Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002713.1 Hibiscus syriacus cultivar Beakdansim tig00005599_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: 63443
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:21347 original size:108 final size:108
Alignment explanation
Indices: 21158--21373 Score: 423
Period size: 108 Copynumber: 2.0 Consensus size: 108
21148 ACGACGTTAA
21158 ACGAATATATTGACGAATATAGACGTTAGAATATAGATGTTAAACAAACGTATTCGTGAACACAA
1 ACGAATATATTGACGAATATAGACGTTAGAATATAGATGTTAAACAAACGTATTCGTGAACACAA
21223 ATACGACCTTATCAGTTTAAATTTGATTCATTTACACCATTAT
66 ATACGACCTTATCAGTTTAAATTTGATTCATTTACACCATTAT
21266 ACGAATATATTGACGAATATAGACGTTAGAATATAGATGTTAAACAAACGTATTCGTGAACACAA
1 ACGAATATATTGACGAATATAGACGTTAGAATATAGATGTTAAACAAACGTATTCGTGAACACAA
*
21331 ATACGGCCTTATCAGTTTAAATTTGATTCATTTACACCATTAT
66 ATACGACCTTATCAGTTTAAATTTGATTCATTTACACCATTAT
21374 TTCCACAGGA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.32
Consensus pattern (108 bp):
ACGAATATATTGACGAATATAGACGTTAGAATATAGATGTTAAACAAACGTATTCGTGAACACAA
ATACGACCTTATCAGTTTAAATTTGATTCATTTACACCATTAT
Found at i:24516 original size:11 final size:11
Alignment explanation
Indices: 24500--24524 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24490 TCACTAACCC
24500 TTTTATTTTTT
1 TTTTATTTTTT
24511 TTTTATTTTTT
1 TTTTATTTTTT
24522 TTT
1 TTT
24525 GTTCTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:25181 original size:19 final size:19
Alignment explanation
Indices: 25157--25202 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
25147 ATTTAGACAT
25157 TTTGCATTTCGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
25176 TTTGCATTTTGTTATTTTC
1 TTTGCATTTCGTTATTTTC
25195 TTTGCATT
1 TTTGCATT
25203 CAGATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.11, C:0.13, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTGCATTTCGTTATTTTC
Found at i:28744 original size:84 final size:84
Alignment explanation
Indices: 28595--29221 Score: 823
Period size: 84 Copynumber: 7.5 Consensus size: 84
28585 TTTTAAACAA
* * * * * *
28595 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
*
28659 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * *
28678 GTCATTTGCAGCACAACTTAAGTCGAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
28743 ACGCTCAGCTCCAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
* * *
28762 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
*
28827 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * * * * *
28846 GTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTACCACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
28911 ACGCTCAGCTCCAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
* * * * *** * *
28930 ATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTTGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
* * *
28991 ACACTCAGCTTCGAGGGCAC
66 ACGCTCAGC-TCCAAGGCAC
* *
29011 ATTATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
*
29076 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * * * *
29095 GTCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
29160 ACGCTCAGCTCCAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
* * *
29179 ATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
29222 AGACCTCCGA
Statistics
Matches: 465, Mismatches: 73, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
80 23 0.05
81 43 0.09
82 1 0.00
83 35 0.08
84 340 0.73
85 23 0.05
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (84 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
ACGCTCAGCTCCAAGGCAC
Found at i:29081 original size:249 final size:249
Alignment explanation
Indices: 28596--29252 Score: 1021
Period size: 249 Copynumber: 2.6 Consensus size: 249
28586 TTTAAACAAA
* * * * * *
28596 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACCTTTGAGTTCGACTA
** * * * * *
28660 CGCTCAGCTCCAAGGCATGTCATTTGCAGCACAACTTAAGTCGAGAAGGGTTGTCTGCCAACAAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AA
