Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004205.1 Hibiscus syriacus cultivar Beakdansim tig00009205_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: 58528
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2550 original size:19 final size:19
Alignment explanation
Indices: 2528--2565 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2518 TCAGTTATTT
2528 TATTTTAAATAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
2547 TATTTTAAGTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
2566 GATATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:2705 original size:75 final size:75
Alignment explanation
Indices: 2502--2716 Score: 254
Period size: 77 Copynumber: 2.8 Consensus size: 75
2492 TTTAAACATT
* * * * * * *
2502 ATATTTTATCTTTGTTTCAGTTATTTTATTTTAAATAAGTTTTAGTATTTTAAGTAAGTTTTAGG
1 ATATTTTA-CTTTGTTTTAGGTATTTTAATTTAAAT-AGTTTTAGTATTTTAATTAGGATTTAGA
**
2567 ATATTATTTTTT
64 ATATTATTTTAA
*
2579 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGA
1 ATATTTTA-CTTTGTTTTAGGTATTTTAATTTAAATA-GTTTTAGTATTTTAATTAGGATTTAGA
2644 ATATTATTTTAA
64 ATATTATTTTAA
* *
2656 ATATTATTA-TTT-TTTTAGGTTTTTTAATTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 ATATT-TTACTTTGTTTTAGGTATTTTAATTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
2717 AGATGTTTTA
Statistics
Matches: 123, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
74 5 0.04
75 40 0.33
76 4 0.03
77 71 0.58
78 3 0.02
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (75 bp):
ATATTTTACTTTGTTTTAGGTATTTTAATTTAAATAGTTTTAGTATTTTAATTAGGATTTAGAAT
ATTATTTTAA
Found at i:5727 original size:31 final size:30
Alignment explanation
Indices: 5692--5780 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 30
5682 CTAAGGTGTC
5692 CCTTGGGTAGGCTCTCAGACCCCAAGGTATT
1 CCTTGGGTAGGCTCT-AGACCCCAAGGTATT
* *
5723 CCTTGGGTAGTCTCTAAAGCCCCAAGGTATT
1 CCTTGGGTAGGCTCTAGA-CCCCAAGGTATT
* *
5754 TCTTGGGTAGGCTCTAAGGCCCCAAGG
1 CCTTGGGTAGGCTCT-AGACCCCAAGG
5781 CATCCCCTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.04
31 47 0.94
32 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.26
Consensus pattern (30 bp):
CCTTGGGTAGGCTCTAGACCCCAAGGTATT
Found at i:12009 original size:97 final size:96
Alignment explanation
Indices: 11869--12128 Score: 389
Period size: 96 Copynumber: 2.7 Consensus size: 96
11859 TTCAAGTAAT
* *
11869 AACCAGTAGATTCCATGATCCATAAATCAGGAA-TAATCCTAT-TTTTCCAGTGAAAACATGAAA
1 AACCAGTAGATTCCATGATCCATAAATCAGGAACT-AT--TATATTTTCAAGTGAAAACAGGAAA
* * *
11932 TCAGATAACACATTTCAGGTAATCATAGTTCATA
63 CCAGATAACACATTTCAAGTAACCATAGTTCATA
* * *
11966 AACCAGTAGATTCCATGACCCATCAATCAGGAACTATTATATTTTCAAGTGAAAACAGGAAGCCA
1 AACCAGTAGATTCCATGATCCATAAATCAGGAACTATTATATTTTCAAGTGAAAACAGGAAACCA
12031 GATAACACATTTCAAGTAACCATAGTTCATA
66 GATAACACATTTCAAGTAACCATAGTTCATA
* *
12062 AACCAGTAGATTCCATGATCCATAAATCAGGAACTATTATATTTTCTAGTGAAAACAGGTAACCA
1 AACCAGTAGATTCCATGATCCATAAATCAGGAACTATTATATTTTCAAGTGAAAACAGGAAACCA
12127 GA
66 GA
12129 GAATCTAGAT
Statistics
Matches: 148, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
95 3 0.02
96 111 0.75
97 33 0.22
98 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (96 bp):
AACCAGTAGATTCCATGATCCATAAATCAGGAACTATTATATTTTCAAGTGAAAACAGGAAACCA
GATAACACATTTCAAGTAACCATAGTTCATA
Found at i:14392 original size:19 final size:19
Alignment explanation
Indices: 14368--14437 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 19
14358 TGGTATCCTT
14368 TTATGCCTTTAATGCACCA
1 TTATGCCTTTAATGCACCA
* *
14387 TTATGCATTTCATTTATGGCATCCT
1 TTATGCCTTT-A---AT-GCA-CCA
14412 TTCATGCCTTTAATGCACCA
