Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000159.1 Hibiscus syriacus cultivar Beakdansim tig00000281_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: 85810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1763 original size:20 final size:20
Alignment explanation
Indices: 1740--1922 Score: 128
Period size: 20 Copynumber: 9.2 Consensus size: 20
1730 AGAATCTCGT
*
1740 TGCGATTTACAAAATCGCAA
1 TGCGATTTACTAAATCGCAA
*
1760 TGCGA-ATACGTAAATCGCAA
1 TGCGATTTAC-TAAATCGCAA
1780 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTAC-TAAATCGCAA
1800 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTAC-TAAATCGCAA
* *
1820 TGCGA-ATACGT-AATCGCAT
1 TGCGATTTAC-TAAATCGCAA
* *
1839 TACGATTTACGT-AATCGCAT
1 TGCGATTTAC-TAAATCGCAA
* * *
1859 TGCGATTTTCCTAATTCGCAT
1 TGCGA-TTTACTAAATCGCAA
* *
1880 TGCGATTTACT-ATTCGCAT
1 TGCGATTTACTAAATCGCAA
* **
1899 TGCAATTTAGGAAAATCGCAA
1 TGCGATTTA-CTAAATCGCAA
1920 TGC
1 TGC
1923 AATAGTCAGA
Statistics
Matches: 141, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
19 30 0.21
20 86 0.61
21 25 0.18
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (20 bp):
TGCGATTTACTAAATCGCAA
Found at i:1784 original size:40 final size:40
Alignment explanation
Indices: 1740--1865 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 40
1730 AGAATCTCGT
1740 TGCGATTTAC-AAAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGA-TTACGAAAATCGCAATGCGAATACGTAAATCGCAA
* *
1780 TGCGATTACGTAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATTACGAAAATCGCAATGCGAATACGTAAATCGCAA
* * * * * *
1820 TGCGAATACG-TAATCGCATTACGATTTACGT-AATCGCAT
1 TGCGATTACGAAAATCGCAATGCGA-ATACGTAAATCGCAA
1859 TGCGATT
1 TGCGATT
1866 TTCCTAATTC
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
39 28 0.37
40 48 0.63
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (40 bp):
TGCGATTACGAAAATCGCAATGCGAATACGTAAATCGCAA
Found at i:1896 original size:19 final size:19
Alignment explanation
Indices: 1833--1907 Score: 87
Period size: 19 Copynumber: 3.8 Consensus size: 19
1823 GAATACGTAA
* *
1833 TCGCATTACGATTTACGTAA
1 TCGCATTGCGATTTAC-TAT
*
1853 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTTACT-AT
1874 TCGCATTGCGATTTACTAT
1 TCGCATTGCGATTTACTAT
*
1893 TCGCATTGCAATTTA
1 TCGCATTGCGATTTA
1908 GGAAAATCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
19 16 0.33
20 16 0.33
21 16 0.33
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (19 bp):
TCGCATTGCGATTTACTAT
Found at i:1897 original size:60 final size:60
Alignment explanation
Indices: 1751--1922 Score: 179
Period size: 60 Copynumber: 2.9 Consensus size: 60
1741 GCGATTTACA
* * *
1751 AAATCGCAATGCGAATACGTAAATCGCAATGCGA-TTACGTAAATCGCAATGCGATTACGT
1 AAATCGCAATGCGAATACGT-AATCGCATTACGATTTACGTAAATCGCAATGCGATTACCT
* *
1811 AAATCGCAATGCGAATACGTAATCGCATTACGATTTACGT-AATCGCATTGCGATTTTCCT
1 AAATCGCAATGCGAATACGTAATCGCATTACGATTTACGTAAATCGCAATGCGA-TTACCT
* * * * * * * *
1871 AATTCGCATTGCGATTTAC-TATTCGCATTGCAATTTAGGAAAATCGCAATGC
1 AAATCGCAATGCGA-ATACGTAATCGCATTACGATTTACGTAAATCGCAATGC
1923 AATAGTCAGA
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
59 23 0.24
60 58 0.62
