Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 16
Found at i:484235 original size:19 final size:19
Alignment explanation
Indices: 484211--484310 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
484201 AAAATTGACT
484211 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
484230 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
484249 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
484263 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
484282 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
484302 ATCGCAATG
1 ATCGCAATG
484311 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:484340 original size:53 final size:53
Alignment explanation
Indices: 484211--484327 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
484201 AAAATTGACT
484211 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
484263 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
484316 ATCGCAATGCGA
1 ATCGCAATGCGA
484328 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:484345 original size:19 final size:19
Alignment explanation
Indices: 484317--484484 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
484307 AATGGGAGAA
* *
484317 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
484336 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
484352 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
484369 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
484388 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
484404 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
484421 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
484440 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
484456 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
484473 TCCGCATTGCGA
1 T-CGCATTGCGA
484485 AATGTAATGG
Statistics
Matches: 123, Mismatches: 10, Indels: 31
0.75 0.06 0.19
Matches are distributed among these distances:
14 18 0.15
16 20 0.16
17 18 0.15
18 2 0.02
19 59 0.48
20 6 0.05
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:484360 original size:33 final size:33
Alignment explanation
Indices: 484323--484484 Score: 150
Period size: 33 Copynumber: 4.7 Consensus size: 33
484313 AGAATCGCAA
*
484323 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* *
484356 TGCGATTTTTATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
484394 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
484427 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
484460 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
484485 AATGTAATGG
Statistics
Matches: 103, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 49 0.48
34 10 0.10
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 8 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:484380 original size:52 final size:52
Alignment explanation
Indices: 484317--484484 Score: 300
Period size: 52 Copynumber: 3.2 Consensus size: 52
484307 AATGGGAGAA
* * *
484317 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
484369 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
484421 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
484473 TCCGCATTGCGA
1 T-CGCATTGCGA
484485 AATGTAATGG
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
52 102 0.91
53 10 0.09
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:484567 original size:19 final size:19
Alignment explanation
Indices: 484543--484689 Score: 188
Period size: 19 Copynumber: 8.2 Consensus size: 19
484533 AAAATTGACT
484543 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
484562 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
484581 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
484595 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
484614 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
*
484634 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
484648 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
484667 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
484687 ATC
1 ATC
484690 ACAACGAGAG
Statistics
Matches: 112, Mismatches: 4, Indels: 23
0.81 0.03 0.17
Matches are distributed among these distances:
14 20 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 52 0.46
20 28 0.25
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:484603 original size:33 final size:34
Alignment explanation
Indices: 484561--484712 Score: 136
Period size: 33 Copynumber: 4.4 Consensus size: 34
484551 GCGAAATGAA
484561 AATCGCAATGCGAAATGAAAATCGCAA-CGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAGAG
484594 AATCGCAATGCGAAATGAAAATCGCAATGCG-GA-
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAGAG
* * * *
484627 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA-GCG--A-GAG
*
484666 AATCGCAATGCGGAAATGAAAATCACAA-CGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAAGCGAGAG
484700 AATCGCAATGCGA
1 AATCGCAATGCGA
484713 TTTTCATTTC
Statistics
Matches: 98, Mismatches: 8, Indels: 26
0.74 0.06 0.20
Matches are distributed among these distances:
32 7 0.07
33 36 0.37
34 27 0.28
35 3 0.03
37 2 0.02
38 2 0.02
39 13 0.13
40 3 0.03
41 5 0.05
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCGAGAG
Found at i:484725 original size:53 final size:53
Alignment explanation
Indices: 484543--484712 Score: 324
Period size: 53 Copynumber: 3.2 Consensus size: 53
484533 AAAATTGACT
484543 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
484595 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
484648 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
484701 ATCGCAATGCGA
1 ATCGCAATGCGA
484713 TTTTCATTTC
Statistics
Matches: 116, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 29 0.25
53 87 0.75
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:487251 original size:23 final size:23
Alignment explanation
Indices: 487218--487262 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
487208 CTGAAACATC
487218 ATCAAAATCCGTG-TATTGACCAT
1 ATCAAAATCCG-GATATTGACCAT
*
487241 ATCAAAGTCCGGATATTGACCA
1 ATCAAAATCCGGATATTGACCA
487263 AGACCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (23 bp):
ATCAAAATCCGGATATTGACCAT
Found at i:487973 original size:20 final size:20
Alignment explanation
Indices: 487945--488214 Score: 281
Period size: 20 Copynumber: 13.5 Consensus size: 20
487935 AAATTTCAGT
* * *
487945 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
487965 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
487985 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
488005 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
488025 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
488045 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
488065 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
488085 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
488105 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
488125 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
488145 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
488165 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
488185 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
488205 GTTGCGATTT
1 GTTGCGATTT
488215 TGGAAAATCG
Statistics
Matches: 220, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 219 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:488644 original size:24 final size:23
