Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006362.1 Hibiscus syriacus cultivar Beakdansim tig00015261_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: 71628
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Found at i:1134 original size:64 final size:62
Alignment explanation
Indices: 1001--1161 Score: 211
Period size: 64 Copynumber: 2.6 Consensus size: 62
991 TTGTATGAAT
** ** *
1001 GTGCATCGATGCATTGGTAGTGCATCGATGC-T-CTTTTAAATAAGACATCGAATGCAATTC
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAAATAAGACAACGAATGCAATTC
*
1061 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAA-ACAACGAATGCAATTG
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAA-A-T-AAGACAACGAATGCAATTC
*
1125 GTGCATCGATGCATAAGGAGTGCATCGATGCATCCCA
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCA
1162 GCAATAATAC
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
60 29 0.33
61 1 0.01
62 5 0.06
63 1 0.01
64 51 0.57
65 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (62 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAAATAAGACAACGAATGCAATTC
Found at i:1525 original size:12 final size:12
Alignment explanation
Indices: 1507--1542 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1497 TATATATGTT
1507 CATGTGATATGA
1 CATGTGATATGA
*
1519 TATGTGATATGA
1 CATGTGATATGA
*
1531 CCTGTGATATGA
1 CATGTGATATGA
1543 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:1619 original size:29 final size:29
Alignment explanation
Indices: 1558--1659 Score: 163
Period size: 29 Copynumber: 3.6 Consensus size: 29
1548 TGATATGAAG
*
1558 TGACATGAGCTACATGAT-GCAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
1586 TGACATGAGCTATATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
1615 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
1644 TGATATGAG-TACATGA
1 TGACATGAGCTACATGA
1660 GCATATGAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 24 0.35
29 45 0.65
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.21
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:4149 original size:31 final size:31
Alignment explanation
Indices: 4111--4222 Score: 206
Period size: 31 Copynumber: 3.6 Consensus size: 31
4101 TACATAGATT
*
4111 CCGAAGAACCTAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
4142 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
4173 CCAAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
4204 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
4223 CCTCGACCCT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:4986 original size:64 final size:64
Alignment explanation
Indices: 4878--5101 Score: 240
Period size: 64 Copynumber: 3.5 Consensus size: 64
4868 TAATGAAGGT
* * * **
4878 ATGCATCGATGCACTACTGATGCATC-AGTGCATAAAATGTATTCGATGTTGT-ATTATTGCTGA
1 ATGCATCGATGCACTACTTATGCATCGA-TGCATAAATTGCATTCGATGTT-TCATTATTAATGA
4941 G
64 G
* ** *
4942 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
* * * *
5006 ATGCATCGATGCACTACTTATGCATCGATTCATGAATTGCATTCGATGTCTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCATTATTAATGAG
** *
5069 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
5102 CATTCAAACA
Statistics
Matches: 136, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
63 3 0.02
64 127 0.93
65 6 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
Found at i:7916 original size:31 final size:31
Alignment explanation
Indices: 7892--8002 Score: 195
Period size: 31 Copynumber: 3.6 Consensus size: 31
7882 CCATAGATTT
* *
7892 CGAAGAACCTAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
7923 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
*
7954 CGAAGAACATAGGTAAACTGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
