Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007816.1 Hibiscus syriacus cultivar Beakdansim tig00110151_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: 3994936
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:3204593 original size:22 final size:21
Alignment explanation
Indices: 3204564--3204621 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
3204554 CGGTAACATA
3204564 ATAGAGTATC-AGTACCATGGT
1 ATAGAGTATCGA-TACCATGGT
3204585 ATAGTAGTATCGATACCATGGT
1 ATAG-AGTATCGATACCATGGT
** *
3204607 AGGGGGTATCGATAC
1 ATAGAGTATCGATAC
3204622 TCACGAGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 14 0.44
22 17 0.53
23 1 0.03
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (21 bp):
ATAGAGTATCGATACCATGGT
Found at i:3205034 original size:56 final size:56
Alignment explanation
Indices: 3204956--3205162 Score: 292
Period size: 56 Copynumber: 3.6 Consensus size: 56
3204946 CTATGTGTAC
*
3204956 AAAGTTAAGAAATTCATAATAAGTTTATGCATTTCCTTATGGGCACTTTGTGTGCA
1 AAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGTGTGCA
* *
3205012 AAAGTTAAGAAATTCATAATAAGTTTATGAATTT-ATGTATGGGCATTTTGTGTGCA
1 AAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCT-TATGGGCACTTTGTGTGCA
* * *
3205068 AAAGTAAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCA
1 AAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGTGTGCA
3205124 AAAGTTAAGATAATAAATTCATAATAAGTTTATG-ATTTC
1 AAAGTTAAG-----AAATTCATAATAAGTTTATGAATTTC
3205163 GGTATTGGTA
Statistics
Matches: 135, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
55 1 0.01
56 110 0.81
60 4 0.03
61 20 0.15
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (56 bp):
AAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGTGTGCA
Found at i:3205534 original size:81 final size:80
Alignment explanation
Indices: 3205312--3205875 Score: 614
Period size: 81 Copynumber: 7.1 Consensus size: 80
3205302 ACTATTTCAA
* * *
3205312 AGTAAAAGATTAATGGCCTAGCTGTGTATTTGGAAGAAATGTGTCAATTATGCCAATTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGCAA-AAATGTGTCAATTATGCCAGTTAGATGAA
*
3205377 AGGTTAAATATCTTTG
65 AGGTTAAATACCTTTG
* * * *
3205393 AGTAAAAGATTAAT-GACTAGCTGTGCATTTGGC-AGAATAGTGCCAATTATGCCAGTTAGATGT
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTT-GCAAAAAT-GTGTCAATTATGCCAGTTAGATGA
*
3205456 AAGGTTAAATACCTTTC
64 AAGGTTAAATACCTTTG
*
3205473 AGTAAAAGATTAATGGCCTAGTTGTGCATTTCGCAAAAATGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTT-GCAAAAATGTGTCAATTATGCCAGTTAGATGAA
3205538 AGGTTAAATACCTTTG
65 AGGTTAAATACCTTTG
* * * * *
3205554 AGTAAAAGATTAATGGCCTAGCTGTGCTTTTGGCAAAAAGGTGTCAATTATGACAATTCGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTT-GCAAAAATGTGTCAATTATGCCAGTTAGATGAA
* *
3205619 ATGTTAAATTCCTTTG
65 AGGTTAAATACCTTTG
*
3205635 AGTAAAAGATTAATGGCCTAGC--T--A--TGC----ATTTGTCAATTATGCCAGTTAGATGAAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGCAAAAATGTGTCAATTATGCCAGTTAGATGAAA
*
3205690 GGTTAAATACATTTG
66 GGTTAAATACCTTTG
* * * * * * * *
3205705 AGTAAAATATTAACGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAGTTATGCTAGTAAGGTGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTG-CAAAAATGTGTCAATTATGCCAGTTAGATGAA
3205770 AGGTTAAATACCTTTG
65 AGGTTAAATACCTTTG
* * * * * * * *
3205786 ACTAAAATATTAACGCCCTAGCTGTACATTTGACAGGAAA-GTGTCAATCATGCAAGTTAGATGA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTG-CA-AAAATGTGTCAATTATGCCAGTTAGATGA
* * **
3205850 AAGGCTATATGTCTTTG
64 AAGGTTAAATACCTTTG
3205867 AGTAAAAGA
1 AGTAAAAGA
3205876 CTAAATGCTT
Statistics
Matches: 410, Mismatches: 57, Indels: 32
0.82 0.11 0.06
Matches are distributed among these distances:
70 55 0.13
72 1 0.00
74 3 0.01
75 1 0.00
76 2 0.00
77 1 0.00
79 4 0.01
80 65 0.16
81 270 0.66
82 8 0.02
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (80 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGCAAAAATGTGTCAATTATGCCAGTTAGATGAAA
GGTTAAATACCTTTG
Found at i:3205708 original size:70 final size:70
Alignment explanation
Indices: 3205595--3205736 Score: 203
Period size: 70 Copynumber: 2.0 Consensus size: 70
3205585 GGCAAAAAGG
* * * * *
3205595 TGTCAATTATGACAATTCGATGAAATGTTAAATTCCTTTGAGTAAAAGATTAATGGCCTAGCTAT
1 TGTCAATTATGACAATTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCCTAGCTAT
3205660 GCATT
66 GCATT
* * * *
3205665 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAATATTAACGGCCTAGCTGT
1 TGTCAATTATGACAATTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCCTAGCTAT
3205730 GCATT
66 GCATT
3205735 TG
1 TG
3205737 ACAGAAAGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (70 bp):
TGTCAATTATGACAATTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCCTAGCTAT
GCATT
Found at i:3205783 original size:232 final size:233
Alignment explanation
Indices: 3205312--3205875 Score: 658
Period size: 232 Copynumber: 2.4 Consensus size: 233
3205302 ACTATTTCAA
3205312 AGTAAAAGATTAATGGCCTAGCTGTG-TATTTGG-AAGAAATGTGTCAATTATGCCAATTAGATG
1 AGTAAAAGATTAATGGCCTAGCTGTGCT-TTTGGCAA-AAA-GTGTCAATTATG-CAATTAGATG
*
3205375 AAAGGTTAAATATCTTTGAGTAAAAGATTAATGACTAGCTGTGCATTTGGCAGAATAGTGCCAAT
62 AAAGGTTAAATATCTTTGAGTAAAAGATTAATGACTAGCTATGCATTT------ATAGT-CCAAT
* * * *
3205440 TATGCCAGTTAGATGTAAGGTTAAATACCTTTCAGTAAAAGATTAATGGCCTAGTTGTGCATTTC
120 TATGCCAGTTAGATGAAAGGTTAAATACATTTCAGTAAAAGATTAACGGCCTAGCTGTGCATTTC
* *
3205505 GCAAAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG
185 GCAAAAAGGTGTCAATTATGCCAGTAAGATGAAAGGTTAAATACCTTTG
*
3205554 AGTAAAAGATTAATGGCCTAGCTGTGCTTTTGGCAAAAAGGTGTCAATTATGACAATTCGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCTTTTGGCAAAAA-GTGTCAATTATG-CAATTAGATGAA
* *
3205619 ATGTTAAAT-TCCTTTGAGTAAAAGATTAATGGCCTAGCTATGCA-TT-T-GT-CAATTATGCCA
64 AGGTTAAATAT-CTTTGAGTAAAAGATTAAT-GACTAGCTATGCATTTATAGTCCAATTATGCCA
* * *
3205679 GTTAGATGAAAGGTTAAATACATTTGAGTAAAATATTAACGGCCTAGCTGTGCATTT-GACAGAA
127 GTTAGATGAAAGGTTAAATACATTTCAGTAAAAGATTAACGGCCTAGCTGTGCATTTCG-CAAAA
* * *
3205743 AGGTGTCAGTTATGCTAGTAAGGTGAAAGGTTAAATACCTTTG
191 AGGTGTCAATTATGCCAGTAAGATGAAAGGTTAAATACCTTTG
* * * * * * * * *
3205786 ACTAAAATATTAACGCCCTAGCTGTACATTTGACAGGAAAGTGTCAATCATGCAAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCTTTTGGCA-AAAAGTGTCAATTATGCAA-TTAGATGAA
* * *
3205851 AGGCTATATGTCTTTGAGTAAAAGA
64 AGGTTAAATATCTTTGAGTAAAAGA
3205876 CTAAATGCTT
Statistics
Matches: 283, Mismatches: 31, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
231 4 0.01
232 171 0.60
233 4 0.01
234 2 0.01
235 1 0.00
241 1 0.00
242 86 0.30
243 14 0.05
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31
Consensus pattern (233 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCTTTTGGCAAAAAGTGTCAATTATGCAATTAGATGAAAG
GTTAAATATCTTTGAGTAAAAGATTAATGACTAGCTATGCATTTATAGTCCAATTATGCCAGTTA
GATGAAAGGTTAAATACATTTCAGTAAAAGATTAACGGCCTAGCTGTGCATTTCGCAAAAAGGTG
TCAATTATGCCAGTAAGATGAAAGGTTAAATACCTTTG
Found at i:3205792 original size:151 final size:151
Alignment explanation
Indices: 3205514--3205817 Score: 421
Period size: 151 Copynumber: 2.0 Consensus size: 151
3205504 CGCAAAAATG
* *
3205514 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGT
1 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCCTAGCTGT
* * ** * * *
3205579 GCTTTTGGCAAAAAGGTGTCAATTATGACAATTCGATGAAATGTTAAATTCCTTTGAGTAAAAGA
66 GCATTTGACAAAAAGGTGTCAATTATGACAATAAGATGAAAGGTTAAATACCTTTGACTAAAAGA
* * *
3205644 TTAATGGCCTAGCTATGCATT
131 TTAACGCCCTAGCTATACATT
*
3205665 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAATATTAACGGCCTAGCTGT
1 TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCCTAGCTGT
* * * * *
3205730 GCATTTGACAGAAAGGTGTCAGTTATG-CTAGTAAGGTGAAAGGTTAAATACCTTTGACTAAAAT
66 GCATTTGACAAAAAGGTGTCAATTATGAC-AATAAGATGAAAGGTTAAATACCTTTGACTAAAAG
*
3205794 ATTAACGCCCTAGCTGTACATT
130 ATTAACGCCCTAGCTATACATT
3205816 TG
1 TG
3205818 ACAGGAAAGT
Statistics
Matches: 133, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
150 1 0.01
151 132 0.99
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (151 bp):
TGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAACGGCCTAGCTGT
GCATTTGACAAAAAGGTGTCAATTATGACAATAAGATGAAAGGTTAAATACCTTTGACTAAAAGA
TTAACGCCCTAGCTATACATT
Found at i:3214964 original size:24 final size:24
Alignment explanation
Indices: 3214889--3214967 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
3214879 GGCAGTGTGG
* *
3214889 ATCGATGCACATTGAAAGGAATGC
1 ATCGATGCACATTCAAAGGGATGC
* * * *
3214913 ATCGGTGCACCTTC--ATGG-TGT
1 ATCGATGCACATTCAAAGGGATGC
3214934 ATCGATGCACATTCAAAGGGATGC
1 ATCGATGCACATTCAAAGGGATGC
3214958 ATCGATGCAC
1 ATCGATGCAC
3214968 TGTTAAGTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
21 14 0.33
22 2 0.05
23 3 0.07
24 23 0.55
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (24 bp):
ATCGATGCACATTCAAAGGGATGC
Found at i:3216755 original size:18 final size:18
Alignment explanation
Indices: 3216732--3216767 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3216722 CTTTCATAGA
3216732 CATAATCCAATGTTCATC
1 CATAATCCAATGTTCATC
3216750 CATAATCCAATGTTCATC
1 CATAATCCAATGTTCATC
3216768 ATTTAATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (18 bp):
CATAATCCAATGTTCATC
Found at i:3218845 original size:22 final size:21
Alignment explanation
Indices: 3218803--3218842 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3218793 GAGCTTATTT
*
3218803 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3218824 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3218843 ACAATTTCTC
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:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3220921 original size:65 final size:64
Alignment explanation
Indices: 3220785--3220934 Score: 171
Period size: 65 Copynumber: 2.3 Consensus size: 64
3220775 TGCACTAAGA
* * * *
3220785 GTGCATCTATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTTCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTAAGTGCATCGATGCATAGCTG
* *
3220849 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTAAGTGCGTCGATGCATAG-
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGC-CTAAGTGCATCGATGCATAGC
*
3220911 TAT
63 T-G
*
3220914 GTGCATCGATGCATGAAATGC
1 GTGCATCGATGCATAAAATGC
3220935 GATGTTCAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
64 29 0.39
65 42 0.57
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTAAGTGCATCGATGCATAGCTG
Found at i:3224186 original size:16 final size:16
Alignment explanation
Indices: 3224165--3224206 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3224155 TAGCAAAAAG
3224165 AAGAGAAAAACATAAA-
1 AAGAGAAAAA-ATAAAT
*
3224181 AAGAGAGAAAATAAAT
1 AAGAGAAAAAATAAAT
3224197 AA-AGAAAAAA
1 AAGAGAAAAAA
3224207 AAGAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.07
Consensus pattern (16 bp):
AAGAGAAAAAATAAAT
Found at i:3224204 original size:13 final size:13
Alignment explanation
Indices: 3224186--3224258 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
3224176 ATAAAAAGAG
3224186 AGAAAATAAATAA
1 AGAAAATAAATAA
* *
3224199 AGAAAAAAAAGAA
1 AGAAAATAAATAA
* *
3224212 AGAAAA-AAGAGAG
1 AGAAAATAA-ATAA
3224225 AGAAAATAAAGTAAA