Alignment explanation
Indices: 488612--488671 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
488602 AAAAAAAATT
* *
488612 AAATAAATATTTATTTATTTTATA
1 AAATTAATATTTATTTATTCTA-A
*
488636 AAATTAATATTAATTTATTCTAA
1 AAATTAATATTTATTTATTCTAA
*
488659 AAACTAA-ATTTAT
1 AAATTAATATTTAT
488672 GATATTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 5 0.16
23 7 0.23
24 19 0.61
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATTAATATTTATTTATTCTAA
Found at i:488875 original size:30 final size:30
Alignment explanation
Indices: 488810--488875 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
488800 AAAAATAAAA
488810 AATTTAATAAATAAAATTATTATTTATATT
1 AATTTAATAAATAAAATTATTATTTATATT
* * *
488840 TATTTAAT-AAT-AAATTTTTAATTTGTAATT
1 AATTTAATAAATAAAATTATT-ATTTAT-ATT
488870 AATTTA
1 AATTTA
488876 TGAAAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 7 0.23
29 8 0.27
30 15 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
AATTTAATAAATAAAATTATTATTTATATT
Found at i:493655 original size:25 final size:26
Alignment explanation
Indices: 493624--493673 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
493614 ATAAGACACT
*
493624 AAAAGTGAC-ATTTTATTATTGTCAC
1 AAAAGTGACAATTTAATTATTGTCAC
493649 AAAAGTGACAATTTAATTATTGTCA
1 AAAAGTGACAATTTAATTATTGTCA
493674 TATTTGAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (26 bp):
AAAAGTGACAATTTAATTATTGTCAC
Found at i:493976 original size:18 final size:18
Alignment explanation
Indices: 493953--493992 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
493943 TTTTAAATTA
493953 TTTTTA-ATTTATCTAAAT
1 TTTTTATATTTATCT-AAT
*
493971 TTTTTATATTTTTCTAAT
1 TTTTTATATTTATCTAAT
493989 TTTT
1 TTTT
493993 AATAATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTATATTTATCTAAT
Found at i:494322 original size:82 final size:82
Alignment explanation
Indices: 494155--494560 Score: 399
Period size: 82 Copynumber: 4.9 Consensus size: 82
494145 ACAAAATGGT
* * **
494155 AACTTTAGCGGTGTTTCTT-TACAAATG-TCGTAATAGGGTTCATCTATAGTGGCGTTTTTTTGA
1 AACTTTAGCGGTGTTT-TTATACAAACGCT-GTAATA-GGTTCACCTATAGTGGCGTTTTTTCAA
** * **
494218 TAAACGATGCAACAGAGAAG
63 TAAACGCCGCAATAGATTAG
* * * *
494238 TACTTTAGCGGTATTTTTATACAAACGCTGTAATAGGTCCATCTATAGTGGCGTTTTTTCAATAA
1 AACTTTAGCGGTGTTTTTATACAAACGCTGTAATAGGTTCACCTATAGTGGCGTTTTTTCAATAA
494303 ACGCCGCAATAGATTAG
66 ACGCCGCAATAGATTAG
* * * * ** * *
494320 TACTTTAGTGGCGTTTTTATACAAATGCCATAATAGGGTTCACCTATAGTGGCATTTTAT-AATA
1 AACTTTAGCGGTGTTTTTATACAAACGCTGTAATA-GGTTCACCTATAGTGGCGTTTTTTCAATA
*
494384 AACGCCGCAATAAATTAG
65 AACGCCGCAATAGATTAG
* * * *
494402 AACTTTAGTC-GTGCTTTTATACAAACGCCGTAATAGAGTTCACCTATAGTGGTGTTTTGTCAAT
1 AACTTTAG-CGGTGTTTTTATACAAACGCTGTAATAG-GTTCACCTATAGTGGCGTTTTTTCAAT
* * *
494466 AAACACCACAACAGATTAG
64 AAACGCCGCAATAGATTAG
* * * *
494485 AACTTTAGCGGCGTTTTTATACAAACG-TCGCAATAGTGTTTACCTATAGTGGCGCTTTTTCAAT
1 AACTTTAGCGGTGTTTTTATACAAACGCT-GTAATAG-GTTCACCTATAGTGGCGTTTTTTCAAT
*
494549 AAACGTCGCAAT
64 AAACGCCGCAAT
494561 GTTTGAATTT
Statistics
Matches: 267, Mismatches: 48, Indels: 16
0.81 0.15 0.05
Matches are distributed among these distances:
81 1 0.00
82 140 0.52
83 125 0.47
84 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (82 bp):
AACTTTAGCGGTGTTTTTATACAAACGCTGTAATAGGTTCACCTATAGTGGCGTTTTTTCAATAA
ACGCCGCAATAGATTAG
Found at i:494600 original size:22 final size:22
Alignment explanation
Indices: 494575--494631 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
494565 GAATTTATAC
*
494575 AAAATGTTATTAAAATTAAAGG
1 AAAATATTATTAAAATTAAAGG
* *
494597 AAAATATTATTATAATTAATGG
1 AAAATATTATTAAAATTAAAGG
494619 -AAATATTATTAAA
1 AAAATATTATTAAA
494632 TTATGAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (22 bp):
AAAATATTATTAAAATTAAAGG
Found at i:494644 original size:21 final size:21
Alignment explanation
Indices: 494575--494638 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 21
494565 GAATTTATAC
* * *
494575 AAAATGTTATTAAAATTAAAGG
1 AAAATATTATTATAATT-AATG
494597 AAAATATTATTATAATTAATG
1 AAAATATTATTATAATTAATG
*
494618 GAAATATTATTA-AATT-ATG
1 AAAATATTATTATAATTAATG
494637 AA
1 AA
494639 TTAATAACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 14 0.38
22 15 0.41
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (21 bp):
AAAATATTATTATAATTAATG
Found at i:499605 original size:21 final size:21
Alignment explanation
Indices: 499579--499628 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
499569 AATTTACAAC
499579 TTGCTTTTGAACTTTGACATA
1 TTGCTTTTGAACTTTGACATA
499600 TTGCTTTTGAACTTTGACATA
1 TTGCTTTTGAACTTTGACATA
*
499621 TTTCTTTT
1 TTGCTTTT
499629 TATATCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.14, G:0.12, T:0.54
Consensus pattern (21 bp):
TTGCTTTTGAACTTTGACATA
Found at i:500660 original size:156 final size:156
Alignment explanation
Indices: 500390--500670 Score: 400
Period size: 156 Copynumber: 1.8 Consensus size: 156
500380 GAAAAGTTGT
* * * *
500390 CTGTCAACAAACAACTTTCCAGTTTCATTTAGAGTCAATTTCAACTTCATAACGAAGGATATTGG
1 CTGTCAACAAACAACTTTCCAGTTTCATTCAGACTCAATTTCAACTTCACAACGAAGGATATTGA
** * * * * *
500455 ACTCGAAACAATGCAACTAACACCAGATTTCATTTCAACTTCACGACGAAGGATATCCAATTGAA
66 ACTCGAAACAACACAACTAACACAAAATTGCATTTCAACTTAACAACGAAGGATATCCAATTGAA
500520 AGCTCAACTTCACAGCGAAGGGGCGA
131 AGCTCAACTTCACAGCGAAGGGGCGA
*
500546 CTGTCAACAAACAACTTTCCAGTTTCATTCAGACTCAATTTCAACTTCACAGCGAAGGATATTGA
1 CTGTCAACAAACAACTTTCCAGTTTCATTCAGACTCAATTTCAACTTCACAACGAAGGATATTGA
** * * * *
500611 ACTCGAAGTAACACAATTTACTCAAAATTGGATTTCAACTTAACAACGAAGGATATCCAA
66 ACTCGAAACAACACAACTAACACAAAATTGCATTTCAACTTAACAACGAAGGATATCCAA
500671 CTCAAAACCA
Statistics
Matches: 107, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
156 107 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (156 bp):
CTGTCAACAAACAACTTTCCAGTTTCATTCAGACTCAATTTCAACTTCACAACGAAGGATATTGA
ACTCGAAACAACACAACTAACACAAAATTGCATTTCAACTTAACAACGAAGGATATCCAATTGAA
AGCTCAACTTCACAGCGAAGGGGCGA
Found at i:500732 original size:65 final size:65
Alignment explanation
Indices: 500628--500757 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 65
500618 GTAACACAAT
500628 TTACTCAAAATTGGATTTCAACTTAACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
1 TTACTCAAAATTGGATTTCAACTTAACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
* * *
500693 TTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
1 TTACTCAAAATTGGATTTCAACTTAACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
500758 AATCCTTTGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (65 bp):
TTACTCAAAATTGGATTTCAACTTAACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
Found at i:500992 original size:281 final size:281
Alignment explanation
Indices: 500489--501298 Score: 1285
Period size: 281 Copynumber: 2.9 Consensus size: 281
500479 AGATTTCATT
* * * *
500489 TCAACTTCAC-GACGAAGGATATCCAATTGAAAGCTCAACTTCACAGCGAAGGGGCGACTGTCAA
1 TCAACTTCACAG-CGATGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGAGCGTCTGTCAA
*
500553 CAAACAACTTTCCAGTTTCATTCAGACTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAA
65 CAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAA
* * *
500618 GTAACACAATTTACTCAAAATTGGATTTCAACTTAACAACGAAGGATATCCAACTCAAAACCAAT
130 GTGACACAATTTACTCAATATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAAT
500683 TTGGTGAAACTTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAAT
195 TTGGTGAAACTTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAAT
*
500748 TTGGTGAAACAATCCTTTGATC
260 TTGGTGAAACAATCCTTGGATC
*
500770 TCAACTTCACAGCGATGGATATCCAATTCAAAGCTCAACTTCACAGCGAATGAGCGTCTGTCAAC
1 TCAACTTCACAGCGATGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGAGCGTCTGTCAAC
* *
500835 AAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGAACTTGAAG
66 AAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAAG
* * *
500900 TGACACAATTTACTCAATATTGTATTTCAACTTCACAACAAAGGATATCCAACTCAAAATCAATT
131 TGACACAATTTACTCAATATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATT
* *
500965 TGGTGAAACTTACTCAAGATTGGATTTCAACTTCATGACAAAGGATATCCAACTCAAAACCAATT
196 TGGTGAAACTTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATT
*
501030 TGGTGAAACAATCCTTGGATT
261 TGGTGAAACAATCCTTGGATC
*
501051 TCAACTTCACAACGAAT-GATATCCAATTCAAAGCTCAACTTCACAGCGAAGGAGCGTCTGTCAA
1 TCAACTTCACAGCG-ATGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGAGCGTCTGTCAA
* * * *
501115 CAAACAACTTTCCAGTTCCATTTAGAGTCAATTTCAACTTCACAACGAAGGATATTAAACTCGAA
65 CAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAA
*
501180 GTGACAAAATTTACTCAAGT-TTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAA
130 GTGACACAATTTACTCAA-TATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAA
* * * *
501244 TTTGGTGAAAC--AATC---ATTGGATTTCAACTTCACAACGAATGATATCCAATTCAAA
194 TTTGGTGAAACTTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAA
501299 GCTAAACTTC
Statistics
Matches: 490, Mismatches: 36, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
276 35 0.07
279 3 0.01
281 448 0.91
282 4 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (281 bp):
TCAACTTCACAGCGATGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGAGCGTCTGTCAAC
AAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAAG
TGACACAATTTACTCAATATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATT
TGGTGAAACTTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATT
TGGTGAAACAATCCTTGGATC
Found at i:501013 original size:65 final size:65
Alignment explanation
Indices: 500909--501082 Score: 223
Period size: 65 Copynumber: 2.8 Consensus size: 65
500899 GTGACACAAT
* * *
500909 TTACTCAATATTGTATTTCAACTTCACAACAAAGGATATCCAACTCAAAATCAATTTGGTGAAAC
1 TTACTCAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
**
500974 TTACTCAAGATTGGATTTCAACTTCATGACAAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
1 TTACTCAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
* * * * *
501039 --AATC---CTTGGATTTCAACTTCACAACGAATGATATCCAATTCAAA
1 TTACTCAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAA
501083 GCTCAACTTC
Statistics
Matches: 97, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
60 34 0.35
63 3 0.03
65 60 0.62
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (65 bp):
TTACTCAAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
Found at i:501730 original size:85 final size:84
Alignment explanation
Indices: 501497--501754 Score: 390
Period size: 85 Copynumber: 3.0 Consensus size: 84
501487 CGAAGGTCTT
* *
501497 GGTTATCTGTCATCAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCAAATTTACA
1 GGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-AATTTACA
* *
501562 GCATAGCTCAAGGCGATAAG
65 ACATAGCTCAAGGCGAGAAG
* * * *
501582 GGCTATCTATCAACAAAAGACCTTCGAGATCGATTACACTCAGCTCAAAGGCACATCCAATTTAT
1 GGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-CAATTTAC
*
501647 AACATAACTCAAGGCGAGAAG
64 AACATAGCTCAAGGCGAGAAG
*
501668 GGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATATTTACA
1 GGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCA-ATTTACA
501733 ACATAGCTCAAGGCGAGAAG
65 ACATAGCTCAAGGCGAGAAG
501753 GG
1 GG
501755 CTATTTATAA
Statistics
Matches: 155, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
84 2 0.01
85 77 0.50
86 75 0.48
87 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (84 bp):
GGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAATTTACAA
CATAGCTCAAGGCGAGAAG
Found at i:503556 original size:10 final size:9
Alignment explanation
Indices: 503521--503555 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
503511 TCTTTCTTGT
*
503521 TTTATTTAA
1 TTTATTTAC
503530 TTTATTTAC
1 TTTATTTAC
503539 TTTATTTTAC
1 TTTA-TTTAC
503549 TTTATTT
1 TTTATTT
503556 TTCTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTATTTAC
Found at i:503625 original size:81 final size:81
Alignment explanation
Indices: 503530--503708 Score: 183
Period size: 81 Copynumber: 2.2 Consensus size: 81
503520 TTTTATTTAA
* * *
503530 TTTAT-TTACTTTATTTTACT-TTATTTTTCTATTT-TTTCGTTAATATTATGTATATA-TATAT
1 TTTATCTTATTTTATTTTAATGTT-TTTTTATATTTGTTTCGTT--T-TTATGTATATATTATAT
503591 TTATTATTA-TTTTT-ATTTC
62 TTATT-TTATTTTTTCATTTC
* * * * *
503610 TTT-TCCTTATTTTATTTAAATGTTTTTTTATATTTGTTTGGTTTTTATTTATTTATTTTATTTA
1 TTTAT-CTTATTTTATTTTAATGTTTTTTTATATTTGTTTCGTTTTTATGTATATATTATATTTA
503674 TTTTATTTTTTCATTTC
65 TTTTATTTTTTCATTTC
503691 TTTATCTTATTTTATTTT
1 TTTATCTTATTTTATTTT
503709 TTCATTTCTT
Statistics
Matches: 82, Mismatches: 9, Indels: 15
0.77 0.08 0.14
Matches are distributed among these distances:
79 13 0.16
80 18 0.22
81 42 0.51
82 9 0.11
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (81 bp):
TTTATCTTATTTTATTTTAATGTTTTTTTATATTTGTTTCGTTTTTATGTATATATTATATTTAT
TTTATTTTTTCATTTC
Found at i:503700 original size:26 final size:26
Alignment explanation
Indices: 503666--503736 Score: 126
Period size: 26 Copynumber: 2.8 Consensus size: 26
503656 ATTTATTTAT
503666 TTTAT-TTATTTTATTTTTTCATTTC
1 TTTATCTTATTTTATTTTTTCATTTC
503691 TTTATCTTATTTTATTTTTTCATTTC
1 TTTATCTTATTTTATTTTTTCATTTC
*
503717 TTTATCTTATTTTAATTTTT
1 TTTATCTTATTTTATTTTTT
503737 ACTTATTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 5 0.11
26 39 0.89
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTATCTTATTTTATTTTTTCATTTC
Found at i:503837 original size:12 final size:12
Alignment explanation
Indices: 503816--503864 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
503806 CCTTATTTTT
503816 TTTTCCTTCTTA
1 TTTTCCTTCTTA
* *
503828 TTTTCTTTCTTTTG
1 TTTTCCTTC--TTA
503842 TTTTCCTTCTTA
1 TTTTCCTTCTTA
*
503854 TTTTCTTTCTT
1 TTTTCCTTCTT
503865 TTGTTTTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 20 0.67
14 10 0.33
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTTCCTTCTTA
Found at i:503884 original size:26 final size:26
Alignment explanation
Indices: 503811--503871 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
503801 TGTCCCCTTA
*
503811 TTTTTTTTTCCTTCTTATTTTCTTTC
1 TTTTGTTTTCCTTCTTATTTTCTTTC
503837 TTTTGTTTTCCTTCTTATTTTCTTTC
1 TTTTGTTTTCCTTCTTATTTTCTTTC
503863 TTTTGTTTT
1 TTTTGTTTT
503872 TGTTTATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (26 bp):
TTTTGTTTTCCTTCTTATTTTCTTTC
Found at i:504254 original size:3 final size:3
Alignment explanation
Indices: 504217--504270 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
504207 TTTCCCTTAC
* *
504217 ATT ATT -TT ATT TTT ATTT ATTT ATTT ATC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT
504264 ATT ATT A
1 ATT ATT A
504271 ATTTTCATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.04
3 32 0.71
4 11 0.24
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:506147 original size:5 final size:4
