Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold244
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: 271570
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 1 of 2
Found at i:292 original size:16 final size:16
Alignment explanation
Indices: 273--366 Score: 79
Period size: 16 Copynumber: 5.9 Consensus size: 16
263 AATTTGGATA
273 TAAAATAATTTAAATT
1 TAAAATAATTTAAATT
289 T-AAATAATTT--A-T
1 TAAAATAATTTAAATT
*
301 TAAAATTAAAATTACAATT
1 TAAAA-T-AATTTA-AATT
** *
320 TAACTTAATTTAAATA
1 TAAAATAATTTAAATT
*
336 TAAAATTATTTAAATT
1 TAAAATAATTTAAATT
*
352 TAAATTAATTTAAAT
1 TAAAATAATTTAAAT
367 AATTAATTCA
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
12 2 0.03
13 4 0.07
14 1 0.02
15 13 0.22
16 29 0.48
17 5 0.08
18 2 0.03
19 4 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATAATTTAAATT
Found at i:351 original size:22 final size:22
Alignment explanation
Indices: 270--356 Score: 67
Period size: 22 Copynumber: 4.1 Consensus size: 22
260 CAAAATTTGG
*
270 ATATAAAATAATTTAAATTT-A
1 ATATAAAATTATTTAAATTTAA
* * *
291 A-AT-AATTTATTAAAATTAAA
1 ATATAAAATTATTTAAATTTAA
* *
311 AT-TACAATTTAACTT-AATTTAA
1 ATATA-AAATT-ATTTAAATTTAA
333 ATATAAAATTATTTAAATTTAA
1 ATATAAAATTATTTAAATTTAA
355 AT
1 AT
357 TAATTTAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 13
0.69 0.12 0.18
Matches are distributed among these distances:
19 11 0.22
20 5 0.10
21 4 0.08
22 26 0.52
23 4 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAAAATTATTTAAATTTAA
Found at i:423 original size:17 final size:17
Alignment explanation
Indices: 403--454 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
393 AATTTTATTT
403 TAAAAATATTAATTTAA
1 TAAAAATATTAATTTAA
*
420 TAAAAATAATAATTATAA
1 TAAAAATATTAATT-TAA
* *
438 CATAAATTATTAATTTA
1 TA-AAAATATTAATTTA
455 TTTTAATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 13 0.45
18 6 0.21
19 10 0.34
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAAATATTAATTTAA
Found at i:8435 original size:19 final size:19
Alignment explanation
Indices: 8411--8447 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8401 TGATCATAAT
8411 CAAAAGTCAACAAAAAAGA
1 CAAAAGTCAACAAAAAAGA
*
8430 CAAAAGTCAACAATAAAG
1 CAAAAGTCAACAAAAAAG
8448 TGGACTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.16, G:0.11, T:0.08
Consensus pattern (19 bp):
CAAAAGTCAACAAAAAAGA
Found at i:9384 original size:72 final size:72
Alignment explanation
Indices: 9299--9493 Score: 261
Period size: 69 Copynumber: 2.8 Consensus size: 72
9289 ACTATTGAAG
* *
9299 TAAGCTTAAATCCTAGTGTTTAGAGTTTAGATTACATGATTTTGATGTAAGATCTGATGATTCAA
1 TAAGCTTAAATCCTAGTGTTTAGAGTTGAGATTACATGATTTTGAAGTAAGATCTGATGATTCAA
9364 GTTAAAA
66 GTTAAAA
* * * * * *
9371 TAAGCCTAAATCCTTGTGTTTAGAGTTGAAATTACATGA--TT-AAATAGGATTTGATGATTCAA
1 TAAGCTTAAATCCTAGTGTTTAGAGTTGAGATTACATGATTTTGAAGTAAGATCTGATGATTCAA
9433 GTTAAAA
66 GTTAAAA
* * * *
9440 TGAGCTTAGATCCTAGTGTTTAGAATTGAGATTACATGATTTTGAGGTAAGATC
1 TAAGCTTAAATCCTAGTGTTTAGAGTTGAGATTACATGATTTTGAAGTAAGATC
9494 ACACTCCTCA
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
69 57 0.56
70 2 0.02
71 2 0.02
72 41 0.40
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.37
Consensus pattern (72 bp):
TAAGCTTAAATCCTAGTGTTTAGAGTTGAGATTACATGATTTTGAAGTAAGATCTGATGATTCAA
GTTAAAA
Found at i:11008 original size:28 final size:28
Alignment explanation
Indices: 10952--11008 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
10942 TTTTACTTAA
10952 CTTTTATTTACTTATTTATTATTTTTTC
1 CTTTTATTTACTTATTTATTATTTTTTC
* * *
10980 CTTTTTTTTGCTT-TTTTTTATTTTATTC
1 CTTTTATTTACTTATTTATTATTTT-TTC
11008 C
1 C
11009 CTTCCATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.74
Consensus pattern (28 bp):
CTTTTATTTACTTATTTATTATTTTTTC
Found at i:19821 original size:41 final size:41
Alignment explanation
Indices: 19764--19845 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
19754 TGGTTGGACC
19764 ACAACATACTATGTGCATGTCGTTACTGTCGAACTGAGGTT
1 ACAACATACTATGTGCATGTCGTTACTGTCGAACTGAGGTT
19805 ACAACATACTATGTGCATGTCGTTACTGTCGAACTGAGGTT
1 ACAACATACTATGTGCATGTCGTTACTGTCGAACTGAGGTT
19846 GGGCTCTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (41 bp):
ACAACATACTATGTGCATGTCGTTACTGTCGAACTGAGGTT
Found at i:20942 original size:2 final size:2
Alignment explanation
Indices: 20870--20926 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
20860 CCAGCAATAC
20870 TA TA 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 TA TA
20912 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
20927 TCCATGCTCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21985 original size:2 final size:2
Alignment explanation
Indices: 21973--22029 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
21963 CAGGATTGCA
* * * * * * *
21973 AT AT GT AT AT AT AT AT AT AT AT AT GT GT GT GT AT GT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22015 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
22030 ATGGGGGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23292 original size:17 final size:19
Alignment explanation
Indices: 23270--23311 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
23260 AAAACACAAC
23270 ATAAAAA-A-ATAAATATA
1 ATAAAAATATATAAATATA
23287 ATAAAAATATATAAATATA
1 ATAAAAATATATAAATATA
*
23306 TTAAAA
1 ATAAAA
23312 TATGTACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 14 0.64
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAAAAATATATAAATATA
Found at i:24877 original size:2 final size:2
Alignment explanation
Indices: 24870--24907 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
24860 TACTCTATTC
*
24870 CT CT CT CT CT CT CT CT CT CT CT CT AT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
24908 ATATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:24879 original size:14 final size:15
Alignment explanation
Indices: 24862--24909 Score: 66
Period size: 14 Copynumber: 3.4 Consensus size: 15
24852 TGCATCAGTA
24862 CTCTATTC-CTCTCT
1 CTCTATTCTCTCTCT
*
24876 CTCT-CTCTCTCTCT
1 CTCTATTCTCTCTCT
24890 CTCTA-TCTCTCTCT
1 CTCTATTCTCTCTCT
24904 CTCTAT
1 CTCTAT
24910 ATATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.07
14 28 0.93
ACGTcount: A:0.06, C:0.44, G:0.00, T:0.50
Consensus pattern (15 bp):
CTCTATTCTCTCTCT
Found at i:29277 original size:17 final size:17
Alignment explanation
Indices: 29236--29277 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
29226 AACCAAAAAA
*
29236 AAAAAAAGAAAATGTGT
1 AAAAAAATAAAATGTGT
*
29253 AAATAAATAAAATAGTG-
1 AAAAAAATAAAAT-GTGT
29270 AAAAAAAT
1 AAAAAAAT
29278 GAAGTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (17 bp):
AAAAAAATAAAATGTGT
Found at i:29718 original size:10 final size:10
Alignment explanation
Indices: 29703--29734 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
29693 TAGCTTTGTC
*
29703 TTGTTTTATT
1 TTGTTTCATT
29713 TTGTTTCATT
1 TTGTTTCATT
29723 TTGTTTCATT
1 TTGTTTCATT
29733 TT
1 TT
29735 AATTCGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.75
Consensus pattern (10 bp):
TTGTTTCATT
Found at i:29724 original size:15 final size:15
Alignment explanation
Indices: 29720--29765 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
29710 ATTTTGTTTC
29720 ATTTTGTTTCATTTT
1 ATTTTGTTTCATTTT
* *
29735 AATTCGTTTCATTTT
1 ATTTTGTTTCATTTT
29750 ATTTTGTCTT-ATTTT
1 ATTTTGT-TTCATTTT
29765 A
1 A
29766 CTTGAAACCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 24 0.92
16 2 0.08
ACGTcount: A:0.17, C:0.09, G:0.07, T:0.67
Consensus pattern (15 bp):
ATTTTGTTTCATTTT
Found at i:35984 original size:302 final size:302
Alignment explanation
Indices: 35356--36565 Score: 2095
Period size: 302 Copynumber: 4.0 Consensus size: 302
35346 GATTTTGAAG
* * *
35356 CTCCAACAGCTTTTTTCCATCTCAATAAAGTCTAAATAGCTAAAAATTACTCTCAAGTTATAAAT
1 CTCCAATAGCTTTTTTCCATCTCAATCAAGTCTAAATAGCTAAAAATTACTCTCAAGCTATAAAT
* *
35421 AAGTATATCCAACACTTTCATATGTAAAGGCATCAAGAAAACATCAATAGAAATATCATTTATAA
66 AAGTATATCCAACACTTCCATACGTAAAGGCATCAAGAAAACATCAATAGAAATATCATTTATAA
*
35486 AAATAGAAGATCATAGTCATATTTATTCATGTGTCACAATCTTTTAAGGATTTTTTTCATTATTC
131 AAATAGAAGATCATAGTCATATTTATTCATGTGTCACAATCTTTTAAGAATTTTTTTCATTATTC
*
35551 TAAGTTTATAATTCCTATCATTCTTAAATTTTTTTG-TTTTTTACATTTGTTTAGCCATTTTTTA
196 TAAGTTTATAATTCCTATCATTCTTAAATTCTTTTGTTTTTTTACATTTGTTTAGCCATTTTTTA
*
35615 TTGATCTTAAACCTCATAAATACTTAATCTTTTAGAGATTCT
261 TTGATCTTAAACCTCATAAACACTTAATCTTTTAGAGATTCT
** * * *
35657 CTTTAATGGCTTTTTTCCATCTCAATCAAGTTTAAATAACTAAAAATTACTCTCAAGCTATAAAT
1 CTCCAATAGCTTTTTTCCATCTCAATCAAGTCTAAATAGCTAAAAATTACTCTCAAGCTATAAAT
*
35722 AAGTATATCCAACACTTCCATACGTAAAGGCATTAAGAAAACATCAATAGAAATATCATTTATAA
66 AAGTATATCCAACACTTCCATACGTAAAGGCATCAAGAAAACATCAATAGAAATATCATTTATAA
*
