Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003808.1 Hibiscus syriacus cultivar Beakdansim tig00008163_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: 62748
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1471 original size:30 final size:32
Alignment explanation
Indices: 1437--1506 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 32
1427 CTTGTAGCTA
* *
1437 TTCAATCATTATATTA-TGTACTTTTC-TATT
1 TTCAATCATTATATAACTATACTTTTCATATT
1467 TTCAA-C-TTATATAACCTATACTTTTCATATT
1 TTCAATCATTATATAA-CTATACTTTTCATATT
1498 TTCCAATCA
1 TT-CAATCA
1507 CAACCCAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
28 7 0.22
29 1 0.03
30 14 0.44
31 6 0.19
32 3 0.09
33 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.01, T:0.50
Consensus pattern (32 bp):
TTCAATCATTATATAACTATACTTTTCATATT
Found at i:1621 original size:25 final size:26
Alignment explanation
Indices: 1555--1625 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
1545 TTGAGTGTTC
1555 ATAATATGAACTC-AAAAGTGCCTCGT
1 ATAAT-TGAACTCGAAAAGTGCCTCGT
* * * *
1581 ATAATTGTATTTGAAAA-TGCCTTGT
1 ATAATTGAACTCGAAAAGTGCCTCGT
1606 ATAATTGAACTCG-AAAGTGC
1 ATAATTGAACTCGAAAAGTGC
1626 TAAACAGGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
24 3 0.08
25 24 0.67
26 9 0.25
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (26 bp):
ATAATTGAACTCGAAAAGTGCCTCGT
Found at i:1853 original size:24 final size:24
Alignment explanation
Indices: 1823--1985 Score: 111
Period size: 24 Copynumber: 6.8 Consensus size: 24
1813 TGCATGAATA
*
1823 CACTAATATAGGAGTACAC-ATTG
1 CACTAATATAGGAGTACACAAATG
* * * *
1846 ATATTAATACAGGAGTGCACAAATG
1 -CACTAATATAGGAGTACACAAATG
*
1871 CACTAAT-TCAGGAGTACACGAATG
1 CACTAATAT-AGGAGTACACAAATG
*
1895 CACTAATATAGGAGTACAC-ATTGG
1 CACTAATATAGGAGTACACAAAT-G
* * **
1919 TATTAATACGGGAG-AGCACAAATG
1 CACTAATATAGGAGTA-CACAAATG
* *
1943 CACTAAT-TCAGGAGTGCACGAATG
1 CACTAATAT-AGGAGTACACAAATG
* *
1967 CATTAATATAGGAGCACAC
1 CACTAATATAGGAGTACAC
1986 TTTGGTACTA
Statistics
Matches: 105, Mismatches: 25, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
23 3 0.03
24 95 0.90
25 7 0.07
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (24 bp):
CACTAATATAGGAGTACACAAATG
Found at i:1905 original size:72 final size:72
Alignment explanation
Indices: 1778--2000 Score: 302
Period size: 72 Copynumber: 3.1 Consensus size: 72
1768 TAATGGTACA
* * ** * * *
1778 AATACATGAGTACACAAATTTACTAGAATCAGGAGTGCATGAATACACTAATATAGGAGTACACA
1 AATACAGGAGTGCACAAATGCACTA-ATTCAGGAGTGCACGAATGCACTAATATAGGAGTACACA
*
1843 TTGATATT
65 TTGGTATT
*
1851 AATACAGGAGTGCACAAATGCACTAATTCAGGAGTACACGAATGCACTAATATAGGAGTACACAT
1 AATACAGGAGTGCACAAATGCACTAATTCAGGAGTGCACGAATGCACTAATATAGGAGTACACAT
1916 TGGTATT
66 TGGTATT
* * * * *
1923 AATACGGGAGAGCACAAATGCACTAATTCAGGAGTGCACGAATGCATTAATATAGGAGCACACTT
1 AATACAGGAGTGCACAAATGCACTAATTCAGGAGTGCACGAATGCACTAATATAGGAGTACACAT
*
1988 TGGTACT
66 TGGTATT
1995 AATACA
1 AATACA
2001 AGATTGTTCA
Statistics
Matches: 133, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 112 0.84
73 21 0.16
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (72 bp):
AATACAGGAGTGCACAAATGCACTAATTCAGGAGTGCACGAATGCACTAATATAGGAGTACACAT
TGGTATT
Found at i:1974 original size:48 final size:47
Alignment explanation
Indices: 1778--1985 Score: 134
Period size: 48 Copynumber: 4.3 Consensus size: 47
1768 TAATGGTACA
