Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009192.1 Hibiscus syriacus cultivar Beakdansim tig00112774_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: 88554
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:528 original size:11 final size:13
Alignment explanation
Indices: 496--525 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
486 TGGCCAAAGA
496 TGAAAAGGTATGT
1 TGAAAAGGTATGT
509 TGAAAAGGTATG-
1 TGAAAAGGTATGT
521 TGAAA
1 TGAAA
526 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:12427 original size:22 final size:22
Alignment explanation
Indices: 12402--12443 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
12392 CAATTCATTT
12402 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
12424 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
12444 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:19516 original size:22 final size:22
Alignment explanation
Indices: 19491--19532 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
19481 CAATTCATTT
19491 ATCTT-TTATTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
19513 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
19533 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:23474 original size:19 final size:20
Alignment explanation
Indices: 23423--23479 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
23413 TTTGAATTTC
23423 TTTTCTTTTCTTATTT-TCTGA
1 TTTTCTTTTCTT-TTTGTCT-A
*
23444 TTTTTTTCTTCTTTTTGTCT-
1 TTTTCTT-TTCTTTTTGTCTA
23464 TTTTCTTTTCTTTTTG
1 TTTTCTTTTCTTTTTG
23480 CACTCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 9 0.28
20 6 0.19
21 9 0.28
22 8 0.25
ACGTcount: A:0.04, C:0.14, G:0.05, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTGTCTA
Found at i:24609 original size:33 final size:33
Alignment explanation
Indices: 24584--24660 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
24574 GCAGCTCCTT
24584 GTGAAAAGGTACCTCTTGAGTTGGCAACTATTC
1 GTGAAAAGGTACCTCTTGAGTTGGCAACTATTC
24617 GTGAAAAGGTACCTCTTGAGTTGGCAACTATTC
1 GTGAAAAGGTACCTCTTGAGTTGGCAACTATTC
*
24650 GCGAAAAGGTA
1 GTGAAAAGGTA
24661 TGATTTCATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (33 bp):
GTGAAAAGGTACCTCTTGAGTTGGCAACTATTC
Found at i:27867 original size:91 final size:91
Alignment explanation
Indices: 27708--27881 Score: 240
Period size: 91 Copynumber: 1.9 Consensus size: 91
27698 CCCATGTGCC
* * * * * * *
27708 TTGCATATGACCAGCCTCTATGTGCCTTTCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCAAGTGGATAATTTAGGCACCAAGATGAAGAGTTAT
*
27773 CTCCCCATTCGGCCAAGCCAAGTGTT
66 CTCCCCATTCGACCAAGCCAAGTGTT
* * *
27799 TTGCATGTGATCAGCCCCCATGTGCCTTGCAAGTGGTTAATTTAGGCACCAAGATGAAGAGTTAT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCAAGTGGATAATTTAGGCACCAAGATGAAGAGTTAT
*
27864 CTCCCTATTCGACCAAGC
66 CTCCCCATTCGACCAAGC
27882 ATCAACTACA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
91 71 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.29
Consensus pattern (91 bp):
TTGCATATGACCAGCCCCCATGTGCCTTGCAAGTGGATAATTTAGGCACCAAGATGAAGAGTTAT
CTCCCCATTCGACCAAGCCAAGTGTT
Found at i:28688 original size:24 final size:24
Alignment explanation
Indices: 28661--28713 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
28651 ATCAGCAAAT
*
28661 AAAAGTCAAGCACTCCAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAGAAG
* *
28685 AAAAATCCAGCACTCAAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAGAAG
28709 AAAAG
1 AAAAG
28714 CAAAGAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.19, G:0.15, T:0.08
Consensus pattern (24 bp):
AAAAGTCAAGCACTCAAAAAGAAG
Found at i:28717 original size:15 final size:15
Alignment explanation
Indices: 28706--28734 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28696 ACTCAAAAAG
28706 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