35787 AAATAGAAAATCATAGTCATATTTATTCATGTGTCACAATCTTTTAAGAATTTTTTTTCATTATT
131 AAATAGAAGATCATAGTCATATTTATTCATGTGTCACAATCTTTTAAGAA-TTTTTTTCATTATT
35852 CTAAGTTTATAATTCCTATCATTCTTAAATTCTTTTG-TTTTTTACATTTGTTTAGCCATTTTTT
195 CTAAGTTTATAATTCCTATCATTCTTAAATTCTTTTGTTTTTTTACATTTGTTTAGCCATTTTTT
*
35916 ATTGATCTTAAACGTCATAAACACTTAATCTTTTAGAGATTCT
260 ATTGATCTTAAACCTCATAAACACTTAATCTTTTAGAGATTCT
35959 CTCCAATAGCTTTTTTCCATCTCAATCAAGTCTAAATAGCTAAAAATTACTCTCAAGCTATAAAT
1 CTCCAATAGCTTTTTTCCATCTCAATCAAGTCTAAATAGCTAAAAATTACTCTCAAGCTATAAAT
* *
36024 AAGTATATCCAACACTTTCATACATAAAGGCATCAAGAAAACATCAATAGAAATATCATTTATAA
66 AAGTATATCCAACACTTCCATACGTAAAGGCATCAAGAAAACATCAATAGAAATATCATTTATAA
*
36089 AAATAGAAGATCATAGTCATATTTATTCATTTGTCACAATCTTTTAAGAA-TTTTTTCATTATTC
131 AAATAGAAGATCATAGTCATATTTATTCATGTGTCACAATCTTTTAAGAATTTTTTTCATTATTC
** *
36153 TAAGTTTATAATTCCTATCATTCTTAAATTCTTTTGTTTTTTTACATTTGTTTAGCCGCTTTTTG
196 TAAGTTTATAATTCCTATCATTCTTAAATTCTTTTGTTTTTTTACATTTGTTTAGCCATTTTTTA
36218 TTGATCTTAAACCTCATAAACACTTAATCTTTTAGA-ATTCT
261 TTGATCTTAAACCTCATAAACACTTAATCTTTTAGAGATTCT
* * *
36259 GTCCAATGGTTTTTTTTTTCCATCTCAATCAAGTCTAAATAGCTAAAAATTACTCTCAAGCTATA
1 CTCCAATAG---CTTTTTTCCATCTCAATCAAGTCTAAATAGCTAAAAATTACTCTCAAGCTATA
*
36324 AATAAGTATATCCAACACTTCCATACGTAAAGGCATCAAGAAAACATCAATAGAAATATCAATTA
63 AATAAGTATATCCAACACTTCCATACGTAAAGGCATCAAGAAAACATCAATAGAAATATCATTTA
36389 TAAAAATAGAAGATCATAGTCATATTTATTCATGTGTCACAATCTTTTAAGAATTTTTTTCATTA
128 TAAAAATAGAAGATCATAGTCATATTTATTCATGTGTCACAATCTTTTAAGAATTTTTTTCATTA
*
36454 TTCTAAGTTTATAATTCCTATCATTCTTAAATTCTTTTGTTTTTTTATATTTGTTTAGCCATTTT
193 TTCTAAGTTTATAATTCCTATCATTCTTAAATTCTTTTGTTTTTTTACATTTGTTTAGCCATTTT
* *
36519 TTGTTGAGCTTAAACCTCATAAACACTTAATCTTTTAGAGATTCT
258 TTATTGATCTTAAACCTCATAAACACTTAATCTTTTAGAGATTCT
36564 CT
1 CT
36566 TTGTTTAAAC
Statistics
Matches: 860, Mismatches: 42, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
300 62 0.07
301 227 0.26
302 288 0.33
303 166 0.19
304 111 0.13
305 6 0.01
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (302 bp):
CTCCAATAGCTTTTTTCCATCTCAATCAAGTCTAAATAGCTAAAAATTACTCTCAAGCTATAAAT
AAGTATATCCAACACTTCCATACGTAAAGGCATCAAGAAAACATCAATAGAAATATCATTTATAA
AAATAGAAGATCATAGTCATATTTATTCATGTGTCACAATCTTTTAAGAATTTTTTTCATTATTC
TAAGTTTATAATTCCTATCATTCTTAAATTCTTTTGTTTTTTTACATTTGTTTAGCCATTTTTTA
TTGATCTTAAACCTCATAAACACTTAATCTTTTAGAGATTCT
Found at i:38196 original size:28 final size:29
Alignment explanation
Indices: 38140--38210 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
38130 GCAAGTTTTG
*
38140 AAATGATAATTTTTTAATATTATTAAATTAA
1 AAATAATAA-TTTTTAATATTATTAAATT-A
38171 AAATAATAATTTTTAATATTA-T-AATTA
1 AAATAATAATTTTTAATATTATTAAATTA
38198 AAA-AATAATTTTT
1 AAATAATAATTTTT
38211 TTAATCATCT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 10 0.26
27 4 0.10
28 4 0.10
29 1 0.03
30 12 0.31
31 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (29 bp):
AAATAATAATTTTTAATATTATTAAATTA
Found at i:38211 original size:28 final size:29
Alignment explanation
Indices: 38145--38215 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
38135 TTTTGAAATG
38145 ATAA-TTTTTTAATATTATTAAATTAAAA
1 ATAATTTTTTTAATATTATTAAATTAAAA
*
38173 ATAATAATTTTTAATATTA-T-AATTAAAAA
1 ATAAT-TTTTTTAATATTATTAAATT-AAAA
38202 ATAATTTTTTTAAT
1 ATAATTTTTTTAAT
38216 CATCTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 16 0.42
29 10 0.26
30 12 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAATTTTTTTAATATTATTAAATTAAAA
Found at i:40359 original size:22 final size:25
Alignment explanation
Indices: 40310--40363 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
40300 TTTTTTTATC
40310 AAATTAGATTAAATTAAATTTAAATTT
1 AAATTAGATTAAATTAAATTT--ATTT
40337 AAATTA-ATT-AATTAAATTT-TTT
1 AAATTAGATTAAATTAAATTTATTT
40359 AAATT
1 AAATT
40364 CGAATCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 8 0.30
25 10 0.37
26 3 0.11
27 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
AAATTAGATTAAATTAAATTTATTT
Found at i:42265 original size:2 final size:2
Alignment explanation
Indices: 42258--42285 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42248 TTGCAAAGAT
42258 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
42286 AGTGATCTTA
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):
TA
Found at i:43091 original size:22 final size:22
Alignment explanation
Indices: 43038--43093 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
43028 AATTAAATTA
** *
43038 AATTATATTATTTATTGGGTGTC
1 AATTA-ATTATTTATTAAGTATC
* *
43061 ACTTTATTATTTATTAAGTATC
1 AATTAATTATTTATTAAGTATC
43083 AATTAATTATT
1 AATTAATTATT
43094 AGTTATATAG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (22 bp):
AATTAATTATTTATTAAGTATC
Found at i:46945 original size:28 final size:28
Alignment explanation
Indices: 46909--46982 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
46899 AAAAAAAAAT
* **
46909 CGGGATTGGAGTATCCTTTCGAAAATAA
1 CGGGGTTGGAGTATCCCCTCGAAAATAA
** *
46937 CGGGGTTGGAGTATCCCCTCGGGAGTAA
1 CGGGGTTGGAGTATCCCCTCGAAAATAA
46965 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
46983 GATGAGATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAA
Found at i:46993 original size:28 final size:29
Alignment explanation
Indices: 46933--47013 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 29
46923 CCTTTCGAAA
*
46933 ATAACGGGGTTGGAGTATCCCC--TCGGG
1 ATAACGGGGTTGGAGTATCCCCGATCGAG
46960 AGTAACGGGGTTGGAGTATCCCCGAT-GAG
1 A-TAACGGGGTTGGAGTATCCCCGATCGAG
* * *
46989 ATAACGAGGTTTGAGTATCCTCGAT
1 ATAACGGGGTTGGAGTATCCCCGAT
47014 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 1 0.02
28 42 0.89
29 3 0.06
30 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (29 bp):
ATAACGGGGTTGGAGTATCCCCGATCGAG
Found at i:47060 original size:52 final size:51
Alignment explanation
Indices: 46996--47218 Score: 241
Period size: 52 Copynumber: 4.3 Consensus size: 51
46986 GAGATAACGA
* * * * *
46996 GGTTTGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAACCGG
** * *
47048 AATTGGAGTATCCCCGATTAAAG-GAAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT---GTGAAAAATTAGTGTTTTGGAAATAAAACCGG
* *
47101 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * **
47153 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGG
47204 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
47219 TCGGAAATAA
Statistics
Matches: 145, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.01
51 38 0.26
52 61 0.42
53 33 0.23
54 11 0.08
55 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:47119 original size:105 final size:103
Alignment explanation
Indices: 46996--47218 Score: 259
Period size: 105 Copynumber: 2.1 Consensus size: 103
46986 GAGATAACGA
* * * * * *
46996 GGTTTGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATC
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTTAGAAATAAAACCGGAATTGGAGTATC
*** *
47060 CCCGATTAAAGGAAAAATTGGTGTTTTGAAAATAAAACCGG
65 CCCGATT--AGGAAAAATCAATATTTTGAAAATAAAACCGG
* **
47101 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAATTGGAGTATCC
* * **
47166 CCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
66 CCGATTAGGAAAAATCAATATTTTGAAAATAAAACCGG
47204 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
47219 TCGGAAATAA
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
103 39 0.39
105 51 0.51
106 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (103 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAATTGGAGTATCC
CCGATTAGGAAAAATCAATATTTTGAAAATAAAACCGG
Found at i:47236 original size:28 final size:28
Alignment explanation
Indices: 47201--47273 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 28
47191 GAAATAAAGT
47201 CGGGGTTGGAGTATCCCCTCG-GAAATAA
1 CGGGGTTGGAGTATCCCCTCGAG-AATAA
*
47229 CGGGGTTGGAGTAT--CCTCGATGATTAA
1 CGGGGTTGGAGTATCCCCTCGA-GAATAA
47256 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
47274 GATTGTGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 5 0.12
27 18 0.45
28 15 0.38
29 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGAGAATAA
Found at i:49767 original size:13 final size:13
Alignment explanation
Indices: 49749--49774 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49739 ACAAAGATCC
49749 ATGTATCGATACA
1 ATGTATCGATACA
49762 ATGTATCGATACA
1 ATGTATCGATACA
49775 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:49771 original size:33 final size:33
Alignment explanation
Indices: 49728--49794 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
49718 AAAATTTTCA
* ***
49728 AATGTTTCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
49761 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
49794 A
1 A
49795 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:49838 original size:19 final size:18
