Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020612.1 Corchorus olitorius cultivar O-4 contig20645, 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: 166072
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13297 original size:3 final size:3
Alignment explanation
Indices: 13289--13332 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
13279 ATATATATAT
13289 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
13333 GTAACTAGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:15132 original size:22 final size:22
Alignment explanation
Indices: 15102--15177 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
15092 GCATGACACG
***
15102 GCACAACCCACGTGCCGGCACA
1 GCACAACCCACGTGCCGATGCA
* *
15124 GCACGACCCACGTGCCAATGCA
1 GCACAACCCACGTGCCGATGCA
15146 GCACAACCCACGTGCCGATGCA
1 GCACAACCCACGTGCCGATGCA
*
15168 GCACGACCCA
1 GCACAACCCA
15178 TTTTTAATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.28, C:0.43, G:0.22, T:0.07
Consensus pattern (22 bp):
GCACAACCCACGTGCCGATGCA
Found at i:25850 original size:19 final size:19
Alignment explanation
Indices: 25830--25866 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
25820 AATTAATTAT
25830 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
25848 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
25867 CTTAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:28391 original size:240 final size:240
Alignment explanation
Indices: 27961--28406 Score: 639
Period size: 240 Copynumber: 1.9 Consensus size: 240
27951 ATGACCAACT
* * * *
27961 TGTGCACTAGGAGAGGAGGATGAGTTGAATTTATAGGAGAACTGCGGCAATGTTACCAATGTTAG
1 TGTGCACTAGGAGAAGAGGATGAGTTGAATTTATAGGAGAACTGCGACAATATTACCAATATTAG
*
28026 TAGTTTAAATATTTTTAAAAATAAAGAAAATGAAAAACATCTTCACGTGATTTACAGGATGTTAA
66 CAGTTTAAATATTTTTAAAAATAAAGAAAATGAAAAACATCTTCACGTGATTTACAGGATGTTAA
28091 TCAATAGAATTTCTTTCTAAAATTGGAAAAAACATCATCACGTGACATTTGAGCGTTACTACCAA
131 TCAATAGAATTTCTTTCTAAAATTGGAAAAAACATCATCACGTGACATTTGAGCGTTACTACCAA
*
28156 ATATTTATTTTTATTACATTGCCTTTAGTTGTTACAGAATTCAAA
196 ATATATATTTTTATTACATTGCCTTTAGTTGTTACAGAATTCAAA
* * *
28201 TGTGCACTAGGAGAAGAGGATG-GATTGAATTTATAGGAGAAGTGTGACATTATTACCAATATTA
1 TGTGCACTAGGAGAAGAGGATGAG-TTGAATTTATAGGAGAACTGCGACAATATTACCAATATTA
* *
28265 GCAGTTTAAATATTTTTAAATATAAAGAAAATGAAAAACATCTTCATGTGATTTACATGG-TGTT
65 GCAGTTTAAATATTTTTAAAAATAAAGAAAATGAAAAACATCTTCACGTGATTTACA-GGATGTT
* * * *** * * * *
28329 AA-CTAATATAATTTCTTTTTTTAAATTGGACCTAA-ATCATGATGTGATATTTGAGTGTTACTA
129 AATC-AATAGAATTTC-TTTCTAAAATTGGAAAAAACATCATCACGTGACATTTGAGCGTTACTA
28392 CCAAATATATATTTT
192 CCAAATATATATTTT
28407 GACTCAGATT
Statistics
Matches: 181, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
239 2 0.01
240 163 0.90
241 16 0.09
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (240 bp):
TGTGCACTAGGAGAAGAGGATGAGTTGAATTTATAGGAGAACTGCGACAATATTACCAATATTAG
CAGTTTAAATATTTTTAAAAATAAAGAAAATGAAAAACATCTTCACGTGATTTACAGGATGTTAA
TCAATAGAATTTCTTTCTAAAATTGGAAAAAACATCATCACGTGACATTTGAGCGTTACTACCAA
ATATATATTTTTATTACATTGCCTTTAGTTGTTACAGAATTCAAA
Found at i:30801 original size:21 final size:22
Alignment explanation
Indices: 30762--30803 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
30752 TCTTTATTTT
**
30762 CCTTATTTCTTTTTTTTTTCTA
1 CCTTATTTCTTTTCCTTTTCTA
30784 CCTT-TTTCTTTTCCTTTTCT
1 CCTTATTTCTTTTCCTTTTCT
30804 TTCTTTCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (22 bp):
CCTTATTTCTTTTCCTTTTCTA
Found at i:30987 original size:38 final size:37
Alignment explanation
Indices: 30912--30998 Score: 122
Period size: 38 Copynumber: 2.3 Consensus size: 37
30902 ACCAGGCCGC
* *
30912 GCGGGGCAGCCAGGCGCTGGCCTGCTAAGCAGGCCAT
1 GCGGGCCAGCCAAGCGCTGGCCTGCTAAGCAGGCCAT
30949 GCGGGCCAGCCAAGCGCATGGCCTGCTAAGC-GGACCAT
1 GCGGGCCAGCCAAGCGC-TGGCCTGCTAAGCAGG-CCAT
*
30987 GCAGGCCAGCCA
1 GCGGGCCAGCCA
30999 GGCGGCCTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 17 0.38
38 28 0.62
ACGTcount: A:0.20, C:0.34, G:0.37, T:0.09
Consensus pattern (37 bp):
GCGGGCCAGCCAAGCGCTGGCCTGCTAAGCAGGCCAT
Found at i:34878 original size:1 final size:1
Alignment explanation
Indices: 34874--34905 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
34864 AAGGAGAAGG
34874 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
34906 GCTCCCATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:37421 original size:16 final size:16
Alignment explanation
Indices: 37397--37430 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
37387 GTGTCTTCTC
*
37397 TTTTCTTTCTTTCTTT
1 TTTTCTTTCATTCTTT
*
37413 TTTTTTTTCATTCTTT
1 TTTTCTTTCATTCTTT
37429 TT
1 TT
37431 AGTTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTCATTCTTT
Found at i:43731 original size:41 final size:41
Alignment explanation
Indices: 43681--43761 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
43671 GTTATGGAAA
*
43681 GACATGTGTTGATCATAAAGTTATGTCTATATGAAAAGACG
1 GACATGTGTTGATCATAAAGTTATGTCTATATAAAAAGACG
43722 GACATGTGTTGATCATAAAGTTATGTCTATATAAAAAGAC
1 GACATGTGTTGATCATAAAGTTATGTCTATATAAAAAGAC
43762 ATGTATGTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (41 bp):
GACATGTGTTGATCATAAAGTTATGTCTATATAAAAAGACG
Found at i:53688 original size:23 final size:22
Alignment explanation
Indices: 53634--53713 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
53624 TAAAAACTTA
*
53634 TATATATATTAATAAATTAGAAT
1 TATATATATTAAT-TATTAGAAT
* * *
53657 TAAAAATATTAATTTTTAGATAT
1 TATATATATTAATTATTAGA-AT
*
53680 TATATATA-TAATTATATAAAAT
1 TATATATATTAATTAT-TAGAAT
53702 ATAATATATATT
1 -T-ATATATATT
53714 TTAGTGACGG
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
22 13 0.30
23 23 0.52
24 7 0.16
25 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (22 bp):
TATATATATTAATTATTAGAAT