Alignment explanation
Indices: 506121--506200 Score: 54
Period size: 4 Copynumber: 18.8 Consensus size: 4
506111 GTTTTTACTT
* *
506121 TTTA TTTC TTTT TTTA TTTA CTTTA CTTTA TTTA TTTTA TTT- TTTCA
1 TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA -TTTA TTTA TTT-A
* * *
506168 TTTC TTTA TCTTA TTTTA TTTT TTTA CTTA TTT
1 TTTA TTTA T-TTA -TTTA TTTA TTTA TTTA TTT
506201 TATATTATAT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
3 3 0.05
4 35 0.57
5 22 0.36
6 1 0.02
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:506157 original size:30 final size:29
Alignment explanation
Indices: 506114--506192 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 29
506104 TTGTTTGGTT
506114 TTTAC-TT-TTTATTTCTTTTTTT-ATTTAC
1 TTTACTTTATTTATTT-TTTTTTTCATTT-C
506142 TTTACTTTATTTATTTTATTTTTTCATTTC
1 TTTACTTTATTTATTTT-TTTTTTCATTTC
506172 TTTA-TCTTATTTTATTTTTTT
1 TTTACT-TTA-TTTATTTTTTT
506193 ACTTATTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
28 5 0.11
29 4 0.09
30 24 0.53
31 12 0.27
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (29 bp):
TTTACTTTATTTATTTTTTTTTTCATTTC
Found at i:506158 original size:26 final size:25
Alignment explanation
Indices: 506112--506213 Score: 86
Period size: 26 Copynumber: 4.0 Consensus size: 25
506102 ATTTGTTTGG
* *
506112 TTTTTAC-TT-TTTATTTCTTTTTT
1 TTTTTACTTTCTTTATTTATTTTAT
*
506135 TATTTACTTTACTTTATTTATTTTAT
1 TTTTTACTTT-CTTTATTTATTTTAT
506161 TTTTT-CATTTCTTTATCTTATTTTATT
1 TTTTTAC-TTTCTTTAT-TTATTTTA-T
*
506188 TTTTTACTTAT-TTTATATTATATTAT
1 TTTTTACTT-TCTTTAT-TTATTTTAT
506214 ACCTACATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
23 6 0.09
24 2 0.03
25 7 0.11
26 28 0.43
27 20 0.31
28 2 0.03
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTTACTTTCTTTATTTATTTTAT
Found at i:506466 original size:4 final size:5
Alignment explanation
Indices: 506445--506540 Score: 58
Period size: 5 Copynumber: 19.6 Consensus size: 5
506435 TCTTCCCTTC
* *
506445 ATTTT GTTTT ATTTT A-TTT ATTTT ATTTT A--TT ATTTC ACTTTT -TTTCT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT ATTT-T
* * ** * *
506493 ATTTT A-TTT ATTTT ACTTT GTTTT CGTTT ATTTTT CTTTT CTTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT ATTTT ATTTT ATT
506541 CTTTAGCCAT
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
3 3 0.04
4 11 0.16
5 47 0.67
6 9 0.13
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:506495 original size:24 final size:26
Alignment explanation
Indices: 506468--506517 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
506458 TTATTTATTT
506468 TATTTTA-TTATTTCACTTT-TTTTC
1 TATTTTATTTATTTCACTTTGTTTTC
*
506492 TATTTTATTTATTTTACTTTGTTTTC
1 TATTTTATTTATTTCACTTTGTTTTC
506518 GTTTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 11 0.48
26 5 0.22
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.72
Consensus pattern (26 bp):
TATTTTATTTATTTCACTTTGTTTTC
Found at i:506675 original size:10 final size:10
Alignment explanation
Indices: 506652--506685 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
506642 TTCCCTTACA
506652 TTATTTTATTT
1 TTATTTT-TTT
506663 TTATTTTTTT
1 TTATTTTTTT
506673 TTATTATTTTT
1 TTATT-TTTTT
506684 TT
1 TT
506686 CATGAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:507072 original size:5 final size:5
Alignment explanation
Indices: 507062--507099 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
507052 ATGATTAAAG
* *
507062 AATAA AATAA AATAA AACAA AGTAA AAT-A AATAA AATA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATA
507100 GAAAACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:507122 original size:29 final size:27
Alignment explanation
Indices: 507057--507126 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 27
507047 AGAAAATGAT
* *
507057 TAAAGAATAAAATAAAATAAAACAAAG
1 TAAAAAATAAAATAAAACAAAACAAAG
507084 TAAAATAAATAAAATAGAAAACAAAACGAAA-
1 T-AAA-AAATAAAAT--AAAACAAAAC-AAAG
507115 TAAAAAATAAAA
1 TAAAAAATAAAA
507127 AAATGAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
27 1 0.03
28 3 0.08
29 16 0.44
30 3 0.08
31 10 0.28
32 3 0.08
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (27 bp):
TAAAAAATAAAATAAAACAAAACAAAG
Found at i:507424 original size:4 final size:4
Alignment explanation
Indices: 507415--507480 Score: 57
Period size: 4 Copynumber: 16.8 Consensus size: 4
507405 AATATAGTAT
* ***
507415 TAAA TAAA TAAA TAAA -AGA TAAA GCGA TGAAA -AAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA
507462 TAAA GTAAA TAAA -AAA TAA
1 TAAA -TAAA TAAA TAAA TAA
507481 GAAAACCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
3 8 0.16
4 36 0.73
5 5 0.10
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.20
Consensus pattern (4 bp):
TAAA
Found at i:507600 original size:9 final size:9
Alignment explanation
Indices: 507588--507612 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
507578 AAAATAAGTA
507588 AAATAAATT
1 AAATAAATT
507597 AAATAAATT
1 AAATAAATT
507606 AAATAAA
1 AAATAAA
507613 ACAAGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAATAAATT
Found at i:508958 original size:2 final size:2
Alignment explanation
Indices: 508951--508989 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
508941 TCATATTTGT
508951 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 T
508990 TATTTTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:509016 original size:10 final size:9
Alignment explanation
Indices: 508987--509058 Score: 60
Period size: 8 Copynumber: 8.1 Consensus size: 9
508977 TATATATATA
508987 TATTATTTT
1 TATTATTTT
508996 TATT-TTTT
1 TATTATTTT
509004 TATTATCTTT
1 TATTAT-TTT
509014 TATTATTTT
1 TATTATTTT
** *
509023 T-GGACTTT
1 TATTATTTT
* *
509031 TCTT-TATT
1 TATTATTTT
509039 TATTATTTT
1 TATTATTTT
509048 TATATATTTT
1 TAT-TATTTT
509058 T
1 T
509059 TTTGGAATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
8 18 0.37
9 15 0.31
10 16 0.33
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (9 bp):
TATTATTTT
Found at i:509055 original size:17 final size:17
Alignment explanation
Indices: 508979--509056 Score: 61
Period size: 17 Copynumber: 4.5 Consensus size: 17
508969 TATATATATA
*
508979 TATATATATATTATTTT
1 TATATATTTATTATTTT
* *
508996 TATTTTTTTATTATCTTT
1 TATATATTTATTAT-TTT
*
509014 TAT-TATTT-TTGGACTTT
1 TATATATTTATT--ATTTT
* *
509031 TCTTTATTTATTATTTT
1 TATATATTTATTATTTT
509048 TATATATTT
1 TATATATTT
509057 TTTTTGGAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
16 2 0.04
17 31 0.66
18 12 0.26
19 2 0.04
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.71
Consensus pattern (17 bp):
TATATATTTATTATTTT
Found at i:509210 original size:6 final size:6
Alignment explanation
Indices: 509201--509295 Score: 59
Period size: 6 Copynumber: 14.7 Consensus size: 6
509191 TATTATGTCC
* * * *
509201 TTTTTA TTTTTA TTTTT- TCTTTA TTTTT- TTTTGTC TCTTTA TCTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA TTTTTA TTTTTA
509248 TTCTATTTA TTTTTA TTTTTTTA TATTTTA TTTATTTA TTTTTA TTTT
1 -T-T-TTTA TTTTTA --TTTTTA T-TTTTA -TT-TTTA TTTTTA TTTT
509296 CTTATTGTTC
Statistics
Matches: 73, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
5 8 0.11
6 36 0.49
7 13 0.18
8 12 0.16
9 4 0.05
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:509239 original size:18 final size:17
Alignment explanation
Indices: 509203--509280 Score: 67
