Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008201.1 Hibiscus syriacus cultivar Beakdansim tig00110821_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: 276706
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1466 original size:93 final size:93
Alignment explanation
Indices: 1136--1603 Score: 876
Period size: 92 Copynumber: 5.1 Consensus size: 93
1126 TAGATTGCTT
*
1136 AGTAAATTTATTCGGTTGCTGCCAATT-T-CT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1198 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1226 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1290 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1317 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1382 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1410 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1475 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1502 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1567 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1595 AGTAAATTT
1 AGTAAATTT
1604 ATCCATTCAA
Statistics
Matches: 369, Mismatches: 3, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
90 26 0.07
91 68 0.18
92 141 0.38
93 134 0.36
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1687 original size:19 final size:19
Alignment explanation
Indices: 1647--1775 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1637 TAGTTTACTT
* *
1647 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1667 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1686 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1705 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1719 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1738 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1752 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1771 TCGCA
1 TCGCA
1776 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1726 original size:33 final size:32
Alignment explanation
Indices: 1683--1775 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1673 CGCGAAACCA
**
1683 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1715 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1748 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1776 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1773 original size:52 final size:52
Alignment explanation
Indices: 1647--1775 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1637 TAGTTTACTT
**
1647 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1699 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1752 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1776 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1793 original size:19 final size:19
Alignment explanation
Indices: 1771--1905 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1761 GAAACCAAAA
*
1771 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1790 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1806 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1823 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1839 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
1856 TCGCGTTGTGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1875 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1895 TCGTGTTGCGA
1 TCGCGTTGCGA
1906 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 44 0.47
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1812 original size:14 final size:14
Alignment explanation
Indices: 1793--1849 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1783 TTTCATTTCG
1793 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1807 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1824 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1840 CGTTGCGATT
1 CGTTGCGATT
1850 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1818 original size:33 final size:33
Alignment explanation
Indices: 1776--1868 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1766 CAAAATCGCA
*
1776 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1809 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1842 TTGCGATTTTCATTTCGCGTTGTGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1869 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3845 original size:14 final size:14
Alignment explanation
Indices: 3826--3861 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3816 ATTGTTTAAT
3826 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3840 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3854 TGATTTGT
1 TGATTTGT
3862 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3992 original size:19 final size:19
Alignment explanation
Indices: 3968--4065 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
3958 AAAATTGACT
3968 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3987 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4006 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4020 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4039 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
4059 ATCGCAA
1 ATCGCAA
4066 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4097 original size:53 final size:53
Alignment explanation
Indices: 3968--4084 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
3958 AAAATTGACT
3968 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
4020 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
4073 ATCGCAATGCGA
1 ATCGCAATGCGA
4085 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:6411 original size:12 final size:12
Alignment explanation
Indices: 6394--6418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6384 TCTTCGGGGA
6394 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6406 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6418 C
1 C
6419 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:6627 original size:24 final size:24
Alignment explanation
Indices: 6593--6639 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6583 CTGAAACATC
6593 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
6617 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
6640 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:7572 original size:20 final size:20
Alignment explanation
Indices: 7322--7571 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
7312 AAATTTCAGT
* * *
7322 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
7342 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
7362 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
7382 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
7402 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
7422 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
7442 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
7462 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
7482 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
7502 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
7522 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
7542 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
7562 GTTGCGATTT
1 GTTGCGATTT
7572 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:7588 original size:21 final size:21
Alignment explanation
Indices: 7558--7640 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
7548 ATTTTCATAT
*
7558 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
7579 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
7600 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
7621 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
7641 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:7631 original size:42 final size:43
Alignment explanation
Indices: 7538--7636 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
7528 ATTTATGTGT
* *
7538 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
7579 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
7621 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
7637 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:16103 original size:18 final size:18
Alignment explanation
Indices: 16080--16115 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16070 GAAATGAAAT
* *
16080 ATTATAGTATTAAATAAA
1 ATTATAGAATAAAATAAA
16098 ATTATAGAATAAAATAAA
1 ATTATAGAATAAAATAAA
16116 TAATACTAGG
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:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
ATTATAGAATAAAATAAA
Found at i:17847 original size:3 final size:3
Alignment explanation
Indices: 17839--17868 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17829 TATTTTATGA
17839 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17869 TTGACCCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18583 original size:19 final size:20
