Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007816.1 Hibiscus syriacus cultivar Beakdansim tig00110151_pilon, whole genome shotgun sequence
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: 3994936
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:352257 original size:9 final size:9
Alignment explanation
Indices: 352245--352286 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
352235 CAAAAGCAAC
352245 AAAAAGAAG
1 AAAAAGAAG
352254 AAAAAGAAG
1 AAAAAGAAG
352263 AAAAAGAA-
1 AAAAAGAAG
352271 AAAGAA-AAG
1 AAA-AAGAAG
352280 AAAAAGA
1 AAAAAGA
352287 CTCCTACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:352269 original size:6 final size:6
Alignment explanation
Indices: 352245--352286 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
352235 CAAAAGCAAC
*
352245 AAAAAG AAGAAA- AAGAAG AAAAAG AAAAAG -AAAAG AAAAAG A
1 AAAAAG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
352287 CTCCTACATC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 7 0.23
6 21 0.68
7 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:353713 original size:17 final size:17
Alignment explanation
Indices: 353691--353723 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
353681 ATCCTACCCT
353691 TATACCATAACCATTTC
1 TATACCATAACCATTTC
*
353708 TATACCCTAACCATTT
1 TATACCATAACCATTT
353724 GTTTAAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
TATACCATAACCATTTC
Found at i:358218 original size:15 final size:15
Alignment explanation
Indices: 358207--358235 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
358197 ACTCAAAAAG
358207 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
358222 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
358236 GTTGAAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:358796 original size:72 final size:72
Alignment explanation
Indices: 358679--358813 Score: 261
Period size: 72 Copynumber: 1.9 Consensus size: 72
358669 TTCACTAACC
*
358679 ATGTCTCGAAGTCCAGGACGAACCCCTAAAAGAGATGCCCCTAATTTGCAAACTCAAACAATCAT
1 ATGTCTCGAAGTCCAGGACGAACCCCTAAAAGAGATGCCCCTAATTTGCAAAATCAAACAATCAT
358744 GCATTAA
66 GCATTAA
358751 ATGTCTCGAAGTCCAGGACGAACCCCTAAAAGAGATGCCCCTAATTTGCAAAATCAAACAATC
1 ATGTCTCGAAGTCCAGGACGAACCCCTAAAAGAGATGCCCCTAATTTGCAAAATCAAACAATC
358814 CTTTGCATGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.20
Consensus pattern (72 bp):
ATGTCTCGAAGTCCAGGACGAACCCCTAAAAGAGATGCCCCTAATTTGCAAAATCAAACAATCAT
GCATTAA
Found at i:368030 original size:35 final size:37
Alignment explanation
Indices: 367961--368040 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
367951 ATACTATTTC
*
367961 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
367998 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
368033 CATCACCA
1 CATCACCA
368041 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:368669 original size:16 final size:16
Alignment explanation
Indices: 368648--368701 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
368638 GTAAGTTATC
368648 TTCATTTTTTTATCAT
1 TTCATTTTTTTATCAT
*
368664 TTCATTTCTTTATTC-T
1 TTCATTTTTTTA-TCAT
* * *
368680 TTCATCTTTTTCTTAT
1 TTCATTTTTTTATCAT
368696 TTCATT
1 TTCATT
368702 ACCATATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 1 0.03
16 27 0.90
17 2 0.07
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCATTTTTTTATCAT
Found at i:370175 original size:35 final size:37
Alignment explanation
Indices: 370106--370185 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
370096 ATACTATTTC
*
370106 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
370143 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
370178 CATCACCA
1 CATCACCA
370186 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:372474 original size:36 final size:36
Alignment explanation
Indices: 372415--372491 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
372405 GATATGGTGG
* * *
372415 TGGAATATGGTGATTATATAGGCGTGATAATGGA-GA
1 TGGACTATGGTGATGATAAAGGCGTGATAAT-GATGA
372451 TGGACTATGGTGATGATAAAGGCGTGATAATGATGA
1 TGGACTATGGTGATGATAAAGGCGTGATAATGATGA
372487 TGGAC
1 TGGAC
372492 AGATTGTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 2 0.05
36 35 0.95
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (36 bp):
TGGACTATGGTGATGATAAAGGCGTGATAATGATGA
Found at i:376994 original size:36 final size:36
Alignment explanation
Indices: 376919--377011 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
376909 GTGAGAATAT
* * * * *
376919 AGGCGTGAT-ATGGTGGTGGAATATGGTGATTATAT
1 AGGCGTGATAATGGAGATGGACTATGGTGATGATAA
376954 AGGCGTGATAATGGAGATGGACTATGGTGATGATAA
1 AGGCGTGATAATGGAGATGGACTATGGTGATGATAA
376990 AGGCGTGATAAT-GATGATGGAC
1 AGGCGTGATAATGGA-GATGGAC
377012 AGATTGTATC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
35 11 0.22
36 40 0.78
ACGTcount: A:0.30, C:0.05, G:0.37, T:0.28
Consensus pattern (36 bp):
AGGCGTGATAATGGAGATGGACTATGGTGATGATAA
Found at i:379206 original size:33 final size:33
Alignment explanation
Indices: 379164--379232 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
379154 ATTGATGAAT
*
379164 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
379197 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
379230 GAA
1 GAA
379233 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:379237 original size:13 final size:12
Alignment explanation
Indices: 379218--379314 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
379208 TTATTGGCGT
379218 GATATGGTGATG
1 GATATGGTGATG
379230 GAATATGGTGAT-
1 G-ATATGGTGATG
*
379242 GATATAGGCG-T-
1 GATAT-GGTGATG
379253 GATAATGGTGATG
1 GAT-ATGGTGATG
379266 GACTATGGTGAT-
1 GA-TATGGTGATG
*
379278 GATATAGGCG-T-
1 GATAT-GGTGATG
*
379289 GATAATGGAGATG
1 GAT-ATGGTGATG
379302 GATTATGGTGATG
1 GA-TATGGTGATG
379315 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:379273 original size:36 final size:36
Alignment explanation
Indices: 379203--379315 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
379193 AATGGAAGGA
* *
379203 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
379238 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
379274 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
379310 TGATGA
1 TGATGA
379316 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:381509 original size:33 final size:33
Alignment explanation
Indices: 381467--381535 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
381457 ATTGATGAAT
*
381467 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
381500 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
381533 GAA
1 GAA
381536 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:381540 original size:13 final size:12
Alignment explanation
Indices: 381521--381617 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
381511 TTATTGGCGT
381521 GATATGGTGATG
1 GATATGGTGATG
381533 GAATATGGTGAT-
1 G-ATATGGTGATG
*
381545 GATATAGGCG-T-
1 GATAT-GGTGATG
381556 GATAATGGTGATG
1 GAT-ATGGTGATG
381569 GACTATGGTGAT-
1 GA-TATGGTGATG
*
381581 GATATAGGCG-T-
1 GATAT-GGTGATG
*
381592 GATAATGGAGATG
1 GAT-ATGGTGATG
381605 GATTATGGTGATG
1 GA-TATGGTGATG
381618 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:381576 original size:36 final size:36
Alignment explanation
Indices: 381506--381618 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
381496 AATGGAAGGA
* *
381506 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
381541 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
