Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000036.1 Hibiscus syriacus cultivar Beakdansim tig00000057_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: 66312
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:843 original size:2 final size:2
Alignment explanation
Indices: 830--874 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
820 TTTTATAGGG
* *
830 TA TA TA TC TA TA TA TA TA TA TA TA TA TA -A TA TA GA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
870 TA TA T
1 TA TA T
875 GGGGGGAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1577 original size:73 final size:73
Alignment explanation
Indices: 1406--1651 Score: 387
Period size: 72 Copynumber: 3.4 Consensus size: 73
1396 GTTTTTATAT
*
1406 TATTTAAATTTTACATATTTTTATTAAATTGAGTATTTATAGCACTTTATT-AAAAAAC-TCTCT
1 TATTT-AATTTTACATATTTTTATTAAATTGAGTATTTATACCACTTTATTAAAAAAACATCTCT
1469 CTTGAATTC
65 CTTGAATTC
*
1478 TA-TTAA-TTTACATATTTTTATTAAATTGAGCATTTATACCACTTTATTAAAAAAACATCTCTC
1 TATTTAATTTTACATATTTTTATTAAATTGAGTATTTATACCACTTTATTAAAAAAACATCTCTC
1541 TTGAATTC
66 TTGAATTC
**
1549 TATTTAATTTTACATATTTTTATTAAATTGAGTATTTATACCACTTTATTTAAAAAATTATCT-T
1 TATTTAATTTTACATATTTTTATTAAATTGAGTATTTATACCACTTTA-TTAAAAAAACATCTCT
1613 -TTGAATTC
65 CTTGAATTC
*
1621 TATTTAATTTTACATATTTTTATTGAATTGA
1 TATTTAATTTTACATATTTTTATTAAATTGA
1652 ACTTAATCTT
Statistics
Matches: 163, Mismatches: 6, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
69 40 0.25
70 9 0.06
71 18 0.11
72 44 0.27
73 40 0.25
74 12 0.07
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (73 bp):
TATTTAATTTTACATATTTTTATTAAATTGAGTATTTATACCACTTTATTAAAAAAACATCTCTC
TTGAATTC
Found at i:1625 original size:72 final size:71
Alignment explanation
Indices: 1406--1651 Score: 370
Period size: 69 Copynumber: 3.4 Consensus size: 71
1396 GTTTTTATAT
* * * *
1406 TATTTAAATTTTACATATTTTTATTAAATTGAGTATTTATAGCACTTTATTAAAAAACTCTCTCT
1 TATTT-AATTTTACATATTTTTATTAAATTGAGTATTTATACCACTTTATTAAAAAAATATCTTT
1471 TGAATTC
65 TGAATTC
* *
1478 TA-TTAA-TTTACATATTTTTATTAAATTGAGCATTTATACCACTTTATTAAAAAAACATCTCTC
1 TATTTAATTTTACATATTTTTATTAAATTGAGTATTTATACCACTTTATTAAAAAAATATCT-T-
1541 TTGAATTC
64 TTGAATTC
*
1549 TATTTAATTTTACATATTTTTATTAAATTGAGTATTTATACCACTTTATTTAAAAAATTATCTTT
1 TATTTAATTTTACATATTTTTATTAAATTGAGTATTTATACCACTTTA-TTAAAAAAATATCTTT
1614 TGAATTC
65 TGAATTC
*
1621 TATTTAATTTTACATATTTTTATTGAATTGA
1 TATTTAATTTTACATATTTTTATTAAATTGA
1652 ACTTAATCTT
Statistics
Matches: 159, Mismatches: 10, Indels: 10
0.89 0.06 0.06
Matches are distributed among these distances:
69 49 0.31
70 2 0.01
71 12 0.08
72 44 0.28
73 40 0.25
74 12 0.08
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (71 bp):
TATTTAATTTTACATATTTTTATTAAATTGAGTATTTATACCACTTTATTAAAAAAATATCTTTT
GAATTC
Found at i:5589 original size:15 final size:15
Alignment explanation
Indices: 5569--5599 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5559 CAACAAATAG
5569 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
5584 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
5599 A
1 A
5600 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:8297 original size:27 final size:27
Alignment explanation
Indices: 8266--8325 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
8256 TCTATTTACA
*
8266 AAATCACATCTCAATAGGAATGGTAAC
1 AAATCACATCTCAATAGGAATGATAAC
* * *
8293 AAATCATATTTCTATAGGAATGATAAC
1 AAATCACATCTCAATAGGAATGATAAC
8320 AAATCA
1 AAATCA
8326 TCTCTATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.27
Consensus pattern (27 bp):
AAATCACATCTCAATAGGAATGATAAC
Found at i:12053 original size:27 final size:27
Alignment explanation
Indices: 12022--12089 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
12012 TCTATTTACA
12022 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
