Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_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: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 16
Found at i:2422649 original size:43 final size:43
Alignment explanation
Indices: 2422580--2422669 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
2422570 TATAGTGGCA
2422580 TTTGTCAATAAAAACGCCATTATATATGTAATCAATGGCGGTG
1 TTTGTCAATAAAAACGCCATTATATATGTAATCAATGGCGGTG
* * * *
2422623 TTTGTTAATACAAACGTCACTT-TATATGTAATCAATTGCGGTG
1 TTTGTCAATAAAAACGCCA-TTATATATGTAATCAATGGCGGTG
2422666 TTTG
1 TTTG
2422670 GGATAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 40 0.95
44 2 0.05
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (43 bp):
TTTGTCAATAAAAACGCCATTATATATGTAATCAATGGCGGTG
Found at i:2422705 original size:43 final size:43
Alignment explanation
Indices: 2422658--2422782 Score: 155
Period size: 43 Copynumber: 2.9 Consensus size: 43
2422648 ATGTAATCAA
* * * * *
2422658 TTGCGGTGTTTGGGATAAAAATGCCCCTATATAACATGAGATT
1 TTGCGGCGTTTGAGAAAAAAATGCCGCTATATAACATGACATT
* **
2422701 TTGCGGCGTTTGTA-AGAAAAGCGCCGCTATATAACATGACATT
1 TTGCGGCGTTTG-AGAAAAAAATGCCGCTATATAACATGACATT
2422744 TTGCGGCGTTT-AGAAAAAAATGCCGCTATATAACATGAC
1 TTGCGGCGTTTGAGAAAAAAATGCCGCTATATAACATGAC
2422783 CTTTAGTTGC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.01
42 23 0.33
43 46 0.66
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (43 bp):
TTGCGGCGTTTGAGAAAAAAATGCCGCTATATAACATGACATT
Found at i:2422782 original size:42 final size:43
Alignment explanation
Indices: 2422674--2422782 Score: 159
Period size: 43 Copynumber: 2.6 Consensus size: 43
2422664 TGTTTGGGAT
* *
2422674 AAAAATGCCCCTATATAACATGAGATTTTGCGGCGTTTGTAAG
1 AAAAATGCCGCTATATAACATGACATTTTGCGGCGTTTGTAAG
**
2422717 AAAAGCGCCGCTATATAACATGACATTTTGCGGCGTTTAG-AA-
1 AAAAATGCCGCTATATAACATGACATTTTGCGGCGTTT-GTAAG
2422759 AAAAATGCCGCTATATAACATGAC
1 AAAAATGCCGCTATATAACATGAC
2422783 CTTTAGTTGC
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 22 0.37
43 36 0.61
44 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (43 bp):
AAAAATGCCGCTATATAACATGACATTTTGCGGCGTTTGTAAG
Found at i:2425320 original size:2 final size:2
Alignment explanation
Indices: 2425313--2425348 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2425303 TTTACCCTAA
2425313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2425349 TAATTAGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2426461 original size:6 final size:6
Alignment explanation
Indices: 2426450--2426537 Score: 72
Period size: 6 Copynumber: 14.8 Consensus size: 6
2426440 TTATGGCCTG
* * * * * *
2426450 TAATAA TAATAA TATTAA TAATAT TAATAT TAATAT TAATAT TAATAT
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
* * *
2426498 TAATAT TAATAA T-ATGGA TAA-AA TAATAA TAATAT TAATA
1 TAATAA TAATAA TAAT-AA TAATAA TAATAA TAATAA TAATA
2426538 CGAATGACGA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
5 6 0.08
6 65 0.90
7 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (6 bp):
TAATAA
Found at i:2426468 original size:9 final size:9
Alignment explanation
Indices: 2426450--2426537 Score: 70
Period size: 9 Copynumber: 9.2 Consensus size: 9
2426440 TTATGGCCTG
*
2426450 TAATAATAA
1 TAATATTAA
2426459 TAATATTAA
1 TAATATTAA
2426468 TAATATTAATA
1 TAATATT-A-A
2426479 TTAATATTAA
1 -TAATATTAA
* * *
2426489 TATTAATAT
1 TAATATTAA
2426498 TAATATTAA
1 TAATATTAA
2426507 TAATATGGATAA
1 TAATAT---TAA
*
2426519 -AATAATAA
1 TAATATTAA
2426527 TAATATTAA
1 TAATATTAA
2426536 TA
1 TA
2426538 CGAATGACGA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
8 3 0.05
9 42 0.67
10 2 0.03
11 6 0.10
12 10 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (9 bp):
TAATATTAA
Found at i:2426470 original size:12 final size:12
Alignment explanation
Indices: 2426450--2426537 Score: 81
Period size: 12 Copynumber: 7.4 Consensus size: 12
2426440 TTATGGCCTG
*
2426450 TAATAATAATAA
1 TAATAATAATAT
*
2426462 TATTAATAATAT
1 TAATAATAATAT
*
2426474 TAATATTAATAT
1 TAATAATAATAT
*
2426486 TAATATTAATAT
1 TAATAATAATAT
* *
2426498 TAATATTAATAA
1 TAATAATAATAT
* *
2426510 T-ATGGATAA-AA
1 TAAT-AATAATAT
2426521 TAATAATAATAT
1 TAATAATAATAT
2426533 TAATA
1 TAATA
2426538 CGAATGACGA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
11 9 0.14
12 55 0.86
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:2426937 original size:123 final size:119
Alignment explanation
Indices: 2426668--2426981 Score: 400
Period size: 123 Copynumber: 2.6 Consensus size: 119
2426658 AAACGGAAAT
* * * *
2426668 GTTGAACATGTTCTTCTTATTATGAACTTCTTATTCTTCTTCAGATGAGTTCTTCTTATTATGAA
1 GTTGAATAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTATGAA
* * * * *
2426733 CTCTTCTACTGGGAATGTTGATCCATCTCCTTCTGTGATGGAATCTATCAAAAT
66 CTCTTCTACTGGAAATGTTGATCCATCTCCTTCTGCGATAGAATCTAGCAAAAG
* * *
2426787 GTTGAATAAGCTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGACGAGTTCTTCTTATTATGAA
1 GTTGAATAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTATGAA
*
2426852 CTCTT-T-CTGGAAATGTTGATGTAGCTCTATCTCCTTCTGCGATAGAAT-TGGGCAAAAG
66 CTCTTCTACTGGAAATGTTGA--T--C-C-ATCTCCTTCTGCGATAGAATCT-AGCAAAAG
**
2426910 GTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTATGAA
1 GTTGAATAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTATGAA
2426975 CTTCTTC
66 C-TCTTC
2426982 CTCCTCTTTA
Statistics
Matches: 168, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
117 12 0.07
118 1 0.01
119 64 0.38
121 1 0.01
122 2 0.01
123 84 0.50
124 4 0.02
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (119 bp):
GTTGAATAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTATGAA
CTCTTCTACTGGAAATGTTGATCCATCTCCTTCTGCGATAGAATCTAGCAAAAG
Found at i:2426972 original size:39 final size:39
Alignment explanation
Indices: 2426918--2427019 Score: 159
Period size: 39 Copynumber: 2.6 Consensus size: 39
2426908 AGGTTGAATA
** *
2426918 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATG
1 AGTTCTTCTTATTATGAACTTCTTCCTCCTCTTCAGATG
*
2426957 AGTTCTTCTTATTATGAACTTCTTCCTCCTCTTTAGATG
1 AGTTCTTCTTATTATGAACTTCTTCCTCCTCTTCAGATG
*
2426996 AGTTCTTCTTATTACGAACTTCTT
1 AGTTCTTCTTATTATGAACTTCTT
2427020 TTAGAAATGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.47
Consensus pattern (39 bp):
AGTTCTTCTTATTATGAACTTCTTCCTCCTCTTCAGATG
Found at i:2426978 original size:162 final size:164
Alignment explanation
Indices: 2426798--2427129 Score: 501
Period size: 162 Copynumber: 2.0 Consensus size: 164
2426788 TTGAATAAGC
* * * *
2426798 TCTTCTTATTATGAACTTCTTCTTCCTCTTCGGACGAGTTCTTCTTATTATGAAC-TCTTTCTGG
1 TCTTCTTATTATGAACTTCTTCCTCCTCTTCAGACGAGTTCTTCTTATTACGAACTTCTTT-TAG
** *
2426862 AAATGTTGATGTAGCTCTATCTCCTTCTGCGATAGAA-TTGGGCAAAAGGTTGAATAAGTTCTTC
65 AAATGTTGATGTAGCTCTATCTCCTTCTGCGATA-AAGACGAGCAAAAGGTTGAATAAGTTCTTC
2426926 AGATTATG-A-ACTTCTTCTTCCTCTTCAGATGAGT
129 AGATTATGAATACTTCTTCTTCCTCTTCAGATGAGT
* *
2426960 TCTTCTTATTATGAACTTCTTCCTCCTCTTTAGATGAGTTCTTCTTATTACGAACTTCTTTTAGA
1 TCTTCTTATTATGAACTTCTTCCTCCTCTTCAGACGAGTTCTTCTTATTACGAACTTCTTTTAGA
* *
2427025 AATGTTGATGTTGCTCTATCTCCTTCTGCGATAAAGACGAGCAAAATGTTGAATAAGTTCTTCAG
66 AATGTTGATGTAGCTCTATCTCCTTCTGCGATAAAGACGAGCAAAAGGTTGAATAAGTTCTTCAG
2427090 ATTATGAACTTACTTCTTCTTCCTCTTCAGATGAGT
131 ATTATGAA--TACTTCTTCTTCCTCTTCAGATGAGT
2427126 TCTT
1 TCTT
2427130 ATTACGAACT
Statistics
Matches: 153, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
161 2 0.01
162 116 0.76
163 6 0.04
166 29 0.19
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (164 bp):
TCTTCTTATTATGAACTTCTTCCTCCTCTTCAGACGAGTTCTTCTTATTACGAACTTCTTTTAGA
AATGTTGATGTAGCTCTATCTCCTTCTGCGATAAAGACGAGCAAAAGGTTGAATAAGTTCTTCAG
ATTATGAATACTTCTTCTTCCTCTTCAGATGAGT
Found at i:2427095 original size:123 final size:123
Alignment explanation
Indices: 2426957--2427403 Score: 666
Period size: 123 Copynumber: 3.6 Consensus size: 123
2426947 TCTTCAGATG
** * *
2426957 AGTTCTTCTTATTATGAACTTCTTCCTCCTCTTTAGATGAGTTCTTCTTATTACGAACTTCTTTT
1 AGTTCTTCAGATTATGAACTTCTTCCTCCTCTTCAGATGAGTTCTTCTTATTACGAACTTCTTCT
* *
2427022 AGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAAAGACGAGCAAAATGTTGAATA
66 AGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAATGTTGAATA
*
2427080 AGTTCTTCAGATTATGAACTTACTTCTTCTTCCTCTTCAGATGAG---TTCTTATTACGAACTTT
1 AGTTCTTCAGATTATGAACTT-CTTC--C-TCCTCTTCAGATGAGTTCTTCTTATTACGAACTTC
* *
2427142 TTCTAGAAATATTGATGTCGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAATGTTGAATA
62 TTCTAGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAATGTTGAATA
* * *
2427204 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCATATGAGTTCTTCTTATTACAAACTTCTTCT
1 AGTTCTTCAGATTATGAACTTCTTCCTCCTCTTCAGATGAGTTCTTCTTATTACGAACTTCTTCT
* * * *
2427269 GGAAATGTTGATGCTGCTCTATCTCCTTTTGTGATAGAGTCGAGCAAAATGTTGAATA
66 AGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAATGTTGAATA
* *
2427327 AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCT
1 AGTTCTTCAGATTATGAACTTCTTCCTCCTCTTCAGATGAGTTCTTCTTATTACGAACTTCTTCT
*
2427392 GGAAATGTTGAT
66 AGAAATGTTGAT
2427404 CCATTGAGTG
Statistics
Matches: 295, Mismatches: 22, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
120 14 0.05
123 168 0.57
124 98 0.33
126 1 0.00
127 14 0.05
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (123 bp):
AGTTCTTCAGATTATGAACTTCTTCCTCCTCTTCAGATGAGTTCTTCTTATTACGAACTTCTTCT
AGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAATGTTGAATA
Found at i:2427179 original size:286 final size:279
Alignment explanation
Indices: 2426677--2427267 Score: 765
Period size: 286 Copynumber: 2.1 Consensus size: 279
2426667 TGTTGAACAT
** * * *
2426677 GTTCTTCTTATTATGAACTTCTTATTCTTCTTCAGATGAGTTCTTCTTATTATGAACTCTTCTAC
1 GTTCTTCTTATTATGAACTTCTTCCTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTTCTAA
* * * * * **
2426742 TGGGAATGTTGATCCATCTCCTTCTGTGATGGAATCTATCAAAATGTTGAATAAGCTCTTCTTAT
66 TGGGAATGTTGATCCATCTCCTTCTGCGATGAAAACGAGCAAAATGTTGAATAAGCTCTTCAGAT
* * * *
2426807 TATGAACTTCTTCTTCCTCTTCGGACGAGTTCTTCTTATTATGAACTCTTTCTGGAAATGTTGAT
131 TATGAACTTCTTCTTCCTCTTCAGACGAG-T-TTCTTATTACGAACTCTTTCTAGAAATATTGAT
* *
2426872 GTAGCTCTATCTCCTTCTGCGATAGAATTGGGCAAAAGGTTGAATAAGTTCTTCAGATTATGAAC
194 GTAGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAAC
2426937 TTCTTCTTCCTCTTCAGATGA
259 TTCTTCTTCCTCTTCAGATGA
* *
2426958 GTTCTTCTTATTATGAACTTCTTCCTCCTCTTTAGATGAGTTCTTCTTATTACGAACTTCTTTTA
1 GTTCTTCTTATTATGAACTTCTTCCTCCTCTTCAGATGAGTTCTTCTTATTACGAAC-TCTTCT-
* * * *
2427023 GAAATGTTG-ATGTTGCTCTATCTCCTTCTGCGAT-AAAGACGAGCAAAATGTTGAATAAGTTCT
64 --AATG-GGAATGTTGATCCATCTCCTTCTGCGATGAAA-ACGAGCAAAATGTTGAATAAGCTCT
* *
2427086 TCAGATTATGAACTTACTTCTTCTTCCTCTTCAGATGAG-TTCTTATTACGAACTTTTTCTAGAA
125 TCAGATTATG-A---ACTTCTTCTTCCTCTTCAGACGAGTTTCTTATTACGAACTCTTTCTAGAA
* * *
2427150 ATATTGATGTCGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAATGTTGAATAAGTTCTTCAGA
186 ATATTGATGTAGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTCAGA
*
2427215 TTATGAACTTCTTCTTCCTCTTCATATGA
251 TTATGAACTTCTTCTTCCTCTTCAGATGA
**
2427244 GTTCTTCTTATTACAAACTTCTTC
1 GTTCTTCTTATTATGAACTTCTTC
2427268 TGGAAATGTT
Statistics
Matches: 268, Mismatches: 32, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
281 52 0.19
282 5 0.02
284 2 0.01
285 54 0.20
286 133 0.50
289 22 0.08
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.42
Consensus pattern (279 bp):