Alignment explanation
Indices: 18542--18580 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18532 TTTGTACTTA
18542 AAAAATATTTTTACGTTTTT
1 AAAAATATTTTTACGTTTTT
* *
18562 AAAATTATTTTTATGTTTT
1 AAAAATATTTTTACGTTTT
18581 AAATAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (20 bp):
AAAAATATTTTTACGTTTTT
Found at i:19968 original size:34 final size:36
Alignment explanation
Indices: 19930--20011 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
19920 TAAAAGTTAG
19930 TTTAAAGTTTGGCAAAT-AAT-TTTGAAAAATGTTT
1 TTTAAAGTTTGGCAAATGAATCTTTGAAAAATGTTT
* **
19964 TTTAAAGTTTGGTAAATGTTTCTTTGAAAAATGTTT
1 TTTAAAGTTTGGCAAATGAATCTTTGAAAAATGTTT
*
20000 TTCAAAGTTTGG
1 TTTAAAGTTTGG
20012 TATATGTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 16 0.38
35 1 0.02
36 25 0.60
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (36 bp):
TTTAAAGTTTGGCAAATGAATCTTTGAAAAATGTTT
Found at i:19997 original size:36 final size:35
Alignment explanation
Indices: 19949--20028 Score: 124
Period size: 36 Copynumber: 2.3 Consensus size: 35
19939 TGGCAAATAA
*
19949 TTTTGAAAAATGTTTTTTAAAGTTTGGTAAATGTT
1 TTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTT
*
19984 TCTTTGAAAAATGTTTTTCAAAGTTTGGTATATGTT
1 T-TTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTT
*
20020 TGTTGAAAA
1 TTTTGAAAA
20029 TAGGAATGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 8 0.20
36 33 0.80
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (35 bp):
TTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTT
Found at i:21231 original size:15 final size:15
Alignment explanation
Indices: 21207--21238 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21197 TGGCAGATCC
*
21207 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
21222 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
21237 AA
1 AA
21239 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:21691 original size:24 final size:23
Alignment explanation
Indices: 21648--21696 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
21638 TATGAGCGAG
21648 AAAGGGATGAAGACACTTTTGTCA
1 AAAGGGATGAAGACACTTTTG-CA
* *
21672 AAAGGGATGAAGATAGTTTTGCA
1 AAAGGGATGAAGACACTTTTGCA
21695 AA
1 AA
21697 GATTGGCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (23 bp):
AAAGGGATGAAGACACTTTTGCA
Found at i:24341 original size:35 final size:35
Alignment explanation
Indices: 24290--24359 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
24280 TGACAACCAA
24290 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
24326 CTTTG-AAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
24360 GGTAGATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 4 0.12
35 25 0.74
36 5 0.15
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
Found at i:40662 original size:1 final size:1
Alignment explanation
Indices: 40656--40712 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
40646 ATGCTTGAAG
** * * * * *
40656 AAAAAAAAAATGAAAAAAAAAGAAGAAAAAAAAAAAAGAAAAAAAAAGAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40713 TGAAGAAGGA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.88, C:0.00, G:0.11, T:0.02
Consensus pattern (1 bp):
A
Found at i:40687 original size:16 final size:15
Alignment explanation
Indices: 40668--40712 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
40658 AAAAAAAATG
40668 AAAAAAAAAGAAGAAA
1 AAAAAAAAAGAA-AAA
40684 AAAAAAAAAG-AAAA
1 AAAAAAAAAGAAAAA
*
40698 AAAAAGAAAGAAAAA
1 AAAAAAAAAGAAAAA
40713 TGAAGAAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 12 0.44
15 5 0.19
16 10 0.37
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAAA
Found at i:40696 original size:26 final size:26
Alignment explanation
Indices: 40652--40712 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
40642 TACTATGCTT
*
40652 GAAG-AAAAAAAAAATGAAAAAAAAA
1 GAAGAAAAAAAAAAAAGAAAAAAAAA
40677 GAAGAAAAAAAAAAAAGAAAAAAAAA
1 GAAGAAAAAAAAAAAAGAAAAAAAAA
40703 GAAAGAAAAA
1 G-AAGAAAAA
40713 TGAAGAAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
25 4 0.12
26 21 0.64
27 8 0.24
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (26 bp):
GAAGAAAAAAAAAAAAGAAAAAAAAA
Found at i:40719 original size:14 final size:14
Alignment explanation
Indices: 40656--40712 Score: 84
Period size: 13 Copynumber: 4.3 Consensus size: 14
40646 ATGCTTGAAG
*
40656 AAAAAAAA-AATGA
1 AAAAAAAAGAAAGA
40669 AAAAAAAAG-AAGA
1 AAAAAAAAGAAAGA
40682 AAAAAAAA-AAAGA
1 AAAAAAAAGAAAGA
40695 AAAAAAAAGAAAGA
1 AAAAAAAAGAAAGA
40709 AAAA
1 AAAA
40713 TGAAGAAGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
13 31 0.77
14 9 0.22
ACGTcount: A:0.88, C:0.00, G:0.11, T:0.02
Consensus pattern (14 bp):
AAAAAAAAGAAAGA
Found at i:41858 original size:136 final size:135
Alignment explanation
Indices: 41678--42031 Score: 523
Period size: 136 Copynumber: 2.6 Consensus size: 135
41668 AAAGAGGTGG
* *
41678 ATCAGCATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCA
1 ATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-AAAGGGAGAAGAAGTTCA
* *
41743 TAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-TGACATTTCGAATCAGTGACACCTCGC
65 TAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAG-CATTTCGAATCAGGGACACCTCGC
41807 TTGAGGA
129 TTGAGGA
** *
41814 ATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCA
1 ATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCG-AAAAGGGAGAAGAAGTTCA
* *
41879 TAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAGCATTTCGAGTCAGGGACGCCTCGCT
65 TAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAGCATTTCGAATCAGGGACACCTCGCT
*
41944 TGAGGG
130 TGAGGA
* * * *
41950 ATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCC-AAAAGAGAGAAGAAGTTCAT
1 ATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAGAAGTTCAT
* *
42014 AATGCGAAGAACTTGTTC
66 AATGAGAAGAGCTTGTTC
42032 AATCTAACAA
Statistics
Matches: 197, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
134 35 0.18
136 160 0.81
137 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (135 bp):
ATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAGGGAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAGCATTTCGAATCAGGGACACCTCGCTT
GAGGA
Found at i:47112 original size:25 final size:25
Alignment explanation
Indices: 47078--47129 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
47068 AAACCTTTCC
47078 ATGATTGTTATCTTCTAATACTTAA
1 ATGATTGTTATCTTCTAATACTTAA
*
47103 ATGATTGTTATCTTCTAGTACTTAA
1 ATGATTGTTATCTTCTAATACTTAA
47128 AT
1 AT
47130 ATGCTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (25 bp):
ATGATTGTTATCTTCTAATACTTAA
Found at i:47591 original size:3 final size:3
Alignment explanation
Indices: 47583--47610 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47573 TAGTTTTGGC
47583 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
47611 TCTCCATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:58173 original size:17 final size:17
Alignment explanation
Indices: 58151--58222 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
58141 TAACTATGAG
58151 ATTAAAAAATCTAAGAA
1 ATTAAAAAATCTAAGAA
****
58168 ATTAAAATGGATAA-AA
1 ATTAAAAAATCTAAGAA
58184 A-T-AAAAATCTAAGAA
1 ATTAAAAAATCTAAGAA
58199 ATTAAAAAAT-TAAGAA
1 ATTAAAAAATCTAAGAA
58215 ACTTAAAA
1 A-TTAAAA
58223 TTTATAAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
14 6 0.14
15 4 0.09
16 11 0.26
17 22 0.51
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (17 bp):
ATTAAAAAATCTAAGAA
Found at i:58204 original size:16 final size:16
Alignment explanation
Indices: 58155--58222 Score: 63
Period size: 16 Copynumber: 4.2 Consensus size: 16
58145 TATGAGATTA
58155 AAAAATCTAAGAAATT
1 AAAAATCTAAGAAATT
*
58171 -AAAATGGATAA-AAA-T
1 AAAAAT--CTAAGAAATT
58186 AAAAATCTAAGAAATT
1 AAAAATCTAAGAAATT
58202 AAAAAAT-TAAGAAACTT
1 -AAAAATCTAAGAAA-TT
58219 AAAA
1 AAAA
58223 TTTATAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
14 3 0.07
15 9 0.21
16 20 0.47
17 11 0.26
ACGTcount: A:0.66, C:0.04, G:0.07, T:0.22
Consensus pattern (16 bp):
AAAAATCTAAGAAATT
Found at i:58211 original size:56 final size:55
Alignment explanation
Indices: 58099--58220 Score: 122
Period size: 56 Copynumber: 2.2 Consensus size: 55
58089 CAACATATGA
** * ** *
58099 AAAAAATTAAGAAATTAAAATGGATAAAAATAAATTTTGCTATAACTATGAGATT
1 AAAAAATTAAGAAATTAAAATGGATAAAAATAAATAATGCTAAAACTAAAAAATT
*
58154 AAAAAATCTAAGAAATTAAAATGGATAAAAATAAA-AAT-CTAAGAAATTAAAAAATT
1 AAAAAAT-TAAGAAATTAAAATGGATAAAAATAAATAATGCT-A-AAACTAAAAAATT
*
58210 AAGAAACTTAA
1 AA-AAAATTAA
58221 AATTTATAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
54 2 0.04
55 9 0.16
56 40 0.73
57 4 0.07
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26
Consensus pattern (55 bp):
AAAAAATTAAGAAATTAAAATGGATAAAAATAAATAATGCTAAAACTAAAAAATT