381577 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
381613 TGATGA
1 TGATGA
381619 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:383834 original size:429 final size:429
Alignment explanation
Indices: 383003--383855 Score: 1368
Period size: 429 Copynumber: 2.0 Consensus size: 429
382993 AAGATCTAAC
* *
383003 TTGTATGCATTGTCATTAATCTTCTCAATGATTTGAAAGGGACCATCTCCTCTTGGTAAAAGCTT
1 TTGTATGCATTGTCATTAATCTTCTCAATAATTTGAAAGGGACCATCACCTCTTGGTAAAAGCTT
* *
383068 AGATTTCCTTTTAGTAGGAAACCTTTCCTTTCACAAATGCACCCATACCAAATCTCCAACTTCCA
66 AGACTTCCTTTTAGTAGGAAACCTTTCCTTACACAAATGCACCCATACCAAATCTCCAACTTCCA
*
383133 AATGGAGTGGTTTACGTCCCTTATTGGCTTGTTGCTCATACTGATTTGTTCTTCTCTCAATATTG
131 AATAGAGTGGTTTACGTCCCTTATTGGCTTGTTGCTCATACTGATTTGTTCTTCTCTCAATATTG
* *
383198 TGCCGAACTTGTTCATGTAACTTCTTGATGAACTCAGCCTTGTTCTTTCCATCCTTGTGAACCAT
196 TGCCGAACTTGTTCATGTAACTTCTTGATGAACTCAGCCTTGTTCTTACCATCCTTGTGAACCAA
* * *
383263 TTGTTCTTGAGGTAGAGGAAGAAGGTCCAAAGGAGTTAAGGGATTGAATCCATACACTACCTCGA
261 TTATTCTCGAGGTAGAGGAAGAAGATCCAAAGGAGTTAAGGGATTGAATCCATACACTACCTCGA
* * *
383328 ATGGTGAAATTTTTATGGCCGAATGAACTGACCGGTTGTAAGCAAATTCAAATGTGGTAGGCAAT
326 ATGGTGAAATTTTTATGGCCGAATGAACTGACCGATTGCAAGCAAATTCAAATGTGGAAGGCAAT
* *
383393 CTTCCCAAGTCTTTATGTTTTTCTTGATGATGGCCCAAT
391 CTTCCCAAGTCTTTATATTATTCTTGATGATGGCCCAAT
* * **
383432 TTGTATGCATTGTCATTAATCTTCTCGATAATTTGAAAGGGATCATCACCTCTTGGTAGCAGCTT
1 TTGTATGCATTGTCATTAATCTTCTCAATAATTTGAAAGGGACCATCACCTCTTGGTAAAAGCTT
* * *
383497 AGACTTCCTTTTAGTTGGAAACCTTTCCTTACGCAAATGCACCCATACCCAATCTCCAACTTCCA
66 AGACTTCCTTTTAGTAGGAAACCTTTCCTTACACAAATGCACCCATACCAAATCTCCAACTTCCA
* * * * *
383562 AATAGAGTGGTTTGCGTCCCTTATTGGCTTGTTGTTCGTACTGCTTTGTTTTTCTCTCAATATTG
131 AATAGAGTGGTTTACGTCCCTTATTGGCTTGTTGCTCATACTGATTTGTTCTTCTCTCAATATTG
* *
383627 TGCCGAA-TCTGTTCATGTAAC-TCTTGATGAACTCGGCCTTGTTCTTACCATCCTTGTTAACCA
196 TGCCGAACT-TGTTCATGTAACTTCTTGATGAACTCAGCCTTGTTCTTACCATCCTTGTGAACCA
383690 ATTATTCTCGAGGTAGAGGAAGAAGATCCAAAGGAGTTAAGGGATTGAATCCATACACTACCTCG
260 ATTATTCTCGAGGTAGAGGAAGAAGATCCAAAGGAGTTAAGGGATTGAATCCATACACTACCTCG
* * *
383755 AATGGTGAAGTTTTTATGGCTGAATGAACTGACCGATTGCAAGCAAATTCCACATGTGGAAGGCA
325 AATGGTGAAATTTTTATGGCCGAATGAACTGACCGATTGCAAGCAAATT-CAAATGTGGAAGGCA
* *
383820 TTCTTCCTAAGTCTTTATATTATTCTTGATGATGGC
389 ATCTTCCCAAGTCTTTATATTATTCTTGATGATGGC
383856 TCTCAACAAT
Statistics
Matches: 388, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
428 146 0.38
429 242 0.62
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (429 bp):
TTGTATGCATTGTCATTAATCTTCTCAATAATTTGAAAGGGACCATCACCTCTTGGTAAAAGCTT
AGACTTCCTTTTAGTAGGAAACCTTTCCTTACACAAATGCACCCATACCAAATCTCCAACTTCCA
AATAGAGTGGTTTACGTCCCTTATTGGCTTGTTGCTCATACTGATTTGTTCTTCTCTCAATATTG
TGCCGAACTTGTTCATGTAACTTCTTGATGAACTCAGCCTTGTTCTTACCATCCTTGTGAACCAA
TTATTCTCGAGGTAGAGGAAGAAGATCCAAAGGAGTTAAGGGATTGAATCCATACACTACCTCGA
ATGGTGAAATTTTTATGGCCGAATGAACTGACCGATTGCAAGCAAATTCAAATGTGGAAGGCAAT
CTTCCCAAGTCTTTATATTATTCTTGATGATGGCCCAAT
Found at i:387200 original size:12 final size:13
Alignment explanation
Indices: 387183--387212 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
387173 TTTGTTGGAG
387183 TCTTTTCTTTTC-
1 TCTTTTCTTTTCT
387195 TCTTTTCTTTTCT
1 TCTTTTCTTTTCT
387208 TCTTT
1 TCTTT
387213 CTTGTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTCT
Found at i:387610 original size:33 final size:33
Alignment explanation
Indices: 387568--387636 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
387558 GTTGATGAAT
*
387568 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
387601 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
387634 GAA
1 GAA
387637 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:387641 original size:13 final size:12
Alignment explanation
Indices: 387622--387718 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
387612 TTATTGGCGT
387622 GATATGGTGATG
1 GATATGGTGATG
387634 GAATATGGTGAT-
1 G-ATATGGTGATG
*
387646 GATATAGGCG-T-
1 GATAT-GGTGATG
387657 GATAATGGTGATG
1 GAT-ATGGTGATG
387670 GACTATGGTGAT-
1 GA-TATGGTGATG
*
387682 GATATAGGCG-T-
1 GATAT-GGTGATG
*
387693 GATAATGGAGATG
1 GAT-ATGGTGATG
387706 GATTATGGTGATG
1 GA-TATGGTGATG
387719 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:387677 original size:36 final size:36
Alignment explanation
Indices: 387607--387719 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
387597 AATGGAAGGA
* *
387607 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
387642 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
387678 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
387714 TGATGA
1 TGATGA
387720 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:391671 original size:28 final size:28
Alignment explanation
Indices: 391640--391704 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
391630 TGCTTATTTC
*
391640 ATATGTTATA-AGATAGTTATTTTGATA
1 ATATGTTATACAGATAGTTATTATGATA
* **
391667 TATATATTATACCTATAGTTATTATGATA
1 -ATATGTTATACAGATAGTTATTATGATA
*
391696 ATAAGTTAT
1 ATATGTTAT
391705 CCATTTATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (28 bp):
ATATGTTATACAGATAGTTATTATGATA
Found at i:395144 original size:20 final size:19
Alignment explanation
Indices: 395121--395178 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
395111 ATGGTCTTAA
*
395121 GAAATGAATATATAATAAAG
1 GAAATGAAAATA-AATAAAG
*
395141 GAAATGAAAATAAATAATAA
1 GAAATGAAAATAAATAA-AG
395161 G-AATG-AAATGAAATAAAG
1 GAAATGAAAAT-AAATAAAG
395179 AAAGGATAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.15
19 15 0.45
20 13 0.39
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.21
Consensus pattern (19 bp):
GAAATGAAAATAAATAAAG
Found at i:398781 original size:13 final size:12
Alignment explanation
Indices: 398756--398815 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 12
398746 CTTGGCTTGC
398756 TTTCTCTTTTTCT
1 TTTCT-TTTTTCT
398769 TTTCTTTTCTTCT
1 TTTCTTTT-TTCT
*
398782 TATCTGATTTTTCT
1 TTTCT--TTTTTCT
*
398796 CTTCTTTTTGTCT
1 TTTCTTTTT-TCT
398809 TTTCTTT
1 TTTCTTT
398816 CTTTTTGCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 7 0.18
13 22 0.56
14 7 0.18
15 3 0.08
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:401365 original size:19 final size:21
Alignment explanation
Indices: 401341--401392 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
401331 CAGCCACAAG
*
401341 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
401360 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
401381 CATGTATTTTCA
1 CATGTATTTTCA
401393 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:423212 original size:55 final size:56
Alignment explanation
Indices: 423141--423247 Score: 198
Period size: 55 Copynumber: 1.9 Consensus size: 56
423131 GATGGAAATA
*
423141 ATAATATGATAATTTATACTAACATGTGAATGAATGCTTATGATAGAATAGAATGT
1 ATAATATGATAATTTATACTAACATGTGAATGAATACTTATGATAGAATAGAATGT
423197 ATAA-ATGATAATTTATACTAACATGTGAATGAATACTTATGATAGAATAGA
1 ATAATATGATAATTTATACTAACATGTGAATGAATACTTATGATAGAATAGA
423248 CATTATTATC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 46 0.92
56 4 0.08
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.35
Consensus pattern (56 bp):
ATAATATGATAATTTATACTAACATGTGAATGAATACTTATGATAGAATAGAATGT
Found at i:427701 original size:19 final size:19
Alignment explanation
Indices: 427677--427722 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
427667 GATAATGAAT
427677 AGAAATGATGAAAGAAAAA