GTTCTTCTTATTATGAACTTCTTCCTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTTCTAA
TGGGAATGTTGATCCATCTCCTTCTGCGATGAAAACGAGCAAAATGTTGAATAAGCTCTTCAGAT
TATGAACTTCTTCTTCCTCTTCAGACGAGTTTCTTATTACGAACTCTTTCTAGAAATATTGATGT
AGCTCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTT
CTTCTTCCTCTTCAGATGA
Found at i:2432151 original size:6 final size:6
Alignment explanation
Indices: 2432142--2432167 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2432132 CAAAAATGGG
2432142 AATGCA AATGCA AATGCA AATGCA AA
1 AATGCA AATGCA AATGCA AATGCA AA
2432168 GATGTTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AATGCA
Found at i:2434310 original size:836 final size:836
Alignment explanation
Indices: 2432698--2437715 Score: 9874
Period size: 836 Copynumber: 6.0 Consensus size: 836
2432688 AGCACTATTC
2432698 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
1 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
*
2432763 AATCCGTAAATCATGAGAAAACTTTTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
66 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
2432828 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
131 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
2432893 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
196 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
2432958 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
261 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
2433023 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
326 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
2433088 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
391 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
2433153 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
456 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
2433218 ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAACCGCTTCTC
521 ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAACCGCTTCTC
2433283 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
586 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
*
2433348 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAAGAGCTGACTAAACCTTGATGATTTCAG
651 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
*
2433413 ATTGCATGATTTCTTCTCACTTCTGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
716 ATTGCATGATTTCTTCTCACTTATGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
2433478 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
781 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
2433534 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
1 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
2433599 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
66 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
*
2433664 GTTCGGCATCATTTTTCAATTTAATGACCAATGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
131 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
2433729 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
196 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
2433794 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
261 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
2433859 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
326 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
2433924 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
391 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
2433989 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
456 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
* *
2434054 ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAACCGATTCTT
521 ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAACCGCTTCTC
2434119 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
586 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
2434184 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
651 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
2434249 ATTGCATGATTTCTTCTCACTTATGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
716 ATTGCATGATTTCTTCTCACTTATGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
2434314 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
781 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
2434370 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
1 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
2434435 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
66 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
2434500 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
131 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
2434565 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
196 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
2434630 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
261 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
2434695 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
326 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
2434760 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
391 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
*
2434825 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCAGAATGAAC
456 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
* *
2434890 ATTGATATCATACCAATTCGGATATGGAGGTTATAATGGTTTCACATAATGCGGAACCGCTTCTC
521 ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAACCGCTTCTC
2434955 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
586 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
2435020 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
651 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
2435085 ATTGCATGATTTCTTCTCACTTATGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
716 ATTGCATGATTTCTTCTCACTTATGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
2435150 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
781 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
2435206 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
1 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
2435271 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
66 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
2435336 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
131 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
2435401 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
196 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
2435466 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
261 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
2435531 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
326 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
2435596 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
391 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
2435661 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
456 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
*
2435726 ATTGATATCATACCAATTCGGATACGGATGTTACAATGGTTTCACATAATGCGGAACCGCTTCTC
521 ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAACCGCTTCTC
2435791 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
586 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
2435856 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
651 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
2435921 ATTGCATGATTTCTTCTCACTTATGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
716 ATTGCATGATTTCTTCTCACTTATGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
2435986 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
781 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
2436042 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
1 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
2436107 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
66 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
*
2436172 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTATTTCCCATGCCA
131 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
2436237 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
196 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
2436302 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
261 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
2436367 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
326 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
2436432 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
391 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
2436497 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
456 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
2436562 ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAACCGCTTCTC
521 ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAACCGCTTCTC
*
2436627 GGGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
586 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
2436692 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
651 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
*
2436757 ATTGCATGATTTCTTCTCACTTCTGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
716 ATTGCATGATTTCTTCTCACTTATGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
2436822 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
781 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
2436878 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
1 AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
*
2436943 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTTTGTGTCTTGACATTTATTTTCCATT
66 AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
2437008 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
131 GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
2437073 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
196 GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
2437138 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
261 TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
2437203 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
326 GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
2437268 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
391 CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
2437333 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
456 TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
*
2437398 ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAATCGCTTCTC
521 ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAACCGCTTCTC
2437463 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
586 GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
*
2437528 CCTTTCGTCTTGGATTGAATCAGAGTTTTCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
651 CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
*
2437593 ATTGCATGATTTCTTCTCACTTCTGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
716 ATTGCATGATTTCTTCTCACTTATGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
*
2437658 ACAACTTGTGAATACGAAGGATGACTGTATATAATTTCTCAATTGGTTAGGATCAG
781 ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
2437714 AA
1 AA
2437716 GTCCATTGTA
Statistics
Matches: 4156, Mismatches: 26, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
836 4156 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (836 bp):
AACATTTGATTTTTGGCTTAACATCTTCCCAATTCAATGATATATGTATTGTGTCTTTCTTCTGC
