Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008315.1 Hibiscus syriacus cultivar Beakdansim tig00111011_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: 178499
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:4660 original size:13 final size:14
Alignment explanation
Indices: 4642--4671 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4632 GTCAAAGAAA
4642 GTCAACGGTC-ACG
1 GTCAACGGTCAACG
4655 GTCAACGGTCAACG
1 GTCAACGGTCAACG
4669 GTC
1 GTC
4672 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:4683 original size:17 final size:17
Alignment explanation
Indices: 4661--4718 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
4651 CACGGTCAAC
4661 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
4678 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
* *
4695 GGTCAACAGTCGGGTCA
1 GGTCAACGGTCGGGTCG
4712 GGTCAAC
1 GGTCAAC
4719 CCAGTTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:4688 original size:7 final size:7
Alignment explanation
Indices: 4642--4671 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4632 GTCAAAGAAA
4642 GTCAACG
1 GTCAACG
4649 GTC-ACG
1 GTCAACG
4655 GTCAACG
1 GTCAACG
4662 GTCAACG
1 GTCAACG
4669 GTC
1 GTC
4672 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:4759 original size:9 final size:9
Alignment explanation
Indices: 4728--4800 Score: 65
Period size: 9 Copynumber: 7.7 Consensus size: 9
4718 CCCAGTTCAG
4728 ACCGGTCAA
1 ACCGGTCAA
* *
4737 ATCGGTTCAG
1 ACCGG-TCAA
4747 ACCGGTCAA
1 ACCGGTCAA
*
4756 ACCGGTTCGA
1 ACCGG-TCAA
*
4766 ACTGGTCAA
1 ACCGGTCAA
4775 ACCGGTTCAAA
1 ACCGG-TC-AA
*
4786 ACTGGTCAA
1 ACCGGTCAA
4795 ACCGGT
1 ACCGGT
4801 TTTCATGCAG
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
9 26 0.52
10 18 0.36
11 6 0.12
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:4790 original size:20 final size:19
Alignment explanation
Indices: 4712--4801 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
4702 AGTCGGGTCA
* * * *
4712 GGTCAACCCAGTTCAGACC
1 GGTCAAACCGGTTCAAACT
* * *
4731 GGTCAAATCGGTTCAGACC
1 GGTCAAACCGGTTCAAACT
*
4750 GGTCAAACCGGTTCGAACT
1 GGTCAAACCGGTTCAAACT
4769 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACT
4789 GGTCAAACCGGTT
1 GGTCAAACCGGTT
4802 TTCATGCAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
19 45 0.73
20 17 0.27
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACT
Found at i:15864 original size:47 final size:48
Alignment explanation
Indices: 15795--15891 Score: 151
Period size: 47 Copynumber: 2.0 Consensus size: 48
15785 TAGCTTATTG
*
15795 ATTTCTCCATAGTCATCTCCTATTACGATAATGTCATCAACAT-AACA
1 ATTTCTCCAAAGTCATCTCCTATTACGATAATGTCATCAACATAAACA
* * *
15842 ATTTCTTCAAAGTCATCTCCTATTATGATAATGTCATCAATATAAACA
1 ATTTCTCCAAAGTCATCTCCTATTACGATAATGTCATCAACATAAACA
15890 AT
1 AT
15892 AAGTATGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 39 0.87
48 6 0.13
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (48 bp):
ATTTCTCCAAAGTCATCTCCTATTACGATAATGTCATCAACATAAACA
Found at i:17337 original size:23 final size:23
Alignment explanation
Indices: 17305--17356 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
17295 GTCTTGTCTT
* *
17305 CCTCCAGCCGTTTCTGTTCATCG
1 CCTCCTGCCGTTTCCGTTCATCG
17328 CCTCCTGCCGTTTCCGTTCATCG
1 CCTCCTGCCGTTTCCGTTCATCG
17351 CCTCCT
1 CCTCCT
17357 TACCGGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.06, C:0.44, G:0.15, T:0.35
Consensus pattern (23 bp):
CCTCCTGCCGTTTCCGTTCATCG
Found at i:21806 original size:17 final size:18
Alignment explanation
Indices: 21784--21841 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
21774 AAAATAAAAT
21784 ATATAAAAT-ACATTTAA
1 ATATAAAATAACATTTAA
*
21801 ATATAACATGAA-ATTTAA
1 ATATAAAAT-AACATTTAA
* *
21819 TTAAAAAATAACA-TTAA
1 ATATAAAATAACATTTAA
21836 ATATAA
1 ATATAA
21842 CTTGATATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
17 18 0.56
18 13 0.41
19 1 0.03
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (18 bp):
ATATAAAATAACATTTAA
Found at i:31660 original size:17 final size:17
Alignment explanation
Indices: 31638--31670 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31628 AGCAGAGGTG
31638 ATATTAGTTTAGGTTTA
1 ATATTAGTTTAGGTTTA
31655 ATATTAGTTTAGGTTT
1 ATATTAGTTTAGGTTT
31671 TATGTAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (17 bp):
ATATTAGTTTAGGTTTA
Found at i:34856 original size:9 final size:9
Alignment explanation
Indices: 34842--34872 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34832 AGAGCACAAG
*
34842 GAGATAAGA
1 GAGATAAAA
34851 GAGATAAAA
1 GAGATAAAA
34860 GAGATAAAA
1 GAGATAAAA
34869 GAGA
1 GAGA
34873 AGATATCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.29, T:0.10
Consensus pattern (9 bp):
GAGATAAAA
Found at i:45573 original size:22 final size:21
Alignment explanation
Indices: 45545--45615 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
45535 CATCAGTAAG
45545 TCTTTCGAGCATGATGATGAAA
1 TCTTTCGAGCATGATGAT-AAA
* * *
45567 TCTTTCGGGCCATCA-G-TAAG
1 TCTTTCGAG-CATGATGATAAA
45587 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGA-TAAA
*
45609 TCCTTCG
1 TCTTTCG
45616 GGTAATTTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 4 0.11
