Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 79 of 182
Found at i:24865509 original size:13 final size:13
Alignment explanation
Indices: 24865491--24865528 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
24865481 TAACAATATT
24865491 TCTTTTTCTTTTC
1 TCTTTTTCTTTTC
*
24865504 TCTTTTTCTCTTTT
1 TCTTTTTCT-TTTC
24865518 TC-TTTTCTTTT
1 TCTTTTTCTTTT
24865529 TCTCAATCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 3 0.13
13 15 0.65
14 5 0.22
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTTTTTCTTTTC
Found at i:24865516 original size:21 final size:20
Alignment explanation
Indices: 24865491--24865529 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
24865481 TAACAATATT
24865491 TCTTTTTCTTTTCTCTTTTTC
1 TCTTTTTCTTTTCT-TTTTTC
24865512 TCTTTTTCTTTTCTTTTT
1 TCTTTTTCTTTTCTTTTT
24865530 CTCAATCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTTTTCTTTTCTTTTTTC
Found at i:24868498 original size:15 final size:15
Alignment explanation
Indices: 24868480--24868509 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24868470 AATTTAAATA
*
24868480 TGAAACAAGTAAAAG
1 TGAAACAAATAAAAG
24868495 TGAAACAAATAAAAG
1 TGAAACAAATAAAAG
24868510 AAAATGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
TGAAACAAATAAAAG
Found at i:24879313 original size:16 final size:17
Alignment explanation
Indices: 24879292--24879331 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
24879282 TTTAACCTAA
24879292 TTATTTATCTT-ATTAT
1 TTATTTATCTTCATTAT
*
24879308 TTATTTA-CTTCTTTAT
1 TTATTTATCTTCATTAT
24879324 TTATTTAT
1 TTATTTAT
24879332 TCGCCCACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTATCTTCATTAT
Found at i:24890436 original size:18 final size:18
Alignment explanation
Indices: 24890410--24890447 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
24890400 ATGCATATCA
24890410 TTTAATTGTCATTGCATT
1 TTTAATTGTCATTGCATT
* *
24890428 TTTATTTGTCTTTGCATT
1 TTTAATTGTCATTGCATT
24890446 TT
1 TT
24890448 ACTCATTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.63
Consensus pattern (18 bp):
TTTAATTGTCATTGCATT
Found at i:24893516 original size:7 final size:7
Alignment explanation
Indices: 24893504--24893537 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
24893494 GCTACAAATA
24893504 GAAGAAT
1 GAAGAAT
24893511 GAAGAAT
1 GAAGAAT
24893518 GAAGAAT
1 GAAGAAT
24893525 GAAGAAT
1 GAAGAAT
24893532 GAAGAA
1 GAAGAA
24893538 ATCATCTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (7 bp):
GAAGAAT
Found at i:24895601 original size:14 final size:14
Alignment explanation
Indices: 24895582--24895613 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
24895572 TACACCCTTG
24895582 GAAGTGTTTTGGAC
1 GAAGTGTTTTGGAC
24895596 GAAGTGTTTTGGAC
1 GAAGTGTTTTGGAC
24895610 -AAGT
1 GAAGT
24895614 AGACTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.25, C:0.06, G:0.34, T:0.34
Consensus pattern (14 bp):
GAAGTGTTTTGGAC
Found at i:24909310 original size:21 final size:21
Alignment explanation
Indices: 24909278--24909324 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
24909268 TTTCTTTTGC
24909278 TTACCTTGTGTTTAGCAATTTT
1 TTACCTTGTG-TTAGCAATTTT
* *
24909300 TTACC-TGTGTTGGCCATTTT
1 TTACCTTGTGTTAGCAATTTT
24909320 TTACC
1 TTACC
24909325 AATGCTGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
21 4 0.17
22 5 0.22
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.51
Consensus pattern (21 bp):
TTACCTTGTGTTAGCAATTTT
Found at i:24909320 original size:20 final size:20
Alignment explanation
Indices: 24909295--24909340 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
24909285 GTGTTTAGCA
** *
24909295 ATTTTTTACCTGTGTTGGCC
1 ATTTTTTACCAATGCTGGCC
24909315 ATTTTTTACCAATGCTGGCC
1 ATTTTTTACCAATGCTGGCC
24909335 ATTTTT
1 ATTTTT
24909341 AATCTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (20 bp):
ATTTTTTACCAATGCTGGCC
Found at i:24910045 original size:99 final size:99
Alignment explanation
Indices: 24909942--24910783 Score: 517
Period size: 99 Copynumber: 8.4 Consensus size: 99
24909932 AAAGGTCTTT
* * * * *
24909942 ATCTCCTTGAGGTTACAGTGGAATGGACTAAAGTTACAACACCAAATCCCATACCCCTGAAGTTG
1 ATCTCCTTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTAAAGTTG
* * *
24910007 CAATGGGTTAGATTAAAGCCAAAAGTGAATCTCA
66 CAGTGGGTCAGATTAAAGACAAAAGTGAATCTCA
** * * *** * * ** *
24910041 ATCT-CTCCGACGTTATAGTGGAATGGAGTGAAGCTT-CAACATTGACTTCTATACCTTTAAAAT
1 ATCTCCT-TAAGGTTACAGTGGAATGGAGTGAAG-TTACAACACCAAATCCTATACCCCTAAAGT
* * * * * * *
24910104 TACAGAAGAGT-GGAGTAAA-ACAAGTAA-CGAATCTTA
64 TGCAG-TGGGTCAGATTAAAGACAA--AAGTGAATCTCA
* * *
24910140 ATCTCC-TAGAGGTTACAATGGAATGGAGTGAAGTTACAACACCAAATCATATGCCCCTAAAGTT
1 ATCTCCTTA-AGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTAAAGTT
* * *
24910204 GCAGTAGGTCAGATTAAAGCCAAAAGAGAATCTCA
65 GCAGTGGGTCAGATTAAAGACAAAAGTGAATCTCA
* * * *** *
24910239 ATCTCCTTAAGGTTACAGTGGAATGAAGTAAAGCTTA-AACACCAACT-CTAATACTTTTAAAAT
1 ATCTCCTTAAGGTTACAGTGGAATGGAGTGAAG-TTACAACACCAAATCCT-ATACCCCTAAAGT
* *
24910302 TGCAGAAGGGT-AGAGTAAA-ACAAGTAACG-G-ATCTCA
64 TGCAG-TGGGTCAGATTAAAGACAA--AA-GTGAATCTCA
* * * * *
24910338 ATCTCCCTAAGGTTACAGTGGAATGGAGTGAAGTTACAGCACAAAATCCTATACCCCTGAAGTTA
1 ATCTCCTTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTAAAGTTG
*
24910403 CAGTAGGTCAGATTAAAGTTACAAAAGT-AGATCTCA
66 CAGTGGGTCAGATTAAAG--ACAAAAGTGA-ATCTCA
* * * * * * *
24910439 ATCTTCC-TGAGGTTATAGTGGAATGTAGTGAAACTT-CAACACGAAATCTTATATCCCTAAAGT
1 ATC-TCCTTAAGGTTACAGTGGAATGGAGTG-AAGTTACAACACCAAATCCTATACCCCTAAAGT
* * *
24910502 TGTAGTGGATCAGATTAAA-ATAAGTAACG-G-ATCTCA
64 TGCAGTGGGTCAGATTAAAGACAA--AA-GTGAATCTCA
* * * * * *
24910538 ATCTCCCTAAGGTTATAATGGAATAGAGTGAAGTTACAACACCAATTCCTATACCCCTGAAGTTG
1 ATCTCCTTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTAAAGTTG
* * *
24910603 CAGTGGGTCGGATTAAAGTTTCAAAAG-CATATCTCA
66 CAGTGGGTCAGATTAAAG--ACAAAAGTGA-ATCTCA
* * * * * *
24910639 AACTCCCTAAGGTTACAGTGGAATGGAGAGAAGCTT-CAAAACCAAATCCTAT-CTTCCTGAAGT
1 ATCTCCTTAAGGTTACAGTGGAATGGAGTGAAG-TTACAACACCAAATCCTATAC-CCCTAAAGT
* * * *
24910702 TGTAGTGAAG-CAAATTAAA-ACTAAAGTAGTGGATCTCA
64 TGCAGTG-GGTCAGATTAAAGAC-AAA--AGTGAATCTCA
** * *
24910740 ATCTCCTTGAA-GTTGTAGTGGAATAGAGTGAAGTTACATCACCA
1 ATCTCCTT-AAGGTTACAGTGGAATGGAGTGAAGTTACAACACCA
24910784 TCCAATCTTA
Statistics
Matches: 564, Mismatches: 130, Indels: 96
0.71 0.16 0.12
Matches are distributed among these distances:
98 32 0.06
99 306 0.54
100 33 0.06
101 175 0.31
102 18 0.03
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (99 bp):
ATCTCCTTAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTAAAGTTG
CAGTGGGTCAGATTAAAGACAAAAGTGAATCTCA
Found at i:24910549 original size:200 final size:198
Alignment explanation
Indices: 24909886--24910783 Score: 769
Period size: 198 Copynumber: 4.5 Consensus size: 198
24909876 GGTAAACAGT
* * * ** *
24909886 AAATCCTATATCACTAAAGTTACAGTGGATACGATTAAAATAAGTAAAAGG-TCTTTATCTCCTT
1 AAATCCTATATCCCTAAAGTTGCAGTGGATA-GATTAAAATAAGT-AACGGATCTCAATCTCCCT
* * * * * *
24909950 GAGGTTACAGTGGAATGGACTAAAGTTACAACACCAAATCCCATACCCCTGAAGTTGCAATGGGT
64 AAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTGAAGTTGCAGTAGGT
* * * * *
24910015 TAGATTAAAGCCAAAAGT-GAATCTCAATCTCTCC-GACGTTATAGTGGAATGGAGTGAAGCTTC
129 CAGATTAAAGCCAAAAGTAGAATCTCAATCT-TCCTAAGGTTACAGTGGAATGGAGTGAAACTTC
**
24910078 AACATT
193 AACACC
* * * * * * ** * * * * *
24910084 GACTTCTATA-CCTTTAAAATTACAGAAGAGTGGAGTAAAACAAGTAACGAATCTTAATCT-CCT
1 AAATCCTATATCC-CTAAAGTTGCAGTGGA-TAGATTAAAATAAGTAACGGATCTCAATCTCCCT
* * * *
24910147 AGAGGTTACAATGGAATGGAGTGAAGTTACAACACCAAATCATATGCCCCTAAAGTTGCAGTAGG
64 A-AGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTGAAGTTGCAGTAGG
*
24910212 TCAGATTAAAGCCAAAAG-AGAATCTCAATC-TCCTTAAGGTTACAGTGGAATGAAGT-AAAGCT
128 TCAGATTAAAGCCAAAAGTAGAATCTCAATCTTCC-TAAGGTTACAGTGGAATGGAGTGAAA-CT
*
24910274 TAAACACC
191 TCAACACC
* ** * * * * *
24910282 AACT-CTA-ATACTTTTAAAATTGCAGAAGGGTAGAGTAAAACAAGTAACGGATCTCAATCTCCC
1 AAATCCTATAT-C-CCTAAAGTTGCAG-TGGATAGATTAAAATAAGTAACGGATCTCAATCTCCC
* * *
24910345 TAAGGTTACAGTGGAATGGAGTGAAGTTACAGCACAAAATCCTATACCCCTGAAGTTACAGTAGG
63 TAAGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTGAAGTTGCAGTAGG
* * * *
24910410 TCAGATTAAAGTTACAAAAGTAG-ATCTCAATCTTCCTGAGGTTATAGTGGAATGTAGTGAAACT
128 TCAGATTAAAG--CCAAAAGTAGAATCTCAATCTTCCTAAGGTTACAGTGGAATGGAGTGAAACT
*
24910474 TCAACACG
191 TCAACACC
* *
24910482 AAATCTTATATCCCTAAAGTTGTAGTGGATCAGATTAAAATAAGTAACGGATCTCAATCTCCCTA
1 AAATCCTATATCCCTAAAGTTGCAGTGGAT-AGATTAAAATAAGTAACGGATCTCAATCTCCCTA
* * * * *
24910547 AGGTTATAATGGAATAGAGTGAAGTTACAACACCAATTCCTATACCCCTGAAGTTGCAGTGGGTC
65 AGGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTGAAGTTGCAGTAGGTC
* * * * * * * *
24910612 GGATTAAAGTTTCAAAAGCA-TATCTCAAACTCCCTAAGGTTACAGTGGAATGGAGAGAAGCTTC
130 AGATTAAAG--CCAAAAGTAGAATCTCAATCTTCCTAAGGTTACAGTGGAATGGAGTGAAACTTC
*
24910676 AAAACC
193 AACACC
* * * * * * * ** *
24910682 AAATCCTATCTTCCTGAAGTTGTAGTGAAGCAAATTAAAACTAAAGTAGTGGATCTCAATCTCCT
1 AAATCCTATATCCCTAAAGTTGCAGTGGA-TAGATTAAAA-T-AAGTAACGGATCTCAATCTCCC
** * *
24910747 TGAA-GTTGTAGTGGAATAGAGTGAAGTTACATCACCA
63 T-AAGGTTACAGTGGAATGGAGTGAAGTTACAACACCA
24910784 TCCAATCTTA
Statistics
Matches: 576, Mismatches: 98, Indels: 48
0.80 0.14 0.07
Matches are distributed among these distances:
196 4 0.01
197 11 0.02
198 253 0.44
199 10 0.02
200 232 0.40
201 12 0.02
202 52 0.09
203 2 0.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (198 bp):
AAATCCTATATCCCTAAAGTTGCAGTGGATAGATTAAAATAAGTAACGGATCTCAATCTCCCTAA
GGTTACAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTGAAGTTGCAGTAGGTCA
GATTAAAGCCAAAAGTAGAATCTCAATCTTCCTAAGGTTACAGTGGAATGGAGTGAAACTTCAAC
ACC
Found at i:24910831 original size:46 final size:46
Alignment explanation
Indices: 24910779--24911013 Score: 283
Period size: 46 Copynumber: 5.0 Consensus size: 46
24910769 GAAGTTACAT
* * *
24910779 CACCATCCAATCTTATACCCCCAAATCCAAAGGGGTAGATTGAAGC
1 CACCATCCAATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGC
** * * **
24910825 CACCATCCAATCTTATACCTTTAAATCTAGTGGGAAAGATTGAAGC
1 CACCATCCAATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * *
24910871 CACCACCCAATCTTATACCCCTAAATCTAGAGGGACAGATTGAAGC
1 CACCATCCAATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGC
*
24910917 CACCACATCCAATCTTATACACCTAAATCCAGAGGGGCAGA-TGAAGC
1 CA-C-CATCCAATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * *
24910964 CACCATATCCAATCTTATACCCTTAAATCAAGAGGGGCAAATTGAAGC
1 CACC--ATCCAATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGC
24911012 CA
1 CA
24911014 TACACAACTC
Statistics
Matches: 163, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
45 1 0.01
46 82 0.50
47 40 0.25
48 40 0.25
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (46 bp):
CACCATCCAATCTTATACCCCTAAATCCAGAGGGGCAGATTGAAGC
Found at i:24924280 original size:16 final size:17
Alignment explanation
Indices: 24924259--24924298 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
