Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002190.1 Kokia drynarioides strain JFW-HI SEQ_114163, 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: 188926
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:323 original size:16 final size:16
Alignment explanation
Indices: 302--332 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
292 TTATTTAGTT
*
302 TTTAAAATAAAATACC
1 TTTAAAAGAAAATACC
318 TTTAAAAGAAAATAC
1 TTTAAAAGAAAATAC
333 AGTGATACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (16 bp):
TTTAAAAGAAAATACC
Found at i:12751 original size:19 final size:19
Alignment explanation
Indices: 12723--12771 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
12713 TTAATATTTT
12723 TTATTTTTTTCTGCAAT-CAA
1 TTATTTTTTTC--CAATACAA
*
12743 TTATTTTTTTCCATTACAA
1 TTATTTTTTTCCAATACAA
12762 TTATTTTTTT
1 TTATTTTTTT
12772 TTTTGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.11
19 13 0.48
20 11 0.41
ACGTcount: A:0.22, C:0.12, G:0.02, T:0.63
Consensus pattern (19 bp):
TTATTTTTTTCCAATACAA
Found at i:15869 original size:20 final size:20
Alignment explanation
Indices: 15806--15875 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
15796 GCCTAGAACA
* *
15806 ATTTTGACTTGTTTGAACA-C
1 ATTTTGACTTGGTT-AAAATC
* * *
15826 AGTTTGA-TTTGTTAAAATG
1 ATTTTGACTTGGTTAAAATC
*
15845 GTTTTGACTTGGTTAAAATC
1 ATTTTGACTTGGTTAAAATC
*
15865 ATTTTAACTTG
1 ATTTTGACTTG
15876 ATTTTAAAGT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
18 3 0.08
19 9 0.24
20 25 0.68
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (20 bp):
ATTTTGACTTGGTTAAAATC
Found at i:33614 original size:21 final size:20
Alignment explanation
Indices: 33590--33640 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
33580 AGAGCAATTC
33590 TGACTTGATTGAGAAA-CAGTT
1 TGACTTGATT-A-AAATCAGTT
*
33611 TGACTTGGTTAAAATCAGTT
1 TGACTTGATTAAAATCAGTT
*
33631 TAACTTGATT
1 TGACTTGATT
33641 TTAAAGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.12
20 14 0.54
21 9 0.35
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (20 bp):
TGACTTGATTAAAATCAGTT
Found at i:35054 original size:157 final size:157
Alignment explanation
Indices: 34729--35061 Score: 353
Period size: 157 Copynumber: 2.1 Consensus size: 157
34719 TAAAAGTTTA
*
34729 GGGAAAAATAAAAAGTTTTAAGGGTTTTGGGAGTAAAATTTGAGGGAAAGTAAATAAGGGGAGTA
1 GGGAAAAATAAAAAGTTTTGAGGGTTTTGGGAGTAAAATTTGAGGGAAAGTAAATAAGGGGAGTA
** * * * * *
34794 AAATTTTGGAGGAAAAATATTCCAAAAAATTGGGAGGAGGAATGAGTTTGGGGTAGATGAGAGGT
66 AAATTTCAGAGGAAAAATATTCAAAAAAATTAGGAGGAGAAATGAGTTTGAGGTAAATGAGAGGT
* * *
34859 GGGATGGGAGGGAGTAAAAGTTATTTG
131 GGGATGGGAGGGAGAAAAAATTATTGG
* *
34886 GGG-AAATTAAAAAGTTTTGAGGGTTTTTGGGGAG-AAAATTTTTG-GGAGAAAGTAAAT-GGGG
1 GGGAAAAATAAAAAGTTTTGAGGG-TTTT-GGGAGTAAAA--TTTGAGG-GAAAGTAAATAAGGG
* *
34947 GAGTAAAATTTCAGAGGGAAAATATT-AAAAATAATCTAGG-GGA-AAATGGGTTTGAGGTAAAT
61 GAGTAAAATTTCAGAGGAAAAATATTCAAAAA-AAT-TAGGAGGAGAAATGAGTTTGAGGTAAAT
*
35009 CG-GGGGTGGGATGGGA-GGAGAAAAAAATT-TTGG
124 -GAGAGGTGGGATGGGAGGGAG-AAAAAATTATTGG
* *
35042 GGGAAAAGTAAAAAGGTTTG
1 GGGAAAAATAAAAAGTTTTG
35062 GAAATAGATT
Statistics
Matches: 148, Mismatches: 18, Indels: 20
0.80 0.10 0.11
Matches are distributed among these distances:
156 28 0.19
157 63 0.43
158 40 0.27
159 17 0.11
ACGTcount: A:0.39, C:0.02, G:0.35, T:0.25
Consensus pattern (157 bp):
GGGAAAAATAAAAAGTTTTGAGGGTTTTGGGAGTAAAATTTGAGGGAAAGTAAATAAGGGGAGTA
AAATTTCAGAGGAAAAATATTCAAAAAAATTAGGAGGAGAAATGAGTTTGAGGTAAATGAGAGGT
GGGATGGGAGGGAGAAAAAATTATTGG
Found at i:41050 original size:18 final size:18
Alignment explanation
Indices: 41009--41064 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
40999 ATGCAACTAC
41009 AATGCAAATGCACTAAAT-AA
1 AATGC-AATG-AC-AAATAAA
* *
41029 AATGTAGTGACAAATAAA
1 AATGCAATGACAAATAAA
*
41047 AATGCAATGACAACTAAA
1 AATGCAATGACAAATAAA
41065 TTCTATGCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.13
18 19 0.63
19 3 0.10
20 4 0.13
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (18 bp):
AATGCAATGACAAATAAA
Found at i:43333 original size:16 final size:17
Alignment explanation
Indices: 43308--43339 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43298 GGGAAACAGA
43308 TAAAAGAAGAAATAAAG
1 TAAAAGAAGAAATAAAG
43325 TAAAA-AAGAAATAAA
1 TAAAAGAAGAAATAAA
43340 CATAAATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
TAAAAGAAGAAATAAAG
Found at i:43345 original size:17 final size:17
Alignment explanation
Indices: 43307--43345 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
43297 AGGGAAACAG
43307 ATAAAAGAAGAAATAAA
1 ATAAAAGAAGAAATAAA
*
43324 GTAAAA-AAGAAATAAA
1 ATAAAAGAAGAAATAAA
43340 CATAAA
1 -ATAAA
43346 TGTAAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (17 bp):
ATAAAAGAAGAAATAAA
Found at i:54499 original size:71 final size:71
Alignment explanation
Indices: 54384--54678 Score: 387
Period size: 71 Copynumber: 4.2 Consensus size: 71
54374 ACTGAAACTT
* ** *
54384 CTCAAGTCAGTAGCCATGGTATTTTTTCCC-TGAACATT-TACCGATACTTAGTTGAGTTGTTCC
1 CTCAAGTCAGTAGCCAAGGTATCCTTTCCCTTGAAC-TTCTACCGATACTTTGTTGAGTTGTTCC
54447 AAAACAA
65 AAAACAA
* * * * * *
54454 CTCAAGTCAGTAACCAAGATATCCTGTACCTTGAACTCCTACCGATACTTTGTTGAGTTGTTCCG
1 CTCAAGTCAGTAGCCAAGGTATCCTTTCCCTTGAACTTCTACCGATACTTTGTTGAGTTGTTCCA
54519 AAACAA
66 AAACAA
* * *
54525 GTCAAGTCAGTAGCCAAGGTATCCTTTCCCCTGAACTTCTACCAATACTTTGTTGAGTTGTTCCA
1 CTCAAGTCAGTAGCCAAGGTATCCTTTCCCTTGAACTTCTACCGATACTTTGTTGAGTTGTTCCA
*
54590 AAATAA
66 AAACAA
* * * * * *
54596 CTTAAGTCAGTAGCCAAGGTATCCTTTCCCTTGAACTTCTACTGATACTTTTTTAAGTTGTTTCG
1 CTCAAGTCAGTAGCCAAGGTATCCTTTCCCTTGAACTTCTACCGATACTTTGTTGAGTTGTTCCA
54661 AAACAA
66 AAACAA
54667 CTCAAGTCAGTA
1 CTCAAGTCAGTA
54679 TCAAAATTTG
Statistics
Matches: 192, Mismatches: 31, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
70 24 0.12
71 168 0.88
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (71 bp):
CTCAAGTCAGTAGCCAAGGTATCCTTTCCCTTGAACTTCTACCGATACTTTGTTGAGTTGTTCCA
AAACAA
Found at i:55209 original size:24 final size:24
Alignment explanation
Indices: 55182--55244 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
55172 CTTGCACACC
*
55182 TTTATGCTCGTCAGCTTATATATG
1 TTTACGCTCGTCAGCTTATATATG
* *
55206 TTTACACTAGTCAGCTTATATATG
1 TTTACGCTCGTCAGCTTATATATG
55230 TTTACGCTCGTCAGC
1 TTTACGCTCGTCAGC
55245 ATGCACACGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTTATATATG
Found at i:55256 original size:24 final size:24
Alignment explanation
Indices: 55155--55258 Score: 82
Period size: 24 Copynumber: 4.3 Consensus size: 24
55145 CATCTTATTT
* *
55155 ACGTCTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTACAC
* * * *
55179 ACCTTTATGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTACAC
* * * * *
55203 ATGTTTACACTAGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTACAC
* * *
55227 ATGTTTACGCTCGTCAGCATGCAC
1 ACGTTTACGCTCGTCAGCTTACAC
55251 ACGTTTAC
1 ACGTTTAC
55259 ATTACTTTGT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (24 bp):
ACGTTTACGCTCGTCAGCTTACAC
Found at i:58011 original size:15 final size:15
Alignment explanation
Indices: 57993--58048 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 15
57983 GATTGGTTGA
57993 ATATTTTATTATAAG
1 ATATTTTATTATAAG
58008 ATATTTGGTATTA-AATTG
1 ATATTT--TATTATAA--G
58026 TAATATTTTATTATAAG
1 --ATATTTTATTATAAG
58043 ATATTT
1 ATATTT
58049 GCATGGAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
15 12 0.35
16 2 0.06
17 6 0.18
18 6 0.18
19 2 0.06
20 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.54
Consensus pattern (15 bp):
ATATTTTATTATAAG
Found at i:59903 original size:19 final size:19
Alignment explanation
Indices: 59879--59919 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
59869 TCTATTGTTT
*
59879 TTATT-AATTTACAATTTTA
1 TTATTAAATTTA-AATTGTA
59898 TTATTAAATTTAAATTGTA
1 TTATTAAATTTAAATTGTA
59917 TTA
1 TTA
59920 ATATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTAAATTTAAATTGTA
Found at i:62701 original size:19 final size:20
Alignment explanation
Indices: 62673--62712 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
62663 AAGAATAAAC
62673 AGAATAAAA-GCATTAAATA
1 AGAATAAAAGGCATTAAATA
* *
62692 AGAATCAAAGGGATTAAATA
1 AGAATAAAAGGCATTAAATA
62712 A
1 A
62713 TGAAAGATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.60, C:0.05, G:0.15, T:0.20
Consensus pattern (20 bp):
AGAATAAAAGGCATTAAATA
Found at i:64471 original size:30 final size:30
Alignment explanation
Indices: 64435--64495 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
64425 GATAAAAATT
64435 CATGAAAACTATCTAAAAGAAATGTACTAA
1 CATGAAAACTATCTAAAAGAAATGTACTAA
64465 CATGAAAACTATCTAAAAGAAATGTACTAA
1 CATGAAAACTATCTAAAAGAAATGTACTAA
64495 C
1 C
64496 TTATTCGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.23
Consensus pattern (30 bp):
CATGAAAACTATCTAAAAGAAATGTACTAA
Found at i:66739 original size:20 final size:21
Alignment explanation
Indices: 66714--66752 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
66704 GCAAGGAATT
66714 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
66734 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
66753 TAGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:70028 original size:102 final size:102
Alignment explanation
Indices: 69899--70100 Score: 377
Period size: 102 Copynumber: 2.0 Consensus size: 102
69889 TGATGACATT
*
69899 GCTCTTTGGCTCCAGACGGAGATGCCTCAAACACACTAAAGGTCACATGCTCATCATTATGACGC
1 GCTCTTTAGCTCCAGACGGAGATGCCTCAAACACACTAAAGGTCACATGCTCATCATTATGACGC
69964 ATGATAAGTTCTCCCTTGAACACATCGATAAGTGTAC
66 ATGATAAGTTCTCCCTTGAACACATCGATAAGTGTAC
* *
70001 GCTCTTTAGTTCCAGACGGAGATGCCTCAATCACACTAAAGGTCACATGCTCATCATTATGACGC
1 GCTCTTTAGCTCCAGACGGAGATGCCTCAAACACACTAAAGGTCACATGCTCATCATTATGACGC
70066 ATGATAAGTTCTCCCTTGAACACATCGATAAGTGT
66 ATGATAAGTTCTCCCTTGAACACATCGATAAGTGT
70101 GCGACCCGTT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 97 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (102 bp):
GCTCTTTAGCTCCAGACGGAGATGCCTCAAACACACTAAAGGTCACATGCTCATCATTATGACGC
ATGATAAGTTCTCCCTTGAACACATCGATAAGTGTAC
Found at i:73311 original size:20 final size:19
Alignment explanation
Indices: 73272--73311 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
73262 AAGAATAAAC
*
73272 AGAATAAAAGCATTAAATA
1 AGAATAAAAGCATCAAATA
*
73291 AGAATAAAAGGGATCAAATA
1 AGAATAAAA-GCATCAAATA
73311 A
1 A
73312 TGAAAGATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.62, C:0.05, G:0.15, T:0.17
Consensus pattern (19 bp):
AGAATAAAAGCATCAAATA
Found at i:77859 original size:18 final size:19
Alignment explanation
Indices: 77838--77876 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
77828 TTATTTGTTT
77838 TTATT-AATTTACAATT-TA
1 TTATTAAATTTA-AATTGTA
77856 TTATTAAATTTAAATTGTA
1 TTATTAAATTTAAATTGTA
77875 TT
1 TT
77877 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTAAATTTAAATTGTA
Found at i:79184 original size:26 final size:26
Alignment explanation
Indices: 79155--79226 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
79145 AACGAGTTCC
79155 TGCAGCGACAATTCTGGGCATGC-TCA
1 TGCAGCGACAATTCTGGGCAT-CATCA
* *
79181 TGCAGCGACATTTCTGGACATCATCA
1 TGCAGCGACAATTCTGGGCATCATCA
** *
79207 TGCAATGACAATTTTGGGCA
1 TGCAGCGACAATTCTGGGCA
79227 CAATTTTAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (26 bp):
TGCAGCGACAATTCTGGGCATCATCA
Found at i:79739 original size:3 final size:3
Alignment explanation
Indices: 79733--79785 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
79723 TACATATATC
79733 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
79781 ATT AT
1 ATT AT
79786 GTGACTGAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:80349 original size:47 final size:47
Alignment explanation
Indices: 80280--80374 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
80270 TCCAAACTCC
*
80280 ATATGCCTTCCCCTAAACATAAAGTTTGCATTGTCCCCAATGCACTA
1 ATATGCCTTCCCCCAAACATAAAGTTTGCATTGTCCCCAATGCACTA
*
80327 ATATGCCTTCCCCCAAACATAAAGTTTGCATTGTCCCTAATGCACTA
1 ATATGCCTTCCCCCAAACATAAAGTTTGCATTGTCCCCAATGCACTA
80374 A
1 A
80375 CACTAAAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (47 bp):
ATATGCCTTCCCCCAAACATAAAGTTTGCATTGTCCCCAATGCACTA
Found at i:80401 original size:17 final size:17
Alignment explanation
Indices: 80379--80412 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
80369 CACTAACACT
*
80379 AAAATGCAATGACAATG
1 AAAATGCAACGACAATG
80396 AAAATGCAACGACAATG
1 AAAATGCAACGACAATG
80413 CTTACTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATG
Found at i:81796 original size:23 final size:20
Alignment explanation
Indices: 81747--81796 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
81737 ACGACATTAG
*
81747 ACAATTAAATAAATTAATGC
1 ACAAATAAATAAATTAATGC
*
81767 ACGAATAAATAAATCTAATATGC
1 ACAAATAAATAAAT-T-A-ATGC
81790 ACAAATA