Period size: 15 Copynumber: 4.8 Consensus size: 17
509193 TTATGTCCTT
509203 TTTATTTTTATTTTTTC
1 TTTATTTTTATTTTTTC
509220 TTTATTTTT-TTTTGTCTC
1 TTTATTTTTATTTT-T-TC
* * *
509238 TTTATCTTTA--TTCTA
1 TTTATTTTTATTTTTTC
509253 TTTATTTTTATTTTTT-
1 TTTATTTTTATTTTTTC
*
509269 TATA-TTTTATTT
1 TTTATTTTTATTT
509281 ATTTATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
15 18 0.36
16 7 0.14
17 15 0.30
18 10 0.20
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.78
Consensus pattern (17 bp):
TTTATTTTTATTTTTTC
Found at i:509262 original size:15 final size:14
Alignment explanation
Indices: 509201--509319 Score: 91
Period size: 14 Copynumber: 8.2 Consensus size: 14
509191 TATTATGTCC
509201 TTTTTA-TT-TTTA
1 TTTTTATTTATTTA
* *
509213 TTTTTTCTTTATTTT
1 -TTTTTATTTATTTA
* * *
509228 TTTTTGTCTCTTTA
1 TTTTTATTTATTTA
*
509242 TCTTTATTCTATTTA
1 TTTTTATT-TATTTA
*
509257 TTTTTATTTTTTTA
1 TTTTTATTTATTTA
509271 TATTTTATTTATTTA
1 T-TTTTATTTATTTA
509286 TTTTTATTT-TCTTA
1 TTTTTATTTAT-TTA
509300 TTGTTCTTATTTATTTA
1 -T-TT-TTATTTATTTA
509317 TTT
1 TTT
509320 ATTGTATATG
Statistics
Matches: 84, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
13 6 0.07
14 34 0.40
15 31 0.37
16 3 0.04
17 9 0.11
18 1 0.01
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:509270 original size:29 final size:29
Alignment explanation
Indices: 509220--509319 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 29
509210 TTATTTTTTC
* * * *
509220 TTTATTTTTTTTTGTCTCTTTAT-CTTTA
1 TTTATTTATTTTTATTTTTTTATACTTTA
*
509248 TTCTATTTATTTTTATTTTTTTATATTTTA
1 TT-TATTTATTTTTATTTTTTTATACTTTA
* **
509278 TTTATTTATTTTTATTTTCTTATTGTTCTTA
1 TTTATTTATTTTTATTTTTTTA-TACT-TTA
509309 TTTATTTATTT
1 TTTATTTATTT
509320 ATTGTATATG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
28 2 0.03
29 36 0.59
30 9 0.15
31 14 0.23
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (29 bp):
TTTATTTATTTTTATTTTTTTATACTTTA
Found at i:509283 original size:4 final size:4
Alignment explanation
Indices: 509244--509322 Score: 55
Period size: 4 Copynumber: 20.5 Consensus size: 4
509234 TCTCTTTATC
* *
509244 TTTA TTCTA TTTA -TT- TTTA TTTT TTTA TAT- TTTA TTTA TTTA -TT-
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
509288 TTTA TTT- TCTTA TTGT- TCTTA TTTA TTTA TTTA TT
1 TTTA TTTA T-TTA TT-TA T-TTA TTTA TTTA TTTA TT
509323 GTATATGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 22
0.70 0.05 0.26
Matches are distributed among these distances:
3 11 0.18
4 41 0.68
5 8 0.13
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:510603 original size:21 final size:21
Alignment explanation
Indices: 510555--510603 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
510545 TTTAGGGTTT
*
510555 GATTTTAAGTGTTATAATTTA
1 GATTTTAAATGTTATAATTTA
* * * *
510576 GAGTTTAAATGTTGTGATTTG
1 GATTTTAAATGTTATAATTTA
510597 GATTTTA
1 GATTTTA
510604 GGATTCTGAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (21 bp):
GATTTTAAATGTTATAATTTA
Found at i:510995 original size:6 final size:6
Alignment explanation
Indices: 510984--511016 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
510974 ACAAATTCAG
510984 ATGTAA ATGTAA ATGTAA ATGTAA ATGTAA ATG
1 ATGTAA ATGTAA ATGTAA ATGTAA ATGTAA ATG
511017 CATTCAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (6 bp):
ATGTAA
Found at i:516144 original size:15 final size:15
Alignment explanation
Indices: 516124--516155 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
516114 TAAATTTTTT
516124 AAGATTCTTACCTAC
1 AAGATTCTTACCTAC
516139 AAGATTCTTACCTAC
1 AAGATTCTTACCTAC
516154 AA
1 AA
516156 CAACCAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (15 bp):
AAGATTCTTACCTAC
Found at i:517485 original size:10 final size:9
Alignment explanation
Indices: 517470--517494 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
517460 ATAATTATAT
517470 ATAAAAAAA
1 ATAAAAAAA
517479 ATAAAAAAA
1 ATAAAAAAA
517488 ATAAAAA
1 ATAAAAA
517495 CTAACCGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:518045 original size:75 final size:75
Alignment explanation
Indices: 517914--518246 Score: 445
Period size: 75 Copynumber: 4.4 Consensus size: 75
517904 CTTAATCAGT
* * * * * *
517914 TAAAATAAAATAAGCATTACCTATTATGTTAAACTACATACCGGTTTATTTGAAGGTTATTAATA
1 TAAAATAAAATAAGCACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
517979 ATGTAAACGG
66 ATGTAAACGG
* ** *
517989 TAAAATAAAATAGGCACTAGATATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAAT-
1 TAAAATAAAATAAGCACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
518053 ATGTAAACGG
66 ATGTAAACGG
* *
518063 TAAAATAAAATAAGCACTACCTATTACGTTAAACTACCTACTGTTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAAGCACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
*
518128 ATGTAAAAGG
66 ATGTAAACGG
* ** * * *
518138 TAAAATAAAATATGTGCTACCCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAAT
1 TAAAATAAAATAAGCACTA-CCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAAT
518203 AATGTAAACGG
65 AATGTAAACGG
* *
518214 TAAAATAAAAT-AGACACTACTTATTATGTTAAA
1 TAAAATAAAATAAG-CACTACCTATTACGTTAAA
518247 TAGACGTTAC
Statistics
Matches: 224, Mismatches: 31, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
74 68 0.30
75 92 0.41
76 64 0.29
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (75 bp):
TAAAATAAAATAAGCACTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGG
Found at i:518094 original size:149 final size:151
Alignment explanation
Indices: 517914--518246 Score: 465
Period size: 149 Copynumber: 2.2 Consensus size: 151
517904 CTTAATCAGT
* * *
517914 TAAAATAAAATAAGCATTACCTATTATGTTAAACTACATACCGGTTTATTTGAAGGTTATTAATA
1 TAAAATAAAATAAGCACTACCTATTATGTTAAACTACATACCGGTTTATTTAAAGGTTACTAATA
* * *
517979 ATGTAAACGGTAAAATAAAATAGGCACTA-GATATTACGTTAAAATACCTACCGGTTTGTTTAAA
66 ATGTAAAAGGTAAAATAAAATAGGCACTACCATATTACGTTAAAATACCTACCAGTTTGTTTAAA
*
518043 GGTTACTAAT-ATGTAAACGG
131 GGTTAATAATAATGTAAACGG
* * * * *
518063 TAAAATAAAATAAGCACTACCTATTACGTTAAACTACCTACTGTTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAAGCACTACCTATTATGTTAAACTACATACCGGTTTATTTAAAGGTTACTAATA
* ** * * *
518128 ATGTAAAAGGTAAAATAAAATATGTGCTACCCTATTACGTTAAACTAGCTACCAGTTTGTTTAAA
66 ATGTAAAAGGTAAAATAAAATAGGCACTACCATATTACGTTAAAATACCTACCAGTTTGTTTAAA
518193 GGTTAATAATAATGTAAACGG
131 GGTTAATAATAATGTAAACGG
*
518214 TAAAATAAAAT-AGACACTACTTATTATGTTAAA
1 TAAAATAAAATAAG-CACTACCTATTATGTTAAA
518247 TAGACGTTAC
Statistics
Matches: 161, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
149 82 0.51
150 41 0.25
151 38 0.24
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (151 bp):
TAAAATAAAATAAGCACTACCTATTATGTTAAACTACATACCGGTTTATTTAAAGGTTACTAATA
ATGTAAAAGGTAAAATAAAATAGGCACTACCATATTACGTTAAAATACCTACCAGTTTGTTTAAA
GGTTAATAATAATGTAAACGG
Found at i:518247 original size:23 final size:23
Alignment explanation
Indices: 518221--518313 Score: 93
Period size: 23 Copynumber: 4.1 Consensus size: 23
518211 CGGTAAAATA
* *
518221 AAATAGACACTACTTATTATGTT
1 AAATAGACGCTACCTATTATGTT
* *
518244 AAATAGACGTTACCTATTACGTT
1 AAATAGACGCTACCTATTATGTT
*
518267 AAACT--A-GTTACCTATTATGTT
1 AAA-TAGACGCTACCTATTATGTT
**
518288 AAATAGGTGCTACCTATTATGTT
1 AAATAGACGCTACCTATTATGTT
518311 AAA
1 AAA
518314 CTATCGGTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.02
21 17 0.29
22 1 0.02
23 39 0.66
