Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003852.1 Hibiscus syriacus cultivar Beakdansim tig00008270_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: 155662
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:764 original size:106 final size:108
Alignment explanation
Indices: 459--1082 Score: 555
Period size: 109 Copynumber: 5.9 Consensus size: 108
449 GTTCCGAGTC
* * ** * **
459 CAATATCCTCCG-CTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGATGACAGTCAG
1 CAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* * * * *
523 CCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-C-
65 CTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * * * *
565 TAATATCTTTCG-CTGTGAAGTTGAAATTGACTCTG-AA---CGAAA-T-CTTGTTGACAATCAG
1 CAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* *
623 CCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGT-C-
65 CTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * *
665 CAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACAACCAG
1 CAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
*
729 CTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCA
65 CTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * ** * * *
774 CGATATCCTCCGTCGTGGAGTTGAAAATCGCGATGAAACT-GAAAAGTTGTTTATTGACAACCAG
1 CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACAACCAG
* * * *
838 -TCATCCCTTCGTTGTGAAGTTGGACTTGTGTTTTCTCGGGTAGCA
65 CT-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * * * *
883 CGATATCCTCCGTCGTGGAGTTGAAATCGGTTCTGGAATTGGGAAGTTGTTCGTTGACAACCAG-
1 CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGC
*
947 TCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCA
66 T-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * * *
992 CGATATCCTCCGTCGTGGAGTTGAAATCGGTTCCGAAATTGGGAAATTG-TTGTTGGCAACCAGA
1 CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG-
1056 C-GTCCCTTCGTTGTGAAGTTGAACTTG
65 CTGTCCCTTCGTTGTGAAGTTGAACTTG
1083 ACTCTAGCTA
Statistics
Matches: 445, Mismatches: 58, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
100 81 0.18
101 3 0.01
102 4 0.01
104 3 0.01
105 3 0.01
106 83 0.19
108 45 0.10
109 219 0.49
110 4 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (108 bp):
CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGC
TGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
Found at i:1590 original size:61 final size:65
Alignment explanation
Indices: 1440--1894 Score: 241
Period size: 73 Copynumber: 6.8 Consensus size: 65
1430 AAGATATCTG
* * * *
1440 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTCTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGT-TTAAGGGAAATAAATTTCAAGAT
1505 TT
64 TT
* * *
1507 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAATAAA-TTCAA-A-T
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAGGGAAATAAATTTCAAGATT
1569 T
65 T
** * * **
1570 TTGTTTCAAG-GAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT-AAGGGAAA-----T-AA-A-TT
* **
1634 ACAA-AACT
57 TCAAGATTT
* * * ** * * *
1642 TAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAA-AGAAA-ACATATCAA-ATA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT-AAGGGAAATAAATTTCAAGAT-
1704 TT
64 TT
* * * **
1706 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT-AAGGGAAA-----T-AA-A-TT
* *
1771 ACAA-AATT
57 TCAAGATTT
* * * * **
1779 TTGTTTCAAGGGAAACTAG-CTCAAGAGAGACGAAATTTATTTCAAGGGAAAT-GTTTTCAATG-
1 TTGTTTCAAGAGAAACT-GTCTCAAGGGAGACAAAATTTGTTT-AAGGGAAATAAATTTCAA-GA
1841 TTT
63 TTT
*
1844 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT-AAGGGAAA
1895 CTGTCTCAAG
Statistics
Matches: 305, Mismatches: 55, Indels: 58
0.73 0.13 0.14
Matches are distributed among these distances:
61 27 0.09
62 14 0.05
63 7 0.02
64 44 0.14
65 55 0.18
66 12 0.04
67 5 0.02
68 35 0.11
69 1 0.00
71 4 0.01
72 14 0.05
73 82 0.27
74 5 0.02
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAGGGAAATAAATTTCAAGATTT
Found at i:1620 original size:36 final size:36
Alignment explanation
Indices: 1564--1914 Score: 299
Period size: 36 Copynumber: 10.1 Consensus size: 36
1554 GGAATAAATT
* *
1564 CAAATTTTGTTTCAA-GGAAACTGTCTCAAGATAGA
1 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* *
1599 CGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* * ** *
1635 CAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGA
1 CAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
** * * * *
1672 TGAAATTTGTTTCAAAGAAAAC-ATATC-----A-A
1 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* *
1701 -ATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
*
1736 CAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1772 CAAAATTTTGTTTCAAGGGAAACTAG-CTCAAGAGAGA
1 CAAAA-TTTGTTTCAAGGGAAACT-GTCTCAAGAGAGA
* * * *
1809 CGAAATTTATTTCAAGGGAAA-TGTTTTC-A-A-TG-
1 CAAAATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGA
* * *
1841 ----TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 CAAAATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGA
1874 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1910 CAAAA
1 CAAAA
1915 CTCTTCTAGT
Statistics
Matches: 251, Mismatches: 41, Indels: 47
0.74 0.12 0.14
Matches are distributed among these distances:
28 18 0.07
29 19 0.08
30 4 0.02
32 1 0.00
33 1 0.00
34 3 0.01
35 19 0.08
36 121 0.48
37 64 0.25
38 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
Found at i:1665 original size:37 final size:36
Alignment explanation
Indices: 1580--1671 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
1570 TTGTTTCAAG
* * * * *
1580 GAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
1616 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
*
1653 GAAACTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
1672 TGAAATTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 22 0.45
37 27 0.55
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:1733 original size:101 final size:101
Alignment explanation
Indices: 1604--1787 Score: 280
Period size: 101 Copynumber: 1.8 Consensus size: 101
1594 ATAGACGAAA
*
1604 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAG
**
1669 AGATGAAA-TTTGTTTCAAAGAAAACATATCAAATAT
65 AGACAAAATTTTGTTTCAAAGAAAACATATCAAATAT
* * * **
1705 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
1770 GACAAAATTTTGTTTCAA
66 GACAAAATTTTGTTTCAA
1788 GGGAAACTAG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
100 26 0.35
101 48 0.65
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (101 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTTGTTTCAAAGAAAACATATCAAATAT
Found at i:1764 original size:137 final size:134
Alignment explanation
Indices: 1521--1916 Score: 492
Period size: 137 Copynumber: 2.9 Consensus size: 134
1511 TTTCAAGAGT
* * *
1521 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAATAAATTCAA-ATTTTGTTTCAA-GGAAA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCA-AGGAA-AAATTCAATATTTTGTTTCAAGGGAAA
* * *
1584 CTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC
64 CTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC
1649 AAAAGA
129 AAAAGA
* *
1655 AACTGTCTCAAGGGAGATGAAATTTGTTTCAAAGAAAACATATCAAATATTTTGTTTCAAGGGAA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAA-AT-TC-AATATTTTGTTTCAAGGGAA
* * * *
1720 ACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTT
63 ACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTC
**
1785 CAAGGGA
128 CAAAAGA
* * ** * *
1792 AACTAG-CTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAG
1 AACT-GTCTCAAGGGAGACGAAATTTGTTTCAA-GGAAA--AATTCAATATTT-TGTTTCAAGGG
*
1856 AAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
