Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 14 of 425
Found at i:3841013 original size:24 final size:26
Alignment explanation
Indices: 3840986--3841039 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
3840976 AAGACGTAAA
*
3840986 AAAAGGA-TTAAAATAAGTAATA-AT
1 AAAAGGATTTAAAATAAATAATATAT
*
3841010 AAAATGATTTAAAATAAATAATATAT
1 AAAAGGATTTAAAATAAATAATATAT
3841036 AAAA
1 AAAA
3841040 AACTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 6 0.23
25 14 0.54
26 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (26 bp):
AAAAGGATTTAAAATAAATAATATAT
Found at i:3841046 original size:25 final size:26
Alignment explanation
Indices: 3840993--3841058 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
3840983 AAAAAAAGGA
* * *
3840993 TTAAAATAAGTAATA-ATAAAATGAT
1 TTAAAATAAATAATATATAAAATAAC
3841018 TTAAAATAAATAATATATAAAA-AAC
1 TTAAAATAAATAATATATAAAATAAC
3841043 TTAAAA-AGAATAATAT
1 TTAAAATA-AATAATAT
3841059 TAACAGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 29 0.81
26 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:3848778 original size:51 final size:54
Alignment explanation
Indices: 3848713--3848824 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
3848703 ACGATAAATA
* * * *
3848713 ATAAAAGAATTTAAAATAG-T-TTACATATAAAATAGTAT-AACTAAATAAAGT
1 ATAAAAAAACTTAAAATAGATAATACATATAAAATAGTATAAAATAAATAAAGT
* * * *
3848764 ATAAAAAAACTTAAAATAGATAATACATATATAATGGTTTAAAATAAATAACGT
1 ATAAAAAAACTTAAAATAGATAATACATATAAAATAGTATAAAATAAATAAAGT
3848818 ATAAAAA
1 ATAAAAA
3848825 TATTTCAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
51 17 0.34
52 1 0.02
53 14 0.28
54 18 0.36
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.29
Consensus pattern (54 bp):
ATAAAAAAACTTAAAATAGATAATACATATAAAATAGTATAAAATAAATAAAGT
Found at i:3848884 original size:27 final size:26
Alignment explanation
Indices: 3848774--3848905 Score: 88
Period size: 27 Copynumber: 5.0 Consensus size: 26
3848764 ATAAAAAAAC
* * * *
3848774 TTAAAATAGATAATACATATATAATGGT
1 TTAAAATAAATAATATAT-TAAAAT-AT
** *
3848802 TTAAAATAAATAACGTATAAAAATAT
1 TTAAAATAAATAATATATTAAAATAT
* * * *
3848828 TTCAAAATAAGTAATAT-TTATAGTAG
1 TT-AAAATAAATAATATATTAAAATAT
3848854 TTAAAATAAATAATATATGTAAAATAT
1 TTAAAATAAATAATATAT-TAAAATAT
**
3848881 TTAAAATTTATAATA-ATTTAAAATA
1 TTAAAATAAATAATATA-TTAAAATA
3848906 CATAAGATGT
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
25 13 0.16
26 19 0.24
27 34 0.43
28 14 0.17
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
TTAAAATAAATAATATATTAAAATAT
Found at i:3848946 original size:24 final size:26
Alignment explanation
Indices: 3848919--3848972 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
3848909 AAGATGTAAA
*
3848919 AAAAGGA-TTAAAATAAGTAATA-AT
1 AAAAGGATTTAAAATAAATAATATAT
*
3848943 AAAATGATTTAAAATAAATAATATAT
1 AAAAGGATTTAAAATAAATAATATAT
3848969 AAAA
1 AAAA
3848973 AACTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 6 0.23
25 14 0.54
26 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (26 bp):
AAAAGGATTTAAAATAAATAATATAT
Found at i:3848979 original size:25 final size:26
Alignment explanation
Indices: 3848926--3848991 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
3848916 AAAAAAAGGA
* * *
3848926 TTAAAATAAGTAATA-ATAAAATGAT
1 TTAAAATAAATAATATATAAAATAAC
3848951 TTAAAATAAATAATATATAAAA-AAC
1 TTAAAATAAATAATATATAAAATAAC
3848976 TTAAAA-ATAATAATAT
1 TTAAAATA-AATAATAT
3848992 TAACAGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 29 0.81
26 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:3850334 original size:30 final size:30
Alignment explanation
Indices: 3850298--3850491 Score: 257
Period size: 30 Copynumber: 6.8 Consensus size: 30
3850288 ACTTTTCTCA
3850298 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
*
3850328 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
*
3850358 ACTAGCCACT-CTTTT---------TCTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
3850378 ACTAGCCACT-CTTTTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
*
3850407 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
*
3850437 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCC
* *
3850467 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCCTTTTCCACCACCA
3850492 CTTGTACCTA
Statistics
Matches: 144, Mismatches: 10, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
20 19 0.13
29 18 0.12
30 107 0.74
ACGTcount: A:0.24, C:0.48, G:0.04, T:0.24
Consensus pattern (30 bp):
ACTAGCCACTCCTTTTCCACCACCAACTCC
Found at i:3850379 original size:20 final size:20
Alignment explanation
Indices: 3850354--3850392 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3850344 CCACCACCAA
3850354 CTCCACTAGCCACTCTTTTT
1 CTCCACTAGCCACTCTTTTT
3850374 CTCCACTAGCCACTCTTTT
1 CTCCACTAGCCACTCTTTT
3850393 CCACCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.41, G:0.05, T:0.38
Consensus pattern (20 bp):
CTCCACTAGCCACTCTTTTT
Found at i:3850399 original size:20 final size:20
Alignment explanation
Indices: 3850356--3850399 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3850346 ACCACCAACT
* *
3850356 CCACTAGCCACTCTTTTTCT
1 CCACTAGCCACTCTTTTCCA
3850376 CCACTAGCCACTCTTTTCCA
1 CCACTAGCCACTCTTTTCCA
3850396 CCAC
1 CCAC
3850400 CAACTCCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.45, G:0.05, T:0.32
Consensus pattern (20 bp):
CCACTAGCCACTCTTTTCCA
Found at i:3850420 original size:79 final size:80
Alignment explanation
Indices: 3850290--3850453 Score: 312
Period size: 79 Copynumber: 2.1 Consensus size: 80
3850280 CAACTTAAAC
3850290 TTTTCTCAACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAAC
1 TTTTCTCAACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAAC
3850355 TCCACTAGCCACTCT
66 TCCACTAGCCACTCT
*
3850370 TTTTCTCCACTAGCCACT-CTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAAC
1 TTTTCTCAACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAAC
3850434 TCCACTAGCCACTCT
66 TCCACTAGCCACTCT
3850449 TTTTC
1 TTTTC
3850454 CACCACCAAC
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 66 0.80
80 17 0.20
ACGTcount: A:0.23, C:0.46, G:0.04, T:0.28
Consensus pattern (80 bp):
TTTTCTCAACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAAC
TCCACTAGCCACTCT
Found at i:3851092 original size:25 final size:24
Alignment explanation
Indices: 3851063--3851133 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
3851053 TACGTATATA
3851063 TATATATATTTTATACTATTTTATG
1 TATATATATTTTATA-TATTTTATG
* * * *
3851088 TATATATCTTTAATATTATATTATT
1 TATATATATTTTATA-TATTTTATG
*
3851113 TATATATA-TATATATATTTTA
1 TATATATATTTTATATATTTTA
3851134 CATGTTATCT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 6 0.16
24 4 0.11
25 27 0.73
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (24 bp):
TATATATATTTTATATATTTTATG
Found at i:3851152 original size:35 final size:35
Alignment explanation
Indices: 3851088--3851154 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
3851078 CTATTTTATG
*
3851088 TATATATCTTTAATATTATATTATTTATATATATA
1 TATATATCTTTAATATTATATTATGTATATATATA
* *
3851123 TATATAT-TTTACATGTTATCTTATGTATATAT
1 TATATATCTTTA-ATATTATATTATGTATATAT
3851155 CTTAACTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 4 0.14
35 24 0.86
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (35 bp):
TATATATCTTTAATATTATATTATGTATATATATA
Found at i:3851171 original size:22 final size:24
Alignment explanation
Indices: 3851143--3851201 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
3851133 ACATGTTATC
3851143 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
3851165 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
3851190 TTATGTACATAT
1 TTATGTATATAT
3851202 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:3851191 original size:25 final size:25
Alignment explanation
Indices: 3851159--3851207 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3851149 ATATATCTTA
**
3851159 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
3851184 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
3851208 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:3851385 original size:16 final size:15
Alignment explanation
Indices: 3851361--3851408 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3851351 TAATTATTAT
*
3851361 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
3851377 TATTTTAATATTTTA
1 TATTTTAATATTTTA
3851392 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
3851408 T
1 T
3851409 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:3851396 original size:7 final size:8
Alignment explanation
Indices: 3851361--3851412 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3851351 TAATTATTAT
*
3851361 TATTCTAA
1 TATTTTAA
*
3851369 TATTTTGA
1 TATTTTAA
3851377 TATTTTAA
1 TATTTTAA
3851385 TATTTT-A
1 TATTTTAA
3851392 TATTTTATA
1 TATTTTA-A
*
3851401 TATTTTAT
1 TATTTTAA
3851409 TATT
1 TATT
3851413 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:3864632 original size:73 final size:73
Alignment explanation
Indices: 3864454--3864820 Score: 515
Period size: 73 Copynumber: 5.0 Consensus size: 73
3864444 CTTTTCAAGG
* * * * * * *
3864454 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGATACTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* *
3864519 TTTTTTC-
66 GTTTGTCA
*
3864526 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
3864591 GTTTGTCA
66 GTTTGTCA
* * *
