Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006526.1 Hibiscus syriacus cultivar Beakdansim tig00015905_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: 502317
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:331218 original size:166 final size:166
Alignment explanation
Indices: 330917--332100 Score: 1241
Period size: 166 Copynumber: 7.1 Consensus size: 166
330907 CTGAGGTGCA
* * * * *
330917 TGTAATTGAACTCGGAGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAACTATACTGCAAAT
1 TGTAATCGAACTCGAAGGTCTT---TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
*
330982 GATATGTCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGG-AGAATAACCCTTCTCG
63 GATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAG-ATAACCCTTCTCG
* *
331046 ACTTAAGTTATGCCGTAAATGATGTGCCCTCGAAGCTGAG
127 ACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* * * **
331086 TGTAATCGAACTC-AGGGGTCTTTTGGCAGATAACCCTTCTTGACTTAAACTATATTGCAAATGA
1 TGTAATCGAACTCGA-AGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA
* *
331150 TATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCGGATAACCCTTCTCAACT
65 TATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACT
* * *
331215 TAAGTTATGCCGCAAATAATGTTCCCTCGAAGCTGAG
130 TAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* *
331252 TGTAATCGAACTC-AGGGGTCTTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 TGTAATCGAACTCGA-AGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA
* *
331316 TGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTCGAC
65 TATGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAC
* * * * *
331380 TTAAGTTATACTGCAAATGATAT-ACCTTGGAGCTGAG
129 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* * * * * * * *
331417 CGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
1 TGTAATCGAACTCGAAGGTCTTT--TGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
** * * * * *** *
331482 ACGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGA
64 ATATG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA
* * * * *
331543 CTTAAGCTATGTTGTAAATGATGTG-CCTTGGAGCTGAG
128 CTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* ** * *
331581 CGTGGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAAT
1 TGTAATCGAACTCGAAGGTC-TT--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
* * * *
331646 GATATACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG-TGACAGATAACCCTTCTAGC
63 GATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA
* * * *
331710 CTTGAGTTATGCTGTAAATGATGTGCCCTCTAAGCTAAG
128 CTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* *
331749 TGTAATCGAACTCGAGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
1 TGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAT
* * * * * * *
331813 GTGCCTTGGAGCTGGGCGTGGTCGAACTCGAAGGTCTTTAGTTGGCATATAACCCTTCTCGATTT
66 ATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT
*
331878 AAGTTATGCTGCAAATGATGTACCCTCGAAGCTGAG
131 AAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* * * * * *
331914 TGTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
1 TGTAATCGAACTCGAAGGTCTTT--TGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
* * * ** * * *** *
331979 ATGTGCCCTCGAAGAAGAGTGTAATCGAACTCGTGGGTC--T--TTGGCAGATAGCCCTTCTCGA
64 ATATG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGA
* * * *
332040 CTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAG
128 CTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
* *
332078 CGTAGTCGAACTCGAAGGTCTTT
1 TGTAATCGAACTCGAAGGTCTTT
332101 GGTTGGCAAA
Statistics
Matches: 864, Mismatches: 129, Indels: 49
0.83 0.12 0.05
Matches are distributed among these distances:
164 204 0.24
165 175 0.20
166 276 0.32
167 81 0.09
168 87 0.10
169 41 0.05
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (166 bp):
TGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAT
ATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT
AAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAG
Found at i:331319 original size:248 final size:247
Alignment explanation
Indices: 331037--332143 Score: 1578
Period size: 248 Copynumber: 4.5 Consensus size: 247
331027 TGGAGAATAA
* * * * * * *
331037 CCCTTCTCGACTTAAGTTATGCCGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC-AG
1 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGA-
* * ** * *
331101 GGGTC-TT-TTGGCAGATAACCCTTCTTGACTTAAACTATATTGCAAATGATATGCCTTGGAGCT
64 AGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATACCTTGGAGCT
* * * * * *
331164 GAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCGGATAACCCTTCTCA-ACTTAAGTTATGCCGC
129 GAGCGTAGTCGAACTCAAAGGTCTTTGG-TGACAGATAACCCTTCT-AGCCTTGAGTTATGCTGT
* *
331228 AAATAATGTTCCCTCGAAGCTGAGTGTAATCGAACTC-AGGGGTCTTTTGGCAGATAG
192 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGA-GGGTC-TTTGGCAGATAG
*
331285 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAA
1 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAA
331349 GGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATACCTTGGAGCT
65 GGTC-TTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATACCTTGGAGCT
*
331414 GAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA
129 GAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA
* *
331479 ATGACGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAG
194 ATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAG
* * *
331533 CCCTTCTCGACTTAAGCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTGGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
331598 GTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATACCTTGGAGCTG
66 GTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATACCTTGGAGCTG
331663 AGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
130 AGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
* *
331728 TGATGTGCCCTCTAAGCTAAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAG
195 TGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAG
* *
331781 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGGGCGTGGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * * * *
331846 GTCTTTAGTTGGCATATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATGTACCCTCGAAGCT
66 GTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATA-CCTTGGAGCT
* * *
331911 GAGTGTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA
129 GAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA
** *
331976 ATGATGTGCCCTCGAAGAAGAGTGTAATCGAACTCGTGGGTCTTTGGCAGATAG
194 ATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAG
*
332030 CCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * * * * *
332095 GTCTTTGGTTGGCAAATAGCCCTTCTTGTCTTGAGCTATATTGCAAATG
66 GTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATG
332144 TTATCTTTAA
Statistics
Matches: 785, Mismatches: 64, Indels: 19
0.90 0.07 0.02
Matches are distributed among these distances:
247 29 0.04
248 390 0.50
249 288 0.37
250 78 0.10
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (247 bp):
CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATACCTTGGAGCTGA
GCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
GATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAG
Found at i:332009 original size:497 final size:498
Alignment explanation
Indices: 331037--332143 Score: 1638
Period size: 497 Copynumber: 2.2 Consensus size: 498
331027 TGGAGAATAA
* * * * * *
331037 CCCTTCTCGACTTAAGTTATGCCGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC-AG
1 CCCTTCTCGACTTAAGCTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGA-
* * * *
331101 GGGTC-TT--TTGGCAGATAACCCTTCTTGACTTAAACTATATTGCAAATGATATGCCTTGGAGC
64 AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAACTATACTGCAAATGATATACCTTGGAGC
* *
331163 TGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCGGATAACCCTTCTCAACTTAAGTTATGCCGC
129 TGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGACAGATAACCCTTCTCAACTTAAGTTATGCCGC
* *
331228 AAATAATGTTCCCTCGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTTGGCAGATAGCCCTTCTC
194 AAATAATGTGCCCTCGAAGCTAAGTGTAATCGAACTCAGGGGTCTTTTGGCAGATAGCCCTTCTC
*
331293 GACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
259 GACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTAG
* * *
331358 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATACCTTGGAGCTGAGCGTAGT
324 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATACCTCGAAGCTGAGCGTAAT
331423 CGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGACGTGC
389 CGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGACGTGC
**
331488 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAG
454 CCTCGAAGAAGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAG
* *
331533 CCCTTCTCGACTTAAGCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTGGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* ** *
331598 GTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATACCTTGGAGCTG
66 GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAACTATACTGCAAATGATATACCTTGGAGCTG
* * * *
331663 AGCGTAGTCGAACTCAAAGGTCTTTGG-TGACAGATAACCCTTCT-AGCCTTGAGTTATGCTGTA
131 AGCGTAGTCGAACTCAAAGGTCTTTGGTTGACAGATAACCCTTCTCA-ACTTAAGTTATGCCGCA
* *
331726 AATGATGTGCCCTCTAAGCTAAGTGTAATCGAACTC-GAGGGTC-TTTGGCAGATAGCCCTTCTC
195 AATAATGTGCCCTCGAAGCTAAGTGTAATCGAACTCAG-GGGTCTTTTGGCAGATAGCCCTTCTC
* * *
331789 GACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGGGCGTGGTCGAACTCGAAGGTCTTTA
259 GACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTA
* * * * *
331853 GTTGGCATATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATGTACCCTCGAAGCTGAGTGTA
323 GTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATA-CCTCGAAGCTGAGCGTA
*
331918 ATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
387 ATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGACGT
*
331983 GCCCTCGAAGAAGAGTGTAATCGAACTCGTGGGTCTTTGGCAGATAG
452 GCCCTCGAAGAAGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAG
* *
332030 CCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * * * * *
332095 GTCTTTGGTTGGCAAATAGCCCTTCTTGTCTTGAGCTATATTGCAAATG
66 GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAACTATACTGCAAATG
332144 TTATCTTTAA
Statistics
Matches: 548, Mismatches: 55, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
495 27 0.05
496 157 0.29