61 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
1917 CTTCTAGTGA
Statistics
Matches: 227, Mismatches: 25, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
132 2 0.01
133 5 0.02
134 30 0.13
135 2 0.01
136 12 0.05
137 100 0.44
138 75 0.33
139 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (134 bp):
AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAAATTCAATATTTTGTTTCAAGGGAAACT
GTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA
AAGA
Found at i:1822 original size:73 final size:73
Alignment explanation
Indices: 1698--1914 Score: 267
Period size: 73 Copynumber: 3.1 Consensus size: 73
1688 GAAAACATAT
1698 CAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCT
1 CAAA-ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCT
1763 CAAGAGAGA
65 CAAGAGAGA
* *
1772 CAAAATTTTGTTTCAAGGGAAACTAG-CTCAAGAGAGACGAAATTTATTTCAAGGGAAA-TGTTT
1 CAAAATTTTGTTTCAAGGGAAACT-GTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTG-TC
*
1835 TC-A-A-TG-
64 TCAAGAGAGA
* * *
1841 -----TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCT
1 CAAAATTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCT
1901 CAAGAGAGA
65 CAAGAGAGA
1910 CAAAA
1 CAAAA
1915 CTCTTCTAGT
Statistics
Matches: 120, Mismatches: 9, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
64 4 0.03
65 47 0.39
66 3 0.03
67 1 0.01
68 1 0.01
70 1 0.01
71 1 0.01
72 3 0.03
73 54 0.45
74 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.28
Consensus pattern (73 bp):
CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTC
AAGAGAGA
Found at i:2423 original size:18 final size:18
Alignment explanation
Indices: 2392--2427 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2382 TGTTGAATCC
* *
2392 CCAAAGATGTCCCAATAT
1 CCAAAAATGCCCCAATAT
2410 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
2428 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:2880 original size:22 final size:22
Alignment explanation
Indices: 2855--2898 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2845 CATTTTTGTT
2855 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
2877 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
2899 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:3475 original size:16 final size:17
Alignment explanation
Indices: 3454--3517 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 17
3444 TTTGCATGTG
3454 CTTTTTGTCTTTT-TTT
1 CTTTTTGTCTTTTCTTT
*
3470 CTTTTTGATTTTGTTCTTT
1 CTTTTTG-TCTT-TTCTTT
* *
3489 CTCTTT-TCTTTTGTTT
1 CTTTTTGTCTTTTCTTT
*
3505 CTCTTTTTTCTTT
1 CT-TTTTGTCTTT
3518 GTTTTTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 14 0.37
17 9 0.24
18 7 0.18
19 8 0.21
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.77
Consensus pattern (17 bp):
CTTTTTGTCTTTTCTTT
Found at i:3515 original size:18 final size:18
Alignment explanation
Indices: 3478--3521 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3468 TTCTTTTTGA
*
3478 TTTTGTTCTTTCTCTTTTC
1 TTTTGTT-TCTCTCTTTTC
*
3497 TTTTGTTTCTCTTTTTTC
1 TTTTGTTTCTCTCTTTTC
3515 -TTTGTTT
1 TTTTGTTT
3522 TTGATTGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 9 0.39
19 7 0.30
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (18 bp):
TTTTGTTTCTCTCTTTTC
Found at i:3518 original size:17 final size:16
Alignment explanation
Indices: 3486--3521 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3476 GATTTTGTTC
3486 TTTCTCTTTTCTTTTG
1 TTTCTCTTTTCTTTTG
*
3502 TTTCTCTTTTTTCTTTG
1 TTTCTCTTTTCT-TTTG
3519 TTT
1 TTT
3522 TTGATTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.78
Consensus pattern (16 bp):
TTTCTCTTTTCTTTTG
Found at i:4639 original size:8 final size:8
Alignment explanation
Indices: 4623--4661 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
4613 AATGTTGATG
4623 AAAATGCA
1 AAAATGCA
*
4631 AAAAGGCA
1 AAAATGCA
4639 AAAATGC-
1 AAAATGCA
4646 AAAATGCA
1 AAAATGCA
*
4654 AGAATGCA
1 AAAATGCA
4662 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:4649 original size:15 final size:15
Alignment explanation
Indices: 4623--4661 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4613 AATGTTGATG
4623 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
4639 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
4654 AGAATGCA
1 AAAATGCA
4662 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:7099 original size:15 final size:15
Alignment explanation
Indices: 7081--7110 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7071 AAAACCATAT
7081 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
7096 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
7111 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:7117 original size:15 final size:15
Alignment explanation
Indices: 7084--7118 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7074 ACCATATTAG
* *
7084 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
7099 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
7114 ATAAA
1 ATAAA
7119 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:7221 original size:13 final size:12
Alignment explanation
Indices: 7203--7308 Score: 76
Period size: 13 Copynumber: 8.8 Consensus size: 12
7193 AATAGTAAGT
7203 AAAATAAATATAA
1 AAAATAAATA-AA
*
7216 AAAATAAAGAAA
1 AAAATAAATAAA
*
7228 AAGAAGAAA-AAA
1 AA-AATAAATAAA
* *
7240 ATATAGAAATAAA
1 A-AAATAAATAAA
7253 ACAAATAAATAAA
1 A-AAATAAATAAA
*
7266 ATAAT-AATAAA
1 AAAATAAATAAA
* *
7277 AAAGTAAA-AAT
1 AAAATAAATAAA
7288 AAAA-AAATAAA
1 AAAATAAATAAA
*
7299 AAAGTAAATA
1 AAAATAAATA
7309 TATATATATA
Statistics
Matches: 74, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
10 3 0.04
11 19 0.26
12 23 0.31
13 29 0.39
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:7240 original size:21 final size:21
Alignment explanation
Indices: 7214--7265 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
7204 AAATAAATAT
*
7214 AAAAAATAAAGAAA-AAGAAGA
1 AAAAAATAAAGAAATAA-AACA
*
7235 AAAAAATATAGAAATAAAACA
1 AAAAAATAAAGAAATAAAACA
*
7256 AATAAATAAA
1 AAAAAATAAA
7266 ATAATAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAAAATAAAGAAATAAAACA
Found at i:7290 original size:14 final size:14
Alignment explanation
Indices: 7203--7300 Score: 69
Period size: 14 Copynumber: 6.7 Consensus size: 14
7193 AATAGTAAGT
*
7203 AAAATAAATAT-AA
1 AAAATAAAAATAAA
7216 AAAATAAAGAA-AAA
1 AAAATAAA-AATAAA
7230 GAAGAA-AAAAATATAGA
1 -AA-AATAAAAATA-A-A
7247 AATAA-AACAAATAAA
1 AA-AATAA-AAATAAA
*
7262 TAAAATAATAATAAA
1 -AAAATAAAAATAAA
*
7277 AAAGTAAAAATAAA
1 AAAATAAAAATAAA
7291 AAAATAAAAA
1 AAAATAAAAA
7301 AGTAAATATA
Statistics
Matches: 69, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
13 8 0.12
14 26 0.38
15 15 0.22
16 14 0.20
17 6 0.09
ACGTcount: A:0.79, C:0.01, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:7300 original size:9 final size:9
Alignment explanation
Indices: 7202--7301 Score: 53
Period size: 9 Copynumber: 10.8 Consensus size: 9
7192 AAATAGTAAG
*
7202 TAAAATAAA
1 TAAAAAAAA
*
7211 TATAAAAAA
1 TAAAAAAAA
7220 TAAAGAAAAA
1 TAAA-AAAAA
*
7230 GAAGAAAAAA
1 TAA-AAAAAA
* *
7240 -ATATAGAAA
1 TA-AAAAAAA
*
7249 TAAAACAAA
1 TAAAAAAAA
*
7258 TAAATAAAA
1 TAAAAAAAA
7267 TAATAATAAAA
1 TAA-AA-AAAA
*
7278 -AAGTAAAAA
1 TAA-AAAAAA
7287 T-AAAAAAA
1 TAAAAAAAA
7295 TAAAAAA
1 TAAAAAA
7302 GTAAATATAT
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
8 6 0.09
9 40 0.58
10 18 0.26
11 5 0.07
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:7773 original size:36 final size:37
Alignment explanation
Indices: 7701--7801 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 37