AATCCGTAAATCATGAGAAAACTTCTTCGCTCGATTTTTGTGTGTCTTGACATTTATTTTCCATT
GTTCGGCATCATTTTTCAATTTAATGACCACTGTTGTCCATTCTTCTGGGGTGTTTCCCATGCCA
GCATTTTGAAAGGTTTGACTGACCTTTGGAAATCCTTACGAATGGTTTCCATTTTTGTGCTCAGT
TTATCGTTTTCAATCTTTAAATGATGTATTTGAGCCTCGTACATCAGAAAATCTTCTTTCTTCTA
GATGCCCCTACTGATACTCTTACCTTTGAATACTTTTGGTATTAATCTAGCAGGACCTTCAGTTA
CCAAACTAGGTCGATTATTTATCATAAACTCTAAGATTCCATGATCCAAAAGACATTGGACTTGA
TGGTTGAAGGCAATGCAATTTTCAATGGAATGTTCTTGAGCTCCAACATGATATTCACAATGAAC
ATTGATATCATACCAATTCGGATACGGAGGTTACAATGGTTTCACATAATGCGGAACCGCTTCTC
GCGCTTCAAGTAGCTTCTCGTACAATTCTTTATATGATATAGGGATAGCACAAAAATGATAACCG
CCTTTCGTCTTGGATTGAATCAGAGTTTCCGACGTCAGGAGCTGACTAAACCTTGATGATTTCAG
ATTGCATGATTTCTTCTCACTTATGGGAGATTTTATAGTTGTCACCATTTCCTGGGTATTTCCAG
ACAACTTGTGAATACGAAGGATGACTGTATGTAATTTCTCAATTGGTTAGGATCAG
Found at i:2439983 original size:2 final size:2
Alignment explanation
Indices: 2439976--2440009 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2439966 TTTACCCTAA
2439976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2440010 TAATTAGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2440268 original size:23 final size:23
Alignment explanation
Indices: 2440238--2440356 Score: 238
Period size: 23 Copynumber: 5.2 Consensus size: 23
2440228 CATTTTTTTA
2440238 TTCTCTCTATAACGAGAGAACTC
1 TTCTCTCTATAACGAGAGAACTC
2440261 TTCTCTCTATAACGAGAGAACTC
1 TTCTCTCTATAACGAGAGAACTC
2440284 TTCTCTCTATAACGAGAGAACTC
1 TTCTCTCTATAACGAGAGAACTC
2440307 TTCTCTCTATAACGAGAGAACTC
1 TTCTCTCTATAACGAGAGAACTC
2440330 TTCTCTCTATAACGAGAGAACTC
1 TTCTCTCTATAACGAGAGAACTC
2440353 TTCT
1 TTCT
2440357 ATTCTCTCTA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 96 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (23 bp):
TTCTCTCTATAACGAGAGAACTC
Found at i:2441179 original size:3 final size:3
Alignment explanation
Indices: 2441171--2441241 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
2441161 ATTATGGACT
* * * * *
2441171 ATA ATA ATA ATA TTA ATA TTA ATA ATA ATA ATA TTG ATA A-A ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2441218 ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
2441242 CGAATGTCGA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:2441525 original size:36 final size:37
Alignment explanation
Indices: 2441480--2441559 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 37
2441470 CAACATTTCC
2441480 AGAAGAAGTTCGTAAT-AAGAACTCATCTGAAGAGGA
1 AGAAGAAGTTCGTAATAAAGAACTCATCTGAAGAGGA
*
2441516 AGAAGAAGTTCGTAATAAGAAGAATTCATCTGAAGAGGA
1 AGAAGAAGTTCGTAAT-A-AAGAACTCATCTGAAGAGGA
2441555 AGAAG
1 AGAAG
2441560 TTCATAATCT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
36 16 0.40
39 24 0.60
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.19
Consensus pattern (37 bp):
AGAAGAAGTTCGTAATAAAGAACTCATCTGAAGAGGA
Found at i:2441574 original size:36 final size:37
Alignment explanation
Indices: 2441480--2441577 Score: 114
Period size: 36 Copynumber: 2.7 Consensus size: 37
2441470 CAACATTTCC
2441480 AGAAGAAGTTCGTAA-T-AAGAACTCATCTGAAGAGG
1 AGAAGAAGTTCGTAATTGAAGAACTCATCTGAAGAGG
* *
2441515 AAGAAGAAGTTCGTAATAAGAAGAATTCATCTGAAGA-G
1 -AGAAGAAGTTCGTAAT-TGAAGAACTCATCTGAAGAGG
*
2441553 -GAAGAAGTTCATAATCTGAAGAACT
1 AGAAGAAGTTCGTAAT-TGAAGAACT
2441578 TATTCAACCT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
36 36 0.68
38 1 0.02
39 16 0.30
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.21
Consensus pattern (37 bp):
AGAAGAAGTTCGTAATTGAAGAACTCATCTGAAGAGG
Found at i:2441585 original size:156 final size:158
Alignment explanation
Indices: 2441357--2441697 Score: 499
Period size: 156 Copynumber: 2.1 Consensus size: 158
2441347 CAACATTTCC
*
2441357 AGAAGAAGTTCGTAATAAGAAGGACTCATCTGAAGAGAAAGAACAAATTCATAATCTGAAGAACT
1 AGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAG--AGAACAAATTCATAATCTGAAGAACT
* * * *
2441422 TATTCAACCTTTTGCTCGACTCTATCGCAGATGGAGATAGAGTAGCATCAACATTTCCAGAAGA-
64 TATTCAACCTTTTGCTCGACTATATCCCAGAAGGAGATAGAGCAGCATCAACATTTCCAGAA-AT
* *
2441486 AGTTCGTAATAAG-AACTCATCTGAAGAGGA
128 AGTTCATAATAAGAAACTCATCCGAAGAGGA
* * *
2441516 AGAAGAAGTTCGTAATAAGAAGAATTCATCTGAAGAG-GAAGAAGTTCATAATCTGAAGAACTTA
1 AGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGAGAACAAATTCATAATCTGAAGAACTTA
*
2441580 TTCAACCTTTTGCTCGATTATATCCCAGAAGGAGATAGAGCAGCATCAACATTTCCAGAAATAGT
66 TTCAACCTTTTGCTCGACTATATCCCAGAAGGAGATAGAGCAGCATCAACATTTCCAGAAATAGT
*
2441645 TCATAATAAGAAAAACTCGTCCGAAGAGGA
131 TCATAATAAG--AAACTCATCCGAAGAGGA
*
2441675 AGAAGAAGTTCATAATAAGAAGA
1 AGAAGAAGTTCGTAATAAGAAGA
2441698 GCTTATTCAA
Statistics
Matches: 165, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
155 1 0.01
156 92 0.56
159 72 0.44
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.23
Consensus pattern (158 bp):
AGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGAGAACAAATTCATAATCTGAAGAACTTA
TTCAACCTTTTGCTCGACTATATCCCAGAAGGAGATAGAGCAGCATCAACATTTCCAGAAATAGT
TCATAATAAGAAACTCATCCGAAGAGGA
Found at i:2441738 original size:123 final size:115
Alignment explanation
Indices: 2441516--2441823 Score: 296
Period size: 123 Copynumber: 2.6 Consensus size: 115
2441506 CTGAAGAGGA
* * * * * * **
2441516 AGAAGAAGTTCGTAATAAGAAGAATTCATCTGAAGAGGAAGAAGTTCATAATCTGAAGAACTTAT
1 AGAAG-AGTTCATAATAAGAAAAACTCATCCGAAAAAGAAGAAGTTCATAATAAGAAGAACTTAT
* * * * * *
2441581 TCAACCTTTTGCTCGATTATATCCCAGAAGGAGATAGAGCAGCATCAACATTTCCAG
65 TCAACCTTTTGATAGATTACATCACAAAAGGAGAT---G--G-ATCAACATTCCCAG
* * *
2441638 A-AATAGTTCATAATAAGAAAAACTCGTCCGAAGAGGAAGAAGAAGTTCATAATAAGAAGAGCTT
1 AGAAGAGTTCATAATAAGAAAAACTCATCCGAA-A--AAGAAGAAGTTCATAATAAGAAGAACTT
* * *
2441702 ATTCAACCTTTTGATAGATTCCATCACAAAAGGAGATGGATCAATATTCCCAT
63 ATTCAACCTTTTGATAGATTACATCACAAAAGGAGATGGATCAACATTCCCAG
* * *
2441755 ATGAAGAGTTCATAATAAGAAGAACTCATCTGAAAAA-AAGAAGTTCATAATAAGAAGAACTTGT
1 A-GAAGAGTTCATAATAAGAAAAACTCATCCGAAAAAGAAGAAGTTCATAATAAGAAGAACTTAT
2441819 TCAAC
65 TCAAC
2441824 ATTTCCGTTT
Statistics
Matches: 155, Mismatches: 26, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
115 30 0.19
116 2 0.01
117 12 0.08
118 2 0.01
119 27 0.17
120 24 0.15
121 2 0.01
122 1 0.01
123 55 0.35
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.25
Consensus pattern (115 bp):
AGAAGAGTTCATAATAAGAAAAACTCATCCGAAAAAGAAGAAGTTCATAATAAGAAGAACTTATT
CAACCTTTTGATAGATTACATCACAAAAGGAGATGGATCAACATTCCCAG
Found at i:2441963 original size:3 final size:3
Alignment explanation
Indices: 2441955--2442015 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
2441945 CCGTCATTCG
* * *
2441955 TAT TAT TAT TAT TAA TAT TAT TAT TAT T-T TAT CAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2442002 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
2442016 CATGCTATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2443221 original size:20 final size:20
Alignment explanation
Indices: 2443196--2443233 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2443186 TATTAATTTA
2443196 TATATTTTATAATTTAATTC
1 TATATTTTATAATTTAATTC
* *
2443216 TATATTTTTTATTTTAAT
1 TATATTTTATAATTTAAT
2443234 CGCATGAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (20 bp):
TATATTTTATAATTTAATTC
Found at i:2449156 original size:12 final size:12
Alignment explanation
Indices: 2449141--2449167 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2449131 TGTCATACGT
2449141 GTTGTCAATGTG
1 GTTGTCAATGTG
2449153 GTTGTCAATGTG
1 GTTGTCAATGTG
2449165 GTT
1 GTT
2449168 TTGATGCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.33, T:0.44
Consensus pattern (12 bp):
GTTGTCAATGTG
Found at i:2450380 original size:31 final size:31
Alignment explanation
Indices: 2450345--2450409 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
2450335 ATACAATACA
* *
2450345 GTCCCTCAACATTTAGTCCGTTTATAAAATG
1 GTCCCCCAACATTTAGTCCGTTTACAAAATG
* *
2450376 GTCCCCCAACATTTAGTCTGTTTACAATATG
1 GTCCCCCAACATTTAGTCCGTTTACAAAATG
2450407 GTC
1 GTC
2450410 TCCGACCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCCGTTTACAAAATG
Found at i:2452543 original size:19 final size:19
Alignment explanation
Indices: 2452499--2452544 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
2452489 CTTTACCCTT
*
2452499 TTTTATATATTAAAATATA
1 TTTTATTTATTAAAATATA
2452518 TTTTATTTATTAAAA-ATA
1 TTTTATTTATTAAAATATA
2452536 TTATTATTT
1 TT-TTATTT
2452545 CAAAAAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATTTATTAAAATATA
Found at i:2463757 original size:81 final size:81
Alignment explanation
Indices: 2463655--2464174 Score: 713
Period size: 81 Copynumber: 6.4 Consensus size: 81
2463645 ACACCGTTTA
* * * * *
2463655 TGTCAAAATGCACAGCTAGGCATTTAATCTTTAACCCAAAGGCATTTAGCCTTTCATCTAACTGA
1 TGTC-AAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA
* *
2463720 TATAATTTACACATTTC
65 CATAATTGACACATTTC
* *
2463737 TGTCAAATACACAGCTAGGCAATTAATCTTTTACTCAAAAGTATTTAACCTTTCATCTAACT-AC
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA-
*
2463801 CATAATTGACACCTTTC
65 CATAATTGACACATTTC
* * *
2463818 TATCAAATGTACAGCTAGGCAATTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGA
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GA
2463883 -ATAATTGACACATTTC
65 CATAATTGACACATTTC
* *
2463899 TGTCAAATGCATAGCTAGGCAATTAATCTTTTACTCTAAGGTATTTAACCTTTCATCTAACTCG-
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GA
* *
2463963 CATAATTGGCACCTTTC
65 CATAATTGACACATTTC
* * * *
2463980 TGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAATGTATTTAACCTTTCATTTAACTGGC
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGAC
2464045 ATAATTGACACATTTC
66 ATAATTGACACATTTC
* * * * * * *
2464061 TTTCAAATGCATAGCTAGACAATTCATTTTTTACTCAAAGGTATTTAACCTTTTATCTAACTGGC
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGAC
*
2464126 ATAATTGACACCTTTC
66 ATAATTGACACATTTC
*
2464142 TGTCAAATGCACAGCTAGACAATTAATCTTTTA
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTA
2464175 TTTAAAACAG
Statistics
Matches: 388, Mismatches: 45, Indels: 11
0.87 0.10 0.02
Matches are distributed among these distances:
80 2 0.01
81 381 0.98
82 4 0.01
83 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (81 bp):
TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGAC
ATAATTGACACATTTC
Found at i:2464479 original size:19 final size:19
Alignment explanation
Indices: 2464455--2464495 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
2464445 ATACCACTTG
*
2464455 TTAGTATATTTCATAACAT
1 TTAGTATATTCCATAACAT
2464474 TTAGTATATTCCATAACAT
1 TTAGTATATTCCATAACAT
2464493 TTA
1 TTA
2464496 TACTTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (19 bp):
TTAGTATATTCCATAACAT
Found at i:2468839 original size:19 final size:21
Alignment explanation
Indices: 2468815--2468866 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2468805 CGGCCAAGAG
*
2468815 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
2468834 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
2468855 CATGTATTTTCA
1 CATGTATTTTCA
2468867 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:2472839 original size:19 final size:21
Alignment explanation
Indices: 2472815--2472866 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2472805 CTGCCAAGAG
*
2472815 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
2472834 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
2472855 CATGTATTTTCA
1 CATGTATTTTCA
2472867 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:2475827 original size:23 final size:23