24 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
AAATAGACGCTACCTATTATGTT
Found at i:518278 original size:21 final size:22
Alignment explanation
Indices: 518235--518316 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 22
518225 AGACACTACT
518235 TATTATGTTAAA-TAGACGTTACC
1 TATTATGTTAAACTAG--GTTACC
*
518258 TATTACGTTAAACTA-GTTACC
1 TATTATGTTAAACTAGGTTACC
518279 TATTATGTTAAA-TAGGTGCTACC
1 TATTATGTTAAACTAGGT--TACC
518302 TATTATGTTAAACTA
1 TATTATGTTAAACTA
518317 TCGGTTTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.04
21 19 0.37
23 27 0.52
24 4 0.08
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (22 bp):
TATTATGTTAAACTAGGTTACC
Found at i:518628 original size:18 final size:17
Alignment explanation
Indices: 518594--518630 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
518584 CTCTAAATGT
*
518594 TAATAATAATGTATCCA
1 TAATAATAATATATCCA
518611 TAATAATAAATATATCCA
1 TAATAAT-AATATATCCA
518629 TA
1 TA
518631 CTTACTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (17 bp):
TAATAATAATATATCCA
Found at i:518962 original size:109 final size:108
Alignment explanation
Indices: 518848--519341 Score: 413
Period size: 109 Copynumber: 4.5 Consensus size: 108
518838 TATTTACAAT
* * * * * * *
518848 AAAATAAGAAATTAACCTATTTTGTTGTCTTAAGATTTCGAAGGATCCATCAGCTTAAACTTTGA
1 AAAATAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGACCCATCAACTTAAACTTTGA
518913 TAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAAC
66 TAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAAC
* * *
518956 AAAAATAAGTAATTAACTTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAACTTAAACTTTG
1 -AAAATAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGACCCATCAACTTAAACTTTG
* *
519021 ATAATATTTTAGGCGCTACCTAATATTTTGATAATATTAATAAC
65 ATAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAAC
* *
519065 AAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAACTTTTAAAAGAC
1 AAAATAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGACCCATCAAC--TT--AA-AC
* ** * ** * * ** * * ** * *
519130 GCTACATATTACATTAAATAAACACTACTTGTTATGTT-ATTATGTTTGTTAT
61 -TTTGATA--ACATT--TTAGGCGCTACCTAATATGTTGATAATATTAATAAC
**** * * ** * *
519182 TGTTTCTAGTAATTAACATATTTTGTTATCGTTGGATTTTTAAGG-CTCCATCAGCTTAAAC-TT
1 AAAAT-AAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGAC-CCATCAACTTAAACTTT
* *
519245 GGTAACATTTTAGGCGCTACCTAATATGTTGATAATATTGATAA-
64 GATAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAAC
* * *
519289 AAAATCAAGTAATTGACCTATTTTGTTATTGTCGGATTTCTAAGG-CCACATCA
1 AAAAT-AAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGACC-CATCA
519342 GTGTTAAAAA
Statistics
Matches: 304, Mismatches: 67, Indels: 30
0.76 0.17 0.07
Matches are distributed among these distances:
106 1 0.00
107 55 0.18
108 59 0.19
109 101 0.33
110 2 0.01
111 3 0.01
112 2 0.01
113 4 0.01
114 6 0.02
116 6 0.02
117 11 0.04
118 54 0.18
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (108 bp):
AAAATAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGACCCATCAACTTAAACTTTGA
TAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAAC
Found at i:519301 original size:225 final size:225
Alignment explanation
Indices: 518963--519422 Score: 627
Period size: 225 Copynumber: 2.0 Consensus size: 225
518953 AACAAAAATA
* *
518963 AGTAATTAACTTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAACTTAAACTTTGATAATAT
1 AGTAATTAACATATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAACTTAAACTTTGATAACAT
* * *
519028 TTTAGGCGCTACCTAATATTTTGATAATATTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCGCTACCTAATATGTTGATAATATTAATAAAAAATCAAGTAATTAACCTATTTTGTTAT
* *
519093 CGTCAGATTTCTAAGGCCCCATCAACT-TTTAAAAGACGCTACATATTACATTAAATAAACACTA
131 CGTCAGATTTCTAAGGCCACATC-ACTGTTAAAAAGACGCTACATATTACATT-AATAAACACTA
* * * * *
519157 CTTGTTATGTTATTATGTTTGTTATTGTTTCT
194 CCTGTTATGTTATTATGGTTGATAATGTTTCC
* * * * *
519189 AGTAATTAACATATTTTGTTATCGTTGGATTTTTAAGGCTCCATCAGCTTAAAC-TTGGTAACAT
1 AGTAATTAACATATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAACTTAAACTTTGATAACAT
* *
519253 TTTAGGCGCTACCTAATATGTTGATAATATTGATAAAAAATCAAGTAATTGACCTATTTTGTTAT
66 TTTAGGCGCTACCTAATATGTTGATAATATTAATAAAAAATCAAGTAATTAACCTATTTTGTTAT
* * * * * * * * * *
519318 TGTCGGATTTCTAAGGCCACATCAGTGTTAAAAAGGCGCTACCTATTACGTTCATTAGCGCTACC
131 CGTCAGATTTCTAAGGCCACATCACTGTTAAAAAGACGCTACATATTACATTAATAAACACTACC
519383 TGTTATGTTATTATGGTTGATAATGTTTCC
196 TGTTATGTTATTATGGTTGATAATGTTTCC
519413 AGTAATTAAC
1 AGTAATTAAC
519423 CGATTATGTT
Statistics
Matches: 204, Mismatches: 29, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
224 46 0.23
225 109 0.53
226 49 0.24
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (225 bp):
AGTAATTAACATATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAACTTAAACTTTGATAACAT
TTTAGGCGCTACCTAATATGTTGATAATATTAATAAAAAATCAAGTAATTAACCTATTTTGTTAT
CGTCAGATTTCTAAGGCCACATCACTGTTAAAAAGACGCTACATATTACATTAATAAACACTACC
TGTTATGTTATTATGGTTGATAATGTTTCC
Found at i:522635 original size:74 final size:74
Alignment explanation
Indices: 522514--522661 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
522504 AAAACACATA
*
522514 AACTGCCAGTACTCTCAAACCAGGACTAAGTAGCCCATCAATCGACACTATGGGCACGACGAATA
1 AACTGCCAGTACTCTCAAACCAGGACTAAGCAGCCCATCAATCGACACTATGGGCACGACGAATA
522579 AACAATTAG
66 AACAATTAG
522588 AACTGCCAGTACTCTCAAACCAGGACTAAGCAGCCCATCAATCGACACTATGGGCACGACGAATA
1 AACTGCCAGTACTCTCAAACCAGGACTAAGCAGCCCATCAATCGACACTATGGGCACGACGAATA
522653 AACAATTAG
66 AACAATTAG
522662 CGACATCACC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.17
Consensus pattern (74 bp):
AACTGCCAGTACTCTCAAACCAGGACTAAGCAGCCCATCAATCGACACTATGGGCACGACGAATA
AACAATTAG
Found at i:527523 original size:20 final size:22
Alignment explanation
Indices: 527476--527526 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
527466 GAATACCCTC
* *
527476 TGTGCTAGGGTTTTGTGTCGTT
1 TGTGATAGGGTTTTGTGTCGTA
527498 TGTGATAGGGTTTTGT-T-GTA
1 TGTGATAGGGTTTTGTGTCGTA
527518 TGTGATAGG
1 TGTGATAGG
527527 TGTTCCGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 11 0.41
21 1 0.04
22 15 0.56
ACGTcount: A:0.12, C:0.04, G:0.37, T:0.47
Consensus pattern (22 bp):
TGTGATAGGGTTTTGTGTCGTA
Found at i:539933 original size:82 final size:82
Alignment explanation
Indices: 539834--540439 Score: 725
Period size: 82 Copynumber: 7.4 Consensus size: 82
539824 AACGTCGAGC
* * *
539834 CTGATCTCCCCTAAATGAATAATGAAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAGA
1 CTGATCTCCCCTGAATGAATAGTGAAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAAA
* *
539899 AGTGGCACAAATCTAGT
66 AGTGGCACAGATCCAGT
* * * * * * *
539916 ATAATCTCCCCTGAATGAATAGT-AGAGAAGATGCATATTCAAAAATTGATTTGAATACCCGAAG
1 CTGATCTCCCCTGAATGAATAGTGA-AGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAA
539980 AAGTGGCACAGATCCAGT
65 AAGTGGCACAGATCCAGT
* * *
539998 CTGATCTCCCCTGAATGAATAGTGGAGCATATACATCTTCAAAAATTGATCTGAATACCCAAAAA
1 CTGATCTCCCCTGAATGAATAGTGAAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAAA
* * **
540063 AGAGGCACAAATATAGT
66 AGTGGCACAGATCCAGT
* * * * * * *
540080 ATGATCTCCTCTAAATGAATAGTGGAGAAGATACATATTCAAAAATTGATTTGAATACCCGAAAA
1 CTGATCTCCCCTGAATGAATAGTGAAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAAA
* *
540145 AGAGGCACAAATCCAGT
66 AGTGGCACAGATCCAGT
* *
540162 CTGATCTCCCCTGAATGAATAAT-AGAGCAGATACATCTTCAAAAATTGATCTGAATACCCCAAG
