Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3470.1
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: 127577
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.31
Warning! 13258 characters in sequence are not A, C, G, or T
Found at i:114 original size:13 final size:13
Alignment explanation
Indices: 98--122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88 TTTTATTATT
98 TTACATTATTTTA
1 TTACATTATTTTA
111 TTACATTATTTT
1 TTACATTATTTT
123 TGAAGTGTAT
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:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (13 bp):
TTACATTATTTTA
Found at i:676 original size:310 final size:297
Alignment explanation
Indices: 1--765 Score: 970
Period size: 310 Copynumber: 2.5 Consensus size: 297
* * * * *
1 AATTTAGTAAAAACCCTTATTTCGGCCATTTATTCGTACTATTTTCT-CGAATTTTATTACTTTC
1 AATTTAGTAAAAACTCTTACTTCGGCC-TTTGTTCGTA-TTTTTTCTCCGCATTTTATTACTTTC
* * * * * *
65 AATAAAAATAAATTACTTTCGT-TTTTTATTATTTTACATTATTTTATTACATTATTTTTGAAGT
64 -A-AAAAAT-CA-TATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
* *
129 GTATTAATTTATGTGTTTTTTAAAT-AATTTTTAAAAAAAAAAACCCTTATTCCTACCCTTTGCT
124 TTATTAATTTATGTATTTTTTAAATAAATTTTT---AAAAAAAACCCTTATTCCTACCCTTTGCT
* *
193 CGTATTATTTTCCCGAATTTTAATACTTTTAATAAAAATATATTATTTTTGTATTTTATTATTTT
186 CGTATTATTTTCCCGAATTTTAATACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTT
* * *
258 ATATTATTTCAGTACATTTTGTATTAATTATTTCTGAATTTTTAAAA
251 ATATTATTTCAGTAAATTTTGTATTAATTATTTCTAAATTTTAAAAA
*
305 AATTTAGTAAAACACTCTTACTTTGGCCCTTTGTTCGTATTTTTT-TCCGCATTTTATTACTTT-
1 AATTTAGTAAAA-ACTCTTACTTCGG-CCTTTGTTCGTATTTTTTCTCCGCATTTTATTACTTTC
368 AAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
64 AAAAA-ATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
* *
433 TAATTTAGTGT-TTTTTTAAATAAATTTTT-AAAAGAACCCTTATTCCTGCCCTTTGCTCGTATT
128 TAATTTA-TGTATTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGCTCGTATT
** *
496 ATTTTCCCGAATTTTTTTTACTTTCAATAACAATATATTATTTTCGTATTTT-TTATTTTATATT
192 ATTTTCCCGAA-TTTTAATACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATT
560 ATTTTAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTAAAAA
256 A--TT--T-CA----G--T-AAAT-TTTGTATTAATTATTTCTAAATTTTAAAAA
* *
615 AATTTAGTAAAAAATCTTACTTCGGCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTGA
1 AATTTAGTAAAAACTCTTACTTCGGCCTTTGTTCGTA-TTTTTTCTCCGCATTTTATTACTTTCA
680 AAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTA
65 AAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTA
745 ATTTACTGTATTTTTTAAATA
130 ATTTA-TGTATTTTTTAAATA
766 TACCATTTTT
Statistics
Matches: 410, Mismatches: 26, Indels: 43
0.86 0.05 0.09
Matches are distributed among these distances:
297 56 0.14
298 35 0.09
299 3 0.01
300 64 0.16
301 16 0.04
302 5 0.01
303 1 0.00
304 32 0.08
305 19 0.05
306 3 0.01
308 13 0.03
309 20 0.05
310 127 0.31
311 16 0.04
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (297 bp):
AATTTAGTAAAAACTCTTACTTCGGCCTTTGTTCGTATTTTTTCTCCGCATTTTATTACTTTCAA
AAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAA
TTTATGTATTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGCTCGTATTATTT
TCCCGAATTTTAATACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTC
AGTAAATTTTGTATTAATTATTTCTAAATTTTAAAAA
Found at i:1064 original size:10 final size:10
Alignment explanation
Indices: 1047--1147 Score: 59
Period size: 10 Copynumber: 10.0 Consensus size: 10
1037 TTCCTTCCCA
1047 CTTC-TTCTT
1 CTTCTTTCTT
1056 CTTCTTTCTT
1 CTTCTTTCTT
* *
1066 TTTTTTTCTT
1 CTTCTTTCTT
* *
1076 CTCCGTTCCTT
1 CTTC-TTTCTT
1087 -TTCTTTCCTT
1 CTTCTTT-CTT
1097 CTT-TTTCTT
1 CTTCTTTCTT
*
1106 TTTCTTTTTCTT
1 CTTC--TTTCTT
*
1118 CTCCTTTCCTT
1 CTTCTTT-CTT
1129 -TTCTTTCCTT
1 CTTCTTT-CTT
1139 CTT-TTTCTT
1 CTTCTTTCTT
1148 TTTTTCCTCT
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
9 14 0.20
10 37 0.52
11 12 0.17
12 8 0.11
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (10 bp):
CTTCTTTCTT
Found at i:1085 original size:44 final size:40
Alignment explanation
Indices: 1019--1152 Score: 126
Period size: 42 Copynumber: 3.2 Consensus size: 40
1009 AAAAATTACC
* *
1019 CTTTTTCTTTT-TTTTCCCTTCCTTCCCACTTCTTCTTCTTCTTT
1 CTTTTT-TTTTCTTCTCCCTTCCTT--CACTT-TCCTTCTT-TTT
* **
1063 CTTTTTTTTTCTTCTCCGTTCCTTTTCTTTCCTTCTTTTT
1 CTTTTTTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
* **
1103 CTTTTTCTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTT
1 C-TTTT-TTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
1145 CTTTTTTT
1 CTTTTTTT
1153 CCTCTCTGTT
Statistics
Matches: 81, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
40 7 0.09
41 15 0.19
42 38 0.47
43 4 0.05
44 17 0.21
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (40 bp):
CTTTTTTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
Found at i:1097 original size:21 final size:21
Alignment explanation
Indices: 1053--1155 Score: 90
Period size: 21 Copynumber: 5.1 Consensus size: 21
1043 CCCACTTCTT
* * *
1053 CTTCTTCTTT-CTTTTTTTTT
1 CTTCTCCTTTCCTTTTCTTTC
*
1073 CTTCTCCGTTCCTTTTCTTTC
1 CTTCTCCTTTCCTTTTCTTTC
* * *
1094 CTTCT-TTTTCTTTTTCTTTTT
1 CTTCTCCTTTCCTTTTC-TTTC
1115 CTTCTCCTTTCCTTTTCTTTC
1 CTTCTCCTTTCCTTTTCTTTC
*
1136 CTTCT--TTTTCTTTT-TTTC
1 CTTCTCCTTTCCTTTTCTTTC
1154 CT
1 CT
1156 CTCTGTTGAC
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
18 6 0.09
19 8 0.12
20 16 0.24
21 29 0.43
22 9 0.13
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (21 bp):
CTTCTCCTTTCCTTTTCTTTC
Found at i:1127 original size:42 final size:41
Alignment explanation
Indices: 1053--1152 Score: 166
Period size: 42 Copynumber: 2.4 Consensus size: 41
1043 CCCACTTCTT
1053 CTTCTTCTTTC-TTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
1 CTTCTT-TTTCTTTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
*
1094 CTTCTTTTTCTTTTTCTTTTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTTT-TTTTTCTTCTCCGTTCCTTTTCTTTC
1136 CTTCTTTTTCTTTTTTT
1 CTTCTTTTTCTTTTTTT
1153 CCTCTCTGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
40 4 0.07
41 12 0.21
42 40 0.71
ACGTcount: A:0.00, C:0.27, G:0.01, T:0.72
Consensus pattern (41 bp):
CTTCTTTTTCTTTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
Found at i:1146 original size:6 final size:6
Alignment explanation
Indices: 1048--1150 Score: 57
