Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold437
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: 325478
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 2 of 3
Found at i:147402 original size:50 final size:48
Alignment explanation
Indices: 147317--147412 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 48
147307 CCGGAGACTG
147317 CAAATACATGAAAAAATTTAAAAAAAAAAAATGGGTCAGATACAGGCTC
1 CAAATACATGAAAAAATTT-AAAAAAAAAAATGGGTCAGATACAGGCTC
** *
147366 CAAATACATGAAAAAAAACTTT-AAAAAAAATTTGGGTCGGATACAGG
1 CAAATACATG--AAAAAA-TTTAAAAAAAAAAATGGGTCAGATACAGG
147413 TAAGTATCCG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 10 0.24
50 22 0.54
51 6 0.15
52 3 0.07
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (48 bp):
CAAATACATGAAAAAATTTAAAAAAAAAAATGGGTCAGATACAGGCTC
Found at i:148339 original size:23 final size:23
Alignment explanation
Indices: 148283--148339 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 23
148273 ATTAGTTTCT
*
148283 AATAATA-TATT-TTTAAATTAA
1 AATAATATTATTATTTAAATAAA
** * *
148304 TTTATTATAATTATTTAAATAAA
1 AATAATATTATTATTTAAATAAA
148327 AATAATATTATTA
1 AATAATATTATTA
148340 AAATAACTAT
Statistics
Matches: 25, Mismatches: 9, Indels: 2
0.69 0.25 0.06
Matches are distributed among these distances:
21 4 0.16
22 3 0.12
23 18 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATAATATTATTATTTAAATAAA
Found at i:148478 original size:22 final size:22
Alignment explanation
Indices: 148428--148488 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
148418 TAAGTTTAGC
148428 TTTAA-ATTAAT-TTAAAAATA
1 TTTAATATTAATATTAAAAATA
*
148448 TATT-TTATTAATATTAAAAATA
1 T-TTAATATTAATATTAAAAATA
*
148470 TTTAATATTTATAATTAAA
1 TTTAATATTAAT-ATTAAA
148489 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 1 0.03
21 10 0.30
22 16 0.48
23 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAATATTAATATTAAAAATA
Found at i:148504 original size:29 final size:27
Alignment explanation
Indices: 148429--148513 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
148419 AAGTTTAGCT
**
148429 TTAAATTAATTTAAAAAT-ATATTTTA
1 TTAAATTAAAATAAAAATAATATTTTA
* **
148455 TTAATATTAAAA-ATATTTAATATTTATAA
1 TTAA-ATTAAAATAAAAATAATATTT-T-A
148484 TTAAATTAAAATAAAAATAATATTTTA
1 TTAAATTAAAATAAAAATAATATTTTA
148511 TTA
1 TTA
148514 TATAAATAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
26 7 0.15
27 15 0.33
28 9 0.20
29 15 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAATTAAAATAAAAATAATATTTTA
Found at i:148805 original size:16 final size:16
Alignment explanation
Indices: 148758--148798 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
148748 TCTTTAATCG
148758 AAAAAT-TTTAAATTTT
1 AAAAATATTTAAA-TTT
148774 AAAAATATTTAAATTT
1 AAAAATATTTAAATTT
148790 AAAAATATT
1 AAAAATATT
148799 ATTATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAAATATTTAAATTT
Found at i:148807 original size:17 final size:16
Alignment explanation
Indices: 148758--148808 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
148748 TCTTTAATCG
148758 AAAAAT-TTTAAATTTT
1 AAAAATATTT-AATTTT
*
148774 AAAAATATTTAAATTT
1 AAAAATATTTAATTTT
*
148790 AAAAATATTATTATTTT
1 AAAAATATT-TAATTTT
148807 AA
1 AA
148809 TCCATCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 20 0.67
17 10 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATATTTAATTTT
Found at i:151333 original size:17 final size:17
Alignment explanation
Indices: 151311--151343 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
151301 TTGGCATAAA
151311 GAGATGCAGCAGTGGAG
1 GAGATGCAGCAGTGGAG
151328 GAGATGCAGCAGTGGA
1 GAGATGCAGCAGTGGA
151344 AGAAGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.45, T:0.12
Consensus pattern (17 bp):
GAGATGCAGCAGTGGAG
Found at i:157503 original size:2 final size:2
Alignment explanation
Indices: 157496--157535 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
157486 CTTCTACTTA
157496 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
157536 TCAGAAACTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:161175 original size:3 final size:3
Alignment explanation
Indices: 161167--161196 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
161157 GAAACGTTGG
161167 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
161197 TTCTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:162112 original size:12 final size:13
Alignment explanation
Indices: 162085--162117 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
162075 TAAAGTAAGC
162085 AAATAATATATTA
1 AAATAATATATTA
*
162098 AAATAATCT-TTA
1 AAATAATATATTA
162110 AAATAATA
1 AAATAATA
162118 ATTTTTAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATAATATATTA
Found at i:162707 original size:12 final size:12
Alignment explanation
Indices: 162692--162717 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
162682 CATTTTTTTA
162692 AACACTTTTAAC
1 AACACTTTTAAC
162704 AACACTTTTAAC
1 AACACTTTTAAC
162716 AA
1 AA
162718 AAGATAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (12 bp):
AACACTTTTAAC
Found at i:169339 original size:20 final size:22
Alignment explanation
Indices: 169306--169345 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
169296 TTGTTAGTAA
*
169306 AAAATAAAGGAAATT-ATTTGG
1 AAAATAAAGAAAATTGATTTGG
169327 AAAA-AAAGAAAATTGATTT
1 AAAATAAAGAAAATTGATTT
169346 TTTTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (22 bp):
AAAATAAAGAAAATTGATTTGG
Found at i:169871 original size:31 final size:31
Alignment explanation
Indices: 169831--169891 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
169821 ACTTCTAAAC
*
169831 AAAATTTTTA-ATATATAATATACTTATATTT
1 AAAAATTTTACATATATAATA-ACTTATATTT
* *
169862 AAAAATTTTACATATTTAATAATTTATATT
1 AAAAATTTTACATATATAATAACTTATATT
169892 ATATTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (31 bp):
AAAAATTTTACATATATAATAACTTATATTT
Found at i:169897 original size:19 final size:19
Alignment explanation
Indices: 169849--169898 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
169839 TAATATATAA
169849 TATACTTATATTTAAAAATT
1 TATA-TTATATTTAAAAATT
* *
169869 T-TA-CATATTTAATAATT
1 TATATTATATTTAAAAATT
169886 TATATTATATTTA
1 TATATTATATTTA
169899 TTTTTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 13 0.52
18 2 0.08
19 9 0.36
20 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATTATATTTAAAAATT
Found at i:170001 original size:15 final size:17
Alignment explanation
Indices: 169976--170007 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
169966 AACTCGTTAA
169976 AAAAATAATTTT-TTTT
1 AAAAATAATTTTATTTT
169992 AAAAAT-ATTTTATTTT
1 AAAAATAATTTTATTTT
170008 TTTCAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAAAATAATTTTATTTT
Found at i:178335 original size:3 final size:3
Alignment explanation
Indices: 178327--178379 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
178317 AGCATTTCTT
178327 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
178375 TTA TT
1 TTA TT
178380 TAAAGTTGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:178523 original size:19 final size:20
Alignment explanation
Indices: 178501--178544 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
178491 ATTTATTTAT
**
178501 ATTAAAAA-AATATTTTAAA
1 ATTAAAAATAATATTAAAAA
178520 ATTAAAAATAATATTAAAAA
1 ATTAAAAATAATATTAAAAA
178540 ATTAA
1 ATTAA
178545 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTAAAAATAATATTAAAAA
Found at i:183063 original size:188 final size:179
Alignment explanation
Indices: 182696--183067 Score: 532
Period size: 188 Copynumber: 2.0 Consensus size: 179
182686 GCTCACCAGC
* * *
182696 AACCTTAAAATCTGTGTTCATATGTTGTAATAACTTCAAAAGAACCCCTGGGACAAGATTTGCCA
1 AACCTTAAAATCTGTGTTCATATGTTGTAATAACTTCAAAAGAAACCCTGGAACAAGATTTGCAA
* * *
182761 TTTTGGGTGCCTTCTCCAATTTGCATTACTCTTACCAAAAAAAAAAGACAAAGAAAAAAGATTCT
66 TTCTGGGTGCCTTCTCCAATTTGCATTACCCTTACAAAAAAAAAAAGACAAAGAAAAAAGATTCT
* *
