Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009568.1 Hibiscus syriacus cultivar Beakdansim tig00116927_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: 696633
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1211 original size:184 final size:185
Alignment explanation
Indices: 903--1365 Score: 871
Period size: 184 Copynumber: 2.5 Consensus size: 185
893 TAGATTGCTT
* *
903 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATAG-A
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
967 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1032 G-GTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTC-TTTGGTTGAA
1086 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1151 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1216 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
1271 AGTAAATTTG-TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1335 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
1366 TTCAATTTGC
Statistics
Matches: 275, Mismatches: 2, Indels: 5
0.98 0.01 0.02
Matches are distributed among these distances:
183 61 0.22
184 152 0.55
185 43 0.16
186 19 0.07
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
Found at i:1214 original size:93 final size:93
Alignment explanation
Indices: 903--1365 Score: 873
Period size: 91 Copynumber: 5.0 Consensus size: 93
893 TAGATTGCTT
* *
903 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATAG-A
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
967 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
995 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG-GTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1058 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1086 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1151 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1179 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1244 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1271 AGTAAATTTG-TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1335 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1363 AGT
1 AGT
1366 TTCAATTTGC
Statistics
Matches: 365, Mismatches: 2, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
91 160 0.44
92 93 0.25
93 112 0.31
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1437 original size:19 final size:19
Alignment explanation
Indices: 1397--1524 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1387 TAGTTTACTT
* *
1397 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1417 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1436 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1455 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1469 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1488 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1502 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
1520 TCGCA
1 TCGCA
1525 TTGCGATTTC
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 9 0.10
19 38 0.43
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1476 original size:33 final size:32
Alignment explanation
Indices: 1433--1524 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
1423 CGCGAAACCA
**
1433 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1465 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1498 AAGATCGCAACGCGAAACC-AAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1525 TTGCGATTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 10 0.18
33 46 0.82
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1541 original size:18 final size:18
Alignment explanation
Indices: 1520--1581 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
1510 CGAAACCAAA
1520 TCGCATTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
1538 TCGCGTTGCGA-TTC-TT
1 TCGCATTGCGATTTCATT
1554 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
1570 TCGCATTGCGAT
1 TCGCATTGCGAT
1582 CTGTCGTTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 6 0.15
15 3 0.08
16 10 0.26
17 3 0.08
18 17 0.44
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:1560 original size:14 final size:14
Alignment explanation
Indices: 1541--1595 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
1531 TTTCATTTCG
1541 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1555 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
1571 CGCATTGCGA-TCTGT
1 CG--TTGCGATTCTTT
1586 CGTTGCGATT
1 CGTTGCGATT
1596 TTCATTCGCG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 6 0.17
14 9 0.26
15 7 0.20
16 7 0.20
18 6 0.17
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1566 original size:32 final size:32
Alignment explanation
Indices: 1525--1613 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 32
1515 CCAAATCGCA
*
1525 TTGCGATTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
*
1557 TTGCGATTTCATTTCGCATTGCGA-TCTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
1588 TTGCGATTTTCA-TTCGCGTTGCGATT
1 TTGCGA-TTTCATTTCGCGTTGCGATT
1614 TTGGTTTCGC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 23 0.44
32 29 0.56
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.45
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1624 original size:19 final size:18
Alignment explanation
Indices: 1586--1650 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
1576 TGCGATCTGT
**
1586 CGTTGCGATTTTCATTCG
1 CGTTGCGATTTTGTTTCG
1604 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-GTTTCG
1623 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT--GTTTCG
*
1643 TGTTGCGA
1 CGTTGCGA
1651 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.29
19 16 0.39
20 13 0.32
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.45
Consensus pattern (18 bp):
CGTTGCGATTTTGTTTCG
Found at i:3576 original size:14 final size:14
Alignment explanation
Indices: 3557--3592 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3547 ATTGTTTAAT
3557 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3571 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3585 TGATTTGT
1 TGATTTGT
3593 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:3712 original size:19 final size:19
Alignment explanation
Indices: 3696--3796 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
3686 AAAAATGACT
3696 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3715 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3734 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3748 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3767 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
3786 ATCGCAATGCG
1 ATCGCAATGCG
3797 TTTATAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 51 0.69
20 6 0.08
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3861 original size:19 final size:19
Alignment explanation
Indices: 3825--4141 Score: 333
Period size: 19 Copynumber: 18.4 Consensus size: 19
3815 GATTATCTCG
3825 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
3843 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3862 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3876 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3895 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3909 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3928 TTGCGA-TTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3946 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
3960 -TGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3978 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3997 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4016 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4030 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4048 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4067 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4081 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
4101 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
4115 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
4134 TTGCGATT
1 TTGCGATT
4142 GTATTTTCCG
Statistics
Matches: 256, Mismatches: 10, Indels: 65
0.77 0.03 0.20
Matches are distributed among these distances:
13 5 0.02
14 35 0.14
15 6 0.02
16 41 0.16
17 27 0.11
18 38 0.15
19 92 0.36
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3863 original size:51 final size:52
Alignment explanation
Indices: 3803--4113 Score: 376
Period size: 51 Copynumber: 6.0 Consensus size: 52
3793 TGCGTTTATA
*
3803 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCA-TTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
3854 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
3904 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA-TTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
3959 -GTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4008 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4059 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
4112 AT
1 AT
4114 GTTGGGATTT
Statistics
Matches: 226, Mismatches: 15, Indels: 36
0.82 0.05 0.13
Matches are distributed among these distances:
47 6 0.03
49 10 0.04
50 21 0.09
51 123 0.54
52 37 0.16
53 17 0.08
54 3 0.01
55 5 0.02
56 1 0.00
57 3 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:3883 original size:33 final size:34
Alignment explanation
Indices: 3837--4141 Score: 275
Period size: 33 Copynumber: 8.9 Consensus size: 34
3827 GCGATTTTCA
3837 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCT
1 TTCG-ATTGCGATTTTCATTTCGCATTGCGATTCT
3872 TTCG-TTGCGATTTTCATTTCGCATTGCGATTCT
1 TTCGATTGCGATTTTCATTTCGCATTGCGATTCT
*
3905 TTCG-TTGCGATTTTCATTTCGCATTGCGATTTAAT
1 TTCGATTGCGATTTTCATTTCGCATTGCGA-TT-CT
*
3940 TTCGCATTGCGA--TTC-TGTCG---TGCGATTTTCAT
1 TTCG-ATTGCGATTTTCATTTCGCATTGCGA--TTC-T
3972 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTCG-ATTGCGATTTTCATTTCGCATTGCGA--TTC-T
*
4010 TTCGCATTGCGA--TTC-TCTCG--TTGCGATTTCAT
1 TTCG-ATTGCGATTTTCATTTCGCATTGCGA-TTC-T
4042 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCT
1 TTCG-ATTGCGATTTTCATTTCGCATTGCGATTCT
*
4077 CTCG-TTGCGATTTTCATTTCCGCATTGCGA-T-T
1 TTCGATTGCGATTTTCATTT-CGCATTGCGATTCT
* *
4109 TTC-ATGTTGGGATTTTCATTTCGCGTTGCGATT
1 TTCGA--TTGCGATTTTCATTTCGCATTGCGATT
4142 GTATTTTCCG
Statistics
Matches: 238, Mismatches: 10, Indels: 45
0.81 0.03 0.15