Found at i:55576 original size:40 final size:40
Alignment explanation
Indices: 55514--55594 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
55504 ACTTGACCCT
*
55514 CCTAATAATTAAGGAAATAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
*
55554 CCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
55594 C
1 C
55595 TAGTTATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (40 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
Found at i:55712 original size:13 final size:13
Alignment explanation
Indices: 55694--55728 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
55684 TGATACGTCA
55694 GGAGGGACAAACT
1 GGAGGGACAAACT
**
55707 GGAGGGACAAGTT
1 GGAGGGACAAACT
55720 GGAGGGACA
1 GGAGGGACA
55729 TGTTTCACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.46, T:0.09
Consensus pattern (13 bp):
GGAGGGACAAACT
Found at i:56114 original size:7 final size:7
Alignment explanation
Indices: 56104--56132 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
56094 CAAAAGTTTT
56104 GTTGAGA
1 GTTGAGA
56111 GTTGAGA
1 GTTGAGA
56118 GTTGAGA
1 GTTGAGA
56125 G-TGAGA
1 GTTGAGA
56131 GT
1 GT
56133 GTCTTGGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (7 bp):
GTTGAGA
Found at i:57609 original size:30 final size:32
Alignment explanation
Indices: 57566--57633 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
57556 TTAAATTGCA
* * *
57566 ATAATTTGTTTCCT-AATTTTTCAAATTTAGG
1 ATAATTAGTTTCCTAAACTTTTCAAATTTAAG
57597 ATAATTAG-TTCCTAAACTTTTCAAATTTAAG
1 ATAATTAGTTTCCTAAACTTTTCAAATTTAAG
57628 ATAATT
1 ATAATT
57634 TACCCCAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (32 bp):
ATAATTAGTTTCCTAAACTTTTCAAATTTAAG
Found at i:59166 original size:22 final size:22
Alignment explanation
Indices: 59141--59182 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
59131 ATGTTATAAG
*
59141 ATATATGAGAAAAATTAAAAAA
1 ATATATCAGAAAAATTAAAAAA
*
59163 ATATATCAGAAAATTTAAAA
1 ATATATCAGAAAAATTAAAA
59183 GAAAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.26
Consensus pattern (22 bp):
ATATATCAGAAAAATTAAAAAA
Found at i:68762 original size:22 final size:21
Alignment explanation
Indices: 68737--68797 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 21
68727 TTGAATATTT
68737 TTATGAAATTTTGATAA-ATAG
1 TTATGAAATTTTGATAACAT-G
*
68758 CTTATTAAATTTTGATAACCATG
1 -TTATGAAATTTTGATAA-CATG
68781 TTATGAAATTTTGATAA
1 TTATGAAATTTTGATAA
68798 TTTACCTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 32 0.91
23 1 0.03
24 2 0.06
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.44
Consensus pattern (21 bp):
TTATGAAATTTTGATAACATG
Found at i:68837 original size:29 final size:29
Alignment explanation
Indices: 68782--68840 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
68772 ATAACCATGT
* * *
68782 TATGAAATTTTGATAATTTACCTATGAAA
1 TATGAAACTTTGATAACTAACCTATGAAA
68811 TATGAAACTTTGATAACCTAACC-ATGAAA
1 TATGAAACTTTGATAA-CTAACCTATGAAA
68840 T
1 T
68841 TTTATTAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (29 bp):
TATGAAACTTTGATAACTAACCTATGAAA
Found at i:68874 original size:21 final size:21
Alignment explanation
Indices: 68811--68881 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 21
68801 ACCTATGAAA
* *
68811 TATGAAACTTTGATAACCTAACC
1 TATGAAATTTTG-TAACCT-TCC
*
68834 -ATGAAATTTTATTAAACCTTCC
1 TATGAAATTTT-GT-AACCTTCC
68856 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTGTAACCTTCC
68877 TATGA
1 TATGA
68882 TTTTTAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 13 0.32
22 13 0.32
23 15 0.37
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGTAACCTTCC
Found at i:68892 original size:21 final size:21
Alignment explanation
Indices: 68811--68894 Score: 73
Period size: 21 Copynumber: 3.9 Consensus size: 21
68801 ACCTATGAAA
* *
68811 TATGAAACTTTGATAACCTAACC
1 TATGAAA-TTTTATAACCT-TCC
68834 -ATGAAATTTTATTAAACCTTCC
1 TATGAAATTTTA-T-AACCTTCC
*
68856 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTATAACCTTCC
*
68877 TATG-ATTTTTAATAACCT
1 TATGAAATTTT-ATAACCT
68895 CTCTGTGAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
20 5 0.10
21 22 0.42
22 10 0.19
23 15 0.29
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTATAACCTTCC
Found at i:70195 original size:145 final size:145
Alignment explanation
Indices: 69932--70222 Score: 557
Period size: 145 Copynumber: 2.0 Consensus size: 145
69922 TCCATGAAAC
*
69932 CAAATTACCAAGCCAGATGTCTTGAAGGCTAAATCTGATATTCTTAGGTCCAATTCGTTAATATG
1 CAAATTACCAAGCCAGATGTCTTGAAGGCTAAATCTGATATTCTTAGATCCAATTCGTTAATATG
69997 GAAGCCCAAAGAAGGAGTTCAAGTTCCATCAGTAATTATGATGCAGTAATGATTCAGTCATGATG
66 GAAGCCCAAAGAAGGAGTTCAAGTTCCATCAGTAATTATGATGCAGTAATGATTCAGTCATGATG
70062 CAAGCATTGTTAAAT
131 CAAGCATTGTTAAAT
70077 CAAATTACCAAGCCAGATGTCTTGAAGGCTAAATCTGATATTCTTAGATCCAATTCGTTAATATG
1 CAAATTACCAAGCCAGATGTCTTGAAGGCTAAATCTGATATTCTTAGATCCAATTCGTTAATATG
70142 GAAGCCCAAAGAAGGAGTTCAAG-TCCAATCAGTAATTATGATGCAGTAATGATTCAGTCATGAT
66 GAAGCCCAAAGAAGGAGTTCAAGTTCC-ATCAGTAATTATGATGCAGTAATGATTCAGTCATGAT
70206 GCAAGCATTGTTAAAT
130 GCAAGCATTGTTAAAT
70222 C
1 C
70223 CTATTTAAAG
Statistics
Matches: 144, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
144 3 0.02
145 141 0.98
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (145 bp):
CAAATTACCAAGCCAGATGTCTTGAAGGCTAAATCTGATATTCTTAGATCCAATTCGTTAATATG
GAAGCCCAAAGAAGGAGTTCAAGTTCCATCAGTAATTATGATGCAGTAATGATTCAGTCATGATG
CAAGCATTGTTAAAT
Found at i:71621 original size:20 final size:20
Alignment explanation
Indices: 71596--71652 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
71586 AGAGTGAGAA
*
71596 TGACACGTGGCTAAAAGGAT
1 TGACACGTGGCTAAAAGGAC
* * *
71616 TGACACATGGTTAAAAAGAC
1 TGACACGTGGCTAAAAGGAC
71636 TGACACGTGGCTAAAAG
1 TGACACGTGGCTAAAAG
