Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007529.1 Hibiscus syriacus cultivar Beakdansim tig00021014_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: 141296
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:18522 original size:15 final size:15
Alignment explanation
Indices: 18499--18540 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
18489 TCGTGGTGGT
*
18499 GGTGGTGGAGATGGA
1 GGTGATGGAGATGGA
18514 GGTGATGGAGATGGA
1 GGTGATGGAGATGGA
* *
18529 GATGATGAAGAT
1 GGTGATGGAGAT
18541 AAAGATGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.50, T:0.21
Consensus pattern (15 bp):
GGTGATGGAGATGGA
Found at i:20007 original size:44 final size:45
Alignment explanation
Indices: 19935--20111 Score: 277
Period size: 44 Copynumber: 4.0 Consensus size: 45
19925 ATTAGCATAG
* *
19935 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
1 CCAATTTACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
*
19980 -CAATTTAATTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
1 CCAATTTACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
** *
20024 TAAATTTACTTGCCATTTATTCCATAAGCTCGTAAGCTTATTTTA
1 CCAATTTACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
*
20069 CCAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CCAATTTACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
20112 TCCTGGTTAC
Statistics
Matches: 121, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
44 69 0.57
45 52 0.43
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
CCAATTTACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
Found at i:20092 original size:89 final size:89
Alignment explanation
Indices: 19941--20111 Score: 290
Period size: 89 Copynumber: 1.9 Consensus size: 89
19931 ATAGCCAATA
*
19941 TACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACAATTTAATTACCATTTATTCCATAA
1 TACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACAATATAATTACCATTTATTCCATAA
20006 GCTCGTAAGCTTATTTTATAAATT
66 GCTCGTAAGCTTATTTTATAAATT
* * *
20030 TACTTGCCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA-TTATTCCATA
1 TACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA-CAATATAATTACCATTTATTCCATA
20094 AGCTCGTAAGCTTATTTT
65 AGCTCGTAAGCTTATTTT
20112 TCCTGGTTAC
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 65 0.84
90 12 0.16
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (89 bp):
TACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACAATATAATTACCATTTATTCCATAA
GCTCGTAAGCTTATTTTATAAATT
Found at i:20270 original size:40 final size:40
Alignment explanation
Indices: 20216--20377 Score: 306
Period size: 40 Copynumber: 4.0 Consensus size: 40
20206 ACCGTAGTGC
20216 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
20256 TACATATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
20296 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
20336 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
20376 TA
1 TA
20378 TAAACCTGCA
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 119 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:22025 original size:23 final size:23
Alignment explanation
Indices: 21999--22046 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
21989 ATTTTGACTT
21999 TTAATTCCGAAATTCCCCTTGAA
1 TTAATTCCGAAATTCCCCTTGAA
22022 TTAATTCCGAAATTCCCCTTGAA
1 TTAATTCCGAAATTCCCCTTGAA
22045 TT
1 TT
22047 TTCAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (23 bp):
TTAATTCCGAAATTCCCCTTGAA
Found at i:26739 original size:2 final size:2
Alignment explanation
Indices: 26732--26771 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
26722 ATAAATTTTA
26732 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
26772 GCACGAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28400 original size:21 final size:22
