Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014941.1 Kokia drynarioides strain JFW-HI SEQ_129984, 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: 135485
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 396 characters in sequence are not A, C, G, or T
Found at i:1203 original size:25 final size:28
Alignment explanation
Indices: 1170--1228 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1160 TCCTTTTACC
1170 TTTTTTCTC-TTT-TTTG-TTTTTCTTA
1 TTTTTTCTCTTTTATTTGCTTTTTCTTA
*
1195 TTTTTTCTCTTTTATTTGCTTTTTCTTG
1 TTTTTTCTCTTTTATTTGCTTTTTCTTA
1223 TTTTTT
1 TTTTTT
1229 TTCACTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 9 0.30
26 3 0.10
27 4 0.13
28 14 0.47
ACGTcount: A:0.03, C:0.12, G:0.05, T:0.80
Consensus pattern (28 bp):
TTTTTTCTCTTTTATTTGCTTTTTCTTA
Found at i:2124 original size:15 final size:16
Alignment explanation
Indices: 2092--2124 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2082 TCGTCTTGAC
*
2092 TTTTCTTTCTTTTCTT
1 TTTTCTTCCTTTTCTT
2108 TTTTCTTCCTTTT-TT
1 TTTTCTTCCTTTTCTT
2123 TT
1 TT
2125 ATTGGGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTCCTTTTCTT
Found at i:3206 original size:231 final size:231
Alignment explanation
Indices: 2796--3251 Score: 867
Period size: 231 Copynumber: 2.0 Consensus size: 231
2786 AAACTACAGA
*
2796 AAGCTCCTCCACAGTCTAGTTGTCTAAAACACTTCCAAGGGTGTATAAACGAACTCTCAACAGGC
1 AAGCTCCTCCACAGTCTAGTTGTCTAAAACACTTCCAAGGGTGTAGAAACGAACTCTCAACAGGC
2861 TCAAATTTTAGCATTCCCTATCTTGATTTATCACATTTCCTCTCAGTTTTCATTTAAGGTTGATG
66 TCAAATTTTAGCATTCCCTATCTTGATTTATCACATTTCCTCTCAGTTTTCATTTAAGGTTGATG
* *
2926 ACTCTCTCTCACACGAATGTTTCAAATATGGGGAATTTCATTGAAATTTAATGCATGAAGTGCAA
131 ACTCTCTCTCACACAAATGTTTCAAATATGGGGAATTTCATTCAAATTTAATGCATGAAGTGCAA
2991 TGCAAATGAATGGTAAAATGCATGCAAAAATTCATG
196 TGCAAATGAATGGTAAAATGCATGCAAAAATTCATG
*
3027 AAGCTCCTCCACAGTCTAGTTGTCTAAAACACTTCCAAGGGTGTAGAGACGAACTCTCAACAGGC
1 AAGCTCCTCCACAGTCTAGTTGTCTAAAACACTTCCAAGGGTGTAGAAACGAACTCTCAACAGGC
3092 TCAAATTTTAGCATTCCCTATCTTGATTTATCACATTTCCTCTCAGTTTTCATTTAAGGTTGATG
66 TCAAATTTTAGCATTCCCTATCTTGATTTATCACATTTCCTCTCAGTTTTCATTTAAGGTTGATG
*
3157 ACTCTCTCTGACACAAATGTTTCAAATATGGGGAATTTCATTCAAATTTAATGCATGAAGTGCAA
131 ACTCTCTCTCACACAAATGTTTCAAATATGGGGAATTTCATTCAAATTTAATGCATGAAGTGCAA
3222 TGCAAATGAATGGTAAAATGCATGCAAAAA
196 TGCAAATGAATGGTAAAATGCATGCAAAAA
3252 GGCATTGATT
Statistics
Matches: 220, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 220 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (231 bp):
AAGCTCCTCCACAGTCTAGTTGTCTAAAACACTTCCAAGGGTGTAGAAACGAACTCTCAACAGGC
TCAAATTTTAGCATTCCCTATCTTGATTTATCACATTTCCTCTCAGTTTTCATTTAAGGTTGATG
ACTCTCTCTCACACAAATGTTTCAAATATGGGGAATTTCATTCAAATTTAATGCATGAAGTGCAA
TGCAAATGAATGGTAAAATGCATGCAAAAATTCATG
Found at i:6607 original size:30 final size:29
Alignment explanation
Indices: 6573--6669 Score: 92
Period size: 28 Copynumber: 3.3 Consensus size: 29
6563 ATGAAAACGT
*
6573 AATTTTGAGGAATTTGGGGATCAAAATTGA
1 AATTTTG-GAAATTTGGGGATCAAAATTGA
*
6603 AATTTTTGGAAAATTT-GGGATTAAAATTGA
1 AA-TTTTGG-AAATTTGGGGATCAAAATTGA
* * *
6633 ACTTTTGGAAATTTGAGGG--CAAAATGGT
1 AATTTTGGAAATTTG-GGGATCAAAATTGA
6661 AATTTTGGA
1 AATTTTGGA
6670 TGTTCAAGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
28 20 0.36
29 6 0.11
30 20 0.36
31 10 0.18
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
AATTTTGGAAATTTGGGGATCAAAATTGA
Found at i:6613 original size:29 final size:29
Alignment explanation
Indices: 6583--6647 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
6573 AATTTTGAGG
*
6583 AATTTGGGGATCAAAATTGAAATTTTTGGAA
1 AATTTGGGGATCAAAATTG-AACTTTTGG-A
*
6614 AATTT-GGGATTAAAATTGAACTTTTGGA
1 AATTTGGGGATCAAAATTGAACTTTTGGA
6642 AATTTG
1 AATTTG
6648 AGGGCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 6 0.19
29 8 0.26
30 12 0.39
31 5 0.16
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTGGGGATCAAAATTGAACTTTTGGA
Found at i:6666 original size:28 final size:28
Alignment explanation
Indices: 6635--6756 Score: 86
Period size: 28 Copynumber: 4.3 Consensus size: 28
6625 AAAATTGAAC
*
6635 TTTTGGAAATTTGAGGGCAAAATGGTAA
1 TTTTGGAAGTTTGAGGGCAAAATGGTAA
* ** **
6663 TTTTGGATGTTCAAGGATAAAATGGTAA
1 TTTTGGAAGTTTGAGGGCAAAATGGTAA
* * *
6691 TTTTTGGATGTTTGGGGGCAAAAAT-GTAGT
1 -TTTTGGAAGTTTGAGGGC-AAAATGGTA-A
* **
6721 TTTTGGAAGTTT-ATAGGCAAAATTATAA
1 TTTTGGAAGTTTGA-GGGCAAAATGGTAA
6749 TTTTGGAA
1 TTTTGGAA
6757 AAGTTTAAGG
Statistics
Matches: 72, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
28 35 0.49
29 32 0.44
30 5 0.07
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (28 bp):
TTTTGGAAGTTTGAGGGCAAAATGGTAA
Found at i:6713 original size:29 final size:29
Alignment explanation
Indices: 6635--7032 Score: 104
Period size: 29 Copynumber: 13.8 Consensus size: 29
6625 AAAATTGAAC
*
6635 TTTTGGAAATTTGAGGGCAAAATGGTAA-
1 TTTTGGAAGTTTGAGGGCAAAATGGTAAT
* ** **
6663 TTTTGGATGTTCAAGGATAAAATGGTAAT
1 TTTTGGAAGTTTGAGGGCAAAATGGTAAT
* * *
6692 TTTTGGATGTTTGGGGGCAAAAAT-GTAGT
1 TTTTGGAAGTTTGAGGGC-AAAATGGTAAT
* **
6721 TTTTGGAAGTTT-ATAGGCAAAATTATAA-
1 TTTTGGAAGTTTGA-GGGCAAAATGGTAAT
*
6749 TTTTGGAAAAGTTT-AAGG-----TGGTAATCT
1 TTTTGG--AAGTTTGAGGGCAAAATGGTAA--T
* **
6776 TTTTGGATA-TTCGA-GATAAAATGGTAAT
1 TTTTGGA-AGTTTGAGGGCAAAATGGTAAT
* * * * *
6804 TTTTAGATGTTCGAGGGTAAAAAT-GTGAT
1 TTTTGGAAGTTTGAGGG-CAAAATGGTAAT
* * *
6833 TTTTGGAAGTTCGAGGGTAAAAAT-GTGAT
1 TTTTGGAAGTTTGAGGG-CAAAATGGTAAT
* *
6862 TTTTGGAAGTTT-AGGGGTAAAAAT-GTGAT
1 TTTTGGAAGTTTGA-GGG-CAAAATGGTAAT
* ** * *
6891 TTTTGAAAGTTCAAGGGTAAAAAT-GTGAT
1 TTTTGGAAGTTTGAGGG-CAAAATGGTAAT
* * *
6920 TTTTGAAAG-TTCAGGGGAAAAAT-GTAAT
1 TTTTGGAAGTTTGA-GGGCAAAATGGTAAT
* *
6948 TTTTGAGAAGTTT-AGGGGTAAAATTGTAAT
1 TTTTG-GAAGTTTGA-GGGCAAAATGGTAAT
*
6978 TTTTGAAAAGTTT-AGGGGTCAAAAT-GTAA-
1 TTTTG-GAAGTTTGA-GGG-CAAAATGGTAAT
* *
7007 TTTTGAAAAGTTTAAGGGTCAAAATG
1 TTTTG-GAAGTTTGAGGG-CAAAATG
7033 TTATTTTATG
Statistics
Matches: 304, Mismatches: 38, Indels: 54
0.77 0.10 0.14
Matches are distributed among these distances:
24 4 0.01
25 4 0.01
26 2 0.01
27 6 0.02
28 63 0.21
29 167 0.55
30 53 0.17
31 5 0.02
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
TTTTGGAAGTTTGAGGGCAAAATGGTAAT
