Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_pilon, 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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 38
Found at i:3970197 original size:21 final size:21
Alignment explanation
Indices: 3970069--3970210 Score: 124
Period size: 21 Copynumber: 6.7 Consensus size: 21
3970059 GGTTCTACGC
*
3970069 GGTCCTTCGGGACATATATGT
1 GGTCCTTAGGGACATATATGT
* * * *
3970090 GATCCTTTGGAACATATATGC
1 GGTCCTTAGGGACATATATGT
** *
3970111 ATTCCTTCA-GGACATATATTT
1 GGTCCTT-AGGGACATATATGT
** *
3970132 GGTCCTTTTGAACATATATGT
1 GGTCCTTAGGGACATATATGT
*
3970153 GGTCCTTAGGGACAATTCTATGT
1 GGTCCTTAGGGAC-A-TATATGT
*
3970176 GGTCCTTAGGGATATATATGT
1 GGTCCTTAGGGACATATATGT
*
3970197 GGTCCTTCGGGACA
1 GGTCCTTAGGGACA
3970211 ATTCTATGAG
Statistics
Matches: 94, Mismatches: 23, Indels: 8
0.75 0.18 0.06
Matches are distributed among these distances:
21 74 0.79
22 2 0.02
23 18 0.19
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (21 bp):
GGTCCTTAGGGACATATATGT
Found at i:3970236 original size:23 final size:23
Alignment explanation
Indices: 3970148--3970226 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
3970138 TTTGAACATA
3970148 TATGTGGTCCTTAGGGACAATTC
1 TATGTGGTCCTTAGGGACAATTC
* *
3970171 TATGTGGTCCTTAGGGA-TA-TA
1 TATGTGGTCCTTAGGGACAATTC
*
3970192 TATGTGGTCCTTCGGGACAATTC
1 TATGTGGTCCTTAGGGACAATTC
*
3970215 TATGAGGTCCTT
1 TATGTGGTCCTT
3970227 CGGAATAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.35
22 2 0.04
23 29 0.60
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (23 bp):
TATGTGGTCCTTAGGGACAATTC
Found at i:3971918 original size:24 final size:24
Alignment explanation
Indices: 3971852--3971920 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
3971842 AATATATATA
* *
3971852 TATAAAGAGAATCGAGTAAACGAGCT
1 TATAAACA-AATCG-GTAAACAAGCT
* *
3971878 TATAAAC-AACCAAGTAAACAAGCT
1 TATAAACAAATC-GGTAAACAAGCT
3971902 TATAAACAAATCGGTAAAC
1 TATAAACAAATCGGTAAAC
3971921 GAGTTTGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
24 26 0.74
25 3 0.09
26 6 0.17
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (24 bp):
TATAAACAAATCGGTAAACAAGCT
Found at i:3973227 original size:14 final size:14
Alignment explanation
Indices: 3973208--3973234 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3973198 GAAAATGTCT
3973208 ATTTTATTTATTTG
1 ATTTTATTTATTTG
3973222 ATTTTATTTATTT
1 ATTTTATTTATTT
3973235 TGTTTAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (14 bp):
ATTTTATTTATTTG
Found at i:3973416 original size:2 final size:2
Alignment explanation
Indices: 3973409--3973444 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3973399 CTATAATTGA
*
3973409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3973445 GAGTTAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3974594 original size:2 final size:2
Alignment explanation
Indices: 3974587--3974677 Score: 73
Period size: 2 Copynumber: 47.0 Consensus size: 2
3974577 GATCTTATTC
* * * *
3974587 AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AA AA AA AT CT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
3974626 AC AA AT AA AT -T AT AT TT CAT 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
3974668 AT AT AT AT AT
1 AT AT AT AT AT
3974678 TAAATTATAG
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
1 4 0.05
2 69 0.93
3 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3975240 original size:25 final size:26
Alignment explanation
Indices: 3975209--3975268 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
3975199 TTTTATAACA
3975209 TTTAAAATTGTTATA-AAAACAAAAT
1 TTTAAAATTGTTATATAAAACAAAAT
* * ** *
3975234 TTTAAAAGTGTTGTATAAAAGTATAT
1 TTTAAAATTGTTATATAAAACAAAAT
3975260 TTTAAAATT
1 TTTAAAATT
3975269 TAATTGTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (26 bp):
TTTAAAATTGTTATATAAAACAAAAT
Found at i:3975898 original size:29 final size:28
Alignment explanation
Indices: 3975868--3975930 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
3975858 AAAATATGAT
3975868 AAAAATAAAAGAAAAACAACATAAAAAATA
1 AAAAAT-AAAGAAAAACAA-ATAAAAAATA
* *
3975898 AAAAATGAAGAAAAACAAATAACAAATA
1 AAAAATAAAGAAAAACAAATAAAAAATA
3975926 AAAAA
1 AAAAA
3975931 AGTTAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 14 0.45
29 11 0.35
30 6 0.19
ACGTcount: A:0.79, C:0.06, G:0.05, T:0.10
Consensus pattern (28 bp):
AAAAATAAAGAAAAACAAATAAAAAATA
Found at i:3975919 original size:21 final size:19
Alignment explanation
Indices: 3975893--3975931 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
3975883 ACAACATAAA
3975893 AAATAAAAAATGAAGAAAAAC
1 AAATAAAAAAT-AA-AAAAAC
*
3975914 AAATAACAAATAAAAAAA
1 AAATAAAAAATAAAAAAA
3975932 GTTAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.10
Consensus pattern (19 bp):
AAATAAAAAATAAAAAAAC
Found at i:3975931 original size:29 final size:29
Alignment explanation
Indices: 3975876--3975930 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
3975866 ATAAAAATAA
3975876 AAGAAAAACAACATAAAAAATAAAAAATG
1 AAGAAAAACAACATAAAAAATAAAAAATG
*
3975905 AAGAAAAACAA-ATAACAAATAAAAAA
1 AAGAAAAACAACATAAAAAATAAAAAA
3975931 AGTTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.09
Consensus pattern (29 bp):
AAGAAAAACAACATAAAAAATAAAAAATG
Found at i:3977007 original size:24 final size:24
Alignment explanation
Indices: 3976978--3977024 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3976968 CGTTGGGCAA
*
3976978 CCCCTTAAACTGGACTGAAACATG
1 CCCCTTAAACTGGACCGAAACATG
* *
3977002 CCCCTTTAATTGGACCGAAACAT
1 CCCCTTAAACTGGACCGAAACAT
3977025 TGGACCCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (24 bp):
CCCCTTAAACTGGACCGAAACATG
Found at i:3977126 original size:9 final size:8
Alignment explanation
Indices: 3977085--3977125 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
3977075 AAATTAAACG
3977085 AATAA-AT
1 AATAATAT
3977092 AATAATAAT
1 AATAAT-AT
3977101 AATAATAT
1 AATAATAT
3977109 AATATATAT
1 AATA-ATAT
3977118 AAT-ATAT
1 AATAATAT
3977125 A
1 A
3977126 TTTCAAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 10 0.32
8 6 0.19
9 15 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AATAATAT
Found at i:3977332 original size:36 final size:38
Alignment explanation
Indices: 3977172--3977413 Score: 269
Period size: 37 Copynumber: 6.6 Consensus size: 38
3977162 TTTAAACAAG
* *
3977172 TTTTCAAAACCATATATCATATAA-TTTTCAAAAATGA
1 TTTTCAAAACTATATATTATATAAGTTTTCAAAAATGA
* *
3977209 TTTT-AAAA--A-ATATCATATAAGTTTTCAAAAAATGG
1 TTTTCAAAACTATATATTATATAAGTTTTC-AAAAATGA
3977244 TTTT-AAAACTATATATTATATAAGTTTTCAAAAAAT-A
1 TTTTCAAAACTATATATTATATAAGTTTTC-AAAAATGA
3977281 TTTTCAAAA-TCATATATTATATAAGTTTTC-AAAATGA
1 TTTTCAAAACT-ATATATTATATAAGTTTTCAAAAATGA
3977318 TTTT-AAAACTATATATTATATAAGTTTTC-AAAATGA
1 TTTTCAAAACTATATATTATATAAGTTTTCAAAAATGA
* *
3977354 TTTTAAAAACTATATATTATATATA-TTTTCAAAAACCG-
1 TTTTCAAAACTATATATTATATA-AGTTTTCAAAAA-TGA
* *
3977392 TTTGC-AAACTATATAATATATA
1 TTTTCAAAACTATATATTATATA
3977414 TATATATATA
Statistics
Matches: 185, Mismatches: 7, Indels: 26
0.85 0.03 0.12
Matches are distributed among these distances:
33 11 0.06
34 6 0.03
35 15 0.08
36 43 0.23
37 55 0.30
38 54 0.29
39 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (38 bp):
TTTTCAAAACTATATATTATATAAGTTTTCAAAAATGA
Found at i:3977332 original size:74 final size:72
Alignment explanation
Indices: 3977172--3977387 Score: 273
Period size: 73 Copynumber: 3.0 Consensus size: 72
3977162 TTTAAACAAG
* * *
3977172 TTTTCAAAACCATATATCATATAA-TTTTCAAAAATGATTTTAAAA-A-ATATCATATAAGTTTT
1 TTTT-AAAACTATATATTATATAAGTTTTCAAAAATGATTTTAAAACATATATTATATAAGTTTT
*
3977234 CAAAAAATGG
65 C--AAAATGA
3977244 TTTTAAAACTATATATTATATAAGTTTTCAAAAAAT-ATTTTCAAAATCATATATTATATAAGTT
1 TTTTAAAACTATATATTATATAAGTTTTC-AAAAATGATTTT-AAAA-CATATATTATATAAGTT
3977308 TTCAAAATGA
63 TTCAAAATGA
3977318 TTTTAAAACTATATATTATATAAGTTTTC-AAAATGATTTTAAAAACTATATATTATATATA-TT
1 TTTTAAAACTATATATTATATAAGTTTTCAAAAATGATTTT-AAAAC-ATATATTATATA-AGTT
3977381 TTCAAAA
63 TTCAAAA
3977388 ACCGTTTGCA
Statistics
Matches: 130, Mismatches: 5, Indels: 17
0.86 0.03 0.11
Matches are distributed among these distances:
71 17 0.13
72 20 0.15
73 40 0.31
74 36 0.28
75 1 0.01
76 16 0.12
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (72 bp):
TTTTAAAACTATATATTATATAAGTTTTCAAAAATGATTTTAAAACATATATTATATAAGTTTTC
AAAATGA
Found at i:3978545 original size:165 final size:164
Alignment explanation
Indices: 3977967--3979324 Score: 1469
Period size: 165 Copynumber: 8.2 Consensus size: 164
3977957 ATAATTTTAT
* * * * * * *
3977967 TGACAGATAGCCCTTCTTGCCTT-AGGCTATGCTGTAAATGATGTGCCCTAG-AGCCGAGTGTAG
1 TGACAGATAACCCTTCTAGCCTTGA-GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAA
* * * * * * *
3978030 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTAGCCTTGAGTTATACCGTAAATGATGTGCCG
65 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-
* * * *
3978095 TT-GAGCCGAGTGTAATCGAACTCAAAGGTCTTTGT
129 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* * * *
3978130 TGACAGATAACTCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCATTGAAGCTGAGCG-AAG
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAA-
*
3978194 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGTGCCT
65 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
* *
3978259 TGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGG
130 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* * * * *
3978294 TGACAGTTAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATGTGCCCTCGAAGCTAAGCGTAGT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAAT
* * * *
3978359 CGAACTCGAGGGTCTTTGGCAGACAGCCCTTCTCGACTTAAGCTATGCAGCAAATGATATGCCTT
66 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
3978424 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
131 GGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGG
** * *
3978459 TGACAGATAACCCTTCTAGCCTTGAGTTATTTTGTAAATGATGTGCACTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAAT
* *
3978524 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATATGCCTT
66 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
3978589 GGAGCTGAGCGTAGTCGAACT-AGAAGGTCTTTTGG
131 GGAGCTGAGCGTAGTCGAACTCA-AAGGTC-TTTGG
* * * * *
3978624 TGACAGATAACCCTTCTAGCATTGAGTTATTCTGTAAATGATGTACCCTCGAAGCCGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAAT
* * * *
3978689 CAAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGTTGCAAATGATATGCCTT
66 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* ** *
3978754 GGAGATGAGCGTAGTTAAACTCGAAGGTCTTTTGG
131 GGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGG
* * * *
3978789 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTTTAAATGATGTTCCCTCGCAGCTGAGCATAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAAT
* * * * * *
3978854 CAAACTCGAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGTTGCAAATGATGCGCCTT
66 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* * *
3978919 GGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGG
131 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* * * ** * ** * * * * *
3978953 TTGGCATATAACCCTTCTCGATTTAAGTTATGCTACAAATGATATG-CCTTGGAGATGAGCGTAG
1 -TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAA
* * * * * * * * * *
3979017 TCGAGCTTGAAGGTATTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTG
65 TCGAACTCGAAGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * * *
3979082 CCCTCGAAGTTGAGCGTAGTCGAACTCGATGGTCTTT-G
127 -CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* * ** * * * *
3979120 -G-CAGATAGCCCTTCTCA-ACTAAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 TGACAGATAACCCTTCT-AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAA
* * *** * *
3979181 TCGAACTCGAAGGTCTTTTTTTGGCAAATAGCCTTTCTTTCCTTGAGCTATGTTGCAAATGATGT
65 TCGAACTCGAAGGTC----TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* *
3979246 GCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGT
126 GCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
* *
3979285 TGGCATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
3979325 TTGTCTTAAA
Statistics
Matches: 1027, Mismatches: 146, Indels: 40
0.85 0.12 0.03
Matches are distributed among these distances:
163 45 0.04
164 357 0.35
165 521 0.51
166 4 0.00
167 67 0.07
168 33 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (164 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAAT
CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG
Found at i:3992630 original size:14 final size:15
Alignment explanation
Indices: 3992599--3992640 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
3992589 AAATATGATA
3992599 AAAATAAAAGAATAAC
1 AAAATAAAA-AATAAC
*
3992615 AACATAAAAAAT-AC
1 AAAATAAAAAATAAC
*
3992629 AAAATACAAAAT
1 AAAATAAAAAAT
3992641 GAAGAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 3 0.13
16 8 0.35
ACGTcount: A:0.74, C:0.10, G:0.02, T:0.14
Consensus pattern (15 bp):
AAAATAAAAAATAAC
Found at i:3993643 original size:24 final size:27
Alignment explanation
Indices: 3993615--3993684 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 27
3993605 TCGTTGGGCA
3993615 ACCCCTTGAACTGGACCGAAACA-T-G
1 ACCCCTTGAACTGGACCGAAACATTGG
*
3993640 -CCCCTTGAATTGGACCGAAACATTGG
1 ACCCCTTGAACTGGACCGAAACATTGG
3993666 ACCCCTTGAACTGGACCGA
1 ACCCCTTGAACTGGACCGA
3993685 GACCTGGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 21 0.52
25 1 0.03
26 1 0.03
27 17 0.43
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (27 bp):
ACCCCTTGAACTGGACCGAAACATTGG
Found at i:3993737 original size:3 final size:3
Alignment explanation
Indices: 3993729--3993773 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
3993719 AATTAAACGA
* *
3993729 AAT AAT AAT AAT AAT AGT AAT -AT ACT AAT AAT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3993774 CTATATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:3993957 original size:37 final size:37
Alignment explanation
Indices: 3993834--3994049 Score: 245
Period size: 37 Copynumber: 5.9 Consensus size: 37
3993824 TTTAAACAAG
* *
3993834 TTTTCAAAACCATATATCATAT-AGTTTTC-AAAAATGA
1 TTTT-AAAACTATATATTATATAAGTTTTCAAAAAAT-A
* *
3993871 TTTTAAAA--A-ATATCATATAAGTTTTCAAAAAATGT
1 TTTTAAAACTATATATTATATAAGTTTTCAAAAAAT-A
3993906 TTTTAAAACTATATATTATATAAGTTTTCAAAAAATA
1 TTTTAAAACTATATATTATATAAGTTTTCAAAAAATA
* *
3993943 TTTTCAAA-TCATATATTATATAAGTTTTCAAAATA-A
1 TTTTAAAACT-ATATATTATATAAGTTTTCAAAAAATA
3993979 TTTTAAAACTATATATTATATAAGTTTTC--AAAATGA
1 TTTTAAAACTATATATTATATAAGTTTTCAAAAAAT-A
3994015 TTTTAAAAACTATATATTATATATA-TTTTCAAAAA
1 TTTT-AAAACTATATATTATATA-AGTTTTCAAAAA
3994050 CCGTTTGCAA
Statistics
Matches: 159, Mismatches: 7, Indels: 24
0.84 0.04 0.13
Matches are distributed among these distances:
33 9 0.06
34 11 0.07
35 15 0.09
36 37 0.23
37 60 0.38
38 24 0.15
39 3 0.02
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (37 bp):
TTTTAAAACTATATATTATATAAGTTTTCAAAAAATA
Found at i:3994072 original size:73 final size:71
Alignment explanation
Indices: 3993821--3994074 Score: 261
Period size: 73 Copynumber: 3.5 Consensus size: 71
3993811 TTATATATTA
* *
3993821 AATTTT-AAACAAGTTTTCAAAACCATATATCATAT-AGTTTTCAAAAATGATTTTAAAAA-ATA
1 AATTTTCAAA-AAGTTTT-AAAACTATATATTATATAAGTTTTCAAAAATGATTTTAAAAACATA
3993883 TCA-TATA-
64 T-ATTATAT
* * *
3993890 AGTTTTCAAAAAATGTTTTTAAAACTATATATTATATAAGTTTTCAAAAAAT-ATTTTCAAATCA
1 AATTTTC-AAAAA-G-TTTTAAAACTATATATTATATAAGTTTTC-AAAAATGATTTTAAAAACA
3993954 TATATTATAT
62 TATATTATAT
*
3993964 AAGTTTTCAAAATAATTTTAAAACTATATATTATATAAGTTTTC-AAAATGATTTTAAAAACTAT
1 AA-TTTTCAAAA-AGTTTTAAAACTATATATTATATAAGTTTTCAAAAATGATTTTAAAAAC-AT
3994028 ATATTATAT
63 ATATTATAT
**
3994037 ATATTTTCAAAAACCGTTTGCAAACTATATATATATAT
1 A-ATTTTCAAAAA--GTTTTAAAACTATATAT-TATAT
3994075 GTGTGTGTGT
Statistics
Matches: 156, Mismatches: 12, Indels: 28
0.80 0.06 0.14
Matches are distributed among these distances:
69 5 0.03
70 2 0.01
71 24 0.15
72 30 0.19
73 64 0.41
74 20 0.13
75 11 0.07
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (71 bp):
AATTTTCAAAAAGTTTTAAAACTATATATTATATAAGTTTTCAAAAATGATTTTAAAAACATATA
TTATAT
Found at i:3994079 original size:2 final size:2
Alignment explanation
Indices: 3994074--3994102 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3994064 TATATATATA
3994074 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3994103 AAAAAAATAT
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:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3994270 original size:14 final size:14
Alignment explanation
Indices: 3994231--3994270 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3994221 ATATCAATTT
*
3994231 AAATAATAATAATAC
1 AAATAA-AAAAATAC
*
3994246 AAATATAAAAATAC
1 AAATAAAAAAATAC
3994260 AAATAAAAAAA
1 AAATAAAAAAA
3994271 ATTATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAAAAAATAC
Found at i:4002207 original size:18 final size:18
Alignment explanation
Indices: 4002174--4002208 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4002164 CCTCATTTCC
* *
4002174 TCCTCTTCCTCTCCCTCT
1 TCCTCTTCCACGCCCTCT
4002192 TCCTCTTCCACGCCCTC
1 TCCTCTTCCACGCCCTC
4002209 CTCGATAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.57, G:0.03, T:0.37
Consensus pattern (18 bp):
TCCTCTTCCACGCCCTCT
Found at i:4003180 original size:24 final size:24
Alignment explanation
Indices: 4003128--4003187 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
4003118 TTTGGTGGTT
* *
4003128 GTTGTGGTGCTTGTGCTGACAACG
1 GTTGTGGTGCTTGTCCTAACAACG
*
4003152 ATTGTGGTGCTTGTCCTAAC-ACAG
1 GTTGTGGTGCTTGTCCTAACAAC-G
*
4003176 GTTGTGATGCTT
1 GTTGTGGTGCTT
4003188 TTGCAGGCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.15, C:0.17, G:0.32, T:0.37
Consensus pattern (24 bp):
GTTGTGGTGCTTGTCCTAACAACG
Found at i:4006829 original size:16 final size:16
Alignment explanation
Indices: 4006808--4006844 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
4006798 CATTTAATAA
4006808 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
4006824 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
4006840 ATAAA
1 ATAAA
4006845 CGTTTGAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:4007923 original size:10 final size:10
Alignment explanation
Indices: 4007910--4007939 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
4007900 TTAAACATAA
4007910 ATAAACGAAC
1 ATAAACGAAC
4007920 ATAAACGAAC
1 ATAAACGAAC
*
4007930 ATAACCGAAC
1 ATAAACGAAC
4007940 GTTCACGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.23, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:4009202 original size:60 final size:59
Alignment explanation
Indices: 4009057--4009202 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 59
4009047 AATATAGGGT
* * *
4009057 AAAGTATAC-AAATAGTC-CTCGAATATAAGATATTATTTTATTAAAATTCTCGATTATTA
1 AAAGT-TACAAAATAGTCTCT-GACTATAAAATATTATTTTATTAAAATTCTCGACTATTA
* * * * **
4009116 AAAGTTATAAAATGATTCTCTTACTATAAAATATTGTTTTATTAAGCTTCTCGACTATTA
1 AAAGTTACAAAAT-AGTCTCTGACTATAAAATATTATTTTATTAAAATTCTCGACTATTA
4009176 AAAGTTACAAAATAGTCATCTGACTAT
1 AAAGTTACAAAATAGTC-TCTGACTAT
4009203 TAATTATGTT
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
58 2 0.03
59 12 0.17
60 55 0.77
61 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (59 bp):
AAAGTTACAAAATAGTCTCTGACTATAAAATATTATTTTATTAAAATTCTCGACTATTA
Found at i:4011426 original size:35 final size:35
Alignment explanation
Indices: 4011379--4011445 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
4011369 GTCATTCAAG
4011379 GGGTATCAATACCAAATGAGC-AGTATCGATACTGA
1 GGGTATCAATACCAAAT-AGCAAGTATCGATACTGA
* **
4011414 GGGTATCGATACCATCTAGCAAGTATCGATAC
1 GGGTATCAATACCAAATAGCAAGTATCGATAC
4011446 CATTTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 3 0.11
35 25 0.89
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (35 bp):
GGGTATCAATACCAAATAGCAAGTATCGATACTGA
Found at i:4016445 original size:17 final size:17
Alignment explanation
Indices: 4016425--4016457 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4016415 CGGTTCAGTC
4016425 AAGTCAACGAGTCGGGT
1 AAGTCAACGAGTCGGGT
*
4016442 AAGTCAACGGGTCGGG
1 AAGTCAACGAGTCGGG
4016458 CAGATGGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.18, G:0.39, T:0.15
Consensus pattern (17 bp):
AAGTCAACGAGTCGGGT
Found at i:4018517 original size:36 final size:37
Alignment explanation
Indices: 4018476--4018547 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
4018466 ATTTTAATAC
4018476 TATTTAAT-GT-TGTTTTATTATTACAGGATTTATAAA
1 TATTTAATAGTAT-TTTTATTATTACAGGATTTATAAA
*
4018512 TATTTAATAGTATTTTTATTATTATAGGATTTATAA
1 TATTTAATAGTATTTTTATTATTACAGGATTTATAA
4018548 CAAATATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 8 0.24
37 24 0.73
38 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.54
Consensus pattern (37 bp):
TATTTAATAGTATTTTTATTATTACAGGATTTATAAA
Found at i:4018785 original size:23 final size:23
Alignment explanation
Indices: 4018741--4018785 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
4018731 TAACAAATTT
* * *
4018741 ATTTAATCATAATAATATATTAA
1 ATTTAATCAAAATAAGAAATTAA
*
4018764 ATTTTATCAAAATAAGAAATTA
1 ATTTAATCAAAATAAGAAATTA
4018786 TGTCAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTTAATCAAAATAAGAAATTAA
Found at i:4019272 original size:17 final size:19
Alignment explanation
Indices: 4019236--4019275 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
4019226 GTTCGATGTT
4019236 ATAATTTAAGTTAATTGTG
1 ATAATTTAAGTTAATTGTG
*
4019255 ATAATTTAA-TT-TTTGTG
1 ATAATTTAAGTTAATTGTG
4019272 ATAA
1 ATAA
4019276 AATAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (19 bp):
ATAATTTAAGTTAATTGTG
Found at i:4020694 original size:15 final size:16
Alignment explanation
Indices: 4020658--4020688 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4020648 CTAACAGAGC
4020658 AAAACCACTAGGGTTT
1 AAAACCACTAGGGTTT
4020674 AAAACC-CTAGGGTTT
1 AAAACCACTAGGGTTT
4020689 CCAACCGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (16 bp):
AAAACCACTAGGGTTT
Found at i:4023531 original size:29 final size:29
Alignment explanation
Indices: 4023496--4023589 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
4023486 AGGTTTTATA
*
4023496 TTTAATTTTATATTATATTTAATTTTAAT
1 TTTAATTTTATATTATATTTAATATTAAT
* * * *
4023525 TTTAATTTTTTAAATAAATTAAATATTAAT
1 TTTAATTTTAT-ATTATATTTAATATTAAT
*
4023555 TTT--TTTAATATTATATTATAGATATTAAT
1 TTTAATTTTATATTATATT-TA-ATATTAAT
4023584 TTTAAT
1 TTTAAT
4023590 ATTAATTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
27 6 0.12
28 5 0.10
29 21 0.42
30 17 0.34
31 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TTTAATTTTATATTATATTTAATATTAAT
Found at i:4023532 original size:17 final size:17