Matches are distributed among these distances:
31 5 0.02
32 37 0.16
33 89 0.37
34 37 0.16
35 28 0.12
36 6 0.03
37 12 0.05
38 24 0.10
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (34 bp):
TTCGATTGCGATTTTCATTTCGCATTGCGATTCT
Found at i:6427 original size:12 final size:12
Alignment explanation
Indices: 6410--6434 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6400 TCTTCGGGGA
6410 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6422 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6434 C
1 C
6435 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:6640 original size:24 final size:24
Alignment explanation
Indices: 6606--6652 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6596 CTGAAACATC
6606 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
6630 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
6653 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:7362 original size:20 final size:20
Alignment explanation
Indices: 7334--7703 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
7324 AAATTTCAGT
* * * *
7334 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
7354 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
7374 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
7394 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
7414 GTTGCGATTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
*
7435 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
7455 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
7475 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7495 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7515 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
7535 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
7555 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7575 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
7595 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
7615 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
7635 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
7655 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
7675 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
7695 GTTGCGATT
1 GTTGCGATT
7704 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.01
20 285 0.92
21 21 0.07
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:8321 original size:16 final size:16
Alignment explanation
Indices: 8302--8337 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
8292 AATTAAATAT
8302 TAAATT-TAAAACAACA
1 TAAATTATAAAACAA-A
8318 TAAATTATAAAACAAA
1 TAAATTATAAAACAAA
8334 TAAA
1 TAAA
8338 AATATAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAATTATAAAACAAA
Found at i:8343 original size:17 final size:17
Alignment explanation
Indices: 8303--8345 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
8293 ATTAAATATT
*
8303 AAATTTAAAACAACATA
1 AAATATAAAACAACATA
*
8320 AATTATAAAACAA-ATAA
1 AAATATAAAACAACAT-A
8337 AAATATAAA
1 AAATATAAA
8346 TGAGTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATATAAAACAACATA
Found at i:9930 original size:17 final size:18
Alignment explanation
Indices: 9899--9935 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
9889 ATCTTAATTC
9899 TTATCATTATCATTT-TA
1 TTATCATTATCATTTCTA
9916 TTATCATTCAT-ATTTCTA
1 TTATCATT-ATCATTTCTA
9934 TT
1 TT
9936 CTCTTGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.27, C:0.14, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATCATTATCATTTCTA
Found at i:14680 original size:21 final size:21
Alignment explanation
Indices: 14654--14693 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
14644 CATATAGCTT
*
14654 CTTTTCATGTAATTCATATCA
1 CTTTTCATATAATTCATATCA
14675 CTTTTCATATAATTCATAT
1 CTTTTCATATAATTCATAT
14694 GTTCACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.03, T:0.50
Consensus pattern (21 bp):
CTTTTCATATAATTCATATCA
Found at i:14730 original size:30 final size:30
Alignment explanation
Indices: 14668--14732 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
14658 TCATGTAATT
* *
14668 CATATCACTTTTCATATAATTCATATGTTCA
1 CATATCACTTTTCATAT-ATTCATAGGATCA
*
14699 CATATCTCTTTTCATAT-TCTCATAGGATCA
1 CATATCACTTTTCATATAT-TCATAGGATCA
14729 CATA
1 CATA
14733 GCACATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 13 0.43
31 16 0.53
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.43
Consensus pattern (30 bp):
CATATCACTTTTCATATATTCATAGGATCA
Found at i:17458 original size:12 final size:12
Alignment explanation
Indices: 17443--17523 Score: 69
Period size: 12 Copynumber: 6.7 Consensus size: 12
17433 ATATTTGATT
17443 TTAATTTTAATA
1 TTAATTTTAATA
17455 TTAATTTTTAA-A
1 TTAA-TTTTAATA
* *
17467 -TAAATTAAATA
1 TTAATTTTAATA
*
17478 TTATTTTTTTAATA
1 TTA--ATTTTAATA
*
17492 TT-ATATTATATA
1 TTAATTTTA-ATA
17504 TTAATTTTAATA
1 TTAATTTTAATA
17516 TTAATTTT
1 TTAATTTT
17524 TTAAATAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
10 4 0.07
11 8 0.15
12 23 0.43
13 11 0.20
14 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:17477 original size:23 final size:25
Alignment explanation
Indices: 17451--17519 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 25
17441 TTTTAATTTT
17451 AATATTAATTTTTAA-A-TAAATTA
1 AATATTAATTTTTAATATTAAATTA
* *
17474 AATATTATTTTTTTAATATTATATTA
1 AATATTA-ATTTTTAATATTAAATTA
*
17500 TATATTAA-TTTTAATATTAA
1 AATATTAATTTTTAATATTAA
17520 TTTTTTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 7 0.18
24 18 0.47
25 1 0.03
26 12 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
AATATTAATTTTTAATATTAAATTA
Found at i:17509 original size:61 final size:62
Alignment explanation
Indices: 17428--17551 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 62
17418 ATTTAATTTG
* *
17428 ATATTATATTTGATTTTAATTTTAATATTAA-TTTTTAAATAAATTAAATATTATTTTTTTA
1 ATATTATATTTGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAGTTTTTTA
17489 ATATTATATTAT-ATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAGTTTTTTA
1 ATATTATATT-TGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAGTTTTTTA
17551 A
1 A
17552 GAGAAAATAA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
61 28 0.47
62 31 0.53
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (62 bp):
ATATTATATTTGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAGTTTTTTA
Found at i:17551 original size:38 final size:38
Alignment explanation
Indices: 17474--17547 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 38
17464 AAATAAATTA
* * *
17474 AATATTATTTTTTTAATATTATATTATATATTAATTTT
1 AATATTAATTTTTTAATATTAAATTAAATATTAATTTT
*
17512 AATATTAATTTTTTAA-A-TAAATTAAATATTAGTTTT
1 AATATTAATTTTTTAATATTAAATTAAATATTAATTTT
17548 TTAAGAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 16 0.50
37 1 0.03
38 15 0.47
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (38 bp):
AATATTAATTTTTTAATATTAAATTAAATATTAATTTT
Found at i:17741 original size:21 final size:21
Alignment explanation
Indices: 17717--17894 Score: 127
Period size: 21 Copynumber: 8.5 Consensus size: 21
17707 ATTTCGACTA
* *
17717 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
17738 TCGCGTTGCGGTAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
**
17759 TCGCGTTGCGA-A-TCTGGAAAC
1 TCGCGTTGCGATAGTC--GAAGT
**
17780 T-GATTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* * *
17800 TCGCGTTGCGATTTATTCCAACT
1 TCGCGTTGCGA--TAGTCGAAGT
* * *
17823 T--CGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA--TAGTCGAAGT
17844 T--CGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
17863 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
17884 TCGCGTTGCGA
1 TCGCGTTGCGA
17895 ATCTGGAAAC
Statistics
Matches: 128, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
19 10 0.08
20 12 0.09
21 96 0.75
22 2 0.02
23 8 0.06
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:18106 original size:18 final size:18
Alignment explanation
Indices: 18080--18124 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
18070 ATATCATACA
18080 AATTATTTTATATATTATT
1 AATTATTTTATATATT-TT
*
18099 AA-TATTTTATTTATTTT
1 AATTATTTTATATATTTT
18116 AATTATTTT
1 AATTATTTT
18125 GATTTAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
AATTATTTTATATATTTT
Found at i:18623 original size:31 final size:31
Alignment explanation
Indices: 18586--18645 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
18576 TAGTTGTATG
* *
18586 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
18617 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
18646 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:20652 original size:42 final size:43
Alignment explanation
Indices: 20604--20689 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 43
20594 TTAAGGATTT
*
20604 TTATTAT-TAAAATA-TATTCTTTAATTATTAAAAATATAA-AAA
1 TTATTATATAAAATATTA-T-TTTAATAATTAAAAATATAATAAA
* *
20646 TTATTATATAACATATTATTTTAATAATTTAAAATATAATAAA
1 TTATTATATAAAATATTATTTTAATAATTAAAAATATAATAAA
20689 T
1 T
20690 AAGCGTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
42 25 0.66
43 11 0.29
44 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (43 bp):
TTATTATATAAAATATTATTTTAATAATTAAAAATATAATAAA
Found at i:26328 original size:2 final size:2
Alignment explanation
Indices: 26294--26425 Score: 212
Period size: 2 Copynumber: 66.5 Consensus size: 2
26284 TTGTGTAATG
* * * * *
26294 TA TA T- TA TA CA TA TA AA TA CA TA CA TG TA TA TA TA 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
26335 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
26377 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
26419 TA TA TA T
1 TA TA TA T
26426 TCCTGCTTAC
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
1 1 0.01
2 118 0.99
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28958 original size:6 final size:6
Alignment explanation
Indices: 28949--28995 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
28939 CGGAAGATAC
* * *
28949 GATGGT GATGGT GATGGT GATGGA GATGGA GATGGA GATGGA GATGG
1 GATGGA GATGGA GATGGA GATGGA GATGGA GATGGA GATGGA GATGG
28996 TGGTATAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.26, C:0.00, G:0.51, T:0.23
Consensus pattern (6 bp):
GATGGA
Found at i:31576 original size:13 final size:12
Alignment explanation
Indices: 31551--31580 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31541 ATTTTTAAAA