Period size: 6 Copynumber: 16.3 Consensus size: 6
1038 TCCTTCCCAC
* * ** *
1048 TTCTTC TTCTTCT TTCTTT TTTTTT CTTCTCCG TTCCTT TTCTTT CCTTCTTT
1 TTCTTT TTCTT-T TTCTTT TTCTTT -TTCT-TT TTCTTT TTCTTT --TTCTTT
* * *
1101 TTCTTT TTCTTT TTC-TT CTC-CT TTCCTT TTCTTT CCTTCTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT --TTCTTT TTCTTT
1149 TT
1 TT
1151 TTCCTCTCTG
Statistics
Matches: 75, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
5 7 0.09
6 45 0.60
7 11 0.15
8 12 0.16
ACGTcount: A:0.00, C:0.27, G:0.01, T:0.72
Consensus pattern (6 bp):
TTCTTT
Found at i:1264 original size:24 final size:24
Alignment explanation
Indices: 1232--1280 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1222 AGTGGGAGTC
1232 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
1256 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
1280 G
1 G
1281 TGATCGGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (24 bp):
GCCACCAATCCTTTTTATTTAGGT
Found at i:2282 original size:107 final size:106
Alignment explanation
Indices: 2097--2316 Score: 300
Period size: 107 Copynumber: 2.1 Consensus size: 106
2087 AAACCCATAC
* * * * *
2097 TTTGAAGTTTTAAGAGGATATTTGGCCATTTGGTTCAACGAGAAATTGAAAACCAGCACATTAGG
1 TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
*
2162 GCACGTTTTCTCGAATTTT-CAAACGCAAAATATCGCTTTAT
66 GCACGTTTTCTCG-ATTTTCCAAACGCAAAATATCGCCTTAT
* * *
2203 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGG-TCGAACGAAAAATCGAAACCCAGCACGTTA
1 TTTGAAATTTTAAAAGGATA-TTTAGCCATTTGGTTC-AACGAAAAATCGAAAACCAGCACATTA
*
2267 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATTGCCTTAT
64 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
*
2310 TTAGAAA
1 TTTGAAA
2317 AATTTTCCTT
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
106 25 0.25
107 75 0.75
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (106 bp):
TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
GCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
Found at i:4377 original size:3 final size:3
Alignment explanation
Indices: 4369--4439 Score: 62
Period size: 3 Copynumber: 24.7 Consensus size: 3
4359 TAAATGAGTA
* * *
4369 AAT AAT AAT AAT GAT TAT AAT AAT AA- ACT AAT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4414 AAT -AT AAT -AT AAT AAT GAAT AGAT AA
1 AAT AAT AAT AAT AAT AAT -AAT A-AT AA
4440 ATATAAAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
2 9 0.16
3 41 0.73
4 6 0.11
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:4413 original size:13 final size:13
Alignment explanation
Indices: 4370--4429 Score: 70
Period size: 13 Copynumber: 4.6 Consensus size: 13
4360 AAATGAGTAA
*
4370 ATAATAATAATGATT
1 ATAATAAT-AT-AAT
4385 ATAATAATA-AA-
1 ATAATAATATAAT
*
4396 CTAATAATATAAT
1 ATAATAATATAAT
4409 ATAATAATATAAT
1 ATAATAATATAAT
4422 ATAATAAT
1 ATAATAAT
4430 GAATAGATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 8 0.20
12 3 0.08
13 20 0.50
14 1 0.03
15 8 0.20
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (13 bp):
ATAATAATATAAT
Found at i:4458 original size:19 final size:20
Alignment explanation
Indices: 4401--4461 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 20
4391 ATAAACTAAT
* *
4401 AATATAATATA-ATAATAT-
1 AATATAATAAAGAAAATATA
* * *
4419 AATATAATAATGAATAGATA
1 AATATAATAAAGAAAATATA
4439 AATATAA-AAAGAAAATATA
1 AATATAATAAAGAAAATATA
4458 AATA
1 AATA
4462 AGATAATAAG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
18 9 0.27
19 17 0.52
20 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AATATAATAAAGAAAATATA
Found at i:14309 original size:42 final size:43
Alignment explanation
Indices: 14263--14366 Score: 122
Period size: 47 Copynumber: 2.4 Consensus size: 43
14253 TTCCCACTTC
14263 TTCTTCTTCTTTCTTTTT-TTTTTCTTCTCCGTTCCGTTCCTT
1 TTCTTCTTCTTTCTTTTTGTTTTTCTTCTCCGTTCCGTTCCTT
* * *
14305 TTCTTTCCTTCTTTTTCTTTTTGTTTTTCTTCTCCTTTCCTTTTCTT
1 TTC-TT-CTTC--TTTCTTTTTGTTTTTCTTCTCCGTTCCGTTCCTT
*
14352 TCCTTCTT-TTTCTTT
1 TTCTTCTTCTTTCTTT
14367 CTTTCCTCTC
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
42 10 0.19
43 2 0.04
44 4 0.08
45 3 0.06
46 11 0.21
47 23 0.43
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (43 bp):
TTCTTCTTCTTTCTTTTTGTTTTTCTTCTCCGTTCCGTTCCTT
Found at i:14314 original size:10 final size:10
Alignment explanation
Indices: 14299--14373 Score: 50
Period size: 10 Copynumber: 7.5 Consensus size: 10
14289 CTCCGTTCCG
14299 TTCCTTTTCT
1 TTCCTTTTCT
14309 TTCCTTCTT-T
1 TTCCTT-TTCT
* *
14319 TTCTTTTTGTT
1 TTCCTTTT-CT
* *
14330 TTTCTTCTCCT
1 TTCCTT-TTCT
14341 TTCCTTTTCT
1 TTCCTTTTCT
14351 TTCCTTCTT-T
1 TTCCTT-TTCT
14361 TT-C-TTTCT
1 TTCCTTTTCT
14369 TTCCT
1 TTCCT
14374 CTCTGTTGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
9 4 0.08
10 24 0.48
11 15 0.30
12 1 0.02
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (10 bp):
TTCCTTTTCT
Found at i:14334 original size:47 final size:41
Alignment explanation
Indices: 14265--14366 Score: 141
Period size: 42 Copynumber: 2.3 Consensus size: 41
14255 CCCACTTCTT
14265 CTTCTTCTTTCTTTTTTTTTTCTTCTCCGTTCCGTTCCTTTTCTTTC
1 CTTCTT-TTTCTTTTTTTTTTCTTCTCC--T---TTCCTTTTCTTTC
14312 CTTCTTTTTCTTTTTGTTTTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTTT-TTTTTCTTCTCCTTTCCTTTTCTTTC
14354 CTTCTTTTTCTTT
1 CTTCTTTTTCTTT
14367 CTTTCCTCTC
Statistics
Matches: 54, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
42 26 0.48
45 1 0.02
46 9 0.17
47 18 0.33
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (41 bp):
CTTCTTTTTCTTTTTTTTTTCTTCTCCTTTCCTTTTCTTTC
Found at i:14483 original size:24 final size:24
Alignment explanation
Indices: 14450--14498 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
14440 AGTGAGAGTC
*
14450 GCCACGAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
14474 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
14498 G
1 G
14499 TGATCGGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (24 bp):
GCCACCAATCCTTTTTATTTAGGT
Found at i:15500 original size:107 final size:106
Alignment explanation
Indices: 15315--15529 Score: 290
Period size: 107 Copynumber: 2.0 Consensus size: 106
15305 AAACCCATAC
* * * * * *
15315 TTTGAAGTTTTAAGAGGATATTTGGCCATTTGGTTCAACGAGAAATTGAAAACTAGCACATTAGG
1 TTTGAACTTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
*