497 287 0.52
498 77 0.14
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (498 bp):
CCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAACTATACTGCAAATGATATACCTTGGAGCTG
AGCGTAGTCGAACTCAAAGGTCTTTGGTTGACAGATAACCCTTCTCAACTTAAGTTATGCCGCAA
ATAATGTGCCCTCGAAGCTAAGTGTAATCGAACTCAGGGGTCTTTTGGCAGATAGCCCTTCTCGA
CTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTAGTT
GGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATACCTCGAAGCTGAGCGTAATCG
AACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGACGTGCCC
TCGAAGAAGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAG
Found at i:339574 original size:12 final size:11
Alignment explanation
Indices: 339540--339575 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
339530 CCCAAACAGG
339540 AAAAA-AAATC
1 AAAAACAAATC
339550 AAAAACAAATC
1 AAAAACAAATC
339561 AAAAACAAATTC
1 AAAAACAAA-TC
339573 AAA
1 AAA
339576 CAAGATGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.21
11 14 0.58
12 5 0.21
ACGTcount: A:0.75, C:0.14, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAAACAAATC
Found at i:342182 original size:6 final size:6
Alignment explanation
Indices: 342171--342196 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
342161 AATAAAAAAA
342171 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
342197 TAACTTTCGC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:342597 original size:26 final size:25
Alignment explanation
Indices: 342576--342648 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 25
342566 AGATAATATT
*
342576 ATAACTAAAAATAAAAAAATAAAAAA
1 ATAA-TAAAAATAAAAAAATAAAATA
*
342602 ATAAAAAAAATAAAAAAAATAAAATA
1 ATAATAAAAAT-AAAAAAATAAAATA
* *
342628 ATAATAATAATAATAAAATAA
1 ATAATAAAAATAAAAAAATAA
342649 CTAAATAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 15 0.37
26 26 0.63
ACGTcount: A:0.79, C:0.01, G:0.00, T:0.19
Consensus pattern (25 bp):
ATAATAAAAATAAAAAAATAAAATA
Found at i:342600 original size:9 final size:9
Alignment explanation
Indices: 342582--342645 Score: 78
Period size: 9 Copynumber: 7.1 Consensus size: 9
342572 TATTATAACT
342582 AAAAAT-AA
1 AAAAATAAA
342590 AAAAAT-AA
1 AAAAATAAA
342598 AAAAATAAA
1 AAAAATAAA
342607 AAAAATAAA
1 AAAAATAAA
342616 AAAAATAAA
1 AAAAATAAA
*
342625 ATAATAATAAT
1 A-AA-AATAAA
*
342636 AATAATAAA
1 AAAAATAAA
342645 A
1 A
342646 TAACTAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
8 14 0.28
9 27 0.54
10 3 0.06
11 6 0.12
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAATAAA
Found at i:342608 original size:17 final size:17
Alignment explanation
Indices: 342582--342648 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
342572 TATTATAACT
342582 AAAAATAAAAAAAT-AA
1 AAAAATAAAAAAATAAA
342598 AAAAATAAAAAAAATAAA
1 AAAAAT-AAAAAAATAAA
* *
342616 AAAAATAAAATAATAAT
1 AAAAATAAAAAAATAAA
* *
342633 AATAATAATAAAATAA
1 AAAAATAAAAAAATAA
342649 CTAAATAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
16 6 0.14
17 30 0.68
18 8 0.18
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAATAAAAAAATAAA
Found at i:342653 original size:9 final size:8
Alignment explanation
Indices: 342582--342648 Score: 80
Period size: 8 Copynumber: 8.0 Consensus size: 8
342572 TATTATAACT
342582 AAAAATAA
1 AAAAATAA
342590 AAAAATAA
1 AAAAATAA
342598 AAAAATAAA
1 AAAAAT-AA
342607 AAAAATAAA
1 AAAAAT-AA
342616 AAAAATAA
1 AAAAATAA
*
342624 AATAATAA
1 AAAAATAA
*
342632 TAATAATAA
1 -AAAAATAA
*
342641 TAAAATAA
1 AAAAATAA
342649 CTAAATAGAG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
8 29 0.54
9 25 0.46
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAAATAA
Found at i:342799 original size:4 final size:4
Alignment explanation
Indices: 342786--342829 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
342776 TATATATAGG
* *
342786 TAAA TGAA TAAA TAAT TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
342830 AGGGACCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:344052 original size:3 final size:3
Alignment explanation
Indices: 344044--344080 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
344034 AATGAAAAGA
* *
344044 AAT AAT AAT AAT AAT AAT AAT AAC ACT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
344081 TAGACTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:344097 original size:16 final size:16
Alignment explanation
Indices: 344055--344098 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
344045 ATAATAATAA
*
344055 TAATAATAATA-ACAC
1 TAATAATAATATAGAC
344070 TAATAATAATATAGAC
1 TAATAATAATATAGAC
344086 TATATAAT-ATATA
1 TA-ATAATAATATA
344099 TCTCTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (16 bp):
TAATAATAATATAGAC
Found at i:344200 original size:32 final size:32
Alignment explanation
Indices: 344164--344231 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
344154 ACTATATACC
344164 ATAT-AGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
344196 ATATAAGTTTTCCAAAATATTTTTAAAACTAT
1 ATATAAGTTTTCAAAAATATTTTTAAAAATAT
344228 ATAT
1 ATAT
344232 TATATAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (32 bp):
ATATAAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:344249 original size:37 final size:37
Alignment explanation
Indices: 344191--344392 Score: 120
Period size: 35 Copynumber: 5.5 Consensus size: 37
344181 GATTTTAAAA
* * *
344191 ATATTATATAAGTTTTCCAAAATATTTTTAAAACTAT
1 ATATTATATAAATTTTTCAAAATAGTTTTAAAACTAT
*
344228 ATATTATATAAATTTTTCAAAA-ATGTTTTTTTTAAACTAT
1 ATATTATATAAATTTTTCAAAATA-G---TTTTAAAACTAT
* * *
344268 ACA-T-TAT--A-TTTTCAAAAT-GATTTCAAAAATAT
1 ATATTATATAAATTTTTCAAAATAG-TTTTAAAACTAT
*
344300 ATGTTATAT-AA-TTTTCAAAAT-GTTTTAAAACTTAT
1 ATATTATATAAATTTTTCAAAATAGTTTTAAAAC-TAT
* * **
344335 ATATTGTATATAAGTTTTCAAAA-ACGTTTTAAAAAAACT
1 ATATTATATA-AATTTTTCAAAATA-GTTTTAAAACTA-T
344374 ATATTATATATATATTTTT
1 ATATTATATA-A-ATTTTT
344393 GGAAACCGTT
Statistics
Matches: 130, Mismatches: 19, Indels: 29
0.73 0.11 0.16
Matches are distributed among these distances:
32 10 0.08
33 1 0.01
34 11 0.08
35 31 0.24
36 2 0.02
37 22 0.17
38 13 0.10
39 22 0.17
40 18 0.14
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (37 bp):
ATATTATATAAATTTTTCAAAATAGTTTTAAAACTAT
Found at i:344319 original size:107 final size:108
Alignment explanation
Indices: 344165--344364 Score: 268
Period size: 107 Copynumber: 1.9 Consensus size: 108
344155 CTATATACCA
* *
344165 TATAGTTTTCAAAAATGATTTTAAAAATATTATATAAGTTTTCCAAAATATTTTTAAAAC-TATA
1 TATAGTTTTCAAAAATGATTTAAAAAATATTATATAAGTTTTCCAAAAT-GTTTTAAAACTTATA
* *
344229 TATTATATA-AATTTTTCAAAAATGTTTTTTTTAAACTATACAT
65 TATTATATATAAGTTTTCAAAAACGTTTTTTTTAAACTATACAT
344272 TATA-TTTTC-AAAATGATTTCAAAAATATATGTTATATAA-TTTT-CAAAATGTTTTAAAACTT
1 TATAGTTTTCAAAAATGATTT-AAAAA-ATA--TTATATAAGTTTTCCAAAATGTTTTAAAACTT
*
344333 ATATATTGTATATAAGTTTTCAAAAACGTTTT
62 ATATATTATATATAAGTTTTCAAAAACGTTTT
344365 AAAAAAACTA
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
105 10 0.12
106 18 0.22
107 25 0.30
108 21 0.26
109 8 0.10
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (108 bp):
TATAGTTTTCAAAAATGATTTAAAAAATATTATATAAGTTTTCCAAAATGTTTTAAAACTTATAT
ATTATATATAAGTTTTCAAAAACGTTTTTTTTAAACTATACAT
Found at i:344377 original size:39 final size:36
Alignment explanation
Indices: 344275--344391 Score: 103
Period size: 39 Copynumber: 3.1 Consensus size: 36
344265 TATACATTAT
* * *
344275 ATTTTCAAAATGATTT-CAAAAATATAT-GTTATATA
1 ATTTTCAAAACGTTTTAAAAAAATATATTG-TATATA
* **
344310 ATTTTCAAAATGTTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAACGTTTTAAAA-AAATATATTGTATATA
*
344347 AGTTTTCAAAAACGTTTTAAAAAAACTATATTATATATA
1 A-TTTTC-AAAACGTTTTAAAAAAA-TATATTGTATATA
344386 TATTTT
1 -ATTTT
344392 TGGAAACCGT
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
35 15 0.22
36 2 0.03
37 13 0.19
38 7 0.10
39 29 0.43
40 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (36 bp):
ATTTTCAAAACGTTTTAAAAAAATATATTGTATATA
Found at i:344853 original size:80 final size:79
Alignment explanation
Indices: 344766--345013 Score: 260
Period size: 77 Copynumber: 3.2 Consensus size: 79
344756 AAACATTTCC
* * *
344766 TAATGAGAATAACTTGTTCAATCTTTGCTCGATTTCATCACAGAAAGAGGTGGATTAGTATTTCC
1 TAATGAGAAGAACTTGTTCAATCTTTGCTTGATTTCATCACAGAAAGAGGTGGATTAGCATTTCC
344831 TAGAGAAGAGGTTCA
66 TA-AGAAGAGGTTCA
* * * * * *
344846 TAATGAGAAGAATTTGTTC-ACCTTTAGTTTG-TCT-ATCACAGAAGGAGGTGGATTAACATTTC
1 TAATGAGAAGAACTTGTTCAATCTTT-GCTTGATTTCATCACAGAAAGAGGTGGATTAGCATTTC
*
344908 C-AATGAAGATGTTCA
65 CTAA-GAAGAGGTTCA
* *
344923 TAATGAGAAGAACTTGTTCAATC--TGCTTGATTCCATCACA-AAAGAAGATGGATTAGCATTT-
1 TAATGAGAAGAACTTGTTCAATCTTTGCTTGATTTCATCACAGAAAG-AGGTGGATTAGCATTTC
* *
344984 CTAATAAAAGGTTTCA
65 CTAAGAAGAGG-TTCA
*
345000 TAATGAGAATAACT
1 TAATGAGAAGAACT
345014 CGTCCGATGA
Statistics
Matches: 138, Mismatches: 22, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
75 4 0.03
76 11 0.08
77 68 0.49
78 28 0.20
79 7 0.05
80 20 0.14
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (79 bp):
TAATGAGAAGAACTTGTTCAATCTTTGCTTGATTTCATCACAGAAAGAGGTGGATTAGCATTTCC
TAAGAAGAGGTTCA
Found at i:345891 original size:44 final size:44
Alignment explanation
Indices: 345828--346030 Score: 253
Period size: 44 Copynumber: 4.6 Consensus size: 44
345818 AAGCCTATTG
* * *
345828 GATTCCATCACATAGGGAGTTGGATCAACATCACCATTTTACTC
1 GATTCCATCACACAAGGAGTTGGATCAACATCACCATTTTGCTC
* * ** *
345872 GATTCTATCACATAAGGAGTTGGATCAACATCATTATTTTGCTT
1 GATTCCATCACACAAGGAGTTGGATCAACATCACCATTTTGCTC
* * ** *
345916 GATTTCATCACACAAGGAGTTTGATCTGCATCACCATTTTGTTC
1 GATTCCATCACACAAGGAGTTGGATCAACATCACCATTTTGCTC
* *
345960 GATTCCATCACACAAGGAGTTTGATCAGCATCACCATTTTGCTC
1 GATTCCATCACACAAGGAGTTGGATCAACATCACCATTTTGCTC
* *
346004 GATTCCATCACAAAAGGAGGTGGATCA
1 GATTCCATCACACAAGGAGTTGGATCA
346031 CCATATCAAC
Statistics
Matches: 137, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 137 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (44 bp):
GATTCCATCACACAAGGAGTTGGATCAACATCACCATTTTGCTC
Found at i:345948 original size:23 final size:23
Alignment explanation
Indices: 345921--345993 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 23
345911 TGCTTGATTT
345921 CATCACACAAGGAGTTTGATCTG
1 CATCACACAAGGAGTTTGATCTG
**** * *
345944 CATCAC-CATTTTGTTCGAT-TC
1 CATCACACAAGGAGTTTGATCTG
*
345965 CATCACACAAGGAGTTTGATCAG
1 CATCACACAAGGAGTTTGATCTG
345988 CATCAC