61 13 0.14
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (60 bp):
AAATCGCAATGCGAATACGTAATCGCATTACGATTTACGTAAATCGCAATGCGATTACCT
Found at i:2439 original size:19 final size:18
Alignment explanation
Indices: 2397--2447 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
2387 ATAATATCTG
*
2397 TTAAATTTTTGTAAGAAA
1 TTAAATTTTTATAAGAAA
* *
2415 TTAAATTATTTATAATAAT
1 TTAAATT-TTTATAAGAAA
*
2434 TTAAATTTTAATAA
1 TTAAATTTTTATAA
2448 AACCATATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TTAAATTTTTATAAGAAA
Found at i:8616 original size:31 final size:29
Alignment explanation
Indices: 8559--8664 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 29
8549 GTTTTTACTA
8559 TTACTATTTTAGTCCCTAAGTTTCTATTT
1 TTACTATTTTAGTCCCTAAGTTTCTATTT
* * *
8588 TATGCTATTTTAGTCCTTTAGGTTTCTATTT
1 T-TACTATTTTAGTCC-CTAAGTTTCTATTT
* * *
8619 TTACTATTTTGGTCCCTTAACTTTCTGTTT
1 TTACTATTTTAGTCCC-TAAGTTTCTATTT
* *
8649 TTTCTATTATAG-CCCT
1 TTACTATTTTAGTCCCT
8665 TTAAGCGTCT
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
28 1 0.02
29 4 0.06
30 44 0.71
31 13 0.21
ACGTcount: A:0.17, C:0.18, G:0.09, T:0.56
Consensus pattern (29 bp):
TTACTATTTTAGTCCCTAAGTTTCTATTT
Found at i:15074 original size:27 final size:27
Alignment explanation
Indices: 15027--15106 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 27
15017 AGACAGTTTA
*
15027 TCTTGAAACAAATATTTGAGTCTGTTCC
1 TCTTGAAA-AAATCTTTGAGTCTGTTCC
* * *
15055 TTTTGAAAAAATCTTTGAGTTTGTTTC
1 TCTTGAAAAAATCTTTGAGTCTGTTCC
*
15082 TCTTAACAAAATCATCTTTGAGTCT
1 TCTTGA-AAAA--ATCTTTGAGTCT
15107 ATTTCTTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
27 20 0.48
28 11 0.26
30 11 0.26
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (27 bp):
TCTTGAAAAAATCTTTGAGTCTGTTCC
Found at i:15501 original size:65 final size:66
Alignment explanation
Indices: 15350--15527 Score: 184
Period size: 65 Copynumber: 2.7 Consensus size: 66
15340 ACAAAACAAA
* *
15350 CATCTTTGAGATCGTTTCCCTTAAAAA-AAA-TTTATCTTATTTGAGACAGTTTCCCATGAAACA
1 CATCTTTGAGATCGTTTCCCTTAAAAACAAATTTTGTCTCATTTGAGACAGTTTCCCATGAAACA
15413 C
66 C
* * ** ** * * *
15414 CGATGTTTGAGAACGTCCCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTTAAAT
1 C-ATCTTTGAGATCGTTTCCCTTAAAAACAAATTTTGTCTCATTTGAGACAGTTTCCCATGAAAC
**
15479 GT
65 AC
* *
15481 CATCTTTGAG-TCGTTTCCCTT-TAAACAAATTTTGTCTCTTTTGAGAC
1 CATCTTTGAGATCGTTTCCCTTAAAAACAAATTTTGTCTCATTTGAGAC
15528 GGTTGCTTTT
Statistics
Matches: 91, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
64 24 0.26
65 30 0.33
66 11 0.12
67 26 0.29
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (66 bp):
CATCTTTGAGATCGTTTCCCTTAAAAACAAATTTTGTCTCATTTGAGACAGTTTCCCATGAAACA
C
Found at i:15629 original size:28 final size:28
Alignment explanation
Indices: 15548--15613 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
15538 GAAACACATC
15548 ATCTTTGAGTTTGTTTTTCTTGAAACAA
1 ATCTTTGAGTTTGTTTTTCTTGAAACAA
*
15576 ATATTTGAGTTTGTTTTTCTTGAAACAA
1 ATCTTTGAGTTTGTTTTTCTTGAAACAA
15604 ATCTTTGAGT
1 ATCTTTGAGT
15614 CAGTTTCCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (28 bp):
ATCTTTGAGTTTGTTTTTCTTGAAACAA