182826 AAGAGAAACTGAAAAATAAAGAATTTTGTCCAATACCCAGATTAAGAAA
131 AAAAGAAACCGAAAAATAAAGAATTTTGTCCAATACCCAGATTAAGAAA
*
182875 AACCTTAAAATCTGTGTTCATATGTTGTAATAACTTCAAAAGAAACTC-GGAACAAGATTTGCAA
1 AACCTTAAAATCTGTGTTCATATGTTGTAATAACTTCAAAAGAAACCCTGGAACAAGATTTGCAA
*
182939 TTCTGGGTGCCTTCTCCAATTTGCGTTACCCTTACAAAACACAAAAACCCCAGACAAAGAAACTC
66 TTCTGGGTGCCTTCTCCAATTTGCATTACCCTTACAAAA-A-AAAAA----AGACAAAG-AA---
*
183004 AAAAGATTCTAAAAGAAACCGAAAAATAAAGAATTTTGGT-CAATATCCAGATTAAGAAA
121 AAAAGATTCTAAAAGAAACCGAAAAATAAAGAATTTT-GTCCAATACCCAGATTAAGAAA
183063 AACCT
1 AACCT
183068 CAACTTGAAA
Statistics
Matches: 171, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
178 49 0.29
179 47 0.27
180 5 0.03
184 8 0.05
185 2 0.01
188 58 0.34
189 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (179 bp):
AACCTTAAAATCTGTGTTCATATGTTGTAATAACTTCAAAAGAAACCCTGGAACAAGATTTGCAA
TTCTGGGTGCCTTCTCCAATTTGCATTACCCTTACAAAAAAAAAAAGACAAAGAAAAAAGATTCT
AAAAGAAACCGAAAAATAAAGAATTTTGTCCAATACCCAGATTAAGAAA
Found at i:183711 original size:15 final size:15
Alignment explanation
Indices: 183693--183847 Score: 77
Period size: 15 Copynumber: 10.9 Consensus size: 15
183683 TTACAGCACG
183693 TAATATTAAATATTA
1 TAATATTAAATATTA
*
183708 TAATA-TAAATATAA
1 TAATATTAAATATTA
* *
183722 TATTA-AAAATAATTA
1 TAATATTAAAT-ATTA
*
183737 AAATA-T-AATA-TA
1 TAATATTAAATATTA
* *
183749 TTAT-TTAAA-AATA
1 TAATATTAAATATTA
183762 TAAATATTAAA-ATATA
1 T-AATATTAAATAT-TA
183778 TAATA-TATAA-ATTA
1 TAATATTA-AATATTA
* *
183792 TTATATTAAATTTATA
1 TAATATTAAATAT-TA
183808 TAAT-TTAAATATTA
1 TAATATTAAATATTA
*
183822 T-ATATATAAATATAA
1 TAATAT-TAAATATTA
183837 TAA-A-TAAATAT
1 TAATATTAAATAT
183848 CAGGAAAGAG
Statistics
Matches: 110, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
12 6 0.05
13 15 0.14
14 35 0.32
15 45 0.41
16 9 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATATTAAATATTA
Found at i:183722 original size:11 final size:11
Alignment explanation
Indices: 183706--183748 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
183696 TATTAAATAT
183706 TATAATATAAA
1 TATAATATAAA
183717 TATAATATTAAA
1 TATAATA-TAAA
*
183729 AATAAT-TAAAA
1 TATAATAT-AAA
183740 TATAATATA
1 TATAATATA
183749 TTATTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 16 0.59
12 10 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAATATAAA
Found at i:183746 original size:28 final size:29
Alignment explanation
Indices: 183693--183761 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
183683 TTACAGCACG
*
183693 TAATATT--AAAT-ATTATAATATAAATA
1 TAATATTAAAAATAATTAAAATATAAATA
183719 TAATATTAAAAATAATTAAAATAT-AATA
1 TAATATTAAAAATAATTAAAATATAAATA
*
183747 TATTATTTAAAAATA
1 TAATA-TTAAAAATA
183762 TAAATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 7 0.19
28 12 0.32
29 18 0.49
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATATTAAAAATAATTAAAATATAAATA
Found at i:183789 original size:29 final size:28
Alignment explanation
Indices: 183757--183847 Score: 63
Period size: 28 Copynumber: 3.4 Consensus size: 28
183747 TATTATTTAA
183757 AAATATAAATATTAAAATATATAATATAT
1 AAATATAAATATTAAAATATATAA-ATAT
*
183786 AAAT-TATTATATT-AAAT-T-T--ATAT
1 AAATATA-AATATTAAAATATATAAATAT
* *
183809 -AATTTAAATATT-ATATATATAAATAT
1 AAATATAAATATTAAAATATATAAATAT
*
183835 AATAAATAAATAT
1 AA-ATATAAATAT
183848 CAGGAAAGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
22 11 0.22
23 7 0.14
24 1 0.02
26 5 0.10
27 2 0.04
28 14 0.29
29 9 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AAATATAAATATTAAAATATATAAATAT
Found at i:183801 original size:44 final size:44
Alignment explanation
Indices: 183693--183832 Score: 127
Period size: 43 Copynumber: 3.3 Consensus size: 44
183683 TTACAGCACG
* *
183693 TAATAT-TAAA-TATTATAATATAAATAT-AATATTAAAA-ATAA
1 TAATATATAAATTATTATATTAAAAATATAAATATTAAAATAT-A
*
183734 TTAAAATAT-AATATATTAT-TTAAAAATATAAATATTAAAATATA
1 -TAATATATAAAT-TATTATATTAAAAATATAAATATTAAAATATA
**
183778 TAATATATAAATTATTATATTAAATTTATATAAT-TT-AAATAT-
1 TAATATATAAATTATTATATTAAAAATATA-AATATTAAAATATA
183820 TATATATATAAAT
1 TA-ATATATAAAT
183833 ATAATAAATA
Statistics
Matches: 83, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
42 9 0.11
43 38 0.46
44 31 0.37
45 5 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (44 bp):
TAATATATAAATTATTATATTAAAAATATAAATATTAAAATATA
Found at i:183844 original size:28 final size:28
Alignment explanation
Indices: 183699--183847 Score: 82
Period size: 29 Copynumber: 5.2 Consensus size: 28
183689 CACGTAATAT
183699 TAAATATTATA-ATATAAATATAATATTAA
1 TAAATATTATATATATAAATATAATA--AA
* * *
183728 -AAATAATTA-AAATATAATATATTATTTAA
1 TAAAT-ATTATATATATAA-ATA-TAATAAA
*
183757 -AAATA-TAAATAT-TAAA-ATATATAATA
1 TAAATATTATATATATAAATATA-ATAA-A
* *
183783 TATAA-ATTAT-TATATTAAATTTATATAATT
1 TA-AATATTATATATA-TAAATATA-ATAA-A
183813 TAAATATTATATATATAAATATAATAAA
1 TAAATATTATATATATAAATATAATAAA
183841 TAAATAT
1 TAAATAT
183848 CAGGAAAGAG
Statistics
Matches: 95, Mismatches: 10, Indels: 31
0.70 0.07 0.23
Matches are distributed among these distances:
24 2 0.02
25 3 0.03
26 2 0.02
27 10 0.11
28 20 0.21
29 26 0.27
30 25 0.26
31 7 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAATATTATATATATAAATATAATAAA
Found at i:184201 original size:19 final size:19
Alignment explanation
Indices: 184162--184243 Score: 59
Period size: 18 Copynumber: 4.5 Consensus size: 19
184152 TATATATAAA
184162 TTTAATATTTATT-AATAATT
1 TTTAA-ATTTATTAAAT-ATT
184182 TTTAAATTTATTAAATA--
1 TTTAAATTTATTAAATATT
* *
184199 TTT--ATTTAATAAATAAT
1 TTTAAATTTATTAAATATT
* *
184216 TTAAAATATA-TAAATATT
1 TTTAAATTTATTAAATATT
*
184234 TATAAATTTA
1 TTTAAATTTA
184244 AAATTTATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
15 11 0.22
17 5 0.10
18 14 0.28
19 12 0.24
20 8 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAAATTTATTAAATATT
Found at i:184241 original size:25 final size:23
Alignment explanation
Indices: 184213--184260 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
184203 TTTAATAAAT
184213 AATTTAAAATATATAAATATTTATA
1 AATTTAAAATATAT-AAT-TTTATA
*
184238 AATTTAAAATTTATAATTTTATA
1 AATTTAAAATATATAATTTTATA
184261 CCTTTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.27
24 3 0.14
25 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATTTAAAATATATAATTTTATA
Found at i:184290 original size:24 final size:23
Alignment explanation
Indices: 184234--184292 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
184224 TATAAATATT
* *
184234 TATAAATTTAAAATTTATAATTT
1 TATAAATTTTAAATTTATAATTA
** *
184257 TATACCTTTTAAATTTGTAATTA
1 TATAAATTTTAAATTTATAATTA
184280 TATTAAATTTTAA
1 TA-TAAATTTTAA
184293 TTATTTTATA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (23 bp):
TATAAATTTTAAATTTATAATTA
Found at i:184295 original size:16 final size:17
Alignment explanation
Indices: 184265--184296 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
184255 TTTATACCTT
184265 TTAAATTTGTAATTATA
1 TTAAATTTGTAATTATA
184282 TTAAATTT-TAATTAT
1 TTAAATTTGTAATTAT
184297 TTTATACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTAAATTTGTAATTATA
Found at i:185392 original size:20 final size:19
Alignment explanation
Indices: 185369--185430 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 19
185359 ATTCAAAATT
185369 TAATTTATATAAATAAAAAA
1 TAATTTA-ATAAATAAAAAA
** *
185389 TAATTTAATTTAT-AAATA
1 TAATTTAATAAATAAAAAA
*
185407 -AATTTAATAAATAAAAAT
1 TAATTTAATAAATAAAAAA
185425 TAATTT
1 TAATTT
185431 TTTATTCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 10 0.30
18 7 0.21
19 9 0.27
20 7 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTTAATAAATAAAAAA
Found at i:185442 original size:36 final size:38
Alignment explanation
Indices: 185355--185456 Score: 122
Period size: 36 Copynumber: 2.7 Consensus size: 38
185345 ATTTATAAAA
*
185355 TTTTATTCAAAATTTAATTTATATAAATAAAAAATAATT
1 TTTTATTCAAAA-TAAATTTATATAAATAAAAAATAATT
*
185394 TAATTTA-T--AAATAAATTTA-ATAAATAAAAATTAATT
