Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold315
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: 271854
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
File 2 of 2
Found at i:169865 original size:42 final size:42
Alignment explanation
Indices: 169810--169928 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
169800 TTCTTCTCTC
* *
169810 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
169852 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
169894 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
169929 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:169869 original size:12 final size:11
Alignment explanation
Indices: 169843--169918 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
169833 TCTATTATCT
*
169843 CTCCTGTCTCTC
1 CTCCTATCTC-C
169855 CTCCTATCATCC
1 CTCCTATC-TCC
169867 CTCCTATCT--
1 CTCCTATCTCC
*
169876 CTACTATCT--
1 CTCCTATCTCC
*
169885 CTCCTGTCTCTC
1 CTCCTATCTC-C
169897 CTCCTATCATCC
1 CTCCTATC-TCC
*
169909 CTCCTCTCTC
1 CTCCTATCTC
169919 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:169870 original size:24 final size:24
Alignment explanation
Indices: 169834--169919 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
169824 CCTCCTCTCT
* *
169834 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
169858 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
169879 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
169900 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
169920 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:169894 original size:18 final size:18
Alignment explanation
Indices: 169825--169895 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
169815 CCTGTCATCC
* *
169825 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
169843 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
169865 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
169885 CTCCTGTCTCT
1 CTCCTGTCTCT
169896 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:172020 original size:42 final size:42
Alignment explanation
Indices: 171959--172077 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
171949 TAGCCCTCAA
* *
171959 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
172001 AGAGATAGTAGAGATAGGAGGTATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
172043 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
172078 GAGAGAAGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.43, C:0.03, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:180436 original size:12 final size:11
Alignment explanation
Indices: 180419--180489 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
180409 AAGAAAAGAG
180419 AGGAGGGATGAT
1 AGGAGGGA-GAT
*
180431 AGGAGGAGAGAC
1 AGGAGG-GAGAT
180443 AGGA--GAGAT
1 AGGAGGGAGAT
*
180452 AGTA--GAGAT
1 AGGAGGGAGAT
180461 AGGAGGGATGAT
1 AGGAGGGA-GAT
*
180473 AGGAGGAGAGAC
1 AGGAGG-GAGAT
180485 AGGAG
1 AGGAG
180490 AGATAATAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
9 15 0.31
11 2 0.04
12 28 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.48, T:0.10
Consensus pattern (11 bp):
AGGAGGGAGAT
Found at i:180465 original size:42 final size:42
Alignment explanation
Indices: 180415--180522 Score: 189
Period size: 42 Copynumber: 2.6 Consensus size: 42
180405 GAGAAAGAAA
*
180415 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAG
1 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
*
180457 AGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
1 AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
*
180499 AGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGGAGGGATGATAGGAGGAG
180523 GAGAGAAGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.41, C:0.03, G:0.47, T:0.09
Consensus pattern (42 bp):
AGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAG
Found at i:189588 original size:37 final size:36
Alignment explanation
Indices: 189547--189631 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 36
189537 CAGCTTGTAC
189547 GGGCTTTGACTCAAACTTGGGTGCCACCAACTCGTGT
1 GGGCTTTGACTCAAAC-TGGGTGCCACCAACTCGTGT
*
189584 GGGCTTTGACT----C-GGGTGTCACCAACTCGTGT
1 GGGCTTTGACTCAAACTGGGTGCCACCAACTCGTGT
* *
189615 GGGGTTTAACTCAAACT
1 GGGCTTTGACTCAAACT
189632 AGGTTGCTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
31 27 0.68
33 1 0.03
35 1 0.03
37 11 0.28
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (36 bp):
GGGCTTTGACTCAAACTGGGTGCCACCAACTCGTGT
Found at i:189826 original size:28 final size:27
Alignment explanation
Indices: 189795--189866 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 27
189785 TTATGGACTT
189795 TAAAGTAGGTGCCACAGATTTGTAGGCC
1 TAAAG-AGGTGCCACAGATTTGTAGGCC
* ** *
189823 TAAAAAAGGTGCCATTGATTTGTAGGCT
1 T-AAAGAGGTGCCACAGATTTGTAGGCC
189851 TAAGAGAGGATGCCAC
1 TAA-AGAGG-TGCCAC
189867 TAACTTGTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 2 0.06
28 25 0.71
29 8 0.23
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (27 bp):
TAAAGAGGTGCCACAGATTTGTAGGCC
Found at i:189893 original size:29 final size:29
Alignment explanation
Indices: 189861--189923 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
189851 TAAGAGAGGA
* *
189861 TGCCACTAACTTGTGGACTTTTGAAGGGG
1 TGCCACTAACGTGTGGACTTTTGAAAGGG
* *
189890 TGCCATTACCGTGTGGACTTTTGAAAGGG
1 TGCCACTAACGTGTGGACTTTTGAAAGGG
189919 TGCCA
1 TGCCA
189924 TTGACTTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (29 bp):
TGCCACTAACGTGTGGACTTTTGAAAGGG
Found at i:189939 original size:29 final size:28
Alignment explanation
Indices: 189869--189939 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