Alignment explanation
Indices: 4023489--4023532 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
4023479 TTTAAAAAGG
4023489 TTTTATATTTAATTTTA
1 TTTTATATTTAATTTTA
*
4023506 TATTATATTTAATTTTAA
1 TTTTATATTTAATTTT-A
4023524 TTTTA-ATTT
1 TTTTATATTT
4023533 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATATTTAATTTTA
Found at i:4023566 original size:15 final size:14
Alignment explanation
Indices: 4023518--4023602 Score: 58
Period size: 14 Copynumber: 6.4 Consensus size: 14
4023508 TTATATTTAA
*
4023518 TTTTAATTTTAATT
1 TTTTAATATTAATT
4023532 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
4023542 ATTAAATATTAATTT
1 TTTTAATATTAA-TT
*
4023557 TTTTAATATT-ATA
1 TTTTAATATTAATT
*
4023570 TTATAGATATTAA--
1 TTTTA-ATATTAATT
4023583 TTTTAATATTAATT
1 TTTTAATATTAATT
4023597 TTTTAA
1 TTTTAA
4023603 ATAAATTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
10 4 0.07
11 1 0.02
12 13 0.24
13 9 0.17
14 18 0.33
15 9 0.17
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:4023595 original size:65 final size:64
Alignment explanation
Indices: 4023496--4023652 Score: 239
Period size: 65 Copynumber: 2.5 Consensus size: 64
4023486 AGGTTTTATA
* * *
4023496 TTTAATTTTATATTAT--AT-TTAATTTTAATTTTAATTTTTTAAATAAATTAAATATTAATTTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAA-GTT
4023558 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAGTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAGTT
*
4023622 TTGAATATTATATTATAGATATTTAATTTTA
1 TTTAATATTATATTATAGATA-TTAATTTTA
4023653 TATCATATAA
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
62 15 0.17
64 24 0.28
65 48 0.55
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (64 bp):
TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAGTT
Found at i:4025776 original size:21 final size:21
Alignment explanation
Indices: 4025752--4025792 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4025742 AGTTATTAAT
*
4025752 CATCATGGATTGTCACGTCAA
1 CATCATGAATTGTCACGTCAA
4025773 CATCATGAATTGTCACGTCA
1 CATCATGAATTGTCACGTCA
4025793 GCACCGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (21 bp):
CATCATGAATTGTCACGTCAA
Found at i:4026446 original size:21 final size:21
Alignment explanation
Indices: 4026399--4026449 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
4026389 TTATTCTACC
*
4026399 AATTTAAATTTTCTAAAAAAT
1 AATTTAAAATTTCTAAAAAAT
* * **
4026420 ATTTTAAAATTTGTAAAATTT
1 AATTTAAAATTTCTAAAAAAT
4026441 AATTTAAAA
1 AATTTAAAA
4026450 CTCATAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTTAAAATTTCTAAAAAAT
Found at i:4032292 original size:76 final size:74
Alignment explanation
Indices: 4032168--4032365 Score: 283
Period size: 76 Copynumber: 2.7 Consensus size: 74
4032158 GTTATAGATG
* *
4032168 GGGGGTATCAGTA-CCTCCT-GGGGGTATCAGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCC
1 GGGGGTATCAGTACCCT-CTGGGGGGTATCGGTACCCTCAGAGCAATCTGTTATTTCTCGGAGCC
4032231 AAATCTTACAA
65 AAATCTTAC-A
* *
4032242 GGGGGTATCAATACCCTCTTGGGGGGTATCGGTACCCTCAGAGCAATCTGTTATTTCTCGGAGTC
1 GGGGGTATCAGTACCCTC-TGGGGGGTATCGGTACCCTCAGAGCAATCTGTTATTTCTCGGAGCC
4032307 AAATCTTACA
65 AAATCTTACA
** * *
4032317 GGGGGTATTTGTACCCTCTGGGGGGTATCGGTACCCTCTGGGCAATCTG
1 GGGGGTATCAGTACCCTCTGGGGGGTATCGGTACCCTCAGAGCAATCTG
4032366 CCTTTTAAGG
Statistics
Matches: 112, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
74 42 0.38
75 20 0.18
76 50 0.45
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (74 bp):
GGGGGTATCAGTACCCTCTGGGGGGTATCGGTACCCTCAGAGCAATCTGTTATTTCTCGGAGCCA
AATCTTACA
Found at i:4032342 original size:20 final size:20
Alignment explanation
Indices: 4032317--4032358 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
4032307 AAATCTTACA
**
4032317 GGGGGTATTTGTACCCTCTG
1 GGGGGTATCGGTACCCTCTG
4032337 GGGGGTATCGGTACCCTCTG
1 GGGGGTATCGGTACCCTCTG
4032357 GG
1 GG
4032359 CAATCTGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.21, G:0.40, T:0.29
Consensus pattern (20 bp):
GGGGGTATCGGTACCCTCTG
Found at i:4040425 original size:22 final size:22
Alignment explanation
Indices: 4040397--4040450 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
4040387 GGAATTGATA
* *
4040397 CCCCCTTGCATGGGTACCGATT
1 CCCCCTTGAATGGGTACCAATT
4040419 CCCCCTTTGAATGGGTACCAATT
1 CCCCC-TTGAATGGGTACCAATT
4040442 CCCCCTTGA
1 CCCCCTTGA
4040451 GGGAACCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.17, C:0.37, G:0.19, T:0.28
Consensus pattern (22 bp):
CCCCCTTGAATGGGTACCAATT
Found at i:4042404 original size:16 final size:16
Alignment explanation
Indices: 4042383--4042415 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4042373 TTGATGCTTA
*
4042383 TGGATGTTTGAATTTG
1 TGGATGTTTAAATTTG
4042399 TGGATGTTTAAATTTG
1 TGGATGTTTAAATTTG
4042415 T
1 T
4042416 TTTAGATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (16 bp):
TGGATGTTTAAATTTG
Found at i:4044246 original size:202 final size:202
Alignment explanation
Indices: 4043900--4044285 Score: 709
Period size: 202 Copynumber: 1.9 Consensus size: 202
4043890 TGACTAAGAA
*
4043900 AATCGGAATAGAAAGATTAACCTGCAATTTTAAAACACATGTATGCAATAATATCAATCCCATAA
1 AATCGGAATAGAAAGATTAACCTGCAATTTTAAAACACATGTATGCAATAATATCAATCCCAAAA
* * *
4043965 CTCAAATGAGTCCTCATTATTTCAAGGTTCTCTAAAATGATCCTAATGGACAATTTTTGAAAATC
66 CGCAAATGAGTCATCATTATTTCAAGGTTCTCTAAAATGATCCTAATGGACAATTTTTGAAAACC
4044030 GAGTTTGAAAACAAGGTTTAAAAATCAATATATGTATAATATTTCATGTAAACACATGTATGCAA
131 GAGTTTGAAAACAAGGTTTAAAAATCAATATATGTATAATATTTCATGTAAACACATGTATGCAA
4044095 TAATATC
196 TAATATC
*
4044102 AATCGGAATAGAAAGATTAACCTGCAATTTTAAAATACATGTATGCAATAATATCAATCCCAAAA
1 AATCGGAATAGAAAGATTAACCTGCAATTTTAAAACACATGTATGCAATAATATCAATCCCAAAA
* *
4044167 CGCAATTGAGTCATCATTATTTCAAGGTTCTCTAAAATGATCCTAATGGATAATTTTTGAAAACC
66 CGCAAATGAGTCATCATTATTTCAAGGTTCTCTAAAATGATCCTAATGGACAATTTTTGAAAACC
4044232 GAGTTTGAAAACAAGGTTTAAAAATCAATATATGTATAATATTTCATGTAAACA
131 GAGTTTGAAAACAAGGTTTAAAAATCAATATATGTATAATATTTCATGTAAACA
4044286 ACATAATTAA
Statistics
Matches: 177, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
202 177 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (202 bp):
AATCGGAATAGAAAGATTAACCTGCAATTTTAAAACACATGTATGCAATAATATCAATCCCAAAA
CGCAAATGAGTCATCATTATTTCAAGGTTCTCTAAAATGATCCTAATGGACAATTTTTGAAAACC
GAGTTTGAAAACAAGGTTTAAAAATCAATATATGTATAATATTTCATGTAAACACATGTATGCAA
TAATATC
Found at i:4044753 original size:21 final size:22
Alignment explanation
Indices: 4044729--4044786 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
4044719 ACCCCGTGGA
*
4044729 GGGTATCGATACCCTC-ATGGG
1 GGGTATCGATACCCTCAAAGGG
*
4044750 GGGTATCGGTACCCACTCAAAGGG
1 GGGTATCGATA-CC-CTCAAAGGG
4044774 GGG-ATCGATACCC
1 GGGTATCGATACCC
4044787 CTTCTAGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 11 0.35
22 4 0.13
23 9 0.29
24 7 0.23
ACGTcount: A:0.22, C:0.26, G:0.33, T:0.19
Consensus pattern (22 bp):
GGGTATCGATACCCTCAAAGGG
Found at i:4044809 original size:20 final size:21
Alignment explanation
Indices: 4044770--4044811 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
4044760 ACCCACTCAA
4044770 AGGGGGGATCGATACCCCTTCT
1 AGGGGGGATCGATA-CCCTTCT
*
4044792 AGGGGGGATTGATA-CCTTCT
1 AGGGGGGATCGATACCCTTCT
4044812 GCACTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.26
Consensus pattern (21 bp):
AGGGGGGATCGATACCCTTCT
Found at i:4049382 original size:973 final size:973
Alignment explanation
Indices: 4047496--4049441 Score: 3759
Period size: 973 Copynumber: 2.0 Consensus size: 973
4047486 ACTAGTGGAT
*
4047496 ACGTCATTAATGGATTTAAAAGAATTTCGCTTTTGTCTTCCTTTAGCACAAGCATCACAGATTTT
1 ACGTCATTAATGGATTTAAAAGAAATTCGCTTTTGTCTTCCTTTAGCACAAGCATCACAGATTTT
4047561 ATCATTATCAAATTTTAGTTTAGGCAACCCTCGAACTAAATCTCCTCGAATTAACCGTTGCAAAA
66 ATCATTATCAAATTTTAGTTTAGGCAACCCTCGAACTAAATCTCCTCGAATTAACCGTTGCAAAA
4047626 CACTCATACTAGCATGTCCTAGTCTCCTATGTCATAACCAACTATCATGCTCATCCTTAGAAACT
131 CACTCATACTAGCATGTCCTAGTCTCCTATGTCATAACCAACTATCATGCTCATCCTTAGAAACT
*
4047691 AGGCATATATTAGTCATATCTATAGAATCTAAATGCATCATGTATATGTTTCCTATTGTATGACG
196 AGGCATATATTAGTCATATCTATAGAATCTAAATGCATCATGTATATGTTTCCTATTGTATGACC
4047756 AACAAGCATAATCCGATTAGATGCAATGTCAATAACTTTACAACCATTAGTTTCAAACATGACAT
261 AACAAGCATAATCCGATTAGATGCAATGTCAATAACTTTACAACCATTAGTTTCAAACATGACAT
*
4047821 TGAATCCCTTATCGCATAATTAGCTAATACTCAATAGATTATACTTTAATTCATTCACATATAAA
326 TGAATCCCTTATCGAATAATTAGCTAATACTCAATAGATTATACTTTAATTCATTCACATATAAA
*
4047886 ACATTCTTAATTTGTATTAAAGATGTATTACCTATAGTGCCTATACCTTCAAAATGACATTTTGA
391 ACATTCTTAATTTGTATTAAAGATGTATTACCTATAGTGCCTATACATTCAAAATGACATTTTGA
4047951 ATTATCACCAAAAGTCACATCTCCTCCATTTTAGGCGTTAAGCTTTATGAACCGGTTTTTGTCTC
456 ATTATCACCAAAAGTCACATCTCCTCCATTTTAGGCGTTAAGCTTTATGAACCGGTTTTTGTCTC
*
4048016 CGGTCATGTGTCTTGAGCATCCACTATCAAGGTACCATGAATTTGAATTTGTTTCCCTTGCCCTG
521 CAGTCATGTGTCTTGAGCATCCACTATCAAGGTACCATGAATTTGAATTTGTTTCCCTTGCCCTG
*
4048081 TAGCAATGCTCATTTCCCTACAAACATATATTAATTTTTTATTTTTGGTACCCAAATCCTTTTGG
586 TAGCAATGCTCATTTCCCTACAAACATAGATTAATTTTTTATTTTTGGTACCCAAATCCTTTTGG
4048146 GTCCATATTCATTAGTTTCCAAAATTCTAGTCCCCTTAGGTATCCATTTGTGTAGGATATACTTA
651 GTCCATATTCATTAGTTTCCAAAATTCTAGTCCCCTTAGGTATCCATTTGTGTAGGATATACTTA
4048211 TCTTTAGTAGTTATGAGTTCTTTAGGAACCCATATACTTCTAATGATTTTTCCATTAGAGGTTCT
716 TCTTTAGTAGTTATGAGTTCTTTAGGAACCCATATACTTCTAATGATTTTTCCATTAGAGGTTCT
*
4048276 TTGGGGACCTCTATGATTGTAGTTTTTAAAACTTTTTCTAACAAAGTTGGATTTTGAATTTTTAT
781 TTGGGGACCTCTATGATTGTAGTTTTTAAAACTTTTTCTAACAAAGTTGGAGTTTGAATTTTTAT
4048341 TTATTTCCAAAACGTTTTGTTCAAATTTTATCAAAAGAAGCTTTAAGATCATCAATTTTCTTTTG
846 TTATTTCCAAAACGTTTTGTTCAAATTTTATCAAAAGAAGCTTTAAGATCATCAATTTTCTTTTG
*
4048406 ATGATCATCATTGACCTTAGAAAGCAAATTATACAAATCATAAATTTTCTTTTCAAACTCTTC
911 ATGATAATCATTGACCTTAGAAAGCAAATTATACAAATCATAAATTTTCTTTTCAAACTCTTC
4048469 ACGTCATTAATGGATTTAAAAGAAATTCGCTTTTGTCTTCCTTTAGCACAAGCATCACAGATTTT
1 ACGTCATTAATGGATTTAAAAGAAATTCGCTTTTGTCTTCCTTTAGCACAAGCATCACAGATTTT
4048534 ATCATTATCAAATTTTAGTTTAGGCAACCCTCGAACTAAATCTCCTCGAATTAACCGTTGCAAAA
66 ATCATTATCAAATTTTAGTTTAGGCAACCCTCGAACTAAATCTCCTCGAATTAACCGTTGCAAAA
4048599 CACTCATACTAGCATGTCCTAGTCTCCTATGTCATAACCAACTATCATGCTCATCCTTAGAAACT
131 CACTCATACTAGCATGTCCTAGTCTCCTATGTCATAACCAACTATCATGCTCATCCTTAGAAACT
4048664 AGGCATATATTAGTCATATCTATAGAATCTAAATGCATCATGTATATGTTTCCTATTGTATGACC
196 AGGCATATATTAGTCATATCTATAGAATCTAAATGCATCATGTATATGTTTCCTATTGTATGACC
4048729 AACAAGCATAATCCGATTAGATGCAATGTCAATAACTTTACAACCATTAGTTTCAAACATGACAT
261 AACAAGCATAATCCGATTAGATGCAATGTCAATAACTTTACAACCATTAGTTTCAAACATGACAT
*
4048794 TGAATCCCTTATCGAATAATTGGCTAATACTCAATAGATTATACTTTAATTCATTCACATATAAA
326 TGAATCCCTTATCGAATAATTAGCTAATACTCAATAGATTATACTTTAATTCATTCACATATAAA
*
4048859 ACATTCTTAATTTGTATTGAAGATGTATTACCTATAGTGCCTATACATTCAAAATGACATTTTGA
391 ACATTCTTAATTTGTATTAAAGATGTATTACCTATAGTGCCTATACATTCAAAATGACATTTTGA
* *
4048924 ATTATCACCAAAAGTCACATCTCCTCTATTTTATGCGTTAAGCTTTATGAACCGGTTTTTGTCTC
456 ATTATCACCAAAAGTCACATCTCCTCCATTTTAGGCGTTAAGCTTTATGAACCGGTTTTTGTCTC
4048989 CAGTCATGTGTCTTGAGCATCCACTATCAAGGTACCATGAATTTGAATTTGTTTCCCTTGCCCTG
521 CAGTCATGTGTCTTGAGCATCCACTATCAAGGTACCATGAATTTGAATTTGTTTCCCTTGCCCTG
*
4049054 TAGCAATGCTCCTTTCCCTACAAACATAGATTAATTTTTTATTTTTGGTACCCAAATCCTTTTGG
586 TAGCAATGCTCATTTCCCTACAAACATAGATTAATTTTTTATTTTTGGTACCCAAATCCTTTTGG
4049119 GTCCATATTCATTAGTTTCCAAAATTCTAGTCCCCTTAGGTATCCATTTGTGTAGGATATACTTA
651 GTCCATATTCATTAGTTTCCAAAATTCTAGTCCCCTTAGGTATCCATTTGTGTAGGATATACTTA
