Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010898.1 Corchorus capsularis cultivar CVL-1 contig10919, 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: 293980
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1099 original size:321 final size:320
Alignment explanation
Indices: 1--1108 Score: 1628
Period size: 321 Copynumber: 3.4 Consensus size: 320
*
1 AAAATATCTATATTCATCGAAGCAAATCTCAGCATTATTGGATATAAGGATTTGTTTTACGAGCA
1 AAAATATCTATATTCATCGAAGCAAATCTCAGCCTTATTGGATATAAGGATTTGTTTTACGAGCA
* * *
66 TCTTAATCTTTTTTCAATTTAATTAGAAATTAATTCGG-AAAAAATGGGAAAACGATATTAGAAG
66 TCTCAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAG
* *
130 CGTGAAAAGCCCGCCAATATTATTGGCGTTGAATTATATATTGATTCTATGTATCTTGGCAAAAA
131 CGTGAAAAGCCCGCCAATCTTATTGGCGTTGAATTATATATTGATTCTATGTATCGTGGCAAAAA
* * *
195 ATTAAGAAAAAAAATTTCGAGACAGTTTTTTGTCGAAATCGTGTACTTACCATCACGGTTTTTGG
196 ATTAAGAAAAAAATTTTCGGGACAGTTTTTTGTCGAAATCGTGTACTAACCATCACGGTTTTTGG
* ** *
260 CTAAAAACGCGTTCCGGAGTCACGACTCAATTTTGCATGATTTTTGTCGCAAAGACTCCTT
261 CTAAAAACGCGTTCCGAAACCACGA-TCAATTTTGCATGATTTTTGGCGCAAAGACTCCTT
* * ** * * *
321 AAAATATCTGTATTCATCAAAGCAAAATCTCAGTGTGATTGGATATAAGGATTTTTTTTACGAGT
1 AAAATATCTATATTCATCGAAGC-AAATCTCAGCCTTATTGGATATAAGGATTTGTTTTACGAGC
* * *
386 ATCTCAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAGAAAATGGAAAAACGATATTATA
65 ATCTCAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAA-AAAATGGAAAAACGATATTAGA
* * * * * * * *
451 ATCATGAAAAGCCCGCCAATCTTTTTGGCTTTGAATTATATAATT-TTTCTGTGTATTGTGGGAA
129 AGCGTGAAAAGCCCGCCAATCTTATTGGCGTTGAATTATAT-ATTGATTCTATGTATCGTGGCAA
* * * *
515 AATATTGAGAAAAAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGTTT
193 AAAATTAAGAAAAAAA-TTTTCGGGACAGTTTTTTGTCGAAATCGTGTACTAACCATCACGGTTT
* * *
580 TTGGCTAAAAACGCGTTCTGAAACCTCGGATCAATTTTGCATGATTTTTGGTGCAAAGACTCCTT
257 TTGGCTAAAAACGCGTTCCGAAACCAC-GATCAATTTTGCATGATTTTTGGCGCAAAGACTCCTT
* * * *
645 AAAATATCTAAATTTATCGAAGCAAATCTCAACCTTATTGGATATAAGGATTTGTTTTACAAGCA
1 AAAATATCTATATTCATCGAAGCAAATCTCAGCCTTATTGGATATAAGGATTTGTTTTACGAGCA
* *
710 TCTCAATCTTGTTTCAATTTAATGAGAAATTAATTCGGAAAAAAATGGGAAAACGATATTAGAAG
66 TCTCAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAG
** *
775 CGTGAAAAGCCCTTCAATCTTATTGGCGTTGAATTATATATTGATCCTATGTATCGTGGCAAAAA
131 CGTGAAAAGCCCGCCAATCTTATTGGCGTTGAATTATATATTGATTCTATGTATCGTGGCAAAAA
* *
840 ATTAAGAAAAAAATTTTCGGGACAGTTTTTTGTCGAAATCGTGTAC-AAGCATCATGGTTTTTGG
196 ATTAAGAAAAAAATTTTCGGGACAGTTTTTTGTCGAAATCGTGTACTAACCATCACGGTTTTTGG
*
904 CTAAAAACGCGTTCCGAAACCCCTGATCAATTTTGCATGATTTTTGGCGCAAAGACTCCTT
261 CTAAAAACGCGTTCCGAAACCAC-GATCAATTTTGCATGATTTTTGGCGCAAAGACTCCTT
* * *
965 AAAATATCTATATTCATCGAAGCAAATCTCCGCCTTATTGGATATAAAGATTTCTTTTTACGAGC
1 AAAATATCTATATTCATCGAAGCAAATCTCAGCCTTATTGGATATAAGGATTT-GTTTTACGAGC
* *
1030 ATCTCAATCTTGTTTCGATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAA
65 ATCTCAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAA
1095 GCGTGAAAAGCCCG
130 GCGTGAAAAGCCCG
1109 GGTAAAAGTA
Statistics
Matches: 695, Mismatches: 85, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
320 142 0.20
321 189 0.27
322 85 0.12
323 157 0.23
324 120 0.17
325 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (320 bp):
AAAATATCTATATTCATCGAAGCAAATCTCAGCCTTATTGGATATAAGGATTTGTTTTACGAGCA
TCTCAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAG
CGTGAAAAGCCCGCCAATCTTATTGGCGTTGAATTATATATTGATTCTATGTATCGTGGCAAAAA
ATTAAGAAAAAAATTTTCGGGACAGTTTTTTGTCGAAATCGTGTACTAACCATCACGGTTTTTGG
CTAAAAACGCGTTCCGAAACCACGATCAATTTTGCATGATTTTTGGCGCAAAGACTCCTT
Found at i:46562 original size:2 final size:2
Alignment explanation
Indices: 46557--46591 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
46547 AAAAAAAAAC
46557 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
46592 AGAAACTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48279 original size:15 final size:15
Alignment explanation
Indices: 48251--48292 Score: 63
Period size: 13 Copynumber: 3.0 Consensus size: 15
48241 CAGTCACAAC
48251 TTTT-CTTTTCTTTT
1 TTTTCCTTTTCTTTT
48265 TTTT--TTTTCTTTT
1 TTTTCCTTTTCTTTT
48278 TTTTCCTTTTCTTTT
1 TTTTCCTTTTCTTTT
48293 AGATCAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.50
14 4 0.15
15 9 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTCCTTTTCTTTT
Found at i:48287 original size:6 final size:5
Alignment explanation
Indices: 48250--48292 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
48240 CCAGTCACAA
48250 CTTTT CTTTT CTTTT -TTTT -TTTT CTTTT -TTTT CCTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT -CTTTT CTTTT
48293 AGATCAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 12 0.34
5 19 0.54
6 4 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
CTTTT
Found at i:53543 original size:15 final size:16
Alignment explanation
Indices: 53525--53554 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53515 CACTTTTTGA
53525 TCTTCTTC-TTCTTTT
1 TCTTCTTCTTTCTTTT
53540 TCTTCTTCTTTCTTT
1 TCTTCTTCTTTCTTT
53555 CCCAATCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
TCTTCTTCTTTCTTTT
Found at i:58781 original size:7 final size:7
Alignment explanation
Indices: 58769--58803 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
58759 TTCACTTTCT
58769 CCAGAAG
1 CCAGAAG
58776 CCAGAAG
1 CCAGAAG
58783 CCAGAAG
1 CCAGAAG
58790 CCAGAAG
1 CCAGAAG
58797 CCAGAAG
1 CCAGAAG
58804 AAAACAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.29, G:0.29, T:0.00
Consensus pattern (7 bp):
CCAGAAG
Found at i:69515 original size:57 final size:56
Alignment explanation
Indices: 69412--69526 Score: 144
Period size: 57 Copynumber: 2.0 Consensus size: 56
69402 ATCCTAGAGA
* *
69412 AAGCAATTCCCCAAACATCCCATTCTAACTCAATCTTGCGCGGGATCAAAAATTAGT
1 AAGCAACTCCCCAAACATCCCATTCTAACTCAATCTT-CGCAGGATCAAAAATTAGT
* *
69469 AAGCAACTCCCCAAGCATCATCCCATTCTAACTCAATCTT-G-AGGATCCAAGATTAGT
1 AAGCAACTCCCCAA--A-CATCCCATTCTAACTCAATCTTCGCAGGATCAAAAATTAGT
69526 A
1 A
69527 GGTCGAAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
57 27 0.53
58 1 0.02
59 1 0.02
60 22 0.43
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (56 bp):
AAGCAACTCCCCAAACATCCCATTCTAACTCAATCTTCGCAGGATCAAAAATTAGT
Found at i:73776 original size:31 final size:31
Alignment explanation
Indices: 73715--73851 Score: 186
Period size: 31 Copynumber: 4.5 Consensus size: 31
73705 TTTTGTGCAC
* * **
73715 GTGGCATGCCACGTGCCA-TTTTTGAAACAT
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
*
73745 GTGGCATGCCACGTGTCACTTTTTGGTACAT
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
* *
73776 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
* *
73807 GTGGCGTGCCACATGTCACTTTTTGGTACAC
1 GTGGCGTGCCACGTGTCACTTTTTGGTACAT
73838 GTGGCGTGCCACGT
1 GTGGCGTGCCACGT
73852 CGGACACCGT
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 17 0.18
31 78 0.82
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.33
Consensus pattern (31 bp):
GTGGCGTGCCACGTGTCACTTTTTGGTACAT
Found at i:85799 original size:7 final size:7
Alignment explanation
Indices: 85787--85830 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
85777 CCTAACCCCT
85787 TCTTCCC
1 TCTTCCC
85794 TCTTCCC
1 TCTTCCC
85801 TCTTCCC
1 TCTTCCC
*
