Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000759.1 Hibiscus syriacus cultivar Beakdansim tig00001467_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: 59840
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1521 original size:35 final size:36
Alignment explanation
Indices: 1481--1555 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
1471 GATTTCGGGA
*
1481 TTTTGCTA-TTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1516 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1552 TTTT
1 TTTT
1556 TTAGCTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 8 0.21
36 30 0.79
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:3854 original size:36 final size:36
Alignment explanation
Indices: 3813--3890 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
3803 GTCGGGTTTA
* * *
3813 GGTCGGTGAAGGGTATATATTTTTCGGGTAAGGTCG
1 GGTCGGTGAAGGATATAGAATTTTCGGGTAAGGTCG
* **
3849 GGTCGGTGAAGGATGTAGAATTTTCGGGTCGGGTCG
1 GGTCGGTGAAGGATATAGAATTTTCGGGTAAGGTCG
3885 GGTCGG
1 GGTCGG
3891 GTTGGCCCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.17, C:0.10, G:0.44, T:0.29
Consensus pattern (36 bp):
GGTCGGTGAAGGATATAGAATTTTCGGGTAAGGTCG
Found at i:10641 original size:132 final size:134
Alignment explanation
Indices: 10404--10671 Score: 504
Period size: 132 Copynumber: 2.0 Consensus size: 134
10394 AAAGTGGAGC
10404 AATTTAGTTCATATAAGTTATTTGCAACTATTAATTATTGAAAATTTTATTAAAATAATTGATGT
1 AATTTAGTTCATATAAGTTATTTGCAACTATTAATTATTGAAAATTTTATTAAAATAATTGATGT
10469 TACAGTTAATACTCTAGTCTTGTTTATGATTATTATTCTATGAACAGATATTACC-T-TACTCAT
66 TACAGTTAATACTCTAGTCTTGTTTATGATTATTATTCTATGAACAGATATTACCTTATACTCAT
10532 TGTA
131 TGTA
10536 AATTTAGTTCATATAAGTTATTTGCAACTATTAATTATTGAAAATTTTATTAAAATAATTGATGT
1 AATTTAGTTCATATAAGTTATTTGCAACTATTAATTATTGAAAATTTTATTAAAATAATTGATGT
* *
10601 TACAGTTAGTACTCTAGTCTTGTTTATGATTATTATTCTATGAACATATATTACCTTATACTCAT
66 TACAGTTAATACTCTAGTCTTGTTTATGATTATTATTCTATGAACAGATATTACCTTATACTCAT
10666 TGTA
131 TGTA
10670 AA
1 AA
10672 CTTCAAATTT
Statistics
Matches: 132, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
132 118 0.89
133 1 0.01
134 13 0.10
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (134 bp):
AATTTAGTTCATATAAGTTATTTGCAACTATTAATTATTGAAAATTTTATTAAAATAATTGATGT
TACAGTTAATACTCTAGTCTTGTTTATGATTATTATTCTATGAACAGATATTACCTTATACTCAT
TGTA
Found at i:32510 original size:25 final size:26
Alignment explanation
Indices: 32476--32557 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 26
32466 CACATTTTAA
* * *
32476 TAAATTAAAAT-AAATTATATATTTT
1 TAAATGAAAATAAAATAAAATATTTT
32501 TAAATGAAAATAAAAATAAAATATTTT
1 TAAATGAAAAT-AAAATAAAATATTTT
* ** *
32528 TAAATTAAGTTAATAATAAAATATATT
1 TAAATGAAAATAA-AATAAAATATTTT
32555 TAA
1 TAA
32558 TAAGTTGATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
25 10 0.21
26 2 0.04
27 35 0.74
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
TAAATGAAAATAAAATAAAATATTTT
Found at i:32545 original size:27 final size:27
Alignment explanation
Indices: 32494--32572 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
32484 AATAAATTAT
* ** *
32494 ATATTTTTAAATGAAAATAAAAATAAA
1 ATATTTTTAAATTAAGTTAATAATAAA
32521 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATTAAGTTAATAATAAA
* *
32548 ATATATTT-AA-TAAGTTGAT-ATAAA
1 ATATTTTTAAATTAAGTTAATAATAAA
32572 A
1 A
32573 ACATTTTCAG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
24 6 0.13
25 8 0.17
26 2 0.04
27 30 0.65
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (27 bp):
ATATTTTTAAATTAAGTTAATAATAAA
Found at i:34593 original size:22 final size:22
Alignment explanation
Indices: 34575--34621 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
34565 AAGTAACTAG
34575 AACCGAAATTAACCCTAACCAA
1 AACCGAAATTAACCCTAACCAA
34597 AACCGAAATTAA-CCTGAACCAA
1 AACCGAAATTAACCCT-AACCAA
34619 AAC
1 AAC
34622 TGACCCTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.51, C:0.30, G:0.06, T:0.13
Consensus pattern (22 bp):
AACCGAAATTAACCCTAACCAA
Found at i:37351 original size:20 final size:21
Alignment explanation
Indices: 37323--37361 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
37313 GATTACTAAA
37323 AATTCTTAGAA-AATAATATT
1 AATTCTTAGAATAATAATATT
*
37343 AATTTTTAGAATAATAATA
1 AATTCTTAGAATAATAATA
37362 ACTATCGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (21 bp):
AATTCTTAGAATAATAATATT
