Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008204.1 Hibiscus syriacus cultivar Beakdansim tig00110826_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: 64041
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:10647 original size:20 final size:20
Alignment explanation
Indices: 10624--10675 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
10614 AACGCGATCC
10624 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
10644 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
10664 CCAAAATCGCAA
1 CCAGAATCGCAA
10676 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:10692 original size:21 final size:20
Alignment explanation
Indices: 10666--10763 Score: 70
Period size: 21 Copynumber: 4.8 Consensus size: 20
10656 ATCAGTTTCC
10666 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * * *
10687 AAAATCGCGATGCGATAGTAG
1 AAAATCGCAACGCGAT-TTTG
* ** *
10708 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-G
* * *
10729 ATAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
10749 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
10764 ACACATAAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 5
0.71 0.22 0.06
Matches are distributed among these distances:
20 15 0.26
21 42 0.74
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:10756 original size:20 final size:20
Alignment explanation
Indices: 10731--10924 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
10721 GATTTTCCAT
* *
10731 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
10751 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
10771 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
10791 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
10811 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
10831 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
10851 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
10871 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
10892 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
10912 AATCGCAACGCGA
1 AATCGCAACGCGA
10925 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:10776 original size:40 final size:39
Alignment explanation
Indices: 10727--10924 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
10717 TTGCGATTTT
* ** *
10727 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
10765 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
10806 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
10846 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
10885 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
10925 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:10814 original size:60 final size:60
Alignment explanation
Indices: 10731--10923 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
10721 GATTTTCCAT
* ** * *
10731 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
10791 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
10851 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
10912 AATCGCAACGCG
1 AATCGCAACGCG
10924 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:11345 original size:33 final size:32
Alignment explanation
Indices: 11301--11370 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
11291 TTCACTTAGA
*
11301 TTTCATTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTCGCGTTACGATTCTCTCGTTGCGAT
* *
11333 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCA-TTCGCGTTACGATTCTCTCGTTGCGAT
11366 TTTCA
1 TTTCA
11371 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 5 0.15
33 29 0.85
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (32 bp):
TTTCATTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:11540 original size:33 final size:31
Alignment explanation
Indices: 11491--11559 Score: 102
Period size: 33 Copynumber: 2.2 Consensus size: 31
11481 AGAATGACTG
**
11491 TCGCAACGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAATCGCAACGCGAAACCAAAA
11522 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAAC--GAGAATCGCAACGCGAAACCAAAA
11555 TCGCA
1 TCGCA
11560 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 7 0.21
33 27 0.79
ACGTcount: A:0.43, C:0.26, G:0.22, T:0.09
Consensus pattern (31 bp):
TCGCAACGAGAATCGCAACGCGAAACCAAAA
Found at i:11596 original size:14 final size:14
Alignment explanation
Indices: 11577--11666 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
11567 TTTCATTTCG
11577 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
11591 CGTTGCGACAGTCATTTCG
1 CGTTGCG--A-T--TCTCT