1 T--TTTATTCAAAATAAATTTATATAAATAAAAAATAATT
185430 TTTTATTCAAATATAAATTTATATAAA
1 TTTTATTCAAA-ATAAATTTATATAAA
185457 AAGATGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
34 4 0.07
35 1 0.02
36 17 0.31
37 9 0.17
38 12 0.22
39 6 0.11
40 1 0.02
41 4 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (38 bp):
TTTTATTCAAAATAAATTTATATAAATAAAAAATAATT
Found at i:185498 original size:3 final size:3
Alignment explanation
Indices: 185490--185518 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
185480 TTTCAATTTT
185490 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
185519 TTTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:185636 original size:15 final size:15
Alignment explanation
Indices: 185610--185757 Score: 85
Period size: 15 Copynumber: 10.0 Consensus size: 15
185600 TTAGTTAAAT
185610 TTAATATTTAAATTAA
1 TTAAT-TTTAAATTAA
185626 TTAATTTTAAATTAA
1 TTAATTTTAAATTAA
* * *
185641 TT-A-TATAGATCAA
1 TTAATTTTAAATTAA
* *
185654 TTTAAATTTAAATTTA
1 -TTAATTTTAAATTAA
* *
185670 TTAAATTTAAATTATT
1 TTAATTTTAAATTA-A
* **
185686 TTAA-ATT-AATTGTT
1 TTAATTTTAAATT-AA
**
185700 TTAAACTTAAATTAA
1 TTAATTTTAAATTAA
185715 TT-ATTTTAAATT-A
1 TTAATTTTAAATTAA
*
185728 TTAATTTTTAATTAA
1 TTAATTTTAAATTAA
185743 TTTAA-TTTAAATTAA
1 -TTAATTTTAAATTAA
185758 ACAAAATGAT
Statistics
Matches: 104, Mismatches: 18, Indels: 21
0.73 0.13 0.15
Matches are distributed among these distances:
13 10 0.10
14 29 0.28
15 42 0.40
16 23 0.22
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (15 bp):
TTAATTTTAAATTAA
Found at i:185665 original size:44 final size:45
Alignment explanation
Indices: 185607--185757 Score: 134
Period size: 44 Copynumber: 3.4 Consensus size: 45
185597 GAATTAGTTA
*
185607 AATTTAATATTTAAATTAATTAATTTTAAATTA-ATTATA-TAGATC
1 AATTTAA-ATTTAAATTAATTAATTTTAAATTATATTAAATTA-ATC
* * * *
185652 AATTTAAATTTAAATTTATTAAATTTAAATTATTTTAAATTAATT
1 AATTTAAATTTAAATTAATTAATTTTAAATTATATTAAATTAATC
** * * *
185697 GTTTTAAACTTAAATTAATT-ATTTTAAA-T-TATTAATTTTTAATT
1 AATTTAAATTTAAATTAATTAATTTTAAATTATATTAA--ATTAATC
185741 AATTT-AATTTAAATTAA
1 AATTTAAATTTAAATTAA
185758 ACAAAATGAT
Statistics
Matches: 87, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
42 5 0.06
43 12 0.14
44 39 0.45
45 29 0.33
46 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (45 bp):
AATTTAAATTTAAATTAATTAATTTTAAATTATATTAAATTAATC
Found at i:185696 original size:14 final size:14
Alignment explanation
Indices: 185679--185757 Score: 52
Period size: 14 Copynumber: 5.1 Consensus size: 14
185669 ATTAAATTTA
185679 AATTATTTTAAATT
1 AATTATTTTAAATT
*
185693 AATTGTTTTAAACTTAAATT
1 AATTATTTT--A---AA-TT
185713 AATTATTTTAAATT
1 AATTATTTTAAATT
*
185727 -ATTAATTTTTAATT
1 AATT-ATTTTAAATT
*
185741 AATTTAATTTAAATT
1 AA-TTATTTTAAATT
185756 AA
1 AA
185758 ACAAAATGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
13 3 0.06
14 19 0.37
15 13 0.25
16 3 0.06
18 1 0.02
19 2 0.04
20 10 0.20
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (14 bp):
AATTATTTTAAATT
Found at i:185709 original size:20 final size:20
Alignment explanation
Indices: 185686--185724 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
185676 TTAAATTATT
*
185686 TTAAATTAATTGTTTTAAAC
1 TTAAATTAATTATTTTAAAC
185706 TTAAATTAATTATTTTAAA
1 TTAAATTAATTATTTTAAA
185725 TTATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TTAAATTAATTATTTTAAAC
Found at i:187126 original size:22 final size:21
Alignment explanation
Indices: 187101--187188 Score: 71
Period size: 22 Copynumber: 4.3 Consensus size: 21
187091 AATTAATTTT
187101 ATATTTAAAT-TTAATTATAAAA
1 ATATTTAAATATTAA-TAT-AAA
*
187123 ATATATAAATATTAATATAAA
1 ATATTTAAATATTAATATAAA
*
187144 AT-TTTAAATATT--T-TAAT
1 ATATTTAAATATTAATATAAA
* *
187161 A-ATTTAAATAAATAAAATAAA
1 ATATTTAAAT-ATTAATATAAA
187182 ATATTTA
1 ATATTTA
187189 TTATTTAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
17 11 0.21
18 3 0.06
20 9 0.17
21 9 0.17
22 17 0.32
23 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATTTAAATATTAATATAAA
Found at i:187461 original size:17 final size:17
Alignment explanation
Indices: 187439--187489 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
187429 TACATCATCA
*
187439 ATTATCTTTATGTATAT
1 ATTATCTTTATATATAT
*
187456 ATTATCTATATATATAT
1 ATTATCTTTATATATAT
*
187473 ATTAT-TTTATAAATAT
1 ATTATCTTTATATATAT
187489 A
1 A
187490 AATATAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTATCTTTATATATAT
Found at i:187496 original size:6 final size:6
Alignment explanation
Indices: 187480--187532 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
187470 TATATTATTT
* *
187480 TATAAA TATAAA TAT-AA TAAAAA TAT-AA TAT-AA T-TAAA AAT-AA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
187523 TATAAA TATA
1 TATAAA TATA
187533 TTAAAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 1 0.03
5 18 0.46
6 20 0.51
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TATAAA
Found at i:187511 original size:28 final size:28
Alignment explanation
Indices: 187480--187553 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 28
187470 TATATTATTT
187480 TATAAATATAAATATAATAAAAATATAA
1 TATAAATATAAATATAATAAAAATATAA
* * *
187508 TAT-AAT-TAAAAATAATATAAATATAT
1 TATAAATATAAATATAATAAAAATATAA
*
187534 TAAAAAATATATAATATAAT
1 T-ATAAATATA-AATATAAT
187554 TTAATAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
26 18 0.49
27 4 0.11
28 6 0.16
29 2 0.05
30 7 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
TATAAATATAAATATAATAAAAATATAA
Found at i:187562 original size:20 final size:20
Alignment explanation
Indices: 187463--187565 Score: 85
Period size: 20 Copynumber: 5.3 Consensus size: 20
187453 TATATTATCT
* *
187463 ATATATATATATTATTTTATAA
1 ATATATA-ATA-TAATTTAAAA
187485 ATATA-AATATAA--T-AAA
1 ATATATAATATAATTTAAAA
187501 A-ATATAATATAA-TTAAAA
1 ATATATAATATAATTTAAAA
*
187519 ATAATATAA-ATATATTAAAAA
1 AT-ATATAATATA-ATTTAAAA
*
187540 ATATATAATATAATTTAATA
1 ATATATAATATAATTTAAAA
187560 ATATAT
1 ATATAT
187566 TAAAATTCAT
Statistics
Matches: 68, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
15 3 0.04
16 10 0.15
17 2 0.03
18 4 0.06
19 5 0.07
20 28 0.41
21 11 0.16
22 5 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATATAATATAATTTAAAA
Found at i:190133 original size:24 final size:26
Alignment explanation
Indices: 190106--190160 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
190096 TTTATCCACG
*
190106 AATTATA-TAATTTATTTAATTT-AA
1 AATTATATTAAGTTATTTAATTTAAA
*
190130 AATTA-ATTAAGTTATTTATTTTAAA
1 AATTATATTAAGTTATTTAATTTAAA
190155 AATTAT
1 AATTAT
190161 TCATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 18 0.69
25 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AATTATATTAAGTTATTTAATTTAAA
Found at i:198927 original size:55 final size:55
Alignment explanation
Indices: 198863--198970 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 55
198853 ATTTAATTCA
198863 AATTTAATTAATATTTATTTTTAAAATTTAAGTTAAATTAAAGATAAAATTAAGT
1 AATTTAATTAATATTTATTTTTAAAATTTAAGTTAAATTAAAGATAAAATTAAGT
* *
198918 AATTTAATTAATATTTATTTTTAAAGTTTAAGTTGAATTAAAGATAAAATTAA
1 AATTTAATTAATATTTATTTTTAAAATTTAAGTTAAATTAAAGATAAAATTAA
198971 ATTATTTATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (55 bp):
AATTTAATTAATATTTATTTTTAAAATTTAAGTTAAATTAAAGATAAAATTAAGT
Found at i:199073 original size:6 final size:6
Alignment explanation
Indices: 199062--199093 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
199052 TATATTTAAT
199062 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TT
199094 CTTTAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:202056 original size:15 final size:15
Alignment explanation
Indices: 202008--202047 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
201998 TTTAACTTAA
* *
202008 TATATTTTTTAATGT
1 TATATATTTTAATAT
202023 T-TATATTTTAATAT
1 TATATATTTTAATAT
202037 TATATATTTTA
1 TATATATTTTA