Found at i:15873 original size:131 final size:131
Alignment explanation
Indices: 15634--15886 Score: 317
Period size: 131 Copynumber: 1.9 Consensus size: 131
15624 TGAAACCAAA
* * *
15634 ATCCCTAAAGATGGCCAACCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCT
1 ATCCCTAAAGATGGCCAACCGTCCTCATCACATAAGAACCGTGTCATCCCCTGACCAGACATCCT
* * * *
15699 CATCACGTAAGAGCCGTGTTAACCATAGATAACCAATCGTCCTCATCACGTAGGAACTGTGTTAT
66 CATCACGTAAGAGCCGTGTCAACCATAGATAACCAACCATCCTCATCACGTAAGAACTGTGTTAT
15764 C
131 C
** * * * * *
15765 ATCCCTAAAGATGGCTTACCGTCCTCATCGCATAAGAACCGTTTCATCCCTTGACCATACATTCT
1 ATCCCTAAAGATGGCCAACCGTCCTCATCACATAAGAACCGTGTCATCCCCTGACCAGACATCCT
* * * * * * *
15830 CATCGCGTAGGAGCTGTGTCACCCCTAGATAACCAGCCATCCTCATCGCGTAAGAAC
66 CATCACGTAAGAGCCGTGTCAACCATAGATAACCAACCATCCTCATCACGTAAGAAC
15887 CTAATTATCA
Statistics
Matches: 101, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
131 101 1.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGGCCAACCGTCCTCATCACATAAGAACCGTGTCATCCCCTGACCAGACATCCT
CATCACGTAAGAGCCGTGTCAACCATAGATAACCAACCATCCTCATCACGTAAGAACTGTGTTAT
C
Found at i:15895 original size:131 final size:131
Alignment explanation
Indices: 15634--15915 Score: 314
Period size: 131 Copynumber: 2.1 Consensus size: 131
15624 TGAAACCAAA
* * *
15634 ATCCCTAAAGATGGCCAACCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCT
1 ATCCCTAAAGATGGCCAACCGTCCTCATCACATAAGAACCGTGTCATCCCCTGACCAGACATCCT
* * * * **
15699 CATCACGTAAGAGCCGTGTTAACCATAGATAACCAATCGTCCTCATCACGTAGGAACTGTGTTAT
66 CATCACGTAAGAGCCGTGTCAACCATAGATAACCAACCATCCTCATCACGTAAGAACTGAATTAT
15764 C
131 C
** * * * * *
15765 ATCCCTAAAGATGGCTTACCGTCCTCATCGCATAAGAACCGTTTCATCCCTTGACCATACATTCT
1 ATCCCTAAAGATGGCCAACCGTCCTCATCACATAAGAACCGTGTCATCCCCTGACCAGACATCCT
* * * * * * *
15830 CATCGCGTAGGAGCTGTGTCACCCCTAGATAACCAGCCATCCTCATCGCGTAAGAACCT-AATTA
66 CATCACGTAAGAGCCGTGTCAACCATAGATAACCAACCATCCTCATCACGTAAGAA-CTGAATTA
15894 TC
130 TC
15896 ACCGTCCCTAAAGATGGCCA
1 A---TCCCTAAAGATGGCCA
15916 GAACTCTTCA
Statistics
Matches: 122, Mismatches: 25, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
131 106 0.87
132 2 0.02
134 14 0.11
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGGCCAACCGTCCTCATCACATAAGAACCGTGTCATCCCCTGACCAGACATCCT
CATCACGTAAGAGCCGTGTCAACCATAGATAACCAACCATCCTCATCACGTAAGAACTGAATTAT
C
Found at i:16174 original size:3 final size:3
Alignment explanation
Indices: 16158--16217 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
16148 GTGTCTTTTT
16158 TTA TT- TTA TT- TTA TTA -TA TTTA TT- TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
16199 TTA TTA TTA TTAA TTA TTA
1 TTA TTA TTA TT-A TTA TTA
16218 CATCATTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
2 10 0.20
3 35 0.70
4 5 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16217 original size:19 final size:18
Alignment explanation
Indices: 16158--16216 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
16148 GTGTCTTTTT
16158 TTATTTTATT-TTATTATA
1 TTATTTTATTATTATTA-A
16176 TTTATTTTA-TATTATT-A
1 -TTATTTTATTATTATTAA
16193 TTATTATTATTATTATTAA
1 TTATT-TTATTATTATTAA
16212 TTATT
1 TTATT