11610 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
11624 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
11641 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
11657 CGTTGCGATT
1 CGTTGCGATT
11667 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 7 0.11
17 7 0.11
18 1 0.02
19 18 0.29
ACGTcount: A:0.10, C:0.27, G:0.24, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:11646 original size:19 final size:18
Alignment explanation
Indices: 11555--11667 Score: 70
Period size: 19 Copynumber: 6.8 Consensus size: 18
11545 GAAACCAAAA
* *
11555 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
11574 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
** *
11590 T--CGTTGCGACAGTCATT
1 TCGCGTTGCGA-TTTCATC
11607 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
11623 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
11640 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
11656 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
11668 TCATTTCAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 26
0.71 0.06 0.24
Matches are distributed among these distances:
14 24 0.31
15 3 0.04
16 11 0.14
17 12 0.16
18 1 0.01
19 26 0.34
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.41
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:11665 original size:33 final size:33
Alignment explanation
Indices: 11560--11674 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
11550 CAAAATCGCA
*
11560 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
**
11593 TTGCGACAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
11626 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
11659 TTGCGATTTTCATTTC
1 TTGCGATTGTCATTTC
11675 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:13749 original size:93 final size:93
Alignment explanation
Indices: 13365--13926 Score: 1078
Period size: 92 Copynumber: 6.1 Consensus size: 93
13355 TAGATTGCTT
*
13365 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
13430 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
13458 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
13521 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
13549 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
13613 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
13641 AGTAAATTTGTTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
13706 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
13734 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
13799 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
13827 AGTAAATTTGTTCGGTTGCTGCCAATT-TGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
13891 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
13919 AGTAAATT
1 AGTAAATT
13927 ATCCATTCAA
Statistics
Matches: 464, Mismatches: 3, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
91 75 0.16
92 196 0.42
93 193 0.42
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:13779 original size:185 final size:186
Alignment explanation
Indices: 13365--13926 Score: 1078
Period size: 185 Copynumber: 3.0 Consensus size: 186
13355 TAGATTGCTT
*
13365 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
13430 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
13495 GTGTATTC-TTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
13549 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
13613 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTACTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
13678 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
13734 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
13799 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATT-TGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
13863 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
13919 AGTAAATT
1 AGTAAATT
13927 ATCCATTCAA
Statistics
Matches: 372, Mismatches: 3, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
183 74 0.20
184 77 0.21
185 165 0.44
186 56 0.15
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:14010 original size:19 final size:19
Alignment explanation
Indices: 13970--14092 Score: 113
Period size: 19 Copynumber: 6.9 Consensus size: 19
13960 TAGTTTACTT
* *
13970 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
13990 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
14009 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
14028 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
14042 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