3864599 AAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-ATTTCAATTTC
*
3864664 TGTTTTTCA
65 TGTTTGTCA
*
3864673 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
3864738 GTTTGTCA
66 GTTTGTCA
* **
3864746 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTCTTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAATT
3864810 TCTGTTT-TCA
63 TCTGTTTGTCA
3864820 A
1 A
3864821 TTTCTGTTCG
Statistics
Matches: 266, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
72 63 0.24
73 105 0.39
74 72 0.27
75 26 0.10
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTTGTCA
Found at i:3864719 original size:147 final size:145
Alignment explanation
Indices: 3864454--3864817 Score: 561
Period size: 147 Copynumber: 2.5 Consensus size: 145
3864444 CTTTTCAAGG
* * * * *
3864454 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGATACTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTACTTTTAATTTCT
* * *
3864519 TTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
66 GTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTC
3864584 AATTTCTGTTTGTCA
131 AATTTCTGTTTGTCA
* *
3864599 AAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTACTTTT-AATTTC
3864664 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATT
65 TGTTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATT
3864729 TCAATTTCTGTTTGTCA
129 TCAATTTCTGTTTGTCA
*
3864746 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGT-CTTTTCAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTACTTTT-AAT
3864809 TTCTGTTTT
62 TTCTGTTTT
3864818 CAATTTCTGT
Statistics
Matches: 200, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
145 52 0.26
146 14 0.07
147 107 0.54
148 16 0.08
149 11 0.05
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (145 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTACTTTTAATTTCT
GTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTC
AATTTCTGTTTGTCA
Found at i:3864819 original size:13 final size:13
Alignment explanation
Indices: 3864801--3864828 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3864791 TGCTGAGGTC
3864801 TTTTCAATTTCTG
1 TTTTCAATTTCTG
3864814 TTTTCAATTTCTG
1 TTTTCAATTTCTG
3864827 TT
1 TT
3864829 CGTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:3864881 original size:239 final size:237
Alignment explanation
Indices: 3864598--3865540 Score: 1274
Period size: 239 Copynumber: 3.9 Consensus size: 237
3864588 TCTGTTTGTC
*
3864598 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
*
3864663 CTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAAT
66 CTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
*
3864728 TTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATG
131 TTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--CACACG
3864793 CTGAGGTCTTTTCAATTTCTGTTTTCAATTTCTGTTCGTAAAAA
194 CTGAGGTCTTTTCAATTTCTGTTTTCAATTTCTGTTCGTAAAAA
3864837 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
* * *
3864902 TTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAAT
66 CTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
* *
3864967 TTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATG
131 TTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--CACACG
3865032 CTGAGGTCTTTTCAATTTCTGTTTTTCAATTTCTGTTCGTAAAAAAA
194 CTGAGGTCTTTTCAATTTCTG-TTTTCAATTTCTGTTCGT--AAAAA
3865079 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
* *
3865144 CTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAAT
66 CTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
*
3865209 TTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCT
131 TTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGCT
* *
3865274 GAGG-----T-AA-------TTTCAATTTCTGTTTGT----C
196 GAGGTCTTTTCAATTTCTGTTTTCAATTTCTGTTCGTAAAAA
* * *
3865299 AAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTC-GGCTCACATGCTGAGGTCTTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGG-----T--A-
* *
3865363 TTTGTTCTTCAATTTCTGTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
55 --T-TT-TTAAATTTCTGTTTTT---CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * * * *
3865428 AGGACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAAAGGTG
113 AGGACACGCTGAGGTA-ATTTCAATTTCTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTG
* *
3865493 AGTTGAGCCTCGGGACACGCTGAGGTCATTTCAATTTCTGTTTGTCAA
175 AGTTGAGCCTCGGCACACGCTGAGGTCTTTTCAATTTCTGTTT-TCAA
3865541 AAATTAACTC
Statistics
Matches: 640, Mismatches: 26, Indels: 61
0.88 0.04 0.08
Matches are distributed among these distances:
219 2 0.00
220 36 0.06
222 10 0.02
226 16 0.03
227 1 0.00
229 1 0.00
232 1 0.00
233 2 0.00
234 16 0.03
235 1 0.00
237 53 0.08
238 16 0.03
239 210 0.33
240 78 0.12
242 188 0.29
245 1 0.00
246 2 0.00
253 2 0.00
254 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (237 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
CTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
TTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGCT
GAGGTCTTTTCAATTTCTGTTTTCAATTTCTGTTCGTAAAAA
Found at i:3864980 original size:73 final size:73
Alignment explanation
Indices: 3864837--3865060 Score: 331
Period size: 73 Copynumber: 3.0 Consensus size: 73
3864827 TTCGTAAAAA
* *
3864837 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA-TTTTCAATTT
*
3864902 TTGTTTTTC
65 CTGTTTTTC
* *
3864911 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTC
*
3864976 TGTTTGTC
66 TGTTTTTC
* * * *
3864984 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACACGCTGAGGTATTTTCAATT
3865049 TCTGTTTTTC
64 TCTGTTTTTC
3865059 AA
1 AA
3865061 TTTCTGTTCG
Statistics
Matches: 135, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
73 53 0.39
74 52 0.39
75 30 0.22
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTC
TGTTTTTC
Found at i:3865059 original size:14 final size:14
Alignment explanation
Indices: 3865040--3865068 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3865030 TGCTGAGGTC
3865040 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
3865054 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
3865068 T
1 T
3865069 CGTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:3865103 original size:168 final size:167
Alignment explanation
Indices: 3864911--3865227 Score: 501
Period size: 169 Copynumber: 1.9 Consensus size: 167
3864901 TTTGTTTTTC
* *
3864911 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA-ATTTCAATTT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATATTTAAATTT
* * * *
3864975 CTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTC
66 CTATTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--CACACGCTGAGGTA
* *
3865040 TTTTCAATTTCTGTTTTTCAATTTCTGTTCGTAAAAAAA
129 ATTTCAATTTCTGTTTGTCAATTTCTGTTCGTAAAAAAA
* *
3865079 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATATTTAAATTT
* *
3865144 CTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAAT
66 CTATTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGCTGAGGTAAT
3865209 TTCAATTTCTGTTTGTCAA
131 TTCAATTTCTGTTTGTCAA
3865228 AAATCAACTC
Statistics
Matches: 136, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
167 30 0.22
168 52 0.38
169 54 0.40
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (167 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATATTTAAATTT
CTATTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGCTGAGGTAAT
TTCAATTTCTGTTTGTCAATTTCTGTTCGTAAAAAAA
Found at i:3865258 original size:73 final size:73
Alignment explanation
Indices: 3865079--3865578 Score: 484
Period size: 73 Copynumber: 6.5 Consensus size: 73
3865069 CGTAAAAAAA
* * *
3865079 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA-ATTTCAATTT
* *
3865144 CTATTTTTC
65 CTGTTTGTC
3865153 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
3865218 TGTTTGTC
66 TGTTTGTC
3865226 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
3865291 TGTTTGTC
66 TGTTTGTC
* * * * **
3865299 AAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACACGCTGAGGTAATTTCAA--
* *
3865364 TTGTTCTTCAATTTCTGTTTT
62 -T-TTC-T---GTT-TG--TC
* ** * * * * * * *
3865385 TAAAAAAAAATCA-ACT-C-ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTT
1 AAAAATCAACTCATATTGCGAGA--G-GTGAGTTGAG-----CCTCGGGACACGCTGAGGTA-AT
* *
3865447 TTAAATTTCTGTTTTTC
57 TTCAATTTCTGTTTGTC
* * *
3865464 AAAAAAATCAACTCATATTACGAAAGGTGAGTTGAGCCTCGGGACACGCTGAGGTCATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATT
3865529 TCTGTTTGTC
64 TCTGTTTGTC
* *
3865539 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGG
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
3865579 CTCACATGCT
Statistics
Matches: 352, Mismatches: 47, Indels: 55
0.78 0.10 0.12
Matches are distributed among these distances:
73 162 0.46
74 53 0.15
75 33 0.09
76 18 0.05
78 1 0.00
79 4 0.01
80 1 0.00
81 18 0.05
82 5 0.01
83 5 0.01
84 5 0.01
85 4 0.01
86 20 0.06
87 1 0.00
89 11 0.03
90 6 0.02
91 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
TGTTTGTC
Found at i:3865465 original size:91 final size:89
Alignment explanation
Indices: 3865299--3865465 Score: 228
Period size: 91 Copynumber: 1.8 Consensus size: 89
3865289 TCTGTTTGTC
* * *
3865299 AAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGG--CACACGCTGAGGTCTTTTAAATT
3865364 TTGTTCTTCAATTTCTGTTTTTAAAA
64 TTGTTCTTCAATTTCTGTTTTTAAAA
* *
3865390 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTATTTTTAAATT
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTC-GGCACACGCTGAGGT-CTTTTAAATT
*
3865454 TCTGTTTTTCAA
64 T-TGTTCTTCAA
3865466 AAAAATCAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
89 11 0.16
90 9 0.13
91 45 0.67
92 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (89 bp):
AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCACACGCTGAGGTCTTTTAAATTTT
GTTCTTCAATTTCTGTTTTTAAAA
Found at i:3865500 original size:240 final size:238
Alignment explanation
Indices: 3865153--3865626 Score: 808
Period size: 240 Copynumber: 2.0 Consensus size: 238
3865143 TCTATTTTTC
* *
3865153 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTAAATTTC
* *
3865218 TGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATT
66 TGTTTGTCAAAAATCAACTCATATTACGAAAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATT
3865283 TCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACATGC
131 TCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACATGC
3865348 TGAGGTCTTTTCAATTT-TG-TTCTTCAATTTCTGTTTTTAAAA
196 TGAGGTCTTTTCAATTTCTGCTT-TTCAATTTCTGTTTTTAAAA
*
3865390 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-ATTTAAATTT
* *
3865455 CTGTTTTTCAAAAAAATCAACTCATATTACGAAAGGTGAGTTGAGCCTCGGGACACGCTGAGGTC
65 CTGTTTGTC--AAAAATCAACTCATATTACGAAAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
* *
3865520 ATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACA
128 ATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACA
*
3865585 TGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTGTTTTT
193 TGCTGAGGTCTTTTCAATTTCTGCTTTTCAATTTCTGTTTTT
3865627 TCAATTTATA
Statistics
Matches: 222, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
237 53 0.24
238 16 0.07
240 133 0.60
241 18 0.08
242 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (238 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTAAATTTC
TGTTTGTCAAAAATCAACTCATATTACGAAAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATT
TCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACATGC
TGAGGTCTTTTCAATTTCTGCTTTTCAATTTCTGTTTTTAAAA
Found at i:3865514 original size:76 final size:75
Alignment explanation
Indices: 3865373--3865615 Score: 312
Period size: 76 Copynumber: 3.2 Consensus size: 75
3865363 TTTGTTCTTC
* *
3865373 AATTTCTGTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1 AATTTCTGTTTTT-CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCT
3865438 GAGGTATTTTT
65 GAGGTATTTTT
* *
3865449 AAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAAAGGTGAGTTGAGCCTCGGGACACGCT
1 -AATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCT
*
3865514 GAGGTCA-TTTC
65 GAGGT-ATTTTT
* * * * *
3865525 AATTTCTGTTTGTC--AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACATGC
1 AATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACACGC
*
3865588 TGAGGTCTTTTT
64 TGAGGTATTTTT
*
3865600 AATTTCTGCTTTTCAA
1 AATTTCTGTTTTTCAA
3865616 TTTCTGTTTT
Statistics
Matches: 144, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
73 36 0.25
75 39 0.27
76 55 0.38
77 14 0.10
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (75 bp):
AATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTG
AGGTATTTTT
Found at i:3865607 original size:315 final size:315
Alignment explanation
Indices: 3864835--3865578 Score: 1282
Period size: 315 Copynumber: 2.4 Consensus size: 315
3864825 TGTTCGTAAA
* *
3864835 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAAT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA--TTTCAAT
* * *
3864900 TTTTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
64 TTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
*
3864965 ATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACA
129 ATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACA
*
3865030 TGCTGAGGTCTTTTCAATTTCTGTTTTTCAATTTCTGTTCGTAAAAAAAAAAAATCAACTCATAT
194 TGCTGAGGTCTTTTCAATTTCTGTTCTTCAATTTCTGTTC-TAAAAAAAAAAAATCAACTCATAT
3865095 TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTCTATTTTTC
258 TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTCTATTTTTC
3865153 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT-ATTTCAATT
3865216 TCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAA
65 TCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAA
3865281 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACAT
130 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACAT
**
3865346 GCTGAGGTCTTTTCAATTT-TGTTCTTCAATTTCTGTT-T-TTAAAAAAAAATCAACTCATATTG
195 GCTGAGGTCTTTTCAATTTCTGTTCTTCAATTTCTGTTCTAAAAAAAAAAAATCAACTCATATTG
*
3865408 CGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTCTGTTTTTC
260 CGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTCTATTTTTC
* *
3865464 AAAAAAATCAACTCATATTACGAAAGGTGAGTTGAGCCTCGGGACACGCTGAGGTCATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT-ATTTCAATT
* *
3865529 TCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGG
65 TCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
3865579 CTCACATGCT
Statistics
Matches: 408, Mismatches: 15, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
311 77 0.19
312 1 0.00
313 108 0.26
314 17 0.04
315 152 0.37
316 52 0.13
317 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (315 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTCAATTT
CTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAAT
TTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACATG
CTGAGGTCTTTTCAATTTCTGTTCTTCAATTTCTGTTCTAAAAAAAAAAAATCAACTCATATTGC
GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTCTATTTTTC
Found at i:3865617 original size:14 final size:15
Alignment explanation
Indices: 3865592--3865633 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
3865582 ACATGCTGAG
*
3865592 GTCTTTTTAATTTCT
1 GTCTTTTCAATTTCT
3865607 G-CTTTTCAATTTCT
1 GTCTTTTCAATTTCT
*
3865621 GTTTTTTCAATTT
1 GTCTTTTCAATTT
3865634 ATATTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (15 bp):
GTCTTTTCAATTTCT
Found at i:3865629 original size:15 final size:14
Alignment explanation
Indices: 3865595--3865644 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
3865585 TGCTGAGGTC
3865595 TTTTT-AATTTCTG
1 TTTTTCAATTTCTG
*
3865608 CTTTTCAATTTCTG
1 TTTTTCAATTTCTG
* *
3865622 TTTTTTCAATTTATA
1 -TTTTTCAATTTCTG
3865637 TTTTTCAA
1 TTTTTCAA
3865645 AAATCAACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 16 0.52
15 11 0.35
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.64
Consensus pattern (14 bp):
TTTTTCAATTTCTG
Found at i:3866459 original size:30 final size:30
Alignment explanation
Indices: 3866392--3866565 Score: 269
Period size: 30 Copynumber: 5.8 Consensus size: 30
3866382 ACTTTTCTCA
* *
3866392 ACTAGCCACTCCTTTTCCACCACCAACTCT
1 ACTAGCCACACCTTTTCCACCACCAACTCC
3866422 A-TAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
3866451 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
3866481 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
3866511 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
3866541 ACTAGCCACACCTTCTCCACTACCA
1 ACTAGCCACACCTTTTCCACCACCA
3866566 CTTGTACCTA
Statistics
Matches: 131, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
29 27 0.21
30 104 0.79
ACGTcount: A:0.25, C:0.48, G:0.03, T:0.24
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:3866510 original size:60 final size:60
Alignment explanation
Indices: 3866392--3866565 Score: 305
Period size: 60 Copynumber: 2.9 Consensus size: 60
3866382 ACTTTTCTCA
* *
3866392 ACTAGCCACTCCTTTTCCACCACCAACTCTA-TAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
3866451 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
* *
3866511 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACTACCA
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCA
3866566 CTTGTACCTA
Statistics
Matches: 110, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 29 0.26
60 81 0.74
ACGTcount: A:0.25, C:0.48, G:0.03, T:0.24
Consensus pattern (60 bp):
ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:3867166 original size:53 final size:54
Alignment explanation
Indices: 3867079--3867206 Score: 136
Period size: 55 Copynumber: 2.3 Consensus size: 54
3867069 TTCTTAATAT
3867079 TATATTATATATATTCTTTTAATATATTAGGTATAT-T-TTAAAT-TCTATATTACG
1 TATA-TATATATATT-TTTTAATATATTAGGTATATATCTTAAATAT-TATATTACG
* * * * **
3867133 TATATATATATATTTTTATACTATTTTATGTATATATCTTTAATATTATATTATT
1 TATATATATATATTTTT-TAATATATTAGGTATATATCTTAAATATTATATTACG
3867188 TATATATATATATATTTTT
1 TATATATATATAT-TTTTT
3867207 TACATGTTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
52 3 0.05
53 24 0.38
54 5 0.08
55 26 0.41
56 5 0.08
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (54 bp):
TATATATATATATTTTTTAATATATTAGGTATATATCTTAAATATTATATTACG
Found at i:3867183 original size:55 final size:57
Alignment explanation
Indices: 3867124--3867232 Score: 141
Period size: 55 Copynumber: 1.9 Consensus size: 57
3867114 TTTTAAATTC
*
3867124 TATATTACGTATATATATATAT-TTTTATAC-TATTTTATGTATATATCTTTAATAT
1 TATATTACGTATATATATATATATTTTATACTTATCTTATGTATATATCTTTAATAT
** *
3867179 TATATTATTTATATATATATATATTTTTTACATGTTATCTTATGTATATATCTT
1 TATATTACGTATATATATATATATTTTATAC---TTATCTTATGTATATATCTT
3867233 AACTACATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
55 20 0.44
56 7 0.16
60 18 0.40
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.58
Consensus pattern (57 bp):
TATATTACGTATATATATATATATTTTATACTTATCTTATGTATATATCTTTAATAT
