Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003253.1 Hibiscus syriacus cultivar Beakdansim tig00006836_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: 76957
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:151 original size:21 final size:21
Alignment explanation
Indices: 128--167 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
118 ATACTGACAA
*
128 AAAATAGAAAAA-TGACATGG
1 AAAATAAAAAAATTGACATGG
148 AAAATAAAAAAATTGACATG
1 AAAATAAAAAAATTGACATG
168 ACATGTCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.62, C:0.05, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAATAAAAAAATTGACATGG
Found at i:2296 original size:26 final size:27
Alignment explanation
Indices: 2233--2312 Score: 80
Period size: 25 Copynumber: 3.1 Consensus size: 27
2223 TTTTATTTTT
*
2233 AAATT-TTTATTATTTATCTCATATAA
1 AAATTATTTATTATATATCTCATATAA
2259 AAATTATGTTATTATATATACTC-T-TAA
1 AAATTAT-TTATTATATAT-CTCATATAA
* *
2286 AATTTATTTA-TATTTATCTCATA-AA
1 AAATTATTTATTATATATCTCATATAA
2311 AA
1 AA
2313 TATATTGAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
24 3 0.07
25 11 0.24
26 8 0.17
27 10 0.22
28 11 0.24
29 3 0.07
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.50
Consensus pattern (27 bp):
AAATTATTTATTATATATCTCATATAA
Found at i:4583 original size:15 final size:15
Alignment explanation
Indices: 4545--4585 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
4535 AATCCTCTCA
4545 TCTCTTCTTCCTTCT
1 TCTCTTCTTCCTTCT
4560 TCT-TATCTTCAC-TCT
1 TCTCT-TCTTC-CTTCT
4575 TCTCTTCTTCC
1 TCTCTTCTTCC
4586 AAACGTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.09
15 19 0.83
16 2 0.09
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.56
Consensus pattern (15 bp):
TCTCTTCTTCCTTCT
Found at i:5078 original size:21 final size:21
Alignment explanation
Indices: 5036--5078 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5026 TTTCTGGGCT
* *
5036 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
5057 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
5078 A
1 A
5079 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:5814 original size:23 final size:23
Alignment explanation
Indices: 5770--5814 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5760 ATTATTATAT
*
5770 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
5793 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
5815 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:7549 original size:17 final size:18
Alignment explanation
Indices: 7523--7557 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
7513 GGCGCTCCCC
7523 GATATATTTTAA-ATTTT
1 GATATATTTTAATATTTT
*
7540 GATATTTTTTAATATTTT
1 GATATATTTTAATATTTT
7558 CTGTTAATAA
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:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
GATATATTTTAATATTTT
Found at i:16374 original size:42 final size:42
Alignment explanation
Indices: 16315--16397 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
16305 AAGAGCTGTA
16315 GTTGGTGGTATGGAGAAAGGAAAAGAAAGGATTGTAGAAGAT
1 GTTGGTGGTATGGAGAAAGGAAAAGAAAGGATTGTAGAAGAT
16357 GTTGGTGGTATGGAGAAAGGAAAAGAAAGGATTGTAGAAGA
1 GTTGGTGGTATGGAGAAAGGAAAAGAAAGGATTGTAGAAGA
16398 CGATGAACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (42 bp):
GTTGGTGGTATGGAGAAAGGAAAAGAAAGGATTGTAGAAGAT
Found at i:25524 original size:6 final size:6
Alignment explanation
Indices: 25513--25539 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
25503 GTATACGTGA
25513 TGCAAG TGCAAG TGCAAG TGCAAG TGC
1 TGCAAG TGCAAG TGCAAG TGCAAG TGC
25540 TTTTGCTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.19
Consensus pattern (6 bp):
TGCAAG
Found at i:35310 original size:16 final size:18
Alignment explanation
Indices: 35271--35311 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
35261 TAATTTACTT
35271 AATTTATTATATTAATAA
1 AATTTATTATATTAATAA
*
35289 AGATTTA-TATTTTAA-AA
1 A-ATTTATTATATTAATAA
35306 AATTTA
1 AATTTA
35312 CAACTAGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 3 0.14
18 8 0.38
19 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AATTTATTATATTAATAA
Found at i:36996 original size:33 final size:34
Alignment explanation
Indices: 36959--37025 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
36949 ACTGAGGCTT
* *
36959 CAACGGAAGTGG-CAGCAACAACAACCGAGACTC
1 CAACGGAACTGGACAACAACAACAACCGAGACTC
36992 CAACGGAACTGGTAACAACAACAACAACCGAGAC
1 CAACGGAACTGG--ACAACAACAACAACCGAGAC
37026 GACGGAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 11 0.38
36 18 0.62
ACGTcount: A:0.43, C:0.30, G:0.21, T:0.06