1 CTGATCTCCCCTGAATGAATAGTGA-AGCAGATACATCTTCAAAAATTGATCTGAATACCCGAA-
*
540226 AAA-TGGCACAGATCTAGT
64 AAAGTGGCACAGATCCAGT
540244 CTGATCTCCCCTGAATGAATAGT-ATAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAA
1 CTGATCTCCCCTGAATGAATAGTGA-AGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAA
* *
540308 AAGAGGCACAGATCCAAT
65 AAGTGGCACAGATCCAGT
* * * ** * * *
540326 CTGATCTCCCCTGAACGAATAGTGGAGCATATATGTCTTTAAAAATTGATCTAAATACTCGAAAA
1 CTGATCTCCCCTGAATGAATAGTGAAGCAGATACATCTTCAAAAATTGATCTGAATACCCG-AAA
* *
540391 AAGTGGCATAGATCCAAT
65 AAGTGGCACAGATCCAGT
* * *
540409 CTGATCTCCTCTGAATGAATAATGGAGCAGA
1 CTGATCTCCCCTGAATGAATAGTGAAGCAGA
540440 CCCATCATCC
Statistics
Matches: 451, Mismatches: 66, Indels: 13
0.85 0.12 0.02
Matches are distributed among these distances:
81 4 0.01
82 398 0.88
83 49 0.11
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (82 bp):
CTGATCTCCCCTGAATGAATAGTGAAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAAA
AGTGGCACAGATCCAGT
Found at i:540110 original size:164 final size:164
Alignment explanation
Indices: 539834--540429 Score: 816
Period size: 164 Copynumber: 3.6 Consensus size: 164
539824 AACGTCGAGC
* * * *
539834 CTGATCTCCCCTAAATGAATAATGAAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAGA
1 CTGATCTCCCCTGAATGAATAATGGAGCAGATACATCTTCAAAAATTGATCTGAATACCCAAAAA
* *
539899 AGTGGCACAAATCTAGTATAATCTCCCCTGAATGAATAGTAGAGAAGATGCATATTCAAAAATTG
66 AGTGGCACAAATCTAGTATGATCTCCCCTGAATGAATAGTAGAGAAGATACATATTCAAAAATTG
* *
539964 ATTTGAATACCCGAAGAAGTGGCACAGATCCAGT
131 ATTTGAATACCCGAAAAAGAGGCACAGATCCAGT
* *
539998 CTGATCTCCCCTGAATGAATAGTGGAGCATATACATCTTCAAAAATTGATCTGAATACCCAAAAA
1 CTGATCTCCCCTGAATGAATAATGGAGCAGATACATCTTCAAAAATTGATCTGAATACCCAAAAA
* * * * *
540063 AGAGGCACAAATATAGTATGATCTCCTCTAAATGAATAGTGGAGAAGATACATATTCAAAAATTG
66 AGTGGCACAAATCTAGTATGATCTCCCCTGAATGAATAGTAGAGAAGATACATATTCAAAAATTG
*
540128 ATTTGAATACCCGAAAAAGAGGCACAAATCCAGT
131 ATTTGAATACCCGAAAAAGAGGCACAGATCCAGT
* *
540162 CTGATCTCCCCTGAATGAATAATAGAGCAGATACATCTTCAAAAATTGATCTGAATACCCCAAGA
1 CTGATCTCCCCTGAATGAATAATGGAGCAGATACATCTTCAAAAATTGATCTGAATA-CCCAAAA
* * * * *
540227 AA-TGGCACAGATCTAGTCTGATCTCCCCTGAATGAATAGTATAGCAGATACATCTTCAAAAATT
65 AAGTGGCACAAATCTAGTATGATCTCCCCTGAATGAATAGTAGAGAAGATACATATTCAAAAATT
* *
540291 GATCTGAATACCCGAAAAAGAGGCACAGATCCAAT
130 GATTTGAATACCCGAAAAAGAGGCACAGATCCAGT
* * * ** * * *
540326 CTGATCTCCCCTGAACGAATAGTGGAGCATATATGTCTTTAAAAATTGATCTAAATACTCGAAAA
1 CTGATCTCCCCTGAATGAATAATGGAGCAGATACATCTTCAAAAATTGATCTGAATAC-CCAAAA
* * * * * *
540391 AAGTGGCATAGATCCAATCTGATCTCCTCTGAATGAATA
65 AAGTGGCACAAATCTAGTATGATCTCCCCTGAATGAATA
540430 ATGGAGCAGA
Statistics
Matches: 382, Mismatches: 47, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
163 1 0.00
164 341 0.89
165 40 0.10
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (164 bp):
CTGATCTCCCCTGAATGAATAATGGAGCAGATACATCTTCAAAAATTGATCTGAATACCCAAAAA
AGTGGCACAAATCTAGTATGATCTCCCCTGAATGAATAGTAGAGAAGATACATATTCAAAAATTG
ATTTGAATACCCGAAAAAGAGGCACAGATCCAGT
Found at i:540280 original size:246 final size:246
Alignment explanation
Indices: 539835--540439 Score: 832
Period size: 246 Copynumber: 2.5 Consensus size: 246
539825 ACGTCGAGCC
* * *
539835 TGATCTCCCCTAAATGAATAATGAAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAGAA
1 TGATCTCCCCTAAATGAATAGTGGAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAAAA
* * * * * *
539900 GTGGCACAAATCTAGTATAATCTCCCCTGAATGAATAGTAGAGAAGATGCATATTCAAAAATTGA
66 GTGGCACAAATCCAGTCTGATCTCCCCTGAATGAATAATAGAGCAGATACATATTCAAAAATTGA
* * * * *
539965 TTTGAATACCCGAAGAAGTGGCACAGATCCAGTCTGATCTCCCCTGAATGAATAGTGGAGCATAT
131 TCTGAATACCCCAAGAAATGGCACAGATCCAGTCTGATCTCCCCTGAATGAATAGTAGAGCAGAT
* *
540030 ACATCTTCAAAAATTGATCTGAATACCCAAAAAAGAGGCACAAATATAGTA
196 ACATCTTCAAAAATTGATCTGAATACCCAAAAAAGAGGCACAAATACAATA
* * * *
540081 TGATCTCCTCTAAATGAATAGTGGAGAAGATACATATTCAAAAATTGATTTGAATACCCGAAAAA
1 TGATCTCCCCTAAATGAATAGTGGAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAAAA
* *
540146 GAGGCACAAATCCAGTCTGATCTCCCCTGAATGAATAATAGAGCAGATACATCTTCAAAAATTGA
66 GTGGCACAAATCCAGTCTGATCTCCCCTGAATGAATAATAGAGCAGATACATATTCAAAAATTGA
* *
540211 TCTGAATACCCCAAGAAATGGCACAGATCTAGTCTGATCTCCCCTGAATGAATAGTATAGCAGAT
131 TCTGAATACCCCAAGAAATGGCACAGATCCAGTCTGATCTCCCCTGAATGAATAGTAGAGCAGAT
* * * *
540276 ACATCTTCAAAAATTGATCTGAATACCCGAAAAAGAGGCACAGATCCAATC
196 ACATCTTCAAAAATTGATCTGAATACCCAAAAAAGAGGCACAAATACAATA
* * * ** * * *
540327 TGATCTCCCCTGAACGAATAGTGGAGCATATATGTCTTTAAAAATTGATCTAAATACTCGAAAAA
1 TGATCTCCCCTAAATGAATAGTGGAGCAGATACATCTTCAAAAATTGATCTGAATACCCG-AAAA
* * * * *
540392 AGTGGCATAGATCCAATCTGATCTCCTCTGAATGAATAATGGAGCAGA
65 AGTGGCACAAATCCAGTCTGATCTCCCCTGAATGAATAATAGAGCAGA
540440 CCCATCATCC
Statistics
Matches: 312, Mismatches: 46, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
246 266 0.85
247 46 0.15
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (246 bp):
TGATCTCCCCTAAATGAATAGTGGAGCAGATACATCTTCAAAAATTGATCTGAATACCCGAAAAA
GTGGCACAAATCCAGTCTGATCTCCCCTGAATGAATAATAGAGCAGATACATATTCAAAAATTGA
TCTGAATACCCCAAGAAATGGCACAGATCCAGTCTGATCTCCCCTGAATGAATAGTAGAGCAGAT
ACATCTTCAAAAATTGATCTGAATACCCAAAAAAGAGGCACAAATACAATA
Found at i:547516 original size:77 final size:76
Alignment explanation
Indices: 547400--548001 Score: 606
Period size: 77 Copynumber: 7.8 Consensus size: 76
547390 TGTACCTAAA
* * * * *
547400 AATGTCATGGTTCACCAAAAAAGTAGGTTGCGATATGAAATGTTAATATTTTTATTAATAAAATA
1 AATGTCATGGTTCACTAATAAA-TATGTTGCGATCTGAAATGTTAATATTTTTATTAATAAAATG
* * * *
547465 GATTACGCCAAAA
65 GGTTGCACC-AAG
*
547478 AATGTCATGGTTCACTAAGAAATATGTTGCGATCTGAAATGTTAATATTTTTATTAATAAAATGG
1 AATGTCATGGTTCACTAATAAATATGTTGCGATCTGAAATGTTAATATTTTTATTAATAAAATGG
547543 GTTGCACCCAAG
66 GTTGCA-CCAAG
* ** ** * *
547555 AATATCATAATTCACTAATAAA-ATAGTTATGATCTGGAATATTAATATTTTTATTAATAAAATG
1 AATGTCATGGTTCACTAATAAATAT-GTTGCGATCTGAAATGTTAATATTTTTATTAATAAAATG
*
547619 GGTTGCATCCAAT
65 GGTTGCA-CCAAG
* * * * *
547632 AATGTCATGATTCACTAATAAATAGGTTGTGATATGAAATATTAATATTTTTATTAATAAAATGG
1 AATGTCATGGTTCACTAATAAATATGTTGCGATCTGAAATGTTAATATTTTTATTAATAAAATGG
* *
547697 ATTGCCTCCAAG
66 GTTG-CACCAAG
* * * * * *
547709 AATGTCATGATTCATTAATAAATAGGTTACGA-CGTGGAATATTAATATTTTTATTAATAAAATG
1 AATGTCATGGTTCACTAATAAATATGTTGCGATC-TGAAATGTTAATATTTTTATTAATAAAATG
*
547773 GGTTGCGTCCAAG
65 GGTTGC-ACCAAG
* *
547786 AATGTCATAGTTCACTAATAAAT-TGGTTACGATCT-AGAATGTTAATATTTTTATTAATAAAAT
1 AATGTCATGGTTCACTAATAAATAT-GTTGCGATCTGA-AATGTTAATATTTTTATTAATAAAAT
* *
547849 GGGTTACATCTAAG
64 GGGTTGCA-CCAAG
* * *
547863 AACGTCATGGTTCACAAATAAATATGTTGCGATAT-AGAATGTTAATATTTTTATTAATAAAATG
1 AATGTCATGGTTCACTAATAAATATGTTGCGATCTGA-AATGTTAATATTTTTATTAATAAAATG
*
547927 GGTTGCATACAAG
65 GGTTGCA-CCAAG
* * * * * *
547940 AATGTTATGGTTCACTAATAAAACAAGTTGAGATTTGGAATGTTAAT-TTTTCTATT-ATAAAA
1 AATGTCATGGTTCACTAAT-AAATATGTTGCGATCTGAAATGTTAATATTTT-TATTAATAAAA
548002 AATTTAAAAG
Statistics
Matches: 451, Mismatches: 59, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
76 3 0.01
77 397 0.88
78 51 0.11
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (76 bp):
AATGTCATGGTTCACTAATAAATATGTTGCGATCTGAAATGTTAATATTTTTATTAATAAAATGG
GTTGCACCAAG
Found at i:547827 original size:37 final size:37
Alignment explanation
Indices: 547784--547904 Score: 93
Period size: 37 Copynumber: 3.2 Consensus size: 37