Alignment explanation
Indices: 2475798--2475888 Score: 137
Period size: 23 Copynumber: 4.0 Consensus size: 23
2475788 TTGTGACATA
* * *
2475798 TATGTGGTCGTTCGAGACAATTC
1 TATGTGGTCCTTCGGGACATTTC
2475821 TATGTGGTCCTTCGGGACATTTC
1 TATGTGGTCCTTCGGGACATTTC
2475844 TATGTGGTCCTTCGGGACATTTC
1 TATGTGGTCCTTCGGGACATTTC
* *
2475867 TATGGGGTCCTTTGGGACATTT
1 TATGTGGTCCTTCGGGACATTT
2475889 TATATGGCAC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.38
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACATTTC
Found at i:2478185 original size:80 final size:80
Alignment explanation
Indices: 2477977--2478411 Score: 492
Period size: 81 Copynumber: 5.4 Consensus size: 80
2477967 ACACTGTTTA
* * * * * * * * *
2477977 TGTCAAAATGCACTGTTAAGCATTTAGTCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTA
1 TGTC-AAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAAC-TG
* *
2478042 CATGATTGACACATTTT
64 CATAATTGACACATTTC
* * * * * * * * *
2478059 TGCCAAATGCATAGCTAGGCATTTAATCTTTAACCCAAAAGCATTTAGCCTTTCATCTAACTACA
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCA
* * *
2478124 CAATTAACACTTTTC
66 TAATTGACACATTTC
* * *
2478139 TGTCAAATGCACAGCTAGGTAATTAATCTTTTACTCAAAGGTATTTAACTTTTCAACTAACTGGC
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GC
*
2478204 ATAATTGACACATTTA
65 ATAATTGACACATTTC
* * * *
2478220 TGTCGAATACACAGCTAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCTTCTAACTGCA
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCA
* *
2478285 TAATTGAAACCTTTC
66 TAATTGACACATTTC
* * *
2478300 TTTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGTATGTAACCTTTCATCTAACTGGC
1 TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GC
2478365 ATAATTGACACATTTC
65 ATAATTGACACATTTC
* *
2478381 TATCAAATGCACAGCGAGGCAATTAATCTTT
1 TGTCAAATGCACAGCTAGGCAATTAATCTTT
2478412 AATTTAAAAC
Statistics
Matches: 300, Mismatches: 51, Indels: 5
0.84 0.14 0.01
Matches are distributed among these distances:
80 135 0.45
81 162 0.54
82 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (80 bp):
TGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCA
TAATTGACACATTTC
Found at i:2478281 original size:161 final size:161
Alignment explanation
Indices: 2478004--2478413 Score: 516
Period size: 161 Copynumber: 2.5 Consensus size: 161
2477994 AAGCATTTAG
* * * ** * * *
2478004 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTACATGATTGACACATTTTTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGC
* * * *
2478069 ATAGCTAGGCATTTAATCTTTAACCCAAAAGCATTTAGCCTTTCATCTAACTACACAATT-AACA
66 ACAGCTAGGCAATTAATATTTAACCCAAAAGCATTTAACCTTTCATCTAACTACACAATTGAA-A
* * *
2478133 CTTTTCTGTCAAATGCACAGCTAGGTAATTAA
130 CCTTTCTGTCAAATGCACAACTAGGCAATTAA
* * * *
2478165 TCTTTTACTCAAAGGTATTTAACTTTTCAACTAACTGGCATAATTGACACATTTATGTCGAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGC
* * * * * * *
2478230 ACAGCTAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCTTCTAACTGCATAATTGAAAC
66 ACAGCTAGGCAATTAATATTTAACCCAAAAGCATTTAACCTTTCATCTAACTACACAATTGAAAC
*
2478295 CTTTCTTTCAAATGCACAACTAGGCAATTAA
131 CTTTCTGTCAAATGCACAACTAGGCAATTAA
* * *
2478326 TCTTTTACTCAAAGGTATGTAACCTTTCATCTAACTGGCATAATTGACACATTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGC
* *
2478391 ACAGCGAGGCAATTAATCTTTAA
66 ACAGCTAGGCAATTAATATTTAA
2478414 TTTAAAACAG
Statistics
Matches: 211, Mismatches: 37, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
161 209 0.99
162 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (161 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGC
ACAGCTAGGCAATTAATATTTAACCCAAAAGCATTTAACCTTTCATCTAACTACACAATTGAAAC
CTTTCTGTCAAATGCACAACTAGGCAATTAA
Found at i:2481112 original size:17 final size:17
Alignment explanation
Indices: 2481090--2481216 Score: 119
Period size: 17 Copynumber: 7.4 Consensus size: 17
2481080 AGTTTAGTAT
* *
2481090 ATGAACTATTTTGATGA
1 ATGAACTAGTTTAATGA
*
2481107 ATGAACTAGTTTAATTA
1 ATGAACTAGTTTAATGA
* * *
2481124 ATGAACTAACTTTATTCA
1 ATGAACT-AGTTTAATGA
* * **
2481142 ATGAACTTGTAATCTTGA
1 ATGAACTAGT-TTAATGA
*
2481160 ATGAACTAGTTTGATGA
1 ATGAACTAGTTTAATGA
2481177 ATGAACTAGTTTAATGA
1 ATGAACTAGTTTAATGA
* *
2481194 ATGAACTCGTTTAATCA
1 ATGAACTAGTTTAATGA
2481211 ATGAAC
1 ATGAAC
2481217 AACTTAGTTA
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
17 63 0.70
18 27 0.30
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (17 bp):
ATGAACTAGTTTAATGA
Found at i:2483077 original size:20 final size:20
Alignment explanation
Indices: 2483052--2483091 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
2483042 CATAATTAAT
2483052 AATAAAA-AAATAACCTCACA
1 AATAAAAGAAA-AACCTCACA
2483072 AATAAAAGGAAAAACCTCAC
1 AATAAAA-GAAAAACCTCAC
2483092 CAAACACTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 8 0.44
22 3 0.17
ACGTcount: A:0.62, C:0.20, G:0.05, T:0.12
Consensus pattern (20 bp):
AATAAAAGAAAAACCTCACA
Found at i:2484913 original size:21 final size:17
Alignment explanation
Indices: 2484759--2484912 Score: 137
Period size: 17 Copynumber: 8.9 Consensus size: 17
2484749 AATTAAGATT
* *
2484759 TAGTTTAGTAAATGAAC
1 TAGTTTAATGAATGAAC
* * *
2484776 TAGTTTGATTAATGAAA
1 TAGTTTAATGAATGAAC
*
2484793 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * * *
2484810 TAACTTTATTCAATGAAT
1 T-AGTTTAATGAATGAAC
* * *
2484828 TTGTAATCATGAATGAAC
1 TAGT-TTAATGAATGAAC
* *
2484846 TAGCTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
2484863 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
2484880 TAGTTTAATGAATGAAC
1 TAGTTTAATGAATGAAC
*
2484897 TAGTTTAATCAATGAA
1 TAGTTTAATGAATGAA
2484913 TTACTTAGTT
Statistics
Matches: 111, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
17 88 0.79
18 23 0.21
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:2488247 original size:13 final size:13
Alignment explanation
Indices: 2488229--2488253 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2488219 CAAATAATAA
2488229 GAATAAAATAATG
1 GAATAAAATAATG
2488242 GAATAAAATAAT
1 GAATAAAATAAT
2488254 AATAATAGTA
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:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
GAATAAAATAATG
Found at i:2488256 original size:3 final size:3
Alignment explanation
Indices: 2488221--2488275 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
2488211 ATATCTTTCA
* *
2488221 AAT AAT AAG AAT AA- AAT AAT GGAAT AA- AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT AAT AAT AAT AAT AAT
2488266 AAT AAT AAT A
1 AAT AAT AAT A
2488276 TATTTTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
5 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:2488424 original size:37 final size:38
Alignment explanation
Indices: 2488358--2488434 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 38
2488348 ATAAACAGTA
*
2488358 AAAAGCAACGACAACAAAAACAATAAACTAATTCAATT
1 AAAAGCAACAACAACAAAAACAATAAACTAATTCAATT
2488396 AAAAGCAACAACAAC-AAAACAATAAACTAATTCAATT
1 AAAAGCAACAACAACAAAAACAATAAACTAATTCAATT
2488433 AA
1 AA
2488435 TTTGATTACA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 24 0.63
38 14 0.37
ACGTcount: A:0.62, C:0.18, G:0.04, T:0.16
Consensus pattern (38 bp):
AAAAGCAACAACAACAAAAACAATAAACTAATTCAATT
Found at i:2490164 original size:13 final size:13
Alignment explanation
Indices: 2490146--2490174 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2490136 TTGAGGTTAA
2490146 ATCATCGCAAGTC
1 ATCATCGCAAGTC
2490159 ATCATCGCAAGTC
1 ATCATCGCAAGTC
2490172 ATC
1 ATC
2490175 CTCATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (13 bp):
ATCATCGCAAGTC
Found at i:2490185 original size:2 final size:2
Alignment explanation
Indices: 2490178--2490258 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
2490168 AGTCATCCTC
2490178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2490220 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2490259 AAGATAGGTA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2494796 original size:29 final size:29
Alignment explanation
Indices: 2494753--2494835 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
2494743 CTCACCTAAC
2494753 TAAATTGATGTAAGCAATGACATCATCACT
1 TAAA-TGATGTAAGCAATGACATCATCACT
* *
2494783 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATCACT
2494812 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2494836 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATCACT
Found at i:2499391 original size:24 final size:24
Alignment explanation
Indices: 2499356--2499410 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2499346 TTAAAATGAT
* *
2499356 AAACAAACGTAAATGAACATAAAC
1 AAACAAACGTAAACGAACACAAAC
* *
2499380 AAACAAATGTAAACGGACACAAAC
1 AAACAAACGTAAACGAACACAAAC
*
2499404 GAACAAA
1 AAACAAA
2499411 AATGAAAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.62, C:0.18, G:0.11, T:0.09
Consensus pattern (24 bp):
AAACAAACGTAAACGAACACAAAC
Found at i:2499456 original size:24 final size:24
Alignment explanation
Indices: 2499400--2499460 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
2499390 AAACGGACAC
* *
2499400 AAACGAACAAAAATGAAAGAACTT
1 AAACGAACATAAATGAAAGAACGT
2499424 AAACGAACATAAATGAAAGAACGT
1 AAACGAACATAAATGAAAGAACGT
2499448 AAA-GAAACATAAA
1 AAACG-AACATAAA
2499461 CAAATGTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.64, C:0.11, G:0.13, T:0.11
Consensus pattern (24 bp):
AAACGAACATAAATGAAAGAACGT
Found at i:2517088 original size:14 final size:14
Alignment explanation
Indices: 2517051--2517090 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2517041 TTAGTATAGT
*
2517051 TTTTTAAAAATGAC
1 TTTTTAAAAGTGAC
*
2517065 TTTTCAAAAGTGAC
1 TTTTTAAAAGTGAC
2517079 TTTTTAAAAGTG
1 TTTTTAAAAGTG
2517091 TTGTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (14 bp):
TTTTTAAAAGTGAC
Found at i:2517245 original size:15 final size:15
Alignment explanation
Indices: 2517227--2517258 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2517217 AAAAATATAG
2517227 AATTTAAATCATATT
1 AATTTAAATCATATT
*
2517242 AATTTAAATTATATT
1 AATTTAAATCATATT
2517257 AA
1 AA
2517259 ATTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAAATCATATT
Found at i:2521361 original size:22 final size:22
Alignment explanation
Indices: 2521333--2521378 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2521323 CTAGGAATGA
2521333 AATAAATAAAAATAATA-ATAAT
1 AATAAAT-AAAATAATAGATAAT
*
2521355 AATAAATAAAATACTAGATAAT
1 AATAAATAAAATAATAGATAAT
2521377 AA
1 AA
2521379 ATCAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
AATAAATAAAATAATAGATAAT
Found at i:2521387 original size:22 final size:20
Alignment explanation
Indices: 2521333--2521387 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 20
2521323 CTAGGAATGA
2521333 AATAAAT-AAAAATAATAAT
1 AATAAATAAAAAATAATAAT
*
2521352 AAT-AATAAATAAAATACTAGAT
1 AATAAAT-AA-AAAATAATA-AT
2521374 AATAAATCAAAAAA
1 AATAAAT-AAAAAA
2521388 GAAGAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 3 0.10
19 3 0.10
20 1 0.03
21 8 0.28
22 9 0.31
23 5 0.17
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
AATAAATAAAAAATAATAAT
Found at i:2521480 original size:37 final size:36
Alignment explanation
Indices: 2521412--2521481 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
2521402 AAATAAGGAG
* *
2521412 TAAATAAAAAAAGTCAAAAGAAAAAAGAAATGAATA
1 TAAATAAAAAAAGTCAAAAAAAAAAAAAAATGAATA
*
2521448 TAAATTAAAGAAAGT-AAAAAAATAAAAAAAATGA
1 TAAA-TAAAAAAAGTCAAAAAAA-AAAAAAAATGA
