Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001925.1 Hibiscus syriacus cultivar Beakdansim tig00003896_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: 62712
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:251 original size:58 final size:59
Alignment explanation
Indices: 151--524 Score: 467
Period size: 58 Copynumber: 6.6 Consensus size: 59
141 AAATTACCAA
* * *
151 AGGGCACTTTGTGTGATAAAATGGTAAG-GAATCATACTAAGTGTATGAATTTCCAAAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
209 AGGGAACTTTGTGTGCTAAAATGGT-AGAAAATCATACCAAGTGTATGAATTTCTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
267 AGGGCATTTTGTGTGCTAAAATGGTAAGGAAACCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGAT
* * * *
326 AGGGCACTTTGTGTGTTAAAATGGTAAGGAAACCATACTAGGTGTA-GAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
384 AGGGCAC-TTGTGTGCTAAAATGGTAAGGAAATTATACTAAGTGTATTAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGAT
*
442 AGGGCACTTTGTGTGC-----------GAAAATCATAC-AGGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGAT
*
489 A-GGCACTTTATGTGCTAAAATGGTAAGAAAATCATA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATA
525 TTGATTGTAT
Statistics
Matches: 276, Mismatches: 25, Indels: 31
0.83 0.08 0.09
Matches are distributed among these distances:
46 13 0.05
47 19 0.07
48 9 0.03
57 46 0.17
58 109 0.39
59 80 0.29
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:1494 original size:43 final size:44
Alignment explanation
Indices: 1428--1599 Score: 276
Period size: 44 Copynumber: 4.0 Consensus size: 44
1418 GTTACCAAAT
* *
1428 AATG-AAATGCATAACGGTACATTATTGGCAGAAAGATGCCATA
1 AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATA
* *
1471 AATG-AAATGTATAATGGTGCATTATTGGCAGAAAGGTGCCATA
1 AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATA
*
1514 AATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCCATA
1 AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATA
*
1558 AATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGCCA
1 AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCA
1600 CTCATGTTGT
Statistics
Matches: 119, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
43 43 0.36
44 76 0.64
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (44 bp):
AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATA
Found at i:1529 original size:87 final size:87
Alignment explanation
Indices: 1428--1599 Score: 274
Period size: 87 Copynumber: 2.0 Consensus size: 87
1418 GTTACCAAAT
* * **
1428 AATGAAATGCATAACGGTACATTATTGGCAGAAAGATGCCATAAATG-AAATGTATAATGGTGCA
1 AATGAAATGCATAACGATACATTATTGGCAGAAAGATGCCATAAATGAAAATGCATAACAGTGCA
1492 TTATTGGCAGAAAGGTGCCATA
66 TTATTGGCAGAAAGGTGCCATA
* *
1514 AATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACAGTGC
1 AATG-AAATGCATAACGATACATTATTGGCAGAAAGATGCCATAAATGAAAATGCATAACAGTGC
1579 ATTATTGGCAGAAAGGTGCCA
65 ATTATTGGCAGAAAGGTGCCA
1600 CTCATGTTGT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
86 4 0.05
87 40 0.51
88 34 0.44
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (87 bp):
AATGAAATGCATAACGATACATTATTGGCAGAAAGATGCCATAAATGAAAATGCATAACAGTGCA
TTATTGGCAGAAAGGTGCCATA
Found at i:6202 original size:129 final size:131
Alignment explanation
Indices: 5993--6227 Score: 314
Period size: 129 Copynumber: 1.8 Consensus size: 131
5983 ATATGGCTGG
* * *
5993 CCATCTTTAGGGATGATGATACACGATTCTTACGTGATGGGACGACTGGTTATCTAGGGGTAACG
1 CCATCTTTAGGGATGATGATACACGATTCATACGTGATGAGACGACTGGTTATCTAGGGGTAACA
* *
6058 CAGCTCCTATTTGATGAGGAGATATGGTCAGTGGATGACACGGTGCCTACGCGTGAGGATGACAA