Found at i:6880 original size:58 final size:58
Alignment explanation
Indices: 6818--7039 Score: 268
Period size: 58 Copynumber: 3.8 Consensus size: 58
6808 AGATGTTCGA
* * *
6818 GGGTAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTTAG
1 GGGTAAAAATGTAATTTTTGGAAGTTCAAGGGTAAAAATGTGATTTTTGAAAGTTTAG
* * *
6876 GGGTAAAAATGTGATTTTTGAAAGTTCAAGGGTAAAAATGTGATTTTTGAAAGTTCAG
1 GGGTAAAAATGTAATTTTTGGAAGTTCAAGGGTAAAAATGTGATTTTTGAAAGTTTAG
* * * *
6934 GGG-AAAAATGTAATTTTTGAGAAGTTTAGGGGTAAAATTGTAATTTTTGAAAAGTTTAG
1 GGGTAAAAATGTAATTTTTG-GAAGTTCAAGGGTAAAAATGTGATTTTTG-AAAGTTTAG
* * * * *
6993 GGGTCAAAATGTAA-TTTTGAAAAGTTTAAGGGTCAAAATGTTATTTT
1 GGGTAAAAATGTAATTTTTG-GAAGTTCAAGGGTAAAAATGTGATTTT
7040 ATGTAATAAA
Statistics
Matches: 144, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
57 15 0.10
58 81 0.56
59 39 0.27
60 9 0.06
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.36
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGGAAGTTCAAGGGTAAAAATGTGATTTTTGAAAGTTTAG
Found at i:6893 original size:141 final size:139
Alignment explanation
Indices: 6653--6906 Score: 314
Period size: 141 Copynumber: 1.8 Consensus size: 139
6643 ATTTGAGGGC
* * * *
6653 AAAATGGTAATTTTGGATGTTCAAGGATAAAATGGTAATTTTTGGATGTTTGGGGGCAAAAATGT
1 AAAATGGTAATTTTAGATGTTCAAGGATAAAATGGTAATTTTTGGAAGTTCGAGGGCAAAAATGT
* * *
6718 AGTTTTTGGAAGTTTATAGGCAAAATTATAATTTTGGAAAAGTTTAAGGTGGTAATCTTTTTGGA
66 AGTTTTTGGAAGTTTAGAGGCAAAAATATAATTTTGG-AAAGTTCAAGGTGGTAATCTTTTTGGA
6783 TATTCGAGAT
130 TATTCGAGAT
* * * *
6793 AAAATGGTAATTTTTAGATGTTCGAGGGTAAAAAT-GTGATTTTTGGAAGTTCGAGGGTAAAAAT
1 AAAATGGTAA-TTTTAGATGTTCAAGGAT-AAAATGGTAATTTTTGGAAGTTCGAGGGCAAAAAT
* * * * *
6857 GT-GATTTTTGGAAGTTTAGGGGTAAAAATGTGATTTTTGAAAGTTCAAGG
64 GTAG-TTTTTGGAAGTTTAGAGGCAAAAATATAATTTTGGAAAGTTCAAGG
6907 GTAAAAATGT
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
140 21 0.22
141 69 0.73
142 5 0.05
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.37
Consensus pattern (139 bp):
AAAATGGTAATTTTAGATGTTCAAGGATAAAATGGTAATTTTTGGAAGTTCGAGGGCAAAAATGT
AGTTTTTGGAAGTTTAGAGGCAAAAATATAATTTTGGAAAGTTCAAGGTGGTAATCTTTTTGGAT
ATTCGAGAT
Found at i:6908 original size:87 final size:88
Alignment explanation
Indices: 6793--7014 Score: 290
Period size: 87 Copynumber: 2.5 Consensus size: 88
6783 TATTCGAGAT
* * * * *
6793 AAAATGGTAATTTTT-AGATGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAAAT
1 AAAAT-GTAATTTTTGAAAAGTTCAAGGGTAAAAATGTGATTTTTGAAAGTTC-AGGGGAAAAAT
*
6857 GTGATTTTTG-GAAGTTTAGGGGTA
64 GTAATTTTTGAGAAGTTTAGGGGTA
*
6881 AAAATGTGATTTTTG-AAAGTTCAAGGGTAAAAATGTGATTTTTGAAAGTTCAGGGGAAAAATGT
1 AAAATGTAATTTTTGAAAAGTTCAAGGGTAAAAATGTGATTTTTGAAAGTTCAGGGGAAAAATGT
6945 AATTTTTGAGAAGTTTAGGGGTA
66 AATTTTTGAGAAGTTTAGGGGTA
* * * * *
6968 AAATTGTAATTTTTGAAAAGTTTAGGGGTCAAAATGT-AATTTTGAAA
1 AAAATGTAATTTTTGAAAAGTTCAAGGGTAAAAATGTGATTTTTGAAA
7015 AGTTTAAGGG
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
86 19 0.16
87 76 0.64
88 23 0.19
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (88 bp):
AAAATGTAATTTTTGAAAAGTTCAAGGGTAAAAATGTGATTTTTGAAAGTTCAGGGGAAAAATGT
AATTTTTGAGAAGTTTAGGGGTA
Found at i:7033 original size:29 final size:28
Alignment explanation
Indices: 6817--7039 Score: 196
Period size: 29 Copynumber: 7.7 Consensus size: 28
6807 TAGATGTTCG
* * **
6817 AGGGTAAAAATGTGATTTTTGGAAGTTCG
1 AGGGTAAAAATGT-AATTTTGAAAGTTTA
* *
6846 AGGGTAAAAATGTGATTTTTGGAAGTTTA
1 AGGGTAAAAATGT-AATTTTGAAAGTTTA
* * *
6875 GGGGTAAAAATGTGATTTTTGAAAGTTCA
1 AGGGTAAAAATGT-AATTTTGAAAGTTTA
* *
6904 AGGGTAAAAATGTGATTTTTGAAAG-TTC
1 AGGGTAAAAATGT-AATTTTGAAAGTTTA
*
6932 AGGGGAAAAATGTAATTTTTGAGAAGTTTA
1 AGGGTAAAAATGTAA-TTTTGA-AAGTTTA
* *
6962 GGGGTAAAATTGTAATTTTTGAAAAGTTTA
1 AGGGTAAAAATGTAA-TTTTG-AAAGTTTA
* *
6992 GGGGTCAAAATGTAATTTTGAAAAGTTTA
1 AGGGTAAAAATGTAATTTTG-AAAGTTTA
* *
7021 AGGGTCAAAATGTTATTTT
1 AGGGTAAAAATGTAATTTT
7040 ATGTAATAAA
Statistics
Matches: 172, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.01
28 19 0.11
29 111 0.65
30 40 0.23
31 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.36
Consensus pattern (28 bp):
AGGGTAAAAATGTAATTTTGAAAGTTTA
Found at i:8770 original size:7 final size:6
Alignment explanation
Indices: 8752--8870 Score: 97
Period size: 6 Copynumber: 20.8 Consensus size: 6
8742 TAATTTTTAA
* * * *
8752 TTAAAT TTAAAT TTAAA- ATGAAT TTAAAT TCAAA- ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * *
8798 TTAAA- ATGAAT TTAAAT TCAAA- ATAAAT TTAAAT TTAAA- CTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
8843 TTAAAC TTAAA- ATAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
8871 AAATGGGTCC
Statistics
Matches: 86, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
5 20 0.23
6 66 0.77
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:8775 original size:17 final size:17
Alignment explanation
Indices: 8753--8871 Score: 184
Period size: 17 Copynumber: 7.0 Consensus size: 17
8743 AATTTTTAAT
8753 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
8770 TGAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
8787 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
8804 TGAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
8821 TAAATTTAAATTTAAAC
1 TAAATTTAAATTTAAAA
*
8838 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
8855 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
8872 AATGGGTCCA
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 90 1.00
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:8791 original size:34 final size:34
Alignment explanation
Indices: 8753--8871 Score: 204
Period size: 34 Copynumber: 3.5 Consensus size: 34
8743 AATTTTTAAT
8753 TAAATTTAAATTTAAAATGAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAATGAATTTAAATTCAAAA
8787 TAAATTTAAATTTAAAATGAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAATGAATTTAAATTCAAAA
* *
8821 TAAATTTAAATTTAAACTAAATTTAAACTT-AAAA
1 TAAATTTAAATTTAAAATGAATTTAAA-TTCAAAA
8855 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
8872 AATGGGTCCA
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
34 79 0.98
35 2 0.02
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (34 bp):
TAAATTTAAATTTAAAATGAATTTAAATTCAAAA
Found at i:9240 original size:12 final size:12