85808 TCTT-CA
1 TCTTCCC
85814 TCTT-CC
1 TCTTCCC
85820 TCTT-CC
1 TCTTCCC
85826 TCTTC
1 TCTTC
85831 TCTCACTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 16 0.47
7 18 0.53
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (7 bp):
TCTTCCC
Found at i:85804 original size:14 final size:13
Alignment explanation
Indices: 85787--85830 Score: 63
Period size: 12 Copynumber: 3.4 Consensus size: 13
85777 CCTAACCCCT
85787 TCTTCCCTCTTCCC
1 TCTTCCCTCTT-CC
*
85801 TCTTCCCTCTTCA
1 TCTTCCCTCTTCC
85814 TCTT-CCTCTTCC
1 TCTTCCCTCTTCC
85826 TCTTC
1 TCTTC
85831 TCTCACTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 11 0.41
13 5 0.19
14 11 0.41
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (13 bp):
TCTTCCCTCTTCC
Found at i:95824 original size:6 final size:6
Alignment explanation
Indices: 95791--95820 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
95781 TGAAGTAGTT
*
95791 TCTTCA TCTTCA TCTTCA TCTTCA CCTTCA
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA
95821 CCTTGTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.47
Consensus pattern (6 bp):
TCTTCA
Found at i:99953 original size:15 final size:15
Alignment explanation
Indices: 99933--99965 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
99923 GTTTACGCCT
99933 TATGCGTAGGAACAG
1 TATGCGTAGGAACAG
99948 TATGCGTAGGAACAG
1 TATGCGTAGGAACAG
99963 TAT
1 TAT
99966 AAATTTCGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.24
Consensus pattern (15 bp):
TATGCGTAGGAACAG
Found at i:106392 original size:26 final size:27
Alignment explanation
Indices: 106362--106423 Score: 72
Period size: 31 Copynumber: 2.2 Consensus size: 27
106352 AAGTAAAGAT
*
106362 AAATATTGTT-GCTTTAGTTAAGAAAG
1 AAATATTCTTAGCTTTAGTTAAGAAAG
106388 AAATAAAATTCTTAAGCTTTAGTTAAGAAAG
1 AAAT---ATTCTT-AGCTTTAGTTAAGAAAG
106419 AAATA
1 AAATA
106424 ATATTCTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
26 4 0.13
28 1 0.03
29 5 0.17
31 20 0.67
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.34
Consensus pattern (27 bp):
AAATATTCTTAGCTTTAGTTAAGAAAG
Found at i:106407 original size:31 final size:31
Alignment explanation
Indices: 106372--106438 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
106362 AAATATTGTT
106372 GCTTTAGTTAAGAAAGAAATAAAATTCTTAA
1 GCTTTAGTTAAGAAAGAAATAAAATTCTTAA
*
106403 GCTTTAGTTAAGAAAGAAATAATATTCTTAA
1 GCTTTAGTTAAGAAAGAAATAAAATTCTTAA
106434 GCTTT
1 GCTTT
106439 CAACATTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (31 bp):
GCTTTAGTTAAGAAAGAAATAAAATTCTTAA
Found at i:108078 original size:49 final size:49
Alignment explanation
Indices: 108006--108106 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
107996 CTTGTGGGAC
108006 ATCACCAGCGTTTCCAGGACAAATTCCAGAAACCCTTTCTTCAGCCTCA
1 ATCACCAGCGTTTCCAGGACAAATTCCAGAAACCCTTTCTTCAGCCTCA
108055 ATCACCAGCGTTTCCAGGACAAATTCCAGAAACCCTTTCTTCAGCCTCA
1 ATCACCAGCGTTTCCAGGACAAATTCCAGAAACCCTTTCTTCAGCCTCA
108104 ATC
1 ATC
108107 GCAGTGGCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.25
Consensus pattern (49 bp):
ATCACCAGCGTTTCCAGGACAAATTCCAGAAACCCTTTCTTCAGCCTCA
Found at i:126311 original size:1 final size:1
Alignment explanation
Indices: 126305--126335 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
126295 TGCAAAAGTG
126305 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
126336 CTTATTTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:134257 original size:13 final size:13
Alignment explanation
Indices: 134239--134267 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
134229 CGGTGGAGGG
134239 AAATAAAAAAAAC
1 AAATAAAAAAAAC
134252 AAATAAAAAAAAC
1 AAATAAAAAAAAC
134265 AAA
1 AAA
134268 AGGAGAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (13 bp):
AAATAAAAAAAAC
Found at i:135764 original size:2 final size:2
Alignment explanation
Indices: 135757--135782 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
135747 ACCATTAACC
135757 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
135783 GTAGCTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:138758 original size:16 final size:18
Alignment explanation
Indices: 138737--138772 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
138727 CTAAAATTAC
138737 AGTTTTAC-T-TTCATAA
1 AGTTTTACTTCTTCATAA
138753 AGTTTTACTTCTTCATAA
1 AGTTTTACTTCTTCATAA
138771 AG
1 AG
138773 AATGTGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 1 0.06
18 9 0.50
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (18 bp):
AGTTTTACTTCTTCATAA
Found at i:139382 original size:14 final size:16
Alignment explanation
Indices: 139363--139394 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
139353 TTTTTTCCTT
139363 TCTCTCC-CT-GAATC
1 TCTCTCCTCTAGAATC
139377 TCTCTCCTCTAGAATC
1 TCTCTCCTCTAGAATC
139393 TC
1 TC
139395 GCGACGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.16, C:0.41, G:0.06, T:0.38
Consensus pattern (16 bp):
TCTCTCCTCTAGAATC
Found at i:139664 original size:12 final size:13
Alignment explanation
Indices: 139635--139665 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
139625 TCACTATTTA
139635 ATATTTGCTTTCC
1 ATATTTGCTTTCC
139648 ATATTTGCTTT-C
1 ATATTTGCTTTCC
139660 ATATTT
1 ATATTT
139666 AACCTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.58
Consensus pattern (13 bp):
ATATTTGCTTTCC
Found at i:139723 original size:41 final size:41
Alignment explanation
Indices: 139674--139754 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
139664 TTAACCTATT
* * *
139674 TTATTTAATATTTACTTTA-TCGTTTTCCCTCAAATTTAGGA
1 TTATTTAATAATTACTTTATTC-ATTTCCCTCAAATCTAGGA
*
139715 TTATTTAATAATTGCTTTATTCATTTCCCTCAAATCTAGG
1 TTATTTAATAATTACTTTATTCATTTCCCTCAAATCTAGG
139755 GTGAAGAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.49
Consensus pattern (41 bp):
TTATTTAATAATTACTTTATTCATTTCCCTCAAATCTAGGA
Found at i:140342 original size:30 final size:28
Alignment explanation
Indices: 140307--140369 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
140297 CACATATGTA
*
140307 TATTTTATGCGATTTAATCTCTAGAAATTT
1 TATTTTATACGATTTAATC-CT-GAAATTT
* *
140337 TATTTTATACGATTTAGTCCTTAAATTT
1 TATTTTATACGATTTAATCCTGAAATTT
140365 TATTT
1 TATTT
140370 CTTTTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 11 0.37
29 2 0.07
30 17 0.57
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.54
Consensus pattern (28 bp):
TATTTTATACGATTTAATCCTGAAATTT
Found at i:140801 original size:22 final size:22
Alignment explanation
Indices: 140773--140841 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
140763 ATGTTCATAC
140773 CCCTTATTCCTTCTTAATTTTT
1 CCCTTATTCCTTCTTAATTTTT
*
140795 CCCTTA-T--TT-TT--TTTTA
1 CCCTTATTCCTTCTTAATTTTT
**
140811 CTAATTATTCCTTCTTAATTTTT
1 C-CCTTATTCCTTCTTAATTTTT
140834 CCCTTATT
1 CCCTTATT
140842 TTTTTTTCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
16 5 0.15
17 3 0.09
18 3 0.09
19 2 0.06
20 2 0.06
21 3 0.09
22 11 0.32
23 5 0.15
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (22 bp):
CCCTTATTCCTTCTTAATTTTT
Found at i:140819 original size:39 final size:38
Alignment explanation
Indices: 140776--140852 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 38
140766 TTCATACCCC
140776 TTATTCCTTCTTAATTTTTCCCTTATTTTTTTTTACTAA