Found at i:37908 original size:18 final size:19
Alignment explanation
Indices: 37871--37920 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
37861 GGAAATTTAC
*
37871 TTTAATTTAAATGATAAAA
1 TTTAATTTAAATAATAAAA
*
37890 TTTATTTTAAATAAT-AAA
1 TTTAATTTAAATAATAAAA
37908 -TTAATTTAAATAA
1 TTTAATTTAAATAA
37921 AATTGGCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 12 0.43
18 3 0.11
19 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTAATTTAAATAATAAAA
Found at i:38067 original size:20 final size:20
Alignment explanation
Indices: 38042--38080 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
38032 CTTATCTTAC
*
38042 TTATAATAAAAATATTAGAT
1 TTATAATAAAAATAATAGAT
38062 TTATAATAAAAATAATAGA
1 TTATAATAAAAATAATAGA
38081 AAACGACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
TTATAATAAAAATAATAGAT
Found at i:38717 original size:64 final size:64
Alignment explanation
Indices: 38571--38717 Score: 147
Period size: 64 Copynumber: 2.3 Consensus size: 64
38561 GGTTGATCTA
* * * * *
38571 AACCGAAAATCAACCGATCCAATATTGACAATACCTGAAATATAATCGATCCAATATTAATCTG
1 AACCAAAAATCAACCGATCCAATATTGACAATACCTAAAAAATAACCGATCCAATATTAATCCG
* ** ** *
38635 ACCCAAAAATCATTCGATCCAATATTGACCCAA-A-C-AAAAAATCAACCGATCTGATATTGATC
1 AACCAAAAATCAACCGATCCAATATTGA--CAATACCTAAAAAAT-AACCGATCCAATATTAATC
38697 CG
63 CG
38699 AACCAAAAATCAACCGATC
1 AACCAAAAATCAACCGATC
38718 TGATAATCAT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
63 5 0.08
64 57 0.86
65 1 0.02
66 3 0.05
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.22
Consensus pattern (64 bp):
AACCAAAAATCAACCGATCCAATATTGACAATACCTAAAAAATAACCGATCCAATATTAATCCG
Found at i:38718 original size:32 final size:32
Alignment explanation
Indices: 38637--38740 Score: 109
Period size: 32 Copynumber: 3.2 Consensus size: 32
38627 TTAATCTGAC
** ** * *
38637 CCAAAAATCATTCGATCCAATATTGACCCAAA
1 CCAAAAATCAACCGATCTGATATTGATCCGAA
*
38669 CAAAAAATCAACCGATCTGATATTGATCCGAA
1 CCAAAAATCAACCGATCTGATATTGATCCGAA
* * *
38701 CCAAAAATCAACCGATCTGATAATCATCCGAC
1 CCAAAAATCAACCGATCTGATATTGATCCGAA
*
38733 CCGAAAAT
1 CCAAAAAT
38741 TGACCTGACA
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (32 bp):
CCAAAAATCAACCGATCTGATATTGATCCGAA
Found at i:39586 original size:182 final size:181
Alignment explanation
Indices: 39370--39841 Score: 678
Period size: 180 Copynumber: 2.6 Consensus size: 181
39360 GATCCAAATT
* * * **
39370 AAAAATGTGTCGATCCAAAACGATATAACATGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
39435 AAACCGGTAAAGCGCTACCGGAT-TCATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
66 AAACCGGTAAAACGATACCGGATAT-ATTGAAAGTGTCGATACTTT-ATATAAGGATCAACACTT
*
39499 CGTGAATTTAAAAGAGAAGCAATTTTAAATCATATAAAGTGTCGATACTTTTA
129 CGTGAATTTAAAAGAGAAGCAATTTTAAAGCATATAAAGTGTCGATACTTTTA
* * *
39552 AAAAATGTATCGATCCAAAATGATATACCATGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
39617 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCAACATTTTG
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCAACACTTCG
* ** * *
39682 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTTA
131 TGAATTTAAAAGAGAAGCAATTTTAAAGCATATAAAGTGTCGATACTTTTA
* * *
39733 AAAAA-ATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
39797 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
39842 CGTAAGTACG
Statistics
Matches: 260, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
180 96 0.37
181 67 0.26
182 96 0.37
183 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (181 bp):
AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCAACACTTCG
TGAATTTAAAAGAGAAGCAATTTTAAAGCATATAAAGTGTCGATACTTTTA
Found at i:39606 original size:20 final size:19
Alignment explanation
Indices: 39583--39628 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
39573 GATATACCAT
39583 GTAAAAATATGATAAAACCG
1 GTAAAAA-ATGATAAAACCG
39603 GTAACAAAATGATAAAACCG
1 GTAA-AAAATGATAAAACCG
39623 GTAAAA
1 GTAAAA
39629 CGTTACCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (19 bp):
GTAAAAAATGATAAAACCG
Found at i:39785 original size:20 final size:19
Alignment explanation
Indices: 39762--39808 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
39752 CGATATAACA
39762 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
39782 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
39802 GGTAAAA
1 GGTAAAA