2521482 GGAAAACCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 10 0.34
37 19 0.66
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (36 bp):
TAAATAAAAAAAGTCAAAAAAAAAAAAAAATGAATA
Found at i:2522604 original size:4 final size:4
Alignment explanation
Indices: 2522595--2522641 Score: 51
Period size: 4 Copynumber: 11.2 Consensus size: 4
2522585 CAAAAACATA
*
2522595 AAAT AAAT AAAT -AAT AAAAT AAAAT AAAAT AAAT AAAT AGAT AAAT A
1 AAAT AAAT AAAT AAAT -AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT A
2522642 TTGTTGGAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 3 0.08
4 23 0.59
5 13 0.33
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2523111 original size:20 final size:20
Alignment explanation
Indices: 2523088--2523126 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2523078 AAATTAATAA
*
2523088 AAATAATAAAAAAACGAAAT
1 AAATAATAAAAAAAAGAAAT
2523108 AAATAATAAAAAAAAGAAA
1 AAATAATAAAAAAAAGAAA
2523127 AAAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (20 bp):
AAATAATAAAAAAAAGAAAT
Found at i:2523116 original size:3 final size:3
Alignment explanation
Indices: 2523018--2523096 Score: 58
Period size: 3 Copynumber: 26.7 Consensus size: 3
2523008 GAAAAAGAAA
* * * *
2523018 AAT AAT AAT ATT AAT ATT AAT ATT AAT -AT AAT AAT ACT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2523064 AA- AAT AGAT GAAT AA- AATT AAT AAA AAT AAT AA
1 AAT AAT A-AT -AAT AAT AA-T AAT AAT AAT AAT AA
2523097 AAAAACGAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
2 8 0.14
3 44 0.75
4 6 0.10
5 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2523138 original size:20 final size:20
Alignment explanation
Indices: 2523095--2523138 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2523085 TAAAAATAAT
* * * *
2523095 AAAAAAACGAAATAAATAAT
1 AAAAAAAAGAAAAAAAAAAG
2523115 AAAAAAAAGAAAAAAAAAAG
1 AAAAAAAAGAAAAAAAAAAG
2523135 AAAA
1 AAAA
2523139 TGCAAAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAAAAG
Found at i:2525153 original size:43 final size:43
Alignment explanation
Indices: 2525090--2525171 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
2525080 AGCCTCAAAT
*
2525090 GGTACAATATCCTCTATTGTGGAGTTGAAATCGTGGATGTGTG
1 GGTACAATATCCTCCATTGTGGAGTTGAAATCGTGGATGTGTG
* * *
2525133 GGTACGATATCCTCCGTTGTGGAGTTGAAATTGTGGATG
1 GGTACAATATCCTCCATTGTGGAGTTGAAATCGTGGATG
2525172 GCCTCTTCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (43 bp):
GGTACAATATCCTCCATTGTGGAGTTGAAATCGTGGATGTGTG
Found at i:2525376 original size:110 final size:110
Alignment explanation
Indices: 2525249--2525727 Score: 771
Period size: 110 Copynumber: 4.3 Consensus size: 110
2525239 TATTGTTTCA
* * * * *
2525249 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAT-AAAATTAGGAAGTTGTTTATTG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA-AAAGTTGTTTGTTG
*
2525313 ACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
65 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
*
2525359 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTTG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTG-TTG
* * *
2525424 ATAGTCATTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTCTCTCG
65 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
* * * * *
2525470 AGTCTAATATCCTTCACTGTGAAGTTTAAATTGACTCTAAAGGAAACTGAAAAGTTGTTTGTTGA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
*
2525535 CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTATGTTGTCTCG
66 CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
*
2525580 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
*
2525645 CAGTCAGTTGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
66 CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
2525690 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
2525728 AAAAGATGTA
Statistics
Matches: 338, Mismatches: 29, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
110 233 0.69
111 105 0.31
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (110 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
Found at i:2525527 original size:221 final size:220
Alignment explanation
Indices: 2525249--2525730 Score: 779
Period size: 221 Copynumber: 2.2 Consensus size: 220
2525239 TATTGTTTCA
* * * * *
2525249 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATAAAATTAGGAAGTTGTTTATTGA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAAGAAAATGAGAAAGTTGTTTATTGA
*
2525314 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGT
66 CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTATGTTGTCTCGAGTCCAATATCCTTCGCTGT
*
2525379 GAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTTGATAGTCA-TTCGCCCCTTCG
131 GAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTG-TTGACAGTCAGTT-GCCCCTTCG
2525443 CTGTGAAGTTGAGCTTGTGTTCTCTCG
194 CTGTGAAGTTGAGCTTGTGTTCTCTCG
* * * * *
2525470 AGTCTAATATCCTTCACTGTGAAGTTTAAATTGACTCTAAAGGAAACTGA-AAAGTTGTTTGTTG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAA-GAAAATGAGAAAGTTGTTTATTG
* *
2525534 ACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTATGTTGTCTCGAGTCCAATATCCTTCGTTG
65 ACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTATGTTGTCTCGAGTCCAATATCCTTCGCTG
*
2525599 TGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTTGCCCCTTCGC
130 TGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTTGCCCCTTCGC
*
2525664 TGTGAAGTTGAGCTTGTGTTGTCTCG
195 TGTGAAGTTGAGCTTGTGTTCTCTCG
2525690 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAA
2525731 AGATGTAAAA
Statistics
Matches: 240, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
220 82 0.34
221 153 0.64
222 5 0.02
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (220 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAAGAAAATGAGAAAGTTGTTTATTGA
CAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTATGTTGTCTCGAGTCCAATATCCTTCGCTGT
GAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAGTTGCCCCTTCGCT
GTGAAGTTGAGCTTGTGTTCTCTCG
Found at i:2527540 original size:37 final size:37
Alignment explanation
Indices: 2527496--2527570 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2527486 TAGATATGTG
2527496 AATGTAATAAAAAAGAGAAAAGTAATGCGAAATATGC
1 AATGTAATAAAAAAGAGAAAAGTAATGCGAAATATGC
2527533 AATGTAATAAAAAAGAGAAAAGTAATGCGAAATATGC
1 AATGTAATAAAAAAGAGAAAAGTAATGCGAAATATGC
2527570 A
1 A
2527571 GGAATGCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (37 bp):
AATGTAATAAAAAAGAGAAAAGTAATGCGAAATATGC
Found at i:2529455 original size:14 final size:14
Alignment explanation
Indices: 2529420--2529462 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
2529410 AGAATAATAT
2529420 TAATATTAATAT--
1 TAATATTAATATAA
2529432 TAATATTAATATAA
1 TAATATTAATATAA
* *
2529446 TAATACTAATAAAA
1 TAATATTAATATAA
2529460 TAA
1 TAA
2529463 AATAGATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 12 0.44
14 15 0.56
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATATTAATATAA
Found at i:2529485 original size:9 final size:9
Alignment explanation
Indices: 2529471--2529496 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2529461 AAAATAGATG
2529471 AATAAAAAT
1 AATAAAAAT
2529480 AATAAAAAT
1 AATAAAAAT
2529489 AATAAAAA
1 AATAAAAA
2529497 ACGAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AATAAAAAT
Found at i:2529496 original size:19 final size:19
Alignment explanation
Indices: 2529483--2529525 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2529473 TAAAAATAAT
2529483 AAAAATAATAAAAAACGAA
1 AAAAATAATAAAAAACGAA
* *
2529502 ATAAATAATAAAAAAAGAA
1 AAAAATAATAAAAAACGAA
2529521 AAAAA
1 AAAAA
2529526 ATGCAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAAATAATAAAAAACGAA
Found at i:2529512 original size:3 final size:3
Alignment explanation
Indices: 2529412--2529493 Score: 62
Period size: 3 Copynumber: 27.7 Consensus size: 3
2529402 AAAGGAAAAG
* * * * *
2529412 AAT AAT ATT AAT ATT AAT ATT AAT ATT AAT -AT AAT AAT ACT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2529458 AAT AA- AAT AGAT GAAT AAA AAT AAT AAA AAT AAT AA
1 AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AA
2529494 AAAACGAAAT
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
2 6 0.10
3 49 0.82
4 4 0.07
5 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2530824 original size:30 final size:30
Alignment explanation
Indices: 2530779--2530835 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2530769 ATTTAAAAAA
* *
2530779 ATATTTTTCAAAACTATATAATATATATAT
1 ATATATTTAAAAACTATATAATATATATAT
*
2530809 ATATATTTAAAAACTATATATTATATA
1 ATATATTTAAAAACTATATAATATATA
2530836 ATTTTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (30 bp):
ATATATTTAAAAACTATATAATATATATAT
Found at i:2532078 original size:62 final size:62
Alignment explanation
Indices: 2531981--2532107 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
2531971 TGCAATGATC
2531981 TTCCATGACATGTACAACCCTTATAAAATTTTTAAAAAATAGATACTCCTTTTTATAAATAT
1 TTCCATGACATGTACAACCCTTATAAAATTTTTAAAAAATAGATACTCCTTTTTATAAATAT
2532043 TTCCATGACATGTACAACCCTTATAAAATTTTTAAAAAATAGATACTCCTTTTTATAAATAT
1 TTCCATGACATGTACAACCCTTATAAAATTTTTAAAAAATAGATACTCCTTTTTATAAATAT
2532105 TTC
1 TTC
2532108 TTCTTCTTCT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (62 bp):
TTCCATGACATGTACAACCCTTATAAAATTTTTAAAAAATAGATACTCCTTTTTATAAATAT
Found at i:2532113 original size:3 final size:3
Alignment explanation
Indices: 2532105--2533422 Score: 1598
Period size: 3 Copynumber: 439.3 Consensus size: 3
2532095 TTATAAATAT
2532105 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2532153 TTC TTC TTC TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC
2532199 TT- TTC TTC TT- TTC TTC TTC TTC TTC TTTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC
2532243 TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC
*
2532288 TTC TTC TTTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTTC TTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC
2532335 TTC TTC -TC TTC TTC TT- TTC TTC TTTC TTC TTC TT- TCTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC T-TC TTC TTC
2532379 TTC TTTC TTC TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC -TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC
2532426 TTC TTC -TC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TT-
1 TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2532469 TCTC TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
2532514 TTT TTC TT- TCTC TTC TTC TTC TTC TTC TTC TTT TTC TTTC TTC TTC
1 TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
* *
2532560 TTC TTC -TC TTC TTT TTT TTC TTC TT- TTC TTC TT- TCTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC
*
2532603 TTC TTC TTC TTTC TTC TTC TTC TT- TTC TTC TTC TTC TTT TTC TTC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2532648 TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTTC TT- TTC TTC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC
*
2532694 TTC TTC TTC TTC TTC TTC -TC TTC TTC TTT TTC TCTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC
2532739 TTC TTC TT- TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC TT- TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* ** * * ** *** ** *
2532784 TTC TT- TTC TTC -TC ACTC AATGAA GTA GAC GGTTC AAA TGA TATC TCC
1 TTC TTC TTC TTC TTC -TTC --T-TC TTC TTC --TTC TTC TTC T-TC TTC