12049 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
12076 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
12090 ATTCCTACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:19181 original size:27 final size:27
Alignment explanation
Indices: 19151--19221 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
19141 AGATTGAAGG
* *
19151 AAATGACCAAAATGCCC-TCGAAGTGTA
1 AAATGACCAAAATACCCAT-AAAGTGTA
*
19178 AAATAACCAAAATACCCATAAAGTGTA
1 AAATGACCAAAATACCCATAAAGTGTA
*
19205 AAATGACCTAAAGTACC
1 AAATGACC-AAAATACC
19222 TCCAAGCCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 29 0.78
28 8 0.22
ACGTcount: A:0.48, C:0.21, G:0.13, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCATAAAGTGTA
Found at i:20392 original size:21 final size:21
Alignment explanation
Indices: 20366--20426 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
20356 GGCACATAGA
*
20366 ATTTGTCCCGAATGACCACAT
1 ATTTGTCCCGAATAACCACAT
*
20387 ATTTGTCTCGAATAACCACAT
1 ATTTGTCCCGAATAACCACAT
** *
20408 AGATGTCCCGAATTACCAC
1 ATTTGTCCCGAATAACCAC
20427 TCCTTAAGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (21 bp):
ATTTGTCCCGAATAACCACAT
Found at i:20709 original size:15 final size:15
Alignment explanation
Indices: 20678--20725 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
20668 CTTGTGATCA
* *
20678 TATAATCACATAACT
1 TATAGTCACATAGCT
** *
20693 TATTTTCGCATAGCT
1 TATAGTCACATAGCT
20708 TATAGTCACATAGCT
1 TATAGTCACATAGCT
20723 TAT
1 TAT
20726 CTCACAGGCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (15 bp):
TATAGTCACATAGCT
Found at i:21184 original size:18 final size:18
Alignment explanation
Indices: 21158--21192 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21148 AGTACTACAA
*
21158 ACACAGTATCTATACCCT
1 ACACAGTATCGATACCCT
*
21176 ACACGGTATCGATACCC
1 ACACAGTATCGATACCC
21193 ATTTTGGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.11, T:0.23
Consensus pattern (18 bp):
ACACAGTATCGATACCCT
Found at i:22880 original size:23 final size:23
Alignment explanation
Indices: 22851--22914 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
22841 CAACTCGTAT
*
22851 AAATGCACTGAAGTGCCACGTAG
1 AAATGCACTGAAGTGCCACCTAG
* *
22874 AATTGCACTGAAGTGCCGCCTAG
1 AAATGCACTGAAGTGCCACCTAG
* *
22897 AAATGCACCGTAGTGCCA
1 AAATGCACTGAAGTGCCA
22915 TATAAGATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
AAATGCACTGAAGTGCCACCTAG
Found at i:28874 original size:19 final size:20
Alignment explanation
Indices: 28850--28923 Score: 89
Period size: 19 Copynumber: 3.7 Consensus size: 20
28840 CAACGAATTT
28850 TCGCAACG-AATTTGGAAAA
1 TCGCAACGCAATTTGGAAAA
* **
28869 TCGCAACGACAATTGTAGACTA
1 TCGCAACG-CAATT-TGGAAAA
28891 TCGCAACG-AATTTGGAAAA
1 TCGCAACGCAATTTGGAAAA
28910 TCGCAACGCAATTT
1 TCGCAACGCAATTT
28924 TCAACTATCG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 20 0.44
20 9 0.20
21 4 0.09
22 12 0.27
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCAATTTGGAAAA
Found at i:28933 original size:40 final size:41
Alignment explanation
Indices: 28850--28938 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
28840 CAACGAATTT
28850 TCGCAACGAATTTGGAAAATCGCAACGACAATTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAATTGTAGACTA
*
28891 TCGCAACGAATTTGGAAAATCGCAACG-CAATTTTCA-ACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAATTGT-AGACTA
28931 TCGCAACG
1 TCGCAACG
28939 CGAATTTACG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
40 18 0.39
41 28 0.61
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAATTGTAGACTA
Found at i:28935 original size:21 final size:20
Alignment explanation
Indices: 28868--28945 Score: 70
Period size: 22 Copynumber: 3.8 Consensus size: 20
28858 AATTTGGAAA
*
28868 ATCGCAACGACAATTGTAGACT
1 ATCGCAACG-CAATTTTA-ACT
* *
28890 ATCGCAACG-AATTTGGAA-A
1 ATCGCAACGCAATTT-TAACT
28909 ATCGCAACGCAATTTTCAACT
