Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003312.1 Hibiscus syriacus cultivar Beakdansim tig00006971_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: 51987
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1482 original size:42 final size:42
Alignment explanation
Indices: 1415--1538 Score: 166
Period size: 42 Copynumber: 3.0 Consensus size: 42
1405 CCCCACTTTT
* *
1415 TCATCGAG-TCGATTCTCCACTTCGACACCGAGATCTATCACC
1 TCATCGAGCT-GATTCTACACCTCGACACCGAGATCTATCACC
*
1457 TCATCGAGCTGATTCTACACCTCGACACCAAGATCTATCACC
1 TCATCGAGCTGATTCTACACCTCGACACCGAGATCTATCACC
* *
1499 TC-T--AACTGATTCTACACCTCGACACCGAGATCCATCACC
1 TCATCGAGCTGATTCTACACCTCGACACCGAGATCTATCACC
1538 T
1 T
1539 ATTCCATCAA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
39 34 0.45
41 1 0.01
42 39 0.52
43 1 0.01
ACGTcount: A:0.27, C:0.36, G:0.12, T:0.25
Consensus pattern (42 bp):
TCATCGAGCTGATTCTACACCTCGACACCGAGATCTATCACC
Found at i:1519 original size:39 final size:41
Alignment explanation
Indices: 1425--1538 Score: 160
Period size: 39 Copynumber: 2.8 Consensus size: 41
1415 TCATCGAGTC
* * *
1425 GATTCTCCACTTCGACACCGAGATCTATCACCTCATCGAGCT
1 GATTCTACACCTCGACACCGAGATCTATCACCTCATC-AACT
*
1467 GATTCTACACCTCGACACCAAGATCTATCACCTC-T-AACT
1 GATTCTACACCTCGACACCGAGATCTATCACCTCATCAACT
*
1506 GATTCTACACCTCGACACCGAGATCCATCACCT
1 GATTCTACACCTCGACACCGAGATCTATCACCT
1539 ATTCCATCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 34 0.52
41 1 0.02
42 31 0.47
ACGTcount: A:0.27, C:0.37, G:0.11, T:0.25
Consensus pattern (41 bp):
GATTCTACACCTCGACACCGAGATCTATCACCTCATCAACT
Found at i:1660 original size:21 final size:21
Alignment explanation
Indices: 1631--1724 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
1621 TCTTCACCTC
* * *
1631 TACGGGATGAGTTAGGTGTTT
1 TACGTGATGAGATAGGTGCTT
*
1652 TACGTGATGAGGTAGGTGCTT
1 TACGTGATGAGATAGGTGCTT
*
1673 TACGTGATGACA-ATGGTGCTT
1 TACGTGATGAGATA-GGTGCTT
1694 TACGTGATGAGATAGGTGCTT
1 TACGTGATGAGATAGGTGCTT
1715 TACGTGATGA
1 TACGTGATGA
1725 TAATGGTGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.10, G:0.34, T:0.34
Consensus pattern (21 bp):
TACGTGATGAGATAGGTGCTT
Found at i:1697 original size:42 final size:42
Alignment explanation
Indices: 1645--1732 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
1635 GGATGAGTTA
* *
1645 GGTGTTTTACGTGATGAGGTAGGTGCTTTACGTGATGACAAT
1 GGTGCTTTACGTGATGAGATAGGTGCTTTACGTGATGACAAT
*
1687 GGTGCTTTACGTGATGAGATAGGTGCTTTACGTGATGATAAT
1 GGTGCTTTACGTGATGAGATAGGTGCTTTACGTGATGACAAT
1729 GGTG
1 GGTG
1733 GTAGGTGCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.09, G:0.34, T:0.35
Consensus pattern (42 bp):
GGTGCTTTACGTGATGAGATAGGTGCTTTACGTGATGACAAT
Found at i:1732 original size:21 final size:21
Alignment explanation
Indices: 1666--1773 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 21
1656 TGATGAGGTA
1666 GGTGCTTTACGTGATGACAAT
1 GGTGCTTTACGTGATGACAAT
*
1687 GGTGCTTTACGTGATGA-GAT
1 GGTGCTTTACGTGATGACAAT
*
1707 AGGTGCTTTACGTGATGATAATGGTGGT
1 -GGTGCTTTACGTGATGACAA------T
*
1735 AGGTGCTTTATGTGATGACAAT
1 -GGTGCTTTACGTGATGACAAT
1757 GGTGCTTTACGTGATGA
1 GGTGCTTTACGTGATGA
1774 AGTATGTGCT
Statistics
Matches: 74, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
20 2 0.03
21 50 0.68
22 2 0.03
28 20 0.27
ACGTcount: A:0.22, C:0.10, G:0.32, T:0.35
Consensus pattern (21 bp):
GGTGCTTTACGTGATGACAAT
Found at i:1749 original size:28 final size:28
Alignment explanation
Indices: 1706--1760 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1696 CGTGATGAGA
*
1706 TAGGTGCTTTACGTGATGATAATGGTGG
1 TAGGTGCTTTACGTGATGACAATGGTGG
*
1734 TAGGTGCTTTATGTGATGACAATGGTG
1 TAGGTGCTTTACGTGATGACAATGGTG
1761 CTTTACGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.07, G:0.35, T:0.36
Consensus pattern (28 bp):
TAGGTGCTTTACGTGATGACAATGGTGG
Found at i:2156 original size:21 final size:21
Alignment explanation
Indices: 2122--2173 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
2112 GAAGAAGCCT
* *
2122 GATCCACCTACCATTATTCAG
1 GATCCATCTCCCATTATTCAG
* *
2143 GGTCCATCTCCCATTCTTCAG
1 GATCCATCTCCCATTATTCAG
*
2164 GATTCATCTC
1 GATCCATCTC