31551 TAAAATATTTTT
1 TAAAATATTTTT
31563 TAAAATATTTTT
1 TAAAATATTTTT
*
31575 TTAAAT
1 TAAAAT
31581 CTAAACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TAAAATATTTTT
Found at i:37187 original size:2 final size:2
Alignment explanation
Indices: 37180--37218 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
37170 ACATACATAC
* * *
37180 AT AT AT AT AT AC AT AC AT AT AT GT 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 AT AT A
37219 CCAAAACTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:37191 original size:20 final size:20
Alignment explanation
Indices: 37162--37210 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
37152 CTTTATGGGA
*
37162 ATATAAATACATACATACAT
1 ATATATATACATACATACAT
*
37182 ATATATATACATACATATAT
1 ATATATATACATACATACAT
*
37202 GTATATATA
1 ATATATATA
37211 TATATATACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (20 bp):
ATATATATACATACATACAT
Found at i:37193 original size:16 final size:16
Alignment explanation
Indices: 37172--37218 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
37162 ATATAAATAC
37172 ATACATACATATATAT
1 ATACATACATATATAT
*
37188 ATACATACATATATGT
1 ATACATACATATATAT
* *
37204 ATATATATATATATA
1 ATACATACATATATA
37219 CCAAAACTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (16 bp):
ATACATACATATATAT
Found at i:37781 original size:21 final size:21
Alignment explanation
Indices: 37751--37812 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
37741 GATTTACATA
*
37751 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
37772 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
37795 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
37813 AATCGCAACG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 7 0.19
21 19 0.53
23 10 0.28
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:38451 original size:16 final size:16
Alignment explanation
Indices: 38417--38472 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
38407 GCCGTCCGTC
38417 TCGGGTCGGGTCG-GG
1 TCGGGTCGGGTCGTGG
38432 TCGGGTCGGGTCGTGG
1 TCGGGTCGGGTCGTGG
*
38448 TCGGGTCAGGTCGTGG
1 TCGGGTCGGGTCGTGG
38464 TCGTGGTCG
1 TCG-GGTCG
38473 TGGTAATACG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.35
16 20 0.54
17 4 0.11
ACGTcount: A:0.02, C:0.20, G:0.54, T:0.25
Consensus pattern (16 bp):
TCGGGTCGGGTCGTGG
Found at i:38476 original size:6 final size:5
Alignment explanation
Indices: 38417--38472 Score: 76
Period size: 5 Copynumber: 10.6 Consensus size: 5
38407 GCCGTCCGTC
*
38417 TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGGG TCAGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCGGG TCGGG TCG-GG TCG-GG
38470 TCG
1 TCG
38473 TGGTAATACG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
5 31 0.66
6 16 0.34
ACGTcount: A:0.02, C:0.20, G:0.54, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:38635 original size:21 final size:21
Alignment explanation
Indices: 38603--38683 Score: 119
Period size: 21 Copynumber: 3.9 Consensus size: 21
38593 AATCACAACG
38603 CGAACTTCGACTATCGCAATA
1 CGAACTTCGACTATCGCAATA
*
38624 CGATA-GTCGACTATCGCAATA
1 CGA-ACTTCGACTATCGCAATA
* *
38645 CGAACTTGGACTATCGCAATG
1 CGAACTTCGACTATCGCAATA
38666 CGAACTTCGACTATCGCA
1 CGAACTTCGACTATCGCA
38684 TTGCGATTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (21 bp):
CGAACTTCGACTATCGCAATA
Found at i:38727 original size:21 final size:21
Alignment explanation
Indices: 38698--38744 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
38688 GATTTACATA
*
38698 TTCGTATTGCGACAGTCCAAG
1 TTCGCATTGCGACAGTCCAAG
* *
38719 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGACAGTCCAAG
38740 TTCGC
1 TTCGC
38745 GTTACGAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGACAGTCCAAG
Found at i:42971 original size:46 final size:46
Alignment explanation
Indices: 42851--43058 Score: 291
Period size: 46 Copynumber: 4.6 Consensus size: 46
42841 TGGTATATGG
* *
42851 TTATGG-AAT-AATAGTAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGTAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
42895 TTAT-G-AATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGTAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* **
42939 TTATGGTATTAAATGGTAAGTATATTAATAAAATAAGCTTACGAGC
1 TTATGGTAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* * *
42985 TTATGGTATTAAATGATAAGTATTTTGGTAAAATAAGCTTACGAGC
1 TTATGGTAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
43031 TTATGGTTAATAAATGGTAA-AATATTGG
1 TTATGG-TAATAAATGGTAAGTATATTGG
43059 ATATGCAAAT
Statistics
Matches: 147, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
43 4 0.03
44 41 0.28
45 1 0.01
46 90 0.61
47 11 0.07
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (46 bp):
TTATGGTAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:46551 original size:26 final size:26
Alignment explanation
Indices: 46520--46573 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
46510 GGTTGATTCC
46520 AACGGATCATCTGTAATCAGAACCAT
1 AACGGATCATCTGTAATCAGAACCAT
46546 AACGGATCATCTGTAATCAGAACCAT
1 AACGGATCATCTGTAATCAGAACCAT
46572 AA
1 AA
46574 GCCTAACTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (26 bp):
AACGGATCATCTGTAATCAGAACCAT
Found at i:46866 original size:34 final size:34
Alignment explanation
Indices: 46807--46872 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
46797 ACATATATAC
*
46807 ATATACACACACCATTACTACCTATTTTAAGCAA
1 ATATACACACACCATTACTACCTATTTCAAGCAA
* * **
46841 ATATATACACACCTTTACTTGCTATTTCAAGC
1 ATATACACACACCATTACTACCTATTTCAAGC
46873 TACTATTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (34 bp):
ATATACACACACCATTACTACCTATTTCAAGCAA
Found at i:59050 original size:6 final size:6
Alignment explanation
Indices: 59041--59074 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
59031 TTTGACCCTT
59041 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTC
59075 TCCTTTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
TCTCCC
Found at i:68328 original size:21 final size:21
Alignment explanation
Indices: 68302--68341 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
68292 CATAACCCCA
*
68302 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
68323 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
68342 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:74837 original size:25 final size:25
Alignment explanation
Indices: 74763--74841 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 25
74753 GAGAGTTTAT
* *
74763 AATTTTGAAAGTTTAATTTAA-CTAT
1 AATTTTGAAATTTTAATTTAATC-AC
*
74788 AATTTTGGGAATATTTTTTTATTTAATCAC
1 AATTTT--GAA-A--TTTTAATTTAATCAC
74818 AATTTTGAAATTTTAATTTAATCA
1 AATTTTGAAATTTTAATTTAATCA
74842 GTATTATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
25 19 0.43
27 4 0.09
28 4 0.09
30 16 0.36
31 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.51
Consensus pattern (25 bp):
AATTTTGAAATTTTAATTTAATCAC
Found at i:75421 original size:20 final size:19
Alignment explanation
Indices: 75389--75432 Score: 79
Period size: 20 Copynumber: 2.3 Consensus size: 19
75379 CTAATTTTTC
75389 ATTTTAAAATTATTTTAGA
1 ATTTTAAAATTATTTTAGA
75408 ATTTTAATAATTATTTTAGA
1 ATTTTAA-AATTATTTTAGA
75428 ATTTT
1 ATTTT
75433 TCTTTCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTTTAAAATTATTTTAGA
Found at i:94359 original size:80 final size:80
Alignment explanation
Indices: 94113--94364 Score: 287
Period size: 80 Copynumber: 3.1 Consensus size: 80
94103 GTAAAGGGTC
* * *
94113 AACTACTTAAAATAATCGCTTAACTATGGAGTTGGGATCGATTTGATCATAATGCTTTAAATTTG
1 AACTACTTAAAATAATCGATTAACTATGGAGTTGGCATCGATTTGATCATTATGCTTTAAATTTG
*
94178 GCAATATGATCATAT
66 GCAATATGATTATAT
* *** ** *
94193 AACTACTTAAACGATATTTTTTTTGCTATGGAGTTGGCATCGATTTGATCATTATGCTTTTAA--
1 AACTACTTAAA--ATAATCGATTAACTATGGAGTTGGCATCGATTTGATCATTATGCTTTAAATT
* *
94256 TGATC-ATATAAATT-TGAT
64 TG-GCAATAT-GATTAT-AT
*
94274 CAACTACTTAAATTAATCGATTAACTATGGAGTTGGCATCGATTTGATCATTATGCTTTAAATTT
1 -AACTACTTAAAATAATCGATTAACTATGGAGTTGGCATCGATTTGATCATTATGCTTTAAATTT
94339 GGCAATATGATTATAT
65 GGCAATATGATTATAT
*
94355 AACTATTTAA
1 AACTACTTAA
94365 GTGGTTTCAA
Statistics
Matches: 139, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
80 69 0.50
81 11 0.08
82 59 0.42
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (80 bp):
AACTACTTAAAATAATCGATTAACTATGGAGTTGGCATCGATTTGATCATTATGCTTTAAATTTG
GCAATATGATTATAT
Found at i:96016 original size:18 final size:19
Alignment explanation
Indices: 95993--96039 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
95983 AACAGACCCT
*
95993 AAATTAAAGAAAT-CAATA
1 AAATTAAAGAAATGAAATA
*
96011 AAATT-AAGATATGAAATA
1 AAATTAAAGAAATGAAATA
*
96029 AAAGTAAAGAA
1 AAATTAAAGAA
96040 GAAAGATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.21
Consensus pattern (19 bp):
AAATTAAAGAAATGAAATA
Found at i:96789 original size:21 final size:21
Alignment explanation
Indices: 96763--96812 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
96753 TATTTTGCAG
96763 GGTTGGGTGAAACTTTATTTT
1 GGTTGGGTGAAACTTTATTTT
96784 GGTTGGGTGAAACTTTATTTT
1 GGTTGGGTGAAACTTTATTTT
*
96805 GGTCGGGT
1 GGTTGGGT
96813 CGTGTTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.06, G:0.34, T:0.44
Consensus pattern (21 bp):
GGTTGGGTGAAACTTTATTTT
Found at i:96943 original size:2 final size:2
Alignment explanation
Indices: 96936--96967 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
96926 AATAATACCC
96936 AT AT AT 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 AT AT AT
96968 CTTCAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97451 original size:18 final size:17
Alignment explanation
Indices: 97413--97460 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
97403 ATATAGAATT
*
97413 AGATTCCAATTCTTGAC
1 AGATTCCAATTCTTCAC
*
97430 AGATTTCAATTCCTTCAC
1 AGATTCCAATT-CTTCAC
*
97448 AGATTCTAATTCT
1 AGATTCCAATTCT
97461 ATCAGAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (17 bp):
AGATTCCAATTCTTCAC
Found at i:97816 original size:8 final size:7
Alignment explanation
Indices: 97783--97868 Score: 51
Period size: 7 Copynumber: 12.9 Consensus size: 7
97773 TATTAACATA
97783 AATA-AT
1 AATATAT
97789 AATA-AT
1 AATATAT
97795 AAT-TA-
1 AATATAT
*
97800 AATAGAT
1 AATATAT
97807 AATACTAT
1 AATA-TAT
97815 AATATAT
1 AATATAT
97822 -ATATAT
1 AATATAT
*
97828 -ATATAC
1 AATATAT
*
97834 CATACT-T
1 AATA-TAT
*
