Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008374.1 Hibiscus syriacus cultivar Beakdansim tig00111131_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: 1731758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:245367 original size:41 final size:41
Alignment explanation
Indices: 245322--245417 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
245312 CGATTTTCCC
245322 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
245363 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
245404 AAATCGCAATGCGA
1 AATTCGCAATGCGA
245418 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:245371 original size:21 final size:20
Alignment explanation
Indices: 245325--245417 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
245315 TTTTCCCAAT
*
245325 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
245345 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
245365 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
245386 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
245407 TCGCAATGCGA
1 TCGCAATGCGA
245418 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:245430 original size:41 final size:41
Alignment explanation
Indices: 245344--245478 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
245334 GAATAAGTAA
* * *
245344 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
245385 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
245426 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
245467 TTCGCAACGCGA
1 ATCGCAACGCGA
245479 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:245431 original size:20 final size:20
Alignment explanation
Indices: 245406--245499 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
245396 AATTGGGAAA
*
245406 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
245426 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
245447 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
245467 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
245487 TTCGCAACGCGAT
1 ATCGCAACGCGAT
245500 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:246254 original size:20 final size:20
Alignment explanation
Indices: 246229--246279 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
246219 ATTCATTTGA
246229 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
246249 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
* *
246269 TTATCACAACG
1 CTATCGCAACG
246280 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (20 bp):
CTATCGCAACGTGAAAATGG
Found at i:246329 original size:14 final size:15
Alignment explanation
Indices: 246309--246381 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
246299 TGATAATCGC
246309 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
246324 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
246341 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
246359 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
246375 -TTGCGAT
1 ATTGCGAT
246382 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:246346 original size:19 final size:19
Alignment explanation
Indices: 246305--246371 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
246295 GAAATGATAA
246305 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
246321 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
246338 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
246356 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
246372 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:246506 original size:14 final size:14
Alignment explanation
Indices: 246487--246523 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
246477 CATCAATTAA
246487 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
246501 ACAAATCATCTTTT
1 ACAAATCAACATTT
246515 ACAAATCAA
1 ACAAATCAA
246524 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:249003 original size:20 final size:19
Alignment explanation
Indices: 248968--249034 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
248958 GAAACTTAAA
248968 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
248987 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
249007 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
249026 ATCGCAACG
1 ATCGCAACG
249035 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:249042 original size:14 final size:14
Alignment explanation
Indices: 249023--249080 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
249013 ATGCGAAATG
249023 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
249037 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
249053 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
249069 AAAATCGCAACG
1 AAAATCGCAACG
249081 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:249065 original size:32 final size:33
Alignment explanation
Indices: 249007--249085 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
248997 GGAAATGGCT
*
249007 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
249040 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
249072 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
249086 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:249114 original size:19 final size:17
Alignment explanation
Indices: 249092--249187 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
249082 GAAACACAAA
249092 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
249111 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
249127 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
249143 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
249159 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
249176 TCGCATTGCGAT
1 TCGC-TTGCGAT
249188 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:249133 original size:14 final size:14
Alignment explanation
Indices: 249114--249171 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
249104 TTTCATTTCG
249114 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
249128 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
249144 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
249160 CGTTGCGATTTT
1 CGTTGCGATTTT
249172 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:249178 original size:33 final size:33
Alignment explanation
Indices: 249097--249187 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
249087 ACAAATCGCA
249097 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
249130 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
249162 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
249188 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:249206 original size:20 final size:19
Alignment explanation
Indices: 249172--249226 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
249162 TTGCGATTTT
*
249172 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
249191 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
249211 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
249227 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:249313 original size:18 final size:19
Alignment explanation
Indices: 249280--249317 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
249270 GCATTACTTC
249280 AACCAAAAGACAAAAACAA
1 AACCAAAAGACAAAAACAA
*
249299 AACCAAAA-CCAAAAACAA
1 AACCAAAAGACAAAAACAA
249317 A
1 A
249318 TACTAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.74, C:0.24, G:0.03, T:0.00
Consensus pattern (19 bp):
AACCAAAAGACAAAAACAA
Found at i:249731 original size:18 final size:18
Alignment explanation
Indices: 249705--249749 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
249695 GTCGATCAGA
*
249705 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
249723 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
249741 TGATGGCTC
1 TGATGGCTC
249750 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:251093 original size:20 final size:20
Alignment explanation
Indices: 251068--251105 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
251058 AATAGTTTCT
251068 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
251088 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
251106 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:251394 original size:22 final size:22
Alignment explanation
Indices: 251369--251412 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
251359 GATTTAGATA
251369 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
251391 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
251413 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:251625 original size:20 final size:20
Alignment explanation
Indices: 251600--251693 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
251590 GATTATGTAT
251600 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
251620 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
251640 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
251661 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
251681 TATCGCATTGCGA
1 TATCGCGTTGCGA
251694 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:251665 original size:41 final size:42
Alignment explanation