16217 ACATCATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 8 0.22
19 19 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTTATTATTATTAA
Found at i:19320 original size:254 final size:257
Alignment explanation
Indices: 18780--19498 Score: 734
Period size: 254 Copynumber: 2.8 Consensus size: 257
18770 ACAATTACAG
* * * * *
18780 ATCGCAACCTATTTCTTAGTGAACCATGACTTTATTGGGCACAACCTTATTTATTATATATATTC
1 ATCGCAATCTATTTCTTAGTGAACCATGACATTATTAGGCGCAACC--A--T-GTATATATATTC
** * * *
18845 ATAACATTTTCTGCTTTTTACCTTATTTTCTTATCATGGGAAAATCTAAGGCTCTATCAGCTTAA
61 ATAACATTTTAAGC-TTTTAACTTATTTTCTTATCGT-GGAAAATCAAAGGCTCTATCAGCTTAA
* * ** *
18910 ACTTTGATAATATTTTAGG-CGCAAACCATTTTATTATTAAAAATATTAAGATTCGTGGTTGCAA
124 ACTTTGATAATATTTTAGGTC-CAACCCATTTTATTATTAAAAATAGTAAGATTCCAGATTGCAA
** * *
18974 CATGCTTTCTTCAAAACCATGACATTCATAGTTGGAACCTATTTTACTAATAGAAATATTAACAT
188 CATGCTTTCTTCAAAACCATGACATTCATAGACGCAACCTATTTTACTAATAAAAATATTAACAT
*
19039 CACAT
253 CACAA
* * *
19044 ATCGCAATCTATTTCTTAGTGAACCATGACATTATTGGGTGCAA-C-TGTA-GT-TATT-ATAAC
1 ATCGCAATCTATTTCTTAGTGAACCATGACATTATTAGGCGCAACCATGTATATATATTCATAAC
* * *
19104 ATTTTAAGCTTTTAACTTATTTTTTTATCGTGGAAACTCCAAGGCTCTATCAGCTTAAACTTTGA
66 ATTTTAAGCTTTTAACTTATTTTCTTATCGTGGAAAATCAAAGGCTCTATCAGCTTAAACTTTGA
* * * *
19169 TAATATTTTAGGTCCAACCCATTTTATTATTATAGATAGTAATATTCCAGATTGCAACATGTTTT
131 TAATATTTTAGGTCCAACCCATTTTATTATTAAAAATAGTAAGATTCCAGATTGCAACATGCTTT
* * * * * * *
19234 TTTTATTGAACTATGACATTCTTCA-ACGCAACCTATTTTATTAATAAAAATATTAACATTACAA
196 CTTCA--AAACCATGACATTCAT-AGACGCAACCTATTTTACTAATAAAAATATTAACATCACAA
* * * *
19298 ATCGCAA-CTTGTTTCTTAGTGAACTATGATATTATTAGGCGCAACCGTATTTATTATACATATT
1 ATCGCAATC-TATTTCTTAGTGAACCATGACATTATTAGGCGCAACC--ATGTA-TAT--ATATT
* * * *
19362 CATAACATTTTAAGCTTTTAACTTATTTTCTTATCGTGAGAAATTAAAAGTCTCTATCAGTTTAA
60 CATAACATTTTAAGCTTTTAACTTATTTTCTTATCGTG-GAAAATCAAAGGCTCTATCAGCTTAA
* * * * * * * *
19427 ACTCTGATAACATTTTAGGTACAACTCATTTTATTATTCAAAATATTAAGATTCCAAATTACAAC
124 ACTTTGATAATATTTTAGGTCCAACCCATTTTATTATTAAAAATAGTAAGATTCCAGATTGCAAC
*
19492 ATTCTTT
189 ATGCTTT
19499 TTTACTTAAA
Statistics
Matches: 379, Mismatches: 60, Indels: 31
0.81 0.13 0.07
Matches are distributed among these distances:
252 89 0.23
253 21 0.06
254 94 0.25
255 6 0.02
256 1 0.00
257 2 0.01
258 4 0.01
260 1 0.00
263 5 0.01
264 76 0.20
265 80 0.21
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (257 bp):
ATCGCAATCTATTTCTTAGTGAACCATGACATTATTAGGCGCAACCATGTATATATATTCATAAC
ATTTTAAGCTTTTAACTTATTTTCTTATCGTGGAAAATCAAAGGCTCTATCAGCTTAAACTTTGA
TAATATTTTAGGTCCAACCCATTTTATTATTAAAAATAGTAAGATTCCAGATTGCAACATGCTTT
CTTCAAAACCATGACATTCATAGACGCAACCTATTTTACTAATAAAAATATTAACATCACAA
Found at i:26965 original size:23 final size:23
Alignment explanation
Indices: 26939--27006 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
26929 CCACAACTCA
*
26939 TATAATTGCACCAAAGTGCCATG
1 TATAATTGCACCGAAGTGCCATG
* **
26962 TATAATTGCACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCATG
* *
26985 TAGAATTGCACCGTAGTGCCAT
1 TATAATTGCACCGAAGTGCCAT
27007 ATAATAATGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCATG
Found at i:27194 original size:103 final size:103