97841 AATACAT
1 AATATAT
*
97848 AATATGT
1 AATATAT
97855 AATATATT
1 AATATA-T
97863 AATATA
1 AATATA
97869 AGAATGTTCG
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
5 3 0.05
6 22 0.35
7 24 0.38
8 14 0.22
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (7 bp):
AATATAT
Found at i:99490 original size:31 final size:31
Alignment explanation
Indices: 99452--99511 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
99442 AACTTAAAAG
99452 AGTTTTATAATACTGAAATTTAAATAATTTT
1 AGTTTTATAATACTGAAATTTAAATAATTTT
99483 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTATAATACTGAAATTTAAATAATT
99512 CATACAACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (31 bp):
AGTTTTATAATACTGAAATTTAAATAATTTT
Found at i:99562 original size:22 final size:22
Alignment explanation
Indices: 99534--99721 Score: 242
Period size: 22 Copynumber: 8.5 Consensus size: 22
99524 ATAATAATTT
99534 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
99556 TTTTAAAATAAATAAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
99578 TTTTAAAAGAAATCAAT-CATA
1 TTTTAAAATAAATCAATCCATA
99599 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *
99621 --TTAAAATAAA--ATTTTCATA
1 TTTTAAAATAAATCA-ATCCATA
99640 TTTTAAAATAAATCAATCCATACAA
1 TTTTAAAATAAATCAATCCAT---A
* *
99665 CTATAATAATAAATCAATCCATA
1 TTTTAA-AATAAATCAATCCATA
99688 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
99710 TTTTAAAATAAA
1 TTTTAAAATAAA
99722 ATTTTAAAAT
Statistics
Matches: 144, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.01
19 5 0.03
20 10 0.07
21 30 0.21
22 72 0.50
23 6 0.04
25 5 0.03
26 15 0.10
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.36
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:100263 original size:21 final size:21
Alignment explanation
Indices: 100234--100286 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
100224 ATTCTGACTA
100234 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
100255 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
100276 TCGCAATGCGA
1 TCGCATTGCGA
100287 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:100348 original size:20 final size:20
Alignment explanation
Indices: 100276--100341 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
100266 TTTTCCTAAT
*
100276 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
100296 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
100316 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
100336 TCGCAA
1 TCGCAA
100342 CGAGATTCTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:117043 original size:12 final size:12
Alignment explanation
Indices: 117026--117050 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
117016 TTTATTGATA
117026 ATTTATTTTTCT
1 ATTTATTTTTCT
117038 ATTTATTTTTCT
1 ATTTATTTTTCT
117050 A
1 A
117051 ACATAAAATT
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:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTATTTTTCT
Found at i:123219 original size:3 final size:3
Alignment explanation
Indices: 123211--123252 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
123201 AATTATTTTT
123211 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
123253 AATGAGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:125120 original size:10 final size:10
Alignment explanation
Indices: 125107--125141 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
125097 TGTTGTGAAG
125107 GGTTGTTTTT
1 GGTTGTTTTT
125117 GGTTGTTTTCT
1 GGTTGTTTT-T
125128 GGTTTGTTTTT
1 GG-TTGTTTTT
125139 GGT
1 GGT
125142 GGGGGTTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.43
11 6 0.26
12 7 0.30
ACGTcount: A:0.00, C:0.03, G:0.31, T:0.66
Consensus pattern (10 bp):
GGTTGTTTTT
Found at i:130286 original size:31 final size:32
Alignment explanation
Indices: 130184--130313 Score: 113
Period size: 31 Copynumber: 4.2 Consensus size: 32
130174 CCTTTTAAAT
* * ** *
130184 ATTATAAAATAGTCATT-AAACTTCCCAAATA
1 ATTATAAAATAATCATTAAAATTTATCAAAAA
**
130215 ATTATAAAATGGTCATTAAAATTTATC-AAAA
1 ATTATAAAATAATCATTAAAATTTATCAAAAA
* *
130246 TTTGTAAAATAATCATT-AAATTTATCAAAAA
1 ATTATAAAATAATCATTAAAATTTATCAAAAA
* * * * *
130277 ATTAAAAAATAATCTTTCAAATTAATCAAAAT
1 ATTATAAAATAATCATTAAAATTTATCAAAAA
130309 ATTAT
1 ATTAT
130314 GATATTAATT
Statistics
Matches: 80, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
30 9 0.11
31 49 0.61
32 22 0.28
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (32 bp):
ATTATAAAATAATCATTAAAATTTATCAAAAA
Found at i:130299 original size:62 final size:62
Alignment explanation
Indices: 130188--130308 Score: 143
Period size: 62 Copynumber: 2.0 Consensus size: 62
130178 TTAAATATTA
* * * * ** *
130188 TAAAATAGTCATTAAACTTCCCAAATAATTATAAAATGGTCATTAAAATTTATCAAAATTTG
1 TAAAATAATCATTAAACTTACCAAAAAATTAAAAAATAATCATTAAAATTAATCAAAATTTG
* * * *
130250 TAAAATAATCATTAAATTTATCAAAAAATTAAAAAATAATCTTTCAAATTAATCAAAAT
1 TAAAATAATCATTAAACTTACCAAAAAATTAAAAAATAATCATTAAAATTAATCAAAAT
130309 ATTATGATAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
62 48 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (62 bp):
TAAAATAATCATTAAACTTACCAAAAAATTAAAAAATAATCATTAAAATTAATCAAAATTTG
Found at i:146343 original size:105 final size:104
Alignment explanation
Indices: 146229--146420 Score: 242
Period size: 104 Copynumber: 1.8 Consensus size: 104
146219 AATCATCGTA
* * *
146229 TTCTTCTTTATCA-CATAATCTCCTTCCCCAATCTTAAAGCATCATATCTCCGTGTTTTGCTCTA
1 TTCTTCTTTAT-ATCATAATCTCCTTCCCCAATCTT-AAGCATCAAATCTCCATGTTTTGCTATA
146293 CTCTTTCTTTAATCCACCATTATAATCTAATTAAAAATCAC
64 CTCTTTCTTTAATCCACCATTATAATCTAATTAAAAATCAC
** * * * * *
146334 TTCTTCTTTATATCATCCTTTTCTTCCCCAATCTTAAGCATTAAATCTCCATGTTTTGTTATGCT
1 TTCTTCTTTATATCATAATCTCCTTCCCCAATCTTAAGCATCAAATCTCCATGTTTTGCTATACT
** *
146399 CTTTCTTTGGTTCACCATTATA
66 CTTTCTTTAATCCACCATTATA
146421 TTTAAGATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
104 44 0.60
105 29 0.40
ACGTcount: A:0.24, C:0.26, G:0.05, T:0.45
Consensus pattern (104 bp):
TTCTTCTTTATATCATAATCTCCTTCCCCAATCTTAAGCATCAAATCTCCATGTTTTGCTATACT
CTTTCTTTAATCCACCATTATAATCTAATTAAAAATCAC
Found at i:147464 original size:20 final size:20
Alignment explanation
Indices: 147441--147505 Score: 105
Period size: 20 Copynumber: 3.2 Consensus size: 20
147431 CGATATACCA
147441 GGTAA-AAATATGATAAAACC
1 GGTAACAAA-ATGATAAAACC
*
147461 GGTAACAAAATGATAAAACT
1 GGTAACAAAATGATAAAACC
147481 GGTAACAAAATGATAAAACC
1 GGTAACAAAATGATAAAACC
147501 GGTAA
1 GGTAA
147506 AACGTTACCG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 39 0.93
21 3 0.07
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.18
Consensus pattern (20 bp):
GGTAACAAAATGATAAAACC
Found at i:147636 original size:201 final size:202
Alignment explanation
Indices: 147268--147686 Score: 642
Period size: 201 Copynumber: 2.1 Consensus size: 202
147258 AAGTAAAACT
* *** * * *
147268 ATGACAAAACCGGTATTGAAATGATAAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGG
1 ATGATAAAACCGGTAACAAAATGATAAAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGA
*
147333 TACTTTAATATAAGGATCGACACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGT
66 TACTTTAATATAAGGATCGACACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGT
* * *
147398 GTCGATACTTTTAAAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGG
131 GTCGATACTTTAAAAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGG
147463 TAACAAA
196 TAACAAA
* * *
147470 ATGATAAAACTGGTAACAAAATGATAAAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGA
1 ATGATAAAACCGGTAACAAAATGATAAAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGA
* * ** *
147535 TACTTT-ATATAAGGATCGACACTTTGTGAATTTAAAAGAGAAGTAGTTTTAGCGCCTATAATGT
66 TACTTTAATATAAGGATCGACACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGT
*
147599 GTCGATACTTTAAAAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGG
131 GTCGATACTTTAAAAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGG
*
147664 TATCAAA
196 TAACAAA
147671 ATGATAAAACCGGTAA
1 ATGATAAAACCGGTAA
147687 AATGATACCG
Statistics
Matches: 195, Mismatches: 22, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
201 134 0.69
202 61 0.31
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (202 bp):
ATGATAAAACCGGTAACAAAATGATAAAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGA
TACTTTAATATAAGGATCGACACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGT
GTCGATACTTTAAAAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGG
TAACAAA
Found at i:147665 original size:20 final size:19
Alignment explanation
Indices: 147642--147688 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
147632 CGATATAACA
147642 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
147662 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
147682 GGTAAAA
1 GGTAAAA
147689 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:147690 original size:17 final size:19
Alignment explanation
Indices: 147651--147693 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
147641 AGGTAAAAAT
147651 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
147671 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
147688 ATGATA
1 ATGATA
147694 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:149978 original size:21 final size:21
Alignment explanation
Indices: 149919--149983 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
149909 AAGACAATCA
* *
149919 AGAGTCGAAGAGAAACTCGAT
1 AGAGTCGAAGAGAAACTTGAG
149940 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
149961 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
149982 AG
1 AG
149984 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.12, G:0.31, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:150059 original size:33 final size:33
Alignment explanation
Indices: 150017--150082 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
150007 AAATAGATGG
*
150017 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
150050 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
150083 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:151898 original size:19 final size:19
Alignment explanation
Indices: 151874--151922 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
151864 AATGTAGGGT
151874 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
151893 TAATTTTGTATATGATTTA
1 TAATTTTGTATAAGATTTA
151912 TAATTTTGTAT
1 TAATTTTGTAT