*** *
2532831 GAA TAAC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2532877 TTC TTC TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC
2532922 TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2532968 TTTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC
1 -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
2533013 TTC TTC TCTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
2533059 TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTA TTC TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2533105 TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2533151 TTTC TTC TTC TTC TT- TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
2533195 TTC -TC TTT TTC TTC TTTC TTC TTC TTC TTC TTC TTC -TC TTC TTC
1 TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* ** * * ** *** ** *
2533239 TTC TTC TTC TTC -TC ACTC AATGAA GTA GAC GGTTC AAA TGA TAC -TC
1 TTC TTC TTC TTC TTC -TTC --T-TC TTC TTC --TTC TTC TTC TTC TTC
* *** *
2533285 TCC GAA TAAC TTC TT- TTC TTC TTC TTC TTC TTC TTC TT- TTC TTTC
1 TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC
*
2533330 TTC TTA TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2533377 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2533423 CACTCAATGA
Statistics
Matches: 1173, Mismatches: 67, Indels: 150
0.84 0.05 0.11
Matches are distributed among these distances:
2 73 0.06
3 1023 0.87
4 73 0.06
5 4 0.00
ACGTcount: A:0.03, C:0.31, G:0.01, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:2537613 original size:20 final size:20
Alignment explanation
Indices: 2537580--2537620 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2537570 TAATTTAATT
* *
2537580 TAAATTAAATAAATATTAAA
1 TAAATAAAAGAAATATTAAA
*
2537600 TAAATAAAAGAAATTTTAAA
1 TAAATAAAAGAAATATTAAA
2537620 T
1 T
2537621 TAATTGAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAATAAAAGAAATATTAAA
Found at i:2539054 original size:7 final size:7
Alignment explanation
Indices: 2539028--2539165 Score: 94
Period size: 7 Copynumber: 19.6 Consensus size: 7
2539018 TTAAATAAAA
2539028 ATATAAT
1 ATATAAT
* *
2539035 AAAAAAT
1 ATATAAT
*
2539042 AAATAAT
1 ATATAAT
2539049 ATATAAT
1 ATATAAT
2539056 ATAT-AT
1 ATATAAT
2539062 AATATACCAT
1 -ATATA--AT
2539072 A-AT-AT
1 ATATAAT
2539077 AATATAAT
1 -ATATAAT
2539085 ATATAAT
1 ATATAAT
2539092 ATAT-AT
1 ATATAAT
2539098 AATATAAT
1 -ATATAAT
2539106 ACTAT-AT
1 A-TATAAT
2539113 ACTATAAT
1 A-TATAAT
2539121 ATA-ATAT
1 ATATA-AT
2539128 ATATACA-
1 ATATA-AT
2539135 ATATAAT
1 ATATAAT
2539142 ATATAAT
1 ATATAAT
*
2539149 ATA-CAT
1 ATATAAT
*
2539155 ATATATT
1 ATATAAT
2539162 ATAT
1 ATAT
2539166 TTTTAAAAAC
Statistics
Matches: 108, Mismatches: 8, Indels: 30
0.74 0.05 0.21
Matches are distributed among these distances:
5 2 0.02
6 12 0.11
7 77 0.71
8 14 0.13
9 1 0.01
10 2 0.02
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (7 bp):
ATATAAT
Found at i:2539085 original size:36 final size:34
Alignment explanation
Indices: 2539028--2539165 Score: 153
Period size: 36 Copynumber: 4.1 Consensus size: 34
2539018 TTAAATAAAA
2539028 ATATAATA-AA-AA-ATAA-ATAATATATAATAT
1 ATATAATATAATAATATAATATAATATATAATAT
2539058 ATATAATATACCATAATATAATATAATATATAATAT
1 ATATAATATA--ATAATATAATATAATATATAATAT
*
2539094 ATATAATATAATACTATATACTATAATATA-ATATAT
1 ATATAATATAATA--ATATAATATAATATATA-ATAT
* *
2539130 ATACAATATAAT-ATATAATATACATATATATTAT
1 ATATAATATAATAATATAATATA-ATATATAATAT
2539164 AT
1 AT
2539166 TTTTAAAAAC
Statistics
Matches: 93, Mismatches: 4, Indels: 18
0.81 0.03 0.16
Matches are distributed among these distances:
30 8 0.09
31 1 0.01
33 10 0.11
34 15 0.16
35 6 0.06
36 53 0.57
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (34 bp):
ATATAATATAATAATATAATATAATATATAATAT
Found at i:2539151 original size:5 final size:5
Alignment explanation
Indices: 2539027--2539144 Score: 100
Period size: 5 Copynumber: 23.2 Consensus size: 5
2539017 CTTAAATAAA
* * **
2539027 AATAT AATAA AAAAT AA-AT AATAT -ATAAT ATATAT AATAT ACCAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AAT-AT A-ATAT AATAT AATAT AATAT
*
2539077 AATAT AATAT -ATAAT ATATAT AATAT AATACT -ATAT ACTAT AATAT
1 AATAT AATAT AAT-AT A-ATAT AATAT AATA-T AATAT AATAT AATAT
*
2539123 AATAT ATATAC AATAT AATAT A
1 AATAT A-ATAT AATAT AATAT A
2539145 TAATATACAT
Statistics
Matches: 92, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
4 9 0.10
5 68 0.74
6 11 0.12
7 4 0.04
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:2539179 original size:20 final size:21
Alignment explanation
Indices: 2539153--2539207 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
2539143 TATAATATAC
2539153 ATATATATTATATTTT-TAAA
1 ATATATATTATATTTTCTAAA
* *
2539173 A-ACTATAATATGTTTTCTAAA
1 ATA-TATATTATATTTTCTAAA
2539194 ATTATATATTATAT
1 A-TATATATTATAT
2539208 ATGTTTCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
19 1 0.04
20 12 0.44
21 5 0.19
22 8 0.30
23 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (21 bp):
ATATATATTATATTTTCTAAA
Found at i:2539245 original size:36 final size:35
Alignment explanation
Indices: 2539191--2539322 Score: 138
Period size: 36 Copynumber: 3.6 Consensus size: 35
2539181 TATGTTTTCT
*
2539191 AAAATTATATATTATATATGTTTCCAAAAACCGTTTTA
1 AAAACTATATA-T-TATATGTTT-CAAAAACCGTTTTA
* ** *
2539229 AAAATTATATATTATATGCTTTCAAAAACTATTTTTT
1 AAAACTATATATTATATG-TTTCAAAAAC-CGTTTTA
* *
2539266 AAAACTATATATTATATGTTTAAAAAAATCGTTTTA
1 AAAACTATATATTATATGTTT-CAAAAACCGTTTTA
*
2539302 AAAACTATATATTACATGTTT
1 AAAACTATATATTATATGTTT
2539323 TCATAAAATA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
36 40 0.49
37 30 0.37
38 11 0.14
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (35 bp):
AAAACTATATATTATATGTTTCAAAAACCGTTTTA
Found at i:2539293 original size:73 final size:75
Alignment explanation
Indices: 2539185--2539355 Score: 206
Period size: 73 Copynumber: 2.3 Consensus size: 75
2539175 CTATAATATG
* ** * *
2539185 TTTTCTAAAATTATATATTATATATGTTTCCAAAAACCGTTTTAAAAATTATATATTATATGCTT
1 TTTTCTAAAACTATATATTATATATGTTTAAAAAAACCGTTTTAAAAACTATATATTACATGCTT
2539250 TCA-AAAACTA
66 TCATAAAA-TA
* * *
2539260 TTTTTTAAAACTATATA-T-TATATGTTTAAAAAAATCGTTTTAAAAACTATATATTACATGTTT
1 TTTTCTAAAACTATATATTATATATGTTTAAAAAAACCGTTTTAAAAACTATATATTACATGCTT
2539323 TCATAAAATA
66 TCATAAAATA
* *
2539333 TTTTCGAAAGCTATACTA-TATAT
1 TTTTCTAAAACTATA-TATTATAT
2539356 CTTCAAAACT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
73 56 0.68
74 8 0.10
75 18 0.22
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (75 bp):
TTTTCTAAAACTATATATTATATATGTTTAAAAAAACCGTTTTAAAAACTATATATTACATGCTT
TCATAAAATA
Found at i:2551418 original size:19 final size:20
Alignment explanation
Indices: 2551370--2551418 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2551360 GTAAATAAAT
*
2551370 AATTAAAATAAAATAAAAGA
1 AATTTAAATAAAATAAAAGA
*
2551390 ATTATTAAAT-AAATAAAAGA
1 AAT-TTAAATAAAATAAAAGA
2551410 AATTTAAAT
1 AATTTAAAT
2551419 TAATTGAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.24
20 14 0.56
21 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
AATTTAAATAAAATAAAAGA
Found at i:2561616 original size:22 final size:22
Alignment explanation
Indices: 2561575--2561624 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
2561565 ATATATATAT
2561575 AAATAAAAAATAAAGTATAAAT-G
1 AAATAAAAAATAAAG-AT-AATGG
2561598 AAATAAAAAATAATA-ATAATGG
1 AAATAAAAAATAA-AGATAATGG
2561620 AAATA
1 AAATA
2561625 TAAGTAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 13 0.52
24 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (22 bp):
AAATAAAAAATAAAGATAATGG
Found at i:2562136 original size:35 final size:35
Alignment explanation
Indices: 2562097--2562168 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
2562087 TTAAAAAACC
*
2562097 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
2562132 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
2562167 CT
1 CT
2562169 TCTTTGTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (35 bp):
CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:2563067 original size:109 final size:109
Alignment explanation
Indices: 2562623--2563056 Score: 751
Period size: 109 Copynumber: 4.0 Consensus size: 109
2562613 CCAATACAAG
* **
2562623 TTAAAATCGACTCTGAAATTGGGAAGTTGTTTGTTGACAACCAATCGTCCCTTCGTTGTGAAGTT
1 TTAAAATCGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
* ** *
2562688 GAACTTGTGTTGTCTCGGGTAGCACAATATCCTCCACCGTGCAA
66 GAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAA
2562732 TTAAAATCGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
1 TTAAAATCGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
*
2562797 GAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAG
66 GAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAA
*
2562841 TTAAAATCGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTT
1 TTAAAATCGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
*
2562906 GAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTTGTGGAA
66 GAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAA
* * *
2562950 TTGAAATCGGCTCTAAAATTGGGAAGTTGTTTGTCGACAACCAGCCGTCCCTTCGTTGTGAAGTT
1 TTAAAATCGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
2563015 GAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGG
66 GAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGG
2563057 GGTTGAAATC
Statistics
Matches: 309, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 309 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (109 bp):
TTAAAATCGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTT
GAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAA
Found at i:2563979 original size:16 final size:16
Alignment explanation
Indices: 2563967--2563997 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2563957 TTATTTTTTG
2563967 TTCTTTCTCTTTTTCT
1 TTCTTTCTCTTTTTCT
*
2563983 TTTTTTCTCTTTTTC
1 TTCTTTCTCTTTTTC
2563998 AATTTTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTTCTCTTTTTCT
Found at i:2564003 original size:16 final size:16
Alignment explanation
Indices: 2563970--2564004 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2563960 TTTTTTGTTC
**
2563970 TTTCTCTTTTTCTTTT
1 TTTCTCTTTTTCAATT
2563986 TTTCTCTTTTTCAATT
1 TTTCTCTTTTTCAATT
2564002 TTT
1 TTT
2564005 TCAATTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTCTTTTTCAATT
Found at i:2574499 original size:14 final size:14
Alignment explanation
Indices: 2574480--2574526 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
2574470 AAATAACACG
* *
2574480 GATAAACAAAATGA
1 GATAAAAAAAATAA
2574494 GATAAAAAAAATAA
1 GATAAAAAAAATAA
*
2574508 GA-AAATAAAATAA
1 GATAAAAAAAATAA
2574521 G-TAAAA
1 GATAAAA
2574527 GTAAAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 14 0.50
14 14 0.50
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (14 bp):
GATAAAAAAAATAA
Found at i:2574532 original size:32 final size:33
Alignment explanation
Indices: 2574496--2574557 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2574486 CAAAATGAGA
*
2574496 TAAAAA-AAATAAGAAAATAAAATAA-GTAAAAG
1 TAAAAATAAACAAGAAAA-AAAATAACGTAAAAG
2574528 TAAAAATAAACAAGAAAAAAAATAACGTAA
1 TAAAAATAAACAAGAAAAAAAATAACGTAA
2574558 CGAATCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (33 bp):
TAAAAATAAACAAGAAAAAAAATAACGTAAAAG
Found at i:2576956 original size:19 final size:20
Alignment explanation