1 TT-ATGCCTTTAATGCACCA
14432 TTATGC
1 TTATGC
14438 ATTTCATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
19 13 0.32
20 5 0.12
21 3 0.08
22 2 0.05
23 2 0.05
24 3 0.08
25 5 0.12
26 7 0.17
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.41
Consensus pattern (19 bp):
TTATGCCTTTAATGCACCA
Found at i:14398 original size:45 final size:45
Alignment explanation
Indices: 14349--14512 Score: 292
Period size: 45 Copynumber: 3.6 Consensus size: 45
14339 TATTCATTAT
*
14349 TTTCATTTATGGTATCCTTTTATGCCTTTAATGCACCATTATGCA
1 TTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCATTATGCA
*
14394 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCA
1 TTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCATTATGCA
* *
14439 TTTCATTTATGGAATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCATTATGCA
14484 TTTCATTTATGGTATCCTTTCATGCCTTT
1 TTTCATTTATGGTATCCTTTCATGCCTTT
14513 TCATATGCAT
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 114 1.00
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.46
Consensus pattern (45 bp):
TTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCATTATGCA
Found at i:21148 original size:45 final size:45
Alignment explanation
Indices: 21099--21217 Score: 202
Period size: 45 Copynumber: 2.6 Consensus size: 45
21089 TATTCATTAT
* *
21099 TTTCATTTATGACATTCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
21144 TTTCATTTATGGCATCCATTCATGCCTTTAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
21189 TTTCATTTATGGCATCCTTTCATGCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTT
21218 TAATATGCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:21758 original size:19 final size:19
Alignment explanation
Indices: 21734--21773 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21724 ATTTTGTGAA
*
21734 AATCAAGCAAGAAACTTTG
1 AATCAAACAAGAAACTTTG
**
21753 AATCAAATGAGAAACTTTG
1 AATCAAACAAGAAACTTTG
21772 AA
1 AA
21774 AATCATTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (19 bp):
AATCAAACAAGAAACTTTG
Found at i:22039 original size:19 final size:19
Alignment explanation
Indices: 22012--22049 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
22002 TTTTGGAAAG
*
22012 TCAAGTAAGAAACTTTGAA
1 TCAAATAAGAAACTTTGAA
22031 TCAAATAAGAAACTTTGAA
1 TCAAATAAGAAACTTTGAA
22050 AATCGTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (19 bp):
TCAAATAAGAAACTTTGAA
Found at i:22172 original size:42 final size:42
Alignment explanation
Indices: 22110--22207 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 42
22100 TAAATGGCCT
*
22110 AGAGGACTT-ATCATCTTGCTCGGAAGACTCACAGATGACCC
1 AGAGGACTTAATCATCATGCTCGGAAGACTCACAGATGACCC
* * * * *
22151 GGAGGATTTAATCATCATGCTCGGAAGACTTACTGATGCCCC
1 AGAGGACTTAATCATCATGCTCGGAAGACTCACAGATGACCC
*
22193 AAAGGACTTAATCAT
1 AGAGGACTTAATCAT
22208 AATGGAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 7 0.15
42 40 0.85
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (42 bp):
AGAGGACTTAATCATCATGCTCGGAAGACTCACAGATGACCC
Found at i:22219 original size:270 final size:272
Alignment explanation
Indices: 21547--22268 Score: 898
Period size: 276 Copynumber: 2.6 Consensus size: 272
21537 TTTATGCCTA
* * * * * *
21547 TCTTATATATATGGCCGAGAGGATTTTTCATCTTGCTCGGAATACTAACATATGACCTGGAGGAT
1 TCTTATA-A-ATGGCCTAGAGGACTTATCATCTTGCTCGGAAGACTCACAGATGACCTGGAGGAT
* * *
21612 TTAATCATCATTCTCGAAAGACTTACTGATGGCCAGAAGGACTTACTCATTTTGGAAATATTCTA
64 TTAATCATCATGCTCGGAAGACTTACTGATGCCCA-AAGGACTTACTCATTTTGGAAATATTCTA
* *
21677 CTGGGA-AAGAAACTTTGAAAATCACTTTCTTACTTTTCAAAAATTTCATTTTGTGAAAATCAAG
128 CT-AGATAAGAAACTTTGAAAATCACTTTCTTACTTTTCAAAAATTTAATTTTGTGAAAATCAAG