24924249 TTTAACCTAA
24924259 TTATTTATCTT-ATTAT
1 TTATTTATCTTCATTAT
*
24924275 TTATTTA-CTTCTTTAT
1 TTATTTATCTTCATTAT
24924291 TTATTTAT
1 TTATTTAT
24924299 TCATTCACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTATCTTCATTAT
Found at i:24929660 original size:18 final size:18
Alignment explanation
Indices: 24929639--24929679 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
24929629 AGAACATGAT
* *
24929639 GAGGATGAAACTGAAGAG
1 GAGGAAGAAACTGAAGAA
*
24929657 GAGGAAGAAAGTGAAGAA
1 GAGGAAGAAACTGAAGAA
24929675 GAGGA
1 GAGGA
24929680 GAATGAGGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.41, T:0.07
Consensus pattern (18 bp):
GAGGAAGAAACTGAAGAA
Found at i:24949700 original size:37 final size:35
Alignment explanation
Indices: 24949659--24949727 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 35
24949649 TTCTCTATTT
*
24949659 ATTTTGCC-CATTTTCTTATATTTTTTCTCATCAAGCA
1 ATTTT-CCACATTTTCTTACA--TTTTCTCATCAAGCA
*
24949696 ATTTTCCAGATTTTCTTACATTTTCTCATCAA
1 ATTTTCCACATTTTCTTACATTTTCTCATCAA
24949728 CCAAACACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 12 0.41
36 2 0.07
37 15 0.52
ACGTcount: A:0.23, C:0.22, G:0.04, T:0.51
Consensus pattern (35 bp):
ATTTTCCACATTTTCTTACATTTTCTCATCAAGCA
Found at i:24952172 original size:16 final size:17
Alignment explanation
Indices: 24952153--24952188 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
24952143 TTATTTATTA
*
24952153 AATTAATTAATTTT-TC
1 AATTAAATAATTTTCTC
24952169 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
24952186 AAT
1 AAT
24952189 CCAATTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:24954701 original size:38 final size:34
Alignment explanation
Indices: 24954581--24954693 Score: 163
Period size: 34 Copynumber: 3.3 Consensus size: 34
24954571 TTATAGTGCT
* *
24954581 TTTGGTGTTCTGGATGGATTAGTTCTTACGAGCA
1 TTTGGTGTGCTGGATGGATTAGCTCTTACGAGCA
* *
24954615 TTTGGTATGCTGGATGGATTAGCTCTTATGAGCA
1 TTTGGTGTGCTGGATGGATTAGCTCTTACGAGCA
* *
24954649 TTTGATGTGCTGGATGGATAAGCTCTTACGAGCA
1 TTTGGTGTGCTGGATGGATTAGCTCTTACGAGCA
*
24954683 TCTGGTGTGCT
1 TTTGGTGTGCT
24954694 AGTTGGATAA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.38
Consensus pattern (34 bp):
TTTGGTGTGCTGGATGGATTAGCTCTTACGAGCA
Found at i:24955710 original size:21 final size:21
Alignment explanation
Indices: 24955666--24955710 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
24955656 TCGGGCTGAG
* * *
24955666 ACACGGGCATGTGGGGTAGTC
1 ACACGGGCATGTGAGATAGCC
24955687 ACACGGGCATGTGAGATAGCC
1 ACACGGGCATGTGAGATAGCC
24955708 ACA
1 ACA
24955711 AGTCCATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.22, G:0.36, T:0.16
Consensus pattern (21 bp):
ACACGGGCATGTGAGATAGCC
Found at i:24961019 original size:20 final size:22
Alignment explanation
Indices: 24960990--24961035 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
24960980 TTAGCATGCA
24960990 TGTTTAGCA-TTTC-ATACTTAG
1 TGTTTAGCATTTTCTA-ACTTAG
24961011 TGTTT-GCATTTTCTAACTTAG
1 TGTTTAGCATTTTCTAACTTAG
24961032 TGTT
1 TGTT
24961036 GTATGGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.13
21 19 0.83
22 1 0.04
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.52
Consensus pattern (22 bp):
TGTTTAGCATTTTCTAACTTAG
Found at i:24969372 original size:24 final size:24
Alignment explanation
Indices: 24969342--24969387 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
24969332 TTTTTTAATA
24969342 TTATTTTGTATGTTGTTCTTTATT
1 TTATTTTGTATGTTGTTCTTTATT
*
24969366 TTATTTTGTATGTTGTTTTTTA
1 TTATTTTGTATGTTGTTCTTTA
24969388 ATACCTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.02, G:0.13, T:0.72
Consensus pattern (24 bp):
TTATTTTGTATGTTGTTCTTTATT
Found at i:24969461 original size:33 final size:33
Alignment explanation
Indices: 24969398--24969467 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
24969388 ATACCTTGAA
* * *
24969398 TTTATTATGACTTGTATGCTGTGTTTTGTTGGT
1 TTTATGATGACTTGTATGCTGTCTTTTGTTGGC
* *
24969431 TTTATGATGACTT-TATGTTTTCTTTATGTTGGC
1 TTTATGATGACTTGTATGCTGTCTTT-TGTTGGC
24969464 TTTA
1 TTTA
24969468 ATGTTGGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.14, C:0.07, G:0.20, T:0.59
Consensus pattern (33 bp):
TTTATGATGACTTGTATGCTGTCTTTTGTTGGC
Found at i:24969466 original size:11 final size:11
Alignment explanation
Indices: 24969424--24969485 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
24969414 TGCTGTGTTT
*
24969424 TGTTGGTTTTA
1 TGTTGGCTTTA
* *
24969435 TGATGACTTTA
1 TGTTGGCTTTA
**
24969446 TGTTTTCTTTA
1 TGTTGGCTTTA
24969457 TGTTGGCTTTAA
1 TGTTGGCTTT-A
*
24969469 TGTTGGATTTA
1 TGTTGGCTTTA
*
24969480 TATTGG
1 TGTTGG
24969486 ATGTTGTGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
11 30 0.75
12 10 0.25
ACGTcount: A:0.16, C:0.05, G:0.23, T:0.56
Consensus pattern (11 bp):
TGTTGGCTTTA
Found at i:24970189 original size:21 final size:21
Alignment explanation
Indices: 24970162--24970211 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
24970152 GTGAGGACCC
24970162 CAACTCAG-AGAGTGAGCAGCA
1 CAACTCAGCA-AGTGAGCAGCA
* *
24970183 CATCTCAGCAAGTGAGTAGCA
1 CAACTCAGCAAGTGAGCAGCA
24970204 CAACTCAG
1 CAACTCAG
24970212 TTGCAAATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.36, C:0.26, G:0.24, T:0.14
Consensus pattern (21 bp):
CAACTCAGCAAGTGAGCAGCA
Found at i:24971508 original size:13 final size:13
Alignment explanation
Indices: 24971479--24971519 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
24971469 ATATCCACTT
24971479 TCTTCTTCTTCTTC
1 TCTTCTT-TTCTTC
*
24971493 TCTTCTTTTATTC
1 TCTTCTTTTCTTC
24971506 TCTTCTTTTCTTC
1 TCTTCTTTTCTTC
24971519 T
1 T
24971520 TAAACCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTTCTTTTCTTC
Found at i:24977862 original size:12 final size:12
Alignment explanation
Indices: 24977845--24977870 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24977835 CAAATACAAC
24977845 AATCTAATACAT
1 AATCTAATACAT
24977857 AATCTAATACAT
1 AATCTAATACAT
24977869 AA
1 AA
24977871 CAATTTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (12 bp):
AATCTAATACAT
Found at i:24978135 original size:27 final size:28
Alignment explanation
Indices: 24978087--24978142 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
24978077 ATCTGTCGAG
* *
24978087 TAACAAATAATGCAATAGAGATCGCCAA
1 TAACAAATAACGCAATAAAGATCGCCAA
* *
24978115 TAAC-AATAACGCGATAAAGATTGCCAA
1 TAACAAATAACGCAATAAAGATCGCCAA
24978142 T
1 T
24978143 CCCCTTGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (28 bp):
TAACAAATAACGCAATAAAGATCGCCAA
Found at i:24979778 original size:46 final size:46
Alignment explanation
Indices: 24979724--24979819 Score: 174
Period size: 46 Copynumber: 2.1 Consensus size: 46
24979714 AGATTGGGAG
24979724 AGGGAGAAGAGGTTAGGGACGACTCAAGAGGAGAAAATAATGATTT
1 AGGGAGAAGAGGTTAGGGACGACTCAAGAGGAGAAAATAATGATTT
* *
24979770 AGGGAGAAGTGGTTAGGGACGACTCAAGGGGAGAAAATAATGATTT
1 AGGGAGAAGAGGTTAGGGACGACTCAAGAGGAGAAAATAATGATTT
24979816 AGGG
1 AGGG
24979820 CTGATTAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.39, C:0.06, G:0.38, T:0.18
Consensus pattern (46 bp):
AGGGAGAAGAGGTTAGGGACGACTCAAGAGGAGAAAATAATGATTT
Found at i:24987254 original size:21 final size:21
Alignment explanation
Indices: 24987228--24987269 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
24987218 TAGATCTTCG
24987228 TACTTAAAATTTCATATTTGA
1 TACTTAAAATTTCATATTTGA
24987249 TACTTAAAATTTCATATTTGA
1 TACTTAAAATTTCATATTTGA
24987270 AGTTATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (21 bp):
TACTTAAAATTTCATATTTGA
Found at i:24991906 original size:14 final size:15
Alignment explanation
Indices: 24991887--24991917 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
24991877 TTTTACTTTG
24991887 TTTTATTTTTAT-CT
1 TTTTATTTTTATGCT
24991901 TTTTATTTTTATGCT
1 TTTTATTTTTATGCT
24991916 TT
1 TT
24991918 CAGACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTATGCT
Found at i:25012783 original size:29 final size:28
Alignment explanation
Indices: 25012724--25012795 Score: 126
Period size: 28 Copynumber: 2.5 Consensus size: 28
25012714 CCCGGGGGTG
*
25012724 AAATGGTAATTTTTTACTTTCGAGGGTAA
1 AAAT-GTAATTTTTGACTTTCGAGGGTAA
25012753 AAATGTAATTTTTGACTTTCGAGGGTAA
1 AAATGTAATTTTTGACTTTCGAGGGTAA
25012781 AAATGTAATTTTTGA
1 AAATGTAATTTTTGA
25012796 TGAAACTAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 38 0.90
29 4 0.10
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (28 bp):
AAATGTAATTTTTGACTTTCGAGGGTAA
Found at i:25012853 original size:59 final size:58
Alignment explanation
Indices: 25012775--25013090 Score: 343
Period size: 59 Copynumber: 5.3 Consensus size: 58
25012765 TGACTTTCGA
* * *
25012775 GGGTAAAAAT-GTAATTTTTGATGAAACTAGGGTTAAAAATGGAATTTTGGAGAGTTTG
1 GGGT-AAAATGGTAATTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGTTTG
* * * ** *
25012833 GGGATAAAACGATAATTTTTGGTAGAATC-GGGGTTAAAAATGGGGTTTTGGAAAGTTCTA
1 GGG-TAAAATGGTAATTTTTGGT-GAAACTGGGGTTAAAAATGGAATTTTGGAAAGTT-TG
* *
25012893 GGGTGAAATGGTAATTTTTGGT-AAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAACT-GGGGTTAAAAATGGAATTTTGGAAAGTTT-G
* * *
25012952 AGGTAAAATGGTAATTTTTGGTGAAA-TCGAGGTTAAAAATGGAATTTTGGAAAGTTCG
1 GGGTAAAATGGTAATTTTTGGTGAAACT-GGGGTTAAAAATGGAATTTTGGAAAGTTTG
* * * *
25013010 GGAGTAAAATGGTAATTTTTTTGGTGAAACCGGGGTTGAGAATGGGATTTTGGAAAGTTTGG
1 GG-GTAAAATGGTAA--TTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGTTT-G
25013072 GGGTAAAATGGTAATTTTT
1 GGGTAAAATGGTAATTTTT
25013091 TGAAAGTTTT
Statistics
Matches: 217, Mismatches: 28, Indels: 25
0.80 0.10 0.09
Matches are distributed among these distances:
57 2 0.01
58 10 0.05
59 143 0.66
60 11 0.05
61 48 0.22
62 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGTGAAACTGGGGTTAAAAATGGAATTTTGGAAAGTTTG
Found at i:25012910 original size:29 final size:28
Alignment explanation
Indices: 25012878--25013028 Score: 105
Period size: 29 Copynumber: 5.1 Consensus size: 28
25012868 AAAAATGGGG
*
25012878 TTTTGGAAAGTTCTAGGGTGAAATGGTAA
1 TTTTGGAAAGTTC-AGGGTAAAATGGTAA
* *
25012907 TTTTTGGTAAA-ATCGGGGTTAAAAATGG-AA
1 -TTTTGG-AAAGTTCAGGG-T-AAAATGGTAA
*
25012937 TTTTGGAAAGTTTAGAGGTAAAATGGTAA
1 TTTTGGAAAGTTCAG-GGTAAAATGGTAA
*
25012966 TTTTTGGTGAAA--TCGAGGTTAAAAATGG-AA
1 -TTTT-G-GAAAGTTC-AGGGT-AAAATGGTAA
*
25012996 TTTTGGAAAGTTCGGGAGTAAAATGGTAA
1 TTTTGGAAAGTTCAGG-GTAAAATGGTAA
25013025 TTTT
1 TTTT
25013029 TTTGGTGAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 31
0.70 0.07 0.23
Matches are distributed among these distances:
27 4 0.04
28 20 0.21
29 27 0.28
30 22 0.23
31 19 0.20
32 4 0.04
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (28 bp):
TTTTGGAAAGTTCAGGGTAAAATGGTAA
Found at i:25012913 original size:30 final size:30
Alignment explanation
Indices: 25012878--25013029 Score: 108
Period size: 30 Copynumber: 5.1 Consensus size: 30
25012868 AAAAATGGGG
*
25012878 TTTTGGAAAGTTCTAGGGTGAAATGGTAAT
1 TTTTGGAAAGTTCTAGGGTAAAATGGTAAT
* *
25012908 TTTTGGTAAA-ATC-GGGGTTAAAAATGG-AA-