66 CAGCTCCTATGTGATGAGGAGATATGGTCAGGGGATGACACGGTGCCTACGCGTGAGGATGACAA
6123 A
131 A
* * ** * *
6124 CCATCTTTAGGGATGAT-A-ACACGGTTCATACGTGATGAGATGGTTGGTTATCT-GAGGTTGAC
1 CCATCTTTAGGGATGATGATACACGATTCATACGTGATGAGACGACTGGTTATCTAG-GGGTAAC
** *
6186 ATGGCTCCTATGTGATGAGGAGATCTGGTCAGGGGATGACAC
65 ACAGCTCCTATGTGATGAGGAGATATGGTCAGGGGATGACAC
6228 ACTTCTTACG
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
128 1 0.01
129 70 0.79
130 1 0.01
131 17 0.19
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (131 bp):
CCATCTTTAGGGATGATGATACACGATTCATACGTGATGAGACGACTGGTTATCTAGGGGTAACA
CAGCTCCTATGTGATGAGGAGATATGGTCAGGGGATGACACGGTGCCTACGCGTGAGGATGACAA
A
Found at i:6256 original size:129 final size:130
Alignment explanation
Indices: 5993--6266 Score: 295
Period size: 129 Copynumber: 2.1 Consensus size: 130
5983 ATATGGCTGG
* * *
5993 CCATCTTTAGGGATGATGATACACGATTCTTACGTGATGGGACGACTGGTTATCTAGGGGTAACG
1 CCATCTTTAGGGATGATGATACACGATTCATACGTGATGAGACGACTGGTTATCTAGGGGTAACA
* * ** *
6058 CAGCTCCTATTTGATGAGGAGATATGGTCAGTGGATGACACGGTGCCTACGCGTGAGGATGACAA
66 CAGCTCCTATGTGATGAGGAGATATGGTCAGGGGATGACACACTGCCTAC-CGTGAGGAGGACAA
6123 A
130 A
* * ** * *
6124 CCATCTTTAGGGATGAT-A-ACACGGTTCATACGTGATGAGATGGTTGGTTATCT-GAGGTTGAC
1 CCATCTTTAGGGATGATGATACACGATTCATACGTGATGAGACGACTGGTTATCTAG-GGGTAAC
** * * * *
6186 ATGGCTCCTATGTGATGAGGAGATCTGGTCAGGGGATGACACACTTCTTA-CGTGATGAGGACAG
65 ACAGCTCCTATGTGATGAGGAGATATGGTCAGGGGATGACACACTGCCTACCGTGAGGAGGACA-
*
6250 TTA
129 -AA
6253 CCATCTTTAGGGAT
1 CCATCTTTAGGGAT
6267 TTGTTTCAAG
Statistics
Matches: 119, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
127 11 0.09
128 1 0.01
129 89 0.75
130 1 0.01
131 17 0.14
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (130 bp):
CCATCTTTAGGGATGATGATACACGATTCATACGTGATGAGACGACTGGTTATCTAGGGGTAACA
CAGCTCCTATGTGATGAGGAGATATGGTCAGGGGATGACACACTGCCTACCGTGAGGAGGACAAA
Found at i:6468 original size:64 final size:64
Alignment explanation
Indices: 6275--6469 Score: 200
Period size: 63 Copynumber: 3.0 Consensus size: 64
6265 ATTTGTTTCA
* * * *
6275 AGAGACAAAATTTGTTTCAAGGGAAACAACTCAAAGA--TGATGTTTCAAGAGAAACTTTTTAAG
1 AGAGACAAAATTTGTTTCAAGGGAAAAAACTCAAAGATTTG-TGTTTCAAGAGAAACGTCTCAAG
* * *
6338 AGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATGATTTTTTTTCCAAGAGAAACTGTCT
1 AGAGACAAAATTTGTTTCAAGGGAAA-AAACTCAAAGAT--TTGTGTTT-CAAGAGAAAC-GTCT
6403 CAAG
61 CAAG
* * *
6407 AGAGAC-AAATTT-TTTTAAGAGAAAAAGACTCAAAGATTTGTGTTTCAAGGGAAACGATCTCAA
1 AGAGACAAAATTTGTTTCAAGGGAAAAA-ACTCAAAGATTTGTGTTTCAAGAGAAACG-TCTCAA
6470 AGATGAATTT
Statistics
Matches: 110, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
63 27 0.25
64 24 0.22
65 6 0.05
66 2 0.02
67 23 0.21
68 17 0.15
69 11 0.10
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (64 bp):
AGAGACAAAATTTGTTTCAAGGGAAAAAACTCAAAGATTTGTGTTTCAAGAGAAACGTCTCAAG
Found at i:6492 original size:81 final size:81
Alignment explanation
Indices: 6402--6551 Score: 248
Period size: 81 Copynumber: 1.9 Consensus size: 81
6392 AGAAACTGTC
* *
6402 TCAAGAGAGAC-AAATTTTTTTAAGAGAAAAAGACTCAAAGATTTGTGTTTCAAGGGAAACGATC
1 TCAAGAGAGACAAAATTTTTTTAAGAG-AAAAGACTCAAAGATTTATGTTTCAAGGGAAACAATC
6466 TCAAAGATGAATTTTTT
65 TCAAAGATGAATTTTTT
* *
6483 TCAAGAGAGACAAAATTTTTTTAAGAGAAAAGACTCAAAGATTTATGTTTTAAGGGAAACAATTT
1 TCAAGAGAGACAAAATTTTTTTAAGAGAAAAGACTCAAAGATTTATGTTTCAAGGGAAACAATCT
6548 CAAA
66 CAAA
6552 TTTTATTTTA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
81 49 0.77
82 15 0.23
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (81 bp):