7985 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
8003 CCTCGACCCT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:8769 original size:64 final size:64
Alignment explanation
Indices: 8661--8884 Score: 229
Period size: 64 Copynumber: 3.5 Consensus size: 64
8651 TAATGAAGGT
* * * * * **
8661 ATGCATCAATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTGTTGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTT-TCATTATTAATGAG
* ** *
8725 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
* * * * *
8789 ATGCATCGATACACTACTTATGCATCGATTCATGAATTGCATTCGATGTCTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCATTATTAATGAG
** *
8852 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
8885 CATTCAAACA
Statistics
Matches: 133, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
63 3 0.02
64 125 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
Found at i:11694 original size:31 final size:31
Alignment explanation
Indices: 11656--11811 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
11646 CCCGAAGGAC
* *
11656 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
11687 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
11718 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
11749 CAGTCCATATGTCCCGAAGAACTTAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
11780 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
11811 C
1 C
11812 CCTCGACCCT
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:12580 original size:64 final size:64
Alignment explanation
Indices: 12468--12691 Score: 247
Period size: 64 Copynumber: 3.5 Consensus size: 64
12458 TAATGAAGGT
* * * * * **
12468 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTTGATGTTGT-ATTATTGTTGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTT-TCATTATTAATGAG
* ** *
12532 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
* * *
12596 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCATTATTAATGAG
** *
12659 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
12692 CATTCAAACA
Statistics
Matches: 137, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 3 0.02
64 129 0.94
65 5 0.04
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
Found at i:13860 original size:16 final size:17
Alignment explanation
Indices: 13835--13868 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13825 ATGAGGTGTC
13835 ACATTAACTTTT-CAAA
1 ACATTAACTTTTACAAA
*
13851 ACATTTACTTTTACAAA
1 ACATTAACTTTTACAAA
13868 A
1 A
13869 TCTCATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (17 bp):
ACATTAACTTTTACAAA
Found at i:14510 original size:21 final size:21
Alignment explanation
Indices: 14477--14554 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
14467 ACCACTCCTT
* *
14477 AAGGATCACATATATATTCCA
1 AAGGACCACATATATGTTCCA
* *
14498 AAGGACCAAATATGTGTTCCA
1 AAGGACCACATATATGTTCCA
* *
14519 AAGAACCACATATATGTTCCC
1 AAGGACCACATATATGTTCCA
**
14540 AAGGATTACATATAT
1 AAGGACCACATATAT
14555 ATCCCGAATG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:21647 original size:21 final size:21
Alignment explanation
Indices: 21600--21648 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
21590 TTTTGAAGAG
*
21600 CCACATATATGTTCCCAAGGA
1 CCACATATATGATCCCAAGGA
**
21621 TTACATATAT-ATCCCGAAGGA
1 CCACATATATGATCCC-AAGGA
21642 CCACATA
1 CCACATA
21649 GAACCCTCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (21 bp):
CCACATATATGATCCCAAGGA
Found at i:28480 original size:10 final size:9
Alignment explanation
Indices: 28455--28490 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
28445 GAGGAAAAAG
28455 TGACCGGTT
1 TGACCGGTT
*
28464 TGGCCGGTTT
1 TGACCGG-TT
28474 TGACCGGTT
1 TGACCGGTT
28483 TGACCGGT
1 TGACCGGT