20 11 0.29
21 1 0.03
22 18 0.47
23 4 0.11
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (21 bp):
TCTTTCGAGCATGATGATAAA
Found at i:45592 original size:20 final size:20
Alignment explanation
Indices: 45533--45596 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
45523 ATCAATAAGT
45533 GCCATCAGTAAGTCTTTCGA
1 GCCATCAGTAAGTCTTTCGA
* * *
45553 G-CATGATGATGAAATCTTTCGG
1 GCCATCA-G-T-AAGTCTTTCGA
45575 GCCATCAGTAAGTCTTTCGA
1 GCCATCAGTAAGTCTTTCGA
45595 GC
1 GC
45597 ATGATGATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.12
20 13 0.38
21 2 0.06
22 11 0.32
23 4 0.12
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (20 bp):
GCCATCAGTAAGTCTTTCGA
Found at i:45592 original size:42 final size:42
Alignment explanation
Indices: 45533--45752 Score: 210
Period size: 42 Copynumber: 5.0 Consensus size: 42
45523 ATCAATAAGT
*
45533 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCTTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
*
45575 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
** ** * * * *
45617 GTAATTTGTAAGCCTTCACCGAAG-A-GTAGTGAAGCAAATCCATCAGTAAG
1 GCCATCAGTAAGTCTT--TCG-AGCATG-A-TGATG-AAATCCTTC-G---G
45667 TGCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
1 -GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
* * *
45710 GCCATAAGTAAGTCTTTCGAGCATGATGATTAAATTCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
45752 G
1 G
45753 TAATTTGTAA
Statistics
Matches: 143, Mismatches: 22, Indels: 26
0.75 0.12 0.14
Matches are distributed among these distances:
42 91 0.64
43 2 0.01
44 4 0.03
45 5 0.03
46 9 0.06
47 9 0.06
48 6 0.04
49 4 0.03
50 2 0.01
51 11 0.08
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
Found at i:45674 original size:13 final size:13
Alignment explanation
Indices: 45656--45680 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45646 TGAAGCAAAT
45656 CCATCAGTAAGTG
1 CCATCAGTAAGTG
45669 CCATCAGTAAGT
1 CCATCAGTAAGT
45681 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:45677 original size:135 final size:135
Alignment explanation
Indices: 45432--45802 Score: 652
Period size: 135 Copynumber: 2.7 Consensus size: 135
45422 TCAATTTAAG
*
45432 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCT
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCT
* * *
45497 TCACCGAAGAGTTGTGAAGCAAACCCATCAATAAGTGCCATCAGTAAGTCTTTCGAGCATGATGA
66 TCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGA
45562 TGAAA
131 TGAAA
*
45567 TCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCT
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCT
45632 TCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGA
66 TCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGA
45697 TGAAA
131 TGAAA
* *
45702 TCCTTCGGGCCATAAGTAAGTCTTTCGAGCATGATGATTAAATTCTTCGGGTAATTTGTAAGCCT
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCT
* * *
45767 CCACCGAAGAGTATTGAAGCAAATTCATCAGTAAGT
66 TCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGT
45803 CTTTCGAGCA
Statistics
Matches: 225, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
135 225 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (135 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCT
TCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGA
TGAAA
Found at i:49649 original size:17 final size:17
Alignment explanation
Indices: 49627--49659 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
49617 GGTAGAGGTG
49627 ATATTAGTTTAGGTTTA
1 ATATTAGTTTAGGTTTA
49644 ATATTAGTTTAGGTTT
1 ATATTAGTTTAGGTTT
49660 TATGTAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (17 bp):
ATATTAGTTTAGGTTTA
Found at i:52688 original size:28 final size:28
Alignment explanation
Indices: 52656--52730 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
52646 ATAATATGTA
52656 AAATAATATCCTACATTAACTATTAACT
1 AAATAATATCCTACATTAACTATTAACT
* *
52684 AAATAATATCCTACAATAACTATTACCT
1 AAATAATATCCTACATTAACTATTAACT
***
52712 GTGTAATATCCTACATTAA
1 AAATAATATCCTACATTAA
52731 ATAAAATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.35
Consensus pattern (28 bp):
AAATAATATCCTACATTAACTATTAACT
Found at i:55486 original size:37 final size:37
Alignment explanation
Indices: 55410--55486 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
55400 TTTTTATATT
*
55410 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
55447 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
55484 TTT
1 TTT
55487 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:55648 original size:18 final size:19
Alignment explanation
Indices: 55625--55669 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
55615 CTCAGTAATC
55625 TTATTCC-CTGGTAATCTT
1 TTATTCCACTGGTAATCTT
55643 TTATTCCCACTGGTAATCTT
1 TTATT-CCACTGGTAATCTT
*
55663 ATATTCC
1 TTATTCC
55670 GTGAACCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 15 0.62
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.47
Consensus pattern (19 bp):
TTATTCCACTGGTAATCTT
Found at i:55657 original size:20 final size:20
Alignment explanation
Indices: 55632--55669 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55622 ATCTTATTCC
*
55632 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