Alignment explanation
Indices: 9184--9243 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
9174 ATAACATTCT
9184 AATGA-AATAAC
1 AATGATAATAAC
9195 AATGCAATAAATAA-
1 AATG--AT-AATAAC
* *
9209 AATGATAGTAAA
1 AATGATAATAAC
*
9221 AATAATAATAAC
1 AATGATAATAAC
9233 AATGATAATAA
1 AATGATAATAA
9244 TGGAAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
11 8 0.21
12 21 0.54
13 1 0.03
14 4 0.10
15 5 0.13
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.23
Consensus pattern (12 bp):
AATGATAATAAC
Found at i:9414 original size:15 final size:14
Alignment explanation
Indices: 9387--9484 Score: 71
Period size: 15 Copynumber: 6.7 Consensus size: 14
9377 AAATATATTA
9387 AAATAAT-AA-AAT
1 AAATAATAAATAAT
9399 AAATAATAGAATAAT
1 AAATAATA-AATAAT
9414 AAATAAAATAAATAAT
1 AAAT--AATAAATAAT
9430 AGAATAATAAAT-A-
1 A-AATAATAAATAAT
9443 AAATAAATAAA-AGAT
1 AAAT-AATAAATA-AT
9458 AAATACATAAAATATAT
1 AAATA-AT-AAATA-AT
*
9475 AAAAAATAAA
1 AAATAATAAA
9485 AAAATGAAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 23
0.74 0.02 0.24
Matches are distributed among these distances:
12 10 0.14
13 7 0.10
14 5 0.07
15 23 0.32
16 12 0.17
17 14 0.20
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.23
Consensus pattern (14 bp):
AAATAATAAATAAT
Found at i:9420 original size:24 final size:24
Alignment explanation
Indices: 9391--9476 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
9381 ATATTAAAAT
9391 AATAAAATAAATAATAGAATAATA
1 AATAAAATAAATAATAGAATAATA
9415 AATAAAATAAATAATAGAATAATA
1 AATAAAATAAATAATAGAATAATA
*
9439 AATAAAATAAATAAAAG-ATAAATA
1 AATAAAATAAATAATAGAAT-AATA
* *
9463 CATAAAATATATAA
1 AATAAAATAAATAA
9477 AAAATAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 2 0.03
24 56 0.97
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.24
Consensus pattern (24 bp):
AATAAAATAAATAATAGAATAATA
Found at i:9480 original size:11 final size:11
Alignment explanation
Indices: 9387--9488 Score: 66
Period size: 12 Copynumber: 8.7 Consensus size: 11
9377 AAATATATTA
9387 AAATAATAAAAT
1 AAATAA-AAAAT
*
9399 AAATAATAGAAT
1 AAATAA-AAAAT
9411 -AATAAATAAAAT
1 AAAT-AA-AAAAT
*
9423 AAATAATAGAAT
1 AAATAA-AAAAT
9435 -AATAAATAAAAT
1 AAAT-AA-AAAAT
*
9447 AAATAAAAGAT
1 AAATAAAAAAT
9458 AAATACATAAAAT
1 AAATA-A-AAAAT
*
9471 ATATAAAAAAT
1 AAATAAAAAAT
9482 AAA-AAAA
1 AAATAAAA
9489 TGAAAGACCA
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
10 4 0.05
11 22 0.29
12 36 0.47
13 14 0.18
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.23
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:9483 original size:24 final size:25
Alignment explanation
Indices: 9387--9489 Score: 117
Period size: 24 Copynumber: 4.3 Consensus size: 25
9377 AAATATATTA
*
9387 AAAT-AATAAAATAAATAATAGAAT
1 AAATAAATAAAATAAATAATAAAAT
*
9411 -AATAAATAAAATAAATAATAGAAT
1 AAATAAATAAAATAAATAATAAAAT
*
9435 -AATAAATAAAATAAATAA-AAGAT
1 AAATAAATAAAATAAATAATAAAAT
* *
9458 AAATACATAAAATATATAA-AAAAT
1 AAATAAATAAAATAAATAATAAAAT
*
9482 AAAAAAAT
1 AAATAAAT
9490 GAAAGACCAA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.09
24 64 0.91
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (25 bp):
AAATAAATAAAATAAATAATAAAAT
Found at i:9740 original size:122 final size:123
Alignment explanation
Indices: 9547--9793 Score: 424
Period size: 122 Copynumber: 2.0 Consensus size: 123
9537 AAACACAAGA
9547 AAAACAATTAAAGGACCAAATTGAAATTTAAAAAAAATTTAAGGCAAAAATTAAAAAATGAAATA
1 AAAACAATTAAAGGACCAAATTGAAATTTAAAAAAAATTTAAGGCAAAAATTAAAAAATGAAATA
* **
9612 AGGGTTAAGTTGGAACACGTGAAACCCCAAGGACTAAAAGTTATATTATCCCAATCCT
66 AGGGTTAAATTGGAACACGTGAAACCCCAAGGACTAAAAGGGATATTATCCCAATCCT
*
9670 AAAACAATTAAAGGACCAAATTGAAATTT-AAAAAAATTTAAGGCAAAAATTAAAAAATGGAATA
1 AAAACAATTAAAGGACCAAATTGAAATTTAAAAAAAATTTAAGGCAAAAATTAAAAAATGAAATA
* * *
9734 AGGGTTAAATTGGAACACGTGATACCCCAGGGATTAAAAGGGATATTATCCCAATCCT
66 AGGGTTAAATTGGAACACGTGAAACCCCAAGGACTAAAAGGGATATTATCCCAATCCT
9792 AA
1 AA
9794 TACACGTGTC
Statistics
Matches: 117, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
122 88 0.75
123 29 0.25
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.23
Consensus pattern (123 bp):
AAAACAATTAAAGGACCAAATTGAAATTTAAAAAAAATTTAAGGCAAAAATTAAAAAATGAAATA
AGGGTTAAATTGGAACACGTGAAACCCCAAGGACTAAAAGGGATATTATCCCAATCCT
Found at i:11032 original size:33 final size:33
Alignment explanation
Indices: 10990--11054 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
10980 AGTTTATAAA
10990 TAACATCTTAGTAGAATCAAAACACAAAGTAGG
1 TAACATCTTAGTAGAATCAAAACACAAAGTAGG
*
11023 TAACATCTTAGTAGAATCAAAACACAATGTAG
1 TAACATCTTAGTAGAATCAAAACACAAAGTAG
11055 AAAATTGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (33 bp):
TAACATCTTAGTAGAATCAAAACACAAAGTAGG
Found at i:14744 original size:19 final size:20
Alignment explanation
Indices: 14722--14759 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
14712 AAAAGTTATA
*
14722 AAAAAGATTAAAT-TTTAAT
1 AAAAAGATAAAATATTTAAT
*
14741 AAAAATATAAAATATTTAA
1 AAAAAGATAAAATATTTAA
14760 AATTTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAAAGATAAAATATTTAAT
Found at i:14801 original size:40 final size:40
Alignment explanation
Indices: 14741--14820 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
14731 AAATTTTAAT
* *
14741 AAAAATATAAAATATTTAAAATTTATTAAAA-AT-TAGAAA
1 AAAAATATAAAATATGTAAAAATTA-TAAAATATATAGAAA
14780 AAAAATTATAAAA-ATCGTAAAAATTATAAAATATATAGAAA
1 AAAAA-TATAAAATAT-GTAAAAATTATAAAATATATAGAAA
14821 TATGGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 12 0.34
40 17 0.49
41 6 0.17
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (40 bp):
AAAAATATAAAATATGTAAAAATTATAAAATATATAGAAA
Found at i:14821 original size:18 final size:18
Alignment explanation
Indices: 14780--14907 Score: 59
Period size: 18 Copynumber: 6.8 Consensus size: 18
14770 AAATTAGAAA
*
14780 AAAAATTATAAAAATCGT
1 AAAAATTATAAAAATCAT
14798 AAAAATTATAAAATAT-AT
1 AAAAATTATAAAA-ATCAT
* *
14816 AGAAA-TATGGAAAAAATTAT
1 AAAAATTAT---AAAAATCAT
* * *
14836 -AAAATTTTATAAAGTCGT
1 AAAAATTATA-AAAATCAT
14854 AAGAAAATTATAGAAAAAT-AT
1 -A-AAAATTAT--AAAAATCAT
* *
14875 AAAGAAATATAAAATTCAT
1 AAA-AATTATAAAAATCAT
14894 AAAAA-TATAAAAAT
1 AAAAATTATAAAAAT
14908 TATCGTATAA
Statistics
