Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007692.1 Hibiscus syriacus cultivar Beakdansim tig00109883_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: 180478
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:51 original size:33 final size:33
Alignment explanation
Indices: 1--77 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
* *
1 TTGCGATTGTCTGGTTGCGATAGTCATTTAGCG
1 TTGCGATTCTCTCGTTGCGATAGTCATTTAGCG
*
34 TTGCGATTCTCTCGTTGCGATAGTCATTTCGCG
1 TTGCGATTCTCTCGTTGCGATAGTCATTTAGCG
67 TTGCGATTCTC
1 TTGCGATTCTC
78 ATTATCTCGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.21, G:0.26, T:0.40
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGCGATAGTCATTTAGCG
Found at i:79 original size:19 final size:19
Alignment explanation
Indices: 14--102 Score: 71
Period size: 19 Copynumber: 4.9 Consensus size: 19
4 CGATTGTCTG
** *
14 GTTGCGATAGTCATTTAGC
1 GTTGCGATTCTCATTTCGC
33 GTTGCGATTCTC---T--C
1 GTTGCGATTCTCATTTCGC
**
47 GTTGCGATAGTCATTTCGC
1 GTTGCGATTCTCATTTCGC
*
66 GTTGCGATTCTCATTATCTC
1 GTTGCGATTCTCATT-TCGC
*
86 GTTGCGATTTTCATTTC
1 GTTGCGATTCTCATTTC
103 AACCAAAAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
14 11 0.20
16 1 0.02
17 1 0.02
19 26 0.46
20 17 0.30
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
GTTGCGATTCTCATTTCGC
Found at i:90 original size:20 final size:19
Alignment explanation
Indices: 43--102 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
33 GTTGCGATTC
**
43 TCTCGTTGCGATAGTCATT
1 TCTCGTTGCGATTCTCATT
*
62 TCGCGTTGCGATTCTCATT
1 TCTCGTTGCGATTCTCATT
*
81 ATCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATTCTCATT
101 TC
1 TC
103 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCTCGTTGCGATTCTCATT
Found at i:2140 original size:21 final size:21
Alignment explanation
Indices: 2116--2182 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2106 TCATTCCTCG
2116 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2137 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2158 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2179 AGAG
1 AGAG
2183 CCGATTCACA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2140 original size:42 final size:42
Alignment explanation
Indices: 2060--2182 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
2050 GCCCGACTCG
* * ** * * *
2060 CCTATCATCCCTCAAGAGTCAACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
2102 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
2144 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
2183 CCGATTCACA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:3541 original size:14 final size:14
Alignment explanation
Indices: 3522--3557 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3512 ATTGTTTAAT
3522 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3536 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3550 TGATTTGT
1 TGATTTGT
3558 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:4609 original size:22 final size:22
Alignment explanation
Indices: 4584--4627 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4574 GATTTAGATA
4584 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
4606 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
4628 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:4838 original size:20 final size:20
Alignment explanation
Indices: 4813--4862 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
4803 GATTATGTAT
*
4813 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
4833 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
4853 TATCTCGTTG
1 TATCGCGTTG
4863 GGATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:4899 original size:20 final size:20
Alignment explanation
Indices: 4793--4907 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
4783 CGCTTTGAAA
*
4793 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
4814 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
4834 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * * ** * *
4854 ATCTCGTTGGGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
4875 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
4895 ATCGCATTGCGAT
1 ATCGCATTGCGAT
4908 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.66
21 23 0.31
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:4909 original size:41 final size:41
Alignment explanation
Indices: 4833--4910 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
4823 CGAAAGTCAG
* * * *
4833 TATCGCGTTGCGAAAGTAAGTATCTCGTTGGGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
4874 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
4911 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:4926 original size:41 final size:41
Alignment explanation
Indices: 4896--4991 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
4886 ATAGTCAGTA
* * *
4896 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
4937 TCGCATTGCGAATTTCCCAATTCGTGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
4978 TCGCATTGCGAATT
1 TCGCATTGCGAATT
4992 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:4940 original size:20 final size:20
Alignment explanation
Indices: 4896--4988 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
4886 ATAGTCAGTA
* **
4896 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
4917 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
4937 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
**
4958 TCGTGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
4978 TCGCATTGCGA
1 TCGCATTGCGA
4989 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:6395 original size:35 final size:35
Alignment explanation
Indices: 6318--6397 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 35
6308 GTATTCTAAG
* * * *
6318 CCCCAAAATCCAAAATACTTCAATTACATTATAAA
1 CCCCAAATTCCAAAACACTTCAATTACATGACAAA
* * * *
6353 CCTCAAATTCCAAAACACTTCAATTATATGCCCAA
1 CCCCAAATTCCAAAACACTTCAATTACATGACAAA
6388 CCCCAAATTC
1 CCCCAAATTC
6398 ACAATCTATT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.25
Consensus pattern (35 bp):
CCCCAAATTCCAAAACACTTCAATTACATGACAAA
Found at i:9292 original size:125 final size:125
Alignment explanation
Indices: 9048--9301 Score: 359
Period size: 125 Copynumber: 2.0 Consensus size: 125
9038 CCAGTATAAG
* * *
9048 TAGGATAAAAGTCGTGATGATATAATTTACAGAGGAGATCCGAAAGAGATGCAACAAATTCAAAA
1 TAGGATAAAAGTCGCGAAGATATAATTTACAGAAGAGATCCGAAAGAGATGCAACAAATTCAAAA
* * *
9113 TAAACACTACCGATCAATTTAACCCAAAAAATCTTTACAGACCAAAGTAAAAAAATGAGAT
66 TAAACACAAACAATCAATTTAACCCAAAAAATCTTTACAGACCAAAG-AAAAAAATGAGAT
9174 TAGGATAAAAGTCGCGAAGATATAA-TTACAGAAGAGATCCGAAAGAGATGCAACAAATTCAAAA
1 TAGGATAAAAGTCGCGAAGATATAATTTACAGAAGAGATCCGAAAGAGATGCAACAAATTCAAAA
* * *
9238 TCAACTAACAAAATAATCAATTTAACCC-AAAAATCTTTACAGACCAAAATAAAAAAAATGAGAT
66 TAAAC--AC-AAACAATCAATTTAACCCAAAAAATCTTTACAGACC-AAA-GAAAAAAATGAGAT
9302 GTATGTTAGG
Statistics
Matches: 114, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
125 42 0.37
126 23 0.20
127 19 0.17
128 30 0.26
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.20
Consensus pattern (125 bp):
TAGGATAAAAGTCGCGAAGATATAATTTACAGAAGAGATCCGAAAGAGATGCAACAAATTCAAAA
TAAACACAAACAATCAATTTAACCCAAAAAATCTTTACAGACCAAAGAAAAAAATGAGAT
Found at i:11538 original size:28 final size:29
Alignment explanation
Indices: 11498--11560 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
11488 TGGCCCTCTC
* *
11498 TTTGA-ATTTCAATGTTTT-TTTTAATAG
1 TTTGAGATCTCAATGTTTTCTTTGAATAG
11525 TTTGAGATCTCAATGTTTTCTTTGAATAG
1 TTTGAGATCTCAATGTTTTCTTTGAATAG
11554 TTTGAGA
1 TTTGAGA
11561 ACGCACATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 5 0.16
28 12 0.38
29 15 0.47
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.52
Consensus pattern (29 bp):
TTTGAGATCTCAATGTTTTCTTTGAATAG
Found at i:13580 original size:20 final size:21
Alignment explanation
Indices: 13555--13599 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
13545 TCAGTGTTTT
*
13555 TTTAG-AAATTATTTTTAAAA
1 TTTAGAAAATTATTTTCAAAA
*
13575 TTTAGAAAATTGTTTTCAAAA
1 TTTAGAAAATTATTTTCAAAA
13596 TTTA
1 TTTA
13600 AAAGAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAGAAAATTATTTTCAAAA
Found at i:14474 original size:27 final size:26
Alignment explanation
Indices: 14420--14486 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
14410 ATTAACCAAT
14420 ATATTTTT-TAGAAAATTAAAAATGAA
1 ATATTTTTCT-GAAAATTAAAAATGAA
14446 AT-TGTTTTCTGAAAA-TAAAAATAGAAA
1 ATAT-TTTTCTGAAAATTAAAAAT-G-AA
14473 ATATTTTTCT-AAAA
1 ATATTTTTCTGAAAA
14487 CCAAACATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
25 8 0.22
26 16 0.44
27 11 0.31
28 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (26 bp):
ATATTTTTCTGAAAATTAAAAATGAA
Found at i:27778 original size:13 final size:13
Alignment explanation
Indices: 27757--27805 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
27747 TTAATTAATG
27757 ATATTATTTTATA
1 ATATTATTTTATA
*
27770 ATATAATTTTATGA
1 ATATTATTTTAT-A
27784 ATATTA-TTTATA
1 ATATTATTTTATA
27796 AT-TTATTTTA
1 ATATTATTTTA
27806 AAAAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 3 0.09
12 7 0.22
13 16 0.50
14 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
ATATTATTTTATA
Found at i:27812 original size:26 final size:27
Alignment explanation
Indices: 27757--27809 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
27747 TTAATTAATG
**
27757 ATATTATTTTATAATATAATTTTATGA
1 ATATTATTTTATAATATAATTTTAAAA
*
27784 ATATTA-TTTATAAT-TTATTTTAAAA
1 ATATTATTTTATAATATAATTTTAAAA
27809 A
1 A
27810 ATAAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
26 8 0.35
27 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
ATATTATTTTATAATATAATTTTAAAA
Found at i:27823 original size:20 final size:19
Alignment explanation
Indices: 27798--27845 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
27788 TATTTATAAT
27798 TTATTTTAAAAAATAAAATA
1 TTATTTTAAAAAA-AAAATA
* *
27818 TTATTTGTAATAAAAATATA
1 TTATTT-TAAAAAAAAAATA
27838 TTATTTTA
1 TTATTTTA
27846 CATATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 17 0.68
21 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTATTTTAAAAAAAAAATA
Found at i:29526 original size:26 final size:26
Alignment explanation
Indices: 29486--29540 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
29476 GGGGACGGAA
*
29486 GTGGAGGTCGGAGGAGTAGGAAGATATG
1 GTGGAGGTCGGAGGAGGAGG-AGA-ATG
29514 GTGGA-GT-GGAGGAGGAGGAGAATG
1 GTGGAGGTCGGAGGAGGAGGAGAATG
29538 GTG
1 GTG
29541 ATGCTAGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 3 0.12
26 10 0.38
27 2 0.08
28 5 0.19
ACGTcount: A:0.27, C:0.02, G:0.55, T:0.16
Consensus pattern (26 bp):
GTGGAGGTCGGAGGAGGAGGAGAATG
Found at i:29593 original size:20 final size:20
Alignment explanation
Indices: 29557--29596 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29547 GTGGGGTGAC
*
29557 CAGTCAACGGGTCAGGTAAG
1 CAGTCAACGAGTCAGGTAAG
29577 CAGTCAAC-AGTCTAGGTAAG
1 CAGTCAACGAGTC-AGGTAAG
29597 TATTTAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (20 bp):
CAGTCAACGAGTCAGGTAAG
Found at i:34358 original size:17 final size:17
Alignment explanation
Indices: 34333--34368 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34323 AATGGAAATT
* *
34333 TGAAGTTTGAAATCGCC
1 TGAAATTTGAAAACGCC
34350 TGAAATTTGAAAACGCC
1 TGAAATTTGAAAACGCC
34367 TG
1 TG
34369 GTTAGAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (17 bp):
TGAAATTTGAAAACGCC
Found at i:36842 original size:37 final size:37
Alignment explanation
Indices: 36792--36865 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
36782 AAAGTCATAA
*
36792 CTGGGCAAGTAAAATCCAACCAGCATATGTACCAGAT
1 CTGGGCAAGTAAAATCCAACCAGCATATGTAACAGAT
36829 CTGGGCAAGTAAAATCCAACCAGCATATGTAACAGAT
1 CTGGGCAAGTAAAATCCAACCAGCATATGTAACAGAT
36866 AGAGTCATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (37 bp):
CTGGGCAAGTAAAATCCAACCAGCATATGTAACAGAT
Found at i:39073 original size:14 final size:14
Alignment explanation
Indices: 39035--39096 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
39025 CGTTTGGTAA
39035 TATGTTCGTTCATT
1 TATGTTCGTTCATT
*
39049 TAT-CTCAGTTCATT
1 TATGTTC-GTTCATT
*
39063 TATGTTCGTTCGTT
1 TATGTTCGTTCATT
*
39077 TATGTGT-GTTTATT
1 TATGT-TCGTTCATT
39091 TATGTT
1 TATGTT
39097 TAGCTCAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
13 3 0.08
14 34 0.85
15 3 0.08
ACGTcount: A:0.15, C:0.11, G:0.16, T:0.58
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:39335 original size:24 final size:24
Alignment explanation
Indices: 39308--39383 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
39298 CGTTTACGCT
*
39308 TGTTCGTTTACAATTGTTTGTTTG
1 TGTTCGTTTACAATCGTTTGTTTG
39332 TGTTCGTTTACAATCGTTTGTTTG
1 TGTTCGTTTACAATCGTTTGTTTG
* * *
39356 TGTTCGTTTACATTCATTTGTTTA
1 TGTTCGTTTACAATCGTTTGTTTG
39380 TGTT
1 TGTT
39384 TGTTCATTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.13, C:0.11, G:0.18, T:0.58
Consensus pattern (24 bp):
TGTTCGTTTACAATCGTTTGTTTG
Found at i:40373 original size:22 final size:22
Alignment explanation
Indices: 40274--40365 Score: 112
Period size: 22 Copynumber: 4.2 Consensus size: 22
40264 TAAACATATA
* *
40274 AACATAAATGAACGAATTACCG
1 AACATAAACGAATGAATTACCG
* * *
40296 AATATAAACAAACGAATTACCG
1 AACATAAACGAATGAATTACCG
* *
40318 AATATAAACGAATGAATTATCG
1 AACATAAACGAATGAATTACCG
*
40340 AACATAAACGAATGGATTACCG
1 AACATAAACGAATGAATTACCG
40362 AACA
1 AACA
40366 ATCACGAACG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (22 bp):
AACATAAACGAATGAATTACCG
Found at i:41264 original size:25 final size:25
Alignment explanation
Indices: 41217--41264 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41207 TGAATGAATG
**
41217 AACTTCTAAAATTTTAGGGATAATA
1 AACTTCTAAAATTTTAGAAATAATA
*
41242 AACTTGTAAAATTTTAGAAATAA
1 AACTTCTAAAATTTTAGAAATAA
41265 AAATGATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (25 bp):
AACTTCTAAAATTTTAGAAATAATA
Found at i:42875 original size:16 final size:16
Alignment explanation
Indices: 42854--42912 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
42844 TCGGATTCGG
*
42854 ATCCGAATATTTGGAT
1 ATCCGAAAATTTGGAT
42870 ATCCGATCCGAAATTTCGGAT
1 ATCCGA----AAATTT-GGAT
*
42891 ATCCGAAAATTCGGAT
1 ATCCGAAAATTTGGAT
42907 ATCCGA
1 ATCCGA
42913 TTTTTTCGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
16 16 0.44
17 5 0.14
20 5 0.14
21 10 0.28
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (16 bp):
ATCCGAAAATTTGGAT
Found at i:42877 original size:21 final size:21
Alignment explanation
Indices: 42844--42896 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
42834 CAAAAAAAAG
*
42844 TCGGAT-TCGGATCCGAATATT
1 TCGGATATCCGATCCGAA-ATT
42865 T-GGATATCCGATCCGAAATT
1 TCGGATATCCGATCCGAAATT
42885 TCGGATATCCGA
1 TCGGATATCCGA
42897 AAATTCGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (21 bp):
TCGGATATCCGATCCGAAATT
Found at i:47113 original size:47 final size:47
Alignment explanation
Indices: 47026--47125 Score: 128
Period size: 47 Copynumber: 2.1 Consensus size: 47
47016 TATACCCAAT
* * * * * * *
47026 ATTAAAATAAAGAAATTATATAAACAATCTCTTGATTGATCTTAATG
1 ATTAAAATAAAAAAATTATATAAAAAATCTATTAAGTGATCGTAATA
*
47073 ATTAAAATAAAAAAATTATATAAAAAATTTATTAAGTGATCGTAATA
1 ATTAAAATAAAAAAATTATATAAAAAATCTATTAAGTGATCGTAATA
47120 ATTAAA
1 ATTAAA
47126 GATTAATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (47 bp):
ATTAAAATAAAAAAATTATATAAAAAATCTATTAAGTGATCGTAATA
Found at i:53610 original size:16 final size:16
Alignment explanation
Indices: 53563--53611 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
53553 AATCCCTTGA
*
53563 ATTTAGTGTCAATTTGC
1 ATTT-GTGTCAATTTGT
*
53580 ATTTGAGTCAA--TGT
1 ATTTGTGTCAATTTGT
53594 ATTTGTGTCAATTTGT
1 ATTTGTGTCAATTTGT
53610 AT
1 AT
53612 GTATATAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 12 0.44
16 11 0.41
17 4 0.15
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.49
Consensus pattern (16 bp):
ATTTGTGTCAATTTGT
Found at i:60795 original size:23 final size:23
Alignment explanation
Indices: 60760--60807 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
60750 ATCAAGTACA
*
60760 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
60783 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
60806 AT
1 AT
60808 TGACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:61128 original size:20 final size:20
Alignment explanation