Alignment explanation
Indices: 49814--49879 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
49804 CAGTAGCTAA
49814 TTATGTATCGATACAATAC
1 TTATGTATCGATAC-ATAC
49833 TTATGTATCGATAC--A-
1 TTATGTATCGATACATAC
49848 -T-TGTATCGATACATAAC
1 TTATGTATCGATACAT-AC
49865 TTATGTATCGATACA
1 TTATGTATCGATACA
49880 AATTGTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.27
14 1 0.02
16 2 0.05
18 1 0.02
19 26 0.63
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
TTATGTATCGATACATAC
Found at i:49854 original size:13 final size:13
Alignment explanation
Indices: 49836--49861 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49826 ACAATACTTA
49836 TGTATCGATACAT
1 TGTATCGATACAT
49849 TGTATCGATACAT
1 TGTATCGATACAT
49862 AACTTATGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:49858 original size:32 final size:32
Alignment explanation
Indices: 49817--49879 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
49807 TAGCTAATTA
49817 TGTATCGATACA-ATACTTATGTATCGATACAT
1 TGTATCGATACATA-ACTTATGTATCGATACAT
49849 TGTATCGATACATAACTTATGTATCGATACA
1 TGTATCGATACATAACTTATGTATCGATACA
49880 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAACTTATGTATCGATACAT
Found at i:50158 original size:21 final size:21
Alignment explanation
Indices: 50128--50171 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
50118 AAGGGAGCCC
* * *
50128 TTCTTTATTTTGTTATATAGA
1 TTCTTAATTTTATTACATAGA
50149 TTCTTAATTTTATTACATAGA
1 TTCTTAATTTTATTACATAGA
50170 TT
1 TT
50172 TATTATATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (21 bp):
TTCTTAATTTTATTACATAGA
Found at i:50256 original size:21 final size:21
Alignment explanation
Indices: 50232--50271 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
50222 TTTATCAGTA
*
50232 ATTCTATTTCATTTATATTAT
1 ATTCTATATCATTTATATTAT
*
50253 ATTCTATATCATTTCTATT
1 ATTCTATATCATTTATATT
50272 CTATAGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTCTATATCATTTATATTAT
Found at i:53211 original size:23 final size:22
Alignment explanation
Indices: 53166--53209 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
53156 TAACCCATTC
*
53166 ATATTTTTTTTTATTTTTAAAT
1 ATATTTTTTTTAATTTTTAAAT
53188 ATATTTTTAATTTAATTTTTAA
1 ATATTTTT--TTTAATTTTTAA
53210 TAGTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
ATATTTTTTTTAATTTTTAAAT
Found at i:54557 original size:2 final size:2
Alignment explanation
Indices: 54550--54574 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54540 AAAGACTAAT
54550 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
54575 GTTTATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56225 original size:2 final size:2
Alignment explanation
Indices: 56218--56260 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
56208 AGGAAAATTA
*
56218 AT AT AT AT AT AT AT AT AT AT AT CT 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
56260 A
1 A
56261 CAAAAAGTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57529 original size:15 final size:15
Alignment explanation
Indices: 57509--57539 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57499 ATTTTCATGC
57509 AAGATCATGTTTAGT
1 AAGATCATGTTTAGT
57524 AAGATCATGTTTAGT
1 AAGATCATGTTTAGT
57539 A
1 A
57540 GAGTTAGAAT
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:0.35, C:0.06, G:0.19, T:0.39
Consensus pattern (15 bp):
AAGATCATGTTTAGT
Found at i:57581 original size:27 final size:27
Alignment explanation
Indices: 57543--57596 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
57533 TTTAGTAGAG
57543 TTAGAATATATAATTATTGAGTTAAGA
1 TTAGAATATATAATTATTGAGTTAAGA
57570 TTAGAATATATAATTATTGAGTTAAGA
1 TTAGAATATATAATTATTGAGTTAAGA
57597 AATCTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (27 bp):
TTAGAATATATAATTATTGAGTTAAGA
Found at i:59101 original size:154 final size:153
Alignment explanation
Indices: 58438--59110 Score: 527
Period size: 154 Copynumber: 4.4 Consensus size: 153
58428 TTTCATATCC
* * * *
58438 TTTAGGATTACTAAAATACTTTCACGTCAAAGGTATATCTTAAGAGCATTTTGGTAA-TTTTCCT
1 TTTAGGATTACTAAGATACTTTCACGTCAAAAGTATACCTTAAGGGCATTTTGGTAATTTTTCC-
* * * * *
58502 TATAACCGAGTCTTAGGTAGCCACCGAGTTGCTTTTATGTCAAAGGTATACGTTTAGGATAGGTT
65 TAGAACCGAGTCTTAGGTAGTCACTGA-TTGCTTTTATGCCAAAGGTATATGTTTAGGATAGGTT
* * *
58567 CATCATTTTATGATATTTTCCTGTCC
129 CATC-TTTTATGATCTTTTCGTGTCT
* ** * * * *
58593 TTTATGATTA-TCGGGATATTTTCATGT-TAAAGATATACTTTAA-GGCATTTTGGTAATTTTTC
1 TTTAGGATTACT-AAGATACTTTCACGTCAAAAG-TATACCTTAAGGGCATTTTGGTAATTTTTC
* * ** * * *
58655 CTAGAGCCAAGTCTTAGGTAGTCACTGGGT-CATTTATGTGCCGAAGGTATATATTTAGGATAGG
64 CTAGAACCGAGTCTTAGGTAGTCACTGATTGC-TTT-TATGCCAAAGGTATATGTTTAGGATAGG
58719 TTCATTCTTTTATGATAC-TTTCGTGTCT
127 TTCA-TCTTTTATGAT-CTTTTCGTGTCT
* * *
58747 TTTAGGGTTA-TCAAGATACTTTCACGTCAAAAGTATACCTTAAGGGTATTTTGATAATTTTT-C
1 TTTAGGATTACT-AAGATACTTTCACGTCAAAAGTATACCTTAAGGGCATTTTGGTAATTTTTCC
** * ** * ** * **
58810 TAGAGTCGAGTCCTAAATAGTCACTAGGTTTTTTTTATGCCAAATGTATA-CATT---ATAGGTT
65 TAGAACCGAGTCTTAGGTAGTCACT-GATTGCTTTTATGCCAAAGGTATATGTTTAGGATAGGTT
* *
58871 TATCCTTTTATGA-CATTTTTGTGTCT
129 CAT-CTTTTATGATC-TTTTCGTGTCT
* **
58897 TTTAAGATTAAC-AAGATACTTTCACGTCAAAAGTATATCC-T-AGAAACATTTTGGTAATTTTT
1 TTTAGGATT-ACTAAGATACTTTCACGTCAAAAGTATA-CCTTAAG-GGCATTTTGGTAATTTTT
* * * * * *
58959 TCTAGAATCGAGTCTGAGGTAATGACCTGATTGCTTTTATGCCAAAGG-ATATGTTTAGAATAGG
63 CCTAGAACCGAGTCTTAGGTAGTCA-CTGATTGCTTTTATGCCAAAGGTATATGTTTAGGATAGG
*
59023 TTCATCGTTTTATGATCTTTTCGTGTTT
127 TTCATC-TTTTATGATCTTTTCGTGTCT
* * * * * * *
59051 TTTAGGGTTACTAGGATACTTTCATGTCGAAAGTATACCATAGGGGCA-TTTGATAATTTT
1 TTTAGGATTACTAAGATACTTTCACGTCAAAAGTATACCTTAAGGGCATTTTGGTAATTTT
59111 CCCATGGCCG
Statistics
Matches: 408, Mismatches: 81, Indels: 60
0.74 0.15 0.11
Matches are distributed among these distances:
148 1 0.00
149 3 0.01
150 76 0.19
151 38 0.09
152 3 0.01
153 22 0.05
154 202 0.50
155 63 0.15
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (153 bp):
TTTAGGATTACTAAGATACTTTCACGTCAAAAGTATACCTTAAGGGCATTTTGGTAATTTTTCCT
AGAACCGAGTCTTAGGTAGTCACTGATTGCTTTTATGCCAAAGGTATATGTTTAGGATAGGTTCA
TCTTTTATGATCTTTTCGTGTCT
Found at i:60392 original size:2 final size:2
Alignment explanation
Indices: 60385--60433 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
60375 GACATATTTG
60385 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
60427 AT AT AT A
1 AT AT AT A
60434 GATAATGATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62223 original size:38 final size:39
Alignment explanation
Indices: 62128--62223 Score: 90
Period size: 44 Copynumber: 2.4 Consensus size: 39
62118 AATAGTTCTT
62128 TTTATTTAAATTTAATTTTAAAAAATATTAATATAAAAA
1 TTTATTTAAATTTAATTTTAAAAAATATTAATATAAAAA
** *
62167 TAATT-TTATAATATTTTAATATTTTTAAAATATTAA-A-AGAAA
1 T--TTATT-TAA-A-TTTAAT-TTTAAAAAATATTAATATAAAAA
62209 TTTATTTAAATTTAA
1 TTTATTTAAATTTAA
62224 ATAAAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
38 5 0.11
39 2 0.04
40 7 0.15
41 7 0.15
42 6 0.13
43 7 0.15
44 13 0.28
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (39 bp):
TTTATTTAAATTTAATTTTAAAAAATATTAATATAAAAA
Found at i:62898 original size:1 final size:1
Alignment explanation
Indices: 62892--62917 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
62882 ATCTATTTAT
62892 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
62918 GCTTCTCACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:68487 original size:6 final size:6
Alignment explanation
Indices: 68476--68545 Score: 56
Period size: 6 Copynumber: 11.3 Consensus size: 6
68466 ATTAAAATTT
* *
68476 ATATAA ATATAA TATCATAA ATATAA TTATAA A-ATAA A-AAATA ATATAA
1 ATATAA ATATAA -AT-ATAA ATATAA ATATAA ATATAA ATATA-A ATATAA
68525 ATAT-A ATATCAA TATATAA AT
1 ATATAA ATAT-AA -ATATAA AT
68546 TATTAAATCT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
5 12 0.23
6 24 0.45
7 9 0.17
8 8 0.15
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:68490 original size:11 final size:11
Alignment explanation
Indices: 68444--68540 Score: 66
Period size: 11 Copynumber: 9.5 Consensus size: 11
68434 AAAAAATTTT
68444 ATATAATATAA
1 ATATAATATAA
68455 AT-T-AT-T-A
1 ATATAATATAA
*
68462 ATATATTA-AA
1 ATATAATATAA
*
68472 AT-TTATATAA
1 ATATAATATAA
*
68482 ATATAATAT-C
1 ATATAATATAA
68492 ATA-AATATAA
1 ATATAATATAA
* *
68502 TTATAAAATAAA
1 ATATAATAT-AA
*
68514 AAATAATATAA
1 ATATAATATAA
*
68525 ATATAATATCA
1 ATATAATATAA
68536 ATATA
1 ATATA
68541 TAAATTATTA
Statistics
Matches: 64, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
7 3 0.05
8 2 0.03
9 11 0.17
10 13 0.20
11 27 0.42
12 8 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAATATAA
Found at i:68746 original size:25 final size:25
Alignment explanation
Indices: 68712--68769 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