Matches: 83, Mismatches: 13, Indels: 29
0.66 0.10 0.23
Matches are distributed among these distances:
17 12 0.14
18 30 0.36
19 14 0.17
20 14 0.17
21 8 0.10
22 4 0.05
23 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.28
Consensus pattern (18 bp):
AAAAATTATAAAAATCAT
Found at i:15109 original size:19 final size:19
Alignment explanation
Indices: 15077--15170 Score: 64
Period size: 19 Copynumber: 4.8 Consensus size: 19
15067 TTAAAGGGCC
**
15077 TTTTTATGCGTTTTATAAT
1 TTTTTATGATTTTTATAAT
15096 TTTTTATGATTTTTATATAAT
1 TTTTTATGA-TTTT-TATAAT
** ** *
15117 TTTACATTTTTTTTATGAT
1 TTTTTATGATTTTTATAAT
*
15136 TTTTTACG-TTCTTTATAATT
1 TTTTTATGATT-TTTATAA-T
*
15156 TTTTTATAATTTTTA
1 TTTTTATGATTTTTA
15171 ATAAAATTTA
Statistics
Matches: 56, Mismatches: 14, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
18 2 0.04
19 23 0.41
20 18 0.32
21 13 0.23
ACGTcount: A:0.23, C:0.04, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTATGATTTTTATAAT
Found at i:15118 original size:11 final size:10
Alignment explanation
Indices: 15087--15174 Score: 63
Period size: 10 Copynumber: 8.8 Consensus size: 10
15077 TTTTTATGCG
15087 TTTTATAATT
1 TTTTATAATT
*
15097 TTTTATGATT
1 TTTTATAATT
15107 TTTATATAATT
1 TTT-TATAATT
** *
15118 TTACAT-TTT
1 TTTTATAATT
*
15127 TTTTATGATT
1 TTTTATAATT
**
15137 TTTTA-CGTT
1 TTTTATAATT
*
15146 CTTTATAATTT
1 TTTTATAA-TT
15157 TTTTATAATT
1 TTTTATAATT
*
15167 TTTAATAA
1 TTTTATAA
15175 AATTTAATTT
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
9 12 0.20
10 30 0.51
11 17 0.29
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:15158 original size:30 final size:30
Alignment explanation
Indices: 15087--15215 Score: 94
Period size: 30 Copynumber: 4.5 Consensus size: 30
15077 TTTTTATGCG
*
15087 TTTTATAA-TTTTTTATGATTTTTATATAA
1 TTTTATAATTTTTTTATGATTTTTATACAA
* * **
15116 TTTTACATTTTTTTTATGATTTTT-TACGT
1 TTTTATAATTTTTTTATGATTTTTATACAA
*
15145 TCTTTATAATTTTTTTATAATTTTTAATA-AA
1 T-TTTATAATTTTTTTATGATTTTT-ATACAA
* *
15176 -ATT-TAA-TTTTTTAT-ATTTTTATTAAAA
1 TTTTATAATTTTTTTATGATTTTTA-TACAA
*
15203 TTTAAT-ATTTTTT
1 TTTTATAATTTTTT
15216 ATAACTTTTA
Statistics
Matches: 78, Mismatches: 13, Indels: 18
0.72 0.12 0.17
Matches are distributed among these distances:
25 1 0.01
26 8 0.10
27 10 0.13
28 5 0.06
29 17 0.22
30 35 0.45
32 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (30 bp):
TTTTATAATTTTTTTATGATTTTTATACAA
Found at i:15193 original size:26 final size:27
Alignment explanation
Indices: 15155--15225 Score: 99
Period size: 26 Copynumber: 2.6 Consensus size: 27
15145 TCTTTATAAT
15155 TTTTTTATAATTTTTAATAAAATTTAA
1 TTTTTTATAATTTTTAATAAAATTTAA
*
15182 TTTTTTAT-ATTTTTATTAAAATTTAATA
1 TTTTTTATAATTTTTAATAAAATTT-A-A
*
15210 TTTTTTATAACTTTTA
1 TTTTTTATAATTTTTA
15226 TTGATTTCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 15 0.38
27 9 0.23
28 9 0.23
29 6 0.15
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTTTTATAATTTTTAATAAAATTTAA
Found at i:24064 original size:23 final size:22
Alignment explanation
Indices: 24038--24131 Score: 111
Period size: 23 Copynumber: 4.1 Consensus size: 22
24028 ACACTAGCGC
24038 GCTTACTGTTCAGCACTGT-GTGT
1 GCTTACTGTTC-GCACT-TCGTGT
*
24061 GCTTACTATTTCGCACTTCGTGT
1 GCTTACT-GTTCGCACTTCGTGT
24084 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTG-TTCGCACTTCGTGT
24107 GCTTACTGTTTCGCA-TCTCGTGT
1 GCTTACTG-TTCGCACT-TCGTGT
24130 GC
1 GC
24132 CTAATGATTT
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
22 2 0.03
23 60 0.92
24 3 0.05
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.41
Consensus pattern (22 bp):
GCTTACTGTTCGCACTTCGTGT
Found at i:24107 original size:46 final size:46
Alignment explanation
Indices: 24038--24131 Score: 131
Period size: 46 Copynumber: 2.0 Consensus size: 46
24028 ACACTAGCGC
24038 GCTTACTGTTCAGCACTGTGTGTGCTTACTATTTCGCA-CTTCGTGT
1 GCTTACTGTTCAGCACTGTGTGTGCTTACTATTTCGCATC-TCGTGT
*
24084 GCTTACTGTTTC-GCACT-TCGTGTGCTTACTGTTTCGCATCTCGTGT
1 GCTTACTG-TTCAGCACTGT-GTGTGCTTACTATTTCGCATCTCGTGT
24130 GC
1 GC
24132 CTAATGATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
45 1 0.02
46 39 0.89
47 4 0.09
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.41
Consensus pattern (46 bp):
GCTTACTGTTCAGCACTGTGTGTGCTTACTATTTCGCATCTCGTGT
Found at i:24173 original size:22 final size:22
Alignment explanation
Indices: 24050--24205 Score: 95
Period size: 23 Copynumber: 6.9 Consensus size: 22
24040 TTACTGTTCA
*
24050 GCACTGTGTGTGCTTACT-ATTT
1 GCACTGTGTGTGCCTACTGA-TT
* *
24072 CGCACT-TCGTGTGCTTACTGTTT
1 -GCACTGT-GTGTGCCTACTGATT
* *
24095 CGCACT-TCGTGTGCTTACTGTTT
1 -GCACTGT-GTGTGCCTACTGATT
* *
24118 CGCATCT-CGTGTGCCTAATGATTT
1 -GCA-CTGTGTGTGCCTACTGA-TT
** * *
24142 GCGTTATGTGCGCCTACTGATT
1 GCACTGTGTGTGCCTACTGATT
24164 GCACTGTGTGTGCCTACTGGATT
1 GCACTGTGTGTGCCTACT-GATT
*
24187 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCCTACTG
24206 TTTCCCCAGC
Statistics
Matches: 112, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
22 19 0.17
23 89 0.79
24 4 0.04
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (22 bp):
GCACTGTGTGTGCCTACTGATT
Found at i:25344 original size:2 final size:2
Alignment explanation
Indices: 25337--25366 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25327 GACATGATCG
25337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25367 GCTCTAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30592 original size:2 final size:2
Alignment explanation
Indices: 30587--30625 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
30577 TTCATATATA
30587 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
30626 ACATAAACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:34247 original size:2 final size:2
Alignment explanation
Indices: 34240--34270 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
34230 AACTTTAGTG
34240 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34271 AAATTTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40317 original size:164 final size:164
Alignment explanation
Indices: 40033--40334 Score: 469
Period size: 164 Copynumber: 1.8 Consensus size: 164
40023 AAGATTATTT
* *
40033 TTTTTCCCTTTTATTGAGGTTTGGTCATTCAAAAAAGCGTATATGGATTTCATTTTTAATTATGA