Found at i:3867192 original size:25 final size:24
Alignment explanation
Indices: 3867139--3867194 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
3867129 TACGTATATA
* *
3867139 TATATATTTTTATACTATTTTATG
1 TATATATTTTAATACTATATTATG
* *
3867163 TATATATCTTTAATATTATATTATT
1 TATATAT-TTTAATACTATATTATG
3867188 TATATAT
1 TATATAT
3867195 ATATATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
TATATATTTTAATACTATATTATG
Found at i:3867267 original size:25 final size:25
Alignment explanation
Indices: 3867234--3867282 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3867224 ATATATCTTA
**
3867234 ACTACATTATGTATGTATTTTTAAC
1 ACTACATTATGTACATATTTTTAAC
*
3867259 ACTATATTATGTACATATTTTTAA
1 ACTACATTATGTACATATTTTTAA
3867283 TATTATCACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (25 bp):
ACTACATTATGTACATATTTTTAAC
Found at i:3867463 original size:16 final size:15
Alignment explanation
Indices: 3867439--3867486 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3867429 TAATTATTAT
*
3867439 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
3867455 TATTTTAATATTTTA
1 TATTTTAATATTTTA
3867470 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
3867486 T
1 T
3867487 TATTCACATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:3867474 original size:7 final size:8
Alignment explanation
Indices: 3867439--3867490 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3867429 TAATTATTAT
*
3867439 TATTCTAA
1 TATTTTAA
*
3867447 TATTTTGA
1 TATTTTAA
3867455 TATTTTAA
1 TATTTTAA
3867463 TATTTT-A
1 TATTTTAA
3867470 TATTTTATA
1 TATTTTA-A
*
3867479 TATTTTAT
1 TATTTTAA
3867487 TATT
1 TATT
3867491 CACATTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:3873016 original size:31 final size:30
Alignment explanation
Indices: 3872978--3873050 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
3872968 AACCCAACAC
*
3872978 AAATTAAATTTAAATAATAAAAAATATTTTT
1 AAATTAAATTT-AATAATAAAAAATATATTT
* *
3873009 AAATTAAAATTTAATCATAAAATATATATTT
1 AAATT-AAATTTAATAATAAAAAATATATTT
*
3873040 AATATTTAATT
1 AA-ATTAAATT
3873051 AATTTTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 27 0.75
32 9 0.25
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATTAAATTTAATAATAAAAAATATATTT
Found at i:3876515 original size:36 final size:36
Alignment explanation
Indices: 3876475--3876553 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
3876465 AAATAAAATG
*
3876475 TTTATAATTTTTA-TTTATAATTTAGCA-TAAATATAA
1 TTTATAATTTATATTTTATAATTT-G-ATTAAATATAA
*
3876511 TTTAT-ATTTATATTTTATTATTTGATTTAAATATAA
1 TTTATAATTTATATTTTATAATTTGA-TTAAATATAA
3876547 TTTATAA
1 TTTATAA
3876554 AATATTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
34 1 0.03
35 7 0.19
36 28 0.76
37 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (36 bp):
TTTATAATTTATATTTTATAATTTGATTAAATATAA
Found at i:3893228 original size:30 final size:31
Alignment explanation
Indices: 3893192--3893251 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
3893182 AAAAAAAATC
3893192 TTATAATTTTA-AATTTTTTA-TAAATTTTGT
1 TTATAATTTTACAATTTTTTACT-AATTTTGT
3893222 TTATAATTTTACTAATTTTTTACTAATTTT
1 TTATAATTTTAC-AATTTTTTACTAATTTT
3893252 AAAATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 11 0.41
32 15 0.56
33 1 0.04
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (31 bp):
TTATAATTTTACAATTTTTTACTAATTTTGT
Found at i:3895993 original size:16 final size:16
Alignment explanation
Indices: 3895972--3896020 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
3895962 ATATTTAGTC
3895972 ATATAATAAATTATTA
1 ATATAATAAATTATTA
3895988 ATATAAT---TTATTA
1 ATATAATAAATTATTA
3896001 A-ATAATAAATTATTTA
1 ATATAATAAATTA-TTA
3896017 ATAT
1 ATAT
3896021 TTCAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 5 0.18
13 7 0.25
15 3 0.11
16 11 0.39
17 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:3896006 original size:28 final size:28
Alignment explanation
Indices: 3895974--3896060 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 28
3895964 ATTTAGTCAT
3895974 ATAATAAATTATTAATATAATTTATTAA
1 ATAATAAATTATTAATATAATTTATTAA
*
3896002 ATAATAAATTATTTAATATTTCAATTTTATTTTA
1 ATAATAAATTA-TTAATA--T-AA-TTTA-TTAA
3896036 ATAATAAATT-TTAA-ATAATATTATT
1 ATAATAAATTATTAATATAAT-TTATT
3896061 CACATATTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
27 3 0.06
28 16 0.31
29 7 0.14
31 2 0.04
32 6 0.12
33 4 0.08
34 13 0.25
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
ATAATAAATTATTAATATAATTTATTAA
Found at i:3896108 original size:15 final size:15
Alignment explanation
Indices: 3896088--3896144 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
3896078 ATTCAATATT
3896088 AATATTTTAATAATA
1 AATATTTTAATAATA
*
3896103 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
3896122 AATATATTAATAATA
1 AATATTTTAATAATA
3896137 AATATTTT
1 AATATTTT
3896145 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:3896616 original size:14 final size:14
Alignment explanation
Indices: 3896597--3896635 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3896587 TCAGAAAAGT
*
3896597 AAATCATTTTTCAG
1 AAATCATTTTCCAG
*
3896611 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
3896625 AAGTCATTTTC
1 AAATCATTTTC
3896636 AGTGAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:3896842 original size:15 final size:15
Alignment explanation
Indices: 3896822--3896854 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3896812 CTCCTTACTA
3896822 AGTTACATCTCTTTT
1 AGTTACATCTCTTTT
3896837 AGTTACATCTCTTTT
1 AGTTACATCTCTTTT
3896852 AGT
1 AGT
3896855 GTTATTTAAG
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:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (15 bp):
AGTTACATCTCTTTT
Found at i:3898979 original size:18 final size:18
Alignment explanation
Indices: 3898956--3898991 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3898946 ACTCACTTCT
3898956 CCTTCGCCTCCGCCTCCG
1 CCTTCGCCTCCGCCTCCG
* *
3898974 CCTTCGTCTCCGTCTCCG
1 CCTTCGCCTCCGCCTCCG
3898992 TCGGATTCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.56, G:0.17, T:0.28
Consensus pattern (18 bp):
CCTTCGCCTCCGCCTCCG
Found at i:3903359 original size:98 final size:98
Alignment explanation
Indices: 3903190--3903387 Score: 387
Period size: 98 Copynumber: 2.0 Consensus size: 98
3903180 TGAAAATTAC
3903190 TATAAAGTGCTTAATTTTTGTGATATTTTTCTCTTTGTCTTCTCTTTTCAAATGCTTGTAATCTT
1 TATAAAGTGCTTAATTTTTGTGATATTTTTCTCTTTGTCTTCTCTTTTCAAATGCTTGTAATCTT
3903255 GCAAACTCTGTAATGCTGTATGGTCACATCAGT
66 GCAAACTCTGTAATGCTGTATGGTCACATCAGT
3903288 TATAAAGTGCTTAATTTTTGTGATATTTTTCTCTTTGTCTTCTCTTTTCAAATGCTTGTAATCTT
1 TATAAAGTGCTTAATTTTTGTGATATTTTTCTCTTTGTCTTCTCTTTTCAAATGCTTGTAATCTT
*
3903353 GCAAACTCTGTAATGCTGTATGGTCAGATCAGT
66 GCAAACTCTGTAATGCTGTATGGTCACATCAGT
3903386 TA
1 TA
3903388 GAATGCTTTA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.47
Consensus pattern (98 bp):
TATAAAGTGCTTAATTTTTGTGATATTTTTCTCTTTGTCTTCTCTTTTCAAATGCTTGTAATCTT
GCAAACTCTGTAATGCTGTATGGTCACATCAGT
Found at i:3918206 original size:26 final size:24
Alignment explanation
Indices: 3918166--3918225 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
3918156 TTATTTTATT
* * *
3918166 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
3918190 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
3918216 AAATAAATAT
1 AAATAAATAT
3918226 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:3918237 original size:22 final size:22
Alignment explanation
Indices: 3918196--3918254 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
3918186 ATAATAAATC
* *
3918196 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
3918216 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
3918238 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
3918255 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:3922638 original size:47 final size:47
Alignment explanation
Indices: 3922574--3922684 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
3922564 GACATTGAGT
* *
3922574 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGCTC
* * *
3922621 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGCTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGCTC
3922668 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
3922685 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGCTC
Found at i:3927438 original size:34 final size:34
Alignment explanation
Indices: 3927400--3927468 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
3927390 CCTTACTTAA
3927400 AGAATTTCTTCATGAAACTTTAACACATGCATAT
1 AGAATTTCTTCATGAAACTTTAACACATGCATAT
3927434 AGAATTTCTTCATGAAACTTTAACACATGCATAT
1 AGAATTTCTTCATGAAACTTTAACACATGCATAT
3927468 A
1 A
3927469 CTCATATTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (34 bp):
AGAATTTCTTCATGAAACTTTAACACATGCATAT
Found at i:3929804 original size:92 final size:89
Alignment explanation
Indices: 3929693--3929870 Score: 275
Period size: 92 Copynumber: 2.0 Consensus size: 89
3929683 ATCTCCATTA
*
3929693 CCCAATCTCTCATTGGAATTTTATTAAAAATTTATATTGATATATTAATAATATTATTAAATAAT
1 CCCAATCTCTCATTGGAATTTTATTAAAAATTTATAGTGATATATTAATAATATTATTAAATAAT
3929758 AATTAAAAAATGAAATTAAAATTGCTG
66 AA-T--AAAATGAAATTAAAATTGCTG
* * ** *
3929785 CCCACTCTCTCATTGGAATTTTATTAAATATTTATAGTGATATATTAATTTTATTATTAGATAAT
1 CCCAATCTCTCATTGGAATTTTATTAAAAATTTATAGTGATATATTAATAATATTATTAAATAAT
3929850 AATAAAATGAAATTAAAATTG