55652 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
55670 GTGAACCAAA
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:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:64912 original size:60 final size:59
Alignment explanation
Indices: 64820--64932 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
64810 TTCAGATATG
* ** * *
64820 AAATTGGAATATTCAAAGTTTGGGGAATAATTTAGAAA-GAGAGTCATAGTTTATGGATA
1 AAATTAGAATATTCAAAGTTTAAGGAATAATTTA-AAATAAAAGTCATAGTTTATGGATA
* *
64879 AAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAAAATAAAAGTCATAGTTTA
1 AAATTAGAATATTC-AAAGTTTAAGGAATAATTTAAAATAAAAGTCATAGTTTA
64933 GAGAAGAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 15 0.33
60 30 0.67
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (59 bp):
AAATTAGAATATTCAAAGTTTAAGGAATAATTTAAAATAAAAGTCATAGTTTATGGATA
Found at i:65307 original size:53 final size:53
Alignment explanation
Indices: 65240--65342 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 53
65230 GTGATTTACA
* * * *
65240 TTAATTCTGGATTTGACAACAT-TTTTAAGTTTGGTTCTTTAATTTGAAGACTT
1 TTAATTCTGAATTTGAAAACATCTTTTAA-TTTGATTCTTAAATTTGAAGACTT
65293 TTAATTCTGAATTTGAAAACATCTTTTAATTTGATTCTTAAATTTGAAGA
1 TTAATTCTGAATTTGAAAACATCTTTTAATTTGATTCTTAAATTTGAAGA
65343 TATTTTCATA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 39 0.87
54 6 0.13
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.48
Consensus pattern (53 bp):
TTAATTCTGAATTTGAAAACATCTTTTAATTTGATTCTTAAATTTGAAGACTT
Found at i:71059 original size:18 final size:18
Alignment explanation
Indices: 71013--71059 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
71003 TTTGGGTTGG
*
71013 GTTTAGGGTTCGAGTCAA
1 GTTTAGGGTTTGAGTCAA
71031 GTTTAGGGTTTG-GCTCAA
1 GTTTAGGGTTTGAG-TCAA
71049 GTTTAGGGTTT
1 GTTTAGGGTTT
71060 TTTTAAGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (18 bp):
GTTTAGGGTTTGAGTCAA
Found at i:71530 original size:18 final size:17
Alignment explanation
Indices: 71491--71531 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
71481 AAACAGGTTT
*
71491 CAGATTCCAATTCCTGA
1 CAGATTCCAATTCCTCA
71508 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCC-TCA
71526 CAGATT
1 CAGATT
71532 TTAATTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (17 bp):
CAGATTCCAATTCCTCA
Found at i:74475 original size:2 final size:2
Alignment explanation
Indices: 74468--74515 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
74458 TCTCCACTTC
74468 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
74510 TA TA TA
1 TA TA TA
74516 AAAGTAGGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:80378 original size:31 final size:31
Alignment explanation
Indices: 80357--80466 Score: 202
Period size: 31 Copynumber: 3.5 Consensus size: 31
80347 CATAGATTCT
* *
80357 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
80388 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
80419 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
80450 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
80467 CCTCGACCCT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:84665 original size:31 final size:31
Alignment explanation
Indices: 84627--84751 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
84617 CCCAAAGAAC
* * * *
84627 CAGTCCATA-GATTCCGAAAAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
84658 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
84689 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
84720 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
84751 C
1 C
84752 CCTCGACCCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:88319 original size:13 final size:13
Alignment explanation
Indices: 88303--88347 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
88293 GACATAAATC
*
88303 TATGACACGCATT
1 TATGACACACATT
88316 TATGACACACATT
1 TATGACACACATT
* *
88329 TATGACGCATATT
1 TATGACACACATT
88342 TATGAC
1 TATGAC
88348 GTTCATTGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (13 bp):
TATGACACACATT
Found at i:88332 original size:26 final size:28
Alignment explanation
Indices: 88276--88334 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 28
88266 TGAATTTTAG
* *
88276 ATGACACGCAATTGTGTGACATAAATCT
1 ATGACACGCAATTGTATGACACAAATCT
* *
88304 ATGACACGC-ATT-TATGACACACATTT
1 ATGACACGCAATTGTATGACACAAATCT
88330 ATGAC
1 ATGAC
88335 GCATATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 15 0.56
27 3 0.11
28 9 0.33
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (28 bp):
ATGACACGCAATTGTATGACACAAATCT
Found at i:98119 original size:21 final size:22
Alignment explanation
Indices: 98095--98137 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
98085 ATAAAGTTAT
98095 ACAAAGACAAGAATACC-CTTC
1 ACAAAGACAAGAATACCACTTC
*
98116 ACAAAGACATGAATACCACTTC
1 ACAAAGACAAGAATACCACTTC
98138 GTATTGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.47, C:0.28, G:0.09, T:0.16
Consensus pattern (22 bp):
ACAAAGACAAGAATACCACTTC
Found at i:104547 original size:13 final size:13
Alignment explanation
Indices: 104529--104553 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
104519 TGAAACAAAC
104529 CCATCAGTAAGTG