2174 TCATCGTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.33
Consensus pattern (21 bp):
GATCCATCTCCCATTATTCAG
Found at i:3614 original size:13 final size:13
Alignment explanation
Indices: 3596--3624 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3586 ATTTTCTTTA
3596 AAAATCAATTTTG
1 AAAATCAATTTTG
3609 AAAATCAATTTTG
1 AAAATCAATTTTG
3622 AAA
1 AAA
3625 TTACTCCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (13 bp):
AAAATCAATTTTG
Found at i:5786 original size:23 final size:23
Alignment explanation
Indices: 5756--5836 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
5746 TGCATGGCCT
5756 TGTGCATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGG
* * *
5779 TGTGCATCGGTGCACCTTCATGG
1 TGTGCATCGATGCACATTCAAGG
5802 TGT--ATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGG
*
5823 -ATGCATCGATGCAC
1 TGTGCATCGATGCAC
5837 TGTTAGGTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.31
22 10 0.20
23 23 0.47
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.27
Consensus pattern (23 bp):
TGTGCATCGATGCACATTCAAGG
Found at i:5811 original size:44 final size:42
Alignment explanation
Indices: 5735--5855 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 42
5725 AAAACCTGAT
* ** *
5735 GGATGCATCGATGCA-TGGCCTTGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACT-GTCAGGTGTATCGATGCACATTCAA
* *
5777 GGTGTGCATCGGTGCACCT-TCATGGTGTATCGATGCACATTCAA
1 GG-ATGCATCGATGCA-CTGTCA-GGTGTATCGATGCACATTCAA
*
5821 GGATGCATCGATGCACTGTTAGGTGTATCGATGCA
1 GGATGCATCGATGCACTGTCAGGTGTATCGATGCA
5856 TTAAGCACAA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
42 18 0.28
43 25 0.38
44 21 0.32
45 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (42 bp):
GGATGCATCGATGCACTGTCAGGTGTATCGATGCACATTCAA
Found at i:5852 original size:20 final size:21
Alignment explanation
Indices: 5761--5855 Score: 95
Period size: 21 Copynumber: 4.4 Consensus size: 21
5751 GGCCTTGTGC
5761 ATCGATGCACATTCAAGGTGT
1 ATCGATGCACATTCAAGGTGT
* * *
5782 GCATCGGTGCACCTTCATGGTGT
1 --ATCGATGCACATTCAAGGTGT
*
5805 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
5827 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
5847 ATCGATGCA
1 ATCGATGCA
5856 TTAAGCACAA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.18
21 19 0.31
22 13 0.21
23 18 0.30
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:6523 original size:28 final size:27
Alignment explanation
Indices: 6476--6534 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
6466 CATAATTTTG
* *
6476 TTTCTTTGAAACCAATAGATTAGCATA
1 TTTCATTGAAACCAAGAGATTAGCATA
*
6503 TTTCATTGAAAACCAAGAGATTATCATA
1 TTTCATTG-AAACCAAGAGATTAGCATA
6531 TTTC
1 TTTC
6535 CAAGGAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (27 bp):
TTTCATTGAAACCAAGAGATTAGCATA
Found at i:7737 original size:34 final size:30
Alignment explanation
Indices: 7699--7773 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 30
7689 TTGATATAAC
7699 AATTTATGGCAAAATAGTTTTTGGACTTGAATTG
1 AATTTAT--CAAAAT-GTTTTTGGACTT-AATTG
7733 AATTTA-CAAAATGTTTTTGGACTTAATTG
1 AATTTATCAAAATGTTTTTGGACTTAATTG
7762 AATTTATTCAAA
1 AATTTA-TCAAA
7774 GTTTTAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.28
30 12 0.31
31 10 0.26
34 6 0.15
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
AATTTATCAAAATGTTTTTGGACTTAATTG
Found at i:7749 original size:30 final size:30
Alignment explanation
Indices: 7708--7767 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
7698 CAATTTATGG
7708 CAAAATAGTTTTTGGACTTGAATTGAATTTA
1 CAAAATAGTTTTTGGACTT-AATTGAATTTA
7739 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATAGTTTTTGGACTTAATTGAATTTA
7768 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATAGTTTTTGGACTTAATTGAATTTA
Found at i:7970 original size:20 final size:20
Alignment explanation
Indices: 7945--8018 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
7935 AATGCAATTA
* *
7945 GTGCATCAATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
**
7965 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
7986 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
8006 GTGCATCCATGCA
1 GTGCATCGATGCA