202048 TTTTTATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TATATATTTTAATAT
Found at i:202527 original size:16 final size:16
Alignment explanation
Indices: 202506--202569 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
202496 CATATTATAA
202506 TTATATTTAA-AATATT
1 TTATATTTAATAA-ATT
202522 TTATATTTATATAAATT
1 TTATATTTA-ATAAATT
*
202539 TTATACTTTAAT-TATT
1 TTATA-TTTAATAAATT
202555 TT-TA-TT-ATAAATT
1 TTATATTTAATAAATT
202568 TT
1 TT
202570 TTAAAAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 2 0.05
13 7 0.17
15 2 0.05
16 14 0.33
17 11 0.26
18 6 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTTAATAAATT
Found at i:209409 original size:19 final size:18
Alignment explanation
Indices: 209387--209470 Score: 79
Period size: 19 Copynumber: 4.8 Consensus size: 18
209377 CATATAAATT
209387 TATTTAATATATATTTAAA
1 TATTTAATATA-ATTTAAA
*
209406 TATTTATTATAATTTAAA
1 TATTTAATATAATTTAAA
209424 TA--T-A-ATAA-TTAAA
1 TATTTAATATAATTTAAA
*
209437 TCTTTTAATATCAATTTAAA
1 T-ATTTAATAT-AATTTAAA
*
209457 TATTTAAAATAATT
1 TATTTAATATAATT
209471 AATCATCCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
13 6 0.11
14 4 0.08
16 2 0.04
17 1 0.02
18 15 0.28
19 19 0.36
20 6 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTAATATAATTTAAA
Found at i:210270 original size:22 final size:21
Alignment explanation
Indices: 210239--210295 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
210229 ATTATAAAAA
* *
210239 TAAAAAATTTTAATTAAAT-T
1 TAAAATATTTAAATTAAATAT
*
210259 TATAAATTATTTAAATTTAATAT
1 TA-AAA-TATTTAAATTAAATAT
210282 TAAAATATTTAAAT
1 TAAAATATTTAAAT
210296 GTAACTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.06
21 12 0.39
22 14 0.45
23 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATATTTAAATTAAATAT
Found at i:210536 original size:2 final size:2
Alignment explanation
Indices: 210529--210593 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
210519 AGTAGGTCAC
210529 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
210571 AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
210594 TTTTACACAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:211642 original size:25 final size:26
Alignment explanation
Indices: 211604--211667 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
211594 ATTATTTAAT
211604 AAATTTAATA-ATAAAA-AA-TATTA
1 AAATTTAATATATAAAATAATTATTA
*
211627 AAATATTAATATATAAAATAATTTTTA
1 AAAT-TTAATATATAAAATAATTATTA
*
211654 ATATTTTAATATAT
1 A-AATTTAATATAT
211668 TTTAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 4 0.12
24 6 0.18
25 6 0.18
26 2 0.06
27 14 0.41
28 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATTTAATATATAAAATAATTATTA
Found at i:211656 original size:19 final size:18
Alignment explanation
Indices: 211632--211692 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
211622 TATTAAAATA
211632 TTAATATATAAAATAATTT
1 TTAATAT-TAAAATAATTT
**
211651 TTAATATTTTAATATATTT
1 TTAATATTAAAATA-ATTT
* *
211670 TAAAAATTAAAATGAATTT
1 TTAATATTAAAAT-AATTT
211689 TTAA
1 TTAA
211693 GTTTAATATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 5 0.15
19 27 0.82
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAATATTAAAATAATTT
Found at i:214018 original size:8 final size:8
Alignment explanation
Indices: 214007--214031 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
213997 ATTATTTATA
214007 ATTTTAAT
1 ATTTTAAT
214015 ATTTTAAT
1 ATTTTAAT
214023 ATTTTAAT
1 ATTTTAAT
214031 A
1 A
214032 CTAAAGCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTAAT
Found at i:214699 original size:8 final size:8
Alignment explanation
Indices: 214647--214701 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
214637 AAAGAAAAAC
214647 TATATGTAA
1 TATATGT-A
*
214656 TATATATA
1 TATATGTA
214664 TATATGTA
1 TATATGTA
*
214672 TGTAT-T-
1 TATATGTA
* *
214678 TATATTTG
1 TATATGTA
214686 TATATGTA
1 TATATGTA
214694 TATATGTA
1 TATATGTA
214702 CATAAATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
6 4 0.11
7 2 0.05
8 26 0.68
9 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:215151 original size:18 final size:18
Alignment explanation
Indices: 215139--215192 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 18
215129 CTATTAAATT
215139 ATAAAAAAATATTTAAAA
1 ATAAAAAAATATTTAAAA
215157 ATAAAAAAATA---AAAA
1 ATAAAAAAATATTTAAAA
* *
215172 ATAATATAA-ATTTAAAA
1 ATAAAAAAATATTTAAAA
215189 ATAA
1 ATAA
215193 TTATATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.35
17 8 0.26
18 11 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAAAAATATTTAAAA
Found at i:216071 original size:21 final size:22
Alignment explanation
Indices: 216040--216081 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
216030 TATTATTATT
216040 ATTTAATTAGAATAAAATATAA
1 ATTTAATTAGAATAAAATATAA
*
216062 ATTT-ATTAGATTAAAATATA
1 ATTTAATTAGAATAAAATATA
216082 CCTCGTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTTAATTAGAATAAAATATAA
Found at i:217449 original size:21 final size:21
Alignment explanation
Indices: 217420--217462 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
217410 ACTCTCTCAT
* *
217420 TGGCTTCTTAGATTATGACTG
1 TGGCGTCTTAGATGATGACTG
*
217441 TGGCGTCTTAGATGATGGCTG
1 TGGCGTCTTAGATGATGACTG
217462 T
1 T
217463 TATGAGGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.14, G:0.30, T:0.40
Consensus pattern (21 bp):
TGGCGTCTTAGATGATGACTG
Found at i:218053 original size:15 final size:16
Alignment explanation
Indices: 218033--218067 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
218023 AAATCGTTAA
*
218033 TTAAAAATTAAA-AAT
1 TTAAAAATAAAATAAT
218048 TTAAAAATAAAATAAT
1 TTAAAAATAAAATAAT
218064 TTAA
1 TTAA
218068 TGTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAAATAAAATAAT
Found at i:220265 original size:6 final size:7
Alignment explanation
Indices: 220237--220267 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
220227 TTTTAATATT
220237 AATTTAA
1 AATTTAA
220244 AATTTAA
1 AATTTAA
220251 AATTTAA
1 AATTTAA
*
220258 AATTAAA
1 AATTTAA
220265 AAT
1 AAT
220268 AATTTAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AATTTAA
Found at i:220448 original size:4 final size:4
Alignment explanation
Indices: 220430--220473 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
220420 TCTAATTATT
** **
220430 TTTA TTTA TCAA TTTA TTTA TTTA TCAA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
220474 CTAAATATCT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:220451 original size:16 final size:16
Alignment explanation
Indices: 220430--220470 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
220420 TCTAATTATT
220430 TTTATTTATCAATTTA
1 TTTATTTATCAATTTA
220446 TTTATTTATCAATTTA
1 TTTATTTATCAATTTA
220462 TTTATTTAT
1 TTTATTTAT
220471 TTACTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTTATCAATTTA
Found at i:228809 original size:16 final size:16
Alignment explanation
Indices: 228768--228821 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
228758 AAATATATAA
228768 AATATATTAAA--ATT
1 AATATATTAAATTATT
*
228782 TATATAATTTAAATTATT
1 AATAT-A-TTAAATTATT
228800 AATATATTAAAATT-TT
1 AATATATT-AAATTATT
228816 AATATA
1 AATATA
228822 ATTATATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 4 0.12
15 1 0.03
16 15 0.45
17 6 0.18
18 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATATTAAATTATT
Found at i:229323 original size:30 final size:30
Alignment explanation
Indices: 229287--229456 Score: 192
Period size: 29 Copynumber: 5.8 Consensus size: 30
229277 ATTAATTTAT
* *
229287 ATTAAAAATTTCTTTACATATAAATTAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
*
229317 ATTAAAAATTTATTTAAAAATAAATTAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
* *
229347 ATTGAAACTTTATTT-AATATAAATTAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
229376 ATTAAAAATTTATTTAAATAT-AA-TAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
* *
229404 ATATAATAACTTATTTAAATAT-AA-TAAAA