1 CCATCAGTAAGTG
104542 CCATCAGTAAGT
1 CCATCAGTAAGT
104554 CTTTCGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:104575 original size:22 final size:21
Alignment explanation
Indices: 104549--104623 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
104539 GTGCCATCAG
104549 TAAGTCTTTCGACCATGATGA
1 TAAGTCTTTCGACCATGATGA
* * *
104570 TGAAGTCCTTCGGGCCATCA-G-
1 T-AAGTCTTTC-GACCATGATGA
*
104591 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGACCATGATGA
*
104612 TTAAATCTTTCG
1 -TAAGTCTTTCG
104624 GGTAATTTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
19 5 0.12
20 9 0.22
21 2 0.05
22 19 0.46
23 6 0.15
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (21 bp):
TAAGTCTTTCGACCATGATGA
Found at i:104601 original size:20 final size:20
Alignment explanation
Indices: 104541--104601 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
104531 ATCAGTAAGT
104541 GCCATCAGTAAGTCTTTC-G
1 GCCATCAGTAAGTCTTTCGG
* * *
104560 ACCATGATGATGAAGTCCTTCGG
1 GCCATCA-G-T-AAGTCTTTCGG
104583 GCCATCAGTAAGTCTTTCG
1 GCCATCAGTAAGTCTTTCG
104602 AGCATGATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
19 5 0.16
20 10 0.31
21 2 0.06
22 9 0.28
23 6 0.19
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (20 bp):
GCCATCAGTAAGTCTTTCGG
Found at i:104752 original size:22 final size:21
Alignment explanation
Indices: 104684--104783 Score: 57
Period size: 22 Copynumber: 4.8 Consensus size: 21
104674 GTGCCATCAT
*
104684 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATAATGA
* * * *
104705 TTAAATCCTTCGGGTCATCA-G-
1 -TAAGTCTTTCGAG-CATAATGA
104726 TAAGTCTTTCGAGCATAATGA
1 TAAGTCTTTCGAGCATAATGA
* *
104747 TGAAGTCCTTT-GGGCCATCA-G-
1 T-AAGT-CTTTCGAG-CATAATGA
104768 TAAGTCTTTCGAGCAT
1 TAAGTCTTTCGAGCAT
104784 GATAATTAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 17
0.68 0.12 0.19
Matches are distributed among these distances:
19 11 0.18
20 17 0.28
21 2 0.03
22 18 0.30
23 12 0.20
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATAATGA
Found at i:104771 original size:135 final size:135
Alignment explanation
Indices: 104436--104760 Score: 456
Period size: 135 Copynumber: 2.4 Consensus size: 135
104426 AGTAAAAAAT
* * * *
104436 TTAAGTCCTTTGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAGTCTTTTAGGTCATTTGTA
1 TTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAGTCCTTTGGGTCATTTGTA
**
104501 A-CCTTCATTGAAGAGTAGTGAAACAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGACCAT
66 AGCCTTCACCGAAGAGTAGTGAAACAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGACCAT
104565 GATGA
131 GATGA
* * *
104570 TGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAAT-CTTTCGGGTAATTTGT
1 TTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAGTCCTTT-GGGTCATTTGT
** * * * *
104634 AAGCCTTCACCGAAGAGTAGTGAAGTAAATCCATTAGTAAGTGCCATCATTAAGTCTTTCGAGCA
65 AAGCCTTCACCGAAGAGTAGTGAAACAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGACCA
104699 TGATGA
130 TGATGA
* * * *
104705 TTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATAATGATGAAGTCCTTTGGG
1 TTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAGTCCTTTGGG
104761 CCATCAGTAA
Statistics
Matches: 167, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
133 3 0.02
134 55 0.33
135 105 0.63
136 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (135 bp):
TTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAGTCCTTTGGGTCATTTGTA
AGCCTTCACCGAAGAGTAGTGAAACAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGACCAT
GATGA
Found at i:104843 original size:177 final size:177
Alignment explanation
Indices: 104543--104979 Score: 757
Period size: 177 Copynumber: 2.5 Consensus size: 177
104533 CAGTAAGTGC
*
104543 CATCAGTAAGTCTTTCGACCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * *
104608 ATGATTAAATCTTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGTAAATCCATTAGTA
66 ATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTA
*
104673 AGTGCCATCATTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
131 AGTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* *
104720 CATCAGTAAGTCTTTCGAGCATAATGATGAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATG
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
*
104785 ATAATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTA
66 ATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTA
*
104850 AGTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGT
131 AGTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* * * *
104897 CAACAGTAAGTCTTTCAAGCATGATGATGAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGAATG
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
104962 ATGATTAAATCATTCGGG
66 ATGATTAAATCATTCGGG
104980 CCATCAGTAA
Statistics
Matches: 244, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
177 244 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (177 bp):
CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
ATGATTAAATCATTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTA
AGTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
Found at i:104859 original size:13 final size:13
Alignment explanation