1 ACAAATA
81797 CTAAAAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.50
21 1 0.04
22 1 0.04
23 10 0.42
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (20 bp):
ACAAATAAATAAATTAATGC
Found at i:83221 original size:10 final size:10
Alignment explanation
Indices: 83173--83227 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
83163 GTAAAAAATC
*
83173 ATAAATATAA
1 ATAAATAAAA
*
83183 ATAGACATGAAA
1 ATA-A-ATAAAA
83195 ATAAATAAAA
1 ATAAATAAAA
*
83205 ATGAAATAAGA
1 AT-AAATAAAA
83216 ATAAATAAAA
1 ATAAATAAAA
83226 AT
1 AT
83228 TATTCAAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
10 19 0.51
11 11 0.30
12 7 0.19
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:84189 original size:149 final size:147
Alignment explanation
Indices: 83720--84224 Score: 519
Period size: 151 Copynumber: 3.4 Consensus size: 147
83710 ACAAAATTAC
* * *
83720 TACTTTATTTTAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTGTTTAAAA
1 TACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTGTTTAAAA
* *
83785 ATTTAAACTTTTTCTTTAAAATTACTA-AAAAACAAATTTTTATTTTTTTAAA--TAAA--TCTA
66 A---AAA-TTTTTCTTTAAAATAACTAGAAAAACATATTTTTATTTTTTTAAATCTAAATTTCTA
**
83845 AATTTTTTTAAATGAAAATCAT
127 TTTTTTTTTAAA-GAAAATCAT
* *
83867 TACTTTACTTAAAAATTC-AAACATTTATTTTGAAATAGTT-AAAAAA--AAAACTTTGTTTAAA
1 TACTTTACTTAAAAA-TCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTGTTTAAA
* * * ** *
83928 AATTTAAACTTTTCTTTAAAATGATTAAGAAAGCAATTTTTTTATTATTTTTTTAAATCTAAACT
65 AA---AAATTTTTCTTTAAAATAACT-AGAAA--AACATATTT-TTATTTTTTTAAATCTAAA-T
* * *
83993 TTC-ATTTTTTTTTAATGAAAAACAC
122 TTCTATTTTTTTTTAAAGAAAATCAT
* *
84018 TATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAATCAAAACTTTGTTTAAAA
1 TACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTGTTTAAAA
* ** *
84082 AAAGTTTTTCTTTAAAATAACTAGAAAAACATATTTTTATTTTTAAAAATCTAAATTTTCTCTTT
66 AAAATTTTTCTTTAAAATAACTAGAAAAACATATTTTTATTTTTTTAAATCTAAA--TT-TCTAT
84147 TTTTTTTTAAAGAAAATCAT
128 TTTTTTTTAAAGAAAATCAT
* * * *
84167 TACTTTCCTTAAAAATCAAAACTTTAATTTCGAAATTGTTTAAAAAAACCAAAACTTT
1 TACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAG-TTAAAAAAATCAAAACTTT
84225 TCCCAAAATC
Statistics
Matches: 299, Mismatches: 40, Indels: 34
0.80 0.11 0.09
Matches are distributed among these distances:
143 15 0.05
144 23 0.08
145 3 0.01
146 23 0.08
147 46 0.15
148 17 0.06
149 56 0.19
150 25 0.08
151 62 0.21
152 10 0.03
153 19 0.06
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (147 bp):
TACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTTGTTTAAAA
AAAATTTTTCTTTAAAATAACTAGAAAAACATATTTTTATTTTTTTAAATCTAAATTTCTATTTT
TTTTTAAAGAAAATCAT
Found at i:84644 original size:3 final size:3
Alignment explanation
Indices: 84636--84684 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
84626 TCATGAACCC
84636 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
84684 T
1 T
84685 TTGGGCCCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:85109 original size:20 final size:19
Alignment explanation
Indices: 85086--85145 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
85076 ATCAATTAGC
85086 ATTTACAATGCAATATAAAA
1 ATTTACAAT-CAATATAAAA
**
85106 ATTT--AATCAAT-T-AGC
1 ATTTACAATCAATATAAAA
85121 ATTTACAATACAATATAAAA
1 ATTTACAAT-CAATATAAAA
85141 ATTTA
1 ATTTA
85146 TCTAATTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 5 0.16
16 1 0.03
17 7 0.23
18 7 0.23
19 1 0.03
20 10 0.32
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (19 bp):
ATTTACAATCAATATAAAA
Found at i:85116 original size:35 final size:35
Alignment explanation
Indices: 85076--85145 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
85066 AATTACTAAG
*
85076 ATCAATTAGCATTTACAATGCAATATAAAAATTTA
1 ATCAATTAGCATTTACAATACAATATAAAAATTTA
85111 ATCAATTAGCATTTACAATACAATATAAAAATTTA
1 ATCAATTAGCATTTACAATACAATATAAAAATTTA
85146 TCTAATTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.34
Consensus pattern (35 bp):
ATCAATTAGCATTTACAATACAATATAAAAATTTA
Found at i:85292 original size:22 final size:22
Alignment explanation
Indices: 85237--85292 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
85227 TCGAGCCATT
*
85237 GTCGCGACGTCATGAACCTGTC
1 GTCGCGACGTCGTGAACCTGTC
* * *
85259 GTCGCAATGTCGTGAGCCTGTC
1 GTCGCGACGTCGTGAACCTGTC
*
85281 GTCGTGACGTCG
1 GTCGCGACGTCG
85293 ATTCTGTGTC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.14, C:0.29, G:0.32, T:0.25
Consensus pattern (22 bp):
GTCGCGACGTCGTGAACCTGTC
Found at i:85721 original size:38 final size:38
Alignment explanation
Indices: 85679--85753 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
85669 GAGTCTATTC
* *
85679 AGAATTGCGCCCAGAATTGTCACTGCATGATGATGTCT
1 AGAATTGCGCCCAAAATTGTCACTGCACGATGATGTCT
*
85717 AGAATTGCGTCCAAAATTGTCACTGCACGATGATGTC
1 AGAATTGCGCCCAAAATTGTCACTGCACGATGATGTC
85754 CAAAAATGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (38 bp):
AGAATTGCGCCCAAAATTGTCACTGCACGATGATGTCT
Found at i:87086 original size:5 final size:5
Alignment explanation
Indices: 87047--87073 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
87037 ATTTCAGGTG
87047 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
87074 CAAGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:90364 original size:25 final size:26
Alignment explanation
Indices: 90325--90374 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
90315 AGCTAACTTA
* *
90325 TCTGGGCTAGTATGAG-TTAATTTTG
1 TCTGGGCTAGCATGAGCTAAATTTTG
*
90350 TCTGGGCTCGCATGAGCTAAATTTT
1 TCTGGGCTAGCATGAGCTAAATTTT
90375 TGAAAGATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (26 bp):
TCTGGGCTAGCATGAGCTAAATTTTG
Found at i:92249 original size:4 final size:4
Alignment explanation
Indices: 92235--92300 Score: 64
Period size: 4 Copynumber: 16.8 Consensus size: 4
92225 GTGCCTCAAT
* * * *
92235 TTCA ATCA TTCA TTCA TTCG TTCG TTCG TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
*
92283 -TCTA TTCA -TCA CTCA TTC
1 TTC-A TTCA TTCA TTCA TTC
92301 GCTCATTTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
3 5 0.09
4 47 0.87
5 2 0.04
ACGTcount: A:0.21, C:0.27, G:0.05, T:0.47
Consensus pattern (4 bp):
TTCA
Found at i:95570 original size:34 final size:33
Alignment explanation
Indices: 95520--95595 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 33
95510 AATCTCCTTC
* *
95520 TGAAAAAGAAAAAAAAAAGAAGAAATAAGGAAAG
1 TGAAAAAGAAAAAAAAAA-AAGAAAGAAAGAAAG
* *