Found at i:59465 original size:6 final size:6
Alignment explanation
Indices: 59454--59480 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
59444 CCAAAGTCCC
59454 TTCATT TTCATT TTCATT TTCATT TTC
1 TTCATT TTCATT TTCATT TTCATT TTC
59481 GTTTACAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCATT
Found at i:60038 original size:31 final size:31
Alignment explanation
Indices: 60000--60060 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
59990 CTTTTACCCC
60000 TAAACTATGATTTTATAAAGAGGAAAGATAT
1 TAAACTATGATTTTATAAAGAGGAAAGATAT
60031 TAAACTATGATTTTATAAAGAGGAAAGATA
1 TAAACTATGATTTTATAAAGAGGAAAGATA
60061 AAACTAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.31
Consensus pattern (31 bp):
TAAACTATGATTTTATAAAGAGGAAAGATAT
Found at i:63306 original size:16 final size:15
Alignment explanation
Indices: 63287--63324 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
63277 TCTCACTAAC
63287 TTTTTTTCTCCTTT-CA
1 TTTTTTTCT--TTTGCA
63303 TTTTTTTCTTTTGCA
1 TTTTTTTCTTTTGCA
63318 TTTTTTT
1 TTTTTTT
63325 TATCATTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.43
16 9 0.43
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTTTCTTTTGCA
Found at i:66039 original size:106 final size:106
Alignment explanation
Indices: 65888--67082 Score: 2076
Period size: 106 Copynumber: 11.3 Consensus size: 106
65878 CTCGAGAGTA
* * *
65888 AATTTCAACTTCTCAACGAAGGATCTT-GACTCTAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
65952 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCT
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
* *
65993 AATTTCAACTTCACCACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
66058 GACCGCTGGTTGTCAACAAAC-ATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
66098 AATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
66163 GACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
66203 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
66268 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
66309 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
66374 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66415 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
66480 GACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
66521 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
66586 GACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
66626 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
66691 GATCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66732 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
66797 GACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
66838 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
66903 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66944 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * *
67009 GACCGCTGGTTGTCAACAAACAACTTCTCAGTTCCAGAACC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
67050 AATTTCAACTTCACGAC-AGAGGATATTGGACTC
1 AATTTCAACTTCACAACGA-AGGATATTGGACTC
67083 GGAACAGTGC
Statistics
Matches: 1053, Mismatches: 33, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
105 330 0.31
106 723 0.69
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
Found at i:66706 original size:423 final size:423
Alignment explanation
Indices: 65888--67082 Score: 2144
Period size: 423 Copynumber: 2.8 Consensus size: 423
65878 CTCGAGAGTA
* * *
65888 AATTTCAACTTCTCAACGAAGGATCTT-GACTCTAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * * *
65952 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCTAATTTCAACTTCACCACAAAGGAT
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
66017 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-AT
131 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
* *
66081 TTCCCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACGCAAGTT
196 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
66146 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
261 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
66211 CTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTG
326 CTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTG
66276 GTTGTCAATAAACAACTTCTCAATTTCAGAGCC
391 GTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
66309 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
66374 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
66439 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAAC
131 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
*
66504 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTT
196 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
66569 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
261 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
*
66634 CTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGATCGCTG
326 CTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTG
66699 GTTGTCAATAAACAACTTCTCAATTTCAGAGCC
391 GTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66732 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
66797 GACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
66862 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
131 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
66927 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
196 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
* * * *
66992 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAGTTCCAGAACCAATTTCA
261 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCA
*
67057 ACTTCACGAC-AGAGGATATTGGACTC
325 ACTTCACAACGA-AGGATATTGGACTC
67083 GGAACAGTGC
Statistics
Matches: 743, Mismatches: 27, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
421 25 0.03
422 155 0.21
423 518 0.70
424 45 0.06
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (423 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC
TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT
CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAA
CTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTG
GTTGTCAATAAACAACTTCTCAATTTCAGAGCC
Found at i:74350 original size:2 final size:2
Alignment explanation
Indices: 74343--74368 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
74333 CATTGTTGCC
74343 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
74369 CTTTTACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78966 original size:32 final size:32
Alignment explanation
Indices: 78888--78966 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
78878 CCTAAGGTGA
*
78888 CCCTTGGGTAGGCTCTGAGGCCCCAAGAAACT
1 CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
** **
78920 TTCTTGGGTAGGCTCTCAGGCCCCAAGGCACT
1 CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
78952 CCCTTAGGGT-GGCTC
1 CCCTT-GGGTAGGCTC
78967 CTTTGTCGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 35 0.90
33 4 0.10
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
Found at i:83156 original size:85 final size:87
Alignment explanation
Indices: 83067--83251 Score: 295
Period size: 91 Copynumber: 2.1 Consensus size: 87
83057 TTACTTTAAT
83067 TCTTATATTATTATTTGAACAATTTGTATTAAAAAATTATATTAATCTATTTCAT-C-A-TATTA
1 TCTTATATTATTATTTGAACAATTTGTATT-AAAAATTATATTAATCTATTTCATACTACTATTA
83129 TCTTGATCAATAAAATCCATTTA
65 TCTTGATCAATAAAATCCATTTA
*
83152 TCTTATATTTTTATTTGAACAATTTGTATTAAAAATTATATTAATCTATTTCATCACATTATCTA
1 TCTTATATTATTATTTGAACAATTTGTATTAAAAATTATATTAATCTATTTCAT-AC--TA-CTA
83217 TTATCTTGATCAATAAAATCCATTTA
62 TTATCTTGATCAATAAAATCCATTTA
83243 TCTTATATT
1 TCTTATATT
83252 TTTTCATGTC
Statistics
Matches: 92, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
84 24 0.26
85 29 0.32
86 1 0.01
89 1 0.01
91 37 0.40
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (87 bp):
TCTTATATTATTATTTGAACAATTTGTATTAAAAATTATATTAATCTATTTCATACTACTATTAT
CTTGATCAATAAAATCCATTTA
Found at i:83693 original size:20 final size:20
Alignment explanation
Indices: 83663--83838 Score: 113
Period size: 20 Copynumber: 8.7 Consensus size: 20
83653 ATTTCCAGAT
*
83663 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
83683 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
** *
83703 TTCGCGTTGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
83726 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
83746 TCGCAATGCGAGTATGACTA
1 TCGCAATGCGATTCTGACTA
83766 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
*** *
83786 TCGCAACAAGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
* * *
83806 TCGCAACGCGATGCTAACTA
1 TCGCAATGCGATTCTGACTA
83826 TCGCAATGCGATT
1 TCGCAATGCGATT
83839 TTCAAAGCGC
Statistics
Matches: 118, Mismatches: 31, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
19 3 0.03
20 91 0.77
21 11 0.09
22 9 0.08