1 AT-TAAAAATTTATTTAAATATAAATTAAAA
* *
229433 A-TATAAAACTTATCTAAATA-AAAT
1 ATTA-AAAATTTATTTAAATATAAAT
229457 GATAAGTTCA
Statistics
Matches: 123, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 53 0.43
30 45 0.37
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.38
Consensus pattern (30 bp):
ATTAAAAATTTATTTAAATATAAATTAAAA
Found at i:229368 original size:59 final size:58
Alignment explanation
Indices: 229299--229440 Score: 184
Period size: 59 Copynumber: 2.4 Consensus size: 58
229289 TAAAAATTTC
*
229299 TTTACATATAAATTAAAAATTAAAAATTTATTTAAAAATAAATTAAAAAT-TGA-AACTTTA
1 TTTA-ATATAAATTAAAAATTAAAAATTTATTTAAAAAT-AA-TAAAAATATAATAAC-TTA
*
229359 TTTAATATAAATTAAAAATTAAAAATTTATTTAAATATAATAAAAATATAATAACTTA
1 TTTAATATAAATTAAAAATTAAAAATTTATTTAAAAATAATAAAAATATAATAACTTA
229417 TTTAA-ATATAA-TAAAAATATAAAA
1 TTTAATATA-AATTAAAAAT-TAAAA
229441 CTTATCTAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
57 17 0.22
58 19 0.25
59 36 0.47
60 4 0.05
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (58 bp):
TTTAATATAAATTAAAAATTAAAAATTTATTTAAAAATAATAAAAATATAATAACTTA
Found at i:230229 original size:34 final size:34
Alignment explanation
Indices: 230186--230254 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
230176 CATCAATGAC
230186 TTAGTTTAAACAATTTAAATTGATGAAGAGTTGA
1 TTAGTTTAAACAATTTAAATTGATGAAGAGTTGA
230220 TTAGTTTAAACAATTTAAATTGATGAAGAGTTGA
1 TTAGTTTAAACAATTTAAATTGATGAAGAGTTGA
230254 T
1 T
230255 GAACCAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (34 bp):
TTAGTTTAAACAATTTAAATTGATGAAGAGTTGA
Found at i:230813 original size:152 final size:152
Alignment explanation
Indices: 230537--230837 Score: 575
Period size: 152 Copynumber: 2.0 Consensus size: 152
230527 CATAAAGACA
*
230537 CACGCAAATGAACAATTAAGATCTTGTAATAATCGAGCATAATCTGAGAGTTACTCCTGCATCTC
1 CACGCAAATGAACAATTAAGATCTTGTAATAATCAAGCATAATCTGAGAGTTACTCCTGCATCTC
230602 CTACATGATGCTCTAGAAGAGCACCGATAAACTAGAACTTCATTTGAGTTTTCTCAACAATATTT
66 CTACATGATGCTCTAGAAGAGCACCGATAAACTAGAACTTCATTTGAGTTTTCTCAACAATATTT
230667 GGGAATCTTCAAAATTTTTACT
131 GGGAATCTTCAAAATTTTTACT
*
230689 CACGCAAATGAACAATTAAGATCTTGTAATAATCAAGCATAATCTGAGAGTTATTCCTGCATCTC
1 CACGCAAATGAACAATTAAGATCTTGTAATAATCAAGCATAATCTGAGAGTTACTCCTGCATCTC
*
230754 CTACATGATGCTCTAGAAGAGCACCGCTAAACTAGAACTTCATTTGAGTTTTCTCAACAATATTT
66 CTACATGATGCTCTAGAAGAGCACCGATAAACTAGAACTTCATTTGAGTTTTCTCAACAATATTT
230819 GGGAATCTTCAAAATTTTT
131 GGGAATCTTCAAAATTTTT
230838 GCTCTACTGG
Statistics
Matches: 146, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
152 146 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (152 bp):
CACGCAAATGAACAATTAAGATCTTGTAATAATCAAGCATAATCTGAGAGTTACTCCTGCATCTC
CTACATGATGCTCTAGAAGAGCACCGATAAACTAGAACTTCATTTGAGTTTTCTCAACAATATTT
GGGAATCTTCAAAATTTTTACT
Found at i:233863 original size:2 final size:2
Alignment explanation
Indices: 233856--233888 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
233846 AGAAGAAGGG
*
233856 GA GA GA GA GT GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
233889 TTAGGGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.03
Consensus pattern (2 bp):
GA
Found at i:234454 original size:21 final size:21
Alignment explanation
Indices: 234428--234495 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 21
234418 TATTATTTTA
234428 TAATTAAAAAATTATTTAAAT
1 TAATTAAAAAATTATTTAAAT
*
234449 TAATTATAAAAA-TATATAAATAT
1 TAATTA-AAAAATTAT-TTAA-AT
234472 TAATATAAAAATAATT-TTTAAAT
1 TAAT-T-AAAA-AATTATTTAAAT
234495 T
1 T
234496 TTTTATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
21 9 0.24
22 8 0.21
23 9 0.24
24 7 0.18
25 4 0.11
26 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATTAAAAAATTATTTAAAT
Found at i:245907 original size:30 final size:32
Alignment explanation
Indices: 245854--245913 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
245844 TGATATGGTG
245854 TAAAATATTATGTATAAATTTTAATATATTAA
1 TAAAATATTATGTATAAATTTTAATATATTAA
*
245886 TAAAATA-TAT-TATATATTTTAATATATT
1 TAAAATATTATGTATAAATTTTAATATATT
245914 TATTTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 17 0.63
31 3 0.11
32 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (32 bp):
TAAAATATTATGTATAAATTTTAATATATTAA
Found at i:246058 original size:17 final size:17
Alignment explanation
Indices: 246021--246060 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
246011 TAATTAAAAA
246021 TAATAT-TATTTAAATT
1 TAATATATATTTAAATT
246037 T-ATATATA-TTAAATAT
1 TAATATATATTTAAAT-T
246053 TAATATAT
1 TAATATAT
246061 TTGACATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 10 0.48
16 5 0.24
17 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATATATTTAAATT
Found at i:246541 original size:19 final size:19
Alignment explanation
Indices: 246519--246605 Score: 67
Period size: 19 Copynumber: 4.8 Consensus size: 19
246509 GTTATAATTA
246519 TATTTATAATATTTTATAT
1 TATTTATAATATTTTATAT
* * *
246538 TATTAATAGTATTATATAT
1 TATTTATAATATTTTATAT
*
246557 AATTT-T-ATATTTTA-A-
1 TATTTATAATATTTTATAT
* *
246572 AATTTTTAATATATTTATAT
1 TATTTATAATAT-TTTATAT
*
246592 TA-TTATTATATTTT
1 TATTTATAATATTTT
246606 TATCGTGATT
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
15 5 0.09
16 2 0.04
17 10 0.19
18 8 0.15
19 27 0.51
20 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (19 bp):
TATTTATAATATTTTATAT
Found at i:246565 original size:45 final size:44
Alignment explanation
Indices: 246516--246608 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 44
246506 CGTGTTATAA
*
246516 TTATA-TTTATAATATTTT-ATATTATTAATAGTATTATATATAATT
1 TTATATTTTAAAAT-TTTTAATA-TATTAATAGTATTAT-TATAATT
* * *
246561 TTATATTTTAAAATTTTTAATATATTTATATTATTATTATATTT
1 TTATATTTTAAAATTTTTAATATATTAATAGTATTATTATAATT
246605 TTAT
1 TTAT
246609 CGTGATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
44 10 0.24
45 22 0.52
46 10 0.24
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (44 bp):
TTATATTTTAAAATTTTTAATATATTAATAGTATTATTATAATT
Found at i:246601 original size:36 final size:37
Alignment explanation
Indices: 246517--246605 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 37
246507 GTGTTATAAT
* * *
246517 TATATTTATAATATTTTATATTATTAATAGTATTATA
1 TATAATTATTATATTTTAAATTATTAATAGTATTATA
*
246554 TATAATT-TTATATTTTAAAATTTTTAATA-TATT-TA
1 TATAATTATTATATTTT-AAATTATTAATAGTATTATA
*
246589 TATTATTATTATATTTT
1 TATAATTATTATATTTT
246606 TATCGTGATT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
35 8 0.18
36 21 0.47
37 16 0.36
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (37 bp):
TATAATTATTATATTTTAAATTATTAATAGTATTATA
Found at i:253065 original size:3 final size:3
Alignment explanation
Indices: 253057--253114 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
253047 ATTTCAAGAC
253057 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
253105 ATA ATA ATA A
1 ATA ATA ATA A
253115 AGCGAATCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:254544 original size:10 final size:10
Alignment explanation
Indices: 254524--254554 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
254514 AAACATGATG
254524 TAAATATAATA
1 TAAA-ATAATA
254535 TAAAATAATA
1 TAAAATAATA
254545 TAAAATAATA
1 TAAAATAATA
254555 AATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAAATAATA
Found at i:256927 original size:26 final size:28
Alignment explanation
Indices: 256854--256927 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 28
256844 TATTAATAAC
*
256854 TATATTTAAATTT-AAATATTTTTATATT
1 TATA-TTATATTTAAAATATTTTTATATT
* ***
256882 TATATCATATTTATTTTATTTTT-TA-T
1 TATATTATATTTAAAATATTTTTATATT
256908 TATATTATATTTAAAATATT
1 TATATTATATTTAAAATATT
256928 ATATAATATA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
26 17 0.47
27 8 0.22
28 11 0.31
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (28 bp):
TATATTATATTTAAAATATTTTTATATT
Found at i:256952 original size:15 final size:15
Alignment explanation