95554 TGAATAAGAAACAAAAAAAAGAAAGAAAGAAAG
1 TGAAAAAGAAAAAAAAAAAAGAAAGAAAGAAAG
*
95587 -GAAATAGAA
1 TGAAAAAGAA
95596 GGAGTAAGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
32 7 0.19
33 13 0.36
34 16 0.44
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.07
Consensus pattern (33 bp):
TGAAAAAGAAAAAAAAAAAAGAAAGAAAGAAAG
Found at i:96158 original size:7 final size:7
Alignment explanation
Indices: 96148--96172 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
96138 AATAAAAAAA
96148 AAAAGAG
1 AAAAGAG
96155 AAAAGAG
1 AAAAGAG
96162 AAAAGAG
1 AAAAGAG
96169 AAAA
1 AAAA
96173 AAAAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAGAG
Found at i:96181 original size:14 final size:14
Alignment explanation
Indices: 96141--96193 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
96131 TTTTTTAAAT
*
96141 AAAAAAAAAAAGAG
1 AAAAAAAAGAAGAG
*
96155 AAAAGAGAA-AAGAG
1 AAAA-AAAAGAAGAG
*
96169 AAAAAAAAGAAGAA
1 AAAAAAAAGAAGAG
96183 AAAAATAAAGA
1 AAAAA-AAAGA
96194 GAGCAAGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 3 0.09
14 22 0.67
15 8 0.24
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAAAAAAGAAGAG
Found at i:96192 original size:26 final size:25
Alignment explanation
Indices: 96144--96195 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
96134 TTTAAATAAA
*
96144 AAAAAAAAGAGAAAAGAGAAAAGAG
1 AAAAAAAAGAGAAAAGAAAAAAGAG
96169 AAAAAAAAGAAGAAAA-AAATAAAGAG
1 AAAAAAAAG-AGAAAAGAAA-AAAGAG
96195 A
1 A
96196 GCAAGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (25 bp):
AAAAAAAAGAGAAAAGAAAAAAGAG
Found at i:97053 original size:42 final size:42
Alignment explanation
Indices: 96564--97044 Score: 656
Period size: 42 Copynumber: 11.5 Consensus size: 42
96554 AAGGAAAGCA
**
96564 TTCATTGCATTTAGAGGCCCAAATGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
96606 TTCATTGCATTTAGAGGCCAAGGTGTGAAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
96648 TTCATTACATTTAGAGGCCCAGGTGTGGAGGCCCGTTCATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
96690 TTCATTGCATTTAAAGGCACAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
96732 TTCATTGCATTTAGAGGCTCAGGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
96774 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** * * * *
96816 TTCATCCCATTTAGAGACCCAAGTGTGTAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
96858 TTCATCGCATGTAGAGGCACAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
96900 TTCATCGTATTTAGAGGCCCATGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
96942 TTCATCGCATTTAGAGGCCCAGGTTTGGAGGTCCATTTAATT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
96984 TTCATTGCATTTAGAGGCCTAGGTGTGAAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
97026 TTTATTGCATTTAGAGGCC
1 TTCATTGCATTTAGAGGCC
97045 TAAATGTGAG
Statistics
Matches: 389, Mismatches: 50, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 389 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:97421 original size:3 final size:3
Alignment explanation
Indices: 97413--97455 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
97403 AAGGGCCCAA
*
97413 ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
97456 AGGTTTCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:98182 original size:20 final size:20
Alignment explanation
Indices: 98139--98181 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
98129 TTCTTAGTTA
*
98139 TTTTAAATAAAAGTTTAAAT
1 TTTTAAACAAAAGTTTAAAT
98159 TTTTAAAC-AAAGATTT-AAT
1 TTTTAAACAAAAG-TTTAAAT
98178 TTTT
1 TTTT
98182 TTAACTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTAAACAAAAGTTTAAAT
Found at i:98246 original size:150 final size:154
Alignment explanation
Indices: 97888--98252 Score: 432
Period size: 150 Copynumber: 2.4 Consensus size: 154
97878 TTATTAATCA
* * * ** * *
97888 ATTTCGAAATAAAAATTTTG-ATTTTTTAAGAAAAATAGTTTTTTTC-TT---TAAAAAAGAGAA
1 ATTTCGAAATAAAAA-CTTGAATTTTTTAAGTAAAATAATAATTTTCATTAAAAAAAAAAAAGAA
*
97948 AATTTAGATTTTTAAAAATAAAAATATGTTTTTCTAGTTATTTTAAAGAAAAAGTTTAAATTTTT
65 AATTTAGATTTTTAAAAATAAAAATATGTTTCTCTAGTTATTTTAAAGAAAAAGTTTAAATTTTT
* *
98013 AAACAAAGTTTCGATTTTTTTAATT
130 AAACAAAGTTTCAATTTTTTTAACT
* * *
98038 ATTTCGAAATAAAAGCTTGAATTTTTTTAAGTAAAATAGTGATTTTCATTAAAAAAAAAAAAGAA
1 ATTTCGAAATAAAAACTTGAA-TTTTTTAAGTAAAATAATAATTTTCATTAAAAAAAAAAAAGAA
* ** *
98103 AGTTTAGA-TTTTAAAAA-AAATCTAT-TTTCT-TAGTTATTTTAAA-TAAAAGTTTAAATTTTT
65 AATTTAGATTTTTAAAAATAAAAATATGTTTCTCTAGTTATTTTAAAGAAAAAGTTTAAATTTTT
98163 AAACAAAGATTT-AATTTTTTTAACT
130 AAACAAAG-TTTCAATTTTTTTAACT
* *
98188 ATTTCGAAGTAAAAA-TTTAGA-TTTTTAAGTAAAATAATAATTTTCATTAAAAAAAAAAAAGAA
1 ATTTCGAAATAAAAACTTGA-ATTTTTTAAGTAAAATAATAATTTTCATTAAAAAAAAAAAAGAA
98251 AA
65 AA
98253 AAGAAAGTTC
Statistics
Matches: 187, Mismatches: 20, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
148 41 0.22
149 6 0.03
150 64 0.34
151 38 0.20
152 6 0.03
153 6 0.03
154 9 0.05
155 17 0.09
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (154 bp):
ATTTCGAAATAAAAACTTGAATTTTTTAAGTAAAATAATAATTTTCATTAAAAAAAAAAAAGAAA
ATTTAGATTTTTAAAAATAAAAATATGTTTCTCTAGTTATTTTAAAGAAAAAGTTTAAATTTTTA
AACAAAGTTTCAATTTTTTTAACT
Found at i:103957 original size:92 final size:92
Alignment explanation
Indices: 103853--104042 Score: 335
Period size: 92 Copynumber: 2.1 Consensus size: 92
103843 TTTTAGTATC
*
103853 ATTTAATAATTAAATTAACGATTTTAATAATAAAATCACCTAATTAATATAAGATGAATGGTTTA
1 ATTTAATAATTAAATTAACGATTTTAATAATAAAATCACCTAATTAATATAAGATGAATAGTTTA
*
103918 AAATGTAATTAAAATATTGTGAGGTCA
66 AAATGTAATTAAAATATTGTGAGGCCA
* * *
103945 ATTTAATAATTAAATTAACGATTTTAATAATAGAATCACGTAATTAATATAAGATGAATAGTTTG
1 ATTTAATAATTAAATTAACGATTTTAATAATAAAATCACCTAATTAATATAAGATGAATAGTTTA
104010 AAATGTAATTAAAATATTGTGAGGCCA
66 AAATGTAATTAAAATATTGTGAGGCCA
104037 ATTTAA
1 ATTTAA
104043 AATAAAAGTA
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (92 bp):
ATTTAATAATTAAATTAACGATTTTAATAATAAAATCACCTAATTAATATAAGATGAATAGTTTA
AAATGTAATTAAAATATTGTGAGGCCA
Found at i:104129 original size:61 final size:61
Alignment explanation
Indices: 104054--104176 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
104044 ATAAAAGTAT
104054 AATTTGAGGAGGTTTCATGCATTTACCTTTTAAAATAACCTACGAGGACGACGAGGCATAC
1 AATTTGAGGAGGTTTCATGCATTTACCTTTTAAAATAACCTACGAGGACGACGAGGCATAC
*
104115 AATTTGAGGCGGTTTCATGCATTTACCTTTTAAAATAACCTACGAGGACGACGAGGCATAC
1 AATTTGAGGAGGTTTCATGCATTTACCTTTTAAAATAACCTACGAGGACGACGAGGCATAC