Indices: 251620--251755 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
251610 CGAAAGTCAG
* * * *
251620 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
251661 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
251703 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
251744 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
251756 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:251694 original size:20 final size:20
Alignment explanation
Indices: 251580--251694 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
251570 CGCTTTGAAA
*
251580 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
251601 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
251621 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
251641 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
251662 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
251682 ATCGCATTGCGAT
1 ATCGCATTGCGAT
251695 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:251727 original size:20 final size:20
Alignment explanation
Indices: 251683--251775 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
251673 ATAGTCAGTA
*
251683 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
251704 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
251724 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
251745 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
251765 TCGCATTGCGA
1 TCGCATTGCGA
251776 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:251756 original size:41 final size:41
Alignment explanation
Indices: 251683--251778 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
251673 ATAGTCAGTA
* *
251683 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
251724 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
251765 TCGCATTGCGAATT
1 TCGCATTGCGAATT
251779 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:253316 original size:130 final size:130
Alignment explanation
Indices: 253170--253417 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
253160 TATTTATATA
* **
253170 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
253235 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
253300 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
253365 TTAACACATGATCATGACATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
253418 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:253383 original size:23 final size:21
Alignment explanation
Indices: 253344--253390 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
253334 AATTAATCAT
*
253344 TTAACCAGGATCTGACATGTG
1 TTAACCAGGATCTGACATATG
*
253365 TTAACACATGATCATGACATATG
1 TTAAC-CAGGATC-TGACATATG
253388 TTA
1 TTA
253391 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (21 bp):
TTAACCAGGATCTGACATATG
Found at i:253448 original size:130 final size:129
Alignment explanation
Indices: 253184--253448 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
253174 ATTTGGTCCT
* ** *
253184 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
253249 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
253314 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *
253379 TGACATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
253443 -A
128 CA
253444 AAATT
1 AAATT
253449 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:253775 original size:28 final size:27
Alignment explanation
Indices: 253744--253806 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
253734 AGTTGATACA
*
253744 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
253772 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
253800 ATATTTT
1 ATATTTT
253807 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:253902 original size:16 final size:18
Alignment explanation
Indices: 253881--253914 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
253871 ATTTCTTATT
253881 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
253897 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
253915 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:255039 original size:20 final size:21
Alignment explanation
Indices: 255014--255053 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
255004 CAACGCTTGA
255014 TTATATGATTA-ATTTACGAT
1 TTATATGATTATATTTACGAT
255034 TTATATGATTATATTTACGA
1 TTATATGATTATATTTACGA
255054 CGCTTGAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (21 bp):
TTATATGATTATATTTACGAT
Found at i:255886 original size:22 final size:23
Alignment explanation
Indices: 255860--255903 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
255850 GTTTTAACCG
255860 GTTTAAATTTCTT-CCCTTTTTC
1 GTTTAAATTTCTTGCCCTTTTTC
* *
255882 GTTTAATTTTCTTGCTCTTTTT
1 GTTTAAATTTCTTGCCCTTTTT
255904 TATTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.11, C:0.18, G:0.07, T:0.64
Consensus pattern (23 bp):
GTTTAAATTTCTTGCCCTTTTTC
Found at i:262707 original size:29 final size:28
Alignment explanation
Indices: 262627--262707 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 28
262617 CATATATATT
* *
262627 TATATATTAAA-T-TATTAAAACAAATC
1 TATATATTAAATTATATTAAAACACATA
* * *
262653 TA-ATAAATAAATTATATTTCACACACATA
1 TATAT-ATTAAATTATA-TTAAAACACATA
262682 TATATATTAAATTATAGTTAAAACAC
1 TATATATTAAATTATA-TTAAAACAC
262708 GATTTAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
25 2 0.05
26 7 0.17
27 1 0.02
28 2 0.05
29 27 0.66
30 2 0.05
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (28 bp):
TATATATTAAATTATATTAAAACACATA
Found at i:263169 original size:19 final size:17
Alignment explanation
Indices: 263129--263163 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
263119 TCTTATTTTA
263129 ACTTAAAAATATATCTT
1 ACTTAAAAATATATCTT
263146 ACTTAAAAATATATCTT
1 ACTTAAAAATATATCTT
263163 A
1 A
263164 TTCTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (17 bp):
ACTTAAAAATATATCTT
Found at i:267179 original size:147 final size:147
Alignment explanation
Indices: 266902--267316 Score: 469
Period size: 147 Copynumber: 2.8 Consensus size: 147
266892 TAAGCTTCAA
* ** * * * * **
266902 CCAAAAAGGTCAAAACGAGCCATTAATAATAATAAGAAAATGCCCTCAATAATGCAACATGGTAG
1 CCAAAAATGTCAAAACGAGCCATTAATAATCTTCAGAAAATG-CATTAATAATGCAGCATGCCAG
*
266967 AAAATGTAAGCAACTTTTCAGTGCCCCATCAAT-AGTC-TCTAGCAACTTTTCAGTGAAATGTCA
65 AAAATGTAAGCAACTTTTCAGTGCCCCATCAATCA-TCTTC-AGCAACTTTTCAGTGAAATGCCA
* *
267030 TCTTTAATAATGCACCATGC
128 TCTCTAATAATGCACCAAGC
* *
267050 CCGAAAATGTCAAAACGAACCATTAATAATCTTCAGAAAATGTCATTAATAATGCAGCATGCCA-
1 CCAAAAATGTCAAAACGAGCCATTAATAATCTTCAGAAAATG-CATTAATAATGCAGCATGCCAG
* * * * * * **
267114 AAAATGTTAGTAACTTTTTAGTGCCCAATCAATCATCTTCAGAAACGTTTCAGTGAGCTGCCATC
65 AAAATGTAAGCAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTTCAGTGAAATGCCATC
* *
267179 TCTATTAATGCATCAAGC
130 TCTAATAATGCACCAAGC
* * * * * *
267197 CCAAAAATGTCAAAATGGGTCATTGATAACCTTCAG-AAATGCTATTAATAATGCAGCATGCCAT
1 CCAAAAATGTCAAAACGAGCCATTAATAATCTTCAGAAAATGC-ATTAATAATGCAGCATGCCAG
**
267261 AAAATGCCAGCAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTTCAGTGA
65 AAAATGTAAGCAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTTCAGTGA
267317 TATATCAAAT
Statistics
Matches: 224, Mismatches: 39, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
145 1 0.00
146 25 0.11
147 143 0.64
148 55 0.25
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (147 bp):
CCAAAAATGTCAAAACGAGCCATTAATAATCTTCAGAAAATGCATTAATAATGCAGCATGCCAGA
AAATGTAAGCAACTTTTCAGTGCCCCATCAATCATCTTCAGCAACTTTTCAGTGAAATGCCATCT
CTAATAATGCACCAAGC
Found at i:267324 original size:32 final size:32
Alignment explanation
Indices: 267268--267344 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
267258 CATAAAATGC
* *
267268 CAGCAACTTTTCAGTGCCCCATC-AATCATCTT
1 CAGCAACTTTTCAGTGACACATCAAATCAT-TT
* *
267300 CAGCAACTTTTCAGTGATATATCAAATCATTT
1 CAGCAACTTTTCAGTGACACATCAAATCATTT
* *
267332 CAGAAAATTTTCA
1 CAGCAACTTTTCA
267345 ATATTGATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 32 0.84
33 6 0.16
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (32 bp):
CAGCAACTTTTCAGTGACACATCAAATCATTT
Found at i:273412 original size:18 final size:20
Alignment explanation
Indices: 273374--273412 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
273364 TATATATATA
*
273374 TATATAATGATATAAAGATT
1 TATATAATGAAATAAAGATT
273394 TATATAAT-AAATAAA-ATT
1 TATATAATGAAATAAAGATT
273412 T
1 T
273413 TAAAGTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TATATAATGAAATAAAGATT
Found at i:278338 original size:21 final size:21
Alignment explanation
Indices: 278268--278338 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
278258 CTTGTTTTTA
*
278268 TTTATTTTGTTTCTTAATTTT
1 TTTATTTTGTTTCTTAATGTT
** *
278289 TTTATTTAATTATGGACTT--TGTA
1 TTTATTTTGTT-T---CTTAATGTT
278312 TTTATTTTGTTTCTTAATGTT
1 TTTATTTTGTTTCTTAATGTT
278333 TTTATT
1 TTTATT
278339 ATTTAATTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
19 3 0.08
21 18 0.49
22 2 0.05
23 11 0.30
25 3 0.08
ACGTcount: A:0.18, C:0.04, G:0.08, T:0.69
Consensus pattern (21 bp):
TTTATTTTGTTTCTTAATGTT
Found at i:282556 original size:20 final size:20
Alignment explanation
Indices: 282525--282576 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
