Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004389.1 Hibiscus syriacus cultivar Beakdansim tig00009623_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: 57270
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3987 original size:31 final size:31
Alignment explanation
Indices: 3952--4011 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
3942 AGTTACGATA
3952 GGGACCATATTGCAAATGGACTAAATGTTAG
1 GGGACCATATTGCAAATGGACTAAATGTTAG
3983 GGGACCATATTGCAAATGGACTAAATGTT
1 GGGACCATATTGCAAATGGACTAAATGTT
4012 GGAGGACTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (31 bp):
GGGACCATATTGCAAATGGACTAAATGTTAG
Found at i:4105 original size:3 final size:3
Alignment explanation
Indices: 4097--4172 Score: 125
Period size: 3 Copynumber: 24.3 Consensus size: 3
4087 TACTTTACCC
4097 TAA TAA TAA TAA TAA TAAA TAA TAAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA T-AA TAA T-AA TAA TAA TAA TAA TAA
4145 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4173 TATTATTATT
Statistics
Matches: 70, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
3 61 0.87
4 9 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9305 original size:15 final size:15
Alignment explanation
Indices: 9287--9319 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
9277 AAAATCTTTT
*
9287 TTTTCCCGTTCTTGA
1 TTTTCCCGTTCTGGA
9302 TTTTCCCGTTCTGGA
1 TTTTCCCGTTCTGGA
9317 TTT
1 TTT
9320 GGATCTGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.15, T:0.55
Consensus pattern (15 bp):
TTTTCCCGTTCTGGA
Found at i:10558 original size:36 final size:36
Alignment explanation
Indices: 10518--10589 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
10508 TATTTCCAAC
*
10518 AAACATGTACCAAACTTTGAAAAATATTTTTCAAAG
1 AAACATGTACCAAACTTTGAAAAACATTTTTCAAAG
*
10554 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACATGTACCAAACTTTGAAAAACATTTTTCAAAG
10590 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (36 bp):
AAACATGTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:10588 original size:21 final size:21
Alignment explanation
Indices: 10528--10588 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
10518 AAACATGTAC
*
10528 CAAACTTTGAAAAATATTTTT
1 CAAACTTTGAAAAACATTTTT
**
10549 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
10564 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
10585 CAAA
1 CAAA
10589 GTTGGTTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 11 0.38
17 1 0.03
19 1 0.03
21 16 0.55
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:13793 original size:37 final size:36
Alignment explanation
Indices: 13752--13875 Score: 92
Period size: 42 Copynumber: 3.3 Consensus size: 36
13742 TATTTCTAGT
*
13752 ATATATATTTTAATAAAATTTATATACGAATAATTTA
1 ATATATATTTTAATAAAATTTATATA-AAATAATTTA
* * * *
13789 ATATATACTTTTATTACATTTATTTTTTGATAAAATTATTT-
1 ATATATA-TTTTAATA-A---AATTTAT-ATAAAATAATTTA
*
13830 ATATAT-TTTTAATAAAATTTATA-AATTAATAACTTA
1 ATATATATTTTAATAAAATTTATATAA--AATAATTTA
13866 ATATATATTT
1 ATATATATTT
13876 ATTATATTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
33 2 0.03
34 1 0.01
35 11 0.16
36 6 0.09
37 10 0.15
38 8 0.12