28721 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
28735 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:31830 original size:91 final size:91
Alignment explanation
Indices: 31674--31847 Score: 276
Period size: 91 Copynumber: 1.9 Consensus size: 91
31664 CCCATGTGCC
* * *
31674 TTGCATATGACCAGCCTCCATGTGCCTTGCATGTAGATCATTTAGGCGCCAAGATGAAGATTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTAGATCATTTAGGCACCAAGATGAAGAGTTCT
31739 CTCCCTATTCGGCCAAGCCAAGTGTT
66 CTCCCTATTCGGCCAAGCCAAGTGTT
* * * *
31765 TTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCACCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTAGATCATTTAGGCACCAAGATGAAGAGTTCT
*
31830 CTCCCTATTTGGCCAAGC
66 CTCCCTATTCGGCCAAGC
31848 ATCAACTACC
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (91 bp):
TTGCATATGACCAGCCCCCATGTGCCTTGCATGTAGATCATTTAGGCACCAAGATGAAGAGTTCT
CTCCCTATTCGGCCAAGCCAAGTGTT
Found at i:38479 original size:21 final size:20
Alignment explanation
Indices: 38439--38510 Score: 110
Period size: 21 Copynumber: 3.6 Consensus size: 20
38429 CGGCCAAGAG
*
38439 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
38458 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTT-AAAAT
38479 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
*
38499 CATCTATTTTCA
1 CATGTATTTTCA
38511 AAGGGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
19 11 0.22
20 18 0.37
21 20 0.41
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:39277 original size:25 final size:24
Alignment explanation
Indices: 39222--39280 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
39212 AAAGAAAAGA
**
39222 CAAAAAGAAAAAAAATCAAAATAT
1 CAAAAAGAAAAAAAAAAAAAATAT
* *
39246 AAGAAAAGAAAAAAAAAAAAGAATTT
1 CA-AAAAGAAAAAAAAAAAA-AATAT
39272 CAAAAAGAA
1 CAAAAAGAA
39281 GCAAAGCCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.79
26 5 0.18
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.10
Consensus pattern (24 bp):
CAAAAAGAAAAAAAAAAAAAATAT
Found at i:41779 original size:18 final size:18
Alignment explanation
Indices: 41756--41791 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41746 ATTTACATAT
41756 CAAGACAGCATGTATTCA
1 CAAGACAGCATGTATTCA
41774 CAAGACAGCATGTATTCA
1 CAAGACAGCATGTATTCA
41792 TTCATTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (18 bp):
CAAGACAGCATGTATTCA
Found at i:42909 original size:28 final size:27
Alignment explanation
Indices: 42858--42924 Score: 63
Period size: 28 Copynumber: 2.6 Consensus size: 27
42848 AGAAAAAAAG
*
42858 AAAAG-AA-AAAGAAATTGAAGCACTCC
1 AAAAGAAAGAAAGAAATTCAAGCACT-C
*
42884 AAAAGAAAGAAAGAAATTCCAA-CACTT
1 AAAAGAAAGAAAGAAATT-CAAGCACTC
42911 AAAA-AAAG-AAGAAA
1 AAAAGAAAGAAAGAAA
42925 AGCAAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 6 0.17
26 9 0.25
27 6 0.17
28 13 0.36
29 2 0.06
ACGTcount: A:0.64, C:0.12, G:0.13, T:0.10
Consensus pattern (27 bp):
AAAAGAAAGAAAGAAATTCAAGCACTC
Found at i:44984 original size:17 final size:16
Alignment explanation
Indices: 44953--44986 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
44943 CACGTGAGGA
44953 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
44969 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
44986 T
1 T
44987 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:60622 original size:30 final size:31
Alignment explanation
Indices: 60586--60645 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
60576 CTTAGCTTTA
**
60586 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
60616 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
60646 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:62022 original size:19 final size:20
Alignment explanation
Indices: 61998--62037 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