1 CATCAC
345994 CATTTTGCTC
Statistics
Matches: 35, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
21 7 0.20
22 16 0.46
23 12 0.34
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (23 bp):
CATCACACAAGGAGTTTGATCTG
Found at i:345970 original size:21 final size:21
Alignment explanation
Indices: 345944--346014 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
345934 GTTTGATCTG
345944 CATCACCATTTTGTTCGATTC
1 CATCACCATTTTGTTCGATTC
**** *
345965 CATCACACAAGGAGTTTGA-TC
1 CATCAC-CATTTTGTTCGATTC
*
345986 AGCATCACCATTTTGCTCGATTC
1 --CATCACCATTTTGTTCGATTC
346009 CATCAC
1 CATCAC
346015 AAAAGGAGGT
Statistics
Matches: 35, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
21 14 0.40
22 13 0.37
23 8 0.23
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (21 bp):
CATCACCATTTTGTTCGATTC
Found at i:351940 original size:21 final size:21
Alignment explanation
Indices: 351914--351970 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
351904 CTCATGGGAC
351914 TATCGATACCCAGGATGTGAG
1 TATCGATACCCAGGATGTGAG
*
351935 TATCGATACTCTA-GA-GTGAG
1 TATCGATAC-CCAGGATGTGAG
*
351955 TATCGAT-TCCAGGATG
1 TATCGATACCCAGGATG
351971 ATTTTTGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.07
19 2 0.07
20 13 0.43
21 11 0.37
22 2 0.07
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (21 bp):
TATCGATACCCAGGATGTGAG
Found at i:359968 original size:2 final size:2
Alignment explanation
Indices: 359961--359987 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
359951 TAACTTGTGT
359961 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
359988 TGATATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:365451 original size:20 final size:20
Alignment explanation
Indices: 365426--365478 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
365416 TTTCTTTGAT
365426 ATTAAAAAAATAAATAAATA
1 ATTAAAAAAATAAATAAATA
* * *
365446 ATTAAAATAATTAATATATA
1 ATTAAAAAAATAAATAAATA
* *
365466 ATTTATAAAATAA
1 ATTAAAAAAATAA
365479 GATATTTATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTAAAAAAATAAATAAATA
Found at i:365542 original size:122 final size:117
Alignment explanation
Indices: 365333--365573 Score: 268
Period size: 120 Copynumber: 2.0 Consensus size: 117
365323 AAATATATAT
* * * *
365333 TAATTTATATATATTTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACTTCTAG
1 TAATTAATATATAATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAG
* * *
365398 GTGCCTTAAGACAGCTCTTTTCTTTGATATTAAAAAAATAAATAAATAATTAAAA
66 GTACCTTAAGACAGCTCCTTTC-TTAATATT-AAAAAATAAATAAAT-ATTAAAA
* ***
365453 TAATTAATATATAATTTATAAAATAAGATATTTATTTATTTTTTTAATATCAGAAAATGGACATC
1 TAATTAATATATAATTTAT-AAATAAAATATTTATTTA-TTTAAAAATATCAGAAAAT-GACATC
* ** * **
365518 CAGTTATTTTAAGACTGC-CCTTTCTTAATATTGGAAAATAAATAAATATTAAAA
63 CAGGTACCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATATTAAAA
365572 TA
1 TA
365574 GGATTAAAAT
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
119 9 0.09
120 30 0.30
121 24 0.24
122 21 0.21
123 17 0.17
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (117 bp):
TAATTAATATATAATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAG
GTACCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATATTAAAA
Found at i:367007 original size:3 final size:3
Alignment explanation
Indices: 366999--367064 Score: 73
Period size: 3 Copynumber: 21.0 Consensus size: 3
366989 AGCCTGTTTG
366999 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAAA TAAA TAAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA T-AA T-AA T-AA
367049 TAA -AA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
367065 CATTAAAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.07
3 38 0.62
4 19 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:367036 original size:4 final size:4
Alignment explanation
Indices: 367027--367078 Score: 58
Period size: 4 Copynumber: 13.5 Consensus size: 4
367017 TAATAATAAT
367027 AATA AATA AATA AATA AATA AATA AA-A AAT- AAT- AATA ACATTA AA-A
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-A-TA AATA
367073 AATA AA
1 AATA AA
367079 AAAAATGGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 12 0.28
4 26 0.60
5 2 0.05
6 3 0.07
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:367342 original size:17 final size:17
Alignment explanation
Indices: 367320--367378 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
367310 TTGAACAAGC
367320 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
367337 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
367356 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
367373 CCTTCT
1 TCTTCT
367379 GAAATGCTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 2 0.06
17 15 0.45
18 4 0.12
19 10 0.30
20 2 0.06
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.47
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:367984 original size:225 final size:226
Alignment explanation
Indices: 367547--368202 Score: 1029
Period size: 225 Copynumber: 2.9 Consensus size: 226
367537 AGAGTCATGA
367547 AAAAGGTTGAACAAAATT-TTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCA
1 AAAAGGTTGAAC-AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
*
367610 TTATGAAC-TT-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAAT
65 TTATGAACTTTCTCTGGAAAAGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAAT
367673 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGG
130 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGG
*
367738 CAATGATGATCCATCAAATGATGAATTCAAAC
195 CAATGTTGATCCATCAAATGATGAATTCAAAC
*
367770 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
* * * ** * *
367835 TATGAACTTTCTCTGGAAAAGCTGACCCATC-AAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCGAA-TGATGAATTCAAACAAAAAGTTGAACAAAT
*
367899 TCTTCTCATTATGAATTTCTTCTT-CTTCAT-ATGACGAGTTCTTCTCATTATGAACTCTACCTG
130 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCA-GACGAGTTCTTCTCATTATGAACTCTACCTG
*
367962 GCAATGTTGATCCATCAAATGATGAATTGAAAC
194 GCAATGTTGATCCATCAAATGATGAATTCAAAC
**
367995 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
* * * *
368060 TATGAACTTTCTTTTGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAGTT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATT
* * * *
368125 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATTATGAACTCTAACTGGC
131 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGGC
*
368190 ACTGTTGATCCAT
196 AATGTTGATCCAT
368203 TGAGTGATGG
Statistics
Matches: 393, Mismatches: 31, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
222 5 0.01
223 36 0.09
224 29 0.07
225 206 0.52
226 116 0.30
227 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (226 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATT
CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGGC
AATGTTGATCCATCAAATGATGAATTCAAAC
Found at i:368054 original size:338 final size:341
Alignment explanation
Indices: 367422--368180 Score: 1036
Period size: 338 Copynumber: 2.2 Consensus size: 341
367412 TAGAGTCATG
* * *
367422 CAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
367487 TTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCATGAAAAAG
66 TTATGAACTTTCTCTGGAAAA---GATGCTG---TATCTCCATCAATGATAGAGTCATGAAAAAG
* *
367552 GTTGAACAAAATTTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA
125 GTTGAACAAAATTTTCTCATTATGAACTTCTTCTTCCTCATCAGACAAGTTCTTCTCATTATGAA
* * *
367617 CTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCAT
190 CTTCCTGGAAAAGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAACTCTTCTCAT
* * *
367682 TATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGATG
255 TATGAACTTCTTCTTCCTTCTTCAGACAAGTTCTTCTCATTATGAACT-TACTCTGGAAATGATG
367746 ATCCATCAAATGATGAATTCAAA
319 ATCCATCAAATGATGAATTCAAA
*
367769 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
367834 TTATGAACTTTCTCTGG-AAA-A-GCTG-A-C-CCATCAAGTGATGGA-T-TTGAGCAAAAGGTT
66 TTATGAACTTTCTCTGGAAAAGATGCTGTATCTCCATCAA-TGATAGAGTCATGA--AAAAGGTT
* * *
367891 GAAC-AAATTCTTCTCATTATGAATTTCTTCTTCTTCAT-ATGACGAGTTCTTCTCATTATGAAC
128 GAACAAAATT-TTCTCATTATGAACTTCTTCTTCCTCATCA-GACAAGTTCTTCTCATTATGAAC
* * * * *
367954 TCTACCTGGCAATGTTGATCCATCAAATGATGAATTGAAACAAAAGGTTGAACAAGCTCTTCTCA
191 T-T-CCTGGAAAAGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAACTCTTCTCA
* * * *
368019 TTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTTTTGAAATGATG
254 TTATGAACTTCTTCTTCCTTCTTCAGACAAGTTCTTCTCATTATGAACTTACTCTGGAAATGATG
*
368084 ATCCATCGAATGATGAATTCAAA
319 ATCCATCAAATGATGAATTCAAA
* *
368107 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
368172 TTATGAACT
66 TTATGAACT
368181 CTAACTGGCA
Statistics
Matches: 372, Mismatches: 32, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
334 3 0.01
335 12 0.03
336 66 0.18
337 4 0.01
338 201 0.54
341 4 0.01
342 1 0.00
346 3 0.01
347 78 0.21
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (341 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGATGCTGTATCTCCATCAATGATAGAGTCATGAAAAAGGTTGAA
CAAAATTTTCTCATTATGAACTTCTTCTTCCTCATCAGACAAGTTCTTCTCATTATGAACTTCCT
GGAAAAGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAACTCTTCTCATTATGAA
CTTCTTCTTCCTTCTTCAGACAAGTTCTTCTCATTATGAACTTACTCTGGAAATGATGATCCATC
AAATGATGAATTCAAA
Found at i:368211 original size:113 final size:113
Alignment explanation
Indices: 367546--368202 Score: 876
Period size: 113 Copynumber: 5.8 Consensus size: 113
367536 TAGAGTCATG
*
367546 AAAAAGGTTGAACAAAATT-TTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
1 AAAAA-GTTGAAC-AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
367609 ATTATGAACT-T-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
64 ATTATGAACTCTATCTGGAAATGTTGATCCATCAAATGATGAATTCAAAC
* *
367657 AAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
367722 TATGAACTCTACCTGGCAATGATGATCCATCAAATGATGAATTCAAAC
66 TATGAACTCTATCTGGAAATGTTGATCCATCAAATGATGAATTCAAAC
*
367770 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * * ** *
367835 TATGAACTTTCTCTGGAAAAGCTGACCCATCAAGTGATGGATTTGAGC
66 TATGAACTCTATCTGGAAATGTTGATCCATCAAATGATGAATTCAAAC
* * * *
367883 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-CTTCAT-ATGACGAGTTCTTCTCA
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCA
* * *
367946 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTGAAAC
65 TTATGAACTCTATCTGGAAATGTTGATCCATCAAATGATGAATTCAAAC
* ** *
367995 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
368060 TATGAACTTTCTTTTGAAATGATGATCCATCGAATGATGAATTCAAAC
66 TATGAACTCTATCTGGAAATGTTGATCCATCAAATGATGAATTCAAAC
* *
368108 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
368173 TATGAACTCTAACTGGCACTGTTGATCCAT
66 TATGAACTCTATCTGGAAATGTTGATCCAT
368203 TGAGTGATGG
Statistics
Matches: 474, Mismatches: 65, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
109 5 0.01
110 30 0.06
111 34 0.07
112 94 0.20
113 310 0.65
114 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (113 bp):
AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTATCTGGAAATGTTGATCCATCAAATGATGAATTCAAAC
Found at i:369367 original size:19 final size:17
Alignment explanation
Indices: 369339--369387 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
369329 CAAATAAAAG
*
369339 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
369358 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
369374 AATAAATTGAATTT
1 AATAAATTGAATTT
369388 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:369756 original size:9 final size:9
Alignment explanation
Indices: 369742--369813 Score: 76
Period size: 10 Copynumber: 7.7 Consensus size: 9
369732 TTGACCCCCC
369742 TTTTTTCTT
1 TTTTTTCTT
369751 TTTTTTC--
1 TTTTTTCTT
369758 TTTTTTCTT
1 TTTTTTCTT
369767 TTTTCTTCTT
1 TTTT-TTCTT
*
369777 CTTCTTCTCTT
1 -TT-TTTTCTT
369788 TTTTTTCTTT
1 TTTTTTC-TT
369798 TTTTTTCCTT
1 TTTTTT-CTT
369808 TTTTTT
1 TTTTTT
369814 TTAATTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
7 7 0.13
9 15 0.28
10 23 0.43
11 7 0.13
12 2 0.04
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:369771 original size:23 final size:22
Alignment explanation
Indices: 369742--369826 Score: 52
Period size: 22 Copynumber: 3.9 Consensus size: 22
369732 TTGACCCCCC
369742 TTTTTTCTTTTTTTTCTTTT-TT
1 TTTTTTCTTTTTTTT-TTTTCTT
* * * *
369764 CTTTTTTC-TTCTTCTTCTTCTC
1 -TTTTTTCTTTTTTTTTTTTCTT
*
369786 TTTTTT-TTCTTTTTTTTTCCTT
1 TTTTTTCTT-TTTTTTTTTTCTT
**
369808 TTTTTT-TTAATTTTTTTTC
1 TTTTTTCTTTTTTTTTTTTC
369827 AAGCATAATA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
21 18 0.38
22 22 0.47
23 7 0.15
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTCTTTTTTTTTTTTCTT
Found at i:377065 original size:15 final size:15
Alignment explanation
Indices: 377042--377073 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
377032 TGCAATGAAT
377042 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
377057 AATGCATGTATGCAA
1 AATGAATGTATGCAA
377072 AA
1 AA
377074 GGTATTGATC
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:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:381034 original size:20 final size:19
Alignment explanation
Indices: 380995--381046 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
380985 TTTCTTTGAT
380995 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
381014 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
381034 ATTTATAAAATAA
1 A-TTAAAAAATAA
381047 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:382608 original size:3 final size:3
Alignment explanation
Indices: 382600--382656 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
382590 AGCCTGTTTG
*
382600 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA -AA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
382645 TAA TAA CAA TAA
1 TAA TAA TAA TAA
382657 ATAAATAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:382667 original size:21 final size:21
Alignment explanation
Indices: 382604--382668 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
382594 TGTTTGTAAT
382604 AATAATAATAAT-AAT-AAT-
1 AATAATAATAATAAATAAATA
382622 AATAATAATAATAAATAAA-A
1 AATAATAATAATAAATAAATA
*
382642 CAATAATAACAATAAATAAATA
1 -AATAATAATAATAAATAAATA
382664 AATAA
1 AATAA
382669 AATGGGTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
18 12 0.29
19 3 0.07
20 2 0.05
21 23 0.56
22 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (21 bp):
AATAATAATAATAAATAAATA
Found at i:382671 original size:9 final size:10
Alignment explanation
Indices: 382600--382668 Score: 60
Period size: 9 Copynumber: 7.3 Consensus size: 10
382590 AGCCTGTTTG
382600 TAATAAT-AA
1 TAATAATAAA
382609 TAATAAT-AA
1 TAATAATAAA
382618 TAATAAT-AA
1 TAATAATAAA
382627 TAATAATAAA
1 TAATAATAAA
*
382637 TAA-AA-CAA
1 TAATAATAAA
*
382645 TAATAA-CAA
1 TAATAATAAA
382654 TAAATAAATAAA
1 T-AAT-AATAAA
382666 TAA
1 TAA
382669 AATGGGTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
8 5 0.09
9 33 0.62
10 8 0.15
11 4 0.08
12 3 0.06
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (10 bp):
TAATAATAAA
Found at i:383388 original size:2 final size:2
Alignment explanation
Indices: 383381--383406 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
383371 TCGCGAGTAA
383381 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
383407 TTTAAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:384022 original size:2 final size:2
Alignment explanation
Indices: 384015--384055 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
384005 CGCGTCTTAT
384015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
384056 TCGTTTCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:385819 original size:2 final size:2
Alignment explanation
Indices: 385812--385852 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
385802 TTTAATTTTG
385812 AT 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 AT A
385853 GTTTTATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:386377 original size:2 final size:2
Alignment explanation
Indices: 386370--386409 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
386360 TTTAATTTAG
386370 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
386410 AAAATATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:390432 original size:2 final size:2
Alignment explanation
Indices: 390425--390455 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
390415 ATCATATAAG
390425 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
390456 TCTCCATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:392295 original size:62 final size:62
Alignment explanation
Indices: 392198--392327 Score: 158
Period size: 62 Copynumber: 2.1 Consensus size: 62
392188 TATTCTTTAT
* * * *
392198 TTTCATTGATAGCATCCATTCATGCTTATAATACAC-CTATATGCATTTCAATTT-TGTCATCC
1 TTTCATTGATAACATCCATTCATGCTTATAATACACGAT-TATACATTTC-ATTTATGGCATCC
* *
392260 TTTCATTTATAACATCCATTCATGCCTT-TGATACACGATTATACATTTCATTTATGGCATCC
1 TTTCATTGATAACATCCATTCATG-CTTATAATACACGATTATACATTTCATTTATGGCATCC
392322 TTTCAT
1 TTTCAT
392328 GCCTTTTATG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
61 4 0.07
62 51 0.86
63 4 0.07
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (62 bp):
TTTCATTGATAACATCCATTCATGCTTATAATACACGATTATACATTTCATTTATGGCATCC
Found at i:392404 original size:2 final size:2
Alignment explanation
Indices: 392397--392429 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
392387 GTTGTACATA
392397 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 A
392430 ATCCCTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:392617 original size:81 final size:81
Alignment explanation
Indices: 392482--392803 Score: 493
Period size: 81 Copynumber: 4.0 Consensus size: 81
392472 TAAAATTCCT
* * * * *
392482 TTATTCTCTAACTCAACAGTATTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTGCCAA
1 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
392547 TTGCATAGTTAGGCCA
66 TTGCACAGTTAGGCCA
*
392563 TTATTCTTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
1 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
392628 CTGCACAGTTAGGCCA
66 TTGCACAGTTAGGCCA
* * *
392644 TTTTTCTTTTACTCAACGGTACTTAACCGTTCATCTGACTGGCATAATTGACACCTTTATGCCAA
1 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
392709 TTGCATAGTTAGG-CA
66 TTGCACAGTTAGGCCA
* * *
392724 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAATTGGCATAATTTACACCTTTCTGCCAG
1 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
392789 TTGCACAATTAGGCC
66 TTGCACAGTTAGGCC
392804 TCAAAGACAC
Statistics
Matches: 218, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
80 72 0.33
81 146 0.67
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.36
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
TTGCACAGTTAGGCCA
Found at i:392781 original size:161 final size:162
Alignment explanation
Indices: 392492--392803 Score: 518
Period size: 161 Copynumber: 1.9 Consensus size: 162
392482 TTATTCTCTA
* *
392492 ACTCAACAGTATTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTGCCAATTGCATAGTT
1 ACTCAACAGTACTTAACCGTTCATCTAACTGACATAATTGACACCTTTATGCCAATTGCATAGTT
392557 AGGCCATTATTCTTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTC
66 AGGCCATTATTCTTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTC
*
392622 TGCCAACTGCACAGTTAGGCCATTTTTCTTTT
131 TGCCAACTGCACAATTAGGCCATTTTTCTTTT
* * *
392654 ACTCAACGGTACTTAACCGTTCATCTGACTGGCATAATTGACACCTTTATGCCAATTGCATAGTT
1 ACTCAACAGTACTTAACCGTTCATCTAACTGACATAATTGACACCTTTATGCCAATTGCATAGTT
* * *
392719 AGG-CATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAATTGGCATAATTTACACCTTTC
66 AGGCCATTATTCTTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTC
**
392783 TGCCAGTTGCACAATTAGGCC
131 TGCCAACTGCACAATTAGGCC
392804 TCAAAGACAC
Statistics
Matches: 139, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
161 76 0.55
162 63 0.45
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (162 bp):
ACTCAACAGTACTTAACCGTTCATCTAACTGACATAATTGACACCTTTATGCCAATTGCATAGTT
AGGCCATTATTCTTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTC
TGCCAACTGCACAATTAGGCCATTTTTCTTTT
Found at i:392827 original size:68 final size:68
Alignment explanation
Indices: 392753--393003 Score: 369
Period size: 68 Copynumber: 3.7 Consensus size: 68
392743 TACTTAACCG
* * * * * *
392753 TTCATCTAATTGGCATAATTTACACCTTTCTGCCAGT-TGCACAATTAGGCCTCAAAGACACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCA-TATGCACAGTTAGGCCTCAAAGACACTCA
392817 GTCT
65 GTCT
* *
392821 TTCATCTAACTGGCATAAATGACAACTTTATGTCATATGCACAGTTAGGCCTCAAAGACACTCAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTCAG
392886 TCT
66 TCT
* * *
392889 TTCATCTAACTAGCATAAATGAAACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGACACCCAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTCAG
392954 TCT
66 TCT
* *
392957 TTCATCTAACTGGCATAAATGACACCTTTGTATCATATGCACAGTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTA
393004 AAATATAATA
Statistics
Matches: 165, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
67 1 0.01
68 164 0.99
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTCAG
TCT
Found at i:394610 original size:32 final size:31
Alignment explanation
Indices: 394574--394649 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
394564 CGGGGCCGTG
*
394574 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
394606 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
394637 GAGCCTACCTAAG
1 GGGCCTACCTAAG
394650 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:394633 original size:63 final size:63
Alignment explanation
Indices: 394527--394649 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
394517 ACCTAAGGGA
* * ** *
394527 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
394590 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
394650 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:396184 original size:18 final size:18
Alignment explanation
Indices: 396161--396195 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
396151 TTCCATCCGG
*
396161 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
396179 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
396196 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:397505 original size:15 final size:15
Alignment explanation
Indices: 397485--397518 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
397475 GGTCAACTCC
397485 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
397500 GGTCAACGGTCAATG
1 GGTCAACGGTCAACG
397515 GGTC
1 GGTC
397519 GGGTCGGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:397530 original size:18 final size:18
Alignment explanation
Indices: 397507--397607 Score: 105
Period size: 18 Copynumber: 6.2 Consensus size: 18
397497 ACGGGTCAAC
*
397507 GGTCAATGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
397525 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
*
397538 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
397556 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
*
397569 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
397587 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
397605 GGT
1 GGT
397608 TGTGACCGGT
Statistics
Matches: 69, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
13 24 0.35
18 45 0.65
ACGTcount: A:0.14, C:0.19, G:0.50, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:397552 original size:31 final size:31
Alignment explanation
Indices: 397514--397602 Score: 178
Period size: 31 Copynumber: 2.9 Consensus size: 31
397504 AACGGTCAAT
397514 GGGTCGGGTCGGGTCAACGGGTCGGGTAAAC
1 GGGTCGGGTCGGGTCAACGGGTCGGGTAAAC
397545 GGGTCGGGTCGGGTCAACGGGTCGGGTAAAC
1 GGGTCGGGTCGGGTCAACGGGTCGGGTAAAC
397576 GGGTCGGGTCGGGTCAACGGGTCGGGT
1 GGGTCGGGTCGGGTCAACGGGTCGGGT
397603 CGGGTTGTGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.13, C:0.19, G:0.51, T:0.17
Consensus pattern (31 bp):
GGGTCGGGTCGGGTCAACGGGTCGGGTAAAC
Found at i:397603 original size:13 final size:13
Alignment explanation
Indices: 397518--397585 Score: 73
Period size: 13 Copynumber: 4.8 Consensus size: 13
397508 GTCAATGGGT
397518 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
397531 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
397544 CGGGTCGGGTCGGGTCAA
1 -----CGGGTCGGGTCAA
*
397562 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
397575 CGGGTCGGGTC
1 CGGGTCGGGTC
397586 GGGTCAACGG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
13 34 0.74
18 12 0.26
ACGTcount: A:0.15, C:0.21, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:399372 original size:81 final size:81
Alignment explanation
Indices: 399245--399884 Score: 904
Period size: 81 Copynumber: 7.9 Consensus size: 81
399235 CTTTATTATC
* ** * *
399245 TTACTCAACAGTGTTTAACCGTTCATCTAATTGCCATAATTGACACCTTTCTGCCAATTGCACAG
1 TTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAG
*
399310 TTAGGCCATTATTCTT
66 TTAGGCCATTTTTCTT
* *
399326 TTACTCAATGGTACTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCTGCCAATTGCACAG
1 TTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAG
*
399391 TTAGGTCATTTTTCTT
66 TTAGGCCATTTTTCTT
* * * * *
399407 TTACTCAACGGTACTAAACCGTTCATCTAACTAGCATAATTGACACCTTTATGCCAATTGCATAA
1 TTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAG
*
399472 TTAGGGCATTTTTCTT
66 TTAGGCCATTTTTCTT
*
399488 TTACTCAACGATACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAG
1 TTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAG
399553 TTAGGCCATTTTTCTT
66 TTAGGCCATTTTTCTT
* * *
399569 TTACTCAACGATACTT-ACCGTTCATCTAACTGGCATAATTGACACATTTATGCCAATTGCACAG
1 TTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAG
*
399633 TTAGGCCATTATTCTT
66 TTAGGCCATTTTTCTT
* * * * * * * * * * *
399649 TCACTCAACGATGCTTAATCGTTCATCTAACTGACATAATTGAAACCTTTTTTCTAATTGTACAA
1 TTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAG
* *
399714 TTAGCCCATTATTCTT
66 TTAGGCCATTTTTCTT
* * * *
399730 TTACTCAATGGTACTTAACCATTAATCTAACTGGCATAATTGACACCTTTCTGCCAATTACACAG
1 TTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAG
399795 TTAGGCCATTTTTCTT
66 TTAGGCCATTTTTCTT
* *
399811 TTACTCAACGGTACTTTACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATATTGCAC
1 TTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCC-A-ATTGCAC
399876 AGTTAGGCC
64 AGTTAGGCC
399885 TCAAAGAAAC
Statistics
Matches: 496, Mismatches: 60, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
80 75 0.15
81 405 0.82
82 1 0.00
83 15 0.03
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (81 bp):
TTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACAG
TTAGGCCATTTTTCTT
Found at i:399850 original size:323 final size:325
Alignment explanation
Indices: 399262--399884 Score: 935
Period size: 323 Copynumber: 1.9 Consensus size: 325
399252 ACAGTGTTTA
* * *
399262 ACCGTTCATCTAATTGCCATAATTGACACCTTTCTGCCAATTGCACAGTTAGGCCATTATTCTTT
1 ACCGTTCATCTAACTGCCATAATTGACACATTTATGCCAATTGCACAGTTAGGCCATTATTCTTT
* * * * * * *
399327 TACTCAATGGTACTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCTGCCAATTGCACAGT
66 CACTCAACGATACTTAACCGTTCATCTAACTGACATAATTGAAACCTTTCTGCCAATTGCACAAT
** * * *
399392 TAGGTCATTTTTCTTTTACTCAACGGTACTAAACCGTTCATCTAACTAGCATAATTGACACCTTT
131 TAGCCCATTATTCTTTTACTCAACGGTACTAAACCATTAATCTAACTAGCATAATTGACACCTTT
* * *
399457 ATGCCAATTGCATAATTAGGGCATTTTTCTTTTACTCAACGATACTTAACCGTTCATCTAACTGG
196 ATGCCAATTACACAATTAGGCCATTTTTCTTTTACTCAACGATACTTAACCGTTCATCTAACTGG
399522 CATAATTGACACCTTTCTGCC-A-ATTGCACAGTTAGGCCATTTTTCTTTTACTCAACGATACTT
261 CATAATTGACACCTTTCTGCCAATATTGCACAGTTAGGCCATTTTTCTTTTACTCAACGATACTT
*
399585 ACCGTTCATCTAACTGGCATAATTGACACATTTATGCCAATTGCACAGTTAGGCCATTATTCTTT
1 ACCGTTCATCTAACTGCCATAATTGACACATTTATGCCAATTGCACAGTTAGGCCATTATTCTTT
* * * * * *
399650 CACTCAACGATGCTTAATCGTTCATCTAACTGACATAATTGAAACCTTTTTTCTAATTGTACAAT
66 CACTCAACGATACTTAACCGTTCATCTAACTGACATAATTGAAACCTTTCTGCCAATTGCACAAT
* * *
399715 TAGCCCATTATTCTTTTACTCAATGGTACTTAACCATTAATCTAACTGGCATAATTGACACCTTT
131 TAGCCCATTATTCTTTTACTCAACGGTACTAAACCATTAATCTAACTAGCATAATTGACACCTTT
* * * * *
399780 CTGCCAATTACACAGTTAGGCCATTTTTCTTTTACTCAACGGTACTTTACTGTTCATCTAACTGG
196 ATGCCAATTACACAATTAGGCCATTTTTCTTTTACTCAACGATACTTAACCGTTCATCTAACTGG
399845 CATAATTGACACCTTTCTGCCAATATTGCACAGTTAGGCC
261 CATAATTGACACCTTTCTGCCAATATTGCACAGTTAGGCC
399885 TCAAAGAAAC
Statistics
Matches: 265, Mismatches: 33, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
323 248 0.94
324 1 0.00
325 16 0.06
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (325 bp):
ACCGTTCATCTAACTGCCATAATTGACACATTTATGCCAATTGCACAGTTAGGCCATTATTCTTT
CACTCAACGATACTTAACCGTTCATCTAACTGACATAATTGAAACCTTTCTGCCAATTGCACAAT
TAGCCCATTATTCTTTTACTCAACGGTACTAAACCATTAATCTAACTAGCATAATTGACACCTTT
ATGCCAATTACACAATTAGGCCATTTTTCTTTTACTCAACGATACTTAACCGTTCATCTAACTGG
CATAATTGACACCTTTCTGCCAATATTGCACAGTTAGGCCATTTTTCTTTTACTCAACGATACTT
Found at i:399983 original size:68 final size:68
Alignment explanation
Indices: 399832--400021 Score: 272
Period size: 68 Copynumber: 2.8 Consensus size: 68
399822 TACTTTACTG
* * * *
399832 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAATATTGCACAGTTAGGCCTCAAAGAAACTT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTC-ATA-TGCACAGTTAGGCATCAAAGAAACTC
*
399897 AGTCT
64 AATCT
* *
399902 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCATCATAGACACTCAA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCATCAAAGAAACTCAA
399967 TCT
66 TCT
* * *
399970 TTCATTTATCTGGCATAAATGACACCTTTCTGTCATATGCACAATTAGGCAT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCAT
400022 ATTAATCTTT
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
68 75 0.68
69 3 0.03
70 32 0.29
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCATCAAAGAAACTCAA
TCT
Found at i:400021 original size:36 final size:36
Alignment explanation
Indices: 399913--400022 Score: 90
Period size: 36 Copynumber: 3.2 Consensus size: 36
399903 TCATCTAACT
*
399913 GGCATAAATGACACCTTTCTGTCATATGCACAGTTA
1 GGCATAAATGACACCTTTCTGTCATATGCACAATTA
* ** * *
399949 GGCAT-CATAGACACTCAATCTTTCAT-T----TATCT-
1 GGCATAAAT-GACAC-CTTTCTGTCATATGCACAAT-TA
399981 GGCATAAATGACACCTTTCTGTCATATGCACAATTA
1 GGCATAAATGACACCTTTCTGTCATATGCACAATTA
400017 GGCATA
1 GGCATA
400023 TTAATCTTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 20
0.63 0.13 0.24
Matches are distributed among these distances:
31 8 0.15
32 12 0.23
33 3 0.06
35 3 0.06
36 19 0.36
37 8 0.15
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (36 bp):
GGCATAAATGACACCTTTCTGTCATATGCACAATTA
Found at i:400339 original size:55 final size:54
Alignment explanation
Indices: 400217--400384 Score: 187
Period size: 55 Copynumber: 3.1 Consensus size: 54
400207 CATATATTTC
* * * *
400217 CCATAC-GAAAATTCATACACTTAGTATGGATTTCTCAG-TTTGCACCCATAGTG
1 CCATACAG-AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
*
400270 CTCCTACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGG
1 C-CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGT-G
* * * * **
400326 CCATACAGAAATTCATACATTTAGTATGTATTTATTATATTTTGCACACTTAGTG