189859 GATGCCACTA
*
189869 ACTTGTGGACTTTTGAAGGGGTGCCATT
1 ACTTGTGGACTTTTGAAAGGGTGCCATT
*
189897 ACCGTGTGGACTTTTGAAAGGGTGCCATT
1 A-CTTGTGGACTTTTGAAAGGGTGCCATT
* *
189926 GACTTATGGGCTTT
1 -ACTTGTGGACTTT
189940 AAAAGGATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.03
29 34 0.94
30 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.35
Consensus pattern (28 bp):
ACTTGTGGACTTTTGAAAGGGTGCCATT
Found at i:190073 original size:28 final size:28
Alignment explanation
Indices: 190024--190122 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 28
190014 CTAGCTAGTG
* *
190024 TGGGCTTTAAAGAGCTGCCACTAATTCA
1 TGGGCTTTAAAAAGGTGCCACTAATTCA
* * *
190052 TGGGATTTAAAAAGGTGTCACTGACTTC-
1 TGGGCTTTAAAAAGGTGCCACT-AATTCA
190080 TGGGCTTTGAAAAAGGTGCCACTAACTT-A
1 TGGGCTTT-AAAAAGGTGCCACTAA-TTCA
*
190109 TGGGCTTTGAAAAG
1 TGGGCTTTAAAAAG
190123 ATTGCCACCA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
28 31 0.53
29 27 0.47
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (28 bp):
TGGGCTTTAAAAAGGTGCCACTAATTCA
Found at i:190128 original size:29 final size:29
Alignment explanation
Indices: 190024--190153 Score: 99
Period size: 29 Copynumber: 4.5 Consensus size: 29
190014 CTAGCTAGTG
190024 TGGGCTTT--AAAGAGCTGCCACTAA-TTCA
1 TGGGCTTTGAAAAGAG-TGCCACTAACTT-A
* * * * *
190052 TGGGATTTAAAAAG-GTGTCACTGACTTC
1 TGGGCTTTGAAAAGAGTGCCACTAACTTA
190080 TGGGCTTTGAAAA-AGGTGCCACTAACTTA
1 TGGGCTTTGAAAAGA-GTGCCACTAACTTA
* * *
190109 TGGGCTTTGAAAAGATTGCCACCAACTCGTG
1 TGGGCTTTGAAAAGAGTGCCACTAACT--TA
*
190140 TGGACTTTGAAAAG
1 TGGGCTTTGAAAAG
190154 GTTGTCACCA
Statistics
Matches: 81, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
28 25 0.31
29 37 0.46
30 5 0.06
31 14 0.17
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (29 bp):
TGGGCTTTGAAAAGAGTGCCACTAACTTA
Found at i:190151 original size:31 final size:31
Alignment explanation
Indices: 190084--190382 Score: 241
Period size: 31 Copynumber: 9.4 Consensus size: 31
190074 GACTTCTGGG
* * *
190084 CTTTGAAAAAGG-TGCCACTAACT--TATGGG
1 CTTTG-AAAAGGTTGCCACCAACTCGTGTGGA
*
190113 CTTTGAAAAGATTGCCACCAACTCGTGTGGA
1 CTTTGAAAAGGTTGCCACCAACTCGTGTGGA
*
190144 CTTTGAAAAGGTTGTCACCAACTCGTGTGGA
1 CTTTGAAAAGGTTGCCACCAACTCGTGTGGA
** *
190175 CTTTGAAAAGTTTTGGTTGCCACTGACTTGTGTGGA
1 CTTTGAAAA-----GGTTGCCACCAACTCGTGTGGA
* *
190211 CTTTGAATGAGG-TGCCACCAACTTGTGTGGA
1 CTTTGAA-AAGGTTGCCACCAACTCGTGTGGA
* *
190242 CTTT-AATTATGG-TGCCACCAACTCATGTGGA
1 CTTTGAA--AAGGTTGCCACCAACTCGTGTGGA
* **
190273 CTTTGAAATGGTTGCCACCAACTCGCATGGA
1 CTTTGAAAAGGTTGCCACCAACTCGTGTGGA
*** * * *
190304 CTTTGATTGGGGTGCCACCAACTCATCTGGA
1 CTTTGAAAAGGTTGCCACCAACTCGTGTGGA
*
190335 CTTTGAAAAGGATTGTGCCACCAACTTGTGTGGA
1 CTTTGAAAAGG--T-TGCCACCAACTCGTGTGGA
190369 CTTTGGAAAAGGTT
1 CTTT-GAAAAGGTT
190383 TGGTTGCCAC
Statistics
Matches: 220, Mismatches: 34, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
28 5 0.02
29 15 0.07
30 6 0.03
31 135 0.61
32 5 0.02
33 1 0.00
34 20 0.09
35 7 0.03
36 25 0.11
37 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (31 bp):
CTTTGAAAAGGTTGCCACCAACTCGTGTGGA
Found at i:190402 original size:35 final size:34
Alignment explanation
Indices: 190316--190486 Score: 121
Period size: 35 Copynumber: 4.8 Consensus size: 34
190306 TTGATTGGGG
* * *
190316 TGCCACCAACTCATCTGGACTTTGAAAAGGATT-G-
1 TGCCACCAACT--TGTGGACTTTAAAAAGGTTTGGT
*
190350 TGCCACCAACTTGTGTGGACTTTGGAAAAGGTTTGGT
1 TGCCACCAAC-T-TGTGGACTTT-AAAAAGGTTTGGT
* ** *
190387 TGCCACCAAGTTGTGGACTCCGAAAAAAGTTTGGT
1 TGCCACCAACTTGTGGACT-TTAAAAAGGTTTGGT
* * **
190422 TACCACCGACTTGTGTAGACTTTAAAAATTATTTGGT
1 TGCCACCAACTTGTG--GACTTTAAAAA-GGTTTGGT
190459 TGCCACCAACTTGTGTGGACTTTAAAAA
1 TGCCACCAAC-T-TGTGGACTTTAAAAA
190487 TGATTTAATT
Statistics
Matches: 110, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
34 19 0.17
35 41 0.37
36 7 0.06
37 38 0.35
38 1 0.01
39 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (34 bp):
TGCCACCAACTTGTGGACTTTAAAAAGGTTTGGT
Found at i:190482 original size:37 final size:36
Alignment explanation
Indices: 190124--190492 Score: 172
Period size: 31 Copynumber: 10.9 Consensus size: 36
190114 TTTGAAAAGA
* *
190124 TTGCCACCAACTCGTGTGGACTTT-GAAA-A---GG
1 TTGCCACCAACTTGTGTGGACTTTAAAAAGATTTGG
* * * *
190155 TTGTCACCAACTCGTGTGGACTTTGAAAAGTTTTGG
1 TTGCCACCAACTTGTGTGGACTTTAAAAAGATTTGG
** * *
190191 TTGCCACTGACTTGTGTGGACTTT-GAATGA---GG
1 TTGCCACCAACTTGTGTGGACTTTAAAAAGATTTGG
190223 -TGCCACCAACTTGTGTGGACTTT----A-ATTATGG
1 TTGCCACCAACTTGTGTGGACTTTAAAAAGATT-TGG
** *
190254 -TGCCACCAACTCATGTGGACTTT--GAA-A--TGG
1 TTGCCACCAACTTGTGTGGACTTTAAAAAGATTTGG
* ** *
190284 TTGCCACCAACTCGCATGGACTTT-----GATTGGG
1 TTGCCACCAACTTGTGTGGACTTTAAAAAGATTTGG
* ** * *
190315 GTGCCACCAACTCATCTGGACTTTGAAAAGGA-TT-G
1 TTGCCACCAACTTGTGTGGACTTT-AAAAAGATTTGG
* *
190350 -TGCCACCAACTTGTGTGGACTTTGGAAAAGGTTTGG
1 TTGCCACCAACTTGTGTGGACTTT-AAAAAGATTTGG
* **
190386 TTGCCACCAA-GT-TGTGGACTCCGAAAAA-AGTTTGG
1 TTGCCACCAACTTGTGTGGACT-TTAAAAAGA-TTTGG
* * * *
190421 TTACCACCGACTTGTGTAGACTTTAAAAATTATTTGG
1 TTGCCACCAACTTGTGTGGACTTTAAAAA-GATTTGG
190458 TTGCCACCAACTTGTGTGGACTTTAAAAATGATTT
1 TTGCCACCAACTTGTGTGGACTTTAAAAA-GATTT
190493 AATTTGTGTT
Statistics
Matches: 263, Mismatches: 45, Indels: 54
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.00
29 1 0.00
30 3 0.01
31 109 0.41
32 5 0.02
33 2 0.01
34 25 0.10
35 31 0.12
36 31 0.12
37 54 0.21
38 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (36 bp):
TTGCCACCAACTTGTGTGGACTTTAAAAAGATTTGG
Found at i:201287 original size:31 final size:31
Alignment explanation