15380 GCACGTTTTCTCGAATTTT-CAAACGCAAAATATCGCTTTAT
66 GCACGTTTTCTCG-ATTTTCCAAACGCAAAATATCGCCTTAT
* * *
15421 TTTGAACTTTTAAAAGGATATTTTAGCTATTTGG-TCGAACGAAAAATCGAAACCCAGCACGTTA
1 TTTGAACTTTTAAAAGGATA-TTTAGCCATTTGGTTC-AACGAAAAATCGAAAACCAGCACATTA
*
15485 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATTGCCTTAT
64 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
15528 TT
1 TT
15530 AGAAAAATTT
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
106 25 0.26
107 70 0.74
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (106 bp):
TTTGAACTTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
GCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
Found at i:15922 original size:21 final size:21
Alignment explanation
Indices: 15883--15941 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
15873 TATAAAAAAT
15883 ATGATTAACAAAT-ATAACCC
1 ATGATTAACAAATAATAACCC
15903 ATGATTAACAAATAATAACCC
1 ATGATTAACAAATAATAACCC
15924 ATGATTAACAAATAATAA
1 ATGATTAACAAATAATAA
15942 ATCATACTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.25
Consensus pattern (21 bp):
ATGATTAACAAATAATAACCC
Found at i:16357 original size:159 final size:152
Alignment explanation
Indices: 16023--16465 Score: 409
Period size: 159 Copynumber: 2.8 Consensus size: 152
16013 GCAAGTTCAA
* * * * * *
16023 AAAAAATTTAGTAAAAACTCTTATTTCGGTCATTTATTCGTACTATTTTCCCGAATTTTATTACT
1 AAAAAATTTAGTAAAAACTCTTA-TTCGGCCCTTTGTTCGTATTATTTTCTCGAATTTTATTACC
* * * *
16088 TTCAATAAAAATAAATTACTTTC-ATTTTATATTATTTTACATTATTTTATTACATTATGTTTGA
65 TTCAATAAAAATATATTATTTTCTA-TTT-TATTATTTTACATTATTTTAGTACATTATGTTTAA
* *
16152 AGTGTATTAATTTAGTGTGTTTTTT
128 AGTGTATTAATTTAGTCTGATTTTT
** * * * *
16177 AAATAAATTTTTTTAAAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTACTTTCTCGAATTTTA
1 AAA-AAA----TTTAGTAAAAACTCTTATT-CGGCCCTTTGTTCGTATTATTTTCTCGAATTTTA
* * *
16242 TTACCTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGT
60 TTACCTTCAATAAAAATATATTATTTTC-TATTTTATTATTTTACATTATTTTAGTACATTATGT
* *
16307 TTAAAATATTTGTATTAA-TTATTTCTGAATTTTT
124 TT--AA-A-GTGTATTAATTTA-GTCTG-ATTTTT
*
16341 AAAAAATTTAGTAAAAAACTCTTACTTCGGCCCTTTGTTCGTATT-TTTTCTCCGCATTTTATTA
1 AAAAAATTTAGT-AAAAACTCTTA-TTCGGCCCTTTGTTCGTATTATTTTCT-CGAATTTTATTA
16405 -CTT---TAAAAAGTATCA-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTAT-TT
63 CCTTCAATAAAAA-TAT-ATTATTTTCT-ATTTTATTATTTTACATTATTTTAGTACATTATGTT
16464 TA
125 TA
16466 TTACTTTAAA
Statistics
Matches: 236, Mismatches: 33, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
154 4 0.02
155 3 0.01
156 10 0.04
157 40 0.17
158 3 0.01
159 106 0.45
160 40 0.17
161 4 0.02
162 4 0.02
163 14 0.06
164 8 0.03
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.51
Consensus pattern (152 bp):
AAAAAATTTAGTAAAAACTCTTATTCGGCCCTTTGTTCGTATTATTTTCTCGAATTTTATTACCT
TCAATAAAAATATATTATTTTCTATTTTATTATTTTACATTATTTTAGTACATTATGTTTAAAGT
GTATTAATTTAGTCTGATTTTT
Found at i:16448 original size:13 final size:13
Alignment explanation
Indices: 16441--16465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16431 TTTATTATTT
16441 TACATTATTTTAG
1 TACATTATTTTAG
16454 TACATTATTTTA
1 TACATTATTTTA
16466 TTACTTTAAA
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:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TACATTATTTTAG
Found at i:18115 original size:49 final size:49
Alignment explanation
Indices: 18062--18189 Score: 139
Period size: 49 Copynumber: 2.6 Consensus size: 49
18052 AGTCCAACCG
* ** *
18062 TGGTCTTACACATAATCAGTTATCACATACCGATGCAATAGCCCAGCTA
1 TGGTCTTACACAGAATCACATATCACATACCGATGCAATAGCCCAGATA
* * * * *
18111 TGGTCTTATACGGAATCACATATCACTTACCGATGCCATATCCCAGATA
1 TGGTCTTACACAGAATCACATATCACATACCGATGCAATAGCCCAGATA
* *
18160 TGGTCTTATATAGAAATCACATAATCACAT
1 TGGTCTTACACAG-AATCACAT-ATCACAT
18190 TTTCACATGT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 51 0.78
50 8 0.12
51 6 0.09
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (49 bp):
TGGTCTTACACAGAATCACATATCACATACCGATGCAATAGCCCAGATA
Found at i:19985 original size:41 final size:41
Alignment explanation
Indices: 19901--20057 Score: 233
Period size: 41 Copynumber: 3.8 Consensus size: 41
19891 TTGTATATAA
* ** * * *
19901 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* * *
19942 CACCAGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
19983 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
20024 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
20058 ACTTACAAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 104 1.00
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:23192 original size:16 final size:18
Alignment explanation
Indices: 23167--23268 Score: 59
Period size: 18 Copynumber: 5.6 Consensus size: 18
23157 TCCTTCCCAC
23167 TTCTTCTTCTTCTTT-CTT
1 TTCTT-TTCTTCTTTCCTT
23185 TT-TTTTCTTCTCCGTTCCTT
1 TTCTTTTCTTCT---TTCCTT
*
23205 TTCTTTTCTTCTTT-TTT
1 TTCTTTTCTTCTTTCCTT
** * *
23222 CTTCTCCTCTCCTCTCCTT
1 -TTCTTTTCTTCTTTCCTT
* *
23241 TCCTTTTCTTTCTTTTC-T
1 TTCTTTTC-TTCTTTCCTT
23259 TTCTTTTCTT
1 TTCTTTTCTT
23269 TATTTCTTTC
Statistics
Matches: 63, Mismatches: 13, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
16 7 0.11
17 6 0.10
18 27 0.43
19 9 0.14
20 5 0.08
21 9 0.14
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (18 bp):
TTCTTTTCTTCTTTCCTT
Found at i:23223 original size:31 final size:29
Alignment explanation
Indices: 23179--23290 Score: 102
Period size: 31 Copynumber: 3.7 Consensus size: 29
23169 CTTCTTCTTC
23179 TTTCTTTTTTTTCTTCTCCGTTCCTTTTCT
1 TTTCTTTTTTTTCTTCTCC-TTCCTTTTCT
* *
23209 TTTCTTCTTTTTTCTTCTCCTCTCCTCTCCT
1 TTTCTT-TTTTTTCTTCTCCT-TCCTTTTCT
* * * *
23240 TTCCTTTTCTTTCTT-TTCTTTCTTTTCT
1 TTTCTTTTTTTTCTTCTCCTTCCTTTTCT
23268 TTAT-TTCTTTCTTTCTTCTCCTT
1 TT-TCTT-TTT-TTTCTTCTCCTT
23291 TCCCTCTCCT
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
28 10 0.15
29 5 0.08
30 21 0.32
31 29 0.45
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (29 bp):
TTTCTTTTTTTTCTTCTCCTTCCTTTTCT
Found at i:23240 original size:36 final size:36
Alignment explanation
Indices: 23167--23256 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 36
23157 TCCTTCCCAC
* * *
23167 TTCTTCTTCTTCTTTCTTTTTTTTCTTCTCCGTTCCTT
1 TTCTT-TTCTTCTTT-TTTCTTCTCCTCTCCGTTCCTT
23205 TTCTTTTCTTCTTTTTTCTTCTCCTCTCC-TCTCCTT
1 TTCTTTTCTTCTTTTTTCTTCTCCTCTCCGT-TCCTT