7691 GTGCTTGTGG
* * * *
7701 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
7738 ATCCTATTTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
7774 ATCCTATTTTT-GAGAGTTTGAATCCTAG
1 ATCCTATTTTTAG-GAGTTTGAATCCTAG
7802 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.02
36 30 0.53
37 26 0.46
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:14512 original size:55 final size:55
Alignment explanation
Indices: 14440--14557 Score: 166
Period size: 55 Copynumber: 2.1 Consensus size: 55
14430 CAGTGTTGTG
* * * *
14440 TCCAGATTGACCTGATTTCCTCATAGAGAATG-AACAATGTTAACACCAAATTATC
1 TCCAGATTAACCAGATTTCCTCAAAGAGAA-GAAACAATGTCAACACCAAATTATC
* *
14495 TTCAGATTAACCAGATTTCCTCAAAGAGAAGAAACAGTGTCAACACCAAATTATC
1 TCCAGATTAACCAGATTTCCTCAAAGAGAAGAAACAATGTCAACACCAAATTATC
14550 TCCAGATT
1 TCCAGATT
14558 GACTCGACGT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 1 0.02
55 54 0.98
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (55 bp):
TCCAGATTAACCAGATTTCCTCAAAGAGAAGAAACAATGTCAACACCAAATTATC
Found at i:14582 original size:55 final size:55
Alignment explanation
Indices: 14457--14591 Score: 148
Period size: 55 Copynumber: 2.5 Consensus size: 55
14447 TGACCTGATT
* * * * **
14457 TCCTCATAGAGAATG-AACAATGTTAACACCAAATTATCTTCAGATTAACCAGATT
1 TCCTCAAAGAGAA-GAAACAGTGTCAACACCAAATTATCTCCAGATTAACCAGACG
*
14512 TCCTCAAAGAGAAGAAACAGTGTCAACACCAAATTATCTCCAGATTGACTC-GACG
1 TCCTCAAAGAGAAGAAACAGTGTCAACACCAAATTATCTCCAGATTAAC-CAGACG
* * *
14567 TCCTTATAGATAAGAAACAGTGTCA
1 TCCTCAAAGAGAAGAAACAGTGTCA
14592 TCACGCGAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
54 1 0.01
55 66 0.97
56 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (55 bp):
TCCTCAAAGAGAAGAAACAGTGTCAACACCAAATTATCTCCAGATTAACCAGACG
Found at i:14838 original size:290 final size:290
Alignment explanation
Indices: 14318--14840 Score: 806
Period size: 290 Copynumber: 1.8 Consensus size: 290
14308 TGTGATGGCC
* *
14318 AGATCTCTTCAATGCAGATGAGAAATGTCGTATTCAGATTGACCTGACGTCCTCAGAGAGAAGGA
1 AGATCTCTTCAATGCAGATGAGAAATGTCGTATCCAGATTGACCCGACGTCCTCAGAGAGAAGGA
* * * * *
14383 ACACTATCATCACCCTAAAACATCCAGATCTCTTCAATGTGGATGAGCAGTGTTGTGTCCAGATT
66 ACAATATAATCACCCTAAAACATCCAGATCTCTTCAATGCGGATAAGCAGTGTTGTCTCCAGATT
* * * * *
14448 GACCTGATTTCCTCATAGAGAATGAACAATGTTAACACCAAATTATCTTCAGATTAACCAGATTT
131 GACCCGATTTCCTCAGAGAGAATGAACAATATCAACACCAAATTATCTCCAGATTAACCAGATTT
14513 CCTCAAAGAGAAGAAACAGTGTCAACACCAAATTATCTCCAGATTGACTCGACGTCCTTATAGAT
196 CCTCAAAGAGAAGAAACAGTGTCAACACCAAATTATCTCCAGATTGACTCGACGTCCTTATAGAT
14578 AAGAAACAGTGTCATCACGCGAAAGTGCCT
261 AAGAAACAGTGTCATCACGCGAAAGTGCCT
*
14608 AGATCTCTTCAATGCAGATGA-ACAATGTCGTCTCCAGATTGACCCGACGTCCTCAGA-ATGAAG
1 AGATCTCTTCAATGCAGATGAGA-AATGTCGTATCCAGATTGACCCGACGTCCTCAGAGA-GAAG
*
14671 GAACAATATAATCACCCTAAAATCA-CCAGATCTCTTCAATGCGGATAAGCAGTGTTGTCTCTAG
64 GAACAATATAATCACCCTAAAA-CATCCAGATCTCTTCAATGCGGATAAGCAGTGTTGTCTCCAG
*
14735 ATTGACCCGATTTCCTCAGAGAGAAAT-AACATTATCAACACCAAATTATCTCCAGATTAACCTA
128 ATTGACCCGATTTCCTCAGAGAG-AATGAACAATATCAACACCAAATTATCTCCAGATTAACC-A
*
14799 -ATTTCCTCATAGAGAATG-AACAGTGTCAACACCAAATTATCT
191 GATTTCCTCAAAGAGAA-GAAACAGTGTCAACACCAAATTATCT
14841 TCATATTAAC
Statistics
Matches: 211, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
289 2 0.01
290 202 0.96
291 7 0.03
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (290 bp):
AGATCTCTTCAATGCAGATGAGAAATGTCGTATCCAGATTGACCCGACGTCCTCAGAGAGAAGGA
ACAATATAATCACCCTAAAACATCCAGATCTCTTCAATGCGGATAAGCAGTGTTGTCTCCAGATT
GACCCGATTTCCTCAGAGAGAATGAACAATATCAACACCAAATTATCTCCAGATTAACCAGATTT
CCTCAAAGAGAAGAAACAGTGTCAACACCAAATTATCTCCAGATTGACTCGACGTCCTTATAGAT
AAGAAACAGTGTCATCACGCGAAAGTGCCT
Found at i:14958 original size:55 final size:55
Alignment explanation
Indices: 14728--14959 Score: 304
Period size: 55 Copynumber: 4.2 Consensus size: 55
14718 AGCAGTGTTG
* * *
14728 TCTCTAGATTGACCCGATTTCCTCAGAGAGAAAT-AACATTATCAACACCAAATTA
1 TCTCCAGATTGACCCGATTTCCTCATAGAG-AATGAACAGTATCAACACCAAATTA
* ** *
14783 TCTCCAGATTAACCTAATTTCCTCATAGAGAATGAACAGTGTCAACACCAAATTA
1 TCTCCAGATTGACCCGATTTCCTCATAGAGAATGAACAGTATCAACACCAAATTA
* * * * *
14838 TCTTCATATTAACCCGATTTTCTCATAGAGAATGAACAGTTTCAACACCAAATTA
1 TCTCCAGATTGACCCGATTTCCTCATAGAGAATGAACAGTATCAACACCAAATTA
* * * *
14893 TCTTCAGATTGACCCGATTGCCTCATAGAGAATGAACAATATCAATACCAAATTA
1 TCTCCAGATTGACCCGATTTCCTCATAGAGAATGAACAGTATCAACACCAAATTA
14948 TCTCCAGATTGA
1 TCTCCAGATTGA
14960 TCCAACGTCC
Statistics
Matches: 155, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
54 3 0.02
55 152 0.98
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (55 bp):
TCTCCAGATTGACCCGATTTCCTCATAGAGAATGAACAGTATCAACACCAAATTA
Found at i:15342 original size:3 final size:3
Alignment explanation
Indices: 15334--15369 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
15324 ATTTTACGTT
15334 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15370 GTACATTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16755 original size:31 final size:31
Alignment explanation
Indices: 16720--16797 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
16710 CAGTTACGTC
16720 GGGGACCATATTGCAAACAAACTAAATGTTG
1 GGGGACCATATTGCAAACAAACTAAATGTTG
* *
16751 GGGGACCATATTGAAAACGAACTAAATGTTG
1 GGGGACCATATTGCAAACAAACTAAATGTTG
* **
16782 GGAGACTGTATTGCAA
1 GGGGACCATATTGCAA
16798 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAAACTAAATGTTG
Found at i:19443 original size:31 final size:31
Alignment explanation
Indices: 19384--19443 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
19374 TTACAATGCA
* * *
19384 ATCCCCTAATATTTAGTCCATTTTCAATATG
1 ATCCCCCAACATTTAGTCCATTTGCAATATG
**
19415 ATCCCCCAACATTTAGTCTGTTTGCAATA
1 ATCCCCCAACATTTAGTCCATTTGCAATA
19444 CGGCCCCTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (31 bp):
ATCCCCCAACATTTAGTCCATTTGCAATATG
Found at i:19717 original size:2 final size:2
Alignment explanation
Indices: 19706--19745 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
19696 TATTTTTACC
19706 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19746 TTTTCTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27479 original size:20 final size:20
Alignment explanation
Indices: 27451--27491 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27441 TTTTAATTTT
* *
27451 AAATCAAATACTTAAATATA
1 AAATAAAATAATTAAATATA
*
27471 AAATAAAATAATTCAATATA
1 AAATAAAATAATTAAATATA
27491 A
1 A
27492 TTATTTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAAATAATTAAATATA
Found at i:28779 original size:174 final size:174
Alignment explanation
Indices: 28489--28831 Score: 569
Period size: 174 Copynumber: 2.0 Consensus size: 174
28479 TTCCAGTCTA
*
28489 GTGAAATTACGAACATACATTGATGTTGCATGACTTTTATTTTTGGTCATTACTTTCTCCAAATC
1 GTGAAATTACGAACATACATTGATGTTGCATGACTTTGATTTTTGGTCATTACTTTCTCCAAATC
* * *
28554 TAGAGCCCAATTTCTACCTTCGTTGAGCATTGCCTCTAGCTAGGCACTTTTGTCTGCCCAAACTT
66 TAGAGCCCAATTTCTAACTTCATTGAGCATTGCCTCTACCTAGGCACTTTTGTCTGCCCAAACTT
* *
28619 TACCCAATTTGAAGTATGTCTCCCGAACAATACTTACCAGTTTG
131 TACCCAATTTGAAGTATGTCTCCCAAACAATAATTACCAGTTTG
* * * * *
28663 GTGAAATTATGAACATACATTGATGTTGGATGAGTTTGATTTTTGGTCATTGCTTTCTCCAGATC
1 GTGAAATTACGAACATACATTGATGTTGCATGACTTTGATTTTTGGTCATTACTTTCTCCAAATC
* *
28728 TAGAGCCCAATTTCTAACTTCATTGAGCATTGCCTTTACCTGGGCACTTTTGTCTGCCCAAACTT
66 TAGAGCCCAATTTCTAACTTCATTGAGCATTGCCTCTACCTAGGCACTTTTGTCTGCCCAAACTT
28793 TACCCAATTTGAAGTATGTCTCCCAAACAATAATTACCA
131 TACCCAATTTGAAGTATGTCTCCCAAACAATAATTACCA
28832 CCGAAAGATG
Statistics
Matches: 156, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
174 156 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (174 bp):