Indices: 201230--201382 Score: 181
Period size: 31 Copynumber: 5.0 Consensus size: 31
201220 AAGTCAATGG
**
201230 CTTTCCAAAGTCC-C-CAAGTTAATGGCACC
1 CTTTCCAAAGTCCACACAAGTTGGTGGCACC
201259 GC-TTCCAAAGTCCACACAAGTTGGTGGCACC
1 -CTTTCCAAAGTCCACACAAGTTGGTGGCACC
*
201290 CTTTCCAAAGTCCACACAAGTCGGTGGCACAACC
1 CTTTCCAAAGTCCACACAAGTTGGTGG--C-ACC
***
201324 CTTTCCAAAGT-C-CACAAGTCAATGGCACC
1 CTTTCCAAAGTCCACACAAGTTGGTGGCACC
201353 CTTTCCAAAGTCCACACAAGTTGGTGGCAC
1 CTTTCCAAAGTCCACACAAGTTGGTGGCAC
201383 AATCCTTCCT
Statistics
Matches: 107, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
29 25 0.23
30 5 0.05
31 50 0.47
32 11 0.10
33 2 0.02
34 14 0.13
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (31 bp):
CTTTCCAAAGTCCACACAAGTTGGTGGCACC
Found at i:201352 original size:63 final size:64
Alignment explanation
Indices: 201283--201433 Score: 232
Period size: 63 Copynumber: 2.4 Consensus size: 64
201273 CACAAGTTGG
* *
201283 TGGCACCCTTTCCAAAGTCCACACAAGTCGGTGGCACAACCCTTTC-CAAAGTCCACAAGTCAA
1 TGGCACCCTTTCCAAAGTCCACACAAGTCGGTGGCACAACCCTTCCTCAAAGACCACAAGTCAA
* * *
201346 TGGCACCCTTTCCAAAGTCCACACAAGTTGGTGGCACAATCCTTCCTCAAAGACCACAAGTCAG
1 TGGCACCCTTTCCAAAGTCCACACAAGTCGGTGGCACAACCCTTCCTCAAAGACCACAAGTCAA
*
201410 TGGCATCCTTTCTCAAAGTCCACA
1 TGGCACCCTTTC-CAAAGTCCACA
201434 AGTCAATGAC
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 43 0.54
64 26 0.32
65 11 0.14
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (64 bp):
TGGCACCCTTTCCAAAGTCCACACAAGTCGGTGGCACAACCCTTCCTCAAAGACCACAAGTCAA
Found at i:201363 original size:29 final size:29
Alignment explanation
Indices: 201152--201438 Score: 181
Period size: 29 Copynumber: 9.6 Consensus size: 29
201142 CAAACAGTTT
* * * *
201152 CAAACTCCACAAATTAGTGGCATCCTCTT-
1 CAAAGTCCACAAGTCAGTGGCACCCT-TTC
* * * *
201181 CAAAGTCCATAAGTTAGTGGCACTCTTTT
1 CAAAGTCCACAAGTCAGTGGCACCCTTTC
* * *
201210 TAAAGTCCATAAGTCAATGG----CTTTC
1 CAAAGTCCACAAGTCAGTGGCACCCTTTC
* * *
201235 CAAAGTCCCCAAGTTAATGGCACCGC-TTC
1 CAAAGTCCACAAGTCAGTGGCACC-CTTTC
**
201264 CAAAGTCCACACAAGTTGGTGGCACCCTTTC
1 CAAAGT-C-CACAAGTCAGTGGCACCCTTTC
*
201295 CAAAGTCCACACAAGTCGGTGGCACAACCCTTTC
1 CAAAGT-C-CACAAGTCAGTGG--C-ACCCTTTC
*
201329 CAAAGTCCACAAGTCAATGGCACCCTTTC
1 CAAAGTCCACAAGTCAGTGGCACCCTTTC
** *
201358 CAAAGTCCACACAAGTTGGTGGCACAATCCTTCC
1 CAAAGT-C-CACAAGTCAGTGGCAC---CCTTTC
* *
201392 TCAAAGACCACAAGTCAGTGGCATCCTTTC
1 -CAAAGTCCACAAGTCAGTGGCACCCTTTC
201422 TCAAAGTCCACAAGTCA
1 -CAAAGTCCACAAGTCA
201439 ATGACATTCT
Statistics
Matches: 211, Mismatches: 29, Indels: 35
0.77 0.11 0.13
Matches are distributed among these distances:
25 20 0.09
28 2 0.01
29 61 0.29
30 26 0.12
31 51 0.24
32 11 0.05
33 15 0.07
34 20 0.09
35 5 0.02
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (29 bp):
CAAAGTCCACAAGTCAGTGGCACCCTTTC
Found at i:201425 original size:30 final size:30
Alignment explanation
Indices: 201151--201480 Score: 155
Period size: 29 Copynumber: 11.0 Consensus size: 30
201141 CCAAACAGTT
* * * *
201151 TCAAACTCCACAAATTAGTGGCATCCTCT-
1 TCAAAGTCCACAAGTCAGTGGCATCCTTTC
* *
201180 TCAAAGTCCATAAGTTAGTGGCA-CTCTTT-
1 TCAAAGTCCACAAGTCAGTGGCATC-CTTTC
* * *
201209 TTAAAGTCCATAAGTCAATGG----CTTTC
1 TCAAAGTCCACAAGTCAGTGGCATCCTTTC
* * * *
201235 -CAAAGTCCCCAAGTTAATGGCA-CCGCTTC
1 TCAAAGTCCACAAGTCAGTGGCATCC-TTTC
** *
201264 -CAAAGTCCACACAAGTTGGTGGCACCCTTTC
1 TCAAAGT-C-CACAAGTCAGTGGCATCCTTTC
* *
201295 -CAAAGTCCACACAAGTCGGTGGCACAACCCTTTC
1 TCAAAGT-C-CACAAGTCAGTGG--C-ATCCTTTC
* *
201329 -CAAAGTCCACAAGTCAATGGCACCCTTTC
1 TCAAAGTCCACAAGTCAGTGGCATCCTTTC
** *
201358 -CAAAGTCCACACAAGTTGGTGGCACAATCCTTCC
1 TCAAAGT-C-CACAAGTCAGTGG--C-ATCCTTTC
*
201392 TCAAAGACCACAAGTCAGTGGCATCCTTTC
1 TCAAAGTCCACAAGTCAGTGGCATCCTTTC
* * * *
201422 TCAAAGTCCACAAGTCAATGACATTCTTTT
1 TCAAAGTCCACAAGTCAGTGGCATCCTTTC
* * * *
201452 TCAAAGTTCATAAGTCAGTTGCAACCTTT
1 TCAAAGTCCACAAGTCAGTGGCATCCTTT
201481 TAAAAGCCCA
Statistics
Matches: 243, Mismatches: 40, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
25 20 0.08
28 2 0.01
29 64 0.26
30 57 0.23
31 47 0.19
32 13 0.05
33 14 0.06
34 21 0.09
35 5 0.02
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (30 bp):
TCAAAGTCCACAAGTCAGTGGCATCCTTTC
Found at i:201427 original size:94 final size:93
Alignment explanation
Indices: 201230--201441 Score: 272
Period size: 94 Copynumber: 2.3 Consensus size: 93
201220 AAGTCAATGG
* * *
201230 CTTTCCAAAGTCCCCAAGTTAATGGCACCGCTTCCAAAGTCCACACAAGTTGGTGGCACCCTTTC
1 CTTTCCAAAGTCCACAAGTCAATGGCACCGCTTCCAAAGTCCACACAAGTTGGTGGCACCCTTCC
* *
201295 CAAAGTCCACACAAGTCGGTGGCACAACC
66 CAAAGTACACACAAGTCAGTGG-ACAACC
201324 CTTTCCAAAGTCCACAAGTCAATGGCACC-CTTTCCAAAGTCCACACAAGTTGGTGGCACAATCC
1 CTTTCCAAAGTCCACAAGTCAATGGCACCGC-TTCCAAAGTCCACACAAGTTGGTGGCAC---CC
*
201388 TTCCTCAAAG-AC-CACAAGTCAGTGG-C-ATC
62 TTCC-CAAAGTACACACAAGTCAGTGGACAACC
201417 CTTTCTCAAAGTCCACAAGTCAATG
1 CTTTC-CAAAGTCCACAAGTCAATG
201442 ACATTCTTTT
Statistics
Matches: 106, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
93 8 0.08
94 75 0.71
96 12 0.11
97 6 0.06
98 5 0.05
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.22
Consensus pattern (93 bp):
CTTTCCAAAGTCCACAAGTCAATGGCACCGCTTCCAAAGTCCACACAAGTTGGTGGCACCCTTCC
CAAAGTACACACAAGTCAGTGGACAACC
Found at i:201481 original size:30 final size:30
Alignment explanation
Indices: 201392--201481 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
201382 CAATCCTTCC
* * *
201392 TCAAAGACCACAAGTCAGTGGCATCCTTTC
1 TCAAAGTCCACAAGTCAGTTGCATCCTTTT
* *
201422 TCAAAGTCCACAAGTCA-ATGACATTCTTTT
1 TCAAAGTCCACAAGTCAGTTG-CATCCTTTT
* * *
201452 TCAAAGTTCATAAGTCAGTTGCAACCTTTT