1 TTTTGG-AAAGTTCTAGGG-T-AAAATGGTAAT
25012937 TTTTGGAAAGTT-TAGAGGTAAAATGGTAAT
1 TTTTGGAAAGTTCTAG-GGTAAAATGGTAAT
* *
25012967 TTTTGGTGAAA--TCGAGGTTAAAAATGG-AA-
1 TTTT-G-GAAAGTTCTAGGGT-AAAATGGTAAT
*
25012996 TTTTGGAAAGTTC-GGGAGTAAAATGGTAAT
1 TTTTGGAAAGTTCTAGG-GTAAAATGGTAAT
25013026 TTTT
1 TTTT
25013030 TTGGTGAAAC
Statistics
Matches: 96, Mismatches: 9, Indels: 34
0.69 0.06 0.24
Matches are distributed among these distances:
27 4 0.04
28 20 0.21
29 23 0.24
30 26 0.27
31 19 0.20
32 4 0.04
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.36
Consensus pattern (30 bp):
TTTTGGAAAGTTCTAGGGTAAAATGGTAAT
Found at i:25013095 original size:118 final size:116
Alignment explanation
Indices: 25012717--25013093 Score: 384
Period size: 118 Copynumber: 3.2 Consensus size: 116
25012707 TTGGATGCCC
* ** * * * **
25012717 GGGGGTGAAATGGTAATTTTTT-ACTTTCGAGGGTAAAAATGTAATTTTTG-ACTTTCGAGGGTA
1 GGGGGTAAAATGGTAATTTTTTGACAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCG-GGGT-
* ** *
25012780 AAAAT-GTAATTTTTGATGAAACTAGGGTTAAAAATGGAATTTTGGAGAGTTT
64 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * * * * * ** *
25012832 GGGGATAAAACGATAATTTTTGGTAGAATCGGGGTTAAAAATGGGGTTTTGGAAAGTTCTAGGGT
1 GGGGGTAAAATGGTAATTTTTTG-ACAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC-GGGGT
* * *
25012897 GAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
64 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* *
25012950 AGAGGTAAAATGGTAATTTTTGGTGA-AATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGAG
1 GGGGGTAAAATGGTAATTTTT--TGACAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGG-G
* * *
25013014 TAAAATGGTAATTTTTTTGGTGAAACCGGGGTTGAGAATGGGATTTTGGAAAGTTT
63 TAAAATGGTAA--TTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTT
25013070 GGGGGTAAAATGGTAATTTTTTGA
1 GGGGGTAAAATGGTAATTTTTTGA
25013094 AAGTTTTGGG
Statistics
Matches: 210, Mismatches: 42, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
115 17 0.08
117 25 0.12
118 109 0.52
119 1 0.00
120 58 0.28
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (116 bp):
GGGGGTAAAATGGTAATTTTTTGACAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAA
AATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTT
Found at i:25013117 original size:30 final size:30
Alignment explanation
Indices: 25013057--25013118 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
25013047 GAGAATGGGA
*
25013057 TTTTGGAAAGTTTGGGGGTAAAATGGTAAT
1 TTTTGGAAAGTTTGGGGGTAAAATGATAAT
* * *
25013087 TTTTTGAAAGTTTTGGGGTCAAA-GTATAAT
1 TTTTGGAAAGTTTGGGGGTAAAATG-ATAAT
25013117 TT
1 TT
25013119 ATGACAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.42
Consensus pattern (30 bp):
TTTTGGAAAGTTTGGGGGTAAAATGATAAT
Found at i:25015085 original size:17 final size:17
Alignment explanation
Indices: 25015065--25015115 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 17
25015055 GTTTCAAATT
**
25015065 ATTTTAAATGTATTTAA
1 ATTTTAAATAAATTTAA
*
25015082 ATTTAAAATAAATTTAA
1 ATTTTAAATAAATTTAA
25015099 A-TTTAAATAAATTTAA
1 ATTTTAAATAAATTTAA
25015115 A
1 A
25015116 ATTAATTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 15 0.50
17 15 0.50
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTTTAAATAAATTTAA
Found at i:25015087 original size:6 final size:6
Alignment explanation
Indices: 25015076--25015120 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
25015066 TTTTAAATGT
* *
25015076 ATTTAA ATTTAA A-ATAA ATTTAA ATTTAA A--TAA ATTTAA AATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
25015121 TTCAAACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.12
5 4 0.12
6 25 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:25015090 original size:27 final size:27
Alignment explanation
Indices: 25015050--25015122 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
25015040 TTAATTTAAT
* * *
25015050 TTTAAGTTTCAAATTATTTTAAATGTA
1 TTTAAATTTAAAATTAATTTAAATGTA
* *
25015077 TTTAAATTTAAAATAAATTTAAATTTA
1 TTTAAATTTAAAATTAATTTAAATGTA
**
25015104 AATAAATTTAAAATTAATT
1 TTTAAATTTAAAATTAATT
25015123 CAAACTTAGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (27 bp):
TTTAAATTTAAAATTAATTTAAATGTA
Found at i:25015117 original size:17 final size:17
Alignment explanation
Indices: 25015076--25015120 Score: 74
Period size: 16 Copynumber: 2.7 Consensus size: 17
25015066 TTTTAAATGT
25015076 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
25015093 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAATAA
*
25015109 ATTTAAAATTAA
1 ATTTAAATTTAA
25015121 TTCAAACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:25015182 original size:3 final size:3
Alignment explanation
Indices: 25015174--25015203 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25015164 GGCTTCAATA
25015174 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25015204 TGTTTGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25017480 original size:12 final size:13
Alignment explanation
Indices: 25017463--25017491 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25017453 ATACAATATT
25017463 GGGGGAGGGGG-A
1 GGGGGAGGGGGAA
25017475 GGGGGAGGGGGAA
1 GGGGGAGGGGGAA
25017488 GGGG
1 GGGG
25017492 TTAACAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (13 bp):
GGGGGAGGGGGAA
Found at i:25020460 original size:2 final size:2
Alignment explanation
Indices: 25020453--25020493 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
25020443 TTATTGTATT
25020453 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
25020494 CTATATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:25024523 original size:28 final size:29
Alignment explanation
Indices: 25024467--25024523 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
25024457 CGGATTGTTG
*
25024467 AACTTATTGATTTTTTTATTTTTCTAAAAT
1 AACTTATTGATTTTTTTA-TTTTCGAAAAT
25024497 AACTT-TTAGATTTTTTTA-TTTCGAAAA
1 AACTTATT-GATTTTTTTATTTTCGAAAA
25024524 GAAAACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 8 0.32
29 2 0.08
30 15 0.60
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (29 bp):
AACTTATTGATTTTTTTATTTTCGAAAAT
Found at i:25039544 original size:105 final size:104
Alignment explanation
Indices: 25039362--25039566 Score: 338
Period size: 105 Copynumber: 2.0 Consensus size: 104
25039352 AATTATGAAT
* *
25039362 AATAATAAATTAGGAGTGTGTTGGACTGAGTAACCGAGATGGGGTGCTTGGGTTGTTATTCCATT
1 AATAATAAATTAGGAGTATGTTGGACTGAGTAACCGAGATGGGGTGCTTGGGTTGTCATTCCATT
*
25039427 TCACGTCAAAAGGGCCAATACATTCTTAAGTAAAAAAAGA
66 TCACGTCAAAAGGACCAATACATTCTTAAG-AAAAAAAGA
* *
25039467 AATAATAAATTAGGAGTATGTTGGGCTGAGTAACCGAGATGGGTTGCTTGGGTTGTCATTCCATT
1 AATAATAAATTAGGAGTATGTTGGACTGAGTAACCGAGATGGGGTGCTTGGGTTGTCATTCCATT
* *
25039532 TCGCGTCAAAAGGACCAATATATTCTTAAGAAAAA
66 TCACGTCAAAAGGACCAATACATTCTTAAGAAAAA
25039567 GAAAAAAAAG
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
104 5 0.05
105 88 0.95
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (104 bp):
AATAATAAATTAGGAGTATGTTGGACTGAGTAACCGAGATGGGGTGCTTGGGTTGTCATTCCATT
TCACGTCAAAAGGACCAATACATTCTTAAGAAAAAAAGA
Found at i:25039595 original size:15 final size:15
Alignment explanation
Indices: 25039559--25039587 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25039549 ATATATTCTT
25039559 AAGAAAAAGAAAAAA
1 AAGAAAAAGAAAAAA
25039574 AAGAAAAAGAAAAA
1 AAGAAAAAGAAAAA
25039588 GACGAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAAA
Found at i:25044760 original size:17 final size:17
Alignment explanation
Indices: 25044740--25044791 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
25044730 GTAAATATAT
25044740 ATAAAAAATAAAAATAA
1 ATAAAAAATAAAAATAA
* * *
25044757 ATAAAATACT-GAAATAT
1 ATAAAA-AATAAAAATAA
*
25044774 ATAAAGAATAAAAATAA
1 ATAAAAAATAAAAATAA
25044791 A
1 A
25044792 CTAAGTACTG
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (17 bp):
ATAAAAAATAAAAATAA
Found at i:25044784 original size:34 final size:34
Alignment explanation
Indices: 25044736--25044849 Score: 131
Period size: 34 Copynumber: 3.2 Consensus size: 34
25044726 ATATGTAAAT
*
25044736 ATATATAAAAAATAAAAATAAATAAAATACTGAA
1 ATATATAAAGAATAAAAATAAATAAAATACTGAA
*
25044770 ATATATAAAGAATAAAAATAAACT-AAGTACTGTAAA
1 ATATATAAAGAATAAAAATAAA-TAAAATACTG--AA
* *
25044806 TATATATATATAGAATAAAAGTAAACAAAATACTGAA
1 -ATATATA-A-AGAATAAAAATAAATAAAATACTGAA
25044843 ATATATA
1 ATATATA
25044850 TATATATATA
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
34 28 0.41
35 1 0.01
36 9 0.13
37 9 0.13
38 1 0.01
39 20 0.29
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.26
Consensus pattern (34 bp):
ATATATAAAGAATAAAAATAAATAAAATACTGAA
Found at i:25044850 original size:2 final size:2
Alignment explanation
Indices: 25044843--25044870 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25044833 AAATACTGAA
25044843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25044871 CACTACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25048845 original size:97 final size:97
Alignment explanation
Indices: 25048670--25048863 Score: 264
Period size: 97 Copynumber: 2.0 Consensus size: 97
25048660 AACTTTGGAA
* * *
25048670 AAGGGTATTCGATTATCTCGATTTGAAGAAAAGTCGCACTTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTCA
* * *
25048735 GAATCAGAGATAAAGAAACATTACCTCGATTT
66 AAATCAGAAATAAAAAAACATTACCTCGATTT
* * * *
25048767 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGCACCTAGTAAGTTTAGGCACAAAATTTCA
1 AAGGGTATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTCA
* *
25048832 AAACTC-GAAATAAAAAAATATTGCCTCGATTT
66 AAA-TCAGAAATAAAAAAACATTACCTCGATTT
25048864 TAAAGTTTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
97 82 0.98
98 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (97 bp):
AAGGGTATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAAATTTCA
AAATCAGAAATAAAAAAACATTACCTCGATTT
Found at i:25049204 original size:58 final size:59
Alignment explanation
Indices: 25049089--25049580 Score: 350
Period size: 59 Copynumber: 8.4 Consensus size: 59
25049079 GATACCCGAT
* ** * * * *
25049089 GGTAAAATGGTAATTTTGGGAAAGTTAGGGCTCAAAAATGGAATTTTTAGATA-TTCGAG
1 GGTAAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGAAATTTTTGGA-AGTTCGAG
* * * *
25049148 GATAAAATGCT-ACTTTTGGAAGAATCGGGGTCAAAAATGAAATTTTTGGAAGTTCGAG
1 GGTAAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGAAATTTTTGGAAGTTCGAG
* * *
25049206 GGTAAAATGGTAATTTTTAGAAAAATCAGGGTCAAAAAT-AGAA-TTTTGGAAGTTTGAG
1 GGTAAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGA-AATTTTTGGAAGTTCGAG
* * *
25049264 GGTAAAATGGTAATTTTTGGAAAAATCGAGGCCAAAAATGGAATTTTTGGAAGTTCGAG
1 GGTAAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGAAATTTTTGGAAGTTCGAG
* * * * * * *
25049323 GGTAAAATGGTAATTTTT-GAAAAATTTGAGGTAAAAAATGGAA-GTTTGGAAAATTTG-G
1 GGTAAAATGGTAATTTTTGGAAAAA-TCGGGGTCAAAAATGAAATTTTTGG-AAGTTCGAG
* * ** *
25049381 GGTCAAAAATGG-AA-TTTT-GAAAAATTCGAGGGT-AATAATGTAATTTTTGGAAAAATCAAG