68702 TTTAATTCAT
*
68712 TTATTATTT-ATTTTAAATTTAAATA
1 TTATTATTTAAATTT-AATTTAAATA
68737 TTATTATTTAAATTTAATTTAAATA
1 TTATTATTTAAATTTAATTTAAATA
*
68762 ATATTATT
1 TTATTATT
68770 CGAAAGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTATTTAAATTTAATTTAAATA
Found at i:68747 original size:14 final size:14
Alignment explanation
Indices: 68728--68769 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
68718 TTTATTTTAA
68728 ATTTAAATATTATT
1 ATTTAAATATTATT
68742 ATTTAAAT-TTA--
1 ATTTAAATATTATT
*
68753 ATTTAAATAATATT
1 ATTTAAATATTATT
68767 ATT
1 ATT
68770 CGAAAGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 8 0.33
12 2 0.08
13 3 0.12
14 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTAAATATTATT
Found at i:68748 original size:20 final size:22
Alignment explanation
Indices: 68713--68753 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
68703 TTAATTCATT
68713 TATTATTTATTTTAAATTTAAA
1 TATTATTTATTTTAAATTTAAA
68735 TATTA-TTA-TTTAAATTTAA
1 TATTATTTATTTTAAATTTAA
68754 TTTAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTATTTATTTTAAATTTAAA
Found at i:70378 original size:13 final size:13
Alignment explanation
Indices: 70360--70390 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
70350 CTCTCTCATA
70360 TTTCGAGTTAGTT
1 TTTCGAGTTAGTT
70373 TTTCGAGTTAGTT
1 TTTCGAGTTAGTT
70386 TTTCG
1 TTTCG
70391 TTTAATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.23, T:0.55
Consensus pattern (13 bp):
TTTCGAGTTAGTT
Found at i:71562 original size:20 final size:19
Alignment explanation
Indices: 71539--71578 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
71529 GTTAAATGAA
71539 AAATCTTAATCTTAAATTTT
1 AAATCTTAATC-TAAATTTT
* *
71559 AAATTTTAGTCTAAATTTT
1 AAATCTTAATCTAAATTTT
71578 A
1 A
71579 TTTATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (19 bp):
AAATCTTAATCTAAATTTT
Found at i:77872 original size:13 final size:13
Alignment explanation
Indices: 77854--77879 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
77844 TACAGCAAGT
77854 ATGTATCGATACA
1 ATGTATCGATACA
77867 ATGTATCGATACA
1 ATGTATCGATACA
77880 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:80148 original size:21 final size:21
Alignment explanation
Indices: 80115--80159 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
80105 TTGCAAGTTG
*
80115 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
80137 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
80157 AAA
1 AAA
80160 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:81983 original size:15 final size:15
Alignment explanation
Indices: 81963--81993 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
81953 TAAAAATGTC
*
81963 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
81978 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
81993 C
1 C
81994 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:84071 original size:13 final size:13
Alignment explanation
Indices: 84053--84090 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
84043 GGAAATTCAA
84053 TGTATCGATACAT
1 TGTATCGATACAT
84066 TGTATCGATACAT
1 TGTATCGATACAT
84079 TGTATCGATACA
1 TGTATCGATACA
84091 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:84235 original size:21 final size:21
Alignment explanation
Indices: 84211--84257 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
84201 AAATCTTTTG
84211 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
84232 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
84252 CAAAAT
1 CAAAAT
84258 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:84254 original size:20 final size:19
Alignment explanation
Indices: 84213--84255 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
84203 ATCTTTTGCA
84213 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
84233 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
84253 AAA
1 AAA
84256 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:86657 original size:13 final size:13
Alignment explanation
Indices: 86639--86664 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
86629 TACAGCAAGT
86639 ATGTATCGATACA
1 ATGTATCGATACA
86652 ATGTATCGATACA
1 ATGTATCGATACA
86665 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:93476 original size:12 final size:12
Alignment explanation
Indices: 93461--93489 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
93451 TATATTTTTT
93461 AAAATATAATTA
1 AAAATATAATTA
93473 AAAAT-TAATTA
1 AAAATATAATTA
93484 AAAATA
1 AAAATA
93490 AAAACAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATATAATTA
Found at i:108480 original size:20 final size:20
Alignment explanation
Indices: 108448--108518 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
108438 TTTTACCCAG
*
108448 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
108468 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
108488 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
108508 ATGTATCGATA
1 ATGTATCGATA
108519 TATTCTGTCT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:108519 original size:20 final size:20
Alignment explanation
Indices: 108487--108524 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
108477 TACATGTATG
108487 AATGTATCGATATATTCTTC
1 AATGTATCGATATATTCTTC
108507 AATGTATCGATATATTCT
1 AATGTATCGATATATTCT
108525 GTCTTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (20 bp):
AATGTATCGATATATTCTTC
Found at i:116556 original size:2 final size:2
Alignment explanation
Indices: 116549--116582 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
116539 AAATCAGTTG
116549 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
116583 TTGATTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116988 original size:22 final size:22
Alignment explanation
Indices: 116959--117012 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
116949 TACAAATATT
*
116959 AATT-TAATAAATTTTATATA-
1 AATTATAATAAATTTTAAATAC
116979 AATATATAAT-AA-TTTAAATAC
1 AAT-TATAATAAATTTTAAATAC
117000 AATTATAATAAAT
1 AATTATAATAAAT
117013 AAAAATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
20 16 0.57
21 8 0.29
22 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTATAATAAATTTTAAATAC
Found at i:120105 original size:2 final size:2
Alignment explanation
Indices: 120098--120141 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
120088 GTTATTAATT
* *
120098 TA TA TA TA CA TA TA TA TA TA TA TA TA TA CA 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 TA
120140 TA
1 TA
120142 CACACACACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:124320 original size:31 final size:31
Alignment explanation
Indices: 124284--124342 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
124274 AATTAAAGTG
* *
124284 TATAGTAATATAGTAACT-TAAAATATATTTA
1 TATAGTAATACAGCAA-TATAAAATATATTTA
124315 TATAGTAATACAGCAATATAAAATATAT
1 TATAGTAATACAGCAATATAAAATATAT
124343 AGTAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (31 bp):
TATAGTAATACAGCAATATAAAATATATTTA
Found at i:124376 original size:22 final size:20
Alignment explanation
Indices: 124329--124376 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
124319 GTAATACAGC
124329 AATATAAAATATATAGTAAT
1 AATATAAAATATATAGTAAT
** *
124349 TTTATAAAATTATATTATTAAT
1 AATATAAAA-TATA-TAGTAAT
124371 AATATA
1 AATATA
124377 GACATATAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 7 0.33
21 4 0.19
22 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATATAAAATATATAGTAAT
Found at i:124432 original size:17 final size:18
Alignment explanation
Indices: 124405--124438 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
124395 TGTAATTATT
*
124405 ATAAATCATATGTTATAA
1 ATAAATCATATGATATAA
124423 ATAAAT-ATATGATATA
1 ATAAATCATATGATATA
124439 GTGTAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (18 bp):
ATAAATCATATGATATAA
Found at i:125049 original size:15 final size:17
Alignment explanation
Indices: 125029--125102 Score: 66
Period size: 15 Copynumber: 4.4 Consensus size: 17
125019 TATTATAATT
125029 ATATTATATAA-A-ATA
1 ATATTATATAATATATA
125044 ATATTATATAATATATA
1 ATATTATATAATATATA
* *
125061 ATATT-TA-ACTATATT
1 ATATTATATAATATATA
*
125076 ATTTATATATAATATTATAA
1 ATAT-TATATAATA-TAT-A
125096 ATATTAT
1 ATATTAT
125103 GTATTCTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
15 20 0.43
16 4 0.09
17 10 0.22
18 3 0.07
19 6 0.13
20 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTATATAATATATA
Found at i:125051 original size:20 final size:20
Alignment explanation
Indices: 125026--125063 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
125016 TCGTATTATA
*
125026 ATTATATTATATAAAATAAT
1 ATTATATAATATAAAATAAT
*
125046 ATTATATAATATATAATA
1 ATTATATAATATAAAATA