39 8 0.12
41 6 0.09
42 12 0.18
43 3 0.04
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (36 bp):
ATATATATTTTAATAAAATTTATATAAAATAATTTA
Found at i:14288 original size:18 final size:17
Alignment explanation
Indices: 14232--14288 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
14222 CATCACCTTA
14232 AAAAAG-GGTTGCAACCT
1 AAAAAGTGG-TGCAACCT
* *
14249 AAAATGTGGTGCAACTT
1 AAAAAGTGGTGCAACCT
14266 GAAAAAGTGGTGCAACCAT
1 -AAAAAGTGGTGCAACC-T
14285 AAAA
1 AAAA
14289 TAAGTTGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 12 0.36
18 20 0.61
19 1 0.03
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (17 bp):
AAAAAGTGGTGCAACCT
Found at i:18044 original size:15 final size:15
Alignment explanation
Indices: 18024--18076 Score: 97
Period size: 15 Copynumber: 3.5 Consensus size: 15
18014 CTTGAAAGTA
18024 AAATCAAAGATTTGC
1 AAATCAAAGATTTGC
*
18039 AAATCAAATATTTGC
1 AAATCAAAGATTTGC
18054 AAATCAAAGATTTGC
1 AAATCAAAGATTTGC
18069 AAATCAAA
1 AAATCAAA
18077 CTAGAAGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.26
Consensus pattern (15 bp):
AAATCAAAGATTTGC
Found at i:21928 original size:21 final size:21
Alignment explanation
Indices: 21837--21929 Score: 114
Period size: 21 Copynumber: 4.3 Consensus size: 21
21827 GGAATCAATA
21837 CCCCCTTGAAGGGGAACCGATT
1 CCCCC-TGAAGGGGAACCGATT
21859 CCCCCTTTGAAGGGGAACCGATT
1 CCCCC--TGAAGGGGAACCGATT
* *
21882 CTCCCTGTAGGGGAACCGATT
1 CCCCCTGAAGGGGAACCGATT
* * *
21903 CCCCCTGTAGGGGAATCGATA
1 CCCCCTGAAGGGGAACCGATT
21924 CCCCCT
1 CCCCCT
21930 ATGGTTCTGG
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
21 39 0.60
22 5 0.08
23 21 0.32
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.20
Consensus pattern (21 bp):
CCCCCTGAAGGGGAACCGATT
Found at i:27473 original size:105 final size:105
Alignment explanation
Indices: 27291--27501 Score: 422
Period size: 105 Copynumber: 2.0 Consensus size: 105
27281 GAAGGAGAAA
27291 ACCAGAGAAGAAATTGAATTTTTTTTCTAATCAACGGACAAAATAAAACTAGGGATTTATCATAA
1 ACCAGAGAAGAAATTGAATTTTTTTTCTAATCAACGGACAAAATAAAACTAGGGATTTATCATAA
27356 ATGAAAAGGTAGTTTTGAAATATTTCTTTTATTTTAAGGT
66 ATGAAAAGGTAGTTTTGAAATATTTCTTTTATTTTAAGGT
27396 ACCAGAGAAGAAATTGAATTTTTTTTCTAATCAACGGACAAAATAAAACTAGGGATTTATCATAA
1 ACCAGAGAAGAAATTGAATTTTTTTTCTAATCAACGGACAAAATAAAACTAGGGATTTATCATAA
27461 ATGAAAAGGTAGTTTTGAAATATTTCTTTTATTTTAAGGT
66 ATGAAAAGGTAGTTTTGAAATATTTCTTTTATTTTAAGGT
27501 A
1 A
27502 TTTCTGTTAA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (105 bp):
ACCAGAGAAGAAATTGAATTTTTTTTCTAATCAACGGACAAAATAAAACTAGGGATTTATCATAA
ATGAAAAGGTAGTTTTGAAATATTTCTTTTATTTTAAGGT
Found at i:33177 original size:17 final size:17
Alignment explanation
Indices: 33155--33193 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
33145 ATTTAATGGT
*
33155 ATAATAATGATTATTTA
1 ATAATAATGATGATTTA
33172 ATAATAATGATGATTTA
1 ATAATAATGATGATTTA
33189 ATAAT
1 ATAAT
33194 GTTAATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (17 bp):
ATAATAATGATGATTTA
Found at i:33277 original size:23 final size:24
Alignment explanation
Indices: 33251--33295 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
33241 AAAAAAGTTG