1 GGT--AAAATGGTAATTTTTGGAAAAA-TCG-GGGTCAAAAATGAAATTTTTGG-AAGTTCGAG
* ** * ** * * *
25049441 GTTAAAAATGG-AA-TTTTGGAAAGTTCAAGGGT-AAAAATGTGATTTTTGTAAAATTAGAG
1 GGT-AAAATGGTAATTTTTGGAAAAATC-GGGGTCAAAAATGAAATTTTTG-GAAGTTCGAG
* * * * * *
25049500 GTTAAAAATGG-AA-TTTTGGAAAATTCGAGGTCAAAAATGGAATTTTAGAAAGTTCGAG
1 GGT-AAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGAAATTTTTGGAAGTTCGAG
*
25049558 GGTAAAATTGTAATTTTTGGAAA
1 GGTAAAATGGTAATTTTTGGAAA
25049581 GTTTAGTGGT
Statistics
Matches: 357, Mismatches: 58, Indels: 36
0.79 0.13 0.08
Matches are distributed among these distances:
57 7 0.02
58 148 0.41
59 188 0.53
60 14 0.04
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (59 bp):
GGTAAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGAAATTTTTGGAAGTTCGAG
Found at i:25049462 original size:29 final size:29
Alignment explanation
Indices: 25049161--25049580 Score: 244
Period size: 29 Copynumber: 14.3 Consensus size: 29
25049151 AAAATGCTAC
* * * *
25049161 TTTTGGAAGAATCGGGGTCAAAAATGAAA
1 TTTTGGAAAAATCGAGGTTAAAAATGGAA
** *
25049190 TTTTTGG-AAGTTCGAGGGT-AAAATGGTAA
1 -TTTTGGAAAAATCGAGGTTAAAAATGG-AA
* * *
25049219 TTTTTAGAAAAATC-AGGGTCAAAAATAGAA
1 -TTTTGGAAAAATCGA-GGTTAAAAATGGAA
** * *
25049249 TTTTGG-AAGTTTGAGGGT-AAAATGGTAA
1 TTTTGGAAAAATCGAGGTTAAAAATGG-AA
**
25049277 TTTTTGGAAAAATCGAGGCCAAAAATGGAA
1 -TTTTGGAAAAATCGAGGTTAAAAATGGAA
** *
25049307 TTTTTGG-AAGTTCGAGGGT-AAAATGGTAA
1 -TTTTGGAAAAATCGAGGTTAAAAATGG-AA
* * *
25049336 TTTTTGAAAAATTTGAGGTAAAAAATGGAA
1 TTTTGGAAAAA-TCGAGGTTAAAAATGGAA
* * * * *
25049366 GTTTGGAAAATTTGGGGTCAAAAATGGAA
1 TTTTGGAAAAATCGAGGTTAAAAATGGAA
* * *
25049395 TTTT-GAAAAATTCGAGGGTAATAATGTAA
1 TTTTGGAAAAA-TCGAGGTTAAAAATGGAA
*
25049424 TTTTTGGAAAAATCAAGGTTAAAAATGGAA
1 -TTTTGGAAAAATCGAGGTTAAAAATGGAA
** * * *
25049454 TTTTGGAAAGTTCAAGGGTAAAAATGTGAT
1 TTTTGGAAAAATCGAGGTTAAAAATG-GAA
* * *
25049484 TTTTGTAAAATTAGAGGTTAAAAATGGAA
1 TTTTGGAAAAATCGAGGTTAAAAATGGAA
* *
25049513 TTTTGGAAAATTCGAGGTCAAAAATGGAA
1 TTTTGGAAAAATCGAGGTTAAAAATGGAA
* ** * * *
25049542 TTTTAGAAAGTTCGAGGGTAAAATTGTAA
1 TTTTGGAAAAATCGAGGTTAAAAATGGAA
25049571 TTTTTGGAAA
1 -TTTTGGAAA
25049581 GTTTAGTGGT
Statistics
Matches: 300, Mismatches: 72, Indels: 36
0.74 0.18 0.09
Matches are distributed among these distances:
27 6 0.02
28 30 0.10
29 144 0.48
30 94 0.31
31 26 0.09
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (29 bp):
TTTTGGAAAAATCGAGGTTAAAAATGGAA
Found at i:25049551 original size:88 final size:89
Alignment explanation
Indices: 25049161--25049576 Score: 331
Period size: 88 Copynumber: 4.7 Consensus size: 89
25049151 AAAATGCTAC
* * *
25049161 TTTTGGAAGAA-TCGGGGTCAAAAATGAAATTTTTGG-AAGTTCGAGGGT-AAAATGGTAATTTT
1 TTTTGGAA-AATTCGAGGTCAAAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAAAT-GTGATTTT
* *
25049223 TAGAAAAA-T-CAGGGTCAAAAATAGAA-
63 T-GAAAAATTAGAGGGT-AAAAATGGAAT
* * ** **
25049249 TTTTGG-AAGTTTGAGGGT--AAAATGGTAATTTTTGGAAAAATCGAGGCCAAAAATG-GAATTT
1 TTTTGGAAAATTCGA-GGTCAAAAATGG-AA-TTTTGGAAAGTTCGAGGGTAAAAATGTG-ATTT
* * *
25049310 TTG-GAAGTTCGAGGGT-AAAATGGTAAT
62 TTGAAAAATTAGAGGGTAAAAATGG-AAT
* * * * * * *
25049337 TTTTGAAAAATTTGAGGTAAAAAATGGAAGTTTGGAAAATTTG-GGGTCAAAAATG-GAATTTTG
1 TTTTGGAAAATTCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT-AAAAATGTGATTTTTG
* * *
25049400 AAAAATTCGAGGGTAATAATGTAAT
65 AAAAATTAGAGGGTAAAAATGGAAT
* * * * *
25049425 TTTTGGAAAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAAATGTGATTTTTGT
1 TTTTGGAAAATTCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTGATTTTTGA
*
25049490 AAAATTAGAGGTTAAAAATGGAA-
66 AAAATTAGAGGGTAAAAATGGAAT
* * *
25049513 TTTTGGAAAATTCGAGGTCAAAAATGGAATTTTAGAAAGTTCGAGGGTAAAATTGTAATTTTTG
1 TTTTGGAAAATTCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTGATTTTTG
25049577 GAAAGTTTAG
Statistics
Matches: 263, Mismatches: 47, Indels: 36
0.76 0.14 0.10
Matches are distributed among these distances:
86 15 0.06
87 24 0.09
88 168 0.64
89 49 0.19
90 7 0.03
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (89 bp):
TTTTGGAAAATTCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTGATTTTTGA
AAAATTAGAGGGTAAAAATGGAAT
Found at i:25049595 original size:29 final size:29
Alignment explanation
Indices: 25049563--25049622 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
25049553 TCGAGGGTAA
25049563 AATTGTAATTTTTGGAAAGTTT-AGTGGTC
1 AATTGTAATTTTTGGAAAGTTTAAG-GGTC
25049592 AATTGTAATTTTTGGAAAGTTTAAGGGTC
1 AATTGTAATTTTTGGAAAGTTTAAGGGTC
25049621 AA
1 AA
25049623 AATATGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (29 bp):
AATTGTAATTTTTGGAAAGTTTAAGGGTC
Found at i:25049605 original size:88 final size:87
Alignment explanation
Indices: 25049092--25049609 Score: 321
Period size: 88 Copynumber: 5.9 Consensus size: 87
25049082 ACCCGATGGT
* * * *
25049092 AAAATGGTAATTTTGGGAAAGTT--AGGGCTCAAAAATGGAATTTTTAG-ATATTCGAGGATAAA
1 AAAATGG-AATTTT-GGAAAGTTCGAGGG-T-AAAAATGTAATTTTTGGAAAATT-GAGGGTAAA
* * *
25049154 ATGCT-ACTTTTGGAAGAA-TCGGGGTCA
61 TTG-TAATTTTTGGAA-AATTCGAGGTCA
* * * *
25049181 AAAATGAAATTTTTGG-AAGTTCGAGGGT-AAAATGGTAATTTTTAGAAAAATCAGGGTCAAAAA
1 AAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAAAT-GTAATTTTTGGAAAATTGAGGGT---AAA
* * *
25049244 TAG-AA-TTTTGG-AAGTTTGAGGGT--
61 TTGTAATTTTTGGAAAATTCGA-GGTCA
** ** * *
25049267 AAAATGGTAATTTTTGGAAAAATCGAGGCCAAAAATGGAATTTTTGG-AAGTTCGAGGGTAAAAT
1 AAAATGG-AA-TTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAATT-GAGGGT-AAAT
* * * *
25049331 GGTAATTTTTGAAAAATTTGAGGTAA
62 TGTAATTTTTGGAAAATTCGAGGTCA
* * * * * *
25049357 AAAATGGAAGTTTGGAAAATTTG-GGGTCAAAAATGGAA-TTTTGAAAAATTCGAGGGTAATAAT
1 AAAATGGAATTTTGGAAAGTTCGAGGGT-AAAAATGTAATTTTTGGAAAATT-GAGGGTAA-ATT
* * *
25049420 GTAATTTTTGGAAAAATCAAGGTTA
63 GTAATTTTTGGAAAATTCGAGGTCA
* * * * *
25049445 AAAATGGAATTTTGGAAAGTTCAAGGGTAAAAATGTGATTTTTGTAAAATTAGAGGTTAAAAATG
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAATT-GAGGGT-AAATTG
*
25049510 GAA-TTTTGGAAAATTCGAGGTCA
64 TAATTTTTGGAAAATTCGAGGTCA
* * * * *
25049533 AAAATGGAATTTTAGAAAGTTCGAGGGTAAAATTGTAATTTTTGGAAAGTTTAGTGGTCAATTGT
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAATTGAG-GGTAAATTGT
25049598 AATTTTTGGAAA
65 AATTTTTGGAAA
25049610 GTTTAAGGGT
Statistics
Matches: 339, Mismatches: 62, Indels: 57
0.74 0.14 0.12
Matches are distributed among these distances:
86 18 0.05
87 53 0.16
88 200 0.59
89 55 0.16
90 13 0.04
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (87 bp):
AAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAATTGAGGGTAAATTGTA
ATTTTTGGAAAATTCGAGGTCA
Found at i:25051400 original size:17 final size:17
Alignment explanation
Indices: 25051375--25051423 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
25051365 ACTCAACATG
* *
25051375 AATTTAAATTTAGAATA
1 AATTAAAATTTAAAATA
* *
25051392 ACTTCAAATTTAAAATA
1 AATTAAAATTTAAAATA
25051409 AATTAAAATTTAAAA
1 AATTAAAATTTAAAA
25051424 ATTAAAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (17 bp):
AATTAAAATTTAAAATA
Found at i:25051752 original size:20 final size:21
Alignment explanation
Indices: 25051727--25051765 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25051717 GTTAAAAAAA
25051727 GTCAACGA-TCAAAGTCAATG
1 GTCAACGAGTCAAAGTCAATG
25051747 GTCAACGAGTCAAAGTCAA
1 GTCAACGAGTCAAAGTCAA
25051766 CGATTGAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (21 bp):
GTCAACGAGTCAAAGTCAATG
Found at i:25057818 original size:17 final size:18
Alignment explanation
Indices: 25057778--25057815 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25057768 ATGCATATCA
*
25057778 TTTAGTTGTCATTGCATT
1 TTTATTTGTCATTGCATT
*
25057796 TTTATTTGTCTTTGCATT
1 TTTATTTGTCATTGCATT
25057814 TT
1 TT
25057816 ATTCATTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.63
Consensus pattern (18 bp):
TTTATTTGTCATTGCATT
Found at i:25058441 original size:115 final size:115
Alignment explanation
Indices: 25058239--25058468 Score: 460
Period size: 115 Copynumber: 2.0 Consensus size: 115
25058229 ATCAAGGGAG
25058239 AACACTCCGCTGCATGTGTTATTAAAATATTCTAGCCAAAGGCTATCACTGCAAGAGTGTGTGTC
1 AACACTCCGCTGCATGTGTTATTAAAATATTCTAGCCAAAGGCTATCACTGCAAGAGTGTGTGTC
25058304 GGTGTAATAACATGCTCCCTAGGGGTTTGTTTCACCCTATCGTTACTGCC
66 GGTGTAATAACATGCTCCCTAGGGGTTTGTTTCACCCTATCGTTACTGCC
25058354 AACACTCCGCTGCATGTGTTATTAAAATATTCTAGCCAAAGGCTATCACTGCAAGAGTGTGTGTC
1 AACACTCCGCTGCATGTGTTATTAAAATATTCTAGCCAAAGGCTATCACTGCAAGAGTGTGTGTC
25058419 GGTGTAATAACATGCTCCCTAGGGGTTTGTTTCACCCTATCGTTACTGCC
66 GGTGTAATAACATGCTCCCTAGGGGTTTGTTTCACCCTATCGTTACTGCC
25058469 TAGGACCAAG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (115 bp):
AACACTCCGCTGCATGTGTTATTAAAATATTCTAGCCAAAGGCTATCACTGCAAGAGTGTGTGTC
GGTGTAATAACATGCTCCCTAGGGGTTTGTTTCACCCTATCGTTACTGCC
Found at i:25058820 original size:21 final size:21
Alignment explanation
Indices: 25058777--25058822 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
25058767 TTAGCATGCA
*
25058777 TGTTTAGCATTTTATACTTAG
1 TGTTTAGCATTTTATACTCAG
*
25058798 TGTTT-GCATTTTCTAACTCAG
1 TGTTTAGCATTTTAT-ACTCAG
25058819 TGTT
1 TGTT
25058823 GTATGGCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.52
Consensus pattern (21 bp):
TGTTTAGCATTTTATACTCAG
Found at i:25069983 original size:21 final size:21
Alignment explanation
Indices: 25069957--25070004 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
25069947 ATGATCAGTT
*
25069957 GAAGGAAAAAGAAGAA-GAAGA
1 GAAGGAAAAAG-AGAATAAAGA
25069978 GAAGGAAAAAGAGAATAAAGA
1 GAAGGAAAAAGAGAATAAAGA
25069999 GAAGGA
1 GAAGGA
25070005 CCCTGCCGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (21 bp):
GAAGGAAAAAGAGAATAAAGA
Found at i:25072450 original size:21 final size:21
Alignment explanation
Indices: 25072426--25072465 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
25072416 TTTATGACTT
25072426 TTTTGA-ATACTTTTTGTGACG
1 TTTTGAGAT-CTTTTTGTGACG
25072447 TTTTGAGATCTTTTTGTGA
1 TTTTGAGATCTTTTTGTGA
25072466 TGCTTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.55
Consensus pattern (21 bp):
TTTTGAGATCTTTTTGTGACG
Found at i:25074986 original size:28 final size:27
Alignment explanation
Indices: 25074907--25074986 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 27
25074897 CATATAACAT
*
25074907 AGACAGAACACACATTAAATACGTAGCAC
1 AGACAGAACACACATCAAAT--GTAGCAC
* *
25074936 A-ATAGAAACACACAACAACATGTAGCAC
1 AGACAG-AACACACATCAA-ATGTAGCAC
*
25074964 AGACAGAGACACACCTCAAATGT
1 AGACAGA-ACACACATCAAATGT
25074987 GCAGAAGCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
28 16 0.39
29 23 0.56
30 2 0.05
ACGTcount: A:0.49, C:0.25, G:0.14, T:0.12
Consensus pattern (27 bp):
AGACAGAACACACATCAAATGTAGCAC
Found at i:25075451 original size:25 final size:25
Alignment explanation
Indices: 25075423--25075471 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
25075413 TGGTCAACAG
* *
25075423 GTCAAAGTCAACGATTAAGGTTAAA
1 GTCAAAGTCAACGATCAAAGTTAAA
25075448 GTCAAAGTCAACGATCAAAGTTAA
1 GTCAAAGTCAACGATCAAAGTTAA
25075472 CGGGTCAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.22