Indices: 104841--104865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
104831 TGAAGCAAAT
104841 CCATCAGTAAGTG
1 CCATCAGTAAGTG
104854 CCATCAGTAAGT
1 CCATCAGTAAGT
104866 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:104918 original size:42 final size:42
Alignment explanation
Indices: 104543--105080 Score: 404
Period size: 42 Copynumber: 12.4 Consensus size: 42
104533 CAGTAAGTGC
* * * *
104543 CATCAGTAAGTCTTTCGACCATGATGATGAAGTCCTTCGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
*
104585 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* ** * * * * *
104627 AATTTGTAAGCCTTCACCGAAG-A-GTAGTGAAGTAAATCCATTAGTAAGTGC
1 CATCAGTAAGTCTT--TCG-AGCATG-A-TG-ATTAAATCC-TTCG---G-GT
*
104678 CATCATTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* * * * *
104720 CATCAGTAAGTCTTTCGAGCATAATGATGAAGTCCTTTGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* *
104762 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* ** * * ** * *
104804 AATTTGTAAGCCTTCACCGAAG-A-GTAGTGAAGCAAATCCATCAGTAAGTGC
1 CATCAGTAAGTCTT--TCG-AGCATG-A-TG-ATTAAATCCTTC-G---G-GT
*
104855 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* * * *
104897 CAACAGTAAGTCTTTCAAGCATGATGATGAAGTCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* * *
104939 CATCAGTAAGTCTTTCGAGAATGATGATTAAATCATTCGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
*
104981 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
*** * * * *
105023 CATTTTTTAGTCTTTCAAGCAAGAT-AATAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
*
105064 CATCCA-TAAGTCCTTCG
1 CAT-CAGTAAGTCTTTCG
105081 GGTAGGATGT
Statistics
Matches: 385, Mismatches: 84, Indels: 55
0.73 0.16 0.10
Matches are distributed among these distances:
41 25 0.06
42 261 0.68
43 4 0.01
44 8 0.02
45 7 0.02
46 19 0.05
47 20 0.05
48 8 0.02
49 8 0.02
50 4 0.01
51 21 0.05
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
Found at i:105567 original size:53 final size:53
Alignment explanation
Indices: 105504--105813 Score: 390
Period size: 53 Copynumber: 5.8 Consensus size: 53
105494 ATCACACCAA
* * **
105504 AAGATTGTTCGAGTTCTACTCCCTGAAGTAAGAGGGAGCAAACCTATAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* *
105557 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGC-AACCCGTAGACAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * *
105609 AAGATTATTCGAGTTCTACTCCCTAAAGCAAGAGGGAGTGAACCCGTGGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
105662 AAGATTGTTCGAGTTCTACCCCCTGAAGCAAGACGGAGCGAACCCGTAAGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * ****
105715 AAGATTATTCGAGTTCTACTCCCTGAATCAATAGGGAGCGAACCCATTTTTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
*
105768 AAGATTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGCGAACCC
1 AAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCC
105814 ATCATTTGAA
Statistics
Matches: 223, Mismatches: 31, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
52 45 0.20
53 151 0.68
54 17 0.08
55 10 0.04
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:105686 original size:105 final size:106
Alignment explanation
Indices: 105504--105813 Score: 410
Period size: 105 Copynumber: 2.9 Consensus size: 106
105494 ATCACACCAA
* * * *
105504 AAGATTGTTCGAGTTCTACTCCCTGAAGTAAGAGGGAGCAAACCTATAGGCAGAAGATTGTTCGA
1 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAAGATTGTTCGA
*
105569 GTTTTACTCCCTGAAGCAAGAGGGAGC-AACCCGT-AGACAG
66 GTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG-CAG
* * * *
105609 AAGATTATTCGAGTTCTACTCCCTAAAGCAAGAGGGAGTGAACCCGTGGGCAGAAGATTGTTCGA
1 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAAGATTGTTCGA
* *
105674 GTTCTACCCCCTGAAGCAAGACGGAGCGAACCCGTAAGCAG
66 GTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAG
* * ****
105715 AAGATTATTCGAGTTCTACTCCCTGAATCAATAGGGAGCGAACCCATTTTTAGAAGATTGTTCGA
1 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAAGATTGTTCGA
*
105780 GTTCCTTAATCCCTGAA-CAAGAGGGAGCGAACCC
66 GTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCC
105814 ATCATTTGAA
Statistics
Matches: 178, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
105 81 0.46
106 69 0.39
107 19 0.11
108 9 0.05
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (106 bp):
AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAAGATTGTTCGA
GTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAG
Found at i:105849 original size:54 final size:55
Alignment explanation
Indices: 105504--105850 Score: 175
Period size: 53 Copynumber: 6.5 Consensus size: 55
105494 ATCACACCAA
* * * * ***
105504 AAGATTGTTCGAGTTC--TACTCCCTGAAGT-AAGAGGGAGCAAACCTATAGGCAG
1 AAGATTGTTCAAGTTCATTAATCCCTGAA-TCAAGAGGGAGCGAACCCATATTTAG
* * * * ***
105557 AAGATTGTTCGAGTT--TTACTCCCTGAAGCAAGAGGGAGC-AACCCGTAGACAG
1 AAGATTGTTCAAGTTCATTAATCCCTGAATCAAGAGGGAGCGAACCCATATTTAG
* * * * * * * ****
105609 AAGATTATTCGAGTTC--TACTCCCTAAAGCAAGAGGGAGTGAACCCGTGGGCAG
1 AAGATTGTTCAAGTTCATTAATCCCTGAATCAAGAGGGAGCGAACCCATATTTAG
* ** * * * ***
105662 AAGATTGTTCGAGTTC--TACCCCCTGAAGCAAGACGGAGCGAACCCGTAAGCAG
1 AAGATTGTTCAAGTTCATTAATCCCTGAATCAAGAGGGAGCGAACCCATATTTAG
* * * * *
105715 AAGATTATTCGAGTTC--TACTCCCTGAATCAATAGGGAGCGAACCCATTTTTAG