125064 TTTAACTATA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTATATAATATAAAATAAT
Found at i:125073 original size:13 final size:13
Alignment explanation
Indices: 125054--125091 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
125044 ATATTATATA
125054 ATATATAATATTT
1 ATATATAATATTT
*
125067 A-ACTATATTATTT
1 ATA-TATAATATTT
125080 ATATATAATATT
1 ATATATAATATT
125092 ATAAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.05
13 19 0.90
14 1 0.05
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATATAATATTT
Found at i:125153 original size:25 final size:25
Alignment explanation
Indices: 125118--125184 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
125108 CTTATCCTAC
*
125118 ATAATGATATAACTATTG-AT-ATTATT
1 ATAAT-ATATAA-TATTGTATCATT-TG
*
125144 ATAATATATAATATGGTATCATTTG
1 ATAATATATAATATTGTATCATTTG
125169 ATAATATATAAGTATT
1 ATAATATATAA-TATT
125185 TAGTAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 4 0.11
25 20 0.57
26 11 0.31
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (25 bp):
ATAATATATAATATTGTATCATTTG
Found at i:125295 original size:18 final size:17
Alignment explanation
Indices: 125274--125307 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
125264 GTATTATATT
*
125274 ATAATATATATATATACA
1 ATAAAATATAT-TATACA
125292 ATAAAATATATTATAC
1 ATAAAATATATTATAC
125308 TTTATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAATATATTATACA
Found at i:125519 original size:24 final size:22
Alignment explanation
Indices: 125476--125519 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
125466 TAATAACCAA
* *
125476 TTATTATATAAATTATATATTT
1 TTATTATATAAATAAAATATTT
125498 TTATTATATTTAAATAAAATAT
1 TTATTATA--TAAATAAAATAT
125520 AGATATATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
24 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTATATAAATAAAATATTT
Found at i:127920 original size:62 final size:62
Alignment explanation
Indices: 127807--127927 Score: 179
Period size: 62 Copynumber: 2.0 Consensus size: 62
127797 GTTAATGCCA
* *
127807 TTTCTTTAATCAATTATTTATGCATGCATTGCTTGATCTACTATTTCTAAGTAAAGAGACAT
1 TTTCCTTAATCAATTATTTATGCATGCATTGCTTAATCTACTATTTCTAAGTAAAGAGACAT
* * * * *
127869 TTTCCTTAATCGATTATTTATGCATGTATTGCTTAATCTATTCTTTTTAAGTAAAGAGA
1 TTTCCTTAATCAATTATTTATGCATGCATTGCTTAATCTACTATTTCTAAGTAAAGAGA
127928 TGTTCATACA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (62 bp):
TTTCCTTAATCAATTATTTATGCATGCATTGCTTAATCTACTATTTCTAAGTAAAGAGACAT
Found at i:129077 original size:30 final size:30
Alignment explanation
Indices: 129043--129104 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
129033 TTTTTTTTAA
129043 TTTCAAATCCCAAAAATATTACCAAGCTAT
1 TTTCAAATCCCAAAAATATTACCAAGCTAT
129073 TTTCAAATCCCAAAAATATTACCAAGCTAT
1 TTTCAAATCCCAAAAATATTACCAAGCTAT
129103 TT
1 TT
129105 CTCCCATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.32
Consensus pattern (30 bp):
TTTCAAATCCCAAAAATATTACCAAGCTAT
Found at i:130342 original size:16 final size:17
Alignment explanation
Indices: 130318--130355 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
130308 AACTATCTTA
*
130318 TTTTCAAATA-AATTAT
1 TTTTAAAATATAATTAT
*
130334 TTTTAAAATATTATTAT
1 TTTTAAAATATAATTAT
130351 TTTTA
1 TTTTA
130356 TTCATAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAAAATATAATTAT
Found at i:130937 original size:368 final size:359
Alignment explanation
Indices: 130502--131332 Score: 1017
Period size: 368 Copynumber: 2.3 Consensus size: 359
130492 TATTTCTTTA
* * * *
130502 TTTTTATTC-GATAAATA-ATTTTATTAAT-AGAATTTAAAATTATCTATAAACATTTAAAAATT
1 TTTTTATTCAG-TAAATATATTTTATTATTAAAAATTTAAAATTATCAATAAATATTTAAAAA-T
130564 TTTAATATATAAAAATTTAAAATTATGTAAAATAAATTTTTTATACTTAA-AAGACTA-TCATAT
64 TTTAATATATAAAAATTTAAAATTATGTAAAATAAATTTTTTATACTTAAGAA-ACTACT-ATAT
* * *
130627 TTTAATATGAAAGTACTAATTTACATTTTTCTTTAAAACTTATTATTTTTTACTTTTTTTATTTG
127 TTTAATATGAAAGTACTAATTTACAATTTTCTTTAAAACTTATTATTTTGTA-TTTTTTTATTTA
* * * **
130692 GTAAATGGATTTTATTATTAAAACAATCTAAACTTTTTTGGTAAATACTT-AAAAATTTTAATAC
191 GTAAATAGATTTTATTATTAAAA-AATC-AAAATTATTCAGTAAATACTTAAAAAATTTTAA-A-
* *
130756 AT-AAA-AATCTAAAATGATATCAAATGAATTTTTCGA-CTTAAGATATTGTTGTATCTTTTAA-
252 ATAAAATAATCTAAAATGATATAAAATGAATTTTT-GAGCTTAAGATATTATTGTATCTTTTAAT
* * *
130817 AATGAAAGCACCAATTTATATTTTTCTTTGAGATGTATTACTTTATAAT
316 AA-GAAAACACCAATTTA-A-ATTT-TTT-AGATATATTACTTTATAAT
**
130866 TTTTTATTTGGTAAATACT-TTTTATTATTAAAAATTTAAAAATTATCCAATAAATATTTAAAAA
1 TTTTTATTCAGTAAATA-TATTTTATTATTAAAAATTT-AAAATTAT-CAATAAATATTTAAAAA
* ** * *
130930 CTTTTAATATATGAAAATTTAAAATTATGTAGAAA-ATTTTTTTTATGCTTAAGAAACTACTGTA
63 -TTTTAATATATAAAAATTTAAAATTATGTA-AAATAAATTTTTTATACTTAAGAAACTACTATA
* * * *
130994 TTTTAATATGTAAGTGCTAATTTACAATTTTCTTTGAAAGTTATTATTTTGTATTTTTTTATTTA
126 TTTTAATATGAAAGTACTAATTTACAATTTTCTTTAAAACTTATTATTTTGTATTTTTTTATTTA
* *
131059 GTAAATAGATTTTATTATTAAAAATTCAAAATTATTCAGTATATACTTAAAAAATTTTAAAATAA
191 GTAAATAGATTTTATTATTAAAAAATCAAAATTATTCAGTAAATACTTAAAAAATTTTAAAATAA
* * *
131124 AATAATCTAAAATTATGTAAAATGAATTTTTTAGCTTAAGATATTATTGTATCTTTTAATAAGAA
256 AATAATCTAAAATGATATAAAATGAATTTTTGAGCTTAAGATATTATTGTATCTTTTAATAAGAA
** *
131189 AACGTCAATTTAAATTTTTTAGATATATTATTTTATAAT
321 AACACCAATTTAAATTTTTTAGATATATTACTTTATAAT
*
131228 TTTTTATTCAGTAAATATATTTTATT-TATAAAAATTTAAAATTATTAGATAAATATTTAAAAAT
1 TTTTTATTCAGTAAATATATTTTATTAT-TAAAAATTTAAAATTATCA-ATAAATATTTAAAAAT
*
131292 TTT-A-ATATAAAAATTTAAAATTATGAAAAATAAATTTTTTA
64 TTTAATATATAAAAATTTAAAATTATGTAAAATAAATTTTTTA
131333 AATTCAAAAA
Statistics
Matches: 406, Mismatches: 43, Indels: 42
0.83 0.09 0.09
Matches are distributed among these distances:
357 3 0.01
358 29 0.07
359 1 0.00
360 5 0.01
361 25 0.06
362 48 0.12
363 3 0.01
364 19 0.05
365 32 0.08
366 81 0.20
367 43 0.11
368 111 0.27
369 6 0.01
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (359 bp):
TTTTTATTCAGTAAATATATTTTATTATTAAAAATTTAAAATTATCAATAAATATTTAAAAATTT
TAATATATAAAAATTTAAAATTATGTAAAATAAATTTTTTATACTTAAGAAACTACTATATTTTA
ATATGAAAGTACTAATTTACAATTTTCTTTAAAACTTATTATTTTGTATTTTTTTATTTAGTAAA
TAGATTTTATTATTAAAAAATCAAAATTATTCAGTAAATACTTAAAAAATTTTAAAATAAAATAA
TCTAAAATGATATAAAATGAATTTTTGAGCTTAAGATATTATTGTATCTTTTAATAAGAAAACAC
CAATTTAAATTTTTTAGATATATTACTTTATAAT
Found at i:131065 original size:183 final size:178
Alignment explanation
Indices: 130513--131332 Score: 684
Period size: 183 Copynumber: 4.5 Consensus size: 178
130503 TTTTATTCGA
* * * *
130513 TAAATA-ATTTTATTAAT-AGAATTTAAAATTATCTATAAACATTTAAAAATTTTTAATATATAA
1 TAAATAGATTTTATTATTAAAAATTTAAAATTATCAATAAATATTTAAAAA-TTTTAATATATAA
* * **
130576 AAATTTAAAATTATGTAAAATAAATTTTTTATACTTAA-AAGACTATCATA-TTTTAATATGAAA
65 AAATTTAAAATTATGTAAAA-ATATTTTTTA-GCTTAAGAA-ACTATTGTACTTTTAATATGAAA
* * * * *
130639 GTACTAATTTACATTTTTCTTTAAAACTTATTATTTTTTACTTTTTTTATTTGG
127 GTACTAATTTACAATTTTCTTTGAAA-TTATTATTTTATA-ATTTTTTATTTAG
* * * * *** * *
130693 TAAATGGATTTTATTATTAAAACAATCTAAACTTTTTTGGTAAATACTTAAAAATTTTAATACAT
1 TAAATAGATTTTATTATT-AAA-AATTTAAA-ATTATCAATAAATATTTAAAAATTTTAATATAT
* * * * * * * * * *
130758 AAAAATCTAAAATGATAT-CAAATGAATTTTTCGACTTAAGATATTGTTGTATCTTTTAAAATGA
63 AAAAATTTAAAATTATGTAAAAAT-ATTTTTTAG-CTTAAGAAACTATTGTA-CTTTTAATATGA
* * * * * * *
130822 AAGCACCAATTTATATTTTTCTTTGAGATGTATTACTTTATAATTTTTTATTTGG
125 AAGTACTAATTTACAATTTTCTTTGAAAT-TATTATTTTATAATTTTTTATTTAG
**
130877 TAAATACTTTTTATTATTAAAAATTTAAAAATTATCCAATAAATATTTAAAAACTTTTAATATAT
1 TAAATAGATTTTATTATTAAAAATTT-AAAATTAT-CAATAAATATTTAAAAA-TTTTAATATAT
* * * *
130942 GAAAATTTAAAATTATGTAGAAAATTTTTTTTATGCTTAAGAAACTACTGTA-TTTTAATATGTA
63 AAAAATTTAAAATTATGTA-AAAATATTTTTTA-GCTTAAGAAACTATTGTACTTTTAATATGAA
* * *
131006 AGTGCTAATTTACAATTTTCTTTGAAAGTTATTATTTTGTATTTTTTTATTTAG
126 AGTACTAATTTACAATTTTCTTTGAAA-TTATTATTTTATAATTTTTTATTTAG
* * * * *
131060 TAAATAGATTTTATTATTAAAAATTCAAAATTATTCAGTATATACTTAAAAAATTTTAAAATA-A
1 TAAATAGATTTTATTATTAAAAATTTAAAATTA-TCAATAAATA-TTTAAAAATTTTAATATATA
* * * *
131124 AATAATCTAAAATTATGT-AAAATGAATTTTTTAGCTTAAGATATTATTGTATCTTTTAATAAGA
64 AA-AATTTAAAATTATGTAAAAAT--ATTTTTTAGCTTAAGAAACTATTGTA-CTTTTAATATGA
* * *
131188 AA--ACGTCAATTTA-AATTTT-TTAGATA-TATTATTTTATAATTTTTTATTCAG
125 AAGTAC-T-AATTTACAATTTTCTTTGAAATTATTATTTTATAATTTTTTATTTAG
* *
131239 TAAATATATTTTATT-TATAAAAATTTAAAATTATTAGATAAATATTTAAAAATTTT-A-ATATA
1 TAAATAGATTTTATTAT-TAAAAATTTAAAATTATCA-ATAAATATTTAAAAATTTTAATATATA
131301 AAAATTTAAAATTATG-AAAAATAAATTTTTTA
64 AAAATTTAAAATTATGTAAAAAT--ATTTTTTA
131333 AATTCAAAAA
Statistics
Matches: 511, Mismatches: 98, Indels: 66
0.76 0.15 0.10
Matches are distributed among these distances:
176 30 0.06
177 4 0.01
178 14 0.03
179 56 0.11
180 10 0.02
181 33 0.06
182 59 0.12
183 138 0.27
184 86 0.17
185 76 0.15
186 5 0.01
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (178 bp):