Consensus pattern (25 bp):
GTCAAAGTCAACGATCAAAGTTAAA
Found at i:25081748 original size:20 final size:22
Alignment explanation
Indices: 25081719--25081764 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
25081709 TTAGCATGCA
25081719 TGTTTAGCA-TTTCATAA-TTAG
1 TGTTTAGCATTTTC-TAACTTAG
25081740 TGTTT-GCATTTTCTAACTTAG
1 TGTTTAGCATTTTCTAACTTAG
25081761 TGTT
1 TGTT
25081765 GTATGGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (22 bp):
TGTTTAGCATTTTCTAACTTAG
Found at i:25097215 original size:21 final size:20
Alignment explanation
Indices: 25097191--25097504 Score: 73
Period size: 21 Copynumber: 16.6 Consensus size: 20
25097181 TGTGCCTAGT
25097191 AGGCTTCGTGCCTGTGTATTC
1 AGGCTT-GTGCCTGTGTATTC
*
25097212 AGGCTGTGTGCC----TA-GC
1 AGGCT-TGTGCCTGTGTATTC
*
25097228 AGGCTTCGTGCCGGTGTATTC
1 AGGCTT-GTGCCTGTGTATTC
* *
25097249 AGGCTTAGTGCCAGTGTATTT
1 AGGCTT-GTGCCTGTGTATTC
*
25097270 AGGCTGTGTGCC----TA-GC
1 AGGCT-TGTGCCTGTGTATTC
25097286 AGGCTTTGTGCC-GATGTATTC
1 AGGC-TTGTGCCTG-TGTATTC
** *
25097307 AGG-TTGTG--TGCCTAGT-
1 AGGCTTGTGCCTGTGTATTC
* *
25097323 AGGCTTCGTGCCGGTGTTTTC
1 AGGCTT-GTGCCTGTGTATTC
* * *
25097344 AAGCTT-TG--TGTCTAGT-
1 AGGCTTGTGCCTGTGTATTC
*
25097360 AGGCTTCGTGCCGGTGTATTC
1 AGGCTT-GTGCCTGTGTATTC
25097381 AGGCTGTGTGCCT-TG----C
1 AGGCT-TGTGCCTGTGTATTC
*
25097397 AGGCTTAGTGCCGGTGTATTC
1 AGGCTT-GTGCCTGTGTATTC
*
25097418 AGGC-TGTG--TGCT-TAGT-
1 AGGCTTGTGCCTG-TGTATTC
*
25097434 AGGCTTTGTGCCGGTGTATTC
1 AGGC-TTGTGCCTGTGTATTC
** *
25097455 AGG-TTGTG--TGCCTA-GC
1 AGGCTTGTGCCTGTGTATTC
*
25097471 AGGCTTAGTGCCGGTGTATTC
1 AGGCTT-GTGCCTGTGTATTC
25097492 AGGCTGTGTGCCT
1 AGGCT-TGTGCCT
25097505 AGTAGGCTTT
Statistics
Matches: 208, Mismatches: 40, Indels: 90
0.62 0.12 0.27
Matches are distributed among these distances:
15 2 0.01
16 48 0.23
17 25 0.12
18 14 0.07
19 16 0.08
20 22 0.11
21 77 0.37
22 4 0.02
ACGTcount: A:0.12, C:0.20, G:0.33, T:0.35
Consensus pattern (20 bp):
AGGCTTGTGCCTGTGTATTC
Found at i:25097215 original size:37 final size:37
Alignment explanation
Indices: 25097172--25097260 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
25097162 TTACACAATT
* *
25097172 TTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCTGTGTA
1 TTCAGGCTTTGTGCCTAGCAGGCTTCGTGCCGGTGTA
*
25097209 TTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTA
1 TTCAGGCTTTGTGCCTAGCAGGCTTCGTGCCGGTGTA
*
25097246 TTCAGGCTTAGTGCC
1 TTCAGGCTTTGTGCC
25097261 AGTGTATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.11, C:0.24, G:0.31, T:0.34
Consensus pattern (37 bp):
TTCAGGCTTTGTGCCTAGCAGGCTTCGTGCCGGTGTA
Found at i:25097318 original size:58 final size:58
Alignment explanation
Indices: 25097191--25097309 Score: 193
Period size: 58 Copynumber: 2.1 Consensus size: 58
25097181 TGTGCCTAGT
* * *
25097191 AGGCTTCGTGCCTGTGTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTATTC
1 AGGCTTAGTGCCAGTGTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGATGTATTC
* *
25097249 AGGCTTAGTGCCAGTGTATTTAGGCTGTGTGCCTAGCAGGCTTTGTGCCGATGTATTC
1 AGGCTTAGTGCCAGTGTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGATGTATTC
25097307 AGG
1 AGG
25097310 TTGTGTGCCT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.13, C:0.21, G:0.33, T:0.33
Consensus pattern (58 bp):
AGGCTTAGTGCCAGTGTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGATGTATTC
Found at i:25097338 original size:95 final size:95
Alignment explanation
Indices: 25097175--25097349 Score: 271
Period size: 95 Copynumber: 1.8 Consensus size: 95
25097165 CACAATTTTC
* *
25097175 AGGCTTTGTGCCTAGTAGGCTTCGTGCCTGTGTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCC
1 AGGCTGTGTGCCTAGCAGGCTTCGTGCCTGTGTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCC
*
25097240 GGTGTATTCAGGCTTAGTGCCAGTGTATTT
66 GGTGTATTCAAGCTTAGTGCCAGTGTATTT
* * *
25097270 AGGCTGTGTGCCTAGCAGGCTTTGTGCC-GATGTATTCAGGTTGTGTGCCTAGTAGGCTTCGTGC
1 AGGCTGTGTGCCTAGCAGGCTTCGTGCCTG-TGTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGC
*
25097334 CGGTGTTTTCAAGCTT
65 CGGTGTATTCAAGCTT
25097350 TGTGTCTAGT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 1 0.01
95 71 0.99
ACGTcount: A:0.13, C:0.21, G:0.32, T:0.35
Consensus pattern (95 bp):
AGGCTGTGTGCCTAGCAGGCTTCGTGCCTGTGTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCC
GGTGTATTCAAGCTTAGTGCCAGTGTATTT
Found at i:25097422 original size:58 final size:57
Alignment explanation
Indices: 25097191--25097422 Score: 192
Period size: 58 Copynumber: 4.1 Consensus size: 57
25097181 TGTGCCTAGT
*
25097191 AGGCTTCGTGCCTGTGTATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCCGGTGTATTC
1 AGGCTTCGTGCCAGTGTATTCAGGCTGTGTGCCTAGCAGGCTT-GTGCCGGTGTATTC
* * *
25097249 AGGCTTAGTGCCAGTGTATTTAGGCTGTGTGCCTAGCAGGCTTTGTGCCGATGTATTC
1 AGGCTTCGTGCCAGTGTATTCAGGCTGTGTGCCTAGCAGGC-TTGTGCCGGTGTATTC
* ** * * ** * * * *
25097307 AGG-TTGTGTGCCTAGTAGGCTTC-GTGCCG-GTG-TTTTCAAGCTT-TG--TGTCTAGT-
1 AGGCTT-CGTGCC-AGT-GTATTCAG-GCTGTGTGCCTAGCAGGCTTGTGCCGGTGTATTC
* *
25097360 AGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTTGCAGGCTTAGTGCCGGTGTATTC
1 AGGCTTCGTGCCAGTGTATTCAGGCTGTGTGCCTAGCAGGCTT-GTGCCGGTGTATTC
25097418 AGGCT
1 AGGCT
25097423 GTGTGCTTAG
Statistics
Matches: 132, Mismatches: 28, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
51 7 0.05
52 6 0.05
53 16 0.12
54 6 0.05
55 2 0.02
56 2 0.02
57 9 0.07
58 69 0.52
59 9 0.07
60 6 0.05
ACGTcount: A:0.12, C:0.21, G:0.33, T:0.34
Consensus pattern (57 bp):
AGGCTTCGTGCCAGTGTATTCAGGCTGTGTGCCTAGCAGGCTTGTGCCGGTGTATTC
Found at i:25097708 original size:37 final size:37
Alignment explanation
Indices: 25097248--25097705 Score: 529
Period size: 37 Copynumber: 12.4 Consensus size: 37
25097238 CCGGTGTATT
* * *
25097248 CAGGCTTAGTGCCAGTGTATTTAGGCTGTGTGCCTAG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
* * *
25097285 CAGGCTTTGTGCCGATGTATTCAGGTTGTGTGCCTAG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
* * * * *
25097322 TAGGCTTCGTGCCGGTGTTTTCAAGCTTTGTGTCTAG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
* *
25097359 TAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTTG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
* *
25097396 CAGGCTTAGTGCCGGTGTATTCAGGCTGTGTGCTTAG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
* * *
25097433 TAGGCTTTGTGCCGGTGTATTCAGGTTGTGTGCCTAG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
*
25097470 CAGGCTTAGTGCCGGTGTATTCAGGCTGTGTGCCTAG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
* ** *
25097507 TAGGCTTTATGCCGGTGTATTCAAGCTGTGTGCCTAG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
* * *
25097544 CAGGCTTCGTGCCGATATATTCAAGCTGTGTGCCTAG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
* * *
25097581 CAGGCTTAGTGTCGGTGTATTCAGACTGTGTGCCTAG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
** * * * *
25097618 CAGGCTTCGTGCTAGTATATTCATGCTGTGTACCTTG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
* * * * * * *
25097655 CTGGCTTCATGTCGATGTATTCGGGCTATGTGGCTAG
1 CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
*
25097692 CAGGCTTTGTGCCG
1 CAGGCTTCGTGCCG
25097706 ATGATCCAAG
Statistics
Matches: 351, Mismatches: 70, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 351 1.00
ACGTcount: A:0.14, C:0.20, G:0.32, T:0.34
Consensus pattern (37 bp):
CAGGCTTCGTGCCGGTGTATTCAGGCTGTGTGCCTAG
Found at i:25100779 original size:39 final size:39
Alignment explanation
Indices: 25100728--25100817 Score: 171
Period size: 39 Copynumber: 2.3 Consensus size: 39
25100718 CAAGGATAAA
*
25100728 AAGAAGAAGAAGCACCAGGACGAGGGTGAGCACCCAAAG
1 AAGAAGAAGAAGCACCAAGACGAGGGTGAGCACCCAAAG
25100767 AAGAAGAAGAAGCACCAAGACGAGGGTGAGCACCCAAAG
1 AAGAAGAAGAAGCACCAAGACGAGGGTGAGCACCCAAAG
25100806 AAGAAGAAGAAG
1 AAGAAGAAGAAG
25100818 AAAATAAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.48, C:0.18, G:0.32, T:0.02
Consensus pattern (39 bp):
AAGAAGAAGAAGCACCAAGACGAGGGTGAGCACCCAAAG
Found at i:25100908 original size:18 final size:18
Alignment explanation
Indices: 25100885--25100926 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
25100875 GATATTTTCA
*
25100885 TGCATTTT-TTATTGTCCT
1 TGCATTTTATT-TTGTCAT
25100903 TGCATTTTATTTTGTCAT
1 TGCATTTTATTTTGTCAT
25100921 TGCATT
1 TGCATT
25100927 CCTTTTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (18 bp):
TGCATTTTATTTTGTCAT
Found at i:25110156 original size:17 final size:18
Alignment explanation
Indices: 25110134--25110168 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
25110124 AGTAATTCTA
*
25110134 TTAATTCT-TTTTATTAT
1 TTAATTCTATTTGATTAT
25110151 TTAATTCTATTTGATTAT
1 TTAATTCTATTTGATTAT
25110169 ATTTTAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (18 bp):
TTAATTCTATTTGATTAT
Found at i:25111945 original size:62 final size:60
Alignment explanation
Indices: 25111845--25112021 Score: 228
Period size: 61 Copynumber: 2.9 Consensus size: 60
25111835 TTGTATTTTT
* * * * *
25111845 TTAATTAGATTCAGCTGCTCTTTGAAACTCTGATTACTGTTTTGGTTTGTGTTTCTTTTTGA
1 TTAATTAGATTCAGCTGCTATTTGAAAC-CTGAATACTGATTTGATTTGTATTTC-TTTTGA
25111907 TTAATTAGATTCAGCTGCTATTTGAAATCCTGAATACTGATTTGATTTGTATTTCTTTTGA
1 TTAATTAGATTCAGCTGCTATTTGAAA-CCTGAATACTGATTTGATTTGTATTTCTTTTGA
* ** * *
25111968 TTTATTAGATTCAGCTGCTATTCAAAACCCTGAATATTGAGTTGATTTGTATTT
1 TTAATTAGATTCAGCTGCTATTTGAAA-CCTGAATACTGATTTGATTTGTATTT
25112022 GTTTCAGCTG
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
61 54 0.52
62 48 0.47
63 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (60 bp):
TTAATTAGATTCAGCTGCTATTTGAAACCTGAATACTGATTTGATTTGTATTTCTTTTGA
Found at i:25121707 original size:18 final size:19
Alignment explanation
Indices: 25121675--25121715 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
25121665 CAACCTCAAA
25121675 ACCCGTAAACCTGGCAACG
1 ACCCGTAAACCTGGCAACG
*
25121694 ACCCG-AAACTTGGCAACG
1 ACCCGTAAACCTGGCAACG
25121712 ACCC
1 ACCC
25121716 AGCAATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.32, C:0.39, G:0.20, T:0.10
Consensus pattern (19 bp):
ACCCGTAAACCTGGCAACG
Found at i:25125710 original size:27 final size:27
Alignment explanation
Indices: 25125669--25125773 Score: 95
Period size: 27 Copynumber: 3.8 Consensus size: 27
25125659 GACTTAATGA
*
25125669 ATATTCTGGATTTTGACTCGAAAGAAAG
1 ATATTCT-GATTTTGGCTCGAAAGAAAG
* **
25125697 TTATTCTGATTTTGGCTCGAAAGAGTG
1 ATATTCTGATTTTGGCTCGAAAGAAAG
* * *
25125724 ATATTCAGATTCTGGCTCGAAAGAGCA-
1 ATATTCTGATTTTGGCTCGAAAGA-AAG
* *
25125751 ATATTCTGGACTCTGGCTCGAAA
1 ATATTCT-GATTTTGGCTCGAAA
25125774 TGGGTGTTAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
27 44 0.69
28 20 0.31
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (27 bp):
ATATTCTGATTTTGGCTCGAAAGAAAG
Found at i:25125832 original size:27 final size:27
Alignment explanation
Indices: 25125802--25125855 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
25125792 TGGCTCGTAA
* *
25125802 GAGCAAAAATCTGTTCTGGGCTCAAAT
1 GAGCAAAAATCTATTATGGGCTCAAAT