151923 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:151933 original size:18 final size:19
Alignment explanation
Indices: 151874--151937 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
151864 AATGTAGGGT
* *
151874 TAATTTTGTATAAGATTTA
1 TAATTTTGTATATGATATA
*
151893 TAATTTTGTATATGATTTA
1 TAATTTTGTATATGATATA
*
151912 TAATTTTGTATGTGA-ATA
1 TAATTTTGTATATGATATA
151930 TAATTTTG
1 TAATTTTG
151938 AATGAGATGA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
18 10 0.24
19 32 0.76
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATATGATATA
Found at i:152917 original size:201 final size:200
Alignment explanation
Indices: 152035--152993 Score: 1650
Period size: 200 Copynumber: 4.8 Consensus size: 200
152025 AATTTACAAT
152035 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
152100 CAAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCAGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
* * *
152165 ATAAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTCTGATCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
152230 AATGA
196 AATGA
*
152235 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
152300 AGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
*
152365 ATGAGAGAATATGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
152430 AATGA
196 AATGA
*
152435 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGTTCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
152500 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
* *
152565 ATGAGAGAATAAGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
152630 AATGA
196 AATGA
* *
152635 ATGGCAAACAGGGTGCAAACATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAATAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
152700 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
* * *
152765 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTTTGTTTGTGTCGATATTTTTGGTCCA
131 ATGAGAGAATAGGTCTAAATAATGTATCGACAC-TTTTGTAGTTTGTGTCGATATTTTTGGTCCA
152830 GAATGA
195 GAATGA
* *
152836 ATGGCAAATAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
152901 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACTGGTACAAGTATACCAGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
* *
152966 ATGAGAGAATTGGTATATAAT-ATGTATC
131 ATGAGAGAATAGGTCTA-AATAATGTATC
152994 AAAACTGTTT
Statistics
Matches: 723, Mismatches: 34, Indels: 3
0.95 0.04 0.00
Matches are distributed among these distances:
200 541 0.75
201 179 0.25
202 3 0.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:154505 original size:6 final size:6
Alignment explanation
Indices: 154494--154593 Score: 74
Period size: 6 Copynumber: 16.7 Consensus size: 6
154484 CAAGCGGTCA
* * * * *
154494 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * ** * * *
154542 ATGACG ATAAAG CTGACG ATGAAG ATGTCG ATGATG ATGATG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
154590 ATGA
1 ATGA
154594 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.22
Consensus pattern (6 bp):
ATGAAG
Found at i:154597 original size:12 final size:12
Alignment explanation
Indices: 154494--154593 Score: 119
Period size: 12 Copynumber: 8.3 Consensus size: 12
154484 CAAGCGGTCA
*
154494 ATGAAGATGAAG
1 ATGACGATGAAG
*
154506 CTGACGATGAAG
1 ATGACGATGAAG
154518 ATGACGATGAAG
1 ATGACGATGAAG
*
154530 ATGACGATGATG
1 ATGACGATGAAG
*
154542 ATGACGATAAAG
1 ATGACGATGAAG
*
154554 CTGACGATGAAG
1 ATGACGATGAAG
* *
154566 ATGTCGATGATG
1 ATGACGATGAAG
* *
154578 ATGATGATGATG
1 ATGACGATGAAG
154590 ATGA
1 ATGA
154594 TGATCCAAAC
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 75 1.00
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:156150 original size:183 final size:183
Alignment explanation
Indices: 155807--156572 Score: 1349
Period size: 183 Copynumber: 4.2 Consensus size: 183
155797 CAAAGTTTTC
*
155807 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCATT-
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACC-TTG
* * *
155871 TCAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGAATTATAATGTAATAGATAATTTTTTA
65 TCAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTA
155934 ATATAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
127 ATATAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
155991 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
156056 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
156121 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
*
156174 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
*
156239 CAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
156304 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
156357 ACACTTTTTAATATTGTGTCGGTACTTTATGTTCAGATTAGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
*
156422 CAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
156487 AACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
*
156540 ACACTTTTTAATATTGTGTCGGTAATTTTATGT
1 ACACTTTTTAATATTGTGTCGGT-ACTTTATGT
156573 AACGCGGTTT
Statistics
Matches: 566, Mismatches: 12, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
183 482 0.85
184 81 0.14
186 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:159061 original size:25 final size:25
Alignment explanation
Indices: 159033--159097 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
159023 TTATCATTAA
159033 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
159058 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
159083 ATTTAGGTATGTACA
1 ATTTAGGTATGTACA
159098 TCTTTTGAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:159478 original size:23 final size:23
Alignment explanation
Indices: 159452--159516 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
159442 AAATATGATG
159452 TAATAGGTAGCGCTTATATAATA
1 TAATAGGTAGCGCTTATATAATA
* *
159475 TAATAGGTAGCGTTTATATAATG
1 TAATAGGTAGCGCTTATATAATA
*
159498 TAATAGGTAGTGCTTATAT
1 TAATAGGTAGCGCTTATAT
159517 TGTAAAGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
TAATAGGTAGCGCTTATATAATA
Found at i:159520 original size:21 final size:22
Alignment explanation
Indices: 159444--159521 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
159434 ATAAGTAAAA
159444 ATATGATGTAATAGGTAGCGCTT
1 ATAT-ATGTAATAGGTAGCGCTT
* *
159467 ATATAATATAATAGGTAGCGTTT
1 ATAT-ATGTAATAGGTAGCGCTT
*
159490 ATATAATGTAATAGGTAGTGCTT
1 ATAT-ATGTAATAGGTAGCGCTT
159513 ATAT-TGTAA
1 ATATATGTAA
159522 AGTATCTATC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 5 0.10
23 44 0.90
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (22 bp):
ATATATGTAATAGGTAGCGCTT
Found at i:160005 original size:23 final size:23
Alignment explanation
Indices: 159935--160007 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
159925 ATAGGTAAAA
* *
159935 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
159958 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
**
159981 ATATAATGTAATAGGTAATGCTT
1 ATATAATGTAATAGGTAGCGCTT
160004 ATAT
1 ATAT
160008 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:160232 original size:487 final size:489
Alignment explanation
Indices: 159097--160405 Score: 2295
Period size: 490 Copynumber: 2.7 Consensus size: 489
159087 AGGTATGTAC
159097 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
*
159162 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
* *
159227 TTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
* * * * *
159292 CTTTTTTATGTAAATGAAATTATTAAATTAATATTGTATGTGGAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGCAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
*
159357 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTAT-AAAAAGTATGGA
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAAGTATGAA
*
159421 CACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCGCTTATATAATATAATAGGTAGC
326 CACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCACTTATATAATATAATAGGTAGC
* *
159486 GTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCTTTTTTATAAAAGTGTTCA
391 GTTTATATAATGTAATAGGTAATGCTTATATTGTAAAGTATCTA--TTTTTTATAAAAGTGTCCA
* * *
159551 TACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
454 TACTTATTTCACTGTGGAAAACATTAAATTAAGATT
159587 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
159652 GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
159717 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
159782 ATTTTTTGTGCAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGCAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
* * *
159847 AAAATTGAAACATAAATTACATAACTTTAAAAAAAATATCGATCCTTTTTATAAAAAAATATGTA
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAAGTATGAA
* *
159912 CACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCACTTATATAATGTAATAGGTAGC
326 CACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCACTTATATAATATAATAGGTAGC
159977 GTTTATATAATGTAATAGGTAATGCTTATATTGTAAAGTATC-A-TTTTTATAAAAGTGTCCATA
391 GTTTATATAATGTAATAGGTAATGCTTATATTGTAAAGTATCTATTTTTTATAAAAGTGTCCATA
*
160040 CTTATTTCACTGTGGAAAACATTAAATTAATATT
456 CTTATTTCACTGTGGAAAACATTAAATTAAGATT
**** *
160074 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATATATCTAATGATTTATTTTTTAT
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
* *
160139 GTTACAATATATATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
160204 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
160269 ATTTTTTGTGCAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT--AA
196 ATTTTTTGTGCAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
* *
160332 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCTTTTTTATAAAAAAGTATAAA
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAAGTATGAA
160397 CACTTTCAA
326 CACTTTCAA
160406 CATATTATAA
Statistics
Matches: 786, Mismatches: 32, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
485 71 0.09
487 298 0.38
490 304 0.39
491 113 0.14
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (489 bp):
ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
ATTTTTTGTGCAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAAGTATGAA
CACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCACTTATATAATATAATAGGTAGC
GTTTATATAATGTAATAGGTAATGCTTATATTGTAAAGTATCTATTTTTTATAAAAGTGTCCATA
CTTATTTCACTGTGGAAAACATTAAATTAAGATT
Found at i:166197 original size:23 final size:23
Alignment explanation