39809 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:39810 original size:17 final size:19
Alignment explanation
Indices: 39771--39813 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
39761 AGGTAAAAAT
39771 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
39791 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
39808 ATGATA
1 ATGATA
39814 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:41925 original size:15 final size:15
Alignment explanation
Indices: 41902--41945 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
41892 GTTGTATTGG
*
41902 GGGATGACGGTGAGT
1 GGGACGACGGTGAGT
41917 GGGACGACGGTGAGT
1 GGGACGACGGTGAGT
41932 GGGACGACGGTGAG
1 GGGACGACGGTGAG
41946 GGAAAACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.20, C:0.11, G:0.55, T:0.14
Consensus pattern (15 bp):
GGGACGACGGTGAGT
Found at i:42149 original size:33 final size:33
Alignment explanation
Indices: 42107--42172 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
42097 AAATAGATGG
*
42107 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
42140 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
42173 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:43986 original size:19 final size:19
Alignment explanation
Indices: 43962--44010 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
43952 AATGTAGGGT
43962 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
43981 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
44000 TAATTTTGTAT
1 TAATTTTGTAT
44011 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:44471 original size:200 final size:200
Alignment explanation
Indices: 44123--44828 Score: 968
Period size: 200 Copynumber: 3.6 Consensus size: 200
44113 AATTTACAAT
* *
44123 ATGGCAAACAGGATGTAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGATGCAACCATAAAGTATCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
* *
44188 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTGCAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTGCAAGTATACCGGTTTT
* * *
44253 ATGAGAGAATAGGTCTAAATAATGTATCGATACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAG
131 ATGAGAGAATAAGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAA
44318 AATGA
196 AATGA
* * *
44323 ATGGAAAACAGGCTGCAACCATAAAGTATCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGATGCAACCATAAAGTATCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
*
44388 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTGCAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTGCAAGTATACCGGTTTT
*
44453 ATGAGAGAATAAGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAA
131 ATGAGAGAATAAGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAA
44518 AATGA
196 AATGA
* * * * * *
44523 ATGTCAAACAGGGTGCAACCATAAAGTGTCAATCC---CATAAACA-T-T-G-------AAAC--
1 ATGGCAAACAGGATGCAACCATAAAGTATCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
* * * **
44573 C--CAA--AA--GTATAATGTAATATGCAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTGCAAGTATACCGGTTTT
* * * *
44632 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAAGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAA
44697 AATGA
196 AATGA
* * *
44702 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGATGCAACCATAAAGTATCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
* * *
44767 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGT
66 CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTGCAAGTATACCGGT
44829 ATAAATATAC
Statistics
Matches: 451, Mismatches: 34, Indels: 42
0.86 0.06 0.08
Matches are distributed among these distances:
179 150 0.33
181 2 0.00
182 6 0.01
183 3 0.01
184 1 0.00
185 2 0.00
187 4 0.01
192 4 0.01
194 2 0.00
195 1 0.00
196 2 0.00
197 6 0.01
198 2 0.00
200 266 0.59
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGATGCAACCATAAAGTATCGATCCATATATAAAAAGTGTCGATCCCAAAAACAT
CGAAAACCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTGCAAGTATACCGGTTTT
ATGAGAGAATAAGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGGTCCAA
AATGA
Found at i:44666 original size:179 final size:179
Alignment explanation
Indices: 44366--44736 Score: 652
Period size: 179 Copynumber: 2.1 Consensus size: 179
44356 CCATATATAA
*
44366 AAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGCAATTTTTCAATCTAA
*