* *
25125829 GAGCAATACTCTATTATGGGCTCAAAT
1 GAGCAAAAATCTATTATGGGCTCAAAT
25125856 AAGTAATTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (27 bp):
GAGCAAAAATCTATTATGGGCTCAAAT
Found at i:25125885 original size:28 final size:27
Alignment explanation
Indices: 25125818--25125887 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
25125808 AAATCTGTTC
* *
25125818 TGGGCTCAAATGAGCAATACTCTATTA
1 TGGGCTCAAATAAGTAATACTCTATTA
* *
25125845 TGGGCTCAAATAAGTAATTCTCTATTG
1 TGGGCTCAAATAAGTAATACTCTATTA
*
25125872 TGGGGCTCTAATAAGT
1 T-GGGCTCAAATAAGT
25125888 TATATTTTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.65
28 13 0.35
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (27 bp):
TGGGCTCAAATAAGTAATACTCTATTA
Found at i:25131803 original size:27 final size:27
Alignment explanation
Indices: 25131765--25131913 Score: 106
Period size: 27 Copynumber: 5.4 Consensus size: 27
25131755 AGGGGTTTCA
*
25131765 GGCTCGAAAGAGTGTTATTCTGATTCT
1 GGCTCAAAAGAGTGTTATTCTGATTCT
* *
25131792 GGCTCAAAAGAGCT-ATATTCTGATTTT
1 GGCTCAAAAGAG-TGTTATTCTGATTCT
* * * *
25131819 AGCTCAAAAGAGCGATATTCTAATTCT
1 GGCTCAAAAGAGTGTTATTCTGATTCT
* * *
25131846 GGCTCATAAGAGCGATAATT-TGAACTT-T
1 GGCTCAAAAGAGTG-TTATTCTG-A-TTCT
* * *
25131874 GGCTCGAAAAGGGTGTTACTCTGTTTCT
1 GGCTC-AAAAGAGTGTTATTCTGATTCT
*
25131902 GGCTCATAAGAG
1 GGCTCAAAAGAG
25131914 CGAAAATTTG
Statistics
Matches: 94, Mismatches: 20, Indels: 16
0.72 0.15 0.12
Matches are distributed among these distances:
27 64 0.68
28 20 0.21
29 10 0.11
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (27 bp):
GGCTCAAAAGAGTGTTATTCTGATTCT
Found at i:25131905 original size:56 final size:55
Alignment explanation
Indices: 25131765--25131923 Score: 180
Period size: 54 Copynumber: 2.9 Consensus size: 55
25131755 AGGGGTTTCA
* * *
25131765 GGCTCG-AAAGAGTGTTATTCTGATTCTGGCTCAAAAGAGCTAT-ATTCTGATTTT
1 GGCTCGAAAAGAGTGTTATTCTGATTCTGGCTCATAAGAGCGATAATT-TGACTTT
* * * *
25131819 AGCTC-AAAAGAGCGATATTCTAATTCTGGCTCATAAGAGCGATAATTTGAACTTT
1 GGCTCGAAAAGAGTGTTATTCTGATTCTGGCTCATAAGAGCGATAATTTG-ACTTT
* * * *
25131874 GGCTCGAAAAGGGTGTTACTCTGTTTCTGGCTCATAAGAGCGAAAATTTG
1 GGCTCGAAAAGAGTGTTATTCTGATTCTGGCTCATAAGAGCGATAATTTG
25131924 TTTCGGGCTC
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
54 38 0.44
55 11 0.13
56 37 0.43
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (55 bp):
GGCTCGAAAAGAGTGTTATTCTGATTCTGGCTCATAAGAGCGATAATTTGACTTT
Found at i:25131941 original size:27 final size:27
Alignment explanation
Indices: 25131895--25131971 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
25131885 GGTGTTACTC
*
25131895 TGTTTCTGGCTCATAA-GAGCGAA-AATT
1 TGTTTCGGGCTCA-AATGAGC-AATAATT
*
25131922 TGTTTCGGGCTCAAATGAGCAATACTT
1 TGTTTCGGGCTCAAATGAGCAATAATT
*
25131949 TG-TTCTGAGCTCAAATGAGCAAT
1 TGTTTC-GGGCTCAAATGAGCAAT
25131972 TCTATGTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.16
27 37 0.84
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (27 bp):
TGTTTCGGGCTCAAATGAGCAATAATT
Found at i:25131979 original size:27 final size:27
Alignment explanation
Indices: 25131929--25132005 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
25131919 ATTTGTTTCG
* * *
25131929 GGCTCAAATGAGCAATACTTTGTTCT-
1 GGCTCAAATGAGCAATTCTATGTTATA
25131955 GAGCTCAAATGAGCAATTCTATGTTATA
1 G-GCTCAAATGAGCAATTCTATGTTATA
*
25131983 GGCTCAAATAAGCTATATTCTAT
1 GGCTCAAATGAGC-A-ATTCTAT
25132006 TATGGTGCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
26 1 0.02
27 33 0.77
28 2 0.05
29 7 0.16
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (27 bp):
GGCTCAAATGAGCAATTCTATGTTATA
Found at i:25134463 original size:20 final size:20
Alignment explanation
Indices: 25134438--25134475 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25134428 AATTTTTACA
25134438 AAGCCCAAAAATAAAAAAAT
1 AAGCCCAAAAATAAAAAAAT
* *
25134458 AAGCCCTAAACTAAAAAA
1 AAGCCCAAAAATAAAAAA
25134476 TGAAAAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.18, G:0.05, T:0.11
Consensus pattern (20 bp):
AAGCCCAAAAATAAAAAAAT
Found at i:25135122 original size:20 final size:20
Alignment explanation
Indices: 25135094--25135131 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25135084 CCCTGTAATT
* *
25135094 TTTATTTTATTTTAATTTCG
1 TTTAATTTAATTTAATTTCG
25135114 TTTAATTTAATTTAATTT
1 TTTAATTTAATTTAATTT
25135132 TTGTTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTAATTTAATTTAATTTCG
Found at i:25135335 original size:22 final size:22
Alignment explanation
Indices: 25135303--25135364 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
25135293 TTATTTATAG
* * *
25135303 TTTTGTTATTTATTCTTCTTC-
1 TTTTTTTATTTATTATTATTCA
25135324 TTTTATTTATTTATTATTATTCA
1 TTTT-TTTATTTATTATTATTCA
*
25135347 TTTTTTTATGTATT-TTAT
1 TTTTTTTATTTATTATTAT
25135365 ATTCTTGCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 8 0.23
22 23 0.66
23 4 0.11
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (22 bp):
TTTTTTTATTTATTATTATTCA
Found at i:25135337 original size:26 final size:26
Alignment explanation
Indices: 25135308--25135394 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
25135298 TATAGTTTTG
25135308 TTATTTATTCTTCTTCTTTTATTTAT
1 TTATTTATTCTTCTTCTTTTATTTAT
* * *
25135334 TTA-TTATTATTCATTTTTTTATGTAT
1 TTATTTATTCTTC-TTCTTTTATTTAT
* *
25135360 TT-TATATTCTTGCCTTCATTTAACTTTAT
1 TTATTTATTCTT--CTTC-TTTTA-TTTAT
25135389 TTATTT
1 TTATTT
25135395 TTATGTATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
25 8 0.18
26 22 0.49
27 2 0.04
28 5 0.11
29 6 0.13
30 2 0.04
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.68
Consensus pattern (26 bp):
TTATTTATTCTTCTTCTTTTATTTAT
Found at i:25139484 original size:31 final size:31
Alignment explanation
Indices: 25139427--25139486 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
25139417 GACAAATTGT
* *
25139427 ACAATAAATACATGAATATAAAAATAATACA
1 ACAATAAATAAATGAAAATAAAAATAATACA
*
25139458 ACAATTAAATAAAT-AAAATAATAATAATA
1 ACAA-TAAATAAATGAAAATAAAAATAATA
25139487 ATAATGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.25
Consensus pattern (31 bp):
ACAATAAATAAATGAAAATAAAAATAATACA
Found at i:25139704 original size:24 final size:24
Alignment explanation
Indices: 25139635--25139706 Score: 60
Period size: 24 Copynumber: 2.9 Consensus size: 24
25139625 ATGTATGTAC
25139635 TAAAAATACTAAAG-AAAATAAACA
1 TAAAAATA-TAAAGAAAAATAAACA
* *
25139659 TAATTAACATA-AAATAATAATAAA-A
1 TAA--AA-ATATAAAGAAAAATAAACA
25139684 TAAAAATATAAAGAAACAATAAA
1 TAAAAATATAAAGAAA-AATAAA
25139707 TGGACTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
22 3 0.08
23 7 0.18
24 9 0.24
25 7 0.18
26 9 0.24
27 3 0.08
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.21
Consensus pattern (24 bp):
TAAAAATATAAAGAAAAATAAACA
Found at i:25139818 original size:25 final size:25
Alignment explanation
Indices: 25139751--25139831 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
25139741 TATAAATTGC
* *
25139751 TAAAAATAGAAATTAAAAGGATTTAAT
1 TAAAAA-ACAAATTAAAA-GATTAAAT
*
25139778 TAAAAAATAAATTAAAAG-TTAAAAT
1 TAAAAAACAAATTAAAAGATT-AAAT
*
25139803 TAAAAAACAGAA-TAAAGGATTAAAT
1 TAAAAAACA-AATTAAAAGATTAAAT
25139828 TAAA
1 TAAA
25139832 GCAATATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
24 2 0.04
25 25 0.53
26 14 0.30
27 6 0.13
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (25 bp):
TAAAAAACAAATTAAAAGATTAAAT
Found at i:25141650 original size:101 final size:101
Alignment explanation
Indices: 25141462--25141756 Score: 286
Period size: 101 Copynumber: 3.0 Consensus size: 101
25141452 TCTATTATAG
*
25141462 CTTCACTCCATTCCAATGTAACTCTAGGGAGATTGAGATTCGCTATCGTAGTTTTAATCCGATCC
1 CTTCACTCCATTCCAATGCAACTCTAGGGAGATTGAGATTCGCTATCGTAGTTTTAATCCGATCC
25141527 ACTACAACTTCAACGATATAGGATTTGGTGTTGTAA
66 ACTACAACTTCAACGATATAGGATTTGGTGTTGTAA
* * *
25141563 CTTCACTCCATTCCACTGCATCTTTAGGGAGATTGAGATAT-GCTA-CTGTAGTTTTAATCCGAT
1 CTTCACTCCATTCCAATGCAACTCTAGGGAGATTGAGAT-TCGCTATC-GTAGTTTTAATCCGAT
* ** * * *
25141626 CCACTACAACTTTAGGGATGTAGGATTTGATGGTTATAA
64 CCACTACAACTTCAACGATATAGGATTTGGT-GTTGTAA
* * * * * * **
25141665 CCTCA-T-C-TT----TGCAACTTTAGGGAGA-TAAGATTCGCTATCATAATTTTGATTTGATCC
1 CTTCACTCCATTCCAATGCAACTCTAGGGAGATTGAGATTCGCTATCGTAGTTTTAATCCGATCC
* * ** *
25141722 ACTGCCACTTCAGGGATTTAGGATTTGGTGTTGTA
66 ACTACAACTTCAACGATATAGGATTTGGTGTTGTA
25141757 TTTTTGTCTT
Statistics
Matches: 165, Mismatches: 24, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
93 6 0.04
94 46 0.28
95 16 0.10
99 2 0.01
100 2 0.01
101 82 0.50
102 11 0.07
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (101 bp):
CTTCACTCCATTCCAATGCAACTCTAGGGAGATTGAGATTCGCTATCGTAGTTTTAATCCGATCC
ACTACAACTTCAACGATATAGGATTTGGTGTTGTAA
Found at i:25142199 original size:29 final size:29
Alignment explanation
Indices: 25142158--25142222 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
25142148 GTTAGATTTG
25142158 GAGGA-AAGGACACCTGTACTATTGATCT
1 GAGGATAAGGACACCTGTACTATTGATCT
25142186 GAGGATAAGGACACCTGTACTATTGATCT
1 GAGGATAAGGACACCTGTACTATTGATCT
25142215 GAGGATAA
1 GAGGATAA
25142223 ATACTCATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (29 bp):
GAGGATAAGGACACCTGTACTATTGATCT
Found at i:25143248 original size:68 final size:68
Alignment explanation
Indices: 25143169--25143298 Score: 251
Period size: 68 Copynumber: 1.9 Consensus size: 68
25143159 GTTTTTCTTT
25143169 TTGTTGCTACTTTTACATTTTATTTTAGGTGTTTTATGACCCGGAGAAATTTGGAATTTATTGCT
1 TTGTTGCTACTTTTACATTTTATTTTAGGTGTTTTATGACCCGGAGAAATTTGGAATTTATTGCT
25143234 GGC
66 GGC
*
25143237 TTGTTGCTACTTTTACATTTTATTTTAGGTGTTTTATGAGCCGGAGAAATTTGGAATTTATT
1 TTGTTGCTACTTTTACATTTTATTTTAGGTGTTTTATGACCCGGAGAAATTTGGAATTTATT
25143299 ATTTGTTAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (68 bp):
TTGTTGCTACTTTTACATTTTATTTTAGGTGTTTTATGACCCGGAGAAATTTGGAATTTATTGCT
GGC
Found at i:25151207 original size:5 final size:5
Alignment explanation
Indices: 25151197--25151224 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
25151187 TATAAAAAAG
25151197 AGAAA AGAAA AGAAA AGAAA AGAAA AGA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGA
25151225 TATATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:25154471 original size:37 final size:36
Alignment explanation
Indices: 25154421--25154492 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
25154411 GTCCTCAAGT
*
25154421 AAAATAGAAATTAGCAAGACTATATCAAAATTTTAAC
1 AAAATAGAAATTAGCAAGAC-ATATCAAAATCTTAAC
25154458 AAAATAGAAATTAGCAAGACATATCAAAATCTTAA
1 AAAATAGAAATTAGCAAGACATATCAAAATCTTAA
25154493 TAAGGCAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 14 0.41
37 20 0.59
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (36 bp):
AAAATAGAAATTAGCAAGACATATCAAAATCTTAAC
Found at i:25164823 original size:18 final size:18
Alignment explanation
Indices: 25164802--25164866 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
25164792 ATGCTCTTAT
*
25164802 GAGCCAATATGCTCAAAC
1 GAGCCAGTATGCTCAAAC
*
25164820 GAGCCAGTATGCCCAAAC
