Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001238.1 Hibiscus syriacus cultivar Beakdansim tig00002434_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: 63956
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2310 original size:21 final size:21
Alignment explanation
Indices: 2286--2325 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2276 TTTATTTTAT
2286 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
2307 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
2326 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:2373 original size:33 final size:33
Alignment explanation
Indices: 2320--2418 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2310 TTTGTTTCAA
2320 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2352 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
2385 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2418 T
1 T
2419 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:2447 original size:13 final size:13
Alignment explanation
Indices: 2404--2459 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
2394 TTGGAAGTAT
2404 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
2417 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
2431 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
2444 TTAAGTATTTGAA
1 TTAAGTATTTCAA
2457 TTA
1 TTA
2460 TCGAACTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 22 0.63
14 7 0.20
15 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:2900 original size:15 final size:15
Alignment explanation
Indices: 2848--2900 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
2838 ATCTGGAATA
2848 TTAAAATCGGTTTTT
1 TTAAAATCGGTTTTT
* *
2863 TTATAACCGGTTTTT
1 TTAAAATCGGTTTTT
*
2878 TAAAAAAATCGGTTTTT
1 T--TAAAATCGGTTTTT
2895 TTAAAA
1 TTAAAA
2901 CCGAAACCGG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 18 0.60
17 12 0.40
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (15 bp):
TTAAAATCGGTTTTT
Found at i:3020 original size:15 final size:17
Alignment explanation
Indices: 2994--3025 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2984 TTCTATGGGA
2994 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
3010 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
3026 CAGATTGAAA
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:13510 original size:9 final size:10
Alignment explanation
Indices: 13487--13541 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
13477 TCACTTTTTA
13487 AAAAATCAAT
1 AAAAATCAAT
13497 AAAAATCAAT
1 AAAAATCAAT
13507 AAAAAT-AATT
1 AAAAATCAA-T
* *
13517 AAAAGTGAAT
1 AAAAATCAAT
* *
13527 AAAATTTAAT
1 AAAAATCAAT
13537 AAAAA
1 AAAAA
13542 AATAATGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 2 0.05
10 35 0.90
11 2 0.05
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (10 bp):
AAAAATCAAT
Found at i:14006 original size:33 final size:33
Alignment explanation
Indices: 13969--14071 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
13959 ATCAAAATAA
13969 TTTTATTAAAAATGAATAAACATTATTAATTGT
1 TTTTATTAAAAATGAATAAACATTATTAATTGT
* ** * * *
14002 TTTTA-AAAATAAT-AATTAATGAATAATAATT-C
1 TTTTATTAAA-AATGAA-TAAACATTATTAATTGT
*
14034 ATTTATTAAAAATGAATAAACATTATTAATTGT
1 TTTTATTAAAAATGAATAAACATTATTAATTGT
14067 TTTTA
1 TTTTA