Indices: 256897--256954 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
256887 CATATTTATT
*
256897 TTATTTTTTATTATA
1 TTATTTTTTATAATA
* *
256912 TTA-TATTTAAAATA
1 TTATTTTTTATAATA
* **
256926 TTATATAATATAATA
1 TTATTTTTTATAATA
256941 TTATTTTTTATAAT
1 TTATTTTTTATAAT
256955 CTATTATGTT
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTTTTTATAATA
Found at i:257080 original size:25 final size:24
Alignment explanation
Indices: 257043--257089 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
257033 ATAATAAAAA
257043 TTTAAATAATAAATTAATAATATTT
1 TTTAAATAATAAATTAA-AATATTT
*
257068 TTTAAATATTAAATTAAAATAT
1 TTTAAATAATAAATTAAAATAT
257090 AAAAATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTAAATAATAAATTAAAATATTT
Found at i:258894 original size:13 final size:13
Alignment explanation
Indices: 258878--258918 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
258868 TTTTTTTTAA
258878 AAATTTATTATTT
1 AAATTTATTATTT
*
258891 AAATTTA-GA-TT
1 AAATTTATTATTT
258902 AAATTTAATTATTT
1 AAATTT-ATTATTT
258916 AAA
1 AAA
258919 AAAATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 8 0.35
14 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
AAATTTATTATTT
Found at i:259263 original size:32 final size:33
Alignment explanation
Indices: 259200--259265 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 33
259190 TATAATATAC
*
259200 TAAATTAAATTTAATAATTTATATAATTATTTT
1 TAAATTAAATTTAATAATTTATATAACTATTTT
259233 TAAATTTAAATTT--TAATATT-TATAACTATTTT
1 TAAA-TTAAATTTAATAAT-TTATATAACTATTTT
259265 T
1 T
259266 CTTTTTTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 16 0.53
33 6 0.20
34 8 0.27
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (33 bp):
TAAATTAAATTTAATAATTTATATAACTATTTT
Found at i:260313 original size:18 final size:18
Alignment explanation
Indices: 260269--260314 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
260259 TTATTTTAAA
*
260269 TTAATTTAAAATAATATT
1 TTAAATTAAAATAATATT
*
260287 TTAAAATTAAAATATTATT
1 TT-AAATTAAAATAATATT
260306 TTAAATTAA
1 TTAAATTAA
260315 TTTAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATTAAAATAATATT
Found at i:262987 original size:25 final size:27
Alignment explanation
Indices: 262959--263027 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
262949 TATTCATAAA
*
262959 ATAATAAAATATTAA-AA-ATATTTTT
1 ATAATTAAATATTAATAATATATTTTT
262984 ATAATTAAAT-TTAAATAATATATTTTT
1 ATAATTAAATATT-AATAATATATTTTT
263011 ATTAATTAAATATTAAT
1 A-TAATTAAATATTAAT
263028 TTAAATTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
24 2 0.05
25 11 0.29
26 2 0.05
27 9 0.24
28 12 0.32
29 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATAATTAAATATTAATAATATATTTTT
Found at i:263497 original size:2 final size:2
Alignment explanation
Indices: 263490--263516 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
263480 TCTTGTATTT
263490 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
263517 TTGATTACTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:264022 original size:2 final size:2
Alignment explanation
Indices: 264015--264051 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
264005 TTCACACGTT
264015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
264052 GTAAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:264129 original size:15 final size:15
Alignment explanation
Indices: 264086--264136 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
264076 AATCTTAAAT
*
264086 TAATTTAAATTTATA
1 TAATTTATATTTATA
* *
264101 TATTATTATTTTTATA
1 TAAT-TTATATTTATA
*
264117 TAATTTATATTTATT
1 TAATTTATATTTATA
264132 TAATT
1 TAATT
264137 CAATAATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TAATTTATATTTATA
Found at i:264341 original size:13 final size:13
Alignment explanation
Indices: 264325--264384 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
264315 CAATAAATAT
264325 AATTATATAATTA
1 AATTATATAATTA
*
264338 AATTAAATAATTA
1 AATTATATAATTA
* * *
264351 ATTTATTAAAATATT
1 AATTA-TATAAT-TA
*
264366 AATTATAT-ATAA
1 AATTATATAATTA
264378 AATTATA
1 AATTATA
264385 AAAAATACCT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
12 7 0.19
13 18 0.50
14 6 0.17
15 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTATATAATTA
Found at i:264360 original size:16 final size:16
Alignment explanation
Indices: 264342--264380 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 16
264332 TAATTAAATT
264342 AAATAATTAATTTATTA
1 AAAT-ATTAATTTATTA
264359 AAATATTAATTATATATA
1 AAATATTAATT-TAT-TA
264377 AAAT
1 AAAT
264381 TATAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 7 0.35
18 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATTAATTTATTA
Found at i:264586 original size:2 final size:2
Alignment explanation
Indices: 264579--264604 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
264569 CTCAGTTACA
264579 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
264605 TAAAATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:269619 original size:26 final size:27
Alignment explanation
Indices: 269588--269646 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 27
269578 ATAATAAATA
269588 ATTAAAATAATT-AAAATTATATTTAT
1 ATTAAAATAATTAAAAATTATATTTAT
269614 ATT-AAATAATTAAAAATTATATTTAT
1 ATTAAAATAATTAAAAATTATATTTAT
269640 ATTAAAA
1 ATTAAAA
269647 AATAAATTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 8 0.26
26 20 0.65
27 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATTAAAATAATTAAAAATTATATTTAT
Found at i:269981 original size:31 final size:31
Alignment explanation
Indices: 269946--270007 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
269936 TTGGCAAATT
*
269946 TTTAAAAGTATAATCTAAATTTAATTTAATA
1 TTTAAAAATATAATCTAAATTTAATTTAATA
*
269977 TTTAAAAATATAATTTAAATTTAATTTAATA
1 TTTAAAAATATAATCTAAATTTAATTTAATA
270008 CGATTTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (31 bp):
TTTAAAAATATAATCTAAATTTAATTTAATA
Found at i:269990 original size:20 final size:19
Alignment explanation
Indices: 269962--270000 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
269952 AGTATAATCT
*
269962 AAATTTAATTTAATATTTAA
1 AAATATAATTTAA-ATTTAA
269982 AAATATAATTTAAATTTAA
1 AAATATAATTTAAATTTAA
270001 TTTAATACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATATAATTTAAATTTAA
Found at i:270001 original size:11 final size:11
Alignment explanation
Indices: 269956--270005 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
269946 TTTAAAAGTA
*
269956 TAATCTAAATT
1 TAATTTAAATT
269967 TAATTTAATATT
1 TAATTTAA-ATT
*
269979 TAA---AAATA
1 TAATTTAAATT
269987 TAATTTAAATT
1 TAATTTAAATT
269998 TAATTTAA
1 TAATTTAA
270006 TACGATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
8 5 0.16
9 2 0.06
11 19 0.59
12 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
TAATTTAAATT
Found at i:271103 original size:13 final size:12
Alignment explanation
Indices: 271079--271103 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
271069 ATATATATAT
271079 AGTTTTAAAAAA
1 AGTTTTAAAAAA
271091 AGTTTTAAAAAA
1 AGTTTTAAAAAA
271103 A
1 A
271104 TGTTAGATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AGTTTTAAAAAA
Found at i:271760 original size:1 final size:1
Alignment explanation
Indices: 271756--271782 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
271746 TTGTGCTTTG
271756 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
271783 GCTCTTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:279680 original size:2 final size:2
Alignment explanation
Indices: 279673--279707 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
279663 TCTTAGGGTC
279673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
279708 GGAGTAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:280204 original size:7 final size:7
Alignment explanation
Indices: 280187--280224 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
280177 TATAGTTATA
280187 TTATA-T
1 TTATATT
280193 TTATATT