23 3 0.03
24 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:83735 original size:22 final size:22
Alignment explanation
Indices: 83678--83736 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
83668 ACGCGATTCT
83678 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
83700 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
83721 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
83737 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:84500 original size:20 final size:20
Alignment explanation
Indices: 84475--84526 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
84465 ATTGCGATTC
84475 TCGCGTTGCGATAGTCAAAT
1 TCGCGTTGCGATAGTCAAAT
**
84495 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCAAAT
*
84515 TCGTGTTGCGAT
1 TCGCGTTGCGAT
84527 TTTCATTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATAGTCAAAT
Found at i:84532 original size:20 final size:20
Alignment explanation
Indices: 84494--84549 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
84484 GATAGTCAAA
* **
84494 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
84514 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
84534 TTCGTGTTACGATTTT
1 TTCGTGTTGCGATTTT
84550 AAGTTTCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:84556 original size:20 final size:20
Alignment explanation
Indices: 84513--84556 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
84503 CGATAGTCAT
* * *
84513 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTACGATTTTAAG
84533 TTTCGTGTTACGATTTTAAG
1 TTTCGTGTTACGATTTTAAG
84553 TTTC
1 TTTC
84557 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAG
Found at i:86152 original size:21 final size:21
Alignment explanation
Indices: 86123--86168 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
86113 TGGTGCATGG
* *
86123 CGTGTTGAGGT-GTCTACTTTA
1 CGTGGTGAGGTAGTC-ACTCTA
86144 CGTGGTGAGGTAGTCACTCTA
1 CGTGGTGAGGTAGTCACTCTA
86165 CGTG
1 CGTG
86169 AGATGGTAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.15, C:0.17, G:0.33, T:0.35
Consensus pattern (21 bp):
CGTGGTGAGGTAGTCACTCTA
Found at i:86537 original size:20 final size:19
Alignment explanation
Indices: 86512--86578 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
86502 GCGATTCTCT
86512 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
*
86532 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-ATTCG
86552 CGTTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
86570 TGTTGCGAT
1 CGTTGCGAT
86579 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 12 0.28
19 1 0.02
20 30 0.70
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:87157 original size:21 final size:21
Alignment explanation
Indices: 87066--87169 Score: 70
Period size: 21 Copynumber: 5.0 Consensus size: 21
87056 GACTCACCTG
*
87066 TCATCGTTCAAGAGGCCTCCC-C
1 TCATCGTTCAAGAGG--TCCCTA
*
87088 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGTCCCTA
** *
87108 TCATCCCTCAAGA-GTCCCCTC
1 TCATCGTTCAAGAGGT-CCCTA
* * *
87129 CCACCGTTCAAGAGGTCACTA
1 TCATCGTTCAAGAGGTCCCTA
* *
87150 TCATCGTTGAAGATGTCCCT
1 TCATCGTTCAAGAGGTCCCT
87170 CCCAACATTA
Statistics
Matches: 61, Mismatches: 17, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
19 3 0.05
20 2 0.03
21 53 0.87
22 3 0.05
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGTCCCTA
Found at i:88600 original size:14 final size:14
Alignment explanation
Indices: 88566--88627 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
88556 TTACTTGTTT
*
88566 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
88580 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
88594 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
88609 TATTGATGTGTAAA
1 AATTGATTTGTAAA
88623 TAATT
1 -AATT
88628 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:88751 original size:20 final size:20
Alignment explanation
Indices: 88726--88778 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
88716 AGGTACACTT
* **
88726 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACAAAAAA
* *
88746 TCGCAATGCGAAAGAAAAAA
1 TCGCAACGCGAAACAAAAAA
88766 TCGCAACGCGAAA
1 TCGCAACGCGAAA
88779 GTCAATTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACAAAAAA
Found at i:88779 original size:20 final size:20
Alignment explanation
Indices: 88742--88779 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
88732 CGCTAAACTC
*
88742 AAAATCGCAATGCGAAAGAA
1 AAAATCGCAACGCGAAAGAA
88762 AAAATCGCAACGCGAAAG
1 AAAATCGCAACGCGAAAG
88780 TCAATTCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.21, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAGAA
Found at i:88831 original size:34 final size:34
Alignment explanation
Indices: 88788--89039 Score: 159
Period size: 40 Copynumber: 6.9 Consensus size: 34
88778 AGTCAATTCG
* * *
88788 CGTTGCGATAGTCTAATACGCTTTGTGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* *
88822 CGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATACGCGTTGCGAT--T----TTCT
*
88862 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* * *
88896 CGTTGCGATAGTTAAATA-GCCGCTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATACG-CGTTGCGAT--T----TTCT
* *
88936 CGTTGCGATAGACAAATTCGCGTTGCGATAGTCATAT-T
1 CGTTGCGATAGTCAAATACGCGTTGCGAT--T--T-TCT
* *
88974 CGTGTTGCAATAGTCAAATTCGCGTTGCGATTTTCT
1 C--GTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* *
89010 CATTGCGATAGTTAAATA-GCCGTTGCGATT
1 CGTTGCGATAGTCAAATACG-CGTTGCGATT
89040 GTCAAATTCG
Statistics
Matches: 175, Mismatches: 24, Indels: 38
0.74 0.10 0.16
Matches are distributed among these distances:
33 2 0.01
34 75 0.43
35 1 0.01
36 5 0.03
38 5 0.03
39 1 0.01
40 85 0.49
41 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
Found at i:88847 original size:20 final size:20
Alignment explanation
Indices: 88822--89098 Score: 267
Period size: 20 Copynumber: 14.4 Consensus size: 20
88812 GTGATTTTCT
* *
88822 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
88842 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
88862 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
88882 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* *
88896 CGTTGCGATAGTTAAA-TAG
1 CGTTGCGATAGTCAAATTCG
*
88915 CCGCTGCGATAGTCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
*
88936 CGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
88956 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
88976 TGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
88996 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* * *
89010 CATTGCGATAGTTAAA-TAG
1 CGTTGCGATAGTCAAATTCG
*
89029 CCGTTGCGATTGTCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
*
89050 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
89070 TGTTGCGATAGTCAAAATCG
1 CGTTGCGATAGTCAAATTCG
89090 CGTTGCGAT
1 CGTTGCGAT
89099 TTTTGAGTTA
Statistics
Matches: 208, Mismatches: 33, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
14 23 0.11
16 2 0.01
18 2 0.01
19 2 0.01
20 175 0.84
21 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:88871 original size:74 final size:74
Alignment explanation
Indices: 88782--88964 Score: 276
Period size: 74 Copynumber: 2.5 Consensus size: 74
88772 CGCGAAAGTC
* * * *
88782 AATTCGCGTTGCGATAGTCTAATACGCTTTGTGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGCTG
88847 CGATAATCA
66 CGATAATCA
* * *
88856 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTTAAATAGCCGCTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGCTG
*
88921 CGATAGTCA
66 CGATAATCA
* *
88930 AATTCGCGTTGCGATAGACAAATTCGCGTTGCGAT
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGAT
88965 AGTCATATTC
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 100 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGCTG
CGATAATCA
Found at i:88963 original size:114 final size:114
Alignment explanation
Indices: 88822--89098 Score: 437
Period size: 114 Copynumber: 2.4 Consensus size: 114
88812 GTGATTTTCT
* * *
88822 CGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
*
88887 CGATTTTCTCGTTGCGATAGTTAAATAGCCGCTGCGATAGTCAAATTCG
66 CGATTTTCTCATTGCGATAGTTAAATAGCCGCTGCGATAGTCAAATTCG
* * * *
88936 CGTTGCGATAGACAAATTCGCGTTGCGATAGTCATATTCGTGTTGCAATAGTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
* *
89001 CGATTTTCTCATTGCGATAGTTAAATAGCCGTTGCGATTGTCAAATTCG
66 CGATTTTCTCATTGCGATAGTTAAATAGCCGCTGCGATAGTCAAATTCG
* * *
89050 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAAATCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
89099 TTTTGAGTTA
Statistics
Matches: 146, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 146 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (114 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
CGATTTTCTCATTGCGATAGTTAAATAGCCGCTGCGATAGTCAAATTCG