4049184 TCTTTAGTAGTTATGAGTTCTTTAGGAACCCATATACTTCTAATGATTTTTCCATTAGAGGTTCT
716 TCTTTAGTAGTTATGAGTTCTTTAGGAACCCATATACTTCTAATGATTTTTCCATTAGAGGTTCT
4049249 TTGGGGACCTCTATGATTGTAGTTTTTAAAACTTTTTTCTAACAAAGTTGGAGTTTGAATTTTT-
781 TTGGGGACCTCTATGATTGTAGTTTTTAAAAC-TTTTTCTAACAAAGTTGGAGTTTGAATTTTTA
4049313 TTTATTTCCAAAACGTTTTGTTCAAATTTTATCAAAAGAAGCTTTAAGATCATCAATTTTCTTTT
845 TTTATTTCCAAAACGTTTTGTTCAAATTTTATCAAAAGAAGCTTTAAGATCATCAATTTTCTTTT
4049378 GATGATAATCATTGACCTTAGAAAGCAAATTATACAAATCATAAATTTTCTTTTCAAACTCTTC
910 GATGATAATCATTGACCTTAGAAAGCAAATTATACAAATCATAAATTTTCTTTTCAAACTCTTC
4049442 TAGTTTGATT
Statistics
Matches: 959, Mismatches: 13, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
973 929 0.97
974 30 0.03
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (973 bp):
ACGTCATTAATGGATTTAAAAGAAATTCGCTTTTGTCTTCCTTTAGCACAAGCATCACAGATTTT
ATCATTATCAAATTTTAGTTTAGGCAACCCTCGAACTAAATCTCCTCGAATTAACCGTTGCAAAA
CACTCATACTAGCATGTCCTAGTCTCCTATGTCATAACCAACTATCATGCTCATCCTTAGAAACT
AGGCATATATTAGTCATATCTATAGAATCTAAATGCATCATGTATATGTTTCCTATTGTATGACC
AACAAGCATAATCCGATTAGATGCAATGTCAATAACTTTACAACCATTAGTTTCAAACATGACAT
TGAATCCCTTATCGAATAATTAGCTAATACTCAATAGATTATACTTTAATTCATTCACATATAAA
ACATTCTTAATTTGTATTAAAGATGTATTACCTATAGTGCCTATACATTCAAAATGACATTTTGA
ATTATCACCAAAAGTCACATCTCCTCCATTTTAGGCGTTAAGCTTTATGAACCGGTTTTTGTCTC
CAGTCATGTGTCTTGAGCATCCACTATCAAGGTACCATGAATTTGAATTTGTTTCCCTTGCCCTG
TAGCAATGCTCATTTCCCTACAAACATAGATTAATTTTTTATTTTTGGTACCCAAATCCTTTTGG
GTCCATATTCATTAGTTTCCAAAATTCTAGTCCCCTTAGGTATCCATTTGTGTAGGATATACTTA
TCTTTAGTAGTTATGAGTTCTTTAGGAACCCATATACTTCTAATGATTTTTCCATTAGAGGTTCT
TTGGGGACCTCTATGATTGTAGTTTTTAAAACTTTTTCTAACAAAGTTGGAGTTTGAATTTTTAT
TTATTTCCAAAACGTTTTGTTCAAATTTTATCAAAAGAAGCTTTAAGATCATCAATTTTCTTTTG
ATGATAATCATTGACCTTAGAAAGCAAATTATACAAATCATAAATTTTCTTTTCAAACTCTTC
Found at i:4049551 original size:22 final size:21
Alignment explanation
Indices: 4049509--4049548 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4049499 GAGATTATTT
*
4049509 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
4049530 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4049549 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:4050936 original size:23 final size:22
Alignment explanation
Indices: 4050892--4050936 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4050882 AATGTCATGG
*
4050892 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
4050914 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
4050937 AAGTTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:4051545 original size:2 final size:2
Alignment explanation
Indices: 4051538--4051563 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4051528 AGATTAATAG
4051538 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
4051564 TAGGAGATAT
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:4052529 original size:23 final size:22
Alignment explanation
Indices: 4052502--4052569 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 22
4052492 ATTATTATAT
4052502 GGCACTATGGTGCAATTCTACGC
1 GGCACT-TGGTGCAATTCTACGC
*
4052525 GGCACTCTGGTGCAATTCTACGT
1 GGCACT-TGGTGCAATTCTACGC
*
4052548 GGCACTTCGGTGCAATTATACG
1 GGCACTT-GGTGCAATTCTACG
4052570 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 1 0.02
23 40 0.98
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (22 bp):
GGCACTTGGTGCAATTCTACGC
Found at i:4053679 original size:21 final size:21
Alignment explanation
Indices: 4053653--4053697 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4053643 GATTTCTGGG
* *
4053653 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4053674 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4053695 CAA
1 CAA
4053698 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4055424 original size:13 final size:13
Alignment explanation
Indices: 4055406--4055468 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
4055396 TCTACGGGCA
4055406 CTACGGTGCAATT
1 CTACGGTGCAATT
4055419 CTACGG-GC-A--
1 CTACGGTGCAATT
4055428 CTACGGTGCAATT
1 CTACGGTGCAATT
4055441 CTACGG-GC-A--
1 CTACGGTGCAATT
*
4055450 CTTCGGTGCAATT
1 CTACGGTGCAATT
4055463 CTACGG
1 CTACGG
4055469 GGCACTTCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 11 0.28
10 4 0.10
11 4 0.10
12 4 0.10
13 17 0.43
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:4055490 original size:23 final size:22
Alignment explanation
Indices: 4055394--4055482 Score: 151
Period size: 22 Copynumber: 4.0 Consensus size: 22
4055384 TATGGACATC
4055394 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
4055416 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
4055438 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
4055460 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTACGGTGCA
4055483 TTTATACGAG
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
22 50 0.77
23 15 0.23
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:4058646 original size:21 final size:21
Alignment explanation
Indices: 4058620--4058664 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4058610 GATTTCTGGG
* *
4058620 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4058641 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4058662 CAA
1 CAA
4058665 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4060391 original size:13 final size:13
Alignment explanation
Indices: 4060373--4060435 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
4060363 TCTACGGGCA
4060373 CTACGGTGCAATT
1 CTACGGTGCAATT
4060386 CTACGG-GC-A--
1 CTACGGTGCAATT
4060395 CTACGGTGCAATT
1 CTACGGTGCAATT
4060408 CTACGG-GC-A--
1 CTACGGTGCAATT
*
4060417 CTTCGGTGCAATT
1 CTACGGTGCAATT
4060430 CTACGG
1 CTACGG
4060436 GGCACTTCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 11 0.28
10 4 0.10
11 4 0.10
12 4 0.10
13 17 0.43
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:4060457 original size:23 final size:22
Alignment explanation
Indices: 4060361--4060449 Score: 151
Period size: 22 Copynumber: 4.0 Consensus size: 22
4060351 TATGGACATC
4060361 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
4060383 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
4060405 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
4060427 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTACGGTGCA
4060450 TTTATACGAG
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
22 50 0.77
23 15 0.23
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:4062962 original size:76 final size:73
Alignment explanation
Indices: 4062835--4063018 Score: 228
Period size: 76 Copynumber: 2.5 Consensus size: 73
4062825 GTTATAGATG
* * ** *
4062835 GGGGTATCAGTA-CCTCCTGGGGGTATCGGTACCATCTGAGCAATCTATTATTTCTCT-GAGCCA
1 GGGGTATCGGTACCCT-CTGGGGGTATCGGTACCCTCAAAGCAATATATTATTTCT-TGGAGCCA
4062898 AATCTTACAA
64 AATCTTACAA
* * *
4062908 GGGGTATCGGTACCCTCTTGGGAGGATATCGGTACCCTCAAAGCCATATGTTATTTCTTGGAGTC
1 GGGGTATCGGTACCCTC-TGGG-GG-TATCGGTACCCTCAAAGCAATATATTATTTCTTGGAGCC
4062973 AAATCTTACAA
63 AAATCTTACAA
*
4062984 GGGGTATCGGTACCCTCTGGGGGTATCGATACCCT
1 GGGGTATCGGTACCCTCTGGGGGTATCGGTACCCT
4063019 ATGGGCAATC
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
73 23 0.24
74 9 0.09
75 7 0.07
76 58 0.60
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (73 bp):
GGGGTATCGGTACCCTCTGGGGGTATCGGTACCCTCAAAGCAATATATTATTTCTTGGAGCCAAA
TCTTACAA
Found at i:4063008 original size:19 final size:19
Alignment explanation
Indices: 4062984--4063023 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4062974 AATCTTACAA
* *
4062984 GGGGTATCGGTACCCTCTG
1 GGGGTATCGATACCCTATG
4063003 GGGGTATCGATACCCTATG
1 GGGGTATCGATACCCTATG
4063022 GG
1 GG
4063024 CAATCTGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (19 bp):
GGGGTATCGATACCCTATG
Found at i:4064098 original size:7 final size:7
Alignment explanation
Indices: 4064083--4064115 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
4064073 TTTGTGGTCA
*
4064083 TTTCTAC
1 TTTCCAC
4064090 TTTCCAC
1 TTTCCAC
4064097 TTTCCAC
1 TTTCCAC
4064104 TTTCCAC
1 TTTCCAC
4064111 TTTCC
1 TTTCC
4064116 GTCTCTCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.39, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTCCAC
Found at i:4090879 original size:7 final size:7
Alignment explanation
Indices: 4090856--4090890 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
4090846 GGTCAAAGGA
4090856 GGTCAAC
1 GGTCAAC
*
4090863 GATC-AC
1 GGTCAAC
4090869 GGTCAAC
1 GGTCAAC
4090876 GGTCAAC
1 GGTCAAC
4090883 GGTCAAC
1 GGTCAAC
4090890 G
1 G
4090891 ATCGGGTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (7 bp):
GGTCAAC
Found at i:4094031 original size:21 final size:21
Alignment explanation
Indices: 4094005--4094045 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4093995 GTTGAATATT
4094005 ATTATTCTGCCACTTGGTTTA
1 ATTATTCTGCCACTTGGTTTA
4094026 ATTATTCTGCCACTTGGTTT
1 ATTATTCTGCCACTTGGTTT
4094046 TTGTTGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.49
Consensus pattern (21 bp):
ATTATTCTGCCACTTGGTTTA
Found at i:4098181 original size:24 final size:24
Alignment explanation
Indices: 4098137--4098182 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4098127 GTGGGATGAA
* *
4098137 GCCTCTGGTTATTATTTTGATGCT
1 GCCTCTGGTTATTACTATGATGCT
4098161 GCCTCTGGGTT-TTACTATGATG
1 GCCTCT-GGTTATTACTATGATG
4098183 GAAATACAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (24 bp):
GCCTCTGGTTATTACTATGATGCT
Found at i:4101206 original size:130 final size:128
Alignment explanation
Indices: 4101013--4101275 Score: 395
Period size: 130 Copynumber: 2.0 Consensus size: 128
4101003 GTGTAGGTTT
* * *
4101013 GGACATTTATTGTCAAATGGTTGGGAGTTTGAATATATATTATTTTGTATTCACCTTAGATTTAT
1 GGACATTTATTGTCAAATGATTGGGAGTTTGAATATATATTATCTTGTATTCACCTTAAATTTAT
* * *
4101078 GAAAAAATTTCGAATCTTCACATTGTTAGGAGGGATAAAATCTCTTTAAAATAGATGGCAAAATA
66 GAAAAAATTTCGAATCCTAACATTGTTAGGAGGGAT-AAA-CTCTTTAAAATAGATCGCAAAATA
*
4101143 GGACATTTATTGTCAAATTATTGGGAGTTTGAATATATATTATCTTGTATTCA-CTTCAAATTTA
1 GGACATTTATTGTCAAATGATTGGGAGTTTGAATATATATTATCTTGTATTCACCTT-AAATTTA
* * *
4101207 TGAAAAAATTTGGAATCCTAACATTGTTAGGATGGATAAAGTCTTTAAAATAGATCGCAAAATA
65 TGAAAAAATTTCGAATCCTAACATTGTTAGGAGGGATAAACTCTTTAAAATAGATCGCAAAATA
4101271 -GACAT
1 GGACAT
4101276 GAAAGGTATA
Statistics
Matches: 122, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
127 5 0.04
128 22 0.18
129 6 0.05
130 89 0.73
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (128 bp):
GGACATTTATTGTCAAATGATTGGGAGTTTGAATATATATTATCTTGTATTCACCTTAAATTTAT
GAAAAAATTTCGAATCCTAACATTGTTAGGAGGGATAAACTCTTTAAAATAGATCGCAAAATA
Found at i:4102176 original size:18 final size:17
Alignment explanation
Indices: 4102146--4102180 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4102136 TTTTTAAATT
4102146 TAAAAAATAAAATAAAA
1 TAAAAAATAAAATAAAA
*
4102163 TAAAAAGTATAAATAAAA
1 TAAAAAATA-AAATAAAA
4102181 AATTAAGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
TAAAAAATAAAATAAAA
Found at i:4103800 original size:26 final size:26
Alignment explanation
Indices: 4103766--4103817 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
4103756 ATGGGAACAT
4103766 CAGCAGGCCACATGCACCAAGTCCAA
1 CAGCAGGCCACATGCACCAAGTCCAA
4103792 CAGCAGGCCACATGCACCAAGTCCAA
1 CAGCAGGCCACATGCACCAAGTCCAA
4103818 GTCCAAGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.38, G:0.19, T:0.08