1 AGAAATGATGAAAGAAAAA
427696 AGAAATGATGAAAGAAAAA
1 AGAAATGATGAAAGAAAAA
*
427715 GGAAATGA
1 AGAAATGA
427723 AGATAACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.11
Consensus pattern (19 bp):
AGAAATGATGAAAGAAAAA
Found at i:429584 original size:19 final size:20
Alignment explanation
Indices: 429560--429611 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
429550 CGGCCAAGAG
* *
429560 CATGTATCTTCATT-TAAAT
1 CATGTATTTTCATTAAAAAT
429579 CATGTATTTTCATTAAAAAAT
1 CATGTATTTTCATT-AAAAAT
429600 CATGTATTTTCA
1 CATGTATTTTCA
429612 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
21 16 0.55
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:433259 original size:24 final size:21
Alignment explanation
Indices: 433224--433266 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
433214 GGCTCATTCT
*
433224 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
433247 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
433267 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:437660 original size:19 final size:19
Alignment explanation
Indices: 437636--437682 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
437626 GTGCAAAGCA
*
437636 AAAGAAAAATAAAAAAAAG
1 AAAGAAAAAGAAAAAAAAG
*
437655 AAAG-AAAAGACAAAAAAG
1 AAAGAAAAAGAAAAAAAAG
437673 AAGAGAAAAA
1 AA-AGAAAAA
437683 AGGCAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.58
19 6 0.25
20 4 0.17
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAGAAAAAAAAG
Found at i:437670 original size:21 final size:21
Alignment explanation
Indices: 437636--437717 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
437626 GTGCAAAGCA
*
437636 AAAGAAAA-ATAAAAAA-AAG
1 AAAGAAAAGACAAAAAAGAAG
437655 AAAGAAAAGACAAAAAAGAAG
1 AAAGAAAAGACAAAAAAGAAG
* * *
437676 AGAA-AAAAGGCAGAAAAGGAG
1 A-AAGAAAAGACAAAAAAGAAG
*
437697 AAAAGAAAAGA-AAAAGAGAAG
1 -AAAGAAAAGACAAAAAAGAAG
437718 TTCAAAAAGA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
19 8 0.16
20 7 0.14
21 27 0.54
22 8 0.16
ACGTcount: A:0.74, C:0.02, G:0.22, T:0.01
Consensus pattern (21 bp):
AAAGAAAAGACAAAAAAGAAG
Found at i:437674 original size:14 final size:13
Alignment explanation
Indices: 437630--437716 Score: 61
Period size: 13 Copynumber: 6.5 Consensus size: 13
437620 ATTGGCGTGC
437630 AAAGCAAAAGAAAA
1 AAAG-AAAAGAAAA
* *
437644 ATA-AAAA-AAAG
1 AAAGAAAAGAAAA
437655 AAAGAAAAGACAAA
1 AAAGAAAAGA-AAA
*
437669 AAAGAAGAGAAAA
1 AAAGAAAAGAAAA
* *
437682 AAGGCAGAAAAGGAGA
1 AA---AGAAAAGAAAA
437698 AAAGAAAAGAAAA
1 AAAGAAAAGAAAA
*
437711 AGAGAA
1 AAAGAA
437717 GTTCAAAAAG
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
11 5 0.09
12 8 0.14
13 20 0.36
14 13 0.23
16 10 0.18
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (13 bp):
AAAGAAAAGAAAA
Found at i:437684 original size:30 final size:29
Alignment explanation
Indices: 437630--437716 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
437620 ATTGGCGTGC
*
437630 AAAGCAAAAGAA-AAATAAAAAAAAGAAAGA
1 AAAGCAAAA-AAGAAA-AGAAAAAAGAAAGA
* **
437660 AAAGACAAAAAAGAAGAGAAAAAAGGCAGA
1 AAAG-CAAAAAAGAAAAGAAAAAAGAAAGA
* *
437690 AAAGGAGAAAAGAAAAGAAAAAGAGAA
1 AAAGCAAAAAAGAAAAGAAAAA-AGAA
437717 GTTCAAAAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
29 15 0.33
30 23 0.51
31 7 0.16
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (29 bp):
AAAGCAAAAAAGAAAAGAAAAAAGAAAGA
Found at i:443538 original size:20 final size:21
Alignment explanation
Indices: 443495--443551 Score: 98
Period size: 20 Copynumber: 2.8 Consensus size: 21
443485 AAGATCATTT
443495 AAATCATGTATTTTCATAAAA
1 AAATCATGTATTTTCATAAAA
*
443516 AAATCAGGTATTTTCAT-AAA
1 AAATCATGTATTTTCATAAAA
443536 AAATCATGTATTTTCA
1 AAATCATGTATTTTCA
443552 AAGTGGTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (21 bp):
AAATCATGTATTTTCATAAAA
Found at i:446079 original size:19 final size:20
Alignment explanation
Indices: 446055--446103 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
446045 TATCCTTTCT
446055 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
446074 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
446094 -TATTATTATT
1 TTATT-TTATT
446104 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:452486 original size:19 final size:20
Alignment explanation
Indices: 452462--452510 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
452452 TGTCCTTTCT
452462 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
452481 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
452501 -TATTATTATT
1 TTATT-TTATT
452511 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:492098 original size:12 final size:13
Alignment explanation
Indices: 492081--492110 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
492071 GATGTAGGAG
492081 TCTTTTCTTTTC-
1 TCTTTTCTTTTCT
492093 TCTTTTCTTTTCT
1 TCTTTTCTTTTCT
492106 TCTTT
1 TCTTT
492111 CTTGTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTCT
Found at i:496569 original size:12 final size:13
Alignment explanation
Indices: 496552--496581 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
496542 GATGTAGGAG
496552 TCTTTTCTTTTC-
1 TCTTTTCTTTTCT
496564 TCTTTTCTTTTCT
1 TCTTTTCTTTTCT
496577 TCTTT
1 TCTTT
496582 CTTGTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTCT
Found at i:531225 original size:22 final size:22
Alignment explanation
Indices: 531178--531226 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
531168 AATTCATCCT
****
531178 GAAAATTAAAAAAAAAAATTCC
1 GAAAATTAAAAAAAAAAAAAAA
531200 GAAAATTAAAAAAAAAAAAAAA
1 GAAAATTAAAAAAAAAAAAAAA
531222 GAAAA
1 GAAAA
531227 AGAATTCTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.12
Consensus pattern (22 bp):
GAAAATTAAAAAAAAAAAAAAA
Found at i:539210 original size:12 final size:12
Alignment explanation
Indices: 539193--539217 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
539183 GATGTAGGAG
539193 TCTTTTCTTTTC
1 TCTTTTCTTTTC
539205 TCTTTTCTTTTC
1 TCTTTTCTTTTC
539217 T
1 T
539218 TCATTCTTGT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTTCTTTTC
Found at i:550177 original size:21 final size:17
Alignment explanation
Indices: 550133--550175 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
550123 CATGCTTGCT
550133 AAGCTAGCTTCACATAC
1 AAGCTAGCTTCACATAC
550150 AAGCTAGCTTCACATAC
1 AAGCTAGCTTCACATAC
550167 AAGCTAGCT
1 AAGCTAGCT
550176 AGGAGGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (17 bp):
AAGCTAGCTTCACATAC
Found at i:551217 original size:23 final size:23
Alignment explanation
Indices: 551189--551242 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
551179 AAAAATTAGA
* *
551189 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
551212 AAAGAAAAATCCAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
551236 -AAGAAAA
1 AAAGAAAA
551243 AGCAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.61, C:0.15, G:0.17, T:0.07
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:552479 original size:44 final size:44
Alignment explanation
Indices: 552411--552512 Score: 195
Period size: 44 Copynumber: 2.3 Consensus size: 44
552401 GCTCAAAGAA
*
552411 GAACCAATGCTATAGAGAGCAAAGACCCAATCTTTATATTGTTT
1 GAACCAATGCTATAGAGAGAAAAGACCCAATCTTTATATTGTTT
552455 GAACCAATGCTATAGAGAGAAAAGACCCAATCTTTATATTGTTT
1 GAACCAATGCTATAGAGAGAAAAGACCCAATCTTTATATTGTTT
552499 GAACCAATGCTATA
1 GAACCAATGCTATA
552513 AAGGGTGGTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (44 bp):
GAACCAATGCTATAGAGAGAAAAGACCCAATCTTTATATTGTTT