71653 ACCAAATGAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (20 bp):
TGACACGTGGCTAAAAGGAC
Found at i:73621 original size:31 final size:28
Alignment explanation
Indices: 73597--73654 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
73587 AATCCCTTAG
*
73597 CTTTTTC--ATTTGGGACAAATAAATCC
1 CTTTTTCTTATTTGAGACAAATAAATCC
*
73623 CTTTTTCTTTTTTGAGACAAATAAATCC
1 CTTTTTCTTATTTGAGACAAATAAATCC
73651 CTTT
1 CTTT
73655 ACTTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.25
28 21 0.75
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (28 bp):
CTTTTTCTTATTTGAGACAAATAAATCC
Found at i:74737 original size:45 final size:45
Alignment explanation
Indices: 74673--74767 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
74663 AATCGACCAA
74673 GAAAATGAATAGGAGAATCGGGCAAGCAAGAATGAATGATGAAGG
1 GAAAATGAATAGGAGAATCGGGCAAGCAAGAATGAATGATGAAGG
74718 GAAAATGAATAGGAGAATCGGGCAAGCAAGAATGAATGATGAAGG
1 GAAAATGAATAGGAGAATCGGGCAAGCAAGAATGAATGATGAAGG
*
74763 AAAAA
1 GAAAA
74768 AAATTATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.49, C:0.06, G:0.32, T:0.13
Consensus pattern (45 bp):
GAAAATGAATAGGAGAATCGGGCAAGCAAGAATGAATGATGAAGG
Found at i:75083 original size:28 final size:29
Alignment explanation
Indices: 75052--75125 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 29
75042 CTCACTTTTG
75052 AAAGCAAAGGGATTTATTTGT-AAATAAA
1 AAAGCAAAGGGATTTATTTGTCAAATAAA
*
75080 AAAG-ATAAGGGATTTATTTGTCCCAAATGAA
1 AAAGCA-AAGGGATTTATTTGT--CAAATAAA
*
75111 AAAGCTAAGGGATTT
1 AAAGCAAAGGGATTT
75126 TCTGGTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 1 0.03
28 19 0.49
31 19 0.49
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (29 bp):
AAAGCAAAGGGATTTATTTGTCAAATAAA
Found at i:75120 original size:31 final size:28
Alignment explanation
Indices: 75052--75125 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 28
75042 CTCACTTTTG
*
75052 AAAGCAAAGGGATTTATTTGTAAATAAA
1 AAAGCTAAGGGATTTATTTGTAAATAAA
* *
75080 AAAGATAAGGGATTTATTTGTCCCAAATGAA
1 AAAGCTAAGGGATTTATTTGT---AAATAAA
75111 AAAGCTAAGGGATTT
1 AAAGCTAAGGGATTT
75126 TCTGGTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 19 0.49
31 20 0.51
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (28 bp):
AAAGCTAAGGGATTTATTTGTAAATAAA
Found at i:78528 original size:26 final size:25
Alignment explanation
Indices: 78489--78554 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
78479 AAAAAGAAAT
*
78489 AAAAAATAAAAAAT-CAGAATTAATTA
1 AAAAAATAATAAATACA-AATTAA-TA
* * *
78515 AAAAAATATTAAATACACATTTATA
1 AAAAAATAATAAATACAAATTAATA
78540 AAAAAATAATAAATA
1 AAAAAATAATAAATA
78555 ATTAATAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 16 0.47
26 16 0.47
27 2 0.06
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.26
Consensus pattern (25 bp):
AAAAAATAATAAATACAAATTAATA
Found at i:80173 original size:8 final size:8
Alignment explanation
Indices: 80160--80209 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
80150 CTTTTAAAAA
*
80160 TTAATTAC
1 TTAATTAT
*
80168 TTAATTTT
1 TTAATTAT
*
80176 TTAATTAC
1 TTAATTAT
*
80184 TT-ATTTT
1 TTAATTAT
80191 TTAATTAT
1 TTAATTAT
80199 TTAATT-T
1 TTAATTAT
80206 TTAA
1 TTAA
80210 GTTCTGAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
7 10 0.29
8 24 0.71
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (8 bp):
TTAATTAT
Found at i:80181 original size:16 final size:16
Alignment explanation
Indices: 80160--80207 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
80150 CTTTTAAAAA
80160 TTAATTACTTAATTTT
1 TTAATTACTTAATTTT
80176 TTAATTACTT-ATTTT
1 TTAATTACTTAATTTT
*
80191 TTAATTATTTAATTTT
1 TTAATTACTTAATTTT
80207 T
1 T
80208 AAGTTCTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 14 0.47
16 16 0.53
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATTACTTAATTTT
Found at i:80189 original size:15 final size:15
Alignment explanation
Indices: 80160--80209 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
80150 CTTTTAAAAA
80160 TTAATTACTTAATTTT
1 TTAATTACTT-ATTTT
80176 TTAATTACTTATTTT
1 TTAATTACTTATTTT
* *
80191 TTAATTATTTAATTT
1 TTAATTACTTATTTT
80206 TTAA
1 TTAA
80210 GTTCTGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 22 0.69
16 10 0.31
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (15 bp):
TTAATTACTTATTTT
Found at i:83180 original size:93 final size:93
Alignment explanation
Indices: 83095--83279 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 93
83085 ACTTTTTAAT
* *
83095 TAAATTAGTAATATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
83160 AGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGTTTTTAGTTGACTAAAACTATAAAAG
* * *
83188 TAAAATAGTAAAATGGTAAAAATAAAATAGTTTTAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
83253 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAACTATAAAA
83280 TTTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:83197 original size:22 final size:22
Alignment explanation
Indices: 83172--83218 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
83162 TTTTTAGTTG
*
83172 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
83194 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
83216 AGT
1 AGT
83219 TTTAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:83350 original size:31 final size:32
Alignment explanation
Indices: 83315--83378 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
83305 ATATTCGAAA
* *
83315 AATAAGGGTATGATAGGCTATTCAAAA-TTTT
1 AATAAGGGTATAATAGGCGATTCAAAAGTTTT
83346 AATAAGGGTATAATAGGCGATTCAAAAGTTTT
1 AATAAGGGTATAATAGGCGATTCAAAAGTTTT
83378 A
1 A
83379 CAAAACTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (32 bp):
AATAAGGGTATAATAGGCGATTCAAAAGTTTT
Found at i:104188 original size:39 final size:39
Alignment explanation