Alignment explanation
Indices: 28353--28400 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
28343 AAAAATAAAA
28353 ATAAAAACAAAGAAAAATTTTG
1 ATAAAAACAAAGAAAAATTTTG
*
28375 A-AAAAGA-AAAGAAAACTTTT-
1 ATAAAA-ACAAAGAAAAATTTTG
28395 ATAAAA
1 ATAAAA
28401 CCCAGAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (22 bp):
ATAAAAACAAAGAAAAATTTTG
Found at i:30692 original size:23 final size:22
Alignment explanation
Indices: 30661--30703 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
30651 TTTATTATTT
*
30661 ATTTTTTCTTTTCTTTTTTTCTC
1 ATTTGTTCTTTT-TTTTTTTCTC
30684 ATTTGTTCTTTTTTTTTTTC
1 ATTTGTTCTTTTTTTTTTTC
30704 AGGTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (22 bp):
ATTTGTTCTTTTTTTTTTTCTC
Found at i:36046 original size:20 final size:21
Alignment explanation
Indices: 36021--36065 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
36011 AGAAAAAAGT
36021 AAAAA-TTAAGAATGAAAGAG
1 AAAAATTTAAGAATGAAAGAG
36041 AAAAATTTAAGAATGAAAGAG
1 AAAAATTTAAGAATGAAAGAG
36062 AAAA
1 AAAA
36066 GAAAAAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.16
Consensus pattern (21 bp):
AAAAATTTAAGAATGAAAGAG
Found at i:40650 original size:21 final size:21
Alignment explanation
Indices: 40626--40667 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40616 TAAGCTATGG
*
40626 CTTTGAAGTAAGACGCCTTGA
1 CTTTGAAGTAAAACGCCTTGA
*
40647 CTTTGAAGTAAAACTCCTTGA
1 CTTTGAAGTAAAACGCCTTGA
40668 TTCTTAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (21 bp):
CTTTGAAGTAAAACGCCTTGA
Found at i:41995 original size:16 final size:16
Alignment explanation
Indices: 41961--41998 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41951 ACACTAAATA
*
41961 AAACTAAAAAATAATT
1 AAACTAAAAAATAAGT
41977 AAAC-AAAAAATAAAGT
1 AAACTAAAAAAT-AAGT
41993 AAACTA
1 AAACTA
41999 TACACAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 11 0.58
17 1 0.05
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (16 bp):
AAACTAAAAAATAAGT
Found at i:44033 original size:23 final size:23
Alignment explanation
Indices: 44003--44051 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
43993 TGGTGGTTGG
*
44003 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
44026 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
44049 TTT
1 TTT
44052 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:52972 original size:2 final size:2
Alignment explanation
Indices: 52965--53039 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
52955 TCCTAACAGC
52965 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
53007 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 A
53040 AAGTTCAGAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:73648 original size:5 final size:5
Alignment explanation
Indices: 73637--73679 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
73627 TTGCTCAATC
* *
73637 AAAAT GAAAT GAAAT AAAAT AAAAT AAAAT AATAA- AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAA
73680 CAATGGGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 2 0.06
5 30 0.88
6 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:79574 original size:3 final size:3
Alignment explanation
Indices: 79561--79620 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
79551 TTTTTCATTC
* * *
79561 TAT TTT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
79607 TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TA
79621 AAAAAATAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:81582 original size:140 final size:141
Alignment explanation
Indices: 81316--81583 Score: 350
Period size: 140 Copynumber: 1.9 Consensus size: 141
81306 ATATTTTTGA
*
81316 TATTTAGTTATTTTTTAATATCAAAGAAATTGACTGTCTTAAAGCACCTAGAAGTCCCTTTCTGA
