCCCATCTCTA
*
80593 GCGAAATCCGTCCCCATCTCTG
1 GCGAAATCCGTCCCCATCTCTA
*
80615 GTGAAATCC
1 GCGAAATCC
80624 ATCTATCTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.25
Consensus pattern (22 bp):
GCGAAATCCGTCCCCATCTCTA
Found at i:82597 original size:21 final size:21
Alignment explanation
Indices: 82573--82622 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
82563 GTTAGGGGAG
* *
82573 TTACGTGATGAGGTCAATGCT
1 TTACGTGAGGAGGTCAATACT
**
82594 TTACGTGAGGAGGTCGGTACT
1 TTACGTGAGGAGGTCAATACT
82615 TTACGTGA
1 TTACGTGA
82623 AGACAATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Done.