1 GAGCCAGTATGCTCAAAC
25164838 GAGCCAGTATGCTCAAAC
1 GAGCCAGTATGCTCAAAC
*
25164856 AAGCCAGTATG
1 GAGCCAGTATG
25164867 TTAATCCTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (18 bp):
GAGCCAGTATGCTCAAAC
Found at i:25173709 original size:38 final size:38
Alignment explanation
Indices: 25173623--25173710 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
25173613 GCAACAACAT
* * *
25173623 TCTTGGTTGCAA-TTGAAGAATACTTATGCAGTGATAG
1 TCTTGGATGCAATTTGAAGAATACTTATGCAGCGACAG
* *
25173660 T-TCTGGATGCAATTTGAATAATATTTATGCAGCGACAG
1 TCT-TGGATGCAATTTGAAGAATACTTATGCAGCGACAG
*
25173698 TCTTGGGTGCAAT
1 TCTTGGATGCAAT
25173711 CTAGAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
36 1 0.02
37 9 0.21
38 31 0.74
39 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.35
Consensus pattern (38 bp):
TCTTGGATGCAATTTGAAGAATACTTATGCAGCGACAG
Found at i:25174663 original size:29 final size:29
Alignment explanation
Indices: 25174630--25174696 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
25174620 TAATGATATT
25174630 ATTCATCCATTACTAATGCAATCTAAATC
1 ATTCATCCATTACTAATGCAATCTAAATC
*
25174659 ATTCATCCATTACTAATGCAATTTAAATC
1 ATTCATCCATTACTAATGCAATCTAAATC
25174688 ATTCATCCA
1 ATTCATCCA
25174697 AAAATTGAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
ATTCATCCATTACTAATGCAATCTAAATC
Found at i:25174982 original size:17 final size:17
Alignment explanation
Indices: 25174943--25174998 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
25174933 ATATAAATGG
**
25174943 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
25174960 AGATGCAACGACAATAA
1 AAATGCAATGACAATAA
*
25174977 AAATGCAGTGACAATAA
1 AAATGCAATGACAATAA
25174994 AAATG
1 AAATG
25174999 TAGAGACAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:25175006 original size:17 final size:17
Alignment explanation
Indices: 25174969--25175008 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
25174959 TAGATGCAAC
*
25174969 GACAATAAAAATGCAGT
1 GACAATAAAAATGCAGA
*
25174986 GACAATAAAAATGTAGA
1 GACAATAAAAATGCAGA
25175003 GACAAT
1 GACAAT
25175009 TATACTATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (17 bp):
GACAATAAAAATGCAGA
Found at i:25181700 original size:10 final size:10
Alignment explanation
Indices: 25181671--25181704 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
25181661 TTATCAAAAA
25181671 TTTCTTTCTT
1 TTTCTTTCTT
25181681 TTT-TTTCTT
1 TTTCTTTCTT
*
25181690 TTTCTTCCTT
1 TTTCTTTCTT
25181700 TTTCT
1 TTTCT
25181705 AATTTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:25199496 original size:15 final size:15
Alignment explanation
Indices: 25199449--25199523 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
25199439 AATGTAAATT
*
25199449 AAATAAA-AATAATA
1 AAATAAATAACAATA
*
25199463 AAAGAAATAACAAT-
1 AAATAAATAACAATA
25199477 --A-AAATAAC-ATGA
1 AAATAAATAACAAT-A
25199489 AAATAAATAACAATA
1 AAATAAATAACAATA
* *
25199504 ATATAAATAAACAAAA
1 AAATAAAT-AACAATA
25199520 AAAT
1 AAAT
25199524 GCTAAAATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
10 2 0.04
11 7 0.15
12 1 0.02
14 7 0.15
15 20 0.42
16 11 0.23
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (15 bp):
AAATAAATAACAATA
Found at i:25199548 original size:19 final size:20
Alignment explanation
Indices: 25199488--25199548 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
25199478 AAATAACATG
25199488 AAAATAAAT-AAC-AATAAT
1 AAAATAAATAAACAAATAAT
* * **
25199506 ATAAATAAACAAAAAAATGCT
1 A-AAATAAATAAACAAATAAT
25199527 AAAATAAATAAACAAAT-AT
1 AAAATAAATAAACAAATAAT
25199546 AAA
1 AAA
25199549 CAATAAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.03
19 11 0.33
20 16 0.48
21 5 0.15
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAATAAATAAACAAATAAT
Found at i:25200533 original size:49 final size:49
Alignment explanation
Indices: 25200421--25201067 Score: 376
Period size: 49 Copynumber: 13.2 Consensus size: 49
25200411 TTCAATCTGT
** * * * * *
25200421 TCCCTCTTTGGTTTTAAGGTGTTAGATCCATCATCATGGCTTCAATCTA
1 TCCCTCTTCAGTTTTAAGGTGTTAGGTCCATCGTTACGGCTTCAACCTA
* ** * * * *
25200470 TCCCTATTTGGTTTTAGGGTATTAGGTCTATCGTTGA-GGCTTAAACCTA
1 TCCCTCTTCAGTTTTAAGGTGTTAGGTCCATCGTT-ACGGCTTCAACCTA
* ** * * * * *
25200519 TCCCTCTTCAGTTTTAAGGTGTAAGACCCGTCGTTATGACTTCAATCTT
1 TCCCTCTTCAGTTTTAAGGTGTTAGGTCCATCGTTACGGCTTCAACCTA
** *
25200568 TCCCTCTTCAGTTTTGGGGTGTTAGGTTCATCGTTACGGCTTCAACCTA
1 TCCCTCTTCAGTTTTAAGGTGTTAGGTCCATCGTTACGGCTTCAACCTA
* * * * * *
25200617 TTCCTCTTCAATTTTAAGGTGTAAGGTCCACCGTTACGGCTTTAACCTT
1 TCCCTCTTCAGTTTTAAGGTGTTAGGTCCATCGTTACGGCTTCAACCTA
** * * * * *
25200666 TCCCTCTTTGGTTTTAGGGTGTTTA-ATCCATCGTTACAGCTTTAATCTA
1 TCCCTCTTCAGTTTTAAGGTG-TTAGGTCCATCGTTACGGCTTCAACCTA
* * * * *
25200715 TCCCTCTTC-GATTTTAAGGTGTTAGGCCCGTCATTGCGACTTCAACCTA
1 TCCCTCTTCAG-TTTTAAGGTGTTAGGTCCATCGTTACGGCTTCAACCTA
* * * * * * *
25200764 TCCCTCTTCAGTTTTAAGGTGTAAGATCCGTCGTTGCGACTTCAATCTT
1 TCCCTCTTCAGTTTTAAGGTGTTAGGTCCATCGTTACGGCTTCAACCTA
* * * *
25200813 TCCCTCTTC-GATTTT-TGGATGTTAGGTCTA-CTGTTATGACTTCAACCTA
1 TCCCTCTTCAG-TTTTAAGG-TGTTAGGTCCATC-GTTACGGCTTCAACCTA
* * * * ** * * *
25200862 TCCCTCTTTAGTTTTAAGGTGTAAGATCCACCGTTGTGGCTTTAATCTT
1 TCCCTCTTCAGTTTTAAGGTGTTAGGTCCATCGTTACGGCTTCAACCTA
* ** * * * * *
25200911 TCCCTCTTCAGTTTTAAGGTGTTAGATCTGTCATTGCGGGTTTAATCTA
1 TCCCTCTTCAGTTTTAAGGTGTTAGGTCCATCGTTACGGCTTCAACCTA
* * * * * * * * *
25200960 TCCGT-TTATAATTTTAGGGTATTAGATCCGTCATTATGAG-TTCAACCTA
1 TCCCTCTT-CAGTTTTAAGGTGTTAGGTCCATCGTTACG-GCTTCAACCTA
* * * * *
25201009 TCCCTTTTCAGTTTT-AGGATGCTAGGTCCGTTGTTACGACTTCAACCTA
1 TCCCTCTTCAGTTTTAAGG-TGTTAGGTCCATCGTTACGGCTTCAACCTA
*
25201058 TTCCTCTTCA
1 TCCCTCTTCA
25201068 AACTGTATGA
Statistics
Matches: 459, Mismatches: 122, Indels: 34
0.75 0.20 0.06
Matches are distributed among these distances:
48 13 0.03
49 435 0.95
50 11 0.02
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (49 bp):
TCCCTCTTCAGTTTTAAGGTGTTAGGTCCATCGTTACGGCTTCAACCTA
Found at i:25204403 original size:391 final size:391
Alignment explanation
Indices: 25203682--25204468 Score: 1556
Period size: 391 Copynumber: 2.0 Consensus size: 391
25203672 TGAACCAAGT
*
25203682 AATGTAATTTAATCTCCCTAGGAATCCTCGAACTTCCTTTTGGGTACGTGGAAGTGGTAACTCTT
1 AATGTAATTTAATCTCCCTAGGAATCCTCAAACTTCCTTTTGGGTACGTGGAAGTGGTAACTCTT
25203747 ATATAGCTTTGACCTTATCAGGATCAATCTCAATTCCTCTTCTACTGACCACAAAGCCTAACAGC
66 ATATAGCTTTGACCTTATCAGGATCAATCTCAATTCCTCTTCTACTGACCACAAAGCCTAACAGC
25203812 TTACCTGAAGTAGCCTCAAAAGTACATTTGTTTGGGTTCAACTTCAACTAGAACTTTCTCAATCT
131 TTACCTGAAGTAGCCTCAAAAGTACATTTGTTTGGGTTCAACTTCAACTAGAACTTTCTCAATCT
25203877 CAAGAATAATTTTCTCAAAACCTTTACGTGTTCTTCTCCTGTTCAAGACTTTGCAATCATATCGT
196 CAAGAATAATTTTCTCAAAACCTTTACGTGTTCTTCTCCTGTTCAAGACTTTGCAATCATATCGT
25203942 CAAGATAGACCTCAATCTCCTTATGTATCATGTCATGCAACAGAGTTACCATAGCCCTTTGATAT
261 CAAGATAGACCTCAATCTCCTTATGTATCATGTCATGCAACAGAGTTACCATAGCCCTTTGATAT
25204007 GTTTCCTCTGCATTCTTTAGTCCAAATGGCATGACTTTTCAGTAAAAGGTTCCTTACATGGTAAC
326 GTTTCCTCTGCATTCTTTAGTCCAAATGGCATGACTTTTCAGTAAAAGGTTCCTTACATGGTAAC
25204072 A
391 A
25204073 AATGTAATTTAATCTCCCTAGGAATCCTCAAACTTCCTTTTGGGTACGTGGAAGTGGTAACTCTT
1 AATGTAATTTAATCTCCCTAGGAATCCTCAAACTTCCTTTTGGGTACGTGGAAGTGGTAACTCTT
25204138 ATATAGCTTTGACCTTATCAGGATCAATCTCAATTCCTCTTCTACTGACCACAAAGCCTAACAGC
66 ATATAGCTTTGACCTTATCAGGATCAATCTCAATTCCTCTTCTACTGACCACAAAGCCTAACAGC
25204203 TTACCTGAAGTAGCCTCAAAAGTACATTTGTTTGGGTTCAACTTCAACTAGAACTTTCTCAATCT
131 TTACCTGAAGTAGCCTCAAAAGTACATTTGTTTGGGTTCAACTTCAACTAGAACTTTCTCAATCT
25204268 CAAGAATAATTTTCTCAAAACCTTTACGTGTTCTTCTCCTGTTCAAGACTTTGCAATCATATCGT
196 CAAGAATAATTTTCTCAAAACCTTTACGTGTTCTTCTCCTGTTCAAGACTTTGCAATCATATCGT
*
25204333 CGAGATAGACCTCAATCTCCTTATGTATCATGTCATGCAACAGAGTTACCATAGCCCTTTGATAT
261 CAAGATAGACCTCAATCTCCTTATGTATCATGTCATGCAACAGAGTTACCATAGCCCTTTGATAT
25204398 GTTTCCTCTGCATTCTTTAGTCCAAATGGCATGACTTTTCAGTAAAAGGTTCCTTACATGGTAAC
326 GTTTCCTCTGCATTCTTTAGTCCAAATGGCATGACTTTTCAGTAAAAGGTTCCTTACATGGTAAC
25204463 A
391 A
25204464 AATGT
1 AATGT
25204469 GATTGTTTCC
Statistics
Matches: 394, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
391 394 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (391 bp):
AATGTAATTTAATCTCCCTAGGAATCCTCAAACTTCCTTTTGGGTACGTGGAAGTGGTAACTCTT
ATATAGCTTTGACCTTATCAGGATCAATCTCAATTCCTCTTCTACTGACCACAAAGCCTAACAGC
TTACCTGAAGTAGCCTCAAAAGTACATTTGTTTGGGTTCAACTTCAACTAGAACTTTCTCAATCT
CAAGAATAATTTTCTCAAAACCTTTACGTGTTCTTCTCCTGTTCAAGACTTTGCAATCATATCGT
CAAGATAGACCTCAATCTCCTTATGTATCATGTCATGCAACAGAGTTACCATAGCCCTTTGATAT
GTTTCCTCTGCATTCTTTAGTCCAAATGGCATGACTTTTCAGTAAAAGGTTCCTTACATGGTAAC
A
Found at i:25208348 original size:13 final size:13
Alignment explanation
Indices: 25208330--25208355 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25208320 ACATACATAC
25208330 AATAAAATGCAAA
1 AATAAAATGCAAA
25208343 AATAAAATGCAAA
1 AATAAAATGCAAA
25208356 GGATCACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AATAAAATGCAAA
Found at i:25210690 original size:49 final size:49
Alignment explanation
Indices: 25210637--25210779 Score: 137
Period size: 49 Copynumber: 2.9 Consensus size: 49
25210627 AAAAGGTGTA
* **
25210637 AGATTCACCGTTGCAGCTTCAGTCTATTCCCTCTTTGG-TTTAAGGTATT
1 AGATTCACCGTCGCAGCTTCAAACTA-TCCCTCTTTGGTTTTAAGGTATT
** *
25210686 AGATTCACCGTCGTGGTTTCAAACTATCCCTCTTTGGTTTTAAGGTATT
1 AGATTCACCGTCGCAGCTTCAAACTATCCCTCTTTGGTTTTAAGGTATT
* * * * * **
25210735 A-AGTCTGCCTTCACAGCTTCAACCTATCCCTCTTCAGTTTTAAGG
1 AGATTC-ACCGTCGCAGCTTCAAACTATCCCTCTTTGGTTTTAAGG
25210780 AGTAAGATTC
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
48 14 0.18
49 62 0.82
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.38
Consensus pattern (49 bp):
AGATTCACCGTCGCAGCTTCAAACTATCCCTCTTTGGTTTTAAGGTATT
Found at i:25210804 original size:98 final size:97
Alignment explanation
Indices: 25210702--25210971 Score: 253
Period size: 98 Copynumber: 2.8 Consensus size: 97
25210692 ACCGTCGTGG
*
25210702 TTTCAAACTATCCCTCTTTGGTTTTAAGGTATTAAGT-C-TGCCTTCACAGCTTCAACCTATCCC
1 TTTCAAACTTTCCCTCTTTGGTTTTAAGGTATTAAGTCCATG--TTCACA-CTTCAACCTATCCC
* * *
25210765 TCTTCAGTTTTAAGGAGTAAGATTCGTCGTTGCGA
63 TCTTCAATTTTAAGGAGTAAGATTCGCCGTTACGA
* * * * * * * * *
25210800 TTTCAATCTTTCCCTCTTCGATATTAGGGTGTTAGGTCCATTGTTGAGACTTCAACCTATCCCTC
1 TTTCAAACTTTCCCTCTTTGGTTTTAAGGTATTAAGTCCA-TGTTCACACTTCAACCTATCCCTC
* * * *
25210865 TTCAATTTTAAGGTGTAAGGTTTGCCGTTACGC
65 TTCAATTTTAAGGAGTAAGATTCGCCGTTACGA
* * **
25210898 TTT-AACCTTTCCCTCTTTGGTTTTAAGGTGTT-AGATCCATCGTT-ACAACTTCAATTTATCCC
1 TTTCAAACTTTCCCTCTTTGGTTTTAAGGTATTAAG-TCCAT-GTTCAC-ACTTCAACCTATCCC
25210960 TCTTCAATTTTA
63 TCTTCAATTTTA
25210972 GGGTGTTAGG
Statistics
Matches: 140, Mismatches: 26, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
96 3 0.02
97 56 0.40
98 74 0.53
99 5 0.04
101 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (97 bp):
TTTCAAACTTTCCCTCTTTGGTTTTAAGGTATTAAGTCCATGTTCACACTTCAACCTATCCCTCT
TCAATTTTAAGGAGTAAGATTCGCCGTTACGA
Found at i:25210805 original size:49 final size:49