282515 CAAAGGGGGA
*
282525 ATCGGTTCCCTCATGAGGGT
1 ATCGATTCCCTCATGAGGGT
*
282545 ATCGATTTCCTCATGAGGGT
1 ATCGATTCCCTCATGAGGGT
282565 ATCGATTCCCTC
1 ATCGATTCCCTC
282577 TGCACAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (20 bp):
ATCGATTCCCTCATGAGGGT
Found at i:285951 original size:22 final size:21
Alignment explanation
Indices: 285909--285948 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
285899 GAGTTTATTT
*
285909 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
285930 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
285949 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:290339 original size:51 final size:50
Alignment explanation
Indices: 290245--290345 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 50
290235 GCCGGATTAG
290245 CCATGATATTCGGCATTGAAAATCCAAGTTAAAGATTTGTTTACACAACT
1 CCATGATATTCGGCATTGAAAATCCAAGTTAAAGATTTGTTTACACAACT
290295 CCATGATATTCGGCATTGAAAAGTCCAAGTTAAAGATTTGTTTACACAACT
1 CCATGATATTCGGCATTGAAAA-TCCAAGTTAAAGATTTGTTTACACAACT
290346 GTACGGAGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 22 0.44
51 28 0.56
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (50 bp):
CCATGATATTCGGCATTGAAAATCCAAGTTAAAGATTTGTTTACACAACT
Found at i:290850 original size:19 final size:20
Alignment explanation
Indices: 290826--290876 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
290816 AATGACCAAT
290826 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
290845 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
290865 AAAATCGCAACG
1 AAAATCGCAACG
290877 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:290870 original size:20 final size:20
Alignment explanation
Indices: 290826--291163 Score: 164
Period size: 20 Copynumber: 16.6 Consensus size: 20
290816 AATGACCAAT
*
290826 AAAATCGCAACGCGA-T-ATC
1 AAAATCGCAACGCGATTGA-G
*
290845 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
** ***
290865 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTGAG
**
290885 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TGAG
**
290905 AAAATCGCAACGCGAGCTT-CC
1 AAAATCGCAACGCGA--TTGAG
**
290926 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* *
290949 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTGAG
** * *
290969 TGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTGAG
** * *
290989 TGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTGAG
** *
291009 TGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
* *
291029 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* * *
291052 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* * * *
291072 AGATTCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* *
291092 AGAATCGCAACGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* *
291112 AGAATCGCAACGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* *
291132 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
*
291152 AAAATCACAACG
1 AAAATCGCAACG
291164 TTAAAAGAAA
Statistics
Matches: 269, Mismatches: 36, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
19 15 0.06
20 203 0.75
21 19 0.07
22 4 0.01
23 27 0.10
24 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTGAG
Found at i:291002 original size:40 final size:40
Alignment explanation
Indices: 290951--291157 Score: 225
Period size: 40 Copynumber: 5.1 Consensus size: 40
290941 TTTAGAAGAA
** **
290951 AATCGCAATGCGATTGATTGAATCGCAATGCGATTGATTG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
**
290991 AATCGCAATGCGATTGATTGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * *
291031 AGTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGA-TT-G-AGAGAATCGCAATGCGATTGAGAG
* * * *
291074 ATTCGCAATGCGACTGAGAGAATCGCAACGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * * * *
291114 AATCGCAACGCGACTGAGAGAATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
291154 AATC
1 AATC
291158 ACAACGTTAA
Statistics
Matches: 148, Mismatches: 16, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
40 111 0.75
41 3 0.02
42 2 0.01
43 32 0.22
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
Found at i:291057 original size:83 final size:80
Alignment explanation
Indices: 290951--291157 Score: 225
Period size: 83 Copynumber: 2.5 Consensus size: 80
290941 TTTAGAAGAA
* * ** ** * **
290951 AATCGCAATGCGATTGATTGAATCGCAATGCGATTGATTGAATCGCAATGCGATTGATTGAATCG
1 AATCGCAACGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAATCG
* *
291016 CAATGCGATTGAGAG
66 CAACGCGACTGAGAG
* * * *
291031 AGTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGATTCGCAATGCGACTGAGAGAA
1 AATCGCAACGCGA-CT-G-AGAGAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAA
291096 TCGCAACGCGACTGAGAG
63 TCGCAACGCGACTGAGAG
* * *
291114 AATCGCAACGCGACTGAGAGAATCGCAACGCGATTTAGAAAATC
1 AATCGCAACGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
291158 ACAACGTTAA
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
80 34 0.33
81 3 0.03
82 2 0.02
83 65 0.62
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (80 bp):
AATCGCAACGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAATCG
CAACGCGACTGAGAG
Found at i:291063 original size:103 final size:103
Alignment explanation
Indices: 290930--291153 Score: 313
Period size: 103 Copynumber: 2.2 Consensus size: 103
290920 GCTTCCAAGT
* ** * **
290930 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTGATTGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* * ** * * *
290995 GCAATGCGATTGATTGAATCGCAATGCGATTGAGAGAG
66 GCAACGCGACTGAGAGAATCGCAACGCGACTGAGAGAA
* *
291033 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGATTCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
291098 GCAACGCGACTGAGAGAATCGCAACGCGACTGAGAGAA
66 GCAACGCGACTGAGAGAATCGCAACGCGACTGAGAGAA
291136 TCGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
291154 AATCACAACG
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (103 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAACGCGACTGAGAGAATCGCAACGCGACTGAGAGAA
Found at i:291092 original size:63 final size:60
Alignment explanation
Indices: 290951--291146 Score: 221
Period size: 60 Copynumber: 3.2 Consensus size: 60
290941 TTTAGAAGAA
* ** * * ** * **
290951 AATCGCAATGCGATTGATTGAATCGCAATGCGATTGATTGAATCGCAATGCGATTGATTG
1 AATCGCAATGCGACTGAGAGAATCGCAACGCGACTGAGAGAATCGCAATGCGACTGAGAG
* * *
291011 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAGAATCGCAACGCGA-CT-G-AGAGAATCGCAATGCGACTGAGAG
* *
291074 ATTCGCAATGCGACTGAGAGAATCGCAACGCGACTGAGAGAATCGCAACGCGACTGAGAG
1 AATCGCAATGCGACTGAGAGAATCGCAACGCGACTGAGAGAATCGCAATGCGACTGAGAG
*
291134 AATCGCAACGCGA
1 AATCGCAATGCGA
291147 TTTAGAAAAT
Statistics
Matches: 117, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
60 63 0.54
61 3 0.03
62 2 0.02
63 49 0.42
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.19
Consensus pattern (60 bp):
AATCGCAATGCGACTGAGAGAATCGCAACGCGACTGAGAGAATCGCAATGCGACTGAGAG
Found at i:291174 original size:19 final size:20
Alignment explanation
Indices: 291150--291192 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
291140 AACGCGATTT
*
291150 AGAAAATCACAAC-GTTAAA
1 AGAAAATCACAACGGTCAAA
*
291169 AGAAAATCGCAACGGTCAAA
1 AGAAAATCACAACGGTCAAA
291189 AGAA
1 AGAA
291193 TAGTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (20 bp):
AGAAAATCACAACGGTCAAA
Found at i:291280 original size:6 final size:6
Alignment explanation
Indices: 291269--291354 Score: 165
Period size: 6 Copynumber: 14.5 Consensus size: 6
291259 GACACGTATT
291269 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
291317 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
291355 CGAGACGAGA
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.06
6 75 0.94
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:292036 original size:6 final size:6
Alignment explanation
Indices: 292007--292086 Score: 121
Period size: 6 Copynumber: 13.5 Consensus size: 6
291997 GGGACTCTCG
292007 GGTCG- GGTCG- GGTCGT CGGGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT --GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
292055 GGTCGT GGTC-T GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
292087 AATACGTGTC
Statistics
Matches: 71, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
5 15 0.21
6 50 0.70
8 6 0.08
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:292070 original size:35 final size:36
Alignment explanation
Indices: 292007--292086 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 36
291997 GGGACTCTCG
292007 GGTCG-GGTCGGGTCGTCGGGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGGGTCGTC-GGTCGTGGTCGTGGTCGT
292043 GGTCGTGGTCGTGGTCGT-GGTC-TGGTCGTGGTCGT
1 GGTCGTGGTCG-GGTCGTCGGTCGTGGTCGTGGTCGT
292078 GGTCGTGGT
1 GGTCGTGGT
292087 AATACGTGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
35 22 0.52
36 9 0.21
37 5 0.12
38 6 0.14
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.31
Consensus pattern (36 bp):
GGTCGTGGTCGGGTCGTCGGTCGTGGTCGTGGTCGT
Found at i:292184 original size:20 final size:20
Alignment explanation
Indices: 292159--292202 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
292149 TTTTTAACTA
