Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 71 of 91
Found at i:25583766 original size:27 final size:27
Alignment explanation
Indices: 25583729--25583810 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
25583719 TTTTTATTTT
25583729 ATTT-TTT-AAATATTTATAATTTATA
1 ATTTATTTAAAATATTTATAATTTATA
* * *
25583754 ATTTATTTAAAATATTAATAATTGATC
1 ATTTATTTAAAATATTTATAATTTATA
** *
25583781 ATTTAAATATTAATATTT-T-ATTTATA
1 ATTTATTTA-AAATATTTATAATTTATA
25583807 ATTT
1 ATTT
25583811 GATCATTAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
25 4 0.09
26 12 0.27
27 23 0.51
28 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (27 bp):
ATTTATTTAAAATATTTATAATTTATA
Found at i:25583802 original size:42 final size:42
Alignment explanation
Indices: 25583755--25583854 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
25583745 TAATTTATAA
* *
25583755 TTTATTTAAAATATTAATAATTGATCATT-T-AAATATTAATAT
1 TTTATTTATAAT-TTAATAATT-AACATTATAAAATATTAATAT
* *
25583797 TTTATTTATAATTTGATCATTAACATTATAAAATATTAATAT
1 TTTATTTATAATTTAATAATTAACATTATAAAATATTAATAT
25583839 TTTATTTATAATTTAA
1 TTTATTTATAATTTAA
25583855 ATATTATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 5 0.10
41 8 0.16
42 38 0.75
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (42 bp):
TTTATTTATAATTTAATAATTAACATTATAAAATATTAATAT
Found at i:25583884 original size:52 final size:51
Alignment explanation
Indices: 25583827--25584102 Score: 152
Period size: 48 Copynumber: 5.7 Consensus size: 51
25583817 TAACATTATA
*
25583827 AAATATTAATATTTTATTTATAATTTAAATATTATTATGATTATTTATTTTT
1 AAATATTAATATTTTATTTATAATTTAAATATTATTAT-ATTATTGATTTTT
* * * *
25583879 AAATA-TAAGTA----ATTTATAATTT-GATCATTA-TATTAATAATTGATAATTA
1 AAATATTAA-TATTTTATTTATAATTTAAAT-ATTATTA-T-ATTATTGAT-TTTT
* *
25583928 AAATATTAATATTTTA-TTAT-ATTTTAATCATTA--ATA-T-TT-A----A
1 AAATATTAATATTTTATTTATAATTTAAAT-ATTATTATATTATTGATTTTT
* *
25583969 AAAAATTAATATTTTATTTATACA-TTAAATATTATTATGATTATTAATTTTT
1 AAATATTAATATTTTATTTATA-ATTTAAATATTATTAT-ATTATTGATTTTT
* *
25584021 AAATATTAATAATTTATAATT-T-ATTTAAATATCA--ATA--ATTGATTATTT
1 AAATATTAAT-ATTT-TATTTATAATTTAAATATTATTATATTATTGATT-TTT
* *
25584069 ACATATTAATATTTTATTTATAATTTAATTATTA
1 AAATATTAATATTTTATTTATAATTTAAATATTA
25584103 ATATTTGAGG
Statistics
Matches: 176, Mismatches: 19, Indels: 62
0.68 0.07 0.24
Matches are distributed among these distances:
41 16 0.09
42 8 0.05
43 5 0.03
44 3 0.02
45 1 0.01
46 6 0.03
47 19 0.11
48 46 0.26
49 11 0.06
50 6 0.03
51 9 0.05
52 36 0.20
53 6 0.03
54 4 0.02
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (51 bp):
AAATATTAATATTTTATTTATAATTTAAATATTATTATATTATTGATTTTT
Found at i:25584006 original size:300 final size:296
Alignment explanation
Indices: 25583418--25584013 Score: 796
Period size: 300 Copynumber: 2.0 Consensus size: 296
25583408 TATATATATA
25583418 ATTTATATTTTATTTTTTAAATATCAATAATTTATAATTTATTTAAAATATGAATAATTAAAAAT
1 ATTTATATTTTATTTTTTAAATATCAATAATTTATAATTTATTTAAAATATGAATAATTAAAAAT
* * * *
25583483 TTAAATGTTAATATTTTATTTATAATTTAATCCTTAGCATTATATAATATCAATATTTTATTATA
66 TTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATATCAATATTTTATTATA
*
25583548 ATTTAAATGTTATTATGATTATTTTTATATAATTTTTTAAATATTAATAATTTATAATTTATTTC
131 ATTTAAATATTATTATGATTA---TTATATAATTTTTTAAATATTAATAATTTATAATTTA-TTC
* *
25583613 AAATATTAATAATTGATAATTGAAATAATATTTTATAATTTAATAATTAACATTATAAAATATTA
192 AAATATTAATAATTGATAATTAAAATAATATTTTATAATTTAATAATTAACATTATAAAAAATTA
*
25583678 ATATTTTATTATAATTTAAATGTTATTATGATTATTTTTT
257 ATATTTTATTATAATTTAAATATTATTATGATTATTTTTT
* ** * * **
25583718 ATTTTTATTTTATTTTTTAAATATTTATAATTTATAATTTATTTAAAATATTAATAATTGATCAT
1 ATTTATATTTTATTTTTTAAATATCAATAATTTATAATTTATTTAAAATATGAATAATTAAAAAT
* *
25583783 TTAAATATTAATATTTTATTTATAATTTGATCATTAACATTATAAAATATTAATATTTTATTTAT
66 TTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATATCAATATTTTA-TTAT
25583848 AATTTAAATATTATTATGATTA-T-T-T-A-TTTTTAAATA-TAAGTAATTTATAATTTGA-TCA
130 AATTTAAATATTATTATGATTATTATATAATTTTTTAAATATTAA-TAATTTATAATTT-ATTCA
* * *
25583906 TTATATTAATAATTGATAATTAAAATATTAATATTTTATTATATTTTAATCATTAATATT-TAAA
193 -AATATTAATAATTGATAATT-AAA-A-TAATATTTTA-TA-A-TTTAATAATTAACATTAT-AA
25583970 AAAATTAATATTTTATTTATACA-TTAAATATTATTATGATTATT
250 AAAATTAATATTTTA-TTATA-ATTTAAATATTATTATGATTATT
25584014 AATTTTTAAA
Statistics
Matches: 263, Mismatches: 20, Indels: 26
0.85 0.06 0.08
Matches are distributed among these distances:
292 6 0.02
293 42 0.16
294 4 0.02
295 2 0.01
296 11 0.04
297 3 0.01
298 2 0.01
299 30 0.11
300 137 0.52
301 26 0.10
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (296 bp):
ATTTATATTTTATTTTTTAAATATCAATAATTTATAATTTATTTAAAATATGAATAATTAAAAAT
TTAAATATTAATATTTTATTTATAATTTAATCATTAACATTATAAAATATCAATATTTTATTATA
ATTTAAATATTATTATGATTATTATATAATTTTTTAAATATTAATAATTTATAATTTATTCAAAT
ATTAATAATTGATAATTAAAATAATATTTTATAATTTAATAATTAACATTATAAAAAATTAATAT
TTTATTATAATTTAAATATTATTATGATTATTTTTT
Found at i:25584047 original size:26 final size:26
Alignment explanation
Indices: 25584018--25584069 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
25584008 ATTATTAATT
* *
25584018 TTTAAATATTAATAATTTATAATTTA
1 TTTAAATATCAATAATTGATAATTTA
*
25584044 TTTAAATATCAATAATTGATTATTTA
1 TTTAAATATCAATAATTGATAATTTA
25584070 CATATTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTAAATATCAATAATTGATAATTTA
Found at i:25584090 original size:142 final size:143
Alignment explanation
Indices: 25583731--25584108 Score: 545
Period size: 142 Copynumber: 2.7 Consensus size: 143
25583721 TTTATTTTAT
* *
25583731 TTTTTAAATATTTATAATTTATAATTTATTTAAAATATTAATAATTGATCATTTAAATATTAATA
1 TTTTTAAATATTAATAATTTATAATTTATTT-AAATATTAATAATTGATAATTTAAATATTAATA
* * *
25583796 TTTTATTTATAATTTGATCATTAACA-TTATAAAATATTAATATTTTATTTATAATTTAAATATT
65 TTTTATTTATAATTTAATCATTAATATTTATAAAAAATTAATATTTTATTTATAATTTAAATATT
*
25583860 ATTATGATTATTTA
130 ATTATGATTATTAA
*
25583874 TTTTTAAATA-TAAGTAATTTATAATTTGATCATT--ATATTAATAATTGATAATTAAAATATTA
1 TTTTTAAATATTAA-TAATTTATAATTT-AT--TTAAATATTAATAATTGATAATTTAAATATTA
*
25583936 ATATTTTA-TTATATTTTAATCATTAATATTTA-AAAAAATTAATATTTTATTTATACA-TTAAA
62 ATATTTTATTTATAATTTAATCATTAATATTTATAAAAAATTAATATTTTATTTATA-ATTTAAA
25583998 TATTATTATGATTATTAA
126 TATTATTATGATTATTAA
* * *
25584016 TTTTTAAATATTAATAATTTATAATTTATTTAAATATCAATAATTGATTATTTACATATTAATAT
1 TTTTTAAATATTAATAATTTATAATTTATTTAAATATTAATAATTGATAATTTAAATATTAATAT
*
25584081 TTTATTTATAATTTAATTATTAATATTT
66 TTTATTTATAATTTAATCATTAATATTT
25584109 GAGGGTTGTA
Statistics
Matches: 211, Mismatches: 14, Indels: 21
0.86 0.06 0.09
Matches are distributed among these distances:
139 2 0.01
141 34 0.16
142 107 0.51
143 64 0.30
144 2 0.01
146 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (143 bp):
TTTTTAAATATTAATAATTTATAATTTATTTAAATATTAATAATTGATAATTTAAATATTAATAT
TTTATTTATAATTTAATCATTAATATTTATAAAAAATTAATATTTTATTTATAATTTAAATATTA
TTATGATTATTAA
Found at i:25595836 original size:14 final size:14
Alignment explanation
Indices: 25595817--25595860 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
25595807 CTTTCTTCTC
25595817 TTTTCTTCTATTAA
1 TTTTCTTCTATTAA
*
25595831 TTTTCTTC---T-C
1 TTTTCTTCTATTAA
25595841 TTTTCTTCTATTAA
1 TTTTCTTCTATTAA
25595855 TTTTCT
1 TTTTCT
25595861 AACAATCTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 8 0.33
11 1 0.04
13 1 0.04
14 14 0.58
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTCTTCTATTAA
Found at i:25595840 original size:24 final size:24
Alignment explanation
Indices: 25595808--25595860 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
25595798 TCAAGCCTAC
25595808 TTTCTTCTCTTTTCTTCTATTAAT
1 TTTCTTCTCTTTTCTTCTATTAAT
25595832 TTTCTTCTCTTTTCTTCTATTAAT
1 TTTCTTCTCTTTTCTTCTATTAAT
25595856 TTTCT
1 TTTCT
25595861 AACAATCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTCTTCTCTTTTCTTCTATTAAT
Found at i:25597659 original size:213 final size:213
Alignment explanation
Indices: 25597276--25597661 Score: 457
Period size: 213 Copynumber: 1.8 Consensus size: 213
25597266 TTTTTATTAA
* *
25597276 AATTGAAAAAATATCTAAATCATGTATAAAGAATGATTGAGACACAAAAAACAGTGATATTTTGT
1 AATTGAAAAAATATCTAAATCATGTATAAAGAATGATTGAGACACAAAAAACAGTAATATGTTGT
* * * *
25597341 TAAAAAGCATAACAAAAAATATAAAAATACCAAAAAGTAGATAAATACATGTTTTTAATTTACTA
66 TAAAAAGCATAACAAAAAATACAAAAATACCAAAAAATAGATAAATACATGTTTTCAATTTAATA
* *
25597406 TAGAGTAAAATACTAAAAAACATCTGTTAAAAAAATATAAAATAATTATAATACCTTCTATAAGT
131 AAGAGTAAAATACTAAAAAACACCTGTTAAAAAAATATAAAATAATTATAATACCTTCTATAAGT
25597471 GAGGATCATGATGGTTTT