GTGAAATTACGAACATACATTGATGTTGCATGACTTTGATTTTTGGTCATTACTTTCTCCAAATC
TAGAGCCCAATTTCTAACTTCATTGAGCATTGCCTCTACCTAGGCACTTTTGTCTGCCCAAACTT
TACCCAATTTGAAGTATGTCTCCCAAACAATAATTACCAGTTTG
Found at i:33564 original size:19 final size:19
Alignment explanation
Indices: 33544--33579 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
33534 CTTCAATTAT
33544 TTTAAT-TTTATTTATTTA
1 TTTAATATTTATTTATTTA
33562 TTTAATATTTATTTATTT
1 TTTAATATTTATTTATTT
33580 TGGCCACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTAATATTTATTTATTTA
Found at i:36386 original size:20 final size:20
Alignment explanation
Indices: 36361--36495 Score: 114
Period size: 20 Copynumber: 6.7 Consensus size: 20
36351 AATTGGGAAA
36361 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
36381 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
36401 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
36422 ATCGCAACGAGATACTGACCT
1 ATCGCAATGCGATACTGA-CT
* *
36443 -TCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
36462 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
36482 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
36496 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.06
20 63 0.66
21 24 0.25
22 1 0.01
23 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:36407 original size:61 final size:61
Alignment explanation
Indices: 36358--36489 Score: 176
Period size: 61 Copynumber: 2.2 Consensus size: 61
36348 GCGAATTGGG
* * * * *
36358 AAAATCGCAATGCGATACTGA-CTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACCT-TCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
36419 AAAATCGCAACGAGATACTGACCTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACCTTCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
36480 ATAATCGCAA
1 AAAATCGCAA
36490 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACCTTCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:36691 original size:22 final size:22
Alignment explanation
Indices: 36663--36706 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
36653 CACTCTCTCA
36663 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
36685 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
36707 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:36997 original size:20 final size:20
Alignment explanation
Indices: 36948--37011 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
36938 GCGATTTTAG
*
36948 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
* *
36968 ATTCACGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
36988 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
37008 TTTC
1 TTTC
37012 AGAAAATATT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:38347 original size:18 final size:18
Alignment explanation
Indices: 38326--38370 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
38316 TCCACTTCGG
*
38326 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
38344 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
38362 GAGCCATCA
1 GAGCCATCA
38371 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:38906 original size:19 final size:20
Alignment explanation
Indices: 38852--38918 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
38842 TAATTTACTT
* *
38852 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
38872 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
38892 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
38911 TCGCAACG
1 TCGCAACG
38919 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:38985 original size:14 final size:14
Alignment explanation
Indices: 38966--39055 Score: 81
Period size: 14 Copynumber: 5.8 Consensus size: 14
38956 TTGTGTTTCG
38966 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
38980 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
38996 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
39012 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
39029 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
39045 CGTTGCGATTT
1 CGTTGCGATTT
39056 GCATTTCGCA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 26 0.41
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.10
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:39030 original size:33 final size:33
Alignment explanation
Indices: 38961--39072 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
38951 GCGATTTGTG
*
38961 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
38993 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
39026 TTTCGCATTGCGATTTTGTCGTTGCGATTTGCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
39059 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
39073 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 26 0.34
33 51 0.66
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:39091 original size:20 final size:19
Alignment explanation
Indices: 39057--39112 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
39047 TTGCGATTTG
*
39057 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
39076 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
39096 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
39113 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:39572 original size:40 final size:40
Alignment explanation
Indices: 39477--39563 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
39467 GACTCACCTG
* *
39477 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CC-ACCGTTCAAGAGGCCACTA
* *
39519 TCCTCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTA
39559 TCATC
1 TCATC
39564 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 20 0.50
41 2 0.05
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.21
Consensus pattern (40 bp):
TCATCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTA
Found at i:40991 original size:13 final size:13
Alignment explanation
Indices: 40973--40998 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40963 TTGATTGTTT
40973 AATGATTTGTAAA
1 AATGATTTGTAAA
40986 AATGATTTGTAAA
1 AATGATTTGTAAA
40999 TGTTGATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
AATGATTTGTAAA
Found at i:41169 original size:19 final size:17
Alignment explanation
Indices: 41144--41193 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
41134 TATCCCAACG
41144 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
41162 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
41177 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
41194 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:41278 original size:20 final size:20
Alignment explanation
Indices: 41220--41288 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
41210 CGATTTTCTA
41220 GTTGCGATAGCCATTTTTCGC
1 GTTGCGATAGCCA-TTTTCGC
***
41241 GTTGCGATTTTTCA-TTTCGC
1 GTTGCGA-TAGCCATTTTCGC
41261 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*
41281 GCTGCGAT
1 GTTGCGAT
41289 TTCCCCGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.08
20 26 0.67
21 7 0.18
22 3 0.08
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:42659 original size:12 final size:12
Alignment explanation
Indices: 42642--42678 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
42632 ATATAATCCT
42642 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42654 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42666 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42678 G
1 G
42679 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:44369 original size:40 final size:37
Alignment explanation
Indices: 44325--44437 Score: 126
Period size: 33 Copynumber: 3.1 Consensus size: 37