* ** * * * *
1778 AATACATGAGTACACAAATTTACTAGAATCAGGAGTGCATGAATACACT
1 AATACAGGAGTACACAAATGCACTA-ATTCAGGAGTGCA-CAATGCATT
* * * * * *
1827 AATATAGGAGTACAC-ATTGATATTAATACAGGAGTGCACAAATGCACT
1 AATACAGGAGTACACAAATG-CACTAATTCAGGAGTGCAC-AATGCATT
* * * * *
1875 AATTCAGGAGTACACGAATGCACTAATAT-AGGAGTACACATTGGTATT
1 AATACAGGAGTACACAAATGCACTAAT-TCAGGAGTGCACAAT-GCATT
*
1923 AATACGGGAG-AGCACAAATGCACTAATTCAGGAGTGCACGAATGCATT
1 AATACAGGAGTA-CACAAATGCACTAATTCAGGAGTGCAC-AATGCATT
* *
1971 AATATAGGAGCACAC
1 AATACAGGAGTACAC
1986 TTTGGTACTA
Statistics
Matches: 123, Mismatches: 27, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
47 4 0.03
48 96 0.78
49 23 0.19
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.23
Consensus pattern (47 bp):
AATACAGGAGTACACAAATGCACTAATTCAGGAGTGCACAATGCATT
Found at i:7757 original size:26 final size:26
Alignment explanation
Indices: 7728--7780 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
7718 TAAGAAAATG
7728 TTGTGAACACTTAGAGGAAAGATTGA
1 TTGTGAACACTTAGAGGAAAGATTGA
*
7754 TTGTGAACCCTTAGAGGAAAGATTGA
1 TTGTGAACACTTAGAGGAAAGATTGA
7780 T
1 T
7781 CTTTGTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.28
Consensus pattern (26 bp):
TTGTGAACACTTAGAGGAAAGATTGA
Found at i:15300 original size:28 final size:28
Alignment explanation
Indices: 15259--15315 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
15249 AACAAAATCA
* * *
15259 TGCTTCACTAACCGGTTGCTTTGAATTT
1 TGCTCCACCAACCGGCTGCTTTGAATTT
15287 TGCTCCACCAACCGGCTGCTTTGAATTT
1 TGCTCCACCAACCGGCTGCTTTGAATTT
15315 T
1 T
15316 CAACAAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.39
Consensus pattern (28 bp):
TGCTCCACCAACCGGCTGCTTTGAATTT
Found at i:18136 original size:13 final size:13
Alignment explanation
Indices: 18118--18167 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
18108 AGATACAAAT
18118 ATGCAAATACCAA
1 ATGCAAATACCAA
18131 ATGCAAATA-C--
1 ATGCAAATACCAA
18141 --GCAAATACCAA
1 ATGCAAATACCAA
18152 ATGCAAATACGCAA
1 ATGCAAATAC-CAA
18166 AT
1 AT
18168 ACAAGATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
12 1 0.03
13 17 0.55
14 5 0.16
ACGTcount: A:0.52, C:0.22, G:0.10, T:0.16
Consensus pattern (13 bp):
ATGCAAATACCAA
Found at i:18137 original size:21 final size:21
Alignment explanation
Indices: 18113--18169 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
18103 TACAAAGATA
*
18113 CAAATATGCAAATACCAAATG
1 CAAATACGCAAATACCAAATG
18134 CAAATACGCAAATACCAAATG
1 CAAATACGCAAATACCAAATG
18155 CAAATACGCAAATAC
1 CAAATACGCAAATAC
18170 AAGATGTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.53, C:0.23, G:0.09, T:0.16
Consensus pattern (21 bp):
CAAATACGCAAATACCAAATG
Found at i:18169 original size:8 final size:8
Alignment explanation
Indices: 18113--18169 Score: 63
Period size: 8 Copynumber: 7.9 Consensus size: 8
18103 TACAAAGATA
*
18113 CAAATATG
1 CAAATACG
18121 CAAATAC-
1 CAAATACG
18128 CAAAT--G
1 CAAATACG
18134 CAAATACG
1 CAAATACG
18142 CAAATAC-
1 CAAATACG
18149 CAAAT--G
1 CAAATACG
18155 CAAATACG
1 CAAATACG
18163 CAAATAC
1 CAAATAC
18170 AAGATGTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
6 10 0.24
7 10 0.24
8 22 0.52
ACGTcount: A:0.53, C:0.23, G:0.09, T:0.16
Consensus pattern (8 bp):
CAAATACG
Found at i:20793 original size:24 final size:24
Alignment explanation
Indices: 20765--20812 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