Alignment explanation
Indices: 27021--27238 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
27011 TAATGTCCAT
*
27021 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
*
27086 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
27124 AAGGACCACATATCATTCCTTAAGAATCATATACATATGA-TAAGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACTAAGGATCAAGTATGTGTCTCACC
*
27188 ATACTTCACACATGTTCCAAAGAATACATATATATCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATATCCCG
27227 AAGGACCACATA
1 AAGGACCACATA
27239 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 110 0.99
104 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:37018 original size:45 final size:44
Alignment explanation
Indices: 36856--37117 Score: 230
Period size: 44 Copynumber: 5.9 Consensus size: 44
36846 AATTTTATGT
* *
36856 GATTGAAAAAAA-TTAGAGGCTTTAATTATAAAGGTAGAAATTGA
1 GATTGAAAAAAACTTAG-GGCCTCAATTATAAAGGTAGAAATTGA
* *
36900 GATTGAAAAAAAATTAGGGGCTCAATTATAAAGGTAGAAATTGA
1 GATTGAAAAAAACTTAGGGCCTCAATTATAAAGGTAGAAATTGA
* * * * *
36944 GATCG-AAAAAACTCGAGGGCCTAAATTATAAAGGTAAAAAGTGA
1 GATTGAAAAAAACT-TAGGGCCTCAATTATAAAGGTAGAAATTGA
* ** * *
36988 GATTGAAAAAAACTTAAGGGCCTCAGTTATAAAATTAAAAAACT-A
1 GATTGAAAAAAACTT-AGGGCCTCAATTATAAAGGT-AGAAATTGA
* * * *
37033 GGATT---AAAAAGTTAGGTGCCTCAATTGTAAAGGCAGAAGTTGA
1 -GATTGAAAAAAACTTAGG-GCCTCAATTATAAAGGTAGAAATTGA
* *
37076 GATTGAAAGAAAACTTAGAGGCCTCAATTGTAAAGATAGAAA
1 GATTGAAA-AAAACTTAG-GGCCTCAATTATAAAGGTAGAAA
37118 ATGTAGAAAG
Statistics
Matches: 175, Mismatches: 30, Indels: 24
0.76 0.13 0.10
Matches are distributed among these distances:
42 11 0.06
43 27 0.15
44 69 0.39
45 30 0.17
46 37 0.21
47 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (44 bp):
GATTGAAAAAAACTTAGGGCCTCAATTATAAAGGTAGAAATTGA
Found at i:37211 original size:42 final size:44
Alignment explanation
Indices: 37115--37212 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 44
37105 GTAAAGATAG
* *
37115 AAAATGTAGAAAGTGAGATTGAAAAAAGTTAAGGGCCTCAATTAT
1 AAAA-GTAAAAAGTAAGATTGAAAAAAGTTAAGGGCCTCAATTAT
* *
37160 -GAAGTTAAAAAGTAAGATT-AAAAAA-TT-AGAGGTCTCAATTAT
1 AAAAG-TAAAAAGTAAGATTGAAAAAAGTTAAG-GGCCTCAATTAT
37202 AAAAGTAAAAA
1 AAAAGTAAAAA
37213 AAGAATTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
41 2 0.04
42 19 0.42
43 10 0.22
44 14 0.31
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.24
Consensus pattern (44 bp):
AAAAGTAAAAAGTAAGATTGAAAAAAGTTAAGGGCCTCAATTAT
Found at i:37215 original size:44 final size:44
Alignment explanation
Indices: 37124--37213 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 44
37114 GAAAATGTAG
* * *
37124 AAAGTGAGATTGAAAAAAGTTAAGGGCCTCAATTATGAAGTTAA
1 AAAGTAAGATTGAAAAAAGTTAAGGGCCTCAATTATAAAGTAAA
*
37168 AAAGTAAGATT-AAAAAA-TT-AGAGGTCTCAATTATAAAAGTAAA
1 AAAGTAAGATTGAAAAAAGTTAAG-GGCCTCAATTAT-AAAGTAAA
37211 AAA
1 AAA
37214 AGAATTGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 2 0.05
42 13 0.32
43 15 0.38
44 10 0.25
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (44 bp):
AAAGTAAGATTGAAAAAAGTTAAGGGCCTCAATTATAAAGTAAA
Found at i:46627 original size:22 final size:21
Alignment explanation