Indices: 166171--166215 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
166161 CACCACATCT
*
166171 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
166194 CGTAGAATTGCACTGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
166216 ATATAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:179234 original size:200 final size:198
Alignment explanation
Indices: 178857--179322 Score: 634
Period size: 200 Copynumber: 2.3 Consensus size: 198
178847 TTTTCTAACT
* *
178857 AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGA
1 AAACCGATATATTTATACCGGT-ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
178922 TGTTTTTGGAATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGACATTC
65 TGTTTTTGGAATCGATACAATTTTAAATGTATCGACACTTTATGCGTACACCTCGTTGGACATTC
* * *
178987 ATTCTGGAAAATAAATATCGACACAAACTTAAAACGTGTCGATACATTATGTAGACCTATTTTCT
130 ATTCTGGAAAATAAATATCGACACAAACTTAAAACGTGTCAATACATTATGTAGACCTATTATAT
179052 CATA
195 CATA
* *
179056 AAACCGATATATTTCTACCGGATACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGA
1 AAACCGATATATTTATACCGG-TACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
179121 TGTTTTTCGG-ATCGATA-ATTTTAATAAATGTATCGACACTTTATGCGTACACCTCGTTTGACA
65 TGTTTTT-GGAATCGATACAATTT--TAAATGTATCGACACTTTATGCGTACACCTCGTTGGACA
** *** ** * *
179184 TTCATTCTGGACAAA-ATGTATCGACAC-TTTTTAAATTTGTTTCAATACATTATGTTGACCTAT
127 TTCATTCTGGA-AAATAAATATCGACACAAACTTAAA-ACGTGTCAATACATTATGTAGACCTAT
179247 TATATCATA
190 TATATCATA
* *
179256 AAATCGATATATTTATACCGTTTACATTGTAAAATTTACCTATTACATTATAATTATCGGTTTCG
1 AAACCGATATATTTATACCG-GTACATTGT-AAATTTACCTATTACATTATAATTATCGGTTTCG
179321 AT
64 AT
179323 ATAACATATG
Statistics
Matches: 236, Mismatches: 23, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
198 4 0.02
199 78 0.33
200 116 0.49
201 38 0.16
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.39
Consensus pattern (198 bp):
AAACCGATATATTTATACCGGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGAT
GTTTTTGGAATCGATACAATTTTAAATGTATCGACACTTTATGCGTACACCTCGTTGGACATTCA
TTCTGGAAAATAAATATCGACACAAACTTAAAACGTGTCAATACATTATGTAGACCTATTATATC
ATA
Found at i:179466 original size:31 final size:30
Alignment explanation
Indices: 179425--179518 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
179415 TTATAATAAA
*
179425 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
179455 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
* * *
179485 TTATAAAAT-T-ATAGAT-ATAATATTTTAA
1 TAATAAAATATAATA-ATAATAATTTTTTAT
179513 TAATAA
1 TAATAA
179519 TATTGACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
28 18 0.33
29 5 0.09
30 24 0.44
31 8 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:179518 original size:14 final size:14
Alignment explanation
Indices: 179436--179522 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
179426 AATAAATATA
**
179436 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
179451 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
179464 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
179478 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
179492 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
179506 ATTTTAATAATAAT
1 ATTTTAATAATAAT
179520 ATT
1 ATT
179523 GACATAAATA
Statistics
Matches: 53, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
13 10 0.19
14 38 0.72
15 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:179518 original size:28 final size:28
Alignment explanation
Indices: 179450--179518 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
179440 ATAATAATTT
*
179450 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
179477 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
179505 TATTTTAATAATAA
1 TATTTTAATAATAA
179519 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:184891 original size:33 final size:33
Alignment explanation
Indices: 184853--184919 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
184843 CCACCCCTAC
184853 CTTCTTTTTAACTGTTATTACGCTTATACTGCA
1 CTTCTTTTTAACTGTTATTACGCTTATACTGCA
184886 CTTCTTTTTAACTGTTATTACGCTTATACTGCA
1 CTTCTTTTTAACTGTTATTACGCTTATACTGCA
184919 C
1 C
184920 ACCTTTCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.48
Consensus pattern (33 bp):
CTTCTTTTTAACTGTTATTACGCTTATACTGCA
Found at i:197104 original size:29 final size:29
Alignment explanation
Indices: 197028--197134 Score: 85
Period size: 29 Copynumber: 3.7 Consensus size: 29
197018 AGAAATCTCA
* *
197028 AAACAAATCAGGG-AACAAATCTCATACAG
1 AAACAGATC-GGGAAACAAATCCCATACAG
* * * *
197057 -AACATATCGATG-AGCAAATCTCATACAG
1 AAACAGATCG-GGAAACAAATCCCATACAG
* *
197085 AAACAGATCGGGAAATAAATCCCATACAT
1 AAACAGATCGGGAAACAAATCCCATACAG
* *
197114 AAATAGATCGGGGAACAAATC
1 AAACAGATCGGGAAACAAATC
197135 ATGTACTAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
27 1 0.02
28 24 0.38
29 38 0.60
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.17
Consensus pattern (29 bp):
AAACAGATCGGGAAACAAATCCCATACAG
Found at i:198738 original size:20 final size:21
Alignment explanation
Indices: 198694--198738 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
198684 CGATAAAAAA
*
198694 TTTATTTAAAATATTATTATT
1 TTTATTTAAAATATTAATATT
198715 TTTATTTAAAATATTAAT-TT
1 TTTATTTAAAATATTAATATT
198735 TTTA
1 TTTA
198739 ATATTTTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTTAAAATATTAATATT
Found at i:205587 original size:2 final size:2
Alignment explanation
Indices: 205580--205644 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
205570 TTTTAACATT
205580 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
205622 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
205645 TTGAAGAATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:207781 original size:2 final size:2
Alignment explanation
Indices: 207774--207812 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
207764 GTGTTATGTG
207774 AT AT 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 AT AT A
207813 ATGTGAGCAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:208164 original size:36 final size:36
Alignment explanation
Indices: 208117--208256 Score: 253
Period size: 36 Copynumber: 3.9 Consensus size: 36
208107 TTGAGTATTT
208117 ATATCAGCTTTGGTACATTCATGTATCAATGTTATC
1 ATATCAGCTTTGGTACATTCATGTATCAATGTTATC
*
208153 ATATCAGCTTTGGTACATTCGTGTATCAATGTTATC
1 ATATCAGCTTTGGTACATTCATGTATCAATGTTATC
*
208189 ATATCAGCTTTGGTACATTCATGTATCAATGTTATT
1 ATATCAGCTTTGGTACATTCATGTATCAATGTTATC
*
208225 ATATCAGCTTTGGTACATTCGTGTATCAATGT
1 ATATCAGCTTTGGTACATTCATGTATCAATGT
208257 CCAGTACCGT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (36 bp):
ATATCAGCTTTGGTACATTCATGTATCAATGTTATC
Found at i:208554 original size:28 final size:28
Alignment explanation
Indices: 208523--208580 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
208513 ATTATATGAT
* *
208523 ATGTTACAAA-TGTTGAGTATAAGATAAC
1 ATGTTACAAAGT-TTAAGTACAAGATAAC
208551 ATGTTACAAAGTTTAAGTACAAGATAAC
1 ATGTTACAAAGTTTAAGTACAAGATAAC
208579 AT
1 AT
208581 ATTTTAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.31
Consensus pattern (28 bp):
ATGTTACAAAGTTTAAGTACAAGATAAC
Found at i:210493 original size:18 final size:18
Alignment explanation
Indices: 210470--210507 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
210460 TCATCATCAT
210470 CATTTTGTAAAAAAAATA
1 CATTTTGTAAAAAAAATA
*
210488 CATTTTGTTAAAAAAATA
1 CATTTTGTAAAAAAAATA
210506 CA
1 CA
210508 AGTTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (18 bp):
CATTTTGTAAAAAAAATA
Found at i:211253 original size:328 final size:334
Alignment explanation
Indices: 210488--211946 Score: 1955
Period size: 328 Copynumber: 4.4 Consensus size: 334
210478 AAAAAAAATA
* * *
210488 CATTTTGTTAAAA-AAATACAAGTTATAAAATTTTTATAAAATTATTCATATTTTAAAATATTTA
1 CATTTTG-TAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTA
* * * * *
210552 CCCTTAAAGTTTTCTTATACTAGATTATATGGATTGTGTAATTTCATGCAAAAATCAAATTAATT
65 CCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCATGCAAAAATCAAAATAACT
* ** * * *
210617 TTACTAAAAATGAATAAACAAAATCAACTGTTGTTAAAAAATAATAATTATTGTATTATAATTCA
130 TTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAAT-AATAATAATTCA
210682 TTTGATCCCTCAAATGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTAATTT
194 TTTGATCCCTCAAATGTAATTAAAAGTTTATTTT-ATA-----TATATTTTTAAACAATTAATTT
* *
210747 TAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTAT-AAA-A--TAT
253 TAAAAATCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTAT
210808 T-TATCATCATCATCAT
318 TATATCATCATCATCAT
* * *
210824 CATTTTATAAAATAAATACTAGTTATAAAACTTTTATAAAAGTATTCATATTTTAAAACACTTAC
1 CATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTAC
* * * * * * *
210889 TCACAAAGTTTTCCTATACTGGATTATACGTATTGTGTAATTTTATGAAAAAATTAAAATAACTT
66 CCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCATGCAAAAATCAAAATAACTT
* * *
210954 TATTATAAA-GAATAAGCATTATCAACCGTTGTTAAAAAATAATAATTAATACATAATAATTCAT
131 TATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATA-ATAATAATTCAT
*
211018 TTGATCCCTCAAATGTAATTAAAAG-TT-TTTT-TA-ATATTTTTAAACAATTAATTTTAAAAGT
195 TTGATCCCTCAAATGTAATTAAAAGTTTATTTTATATATATTTTTAAACAATTAATTTTAAAAAT
*
211079 TAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATTAT-T-A
260 CAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATTATATCA
211142 TCATCATCAT
325 TCATCATCAT
* *
211152 CATTTTGTAAAATAAATACTAGTTGTAAAACTTTTATAAAATTATTCATATTTTAAAGTACTTAC
1 CATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTAC
* * *
211217 CCTCAAAGTTTTTCAATACTAGATTATATGTATTGTGTAATTTCATGCAAAAATCAAAATAATTT
66 CCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCATGCAAAAATCAAAATAACTT
* *
211282 TATTTAAAATGAATAAAAATTATCAACTGTTGTTAAAAAATAATAATTAATGAATAATAATTCAT
131 TATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAAT-AATAATAATTCAT
* * * *
211347 TTTATTCCTCAATTTTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTAATTTT
195 TTGATCCCTCAAATGTAATTAAAAGTTTATTTT-ATA-----TATATTTTTAAACAATTAATTTT
211412 AAAAATCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATT
254 AAAAATCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATT
*
211477 ATCATCATCAACATCAT
319 AT-ATCATCATCATCAT
* * *
211494 CATTTTGTAAAATAAATACCAATTATAAAACTTTTATAAAATTATTCATATTTTAAAATATTTAC
1 CATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTAC
*
211559 CTTCAAAGTTTTCCTATACTAGATTATACT-TATTGTGTAATTTCATGCAAAAATCAAAATAACT