* *
21741 CAAGAAACTTTGAATCAAATGAGAAACTTTGAAAATCATTTTCTTATTTTCACAAATATCATACA
192 CAAGAAACTTTGAATCAAATAAGAAACTTTGAAAATC--TGTC-TATTTTCACAAATATCATACA
21806 AAAACACCATGCCCGAAGG
254 AAAACACCATGCCCGAAGG
* * * * * * *
21825 CCTTATAGATGGCCTCGGGGACTTATCATCATGCTCTGAAGACTCATAGATGACCTGGAGGATTT
1 TCTTATAAATGGCCTAGAGGACTTATCATCTTGCTCGGAAGACTCACAGATGACCTGGAGGATTT
* * * ** * *
21890 AACCATCATGCTCAGAATACTTACTGATGGTACAGAGGACTTACTCATTTTGGAAATATTATACT
66 AATCATCATGCTCGGAAGACTTACTGAT-GCCCAAAGGACTTACTCATTTTGGAAATATTCTACT
* * * * * *
21955 ACATAAGAAACATTGAAAATCACTTTATTACTTTTCAAATATTTAATTTT-TGGAAAGTCAAGTA
130 AGATAAGAAACTTTGAAAATCACTTTCTTACTTTTCAAAAATTTAATTTTGT-GAAAATCAAGCA
* *
22019 AGAAACTTTGAATCAAATAAGAAACTTTGAAAATC-GTC-ATTTTCATAAATATCATACAACAA-
194 AGAAACTTTGAATCAAATAAGAAACTTTGAAAATCTGTCTATTTTCACAAATATCATACAAAAAC
* *
22081 ATCATGCCC-AGGTG
259 ACCATGCCCGAAG-G
*
22095 TCTTATAAATGGCCTAGAGGACTTATCATCTTGCTCGGAAGACTCACAGATGACCCGGAGGATTT
1 TCTTATAAATGGCCTAGAGGACTTATCATCTTGCTCGGAAGACTCACAGATGACCTGGAGGATTT
* **
22160 AATCATCATGCTCGGAAGACTTACTGATGCCCCAAAGGACTTAATCATAATGGAAATATTCTACT
66 AATCATCATGCTCGGAAGACTTACTGATG-CCCAAAGGACTTACTCATTTTGGAAATATTCTACT
* ** *
22225 AGGTAAGAAACTTTGAAAATTGCTTTCTTACTTTTAAAAAATTT
130 AGATAAGAAACTTTGAAAATCACTTTCTTACTTTTCAAAAATTT
22269 CATATAAATA
Statistics
Matches: 377, Mismatches: 62, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
269 3 0.01
270 155 0.41
271 22 0.06
273 2 0.01
275 2 0.01
276 184 0.49
277 3 0.01
278 6 0.02
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (272 bp):
TCTTATAAATGGCCTAGAGGACTTATCATCTTGCTCGGAAGACTCACAGATGACCTGGAGGATTT
AATCATCATGCTCGGAAGACTTACTGATGCCCAAAGGACTTACTCATTTTGGAAATATTCTACTA
GATAAGAAACTTTGAAAATCACTTTCTTACTTTTCAAAAATTTAATTTTGTGAAAATCAAGCAAG
AAACTTTGAATCAAATAAGAAACTTTGAAAATCTGTCTATTTTCACAAATATCATACAAAAACAC
CATGCCCGAAGG
Found at i:22514 original size:20 final size:21
Alignment explanation
Indices: 22489--22527 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22479 ATATATGCAA
*
22489 ATAATG-GTTTCATGAATATG
1 ATAATGTGATTCATGAATATG
22509 ATAATGTGATTCATGAATA
1 ATAATGTGATTCATGAATA
22528 ACTTTATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38
Consensus pattern (21 bp):
ATAATGTGATTCATGAATATG
Found at i:28208 original size:42 final size:40
Alignment explanation
Indices: 28139--28427 Score: 248
Period size: 42 Copynumber: 7.0 Consensus size: 40
28129 TTATTACAAA
* * *
28139 TTCGTTGCGA--TAGTCTAAGTTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAG
* *
28177 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
1 TT--CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAG
* *
28219 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAA
1 TT--CGTTGCGATTTATTCCAAGTTCGTTGCGA--TAGTCCAAG
* * * *
28263 TTCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAA
1 TTCGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCCAAG
* * * *
28305 TTCGTTACGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAG
1 TTCGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCCAAG
*
28347 TTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
1 TTCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAG
28387 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
1 TT--CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
28428 AATCGCAACG
Statistics
Matches: 222, Mismatches: 17, Indels: 20
0.86 0.07 0.08
Matches are distributed among these distances:
38 2 0.01
40 27 0.12
42 177 0.80
44 16 0.07
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (40 bp):
TTCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAG
Found at i:28259 original size:63 final size:61
Alignment explanation
Indices: 28120--28378 Score: 292
Period size: 63 Copynumber: 4.1 Consensus size: 61
28110 TCGAAGTTCG
* * * * *
28120 CGTTGCGATTTATTACAAATTCGTTGCGATAGTCTAAGTTCGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGTTGCGATTTATTCCAAATT
*
28179 CGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTT--CGTTGCGATTTATTCCAAATT
28244 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTT--CGTTGCGATTTATTCCAAATT
* * * * * *
28307 CGTTACGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT--CGTTGCGA--TAGTCGAAGTTCGTTGCGATTTATTCCAAATT
28370 CGTTGCGAT
1 CGTTGCGAT
28379 AGTCCAAGTT
Statistics
Matches: 177, Mismatches: 12, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
61 46 0.26
63 113 0.64
65 18 0.10
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (61 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGTTGCGATTTATTCCAAATT
Found at i:28302 original size:105 final size:105
Alignment explanation
Indices: 28105--28424 Score: 554
Period size: 105 Copynumber: 3.1 Consensus size: 105
28095 ACTGATTTGT
* * * * *
28105 GATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGA--TAGTCTAAGTTCGTTGCGA
1 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCGTTGCGA
28168 TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
66 TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
28208 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCGTTGCGA
1 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCGTTGCGA
*
28273 TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTAC
66 TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
28313 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCGTTGCGA
1 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCGTTGCGA
* *
28378 TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGC
66 TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
28418 GATAGTC
1 GATAGTC
28425 CAAAATCGCA
Statistics
Matches: 206, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
103 42 0.20
105 164 0.80
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.37
Consensus pattern (105 bp):
GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATTCGTTGCGA
TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
Found at i:28379 original size:63 final size:63
Alignment explanation
Indices: 28223--28420 Score: 269
Period size: 63 Copynumber: 3.1 Consensus size: 63
28213 TCGAAGTTCG
* * * * *
28223 CGTTGCGATTTATTCCAAGTTCGTTGCGATTTATTCCAAATT--CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
* *
28284 CGCGTTGCGATTTATTCCAAATTCGTTACGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
28349 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
28412 CGTTGCGAT
1 CGTTGCGAT
28421 AGTCCAAAAT
Statistics
Matches: 122, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
61 8 0.07
63 105 0.86
65 9 0.07
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (63 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
Found at i:29351 original size:42 final size:42
Alignment explanation
Indices: 29292--29696 Score: 620
Period size: 42 Copynumber: 9.7 Consensus size: 42
29282 TGAGATTTTG
*
29292 GACTATCGCAACGAACTTGGAATAAATCGCATCGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
29334 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
29376 GACTATAGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
29418 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
29460 GACTATAGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
29502 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