Found at i:553041 original size:19 final size:20
Alignment explanation
Indices: 553002--553037 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
552992 GGATAATAAT
553002 ATAAGAAATGAAAATGAATA
1 ATAAGAAATGAAAATGAATA
553022 ATAAG-AATG-AAATGAA
1 ATAAGAAATGAAAATGAA
553038 ATAAATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 4 0.25
20 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (20 bp):
ATAAGAAATGAAAATGAATA
Found at i:553044 original size:20 final size:21
Alignment explanation
Indices: 552996--553045 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
552986 TAAAGGGGAT
552996 AATAATATAAGAAATGAAAATG
1 AATAA-ATAAGAAATGAAAATG
553018 AAT-AATAAG-AATG-AAATG
1 AATAAATAAGAAATGAAAATG
553036 AAATAAATAA
1 -AATAAATAA
553046 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.19
19 7 0.27
20 10 0.38
21 1 0.04
22 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (21 bp):
AATAAATAAGAAATGAAAATG
Found at i:558290 original size:13 final size:12
Alignment explanation
Indices: 558268--558349 Score: 62
Period size: 13 Copynumber: 6.4 Consensus size: 12
558258 TTTGAACTTC
558268 TCTTTTTTCTTT
1 TCTTTTTTCTTT
558280 TCTTTTCTTCTTT
1 TCTTTT-TTCTTT
558293 TCTGATTTTT-TTACT
1 TCT--TTTTTCTT--T
558308 TCTTTTTGTCTTT
1 TCTTTTT-TCTTT
558321 TCTTTCTTT-TTT
1 TCTTT-TTTCTTT
*
558333 T-ATTTTTCTTT
1 TCTTTTTTCTTT
558344 TGCTTT
1 T-CTTT
558350 GCACGCCAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 21
0.71 0.03 0.26
Matches are distributed among these distances:
10 3 0.05
11 6 0.11
12 10 0.18
13 24 0.42
14 5 0.09
15 9 0.16
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.77
Consensus pattern (12 bp):
TCTTTTTTCTTT
Found at i:558291 original size:20 final size:21
Alignment explanation
Indices: 558268--558344 Score: 69
Period size: 20 Copynumber: 3.9 Consensus size: 21
558258 TTTGAACTTC
558268 TCTTTTT-TCTTTTCTTTTCT
1 TCTTTTTATCTTTTCTTTTCT
*
558288 TCTTTTCTGA--TTTT-TTTACT
1 TCTTTT-T-ATCTTTTCTTTTCT
*
558308 TCTTTTTGTCTTTTC-TTTCT
1 TCTTTTTATCTTTTCTTTTCT
558328 T-TTTTTAT-TTTTCTTTT
1 TCTTTTTATCTTTTCTTTT
558345 GCTTTGCACG
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
18 5 0.11
19 10 0.22
20 26 0.57
21 5 0.11
ACGTcount: A:0.04, C:0.16, G:0.03, T:0.78
Consensus pattern (21 bp):
TCTTTTTATCTTTTCTTTTCT
Found at i:560723 original size:11 final size:11
Alignment explanation
Indices: 560693--560727 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
560683 ATCATGCCTA
560693 TCATCACCATAT
1 TCATCACCAT-T
560705 TCCATCACCATT
1 T-CATCACCATT
560717 TCATCACCATT
1 TCATCACCATT
560728 AAATCATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.45
12 3 0.14
13 9 0.41
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (11 bp):
TCATCACCATT
Found at i:562054 original size:22 final size:22
Alignment explanation
Indices: 562029--562073 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
562019 CTCCTCCAGC
562029 TGAATCGAGCTTCCCTTAGTGT
1 TGAATCGAGCTTCCCTTAGTGT
562051 TGAATCGAGCTTCCCTTAGTGT
1 TGAATCGAGCTTCCCTTAGTGT
562073 T
1 T
562074 CCATGAGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (22 bp):
TGAATCGAGCTTCCCTTAGTGT
Found at i:565530 original size:11 final size:11
Alignment explanation
Indices: 565474--565530 Score: 62
Period size: 11 Copynumber: 4.9 Consensus size: 11
565464 ACAATCTGTC
565474 CATCACCATTAT
1 CATCACCATT-T
*
565486 CAT-ACCTATAT
1 CATCACC-ATTT
565497 CATCACCATATT
1 CATCACCAT-TT
565509 CCATCACCATTT
1 -CATCACCATTT
565521 CATCACCATT
1 CATCACCATT
565531 AAATCATCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 19 0.49
12 11 0.28
13 9 0.23
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.33
Consensus pattern (11 bp):
CATCACCATTT
Found at i:566858 original size:22 final size:22
Alignment explanation
Indices: 566833--566877 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
566823 CTCCTCCAGC
566833 TGAATCGAGCTTCCCTTAGTGT
1 TGAATCGAGCTTCCCTTAGTGT
566855 TGAATCGAGCTTCCCTTAGTGT
1 TGAATCGAGCTTCCCTTAGTGT
566877 T
1 T
566878 CCATGAGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (22 bp):
TGAATCGAGCTTCCCTTAGTGT
Found at i:570323 original size:13 final size:11
Alignment explanation
Indices: 570301--570367 Score: 64
Period size: 13 Copynumber: 5.6 Consensus size: 11
570291 TATCACGCCT
570301 ATATCATCACC
1 ATATCATCACC
570312 ATAGTCCATCACC
1 ATA-T-CATCACC
*
570325 ATTATCA-CGCC
1 A-TATCATCACC
570336 TATATCATCACC
1 -ATATCATCACC
570348 ATATTCCATCACC
1 ATA-T-CATCACC
570361 ATATCAT
1 ATATCAT
570368 GCCAATAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
11 17 0.36
12 9 0.19
13 19 0.40
14 2 0.04
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.30
Consensus pattern (11 bp):
ATATCATCACC
Found at i:570328 original size:36 final size:36
Alignment explanation
Indices: 570273--570380 Score: 146
Period size: 36 Copynumber: 3.0 Consensus size: 36
570263 ACTATTTCAT
570273 CATAATCCATCCATCCATTATCACGCCTATATCATCAC
1 CATAATCCAT-CA-CCATTATCACGCCTATATCATCAC
*
570311 CATAGTCCATCACCATTATCACGCCTATATCATCAC
1 CATAATCCATCACCATTATCACGCCTATATCATCAC
* * * *
570347 CATATTCCATCACCA-TATCATGCCAATAACATCA
1 CATAATCCATCACCATTATCACGCCTATATCATCA
570381 TCCTTCCATT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
35 16 0.25
36 38 0.58
37 2 0.03
38 9 0.14
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
CATAATCCATCACCATTATCACGCCTATATCATCAC
Found at i:570395 original size:33 final size:33
Alignment explanation
Indices: 570351--570419 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
570341 CATCACCATA
*
570351 TTCCATCACCATATCAT-GCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
570384 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
570417 TTC
1 TTC
570420 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:570798 original size:17 final size:19
Alignment explanation
Indices: 570756--570801 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
570746 ACAAAGTGCT
570756 ACAAAA-AAAACCAACAAG
1 ACAAAAGAAAACCAACAAG
570774 A-AAGAAGAAAA-CAA-AAG
1 ACAA-AAGAAAACCAACAAG
570791 ACAAAAGAAAA
1 ACAAAAGAAAA
570802 AGACTCCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 13 0.52
18 8 0.32
19 4 0.16
ACGTcount: A:0.76, C:0.13, G:0.11, T:0.00
Consensus pattern (19 bp):
ACAAAAGAAAACCAACAAG
Found at i:574737 original size:36 final size:36
Alignment explanation
Indices: 574685--574797 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
574675 GATACTATTT
* *
574685 TCATCACCATAATCCATCTCCATTATCGCGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
574721 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
574757 TCATCACCATATTCCATCACCA-TATCATGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
574792 ACATCA
1 TCATCA
574798 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:574740 original size:13 final size:11
Alignment explanation
Indices: 574718--574784 Score: 64
Period size: 13 Copynumber: 5.6 Consensus size: 11
574708 TATCGCGCCT
574718 ATATCATCACC
1 ATATCATCACC
574729 ATAGTCCATCACC
1 ATA-T-CATCACC
*
574742 ATTATCA-CGCC
1 A-TATCATCACC
574753 TATATCATCACC
1 -ATATCATCACC
574765 ATATTCCATCACC
1 ATA-T-CATCACC
574778 ATATCAT
1 ATATCAT
574785 GCCAATAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
11 17 0.36
12 9 0.19
13 19 0.40
14 2 0.04
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.30
Consensus pattern (11 bp):
ATATCATCACC
Found at i:574812 original size:33 final size:33
Alignment explanation