1 TCAAAGTCCACAAGTCAGTTGCATCCTTTT
201482 AAAAGCCCAT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
29 1 0.02
30 45 0.94
31 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (30 bp):
TCAAAGTCCACAAGTCAGTTGCATCCTTTT
Found at i:201554 original size:31 final size:31
Alignment explanation
Indices: 201472--201731 Score: 293
Period size: 31 Copynumber: 8.5 Consensus size: 31
201462 TAAGTCAGTT
* *
201472 GCAACCTTTTAAAAGCCCATACGAGTTGGTG
1 GCAACCTTTTCAAAGCCCACACGAGTTGGTG
** * * *
201503 GTGACCTCTTCTTAAGCCCACACGAGTTGATG
1 GCAACCTTTTC-AAAGCCCACACGAGTTGGTG
201535 GCAACCTTTTCAAAGCCCACACGAGTTGGTG
1 GCAACCTTTTCAAAGCCCACACGAGTTGGTG
201566 GCAA-CTTCTTCAAAGCCCACACGAGTTGGTG
1 GCAACCTT-TTCAAAGCCCACACGAGTTGGTG
*
201597 GCAACCTCTTCAAAGCCCACACGAGTTGGTG
1 GCAACCTTTTCAAAGCCCACACGAGTTGGTG
* *
201628 GC-A-----TCAAAGCCAACACAAGTTGGTG
1 GCAACCTTTTCAAAGCCCACACGAGTTGGTG
* *
201653 GCAACATTTTCAAAGCCCACACGAGTTAGTG
1 GCAACCTTTTCAAAGCCCACACGAGTTGGTG
* * *
201684 GCAACCTTTTCAAAGTCTACACGAGTTAGTG
1 GCAACCTTTTCAAAGCCCACACGAGTTGGTG
201715 G-AATCCTTTCTCAAAGC
1 GCAA-CCTTT-TCAAAGC
201732 TCGCATGAGC
Statistics
Matches: 196, Mismatches: 22, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
25 22 0.11
26 1 0.01
30 6 0.03
31 134 0.68
32 33 0.17
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (31 bp):
GCAACCTTTTCAAAGCCCACACGAGTTGGTG
Found at i:201643 original size:25 final size:25
Alignment explanation
Indices: 201606--201655 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
201596 GGCAACCTCT
* *
201606 TCAAAGCCCACACGAGTTGGTGGCA
1 TCAAAGCCAACACAAGTTGGTGGCA
201631 TCAAAGCCAACACAAGTTGGTGGCA
1 TCAAAGCCAACACAAGTTGGTGGCA
201656 ACATTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (25 bp):
TCAAAGCCAACACAAGTTGGTGGCA
Found at i:201668 original size:87 final size:88
Alignment explanation
Indices: 201472--201715 Score: 285
Period size: 87 Copynumber: 2.7 Consensus size: 88
201462 TAAGTCAGTT
* * ** * *
201472 GCAACCTTTTAAAAGCCCATACGAGTTGGTGGTGACCTCTTCTTAAGCCCACACGAGTTGATGGC
1 GCAA-CTTTTCAAAGCCCACACGAGTTGGTGGCAACCTCTTC-AAAGCCCACACGAGTTGGTGGC
* *
201537 AACCTTTTCAAAGCCCACACGAGTTGGTG
64 AA----TTCAAAGCCAACACAAGTTGGTG
201566 GCAACTTCTTCAAAGCCCACACGAGTTGGTGGCAACCTCTTCAAAGCCCACACGAGTTGGTGGC-
1 GCAACTT-TTCAAAGCCCACACGAGTTGGTGGCAACCTCTTCAAAGCCCACACGAGTTGGTGGCA
201630 A-TCAAAGCCAACACAAGTTGGTG
65 ATTCAAAGCCAACACAAGTTGGTG
* * * * *
201653 GCAACATTTTCAAAGCCCACACGAGTTAGTGGCAACCTTTTCAAAGTCTACACGAGTTAGTGG
1 GCAAC-TTTTCAAAGCCCACACGAGTTGGTGGCAACCTCTTCAAAGCCCACACGAGTTGGTGG
201716 AATCCTTTCT
Statistics
Matches: 135, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
87 75 0.56
88 2 0.01
92 1 0.01
93 23 0.17
94 34 0.25
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (88 bp):
GCAACTTTTCAAAGCCCACACGAGTTGGTGGCAACCTCTTCAAAGCCCACACGAGTTGGTGGCAA
TTCAAAGCCAACACAAGTTGGTG
Found at i:201949 original size:80 final size:80
Alignment explanation
Indices: 201786--201987 Score: 203
Period size: 80 Copynumber: 2.5 Consensus size: 80
201776 ATCTCCTTCT
* * * * * *
201786 AAGCCCAATGTCGTTGGCCTTGAATTAGCACATTGGCACCCTGCCTATGTCAAAAGGCACTTGTC
1 AAGCCCAATGTCGTTGGCCTTGAATCAGCACATTAGCACCTTGCCTAAGTCAAAAGGCACATCTC
201851 AAATCTTCTTCACTA
66 AAATCTTCTTCACTA
* ***
201866 AAGCCCAATGTTGTTGGCCTTGAATCAGCACATTAGCACCTTGCCCTAAGTCATGCGGCATCCAT
1 AAGCCCAATGTCGTTGGCCTTGAATCAGCACATTAGCACCTTG-CCTAAGTCAAAAGGCA--CAT
*
201931 CT-AAATCTTCTT-TC-A
63 CTCAAATCTTCTTCACTA
** * * * *
201946 AAGCTTAATATCATTGGCCTTGGATCAACACATTAGCACCTT
1 AAGCCCAATGTCGTTGGCCTTGAATCAGCACATTAGCACCTT
201988 TGCCATCCTT
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
80 75 0.74
81 13 0.13
82 10 0.10
83 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (80 bp):
AAGCCCAATGTCGTTGGCCTTGAATCAGCACATTAGCACCTTGCCTAAGTCAAAAGGCACATCTC
AAATCTTCTTCACTA
Found at i:202037 original size:52 final size:51
Alignment explanation
Indices: 201968--202191 Score: 166
Period size: 52 Copynumber: 4.3 Consensus size: 51
201958 ATTGGCCTTG
* * * * *
201968 GATCAACACATTAGCACCTTTGCCATC-CTTAAGTCCAATGTCATTGGCC-AA
1 GATCAGCACATTGGCACCTTTGCCATCTC-TAAGACC-ATGTCACTAGCCTAA
* * * *
202019 GAATCAGCACATTGGCACCTTTGTCATTTCTAAGACCATGTCGCTAGCCTTA
1 G-ATCAGCACATTGGCACCTTTGCCATCTCTAAGACCATGTCACTAGCCTAA
* * * *** * **
202071 GATCAGCACATTGGCACCTTTGTCATTTCTATGACCAATGTTGTTGGCCTTC
1 GATCAGCACATTGGCACCTTTGCCATCTCTAAGACC-ATGTCACTAGCCTAA
* * *
202123 GATCAACACATTGGCACCTTTGTCATCTCTAAAACCAGTGTCACTAGCCATAA
1 GATCAGCACATTGGCACCTTTGCCATCTCTAAGACCA-TGTCACTAGCC-TAA
* *
202176 -ATTAGCATATTGGCAC
1 GATCAGCACATTGGCAC
202192 GTTATCATTT
Statistics
Matches: 140, Mismatches: 27, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
51 45 0.32
52 93 0.66
53 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (51 bp):
GATCAGCACATTGGCACCTTTGCCATCTCTAAGACCATGTCACTAGCCTAA
Found at i:202081 original size:51 final size:52
Alignment explanation
Indices: 202021--202251 Score: 243
Period size: 51 Copynumber: 4.5 Consensus size: 52
202011 TTGGCCAAGA
202021 ATCAGCACATTGGCACCTTTGTCATTTCTAAGACC-ATGTCGCTAGCCTTAG
1 ATCAGCACATTGGCACCTTTGTCATTTCTAAGACCAATGTCGCTAGCCTTAG
* * * * *
202072 ATCAGCACATTGGCACCTTTGTCATTTCTATGACCAATGTTGTTGGCCTTCG
1 ATCAGCACATTGGCACCTTTGTCATTTCTAAGACCAATGTCGCTAGCCTTAG
* * * * * * *
202124 ATCAACACATTGGCACCTTTGTCATCTCTAAAACCAGTGTCACTAGCCATAA
1 ATCAGCACATTGGCACCTTTGTCATTTCTAAGACCAATGTCGCTAGCCTTAG
* * * * *
202176 ATTAGCATATTGGCA-CGTTATCATTTTTAAGACCAATGTCGCTAGCCTT-G
1 ATCAGCACATTGGCACCTTTGTCATTTCTAAGACCAATGTCGCTAGCCTTAG
* * * *
202226 AATCAACACGTTGACACCTATGTCAT
1 -ATCAGCACATTGGCACCTTTGTCAT
202252 CTTTAAGTCT
Statistics