Indices: 104134--104213 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
104124 TCGAACCTGA
104134 AACATGCTTCACTTGAACATGCTTAACTTACAGGGTTTC
1 AACATGCTTCACTTGAACATGCTTAACTTACAGGGTTTC
104173 AACATGCTTCACTTGAACATGCTTAACTTACAGGGTTTC
1 AACATGCTTCACTTGAACATGCTTAACTTACAGGGTTTC
104212 AA
1 AA
104214 ACCGGGACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (39 bp):
AACATGCTTCACTTGAACATGCTTAACTTACAGGGTTTC
Found at i:109068 original size:294 final size:293
Alignment explanation
Indices: 108511--109097 Score: 1003
Period size: 294 Copynumber: 2.0 Consensus size: 293
108501 ATTTTTAGTG
* *
108511 ACTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCTTTTTTTGG
1 ACTATGGAAATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTAGCTTTTTTTGG
* * * * *
108576 TCTTTTCTCACTTTTCGGGTGGCTAAAAAGGCCCTTGATAAATTTTCTCCCTTACTTTTCCTGCT
66 TCTTTTCTCACTTTTCGGGTGACTAAAAAGACCCTCGATAAATTTCCTCACTTACTTTTCCTGCT
108641 GCCCTTTTTTGAAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTGATTG
131 GCCCTTTTTTGAAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTGATTG
* *
108706 TGTGTGGATATTATGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTGGTGCTATAA
196 TGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTATAA
108771 ATGTATCTACCCGAGTTCATTAATTTAACAATT
261 ATGTATCTACCCGAGTTCATTAATTTAACAATT
* *
108804 ACTATGGAAATTACCTAAAAGGCCAAATTGAGGATTAATGTGGTGCTTCCTTTTAGCTTTTTTTT
1 ACTATGGAAATTA-CTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTAGCTTTTTTTG
*
108869 GTCTTTTCTCACTTTTCGGGTGACTAAAAAGACCCTCGATGAATTTCCTCACTTACTTTTCCTGC
65 GTCTTTTCTCACTTTTCGGGTGACTAAAAAGACCCTCGATAAATTTCCTCACTTACTTTTCCTGC
*
108934 TGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTGATT
130 TGCCCTTTTTTGAAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTGATT
* * *
108999 GTGTGTGGATATTAGGATTTGCCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGTTGTA
195 GTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTATA
* *
109064 AATGTCTTTACCCGAGTTCATTAATTTAACAATT
260 AATGTATCTACCCGAGTTCATTAATTTAACAATT
109098 GCAATCAAGA
Statistics
Matches: 275, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
293 13 0.05
294 262 0.95
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (293 bp):
ACTATGGAAATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTAGCTTTTTTTGG
TCTTTTCTCACTTTTCGGGTGACTAAAAAGACCCTCGATAAATTTCCTCACTTACTTTTCCTGCT
GCCCTTTTTTGAAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTGATTG
TGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTATAA
ATGTATCTACCCGAGTTCATTAATTTAACAATT
Found at i:109937 original size:22 final size:22
Alignment explanation
Indices: 109886--109943 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
109876 GCATTAAAGT
*
109886 TAGATTATTAGTTTAATCATCG
1 TAGATTATTAGTTTAATCAACG
* *
109908 TATA-TATTAGTTATAAT-AAGG
1 TAGATTATTAGTT-TAATCAACG
109929 TAGATTATTAGTTTA
1 TAGATTATTAGTTTA
109944 TTATAACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (22 bp):
TAGATTATTAGTTTAATCAACG
Found at i:127060 original size:1 final size:1
Alignment explanation
Indices: 127054--127083 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
127044 AGAAACCAAG
127054 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
127084 CTAGTTAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:129468 original size:495 final size:496
Alignment explanation
Indices: 128330--129824 Score: 2722
Period size: 495 Copynumber: 3.0 Consensus size: 496
128320 GAGGGTTATT
*
128330 TGATAAATAATCCAAATAAGAAAATGTTTATTAATGGAGATCTTGAAGCATAAAAACTCCCTTTT
1 TGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAACTCCCTTTT
*
128395 GAGCCCTTTATGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCAAGAAAGTCGTAAATCAT
66 GAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCAAGAAAGTCGTAAATCAT
128460 GCAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGATATGTGGACAAAAAATTATACGAT
131 GCAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGATATGTGGACAAAAAATTATACGAT
*
128525 ATTAAATTGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTATA
196 ATTAAATTGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAA
128590 ATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAAT
261 ATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAAT
* * * *
128655 CACCTTAATCGGACAAATAGGAAAAAAATACAAAAATAAATACGAACGCGTTAAATTGTGCAACA
326 CACCTTAATCGGACAAATAAG-AAAAAATACAAAAATAAATACGAACGCGTTAAATCGTCCAACC
*
128720 TATAATTGTAAAGGACTAAATAACATAAAGCATAAAAGTATGAGGATCATTAGATAAATAATCCA
390 TATAATTGTAAAGGACTAAATAGCATAAAGCATAAAAGTATGAGGATCATTAGATAAATAATCCA
*
128785 ATAAAAATATATTAGTTTATGGAGAATGGGACCCATAAATAAATAG
455 ACAAAAATATATTAGTTTATGGAGAATGGGACCC----ATAAATAG
128831 TGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAACTCCCTTTT
1 TGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAACTCCCTTTT
* *
128896 GAGCCCTTCATGAAACTTGTAGATCAAATTTAGCTTTCAGGTCCTTCAAGAAAGTCGTAAATCAT
66 GAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCAAGAAAGTCGTAAATCAT
128961 GCAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGATATGTGGACAAAAAATTATACGAT
131 GCAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGATATGTGGACAAAAAATTATACGAT
129026 ATTAAATTGACCGGCAATCAAAACCACAAAATTTCAGAAGCA-TTTTTAGAATCAAAACATTAAA
196 ATTAAATTGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAA
129090 ATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAAT
261 ATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAAT
*
129155 CACCTTAATCGGACAAATAAGAAAAAATACAAAAATAAAAACGAACGCGTTAAATCGTCCAACCT
326 CACCTTAATCGGACAAATAAGAAAAAATACAAAAATAAATACGAACGCGTTAAATCGTCCAACCT
*
129220 ATAATTGTAAAGGACTAAATAGCATAAAACATAAAAGTATGAGGATCATTAGATAAATAATCCAA
391 ATAATTGTAAAGGACTAAATAGCATAAAGCATAAAAGTATGAGGATCATTAGATAAATAATCCAA