Indices: 574768--574836 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
574758 CATCACCATA
*
574768 TTCCATCACCATATCAT-GCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
574801 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
574834 TTC
1 TTC
574837 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:584864 original size:19 final size:20
Alignment explanation
Indices: 584840--584882 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
584830 AGCATTTATC
*
584840 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
584859 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
584879 TTCA
1 TTCA
584883 AAGGGTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:585922 original size:23 final size:23
Alignment explanation
Indices: 585877--585922 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
585867 TTATACCTAT
*
585877 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
585900 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
585923 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:588441 original size:19 final size:21
Alignment explanation
Indices: 588417--588468 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
588407 CGGCCAAGAG
588417 CATGTATCTTC-TTTAAAA-T
1 CATGTATCTTCATTTAAAAGT
*
588436 CATGTATGTTCATTTAAAAGT
1 CATGTATCTTCATTTAAAAGT
*
588457 CATGTATTTTCA
1 CATGTATCTTCA
588469 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.34
20 7 0.24
21 12 0.41
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (21 bp):
CATGTATCTTCATTTAAAAGT
Found at i:592341 original size:21 final size:20
Alignment explanation
Indices: 592297--592348 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
592287 CGGCCAAGAG
*
592297 CATGTATCTTC-TTTAAAAT
1 CATGTATTTTCATTTAAAAT
592316 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAA-T
592337 CATGTATTTTCA
1 CATGTATTTTCA
592349 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 10 0.33
20 7 0.23
21 13 0.43
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:594300 original size:16 final size:16
Alignment explanation
Indices: 594266--594312 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
594256 ATAACATCTC
*
594266 TATCCATTTTATTTCT
1 TATCCATTTCATTTCT
594282 TATCC-TTTCATTTCT
1 TATCCATTTCATTTCT
594297 T-T--ATTTCATTTCT
1 TATCCATTTCATTTCT
594310 TAT
1 TAT
594313 TTCTAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 10 0.36
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTCATTTCT
Found at i:594314 original size:12 final size:13
Alignment explanation
Indices: 594287--594315 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
594277 TTTCTTATCC
594287 TTTCATTTCTTTA
1 TTTCATTTCTTTA
594300 TTTCATTTC-TTA
1 TTTCATTTCTTTA
594312 TTTC
1 TTTC
594316 TAATATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:597455 original size:13 final size:13
Alignment explanation
Indices: 597437--597494 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
597427 CTACCTATAA
597437 CATCACCATCTTC
1 CATCACCATCTTC
*
597450 CATCACCAT-TTT
1 CATCACCATCTTC
* * **
597462 CA-CGCC-TATAA
1 CATCACCATCTTC
597473 CATCACCATCTTC
1 CATCACCATCTTC
597486 CATCACCAT
1 CATCACCAT
597495 TGCACGCCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
10 1 0.03
11 6 0.18
12 7 0.21
13 20 0.59
ACGTcount: A:0.28, C:0.41, G:0.02, T:0.29
Consensus pattern (13 bp):
CATCACCATCTTC
Found at i:597477 original size:36 final size:35
Alignment explanation
Indices: 597430--597541 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
597420 TAAGATACTA
597430 CCTATAACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
*
597466 CCTATAACATCACCATCTTCCATCACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
** ** ** *
597501 CCTATATTATCATAAAGTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
597536 CCTATA
1 CCTATA
597542 TAACCACTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 39 0.58
36 28 0.42
ACGTcount: A:0.29, C:0.35, G:0.04, T:0.31
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:599770 original size:2 final size:2
Alignment explanation
Indices: 599763--599793 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
599753 ATCACCAACT
599763 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 T
599794 TCCACTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:604378 original size:19 final size:21
Alignment explanation
Indices: 604335--604386 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
604325 GAAACCCCTT
604335 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
604356 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
604375 TGAAGATACATG
1 TGAAAATACATG
604387 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:607337 original size:33 final size:33
Alignment explanation
Indices: 607258--607361 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
607248 ATACAATCTG
* *
607258 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
607294 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
607327 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
607360 TC
1 TC
607362 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:611802 original size:33 final size:33
Alignment explanation
Indices: 611723--611826 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
611713 ATACAATCTG
* *
611723 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
611759 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
611792 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
611825 TC
1 TC
611827 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:616281 original size:33 final size:33
Alignment explanation
Indices: 616202--616305 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
616192 ATACAATCTG
* *
616202 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
616238 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
616271 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
616304 TC
1 TC
616306 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:619193 original size:19 final size:19
Alignment explanation
Indices: 619158--619205 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
619148 ACCCCTTTGA
619158 AAATACATGATTTTTAAATG
1 AAATACATGATTTTT-AATG
619178 AAATACATGA-TTTTAATG
1 AAATACATGATTTTTAATG
619196 AAGATACATG
1 AA-ATACATG
619206 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.22
19 11 0.41
20 10 0.37
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (19 bp):
AAATACATGATTTTTAATG
Found at i:640629 original size:9 final size:9
Alignment explanation
Indices: 640610--640649 Score: 71
Period size: 9 Copynumber: 4.3 Consensus size: 9
640600 TTAGAGTGTA
640610 AAAAGAAAAG
1 AAAA-AAAAG
640620 AAAAAAAAG
1 AAAAAAAAG
640629 AAAAAAAAG
1 AAAAAAAAG
640638 AAAAAAAAG
1 AAAAAAAAG
640647 AAA
1 AAA
640650 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 26 0.87
10 4 0.13
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:643754 original size:24 final size:24
Alignment explanation
Indices: 643727--643784 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
643717 TCAAGCTATA
643727 ACTCACCTAGTTAGCTACCAAGAC
1 ACTCACCTAGTTAGCTACCAAGAC
643751 ACTCACCTAGTTAGCTACCAAGAC
1 ACTCACCTAGTTAGCTACCAAGAC
643775 ACTCACCTAG
1 ACTCACCTAG
643785 CTTACCTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.33, C:0.34, G:0.12, T:0.21
Consensus pattern (24 bp):
ACTCACCTAGTTAGCTACCAAGAC
Found at i:645701 original size:12 final size:12
Alignment explanation