Indices: 61078--61129 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
61068 TGGGTAGCGC
61078 TTTACCTGTTTTGTCATTTA
1 TTTACCTGTTTTGTCATTTA
** * *
61098 TAGACCGGTTTTGTCATTTT
1 TTTACCTGTTTTGTCATTTA
61118 TTTACCTGTTTT
1 TTTACCTGTTTT
61130 ATTGTTATGG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTACCTGTTTTGTCATTTA
Found at i:61320 original size:182 final size:182
Alignment explanation
Indices: 61070--61899 Score: 1327
Period size: 182 Copynumber: 4.6 Consensus size: 182
61060 CATGTTTCTG
*
61070 GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTTTATTGT
1 GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGT
* *
61135 TATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAA
66 TATGGATCGATACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAA
* *
61200 ATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTTTCAATATATCC
131 ATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCC
* * ** * * *
61252 GGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCGTTTTTGTCATATTTTTAACTGTTATATTGT
1 GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGT
*
61317 TATGGATCGATACATTTTTATAAAGTATCGTCACTTTATTAGCGCTATAACTTCTTCTCTTTTAA
66 TATGGATCGATACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAA
61382 ATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCC
131 ATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCC
*
61434 GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACCTGTTATATTGT
1 GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGT
* * *
61499 TATGGATCGATACATTTTTATAAAGTATCGACATTTTATTAGCACTATAACTTCTTTTCTTTTAA
66 TATGGATCGATACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAA
* * *
61564 ATTCCAAAAGTGTCTATACTTATAATAAAATATCGACACTTTCAACATATCC
131 ATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCC
* * * ** * *
61616 GATAGCTCTTTACCGGTTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACCTGTTATATTGT
1 GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGT
** * *
61681 TATGGATTAATACATTTTTATAAAGTATCAACACTTTATTAGCGCTATAACTTATTCTCTTTTAA
66 TATGGATCGATACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAA
* * *
61746 ATTCTAAAAGTGTCGATAGTTATAATAAAGTATCGACACTATCAACATATTC
131 ATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCC
* *
61798 GATAGCGCTTTACCTGTTTTATCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGT
1 GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGT
*
61863 TATGGATCAATACATTTTTATAAAGTATCGACACTTT
66 TATGGATCGATACATTTTTATAAAGTATCGACACTTT
61900 CAATATATCC
Statistics
Matches: 591, Mismatches: 57, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
182 591 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGT
TATGGATCGATACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAA
ATTCCAAAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCC
Found at i:62009 original size:111 final size:112
Alignment explanation
Indices: 61770--62230 Score: 746
Period size: 111 Copynumber: 4.1 Consensus size: 112
61760 GATAGTTATA
* * * *
61770 ATAAAGTATCGACACTATCAACATATTCGATAGCGCTTTACCTGTTTTATCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
61835 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* *
61882 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGATTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
61947 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* * * *
61993 ATAAAGTATCGACACTTTTAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
62058 TTTGTCA-TTTTTTACCTGTTTTATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
**
62104 ATAAAGTATCGACACTTTCAATATATCTAATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
62169 TTTGTCATTTTTTTAACTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
*
62216 ATAGAGTATCGACAC
1 ATAAAGTATCGACAC
62231 AAACCGACAA
Statistics
Matches: 325, Mismatches: 23, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
111 208 0.64
112 117 0.36
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
Found at i:63622 original size:83 final size:82
Alignment explanation
Indices: 63535--63739 Score: 234
Period size: 82 Copynumber: 2.5 Consensus size: 82
63525 CGTAATAGAA
63535 TGGTAATTTAGCGGCGTTTATAGCTA-AAACGCCACAATAGAT-TTGTTTATAGTGGCGTTTCTT
1 TGGTAATTTAGCGGCGTTTATA--TACAAACGCCACAATAG-TGTTGTTTATAGTGGCGTTTCTT
* *
63598 CAACAAATGCCGCAACATAG
63 CAACAAACGACGCAACATAG
* *** * *
63618 TGGTAATTTAGCGGCGTTTTTATACAAACGCCGTTATTGTGTTGTTTATAGTGGCGTTTGTTCAA
1 TGGTAATTTAGCGGCGTTTATATACAAACGCCACAATAGTGTTGTTTATAGTGGCGTTTCTTCAA
* *
63683 CAAACGACGCTATATAG
66 CAAACGACGCAACATAG
** * *
63700 AAGTAATTTAGCGGCGTTTATGAAACAAACGCCGCAATAG
1 TGGTAATTTAGCGGCGTTTAT-ATACAAACGCCACAATAG
63740 AGTATTTATT
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
81 3 0.03
82 64 0.63
83 35 0.34
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (82 bp):
TGGTAATTTAGCGGCGTTTATATACAAACGCCACAATAGTGTTGTTTATAGTGGCGTTTCTTCAA
CAAACGACGCAACATAG
Found at i:64233 original size:22 final size:22
Alignment explanation
Indices: 64207--64256 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
64197 AAGTGTTTTG
64207 TTGCTTTCGAATAGAAAAATAA
1 TTGCTTTCGAATAGAAAAATAA
* *
64229 TTGCTTTCTAATAGGAAAATAA
1 TTGCTTTCGAATAGAAAAATAA
*
64251 TAGCTT
1 TTGCTT
64257 CTGAAAACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TTGCTTTCGAATAGAAAAATAA
Found at i:65472 original size:42 final size:43
Alignment explanation
Indices: 65425--65515 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 43
65415 GTTTGGTGGT
* * *
65425 GTTTTTAAAAAAAATGTTACAATAGGGTTAATTTATAGCGGC-
1 GTTTTTAAAAAAAATATCACAATAGGGTTAATTTATAGCAGCG
** ** *
65467 GTTTTTACTAAAAATATCGTAATAGGGTTAGTTTATAGCAGCG
1 GTTTTTAAAAAAAATATCACAATAGGGTTAATTTATAGCAGCG
65510 GTTTTT
1 GTTTTT
65516 GATTAAACGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 34 0.85
43 6 0.15
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.40
Consensus pattern (43 bp):
GTTTTTAAAAAAAATATCACAATAGGGTTAATTTATAGCAGCG
Found at i:66929 original size:22 final size:22
Alignment explanation
Indices: 66904--66946 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
66894 ATGTATGTAT
*
66904 ATGTAAATTAAGCTTATGATAA
1 ATGTAAATTAAGCTTAGGATAA
66926 ATGTAAATTAAGCTTAGGATA
1 ATGTAAATTAAGCTTAGGATA
66947 TATAATTACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (22 bp):
ATGTAAATTAAGCTTAGGATAA
Found at i:74309 original size:23 final size:23
Alignment explanation
Indices: 74242--74310 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
74232 CACCACAGGT
* *
74242 CGTATAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
74265 CATAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
74288 CGTAGAAATGCACCGAAATGCCA
1 CGTAGAAATGCACCGAAGTGCCA
74311 TATAATATGT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:78703 original size:19 final size:19
Alignment explanation
Indices: 78681--78717 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
78671 TTCATTCTTA
78681 TGGGAATCTCACATTCCCC
1 TGGGAATCTCACATTCCCC
78700 TGGGAATCTCACATTCCC
1 TGGGAATCTCACATTCCC
78718 ATGACCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.27
Consensus pattern (19 bp):
TGGGAATCTCACATTCCCC
Found at i:80880 original size:33 final size:34
Alignment explanation
Indices: 80838--80919 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 34
80828 GTCCAACACT
* * *
80838 GCCTTGGGCTGAGGC-CGCCGCACACCAAGGGTC
1 GCCTAGGGCTGAGGCTCGCCACACACCAAAGGTC
*
80871 GCCTAGGGCTGA-GCTCGCCATACACCAAAGGTC
1 GCCTAGGGCTGAGGCTCGCCACACACCAAAGGTC
** *
80904 ATCTAGGGCCGAGGCT
1 GCCTAGGGCTGAGGCT
80920 GACACACTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 2 0.05
33 35 0.88
34 3 0.08
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.15
Consensus pattern (34 bp):
GCCTAGGGCTGAGGCTCGCCACACACCAAAGGTC
Found at i:81593 original size:19 final size:19
Alignment explanation
Indices: 81571--81609 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
81561 GAAAAGAGAA
* *
81571 ATTATATAAAAAATGAAAT
1 ATTAAATAAAAAATAAAAT
*
81590 ATTAAATTAAAAATAAAAT
1 ATTAAATAAAAAATAAAAT
81609 A
1 A
81610 AAATGTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
ATTAAATAAAAAATAAAAT
Found at i:82349 original size:20 final size:21
Alignment explanation