1 AGAAAATAAA-T-AA
3224240 AGAGAAATAAATAA
1 AGA-AAATAAATAA
3224254 A-AAAA
1 AGAAAA
3224259 GATCAAATCC
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
12 5 0.10
13 28 0.56
14 5 0.10
15 5 0.10
16 7 0.14
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (13 bp):
AGAAAATAAATAA
Found at i:3224254 original size:15 final size:17
Alignment explanation
Indices: 3224223--3224255 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3224213 GAAAAAAGAG
3224223 AGAGAAAATAAAGTAAA
1 AGAGAAAATAAAGTAAA
3224240 AGAG-AAATAAA-TAAA
1 AGAGAAAATAAAGTAAA
3224255 A
1 A
3224256 AAAGATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (17 bp):
AGAGAAAATAAAGTAAA
Found at i:3224257 original size:17 final size:16
Alignment explanation
Indices: 3224160--3224257 Score: 54
Period size: 17 Copynumber: 5.4 Consensus size: 16
3224150 ATATATAGCA
3224160 AAAAGAAGAGAAAAACAT
1 AAAA-AAGAGAAAAA-AT
3224178 AAAAAGAGAGAAAATAAAT
1 AAAAA-AGAG-AAA-AAAT
* *
3224197 AAAGAAA-AAAAAGAAAG
1 AAA-AAAGAGAAA-AAAT
3224214 AAAAAAGAGAGAGAAAAT
1 AAAAAAGAGA-A-AAAAT
3224232 AAAGTAAAAGAGAAATAAAT
1 -AA--AAAAGAGAAA-AAAT
3224252 AAAAAA
1 AAAAAA
3224258 AGATCAAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 23
0.70 0.05 0.25
Matches are distributed among these distances:
16 3 0.05
17 16 0.25
18 13 0.20
19 15 0.23
20 9 0.14
21 8 0.12
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (16 bp):
AAAAAAGAGAAAAAAT
Found at i:3225040 original size:28 final size:28
Alignment explanation
Indices: 3224993--3225060 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
3224983 CAAAGAAGCC
*
3224993 AACCTGAAACACATTGCCTCGCC-AAATT
1 AACCTGAAACACATTACCTC-CCTAAATT
3225021 AA-CTAGAAACACATTACCTCCCTAAATT
1 AACCT-GAAACACATTACCTCCCTAAATT
3225049 AACCTGAAACAC
1 AACCTGAAACAC
3225061 TCTACTTTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 4 0.11
28 30 0.83
29 2 0.06
ACGTcount: A:0.41, C:0.31, G:0.07, T:0.21
Consensus pattern (28 bp):
AACCTGAAACACATTACCTCCCTAAATT
Found at i:3230994 original size:14 final size:14
Alignment explanation
Indices: 3230930--3230994 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
3230920 CCCATGAGAA
*
3230930 ATGATATAAGTTAT
1 ATGATATATGTTAT
3230944 ATGATATGAT-TTAT
1 ATGATAT-ATGTTAT
* **
3230958 ATGATTACATGCACAT
1 ATGA-TATATG-TTAT
*
3230974 GTGATATATGTTAT
1 ATGATATATGTTAT
3230988 ATGATAT
1 ATGATAT
3230995 GGATCGATGT
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
14 25 0.66
15 8 0.21
16 5 0.13
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (14 bp):
ATGATATATGTTAT
Found at i:3231403 original size:23 final size:23
Alignment explanation
Indices: 3231367--3231410 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3231357 CAATCTTATA
3231367 TGGCACTACAGTGCAATTCTATG
1 TGGCACTACAGTGCAATTCTATG
* * *
3231390 TGGCACTTCGGTGCATTTCTA
1 TGGCACTACAGTGCAATTCTA
3231411 CGCGGTCCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (23 bp):
TGGCACTACAGTGCAATTCTATG
Found at i:3232222 original size:23 final size:21
Alignment explanation
Indices: 3232175--3232222 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
3232165 AAAGTACTAT
**
3232175 AGCAGGGAATCGGTACCCTGT
1 AGCAGGGAATCGGTACCCTCA
*
3232196 AGCAGGGGAATCGGTTCCCCTCA
1 AGCA-GGGAATCGG-TACCCTCA
3232219 AGCA
1 AGCA
3232223 ATCTGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 9 0.41
23 9 0.41
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.17
Consensus pattern (21 bp):
AGCAGGGAATCGGTACCCTCA
Found at i:3235593 original size:104 final size:104
Alignment explanation
Indices: 3235388--3235593 Score: 290
Period size: 104 Copynumber: 2.0 Consensus size: 104
3235378 TCACAGGATG
* *
3235388 ACTCTACCTGACTAGCTCGGGGATGGAAGTTATGCTCCCTTTCACTTAGAGTGTGGGATGTTAGG
1 ACTCTACCTGACTAGCTCGGGGATGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGG
* * *
3235453 TGTGATGGGCTGAATCCCCTCGAAGCAGTGTTAAAAAAA
66 TGTGATGAGATGAATCCCCTCAAAGCAGTGTTAAAAAAA
* * *
3235492 ACTCTACTTGACTAGCTTGGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTA-G
1 ACTCTACCTGACTAGCTCGGGGATGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGG
* * *
3235556 TGTGATGAGATGACTCCCCTTAAAGTA-TGCTTAAAAAA
66 TGTGATGAGATGAATCCCCTCAAAGCAGTG-TTAAAAAA
3235594 GAGAGTTGAA
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
102 2 0.02
103 30 0.33
104 58 0.64
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (104 bp):
ACTCTACCTGACTAGCTCGGGGATGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGG
TGTGATGAGATGAATCCCCTCAAAGCAGTGTTAAAAAAA
Found at i:3238067 original size:44 final size:45
Alignment explanation
Indices: 3237935--3238068 Score: 209
Period size: 45 Copynumber: 3.0 Consensus size: 45
3237925 ATCAATAAAT
* *
3237935 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
3237980 TTACCATTTAATTCCATAAGCTCGT-AGCTTATTTTGCCAATATAC
1 TTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
3238025 TTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACTAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
3238069 ATGCCATTAA
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
43 15 0.18
44 20 0.24
45 33 0.40
46 14 0.17
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:3238229 original size:59 final size:58
Alignment explanation
Indices: 3238166--3238637 Score: 437
Period size: 58 Copynumber: 8.1 Consensus size: 58
3238156 TATCACTCTC
* * * *
3238166 AGTGCTCTATCTGGAAAATCATACGCTTAGTATGCTTTCCCTT-TCATTTTAGCACACGA
1 AGTGCTCTATATGG-AAATCATACACTTAGTATGATTT-CCTTATCATTTTAGCACACTA
* ** ** *
3238225 AGTGCCCTAT-TAAAAATTCATAC-CATTAGTATGATTTTGTTACCATTTTAGCACA-TGA
1 AGTGCTCTATATGGAAA-TCATACAC-TTAGTATGATTTCCTTATCATTTTAGCACACT-A
* * * * * *
3238283 AATGCCCTATGTGAAAATCCATAC-CATTAGTATGATTTCCTTATC-TTTGTAGCACCCTT
1 AGTGCTCTATATGGAAAT-CATACAC-TTAGTATGATTTCCTTATCATTT-TAGCACACTA
* * *
3238342 AGTGCTTTATCTGGAAATCCATACACTTAGTATGATTCCCTTA-CATTTTTAGCACA-TAA
1 AGTGCTCTATATGGAAAT-CATACACTTAGTATGATTTCCTTATCA-TTTTAGCACACT-A
* * * *
3238401 AATGC-CGTATCTGAAAATCCATACACTTAGTATGATTTCCTTATCA-TTTAGCACACTC
1 AGTGCTC-TATATGGAAAT-CATACACTTAGTATGATTTCCTTATCATTTTAGCACACTA
* * *
3238459 AGTGCTCAATATGGAAATCTATACACTCAGTATGATTTCCTTATCA-TTTAGCACACTC
1 AGTGCTCTATATGGAAATC-ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTA
* * *
3238517 AGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCCTTATCA-TTTAGCACACTC
1 AGTGCTCTATATGGAAATC-ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTA
* *
3238575 AGTGCTCCATATGGAAATCTATACACTTAGTATGATTTCCTTATCATTTTAGCACACAA
1 AGTGCTCTATATGGAAATC-ATACACTTAGTATGATTTCCTTATCATTTTAGCACACTA
3238634 AGTG
1 AGTG
3238638 TCATTCGGTA
Statistics
Matches: 358, Mismatches: 37, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
57 7 0.02
58 206 0.58
59 138 0.39
60 7 0.02
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (58 bp):
AGTGCTCTATATGGAAATCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTA
Found at i:3238254 original size:58 final size:60
Alignment explanation
Indices: 3238180--3238456 Score: 184
Period size: 59 Copynumber: 4.8 Consensus size: 60
3238170 CTCTATCTGG
* * *
3238180 AAAA-TCATACGC-TTAGTATGCTTTCCCTT-TCATTTTAGCACACGAAGTGCCCTAT-TA
1 AAAATTCATAC-CATTAGTATGATTTCCCTTACCATTTTAGCACACGAAATGCCCTATGTA
** * *
3238237 AAAATTCATACCATTAGTATGATTT-TGTTACCATTTTAGCACATGAAATGCCCTATGTG
1 AAAATTCATACCATTAGTATGATTTCCCTTACCATTTTAGCACACGAAATGCCCTATGTA
* * * ** * ** * *
3238296 AAAATCCATACCATTAGTATGATTT-CCTTATC-TTTGTAGCACCCTTAGTGCTTTATCTG
1 AAAATTCATACCATTAGTATGATTTCCCTTACCATTT-TAGCACACGAAATGCCCTATGTA
* * ** * * *
3238355 GAAATCCATA-CACTTAGTATGA-TTCCCTTA-CATTTTTAGCACATAAAATGCCGTATCTG
1 AAAATTCATACCA-TTAGTATGATTTCCCTTACCA-TTTTAGCACACGAAATGCCCTATGTA
* *
3238414 AAAATCCATA-CACTTAGTATGATTT-CCTTATCA-TTTAGCACAC
1 AAAATTCATACCA-TTAGTATGATTTCCCTTACCATTTTAGCACAC
3238457 TCAGTGCTCA
Statistics
Matches: 180, Mismatches: 29, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
57 7 0.04
58 57 0.32
59 109 0.61
60 7 0.04
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (60 bp):
AAAATTCATACCATTAGTATGATTTCCCTTACCATTTTAGCACACGAAATGCCCTATGTA
Found at i:3238517 original size:30 final size:30
Alignment explanation
Indices: 3238481--3238577 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
3238471 GGAAATCTAT
3238481 ACACTCAGTATGATTTCCTTATCATTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTAGC
* * * * *
3238511 ACACTCAG--TG--CTCCATATGGAAATCTA-T
1 ACACTCAGTATGATTTCCTTAT---CATTTAGC
3238539 ACACTCAGTATGATTTCCTTATCATTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTAGC
3238569 ACACTCAGT
1 ACACTCAGT
3238578 GCTCCATATG
Statistics
Matches: 49, Mismatches: 10, Indels: 16
0.65 0.13 0.21
Matches are distributed among these distances:
26 6 0.12
28 10 0.20
29 8 0.16
30 19 0.39
32 6 0.12
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (30 bp):
ACACTCAGTATGATTTCCTTATCATTTAGC
Found at i:3239731 original size:25 final size:25
Alignment explanation
Indices: 3239703--3239753 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3239693 TAAAATTCTT
3239703 TTTAGGAAATTATCACTTAATTCCC
1 TTTAGGAAATTATCACTTAATTCCC
3239728 TTTAGGAAATTATCACTTAATTCCC
1 TTTAGGAAATTATCACTTAATTCCC
3239753 T
1 T
3239754 AAACGTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (25 bp):
TTTAGGAAATTATCACTTAATTCCC
Found at i:3245512 original size:17 final size:17
Alignment explanation
Indices: 3245486--3245534 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
3245476 GGGAAAGTAA
* *
3245486 AAAAAATAAACCAAAAG
1 AAAAAGTAAACAAAAAG
* *
3245503 TAAAAGTAAATAAAAAG
1 AAAAAGTAAACAAAAAG
3245520 AAAAAGTGAAACAAA
1 AAAAAGT-AAACAAA
3245535 GTTTCCCTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAAGTAAACAAAAAG
Found at i:3251241 original size:11 final size:11
Alignment explanation
Indices: 3251225--3251273 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
3251215 CAAGAAAAAC
3251225 AAGAAAAATAT
1 AAGAAAAATAT
*
3251236 AAGAAAAATAA
1 AAGAAAAATAT
*
3251247 AAGTAAAACTAT
1 AAG-AAAAATAT
3251259 ATAGAAGAAATAT
1 A-AGAA-AAATAT
3251272 AA
1 AA
3251274 ACAAGTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 13 0.42
12 10 0.32
13 8 0.26
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.18
Consensus pattern (11 bp):
AAGAAAAATAT
Found at i:3251641 original size:23 final size:24
Alignment explanation
Indices: 3251590--3251641 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
3251580 ATGTGGTCGC
* *
3251590 AATTGAATATGTCGTGGCAAGTTG
1 AATTGAATATGTCGTGGAAAATTG
* *
3251614 GATTGAA-ATGTCGTGGAAAATTT
1 AATTGAATATGTCGTGGAAAATTG
3251637 AATTG
1 AATTG
3251642 TGATAAGTGC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.35
Consensus pattern (24 bp):
AATTGAATATGTCGTGGAAAATTG
Found at i:3258232 original size:54 final size:55
Alignment explanation
Indices: 3258096--3258303 Score: 196
Period size: 54 Copynumber: 3.8 Consensus size: 55
3258086 TGATTTTTTT
* * *
3258096 AGAAACTAAG-CTTGATTTTCA-AGGGTTTCTTGAT-ATTTTCAAATGAATTTTAAA
1 AGAAACTAAGTC-TGATTTTCAGA-AGTTTCTTGATGGTTTTCAAATGAATTTTCAA
* * *
3258150 AGAAGA-TAAGCCTGATTTCTAAG-GGTTTCTTGAT-GTTTTCAAATGAATTTTCAA