29544 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
** *
29586 GACTATCGCAACGAACTTGGAATAAATCGCAACATGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
29628 GACTATCGCAACAAACTTGGACT--ATCGCAATGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
29668 GACTATCGCAACGAA-TTTGAA-AAATCGCA
1 GACTATCGCAACGAACTTGGAATAAATCGCA
29697 TTGCGATAGT
Statistics
Matches: 332, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
39 4 0.01
40 33 0.10
42 295 0.89
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:29721 original size:21 final size:21
Alignment explanation
Indices: 29692--29744 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
29682 ATTTGAAAAA
*
29692 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* *
29713 TCGCGTTGCGATATTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
29734 TCGCGTTGCGA
1 TCGCGTTGCGA
29745 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:39070 original size:2 final size:2
Alignment explanation
Indices: 39063--39145 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
39053 AAATGATGGA
39063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39146 GAATTTCAGG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39409 original size:28 final size:28
Alignment explanation
Indices: 39355--39427 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
39345 TACCATTTTT
*
39355 TTCTTTTAAAAT--GATTTTTCTTAAAA
1 TTCTTTTAAAATACGTTTTTTCTTAAAA
39381 TTCTTTTAAAATACGTTTTTTCTTAAAA
1 TTCTTTTAAAATACGTTTTTTCTTAAAA
39409 TTCTTTTAAAATACGTTTT
1 TTCTTTTAAAATACGTTTT
39428 CTTAAGTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 12 0.27
28 32 0.73
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.55
Consensus pattern (28 bp):
TTCTTTTAAAATACGTTTTTTCTTAAAA
Found at i:52664 original size:2 final size:2
Alignment explanation
Indices: 52657--52685 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52647 TTCATTTTCG
52657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52686 GGAAAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53622 original size:126 final size:130
Alignment explanation
Indices: 53294--53727 Score: 425
Period size: 134 Copynumber: 3.3 Consensus size: 130
53284 CAAATTAATC
* * * * *
53294 GATTTGCTTCACTGCTCTTCAAGGAAGATCAAATCTGAAAGAAGAAGAATCTGCTCCACTACTTT
1 GATTTGCTTCGCTGCTCTTC-AGGAAGACCGAATCTGAAAGAAGAAGAATCTGCTCCAATACTCT
*
53359 TTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCATTTCTCTTCAGGGAATATTGAATCA
65 TTAGGGGAGATCAGACTCGAGAAAACTTT-ATCCA--TCA-TTCTCTTCAGGGAAGATTGAATCA
*
53424 AACGT
126 AACAT
* * * * * * * * *
53429 GATTTACTTCGCTGTTGTTCAGGAATACTGAATCTGAAAGAAGAAAAATATGTTCCACA-ACTGT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCGAATCTGAAAGAAGAAGAATCTGCTCCA-ATACTCT
* *
53493 TTAGGGGAAATCAGACTCGAGAAAACTTT-T-CA-C-TTCTCTTCAGGGAAGATTGAATCGAACA
65 TTAGGGGAGATCAGACTCGAGAAAACTTTATCCATCATTCTCTTCAGGGAAGATTGAATCAAACA
53554 T
130 T
*
53555 GATTTGC-TCGCTGCTCTTCAGGAAGACCGAATCTGAAAAAAAGAAGAATCTGCTCCAATACTCT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCGAATCTG-AAAGAAGAAGAATCTGCTCCAATACTCT
* * * * * *
53619 TTAGGGGAGACCAGACTCAAGAAATCTTTGACCCACTTCATTGTTCTTCAGGGAATATTGAATCA
65 TTAGGGGAGATCAGACTCGAGAAAACTTT-ATCCA--TCATT-CTCTTCAGGGAAGATTGAATCA
53684 AA-AGT
126 AACA-T
* ** * *
53689 GATTTGTTTCATTTG-TCTTCAAGAAGACCAAATCTGAAA
1 GATTTGCTTC-GCTGCTCTTCAGGAAGACCGAATCTGAAA
53728 ATCTAACATC
Statistics
Matches: 245, Mismatches: 40, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
125 25 0.10
126 78 0.32
128 1 0.00
129 2 0.01
131 2 0.01
132 2 0.01
133 3 0.01
134 93 0.38
135 37 0.15
