Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002451.1 Hibiscus syriacus cultivar Beakdansim tig00005023_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: 17280
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:814 original size:21 final size:20
Alignment explanation
Indices: 728--885 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
718 AAATGACCAA
**
728 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
747 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
767 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
787 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
808 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
829 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
849 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
870 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
886 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:878 original size:20 final size:20
Alignment explanation
Indices: 853--1046 Score: 87
Period size: 20 Copynumber: 9.7 Consensus size: 20
843 GATTTTCAAG
* *
853 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
873 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
893 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
913 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
933 AATCGCAACGCGTATCA-GTA
1 AATCGCAACGCG-AACACATA
* * *
953 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
973 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
993 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1014 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1034 AATCGCAACGCGA
1 AATCGCAACGCGA
1047 TATTTAAAGC
Statistics
Matches: 147, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.02
20 128 0.87
21 15 0.10
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:900 original size:40 final size:39
Alignment explanation
Indices: 853--1046 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 39
843 GATTTTCAAG
* ** *
853 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
893 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* * * *
933 AATCGCAACGCGTATCAGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
973 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
1014 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1047 TATTTAAAGC
Statistics
Matches: 130, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 96 0.74
41 33 0.25
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:936 original size:60 final size:60
Alignment explanation
Indices: 853--1045 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
843 GATTTTCAAG
* ** *
853 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
* * * *
913 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATCA-GTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
* ** *
973 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT-AAATCGCAACGCGTATCCGTA
1034 AATCGCAACGCG
1 AATCGCAACGCG
1046 ATATTTAAAG
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
59 2 0.02
60 77 0.68
61 34 0.30
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
Found at i:1464 original size:33 final size:33
Alignment explanation
Indices: 1425--1495 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1415 TTCACTTAGA
1425 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1458 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1491 TTTCA
1 TTTCA
1496 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1619 original size:20 final size:20
Alignment explanation
Indices: 1575--1684 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
1565 TGCAGAAGAG
*
1575 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1596 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1616 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1637 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
1651 TCGCAACGTGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
1670 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1685 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1632 original size:41 final size:38
Alignment explanation
Indices: 1568--1684 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
1558 TTCAATTTGC
* *
1568 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1606 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1647 AG-A-A-TCGCAAC--GTGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1680 AGAAT
1 AGAAT
1685 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.16, G:0.26, T:0.12
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:1654 original size:14 final size:14
Alignment explanation
Indices: 1635--1691 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1625 GAGAAATGAA
1635 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1649 AATCGCAACGTGAAATGAA
1 AATCGCAAC--G--A-GAG
1668 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1682 AATCGCAACG
1 AATCGCAACG
1692 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1667 original size:33 final size:33
Alignment explanation
Indices: 1627--1707 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1617 CGCAACGAGA
*
1627 GAAATGAAAATCGCAACGAGAGAATCGCAACGT
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1660 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1693 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1708 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1725 original size:19 final size:19
Alignment explanation
Indices: 1703--1830 Score: 96
Period size: 19 Copynumber: 7.1 Consensus size: 19
1693 GAAACCAAAA
*
1703 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1722 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1738 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1755 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1769 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
1789 ATCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
1809 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1829 TC
1 TC
1831 AACCAAAAGA
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
14 18 0.20
16 9 0.10
17 9 0.10
19 20 0.23
20 18 0.20
21 14 0.16
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1744 original size:14 final size:14
Alignment explanation
Indices: 1725--1781 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1715 TTTCATTTCG
1725 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1739 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1756 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTTT
1772 CGTTGCGATT
1 CGTTGCGATT
1782 TTCATTTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1750 original size:33 final size:33
Alignment explanation
Indices: 1708--1830 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
1698 CAAAATCGCA
*
1708 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1741 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1774 TTGCGATTTTCATTTATCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
1815 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1831 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
33 44 0.55
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.26
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1815 original size:20 final size:20
Alignment explanation
Indices: 1765--1820 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
1755 TCGCGTTGCG
***
1765 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
*
1785 ATTTATCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGACAGTC
1806 ATTCTCTCGTTGCGA
1 ATTCTCTCGTTGCGA
1821 TTTTCATTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:1827 original size:20 final size:20
Alignment explanation
Indices: 1765--1828 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
1755 TCGCGTTGCG
1765 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* ***
1785 ATTTATCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
1806 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1826 ATT
1 ATT
1829 TCAACCAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:2284 original size:11 final size:11
Alignment explanation
Indices: 2270--2296 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2260 GACACGATGA