28491 CACAACTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.08, C:0.22, G:0.36, T:0.33
Consensus pattern (9 bp):
TGACCGGTT
Found at i:28521 original size:18 final size:18
Alignment explanation
Indices: 28498--28533 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28488 GGTCACAACT
28498 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
28516 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
28534 GTTGACCCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.50, G:0.22, T:0.11
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:28537 original size:7 final size:7
Alignment explanation
Indices: 28525--28556 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
28515 CCGACCCGAC
28525 CCGTTGA
1 CCGTTGA
28532 CCGTTGA
1 CCGTTGA
28539 CCCGTTGA
1 -CCGTTGA
28547 CCGTTGA
1 CCGTTGA
28554 CCG
1 CCG
28557 GCGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:28542 original size:15 final size:15
Alignment explanation
Indices: 28522--28565 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 15
28512 GACCCGACCC
28522 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
28537 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
28552 GACCGGCGTTGACC
1 GACC--CGTTGACC
28566 ACTGTTGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 19 0.70
17 8 0.30
ACGTcount: A:0.14, C:0.34, G:0.30, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:29894 original size:18 final size:18
Alignment explanation
Indices: 29868--29903 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29858 TCGAAAGGAC
*
29868 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
29886 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
29904 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:31127 original size:24 final size:24
Alignment explanation
Indices: 31031--31139 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
31021 GAATATTTTA
* *
31031 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
31055 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
31079 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
31103 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
31127 TTTGATTTCTGAT
1 TCTGATATCTGAT
31140 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:31307 original size:2 final size:2
Alignment explanation
Indices: 31300--31338 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
31290 CGGATGGGGG
31300 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
31339 GTTTTAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32558 original size:36 final size:36
Alignment explanation
Indices: 32511--32582 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
32501 TTATGTAAAC
32511 AACTTGGAAAAGGAAAAATGCAAGTAGAATATTTTT
1 AACTTGGAAAAGGAAAAATGCAAGTAGAATATTTTT
32547 AACTTGGAAAAGGAAAAATGCAAGTAGAATATTTTT
1 AACTTGGAAAAGGAAAAATGCAAGTAGAATATTTTT
32583 TAGCTACCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (36 bp):
AACTTGGAAAAGGAAAAATGCAAGTAGAATATTTTT
Found at i:33029 original size:27 final size:27
Alignment explanation
Indices: 32998--33057 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
32988 ACTACAAAGG
*
32998 ATTTATGATTTATTGACTATTTTAAGA
1 ATTTATGATTTATTGACTATTGTAAGA
* *
33025 ATTTATGGTTTATTGATTATTGTAAGA
1 ATTTATGATTTATTGACTATTGTAAGA
33052 ATTTAT
1 ATTTAT
33058 AGTTTTGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (27 bp):
ATTTATGATTTATTGACTATTGTAAGA
Found at i:34995 original size:23 final size:23
Alignment explanation
Indices: 34963--35055 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
34953 AGTCGAGGGT
34963 TCTATGTGGTCATTCGGGACAAA
1 TCTATGTGGTCATTCGGGACAAA
* ** *
34986 TCTGTGTGGTTTTTTGGGACAAA
1 TCTATGTGGTCATTCGGGACAAA
* *
35009 CCTATGTGGTCATTCGGGATAAA