1 TTTTTCCCTTTTATTGAGGTTTGATCATTCAAAAAAGCATATATGGATTTCATTTTTAATTATGA
* * **
40098 TTATACTTGCCATATATGGATTTCAGTTTTCTCTGACATGAACGTTCTGTTGCTGCTGCTCTCAC
66 TTATACTTACCATATATGGAATTCAGTTTTCTCTGACATGAACGTTCCATTGCTGCTGCTCTCAC
40163 TGTTCCTGTTGCACTTCCAATTTAAGATTAAATA
131 TGTTCCTGTTGCACTTCCAATTTAAGATTAAATA
** *
40197 TTTTTCCCTTTTATTGAGGTTTGATCATTTGAAAAGGCATATATGGATTTCATTTTTAATTATGA
1 TTTTTCCCTTTTATTGAGGTTTGATCATTCAAAAAAGCATATATGGATTTCATTTTTAATTATGA
** * * * *
40262 TTATACTTACTGTATATGGAATTCATTTTTCTTTGATATGAACTTTCCATTGCTGCTGCTCTCAC
66 TTATACTTACCATATATGGAATTCAGTTTTCTCTGACATGAACGTTCCATTGCTGCTGCTCTCAC
40327 TGTTCCTG
131 TGTTCCTG
40335 ATAGTCATGT
Statistics
Matches: 123, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
164 123 1.00
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (164 bp):
TTTTTCCCTTTTATTGAGGTTTGATCATTCAAAAAAGCATATATGGATTTCATTTTTAATTATGA
TTATACTTACCATATATGGAATTCAGTTTTCTCTGACATGAACGTTCCATTGCTGCTGCTCTCAC
TGTTCCTGTTGCACTTCCAATTTAAGATTAAATA
Found at i:43302 original size:6 final size:6
Alignment explanation
Indices: 43291--43324 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
43281 ACACTTCTCT
43291 TCTTCA TCTTCA TCTTCA T-TTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
43325 TTCCTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.53
Consensus pattern (6 bp):
TCTTCA
Found at i:43315 original size:11 final size:12
Alignment explanation
Indices: 43291--43324 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
43281 ACACTTCTCT
43291 TCTTCATCTTCA
1 TCTTCATCTTCA
43303 TCTTCAT-TTCA
1 TCTTCATCTTCA
43314 TCTTCATCTTC
1 TCTTCATCTTC
43325 TTCCTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.53
Consensus pattern (12 bp):
TCTTCATCTTCA
Found at i:48094 original size:25 final size:26
Alignment explanation
Indices: 48066--48115 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
48056 TTCTTGAGCG
* * *
48066 AGACTTGATTA-ATGACTGTTGAGAT
1 AGACTTCATTAGAAGACTGTAGAGAT
48091 AGACTTCATTAGAAGACTGTAGAGA
1 AGACTTCATTAGAAGACTGTAGAGA
48116 CTTCTACGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (26 bp):
AGACTTCATTAGAAGACTGTAGAGAT
Found at i:55097 original size:15 final size:15
Alignment explanation
Indices: 55064--55106 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55054 TATTTGGTAT
*
55064 AAATATTT-TTTTTC
1 AAATATTTATTTTTA
*
55078 TAATATTTATTTTTA
1 AAATATTTATTTTTA
55093 AAATATTTTATTTT
1 AAATA-TTTATTTT
55107 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 7 0.29
15 9 0.38
16 8 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
AAATATTTATTTTTA
Found at i:55106 original size:5 final size:5
Alignment explanation
Indices: 55096--55121 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55086 ATTTTTAAAA
55096 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
55122 TATAAGACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:55590 original size:19 final size:21
Alignment explanation
Indices: 55547--55591 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
55537 TTCTTGTATT
*
55547 AATTATAAATAAACTAAAAGT
1 AATTATAAATAAACTAAAAGA
*
55568 AATTATAAA-AAA-TAAAGGA
1 AATTATAAATAAACTAAAAGA
55587 AATTA
1 AATTA
55592 AAAGGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 3 0.14
21 9 0.41
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (21 bp):
AATTATAAATAAACTAAAAGA
Found at i:55943 original size:28 final size:30
Alignment explanation
Indices: 55912--55974 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
55902 AGAGAAATAA
55912 AAAATAAAAAATGA-TAAA-ATGAGTGACC
1 AAAATAAAAAATGACTAAATATGAGTGACC
* * * *
55940 AAAATGAAAATTGACTAAATTTGAGTGACT
1 AAAATAAAAAATGACTAAATATGAGTGACC
55970 AAAAT
1 AAAAT
55975 GAGTGCATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 12 0.41
29 4 0.14
30 13 0.45
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (30 bp):
AAAATAAAAAATGACTAAATATGAGTGACC
Found at i:56627 original size:20 final size:21
Alignment explanation
Indices: 56582--56627 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
56572 TACAAAAAAA
56582 AAAAAAGTTCAAAATAATTTT
1 AAAAAAGTTCAAAATAATTTT
* *
56603 CAAAAAG-TCGAAAT-ATTTAT
1 AAAAAAGTTCAAAATAATTT-T
56623 AAAAA
1 AAAAA
56628 TTTCAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.19
20 11 0.52
21 6 0.29
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (21 bp):
AAAAAAGTTCAAAATAATTTT
Found at i:70116 original size:39 final size:39
Alignment explanation
Indices: 70057--70173 Score: 216
Period size: 39 Copynumber: 3.0 Consensus size: 39
70047 TATAAGTAAG
*
70057 CTAATAGACCTAGATAGTTTGATGATGAGGATAACTTTA
1 CTAAAAGACCTAGATAGTTTGATGATGAGGATAACTTTA
70096 CTAAAAGACCTAGATAGTTTGATGATGAGGATAACTTTA
1 CTAAAAGACCTAGATAGTTTGATGATGAGGATAACTTTA
*
70135 CTAAAAGACCTAGATAGTTTGATGATGGGGATAACTTTA
1 CTAAAAGACCTAGATAGTTTGATGATGAGGATAACTTTA
70174 AGCGTCAATC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (39 bp):
CTAAAAGACCTAGATAGTTTGATGATGAGGATAACTTTA
Found at i:74235 original size:14 final size:14
Alignment explanation
Indices: 74196--74240 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
74186 AATTAAATTA
* *
74196 AAAAATAAGTAATT
1 AAAAATAAATAAAT
74210 AAACATATAAATAAAT
1 AAA-A-ATAAATAAAT
74226 AAAAATAAATAAAT
1 AAAAATAAATAAAT
74240 A
1 A
74241 CTAAACATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 14 0.52
15 2 0.07
16 11 0.41
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:74381 original size:6 final size:6
Alignment explanation
Indices: 74363--74402 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
74353 TATAATATAC
*
74363 TTAATT TTGATT TTAATT TTAATT TATATATT TTAATT TT
1 TTAATT TTAATT TTAATT TTAATT T-TA-ATT TTAATT TT
74403 TAATATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 22 0.73
7 4 0.13
8 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:74414 original size:17 final size:17
Alignment explanation
Indices: 74388--74470 Score: 55
Period size: 17 Copynumber: 4.8 Consensus size: 17
74378 ATTTTAATTT
*
74388 ATATATTTTAATTTTTA
1 ATATAATTTAATTTTTA
*
74405 ATATAATTTAATTTCT-
1 ATATAATTTAATTTTTA
**
74421 ATATTTTTATAATTTTTTTA
1 ATATAATT-TAA--TTTTTA
*
74441 AT-TAATTTAAATTGTTA
1 ATATAATTT-AATTTTTA
*
74458 ATATCA-TTAATTT