136 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (130 bp):
GATTTGCTTCGCTGCTCTTCAGGAAGACCGAATCTGAAAGAAGAAGAATCTGCTCCAATACTCTT
TAGGGGAGATCAGACTCGAGAAAACTTTATCCATCATTCTCTTCAGGGAAGATTGAATCAAACAT
Found at i:54485 original size:45 final size:45
Alignment explanation
Indices: 54397--54485 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
54387 GAATGAAATC
* * ** *
54397 ACTAAAATATTGACTCTTCTTCGCGAGAAAGTCAAGAAGGACAAT
1 ACTAAAATAATGACTCCTCTTAACGAGAAAGTAAAGAAGGACAAT
*
54442 ACTAAAATAATGACTCCTCTTAATGAGAAAGTAAAGGAA-GACAA
1 ACTAAAATAATGACTCCTCTTAACGAGAAAGTAAA-GAAGGACAA
54486 CACCGAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
45 34 0.92
46 3 0.08
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (45 bp):
ACTAAAATAATGACTCCTCTTAACGAGAAAGTAAAGAAGGACAAT
Found at i:54588 original size:38 final size:38
Alignment explanation
Indices: 54491--55204 Score: 538
Period size: 38 Copynumber: 18.0 Consensus size: 38
54481 GACAACACCG
* * * *
54491 AAAGATTGAATCCTCTTCGCGAGAAAGTCAAGAATAACAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-AC
*
54531 TGAAAGATTGAC-TCATCTTCACGAGGAAATCAAGAATAAC
1 --AAAGATTGACTTC-TCTTCACGAGGAAGTCAAGAATAAC
* *
54571 AAAGATTGACTACTCTTCACGAGGAAGTCCAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
54609 AAAGATTGACTTCTCTTCACGAGGAAGTCGAGAATAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
54647 AAAGATTGACTTCACTTTACGAGGAAGTCCAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
54685 ATTGGGAGAATGAC-TCATCTTCACGAGGAATTCAAGAATAA-
1 A----AAGATTGACTTC-TCTTCACGAGGAAGTCAAGAATAAC
* * * *
54726 AAAGATTAACTCCTCTTCACGAGAAAGTCAAGAACAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
54764 AAAGATCGACTTCTCTTCACGAGGAAGTCCAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
54802 AAAGATTTACTTCTCTTCATGATGAAGTCCAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** * *
54840 ACTAGGAGATTGACTCCTCTTCGTGAGGGAGTCAGGAATAAC
1 A--A--AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * ** *
54882 AAAGATTGATTTCTCTTTATAAGAAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** * * *
54920 AAAGACCGACTTTTGTTCACGAGGAAGTCGAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
54958 AAAGATTGATTTCTCTTCATGAGGAAGTCAAGAATGACAATAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT----A-AC
* * * * * *
55001 TGAGAGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACATAC
1 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT---A-AC
* * * * * *
55045 TGAGAGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATAC
1 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT----A-AC
* *
55090 TGAAAGATTAACTTCTCTTCACGAGAAAGTCAAGAATAAC
1 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
55130 AAAGATTGACTCCTCTTCACGAGGGAGTCAAGAATAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
55168 AAGGATTGACTTCTCTT--CGAGGAAGTTAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
55204 A
1 A
55205 TTGGAATATT
Statistics
Matches: 553, Mismatches: 98, Indels: 48
0.79 0.14 0.07
Matches are distributed among these distances:
36 17 0.03
37 27 0.05
38 303 0.55
39 1 0.00
40 6 0.01
41 6 0.01
42 86 0.16
43 2 0.00
44 41 0.07
45 64 0.12
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:54954 original size:156 final size:157
Alignment explanation
Indices: 54491--55166 Score: 626
Period size: 156 Copynumber: 4.2 Consensus size: 157
54481 GACAACACCG
* * ** * *
54491 AAAGATTGAATCCTCTTCGCGAGAAAGTCAAGAATAACACT-GAAAGATTGACTCATCTTCACGA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTAGAGAGATTGACTCATCTTCACGA
* * *
54555 GGAAATCAAGAATAACAAAGATTGACTACTCTTCACGAGGAAGTCCAGAATAACAAAGATTGACT