*
23241 TCCTTTTCTTTCTTTT
1 TTCTTTTC-TTCTTTT
23257 CTTTCTTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 1 0.02
36 24 0.52
37 16 0.35
38 5 0.11
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (36 bp):
TTCTTTTCTTCTTTTTTCTTCTCCTCTCCGTTCCTT
Found at i:23254 original size:4 final size:4
Alignment explanation
Indices: 23245--23284 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
23235 CTCCTTTCCT
*
23245 TTTC TTTC TTTTC TTTC TTTTC TTTA TTTC TTTC TTTC TT
1 TTTC TTTC -TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TT
23285 CTCCTTTCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 24 0.75
5 8 0.25
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:23566 original size:9 final size:9
Alignment explanation
Indices: 23552--23621 Score: 86
Period size: 9 Copynumber: 7.6 Consensus size: 9
23542 TTTGGTTAAA
23552 AATTACCCG
1 AATTACCCG
*
23561 AATTACCCA
1 AATTACCCG
23570 AATTACCCG
1 AATTACCCG
*
23579 ACTTACCCG
1 AATTACCCG
*
23588 ACTTACCCG
1 AATTACCCG
*
23597 AAAATTACCCA
1 --AATTACCCG
23608 AATTACCCG
1 AATTACCCG
23617 AATTA
1 AATTA
23622 AATCACTACA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
9 46 0.87
11 7 0.13
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:23574 original size:18 final size:18
Alignment explanation
Indices: 23551--23621 Score: 97
Period size: 18 Copynumber: 3.8 Consensus size: 18
23541 TTTTGGTTAA
23551 AAATTACCCGAATTACCC
1 AAATTACCCGAATTACCC
*
23569 AAATTACCCGACTTACCC
1 AAATTACCCGAATTACCC
* *
23587 GACTTACCCGAAAATTACCC
1 AAATTACCCG--AATTACCC
23607 AAATTACCCGAATTA
1 AAATTACCCGAATTA
23622 AATCACTACA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.67
20 15 0.33
ACGTcount: A:0.38, C:0.32, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATTACCCGAATTACCC
Found at i:23687 original size:17 final size:17
Alignment explanation
Indices: 23628--23687 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
23618 ATTAAATCAC
23628 TACATAATTAAAAGC-AT
1 TACATAATTAAAA-CTAT
* * *
23645 TACATAAATCTTTAAATTAC
1 TACAT-AA--TTAAAACTAT
23665 TACATAATTAAAACTAT
1 TACATAATTAAAACTAT
23682 TACATA
1 TACATA
23688 CGTCTTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 18 0.55
18 2 0.06
19 2 0.06
20 11 0.33
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAACTAT
Found at i:23724 original size:17 final size:17
Alignment explanation
Indices: 23702--23764 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 17
23692 TTTGAATCAC
23702 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
* *
23719 TACATAAGTCTTGAATTAACAC
1 TACATAA---TT-AA-AAACAT
23741 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
23758 TACATAA
1 TACATAA
23765 GTCTTGAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
17 18 0.49
18 2 0.05
19 2 0.05
20 2 0.05
21 2 0.05
22 11 0.30
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.30
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:23744 original size:22 final size:22
Alignment explanation
Indices: 23714--23779 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
23704 CATAATTAAA
*
23714 AACATTACATAAGTCTTGAATT
1 AACACTACATAAGTCTTGAATT
*
23736 AACACTACATAA---TT-AA-A
1 AACACTACATAAGTCTTGAATT
*
23753 AACATTACATAAGTCTTGAATT
1 AACACTACATAAGTCTTGAATT
23775 AACAC
1 AACAC
23780 ATAATTGACA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
17 11 0.32
18 2 0.06
19 2 0.06
20 2 0.06
21 2 0.06
22 15 0.44
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (22 bp):
AACACTACATAAGTCTTGAATT
Found at i:23751 original size:39 final size:40
Alignment explanation
Indices: 23616--23779 Score: 202
Period size: 37 Copynumber: 4.2 Consensus size: 40
23606 CAAATTACCC
* *
23616 GAATTAAATCACTACATAATTAAAAGCATTACATAAATCTTT
1 GAATT-AA-CACTACATAATTAAAAACATTACATAAGTCTTT
* *
23658 AAATT---ACTACATAATT-AAAACTATTACATACGTCTTT
1 GAATTAACACTACATAATTAAAAAC-ATTACATAAGTCTTT
23695 GAA-T--CACTACATAATTAAAAACATTACATAAGTC-TT
1 GAATTAACACTACATAATTAAAAACATTACATAAGTCTTT
23731 GAATTAACACTACATAATTAAAAACATTACATAAGTC-TT
1 GAATTAACACTACATAATTAAAAACATTACATAAGTCTTT
23770 GAATTAACAC
1 GAATTAACAC
23780 ATAATTGACA
Statistics
Matches: 110, Mismatches: 6, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
36 10 0.09
37 49 0.45
38 5 0.05
39 42 0.38
42 4 0.04
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (40 bp):
GAATTAACACTACATAATTAAAAACATTACATAAGTCTTT
Found at i:26597 original size:16 final size:16
Alignment explanation
Indices: 26576--26631 Score: 96
Period size: 17 Copynumber: 3.5 Consensus size: 16
26566 TGGCCTTGAT
26576 ATTATAATGATGAAAA
1 ATTATAATGATGAAAA
26592 ATTATAATGATGAAAAA
1 ATTATAATGATG-AAAA
26609 ATTATAATGATG-AAA
1 ATTATAATGATGAAAA
26624 ATTATAAT
1 ATTATAAT
26632 ATTAGTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 11 0.28
16 12 0.31
17 16 0.41
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (16 bp):
ATTATAATGATGAAAA
Found at i:26857 original size:16 final size:15
Alignment explanation
Indices: 26821--26853 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
26811 ATGTGTAAAG
26821 AAATTTGTAAGTAAT
1 AAATTTGTAAGTAAT
26836 AAATTTGTAAGTAAT
1 AAATTTGTAAGTAAT
26851 AAA
1 AAA
26854 ATTTTACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (15 bp):
AAATTTGTAAGTAAT
Found at i:26925 original size:42 final size:43
Alignment explanation
Indices: 26836--26930 Score: 140
Period size: 42 Copynumber: 2.2 Consensus size: 43
26826 TGTAAGTAAT
26836 AAATTTGTAAGTAATAAAATTTTACTTACACTGGATGTGTAAAG
1 AAATTTGTAAGTAATAAAATTTTAC-TACACTGGATGTGTAAAG
**
26880 AAATTTGTAAGTAAT-AAATTTATA-TATGCTGGATGTGTAAAG
1 AAATTTGTAAGTAATAAAATTT-TACTACACTGGATGTGTAAAG
26922 AAATTTGTA
1 AAATTTGTA
26931 CACTGGATGT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 25 0.52
43 6 0.12
44 17 0.35
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.38
Consensus pattern (43 bp):
AAATTTGTAAGTAATAAAATTTTACTACACTGGATGTGTAAAG
Found at i:26938 original size:25 final size:25
Alignment explanation
Indices: 26908--26955 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
26898 TTTATATATG
26908 CTGGATGTGTAAAGAAATTTGTACA
1 CTGGATGTGTAAAGAAATTTGTACA
26933 CTGGATGTGTAAAGAAATTTGTA
1 CTGGATGTGTAAAGAAATTTGTA
26956 AGTAATAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.33
Consensus pattern (25 bp):
CTGGATGTGTAAAGAAATTTGTACA