1 TCTATGTGGTCATTCGGGACAAA
* * *
35032 ACTATATGGTCCTTCGGGACAAA
1 TCTATGTGGTCATTCGGGACAAA
35055 T
1 T
35056 ATGTGGCACT
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (23 bp):
TCTATGTGGTCATTCGGGACAAA
Found at i:35051 original size:46 final size:45
Alignment explanation
Indices: 34964--35061 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 45
34954 GTCGAGGGTT
* * * ** *
34964 CTATGTGGTCATTCGGGACAAATCTGTGTGGTTTTTTGGGACAAA
1 CTATGTGGTCATTCGGGACAAAACTATATGGTCCTTCGGGACAAA
*
35009 CCTATGTGGTCATTCGGGATAAAACTATATGGTCCTTCGGGACAAA
1 -CTATGTGGTCATTCGGGACAAAACTATATGGTCCTTCGGGACAAA
35055 -TATGTGG
1 CTATGTGG
35062 CACTTCAGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 7 0.16
46 38 0.84
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (45 bp):
CTATGTGGTCATTCGGGACAAAACTATATGGTCCTTCGGGACAAA
Found at i:37054 original size:7 final size:7
Alignment explanation
Indices: 37042--37086 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
37032 TTAGATCTTG
37042 AAATTAT
1 AAATTAT
37049 AAATTAT
1 AAATTAT
*
37056 AAAGTAT
1 AAATTAT
37063 AAATTAT
1 AAATTAT
*
37070 AAATTGT
1 AAATTAT
*
37077 AAATTGT
1 AAATTAT
37084 AAA
1 AAA
37087 ATTTACAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (7 bp):
AAATTAT
Found at i:37895 original size:21 final size:21
Alignment explanation
Indices: 37845--37897 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
37835 ATGTATAATT
37845 ATAAATTAGTTTAAAATTTAAAG
1 ATAAATTA-TTTAAAA-TTAAAG
37868 ATAAATTATTTAAAA-TAAAGG
1 ATAAATTATTTAAAATTAAA-G
*
37889 GTAAATTAT
1 ATAAATTAT
37898 ACCAGTGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 4 0.14
21 9 0.32
22 7 0.25
23 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (21 bp):
ATAAATTATTTAAAATTAAAG
Found at i:41411 original size:11 final size:11
Alignment explanation
Indices: 41395--41419 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41385 TTGAAACTCT
41395 TTTTAAAATTA
1 TTTTAAAATTA
41406 TTTTAAAATTA
1 TTTTAAAATTA
41417 TTT
1 TTT
41420 CCAGTATATG
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:41718 original size:21 final size:20
Alignment explanation
Indices: 41676--41721 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
41666 CCCCCTTTAG
**
41676 TTAAATAAAAAAATTATTAA
1 TTAAATAAAAAAATTAAAAA
*
41696 TTAAATCAAAAAAGTTAAAAA
1 TTAAAT-AAAAAAATTAAAAA
41717 TTAAA
1 TTAAA
41722 CTATATACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
TTAAATAAAAAAATTAAAAA
Found at i:48598 original size:31 final size:31
Alignment explanation
Indices: 48563--48626 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
48553 TAATGACTAA
*
48563 ACATACT-ATGCATTATCTAAATGCGAACCTG
1 ACATACTGA-GCATTATCTAAATGCAAACCTG
*
48594 ACATACTGAGCATTATCTGAATGCAAACCTG
1 ACATACTGAGCATTATCTAAATGCAAACCTG
48625 AC
1 AC
48627 TAGTATCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (31 bp):
ACATACTGAGCATTATCTAAATGCAAACCTG
Found at i:49940 original size:32 final size:32
Alignment explanation
Indices: 49900--49978 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 32
49890 TGGGTACTCT
* *
49900 AACAATATTGATATTAGTGTCGGTATT-CTAAG
1 AACAATATTGATATTAGTATCGATATTAC-AAG
*
49932 AACAATATTGATATGAGTATCGATATTACAAG
1 AACAATATTGATATTAGTATCGATATTACAAG
*
49964 AACAATATCGATATT
1 AACAATATTGATATT
49979 GTCACCTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
32 40 0.98
33 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (32 bp):
AACAATATTGATATTAGTATCGATATTACAAG
Found at i:62014 original size:23 final size:22
Alignment explanation
Indices: 61957--62037 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 22
61947 AGAACCTCCA
* * *
61957 GGGGTATCGATTCCCCTAC-AG
1 GGGGAATCGGTTCCCCTTCAAG
61978 GGGGAATCGG-TCCCCTTCAAAG