Matches: 140, Mismatches: 37, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
51 70 0.50
52 70 0.50
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (52 bp):
ATCAGCACATTGGCACCTTTGTCATTTCTAAGACCAATGTCGCTAGCCTTAG
Found at i:202141 original size:103 final size:103
Alignment explanation
Indices: 202019--202253 Score: 276
Period size: 103 Copynumber: 2.3 Consensus size: 103
202009 CATTGGCCAA
* * * * * *
202019 GAATCAGCACATTGGCACCTTTGTCATTTCTAAGACCA-TGTCGCTAGCCTTAGATCAGCACATT
1 GAATCAACACATTGGCACCTTTGTCATCTCTAAAACCAGTGTCACTAGCCATAAATCAGCACATT
* * * * * *
202083 GGCACCTTTGTCATTTCTATGACCAATGTTGTTGGCCTT
66 GGCA-CGTTATCATTTCTAAGACCAATGTCGCTAGCCTT
* *
202122 CG-ATCAACACATTGGCACCTTTGTCATCTCTAAAACCAGTGTCACTAGCCATAAATTAGCATAT
1 -GAATCAACACATTGGCACCTTTGTCATCTCTAAAACCAGTGTCACTAGCCATAAATCAGCACAT
*
202186 TGGCACGTTATCATTTTTAAGACCAATGTCGCTAGCCTT
65 TGGCACGTTATCATTTCTAAGACCAATGTCGCTAGCCTT
* * *
202225 GAATCAACACGTTGACACCTATGTCATCT
1 GAATCAACACATTGGCACCTTTGTCATCT
202254 TTAAGTCTAG
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
102 1 0.01
103 84 0.76
104 26 0.23
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (103 bp):
GAATCAACACATTGGCACCTTTGTCATCTCTAAAACCAGTGTCACTAGCCATAAATCAGCACATT
GGCACGTTATCATTTCTAAGACCAATGTCGCTAGCCTT
Found at i:202244 original size:155 final size:155
Alignment explanation
Indices: 201959--202251 Score: 369
Period size: 155 Copynumber: 1.9 Consensus size: 155
201949 CTTAATATCA
* ** * *
201959 TTGGCCTTGGATCAACACATTAGCACCTTTGCCATCCTTAAGTCCAATGTCATTGGCCAAGAATC
1 TTGGCCTTCGATCAACACATTAGCACCTTTGCCATCCTTAAAACCAATGTCACTAGCCAAGAATC
* * * *
202024 AGCACATTGGCACCTTTGTCATTTCTAAGACCATGTCGCTAGCCTTAGATCAGCACATTGGCACC
66 AGCACATTGGCACCGTTATCATTTCTAAGACCATGTCGCTAGCCTTAGATCAACACATTGACACC
*
202089 TTTGTCATTTCTATGACCAATGTTG
131 TATGTCATTTCTATGACCAATGTTG
* * *
202114 TTGGCCTTCGATCAACACATTGGCACCTTTGTCAT-CTCTAAAACCAGTGTCACTAGCCATA-AA
1 TTGGCCTTCGATCAACACATTAGCACCTTTGCCATCCT-TAAAACCAATGTCACTAGCCA-AGAA
* * * *
202177 TTAGCATATTGGCA-CGTTATCATTTTTAAGACCAATGTCGCTAGCCTT-GAATCAACACGTTGA
64 TCAGCACATTGGCACCGTTATCATTTCTAAGACC-ATGTCGCTAGCCTTAG-ATCAACACATTGA
202240 CACCTATGTCAT
127 CACCTATGTCAT
202252 CTTTAAGTCT
Statistics
Matches: 117, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
154 19 0.16
155 97 0.83
156 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (155 bp):
TTGGCCTTCGATCAACACATTAGCACCTTTGCCATCCTTAAAACCAATGTCACTAGCCAAGAATC
AGCACATTGGCACCGTTATCATTTCTAAGACCATGTCGCTAGCCTTAGATCAACACATTGACACC
TATGTCATTTCTATGACCAATGTTG
Found at i:202532 original size:43 final size:43
Alignment explanation
Indices: 202471--202558 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
202461 TTTAAGCCTA
*
202471 CATGAGCTGGTGGCACCAAACCTGTCCACAAGCAGCCGAACGC
1 CATGAGCTGGTGGCACCAAACCTATCCACAAGCAGCCGAACGC
*
202514 CATGAGCTGGTGGCACCAAACTTATCCACAAGCAGCCGAACGC
1 CATGAGCTGGTGGCACCAAACCTATCCACAAGCAGCCGAACGC
202557 CA
1 CA
202559 ATTGCACTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.34, G:0.24, T:0.12
Consensus pattern (43 bp):
CATGAGCTGGTGGCACCAAACCTATCCACAAGCAGCCGAACGC
Found at i:204738 original size:12 final size:12
Alignment explanation
Indices: 204718--204752 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
204708 AAGAGAAAGA
204718 AGAGATAGGAGG
1 AGAGATAGGAGG
204730 -GATGATAGGAGG
1 AGA-GATAGGAGG
204742 AGAGATAGGAG
1 AGAGATAGGAG
204753 AGATAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:204761 original size:12 final size:12
Alignment explanation
Indices: 204721--204766 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
204711 AGAAAGAAGA
*
204721 GATAGGAGGGAT
1 GATAGGAGAGAT
204733 GATAGGAGGAGA-
1 GATAGGA-GAGAT
204745 GATAGGAGAGAT
1 GATAGGAGAGAT
*
204757 AATA-GAGAGA
1 GATAGGAGAGA
204767 GGAGGGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 10 0.33
12 17 0.57
13 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:213136 original size:23 final size:25
Alignment explanation
Indices: 213091--213136 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
213081 GCCTTTGCTC
* *
213091 TGTTTTTCATTTTTTGTTTCTTTCG
1 TGTTTCTCATTTTTTGTTGCTTTCG
213116 TGTTTCTCA-TTTTTG-TGCTTT
1 TGTTTCTCATTTTTTGTTGCTTT
213137 TGCTTTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 6 0.32
25 8 0.42
ACGTcount: A:0.04, C:0.13, G:0.13, T:0.70
Consensus pattern (25 bp):
TGTTTCTCATTTTTTGTTGCTTTCG
Found at i:214748 original size:21 final size:21
Alignment explanation
Indices: 214703--214771 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
214693 TAGTTTTTTA
* *
214703 AAAAAGAAAAAGAAAAAAAAG
1 AAAAAGAATAAGAAAAAAAAC
* *
214724 AAAAAGAATAAGAAAGAACAC
1 AAAAAGAATAAGAAAAAAAAC
* *
214745 AAAAA-AATCAGAAAAAAATAA
1 AAAAAGAATAAGAAAAAAA-AC
214766 AAAAAG
1 AAAAAG
214772 GAAAAACTAG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 10 0.26
21 28 0.74
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (21 bp):
AAAAAGAATAAGAAAAAAAAC
Found at i:220359 original size:9 final size:9
Alignment explanation
Indices: 220347--220449 Score: 83
Period size: 9 Copynumber: 12.1 Consensus size: 9
220337 CTCTCTCTAT
220347 TATCTCTCC
1 TATCTCTCC
220356 TATCTCTCC
1 TATCTCTCC
**
220365 --TC-CTAT
1 TATCTCTCC
*
220371 TATCCCTCC
1 TATCTCTCC
*
220380 TATCTCTAC
1 TATCTCTCC
220389 TATCTCTCC
1 TATCTCTCC
220398 TATCTCTCC
1 TATCTCTCC
* *
220407 T-CCTAT-C
1 TATCTCTCC
*
220414 -ATCCCTCC
1 TATCTCTCC
* *
220422 TACCTCTAC
1 TATCTCTCC
220431 TATCTCTCC
1 TATCTCTCC
220440 TATCTCTCC
1 TATCTCTCC
220449 T
1 T
220450 CCTATCTCTT
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
6 2 0.03
7 5 0.07
8 6 0.08
9 58 0.82