129285 CAAAAATATATTAGTTTATGGAGAATGGGACCCATAAATAG
456 CAAAAATATATTAGTTTATGGAGAATGGGACCCATAAATAG
129326 TGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAACTCCCTTTT
1 TGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAACTCCCTTTT
* * *
129391 GAGCCATTCATGAAACTCGTAGATCAAATTTAGATTTCGGGTCATTCAAGAAAGTCGTAAATCAT
66 GAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCAAGAAAGTCGTAAATCAT
129456 GCAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGATATGTGGACAAAAAATTATACGAT
131 GCAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGATATGTGGACAAAAAATTATACGAT
*
129521 ATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAAGCATTTTTTAGAATCAAAACATTAAA
196 ATTAAATTGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAA
*
129586 ATTGACTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAAT
261 ATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAAT
* * *
129651 CACCTTAATCGGACAAATAGGAAAAAAAATACTAAAATAAATGCGAACGCGTTAAATCGTCCAAC
326 CACCTTAATCGGACAAATA--AGAAAAAATACAAAAATAAATACGAACGCGTTAAATCGTCCAAC
129716 CTATAATTGTAAAGGACTAAATAGCATAAAGCATAAAAGTATGAGGATCATTAGATAAATAATCC
389 CTATAATTGTAAAGGACTAAATAGCATAAAGCATAAAAGTATGAGGATCATTAGATAAATAATCC
*
129781 AACAAAAATATATTAGTTTATGGAGAATGGGACCCACAAATAG
454 AACAAAAATATATTAGTTTATGGAGAATGGGACCCATAAATAG
129824 T
1 T
129825 AGCTTTTTCA
Statistics
Matches: 965, Mismatches: 26, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
495 239 0.25
496 105 0.11
498 147 0.15
499 135 0.14
500 106 0.11
501 233 0.24
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (496 bp):
TGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAAAACTCCCTTTT
GAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCAAGAAAGTCGTAAATCAT
GCAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGATATGTGGACAAAAAATTATACGAT
ATTAAATTGACCGGCAATCAAAACCACAAAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAA
ATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAAT
CACCTTAATCGGACAAATAAGAAAAAATACAAAAATAAATACGAACGCGTTAAATCGTCCAACCT
ATAATTGTAAAGGACTAAATAGCATAAAGCATAAAAGTATGAGGATCATTAGATAAATAATCCAA
CAAAAATATATTAGTTTATGGAGAATGGGACCCATAAATAG
Found at i:129990 original size:18 final size:18
Alignment explanation
Indices: 129967--130003 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
129957 TTTCAAATCC
129967 TCCTATTATTGTTTCTTA
1 TCCTATTATTGTTTCTTA
129985 TCCTATTATTGTTTCTTA
1 TCCTATTATTGTTTCTTA
130003 T
1 T
130004 AATATAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.62
Consensus pattern (18 bp):
TCCTATTATTGTTTCTTA
Found at i:132670 original size:17 final size:18
Alignment explanation
Indices: 132638--132671 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
132628 GCTGTAAATG
*
132638 GATCAATTAAATGAAAAA
1 GATCAATTAAAGGAAAAA
132656 GATCAA-TAAAGGAAAA
1 GATCAATTAAAGGAAAA
132672 GTGAAGATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.18
Consensus pattern (18 bp):
GATCAATTAAAGGAAAAA
Found at i:137233 original size:18 final size:18
Alignment explanation
Indices: 137212--137253 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
137202 AAAATGATTT
*
137212 TTTTTTGTAAAAAAATAA
1 TTTTTCGTAAAAAAATAA
**
137230 TTTTTCGTAAAATGATAA
1 TTTTTCGTAAAAAAATAA
137248 TTTTTC
1 TTTTTC
137254 CATGTGGAAT
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:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (18 bp):
TTTTTCGTAAAAAAATAA
Found at i:138712 original size:39 final size:39
Alignment explanation
Indices: 138651--138726 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
138641 TGTCTTCCCC
* * *
138651 CTGTTTGTTTTTGCTTCTCTTGAGTTGGACTGTTTTGCT
1 CTGTTTGCTTTTGCTTCTCTTGAGCTAGACTGTTTTGCT
*
138690 CTGTTTGCTTTTG-TTATCCTTGAGCTAGACTGTTTTG
1 CTGTTTGCTTTTGCTTCT-CTTGAGCTAGACTGTTTTG
138727 GTGGCTCGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.09
39 29 0.91
ACGTcount: A:0.08, C:0.16, G:0.22, T:0.54
Consensus pattern (39 bp):
CTGTTTGCTTTTGCTTCTCTTGAGCTAGACTGTTTTGCT
Found at i:142859 original size:22 final size:22
Alignment explanation
Indices: 142834--143396 Score: 148
Period size: 22 Copynumber: 25.5 Consensus size: 22
142824 GACCATCAAC
*
142834 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
142856 CAAAATTTAAGAGTG-TGGTTA-
1 CAAAATTTCATAG-GAAGGTTAT
* * **
142877 CTGAAATTTCATATGAAAATTAT
1 C-AAAATTTCATAGGAAGGTTAT
*
142900 CAAAACTTT-ATAGTGTA-GTTAT
1 CAAAA-TTTCATAG-GAAGGTTAT
* *
142922 CAAAATTTCATAAGAAGGTTAC
1 CAAAATTTCATAGGAAGGTTAT
**
142944 CAAAATTTCATAAAAAAGGTTAT
1 CAAAATTTCAT-AGGAAGGTTAT
* * * *
142967 CAAAATTTCTTAGGGAGGCTAA
1 CAAAATTTCATAGGAAGGTTAT
*
142989 C-AAATTCCATACGGAA-GTTAT
1 CAAAATTTCATA-GGAAGGTTAT
* *
143010 CAAAATTTTATAGTG-TGGTTAT
1 CAAAATTTCATAG-GAAGGTTAT
* * * *
143032 GAAAAATTCATAAGAAGGTTAA
1 CAAAATTTCATAGGAAGGTTAT
*
143054 CAAAATTTCATAGGGAGGGAATTTAT
1 CAAAATTTCATA-GGAAGG---TTAT
* *
143080 CAAAA-TT--T--G-TGCTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * * * * *
143096 TAAAATTTCCTAGGGACGTGAA
1 CAAAATTTCATAGGAAGGTTAT
* *
143118 CAAAATTTCATTGGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * * *
143140 GAAAATTTTAT-GGAGAGCTTAC
1 CAAAATTTCATAGGA-AGGTTAT
* *
143162 CAAAATTACATA-GAGAGGATAT
1 CAAAATTTCATAGGA-AGGTTAT
* *
143184 CACAGGTTCATTCTCATAGGGAGGTTAT
1 CA-A----AATT-TCATAGGAAGGTTAT
**
143212 CAAAATTTCAT-GGTGTGGTTAT
1 CAAAATTTCATAGG-AAGGTTAT
*
143234 CAAAATTTTCATAGTGCA-GTTA-
1 CAAAA-TTTCATAG-GAAGGTTAT
* * *
143256 C-CAATTTTATA--ATGTGATTAT
1 CAAAATTTCATAGGAAG-G-TTAT
* **
143277 CAAAATTTCATAGGGACATTAT
1 CAAAATTTCATAGGAAGGTTAT
* * * *
143299 CAAAATTTCAAACTG-AGATTAA
1 CAAAATTTCATA-GGAAGGTTAT
*
143321 CAAAATTTCATA-G-TGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * * *
143341 CAAAAGTTCACAGTATGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