Consensus pattern (26 bp):
CAGCAGGCCACATGCACCAAGTCCAA
Found at i:4109772 original size:33 final size:33
Alignment explanation
Indices: 4109730--4109797 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
4109720 AATATATAAG
4109730 TAAGGTTATATGAATACACATGCCCACTAAAGC
1 TAAGGTTATATGAATACACATGCCCACTAAAGC
4109763 TAAGGTTATATGAATACACATGCCCACTAAAGC
1 TAAGGTTATATGAATACACATGCCCACTAAAGC
4109796 TA
1 TA
4109798 CAGTACAATA
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:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (33 bp):
TAAGGTTATATGAATACACATGCCCACTAAAGC
Found at i:4111413 original size:41 final size:40
Alignment explanation
Indices: 4111367--4111486 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 40
4111357 CTTTCTAAGG
*
4111367 ATCGATCATTTTCTCCAAGGGATCGAACCTTTTGAAAAGAA
1 ATCGATCA-TTTCTCCGAGGGATCGAACCTTTTGAAAAGAA
* * * **
4111408 ATCGATCATTTCTTTCGAGGGATTGATCCTTTTGAAAAGTG
1 ATCGATCATTTC-TCCGAGGGATCGAACCTTTTGAAAAGAA
*
4111449 ATTGATCATTTCTCTCGAGGGATC-AATCCTTTTGAAAA
1 ATCGATCATTTCTC-CGAGGGATCGAA-CCTTTTGAAAA
4111487 AGGATCGATC
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
40 6 0.09
41 60 0.91
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (40 bp):
ATCGATCATTTCTCCGAGGGATCGAACCTTTTGAAAAGAA
Found at i:4112823 original size:19 final size:21
Alignment explanation
Indices: 4112799--4112838 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4112789 CCAACTCATG
*
4112799 TTATCAT-TC-ATATGATAGA
1 TTATCATATCAATATCATAGA
4112818 TTATCATATCAATATCATAGA
1 TTATCATATCAATATCATAGA
4112839 CGGTTATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (21 bp):
TTATCATATCAATATCATAGA
Found at i:4113975 original size:25 final size:24
Alignment explanation
Indices: 4113937--4113984 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
4113927 TGAAAATAAA
* *
4113937 ATAAAAATTGCATAACATGCATAC
1 ATAAAAATTACATAACATACATAC
*
4113961 ATAAAAATGTACATACCATACATA
1 ATAAAAAT-TACATAACATACATA
4113985 AAATAGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (24 bp):
ATAAAAATTACATAACATACATAC
Found at i:4116135 original size:54 final size:54
Alignment explanation
Indices: 4115948--4116320 Score: 332
Period size: 55 Copynumber: 6.9 Consensus size: 54
4115938 TCTTCAAAAT
* * ** * ***
4115948 CGGGTTCGCTCCCTATCGTTTCAGGGAACATAGAACTTGAAGAATCTTCTGGGGA
1 CGGGTTCGCTCCCTCT-TTTTCAGGGAGTATAGAACTCGAAGAATCTTCTGCTAA
* *
4116003 CGGGTTCGCTCCCTATTGTTTCAGGGAGTATAGAACTCGAATAATCTTCTGCTAA
1 CGGGTTCGCTCCCTCTT-TTTCAGGGAGTATAGAACTCGAAGAATCTTCTGCTAA
*
4116058 CGGGTTCGCTCCCTATTGTTTCAGGGAGTATAGAACTC-AAGAATCTTCTGCTAA
1 CGGGTTCGCTCCCTCTT-TTTCAGGGAGTATAGAACTCGAAGAATCTTCTGCTAA
* * *
4116112 CTGGTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACTCGAACAATCTTCTGC-AA
1 CGGGTTCGCTCCCTCTTT-TTCAGGGAGTATAGAACTCGAAGAATCTTCTGCTAA
** * * * *
4116166 GCGGGTTCATTCCCTCTTTATCTAGGGAGTGTGGAACTCGAACG--TCTT-T--AAA
1 -CGGGTTCGCTCCCTCTTTTTC-AGGGAGTATAGAACTCGAA-GAATCTTCTGCTAA
* * * * * *
4116218 CGGGTTCACTCCCTCTTTCCTCAGGGAGAATAGAACTCGAA-TATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTT-TTCAGGGAGTATAGAACTCGAAGAATCTTCTGCTAA
* * *
4116272 CGGGTTTGCTCCCTCTTTCTCTAGGGAGTAT-GAAACTCGAACAATCTTC
1 CGGGTTCGCTCCCTCTTTTTC-AGGGAGTATAG-AACTCGAAGAATCTTC
4116321 AACAATCGTG
Statistics
Matches: 274, Mismatches: 28, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
51 37 0.14
52 5 0.02
53 6 0.02
54 91 0.33
55 135 0.49
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (54 bp):
CGGGTTCGCTCCCTCTTTTTCAGGGAGTATAGAACTCGAAGAATCTTCTGCTAA
Found at i:4116137 original size:109 final size:108
Alignment explanation
Indices: 4115948--4116485 Score: 354
Period size: 110 Copynumber: 5.0 Consensus size: 108
4115938 TCTTCAAAAT
* ** * ***
4115948 CGGGTTCGCTCCCTATCGTTTC-AGGGAACATAGAACTTGAAGAATCTTCTGGGGACGGGTTCGC
1 CGGGTTCGCTCCCTAT-TTTTCTAGGGAGTATAGAAC-TCAAGAATCTTCTGCTAACGGGTTCGC
*
4116012 TCCCTATTGT-TTCAGGGAGTATAGAACTCGAATAATCTTCTGCTAA
64 TCCCTCTT-TCTTCAGGGAGTATAGAACTCGAATAATCTTCTGC-AA
*
4116058 CGGGTTCGCTCCCTATTGTTTC-AGGGAGTATAGAACTCAAGAATCTTCTGCTAACTGGTTCGCT
1 CGGGTTCGCTCCCTATT-TTTCTAGGGAGTATAGAACTCAAGAATCTTCTGCTAACGGGTTCGCT
* *
4116122 CCCTCTTTCTTCAGGGAGTATGGAACTCGAACAATCTTCTGCAA
65 CCCTCTTTCTTCAGGGAGTATAGAACTCGAATAATCTTCTGCAA
** * * * * * * *
4116166 GCGGGTTCATTCCCTCTTTATCTAGGGAGTGTGGAACTC--GAA-CGTCT-TTAAACGGGTTCAC
1 -CGGGTTCGCTCCCTATTTTTCTAGGGAGTATAGAACTCAAGAATCTTCTGCT-AACGGGTTCGC
* * *
4116227 TCCCTCTTTCCTCAGGGAGAATAGAACTCGAAT-ATCTTCTTCAAA
64 TCCCTCTTTCTTCAGGGAGTATAGAACTCGAATAATCTTCTGC-AA
* * * * ** *
4116272 CGGGTTTGCTCCCTCTTTCTCTAGGGAGTAT-GAAACTCGAACAATCTTCAAC-AATCGTG-TCT
1 CGGGTTCGCTCCCTATTTTTCTAGGGAGTATAG-AACTC-AAGAATCTTCTGCTAA-CGGGTTC-
* * * * **
4116334 GCTCCCTATTTCTTCAGAGAGTAT-GAGATTCGAACAATCTTCAACAA
62 GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAATAATCTTCTGCAA
** * * ** *
4116381 TCATG-TCTGCTCCCTATTTCTTC-AGAGAGTAT-GAGACTCGAACAATCTTCAAC-AATCGTG-
1 -CGGGTTC-GCTCCCTATTT-TTCTAGGGAGTATAGA-ACTC-AAGAATCTTCTGCTAA-CGGGT
* * * *
4116441 TCTGCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACAATCTTC
60 TC-GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAATAATCTTC
4116486 AATAATCGTT
Statistics
Matches: 354, Mismatches: 53, Indels: 42
0.79 0.12 0.09
Matches are distributed among these distances:
104 1 0.00
105 40 0.11
106 44 0.12
107 3 0.01
108 14 0.04
109 123 0.35
110 126 0.36
111 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (108 bp):
CGGGTTCGCTCCCTATTTTTCTAGGGAGTATAGAACTCAAGAATCTTCTGCTAACGGGTTCGCTC
CCTCTTTCTTCAGGGAGTATAGAACTCGAATAATCTTCTGCAA
Found at i:4116180 original size:55 final size:54
Alignment explanation
Indices: 4116003--4116485 Score: 348
Period size: 55 Copynumber: 8.9 Consensus size: 54
4115993 CTTCTGGGGA
* * *
4116003 CGGGTTCGCTCCCTATTGT-TTCAGGGAGTATAGAACTCGAATAATCTTCTGCTAA-
1 CGGGTTC-CTCCCTATT-TCTTCAGGGAGTATGGAACTCGAACAATCTTCTAC-AAT
* * *
4116058 CGGGTTCGCTCCCTATTGT-TTCAGGGAGTATAGAACTC-AAGAATCTTCTGCTAA-
1 CGGGTTC-CTCCCTATT-TCTTCAGGGAGTATGGAACTCGAACAATCTTCTAC-AAT
* * * *
4116112 CTGGTTCGCTCCCTCTTTCTTCAGGGAGTATGGAACTCGAACAATCTTCTGCAAG
1 CGGGTTC-CTCCCTATTTCTTCAGGGAGTATGGAACTCGAACAATCTTCTACAAT
* * * * *
4116167 CGGGTTCATTCCCTCTTT-ATCTAGGGAGTGTGGAACTCGAAC-GTCTT-TA-AA-
1 CGGGTTC-CTCCCTATTTCTTC-AGGGAGTATGGAACTCGAACAATCTTCTACAAT
* * * * * * *
4116218 CGGGTTCACTCCCTCTTTCCTCAGGGAGAATAGAACTCGAA-TATCTTCTTCAAA
1 CGGGTTC-CTCCCTATTTCTTCAGGGAGTATGGAACTCGAACAATCTTCTACAAT
* * * *
4116272 CGGGTTTGCTCCCTCTTTC-TCTAGGGAGTATGAAACTCGAACAATCTTCAACAAT
1 CGGG-TTCCTCCCTATTTCTTC-AGGGAGTATGGAACTCGAACAATCTTCTACAAT
* * * * *
4116327 CGTGTCTGCTCCCTATTTCTTCAGAGAGTAT-GAGATTCGAACAATCTTCAACAAT
1 CGGGT-TCCTCCCTATTTCTTCAGGGAGTATGGA-ACTCGAACAATCTTCTACAAT
** * * *
4116382 CATGTCTGCTCCCTATTTCTTCAGAGAGTAT-GAGACTCGAACAATCTTCAACAAT
1 CGGGT-TCCTCCCTATTTCTTCAGGGAGTATGGA-ACTCGAACAATCTTCTACAAT
* * *
4116437 CGTGTCTGCTCCCTATTTCTTCAGAGAGTATAGG-ACTCGAACAATCTTC
1 CGGGT-TCCTCCCTATTTCTTCAGGGAGTAT-GGAACTCGAACAATCTTC
4116486 AATAATCGTT
Statistics
Matches: 376, Mismatches: 35, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
51 37 0.10
52 5 0.01
53 6 0.02
54 89 0.24
55 236 0.63
56 2 0.01
57 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (54 bp):
CGGGTTCCTCCCTATTTCTTCAGGGAGTATGGAACTCGAACAATCTTCTACAAT
Found at i:4117510 original size:10 final size:11
Alignment explanation
Indices: 4117495--4117535 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
4117485 TGAACCCTCA
4117495 TTTTTCATT-T
1 TTTTTCATTAT
4117505 TTTTTCATTCAT
1 TTTTTCATT-AT
*
4117517 TTTTT-TTTAT
1 TTTTTCATTAT
4117527 TTTTTCATT
1 TTTTTCATT
4117536 TTCACTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 16 0.62
11 4 0.15
12 6 0.23
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCATTAT
Found at i:4117567 original size:28 final size:26
Alignment explanation
Indices: 4117502--4117567 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
4117492 TCATTTTTCA
* *
4117502 TTTTTTTTCATTCATTTTTTTTTATT
1 TTTTTTTTCACTCATTTTTTCTTATT
*
4117528 TTTTCATTTTCACTCATTTTTTCTTCTT
1 TTTT--TTTTCACTCATTTTTTCTTATT
4117556 CTTTTTTCTTCA
1 -TTTTTT-TTCA
4117568 AGCAAAATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 4 0.12
27 2 0.06
28 23 0.70
29 4 0.12
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTTTTTCACTCATTTTTTCTTATT
Found at i:4128908 original size:25 final size:24
Alignment explanation
Indices: 4128870--4128917 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
4128860 TGAAAATAAA
* *
4128870 ATAAAAATTGCATAACATGCATAC
1 ATAAAAATTACATAACATACATAC
*
4128894 ATAAAAATGTACATACCATACATA
1 ATAAAAAT-TACATAACATACATA
4128918 AAATAGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (24 bp):
ATAAAAATTACATAACATACATAC
Found at i:4131052 original size:6 final size:6
Alignment explanation
Indices: 4131041--4131083 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
4131031 ACGCAATTAA
**
4131041 ACATAT ACATAT ACATAT ACATAT ATGTAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT A
4131084 GTATGTTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (6 bp):
ACATAT
Found at i:4134595 original size:185 final size:185
Alignment explanation
Indices: 4134266--4134949 Score: 837
Period size: 179 Copynumber: 3.8 Consensus size: 185
4134256 ACTTTATGTT
* * * * * * * *
4134266 GACCTATTTTCTCATATTTTTAGCTGTTATATTTTTATCGATTGATACATTTTCATAAAGTGTTG
1 GACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCG
* *
4134331 ACACTTTTTAGGCGCTATAACTT-AT-T-TTCTTTTAAATTCAGAAAGTGTCGATACTTATATTA
66 ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTTTTAAATTCAGAAAGTGTCGATACTTATATTA
*
4134393 AATTATCGACACTTTCAACATATCCGGTAGTCTTTTACCAGTTTTGTCATTTTGA
131 AATTATCGACACTTTCAACATATCTGGTAGTCTTTTACCAGTTTTGTCATTTTGA
* *
4134448 GACCGATTTTGTCTTATTTTTACCTGTTATATTGTTATGGATCGATACATTTT-TTAAAGTATCG
1 GACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCG
* * * *
4134512 ACACTTTATAGGCGTTATAACTTCTTCTCTTTTATTTAAATACAAAAAGTGTCGATACTTATATT
66 ACACTTTTTAGGCGCTATAACTTCTTCTCTTTT-TTTAAATTCAGAAAGTGTCGATACTTATATT
* * *
4134577 TAAGTATCGACGCTTTCAACATATCTGGTAGT-TATTTA-CATGTTTTGTCATTTTGA
130 AAATTATCGACACTTTCAACATATCTGGTAGTCT-TTTACCA-GTTTTGTCATTTTGA
* * *
4134633 GACC-AGTTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTC
1 GACCGA-TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATC
4134697 GACACTTTTTAGGCGCTAT-A--TCTTCTC---TTTTAAATTCAGAAAGTGTCGATACTTATATT
65 GACACTTTTTAGGCGCTATAACTTCTTCTCTTTTTTTAAATTCAGAAAGTGTCGATACTTATATT
** *
4134756 AAATTATCGACACTTGAAACATATCTGGTAG-CGTTTTACCGGTTTTGTCATTTTGA
130 AAATTATCGACACTTTCAACATATCTGGTAGTC-TTTTACCAGTTTTGTCATTTTGA
* * * * **
4134812 GATCGGTTTTATCATATTTTTACCTGTAATATTGTTATGGATCGATACATTTTTTTAAAGTATCG
1 GACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCG
* * * * * *
4134877 ATAATTTTTAGGCGCTATAACTTATTTTCTTTTTATT---TCCA-AAAGTGTCGATATTTATATT
66 ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTT-TTAAATTCAGAAAGTGTCGATACTTATATT
*
4134938 AAAATATCGACA
130 AAATTATCGACA
4134950 TTGTTAATTT
Statistics
Matches: 432, Mismatches: 51, Indels: 38
0.83 0.10 0.07
Matches are distributed among these distances:
179 145 0.34
180 4 0.01
181 29 0.07
182 82 0.19
183 11 0.03
184 7 0.02
185 127 0.29
186 27 0.06
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (185 bp):
GACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCG
ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTTTTAAATTCAGAAAGTGTCGATACTTATATTA
AATTATCGACACTTTCAACATATCTGGTAGTCTTTTACCAGTTTTGTCATTTTGA
Found at i:4137589 original size:18 final size:18
Alignment explanation
Indices: 4137566--4137600 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4137556 GTCACAACCT
4137566 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
4137584 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
4137601 GTTGACCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:4137600 original size:13 final size:13
Alignment explanation
Indices: 4137565--4137589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4137555 AGTCACAACC
4137565 TGACCCGACCCGT
1 TGACCCGACCCGT
4137578 TGACCCGACCCG
1 TGACCCGACCCG
4137590 ACCCGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:4139177 original size:24 final size:24
Alignment explanation
Indices: 4139150--4139197 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
4139140 CCTTAGATTA
4139150 ATTAAGGAATCCAAATAAGCATAG
1 ATTAAGGAATCCAAATAAGCATAG
4139174 ATTAAGGAATCCAAATAAGCATAG
1 ATTAAGGAATCCAAATAAGCATAG
4139198 GTATTGGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (24 bp):
ATTAAGGAATCCAAATAAGCATAG
Found at i:4140202 original size:24 final size:24
Alignment explanation
Indices: 4140113--4140207 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
4140103 TTATCTGAAT
* * *
4140113 TCTGATTTGAATTATGTTTTGACA
1 TCTGATCTGAATTATGTTCTGATA
*
4140137 TCTGATCTGAAATATGTTCTGAT-
1 TCTGATCTGAATTATGTTCTGATA
* * * *
4140160 TCCTAACCTGGATTCTGTTCTGATA
1 T-CTGATCTGAATTATGTTCTGATA
*
4140185 TCTGATCTGAATTATGTTTTGAT
1 TCTGATCTGAATTATGTTCTGAT
4140208 TTTTTATATC
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
23 1 0.02
24 53 0.96
25 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (24 bp):
TCTGATCTGAATTATGTTCTGATA
Found at i:4142328 original size:13 final size:13
Alignment explanation
Indices: 4142310--4142363 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
4142300 GGTCACAACC
4142310 TGACCCGACCCGT
1 TGACCCGACCCGT
4142323 TGACCCGACCCGACCCAT
1 TGACCCGACCCG-----T
*
4142341 TTACCCGACCCGT
1 TGACCCGACCCGT
4142354 TGACCCGACC
1 TGACCCGACC
4142364 TGACCCGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
13 22 0.65
18 12 0.35
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.15
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:4142334 original size:18 final size:18
Alignment explanation
Indices: 4142311--4142376 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
4142301 GTCACAACCT
4142311 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
*
4142329 GACCCGACCCATT-----
1 GACCCGACCCGTTGACCC
*
4142342 TACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
*
4142360 GACCTGACCCGTTGACC
1 GACCCGACCCGTTGACC
4142377 GTTGACCGGC
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
13 11 0.29
18 27 0.71
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:4144956 original size:24 final size:24
Alignment explanation
Indices: 4144860--4144961 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 24
4144850 GAATATTTTA
* * *
4144860 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTATGT
* * *
4144884 TTTGACATCTGATCTGAAATATGT
1 TCTGATATCTGATCTGAATTATGT
* * * * *
4144908 TATGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
4144932 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
*
4144956 TTTGAT
1 TCTGAT
4144962 TTTTTATATC
Statistics
Matches: 57, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
23 1 0.02
24 55 0.96
25 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:4147899 original size:199 final size:198
Alignment explanation
Indices: 4147427--4148398 Score: 1245
Period size: 200 Copynumber: 4.9 Consensus size: 198
4147417 TGTATTTGGG
* * * * * * *
4147427 GTCGATACTTTTTATTTAGACCTATTTTCTCATAAAATCGGTAAATTTAAACCGGTTATATTGTA
1 GTCGATAC--TTTATGTATACCTGTTTTCTCAT-AAATCGGTATATTTAGACCGGTTACATTGTT
* * *
4147492 AATTTACCCATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGT
63 AATTTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGT
* * * *
4147557 ATCGAAACTTTGTTGTGCACTTGGTTTTGAAAATACACTT-TGGA-CAAAACGTATCAATAATT-
128 ATCGACACTTT-TTGTGCACTTGGTTTTG-AAATACA-TTATGGACCAAAA-GTATCGACACTTG
**
4147619 TTTATATCAGT
189 TTT-TATTTGT
* *
4147630 GTTGATACTTTATGTATACCTGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTAAT
1 GTCGATACTTTATGTATACCTGTTTTCTCATAAATCGGTATATTTAGACCGGTTACATTGTTAAT
*
4147695 TTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTCTTATAAAGGTATC
66 TTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATC
*
4147760 GACACTTTTTAGTACACTTGGTTTTGAAATACATTATGGACCAAAAGTATCGACACTTGTTTTAT
131 GACACTTTTT-GTGCACTTGGTTTTGAAATACATTATGGACCAAAAGTATCGACACTTGTTTTAT
4147825 TTGT
195 TTGT
*
4147829 GTCGATACTTTATGTATACCTGTTTTCTCATAAATCGGTATATTTAGATCGGTTACATTGTTAAT
1 GTCGATACTTTATGTATACCTGTTTTCTCATAAATCGGTATATTTAGACCGGTTACATTGTTAAT
*
4147894 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATC
66 TTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATC
* * * *
4147959 GACACATTTAGTGCAATTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
131 GACACTTTTTGTGCACTTGGTTTTGAAATACATTATGGACCAAAAGTATCGACACTTGTTTTATT
4148024 TGT
196 TGT
* * * * ** *
4148027 GTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACAAGTTAAATTGTTAAT
1 GTCGATACTTTATGTATACCTGTTTTCTCATAAATCGGTATATTTAGACCGGTTACATTGTTAAT
* *
4148092 TTACTTATTAC-TTCATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTAT
66 TTACCTATTACATT-ATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTAT
* *** * * * * *
4148156 CGACACTTTGTTGTGCACTTGGTTTTTAAAATACACGCTGGACAAAAAATATCTACACTTATTGT
130 CGACACTTT-TTGTGCACTTGG-TTTTGAAATACATTATGGACCAAAAGTATCGACACTTGTTTT
4148221 ATTTGT
193 ATTTGT
* * * * * *
4148227 GTCGATACTTTATGTATACTTGTTTTCTCAAAAATCGGTATATTTAGGCTGGTTACATTATTATT
1 GTCGATACTTTATGTATACCTGTTTTCTCATAAATCGGTATATTTAGACCGGTTACATTGTTAAT
* * *
4148292 TTACCTATTACATTAT-ATATATGTA-TTTCAATGTTTTTAGTATCGACACTTCTTATAAATGTA
66 TTACCTATTACATTATAAT-TATG-AGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTA
** * *
4148355 TCGACACTTTTTTCGTGCACTTAATTTGGAAATATATTATGGAC
129 TCGACAC-TTTTT-GTGCACTTGGTTTTGAAATACATTATGGAC
4148399 AACATGTATC
Statistics
Matches: 682, Mismatches: 75, Indels: 27
0.87 0.10 0.03
Matches are distributed among these distances:
197 2 0.00
198 180 0.26
199 172 0.25
200 287 0.42
201 34 0.05
203 7 0.01
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (198 bp):
GTCGATACTTTATGTATACCTGTTTTCTCATAAATCGGTATATTTAGACCGGTTACATTGTTAAT
TTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATC
GACACTTTTTGTGCACTTGGTTTTGAAATACATTATGGACCAAAAGTATCGACACTTGTTTTATT
TGT
Found at i:4148625 original size:24 final size:24
Alignment explanation
Indices: 4148598--4148644 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4148588 ATTTACATTT
4148598 AAATTCAAACTCAAACTCAAATTG
1 AAATTCAAACTCAAACTCAAATTG
* * *
4148622 AAATTTAAATTCAAACTCTAATT
1 AAATTCAAACTCAAACTCAAATT
4148645 ATAAATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTCAAACTCAAACTCAAATTG
Found at i:4152143 original size:30 final size:30
Alignment explanation
Indices: 4152097--4152153 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
4152087 GCAAAAACAT
** *
4152097 AAACTTAAAGTCCCAAAACAATAATTACAG
1 AAACTTAAAGAACCAAAACAAAAATTACAG
*
4152127 AAACTTAAAGAACCAAAATAAAAATTA
1 AAACTTAAAGAACCAAAACAAAAATTA
4152154 AATAAGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (30 bp):
AAACTTAAAGAACCAAAACAAAAATTACAG
Found at i:4153772 original size:3 final size:3
Alignment explanation
Indices: 4153760--4153803 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
4153750 TAATATCAAT
*
4153760 TAA TAT TAA TAA TAAA TAA TAA TAA TAA TAA TTAA TAA TTAA TA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA -TAA TA
4153804 TTTTTTGCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 27 0.75
4 9 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:4153777 original size:13 final size:12
Alignment explanation
Indices: 4153748--4153805 Score: 57
Period size: 13 Copynumber: 4.8 Consensus size: 12
4153738 AAACATGTAA
*
4153748 AATAATATCAAT
1 AATAATATTAAT
4153760 --TAATATTAAT
1 AATAATATTAAT
*
4153770 AATAAATAATAAT
1 AAT-AATATTAAT
4153783 AATAATAATTAAT
1 AATAAT-ATTAAT
4153796 AATTAATATT
1 AA-TAATATT
4153806 TTTTGCCCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 9 0.24
12 4 0.11
13 21 0.55
14 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:4153779 original size:7 final size:6
Alignment explanation
Indices: 4153760--4153803 Score: 52
Period size: 7 Copynumber: 6.8 Consensus size: 6
4153750 TAATATCAAT
*
4153760 TAATAT TAATAA TAAATAA TAATAA TAATAA TTAATAA TTAATA
1 TAATAA TAATAA T-AATAA TAATAA TAATAA -TAATAA -TAATA
4153804 TTTTTTGCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
6 17 0.49
7 18 0.51
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
TAATAA
Found at i:4153779 original size:16 final size:16
Alignment explanation
Indices: 4153760--4153803 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
4153750 TAATATCAAT
4153760 TAATATTAATAATAAA
1 TAATATTAATAATAAA
* *
4153776 TAATAATAATAATAAT
1 TAATATTAATAATAAA
4153792 TAATAATTAATA
1 TAAT-ATTAATA
4153804 TTTTTTGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATTAATAATAAA
Found at i:4153793 original size:26 final size:26
Alignment explanation
Indices: 4153747--4153803 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
4153737 TAAACATGTA
4153747 AAATAATATCAATTAATATTAATAAT
1 AAATAATATCAATTAATATTAATAAT
4153773 AAATAATAAT-AA-TAATAATTAATAAT
1 AAATAAT-ATCAATTAAT-ATTAATAAT
*
4153799 TAATA
1 AAATA
4153804 TTTTTTGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 4 0.14
26 22 0.79
27 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
AAATAATATCAATTAATATTAATAAT
Found at i:4154507 original size:129 final size:128
Alignment explanation
Indices: 4154078--4154505 Score: 425
Period size: 129 Copynumber: 3.3 Consensus size: 128
4154068 TTTAGGAAAA
** * * * *
4154078 GTGATAACTTGGTTCCTACGTGATGTA-GATGGCTGGTTATCTAAGTTGACATAGCTCATACATA
1 GTGATAACACGGTTCCTACGTGATG-AGGACGGCTGGTTATCTAGGTTGACACAGCTCCTACATA
* ** * * * **
4154142 ATGAGGATACCAGGTC-AGGTGATGACACGACTCATACATGATGAAGAGTTC-TGTCCATCTA-A
65 ATGAGGAGACCAGGTCGA-GTGATGACACGGTTCCTACGTGATGAGGACATCATGT-CATCTATA
4154204 CG
128 -G
* * * * * * *
4154206 GTGATAACACGGCTCATACGTGATGAAGA-GTTCTGGTTATCAATGATTGACACTGCTCCTACAT
1 GTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTA-GGTTGACACAGCTCCTACAT
* * * * * *** *
4154270 AATGAGGAGATCAGATCGGGTGATGACATGGTTCCTACGTGATGTGGATGGCATGCCATCTATAG
64 AATGAGGAGACCAGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACATCATGTCATCTATAG
* * * *
4154335 GTGATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCTGGGTTTGACACGGCTCCTACATG
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGG-TTGACACAGCTCCTACATA
*
4154400 ATGAGGAGACCAGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACATCAGGTCATCTATAG
65 ATGAGGAGACCAGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACATCATGTCATCTATAG
* *
4154464 GTGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCT
1 GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
4154506 GGAGTGACAA
Statistics
Matches: 243, Mismatches: 49, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