196 GAGGATCATGATGGTTTT
* * *
25597489 AATTGAAAAAATAT-TCAAATCATG-AGTAAGGAATGACTATGCA-ATACATAAAACAGTAATAT
1 AATTGAAAAAATATCT-AAATCATGTA-TAAAGAATGA-T-TG-AGACACAAAAAACAGTAATAT
* * *
25597551 GTTGTT-AAAAGCAT-A-AAAAAATACCAAAATACCAAAAAAATATTGA-CAATCACGTGTTTTC
61 GTTGTTAAAAAGCATAACAAAAAATACAAAAATACC-AAAAAATA--GATAAAT-ACATGTTTTC
* * * * *
25597612 CATTTAATAAATAGTAGAATAC-AAAAAGCACCTGTT-AAAAGATATAAAAT
122 AATTTAATAAAGAGTAAAATACTAAAAAACACCTGTTAAAAAAATATAAAAT
25597662 TACTATAAAA
Statistics
Matches: 145, Mismatches: 19, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
212 18 0.12
213 52 0.36
214 24 0.17
215 50 0.34
216 1 0.01
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (213 bp):
AATTGAAAAAATATCTAAATCATGTATAAAGAATGATTGAGACACAAAAAACAGTAATATGTTGT
TAAAAAGCATAACAAAAAATACAAAAATACCAAAAAATAGATAAATACATGTTTTCAATTTAATA
AAGAGTAAAATACTAAAAAACACCTGTTAAAAAAATATAAAATAATTATAATACCTTCTATAAGT
GAGGATCATGATGGTTTT
Found at i:25608538 original size:12 final size:12
Alignment explanation
Indices: 25608521--25608546 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25608511 AGCATCTGAT
25608521 TCACTACCAGAA
1 TCACTACCAGAA
25608533 TCACTACCAGAA
1 TCACTACCAGAA
25608545 TC
1 TC
25608547 TGATTCTGAA
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:0.38, C:0.35, G:0.08, T:0.19
Consensus pattern (12 bp):
TCACTACCAGAA
Found at i:25612444 original size:2 final size:2
Alignment explanation
Indices: 25612437--25612468 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25612427 GCGAGCAAAA
25612437 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25612469 TAGACGCTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25612527 original size:49 final size:48
Alignment explanation
Indices: 25612453--25612548 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 48
25612443 AGAGAGAGAG
25612453 AGAGAGAGAGAGAGAGTAGACGCTGATGATGATGGGCTCCGCTCTCGT
1 AGAGAGAGAGAGAGAGTAGACGCTGATGATGATGGGCTCCGCTCTCGT
25612501 AGNAGAGAGAGAGAGAGTAGACGCTGATGATGATGGGCTCCGCTCTCG
1 AG-AGAGAGAGAGAGAGTAGACGCTGATGATGATGGGCTCCGCTCTCG
25612549 AGTTTGCCTC
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 2 0.04
49 45 0.96
ACGTcount: A:0.27, C:0.17, G:0.38, T:0.18
Consensus pattern (48 bp):
AGAGAGAGAGAGAGAGTAGACGCTGATGATGATGGGCTCCGCTCTCGT
Found at i:25621084 original size:20 final size:19
Alignment explanation
Indices: 25621038--25621086 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
25621028 TCTATTTTTT
25621038 TAACAAAAAATAAAATAAA
1 TAACAAAAAATAAAATAAA
* * *
25621057 AAAGCAAAAATTAAAAGTATA
1 TAA-CAAAAAATAAAA-TAAA
25621078 TAACAAAAA
1 TAACAAAAA
25621087 GAGCCTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.08
20 17 0.71
21 5 0.21
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (19 bp):
TAACAAAAAATAAAATAAA
Found at i:25621531 original size:1 final size:1
Alignment explanation
Indices: 25621527--25621579 Score: 106
Period size: 1 Copynumber: 53.0 Consensus size: 1
25621517 TTAATTTTTT
25621527 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25621580 TTTTATTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25628177 original size:22 final size:24
Alignment explanation
Indices: 25628161--25628205 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
25628151 AATTAAATTT
25628161 TTATTAATTTA-TAATT-AATAAA
1 TTATTAATTTATTAATTAAATAAA
25628183 TTATTAATTTATTAATTAAATAA
1 TTATTAATTTATTAATTAAATAA
25628206 TATCTCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
23 5 0.24
24 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATTAATTTATTAATTAAATAAA
Found at i:25628199 original size:15 final size:16
Alignment explanation
Indices: 25628160--25628206 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
25628150 AAATTAAATT
25628160 TTTATTAATT-TATAA
1 TTTATTAATTATATAA
* *
25628175 TTAATAAATTAT-TAA
1 TTTATTAATTATATAA
*
25628190 TTTATTAATTAAATAA
1 TTTATTAATTATATAA
25628206 T
1 T
25628207 ATCTCAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATTAATTATATAA
Found at i:25631148 original size:20 final size:20
Alignment explanation
Indices: 25631112--25631149 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25631102 TAGATTAGAA
*
25631112 TACTTTCTTATTTTATCATT
1 TACTTTCTTATTATATCATT
25631132 TACTTTACTTA-TATATCA
1 TACTTT-CTTATTATATCA
25631150 AGTATGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (20 bp):
TACTTTCTTATTATATCATT
Found at i:25631498 original size:36 final size:35
Alignment explanation
Indices: 25631426--25631527 Score: 98
Period size: 36 Copynumber: 2.9 Consensus size: 35
25631416 TGATTAAAAC
* * *
25631426 AAGTGAAGTGCTACTTTATGTAGAACCACTAGAAT
1 AAGTGAAGTGCTACTTTATATAAAACAACTAGAAT
* *
25631461 AAGTGAAAGTGCTACTTTATATAAAAGAACTATAAT
1 AAGTG-AAGTGCTACTTTATATAAAACAACTAGAAT
** * *
25631497 AAGT-AGAGCACTACTCTATATGAAACAACTA
1 AAGTGA-AGTGCTACTTTATATAAAACAACTA
25631528 ATACAAGTAG
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
34 1 0.02
35 25 0.45
36 29 0.53
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (35 bp):
AAGTGAAGTGCTACTTTATATAAAACAACTAGAAT
Found at i:25631795 original size:29 final size:29
Alignment explanation
Indices: 25631763--25631896 Score: 135
Period size: 29 Copynumber: 4.6 Consensus size: 29
25631753 ATATACCTTT
25631763 TTCTCTTGTACCTATTCATGTACAGCTTC
1 TTCTCTTGTACCTATTCATGTACAGCTTC
* *
25631792 TTCTTTTGTACCTGTTCATGTACAGCTTC
1 TTCTCTTGTACCTATTCATGTACAGCTTC
* * ** **
25631821 TTCTTTTGTACCTGTTC-TCGTTTAATTTC
1 TTCTCTTGTACCTATTCAT-GTACAGCTTC
* * *
25631850 TTCTCTTGTGCTTATTAATGTACAGCTTC
1 TTCTCTTGTACCTATTCATGTACAGCTTC
* *
25631879 TTCTGTTGTACCTTTTCA
1 TTCTCTTGTACCTATTCA
25631897 CGTGTACCTC
Statistics
Matches: 83, Mismatches: 20, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
28 1 0.01
29 81 0.98
30 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.12, T:0.51
Consensus pattern (29 bp):
TTCTCTTGTACCTATTCATGTACAGCTTC
Found at i:25652394 original size:17 final size:16
Alignment explanation
Indices: 25652352--25652394 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
25652342 TTAATAAAAT
25652352 AAATATTTA-AGTGTA
1 AAATATTTATAGTGTA
*
25652367 AAAGATTTATAGTGTTA
1 AAATATTTATAGTG-TA
*
25652384 AAATATATATA
1 AAATATTTATA
25652395 AATATTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 4 0.17
17 11 0.48
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (16 bp):
AAATATTTATAGTGTA
Found at i:25653359 original size:15 final size:15
Alignment explanation
Indices: 25653301--25653361 Score: 52
Period size: 15 Copynumber: 3.7 Consensus size: 15
25653291 TTAACACCAA
25653301 AAATATTTTACATTT
1 AAATATTTTACATTT
25653316 AAAT-TTTTAGCTTATTAAT
1 AAATATTTTA-C--ATT--T
25653335 AAGTATATTTTACATTT
1 AA--ATATTTTACATTT
25653352 AAATATTTTA
1 AAATATTTTA
25653362 AATATTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
14 5 0.13
15 13 0.34
17 6 0.16
19 6 0.16
21 3 0.08
22 5 0.13
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.52
Consensus pattern (15 bp):
AAATATTTTACATTT
Found at i:25653892 original size:8 final size:8
Alignment explanation
Indices: 25653879--25653905 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
25653869 ACTTCTAAAC
25653879 TATCAAAT
1 TATCAAAT
25653887 TATCAAAT
1 TATCAAAT
25653895 TATCAAAT
1 TATCAAAT
25653903 TAT
1 TAT
25653906 AATTTCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (8 bp):
TATCAAAT
Found at i:25654986 original size:8 final size:8
Alignment explanation
Indices: 25654969--25655006 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
25654959 TATTTTTCAC
25654969 AAAATTAT
1 AAAATTAT
*
25654977 AAAGTTAT
1 AAAATTAT
25654985 AAAATT-T
1 AAAATTAT
25654992 AAAATTAT
1 AAAATTAT
25655000 ATAAATT
1 A-AAATT
25655007 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 7 0.27
8 14 0.54
9 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
AAAATTAT
Found at i:25657562 original size:45 final size:45
Alignment explanation
Indices: 25657468--25657563 Score: 115
Period size: 45 Copynumber: 2.1 Consensus size: 45
25657458 CGTTATAATG
* *
25657468 TTACACGTCATATACAAAAACATGTTACATATCATGAGTAGATTG
1 TTACACGTCATATACAAAAACATGTGACATATCATGAGTAGATTA
* * *
25657513 TTACATGTCATATACAAAAATATGTGACATGA-CATGATTA-AGTTA
1 TTACACGTCATATACAAAAACATGTGACAT-ATCATGAGTAGA-TTA
25657558 TTACAC
1 TTACAC
25657564 ATTATGTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
44 1 0.02
45 41 0.95
46 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (45 bp):
TTACACGTCATATACAAAAACATGTGACATATCATGAGTAGATTA
Found at i:25657653 original size:76 final size:76