44431 CCGGTGCAAGTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTATCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTATCGACACTTTTGTAGTT
*
44496 TGTGTCGATATTTTTGGTCCAAAATGAATGTCAAACAGGGTGCAACCAT
131 TGTGTCGATATTTTTGGTCCAAAATGAATGGCAAACAGGGTGCAACCAT
* * *
44545 AAAGTGTCAATCCCATAAACATTGAAACCCAAAAGTATAATGTAATATGCAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGCAATTTTTCAATCTAA
* * *
44610 CCGGTATAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTATCGACACTTTTGTAGTT
*
44675 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCAT
131 TGTGTCGATATTTTTGGTCCAAAATGAATGGCAAACAGGGTGCAACCAT
44724 AAAGTGTCGATCC
1 AAAGTGTCGATCC
44737 ATATATAAAA
Statistics
Matches: 181, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
179 181 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (179 bp):
AAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGCAATTTTTCAATCTAA
CCGGTACAAGTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTATCGACACTTTTGTAGTT
TGTGTCGATATTTTTGGTCCAAAATGAATGGCAAACAGGGTGCAACCAT
Found at i:44828 original size:14 final size:14
Alignment explanation
Indices: 44809--44842 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44799 TTTCAATCTA
*
44809 ACCGGTACAAGTAT
1 ACCGGTACAAATAT
*
44823 ACCGGTATAAATAT
1 ACCGGTACAAATAT
44837 ACCGGT
1 ACCGGT
44843 TTTATGAGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (14 bp):
ACCGGTACAAATAT
Found at i:45131 original size:183 final size:183
Alignment explanation
Indices: 44823--45264 Score: 785
Period size: 183 Copynumber: 2.4 Consensus size: 183
44813 GTACAAGTAT
* *
44823 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATTGATACTTTTTAATA
1 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATA
* *
44888 TTGTGTCAGTACTTTATGTCTAGATTGGAAGAAAAATATGTCGATACCTTGTCAAAAAGTGTCGA
66 TTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATATGTCGATACCTTGTCAAAAAGTGTCGA
44953 CATTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATATA
131 CATTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATATA
* *
45006 ACCGGTATAAATATACCGGTTTTATGAACTAATAGGTCTACAACCTATATCGACACTTTTTAATA
1 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATA
* *
45071 TTGTGTCGGTACTTTATGTCCAGATTGGAAGAAATATGTGTCGATACCTTGTCAAAAAGTGTCGA
66 TTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATATGTCGATACCTTGTCAAAAAGTGTCGA
* *
45136 CATTTACATATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATA
131 CATTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATATA
*
45189 ATCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATA
1 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATA
45254 TTGTGTCGGTA
66 TTGTGTCGGTA
45265 ATTTTAAGTA
Statistics
Matches: 246, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 246 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (183 bp):
ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATA
TTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATATGTCGATACCTTGTCAAAAAGTGTCGA
CATTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATATA
Found at i:48140 original size:23 final size:23
Alignment explanation
Indices: 48110--48182 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
48100 ATAGGTAAAA
48110 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
48133 ATATAATGTAATAGGTAACGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
48156 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
48179 ATAT
1 ATAT
48183 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:48146 original size:43 final size:44
Alignment explanation
Indices: 48098--48182 Score: 118
Period size: 46 Copynumber: 1.9 Consensus size: 44
48088 ACTTTCAATA
48098 TAATAGGTAA-AAATATAATGTAATAGGTAGCGCTTATATAATG
1 TAATAGGTAACAAATATAATGTAATAGGTAGCGCTTATATAATG
** *
48141 TAATAGGTAACGTTTATATAATGTAATAGGTAGTGCTTATAT
1 TAATAGGTAAC--AAATATAATGTAATAGGTAGCGCTTATAT
48183 TGTAAAGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 10 0.28
46 26 0.72
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (44 bp):
TAATAGGTAACAAATATAATGTAATAGGTAGCGCTTATATAATG
Found at i:54122 original size:15 final size:15
Alignment explanation
Indices: 54110--54139 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54100 ATTCTCAATT
54110 CAATTCATCTCAAAG
1 CAATTCATCTCAAAG
54125 CAATTCATCTCAAAG
1 CAATTCATCTCAAAG
54140 TTTGAGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (15 bp):
CAATTCATCTCAAAG
Done.