14072 AAAATAATTA
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
32 23 0.45
33 28 0.55
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (33 bp):
TTTTATTAAAAATGAATAAACATTATTAATTGT
Found at i:14044 original size:65 final size:65
Alignment explanation
Indices: 13970--14102 Score: 257
Period size: 65 Copynumber: 2.0 Consensus size: 65
13960 TCAAAATAAT
13970 TTTATTAAAAATGAATAAACATTATTAATTGTTTTTAAAAATAATAATTAATGAATAATAATTCA
1 TTTATTAAAAATGAATAAACATTATTAATTGTTTTTAAAAATAATAATTAATGAATAATAATTCA
*
14035 TTTATTAAAAATGAATAAACATTATTAATTGTTTTTAAAAATAATTATTAATGAATAATAATTCA
1 TTTATTAAAAATGAATAAACATTATTAATTGTTTTTAAAAATAATAATTAATGAATAATAATTCA
14100 TTT
1 TTT
14103 GATCCCTCAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (65 bp):
TTTATTAAAAATGAATAAACATTATTAATTGTTTTTAAAAATAATAATTAATGAATAATAATTCA
Found at i:20514 original size:29 final size:29
Alignment explanation
Indices: 20477--20533 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
20467 AGTTAGTATT
20477 AAAATCGAA-ATAAAAAAATAAATAAAAG
1 AAAATCGAATATAAAAAAATAAATAAAAG
* *
20505 AAAATTCGAATTTAAAAAAATAATTAAAA
1 AAAA-TCGAATATAAAAAAATAAATAAAA
20534 ATAATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 16 0.64
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.21
Consensus pattern (29 bp):
AAAATCGAATATAAAAAAATAAATAAAAG
Found at i:20545 original size:29 final size:30
Alignment explanation
Indices: 20487--20547 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
20477 AAAATCGAAA
**
20487 TAAAAAAATAAATAAAAGAAAATTCGAATT
1 TAAAAAAATAAATAAAAGAAAATTAAAATT
* *
20517 TAAAAAAATAATTAAAA-ATAATTAAAATT
1 TAAAAAAATAAATAAAAGAAAATTAAAATT
20546 TA
1 TA
20548 TGGATCAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (30 bp):
TAAAAAAATAAATAAAAGAAAATTAAAATT
Found at i:20635 original size:27 final size:26
Alignment explanation
Indices: 20584--20635 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
20574 TTGCAAAAGA
*
20584 AAAAACATAAAATTAAAGGATTAAAT
1 AAAAACATAAAATTAAAGGACTAAAT
*
20610 AAAAA-ATAGAAATTTAAAGTACTAAA
1 AAAAACATA-AAA-TTAAAGGACTAAA
20636 ATGGCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 3 0.14
26 8 0.36
27 11 0.50
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.23
Consensus pattern (26 bp):
AAAAACATAAAATTAAAGGACTAAAT
Found at i:20956 original size:13 final size:13
Alignment explanation
Indices: 20938--20970 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
20928 TTTCCAGTAG
20938 CCTGCAACGAAAC
1 CCTGCAACGAAAC
20951 CCTGCAACGAAAC
1 CCTGCAACGAAAC
20964 CCTGCAA
1 CCTGCAA
20971 AACAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.39, G:0.15, T:0.09
Consensus pattern (13 bp):
CCTGCAACGAAAC
Found at i:22306 original size:84 final size:84
Alignment explanation
Indices: 21969--22642 Score: 751
Period size: 84 Copynumber: 8.0 Consensus size: 84
21959 ACCATACGGT
* * * * * *
21969 TGATATGCCTATGAGCTGAATGAAATCGAACTCGAAGGTC-TTTGATGACAGATAACCCTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
*
22033 CCTTGAGTTATGCTGTAAA
66 CCTTGAGTTATGCTGCAAA
* * * * * *
22052 TTTGATATACCTTTGAGGTGAGTGTAATCGAACTCAAAGGTC-TTTGTTGACAGATAACCATTCT
1 --TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCT
22116 CGCCTTGAGTTATGCTGCAAA
64 CGCCTTGAGTTATGCTGCAAA
* * *