Indices: 82319--82365 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
82309 TCAAATGACC
*
82319 GAAAAACGTGCCACAAAAATA
1 GAAAAACGTGCCACAAAAACA
*
82340 GAAAAA-GTGCCACAAAGACA
1 GAAAAACGTGCCACAAAAACA
82360 GAAAAA
1 GAAAAA
82366 TATGTCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.60, C:0.17, G:0.17, T:0.06
Consensus pattern (21 bp):
GAAAAACGTGCCACAAAAACA
Found at i:83251 original size:14 final size:14
Alignment explanation
Indices: 83232--83261 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
83222 ATTCATTTAC
83232 AGTCCTATTTCTTG
1 AGTCCTATTTCTTG
83246 AGTCCTATTTCTTG
1 AGTCCTATTTCTTG
83260 AG
1 AG
83262 GTACTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.47
Consensus pattern (14 bp):
AGTCCTATTTCTTG
Found at i:85196 original size:35 final size:34
Alignment explanation
Indices: 85157--85272 Score: 87
Period size: 35 Copynumber: 3.4 Consensus size: 34
85147 AATATTTCAA
85157 ATTAAAAGGTATTTATTATATATTTAACTTTGAAT
1 ATTAAAAGGTATTTATTATATATTTAA-TTTGAAT
* *
85192 ATTAAAA--TA-TAATTATATCATTTTGAATATTTAA-
1 ATTAAAAGGTATTTATTATAT-A-TTT-AAT-TTGAAT
* * * *
85226 GTTAAAAGATATTTATTATCTCTTTAAGTTTGAAT
1 ATTAAAAGGTATTTATTATATATTTAA-TTTGAAT
*
85261 ATTGAAAGGTAT
1 ATTAAAAGGTAT
85273 CTATATCTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
32 8 0.13
33 3 0.05
34 16 0.26
35 26 0.42
36 2 0.03
37 7 0.11
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (34 bp):
ATTAAAAGGTATTTATTATATATTTAATTTGAAT
Found at i:85239 original size:69 final size:69
Alignment explanation
Indices: 85142--85340 Score: 233
Period size: 69 Copynumber: 2.9 Consensus size: 69
85132 TAATTACTCT
* * * *
85142 TTTTAAATATTTCAAATTAAAAGGTATTTATTATATATTTAACTTTGAATATTAAAATATAAT-T
1 TTTTGAATATTTCAAATTAAAAGATATTTATTATATATTTAAATTTGAATATTAAAAGAT-ATCT
85206 ATATC
65 ATATC
* * * * * *
85211 ATTTTGAATATTT-AAGTTAAAAGATATTTATTATCTCTTTAAGTTTGAATATTGAAAGGTATCT
1 -TTTTGAATATTTCAAATTAAAAGATATTTATTATATATTTAAATTTGAATATTAAAAGATATCT
85275 ATATC
65 ATATC
* * * *
85280 TTTTGAATATTTCAAATTAAAATATA-TTATTGTATGTTTAAATTTGATTATTAAAAGATAT
1 TTTTGAATATTTCAAATTAAAAGATATTTATTATATATTTAAATTTGAATATTAAAAGATAT
85341 ATTTTGAGTA
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
68 42 0.39
69 56 0.51
70 11 0.10
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (69 bp):
TTTTGAATATTTCAAATTAAAAGATATTTATTATATATTTAAATTTGAATATTAAAAGATATCTA
TATC
Found at i:85326 original size:68 final size:69
Alignment explanation
Indices: 85113--85339 Score: 221
Period size: 69 Copynumber: 3.3 Consensus size: 69
85103 TATCTTTTCT
* * * * *
85113 AATTTGAATATTAGTAGGATAATTA-CTCTTTTTAAATATTTCAAATTAAAAGGTAT-TTATTAT
1 AATTTGAATATTA-AAAGATAATTATATCATTTTGAATATTTCAAATTAAAA--TATATTATTAT
85176 ATATTTA
63 ATATTTA
* * * * *
85183 ACTTTGAATATTAAAATATAATTATATCATTTTGAATATTT-AAGTTAAAAGATATTTATTATCT
1 AATTTGAATATTAAAAGATAATTATATCATTTTGAATATTTCAAATTAAAATATA-TTATTATAT
*
85247 CTTTA
65 ATTTA
* * * *
85252 AGTTTGAATATTGAAAGGT-ATCTATATC-TTTTGAATATTTCAAATTAAAATATATTATTGTAT
1 AATTTGAATATTAAAAGATAAT-TATATCATTTTGAATATTTCAAATTAAAATATATTATTATAT
*
85315 GTTTA
65 ATTTA
*
85320 AATTTGATTATTAAAAGATA
1 AATTTGAATATTAAAAGATA
85340 TATTTTGAGT
Statistics
Matches: 127, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
67 2 0.02
68 40 0.31
69 60 0.47
70 25 0.20
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (69 bp):
AATTTGAATATTAAAAGATAATTATATCATTTTGAATATTTCAAATTAAAATATATTATTATATA
TTTA
Found at i:88507 original size:21 final size:20
Alignment explanation
Indices: 88466--88521 Score: 96
Period size: 21 Copynumber: 2.8 Consensus size: 20
88456 TTCATTCTTA
88466 TGGGAATCTCACATT-CCCC
1 TGGGAATCTCACATTCCCCC
88485 TGGGAATCTCACATTCCCCCC
1 TGGGAATCTCACATT-CCCCC
88506 TGGGAATCTCACATTC
1 TGGGAATCTCACATTC
88522 TCCTAACTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.43
20 1 0.03
21 19 0.54
ACGTcount: A:0.21, C:0.36, G:0.16, T:0.27
Consensus pattern (20 bp):
TGGGAATCTCACATTCCCCC
Found at i:92074 original size:36 final size:36
Alignment explanation
Indices: 92027--92132 Score: 194
Period size: 36 Copynumber: 2.9 Consensus size: 36
92017 TTTGTGATTT
*
92027 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
1 CATCGACACTTCCGATTCAAGTCGAACGGAAGGAAG
*
92063 CATCGACACTTCCGATTCAAGTCGAACGGAAGAAAG
1 CATCGACACTTCCGATTCAAGTCGAACGGAAGGAAG
92099 CATCGACACTTCCGATTCAAGTCGAACGGAAGGA
1 CATCGACACTTCCGATTCAAGTCGAACGGAAGGA
92133 GACGACACAC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (36 bp):
CATCGACACTTCCGATTCAAGTCGAACGGAAGGAAG
Found at i:96299 original size:6 final size:6
Alignment explanation
Indices: 96288--96350 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
96278 GACAGTTGCA
* * * *
96288 GGAGCC GGAGCC GGAGCT GGAGCT GGAGCC GGAGCC GGAGCT GGAGCT
1 GGAGCC GGAGCC GGAGCC GGAGCC GGAGCC GGAGCC GGAGCC GGAGCC
* *
96336 GGAACC GGAACC GGA
1 GGAGCC GGAGCC GGA
96351 ACTGATCTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.21, C:0.25, G:0.48, T:0.06
Consensus pattern (6 bp):
GGAGCC
Found at i:96320 original size:24 final size:24
Alignment explanation
Indices: 96288--96350 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
96278 GACAGTTGCA
96288 GGAGCCGGAGCCGGAGCTGGAGCT
1 GGAGCCGGAGCCGGAGCTGGAGCT
96312 GGAGCCGGAGCCGGAGCTGGAGCT
1 GGAGCCGGAGCCGGAGCTGGAGCT
* *
96336 GGAACCGGAACCGGA
1 GGAGCCGGAGCCGGA
96351 ACTGATCTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.48, T:0.06
Consensus pattern (24 bp):
GGAGCCGGAGCCGGAGCTGGAGCT
Found at i:98461 original size:3 final size:3
Alignment explanation
Indices: 98453--98487 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
98443 TTATTTTAAT
*
98453 TTA TTA TTA TTA TTA TT- TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
98488 CAAATTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:98474 original size:17 final size:17
Alignment explanation
Indices: 98437--98486 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
98427 ATCTTTTCTA
*
98437 TTTATT-TTATT-TTAA
1 TTTATTATTATTATTAT
98452 TTTATTATTATTATTAT
1 TTTATTATTATTATTAT
*
98469 TTTATTAATATTATTAT
1 TTTATTATTATTATTAT
98486 T
1 T
98487 ACAAATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.19
16 5 0.16
17 20 0.65
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTATTATTATTAT
Found at i:101688 original size:32 final size:28
Alignment explanation
Indices: 101656--101709 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
101646 ACATGTACTA
* *
101656 ACTAAATTCTTTTCTTTTGTTTGTGTAC
1 ACTAACTTATTTTCTTTTGTTTGTGTAC
101684 ACTAACTTATTTTCTTTTGTTTGTGT
1 ACTAACTTATTTTCTTTTGTTTGTGT
101710 CATTTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (28 bp):
ACTAACTTATTTTCTTTTGTTTGTGTAC
Found at i:103687 original size:25 final size:25
Alignment explanation
Indices: 103659--103708 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
103649 AAGTGGGAAG
*
103659 ATCAAACCAAAACAAAGAGAAAAGA
1 ATCAAACAAAAACAAAGAGAAAAGA
* *
103684 ATCAAAGAAAAACAAAGAGCAAAGA
1 ATCAAACAAAAACAAAGAGAAAAGA
103709 GAAAAGGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.68, C:0.14, G:0.14, T:0.04
Consensus pattern (25 bp):
ATCAAACAAAAACAAAGAGAAAAGA
Found at i:103737 original size:30 final size:31
Alignment explanation
Indices: 103669--103744 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
103659 ATCAAACCAA
* *
103669 AACAAAGAGAAAAGAATCAAAGAAAAACAAAG
1 AACAAAGAGAAAAG-AGCAAAGAAAAACAAAC
*
103701 AGCAAAGAGAAAAG-GCAAAGAAAGAA-AAAC
1 AACAAAGAGAAAAGAGCAAAGAAA-AACAAAC
103731 AACAAAGA-AAAAGA
1 AACAAAGAGAAAAGA
103745 AAAAACAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 5 0.13
30 18 0.47
31 2 0.05
32 13 0.34
ACGTcount: A:0.71, C:0.09, G:0.18, T:0.01
Consensus pattern (31 bp):
AACAAAGAGAAAAGAGCAAAGAAAAACAAAC
Found at i:103743 original size:23 final size:23
Alignment explanation
Indices: 103717--103769 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
103707 GAGAAAAGGC
*
103717 AAAGAAAGAA-AAACAACAAAGAA
1 AAAGAAAAAACAAACAA-AAAGAA
*
103740 AAAGAAAAAACAAAGAAAAAGAA
1 AAAGAAAAAACAAACAAAAAGAA
103763 AAAGAAA
1 AAAGAAA
103770 TAAAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAACAAACAAAAAGAA
Found at i:103746 original size:34 final size:34
Alignment explanation
Indices: 103687--103819 Score: 91