1 CCATACAGAAATTCATACACTTAGTATGAATTTCTTA-GTTTTGCACACAAAGTG
400381 CCAT
1 CCAT
400385 TTGGAAATCA
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
53 1 0.01
54 32 0.33
55 50 0.51
56 15 0.15
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (54 bp):
CCATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
Found at i:401137 original size:38 final size:38
Alignment explanation
Indices: 401080--401182 Score: 126
Period size: 33 Copynumber: 2.8 Consensus size: 38
401070 TCGGGTCAAG
*
401080 TTTTTAAGTGTGATCTTCGGGTCGAGTCGGGTCAGGTT
1 TTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCAGGTT
* *
401118 TTTTTAAGTGTGGTATTCGGGTC-A----GATCAGGTT
1 TTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCAGGTT
* *
401151 TTTTTAAGTGTAATATTCGGGTCGGGTCGGGT
1 TTTTTAAGTGTGATATTCGGGTCGAGTCGGGT
401183 TCGGGTTTAG
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
33 29 0.55
37 1 0.02
38 23 0.43
ACGTcount: A:0.16, C:0.11, G:0.33, T:0.41
Consensus pattern (38 bp):
TTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCAGGTT
Found at i:401329 original size:22 final size:22
Alignment explanation
Indices: 401277--401333 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
401267 CCTCTATATA
* * *
401277 TAATTTTTTTTTTCAATTAAGT
1 TAATTTTTTTATTCAATAAAAT
* * *
401299 CAATGTTTTTATTGAATAAAAT
1 TAATTTTTTTATTCAATAAAAT
401321 TAATTTTTTTATT
1 TAATTTTTTTATT
401334 ATTTTGTGAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.60
Consensus pattern (22 bp):
TAATTTTTTTATTCAATAAAAT
Found at i:401799 original size:18 final size:18
Alignment explanation
Indices: 401760--401812 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
401750 TATGGAATTG
* *
401760 GATTCCAATT-CCTGACA
1 GATTCCAATTCCCTCATA
* *
401777 GATTCTAATTCCTTCATA
1 GATTCCAATTCCCTCATA
401795 GATTCCAATTCCCTCATA
1 GATTCCAATTCCCTCATA
401813 AACATTCCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCCTCATA
Found at i:402238 original size:96 final size:98
Alignment explanation
Indices: 402016--402239 Score: 259
Period size: 96 Copynumber: 2.3 Consensus size: 98
402006 TGGCTCTATA
* * *
402016 GTATCGATA-CCTCTATCATGGTATC-A-A-TACTACTATACTATGGTACTAATACGCCCTTCTG
1 GTATCGATACCCT-TACCATGGTATCGATACTACTACTATACTATGGTACCAATACGCCCTTCCG
* *
402077 GTATCGATACCAATTTTTGATTCGATGTTGCTTG
65 GTATCAATACCAATTTTTGATTCGATGTAGCTTG
* * *
402111 GTATCGATACCCTTACCATGGTATTGATACTACTA-TATATTATGGTACCGATAC-CCCTTCCGG
1 GTATCGATACCCTTACCATGGTATCGATACTACTACTATACTATGGTACCAATACGCCCTTCCGG
*
402174 TATCAATACCTATTTTAT-ATTCGATGTAGAC-TG
66 TATCAATACCAATTTT-TGATTCGATGTAG-CTTG
*
402207 GTATCGATACCCTTACCAT-GTAATCGTTACTAC
1 GTATCGATACCCTTACCATGGT-ATCGATACTAC
402240 ATCGTTGGTA
Statistics
Matches: 111, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
95 21 0.19
96 66 0.59
97 19 0.17
98 5 0.05
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (98 bp):
GTATCGATACCCTTACCATGGTATCGATACTACTACTATACTATGGTACCAATACGCCCTTCCGG
TATCAATACCAATTTTTGATTCGATGTAGCTTG
Found at i:403100 original size:2 final size:2
Alignment explanation
Indices: 403053--403088 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
403043 TGACTTTGTA
403053 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
403089 GAAGAAATAT
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:403589 original size:95 final size:96
Alignment explanation
Indices: 403423--403617 Score: 279
Period size: 95 Copynumber: 2.0 Consensus size: 96
403413 TAGATGAAAA
***
403423 TATATTATTATTTATTTTAAAATTCTAAAATCATATTTAAAAATTTGTTTTGATTCTAAATTTAA
1 TATATTATTATTTATTTTAAAATTCTAAAATCATATTTAAAAA--TAAATTGATTCTAAATTTAA
403488 TCATAATTCTACTTAAAGGGAAGAGAAAGAGAC
64 TCATAATTCTACTTAAAGGGAAGAGAAAGAGAC
*
403521 TATATTATTATTTATTTTAAAATTCTTTTAAA-CATATTTAAAAA-AAATT-ATTCTAAATTTAA
1 TATATTATTATTTATTTTAAAATTC--TAAAATCATATTTAAAAATAAATTGATTCTAAATTTAA
* *
403583 TCATAATTCTATTTAGAGGGAAGAGAAAGAGAC
64 TCATAATTCTACTTAAAGGGAAGAGAAAGAGAC
403616 TA
1 TA
403618 CAGGGAAAGG
Statistics
Matches: 89, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
95 46 0.52
96 2 0.02
98 25 0.28
99 12 0.13
100 4 0.04
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.42
Consensus pattern (96 bp):
TATATTATTATTTATTTTAAAATTCTAAAATCATATTTAAAAATAAATTGATTCTAAATTTAATC
ATAATTCTACTTAAAGGGAAGAGAAAGAGAC
Found at i:413852 original size:35 final size:35
Alignment explanation
Indices: 413806--413876 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
413796 GCTTCGGCGG
*
413806 AAGTTTAATATATTCAGGAACAACCTCACATAATC
1 AAGTTTAATATATTCAGGAACAACCTCACACAATC
413841 AAGTTTAATATATTCAGGAACAACCTCACACAATC
1 AAGTTTAATATATTCAGGAACAACCTCACACAATC
413876 A
1 A
413877 GACTTCTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (35 bp):
AAGTTTAATATATTCAGGAACAACCTCACACAATC
Found at i:415347 original size:90 final size:89
Alignment explanation
Indices: 415194--415368 Score: 278
Period size: 90 Copynumber: 2.0 Consensus size: 89
415184 CCTAATACAC
* * * * *
415194 CCTTTTATAGCTAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTAT
*
415259 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
*
415284 CCTTTTATATCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTAT
415349 ATTTAATTAATTGAAATTAA
66 ATTTAATTAATTGAAATTAA
415369 ATATTCGGGA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 7 0.09
90 71 0.91
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:422212 original size:90 final size:90
Alignment explanation
Indices: 422059--422233 Score: 287
Period size: 90 Copynumber: 1.9 Consensus size: 90
422049 TAACACACCC
* * *
422059 TTTATAGCCAAATTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTATATT
1 TTTATAGCCAAATTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTATATT
* *
422124 TAATTAATTGGAATTTAATAATCCT
66 TAATTAATTGAAATTAAATAATCCT
* *
422149 TTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTATATT
1 TTTATAGCCAAATTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTATATT
422214 TAATTAATTGAAATTAAATA
66 TAATTAATTGAAATTAAATA
422234 TTTGGGATTA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.45
Consensus pattern (90 bp):
TTTATAGCCAAATTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTATATT
TAATTAATTGAAATTAAATAATCCT
Found at i:437974 original size:20 final size:20
Alignment explanation
Indices: 437949--438102 Score: 105
Period size: 20 Copynumber: 7.7 Consensus size: 20
437939 AAATGACCAA
*
437949 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGAATTC
* * *
437969 CAAATTTGCAACAC-AATTTA
1 CAAATTCGCAACGCGAA-TTC
*
437989 CAAATTTGCAACGCGAATATC
1 CAAATTCGCAACGCGAAT-TC
* * *
438010 TAAA-TCGCAACGCGAGTTT
1 CAAATTCGCAACGCGAATTC
* *
438029 CAAATTTGCAACGCGATTTC
1 CAAATTCGCAACGCGAATTC
* * *
438049 CAAATTCGCAACACATAATTT
1 CAAATTCGCAACGC-GAATTC
* * *
438070 CAAATTCGTAACTCGATTTC
1 CAAATTCGCAACGCGAATTC
**
438090 TGAATTCGCAACG
1 CAAATTCGCAACG
438103 TGGATTTTGT
Statistics
Matches: 101, Mismatches: 28, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
19 6 0.06
20 74 0.73
21 21 0.21
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTC
Found at i:437993 original size:40 final size:40
Alignment explanation
Indices: 437949--438077 Score: 127
Period size: 40 Copynumber: 3.2 Consensus size: 40
437939 AAATGACCAA
* *
437949 CAAATTCGCAACGCGAACTCCAAATTTGCAACAC-AATTT
1 CAAATTCGCAACGCGAAATCCAAATTCGCAACACAAATTT
* * * * *
437988 ACAAATTTGCAACGCGAATATCTAAA-TCGCAACGCGAGTTT
1 -CAAATTCGCAACGCGAA-ATCCAAATTCGCAACACAAATTT
* **
438029 CAAATTTGCAACGCGATTTCCAAATTCGCAACACATAATTT
1 CAAATTCGCAACGCGAAATCCAAATTCGCAACACA-AATTT
438070 CAAATTCG
1 CAAATTCG
438078 TAACTCGATT
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
39 5 0.07
40 47 0.65
41 20 0.28
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (40 bp):
CAAATTCGCAACGCGAAATCCAAATTCGCAACACAAATTT
Found at i:438137 original size:20 final size:20
Alignment explanation
Indices: 437949--438141 Score: 88
Period size: 20 Copynumber: 9.6 Consensus size: 20
437939 AAATGACCAA
* ** *
437949 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACTCGATTTT
* * * *
437969 CAAATTTGCAACACAATTTA
1 CAAATTCGCAACTCGATTTT
* * * *
437989 CAAATTTGCAACGCGAATAT
1 CAAATTCGCAACTCGATTTT
* *
438009 CTAAA-TCGCAACGCGAGTTT
1 C-AAATTCGCAACTCGATTTT
* * *
438029 CAAATTTGCAACGCGATTTC
1 CAAATTCGCAACTCGATTTT
*
438049 CAAATTCGCAACAC-ATAATTT
1 CAAATTCGCAACTCGAT--TTT
*
438070 CAAATTCGTAACTCGA-TTT
1 CAAATTCGCAACTCGATTTT
* *
438089 CTGAATTCGCAACGTGGATTTT
1 C-AAATTCGCAAC-TCGATTTT
***
438111 -GTTTTCGCAACTCGATTTT
1 CAAATTCGCAACTCGATTTT
*
438130 CGAATTCGCAAC
1 CAAATTCGCAAC
438142 ACAAATTTTA
Statistics
Matches: 134, Mismatches: 30, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
19 16 0.12
20 94 0.70
21 20 0.15
22 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.30
Consensus pattern (20 bp):
CAAATTCGCAACTCGATTTT
Found at i:438150 original size:40 final size:40
Alignment explanation
Indices: 438030--438161 Score: 104
Period size: 40 Copynumber: 3.3 Consensus size: 40
438020 CGCGAGTTTC
* * * * *
438030 AAATTTGCAACGCGATTTCCAAATTCGCAACACATAATTTC
1 AAATTCGCAACTCGATTTTCGAATTCGCAACACA-AATTTT
* ****
438071 AAATTCGTAACTCGA-TTTCTGAATTCGCAACGTGGATTTT
1 AAATTCGCAACTCGATTTTC-GAATTCGCAACACAAATTTT
***
438111 GTTTTCGCAACTCGATTTTCGAATTCGCAACACAAATTTT
1 AAATTCGCAACTCGATTTTCGAATTCGCAACACAAATTTT
* *
438151 AATTTCACAAC
1 AAATTCGCAAC
438162 AGGTTTTATT
Statistics
Matches: 68, Mismatches: 21, Indels: 5
0.72 0.22 0.05
Matches are distributed among these distances:
40 42 0.62
41 26 0.38
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (40 bp):
AAATTCGCAACTCGATTTTCGAATTCGCAACACAAATTTT
Found at i:438337 original size:14 final size:15
Alignment explanation
Indices: 438318--438355 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
438308 TCCCCATCTC
438318 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
438332 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
438348 TAATTTTT
1 TAATTTTT
438356 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:439583 original size:23 final size:23
Alignment explanation
Indices: 439564--439617 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
439554 AAATGCACCT
439564 AAGTGCCACGTAGAATTGCACTG
1 AAGTGCCACGTAGAATTGCACTG
* *
439587 AAGTGCCGCGTAGAATTGTACTG
1 AAGTGCCACGTAGAATTGCACTG
439610 AAGTGCCA
1 AAGTGCCA
439618 TATAAAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACTG
Found at i:442289 original size:24 final size:24
Alignment explanation
Indices: 442232--442291 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
442222 TAGTCAGTAT
*
442232 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTAAATAC
* * *
442256 CCGGACTTTGATCTTGGTAAATAC
1 TCGAAATTTGATCTTGGTAAATAC
*
442280 TCGAATTTTGAT
1 TCGAAATTTGAT
442292 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTAAATAC
Found at i:446329 original size:21 final size:21
Alignment explanation
Indices: 446305--446401 Score: 158
Period size: 21 Copynumber: 4.6 Consensus size: 21
446295 GTTAATTGGG
*
446305 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
446326 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
446347 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
446368 CTCTTGAACGATAGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
446389 CTCTTGAACGATG
1 CTCTTGAACGATG
446402 ACAGGTGAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:446562 original size:4 final size:4
Alignment explanation
Indices: 446546--446591 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
446536 GAGCCGCTAA
* * *
446546 AAAT AAAT TAAT AAAT AAAT AAGT GAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
446592 TGCCAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:446844 original size:21 final size:21
Alignment explanation
Indices: 446820--446860 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
446810 GTCGTCACAT
*
446820 AAAGTACCGACCTCATCACGC
1 AAAGCACCGACCTCATCACGC
*
446841 AAAGCACTGACCTCATCACG
1 AAAGCACCGACCTCATCACG
446861 TAACTCCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.37, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAGCACCGACCTCATCACGC
Found at i:449905 original size:18 final size:18
Alignment explanation
Indices: 449880--449945 Score: 78
Period size: 18 Copynumber: 3.4 Consensus size: 18
449870 GGAGTAGTCA
*
449880 TTCGGGACGTAGTGGTCC
1 TTCGGGACATAGTGGTCC
*
449898 TACGGGACATATACAGTGGTCC
1 TTCGGGAC--AT--AGTGGTCC
449920 TTCGGGACATAGTGGTCC
1 TTCGGGACATAGTGGTCC
449938 TTCGGGAC
1 TTCGGGAC
449946 GAATACTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 23 0.56
20 3 0.07
22 15 0.37
ACGTcount: A:0.18, C:0.23, G:0.33, T:0.26
Consensus pattern (18 bp):
TTCGGGACATAGTGGTCC
Found at i:456250 original size:64 final size:65
Alignment explanation
Indices: 456135--456259 Score: 164
Period size: 64 Copynumber: 1.9 Consensus size: 65
456125 GATGCACTTC
* * * * *
456135 TTAATAATAGAGACATCGAATGCAATTAGTGCATCGATGCATAAGGCGTGCATTGATGCATCCCA
1 TTAATAATAGAAACATCGAATGCAATTAGTGCACCGATGCACAAGGAGTGCATCGATGCATCCCA
* *
456200 TTAATAATA-AAACATCGAATGCAATTTA-TGCACCGATGCACGAGTAGTGCATCGATGCAT
1 TTAATAATAGAAACATCGAATGCAA-TTAGTGCACCGATGCACAAGGAGTGCATCGATGCAT
456260 ACCTTCATTG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 40 0.77
65 12 0.23
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (65 bp):
TTAATAATAGAAACATCGAATGCAATTAGTGCACCGATGCACAAGGAGTGCATCGATGCATCCCA
Found at i:456915 original size:18 final size:18
Alignment explanation
Indices: 456888--456957 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
456878 TTAAGGAGTA
*
456888 GTCCTTCGGGACGTAGTG
1 GTCCTTCGGGACATAGTG
*
456906 GTCCTACGGGACATATACAGTG
1 GTCCTTCGGGAC--AT--AGTG
456928 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
456946 GTCCTTCGGGAC
1 GTCCTTCGGGAC
456958 GAATACTGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 27 0.60
20 3 0.07
22 15 0.33
ACGTcount: A:0.17, C:0.24, G:0.33, T:0.26
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:457886 original size:20 final size:20
Alignment explanation
Indices: 457863--457965 Score: 163
Period size: 20 Copynumber: 5.2 Consensus size: 20
457853 AAACTTAAAT
457863 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
457883 TCGCAACTCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
457903 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
457923 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
** *
457943 TATCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
457962 TCGC
1 TCGC
457966 GTTGCGATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
19 6 0.08
20 70 0.92
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:458531 original size:20 final size:20
Alignment explanation
Indices: 458506--458553 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
458496 TTCAAATTCA
458506 AAAATAAAATTCGCGTTGCG
1 AAAATAAAATTCGCGTTGCG
458526 AAAATAAAATTCGCGTTGCG
1 AAAATAAAATTCGCGTTGCG
458546 AAAATAAA
1 AAAATAAA
458554 CGTGCTTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (20 bp):
AAAATAAAATTCGCGTTGCG
Found at i:458565 original size:19 final size:20
Alignment explanation
Indices: 458506--458566 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
458496 TTCAAATTCA
*
458506 AAAATAAAATTCGCGTTGCG
1 AAAATAAAAGTCGCGTTGCG
*
458526 AAAATAAAATTCGCGTTGCG
1 AAAATAAAAGTCGCGTTGCG
* *
458546 AAAATAAACGT-GCTTTGCG
1 AAAATAAAAGTCGCGTTGCG
458565 AA
1 AA
458567 TTTGACTTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
19 9 0.24
20 29 0.76
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
AAAATAAAAGTCGCGTTGCG
Found at i:460252 original size:24 final size:25
Alignment explanation
Indices: 460220--460267 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
460210 ATTTTGTTTC
*
460220 TAATCATAAAACATT-TTAATTTAA
1 TAATAATAAAACATTATTAATTTAA
460244 TAATAATAAAACATTCATTAATTT
1 TAATAATAAAACATT-ATTAATTT
460268 TTAGTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
26 7 0.33
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (25 bp):
TAATAATAAAACATTATTAATTTAA
Found at i:460677 original size:54 final size:54
Alignment explanation
Indices: 460610--460785 Score: 185
Period size: 54 Copynumber: 3.3 Consensus size: 54
460600 TTTTCTGGTT
* * * *
460610 TTGCACACGTAGTGTCTATACGGTAATTCACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGTCAATACGGTAATTCATAAACTCATTATGAATTACGTAGG
* * * * * *
460664 TTGCACATATAGTGCCAATAC-ATAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGTCAATACGGT-AATTCATAAACTCATTATGAATTACGTAGG
* *** *
460718 TTGCACACATAATGTCAATACAGG-AATTCATAAACTCATTATGAATTTTTTAGA
1 TTGCACACATAGTGTCAATAC-GGTAATTCATAAACTCATTATGAATTACGTAGG
460772 TTGCACACATAGTG
1 TTGCACACATAGTG
460786 CACATTTGGT
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
53 1 0.01
54 100 0.99
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (54 bp):
TTGCACACATAGTGTCAATACGGTAATTCATAAACTCATTATGAATTACGTAGG
Found at i:461862 original size:14 final size:14
Alignment explanation
Indices: 461843--461878 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
461833 CTACAAAAAC
461843 ATTATT-TTA-ATT
1 ATTATTATTATATT
461855 A-TATTATTATATT
1 ATTATTATTATATT
461868 ATTATTATTAT
1 ATTATTATTAT
461879 TTAACAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.19
12 4 0.19
13 4 0.19
14 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:462603 original size:14 final size:14
Alignment explanation
Indices: 462584--462613 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
462574 ACGAAACCAC
*
462584 AAAATCGAGAGAAA
1 AAAATCAAGAGAAA
462598 AAAATCAAGAGAAA
1 AAAATCAAGAGAAA
462612 AA
1 AA
462614 GGAAAGAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCAAGAGAAA
Found at i:463423 original size:30 final size:29
Alignment explanation
Indices: 463373--463723 Score: 154
Period size: 30 Copynumber: 11.8 Consensus size: 29
463363 TAAGCTTATG
*
463373 TTTTGCTATGTTAGTACCTTTAAGTTTCTA
1 TTTTGCTATTTTAGT-CCTTTAAGTTTCTA
* * * *
463403 TTTGAGCTATTTTAGTCCTTTAAATTTATGC
1 TTT-TGCTATTTTAGTCCTTTAAGTTTCT-A
* * * * *
463434 TTATGCTATTTTGGTCCTTTAACTTTTTGTT
1 TTTTGCTATTTTAGTCCTTTAA--GTTTCTA
* * *
463465 TTTTGTTA-TTTAGTCCCTTAAGTGTT-TGT
1 TTTTGCTATTTTAGTCCTTTAAGT-TTCT-A
* * *
463494 TTTTGTTATTTTAGTCCTTTAAATGTCTA
1 TTTTGCTATTTTAGTCCTTTAAGTTTCTA
* * *
463523 TATTTGCTA-TTTAGACCCTTAAGTTTTTA
1 T-TTTGCTATTTTAGTCCTTTAAGTTTCTA
* * *
463552 TTTTCACTATTTTGGCCCTTTAAGTTTCTA
1 TTTT-GCTATTTTAGTCCTTTAAGTTTCTA
* * * *
463582 TTTTGCCATTATAGTCCTTTAAATTT-TGGT
1 TTTTGCTATTTTAGTCCTTTAAGTTTCT--A
* * * * *
463612 TTTTACTTTTTTAGCCCTTTACGTTTCTG
1 TTTTGCTATTTTAGTCCTTTAAGTTTCTA
* * *
463641 TTAATT-CCATTTTAGTCCCTTAAATTTCTA
1 TT--TTGCTATTTTAGTCCTTTAAGTTTCTA
* * * * * *
463671 TTTTTGTTGTTTTAGCCCTTTCAGTTTATGT
1 -TTTTGCTATTTTAGTCCTTTAAGTTTCT-A
* *
463702 TTTTGCTATTTAAGTCTTTTAA
1 TTTTGCTATTTTAGTCCTTTAA
463724 ATTGAATATG
Statistics
Matches: 234, Mismatches: 68, Indels: 38
0.69 0.20 0.11
Matches are distributed among these distances:
28 6 0.03
29 52 0.22
30 149 0.64
31 23 0.10
32 4 0.02
ACGTcount: A:0.18, C:0.14, G:0.12, T:0.56
Consensus pattern (29 bp):
TTTTGCTATTTTAGTCCTTTAAGTTTCTA
Found at i:463501 original size:29 final size:29
Alignment explanation
Indices: 463464--463555 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
463454 AACTTTTTGT
*
463464 TTTTTGTTATTTAGTCCCTTAAGTGTTTG
1 TTTTTGTTATTTAGTCCCTTAAGTGTTTA
* * *
463493 TTTTTGTTATTTTAGTCCTTTAAATGTCTA
1 TTTTTGTTA-TTTAGTCCCTTAAGTGTTTA
* * * *
463523 TATTTGCTATTTAGACCCTTAAGTTTTTA
1 TTTTTGTTATTTAGTCCCTTAAGTGTTTA
463552 TTTT
1 TTTT
463556 CACTATTTTG
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 27 0.54
30 23 0.46
ACGTcount: A:0.18, C:0.11, G:0.12, T:0.59
Consensus pattern (29 bp):
TTTTTGTTATTTAGTCCCTTAAGTGTTTA
Found at i:463563 original size:59 final size:58
Alignment explanation
Indices: 463465--463632 Score: 174
Period size: 59 Copynumber: 2.9 Consensus size: 58
463455 ACTTTTTGTT
* * ** *
463465 TTTTGTTATTTAGTCCCTTAAGTGTTTGTTTTTGTTATTTTAGTCCTTTAAATGTCTA
1 TTTTGCTATTTAGTCCCTTAAGTTTTTGTTTTTACTATTTTAGCCCTTTAAATGTCTA
* * * * * *
463523 TATTTGCTATTTAGACCCTTAAGTTTTTATTTTCACTATTTTGGCCCTTTAAGTTTCTA
1 T-TTTGCTATTTAGTCCCTTAAGTTTTTGTTTTTACTATTTTAGCCCTTTAAATGTCTA
* * * * *
463582 TTTTGCCATTATAGTCCTTTAAATTTTGGTTTTTACTTTTTTAGCCCTTTA
1 TTTTGCTATT-TAGTCCCTTAAGTTTTTGTTTTTACTATTTTAGCCCTTTA
463633 CGTTTCTGTT
Statistics
Matches: 88, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
58 9 0.10
59 79 0.90
ACGTcount: A:0.18, C:0.14, G:0.11, T:0.56
Consensus pattern (58 bp):
TTTTGCTATTTAGTCCCTTAAGTTTTTGTTTTTACTATTTTAGCCCTTTAAATGTCTA
Found at i:463675 original size:60 final size:58
Alignment explanation
Indices: 463473--463697 Score: 170
Period size: 59 Copynumber: 3.8 Consensus size: 58
463463 TTTTTTGTTA