104176 A
1 A
104177 TATGGGAAGC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (61 bp):
AATTTGAGGAGGTTTCATGCATTTACCTTTTAAAATAACCTACGAGGACGACGAGGCATAC
Found at i:105089 original size:11 final size:11
Alignment explanation
Indices: 105073--105110 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
105063 TTTTAACATC
105073 AAAAAATATAT
1 AAAAAATATAT
*
105084 AAAAAATTTAT
1 AAAAAATATAT
105095 -AAAAATATTAT
1 AAAAAATA-TAT
105106 AAAAA
1 AAAAA
105111 CTTATTGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 6 0.26
11 13 0.57
12 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAAATATAT
Found at i:105115 original size:21 final size:21
Alignment explanation
Indices: 105074--105115 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
105064 TTTAACATCA
*
105074 AAAAATATATAAAAAATTTAT
1 AAAAATATATAAAAAACTTAT
105095 AAAAATAT-TATAAAAACTTAT
1 AAAAATATATA-AAAAACTTAT
105116 TGCCATATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATATATAAAAAACTTAT
Found at i:108018 original size:15 final size:16
Alignment explanation
Indices: 107997--108034 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
107987 GGTAATGCGA
107997 AAATTTAAAT-TTAGTT
1 AAATTTAAATATT-GTT
108013 -AATTTAAATATTGTT
1 AAATTTAAATATTGTT
108028 AAATTTA
1 AAATTTA
108035 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
AAATTTAAATATTGTT
Found at i:108802 original size:63 final size:63
Alignment explanation
Indices: 108703--108829 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
108693 CTGCTACTGC
*
108703 TACAGTCGTGGACCTAGTGGTGACTATCGGTTCTACGTCCCAAGGTGATCAACCCATACATTT
1 TACAGTCGTGGACCTAGTGGTGACTACCGGTTCTACGTCCCAAGGTGATCAACCCATACATTT
108766 TACAGTCGTGGACCTAGTGGTGACTACCGGTTCTACGTCCCAAGGTGATCAACCCATACATTT
1 TACAGTCGTGGACCTAGTGGTGACTACCGGTTCTACGTCCCAAGGTGATCAACCCATACATTT
108829 T
1 T
108830 TTCGTTGGTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (63 bp):
TACAGTCGTGGACCTAGTGGTGACTACCGGTTCTACGTCCCAAGGTGATCAACCCATACATTT
Found at i:109807 original size:18 final size:18
Alignment explanation
Indices: 109768--109809 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
109758 ATACTACACC
* *
109768 CCGATGCAGATGTCGGTG
1 CCGATGCAGATGTCGATA
*
109786 CCGATGGAGATGTCGATA
1 CCGATGCAGATGTCGATA
109804 CCGATG
1 CCGATG
109810 TCGGGACAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (18 bp):
CCGATGCAGATGTCGATA
Found at i:110387 original size:4 final size:4
Alignment explanation
Indices: 110370--110534 Score: 170
Period size: 4 Copynumber: 40.5 Consensus size: 4
110360 TTTAACTAAG
* * * *
110370 TAAA TAAG TAAA TAAA TAAC TAAA TAAA CAAAA TAAA CAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA -TAAA TAAA TAAA TAAA TAAA
* *
110419 TAAA TAAA TAAAA TAAC TAAA TAAA TAAAA TAAA TAAC TAAA TAAA TAAA
1 TAAA TAAA T-AAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
* * * * * *
110469 TAAA T-AA CAAA TATA TAAA TAAT TAAC TAAT TAAA TAAAA TAAA TAAC
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA
*
110517 TAAA TAAA TAAA AAAA TA
1 TAAA TAAA TAAA TAAA TA
110535 TTTTTAAATT
Statistics
Matches: 132, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
3 2 0.02
4 115 0.87
5 15 0.11
ACGTcount: A:0.70, C:0.05, G:0.01, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:110405 original size:21 final size:21
Alignment explanation
Indices: 110370--110534 Score: 196
Period size: 21 Copynumber: 7.9 Consensus size: 21
110360 TTTAACTAAG
*
110370 TAAATAAGT-AAATAAATAAC
1 TAAATAAATAAAATAAATAAC
* * *
110390 TAAATAAACAAAATAAACAAA
1 TAAATAAATAAAATAAATAAC
110411 TAAATAAATAAATAAATAAAATAAC
1 TAAATAAAT--A-AAAT-AAATAAC
110436 TAAATAAATAAAATAAATAAC
1 TAAATAAATAAAATAAATAAC
110457 TAAATAAAT-AAATAAATAAC
1 TAAATAAATAAAATAAATAAC
* *
110477 -AAATATAT-AAATAATTAAC
1 TAAATAAATAAAATAAATAAC
*
110496 TAATTAAATAAAATAAATAAC
1 TAAATAAATAAAATAAATAAC
110517 TAAATAAATAAAA-AAATA
1 TAAATAAATAAAATAAATA
110535 TTTTTAAATT
Statistics
Matches: 125, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.14
20 29 0.23
21 55 0.44
22 4 0.03
23 2 0.02
24 4 0.03
25 14 0.11
ACGTcount: A:0.70, C:0.05, G:0.01, T:0.24
Consensus pattern (21 bp):
TAAATAAATAAAATAAATAAC
Found at i:110687 original size:29 final size:30
Alignment explanation
Indices: 110653--110733 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 30
110643 AACTTTTCCC
*
110653 AAAAATGGTCTATTCCTCTAAATATTTTT-
1 AAAAATGGTATATTCCTCTAAATATTTTTA
* * ** * *
110682 AAAAATAGTGTAAACCCCTAATTATTTTTA
1 AAAAATGGTATATTCCTCTAAATATTTTTA
* *
110712 AAAAACGGTATATTCTTCTAAA
1 AAAAATGGTATATTCCTCTAAA
110734 AAAACCTGTA
Statistics
Matches: 37, Mismatches: 14, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (30 bp):
AAAAATGGTATATTCCTCTAAATATTTTTA
Found at i:117595 original size:72 final size:72
Alignment explanation
Indices: 117475--117618 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
117465 ATGACTTTGA
117475 AATACATGCACAATATGATTTATGTTAGCCTTTTTTAATACTAAGTATAAAATTTTGAAATAATG
1 AATACATGCACAATATGATTTATGTTAGCCTTTTTTAATACTAAGTATAAAATTTTGAAATAATG
117540 TTTGCAT
66 TTTGCAT
* *
117547 AATACATGCACAGTATGATTTATGTTAGCCTTTTTTAATACTAGGTATAAAATTTTGAAATAATG
1 AATACATGCACAATATGATTTATGTTAGCCTTTTTTAATACTAAGTATAAAATTTTGAAATAATG
117612 TTTGCAT
66 TTTGCAT
117619 TTGAGCAACT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (72 bp):
AATACATGCACAATATGATTTATGTTAGCCTTTTTTAATACTAAGTATAAAATTTTGAAATAATG
TTTGCAT
Found at i:119428 original size:15 final size:16
Alignment explanation
Indices: 119396--119428 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
119386 TATTCATACA
*
119396 TTGCATTTAGGTTAAT
1 TTGCATTTAGGATAAT
119412 TTGCATTTA-GATAAT
1 TTGCATTTAGGATAAT
119427 TT
1 TT
119429 AGTTTATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (16 bp):
TTGCATTTAGGATAAT
Found at i:121878 original size:27 final size:27
Alignment explanation
Indices: 121815--121885 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
121805 GATTATTGCT
* * *
121815 TATTCGAGCCAAATACATAAAATGGCT
1 TATTCGAGCCAAATACAAAAAATGCCC
* *
121842 TATTCAAGCCCAATACAAAATAATGCCC
1 TATTCGAGCCAAATACAAAA-AATGCCC
*
121870 T-TTCGAGCCAGATACA
1 TATTCGAGCCAAATACA
121886 GAGTAATGCT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 29 0.83
28 6 0.17
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (27 bp):
TATTCGAGCCAAATACAAAAAATGCCC
Found at i:121892 original size:27 final size:28
Alignment explanation