Period size: 33 Copynumber: 4.0 Consensus size: 34
103677 GAAAAGAATC
* * **
103687 AAAGAAAAACAAAGAGCAAAGAGAAAAGGCAAAG
1 AAAGAAAAACAAAAAGCAAAAAGAAAAAACAAAG
103721 AAAGAAAAACAACAAAG-AAAAAGAAAAAACAAAG
1 AAAGAAAAACAA-AAAGCAAAAAGAAAAAACAAAG
* *
103755 AAA-AAGAAA-AAGAAA-TAAAGAA-AAAAATCAAAG
1 AAAGAA-AAACAA-AAAGCAAA-AAGAAAAAACAAAG
* * *
103788 AAA-AAAGAAC-AAAAGAAAAAACAAAGAACAAA
1 AAAGAAA-AACAAAAAGCAAAAAGAAAAAACAAA
103820 AAGAGGACAA
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
32 6 0.07
33 39 0.48
34 34 0.41
35 3 0.04
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.02
Consensus pattern (34 bp):
AAAGAAAAACAAAAAGCAAAAAGAAAAAACAAAG
Found at i:103750 original size:20 final size:19
Alignment explanation
Indices: 103691--103815 Score: 84
Period size: 17 Copynumber: 6.6 Consensus size: 19
103681 AGAATCAAAG
* *
103691 AAAAACAAAGAGCAAAGAGA
1 AAAAACAAAGA-AAAAGAAA
**
103711 AAAGGCAAAG--AAAGAAA
1 AAAAACAAAGAAAAAGAAA
*
103728 AACAACAAAGAAAAAG--A
1 AAAAACAAAGAAAAAGAAA
103745 AAAAACAAAGAAAAAGAAA
1 AAAAACAAAGAAAAAGAAA
*
103764 AAGAAATAAAGAAAAA-AATCA
1 AA-AAACAAAGAAAAAGAA--A
*
103785 AAGAAA-AAAGAACAAA-AGA
1 AA-AAACAAAGAA-AAAGAAA
103804 AAAAACAAAGAA
1 AAAAACAAAGAA
103816 CAAAAAGAGG
Statistics
Matches: 87, Mismatches: 9, Indels: 19
0.76 0.08 0.17
Matches are distributed among these distances:
17 29 0.33
18 3 0.03
19 18 0.21
20 26 0.30
21 11 0.13
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAACAAAGAAAAAGAAA
Found at i:103781 original size:23 final size:25
Alignment explanation
Indices: 103747--103815 Score: 61
Period size: 28 Copynumber: 2.7 Consensus size: 25
103737 GAAAAAGAAA
*
103747 AAACAAAGAA-AAAGAAAAAGAAAT
1 AAACAAAAAACAAAGAAAAAGAAAT
*
103771 AAAGAAAAAAATCAAAGAAAAAAGAACA-
1 AAA-CAAAAAA-CAAAG-AAAAAGAA-AT
*
103799 AAAGAAAAAACAAAGAA
1 AAACAAAAAACAAAGAA
103816 CAAAAAGAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 3 0.08
25 7 0.19
26 5 0.14
27 10 0.27
28 11 0.30
29 1 0.03
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.03
Consensus pattern (25 bp):
AAACAAAAAACAAAGAAAAAGAAAT
Found at i:103803 original size:8 final size:7
Alignment explanation
Indices: 103721--103808 Score: 65
Period size: 7 Copynumber: 12.4 Consensus size: 7
103711 AAAGGCAAAG
103721 AAAG-AA
1 AAAGAAA
* *
103727 AAACAAC
1 AAAGAAA
103734 AAAG-AA
1 AAAGAAA
103740 AAAGAAA
1 AAAGAAA
*
103747 AAACAAA
1 AAAGAAA
*
103754 GAAAAAGAA
1 -AAAGA-AA
103763 AAAGAAA
1 AAAGAAA
103770 TAAAGAAA
1 -AAAGAAA
**
103778 AAA-ATC
1 AAAGAAA
103784 AAAGAAA
1 AAAGAAA
103791 AAAGAACA
1 AAAGAA-A
103799 AAAGAAA
1 AAAGAAA
103806 AAA
1 AAA
103809 CAAAGAACAA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
6 12 0.19
7 28 0.44
8 22 0.34
9 2 0.03
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:103820 original size:13 final size:12
Alignment explanation
Indices: 103721--103821 Score: 66
Period size: 13 Copynumber: 7.9 Consensus size: 12
103711 AAAGGCAAAG
103721 AAAGAAAAACAAC
1 AAAGAAAAA-AAC
103734 AAAGAAAAAGAA-
1 AAAGAAAAA-AAC
*
103746 AAA-ACAAAGAA-
1 AAAGA-AAAAAAC
*
103757 AAAGAAAAAGAAAT
1 AAAG-AAAA-AAAC
103771 AAAGAAAAAAATC
1 AAAGAAAAAAA-C
103784 AAAGAAAAAAGAAC
1 AAAG-AAAAA-AAC
103798 AAA-AGAAAAAAC
1 AAAGA-AAAAAAC
103810 AAAGAACAAAAA
1 AAAGAA-AAAAA
103822 GAGGACAAAG
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
11 6 0.08
12 20 0.27
13 32 0.44
14 13 0.18
15 2 0.03
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAGAAAAAAAC
Found at i:103823 original size:20 final size:19
Alignment explanation
Indices: 103687--103823 Score: 90
Period size: 20 Copynumber: 7.3 Consensus size: 19
103677 GAAAAGAATC
*
103687 AAAG-AAAAACAAAGAGCAA
1 AAAGAAAAAACAAAGA-AAA
* **
103706 AGAGAAAAGGCAAAG-AAA
1 AAAGAAAAAACAAAGAAAA
* *
103724 GAA-AAACAACAAAG--AA
1 AAAGAAAAAACAAAGAAAA
103740 AAAGAAAAAACAAAGAAAA
1 AAAGAAAAAACAAAGAAAA
*
103759 AGAA-AAAGAAATAAAGAAAA
1 A-AAGAAA-AAACAAAGAAAA
* *
103779 AAATCAAAGAAA-AAAGAACA
1 AAA-GAAA-AAACAAAGAAAA
103799 AAAGAAAAAACAAAGAACAA
1 AAAGAAAAAACAAAGAA-AA
103819 AAAGA
1 AAAGA
103824 GGACAAAGAG
Statistics
Matches: 93, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
16 4 0.04
17 18 0.19
18 6 0.06
19 20 0.22
20 38 0.41
21 7 0.08
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (19 bp):
AAAGAAAAAACAAAGAAAA
Found at i:104719 original size:23 final size:23
Alignment explanation
Indices: 104685--104750 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
104675 CGAAAGGGGC
104685 AATA-TTTTCAAACTTTTGATTA
1 AATATTTTTCAAACTTTTGATTA
104707 AATATTTTTCAAAACTTTT--TTA
1 AATATTTTTC-AAACTTTTGATTA
* *
104729 ATTGATATTTTCATACTTTTGA
1 AAT-AT-TTTTCAAACTTTTGA
104751 AAATACAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 9 0.25
23 14 0.39
24 13 0.36
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (23 bp):
AATATTTTTCAAACTTTTGATTA
Found at i:104739 original size:24 final size:24
Alignment explanation
Indices: 104686--104741 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
104676 GAAAGGGGCA
104686 ATATTTTC-AAACTTTTGATTAAAT
1 ATATTTTCAAAACTTTT-ATTAAAT
*
104710 AT-TTTTCAAAACTTTT-TTAATT
1 ATATTTTCAAAACTTTTATTAAAT
104732 GATATTTTCA
1 -ATATTTTCA
104742 TACTTTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 5 0.18
23 7 0.25
24 16 0.57
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATTTTCAAAACTTTTATTAAAT
Found at i:104900 original size:33 final size:33
Alignment explanation
Indices: 104858--104939 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
104848 ATAATCAGTG
* *
104858 TTGAAGCAATCAACATCGAATATTGGGGCATCT
1 TTGAAGCAATCAACATCGAACATTAGGGCATCT
*
104891 TTGAAGCAATCAACATCGAACGTTAGGGCATCT
1 TTGAAGCAATCAACATCGAACATTAGGGCATCT
* *
104924 TTGGAG-ATTCAACATC
1 TTGAAGCAATCAACATC
104940 TTGATGCGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 9 0.20
33 35 0.80
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (33 bp):
TTGAAGCAATCAACATCGAACATTAGGGCATCT
Found at i:105270 original size:36 final size:35
Alignment explanation
Indices: 105230--105329 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 35
105220 TCGTTTTCAC
*
105230 AAAAACAAACTTTGTCTCGCTTAAGACAATTTCTCT
1 AAAAACAAA-TTTGTCTCGCTTAAGACAATTTATCT
105266 AAAAACAAATTTTGTCTCGCTTAAGACAATTTATCT
1 AAAAACAAA-TTTGTCTCGCTTAAGACAATTTATCT
* * *
105302 CAAAGCAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAATTT-GTCTCGCTTAAGACA
105330 TTTTTTTCTC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 3 0.05
36 55 0.95
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (35 bp):
AAAAACAAATTTGTCTCGCTTAAGACAATTTATCT
Found at i:105294 original size:21 final size:20
Alignment explanation
Indices: 105234--105294 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
105224 TTTCACAAAA
105234 ACAAACTTTGTCTCGCTTAAG
1 ACAAA-TTTGTCTCGCTTAAG
* *
105255 AC-AA-TT-TCT--CTAAAA
1 ACAAATTTGTCTCGCTTAAG
105270 ACAAATTTTGTCTCGCTTAAG
1 ACAAA-TTTGTCTCGCTTAAG
105291 ACAA
1 ACAA
105295 TTTATCTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 6 0.20
16 2 0.07
17 3 0.10
18 4 0.13
19 3 0.10
20 2 0.07
21 10 0.33
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ACAAATTTGTCTCGCTTAAG
Found at i:105772 original size:31 final size:31
Alignment explanation
Indices: 105737--105815 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
105727 CCTTGAGGCA
105737 GTTTCT-TTGGAAACACAAA-ATCTTTGAGTTT
1 GTTTCTCTT-GAAACA-AAACATCTTTGAGTTT
*
105768 GTTTCTCTTGAAACAAAACCATCTTTGAG-TC
1 GTTTCTCTTGAAACAAAA-CATCTTTGAGTTT
*
105799 GTTTCCCTTGAAACAAA
1 GTTTCTCTTGAAACAAA
105816 TTTGTCTCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 3 0.07
31 29 0.67
32 11 0.26
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (31 bp):
GTTTCTCTTGAAACAAAACATCTTTGAGTTT
Found at i:105797 original size:32 final size:31
Alignment explanation
Indices: 105756--105815 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
105746 GAAACACAAA
* *
105756 ATCTTTGAGTTTGTTTCTCTTGAAACAAAACC
1 ATCTTTGAG-TCGTTTCCCTTGAAACAAAACC
105788 ATCTTTGAGTCGTTTCCCTTGAAACAAA
1 ATCTTTGAGTCGTTTCCCTTGAAACAAA
105816 TTTGTCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (31 bp):
ATCTTTGAGTCGTTTCCCTTGAAACAAAACC
Found at i:105876 original size:95 final size:98