8019 CGAAGGCTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:7989 original size:21 final size:21
Alignment explanation
Indices: 7963--8027 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
7953 ATGCATCCTT
7963 CTGTGCATCGATGCATCAAGG
1 CTGTGCATCGATGCATCAAGG
**
7984 CTGTGCATCGATGCATC-CTG
1 CTGTGCATCGATGCATCAAGG
*
8004 CTGTGCATCCATGCA-CGAAGG
1 CTGTGCATCGATGCATC-AAGG
8025 CTG
1 CTG
8028 CAACGGCTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.41
21 21 0.57
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.25
Consensus pattern (21 bp):
CTGTGCATCGATGCATCAAGG
Found at i:7992 original size:41 final size:41
Alignment explanation
Indices: 7945--8027 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
7935 AATGCAATTA
* *
7945 GTGCATCAATGCATCCTTCTGTGCATCGATGCATC-AAGGCT
1 GTGCATCAATGCATCCTGCTGTGCATCCATGCA-CGAAGGCT
*
7986 GTGCATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCT
1 GTGCATCAATGCATCCTGCTGTGCATCCATGCACGAAGGCT
8027 G
1 G
8028 CAACGGCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.27
Consensus pattern (41 bp):
GTGCATCAATGCATCCTGCTGTGCATCCATGCACGAAGGCT
Found at i:10394 original size:24 final size:25
Alignment explanation
Indices: 10347--10409 Score: 101
Period size: 24 Copynumber: 2.5 Consensus size: 25
10337 TATTCACAAC
*
10347 TTCATTTTTTTGAATCAATTTTTTTT
1 TTCATTTTTTTCAATCAA-TTTTTTT
10373 TTCATTTTTTTCAATCAA-TTTTTT
1 TTCATTTTTTTCAATCAATTTTTTT
10397 TTCATTTTTTTCA
1 TTCATTTTTTTCA
10410 TTTTTAGTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 19 0.53
26 17 0.47
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.68
Consensus pattern (25 bp):
TTCATTTTTTTCAATCAATTTTTTT
Found at i:24649 original size:45 final size:45
Alignment explanation
Indices: 24600--24687 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
24590 AAAATAGCCA
* * *
24600 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATCGTATGTGCATCGATGCATAAAATGCACT
24645 GAGTGCATCGATGCATCGTATGTGCATCGATGCATAAAATGCA
1 GAGTGCATCGATGCATCGTATGTGCATCGATGCATAAAATGCA
24688 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (45 bp):
GAGTGCATCGATGCATCGTATGTGCATCGATGCATAAAATGCACT
Found at i:28490 original size:3 final size:3
Alignment explanation
Indices: 28482--28527 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
28472 TCTTCAGTGA
28482 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
28528 AGGGGTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:28797 original size:24 final size:24
Alignment explanation
Indices: 28770--28823 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
28760 CTGAAACATC
28770 ATCAAAATATGAGTATTGACCAAG
1 ATCAAAATATGAGTATTGACCAAG
* * * *
28794 ATCAAAGTCTGGGTATTGACCAAT
1 ATCAAAATATGAGTATTGACCAAG
28818 ATCAAA
1 ATCAAA
28824 TTTCAAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATATGAGTATTGACCAAG
Found at i:29832 original size:41 final size:40
Alignment explanation
Indices: 29779--29868 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
29769 ATCGCAACTC
* * *
29779 AAATTCAGAATTCGCAACACGAAAATCACAACTCGAAAATG
1 AAATTC-GAATTCGAAAAACAAAAATCACAACTCGAAAATG
* *
29820 AAATTCGCAATTCGAAAAATAAAAATCGCAACTCGAAAATG
1 AAATTCG-AATTCGAAAAACAAAAATCACAACTCGAAAATG
29861 AAATTCGA
1 AAATTCGA
29869 GTTGCGAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 2 0.05
41 41 0.95
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (40 bp):
AAATTCGAATTCGAAAAACAAAAATCACAACTCGAAAATG
Found at i:29834 original size:20 final size:20
Alignment explanation
Indices: 29807--29867 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
29797 ACGAAAATCA
29807 CAACTCGAAAATGAAATTCG
1 CAACTCGAAAATGAAATTCG
* * *
29827 CAATTCGAAAAATAAAAATCG
1 CAACTCG-AAAATGAAATTCG
29848 CAACTCGAAAATGAAATTCG
1 CAACTCGAAAATGAAATTCG
29868 AGTTGCGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (20 bp):
CAACTCGAAAATGAAATTCG
Found at i:29848 original size:21 final size:21
Alignment explanation
Indices: 29800--29858 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
29790 TCGCAACACG
* *
29800 AAAATCACAACTCG-AAAATG
1 AAAATCGCAACTCGAAAAATA
* *
29820 AAATTCGCAATTCGAAAAATA
1 AAAATCGCAACTCGAAAAATA
29841 AAAATCGCAACTCGAAAA
1 AAAATCGCAACTCGAAAA