Consensus pattern (34 bp):
CAACGGAACTGGACAACAACAACAACCGAGACTC
Found at i:45842 original size:23 final size:24
Alignment explanation
Indices: 45807--45853 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
45797 TTAAGTATGA
* *
45807 AATTAGGGGTTTA-GAAATTTGAG
1 AATTAAGGCTTTATGAAATTTGAG
*
45830 AATTAAGGCTTTATGAATTTTGAG
1 AATTAAGGCTTTATGAAATTTGAG
45854 TGTTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (24 bp):
AATTAAGGCTTTATGAAATTTGAG
Found at i:46951 original size:35 final size:35
Alignment explanation
Indices: 46905--46975 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
46895 CTACTGCTCT
*
46905 ATAGTACTAGTGTGAAGTTCATATAAGAGAAAGAA
1 ATAGTACTAGTGTGAAGTTCATACAAGAGAAAGAA
*
46940 ATAGTACTAGTGTGAAGTTCATGCAAGAGAAAGAA
1 ATAGTACTAGTGTGAAGTTCATACAAGAGAAAGAA
46975 A
1 A
46976 ACAACACATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (35 bp):
ATAGTACTAGTGTGAAGTTCATACAAGAGAAAGAA
Found at i:52209 original size:32 final size:31
Alignment explanation
Indices: 52145--52209 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 31
52135 TGGTGACTAC
* * *
52145 ATCTTGATCAAATAAAAATGAAAGTAATCAT
1 ATCTTAATCAAATAAAAATAAAAGTAACCAT
* *
52176 ATCTTAATTAAATAAAAAATAAAAGTGACCAT
1 ATCTTAATCAAAT-AAAAATAAAAGTAACCAT
52208 AT
1 AT
52210 ATTATGTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (31 bp):
ATCTTAATCAAATAAAAATAAAAGTAACCAT
Found at i:56319 original size:3 final size:3
Alignment explanation
Indices: 56311--56337 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
56301 GTAGTTAAGC
56311 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
56338 TTACAATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:57193 original size:21 final size:21
Alignment explanation
Indices: 57169--57221 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
57159 GGTGGCACTA
57169 TATATACATACATGTCTGGAT
1 TATATACATACATGTCTGGAT
57190 TATATACATACATGTCTGGAT
1 TATATACATACATGTCTGGAT
57211 TATATACATAC
1 TATATACATAC
57222 GTGCATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (21 bp):
TATATACATACATGTCTGGAT
Found at i:57767 original size:2 final size:2
Alignment explanation
Indices: 57760--57809 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
57750 GAATTCTAAA
57760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
57802 AT AA AT AT
1 AT AT AT AT
57810 TTAGTATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58611 original size:21 final size:20
Alignment explanation
Indices: 58571--58612 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
58561 TCAACTTACA
*
58571 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
58591 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
58612 A
1 A
58613 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:63224 original size:21 final size:20
Alignment explanation
Indices: 63184--63225 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
63174 TCAACTTACA
*
63184 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
63204 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
63225 A
1 A
63226 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:64599 original size:2 final size:2
Alignment explanation
Indices: 64592--64619 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
64582 GGATGGAAAC
64592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64620 CCAGTCGGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65456 original size:42 final size:42
Alignment explanation
Indices: 65397--65516 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
65387 TTTCCCCGAA
*
65397 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
65439 TTCCCGTGTTTGTTTCACATAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
65481 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
65517 TGTAATTCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:65752 original size:22 final size:23
Alignment explanation
Indices: 65705--65765 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
65695 TAATTATTAA
* *
65705 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
65726 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
65749 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
65766 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:65781 original size:31 final size:32
Alignment explanation
Indices: 65716--65794 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
65706 ATATTTAAAA
65716 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAATATAATAT
*
65748 TATATTT-TTAATA-TTAT-ATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAATATAAT--AT