Alignment explanation
Indices: 25657513--25657653 Score: 167
Period size: 76 Copynumber: 1.9 Consensus size: 76
25657503 GAGTAGATTG
* * * * **
25657513 TTACATGTCATATACAAAAATATGTGACATGACATGATTAAGTTATTACACATTATGTTGAAAAA
1 TTACACGTCATATACAAAAACATGTGACATGACATAATTAAGTTATTACACATAATGTACAAAAA
25657578 AAATATTGTTA
66 AAATATTGTTA
* * * * *
25657589 TTACACGTCATGTACAAAAACATGAT-ACATGTCATAATTAGGTTGTTACACGTAATGTACAAAA
1 TTACACGTCATATACAAAAACATG-TGACATGACATAATTAAGTTATTACACATAATGTACAAAA
25657653 A
65 A
25657654 TATGTGACAC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
76 52 0.98
77 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.33
Consensus pattern (76 bp):
TTACACGTCATATACAAAAACATGTGACATGACATAATTAAGTTATTACACATAATGTACAAAAA
AAATATTGTTA
Found at i:25657680 original size:45 final size:45
Alignment explanation
Indices: 25657589--25657685 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
25657579 AATATTGTTA
* * * *
25657589 TTACACGTCATGTACAAAAACATGATACATGTCATAATTAGGTTG
1 TTACACGTAATGTACAAAAACATGATACACGTCACAATTAGATTG
* **
25657634 TTACACGTAATGTACAAAAATATG-TGACACGTCACGGTTAGATTG
1 TTACACGTAATGTACAAAAACATGAT-ACACGTCACAATTAGATTG
25657679 TTACACG
1 TTACACG
25657686 CCATGTTGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (45 bp):
TTACACGTAATGTACAAAAACATGATACACGTCACAATTAGATTG
Found at i:25657683 original size:121 final size:120
Alignment explanation
Indices: 25657468--25657728 Score: 308
Period size: 121 Copynumber: 2.2 Consensus size: 120
25657458 CGTTATAATG
* * * *
25657468 TTACACGTCATATACAAAAACATGTTACATATCATGAGTAGATTGTTACATGTCATATACAAAAA
1 TTACACGTCATATACAAAAACATGATACATATCATAAGTAGATTGTTACACGTAATATACAAAAA
* * ** * *
25657533 TATGTGACATGACATGATTAAGTTATTACACATTATGTTGAAAAAAAATATTGTTA
66 TATGTGACACGACACGATTAAGTTATTACACACCATGTTG-AAAAAAATACTATTA
* * * * *
25657589 TTACACGTCATGTACAAAAACATGATACATGTCATAATTAGGTTGTTACACGTAATGTACAAAAA
1 TTACACGTCATATACAAAAACATGATACATATCATAAGTAGATTGTTACACGTAATATACAAAAA
* * * * *
25657654 TATGTGACACGTCACGGTT-AGATTGTTACACGCCATGTTGAAAAAAATACTATTG
66 TATGTGACACGACACGATTAAG-TTATTACACACCATGTTGAAAAAAATACTATTA
*
25657709 TTACATGTCATATACAAAAA
1 TTACACGTCATATACAAAAA
25657729 TGTGTTACAC
Statistics
Matches: 117, Mismatches: 22, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
120 32 0.27
121 85 0.73
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (120 bp):
TTACACGTCATATACAAAAACATGATACATATCATAAGTAGATTGTTACACGTAATATACAAAAA
TATGTGACACGACACGATTAAGTTATTACACACCATGTTGAAAAAAATACTATTA
Found at i:25657791 original size:30 final size:29
Alignment explanation
Indices: 25657676--25657824 Score: 100
Period size: 30 Copynumber: 5.3 Consensus size: 29
25657666 CACGGTTAGA
* *
25657676 TTGTTACACGCCATGTTGAAAAAAATACTA
1 TTGTTACACGCCATGTT-AAAAAAATATTG
* * * *
25657706 TTGTTACATGTCAT-AT-ACAAAA-A-TG
1 TTGTTACACGCCATGTTAAAAAAATATTG
*
25657731 -TGTTACACGCCATGGTT-AAAACA-A--G
1 TTGTTACACGCCAT-GTTAAAAAAATATTG
* **
25657756 TTGTTACATGTTATGTTAAAAAAAATATTG
1 TTGTTACACGCCATGTT-AAAAAAATATTG
* *
25657786 TTGTTATACGCCATGTTGAAAAAATATTG
1 TTGTTACACGCCATGTTAAAAAAATATTG
25657815 TTGTTACACG
1 TTGTTACACG
25657825 TCATATTCAA
Statistics
Matches: 91, Mismatches: 20, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
24 11 0.12
25 5 0.05
26 17 0.19
27 10 0.11
28 1 0.01
29 21 0.23
30 26 0.29
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (29 bp):
TTGTTACACGCCATGTTAAAAAAATATTG
Found at i:25657836 original size:29 final size:29
Alignment explanation
Indices: 25657775--25657837 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
25657765 GTTATGTTAA
* * *
25657775 AAAAAATATTGTTGTTATACGCCATGTTG
1 AAAAAATATTGTTGTTACACGCCATATTC
*
25657804 AAAAAATATTGTTGTTACACGTCATATTC
1 AAAAAATATTGTTGTTACACGCCATATTC
25657833 AAAAA
1 AAAAA
25657838 CATTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (29 bp):
AAAAAATATTGTTGTTACACGCCATATTC
Found at i:25659694 original size:13 final size:13
Alignment explanation
Indices: 25659676--25659708 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
25659666 AATATTCAAG
25659676 AATAAAGACTATC
1 AATAAAGACTATC
*
25659689 ATTAAAGACTATC
1 AATAAAGACTATC
25659702 AATAAAG
1 AATAAAG
25659709 GCTACACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (13 bp):
AATAAAGACTATC
Found at i:25664799 original size:63 final size:62
Alignment explanation
Indices: 25664720--25664841 Score: 149
Period size: 62 Copynumber: 2.0 Consensus size: 62
25664710 TATTACTTAG
* *
25664720 AATATTTTTATCTTTTAACAAAATAAAT-TCTTCAATTTTAAT-AAAGAGTATTTTTTTCATCAT
1 AATATTTTTATCTTTTAACAAAA-AAATCT-TTAAATTTTAATAAAAGA-TATTTTTATCATCAT
* * **
25664783 AATATTTTTGTTTTTTAATTAAAAAATCTTTAAATTTTAATAAAAGATATTTTTATCAT
1 AATATTTTTATCTTTTAACAAAAAAATCTTTAAATTTTAATAAAAGATATTTTTATCAT
25664842 TTACTTATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
62 26 0.51
63 25 0.49
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (62 bp):
AATATTTTTATCTTTTAACAAAAAAATCTTTAAATTTTAATAAAAGATATTTTTATCATCAT
Found at i:25665225 original size:23 final size:22
Alignment explanation
Indices: 25665177--25665231 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
25665167 TTTTATTTAA
* * *
25665177 TTAATTATTAAAGTTTTTAATAT
1 TTAATT-TTAAAATTTTAAAAAT
25665200 TTAATTTTAAAATTTTAAAAATT
1 TTAATTTTAAAATTTTAAAAA-T
25665223 TTAATTTTA
1 TTAATTTTA
25665232 TCCTATAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAATTTTAAAATTTTAAAAAT
Found at i:25673544 original size:3 final size:3
Alignment explanation
Indices: 25673536--25673562 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25673526 CCAAGATACC
25673536 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
25673563 AGAAACACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25696357 original size:27 final size:27
Alignment explanation
Indices: 25696307--25696359 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
25696297 TAAGAATCTA
* * *
25696307 TTTATAATAACTAATTAGACCTAAACC
1 TTTATAATAACCAACTAAACCTAAACC
*
25696334 TTTATAATAACCAACTAAATCTAAAC
1 TTTATAATAACCAACTAAACCTAAAC
25696360 TTACTGCAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (27 bp):
TTTATAATAACCAACTAAACCTAAACC
Found at i:25709975 original size:18 final size:18
Alignment explanation
Indices: 25709952--25709989 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
25709942 CTAGTAACTC
25709952 TTCAATTCCAAAAGACTT
1 TTCAATTCCAAAAGACTT
25709970 TTCAATTCCAAAAGACTT
1 TTCAATTCCAAAAGACTT
25709988 TT
1 TT
25709990 AAGGAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (18 bp):
TTCAATTCCAAAAGACTT
Found at i:25727617 original size:25 final size:24
Alignment explanation
Indices: 25727581--25727635 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
25727571 ATAAAGTAAG
* **
25727581 ATTTATATATTTTTTAAATATATTA
1 ATTTATAAATTTAATAAAT-TATTA
*
25727606 TTTTATAAATTTAATAAATTATTA
1 ATTTATAAATTTAATAAATTATTA
25727630 ATTTAT
1 ATTTAT
25727636 CATGTTAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTATAAATTTAATAAATTATTA
Found at i:25727697 original size:17 final size:17
Alignment explanation
Indices: 25727668--25727702 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25727658 CAATCACAAA
25727668 TATTATTTAATAAAAAT
1 TATTATTTAATAAAAAT
25727685 TATTAATTT-ATAAAAAT
1 TATT-ATTTAATAAAAAT
25727702 T
1 T
25727703 TTACTGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTATTTAATAAAAAT
Found at i:25737455 original size:26 final size:27
Alignment explanation
Indices: 25737419--25737470 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
25737409 TGATATAAAG
25737419 TAAAAATATAAAAATTTAATTGAAATA
1 TAAAAATATAAAAATTTAATTGAAATA
* *
25737446 TAAAAA-ATAAATATTTATTTGAAAT
1 TAAAAATATAAAAATTTAATTGAAAT
25737471 TTTTAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
TAAAAATATAAAAATTTAATTGAAATA
Found at i:25738381 original size:29 final size:26
Alignment explanation
Indices: 25738334--25738390 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 26
25738324 TTATTTAAAA
25738334 TATTTAATAAATTTATATTTGTATTT
1 TATTTAATAAATTTATATTTGTATTT
*
25738360 TATTTAATTAAATTTTTATATTTTTATTT
1 TATTTAA-TAAA--TTTATATTTGTATTT
25738389 TA
1 TA
25738391 AATAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 7 0.26
27 4 0.15
29 16 0.59
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TATTTAATAAATTTATATTTGTATTT
Found at i:25738409 original size:30 final size:29
Alignment explanation
Indices: 25738339--25738432 Score: 111
Period size: 31 Copynumber: 3.2 Consensus size: 29
25738329 TAAAATATTT
* *
25738339 AATAAA-TTTATATTTGTATTTT-ATTTA