1 GGGGAATCGGTTCCCCTTC-AAG
62000 GGGGAATCGGTTCCCCTTCAAG
1 GGGGAATCGGTTCCCCTTCAAG
* *
62022 GGAGGTATCGATTCCC
1 GG-GGAATCGGTTCCC
62038 TCTGCACCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
20 7 0.14
21 8 0.16
22 17 0.33
23 19 0.37
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (22 bp):
GGGGAATCGGTTCCCCTTCAAG
Found at i:62038 original size:22 final size:21
Alignment explanation
Indices: 61957--62038 Score: 67
Period size: 22 Copynumber: 3.8 Consensus size: 21
61947 AGAACCTCCA
* *
61957 GGGGTATCGATTCCCCT-ACAG
1 GGGGAATCGATTCCCTTCA-AG
* *
61978 GGGGAATCGGTCCCCTTCAAAG
1 GGGGAATCGATTCCCTTC-AAG
*
62000 GGGGAATCGGTTCCCCTTCAAG
1 GGGGAATCGATT-CCCTTCAAG
*
62022 GGAGGTATCGATTCCCT
1 GG-GGAATCGATTCCCT
62039 CTGCACCAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 13 0.26
22 22 0.44
23 15 0.30
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.23
Consensus pattern (21 bp):
GGGGAATCGATTCCCTTCAAG
Found at i:69732 original size:4 final size:5
Alignment explanation
Indices: 69726--69782 Score: 53
Period size: 6 Copynumber: 10.6 Consensus size: 5
69716 TCGTCGAATT
*
69726 TATT- TATTA TATTA TATTA TATATA TATATA TATATA TATATA TATAA
1 TATTA TATTA TATTA TATTA TAT-TA TAT-TA TAT-TA TAT-TA TATTA
69774 TATATA TAT
1 TAT-TA TAT
69783 ATAATAAGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
4 4 0.08
5 17 0.35
6 27 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TATTA
Found at i:69750 original size:2 final size:2
Alignment explanation
Indices: 69733--69785 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
69723 ATTTATTTAT
69733 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69773 -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
69786 ATAAGCATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69878 original size:31 final size:32
Alignment explanation
Indices: 69796--69921 Score: 100
Period size: 31 Copynumber: 4.0 Consensus size: 32
69786 ATAAGCATAT
* *
69796 TTTTGAAAATA-TTTT-AAAA-A-ATATATAA
1 TTTTGAAAACAGTTTTGAAAATATATATATAG
* * * *
69824 TTTTAGAAAGCAGTTTTTCGAAAATATATTTTTAT
1 TTTT-GAAAACAG-TTTT-GAAAATATATATATAG
*
69859 TTTTGAAAAC-GTTTTGAAAACATATATATAG
1 TTTTGAAAACAGTTTTGAAAATATATATATAG
* *
69890 TTTTGAAAACATTTTTTAAAATATATAATATA
1 TTTTGAAAACAGTTTTGAAAATATAT-ATATA
69922 TAGTGTTTGA
Statistics
Matches: 76, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
28 4 0.05
29 5 0.07
31 26 0.34
32 16 0.21
33 10 0.13
34 6 0.08
35 9 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (32 bp):
TTTTGAAAACAGTTTTGAAAATATATATATAG
Found at i:69976 original size:36 final size:33
Alignment explanation
Indices: 69882--70093 Score: 99
Period size: 35 Copynumber: 6.5 Consensus size: 33
69872 TTGAAAACAT
69882 ATATATAGTTTTGAAAACATTTTTTAAAATATATA
1 ATATATAGTTTT-AAAAC-TTTTTTAAAATATATA
****
69917 ATATATAGTGTTTGATTTTTTTTTTAAATATATATATA
1 ATATATAGT-TTT-AAAACTTTTTT-AA-A-ATATATA
* *
69955 ATATATAGTTTTTAAACTTTTTTTGAAAACATAT-
1 ATATATAGTTTTAAAAC-TTTTTT-AAAATATATA
* * * *
69989 ATATATGGTTTGAAAAC-------ATACATATA
1 ATATATAGTTTTAAAACTTTTTTAAAATATATA
* *
70015 ATATATAGTTTTTAAAA-TATTTTGAAATATAT-
1 ATATATAG-TTTTAAAACTTTTTTAAAATATATA
* *
70047 ATATA-ATTTTTGAAAACATTTTT-AAATATATA
1 ATATATAGTTTT-AAAACTTTTTTAAAATATATA
*
70079 AT-TATAGTTTGAAAA
1 ATATATAGTTTTAAAA
70094 TGTTTTTGAA
Statistics
Matches: 135, Mismatches: 24, Indels: 40
0.68 0.12 0.20
Matches are distributed among these distances:
25 7 0.05
26 7 0.05
27 7 0.05
30 4 0.03
31 19 0.14
32 15 0.11
33 6 0.04
34 14 0.10
35 20 0.15
36 8 0.06
37 12 0.09
38 16 0.12
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (33 bp):
ATATATAGTTTTAAAACTTTTTTAAAATATATA
Found at i:70049 original size:30 final size:30
Alignment explanation