29859 TGAAATTCGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.54, C:0.19, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCGCAACTCGAAAAATA
Found at i:29876 original size:20 final size:20
Alignment explanation
Indices: 29853--29978 Score: 90
Period size: 20 Copynumber: 6.2 Consensus size: 20
29843 AATCGCAACT
29853 CGAAAATGAAATTCGAGTTG
1 CGAAAATGAAATTCGAGTTG
** ** *
29873 CGAATTTGATTTTCGAGTTA
1 CGAAAATGAAATTCGAGTTG
* * * *
29893 AGAAAACGAAACTCGTGTTG
1 CGAAAATGAAATTCGAGTTG
** * *
29913 CGAATTTAAAAATCGAGTTG
1 CGAAAATGAAATTCGAGTTG
* *
29933 CGAAAAAGAAATTCGTGTTG
1 CGAAAATGAAATTCGAGTTG
*
29953 CGAAAATGTCAAATTCAAGTTG
1 CGAAAATG--AAATTCGAGTTG
29975 CGAA
1 CGAA
29979 TTCGACTTCT
Statistics
Matches: 74, Mismatches: 30, Indels: 2
0.70 0.28 0.02
Matches are distributed among these distances:
20 60 0.81
22 14 0.19
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (20 bp):
CGAAAATGAAATTCGAGTTG
Found at i:29913 original size:40 final size:40
Alignment explanation
Indices: 29854--29956 Score: 116
Period size: 40 Copynumber: 2.6 Consensus size: 40
29844 ATCGCAACTC
* * * ***
29854 GAAAATGAAATTCGAGTTGCGAATTTGATTTTCGAGTTAA
1 GAAAAAGAAATTCGTGTTGCGAATTTAAAAATCGAGTTAA
* * **
29894 GAAAACGAAACTCGTGTTGCGAATTTAAAAATCGAGTTGC
1 GAAAAAGAAATTCGTGTTGCGAATTTAAAAATCGAGTTAA
29934 GAAAAAGAAATTCGTGTTGCGAA
1 GAAAAAGAAATTCGTGTTGCGAA
29957 AATGTCAAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (40 bp):
GAAAAAGAAATTCGTGTTGCGAATTTAAAAATCGAGTTAA
Found at i:29974 original size:22 final size:20
Alignment explanation
Indices: 29928--29978 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
29918 TTAAAAATCG
*
29928 AGTTGCGAAAAAGAAATTCG
1 AGTTGCGAAAAAGAAATTCA
* *
29948 TGTTGCGAAAATGTCAAATTCA
1 AGTTGCGAAAAAG--AAATTCA
29970 AGTTGCGAA
1 AGTTGCGAA
29979 TTCGACTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 11 0.44
22 14 0.56
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (20 bp):
AGTTGCGAAAAAGAAATTCA
Found at i:30014 original size:20 final size:20
Alignment explanation
Indices: 29962--30021 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
29952 GCGAAAATGT
*
29962 CAAATTCAAGTTGCGAATT-
1 CAAATTCGAGTTGCGAATTC
* * *
29981 CGACTTCTGTGTTGCGAATTC
1 CAAATTC-GAGTTGCGAATTC
*
30002 CAAATTCGAGTTGCAAATTC
1 CAAATTCGAGTTGCGAATTC
30022 GGAAACTGTG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 5 0.16
20 21 0.68
21 5 0.16
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (20 bp):
CAAATTCGAGTTGCGAATTC
Found at i:30560 original size:17 final size:17
Alignment explanation
Indices: 30527--30564 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
30517 TGGTAAACAC
30527 AAAACAATTTTTGTCTT
1 AAAACAATTTTTGTCTT
*
30544 AAAA-AATTATTTTTCTT
1 AAAACAATT-TTTGTCTT
30561 AAAA
1 AAAA
30565 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (17 bp):
AAAACAATTTTTGTCTT
Found at i:30703 original size:21 final size:21
Alignment explanation
Indices: 30679--30718 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30669 AGTAAAATCA
* *
30679 TAATTGTTTTTTAAAAATGTT
1 TAATTGCTTTTAAAAAATGTT
30700 TAATTGCTTTTAAAAAATG
1 TAATTGCTTTTAAAAAATG
30719 GTTATGACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (21 bp):
TAATTGCTTTTAAAAAATGTT
Found at i:36144 original size:79 final size:79
Alignment explanation
Indices: 36011--36168 Score: 264
Period size: 79 Copynumber: 2.0 Consensus size: 79
36001 AACAAAAATA
* * *
36011 AATCAAATTTTGTTTAAAATATGTCATGTATTAATATGAATAATTAACACCCTTCTTAGTTGTCC
1 AATCAAATTTTGTTCAAAATATGTCATGTATTAATATGAATAATTAACAACCTTCTTAGTTGTCA
*
36076 TTGTTTACTTAATC
66 TTGATTACTTAATC
36090 AATC-AATTTTAGTTCAAAATATGTCATGTATTAATATGAATAATTAACAACCTTCTTAGTTGTC
1 AATCAAATTTT-GTTCAAAATATGTCATGTATTAATATGAATAATTAACAACCTTCTTAGTTGTC
36154 ATTGATTACTTAATC
65 ATTGATTACTTAATC
36169 GCTTGTGAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
78 6 0.08
79 68 0.92
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (79 bp):
AATCAAATTTTGTTCAAAATATGTCATGTATTAATATGAATAATTAACAACCTTCTTAGTTGTCA
TTGATTACTTAATC
Found at i:40502 original size:21 final size:20
Alignment explanation