33251 CATGCTTCTCCACAAGG-TTGACA
1 CATGCTTCTCCACAAGGCTTGACA
33274 CATGCTTCTCCACAAGGCTTGA
1 CATGCTTCTCCACAAGGCTTGA
33296 TAAATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (24 bp):
CATGCTTCTCCACAAGGCTTGACA
Found at i:35398 original size:20 final size:21
Alignment explanation
Indices: 35373--35414 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
35363 CACTCAAAAG
35373 AAGAAAACA-AAAAG-AAGAAA
1 AAGAAAA-AGAAAAGAAAGAAA
35393 AAGAAAAAGAAAAGAAAGAAA
1 AAGAAAAAGAAAAGAAAGAAA
35414 A
1 A
35415 GTTGAAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.05
20 12 0.60
21 7 0.35
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (21 bp):
AAGAAAAAGAAAAGAAAGAAA
Found at i:35399 original size:15 final size:15
Alignment explanation
Indices: 35368--35414 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
35358 GCAAGCACTC
*
35368 AAAAGAAG-AAAACA
1 AAAAGAAGAAAAAGA
35382 AAAAGAAGAAAAAGA
1 AAAAGAAGAAAAAGA
35397 AAAAGAA-AAGAAAGA
1 AAAAGAAGAA-AAAGA
35412 AAA
1 AAA
35415 GTTGAAAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 10 0.33
15 20 0.67
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAAAAGA
Found at i:38233 original size:29 final size:29
Alignment explanation
Indices: 38191--38250 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
38181 GGCCAAGAGG
38191 GGGGGTGAATTGGCAATTAAAAATTTGGT
1 GGGGGTGAATTGGCAATTAAAAATTTGGT
38220 GGGGGTGAATTGGCAATTAAAAATTTGGT
1 GGGGGTGAATTGGCAATTAAAAATTTGGT
38249 GG
1 GG
38251 AAGCTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.30
Consensus pattern (29 bp):
GGGGGTGAATTGGCAATTAAAAATTTGGT
Found at i:38897 original size:20 final size:19
Alignment explanation
Indices: 38872--38947 Score: 75
Period size: 22 Copynumber: 3.8 Consensus size: 19
38862 ATATGCCTTA
*
38872 GGGTATCGGTACCATCTGAG
1 GGGTATCGATACCAT-TGAG
38892 GGGTATCGATACCATTGCATGG
1 GGGTATCGATACCATTG-A--G
38914 GGGTATCGATACC-TATG-G
1 GGGTATCGATACCAT-TGAG
*
38932 GGGTATCGGTACCATT
1 GGGTATCGATACCATT
38948 CGAGCATTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
18 14 0.29
19 3 0.06
20 15 0.31
21 1 0.02
22 16 0.33
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (19 bp):
GGGTATCGATACCATTGAG
Found at i:38933 original size:18 final size:19
Alignment explanation
Indices: 38872--38946 Score: 80
Period size: 18 Copynumber: 3.8 Consensus size: 19
38862 ATATGCCTTA
* *
38872 GGGTATCGGTACCATCTGAG
1 GGGTATCGATACCATATG-G
38892 GGGTATCGATACCATTGCATGG
1 GGGTATCGATACCA-T--ATGG
38914 GGGTATCGATACC-TATGG
1 GGGTATCGATACCATATGG
*
38932 GGGTATCGGTACCAT
1 GGGTATCGATACCAT
38947 TCGAGCATTC
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 16 0.33
19 1 0.02
20 14 0.29
21 1 0.02
22 14 0.29
23 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (19 bp):
GGGTATCGATACCATATGG
Found at i:41720 original size:44 final size:44
Alignment explanation
Indices: 41668--41792 Score: 148
Period size: 44 Copynumber: 2.8 Consensus size: 44
41658 CGGTACCATC
* *
41668 AGGGGGTATTGATACCCATTCAAGGATGGTATCGATACTTATT-GA
1 AGGGGGTATCGATACCCATTCAAGG--GGTATCGATACTTATTCAA
* * *
41713 A-GGGGTATCGATACCTATTGAAGGGGTATCGATACCTATTCAA
1 AGGGGGTATCGATACCCATTCAAGGGGTATCGATACTTATTCAA