1 AGAA-ACTAAGTCTGATTT-TCAGAAGTTTCTTGATGGTTTTCAAATGAATTTTCAA
* * *
3258204 AGAAACTAAGTCTAATTTTCAGAAGTTTCTT-ATCGGTTTTTAAATGAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGAT-GGTTTTCAAATGAATTTTCAA
* * * *
3258259 AGTAACTAAGTATGATTTTCATAAATTTCTTGATGAGTTTTCAAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG-GTTTTCAAA
3258304 GAAACTAAGT
Statistics
Matches: 129, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
53 6 0.05
54 64 0.50
55 49 0.38
56 10 0.08
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (55 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGGTTTTCAAATGAATTTTCAA
Found at i:3258256 original size:55 final size:55
Alignment explanation
Indices: 3258184--3258303 Score: 152
Period size: 55 Copynumber: 2.2 Consensus size: 55
3258174 GTTTCTTGAT
* *
3258184 GTTTTCAAATGAATTTTCAAAGAAACTAAGTCTAATTTTCAGAAGTTTCTTATCG
1 GTTTTCAAATGAATTTTCAAAGAAACTAAGTATAATTTTCAGAAATTTCTTATCG
* * * * *
3258239 GTTTTTAAATGAGTTTTCAAAGTAACTAAGTATGATTTTCATAAATTTCTTGAT-G
1 GTTTTCAAATGAATTTTCAAAGAAACTAAGTATAATTTTCAGAAATTTCTT-ATCG
3258294 AGTTTTCAAA
1 -GTTTTCAAA
3258304 GAAACTAAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
55 45 0.82
56 10 0.18
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (55 bp):
GTTTTCAAATGAATTTTCAAAGAAACTAAGTATAATTTTCAGAAATTTCTTATCG
Found at i:3258277 original size:22 final size:23
Alignment explanation
Indices: 3258247--3258325 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 23
3258237 CGGTTTTTAA
3258247 ATGAGTTTTCAAAGTAACTAAGT
1 ATGAGTTTTCAAAGTAACTAAGT
* ** *
3258270 ATGA-TTTTCATAAATTTCT-TG-
1 ATGAGTTTTCA-AAGTAACTAAGT
*
3258291 ATGAGTTTTCAAAGAAACTAAGT
1 ATGAGTTTTCAAAGTAACTAAGT
*
3258314 TTGA-TTTTCAAA
1 ATGAGTTTTCAAA
3258326 TGAATATTGA
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
21 8 0.19
22 22 0.52
23 12 0.29
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (23 bp):
ATGAGTTTTCAAAGTAACTAAGT
Found at i:3260006 original size:182 final size:182
Alignment explanation
Indices: 3259692--3260042 Score: 459
Period size: 182 Copynumber: 1.9 Consensus size: 182
3259682 GCCTTAACTC
* * * * *
3259692 GATTCCATCACAGAAGGAGGAGGATCAATATTTCCAGTAGAGGGTTCATAATAAGAATAACTTAT
1 GATTCCATCACAAAAGGAGGAGGATCAACATTTCCAATAGAGGGTTCATAATAAGAAGAACTCAT
* * * * * *
3259757 CCGACGAGGGAGAATAAGTTCATCATGAGAAGAACTTGTTCAAACTTAGCTTGATTCCATCACAT
66 CCAACGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAAACTTAGCTCGATTCCATAACAT
** * * *
3259822 AAGAAGTTGGAACATTGCTAGTATTTGGCTTATCCATCGCATCACTTTGTTG
131 AAGAAGTTGGAACATCACTAATACTTGGCTCATCCATCGCATCACTTTGTTG
* * * * * *
3259874 GATTCCATTACAAAATGAGGTGGATCAACATTTCCAATGGAGGGTTCATAATGAGAAGAACTCGT
1 GATTCCATCACAAAAGGAGGAGGATCAACATTTCCAATAGAGGGTTCATAATAAGAAGAACTCAT
** * *
3259939 TTAATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTCGATTCCATAACAT
66 CCAACGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAAACTTAGCTCGATTCCATAACAT
*
3260004 AAGGAGTTGGAACATCACTAATACTTGGCTCATCCATCG
131 AAGAAGTTGGAACATCACTAATACTTGGCTCATCCATCG
3260043 TATATAGAGT
Statistics
Matches: 142, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
182 142 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (182 bp):
GATTCCATCACAAAAGGAGGAGGATCAACATTTCCAATAGAGGGTTCATAATAAGAAGAACTCAT
CCAACGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAAACTTAGCTCGATTCCATAACAT
AAGAAGTTGGAACATCACTAATACTTGGCTCATCCATCGCATCACTTTGTTG
Found at i:3260692 original size:403 final size:406
Alignment explanation
Indices: 3259861--3260867 Score: 1334
Period size: 403 Copynumber: 2.5 Consensus size: 406
3259851 TTATCCATCG
** * * * * * *
3259861 CATCACTTTGTTGGATTCCATTACAAAATGAGGTGGATCAACATTTCCAATGGAGGGTTCATAAT
1 CATCACTTTGTTCAATTCCATCATAGAAGGAGGTGGATCAACATTTCCAGTGGAGAGTTCATAAT
* * * *
3259926 GAGAAGAACTCGTTTAATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTC
66 GAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACGTTAGCTC
* *
3259991 GATTCCATAACATAAGGAGTTGGAACATCACTAATACTTGGCTCATCCATCGTATATAGAGTTGG
131 GATTCCATCACATAAGGAGTTGGAACAACACTAATACTTGGCTCATCCATCGTATATAGAGTTGG
* * * * *
3260056 ATCA-TAATCATCACTTTGTTCAATTCCATCATAGAAGAAGGTGAATCAATATTTCTAGTGGAGG
196 ATCAGTAATCATCACTTTGTTCAATTCCATCACAGAAGAAGGTGAATCAACATTTCTAATAGAGA
* * * **
3260120 GTTCATAATGAGAAGAACTCATTCGATGAGGGGGAATAAGTTCATAATGAGAAGAACTTGTTCAA
261 GTTCATAATAAGAAGAACACATCCGATGAGGGAAAATAAGTTCATAATGAGAAGAACTTGTTCAA
* ** ** * **
3260185 CCTTAGCTCGATTCCATCACATAAGGAGTTGGAACAGTACCAATACTTGGCTCATCCATAGCATA
326 CCTTAGCTCGATTCCATCACATAAGAAGTTGGAACAACAAAAAAACAAGGCTCATCCATAGCATA
* *
3260250 TGGATTTGGATCATAT
391 TGGAGTTGGATCACAT
** * * *
3260266 CATCACTTT-TTTTATTTCATCATAGAAGGATGTGGATCAACATTTCCAGTTGAGAGTTCATAAT
1 CATCACTTTGTTCAATTCCATCATAGAAGGAGGTGGATCAACATTTCCAGTGGAGAGTTCATAAT
* *
3260330 GAG-AGAAACTCATCTGAT-AGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCAACGTTAGCT
66 GAGAAG-AACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACGTTAGCT
** * * *
3260393 CGATTCCATCACATAATAAGTTGGAACAGCACTAATACTTGGCTCATCCATCGCATATAGAGTTA
130 CGATTCCATCACATAAGGAGTTGGAACAACACTAATACTTGGCTCATCCATCGTATATAGAGTTG
* * * *
3260458 GATCAGT-ATTATCACTTTGTTCGATTCTATCACAGAAGAAGGTGGATCAACATTT-TGAATAGA
195 GATCAGTAATCATCACTTTGTTCAATTCCATCACAGAAGAAGGTGAATCAACATTTCT-AATAGA
* *
3260521 GAGTTCATAATAAGAAGAACACATCCGAT-ATGGAAAAT-ATTTCATAATGAGAAGAACTTGTTC
259 GAGTTCATAATAAGAAGAACACATCCGATGAGGGAAAATAAGTTCATAATGAGAAGAACTTGTTC
3260584 AACCTTAGCTCGATTCCATCACATAAGAAGTTGGAACAACAAAAAAACAAGGCTCATCCATCA-C
324 AACCTTAGCTCGATTCCATCACATAAGAAGTTGGAACAACAAAAAAACAAGGCTCATCCAT-AGC
3260648 ATATGGAGTTGGATCAGCAT
388 ATATGGAGTTGGATCA-CAT
* *
3260668 CATCACTTTGTTCAATTCCATCATAGAAGGAGGTTGATCAACATTTTCAGTGGAGAGTTCATAAT
1 CATCACTTTGTTCAATTCCATCATAGAAGGAGGTGGATCAACATTTCCAGTGGAGAGTTCATAAT
* * * *
3260733 AAGAAGAACTAATCTGATGAGGGAGAAGAAGTTCATAGTGAGAATAACTTGTTCAACCG-TAGCT
66 GAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAA-CGTTAGCT
* * *
3260797 CGTTTCCATCACATAAGGAGTTGGAATAACACCAATACTTGGCTCATCCATCGTATA-AGGAGTT
130 CGATTCCATCACATAAGGAGTTGGAACAACACTAATACTTGGCTCATCCATCGTATATA-GAGTT
3260861 GGATCAG
194 GGATCAG
3260868 CATCATAATT
Statistics
Matches: 523, Mismatches: 69, Indels: 21
0.85 0.11 0.03
Matches are distributed among these distances:
401 93 0.18
402 19 0.04
403 241 0.46
404 159 0.30
405 11 0.02
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (406 bp):
CATCACTTTGTTCAATTCCATCATAGAAGGAGGTGGATCAACATTTCCAGTGGAGAGTTCATAAT
GAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACGTTAGCTC
GATTCCATCACATAAGGAGTTGGAACAACACTAATACTTGGCTCATCCATCGTATATAGAGTTGG
ATCAGTAATCATCACTTTGTTCAATTCCATCACAGAAGAAGGTGAATCAACATTTCTAATAGAGA
GTTCATAATAAGAAGAACACATCCGATGAGGGAAAATAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTAGCTCGATTCCATCACATAAGAAGTTGGAACAACAAAAAAACAAGGCTCATCCATAGCATA
TGGAGTTGGATCACAT
Found at i:3260867 original size:203 final size:203
Alignment explanation
Indices: 3259861--3260873 Score: 1220
Period size: 203 Copynumber: 5.0 Consensus size: 203
3259851 TTATCCATCG
** * * * * * * *
3259861 CATCACTTTGTTGGATTCCATTACAAAATGAGGTGGATCAACATTTCCAATGGAGGGTTCATAAT
1 CATCACTTTGTTCAATTCCATCATAGAAGGAGGTGGATCAACATTTTCAGTGGAGAGTTCATAAT
* * * *
3259926 GAGAAGAACTCGTTTAATGAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTC
66 GAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTC
* * * *
3259991 GATTCCATAACATAAGGAGTTGGAACATCACTAATACTTGGCTCATCCATCGTATATA-GAGTTG
131 GATTCCATCACATAAGGAGTTGGAACAACACCAATACTTGGCTCATCCATCGCATA-AGGAGTTG
**
3260055 GATCATAAT
195 GATCAGCAT
* * * *
3260064 CATCACTTTGTTCAATTCCATCATAGAAGAAGGTGAATCAATA-TTTCTAGTGGAGGGTTCATAA
1 CATCACTTTGTTCAATTCCATCATAGAAGGAGGTGGATCAACATTTTC-AGTGGAGAGTTCATAA
* *
3260128 TGAGAAGAACTCAT-TCGATGAGGGGGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGC
65 TGAGAAGAACTCATCT-GATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGC
** * * *
3260192 TCGATTCCATCACATAAGGAGTTGGAACAGTACCAATACTTGGCTCATCCATAGCATATGGATTT
129 TCGATTCCATCACATAAGGAGTTGGAACAACACCAATACTTGGCTCATCCATCGCATAAGGAGTT
*
3260257 GGATCA-TAT
194 GGATCAGCAT
** * * * *
3260266 CATCACTTT-TTTTATTTCATCATAGAAGGATGTGGATCAACATTTCCAGTTGAGAGTTCATAAT
1 CATCACTTTGTTCAATTCCATCATAGAAGGAGGTGGATCAACATTTTCAGTGGAGAGTTCATAAT
* *
3260330 GAG-AGAAACTCATCTGAT-AGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCAACGTTAGCT
66 GAGAAG-AACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
** * *
3260393 CGATTCCATCACATAATAAGTTGGAACAGCACTAATACTTGGCTCATCCATCGCATATA-GAGTT
130 CGATTCCATCACATAAGGAGTTGGAACAACACCAATACTTGGCTCATCCATCGCATA-AGGAGTT
* *
3260457 AGATCAGTAT
194 GGATCAGCAT
* * * * * * * *
3260467 TATCACTTTGTTCGATTCTATCACAGAAGAAGGTGGATCAACATTTTGAATAGAGAGTTCATAAT
1 CATCACTTTGTTCAATTCCATCATAGAAGGAGGTGGATCAACATTTTCAGTGGAGAGTTCATAAT
* * * * *
3260532 AAGAAGAACACATCCGAT-ATGGA-AA-ATATTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
66 GAGAAGAACTCATCTGATGAGGGAGAAGA-AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
* ** * ** * *
3260594 CGATTCCATCACATAAGAAGTTGGAACAACAAAAAAACAAGGCTCATCCATCACATATGGAGTTG
130 CGATTCCATCACATAAGGAGTTGGAACAACACCAATACTTGGCTCATCCATCGCATAAGGAGTTG
3260659 GATCAGCAT
195 GATCAGCAT
*
3260668 CATCACTTTGTTCAATTCCATCATAGAAGGAGGTTGATCAACATTTTCAGTGGAGAGTTCATAAT
1 CATCACTTTGTTCAATTCCATCATAGAAGGAGGTGGATCAACATTTTCAGTGGAGAGTTCATAAT
* * * * *
3260733 AAGAAGAACTAATCTGATGAGGGAGAAGAAGTTCATAGTGAGAATAACTTGTTCAACCGTAGCTC
66 GAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTC
* * *
3260798 GTTTCCATCACATAAGGAGTTGGAATAACACCAATACTTGGCTCATCCATCGTATAAGGAGTTGG
131 GATTCCATCACATAAGGAGTTGGAACAACACCAATACTTGGCTCATCCATCGCATAAGGAGTTGG
3260863 ATCAGCAT
196 ATCAGCAT
3260871 CAT
1 CAT
3260874 AATTTTGCTT
Statistics
Matches: 693, Mismatches: 102, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
200 107 0.15
201 233 0.34
202 83 0.12
203 269 0.39
204 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (203 bp):
CATCACTTTGTTCAATTCCATCATAGAAGGAGGTGGATCAACATTTTCAGTGGAGAGTTCATAAT
GAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTC
GATTCCATCACATAAGGAGTTGGAACAACACCAATACTTGGCTCATCCATCGCATAAGGAGTTGG
ATCAGCAT
Found at i:3260889 original size:42 final size:42
Alignment explanation
Indices: 3260801--3260955 Score: 163
Period size: 42 Copynumber: 3.7 Consensus size: 42
3260791 GTAGCTCGTT
* * * * *
3260801 TCCATCACATAAGGAGTTGGAAT-AACACCA-ATACTTGGCTCA
1 TCCATCACATAAGGAGTTGG-ATCAGCATCATA-ATTTTGTTCA
** *
3260843 TCCATCGTATAAGGAGTTGGATCAGCATCATAATTTTGCTT-G
1 TCCATCACATAAGGAGTTGGATCAGCATCATAATTTTG-TTCA
* *
3260885 TCCATCACATAAGAAGTTGGATCAGCATCATCATTTTGTTCA
1 TCCATCACATAAGGAGTTGGATCAGCATCATAATTTTGTTCA
*
3260927 TCCATCACATAAGGAATTGGATCAGCATC
1 TCCATCACATAAGGAGTTGGATCAGCATC
3260956 TCCTTGGGTT
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.04
42 88 0.94
43 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (42 bp):
TCCATCACATAAGGAGTTGGATCAGCATCATAATTTTGTTCA
Found at i:3266603 original size:140 final size:140
Alignment explanation
Indices: 3266391--3266963 Score: 765
Period size: 140 Copynumber: 4.1 Consensus size: 140
3266381 TCTGGTCATT
* * * * *