127 2 0.01
128 34 0.14
129 203 0.84
130 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (128 bp):
GTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGTTGACACAGCTCCTACATAA
TGAGGAGACCAGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACATCATGTCATCTATAG
Found at i:4155277 original size:86 final size:83
Alignment explanation
Indices: 4155038--4155352 Score: 362
Period size: 86 Copynumber: 3.7 Consensus size: 83
4155028 GTCATCGAGT
* * * *
4155038 TAAATGGAATCAAACTCGAAGGTGTTTGTTGACAGATAACCCTTTTCGTCTTGAGTTATGCTGA-
1 TAAATGGAATCGAACTCGAAGGT-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCT-AT
* **
4155102 AAATTTGACATGTCCTTGAGC
64 GAATTTG-GTTGTCCTTGAGC
* * * * * *
4155123 TGAATGTAATCGAACTCGAAGGTTTGTGTTGATAGATAATCCTTCTCGCCTTAAGCTATGCTGTG
1 TAAATGGAATCGAACTCGAAGGTTT-TGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTATG
4155188 AATTTGGTTGTCCTTGAGC
65 AATTTGGTTGTCCTTGAGC
* *
4155207 TAAATGGAATCGAACTCAAAGGTCTCTTGCTTGACAAATAACCCTTCTCGCCTTGAGCTATGCTA
1 TAAATGGAATCGAACTCGAAGGT-T-TTG-TTGACAGATAACCCTTCTCGCCTTGAGCTATGCTA
4155272 TGAATTTGGTTGTCCTTGAGC
63 TGAATTTGGTTGTCCTTGAGC
* * * * * *
4155293 TGAATGAAATCGAACTCGAAGGTCTTGGTTGATAGATAACCTTTCTCGCCTTGAGTTATG
1 TAAATGGAATCGAACTCGAAGGT-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
4155353 TTGCCAATAG
Statistics
Matches: 196, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
84 61 0.31
85 61 0.31
86 74 0.38
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (83 bp):
TAAATGGAATCGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTATGA
ATTTGGTTGTCCTTGAGC
Found at i:4155530 original size:86 final size:86
Alignment explanation
Indices: 4155412--4155678 Score: 383
Period size: 86 Copynumber: 3.1 Consensus size: 86
4155402 ACAGGTCATA
* * * *
4155412 ATTCTTCAGGTGGTTCCCCTTAACGAGTCTGAACCAAGTGGGATGATCTTTGGATGACTCCCCTT
1 ATTCCTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCTT
4155477 CATGGGAAAACCATGTGGTAT
66 CATGGGAAAACCATGTGGTAT
* * *
4155498 ATTCCTCAGGTGATTCCCCTTAGCGGGTCTGAACCGAGTGAGATGAAT-TTTGGATGACCCCCCT
1 ATTCCTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATG-ATCTTTGGATGACTCCCCT
*
4155562 TCATAGGAAAACCATGTGGTAT
65 TCATGGGAAAACCATGTGGTAT
* * * * * * *
4155584 ATTTCTCGGGTGGTTCCTCTTAGCAGGTCTGAACCAAGTAAGATGATCTTTAGATGACTCCCATT
1 ATTCCTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCTT
4155649 CATGGGAAAACCATGTGGTAT
66 CATGGGAAAACCATGTGGTAT
4155670 ATTCCTCAG
1 ATTCCTCAG
4155679 TCGGATATCA
Statistics
Matches: 158, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
85 2 0.01
86 154 0.97
87 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (86 bp):
ATTCCTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCTT
CATGGGAAAACCATGTGGTAT
Found at i:4156175 original size:32 final size:32
Alignment explanation
Indices: 4156106--4156190 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 32
4156096 TCGCATCAGG
* *
4156106 ATGTTGAATCTCTAAAGATGCCCCAATATTCA
1 ATGTTGAATCTCCAAAGATGCCCCAACATTCA
* * **
4156138 ATGTTGAATTTCCAAATATGCCCCAACATTTG
1 ATGTTGAATCTCCAAAGATGCCCCAACATTCA
* **
4156170 TTGTTGAATCTTTAAAGATGC
1 ATGTTGAATCTCCAAAGATGC
4156191 ACCATTGTTC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (32 bp):
ATGTTGAATCTCCAAAGATGCCCCAACATTCA
Found at i:4157257 original size:12 final size:11
Alignment explanation
Indices: 4157230--4157282 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 11
4157220 TTCGCATGTG
4157230 CTTTTTTC-TT
1 CTTTTTTCTTT
4157240 CTTTTTTTCTTT
1 C-TTTTTTCTTT
4157252 ACTTTTTTCTTT
1 -CTTTTTTCTTT
4157264 GCTTCTTTTCTTT
1 -CTT-TTTTCTTT
4157277 -TTTTTT
1 CTTTTTT
4157283 ACAAAATGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 5 0.13
11 9 0.24
12 15 0.39
13 9 0.24
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:4159240 original size:2 final size:2
Alignment explanation
Indices: 4159233--4159268 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4159223 ACAACAAGGG
* *
4159233 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4159269 GGATAAATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4161219 original size:51 final size:51
Alignment explanation
Indices: 4161164--4161279 Score: 133
Period size: 57 Copynumber: 2.2 Consensus size: 51
4161154 TGTAAATACT
* *
4161164 GATGCAAAAGTAATGATCCTCTAAAATGCAATGCATCATGCAGAATGCGAA
1 GATGCAAAAGTAATGATCCTCTAAAATACAATGCATCATACAGAATGCGAA
* * *
4161215 GATGCAGATGAAAAATTGATGATCCTCTGAAATACAATGCATCATACAGAATGCGAA
1 GATGC------AAAAGTAATGATCCTCTAAAATACAATGCATCATACAGAATGCGAA
4161272 GATGCAAA
1 GATGCAAA
4161280 TGCAGATGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
51 8 0.15
57 46 0.85
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (51 bp):
GATGCAAAAGTAATGATCCTCTAAAATACAATGCATCATACAGAATGCGAA
Found at i:4161253 original size:57 final size:61
Alignment explanation
Indices: 4161176--4161323 Score: 205
Period size: 63 Copynumber: 2.5 Consensus size: 61
4161166 TGCAAAAGTA
* * *
4161176 ATGATCCTCTAAAATGCAATGCATCATGCAGAATGCG-A-A-G-ATGCAGATGAAAAATTG
1 ATGATCCTCTGAAATACAATGCATCATACAGAATGCGAAGATGAATGCAGATGAAAAATTG
*
4161233 ATGATCCTCTGAAATACAATGCATCATACAGAATGCGAAGATGCAAATGCAGATGCAAAATTG
1 ATGATCCTCTGAAATACAATGCATCATACAGAATGCGAAGATG--AATGCAGATGAAAAATTG
*
4161296 ATAATCCTCTGAAATACAATGCATCATA
1 ATGATCCTCTGAAATACAATGCATCATA
4161324 AAAAATTGAT
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
57 34 0.43
58 1 0.01
59 1 0.01
60 1 0.01
63 43 0.54
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (61 bp):
ATGATCCTCTGAAATACAATGCATCATACAGAATGCGAAGATGAATGCAGATGAAAAATTG
Found at i:4161330 original size:36 final size:36
Alignment explanation
Indices: 4161289--4161358 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
4161279 ATGCAGATGC
4161289 AAAATTGATAATCCTCTGAAATACAATGCATCATAA
1 AAAATTGATAATCCTCTGAAATACAATGCATCATAA
* *
4161325 AAAATTGATGATCCTCTGAAATGCAATGCATCAT
1 AAAATTGATAATCCTCTGAAATACAATGCATCAT
4161359 GCAGAATGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (36 bp):
AAAATTGATAATCCTCTGAAATACAATGCATCATAA
Found at i:4162089 original size:32 final size:32
Alignment explanation
Indices: 4162053--4162131 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
4162043 GTCATGATAT
*
4162053 CTACCCGAACATGCTTTAATTAAATAACATTC
1 CTACCCGAACATGCTTTAATTAAATAAAATTC
*
4162085 CTACCCGGACATGCTTTAATTAAATAAAATTC
1 CTACCCGAACATGCTTTAATTAAATAAAATTC
4162117 CTACCC-AGACATGCT
1 CTACCCGA-ACATGCT
4162132 ATCTACCCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.29
Consensus pattern (32 bp):
CTACCCGAACATGCTTTAATTAAATAAAATTC
Found at i:4162672 original size:17 final size:17
Alignment explanation
Indices: 4162650--4162684 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4162640 TGTGTGAAAA
4162650 GGAACATTCAAACCTTT
1 GGAACATTCAAACCTTT
4162667 GGAACATTCAAACCTTT
1 GGAACATTCAAACCTTT
4162684 G
1 G
4162685 ACTCAAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (17 bp):
GGAACATTCAAACCTTT
Found at i:4163510 original size:30 final size:30
Alignment explanation
Indices: 4163464--4163520 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
4163454 GCAAAAACAT
** *
4163464 AAACTTAAAGTCCCAAAACAATAATTACAG
1 AAACTTAAAGAACCAAAACAAAAATTACAG
*
4163494 AAACTTAAAGAACCAAAATAAAAATTA
1 AAACTTAAAGAACCAAAACAAAAATTA
4163521 AATAAGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (30 bp):
AAACTTAAAGAACCAAAACAAAAATTACAG
Found at i:4165145 original size:16 final size:16
Alignment explanation
Indices: 4165126--4165169 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
4165116 TAATATCAAT
4165126 TAATATTAATAATAAA
1 TAATATTAATAATAAA
* * *
4165142 TAATAATAATAGTAAT
1 TAATATTAATAATAAA
4165158 TAATAATTAATA
1 TAAT-ATTAATA
4165170 TTTTTTGCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
TAATATTAATAATAAA
Found at i:4165671 original size:198 final size:198
Alignment explanation
Indices: 4165197--4165852 Score: 996
Period size: 199 Copynumber: 3.3 Consensus size: 198
4165187 AACAGGTGTC
* * * *
4165197 TACATTCATAATTATAGGTTTCGATGTTTTTAGGATCGACACTTGTTATAAATATATCGACACTT
1 TACATT-ATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTCTTATAAATATATCGACACTT
** * * * *
4165262 TTCCGTGTC-CTTTG-TTAAGAATACATTCTGGACCAAAAGTATCGAAACTTGTTTTAGTTGTTT
65 TTTAGTG-CACTTGGTTTAA-AATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGT
* * *
4165325 CGATACTTTTTGTACACCTGTTTTCTCAAAAACCGATATATTTAGACTGGTTA-ATTGCTAATTT
128 CGATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACTGGTTACATTGTTAATTT
4165389 ACCTAT
193 ACCTAT
*
4165395 TAAATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTCTTATAAATATATCGACACTTT
1 TACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTCTTATAAATATATCGACACTTT
**
4165460 TTAGTAAACTTGGTTTAAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGA
66 TTAGTGCACTTGGTTTAAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGA
* *
4165525 TACTATTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGATTGGTTACATTGTTAATTTACC
131 TACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACTGGTTACATTGTTAATTTACC
4165590 TAT
196 TAT
* *
4165593 TACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTCTTATAAATGTATCGACCCTTT
1 TACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTCTTATAAATATATCGACACTTT
* *
4165658 TTAGTGCACTTGGTTTTGAAATACATTATGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCG
66 TTAGTGCACTTGG-TTTAAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCG
* * * *
4165723 ATACTTTTTATACA-ACTGTTTTCACAAAAACTGGTATATTTAGACCGGTTACATTGTTAATTTA
130 ATACTTTTTGTACACA-TGTTTTCTCAAAAACCGGTATATTTAGACTGGTTACATTGTTAATTTA
4165787 CCTAT
194 CCTAT
*
4165792 TACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTCTTATAAATGTATCGACA
1 TACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTCTTATAAATATATCGACA
4165853 TATATGTTTA
Statistics
Matches: 421, Mismatches: 32, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
197 152 0.36
198 99 0.24
199 170 0.40
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (198 bp):
TACATTATAATTATGGGTTTTGATGTTTTTGGGATCGACACTTCTTATAAATATATCGACACTTT
TTAGTGCACTTGGTTTAAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGA
TACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACTGGTTACATTGTTAATTTACC
TAT
Found at i:4166249 original size:19 final size:19
Alignment explanation
Indices: 4166225--4166274 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
4166215 TTACATTCAC
*
4166225 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
*
4166244 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCGT
4166263 ATACAAAATTAA
1 ATACAAAATTAA
4166275 CCTACATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:4167768 original size:18 final size:18
Alignment explanation
Indices: 4167733--4167771 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4167723 TTCTCCCCAT
**
4167733 TTCCTCAATCTTTTCTTC
1 TTCCTCAATCTTCCCTTC
*
4167751 TTCCTCCATCTTCCCTTC
1 TTCCTCAATCTTCCCTTC
4167769 TTC
1 TTC
4167772 AAATTTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.41, G:0.00, T:0.51
Consensus pattern (18 bp):
TTCCTCAATCTTCCCTTC
Found at i:4168164 original size:9 final size:9
Alignment explanation
Indices: 4168148--4168187 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
4168138 TTCTTCACTC
4168148 CCTCCTCTA
1 CCTCCTCTA
* *
4168157 CTTCCTCTG
1 CCTCCTCTA
*
4168166 CCTCCTCTG
1 CCTCCTCTA
4168175 CCTCCTCTA