66 CCTCAAAGTTTTCCTATACTAGATTATA-TGTATTGTGTAATTTCATGCAAAAATCAAAATAACT
*
211623 TTATTAAAAATGAATAAACATTATCAA---TTGTT-----GT--TAA--AA-AATAATAATTCAT
130 TTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATAATAATAATTCAT
* * * * *
211675 TTGATTCCTCAATTGTAATTAAAATTTTATTTTAATATTTTTTATATTTTTAGATAATTAATTTT
195 TTGATCCCTCAAATGTAATTAAAAGTTTATTTT-ATA-----TATATTTTTAAACAATTAATTTT
**
211740 AAAAATCAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATT
254 AAAAATCAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATT
*
211805 ATCATCATCATCGTCAT
319 AT-ATCATCATCATCAT
* *
211822 CATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTTATAGTTTAAAATACTTAC
1 CATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTAC
* * *
211887 CCTTAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTCATGCAAAAATTAAAAT
66 CCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCATGCAAAAATCAAAAT
211947 TTATCGAGTT
Statistics
Matches: 1013, Mismatches: 86, Indels: 56
0.88 0.07 0.05
Matches are distributed among these distances:
325 73 0.07
326 3 0.00
327 1 0.00
328 399 0.39
329 76 0.08
330 6 0.01
331 6 0.01
332 3 0.00
333 6 0.01
334 3 0.00
335 77 0.08
336 113 0.11
339 92 0.09
341 1 0.00
342 153 0.15
343 1 0.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (334 bp):
CATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTAC
CCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTCATGCAAAAATCAAAATAACTT
TATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATAATAATAATTCATT
TGATCCCTCAAATGTAATTAAAAGTTTATTTTATATATATTTTTAAACAATTAATTTTAAAAATC
AATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATTATATCAT
CATCATCAT
Found at i:211938 original size:670 final size:663
Alignment explanation
Indices: 210314--211946 Score: 2249
Period size: 664 Copynumber: 2.4 Consensus size: 663
210304 ATAATTACTG
* * * * * *
210314 AATAACAATTAATTTGATCCCTTAATTGTAATTGAAAGTTTGTTTTAATATTTTTTATATTTTTA
1 AATAATAATTAATTTGATACCTCAATTGTAATTAAAATTTTATTTTAATATTTTTTATATTTTTA
* *
210379 AACAATTAA-TTTAAAAATTTAATAAATTTTTCAAAAATATATAAAATTTATAA-GTTTTAAATT
66 AACAATTAATTTTAAAAA-TTAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTTAAATT
* *
210442 ATAAAATATTTTTCATCATCATCATCATCATTTTGTAAAAAAAATACATTTTGTTAAAA-AAATA
130 ATAAAATA--TTT-AT--T-ATCATCATCA--TCGT------CAT-CATTTTG-TAAAATAAATA
* * * *
210506 CAAGTTATAAAATTTTTATAAAATTATTCATATTTTAAAATATTTACCCTTAAAGTTTTCTTATA
179 CTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTTAAAGTTTTCCTATA
* *
210571 CTAGATTATATGGATTGTGTAATTTCATGCAAAAATCAAATTAATTTTACTAAAAATGAATAAAC
244 CTAGATTATATGTATTGTGTAATTTCATGCAAAAATCAAAATAATTTTACTAAAAATGAATAAAC
* * *
210636 AAAATCAACTGTTGTTAAAAAATAATAATTATTGTATTATAATTCATTTGATCCCTCAAATGTAA
309 AAAATCAACTGTTGTTAAAAAATAATAATTAATGAATAATAATTCATTTGATCCCTCAAATGTAA
* *
210701 TTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTAATTTTAAAAGTCAATAAATTTTT
374 TTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTAATTTTAAAAATCAATAAAATTTT
210766 CAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATCATCATCATCATCATTTTA
439 CAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATCATCATCATCATCATTTTA
* *
210831 TAAAATAAATACTAGTTATAAAACTTTTATAAAAGTATTCATATTTTAAAACACTTACTCACAAA
504 TAAAATAAATACCAATTATAAAACTTTTATAAAAGTATTCATATTTTAAAACACTTACTCACAAA
* * * *
210896 GTTTTCCTATACTGGATTATACGTATTGTGTAATTTTATGAAAAAATTAAAATAACTTTATTATA
569 GTTTTCCTATACTAGATTATACGTATTGTGTAATTTCATGAAAAAATCAAAATAACTTTATTAAA
*
210961 AAGAATAAGCATTATCAACCGTTGTTAAAA
634 AAGAATAAACATTATCAACCGTTGTTAAAA
* * ** * *** * * * **
210991 AATAATAATTAATACATAATAATTCATTTGATCCCTCAAATGTAATTAAAAGT-TTTTTTAATAT
1 AATAATAATTAAT--TTGATACCTCAATTG-TAATTAAAATTTTATTTTAA-TATTTTTT-ATAT
* *
211055 TTTTAAACAATTAATTTTAAAAGTTAATAAAATTTTCAAAAATATATGAAATTTATAATTTTTTA
61 TTTTAAACAATTAATTTTAAAAATTAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTTA
* *
211120 AATTATAAAATATTTATTAT--T-ATCATCATCATCATTTTGTAAAATAAATACTAGTTGTAAAA
126 AATTATAAAATATTTATTATCATCATCATCGTCATCATTTTGTAAAATAAATACTAGTTATAAAA
* * * *
211182 CTTTTATAAAATTATTCATATTTTAAAGTACTTACCCTCAAAGTTTTTCAATACTAGATTATATG
191 CTTTTATAAAATTATTCATATTTTAAAATACTTACCCTTAAAGTTTTCCTATACTAGATTATATG
* * *
211247 TATTGTGTAATTTCATGCAAAAATCAAAATAATTTTATTTAAAATGAATAAA-AATTATCAACTG
256 TATTGTGTAATTTCATGCAAAAATCAAAATAATTTTACTAAAAATGAATAAACAA-AATCAACTG
* * * *
211311 TTGTTAAAAAATAATAATTAATGAATAATAATTCATTTTATTCCTCAATTTTAATTAAAAGTTTA
320 TTGTTAAAAAATAATAATTAATGAATAATAATTCATTTGATCCCTCAAATGTAATTAAAAGTTTA
211376 TTTTAATATTTTTTATATTTTTAAACAATTAATTTTAAAAATCAATAAAATTTTCAAAAATATAT
385 TTTTAATATTTTTTATATTTTTAAACAATTAATTTTAAAAATCAATAAAATTTTCAAAAATATAT
*
211441 GAAATTTATAATTTTTTAAATTATAAAATATTTATTATCATCATCAACATCATCATTTTGTAAAA
450 GAAATTTATAATTTTTTAAATTATAAAATA--T-TTATCATCAT---CATCATCATTTTATAAAA
* * * *
211506 TAAATACCAATTATAAAACTTTTATAAAATTATTCATATTTTAAAATATTTAC-CTTCAAAGTTT
509 TAAATACCAATTATAAAACTTTTATAAAAGTATTCATATTTTAAAACACTTACTC-ACAAAGTTT
* *
211570 TCCTATACTAGATTATACTTATTGTGTAATTTCATGCAAAAATCAAAATAACTTTATTAAAAATG
573 TCCTATACTAGATTATACGTATTGTGTAATTTCATGAAAAAATCAAAATAACTTTATTAAAAA-G
**
211635 AATAAACATTATCAATTGTTGTTAAAA
637 AATAAACATTATCAACCGTTGTTAAAA
* *
211662 AATAATAATTCATTTGATTCCTCAATTGTAATTAAAATTTTATTTTAATATTTTTTATATTTTTA
1 AATAATAATTAATTTGATACCTCAATTGTAATTAAAATTTTATTTTAATATTTTTTATATTTTTA
* * * *
211727 GATAATTAATTTTAAAAATCAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTA
66 AACAATTAATTTTAAAAATTAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTA
211792 TAAAATATTTATTATCATCATCATCGTCATCATTTTGTAAAATAAATACTAGTTATAAAACTTTT
131 TAAAATATTTATTATCATCATCATCGTCATCATTTTGTAAAATAAATACTAGTTATAAAACTTTT
* * *
211857 ATAAAATTATTTATAGTTTAAAATACTTACCCTTAAAGTTTTCCTATACTAGATTATACGTATTG
196 ATAAAATTATTCATATTTTAAAATACTTACCCTTAAAGTTTTCCTATACTAGATTATATGTATTG
*
211922 TGTAATTTCATGCAAAAATTAAAAT
261 TGTAATTTCATGCAAAAATCAAAAT
211947 TTATCGAGTT
Statistics
Matches: 840, Mismatches: 95, Indels: 49
0.85 0.10 0.05
Matches are distributed among these distances:
663 7 0.01
664 287 0.34
665 2 0.00
666 1 0.00
667 94 0.11
668 18 0.02
669 11 0.01
670 256 0.30
671 39 0.05
673 4 0.00
674 1 0.00
676 2 0.00
677 13 0.02
679 10 0.01
680 19 0.02
681 52 0.06
682 24 0.03
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (663 bp):
AATAATAATTAATTTGATACCTCAATTGTAATTAAAATTTTATTTTAATATTTTTTATATTTTTA
AACAATTAATTTTAAAAATTAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTA
TAAAATATTTATTATCATCATCATCGTCATCATTTTGTAAAATAAATACTAGTTATAAAACTTTT
ATAAAATTATTCATATTTTAAAATACTTACCCTTAAAGTTTTCCTATACTAGATTATATGTATTG
TGTAATTTCATGCAAAAATCAAAATAATTTTACTAAAAATGAATAAACAAAATCAACTGTTGTTA
AAAAATAATAATTAATGAATAATAATTCATTTGATCCCTCAAATGTAATTAAAAGTTTATTTTAA
TATTTTTTATATTTTTAAACAATTAATTTTAAAAATCAATAAAATTTTCAAAAATATATGAAATT
TATAATTTTTTAAATTATAAAATATTTATCATCATCATCATCATTTTATAAAATAAATACCAATT
ATAAAACTTTTATAAAAGTATTCATATTTTAAAACACTTACTCACAAAGTTTTCCTATACTAGAT
TATACGTATTGTGTAATTTCATGAAAAAATCAAAATAACTTTATTAAAAAGAATAAACATTATCA
ACCGTTGTTAAAA
Found at i:213740 original size:24 final size:24
Alignment explanation
Indices: 213708--213765 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
213698 ACCCAAAGGG
213708 GTACCGATACTACTTTACATAGTA
1 GTACCGATACTACTTTACATAGTA
213732 GTACCGATACTACTTTACATAGTA
1 GTACCGATACTACTTTACATAGTA
*
213756 GTATCGATAC
1 GTACCGATAC
213766 CATGAGGACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (24 bp):
GTACCGATACTACTTTACATAGTA
Found at i:219343 original size:22 final size:20
Alignment explanation
Indices: 219299--219345 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
219289 AATTAAATCC
* *
219299 TATTTTTATTGAAAAAATAT
1 TATTTTTAATAAAAAAATAT
219319 TATTTTTAATAAATAAATATAT
1 TATTTTTAATAAA-AAA-ATAT
219341 TATTT
1 TATTT
219346 CAGGTCGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 3 0.13
22 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TATTTTTAATAAAAAAATAT
Found at i:220331 original size:15 final size:16
Alignment explanation
Indices: 220311--220343 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
220301 TGATCCCTCA
220311 TAATAAATATTAA-AG
1 TAATAAATATTAAGAG
*
220326 TAATAAATTTTAAGAG
1 TAATAAATATTAAGAG
220342 TA
1 TA
220344 TATTCGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (16 bp):
TAATAAATATTAAGAG
Found at i:220902 original size:20 final size:20
Alignment explanation
Indices: 220877--221157 Score: 215
Period size: 20 Copynumber: 14.2 Consensus size: 20
220867 TCCAGAATTA
* *
220877 CAACGCGAATATGAAAATCG
1 CAACGCGAATACGTAAATCG
* **
220897 CAACGCGAACATATAAATCG
1 CAACGCGAATACGTAAATCG
* *
220917 CAACGCG-ATTC-TGACTATCG
1 CAACGCGAATACGT-A-AATCG
* * * *
220937 CAACGAGTATCCGTAAAATCA
1 CAACGCGAATACGT-AAATCG
* *
220958 CAACGCGTATCCGTAAATCG
1 CAACGCGAATACGTAAATCG
220978 CAACGAC-AATACGTAAAATCG
1 CAACG-CGAATACGT-AAATCG
* *
220999 CAACGCGTATCCGTAAATCG
1 CAACGCGAATACGTAAATCG
* *
221019 CAAAGAGAATACGTAAATCG
1 CAACGCGAATACGTAAATCG
221039 CAACGCG-----G-AAATCG
1 CAACGCGAATACGTAAATCG
*
221053 CAACGAGAATACGTAAATCG
1 CAACGCGAATACGTAAATCG
* *
221073 CAATGCGTAT-CTGTAAATCG
1 CAACGCGAATAC-GTAAATCG
*
221093 CAATGCGAATACGTAAATCG
1 CAACGCGAATACGTAAATCG
*
221113 CAATGCGAATACGTAAATCG
1 CAACGCGAATACGTAAATCG
*
221133 CAATGCGAAT-CTGTAAATCG
1 CAACGCGAATAC-GTAAATCG
221153 CAACG
1 CAACG
221158 AGATTCTGAC
Statistics
Matches: 215, Mismatches: 30, Indels: 32
0.78 0.11 0.12
Matches are distributed among these distances:
14 12 0.06
15 1 0.00
18 1 0.00
19 5 0.02
20 157 0.73
21 37 0.17
22 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (20 bp):
CAACGCGAATACGTAAATCG
Found at i:220978 original size:41 final size:40
Alignment explanation
Indices: 220933--221157 Score: 248
Period size: 40 Copynumber: 5.7 Consensus size: 40
220923 GATTCTGACT
* * *
220933 ATCGCAACGAGTATCCGTAAAATCACAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
*
220974 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
*
221015 ATCGCAAAGAGAATACGTAAATCGCAACGCG-----G-AA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* *
221049 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* * * * *
221089 ATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* *
221129 ATCGCAATGCGAAT-CTGTAAATCGCAACG
1 ATCGCAACGAGAATAC-GTAAATCGCAACG
221158 AGATTCTGAC
Statistics
Matches: 163, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
34 31 0.19