14061 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
14075 TCGCAACGCGAAACCAAA
1 TCGCAACGCGAAACCAAA
14093 TTGCATTGCG
Statistics
Matches: 84, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.23
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 40 0.48
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.08
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:14049 original size:33 final size:32
Alignment explanation
Indices: 14006--14092 Score: 138
Period size: 33 Copynumber: 2.7 Consensus size: 32
13996 CGCGAAACCA
**
14006 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
14038 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
14071 AAGATCGCAACGCGAAACCAAA
1 AA-ATCGCAACGCGAAACCAAA
14093 TTGCATTGCG
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
32 2 0.04
33 49 0.96
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:14122 original size:19 final size:19
Alignment explanation
Indices: 14098--14226 Score: 109
Period size: 19 Copynumber: 7.3 Consensus size: 19
14088 CCAAATTGCA
14098 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
14117 TTGCGA--TTC-TTT--CG
1 TTGCGATTTTCATTTCGCG
*
14131 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
14149 TTGCGA--TTC-TGT--CG
1 TTGCGATTTTCATTTCGCG
*
14163 TTGCGATTTTAATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
14182 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
14201 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
14221 TTGCGA
1 TTGCGA
14227 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
14 15 0.17
15 3 0.03
16 10 0.11
17 8 0.09
18 7 0.08
19 35 0.39
20 12 0.13
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:14134 original size:14 final size:14
Alignment explanation
Indices: 14115--14170 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
14105 TTTCATTTCG
14115 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
14129 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
14145 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
14161 CGTTGCGATT
1 CGTTGCGATT
14171 TTAATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 16 0.43
15 3 0.08
16 9 0.24
17 3 0.08
18 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:14145 original size:32 final size:33
Alignment explanation
Indices: 14098--14189 Score: 150
Period size: 32 Copynumber: 2.8 Consensus size: 33
14088 CCAAATTGCA
*
14098 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
14131 TTGCGA-TTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
14163 TTGCGATTTTAATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
14190 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:16164 original size:13 final size:14
Alignment explanation
Indices: 16139--16173 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
16129 ATTGTTTAAT
16139 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
16153 TGATTTGT-AAAGT
1 TGATTTGTAAAAGA
16166 TGATTTGT
1 TGATTTGT
16174 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:16296 original size:19 final size:19
Alignment explanation
Indices: 16280--16381 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
16270 AAAAATGACT
16280 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
16299 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
16318 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
16332 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
16351 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
16371 ATCGCAATGCG
1 ATCGCAATGCG
16382 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:16433 original size:19 final size:19
Alignment explanation
Indices: 16409--16696 Score: 338
Period size: 19 Copynumber: 16.4 Consensus size: 19
16399 CGATATCTCG
16409 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
16428 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
16447 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
16461 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
16480 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
16499 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
16518 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
16537 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
16551 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
16570 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
16584 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
16603 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
16622 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