Found at i:89016 original size:74 final size:74
Alignment explanation
Indices: 88938--89078 Score: 185
Period size: 74 Copynumber: 1.9 Consensus size: 74
88928 CAAATTCGCG
* * *
88938 TTGCGATAGACAAAT-TCGCGTTGCGATAGTCATATTCGTGTTGCAATAGTCAAATTCGCGTTGC
1 TTGCGATAGACAAATAGC-CGTTGCGATAGTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGC
89002 GATTTTCTCA
65 GATTTTCTCA
** * * * *
89012 TTGCGATAGTTAAATAGCCGTTGCGATTGTCAAATTCGCGTTGCGATAGTCATATTCGTGTTGCG
1 TTGCGATAGACAAATAGCCGTTGCGATAGTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGCG
89077 AT
66 AT
89079 AGTCAAAATC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
74 56 0.98
75 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (74 bp):
TTGCGATAGACAAATAGCCGTTGCGATAGTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGCG
ATTTTCTCA
Found at i:89017 original size:94 final size:94
Alignment explanation
Indices: 88773--89133 Score: 339
Period size: 94 Copynumber: 3.9 Consensus size: 94
88763 AAATCGCAAC
* * * * * *
88773 GCGAAAGTCA-ATTCGCGTTGCGATAGTCTAATACGCTTTGTGATTTTCTCGTTGCGATAGTCAA
1 GCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCATTGCGATAGTCAA
* *
88837 ATACCCGTTGCGATA-ATCAAATTCGCGTT
66 ATTCGCGTTGCGATAGA-CAAATTCGCGTT
* * **
88866 GCGATAGTCAAATTCGCGTTGCGAT--T----TTCTCGTTGCGATAGTTAAATAGC-CGCTGCGA
1 GCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT--TT---T--CTCATTGCGA
88924 TAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTT
59 TAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTT
* * *
88960 GCGATAGTCATATTCGTGTTGCAATAGTCAAATTCGCGTTGCGATTTTCTCATTGCGATAGTTAA
1 GCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCATTGCGATAGTCAA
* * *
89025 A-TAGCCGTTGCGATTGTCAAATTCGCGTT
66 ATTCG-CGTTGCGATAGACAAATTCGCGTT
* * * * *
89054 GCGATAGTCATATTCGTGTTGCGATAGTCAAAATCGCGTTGCGATTTT-TGAGTTACGATAATCA
1 GCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCA-TTGCGATAGTCA
*
89118 AATTCACGTTGCGATA
65 AATTCGCGTTGCGATA
89134 TTCAAATGAA
Statistics
Matches: 222, Mismatches: 27, Indels: 37
0.78 0.09 0.13
Matches are distributed among these distances:
88 9 0.04
90 2 0.01
92 1 0.00
93 15 0.07
94 176 0.79
95 4 0.02
96 1 0.00
98 2 0.01
100 12 0.05
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (94 bp):
GCGATAGTCATATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCATTGCGATAGTCAA
ATTCGCGTTGCGATAGACAAATTCGCGTT
Found at i:89367 original size:140 final size:140
Alignment explanation
Indices: 89115--89380 Score: 514
Period size: 140 Copynumber: 1.9 Consensus size: 140
89105 GTTACGATAA
89115 TCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
89180 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
89245 CACATAATAG
131 CACATAATAG
* *
89255 TCAAATTCGCGTTGTGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
89320 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
89381 TACAACGTTT
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
TCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
CACATAATAG
Found at i:89463 original size:18 final size:18
Alignment explanation
Indices: 89440--89474 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
89430 AAGCCGGTTG
*
89440 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
89458 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
89475 GTCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:91530 original size:14 final size:14
Alignment explanation
Indices: 91511--91547 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
91501 TCCCGTGTCA
91511 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
91525 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
91539 TTCTTCTTC
1 TT-TTCTTC
91548 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:91771 original size:24 final size:24
Alignment explanation
Indices: 91737--91790 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
91727 CTGAAACATC
91737 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
91761 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
91785 ATCAAA
1 ATCAAA
91791 TTTCGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:92636 original size:20 final size:20
Alignment explanation
Indices: 92612--92722 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
92602 AAATTCAGTG
* *
92612 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
*
92632 TTGCGATAGTCAGAATCGTA
1 TTGCGATAGTCAGAATCGCA
*
92652 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
* * *
92672 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
* * *
92692 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
92712 TTGCGATAGTC
1 TTGCGATAGTC
92723 GGAAAATCGC
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 79 0.98
21 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:92773 original size:20 final size:20
Alignment explanation
Indices: 92620--92780 Score: 94
Period size: 20 Copynumber: 7.9 Consensus size: 20
92610 TGTTGCGACA
* *
92620 GTCAGAATCGCGTTGCGATA
1 GTCAGAATCGCATTGCGATT
* *
92640 GTCAGAATCGTATTGCGATA
1 GTCAGAATCGCATTGCGATT
*
92660 GTCATAATCGCATTGCGATT
1 GTCAGAATCGCATTGCGATT
* *
92680 -TACATATTCGCATTGCGATT
1 GT-CAGAATCGCATTGCGATT
* * *
92700 -TACATATTCGCATTGCGATA
1 GT-CAGAATCGCATTGCGATT
* **
92720 GTCGGAAAATCGCAACGCGAATT
1 GTC--AGAATCGCATTGCG-ATT
* * *
92743 -TGGAAAATCGCAATGCGATT
1 GT-CAGAATCGCATTGCGATT
*
92763 GTCAGAATCGCGTTGCGA
1 GTCAGAATCGCATTGCGA
92781 ATCTGGAAAC
Statistics
Matches: 116, Mismatches: 18, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
19 1 0.01
20 87 0.75
21 15 0.13
22 11 0.09
23 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (20 bp):
GTCAGAATCGCATTGCGATT
Found at i:93129 original size:46 final size:46
Alignment explanation
Indices: 93062--93155 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 46
93052 TTTTTAACAT
* * * *
93062 TTCCGGTAAAAGATTACCTAAATCATTATTATTTCTATCGAAAATG
1 TTCCGGTAAAAGATTAACTAAAACATTATTATTTCTACCAAAAATG
* * *
93108 TTCCGGT-AAAGCGTTAACTAAAACATTATTTTTTTTACCAAAAATG
1 TTCCGGTAAAAG-ATTAACTAAAACATTATTATTTCTACCAAAAATG
93154 TT
1 TT
93156 AATATTGGCA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 4 0.10
46 36 0.90
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (46 bp):
TTCCGGTAAAAGATTAACTAAAACATTATTATTTCTACCAAAAATG
Found at i:93216 original size:21 final size:22
Alignment explanation
Indices: 93182--93227 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
93172 TGGAAATATT
* *
93182 TAAAAAAAATTAATGTTTTAGG
1 TAAAAAAAATTAATATTTTAAG
*
93204 TAAAAATAA-TAATATTTTAAG
1 TAAAAAAAATTAATATTTTAAG
93225 TAA
1 TAA
93228 TTTTTTTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (22 bp):
TAAAAAAAATTAATATTTTAAG
Found at i:93292 original size:11 final size:11
Alignment explanation
Indices: 93276--93301 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
93266 GCGTCTTTCC
93276 TTAACCGTATA
1 TTAACCGTATA
93287 TTAACCGTATA
1 TTAACCGTATA
93298 TTAA
1 TTAA
93302 AGCTGCAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (11 bp):
TTAACCGTATA
Found at i:105113 original size:2 final size:2
Alignment explanation
Indices: 105106--105131 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
105096 TTTCATTCAT
105106 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
105132 AAAAAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107020 original size:12 final size:12
Alignment explanation
Indices: 107003--107029 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
106993 AAATGGATCA
107003 AATGCATGATAT
1 AATGCATGATAT
107015 AATGCATGATAT
1 AATGCATGATAT
107027 AAT
1 AAT
107030 TCTTTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (12 bp):
AATGCATGATAT
Found at i:112258 original size:32 final size:32
Alignment explanation
Indices: 112217--112287 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
112207 ATATATATAT
112217 AATAT-TA-ATAA-ATTTA-AT-TTAAATTAA
1 AATATATATATAATATTTATATATTAAATTAA
* *
112244 AATATATATATAATATTTATATATTTAATTTA
1 AATATATATATAATATTTATATATTAAATTAA
112276 AATATATATATA
1 AATATATATATA
112288 CCCGGCCCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
27 5 0.14
28 2 0.05
29 4 0.11
30 5 0.14
31 2 0.05
32 19 0.51
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
AATATATATATAATATTTATATATTAAATTAA
Found at i:112266 original size:15 final size:15
Alignment explanation
Indices: 112206--112285 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
112196 AATTATTTTA
112206 TATATATATATAATAT
1 TATATATATATAAT-T
* *
112222 TA-ATAAATTTAATT
1 TATATATATATAATT
* *
112236 TA-A-AT-TAAAATA
1 TATATATATATAATT
112248 TATATATA-AT-ATT
1 TATATATATATAATT
112261 TATATAT-T-TAATT
1 TATATATATATAATT
*
112274 TAAATATATATA
1 TATATATATATA
112286 TACCCGGCCC
Statistics
Matches: 48, Mismatches: 9, Indels: 15
0.67 0.12 0.21
Matches are distributed among these distances:
12 7 0.15
13 20 0.42
14 8 0.17
15 11 0.23
16 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:112287 original size:38 final size:37
Alignment explanation
Indices: 112203--112287 Score: 127
Period size: 38 Copynumber: 2.3 Consensus size: 37
112193 AATAATTATT
112203 TTATATATATATATAATATTAATAAATTTAATTTAAA
1 TTATATATATATATAATATTAATAAATTTAATTTAAA
* * *
112240 TTAAAATATATATATAATATTTATATATTTAATTTAAA
1 TT-ATATATATATATAATATTAATAAATTTAATTTAAA
112278 -TATATATATA
1 TTATATATATA
112288 CCCGGCCCGA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 8 0.19
37 3 0.07
38 32 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TTATATATATATATAATATTAATAAATTTAATTTAAA
Found at i:112845 original size:17 final size:17
Alignment explanation
Indices: 112825--112857 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
112815 AGGACTAATT
112825 TTATAAATACCCTAAAC
1 TTATAAATACCCTAAAC
*
112842 TTATAAATATCCTAAA
1 TTATAAATACCCTAAA
112858 GTCTAGGGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (17 bp):
TTATAAATACCCTAAAC
Found at i:135744 original size:9 final size:9
Alignment explanation
Indices: 135730--135754 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
135720 GGTCCTAACT
135730 TTTAATAAA
1 TTTAATAAA
135739 TTTAATAAA
1 TTTAATAAA
135748 TTTAATA
1 TTTAATA
135755 TTCAATCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAATAAA
Found at i:137987 original size:13 final size:12
Alignment explanation
Indices: 137968--138001 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
137958 ATTAAAGATG
*
137968 TACTTAATTAAA
1 TACTTAAATAAA
137980 TCACTTAAATAAA
1 T-ACTTAAATAAA
137993 TACTTAAAT
1 TACTTAAAT
138002 TACATATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (12 bp):
TACTTAAATAAA
Found at i:138983 original size:30 final size:30
Alignment explanation
Indices: 138920--139013 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
138910 GAAGGACCTA
* * *
138920 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
138949 TCCAGAGGTCATAAAGATCCTCAGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
138979 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
139010 TCCA
1 TCCA
139014 TATGTTCCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 16 0.28
30 33 0.57
31 9 0.16
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:139062 original size:31 final size:31
Alignment explanation
Indices: 139001--139068 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
138991 AAAGATCCTC
**
139001 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCAAAGAACATA
* *
139032 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCAAAGAACATA
139063 GGTAAA
1 GGTAAA
139069 ACCCTCGACT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCAAAGAACATA
Found at i:139983 original size:21 final size:21
Alignment explanation
Indices: 139953--139997 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
139943 TTTTGTTTGT
* *
139953 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
139974 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
139995 TTG
1 TTG
139998 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:140730 original size:20 final size:20
Alignment explanation
Indices: 140707--140753 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
140697 TACAGTTTAG
*
140707 GTTGACTCAATTCAGTCCGA
1 GTTGACTCAATCCAGTCCGA
* * *
140727 GTTGACTTAGTCCAGTTCGA
1 GTTGACTCAATCCAGTCCGA
140747 GTTGACT
1 GTTGACT
140754 TGAACTGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (20 bp):
GTTGACTCAATCCAGTCCGA
Found at i:142304 original size:34 final size:32
Alignment explanation
Indices: 142246--142315 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
142236 ACCTTACAAC
* * *
142246 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
142278 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
142312 TCCC
1 TCCC
142316 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:142704 original size:20 final size:21
Alignment explanation
Indices: 142679--142733 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
142669 TTGCAGCCTT
*
142679 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
142699 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
142720 GATGCATCGATGCA
1 GATGCATCGATGCA
142734 CTAATTTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:142799 original size:13 final size:13
Alignment explanation
Indices: 142778--142815 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
142768 TTAGTGCAGA
*
142778 TGCATGGATGCAC
1 TGCAGGGATGCAC
142791 TGCAGGGATGCAC
1 TGCAGGGATGCAC
142804 TGCAGGGATGCA
1 TGCAGGGATGCA
142816 TGGATGCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.24, C:0.21, G:0.37, T:0.18
Consensus pattern (13 bp):
TGCAGGGATGCAC
Found at i:142964 original size:30 final size:30
Alignment explanation
Indices: 142907--142966 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
142897 AACTTTGAAT
142907 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
142937 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
142967 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:144266 original size:19 final size:20
Alignment explanation
Indices: 144223--144270 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
144213 TCTAAATCCT
*
144223 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
144243 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
144262 TTTTCAAAA
1 TTTTCAAAA
144271 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:145167 original size:7 final size:8
Alignment explanation
Indices: 145136--145190 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
145126 TACCCGACCC
145136 GACCCGTT
1 GACCCGTT
145144 GACCCGTT
1 GACCCGTT
*
145152 TACCCGTT
1 GACCCGTT
145160 GA-CCGTT
1 GACCCGTT
145167 GACCGGCGTT
1 GACC--CGTT
145177 GACCACTGTT
1 GACC-C-GTT
145187 GACC
1 GACC
145191 AAAACTTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 7 0.17
8 17 0.43
9 1 0.03
10 15 0.38
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (8 bp):
GACCCGTT
Found at i:147731 original size:24 final size:24
Alignment explanation
Indices: 147642--147743 Score: 89
Period size: 24 Copynumber: 4.2 Consensus size: 24
147632 TTATCCGATT
* * *
147642 TCTGATTTGAATTCTGTTTTGACA
1 TCTGATCTGAATTCTGTTCTGATA
* *
147666 TCTGATCTGAAATCTGCTCTGAT-
1 TCTGATCTGAATTCTGTTCTGATA
* * *
147689 TCCTAACCTGGATTCTGTTCTGATA
1 T-CTGATCTGAATTCTGTTCTGATA
* * *
147714 TCTGATCTGAATTATGTTTTGATT
1 TCTGATCTGAATTCTGTTCTGATA
147738 TCTGAT
1 TCTGAT
147744 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 58 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (24 bp):
TCTGATCTGAATTCTGTTCTGATA
Found at i:149829 original size:18 final size:18
Alignment explanation
Indices: 149806--149840 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
149796 ACCGGTCACA
*
149806 ACCCGACCTGACCCGTTT
1 ACCCGACCCGACCCGTTT
149824 ACCCGACCCGACCCGTT
1 ACCCGACCCGACCCGTT
149841 GACCGTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.49, G:0.17, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:149848 original size:7 final size:7
Alignment explanation
Indices: 149836--149863 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
149826 CCGACCCGAC
149836 CCGTTGA
1 CCGTTGA
149843 CCGTTGA
1 CCGTTGA
149850 CCGTTGA
1 CCGTTGA
149857 CCGTTGA
1 CCGTTGA
149864 TCGGCATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
CCGTTGA
Found at i:152428 original size:24 final size:24
Alignment explanation
Indices: 152339--152440 Score: 98
Period size: 24 Copynumber: 4.2 Consensus size: 24
152329 TTATTCGATT
* * *
152339 TCTGATTTGAATTCTGTTTTGACA
1 TCTGATCTGAATTCTGTTCTGATA
*
152363 TCTGATCTGAAATCTGTTCTGAT-
1 TCTGATCTGAATTCTGTTCTGATA
* * *
152386 TCCTAACCTGGATTCTGTTCTGATA
1 T-CTGATCTGAATTCTGTTCTGATA
* * *
152411 TCTGATCTGAATTATGTTTTGATT
1 TCTGATCTGAATTCTGTTCTGATA
152435 TCTGAT
1 TCTGAT
152441 ATCTCCGTTT
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
23 1 0.02
24 60 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATCTGAATTCTGTTCTGATA
Found at i:152607 original size:2 final size:2
Alignment explanation
Indices: 152600--152638 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
152590 CGGATGGGGG
152600 TA TA 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 T
152639 TAAAAGATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:154404 original size:8 final size:8
Alignment explanation
Indices: 154391--154467 Score: 52
Period size: 8 Copynumber: 11.1 Consensus size: 8
154381 TTGCAGCCTT
154391 GATGCATG
1 GATGCATG
154399 GATGCAT-
1 GATGCATG
154406 G--GCA-G
1 GATGCATG
154411 GATGCATG
1 GATGCATG
154419 GATGCAT-
1 GATGCATG
154426 G--GCAT-
1 GATGCATG
*
154431 GATGCATC
1 GATGCATG
154439 GATGCAT-
1 GATGCATG
154446 G--GCA-G
1 GATGCATG
*
154451 GATGCATC