Indices: 40478--40595 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 20
40468 CAGTTCCCAG
40478 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
40498 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
40519 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
40541 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
40561 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
40581 AATCGCAACGCGATT
1 AATCGCAACGCGATT
40596 CTGACTATCT
Statistics
Matches: 76, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
19 2 0.03
20 36 0.47
21 34 0.45
22 3 0.04
23 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:40566 original size:20 final size:20
Alignment explanation
Indices: 40541--40816 Score: 200
Period size: 20 Copynumber: 13.7 Consensus size: 20
40531 GATTTTCCAG
** *
40541 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
40561 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
40581 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * * *
40600 CTATCTCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
* * *
40622 AATCGCAATGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
*
40642 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
* *
40663 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* * *
40683 ATTCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
40703 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
40723 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
40743 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
40763 AATCGCAATGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
40784 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
40804 AATCGCAACGCGA
1 AATCGCAACGCGA
40817 TCTCCGGTAT
Statistics
Matches: 198, Mismatches: 47, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
19 1 0.01
20 149 0.75
21 47 0.24
22 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:40645 original size:81 final size:81
Alignment explanation
Indices: 40541--40816 Score: 292
Period size: 81 Copynumber: 3.4 Consensus size: 81
40531 GATTTTCCAG
* * * *
40541 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGT-A-TAT
* * *
40604 CTCAACGAGTATCCGTAA
64 CGCAACGAGAATACGTAA
* * * *
40622 AATCGCAATGCGTATCTGTAAATCGCAACGACAATACGTA-AAATCGTAACGCGTATCCGTA-AT
1 AATCGCAACGCGTATCTGTAAATCGCAACG-CGA-ACATATAAATCGCAACGCGTATCCGTATA-
40685 TCGCAACGAGAATACGT-A
63 TCGCAACGAGAATACGTAA
* * ** * *
40703 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTATATCG
* *
40768 CAATGACAATACGTAA
66 CAACGAGAATACGTAA
*
40784 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGA
40817 TCTCCGGTAT
Statistics
Matches: 163, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
79 1 0.01
80 35 0.21
81 90 0.55
82 28 0.17
83 8 0.05
84 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (81 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTATATCG
CAACGAGAATACGTAA
Found at i:40717 original size:40 final size:41
Alignment explanation
Indices: 40606--40813 Score: 303
Period size: 41 Copynumber: 5.1 Consensus size: 41
40596 CTGACTATCT
* * * *
40606 CAACGAGTATCCGTAAAATCGCAATGCGTATCTGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
* * *
40647 CAACGACAATACGTAAAATCGTAACGCGTATCCGTAATTCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
40688 CAACGAGAATACGT-AAATCGCAACGCGTATCTGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
40728 CAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
* *
40768 CAATGACAATACGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
40809 CAACG
1 CAACG
40814 CGATCTCCGG
Statistics
Matches: 149, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 73 0.49
41 76 0.51
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (41 bp):
CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
Found at i:41700 original size:24 final size:24
Alignment explanation
Indices: 41673--41726 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
41663 GTATTCGAAA
41673 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
41697 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
41721 TTTGAT
1 TTTGAT
41727 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:44194 original size:20 final size:20