16636 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
16656 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
16670 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
16689 TTGCGATT
1 TTGCGATT
16697 GTATTTTCCG
Statistics
Matches: 233, Mismatches: 10, Indels: 52
0.79 0.03 0.18
Matches are distributed among these distances:
14 39 0.17
16 27 0.12
17 25 0.11
18 1 0.00
19 126 0.54
20 15 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:16466 original size:33 final size:35
Alignment explanation
Indices: 16409--16696 Score: 241
Period size: 33 Copynumber: 8.2 Consensus size: 35
16399 CGATATCTCG
16409 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGA-TTTC-TTTCG-ATTGCGATTTTCATTTCGCA
16447 TTGCGA-TTCTTTCG-TTGCGATTTTCATTTCGCA
1 TTGCGATTTCTTTCGATTGCGATTTTCATTTCGCA
16480 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGA-TTTC-TTTCG-ATTGCGATTTTCATTTCGCA
* *
16518 TTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--
1 TTGCGA-TTT-CTTTCG-ATTGCGATTTTCATTTCGCA
*
16551 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--
1 TTGCGA-TTTC-TTTCG-ATTGCGATTTTCATTTCGCA
16584 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGA-TTTC-TTTCG-ATTGCGATTTTCATTTCGCA
*
16622 TTGCGA-TTCTCTC-ATTGCGATTTTCATTTCCGCA
1 TTGCGATTTCTTTCGATTGCGATTTTCATTT-CGCA
* * *
16656 TTGCGATTT-TCAT-G-TTGGGATTTTCATTTCGCG
1 TTGCGATTTCT-TTCGATTGCGATTTTCATTTCGCA
16689 TTGCGATT
1 TTGCGATT
16697 GTATTTTCCG
Statistics
Matches: 225, Mismatches: 9, Indels: 37
0.83 0.03 0.14
Matches are distributed among these distances:
33 107 0.48
34 25 0.11
35 21 0.09
36 18 0.08
38 54 0.24
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (35 bp):
TTGCGATTTCTTTCGATTGCGATTTTCATTTCGCA
Found at i:16477 original size:52 final size:52
Alignment explanation
Indices: 16388--16696 Score: 265
Period size: 52 Copynumber: 5.9 Consensus size: 52
16378 TGCGTTTATA
16388 ATTTCGCATTGCGATATC--TCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGAT-TCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
16439 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
16491 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
16546 -TGTCG--TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* * * *
16595 ATTTCGCATTGCGA-T-TTTCATTTCGCA-TTGCGATTCTCTCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* *
16647 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTCTTTC--GTTGCGATTTTCATTTCGCATTGCGATT
16697 GTATTTTCCG
Statistics
Matches: 219, Mismatches: 16, Indels: 44
0.78 0.06 0.16
Matches are distributed among these distances:
45 4 0.02
46 1 0.00
47 12 0.05
49 9 0.04
50 10 0.05
51 15 0.07
52 93 0.42
53 26 0.12
54 11 0.05
55 14 0.06
57 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:18996 original size:12 final size:12
Alignment explanation
Indices: 18979--19003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18969 TCTTCGGGGA
18979 CTTTTTCTTCTT
1 CTTTTTCTTCTT
18991 CTTTTTCTTCTT
1 CTTTTTCTTCTT
19003 C
1 C
19004 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:19212 original size:24 final size:24
Alignment explanation
Indices: 19178--19224 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
19168 CTGAAACATC
19178 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
19202 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
19225 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:19931 original size:20 final size:20
Alignment explanation
Indices: 19903--20271 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
19893 AAATTTCAGT
* * * *
19903 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
19923 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
19943 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
19963 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
19983 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
20003 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
20023 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
20043 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
20063 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
20083 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
20103 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
20123 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
20143 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
20163 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
20183 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