Alignment explanation
Indices: 105682--105876 Score: 220
Period size: 97 Copynumber: 2.0 Consensus size: 98
105672 TATTTCTATT
* *
105682 AAAACCAACCTTTGAGATCGTTTCCATTGAAACAAATTTTGTCTCCCTTGAGGCAGTTTCTTTGG
1 AAAACCAACCTTTGAGATCGTTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTTTGG
* ** *
105747 AAACACAAAATCTTTGAGTTTGTTTCTCTTGAAAC
66 AAACAC--AACCTTTGAGTCGGTTTCCCTTGAAAC
* * * *
105782 AAAACC-ATCTTTGAG-TCGTTTCCCTTGAAACAAA-TTTGTCT-CTTTCGAGACAGCTTCTTTT
1 AAAACCAACCTTTGAGATCGTTTCCATTGAAACAAATTTTGTCTCCCTT-GAGACAGCTTCTTTG
*
105843 GAAGCATC-ACCTTTGAGTCGGTTTCCCTTGAAAC
65 GAAACA-CAACCTTTGAGTCGGTTTCCCTTGAAAC
105877 CATCATTCCA
Statistics
Matches: 82, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
95 22 0.27
96 3 0.04
97 24 0.29
98 19 0.23
99 8 0.10
100 6 0.07
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (98 bp):
AAAACCAACCTTTGAGATCGTTTCCATTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTTTGG
AAACACAACCTTTGAGTCGGTTTCCCTTGAAAC
Found at i:106241 original size:130 final size:128
Alignment explanation
Indices: 105878--106264 Score: 429
Period size: 134 Copynumber: 2.9 Consensus size: 128
105868 CCTTGAAACC
* * *
105878 ATCATTCCAAAATATGGTCAGTCATCCTCATCGTGTAGGAACCGTGTCATCTCCCGACCATACCT
1 ATCATTCCTAAAGATGGTCAGTC-TCCTCATCGTGTAGGAACC-TGTCATC-CCCGACCAAACCT
* * * * * * *
105943 CTTCATCACGTCGGAGCCGTGTCAACCCTAGATAACTAGCCGTCCTTATCGCGTAGGAACCGTGT
63 CATCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTAGGAAACGTGT
106008 T
128 T
* * * * *
106009 ATCGTCATTCCTAAAGATGGTCAGAACTCTTCATCATGTATGAGACGC-GTCATCCCTCGACCAG
1 A---TCATTCCTAAAGATGGTCAG-TCTCCTCATCGTGTAGGA-AC-CTGTCATCCC-CGACCAA
* *
106073 ACCTCATCATCACGTAGGAGCCGTGTCACCCCT-GATAACCAGTCGTCCTCATCACGTAGGAAAT
59 ACCTCATCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTAGGAAAC
106137 GTGTT
124 GTGTT
* *
106142 ATCATTCCTAAAGATGG-CATGTCGTCCTCATCGCGTAGGAACCATATCATCCCCGACCAAACCT
1 ATCATTCCTAAAGATGGTCA-GTC-TCCTCATCGTGTAGGAACC-TGTCATCCCCGACCAAACCT
* * * *
106206 CCTCATCACATAAGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGTGTAGGAA
63 CATCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTAGGAA
106265 CTGATTTATC
Statistics
Matches: 216, Mismatches: 28, Indels: 25
0.80 0.10 0.09
Matches are distributed among these distances:
128 1 0.00
129 41 0.19
130 63 0.29
131 1 0.00
133 33 0.15
134 73 0.34
135 3 0.01
136 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (128 bp):
ATCATTCCTAAAGATGGTCAGTCTCCTCATCGTGTAGGAACCTGTCATCCCCGACCAAACCTCAT
CATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTAGGAAACGTGTT
Found at i:109570 original size:23 final size:23
Alignment explanation
Indices: 109525--109571 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
109515 TCATTAGTAA
*
109525 ATTAATATTTGATCTATTAATCG
1 ATTAATATTTGATATATTAATCG
* * *
109548 ATTAGTATTTGATATGTTGATCG
1 ATTAATATTTGATATATTAATCG
109571 A
1 A
109572 GTTGTCATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (23 bp):
ATTAATATTTGATATATTAATCG
Found at i:109878 original size:3 final size:3
Alignment explanation
Indices: 109872--109990 Score: 202
Period size: 3 Copynumber: 39.7 Consensus size: 3
109862 TTTTTATCCA
* *
109872 TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
109920 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
109968 TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
109991 AATATATTAA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 108 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:112139 original size:18 final size:17
Alignment explanation
Indices: 112116--112166 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
112106 TTCTTTTCAA
112116 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
112133 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
112151 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
112167 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 17 0.63
19 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:112188 original size:13 final size:15
Alignment explanation
Indices: 112157--112193 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
112147 TTATATGTTT
112157 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
112172 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
112185 TA-TTTATTT
1 TATTTTATTT
112194 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:124812 original size:20 final size:20
Alignment explanation
Indices: 124787--124839 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
124777 TCCGAATTCG
124787 CAATGCGAATATGTAAATCA
1 CAATGCGAATATGTAAATCA
*
124807 CAATGCGAATATGTAAATCG
1 CAATGCGAATATGTAAATCA
* *
124827 TAATGCGATTATG
1 CAATGCGAATATG
124840 ACTATCGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (20 bp):
CAATGCGAATATGTAAATCA
Found at i:124907 original size:20 final size:20
Alignment explanation
Indices: 124831--124910 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
124821 AAATCGTAAT
* *
124831 GCGATTATGACTATCGCAAT
1 GCGATTCTGACTATCGCAAC
*
124851 GCGATTCTGACTATCTCAAC
1 GCGATTCTGACTATCGCAAC
124871 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
* *
124891 GAGATTCTGACTGTCGCAAC
1 GCGATTCTGACTATCGCAAC
124911 ACTGAATTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAC
Found at i:125745 original size:24 final size:24
Alignment explanation
Indices: 125713--125766 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
125703 GTATTCGAAA
*
125713 TTTGATCTTGGTTAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
125737 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
125761 TTTGAT
1 TTTGAT
125767 GATGTTTCAG
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:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:125985 original size:14 final size:14
Alignment explanation
Indices: 125956--125992 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
125946 AGAAAAAGAA
125956 GAAGAATAAATCCCC
1 GAAGAA-AAATCCCC
*
125971 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
125985 GAAGAAAA
1 GAAGAAAA
125993 TGCCACGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.19, T:0.08
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:128062 original size:18 final size:18
Alignment explanation
Indices: 128029--128063 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
128019 AGAAAAAGGC
**
128029 AATCAAAATCGTAATCAA
1 AATCAAAATCCCAATCAA
128047 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
128064 TAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:128375 original size:140 final size:140
Alignment explanation
Indices: 128123--128392 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
128113 AAACGTTGTA
* *
128123 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGTTTGAACATTGTTG
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGTTTGAACATTGCTA
*
128188 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
128253 TATGTGTATT
131 TATGTGTATT
* *
128263 TTATGTGTAAACTTTTAATATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGTTTGAACATTGCTA
*
128328 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGTGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
128393 CGCAACGCGA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:128388 original size:20 final size:20
Alignment explanation
Indices: 128363--128616 Score: 151
Period size: 20 Copynumber: 13.8 Consensus size: 20
128353 TTACACATTC
*
128363 ATTTGAATATCGCAACGTGA
1 ATTTGAATATCGCAACGCGA
*
128383 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* * *
128403 ATTTGATTATCGTAACTC--
1 ATTTGAATATCGCAACGCGA
128421 A----AATATCGCAACGCG-
1 ATTTGAATATCGCAACGCGA
* *
128436 A----ACTATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
* *
128452 ATATGACTATCGCAACGC-A
1 ATTTGAATATCGCAACGCGA
128471 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
128486 ATTTGATTATCGCAACAG-GT
1 ATTTGAATATCGCAAC-GCGA
* *
128506 ATTTGACTATCGCAACGAGA
1 ATTTGAATATCGCAACGCGA
128526 A----AAT-T-GCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
128540 ATTTGACTATCACAACGCGA
1 ATTTGAATATCGCAACGCGA
*
128560 ATTTGATTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* * *
128580 ATTTGATTATCGCAACGGGT
1 ATTTGAATATCGCAACGCGA
*