1 TTATTCCTTCTTAATTTTTCCCTTATTTTTTTTT-CTAA
140815 TTATTCCTTCTTAATTTTTCCCTTATTTTTTTTTCTAA
1 TTATTCCTTCTTAATTTTTCCCTTATTTTTTTTTCTAA
140853 ATATACCCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 4 0.11
39 34 0.89
ACGTcount: A:0.17, C:0.18, G:0.00, T:0.65
Consensus pattern (38 bp):
TTATTCCTTCTTAATTTTTCCCTTATTTTTTTTTCTAA
Found at i:140835 original size:14 final size:14
Alignment explanation
Indices: 140779--140835 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
140769 ATACCCCTTA
140779 TTCCTTCTTAATTT
1 TTCCTTCTTAATTT
140793 TTCC--CTT-ATTT
1 TTCCTTCTTAATTT
** *
140804 TTTTTTAC-TAATTA
1 TTCCTT-CTTAATTT
140818 TTCCTTCTTAATTT
1 TTCCTTCTTAATTT
140832 TTCC
1 TTCC
140836 CTTATTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
11 6 0.19
12 3 0.09
13 2 0.06
14 21 0.66
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (14 bp):
TTCCTTCTTAATTT
Found at i:140863 original size:39 final size:39
Alignment explanation
Indices: 140781--140864 Score: 134
Period size: 39 Copynumber: 2.2 Consensus size: 39
140771 ACCCCTTATT
* *
140781 CCTTCTTAATTTTTCCCTTATTTTTTTTTACTAATTATT
1 CCTTCTTAATTTTTCCCTTATTTTTTTTTACTAAATATC
140820 CCTTCTTAATTTTTCCCTTATTTTTTTTT-CTAAATATAC
1 CCTTCTTAATTTTTCCCTTATTTTTTTTTACTAAATAT-C
140859 CCTTCT
1 CCTTCT
140865 ATCAAAGGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 7 0.17
39 35 0.83
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (39 bp):
CCTTCTTAATTTTTCCCTTATTTTTTTTTACTAAATATC
Found at i:141214 original size:30 final size:30
Alignment explanation
Indices: 141172--141245 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
141162 ACGTTGTTTA
*
141172 ACGTGGCATGCCACGTGTACAAAAAATGAC
1 ACGTGACATGCCACGTGTACAAAAAATGAC
* *
141202 ATGTGACATGCCACGTGTACAAAAATTGAC
1 ACGTGACATGCCACGTGTACAAAAAATGAC
141232 ACGTGACATGCCAC
1 ACGTGACATGCCAC
141246 ATCGGATGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (30 bp):
ACGTGACATGCCACGTGTACAAAAAATGAC
Found at i:141713 original size:53 final size:53
Alignment explanation
Indices: 141633--141739 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
141623 CTAACAATCA
* *
141633 CGGTCCAGTCCGTTTCTGATAACTATGCTTAATAGCTTGAACTACCAGTTAGG
1 CGGTCCAGTCCGATTCTAATAACTATGCTTAATAGCTTGAACTACCAGTTAGG
* *
141686 CGGTCCGGTCCGATTCTAATAACTATGCTTAATAGCTTGACCTACCAGTTAGG
1 CGGTCCAGTCCGATTCTAATAACTATGCTTAATAGCTTGAACTACCAGTTAGG
141739 C
1 C
141740 CTAGATACGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (53 bp):
CGGTCCAGTCCGATTCTAATAACTATGCTTAATAGCTTGAACTACCAGTTAGG
Found at i:154874 original size:26 final size:26
Alignment explanation
Indices: 154845--154897 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
154835 TTGAAAGACA
154845 ATCGTATGTAAATGAAATCGAGGATT
1 ATCGTATGTAAATGAAATCGAGGATT
154871 ATCGTATGTAAATGAAATCGAGGATT
1 ATCGTATGTAAATGAAATCGAGGATT
154897 A
1 A
154898 ATTAGTGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.30
Consensus pattern (26 bp):
ATCGTATGTAAATGAAATCGAGGATT
Found at i:158732 original size:14 final size:15
Alignment explanation
Indices: 158708--158752 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
158698 AAATTAGACC
158708 CAAAAACAAAAAAAA
1 CAAAAACAAAAAAAA
158723 CAAAAA-AAAAAAAA
1 CAAAAACAAAAAAAA
*
158737 CAAAAATAAAATAAAA
1 CAAAAACAAAA-AAAA
158753 GAAGGAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.50
15 10 0.36
16 4 0.14
ACGTcount: A:0.87, C:0.09, G:0.00, T:0.04
Consensus pattern (15 bp):
CAAAAACAAAAAAAA
Found at i:159949 original size:31 final size:31
Alignment explanation
Indices: 159875--159969 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 31
159865 AAAGTCGTGT
* **
159875 CACATGTACC-AAAAGTGACACATGTCACGC
1 CACATGTACCAAAAAGTGACACATGGCATAC
*
159905 CACATGTACCAAAAAGTGACACATGGCATAT
1 CACATGTACCAAAAAGTGACACATGGCATAC
** * * * *
159936 CACATGTTTCAAAAAATGGCACGTGGCATGC
1 CACATGTACCAAAAAGTGACACATGGCATAC
159967 CAC
1 CAC
159970 GTGCACAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
30 10 0.19
31 43 0.81
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (31 bp):
CACATGTACCAAAAAGTGACACATGGCATAC
Found at i:162251 original size:40 final size:40
Alignment explanation
Indices: 162195--162272 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
162185 TTTAAGGTAA
* *
162195 TTTCTTAATTTGGATTGTATTCTCATTTTGATGTTTGGAC
1 TTTCTTAATTTAGATTGGATTCTCATTTTGATGTTTGGAC
* *
162235 TTTCTTAGTTTAGATTGGATTCTCATTTTTATGTTTGG
1 TTTCTTAATTTAGATTGGATTCTCATTTTGATGTTTGG
162273 TCATATCGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.17, C:0.09, G:0.18, T:0.56
Consensus pattern (40 bp):
TTTCTTAATTTAGATTGGATTCTCATTTTGATGTTTGGAC
Found at i:162272 original size:20 final size:20
Alignment explanation
Indices: 162213--162272 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
162203 TTTGGATTGT
*
162213 ATTCTCATTTTGATGTTTGG
1 ATTCTCATTTTTATGTTTGG
*
162233 ACTT-TC-TTAGTTTA-GATTGG
1 A-TTCTCATT--TTTATGTTTGG
162253 ATTCTCATTTTTATGTTTGG
1 ATTCTCATTTTTATGTTTGG
162273 TCATATCGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 12
0.67 0.07 0.26
Matches are distributed among these distances:
19 8 0.26
20 16 0.52
21 7 0.23
ACGTcount: A:0.17, C:0.10, G:0.18, T:0.55
Consensus pattern (20 bp):
ATTCTCATTTTTATGTTTGG
Found at i:163642 original size:321 final size:318
Alignment explanation
Indices: 163024--164053 Score: 1388
Period size: 321 Copynumber: 3.2 Consensus size: 318
163014 ATTTCGGAAA
*
163024 AAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTGGCGTTGAATTATAT
1 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTGGCGTTGAATTATAT
* ** *
163089 ATTTTTTCTGAGTATTGTGGCAAAAAATTGA-AAAAAAAAAATTCTGGTCAGTTTTTAGCCGAAA
66 AATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAA
* *
163153 TCGTGTACTTACCATCAC-GATTTTTTGCTAAAAACGCGTTTCGGGACCCAGACTGAGTTTTGCA
131 TCGTGTACTTACCATCACAG-TTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTGAGTTTTGCA
* * * *
163217 TGAAATTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTGACCAAATCTTAGCCACAACGG
195 TGATATTTGGCAGAAAGACT-CTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAA-GA
* *
163282 ATTTAAAATTTTGTTGTTTCGAGCTTCTAAATCTTGTTTCGATATAATTACAAATAAATTCG
258 ATTTAAAATTTT-TTGTTACGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTCG
* *
163344 AAAAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCTTCAACTTTTTTAGCG-TGAATTATA
1 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA-TTTTTTGGCGTTGAATTATA
* *
163408 TAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCATTTTTTAACCGAA
65 TAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAA
* * * *
163473 ATCGTGAACTTACCATTACAGTTTTTGGCTAAAAA-GACGTTTCGGGGCCCCGACTCAGTTTTGC
130 ATCGTGTACTTACCATCACAGTTTTTTGCTAAAAACG-CGTTTCGGGGCCCCGACTGAGTTTTGC
* * ** * * *
163537 ATGATATTTGACTGAAAGACTCTTTGAAATATAAATATTCATTTGAACAAATCTCAGGCACAATG
194 ATGATATTTGGCAGAAAGACTC-TTGAAATATCTATATTCATCTGAACAAATCTTAGACACAA-G
* ** * *
163602 AATTTAAGAGTTTTTTGTTACGAGAATCTGAATATTGTTTCGATATAATTAGAAATAAATTCGG
257 AATTTAA-AATTTTTTGTTACGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTC-G
* * * * *
163666 AAAAAAATGGAAAAACGATATTATAAGCGTGAAAAGCCCTTTAATTTTTTTGCTGTTGAATTACA
1 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTGGC-GTTGAATTATA
* * * * * *