Indices: 645684--645716 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
645674 ACAAAAAGTG
645684 AAAGAAAGAAA-A
1 AAAGAAA-AAAGA
645696 AAAGAAAAAAGA
1 AAAGAAAAAAGA
645708 AAAGAAAAA
1 AAAGAAAAA
645717 GACTCCTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 3 0.15
12 17 0.85
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAGA
Found at i:653651 original size:17 final size:17
Alignment explanation
Indices: 653629--653661 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
653619 CTATCCTAGT
653629 TTTACCATAACCATTTA
1 TTTACCATAACCATTTA
*
653646 TTTACCCTAACCATTT
1 TTTACCATAACCATTT
653662 CTTTTAGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTACCATAACCATTTA
Found at i:654730 original size:30 final size:31
Alignment explanation
Indices: 654678--654737 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
654668 CTTAGCTTTA
**
654678 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
654708 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
654738 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:655670 original size:19 final size:21
Alignment explanation
Indices: 655646--655697 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
655636 CGGCCAAGAG
*
655646 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
655665 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
655686 CATGTATTTTCA
1 CATGTATTTTCA
655698 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:659426 original size:17 final size:17
Alignment explanation
Indices: 659404--659436 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
659394 CTATCCTAGT
659404 TTTACCATAACCATTTA
1 TTTACCATAACCATTTA
*
659421 TTTACCCTAACCATTT
1 TTTACCATAACCATTT
659437 CTTTTAGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTACCATAACCATTTA
Found at i:660962 original size:19 final size:21
Alignment explanation
Indices: 660919--660970 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
660909 GAAACCCCTT
660919 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
660940 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
660959 TGAAGATACATG
1 TGAAAATACATG
660971 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:661919 original size:30 final size:31
Alignment explanation
Indices: 661879--661938 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
661869 ACATGCTGCC
**
661879 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
661910 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
661939 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:668749 original size:17 final size:17
Alignment explanation
Indices: 668727--668759 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
668717 CTATCCTAGT
668727 TTTACCATAACCATTTA
1 TTTACCATAACCATTTA
*
668744 TTTACCCTAACCATTT
1 TTTACCATAACCATTT
668760 CTTTTAGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTACCATAACCATTTA
Found at i:670690 original size:17 final size:17
Alignment explanation
Indices: 670668--670700 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
670658 CTATCCTAGT
670668 TTTACCATAACCATTTA
1 TTTACCATAACCATTTA
*
670685 TTTACCCTAACCATTT
1 TTTACCATAACCATTT
670701 CTTTTAGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTACCATAACCATTTA
Found at i:676426 original size:17 final size:16
Alignment explanation
Indices: 676371--676431 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 16
676361 TTGAGTTGTA
676371 AGTTATC-TTCAT-TT
1 AGTTATCTTTCATCTT
*
676385 TGTTA-CTTTCAT-TT
1 AGTTATCTTTCATCTT
676399 AGTTATCTTTCATCTT
1 AGTTATCTTTCATCTT
676415 AGTTATTCTTTCATCTT
1 AGTTA-TCTTTCATCTT
676432 TTCTATTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
13 1 0.02
14 15 0.37
15 7 0.17
16 7 0.17
17 11 0.27
ACGTcount: A:0.18, C:0.16, G:0.07, T:0.59
Consensus pattern (16 bp):
AGTTATCTTTCATCTT
Found at i:676438 original size:17 final size:17
Alignment explanation
Indices: 676390--676431 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
676380 CATTTTGTTA
676390 CTTTCAT-TTAGTTA-T
1 CTTTCATCTTAGTTATT
676405 CTTTCATCTTAGTTATT
1 CTTTCATCTTAGTTATT
676422 CTTTCATCTT
1 CTTTCATCTT
676432 TTCTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.28
16 7 0.28
17 11 0.44
ACGTcount: A:0.17, C:0.19, G:0.05, T:0.60
Consensus pattern (17 bp):
CTTTCATCTTAGTTATT
Found at i:683353 original size:171 final size:169
Alignment explanation
Indices: 683046--683388 Score: 573
Period size: 171 Copynumber: 2.0 Consensus size: 169
683036 CTAAAATGGT
*
683046 AACCTTTAAAGAACCAATAGGCGTGACTCTTGTGATTCACAAGACATGTCTATTGAGTTTTAATG
1 AACCTTTAAAGAACCAATAGGCGTGACTCTTGTGATTCACAAGACATGTATATTGAGTTTTAATG
*
683111 GTTATACCATTGAAGTTCCAAATAAAGGCGTCACTTGAAGTGCTAGAGAGTTTTGTTCGTTGACA
66 GTTATACCATTGAAGTTCCAAATAAAGGCGTCACTTGAAGTGCTAGAGAGTTTTGTTCATTGACA
*
683176 TCCAAGTGCATTGCCAATCCTGAAAAGAATTCACTAGCC
131 TCCAAGTGCATTGCCAATCCTGAAAAGAATTCAATAGCC
* * *
683215 AACCTTTGAAGAACCAATAGGCGTGACTATTTGTGATTCACAAGACATGTATCTTGATGTTTTGA
1 AACCTTTAAAGAACCAATAGGCGTGACT-CTTGTGATTCACAAGACATGTATATTGA-GTTTT-A
*
683280 A-GGTTATACCATTGAAGTTCCAAATAAAGTCGTCACTTGAAGTGCTA-AGAGTTTTGTTCATTG
63 ATGGTTATACCATTGAAGTTCCAAATAAAGGCGTCACTTGAAGTGCTAGAGAGTTTTGTTCATTG
683343 ACATTCCAAGTGCATTGCCAATCCTGAAAAGAATTCAATAGCC
128 ACA-TCCAAGTGCATTGCCAATCCTGAAAAGAATTCAATAGCC
683386 AAC
1 AAC
683389 TCCCATTAAA
Statistics
Matches: 163, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
169 27 0.17
170 43 0.26
171 91 0.56
172 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (169 bp):
AACCTTTAAAGAACCAATAGGCGTGACTCTTGTGATTCACAAGACATGTATATTGAGTTTTAATG
GTTATACCATTGAAGTTCCAAATAAAGGCGTCACTTGAAGTGCTAGAGAGTTTTGTTCATTGACA
TCCAAGTGCATTGCCAATCCTGAAAAGAATTCAATAGCC
Found at i:684092 original size:17 final size:17
Alignment explanation
Indices: 684070--684102 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
684060 CTATCCTAGT
684070 TTTACCATAACCATTTA
1 TTTACCATAACCATTTA
*
684087 TTTACCCTAACCATTT
1 TTTACCATAACCATTT
684103 CTTTTAGTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTACCATAACCATTTA
Found at i:690847 original size:16 final size:16
Alignment explanation
Indices: 690821--690862 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
690811 GAGTTGTAAG
*
690821 TTATCTTCATTTTGTTA
1 TTAT-TTCATTTAGTTA
690838 TTATTTCATTTAGTTA
1 TTATTTCATTTAGTTA
*
690854 TTCTTTCAT
1 TTATTTCAT
690863 CTTTTCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (16 bp):
TTATTTCATTTAGTTA
Found at i:703054 original size:13 final size:14
Alignment explanation
Indices: 703031--703059 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
703021 ATAAGATACT
703031 ATCTGTCCATCACC
1 ATCTGTCCATCACC
703045 ATCT-TCCATCACC
1 ATCTGTCCATCACC
703058 AT
1 AT
703060 TTCATACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.41, G:0.03, T:0.31
Consensus pattern (14 bp):
ATCTGTCCATCACC
Found at i:703087 original size:35 final size:35
Alignment explanation
Indices: 703038--703113 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
703028 ACTATCTGTC
* *
703038 CATCACCATCTTCCATCACCATTTCATACCTATAT
1 CATCACAATCTTCCATCACCATTTCACACCTATAT
* *
703073 CATCACAATTTTCCATCACCATTTCACGCCTATAT
1 CATCACAATCTTCCATCACCATTTCACACCTATAT
703108 CATCAC
1 CATCAC
703114 CATCCCTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.29, C:0.37, G:0.01, T:0.33
Consensus pattern (35 bp):
CATCACAATCTTCCATCACCATTTCACACCTATAT
Found at i:711714 original size:13 final size:12
Alignment explanation
Indices: 711692--711747 Score: 69
Period size: 13 Copynumber: 4.4 Consensus size: 12