Alignment explanation
Indices: 44157--44245 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
44147 CAACACGGAA
44157 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
* *
44177 ATCGTAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
44197 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
44217 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
44237 ATCGCAACG
1 ATCGCAACG
44246 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 57 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:44267 original size:33 final size:33
Alignment explanation
Indices: 44217--44312 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
44207 GGAATTGACT
* **
44217 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
44251 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
44284 ATCGAAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
44313 CAAAATTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:44510 original size:14 final size:14
Alignment explanation
Indices: 44491--44527 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
44481 CATCAATTAA
44491 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
44505 ACAAATCATCTTTT
1 ACAAATCAACATTT
44519 ACAAATCAA
1 ACAAATCAA
44528 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:46478 original size:20 final size:20
Alignment explanation
Indices: 46455--46541 Score: 140
Period size: 20 Copynumber: 4.3 Consensus size: 20
46445 GAAACTTAAA
*
46455 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
46475 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
46495 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
46515 ATCGCAATGC-AAATTTGACT
1 ATCGCAATGCGAAA-ATGACT
46535 ATCGCAA
1 ATCGCAA
46542 CGAGAGAATC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 3 0.05
20 61 0.95
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:46598 original size:19 final size:19
Alignment explanation
Indices: 46576--46619 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
46566 AAATCGCAAC
46576 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* *
46595 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
46614 GCGATT
1 GCGATT
46620 TTGTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.30, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:46620 original size:19 final size:19
Alignment explanation
Indices: 46585--46670 Score: 101
Period size: 19 Copynumber: 4.8 Consensus size: 19
46575 CGCGATTATA
46585 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
46604 GTTTCGCGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTG
46622 G--T--CGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
* *
46637 GTTTCGTGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTG
* *
46656 ATTTCTCGTTGCGAT
1 GTTTCGCGTTGCGAT
46671 AGTCATTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.21
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 41 0.72
ACGTcount: A:0.07, C:0.16, G:0.28, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:46629 original size:14 final size:14
Alignment explanation
Indices: 46610--46636 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46600 TTTGGTTTCG
46610 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
46624 CGTTGCGATTTTG
1 CGTTGCGATTTTG
46637 GTTTCGTGTT
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:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:46633 original size:33 final size:33
Alignment explanation
Indices: 46591--46654 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
46581 TATAGTTTCG
46591 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
*
46624 CGTTGCGATTTTGGTTTCGTGTTGCGATTTT
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTTT
46655 CATTTCTCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.06, C:0.14, G:0.30, T:0.50
Consensus pattern (33 bp):
CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
Found at i:46904 original size:94 final size:94
Alignment explanation
Indices: 46758--47137 Score: 622
Period size: 94 Copynumber: 4.1 Consensus size: 94
46748 ATGGATTGCA
* *
46758 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