TCAAGAGAGACAAAATTTTTTTAAGAGAAAAGACTCAAAGATTTATGTTTCAAGGGAAACAATCT
CAAAGATGAATTTTTT
Found at i:9992 original size:32 final size:32
Alignment explanation
Indices: 9916--9985 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
9906 GACATGATAT
9916 CTACCCGAACATGCTTTTATTAAATAACATTC
1 CTACCCGAACATGCTTTTATTAAATAACATTC
9948 CTACCCGAACATGCTTTTATTAAATAACATTC
1 CTACCCGAACATGCTTTTATTAAATAACATTC
9980 CTACCC
1 CTACCC
9986 AGACATGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (32 bp):
CTACCCGAACATGCTTTTATTAAATAACATTC
Found at i:12497 original size:19 final size:19
Alignment explanation
Indices: 12473--12520 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
12463 ATTTCTGGTT
12473 CGAATGCTCTCTCCCTCAC
1 CGAATGCTCTCTCCCTCAC
12492 CGAATGCTCTCTCCCTCAC
1 CGAATGCTCTCTCCCTCAC
12511 CGAATGCTCT
1 CGAATGCTCT
12521 TTCGGTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.17, C:0.44, G:0.12, T:0.27
Consensus pattern (19 bp):
CGAATGCTCTCTCCCTCAC
Found at i:12566 original size:48 final size:48
Alignment explanation
Indices: 12504--12614 Score: 177
Period size: 48 Copynumber: 2.3 Consensus size: 48
12494 AATGCTCTCT
* *
12504 CCCTCACCGAATGCTCTTTCGGTTCCTCTTTATTTCTTTTCTCTGTCC
1 CCCTCACCGAATGCTCTTTCGGATCCTCTTTATTTCTTTTCTATGTCC
* *
12552 CCCTCACCGAATGCTCTTTCGGATCCTTTTTATTTTTTTTCTATGTCC
1 CCCTCACCGAATGCTCTTTCGGATCCTCTTTATTTCTTTTCTATGTCC
*
12600 CCCTCACTGAATGCT
1 CCCTCACCGAATGCT
12615 TTCCTTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.12, C:0.33, G:0.11, T:0.44
Consensus pattern (48 bp):
CCCTCACCGAATGCTCTTTCGGATCCTCTTTATTTCTTTTCTATGTCC
Found at i:13582 original size:24 final size:25
Alignment explanation
Indices: 13555--13601 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
13545 GTTTAGGTGT
*
13555 TGGGCTAGGGTTTTGAT-TTGGGCA
1 TGGGCTAGGGTTATGATGTTGGGCA
* *
13579 TGGGTTTGGGTTATGATGTTGGG
1 TGGGCTAGGGTTATGATGTTGGG
13602 TATTGGGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.11, C:0.04, G:0.45, T:0.40
Consensus pattern (25 bp):
TGGGCTAGGGTTATGATGTTGGGCA
Found at i:13626 original size:3 final size:3
Alignment explanation
Indices: 13613--13732 Score: 136
Period size: 3 Copynumber: 38.3 Consensus size: 3
13603 ATTGGGTTTG
* *
13613 TAA TAAA TAA TAA TAA TAA TAA TACT TTA TAA TAAA TAA TAA T-A TAA
1 TAA T-AA TAA TAA TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA
*
13660 TAA TAA TAA TTTA TAA TAAA TAA TAA TAA TATA TAA TAAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
13709 TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
13733 GACTGAAAAA
Statistics
Matches: 102, Mismatches: 6, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.04
3 80 0.78
4 18 0.18
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:13652 original size:20 final size:18
Alignment explanation
Indices: 13622--13725 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 18
13612 GTAATAAATA
13622 ATAATAATAATAATACTTT
1 ATAATAATAATAATA-TTT
*
13641 ATAAT-A-AATAATA-AT
1 ATAATAATAATAATATTT
13656 ATAATAATAAT-A-ATTT
1 ATAATAATAATAATATTT
*
13672 ATAATAAATAATAATAATAT
1 ATAAT-AATAATAAT-ATTT
* *
13692 ATAATAAATAATAATAATA
1 ATAAT-AATAATAATATTT
13711 ATAATAATAATAATA
1 ATAATAATAATAATA
13726 ATATAATGAC
Statistics
Matches: 72, Mismatches: 6, Indels: 15
0.77 0.06 0.16
Matches are distributed among these distances:
15 7 0.10
16 8 0.11
17 16 0.22
18 12 0.17
19 11 0.15
20 18 0.25
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATAATAATAATATTT
Found at i:25513 original size:13 final size:13
Alignment explanation