1 AATAAATTTTATATTTTTATTTTAAATTA
* *
25738366 ATTAAATTTTTATATTTTTATTTTAAATAA
1 AATAAA-TTTTATATTTTTATTTTAAATTA
25738396 AATAAATTATTATATTTTTTATTTTAAATTA
1 AATAAATT-TTATA-TTTTTATTTTAAATTA
25738427 AATAAA
1 AATAAA
25738433 AGTTTATAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.09
29 17 0.30
30 13 0.23
31 21 0.38
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
AATAAATTTTATATTTTTATTTTAAATTA
Found at i:25738538 original size:33 final size:33
Alignment explanation
Indices: 25738488--25738582 Score: 88
Period size: 33 Copynumber: 2.9 Consensus size: 33
25738478 TTTATATTAC
25738488 ATAA-AATTAA-AATTGATATGATATGTTAAAAT
1 ATAATAATTAATAA-TGATATGATATGTTAAAAT
* * * *
25738520 ATTATTATTAATTATGATATG-TCATGTTAATAT
1 ATAATAATTAATAATGATATGAT-ATGTTAAAAT
** *
25738553 ATAATAATTAATAACAATATGATATATTAA
1 ATAATAATTAATAATGATATGATATGTTAA
25738583 TTTGATACGA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
32 4 0.08
33 43 0.88
34 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.42
Consensus pattern (33 bp):
ATAATAATTAATAATGATATGATATGTTAAAAT
Found at i:25742600 original size:94 final size:94
Alignment explanation
Indices: 25742438--25742627 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 94
25742428 TTCTTTAAGA
*
25742438 ATCCATTTCATGAAACAAGAAAAACTTTGCTTGTCCATTATTTATGTGGTCTCTGACATTCTAGC
1 ATCCATTTCATGAAACAAGAAAAACTTTGCTTGTCCATTATTTATGTGGTCTCTGACATTCTAAC
25742503 AGGCCCTGCAGTTGTCATTGTATATATGG
66 AGGCCCTGCAGTTGTCATTGTATATATGG
*
25742532 ATCCATTTCATGAAACAAGAAAAACTTTGCTTTTCCATTATTTATGTGGTCTCTGACATTCTAAC
1 ATCCATTTCATGAAACAAGAAAAACTTTGCTTGTCCATTATTTATGTGGTCTCTGACATTCTAAC
25742597 AGGCCCTGCAGTTGTCATTGTATATATGG
66 AGGCCCTGCAGTTGTCATTGTATATATGG
25742626 AT
1 AT
25742628 GTATATGATG
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (94 bp):
ATCCATTTCATGAAACAAGAAAAACTTTGCTTGTCCATTATTTATGTGGTCTCTGACATTCTAAC
AGGCCCTGCAGTTGTCATTGTATATATGG
Found at i:25759800 original size:18 final size:18
Alignment explanation
Indices: 25759746--25759818 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 18
25759736 TACGGATACG
25759746 TGTATTCAAACAATTATA
1 TGTATTCAAACAATTATA
* * * * *
25759764 TTTGTTCATACGGA-CATA
1 TGTATTCAAAC-AATTATA
25759782 TGTATTCAAACAATTATA
1 TGTATTCAAACAATTATA
* *
25759800 T-TCATTTAAATAATTATA
1 TGT-ATTCAAACAATTATA
25759818 T
1 T
25759819 ATTTTTTTAA
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
17 2 0.05
18 37 0.93
19 1 0.03
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (18 bp):
TGTATTCAAACAATTATA
Found at i:25759821 original size:20 final size:20
Alignment explanation
Indices: 25759796--25759838 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
25759786 TTCAAACAAT
25759796 TATATTCATTTAAATAATTA
1 TATATTCATTTAAATAATTA
** *
25759816 TATATTTTTTTAAATAGTTA
1 TATATTCATTTAAATAATTA
25759836 TAT
1 TAT
25759839 TTATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TATATTCATTTAAATAATTA
Found at i:25759949 original size:7 final size:7
Alignment explanation
Indices: 25759939--25759965 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25759929 TTTTGAGAGA
25759939 TACAATT
1 TACAATT
25759946 TACAATT
1 TACAATT
25759953 TACAATT
1 TACAATT
25759960 TACAAT
1 TACAAT
25759966 CAGTCTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
TACAATT
Found at i:25766015 original size:13 final size:13
Alignment explanation
Indices: 25765997--25766024 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
25765987 ATGATTGCAA
25765997 AATCAAAGAGAAC
1 AATCAAAGAGAAC
25766010 AATCAAAGAGAAC
1 AATCAAAGAGAAC
25766023 AA
1 AA
25766025 ATTTGGTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.14, G:0.14, T:0.07
Consensus pattern (13 bp):
AATCAAAGAGAAC
Found at i:25773993 original size:134 final size:134
Alignment explanation
Indices: 25773748--25774020 Score: 399
Period size: 134 Copynumber: 2.0 Consensus size: 134
25773738 GCACTTAAGT
*** *
25773748 CACAACATATCACTAAAACTTGTTAGATTGCTTTCAATTAATTTAAAAATGTGCAGAACAGTCTG
1 CACAACATATCACTAAAACTTGTTAGATTGCTTTCAATTAATTTAAAAACACGCAGAACAGTCTA
*
25773813 AAAGCAAGTTTTCACACAGCTATTCTTTAATTCTCATAAATTATTTCATTAAGAAT-GGCTGCTG
66 AAAGCAAGTTTT-ACACAGCTATTCTTTAATTCTCATAAATGATTTCATTAAGAATAGGCTGCTG
25773877 AGGAC
130 AGGAC
* *
25773882 CACAACATATCACTAAAACTTGTTAGATTGGTTTCAATTAATTTAAAAACACGCAGAACAGGCTT
1 CACAACATATCACTAAAACTTGTTAGATTGCTTTCAATTAATTTAAAAACACGCAGAACA-G-TC
* * *
25773947 TAAAAGCAA-TTTT-CACAGCTATTCTTTGATTCTCATCAGATGATTTCATTGAGAATAGGCTGC
64 TAAAAGCAAGTTTTACACAGCTATTCTTTAATTCTCAT-AAATGATTTCATTAAGAATAGGCTGC
25774010 TGAGGAC
128 TGAGGAC
25774017 CACA
1 CACA
25774021 CAGACATTGA
Statistics
Matches: 125, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
133 22 0.18
134 72 0.58
135 22 0.18
136 9 0.07
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (134 bp):
CACAACATATCACTAAAACTTGTTAGATTGCTTTCAATTAATTTAAAAACACGCAGAACAGTCTA
AAAGCAAGTTTTACACAGCTATTCTTTAATTCTCATAAATGATTTCATTAAGAATAGGCTGCTGA
GGAC
Found at i:25774281 original size:20 final size:21
Alignment explanation
Indices: 25774234--25774281 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
25774224 AACAAAAAAA
*
25774234 TATTT-ATTATAATAGTTCAT
1 TATTTAATTAAAATAGTTCAT
* *
25774254 TTTTTAATTAAAATA-TTTAT
1 TATTTAATTAAAATAGTTCAT
25774274 TATTTAAT
1 TATTTAAT
25774282 AATTTATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TATTTAATTAAAATAGTTCAT
Found at i:25774493 original size:24 final size:24
Alignment explanation
Indices: 25774449--25774498 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
25774439 ATTAAAATAC
25774449 AAAAAAATTTATAATTAAAATTTT
1 AAAAAAATTTATAATTAAAATTTT
* *
25774473 AANAAAAATTTAT-TTTTAAATTTT
1 AA-AAAAATTTATAATTAAAATTTT
25774497 AA
1 AA
25774499 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAAAAATTTATAATTAAAATTTT
Found at i:25774508 original size:19 final size:19
Alignment explanation
Indices: 25774479--25774543 Score: 78
Period size: 19 Copynumber: 3.2 Consensus size: 19
25774469 TTTTAANAAA
25774479 AATTT-ATTTTTAAATTTT
1 AATTTAATTTTTAAATTTT
25774497 AATTTAATTTTTAAATTTT
1 AATTTAATTTTTAAATTTT
25774516 AAATATTAACTTTTTATAATTTAT
1 -AAT-TTAA-TTTTTA-AATTT-T
25774540 AATT
1 AATT
25774544 AAAACTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.12
19 13 0.32
20 3 0.07
21 4 0.10
22 7 0.17
23 8 0.20
24 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTAATTTTTAAATTTT
Found at i:25774516 original size:14 final size:14
Alignment explanation
Indices: 25774484--25774543 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 14
25774474 ANAAAAATTT
25774484 ATTTTTAAATTTTA
1 ATTTTTAAATTTTA
*
25774498 A--TTTAATTTTTA
1 ATTTTTAAATTTTA
* *
25774510 AATTTTAAATATTA
1 ATTTTTAAATTTTA
25774524 ACTTTTTATAATTTATA
1 A-TTTTTA-AATTT-TA
25774541 ATT
1 ATT
25774544 AAAACTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
12 11 0.31
14 11 0.31
15 5 0.14
16 6 0.17
17 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTTTAAATTTTA
Found at i:25774581 original size:17 final size:17
Alignment explanation
Indices: 25774556--25774610 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
25774546 AACTTAAACC
*
25774556 TTTTTATTTTATATTCA
1 TTTTAATTTTATATTCA
25774573 TTTTAA--TT-T-TTC-
1 TTTTAATTTTATATTCA
25774585 TTTTAATTTTATATTCA
1 TTTTAATTTTATATTCA
25774602 TTTTAATTT
1 TTTTAATTT
25774611 AGTGAGAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
12 6 0.19
13 3 0.09
14 3 0.09
15 3 0.09
16 3 0.09
17 14 0.44
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAATTTTATATTCA
Found at i:25774587 original size:29 final size:29
Alignment explanation
Indices: 25774555--25774610 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
25774545 AAACTTAAAC
*
25774555 CTTTTTATTTTATATTCATTTTAATTTTT
1 CTTTTAATTTTATATTCATTTTAATTTTT
25774584 CTTTTAATTTTATATTCATTTTAATTT
1 CTTTTAATTTTATATTCATTTTAATTT
25774611 AGTGAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (29 bp):
CTTTTAATTTTATATTCATTTTAATTTTT
Found at i:25785797 original size:2 final size:2
Alignment explanation
Indices: 25785790--25785818 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25785780 AGATTTTCTA
25785790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25785819 ATTATAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25791933 original size:47 final size:47
Alignment explanation
Indices: 25791880--25792043 Score: 283
Period size: 47 Copynumber: 3.5 Consensus size: 47
25791870 ATTTTGTATG
*
25791880 ATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATAATGTAATT
1 ATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATAGTGTAATT
* *
25791927 ATTTTACTTATTTGTTAGGTAAAATTTATGAAATGCATGGTGTAATT
1 ATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATAGTGTAATT
25791974 ATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATAGTGTAATT
1 ATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATAGTGTAATT
* *
25792021 ATTTTAATTATTTGTTAAGTAAA
1 ATTTTACTTATTTGTTAGGTAAA
25792044 CTTGTATGCA
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 110 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.48
Consensus pattern (47 bp):
ATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATAGTGTAATT
Found at i:25797739 original size:15 final size:15
Alignment explanation
Indices: 25797719--25797788 Score: 65
Period size: 15 Copynumber: 4.8 Consensus size: 15
25797709 GATAGGATTA
25797719 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
*
25797734 ATTTAAATTTAAATT
1 ATTTAAATTTAATTT
* **
25797749 ATCT--A-TCCATTGT
1 ATTTAAATTTAATT-T
25797762 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
*
25797777 GTTTAAATTTAA
1 ATTTAAATTTAA
25797789 ATAAGGATTA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
12 3 0.07
13 5 0.12
15 30 0.71
16 4 0.10
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (15 bp):
ATTTAAATTTAATTT
Found at i:25797743 original size:21 final size:21
Alignment explanation
Indices: 25797718--25797837 Score: 77
Period size: 21 Copynumber: 5.7 Consensus size: 21
25797708 AGATAGGATT
25797718 AATTTAAATTTAATTTATTTA
1 AATTTAAATTTAATTTATTTA
* *
25797739 AATTTAAA-TT-ATCTATCCATTG
1 AATTTAAATTTAATTTAT---TTA
* *
25797761 TATTTAAATTTAATTTGTTTA
1 AATTTAAATTTAATTTATTTA
* *
25797782 AATTTAAA--TAAGGATTAATTA
1 AATTTAAATTTAA--TTTATTTA
** *
25797803 TTTTTAAATTTAATTTGTTTA
1 AATTTAAATTTAATTTATTTA
*
25797824 AATTTAAATATAAT
1 AATTTAAATTTAAT
25797838 ATCCTATTTT
Statistics
Matches: 72, Mismatches: 18, Indels: 18
0.67 0.17 0.17
Matches are distributed among these distances:
19 8 0.11
20 2 0.03
21 44 0.61
22 9 0.12
23 5 0.07
24 4 0.06
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (21 bp):
AATTTAAATTTAATTTATTTA
Found at i:25797819 original size:42 final size:42
Alignment explanation
Indices: 25797715--25797833 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 42
25797705 TTGAGATAGG
* * * *
25797715 ATTA-ATTTAAATTTAATTTATTTAAATTTAAATTATCTATCC
1 ATTATATTTAAATTTAATTTGTTTAAATTTAAA-TAACGATCA
* * *
25797757 ATTGTATTTAAATTTAATTTGTTTAAATTTAAATAAGGATTA
1 ATTATATTTAAATTTAATTTGTTTAAATTTAAATAACGATCA
*
25797799 ATTATTTTTAAATTTAATTTGTTTAAATTTAAATA
1 ATTATATTTAAATTTAATTTGTTTAAATTTAAATA
25797834 TAATATCCTA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 40 0.60
43 27 0.40
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (42 bp):
ATTATATTTAAATTTAATTTGTTTAAATTTAAATAACGATCA
Found at i:25803828 original size:7 final size:7
Alignment explanation
Indices: 25803810--25803844 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
25803800 TCTTACATAA
25803810 AAAATTT
1 AAAATTT
25803817 AAAAATTT
1 -AAAATTT
25803825 AAAATTT
1 AAAATTT
25803832 AAAATTT
1 AAAATTT
25803839 AAAATT
1 AAAATT
25803845 AATATAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAAATTT
Found at i:25812277 original size:45 final size:45
Alignment explanation
Indices: 25812213--25812302 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
25812203 CGCAATCGAT
25812213 GCCTATGAACAATCAACCCCAACTTCTTTCACAGGCACAACCTCA
1 GCCTATGAACAATCAACCCCAACTTCTTTCACAGGCACAACCTCA
25812258 GCCTATGAACAATCAACCCCAACTTCTTTCACAGGCACAACCTCA
1 GCCTATGAACAATCAACCCCAACTTCTTTCACAGGCACAACCTCA
25812303 AACACAAGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.38, G:0.09, T:0.20
Consensus pattern (45 bp):
GCCTATGAACAATCAACCCCAACTTCTTTCACAGGCACAACCTCA
Found at i:25816996 original size:2 final size:2
Alignment explanation
Indices: 25816989--25817018 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25816979 GTGGAAGTGA
25816989 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25817019 GTTAGACTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25820967 original size:17 final size:19
Alignment explanation
Indices: 25820935--25820974 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
25820925 ATCATCTGTA
*
25820935 TTTTTCTTCTTCTTT-GTT
1 TTTTTCTTCCTCTTTGGTT
25820953 TTTTTCTTCCT-TTTGGTT
1 TTTTTCTTCCTCTTTGGTT
25820971 TTTT
1 TTTT
25820975 GAATGATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (19 bp):
TTTTTCTTCCTCTTTGGTT
Found at i:25824515 original size:30 final size:30
Alignment explanation
Indices: 25824451--25824515 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
25824441 AATCTAATTT
* * *
25824451 TTATATTTTTATTTTGAGGTAAATAAGTTT
1 TTATATATTTATTTTGAGGTAAATAAGCTC
* * *
25824481 TTATATATTTATTTTGAGTTGAATTAGCTC
1 TTATATATTTATTTTGAGGTAAATAAGCTC
25824511 TTATA
1 TTATA
25824516 AATAATAGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.55
Consensus pattern (30 bp):
TTATATATTTATTTTGAGGTAAATAAGCTC
Found at i:25824842 original size:12 final size:13
Alignment explanation
Indices: 25824819--25824844 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25824809 AAAATAATTG
25824819 AAAGATTTTTTTC
1 AAAGATTTTTTTC
25824832 AAAGATTTTTTTC
1 AAAGATTTTTTTC
25824845 TATTAATCAA
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:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
AAAGATTTTTTTC
Found at i:25825335 original size:76 final size:77
Alignment explanation
Indices: 25825238--25825391 Score: 301
Period size: 76 Copynumber: 2.0 Consensus size: 77
25825228 TTTCAATTAT
25825238 AAAAAAAAATCACCAAACATCAAATTCTAAATATCTTTGTCAC-TTTCAAAATTCAGCTTTATCA
1 AAAAAAAAATCACCAAACATCAAATTCTAAATATCTTTGTCACTTTTCAAAATTCAGCTTTATCA
25825302 TGTTTGAAACGC
66 TGTTTGAAACGC
25825314 AAAAAAAAATCACCAAACATCAAATTCTAAATATCTTTGTCACTTTTCAAAATTCAGCTTTATCA
1 AAAAAAAAATCACCAAACATCAAATTCTAAATATCTTTGTCACTTTTCAAAATTCAGCTTTATCA
25825379 TGTTTGAAACGC
66 TGTTTGAAACGC
25825391 A
1 A
25825392 CCAAGTCTTT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 43 0.56
77 34 0.44
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (77 bp):
AAAAAAAAATCACCAAACATCAAATTCTAAATATCTTTGTCACTTTTCAAAATTCAGCTTTATCA
TGTTTGAAACGC
Found at i:25829559 original size:37 final size:37
Alignment explanation
Indices: 25829517--25829590 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
25829507 AATCAACCTG
* *
25829517 AATATGAATTTTACTATTATATAGTATATATTATATT
1 AATATGAATTTTACTATCATATAATATATATTATATT
25829554 AATATGAATTTTACTATCATATAATATATATTATATT
1 AATATGAATTTTACTATCATATAATATATATTATATT
25829591 CTGTCTCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (37 bp):
AATATGAATTTTACTATCATATAATATATATTATATT
Found at i:25829899 original size:25 final size:26
Alignment explanation
Indices: 25829868--25829997 Score: 113
Period size: 26 Copynumber: 5.1 Consensus size: 26
25829858 AATTTTAATT
*
25829868 ATAATTTTACCACAAGAAGTGGAT-A
1 ATAATTTTACCACTAGAAGTGGATGA
* ** *
25829893 ATAATTTTACTA-TCAGAA-TCTAAGA
1 ATAATTTTACCACT-AGAAGTGGATGA
* *
25829918 ATAATTTTACCATTAGAAGTGGATGG
1 ATAATTTTACCACTAGAAGTGGATGA
** *
25829944 ATAATTTTTTCACTAGAAGTGGATGC
1 ATAATTTTACCACTAGAAGTGGATGA
* * *
25829970 ATAATTTTACTACCAGAAATGGATGA
1 ATAATTTTACCACTAGAAGTGGATGA
25829996 AT
1 AT
25829998 GTTGTAATCC
Statistics
Matches: 81, Mismatches: 20, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
24 2 0.02
25 31 0.38
26 48 0.59
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (26 bp):
ATAATTTTACCACTAGAAGTGGATGA
Found at i:25834759 original size:50 final size:50
Alignment explanation
Indices: 25834697--25834791 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
25834687 AGTCTTAATA
*
25834697 ACGTTGCATGTTATCTGACTTAGTCTTAAA-TGTCCAAAATATTTCCTGAG
1 ACGTTGCATGTTATATGACTTAGTCTTAAACT-TCCAAAATATTTCCTGAG
* *
25834747 ACGTTGCTTGTTATATGACTTAGTCTTAAACTTTCAAAATATTTC
1 ACGTTGCATGTTATATGACTTAGTCTTAAACTTCCAAAATATTTC
25834792 TTAAACGTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 40 0.98
51 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (50 bp):
ACGTTGCATGTTATATGACTTAGTCTTAAACTTCCAAAATATTTCCTGAG
Found at i:25835882 original size:2 final size:2
Alignment explanation
Indices: 25835877--25835914 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25835867 TAAAAAACAG
25835877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25835915 ATAACAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25843225 original size:18 final size:18
Alignment explanation