*
41756 AGGGGGTATCGATA-CCAGTCTAAGGGGTATCGATACT
1 AGGGGGTATCGATACCCATTC-AAGGGGTATCGATACT
41793 CTATGCACAA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
42 15 0.22
43 5 0.07
44 47 0.69
45 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (44 bp):
AGGGGGTATCGATACCCATTCAAGGGGTATCGATACTTATTCAA
Found at i:41721 original size:21 final size:21
Alignment explanation
Indices: 41670--41796 Score: 132
Period size: 21 Copynumber: 5.8 Consensus size: 21
41660 GTACCATCAG
* * *
41670 GGGGTATTGATACCCATTCAA
1 GGGGTATCGATACCTATTGAA
*
41691 GGATGGTATCGATACTTATTGAA
1 GG--GGTATCGATACCTATTGAA
41714 GGGGTATCGATACCTATTGAA
1 GGGGTATCGATACCTATTGAA
*
41735 GGGGTATCGATACCTATTCAAA
1 GGGGTATCGATACCTATT-GAA
41757 GGGGGTATCGATACC-AGTCT-AA
1 -GGGGTATCGATACCTA-T-TGAA
41779 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
41797 GCACAAAAAT
Statistics
Matches: 92, Mismatches: 6, Indels: 15
0.81 0.05 0.13
Matches are distributed among these distances:
21 51 0.55
22 7 0.08
23 33 0.36
24 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (21 bp):
GGGGTATCGATACCTATTGAA
Found at i:41754 original size:65 final size:66
Alignment explanation
Indices: 41670--41796 Score: 163
Period size: 65 Copynumber: 1.9 Consensus size: 66
41660 GTACCATCAG
* * *
41670 GGGGTATTGATACCCATTC-AAGGATGGTATCGATACTTA-T-TGAAGGGGTATCGATAC-CTAT
1 GGGGTATCGATACCCATTCAAAGG-GGGTATCGATAC-CAGTCT-AAGGGGTATCGATACTCTAT
41731 TGAA
63 TGAA
*
41735 GGGGTATCGATACCTATTCAAAGGGGGTATCGATACCAGTCTAAGGGGTATCGATACTCTAT
1 GGGGTATCGATACCCATTCAAAGGGGGTATCGATACCAGTCTAAGGGGTATCGATACTCTAT
41797 GCACAAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
64 1 0.02
65 44 0.81
66 9 0.17
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (66 bp):
GGGGTATCGATACCCATTCAAAGGGGGTATCGATACCAGTCTAAGGGGTATCGATACTCTATTGA
A
Found at i:47486 original size:22 final size:20
Alignment explanation
Indices: 47458--47513 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 20
47448 ATATGCCTTA
47458 GGGTATCGATACCATTGCATGG
1 GGGTATCGATACCATT--ATGG
47480 GGGTATCGATACC--TATGG
1 GGGTATCGATACCATTATGG
*
47498 GGGTATCGGTACCATT
1 GGGTATCGATACCATT
47514 CGAGCATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 16 0.52
20 2 0.06
22 13 0.42
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (20 bp):
GGGTATCGATACCATTATGG
Found at i:48966 original size:565 final size:565
Alignment explanation
Indices: 47861--48990 Score: 1850
Period size: 565 Copynumber: 2.0 Consensus size: 565
47851 TTCATCTCTA
*
47861 AGCTGCCCAAGGACTTCAATACATCATCCTATGGTTGCAACCTTACCACAAGCATCCTAGAAAGC
1 AGCTGCCCAAGGACTTCAAGACATCATCCTATGGTTGCAACCTTACCACAAGCATCCTAGAAAGC
* * * * * * **
47926 CATGTGCATGTCTTGTGATCATCCAAGCCATGTGTTATTTGTGTGACTCCATTTAGGCGGCAAGA
66 CATGTGCACGCCTTCTGATAAGCCAAGCCATGTGCTATGCGTGTGACTCCATTTAGGCGGCAAGA
* *
47991 TGAATGGCAACCTCACCATTCGGCCAAGCATCATTTCTCATCCAAATTGGCACCAACTTGAAGGG
131 TGAATGGCAACCTCACCATTCGGCCAAGCATCATTTCTCATCCAAATTGGCACAAACTTAAAGGG
* * *
48056 ATTCAAGTGTTATTCGGCCATGAGACATGCTCCTCTATTCCAACTGAACCAGCACATATATTTTT
196 ATTCAAGTGCTATTCGGCCATGAGACATGCTCCTCTATTCCAACCGAACCAACACATATATTTTT
* *
48121 CATGTTATTAATTAATTAATTATGTCATTATAGAGGGATACAAGGGCTGGCCGAACCACCATATA