1 AAGATTGTTCAAGTTCATTAATCCCTGAATCAAGAGGGAGCGAACCCATATTTAG
* *
105768 AAGATTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGCGAACCCATCATTT-G
1 AAGATTGTTCAAGTTCATTAATCCCTGAATCAAGAGGGAGCGAACCCAT-ATTTAG
* *
105822 AAGATTTTTCAAGTTTCATTTAT-CCTGAA
1 AAGATTGTTCAAG-TTCATTAATCCCTGAA
105851 GTAACAGTGG
Statistics
Matches: 252, Mismatches: 34, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
52 45 0.18
53 151 0.60
54 36 0.14
55 20 0.08
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (55 bp):
AAGATTGTTCAAGTTCATTAATCCCTGAATCAAGAGGGAGCGAACCCATATTTAG
Found at i:109033 original size:15 final size:15
Alignment explanation
Indices: 109009--109039 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
108999 GGTGTCTATT
*
109009 ACATTGAAGATTCAC
1 ACATTCAAGATTCAC
109024 ACATTCAAGATTCAC
1 ACATTCAAGATTCAC
109039 A
1 A
109040 ACCGGTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (15 bp):
ACATTCAAGATTCAC
Found at i:112151 original size:33 final size:34
Alignment explanation
Indices: 112082--112152 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
112072 ATTGTAAAAG
112082 GGGATTGGTTCTATCTTAGCCAATTGAAAAGATA
1 GGGATTGGTTCTATCTTAGCCAATTGAAAAGATA
*
112116 GGGATTGGTTCTAGT-TTAGTC-ATTGAAAA-ACTA
1 GGGATTGGTTCTA-TCTTAGCCAATTGAAAAGA-TA
112149 GGGA
1 GGGA
112153 GCTGTAAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
32 1 0.03
33 14 0.41
34 18 0.53
35 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.32
Consensus pattern (34 bp):
GGGATTGGTTCTATCTTAGCCAATTGAAAAGATA
Found at i:119178 original size:28 final size:27
Alignment explanation
Indices: 119124--119176 Score: 92
Period size: 25 Copynumber: 2.0 Consensus size: 27
119114 AAAGAATTCA
119124 AAAATAATAGTACTTTTGAGTATTATT
1 AAAATAATAGTACTTTTGAGTATTATT
119151 AAAA-AAT-GTACTTTTGAGTATTATT
1 AAAATAATAGTACTTTTGAGTATTATT
119176 A
1 A
119177 TTTTGTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 19 0.73
26 3 0.12
27 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (27 bp):
AAAATAATAGTACTTTTGAGTATTATT
Found at i:129836 original size:3 final size:3
Alignment explanation
Indices: 129818--129866 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
129808 CTTAGATACT
*
129818 TAA TTA TAA T-A TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
129864 TAA
1 TAA
129867 ATCTATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:129895 original size:19 final size:19
Alignment explanation
Indices: 129824--129912 Score: 82
Period size: 19 Copynumber: 4.9 Consensus size: 19
129814 TACTTAATTA
*
129824 TAATATAATAATA-TAATAA
1 TAATA-AATAATATTAATAT
* *
129843 TAAT-AATAATAATAATAA
1 TAATAAATAATATTAATAT
*
129861 TAATAAAT-CTA-T-ATAT
1 TAATAAATAATATTAATAT
129877 TAATTAAA-AATATTAATAT
1 TAA-TAAATAATATTAATAT
129896 TAATAAATAATATTAAT
1 TAATAAATAATATTAAT
129913 TTTTCATTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
16 6 0.10
17 14 0.23
18 17 0.28
19 23 0.38
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATAAATAATATTAATAT
Found at i:129909 original size:32 final size:31
Alignment explanation
Indices: 129823--129913 Score: 94
Period size: 35 Copynumber: 2.8 Consensus size: 31
129813 ATACTTAATT
* *
129823 ATAATATAATAATATAATAATAA-TAATAATA
1 ATAATATAATAA-ATAATATTAATTAAAAATA
129854 ATAATAATAATAAATCTATATATTAATTAAAAATA
1 ATAAT-ATAATAAA--TA-ATATTAATTAAAAATA
*
129889 TTAATATTAATAAATAATATTAATT
1 ATAATA-TAATAAATAATATTAATT
129914 TTTCATTTGG
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
31 6 0.12
32 16 0.31
33 4 0.08
34 7 0.14
35 18 0.35
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (31 bp):
ATAATATAATAAATAATATTAATTAAAAATA
Found at i:131155 original size:28 final size:28
Alignment explanation
Indices: 131089--131156 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
131079 ATGTAACTAT
131089 AATCAA-TCATTATAATATATAAATAAAG
1 AATCAACT-ATTATAATATATAAATAAAG
* * *
131117 AATCAATTATTATAATATATTAATAGATG
1 AATCAACTATTATAATATATAAATA-AAG
131146 AAT-AACTATTA
1 AATCAACTATTA
131157 AAACTTGGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 29 0.83
29 6 0.17
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (28 bp):
AATCAACTATTATAATATATAAATAAAG
Found at i:132342 original size:20 final size:20
Alignment explanation
Indices: 132317--132363 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
132307 AACCGGTTCA
*
132317 AGTCAACTCAAATCGGGCTG
1 AGTCAACTCAAATCGGGCCG
**
132337 AGTCAACTCGGATCGGGCCG
1 AGTCAACTCAAATCGGGCCG
132357 AGTCAAC
1 AGTCAAC
132364 CTGAACCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (20 bp):
AGTCAACTCAAATCGGGCCG
Found at i:134516 original size:27 final size:27
Alignment explanation
Indices: 134485--134544 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
134475 GCCAACCACT
134485 TTTCTTATTACAAATACATACTATACA
1 TTTCTTATTACAAATACATACTATACA
134512 TTTCTTATTACAAATACATACTATACA
1 TTTCTTATTACAAATACATACTATACA
134539 TTTCTT
1 TTTCTT
134545 TTCTGATCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTCTTATTACAAATACATACTATACA
Found at i:135015 original size:31 final size:31
Alignment explanation
Indices: 134972--135122 Score: 243
Period size: 31 Copynumber: 4.9 Consensus size: 31
134962 GAAGGACCAG
*
134972 TCCATATATCCCGAAGAACATAGGTAAACAA