*
292159 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
* *
292179 TTCTTTTTAACGTTGTGATT
1 TTCTTTTGAACGTTGCGATT
292199 TTCT
1 TTCT
292203 AAATCGCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:292212 original size:20 final size:20
Alignment explanation
Indices: 292189--292360 Score: 132
Period size: 20 Copynumber: 8.4 Consensus size: 20
292179 TTCTTTTTAA
* *
292189 CGTTGTGATTTTCTAAATCG
1 CGTTGCGATTCTCTAAATCG
* *
292209 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTCTAAATCG
* *
292229 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTCTAAATCG
*
292249 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TTC-TCTAAATCG
* *
292272 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTCTCTAAATCG
* *
292292 C-ATGCGATTCTATAAATCG
1 CGTTGCGATTCTCTAAATCG
* ** *
292311 CATTGCGATTCAATCAATCG
1 CGTTGCGATTCTCTAAATCG
*
292331 CATTGCGATTTTCTTCT-AATCG
1 CGTTGCGA--TTC-TCTAAATCG
292353 CGTTGCGA
1 CGTTGCGA
292361 ACTAGCAAAC
Statistics
Matches: 125, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
19 15 0.12
20 75 0.60
21 2 0.02
22 18 0.14
23 15 0.12
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTCTCTAAATCG
Found at i:292279 original size:63 final size:62
Alignment explanation
Indices: 292199--292320 Score: 181
Period size: 63 Copynumber: 2.0 Consensus size: 62
292189 CGTTGTGATT
* * * * * *
292199 TTCTAAATCGCGTTGCGATTCTCTCAGTCGCGTTGCGATTCTCTCAGTCGCATTGCGATTTTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGC-ATGCGATTCTATAAATCGCATTGCGATTTTC
292262 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATGCGATTCTATAAATCGCATTGCGATT
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATGCGATTCTATAAATCGCATTGCGATT
292321 CAATCAATCG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
62 24 0.45
63 29 0.55
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (62 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATGCGATTCTATAAATCGCATTGCGATTTTC
Found at i:292328 original size:39 final size:40
Alignment explanation
Indices: 292204--292340 Score: 114
Period size: 43 Copynumber: 3.4 Consensus size: 40
292194 TGATTTTCTA
* * * * * * **
292204 AATCGCGTTGCGATTCTCTCAGTCGCGTTGCGATTCTCTC
1 AATCGCATTGCGATTCTATAAATCGCATTGCGACTCAATC
* * * **
292244 AGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTC
1 AATCGCATTGCGA--TTC-TATAAATCGCATTGCGACTCAATC
*
292287 AATCGCA-TGCGATTCTATAAATCGCATTGCGATTCAATC
1 AATCGCATTGCGATTCTATAAATCGCATTGCGACTCAATC
292326 AATCGCATTGCGATT
1 AATCGCATTGCGATT
292341 TTCTTCTAAT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
39 26 0.32
40 21 0.26
42 8 0.10
43 27 0.33
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.34
Consensus pattern (40 bp):
AATCGCATTGCGATTCTATAAATCGCATTGCGACTCAATC
Found at i:294069 original size:42 final size:42
Alignment explanation
Indices: 293954--294072 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
293944 TTCCCCGAAA
* *
293954 TCCCGTGTTTGTTTCATGTAATTCATTTTCCAGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTT
*
293996 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTT
*
294038 TCCCGTGTTTGTTTCACGTAATTAATTTTCCGGAA
1 TCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAA
294073 CGTAATTCAT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.45
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTT
Found at i:294308 original size:22 final size:22
Alignment explanation
Indices: 294262--294359 Score: 85
Period size: 22 Copynumber: 4.3 Consensus size: 22
294252 AATTATTAAA
* *
294262 ATATTTAAAAT-ATAT-TTATT
1 ATATTTATAATAATATAATATT
294282 AATATTTATAATAATATAATATT
1 -ATATTTATAATAATATAATATT
*
294305 ATATTTTTAGTTTAATACTATAATCATT
1 ATA--TTTA---TAATAATATAAT-ATT
294333 ATA-TTATAATAATATAATATT
1 ATATTTATAATAATATAATATT
294354 ATATTT
1 ATATTT
294360 TTATTTATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
21 16 0.25
22 20 0.31
23 4 0.06
24 4 0.06
25 3 0.05
27 11 0.17
28 6 0.09
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (22 bp):
ATATTTATAATAATATAATATT
Found at i:294368 original size:28 final size:28
Alignment explanation
Indices: 294331--294428 Score: 86
Period size: 28 Copynumber: 3.6 Consensus size: 28
294321 ACTATAATCA
294331 TTATATTATAATAATATAATATTATATTT
1 TTATATTATAATAATATAATATTAT-TTT
294360 TTAT-TTAT-AT-ATATAAT-TT-TTTT
1 TTATATTATAATAATATAATATTATTTT
294383 TATATATT-TAATAATGAATAATATTA-TTT
1 T-TATATTATAATAAT--ATAATATTATTTT
*
294412 ATATATT-TAAATAATAT
1 TTATATTAT-AATAATAT
294429 TTTAGTAAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
23 4 0.07
24 5 0.08
25 6 0.10
26 9 0.15
27 4 0.07
28 16 0.27
29 15 0.25
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
TTATATTATAATAATATAATATTATTTT
Found at i:294369 original size:22 final size:22
Alignment explanation
Indices: 294295--294388 Score: 72
Period size: 22 Copynumber: 4.2 Consensus size: 22
294285 ATTTATAATA
294295 ATATAATATTATATTTTTAGTTTAAT
1 ATATAATATTATATTTTTA--TT--T
* * *
294321 ACTATAATCATTATA-TTATAATA
1 A-TATAAT-ATTATATTTTTATTT
294344 ATATAATATTATATTTTTATTT
1 ATATAATATTATATTTTTATTT
294366 ATAT-ATA-TA-ATTTTT-TTT
1 ATATAATATTATATTTTTATTT
294384 ATATA
1 ATATA
294389 TTTAATAATG
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
18 7 0.12
19 6 0.10
20 2 0.03
21 9 0.16
22 15 0.26
23 1 0.02
25 1 0.02
26 1 0.02
27 10 0.17
28 6 0.10
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (22 bp):
ATATAATATTATATTTTTATTT
Found at i:294379 original size:18 final size:18
Alignment explanation
Indices: 294349--294394 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
294339 TAATAATATA
*
294349 ATAT-TATATTTTTATTT
1 ATATATATAATTTTATTT
*
294366 ATATATATAATTTTTTTT
1 ATATATATAATTTTATTT
*
294384 ATATATTTAAT
1 ATATATATAAT
294395 AATGAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATATATAATTTTATTT
Found at i:294395 original size:49 final size:48
Alignment explanation
Indices: 294278--294376 Score: 148
Period size: 49 Copynumber: 2.0 Consensus size: 48
294268 AAAATATATT
294278 TATTAATATTTATAATAATATAATATTATATTTTTAGTTTAATACTATAA
1 TATT-ATA-TTATAATAATATAATATTATATTTTTAGTTTAATACTATAA
294328 TCATTATATTATAATAATATAATATTATATTTTTA-TTTATATA-TATAA
1 T-ATTATATTATAATAATATAATATTATATTTTTAGTTTA-ATACTATAA
294376 T
1 T
294377 TTTTTTTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
48 10 0.21
49 30 0.64
50 4 0.09
51 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (48 bp):
TATTATATTATAATAATATAATATTATATTTTTAGTTTAATACTATAA
Found at i:294431 original size:52 final size:53
Alignment explanation
Indices: 294262--294431 Score: 134
Period size: 49 Copynumber: 3.4 Consensus size: 53
294252 AATTATTAAA
* *
294262 ATATTTAAA-ATAT-A-TTTATTAATAT-TTATAATAATATAATATTATATTT
1 ATATTTAAATATATAATTTTTTTTATATATTATAATAATATAATATTATATTT
* **
294311 TTAGTTT-AATACTATAA----TCAT-TATATTATAATAATATAATATTATATTT
1 ATA-TTTAAATA-TATAATTTTTTTTATATATTATAATAATATAATATTATATTT
* *
294360 TTATTTATATATATAATTTTTTTTATATATT-TAATAATGAATAATATTAT-TTAT
1 ATATTTAAATATATAATTTTTTTTATATATTATAATAAT--ATAATATTATATT-T
294414 ATATTTAAATA-AT-ATTTT
1 ATATTTAAATATATAATTTT
294432 AGTAAAGATA
Statistics
Matches: 97, Mismatches: 10, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
48 11 0.11
49 34 0.35
50 4 0.04
51 3 0.03
52 15 0.15
53 10 0.10
54 20 0.21
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (53 bp):
ATATTTAAATATATAATTTTTTTTATATATTATAATAATATAATATTATATTT
Found at i:294783 original size:20 final size:20
Alignment explanation
Indices: 294746--294784 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
294736 TTTCCAGATG
**
294746 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
294766 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
294785 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:294800 original size:15 final size:15
Alignment explanation
Indices: 294758--294803 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
294748 TTCCAGAAAT
294758 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
294773 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
294787 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
294802 GT
1 GT
294804 CCAGTAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:294821 original size:20 final size:20
Alignment explanation
Indices: 294783--294823 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
294773 GAATTCAAAT
***
294783 TCCAGTAATTCATTTTCCAG
1 TCCAGTAATTCAAACTCCAG
294803 TCCAGTAATTCAAACTCCAG
1 TCCAGTAATTCAAACTCCAG
294823 T
1 T
294824 AACTCATTTT
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:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (20 bp):
TCCAGTAATTCAAACTCCAG
Found at i:294822 original size:35 final size:34
Alignment explanation
Indices: 294769--294835 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
294759 TAATTCATTT
* *
294769 TCCAGAATTCAAATTCCAGTAATTCATTTTCCAG
1 TCCAGAATTCAAACTCCAGTAACTCATTTTCCAG
294803 TCCAGTAATTCAAACTCCAGTAACTCATTTTCC
1 TCCAG-AATTCAAACTCCAGTAACTCATTTTCC
294836 GGAAAACCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.34
Consensus pattern (34 bp):
TCCAGAATTCAAACTCCAGTAACTCATTTTCCAG
Found at i:296010 original size:21 final size:20