Indices: 121862--121918 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
121852 CAATACAAAA
* *
121862 TAATGCCCTTTCGAGCCAGA-TACAGAG
1 TAATGCCCGTTCAAGCCAGAGTACAGAG
* *
121889 TAATGCTCGTTCAAGCCAGAGTTCAGAG
1 TAATGCCCGTTCAAGCCAGAGTACAGAG
121917 TA
1 TA
121919 TTTCTTCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (28 bp):
TAATGCCCGTTCAAGCCAGAGTACAGAG
Found at i:126713 original size:28 final size:28
Alignment explanation
Indices: 126658--126722 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
126648 AAAGGCTCAC
* * ** *
126658 ACACATAACAGAACATCCGTAAAGGCTT
1 ACACATATCAGAACAACCACAAAAGCTT
126686 ACACATATCAGAACAACCACAAAAGCTT
1 ACACATATCAGAACAACCACAAAAGCTT
126714 -CTACATATC
1 AC-ACATATC
126723 GGTAACTTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.45, C:0.28, G:0.09, T:0.18
Consensus pattern (28 bp):
ACACATATCAGAACAACCACAAAAGCTT
Found at i:129731 original size:11 final size:10
Alignment explanation
Indices: 129692--129733 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
129682 CCGGTATAAT
*
129692 AATATTTATA
1 AATATTTTTA
*
129702 ATTATTTTTA
1 AATATTTTTA
129712 AATATTTTTA
1 AATATTTTTA
129722 AATATCTTTTA
1 AATAT-TTTTA
129733 A
1 A
129734 TTACATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 22 0.79
11 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (10 bp):
AATATTTTTA
Found at i:130794 original size:16 final size:17
Alignment explanation
Indices: 130773--130805 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
130763 ATACTTGACA
130773 AATTATG-CTATGTGTT
1 AATTATGTCTATGTGTT
*
130789 AATTATGTGTATGTGTT
1 AATTATGTCTATGTGTT
130806 GATCTCATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.03, G:0.21, T:0.52
Consensus pattern (17 bp):
AATTATGTCTATGTGTT
Found at i:131657 original size:12 final size:12
Alignment explanation
Indices: 131640--131667 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
131630 TTATCTTAAA
131640 ATCTTTGATCTG
1 ATCTTTGATCTG
131652 ATCTTTGATCTG
1 ATCTTTGATCTG
131664 ATCT
1 ATCT
131668 ATGCTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (12 bp):
ATCTTTGATCTG
Found at i:138262 original size:23 final size:23
Alignment explanation
Indices: 138219--138288 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
138209 TGTGTTTTTC
**
138219 ATTCAATG-CTATATGTGTGTTAT
1 ATTCAATGCCT-TATGCATGTTAT
*
138242 ATTCAATGCCTTGTGCATGTTAT
1 ATTCAATGCCTTATGCATGTTAT
* **
138265 ATTCAGTGTTTTATGCATGTTAT
1 ATTCAATGCCTTATGCATGTTAT
138288 A
1 A
138289 CTGGTATGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 37 0.95
24 2 0.05
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.47
Consensus pattern (23 bp):
ATTCAATGCCTTATGCATGTTAT
Found at i:141294 original size:25 final size:24
Alignment explanation
Indices: 141233--141343 Score: 105
Period size: 26 Copynumber: 4.4 Consensus size: 24
141223 TGTTAAACAT
* * *
141233 TCACCGGCTCGAGGCCTGATAAATA
1 TCACCGGCTCAAAGCCTGCTAAA-A
* *
141258 GTCATCGGCTCAAAGCCTACTAGAAA
1 -TCACCGGCTCAAAGCCTGCTA-AAA
* * *
141284 CCACCGGCTCATAGCCTGCTAATTAT
1 TCACCGGCTCAAAGCCTGCTAA--AA
141310 TCACCGGCTCAAAGCCTGCTAAAA
1 TCACCGGCTCAAAGCCTGCTAAAA
141334 TCACCGGCTC
1 TCACCGGCTC
141344 GAGCCTTACT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
24 12 0.17
25 17 0.25
26 38 0.55
27 2 0.03
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (24 bp):
TCACCGGCTCAAAGCCTGCTAAAA
Found at i:141355 original size:24 final size:24
Alignment explanation
Indices: 141263--141357 Score: 93
Period size: 26 Copynumber: 3.8 Consensus size: 24
141253 AAATAGTCAT
*
141263 CGGCTCAAAGCCTACTAGAAACCAC
1 CGGCTCAAAGCCTACTA-AAATCAC
* * *
141288 CGGCTCATAGCCTGCTAATTATTCAC
1 CGGCTCAAAGCCTACTAA--AATCAC
*
141314 CGGCTCAAAGCCTGCTAAAATCAC
1 CGGCTCAAAGCCTACTAAAATCAC
*
141338 CGGCTC-GAGCCTTACTAAAA
1 CGGCTCAAAGCC-TACTAAAA
141358 ATCATCTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
23 4 0.07
24 19 0.32
25 15 0.25
26 21 0.36
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.20
Consensus pattern (24 bp):
CGGCTCAAAGCCTACTAAAATCAC
Found at i:142724 original size:17 final size:17
Alignment explanation
Indices: 142702--142735 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
142692 CTTAAGTAAC
142702 TAAATTAACTTCTCAAT
1 TAAATTAACTTCTCAAT
**
142719 TAAATTATTTTCTCAAT
1 TAAATTAACTTCTCAAT
142736 CCAATTCTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTAACTTCTCAAT
Found at i:145345 original size:10 final size:10
Alignment explanation
Indices: 145330--145364 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
145320 TTTGTACAAT
145330 TTTTTATTTA
1 TTTTTATTTA
145340 TTTTTATTTTA
1 TTTTTA-TTTA
*
145351 TATTTATTTA
1 TTTTTATTTA
145361 TTTT
1 TTTT
145365 CATGTCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:145374 original size:20 final size:21
Alignment explanation
Indices: 145332--145383 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
145322 TGTACAATTT
* *
145332 TTTATTTATTTTTATTTTATA
1 TTTATTTATTTTCATTGTATA
*
145353 TTTATTTATTTTCA-TGTCTA
1 TTTATTTATTTTCATTGTATA
145373 TTTATTT-TTTT
1 TTTATTTATTTT
145384 ATTAGGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.14
20 11 0.39
21 13 0.46
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTATTTATTTTCATTGTATA
Found at i:145376 original size:16 final size:15
Alignment explanation
Indices: 145342--145380 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
145332 TTTATTTATT
*
145342 TTTATTTTATATTTA
1 TTTATTTTATATCTA
*
145357 TTTATTTTCATGTCTA
1 TTTATTTT-ATATCTA
145373 TTTATTTT
1 TTTATTTT
145381 TTTATTAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTATTTTATATCTA
Found at i:152256 original size:195 final size:195
Alignment explanation
Indices: 151913--152331 Score: 492
Period size: 195 Copynumber: 2.1 Consensus size: 195
151903 CTAGTACCCA
** * *
151913 ATGCTGCTCACACGAGTTGTCGAGGACTCGCAACATATACGGTACACCAGCCATCGATACCATGT
1 ATGCTGCTCACACGAGTTGTCGAGGACTCAAAACAAATACGGTACACCAGCCATCGATACCATCT
* * * *
151978 TTGTCTGTAAACTATCCCCTAATGATGTTGCTCACACGAGCTATCGAGAATATGCATTCAAGCAT
66 ATGTCTATAAACTATCCCCTAATGATGCTGCTCACACGAGCTATCAAGAATATGCATTCAAGCAT
* * * **
152043 AACTCTCAGTCGTCGTAGGGCTTGTAATCCATT-TTAGGATTTCATATCTC-T-TTTTCGACTCA
131 AAATCTCAGTCATCGTAGGGCCTGTAATCCATTCTT-GGA-TTCATATCTCATCTTCCCGACTCA
*
152105 TG
194 CG
* * *
152107 ATGCTACTCACACGAGTTGTCGAGGACTCAAAACAAATGCGGTAC-CTCAGCCATCGATACGGTA