Found at i:28686 original size:14 final size:15
Alignment explanation
Indices: 28654--28687 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28644 TATGTCTAAG
*
28654 TTTTATTGTTTTTAT
1 TTTTATTGTATTTAT
28669 TTTTATT-TATTTAT
1 TTTTATTGTATTTAT
28683 TTTTA
1 TTTTA
28688 AGGTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTATTGTATTTAT
Found at i:28704 original size:37 final size:36
Alignment explanation
Indices: 28603--28705 Score: 95
Period size: 38 Copynumber: 2.8 Consensus size: 36
28593 GATTTGAGCT
*
28603 TTTATTTTTAAGGTGATATTTGTTTGATTTTTTCTTA
1 TTTATTTTTAAGGTGATATTT-TTTTATTTTTTCTTA
**
28640 TTT-TTATGTCTAA-GTTTTATTGTTTTTATTTTTAT-TTA
1 TTTATT-T-T-TAAGGTGATATT-TTTTTATTTTT-TCTTA
28678 TTTATTTTTAAGGTGATATTTATTTTAT
1 TTTATTTTTAAGGTGATATTT-TTTTAT
28706 CTACAATAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
36 6 0.11
37 17 0.32
38 23 0.43
39 7 0.13
ACGTcount: A:0.20, C:0.02, G:0.11, T:0.67
Consensus pattern (36 bp):
TTTATTTTTAAGGTGATATTTTTTTATTTTTTCTTA
Found at i:32738 original size:19 final size:19
Alignment explanation
Indices: 32714--32750 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
32704 AGTCTCTTTC
32714 CAGGGATAGTAAAACACGG
1 CAGGGATAGTAAAACACGG
32733 CAGGGATAGTAAAACACG
1 CAGGGATAGTAAAACACG
32751 AATATTGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.16, G:0.30, T:0.11
Consensus pattern (19 bp):
CAGGGATAGTAAAACACGG
Found at i:43302 original size:6 final size:7
Alignment explanation
Indices: 43277--43301 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43267 ATAATAAATA
43277 TTTTTAT
1 TTTTTAT
43284 TTTTTAT
1 TTTTTAT
43291 TTTTTAT
1 TTTTTAT
43298 TTTT
1 TTTT
43302 AAAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:43574 original size:30 final size:32
Alignment explanation
Indices: 43521--43585 Score: 107
Period size: 30 Copynumber: 2.1 Consensus size: 32
43511 ATTTTACTAA
43521 ATTCAAATTAATTACTGTCATTTTTAAATTAT
1 ATTCAAATTAATTACTGTCATTTTTAAATTAT
*
43553 ATTCAAATTAATTAC-GT-ATTTTTTAATTAT
1 ATTCAAATTAATTACTGTCATTTTTAAATTAT
43583 ATT
1 ATT
43586 GCCCCCAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 15 0.47
31 2 0.06
32 15 0.47
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (32 bp):
ATTCAAATTAATTACTGTCATTTTTAAATTAT
Found at i:48037 original size:18 final size:19
Alignment explanation
Indices: 48000--48037 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
47990 ATATTCACTA
*
48000 AAAAAAATATTATTCCAAC
1 AAAAAAATATTATTCAAAC
*
48019 AAAAAAAT-TTATTTAAAC
1 AAAAAAATATTATTCAAAC
48037 A
1 A
48038 TGGTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAAATATTATTCAAAC
Found at i:48395 original size:53 final size:53
Alignment explanation
Indices: 48331--48436 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
48321 AAATTAAAAG
**
48331 GGAAACAGTTTGAATAAATTGAAAGAAGAATGGCAAGGACTCATGCCAATACC
1 GGAAACAGTTTGAATAAATTGAAAGAAGAATGGCAAACACTCATGCCAATACC
*
48384 GGAAAGAGTTTGAATAAATTGAAAGAAGAATGGCAAACACTCATGCCAATACC
1 GGAAACAGTTTGAATAAATTGAAAGAAGAATGGCAAACACTCATGCCAATACC
48437 CAAGGAGATG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (53 bp):
GGAAACAGTTTGAATAAATTGAAAGAAGAATGGCAAACACTCATGCCAATACC
Found at i:49955 original size:50 final size:50
Alignment explanation
Indices: 49880--49980 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
49870 GTCTGGAACA
49880 GGACTGAAATCCGGTAACTCTGAATAATTTGATCGCTTGGCAAAGAAGGC
1 GGACTGAAATCCGGTAACTCTGAATAATTTGATCGCTTGGCAAAGAAGGC
* *
49930 GGACTGAAATCGGGTAACTCTGAATAATTTGATCGCTTGGCAACGAAGGC
1 GGACTGAAATCCGGTAACTCTGAATAATTTGATCGCTTGGCAAAGAAGGC
49980 G
1 G
49981 CTGTTGCTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.24
Consensus pattern (50 bp):
GGACTGAAATCCGGTAACTCTGAATAATTTGATCGCTTGGCAAAGAAGGC
Found at i:55425 original size:501 final size:502
Alignment explanation
Indices: 54384--55439 Score: 1864
Period size: 501 Copynumber: 2.1 Consensus size: 502
54374 TAATCCTACA
* ** *
54384 ATATTGATGCCCTAAATGAAGGTTAGAGCCCCCCTTCACATCATAATTATTTCTATCCTTGGAAA
1 ATATTGTTGCCCTAAATGAAGGTTAGAG-CCCCCTTCACATGGTAATTATTTCTATCATTGGAAA
* * *
54449 GTGACTGGTTATGCATTTTCCAATGCTGCTTGTCATTGTATTTGGTTTGCTCTAAATGAAGGTTA
65 GTGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTA
* * *
54514 GTGCTATCATAATTATTCCTATCCTTGTAAATTGACTTATTTTTCATTTGCGCGTACTGCTTGTC
130 GTGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGCGCGTAATGCTTGTC
* * *
54579 TTTGCGTTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAT
195 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAA
*
54644 AACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTGGTTGTGTGAAAATGTCTTCCTTTTTCCA
260 AACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCA
*
54709 AGATGAATGAGTGGACTCAGTTTTGTTAGGACTATATGTCATGCTCTTCTTGTTGTTTTGAATGG
325 AGATGAATGAGTGGACTCAGTTTTGTCAGGACTATATGTCATGCTCTTCTTGTTGTTTTGAATGG
54774 GTACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
390 GTACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
54839 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAC
455 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAC
54887 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTCTATCATTGGAAAG
1 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTCTATCATTGGAAAG
* *
54952 TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAATGTTGG
66 TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
55017 TGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGC-CAGTAATGCTTGTC
131 TGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGCGC-GTAATGCTTGTC
*
55081 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTTCCTGTATAA
195 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAA
*
55146 AACTTGAGTAATGCTAAGGTACAAAGAAGTC-GAGTCGTTGTGTGAAAATGTGTTCCTTTTTCCA
260 AACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCA
* *
55210 AGATGAATGAGTGGACTCAGTTTTGTCAGGACTATGTGTCGTGCTCTTCTTGTTGTTTTGAATGG
325 AGATGAATGAGTGGACTCAGTTTTGTCAGGACTATATGTCATGCTCTTCTTGTTGTTTTGAATGG
* *
55275 GTACGAGGCTCCTAGCACCTTTAGGGAACTGGAGCTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
390 GTACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTT
*
55340 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAT
455 TAACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAC
55388 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTC
1 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTC
55440 CATCCTTGAA
Statistics
Matches: 528, Mismatches: 24, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
501 256 0.48
502 245 0.46
503 27 0.05
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (502 bp):
ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTTCTATCATTGGAAAG
TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
TGCCATCATAATTATTCCTATCCTTGTAAATTGACTGATTTTTCATTTGCGCGTAATGCTTGTCA
TTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACATCCTGTATAAA
ACTTGAGTAATGCTAAGGTACAAAGAAGTCTGAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCAA
GATGAATGAGTGGACTCAGTTTTGTCAGGACTATATGTCATGCTCTTCTTGTTGTTTTGAATGGG
TACGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTT
AACCAAAGGCTTGCTATACCCCAAATAGTTGCTTCTATTTTGATGAC
Found at i:62027 original size:4 final size:4
Alignment explanation
Indices: 62018--62051 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
62008 AAGTTTTATT
62018 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
62052 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:62059 original size:22 final size:22
Alignment explanation
Indices: 62001--62060 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
61991 AAGTGGCCCA
*
62001 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
62025 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
62046 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
62061 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:75151 original size:271 final size:271
Alignment explanation
Indices: 74668--75546 Score: 1740
Period size: 271 Copynumber: 3.2 Consensus size: 271
74658 GCAAGGTGTG
*
74668 TGCATGAGAACAAAGTTTATTACCTTATTGTGGATCTAGTCTATTCATTAGACTGGTGGAAATTG
1 TGCATGAGAACAAACTTTATTACCTTATTGTGGATCTAGTCTATTCATTAGACTGGTGGAAATTG
74733 TGGGTTATGGTTAGTAGAATGTATGAATTTCATGAGGCTTGATTATTTAAGCTGTAAGAGTTTAA
66 TGGGTTATGGTTAGTAGAATGTATGAATTTCATGAGGCTTGATTATTTAAGCTGTAAGAGTTTAA
74798 TATATCCATTTCCAATTCTTAATTTAAATGGTATGGGTTTAATGGAACTTTTTCTTGTGGGTTCT
131 TATATCCATTTCCAATTCTTAATTTAAATGGTATGGGTTTAATGGAACTTTTTCTTGTGGGTTCT
74863 GTGGGTAATAAGGGAAATTTTGTATTGCTTTAATGTAGCTTCTTGTTATTCTTGATAATCAATAT
196 GTGGGTAATAAGGGAAATTTTGTATTGCTTTAATGTAGCTTCTTGTTATTCTTGATAATCAATAT
74928 TAATGCACTAA
261 TAATGCACTAA
74939 TGCATGAGAACAAACTTTATTACCTTATTGTGGATCTAGTCTATTCATTAGACTGGTGGAAATTG
1 TGCATGAGAACAAACTTTATTACCTTATTGTGGATCTAGTCTATTCATTAGACTGGTGGAAATTG
75004 TGGGTTATGGTTAGTAGAATGTATGAATTTCATGAGGCTTGATTATTTAAGCTGTAAGAGTTTAA
66 TGGGTTATGGTTAGTAGAATGTATGAATTTCATGAGGCTTGATTATTTAAGCTGTAAGAGTTTAA
75069 TATATCCATTTCCAATTCTTAATTTAAATGGTATGGGTTTAATGGAACTTTTTCTTGTGGGTTCT
131 TATATCCATTTCCAATTCTTAATTTAAATGGTATGGGTTTAATGGAACTTTTTCTTGTGGGTTCT
75134 GTGGGTAATAAGGGAAATTTTGTATTGCTTTAATGTAGCTTCTTGTTATTCTTGATAATCAATAT
196 GTGGGTAATAAGGGAAATTTTGTATTGCTTTAATGTAGCTTCTTGTTATTCTTGATAATCAATAT
75199 TAATGCACTAA
261 TAATGCACTAA
75210 TGCATGAGAACAAACTTTATTACCTTATTGTGGATCTAGTCTATTCATTAGACTGGTGGAAATTG
1 TGCATGAGAACAAACTTTATTACCTTATTGTGGATCTAGTCTATTCATTAGACTGGTGGAAATTG
75275 TGGGTTATGGTTAGTAGAATGTATGAATTTCATGAGGCTTGATTATTTAAGCTGTAAGAGTTTAA
66 TGGGTTATGGTTAGTAGAATGTATGAATTTCATGAGGCTTGATTATTTAAGCTGTAAGAGTTTAA
75340 TATATCCATTTCCAATTCTTAATTTAAATGGTATGGGTTTAATGGAACTTTTTCTTGTGGGTTCT
131 TATATCCATTTCCAATTCTTAATTTAAATGGTATGGGTTTAATGGAACTTTTTCTTGTGGGTTCT
75405 GTGGGTAATAAGGGAAATTTTGTATTGCTTTAATGTAGCTTCTTGTTATTCTTGATAATCAATAT
196 GTGGGTAATAAGGGAAATTTTGTATTGCTTTAATGTAGCTTCTTGTTATTCTTGATAATCAATAT
75470 TAATGCACTAA
261 TAATGCACTAA
*
75481 TGCATGAGAACAAACTTTATTACCTTATTGTGGATCTAGTCTATTCATTGGACTGGTGGAAATTG
1 TGCATGAGAACAAACTTTATTACCTTATTGTGGATCTAGTCTATTCATTAGACTGGTGGAAATTG
75546 T
66 T
75547 AGTGTTGACA
Statistics
Matches: 606, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
271 606 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (271 bp):
TGCATGAGAACAAACTTTATTACCTTATTGTGGATCTAGTCTATTCATTAGACTGGTGGAAATTG
TGGGTTATGGTTAGTAGAATGTATGAATTTCATGAGGCTTGATTATTTAAGCTGTAAGAGTTTAA
TATATCCATTTCCAATTCTTAATTTAAATGGTATGGGTTTAATGGAACTTTTTCTTGTGGGTTCT
GTGGGTAATAAGGGAAATTTTGTATTGCTTTAATGTAGCTTCTTGTTATTCTTGATAATCAATAT
TAATGCACTAA
Found at i:78081 original size:6 final size:6
Alignment explanation
Indices: 78065--78111 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
78055 GCCCCTCCAT
*
78065 TTTTCA TTTTTCA TTTTCA TTTTCA TTTTCA TTTTTA TTTTCA TTTT
1 TTTTCA -TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
78112 TTTTACTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 32 0.84
7 6 0.16
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTCA
Found at i:78942 original size:12 final size:11
Alignment explanation
Indices: 78921--78966 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
78911 ATTTTTCTTC
*
78921 TTTTTCTTTTA
1 TTTTTTTTTTA
78932 TTTTTTATTTTAA
1 TTTTTT-TTTT-A
78945 TTTTTCTTTTTA
1 TTTTT-TTTTTA
78957 TTTTTTTTTT
1 TTTTTTTTTT
78967 GCTTTTGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 10 0.32
12 10 0.32
13 10 0.32
14 1 0.03
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:78948 original size:18 final size:18
Alignment explanation
Indices: 78927--78998 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
78917 CTTCTTTTTC
78927 TTTTATTTTTTATTTTAA
1 TTTTATTTTTTATTTTAA
**
78945 TTTT-TCTTTTTATTTTTT
1 TTTTAT-TTTTTATTTTAA
** * *
78963 TTTTGCTTTTGATTTTGA
1 TTTTATTTTTTATTTTAA
78981 TTTTGATTTTTTGATTTT
1 TTTT-ATTTTTT-ATTTT
78999 TTTTGAATTG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 1 0.02
18 31 0.76
19 4 0.10
20 5 0.12
ACGTcount: A:0.12, C:0.03, G:0.07, T:0.78
Consensus pattern (18 bp):
TTTTATTTTTTATTTTAA
Found at i:78949 original size:24 final size:24
Alignment explanation
Indices: 78921--78966 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
78911 ATTTTTCTTC
78921 TTTTTC-TTTTATTTTTTATTTTAA
1 TTTTTCTTTTTATTTTTT-TTTTAA
78945 TTTTTCTTTTTATTTTTTTTTT
1 TTTTTCTTTTTATTTTTTTTTT
78967 GCTTTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (24 bp):
TTTTTCTTTTTATTTTTTTTTTAA
Found at i:78972 original size:12 final size:12
Alignment explanation
Indices: 78921--79002 Score: 69
Period size: 12 Copynumber: 6.7 Consensus size: 12
78911 ATTTTTCTTC
*
78921 TTTTTCTTTT-A
1 TTTTTTTTTTGA
*
78932 TTTTTTATTTTAA
1 TTTTTT-TTTTGA
78945 TTTTTCTTTTT-A