1 ATATAATTTAATTT
74471 ATCGGTTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
16 10 0.20
17 26 0.52
18 3 0.06
19 9 0.18
20 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (17 bp):
ATATAATTTAATTTTTA
Found at i:74443 original size:31 final size:29
Alignment explanation
Indices: 74373--74448 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 29
74363 TTAATTTTGA
74373 TTTTAATTTTAA-TTTATATATTTTAATTT
1 TTTTAA-TTTAATTTTATATATTTTAATTT
*
74402 TTAATATAATTTAATTTCTATATTTTTATAATTT
1 TT--T-TAATTTAATTT-TATATATTT-TAATTT
74436 TTTTAA-TTAATTT
1 TTTTAATTTAATTT
74449 AAATTGTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
29 2 0.05
30 7 0.17
31 9 0.22
32 6 0.15
33 8 0.20
34 8 0.20
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTAATTTAATTTTATATATTTTAATTT
Found at i:75209 original size:21 final size:23
Alignment explanation
Indices: 75169--75211 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
75159 CATTTTTTAA
75169 ATATAATTTATTTATAAAATTTC
1 ATATAATTTATTTATAAAATTTC
75192 ATATAATTT-TTT-TAAAATTT
1 ATATAATTTATTTATAAAATTT
75212 TCAAGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATAATTTATTTATAAAATTTC
Found at i:79507 original size:156 final size:155
Alignment explanation
Indices: 78912--79823 Score: 915
Period size: 156 Copynumber: 5.8 Consensus size: 155
78902 AGTAAAGCAG
* * * * *
78912 CTCAAATTTTAGCATCATAGA-GCAACAAAACAGAATAAACAAAAATCAATT-AAACGACCACAG
1 CTCAAATTTTAGCATCACAGAGGCAAAAAAAAAGAATAAACAAAAGT-TATTAAAACGACCACAG
*
78975 TGGGAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTC
65 TGGAAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTC
*
79040 TTGGGTGAAATTTAGGGAAACTAAAGTAA
130 TTGGGT-AAA-ATAGGGAAA-TAAAGTAA
* * * * * * *** *
79069 CTCAAATTTTAACATTACAGAGGCAGTAAAATAAGTA-AAAGAATAA--TATTAATTGGACTACA
1 CTCAAATTTTAGCATCACAGAGGCA-AAAAAAAAGAATAAACAA-AAGTTATTAAAACGACCACA
* *
79131 GTGGGAA-TTGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTTCGCTATGCGG
64 GT-GGAAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGG
* * *
79195 TGTTGGGTAAAAACAAGGCAAACTAAAGTAA
128 TCTTGGGT-AAAA-TAGGGAAA-TAAAGTAA
* * * *
79226 CTCAAATTTTAACATCAC-GAAGGCAGTAAAATAAGTAA-AAAGAATAA-TTATTAATCGAACGA
1 CTCAAATTTTAGCATCACAG-AGGCA-AAAAAAAAG-AATAAACAA-AAGTTATTAA---AACGA
*
79288 CCACAGTGGGAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTAT
59 CCACAGTGGAAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTAT
* * *
79353 GCGGTCATAGATAAAGATAAGGGAAATTAAAGTAA
124 GCGGTCTTGGGTAAA-AT-AGGGAAA-TAAAGTAA
** * * *
79388 CAGAAATTTTAGCACCACA-A-CCAAAAAAAAAGAATAAACAAAAGTTATTAAAACGACCACAGA
1 CTCAAATTTTAGCATCACAGAGGCAAAAAAAAAGAATAAACAAAAGTTATTAAAACGACCACAGT
79451 GGAAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTCT
66 GGAAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTCT
* * * *
79516 TGCGG---GAT--GGTAA-AAGGTAG
131 TG-GGTAAAATAGGGAAATAAAGTAA
* * * ** * * *
79536 TTCAAATTTTAGCAACATAGAGGCAGTAAAAAAGAATTAACAAAAGTTAATAAAGACGACCACGG
1 CTCAAATTTTAGCATCACAGAGGCAAAAAAAAAGAATAAACAAAAGTTATTAAA-ACGACCACAG
* * * * * *
79601 AGGAAGTCGAACCAACAACCTTCTGATCCGAAGTCAGACGCGCTAATCTACTGCTCTATGCAGTC
65 TGGAAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTC
* * *
79666 TTGGGTGAAAATATGGTAA-AAAGTAG
130 TTGGGT-AAAATAGGGAAATAAAGTAA
* ** * **
79692 CTCAAATTTTAGCATCATAGAGGCAGTAAAAAAGAATGAACAAAAGTTAACAAAAACGACCACAG
1 CTCAAATTTTAGCATCACAGAGGCAAAAAAAAAGAATAAACAAAAGTT-ATTAAAACGACCACAG
*
79757 TGGGAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTC
65 TGGAAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTC
79822 TT
130 TT
79824 AATTGAGAGG
Statistics
Matches: 640, Mismatches: 86, Indels: 59
0.82 0.11 0.08
Matches are distributed among these distances:
148 19 0.03
149 1 0.00
150 33 0.05
151 72 0.11
153 2 0.00
154 2 0.00
156 204 0.32
157 144 0.22
158 25 0.04
159 33 0.05
160 2 0.00
161 7 0.01
162 96 0.15
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (155 bp):
CTCAAATTTTAGCATCACAGAGGCAAAAAAAAAGAATAAACAAAAGTTATTAAAACGACCACAGT
GGAAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTCT
TGGGTAAAATAGGGAAATAAAGTAA
Found at i:79750 original size:307 final size:309
Alignment explanation
Indices: 78912--79823 Score: 971
Period size: 307 Copynumber: 2.9 Consensus size: 309
78902 AGTAAAGCAG
** * * *
78912 CTCAAATTTTAGCATCATAGA-GCAACAAAACAGAATAAACAAAAATCAATTAA-ACGACCACAG
1 CTCAAATTTTAGCATCATAGAGGCAGTAAAAAAGAATAAAC-AAAATTAATAAAGACGACCACAG
78975 TGGGAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTC
65 TGGGAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTC
** * *
79040 TTGGGTGAAATTTAGGGAAACTAAAGTAACTCAAATTTTAACATTACAGAGGCAGTAAAATAAG-
130 TTGGGTGAAAGATAGGGAAA-TAAAGTAACTCAAATTTTAGCATCACAGAGGCAGTAAAA-AAGA
*** * * *
79104 -TAA-AAGAA--TAATATTAATTGGACTACAGTGGGAA-TTGAACCCACGACCTTCTGATCCGAA
193 ATAACAA-AAGTTAATA--AAAACGACCACAG-AGGAAGTCGAACCCACGACCTTCTGATCCGAA
* *
79164 GTCAGACGCGCTAATCCACTTCGCTATGCGGTGTTGGGTAAAAACAAGGCAAACTAAAGTAA
254 GTCAGACGCGCTAATCCACTGCGCTATGCGGTCTTGGG-----ACAAGGCAAAC-AAAGTAA
* * * * *
79226 CTCAAATTTTAACATCA-CGAAGGCAGTAAAATAAGTAA-AAAGAATAATTATTAATCGAACGAC
1 CTCAAATTTTAGCATCATAG-AGGCAGTAAAA-AAG-AATAAACAA-AATTAATAA-AG-ACGAC
79289 CACAGTGGGAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATG
60 CACAGTGGGAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATG
* * * ** * * **
79354 CGGTCATAGAT-AAAGATAAGGGAAATTAAAGTAACAGAAATTTTAGCACCACA-A-CCAAAAAA
125 CGGTCTTGGGTGAAAGAT-AGGGAAA-TAAAGTAACTCAAATTTTAGCATCACAGAGGCAGTAAA
*
79416 AAAGAATAAACAAAAGTT-ATTAAAACGACCACAGAGGAAGTCGAACCCACGACCTTCTGATCCG
188 AAAGAAT-AACAAAAGTTAATAAAAACGACCACAGAGGAAGTCGAACCCACGACCTTCTGATCCG
* * * * *
79480 AAGTCAGACGCGCTAATCCACTGCGCTATGCGGTCTTGCGG-GATGG-TAA-AAGGTAG
252 AAGTCAGACGCGCTAATCCACTGCGCTATGCGGTCTTG-GGACAAGGCAAACAAAGTAA
* * * *
79536 TTCAAATTTTAGCAACATAGAGGCAGTAAAAAAGAATTAACAAAAGTTAATAAAGACGACCACGG
1 CTCAAATTTTAGCATCATAGAGGCAGTAAAAAAGAATAAACAAAA-TTAATAAAGACGACCACAG
* * * * * * *
79601 AGGAAGTCGAACCAACAACCTTCTGATCCGAAGTCAGACGCGCTAATCTACTGCTCTATGCAGTC
65 TGGGAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTC
* * * *
79666 TTGGGTGAAA-ATATGGTAA-AAAGTAGCTCAAATTTTAGCATCATAGAGGCAGTAAAAAAGAAT
130 TTGGGTGAAAGATAGGGAAATAAAGTAACTCAAATTTTAGCATCACAGAGGCAGTAAAAAAGAAT