3266391 TTTAGGTA-AATTT-GGAGACAACACGGTTCCTACGTGATGAGGAAATCTTGTTATCTAAGGGTA
1 TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATG
* * * * *
3266454 ACGTTGCTCCTAGGTGATGAGGATATCTGGTCGGTGGATGACATTGTTCCTACATGATGAAGACA
66 ACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACATTGTTCCTACATGATGAAGACG
3266519 TCTAGCCATC
131 TCTAGCCATC
* *
3266529 TTTAGGGATAATTTGGGAGACAACAAGGTTCCAACGTGATGAGGAAGTCTGGTTATCTAAGGATG
1 TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATG
* * ** * * * *
3266594 ATGCAGCTCCTACGTGATGAGGAGATCGGGTCAGTGGACGACATTGTTCCTACATGATGAGGATG
66 ACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACATTGTTCCTACATGATGAAGACG
*
3266659 TCTAGCCGTC
131 TCTAGCCATC
* * * *
3266669 TTTAGGGATAATTTAGGAGATAACACTGTTCCTACGTGATGAGGAAGTATGGTTATCTAAGGATG
1 TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATG
* * *
3266734 ACGCTTCTCCTATGTGATGAGGAGATATGGTCGGTGGATGACATTGTTCATACATGATG-AGAAC
66 ACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACATTGTTCCTACATGATGAAG-AC
*
3266798 GTCTAGCCATA
130 GTCTAGCCATC
* * *
3266809 TTTAGGGATAATTTGAGAGACAACACGATTCTTACGTGATGAGGAAGTCTGGTTATCTAAGGATG
1 TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATG
* * * * *
3266874 ACACTGCTCCTACGTGATGATGAGATATGATTGGTGGATGACATTGTTCCTACATGATGAGGACG
66 ACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACATTGTTCCTACATGATGAAGACG
*
3266939 TCTAACCATC
131 TCTAGCCATC
*
3266949 TATAGGGATAATTTG
1 TTTAGGGATAATTTG
3266964 TTTCAAGAGA
Statistics
Matches: 375, Mismatches: 56, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
138 7 0.02
139 6 0.02
140 361 0.96
141 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (140 bp):
TTTAGGGATAATTTGGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATG
ACGCTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACATTGTTCCTACATGATGAAGACG
TCTAGCCATC
Found at i:3267047 original size:29 final size:29
Alignment explanation
Indices: 3266998--3267106 Score: 92
Period size: 29 Copynumber: 3.5 Consensus size: 29
3266988 AGACAAAATT
*
3266998 TGTTTCAAGGGAAACAATCTCAAAGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGTTTA
** ***
3267027 TGTTTCAAGAGAAACTGTCTCATGAGAGACAAAAAA
1 TGTTTCAAGAGAAACAATCTCA--A-AG----TTTA
*
3267063 TATTTCAAGAGAAACAATCTCAAAGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGTTTA
3267092 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
3267107 TGTCTCAAGA
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
29 34 0.57
31 1 0.02
32 2 0.03
33 2 0.03
34 1 0.02
36 20 0.33
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (29 bp):
TGTTTCAAGAGAAACAATCTCAAAGTTTA
Found at i:3267069 original size:65 final size:65
Alignment explanation
Indices: 3266962--3267224 Score: 328
Period size: 65 Copynumber: 4.0 Consensus size: 65
3266952 AGGGATAATT
* * * *
3266962 TGTTTCAAGAGAAATTGTCTTAAGCGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTA
* ** *
3267027 TGTTTCAAGAGAAACTGTCTCATGAGAGACAAAAAATATTTCAAGAGAAACAATCTCAAAGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTA
* * * * *
3267092 TGTTTCAAGAGAAACTGTCTCAAGATAGAGACAATTTGTTTCAAGAGAAACAATCACAAGGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAG-TTT
*
3267157 G
65 A
* ** * * *
3267158 TGTTTCAAGAGAAATTGTCTCAAGAGAGATGAACTTTGTTTCGAGAGAAACAGTCTCAACAGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAA-AGTTT
3267223 A
65 A
3267224 T
1 T
3267225 CAATTTTATT
Statistics
Matches: 167, Mismatches: 29, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
65 109 0.65
66 57 0.34
67 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTA
Found at i:3274024 original size:18 final size:17
Alignment explanation
Indices: 3273993--3274026 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3273983 AAAAAATTAA
3273993 CATAATATACATACATG
1 CATAATATACATACATG
*
3274010 CATATATATATATACAT
1 CATA-ATATACATACAT
3274027 TAATTGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (17 bp):
CATAATATACATACATG
Found at i:3275324 original size:21 final size:21
Alignment explanation
Indices: 3275299--3275359 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
3275289 TGGCGGCTCA
3275299 GGAGTGTTCGGCGGTAGCTTG
1 GGAGTGTTCGGCGGTAGCTTG
***
3275320 GGAGTGTTCGGCGACGGCTTG
1 GGAGTGTTCGGCGGTAGCTTG
* *
3275341 GGAATGTTCAGCGGTAGCT
1 GGAGTGTTCGGCGGTAGCT
3275360 AACGCAGCAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.26
Consensus pattern (21 bp):
GGAGTGTTCGGCGGTAGCTTG
Found at i:3275755 original size:3 final size:3
Alignment explanation
Indices: 3275747--3275811 Score: 67
Period size: 3 Copynumber: 21.7 Consensus size: 3
3275737 TAATTGTTAA
* * * * *
3275747 AAT AAT AAT AAT AAT AAT CAT CAT CAT ACT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
3275795 AAC AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AA
3275812 ATAAATGAGA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3280168 original size:12 final size:12
Alignment explanation
Indices: 3280143--3280235 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
3280133 ATGGAGATAT
* *
3280143 CAGAAATCAAAA
1 CAGAATTCAGAA
3280155 CAGAATTCAGAA
1 CAGAATTCAGAA
3280167 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
*
3280179 CAGAATCCAGATA
1 CAGAATTCAGA-A
* *
3280192 -AGAAATCAGGA
1 CAGAATTCAGAA
**
3280203 CAGAATTCAGGT
1 CAGAATTCAGAA
*
3280215 CATGTA-TCAGAA
1 CA-GAATTCAGAA
3280227 CAGAATTCA
1 CAGAATTCA
3280236 AGTCAGAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
11 5 0.08
12 53 0.84
13 5 0.08
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:3280175 original size:24 final size:24
Alignment explanation
Indices: 3280143--3280249 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
3280133 ATGGAGATAT
*
3280143 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* *
3280167 CAGATATCAGAACAGAATCCAGATA
1 CAGAAATCAGAACAGAATTCAGA-A
* **
3280192 -AGAAATCAGGACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
* *
3280215 CATG-TATCAGAACAGAATTCA-AGT
1 CA-GAAATCAGAACAGAATTCAGA-A
3280239 CAGAAATCAGA
1 CAGAAATCAGA
3280250 TAAAATATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.02
24 63 0.95
25 2 0.03
ACGTcount: A:0.49, C:0.17, G:0.18, T:0.17
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:3280244 original size:48 final size:48
Alignment explanation
Indices: 3280141--3280249 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
3280131 AAATGGAGAT
* *
3280141 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
* * **
3280189 ATAAGAAATCAGGACAGAATTCAGGTCATG-TATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGAACA-GATATCAGAACAGAA-TCAAG
3280238 -TCAGAAATCAGA
1 ATCAGAAATCAGA
3280250 TAAAATATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 46 0.90
49 5 0.10
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCAAG
Found at i:3289170 original size:26 final size:27
Alignment explanation
Indices: 3289108--3289158 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3289098 TAAAACGGTT
*
3289108 CGGTTCAG--TTCGGTTTGGCTTTAAA
1 CGGTTCAGTTTTCGGTTCGGCTTTAAA
3289133 CGGTTCAGTTTTCGGTTCGG-TTTAAA
1 CGGTTCAGTTTTCGGTTCGGCTTTAAA
3289159 GGCTTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 6 0.26
27 9 0.39
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (27 bp):
CGGTTCAGTTTTCGGTTCGGCTTTAAA
Found at i:3289460 original size:5 final size:5
Alignment explanation
Indices: 3289443--3289474 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
3289433 TTTGGTAAAA
*
3289443 AACCG AACTG AACCG AACCG AACCG AACCG AA
1 AACCG AACCG AACCG AACCG AACCG AACCG AA
3289475 TACACCCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.44, C:0.34, G:0.19, T:0.03
Consensus pattern (5 bp):
AACCG
Found at i:3297966 original size:98 final size:101
Alignment explanation
Indices: 3297793--3297998 Score: 301
Period size: 98 Copynumber: 2.1 Consensus size: 101
3297783 AACAACTTTC
* * * *
3297793 CAATTTCAGAGCCGATTTCAACTCCATGACGGAAGATATCGTGCCACTCGAGACAACACAAGCTC
1 CAATTTCAGAGCCAATCTCAACTCCACGACGAAAGATATCGTGCCACTCGAGACAACACAAGCTC
*
3297858 AACTTCACAGCGAAGGGGTGGCTGACTGTCGAAAAA
66 AACTTCACAGCGAAGGGGCGGCTGACTGTCGAAAAA
* * * *
3297894 TAATTTCGGAGCCAATCTCAACTCCACGGCGAAAGATATTG-GCC-C-CGAGACAACACAAGCTC
1 CAATTTCAGAGCCAATCTCAACTCCACGACGAAAGATATCGTGCCACTCGAGACAACACAAGCTC
*
3297956 AACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAA
66 AACTTCACAGCGAAGGGGCGGCTGACTGTCGAAAAA
3297992 CAATTTC
1 CAATTTC
3297999 CCAGTTCCAG
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
98 57 0.61
99 1 0.01
100 3 0.03
101 33 0.35
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.18
Consensus pattern (101 bp):
CAATTTCAGAGCCAATCTCAACTCCACGACGAAAGATATCGTGCCACTCGAGACAACACAAGCTC
AACTTCACAGCGAAGGGGCGGCTGACTGTCGAAAAA
Found at i:3300236 original size:27 final size:29
Alignment explanation
Indices: 3300206--3300263 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
3300196 TTTCTCTTAC
*
3300206 AAACCTAATGACA-ATTTT-TTTATATAT
1 AAACCTAATAACAGATTTTGTTTATATAT
3300233 AAACCTAATAACAGATTTTGGTTTATATAT
1 AAACCTAATAACAGATTTT-GTTTATATAT
3300263 A
1 A
3300264 TGAACCCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 12 0.44
28 5 0.19
30 10 0.37
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (29 bp):
AAACCTAATAACAGATTTTGTTTATATAT
Found at i:3302639 original size:17 final size:17
Alignment explanation
Indices: 3302590--3302639 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
3302580 TTGTTCATGT
3302590 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
3302607 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
3302621 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
3302638 TT
1 TT
3302640 AGAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:3304879 original size:2 final size:2
Alignment explanation
Indices: 3304872--3304908 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3304862 TGGTAAAGAC
3304872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3304909 TGTAACACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3308494 original size:21 final size:21
Alignment explanation
Indices: 3308468--3308507 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3308458 AAGACTTTAT
3308468 TTTCAAAATTAAAAAATGATA
1 TTTCAAAATTAAAAAATGATA
3308489 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
3308508 AAATAGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:3312364 original size:23 final size:22
Alignment explanation
Indices: 3312321--3312363 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3312311 TCGATACCCG
* *
3312321 TTGAAGGGGAACTGATTCCCCT
1 TTGAAAGGGAACCGATTCCCCT
3312343 TTGAAAGGGAACCGATTCCCC
1 TTGAAAGGGAACCGATTCCCC
3312364 CCAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (22 bp):
TTGAAAGGGAACCGATTCCCCT
Found at i:3314322 original size:17 final size:16
Alignment explanation
Indices: 3314294--3314330 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
3314284 ATGTTTTAGC
3314294 ATTT-TGGATGTTTGA
1 ATTTGTGGATGTTTGA
3314309 ATTTGTGGATTGTTTGA
1 ATTTGTGGA-TGTTTGA
3314326 ATTTG
1 ATTTG
3314331 GATGCTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 4 0.20
17 12 0.60