22137 TGATATGCCTTTGAGCTGAGTATAATCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
22201 CCTTGAGTTATGCTGCAAA
66 CCTTGAGTTATGCTGCAAA
* ** * * *
22220 TGATGTGCCTTAGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTAG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
*
22285 CCTTGAGATATGCTGCAAA
66 CCTTGAGTTATGCTGCAAA
* * * * * * *
22304 TGATGTGTCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCATTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
* * **
22369 ACTTAAGTTATTATGCAAA
66 CCTTGAGTTATGCTGCAAA
* * * * * * *
22388 TGATGTACCTCTGTGATGAGTTTAATCGAACTCAAAGGTCTTTTGGTGGCAGATAACCCTTCTCG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
22453 CCTTGAGTTATGCTGCAAA
66 CCTTGAGTTATGCTGCAAA
* * * * * * * * * *
22472 TGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCATATAACCATTATAG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
* * *
22537 CCTTAAGTTATGTTGTAAA
66 CCTTGAGTTATGCTGCAAA
* * * * * *
22556 TGATGTGTCTTTGAGCTAAGTGTAATTGAACTCGAAGGTCTTTTGTTAGCATATAACCCTTCTTG
1 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
* *
22621 CCTTGAGTTAAGATGCAAA
66 CCTTGAGTTATGCTGCAAA
22640 TGA
1 TGA
22643 GCACGATATC
Statistics
Matches: 501, Mismatches: 87, Indels: 3
0.85 0.15 0.01
Matches are distributed among these distances:
83 112 0.22
84 315 0.63
85 74 0.15
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (84 bp):
TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCG
CCTTGAGTTATGCTGCAAA
Found at i:23122 original size:43 final size:43
Alignment explanation
Indices: 23074--23176 Score: 143
Period size: 43 Copynumber: 2.4 Consensus size: 43
23064 TTCGTTGTGA
** *
23074 AGTTGAAACCGTGGATGTGTGGGAACGATATCCTCCATCGTGG
1 AGTTGAAATTGTGGATGCGTGGGAACGATATCCTCCATCGTGG
* * * *
23117 AGTTGAAATTGTGGATCCGTTGGTACGATATCCTCCGTCGTGG
1 AGTTGAAATTGTGGATGCGTGGGAACGATATCCTCCATCGTGG
23160 AGTTGAAATTGTGGATG
1 AGTTGAAATTGTGGATG
23177 ACCCCTTCAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (43 bp):
AGTTGAAATTGTGGATGCGTGGGAACGATATCCTCCATCGTGG
Found at i:23451 original size:64 final size:64
Alignment explanation
Indices: 23370--23497 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
23360 GTGTTATTTC
* *
23370 GAGTTCAATATCCTTCGCTGTCAAGTTGAAATTGACTCTGAATGAAACTAGAAAA-TTGTTTGTT
1 GAGTACAATATCATTCGCTGTCAAGTTGAAATTGACTCTGAATGAAA-TAGAAAAGTTGTTTGTT
* *
23434 GAGTACAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTGTTTGTT
1 GAGTACAATATCATTCGCTGTCAAGTTGAAATTGACTCTGAATGAAATAGAAAAGTTGTTTGTT
23498 AACAAACGCT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 6 0.10
64 53 0.90
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (64 bp):
GAGTACAATATCATTCGCTGTCAAGTTGAAATTGACTCTGAATGAAATAGAAAAGTTGTTTGTT
Found at i:24813 original size:23 final size:23
Alignment explanation
Indices: 24783--24840 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
24773 GAGTCTTGTC
24783 TTATTTTTTCTTCACTTTTTCCT
1 TTATTTTTTCTTCACTTTTTCCT
** *
24806 TTATTTTTGT-TTCTTTTTTTCTT
1 TTATTTTT-TCTTCACTTTTTCCT
*
24829 TTCTTTTTTCTT
1 TTATTTTTTCTT
24841 TTTTGTTCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.03
23 27 0.93
24 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.78
Consensus pattern (23 bp):
TTATTTTTTCTTCACTTTTTCCT
Found at i:30460 original size:16 final size:16
Alignment explanation