1 TCCATATGTCCCGAAGAACATAGGTAAACAA
*
135003 TCCATATGTCCCGAAGAACATAGGTAAACAG
1 TCCATATGTCCCGAAGAACATAGGTAAACAA
*
135034 TCCATATGTCCCGAAGAACATAGGTAAACAG
1 TCCATATGTCCCGAAGAACATAGGTAAACAA
*
135065 TCCATATGTCCCGAAGAATATAGGTAAAC-A
1 TCCATATGTCCCGAAGAACATAGGTAAACAA
*
135095 GCCATATGTCCC-AAGAACATAGGTAAAC
1 TCCATATGTCCCGAAGAACATAGGTAAAC
135123 CCTCGACCCT
Statistics
Matches: 114, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 15 0.13
30 11 0.10
31 88 0.77
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAAACAA
Found at i:138218 original size:16 final size:16
Alignment explanation
Indices: 138197--138228 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
138187 AATAAATAAG
138197 CGAACATAAACGAACA
1 CGAACATAAACGAACA
138213 CGAACATAAACGAACA
1 CGAACATAAACGAACA
138229 AACTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:138309 original size:10 final size:10
Alignment explanation
Indices: 138294--138336 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
138284 CATTTAATAA
138294 ATAAACGAAC
1 ATAAACGAAC
138304 ATAAACGAAC
1 ATAAACGAAC
138314 ----ACGAAC
1 ATAAACGAAC
138320 ATAAACGAAC
1 ATAAACGAAC
138330 ATAAACG
1 ATAAACG
138337 TTAGAGACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.21
10 23 0.79
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:138319 original size:16 final size:16
Alignment explanation
Indices: 138298--138330 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
138288 TAATAAATAA
138298 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
138314 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
138330 A
1 A
138331 TAAACGTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:139604 original size:33 final size:33
Alignment explanation
Indices: 139550--139639 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
139540 GGGAAAGAGA
* *
139550 TGAAGCTCTGTCGAATTGTTGCAGTTGAAGACT
1 TGAAGCTCCGTCGAATCGTTGCAGTTGAAGACT
*
139583 TGAAGCTCCGTCAAATCGTTGCAGTTGAAGACT
1 TGAAGCTCCGTCGAATCGTTGCAGTTGAAGACT
139616 TGAAGCTCCGTCGAATCGTTGCAG
1 TGAAGCTCCGTCGAATCGTTGCAG
139640 AAATGAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (33 bp):
TGAAGCTCCGTCGAATCGTTGCAGTTGAAGACT
Found at i:139897 original size:24 final size:24
Alignment explanation
Indices: 139860--139915 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
139850 TATTAGGTTA
* *
139860 AACATAAATGAACGCACATAAACG
1 AACATAACTAAACGCACATAAACG
*
139884 AACATAACTAAACGCATATAAACG
1 AACATAACTAAACGCACATAAACG
139908 AACATAAC
1 AACATAAC
139916 CGAATGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.55, C:0.21, G:0.09, T:0.14
Consensus pattern (24 bp):
AACATAACTAAACGCACATAAACG
Found at i:140809 original size:13 final size:14
Alignment explanation
Indices: 140788--140821 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
140778 GAATATTATA
140788 ATAACAATA-ATTT
1 ATAACAATATATTT
*
140801 ATAAGAATATATTT
1 ATAACAATATATTT
140815 ATAACAA
1 ATAACAA
140822 GTAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
ATAACAATATATTT
Found at i:142044 original size:47 final size:51
Alignment explanation
Indices: 141987--142083 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 51
141977 GTCCCTTGTC
* * *
141987 TCTGTCTGCTCTTC-ATCT-TTC-TTTATTTTCTGAGGAAGATAGAACACG
1 TCTGTCTGCTCTTCTATATATTCGTTTATTTTCTGAAGAAAATAGAACACG
* *
142035 TCTGT-TGCTCTTCTTTATATTCGTTTATTTTCTTAAGAAAATAGAACAC
1 TCTGTCTGCTCTTCTATATATTCGTTTATTTTCTGAAGAAAATAGAACAC
142084 CAAGGCGCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 8 0.20
48 7 0.17
49 3 0.07
50 23 0.56
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (51 bp):
TCTGTCTGCTCTTCTATATATTCGTTTATTTTCTGAAGAAAATAGAACACG
Found at i:143040 original size:16 final size:17
Alignment explanation
Indices: 143007--143058 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
142997 ATTTCAAAAG
** *
143007 GAAAAAAGTCAAAGGTT
1 GAAAAAAGAAAAAAGTT
143024 GAAAAAAG-AAAAAGTT
1 GAAAAAAGAAAAAAGTT
*
143040 GAAAAATGAAAAAAGTT
1 GAAAAAAGAAAAAAGTT
143057 GA
1 GA
143059 GCCATAACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 13 0.42
17 18 0.58
ACGTcount: A:0.62, C:0.02, G:0.21, T:0.15
Consensus pattern (17 bp):
GAAAAAAGAAAAAAGTT
Found at i:143124 original size:2 final size:2
Alignment explanation
Indices: 143106--143146 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
143096 GCCCACAAAA
*
143106 AT AT AT TT A- AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
143147 AATAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:143236 original size:42 final size:40
Alignment explanation
Indices: 143188--143314 Score: 111
Period size: 45 Copynumber: 3.1 Consensus size: 40
143178 AGAAATAAAC
*
143188 ATAAAAACATATATAAATAAATATTAATATTAAATTGAATAA
1 ATAAAAACATATATAAAT-AATATTAATATTAAA-TAAATAA
* **
143230 ATAAAAAATACATATATATAATAATAATAATAGGAAA-AAAT-A
1 AT--AAAA-ACATATATA-AATAATATTAATATTAAATAAATAA
*
143272 ATAAAAA-ATATATAAAT-ATATT-AGATTAAATAAAATAA
1 ATAAAAACATATATAAATAATATTAATATTAAAT-AAATAA
143310 ATAAA
1 ATAAA
143315 GGAAAAAAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
35 5 0.07
36 4 0.06
37 7 0.10
38 13 0.19
39 1 0.01
40 4 0.06
42 5 0.07
43 3 0.04
44 4 0.06
45 21 0.30