TAAATAGATTTTATTATTAAAAATTTAAAATTATCAATAAATATTTAAAAATTTTAATATATAAA
AATTTAAAATTATGTAAAAATATTTTTTAGCTTAAGAAACTATTGTACTTTTAATATGAAAGTAC
TAATTTACAATTTTCTTTGAAATTATTATTTTATAATTTTTTATTTAG
Found at i:131280 original size:21 final size:22
Alignment explanation
Indices: 131255--131315 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
131245 TATTTTATTT
131255 ATAAAAATTTAAAATTATT-AG
1 ATAAAAATTTAAAATTATTAAG
* *
131276 ATAAATATTTAAAAATT-TTAAT
1 ATAAAAATTT-AAAATTATTAAG
131298 ATAAAAATTTAAAATTAT
1 ATAAAAATTTAAAATTAT
131316 GAAAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
ATAAAAATTTAAAATTATTAAG
Found at i:131779 original size:14 final size:14
Alignment explanation
Indices: 131762--131808 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
131752 TATGTAAAAA
131762 AATAATAATATTTT
1 AATAATAATATTTT
* **
131776 AATAATAATGTTAA
1 AATAATAATATTTT
131790 AATAATAATATTTT
1 AATAATAATATTTT
131804 AATAA
1 AATAA
131809 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:132407 original size:25 final size:25
Alignment explanation
Indices: 132348--132407 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
132338 TCTATATGGG
132348 AAGCTAAAAATTATAAAAATTAAAT
1 AAGCTAAAAATTATAAAAATTAAAT
** * *
132373 AAAATAAAAATTATAAAAGTTAGTAT
1 AAGCTAAAAATTATAAAAATTA-AAT
132399 AAGCTAAAA
1 AAGCTAAAA
132408 GTATTTATAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.27
Consensus pattern (25 bp):
AAGCTAAAAATTATAAAAATTAAAT
Found at i:132707 original size:23 final size:25
Alignment explanation
Indices: 132681--132726 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
132671 ATATATTTTT
132681 TATATAA-TAA-AAATTATATAAGA
1 TATATAATTAATAAATTATATAAGA
*
132704 TATATAATTAATATATTATATAA
1 TATATAATTAATAAATTATATAA
132727 TAGTAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 3 0.15
25 10 0.50
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
TATATAATTAATAAATTATATAAGA
Found at i:133644 original size:37 final size:39
Alignment explanation
Indices: 133601--133743 Score: 125
Period size: 37 Copynumber: 3.7 Consensus size: 39
133591 TATATATAAC
*
133601 TACATAAAATATTATTAATTACGTATAAACATTA-AATT
1 TACATAAAATATTATTAATTACATATAAACATTACAATT
* *
133639 T-CATAAAATATTATTAATTATATATAAATATTACAATT
1 TACATAAAATATTATTAATTACATATAAACATTACAATT
* * * * *
133677 TACATAGAACATTA-T-CTT-CATATATAATTATATAAAATAT
1 TACATAAAATATTATTAATTACATATA-AA-CAT-TACAAT-T
*
133717 TACATATAAATATTATTAGTTACATAT
1 TACATA-AAATATTATTAATTACATAT
133744 GTAATTATAT
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
36 5 0.06
37 33 0.39
38 10 0.12
39 15 0.18
40 7 0.08
41 6 0.07
42 1 0.01
43 2 0.02
44 5 0.06
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (39 bp):
TACATAAAATATTATTAATTACATATAAACATTACAATT
Found at i:133667 original size:20 final size:20
Alignment explanation
Indices: 133607--133947 Score: 98
Period size: 20 Copynumber: 17.4 Consensus size: 20
133597 TAACTACATA
**
133607 AAATATTATTAATTACGTAT
1 AAATATTATTAATTATATAT
*
133627 AAACATTA--AATT-TCATA-
1 AAATATTATTAATTAT-ATAT
133644 AAATATTATTAATTATATAT
1 AAATATTATTAATTATATAT
* *
133664 AAATATTA-CAATT-TACAT
1 AAATATTATTAATTATATAT
* *
133682 AGAACATTATCT--TCATATAT
1 A-AATATTAT-TAATTATATAT
* ** *
133702 AATTATATAAAATATTACATAT
1 AAATAT-TATTA-ATTATATAT
* *
133724 AAATATTATTAGTTACATAT
1 AAATATTATTAATTATATAT
*
133744 --GTA--A-T---TATATA-
1 AAATATTATTAATTATATAT
** *
133755 AAATATTACAAATTACATAT
1 AAATATTATTAATTATATAT
* *
133775 AAATATTATTGATTATATTT
1 AAATATTATTAATTATATAT
* *
133795 AAATATTA-CAAGTTACATA-
1 AAATATTATTAA-TTATATAT
* *
133814 AAATATTACTTTTATAAGTAATTACTT
1 AAATATTA--TTAATTA-T-A-TA--T
**
133841 AAAATATTACCAATTATATAT
1 -AAATATTATTAATTATATAT
*
133862 AAACATTA-TAAGTTATATA-
1 AAATATTATTAA-TTATATAT
** *
133881 AAATATTAAAAATTACATAT
1 AAATATTATTAATTATATAT
* *
133901 AAATATTATCAGTTATATAT
1 AAATATTATTAATTATATAT
133921 AAATATTA-TAAGTTATATA-
1 AAATATTATTAA-TTATATAT
133940 AAATATTA
1 AAATATTA
133948 CCTTTACATG
Statistics
Matches: 231, Mismatches: 53, Indels: 75
0.64 0.15 0.21
Matches are distributed among these distances:
12 5 0.02
13 2 0.01
15 2 0.01
16 1 0.00
17 7 0.03
18 13 0.06
19 59 0.26
20 106 0.46
21 6 0.03
22 12 0.05
23 3 0.01
24 3 0.01
25 1 0.00
26 3 0.01
28 8 0.03
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (20 bp):
AAATATTATTAATTATATAT
Found at i:133856 original size:87 final size:87
Alignment explanation
Indices: 133653--133908 Score: 247
Period size: 87 Copynumber: 2.9 Consensus size: 87
133643 AAAATATTAT
* * * *
133653 TAATTATATATAAATATTACAATTTACATA-GAACATTAT--CTTCATATATAATTATATAAAAT
1 TAATTATATA-AAATATTACAAATTACATATAAACATTATAAGTT-ATATA-AAATAT-TAAAA-
*
133715 ATTACATATAAATATTA-TTAGTTACATATG
61 ATTACATATAAATATTACTT--TT--ATAAG
* * * * *
133745 TAATTATATAAAATATTACAAATTACATATAAATATTAT-TGATTATATTTAAATATTACAAGTT
1 TAATTATATAAAATATTACAAATTACATATAAACATTATAAG-TTATA-TAAAATATTAAAAATT
133809 ACATA-AAATATTACTTTTATAAG
64 ACATATAAATATTACTTTTATAAG
* *
133832 TAATTACT-TAAAATATTACCAATTATATATAAACATTATAAGTTATATAAAATATTAAAAATTA
1 TAATTA-TATAAAATATTACAAATTACATATAAACATTATAAGTTATATAAAATATTAAAAATTA
133896 CATATAAATATTA
65 CATATAAATATTA
133909 TCAGTTATAT
Statistics
Matches: 140, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
86 18 0.13
87 51 0.36
88 2 0.01
89 2 0.01
90 8 0.06
91 27 0.19
92 21 0.15
93 8 0.06
94 3 0.02
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (87 bp):
TAATTATATAAAATATTACAAATTACATATAAACATTATAAGTTATATAAAATATTAAAAATTAC
ATATAAATATTACTTTTATAAG
Found at i:133924 original size:126 final size:130
Alignment explanation
Indices: 133634--133978 Score: 370
Period size: 126 Copynumber: 2.7 Consensus size: 130
133624 TATAAACATT
* * * * *
133634 AAATTTCATA-AAATATTATTAATTATATATAAATATTACAATTTACATAGAACATTA-TCTTCA
1 AAATTACATATAAATATTA-TAGTTATATATAAATATTACAAGTTACATAAAATATTACT-TTCA
* *
133697 TATA-TAATTA-TATAAAATATTA-CATATAAATATTATTAGTTACATATGTAATTATATAAAAT
64 TA-AGTAATTACT-TAAAATATTACCATATAAATATTATTAG-AACATATATAATTATATAAAAT
*
133759 ATTAC
126 ATTAA
* * *
133764 AAATTACATATAAATATTATTGATTATATTTAAATATTACAAGTTACATAAAATATTACTTTTAT
1 AAATTACATATAAATATTATAG-TTATATATAAATATTACAAGTTACATAAAATATTACTTTCAT
*
133829 AAGTAATTACTTAAAATATTACCA-AT-TATA-TA-TA-AACAT-TATAAGTTATATAAAATATT
65 AAGTAATTACTTAAAATATTACCATATAAATATTATTAGAACATATATAA-TTATATAAAATATT
133888 AA
129 AA
* *
133890 AAATTACATATAAATATTATCAGTTATATATAAATATTATAAGTTATATAAAATATTACCTTTAC
1 AAATTACATATAAATATTAT-AGTTATATATAAATATTACAAGTTACATAAAATATTA-CTTT-C
** *
133955 ATGTGTAATTACATAAAATATTAC
63 ATAAGTAATTACTTAAAATATTAC
133979 TCGTTACATA
Statistics
Matches: 185, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
125 4 0.02
126 71 0.38
127 5 0.03
128 23 0.12
129 2 0.01
130 14 0.08
131 62 0.34
132 4 0.02
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (130 bp):
AAATTACATATAAATATTATAGTTATATATAAATATTACAAGTTACATAAAATATTACTTTCATA
AGTAATTACTTAAAATATTACCATATAAATATTATTAGAACATATATAATTATATAAAATATTAA
Found at i:133929 original size:59 final size:58
Alignment explanation
Indices: 133833--133947 Score: 185
Period size: 59 Copynumber: 2.0 Consensus size: 58
133823 TTTTATAAGT
*
133833 AATTACTTAAAATATTACCAATTATATATAAACATTATAAGTTATATAAAATATTAAA
1 AATTACATAAAATATTACCAATTATATATAAACATTATAAGTTATATAAAATATTAAA
* * *
133891 AATTACATATAAATATTATCAGTTATATATAAATATTATAAGTTATATAAAATATTA
1 AATTACATA-AAATATTACCAATTATATATAAACATTATAAGTTATATAAAATATTA
133948 CCTTTACATG
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 8 0.15
59 44 0.85
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (58 bp):
AATTACATAAAATATTACCAATTATATATAAACATTATAAGTTATATAAAATATTAAA
Found at i:133944 original size:39 final size:39
Alignment explanation
Indices: 133748--133947 Score: 143
Period size: 39 Copynumber: 4.9 Consensus size: 39
133738 ACATATGTAA
* * *
133748 TTATATAAAATATTACAAATTACATATAAATATTAT-TG
1 TTATATAAAATATTAAAAATTATATATAAATATTATAAG
* * * * *
133786 ATTATATTTAAATATTACAAGTTACATAAAATATTACTTTTATAAG
1 -TTATA-TAAAATATTAAAAATTATATATAA-A-TA---TTATAAG
* ** *
133832 TAATTACTTAAAATATTACCAATTATATATAAACATTATAAG
1 TTA-TA--TAAAATATTAAAAATTATATATAAATATTATAAG
* *
133874 TTATATAAAATATTAAAAATTACATATAAATATTATCAG
1 TTATATAAAATATTAAAAATTATATATAAATATTATAAG
* *
133913 TTATATATAAATATTATAAGTTATATA-AAATATTA
1 TTATATA-AAATATTAAAAATTATATATAAATATTA
133948 CCTTTACATG
Statistics
Matches: 131, Mismatches: 20, Indels: 20
0.77 0.12 0.12
Matches are distributed among these distances:
39 49 0.37
40 37 0.28
41 3 0.02
42 11 0.08
45 7 0.05
46 4 0.03
47 20 0.15
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (39 bp):
TTATATAAAATATTAAAAATTATATATAAATATTATAAG
Found at i:139162 original size:21 final size:23
Alignment explanation
Indices: 139115--139165 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