Indices: 25497--25542 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
25487 TAAATTGCAC
25497 TTTTAAAAAACAA
1 TTTTAAAAAACAA
**
25510 TTTT--AAAACTTC
1 TTTTAAAAAAC-AA
25522 TTTTAAAAAACAA
1 TTTTAAAAAACAA
25535 TTTTAAAA
1 TTTTAAAA
25543 GTTTTTTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 12 0.46
14 5 0.19
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTTAAAAAACAA
Found at i:28698 original size:20 final size:20
Alignment explanation
Indices: 28673--28715 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28663 TCTAAAGGCC
28673 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
28693 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
28713 CAT
1 CAT
28716 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:51247 original size:2 final size:2
Alignment explanation
Indices: 51240--51284 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
51230 TCAGATTTAT
51240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51281 TA TA
1 TA TA
51285 ATCGCCTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51634 original size:22 final size:21
Alignment explanation
Indices: 51606--51707 Score: 91
Period size: 21 Copynumber: 4.9 Consensus size: 21
51596 CACACTGTCT
*
51606 AGGGGGTACATATTCCCCCTAC
1 AGGGGGTACAGATTCCCCC-AC
* *
51628 AGGGGGTACCGATTCCCCCCC
1 AGGGGGTACAGATTCCCCCAC
* *
51649 AGGGCGTACCGATT-CCCCACC
1 AGGGGGTACAGATTCCCCCA-C
* *
51670 AGGGGGAACAAATTCCCCC-C
1 AGGGGGTACAGATTCCCCCAC
* *
51690 AAGGGGTACCGATTCCCC
1 AGGGGGTACAGATTCCCC
51708 TTGTCTAACG
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
20 19 0.29
21 25 0.38
22 21 0.32
ACGTcount: A:0.22, C:0.37, G:0.25, T:0.16
Consensus pattern (21 bp):
AGGGGGTACAGATTCCCCCAC
Found at i:52099 original size:34 final size:32
Alignment explanation
Indices: 52060--52124 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 32
52050 GTAAAGGGAA
*
52060 AAGGTTCTAGCTTAGCCCGTGTAAAAGCTAGGGT
1 AAGGTTCTAGCTTAGCCCG-G-AAAAACTAGGGT
*
52094 AAGGTTCTAGTTTAGCCCGGAAAAACTAGGG
1 AAGGTTCTAGCTTAGCCCGGAAAAACTAGGG
52125 AGTTTGTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 10 0.34
33 1 0.03
34 18 0.62
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (32 bp):
AAGGTTCTAGCTTAGCCCGGAAAAACTAGGGT
Found at i:55100 original size:22 final size:21
Alignment explanation
Indices: 55072--55178 Score: 133
Period size: 22 Copynumber: 5.0 Consensus size: 21
55062 TCAGATTGTC
*
55072 CAGGGGGTACAGATTCCCCCTA
1 CAGGGGGTACCGATTCCCCC-A
*
55094 CAGGGGGTACCGATTCCCCCCC
1 CAGGGGGTACCGATT-CCCCCA
55116 CAGGGGGTACCGATTCCCCCA
1 CAGGGGGTACCGATTCCCCCA
* * *
55137 CCAGGGGGAACAGATTCCCCCC
1 -CAGGGGGTACCGATTCCCCCA
*
55159 CAGGGGATACCGATTCCCCC
1 CAGGGGGTACCGATTCCCCC
55179 TGTCTAACGG
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.30
22 47 0.64
23 5 0.07
ACGTcount: A:0.20, C:0.39, G:0.27, T:0.14
Consensus pattern (21 bp):
CAGGGGGTACCGATTCCCCCA
Found at i:55171 original size:43 final size:44
Alignment explanation
Indices: 55071--55179 Score: 159
Period size: 44 Copynumber: 2.5 Consensus size: 44
55061 ATCAGATTGT
* * *
55071 CCAGGGGGTACAGATTCCCCCTACAGGGGGTACCGATTCCCCCC
1 CCAGGGGGTACCGATTCCCCCTACAGGGGGAACAGATTCCCCCC
55115 CCAGGGGGTACCGATTCCCCC-ACCAGGGGGAACAGATT-CCCCC
1 CCAGGGGGTACCGATTCCCCCTA-CAGGGGGAACAGATTCCCCCC
*
55158 CCAGGGGATACCGATTCCCCCT
1 CCAGGGGGTACCGATTCCCCCT
55180 GTCTAACGGT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
43 26 0.44
44 33 0.56
ACGTcount: A:0.19, C:0.39, G:0.27, T:0.15
Consensus pattern (44 bp):
CCAGGGGGTACCGATTCCCCCTACAGGGGGAACAGATTCCCCCC
Done.