163731 AAAATTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAAAATTTTTGGATTAGTTTTTAGTCGAA
65 TAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAA
* * * * *
163795 ATCGTCTACTTA-AATCACGATTTTTTTGCTAAAAACGCGTTTCAGGGCGCCGACTGAGTTTTGC
130 ATCGTGTACTTACCATCAC-AGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTGAGTTTTGC
*
163859 ATGATATTTGGCAGAAAGACTACTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAACA
194 ATGATATTTGGCAGAAAGACT-CTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAAGA
* *
163924 GATTTAAAATTTCATTGTTACGAGCTTCTGAATCTTGATTCGATATAATTACAAATAAATTCG
258 -ATTTAAAATTT-TTTGTTACGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTCG
* *
163987 AAAAAAATGGAAAAACGATATTAGAAACGTGAAAAACCCTTCAATTTTTTTGGCGTTCAATTATA
1 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA-TTTTTTGGCGTTGAATTATA
164052 TA
65 TA
164054 TGGCAGAAAG
Statistics
Matches: 616, Mismatches: 79, Indels: 29
0.85 0.11 0.04
Matches are distributed among these distances:
320 84 0.14
321 259 0.42
322 232 0.38
323 41 0.07
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (318 bp):
AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTGGCGTTGAATTATAT
AATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAA
TCGTGTACTTACCATCACAGTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTGAGTTTTGCAT
GATATTTGGCAGAAAGACTCTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAAGAATT
TAAAATTTTTTGTTACGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTCG
Found at i:164528 original size:250 final size:246
Alignment explanation
Indices: 164077--164573 Score: 680
Period size: 250 Copynumber: 2.0 Consensus size: 246
164067 CCTTGAAATA
*
164077 TCTATATTCATCTGAACAAATCTTAGACACAACAGATTTAAAATTTTATTGTTACGAGTTTCTGA
1 TCTATATTCATCTGAACAAATCTTAGACACAACAGATTTAAAATTTTATTGTTACGAGCTTCTGA
** * * * *
164142 ATATGTTTCGATATAATTACAAATAAATTCGAAAAAAATGGAAACACAATATTAGAAGTGTGCAA
66 ATATGTTTCGATATAATTACAAATAAATTAAAAAAAAAAGGAAAAACAATATTAGAAGCGTGAAA
* *
164207 AACTCCTCAATTTTTTGGCATTGAATTATTTTATTTTTTCTGAGTATTGTGGCAAAAATATTGTG
131 AACTCCTCAATTTTTTGGCATTGAATTATTATATTTTTTCTGAGTATTGTGGCAAAAA-AAT-TG
**
164272 AAAAAATTTTTCGGATCAGTTTTTAGCCGAAATCGTGTACTTAACATCACGATT
194 AAAAAA-AATTCGGATCAGTTTTTAGCCGAAATCGTGTACTTAACATCACGATT
* *
164326 TCTATATTCATCTG-ACTAAATCTTA-ACCACAACGGATTTAAAATTTTGTTGTTACGAGCTTCT
1 TCTATATTCATCTGAAC-AAATCTTAGA-CACAACAGATTTAAAATTTTATTGTTACGAGCTTCT
* * *
164389 GAATCTTGTTTCGATATAATTACAATTAAATTAAAAAAAAAAGGAAAAACGATATTAGAAGCGTG
64 GAAT-ATGTTTCGATATAATTACAAATAAATTAAAAAAAAAAGGAAAAACAATATTAGAAGCGTG
* * *
164454 AAAAAAC-CTTCAATTTTTTTGGCGTTGAATTA-TATATTTTTTCTGTGTATTGTGG-AAAAAAA
128 -AAAAACTCCTCAA-TTTTTTGGCATTGAATTATTATATTTTTTCTGAGTATTGTGGCAAAAAAA
* * *
164516 TTGAAAAAAAAATTCGGGTCCGTTTTTAGCCGAAATCGTGTACTTACCATCACGATT
191 TTG-AAAAAAAATTCGGATCAGTTTTTAGCCGAAATCGTGTACTTAACATCACGATT
164573 T
1 T
164574 TTTGCTAAAA
Statistics
Matches: 220, Mismatches: 22, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
247 45 0.20
248 11 0.05
249 64 0.29
250 78 0.35
251 22 0.10
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (246 bp):
TCTATATTCATCTGAACAAATCTTAGACACAACAGATTTAAAATTTTATTGTTACGAGCTTCTGA
ATATGTTTCGATATAATTACAAATAAATTAAAAAAAAAAGGAAAAACAATATTAGAAGCGTGAAA
AACTCCTCAATTTTTTGGCATTGAATTATTATATTTTTTCTGAGTATTGTGGCAAAAAAATTGAA
AAAAAATTCGGATCAGTTTTTAGCCGAAATCGTGTACTTAACATCACGATT
Found at i:165271 original size:323 final size:317
Alignment explanation
Indices: 164326--165529 Score: 1595
Period size: 311 Copynumber: 3.8 Consensus size: 317
164316 CATCACGATT
* *
164326 TCTATATTCATCTGACTAAATCTTAACCACAACGGATTTAAAATTTTGTTGTTACGAGCTTCTGA
1 TCTATATTCATCTGAC-AAATCTTAGCCACAACGGATTTAAAATTTTGTTGTTACGAGCTTCTAA
* * * *
164391 ATCTTGTTTCGATATAATTACAATTAAATTAAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAA
65 ATATTGTTTCGATATAATTACAAATAAATTGAAAAAAATA-GAAAAACGATATTAGAAGCGTGAA
* *
164456 AAAACCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGTGTATTGTGGAAAAAAATTGAA
129 AAAACCTTCAA-TTTTTTGGCGTTGAATTATATAATTTTTCTGAGTATTGTGGAAAAAAATTGAA
* * *
164521 AAAAAA-ATTCGGGTCCGTTTTTAGCCGAAATCGTGTACTTACCATCACGATTTTTTGCTAAAAA
193 AAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACGATTTTTGGCTAAAAA
*
164585 CGCGTTTCGGGGCCCCGACTGAGTTTTGCATGAAATTTGGCAGAAAGACTCCTTGAAATA
258 CGCGTTTCGGGGCCCCGACTGAGTTTTGCATGATATTTGGCAGAAAGACTCCTTGAAATA
* **
164645 TCTATATTCATCTGACCAAATCTTGGCCACAACGGATTTAAAATTTTGTTGTTTTGAGCTTCTAA
1 TCTATATTCATCTGA-CAAATCTTAGCCACAACGGATTTAAAATTTTGTTGTTACGAGCTTCTAA
* *
164710 ATCTTGTTTCGATATAATTACAATTAAATT-----AAA-A-AAAAACGATATTAGAAGCGTGAAA
65 ATATTGTTTCGATATAATTACAAATAAATTGAAAAAAATAGAAAAACGATATTAGAAGCGTGAAA
*
164768 AAACCTTCAATTTTTTGGCGTTGAATTATATAATTTTTCTGAGTATTATGGAAAAAAATTGAAAA
130 AAACCTTCAATTTTTTGGCGTTGAATTATATAATTTTTCTGAGTATTGTGGAAAAAAATTGAAAA
* * *
164833 AAAAATTTCGGGTCA-TTTTTAGCCGAAATCGTGAACTTACCATCACAGTTTTTTGGCTAAAAA-
195 AAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCAC-GATTTTTGGCTAAAAAC
* * ** *
164896 GACGTTTCGGGGCCCCGACTCAGTTTTGCATTATATTTTACGGAAAGACTCCTTGAAATA
259 G-CGTTTCGGGGCCCCGACTGAGTTTTGCATGATATTTGGCAGAAAGACTCCTTGAAATA
* * * * * *
164956 TCAATATTCATTTGATCAAATCTCAGCCACAATGGATTTAAGCATTTT-TTGTTACGAGCATCTA
1 TCTATATTCATCTGA-CAAATCTTAGCCACAACGGATTTAA-AATTTTGTTGTTACGAGCTTCTA
* * *
165020 AATATTGTTTCGATATAATTACAAATAAATTCGTGGAAAAAATAGAAAAACAATATTATAAGCGT
64 AATATTGTTTCGATATAATTACAAATAAA-T--TGAAAAAAATAGAAAAACGATATTAGAAGCGT
* * * *
165085 GAAAAGACCTTTAATTTTTTTGTG-GTTGAATTATAAAATTTTTCTGAGTATTGTGGGAAAAAAT
126 GAAAAAACCTTCAA-TTTTTTG-GCGTTGAATTATATAATTTTTCTGAGTATTGTGGAAAAAAAT
* * *
165149 TGAGAAAAAAATTTTTGGGTCAGTTTTTAGCCGAAATTGTGTTCTTACCATCACGATTTTTGGCT
189 TGA-AAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACGATTTTTGGCT
* * *
165214 AAAAACGCGTTTCAGGACCCCGACTGAGTTTTGCATGATATTTGGCAAAAAGACTCCTTGAAATA
253 AAAAACGCGTTTCGGGGCCCCGACTGAGTTTTGCATGATATTTGGCAGAAAGACTCCTTGAAATA
* *
165279 TCTATATTCATCTGAACAAATCTTAGACACAACGGATTTAAAATTTTGTTGTTACGAGCTTCTGA
1 TCTATATTCATCTG-ACAAATCTTAGCCACAACGGATTTAAAATTTTGTTGTTACGAGCTTCTAA
* *
165344 ATATTGTTTCGATATAATTACAAATAAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGCA
65 ATATTGTTTCGATATAATTACAAATAAATT-GAAAAAAATAGAAAAACGATATTAGAAGCGTGAA
* * * * * * **
165409 AAACCCCTCAATTCTTTGGCATTGAATTATTTTATTTTTTCTGAGTATTGTGGCAAAATTATTGT
129 AAAACCTTCAATTTTTTGGCGTTGAATTA-TATAATTTTTCTGAGTATTGTGG-AAAAAAATTG-
* * ** *
165474 GAAAAAATTTTTCGGGTCAGTTTTTAGCTAAAATCGTGTACTTAACATCACGATTT
191 AAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACGATTT
165530 CTATATTCAT
Statistics
Matches: 773, Mismatches: 85, Indels: 51
0.85 0.09 0.06
Matches are distributed among these distances:
310 87 0.11
311 183 0.24
312 6 0.01
313 1 0.00
314 4 0.01
319 92 0.12
320 17 0.02
321 86 0.11
322 108 0.14
323 159 0.21
324 30 0.04
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (317 bp):
TCTATATTCATCTGACAAATCTTAGCCACAACGGATTTAAAATTTTGTTGTTACGAGCTTCTAAA
TATTGTTTCGATATAATTACAAATAAATTGAAAAAAATAGAAAAACGATATTAGAAGCGTGAAAA
AACCTTCAATTTTTTGGCGTTGAATTATATAATTTTTCTGAGTATTGTGGAAAAAAATTGAAAAA
AAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACGATTTTTGGCTAAAAACGC
GTTTCGGGGCCCCGACTGAGTTTTGCATGATATTTGGCAGAAAGACTCCTTGAAATA