20203 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
20223 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
20243 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
20263 GTTGCGATT
1 GTTGCGATT
20272 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:20654 original size:7 final size:7
Alignment explanation
Indices: 20644--20710 Score: 134
Period size: 7 Copynumber: 9.6 Consensus size: 7
20634 GCTCTGCCAT
20644 CTGCCTA
1 CTGCCTA
20651 CTGCCTA
1 CTGCCTA
20658 CTGCCTA
1 CTGCCTA
20665 CTGCCTA
1 CTGCCTA
20672 CTGCCTA
1 CTGCCTA
20679 CTGCCTA
1 CTGCCTA
20686 CTGCCTA
1 CTGCCTA
20693 CTGCCTA
1 CTGCCTA
20700 CTGCCTA
1 CTGCCTA
20707 CTGC
1 CTGC
20711 AAACATACAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.13, C:0.43, G:0.15, T:0.28
Consensus pattern (7 bp):
CTGCCTA
Found at i:21113 original size:23 final size:24
Alignment explanation
Indices: 21087--21145 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
21077 CCTATTTTTA
*
21087 TTAATTATTTAATTTTATAT-TCT
1 TTAATTATTTAATCTTATATATCT
** *
21110 TTAAAAAATTAATCTTATATATCT
1 TTAATTATTTAATCTTATATATCT
*
21134 TAAATT-TTTAAT
1 TTAATTATTTAAT
21146 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAATTATTTAATCTTATATATCT
Found at i:21401 original size:30 final size:29
Alignment explanation
Indices: 21344--21402 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
21334 ATTCGGTCTG
* *
21344 AAAATAATATAATTATCTTTTGTATATTT
1 AAAATAATATAATAATCTTTTGAATATTT
21373 AAAATAATTATAATAATACTTTT-AATATTT
1 AAAATAA-TATAATAAT-CTTTTGAATATTT
21403 TCCCCTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 7 0.27
30 14 0.54
31 5 0.19
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (29 bp):
AAAATAATATAATAATCTTTTGAATATTT
Found at i:25116 original size:183 final size:184
Alignment explanation
Indices: 24819--25192 Score: 626
Period size: 183 Copynumber: 2.0 Consensus size: 184
24809 ATAAAAATCA
* * *
24819 AATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 AATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAATTATAAAATAAAAAA
24884 TTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTAT
66 TTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTAT
* * * *
24949 TAATTGGGTTTTAAATGGTTTTGGTTTAGCCCATATGTTATATATAATATATAT
131 TAATTGGGTTCTAAATGATTTGGGTTGAGCCCATATGTTATATATAATATATAT
25003 AATATTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTTTTAATTCAAAAAA-AGTTTACAAATAATTTAAATAATATATAATTATAAAATAAAAA
* *
25067 ATTTATAT-ATATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTA
65 ATTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTA
*
25131 TTAATTGGGTTCTAAATGATTTGGGTTGAGCCCATATGTTATATATAATATATTT
130 TTAATTGGGTTCTAAATGATTTGGGTTGAGCCCATATGTTATATATAATATATAT
*
25186 AAAATTT
1 AATATTT
25193 AAAATTTAAT
Statistics
Matches: 178, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
183 117 0.66
184 61 0.34
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (184 bp):
AATATTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAATTATAAAATAAAAAA
TTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTAT
TAATTGGGTTCTAAATGATTTGGGTTGAGCCCATATGTTATATATAATATATAT
Found at i:25217 original size:9 final size:9
Alignment explanation
Indices: 25198--25231 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
25188 AATTTAAAAT
25198 TTAATTTCGG
1 TTAA-TTCGG
25208 TTAATTCGG
1 TTAATTCGG
25217 TTAATTCGG
1 TTAATTCGG
25226 TTAATT
1 TTAATT
25232 AACCGAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (9 bp):
TTAATTCGG
Found at i:25316 original size:17 final size:16
Alignment explanation
Indices: 25294--25338 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
25284 CCGTTAACCG
25294 ACCGAACTAATTCGGTA
1 ACCGAACTAATTC-GTA
*
25311 ACCGAACTAAAT--TA
1 ACCGAACTAATTCGTA
25325 ACCGAACTAATTCG
1 ACCGAACTAATTCG
25339 ATTCGATCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 13 0.54
17 11 0.46
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.22
Consensus pattern (16 bp):
ACCGAACTAATTCGTA
Found at i:25665 original size:25 final size:25
Alignment explanation
Indices: 25629--25679 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
25619 ATTGGTCTCT
* *
25629 CTGTCCCTGTCCCTGTTTAAAAAAC
1 CTGTCCCTGTCCCAGCTTAAAAAAC
25654 CTGTACCC-GTCCCAGCTTAAAAAAC
1 CTGT-CCCTGTCCCAGCTTAAAAAAC
25679 C
1 C
25680 ACGGGGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.25
Consensus pattern (25 bp):
CTGTCCCTGTCCCAGCTTAAAAAAC
Found at i:25761 original size:23 final size:23
Alignment explanation
Indices: 25731--25779 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