Indices: 46600--46682 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 21
46590 TATAGGGCAG
46600 AGGGAATCGATACCCCCTTGA
1 AGGGAATCGATACCCCCTTGA
* *
46621 AGGGGAACCGATTCCCCCTTTGA
1 A-GGGAATCGATACCCCC-TTGA
*
46644 ATGGGAA-CTGATTCCCTCCTTG-
1 A-GGGAATC-GATACCC-CCTTGA
46666 AGGGAATCGATACCCCC
1 AGGGAATCGATACCCCC
46683 CATGGGTTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
20 2 0.04
21 12 0.23
22 17 0.32
23 20 0.38
24 2 0.04
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTTGA
Found at i:52773 original size:23 final size:23
Alignment explanation
Indices: 52747--52793 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
52737 AACATATTAG
* *
52747 GTAGCGCTTATATAATATAATAT
1 GTAGCGATTATATAATAAAATAT
52770 GTAGCGATTATATAATAAAATAT
1 GTAGCGATTATATAATAAAATAT
52793 G
1 G
52794 CATTTAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (23 bp):
GTAGCGATTATATAATAAAATAT
Found at i:52855 original size:87 final size:86
Alignment explanation
Indices: 52703--52869 Score: 271
Period size: 87 Copynumber: 1.9 Consensus size: 86
52693 TGGTTATGTT
* * *
52703 ATATCATTTAGCCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAAT
1 ATATCATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATATAAT
52768 ATGTAGCGATTATATAATAAA
66 ATGTAGCGATTATATAATAAA
* *
52789 ATATGCATTTAACCAGAAATATTATCAAGTACAATAATATATTAGGTAACGCTTATATAATGTAA
1 ATAT-CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATATAA
*
52854 TATGTAGCGCTTATAT
65 TATGTAGCGATTATAT
52870 TGACCTATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
86 4 0.05
87 70 0.95
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (86 bp):
ATATCATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATATAAT
ATGTAGCGATTATATAATAAA
Found at i:53201 original size:18 final size:19
Alignment explanation
Indices: 53178--53219 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
53168 GTAAGAAAAT
*
53178 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
53196 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
53214 ATTAAA
1 ATTAAA
53220 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:54911 original size:21 final size:20
Alignment explanation
Indices: 54865--54914 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
54855 AATGTATTTG
54865 ATTTTTTTCTTTTTTTTCAC
1 ATTTTTTTCTTTTTTTTCAC
* *
54885 ACTTTTGTTGTTTTGTTTTC-C
1 A-TTTTTTTCTTTT-TTTTCAC
54906 ATTTTTTTC
1 ATTTTTTTC
54915 ATGTCTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 7 0.29
21 12 0.50
22 5 0.21
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.72
Consensus pattern (20 bp):
ATTTTTTTCTTTTTTTTCAC
Found at i:58760 original size:17 final size:18
Alignment explanation
Indices: 58738--58775 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
58728 GAAAATAAAA
*
58738 AAATAA-TAAAAGCGATT
1 AAATAAGTAAAAGCAATT
58755 AAATAAGTAAAAGCAATT
1 AAATAAGTAAAAGCAATT
58773 AAA
1 AAA
58776 GTAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (18 bp):
AAATAAGTAAAAGCAATT
Found at i:60424 original size:200 final size:199
Alignment explanation
Indices: 59881--60472 Score: 691
Period size: 199 Copynumber: 3.0 Consensus size: 199