261 CATGTTATTAATTAATTAATTATGTCATTAAAGAGGGACACAAGGGCTGGCCGAACCACCATATA
* * * * *
48186 ACCATTCGACCAAGTTCCTTCAAAAACTATAAATGGGCTAGTACTATTCTTTTGTAAGCACACCT
326 ACAATTCGACCAAGTCCCTTCAAAAACTATAAATAGGATAGTACTATTCATTTGTAAGCACACCT
*
48251 TTCTTATAATTTAAAGTGAGATTATTCTCTTTTCTTAAGTCCTTGTGACTTTTATTGACTTATCA
391 TTCTTATAATTTAAAGTGAGATTATTCTCTTTTCTTAAGTCCTTGTGACTTTTATCGACTTATCA
* **
48316 AGTAATTTATTTACTTGTGGCATCAACCCCTTATTCCCTTGATACTTGTGGTTCATATCTTTCTA
456 AGTAATTTATTTACTTGTGGCATCAACCCCTTATTCCCTTGATACTTATGGTTCATATCTCCCTA
*
48381 TAAATTATGGGTCCAAGTCCTTGTTACCACCCCTTAGAAAGATTT
521 TAAATTATGGGTCAAAGTCCTTGTTACCACCCCTTAGAAAGATTT
48426 AGCTGCCCAAGGACTTCAAGACATCATCCTATGGTTGCAACCTTACCACAAGCATCCTAGAAAGC
1 AGCTGCCCAAGGACTTCAAGACATCATCCTATGGTTGCAACCTTACCACAAGCATCCTAGAAAGC
*
48491 CATGTGCACGCCTTCTGATAAGCCATGCCATGTGCTATGCGTGTGACTCCATTTAGGC-GCAATG
66 CATGTGCACGCCTTCTGATAAGCCAAGCCATGTGCTATGCGTGTGACTCCATTTAGGCGGCAA-G
* *
48555 ATGAATGGTAACCTCACCATTCGGCCAAGCATCATTTCTCATCCAAATTGGCGCAAACTTAAAGG
130 ATGAATGGCAACCTCACCATTCGGCCAAGCATCATTTCTCATCCAAATTGGCACAAACTTAAAGG
*
48620 GATTCAAGTGCTATTCGGCCATGAGACATGCTCCTCTATTCCAACCGAACCAACACCTATATTTT
195 GATTCAAGTGCTATTCGGCCATGAGACATGCTCCTCTATTCCAACCGAACCAACACATATATTTT
*
48685 TCATGTTATTAATTAATTAATTATGTCATTAAAGAGGGACACAAGGGCTGGCCGAACCACCATGT
260 TCATGTTATTAATTAATTAATTATGTCATTAAAGAGGGACACAAGGGCTGGCCGAACCACCATAT
* * * *
48750 AACAATTCGGCTAAGTCCCTTCAAAAACTATAAATAGGATAGTTCTATTCATTTGTAAGCACACT
325 AACAATTCGACCAAGTCCCTTCAAAAACTATAAATAGGATAGTACTATTCATTTGTAAGCACACC
* * *
48815 TTTCTTATAATTTAAAGTTATATTATTCTCTTTTCTTAAGTCCTTGTGATTTTTATCGACTTATC
390 TTTCTTATAATTTAAAGTGAGATTATTCTCTTTTCTTAAGTCCTTGTGACTTTTATCGACTTATC
* * *
48880 AAGTAATTTATTTACTTGTGGCATCAACCTCTTCTTCCCTTGATACTTATGGTTCCTATCTCCCT
455 AAGTAATTTATTTACTTGTGGCATCAACCCCTTATTCCCTTGATACTTATGGTTCATATCTCCCT
*
48945 ATAGA-TAGTGGGTCAAAGTCCTTGTTACCACCCCTTAGAAAGATTT
520 ATAAATTA-TGGGTCAAAGTCCTTGTTACCACCCCTTAGAAAGATTT
48991 GTAAGGCTGG
Statistics
Matches: 521, Mismatches: 42, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
564 6 0.01
565 515 0.99
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (565 bp):
AGCTGCCCAAGGACTTCAAGACATCATCCTATGGTTGCAACCTTACCACAAGCATCCTAGAAAGC
CATGTGCACGCCTTCTGATAAGCCAAGCCATGTGCTATGCGTGTGACTCCATTTAGGCGGCAAGA
TGAATGGCAACCTCACCATTCGGCCAAGCATCATTTCTCATCCAAATTGGCACAAACTTAAAGGG
ATTCAAGTGCTATTCGGCCATGAGACATGCTCCTCTATTCCAACCGAACCAACACATATATTTTT
CATGTTATTAATTAATTAATTATGTCATTAAAGAGGGACACAAGGGCTGGCCGAACCACCATATA
ACAATTCGACCAAGTCCCTTCAAAAACTATAAATAGGATAGTACTATTCATTTGTAAGCACACCT
TTCTTATAATTTAAAGTGAGATTATTCTCTTTTCTTAAGTCCTTGTGACTTTTATCGACTTATCA
AGTAATTTATTTACTTGTGGCATCAACCCCTTATTCCCTTGATACTTATGGTTCATATCTCCCTA
TAAATTATGGGTCAAAGTCCTTGTTACCACCCCTTAGAAAGATTT
Found at i:53765 original size:19 final size:19
Alignment explanation
Indices: 53741--53780 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
53731 TCACCCCTTT
53741 CAATTTCAATCTCAAACTA
1 CAATTTCAATCTCAAACTA
53760 CAATTTCAATCTCAAACTA
1 CAATTTCAATCTCAAACTA
53779 CA
1 CA
53781 CACATGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (19 bp):
CAATTTCAATCTCAAACTA
Done.