20755 TAGGTATCTC
20765 TTTCACTCTCTTTTTTTC-TCCCCT
1 TTTCACTCT-TTTTTTTCTTCCCCT
20789 TTTCACTCTTTTTTTTCTTCCCCT
1 TTTCACTCTTTTTTTTCTTCCCCT
20813 CAAATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTCACTCTTTTTTTTCTTCCCCT
Found at i:25722 original size:65 final size:65
Alignment explanation
Indices: 25618--25798 Score: 220
Period size: 65 Copynumber: 2.8 Consensus size: 65
25608 GCACCAATAT
* * * * *
25618 AGATCACTCATATGACTCATGTACCTTTATTGTACATGAGGTGGAGTGATAATTGAATACTACAC
1 AGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTAAATACTACAA
* *
25683 AGATCACTCATATGACTCATGTACCTTGGTGGTGCATGAGGTGGAGTGATAATTAAATACTGCAA
1 AGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTAAATACTACAA
* * ** * *
25748 AGAACACTCA-ACGAGACTTGTGTACCTTTGTGGTGCATAAGATGGAGTGAT
1 AGATCACTCATA--TGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGAT
25799 TATGTGATAC
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 1 0.01
65 67 0.67
66 32 0.32
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (65 bp):
AGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTAAATACTACAA
Found at i:26008 original size:17 final size:17
Alignment explanation
Indices: 25988--26034 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
25978 TAGATGCAAA
*
25988 ACAATAAAAGATATAGT
1 ACAATAAAAGAAATAGT
*
26005 ACAATAAGAGAAATAGT
1 ACAATAAAAGAAATAGT
**
26022 GTAATAAAAGAAA
1 ACAATAAAAGAAA
26035 GGATGTAGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.04, G:0.15, T:0.19
Consensus pattern (17 bp):
ACAATAAAAGAAATAGT
Found at i:35730 original size:20 final size:19
Alignment explanation
Indices: 35697--35743 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 19
35687 AATGTTTGAG
35697 TAAGTTTTTGTTTTTCCAC
1 TAAGTTTTTGTTTTTCCAC
35716 TAAGTTTTTGTTTTTCCAC
1 TAAGTTTTTGTTTTTCCAC
35735 TAAAGTTTT
1 T-AAGTTTT
35744 AAATATAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (19 bp):
TAAGTTTTTGTTTTTCCAC
Found at i:36484 original size:20 final size:21
Alignment explanation
Indices: 36459--36504 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
36449 TCTTGCAACT
* *
36459 ATCGAATTATTTGA-AAAAGG
1 ATCGAACTATTTCACAAAAGG
36479 ATCGAACTATTTCACAAAAGG
1 ATCGAACTATTTCACAAAAGG
36500 ATCGA
1 ATCGA
36505 TCCCTTGTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGAACTATTTCACAAAAGG
Found at i:40257 original size:23 final size:23
Alignment explanation
Indices: 40227--40272 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
40217 TGAAGGGATG
*
40227 TAAACGAACATAAATGAGCACAA
1 TAAACGAACATAAATGAACACAA
*
40250 TAAACGAACGTAAATGAACACAA
1 TAAACGAACATAAATGAACACAA
40273 ACGAACAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (23 bp):
TAAACGAACATAAATGAACACAA
Found at i:40527 original size:10 final size:10
Alignment explanation
Indices: 40512--40553 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
40502 AAATGTACAC
40512 ACATAAAAGA
1 ACATAAAAGA
*
40522 ACATAAATA-C
1 ACATAAA-AGA
40532 ACATAAAAGA
1 ACATAAAAGA
*
40542 ACATAAACGA
1 ACATAAAAGA
40552 AC
1 AC
40554 GGAAATAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 1 0.04
10 25 0.93
11 1 0.04
ACGTcount: A:0.64, C:0.17, G:0.07, T:0.12
Consensus pattern (10 bp):
ACATAAAAGA
Found at i:40533 original size:20 final size:20
Alignment explanation
Indices: 40510--40548 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40500 ATAAATGTAC