Found at i:166235 original size:321 final size:322
Alignment explanation
Indices: 165532--167978 Score: 2193
Period size: 323 Copynumber: 7.8 Consensus size: 322
165522 CACGATTTCT
* * * * * *
165532 ATATTCATCTGACTAAATCTTAACCACAACAGATTTAAAATTTTGTTGTTACGAGCTTCTGAATC
1 ATATTCATCTGACCAAATCTCAGCCACAACGGATTTAAAATTATGTTGTTACGAGCATCTGAATC
* * * *
165597 TTTTTTCGATATAATTACAATTAAATTCGAAAAAAAAATGGAAAAACGATATTAGAAGCATGAAA
66 TTGTTTCGATATAATTACAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
** *
165662 AACCCTTCAATTTTTTGGCGTTGAATTATATATCTTTTTCTGAGTATTGTGGCAAAAAATT-A-A
131 AACCCTTCAATTTTTTATCGTTGAATTATATA-ATTTTTCTGAGTATTGTGGCAAAAAATTGAGA
* * * *
165725 AAAAAAAATTCGGGTCAGTTTTTAGCTGAAATCGTGTAC---GCA-C-GA-TTTTTGGCTAAAAA
195 AAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAA
* * * * * * *
165784 CG-CGTTTCGGGGTCCCGACTGAGTTTTGCATGAAATTTGGCAGAAAGACTCCTTGAAATATCT
260 -GACGTTTCGGGGCCCCGGCTCAGTTTTGCATGATATTTGACTGAAAGACTCCTTGAAATATCA
* * * * * * *
165847 ATATTCATCTAATCAAATCTTAGCCACAACGGATTTAAAATTTTGTTGTTTCGAGCTTCTAAATC
1 ATATTCATCTGACCAAATCTCAGCCACAACGGATTTAAAATTATGTTGTTACGAGCATCTGAATC
165912 TTGTTTCGATATAATTACAAATAAATTC-G-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
66 TTGTTTCGATATAATTACAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
*
165975 AACCCTTCACTTTTTTATCGTGTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGA
131 AACCCTTCAATTTTTTATCGT-TGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGA
* *
166040 AAAAAAATTTCGGGTCATTTTTTAGCCGAAATTGTGTACTTACCATCACAGTTTTTGG-TGAAAA
195 AAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACAGTTTTTGGCT-AAAA
166104 AGACGTTTCGGGGCCCCGGCTCAGTTTTGCATGATATTTGACTGAAAGACTCCTTGAAATATCA
259 AGACGTTTCGGGGCCCCGGCTCAGTTTTGCATGATATTTGACTGAAAGACTCCTTGAAATATCA
* * *
166168 ATATTCATTTGACCAAATCTCAGCCACAATGGATTTAAGCATTAT-TTGTTACGAGCATCTGAAT
1 ATATTCATCTGACCAAATCTCAGCCACAACGGATTTAA-AATTATGTTGTTACGAGCATCTGAAT
* *
166232 CTTGTTTCGATATAATTAGAAATAAATTCGGGAAAAAAAATGGAAAAACGATATTAGAAGCGTAA
65 CTTGTTTCGATATAATTACAAATAAATTC-GGAAAAAAAATGGAAAAACGATATTAGAAGCGTGA
* * *
166297 AAAACCTTTCAACTTTTTTATCATTGAATTATATAATTTTTCTGAGTATTCTGGCAAAAAATTGA
129 AAAACCCTTCAA-TTTTTTATCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGA
* * * * * * *
166362 CAAAAAAATTTTCGAGTCATTTTTTAGCCGAAATCGTGAACGTA-AATCACAGTTTTTGGCTAAA
193 GAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAA
*
166426 AAGACGTTTCGGGGCCCCGGCTTAGTTTTGCATGATATTTGACTGAAAGACTCCTTGAAATATCA
258 AAGACGTTTCGGGGCCCCGGCTCAGTTTTGCATGATATTTGACTGAAAGACTCCTTGAAATATCA
* *
166491 ATATTCATTTGACCAAATCTCAGCCAC-ACTGGATTTAAGCATTAT-TTGTTACGAGCATCTGAA
1 ATATTCATCTGACCAAATCTCAGCCACAAC-GGATTTAA-AATTATGTTGTTACGAGCATCTGAA
* * * * *
166554 TCTTGTTTCGATATAATTAGAAATAAGTTCGGGAAAAAAATTGGAAAAACGATATTATAAGCGTT
64 TCTTGTTTCGATATAATTACAAATAAATTC-GGAAAAAAAATGGAAAAACGATATTAGAAGCGTG
* *
166619 AAAAGCCCTTCAATTTTTT-TGCCGTTGAATTATAAAATTTTTCTGAGTATTGTGGCAAAAAATT
128 AAAAACCCTTCAATTTTTTAT--CGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATT
* * * * * *
166683 GAGAAAAATATTTTTGGATAAGTTTTTAGCCGAAAATCGTGTACTTACCATCAC-GATATTTGGC
191 GAGAAAAAAAATTTCGGGTCAGTTTTTAGCCG-AAATCGTGTACTTACCATCACAG-TTTTTGGC
* * * ** * * *
166747 -AGAAAGAC---T-------CC--TTGAAATAT-C-T-ATA-TTCA-T--ATGA--CC---AAAT
254 TAAAAAGACGTTTCGGGGCCCCGGCTCAGTTTTGCATGATATTTGACTGAAAGACTCCTTGAAAT
* *
166787 TTTA
319 ATCA
** * * ** * ** ***** * ** * * * *
166791 GCCA--CAACGGATTTAAATTTTTGTTTTTACGAGCTTTTGAATTTTGTT-TT--GA-TATATTT
1 -ATATTCATCTGA-CCAAATCTCAGCCACAACG-GATTTAAAATTATGTTGTTACGAGCAT-CTG
** *** * * ** ** * *** ***
166850 ACAAATAAATTCGAAAAAATTGGAAA-AACGATATTTGAAGCGTGAAAAACT-CTTAAATTTTAT
62 A-ATCTTGTTTCGATATAATTACAAATAA--AT-TCGGAA-----AAAAAATGGAAAAACGATAT
**
166913 T-GTCGC-TG---AA----T--------------T--A-TA-A-AATTTTTCTGAGTATTGTGGC
118 TAGAAGCGTGAAAAACCCTTCAATTTTTTATCGTTGAATTATATAATTTTTCTGAGTATTGTGGC
* ** * * * *
166950 AAAAAATTGAGAAAAAA-TTGTTTTGGTCAGTTTTTAGCCGAAATTGTGTATTTACTATCACGAT
183 AAAAAATTGAGAAAAAAAAT-TTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCAC-AG
** * * * * *
167014 TTTTTGGCTAAAAAGGTGTTTCAGGGG-CCCGACTGAGTTTTGCATGGTATTTGGCAGAAAGACT
246 TTTTTGGCTAAAAAGACGTTTC-GGGGCCCCGGCTCAGTTTTGCATGATATTTGACTGAAAGACT
**
167078 CCTTGAAATATTT
310 CCTTGAAATATCA
* * * * * *
167091 ATATTCATCTGAACAAATCTTAGACACAACGTATTTAAAATTTTGTTGTTACGAGCTTCTGAATC
1 ATATTCATCTGACCAAATCTCAGCCACAACGGATTTAAAATTATGTTGTTACGAGCATCTGAATC
*
167156 TTGTTTCGATATAATTACAAATAAATTC-G-AAAAAAATGGAAAAACGATACTAGAAGCGTGAAA
66 TTGTTTCGATATAATTACAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* *
167219 AACCCTTCAACATTTTTAGCGTTGAATTATAT-ATTTTTCTGAGTATTGTGGCAAAAAATTGAGA
131 AACCCTTCAA-TTTTTTATCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGA
* * * *
167283 AAAAAAATTTCGGGTCATTTTTTAGCCGAAATCGTGAACTTACCGTCACAGTTTTGGGCTAAAAA
195 AAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAA
* *
167348 GACGTTTCGGGG-CCCGGCTCCGTTTTGCATGATATTAGACTGAAAGACTCCTTGAAATATCA
260 GACGTTTCGGGGCCCCGGCTCAGTTTTGCATGATATTTGACTGAAAGACTCCTTGAAATATCA
* * * *
167410 ATATTCATTTGACCAAATCTCAGCCACAATGGATTTAAGCATT-TGTTGTTACGAGCATTTGAAT
1 ATATTCATCTGACCAAATCTCAGCCACAACGGATTTAA-AATTATGTTGTTACGAGCATCTGAAT
* * * *
167474 CTTGTTTCGATATAATTAGAAATAAATTCGG-AAAAAAATGG--AAACAATTTTAGAAGCGTAAA
65 CTTGTTTCGATATAATTACAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAA
* * *
167536 AAACCCTTCAATTTTTT-TGCCATTGAATTATAAAATTTTTCTGAGTATTCTGGCAAAAAATTGA
130 AAACCCTTCAATTTTTTAT--CGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGA
* **
167600 GAAAAAAAAATTCCAGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCAC-GATTTTTGGCTAA
193 GAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACAG-TTTTTGGCTAA
* * * * * * *
167664 AAACG-CGTTTCGGGACCCCGACTGAGTTTTGCATGAAATTTGGCAGAACGACTCCTTGAAATAT
257 AAA-GACGTTTCGGGGCCCCGGCTCAGTTTTGCATGATATTTGACTGAAAGACTCCTTGAAATAT
*
167728 CT
321 CA
* * * * * *
167730 ATATTCATCTGAACAAATCTTAGACACAACGGATTTAAAATTTTGTTGTTATGAGCTTCTGAATC
1 ATATTCATCTGACCAAATCTCAGCCACAACGGATTTAAAATTATGTTGTTACGAGCATCTGAATC
* *
167795 TTGTTTCGATATAATTACAAATAAATTC-G-AAAAATATGGAAAAACGATATTAGAAGCGTGCAA
66 TTGTTTCGATATAATTACAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* ** * * * * *
167858 AACCCCTCAATTTTTTGGCATTGAATTATTTTATTTTTCCTGAGTGTTGTGGCAAAAATATTGTG
131 AACCCTTCAATTTTTTATCGTTGAATTATATAATTTTT-CTGAGTATTGTGGCAAAAA-ATTGAG
* * *
167923 AAAAAAAATTTTCGGATCAATTTTTAGCCGAAATCGTGTACTTACCATCACGGTTT
194 AAAAAAAA-TTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACAGTTT
167979 CTATATTCAT
Statistics
Matches: 1734, Mismatches: 278, Indels: 232
0.77 0.12 0.10
Matches are distributed among these distances:
274 20 0.01
275 61 0.04
276 6 0.00
277 2 0.00
278 1 0.00
279 1 0.00
280 1 0.00
286 2 0.00
288 5 0.00
289 1 0.00
290 1 0.00
291 2 0.00
292 8 0.00
293 6 0.00
294 3 0.00
295 6 0.00
297 5 0.00
298 9 0.01
299 35 0.02
300 43 0.02
301 30 0.02
302 8 0.00
303 5 0.00
304 7 0.00
305 9 0.01
307 1 0.00
308 3 0.00
309 3 0.00
310 1 0.00
311 1 0.00
312 4 0.00
313 78 0.04
314 14 0.01
315 120 0.07
317 6 0.00
318 42 0.02
319 235 0.14
320 177 0.10
321 266 0.15
322 25 0.01
323 318 0.18
324 141 0.08
325 22 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (322 bp):