Indices: 2576929--2576966 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2576919 CAGTTCGCGC
*
2576929 TTTGCTATTATTGT-TTGTG
1 TTTGATATTATTGTGTTGTG
2576948 TTTGATATTATTGTGTTGT
1 TTTGATATTATTGTGTTGT
2576967 TGCTTCAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.13, C:0.03, G:0.21, T:0.63
Consensus pattern (20 bp):
TTTGATATTATTGTGTTGTG
Found at i:2580184 original size:13 final size:13
Alignment explanation
Indices: 2580166--2580194 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2580156 TTCAGCTCAT
2580166 GGCAAAGCATAAA
1 GGCAAAGCATAAA
2580179 GGCAAAGCATAAA
1 GGCAAAGCATAAA
2580192 GGC
1 GGC
2580195 TCATTTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.17, G:0.28, T:0.07
Consensus pattern (13 bp):
GGCAAAGCATAAA
Found at i:2584566 original size:2 final size:2
Alignment explanation
Indices: 2584559--2584600 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2584549 TTTATACTCG
2584559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2584601 TATCTCAACG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2584729 original size:3 final size:3
Alignment explanation
Indices: 2584721--2584755 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2584711 TTAGTACTAT
2584721 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2584756 GAAGAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2584832 original size:22 final size:22
Alignment explanation
Indices: 2584800--2584841 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2584790 AGATTTAATG
2584800 AAAAAATTA-TTAAAAAAAAGA
1 AAAAAATTATTTAAAAAAAAGA
*
2584821 AAAATAATTATTTAAAGAAAA
1 AAAA-AATTATTTAAAAAAAA
2584842 TAATAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 5 0.28
23 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAAAATTATTTAAAAAAAAGA
Found at i:2589047 original size:89 final size:90
Alignment explanation
Indices: 2588896--2589063 Score: 230
Period size: 89 Copynumber: 1.9 Consensus size: 90
2588886 GAAATTACTG
* * * *
2588896 TTTAGTCCATTAACTTTATGTTTTAGCTATTTTAGTCATTTAAGTTTCGATTTTTATTATTTTAG
1 TTTAGTCCATTAACTTTATGTTTTAGCTATTTTAGTCATGTAACTTTCGATTTTTACTATTTTAA
*
2588961 TCTTTTAA-TTTCTTTTAATACCAA
66 TCCTTTAAGTTTCTTTTAATACCAA
* * ** * *
2588985 TTTAGTCCCTTAACTTTCTGTTTTTTCTATTTTAGTCGTGTAACTTTCTATTTTTACTATTTTAA
1 TTTAGTCCATTAACTTTATGTTTTAGCTATTTTAGTCATGTAACTTTCGATTTTTACTATTTTAA
2589050 TCCTTTAAGTTTCT
66 TCCTTTAAGTTTCT
2589064 GTTTTTGTTG
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 62 0.93
90 5 0.07
ACGTcount: A:0.21, C:0.14, G:0.08, T:0.57
Consensus pattern (90 bp):
TTTAGTCCATTAACTTTATGTTTTAGCTATTTTAGTCATGTAACTTTCGATTTTTACTATTTTAA
TCCTTTAAGTTTCTTTTAATACCAA
Found at i:2589069 original size:30 final size:30
Alignment explanation
Indices: 2588896--2589115 Score: 171
Period size: 30 Copynumber: 7.4 Consensus size: 30
2588886 GAAATTACTG
* *
2588896 TTTAGTCCATTAACTTTATG-TTTTAGCTAT
1 TTTAGTCCTTTAACTTTCTGTTTTTA-CTAT
* * *
2588926 TTTAGTCATTTAAGTTTC-GATTTTTATTAT
1 TTTAGTCCTTTAACTTTCTG-TTTTTACTAT
* * * *
2588956 TTTAGTCTTTTAA-TTTCT-TTTAATACCAA
1 TTTAGTCCTTTAACTTTCTGTTT-TTACTAT
* *
2588985 TTTAGTCCCTTAACTTTCTGTTTTTTCTAT
1 TTTAGTCCTTTAACTTTCTGTTTTTACTAT
* * *
2589015 TTTAGTCGTGTAACTTTCTATTTTTACTAT
1 TTTAGTCCTTTAACTTTCTGTTTTTACTAT
* * ** *
2589045 TTTAATCCTTTAAGTTTCTGTTTTTGTTGT
1 TTTAGTCCTTTAACTTTCTGTTTTTACTAT
* * *
2589075 TTTAGTCCTGTAAATTTCTGTTTTTGCTA-
1 TTTAGTCCTTTAACTTTCTGTTTTTACTAT
*
2589104 TTTAGTCTTTTA
1 TTTAGTCCTTTA
2589116 TTTTACTAAG
Statistics
Matches: 148, Mismatches: 36, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
28 3 0.02
29 29 0.20
30 108 0.73
31 8 0.05
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.58
Consensus pattern (30 bp):
TTTAGTCCTTTAACTTTCTGTTTTTACTAT
Found at i:2592962 original size:23 final size:23
Alignment explanation
Indices: 2592930--2592992 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
2592920 CCTGTGGGGG
*
2592930 GAATCAGTTCCCCTTCAAAGAGC
1 GAATCGGTTCCCCTTCAAAGAGC
* * *
2592953 GAATCGGTTCCCCCTC-AAGGGG
1 GAATCGGTTCCCCTTCAAAGAGC
* *
2592975 GTATCGATTCCCCTTCAA
1 GAATCGGTTCCCCTTCAA
2592993 GGGGGGTATC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (23 bp):
GAATCGGTTCCCCTTCAAAGAGC
Found at i:2593001 original size:23 final size:23
Alignment explanation
Indices: 2592906--2593009 Score: 92
Period size: 23 Copynumber: 4.7 Consensus size: 23
2592896 GAACCCTCAA
2592906 GGGGTATCGATTCCCCTGT---GG
1 GGGGTATCGATTCCCCT-TCAAGG
* *
2592927 GGGGAATC-AGTTCCCCTTCAAAG
1 GGGGTATCGA-TTCCCCTTCAAGG
* * * * *
2592950 AGCGAATCGGTTCCCCCTCAA-G
1 GGGGTATCGATTCCCCTTCAAGG
2592972 GGGGTATCGATTCCCCTTCAAGG
1 GGGGTATCGATTCCCCTTCAAGG
2592995 GGGGTATCGATTCCC
1 GGGGTATCGATTCCC
2593010 TCTACACTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.03
21 14 0.21
22 17 0.26
23 33 0.50
ACGTcount: A:0.18, C:0.28, G:0.30, T:0.24
Consensus pattern (23 bp):
GGGGTATCGATTCCCCTTCAAGG
Found at i:2593009 original size:45 final size:45
Alignment explanation
Indices: 2592906--2593009 Score: 104
Period size: 45 Copynumber: 2.3 Consensus size: 45
2592896 GAACCCTCAA
***
2592906 GGGGTATCGATT-CCCCTGTGGGGGGAATCAGTTCCCCTTCAAAG
1 GGGGTATCGATTCCCCCTCAAGGGGGAATCAGTTCCCCTTCAAAG
* * * * * *
2592950 AGCGAATCGGTTCCCCCTCAAGGGGGTATC-GATTCCCCTTCAAGG
1 GGGGTATCGATTCCCCCTCAAGGGGGAATCAG-TTCCCCTTCAAAG
2592995 GGGGTATCGATTCCC
1 GGGGTATCGATTCCC
2593010 TCTACACTAA
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
44 9 0.20
45 36 0.80
ACGTcount: A:0.18, C:0.28, G:0.30, T:0.24
Consensus pattern (45 bp):
GGGGTATCGATTCCCCCTCAAGGGGGAATCAGTTCCCCTTCAAAG
Found at i:2596835 original size:22 final size:21
Alignment explanation
Indices: 2596793--2596832 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2596783 GATCTTATTT
*
2596793 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2596814 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2596833 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2603303 original size:64 final size:64
Alignment explanation
Indices: 2603187--2603323 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 64
2603177 TTCAATGTGT
* * *
2603187 ATCGATGCA-CTCTTAAATAAATAAACATCGAATACAATTAGTGCATCGATGCATA-AGGAGTGC
1 ATCGATGCACCTCTTAAATAAACAAACATCGAATACAATTAGTGCACCAATGCATAGAGG-GTGC
* * * *
2603250 ATCGATGCACCTGCTTAAA-ATACAAACATCGAATGAGATTTA-TGCACCAATGCATAGATGGTG
1 ATCGATGCACCT-CTTAAATAAACAAACATCGAAT-ACAATTAGTGCACCAATGCATAGAGGGTG
2603313 C
64 C
2603314 ATCGATGCAC
1 ATCGATGCAC
2603324 TCATCAAGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
63 9 0.14
64 41 0.65
65 13 0.21
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (64 bp):
ATCGATGCACCTCTTAAATAAACAAACATCGAATACAATTAGTGCACCAATGCATAGAGGGTGC
Found at i:2616827 original size:17 final size:18
Alignment explanation
Indices: 2616801--2616843 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2616791 GTTTGTTAGG
2616801 AGTGGTTCTTT-GGGACAT
1 AGTGG-TCTTTAGGGACAT
2616819 AGTGGTCTTTAGGGACAT
1 AGTGGTCTTTAGGGACAT
*
2616837 ATTGGTC
1 AGTGGTC
2616844 CTTCAAGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.19, C:0.12, G:0.33, T:0.37
Consensus pattern (18 bp):
AGTGGTCTTTAGGGACAT
Found at i:2620259 original size:33 final size:33
Alignment explanation
Indices: 2620217--2620283 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
2620207 TCTAGTACAG
*
2620217 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACAGATT
* *
2620250 ATGGTGGACATGTCCTTATGTGTCATACAGATT
1 ATGGTGGACACGACCTTATGTGTCATACAGATT
2620283 A
1 A
2620284 GCACTACGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACAGATT
Found at i:2620371 original size:20 final size:20
Alignment explanation
Indices: 2620343--2620385 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2620333 TATATTGGGC
* *
2620343 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
2620363 TATTTTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
2620383 TAT
1 TAT
2620386 GGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.58
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:2620456 original size:43 final size:43
Alignment explanation
Indices: 2620382--2620530 Score: 165
Period size: 44 Copynumber: 3.4 Consensus size: 43
2620372 TGGTATATGG
* * * * ** *
2620382 TTATGGAATAATGGCAAGTGTATGGGTAAAATAAGCTTACAATC
1 TTATGGAAAAATGGTAA-CGTATTGGTAAAATAAGCTTATGAGC
2620426 TTATGGAACAAATGGTAA-GTATTGGTAAAATAAGCTTATGAGC
1 TTATGGAA-AAATGGTAACGTATTGGTAAAATAAGCTTATGAGC
* *
2620469 TTATGGAATAATGGTAACTATATTGGTAAAATAAGCTTATGAGC
1 TTATGGAAAAATGGTAAC-GTATTGGTAAAATAAGCTTATGAGC
*
2620513 TTATGGGATAAATGGTAA
1 TTAT-GGAAAAATGGTAA
2620531 ATATATTGGA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
42 8 0.09
43 29 0.32
44 36 0.40
45 18 0.20
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (43 bp):
TTATGGAAAAATGGTAACGTATTGGTAAAATAAGCTTATGAGC
Found at i:2625087 original size:18 final size:18
Alignment explanation
Indices: 2625064--2625116 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
2625054 GTTATTTAGG
*
2625064 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
* *
2625082 AGTGGTCTTTCAGGACAT
1 AGTGGTCATTCGGGACAT
* *
2625100 AGTTGTCATTCGAGACA
1 AGTGGTCATTCGGGACA
2625117 AATCCTAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:2626525 original size:31 final size:31
Alignment explanation
Indices: 2626454--2626531 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
2626444 ACTGATACTC
* * *
2626454 ATGTGCATTATCTGAATGCAAACCCGACATA
1 ATGTGCATTATCTGAAAGCAAACCCGAAACA
* * *
2626485 ATGTACATTATCTGAAAGCGAACCTGAAACA
1 ATGTGCATTATCTGAAAGCAAACCCGAAACA
* *
2626516 TTGTGCATTATTTGAA
1 ATGTGCATTATCTGAA
2626532 TACAATTTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (31 bp):
ATGTGCATTATCTGAAAGCAAACCCGAAACA
Found at i:2628940 original size:18 final size:19
Alignment explanation
Indices: 2628911--2628946 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2628901 TGCAATGCAT
2628911 CACATTCGCATATCACATC
1 CACATTCGCATATCACATC
2628930 CACATTC-CATATCACAT
1 CACATTCGCATATCACAT
2628947 TTCTTATCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (19 bp):
CACATTCGCATATCACATC
Found at i:2631324 original size:45 final size:44
Alignment explanation
Indices: 2631252--2631343 Score: 130
Period size: 45 Copynumber: 2.1 Consensus size: 44
2631242 ATTATGCCAT
* *
2631252 TTTCATTTTGACATTCTTTTATGCCTTTTATACAATATTATACA
1 TTTCATTTTGACATCCTTTCATGCCTTTTATACAATATTATACA
* * *
2631296 TTTCATTTATGGCATCCTTTCATTCCTTTTATACATTATTATACA
1 TTTCATTT-TGACATCCTTTCATGCCTTTTATACAATATTATACA
2631341 TTT
1 TTT
2631344 TTATACATCT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 8 0.19
45 34 0.81
ACGTcount: A:0.25, C:0.17, G:0.04, T:0.53
Consensus pattern (44 bp):
TTTCATTTTGACATCCTTTCATGCCTTTTATACAATATTATACA
Found at i:2631929 original size:59 final size:59
Alignment explanation
Indices: 2631857--2632265 Score: 628
Period size: 59 Copynumber: 7.0 Consensus size: 59
2631847 TTTGTGTACA
* *
2631857 AAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTATCACACG
1 AAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACG
* * *
2631916 AAGTGCCCTATACGAAAATTCATACACTTAGCATGAATTTCTTAACATTTTATCACACG
1 AAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACG
* *
2631975 AAGTGCCCTATATGGAAATTCATACTCTTAGTATGAATTTCTTAACATTTTAGCACACG
1 AAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACG
* * * *
2632034 AAGTGACCTATACGGAAACTCATACACTTAGAATGAATTTCTTAACATTTTAGCACGC-