1 ATCGCAACGCAATTTT-AACT
28930 ATCGCAACGCGAATTT
1 ATCGCAACGC-AATTT
28946 ACGATAGTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
19 9 0.20
20 12 0.26
21 11 0.24
22 14 0.30
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCAATTTTAACT
Found at i:31421 original size:50 final size:49
Alignment explanation
Indices: 31303--31427 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 49
31293 ATAGCAGTAA
* * *
31303 AGCGCGCCCCTGAACCGTGCTATACGCTGATTTGGAGCCACGTGGGTAT
1 AGCGCGCCCCTGAACCGCGCTATACGCTGATCTGGAGCCACATGGGTAT
* ** * * *
31352 AACGCGGCCCCTGCCCCGCGATATACGGTGATCTGGCGCCACATGGGTAT
1 AGCGC-GCCCCTGAACCGCGCTATACGCTGATCTGGAGCCACATGGGTAT
*
31402 AGCGCGCCCCCTGATCCGCGCTATAC
1 AGCGCG-CCCCTGAACCGCGCTATAC
31428 ATGGGTATCT
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
49 5 0.08
50 56 0.92
ACGTcount: A:0.18, C:0.34, G:0.29, T:0.19
Consensus pattern (49 bp):
AGCGCGCCCCTGAACCGCGCTATACGCTGATCTGGAGCCACATGGGTAT
Found at i:31890 original size:111 final size:111
Alignment explanation
Indices: 31696--32028 Score: 603
Period size: 111 Copynumber: 3.0 Consensus size: 111
31686 TGGAAATCAT
*
31696 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
31761 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
31807 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
31872 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
31918 ATATATTGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
31983 TAACTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
32029 TTTTTGTAAT
Statistics
Matches: 214, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 214 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:33874 original size:9 final size:9
Alignment explanation
Indices: 33862--33923 Score: 70
Period size: 9 Copynumber: 6.9 Consensus size: 9
33852 ACCTGCTCAA
*
33862 GACGACGAC
1 GACGACGAT
33871 GACGACGAT
1 GACGACGAT
*
33880 GATGACGAT
1 GACGACGAT
33889 GACGACGAT
1 GACGACGAT
*
33898 GATGACGAT
1 GACGACGAT
* * *
33907 GACAATGGT
1 GACGACGAT
33916 GACGACGA
1 GACGACGA
33924 CGACAGCGAG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.34, C:0.19, G:0.34, T:0.13
Consensus pattern (9 bp):
GACGACGAT
Found at i:33892 original size:18 final size:18
Alignment explanation
Indices: 33865--33909 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
33855 TGCTCAAGAC
*
33865 GACGACGACGACGATGAT
1 GACGATGACGACGATGAT
33883 GACGATGACGACGATGAT
1 GACGATGACGACGATGAT
33901 GACGATGAC
1 GACGATGAC
33910 AATGGTGACG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.13
Consensus pattern (18 bp):
GACGATGACGACGATGAT
Found at i:36888 original size:9 final size:9
Alignment explanation
Indices: 36862--36891 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
36852 AGTCAGGCTG
*
36862 TCAACTTGA
1 TCAACTTGT
36871 TCAACTTGT
1 TCAACTTGT
36880 TCAACTTGT
1 TCAACTTGT
36889 TCA
1 TCA
36892 GCCAGCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (9 bp):
TCAACTTGT
Found at i:37682 original size:12 final size:12
Alignment explanation
Indices: 37655--37688 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
37645 TATAAGAGAT
37655 GAGAGATGCGA-
1 GAGAGATGCGAG
37666 G-GAGATGCGAG
1 GAGAGATGCGAG
37677 GAGAGATGCGAG
1 GAGAGATGCGAG
37689 AACAGGAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.43
11 2 0.10
12 10 0.48
ACGTcount: A:0.32, C:0.09, G:0.50, T:0.09
Consensus pattern (12 bp):
GAGAGATGCGAG
Found at i:42511 original size:60 final size:59
Alignment explanation
Indices: 42440--42594 Score: 168
Period size: 59 Copynumber: 2.6 Consensus size: 59
42430 AGGATATTAC
* * * *
42440 TTTGTCGAGTCTGTCAACTATTAAAAGTTAAAACATAATCCCCTGATTATAAGACGTTGT
1 TTTGTTGAGTCTCTCAACCATTAAAAGTTAAAA-ATAATCCCCTGACTATAAGACGTTGT
* ** * *
42500 TTTGTTGAGTCTCTCGACCATTAAAAGTTAAAAATGGTCTCCTGACTATAAGATGTTGT