1 TTTTT-TTTTTGA
*
78957 TTTTTTTTTTGC
1 TTTTTTTTTTGA
**
78969 TTTTGATTTTGA
1 TTTTTTTTTTGA
78981 TTTTGATTTTTTGA
1 TTTT--TTTTTTGA
78995 TTTTTTTT
1 TTTTTTTT
79003 GAATTGGATC
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
11 10 0.17
12 27 0.47
13 10 0.17
14 11 0.19
ACGTcount: A:0.11, C:0.04, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTTGA
Found at i:84091 original size:60 final size:60
Alignment explanation
Indices: 84027--84150 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
84017 CAAGCATGTG
* * * *
84027 TATATAAAAATTAAAAATATGTATA-AAAGATATATATAT-ATATAAGATTTATTAAATATA
1 TATATAAAAATAAAAAATATGTATATAAAGATATATAAATAATATAAG--GTATAAAATATA
* *
84087 TATATGAAAATAAAAAATGTGTATATAAAGATATATAAATAATATAAGGTATAAAATATA
1 TATATAAAAATAAAAAATATGTATATAAAGATATATAAATAATATAAGGTATAAAATATA
84147 TATA
1 TATA
84151 ATATATATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 36 0.64
61 13 0.23
62 7 0.12
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (60 bp):
TATATAAAAATAAAAAATATGTATATAAAGATATATAAATAATATAAGGTATAAAATATA
Found at i:84149 original size:18 final size:19
Alignment explanation
Indices: 84041--84158 Score: 69
Period size: 18 Copynumber: 6.0 Consensus size: 19
84031 TAAAAATTAA
* * *
84041 AAATATGTATAAAAGATAT
1 AAATATATATAAGATATAT
* *
84060 ATATATATATAAGATTTATT
1 AAATATATATAAGATATA-T
* * *
84080 AAATATATATATGAAAATAAA
1 AAATATATATAAG-ATAT-AT
*
84101 AAATGTGTATATAAAGATATAT
1 AAA--TATATAT-AAGATATAT
*
84123 AAATA-ATATAAGGTATA-
1 AAATATATATAAGATATAT
*
84140 AAATATATATAATATATAT
1 AAATATATATAAGATATAT
84159 TAGAAAAGTA
Statistics
Matches: 73, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
17 5 0.07
18 17 0.23
19 17 0.23
20 13 0.18
21 5 0.07
22 5 0.07
23 9 0.12
24 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (19 bp):
AAATATATATAAGATATAT
Found at i:86644 original size:6 final size:7
Alignment explanation
Indices: 86625--86658 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
86615 TTAGCCTCTC
86625 CATTTTT
1 CATTTTT
86632 CATTTTT
1 CATTTTT
86639 CATTTTT
1 CATTTTT
86646 CA-TTTT
1 CATTTTT
86652 CATTTTT
1 CATTTTT
86659 TTGACTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:86659 original size:14 final size:14
Alignment explanation
Indices: 86625--86658 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
86615 TTAGCCTCTC
86625 CATTTTTCATTTTT
1 CATTTTTCATTTTT
86639 CATTTTTCA-TTTT
1 CATTTTTCATTTTT
86652 CATTTTT
1 CATTTTT
86659 TTGACTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:87475 original size:6 final size:6
Alignment explanation
Indices: 87464--87511 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
87454 CTCATTTTTC
**
87464 TTCTTT TTCTTT TAT-TTT TTCTTT TAATTT TTCTTT TTCTTT TT-TTT
1 TTCTTT TTCTTT T-TCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
87511 T
1 T
87512 CTGCTTTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
5 5 0.14
6 30 0.83
7 1 0.03
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.83
Consensus pattern (6 bp):
TTCTTT
Found at i:87487 original size:18 final size:16
Alignment explanation
Indices: 87458--87511 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 16
87448 TGACCTCTCA
*
87458 TTTTTCTTCTTTTTCTT
1 TTTTTTTTCTTTTT-TT
87475 TTATTTTTTCTTTTAATTT
1 TT-TTTTTTCTTTT--TTT
*
87494 TTCTTTTTCTTTTTTT
1 TTTTTTTTCTTTTTTT
87510 TT
1 TT
87512 CTGCTTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
18 20 0.62
19 4 0.12
20 1 0.03
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTT
Found at i:87506 original size:24 final size:23
Alignment explanation
Indices: 87467--87511 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
87457 ATTTTTCTTC
87467 TTTTTCTTTTATTTTTTCTTTTAA
1 TTTTTCTTTTATTTTTT-TTTTAA
87491 TTTTTCTTTT-TCTTTTTTTTT
1 TTTTTCTTTTAT-TTTTTTTTT
87512 CTGCTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTCTTTTATTTTTTTTTTAA
Found at i:91929 original size:72 final size:72
Alignment explanation
Indices: 91812--91955 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
91802 GAAAATAGGA
91812 AATGAACGGGTAAAAAAAAGAGATGCGAAATGAAAAAAGAAAAAAAAAACCTTGGAGTAAACCTA
1 AATGAACGGGTAAAAAAAAGAGATGCGAAATGAAAAAAGAAAAAAAAAACCTTGGAGTAAACCTA
91877 TTTTTGT
66 TTTTTGT
*
91884 AATGAACGGGTAAAAAAAAGAGATGCGAAATGAAAAAAGAAAAAAAAAACCTTGGAGTAAATCTA
1 AATGAACGGGTAAAAAAAAGAGATGCGAAATGAAAAAAGAAAAAAAAAACCTTGGAGTAAACCTA
91949 TTTTTGT
66 TTTTTGT
91956 TTTTTATTTC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.53, C:0.08, G:0.19, T:0.20
Consensus pattern (72 bp):
AATGAACGGGTAAAAAAAAGAGATGCGAAATGAAAAAAGAAAAAAAAAACCTTGGAGTAAACCTA
TTTTTGT
Found at i:92471 original size:8 final size:8
Alignment explanation
Indices: 92458--92498 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
92448 TATTTTATGC
92458 ATTTTTAT
1 ATTTTTAT
92466 ATTTTTAT
1 ATTTTTAT
*
92474 ATTTTTGT
1 ATTTTTAT
92482 A--TTTAT
1 ATTTTTAT
92488 ATTTTTA-
1 ATTTTTAT
92495 ATTT
1 ATTT
92499 AATTCAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
6 5 0.17
7 4 0.14
8 20 0.69
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (8 bp):
ATTTTTAT
Found at i:92510 original size:17 final size:17
Alignment explanation
Indices: 92488--92521 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
92478 TTGTATTTAT
92488 ATTTTTAATTTAATTCA
1 ATTTTTAATTTAATTCA
* *
92505 ATTTTTATTTTATTTCA
1 ATTTTTAATTTAATTCA
92522 CTTTAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTAATTTAATTCA
Found at i:92670 original size:18 final size:19
Alignment explanation
Indices: 92649--92731 Score: 77
Period size: 18 Copynumber: 4.5 Consensus size: 19
92639 ATAAAAAATA
92649 TTCAAAAAAATT-CGTGTT
1 TTCAAAAAAATTCCGTGTT
92667 TTCAAAAAAAATTCCG-GTGT
1 TTC-AAAAAAATTCCGTGT-T
* * *
92687 TTC-AAAAATTTTCATGTT
1 TTCAAAAAAATTCCGTGTT
92705 TTC--AAAAATTCCCGTGTT
1 TTCAAAAAAATT-CCGTGTT
92723 TTCAAAAAA
1 TTCAAAAAA
92732 TTTCTATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
17 6 0.12
18 23 0.44
19 13 0.25
20 10 0.19
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (19 bp):
TTCAAAAAAATTCCGTGTT
Found at i:92675 original size:20 final size:20
Alignment explanation
Indices: 92652--92694 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
92642 AAAAATATTC
92652 AAAAAAATT-C-GTGTTTTCA
1 AAAAAAATTCCGGTG-TTTCA
92671 AAAAAAATTCCGGTGTTTCA
1 AAAAAAATTCCGGTGTTTCA