66 GGAAATCAAGAATAACAAAGATTGACTACTCTTCACGAGAAAGTCAAGAATAACAAAGATCGACT
*
54620 TCTCTTCACGAGGAAGTCGAGAATAAT
131 TCTCTTCACGAGGAAGTCGAGAATAAC
* * * * * * *
54647 AAAGATTGACTTCACTTTACGAGGAAGTCCAGAATAACA-TTGGGAGAATGACTCATCTTCACGA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTAGAGAGATTGACTCATCTTCACGA
* * * *
54711 GGAATTCAAGAATAA-AAAGATTAACTCCTCTTCACGAGAAAGTCAAGAACAACAAAGATCGACT
66 GGAAATCAAGAATAACAAAGATTGACTACTCTTCACGAGAAAGTCAAGAATAACAAAGATCGACT
*
54775 TCTCTTCACGAGGAAGTCCAGAATAAC
131 TCTCTTCACGAGGAAGTCGAGAATAAC
* * * * **
54802 AAAGATTTACTTCTCTTCATGATGAAGTCCAGAATAACACTAG-GAGATTGACTCCTCTTCGTGA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTAGAGAGATTGACTCATCTTCACGA
* * * * * * ** *
54866 GGGAGTCAGGAATAACAAAGATTGATTTCTCTTTATAAGAAAGTCAAGAATAACAAAGACCGACT
66 GGAAATCAAGAATAACAAAGATTGACTACTCTTCACGAGAAAGTCAAGAATAACAAAGATCGACT
* *
54931 TTTGTTCACGAGGAAGTCGAGAATAAC
131 TCTCTTCACGAGGAAGTCGAGAATAAC
* * * *
54958 AAAGATTGATTTCTCTTCATGAGGAAGTCAAGAATGACAATACTGAGAGATTGACTTC-TCTTAA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTA--GAGAGATTGAC-TCATCTTCA
* * * * * * * * *
55022 TGA-GAAAGTGAAAAATGACATACTGAGAGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACA
63 CGAGGAAA-TCAAGAAT---A-AC--AAAGATTGACTACTCTTCACGAGAAAGTCAAGAAT----
** * *
55086 ATACTGAAAGATTAACTTCTCTTCACGAGAAAGTCAAGAATAAC
117 A-AC--AAAGATCGACTTCTCTTCACGAGGAAGTCGAGAATAAC
* * *
55130 AAAGATTGACTCCTCTTCACGAGGGAGTCAAGAATAA
1 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAA
55167 TAAGGATTGA
Statistics
Matches: 425, Mismatches: 74, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
155 132 0.31
156 169 0.40
158 3 0.01
159 21 0.05
160 2 0.00
162 1 0.00
163 2 0.00
165 29 0.07
169 1 0.00
170 2 0.00
172 63 0.15
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.24
Consensus pattern (157 bp):
AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACACTAGAGAGATTGACTCATCTTCACGA
GGAAATCAAGAATAACAAAGATTGACTACTCTTCACGAGAAAGTCAAGAATAACAAAGATCGACT
TCTCTTCACGAGGAAGTCGAGAATAAC
Found at i:55059 original size:44 final size:45
Alignment explanation
Indices: 54960--55119 Score: 232
Period size: 45 Copynumber: 3.6 Consensus size: 45
54950 AGAATAACAA
* * * * *
54960 AGATTGATTTCTCTTCATGAGGAAGTCAAGAATGACAATACTGAG
1 AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATACTGAG
55005 AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGAC-ATACTGAG
1 AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATACTGAG
*
55049 AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATACTGAA
1 AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATACTGAG
* * *
55094 AGATTAACTTCTCTTCACGAGAAAGT
1 AGATTGACTTCTCTTAATGAGAAAGT
55120 CAAGAATAAC
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
44 44 0.42
45 61 0.58
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (45 bp):
AGATTGACTTCTCTTAATGAGAAAGTGAAAAATGACAATACTGAG
Found at i:55988 original size:43 final size:43
Alignment explanation
Indices: 55912--56043 Score: 151
Period size: 43 Copynumber: 3.0 Consensus size: 43
55902 TATTCCTGGA
* *
55912 TGATATGAGCCTTCAAAAATGTCTCAACATTTATTATTTCTTGC
1 TGATATGAGCCTTC-AAAATGCCCCAACATTTATTATTTCTTGC
* * *
55956 TGATATGGGCCTTCAAAATGCCCCAACATTTATTATTTCTAGA
1 TGATATGAGCCTTCAAAATGCCCCAACATTTATTATTTCTTGC
* *
55999 TGATACAT-A-CCTTCAAAAGTTCCCCAACATTTATCATTTCTTGC
1 TGAT--ATGAGCCTTCAAAA-TGCCCCAACATTTATTATTTCTTGC
56043 T
1 T
56044 CCAGAACTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 38 0.51
44 35 0.47
45 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (43 bp):
TGATATGAGCCTTCAAAATGCCCCAACATTTATTATTTCTTGC
Done.