Alignment explanation
Indices: 295924--296081 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
295914 AAATGACCAA
**
295924 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
295943 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
295963 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
295983 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
296004 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
296025 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
296045 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
296066 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
296082 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:296143 original size:20 final size:20
Alignment explanation
Indices: 296049--296277 Score: 248
Period size: 20 Copynumber: 11.4 Consensus size: 20
296039 GATTTTCCAG
* ** *
296049 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
296069 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
296089 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
296109 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
296129 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
296149 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
296169 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
296189 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
296209 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
296229 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
296249 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
296269 AATCACAAC
1 AATCGCAAC
296278 ACTGAAATTT
Statistics
Matches: 179, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 175 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:297007 original size:24 final size:24
Alignment explanation
Indices: 296968--297014 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
296958 AAATTTGGTC
296968 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
296992 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
297015 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:299412 original size:33 final size:34
Alignment explanation
Indices: 299361--299558 Score: 158
Period size: 33 Copynumber: 5.7 Consensus size: 34
299351 CGGAAATTAC
* *
299361 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
299394 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
* * *
299428 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
299467 AAT-GCGGA-AATG-AAATCGCAATGCGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
* *
299499 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
299532 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
299559 CGAGAGAATC
Statistics
Matches: 131, Mismatches: 15, Indels: 33
0.73 0.08 0.18
Matches are distributed among these distances:
31 1 0.01
32 9 0.07
33 63 0.48
34 19 0.15
35 1 0.01
36 1 0.01
37 1 0.01
38 14 0.11
39 21 0.16
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:299444 original size:19 final size:19
Alignment explanation
Indices: 299375--299597 Score: 227
Period size: 19 Copynumber: 12.7 Consensus size: 19
299365 GCAACGAGAG
299375 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
299394 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
299408 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
299428 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
299447 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
299461 AATCGCAATGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
299480 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
299499 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
299513 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
299532 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
299551 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
299565 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
299585 AATCGCATTGCGA
1 AATCGCAATGCGA
299598 TTCTCTCGTT
Statistics
Matches: 171, Mismatches: 9, Indels: 48
0.75 0.04 0.21
Matches are distributed among these distances:
14 42 0.25
15 3 0.02
16 5 0.03
17 9 0.05
18 7 0.04
19 76 0.44
20 29 0.17
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:299503 original size:52 final size:53
Alignment explanation
Indices: 299375--299597 Score: 389
Period size: 52 Copynumber: 4.2 Consensus size: 53
299365 GCAACGAGAG
* *
299375 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
299428 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATG-A
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
299480 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
299532 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
299585 AATCGCATTGCGA
1 AATCGCAATGCGA
299598 TTCTCTCGTT
Statistics
Matches: 164, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
51 6 0.04
52 90 0.55
53 67 0.41
54 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:299569 original size:33 final size:33
Alignment explanation
Indices: 299428--299591 Score: 156
Period size: 33 Copynumber: 4.8 Consensus size: 33
299418 CGGAAATGAA
299428 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
299461 AATCGCAATGCGGAAATG-AAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
299493 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
299532 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
299565 AATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGC-GAAATGAAAATCGCA
299592 TTGCGATTCT
Statistics
Matches: 106, Mismatches: 11, Indels: 27
0.74 0.08 0.19
Matches are distributed among these distances:
30 4 0.04
31 2 0.02
32 7 0.07
33 44 0.42
34 22 0.21
35 1 0.01
36 2 0.02
38 10 0.09
39 7 0.07
40 7 0.07
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:299646 original size:19 final size:19
Alignment explanation
Indices: 299606--299726 Score: 145
Period size: 19 Copynumber: 6.8 Consensus size: 19
299596 GATTCTCTCG
299606 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
299626 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
299645 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
299659 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
299678 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
299692 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
299711 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
299727 AACATAATGC
Statistics
Matches: 87, Mismatches: 4, Indels: 21
0.78 0.04 0.19
Matches are distributed among these distances:
14 12 0.14
16 14 0.16
17 14 0.16
19 32 0.37
20 15 0.17
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:299664 original size:14 final size:14
Alignment explanation
Indices: 299645--299699 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
299635 TCATTTCGCA
299645 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
299659 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
299676 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
299692 TTGCGATT
1 TTGCGATT
299700 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:299668 original size:33 final size:33
Alignment explanation
Indices: 299626--299718 Score: 186
Period size: 33 Copynumber: 2.8 Consensus size: 33
299616 CATTTCCGCA
299626 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
299659 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
299692 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
299719 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:299837 original size:15 final size:15
Alignment explanation
Indices: 299817--299854 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
299807 CATCAATTAC
299817 ACAAATCAAACTTTT
1 ACAAATCAAACTTTT
*
299832 ACAAATC-ATCTTTT
1 ACAAATCAAACTTTT
299846 ACAAATCAA
1 ACAAATCAA
299855 TTAAACAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (15 bp):
ACAAATCAAACTTTT
Found at i:301864 original size:14 final size:14
Alignment explanation
Indices: 301845--301901 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
301835 ACGCGAATGA
*
301845 AATCGCAACGACAG
1 AATCGCAACGAAAG
301859 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
301876 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
301892 AATCGCAACG
1 AATCGCAACG
301902 CGATATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:301872 original size:50 final size:55
Alignment explanation
Indices: 301753--301887 Score: 154
Period size: 50 Copynumber: 2.5 Consensus size: 55
301743 TAGTTTACTT
* *
301753 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGATAATCGCAACGAGAAACAAAAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAATGATAATCGCAAC-AG-AACAAAAA
*
301811 TCGCAACGCGAAACCAAAATCGCAACGCG-AATGA-AATCGCAAC-G-AC-AGAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGATAATCGCAACAGAACAAAAA
* **
301861 TCGCAATGCGAAATGAAAATCGCAACG
1 TCGCAACGCGAAACCAAAATCGCAACG
301888 AAAGAATCGC
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
50 27 0.38
51 2 0.03
53 1 0.01
55 9 0.13
56 5 0.07
57 14 0.20
58 13 0.18
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (55 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAATGATAATCGCAACAGAACAAAAA
Found at i:301886 original size:33 final size:33