44315 TCTTTTGGTT
44325 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACG-GA-AATGAGAATCGCAACGC
**
44364 GGAAATGACTATCGCAAC---AA-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGGAAATGAGAATCGCAACGC
* *
44398 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACG-GAAATGAGAATCGCAACGC
44436 GA
1 GA
44438 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
33 15 0.24
34 14 0.23
35 2 0.03
37 2 0.03
38 14 0.23
40 15 0.24
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGGAAATGAGAATCGCAACGC
Found at i:44411 original size:19 final size:19
Alignment explanation
Indices: 44325--44437 Score: 119
Period size: 19 Copynumber: 6.1 Consensus size: 19
44315 TCTTTTGGTT
*
44325 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
44344 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
44364 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
44382 --AA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
44398 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
44417 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
44436 GA
1 GA
44438 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 9 0.11
15 2 0.03
16 1 0.01
18 3 0.04
19 35 0.44
20 27 0.34
21 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:44455 original size:19 final size:19
Alignment explanation
Indices: 44433--44477 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
44423 AAAATCGCAA
*
44433 TGCGATTTTGGTTTCACGT
1 TGCGATTTTGATTTCACGT
* *
44452 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCACGT
44471 TGCGATT
1 TGCGATT
44478 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCACGT
Found at i:45059 original size:20 final size:20
Alignment explanation
Indices: 45034--45121 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 20
45024 ATGTAAATCA
45034 CATTGCGATAGTAAG-ATTCG
1 CATTGCGAT-GTAAGTATTCG
* *
45054 CATTGCGATTTACGTATTCG
1 CATTGCGATGTAAGTATTCG
* *
45074 CATTGCGAT-TTACTAATTCG
1 CATTGCGATGTAAGT-ATTCG
* * *
45094 CGTTGCGATTTACGTATTCG
1 CATTGCGATGTAAGTATTCG
45114 CATTGCGA
1 CATTGCGA
45122 ATTATGAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
19 5 0.09
20 48 0.87
21 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
CATTGCGATGTAAGTATTCG
Found at i:45182 original size:21 final size:21
Alignment explanation
Indices: 45111--45183 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
45101 ATTTACGTAT
* *
45111 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
45132 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
45152 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
45173 TCGCATTGCGA
1 TCGCAATGCGA
45184 TAGTCAGTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:45222 original size:21 final size:21
Alignment explanation
Indices: 45196--45285 Score: 96
Period size: 20 Copynumber: 4.4 Consensus size: 21
45186 GTCAGTATCC
45196 CATTGCGATTTTCCAAATTCG
1 CATTGCGATTTTCCAAATTCG
** *
45217 CATTGCGATAGT-C-AGTATCG
1 CATTGCGATTTTCCAAAT-TCG
45237 CATTGCGATTTTCCAAATTCG
1 CATTGCGATTTTCCAAATTCG
* **
45258 CATTGCGA-TTTACTTATTCG
1 CATTGCGATTTTCCAAATTCG
45278 CATTGCGA
1 CATTGCGA
45286 ATTGGGAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.04
20 31 0.54
21 22 0.39
22 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
CATTGCGATTTTCCAAATTCG
Found at i:45278 original size:20 final size:21
Alignment explanation
Indices: 45049--45285 Score: 88
Period size: 20 Copynumber: 11.6 Consensus size: 21
45039 CGATAGTAAG
**
45049 ATTCGCATTGCGA-TTTACGT
1 ATTCGCATTGCGATTTTACAA
*
45069 ATTCGCATTGCGA-TTTACTA
1 ATTCGCATTGCGATTTTACAA
* **
45089 ATTCGCGTTGCGA-TTTACGT
1 ATTCGCATTGCGATTTTACAA
*
45109 ATTCGCATTGCGAATTATGA-AA
1 ATTCGCATTGCG-ATT-TTACAA
** *
45131 A-TCGCAACGCGA--ATACGTAA
1 ATTCGCATTGCGATTTTAC--AA
* * *
45151 A-TCGCAATGCGA-ATTAGGAA
1 ATTCGCATTGCGATTTTA-CAA
* **
45171 AATCGCATTGCGATAGT-C-A
1 ATTCGCATTGCGATTTTACAA
* * *
45190 GTATCCCATTGCGATTTTCCAA
1 AT-TCGCATTGCGATTTTACAA
**
45212 ATTCGCATTGCGATAGT-C-A
1 ATTCGCATTGCGATTTTACAA
* *
45231 GTATCGCATTGCGATTTTCCAA
1 AT-TCGCATTGCGATTTTACAA
**
45253 ATTCGCATTGCGA-TTTACTT
1 ATTCGCATTGCGATTTTACAA
45273 ATTCGCATTGCGA
1 ATTCGCATTGCGA
45286 ATTGGGAAAA
Statistics
Matches: 166, Mismatches: 35, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
17 1 0.01
19 3 0.02
20 106 0.64
21 46 0.28
22 8 0.05
23 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATTCGCATTGCGATTTTACAA
Found at i:45279 original size:41 final size:40
Alignment explanation
Indices: 45049--45285 Score: 149
Period size: 41 Copynumber: 5.8 Consensus size: 40
45039 CGATAGTAAG
* * *
45049 ATTCGCATTGCGATTTACGTATTCGCATTGCGA-TTTACTA
1 ATTCGCATTGCGA-TTACTTATTCGCATTGCGATTTTCCAA
* * * *
45089 ATTCGCGTTGCGATTTACGTATTCGCATTGCGAATTAT-GAA
1 ATTCGCATTGCGA-TTACTTATTCGCATTGCG-ATTTTCCAA
* ** * * * * * ***
45130 AATCGCAACGCGAATACGTAAATCGCAATGCGAATTAGGAA
1 ATTCGCATTGCGATTAC-TTATTCGCATTGCGATTTTCCAA
* * * *
45171 AATCGCATTGCGA-TAGTCAGTATCCCATTGCGATTTTCCAA
1 ATTCGCATTGCGATTACTTA-T-TCGCATTGCGATTTTCCAA
* *
45212 ATTCGCATTGCGA-TAGTCAGTATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGATTACTTA-T-TCGCATTGCGATTTTCCAA
45253 ATTCGCATTGCGATTTACTTATTCGCATTGCGA
1 ATTCGCATTGCGA-TTACTTATTCGCATTGCGA
45286 ATTGGGAAAA
Statistics
Matches: 158, Mismatches: 31, Indels: 15
0.77 0.15 0.07
Matches are distributed among these distances:
39 2 0.01
40 38 0.24
41 111 0.70
42 3 0.02
43 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (40 bp):
ATTCGCATTGCGATTACTTATTCGCATTGCGATTTTCCAA
Found at i:45327 original size:21 final size:22
Alignment explanation
Indices: 45275--45327 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
45265 ATTTACTTAT
45275 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* **
45296 TCACAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
45317 TCGCATTGCGA
1 TCGCATTGCGA
45328 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:46281 original size:27 final size:27
Alignment explanation
Indices: 46251--46309 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 27
46241 TATATTAATG
* *
46251 AATATTATAGGGTTTTTCTCTCTACCC
1 AATATTATAGGGGTTTCCTCTCTACCC
46278 AATA-T-TAGGGGTTTCCTCTCTACCC
1 AATATTATAGGGGTTTCCTCTCTACCC
46303 AATATTA
1 AATATTA
46310 GAGTTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 22 0.79
26 2 0.07
27 4 0.14
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (27 bp):
AATATTATAGGGGTTTCCTCTCTACCC
Found at i:46286 original size:25 final size:25
Alignment explanation
Indices: 46258--46317 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
46248 ATGAATATTA
46258 TAGGGTTTTTCTCTCTACCCAATAT
1 TAGGGTTTTTCTCTCTACCCAATAT
* *
46283 TAGGGGTTTCCTCTCTACCCAATAT
1 TAGGGTTTTTCTCTCTACCCAATAT
*
46308 TAGAGTTTTT
1 TAGGGTTTTT
46318 GACCATGTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (25 bp):
TAGGGTTTTTCTCTCTACCCAATAT
Found at i:79412 original size:26 final size:27
Alignment explanation
Indices: 79377--79428 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
79367 AGATTTAAGG
79377 TTTAAGGTTTATGATTTG-GGTTTGAA
1 TTTAAGGTTTATGATTTGTGGTTTGAA
*
79403 TTTAGGGTTTATGATTTGTGGTTTGA
1 TTTAAGGTTTATGATTTGTGGTTTGA
79429 GGTGGAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (27 bp):
TTTAAGGTTTATGATTTGTGGTTTGAA
Found at i:79874 original size:13 final size:13
Alignment explanation
Indices: 79856--79896 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
79846 CATGAACCGC
79856 GCCTTACGGCCGT
1 GCCTTACGGCCGT
*
79869 GCCTTACGGCCGC
1 GCCTTACGGCCGT
79882 GCCTTACGGCTCGT
1 GCCTTACGGC-CGT
79896 G
1 G
79897 TAAAGATCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 22 0.88