Indices: 30401--30459 Score: 100
Period size: 16 Copynumber: 3.7 Consensus size: 16
30391 TGATTAGATG
30401 TTGTTGAAAAAATAAA
1 TTGTTGAAAAAATAAA
30417 TTGTTGAAAAAATAAA
1 TTGTTGAAAAAATAAA
*
30433 TTGTTGAAAAATTAAA
1 TTGTTGAAAAAATAAA
*
30449 TTGCTGAAAAA
1 TTGTTGAAAAA
30460 TGAATTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.32
Consensus pattern (16 bp):
TTGTTGAAAAAATAAA
Found at i:33932 original size:117 final size:117
Alignment explanation
Indices: 33726--33959 Score: 459
Period size: 117 Copynumber: 2.0 Consensus size: 117
33716 TACGCACTTT
33726 CAAGCATGAAACTCAAATAACAAACTATTATCTCTATCAAGCTTAGACACATAAATCATATTCTT
1 CAAGCATGAAACTCAAATAACAAACTATTATCTCTATCAAGCTTAGACACATAAATCATATTCTT
*
33791 GGTTATATATGGTACAAGTATAGTATTCTTTAAATTCAAAGTGCGTAAATTA
66 GGTTATATATGGTACAAGTATAGTATTCTTTAAATTCAAAGTGCGCAAATTA
33843 CAAGCATGAAACTCAAATAACAAACTATTATCTCTATCAAGCTTAGACACATAAATCATATTCTT
1 CAAGCATGAAACTCAAATAACAAACTATTATCTCTATCAAGCTTAGACACATAAATCATATTCTT
33908 GGTTATATATGGTACAAGTATAGTATTCTTTAAATTCAAAGTGCGCAAATTA
66 GGTTATATATGGTACAAGTATAGTATTCTTTAAATTCAAAGTGCGCAAATTA
33960 GCAAATAAAG
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 116 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (117 bp):
CAAGCATGAAACTCAAATAACAAACTATTATCTCTATCAAGCTTAGACACATAAATCATATTCTT
GGTTATATATGGTACAAGTATAGTATTCTTTAAATTCAAAGTGCGCAAATTA
Found at i:36772 original size:23 final size:23
Alignment explanation
Indices: 36745--36790 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
36735 AAAACAAAAA
*
36745 ATCAAAGGAATGAAGCTTTGATT
1 ATCAAAGAAATGAAGCTTTGATT
36768 ATCAAAGAAATGAAGCTTTGATT
1 ATCAAAGAAATGAAGCTTTGATT
36791 CAATGTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (23 bp):
ATCAAAGAAATGAAGCTTTGATT
Found at i:40175 original size:55 final size:54
Alignment explanation
Indices: 40085--40210 Score: 180
Period size: 55 Copynumber: 2.3 Consensus size: 54
40075 GTACCTCCTA
* * * *
40085 GGGGCTATCGATACCCTCAGAGCAATTTGTTATTTCTCGGAGCAAAATGTTACATT
1 GGGG-TATCGGTACCCTCAGAGCAATCTGTAATTTCTCGGAGCAAAATCTTACA-T
* *
40141 GGGGTATCGGTACCCTCCGAGCAATCTGTAATTTCTCGGAGCTAAATCTTACAT
1 GGGGTATCGGTACCCTCAGAGCAATCTGTAATTTCTCGGAGCAAAATCTTACAT
40195 GGGGTATCGGTACCCT
1 GGGGTATCGGTACCCT
40211 TTTGGGGGGG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 17 0.27
55 43 0.67
56 4 0.06
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (54 bp):
GGGGTATCGGTACCCTCAGAGCAATCTGTAATTTCTCGGAGCAAAATCTTACAT
Found at i:40964 original size:14 final size:13
Alignment explanation
Indices: 40930--40964 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
40920 GTTTAACAAT
40930 TCAAAGTTCTAAA
1 TCAAAGTTCTAAA
40943 TCAGAAGTTCTAAA
1 TCA-AAGTTCTAAA
40957 TCGAAAGT
1 TC-AAAGT
40965 AGGCAAGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 16 0.80
15 1 0.05
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
TCAAAGTTCTAAA
Found at i:42807 original size:12 final size:12
Alignment explanation
Indices: 42790--42821 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
42780 AGCAATGTAG
42790 AGATTAGGAGGA
1 AGATTAGGAGGA
42802 AGATTAGGAGGA
1 AGATTAGGAGGA
*
42814 AGAGTAGG
1 AGATTAGG
42822 GTGAACAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.16
Consensus pattern (12 bp):
AGATTAGGAGGA
Found at i:42925 original size:20 final size:20