ACGTcount: A:0.14, C:0.45, G:0.00, T:0.42
Consensus pattern (9 bp):
TATCTCTCC
Found at i:220367 original size:12 final size:12
Alignment explanation
Indices: 220352--220458 Score: 71
Period size: 12 Copynumber: 9.9 Consensus size: 12
220342 TCTATTATCT
220352 CTCCTATCTCTC
1 CTCCTATCTCTC
*
220364 CTCCTAT-TATCC
1 CTCCTATCTCT-C
220376 CTCCTA--TCT-
1 CTCCTATCTCTC
*
220385 CTACTA--TCT-
1 CTCCTATCTCTC
220394 CTCCTATCTCTC
1 CTCCTATCTCTC
220406 CTCCTATCATC-C
1 CTCCTATC-TCTC
220418 CTCCTA-C-CT-
1 CTCCTATCTCTC
*
220427 CTACTA--TCT-
1 CTCCTATCTCTC
220436 CTCCTATCTCTC
1 CTCCTATCTCTC
220448 CTCCTATCTCT
1 CTCCTATCTCT
220459 TCTTTCTCTT
Statistics
Matches: 79, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
9 26 0.33
11 11 0.14
12 40 0.51
13 2 0.03
ACGTcount: A:0.13, C:0.46, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:220376 original size:42 final size:42
Alignment explanation
Indices: 220322--220455 Score: 207
Period size: 42 Copynumber: 3.2 Consensus size: 42
220312 TTCTCTTCTT
* * *
220322 CTCCTGTCATCCCTTCTCTCTCTATTATCTCTCCTATCTCTC
1 CTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCTCTC
* *
220364 CTCCTATTATCCCTCCTATCTCTACTATCTCTCCTATCTCTC
1 CTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCTCTC
220406 CTCCTATCATCCCTCCTAC-CTCTACTATCTCTCCTATCTCTC
1 CTCCTATCATCCCTCCT-CTCTCTACTATCTCTCCTATCTCTC
220448 CTCCTATC
1 CTCCTATC
220456 TCTTCTTTCT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.13, C:0.45, G:0.01, T:0.42
Consensus pattern (42 bp):
CTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCTCTC
Found at i:220440 original size:30 final size:30
Alignment explanation
Indices: 220406--220467 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
220396 CCTATCTCTC
220406 CTCCTATCATC-CCTCCTACCTCTACTATCT
1 CTCCTATC-TCTCCTCCTACCTCTACTATCT
* * *
220436 CTCCTATCTCTCCTCCTATCTCTTCTTTCT
1 CTCCTATCTCTCCTCCTACCTCTACTATCT
220466 CT
1 CT
220468 TTGAGGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.11, C:0.45, G:0.00, T:0.44
Consensus pattern (30 bp):
CTCCTATCTCTCCTCCTACCTCTACTATCT
Found at i:224387 original size:54 final size:54
Alignment explanation
Indices: 224305--224413 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
224295 GGGACCTTCC
224305 TTAGACTACGTTAAGGCATGAATGCTTTTACATCTTTACCATCCTCATTCACAT
1 TTAGACTACGTTAAGGCATGAATGCTTTTACATCTTTACCATCCTCATTCACAT
224359 TTAGACTACGTTAAGGCATGAATGCTTTTACATCTTTACCATCCTCATTCACAT
1 TTAGACTACGTTAAGGCATGAATGCTTTTACATCTTTACCATCCTCATTCACAT
224413 T
1 T
224414 GGTTTTTTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.38
Consensus pattern (54 bp):
TTAGACTACGTTAAGGCATGAATGCTTTTACATCTTTACCATCCTCATTCACAT
Found at i:225713 original size:23 final size:23
Alignment explanation
Indices: 225669--225715 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
225659 TCCCACGGCT
* *
225669 GCAACCATTTTCAGCTGTTGGCA
1 GCAACCATTTTCAACTGCTGGCA
225692 GCAACCACTTTT-AACTGCTGGCA
1 GCAACCA-TTTTCAACTGCTGGCA
225715 G
1 G
225716 AAACTAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (23 bp):
GCAACCATTTTCAACTGCTGGCA
Found at i:228642 original size:102 final size:101
Alignment explanation
Indices: 228490--228732 Score: 312
Period size: 102 Copynumber: 2.4 Consensus size: 101
228480 TTATTCACGG
* *
228490 GATACTCCAACCCTGACTTTTCG-AGGGATACTCCAACCCTGCTCTTCAAAATTTATCTAGACTT
1 GATACTCCAACCCTGAC-TTT-GAAGGGATACTCCAACCCCGCTCTTCAAAATTTATCAAGACTT
* *
228554 GAACTCCTCCTTTGTCAAAATTATTTGTTATCCAT-AG
64 GAACTCCTCCTTTGCCAAAATTATTTGTTATCCATAAA
* * *
228591 GGTACTCCAACCCTGACCATTTGAAGAGATACTCCAACCCCGCTCTTCAAAATTTATCAAGATTT
1 GATACTCCAACCCTGA-C-TTTGAAGGGATACTCCAACCCCGCTCTTCAAAATTTATCAAGACTT
** *
228656 GAACTCCTTTTTTGCCAAAATTATTTGTTATCTATAAA
64 GAACTCCTCCTTTGCCAAAATTATTTGTTATCCATAAA
*
228694 GATACTCCAACCC-CATCTTCTGAAGGGATACTCCAACCC
1 GATACTCCAACCCTGA-CTT-TGAAGGGATACTCCAACCC
228733 TATTTTTAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
101 18 0.15
102 92 0.75
103 13 0.11
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (101 bp):
GATACTCCAACCCTGACTTTGAAGGGATACTCCAACCCCGCTCTTCAAAATTTATCAAGACTTGA
ACTCCTCCTTTGCCAAAATTATTTGTTATCCATAAA
Found at i:231645 original size:12 final size:11
Alignment explanation
Indices: 231623--231698 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
231613 AGAGAAAGAA
*
231623 GAGAGAGGAGG
1 GAGATAGGAGG
231634 GATGATAGGAGG
1 GA-GATAGGAGG
*
231646 AGAGACAGGA--
1 -GAGATAGGAGG
*
231656 GAGATAGTA--
1 GAGATAGGAGG
231665 GAGATAGGAGG
1 GAGATAGGAGG
231676 GATGATAGGAGG
1 GA-GATAGGAGG
*
231688 AGAGACAGGAG
1 -GAGATAGGAG
231699 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:231655 original size:24 final size:24
Alignment explanation
Indices: 231622--231707 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
231612 AAGAGAAAGA
*
231622 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
231646 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
231664 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
231688 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
231708 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:231674 original size:42 final size:42
Alignment explanation
Indices: 231613--231731 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
231603 TAGCCCTCAA
* *
231613 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
231655 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
231697 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
231732 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:242225 original size:159 final size:159
Alignment explanation
Indices: 241929--242936 Score: 649