1 TATTTAGTTATTTTTTAATATCAAAGAAATAGACTGTCTTAAAGCACCTAGAAGTCCCTTTCTGA
* * *
81381 TATTCTTAAATAAATAAATATCCTATTTTTATAAAATATATATTAATTTATTTTAATTATTTTTA
66 TATTCTTAAATAAATAAATATCCTATTTATATAAAATAAATATTAATTTATATTAATTATTTTTA
81446 GAAAAATGTTT
131 GAAAAATGTTT
* * * *
81457 TATTTATTTA-TTTTTAATATCGAAGAAA-AGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTG
1 TATTTAGTTATTTTTTAATATCAAAGAAATAGA-CTGTCTTAAAGCACCTAGAAGTCCCTTTCTG
* * *
81520 ATATT-TCTAAATAAATAGATGTCTTATTTATA-AAAATAAATA-T-ATGTATATATTAATATAT
65 ATATTCT-TAAATAAATAAATATCCTATTTATATAAAATAAATATTAAT-T-TATATTAAT-TAT
81581 TTT
126 TTT
81584 CTTAAAATTA
Statistics
Matches: 111, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
137 2 0.02
138 2 0.02
139 20 0.18
140 78 0.70
141 9 0.08
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (141 bp):
TATTTAGTTATTTTTTAATATCAAAGAAATAGACTGTCTTAAAGCACCTAGAAGTCCCTTTCTGA
TATTCTTAAATAAATAAATATCCTATTTATATAAAATAAATATTAATTTATATTAATTATTTTTA
GAAAAATGTTT
Found at i:87463 original size:17 final size:16
Alignment explanation
Indices: 87428--87538 Score: 59
Period size: 17 Copynumber: 6.6 Consensus size: 16
87418 CTCATCCAGC
*
87428 AAAGAAAGAAGAAAGAAA
1 AAAGAAA-AAGAGA-AAA
87446 AAAGAAAAAGATG-AAA
1 AAAGAAAAAGA-GAAAA
* *
87462 AAGGAAAAATGAGAAAG
1 AAAGAAAAA-GAGAAAA
*
87479 AAGGAAAAA-AGAAAA
1 AAAGAAAAAGAGAAAA
87494 AATATGAAAAAG-GAAAA
1 AA-A-GAAAAAGAGAAAA
*
87511 ATTGAGAAAAA-ATGAAAA
1 A--AAGAAAAAGA-GAAAA
87529 AAAGGAAAAA
1 AAA-GAAAAA
87539 AAAAGGGAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
15 7 0.09
16 13 0.17
17 41 0.55
18 14 0.19
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAGAAAA
Found at i:87494 original size:7 final size:7
Alignment explanation
Indices: 87432--87558 Score: 60
Period size: 7 Copynumber: 16.6 Consensus size: 7
87422 TCCAGCAAAG
*
87432 AAAGAAG
1 AAAGAAA
87439 AAAGAAA
1 AAAGAAA
87446 AAAGAAA
1 AAAGAAA
87453 AAGATGAAA
1 AA-A-GAAA
*
87462 AAGGAAA
1 AAAGAAA
87469 AATGAGAAA
1 AA--AGAAA
*
87478 GAAGGAAA
1 -AAAGAAA
87486 AAAGAAAA
1 AAAG-AAA
87494 AATATGAAA
1 AA-A-GAAA
*
87503 AAGGAAA
1 AAAGAAA
87510 AATTGAGAAA
1 AA---AGAAA
87520 AAATGAAA
1 AAA-GAAA
*
87528 AAA-AGGA
1 AAAGA-AA
87535 AAA-AAA
1 AAAGAAA
* *
87541 AAGGGAA
1 AAAGAAA
87548 AAAGAAA
1 AAAGAAA
87555 AAAG
1 AAAG
87559 GGGAGAAATT
Statistics
Matches: 93, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
6 4 0.04
7 47 0.51
8 17 0.18
9 16 0.17
10 9 0.10
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (7 bp):
AAAGAAA
Found at i:87539 original size:17 final size:17
Alignment explanation
Indices: 87443--87539 Score: 71
Period size: 17 Copynumber: 5.8 Consensus size: 17
87433 AAGAAGAAAG
87443 AAAAAA-GAAAAAGATG-
1 AAAAAAGGAAAAA-ATGA
87459 -AAAAAGG-AAAAATGA
1 AAAAAAGGAAAAAATGA
*
87474 GAAAGAAGGAAAAAA-GA
1 -AAAAAAGGAAAAAATGA
* *
87491 AAAAATATG-AAAAAGGA
1 AAAAA-AGGAAAAAATGA
**
87508 AAAATTGAGAAAAAATGA
1 AAAAAAG-GAAAAAATGA
87526 AAAAAAGGAAAAAA
1 AAAAAAGGAAAAAA
87540 AAAGGGAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
14 3 0.05
15 9 0.14
16 10 0.16
17 24 0.38
18 17 0.27
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (17 bp):
AAAAAAGGAAAAAATGA
Found at i:91840 original size:22 final size:22
Alignment explanation
Indices: 91812--91891 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
91802 TACATCTACA
*
91812 CTCTTCAAAGATGATAGATTTT
1 CTCTTCAAAGATGATAGATTCT
*
91834 CTCTTCAAAGATGATATATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
91856 CTTTTTAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
91878 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
91892 AAGCTTTATC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:92685 original size:73 final size:73
Alignment explanation
Indices: 92566--93602 Score: 1851