25721 AACCGCAGGA
25731 AAACGGGTATCCCTGTTTAGCAT
1 AAACGGGTATCCCTGTTTAGCAT
*
25754 AAACGGGTATCCCTGTTTAGCTT
1 AAACGGGTATCCCTGTTTAGCAT
25777 AAA
1 AAA
25780 ATATTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (23 bp):
AAACGGGTATCCCTGTTTAGCAT
Found at i:29895 original size:60 final size:60
Alignment explanation
Indices: 29802--29946 Score: 272
Period size: 60 Copynumber: 2.4 Consensus size: 60
29792 CATAATGAAT
29802 GACTATTTTGTAACTTTTTATAGTCAAGAGACTCAAAAAAACAAATCCATATAGTCGAGG
1 GACTATTTTGTAACTTTTTATAGTCAAGAGACTCAAAAAAACAAATCCATATAGTCGAGG
29862 GACTATTTTGTAACTTTTTATAGTCAAGAGACTCAAAAAAACAAATCCATATAGTCGAGG
1 GACTATTTTGTAACTTTTTATAGTCAAGAGACTCAAAAAAACAAATCCATATAGTCGAGG
* *
29922 GACTATTTTATAACTTTTAATAGTC
1 GACTATTTTGTAACTTTTTATAGTC
29947 GGGACTAAAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 83 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (60 bp):
GACTATTTTGTAACTTTTTATAGTCAAGAGACTCAAAAAAACAAATCCATATAGTCGAGG
Found at i:31985 original size:7 final size:7
Alignment explanation
Indices: 31975--32043 Score: 138
Period size: 7 Copynumber: 9.9 Consensus size: 7
31965 CTAACATGAC
31975 GTAAACT
1 GTAAACT
31982 GTAAACT
1 GTAAACT
31989 GTAAACT
1 GTAAACT
31996 GTAAACT
1 GTAAACT
32003 GTAAACT
1 GTAAACT
32010 GTAAACT
1 GTAAACT
32017 GTAAACT
1 GTAAACT
32024 GTAAACT
1 GTAAACT
32031 GTAAACT
1 GTAAACT
32038 GTAAAC
1 GTAAAC
32044 ACAAATCCTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.28
Consensus pattern (7 bp):
GTAAACT
Found at i:35168 original size:4 final size:4
Alignment explanation
Indices: 35159--35183 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
35149 TTTGTTTATT
35159 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
35184 GAGGAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:35836 original size:60 final size:60
Alignment explanation
Indices: 35732--35844 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
35722 CCAGTGATCA
* * *
35732 TTTTGTAACTTTTAATAGTCAGGGTACTCAACAAAGCAACACTCTATAGTTGAAAGACCG
1 TTTTGTAACTTTTAATAGTCAAGGTACTCAACAAAACAACACTCTATAATTGAAAGACCG
* * * * *
35792 TTTTGTAACTTTTAATAGTCGAATG-ACTTAATAAAATAATACTCTATAATTGA
1 TTTTGTAACTTTTAATAGTC-AAGGTACTCAACAAAACAACACTCTATAATTGA
35845 GGGATCATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 42 0.95
61 2 0.05
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (60 bp):
TTTTGTAACTTTTAATAGTCAAGGTACTCAACAAAACAACACTCTATAATTGAAAGACCG
Found at i:36408 original size:14 final size:14
Alignment explanation
Indices: 36389--36415 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36379 TTTTTCTCTC
36389 TCTCAATATTCTAG
1 TCTCAATATTCTAG
36403 TCTCAATATTCTA
1 TCTCAATATTCTA
36416 ATGCCGTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (14 bp):
TCTCAATATTCTAG
Found at i:36889 original size:2 final size:2
Alignment explanation
Indices: 36882--36917 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
36872 TCATTGTTCA
36882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36918 GAAAATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38239 original size:31 final size:31
Alignment explanation
Indices: 38204--38270 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
38194 ATAACTTTTA
38204 ATAGTCAAGGGACTCAATAAAGCATTATCAT
1 ATAGTCAAGGGACTCAATAAAGCATTATCAT
38235 ATAGTCAAGGGACTCAATAAAGCATTATCAT
1 ATAGTCAAGGGACTCAATAAAGCATTATCAT
38266 ATAGT
1 ATAGT
38271 ATGGGGATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (31 bp):
ATAGTCAAGGGACTCAATAAAGCATTATCAT
Found at i:38246 original size:60 final size:60
Alignment explanation
Indices: 38117--38247 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 60
38107 CATAATGAAA
* * ** * *
38117 AGTCAAGTGACCATTTTGTAACTTTTAATAGTTGAGGGACTCAGCAAAGCAATTCTCTAT
1 AGTCAAGGGACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAGCAATTATCTAT
** * *
38177 AGTTGAGGGATCATTTTATAACTTTTAATAGTCAAGGGACTCAATAAAGC-ATTATCATAT
1 AGTCAAGGGACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAGCAATTATC-TAT
38237 AGTCAAGGGAC
1 AGTCAAGGGAC
38248 TCAATAAAGC
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
59 5 0.09
60 52 0.91
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (60 bp):
AGTCAAGGGACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAGCAATTATCTAT
Found at i:40688 original size:21 final size:20
Alignment explanation
Indices: 40664--40718 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
40654 TTCAAAATCC
40664 TAAAAAC-AAGTTAAAACATCT
1 TAAAAACTAA-TTAAAACA-CT
**
40685 TAAATCCTAATTAAAACACT