ATATTCATCTGACCAAATCTCAGCCACAACGGATTTAAAATTATGTTGTTACGAGCATCTGAATC
TTGTTTCGATATAATTACAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
AACCCTTCAATTTTTTATCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAA
AAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCACAGTTTTTGGCTAAAAAG
ACGTTTCGGGGCCCCGGCTCAGTTTTGCATGATATTTGACTGAAAGACTCCTTGAAATATCA
Found at i:166964 original size:275 final size:275
Alignment explanation
Indices: 166459--167013 Score: 748
Period size: 275 Copynumber: 2.0 Consensus size: 275
166449 AGTTTTGCAT
* *
166459 GATATTTGACTGAAAGACTCCTTGAAATATCAATATTCATTTGACCAAATCTCAGCCACACTGGA
1 GATATTTGACAGAAAGACTCCTTGAAATATCAATATTCATATGACCAAATCTCAGCCACACTGGA
* *
166524 TTTAAGCATTATTTGTTACGAGCATCTGAATCTTGTTTCGATATAATTAGAAATAAGTTCGGGAA
66 TTTAA-CATTATTTGTTACGAGCATCTGAATCTTGTTTCGATATAATTACAAATAAATTC-GGAA
* * * * *
166589 AAAAATTGGAAAAACGATATTATAAGCGTTAAAAGCCCTTCAATTTTTTTGCCGTTGAATTATAA
129 AAAAATTGGAAAAACGATATTATAAGCGTGAAAAACCCTTAAATTTTATTGCCGCTGAATTATAA
166654 AATTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAATAT-TTTTGGATAAGTTTTTAGCCGAA
194 AATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAT-TGTTTTGG-TAAGTTTTTAGCCG-A
166717 AATCGTGTACTTACCATCAC
256 AATCGTGTACTTACCATCAC
* * * *
166737 GATATTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATGACCAAATTTTAGCCACAAC-GG
1 GATATTTGACAGAAAGACTCCTTGAAATATCAATATTCATATGACCAAATCTCAGCCAC-ACTGG
* * * * *
166801 ATTTAA-ATT-TTTGTTTTTACGAGCTTTTGAATTTTGTTTTGATATATTTACAAATAAATTC-G
65 ATTTAACATTATTTG---TTACGAGCATCTGAATCTTGTTTCGATATAATTACAAATAAATTCGG
* *
166863 -AAAAAATTGGAAAAACGATATT-TGAAGCGTGAAAAACTCTTAAATTTTATTGTCGCTGAATTA
127 AAAAAAATTGGAAAAACGATATTAT-AAGCGTGAAAAACCCTTAAATTTTATTGCCGCTGAATTA
*
166926 TAAAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTGTTTTGGTCAGTTTTTAGCCGA
191 TAAAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTGTTTTGGTAAGTTTTTAGCCGA
* * *
166991 AATTGTGTATTTACTATCAC
256 AATCGTGTACTTACCATCAC
167011 GAT
1 GAT
167014 TTTTTGGCTA
Statistics
Matches: 246, Mismatches: 24, Indels: 18
0.85 0.08 0.06
Matches are distributed among these distances:
274 22 0.09
275 107 0.43
276 16 0.07
278 99 0.40
279 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (275 bp):
GATATTTGACAGAAAGACTCCTTGAAATATCAATATTCATATGACCAAATCTCAGCCACACTGGA
TTTAACATTATTTGTTACGAGCATCTGAATCTTGTTTCGATATAATTACAAATAAATTCGGAAAA
AAATTGGAAAAACGATATTATAAGCGTGAAAAACCCTTAAATTTTATTGCCGCTGAATTATAAAA
TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTGTTTTGGTAAGTTTTTAGCCGAAATCG
TGTACTTACCATCAC
Found at i:167163 original size:600 final size:594
Alignment explanation
Indices: 166136--167974 Score: 1573
Period size: 639 Copynumber: 3.0 Consensus size: 594
166126 AGTTTTGCAT
* * *
166136 GATATTTGACTGAAAGACTCCTTGAAATATCAATATTCATTTGACCAAATCTCAGCCACAATGGA
1 GATATTTGACAGAAAGACTCCTTGAAATATCAATATTCATATGACCAAATCTCAGCCACAACGGA
*
166201 TTTAAGCATTATTTGTTACGAGCATCTGAATCTTGTTTCGATATAATTAGAAATAAATTCGGGAA
66 TTTAA-CATTATTTGTTACGAGCATCTGAATCTTGTTTCGATATAATTACAAATAAATTC-GGAA
* * *
166266 AAAAAATGGAAAAACGATATTAGAAGCGTAAAAAACCTTTCAACTTTTTTATCATTGAATTATAT
129 AAAAAATGGAAAAACGATATTAGAAGCGTAAAAAACCTTTCAAATTTTTTATCACTGAATTATAA
*
166331 AATTTTTCTGAGTATTCTGGCAAAAAATTGACAAAAAAATTTTCGAGTCATTTTTTAGCCGAAAT
194 AATTTTTCTGAGTATTCTGGCAAAAAATTGACAAAAAAATTTTCGAGTCAGTTTTTAGCCGAAAT
* *
166396 CGTGAACGTAAATCACAGTTTTTGGCTAAAAAGACGTTTCGGGGCCCCGGCTTAGTTTTGCATGA
259 CGTGAACGTAAATCACAGTTTTTGGCTAAAAAGACGTTTCGGGGCCCCGACTGAGTTTTGCATGA
* * * *
166461 TATTTGACTGAAAGACTCCTTGAAATATCAATATTCATTTGACCAAATCTCAGCCACACTGGATT
324 TATTTGACAGAAAGACTCCTTGAAATATCAATATTCATCTGAACAAATCTCAGACACACTGGATT
* * *
166526 TAAGCATTATTTGTTACGAGCATCTGAATCTTGTTTCGATATAATTAGAAATAAGTTCGGGAAAA
389 TAAGAATTATTTGTTACGAGCATCTGAATCTTGTTTCGATATAATTACAAATAAATTC--GAAAA
* * * * * *
166591 AAATTGGAAAAACGATATTATAAGCGTTAAAAGCCCTTCAA-TTTTTTTGCCGTTGAATTATAAA
452 AAA-TGGAAAAACGATACTAGAAGCGTGAAAAACCCTTCAACATTTTTAG-CGTTGAATTAT-AA
* * *
166655 ATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAATATTTTTGGATAAGTTTTTAGCCGAAAAT
514 ATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGATAAGTTTTTAGCCG-AAAT
*
166720 CGTGTACTTACCATCAC
578 CGTGAACTTACCATCAC
* * * *
166737 GATATTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATGACCAAATTTTAGCCACAACGGA
1 GATATTTGACAGAAAGACTCCTTGAAATATCAATATTCATATGACCAAATCTCAGCCACAACGGA
* * * * *
166802 TTTAA-ATT-TTTGTTTTTACGAGCTTTTGAATTTTGTTTTGATATATTTACAAATAAATTC-G-
66 TTTAACATTATTTG---TTACGAGCATCTGAATCTTGTTTCGATATAATTACAAATAAATTCGGA
* * * * *
166863 AAAAAATTGGAAAAACGATATTTGAAGCGTGAAAAA-CTCTT-AAATTTTATTGTCGCTGAATTA
128 AAAAAAATGGAAAAACGATATTAGAAGCGTAAAAAACCT-TTCAAATTTT-TTATCACTGAATTA
* * * *
166926 TAAAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTGTTTTG-GTCAGTTTTTAGCCG
191 TAAAATTTTTCTGAGTATTCTGGCAAAAAATTGACAAAAAAAT-TTTCGAGTCAGTTTTTAGCCG
* * ** * * **
166990 AAATTGTGTATTTACTATCACGATTTTTTGGCTAAAAAGGTGTTTCAGGGG-CCCGACTGAGTTT
255 AAATCGTGAACGTA-AATCAC-AGTTTTTGGCTAAAAAGACGTTTC-GGGGCCCCGACTGAGTTT
* * ** *
167054 TGCATGGTATTTGGCAGAAAGACTCCTTGAAATATTTATATTCATCTGAACAAATCTTAGACACA
317 TGCATGATATTTGACAGAAAGACTCCTTGAAATATCAATATTCATCTGAACAAATCTCAGACAC-
* * *
167119 AC-GTATTTAA-AATTTTGTTGTTACGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAAT
381 ACTGGATTTAAGAATTAT-TTGTTACGAGCATCTGAATCTTGTTTCGATATAATTACAAATAAAT
167182 TCGAAAAAAATGGAAAAACGATACTAGAAGCGTGAAAAACCCTTCAACATTTTTAGCGTTGAATT
445 TCGAAAAAAATGGAAAAACGATACTAGAAGCGTGAAAAACCCTTCAACATTTTTAGCGTTGAATT
* * * *
167247 ATATATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCATTTTTTAGCCGA
510 ATAAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGATAAGTTTTTAGCCGA
*
167312 AATCGTGAACTTACCGTCAC
575 AATCGTGAACTTACCATCAC
* * *** ***** ** * *
167332 -AGT-TTTGGGCTAAAAAGACGTTTCGGGGCCCGGCTCCGTTTTGCATGATATTAGACTGAAAGA
1 GA-TATTT-GAC-AGAAAGAC---TCCTTG-AAATATCAATATT-C---ATA-T-GAC--CAA-A
* *** *** * * * ** * * * *
167395 CTCCTTGAAATATCAATATTCATTTGACCA-AATCTCAGCCACAATGGAT-TTAAGCATTTGTTG
50 -T-C-TCAGCCA-C-A-ACGGATTT-AACATTAT-T-TGTTACGA-GCATCTGAATC--TTG-T-
* * * * * * *
167458 TTACGAGCATTTGAATCTTGTTTC-GATATAATT-AGAAATAAATTCGGAAAAAAATGGAAACAA
101 TT-C--G-ATAT-AA-----TTACAAATA-AATTCGGAAAAAAAAT-GG-----AA---AAACGA
* * * ** *
167521 TTTTAGAAGCGTAAAAAACCCTTCAATTTTTTTGCCATTGAATTATAAAATTTTTCTGAGTATTC
146 TATTAGAAGCGTAAAAAACCTTTCAAATTTTTTATCACTGAATTATAAAATTTTTCTGAGTATTC
* ** * * * *
167586 TGGCAAAAAATTGAGAAAAAAAAATTCCAGTCAGTTTTTAGCCGAAATCGTGTACTTACCATCAC
211 TGGCAAAAAATTGACAAAAAAATTTTCGAGTCAGTTTTTAGCCGAAATCGTGAACGTA-AATCAC
* * * *
167651 -GATTTTTGGCTAAAAACG-CGTTTCGGGACCCCGACTGAGTTTTGCATGAAATTTGGCAGAACG
275 AG-TTTTTGGCTAAAAA-GACGTTTCGGGGCCCCGACTGAGTTTTGCATGATATTTGACAGAAAG
* * *
167714 ACTCCTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAAC-GGATTTAA-AATTTTGTT
338 ACTCCTTGAAATATCAATATTCATCTGAACAAATCTCAGACAC-ACTGGATTTAAGAATTAT-TT
* * *
167777 GTTATGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTCGAAAAATATGGAAAAACGA
401 GTTACGAGCATCTGAATCTTGTTTCGATATAATTACAAATAAATTCGAAAAAAATGGAAAAACGA
* * * * * * ** *
167842 TATTAGAAGCGTGCAAAACCCCTCAA-TTTTTTGGCATTGAATTATTTTATTTTTCCTGAGTGTT
466 TACTAGAAGCGTGAAAAACCCTTCAACATTTTTAGCGTTGAATTA-TAAATTTTT-CTGAGTATT
* *