66 AATAAAATGAAATTAAAATTG
3929871 AACCAGGGCA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 18 0.22
91 1 0.01
92 61 0.76
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (89 bp):
CCCAATCTCTCATTGGAATTTTATTAAAAATTTATAGTGATATATTAATAATATTATTAAATAAT
AATAAAATGAAATTAAAATTGCTG
Found at i:3930890 original size:2 final size:2
Alignment explanation
Indices: 3930883--3930917 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3930873 ATTATGAATA
3930883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3930918 AAAGTATCAA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3934694 original size:175 final size:176
Alignment explanation
Indices: 3934398--3934743 Score: 615
Period size: 175 Copynumber: 2.0 Consensus size: 176
3934388 ATTCAGGAGG
3934398 TTGGGATTGAGAAAACCTGATATCTTGTTCGTGAGCTTGGGAAGATCTAATATTTGATTTTTCTC
1 TTGGGATTGAGAAAACCTGATATCTTGTTCGTGAGCTTGGGAAGATCTAATATTTGATTTTTCTC
* * *
3934463 CACTATTAACAAAAGGTTAAGGAACTGATTGATCATTATTGCTTTTAGTTACCCTTTTTTCGAAA
66 CACTAATAACAAAAGGTTAAGGAACTGATTGATCATAATTGCTTTTAGTCACCCTTTTTTCGAAA
*
3934528 AAAGATTCGGTCTTTTTGTTGACCATTATTTAATCTGAAAAGGAAA
131 AAAGATTCGGTCTTTTTGTTGACCATAATTTAATCTGAAAAGGAAA
3934574 TTGGGATTGAGAAAACCTGATATCTTGTTCGTGAGCTT-GGAAGATCTAATATTTGATTTTTCTC
1 TTGGGATTGAGAAAACCTGATATCTTGTTCGTGAGCTTGGGAAGATCTAATATTTGATTTTTCTC
* *
3934638 CACTAATAACAAAAGGTTAAGGAATTGATTGATCGTAATTGCTTTCT-GTCACCCTTTTTTCGAA
66 CACTAATAACAAAAGGTTAAGGAACTGATTGATCATAATTGCTTT-TAGTCACCCTTTTTTCGAA
3934702 AAAAGATTCGGTCTTTTTGTTGACCATAATTTAATCTGAAAA
130 AAAAGATTCGGTCTTTTTGTTGACCATAATTTAATCTGAAAA
3934744 ACCTGAAGAC
Statistics
Matches: 163, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
175 124 0.76
176 39 0.24
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (176 bp):
TTGGGATTGAGAAAACCTGATATCTTGTTCGTGAGCTTGGGAAGATCTAATATTTGATTTTTCTC
CACTAATAACAAAAGGTTAAGGAACTGATTGATCATAATTGCTTTTAGTCACCCTTTTTTCGAAA
AAAGATTCGGTCTTTTTGTTGACCATAATTTAATCTGAAAAGGAAA
Found at i:3935864 original size:15 final size:15
Alignment explanation
Indices: 3935844--3935900 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
3935834 ATTCAATATT
3935844 AATATTTTAATAATA
1 AATATTTTAATAATA
*
3935859 AATATTTATTACAGTTATA
1 AATA-TT-TTA-A-TAATA
*
3935878 AATATATTAATAATA
1 AATATTTTAATAATA
*
3935893 AATGTTTT
1 AATATTTT
3935901 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 14 0.42
16 3 0.09
17 6 0.18
18 2 0.06
19 8 0.24
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:3941730 original size:26 final size:25
Alignment explanation
Indices: 3941696--3941744 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
3941686 TTTTTTAAGA
*
3941696 ATTTCAAAATTTTGTTAGTGTTCATTT
1 ATTTCAAAATTATG-T-GTGTTCATTT
3941723 ATTT-AAAATTATGTGTGTTCAT
1 ATTTCAAAATTATGTGTGTTCAT
3941745 GTTCGTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 1 0.05
26 8 0.38
27 4 0.19
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (25 bp):
ATTTCAAAATTATGTGTGTTCATTT
Found at i:3941844 original size:35 final size:35
Alignment explanation
Indices: 3941770--3941844 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
3941760 GTTCACAATC
* *
3941770 ATGTTCATTTAACTTAATCAAACATGTTCATGAAT
1 ATGTTCATTTAACTTAACCAAACATGTTCATGAAA
* *
3941805 ATGTTCATTTAACTTAACCGAATATGTTCAT-AACA
1 ATGTTCATTTAACTTAACCAAACATGTTCATGAA-A
3941840 ATGTT
1 ATGTT
3941845 AATAAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (35 bp):
ATGTTCATTTAACTTAACCAAACATGTTCATGAAA
Found at i:3945310 original size:3 final size:3
Alignment explanation
Indices: 3945271--3945397 Score: 62
Period size: 3 Copynumber: 42.3 Consensus size: 3
3945261 AGTTTTATAT
* * * *
3945271 TTA TCA TTA TTA TGT- TTA TTA ATA TTT TTA ATA TTA TTA TT- TCTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * * * *
3945316 TTA TTA CTA TTA CTG TTG TT- TTAA TTA GTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * ** **
3945361 TTG GTA TTA TTA CCA CCA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3945398 CATACTATTA
Statistics
Matches: 93, Mismatches: 25, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
2 4 0.04
3 85 0.91
4 4 0.04
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:3945681 original size:3 final size:3
Alignment explanation
Indices: 3945673--3945718 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3945663 TTTTGTCATA
3945673 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3945719 TTCTTTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3951705 original size:49 final size:48
Alignment explanation
Indices: 3951651--3951747 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
3951641 ATAAAGAGGG
* * *
3951651 TTTAAAATAAATAATATATAAAATAGTTT-AACTACATAATGTATATAAA
1 TTTAAAATAAATAATATAT-AAA-AGTTTAAAATAAATAACGTATATAAA
*
3951700 TTTAAAATAAATAATATGTAAAAGTTTAAAATAAATAACGTATATAAA
1 TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAACGTATATAAA
3951748 AAGAAAATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 5 0.12
48 20 0.47
49 18 0.42
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (48 bp):
TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAACGTATATAAA
Found at i:3951727 original size:24 final size:24
Alignment explanation
Indices: 3951599--3951748 Score: 103
Period size: 24 Copynumber: 6.2 Consensus size: 24
3951589 ATTATATAAA
* * * *
3951599 AAAAATTTAAAATAAACAATGTAG
1 AAAAGTTTAAAATAAATAATATAT
*
3951623 AACAA-TTTAAAATAACTAATA-A-
1 AA-AAGTTTAAAATAAATAATATAT
**
3951645 AGAGGGTTTAAAATAAATAATATAT
1 A-AAAGTTTAAAATAAATAATATAT
* * *
3951670 AAAATAGTTT-AACTACATAATGTAT
1 -AAA-AGTTTAAAATAAATAATATAT
*
3951695 ATAAA-TTTAAAATAAATAATATGT
1 A-AAAGTTTAAAATAAATAATATAT
3951719 AAAAGTTTAAAATAAATAACGTATAT
1 AAAAGTTTAAAATAAATAA--TATAT
3951745 AAAA
1 AAAA
3951749 AGAAAATCAT
Statistics
Matches: 98, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
22 1 0.01
23 23 0.23
24 44 0.45
25 17 0.17
26 13 0.13
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAAGTTTAAAATAAATAATATAT
Found at i:3953570 original size:87 final size:87
Alignment explanation
Indices: 3953468--3954070 Score: 831
Period size: 86 Copynumber: 7.0 Consensus size: 87
3953458 AACTTGTTAT
*
3953468 CCTACTACTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
3953533 CCCTTCGTCTTCGATCTGTTTC
66 CCCTTCGTCTTCGATCTGTTTC
* *
3953555 CCTACTGCTTGGGGGGTTAAGATCTGTAAATTCAGCCAGTTACCCTACTGCTTAGGGGGTTAAGG
1 CCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
*
3953620 CCCTTCGCCTTCGATCTGTTTC
66 CCCTTCGTCTTCGATCTGTTTC
*
3953642 CCTACTGCTTA-GGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
3953706 CCCTTCGTCTTCGATCTGTTTC
66 CCCTTCGTCTTCGATCTGTTTC
*
3953728 CCTACTACTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
3953793 CCCTTCGTCTTCGATCTGTTTC
66 CCCTTCGTCTTCGATCTGTTTC
*** * * * *
3953815 CCTACTGCTTAGAAAGATAAGATCTGT-AATTCAACCTGTTACCTTACTGCTTAGGGGTTTAAGG
1 CCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
** **
3953879 TTCTTCGTCTTCGATCT-ACTC
66 CCCTTCGTCTTCGATCTGTTTC
* * * * * * *
3953900 CACTATTGCTTAGGGAGATAAGATCTG-CAATTTAACCTGTTACCCTACTGCTTAGGGGTTTAAG
1 C-CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
** * *
3953964 GTTCTTCATCTTCGATCTG-CTC
65 GCCCTTCGTCTTCGATCTGTTTC
* * * * * *
3953986 CACTACTGCTTAGGGAGATAAGATCTG-CAATGCAGTCTGTTACCCTACTGCTTAGGGGTTTAAG
1 C-CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
*
3954050 ACCCTTCGTCTTCGATCTGTT
65 GCCCTTCGTCTTCGATCTGTT
3954071 ACACCATTCT
Statistics
Matches: 473, Mismatches: 38, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
85 3 0.01
86 281 0.59
87 189 0.40
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (87 bp):
CCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
CCCTTCGTCTTCGATCTGTTTC
Found at i:3953772 original size:173 final size:173
Alignment explanation
Indices: 3953468--3954070 Score: 829
Period size: 173 Copynumber: 3.5 Consensus size: 173
3953458 AACTTGTTAT
* *
3953468 CCTACTACTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CCTACTGCTTA-GGGGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
* *
3953533 CCCTTCGTCTTCGATCTGTTTCCCTACTGCTTGGGGGGTTAAGATCTGTAAATTCAGCCAGTTAC
65 CCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTAC
*
3953598 CCTACTGCTTAGGGGGTTAAGGCCCTTCGCCTTCGATCTGTTTC
130 CCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTC
* *
3953642 CCTACTGCTTAGGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
1 CCTACTGCTTAGGGGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
*
3953707 CCTTCGTCTTCGATCTGTTTCCCTACTACTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACC
66 CCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACC
3953772 CTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTC
131 CTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTC
** * * *
3953815 CCTACTGCTTAGAAAGATAAGATCTGT-AATTCAACCTGTTACCTTACTGCTTAGGGGTTTAAGG
1 CCTACTGCTTAG-GGGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
** ** * * * * * *
3953879 TTCTTCGTCTTCGATCT-ACTCCACTATTGCTTAGGGAGATAAGATCTG-CAATTTAACCTGTTA
65 CCCTTCGTCTTCGATCTGTTTCC-CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTA
* ** * *
3953942 CCCTACTGCTTAGGGGTTTAAGGTTCTTCATCTTCGATCTG-CTC
129 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTC
* * * *
3953986 CACTACTGCTTAGGGAGATAAGATCTG-CAATGCAGTCTGTTACCCTACTGCTTAGGGGTTTAAG
1 C-CTACTGCTTAGGG-GATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
*
3954050 ACCCTTCGTCTTCGATCTGTT