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (16 bp):
ATTTGTGGATGTTTGA
Found at i:3314367 original size:14 final size:15
Alignment explanation
Indices: 3314327--3314368 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3314317 ATTGTTTGAA
*
3314327 TTTGGATGCTTATATG
1 TTTGGATG-TTATGTG
3314343 TTTGGAT-TTATGT-
1 TTTGGATGTTATGTG
3314356 TTTGGATGTTATG
1 TTTGGATGTTATG
3314369 GATGATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 7 0.29
14 10 0.42
16 7 0.29
ACGTcount: A:0.17, C:0.02, G:0.26, T:0.55
Consensus pattern (15 bp):
TTTGGATGTTATGTG
Found at i:3315057 original size:21 final size:22
Alignment explanation
Indices: 3315023--3315064 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
3315013 CTCGGAGGGA
3315023 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
3315045 ACCGATT-CCCCCCAAGGGGG
1 ACCGATTCCCCCCCAAGGGGG
3315065 GTATCAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.19, C:0.40, G:0.29, T:0.12
Consensus pattern (22 bp):
ACCGATTCCCCCCCAAGGGGGT
Found at i:3315077 original size:21 final size:21
Alignment explanation
Indices: 3315031--3315077 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
3315021 GAACCGATTC
*
3315031 CCCCCCAAGGGGGTACCGATT
1 CCCCCCAAGGGGGTACCAATT
*
3315052 CCCCCCAAGGGGGGTATCAATT
1 CCCCCCAA-GGGGGTACCAATT
3315074 CCCC
1 CCCC
3315078 TTGTTCAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.19, C:0.40, G:0.26, T:0.15
Consensus pattern (21 bp):
CCCCCCAAGGGGGTACCAATT
Found at i:3319677 original size:54 final size:54
Alignment explanation
Indices: 3319581--3319846 Score: 383
Period size: 54 Copynumber: 4.9 Consensus size: 54
3319571 CCGAAATGGA
* ** * *
3319581 AATTCACAAACTTATTATGAATTCCATGGATTGC-CAATATAGTGTCGATACGGT
1 AATTCACAAACTCATTATGAATTCTGTGGGTTGCAC-ACATAGTGTCGATACGGT
* * **
3319635 AATTCACAAAATCATTATGAATTCTGTGTGTTGCATGCATAGTGTCGATACGGT
1 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
3319689 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
1 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
* * *
3319743 AATTCACAAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCTATACGGC
1 AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
*
3319797 AATTCATAAACTCATTATGAATT-TCGTGGGTTGCACACATAGTGTCGATA
1 AATTCACAAACTCATTATGAATTCT-GTGGGTTGCACACATAGTGTCGATA
3319847 GTACACATGG
Statistics
Matches: 191, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
54 191 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (54 bp):
AATTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGT
Found at i:3322655 original size:21 final size:21
Alignment explanation
Indices: 3322631--3322676 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3322621 AAGACAGCTT
*
3322631 GATCGATTCAATTAATGGCTG
1 GATCGATTCAATTAATGGCTC
* **
3322652 GATCGGTTTGATTAATGGCTC
1 GATCGATTCAATTAATGGCTC
3322673 GATC
1 GATC
3322677 TGTTTTGTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (21 bp):
GATCGATTCAATTAATGGCTC
Found at i:3322681 original size:21 final size:21
Alignment explanation
Indices: 3322641--3322681 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3322631 GATCGATTCA
*
3322641 ATTAATGGCTGGATCGGTTTG
1 ATTAATGGCTCGATCGGTTTG
*
3322662 ATTAATGGCTCGATCTGTTT
1 ATTAATGGCTCGATCGGTTT
3322682 TGTCAACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (21 bp):
ATTAATGGCTCGATCGGTTTG
Found at i:3326092 original size:18 final size:19
Alignment explanation
Indices: 3326065--3326111 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
3326055 TGTTGAATAT
*
3326065 TATTTCAACTATTT-AAAA
1 TATTTTAACTATTTAAAAA
3326083 TATTTTAACTATTTAAAAA
1 TATTTTAACTATTTAAAAA
*
3326102 TAGTTTAACT
1 TATTTTAACT
3326112 CGATTCGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (19 bp):
TATTTTAACTATTTAAAAA
Found at i:3326218 original size:18 final size:18
Alignment explanation
Indices: 3326191--3326225 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3326181 ATTCGAATAT
3326191 TATTTCAACTATTTAAAG
1 TATTTCAACTATTTAAAG
*
3326209 TATTTTAACTATTTAAA
1 TATTTCAACTATTTAAA
3326226 AATAGTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (18 bp):
TATTTCAACTATTTAAAG
Found at i:3326222 original size:126 final size:126
Alignment explanation
Indices: 3326059--3326409 Score: 589
Period size: 127 Copynumber: 2.8 Consensus size: 126
3326049 TAAAATTGTT
*
3326059 GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATAGTTTAACTCGATTCGGGTCA
1 GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATAGTTTAACTCGATTCGGGTCG
3326124 AATATTATTTCAACTATTTAAAATATTTTAACTCGATCTAGATCGAATAAATTAAATATTC
66 AATATTATTTCAACTATTTAAAATATTTTAACTCGATCTAGATCGAATAAATTAAATATTC
* *
3326185 GAATATTATTTCAACTATTTAAAGTATTTTAACTATTTAAAAATAGTTTAACTCGATCCGGGTCG
1 GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATAGTTTAACTCGATTCGGGTCG
* * *
3326250 AATATTATTTCAACTATTTAAAAATATTTTAACTCGGTCTGGATCGAATAAATTAAATATTT
66 AATATTATTTCAACTATTT-AAAATATTTTAACTCGATCTAGATCGAATAAATTAAATATTC
*
3326312 GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAA-ATGTTTAACTCGAGTCGGGTC
1 GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATA-GTTTAACTCGATTCGGGTC
* *
3326376 GAATATTATTTCTACTATTTAAAA-AATTTAACTC
65 GAATATTATTTCAACTATTTAAAATATTTTAACTC
3326410 AATATGGGTT
Statistics
Matches: 212, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
125 9 0.04
126 86 0.41
127 117 0.55
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (126 bp):
GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATAGTTTAACTCGATTCGGGTCG
AATATTATTTCAACTATTTAAAATATTTTAACTCGATCTAGATCGAATAAATTAAATATTC
Found at i:3326236 original size:19 final size:18
Alignment explanation
Indices: 3326197--3326237 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
3326187 ATATTATTTC
* *
3326197 AACTATTTAAAGTATTTT
1 AACTATTTAAAATAGTTT
3326215 AACTATTTAAAAATAGTTT
1 AACTATTT-AAAATAGTTT
3326234 AACT
1 AACT
3326238 CGATCCGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (18 bp):
AACTATTTAAAATAGTTT
Found at i:3326259 original size:46 final size:45
Alignment explanation
Indices: 3326209--3326492 Score: 197
Period size: 46 Copynumber: 6.5 Consensus size: 45
3326199 CTATTTAAAG
*
3326209 TATTTTAACTATTTAAAAATAGTTTAACTCGATCCGGGTCGAATAT
1 TATTTTAACTATTTAAAAATA-TTTAACTCGATCTGGGTCGAATAT
* * *
3326255 TATTTCAACTATTTAAAAATATTTTAACTCGGTCTGGATCGAATA-
1 TATTTTAACTATTTAAAAATA-TTTAACTCGATCTGGGTCGAATAT
* * * * *
3326300 -A-ATTAAATATTTGAATATTATTTCAACT--AT-T---T--AA-AA
1 TATTTTAACTATTT-AAAAATATTT-AACTCGATCTGGGTCGAATAT
*
3326336 TATTTTAACTATTTAAAAAATGTTTAACTCGAGTC-GGGTCGAATAT
1 TATTTTAACTATTT-AAAAATATTTAACTCGA-TCTGGGTCGAATAT
* * *
3326382 TATTTCT-ACTATTTAAAAA-ATTTAACTCAATATGGGTTGAATAT
1 TATTT-TAACTATTTAAAAATATTTAACTCGATCTGGGTCGAATAT
** * * *
3326426 TATTTCGATTGTTT-AAAATATTTTAACTCTATCTGGGTCGAATAT
1 TATTTTAACTATTTAAAAATA-TTTAACTCGATCTGGGTCGAATAT
* *
3326471 TA-TTCAACTATTTTAAAATATT
1 TATTTTAACTATTTAAAAATATT
3326493 AATTTATTCG
Statistics
Matches: 186, Mismatches: 31, Indels: 44
0.71 0.12 0.17
Matches are distributed among these distances:
35 1 0.01
36 2 0.01
37 5 0.03
38 17 0.09
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 17 0.09
44 50 0.27
45 36 0.19
46 53 0.28
47 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.43
Consensus pattern (45 bp):
TATTTTAACTATTTAAAAATATTTAACTCGATCTGGGTCGAATAT
Found at i:3326345 original size:18 final size:18
Alignment explanation
Indices: 3326318--3326364 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
3326308 ATTTGAATAT
*
3326318 TATTTCAACTATTTAAAA
1 TATTTTAACTATTTAAAA
3326336 TATTTTAACTATTTAAAA
1 TATTTTAACTATTTAAAA
*
3326354 AATGTTTAACT
1 TAT-TTTAACT
3326365 CGAGTCGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (18 bp):
TATTTTAACTATTTAAAA
Found at i:3326424 original size:44 final size:43
Alignment explanation
Indices: 3326336--3326488 Score: 146
Period size: 44 Copynumber: 3.4 Consensus size: 43
3326326 CTATTTAAAA
* * *
3326336 TATTTTAACTATTTAAAAAATGTTTAACTCGAGTCGGGTCGAATAT
1 TATTTCAACTATTTAAAAAA--TTTAACTC-AATTGGGTCGAATAT
* *
3326382 TATTTCTACTATTTAAAAAATTTAACTCAATATGGGTTGAATAT
1 TATTTCAACTATTTAAAAAATTTAACTCAAT-TGGGTCGAATAT
* * * * *
3326426 TATTTCGATTGTTTAAAATATTTTAACTCTATCTGGGTCGAATAT
1 TATTTCAACTATTTAAAA-AATTTAACTCAAT-TGGGTCGAATAT
*
3326471 TA-TTCAACTATTTTAAAA
1 TATTTCAACTATTTAAAAA
3326489 TATTAATTTA
Statistics
Matches: 89, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
43 3 0.03
44 44 0.49
45 24 0.27
46 18 0.20
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.43
Consensus pattern (43 bp):
TATTTCAACTATTTAAAAAATTTAACTCAATTGGGTCGAATAT
Found at i:3331651 original size:27 final size:26
Alignment explanation
Indices: 3331621--3331726 Score: 64
Period size: 27 Copynumber: 4.1 Consensus size: 26
3331611 ATAAATATGA
3331621 AAAATATTGAATTTAATTTAGAAATAT
1 AAAATATTGAATTTAATTTA-AAATAT
* *
3331648 AAAA-A---AA-TAAATTTAATATGA-
1 AAAATATTGAATTTAATTTAAAAT-AT
3331669 AAAATATTGAATTTAATTTTAAAAATAT
1 AAAATATTGAATTTAA-TTT-AAAATAT
* * *
3331697 AAAAATAAT-AATTTTACTTTAAAATTT
1 -AAAATATTGAA-TTTAATTTAAAATAT
3331724 AAA
1 AAA
3331727 GCTTGTATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 23
0.67 0.08 0.25
Matches are distributed among these distances:
21 7 0.11
22 9 0.15
23 2 0.03
25 2 0.03
26 7 0.11
27 14 0.23
28 9 0.15
29 11 0.18
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.39
Consensus pattern (26 bp):
AAAATATTGAATTTAATTTAAAATAT
Found at i:3331666 original size:48 final size:50
Alignment explanation
Indices: 3331614--3331712 Score: 166
Period size: 48 Copynumber: 2.0 Consensus size: 50
3331604 TAGAAATATA
*
3331614 AATATGAAAAATATTGAATTTAA-TTTAGAAATATAAAAA-AATAAATTT
1 AATATGAAAAATATTGAATTTAATTTTAAAAATATAAAAATAATAAATTT
*
3331662 AATATGAAAAATATTGAATTTAATTTTAAAAATATAAAAATAATAATTTT
1 AATATGAAAAATATTGAATTTAATTTTAAAAATATAAAAATAATAAATTT
3331712 A
1 A
3331713 CTTTAAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 23 0.49
49 15 0.32
50 9 0.19
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (50 bp):
AATATGAAAAATATTGAATTTAATTTTAAAAATATAAAAATAATAAATTT
Found at i:3331681 original size:21 final size:21
Alignment explanation
Indices: 3331657--3331696 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3331647 TAAAAAAATA
3331657 AATTTAATATGAAAAATATTG
1 AATTTAATATGAAAAATATTG
* *
3331678 AATTTAATTTTAAAAATAT
1 AATTTAATATGAAAAATAT
3331697 AAAAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
AATTTAATATGAAAAATATTG
Found at i:3331709 original size:28 final size:30
Alignment explanation
Indices: 3331662--3331720 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
3331652 AAATAAATTT
* *
3331662 AATATGAAAAATATTGAATTTAATTTTAAA
1 AATATGAAAAATAATGAATTTAACTTTAAA
*
3331692 AATAT-AAAAATAAT-AATTTTACTTTAAA
1 AATATGAAAAATAATGAATTTAACTTTAAA
3331720 A
1 A
3331721 TTTAAAGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 13 0.50
29 8 0.31
30 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (30 bp):
AATATGAAAAATAATGAATTTAACTTTAAA
Found at i:3331820 original size:22 final size:22
Alignment explanation
Indices: 3331795--3331840 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3331785 TCTGTTTAAC