Period size: 159 Copynumber: 6.3 Consensus size: 159
241919 TAGGTGTAGG
* ** * * * * *
241929 AAAAGCTTTTCATACCAAACCAAAGCATCAATATCATGTATCCCAAGGAGGAAAACATGTTTTTG
1 AAAAGCTTTTCTTATGAAACCAAAGCATCAATATCGTGTATCCCAATGAGGAGAACATCTTTTTA
* * ** * * *
241994 TTACCTAATCATGAGAACAAT--A-GAGATTATTGGGAGAATCTATGTTTATATCATTTGAGGAA
66 TTGCCCAATCAT-A-AA-AATAGAGGAGATTATTATGAGAATCCATGTTTATCTCATTTGAGGGA
** * * *
242056 CAAACTTTGATTTTAAAGAAAATAATGGAAAC
128 TGAACTTTAATTCTAAAGAAAATAATGGGAAC
*
242088 AAAAGCTTTTCTTATGAAACCAAAGCATCAATATCATGTATCCCAATGAGGAGAACATCTTTTTA
1 AAAAGCTTTTCTTATGAAACCAAAGCATCAATATCGTGTATCCCAATGAGGAGAACATCTTTTTA
* * * * *
242153 TTGCCCAAACACAAAAATAGAGGATATTATTATGAGAATCCATGTTTCTCTCATTTGGGGGATGA
66 TTGCCCAATCATAAAAATAGAGGAGATTATTATGAGAATCCATGTTTATCTCATTTGAGGGATGA
* *
242218 A-TATTGATTCT-AAGAAAAATAAT-GGAAG
131 ACT-TTAATTCTAAAG-AAAATAATGGGAAC
* * * *
242246 AAAACCTTTTCTTACT-AAACTAAAGCATCAAAATCGTGTATCTCAAAT-AGGAGAACATGC-TT
1 AAAAGCTTTTCTTA-TGAAACCAAAGCATCAATATCGTGTATC-CCAATGAGGAGAACAT-CTTT
* * * * *
242308 TTATTGCCTAATCATGAAAATAGTA-GAGATTATTACGGGAATCCATGTTTATCTCATTTAAGGG
63 TTATTGCCCAATCATAAAAATAG-AGGAGATTATTATGAGAATCCATGTTTATCTCATTTGAGGG
* * * *
242372 ATAAACTTTAATT-TTAAGAAAACTAATGAGAAG
127 ATGAACTTTAATTCTAAAGAAAA-TAATGGGAAC
* ** * * *
242405 AAAAGCTTTTTTTGGGAAACCAAAGCATCAATCTCGTGTGTCCCACCCAGTAAGGAG-A-ATCTG
1 AAAAGCTTTTCTTATGAAACCAAAGCATCAATATCGTGTATCCCA---A-TGAGGAGAACATCT-
*** * * * * ** * *
242468 TTTTAGTTGCTTGATTATAAAACA-A-AGGAGATTACTATGACAATCAATGTTTGCCTCAATTAA
61 TTTTA-TTGCCCAATCATAAAA-ATAGAGGAGATTATTATGAGAATCCATGTTTATCTCATTTGA
* * * *
242531 GGGACGAACTTTGATTCTAATGAAAATAATGGGAAG
124 GGGATGAACTTTAATTCTAAAGAAAATAATGGGAAC
* * * * * * ** *
242567 AAAAACTCTACTTATGAAACCAAATG-ATCAATATCGTGCATCTCAATAAGGAGAATGTGTTTTT
1 AAAAGCTTTTCTTATGAAACCAAA-GCATCAATATCGTGTATCCCAATGAGGAGAACATCTTTTT
* * * * * * * **
242631 GTTGCCCAATCATGAAAACA-ATGCAGATTATTATGAGAATCCATGCTTGTCTTATAAGAGGGAT
65 ATTGCCCAATCATAAAAATAGA-GGAGATTATTATGAGAATCCATGTTTATCTCATTTGAGGGAT
* *
242695 GTA-TTTCAATTCTAAGGAAAACT-ATGGGAAC
129 GAACTTT-AATTCTAAAGAAAA-TAATGGGAAC
* * * ** ** * *
242726 -AAAGCTTTTTTTATGAAACCAAAGCACCAATATTGTGTATCTTAATGAAAAAAAAAGTCTTTTT
1 AAAAGCTTTTCTTATGAAACCAAAGCATCAATATCGTGTATCCCAATGAGGAGAACA-TCTTTTT
* * * * * * * * *
242790 CTTGCCCAATGATGAAAACAAAAGAGATTATTACGAGAATCCA--TTTGTCTCATTTGGGGGATG
65 ATTGCCCAATCATAAAAATAGAGGAGATTATTATGAGAATCCATGTTTATCTCATTTGAGGGATG
* * *
242853 AACTTTAATTTTAAAGGAAATAGTGGGAAC
130 AACTTTAATTCTAAAGAAAATAATGGGAAC
** * * * * * * *
242883 -AAAGCTTTTCTTACAAAATCAAAACATCATTGTCATGTATCCCAACGAAGAGAA
1 AAAAGCTTTTCTTATGAAACCAAAGCATCAATATCGTGTATCCCAATGAGGAGAA
242937 TGTGTTTTTA
Statistics
Matches: 664, Mismatches: 148, Indels: 76
0.75 0.17 0.09
Matches are distributed among these distances:
156 4 0.01
157 82 0.12
158 193 0.29
159 259 0.39
160 5 0.01
161 4 0.01
162 90 0.14
163 26 0.04
164 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (159 bp):
AAAAGCTTTTCTTATGAAACCAAAGCATCAATATCGTGTATCCCAATGAGGAGAACATCTTTTTA
TTGCCCAATCATAAAAATAGAGGAGATTATTATGAGAATCCATGTTTATCTCATTTGAGGGATGA
ACTTTAATTCTAAAGAAAATAATGGGAAC
Found at i:245935 original size:12 final size:11
Alignment explanation
Indices: 245913--245988 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
245903 AGAGAAAGAA
*
245913 GAGAGAGGAGG
1 GAGATAGGAGG
245924 GATGATAGGAGG
1 GA-GATAGGAGG
*
245936 AGAGACAGGA--
1 -GAGATAGGAGG
*
245946 GAGATAGTA--
1 GAGATAGGAGG
245955 GAGATAGGAGG
1 GAGATAGGAGG
245966 GATGATAGGAGG
1 GA-GATAGGAGG
245978 AGAGATAGGAG
1 -GAGATAGGAG
245989 AGATAATAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.07
12 31 0.57
13 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.49, T:0.11
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:245945 original size:24 final size:24
Alignment explanation
Indices: 245912--245997 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
245902 AAGAGAAAGA
*
245912 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATAGGAGG
* *
245936 AGAGACAGGA--GA-GAT---AGT
1 AGAGATAGGAGGGATGATAGGAGG
245954 AGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATAGGAGG
* *
245978 AGAGATAGGAGAGATAATAG
1 AGAGATAGGAGGGATGATAG
245998 AGAGAGGAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 29 0.58
ACGTcount: A:0.42, C:0.01, G:0.45, T:0.12
Consensus pattern (24 bp):
AGAGATAGGAGGGATGATAGGAGG
Found at i:245947 original size:9 final size:9
Alignment explanation
Indices: 245933--245993 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
245923 GGATGATAGG
*
245933 AGGAGAGAC
1 AGGAGAGAT
245942 AGGAGAGAT
1 AGGAGAGAT
*
245951 AGTAGAGAT
1 AGGAGAGAT
*
245960 AGGAGGGAT
1 AGGAGAGAT
* *
245969 --GATAG-G
1 AGGAGAGAT
245975 AGGAGAGAT
1 AGGAGAGAT
245984 AGGAGAGAT
1 AGGAGAGAT
245993 A
1 A
245994 ATAGAGAGAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.43, C:0.02, G:0.44, T:0.11
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:245964 original size:42 final size:42
Alignment explanation
Indices: 245903--246021 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
245893 TAGCCCTCAA
* *
245903 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
245945 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
245987 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
246022 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:245997 original size:12 final size:12
Alignment explanation
Indices: 245957--246002 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
245947 AGATAGTAGA
*
245957 GATAGGAGGGAT
1 GATAGGAGAGAT
245969 GATAGGAGGAGA-
1 GATAGGA-GAGAT
245981 GATAGGAGAGAT