Alignment explanation
Indices: 42900--42955 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
42890 AGAACCAGTG
42900 GAGGGTATTGGTACCCTCAA
1 GAGGGTATTGGTACCCTCAA
42920 GAGGGTATTGGTACCCTCAA
1 GAGGGTATTGGTACCCTCAA
* *
42940 GGGGGTATCGGTACCC
1 GAGGGTATTGGTACCC
42956 ACTTAAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.23
Consensus pattern (20 bp):
GAGGGTATTGGTACCCTCAA
Found at i:45485 original size:19 final size:19
Alignment explanation
Indices: 45441--45515 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
45431 TTATAGCCAA
*
45441 GGGGTATGGGTACCCCTGCAGG
1 GGGGTATCGGTACCCCT---GG
45463 GGGGTATCGGTACCCCTGG
1 GGGGTATCGGTACCCCTGG
*
45482 GGGGTATCGGTACCCCTGA
1 GGGGTATCGGTACCCCTGG
45501 GGGGTATCGGTACCC
1 GGGGTATCGGTACCC
45516 TCTTTGCATT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
19 35 0.69
22 16 0.31
ACGTcount: A:0.13, C:0.25, G:0.41, T:0.20
Consensus pattern (19 bp):
GGGGTATCGGTACCCCTGG
Found at i:45759 original size:21 final size:21
Alignment explanation
Indices: 45735--45775 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45725 ATGTTTAATG
*
45735 AAAAATATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
45756 AAAAAGATATCAATTGTTAA
1 AAAAAGATATCAATTGTTAA
45776 AAATATACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:49029 original size:34 final size:32
Alignment explanation
Indices: 48983--49053 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 32
48973 CCTTTTATAA
* * *
48983 AGGGAAATGTTCTAGCTTAGCTCGTGTAAAAGCT
1 AGGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
49017 AGGGAAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
49049 AGGGA
1 AGGGA
49054 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (32 bp):
AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:50560 original size:19 final size:20
Alignment explanation
Indices: 50536--50573 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50526 TAAAGATAAT
50536 TTGATTTT-AAAAGCAAAAG
1 TTGATTTTGAAAAGCAAAAG
*
50555 TTGATTTTGAAAATCAAAA
1 TTGATTTTGAAAAGCAAAA
50574 TGAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (20 bp):
TTGATTTTGAAAAGCAAAAG
Found at i:53090 original size:63 final size:65
Alignment explanation
Indices: 52972--53095 Score: 191
Period size: 63 Copynumber: 1.9 Consensus size: 65
52962 GGTACCCCTA
*
52972 CAGGGGGTATCGGTACCCCTGGGGGGATATCGATACCCTCTTTGTATTCTGGAATTTTTGCCTTT
1 CAGGGGGTATCGGTACCCCTGGGGGGATATCGATACCCTCTTTGAATTCTGGAATTTTTGCCTTT
* *
53037 CAGGGGGTAT-GGATACCCCT-GGGGG-TATCGGTACCCTTTTTGAATTCTGGAATTTTTGC
1 CAGGGGGTATCGG-TACCCCTGGGGGGATATCGATACCCTCTTTGAATTCTGGAATTTTTGC
53096 TCAAATCTGA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
63 31 0.56
64 7 0.13
65 17 0.31
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.35
Consensus pattern (65 bp):
CAGGGGGTATCGGTACCCCTGGGGGGATATCGATACCCTCTTTGAATTCTGGAATTTTTGCCTTT
Found at i:60689 original size:15 final size:15
Alignment explanation
Indices: 60669--60697 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
60659 CTATAGGAGG
60669 GGTATCGATACCATA
1 GGTATCGATACCATA
60684 GGTATCGATACCAT
1 GGTATCGATACCAT
60698 TAGTCAGGTA
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:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (15 bp):
GGTATCGATACCATA
Done.