64 GCCCTTCGTCTTCGATCTGTT
3954071 ACACCATTCT
Statistics
Matches: 383, Mismatches: 40, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
171 3 0.01
172 121 0.32
173 238 0.62
174 21 0.05
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (173 bp):
CCTACTGCTTAGGGGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
CCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACC
CTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTGTTTC
Found at i:3953996 original size:44 final size:44
Alignment explanation
Indices: 3953859--3954000 Score: 141
Period size: 44 Copynumber: 3.3 Consensus size: 44
3953849 CCTGTTACCT
* *
3953859 TACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTACTCCAC
1 TACTGCTTAGGGGTTTAAGGTTCTTCATCTTCGATCTGCTCCAC
* * * * * * *
3953903 TATTGCTTAGGGAG-ATAA-GATCTGCAAT-TT-AACCTGTTACC-C
1 TACTGCTTAGGG-GTTTAAGGTTCTTC-ATCTTCGATCTGCT-CCAC
3953945 TACTGCTTAGGGGTTTAAGGTTCTTCATCTTCGATCTGCTCCAC
1 TACTGCTTAGGGGTTTAAGGTTCTTCATCTTCGATCTGCTCCAC
3953989 TACTGCTTAGGG
1 TACTGCTTAGGG
3954001 AGATAAGATC
Statistics
Matches: 74, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
41 1 0.01
42 21 0.28
43 18 0.24
44 33 0.45
45 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (44 bp):
TACTGCTTAGGGGTTTAAGGTTCTTCATCTTCGATCTGCTCCAC
Found at i:3962129 original size:19 final size:20
Alignment explanation
Indices: 3962105--3962147 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
3962095 GGTCTTTTCG
* *
3962105 TGAAATTTAATGCACATG-A
1 TGAAATGTAATGCAAATGAA
3962124 TGAAATGTAATGCAAATGAA
1 TGAAATGTAATGCAAATGAA
3962144 TGAA
1 TGAA
3962148 TGCAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGAA
Found at i:3966172 original size:49 final size:48
Alignment explanation
Indices: 3966118--3966214 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
3966108 ATAAAGAGGG
* *
3966118 TTTAAAATAAATAATATATAAAATAGTTTAA-CTACATAATGTATATAAA
1 TTTAAAATAAATAATATAT-AAA-AGTTTAAGATAAATAATGTATATAAA
*
3966167 TTTAAAATAAATAATATGTAAAAGTTTAAGATAAATAATGTATATAAA
1 TTTAAAATAAATAATATATAAAAGTTTAAGATAAATAATGTATATAAA
3966215 AGAAAATCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 7 0.16
48 19 0.43
49 18 0.41
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (48 bp):
TTTAAAATAAATAATATATAAAAGTTTAAGATAAATAATGTATATAAA
Found at i:3966194 original size:24 final size:24
Alignment explanation
Indices: 3966060--3966216 Score: 99
Period size: 24 Copynumber: 6.5 Consensus size: 24
3966050 AAGGAACATT
* * *
3966060 ATATAAAAAAATTTAAAATAAACA
1 ATATATAAAAGTTTAAAATAAATA
* * *
3966084 ATGTAGAACAA-TTTAAAATAACTA
1 ATATATAA-AAGTTTAAAATAAATA
**
3966108 ATA-A-AGAGGGTTTAAAATAAATA
1 ATATATA-AAAGTTTAAAATAAATA
* *
3966131 ATATATAAAATAGTTT-AACTACATA
1 ATATAT-AAA-AGTTTAAAATAAATA
*
3966156 ATGTATATAAA-TTTAAAATAAATA
1 ATATATA-AAAGTTTAAAATAAATA
* *
3966180 ATATGTAAAAGTTTAAGATAAATA
1 ATATATAAAAGTTTAAAATAAATA
3966204 ATGTATATAAAAG
1 A--TATATAAAAG
3966217 AAAATCATAA
Statistics
Matches: 102, Mismatches: 19, Indels: 22
0.71 0.13 0.15
Matches are distributed among these distances:
22 1 0.01
23 23 0.23
24 47 0.46
25 17 0.17
26 14 0.14
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.31
Consensus pattern (24 bp):
ATATATAAAAGTTTAAAATAAATA
Found at i:3966397 original size:2 final size:2
Alignment explanation
Indices: 3966390--3966418 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3966380 AAGAGAATTA
3966390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3966419 AAGATCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3974271 original size:29 final size:29
Alignment explanation
Indices: 3974233--3974335 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
3974223 TAATCAGCCG
*
3974233 CGCACACTTAGTGCCATATACTTTAAACT
1 CGCACACTTAGTGCCATACACTTTAAACT
* * * *
3974262 CGCACGCTTAGTGCCATGCATTTTAAGCT
1 CGCACACTTAGTGCCATACACTTTAAACT
* *
3974291 CGCACACTTAGTGCCATGCA-TTTCAAGCT
1 CGCACACTTAGTGCCATACACTTT-AAACT
*
3974320 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
3974336 ATCTCTCAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
28 3 0.05
29 63 0.95
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACACTTTAAACT
Found at i:3978460 original size:34 final size:34
Alignment explanation
Indices: 3978417--3978487 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
3978407 CTGCTTCACC
3978417 TTCCCTACCAACCTTGGGTTTCTTCTCTGCCATT
1 TTCCCTACCAACCTTGGGTTTCTTCTCTGCCATT
3978451 TTCCCTACCAACCTTGGGTTTCTTCTCTGCCATT
1 TTCCCTACCAACCTTGGGTTTCTTCTCTGCCATT
3978485 TTC
1 TTC
3978488 TTACTCAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.11, C:0.35, G:0.11, T:0.42
Consensus pattern (34 bp):
TTCCCTACCAACCTTGGGTTTCTTCTCTGCCATT
Found at i:3979190 original size:29 final size:29
Alignment explanation
Indices: 3979127--3979198 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
3979117 ATTCACAATA
* *
3979127 AATTGAGCCTTCAACATCTATTTTCATGC
1 AATTGACCCTTCAACATCTATTTTCATCC
*
3979156 ATTTGAACCCTTCAA-ATCTATTTTCATCC
1 AATTG-ACCCTTCAACATCTATTTTCATCC
*
3979185 AATTGAGCCTTCAA
1 AATTGACCCTTCAA
3979199 TCTGACAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.22
29 21 0.57
30 8 0.22
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (29 bp):
AATTGACCCTTCAACATCTATTTTCATCC
Found at i:3982692 original size:13 final size:13
Alignment explanation
Indices: 3982674--3982717 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 13
3982664 ACACATACCA
3982674 ATTCTGTAGGAAT
1 ATTCTGTAGGAAT
3982687 ATTCTGTA--AAT
1 ATTCTGTAGGAAT
3982698 ATT-T-TAGGAAT
1 ATTCTGTAGGAAT
*
3982709 ATTTTGTAG
1 ATTCTGTAG
3982718 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
9 2 0.07
10 1 0.04
11 12 0.44
12 1 0.04
13 11 0.41
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (13 bp):
ATTCTGTAGGAAT
Found at i:3982708 original size:22 final size:22
Alignment explanation
Indices: 3982680--3982724 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3982670 ACCAATTCTG
3982680 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
3982702 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
3982724 T
1 T
3982725 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:3987227 original size:22 final size:22
Alignment explanation
Indices: 3987199--3987243 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3987189 AGGGGGAGTG
3987199 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
3987221 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
3987243 T
1 T
3987244 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:3994472 original size:15 final size:15
Alignment explanation
Indices: 3994452--3994500 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
3994442 AACCTTCTGA
*
3994452 TGATTCTCTACCAAT
1 TGATTCTCTACCAGT
*
3994467 TGATTCTCTAACAGT
1 TGATTCTCTACCAGT
3994482 TGATTCTCTACCAGT
1 TGATTCTCTACCAGT
3994497 TGAT
1 TGAT
3994501 GCAATGGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.41
Consensus pattern (15 bp):
TGATTCTCTACCAGT
Found at i:4003261 original size:17 final size:17
Alignment explanation
Indices: 4003215--4003262 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
4003205 AAAATGATCA
* *
4003215 ATTTATTTTTTTATTTT
1 ATTTATTTTATTAATTT
* * *
4003232 ATATATATAATTAATTT
1 ATTTATTTTATTAATTT
4003249 ATTTATTTTATTAA
1 ATTTATTTTATTAA
4003263 ATGAATAAAA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTATTTTATTAATTT
Found at i:4003600 original size:28 final size:28
Alignment explanation
Indices: 4003546--4003606 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
4003536 AAAATTTTAT
* *
4003546 TATAAAAATATTTTATATATTATAAAAA
1 TATAAAAATATTTCATATATTAAAAAAA
* *
4003574 TATAAAAATATATTCATTTA-TAAAAAAT
1 TATAAAAATAT-TTCATATATTAAAAAAA
4003602 TATAA
1 TATAA
4003607 TAGAGTATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TATAAAAATATTTCATATATTAAAAAAA
Found at i:4004571 original size:23 final size:23
Alignment explanation
Indices: 4004541--4004587 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4004531 TGAATATATT
* *
4004541 ATTACATGCGTAAATTTTACGGA
1 ATTACATGCATAAATTTTAAGGA
4004564 ATTACATGCATAAATTTTAAGGA
1 ATTACATGCATAAATTTTAAGGA
4004587 A
1 A
4004588 AAAATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (23 bp):
ATTACATGCATAAATTTTAAGGA
Found at i:4021312 original size:12 final size:13
Alignment explanation
Indices: 4021289--4021317 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4021279 ATTTGACAAA
4021289 AAAAAACAAAAAC
1 AAAAAACAAAAAC
4021302 AAAAAAC-AAAAC
1 AAAAAACAAAAAC
4021314 AAAA
1 AAAA
4021318 CATGCAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:4023005 original size:6 final size:7
Alignment explanation
Indices: 4022987--4023012 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4022977 TACAAATATT
4022987 TAAAAAA
1 TAAAAAA
4022994 TAAAAAA
1 TAAAAAA
4023001 TAAAAAA
1 TAAAAAA
4023008 TAAAA
1 TAAAA
4023013 CTAGATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:4038379 original size:24 final size:25
Alignment explanation
Indices: 4038347--4038397 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
4038337 TAAATACAAT
4038347 GTAATGCAAGCCTAAGAAGATG-AA
1 GTAATGCAAGCCTAAGAAGATGTAA
4038371 GTAATGCAAGCCTAAGAAGATGTAA
1 GTAATGCAAGCCTAAGAAGATGTAA
4038396 GT
1 GT
4038398 TCAAGCCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.20
Consensus pattern (25 bp):
GTAATGCAAGCCTAAGAAGATGTAA
Found at i:4038395 original size:21 final size:21