*
65779 TATATTATAATAATAT
1 TATATT-TATTAATAT
65795 AAGATATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 9 0.22
30 4 0.10
31 14 0.35
32 8 0.20
33 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATATAATAT
Found at i:65862 original size:19 final size:19
Alignment explanation
Indices: 65840--65892 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
65830 ATTTTTTTTT
*
65840 ATATATTTAATAATGAATA
1 ATATATTTAATAATCAATA
*
65859 ATATTATTTATATATTTCAATA
1 ATA-TATTTA-ATA-ATCAATA
65881 ATAT-TTTAATAA
1 ATATATTTAATAA
65893 AGATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATCAATA
Found at i:65912 original size:22 final size:23
Alignment explanation
Indices: 65887--65930 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
65877 AATAATATTT
65887 TAATAAAGA-TATTAAAATATAC
1 TAATAAAGATTATTAAAATATAC
* * *
65909 TAATTAATATTTTTAAAATATA
1 TAATAAAGATTATTAAAATATA
65931 ATATAGTACT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TAATAAAGATTATTAAAATATAC
Found at i:66128 original size:20 final size:20
Alignment explanation
Indices: 66050--66119 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
66040 TTTCCAGATG
*
66050 TTTTTCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
66070 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
66090 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
66110 TTTTCCAGAA
1 TTTTCCAGAA
66120 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:66128 original size:40 final size:40
Alignment explanation
Indices: 66050--66128 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
66040 TTTCCAGATG
* **
66050 TTTTTCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
66090 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
66129 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:66138 original size:15 final size:15
Alignment explanation
Indices: 66102--66183 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
66092 TTACAGAAAT
**
66102 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
66117 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
66131 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
66146 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
66161 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
66176 GTAATTCA
1 GTAATTCA
66184 TTTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:66154 original size:30 final size:30
Alignment explanation
Indices: 66102--66183 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
66092 TTACAGAAAT
66102 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
66131 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
66161 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
66184 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:66176 original size:45 final size:44
Alignment explanation
Indices: 66102--66188 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
66092 TTACAGAAAT
**
66102 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
66146 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
66189 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:66487 original size:5 final size:5
Alignment explanation
Indices: 66477--66510 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
66467 TTATAAATTT
66477 ATCCC ATCCC ATCCC ATCCC ATCCC ATCCC ATCC
1 ATCCC ATCCC ATCCC ATCCC ATCCC ATCCC ATCC
66511 TACCCATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (5 bp):
ATCCC
Found at i:71560 original size:34 final size:33
Alignment explanation
Indices: 71522--71593 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 33
71512 AAATAATATT
71522 TTTAAGGTTAGAGTTTAAAT-TTTAGGGTTTAAGA
1 TTTAAGGTTAGAGTTT--ATGTTTAGGGTTTAAGA
* * *
71556 TTTAAATGTTAGGGTTTATGTTTGGGGTTTAAGA
1 TTT-AAGGTTAGAGTTTATGTTTAGGGTTTAAGA
71590 TTTA
1 TTTA
71594 TGATTGAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
33 3 0.09
34 19 0.58
35 11 0.33
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (33 bp):
TTTAAGGTTAGAGTTTATGTTTAGGGTTTAAGA
Found at i:71944 original size:33 final size:33
Alignment explanation
Indices: 71901--72001 Score: 184
Period size: 33 Copynumber: 3.1 Consensus size: 33
71891 TGATGGAAGG
* *
71901 CCCCACTATTTTGGATTCATTCATTTCAATCAT
1 CCCCAGTATTTTGGGTTCATTCATTTCAATCAT
71934 CCCCAGTATTTTGGGTTCATTCATTTCAATCAT
1 CCCCAGTATTTTGGGTTCATTCATTTCAATCAT
71967 CCCCAGTATTTTGGGTTCATTCATTTCAATCAT
1 CCCCAGTATTTTGGGTTCATTCATTTCAATCAT
72000 CC
1 CC
72002 ATCCAATTCA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.42
Consensus pattern (33 bp):
CCCCAGTATTTTGGGTTCATTCATTTCAATCAT
Done.