61988 TATCCTTTCT
61998 TTATTTCATATCATT-CTTA
1 TTATTTCATATCATTACTTA
* *
62017 TTATTTCTTTTCATTACTTA
1 TTATTTCATATCATTACTTA
62037 T
1 T
62038 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTCATATCATTACTTA
Found at i:64806 original size:30 final size:31
Alignment explanation
Indices: 64770--64829 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
64760 CTTAGCTTTA
**
64770 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
64800 TATTATGTTTACATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
64830 GGCAGAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:65762 original size:19 final size:21
Alignment explanation
Indices: 65738--65789 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
65728 CGGCCAAGAG
*
65738 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
65757 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
65778 CATGTATTTTCA
1 CATGTATTTTCA
65790 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:66229 original size:27 final size:27
Alignment explanation
Indices: 66198--66250 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
66188 ATCTCTATCC
* *
66198 TTTCTTT-ATTTCATATCATTCTTATTA
1 TTTCTTTCATTACATAT-ATTATTATTA
66225 TTTCTTTCATTACATATATTATTATT
1 TTTCTTTCATTACATATATTATTATT
66251 CACTTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTCTTTCATTACATATATTATTATTA
Found at i:67178 original size:19 final size:21
Alignment explanation
Indices: 67135--67186 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
67125 GAAACCCCTT
67135 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
67156 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
67175 TGAAGATACATG
1 TGAAAATACATG
67187 CTCTTGGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:67880 original size:15 final size:15
Alignment explanation
Indices: 67860--67895 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
67850 ATTATTAGCT
*
67860 TTATAATATATGTTA
1 TTATAATATATATTA
67875 TTATAATATATATTA
1 TTATAATATATATTA
*
67890 TGATAA
1 TTATAA
67896 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:75890 original size:17 final size:18
Alignment explanation
Indices: 75858--75892 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
75848 GGTTAGGGTA
*
75858 GAAAGAATATAAGAAATG
1 GAAAGAATAAAAGAAATG
75876 GAAAG-ATAAAAGAAATG
1 GAAAGAATAAAAGAAATG
75893 ATTTAAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.14
Consensus pattern (18 bp):
GAAAGAATAAAAGAAATG
Found at i:76116 original size:8 final size:8
Alignment explanation
Indices: 76103--76137 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
76093 GAATTTCTTT
76103 TTCTTTTC
1 TTCTTTTC
76111 TTCTTTTC
1 TTCTTTTC
76119 -T-TTTTC
1 TTCTTTTC
76125 TTCTTTTC
1 TTCTTTTC
76133 TTCTT
1 TTCTT
76138 CTTTTTGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.20
7 2 0.08
8 18 0.72
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:76116 original size:14 final size:14
Alignment explanation
Indices: 76097--76160 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
76087 CTTTTTGAAT
76097 TTCTTTTTCTTTTC
1 TTCTTTTTCTTTTC
76111 TTC-TTTTCTTTTTC
1 TTCTTTTTC-TTTTC
76125 TTC-TTTTCTTCTTC
1 TTCTTTTTCTT-TTC
*
76139 TT-TTTGTCTTTTC
1 TTCTTTTTCTTTTC
76152 TTTCTTTTT
1 -TTCTTTTT
76161 GTACTCCAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
13 10 0.23
14 29 0.67
15 4 0.09
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:76120 original size:19 final size:19
Alignment explanation
Indices: 76096--76159 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 19
76086 TCTTTTTGAA
76096 TTTCTTTTTCTTTTCTTCT
1 TTTCTTTTTCTTTTCTTCT
76115 TTTCTTTTTCTTCTT-TTCT
1 TTTCTTTTTCTT-TTCTTCT
76134 TCTTCTTTTTGTCTTTTCTTTCT
1 T-TTC-TTTT-TCTTTTC-TTCT
76157 TTT
1 TTT
76160 TGTACTCCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