Alignment explanation
Indices: 301828--301918 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
301818 GCGAAACCAA
*
301828 AATCGCAACGCG-AATG-AAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
301859 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
301892 AATCGCAACGCGATATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
301919 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 11 0.20
32 4 0.07
33 39 0.72
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:301924 original size:19 final size:19
Alignment explanation
Indices: 301753--301923 Score: 141
Period size: 19 Copynumber: 9.6 Consensus size: 19
301743 TAGTTTACTT
* *
301753 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
301773 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
301792 TCGCAACGAGAAACAAAAA
1 TCGCAACGCGAAATGAAAA
**
301811 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
301830 TCGCAACGCG-AATG-AAA
1 TCGCAACGCGAAATGAAAA
*
301847 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
301861 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
301880 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
*
301894 TCGCAACGCGATATGAAAA
1 TCGCAACGCGAAATGAAAA
*
301913 TCGCAATGCGA
1 TCGCAACGCGA
301924 TTTTGGTTTC
Statistics
Matches: 125, Mismatches: 15, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
14 16 0.13
15 3 0.02
16 10 0.08
17 16 0.13
18 2 0.02
19 66 0.53
20 12 0.10
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:301954 original size:14 final size:14
Alignment explanation
Indices: 301935--301961 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
301925 TTTGGTTTCG
301935 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
301949 CGTTGCGATTTTG
1 CGTTGCGATTTTG
301962 ATTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:301961 original size:33 final size:33
Alignment explanation
Indices: 301919--302013 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
301909 AAAATCGCAA
*
301919 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGATTTCGCGTTGCGATTTTGTCGT
*
301952 TGCGATTTTGATTTCGCGTTGCGATTCTT-TTGT
1 TGCGATTTTGATTTCGCGTTGCGATT-TTGTCGT
*
301985 TGCGATTTTCATTTCGCGTTGCGATTTTG
1 TGCGATTTTGATTTCGCGTTGCGATTTTG
302014 GTTTCGCGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 2 0.04
33 53 0.93
34 2 0.04
ACGTcount: A:0.08, C:0.16, G:0.26, T:0.49
Consensus pattern (33 bp):
TGCGATTTTGATTTCGCGTTGCGATTTTGTCGT
Found at i:301973 original size:19 final size:19
Alignment explanation
Indices: 301919--302047 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
301909 AAAATCGCAA
*
301919 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
301938 TGCGATTTTG---T--CGT
1 TGCGATTTTGATTTCGCGT
301952 TGCGATTTTGATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
301971 TGCGATTCT--TTT---GT
1 TGCGATTTTGATTTCGCGT
*
301985 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
302004 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
302023 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTTGA-TTTCGCGT
302043 TGCGA
1 TGCGA
302048 AAGTAAACTA
Statistics
Matches: 92, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 23 0.25
16 4 0.04
17 4 0.04
19 49 0.53
20 12 0.13
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:302228 original size:93 final size:93
Alignment explanation
Indices: 302092--302741 Score: 1231
Period size: 93 Copynumber: 7.1 Consensus size: 93
302082 ATGGATTGCA
302092 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
302156 TAGCAGAATTGGCAACAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
302184 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
302249 TAGCAG-ATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
302276 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
302340 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
302368 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
302433 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
302461 TTACTTTCAACC-AAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
302524 TAGCA-AATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
302551 TTACTTTCAACCAAAAGACAAAACAAAGACAAATGCTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
302616 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
302644 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
302709 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
302737 TTACT
1 TTACT
302742 AAGCAATCTA
Statistics
Matches: 548, Mismatches: 4, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
90 34 0.06
91 107 0.20
92 138 0.25
93 269 0.49
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:302420 original size:184 final size:186
Alignment explanation
Indices: 302092--302741 Score: 1231
Period size: 184 Copynumber: 3.5 Consensus size: 186
302082 ATGGATTGCA
302092 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
302156 TAGCAGAATTGGCAACAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
302221 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAG-ATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
302276 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
302340 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
302405 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
302461 TTACTTTCAACC-AAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
302524 TAGCA-AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATGCT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
302588 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
302644 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
302709 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
302742 AAGCAATCTA
Statistics
Matches: 457, Mismatches: 3, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
183 126 0.28
184 209 0.46
185 96 0.21
186 26 0.06
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:302660 original size:276 final size:277
Alignment explanation
Indices: 302092--302741 Score: 1234
Period size: 276 Copynumber: 2.4 Consensus size: 277
302082 ATGGATTGCA
302092 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
302156 TAGCAGAATTGGCAACAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
302221 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGATTGGCAGCAACCGAACAAATTTACTTTCAA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAAATTGGCAGCAACCGAACAAATTTACTTTCAA
302286 CCAAAAGACAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTG
196 CCAAAAGACAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTG
302351 GCAGCAACCGAACAAAT
261 GCAGCAACCGAACAAAT
302368 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
302433 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACC-AAAGACAAAAC-AAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
302496 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAAATTGGCAGCAACCGAACAAATTTACTTTCAA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAAATTGGCAGCAACCGAACAAATTTACTTTCAA
*
302561 CCAAAAGACAAAACAAAGACAAATGCTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATT
196 CCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATT
302626 GGCAGCAACCGAACAAAT
260 GGCAGCAACCGAACAAAT
302644 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
302709 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
302742 AAGCAATCTA
Statistics
Matches: 368, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
275 85 0.23
276 184 0.50
277 99 0.27
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (277 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAAATTGGCAGCAACCGAACAAATTTACTTTCAA
CCAAAAGACAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTG
GCAGCAACCGAACAAAT
Found at i:304464 original size:20 final size:20
Alignment explanation
Indices: 304433--304529 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
304423 TTTTGGTTGA
304433 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
304453 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
304473 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
304492 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
304507 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
304527 AAT
1 AAT
304530 CGTAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:304485 original size:21 final size:21
Alignment explanation
Indices: 304431--304495 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
304421 TCTTTTGGTT
304431 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
304452 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
304472 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
304493 GAA
1 GAA
304496 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:304499 original size:14 final size:14
Alignment explanation
Indices: 304480--304536 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
304470 GAGAAATGAA
304480 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
304494 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
304513 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
304527 AATCGTAACG
1 AATCGCAACG