1 TTATATT
280200 TTATATT
1 TTATATT
280207 TTATATAT
1 TTATAT-T
280215 TCTATATT
1 T-TATATT
280223 TT
1 TT
280225 CAGCTTCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.17
7 15 0.52
8 4 0.14
9 5 0.17
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (7 bp):
TTATATT
Found at i:280215 original size:16 final size:16
Alignment explanation
Indices: 280194--280224 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
280184 ATATTATATT
*
280194 TATATTTTATATTTTA
1 TATATTCTATATTTTA
280210 TATATTCTATATTTT
1 TATATTCTATATTTT
280225 CAGCTTCTAT
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:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTCTATATTTTA
Found at i:282089 original size:22 final size:23
Alignment explanation
Indices: 282059--282105 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
282049 GAAATCAATG
*
282059 GTTTATACTTGGTAAAGGAAAAA
1 GTTTATACTTAGTAAAGGAAAAA
**
282082 GTTT-TACTTAGTAAATTAAAAA
1 GTTTATACTTAGTAAAGGAAAAA
282104 GT
1 GT
282106 AAATTTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (23 bp):
GTTTATACTTAGTAAAGGAAAAA
Found at i:282450 original size:20 final size:20
Alignment explanation
Indices: 282425--282467 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
282415 AAATGTATAT
282425 CACACTATACAAGAAAATAA
1 CACACTATACAAGAAAATAA
*
282445 CACACTATACAAGGAAATAA
1 CACACTATACAAGAAAATAA
282465 CAC
1 CAC
282468 TTGCATGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.23, G:0.07, T:0.14
Consensus pattern (20 bp):
CACACTATACAAGAAAATAA
Found at i:283145 original size:37 final size:37
Alignment explanation
Indices: 283124--283436 Score: 126
Period size: 37 Copynumber: 8.9 Consensus size: 37
283114 TAAACAACAA
283124 TAATATTAAATTATATTAAATTAATAAAATAATAAAC
1 TAATATTAAATTATATTAAATTAATAAAATAATAAAC
* * * **
283161 TATTATTAAATTATA-T---TCAA-AACA-GCT--A-
1 TAATATTAAATTATATTAAATTAATAAAATAATAAAC
** * * * **
283189 TAATACCAAATTATATTAATTTAACAAACTAATATGC
1 TAATATTAAATTATATTAAATTAATAAAATAATAAAC
* * * * *
283226 TAATATGAAATTAAATT-ACTATAAT-AAAGAATAGAC
1 TAATATTAAATTATATTAAAT-TAATAAAATAATAAAC
* *
283262 TAATATTAAATTATATT-ATTTCAATAAATTAATAAAC
1 TAATATTAAATTATATTAAATT-AATAAAATAATAAAC
* * * * * * *
283299 TATTACTAAACTGTCTTAATTTAATAAACTAATAAAC
1 TAATATTAAATTATATTAAATTAATAAAATAATAAAC
* * *
283336 TATTACTAAATTATA-TAAA-T--T----TAACAAAC
1 TAATATTAAATTATATTAAATTAATAAAATAATAAAC
* * * * **
283365 TAATATCAAATTATATTAATTTAACAAACTAATATGC
1 TAATATTAAATTATATTAAATTAATAAAATAATAAAC
* * *
283402 TAATATTAAATTAAATTGATTTAATAAAATAATAA
1 TAATATTAAATTATATTAAATTAATAAAATAATAA
283437 TATCTTAATA
Statistics
Matches: 201, Mismatches: 54, Indels: 42
0.68 0.18 0.14
Matches are distributed among these distances:
28 12 0.06
29 21 0.10
30 3 0.01
31 2 0.01
32 6 0.03
33 6 0.03
34 1 0.00
35 2 0.01
36 33 0.16
37 111 0.55
38 4 0.02
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.38
Consensus pattern (37 bp):
TAATATTAAATTATATTAAATTAATAAAATAATAAAC
Found at i:283375 original size:29 final size:29
Alignment explanation
Indices: 283343--283399 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
283333 AACTATTACT
283343 AAATTATATAAATTTAACAAACTAATATC
1 AAATTATATAAATTTAACAAACTAATATC
*
283372 AAATTATATTAATTTAACAAACTAATAT
1 AAATTATATAAATTTAACAAACTAATAT
283400 GCTAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (29 bp):
AAATTATATAAATTTAACAAACTAATATC
Found at i:284641 original size:31 final size:31
Alignment explanation
Indices: 284606--284670 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
284596 AACAGTGTAC
*
284606 CAACCACAATTTATAAATGAAAATCCAGAAG
1 CAACCACAATTTATAAATGAAAATCAAGAAG
284637 CAACCACAATTTATAAATGAAAATCAAGAAG
1 CAACCACAATTTATAAATGAAAATCAAGAAG
284668 CAA
1 CAA
284671 TAACTGGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.18
Consensus pattern (31 bp):
CAACCACAATTTATAAATGAAAATCAAGAAG
Found at i:294865 original size:70 final size:71
Alignment explanation
Indices: 294779--294920 Score: 250
Period size: 70 Copynumber: 2.0 Consensus size: 71
294769 CAAAAGCAAA
*
294779 GGGCTAATTCATTTATGTGATCTGCACTGTTCTTTACACC-AAAAAAAAAAAAGAAGGTTAAACA
1 GGGCTAATTCATTTATGTCATCTGCACTGTTCTTTACACCAAAAAAAAAAAAAGAAGGTTAAACA
294843 AATAAT
66 AATAAT
*
294849 GGGCTAATTCATTTATGTCATCTGCGCTGTTCTTTACACCAAAAAAAAAAAAAAGAAGGTTAAAC
1 GGGCTAATTCATTTATGTCATCTGCACTGTTCTTTACACC-AAAAAAAAAAAAAGAAGGTTAAAC
294914 AAATAAT
65 AAATAAT
294921 TAGTTGATTT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
70 38 0.56
72 30 0.44
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (71 bp):
GGGCTAATTCATTTATGTCATCTGCACTGTTCTTTACACCAAAAAAAAAAAAAGAAGGTTAAACA
AATAAT
Found at i:295395 original size:59 final size:59
Alignment explanation
Indices: 295318--295436 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
295308 CTCACCTCGA
*
295318 GTCCGAGTAACATAGATATTCTTAACATTATAACTTATACCAGTTTGATACATTTGCCT
1 GTCCAAGTAACATAGATATTCTTAACATTATAACTTATACCAGTTTGATACATTTGCCT
295377 GTCCAAGTAACATAGATATTCTTAACATTATAACTTATACCAGTTTGATACATTTGCCT
1 GTCCAAGTAACATAGATATTCTTAACATTATAACTTATACCAGTTTGATACATTTGCCT
295436 G
1 G
295437 ACCCCTCTAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (59 bp):
GTCCAAGTAACATAGATATTCTTAACATTATAACTTATACCAGTTTGATACATTTGCCT
Found at i:297533 original size:20 final size:20
Alignment explanation
Indices: 297505--297579 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
297495 TCATACCCTG
297505 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
297525 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
297545 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
297565 ATGTATCGATACATT
1 ATGTATCGATACATT
297580 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:297572 original size:40 final size:39
Alignment explanation
Indices: 297505--297582 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
297495 TCATACCCTG
* *
297505 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
297545 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
297583 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:298517 original size:23 final size:23
Alignment explanation
Indices: 298487--298542 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
298477 AGCCTTTGAC
298487 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
298510 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
298532 CATGCATTTTT
1 CATGCATTTTT
298543 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:298549 original size:20 final size:21
Alignment explanation
Indices: 298495--298549 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
298485 ACCATGCATT
**
298495 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
298516 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
298538 -TTTTTAACATGT
1 TTTTTTAACATGT
298550 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:304734 original size:36 final size:36
Alignment explanation
Indices: 304660--304734 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
304650 AGTTCCCTTC
* *
304660 AAAATGACAAAAAAAAAGTCAAAAGCAAAAGCACAA
1 AAAATGACAAAAAAAAAGTCAAAAGCAAAAGAAAAA
* *
304696 AAAATGA-AAAGAAAAAGTGCAAAAGCAAAATAAAAA
1 AAAATGACAAAAAAAAAGT-CAAAAGCAAAAGAAAAA
304732 AAA
1 AAA
304735 GGGAACAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 10 0.29
36 24 0.71
ACGTcount: A:0.72, C:0.09, G:0.12, T:0.07
Consensus pattern (36 bp):
AAAATGACAAAAAAAAAGTCAAAAGCAAAAGAAAAA
Found at i:306278 original size:26 final size:27
Alignment explanation
Indices: 306082--306568 Score: 646
Period size: 27 Copynumber: 18.0 Consensus size: 27
306072 GTGGCATTTT
* *
306082 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
306110 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
306137 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
306165 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
306192 CTTTTAAATCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
306219 TTTTTAAATCCACAACTCCGTGGCAAAACC