1 ATGCTGCTCACACGAGTTGTCGAGGACTCAAAACAAATACGGTACAC-CAGCCATCGATAC--CA
* * * *
152171 TCTATG-C-ATATAACTGTCCCTTAATGATGCTGCTCACACGAGCTGTCAAGAATATGGACTT-A
63 TCTATGTCTATA-AACTATCCCCTAATGATGCTGCTCACACGAGCTATCAAGAATATGCA-TTCA
* * *
152233 TGCATAAATCTCAGTCATCGTAGGGCCTGTAATCCATTCTTGGATTCATTTCTCATCTTCCCGAT
126 AGCATAAATCTCAGTCATCGTAGGGCCTGTAATCCATTCTTGGATTCATATCTCATCTTCCCGAC
152298 TCACG
191 TCACG
* *
152303 ATGCTGCTCACACGAGTTATTGAGGACTC
1 ATGCTGCTCACACGAGTTGTCGAGGACTC
152332 GTAACATATG
Statistics
Matches: 190, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
193 1 0.01
194 64 0.34
195 81 0.43
196 44 0.23
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (195 bp):
ATGCTGCTCACACGAGTTGTCGAGGACTCAAAACAAATACGGTACACCAGCCATCGATACCATCT
ATGTCTATAAACTATCCCCTAATGATGCTGCTCACACGAGCTATCAAGAATATGCATTCAAGCAT
AAATCTCAGTCATCGTAGGGCCTGTAATCCATTCTTGGATTCATATCTCATCTTCCCGACTCACG
Found at i:155224 original size:25 final size:24
Alignment explanation
Indices: 155178--155224 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
155168 GTCTATGAAT
*
155178 ATTTTGGTATATGTTGTTTCTTTG
1 ATTTTGGTATATGTTGTATCTTTG
* *
155202 ATTTTGGTTTTTGCTTGTATCTT
1 ATTTTGGTATATG-TTGTATCTT
155225 GTTTGAGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.11, C:0.06, G:0.19, T:0.64
Consensus pattern (24 bp):
ATTTTGGTATATGTTGTATCTTTG
Found at i:156500 original size:6 final size:6
Alignment explanation
Indices: 156489--156569 Score: 82
Period size: 6 Copynumber: 14.2 Consensus size: 6
156479 TAAAATTTAT
*
156489 TTTAAA TTTAAA --TAAA TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
156534 TTTATT TTTAAA TTTAAA ATT--A TTCTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA T
156570 AAATAAAAGC
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
4 6 0.10
5 6 0.10
6 46 0.75
7 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:156507 original size:17 final size:17
Alignment explanation
Indices: 156487--156573 Score: 72
Period size: 17 Copynumber: 5.1 Consensus size: 17
156477 TTTAAAATTT
156487 ATTTTAAATTTAAATAA
1 ATTTTAAATTTAAATAA
*
156504 A-TTTAAATTTAAATTTA
1 ATTTTAAATTTAAA-TAA
* *
156521 A-TTTAAGTTTAAATTTA
1 ATTTTAAATTTAAA-TAA
* *
156538 TTTTTAAATTTAAA-ATT
1 ATTTTAAATTTAAATA-A
*
156555 ATTCTAAATTTAAATAA
1 ATTTTAAATTTAAATAA
156572 AT
1 AT
156574 AAAAGCTCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
16 12 0.21
17 33 0.58
18 12 0.21
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
ATTTTAAATTTAAATAA
Found at i:163848 original size:208 final size:209
Alignment explanation
Indices: 163482--164260 Score: 912
Period size: 209 Copynumber: 3.8 Consensus size: 209
163472 TCGCGATTAT
* * * * * *
163482 TCAAAACAA-TGAGGCGGTTATCTTCCTGATAAGATACAGAGAAGTATACCAACTCGATGAAACA
1 TCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAACTCAATGAAACA
* * * * * * *
163546 AAGCTCAAATGTGAATGAAACTTCAAATCCTAGCTTCCTAATGAGATACTGAGAAGCATGTCGAA
66 AAGCTC-AATGTGAACGAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
* *
163611 GCAATAAAGCGGTTACCTTCCTAATGAGATACTGAGAAGTGGACCAGATCCGTCTTCCTGATGAG
130 GCAATAAAGCGGTTACCTTCCTGATGAGATACTGAGAAGTGGACCAGATTCGTCTTCCTGATGAG
* * *
163676 ACACAAAGAAGTTGA
195 ATACAGAGAAGTAGA
* ** *
163691 TCAAAACAAGTGATGCGGTCATCTTCCTAATGAGACATTGAGAAGTAGACCAA-TCAACGAAACA
1 TCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAACTCAATGAAACA
* * * *
163755 AAGCTCGATGTGAGCGAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCTGGTCGAAG
66 AAGCTCAATGTGAACGAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
** * * * * *
163820 CAATAAAATGGTCAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCTTGATGAGA
131 CAATAAAGCGGTTACCTTCCTGATGAGATACTGAGAAGTGGACCAGATTCGTCTTCCTGATGAGA
* *
163885 TGCAGAGAAGCAGA
196 TACAGAGAAGTAGA
* ** * *
163899 TTAAAACAAGTGATGTAGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAACA
1 TCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAACTCAATGAAACA
* * * *
163964 AAGCTCGATGTGAACGAATCTTCGAACCTCAGCTTCTTGATAAGATACTGAGAAGCAGGTCGAAG
66 AAGCTCAATGTGAACGAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* ** * * * *
164029 TAATAAAGCGGTTACCTTCCTGATGAGGCACAGAGAAGTGAACTAGATTCGCCTTCCTGATGAGA
131 CAATAAAGCGGTTACCTTCCTGATGAGATACTGAGAAGTGGACCAGATTCGTCTTCCTGATGAGA
*
164094 TACAGAGAAGTGGA
196 TACAGAGAAGTAGA
** * * *
164108 TTGAAACAAGTAAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAA-G-----
1 TCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAACTCAATGAAACA
* * * *
164167 --GCTCAAAGTGAGCAAATCTTCGAACCCCAGCATCCTGATGAGATACTGAGAAGCAGGTCGAAG
66 AAGCTCAATGTGAACGAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* *
164230 CAATAAAGCAGTTACATTCCTGATGAGATAC
131 CAATAAAGCGGTTACCTTCCTGATGAGATAC
164261 AAAGGAGTGG
Statistics
Matches: 483, Mismatches: 85, Indels: 12
0.83 0.15 0.02
Matches are distributed among these distances:
201 81 0.17
208 162 0.34
209 205 0.42
210 35 0.07
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (209 bp):
TCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAACTCAATGAAACA
AAGCTCAATGTGAACGAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
CAATAAAGCGGTTACCTTCCTGATGAGATACTGAGAAGTGGACCAGATTCGTCTTCCTGATGAGA
TACAGAGAAGTAGA
Found at i:164864 original size:17 final size:17
Alignment explanation
Indices: 164842--164898 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
164832 CAATTTTTTT
164842 AATTTATTTTAAGA-TTA
1 AATTTATTTTAA-ATTTA
164859 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
164876 AAGTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
164893 AATTTA
1 AATTTA
164899 AATTTGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 1 0.03
17 36 0.97
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:164891 original size:7 final size:6
Alignment explanation
Indices: 164856--164941 Score: 83
Period size: 6 Copynumber: 15.0 Consensus size: 6
164846 TATTTTAAGA
* * *
164856 TTAAAT TT-ATT TTAAAT TTAAAG TT-ATT TTAAAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
164902 TT-GAT TTAAAT TTAAAT TTAAAA TT--AT TCTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT
164942 AAATAAAAGC
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
4 2 0.03
5 12 0.19
6 47 0.73
7 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:164892 original size:23 final size:23
Alignment explanation
Indices: 164866--164941 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
164856 TTAAATTTAT
*
164866 TTTAAATTTAAAGTTATTTTAAA