1 AAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACG
* * *
2632092 ACGTTCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACA
1 AAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACG
*
2632151 AAGTGCCCTATACGAAAATTCATACACTTAGTATGAATTTCTT-A-ATTTTAGCACACG
1 AAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACG
* *
2632208 AAGTGCCCTATACGGAAATTTATACACTTAGTAAT-AATTTCTTAACATTTTATCACAC
1 AAGTGCCCTATACGGAAATTCATACACTTAGT-ATGAATTTCTTAACATTTTAGCACAC
2632266 TTGGTGCATT
Statistics
Matches: 319, Mismatches: 27, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
57 50 0.16
58 56 0.18
59 213 0.67
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (59 bp):
AAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACG
Found at i:2632730 original size:95 final size:95
Alignment explanation
Indices: 2632631--2632812 Score: 283
Period size: 95 Copynumber: 1.9 Consensus size: 95
2632621 AATTCTATAT
* * *
2632631 TATGGTATCGATACCCCCTTCCGATATCGATACCAAATTTAGGTTAAATGTTTCCTGGTATCGAT
1 TATGGTACCGATACCCCCTTCCGATATCGATACCAAATTTAGATTAAATGTTGCCTGGTATCGAT
2632696 ACCCTTACAATGGTATCGATACTACAATAC
66 ACCCTTACAATGGTATCGATACTACAATAC
* * ** *
2632726 TATGGTACCGATACCCCCTTCTGATATCGATGCCAAATTTAGATTCGATGTTGCTTGGTATCGAT
1 TATGGTACCGATACCCCCTTCCGATATCGATACCAAATTTAGATTAAATGTTGCCTGGTATCGAT
*
2632791 ACCCTTACCATGGTATCGATAC
66 ACCCTTACAATGGTATCGATAC
2632813 CCTTACCATG
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 78 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (95 bp):
TATGGTACCGATACCCCCTTCCGATATCGATACCAAATTTAGATTAAATGTTGCCTGGTATCGAT
ACCCTTACAATGGTATCGATACTACAATAC
Found at i:2632806 original size:20 final size:20
Alignment explanation
Indices: 2632781--2632832 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2632771 CGATGTTGCT
2632781 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCTTACCA
2632801 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCTTACCA
2632821 TGGTATCGATAC
1 TGGTATCGATAC
2632833 TACCTCATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (20 bp):
TGGTATCGATACCCTTACCA
Found at i:2632869 original size:21 final size:21
Alignment explanation
Indices: 2632843--2632895 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2632833 TACCTCATTG
*
2632843 GTATCGATATTGATAGAATCA
1 GTATCGATACTGATAGAATCA
*
2632864 GTATCGATACTGATTGAATCA
1 GTATCGATACTGATAGAATCA
*
2632885 ATATCGATACT
1 GTATCGATACT
2632896 ACTCATCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (21 bp):
GTATCGATACTGATAGAATCA
Found at i:2633880 original size:21 final size:21
Alignment explanation
Indices: 2633792--2633880 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 21
2633782 ACCCTATCTT
* * *
2633792 TGGTATGAATACAAGTTCAAC
1 TGGTATGGATACTAGTTCATC
* *
2633813 TGGTATGGACATTAGTTCATC
1 TGGTATGGATACTAGTTCATC
** * *
2633834 AT-GTATGGATA--ACGACCCTT
1 -TGGTATGGATACTA-GTTCATC
2633854 TGGTATGGATACTAGTTCATC
1 TGGTATGGATACTAGTTCATC
2633875 TGGTAT
1 TGGTAT
2633881 CGAACAAGTG
Statistics
Matches: 49, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
19 2 0.04
20 12 0.24
21 33 0.67
22 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (21 bp):
TGGTATGGATACTAGTTCATC
Found at i:2638105 original size:48 final size:47
Alignment explanation
Indices: 2638027--2638117 Score: 137
Period size: 48 Copynumber: 1.9 Consensus size: 47
2638017 ATAACAATAT
* *
2638027 ATTATTTTTTAGTAATATGCCAGTAAAATTGTTAACTTTTTAACGAC
1 ATTATTTTTTAGTAATATGCCAATAAAATTGTCAACTTTTTAACGAC
* *
2638074 ATTATTTTTTTAGTAATATGTCAATATAATTGTCAACTTTTTAA
1 ATTA-TTTTTTAGTAATATGCCAATAAAATTGTCAACTTTTTAA
2638118 TGGCATAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 4 0.10
48 35 0.90
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (47 bp):
ATTATTTTTTAGTAATATGCCAATAAAATTGTCAACTTTTTAACGAC
Found at i:2641387 original size:30 final size:31
Alignment explanation
Indices: 2641325--2641428 Score: 140
Period size: 31 Copynumber: 3.4 Consensus size: 31
2641315 TAAGACGACC
*
2641325 CTTGGGTAGGCCCTGTGGCCCTGATATCTTT
1 CTTGGGTAGGCCCTGTGGCCCTGAGATCTTT
*
2641356 CTTGGGTAGGCCCTGTGG-CCTGAGATTTTT
1 CTTGGGTAGGCCCTGTGGCCCTGAGATCTTT
* *
2641386 CTTGGGTAGGCCCCTG-GCCCCAGAGAATCTTT
1 CTTGGGTAGG-CCCTGTGGCCCTGAG-ATCTTT
2641418 CTTGGGTAGGC
1 CTTGGGTAGGC
2641429 TTTCAGGCCT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
30 21 0.32
31 29 0.45
32 15 0.23
ACGTcount: A:0.12, C:0.25, G:0.32, T:0.32
Consensus pattern (31 bp):
CTTGGGTAGGCCCTGTGGCCCTGAGATCTTT
Found at i:2643607 original size:27 final size:27
Alignment explanation
Indices: 2643569--2643638 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
2643559 TCTAGTCCAG
* * *
2643569 TCACTGAGTCAACTTGATTGGGTCAAC
1 TCACCGAGTCAACTCGATTAGGTCAAC
2643596 TCACCGAGTCAACTCGATTAGGTCAAC
1 TCACCGAGTCAACTCGATTAGGTCAAC
2643623 TCACCGAGTCAACTCG
1 TCACCGAGTCAACTCG
2643639 TTAACTTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (27 bp):
TCACCGAGTCAACTCGATTAGGTCAAC
Found at i:2643608 original size:13 final size:13
Alignment explanation
Indices: 2643590--2643637 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
2643580 ACTTGATTGG
2643590 GTCAACTCACCGA
1 GTCAACTCACCGA
**
2643603 GTCAACTCGA-TTA
1 GTCAACTC-ACCGA
2643616 GGTCAACTCACCGA
1 -GTCAACTCACCGA
2643630 GTCAACTC
1 GTCAACTC
2643638 GTTAACTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (13 bp):
GTCAACTCACCGA
Found at i:2644821 original size:19 final size:19
Alignment explanation
Indices: 2644782--2644816 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2644772 AAGTAACCTC
2644782 AATGACTTCGGATTAAGTG
1 AATGACTTCGGATTAAGTG
2644801 AATGACTT-GGA-TAAGT
1 AATGACTTCGGATTAAGT
2644817 CTGAAAACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (19 bp):
AATGACTTCGGATTAAGTG
Found at i:2648375 original size:16 final size:17
Alignment explanation
Indices: 2648354--2648386 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2648344 ACAAATCTAA
2648354 ATAAAAAAT-ATTATTT
1 ATAAAAAATCATTATTT
*
2648370 ATAAAAATTCATTATTT
1 ATAAAAAATCATTATTT
2648387 GATCGTGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAAAAAATCATTATTT
Found at i:2649579 original size:10 final size:10
Alignment explanation
Indices: 2649566--2649626 Score: 68
Period size: 10 Copynumber: 5.7 Consensus size: 10
2649556 GTTCGTGAAC
*
2649566 GTTCGGTTAT
1 GTTCGTTTAT
2649576 GTTCGTTTAT
1 GTTCGTTTAT
*
2649586 GTTCATTCAGTTAT
1 GTTC-GT---TTAT
2649600 GTTCGTTTAT
1 GTTCGTTTAT
2649610 GTTCGTTTAT
1 GTTCGTTTAT
2649620 GTTCGTT
1 GTTCGTT
2649627 CATTTATGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
10 34 0.77
11 1 0.02
13 1 0.02
14 8 0.18
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.56
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:2649604 original size:34 final size:34
Alignment explanation
Indices: 2649566--2649636 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
2649556 GTTCGTGAAC
2649566 GTTCGGTTATGTTCGTTTATGTTCATTCAGTTAT
1 GTTCGGTTATGTTCGTTTATGTTCATTCAGTTAT
* * *
2649600 GTTCGTTTATGTTCGTTTATGTTCGTTCATTTAT
1 GTTCGGTTATGTTCGTTTATGTTCATTCAGTTAT
2649634 GTT
1 GTT
2649637 TAACTCAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (34 bp):
GTTCGGTTATGTTCGTTTATGTTCATTCAGTTAT
Found at i:2649627 original size:24 final size:24
Alignment explanation
Indices: 2649571--2649636 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
2649561 TGAACGTTCG
*
2649571 GTTATGTTCGTTTATGTTCATTCA
1 GTTACGTTCGTTTATGTTCATTCA
* * *
2649595 GTTATGTTCGTTTATGTTCGTTTA
1 GTTACGTTCGTTTATGTTCATTCA
*
2649619 TGTT-CGTTCATTTATGTT
1 -GTTACGTTCGTTTATGTT
2649637 TAACTCAATC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 34 0.92
25 3 0.08
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.58
Consensus pattern (24 bp):
GTTACGTTCGTTTATGTTCATTCA
Found at i:2651051 original size:42 final size:42
Alignment explanation
Indices: 2650989--2651105 Score: 216
Period size: 42 Copynumber: 2.8 Consensus size: 42
2650979 AACAATTATG
* *
2650989 AAACACATGTTATATCTTGCAGATGCTGCAATTATGATTAAT
1 AAACACATATTATATGTTGCAGATGCTGCAATTATGATTAAT
2651031 AAACACATATTATATGTTGCAGATGCTGCAATTATGATTAAT
1 AAACACATATTATATGTTGCAGATGCTGCAATTATGATTAAT
2651073 AAACACATATTATATGTTGCAGATGCTGCAATT
1 AAACACATATTATATGTTGCAGATGCTGCAATT
2651106 TGTAGTTCCG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Consensus pattern (42 bp):
AAACACATATTATATGTTGCAGATGCTGCAATTATGATTAAT
Found at i:2654003 original size:34 final size:34
Alignment explanation
Indices: 2653960--2654032 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
2653950 GTACAATAAC
** *
2653960 CACTCCAGGTGTTATGATCAAAAACAAAAATATG
1 CACTCCAGGTGCAATCATCAAAAACAAAAATATG
* *
2653994 CACTCCAGGTGCAATCATCAAATATAAAAATATG
1 CACTCCAGGTGCAATCATCAAAAACAAAAATATG
*
2654028 AACTC
1 CACTC
2654033 TATATGCAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (34 bp):
CACTCCAGGTGCAATCATCAAAAACAAAAATATG
Found at i:2654041 original size:34 final size:34
Alignment explanation
Indices: 2653976--2654045 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
2653966 AGGTGTTATG
* *
2653976 ATCAAAAACAAAAATATGCACTCCAGGTGCAATC
1 ATCAAAAACAAAAATATGAACTCCAGATGCAATC
* * * *
2654010 ATCAAATATAAAAATATGAACTCTATATGCAATC
1 ATCAAAAACAAAAATATGAACTCCAGATGCAATC
2654044 AT
1 AT
2654046 ATAATGTACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.24
Consensus pattern (34 bp):
ATCAAAAACAAAAATATGAACTCCAGATGCAATC
Found at i:2656466 original size:29 final size:31
Alignment explanation
Indices: 2656411--2656475 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
2656401 ATTTTTATCC
* *
2656411 CTAAACTTTTCCAAAGTTTATAATTTGGCCA
1 CTAAACTTTTCCAAAATTTACAATTTGGCCA
* *
2656442 CTAAAC-TTT-CAAAATTTACATTTTGGTCA
1 CTAAACTTTTCCAAAATTTACAATTTGGCCA
2656471 C-AAAC
1 CTAAAC
2656476 CAAAATTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.13
29 17 0.57
30 3 0.10
31 6 0.20
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (31 bp):
CTAAACTTTTCCAAAATTTACAATTTGGCCA
Found at i:2659088 original size:16 final size:16
Alignment explanation
Indices: 2659031--2659088 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
2659021 ACCCGACCCA
* *
2659031 AAATTTAGCGAAACCG
1 AAATTTAACCAAACCG
*
2659047 AAA-GTAACACAAACCG
1 AAATTTAAC-CAAACCG
*
2659063 AAATTAAACCAAACCG
1 AAATTTAACCAAACCG
*
2659079 AATTTTAACC
1 AAATTTAACC
2659089 CGATCCAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 3 0.09
16 27 0.82
17 3 0.09
ACGTcount: A:0.50, C:0.22, G:0.10, T:0.17
Consensus pattern (16 bp):
AAATTTAACCAAACCG
Found at i:2663289 original size:21 final size:21
Alignment explanation
Indices: 2663250--2663290 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2663240 TACTCATGAG
*
2663250 GTATCGATACTTAGAGGCTTA
1 GTATCGATACTAAGAGGCTTA
2663271 GTATCGATACTCAAG-GGCTT
1 GTATCGATACT-AAGAGGCTT
2663291 GATTAGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (21 bp):
GTATCGATACTAAGAGGCTTA
Found at i:2663343 original size:18 final size:20
Alignment explanation
Indices: 2663316--2663365 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2663306 GCCAATTTTT
*
2663316 GTATCCATACTCAT-GG-GA
1 GTATCGATACTCATGGGAGA
*
2663334 GTATCGATACTGATGGGAGA
1 GTATCGATACTCATGGGAGA
2663354 GTATCGATACTC
1 GTATCGATACTC
2663366 CCAATATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 12 0.44
19 2 0.07
20 13 0.48
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (20 bp):
GTATCGATACTCATGGGAGA
Done.