* * *
79729 GAACAAAAGTTAACAAAAACGACCACAGTGGGAGTCGAACCCACGACCTTCTGATCCGAAGTCAG
195 -AACAAAAGTTAATAAAAACGACCACAGAGGAAGTCGAACCCACGACCTTCTGATCCGAAGTCAG
79794 ACGCGCTAATCCACTGCGCTATGCGGTCTT
259 ACGCGCTAATCCACTGCGCTATGCGGTCTT
79824 AATTGAGAGG
Statistics
Matches: 502, Mismatches: 72, Indels: 55
0.80 0.11 0.09
Matches are distributed among these distances:
304 21 0.04
305 1 0.00
306 27 0.05
307 151 0.30
308 8 0.02
309 13 0.03
310 30 0.06
311 1 0.00
312 2 0.00
313 4 0.01
314 17 0.03
315 9 0.02
316 14 0.03
317 12 0.02
318 74 0.15
319 113 0.23
320 4 0.01
321 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (309 bp):
CTCAAATTTTAGCATCATAGAGGCAGTAAAAAAGAATAAACAAAATTAATAAAGACGACCACAGT
GGGAGTCGAACCCACGACCTTCTGATCCGAAGTCAGACGCGCTAATCCACTGCGCTATGCGGTCT
TGGGTGAAAGATAGGGAAATAAAGTAACTCAAATTTTAGCATCACAGAGGCAGTAAAAAAGAATA
ACAAAAGTTAATAAAAACGACCACAGAGGAAGTCGAACCCACGACCTTCTGATCCGAAGTCAGAC
GCGCTAATCCACTGCGCTATGCGGTCTTGGGACAAGGCAAACAAAGTAA
Found at i:80905 original size:27 final size:27
Alignment explanation
Indices: 80875--80937 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
80865 AATCGGTATA
80875 ATAATAATTTTAACACTC-AAATTTAAC
1 ATAATAATTTTAACACTCAAAATTT-AC
* *
80902 ATAAT-CTATTTAACTCTCAAAATTTAC
1 ATAATAAT-TTTAACACTCAAAATTTAC
80929 A-AATAATTT
1 ATAATAATTT
80938 CAAATTGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
26 6 0.20
27 18 0.60
28 6 0.20
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (27 bp):
ATAATAATTTTAACACTCAAAATTTAC
Found at i:82373 original size:8 final size:8
Alignment explanation
Indices: 82362--82403 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
82352 TTTAATCTTT
82362 TAAAATTA
1 TAAAATTA
*
82370 TAAAAATA
1 TAAAATTA
82378 T-AAATTA
1 TAAAATTA
*
82385 TTAAAATAA
1 -TAAAATTA
82394 TAAAATTA
1 TAAAATTA
82402 TA
1 TA
82404 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 5 0.18
8 18 0.64
9 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAATTA
Found at i:82382 original size:15 final size:17
Alignment explanation
Indices: 82362--82403 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
82352 TTTAATCTTT
82362 TAAAATTATAAAAAT-A
1 TAAAATTATAAAAATAA
*
82378 T-AAATTATTAAAATAA
1 TAAAATTATAAAAATAA
82394 TAAAATTATA
1 TAAAATTATA
82404 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 3 0.14
17 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Found at i:92840 original size:24 final size:24
Alignment explanation
Indices: 92804--92849 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
92794 GGTTAATTAA
** *
92804 GAAAAAAGGTTCAAGTAGCAAATT
1 GAAAAAAAATTCAAGTACCAAATT
*
92828 GAAAAAAAATTCAGGTACCAAA
1 GAAAAAAAATTCAAGTACCAAA
92850 ATAAACATTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (24 bp):
GAAAAAAAATTCAAGTACCAAATT
Found at i:94467 original size:64 final size:64
Alignment explanation
Indices: 94398--94526 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
94388 ATAGCACAAA
94398 TACATTCCCATCCTTTTTTCACCTTTATCCCCAAGAAATACTCGAGGCTTCCAAGGTCTTTAAG
1 TACATTCCCATCCTTTTTTCACCTTTATCCCCAAGAAATACTCGAGGCTTCCAAGGTCTTTAAG
94462 TACATTCCCATCCTTTTTTCACCTTTATCCCCAAGAAATACTCGAGGCTTCCAAGGTCTTTAAG
1 TACATTCCCATCCTTTTTTCACCTTTATCCCCAAGAAATACTCGAGGCTTCCAAGGTCTTTAAG
94526 T
1 T
94527 GAGAACTTAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.35
Consensus pattern (64 bp):
TACATTCCCATCCTTTTTTCACCTTTATCCCCAAGAAATACTCGAGGCTTCCAAGGTCTTTAAG
Found at i:96446 original size:5 final size:5
Alignment explanation
Indices: 96436--96481 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
96426 AAATATCAAT
*
96436 AAATA AAATA AAATA TAAA-A TAATA AAATA AAATA AAATA TAAATA
1 AAATA AAATA AAATA -AAATA AAATA AAATA AAATA AAATA -AAATA
96482 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
4 2 0.06
5 26 0.72
6 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAATA
Found at i:96447 original size:25 final size:26
Alignment explanation
Indices: 96421--96482 Score: 92
Period size: 25 Copynumber: 2.4 Consensus size: 26
96411 AAAATGCCTA
*
96421 AATAAAAATATCAAT-AAATAAAATAA
1 AATATAAATAT-AATAAAATAAAATAA
96447 AATATAAA-ATAATAAAATAAAATAA
1 AATATAAATATAATAAAATAAAATAA
96472 AATATAAATAT
1 AATATAAATAT
96483 TTTTAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
24 3 0.09
25 21 0.64
26 9 0.27
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (26 bp):
AATATAAATATAATAAAATAAAATAA
Found at i:96478 original size:20 final size:21
Alignment explanation
Indices: 96420--96478 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
96410 TAAAATGCCT
*
96420 AAATAAAAATATCAATA-AATA
1 AAAT-AAAATATAAATATAATA
96441 AAATAAAATATAAA-ATAATA
1 AAATAAAATATAAATATAATA
96461 AAATAAAATA-AAATATAA
1 AAATAAAATATAAATATAA
96479 ATATTTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
19 4 0.11
20 27 0.77
21 4 0.11
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATAAAATATAAATATAATA
Found at i:96515 original size:28 final size:27
Alignment explanation
Indices: 96436--96522 Score: 92
Period size: 28 Copynumber: 3.3 Consensus size: 27
96426 AAATATCAAT
96436 AAATAAAATAAAATATAAAATAA---TA
1 AAATAAAATAAAATAT-AAATAAGTTTA
**
96461 AAATAAAATAAAATATAAATATTTTTAA
1 AAATAAAATAAAATATAAATAAGTTT-A
*
96489 AAATAAAA-AATAATATAAGTAAGTTTA
1 AAATAAAATAA-AATATAAATAAGTTTA
96516 AAATAAA
1 AAATAAA
96523 CTTAAGTTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
24 5 0.09
25 16 0.30
27 11 0.21
28 21 0.40
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (27 bp):
AAATAAAATAAAATATAAATAAGTTTA
Found at i:99383 original size:15 final size:15
Alignment explanation
Indices: 99336--99383 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
99326 TGAGTTGACT
* *
99336 AATATTAAGAATAAA
1 AATATTAAAAAAAAA
* *
99351 AATACTTATAAAATAA
1 AATA-TTAAAAAAAAA
99367 AATATTAAAAAAAAA
1 AATATTAAAAAAAAA
99382 AA
1 AA
99384 AATCTTATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (15 bp):
AATATTAAAAAAAAA
Found at i:110940 original size:22 final size:22
Alignment explanation
Indices: 110898--110940 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
110888 AATTAATTAA
*
110898 TTTTAAAATATAGATTTTATTT
1 TTTTAAAATATAGATTATATTT
110920 TTTTAAATATATAG-TTATATT
1 TTTTAAA-ATATAGATTATATT