Alignment explanation
Indices: 4038345--4038404 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 21
4038335 CATAAATACA
4038345 ATGTAATGCAAGCCTAAGAAG
1 ATGTAATGCAAGCCTAAGAAG
4038366 ATGAAGTAATGCAAGCCTAAGAAG
1 AT---GTAATGCAAGCCTAAGAAG
*
4038390 ATGTAAGTTCAAGCC
1 ATGTAA-TGCAAGCC
4038405 AGATGACCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 6 0.18
22 7 0.21
24 21 0.62
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (21 bp):
ATGTAATGCAAGCCTAAGAAG
Found at i:4041907 original size:27 final size:28
Alignment explanation
Indices: 4041855--4041913 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
4041845 ACAGTTTATA
* *
4041855 GTTTAAGATTTAAAGTTTTTGTTTTAGG
1 GTTTAAGAGTTAAAGTTTTAGTTTTAGG
4041883 GTTT-AGAGTTAAAGTTTTAAG-TTTAGG
1 GTTTAAGAGTTAAAGTTTT-AGTTTTAGG
4041910 GTTT
1 GTTT
4041914 TTAAGATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (28 bp):
GTTTAAGAGTTAAAGTTTTAGTTTTAGG
Found at i:4053172 original size:16 final size:15
Alignment explanation
Indices: 4053147--4053180 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
4053137 ACTTTTGTAG
*
4053147 TATATATATATTTTA
1 TATATATATAATTTA
4053162 TATATTATATAATTTA
1 TATA-TATATAATTTA
4053178 TAT
1 TAT
4053181 CACATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATATATAATTTA
Found at i:4055589 original size:20 final size:20
Alignment explanation
Indices: 4055564--4055615 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
4055554 AACGCAAACG
** *
4055564 GAAAAAGATGAGTAAACCTA
1 GAAAAAGAAAAGTAAAACTA
4055584 GAAAAAGAAAAGTAAAACTA
1 GAAAAAGAAAAGTAAAACTA
4055604 GAAAAATGAAAA
1 GAAAAA-GAAAA
4055616 ACCGAATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.65, C:0.06, G:0.17, T:0.12
Consensus pattern (20 bp):
GAAAAAGAAAAGTAAAACTA
Found at i:4059852 original size:33 final size:33
Alignment explanation
Indices: 4059810--4059877 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
4059800 GTGTTTCAGT
4059810 CAAAATGAAAAGTTCAAAAACTATCTCAAAATA
1 CAAAATGAAAAGTTCAAAAACTATCTCAAAATA
4059843 CAAAATGAAAAGTTCAAAAACTATCTCAAAATA
1 CAAAATGAAAAGTTCAAAAACTATCTCAAAATA
4059876 CA
1 CA
4059878 TATTCTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.57, C:0.16, G:0.06, T:0.21
Consensus pattern (33 bp):
CAAAATGAAAAGTTCAAAAACTATCTCAAAATA
Found at i:4061142 original size:20 final size:20
Alignment explanation
Indices: 4061109--4061147 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4061099 GAATTAATTC
4061109 AAATTTAATACAAA-TTAAA
1 AAATTTAATACAAAGTTAAA
*
4061128 AAATTATAATTCAAAGTTAA
1 AAATT-TAATACAAAGTTAA
4061148 GTTTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AAATTTAATACAAAGTTAAA
Found at i:4069018 original size:9 final size:9
Alignment explanation
Indices: 4068998--4069060 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 9
4068988 TATTTTTTTA
4068998 TAAAAAATAT
1 TAAAAAA-AT
4069008 TAAAAAAAT
1 TAAAAAAAT
* *
4069017 TATAAAATT
1 TAAAAAAAT
4069026 TATAAAAAAT
1 TA-AAAAAAT
*
4069036 AGAAAAAATAT
1 -TAAAAAA-AT
4069047 TAAAAAAAT
1 TAAAAAAAT
4069056 ATAAA
1 -TAAA
4069061 CTTTTAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 13 0.30
10 27 0.63
11 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:4069028 original size:30 final size:30
Alignment explanation
Indices: 4068994--4069053 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4068984 CTAATATTTT
* *
4068994 TTTATAAAAAATATTAAAAAA-ATTATAAAA
1 TTTATAAAAAATA-GAAAAAATATTAAAAAA
4069024 TTTATAAAAAATAGAAAAAATATTAAAAAA
1 TTTATAAAAAATAGAAAAAATATTAAAAAA
4069054 ATATAAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (30 bp):
TTTATAAAAAATAGAAAAAATATTAAAAAA
Found at i:4069052 original size:38 final size:38
Alignment explanation
Indices: 4068999--4069084 Score: 111
Period size: 38 Copynumber: 2.2 Consensus size: 38
4068989 ATTTTTTTAT
*
4068999 AAAAAATATTAAAAAAATTATAAAATTTATAAAAAATAG
1 AAAAAATATTAAAAAAAATATAAAATTT-TAAAAAATAG
* * *
4069038 AAAAAATATT-AAAAAAATATAAACTTTTAAAAATTAT
1 AAAAAATATTAAAAAAAATATAAAATTTTAAAAAATAG
4069075 AAAAATATAT
1 AAAAA-ATAT
4069085 ATAATAGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 13 0.31
38 19 0.45
39 10 0.24
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (38 bp):
AAAAAATATTAAAAAAAATATAAAATTTTAAAAAATAG
Found at i:4069053 original size:39 final size:37
Alignment explanation
Indices: 4068999--4069084 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 37
4068989 ATTTTTTTAT
4068999 AAAAAATATTAAAAAAATTATAAAATTTATAAAAAATAG
1 AAAAAATATTAAAAAAA-TATAAAATTT-TAAAAAATAG
* * *
4069038 AAAAAATATTAAAAAAATATAAACTTTTAAAAATTAT
1 AAAAAATATTAAAAAAATATAAAATTTTAAAAAATAG
4069075 AAAAATATAT
1 AAAAA-ATAT
4069085 ATAATAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 13 0.30
38 13 0.30
39 17 0.40
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (37 bp):
AAAAAATATTAAAAAAATATAAAATTTTAAAAAATAG
Found at i:4069067 original size:18 final size:18
Alignment explanation
Indices: 4069001--4069070 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 18
4068991 TTTTTTATAA
*
4069001 AAAATATTAAAAAAATTAT
1 AAAATTTTAAAAAAA-TAT
* *
4069020 AAAATTTATAAAAAATAGAA
1 AAAATTT-TAAAAAA-ATAT
*
4069040 AAAATATTAAAAAAATAT
1 AAAATTTTAAAAAAATAT
*
4069058 AAACTTTTAAAAA
1 AAAATTTTAAAAA
4069071 TTATAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
18 13 0.32
19 13 0.32
20 14 0.34
21 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (18 bp):
AAAATTTTAAAAAAATAT
Found at i:4069079 original size:9 final size:9
Alignment explanation
Indices: 4069001--4069217 Score: 107
Period size: 9 Copynumber: 23.0 Consensus size: 9
4068991 TTTTTTATAA
*
4069001 AAAATATTAA
1 AAAA-ATTAT
4069011 AAAAATTAT
1 AAAAATTAT
*
4069020 AAAATTTAT
1 AAAAATTAT
* *
4069029 AAAAAATAG
1 AAAAATTAT
*
4069038 AAAAAATATT
1 AAAAATTA-T
*
4069048 AAAAA-AAT
1 AAAAATTAT
* *
4069056 ATAAACTTTT
1 A-AAAATTAT
4069066 AAAAATTAT
1 AAAAATTAT
4069075 AAAAATATAT
1 AAAAAT-TAT
* *
4069085 ATAATAGTAT
1 A-AAAATTAT
*
4069095 AAATATTAT
1 AAAAATTAT
4069104 AATAAA-TAT
1 AA-AAATTAT
4069113 AATAAATTAT
1 AA-AAATTAT
4069123 -AAAATTAAT
1 AAAAATT-AT
*
4069132 AAAAATTTT
1 AAAAATTAT
**
4069141 AAATTTTAT
1 AAAAATTAT
*
4069150 AAAAACATATT
1 AAAAA-TTA-T
*
4069161 AAAATTCTAT
1 AAAAAT-TAT
* *
4069171 AACAATCAT
1 AAAAATTAT
*
4069180 AAAAAAGTAT
1 -AAAAATTAT
*
4069190 TAAAATTAT
1 AAAAATTAT
*
4069199 ATAAACTTAT
1 A-AAAATTAT
4069209 AAAAATTAT
1 AAAAATTAT
4069218 TATAAAAACT
Statistics
Matches: 157, Mismatches: 36, Indels: 29
0.71 0.16 0.13
Matches are distributed among these distances:
8 7 0.04
9 89 0.57
10 51 0.32
11 10 0.06
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:4069126 original size:75 final size:74
Alignment explanation
Indices: 4069021--4069159 Score: 165
Period size: 75 Copynumber: 1.9 Consensus size: 74
4069011 AAAAATTATA
* *
4069021 AAATTTATAAAAAATAGAAAAAATATTAAAA-AAATATAAACTTTTAAAAATTATAAAAATATAT
1 AAATTTATAAAAAATAGAAAAAATATTAAAATAAATA-AAAATTTTAAAAATTATAAAAACATAT
4069085 ATAATAGTAT
65 ATAATAGTAT
* * * * **
4069095 AAATATTATAATAAATATAATAAAT-TATAAAATTAATAAAAATTTTAAATTTTATAAAAACATA
1 AAAT-TTATAAAAAATAGAAAAAATAT-TAAAATAAATAAAAATTTTAAAAATTATAAAAACATA
4069159 T
64 T
4069160 TAAAATTCTA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
74 5 0.09
75 45 0.83
76 4 0.07
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (74 bp):
AAATTTATAAAAAATAGAAAAAATATTAAAATAAATAAAAATTTTAAAAATTATAAAAACATATA
TAATAGTAT
Found at i:4069215 original size:19 final size:18
Alignment explanation
Indices: 4069068--4069223 Score: 79
Period size: 19 Copynumber: 8.2 Consensus size: 18
4069058 AAACTTTTAA
4069068 AAATTATAAAAATATATAT
1 AAATTATAAAAAT-TATAT
* *
4069087 AATAGTATAAATATTATAAT
1 AA-ATTATAAAAATTAT-AT
4069107 AAA-TATAATAAATTATA-
1 AAATTATAA-AAATTATAT
4069124 AAATTAATAAAAATT-T-T
1 AAATT-ATAAAAATTATAT
*
4069141 AAATTTTATAAAAA-CATATT
1 AAA--TTATAAAAATTATA-T
* * *
4069161 AAAATTCTATAACAATCATAAA
1 -AAA-T-TATAAAAATTAT-AT
* *
4069183 AAAGTATTAAAATTATAT
1 AAATTATAAAAATTATAT
4069201 AAACTTATAAAAATTATTAT
1 AAA-TTATAAAAATTA-TAT
4069221 AAA
1 AAA
4069224 AACTTGAATT
Statistics
Matches: 107, Mismatches: 13, Indels: 33
0.70 0.08 0.22
Matches are distributed among these distances:
17 7 0.07
18 24 0.22
19 37 0.35
20 22 0.21
21 13 0.12
22 3 0.03
23 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (18 bp):
AAATTATAAAAATTATAT
Found at i:4069978 original size:30 final size:30
Alignment explanation
Indices: 4069935--4070006 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
4069925 GAAATTCAAT
* * *
4069935 AAATAAAAAATAAA-ATTATTAAGATTGATA
1 AAATATAATATAAATATTATTAAAATT-ATA
* * *
4069965 TAATATAATATAAATATTTTTAAAATTTTA
1 AAATATAATATAAATATTATTAAAATTATA
4069995 AAATATAATATA
1 AAATATAATATA
4070007 GGCGGGCTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (30 bp):
AAATATAATATAAATATTATTAAAATTATA
Found at i:4077975 original size:35 final size:36
Alignment explanation
Indices: 4077911--4077995 Score: 120
Period size: 35 Copynumber: 2.4 Consensus size: 36
4077901 GTGGCATTTT
4077911 ATATTTTTAAAAATTTACTTATAAAAATAAAAAAAATG
1 ATATTTTTAAAAA--TACTTATAAAAATAAAAAAAATG
*
4077949 ATATTTTTAAAAA-ATTTATAAAAATAAAAAAAATG
1 ATATTTTTAAAAATACTTATAAAAATAAAAAAAATG
*
4077984 ATA-ATTTAAAAA
1 ATATTTTTAAAAA
4077996 CGTATTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 8 0.18
35 24 0.53
38 13 0.29
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (36 bp):