167906 GTGGCAAAAATATTGTGAAAAAAAATTTTCGGATCAA-TTTTTAGCCGAAATCGTGTACTTACCA
529 GTGGCAAAAA-ATTGAGAAAAAAAA-TTTCGGAT-AAGTTTTTAGCCGAAATCGTGAACTTACCA
167970 TCAC
591 TCAC
167974 G
1 G
167975 GTTTCTATAT
Statistics
Matches: 1015, Mismatches: 145, Indels: 114
0.80 0.11 0.09
Matches are distributed among these distances:
594 4 0.00
595 23 0.02
596 62 0.06
597 52 0.05
598 127 0.13
599 20 0.02
600 144 0.14
601 109 0.11
604 3 0.00
605 1 0.00
606 3 0.00
608 2 0.00
609 1 0.00
610 1 0.00
612 3 0.00
613 1 0.00
614 1 0.00
615 5 0.00
616 7 0.01
617 4 0.00
618 4 0.00
619 2 0.00
620 2 0.00
623 1 0.00
624 3 0.00
625 1 0.00
629 3 0.00
630 8 0.01
631 7 0.01
632 2 0.00
637 2 0.00
638 18 0.02
639 207 0.20
640 125 0.12
641 20 0.02
642 36 0.04
643 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (594 bp):
GATATTTGACAGAAAGACTCCTTGAAATATCAATATTCATATGACCAAATCTCAGCCACAACGGA
TTTAACATTATTTGTTACGAGCATCTGAATCTTGTTTCGATATAATTACAAATAAATTCGGAAAA
AAAATGGAAAAACGATATTAGAAGCGTAAAAAACCTTTCAAATTTTTTATCACTGAATTATAAAA
TTTTTCTGAGTATTCTGGCAAAAAATTGACAAAAAAATTTTCGAGTCAGTTTTTAGCCGAAATCG
TGAACGTAAATCACAGTTTTTGGCTAAAAAGACGTTTCGGGGCCCCGACTGAGTTTTGCATGATA
TTTGACAGAAAGACTCCTTGAAATATCAATATTCATCTGAACAAATCTCAGACACACTGGATTTA
AGAATTATTTGTTACGAGCATCTGAATCTTGTTTCGATATAATTACAAATAAATTCGAAAAAAAT
GGAAAAACGATACTAGAAGCGTGAAAAACCCTTCAACATTTTTAGCGTTGAATTATAAATTTTTC
TGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGATAAGTTTTTAGCCGAAATCGTGAACT
TACCATCAC
Found at i:167465 original size:319 final size:319
Alignment explanation
Indices: 166737--167978 Score: 1613
Period size: 319 Copynumber: 3.9 Consensus size: 319
166727 TTACCATCAC
* * * *
166737 GATATTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATGACCAAATTTTAGCCACAACGGA
1 GATATTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAACGGA
* * * * * *
166802 TTTAAATTTTTGTTTTTACGAGCTTTTGAATTTTGTTTTGATATATTTACAAATAAATTCGAAAA
66 TTTAAAATTTTGTTGTTACGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTCGAAAA
* * * * **
166867 AATTGGAAAAACGATATTTGAAGCGTGAAAAACTCTT-AAATTTTATTGTCGCTGAATTATAAAA
131 AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTT-TTGCCATTGAATTATAAAA
* ** *
166931 TTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAAATTGTTTTGGTCAGTTTTTAGCCGAAATT
195 TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAAT-TTCGGGTCAGTTTTTAGCCGAAATC
* * * *
166995 GTGTATTTACTATCACGATTTTTTGGCTAAAAAGGTGTTTCAGGGGCCCGACTGAGTTTTGCAT
259 GTGTACTTACCATCAC-AGTTTTTGGCTAAAAA-GCGTTTC-GGGGCCCGACTGAGTTTTGCAT
* * *
167059 GGTATTTGGCAGAAAGACTCCTTGAAATATTTATATTCATCTGAACAAATCTTAGACACAACGTA
1 GATATTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAACGGA
167124 TTTAAAATTTTGTTGTTACGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTCGAAAA
66 TTTAAAATTTTGTTGTTACGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTCGAAAA
* * * *
167189 AAATGGAAAAACGATACTAGAAGCGTGAAAAACCCTTCAACATTTTTAG-CGTTGAATTAT-ATA
131 AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA-ATTTTTTGCCATTGAATTATAAAA
*
167252 TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCATTTTTTAGCCGAAATCG
195 TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCG
* * * * **
167317 TGAACTTACCGTCACAGTTTTGGGCTAAAAAGACGTTTCGGGGCCCGGCTCCGTTTTGCAT
260 TGTACTTACCATCACAGTTTTTGGCTAAAAAG-CGTTTCGGGGCCCGACTGAGTTTTGCAT
* * * * * * * * *
167378 GATATTAGACTGAAAGACTCCTTGAAATATCAATATTCATTTGACCAAATCTCAGCCACAATGGA
1 GATATTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAACGGA
* *
167443 TTTAAGCA-TTTGTTGTTACGAGCATT-TGAATCTTGTTTCGATATAATTAGAAATAAATTCGGA
66 TTTAA-AATTTTGTTGTTACGAGC-TTCTGAATCTTGTTTCGATATAATTACAAATAAATTC-GA
* * * *
167506 AAAAAATGG--AAACAATTTTAGAAGCGTAAAAAACCCTTCAATTTTTTTGCCATTGAATTATAA
128 AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTGCCATTGAATTATAA
* * **
167569 AATTTTTCTGAGTATTCTGGCAAAAAATTGAGAAAAAAAAATTCCAGTCAGTTTTTAGCCGAAAT
193 AATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAAT
*
167634 CGTGTACTTACCATCAC-GATTTTTGGCTAAAAACGCGTTTCGGGACCCCGACTGAGTTTTGCAT
258 CGTGTACTTACCATCACAG-TTTTTGGCTAAAAA-GCGTTTCGGG-GCCCGACTGAGTTTTGCAT
* *
167698 GAAATTTGGCAGAACGACTCCTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAACGGA
1 GATATTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAACGGA
*
167763 TTTAAAATTTTGTTGTTATGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTCGAAAA
66 TTTAAAATTTTGTTGTTACGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTCGAAAA
* * * * ***
167828 ATATGGAAAAACGATATTAGAAGCGTGCAAAACCCCTC-AATTTTTTGGCATTGAATTATTTTAT
131 AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTGCCATTGAATTATAAAAT
* * * *
167892 TTTTCCTGAGTGTTGTGGCAAAAATATTGTGAAAAAAAATTTTCGGATCAATTTTTAGCCGAAAT
196 TTTT-CTGAGTATTGTGGCAAAAA-ATTGAGAAAAAAAA-TTTCGGGTCAGTTTTTAGCCGAAAT
*
167957 CGTGTACTTACCATCACGGTTT
258 CGTGTACTTACCATCACAGTTT
167979 CTATATTCAT
Statistics
Matches: 798, Mismatches: 102, Indels: 39
0.85 0.11 0.04
Matches are distributed among these distances:
317 6 0.01
318 39 0.05
319 236 0.30
320 180 0.23
321 107 0.13
322 180 0.23
323 44 0.06
324 6 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (319 bp):
GATATTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTGAACAAATCTTAGACACAACGGA
TTTAAAATTTTGTTGTTACGAGCTTCTGAATCTTGTTTCGATATAATTACAAATAAATTCGAAAA
AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTGCCATTGAATTATAAAAT
TTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGT
GTACTTACCATCACAGTTTTTGGCTAAAAAGCGTTTCGGGGCCCGACTGAGTTTTGCAT
Found at i:168763 original size:33 final size:31
Alignment explanation
Indices: 168712--168772 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
168702 ATTGTACACA
*
168712 AACATATATATATATATATATGTACATAATT
1 AACATATATACATATATATATGTACATAATT
*
168743 AACATATATACATACGTATATATGTTCATA
1 AACATATATACATA--TATATATGTACATA
168773 TGTTCATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 13 0.50
33 13 0.50
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (31 bp):
AACATATATACATATATATATGTACATAATT
Found at i:169358 original size:14 final size:14
Alignment explanation
Indices: 169339--169370 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
169329 TGAGTAATGC
*
169339 AAAATATAATTAAG
1 AAAATATAATGAAG
169353 AAAATATAATGAAG
1 AAAATATAATGAAG
169367 AAAA
1 AAAA
169371 CATTCTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (14 bp):
AAAATATAATGAAG
Found at i:169834 original size:2 final size:2
Alignment explanation
Indices: 169829--169861 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
169819 TGTGTGTGTG
169829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
169862 GATCAAGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:177590 original size:16 final size:16
Alignment explanation
Indices: 177569--177600 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
177559 CATAAAATAA
177569 AATATCATACAATGCG
1 AATATCATACAATGCG
177585 AATATCATACAATGCG
1 AATATCATACAATGCG
177601 TAACTGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
AATATCATACAATGCG
Found at i:180033 original size:31 final size:31
Alignment explanation
Indices: 179993--180060 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
179983 ATGGATATAT
*
179993 ATAAGATTTTCTTTTTGGTA-CTCAAATAAGAG
1 ATAA-ATTTTCTTTTTGG-AGATCAAATAAGAG