711682 TTTGAACTTC
711692 TCTTTTTTCTTT
1 TCTTTTTTCTTT
711704 TCTTTTCTTCTTT
1 TCTTTT-TTCTTT
711717 TCTGATTTTT-TTT
1 TCT--TTTTTCTTT
711730 TCTTTTTATCTTT
1 TCTTTTT-TCTTT
711743 TCTTT
1 TCTTT
711748 CTTTTTGCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.10
12 7 0.18
13 23 0.59
14 2 0.05
15 3 0.08
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (12 bp):
TCTTTTTTCTTT
Found at i:711726 original size:17 final size:17
Alignment explanation
Indices: 711703--711753 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
711693 CTTTTTTCTT
711703 TTCTTTTCTTCTTTTCTGA
1 TTCTTTTCTTCTTTT-T-A
*
711722 TT-TTTTTTTCTTTTTA
1 TTCTTTTCTTCTTTTTA
711738 -TCTTTTCTTTCTTTTT
1 TTCTTTTC-TTCTTTTT
711754 GCACTCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 1 0.04
16 5 0.18
17 9 0.32
18 11 0.39
19 2 0.07
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (17 bp):
TTCTTTTCTTCTTTTTA
Found at i:711752 original size:26 final size:25
Alignment explanation
Indices: 711678--711753 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
711668 GCTTGCTTTC
* * *
711678 TCTTTTTGAACTTCTCTTTTTTCTTT
1 TCTTTTT-ATCTTTTCTTTTTTTTTT
*
711704 TCTTTTCT-TCTTTTCTGATTTTTTTT
1 TCTTTT-TATCTTTTCT-TTTTTTTTT
*
711730 TCTTTTTATCTTTTCTTTCTTTTT
1 TCTTTTTATCTTTTCTTTTTTTTT
711754 GCACTCCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
25 13 0.32
26 27 0.66
27 1 0.02
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (25 bp):
TCTTTTTATCTTTTCTTTTTTTTTT
Found at i:714198 original size:35 final size:33
Alignment explanation
Indices: 714156--714266 Score: 132
Period size: 35 Copynumber: 3.2 Consensus size: 33
714146 TCTTTCCATC
* *
714156 CCCATCTTCCATCACAATTTAACACCTATATCAT
1 CCCATCTTCCATCAC-ATTTCACGCCTATATCAT
*
714190 CCTCATCTTCCATTACCATTTCACGCCTATATCAT
1 CC-CATCTTCCATCA-CATTTCACGCCTATATCAT
*
714225 CACCTTCTTCCATCATCATTTCACGCCTATATCAT
1 C-CCATCTTCCATCA-CATTTCACGCCTATATCAT
714260 CACCATC
1 C-CCATC
714267 CCTTAACCAT
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
34 2 0.03
35 63 0.94
36 2 0.03
ACGTcount: A:0.26, C:0.38, G:0.02, T:0.34
Consensus pattern (33 bp):
CCCATCTTCCATCACATTTCACGCCTATATCAT
Found at i:717176 original size:50 final size:50
Alignment explanation
Indices: 717099--717242 Score: 227
Period size: 50 Copynumber: 2.9 Consensus size: 50
717089 GATACATCTC
717099 CCTTGGCCGAATGGTGATATGCTTGTTCATCTTGGTGCCAAAGTTAACTT
1 CCTTGGCCGAATGGTGATATGCTTGTTCATCTTGGTGCCAAAGTTAACTT
* *
717149 CTTTGGCCGAATGGTGATATGCTTGTTCATCTTGGTGCCAAATTTAACTT
1 CCTTGGCCGAATGGTGATATGCTTGTTCATCTTGGTGCCAAAGTTAACTT
* * *
717199 CCTTGGCCGAATGATGATGTG-TTGGTTCATCTTGGAGCCAAAGT
1 CCTTGGCCGAATGGTGATATGCTT-GTTCATCTTGGTGCCAAAGT
717243 CTTCATGTGC
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 2 0.02
50 84 0.98
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (50 bp):
CCTTGGCCGAATGGTGATATGCTTGTTCATCTTGGTGCCAAAGTTAACTT
Found at i:721417 original size:20 final size:20
Alignment explanation
Indices: 721392--721447 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
721382 GAAACCCATT
721392 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTGA
721412 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTGA
*
721432 TGAAAATACAAGATTT
1 TGAAAATACATGATTT
721448 AAATGAAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTGA
Found at i:723413 original size:24 final size:24
Alignment explanation
Indices: 723386--723436 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
723376 TGTGGATCAC
* *
723386 CAAAAGTCACGTTTATTGATTCTT
1 CAAAAGACACGTTTATTGAATCTT
* *
723410 CAAAAGACATGTTTCTTGAATCTT
1 CAAAAGACACGTTTATTGAATCTT
723434 CAA
1 CAA
723437 CTTGAAATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (24 bp):
CAAAAGACACGTTTATTGAATCTT
Found at i:724659 original size:24 final size:23
Alignment explanation
Indices: 724602--724660 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 23
724592 CTTTTCTTTG
*
724602 TTTCTTCTTCTTTTGAGTGTTGCA
1 TTTCTT-TTCTTTTAAGTGTTGCA
*
724626 TTTTTCTTTCTTTTAAGTGCTT-CA
1 TTTCT-TTTCTTTTAAGTG-TTGCA
724650 CTTTCTTTTCT
1 -TTTCTTTTCT
724661 GATTTTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.08, C:0.19, G:0.10, T:0.63
Consensus pattern (23 bp):
TTTCTTTTCTTTTAAGTGTTGCA
Found at i:728659 original size:24 final size:24
Alignment explanation
Indices: 728632--728703 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
728622 AGTCTTCCTG
*
728632 ATGATATATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
728656 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
728680 ATGACGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
728704 TATGTCATGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:729948 original size:30 final size:30
Alignment explanation
Indices: 729914--729972 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
729904 TTTAGTCCCT
* *
729914 AAACTTT-TCAAAGTTTATACTTTGGTCACC
1 AAACTTTACCAAA-TTTATAATTTGGTCACC
729944 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATTTATAATTTGGTCAC
729973 TAAATAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTTGGTCACC
Found at i:735924 original size:23 final size:23
Alignment explanation
Indices: 735896--736016 Score: 83
Period size: 23 Copynumber: 5.1 Consensus size: 23
735886 ACAATCTGTC
*
735896 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
735919 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
735942 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCACCATA-T
*
735967 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
735991 CATCACCA-TATTCCATCACCATAT
1 CATCACCATTA-T-CATCACCATAT
736015 CA
1 CA
736017 CGCCTATATT
Statistics
Matches: 79, Mismatches: 5, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
22 9 0.11
23 29 0.37
24 17 0.22
25 17 0.22
26 2 0.03
27 5 0.06
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.28
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:735933 original size:36 final size:36
Alignment explanation
Indices: 735893--736033 Score: 257
Period size: 36 Copynumber: 3.9 Consensus size: 36
735883 GATACAATCT
735893 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
735929 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
735965 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
736001 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
736034 ACTTATAAAT
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
35 21 0.20
36 82 0.80
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:735937 original size:13 final size:11
Alignment explanation
Indices: 735896--736016 Score: 86
Period size: 11 Copynumber: 10.2 Consensus size: 11
735886 ACAATCTGTC
735896 CATCACCATTAT
1 CATCACCA-TAT
*
735908 CA-CGCCTATAT
1 CATCACC-ATAT
735919 CATCACCATAGT
1 CATCACCATA-T
735931 CCATCACCATTAT
1 -CATCACCA-TAT
*
735944 CA-CGCCTATAT
1 CATCACC-ATAT
735955 CATCACCATAGT
1 CATCACCATA-T
735967 CCATCACCATTAT
1 -CATCACCA-TAT
*
735980 CA-CGCCTATAT
1 CATCACC-ATAT
735991 CATCACCATATT
1 CATCACCATA-T
736003 CCATCACCATAT
1 -CATCACCATAT
736015 CA
1 CA
736017 CGCCTATATT
Statistics
Matches: 89, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
11 35 0.39
12 22 0.25
13 28 0.31
14 4 0.04
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:736443 original size:17 final size:18
Alignment explanation
Indices: 736415--736449 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
736405 AAAAGCAACG
736415 AGAAAGAAGAAAAGAAAA
1 AGAAAGAAGAAAAGAAAA