Indices: 25843202--25843237 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
25843192 ATAAATACTT
25843202 ATTTAAATTTTTTAAATA
1 ATTTAAATTTTTTAAATA
*
25843220 ATTTAATTTTTTTAAATA
1 ATTTAAATTTTTTAAATA
25843238 TTATGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTAAATTTTTTAAATA
Found at i:25847741 original size:2 final size:2
Alignment explanation
Indices: 25847734--25847761 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25847724 AGTTACGTAT
25847734 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25847762 TGAAGTTTCC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25879167 original size:3 final size:3
Alignment explanation
Indices: 25879161--25879190 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25879151 GATGATGATC
25879161 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25879191 GGGAATGCAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25886834 original size:23 final size:23
Alignment explanation
Indices: 25886804--25886849 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
25886794 TAGAATAACA
*
25886804 ATTCCTAATTCTATTAAGATAAG
1 ATTCCTAATTATATTAAGATAAG
*
25886827 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAAGATAAG
25886850 GTTATTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTATATTAAGATAAG
Found at i:25891181 original size:15 final size:16
Alignment explanation
Indices: 25891150--25891182 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25891140 ATGTCGTTAC
25891150 TTTACCTTAACTTTAA
1 TTTACCTTAACTTTAA
*
25891166 TTTACTTTAA-TTTAA
1 TTTACCTTAACTTTAA
25891181 TT
1 TT
25891183 CTGTAGATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTACCTTAACTTTAA
Found at i:25896471 original size:26 final size:25
Alignment explanation
Indices: 25896418--25896471 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
25896408 GTCGGGTGAA
**
25896418 TTTATTATTTTTTTATTTCATTTGT
1 TTTATTATTTTTTTATTTCATTCAT
* *
25896443 TTTATTTTTATTTTTATTTTATTCAT
1 TTTATTATT-TTTTTATTTCATTCAT
25896469 TTT
1 TTT
25896472 GTTGATGCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.78
Consensus pattern (25 bp):
TTTATTATTTTTTTATTTCATTCAT
Found at i:25896769 original size:23 final size:25
Alignment explanation
Indices: 25896734--25896784 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
25896724 AAATTTTCAA
* *
25896734 AAAAATTAGTATTA-AAAAAA-TTC
1 AAAAACTAATATTAGAAAAAATTTC
25896757 AAAAACTAATATTAGAAAAAATTTC
1 AAAAACTAATATTAGAAAAAATTTC
25896782 AAA
1 AAA
25896785 TAATTAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.50
24 6 0.25
25 6 0.25
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
AAAAACTAATATTAGAAAAAATTTC
Found at i:25897089 original size:28 final size:28
Alignment explanation
Indices: 25897057--25897112 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
25897047 GAACAAGTGG
25897057 TTATGTAATACTAATTGGAAAAAGAAAA
1 TTATGTAATACTAATTGGAAAAAGAAAA
*
25897085 TTATGTAATACTATTTGGAAAAAGAAAA
1 TTATGTAATACTAATTGGAAAAAGAAAA
25897113 GTGAAGATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (28 bp):
TTATGTAATACTAATTGGAAAAAGAAAA
Found at i:25905469 original size:30 final size:30
Alignment explanation
Indices: 25905395--25905484 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
25905385 ACTTTGAGGA
** *
25905395 AAATTCAAATAAATTCATATATTTTTATTGT
1 AAATT-AAATAAATTTTTATATTTTTATTTT
* * *
25905426 -GATCAATTAAATTTTTATATTTTTATTTT
1 AAATTAAATAAATTTTTATATTTTTATTTT
25905455 AAATTAAATAAATTTTTATATTTTTATTTT
1 AAATTAAATAAATTTTTATATTTTTATTTT
25905485 GAGTAAAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 21 0.43
30 28 0.57
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (30 bp):
AAATTAAATAAATTTTTATATTTTTATTTT
Found at i:25905491 original size:29 final size:28
Alignment explanation
Indices: 25905401--25905491 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 28
25905391 AGGAAAATTC
** *
25905401 AAATAAATTCATATATTTTTATTGTGAT
1 AAATAAATTTTTATATTTTTATTTTGAT
* *
25905429 CAATTAAATTTTTATATTTTTATTTTAAATT
1 -AAATAAATTTTTATATTTTTATTTT-GA-T
25905460 AAATAAATTTTTATATTTTTATTTTGAGT
1 AAATAAATTTTTATATTTTTATTTTGA-T
25905489 AAA
1 AAA
25905492 AAAAACTCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
29 26 0.50
30 25 0.48
31 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (28 bp):
AAATAAATTTTTATATTTTTATTTTGAT
Found at i:25905837 original size:18 final size:18
Alignment explanation
Indices: 25905803--25905840 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
25905793 ATAATAATAA
25905803 TAAAAATTAAAATTTTTT
1 TAAAAATTAAAATTTTTT
25905821 TAAATAATTAAAATTTTTT
1 TAAA-AATTAAAATTTTTT
25905840 T
1 T
25905841 CAAACGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAAAATTAAAATTTTTT
Found at i:25913809 original size:18 final size:18
Alignment explanation
Indices: 25913786--25913822 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
25913776 ATTATGATAT
25913786 TTTTATAATTGCAAACAA
1 TTTTATAATTGCAAACAA
*
25913804 TTTTATAATTGTAAACAA
1 TTTTATAATTGCAAACAA
25913822 T
1 T
25913823 CAAATTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (18 bp):
TTTTATAATTGCAAACAA
Found at i:25921045 original size:15 final size:17
Alignment explanation
Indices: 25921017--25921050 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
25921007 ATATATTTTG
25921017 TAATATTATAATTAAAA
1 TAATATTATAATTAAAA
25921034 TAATA-TAT-ATTAAAA
1 TAATATTATAATTAAAA
25921049 TA
1 TA
25921051 TTAATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 3 0.18
17 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATATTATAATTAAAA
Found at i:25925714 original size:2 final size:2
Alignment explanation
Indices: 25925707--25925734 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25925697 TGAAATGAGA
25925707 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
25925735 GATGACTACA
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:25928845 original size:4 final size:4
Alignment explanation
Indices: 25928836--25928860 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25928826 CCACCAAATT
25928836 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
25928861 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:25934058 original size:61 final size:62
Alignment explanation
Indices: 25933963--25934086 Score: 214
Period size: 61 Copynumber: 2.0 Consensus size: 62
25933953 ACCGAGTCCA
*
25933963 TCTGATGTTTCTTCATATACACGCATATGAATAAAATATGC-ATTCCCGATACTCACAAATC
1 TCTGATGTTTCTTCATATACACGCATATGAATAAAATATGCAATTCCAGATACTCACAAATC
* *
25934024 TCTGATGTTTCTTCATTTACACGCATATGAATAAAATATGCAATTCCAGATACTCACATATC
1 TCTGATGTTTCTTCATATACACGCATATGAATAAAATATGCAATTCCAGATACTCACAAATC
25934086 T
1 T
25934087 GCCTTCCTGA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
61 40 0.68
62 19 0.32
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.35
Consensus pattern (62 bp):
TCTGATGTTTCTTCATATACACGCATATGAATAAAATATGCAATTCCAGATACTCACAAATC
Found at i:25942014 original size:31 final size:31
Alignment explanation
Indices: 25941975--25942056 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
25941965 TTTGACCCTC
25941975 AGAAGCAGTATTCCCATAAATAAATAAAAAT
1 AGAAGCAGTATTCCCATAAATAAATAAAAAT
* *
25942006 AGAGGCAGTATTTCCATAAATAAATAAAAAT
1 AGAAGCAGTATTCCCATAAATAAATAAAAAT
25942037 AGAAGCAGTATTCCCA-AAAT
1 AGAAGCAGTATTCCCATAAAT
25942057 TCATCATCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 4 0.09
31 43 0.91
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.23
Consensus pattern (31 bp):
AGAAGCAGTATTCCCATAAATAAATAAAAAT
Found at i:25942249 original size:45 final size:45
Alignment explanation
Indices: 25942167--25942255 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
25942157 TTGAGATCCA
*
25942167 AGATTCAACATAGCATCACTAATCAGATCAACAAAAAATAAATTC
1 AGATCCAACATAGCATCACTAATCAGATCAACAAAAAATAAATTC
*
25942212 AGATCCAACATAGCATCACTAGTCCAGATCAACAAAAAATAAAT
1 AGATCCAACATAGCATCACTAAT-CAGATCAACAAAAAATAAAT
25942256 GATGAAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.51, C:0.21, G:0.08, T:0.20
Consensus pattern (45 bp):
AGATCCAACATAGCATCACTAATCAGATCAACAAAAAATAAATTC
Found at i:25943063 original size:2 final size:2
Alignment explanation
Indices: 25943056--25943081 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25943046 GGCGTCCATT
25943056 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
25943082 AACACCTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:25948334 original size:19 final size:19
Alignment explanation
Indices: 25948312--25948368 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