14 3 0.12
ACGTcount: A:0.07, C:0.39, G:0.32, T:0.22
Consensus pattern (13 bp):
GCCTTACGGCCGT
Found at i:80380 original size:14 final size:13
Alignment explanation
Indices: 80361--80390 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
80351 GGATCAAATG
80361 AATTATTATTTATT
1 AATTATTATTT-TT
80375 AATTATTATTTTT
1 AATTATTATTTTT
80388 AAT
1 AAT
80391 AACAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
AATTATTATTTTT
Found at i:81837 original size:19 final size:20
Alignment explanation
Indices: 81803--81840 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
81793 TATAATTTAA
81803 TTACATTTTAATTATATATC
1 TTACATTTTAATTATATATC
*
81823 TTACGTTTT-ATTATATAT
1 TTACATTTTAATTATATAT
81841 TTTATAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (20 bp):
TTACATTTTAATTATATATC
Found at i:82744 original size:31 final size:30
Alignment explanation
Indices: 82684--82752 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
82674 TTAGCGACTA
* *
82684 AAATTTAATAAATCGATTATATAAATGATT
1 AAATTTAATAAATCAATAATATAAATGATT
*
82714 AAATTTCAATAAATCAATAACT-TAAGTGATT
1 AAATTT-AATAAATCAATAA-TATAAATGATT
82745 AAAGTTTA
1 AAA-TTTA
82753 TGTTTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 6 0.18
31 23 0.70
32 4 0.12
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.38
Consensus pattern (30 bp):
AAATTTAATAAATCAATAATATAAATGATT
Found at i:85958 original size:84 final size:84
Alignment explanation
Indices: 85806--86053 Score: 273
Period size: 84 Copynumber: 2.9 Consensus size: 84
85796 AATTTATTGA
* * * * * * ** *
85806 CAGATAGCCCTTCTTGCCTTGAA-CTATGTTGTAAATTTGATTTGCCTCTGAGTTGAATGTAATC
1 CAGATAGCCCTTCTAGCCTT-AAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGCGTAGTC
* *
85870 GAACTCGAGGGTCTTTGGTTGG
63 GAACTCAAAGGTCTTTGGTTGG
* *
85892 CAGATAGCCCTTCTCGCCTTAAGCTATGCTGCAAAAGATGTGCCTTTGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
*
85957 CTCTAAGGTCTTTGGTTGG
66 CTCAAAGGTCTTTGGTTGG
* * * * * * *
85976 TAGATAACCCTTCTAGCCTTGAGTTATGCTGCAACTGATGTGCCTTGGAGCTAAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
86041 CTCAAAGGTCTTT
66 CTCAAAGGTCTTT
86054 TGTTTCAAGA
Statistics
Matches: 139, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
84 108 0.78
85 2 0.01
86 29 0.21
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (84 bp):
CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTGGTTGG
Found at i:86104 original size:36 final size:35
Alignment explanation
Indices: 86052--86156 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 35
86042 TCAAAGGTCT
* *
86052 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAA
1 TTTGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAA
86088 TTTGTTTCAATGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAA
*
86124 TTTTTTTCAAGGGAAACTGTCTCAAGAGA-ACAA
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAA
86157 TGGTGAGCAC
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 4 0.06
36 59 0.92
37 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (35 bp):
TTTGTTTCAAGGAAACTGTCTCAAGAGAGACAAAA
Found at i:86466 original size:106 final size:106
Alignment explanation
Indices: 86281--86956 Score: 1026
Period size: 106 Copynumber: 6.6 Consensus size: 106
86271 TATTGTTCCA
** * *
86281 AGTCCAATATCC-TCTGCCGTGAAGTTGAAATTGACTCTGGAA-CTGGGAAATTGTTTATTGACA
1 AGTCCAATATCCTTC-GTTGTGAAGTTGAAATTGGCTCTGAAATC-GGGAAATTGTTTATTGACA
*
86344 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
86387 AGTCCAATATCCTTCGTTGTGGAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
*
86452 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
86493 AGTCCAATATCCTTCGTTGTGAAGTTGAAA-------T----T-GGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
*
86546 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
86587 AGTCCAATATCCTTCGTTGTGAAGTTGAAA-------T----T-GGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
86640 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
86681 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
* *
86746 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
86787 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
*
86852 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
86893 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATGTGTTTGTTGACA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAAT-TGTTTATTGACA
86957 GACAACTTTT
Statistics
Matches: 538, Mismatches: 17, Indels: 29
0.92 0.03 0.05
Matches are distributed among these distances:
94 185 0.34
95 1 0.00
99 1 0.00
101 1 0.00
105 1 0.00
106 335 0.62
107 14 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:86521 original size:43 final size:43
Alignment explanation
Indices: 86460--86709 Score: 176
Period size: 43 Copynumber: 5.4 Consensus size: 43
86450 ACCAGCGGTC
86460 CCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT
* * * * ** ***
86503 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG-TT-TGGA-GTCCA-ATAT
86553 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT
* * * * ** ***
86597 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG-TT-TGGA-GTCCA-ATAT
*
86647 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT
*
86691 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
86710 ATTGGCTCTG
Statistics
Matches: 153, Mismatches: 38, Indels: 32
0.69 0.17 0.14
Matches are distributed among these distances:
43 62 0.41
44 2 0.01
45 6 0.04
46 12 0.08
47 7 0.05
48 12 0.08
49 6 0.04
50 2 0.01
51 44 0.29
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATAT
Found at i:86566 original size:51 final size:51
Alignment explanation
Indices: 86503--86666 Score: 182
Period size: 51 Copynumber: 3.4 Consensus size: 51
86493 AGTCCAATAT
*
86503 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
* * * ** ***
86554 CCTTCGTCGTGAAGTTGAACTTGCG---TTG-TT-TGGA-GTCCA-ATAT-
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
*
86597 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
86648 CCTTCGTCGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
86667 CTTGCGTTGT
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
43 22 0.26
44 1 0.01
45 3 0.03
46 6 0.07
47 4 0.05
48 6 0.07
49 3 0.03
50 1 0.01
51 40 0.47
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (51 bp):
CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
Found at i:86585 original size:94 final size:94
Alignment explanation
Indices: 86424--86926 Score: 727
Period size: 94 Copynumber: 5.1 Consensus size: 94
86414 AAATTGGCTC
*
86424 TGAAATCGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
86489 TTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
86518 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
86583 TTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
86612 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
86677 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
86706 TGAAATTGGCTCTGAAATCGGGAAATTATTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTG
1 TGAAA-------T----T-GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
86771 AACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
86812 TGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAA-------T----T-GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
86877 AACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
86918 TGAAATTGG
1 TGAAATTGG
86927 CTCTGAAATC
Statistics
Matches: 388, Mismatches: 9, Indels: 24
0.92 0.02 0.06
Matches are distributed among these distances:
94 193 0.50
95 1 0.00
99 1 0.00
101 1 0.00
105 1 0.00
106 191 0.49