128600 ATTTGACTATCGCAACG
1 ATTTGAATATCGCAACG
128617 AGAAAATCGC
Statistics
Matches: 189, Mismatches: 25, Indels: 40
0.74 0.10 0.16
Matches are distributed among these distances:
14 29 0.15
15 17 0.09
16 3 0.02
18 3 0.02
19 5 0.03
20 131 0.69
21 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:128453 original size:49 final size:49
Alignment explanation
Indices: 128388--128540 Score: 146
Period size: 49 Copynumber: 3.0 Consensus size: 49
128378 CGTGAATTTG
* * * * * *
128388 ACTATCGCAACGCGAATTTGATTATCGTAACTCAAATATCGCAACGCGA
1 ACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCGA
128437 ACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCGAA
1 ACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCG-A
* * * * *
128487 TTTGATTATCGCAACAGGTATTTGACTATCGCAACG-AGAAAATTGCAACGCGA
1 ----ACTATCGCAACACGAATATGACTATCGCAACGCA-AAAATCGCAACGCGA
128540 A
1 A
128541 TTTGACTATC
Statistics
Matches: 87, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
49 43 0.49
50 1 0.01
53 2 0.02
54 41 0.47
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (49 bp):
ACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCGA
Found at i:128513 original size:54 final size:54
Alignment explanation
Indices: 128371--128577 Score: 239
Period size: 54 Copynumber: 3.9 Consensus size: 54
128361 TCATTTGAAT
* * * * *
128371 ATCGCAACGTGAATTTGACTATCGCAACGCGAATTTGATTATCGTAACTCAAAT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* *
128425 ATCGCAACGCG-A----ACTATCGCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* *
128474 ATCGCAACGCGAATTTGATTATCGCAACAG-GTATTTGACTATCGCAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAAC-GCGAATTTGACTATCGCAACGCA-AAA
* * *
128528 ATTGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGC
128578 GAATTTGATT
Statistics
Matches: 128, Mismatches: 16, Indels: 17
0.80 0.10 0.11
Matches are distributed among these distances:
49 42 0.33
50 1 0.01
53 3 0.02
54 82 0.64
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:128591 original size:94 final size:94
Alignment explanation
Indices: 128474--128656 Score: 312
Period size: 94 Copynumber: 1.9 Consensus size: 94
128464 CAACGCAAAA
* *
128474 ATCGCAACGCGAATTTGATTATCGCAACAGGTATTTGACTATCGCAACGAGAAAATTGCAACGCG
1 ATCGCAACGCGAATTTGATTATCGCAACAGGTATTTGACTATCGCAACGAGAAAATCGCAAAGCG
*
128539 AATTTGACTATCACAACGCGAATTTGATT
66 AATTAGACTATCACAACGCGAATTTGATT
*
128568 ATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAAAGCG
1 ATCGCAACGCGAATTTGATTATCGCAACAGGTATTTGACTATCGCAACGAGAAAATCGCAAAGCG
* *
128633 TATTAGACTATCGCAACGCGAATT
66 AATTAGACTATCACAACGCGAATT
128657 GACTTTCGCG
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 83 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGATTATCGCAACAGGTATTTGACTATCGCAACGAGAAAATCGCAAAGCG
AATTAGACTATCACAACGCGAATTTGATT
Found at i:128596 original size:40 final size:40
Alignment explanation
Indices: 128363--128665 Score: 182
Period size: 34 Copynumber: 8.3 Consensus size: 40
128353 TTACACATTC
* *
128363 ATTTGAATATCGCAACGTGAATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
* * *
128403 ATTTGATTATCGTAACTC-AA----A-TATCGCAACGCG-
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
* *
128436 A----ACTATCGCAACACGAATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
* * *
128471 A----A-AATCGCAACGCGAATTTGATTATCGCAACAG-GT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAAC-GCGA
* *
128506 ATTTGACTATCGCAACGAGAA----A--ATTGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
* *
128540 ATTTGACTATCACAACGCGAATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
* * * *
128580 ATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
* * *
128620 A----A--ATCGCAAAGCGTATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
*
128654 A-TTGACTTTCGC
1 ATTTGACTATCGC
128666 GTTGCGATTT
Statistics
Matches: 207, Mismatches: 30, Indels: 53
0.71 0.10 0.18
Matches are distributed among these distances:
29 10 0.05
30 2 0.01
33 2 0.01
34 94 0.45
35 16 0.08
36 2 0.01
37 1 0.00
38 1 0.00
39 7 0.03
40 72 0.35
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (40 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGA
Found at i:128684 original size:20 final size:20
Alignment explanation
Indices: 128659--128697 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
128649 CGCGAATTGA
*
128659 CTTTCGCGTTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
128679 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
128698 AGTTTAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.21, G:0.26, T:0.46
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:128871 original size:14 final size:14
Alignment explanation
Indices: 128811--128872 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
128801 CACAAATAAG
*
128811 AATTATTTACACATC
1 AATT-TTTACAAATC
**
128826 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
128841 AACTTTTACAAATC
1 AATTTTTACAAATC
*
128855 AATTTTTATAAATC
1 AATTTTTACAAATC
128869 AATT
1 AATT
128873 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:130283 original size:21 final size:21
Alignment explanation
Indices: 130254--130354 Score: 80
Period size: 21 Copynumber: 4.8 Consensus size: 21
130244 GGGAGGGACT
* *
130254 TCTTCAACGATGACAGTGGCC
1 TCTTGAACGATGACAGGGGCC
* ** *
130275 TCTTGAACGGTGGGAGGGGAC
1 TCTTGAACGATGACAGGGGCC
** *
130296 TCTTGAGGGATGATAGGGGCC
1 TCTTGAACGATGACAGGGGCC
*
130317 TCTTGAACGAT-A-GGGGATGCC
1 TCTTGAACGATGACAGGG--GCC
130338 TCTTGAACGATGACAGG
1 TCTTGAACGATGACAGG
130355 TGAGTCGGGC
Statistics
Matches: 60, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
19 3 0.05
20 1 0.02
21 53 0.88
22 1 0.02
23 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.23
Consensus pattern (21 bp):
TCTTGAACGATGACAGGGGCC
Found at i:130350 original size:42 final size:42
Alignment explanation
Indices: 130243--130354 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
130233 TCTAGAATGT
* * *
130243 TGGGAG-GGACTTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGAC-TCTTGAACGATGACAGGGGCCTCTTGAACGA
* ** *
130285 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGA
* *
130327 TAGGG-GATGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGACTCTTGAACGATGACAGG
130355 TGAGTCGGGC
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
42 49 0.88
43 7 0.12
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:130863 original size:18 final size:19
Alignment explanation
Indices: 130840--130906 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
130830 GAAACATAAA
*
130840 ATCGCAACAC-AAATGACT
1 ATCGCAACGCGAAATGACT
130858 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
130878 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
130898 ATCGCAACG
1 ATCGCAACG
130907 AGAGAATCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.20
19 2 0.05
20 33 0.75
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:130875 original size:20 final size:20
Alignment explanation
Indices: 130850--130906 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
130840 ATCGCAACAC
130850 AAATGACTATCGCAACGCGA
1 AAATGACTATCGCAACGCGA
130870 AAATGACTATCGCAACGCGA
1 AAATGACTATCGCAACGCGA
**
130890 ATTTGACTATCGCAACG
1 AAATGACTATCGCAACG
130907 AGAGAATCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGA
Found at i:130960 original size:20 final size:20
Alignment explanation
Indices: 130931--130982 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
130921 TGATTTTCAT
130931 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
* **
130951 TTCGCATTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
130971 TTCGCGTTGCGA
1 TTCGCGTTGCGA
130983 AAGTAAACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:132888 original size:20 final size:20
Alignment explanation
Indices: 132859--132953 Score: 102
Period size: 20 Copynumber: 4.8 Consensus size: 20
132849 TCTGAAACTT
*
132859 AAAATCGCAACACGAATATG
1 AAAATCGCAACGCGAATATG
* * *
132879 AAAATTGCAACACGAAAATG
1 AAAATCGCAACGCGAATATG
** *
132899 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAATATG
**
132919 ACTATCGCAACGCGAA-ATG
1 AAAATCGCAACGCGAATATG
132938 AAAATCGCAACGCGAA
1 AAAATCGCAACGCGAA
132954 ACTAAAATCG