25948302 AAGTTTTGAA
25948312 TTTCCTTTTCTTTTTTTTT
1 TTTCCTTTTCTTTTTTTTT
**
25948331 TTTCCCCCTT-TTTTTTTTT
1 TTT-CCTTTTCTTTTTTTTT
25948350 TTT-CTTTTCACTTTTTTTT
1 TTTCCTTTT--CTTTTTTTT
25948369 GCGCTGGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.10
19 15 0.50
20 12 0.40
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCCTTTTCTTTTTTTTT
Found at i:25948366 original size:24 final size:22
Alignment explanation
Indices: 25948315--25948368 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
25948305 TTTTGAATTT
* *
25948315 CCTTTTCTTTTTTTTTTTTCCC
1 CCTTTTTTTTTTTTTTTTTCCA
*
25948337 CCTTTTTTTTTTTTTTCTTTTCA
1 CCTTTTTTTTTTTTTT-TTTCCA
25948360 -CTTTTTTTT
1 CCTTTTTTTT
25948369 GCGCTGGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
CCTTTTTTTTTTTTTTTTTCCA
Found at i:25948533 original size:16 final size:15
Alignment explanation
Indices: 25948512--25948545 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
25948502 ATGTTATTTC
25948512 TTCTTTGCTTTTTCTT
1 TTCTTTG-TTTTTCTT
*
25948528 TTCTTTGTTTTTTTT
1 TTCTTTGTTTTTCTT
25948543 TTC
1 TTC
25948546 GTTTCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (15 bp):
TTCTTTGTTTTTCTT
Found at i:25962327 original size:17 final size:18
Alignment explanation
Indices: 25962290--25962330 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
25962280 CTCAAATCAG
*
25962290 GCCAAGTAGCCAAGATAA
1 GCCAAATAGCCAAGATAA
25962308 GCCAAATAGCCAAG-TAA
1 GCCAAATAGCCAAGATAA
25962325 GCCAAA
1 GCCAAA
25962331 CATAGGAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (18 bp):
GCCAAATAGCCAAGATAA
Found at i:25963315 original size:27 final size:27
Alignment explanation
Indices: 25963282--25963462 Score: 177
Period size: 27 Copynumber: 6.8 Consensus size: 27
25963272 TTTAACTATT
*
25963282 AGAAGTGGATGGATACCTTTACCCGCC
1 AGAAGTGGATGGATACCTTTACCCACC
* *
25963309 AGGAGTGGATAGATACCTTTACCCACC
1 AGAAGTGGATGGATACCTTTACCCACC
* * *
25963336 AGAAGTAGATGAATA-CTTTACCTACC
1 AGAAGTGGATGGATACCTTTACCCACC
* * **
25963362 AGAAGTAGATGAATA-CTTTACCCATA
1 AGAAGTGGATGGATACCTTTACCCACC
* * * *
25963388 AGAAGTGGTTGTATACTTTTAGCCACC
1 AGAAGTGGATGGATACCTTTACCCACC
* * *
25963415 AGAAGTTGATGGATACTTTTACTCACC
1 AGAAGTGGATGGATACCTTTACCCACC
* *
25963442 AAAAGTGAATGGATACCTTTA
1 AGAAGTGGATGGATACCTTTA
25963463 TCCATCAAGA
Statistics
Matches: 126, Mismatches: 27, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
26 45 0.36
27 81 0.64
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (27 bp):
AGAAGTGGATGGATACCTTTACCCACC
Found at i:25963344 original size:23 final size:25
Alignment explanation
Indices: 25963298--25963385 Score: 104
Period size: 26 Copynumber: 3.4 Consensus size: 25
25963288 GGATGGATAC
* * *
25963298 CTTTACCCGCCAGGAGTGGATAGATA
1 CTTTACCCACCAGAAGTAGATA-ATA
25963324 CCTTTACCCACCAGAAGTAGATGAATA
1 -CTTTACCCACCAGAAGTAGAT-AATA
*
25963351 CTTTACCTACCAGAAGTAGATGAATA
1 CTTTACCCACCAGAAGTAGAT-AATA
25963377 CTTTACCCA
1 CTTTACCCA
25963386 TAAGAAGTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 33 0.60
27 21 0.38
28 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
CTTTACCCACCAGAAGTAGATAATA
Found at i:25963414 original size:79 final size:81
Alignment explanation
Indices: 25963284--25963494 Score: 207
Period size: 79 Copynumber: 2.6 Consensus size: 81
25963274 TAACTATTAG
* * ** * * * * *
25963284 AAGTGGATGGATACCTTTACCCGCCAGGAGTGGATAGATACCTTTACCCACCAGAAGTAGATGAA
1 AAGTGAATGAATACCTTTACCCATCAAGAGTGGTTATATACATTTAGCCACCAGAAGTAGATGAA
*
25963349 TAC-TTTAC-CTACCAG
66 TACTTTTACTC-ACCAA
* * *
25963364 AAGT-AGATGAATA-CTTTACCCAT-AAGAAGTGGTTGTATACTTTTAGCCACCAGAAGTTGATG
1 AAGTGA-ATGAATACCTTTACCCATCAAG-AGTGGTTATATACATTTAGCCACCAGAAGTAGATG
*
25963426 GATACTTTTACTCACCAA
64 AATACTTTTACTCACCAA
* * *
25963444 AAGTGAATGGATACCTTTATCCATCAAGAGTGGTTATGTACATTTAGCCAC
1 AAGTGAATGAATACCTTTACCCATCAAGAGTGGTTATATACATTTAGCCAC
25963495 TAGCCACTAG
Statistics
Matches: 106, Mismatches: 18, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
78 2 0.02
79 41 0.39
80 29 0.27
81 31 0.29
82 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (81 bp):
AAGTGAATGAATACCTTTACCCATCAAGAGTGGTTATATACATTTAGCCACCAGAAGTAGATGAA
TACTTTTACTCACCAA
Found at i:25963628 original size:27 final size:27
Alignment explanation
Indices: 25963598--25963713 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 27
25963588 TTTACCAATT
*
25963598 AGAAGTAAATGGAAACATTTACCCACC
1 AGAAGTAAATGGAAACTTTTACCCACC
** * * **
25963625 AGAAGTGGATGGATACTTTTACTCATG
1 AGAAGTAAATGGAAACTTTTACCCACC
* * *
25963652 AGAAGTAGAT-GAATACCTTCACCCACC
1 AGAAGTAAATGGAA-ACTTTTACCCACC
* * * *
25963679 AAAAGTGAATGGATACTTTTACCTACC
1 AGAAGTAAATGGAAACTTTTACCCACC
25963706 AGAAGTAA
1 AGAAGTAA
25963714 GGGATGAACA
Statistics
Matches: 64, Mismatches: 23, Indels: 4
0.70 0.25 0.04
Matches are distributed among these distances:
26 2 0.03
27 60 0.94
28 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (27 bp):
AGAAGTAAATGGAAACTTTTACCCACC
Found at i:25963646 original size:54 final size:53
Alignment explanation
Indices: 25963519--25963701 Score: 165
Period size: 54 Copynumber: 3.4 Consensus size: 53
25963509 GGATGGATGC
* * * * *
25963519 AAGTTGATGGATATCTTTTCCCACTT-GAAGTGAATGGGTAACTTTACCCACCAA
1 AAGTGGATGGATA-CTTTTACCAATTAGAAGTAAAT-GGAAACTTTACCCACCAA
* ** * *
25963573 AAGTGGCTGCTTACCTTTACCAATTAGAAGTAAATGGAAACATTTACCCACCAG
1 AAGTGGATGGATACTTTTACCAATTAGAAGTAAATGGAAAC-TTTACCCACCAA
* * *
25963627 AAGTGGATGGATACTTTTACTC-ATGAGAAGTAGAT-GAATACCTTCACCCACCAA
1 AAGTGGATGGATACTTTTAC-CAATTAGAAGTAAATGGAA-A-CTTTACCCACCAA
*
25963681 AAGTGAATGGATACTTTTACC
1 AAGTGGATGGATACTTTTACC
25963702 TACCAGAAGT
Statistics
Matches: 105, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
53 18 0.17
54 85 0.81
55 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (53 bp):
AAGTGGATGGATACTTTTACCAATTAGAAGTAAATGGAAACTTTACCCACCAA
Found at i:25968137 original size:2 final size:2
Alignment explanation
Indices: 25968130--25968184 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
25968120 ATCTGAATAT
25968130 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
25968172 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
25968185 TAACTTAGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:25968220 original size:44 final size:43
Alignment explanation
Indices: 25968171--25968258 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 43
25968161 CTCTCTCTCT
25968171 CTCTCTCTCTCTCTTAACTTAGTTTAACGAATTAAGTTGCTAA
1 CTCTCTCTCTCTCTTAACTTAGTTTAACGAATTAAGTTGCTAA
* *
25968214 CNTCTCTCTCTCTCTTAACTTAGTTTAACGGATTATGTTGCTAA
1 C-TCTCTCTCTCTCTTAACTTAGTTTAACGAATTAAGTTGCTAA
25968258 C
1 C
25968259 CTAGAGTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.42
Consensus pattern (43 bp):
CTCTCTCTCTCTCTTAACTTAGTTTAACGAATTAAGTTGCTAA
Found at i:25971538 original size:28 final size:28
Alignment explanation
Indices: 25971491--25971544 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
25971481 ATATGCACTG
*
25971491 CACTATTTTTCTTAATTAAGGTTTTTCC
1 CACTATTTTTCTTAATTAAGATTTTTCC
*
25971519 CACTAGTTTTTCTTGA-TAAGATTTTT
1 CACTA-TTTTTCTTAATTAAGATTTTT
25971545 AATGAGGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.22, C:0.15, G:0.09, T:0.54
Consensus pattern (28 bp):
CACTATTTTTCTTAATTAAGATTTTTCC
Found at i:25972577 original size:25 final size:24
Alignment explanation
Indices: 25972529--25972579 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
25972519 AATAAAATAT
*
25972529 ATAATATAAGAATTAAAAATTAAA
1 ATAAAATAAGAATTAAAAATTAAA
25972553 ATAAAATAA-AATATAAGAAATTAAA
1 ATAAAATAAGAAT-TAA-AAATTAAA
25972578 AT
1 AT
25972580 TTATATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 3 0.12
24 11 0.46
25 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (24 bp):
ATAAAATAAGAATTAAAAATTAAA
Found at i:25972579 original size:31 final size:33
Alignment explanation
Indices: 25972513--25972692 Score: 115
Period size: 33 Copynumber: 5.5 Consensus size: 33
25972503 GTAATGTTAT
25972513 AATTAAAATAAAATATATAATATAAGAATTAAA
1 AATTAAAATAAAATATATAATATAAGAATTAAA
25972546 AATTAAAATAAAATA-A-AATATAAGAAATT-AA
1 AATTAAAATAAAATATATAATATAAG-AATTAAA
* * ** *
25972577 AATT--TATATAATATA-GGTAAAAGAAATT-AA
1 AATTAAAATAAAATATATAATATAAG-AATTAAA
* * * * *
25972607 AATATAATATATAATATAAAAAATTAG-ATTAAAGA
1 AAT-TAAAATAAAATATATAATATAAGAATT-AA-A
* * ** *
25972642 AATGAAAATAAAATATATAATATTATTATAAAA
1 AATTAAAATAAAATATATAATATAAGAATTAAA
*
25972675 AATAAAAATAAAATATAT
1 AATTAAAATAAAATATAT
25972693 GACATTAAAA
Statistics