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGT
Found at i:92178 original size:3 final size:3
Alignment explanation
Indices: 92170--92209 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
92160 TTAATAGAAT
* *
92170 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
92210 CATGTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:92206 original size:13 final size:13
Alignment explanation
Indices: 92148--92199 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 13
92138 AGTGGGGCCT
92148 ATAA-AAATAA-A
1 ATAATAAATAATA
92159 ATTAATAGAATTAATA
1 A-TAATA-AA-TAATA
92175 ATAAT-AATAATA
1 ATAATAAATAATA
92187 ATAATAAATAATA
1 ATAATAAATAATA
92200 TTTATAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
11 1 0.03
12 13 0.37
13 10 0.29
14 2 0.06
15 7 0.20
16 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (13 bp):
ATAATAAATAATA
Found at i:96611 original size:21 final size:21
Alignment explanation
Indices: 96585--96631 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
96575 ATAAAGAAAG
96585 TCTTGGAGATTGTTTCAAGGA
1 TCTTGGAGATTGTTTCAAGGA
*
96606 TCTTGGAGATTGTTTCAAGTA
1 TCTTGGAGATTGTTTCAAGGA
96627 TCTTG
1 TCTTG
96632 TCGGGAATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.43
Consensus pattern (21 bp):
TCTTGGAGATTGTTTCAAGGA
Found at i:97234 original size:30 final size:30
Alignment explanation
Indices: 97199--97262 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
97189 TGTTCTCTGA
97199 ATTATCAGGTACTTCTATTTCAGATTCTAT
1 ATTATCAGGTACTTCTATTTCAGATTCTAT
*
97229 ATTATCAGGTACTTCTATTTCAGATTCTGT
1 ATTATCAGGTACTTCTATTTCAGATTCTAT
97259 ATTA
1 ATTA
97263 AAGAAAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (30 bp):
ATTATCAGGTACTTCTATTTCAGATTCTAT
Found at i:97251 original size:15 final size:15
Alignment explanation
Indices: 97203--97251 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
97193 CTCTGAATTA
97203 TCAGGTACTTCTATT
1 TCAGGTACTTCTATT
* * *
97218 TCAGATTC-TATATT
1 TCAGGTACTTCTATT
97232 ATCAGGTACTTCTATT
1 -TCAGGTACTTCTATT
97248 TCAG
1 TCAG
97252 ATTCTGTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 5 0.19
15 16 0.62
16 5 0.19
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (15 bp):
TCAGGTACTTCTATT
Found at i:98196 original size:30 final size:30
Alignment explanation
Indices: 98160--98216 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
98150 CCCGAAGGAC
98160 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
98190 CTATCCAGAGGTCATAAAGATCCTCGG
1 CTATCCAGAGGTCATAAAGATCCTCGG
98217 CATCTGTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:98258 original size:31 final size:31
Alignment explanation
Indices: 98220--98338 Score: 89
Period size: 31 Copynumber: 3.8 Consensus size: 31
98210 TCCTCGGCAT
*
98220 CTGTCCATAGGTTCCGAAGAACCTAGGTAAA
1 CTGTCCATAGGTTCCGAAGAACATAGGTAAA
* ** *
98251 CTGTCCATATGTTCCTTAGAACATAGGTATA
1 CTGTCCATAGGTTCCGAAGAACATAGGTAAA
* * * *
98282 CTGTCTATATG-TCTCGAA-AGGCATAGGTAATT
1 CTGTCCATAGGTTC-CGAAGA-ACATAGGTAA-A
* * *
98314 CTATCCATATGTTCCGTAGAACATA
1 CTGTCCATAGGTTCCGAAGAACATA
98339 TGTATACCCT
Statistics
Matches: 68, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
30 3 0.04
31 46 0.68
32 16 0.24
33 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (31 bp):
CTGTCCATAGGTTCCGAAGAACATAGGTAAA
Found at i:103046 original size:31 final size:31
Alignment explanation
Indices: 102975--103100 Score: 130
Period size: 31 Copynumber: 4.0 Consensus size: 31
102965 TCCTCGGCAT
* * * *
102975 CTGTCCATAGGTTCCGAAGAACCTAGGTAAA
1 CTGTCCATATGTTCCTAAGAACATAGGTATA
* *
103006 CTGTCCATATGTTCCTTAGAACATAGATATA
1 CTGTCCATATGTTCCTAAGAACATAGGTATA
** *
103037 CTGTCCATATGTCTCGAAAG-ACATAGGTAATT
1 CTGTCCATATGT-TCCTAAGAACATAGGT-ATA
103069 CTGTCCATATGTT-CTATAGAACATAGGTATA
1 CTGTCCATATGTTCCTA-AGAACATAGGTATA
103100 C
1 C
103101 CCTCGACTCT
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
30 1 0.01
31 50 0.65
32 26 0.34
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (31 bp):
CTGTCCATATGTTCCTAAGAACATAGGTATA
Found at i:103984 original size:64 final size:64
Alignment explanation
Indices: 103876--103998 Score: 153
Period size: 64 Copynumber: 1.9 Consensus size: 64
103866 TAATGAAGGT
* *
103876 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTT-TCATTATTACTGGG
* **
103940 ATGCATCGATGCA-TACCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCATTATTA
1 ATGCATCGATGCACTA-CTGATGCATCGATGCA-TAAAAGGCATTCGATGTTTCATTATTA
103999 AAAGAGTGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
63 3 0.06
64 47 0.92
65 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTTTCATTATTACTGGG
Found at i:106609 original size:23 final size:25
Alignment explanation
Indices: 106576--106623 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
106566 AAAATTTTAT
*
106576 TAAAATTTTAG-GAG-ATAAAATTA
1 TAAAATCTTAGAGAGTATAAAATTA
*
106599 TAAAATCTTAGAGAGTGTAAAATTA
1 TAAAATCTTAGAGAGTATAAAATTA
106624 AATAATTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 3 0.14
25 8 0.38
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.33
Consensus pattern (25 bp):
TAAAATCTTAGAGAGTATAAAATTA
Found at i:122612 original size:3 final size:3
Alignment explanation
Indices: 122604--122680 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
122594 TCAGGTTTTG
122604 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
122652 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
122681 TAAATACGTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:130174 original size:43 final size:43
Alignment explanation
Indices: 130105--130194 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
130095 ATAAATTGTC
**
130105 TTTGGAGAAGTTGGGAATGAAAGTTATCCCCTATATGTAAAGT
1 TTTGGAGAAGTTAAGAATGAAAGTTATCCCCTATATGTAAAGT
* *
130148 TTTGGAGAAGTTAAGAGTGAAGGTTATCCCCTATATGTAAAGT
1 TTTGGAGAAGTTAAGAATGAAAGTTATCCCCTATATGTAAAGT
130191 TTTG
1 TTTG
130195 TTTGATGTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (43 bp):
TTTGGAGAAGTTAAGAATGAAAGTTATCCCCTATATGTAAAGT
Found at i:130326 original size:20 final size:19
Alignment explanation
Indices: 130290--130336 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
130280 ATTTCGCATC
130290 TTTGTATTTTCATTTTGCA
1 TTTGTATTTTCATTTTGCA
*
130309 TTTGTACTTTT-ATGTTTGCT
1 TTTGTA-TTTTCAT-TTTGCA
130329 TTTGTATT
1 TTTGTATT
130337 GCACAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.13, C:0.09, G:0.13, T:0.66
Consensus pattern (19 bp):
TTTGTATTTTCATTTTGCA
Found at i:130976 original size:19 final size:19
Alignment explanation
Indices: 130952--130988 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
130942 AGATCAAGTT
*
130952 GAAGCGAAGTATAAAAGAG
1 GAAGCGAAATATAAAAGAG
*
130971 GAAGCGAAATATAGAAGA
1 GAAGCGAAATATAAAAGA
130989 TGTTAAAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.30, T:0.11
Consensus pattern (19 bp):
GAAGCGAAATATAAAAGAG
Found at i:135043 original size:33 final size:31
Alignment explanation
Indices: 135006--135081 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
134996 GAGGGGCATT
*
135006 TTGAAGGTCCATATTATCAATGATTGGGACATC
1 TTGAAGGTCCATATCATC-ATG-TTGGGACATC
* * *
135039 TTGAA-GACTCACATCATCATGTTGGGACATT
1 TTGAAGGTC-CATATCATCATGTTGGGACATC
135070 TTGAAGGTCCAT
1 TTGAAGGTCCAT
135082 TTTGACCAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
31 16 0.46
32 7 0.20
33 12 0.34
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (31 bp):
TTGAAGGTCCATATCATCATGTTGGGACATC
Found at i:135124 original size:41 final size:41
Alignment explanation
Indices: 135060--135137 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
135050 CATCATCATG
* *