19 17 0.44
20 5 0.13
21 6 0.15
22 6 0.15
23 5 0.13
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTCTTTTCTTCT
Found at i:78066 original size:909 final size:908
Alignment explanation
Indices: 76310--78130 Score: 3606
Period size: 909 Copynumber: 2.0 Consensus size: 908
76300 TCAGGGAAGT
76310 ACTTTCTCATAAGTGCCTTAATGTTTTTAAATCTTTTAATGAGAAAGAACCATCAGATAATAGGT
1 ACTTTCTCATAAGTGCCTTAATGTTTTTAAATCTTTTAATGAGAAAGAACCATCAGATAATAGGT
76375 TGTTTAATATATTACATATTGAATATTAAATAACCTATAGTCCACATTATTATATAATACATTGT
66 TGTTTAATATATTACATATTGAATATTAAATAACCTATAGTCCACATTATTATATAATACATTGT
76440 ATAAAGTTCATTTACTTAGTTTATTTCTTTATATTATGCGTGTAGGCACATTCGGCCAATACTTG
131 ATAAAGTTCATTTACTTAGTTTATTTCTTTATATTATGCGTGTAGGCACATTCGGCCAATACTTG
76505 GGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGGACGATCAGGGGA
196 GGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGGACGATCAGGGGA
76570 GCTTAAGGAGCAATTTGGTGAAAAGTCGTTTTGAGGCTGCGAGCTCATAGCTGGATTGAGCTGAA
261 GCTTAAGGAGCAATTTGGTGAAAAGTCGTTTTGAGGCTGCGAGCTCATAGCTGGATTGAGCTGAA
76635 GATTTGAGCTACAAGATGAACTCATTTCAGCTGGGGAGTTGCACCATCATCATCACCACTTAGGA
326 GATTTGAGCTACAAGATGAACTCATTTCAGCTGGGGAGTTGCACCATCATCATCACCACTTAGGA
76700 CACTTCAAATATGTCCTACATCAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCCATCTC
391 CACTTCAAATATGTCCTACATCAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCCATCTC
76765 AAGAGGTACCTCTTCACAAGGAGCTGCCCAAACGTTCATCATGTTACAAGTCATCTAAGGTCAGC
456 AAGAGGTACCTCTTCACAAGGAGCTGCCCAAACGTTCATCATGTTACAAGTCATCTAAGGTCAGC
76830 TCACCACCAGCTCATTCACACCCGAAGTAGCTCAAACATGAAGGGGTACCTTTCTCAAACATTGT
521 TCACCACCAGCTCATTCACACCCGAAGTAGCTCAAACATGAAGGGGTACCTTTCTCAAACATTGT
76895 GACCTTTCATGAATGATGCTGCCCATGAAGATGCCTTTTCAACAAGGAACACATCGGTGAAGAGA
586 GACCTTTCATGAATGATGCTGCCCATGAAGATGCCTTTTCAACAAGGAACACATCGGTGAAGAGA
76960 TCACGCCTATTGGATGCTTAAATCATCAAGAAACATGAGCTAGAGGCTCCATGCCTATTCGGCCA
651 TCACGCCTATTGGATGCTTAAATCATCAAGAAACATGAGCTAGAGGCTCCATGCCTATTCGGCCA
77025 CATCACATGCCATACACATGAGAGCCTTTTTGGCGCCAAGCATGAAGAGACACACCACCATTCGG
716 CATCACATGCCATACACATGAGAGCCTTTTTGGCGCCAAGCATGAAGAGACACACCACCATTCGG
77090 CCAAAGGGGGAAAATGGCGCCAAGATGAACCAACATACATATTCGGCCAAGGGAGATGTCTTCCC
781 CCAAAGGGGGAAAATGGCGCCAAGATGAACCAACATACATATTCGGCCAAGGGAGATGTCTTCCC
77155 ATCCTTAGCCGAATCATTAAGGCCTTTCATGAAGAGTTAGCCGAACCATCACAAGCCCAAAGG
846 ATCCTTAGCCGAATCATTAAGGCCTTTCATGAAGAGTTAGCCGAACCATCACAAGCCCAAAGG
77218 ACTTTCTCATAAGTGCCTTAATGTTTTTAAATCTTTTAATGAGAAAGAACCATCAGATAATAGGT
1 ACTTTCTCATAAGTGCCTTAATGTTTTTAAATCTTTTAATGAGAAAGAACCATCAGATAATAGGT
77283 TGTTTAATATATTACATATTGAATATTAAATAACCTATAGTCCACATTATTATATAATACATTGT
66 TGTTTAATATATTACATATTGAATATTAAATAACCTATAGTCCACATTATTATATAATACATTGT
77348 ATAAAGTTCATTTACTTAGTTTATTTCTTTATATTATGCGTGTAGGCACATTCGGCCAATACTTG
131 ATAAAGTTCATTTACTTAGTTTATTTCTTTATATTATGCGTGTAGGCACATTCGGCCAATACTTG
77413 GGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGGAACGATCAGGGG
196 GGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGG-ACGATCAGGGG
*
77478 AGCTTAAGGAGCAATTTGGTGAAAAGTTGTTTTGAGGCTGCGAGCTCATAGCTGGATTGAGCTGA
260 AGCTTAAGGAGCAATTTGGTGAAAAGTCGTTTTGAGGCTGCGAGCTCATAGCTGGATTGAGCTGA
77543 AGATTTGAGCTACAAGATGAACTCATTTCAGCTGGGGAGTTGCACCATCATCATCACCACTTAGG
325 AGATTTGAGCTACAAGATGAACTCATTTCAGCTGGGGAGTTGCACCATCATCATCACCACTTAGG
77608 ACACTTCAAATATGTCCTACATCAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCCATCT
390 ACACTTCAAATATGTCCTACATCAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCCATCT
77673 CAAGAGGTACCTCTTCACAAGGAGCTGCCCAAACGTTCATCATGTTACAAGTCATCTAAGGTCAG
455 CAAGAGGTACCTCTTCACAAGGAGCTGCCCAAACGTTCATCATGTTACAAGTCATCTAAGGTCAG
77738 CTCACCACCAGCTCATTCACACCCGAAGTAGCTCAAACATGAAGGGGTACCTTTCTCAAACATTG
520 CTCACCACCAGCTCATTCACACCCGAAGTAGCTCAAACATGAAGGGGTACCTTTCTCAAACATTG