Period size: 73 Copynumber: 14.2 Consensus size: 73
92556 CTATTTCCAA
*
92566 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
92631 CTCAGGGT
66 CTCAGGGT
* *
92639 CATCTGTAAGACCTACAGTTCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
92704 CTCAGGGT
66 CTCAGGGT
* * * *
92712 CATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGCAGCTTTTTTATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
*
92777 ATCAGGGT
66 CTCAGGGT
92785 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
92850 CTCAGGGT
66 CTCAGGGT
* *
92858 CATCTGTAAGACCTACAGTACATGATGTTCTCAAAAAGCCTTCGAGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
92923 CTCAGGGT
66 CTCAGGGT
*
92931 CATCTGTAAGACCTACAGCGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
92996 CTCAGGGT
66 CTCAGGGT
93004 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
93069 CTCAGGGT
66 CTCAGGGT
93077 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
93142 CTCAGGGT
66 CTCAGGGT
*
93150 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAACCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
93215 CTCAGGGT
66 CTCAGGGT
*
93223 CATCTGTAAGACCTACAGCGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
93288 CTCAGGGT
66 CTCAGGGT
93296 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
93361 CTCAGGGT
66 CTCAGGGT
93369 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
93434 CTCAGGGT
66 CTCAGGGT
*
93442 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAACCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
**
93507 CTCAAAGT
66 CTCAGGGT
* * * * *
93515 CATCTGTAAGACCTACACTGCCTGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATCCTAAAT
1 CATCTGTAAGACCTACAGTGCATGATGTTCTC-AAAAAGCCTTCGGGAGCTTTTTGATCTTAAAG
*
93580 CCTTAGGGT
65 CCTCAGGGT
93589 CAT-TGATAAGACCT
1 CATCTG-TAAGACCT
93603 CTGGGCAAAA
Statistics
Matches: 929, Mismatches: 33, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
73 883 0.95
74 46 0.05
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:93755 original size:3 final size:3
Alignment explanation
Indices: 93742--93804 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
93732 TTTTTCATTC
* * *
93742 TAT TTT TAT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
93791 TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TA
93805 AGAAAATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:95742 original size:140 final size:141
Alignment explanation
Indices: 95476--95743 Score: 341
Period size: 140 Copynumber: 1.9 Consensus size: 141
95466 CATATTTTGA
* *
95476 TATTTAGTTATTTTTTAATATCAAAGAAATTGACTGTCTTAAAGCACCTAGAAGACCTTTTCTGA
1 TATTTAGTTATTTTTTAATATCAAAGAAATAGACTGTCTTAAAGCACCTAGAAGACATTTTCTGA
* * *
95541 TATTCTTAAATAAATAAATATCCTATTTTTATAAAATATATATTAATTTATTTTAATTATTTTTA
66 TATTCTTAAATAAATAAATATCCTATTTATATAAAATAAATATTAATTTATATTAATTATTTTTA
95606 GAAAAATGTTT
131 GAAAAATGTTT
* * * *
95617 TATTTATTTA-TTTTTAATATCGAAGAAA-AGAGCTGTCTTAAGGCACCTAGAAGTCATTTTCTG
1 TATTTAGTTATTTTTTAATATCAAAGAAATAGA-CTGTCTTAAAGCACCTAGAAGACATTTTCTG
* * *
95680 ATATT-TCTAAATAAATAGATGTCTTATTTATA-AAAATAAATA-T-ATGTATATATTAATATAT
65 ATATTCT-TAAATAAATAAATATCCTATTTATATAAAATAAATATTAAT-T-TATATTAAT-TAT
95741 TTT
126 TTT
95744 CTTAAAATTA
Statistics
Matches: 110, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
137 2 0.02
138 2 0.02
139 20 0.18
140 77 0.70
141 9 0.08
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (141 bp):
TATTTAGTTATTTTTTAATATCAAAGAAATAGACTGTCTTAAAGCACCTAGAAGACATTTTCTGA
TATTCTTAAATAAATAAATATCCTATTTATATAAAATAAATATTAATTTATATTAATTATTTTTA
GAAAAATGTTT
Found at i:105908 original size:12 final size:11
Alignment explanation
Indices: 105886--105954 Score: 75
Period size: 11 Copynumber: 6.0 Consensus size: 11
105876 AAATAAAGGG