139105 AACAAAAAAC
139115 ATTATTACTTACTAAAATTTTAA
1 ATTATTACTTACTAAAATTTTAA
*
139138 ATTATTA-TTA-TAAATATTTT-T
1 ATTATTACTTACTAAA-ATTTTAA
139159 ATTATTA
1 ATTATTA
139166 ATAAGATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 11 0.42
22 8 0.31
23 7 0.27
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTATTACTTACTAAAATTTTAA
Found at i:139866 original size:24 final size:22
Alignment explanation
Indices: 139810--139866 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
139800 ATTAACTGTC
*
139810 AAAA-TTTTCTTTTTATTTAAA
1 AAAACTTTTCATTTTATTTAAA
**
139831 AAAACTACTCATTTTATTTGAAA
1 AAAACTTTTCATTTTATTT-AAA
*
139854 ATTAACTTTTCAT
1 A-AAACTTTTCAT
139867 CTTTTTATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 4 0.15
22 11 0.41
23 4 0.15
24 8 0.30
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.49
Consensus pattern (22 bp):
AAAACTTTTCATTTTATTTAAA
Found at i:139886 original size:26 final size:26
Alignment explanation
Indices: 139817--139896 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
139807 GTCAAAATTT
*
139817 TCTTTTTATTT-AAAAAAACTACTCA
1 TCTTTTTATTTGAAAATAACTACTCA
**
139842 ---TTTTATTTGAAAATTAACTTTTCA
1 TCTTTTTATTTGAAAA-TAACTACTCA
139866 TCTTTTTATTTGATAAA-AACTACTCA
1 TCTTTTTATTTGA-AAATAACTACTCA
139892 TCTTT
1 TCTTT
139897 AAATTTTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
22 8 0.18
23 4 0.09
24 7 0.16
26 12 0.27
27 10 0.23
28 3 0.07
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.50
Consensus pattern (26 bp):
TCTTTTTATTTGAAAATAACTACTCA
Found at i:139902 original size:26 final size:23
Alignment explanation
Indices: 139821--139897 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 23
139811 AAATTTTCTT
*
139821 TTTATTTAAAAAAACTACTCAT-
1 TTTATTTGAAAAAACTACTCATC
**
139843 TTTATTTGAAAATTAACTTTTCATC
1 TTTATTTGAAAA--AACTACTCATC
139868 TTTTTATTTGATAAAAACTACTCATC
1 --TTTATTTGA-AAAAACTACTCATC
139894 TTTA
1 TTTA
139898 AATTTTAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
22 11 0.25
24 12 0.27
26 9 0.20
27 9 0.20
28 3 0.07
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.48
Consensus pattern (23 bp):
TTTATTTGAAAAAACTACTCATC
Found at i:144728 original size:15 final size:16
Alignment explanation
Indices: 144701--144731 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
144691 TTTATAAAGA
144701 TTTAATAATAAATATT
1 TTTAATAATAAATATT
144717 TTTAAT-ATAAATATT
1 TTTAATAATAAATATT
144732 AATATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAATAATAAATATT
Found at i:144735 original size:12 final size:12
Alignment explanation
Indices: 144718--144764 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
144708 ATAAATATTT
144718 TTAATATAAATA
1 TTAATATAAATA
**
144730 TTAATAT-TTTA
1 TTAATATAAATA
*
144741 ATAATATAAATA
1 TTAATATAAATA
*
144753 TTAATAGAAATA
1 TTAATATAAATA
144765 ATATTTTAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
TTAATATAAATA
Found at i:144749 original size:23 final size:21
Alignment explanation
Indices: 144711--144758 Score: 78
Period size: 23 Copynumber: 2.2 Consensus size: 21
144701 TTTAATAATA
144711 AATATTTTTAATATAAATATT
1 AATATTTTTAATATAAATATT
144732 AATATTTTAATAATATAAATATT
1 AATATTTT--TAATATAAATATT
144755 AATA
1 AATA
144759 GAAATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 8 0.32
23 17 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATTTTTAATATAAATATT
Found at i:144768 original size:53 final size:53
Alignment explanation
Indices: 144711--144828 Score: 125
Period size: 53 Copynumber: 2.2 Consensus size: 53
144701 TTTAATAATA
*
144711 AATATTTTTAATATAAATATTAATATTTTAATAATATA-AATATTAATAGAAAT
1 AATATTTTTAATATAAATA-TAATATTTAAATAATATAGAATATTAATAGAAAT
* * * * * * *
144764 AATA-TTTTAATGATTATTATAATATTTAAATATTTTAGAATATTTATATAATT
1 AATATTTTTAAT-ATAAATATAATATTTAAATAATATAGAATATTAATAGAAAT
144817 AAT-TTTTTAATA
1 AATATTTTTAATA
144829 ATAACTAGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
52 23 0.43
53 31 0.57
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (53 bp):
AATATTTTTAATATAAATATAATATTTAAATAATATAGAATATTAATAGAAAT
Found at i:144787 original size:20 final size:18
Alignment explanation
Indices: 144762--144809 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
144752 ATTAATAGAA
*
144762 ATAATATTTTAATGATTATT
1 ATAATATTTAAAT-ATT-TT
144782 ATAATATTTAAATATTTT
1 ATAATATTTAAATATTTT
*
144800 AGAATATTTA
1 ATAATATTTA
144810 TATAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
19 3 0.12
20 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
ATAATATTTAAATATTTT
Found at i:144807 original size:18 final size:20
Alignment explanation
Indices: 144764--144809 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
144754 TAATAGAAAT
* *
144764 AATATTTTAATGATTATTAT
1 AATATTTAAATGATTATTAG
144784 AATATTTAAAT-ATT-TTAG
1 AATATTTAAATGATTATTAG
144802 AATATTTA
1 AATATTTA
144810 TATAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
19 3 0.12
20 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
AATATTTAAATGATTATTAG
Found at i:148268 original size:45 final size:45
Alignment explanation
Indices: 148217--148306 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
148207 ATTAACAATA
148217 ATAGAAAT-TCAATTTAATTAGTTAAAACTATTATTAAAATCTTTC
1 ATAGAAATGT-AATTTAATTAGTTAAAACTATTATTAAAATCTTTC
148262 ATAGAAATGTAATTTAATTAGTTAAAACTATTATTAAAATCTTTC
1 ATAGAAATGTAATTTAATTAGTTAAAACTATTATTAAAATCTTTC
148307 TCTCTGTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 43 0.98
46 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (45 bp):
ATAGAAATGTAATTTAATTAGTTAAAACTATTATTAAAATCTTTC
Found at i:148693 original size:3 final size:3
Alignment explanation
Indices: 148685--148709 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
148675 TATGCTACTC
148685 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
148710 AAATCCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:149488 original size:2 final size:2
Alignment explanation
Indices: 149481--149507 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
149471 TTGGAAGGTT
149481 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
149508 GACGCACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:154432 original size:29 final size:30
Alignment explanation
Indices: 154377--154436 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
154367 GATTTCTCTC
*
154377 TTTCACTATCCTAATTAATTAATTTGGCCT
1 TTTCACTATCCTAATTAATCAATTTGGCCT
*
154407 TTTC-CTATCCTAATTTTATCAA-TTGGCCT
1 TTTCACTATCCTAA-TTAATCAATTTGGCCT
154436 T
1 T
154437 CCAATTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.48
Consensus pattern (30 bp):
TTTCACTATCCTAATTAATCAATTTGGCCT
Found at i:159003 original size:2 final size:2
Alignment explanation
Indices: 158996--159047 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
158986 AACTGGGCAT
158996 TA TA 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 TA TA
159038 TA TA TA TA TA
1 TA TA TA TA TA
159048 AATTACGGCC
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):
TA
Found at i:160219 original size:2 final size:2
Alignment explanation
Indices: 160212--160242 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
160202 ATATCTCATG
*
160212 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
160243 GTACATGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:160896 original size:17 final size:17
Alignment explanation
Indices: 160845--160898 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
160835 TGAAATTTTA
160845 AAAATTTATAT-AATAT
1 AAAATTTATATAAATAT
160861 -AAA-TTAT-TAAAATATT
1 AAAATTTATAT-AAATA-T
160877 AAAATTTATATAAATAT
1 AAAATTTATATAAATAT
160894 AAAAT
1 AAAAT
160899 ACGGATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 7 0.22
16 1 0.03
17 9 0.28
18 9 0.28
19 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATTTATATAAATAT
Found at i:161626 original size:2 final size:2
Alignment explanation
Indices: 161619--161649 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
161609 TAAATATCTT
161619 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
161650 TAAGAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:163085 original size:27 final size:26
Alignment explanation
Indices: 163051--163107 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
163041 ATTCCCATAT
*
163051 ATGTAATTGT-CAATTAAAATTTTCAC
1 ATGTAATTGTAAAATTAAAATTTT-AC
*
163077 ATGTAAATTTTAAAATTAAAATTTTAC
1 ATGT-AATTGTAAAATTAAAATTTTAC
163104 ATGT
1 ATGT
163108 CAATATAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 4 0.15
27 11 0.41
28 12 0.44
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (26 bp):
ATGTAATTGTAAAATTAAAATTTTAC
Found at i:164199 original size:25 final size:25
Alignment explanation