* * * * * * *
463473 TTTAGTCCCTTAAGTGTTTGTTTTT-GTTATTTTAGTCCTTTAAATGTCTATATTTGCTA-
1 TTTAGTCCCTTAAAT-TTTATTTTTACTT-TTTTAGCCCTTTAAGTTTCTAT-TTTGCCAT
* * * * *
463532 TTTAGACCCTTAAGTTTTTATTTTCACTATTTTGGCCCTTTAAGTTTCTATTTTGCCAT
1 TTTAGTCCCTTAA-ATTTTATTTTTACTTTTTTAGCCCTTTAAGTTTCTATTTTGCCAT
* * * * *
463591 TATAGTCCTTTAAATTTTGGTTTTTACTTTTTTAGCCCTTTACGTTTCTGTTAATT-CCAT
1 TTTAGTCCCTTAAATTTT-ATTTTTACTTTTTTAGCCCTTTAAGTTTCTATT--TTGCCAT
* *
463651 TTTAGTCCCTTAAATTTCTATTTTT-GTTGTTTTAGCCCTTTCAGTTT
1 TTTAGTCCCTTAAATTT-TATTTTTACTT-TTTTAGCCCTTTAAGTTT
463698 ATGTTTTTGC
Statistics
Matches: 131, Mismatches: 27, Indels: 15
0.76 0.16 0.09
Matches are distributed among these distances:
58 10 0.08
59 76 0.58
60 42 0.32
61 3 0.02
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (58 bp):
TTTAGTCCCTTAAATTTTATTTTTACTTTTTTAGCCCTTTAAGTTTCTATTTTGCCAT
Found at i:466570 original size:12 final size:12
Alignment explanation
Indices: 466553--466577 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
466543 TGTAACCGGA
466553 TCACACTTGGGC
1 TCACACTTGGGC
466565 TCACACTTGGGC
1 TCACACTTGGGC
466577 T
1 T
466578 GCTCTTGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.24, T:0.28
Consensus pattern (12 bp):
TCACACTTGGGC
Found at i:466945 original size:14 final size:14
Alignment explanation
Indices: 466904--466947 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
466894 CTCCCCGCAT
*
466904 CCGCCCCGCATCCA
1 CCGCCCCGCATCCC
*
466918 CCGCCCCGTATCCC
1 CCGCCCCGCATCCC
*
466932 CCGCCCCACATCCC
1 CCGCCCCGCATCCC
466946 CC
1 CC
466948 ACCAGCTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.11, C:0.68, G:0.11, T:0.09
Consensus pattern (14 bp):
CCGCCCCGCATCCC
Found at i:469873 original size:15 final size:16
Alignment explanation
Indices: 469844--469874 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
469834 CGATGTTGTC
469844 ATCCTCTTCAGCAACA
1 ATCCTCTTCAGCAACA
469860 ATCCTCTT-AGCAACA
1 ATCCTCTTCAGCAACA
469875 TCTTCCCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.32, C:0.35, G:0.06, T:0.26
Consensus pattern (16 bp):
ATCCTCTTCAGCAACA
Found at i:474970 original size:23 final size:24
Alignment explanation
Indices: 474929--474973 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
474919 TATTTCTGTG
* *
474929 TTTTTATAATTAATGCATGTAAAA
1 TTTTTATAATAAATACATGTAAAA
474953 TTTTTA-AATAAATACATGTAA
1 TTTTTATAATAAATACATGTAA
474974 TGCAAATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (24 bp):
TTTTTATAATAAATACATGTAAAA
Found at i:476503 original size:18 final size:18
Alignment explanation
Indices: 476482--476524 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
476472 TATCTCCTTG
476482 TGCTCTTCATCAGACATA
1 TGCTCTTCATCAGACATA
476500 TGCTCTTCATCAGACATA
1 TGCTCTTCATCAGACATA
*
476518 TGATCTT
1 TGCTCTT
476525 TATGTGCGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.37
Consensus pattern (18 bp):
TGCTCTTCATCAGACATA
Found at i:476799 original size:6 final size:6
Alignment explanation
Indices: 476790--476831 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
476780 TGCTAATAAG
*
476790 AATGCA AATGCA AATGCA AATGCA AATGCA AATACA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA
476832 CAAGGTGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (6 bp):
AATGCA
Found at i:476799 original size:18 final size:17
Alignment explanation
Indices: 476778--476831 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 17
476768 TAAATAAATT
*
476778 AATGCTAATAAGAATGCA
1 AATGCAAATAA-AATGCA
*
476796 AATGCAAATGCAAATGCA
1 AATGCAAAT-AAAATGCA
476814 AATGCAAATACAAATGCA
1 AATGCAAATA-AAATGCA
476832 CAAGGTGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 30 0.97
19 1 0.03
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (17 bp):
AATGCAAATAAAATGCA
Found at i:479765 original size:17 final size:17
Alignment explanation
Indices: 479743--479775 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
479733 CTTTTACATA
479743 AAACCTAAACTAATATT
1 AAACCTAAACTAATATT
479760 AAACCTAAACTAATAT
1 AAACCTAAACTAATAT
479776 CACCTCTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (17 bp):
AAACCTAAACTAATATT
Found at i:489055 original size:21 final size:21
Alignment explanation
Indices: 489013--489056 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
489003 AACCCGGGAG
*
489013 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
489034 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
489055 CT
1 CT
489057 CCTCCTTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:493834 original size:20 final size:20
Alignment explanation
Indices: 493791--493854 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
493781 GGTTGACTTC
* *
493791 TTTTCCAAGGGATCGATCCT
1 TTTTCAAAGGGATTGATCCT
493811 TTTTCAAAAGGGATTGATCCT
1 TTTTC-AAAGGGATTGATCCT
493832 TTTTCAAAGGGATAT-ATCCT
1 TTTTCAAAGGGAT-TGATCCT
493852 TTT
1 TTT
493855 ACTAGAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 21 0.52
21 19 0.47
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (20 bp):
TTTTCAAAGGGATTGATCCT
Found at i:493851 original size:41 final size:40
Alignment explanation
Indices: 493775--493854 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 40
493765 GCCAAACTTC
* * *
493775 CAAAAGGGTTGACTTCTTTTCCAAGGGATCGATCCTTTTT
1 CAAAAGGGTTGACCTCTTTTCAAAGGGATAGATCCTTTTT
*
493815 CAAAAGGGATTGATCCT-TTTTCAAAGGGATATATCCTTTT
1 CAAAAGGG-TTGA-CCTCTTTTCAAAGGGATAGATCCTTTT
493855 ACTAGAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 8 0.24
41 24 0.71
42 2 0.06
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (40 bp):
CAAAAGGGTTGACCTCTTTTCAAAGGGATAGATCCTTTTT
Found at i:495698 original size:52 final size:51
Alignment explanation
Indices: 495634--495764 Score: 165
Period size: 51 Copynumber: 2.5 Consensus size: 51
495624 GCTTATGCGA
* *
495634 TAGATAAGGATAATTAATT-AGTATTTTAATATAACACTAACTCTTAGAAAGT
1 TAGATAAGGATAACT-ATTAAGTAGTTTAATATAA-ACTAACTCTTAGAAAGT
* * * *
495686 TAGATAAAGATAACTATTAAGTAGTTTAGTTTAAATTAACTCTTAGAAAGT
1 TAGATAAGGATAACTATTAAGTAGTTTAATATAAACTAACTCTTAGAAAGT
* *
495737 TAGATAAGGATAACTACTAAGTAATTTA
1 TAGATAAGGATAACTATTAAGTAGTTTA
495765 GTTTAAATTA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
51 44 0.64
52 25 0.36
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (51 bp):
TAGATAAGGATAACTATTAAGTAGTTTAATATAAACTAACTCTTAGAAAGT
Found at i:495733 original size:51 final size:51
Alignment explanation
Indices: 495671--495775 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
495661 AATATAACAC
* *
495671 TAACTCTTAGAAAGTTAGATAAAGATAACTATTAAGTAGTTTAGTTTAAAT
1 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAATTTAGTTTAAAT
*
495722 TAACTCTTAGAAAGTTAGATAAGGATAACTACTAAGTAATTTAGTTTAAAT
1 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAATTTAGTTTAAAT
495773 TAA
1 TAA
495776 ATACTTGTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (51 bp):
TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAATTTAGTTTAAAT
Found at i:495750 original size:25 final size:24
Alignment explanation
Indices: 495671--495751 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
495661 AATATAACAC
495671 TAACTCTTAGAAAGTTAGATAAAGA
1 TAACTCTTAGAAAGTTAGAT-AAGA
* * *
495696 TAACTATTA-AGTAGTTTAGTTTAA-A
1 TAACTCTTAGA-AAG-TTAG-ATAAGA
495721 TTAACTCTTAGAAAGTTAGATAAGGA
1 -TAACTCTTAGAAAGTTAGATAA-GA
495747 TAACT
1 TAACT
495752 ACTAAGTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
24 4 0.09
25 20 0.47
26 17 0.40
27 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (24 bp):
TAACTCTTAGAAAGTTAGATAAGA
Found at i:499960 original size:26 final size:26
Alignment explanation
Indices: 499931--500010 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 26
499921 TAGATAAAGA
499931 TAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTACTAAGTAGTTTAGTTTAAAT
* * *
499957 TAACT-CTTAGAAAG-TTAG-ATAAGGA-
1 TAACTACTAAG-TAGTTTAGTTTAA--AT
499982 TAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTACTAAGTAGTTTAGTTTAAAT
500008 TAA
1 TAA
500011 AAACTTGTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
24 3 0.07
25 16 0.39
26 19 0.46
27 3 0.07
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (26 bp):
TAACTACTAAGTAGTTTAGTTTAAAT
Found at i:499964 original size:51 final size:51
Alignment explanation
Indices: 499906--500010 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
499896 AATATAACAC
499906 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
*
499957 TAACTCTTAGAAAGTTAGATAAGGATAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
500008 TAA
1 TAA
500011 AAACTTGTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (51 bp):
TAACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAAT
Found at i:499985 original size:25 final size:24
Alignment explanation
Indices: 499906--499986 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
499896 AATATAACAC
499906 TAACTCTTAGAAAGTTAGATAAAGA
1 TAACTCTTAGAAAGTTAGAT-AAGA
* * *
499931 TAACTACTAAG-TAGTTTAGTTTAA-A
1 TAACT-CTTAGAAAG-TTAG-ATAAGA
499956 TTAACTCTTAGAAAGTTAGATAAGGA
1 -TAACTCTTAGAAAGTTAGATAA-GA
499982 TAACT
1 TAACT
499987 ACTAAGTAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
24 3 0.07
25 21 0.49
26 18 0.42
27 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (24 bp):
TAACTCTTAGAAAGTTAGATAAGA
Found at i:499997 original size:25 final size:24
Alignment explanation
Indices: 499918--499997 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
499908 ACTCTTAGAA
499918 AGTTAGATAAAGATAACTACTAAGT
1 AGTTAGAT-AAGATAACTACTAAGT
* * *
499943 AGTTTAGTTTAA-ATTAACT-CTTAGAA
1 AG-TTAG-ATAAGA-TAACTACTAAG-T
499969 AGTTAGATAAGGATAACTACTAAGT
1 AGTTAGATAA-GATAACTACTAAGT
499994 AGTT
1 AGTT
499998 TAGTTTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 3 0.07
25 20 0.48
26 18 0.43
27 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.34
Consensus pattern (24 bp):
AGTTAGATAAGATAACTACTAAGT
Found at i:500450 original size:18 final size:18
Alignment explanation
Indices: 500427--500477 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
500417 CCACTATGAA
500427 ATGTCCCGAAAGACCACT
1 ATGTCCCGAAAGACCACT
*
500445 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAAGACCACT
* *
500463 GTGTCCCGAATGACC
1 ATGTCCCGAAAGACC
500478 GCGTAGACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (18 bp):
ATGTCCCGAAAGACCACT
Done.