77803 TGACCTTTCATGAATGATGCTGCCCATGAAGATGCCTTTTCAACAAGGAACACATCGGTGAAGAG
585 TGACCTTTCATGAATGATGCTGCCCATGAAGATGCCTTTTCAACAAGGAACACATCGGTGAAGAG
77868 ATCACGCCTATTGGATGCTTAAATCATCAAGAAACATGAGCTAGAGGCTCCATGCCTATTCGGCC
650 ATCACGCCTATTGGATGCTTAAATCATCAAGAAACATGAGCTAGAGGCTCCATGCCTATTCGGCC
77933 ACATCACATGCCATACACATGAGAGCCTTTTTGGCGCCAAGCATGAAGAGACACACCACCATTCG
715 ACATCACATGCCATACACATGAGAGCCTTTTTGGCGCCAAGCATGAAGAGACACACCACCATTCG
77998 GCCAAAGGGGGAAAATGGCGCCAAGATGAACCAACATACATATTCGGCCAAGGGAGATGTCTTCC
780 GCCAAAGGGGGAAAATGGCGCCAAGATGAACCAACATACATATTCGGCCAAGGGAGATGTCTTCC
**
78063 CATCCTTAGCCGAATCATTAAGGCCTTTCATGAAGAGTTAGCCGAACCATCACAAGCGTAAAGG
845 CATCCTTAGCCGAATCATTAAGGCCTTTCATGAAGAGTTAGCCGAACCATCACAAGCCCAAAGG
78127 ACTT
1 ACTT
78131 ATTCATTCAT
Statistics
Matches: 909, Mismatches: 3, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
908 248 0.27
909 661 0.73
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (908 bp):
ACTTTCTCATAAGTGCCTTAATGTTTTTAAATCTTTTAATGAGAAAGAACCATCAGATAATAGGT
TGTTTAATATATTACATATTGAATATTAAATAACCTATAGTCCACATTATTATATAATACATTGT
ATAAAGTTCATTTACTTAGTTTATTTCTTTATATTATGCGTGTAGGCACATTCGGCCAATACTTG
GGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGGACGATCAGGGGA
GCTTAAGGAGCAATTTGGTGAAAAGTCGTTTTGAGGCTGCGAGCTCATAGCTGGATTGAGCTGAA
GATTTGAGCTACAAGATGAACTCATTTCAGCTGGGGAGTTGCACCATCATCATCACCACTTAGGA
CACTTCAAATATGTCCTACATCAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCCATCTC
AAGAGGTACCTCTTCACAAGGAGCTGCCCAAACGTTCATCATGTTACAAGTCATCTAAGGTCAGC
TCACCACCAGCTCATTCACACCCGAAGTAGCTCAAACATGAAGGGGTACCTTTCTCAAACATTGT
GACCTTTCATGAATGATGCTGCCCATGAAGATGCCTTTTCAACAAGGAACACATCGGTGAAGAGA
TCACGCCTATTGGATGCTTAAATCATCAAGAAACATGAGCTAGAGGCTCCATGCCTATTCGGCCA
CATCACATGCCATACACATGAGAGCCTTTTTGGCGCCAAGCATGAAGAGACACACCACCATTCGG
CCAAAGGGGGAAAATGGCGCCAAGATGAACCAACATACATATTCGGCCAAGGGAGATGTCTTCCC
ATCCTTAGCCGAATCATTAAGGCCTTTCATGAAGAGTTAGCCGAACCATCACAAGCCCAAAGG
Found at i:78587 original size:15 final size:15
Alignment explanation
Indices: 78567--78608 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
78557 CAGCCATCTC
78567 TTTCATTTCTTTCTA
1 TTTCATTTCTTTCTA
*
78582 TTTCATTTCCTTTTTA
1 TTTCATTT-CTTTCTA
*
78598 TATCATTTCTT
1 TTTCATTTCTT
78609 AAGGCCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTCATTTCTTTCTA
Found at i:78988 original size:19 final size:20
Alignment explanation
Indices: 78952--78991 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
78942 GAATAATAAT
78952 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
78972 ATAAG-AATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
78991 A
1 A
78992 AGAAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:79444 original size:19 final size:21
Alignment explanation
Indices: 79401--79452 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
79391 GAAACCCCTT
**
79401 TGAAAATACACAACTTTTAAA
1 TGAAAATACATGACTTTTAAA
79422 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
79441 TGAAGATACATG
1 TGAAAATACATG
79453 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:83321 original size:19 final size:21
Alignment explanation
Indices: 83278--83329 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
83268 GAAACCCCTT
83278 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
83299 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
83318 TGAAGATACATG
1 TGAAAATACATG
83330 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:88059 original size:19 final size:21
Alignment explanation
Indices: 88016--88067 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
88006 GAAACCCCTT
88016 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
88037 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
88056 TGAAGATACATG
1 TGAAAATACATG
88068 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Done.