2270 TTTAATGTTTG
1 TTTAATGTTTG
2281 TTTAATGTTTG
1 TTTAATGTTTG
2292 TTTAA
1 TTTAA
2297 ACTATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (11 bp):
TTTAATGTTTG
Found at i:3332 original size:20 final size:22
Alignment explanation
Indices: 3309--3349 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
3299 TTGACATAAA
*
3309 TAATAT-TAAATAA-ATTATTC
1 TAATATATAAAAAATATTATTC
3329 TAATATATAAAAAATATTATT
1 TAATATATAAAAAATATTATT
3350 ATTTTGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 6 0.33
22 6 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATATATAAAAAATATTATTC
Found at i:3757 original size:22 final size:21
Alignment explanation
Indices: 3731--3771 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3721 CATAAAATTA
*
3731 TAAACCTTAAACCCTTACACTT
1 TAAACCATAAACCC-TACACTT
3753 TAAACCATAAACCCTACAC
1 TAAACCATAAACCCTACAC
3772 CCTAACCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACCATAAACCCTACACTT
Found at i:3814 original size:14 final size:14
Alignment explanation
Indices: 3753--3814 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
3743 CCTTACACTT
*
3753 TAAACCATAAACCC
1 TAAACCTTAAACCC
* *
3767 TACACCCT-AA-CC
1 TAAACCTTAAACCC
3779 TAAACC-TAAACACC
1 TAAACCTTAAAC-CC
*
3793 -AAAGCTTAAACCC
1 TAAACCTTAAACCC
3806 TAAACCTTA
1 TAAACCTTA
3815 GATCCAAACC
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
11 1 0.03
12 9 0.24
13 8 0.21
14 20 0.53
ACGTcount: A:0.45, C:0.35, G:0.02, T:0.18
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:15201 original size:21 final size:20
Alignment explanation
Indices: 15115--15272 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
15105 AAATGACCAA
**
15115 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
15134 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
15154 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
15174 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
15195 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
15216 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
15236 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
15257 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
15273 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:15265 original size:20 final size:20
Alignment explanation
Indices: 15240--15432 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
15230 GATTTTCAAG
* ** *
15240 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
15260 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
15280 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
15300 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
15320 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGTATCCGTA
*
15340 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
15360 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
15380 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
15401 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
15421 AATCGCAACGCG
1 AATCGCAACGCG
15433 ATATTTAAAG
Statistics
Matches: 147, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:15848 original size:33 final size:33
Alignment explanation
Indices: 15809--15879 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
15799 TTCACTTAGA
15809 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
15842 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
15875 TTTCA
1 TTTCA
15880 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:15984 original size:21 final size:20
Alignment explanation
Indices: 15958--16063 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
15948 TGCAGAAGAG
15958 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
15979 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
15999 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
16020 TCGTAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
16034 TCGCAACGTG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
16053 TCGCAACGAGA
1 TCGCAACGAGA
16064 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:16015 original size:41 final size:38
Alignment explanation
Indices: 15951--16067 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
15941 TTCAATTTGC
* *
15951 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
15989 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGTAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
16030 AG-A-A-TCGCAAC--GTGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
16063 AGAAT
1 AGAAT
16068 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.15, G:0.26, T:0.13
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:16041 original size:14 final size:14
Alignment explanation
Indices: 16018--16074 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
16008 GAGAAATGAA
*
16018 AATCGTAACGAGAG
1 AATCGCAACGAGAG
*
16032 AATCGCAACGTGAAATGAA
1 AATCGCAAC--G--A-GAG
16051 AATCGCAACGAGAG
1 AATCGCAACGAGAG
16065 AATCGCAACG
1 AATCGCAACG
16075 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:16050 original size:33 final size:33
Alignment explanation
Indices: 16010--16090 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
16000 CGCAACGAGA
* *
16010 GAAATGAAAATCGTAACGAGAGAATCGCAACGT
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
16043 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
16076 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
16091 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:16108 original size:19 final size:19
Alignment explanation
Indices: 16086--16213 Score: 96
Period size: 19 Copynumber: 7.1 Consensus size: 19
16076 GAAACCAAAA
*
16086 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
16105 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
16121 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
16138 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
16152 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
16172 ATCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
16192 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
16212 TC
1 TC
16214 AACCAAAGAC
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
14 18 0.20
16 9 0.10
17 9 0.10
19 20 0.23
20 18 0.20
21 14 0.16
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:16127 original size:14 final size:14
Alignment explanation
Indices: 16108--16164 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
16098 TTTCATTTCG
16108 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
16122 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
16139 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTTT
16155 CGTTGCGATT
1 CGTTGCGATT
16165 TTCATTTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:16133 original size:33 final size:33
Alignment explanation
Indices: 16091--16213 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
16081 CAAAATCGCA
*
16091 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
16124 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
16157 TTGCGATTTTCATTTATCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
16198 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
16214 AACCAAAGAC
Statistics
Matches: 80, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
33 44 0.55
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.26
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:16198 original size:20 final size:20
Alignment explanation
Indices: 16148--16203 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
16138 TCGCGTTGCG
***
16148 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
*
16168 ATTTATCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGACAGTC
16189 ATTCTCTCGTTGCGA
1 ATTCTCTCGTTGCGA
16204 TTTTCATTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:16210 original size:20 final size:20
Alignment explanation
Indices: 16148--16211 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
16138 TCGCGTTGCG
16148 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* ***
16168 ATTTATCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
16189 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
16209 ATT
1 ATT
16212 TCAACCAAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Done.