143363 CAAATTTTCATAGGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
**
143385 TGAAATTTCATA
1 CAAAATTTCATA
143397 ATAAGCCCCA
Statistics
Matches: 386, Mismatches: 108, Indels: 94
0.66 0.18 0.16
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
19 3 0.01
20 25 0.06
21 29 0.08
22 244 0.63
23 46 0.12
24 1 0.00
25 3 0.01
26 8 0.02
27 4 0.01
28 12 0.03
29 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:142970 original size:23 final size:22
Alignment explanation
Indices: 142917--142975 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 22
142907 TTATAGTGTA
*
142917 GTTATCAAAATTTCATAAGAAG
1 GTTATCAAAATTTCATAAAAAG
*
142939 GTTACCAAAATTTCATAAAAAAG
1 GTTATCAAAATTTCAT-AAAAAG
142962 GTTATCAAAATTTC
1 GTTATCAAAATTTC
142976 TTAGGGAGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAAAAG
Found at i:143350 original size:20 final size:21
Alignment explanation
Indices: 143321--143366 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
143311 CTGAGATTAA
* *
143321 CAAAATTTCATAG-TGGTTAT
1 CAAAAGTTCACAGATGGTTAT
143341 CAAAAGTTCACAGTATGGTTAT
1 CAAAAGTTCACAG-ATGGTTAT
143363 CAAA
1 CAAA
143367 TTTTCATAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
22 11 0.50
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
CAAAAGTTCACAGATGGTTAT
Found at i:144434 original size:44 final size:44
Alignment explanation
Indices: 144367--144490 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 44
144357 CTGACCATCA
* ** * * *
144367 ACCAAAATTACATAGGAAGATTATTAAAA-TTTAGTAGTGTGGTT
1 ACCAAAATTTCATATAAAGATTATCAAAACTTCA-TAGTGTAGTT
*
144411 ACCGAAATTTCATATAAAGATTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATATAAAGATTATCAAAACTTCATAGTGTAGTT
* * * *
144455 ATCAAAATTTCATA-AGAAGGTTACCAAAATTTCATA
1 ACCAAAATTTCATATA-AAGATTATCAAAACTTCATA
144491 AAAAGGTTAT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 1 0.02
44 62 0.94
45 3 0.05
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (44 bp):
ACCAAAATTTCATATAAAGATTATCAAAACTTCATAGTGTAGTT
Found at i:144477 original size:22 final size:22
Alignment explanation
Indices: 144415--144552 Score: 95
Period size: 22 Copynumber: 6.3 Consensus size: 22
144405 GTGGTTACCG
*
144415 AAATTTCATATA-AAGATTATCA
1 AAATTTCATA-AGAAGGTTATCA
* * *
144437 AAACTTCATAGTGTA-GTTATCA
1 AAATTTCATA-AGAAGGTTATCA
*
144459 AAATTTCATAAGAAGGTTACCA
1 AAATTTCATAAGAAGGTTATCA
*
144481 AAATTTCATAAAAAGGTTAT-A
1 AAATTTCATAAGAAGGTTATCA
* * * *
144502 AGAATTTCTTAGGGAGGTTAAC-
1 A-AATTTCATAAGAAGGTTATCA
* * *
144524 AAATTCCATATGAAAGATTATCA
1 AAATTTCATAAG-AAGGTTATCA
144547 AAATTT
1 AAATTT
144553 TATAGTGTGG
Statistics
Matches: 87, Mismatches: 23, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
21 12 0.14
22 69 0.79
23 6 0.07
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
AAATTTCATAAGAAGGTTATCA
Found at i:144500 original size:44 final size:44
Alignment explanation
Indices: 144452--144552 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 44
144442 TCATAGTGTA
* *
144452 GTTATCAAAATTTCATAAGAAGGTTACCAAAATTTCATA-AAAAG
1 GTTATCAAAATTTCATAAGAAGGTTAAC-AAATTCCATATAAAAG
* * * *
144496 GTTAT-AAGAATTTCTTAGGGAGGTTAACAAATTCCATATGAAAG
1 GTTATCAA-AATTTCATAAGAAGGTTAACAAATTCCATATAAAAG
*
144540 ATTATCAAAATTT
1 GTTATCAAAATTT
144553 TATAGTGTGG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
43 11 0.23
44 34 0.72
45 2 0.04
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.33
Consensus pattern (44 bp):
GTTATCAAAATTTCATAAGAAGGTTAACAAATTCCATATAAAAG
Found at i:144712 original size:22 final size:22
Alignment explanation
Indices: 144668--144720 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
144658 TTTCATTGGT
* ** *
144668 AGGTTATGAAAATTTTATCGAG
1 AGGTTATCAAAATTACATAGAG
144690 AGGTTATCAAAATTACATAGAG
1 AGGTTATCAAAATTACATAGAG
*
144712 AGGATATCA
1 AGGTTATCA
144721 CTGTTTCAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.30
Consensus pattern (22 bp):
AGGTTATCAAAATTACATAGAG
Found at i:144767 original size:22 final size:22
Alignment explanation
Indices: 144734--144909 Score: 153
Period size: 22 Copynumber: 8.2 Consensus size: 22
144724 TTTCAATCTT
*
144734 ATAGGGTGGTTATCAAAATTTC
1 ATAGTGTGGTTATCAAAATTTC
*
144756 ATGGTGTGGTTATCAAAATTTC
1 ATAGTGTGGTTATCAAAATTTC
** * *
144778 ATAGTGCAGTTA-C-TAATTTT
1 ATAGTGTGGTTATCAAAATTTC
* *
144798 ATAGTGTGATTATCAGAATTTC
1 ATAGTGTGGTTATCAAAATTTC
* * *
144820 ATAGGGAGATTATCAAAATTTC
1 ATAGTGTGGTTATCAAAATTTC
* * * *
144842 ACACTGAGATTATCAAAATTTC
1 ATAGTGTGGTTATCAAAATTTC
*
144864 ATA--GTGGTTATCAAAAGTTC
1 ATAGTGTGGTTATCAAAATTTC
* * *
144884 ACAGTATGGTTATCAAATTTTC
1 ATAGTGTGGTTATCAAAATTTC
144906 ATAG
1 ATAG
144910 GCAAATAGAG
Statistics
Matches: 123, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
20 30 0.24
21 2 0.02
22 91 0.74
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (22 bp):
ATAGTGTGGTTATCAAAATTTC
Found at i:144811 original size:42 final size:45
Alignment explanation
Indices: 144743--144909 Score: 159
Period size: 42 Copynumber: 3.9 Consensus size: 45
144733 TATAGGGTGG
* *
144743 TTATCAAAATTTCATGGTGTGGTTATCAAAATTTCATAGTGCAG-
1 TTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAGTGCAGA
* * * *
144787 TTA-C-TAATTTTATAGTGTGATTATCAGAATTTCATAG-GGAGA
1 TTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAGTGCAGA
* * *
144829 TTATCAAAATTTCACACTGAGATTATCAAAATTTCATAGTG--G-
1 TTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAGTGCAGA
* * * * *
144871 TTATCAAAAGTTCACAGTATGGTTATCAAATTTTCATAG
1 TTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAG
144910 GCAAATAGAG
Statistics
Matches: 101, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 3 0.03
42 64 0.63
43 3 0.03
44 30 0.30
45 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAGTGCAGA
Found at i:144875 original size:64 final size:62
Alignment explanation
Indices: 144739--144884 Score: 152
Period size: 64 Copynumber: 2.3 Consensus size: 62
144729 ATCTTATAGG
* * * * * *
144739 GTGGTTATCAAAATTTCATGGTGTGGTTATCAAAATTTCATAGTGCAGTTACTAATTTTATA
1 GTGGTTATCAAAATTTCATGGTGAGATTATCAAAATTTCACACTGCAGTTACAAATTTCATA
*
144801 GTGTGATTATCAGAATTTCATAGG-GAGATTATCAAAATTTCACACTG-AGATTATCAAAATTTC
1 GTG-G-TTATCAAAATTTCAT-GGTGAGATTATCAAAATTTCACACTGCAG-TTA-C-AAATTTC
144864 ATA
60 ATA
*
144867 GTGGTTATCAAAAGTTCA
1 GTGGTTATCAAAATTTCA
144885 CAGTATGGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 48 0.70
65 4 0.06
66 11 0.16
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (62 bp):
GTGGTTATCAAAATTTCATGGTGAGATTATCAAAATTTCACACTGCAGTTACAAATTTCATA
Found at i:157010 original size:27 final size:27
Alignment explanation
Indices: 156970--157024 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
156960 GTTTTTTTGC
156970 AATTTGGATATGAATTTACACGTGAAG
1 AATTTGGATATGAATTTACACGTGAAG
* *
156997 AATTTGGATCTGAATTTAGACGTGAAG
1 AATTTGGATATGAATTTACACGTGAAG
157024 A
1 A
157025 GGCTTGCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (27 bp):
AATTTGGATATGAATTTACACGTGAAG
Found at i:159056 original size:32 final size:32
Alignment explanation
Indices: 159015--159079 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
159005 ATCGAACCAC
159015 TTGATCAATAAAACAATGAAGGGATACTTTAG
1 TTGATCAATAAAACAATGAAGGGATACTTTAG
159047 TTGATCAATAAAACAATGAAGGGATACTTTAG
1 TTGATCAATAAAACAATGAAGGGATACTTTAG
159079 T
1 T
159080 ATGTGAGCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.29
Consensus pattern (32 bp):
TTGATCAATAAAACAATGAAGGGATACTTTAG
Found at i:159159 original size:19 final size:19
Alignment explanation
Indices: 159135--159171 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
159125 GTACAGTACC
159135 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
159154 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
159172 TACTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:160551 original size:130 final size:131
Alignment explanation
Indices: 160351--160613 Score: 402
Period size: 130 Copynumber: 2.0 Consensus size: 131
160341 GTCATTTAAG
* ** * * *
160351 AAATATATTTTAAATTTTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
1 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATA
160416 AAATAGGTATAAGGATATTAAATTTAATTAAATAAAAAAAGAGTTTTTAGTTGAGTAAAACTATA
66 AAATAGGTATAAGGATATTAAATTTAATTAAATAAAAAAAGAGTTTTTAGTTGAGTAAAACTATA
160481 A
131 A
* *
160482 AAATATATTTAAAAAATTCTAATATATATAAG-TTTTTAATTAAAATAGTAAAATGGTAAAAATT
1 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATA
* * * * *
160546 AAATAGTTATGAGGATATTATATTTAATTAAATAAAGATAGAGTTTTTAGTTGAGTAAAACTATA
66 AAATAGGTATAAGGATATTAAATTTAATTAAATAAAAAAAGAGTTTTTAGTTGAGTAAAACTATA
160611 A
131 A
160612 AA
1 AA
160614 GTCTAATGGT
Statistics
Matches: 119, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
130 91 0.76
131 28 0.24
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (131 bp):
AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATA
AAATAGGTATAAGGATATTAAATTTAATTAAATAAAAAAAGAGTTTTTAGTTGAGTAAAACTATA
A
Found at i:161891 original size:31 final size:31
Alignment explanation
Indices: 161850--162018 Score: 129
Period size: 31 Copynumber: 5.6 Consensus size: 31
161840 TTCGGCTAAT
161850 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * * **
161881 TGTTCAAATAAGGGCCCGATCTTTTG---ATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCCAAAA
* *
161910 TGGTCAAATAAGGGCCTAAAGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * **
161941 TACTCAAATAAGGGTCC-AATC-TTT--TAATT
1 TGCTCAAATAAGGG-CCTAA-CGTTTGCCAAAA
*
161970 TGGC-CAAAAAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
162001 TGCTCAAATAAGGGCCTA
1 TGCTCAAATAAGGGCCTA
162019 GCATCGAAAA
Statistics
Matches: 101, Mismatches: 25, Indels: 24
0.67 0.17 0.16
Matches are distributed among these distances:
28 10 0.10
29 31 0.31
30 3 0.03
31 47 0.47
32 10 0.10
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:161948 original size:60 final size:60
Alignment explanation
Indices: 161853--162016 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
161843 GGCTAATTGC
* * *
161853 TCAAATAAGGGCCTAACGTTTGCCAAAATGTTCAAATAAGGGCCCGATCTTTTGATTTGG
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGG
* * *
161913 TCAAATAAGGGCCTAAAGTTTGCCAAAATACTCAAATAAGGGTCCAATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGG
* *
161973 CCAAAAAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
162017 TAGCATCGAA
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGG
Found at i:162095 original size:31 final size:31
Alignment explanation
Indices: 162055--162223 Score: 127
Period size: 31 Copynumber: 5.6 Consensus size: 31
162045 AAACTGACGC
*
162055 TAGGTCCTTATTTGAGCATTTTGGCAAACAT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
* ** * *
162086 TAGGCCCTTATTTTG-CCAAATT--AAAAGAT
1 TAGGCCCTTA-TTTGAGCATTTTGGCAAACAT
** *
162115 CGGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
** *
162146 TAGGCCCTTATTTG-GCCA-AAT--CAAAAGAT
1 TAGGCCCTTATTTGAG-CATTTTGGC-AAACAT
** *
162175 CGGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
162206 TAGGCCCTTATTTGAGCA
1 TAGGCCCTTATTTGAGCA
162224 ATTAACCAAT
Statistics
Matches: 100, Mismatches: 28, Indels: 20
0.68 0.19 0.14
Matches are distributed among these distances:
28 5 0.05
29 35 0.35
30 4 0.04
31 51 0.51
32 5 0.05
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (31 bp):
TAGGCCCTTATTTGAGCATTTTGGCAAACAT
Found at i:162134 original size:60 final size:60
Alignment explanation
Indices: 162060--162219 Score: 293
Period size: 60 Copynumber: 2.7 Consensus size: 60
162050 GACGCTAGGT
* * *