3331795 TAGTTTAGGTGATCTTATATTT
1 TAGTTTAGGTGATCTTATATTT
3331817 TAGTTTAGGTGATCTTATATTT
1 TAGTTTAGGTGATCTTATATTT
3331839 TA
1 TA
3331841 TAATTACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.17, T:0.54
Consensus pattern (22 bp):
TAGTTTAGGTGATCTTATATTT
Found at i:3335047 original size:22 final size:22
Alignment explanation
Indices: 3335022--3335069 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
3335012 CATATTACAA
3335022 ATAGGGAACCAATTCCCCTGCT
1 ATAGGGAACCAATTCCCCTGCT
* *
3335044 ATAGGGAACCGATTCCTCTGCT
1 ATAGGGAACCAATTCCCCTGCT
3335066 ATAG
1 ATAG
3335070 TACTGCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (22 bp):
ATAGGGAACCAATTCCCCTGCT
Found at i:3337540 original size:58 final size:59
Alignment explanation
Indices: 3337471--3337690 Score: 336
Period size: 59 Copynumber: 3.8 Consensus size: 59
3337461 ATGGTACTAA
*
3337471 GTGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTA-TGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
3337528 GTGTACTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTG
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
3337587 GTGTGCTAAAATGTTAAGAAATTCATAATAAGTGTATGAATTTCCGGATTGGGCACATT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
3337646 GTGTGCTAAAATGTAAAGAGATTCATACTAAATGTATGAATTTCC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCC
3337691 ATATGGGAAA
Statistics
Matches: 147, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
57 5 0.03
58 40 0.27
59 102 0.69
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:3338110 original size:68 final size:68
Alignment explanation
Indices: 3337966--3338165 Score: 325
Period size: 68 Copynumber: 3.0 Consensus size: 68
3337956 ATAAAAGATC
* *
3337966 TGAGGCCTAACTGTGCATTTGACAGAAATGTTTCAATTATG-TAGTTAGATGAAAGGCTTAA-TG
1 TGAGGCCTAACTGTGCATTTGACAGAAAGGTTTCAATTATGCCAGTTAGATGAAAGGC-TAAGTG
3338029 CCTT
65 CCTT
* *
3338033 TGAGGCCTAACCGTGCATTTGACAGAAAGGTTTCAATTATGCCAGTTAGATGAAAGTCTAAGTGC
1 TGAGGCCTAACTGTGCATTTGACAGAAAGGTTTCAATTATGCCAGTTAGATGAAAGGCTAAGTGC
3338098 CTT
66 CTT
3338101 TGAGGCCTAACTGTGCATTTGACAGAAAGGTGTT-AATTATGCCAGTTAGATGAAAGGCTAAGTG
1 TGAGGCCTAACTGTGCATTTGACAGAAAGGT-TTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
3338165 C
65 C
3338166 AATACCCTAA
Statistics
Matches: 124, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
67 42 0.34
68 80 0.65
69 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
TGAGGCCTAACTGTGCATTTGACAGAAAGGTTTCAATTATGCCAGTTAGATGAAAGGCTAAGTGC
CTT
Found at i:3340455 original size:33 final size:33
Alignment explanation
Indices: 3340393--3340455 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
3340383 TGTAGCAATC
*
3340393 ACTGTAGCAGTGCATCGATACACTGTTCATGTT
1 ACTGTAGCAGTGCATCGATACACTATTCATGTT
* * *
3340426 ACTGTAGTAGTGCATCGGTACATTATTCAT
1 ACTGTAGCAGTGCATCGATACACTATTCAT
3340456 TGTTCACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (33 bp):
ACTGTAGCAGTGCATCGATACACTATTCATGTT
Found at i:3351478 original size:95 final size:95
Alignment explanation
Indices: 3351303--3351492 Score: 244
Period size: 95 Copynumber: 2.0 Consensus size: 95
3351293 ATACAGACGA
* * * * * * *
3351303 GGTAGTATCGATACCATGGTAAGGGTATCGATACTAATCATCACTGAAGCTAAAATTGGTATCGA
1 GGTAGTATCGATACCACGGTAAGGGTATCGATACCAAGCAACACTAAACCTAAAATTGGTAACGA
*
3351368 TACTGGAAGGAGGTATC-AGTACCATAGTAT
66 TACTCGAAGGAGGTATCGA-TACCATAGTAT
3351398 GGTAGTATCGATACCACGGTAAGGGTATCGATACCAAGCAACA-TCAAACCTAAAATTGGTAACG
1 GGTAGTATCGATACCACGGTAAGGGTATCGATACCAAGCAACACT-AAACCTAAAATTGGTAACG
3351462 ATA-TCGAATGTG-GGTATCGATACCATAGTAT
65 ATACTCGAA-G-GAGGTATCGATACCATAGTAT
3351493 AGAAGTATAG
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
94 5 0.06
95 76 0.92
96 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (95 bp):
GGTAGTATCGATACCACGGTAAGGGTATCGATACCAAGCAACACTAAACCTAAAATTGGTAACGA
TACTCGAAGGAGGTATCGATACCATAGTAT
Found at i:3351500 original size:95 final size:95
Alignment explanation
Indices: 3351306--3351526 Score: 236
Period size: 95 Copynumber: 2.3 Consensus size: 95
3351296 CAGACGAGGT
* * * * * * *
3351306 AGTATCGATACCATGGTAAGGGTATCGATACTAATCATCACTGAAGCTAAAATTGGTATCGATAC
1 AGTATCGATACCAAGGTAAGGGTATCGATACCAAGCAACACTAAACCTAAAATTGGTAACGATAC
* * *
3351371 TGGAAGGAGGTATCAGTACCATAGTATGGT
66 TCGAAGGAGGTATCAGTACCATAGTATAGA
*
3351401 AGTATCGATACCACGGTAAGGGTATCGATACCAAGCAACA-TCAAACCTAAAATTGGTAACGATA
1 AGTATCGATACCAAGGTAAGGGTATCGATACCAAGCAACACT-AAACCTAAAATTGGTAACGATA
3351465 -TCGAATGTG-GGTATC-GATACCATAGTATAGA
65 CTCGAA-G-GAGGTATCAG-TACCATAGTATAGA
* * *
3351496 AGTATAGCTACCAAGGT-AGTAGTATCGATAC
1 AGTATCGATACCAAGGTAAG-GGTATCGATAC
3351527 TATGAAGCCA
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
94 8 0.07
95 98 0.92
96 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (95 bp):
AGTATCGATACCAAGGTAAGGGTATCGATACCAAGCAACACTAAACCTAAAATTGGTAACGATAC
TCGAAGGAGGTATCAGTACCATAGTATAGA
Found at i:3352006 original size:59 final size:59
Alignment explanation
Indices: 3351856--3352086 Score: 288
Period size: 59 Copynumber: 3.9 Consensus size: 59
3351846 ATGGCACTAA
* *
3351856 GTGTGC-AAAATGTCAAGAAATTCATACTAAGTGTATGAATTTTTGTATAGGGAACTTT
1 GTGTGCTAAAATGTCAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGAACTTT
* * * * * * *
3351914 GTTTGCTAAAAATGTCAAGAAATTCATATTAAGTGTATGGACTTCCATATTGGGCACTTT
1 GTGTGCT-AAAATGTCAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGAACTTT
* * *
3351974 GTGTGCTATAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGTACTTT
1 GTGTGCTAAAATGTCAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGAACTTT
* * *
3352033 GTGTGCTAAAATGTAAAGAGATTCATACTAAAG-GTATGAATTTTCATA-TGGGAA
1 GTGTGCTAAAATGTCAAGAAATTCATACT-AAGTGTATGAATTTTCGTATTGGGAA
3352087 ATGTGAGTAT
Statistics
Matches: 147, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
58 10 0.07
59 84 0.57
60 53 0.36
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (59 bp):
GTGTGCTAAAATGTCAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGAACTTT
Found at i:3352461 original size:68 final size:68
Alignment explanation
Indices: 3352352--3352617 Score: 433
Period size: 68 Copynumber: 3.9 Consensus size: 68
3352342 AAATAAAAGA
* * *
3352352 TTTGATGCCTAACTGTGCATTTGACAGAAACGTGTCAATTATGCCAGTTAGATGAAAGGCTAATT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
3352417 GCC
66 GCC
** *
3352420 TTTGAGGCCTAACTGTATATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGCCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
3352485 GCC
66 GCC
* * * *
3352488 TTTGAAGCATAACTGTGCATTTGACAGAAAGATGTCAATTATGCCAGTTAAATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
3352553 GCC
66 GCC
*
3352556 TTTGAGGCCTAAATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTA
1 TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTA
3352618 TTTAACATCC
Statistics
Matches: 180, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 180 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (68 bp):
TTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
GCC
Found at i:3352767 original size:22 final size:22
Alignment explanation
Indices: 3352728--3352770 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3352718 ATTTTTGTAC
*
3352728 TGGATTAAATGGTAATTATGGA
1 TGGATTAAAAGGTAATTATGGA
3352750 TGGATTAAAAGAGT-ATTATGG
1 TGGATTAAAAG-GTAATTATGG
3352771 TAATTTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35
Consensus pattern (22 bp):
TGGATTAAAAGGTAATTATGGA
Found at i:3353943 original size:21 final size:23
Alignment explanation
Indices: 3353914--3353956 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
3353904 TGAATGAAGT
*
3353914 AATTGTATGAGAA-ATG-ATATG
1 AATTATATGAGAACATGTATATG
3353935 AATTATATGAGAACATGTATAT
1 AATTATATGAGAACATGTATAT
3353957 ATGAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (23 bp):
AATTATATGAGAACATGTATATG
Found at i:3354235 original size:18 final size:18
Alignment explanation
Indices: 3354212--3354246 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3354202 ATGTGTTCTA
3354212 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTTGGGACAT
3354230 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTTGGGACA
3354247 AATTCTATGC
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:0.17, G:0.34, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTTGGGACAT
Found at i:3358070 original size:21 final size:21
Alignment explanation
Indices: 3358029--3358080 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
3358019 GTTATAATTG
* * *
3358029 AATGACAT-AATTGTATTAGA
1 AATGATATGAATTATATGAGA
3358049 AATGATATGAATTATATGAGA
1 AATGATATGAATTATATGAGA
3358070 ACATGTATATG
1 A-ATG-ATATG
3358081 CGAATATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 3 0.12
23 5 0.19
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGATATGAATTATATGAGA
Found at i:3358358 original size:18 final size:18
Alignment explanation
Indices: 3358335--3358369 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3358325 ATGTGTTCTA
3358335 AGTGGTCATTT-GGGACAT
1 AGTGGTC-TTTCGGGACAT
3358353 AGTGGTCTTTCGGGACA
1 AGTGGTCTTTCGGGACA
3358370 AATTCTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.31
Consensus pattern (18 bp):
AGTGGTCTTTCGGGACAT
Found at i:3359682 original size:68 final size:68
Alignment explanation
Indices: 3359573--3359930 Score: 527
Period size: 68 Copynumber: 5.3 Consensus size: 68
3359563 GGGATATTAT
*
3359573 AGGCTAAGTGCCTTTGAGTCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
1 AGGCTAAGTGCCTTTGAGGCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
3359638 GAA
66 GAA
* * *
3359641 AGGCTAAGTACCTTTGAGGCATAACTATGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGAT
1 AGGCTAAGTGCCTTTGAGGCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
3359706 GAA
66 GAA
* * * * *
3359709 AGGCTAAGTGCCCTTGAGGCCTAACTGTGCATATGACAAAAAGGTGTCAATTATGCCAGTTAAAT
1 AGGCTAAGTGCCTTTGAGGCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
3359774 GAA
66 GAA
* * * * * * * *
3359777 AGGTTAAGTGCCTTTGAGGACTAACTGTGTATTTGATAAAAAGGTTTCAATTAAGCCAGTTAGAT
1 AGGCTAAGTGCCTTTGAGGCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
3359842 GAA
66 GAA
* *
3359845 AGGCTAAGTGCCTTTGAGGCCTAGCTATGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGAT
1 AGGCTAAGTGCCTTTGAGGCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
3359910 GAA
66 GAA
* *
3359913 AGGTTAAATGCCTTTGAG
1 AGGCTAAGTGCCTTTGAG
3359931 TAAAAGACTA
Statistics
Matches: 257, Mismatches: 33, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 257 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (68 bp):
AGGCTAAGTGCCTTTGAGGCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
GAA
Found at i:3360367 original size:45 final size:46
Alignment explanation
Indices: 3360307--3360432 Score: 125
Period size: 46 Copynumber: 2.8 Consensus size: 46
3360297 ATAAATACAT
* *
3360307 GAAAGGAT-TCATAAATGAAATGCATAATGGTGTAT-AAAAGGCAT
1 GAAAGGATGCCATAAATGAAATGCATAATGGTGTATAAAAAGGCAA
* * * * *
3360351 GAAATGATGCCATAAATGAAATGTATAGTAGTATATAAAAAGGCAA
1 GAAAGGATGCCATAAATGAAATGCATAATGGTGTATAAAAAGGCAA