1 GATGCATG
154459 GATGCATG
1 GATGCATG
154467 G
1 G
154468 CAAGGATGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 22
0.70 0.03 0.28
Matches are distributed among these distances:
5 13 0.23
7 13 0.23
8 30 0.54
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (8 bp):
GATGCATG
Found at i:154416 original size:20 final size:20
Alignment explanation
Indices: 154391--154485 Score: 154
Period size: 20 Copynumber: 4.7 Consensus size: 20
154381 TTGCAGCCTT
*
154391 GATGCATGGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
* *
154411 GATGCATGGATGCATGGCAT
1 GATGCATCGATGCATGGCAG
154431 GATGCATCGATGCATGGCAG
1 GATGCATCGATGCATGGCAG
154451 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGC-AG
154472 GATGCATCGATGCA
1 GATGCATCGATGCA
154486 CTAATTGCAT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
20 55 0.77
21 16 0.23
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:154530 original size:95 final size:97
Alignment explanation
Indices: 154410--154584 Score: 250
Period size: 95 Copynumber: 1.8 Consensus size: 97
154400 ATGCATGGCA
154410 GGATGCATGGATGCATGGCATGATGCATCGATGCA-T-G-GCAGGATGCATCGATGCA-TGGCAA
1 GGATGCATGGATGCATGGCATGATGCATCGATGCATTAGTGCA-GATGCATCGATGCACT-GCAA
154471 GGATGCATCGATGCACTAATTGCATTCGATGTTT
64 GGATGCATCGATGCACTAATTGCATTCGATGTTT
* * * * *
154505 GGATGCATGGATGCATTGCCTGATGCATCGATGCATTAGTGCATATGCATGGATGCACTGCAGGG
1 GGATGCATGGATGCATGGCATGATGCATCGATGCATTAGTGCAGATGCATCGATGCACTGCAAGG
*
154570 ATGCATGGATGCACT
66 ATGCATCGATGCACT
154585 TTGACACCCT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
95 33 0.47
96 1 0.01
97 32 0.46
98 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (97 bp):
GGATGCATGGATGCATGGCATGATGCATCGATGCATTAGTGCAGATGCATCGATGCACTGCAAGG
ATGCATCGATGCACTAATTGCATTCGATGTTT
Found at i:154700 original size:30 final size:30
Alignment explanation
Indices: 154666--154725 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
154656 AACTTTGAAT
*
154666 AAATTCAATTCAAATCCAAAAATATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
154696 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
154726 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:160552 original size:2 final size:2
Alignment explanation
Indices: 160545--160579 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
160535 TCGGGAGTGC
160545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
160580 ACGTTGGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:160619 original size:18 final size:16
Alignment explanation
Indices: 160578--160611 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
160568 TATATATATA
160578 TAACGTTGGCAGAGGC
1 TAACGTTGGCAGAGGC
160594 TAACGTTGGCAGAGGC
1 TAACGTTGGCAGAGGC
160610 TA
1 TA
160612 CAACGTTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (16 bp):
TAACGTTGGCAGAGGC
Found at i:161951 original size:33 final size:33
Alignment explanation
Indices: 161914--161984 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
161904 ACTAATTTTA
*
161914 ATTTTGTTTCCCTC-TTTTTCTATGATTAATTAT
1 ATTTTATTTCCCTCATTTTTC-ATGATTAATTAT
161947 ATTTTATTTCCCTCATTTTTCATGATTAATTAT
1 ATTTTATTTCCCTCATTTTTCATGATTAATTAT
161980 -TTTTA
1 ATTTTA
161985 CCCTCCTCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
32 5 0.14
33 25 0.69
34 6 0.17
ACGTcount: A:0.21, C:0.14, G:0.04, T:0.61
Consensus pattern (33 bp):
ATTTTATTTCCCTCATTTTTCATGATTAATTAT
Found at i:162988 original size:34 final size:35
Alignment explanation
Indices: 162950--163051 Score: 143
Period size: 34 Copynumber: 2.9 Consensus size: 35
162940 TTTCGTCCTA
* *
162950 TTAGGATTCAAACTCTTAAAAATAAGATAGAA-TT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
162984 TTAGGATTCAAACTCCTATAAATAGGATAAAATTT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
163019 TGCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 T--TAGGATTCAAACTCCTAAAAATAGGATAGA
163052 GTTCTACTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
34 28 0.47
35 3 0.05
37 28 0.47
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (35 bp):
TTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:163646 original size:21 final size:19
Alignment explanation
Indices: 163616--163656 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
163606 CTTTTACTTT
163616 TTTATATATTTTACTCATTTA
1 TTTATATATTTTA-T-ATTTA
*
163637 TTTATCTATTTTATATTTA
1 TTTATATATTTTATATTTA
163656 T
1 T
163657 CCTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATATATTTTATATTTA
Found at i:165802 original size:18 final size:18
Alignment explanation
Indices: 165779--165818 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
165769 TTCCTTCAAG
165779 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
165797 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
165815 TCTG
1 TCTG
165819 AAAGACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
TCTGGATTCACATCCACT
Found at i:166351 original size:8 final size:8
Alignment explanation
Indices: 166338--166376 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
166328 GAACATTTCG
*
166338 TGCATTCT
1 TGCATTTT
166346 TGCA-TTT
1 TGCATTTT
166353 TGCATTTT
1 TGCATTTT
*
166361 TGCCTTTT
1 TGCATTTT
166369 TGCATTTT
1 TGCATTTT
166377 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:167568 original size:16 final size:16
Alignment explanation
Indices: 167542--167575 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
167532 AGATCCAATC
167542 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
167557 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
167574 AA
1 AA
167576 AAAAACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:167591 original size:24 final size:23
Alignment explanation
Indices: 167564--167639 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
167554 GAAAAGAAGC
167564 AAAAAAGCAAAAAAAAACACAAA-G
1 AAAAAAG-AAAAAAAAACA-AAAGG
* *
167588 AAAAAGAGAAACAAGAACAAAAGG
1 AAAAA-AGAAAAAAAAACAAAAGG
** * *
167612 AAAAAAGAGCAAAAATCAAAAAG
1 AAAAAAGAAAAAAAAACAAAAGG
167635 AAAAA
1 AAAAA
167640 GGGACAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
23 20 0.48
24 20 0.48
25 2 0.05
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.01
Consensus pattern (23 bp):
AAAAAAGAAAAAAAAACAAAAGG
Found at i:168282 original size:22 final size:22
Alignment explanation
Indices: 168254--168304 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
168244 CCCCATCAAT
168254 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
168276 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
168298 CCTTTGA
1 CCTTTGA
168305 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:168725 original size:18 final size:18
Alignment explanation
Indices: 168702--168737 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
168692 TCAACATCAA
* *
168702 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
168720 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
168738 GGATTCAATA
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:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:169204 original size:36 final size:35
Alignment explanation
Indices: 169164--169459 Score: 169
Period size: 36 Copynumber: 8.4 Consensus size: 35
169154 ACTCATGATT
* * *
169164 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAA-ATTTGTCTCTCTTGAGACA
* * * **
169200 GTTT-TCACTAGAAGAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAATTTGTCTCTCTTGAGACA
* * *
169235 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
* *
169271 GTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* * * * *
169307 GTTTCCCTTGAAACAAA-----ATAT-TTGA-ATA
1 GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
* *
169335 TGTTT-TCTTTGAAACAAATTTCGTCTCCCTTGAGACA
1 -GTTTCTC-TTAAAACAAATTT-GTCTCTCTTGAGACA
* ** *
169372 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAAC-AA-ATTTGTCTCTCTTGAGACA
* * * *
169409 GTTTCTCTTGAATCAATTTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* *
169445 GTTACTCTTGAAACA
1 GTTTCTCTTAAAACA
169460 CAAAATCTTC
Statistics
Matches: 207, Mismatches: 35, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
28 3 0.01
29 18 0.09
30 3 0.01
35 34 0.16
36 116 0.56
37 30 0.14
38 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (35 bp):
GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
Found at i:170371 original size:105 final size:105
Alignment explanation
Indices: 170132--170886 Score: 1105
Period size: 105 Copynumber: 7.3 Consensus size: 105
170122 GCCATCTGCG
* * * * * *
170132 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
170197 GGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
*
170241 ATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
170306 ACCGCTTCCTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
170346 ATTTCAACTTCACAATGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
170411 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
170451 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
170516 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
170556 ATTTCAACTTCACAACGAAGGATATTGGACT-CAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
170620 ACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
170660 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
170725 ACCGCTGCTTGTCAACAA-AAC-T-TC-A-TTCAAGAG-CA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTC-AGAGCCA
*
170760 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCAC-ACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
170824 ACCGCTGGTTGTCAACAA-AA-TT-TC-----CAGAACCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
170856 ATTTCAACTTCACGAA-GGAGGATATTGGACT
1 ATTTCAACTTCAC-AACGAAGGATATTGGACT
170887 TGGAACAATG
Statistics
Matches: 610, Mismatches: 30, Indels: 25
0.92 0.05 0.04
Matches are distributed among these distances:
95 3 0.00
96 30 0.05
97 2 0.00
99 30 0.05
100 57 0.09
101 5 0.01
102 1 0.00
103 1 0.00
104 106 0.17
105 305 0.50
106 44 0.07
107 5 0.01
109 21 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:170698 original size:209 final size:208
Alignment explanation
Indices: 170132--170886 Score: 1112
Period size: 209 Copynumber: 3.7 Consensus size: 208
170122 GCCATCTGCG
* * * * *
170132 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCGAGACAACGCAAGTTCAACTTCACGACGAA
*
170197 GGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
* * *
170261 AATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTTCCTGTCAACAACA
126 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACA
170326 ACTTCTCAATTTCAGAGCCA
191 ACTTC-CAA-TTCAGAGCCA
* *
170346 ATTTCAACTTCACAATGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCATGACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGAC-TCGAGACAACGCAAGTTCAACTTCACGACGAAGG
170410 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
65 GACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
*
170475 TTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT
130 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT
170540 CCCAATCTCAGAGCCA
195 -CCAAT-TCAGAGCCA
170556 ATTTCAACTTCACAACGAAGGATATTGGACTC-AGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
170620 ACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
170685 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AACTT-
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTC
170748 C-ATTCAAGAG-CA
196 CAATTC-AGAGCCA
170760 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCAC-ACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
170824 ACCGCTGGTTGTCAACAA-AA-TT-TC-----CAGAACCAATTTCAACTTCACGAA-GGAGGATA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCAC-AACGAAGGATA
170880 TTGGACT
130 TTGGACT
170887 TGGAACAATG
Statistics
Matches: 510, Mismatches: 24, Indels: 32
0.90 0.04 0.06
Matches are distributed among these distances:
196 33 0.06
197 2 0.00
201 1 0.00
202 2 0.00
203 2 0.00
204 61 0.12
205 29 0.06
206 1 0.00
208 5 0.01
209 152 0.30
210 150 0.29
211 44 0.09
212 7 0.01
214 21 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (208 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTC
CAATTCAGAGCCA
Found at i:171478 original size:34 final size:36
Alignment explanation
Indices: 171434--171535 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
171424 TTTCGTCCTA
171434 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
171469 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
171504 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
171536 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:172040 original size:2 final size:2
Alignment explanation
Indices: 171980--172021 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
171970 TATTATTTAT
171980 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
172021 T
1 T
172022 CCTATTTTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:172155 original size:16 final size:18
Alignment explanation
Indices: 172134--172168 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
172124 TTTACTCATT
172134 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
172150 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
172168 T
1 T
172169 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:174756 original size:3 final size:3
Alignment explanation
Indices: 174748--174782 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
174738 TATTATAACA
174748 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
174783 AAAAAGATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:176698 original size:23 final size:23
Alignment explanation
Indices: 176659--176703 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
176649 TTGATTCTGG
*
176659 TTATAGTTATATAAATATTTTTA
1 TTATAGTTATATAAATAATTTTA
*
176682 TTATA-TTATATCGAATAATTTT
1 TTATAGTTATAT-AAATAATTTT
176704 GACTATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
TTATAGTTATATAAATAATTTTA
Found at i:192742 original size:7 final size:7
Alignment explanation
Indices: 192730--192775 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
192720 TGTCCAAACC
192730 GAATTCA
1 GAATTCA
192737 GAATTCA
1 GAATTCA
192744 GAATTCA
1 GAATTCA
192751 GAATTCA
1 GAATTCA
192758 GAATTCA
1 GAATTCA
*
192765 GAAGTCA
1 GAATTCA
192772 GAAT
1 GAAT
192776 GCAAGGTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (7 bp):
GAATTCA
Found at i:195969 original size:19 final size:18
Alignment explanation
Indices: 195945--195997 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
195935 GAATGTATTT
195945 CATGCATCGATGCACATAC
1 CATGCATCGATGCACA-AC
* *
195964 CATGCACCGATGCACCAGC
1 CATGCATCGATGCA-CAAC
*
195983 CATACATCGATGCAC
1 CATGCATCGATGCAC
195998 TCTGGCTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 1 0.03
19 26 0.90
20 2 0.07
ACGTcount: A:0.30, C:0.36, G:0.17, T:0.17
Consensus pattern (18 bp):
CATGCATCGATGCACAAC
Found at i:196021 original size:83 final size:84
Alignment explanation
Indices: 195881--196042 Score: 204
Period size: 83 Copynumber: 1.9 Consensus size: 84
195871 TTTCAGAGTG
* * * * *
195881 ATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTGAACATCGAATGTATTTC
1 ATGCACCGATGCACCAAGCCATACATCGATGCACCATGAACTAAATTGAACATCGAATGCACTTC
195946 ATGCATCGATGCACATACC
66 ATGCATCGATGCACATACC
* **
195965 ATGCACCGATGCACC-AGCCATACATCGATGCACTC-TG-GCTATTTTGAAACATCGAATGCACT
1 ATGCACCGATGCACCAAGCCATACATCGATGCAC-CATGAACTAAATTG-AACATCGAATGCACT
*
196027 TGATGCATCGATGCAC
64 TCATGCATCGATGCAC
196043 TCTTAGTGCA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
82 5 0.07
83 46 0.69
84 16 0.24
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (84 bp):
ATGCACCGATGCACCAAGCCATACATCGATGCACCATGAACTAAATTGAACATCGAATGCACTTC
ATGCATCGATGCACATACC
Found at i:196042 original size:17 final size:19
Alignment explanation
Indices: 196014--196062 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
196004 TATTTTGAAA
196014 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
196032 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
196051 CACCGATGCACT
1 CATCGATGCACT
196063 GAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:204528 original size:21 final size:23
Alignment explanation
Indices: 204493--204551 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
204483 TTGGTGCAGA
*
204493 GGGAATCGA-TCCCCCCATG-A-
1 GGGAACCGATTCCCCCCATGAAG
* **
204513 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATGAAG
204536 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
204552 ACAGGGGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 7 0.23
21 8 0.26
22 1 0.03
23 15 0.48
ACGTcount: A:0.22, C:0.34, G:0.25, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCATGAAG
Found at i:204559 original size:20 final size:20
Alignment explanation
Indices: 204534--204571 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
204524 CCCCCTTTGA
*
204534 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
204554 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
204572 TGGAGTACTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:206873 original size:18 final size:18
Alignment explanation
Indices: 206850--206907 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
206840 GGAGAAGTGT
206850 TAAATGTGTTTTAAATGA
1 TAAATGTGTTTTAAATGA
*** * *
206868 TAAATG-G-GAGAAGTGT
1 TAAATGTGTTTTAAATGA
206884 TAAATGTGTTTTAAATGA
1 TAAATGTGTTTTAAATGA
206902 TAAATG
1 TAAATG
206908 GGAGAAGTGT
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
16 10 0.36
17 2 0.07
18 16 0.57
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (18 bp):
TAAATGTGTTTTAAATGA
Done.