1 TTTAAATTTAAAATTATTTTAAA
*
164889 TTTAAATTTAAATTTGA-TTTAAA
1 TTTAAATTTAAAATT-ATTTTAAA
*
164912 TTTAAATTTAAAATTATTCTAAA
1 TTTAAATTTAAAATTATTTTAAA
164935 TTTAAAT
1 TTTAAAT
164942 AAATAAAAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
22 1 0.02
23 46 0.96
24 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (23 bp):
TTTAAATTTAAAATTATTTTAAA
Found at i:164908 original size:17 final size:17
Alignment explanation
Indices: 164888--164920 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
164878 GTTATTTTAA
164888 ATTTAAATTTAAATTTG
1 ATTTAAATTTAAATTTG
164905 ATTTAAATTTAAATTT
1 ATTTAAATTTAAATTT
164921 AAAATTATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTAAATTTAAATTTG
Found at i:165572 original size:3 final size:3
Alignment explanation
Indices: 165564--165641 Score: 66
Period size: 3 Copynumber: 26.0 Consensus size: 3
165554 TTAAAACGAT
* * * * * * * *
165564 TAA TAA TAA TAA TAA TAA TAA CAA CAA CAA CAA CAA CAA CAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
165612 TAA TGT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
165642 ATATAAAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.64, C:0.10, G:0.01, T:0.24
Consensus pattern (3 bp):
TAA
Found at i:166811 original size:29 final size:29
Alignment explanation
Indices: 166778--166954 Score: 132
Period size: 29 Copynumber: 6.1 Consensus size: 29
166768 AAAAGTACCA
*
166778 TTTTACCTTAAATTTCCTAAAATT-CCATT
1 TTTTACCCTAAATTT-CTAAAATTACCATT
* * * *
166807 TTTTACCTTGAACTTCCAAAAATTACCA--
1 TTTTACCCT-AAATTTCTAAAATTACCATT
*
166835 TTTTACCCTTAAATTTTTGAAAATT-CCATT
1 TTTTACCC-TAAATTTCT-AAAATTACCATT
* *
166865 TTTAACCCTAAACTTTCCAAAAATTACCATT
1 TTTTACCCTAAA-TTT-CTAAAATTACCATT
* *
166896 TTAT-CCCTAAATTTTTGAAAATT-CCATT
1 TTTTACCCTAAATTTCT-AAAATTACCATT
* * *
166924 TTTGACCCTGAACTTCTAAAATTACCATT
1 TTTTACCCTAAATTTCTAAAATTACCATT
166953 TT
1 TT
166955 ACCCCGAATT
Statistics
Matches: 116, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
28 27 0.23
29 52 0.45
30 30 0.26
31 7 0.06
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTTACCCTAAATTTCTAAAATTACCATT
Found at i:166908 original size:59 final size:57
Alignment explanation
Indices: 166746--167014 Score: 289
Period size: 59 Copynumber: 4.7 Consensus size: 57
166736 TAGAAATCAT
* * * *
166746 ATTTTGACCCTCGAACTTTCCAAAAAGTACCATTTTACCTTAAATTTCCT-AAAATTCC
1 ATTTTTACCCT-GAACTTTCCAAAAATTACCATTTTACCCTAAATTT-TTGAAAATTCC
*
166804 ATTTTTTACCTTGAAC-TTCCAAAAATTACCATTTTACCCTTAAATTTTTGAAAATTCC
1 A-TTTTTACCCTGAACTTTCCAAAAATTACCATTTTACCC-TAAATTTTTGAAAATTCC
*
166862 ATTTTTAACCCTAAACTTTCCAAAAATTACCATTTTATCCCTAAATTTTTGAAAATTCC
1 ATTTTT-ACCCTGAACTTTCCAAAAATTACCATTTTA-CCCTAAATTTTTGAAAATTCC
* ** *
166921 ATTTTTGACCCTGAAC-TT-CTAAAATTACCATTTTACCCCGAA-TTTTCAATAATTCC
1 ATTTTT-ACCCTGAACTTTCCAAAAATTACCATTTTACCCTAAATTTTTGAA-AATTCC
* * * *
166977 ATTTTTGCCCTCG-AGTTTCCAAAAATTATCGTTTTACC
1 ATTTTTACCCT-GAACTTTCCAAAAATTACCATTTTACC
167015 GCCCAAGCAT
Statistics
Matches: 183, Mismatches: 18, Indels: 21
0.82 0.08 0.09
Matches are distributed among these distances:
55 11 0.06
56 20 0.11
57 59 0.32
58 30 0.16
59 60 0.33
60 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (57 bp):
ATTTTTACCCTGAACTTTCCAAAAATTACCATTTTACCCTAAATTTTTGAAAATTCC
Found at i:171364 original size:105 final size:105
Alignment explanation
Indices: 171182--171388 Score: 360
Period size: 105 Copynumber: 2.0 Consensus size: 105
171172 GAAGCCCCTC
171182 CCATAACGACCGAAACACACCCCTTCGGACCTTGAATGTTGGTAAAGTGAAAGAATCGATGGAGG
1 CCATAACGACCGAAACACACCCCTTCGGACCTTGAATGTTGGTAAAGTGAAAGAATCGATGGAGG
171247 GAGACCCGAAACCCGACAATCAACAACCAACAAGGTCCTT
66 GAGACCCGAAACCCGACAATCAACAACCAACAAGGTCCTT
* * ** *
171287 CCATAACGATCGAAACACACCCCTTCGGACCTTGGATGTTGGTGGAGTGAAAGAATTGATGGAGG
1 CCATAACGACCGAAACACACCCCTTCGGACCTTGAATGTTGGTAAAGTGAAAGAATCGATGGAGG
*
171352 GAGATCCGAAACCCGACAATCAACAACCAACAAGGTC
66 GAGACCCGAAACCCGACAATCAACAACCAACAAGGTC
171389 AAACCTTAGG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 96 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (105 bp):
CCATAACGACCGAAACACACCCCTTCGGACCTTGAATGTTGGTAAAGTGAAAGAATCGATGGAGG
GAGACCCGAAACCCGACAATCAACAACCAACAAGGTCCTT
Found at i:178486 original size:18 final size:18
Alignment explanation
Indices: 178448--178486 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
178438 AATATTTTTT
* **
178448 AAAAGTGTTTTTGAATTA
1 AAAAGTATTTTTGAAAAA
178466 AAAAGTATTTTTGAAAAA
1 AAAAGTATTTTTGAAAAA
178484 AAA
1 AAA
178487 TTAAAATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (18 bp):
AAAAGTATTTTTGAAAAA
Found at i:179340 original size:12 final size:12
Alignment explanation
Indices: 179325--179366 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
179315 GTCCAATTAT
*
179325 ATGTTCATGAAC
1 ATGTTCGTGAAC
**
179337 ATGTTCGTTTA-
1 ATGTTCGTGAAC
179348 ATGTTCGTGAAC
1 ATGTTCGTGAAC
179360 ATGTTCG
1 ATGTTCG
179367 ATTAAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:179352 original size:23 final size:23
Alignment explanation
Indices: 179320--179371 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
179310 ACCATGTCCA
179320 ATTATATGTTCATGAACATGTTCG
1 ATTA-ATGTTCATGAACATGTTCG
* *
179344 TTTAATGTTCGTGAACATGTTCG
1 ATTAATGTTCATGAACATGTTCG
179367 ATTAA
1 ATTAA
179372 GTTAAATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (23 bp):
ATTAATGTTCATGAACATGTTCG
Found at i:179381 original size:23 final size:23
Alignment explanation
Indices: 179320--179381 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
179310 ACCATGTCCA
*
179320 ATTATATGTTCATGAACATGTTCG
1 ATTA-ATGTTAATGAACATGTTCG
* **
179344 TTTAATGTTCGTGAACATGTTCG
1 ATTAATGTTAATGAACATGTTCG
179367 ATTAA-GTTAAATGAA
1 ATTAATGTT-AATGAA
179382 TATGATCGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 3 0.09
23 26 0.81
24 3 0.09
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (23 bp):
ATTAATGTTAATGAACATGTTCG
Found at i:182763 original size:6 final size:6
Alignment explanation
Indices: 182697--182761 Score: 94
Period size: 6 Copynumber: 10.8 Consensus size: 6
182687 CTTATTGGTA
*
182697 TCATCC TTATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC
1 TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC
* * *
182745 TCCTCA TCATCA TCATC
1 TCATCC TCATCC TCATC
182762 ATATGATCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.35
Consensus pattern (6 bp):
TCATCC
Done.