46822 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
46851 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACTGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
46916 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
46945 TTACTTTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCACAGTGTTAAAGAATACACACT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
47010 TTAGCAGAACTGGTAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
47039 TTAC-TTCAACCAAAAGACAAAACAAAAGA-AAATTACTAACTTCACAGTGTTAAAGAATAAACA
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAA-TACTAACTTCACAGTGTTAAAGAATACACA
* *
47102 GTTTAGCAGTATTGGCAGCAACCGAATAAAT
64 GTTTAGCAGAATTGGCAGCAACCGAACAAAT
47133 TTACT
1 TTACT
47138 AAGCAATCTA
Statistics
Matches: 269, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
93 26 0.10
94 243 0.90
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:48855 original size:20 final size:20
Alignment explanation
Indices: 48832--48887 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
48822 TGAAATGAAA
*
48832 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATAACT
48852 ATCGCAATGCG-GA-AATAACT
1 ATCGCAA--CGAGAGAATAACT
48872 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
48888 CGCAACACGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 23 0.74
21 2 0.06
22 2 0.06
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATAACT
Found at i:48891 original size:14 final size:14
Alignment explanation
Indices: 48872--48927 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
48862 GGAAATAACT
48872 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
48886 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
48905 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
48919 ATCGCAACG
1 ATCGCAACG
48928 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 17 0.49
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.23
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:48909 original size:33 final size:33
Alignment explanation
Indices: 48872--48946 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
48862 GGAAATAACT
48872 ATCGCAACGAGAGAATCGCAACACGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACACGAAATGAAA
* *
48905 ATCGCAACGAGAGAATCGCAACGCGAAATTAAA
1 ATCGCAACGAGAGAATCGCAACACGAAATGAAA
48938 ATCGCAACG
1 ATCGCAACG
48947 CGAAATGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAACACGAAATGAAA
Found at i:48968 original size:19 final size:19
Alignment explanation
Indices: 48823--48968 Score: 98
Period size: 19 Copynumber: 8.1 Consensus size: 19
48813 GTCTTTGGTT
*
48823 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
48842 GAGAATGACTATCGCAATGC
1 GA-AATGAAAATCGCAACGC
*
48862 GGAAAT-AACTATCGCAA--C
1 -GAAATGAA-AATCGCAACGC
* *
48880 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACGC
48896 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
48913 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
48929 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
48948 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
48967 GA
1 GA
48969 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
14 17 0.17
15 3 0.03
16 4 0.04
17 3 0.03
18 3 0.03
19 44 0.44
20 24 0.24
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:49014 original size:21 final size:20
Alignment explanation
Indices: 48988--49065 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 20
48978 CGCGTTGCGA
*
48988 TTCTCTCGTTGCGATTTTTAT
1 TTCTCT-GTTGCGATTTTCAT
**
49009 TTCTCTCGTTGCGATAGTCAT
1 TTCTCT-GTTGCGATTTTCAT
49030 TT-TCGTGTTGCGATTTTCAT
1 TTCTC-TGTTGCGATTTTCAT
*
49050 TTC-ATGTTGCGATTTT
1 TTCTCTGTTGCGATTTT
49066 AAGTTAGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.24
20 16 0.33
21 21 0.43
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.53
Consensus pattern (20 bp):
TTCTCTGTTGCGATTTTCAT
Found at i:49041 original size:20 final size:19
Alignment explanation
Indices: 49016--49062 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
49006 TATTTCTCTC
*
49016 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCA-TTTCAT