* *
3360397 GAACGGTTGCCATAGTAA--AAATGCATAATGGTGTAT
1 GAAAGGATGCCATA--AATGAAATGCATAATGGTGTAT
3360433 TATAAGCATG
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
44 7 0.11
45 22 0.34
46 33 0.52
48 2 0.03
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.25
Consensus pattern (46 bp):
GAAAGGATGCCATAAATGAAATGCATAATGGTGTATAAAAAGGCAA
Found at i:3360409 original size:46 final size:45
Alignment explanation
Indices: 3360307--3360410 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
3360297 ATAAATACAT
* * * *
3360307 GAAAGGAT-TCATAAATGAAATGCATAATGGTGTATAAAAGGCAT
1 GAAAGGATGCCATAAATGAAATGCATAATAGTATATAAAAGGCAA
* * *
3360351 GAAATGATGCCATAAATGAAATGTATAGTAGTATATAAAAAGGCAA
1 GAAAGGATGCCATAAATGAAATGCATAATAGTATAT-AAAAGGCAA
* *
3360397 GAACGGTTGCCATA
1 GAAAGGATGCCATA
3360411 GTAAAAATGC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
44 7 0.15
45 22 0.46
46 19 0.40
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (45 bp):
GAAAGGATGCCATAAATGAAATGCATAATAGTATATAAAAGGCAA
Found at i:3361705 original size:2 final size:2
Alignment explanation
Indices: 3361698--3361722 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3361688 TGAAATAACA
3361698 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3361723 ATAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3362390 original size:31 final size:31
Alignment explanation
Indices: 3362352--3362417 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
3362342 CAAAAAACAC
3362352 GGGTGATGCTAGAGTGAAACGACGTCGTTTT
1 GGGTGATGCTAGAGTGAAACGACGTCGTTTT
3362383 GGGTGATGCTAGAGTGAAACGACGTCGTTTT
1 GGGTGATGCTAGAGTGAAACGACGTCGTTTT
3362414 GGGT
1 GGGT
3362418 TTAACTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.21, C:0.12, G:0.38, T:0.29
Consensus pattern (31 bp):
GGGTGATGCTAGAGTGAAACGACGTCGTTTT
Found at i:3364478 original size:125 final size:125
Alignment explanation
Indices: 3364272--3364915 Score: 607
Period size: 125 Copynumber: 5.2 Consensus size: 125
3364262 TATAAATAAT
* * * * * *
3364272 GCTAAGTCGTAATTGGTAGATGATACACTTCTTTTACTGAAGGACGTTGAATCTGGTGACAATCT
1 GCTAAGTCGTAATTGGTAGGTGATCCACTCCTTTTGCTGAAGGATGTTGAATCTGGTGACGATCT
* * * *
3364337 CACTCTTTCCTATAAAAGACGTTGAGTCTTGGGATGATCTTACTCATTCCTCTAAAATAC
66 CACTCTTTCCTCTAAAAGACGCTGAGTCGTGGGATGATCTTACTCATTCCTCTAAGATAC
* * * * *
3364397 GCTAAGTCGTATTTGGTAGGTGATCCACTCCTCTTGCTGAAGGATATTGAATCTAGTGATGATCT
1 GCTAAGTCGTAATTGGTAGGTGATCCACTCCTTTTGCTGAAGGATGTTGAATCTGGTGACGATCT
* * * * *
3364462 CACTCTTTCCTCTAAAAGATGCTAAGTCGTGGAATGATCTTACTCCTTTCTCTTAAGGATA-
66 CACTCTTTCCTCTAAAAGACGCTGAGTCGTGGGATGATCTTACTCATTCCTC-TAA-GATAC
** * * ** * * *
3364523 -CTAAGTAATAATTGGTATGTGATCCACTCCTTTTGTTGAAGGATACTAAATCTAGTGATGATCT
1 GCTAAGTCGTAATTGGTAGGTGATCCACTCCTTTTGCTGAAGGATGTTGAATCTGGTGACGATCT
* * * * *
3364587 CACTTTTTCCTCTAAAAGACGCTGAGCCGTGGGACGATCATACTCATTCCTCTGAAG-GAC
66 CACTCTTTCCTCTAAAAGACGCTGAGTCGTGGGATGATCTTACTCATTCCTCT-AAGATAC
* * * * * * *
3364647 CCTAAATTGTAATTGGTAGATGATACACTCCTTTTGTTGAAGGATGCTGAATCTGGTGACGATCT
1 GCTAAGTCGTAATTGGTAGGTGATCCACTCCTTTTGCTGAAGGATGTTGAATCTGGTGACGATCT
* * * * ** * *
3364712 CACTATTTCCTCTGAAAGACACTAAGTCACGGGATGATCTTACTCCTTCCTATGAAGA-AC
66 CACTCTTTCCTCTAAAAGACGCTGAGTCGTGGGATGATCTTACTCATTCCTCT-AAGATAC
* * * * * *
3364772 GCTAAGTTGTAATTCGTAGGTGATCCAATCATTTTGCTAAAGGATGTTGAATCTGGTGACGATGT
1 GCTAAGTCGTAATTGGTAGGTGATCCACTCCTTTTGCTGAAGGATGTTGAATCTGGTGACGATCT
* * * * * ** * *
3364837 CACTCTTT-CTGTTGAAAGACACTGAGCCTTGAAACGATCTTACTCATTCCTCTGAAGGT-C
66 CACTCTTTCCT-CTAAAAGACGCTGAGTCGTGGGATGATCTTACTCATTCCTCT-AAGATAC
*
3364897 GCTAAGTCATAATTGGTAG
1 GCTAAGTCGTAATTGGTAG
3364916 TTGCTCATCT
Statistics
Matches: 426, Mismatches: 85, Indels: 16
0.81 0.16 0.03
Matches are distributed among these distances:
123 1 0.00
124 4 0.01
125 415 0.97
126 3 0.01
127 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (125 bp):
GCTAAGTCGTAATTGGTAGGTGATCCACTCCTTTTGCTGAAGGATGTTGAATCTGGTGACGATCT
CACTCTTTCCTCTAAAAGACGCTGAGTCGTGGGATGATCTTACTCATTCCTCTAAGATAC
Found at i:3365895 original size:18 final size:18
Alignment explanation
Indices: 3365872--3365910 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3365862 AAAATGTTTT
*
3365872 ATGAAA-AAGTTTTGAATA
1 ATGAAAGAA-TTTTGAAAA
3365890 ATGAAAGAATTTTGAAAA
1 ATGAAAGAATTTTGAAAA
3365908 ATG
1 ATG
3365911 TTTGATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (18 bp):
ATGAAAGAATTTTGAAAA
Found at i:3365905 original size:11 final size:11
Alignment explanation
Indices: 3365891--3365955 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 11
3365881 TTTTGAATAA
3365891 TGAAAGAATTT
1 TGAAAGAATTT
3365902 TGAAA-AATGTT
1 TGAAAGAAT-TT
3365913 TGATTAAAGAATTT
1 TG---AAAGAATTT
3365927 TGAAA-AATGTT
1 TGAAAGAAT-TT
3365938 TGATGAAGAATTT
1 TGA--AAGAATTT
3365951 TGAAA
1 TGAAA
3365956 AATGTTGCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 18
0.71 0.00 0.29
Matches are distributed among these distances:
10 6 0.13
11 19 0.42
13 7 0.16
14 10 0.22
15 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (11 bp):
TGAAAGAATTT
Found at i:3365912 original size:43 final size:43
Alignment explanation
Indices: 3365851--3365935 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
3365841 AAAATCGATG
* *
3365851 AAGAAGTTTTGAAAATGTTTTATGAAA-AAGTTTTGAATAATGA
1 AAGAAGTTTTGAAAATGTTTGATGAAAGAA-TTTTGAAAAATGA
*
3365894 AAGAA-TTTTGAAAAATGTTTGATTAAAGAATTTTGAAAAATG
1 AAGAAGTTTTG-AAAATGTTTGATGAAAGAATTTTGAAAAATG
3365936 TTTGATGAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 5 0.14
43 30 0.81
44 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (43 bp):
AAGAAGTTTTGAAAATGTTTGATGAAAGAATTTTGAAAAATGA
Found at i:3365946 original size:24 final size:25
Alignment explanation
Indices: 3365893--3365961 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
3365883 TTGAATAATG
3365893 AAAGAATTTTGAAAAATGTTTGATT
1 AAAGAATTTTGAAAAATGTTTGATT
3365918 AAAGAATTTTGAAAAATGTTTGA-T
1 AAAGAATTTTGAAAAATGTTTGATT
*
3365942 GAAGAATTTTGAAAAATGTT
1 AAAGAATTTTGAAAAATGTT
3365962 GCCCCTTACA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 20 0.47
25 23 0.53
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (25 bp):
AAAGAATTTTGAAAAATGTTTGATT
Found at i:3366892 original size:17 final size:17
Alignment explanation
Indices: 3366854--3366897 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
3366844 ACTTGATATG
*
3366854 TTTTCTTTAT-TCTTTC
1 TTTTCTTTTTGTCTTTC
3366870 -TTTCTTTTTGTCTTTC
1 TTTTCTTTTTGTCTTTC
3366886 TTTTCTTTTTGT
1 TTTTCTTTTTGT
3366898 TTCTCTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 11 0.44
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTTCTTTTTGTCTTTC
Found at i:3366944 original size:41 final size:40
Alignment explanation
Indices: 3366882--3366960 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
3366872 TCTTTTTGTC
* * * *
3366882 TTTCTTTTCTTTTTGTTTCTCTCATTTTTTCTCTTTTTTTAT
1 TTTCTTTTCTTTTTCTATCTCT-ATCTTTTAT-TTTTTTTAT
3366924 TTTC-TTTCTTTTTCTATCTCTATCTTTTATTTTTTTT
1 TTTCTTTTCTTTTTCTATCTCTATCTTTTATTTTTTTT
3366961 GCTCTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 7 0.21
40 7 0.21
41 15 0.45
42 4 0.12
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.76
Consensus pattern (40 bp):
TTTCTTTTCTTTTTCTATCTCTATCTTTTATTTTTTTTAT
Found at i:3372906 original size:23 final size:23
Alignment explanation
Indices: 3372880--3372980 Score: 114
Period size: 23 Copynumber: 4.3 Consensus size: 23
3372870 GAATCGAGGG
* *
3372880 TTCTATGCGGTCCTTCGCGACAA
1 TTCTATGTGGTCCTTCGGGACAA
*
3372903 TTCTATGTGGTCTTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
*
3372926 TTCTACGTGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
* **
3372949 ATCTATGTGG-CACTTCGGTTCATA
1 TTCTATGTGGTC-CTTCGGGACA-A
3372973 TTCTATGT
1 TTCTATGT
3372981 AGCACTTCGG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
22 1 0.02
23 57 0.86
24 8 0.12
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAA
Found at i:3372985 original size:24 final size:24
Alignment explanation
Indices: 3372938--3373001 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
3372928 CTACGTGGTC
*
3372938 CTTCGG-GACAAA-TCTATGTGGCA
1 CTTCGGTG-CAAATTCTATGTAGCA
* *
3372961 CTTCGGTTCATATTCTATGTAGCA
1 CTTCGGTGCAAATTCTATGTAGCA
3372985 CTTCGGTGCAAATTCTA
1 CTTCGGTGCAAATTCTA
3373002 CGTGGCAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 9 0.26
24 25 0.74
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (24 bp):
CTTCGGTGCAAATTCTATGTAGCA
Found at i:3379803 original size:23 final size:23
Alignment explanation
Indices: 3379773--3379879 Score: 126
Period size: 23 Copynumber: 4.7 Consensus size: 23
3379763 TTGAGGGTTT
* *
3379773 TATGTGGTCATTCGGGATAATTC
1 TATGTGGTCCTTCGGGACAATTC
*
3379796 TATGTGGTCCTTCGGGACAATTT
1 TATGTGGTCCTTCGGGACAATTC
*
3379819 TATGTGGTCCTTCGAGACAATTC
1 TATGTGGTCCTTCGGGACAATTC
*** *
3379842 TACACGGTCCTTCGGGACAAATC
1 TATGTGGTCCTTCGGGACAATTC
3379865 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
3379880 TGCATATTTT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
22 1 0.01
23 69 0.99
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAATTC
Found at i:3381291 original size:16 final size:16
Alignment explanation
Indices: 3381270--3381302 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3381260 AATAAAATGC
3381270 AATAAT-ATAAATAATA
1 AATAATAAT-AATAATA
3381286 AATAATAATAATAATA
1 AATAATAATAATAATA
3381302 A
1 A
3381303 TAACCTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:3382908 original size:31 final size:29
Alignment explanation
Indices: 3382852--3382939 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 29
3382842 GAACAAAATG
3382852 TAAATTTTGAAAGTTTAGTGG-CCAAAGAA
1 TAAATTTTGAAAGTTTAG-GGACCAAAGAA
* *
3382881 TAAAGTTTGGAAACGTTTAGGGACCAAAAGGA
1 TAAA-TTTTGAAA-GTTTAGGGACC-AAAGAA
*
3382913 T-AATTTTCAAAAGTTTAGGGACCAAAG
1 TAAATTTT-GAAAGTTTAGGGACCAAAG
3382940 TGTAATTTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
29 8 0.16
30 23 0.46
31 13 0.26
32 6 0.12
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (29 bp):
TAAATTTTGAAAGTTTAGGGACCAAAGAA
Found at i:3382949 original size:29 final size:30
Alignment explanation
Indices: 3382895--3382956 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
3382885 GTTTGGAAAC
3382895 GTTTAGGGACCAAAAGGATAATTTTCAAAA
1 GTTTAGGGACCAAAAGGATAATTTTCAAAA
3382925 GTTTAGGGACC-AAAGTG-TAATTTTCAAAA
1 GTTTAGGGACCAAAAG-GATAATTTTCAAAA
3382954 GTT
1 GTT
3382957 AGGAGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.31
Consensus pattern (30 bp):
GTTTAGGGACCAAAAGGATAATTTTCAAAA
Found at i:3386443 original size:21 final size:21
Alignment explanation
Indices: 3386413--3386528 Score: 155
Period size: 21 Copynumber: 5.6 Consensus size: 21
3386403 GATTTACATA
*
3386413 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
3386434 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
3386455 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
** * *
3386476 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCGAAG
*
3386497 TT--CGTTACGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