35 1 0.01
39 2 0.01
40 76 0.47
41 53 0.33
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
Found at i:221094 original size:74 final size:75
Alignment explanation
Indices: 220972--221115 Score: 236
Period size: 74 Copynumber: 1.9 Consensus size: 75
220962 GCGTATCCGT
220972 AAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAAGAGAATACGTAAAT
1 AAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAAGAGAATACGTAAAT
221037 CGCAACGCGG
66 CGCAACGCGG
* * * * *
221047 AAATCGCAACGAGAATACGT-AAATCGCAATGCGTATCTGTAAATCGCAATGCGAATACGTAAAT
1 AAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAAGAGAATACGTAAAT
221111 CGCAA
66 CGCAA
221116 TGCGAATACG
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 45 0.70
75 19 0.30
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.17
Consensus pattern (75 bp):
AAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAAAGAGAATACGTAAAT
CGCAACGCGG
Found at i:222068 original size:24 final size:24
Alignment explanation
Indices: 222017--222070 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
222007 GTATTCGAAA
*
222017 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
222041 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
222065 TTTGAT
1 TTTGAT
222071 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:224610 original size:20 final size:20
Alignment explanation
Indices: 224585--224622 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
224575 ATCTTAATGT
224585 CTATCGCAACGCGAAAATTA
1 CTATCGCAACGCGAAAATTA
*
224605 CTATCGCAACGTGAAAAT
1 CTATCGCAACGCGAAAAT
224623 CGCAACGCGA
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:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATTA
Found at i:224626 original size:14 final size:14
Alignment explanation
Indices: 224607--224636 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
224597 GAAAATTACT
*
224607 ATCGCAACGTGAAA
1 ATCGCAACGCGAAA
224621 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
224635 AT
1 AT
224637 GACTATCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGCGAAA
Found at i:224688 original size:33 final size:33
Alignment explanation
Indices: 224641--224734 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
224631 GAAAATGACT
*
224641 ATCGAAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
224674 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
224707 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
224735 CGAATTTAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:224756 original size:19 final size:18
Alignment explanation
Indices: 224734--224808 Score: 59
Period size: 19 Copynumber: 4.2 Consensus size: 18
224724 AAATCGCAAC
224734 GCGAATTTAGTTTCGCGTT
1 GCGAATTTA-TTTCGCGTT
*
224753 GCG-ATTT-TGT--CGTT
1 GCGAATTTATTTCGCGTT
*
224767 GCGATTTTAATTTCGCGTT
1 GCGAATTT-ATTTCGCGTT
* *
224786 GCGATTTTCATTTCGCATT
1 GCGAATTT-ATTTCGCGTT
224805 GCGA
1 GCGA
224809 TAGTAATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 7 0.15
15 3 0.07
16 2 0.04
17 2 0.04
18 4 0.09
19 28 0.61
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.44
Consensus pattern (18 bp):
GCGAATTTATTTCGCGTT
Found at i:224809 original size:19 final size:19
Alignment explanation
Indices: 224765--224809 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
224755 GATTTTGTCG
*
224765 TTGCGATTTTAATTTCGCG
1 TTGCGATTTTAATTTCGCA
*
224784 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTAATTTCGCA
224803 TTGCGAT
1 TTGCGAT
224810 AGTAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTAATTTCGCA
Found at i:224817 original size:19 final size:19
Alignment explanation
Indices: 224774--224817 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
224764 GTTGCGATTT
* **
224774 TAATTTCGCGTTGCGATTT
1 TAATTTCGCATTGCGATAG
*
224793 TCATTTCGCATTGCGATAG
1 TAATTTCGCATTGCGATAG
224812 TAATTT
1 TAATTT
224818 TTGCCTTCAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (19 bp):
TAATTTCGCATTGCGATAG
Found at i:224935 original size:14 final size:14
Alignment explanation
Indices: 224916--224952 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
224906 CATCAATTAA
224916 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
224930 ACAAATCATCTTTT
1 ACAAATCAACTTTT
224944 ACAAATCAA
1 ACAAATCAA
224953 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:226388 original size:42 final size:42
Alignment explanation
Indices: 226342--226421 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
226332 CGATGACAGT
* * *
226342 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
226384 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
226422 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:228412 original size:20 final size:20
Alignment explanation
Indices: 228387--228449 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
228377 TTTTGGTTGA
228387 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
228407 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
228426 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
228447 AAT
1 AAT
228450 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:228518 original size:20 final size:20
Alignment explanation
Indices: 228493--228539 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
228483 CATTTCTTTC
*
228493 GTTGCGACAGTCATTTTCGT
1 GTTGCGACAGTCATTTTCAT
***
228513 GTTGCGATTTTCATTTTCAT
1 GTTGCGACAGTCATTTTCAT
228533 GTTGCGA
1 GTTGCGA
228540 TTTTATGTTT
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:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
GTTGCGACAGTCATTTTCAT
Found at i:228540 original size:20 final size:20
Alignment explanation
Indices: 228503--228543 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
228493 GTTGCGACAG
*
228503 TCATTTTCGTGTTGCGATTT
1 TCATTTTCATGTTGCGATTT
228523 TCATTTTCATGTTGCGATTT
1 TCATTTTCATGTTGCGATTT
228543 T
1 T
228544 ATGTTTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (20 bp):
TCATTTTCATGTTGCGATTT
Found at i:229133 original size:20 final size:20
Alignment explanation
Indices: 229104--229237 Score: 144
Period size: 20 Copynumber: 6.6 Consensus size: 20
229094 GCTTTAAAAA
229104 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
* *
229124 TCGAGTTGCGATTTTACGTAT
1 TCGCGTTGCGA-TTTACGGAT
229145 T-GTCGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTACGGAT
* * *
229165 ACGCATTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGGAT
* *
229185 TCTCGTTACGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
*
229205 ACGCGTTGCGATTTTACGGAT
1 TCGCGTTGCGA-TTTACGGAT
* *
229226 ACTCGTTGCGAT
1 TCGCGTTGCGAT
229238 AGTCAAAATC
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
20 58 0.62
21 36 0.38
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGGAT
Found at i:229164 original size:41 final size:41
Alignment explanation
Indices: 229107--229237 Score: 185
Period size: 41 Copynumber: 3.2 Consensus size: 41
229097 TTAAAAATCG
* *
229107 CGTTGCGATTTACGGATTCGAGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGAGTTGCGATTTTACGTATTCT
229148 CGTTGCGATTTACGGATACGCA-TTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACG-AGTTGCGATTTTACGTATTCT
* * * *
229188 CGTTACGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGAGTTGCGATTTTACGTATTCT
229229 CGTTGCGAT
1 CGTTGCGAT
229238 AGTCAAAATC
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
40 36 0.45
41 43 0.54
42 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGAGTTGCGATTTTACGTATTCT
Found at i:229274 original size:20 final size:20
Alignment explanation
Indices: 229251--229298 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
229241 CAAAATCAAT
*
229251 TTGCGATTTAT-ATGTTCGCG
1 TTGCGATTT-TCATATTCGCG
229271 TTGCGATTTTCATATTCGCG
1 TTGCGATTTTCATATTCGCG
229291 TTGCGATT
1 TTGCGATT
229299 ACGGAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATATTCGCG
Found at i:229278 original size:81 final size:81
Alignment explanation
Indices: 229104--229298 Score: 189
Period size: 81 Copynumber: 2.4 Consensus size: 81
229094 GCTTTAAAAA
* * ** * ** *
229104 TCGCGTTGCGATTTACGGATTCGAGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACGGATTCGCGTTGCGATTTTACGGATACTCGTTGCGATTCACAAATACGA
*
229169 ATTGCGATTTACGTAT
66 ATTGCGATTTACATAT
* * *
229185 TCTCGTTACGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-AAAT-C
1 TCGCGTTGCGATTTACGGATTCGCGTTGCGATTTTACGGATACTCGTTGCGAT--TCACAAATAC
* *
229248 -AATTTGCGATTTATATGT
64 GAA-TTGCGATTTACATAT
* **
229266 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACGGATTCGCGTTGCGATT
229299 ACGGAAAATC
Statistics
Matches: 91, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
80 1 0.01
81 86 0.95
82 2 0.02
83 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (81 bp):
TCGCGTTGCGATTTACGGATTCGCGTTGCGATTTTACGGATACTCGTTGCGATTCACAAATACGA
ATTGCGATTTACATAT
Found at i:229397 original size:20 final size:19
Alignment explanation
Indices: 229348--229401 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
229338 ATTCTTCATA
229348 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
229367 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
229388 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
229402 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:240451 original size:35 final size:35
Alignment explanation
Indices: 240405--240479 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
240395 CGTCACGAAC
* *
240405 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAACCGAGGAGCCTCCA
*
240440 AGTAAGGCCCTGAGCACAAAATCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAACCGAGGAGCCTCCA
240475 AGTAA
1 AGTAA
240480 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.27, G:0.28, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAACCGAGGAGCCTCCA
Found at i:240583 original size:24 final size:24
Alignment explanation
Indices: 240556--240646 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
240546 CATAATTCAA
* *
240556 GTCAAGTATTATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
240580 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
240604 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
240627 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
240647 TCAAATTTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 21 0.37
24 36 0.63
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Done.