162060 CCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTTGCCAAATTAAAAGATCGGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATCAAAAGATCGGGC
162120 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATCAAAAGATCGGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATCAAAAGATCGGGC
162180 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
162220 AGCAATTAAC
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATCAAAAGATCGGGC
Found at i:162188 original size:29 final size:29
Alignment explanation
Indices: 162088--162188 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
162078 GCAAACATTA
* *
162088 GGCCCTTATTTTGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATCAAAAGATCG
** * **
162117 GGCCCTTATTTGAG-CATTTTGGCAAACG-TTA
1 GGCCCTTATTTG-GCCA-AAT--CAAAAGATCG
162148 GGCCCTTATTTGGCCAAATCAAAAGATCG
1 GGCCCTTATTTGGCCAAATCAAAAGATCG
162177 GGCCCTTATTTG
1 GGCCCTTATTTG
162189 AGCATTTTGG
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
28 5 0.09
29 26 0.48
30 4 0.07
31 15 0.28
32 4 0.07
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATCAAAAGATCG
Found at i:163350 original size:18 final size:18
Alignment explanation
Indices: 163327--163366 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
163317 GCCCAAAGCG
*
163327 TGGCATCGTGTGCTCTTA
1 TGGCATCGTGCGCTCTTA
163345 TGGCATCGTGCGCTCTTA
1 TGGCATCGTGCGCTCTTA
163363 TGGC
1 TGGC
163367 GTTATGTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.25, G:0.30, T:0.35
Consensus pattern (18 bp):
TGGCATCGTGCGCTCTTA
Found at i:163377 original size:18 final size:18
Alignment explanation
Indices: 163327--163378 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
163317 GCCCAAAGCG
*
163327 TGGCATCGTGTGCTCTTA
1 TGGCATCATGTGCTCTTA
* *
163345 TGGCATCGTGCGCTCTTA
1 TGGCATCATGTGCTCTTA
* *
163363 TGGCGTTATGTGCTCT
1 TGGCATCATGTGCTCT
163379 CCGCCTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.10, C:0.23, G:0.29, T:0.38
Consensus pattern (18 bp):
TGGCATCATGTGCTCTTA
Found at i:164603 original size:29 final size:28
Alignment explanation
Indices: 164547--164603 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
164537 TATGTTTTGC
* *
164547 TTTTGGGACAAAATAATTCCATATGTTT
1 TTTTGGGACAAAATAATCCCATACGTTT
* *
164575 TTTTCGGGACAAATTAATCCCTTACGTTT
1 TTTT-GGGACAAAATAATCCCATACGTTT
164604 AAAAAATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (28 bp):
TTTTGGGACAAAATAATCCCATACGTTT
Found at i:164787 original size:31 final size:30
Alignment explanation
Indices: 164747--164840 Score: 122
Period size: 30 Copynumber: 3.1 Consensus size: 30
164737 AATGGACTAA
*
164747 TTTGTCCAAAA-AAAATATATAAGGGATTTT
1 TTTGTCCAAAAGAAAA-ACATAAGGGATTTT
164777 TTTGTACCAAAAGAAAAACATAAGGGA-TTT
1 TTTGT-CCAAAAGAAAAACATAAGGGATTTT
164807 TTTGTCCCAAAAGAAAAACATTAA-GGATTTT
1 TTTGT-CCAAAAGAAAAACA-TAAGGGATTTT
164838 TTT
1 TTT
164841 AGTATTTAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
30 30 0.52
31 24 0.41
32 4 0.07
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.34
Consensus pattern (30 bp):
TTTGTCCAAAAGAAAAACATAAGGGATTTT
Found at i:164900 original size:6 final size:7
Alignment explanation
Indices: 164883--164907 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
164873 AAAAATTGAT
164883 TTTTTTC
1 TTTTTTC
164890 TTTTTTC
1 TTTTTTC
164897 TTTTTTC
1 TTTTTTC
164904 TTTT
1 TTTT
164908 CTCCTTCTCC
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:165150 original size:126 final size:125
Alignment explanation
Indices: 164998--165236 Score: 338
Period size: 126 Copynumber: 1.9 Consensus size: 125
164988 AATTCCCTAA
* * *
164998 AAAATTGGTAAAGATAAAATAGTTATAAAAATATT-GAATTTAATTAAATAAAAATAGAATTTTT
1 AAAATTGGTAAAAATAAAATAATTATAAAAATATTAG-ATTTAATTAAACAAAAATAGAATTTTT
* *
165062 GGTAAAATAAAACTGTAAAAGTTTAAATAATGTCATTTAAGAAATATATTTAATTAAAATAGT
65 GATAAAA-AAAACTGTAAAAGTTTAAA-AATGACATTTAAGAAATATATTTAATTAAAATAGT
* * *
165125 AAAA-TGGTAAAAATAAAATAATTATAAATATATTAGATTTGATTAAACAAAAATAGAGTTTTTG
1 AAAATTGGTAAAAATAAAATAATTATAAAAATATTAGATTTAATTAAACAAAAATAGAATTTTTG
** *
165189 ATTGAAAAAATTGTAAAAGTTTAAAAATGACATTTAAGAAATATATTT
66 ATAAAAAAAACTGTAAAAGTTTAAAAATGACATTTAAGAAATATATTT
165237 GAAAAATAAG
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
124 22 0.22
125 18 0.18
126 55 0.55
127 5 0.05
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (125 bp):
AAAATTGGTAAAAATAAAATAATTATAAAAATATTAGATTTAATTAAACAAAAATAGAATTTTTG
ATAAAAAAAACTGTAAAAGTTTAAAAATGACATTTAAGAAATATATTTAATTAAAATAGT
Found at i:165346 original size:163 final size:161
Alignment explanation
Indices: 165124--165415 Score: 408
Period size: 163 Copynumber: 1.8 Consensus size: 161
165114 ATTAAAATAG
* * ** *
165124 TAAAATGGTAAAAATAAAATAATTATAAATATATTAGATTTGATTAAACAAAAATAGAGTTTTTG
1 TAAAATAGTAAAAATAAAATAAATATAAATATATTAGATTAAATTAAACAAAAATAGAGTTTTTA
* * *
165189 ATTGA-AAAAATTGTAAAAGTTTAAA-AATGACATTTAAGAAATATATTTGAAAAATAAGGGTAT
66 ATTGAGAAAAATTATAAAAATTTAAACAATGACATTTAA-AAATATAATTGAAAAATAAGGGTAT
165252 TTAAAAATTCTAATATATCTAAGTTTTTAAAT
130 TTAAAAATTCTAATATATCTAAGTTTTTAAAT
* *
165284 TAAAATAGTAAAATGATAATAATAAATATAAATATATTAGATTAAATTAAATAAATATAGAGTTT
1 TAAAATAGTAAAA--ATAA-AATAAATATAAATATATTAGATTAAATTAAACAAAAATAGAGTTT
* * * *
165349 TTAATTGAGTAATATTATAAAAATTTAAACAATGGCATTTAATAATATAATTGAAAAATAAGGGT
63 TTAATTGAGAAAAATTATAAAAATTTAAACAATGACATTTAAAAATATAATTGAAAAATAAGGGT
165414 AT
128 AT
165416 AGTAATCAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
160 12 0.11
162 4 0.04
163 47 0.42
164 39 0.35
165 11 0.10
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (161 bp):
TAAAATAGTAAAAATAAAATAAATATAAATATATTAGATTAAATTAAACAAAAATAGAGTTTTTA
ATTGAGAAAAATTATAAAAATTTAAACAATGACATTTAAAAATATAATTGAAAAATAAGGGTATT
TAAAAATTCTAATATATCTAAGTTTTTAAAT
Done.