40510 ACACATAAAAGAACATAAAT
1 ACACATAAAAGAACATAAAT
40530 ACACATAAAAGAACATAAA
1 ACACATAAAAGAACATAAA
40549 CGAACGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.15, G:0.05, T:0.13
Consensus pattern (20 bp):
ACACATAAAAGAACATAAAT
Found at i:44136 original size:131 final size:131
Alignment explanation
Indices: 43964--44330 Score: 476
Period size: 131 Copynumber: 2.8 Consensus size: 131
43954 TAATTCTAAG
* * * *
43964 AGAGAAAATGATAATATCTTATTATTTCCAATCGAGAATAAATGACCTCTCATGTCTTAAAACAA
1 AGAGAAAAAGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGTCTTAAAGCAA
* * * *
44029 TTATTTATTACTCCAATAGAAATGAAGAGATGTCAGTATT-TCGTCTTAAAATTCAATATTGATT
66 TCATTTATTACTCCAATAGAAATGAAGAGATATCACTATTCT-GTCTTAAAAATCAATATTGATT
44093 CA
130 CA
* * *
44095 AGTGAAAAAGATAATATCTAATGATTTCTAATCGATAATAAATGACCTCT--TGTTCCTTAAAGC
1 AGAGAAAAAGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATG-T-CTTAAAGC
*
44158 AGTCATTTATTACTCCAATTA-AAATGAAGAGATATCACTATTCTGTCTTAAAAATCAATATTGA
64 AATCATTTATTACTCCAA-TAGAAATGAAGAGATATCACTATTCTGTCTTAAAAATCAATATTGA
*
44222 TTCG
128 TTCA
* *
44226 AGAGAAAATA-ATAATATCTAATTATTTCCAATCGATAATGAATGACCTCTCATGCCTTAAAGCA
1 AGAGAAAA-AGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGTCTTAAAGCA
** *
44290 ATCATTTATTACTCCAACCGAAATGAA-ATGATATTACTATT
65 ATCATTTATTACTCCAATAGAAATGAAGA-GATATCACTATT
44331 TTCAATATTG
Statistics
Matches: 205, Mismatches: 22, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
129 2 0.01
130 2 0.01
131 195 0.95
132 4 0.02
133 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (131 bp):
AGAGAAAAAGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGTCTTAAAGCAA
TCATTTATTACTCCAATAGAAATGAAGAGATATCACTATTCTGTCTTAAAAATCAATATTGATTC
A
Found at i:44985 original size:33 final size:35
Alignment explanation
Indices: 44930--45000 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 35
44920 GCATGGGACA
*
44930 AAATTAAAATAAAATAAAATTTTATGTCAAAAT-T
1 AAATTAAAATAAAATAAAATTTTAGGTCAAAATGT
* *
44964 AAATT-AAATAAAA-ATAGATTTTAGGTCGAAATGT
1 AAATTAAAATAAAATA-AAATTTTAGGTCAAAATGT
44998 AAA
1 AAA
45001 CATGCTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.03
33 22 0.69
34 9 0.28
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.32
Consensus pattern (35 bp):
AAATTAAAATAAAATAAAATTTTAGGTCAAAATGT
Found at i:48303 original size:109 final size:108
Alignment explanation
Indices: 48113--48357 Score: 289
Period size: 109 Copynumber: 2.3 Consensus size: 108
48103 GTCACTACAT
* * * * *
48113 ATGACCAAAGTGTAAAAA-ATGATAAACTTATAGGGACTAAACAATAAATAGACCAAAAATTATA
1 ATGACCAAAATGTAAAAACACGCTAAACTTAGAGGGACTAAACAATAAATAGACCAAAAATTACA
* *
48177 TAACATGCAAAGAAAAGGGAAAATAATAGTTTTAGT-CCTCAAAG
66 TAACA-GCAAAGAAAAGGGAAAATAACAGATTTAGTCCCT-AAAG
* * * * *
48221 ATGACCAAAATGCAAAAACACGCTAAAGTTAGAGGGACTAAATAGTGAATAGACCAAAAATTACA
1 ATGACCAAAATGTAAAAACACGCTAAACTTAGAGGGACTAAACAATAAATAGACCAAAAATTACA
* *
48286 TAACA-CATAAGGAAAAGGGAAAATAACAGATTTGGTCCCTACAG
66 TAACAGCA-AA-GAAAAGGGAAAATAACAGATTTAGTCCCTAAAG
* *
48330 GTGACCAAAATGTAAAAGCACGCTAAAC
1 ATGACCAAAATGTAAAAACACGCTAAAC
48358 CTAAGGGGTC
Statistics
Matches: 115, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
107 2 0.02
108 18 0.16
109 92 0.80
110 3 0.03
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (108 bp):
ATGACCAAAATGTAAAAACACGCTAAACTTAGAGGGACTAAACAATAAATAGACCAAAAATTACA