Matches: 119, Mismatches: 18, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
29 7 0.06
30 16 0.13
31 15 0.13
32 8 0.07
33 44 0.37
34 23 0.19
35 6 0.05
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (33 bp):
AATTAAAATAAAATATATAATATAAGAATTAAA
Found at i:25990971 original size:4 final size:4
Alignment explanation
Indices: 25990964--25990990 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
25990954 CACATACAAA
25990964 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
25990991 ACCTTTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:25991935 original size:2 final size:2
Alignment explanation
Indices: 25991928--25991979 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
25991918 GTTTGTTTAC
25991928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25991970 AT AT AT AT AT
1 AT AT AT AT AT
25991980 NTATCAATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25992845 original size:30 final size:28
Alignment explanation
Indices: 25992772--25992846 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 28
25992762 TTAATAAAAT
*
25992772 TTAAATAAATTATTAT-TTTTTATTACG
1 TTAAATAAATTTTTATATTTTTATTACG
* *
25992799 TTCAATCAAATCTTTATATTTTTATTTTA-G
1 TTAAAT-AAATTTTTATATTTTTA--TTACG
25992829 ATTAAATAAATTTTTATA
1 -TTAAATAAATTTTTATA
25992847 GTTAATAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.13
28 8 0.21
29 6 0.16
30 11 0.29
31 8 0.21
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (28 bp):
TTAAATAAATTTTTATATTTTTATTACG
Found at i:25998859 original size:13 final size:13
Alignment explanation
Indices: 25998841--25998865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25998831 TAATAACAAA
25998841 AAATTAAATTAAT
1 AAATTAAATTAAT
25998854 AAATTAAATTAA
1 AAATTAAATTAA
25998866 ATTTATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTAAATTAAT
Found at i:25998864 original size:18 final size:16
Alignment explanation
Indices: 25998838--25998886 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 16
25998828 TATTAATAAC
25998838 AAAAAATTAAATTAAT
1 AAAAAATTAAATTAAT
*
25998854 AAATTAAATTAAATTTAT
1 AAA--AAATTAAATTAAT
*
25998872 AAAAAAATAAATTAA
1 AAAAAATTAAATTAA
25998887 AATTTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 13 0.46
18 15 0.54
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAATTAAATTAAT
Found at i:25999423 original size:91 final size:90
Alignment explanation
Indices: 25999267--25999442 Score: 210
Period size: 91 Copynumber: 1.9 Consensus size: 90
25999257 CTCTCAAGTT
* * * *
25999267 TTGGTGTTATTTTGTTTTCATCATCTTCAAGTTTAAAAAAAATTTCAATTATTAGGTTTTGATTT
1 TTGGTATTATTTTGTTTTCATCATCTTCAAGTTTAAAAAAAATTTAAATGATTAGGTTTTAATTT
* *
25999332 TTGGTTTTAGCAAATCAGGTATATCA
66 TTAGTTGTAGCAAATC-GGTATATCA
* * * ** * *
25999358 TTGGTATTATTTTGTTTTTATCATTTTTAAGCTTT-AAAAGGATTTAAATGGTTAGTTTTTAATT
1 TTGGTATTATTTTGTTTTCATCATCTTCAAG-TTTAAAAAAAATTTAAATGATTAGGTTTTAATT
25999422 TTTAGTTGTAGCAAATCGGTA
65 TTTAGTTGTAGCAAATCGGTA
25999443 ATTGACTTGA
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
90 4 0.06
91 64 0.90
92 3 0.04
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (90 bp):
TTGGTATTATTTTGTTTTCATCATCTTCAAGTTTAAAAAAAATTTAAATGATTAGGTTTTAATTT
TTAGTTGTAGCAAATCGGTATATCA
Found at i:25999782 original size:28 final size:28
Alignment explanation
Indices: 25999712--25999765 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
25999702 TTTACCCATC
* **
25999712 AGGAGTAGATGAATGCTTTTAACTCAAT
1 AGGAATAGATGAATATTTTTAACTCAAT
25999740 AGGAATAGATGAATATTTTTAACTCA
1 AGGAATAGATGAATATTTTTAACTCA
25999766 CTAGAAGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (28 bp):
AGGAATAGATGAATATTTTTAACTCAAT
Found at i:26003787 original size:12 final size:12
Alignment explanation
Indices: 26003770--26003796 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
26003760 GGTCATGGAA
26003770 AAAAAAAGAAAG
1 AAAAAAAGAAAG
26003782 AAAAAAAGAAAG
1 AAAAAAAGAAAG
26003794 AAA
1 AAA
26003797 GAAATAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:26003793 original size:16 final size:15
Alignment explanation
Indices: 26003768--26003800 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
26003758 AAGGTCATGG
26003768 AAAAAAAAAGAAAGA
1 AAAAAAAAAGAAAGA
26003783 AAAAAAGAAAGAAAGA
1 AAAAAA-AAAGAAAGA
26003799 AA
1 AA
26003801 TAATCTCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAGA
Found at i:26009418 original size:21 final size:21
Alignment explanation
Indices: 26009392--26009434 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
26009382 GTCTCCCACT
26009392 AAGGCTAGATTTGCTTCAGTC
1 AAGGCTAGATTTGCTTCAGTC
26009413 AAGGCTAGATTTGCTTCAGTC
1 AAGGCTAGATTTGCTTCAGTC
26009434 A
1 A
26009435 CTTCAGCTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (21 bp):
AAGGCTAGATTTGCTTCAGTC
Found at i:26015369 original size:6 final size:6
Alignment explanation
Indices: 26015358--26015387 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
26015348 CTTCCTTCAC
26015358 ATCAAA ATCAAA ATCAAA ATCAAA ATCAAA
1 ATCAAA ATCAAA ATCAAA ATCAAA ATCAAA
26015388 TTGAATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ATCAAA
Found at i:26015820 original size:4 final size:4
Alignment explanation
Indices: 26015811--26015835 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
26015801 TCTGGACATT
26015811 TGCG TGCG TGCG TGCG TGCG TGCG T
1 TGCG TGCG TGCG TGCG TGCG TGCG T
26015836 TTGTCACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.48, T:0.28
Consensus pattern (4 bp):
TGCG
Found at i:26022628 original size:34 final size:34
Alignment explanation
Indices: 26022585--26022687 Score: 197
Period size: 34 Copynumber: 3.0 Consensus size: 34
26022575 TCCCACACTT
*
26022585 AAAATAAATTAAAAGAAACCATTACATATGGTAC
1 AAAAAAAATTAAAAGAAACCATTACATATGGTAC
26022619 AAAAAAAATTAAAAGAAACCATTACATATGGTAC
1 AAAAAAAATTAAAAGAAACCATTACATATGGTAC
26022653 AAAAAAAATTAAAAGAAACCATTACATATGGTAC
1 AAAAAAAATTAAAAGAAACCATTACATATGGTAC
26022687 A
1 A
26022688 GACTTCCTTA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (34 bp):
AAAAAAAATTAAAAGAAACCATTACATATGGTAC
Found at i:26025332 original size:2 final size:2
Alignment explanation
Indices: 26025327--26025365 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
26025317 ATATATCCNT
26025327 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26025366 ATAAAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26074954 original size:34 final size:32
Alignment explanation
Indices: 26074887--26074960 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 32
26074877 AAAAAAATTT
26074887 AATATTTTTTATTATTTAGATAAATTATCAAAA
1 AATATTTTTTATTATTTAGATAAATTATC-AAA
** *
26074920 AATATTTTTTATTATTTAGATTATTTTATGAAA
1 AATATTTTTTATTATTTAGA-TAAATTATCAAA
26074953 AATATTTT
1 AATATTTT
26074961 CTAGTGGAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 31 0.84
34 6 0.16
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (32 bp):
AATATTTTTTATTATTTAGATAAATTATCAAA
Found at i:26075410 original size:41 final size:36
Alignment explanation
Indices: 26075365--26075445 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 36
26075355 TTCATTAAAA
*
26075365 AATATTTTTTAATTTTAATAATATTGTATAATTTAAATATT
1 AATA-TTTTT-ATTTT-ATAATATT-T-TAAGTTAAATATT
*
26075406 AATATTTTTATTTTTTAATATTTTAAGTTAAATATT
1 AATATTTTTATTTTATAATATTTTAAGTTAAATATT
26075442 AATA
1 AATA
26075446 GTCATCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
36 16 0.42
37 1 0.03
38 7 0.18
39 5 0.13
40 5 0.13
41 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (36 bp):
AATATTTTTATTTTATAATATTTTAAGTTAAATATT
Found at i:26078346 original size:22 final size:23
Alignment explanation
Indices: 26078321--26078368 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
26078311 AAAAATATAT
*
26078321 AACA-CTACACGTCATGTACAAA
1 AACAGCTACACGCCATGTACAAA
*
26078343 AACATGTTACACGCCATGTACAAA
1 AACA-GCTACACGCCATGTACAAA
26078367 AA
1 AA
26078369 TATGTAACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
24 18 0.82
ACGTcount: A:0.46, C:0.25, G:0.10, T:0.19
Consensus pattern (23 bp):
AACAGCTACACGCCATGTACAAA
Found at i:26078353 original size:24 final size:24
Alignment explanation
Indices: 26078326--26078384 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
26078316 TATATAACAC
*
26078326 TACACGTCATGTACAAAAACATGT
1 TACACGACATGTACAAAAACATGT
* *
26078350 TACACGCCATGTACAAAAATATGT
1 TACACGACATGTACAAAAACATGT
*
26078374 AACACGACATG
1 TACACGACATG
26078385 GTTAGGTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (24 bp):
TACACGACATGTACAAAAACATGT
Done.