ATATTTTTAAAAATACTTATAAAAATAAAAAAAATG
Found at i:4077993 original size:17 final size:17
Alignment explanation
Indices: 4077938--4077995 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
4077928 CTTATAAAAA
*
4077938 TAAAAAAAATGATATTT
1 TAAAAAAAATGATAATT
* * * **
4077955 TTAAAAAATTTATAAAAA
1 TAAAAAAAATGAT-AATT
4077973 TAAAAAAAATGATAATT
1 TAAAAAAAATGATAATT
4077990 TAAAAA
1 TAAAAA
4077996 CGTATTAAAA
Statistics
Matches: 29, Mismatches: 11, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
17 18 0.62
18 11 0.38
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
TAAAAAAAATGATAATT
Found at i:4080953 original size:2 final size:2
Alignment explanation
Indices: 4080946--4080978 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4080936 ATATGCAAAG
4080946 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
4080979 TTATGATTAG
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:4086603 original size:25 final size:25
Alignment explanation
Indices: 4086569--4086619 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
4086559 TTCCTTATAA
**
4086569 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
4086594 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
4086619 A
1 A
4086620 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:4086618 original size:12 final size:12
Alignment explanation
Indices: 4086572--4086619 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
4086562 CTTATAAACT
4086572 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
4086584 TTCTATTAGGACT
1 TTAAATTAGGA-A
4086597 TTAAATTAGGAA
1 TTAAATTAGGAA
*
4086609 TTAGATTAGGA
1 TTAAATTAGGA
4086620 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:4091262 original size:25 final size:25
Alignment explanation
Indices: 4091228--4091278 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
4091218 TTCCTTATAA
**
4091228 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
4091253 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
4091278 A
1 A
4091279 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:4091277 original size:12 final size:12
Alignment explanation
Indices: 4091231--4091278 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
4091221 CTTATAAACT
4091231 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
4091243 TTCTATTAGGACT
1 TTAAATTAGGA-A
4091256 TTAAATTAGGAA
1 TTAAATTAGGAA
*
4091268 TTAGATTAGGA
1 TTAAATTAGGA
4091279 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:4095731 original size:15 final size:15
Alignment explanation
Indices: 4095711--4095746 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
4095701 GGAAATGGAA
4095711 AAAAAAAATAATGAC
1 AAAAAAAATAATGAC
4095726 AAAAAAAATAATGAC
1 AAAAAAAATAATGAC
4095741 AAAAAA
1 AAAAAA
4095747 TTTCAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.11
Consensus pattern (15 bp):
AAAAAAAATAATGAC
Found at i:4102648 original size:21 final size:22
Alignment explanation
Indices: 4102622--4102670 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
4102612 AATAAAAATG
*
4102622 TAAATAATAT-ATTTAAGA-ACA
1 TAAATAATATAATTCAAGACA-A
*
4102643 TAAATAGTATAATTCAAGACAA
1 TAAATAATATAATTCAAGACAA
4102665 TAAATA
1 TAAATA
4102671 TCACAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 14 0.58
23 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
TAAATAATATAATTCAAGACAA
Found at i:4104665 original size:2 final size:2
Alignment explanation
Indices: 4104658--4104694 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4104648 GTGATATGGT
*
4104658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4104695 TATTATCTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4104878 original size:38 final size:38
Alignment explanation
Indices: 4104835--4104946 Score: 129
Period size: 39 Copynumber: 2.9 Consensus size: 38
4104825 AAAATTTATG
4104835 TGGTATTATATCCGGGTTAAATCCCGCAGGCTTAATGC
1 TGGTATTATATCCGGGTTAAATCCCGCAGGCTTAATGC
* * *
4104873 TGGTATTATATCCGGACTTATAGT-CCGCAGG-TCTAGTGC
1 TGGTATTATATCCGG-GTTA-AATCCCGCAGGCT-TAATGC
*
4104912 TGGTAATAGATATCCGGGTTAAATCCCGCAGGCTT
1 TGGT-AT-TATATCCGGGTTAAATCCCGCAGGCTT
4104947 TGTGCTAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
38 16 0.26
39 21 0.34
40 15 0.25
41 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (38 bp):
TGGTATTATATCCGGGTTAAATCCCGCAGGCTTAATGC
Found at i:4112746 original size:36 final size:36
Alignment explanation
Indices: 4112694--4112766 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
4112684 TGCTTACTTG
*
4112694 TTATGATATATGTAAACATAGTCTATTTTATAATAT
1 TTATGATATATATAAACATAGTCTATTTTATAATAT
4112730 TTATGATATATATAAACATAGTCTATTTTATAATAT
1 TTATGATATATATAAACATAGTCTATTTTATAATAT
4112766 T
1 T
4112767 GGTTGGCTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (36 bp):
TTATGATATATATAAACATAGTCTATTTTATAATAT
Found at i:4116271 original size:2 final size:2
Alignment explanation
Indices: 4116264--4116298 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4116254 TTGATGTATA
4116264 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4116299 GAGAGTATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
TG
Found at i:4123624 original size:27 final size:27
Alignment explanation
Indices: 4123594--4123648 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
4123584 AAAAAATGTT
4123594 ATTCCTGAATTCATAGACATGTGAATG
1 ATTCCTGAATTCATAGACATGTGAATG
4123621 ATTCCTGAATTCATAGACATGTGAATG
1 ATTCCTGAATTCATAGACATGTGAATG
4123648 A
1 A
4123649 AAGTGAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (27 bp):
ATTCCTGAATTCATAGACATGTGAATG
Found at i:4126437 original size:2 final size:2
Alignment explanation
Indices: 4126430--4126458 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4126420 AAACTCCTTA
4126430 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
4126459 AGAGAGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:4126463 original size:2 final size:2
Alignment explanation
Indices: 4126458--4126506 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
4126448 GTGTGTGTGT
4126458 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4126500 GA GA GA G
1 GA GA GA G
4126507 CTCACAGTCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4127313 original size:43 final size:44
Alignment explanation
Indices: 4127253--4127335 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
4127243 ATTTAACTAT
* *
4127253 TAATTTTTATATATTAT-ATTAA-TTTAGACTTAATTTTAAAAAA
1 TAATTTTTAAATATTATAAATAATTTTA-ACTTAATTTTAAAAAA
*
4127296 TAATTTTTAAA-ATTTATAAATAATTTTAATTTAATTTTAA
1 TAATTTTTAAATA-TTATAAATAATTTTAACTTAATTTTAA
4127336 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
42 1 0.03
43 14 0.41
44 15 0.44
45 4 0.12
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (44 bp):
TAATTTTTAAATATTATAAATAATTTTAACTTAATTTTAAAAAA
Found at i:4127387 original size:21 final size:21
Alignment explanation
Indices: 4127340--4127385 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4127330 TTTTAATTTT
* *
4127340 AAAATTTTTAAAAATATAATA
1 AAAAATTTAAAAAATATAATA
*
4127361 ATAAATTTAAAAAATAT-ATA
1 AAAAATTTAAAAAATATAATA
4127381 AAAAA
1 AAAAA
4127386 ATATAATAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATTTAAAAAATATAATA
Found at i:4127656 original size:14 final size:15
Alignment explanation
Indices: 4127637--4127676 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
4127627 TAATCATTTA
4127637 AAAATTATAAAT-AT
1 AAAATTATAAATAAT
4127651 AAAATTATTAAAATAAT
1 AAAATTA-T-AAATAAT
4127668 AAAATTATA
1 AAAATTATA
4127677 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.30
15 2 0.09
16 5 0.22
17 9 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATTATAAATAAT
Found at i:4128652 original size:2 final size:2
Alignment explanation
Indices: 4128647--4128695 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
4128637 AATGTAAAAG
4128647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4128689 AT AT AT A
1 AT AT AT A
4128696 CATTTATGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4135058 original size:29 final size:29
Alignment explanation
Indices: 4135015--4135078 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
4135005 TTGATAATAT
* *
4135015 TTGATTCTTTTTAATAGTATATGA-ACTAAA
1 TTGA-TCTATTTAATAATATA-GATACTAAA
*
4135045 TTGATCTATTTAATAATATAGATACTAAT
1 TTGATCTATTTAATAATATAGATACTAAA
4135074 TTGAT
1 TTGAT
4135079 AGAAATATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.07
29 24 0.80
30 4 0.13
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (29 bp):
TTGATCTATTTAATAATATAGATACTAAA
Found at i:4145670 original size:7 final size:7
Alignment explanation
Indices: 4145658--4145684 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4145648 GGACTAGAAA
4145658 ATTAATT
1 ATTAATT
4145665 ATTAATT
1 ATTAATT
4145672 ATTAATT
1 ATTAATT
4145679 ATTAAT
1 ATTAAT
4145685 CAACAGTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTAATT
Found at i:4155225 original size:31 final size:29
Alignment explanation
Indices: 4155190--4155249 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
4155180 GTGACCACTT
*
4155190 CGTAACAAAATGATAACATAAGTGACTAAAA
1 CGTAAC-AAATCA-AACATAAGTGACTAAAA
**
4155221 CGTAACATTTCAAACATAAGTGACTAAAA
1 CGTAACAAATCAAACATAAGTGACTAAAA
4155250 TATAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
30 3 0.12
31 6 0.23
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.22
Consensus pattern (29 bp):
CGTAACAAATCAAACATAAGTGACTAAAA
Done.