1 TTTGTTGAGTCTCTCAACCATTAAAAGTTAAAAATAATCCCCTGACTATAAGACGTTGT
* * *
42559 TTTATTGAGTCTCAT-GACAATTAAAAGTTACAAAAT
1 TTTGTTGAGTCTC-TCAACCATTAAAAGTTA-AAAAT
42595 TGTTGTCAGA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
59 47 0.57
60 35 0.43
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (59 bp):
TTTGTTGAGTCTCTCAACCATTAAAAGTTAAAAATAATCCCCTGACTATAAGACGTTGT
Found at i:42567 original size:59 final size:59
Alignment explanation
Indices: 42459--42594 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 59
42449 TCTGTCAACT
* * *
42459 ATTAAAAGTTAAAACATAATCCCCTGATTATAAGACGTTGTTTTGTTGAGTCTC-TCGACC
1 ATTAAAAGTTAAAA-ATAATCCCCTGACTATAAGACGTTGTTTTATTGAGTCTCAT-GACA
** * *
42519 ATTAAAAGTTAAAAATGGTCTCCTGACTATAAGATGTTGTTTTATTGAGTCTCATGACA
1 ATTAAAAGTTAAAAATAATCCCCTGACTATAAGACGTTGTTTTATTGAGTCTCATGACA
42578 ATTAAAAGTTACAAAAT
1 ATTAAAAGTTA-AAAAT
42595 TGTTGTCAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 47 0.70
60 20 0.30
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (59 bp):
ATTAAAAGTTAAAAATAATCCCCTGACTATAAGACGTTGTTTTATTGAGTCTCATGACA
Found at i:42776 original size:28 final size:28
Alignment explanation
Indices: 42732--42788 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
42722 CTGTCGTTGC
42732 TTTCAAGCACTGACTCGACGACATAATA
1 TTTCAAGCACTGACTCGACGACATAATA
* *
42760 TTTCAAGCATTGGCTCGACGACATAATA
1 TTTCAAGCACTGACTCGACGACATAATA
42788 T
1 T
42789 AAACTGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (28 bp):
TTTCAAGCACTGACTCGACGACATAATA
Found at i:43596 original size:2 final size:2
Alignment explanation
Indices: 43589--43613 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43579 ACTATACTAT
43589 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
43614 TCAATTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46136 original size:10 final size:10
Alignment explanation
Indices: 46121--46148 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
46111 TTGCATAGAA
46121 GAAAGAAGGT
1 GAAAGAAGGT
46131 GAAAGAAGGT
1 GAAAGAAGGT
46141 GAAAGAAG
1 GAAAGAAG
46149 TGATCTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.39, T:0.07
Consensus pattern (10 bp):
GAAAGAAGGT
Found at i:48512 original size:24 final size:23
Alignment explanation
Indices: 48445--48522 Score: 95
Period size: 24 Copynumber: 3.4 Consensus size: 23
48435 TGTGTTCGGT
* *
48445 TCGTTTATA-TTCACGAACAAGC
1 TCGTCTATAGTTCATGAACAAGC
* *
48467 TTGTCTATAGTTCATGAGCAAGC
1 TCGTCTATAGTTCATGAACAAGC
48490 TCGTCTATATGTTCATGAACAAGC
1 TCGTCTATA-GTTCATGAACAAGC
*
48514 TCGTTTATA
1 TCGTCTATA
48523 AGCTCATTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.15
23 19 0.40
24 21 0.45
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (23 bp):
TCGTCTATAGTTCATGAACAAGC
Found at i:48527 original size:12 final size:12
Alignment explanation
Indices: 48510--48545 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
48500 GTTCATGAAC
48510 AAGCTCGTTTAT
1 AAGCTCGTTTAT
* *
48522 AAGCTCATTTAG
1 AAGCTCGTTTAT
48534 AAGCTCGTTTAT
1 AAGCTCGTTTAT
48546 TGTTTTATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:53723 original size:2 final size:2
Alignment explanation
Indices: 53716--53751 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
53706 CCTTTTTGTC
53716 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
53752 TAAAATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65640 original size:23 final size:25
Alignment explanation
Indices: 65614--65662 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
65604 TATAATTTAT
65614 TATTTT-TTCATTTA-GTATCTAAA
1 TATTTTATTCATTTAGGTATCTAAA
65637 TATTTTCGATTCATTTAGGTATCTAA
1 TATTTT--ATTCATTTAGGTATCTAA
65663 CGTTTCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.27
26 8 0.36
27 8 0.36
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (25 bp):
TATTTTATTCATTTAGGTATCTAAA
Done.