1 TAAAAACTAATTAAAACACT
*
40705 T-AAAACTATTTAAA
1 TAAAAACTAATTAAA
40719 CTAAAATACC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 13 0.46
22 2 0.07
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.29
Consensus pattern (20 bp):
TAAAAACTAATTAAAACACT
Found at i:40776 original size:19 final size:19
Alignment explanation
Indices: 40720--40782 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
40710 CTATTTAAAC
**
40720 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
40740 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
40760 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
40779 TAAA
1 TAAA
40783 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:40810 original size:64 final size:68
Alignment explanation
Indices: 40685--40882 Score: 208
Period size: 64 Copynumber: 2.8 Consensus size: 68
40675 TAAAACATCT
* ** *
40685 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC--CTA-AAAAAT-AATATAAT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAATAAT
*
40745 ATTC
65 ATCC
40749 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC------AAAGATAAAA-ATAAA
40814 AATAATATCC
59 AATAATATCC
* *
40824 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAA-ATAA
40883 TGTTTAAAAT
Statistics
Matches: 114, Mismatches: 7, Indels: 20
0.81 0.05 0.14
Matches are distributed among these distances:
63 5 0.04
64 36 0.32
70 15 0.13
72 1 0.01
73 4 0.04
74 2 0.02
75 28 0.25
76 23 0.20
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAAATAAAAATAATA
TCC
Found at i:44963 original size:127 final size:126
Alignment explanation
Indices: 44738--44991 Score: 463
Period size: 127 Copynumber: 2.0 Consensus size: 126
44728 GTGTTATGTA
*
44738 ATATCCGATTTTCGTCCGGTCTACCTTTTTACATAATTCAAATATTTTTATTGAAGTTGATTTTA
1 ATATCCAATTTTCGTCCGGTCTACCTTTTTACATAATTCAAATATTTTTATTGAAGTTGATTTTA
*
44803 GGTTCGGTACATCCTTCGACTTGCAATGGATTTTTGGATAAGATCCAAATATTTTTAAGTG
66 GGTTCGGTACATCATTCGACTTGCAATGGATTTTTGGATAAGATCCAAATATTTTTAAGTG
* *
44864 ATATCCAATTTTCGTCCGGTCTGCCTTTTTTTCATAATTCAAATATTTTTATTGAAGTTGATTTT
1 ATATCCAATTTTCGTCCGGTCTACC-TTTTTACATAATTCAAATATTTTTATTGAAGTTGATTTT
44929 AGGTTCGGTACATCATTCGACTTGCAATGGATTTTTGGATAAGATCCAAATATTTTTAAGTG
65 AGGTTCGGTACATCATTCGACTTGCAATGGATTTTTGGATAAGATCCAAATATTTTTAAGTG
44991 A
1 A
44992 AGATTTCTTG
Statistics
Matches: 123, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
126 23 0.19
127 100 0.81
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (126 bp):
ATATCCAATTTTCGTCCGGTCTACCTTTTTACATAATTCAAATATTTTTATTGAAGTTGATTTTA
GGTTCGGTACATCATTCGACTTGCAATGGATTTTTGGATAAGATCCAAATATTTTTAAGTG
Found at i:47575 original size:4 final size:4
Alignment explanation
Indices: 47568--48324 Score: 948
Period size: 4 Copynumber: 187.8 Consensus size: 4
47558 GTTATTTATT
* * * *
47568 TATG TATG TATG TATG TATG CATG TATG CATG TATG CATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
47616 TATG CATG TATG CATG TATG CATG TATG CATG TATG CATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
47664 TATG CATG TATG CATG TATG CATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
47712 TATG CATG CATATG TATG TATG TATG TATG CATG CATATG TATG TATG
1 TATG TATG --TATG TATG TATG TATG TATG TATG --TATG TATG TATG
47760 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
47808 TATG TATG TATG TATG TATG TATG TATG CATG TATG CATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * ** *
47856 TATT TAT- TCAT- TCAAT- TTTG AAT- TAAA T-TT TATG TATG TATG TATG
1 TATG TATG T-ATG T--ATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
47902 TATG CATG TATG TATG TATG TATG CATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
47950 CATG TATG TATG TATA TATG CATG TATG CATG TATG CATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
47998 TATG CATG TATG CATG TATG CATG TATG CATG TATG CATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
48046 TATG CATG TATG CATG TATG CATG TATG CATG TATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
48094 TATG TATG TATG TATG TATG TATG TATG TATG CATG CATATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG --TATG TATG TATG
* *
48144 TATA TATG CATG CATATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG --TATG TATG TATG TATG TATG TATG TATG TATG TATG
48194 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48242 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
48290 TATG TATG TATG TATG TATG CATG CATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
48325 TTATTCATTC
Statistics