1 CCTCCTCTA
4168184 CCTC
1 CCTC
4168188 ATTGACAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.05, C:0.55, G:0.05, T:0.35
Consensus pattern (9 bp):
CCTCCTCTA
Found at i:4169736 original size:19 final size:18
Alignment explanation
Indices: 4169708--4169775 Score: 82
Period size: 19 Copynumber: 3.6 Consensus size: 18
4169698 CATTTATACA
*
4169708 ACCTAAAATATCATTTTCT
1 ACCTATAATATCATTTT-T
*
4169727 ACCTATAATATGATTTTTT
1 ACCTATAATATCA-TTTTT
4169746 ACCTATAATATCATTATTT
1 ACCTATAATATCATT-TTT
*
4169765 ACATATAATAT
1 ACCTATAATAT
4169776 TAAATAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.05
19 37 0.86
20 4 0.09
ACGTcount: A:0.38, C:0.15, G:0.01, T:0.46
Consensus pattern (18 bp):
ACCTATAATATCATTTTT
Found at i:4170609 original size:181 final size:182
Alignment explanation
Indices: 4170204--4170982 Score: 1174
Period size: 182 Copynumber: 4.3 Consensus size: 182
4170194 GTAGTGCTTT
*
4170204 ACCGGTTTTGTCATATTTTTACATGTTATATTGCTATGGATCGATACATTTTTTTAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
* *
4170269 CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATACTTATATTAAATT
66 CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGT
* * *
4170334 ATCGACACTTTCAACATATCTGGTATCTTTTTACCGGTTTTGTCATTTTGAG
131 ATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAG
* * * *
4170386 ACCTGTTTTGTGATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTGTCGA
1 ACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
*
4170451 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTT-TATTAAAGT
66 CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGT
*
4170515 ATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTTGAG
131 ATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAG
* *
4170567 ACCGGTTTTTTCATATTTTTACATGTTATATTGCTATGGATCGATACATTTTTTTAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
*
4170632 CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGT
66 CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGT
* * * * * *
4170697 ATCGACACTTTCAATATAACCGATAG-TTATTTACCTGTTTTATCATTTTGAG
131 ATCGACACTTTCAACATATCCGGTAGCGT-TTTACCGGTTTTGTCATTTTGAG
* ** * *
4170749 ACCGATTTTGTCATATTTTTAGC-TGTTATATTGTTATGGATC-ATTACATTTTCATAAAGTTTG
1 ACCGGTTTTGTCATATTTTTA-CATGTTATATTGTTATGGATCGA-TACATTTTTTTAAAGTATC
* *
4170812 GACACTTTTTAGGCGTTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAA
64 GACACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTATATTAA
* * *
4170876 ATTATTGACACTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCATTTTGAG
128 AGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAG
* * *
4170931 ACCGG-TTTGTCATATTTTTACCTATTATATTGTTATAGATCGATACATTTTT
1 ACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTT
4170983 CATTTGTATC
Statistics
Matches: 539, Mismatches: 50, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
180 1 0.00
181 211 0.39
182 325 0.60
183 2 0.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (182 bp):
ACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGT
ATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAG
Found at i:4170745 original size:363 final size:364
Alignment explanation
Indices: 4170204--4170982 Score: 1237
Period size: 363 Copynumber: 2.1 Consensus size: 364
4170194 GTAGTGCTTT
4170204 ACCGGTTTTGTCATATTTTTACATGTTATATTGCTATGGATCGATACATTTTTTTAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACATGTTATATTGCTATGGATCGATACATTTTTTTAAAGTATCGA
* * *
4170269 CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATACTTATATTAAATT
66 CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGT
* * * * * *
4170334 ATCGACACTTTCAACATATCTGGTATCTTTTTACCGGTTTTGTCATTTTGAGACCTG-TTTTGTG
131 ATCGACACTTTCAACATAACCGATATCTATTTACCGGTTTTATCATTTTGAGACC-GATTTTGTC
**
4170398 ATATTTTTACCTGTTATATTGTTATGGATCGA-TACATTTTTTTAAAGTGTCGACACTTTATAGG
195 ATATTTTTACCTGTTATATTGTTATGGATC-ATTACATTTTCATAAAGTGTCGACACTTTATAGG
4170462 CGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTT-TATTAAAGTATCGACACTT
259 CGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAAGTATCGACACTT
4170525 TCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTTGAG
323 TCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTTGAG
*
4170567 ACCGGTTTTTTCATATTTTTACATGTTATATTGCTATGGATCGATACATTTTTTTAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACATGTTATATTGCTATGGATCGATACATTTTTTTAAAGTATCGA
4170632 CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGT
66 CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGT
* *
4170697 ATCGACACTTTCAATATAACCGATAGT-TATTTACCTGTTTTATCATTTTGAGACCGATTTTGTC
131 ATCGACACTTTCAACATAACCGATA-TCTATTTACCGGTTTTATCATTTTGAGACCGATTTTGTC
* * * *
4170761 ATATTTTTAGCTGTTATATTGTTATGGATCATTACATTTTCATAAAGTTTGGACACTTTTTAGGC
195 ATATTTTTACCTGTTATATTGTTATGGATCATTACATTTTCATAAAGTGTCGACACTTTATAGGC
* * *
4170826 GTTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATTGACACTTTC
260 GCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAGTATCGACACTTTC
* *
4170891 AACATATCTGGTAGCGTTTTACCGGTTTTGTCATTTTGAG
325 AACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTTGAG
* * * *
4170931 ACCGG-TTTGTCATATTTTTACCTATTATATTGTTATAGATCGATACATTTTT
1 ACCGGTTTTGTCATATTTTTACATGTTATATTGCTATGGATCGATACATTTTT
4170983 CATTTGTATC
Statistics
Matches: 383, Mismatches: 28, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
362 4 0.01
363 316 0.83
364 63 0.16
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (364 bp):
ACCGGTTTTGTCATATTTTTACATGTTATATTGCTATGGATCGATACATTTTTTTAAAGTATCGA
CACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGT
ATCGACACTTTCAACATAACCGATATCTATTTACCGGTTTTATCATTTTGAGACCGATTTTGTCA
TATTTTTACCTGTTATATTGTTATGGATCATTACATTTTCATAAAGTGTCGACACTTTATAGGCG
CTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCA
ACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTTGAG
Found at i:4171356 original size:17 final size:16
Alignment explanation
Indices: 4171334--4171367 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4171324 TAAAGACAGT
4171334 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
4171351 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
4171367 A
1 A
4171368 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:4175208 original size:19 final size:20
Alignment explanation
Indices: 4175186--4175229 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4175176 GAGAAAAGGT
4175186 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
4175205 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
4175225 AAAAG
1 AAAAG
4175230 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:4181585 original size:201 final size:200
Alignment explanation
Indices: 4181293--4182313 Score: 1676
Period size: 201 Copynumber: 5.1 Consensus size: 200
4181283 GTAGTGCCTA
* * *
4181293 TAAG-TTGTGTCGATATTTTTTGTCCAAAATTAATGCCCAAACTAGGTGCACACATAAAGTGTCG
1 TAAGTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCG
* *
4181357 ATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATAGGTAAT
66 ATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAT
*
4181422 TTTTCAATGTAACTGGTATAAATATACATGTTTTAAGAGAGAATAGGTCTACATAATGTATCAAC
131 TTTTCAATGTAACTGGTATAAATATAC-TGTTTTAAGAGAGAATAGGTCTACATAATGTATCGAC
4181487 ACTTTT
195 ACTTTT
* * * *
4181493 AAAGTTTGTGTCAATACTTTTTGTCCAGAATGAATGCCCAAACTACGTGCACGCATAAAGTGTCG
1 TAAGTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCG
*
4181558 ATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATATTTATAATGTAATAGGTAAT
66 ATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAT
* *
4181623 TTTTCAGTGTAACTGGTATAAATATACTGATTTTAAGAGAGAATAGGTCTATATAATGTATCGAC
131 TTTTCAATGTAACTGGTATAAATATACTG-TTTTAAGAGAGAATAGGTCTACATAATGTATCGAC
4181688 ACTTTT
195 ACTTTT
* * *
4181694 TAAG-TTGTGTCGATACTTTTTGTCCATAATGAATGCCCAAACTAGGTGCACACATAAAGTGTTG
1 TAAGTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCG
*
4181758 ATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATATGTAAT
66 ATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAT
* *
4181823 TTTTCAATGTAACTGGTATAAATATACATGTTTTAAGAGAGAATATGTCTACATAATGTATCGAA
131 TTTTCAATGTAACTGGTATAAATATAC-TGTTTTAAGAGAGAATAGGTCTACATAATGTATCGAC
4181888 ACTTTT
195 ACTTTT
* *
4181894 TAAGTTTGTGTCGATACTTTTTGTCCATAATGAATGCCCAAACTAGGTGCACGAATAAAGTGTCG
1 TAAGTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCG
4181959 ATACATTTATAAAAAGTATCGATCCCAAAAA-ATCGAAACCCATAATTATAATGTAATAGGTAA-
66 ATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAT
* *
4182022 TTTTCAATGTAACCGGTATAAATATATCGGTTTTAAGAGAGAATAGGTCTACATAATGTATCGAC
131 TTTTCAATGTAACTGGTATAAATATA-CTGTTTTAAGAGAGAATAGGTCTACATAATGTATCGAC
4182087 ACTTTT
195 ACTTTT
*
4182093 TAAG-TT-TGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCATAAAATGTCG
1 TAAGTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCG
* *
4182156 ATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAA
66 ATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAT
* * * *
4182221 TTTCCAATGTAACCGGTATAAATATACCGGTTTTAAGAGAGAATATGTCTACATAATGTATCGAC
131 TTTTCAATGTAACTGGTATAAATATA-CTGTTTTAAGAGAGAATAGGTCTACATAATGTATCGAC
4182286 ACTTTT
195 ACTTTT
*
4182292 TAAATTTGTGTCGATACTTTTT
1 TAAGTTTGTGTCGATACTTTTT
4182314 TAAATTTCAT
Statistics
Matches: 771, Mismatches: 41, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
197 85 0.11
198 33 0.04
199 140 0.18
200 225 0.29
201 288 0.37
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (200 bp):
TAAGTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCATAAAGTGTCG
ATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAT
TTTTCAATGTAACTGGTATAAATATACTGTTTTAAGAGAGAATAGGTCTACATAATGTATCGACA
CTTTT
Found at i:4182554 original size:23 final size:23
Alignment explanation
Indices: 4182524--4182571 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
4182514 TTGGACTCTC
4182524 TTTTTTTCCTTAATGTGTTTGTG
1 TTTTTTTCCTTAATGTGTTTGTG
*
4182547 TTTTTTTCGTTAATGTGTTTGTG
1 TTTTTTTCCTTAATGTGTTTGTG
4182570 TT
1 TT
4182572 CCAATGTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.67
Consensus pattern (23 bp):
TTTTTTTCCTTAATGTGTTTGTG
Found at i:4185237 original size:24 final size:25
Alignment explanation
Indices: 4185210--4185264 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
4185200 TTTTAAGTTC
*
4185210 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
* *
4185234 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
4185258 ATTTCAA
1 ATTTCAA
4185265 TATAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 20 0.77
25 2 0.08
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:4185250 original size:18 final size:18
Alignment explanation
Indices: 4185229--4185265 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4185219 GTAATTGGAG
4185229 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
4185247 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
4185265 T
1 T
4185266 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:4185272 original size:24 final size:24
Alignment explanation
Indices: 4185221--4185273 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4185211 TTTCATATGT
* * *
4185221 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
4185245 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
4185269 AATTT
1 AATTT
4185274 CGACTCTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Done.