** * * * *
28725 AGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
127 AGACCTCCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCAGAATAACTTAAGTCGAG
28789 AAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATG
192 AAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATG
*
28847 TCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTACCACCAAAAGACCTTTGAGTTCGACTA
1 TCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACCTTTGAGTTCGACTA
*
28912 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * * * *
28977 CCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATTATTTGCAGCATAACTTAAGTCGAGAAGG
131 CTCCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCAGAATAACTTAAGTCGAGAAGG
29042 GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATG
196 GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATG
29096 TCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACCTTTGAGTTCGACTA
1 TCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACCTTTGAGTTCGACTA
29161 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
*
29226 CTCCGAGTTCGATTACACTCAACTTCG
131 CTCCGAGTTCGATTACACTCAGCTTCG
29253 GGGTCATATC
Statistics
Matches: 373, Mismatches: 31, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
248 23 0.06
249 243 0.65
251 38 0.10
252 69 0.18
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (249 bp):
TCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCACCAAAAGACCTTTGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
CTCCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTGCAGAATAACTTAAGTCGAGAAGG
GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATG
Found at i:29980 original size:38 final size:37
Alignment explanation
Indices: 29889--30180 Score: 208
Period size: 38 Copynumber: 7.9 Consensus size: 37
29879 GCAAACGGTC
* *
29889 TTTGAAAATACT-TATAATATACATAATTTTTGAAAACA-T
1 TTTGAAAATA-TATATAATAT--ATAGTTTTT-AAAATATT
* *
29928 TTTGAAAATGTATATAATATATAGTTTTAAAAATATTT
1 TTTGAAAATATATATAATATATAGTTTTTAAAATA-TT
* *
29966 TTTGAAACTATATAT--TATATAGTTTTTAAAACATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAATATT
*
30001 TTAGAAAATATATATAATATATAGTTTTTAAAATCATT
1 TTTGAAAATATATATAATATATAGTTTTTAAAAT-ATT
* * *
30039 TTTGAAAA-ATTATATAATATATTG-TTTT-GAATTTT
1 TTTGAAAATA-TATATAATATATAGTTTTTAAAATATT
* * * * * *
30074 TTTAAAACATTTAAATATTATATAATTTTTGAAAA-ACAT
1 TTTGAAA-ATATATATAATATATAGTTTTT-AAAATA-TT
* * ***
30113 TTTAAAAATATATATAATATATAATTTTTAAACCGTT
1 TTTGAAAATATATATAATATATAGTTTTTAAAATATT
* * *
30150 TCTGAAAATATATAT--TATAAAATTTTTAAAA
1 TTTGAAAATATATATAATATATAGTTTTTAAAA
30181 CGTTTTTAAA
Statistics
Matches: 205, Mismatches: 34, Indels: 32
0.76 0.13 0.12
Matches are distributed among these distances:
35 37 0.18
36 35 0.17
37 49 0.24
38 57 0.28
39 27 0.13
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (37 bp):
TTTGAAAATATATATAATATATAGTTTTTAAAATATT
Found at i:30053 original size:73 final size:73
Alignment explanation
Indices: 29911--30180 Score: 230
Period size: 73 Copynumber: 3.7 Consensus size: 73
29901 TATAATATAC
* * * *
29911 ATAATTTTTGAAAACATTTTGAAAATGTATATAATATATAGTTTTAAAAAT-ATTTTTTG-AAAC
1 ATAATTTTT-AAAACATTTTGAAAATATATATAATATATAATTTTTAAAATCA-TTTTTGAAAAA
29974 TATATATTAT
64 TATATATTAT
* *
29984 ATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCATTTTTGAAAAAT
1 ATAATTTTTAAAACATTTT-GAAAATATATATAATATATAATTTTTAAAATCATTTTTGAAAAAT
*
30049 -TATATAAT
65 ATATATTAT
* * *** * * * * *
30057 ATATTGTTTTGAATTTTTTTAAAACATTTAAATATTATATAATTTTTGAAAAACA-TTTT-AAAA
1 ATAAT-TTTTAAAACATTTTGAAA-ATATATATAATATATAATTTTT-AAAATCATTTTTGAAAA
30120 ATATATATAATAT
63 ATATATAT--TAT
* * *
30133 ATAATTTTTAAACCGTTTCTGAAAATATATAT--TATAAAATTTTTAAAA
1 ATAATTTTTAAAACATTT-TGAAAATATATATAATATATAATTTTTAAAA
30181 CGTTTTTAAA
Statistics
Matches: 161, Mismatches: 26, Indels: 21
0.77 0.12 0.10
Matches are distributed among these distances:
72 14 0.09
73 74 0.46
74 42 0.26
75 21 0.13
76 10 0.06
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (73 bp):
ATAATTTTTAAAACATTTTGAAAATATATATAATATATAATTTTTAAAATCATTTTTGAAAAATA
TATATTAT
Found at i:30101 original size:29 final size:31
Alignment explanation
Indices: 30068--30130 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
30058 TATTGTTTTG
** *
30068 AATTTTTTTAAAACA-TTTAAATAT-TATAT
1 AATTTTTGAAAAACATTTTAAAAATATATAT
30097 AATTTTTGAAAAACATTTTAAAAATATATAT
1 AATTTTTGAAAAACATTTTAAAAATATATAT
30128 AAT
1 AAT
30131 ATATAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.45
30 8 0.28
31 8 0.28
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
AATTTTTGAAAAACATTTTAAAAATATATAT
Found at i:30187 original size:112 final size:111
Alignment explanation
Indices: 29977--30197 Score: 265
Period size: 111 Copynumber: 2.0 Consensus size: 111
29967 TTGAAACTAT
* * * *
29977 ATATTATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTTTTTAAAATCATTTTT
1 ATATTATATAATTTTTAAAACATTTTAGAAAATATATATAATATATAATTTTTAAAACCATTTCT
* **
30042 GAAAAATTATATAATATATTGTTTTGAATTTTTTTAAAA-CATTTAA
66 GAAAAATTATATAATATATTG-TTTAAAAGTTTTTAAAAGCATTTAA
*
30088 ATATTATATAATTTTTGAAAAACATTTTA-AAAATATATATAATATATAATTTTT-AAACCGTTT
1 ATATTATATAATTTTT--AAAACATTTTAGAAAATATATATAATATATAATTTTTAAAACCATTT
30151 CTGAAAATATATATTATAA-A-ATT-TTTAAAACGTTTTTAAAAGCATTT
64 CTGAAAA-AT-TA-TATAATATATTGTTTAAAA-GTTTTTAAAAGCATTT
30198 TGGAAATTTA
Statistics
Matches: 95, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
110 5 0.05
111 37 0.39
112 34 0.36
113 14 0.15
114 5 0.05
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (111 bp):
ATATTATATAATTTTTAAAACATTTTAGAAAATATATATAATATATAATTTTTAAAACCATTTCT
GAAAAATTATATAATATATTGTTTAAAAGTTTTTAAAAGCATTTAA
Found at i:30386 original size:9 final size:10
Alignment explanation
Indices: 30356--30394 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
30346 CGATGAACAC
*
30356 AAAATAAAAG
1 AAAATAAAAA
* *
30366 AGAACAAAAA
1 AAAATAAAAA
30376 AAAATAAAAA
1 AAAATAAAAA
30386 AAAATAAAA
1 AAAATAAAA
30395 GGGTTAGTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.85, C:0.03, G:0.05, T:0.08
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:31484 original size:20 final size:19
Alignment explanation
Indices: 31437--31474 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
31427 ATTCAATAAT
31437 AAAAAAAATAAATACAAAC
1 AAAAAAAATAAATACAAAC
*
31456 AAATCAAAATAAATACAAA
1 AAA-AAAAATAAATACAAA
31475 AGGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (19 bp):
AAAAAAAATAAATACAAAC
Found at i:31512 original size:11 final size:11
Alignment explanation
Indices: 31498--31554 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
31488 GGAAAAGAAT
31498 AAATAAAAAAA
1 AAATAAAAAAA
*
31509 AAATAAAATAA
1 AAATAAAAAAA
*** *
31520 GCTTAAAAATA
1 AAATAAAAAAA
*
31531 AAATAAAAAAT
1 AAATAAAAAAA
31542 AAATAGAAAAAA
1 AAATA-AAAAAA
31554 A
1 A
31555 TGATAAATAA
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
11 27 0.82
12 6 0.18
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.16
Consensus pattern (11 bp):
AAATAAAAAAA
Found at i:32955 original size:35 final size:37
Alignment explanation
Indices: 32910--32978 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 37
32900 ATGCTTTTAA
*
32910 AAACGTTTTAAAAATT-T-TATAATATATATTTTCAG
1 AAACGGTTTAAAAATTATATATAATATATATTTTCAG
*
32945 AAACGGTTTAAAAATTATATATTATATATATTTT
1 AAACGGTTTAAAAATTATATATAATATATATTTT
32979 AAAATGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 15 0.50
36 1 0.03
37 14 0.47
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
AAACGGTTTAAAAATTATATATAATATATATTTTCAG
Found at i:32995 original size:37 final size:35
Alignment explanation
Indices: 32904--33200 Score: 185
Period size: 37 Copynumber: 8.1 Consensus size: 35
32894 TCCAAAATGC
* * *
32904 TTTTAAAAACGTTTTAAAAA-T-TTTATAATATATA
1 TTTT-AAAATGTTTTAAAAACTATATATTATATATA