Alignment explanation
Indices: 25210751--25211258 Score: 303
Period size: 49 Copynumber: 10.4 Consensus size: 49
25210741 GCCTTCACAG
* *
25210751 CTTCAACCTATCCCTCTTCAGTTTTAAGGAGTAAGATTCGTCGTTGCGA
1 CTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCGTCGTTGCGA
* * * * * * * * * *
25210800 TTTCAATCTTTCCCTCTTC-GATATTAGGGTGTTAGGTCCATTGTTGAGA
1 CTTCAACCTATCCCTCTTCAG-TTTTAAGGTGTAAGATCCGTCGTTGCGA
* * ** * *
25210849 CTTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGGTTTGCCGTTACG-
1 CTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCGTCGTTGCGA
* * ** * * * *
25210897 CTTTAACCTTTCCCTCTTTGGTTTTAAGGTGTTAGATCCATCGTTACAA
1 CTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCGTCGTTGCGA
** * * * * * * *
25210946 CTTCAATTTATCCCTCTTCAATTTTAGGGTGTTAGGTCCATCATTGTGA
1 CTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCGTCGTTGCGA
* *
25210995 CTTCAACCTATCCCTCTTCAGTTTTAAGGTGAAAGATCCGTCATTGCGA
1 CTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCGTCGTTGCGA
* * ** * * *
25211044 CTTCAATCTTTCCCTCTTC-GATTTTTCGGTGTTAGGTTCCCT-GTTGCGA
1 CTTCAACCTATCCCTCTTCAG-TTTTAAGGTG-TAAGATCCGTCGTTGCGA
* * * * *
25211093 CTTTAACCCATCCCTCTTTAGTTTTAAGGTGTAAGATCCGTCATTAC-A
1 CTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCGTCGTTGCGA
* * * * * * *
25211141 GCTTCAATCTTTCCCTCTT-AGATTTT-AGCGTGTTAGATCTGCCATTACGA
1 -CTTCAACCTATCCCTCTTCAG-TTTTAAG-GTGTAAGATCCGTCGTTGCGA
* * * ** * * * *
25211191 CTTCAATCTATCCCTCTTTAATTTTCGGGTGTTAGGGT-TGTCGTTACGA
1 CTTCAACCTATCCCTCTTCAGTTTTAAGGTG-TAAGATCCGTCGTTGCGA
*
25211240 CCTCAACCTATCCCTCTTC
1 CTTCAACCTATCCCTCTTC
25211259 GATTTTAGGA
Statistics
Matches: 346, Mismatches: 99, Indels: 28
0.73 0.21 0.06
Matches are distributed among these distances:
48 50 0.14
49 283 0.82
50 13 0.04
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (49 bp):
CTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATCCGTCGTTGCGA
Found at i:25210941 original size:146 final size:146
Alignment explanation
Indices: 25210750--25211025 Score: 383
Period size: 146 Copynumber: 1.9 Consensus size: 146
25210740 TGCCTTCACA
* * * * *
25210750 GCTTCAACCTATCCCTCTTCAGTTTTAAGGAGTAAGATTCGTCGTTGCGATTTCAATCTT-TCCC
1 GCTTCAACCTATCCCTCTTCAGTTTTAAGGAGTAAGATCCATCGTTACAACTTCAAT-TTATCCC
* **
25210814 TCTTCGATATTAGGGTGTTAGGTCCATTGTTGAGACTTCAACCTATCCCTCTTCAATTTTAAGGT
65 TCTTCAATATTAGGGTGTTAGGTCCATCATTGAGACTTCAACCTATCCCTCTTCAATTTTAAGGT
25210879 GTAAGGTTTGCCGTTAC
130 GTAAGGTTTGCCGTTAC
* * ** * *
25210896 GCTTTAACCTTTCCCTCTTTGGTTTTAAGGTGTTAGATCCATCGTTACAACTTCAATTTATCCCT
1 GCTTCAACCTATCCCTCTTCAGTTTTAAGGAGTAAGATCCATCGTTACAACTTCAATTTATCCCT
* * *
25210961 CTTCAATTTTAGGGTGTTAGGTCCATCATTGTGACTTCAACCTATCCCTCTTCAGTTTTAAGGTG
66 CTTCAATATTAGGGTGTTAGGTCCATCATTGAGACTTCAACCTATCCCTCTTCAATTTTAAGGTG
25211026 AAAGATCCGT
Statistics
Matches: 112, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
145 2 0.02
146 110 0.98
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (146 bp):
GCTTCAACCTATCCCTCTTCAGTTTTAAGGAGTAAGATCCATCGTTACAACTTCAATTTATCCCT
CTTCAATATTAGGGTGTTAGGTCCATCATTGAGACTTCAACCTATCCCTCTTCAATTTTAAGGTG
TAAGGTTTGCCGTTAC
Found at i:25211047 original size:98 final size:97
Alignment explanation
Indices: 25210848--25211215 Score: 339
Period size: 98 Copynumber: 3.8 Consensus size: 97
25210838 CATTGTTGAG
* * * * **** * * * *
25210848 ACTTCAACCTATCCCTCTTCAATTTTAAGGTGTAAGGTTTGCCGTTACG-CTTTAACCTTTCCCT
1 ACTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCCATCATTGCGACTTCAACCTATCCCT
* * * *
25210912 CTTTGGTTTTAAGGTGTTAGATCCATCGTTAC
66 CTTTAGTTTTAAGGTGTAAGATCCGTCATTAC
*
25210944 AACTTCAAT-TTATCCCTCTTCAATTTTAGGGTGTTAGGTCCATCATTGTGACTTCAACCTATCC
1 -ACTTCAATCTT-TCCCTCTTCAATTTTAGGGTGTTAGGTCCATCATTGCGACTTCAACCTATCC
* * *
25211008 CTCTTCAGTTTTAAGGTGAAAGATCCGTCATTGC
64 CTCTTTAGTTTTAAGGTGTAAGATCCGTCATTAC
* ** * * * *
25211042 GACTTCAATCTTTCCCTCTTCGATTTTTCGGTGTTAGGTTCCCT-GTTGCGACTTTAACCCATCC
1 -ACTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGG-TCCATCATTGCGACTTCAACCTATCC
25211106 CTCTTTAGTTTTAAGGTGTAAGATCCGTCATTAC
64 CTCTTTAGTTTTAAGGTGTAAGATCCGTCATTAC
* * *** * *
25211140 AGCTTCAATCTTTCCCTCTT-AGATTTTAGCGTGTTAGATCTGCCATTACGACTTCAATCTATCC
1 A-CTTCAATCTTTCCCTCTTCA-ATTTTAGGGTGTTAGGTCCATCATTGCGACTTCAACCTATCC
*
25211204 CTCTTTAATTTT
64 CTCTTTAGTTTT
25211216 CGGGTGTTAG
Statistics
Matches: 218, Mismatches: 46, Indels: 13
0.79 0.17 0.05
Matches are distributed among these distances:
96 1 0.00
97 39 0.18
98 172 0.79
99 6 0.03
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.40
Consensus pattern (97 bp):
ACTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCCATCATTGCGACTTCAACCTATCCCT
CTTTAGTTTTAAGGTGTAAGATCCGTCATTAC
Found at i:25211108 original size:244 final size:245
Alignment explanation
Indices: 25210751--25211226 Score: 634
Period size: 244 Copynumber: 1.9 Consensus size: 245
25210741 GCCTTCACAG
* * * *
25210751 CTTCAACCTATCCCTCTTCAGTTTTAAGGAGTAAGATTCGTCGTTGCGATTTCAATCTTTCCCTC
1 CTTCAACCTATCCCTCTTCAGTTTTAAGGAGAAAGATCCGTCATTGCGACTTCAATCTTTCCCTC
* * *
25210816 TTCGATATTAGGGTGTTAGGTCCATTGTTGAGACTTCAACCTATCCCTCTTCAATTTTAAGGTGT
66 TTCGATATTACGGTGTTAGGTCCACTGTTGAGACTTCAACCCATCCCTCTTCAATTTTAAGGTGT
* ** * * * * * *
25210881 AAGGTTTGCCGTTAC-GCTTTAACCTTTCCCTCTTTGGTTTTAAG-GTGTTAGATCCATCGTTAC
131 AAGATCCGCCATTACAGCTTCAACCTTTCCCTCTTAGATTTT-AGCGTGTTAGATCCACCATTAC
*
25210944 AACTTCAATTTATCCCTCTTCAATTTTAGGGTGTTAGGTCCATCATTGTGA
195 AACTTCAATCTATCCCTCTTCAATTTTAGGGTGTTAGGTCCATCATTGTGA
*
25210995 CTTCAACCTATCCCTCTTCAGTTTTAAGGTGAAAGATCCGTCATTGCGACTTCAATCTTTCCCTC
1 CTTCAACCTATCCCTCTTCAGTTTTAAGGAGAAAGATCCGTCATTGCGACTTCAATCTTTCCCTC
* * * * * *
25211060 TTCGATTTTTCGGTGTTAGGTTCC-CTGTTGCGACTTTAACCCATCCCTCTTTAGTTTTAAGGTG
66 TTCGATATTACGGTGTTAGG-TCCACTGTTGAGACTTCAACCCATCCCTCTTCAATTTTAAGGTG
* * **
25211124 TAAGATCCGTCATTACAGCTTCAATCTTTCCCTCTTAGATTTTAGCGTGTTAGATCTGCCATTAC
130 TAAGATCCGCCATTACAGCTTCAACCTTTCCCTCTTAGATTTTAGCGTGTTAGATCCACCATTAC
* * *
25211189 GACTTCAATCTATCCCTCTTTAATTTTCGGGTGTTAGG
195 AACTTCAATCTATCCCTCTTCAATTTTAGGGTGTTAGG
25211227 GTTGTCGTTA
Statistics
Matches: 198, Mismatches: 31, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
244 124 0.63
245 74 0.37
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.40
Consensus pattern (245 bp):
CTTCAACCTATCCCTCTTCAGTTTTAAGGAGAAAGATCCGTCATTGCGACTTCAATCTTTCCCTC
TTCGATATTACGGTGTTAGGTCCACTGTTGAGACTTCAACCCATCCCTCTTCAATTTTAAGGTGT
AAGATCCGCCATTACAGCTTCAACCTTTCCCTCTTAGATTTTAGCGTGTTAGATCCACCATTACA
ACTTCAATCTATCCCTCTTCAATTTTAGGGTGTTAGGTCCATCATTGTGA
Found at i:25217770 original size:40 final size:40
Alignment explanation
Indices: 25217726--25217801 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
25217716 TTTTTGCTAG
* *
25217726 TTTGAGCTACCCTTTCAGGTTTTCAACTCAAACTCTTTTT
1 TTTGAGCCACCCTTTCAAGTTTTCAACTCAAACTCTTTTT
* *
25217766 TTTGAGCCGCCCTTTCAAGTTTTCAACTTAAACTCT
1 TTTGAGCCACCCTTTCAAGTTTTCAACTCAAACTCT
25217802 CTCTCTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (40 bp):
TTTGAGCCACCCTTTCAAGTTTTCAACTCAAACTCTTTTT
Found at i:25240349 original size:15 final size:15
Alignment explanation
Indices: 25240329--25240359 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
25240319 CAACATACAG
25240329 GCAATAAAATGCAAA
1 GCAATAAAATGCAAA
25240344 GCAATAAAATGCAAA
1 GCAATAAAATGCAAA
25240359 G
1 G
25240360 GATCACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (15 bp):
GCAATAAAATGCAAA
Found at i:25253694 original size:21 final size:21
Alignment explanation
Indices: 25253643--25253705 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
25253633 AATCACCATA
*
25253643 AATCAGATGCATTCACAACAC
1 AATCAGATGCATCCACAACAC
** * * *
25253664 ACCCAAATGCATCCACACCAG
1 AATCAGATGCATCCACAACAC
25253685 AATCAGATGCAGT-CACAACAC
1 AATCAGATGCA-TCCACAACAC
25253706 TCTTCAATGC
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.41, C:0.33, G:0.11, T:0.14
Consensus pattern (21 bp):
AATCAGATGCATCCACAACAC
Found at i:25278738 original size:23 final size:23
Alignment explanation
Indices: 25278712--25278757 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
25278702 AATGAAAAAT
*
25278712 CAAAA-AGAAAAGATGAGTAGAGA
1 CAAAAGAGAAAAAATGAGT-GAGA
25278735 CAAAAGAGAAAAAATGAGTGAGA
1 CAAAAGAGAAAAAATGAGTGAGA
25278758 AAGTATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.61, C:0.04, G:0.26, T:0.09
Consensus pattern (23 bp):
CAAAAGAGAAAAAATGAGTGAGA
Found at i:25284071 original size:12 final size:12
Alignment explanation
Indices: 25284054--25284090 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
25284044 TTTATAGAGC
25284054 ATAAAATAAAAG
1 ATAAAATAAAAG
*
25284066 ATAAAATAAAAT
1 ATAAAATAAAAG
*
25284078 AGAAAATAAAAG
1 ATAAAATAAAAG
25284090 A
1 A
25284091 AAATGTTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:25284076 original size:17 final size:17
Alignment explanation
Indices: 25284054--25284094 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
25284044 TTTATAGAGC
25284054 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
25284071 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
*
25284088 AGAAAAT
1 ATAAAAT
25284095 GTTGAGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:25290047 original size:17 final size:17
Alignment explanation
Indices: 25290025--25290061 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
25290015 GTGTTATGAT
*
25290025 TTGGTAGAAAGGGTAAG
1 TTGGTAAAAAGGGTAAG
25290042 TTGGTAAAAAGGGTAAG
1 TTGGTAAAAAGGGTAAG
25290059 TTG
1 TTG
25290062 AGTCCACGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (17 bp):
TTGGTAAAAAGGGTAAG
Found at i:25291780 original size:71 final size:71
Alignment explanation
Indices: 25291700--25291851 Score: 277
Period size: 71 Copynumber: 2.1 Consensus size: 71
25291690 ACCCATGTTT
* * *
25291700 GTATCGGTAGAAGTACAGGGTACGAGAGAGGTTGTTTATTGACTTGAGTTGTATTGGTAGATGCA
1 GTATCGGTAGAAGTACAGGGTACGAGAGAGGTTGTTCATTGACTTGAGTTGTATCGGTAGAGGCA
25291765 TGATAA
66 TGATAA
25291771 GTATCGGTAGAAGTACAGGGTACGAGAGAGGTTGTTCATTGACTTGAGTTGTATCGGTAGAGGCA
1 GTATCGGTAGAAGTACAGGGTACGAGAGAGGTTGTTCATTGACTTGAGTTGTATCGGTAGAGGCA
25291836 TGATAA
66 TGATAA
25291842 GTATCGGTAG
1 GTATCGGTAG
25291852 TTCAATTCAT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.28, C:0.09, G:0.34, T:0.30
Consensus pattern (71 bp):
GTATCGGTAGAAGTACAGGGTACGAGAGAGGTTGTTCATTGACTTGAGTTGTATCGGTAGAGGCA
TGATAA
Found at i:25294390 original size:37 final size:38
Alignment explanation
Indices: 25294359--25294438 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
25294349 AATATTTTTG
25294359 AATTGCACCTAAAACTATCGCTGCATAAATATTCTTCA
1 AATTGCACCTAAAACTATCGCTGCATAAATATTCTTCA
* ** **
25294397 AATTGCATCTTGAACTATCGCTGCATAAGCATTCTT-A
1 AATTGCACCTAAAACTATCGCTGCATAAATATTCTTCA
25294434 AATTG
1 AATTG
25294439 TATCTAGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 6 0.16
38 31 0.84
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (38 bp):
AATTGCACCTAAAACTATCGCTGCATAAATATTCTTCA
Done.