Indices: 164171--164219 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
164161 ATTTACTTGC
164171 TATTATT-ATTATTGTTATTTTAATG
1 TATTATTGATTATT-TTATTTTAATG
* *
164196 TATTGTTGTTTATTTTATTTTAAT
1 TATTATTGATTATTTTATTTTAAT
164220 TCCTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.67
Consensus pattern (25 bp):
TATTATTGATTATTTTATTTTAATG
Found at i:164768 original size:29 final size:27
Alignment explanation
Indices: 164697--164768 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 27
164687 TTTTTAGACC
*
164697 TAAA-TGCATCTTTTAGGGTCATTTTAG
1 TAAATTGCATC-TTTAAGGTCATTTTAG
* *
164724 TAATTTCCATCACTTTAAGGTCATTTTAGG
1 TAAATTGCAT--CTTTAAGGTCATTTTA-G
164754 TATAATTGCATCTTT
1 TA-AATTGCATCTTT
164769 TAAAGTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
27 3 0.09
28 4 0.11
29 18 0.51
30 4 0.11
31 6 0.17
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (27 bp):
TAAATTGCATCTTTAAGGTCATTTTAG
Found at i:166396 original size:20 final size:21
Alignment explanation
Indices: 166371--166420 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
166361 CACAATATCG
**
166371 ATCGATACATG-ACCAAATGT
1 ATCGATACATGTAAAAAATGT
*
166391 ATCGATACTTGTAAAAAATGT
1 ATCGATACATGTAAAAAATGT
166412 ATCGATACA
1 ATCGATACA
166421 GGTCATTGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (21 bp):
ATCGATACATGTAAAAAATGT
Found at i:166499 original size:13 final size:13
Alignment explanation
Indices: 166481--166506 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166471 ACACACAATA
166481 TGTATCGATACAT
1 TGTATCGATACAT
166494 TGTATCGATACAT
1 TGTATCGATACAT
166507 CCTAAAATGT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:166522 original size:33 final size:32
Alignment explanation
Indices: 166461--166528 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
166451 CCTTAACTGT
*
166461 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
166493 TTGTATCGATACATC-CTAAAATGTATCGATACA
1 TTGTATCGATACA-CAC-AAAATGTATCGATACA
166526 TTG
1 TTG
166529 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:172451 original size:8 final size:8
Alignment explanation
Indices: 172438--172463 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
172428 ATTTGATTAA
172438 ATTTTGTG
1 ATTTTGTG
172446 ATTTTGTG
1 ATTTTGTG
172454 ATTTTGTG
1 ATTTTGTG
172462 AT
1 AT
172464 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:172748 original size:20 final size:20
Alignment explanation
Indices: 172713--172754 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
172703 CAAATTTCTT
172713 ATTTTTCACTTCAAAATACATC
1 ATTTTTCAC-TCAAAAT-CATC
172735 ATTTTTCA-TCAAAATCATC
1 ATTTTTCACTCAAAATCATC
172754 A
1 A
172755 ACAAAAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTTTCACTCAAAATCATC
Found at i:174438 original size:22 final size:21
Alignment explanation
Indices: 174412--174478 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 21
174402 CGAAATTGTT
*
174412 AAATTATTTTATTAAAGGGGAG
1 AAATT-TTTTATTAAGGGGGAG
174434 AAATTTTTTTATTAAGGGGGAG
1 AAA-TTTTTTATTAAGGGGGAG
174456 AAATTTTTTGATTAAGGGGGAG
1 AAATTTTTT-ATTAAGGGGGAG
174478 A
1 A
174479 GAAAAGAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
21 6 0.14
22 34 0.81
23 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.37
Consensus pattern (21 bp):
AAATTTTTTATTAAGGGGGAG
Found at i:175052 original size:13 final size:13
Alignment explanation
Indices: 175034--175058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
175024 AGATTGCACA
175034 GTATCGATACATT
1 GTATCGATACATT
175047 GTATCGATACAT
1 GTATCGATACAT
175059 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:175183 original size:20 final size:20
Alignment explanation
Indices: 175140--175211 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
175130 CTTAACTGTT
* *
175140 TGTATCGATACA-CACAATA
1 TGTATCGATACATCCCAAAA
175159 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCCCAAAA
175179 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCCCAAAA
175199 TGTATCGATACAT
1 TGTATCGATACAT
175212 TGGCTTGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 12 0.24
20 38 0.76
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATCCCAAAA
Found at i:180588 original size:330 final size:322
Alignment explanation
Indices: 179967--180591 Score: 704
Period size: 330 Copynumber: 1.9 Consensus size: 322
179957 ATTAGGTATT
* * * ** * *
179967 AATATTGGATCTTATTGTATTAATACATTCAATTGGTTTTTTGAAAATCATGCTTAAAAACTTTT
1 AATATTGGATCTTATTGAATCAATACATTCAACTGGTTTTTTGAAAATCACACTAAAAAACTTAT
* * * *
180032 AATTTTTCATTCCATACCTTACAAATTAAAATCATTATTAAAGCTTGAAGAGTAAAAATCATTAA
66 AATTTTTCATTCCAAAACTTACAAATTAAAATCATTATTAAACCTTGAAGAGTAAAAATCATCAA
* * * *
180097 AATTAAGGCTTGCTAGGTAAAAACTTGGATCAAAAGTGAGTATGCAATTTTTGAACCATGTTGAT
131 AATTAAAGCTTGCTAGGTAAAAACTTGAATCAAAAGTGAGTATGCAATTTTTAAACCATATTGAT
* ** **
180162 CCATATGCAAAGTTGGACATATTTTTGCAACATTGCAATTGAACATTCATCTCCATTTATTCAAG
196 CCATATGCAAAATTAAACATATTTTTGCAACATTGCAATTGAACACGCATCTCCATTTATTCAAG
* * *
180227 AGGAGTAAATTTGTCAACCACAATCATTAAGCACATTTATAATGAAGTTTGAATAGAGTACC
261 AGGAATAAATTTATCAACCACAATAATTAAGCACATTTATAATGAAGTTTGAATAGAGTACC
*
180289 AATATTGGATCTTATTGAATCAATATATTTC-ACTGGTTTTTTGAAAATCACACTAAAAAACTTA
1 AATATTGGATCTTATTGAATCAATACA-TTCAACTGGTTTTTTGAAAATCACACTAAAAAACTTA
* ** * *
180353 TAATTTTTCATTCTAAAACTTATGAATTAAAATCATTATGCATTGTTTAAACCTTGACGAGTAAG
65 TAATTTTTCATTCCAAAACTTACAAATTAAAATCA-T-T--A----TTAAACCTTGAAGAGTAAA
* * *
180418 AATCATCAAAATTAAAG-TT-CTCAAGGTAAAGATTTGAATC-AAAGTTGAGTATGTAATTTTTA
122 AATCATCAAAATTAAAGCTTGCT--AGGTAAAAACTTGAATCAAAAG-TGAGTATGCAATTTTTA
* * * ** **
180480 AACCATATTGTTGCATATGTAAAATTAAATGTATTTTTGCAACATTGTGATTAGAA-ACGCATCT
184 AACCATATTGATCCATATGCAAAATTAAACATATTTTTGCAACATTGCAATT-GAACACGCATCT
** *
180544 TTATTTATTCAAG-GAGAATAAATTTATCAACCATAATAATTAAGCACA
248 CCATTTATTCAAGAG-GAATAAATTTATCAACCACAATAATTAAGCACA
180592 CTCATAATTC
Statistics
Matches: 247, Mismatches: 42, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
322 82 0.33
323 4 0.02
324 1 0.00
326 1 0.00
328 2 0.01
329 7 0.03
330 147 0.60
331 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.36
Consensus pattern (322 bp):
AATATTGGATCTTATTGAATCAATACATTCAACTGGTTTTTTGAAAATCACACTAAAAAACTTAT
AATTTTTCATTCCAAAACTTACAAATTAAAATCATTATTAAACCTTGAAGAGTAAAAATCATCAA
AATTAAAGCTTGCTAGGTAAAAACTTGAATCAAAAGTGAGTATGCAATTTTTAAACCATATTGAT
CCATATGCAAAATTAAACATATTTTTGCAACATTGCAATTGAACACGCATCTCCATTTATTCAAG
AGGAATAAATTTATCAACCACAATAATTAAGCACATTTATAATGAAGTTTGAATAGAGTACC
Found at i:183464 original size:55 final size:57
Alignment explanation
Indices: 183403--183514 Score: 174
Period size: 55 Copynumber: 1.9 Consensus size: 57
183393 TGCATGTACT
*
183403 CATGAAATGAACATATGCATGCATGAAAC-AAGAAAGTAAGCATGAAA-TGTTTATG
1 CATGAAATGAACATATGCATGCATGAAACAAAGAAAATAAGCATGAAATTGTTTATG
183458 CATGAAATGAACATATGCATGCATGAAACATAAAAGAAAATAAGCATGAAATTGTTT
1 CATGAAATGAACATATGCATGCATGAAAC---AAAGAAAATAAGCATGAAATTGTTT
183515 GTGCCATGTG
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
55 29 0.57
59 17 0.33
60 5 0.10
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (57 bp):
CATGAAATGAACATATGCATGCATGAAACAAAGAAAATAAGCATGAAATTGTTTATG
Found at i:183597 original size:23 final size:23
Alignment explanation
Indices: 183585--183648 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 23
183575 CTTTTTTTCC
183585 TTTCTTTGATTTTTTTGTTTTAA
1 TTTCTTTGATTTTTTTGTTTTAA
* *
183608 TTTCTTTGATTTTTGATTTTTTTGA
1 TTTCTTTGATTTTT--TTGTTTTAA
* *
183633 TTTTTTTGAATTTTTT
1 TTTCTTTGATTTTTTT
183649 AAATTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 16 0.46
25 19 0.54
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.75
Consensus pattern (23 bp):
TTTCTTTGATTTTTTTGTTTTAA
Found at i:183601 original size:9 final size:9
Alignment explanation
Indices: 183602--183648 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
183592 GATTTTTTTG
*
183602 TTTTAATTT
1 TTTTGATTT
*
183611 CTTTGA-TT
1 TTTTGATTT
183619 -TTTGATTT
1 TTTTGATTT
183627 TTTTGATTT
1 TTTTGATTT
183636 TTTTGAATTT
1 TTTTG-ATTT
183646 TTT
1 TTT
183649 AAATTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
7 5 0.15
8 4 0.12
9 17 0.52
10 7 0.21
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTGATTT
Found at i:183626 original size:16 final size:16
Alignment explanation
Indices: 183589--183637 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
183579 TTTTCCTTTC
183589 TTTGATTTTTTTG--T
1 TTTGATTTTTTTGATT
* *
183603 TTTAATTTCTTTGATT
1 TTTGATTTTTTTGATT
183619 TTTGATTTTTTTGATT
1 TTTGATTTTTTTGATT
183635 TTT
1 TTT
183638 TTGAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 11 0.38
16 18 0.62
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (16 bp):
TTTGATTTTTTTGATT
Done.