304537 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:304512 original size:33 final size:33
Alignment explanation
Indices: 304431--304552 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 33
304421 TCTTTTGGTT
*
304431 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
304472 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
304505 GAAATGAAAATCGCAACGAGAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
304538 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
304553 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
32 9 0.11
33 39 0.49
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:304588 original size:14 final size:14
Alignment explanation
Indices: 304569--304625 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
304559 TTTGGTTTCG
304569 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
304583 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
304602 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
304616 CGTTGCGATT
1 CGTTGCGATT
304626 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:304601 original size:33 final size:33
Alignment explanation
Indices: 304553--304633 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
304543 GAAATCGCAA
**
304553 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
304586 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
304619 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
304634 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:304667 original size:41 final size:41
Alignment explanation
Indices: 304609--304686 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
304599 TCGCGTTGCG
*
304609 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
*
304650 ATTCTCTCGTTGTGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
304687 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:304671 original size:20 final size:21
Alignment explanation
Indices: 304610--304685 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
304600 CGCGTTGCGA
304610 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
304631 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
304651 TTCTCTCGTTGTGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
304672 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
304686 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:304807 original size:33 final size:33
Alignment explanation
Indices: 304765--304835 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
304755 AATACTAACT
*
304765 TGAAAATCGCAACTAGAGAAAAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAAAAGCAACGCGAAA
** *
304798 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAAAAGCAACGCGAAA
304831 TGAAA
1 TGAAA
304836 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAAAAGCAACGCGAAA
Found at i:305241 original size:20 final size:20
Alignment explanation
Indices: 305211--305403 Score: 201
Period size: 20 Copynumber: 9.6 Consensus size: 20
305201 CTTTAAATAT
*
305211 CGCGTTGCGATTTACGGATT
1 CGCGTTGCGATTTACGGATA
* * * *
305231 CTCGTTACGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
305253 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
305272 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
305292 CACATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
305312 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
305332 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
305352 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
305372 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
305392 CGCGTTGCGATT
1 CGCGTTGCGATT
305404 CTGGAAAATC
Statistics
Matches: 145, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.88
21 15 0.10
22 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:308298 original size:2 final size:2
Alignment explanation
Indices: 308285--308342 Score: 107
Period size: 2 Copynumber: 28.5 Consensus size: 2
308275 TAAATATTAA
308285 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
308328 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
308343 AATCCATATT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 53 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:313208 original size:29 final size:29
Alignment explanation
Indices: 313165--313342 Score: 170
Period size: 29 Copynumber: 6.1 Consensus size: 29
313155 GATCTGACCT
*
313165 AGTGATATTCTGGGAATTTTTGTGAAAAA
1 AGTGACATTCTGGGAATTTTTGTGAAAAA
* *
313194 TGTGACATTATGGGAATTTTTGTGAAAAA
1 AGTGACATTCTGGGAATTTTTGTGAAAAA
* *
313223 AG-GCAACATT-TAGGAATTTTTTTGAAAAAA
1 AGTG--ACATTCTGGGAATTTTTGTG-AAAAA
*
313253 AGTGACATTCGGGGAATTTTT-TGGAAAAA
1 AGTGACATTCTGGGAATTTTTGT-GAAAAA
* * *
313282 AGGTGATATTCTGAGAATTTATGTGAAAAA
1 A-GTGACATTCTGGGAATTTTTGTGAAAAA
313312 A-TGACAATT-TGGGAATTATTT-TGAAAAA
1 AGTGAC-ATTCTGGGAATT-TTTGTGAAAAA
313340 AGT
1 AGT
313343 AAAATTTTGG
Statistics
Matches: 123, Mismatches: 15, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
28 19 0.15
29 57 0.46
30 45 0.37
31 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.35
Consensus pattern (29 bp):
AGTGACATTCTGGGAATTTTTGTGAAAAA
Found at i:313311 original size:59 final size:58
Alignment explanation
Indices: 313166--313341 Score: 182
Period size: 59 Copynumber: 3.0 Consensus size: 58
313156 ATCTGACCTA
* *
313166 GTGATATTCTGGGAATTTTTGTGAAAAATGTGACATTATGGGAA-TTTTTGTGAAAAAAG
1 GTGATATTCTGAGAATTTTTGTGAAAAAAGTGACATT-TGGGAATTTTTTG-GAAAAAAG
** * * *
313225 GCAACATT-T-AGGAATTTTTTTGAAAAAAAGTGACATTCGGGGAATTTTTTGGAAAAAAG
1 GTGATATTCTGA-GAATTTTTGTG-AAAAAAGTGACATT-TGGGAATTTTTTGGAAAAAAG
*
313284 GTGATATTCTGAGAATTTATGTGAAAAAA-TGACAATTTGGGAATTATTTT-GAAAAAAG
1 GTGATATTCTGAGAATTTTTGTGAAAAAAGTGAC-ATTTGGGAATT-TTTTGGAAAAAAG
313342 TAAAATTTTG
Statistics
Matches: 96, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
58 30 0.31
59 49 0.51
60 16 0.17
61 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.35
Consensus pattern (58 bp):
GTGATATTCTGAGAATTTTTGTGAAAAAAGTGACATTTGGGAATTTTTTGGAAAAAAG
Found at i:314312 original size:63 final size:63
Alignment explanation
Indices: 314244--314367 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
314234 CTAATGTGAC
* * *
314244 TCTTAGGTAGGCTCTACGGCC-CTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCCTACGACCTC-GAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
314306 T
63 T
* *
314307 TCTTAGGTAGGCCCTACGACCTCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCTACGACCTCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
314368 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 50 0.94
64 2 0.04
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCTACGACCTCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:314318 original size:32 final size:31
Alignment explanation
Indices: 314244--314324 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
314234 CTAATGTGAC
* *
314244 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** * **
314275 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
314307 TCTTAGGTAGGCCCTACG
1 TCTTAGGTAGGCCCTACG
314325 ACCTCGAAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.59
32 16 0.41
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:320670 original size:28 final size:27
Alignment explanation
Indices: 320630--320795 Score: 167
Period size: 28 Copynumber: 6.0 Consensus size: 27
320620 CCCCGACCCA
*
320630 GTGACATTCTGGGAATTTTTATGAAAAG
1 GTGACA-TCTGGGAATTTTTGTGAAAAG
320658 GTGACATGCTGGGAATTTTTGTGAAAAG
1 GTGACAT-CTGGGAATTTTTGTGAAAAG
*
320686 GTAACATTCTGGGAATTTTTGTGAAAA-
1 GTGACA-TCTGGGAATTTTTGTGAAAAG
* *
320713 ATGACACTATGGGAA-TTTTGTGGAAAAG
1 GTGACA-TCTGGGAATTTTTGT-GAAAAG
* *
320741 GTGAGAATCTGGGAATTTTTGTGAAAAA
1 GTGA-CATCTGGGAATTTTTGTGAAAAG
* *
320769 ATGACAATTTGGGAATTATTT-TGAAAA
1 GTGAC-ATCTGGGAATT-TTTGTGAAAA
320796 AAAGTGACAT
Statistics
Matches: 117, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
26 6 0.05
27 17 0.15
28 83 0.71
29 11 0.09
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (27 bp):
GTGACATCTGGGAATTTTTGTGAAAAG
Found at i:320782 original size:83 final size:83
Alignment explanation
Indices: 320639--320796 Score: 207
Period size: 83 Copynumber: 1.9 Consensus size: 83
320629 AGTGACATTC
* * **
320639 TGGGAATTTTTATGAAAAGGTGACATGCTGGGAATTTTTGTGAAAAGGTAACATTCTGGGAATT-
1 TGGGAATTTTTAGGAAAAGGTGAAATGCTGGGAATTTTTGTGAAAAAATAACATTCTGGGAATTA
320703 TTTGTGAAAAATGACACTA
66 TTT-TGAAAAATGACACTA
*
320722 TGGGAATTTTGT-GGAAAAGGTGAGAAT-CTGGGAATTTTTGTGAAAAAATGACAATT-TGGGAA
1 TGGGAATTTT-TAGGAAAAGGTGA-AATGCTGGGAATTTTTGTGAAAAAATAAC-ATTCTGGGAA
320784 TTATTTTGAAAAA
63 TTATTTTGAAAAA
320797 AAGTGACATT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
83 57 0.86
84 9 0.14
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (83 bp):
TGGGAATTTTTAGGAAAAGGTGAAATGCTGGGAATTTTTGTGAAAAAATAACATTCTGGGAATTA
TTTTGAAAAATGACACTA
Found at i:320796 original size:28 final size:28
Alignment explanation
Indices: 320631--320817 Score: 134
Period size: 28 Copynumber: 6.6 Consensus size: 28
320621 CCCGACCCAG
* **
320631 TGAC-ATTCTGGGAATTTTTATGAAAAGG
1 TGACAATT-TGGGAATTTTTGTGAAAAAA
* **
320659 TGAC-ATGCTGGGAATTTTTGTGAAAAGG
1 TGACAAT-TTGGGAATTTTTGTGAAAAAA
*