92691 AAAA
1 AAAA
92695 TTTTCATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 10 0.45
21 3 0.14
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (20 bp):
AAAAAAATTCCGGTGTTTCA
Found at i:92742 original size:18 final size:18
Alignment explanation
Indices: 92649--92747 Score: 76
Period size: 19 Copynumber: 5.4 Consensus size: 18
92639 ATAAAAAATA
* *
92649 TTCAAAAAAATTCGTGTT
1 TTCAAAAAATTTCATGTT
* **
92667 TTCAAAAAAAATTCCGGTGT
1 TTC-AAAAAATTTCATGT-T
*
92687 TTCAAAAATTTTCATGTT
1 TTCAAAAAATTTCATGTT
* *
92705 TTC-AAAAATTCCCGTGTT
1 TTCAAAAAATT-TCATGTT
92723 TTCAAAAAATTTCTAT-TT
1 TTCAAAAAATTTC-ATGTT
92741 TTCAAAA
1 TTCAAAA
92748 TTTTTATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
17 6 0.09
18 25 0.38
19 30 0.46
20 4 0.06
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.40
Consensus pattern (18 bp):
TTCAAAAAATTTCATGTT
Found at i:92749 original size:35 final size:35
Alignment explanation
Indices: 92649--92747 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 35
92639 ATAAAAAATA
* * *
92649 TTCAAAAAAATTCGTGTTTTCAAAAAAAATTCCGGTGT
1 TTCAAAAAATTTCATGTTTTC---AAAAATTCCCGTGT
*
92687 TTCAAAAATTTTCATGTTTTCAAAAATTCCCGTGTT
1 TTCAAAAAATTTCATGTTTTCAAAAATTCCCGTG-T
92723 TTCAAAAAATTTCTAT-TTTTCAAAA
1 TTCAAAAAATTTC-ATGTTTTCAAAA
92748 TTTTTATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
35 12 0.22
36 22 0.41
37 2 0.04
38 18 0.33
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.40
Consensus pattern (35 bp):
TTCAAAAAATTTCATGTTTTCAAAAATTCCCGTGT
Found at i:92759 original size:17 final size:16
Alignment explanation
Indices: 92728--92758 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
92718 GTGTTTTCAA
92728 AAAATTTCTATTTTTC
1 AAAATTTCTATTTTTC
*
92744 AAAATTTTTATTTTT
1 AAAATTTCTATTTTT
92759 TTATTTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
AAAATTTCTATTTTTC
Found at i:103370 original size:125 final size:125
Alignment explanation
Indices: 103148--103398 Score: 484
Period size: 125 Copynumber: 2.0 Consensus size: 125
103138 GTTCTGATTT
*
103148 TCAGGCTTCTCCTGATTATTGCCCGGCTGCCATCCATGAATTCCCAATTCCTCCTAAAGCTCTTT
1 TCAGGCTTCTCCTGATTATTGCCCGGCTGCCATCCATGAATTCCCAATCCCTCCTAAAGCTCTTT
103213 TAGGACTTCATTCTTATTGCCCTGTTTACTTTGATGCATTTCATGCTGTTCTTGTGGATG
66 TAGGACTTCATTCTTATTGCCCTGTTTACTTTGATGCATTTCATGCTGTTCTTGTGGATG
*
103273 TCAGGCTTCTCCTGATTATTGCCCGGCTGCCATCCATGAATTCCGAATCCCTCCTAAAGCTCTTT
1 TCAGGCTTCTCCTGATTATTGCCCGGCTGCCATCCATGAATTCCCAATCCCTCCTAAAGCTCTTT
103338 TAGGACTTCATTCTTATTGCCCTGTTTACTTTGATGCATTTCATGCTGTTCTTGTGGATG
66 TAGGACTTCATTCTTATTGCCCTGTTTACTTTGATGCATTTCATGCTGTTCTTGTGGATG
103398 T
1 T
103399 AAGTGTTCAC
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (125 bp):
TCAGGCTTCTCCTGATTATTGCCCGGCTGCCATCCATGAATTCCCAATCCCTCCTAAAGCTCTTT
TAGGACTTCATTCTTATTGCCCTGTTTACTTTGATGCATTTCATGCTGTTCTTGTGGATG
Found at i:112822 original size:17 final size:16
Alignment explanation
Indices: 112792--112825 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
112782 ATATCTAAGC
*
112792 AAAAAATTAGATTGAT
1 AAAAAATTAAATTGAT
112808 AAAATAATTAAATTGAT
1 AAAA-AATTAAATTGAT
112825 A
1 A
112826 CGATATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (16 bp):
AAAAAATTAAATTGAT
Found at i:113449 original size:25 final size:25
Alignment explanation
Indices: 113421--113468 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
113411 AAAAGGAATC
113421 TTTATGTTTGT-TTAATAATTATTTT
1 TTTA-GTTTGTCTTAATAATTATTTT
* *
113446 TTTAGTTTTTCTTAATTATTATT
1 TTTAGTTTGTCTTAATAATTATT
113469 ATTCTTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (25 bp):
TTTAGTTTGTCTTAATAATTATTTT
Found at i:116845 original size:130 final size:131
Alignment explanation
Indices: 116584--116853 Score: 400
Period size: 130 Copynumber: 2.1 Consensus size: 131
116574 TCCATGAAAC
* *
116584 TAAAAAATAGATGTTGTAATGAACTTAAATTTAACAAATAATTAGATCTAAATTTTAAAATCTGA
1 TAAAAAATAGACGTTGTAATGAACTTAAAATTAACAAATAATTAGATCTAAATTTTAAAATCTGA
* * **
116649 AAAAATAAAGGGAATAGATTTCAAATTTATGAAAAAATACCGAAACTTATTGCATATCTTAATCA
66 AAAAATAAAGGGAATAAATTTCAAATTTATAAAAAAATACAAAAACTTATTGCATATCTTAATCA
116714 T
131 T
* **
116715 TAAAAAATAGACGTTGTAATGAACTTAAAATTAACAAATAATTAGATCTGAATTTTAAAAT-TTT
1 TAAAAAATAGACGTTGTAATGAACTTAAAATTAACAAATAATTAGATCTAAATTTTAAAATCTGA
* * *
116779 AAAAATAAAGGGACTAAATTTTAAATTTATAAAAAAATACAAAAACTTA-TGACATTTCTTAATC
66 AAAAATAAAGGGAATAAATTTCAAATTTATAAAAAAATACAAAAACTTATTG-CATATCTTAATC
116843 AT
130 AT
*
116845 TAAATAATA
1 TAAAAAATA
116854 ATTGAAACTA
Statistics
Matches: 125, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
129 2 0.02
130 65 0.52
131 58 0.46
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (131 bp):
TAAAAAATAGACGTTGTAATGAACTTAAAATTAACAAATAATTAGATCTAAATTTTAAAATCTGA
AAAAATAAAGGGAATAAATTTCAAATTTATAAAAAAATACAAAAACTTATTGCATATCTTAATCA
T
Found at i:117839 original size:4 final size:4
Alignment explanation
Indices: 117830--117860 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
117820 TGATGTTATG
117830 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
117861 GAGAAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:121050 original size:2 final size:2
Alignment explanation
Indices: 121043--121072 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
121033 GCATAAGTGG
121043 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
121073 TATATATACG
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:121434 original size:16 final size:17
Alignment explanation
Indices: 121413--121448 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
121403 TTATATAAAT
*
121413 TTTGACAT-ATTATTTA
1 TTTGACATAATTATATA
121429 TTTGACATAATTATATA
1 TTTGACATAATTATATA
121446 TTT
1 TTT
121449 TTATTATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTGACATAATTATATA
Found at i:124328 original size:24 final size:22
Alignment explanation
Indices: 124278--124328 Score: 52
Period size: 24 Copynumber: 2.2 Consensus size: 22
124268 GCAGAAAACT
124278 AATA-CTAGAATTTAACCTAAA
1 AATATCTAGAATTTAACCTAAA
124299 ATATATCTA-AATTTGAACCCTAATA
1 A-ATATCTAGAATTT-AA-CCTAA-A
124324 AATAT
1 AATAT
124329 GAAAATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
21 1 0.04
22 8 0.32
23 5 0.20
24 9 0.36
25 2 0.08
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (22 bp):
AATATCTAGAATTTAACCTAAA
Done.