* *
180025 ATAAATTTTTTTTTTGGAGATTAAATAAGAG
1 ATAAATTTTCTTTTTGGAGATCAAATAAGAG
180056 ATAAA
1 ATAAA
180061 ATTACCAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 27 0.84
32 4 0.12
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (31 bp):
ATAAATTTTCTTTTTGGAGATCAAATAAGAG
Found at i:184659 original size:21 final size:21
Alignment explanation
Indices: 184635--184679 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
184625 TGATCCTTCC
184635 AGACTTTATT-TTACATTTATT
1 AGAC-TTATTATTACATTTATT
184656 AGACTTATTATTACATTTATT
1 AGACTTATTATTACATTTATT
184677 AGA
1 AGA
184680 TTCAAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (21 bp):
AGACTTATTATTACATTTATT
Found at i:185715 original size:2 final size:2
Alignment explanation
Indices: 185710--185734 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
185700 ATATTCTTGC
185710 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
185735 GTAGATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:190111 original size:19 final size:19
Alignment explanation
Indices: 190075--190113 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
190065 AATAAGAAAA
*
190075 CTCTGTTTTTTTCTTTTTC
1 CTCTGTTTTTTTCATTTTC
190094 CTCTG-TTTTTTCAATTTTC
1 CTCTGTTTTTTTC-ATTTTC
190113 C
1 C
190114 CGATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.05, C:0.23, G:0.05, T:0.67
Consensus pattern (19 bp):
CTCTGTTTTTTTCATTTTC
Found at i:196631 original size:103 final size:105
Alignment explanation
Indices: 196436--196635 Score: 298
Period size: 103 Copynumber: 1.9 Consensus size: 105
196426 AATCGGAACT
* * * **
196436 CGAACCCTTGCTCTTTAGGTTCAAATGAATCTTATCTAACCACCAGAACAAATGGGAGAACTGAT
1 CGAACCCTTGCTCTTTAGGTCCAAATGAATCTCACCTAACCACCAGAACAAATGGGAGAACCAAT
196501 CAAATTCCTTCAATTTTGTTTTACCAAGAAATGACGTTAC
66 CAAATTCCTTCAATTTTGTTTTACCAAGAAATGACGTTAC
* *
196541 CGAACCCTTGCTCTTTATGTCCAAATGAATC-CACCTAACCACCAGAAC-AA-GGGTTGAACCAA
1 CGAACCCTTGCTCTTTAGGTCCAAATGAATCTCACCTAACCACCAGAACAAATGGG-AGAACCAA
*
196603 TCAAATTCCTTCAATTTTGTTTTGCCAAGAAAT
65 TCAAATTCCTTCAATTTTGTTTTACCAAGAAAT
196636 TTGTAACGTT
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
102 3 0.03
103 39 0.45
104 15 0.17
105 29 0.34
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (105 bp):
CGAACCCTTGCTCTTTAGGTCCAAATGAATCTCACCTAACCACCAGAACAAATGGGAGAACCAAT
CAAATTCCTTCAATTTTGTTTTACCAAGAAATGACGTTAC
Found at i:197740 original size:31 final size:31
Alignment explanation
Indices: 197702--197803 Score: 122
Period size: 31 Copynumber: 3.4 Consensus size: 31
197692 GGCTAATTGT
197702 TCAAATAAGGGCCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCTAACGTTATCGAAAATGC
* * **
197733 TCAAATAAGGGCCTGATC-TT-T-TAATTTGGC
1 TCAAATAAGGGCCT-AACGTTATCGAAAAT-GC
197763 -CAAATAAGGGCCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCTAACGTTATCGAAAATGC
197793 TCAAATAAGGG
1 TCAAATAAGGG
197804 TTTGGTGTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
28 2 0.04
29 18 0.32
30 6 0.11
31 29 0.51
32 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (31 bp):
TCAAATAAGGGCCTAACGTTATCGAAAATGC
Found at i:197935 original size:31 final size:31
Alignment explanation
Indices: 197897--198001 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 31
197887 AAAGATGGGA
197897 CCCTTATTTGAGCATTTTGGCAAACATTAGG
1 CCCTTATTTGAGCATTTTGGCAAACATTAGG
** * * *
197928 CCCTTATTTG-GCCAAATT--AAAATATCAGG
1 CCCTTATTTGAG-CATTTTGGCAAACATTAGG
* * *
197957 TCCTTATTTGAGCATTTTGGCATACGTTAGG
1 CCCTTATTTGAGCATTTTGGCAAACATTAGG
197988 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
198002 ATTAGCCAAT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
29 21 0.38
30 2 0.04
31 33 0.59
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTGGCAAACATTAGG
Found at i:197997 original size:60 final size:60
Alignment explanation
Indices: 197833--197997 Score: 215
Period size: 60 Copynumber: 2.8 Consensus size: 60
197823 AAGCGTGAGA
* ** * *
197833 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAAGTTCTTATTTACCCAAATTCAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGCCCAAATTAAAAGAT
* * * *
197893 -GGGACCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAATAT
1 CAGG-CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGCCCAAATTAAAAGAT
* *
197953 CAGGTCCTTATTTGAGCATTTTGGCATACGTTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
197998 AGCAATTAGC
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 2 0.02
60 86 0.96
61 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGCCCAAATTAAAAGAT
Found at i:201308 original size:16 final size:16
Alignment explanation
Indices: 201287--201346 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
201277 GATTATGATG
*
201287 ATAATTATTAGTAATA
1 ATAATTATTAATAATA
*
201303 ATAATTATTATTAATA
1 ATAATTATTAATAATA
*
201319 TTAA-TATATAATATATA
1 ATAATTAT-TAATA-ATA
*
201336 ATAAATATTAA
1 ATAATTATTAA
201347 AAAAAAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 3 0.08
16 22 0.59
17 9 0.24
18 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
ATAATTATTAATAATA
Found at i:208047 original size:5 final size:5
Alignment explanation
Indices: 208037--208073 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
208027 TTCGACACGC
208037 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TA
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TA
208074 ATCTAGGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (5 bp):
TATCT
Found at i:253128 original size:3 final size:3
Alignment explanation
Indices: 253122--253174 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
253112 AGTGAATGTG
* ** * *
253122 GAT GAT GAT GAT GAT GAT GAT TAT GAT GAT GGG GAT GTT GAT TAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
253170 GAT GA
1 GAT GA
253175 GGAGGAGGAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (3 bp):
GAT
Found at i:253149 original size:21 final size:21
Alignment explanation
Indices: 253123--253177 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
253113 GTGAATGTGG
*
253123 ATGATGATGATGATGATGATT
1 ATGATGATGAGGATGATGATT
* *
253144 ATGATGATGGGGATGTTGATT
1 ATGATGATGAGGATGATGATT
253165 ATGATGATGAGGA
1 ATGATGATGAGGA
253178 GGAGGATGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (21 bp):
ATGATGATGAGGATGATGATT
Found at i:258098 original size:4 final size:4
Alignment explanation
Indices: 258089--258115 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
258079 ATGATATAGT
258089 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
258116 TTTTTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:264345 original size:6 final size:6
Alignment explanation
Indices: 264302--264334 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
264292 GTCGAATAGA
264302 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA- AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
264335 GAACAGAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:272632 original size:2 final size:2
Alignment explanation
Indices: 272627--272653 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
272617 TATATATATA
272627 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
272654 TCTATTGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.