59871 ACTCATCATG
*
59881 CGTGCACCTCG-TTGGGAATTCATTCTGGA-AACAAGTATTGACACAAACTTAAAGAGTGTCGAT
1 CGTGCACCTCGTTTGGGAATTCATTCTGGACAA-AAGTATCGACACAAACTTAAA-AGTGTCGAT
* * * * *
59944 AAATTAT-TTAGACCTATTTTCTCATAAAACTGGTATATTTCTATCGGGTACATTGTAAATTTAC
64 ACATTATGTT-GACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTAC
* * * * *
60008 CTATCAAATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACA
128 ATATTACATTATAATTATCGATTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACA
*
60073 CTTTATG
193 CTTTATA
* * * * * *
60080 TGTGCACC-CGTTT-GGTATTCATTATGGACAAAATGTATCGACACAAATTTAATAACTGTCAAT
1 CGTGCACCTCGTTTGGGAATTCATTCTGGACAAAA-GTATCGACACAAACTTAA-AAGTGTCGAT
* *
60143 ACTTTATGATGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACA
64 ACATTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACA
* *
60208 TATTACATTATAATTATCTATTTCGAT-TTTATTGGGATCGATACTTTTAATAATTGTATCGACA
129 TATTACATTATAATTATCGATTTCGATGTTT-TTGGGATCGATACTTTTAATAAATGTATCGACA
60272 CTTTATA
193 CTTTATA
* *
60279 CGTGCACCTCGTTTGGGCATTCATTCTGGACAATAAGTATCGATACAAA-TTACACAAGTGTCGA
1 CGTGCACCTCGTTTGGGAATTCATTCTGGACAA-AAGTATCGACACAAACTTA-A-AAGTGTCGA
* * * * * *
60343 TACATTATGTTGACATGTTTTCTAAT-TAACCGGTATATTTATACCCGTTACATTGTTAATTTAC
63 TACATTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTAC
* * * * * *
60407 ATATTACATTATAATTATTGGTGTCGATATTTTTTGGG-CCGATACTTTTAGA-AAAAGTATCGA
128 ATATTACATTATAATTATCGATTTCGAT-GTTTTTGGGATCGATACTTTTA-ATAAATGTATCGA
60470 CAC
191 CAC
60473 ATATTTAGGT
Statistics
Matches: 336, Mismatches: 44, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
198 20 0.06
199 156 0.46
200 92 0.27
201 63 0.19
202 5 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (199 bp):
CGTGCACCTCGTTTGGGAATTCATTCTGGACAAAAGTATCGACACAAACTTAAAAGTGTCGATAC
ATTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACATA
TTACATTATAATTATCGATTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTT
TATA
Found at i:64648 original size:3 final size:3
Alignment explanation
Indices: 64640--64780 Score: 255
Period size: 3 Copynumber: 47.0 Consensus size: 3
64630 TGAATCGCAG
64640 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
64688 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
64736 TAA TAA TAG TAA TAA TAA TAG TAA TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
64781 ATCATATATG
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 132 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:83482 original size:2 final size:2
Alignment explanation
Indices: 83471--83514 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
83461 TTCCGCAACA
83471 AT AT -T AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
83509 AT AT AT
1 AT AT AT
83515 CACAAATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84812 original size:16 final size:16
Alignment explanation
Indices: 84787--84820 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
84777 CCCAATAAAG
*
84787 AGCTAGAACACTATTT
1 AGCTAAAACACTATTT
*
84803 AGCTAAAACACTTTTT
1 AGCTAAAACACTATTT
84819 AG
1 AG
84821 TCAAATCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (16 bp):
AGCTAAAACACTATTT
Done.