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
19 16 0.25
20 48 0.75
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:132946 original size:19 final size:19
Alignment explanation
Indices: 132859--132964 Score: 97
Period size: 20 Copynumber: 5.4 Consensus size: 19
132849 TCTGAAACTT
*
132859 AAAATCGCAACACGAATATG
1 AAAATCGCAACGCGAA-ATG
* *
132879 AAAATTGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
132899 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
**
132919 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
132938 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
132957 AAAATCGC
1 AAAATCGC
132965 TTTGCGATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
19 27 0.36
20 45 0.61
21 2 0.03
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:133597 original size:20 final size:20
Alignment explanation
Indices: 133572--133669 Score: 133
Period size: 20 Copynumber: 4.9 Consensus size: 20
133562 GAAAATCACA
* *
133572 TTGCGATAGTCAGCATCGCG
1 TTGCGATAGTCAGAATCGAG
*
133592 TTGCGATAGTCAGAATCTAG
1 TTGCGATAGTCAGAATCGAG
*
133612 TTGCGATAGTCAGAATCTAG
1 TTGCGATAGTCAGAATCGAG
* *
133632 TTGCGATAGTCAGAATTGCG
1 TTGCGATAGTCAGAATCGAG
*
133652 TTGCGATAGTCATAATCG
1 TTGCGATAGTCAGAATCG
133670 CATTGCAATT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGAG
Found at i:133675 original size:20 final size:20
Alignment explanation
Indices: 133565--133760 Score: 121
Period size: 20 Copynumber: 9.7 Consensus size: 20
133555 GCGCTTTGAA
*
133565 AATCACATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
133585 CATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
133605 AATC-TAGTTGCGATAGTCAG
1 AATCGCA-TTGCGATAGTCAG
*
133625 AATC-TAGTTGCGATAGTCAG
1 AATCGCA-TTGCGATAGTCAG
* * *
133645 AATTGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
133665 AATCGCATTGCAAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* *
133685 ATTCGCATTGCGATAGTCGGAA
1 AATCGCATTGCGATAGTC--AG
** * * *
133707 AATCGCAACGCGA-ATTTGGAA
1 AATCGCATTGCGATA-GT-CAG
*
133728 AATCGCAATGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
133748 AATCGCGTTGCGA
1 AATCGCATTGCGA
133761 ATCTGGAAAC
Statistics
Matches: 138, Mismatches: 29, Indels: 18
0.75 0.16 0.10
Matches are distributed among these distances:
19 1 0.01
20 107 0.78
21 17 0.12
22 13 0.09
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:136085 original size:20 final size:20
Alignment explanation
Indices: 136060--136108 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
136050 TGGCCACCAA
136060 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
136080 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
*
136100 CCCTCCACT
1 GCCTCCACT
136109 CACAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.45, G:0.12, T:0.33
Consensus pattern (20 bp):
GCCTCCACTAGTCCTTGTCT
Found at i:136402 original size:25 final size:25
Alignment explanation
Indices: 136342--136394 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
136332 TCTGTTTTGA
*
136342 ATTTTTAATAG-TTTTTATTTATTT
1 ATTTTCAATAGTTTTTTATTTATTT
136366 ATTTTCAATAGTTTTTTA-TTA-TT
1 ATTTTCAATAGTTTTTTATTTATTT
136389 ATTTTC
1 ATTTTC
136395 GAAATAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 13 0.48
25 6 0.22
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (25 bp):
ATTTTCAATAGTTTTTTATTTATTT
Found at i:140762 original size:39 final size:39
Alignment explanation
Indices: 140708--140787 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
140698 CACCCGGAGT
* *
140708 ATTACCCGAGGACTCATCCACTACTAAAGGGAAAGTTGC
1 ATTACCCGAGGACTCATCCACTACCAAAGGGAAAGCTGC
*
140747 ATTACCCG-GTGACTCATCCTCTACCAAAGGGAAAGCTGC
1 ATTACCCGAG-GACTCATCCACTACCAAAGGGAAAGCTGC
140786 AT
1 AT
140788 CTACTGTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (39 bp):
ATTACCCGAGGACTCATCCACTACCAAAGGGAAAGCTGC
Found at i:149230 original size:20 final size:20
Alignment explanation
Indices: 149205--149253 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
149195 TGGCCACCAA
149205 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
149225 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
*
149245 CCCTCCACT
1 GCCTCCACT
149254 CACAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.45, G:0.12, T:0.33
Consensus pattern (20 bp):
GCCTCCACTAGTCCTTGTCT
Found at i:149478 original size:23 final size:23
Alignment explanation
Indices: 149452--149540 Score: 58
Period size: 24 Copynumber: 3.8 Consensus size: 23
149442 CAGTTTCTTT
149452 ATTTTTATTATTATTTTTTATTG
1 ATTTTTATTATTATTTTTTATTG
* * *
149475 ATTTTCTGTT-TTGAATTTTTAAT-
1 ATTTT-TATTATT-ATTTTTTATTG
** *
149498 AGTTTTTATTTATTATTTTCAATAG
1 A-TTTTTA-TTATTATTTTTTATTG
*
149523 -TTTTTTTTATTATTTTTT
1 ATTTTTATTATTATTTTTT
149541 CGAAATAGTA
Statistics
Matches: 48, Mismatches: 12, Indels: 13
0.66 0.16 0.18
Matches are distributed among these distances:
22 10 0.21
23 14 0.29
24 22 0.46
25 2 0.04
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.71
Consensus pattern (23 bp):
ATTTTTATTATTATTTTTTATTG
Found at i:149549 original size:26 final size:23
Alignment explanation
Indices: 149489--149538 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
149479 TCTGTTTTGA
*
149489 ATTTTTAATAGTTTTTATTTATT
1 ATTTTCAATAGTTTTTATTTATT
149512 ATTTTCAATAGTTTTT-TTTATT
1 ATTTTCAATAGTTTTTATTTATT
149534 ATTTT
1 ATTTT
149539 TTCGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (23 bp):
ATTTTCAATAGTTTTTATTTATT
Found at i:153250 original size:29 final size:29
Alignment explanation
Indices: 153195--153249 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
153185 TTTCAAAATT
*
153195 TAAAATTTAGTATTTATACTTTATTTTTA
1 TAAAATTAAGTATTTATACTTTATTTTTA
*
153224 TAAAATTAAGTTTTTATA--TTATTTTT
1 TAAAATTAAGTATTTATACTTTATTTTT
153250 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
29 16 0.67
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (29 bp):
TAAAATTAAGTATTTATACTTTATTTTTA
Found at i:174756 original size:20 final size:21
Alignment explanation
Indices: 174719--174761 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
174709 TTATAAATTT
* *
174719 TTAAAAATATATATATTTAAA
1 TTAAAAATATAAAAATTTAAA
*
174740 TTAAAAAT-TAAAAATTTTAA
1 TTAAAAATATAAAAATTTAAA
174760 TT
1 TT
174762 TTAAGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAAAATATAAAAATTTAAA
Found at i:176119 original size:13 final size:13
Alignment explanation
Indices: 176101--176136 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
176091 TTCCACAAAT
176101 TAACAAAAAAAAA
1 TAACAAAAAAAAA
176114 TAACAAAAAAAAA
1 TAACAAAAAAAAA
176127 -AA-AAAAAAAA
1 TAACAAAAAAAA
176137 TAAAAAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 13 0.57
ACGTcount: A:0.89, C:0.06, G:0.00, T:0.06
Consensus pattern (13 bp):
TAACAAAAAAAAA
Found at i:176119 original size:21 final size:21
Alignment explanation
Indices: 176105--176143 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
176095 ACAAATTAAC
176105 AAAAAAAAATAACAAAAAAAA
1 AAAAAAAAATAACAAAAAAAA
*
176126 AAAAAAAAA-AATAAAAAA
1 AAAAAAAAATAACAAAAAA
176144 CCAAAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.92, C:0.03, G:0.00, T:0.05
Consensus pattern (21 bp):
AAAAAAAAATAACAAAAAAAA
Found at i:176159 original size:1 final size:1
Alignment explanation
Indices: 176105--176143 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
176095 ACAAATTAAC
* * *
176105 AAAAAAAAATAACAAAAAAAAAAAAAAAAAAATAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
176144 CCAAAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.03, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:177577 original size:43 final size:43
Alignment explanation
Indices: 177515--177596 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
177505 ATTTTTATCA
*
177515 TATTTAATTTAAAACACTTTTAAATTAAATAATAACATAATTAT
1 TATTTAATCTAAAACACTTTTAAA-TAAATAATAACATAATTAT
* *
177559 TATTT-ATCTAAAGCACTTTTAAATAAATAATAATATAA
1 TATTTAATCTAAAACACTTTTAAATAAATAATAACATAA
177597 ACATGTCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 14 0.40
43 16 0.46
44 5 0.14
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.41
Consensus pattern (43 bp):
TATTTAATCTAAAACACTTTTAAATAAATAATAACATAATTAT
Done.