**
49036 GTTGCGATTTTCATTTCAT
1 GTTGCGATAGTCATTTCAT
49055 GTTGCGAT
1 GTTGCGAT
49063 TTTAAGTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.47
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCAT
Found at i:49448 original size:22 final size:22
Alignment explanation
Indices: 49396--49448 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
49386 GTGAATGGTT
*
49396 GTGAGGGATTTCGCCGGAGATG
1 GTGAGAGATTTCGCCGGAGATG
* * *
49418 GGGACAGATTTCGCCGTAGA-G
1 GTGAGAGATTTCGCCGGAGATG
49439 AGTGAGAGAT
1 -GTGAGAGAT
49449 GGAGATGGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.25, C:0.13, G:0.42, T:0.21
Consensus pattern (22 bp):
GTGAGAGATTTCGCCGGAGATG
Found at i:49636 original size:20 final size:19
Alignment explanation
Indices: 49601--49882 Score: 174
Period size: 20 Copynumber: 13.9 Consensus size: 19
49591 TTTAAAAATC
*
49601 GCGTTGCGATTTTACGTATT
1 GCGTTGCGA-TTTACGGATT
*
49621 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTACGGAT-T
* *
49642 GCATTGCGATTTACGTATT
1 GCGTTGCGATTTACGGATT
* *
49661 CTCGTTGCGATTTACAGATAT
1 -GCGTTGCGATTTACGGAT-T
*
49682 GCGTTGCGATTTACGTATT
1 GCGTTGCGATTTACGGATT
* * *
49701 CTCGTTGCGATTTATGGATAC
1 -GCGTTGCGATTTACGGAT-T
* *
49722 GCGTTGCGATTTTATGTATT
1 GCGTTGCGA-TTTACGGATT
*
49742 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTACGGAT-T
49763 GCGTTGCGATTTTACGGATACT
1 GCGTTGCGA-TTTACGGAT--T
* * *
49785 -CGTTGCGATAGT-CAGAATC
1 GCGTTGCGAT-TTAC-GGATT
* *
49804 GCGTTGCGATTTATGGATAC
1 GCGTTGCGATTTACGGAT-T
* *
49824 GCGTTGCGATTTTATGTATT
1 GCGTTGCGA-TTTACGGATT
*
49844 GTCGTTGCGATTTAC-GATAC
1 G-CGTTGCGATTTACGGAT-T
49864 GCGTTGCGATTTTACGGAT
1 GCGTTGCGA-TTTACGGAT
49883 ATCGTGCGAT
Statistics
Matches: 206, Mismatches: 35, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
19 15 0.07
20 124 0.60
21 67 0.33
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.39
Consensus pattern (19 bp):
GCGTTGCGATTTACGGATT
Found at i:49660 original size:40 final size:41
Alignment explanation
Indices: 49600--49793 Score: 293
Period size: 40 Copynumber: 4.8 Consensus size: 41
49590 CTTTAAAAAT
*
49600 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* *
49641 CGCATTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* *
49681 TGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* *
49721 CGCGTTGCGATTTTATGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* *
49762 CGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGAT
49794 AGTCAGAATC
Statistics
Matches: 137, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 73 0.53
41 64 0.47
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:49814 original size:102 final size:99
Alignment explanation
Indices: 49703--49933 Score: 392
Period size: 102 Copynumber: 2.3 Consensus size: 99
49693 TACGTATTCT
49703 CGTTGCGATTTATGGATACGCGTTGCGATTTTATGTATTGTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTATGGATACGCGTTGCGATTTTATGTATTGTCGTTGCGATTTAC-GATACGCGTT
49768 GCGATTTTACGGATACTCGTTGCGATAGTCAGAATCG
65 GCGATTTTACGGATA-TCG-TGCGATAGTCAGAATCG
49805 CGTTGCGATTTATGGATACGCGTTGCGATTTTATGTATTGTCGTTGCGATTTACGATACGCGTTG
1 CGTTGCGATTTATGGATACGCGTTGCGATTTTATGTATTGTCGTTGCGATTTACGATACGCGTTG
*
49870 CGATTTTACGGATATCGTGCGATAGTCAGAATTG
66 CGATTTTACGGATATCGTGCGATAGTCAGAATCG
* *
49904 CGTTGCGATTTATATG-TTCGCGTTGCGATT
1 CGTTGCGATTTAT-GGATACGCGTTGCGATT
49934 CTGGAAAATC
Statistics
Matches: 125, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
99 42 0.34
100 4 0.03
101 25 0.20
102 54 0.43
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.38
Consensus pattern (99 bp):
CGTTGCGATTTATGGATACGCGTTGCGATTTTATGTATTGTCGTTGCGATTTACGATACGCGTTG
CGATTTTACGGATATCGTGCGATAGTCAGAATCG
Found at i:50032 original size:20 final size:19
Alignment explanation
Indices: 49982--50036 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
49972 ATTCTTCATA
49982 ATCGCGTTTGCGATTCTGGG
1 ATCGCG-TTGCGATTCTGGG
* **
50002 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
50023 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
50037 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.35
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Done.