110941 CTAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTTAAAATATAGATTATATTT
Found at i:126446 original size:225 final size:225
Alignment explanation
Indices: 126055--126476 Score: 835
Period size: 225 Copynumber: 1.9 Consensus size: 225
126045 GACCTGGTGG
126055 GGCTTCTTGGCTTTGACCTTGCCTTGCTTGACAGGCTTTCATAGAATTGCTACAATCAAACAGCA
1 GGCTTCTTGGCTTTGACCTTGCCTTGCTTGACAGGCTTTCATAGAATTGCTACAATCAAACAGCA
126120 ACCGCAACAAAAAATAAGTACAGAGAAGTGCACGTAGAGAAAACAAAAGTTCCAGTTCTACTTAA
66 ACCGCAACAAAAAATAAGTACAGAGAAGTGCACGTAGAGAAAACAAAAGTTCCAGTTCTACTTAA
126185 TTTGGCGCACATTTCAGTAGACATGCAGTAAATTGAACAGTTCACAGTAAGTGTAAAATAATGGA
131 TTTGGCGCACATTTCAGTAGACATGCAGTAAATTGAACAGTTCACAGTAAGTGTAAAATAATGGA
126250 ACAAAAAATAAGTACAGAGAAGTGTAATTT
196 ACAAAAAATAAGTACAGAGAAGTGTAATTT
126280 GGCTTCTTGGCTTTGACCTTGCCTTGCTTGACAGGCTTTCATAGAATTGCTACAATCAAACAGCA
1 GGCTTCTTGGCTTTGACCTTGCCTTGCTTGACAGGCTTTCATAGAATTGCTACAATCAAACAGCA
*
126345 ACCGCAACAAACAATAAGTACAGAGAAGTGCACGTAGAGAAAACAAAAGTTCCAGTTCTACTTAA
66 ACCGCAACAAAAAATAAGTACAGAGAAGTGCACGTAGAGAAAACAAAAGTTCCAGTTCTACTTAA
126410 TTTGGCGCACATTTCAGTAGACATGCAGTAAATTGAACAGTTCACAGTAAGTGTAAAATAATGGA
131 TTTGGCGCACATTTCAGTAGACATGCAGTAAATTGAACAGTTCACAGTAAGTGTAAAATAATGGA
126475 AC
196 AC
126477 CTCAACTGCA
Statistics
Matches: 196, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
225 196 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (225 bp):
GGCTTCTTGGCTTTGACCTTGCCTTGCTTGACAGGCTTTCATAGAATTGCTACAATCAAACAGCA
ACCGCAACAAAAAATAAGTACAGAGAAGTGCACGTAGAGAAAACAAAAGTTCCAGTTCTACTTAA
TTTGGCGCACATTTCAGTAGACATGCAGTAAATTGAACAGTTCACAGTAAGTGTAAAATAATGGA
ACAAAAAATAAGTACAGAGAAGTGTAATTT
Found at i:128343 original size:16 final size:16
Alignment explanation
Indices: 128296--128348 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
128286 ATTTGAGTCA
* *
128296 ATTTCAGATTTAGATC
1 ATTTTAGATTTAGATT
* *
128312 ATTCTAGATTTTGATT
1 ATTTTAGATTTAGATT
*
128328 ATTTTGGATTTAGATT
1 ATTTTAGATTTAGATT
128344 -TTTTA
1 ATTTTA
128349 ATTGAGTCGT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 4 0.14
16 25 0.86
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (16 bp):
ATTTTAGATTTAGATT
Found at i:132142 original size:21 final size:21
Alignment explanation
Indices: 132116--132156 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
132106 GGTTTAGGAT
*
132116 TTCAAGGTTTAAGATTTAGGG
1 TTCAAGATTTAAGATTTAGGG
*
132137 TTCAAGATTTAGGATTTAGG
1 TTCAAGATTTAAGATTTAGG
132157 ATCCAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.27, T:0.39
Consensus pattern (21 bp):
TTCAAGATTTAAGATTTAGGG
Found at i:132237 original size:10 final size:10
Alignment explanation
Indices: 132222--132261 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
132212 AAAGATGCTG
*
132222 AAATAATATT
1 AAATAATATA
132232 AAATAATTATA
1 AAATAA-TATA
*
132243 AAAAAATATA
1 AAATAATATA
132253 AAATAATAT
1 AAATAATAT
132262 GGTATCTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAATAATATA
Found at i:132375 original size:2 final size:2
Alignment explanation
Indices: 132368--132414 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
132358 GAACAGACAA
* *
132368 AT AT AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
132410 AT AT A
1 AT AT A
132415 AGCAAAAGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:135208 original size:59 final size:59
Alignment explanation
Indices: 135089--135455 Score: 526
Period size: 59 Copynumber: 6.2 Consensus size: 59
135079 AAATAGGTAG
* * * *
135089 TTTTGGAAGGTTCGGAGTCAAAAAT-GGATTTTTGTAAGTTCG-GGGTAAAATGGTTAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
* *
135146 TTTTAGAAGGTTCGGGGTTAAAAATGGGATTTTTGGGAGTTCGAGGGTAAAATGGTAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
* * *
135205 TTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGGAGTTCGGGTGGTAAAATGGTAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAG-GGTAAAATGGTAAT
* * * *
135265 TTTT-GAAAGGTTCGAGGTTAAAAATGAGATTTTTGGAAGTTTGAGGGTAAAATGGTAAT
1 TTTTAG-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
* *
135324 TTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTC-AGGGGTAAAATGGTAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAAT
* *
135383 TTTTAGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAAT
1 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
135442 TTTTAGAAGGTTCG
1 TTTTAGAAGGTTCG
135456 AGGACCTCCG
Statistics
Matches: 280, Mismatches: 23, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
57 22 0.08
58 16 0.06
59 190 0.68
60 52 0.19
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (59 bp):
TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAAT
Found at i:135431 original size:118 final size:115
Alignment explanation
Indices: 135089--135458 Score: 546
Period size: 119 Copynumber: 3.1 Consensus size: 115
135079 AAATAGGTAG
* * *
135089 TTTTGGAAGGTTCG-GAGTCAAAAATGGATTTTTGTAAGTTCGGGGTAAAATGGTTATTTTTAGA
1 TTTTAGAAGGTTCGAG-GTCAAAAATGGATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTTAGA
* *
135153 AGGTTCGGGGTTAAAAATGGGATTTTTGGGAGTTCGAGGGTAAAATGGTAAT
65 AGGTTC-GGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAAT
* * *
135205 TTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGGAGTTCGGGTGGTAAAATGGTAATTTTT-
1 TTTTAGAAGGTTCGAGGTCAAAAAT-GGATTTTTGGAAGTTC-GG-GGTAAAATGGTAATTTTTA
*
135269 GAAAGGTTCGAGGTTAAAAATGAGATTTTTGGAAGTTTGAGGGTAAAATGGTAAT
63 G-AAGGTTCG-GGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAAT
135324 TTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTAG
1 TTTTAGAAGGTTCGAGGTCAAAAATG-GATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTAG
*
135389 AAGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAAT
64 AAGGTTC-GGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAAT
135442 TTTTAGAAGGTTCGAGG
1 TTTTAGAAGGTTCGAGG
135459 ACCTCCGAAG
Statistics
Matches: 231, Mismatches: 14, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
116 21 0.09
117 15 0.06
118 89 0.39
119 106 0.46
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (115 bp):
TTTTAGAAGGTTCGAGGTCAAAAATGGATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTTAGAA
GGTTCGGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAAT
Done.