*
105886 AAATGAAAATA
1 AAATAAAAATA
105897 AAATTAAAAATA
1 AAA-TAAAAATA
*
105909 AAATGAAAATA
1 AAATAAAAATA
*
105920 AAACTGAAAATGA
1 AAA-TAAAAAT-A
105933 AAATAAAAATA
1 AAATAAAAATA
*
105944 AAAGAAAAATA
1 AAATAAAAATA
105955 GGTAGATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
11 24 0.47
12 23 0.45
13 4 0.08
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.17
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:105912 original size:23 final size:22
Alignment explanation
Indices: 105886--105954 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
105876 AAATAAAGGG
105886 AAATGAAAATAAAATTAAAAATA
1 AAATGAAAATAAAA-TAAAAATA
*
105909 AAATGAAAATAAAACTGAAAATGA
1 AAATGAAAATAAAA-TAAAAAT-A
* *
105933 AAATAAAAATAAAAGAAAAATA
1 AAATGAAAATAAAATAAAAATA
105955 GGTAGATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
22 1 0.03
23 25 0.62
24 14 0.35
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.17
Consensus pattern (22 bp):
AAATGAAAATAAAATAAAAATA
Found at i:105917 original size:18 final size:18
Alignment explanation
Indices: 105886--105951 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
105876 AAATAAAGGG
105886 AAATGAAAAT-AAAATTAA
1 AAATGAAAATGAAAA-TAA
105904 AAAT-AAAATGAAAATAA
1 AAATGAAAATGAAAATAA
*
105921 AACTGAAAATGAAAATAA
1 AAATGAAAATGAAAATAA
105939 AAAT-AAAA-GAAAA
1 AAATGAAAATGAAAA
105952 ATAGGTAGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.11
17 15 0.34
18 24 0.55
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.17
Consensus pattern (18 bp):
AAATGAAAATGAAAATAA
Found at i:112850 original size:18 final size:18
Alignment explanation
Indices: 112827--112871 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
112817 AAAATTGTTT
*
112827 TAAAATAAAAGATAAGGA
1 TAAAATAAAAGACAAGGA
*
112845 TAAAATAAAAGACAATGA
1 TAAAATAAAAGACAAGGA
*
112863 TGAAATAAA
1 TAAAATAAA
112872 TAAATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.18
Consensus pattern (18 bp):
TAAAATAAAAGACAAGGA
Found at i:113551 original size:21 final size:22
Alignment explanation
Indices: 113504--113551 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
113494 AAAAATAAAA
*
113504 ATAAAAACAAAGAAAATTTTTG
1 ATAAAAACAAAGAAAACTTTTG
113526 A-AAAATA-AAAGAAAACTTTT-
1 ATAAAA-ACAAAGAAAACTTTTG
113546 ATAAAA
1 ATAAAA
113552 CCCAGAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (22 bp):
ATAAAAACAAAGAAAACTTTTG
Found at i:113678 original size:20 final size:21
Alignment explanation
Indices: 113645--113683 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
113635 AATAAGGAAA
113645 AGATAATTCGTAAA-ATAAAG
1 AGATAATTCGTAAAGATAAAG
113665 AGATAATT-GCTAAAGATAA
1 AGATAATTCG-TAAAGATAA
113684 TTCTTAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 12 0.71
21 4 0.24
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (21 bp):
AGATAATTCGTAAAGATAAAG
Found at i:113897 original size:12 final size:12
Alignment explanation
Indices: 113880--113911 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
113870 GTCATATGCA
113880 TCATGCCCGGAG
1 TCATGCCCGGAG
113892 TCATGCCCGGAG
1 TCATGCCCGGAG
113904 TCATGCCC
1 TCATGCCC
113912 ACTAATCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.38, G:0.28, T:0.19
Consensus pattern (12 bp):
TCATGCCCGGAG
Found at i:122687 original size:90 final size:90
Alignment explanation
Indices: 122571--122748 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
122561 TAATCCCGAA
* * * * *
122571 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
122636 TAGGATAACTTGGATGTAAAAGGAT
66 TAGGATAACTTGGATATAAAAGGAT
122661 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
* *
122726 TAGGGTAACTTGGCTATAAAAGG
66 TAGGATAACTTGGATATAAAAGG
122749 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGATAACTTGGATATAAAAGGAT
Found at i:129190 original size:90 final size:90
Alignment explanation
Indices: 129072--129244 Score: 292
Period size: 90 Copynumber: 1.9 Consensus size: 90
129062 TATATATTTT
* * * *
129072 AATTTCAATTAAGTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTATGG
1 AATTCCAATTAAGTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGG
129137 TAACTTGGATATAAAAGGATTATTA
66 TAACTTGGATATAAAAGGATTATTA
*
129162 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGG
1 AATTCCAATTAAGTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGG
*
129227 TAACTTGGCTATAAAAGG
66 TAACTTGGATATAAAAGG
129245 GTGTGTTAGG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 77 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (90 bp):
AATTCCAATTAAGTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGG
TAACTTGGATATAAAAGGATTATTA
Found at i:131303 original size:74 final size:74
Alignment explanation
Indices: 131182--131320 Score: 233
Period size: 74 Copynumber: 1.9 Consensus size: 74
131172 AGAGCAATTG
* * *
131182 CCCCTCCCAACTTTGATGGTCTAATTACATTTTAGATCATTGATAATTATAAAATCATTATAATT
1 CCCCTCCCAACTTTAATGATCTAATTACATTTTAGATCACTGATAATTATAAAATCATTATAATT
131247 AAGCTTTTA
66 AAGCTTTTA
* *
131256 CCCCTCTCAACTTTAATGATCTAATTACATTTTAGGTCACTGATAATTATAAAATCATTATAATT
1 CCCCTCCCAACTTTAATGATCTAATTACATTTTAGATCACTGATAATTATAAAATCATTATAATT
131321 GAGCCCTTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (74 bp):
CCCCTCCCAACTTTAATGATCTAATTACATTTTAGATCACTGATAATTATAAAATCATTATAATT
AAGCTTTTA
Found at i:131335 original size:74 final size:74
Alignment explanation
Indices: 131182--131337 Score: 222
Period size: 74 Copynumber: 2.1 Consensus size: 74
131172 AGAGCAATTG
* * *
131182 CCCCTCCCAACTTTGATGGTCTAATTACATTTTAGATCATTGATAATTATAAAATCATTATAATT
1 CCCCTCCCAACTTTAATGATCTAATTACATTTTAGATCACTGATAATTATAAAATCATTATAATT
**
131247 AAGCTTTTA
66 AAGCCCTTA
* *
131256 CCCCTCTCAACTTTAATGATCTAATTACATTTTAGGTCACTGATAATTATAAAATCATTATAATT
1 CCCCTCCCAACTTTAATGATCTAATTACATTTTAGATCACTGATAATTATAAAATCATTATAATT
* *
131321 GAGCCCTTG
66 AAGCCCTTA
*
131330 TCCCTCCC
1 CCCCTCCC
131338 CAAATTTTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.38
Consensus pattern (74 bp):
CCCCTCCCAACTTTAATGATCTAATTACATTTTAGATCACTGATAATTATAAAATCATTATAATT
AAGCCCTTA
Found at i:131733 original size:20 final size:20
Alignment explanation
Indices: 131708--131753 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
131698 AAGAGAAGCG
131708 AAGCACTTACCCATTGGACT
1 AAGCACTTACCCATTGGACT
131728 AAGCACTTACCCATTGGACT
1 AAGCACTTACCCATTGGACT
131748 AAGCAC
1 AAGCAC
131754 AATATTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (20 bp):
AAGCACTTACCCATTGGACT
Found at i:136888 original size:30 final size:32
Alignment explanation
Indices: 136826--136888 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 32
136816 ATCATTTTTT
* *
136826 TTAAAACAAAGACCCTAAATTTTTCTAAAATA
1 TTAAAACAAAGACCCTAAAATTTTCAAAAATA
136858 TTAAAA-AAA-ACCCATAAAATTTT-AAAAATA
1 TTAAAACAAAGACCC-TAAAATTTTCAAAAATA
136888 T
1 T
136889 CATAAAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 11 0.39
31 11 0.39
32 6 0.21
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.30
Consensus pattern (32 bp):
TTAAAACAAAGACCCTAAAATTTTCAAAAATA
Found at i:138989 original size:10 final size:10
Alignment explanation
Indices: 138975--139013 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
138965 AGCTCTACAG
138975 TCTTCCA-AT
1 TCTTCCATAT
138984 TCCTTCCATAT
1 T-CTTCCATAT
*
138995 TCTTCCATAC
1 TCTTCCATAT
139005 TCTTCCATA
1 TCTTCCATA
139014 AGGTTCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 1 0.04
10 23 0.85
11 3 0.11
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.44
Consensus pattern (10 bp):
TCTTCCATAT
Done.