* * *
32938 TTTTCAGAAACGGTTTAAAAATTATATATTATATATA
1 TTTT-A-AAATGTTTTAAAAACTATATATTATATATA
* * * *
32975 TTTTAAAATGTTTTTCAAAAATTATATAATATTTAAATG
1 TTTTAAAATG-TTTT-AAAAACTATAT-AT-TATATATA
*** * *
33014 TTTTAAAA-AAATTCAAAACAATATATTATATA-A
1 TTTTAAAATGTTTTAAAAACTATATATTATATATA
33047 TTTTTCAAAAATGATTTTAAAAACTATATATTATATATA
1 -TTTT--AAAATG-TTTTAAAAACTATATATTATATATA
33086 TTTTCTAAAATGTTTTAAAAACTATATA--ATATATA
1 -TTT-TAAAATGTTTTAAAAACTATATATTATATATA
* * * *
33121 GTTTCAAAAATATTTTTAAAACTATATATTATATACA
1 -TTT-TAAAATGTTTTAAAAACTATATATTATATATA
*
33158 TTTTCAAAATGTTTTCAAAAATTATGTATATTATA-AGTA
1 TTTT-AAAATGTTTT-AAAAACTA--TATATTATATA-TA
33197 TTTT
1 TTTT
33201 CAAAGACCGT
Statistics
Matches: 209, Mismatches: 33, Indels: 37
0.75 0.12 0.13
Matches are distributed among these distances:
34 13 0.06
35 50 0.24
36 29 0.14
37 56 0.27
38 28 0.13
39 32 0.15
40 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (35 bp):
TTTTAAAATGTTTTAAAAACTATATATTATATATA
Found at i:33023 original size:29 final size:30
Alignment explanation
Indices: 32965--33026 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
32955 AAAATTATAT
**
32965 ATTATATATATTTTAAAATGTTTTTCAAAA
1 ATTATATATATTTTAAAATGTTTTAAAAAA
32995 ATTATATA-ATATTT-AAATGTTTTAAAAAA
1 ATTATATATAT-TTTAAAATGTTTTAAAAAA
33024 ATT
1 ATT
33027 CAAAACAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
ATTATATATATTTTAAAATGTTTTAAAAAA
Found at i:33161 original size:111 final size:109
Alignment explanation
Indices: 32927--33201 Score: 296
Period size: 111 Copynumber: 2.5 Consensus size: 109
32917 TTAAAAATTT
* * *
32927 TATAATATAT-ATTTTCAGAAACGGTTTAAAAATTATATATTATATATA-TTT-TAAAATGTTTT
1 TATATTATATAATTTTCA-AAATGTTTTAAAAATTATATATTATATATATTTTCTAAAATGTTTT
* *
32989 TCAAAAATTATATAATATTTAAATGTTTTAAAAAAATTCAAAACAA
65 TCAAAAACTATATAATA-TTAAATGTTTCAAAAAAATTCAAAACAA
*
33035 TATATTATATAATTTTTCAAAAATGATTTTAAAAACTATATATTATATATATTTTCTAAAATG-T
1 TATATTATATAA-TTTTC-AAAATG-TTTTAAAAATTATATATTATATATATTTTCTAAAATGTT
* * * *
33099 TTT-AAAAACTATATAATA-TATA-GTTTCAAAAATATTTTTAAAACTA
63 TTTCAAAAACTATATAATATTAAATGTTTCAAAAA-A-ATTCAAAACAA
33145 TATATTATATACATTTTCAAAATGTTTTCAAAAATTATGTATATTATA-AGTATTTTC
1 TATATTATATA-ATTTTCAAAATGTTTT-AAAAATTA--TATATTATATA-TATTTTC
33202 AAAGACCGTT
Statistics
Matches: 143, Mismatches: 11, Indels: 23
0.81 0.06 0.13
Matches are distributed among these distances:
108 22 0.15
109 18 0.13
110 34 0.24
111 55 0.38
112 7 0.05
113 7 0.05
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (109 bp):
TATATTATATAATTTTCAAAATGTTTTAAAAATTATATATTATATATATTTTCTAAAATGTTTTT
CAAAAACTATATAATATTAAATGTTTCAAAAAAATTCAAAACAA
Found at i:34119 original size:21 final size:20
Alignment explanation
Indices: 34077--34119 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
34067 GATAAAGAAA
*
34077 TATCTAAAAATTATTATTTT
1 TATCTAAAAATAATTATTTT
34097 TATCTAAAACATCAATT-TTTT
1 TATCTAAAA-AT-AATTATTTT
34118 TA
1 TA
34120 ATATTTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 8 0.40
22 3 0.15
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (20 bp):
TATCTAAAAATAATTATTTT
Found at i:58207 original size:19 final size:19
Alignment explanation
Indices: 58183--58224 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
58173 ACAAAGTCTC
58183 CTCTGTTGCAACAACTCTT
1 CTCTGTTGCAACAACTCTT
* *
58202 CTCTGTTGTAGCAACTCTT
1 CTCTGTTGCAACAACTCTT
58221 CTCT
1 CTCT
58225 CTTCCCTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40
Consensus pattern (19 bp):
CTCTGTTGCAACAACTCTT
Found at i:58292 original size:30 final size:30
Alignment explanation
Indices: 58249--58306 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
58239 GCAGTTTCAT
* * *
58249 AGGTCGTCGTGTGCTTCTGGAA-ACCTATAA
1 AGGTCGCCATGTGCTCCT-GAAGACCTATAA
58279 AGGTCGCCATGTGCTCCTGAAGACCTAT
1 AGGTCGCCATGTGCTCCTGAAGACCTAT
58307 GGTGATCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (30 bp):
AGGTCGCCATGTGCTCCTGAAGACCTATAA
Done.