1 GATAGGAGAGAT
*
245993 AATA-GAGAGA
1 GATAGGAGAGA
246003 GGAGGGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 10 0.33
12 17 0.57
13 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:255895 original size:158 final size:157
Alignment explanation
Indices: 255592--256268 Score: 646
Period size: 158 Copynumber: 4.3 Consensus size: 157
255582 GTTCTCATCA
* * ** ** * *
255592 GAAAATGATGGTAAGAAATGCTTTTCTTGGGAAACCAAAGCATCAATATCACATATCCCAAGGAG
1 GAAAATGATGGAAAGAAAAGCTTTTCTTATGAAACCAAAGCATCAATATCATGTATCCTAA-TAG
* * ** * *
255657 GAGAA-TGTGCATTGGC-TGCCCAGTCACAAAAAGAATGAAGATTATTATGACAATCCATATTTG
65 AAGAACT-TG-TTTTTCTTGCCCAGTCAC-AAAAGAATGGAGATTATTATGACAATCCATGTTTG
* **
255720 TCTTAAATGAGGGATGAACTTTAATTCTAAG
127 TCTCATTTGAGGGATGAACTTTAATTCTAAG
** * * * ** * *
255751 GAATGTTATGAAAAGAAAAGCTCTTCTTATGAAACCAAAGCATCAATATTGTGCATCCTGATCAG
1 GAAAATGATGGAAAGAAAAGCTTTTCTTATGAAACCAAAGCATCAATATCATGTATCCTAAT-AG
*
255816 AAGAACTTGTTTTTCTTGCCCAGTCACAAAAGAATGGAGATTATTATGACAATCCTTGTTTGTCT
65 AAGAACTTGTTTTTCTTGCCCAGTCACAAAAGAATGGAGATTATTATGACAATCCATGTTTGTCT
* *
255881 CATTTGAGGGATGAACTTTGATTCTAGG
130 CATTTGAGGGATGAACTTTAATTCTAAG
* * * *
255909 GAAAATAATGGGAAGAAAAGCTTTTCTAATGAAACCAAAGCATCAATATCATGTATCCCAAT-GA
1 GAAAATGATGGAAAGAAAAGCTTTTCTTATGAAACCAAAGCATCAATATCATGTATCCTAATAGA
* * * * * *
255973 ATGGAACTTGCTTTTTTTTG-TCTGATCACAAAACAATAGAGATTATTATGAGAATCCATGTTTG
66 A--GAACTTG-TTTTTCTTGCCCAG-TCACAAAAGAATGGAGATTATTATGACAATCCATGTTTG
* * *
256037 TCTCATTTGAAGGATGAACTTTGATTCAAAG
127 TCTCATTTGAGGGATGAACTTTAATTCTAAG
* * * * *
256068 GAAAATGATGGAAAGAGATGTTTTTCTTGTGAAACCAAACCATCAATATCATGTATCCTAATGAG
1 GAAAATGATGGAAAGAAAAGCTTTTCTTATGAAACCAAAGCATCAATATCATGTATCCTAAT-A-
* ** * * * ** * *
256133 GAA-AACATGTTTTGGTTGCCTAATCACAAAAAAATGGATTTTACTATGAGAATCCATGTTTGTC
64 GAAGAACTTGTTTTTCTTGCCCAGTCACAAAAGAATGGAGATTATTATGACAATCCATGTTTGTC
* * *
256197 TCATTTAAGAGATGAACTTTAATTTTAAG
129 TCATTTGAGGGATGAACTTTAATTCTAAG
* * *
256226 AAAAATGATGGGAAGAAAGGCTTTTCTTATGAAACC-AAGCATC
1 GAAAATGATGGAAAGAAAAGCTTTTCTTATGAAACCAAAGCATC
256269 TGTAAGTAAA
Statistics
Matches: 422, Mismatches: 85, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
156 3 0.01
157 6 0.01
158 216 0.51
159 193 0.46
160 1 0.00
162 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (157 bp):
GAAAATGATGGAAAGAAAAGCTTTTCTTATGAAACCAAAGCATCAATATCATGTATCCTAATAGA
AGAACTTGTTTTTCTTGCCCAGTCACAAAAGAATGGAGATTATTATGACAATCCATGTTTGTCTC
ATTTGAGGGATGAACTTTAATTCTAAG
Found at i:256195 original size:317 final size:316
Alignment explanation
Indices: 255695--256268 Score: 736
Period size: 317 Copynumber: 1.8 Consensus size: 316
255685 AAAAGAATGA
* * * ** *
255695 AGATTATTATGACAATCCATATTTGTCTTAAATGAGGGATGAACTTTAATTCTAAGGAATGTTAT
1 AGATTATTATGACAATCCATATTTGTCTCAAATGAAGGATGAACTTTAATTCAAAGGAAAATGAT
* ** * *
255760 GAAAAGAAAAGCTCTTCTTATGAAACCAAAGCATCAATATTGTGCATCCTGATCAGAAGAACTTG
66 GAAAAGAAAAGCTCTTCTTATGAAACCAAACCATCAATATCATGCATCCTAATCAGAAGAACATG
* * * * * * *
255825 TTTTTCTTGCCCAGTCACAAAAGAATGGAGATTATTATGACAATCCTTGTTTGTCTCATTTGAGG
131 TTTTGCTTGCCCAATCACAAAAAAATGGAGATTACTATGACAATCCATGTTTGTCTCATTTAAGA
* * *
255890 GATGAACTTTGATTCTAGGGAAAATAATGGGAAGAAAAGCTTTTCTAATGAAACCAAAGCATCAA
196 GATGAACTTTAATTCTAAGAAAAATAATGGGAAGAAAAGCTTTTCTAATGAAACC-AAGCATCAA
255955 TATCATGTATCCCAATGAATGGAACTTGCTTTTTTTTGTCTGATCACAAAACAATAG
260 TATCATGTATCCCAATGAATGGAACTTGCTTTTTTTTGTCTGATCACAAAACAATAG
* * ** *
256012 AGATTATTATGAGAATCCATGTTTGTCTCATTTGAAGGATGAACTTTGATTCAAAGGAAAATGAT
1 AGATTATTATGACAATCCATATTTGTCTCAAATGAAGGATGAACTTTAATTCAAAGGAAAATGAT
* * * * * * * *
256077 GGAAAGAGATGTTTTTCTTGTGAAACCAAACCATCAATATCATGTATCCTAATGAGGAA-AACAT
66 GAAAAGAAAAGCTCTTCTTATGAAACCAAACCATCAATATCATGCATCCTAATCA-GAAGAACAT
* * ** *
256141 GTTTTGGTTGCCTAATCACAAAAAAATGGATTTTACTATGAGAATCCATGTTTGTCTCATTTAAG
130 GTTTTGCTTGCCCAATCACAAAAAAATGGAGATTACTATGACAATCCATGTTTGTCTCATTTAAG
* * * *
256206 AGATGAACTTTAATTTTAAGAAAAATGATGGGAAGAAAGGCTTTTCTTATGAAACCAAGCATC
195 AGATGAACTTTAATTCTAAGAAAAATAATGGGAAGAAAAGCTTTTCTAATGAAACCAAGCATC
256269 TGTAAGTAAA
Statistics
Matches: 213, Mismatches: 43, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
316 7 0.03
317 203 0.95
318 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (316 bp):
AGATTATTATGACAATCCATATTTGTCTCAAATGAAGGATGAACTTTAATTCAAAGGAAAATGAT
GAAAAGAAAAGCTCTTCTTATGAAACCAAACCATCAATATCATGCATCCTAATCAGAAGAACATG
TTTTGCTTGCCCAATCACAAAAAAATGGAGATTACTATGACAATCCATGTTTGTCTCATTTAAGA
GATGAACTTTAATTCTAAGAAAAATAATGGGAAGAAAAGCTTTTCTAATGAAACCAAGCATCAAT
ATCATGTATCCCAATGAATGGAACTTGCTTTTTTTTGTCTGATCACAAAACAATAG
Found at i:256942 original size:23 final size:24
Alignment explanation
Indices: 256916--256978 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
256906 CTAGTAATTA
*
256916 TAAAAAAATAAAATTAACC-ATAG
1 TAAAAAAATAAAATTAACCAAAAG
* * * *
256939 TAAAATAATCAATTTAACCAAAAT
1 TAAAAAAATAAAATTAACCAAAAG
256963 TAAAATAAATAAAATT
1 TAAAA-AAATAAAATT
256979 CATTATTCCT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
23 16 0.53
24 7 0.23
25 7 0.23
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (24 bp):
TAAAAAAATAAAATTAACCAAAAG
Found at i:266206 original size:38 final size:38
Alignment explanation
Indices: 266131--266206 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
266121 AGATTGTTAG
*
266131 GGAAAGGGTGTGTTCAACCAAAGGCCCTTCACTGAGAT
1 GGAAAGGGTGTGTTCAACCAAAGGCCCTTCACCGAGAT
* **
266169 GGAAAGGGTGTGTTCAGCCAAAGGCCCTTTGCCGAGAT
1 GGAAAGGGTGTGTTCAACCAAAGGCCCTTCACCGAGAT
266207 CAAGACAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (38 bp):
GGAAAGGGTGTGTTCAACCAAAGGCCCTTCACCGAGAT
Done.