46 3 0.04
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (40 bp):
ATAAAAACATATATAAATAATATTAATATTAAATAAATAA
Found at i:144383 original size:3 final size:3
Alignment explanation
Indices: 144365--144410 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
144355 GCAAAAGTTG
*
144365 TAA TAA -AA TAAA TAA TAA TAA TAA T-A TAA TAA GAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
144409 TA
1 TA
144411 TTATATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:144401 original size:17 final size:16
Alignment explanation
Indices: 144366--144408 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
144356 CAAAAGTTGT
*
144366 AATAA-AATAAATAAT
1 AATAATAATAAATAAG
144381 AATAATAATATAATAAG
1 AATAATAATA-AATAAG
144398 AATAATAATAA
1 AATAATAATAA
144409 TATTATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 5 0.20
17 15 0.60
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
AATAATAATAAATAAG
Found at i:148168 original size:35 final size:34
Alignment explanation
Indices: 148083--148169 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
148073 AATATAATTT
*
148083 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
148117 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
148155 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
148170 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:148267 original size:24 final size:24
Alignment explanation
Indices: 148197--148268 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 24
148187 AAATCCAACA
* *
148197 AATTTAACAAAATAAAGTAAGTATT
1 AATTTAACAAAATAAAGTAAATA-C
* * *
148222 AA-ATAA-GAAATAAA-AAAATAC
1 AATTTAACAAAATAAAGTAAATAC
148243 AATTTAACAAAATAAAGTAAATAC
1 AATTTAACAAAATAAAGTAAATAC
148267 AA
1 AA
148269 ATATAATAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
21 2 0.06
22 7 0.19
23 14 0.39
24 11 0.31
25 2 0.06
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (24 bp):
AATTTAACAAAATAAAGTAAATAC
Found at i:149546 original size:31 final size:31
Alignment explanation
Indices: 149508--149632 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
149498 CCCGAATGAC
* * *
149508 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
149539 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
149570 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
149601 CAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
149632 C
1 C
149633 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:150456 original size:21 final size:21
Alignment explanation
Indices: 150432--150476 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
150422 TGTTGTTCGT
* *
150432 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
150453 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
150474 TTG
1 TTG
150477 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:153675 original size:31 final size:31
Alignment explanation
Indices: 153640--153751 Score: 197
Period size: 31 Copynumber: 3.6 Consensus size: 31
153630 TCAATAGATT
* *
153640 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
153671 CCGAAGGACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
153702 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
153733 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
153752 CCTCGACCCT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:154574 original size:21 final size:21
Alignment explanation
Indices: 154550--154594 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
154540 TGTTGTTCGT
* *
154550 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
154571 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
154592 TTG
1 TTG
154595 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:160465 original size:2 final size:2
Alignment explanation
Indices: 160458--160484 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
160448 TACAAATTCA
160458 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 A
160485 AAAGCTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:167464 original size:33 final size:34
Alignment explanation
Indices: 167422--167490 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
167412 CCATCAGGCC
*
167422 TGTTTCCG-AAATTTTAGTGGCACTTGAACGAAT
1 TGTTTCCGAAAATTTTAGTGGCACTCGAACGAAT
167455 TGTTTCCGAAAATTTTAGTGGCACTCGAACGAAT
1 TGTTTCCGAAAATTTTAGTGGCACTCGAACGAAT
167489 TG
1 TG
167491 AAAAATTAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 8 0.24
34 26 0.76
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (34 bp):
TGTTTCCGAAAATTTTAGTGGCACTCGAACGAAT
Found at i:175101 original size:64 final size:65
Alignment explanation
Indices: 175033--175155 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 65
175023 TTAGAACACT
* *
175033 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCC
1 TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC
*****
175097 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAA
1 TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAA
175156 TATTCAGAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 43 0.84
65 8 0.16
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (65 bp):
TGATGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC
Done.