1 CTTTTAAGTCCACAACTCCGTGGC---ACC
306249 CTTTTAAGTCCACAACT-CGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
306275 CTTTTAAGTCCACAACTTCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
306303 CTGTTTAAGACCACAACTCCGTGGCACC
1 CT-TTTAAGTCCACAACTCCGTGGCACC
* * **
306331 CTTTTAAGTCCATAACTTCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
306358 C-TTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
306384 TTTTTAAGT-CACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
306409 CTTTTAAGTCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
306436 C-TTTAAGT-CATAACT-CATGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
306460 CTTGTAAGTCCACACCTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
306487 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
306514 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
306541 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
306568 C
1 C
306569 ATTTCAAAGC
Statistics
Matches: 407, Mismatches: 39, Indels: 27
0.86 0.08 0.06
Matches are distributed among these distances:
24 7 0.02
25 21 0.05
26 83 0.20
27 213 0.52
28 38 0.09
29 27 0.07
30 18 0.04
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:306606 original size:32 final size:32
Alignment explanation
Indices: 306551--307248 Score: 1120
Period size: 32 Copynumber: 21.8 Consensus size: 32
306541 CTTTTAAATC
* *
306551 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
306582 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
306614 CA-AAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
306645 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
306677 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
306709 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
306741 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
306773 CACAAGTCGGTGGCAACCCATTTTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
306805 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
306837 CACAAGTCGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
306867 CACAAGTCGGTGGCAACCCATTGCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
306899 CACAAGTCGGTGGCAACCCATTGCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
306931 CACAAGTCGGTGGCAACCC-TTTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTT-CAAAGCCCA
306963 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
306995 CACAAGTCGGTGGCAACCCATTTC-AAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
307026 CACAAGTCGGTGACAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
307058 CACAAGTCGGGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTC--GGTGGCAACCCATTTCAAAGCCCA
*
307092 CACAAGTCTGGTGGCAACCCATTTCAAAACCCA
1 CACAAGTC-GGTGGCAACCCATTTCAAAGCCCA
* *
307125 CACAAGTCGGTGGCAACTCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
307157 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
307189 CACAAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CAC-AAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
307222 TGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
307249 TCACCATATT
Statistics
Matches: 632, Mismatches: 25, Indels: 19
0.93 0.04 0.03
Matches are distributed among these distances:
30 27 0.04
31 78 0.12
32 434 0.69
33 62 0.10
34 31 0.05
ACGTcount: A:0.31, C:0.35, G:0.19, T:0.15
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:307802 original size:20 final size:20
Alignment explanation
Indices: 307774--307848 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
307764 TCATACCCTG
307774 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
307794 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
307814 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
307834 ATGTATCGATACATT
1 ATGTATCGATACATT
307849 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:307841 original size:40 final size:39
Alignment explanation
Indices: 307774--307851 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
307764 TCATACCCTG
* *
307774 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
307814 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
307852 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:308786 original size:23 final size:23
Alignment explanation
Indices: 308759--308814 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
308749 AGCCTTTGAC
308759 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
308782 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
308804 CATGCATTTTT
1 CATGCATTTTT
308815 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:308821 original size:20 final size:21
Alignment explanation
Indices: 308767--308821 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
308757 ACCATGCATT
**
308767 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
308788 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
308810 -TTTTTAACATGT
1 TTTTTTAACATGT
308822 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:318999 original size:9 final size:9
Alignment explanation
Indices: 318987--319031 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
318977 AGTTGATTAC
318987 TAAGTTTGT
1 TAAGTTTGT
*
318996 TAAGTTGGT
1 TAAGTTTGT
*
319005 TATGTTTGT
1 TAAGTTTGT
319014 T-AGTTTGT
1 TAAGTTTGT
319022 T-AGTTTGT
1 TAAGTTTGT
319030 TA
1 TA
319032 GTTAATTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 15 0.48
9 16 0.52
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (9 bp):
TAAGTTTGT
Found at i:319021 original size:8 final size:8
Alignment explanation
Indices: 318989--319045 Score: 69
Period size: 8 Copynumber: 6.9 Consensus size: 8
318979 TTGATTACTA
318989 AGTTTGTT
1 AGTTTGTT
*
318997 AAGTTGGTT
1 -AGTTTGTT
319006 ATGTTTGTT
1 A-GTTTGTT
319015 AGTTTGTT
1 AGTTTGTT
319023 AGTTTGTT
1 AGTTTGTT
**
319031 AGTTAATT
1 AGTTTGTT
319039 AGTTTGT
1 AGTTTGT
319046 CAATTTTGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
8 27 0.66
9 14 0.34
ACGTcount: A:0.18, C:0.00, G:0.25, T:0.58
Consensus pattern (8 bp):
AGTTTGTT
Found at i:319223 original size:2 final size:2
Alignment explanation
Indices: 319218--319263 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
319208 TATGTGTGTG
319218 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
319260 TA TA
1 TA TA
319264 GTAAAGACTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:319339 original size:18 final size:20
Alignment explanation
Indices: 319316--319356 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
319306 AACTAACAAA
319316 TTAACAAAC-A-TAACCAAC
1 TTAACAAACTAGTAACCAAC
319334 TTAACAAACTTAGTAACCAAC
1 TTAACAAAC-TAGTAACCAAC
319355 TT
1 TT
319357 CCACAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
20 1 0.05
21 10 0.50
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (20 bp):
TTAACAAACTAGTAACCAAC
Found at i:321626 original size:3 final size:3
Alignment explanation
Indices: 321611--321660 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
321601 CATTAGGAAA
* * *
321611 AAT AAT CAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT GAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
321658 AAT
1 AAT
321661 CGTGTTCCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:323042 original size:22 final size:22
Alignment explanation
Indices: 323017--323060 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
323007 GGGTTTGCAA
323017 ACTGCAATGCATCAATTCAAGC
1 ACTGCAATGCATCAATTCAAGC
323039 ACTGCAATGCATCAATTCAAGC
1 ACTGCAATGCATCAATTCAAGC
323061 GCGCACACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (22 bp):
ACTGCAATGCATCAATTCAAGC
Found at i:323161 original size:1 final size:1
Alignment explanation
Indices: 323150--323204 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
323140 TTATATTGAG
* * * * * *
323150 TTTTCTTTTTTTCTTTCTTTTTTCTTCTTCTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
323205 CCTTTCCCCC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Done.