*
3386516 TTCGCGTTACGAT
1 TTCGCGTTGCGAT
3386529 TTATTCCAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
19 14 0.17
21 69 0.83
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:3386465 original size:42 final size:42
Alignment explanation
Indices: 3386412--3386553 Score: 166
Period size: 42 Copynumber: 3.4 Consensus size: 42
3386402 CGATTTACAT
* *
3386412 ATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAA
1 ATTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAA
* **
3386454 GTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAA
1 ATTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAA
* * *
3386496 ATT--CGTTACGATAGTCGAAGTTCGCGTTACGATTTATTCCAA
1 ATTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGA--TAGTCCAA
3386538 ATT--CGTTGCGATAGTC
1 ATTCGCGTTGCGATAGTC
3386554 CAAAATCGTA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 27 0.31
42 61 0.69
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (42 bp):
ATTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAA
Found at i:3386544 original size:21 final size:20
Alignment explanation
Indices: 3386480--3386567 Score: 56
Period size: 19 Copynumber: 4.4 Consensus size: 20
3386470 TCGAAGTTCG
*
3386480 CGTTGCGATT-TTCCAAATT
1 CGTTACGATTATTCCAAATT
* * *
3386499 CGTTACGA-TAGTCGAAGTT
1 CGTTACGATTATTCCAAATT
3386518 CGCGTTACGATTTATTCCAAATT
1 --CGTTACGA-TTATTCCAAATT
* * *
3386541 CGTTGCGA-TAGTCCAAAAT
1 CGTTACGATTATTCCAAATT
*
3386560 CGTAACGA
1 CGTTACGA
3386568 CTTGTGGTAT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.02
19 28 0.54
21 15 0.29
23 8 0.15
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (20 bp):
CGTTACGATTATTCCAAATT
Found at i:3386545 original size:61 final size:60
Alignment explanation
Indices: 3386438--3386567 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 60
3386428 TCGAAGTTCG
* * * * ** *
3386438 CGTTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTACGATAGTCGAAGTTCGCGTTACGATAGTCCAAATTC-CGTTGCGATAGTCCAAAAT
*
3386499 CGTTACGATAGTCGAAGTTCGCGTTACGATTTATTCCAAATT-CGTTGCGATAGTCCAAAAT
1 CGTTACGATAGTCGAAGTTCGCGTTACGA--TAGTCCAAATTCCGTTGCGATAGTCCAAAAT
*
3386560 CGTAACGA
1 CGTTACGA
3386568 CTTGTGGTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
61 50 0.86
63 8 0.14
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (60 bp):
CGTTACGATAGTCGAAGTTCGCGTTACGATAGTCCAAATTCCGTTGCGATAGTCCAAAAT
Found at i:3387312 original size:21 final size:20
Alignment explanation
Indices: 3387286--3387355 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
3387276 ATTTTGGACT
3387286 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTT-GAATAA
*
3387307 ATCGCAATGCGAACTTTGACT--
1 ATCGCAA--CGAA-TTTGAATAA
3387328 ATCGCAACGAATTTTGAATAA
1 ATCGCAACGAA-TTTGAATAA
3387349 ATCGCAA
1 ATCGCAA
3387356 TGCGAAATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
19 10 0.24
21 21 0.51
23 7 0.17
24 3 0.07
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAATTTGAATAA
Found at i:3387373 original size:21 final size:20
Alignment explanation
Indices: 3387307--3387481 Score: 117
Period size: 21 Copynumber: 8.6 Consensus size: 20
3387297 TTTGGAATAA
*
3387307 ATCGCAATGCGAACTTTGACT
1 ATCGCAA-GCGAACTTCGACT
* * *
3387328 ATCGCAA-CGAATTTTGAAT
1 ATCGCAAGCGAACTTCGACT
*
3387347 AAATCGCAATGCGAAATTCGACT
1 --ATCGCAA-GCGAACTTCGACT
* * **
3387370 ATCG-AAACGAA-TTAGGAAA
1 ATCGCAAGCGAACTT-CGACT
*
3387389 ATCGCAATGTGAACTTCGACT
1 ATCGCAA-GCGAACTTCGACT
* * **
3387410 ATCGCAA-CGAATTTGGAAA
1 ATCGCAAGCGAACTTCGACT
3387429 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTCGACT
3387450 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTCGACT
3387471 ATCGCAA-CGAA
1 ATCGCAAGCGAA
3387482 TTTGGAAAAT
Statistics
Matches: 121, Mismatches: 23, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
18 2 0.02
19 38 0.31
20 4 0.03
21 66 0.55
22 2 0.02
23 9 0.07
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAAGCGAACTTCGACT
Found at i:3387407 original size:40 final size:41
Alignment explanation
Indices: 3387282--3387458 Score: 259
Period size: 40 Copynumber: 4.3 Consensus size: 41
3387272 TGCGATTTTG
*
3387282 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTT
1 GACTATCGCAACGAATTTGG-ATAAATCGCAATGCGAACTTC
* *
3387324 GACTATCGCAACGAATTTTGAATAAATCGCAATGCGAAATTC
1 GACTATCGCAACGAA-TTTGGATAAATCGCAATGCGAACTTC
* * *
3387366 GACTATCGAAACGAATTAGGA-AAATCGCAATGTGAACTTC
1 GACTATCGCAACGAATTTGGATAAATCGCAATGCGAACTTC
*
3387406 GACTATCGCAACGAATTTGGA-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGATAAATCGCAATGCGAACTTC
3387446 GACTATCGCAACG
1 GACTATCGCAACG
3387459 CGAACTTCGA
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 66 0.54
41 4 0.03
42 48 0.39
43 4 0.03
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (41 bp):
GACTATCGCAACGAATTTGGATAAATCGCAATGCGAACTTC
Found at i:3387455 original size:61 final size:61
Alignment explanation
Indices: 3387389--3387523 Score: 216
Period size: 61 Copynumber: 2.2 Consensus size: 61
3387379 AATTAGGAAA
* * * *
3387389 ATCGCAATGTGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCACAACGCAAACTTCGACT
* *
3387450 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCACAACGTAAACTTGGACT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCACAACGCAAACTTCGACT
3387511 ATCGCAACGCGAA
1 ATCGCAACGCGAA
3387524 TATGTAAATC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (61 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCACAACGCAAACTTCGACT
Found at i:3387477 original size:82 final size:82
Alignment explanation
Indices: 3387282--3387458 Score: 232
Period size: 82 Copynumber: 2.2 Consensus size: 82
3387272 TGCGATTTTG
* ** *
3387282 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTTGACTATCGCAACGAATTTTGAAT
1 GACTATCGAAACGAATTACG-A-AAATCGCAATGCGAACTTCGACTATCGCAACGAATTTTGAAT
*
3387347 AAATCGCAATGCGAAATTC
64 AAATCGCAACGCGAAATTC
* * *
3387366 GACTATCGAAACGAATTAGGAAAATCGCAATGTGAACTTCGACTATCGCAACGAA-TTTGGA-AA
1 GACTATCGAAACGAATTACGAAAATCGCAATGCGAACTTCGACTATCGCAACGAATTTTGAATAA
*
3387429 ATCGCAACGCGAACTTC
66 ATCGCAACGCGAAATTC
*
3387446 GACTATCGCAACG
1 GACTATCGAAACG
3387459 CGAACTTCGA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
80 29 0.34
81 5 0.06
82 32 0.38
83 1 0.01
84 18 0.21
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (82 bp):
GACTATCGAAACGAATTACGAAAATCGCAATGCGAACTTCGACTATCGCAACGAATTTTGAATAA
ATCGCAACGCGAAATTC
Found at i:3387518 original size:21 final size:20
Alignment explanation
Indices: 3387389--3387519 Score: 104
Period size: 21 Copynumber: 6.5 Consensus size: 20
3387379 AATTAGGAAA
*
3387389 ATCGCAATGTGAACTTCGACT
1 ATCGCAACG-GAACTTCGACT
* * **
3387410 ATCGCAAC-GAATTTGGAAA
1 ATCGCAACGGAACTTCGACT
3387429 ATCGCAACGCGAACTTCGACT
1 ATCGCAACG-GAACTTCGACT
3387450 ATCGCAACGCGAACTTCGACT
1 ATCGCAACG-GAACTTCGACT
* * **
3387471 ATCGCAAC-GAATTTGGAAA
1 ATCGCAACGGAACTTCGACT
* * *
3387490 ATCACAACGTAAACTTGGACT
1 ATCGCAACG-GAACTTCGACT
3387511 ATCGCAACG
1 ATCGCAACG
3387520 CGAATATGTA
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
19 29 0.33
21 58 0.67
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGGAACTTCGACT
Found at i:3387562 original size:21 final size:21
Alignment explanation
Indices: 3387532--3387584 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3387522 AATATGTAAA
*
3387532 TCGCATTGCGATAGTCCAAAT
1 TCGCGTTGCGATAGTCCAAAT
* * *
3387553 TCGTGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAAT
3387574 TCGCGTTGCGA
1 TCGCGTTGCGA
3387585 ATCTGGAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAAT
Found at i:3394194 original size:15 final size:15
Alignment explanation
Indices: 3394176--3394231 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
3394166 TAACCGGTTT
3394176 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
3394191 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
3394208 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
3394223 CGATTTTAA
1 CGGTTTTAA
3394232 TATTTCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:3394204 original size:17 final size:17
Alignment explanation
Indices: 3394179--3394229 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
3394169 CCGGTTTCGG
3394179 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
3394196 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
3394211 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
3394228 TT
1 TT
3394230 AATATTTCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:3394648 original size:13 final size:13
Alignment explanation
Indices: 3394627--3394681 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3394617 AAGTTCGATA
*
3394627 AATTCAAATACTT
1 AATTGAAATACTT
3394640 AATTGAAATACTT
1 AATTGAAATACTT
* *
3394653 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
3394667 AATTGAAATACTT
1 AATTGAAATACTT
3394680 AA
1 AA
3394682 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:3394763 original size:32 final size:33
Alignment explanation
Indices: 3394667--3394765 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
3394657 AACTCAACAT
* * *
3394667 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3394700 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3394733 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3394765 A
1 A
3394766 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:3394784 original size:21 final size:21
Alignment explanation
Indices: 3394760--3394799 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3394750 ACTTCAAGTT
3394760 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
3394781 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
3394800 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:3397088 original size:12 final size:12
Alignment explanation
Indices: 3397071--3397116 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
3397061 TTCGGATAAA
3397071 AACCGGTTTTTT
1 AACCGGTTTTTT
3397083 AACCGGTTTTTTT
1 AACCGG-TTTTTT
3397096 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
3397110 ATCCGGT
1 AACCGGT
3397117 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:3397101 original size:15 final size:14
Alignment explanation
Indices: 3397070--3397109 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
3397060 TTTCGGATAA
3397070 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
3397083 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
3397096 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
3397110 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:3398072 original size:9 final size:9
Alignment explanation
Indices: 3398054--3398106 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
3398044 ATAAACAAAG
*
3398054 ATAAATTAA
1 ATAAAATAA
3398063 ATAAAATAA
1 ATAAAATAA
*
3398072 AT-AAATAG
1 ATAAAATAA
3398080 ATAAAATAA
1 ATAAAATAA
*
3398089 AAAAAATAA
1 ATAAAATAA
3398098 A-AAAA-AA
1 ATAAAATAA
3398105 AT
1 AT
3398107 GTCGAGTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
7 3 0.08
8 11 0.29
9 24 0.63
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
ATAAAATAA
Done.