Indices: 70010--70105 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 30
70000 GAAAACATAC
70010 ATATAATATATAGTTTTTAAAATATTTTGAA
1 ATAT-ATATATAGTTTTTAAAATATTTTGAA
* * *
70041 ATATATATATAATTTTTGAAAACATTTTTAA
1 ATATATATATAGTTTTT-AAAATATTTTGAA
* *
70072 ATATATAATTATAG-TTTGAAAATGTTTTTGAA
1 ATATAT-A-TATAGTTTTTAAAAT-ATTTTGAA
70104 AT
1 AT
70106 TTTGAAAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 12 0.23
31 25 0.47
32 12 0.23
33 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (30 bp):
ATATATATATAGTTTTTAAAATATTTTGAA
Found at i:70059 original size:58 final size:60
Alignment explanation
Indices: 69950--70065 Score: 166
Period size: 58 Copynumber: 2.0 Consensus size: 60
69940 TTAAATATAT
* *
69950 ATATAATATATAGTTTTTAAACTTTTTTTGAAAACATATATATATGGTTTGAAAACATAC
1 ATATAATATATAGTTTTTAAACATATTTTGAAAACATATATATATGGTTTGAAAACATAC
* *
70010 ATATAATATATAGTTTTTAAA-ATATTTTG-AAATATATATATAAT-TTTTGAAAACAT
1 ATATAATATATAGTTTTTAAACATATTTTGAAAACATATATAT-ATGGTTTGAAAACAT
70066 TTTTAAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 22 0.43
59 8 0.16
60 21 0.41
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (60 bp):
ATATAATATATAGTTTTTAAACATATTTTGAAAACATATATATATGGTTTGAAAACATAC
Found at i:70161 original size:16 final size:16
Alignment explanation
Indices: 70140--70184 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
70130 ATAATATTTG
70140 TTTATTATTATTTATT
1 TTTATTATTATTTATT
*
70156 TTTATTATTA-TTGTT
1 TTTATTATTATTTATT
70171 TTTA-T-TTATTTATT
1 TTTATTATTATTTATT
70185 CTTTTGGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 3 0.12
14 5 0.19
15 8 0.31
16 10 0.38
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTATTATTATTTATT
Found at i:70165 original size:19 final size:19
Alignment explanation
Indices: 70141--70180 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
70131 TAATATTTGT
70141 TTATTATTATTTATT-TTTA
1 TTATTATTATTT-TTATTTA
*
70160 TTATTATTGTTTTTATTTA
1 TTATTATTATTTTTATTTA
70179 TT
1 TT
70181 TATTCTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
TTATTATTATTTTTATTTA
Found at i:71180 original size:16 final size:16
Alignment explanation
Indices: 71161--71296 Score: 51
Period size: 16 Copynumber: 7.7 Consensus size: 16
71151 TTATTATATA
71161 TTTTATATTTTATTTT
1 TTTTATATTTTATTTT
*
71177 TTTTTTATTTTATCATTTAT
1 TTTTATA-TTT-T-ATTT-T
*
71197 TTCTTCGATTTCTTTATTTT
1 TT-TT--ATAT-TTTATTTT
* *
71217 TTCTATA-TTTATTTA
1 TTTTATATTTTATTTT
*
71232 TTTTATTTTTTATTCTT
1 TTTTATATTTTATT-TT
71249 CTCTTT-TGATTTTATTATTAT
1 -T-TTTAT-ATTTTA-T-TT-T
* * *
71270 TTTTTTAGTTTATTAT
1 TTTTATATTTTATTTT
71286 TTTTATATTTT
1 TTTTATATTTT
71297 TCTTTGATCT
Statistics
Matches: 89, Mismatches: 14, Indels: 34
0.65 0.10 0.25
Matches are distributed among these distances:
15 12 0.13
16 22 0.25
17 7 0.08
18 4 0.04
19 21 0.24
20 10 0.11
21 8 0.09
22 2 0.02
23 3 0.03
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTTATATTTTATTTT
Found at i:71274 original size:19 final size:18
Alignment explanation
Indices: 71149--71286 Score: 74
Period size: 19 Copynumber: 7.6 Consensus size: 18
71139 TCAGACCCTT
*
71149 TTTTATTATATATTTTATA
1 TTTTATTAT-TATTTTTTA
71168 TTTTATT-TT-TTTTTTA
1 TTTTATTATTATTTTTTA
* *
71184 TTTTATCATTTATTTCTTCGA
1 TTTTATTA-TTATTT-TT-TA
*
71205 TTTCT-TTATT-TTTTCTA
1 TTT-TATTATTATTTTTTA
71222 TATTTA-T-TTATTTTATT-
1 T-TTTATTATTATTTT-TTA
* * *
71239 TTTTATTCTTCTCTTTTGA
1 TTTTATTATTAT-TTTTTA
71258 TTTTATTATTATTTTTTTA
1 TTTTATTATTA-TTTTTTA
*
71277 GTTTATTATT
1 TTTTATTATT
71287 TTTATATTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
16 18 0.20
17 11 0.12
18 11 0.12
19 39 0.43
20 5 0.05
21 6 0.07
22 1 0.01
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTATTATTATTTTTTA
Done.