135060 TTGGGACATTTTGAAGGTCCATTT-TGACCAGAAATGAAAAT
1 TTGGGACATTTGGAAGGTCCATTTCAGA-CAGAAATGAAAAT
*
135101 TTGGTACATTTGGAAGG-CACATTTCAGACAGAAATGA
1 TTGGGACATTTGGAAGGTC-CATTTCAGACAGAAATGA
135138 TCCATGAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 1 0.03
41 29 0.91
42 2 0.06
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (41 bp):
TTGGGACATTTGGAAGGTCCATTTCAGACAGAAATGAAAAT
Found at i:137009 original size:40 final size:42
Alignment explanation
Indices: 136943--137043 Score: 104
Period size: 43 Copynumber: 2.4 Consensus size: 42
136933 TGGCCAAATA
* *
136943 TCCTCATCACGAAGGAACAATGTCAT-C-TA-CCAATCAGAAC-
1 TCCTCATCACGAAGGAACAA-GTCATCCTTAGACAACCAG-ACG
*
136983 TCCTCATCACGAAGGAGTCACA-TCATCCTTAGACAACCAGACG
1 TCCTCATCACGAAGGA-ACA-AGTCATCCTTAGACAACCAGACG
137026 TCCTCATCACGAAGGAAC
1 TCCTCATCACGAAGGAAC
137044 TGTGTTATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
40 20 0.39
41 3 0.06
42 6 0.12
43 22 0.43
ACGTcount: A:0.35, C:0.32, G:0.15, T:0.19
Consensus pattern (42 bp):
TCCTCATCACGAAGGAACAAGTCATCCTTAGACAACCAGACG
Found at i:137146 original size:97 final size:96
Alignment explanation
Indices: 136980--137204 Score: 272
Period size: 97 Copynumber: 2.3 Consensus size: 96
136970 TACCAATCAG
* *
136980 AACTCCTCATCACGAAGGAGTC-ACATCATCCTTAGACAACCAGACGTCCTCATCACGAAGGAAC
1 AACTCCTCATCACGAAGGAG-CAACATCATCCTTAGACAACCAGACGTCATCATCACGAAAGAAC
* * * *
137044 TGTGTTATCTCCAATATCTTCAATGATGGTCA
65 AGTGTTATCTCAAATATCTTCAAAGATGGCCA
* * * * * *
137076 TAACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCATATGTCATCATCATGAAATAAC
1 -AACTCCTCATCACGAAGGAGCAACATCATCCTTAGACAACCAGACGTCATCATCACGAAAGAAC
*
137141 AGTGTTATCTCAAATATCTTTAAAGATGGCCA
65 AGTGTTATCTCAAATATCTTCAAAGATGGCCA
* * *
137173 GACGTCCTCATCACGAAGGAACAATATCATCC
1 AAC-TCCTCATCACGAAGGAGCAACATCATCC
137205 ACCGATAAGA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
96 3 0.03
97 106 0.97
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (96 bp):
AACTCCTCATCACGAAGGAGCAACATCATCCTTAGACAACCAGACGTCATCATCACGAAAGAACA
GTGTTATCTCAAATATCTTCAAAGATGGCCA
Found at i:137251 original size:137 final size:137
Alignment explanation
Indices: 137077--137618 Score: 757
Period size: 137 Copynumber: 4.0 Consensus size: 137
137067 TGATGGTCAT
* * *
137077 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCATATGTCATCATCATGAAATAACA
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
*
137142 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATATCATCCAC
66 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
*
137207 CGATAAG
131 CGATCAG
*
137214 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATATCCTCATCATGAAAGAACA
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
*
137279 TTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
66 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
137344 CGATCAG
131 CGATCAG
* * * * * * *
137351 AACTCCTCATCATGAATGAGCAACATCATTCTTAGATAGCTAGATGTCCTCATCACGAATGAACC
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
* * *
137416 GTGTTATCTCAAATATATTTAAAGATGGCCAGACATCCTCATCACGAAGAAACAATGTCATCCAC
66 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
137481 CGATCAG
131 CGATCAG
* * * * * *
137488 AACTACTCATCACGTAGGAGC--CGAGTCATCCTCAGATAACCAGACGTCCTCATCA-CAAAGGA
1 AACTCCTCATCACGAAGGAGCAAC-A-TCATTCTTAGATAACCAGATGTCCTCATCATGAAA-GA
** * * * * * *
137550 ACCTTGTTATCTTAAATATCTTCAAAGGTGGTCAGACGTCCTCATCATGAAGGAACAATGTCATA
63 ACAGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATC
137615 CACC
128 CACC
137619 AGTTAGATCT
Statistics
Matches: 362, Mismatches: 40, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
135 1 0.00
136 3 0.01
137 358 0.99
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (137 bp):
AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
CGATCAG
Found at i:137363 original size:234 final size:233
Alignment explanation
Indices: 136909--137343 Score: 545
Period size: 234 Copynumber: 1.9 Consensus size: 233
136899 AGAAGGAACC
* * * *
136909 GTGTTATCCTAAATGTCTTAAAGATGGCCAAATATCCTCATCACGAAGGAACAATGTCATCTACC
1 GTGTTATCCTAAATATCTTAAAGATGGCCAAACATCCTCATCACGAAGGAACAATATCATCCACC
* *
136974 AATCAGAACTCCTCATCACGAAGGAGTCACATCATCCTTAGACAACCAGACGTCCTCATCACGAA
66 AATAAGAACTCCTCATCACGAAGGAGTCACATCATCCTTAGACAACCAGACATCCTCATCACGAA
* * * * *
137039 GGAACTGTGTTATCTCCAATATCTTCAATGATGGTCATAACTCCTCATCACGAAGGAGCAACATC
131 AGAACTGTGTTATCTCAAATATCTTCAAAGATGGCCATAACTCCTCATCACGAAGGAACAACATC
* ** * **
137104 ATTCTTAGATAACCATATGTCATCATCATGAAATAACA
196 ATCCACAGATAAACATACCTCATCATCATGAAATAACA
* *
137142 GTGTTAT-CTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATATCATCCA
1 GTGTTATCCT-AAATATC-TTAAAGATGGCCAAACATCCTCATCACGAAGGAACAATATCATCCA
* * * * *
137206 CCGATAAGAACTCCTCATCACGAAGGAG-CAACATCATTCTTAGATAACCAGATATCCTCATCAT
64 CCAATAAGAACTCCTCATCACGAAGGAGTC-ACATCATCCTTAGACAACCAGACATCCTCATCAC
* *
137270 GAAAGAACAT-TGTTATCTCAAATATCTTTAAAGATGGCCA-GACGTCCTCATCACGAAGGAACA
128 GAAAGAAC-TGTGTTATCTCAAATATCTTCAAAGATGGCCATAAC-TCCTCATCACGAAGGAACA
**
137333 ATGTCATCCAC
191 ACATCATCCAC
137344 CGATCAGAAC
Statistics
Matches: 172, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
232 2 0.01
233 16 0.09
234 153 0.89
235 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (233 bp):
GTGTTATCCTAAATATCTTAAAGATGGCCAAACATCCTCATCACGAAGGAACAATATCATCCACC
AATAAGAACTCCTCATCACGAAGGAGTCACATCATCCTTAGACAACCAGACATCCTCATCACGAA
AGAACTGTGTTATCTCAAATATCTTCAAAGATGGCCATAACTCCTCATCACGAAGGAACAACATC
ATCCACAGATAAACATACCTCATCATCATGAAATAACA
Found at i:138916 original size:118 final size:119
Alignment explanation
Indices: 138810--139034 Score: 271
Period size: 118 Copynumber: 1.9 Consensus size: 119
138800 TATTAGTAAT
* *
138810 TATATTTTATAATATTTTGAATTTA-GACTATTAATTTAT-ATATTTTTACAA-TTTAATCAC-T
1 TATATTTCATAATATTTAGAA-TTAGGACTATTAATTT-TGATA-TTTTACAATTTTAATC-CTT
* ** *
138871 GAGGTTTAATATTTTAATTTTAAATAATA-TTTTAGGATTATTTACACTAATAATACA
62 GAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTATTTACACTAATAATACA
* * * * *
138928 TATATTTCATGATATTTAGAATTAGGATTTTTAATTTTGATATTTTACAATTTTAATCCTTTAGT
1 TATATTTCATAATATTTAGAATTAGGACTATTAATTTTGATATTTTACAATTTTAATCCTTGAGG
*
138993 TTTAAAATAATAATTTTAAATATTATTTTTAGAATTATTTAC
66 TTTAAAATAATAATTTTAAATAATATTTTTAGAATTATTTAC
139035 TATTATAGTA
Statistics
Matches: 90, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
117 13 0.14
118 62 0.69
119 15 0.17
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.52
Consensus pattern (119 bp):
TATATTTCATAATATTTAGAATTAGGACTATTAATTTTGATATTTTACAATTTTAATCCTTGAGG
TTTAAAATAATAATTTTAAATAATATTTTTAGAATTATTTACACTAATAATACA
Found at i:148422 original size:18 final size:19
Alignment explanation
Indices: 148399--148436 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
148389 GAACAGGTCT
148399 GACCCGACCCGA-CTGACC
1 GACCCGACCCGACCTGACC
148417 GACCCGACCCGACCTGACC
1 GACCCGACCCGACCTGACC
148436 G
1 G
148437 TTGACCCGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.21, C:0.50, G:0.24, T:0.05
Consensus pattern (19 bp):
GACCCGACCCGACCTGACC
Found at i:148445 original size:22 final size:22
Alignment explanation
Indices: 148398--148464 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
148388 CGAACAGGTC
148398 TGACCCGACCCGA-CTGACC--
1 TGACCCGACCCGACCTGACCGT
148417 -GACCCGACCCGACCTGACCGT
1 TGACCCGACCCGACCTGACCGT
* * *
148438 TGACCCGACCTGACCCGACTGT
1 TGACCCGACCCGACCTGACCGT
148460 TGACC
1 TGACC
148465 GTTGACTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 12 0.29
19 6 0.15
22 23 0.56
ACGTcount: A:0.19, C:0.45, G:0.22, T:0.13
Consensus pattern (22 bp):
TGACCCGACCCGACCTGACCGT
Done.