Matches: 650, Mismatches: 90, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
3 4 0.01
4 631 0.97
5 3 0.00
6 12 0.02
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:49767 original size:60 final size:60
Alignment explanation
Indices: 49703--49815 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
49693 TGTGACTATC
* *
49703 ATTCTAAATTAGTCCTCAAAC-TTTTGAACATTTCAATTTTATCCCTAAACTATGACCTTT
1 ATTCTAAATTAGTCCTCAAACTTTTTGAACATTCCAATTTCATCCC-AAACTATGACCTTT
*
49763 ATTCTAAATTAGTCCTTAAACTTTTTGAACATTCCAATTTCATCCCAAACTAT
1 ATTCTAAATTAGTCCTCAAACTTTTTGAACATTCCAATTTCATCCCAAACTAT
49816 ACATATATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
60 27 0.55
61 22 0.45
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (60 bp):
ATTCTAAATTAGTCCTCAAACTTTTTGAACATTCCAATTTCATCCCAAACTATGACCTTT
Found at i:50041 original size:60 final size:60
Alignment explanation
Indices: 49944--50102 Score: 162
Period size: 60 Copynumber: 2.6 Consensus size: 60
49934 TGAATTTGGA
** ** ** *
49944 GATGAAATTAGAATATTCAAAAG-TTTGGGAACCAATTTAGAAAGGGAGTCATAATTTATG
1 GATG-AATTAGAATATTCAAAAGCTTAAGGAACCAATTTAGAAAGAAACCCATAATTTAAG
* * * *
50004 GATGCAATTAGAATGTTCAAAAGCTTAAGG-ACTAATTTAGAATGAAACCCATAGTTTAAG
1 GATG-AATTAGAATATTCAAAAGCTTAAGGAACCAATTTAGAAAGAAACCCATAATTTAAG
*
50064 GATGATATTAGAATATTCAAAAGCTTAA-GAATCAATTTA
1 GATGA-ATTAGAATATTCAAAAGCTTAAGGAACCAATTTA
50103 AAATAAGGGT
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
59 2 0.02
60 75 0.93
61 4 0.05
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (60 bp):
GATGAATTAGAATATTCAAAAGCTTAAGGAACCAATTTAGAAAGAAACCCATAATTTAAG
Found at i:50448 original size:29 final size:28
Alignment explanation
Indices: 50410--50477 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
50400 AAAAGTGATG
* * *
50410 AATTTGAATTTATGAAATTTTAGAGAATA
1 AATTTAAATTTATAAAAATTTA-AGAATA
*
50439 AATTTAAATTTATAAAAATTTAAGGATA
1 AATTTAAATTTATAAAAATTTAAGAATA
**
50467 AAAATAAATTT
1 AATTTAAATTT
50478 TTAATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 14 0.42
29 19 0.58
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (28 bp):
AATTTAAATTTATAAAAATTTAAGAATA
Found at i:50476 original size:28 final size:29
Alignment explanation
Indices: 50416--50477 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
50406 GATGAATTTG
* * **
50416 AATTTATGAAATTTTAGAGAATAAATTTA
1 AATTTATAAAAATTTAGAGAATAAAAATA
*
50445 AATTTATAAAAATTTA-AGGATAAAAATA
1 AATTTATAAAAATTTAGAGAATAAAAATA
50473 AATTT
1 AATTT
50478 TTAATAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (29 bp):
AATTTATAAAAATTTAGAGAATAAAAATA
Found at i:52823 original size:15 final size:16
Alignment explanation
Indices: 52803--52835 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
52793 GGAAAAATTA
52803 AATTTTAAT-TTTTTT
1 AATTTTAATATTTTTT
52818 AATTTTAATATTTTTT
1 AATTTTAATATTTTTT
52834 AA
1 AA
52836 AATATGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AATTTTAATATTTTTT
Found at i:59607 original size:108 final size:108
Alignment explanation
Indices: 59418--59637 Score: 404
Period size: 108 Copynumber: 2.0 Consensus size: 108
59408 TGAGTTAAAC
* *
59418 ATCCATGTTTTAATTGTTTTCTAATCAGGGCTTTGATTGAAGCTAAAGACGTGGAAGAGAAGAAA
1 ATCCATGTTCTAATTGTTTTCTAATCAGGGCTTTGATTGAAGCTAAAGACATGGAAGAGAAGAAA
59483 AACAGTGGAGGAGAAGTGGTGATTGATGTTCACGGTGAAGAAG
66 AACAGTGGAGGAGAAGTGGTGATTGATGTTCACGGTGAAGAAG
* *
59526 ATCCATGTTCTAATTGTTTTCTAATTAGGGCTTTGATTGAAGCTAAAGACATGGCAGAGAAGAAA
1 ATCCATGTTCTAATTGTTTTCTAATCAGGGCTTTGATTGAAGCTAAAGACATGGAAGAGAAGAAA
59591 AACAGTGGAGGAGAAGTGGTGATTGATGTTCACGGTGAAGAAG
66 AACAGTGGAGGAGAAGTGGTGATTGATGTTCACGGTGAAGAAG
59634 ATCC
1 ATCC
59638 CAAAGGACTG
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (108 bp):
ATCCATGTTCTAATTGTTTTCTAATCAGGGCTTTGATTGAAGCTAAAGACATGGAAGAGAAGAAA
AACAGTGGAGGAGAAGTGGTGATTGATGTTCACGGTGAAGAAG
Found at i:60950 original size:68 final size:68
Alignment explanation
Indices: 60841--60973 Score: 232
Period size: 68 Copynumber: 2.0 Consensus size: 68
60831 AACAATGCTA
60841 GTATGCAATAATCCTAATATATGTTATTCCCTATTTATACTATATAGTTTAAGTTGTTTAAGCTC
1 GTATGCAATAATCCTAATATATGTTATTCCCTATTTATACTATATAGTTTAAGTTGTTTAAGCTC
60906 CTG
66 CTG
* *
60909 GTATGCACTTATCCTAATATGA-GTTATTCCCTATTTATACTATATAGTTTAAGTTGTTTAAGCT
1 GTATGCAATAATCCTAATAT-ATGTTATTCCCTATTTATACTATATAGTTTAAGTTGTTTAAGCT
60973 C
65 C
60974 AAAACTAATG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 61 0.98
69 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (68 bp):
GTATGCAATAATCCTAATATATGTTATTCCCTATTTATACTATATAGTTTAAGTTGTTTAAGCTC
CTG
Done.