320687 TAAC-ATTCTGGGAATTTTTGTG-AAAAA
1 TGACAATT-TGGGAATTTTTGTGAAAAAA
* * **
320714 TGACACTATGGGAA-TTTTGTGGAAAAGG
1 TGACAATTTGGGAATTTTTGT-GAAAAAA
* *
320742 TGAGAATCTGGGAATTTTTGTGAAAAAA
1 TGACAATTTGGGAATTTTTGTGAAAAAA
320770 TGACAATTTGGGAATTATTT-TGAAAAAAA
1 TGACAATTTGGGAATT-TTTGTG-AAAAAA
* *
320799 GTGACATTTTGAGAATTTT
1 -TGACAATTTGGGAATTTT
320818 CGAATGTGGA
Statistics
Matches: 130, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
26 6 0.05
27 13 0.10
28 80 0.62
29 17 0.13
30 14 0.11
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.35
Consensus pattern (28 bp):
TGACAATTTGGGAATTTTTGTGAAAAAA
Found at i:321775 original size:32 final size:31
Alignment explanation
Indices: 321701--321784 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
321691 CTAATGTGAC
* * *
321701 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** **
321732 TCTCGGGTAGGCCCTACGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
321764 TCTTAGGTAGGCCC-ACGGCCC
1 TCTTAGGTAGGCCCTACGGCCC
321785 CGAAATCTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
31 30 0.70
32 13 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:321783 original size:62 final size:63
Alignment explanation
Indices: 321701--321823 Score: 144
Period size: 62 Copynumber: 2.0 Consensus size: 63
321691 CTAATGTGAC
** * *
321701 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCT-ACGGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCTCA-GGCCCTAAGATGTGT
* * *
321764 TCTTAGGTAGGC-CCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCTCTAAGATGT
1 TCTTAGGTAGGCTCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
321824 TCCCTTAGTG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
62 37 0.73
63 14 0.27
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCTCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:323334 original size:3 final size:3
Alignment explanation
Indices: 323321--323354 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
323311 TCAATTAAAT
*
323321 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
323355 AAGTTCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:332098 original size:21 final size:21
Alignment explanation
Indices: 332074--332189 Score: 196
Period size: 21 Copynumber: 5.5 Consensus size: 21
332064 TTCCAGTTGG
* * *
332074 GAGTATCAATACTACTGGAGG
1 GAGTATCGATACTGCTGGAGA
*
332095 GAGTATTGATACTGCTGGAGA
1 GAGTATCGATACTGCTGGAGA
332116 GAGTATCGATACTGCTGGAGA
1 GAGTATCGATACTGCTGGAGA
332137 GAGTATCGATACTGCTGGAGA
1 GAGTATCGATACTGCTGGAGA
332158 GAGTATCGATACTGCTGGAGA
1 GAGTATCGATACTGCTGGAGA
332179 GAGTATCGATA
1 GAGTATCGATA
332190 ATGTCCCTAC
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 90 1.00
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (21 bp):
GAGTATCGATACTGCTGGAGA
Found at i:334880 original size:28 final size:27
Alignment explanation
Indices: 334845--334905 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
334835 TTTTAGTATC
334845 ATTTTAATA-AAAATATTAATTATTAA-A
1 ATTTTAATATAAAATA-TAATT-TTAATA
*
334872 ATATTTAATATATAATATAATTTTAATA
1 AT-TTTAATATAAAATATAATTTTAATA
334900 ATTTTA
1 ATTTTA
334906 TATTTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 10 0.33
28 15 0.50
29 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTTAATATAAAATATAATTTTAATA
Found at i:335440 original size:14 final size:14
Alignment explanation
Indices: 335402--335440 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
335392 CAAAACAACG
335402 TAAAATAATTTAAA
1 TAAAATAATTTAAA
*
335416 -AAAAAATATTTAAA
1 TAAAATA-ATTTAAA
335430 TAAAATAATTT
1 TAAAATAATTT
335441 TAGGGTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 5 0.24
14 11 0.52
15 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAAATAATTTAAA
Found at i:335442 original size:15 final size:15
Alignment explanation
Indices: 335402--335442 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
335392 CAAAACAACG
335402 TAAAATAA-TTTAAA
1 TAAAATAATTTTAAA
335416 -AAAA-AATATTTAAA
1 TAAAATAAT-TTTAAA
335430 TAAAATAATTTTA
1 TAAAATAATTTTA
335443 GGGTTGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.09
13 4 0.17
14 6 0.26
15 8 0.35
16 3 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATAATTTTAAA
Found at i:335804 original size:35 final size:36
Alignment explanation
Indices: 335765--335839 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
335755 ATTAATTATT
*
335765 TATTAAATTAATA-ATTTTATATTATATTT-TAAAAA
1 TATTAAATTAATATATTTTA-AATATATTTATAAAAA
* *
335800 TATT-AATTAGTATATTTTAAATATATTTATTAAAA
1 TATTAAATTAATATATTTTAAATATATTTATAAAAA
335835 TATTA
1 TATTA
335840 TTAGATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 15 0.44
35 19 0.56
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (36 bp):
TATTAAATTAATATATTTTAAATATATTTATAAAAA
Found at i:335816 original size:23 final size:23
Alignment explanation
Indices: 335787--335831 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
335777 AATTTTATAT
335787 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
335810 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
335832 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:335825 original size:34 final size:35
Alignment explanation
Indices: 335765--335843 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
335755 ATTAATTATT
* *
335765 TATTAAATTAATAATTTTATATTATATTT-TAAAAA
1 TATT-AATTAGTAATTTTATAATATATTTATAAAAA
*
335800 TATTAATTAGTATATTTTA-AATATATTTATTAAAA
1 TATTAATTAGTA-ATTTTATAATATATTTATAAAAA
335835 TATT-ATTAG
1 TATTAATTAG
335844 ATTATTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 20 0.51
35 19 0.49
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (35 bp):
TATTAATTAGTAATTTTATAATATATTTATAAAAA
Found at i:335837 original size:23 final size:23
Alignment explanation
Indices: 335788--335856 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
335778 ATTTTATATT
* * **
335788 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
335811 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
335834 ATATTATTAGAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
335857 TATTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:336061 original size:32 final size:32
Alignment explanation
Indices: 335994--336063 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
335984 ATATTATTAT
* **
335994 AATATAATTGATTATTTTATTAGAATATTTAA
1 AATATAATTGATTATATTATTAGAATATGAAA
336026 AATATAA-T-ATTATATTATTAGAAATATGAATA
1 AATATAATTGATTATATTATTAG-AATATGAA-A
336058 AATATA
1 AATATA
336064 TTTTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 12 0.36
31 7 0.21
32 14 0.42
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (32 bp):
AATATAATTGATTATATTATTAGAATATGAAA
Found at i:343618 original size:17 final size:18
Alignment explanation
Indices: 343596--343632 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
343586 TGAAAACATT
*
343596 TTAACTTT-TATTTTTGG
1 TTAACTTTCTATTTTGGG
343613 TTAACTTTCTATTTTGGG
1 TTAACTTTCTATTTTGGG
343631 TT
1 TT
343633 GTCTAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.16, C:0.08, G:0.14, T:0.62
Consensus pattern (18 bp):
TTAACTTTCTATTTTGGG
Found at i:348783 original size:151 final size:151
Alignment explanation
Indices: 348509--348810 Score: 604
Period size: 151 Copynumber: 2.0 Consensus size: 151
348499 ACGAGAGAGG
348509 CTACCTGAGACTGCTGCCGCGCGGCGAATGCTGTGGATGGCTGCTGCTTAGCTCACAAAACGTCT
1 CTACCTGAGACTGCTGCCGCGCGGCGAATGCTGTGGATGGCTGCTGCTTAGCTCACAAAACGTCT
348574 AAAACCCTAGCTGCTTCTTTTTAGAAACAAATGCTTAGAAATATTAATTTGTAGAATCCCCCCTG
66 AAAACCCTAGCTGCTTCTTTTTAGAAACAAATGCTTAGAAATATTAATTTGTAGAATCCCCCCTG
348639 ATCTTTTCCTAAAATTTAATT
131 ATCTTTTCCTAAAATTTAATT
348660 CTACCTGAGACTGCTGCCGCGCGGCGAATGCTGTGGATGGCTGCTGCTTAGCTCACAAAACGTCT
1 CTACCTGAGACTGCTGCCGCGCGGCGAATGCTGTGGATGGCTGCTGCTTAGCTCACAAAACGTCT
348725 AAAACCCTAGCTGCTTCTTTTTAGAAACAAATGCTTAGAAATATTAATTTGTAGAATCCCCCCTG
66 AAAACCCTAGCTGCTTCTTTTTAGAAACAAATGCTTAGAAATATTAATTTGTAGAATCCCCCCTG
348790 ATCTTTTCCTAAAATTTAATT
131 ATCTTTTCCTAAAATTTAATT
348811 TTTGTTCCTT
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 151 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (151 bp):
CTACCTGAGACTGCTGCCGCGCGGCGAATGCTGTGGATGGCTGCTGCTTAGCTCACAAAACGTCT
AAAACCCTAGCTGCTTCTTTTTAGAAACAAATGCTTAGAAATATTAATTTGTAGAATCCCCCCTG
ATCTTTTCCTAAAATTTAATT
Found at i:353043 original size:3 final size:3
Alignment explanation
Indices: 353035--353117 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
353025 TTTTTATCCA
*
353035 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
353083 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
353118 ATTTATATTA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:366281 original size:18 final size:17
Alignment explanation
Indices: 366243--366287 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
366233 CTATTTCAAG
*
366243 TTCAATTTA-TTTGAGA
1 TTCAATTTATTTTGAAA
366259 TTCAATTTATTTTGGAAA
1 TTCAATTTATTTT-GAAA
366277 TTCAATTTATT
1 TTCAATTTATT
366288 CTTTTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 9 0.35
17 3 0.12
18 14 0.54
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (17 bp):
TTCAATTTATTTTGAAA
Done.