TAACAGCAAAGAAAAGGGAAAATAACAGATTTAGTCCCTAAAG
Found at i:49415 original size:3 final size:3
Alignment explanation
Indices: 49407--49454 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
49397 TTGGTTTGTA
* *
49407 AAT AAT AAT ATT TAT AAT -AT AA- ATAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
49451 AAT A
1 AAT A
49455 TAAGGGTGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 3 0.08
3 34 0.89
4 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:49795 original size:10 final size:10
Alignment explanation
Indices: 49789--49815 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49779 ATGTATACTC
49789 TTGTATATTT
1 TTGTATATTT
49799 TTGTATATTT
1 TTGTATATTT
49809 TTGTATA
1 TTGTATA
49816 AACTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (10 bp):
TTGTATATTT
Found at i:49972 original size:25 final size:26
Alignment explanation
Indices: 49938--49995 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
49928 AATATTTATT
*
49938 TTGATAAAAATAATTGAAGG-ATTTA
1 TTGAAAAAAATAATTGAAGGAATTTA
* * *
49963 TTGAAAAAAATATTTGAGGGAATTTT
1 TTGAAAAAAATAATTGAAGGAATTTA
49989 TTGAAAA
1 TTGAAAA
49996 CTTTAACCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 17 0.61
26 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (26 bp):
TTGAAAAAAATAATTGAAGGAATTTA
Found at i:52935 original size:3 final size:3
Alignment explanation
Indices: 52929--53010 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
52919 TATGATGATG
52929 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
52977 ATA ATA ATA ATA ATA ATA ATA ATA A-A GTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
53011 TTGTCGATTG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 1 0.01
3 75 0.99
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53831 original size:60 final size:59
Alignment explanation
Indices: 53726--53897 Score: 183
Period size: 60 Copynumber: 2.9 Consensus size: 59
53716 TATATGCATG
* *
53726 ATTTA-GGATGAAATTGGAATTTTCAAAAAGTTTAGGGACTAATTTAAAAT-AAAGGTT-AT-
1 ATTTAGGGATGAAATT-GAATATTC-AAAAGTTTAGAGACTAATTTAAAATGAAA--TTCATC
* * *
53785 AGTTTGGGGATGAAATTGAAATATTCAAAAGTTT-GAAGACTAATTTAGAATGATATTCATC
1 A-TTTAGGGATGAAATTG-AATATTCAAAAGTTTAG-AGACTAATTTAAAATGAAATTCATC
*
53846 ATTTAGGGATGAAATTTGAATATTTAAAAGTTTAGAGACTAATTTAAAATGA
1 ATTTAGGGATGAAA-TTGAATATTCAAAAGTTTAGAGACTAATTTAAAATGA
53898 CTATTATACT
Statistics
Matches: 96, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
59 4 0.04
60 69 0.72
61 23 0.24
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (59 bp):
ATTTAGGGATGAAATTGAATATTCAAAAGTTTAGAGACTAATTTAAAATGAAATTCATC
Found at i:57107 original size:21 final size:21
Alignment explanation
Indices: 57083--57126 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
57073 TCTATTTTTG
57083 TTTAGATATATTGATCGTA-AA
1 TTTAGATA-ATTGATCGTATAA
**
57104 TTTATTTAATTGATCGTATAA
1 TTTAGATAATTGATCGTATAA
57125 TT
1 TT
57127 ATTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (21 bp):
TTTAGATAATTGATCGTATAA
Found at i:62213 original size:9 final size:9
Alignment explanation
Indices: 62199--62224 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
62189 GAACTCTAAA
62199 TGAAGAAAG
1 TGAAGAAAG
62208 TGAAGAAAG
1 TGAAGAAAG
62217 TGAAGAAA
1 TGAAGAAA
62225 CAAAGAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.12
Consensus pattern (9 bp):
TGAAGAAAG
Done.