736433 AGAAA-AAGAAAAGAAAA
1 AGAAAGAAGAAAAGAAAA
736450 GACTCCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AGAAAGAAGAAAAGAAAA
Found at i:740015 original size:36 final size:36
Alignment explanation
Indices: 739968--740073 Score: 189
Period size: 34 Copynumber: 3.0 Consensus size: 36
739958 GATACAATCT
*
739968 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
740004 GTCCATCACCATTATCACGCCTATATCAT--CCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
740038 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
740074 TCACGCCTAT
Statistics
Matches: 67, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
34 34 0.51
36 33 0.49
ACGTcount: A:0.30, C:0.35, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:740092 original size:22 final size:23
Alignment explanation
Indices: 740044--740093 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
740034 CATAGTCCAT
*
740044 CACCATTATCACGCCTATATCAT
1 CACCATTATCACGCCTATATCAA
*
740067 CACCA-TATCACGCCTATATTAA
1 CACCATTATCACGCCTATATCAA
740089 CACCA
1 CACCA
740094 ACTTATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.34, C:0.36, G:0.04, T:0.26
Consensus pattern (23 bp):
CACCATTATCACGCCTATATCAA
Found at i:748504 original size:22 final size:22
Alignment explanation
Indices: 748450--748504 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
748440 AATAATACTG
* *
748450 TGAACTGTAAGGCATAGTACCA
1 TGAACAGTAATGCATAGTACCA
748472 TGAACAGTAATGCATAGTACCA
1 TGAACAGTAATGCATAGTACCA
748494 TGAACAGTAAT
1 TGAACAGTAAT
748505 TAACATTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (22 bp):
TGAACAGTAATGCATAGTACCA
Found at i:754912 original size:12 final size:11
Alignment explanation
Indices: 754869--754913 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
754859 CCCTCTTTAA
*
754869 TTTTTTCTTTT
1 TTTTTTATTTT
754880 TTTTTTCATTTT
1 TTTTTT-ATTTT
*
754892 TTTTATATTTT
1 TTTTTTATTTT
754903 TTCTTTTATTT
1 TT-TTTTATTT
754914 ACAAATCTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 13 0.45
12 16 0.55
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:763369 original size:19 final size:20
Alignment explanation
Indices: 763330--763380 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
763320 GAAATCCATT
*
763330 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATCTTTAA
763350 TGAAAATACATGA-CTTTAA
1 TGAAAATACATGATCTTTAA
763369 TGAAAATACATG
1 TGAAAATACATG
763381 CTATGGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATCTTTAA
Found at i:768304 original size:6 final size:5
Alignment explanation
Indices: 768269--768325 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
768259 TGGAGTGCAA
*
768269 AAAAG AAAAG AAAAG -ACA- AAAAG AAGAAG AATAAG AAAAG --AAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AA-AAG AAAAG AAAAG AAAAG
768317 AAAAAG AAA
1 -AAAAG AAA
768326 TTAAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
3 3 0.07
4 4 0.09
5 21 0.49
6 15 0.35
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:768304 original size:25 final size:24
Alignment explanation
Indices: 768268--768325 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
768258 TTGGAGTGCA
768268 AAAAAGAAAAGAAAAGACA-AAAAG
1 AAAAAGAAAAGAAAAGA-AGAAAAG
*
768292 AAGAAGAATAAGAAAAGAAGAAAAG
1 AAAAAGAA-AAGAAAAGAAGAAAAG
768317 AAAAAGAAA
1 AAAAAGAAA
768326 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (24 bp):
AAAAAGAAAAGAAAAGAAGAAAAG
Found at i:768309 original size:14 final size:13
Alignment explanation
Indices: 768267--768320 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
768257 ATTGGAGTGC
768267 AAAA-AAGAAAAG
1 AAAAGAAGAAAAG
768279 AAAAGACA-AAAAG
1 AAAAGA-AGAAAAG
768292 --AAGAAGAATAAG
1 AAAAGAAGAA-AAG
768304 AAAAGAAGAAAAG
1 AAAAGAAGAAAAG
768317 AAAA
1 AAAA
768321 AGAAATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
10 1 0.03
11 6 0.17
12 7 0.19
13 13 0.36
14 9 0.25
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAAGAAGAAAAG
Found at i:768314 original size:8 final size:8
Alignment explanation
Indices: 768276--768318 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
768266 CAAAAAAGAA
768276 AAGAAAAG
1 AAGAAAAG
768284 ACA-AAAAG
1 A-AGAAAAG
*
768292 AAGAAGAAT
1 AAGAA-AAG
768301 AAGAAAAG
1 AAGAAAAG
768309 AAGAAAAG
1 AAGAAAAG
768317 AA
1 AA
768319 AAAGAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 1 0.03
8 21 0.70
9 8 0.27
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (8 bp):
AAGAAAAG
Found at i:770560 original size:21 final size:22
Alignment explanation
Indices: 770521--770561 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
770511 GACTATTAAG
* *
770521 CAAAGGATGGTAATTCTTCATC
1 CAAAGGATCGTAATCCTTCATC
770543 CAAAGGA-CGTAATCCTTCA
1 CAAAGGATCGTAATCCTTCA
770562 AGAATCAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (22 bp):
CAAAGGATCGTAATCCTTCATC
Found at i:772411 original size:26 final size:26
Alignment explanation
Indices: 772380--772453 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 26
772370 TATCCCTTAT
772380 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
*
772406 TTATTT-ATTT-A-TTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
* *
772428 TTA-ATCATTTTCCTTTTCTTATCTTT
1 TTATTTCA-TTT-CATTTCTTATCTTT
772454 GTTGTAGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
21 1 0.03
22 9 0.24
23 8 0.21
24 1 0.03
25 4 0.11
26 11 0.29
27 4 0.11
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTATCTTTA
Found at i:782843 original size:17 final size:17
Alignment explanation
Indices: 782821--782854 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
782811 CCGATTCTTC
782821 GGGTAAGCATTCAGATA
1 GGGTAAGCATTCAGATA
782838 GGGTAAGCATTCAGATA
1 GGGTAAGCATTCAGATA
782855 TGTAATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (17 bp):
GGGTAAGCATTCAGATA
Found at i:789464 original size:24 final size:24
Alignment explanation
Indices: 789437--789487 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
789427 TGTGGATCAC
* *
789437 CAAAAGTCACGTTTATTGATTCTT
1 CAAAAGACACGTTTATTGAATCTT
* *
789461 CAAAAGACATGTTTCTTGAATCTT
1 CAAAAGACACGTTTATTGAATCTT
789485 CAA
1 CAA
789488 CTTGAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (24 bp):
CAAAAGACACGTTTATTGAATCTT
Found at i:792931 original size:13 final size:13
Alignment explanation
Indices: 792913--792937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
792903 ACTTTCTTTC
792913 TTTCTTCTTTTTT
1 TTTCTTCTTTTTT
792926 TTTCTTCTTTTT
1 TTTCTTCTTTTT
792938 GAGTGCTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTCTTCTTTTTT
Found at i:792952 original size:24 final size:24
Alignment explanation
Indices: 792925--792979 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
792915 TCTTCTTTTT
*
792925 TTTTCTTCTTTTTGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
*
792949 TTTTGTTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
792973 TTTTCTT
1 TTTTCTT
792980 TGCTGATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.07, C:0.15, G:0.18, T:0.60
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTTGAC
Found at i:793660 original size:19 final size:19
Alignment explanation
Indices: 793619--793669 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
793609 GAAACCCCTT
* **
793619 TGAAAATACATTAATTTTTA
1 TGAAAATACA-TGATTTAAA
793639 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
793658 TGAAGATACATG
1 TGAAAATACATG
793670 CTCATGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Done.