547774 GTTGCGTCCA
547784 AGAATGTCATAGTTCACTAATAAATTGGTTACGATCT
1 AGAATGTCATAGTTCACTAATAAATTGGTTACGATCT
* * * * *
547821 AGAATGTTAATATTTTTATTAATAAAATGGGTTAC-ATCT
1 AGAATG-TCATA-GTTCACTAAT-AAATTGGTTACGATCT
* * * * *
547860 AAGAACGTCATGGTTCACAAATAAATAT-GTTGCGATAT
1 -AGAATGTCATAGTTCACTAATAAAT-TGGTTACGATCT
547898 AGAATGT
1 AGAATGT
547905 TAATATTTTT
Statistics
Matches: 62, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
37 20 0.32
38 13 0.21
39 14 0.23
40 15 0.24
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (37 bp):
AGAATGTCATAGTTCACTAATAAATTGGTTACGATCT
Found at i:547833 original size:231 final size:231
Alignment explanation
Indices: 547400--547961 Score: 754
Period size: 231 Copynumber: 2.4 Consensus size: 231
547390 TGTACCTAAA
547400 AATGTCATGGTTCACCAAA-AAAGTAGGTTGCGATATGAAATGTTAATATTTTTATTAATAAAAT
1 AATGTCATGGTTCA-CAAATAAA-TAGGTTGCGATATGAAATGTTAATATTTTTATTAATAAAAT
* * * * * * * *
547464 AGATTACGC-CAAAAAATGTCATGGTTCACTAAGAAATATGTTGCGATCTGAAATGTTAATATTT
64 GGATTGC-CTCCAAGAATGTCATGGTTCACTAATAAATAGGTTACGATCTGAAATATTAATATTT
* *
547528 TTATTAATAAAATGGGTTGCACCCAAGAATATCATAATTCACTAATAAAATAGTTATGATCTGGA
128 TTATTAATAAAATGGGTTGCACCCAAGAATATCATAATTCACTAATAAAATAGTTACGATCTAGA
* *
547593 ATATTAATATTTTTATTAATAAAATGGGTTGCATCCAAT
193 ATATTAATATTTTTATTAATAAAATGGGTTACATCCAAG
* * * *
547632 AATGTCATGATTCACTAATAAATAGGTTGTGATATGAAATATTAATATTTTTATTAATAAAATGG
1 AATGTCATGGTTCACAAATAAATAGGTTGCGATATGAAATGTTAATATTTTTATTAATAAAATGG
* * *
547697 ATTGCCTCCAAGAATGTCATGATTCATTAATAAATAGGTTACGA-CGTGGAATATTAATATTTTT
66 ATTGCCTCCAAGAATGTCATGGTTCACTAATAAATAGGTTACGATC-TGAAATATTAATATTTTT
** * * * *
547761 ATTAATAAAATGGGTTGCGTCCAAGAATGTCATAGTTCACTAATAAATTGGTTACGATCTAGAAT
130 ATTAATAAAATGGGTTGCACCCAAGAATATCATAATTCACTAATAAAATAGTTACGATCTAGAAT
* *
547826 GTTAATATTTTTATTAATAAAATGGGTTACATCTAAG
195 ATTAATATTTTTATTAATAAAATGGGTTACATCCAAG
* *
547863 AACGTCATGGTTCACAAATAAATATGTTGCGATAT-AGAATGTTAATATTTTTATTAATAAAATG
1 AATGTCATGGTTCACAAATAAATAGGTTGCGATATGA-AATGTTAATATTTTTATTAATAAAATG
* * * *
547927 GGTTGCATACAAGAATGTTATGGTTCACTAATAAA
65 GATTGCCTCCAAGAATGTCATGGTTCACTAATAAA
547962 ACAAGTTGAG
Statistics
Matches: 287, Mismatches: 39, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
230 3 0.01
231 268 0.93
232 16 0.06
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (231 bp):
AATGTCATGGTTCACAAATAAATAGGTTGCGATATGAAATGTTAATATTTTTATTAATAAAATGG
ATTGCCTCCAAGAATGTCATGGTTCACTAATAAATAGGTTACGATCTGAAATATTAATATTTTTA
TTAATAAAATGGGTTGCACCCAAGAATATCATAATTCACTAATAAAATAGTTACGATCTAGAATA
TTAATATTTTTATTAATAAAATGGGTTACATCCAAG
Found at i:547846 original size:39 final size:39
Alignment explanation
Indices: 547722--547930 Score: 126
Period size: 40 Copynumber: 5.4 Consensus size: 39
547712 GTCATGATTC
* * *
547722 ATTAATAAATAGGTTACGA-CGTGGAATATTAATATTTTT
1 ATTAATAAATGGGTTACGATC-TAGAATGTTAATATTTTT
* * * * *
547761 ATTAATAAAATGGGTTGCG-TCCAAGAATG-TCATA-GTTC
1 ATTAAT-AAATGGGTTACGAT-CTAGAATGTTAATATTTTT
* *
547799 ACTAATAAATTGGTTACGATCTAGAATGTTAATATTTTT
1 ATTAATAAATGGGTTACGATCTAGAATGTTAATATTTTT
* * ** *
547838 ATTAATAAAATGGGTTAC-ATCTAAGAACG-TCAT-GGTTC
1 ATTAAT-AAATGGGTTACGATCT-AGAATGTTAATATTTTT
** ** * *
547876 ACAAATAAATATGTTGCGATATAGAATGTTAATATTTTT
1 ATTAATAAATGGGTTACGATCTAGAATGTTAATATTTTT
547915 ATTAATAAAATGGGTT
1 ATTAAT-AAATGGGTT
547931 GCATACAAGA
Statistics
Matches: 121, Mismatches: 37, Indels: 23
0.67 0.20 0.13
Matches are distributed among these distances:
37 30 0.25
38 24 0.20
39 30 0.25
40 36 0.30
41 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (39 bp):
ATTAATAAATGGGTTACGATCTAGAATGTTAATATTTTT
Found at i:548271 original size:133 final size:134
Alignment explanation
Indices: 548032--548279 Score: 399
Period size: 133 Copynumber: 1.9 Consensus size: 134
548022 TTTCCGAAAG
* *
548032 TCGATACTTTCGAATTTAAAGAAAAACATGGAAAATGAGAAGGATGCAAAGTATCGATATTTTTA
1 TCGATACTTTCGAATTTAAAGAAAAACATGGAAAATGAGAAGGATGCAAAGTATCAATAATTTTA
* * * *
548097 CAGAAGTATCGATACTTTTAAATTCGAAAGTTAAAATATCATTTTTCATTTTTTAAAAATTCAAA
66 CAAAAATATCGATACTTTTAAATTCAAAAGTTAAAATATCATTTTCCATTTTTTAAAAATTCAAA
548162 AATA
131 AATA
* * *
548166 TCGATACTTTCGAATTTAAA-TAAAACATGGAAAATGAGAAGGTTGCAAAGTATCAATAATTTTC
1 TCGATACTTTCGAATTTAAAGAAAAACATGGAAAATGAGAAGGATGCAAAGTATCAATAATTTTA
*
548230 CAAAAATATCGATACTTTTAACTTCAAAAGTTAAAATATCATTTTCCATT
66 CAAAAATATCGATACTTTTAAATTCAAAAGTTAAAATATCATTTTCCATT
548280 AATATTTTTC
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
133 84 0.81
134 20 0.19
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (134 bp):
TCGATACTTTCGAATTTAAAGAAAAACATGGAAAATGAGAAGGATGCAAAGTATCAATAATTTTA
CAAAAATATCGATACTTTTAAATTCAAAAGTTAAAATATCATTTTCCATTTTTTAAAAATTCAAA
AATA
Found at i:549268 original size:77 final size:77
Alignment explanation
Indices: 549130--549671 Score: 631
Period size: 77 Copynumber: 7.1 Consensus size: 77
549120 CTAAGGTTAG
* * * * *
549130 CATTCTTGTGCGCAACCTATTTTATTAATAAAAATATTAACATTCCATATCGTAATCTATTTATT
1 CATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCTT
549195 AGTGAACCATGA
66 AGTGAACCATGA
* * * * * * *
549207 TATTCTTGGGCGTAACCCATTTTATTGATAAAAATATTAATATTACAGATCGCAACTTATTTCTT
1 CATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCTT
*
549272 AGTGAACTATGA
66 AGTGAACCATGA
* *
549284 CATTCTTGGG-GACAACCCATTTTATTAATAAAAATATTAAAATTCCATATTGCAACCTATTTCT
1 CATTCTTGGGCG-CAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCT
549348 TAGTGAACCATGA
65 TAGTGAACCATGA
* * * * * * *
549361 CATTCGTGGGCACAACCCATTTTATTAATAAAAATATTAACATGCCAGATCACAACATGTTTCTT
1 CATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCTT
* *
549426 AGTGACCCGTGA
66 AGTGAACCATGA
* * * * * *
549438 CATTTTTGGGCGCAATCAATTATATTAATAAAAATGTTAACATTTCCATATCACAACCTATTTCT
1 CATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACA-TTCCATATCGCAACCTATTTCT
*
549503 TAGTGAATCATGA
65 TAGTGAACCATGA
* * * * * * * * *
549516 CATTATTGGGAGTAACCCATTTTATTAATAAAAATATTAATATTCTAGATTGCAACATGTTTCTT
1 CATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCTT
*
549581 GGTGAACCATGA
66 AGTGAACCATGA
* * * *
549593 TATTTTTGGGC-TAACCCATTTTATTAAT-AAAATATTAACATTCCATATCGCAACCTATTTCCT
1 CATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCTT
*
549656 AATGAACCATGA
66 AGTGAACCATGA
549668 CATT
1 CATT
549672 TTTAGGTGCA
Statistics
Matches: 386, Mismatches: 76, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
75 41 0.11
76 18 0.05
77 265 0.69
78 62 0.16
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (77 bp):
CATTCTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCTT
AGTGAACCATGA
Found at i:549547 original size:155 final size:154
Alignment explanation
Indices: 549130--549671 Score: 696
Period size: 154 Copynumber: 3.5 Consensus size: 154
549120 CTAAGGTTAG
* * * * * *
549130 CATTCTTGTGCGCAACCTATTTTATTAATAAAAATATTAACATTCCATATCGTAATCTATTTATT
1 CATTTTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCTT
* * * *
549195 AGTGAACCATGATATTCTTGGGCGTAACCCATTTTATTGATAAAAATATTAATATTACAGATCGC
66 AGTGAACCATGACATTCTTGGGAGTAACCCATTTTATTAATAAAAATATTAATATTCCAGATCGC
* * *
549260 AACTTATTTCTTAGTGAACTATGA
131 AACATGTTTCTTAGTGAACCATGA
* * *
549284 CATTCTTGGG-GACAACCCATTTTATTAATAAAAATATTAAAATTCCATATTGCAACCTATTTCT
1 CATTTTTGGGCG-CAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCT
* * * *
549348 TAGTGAACCATGACATTCGTGGGCA-CAACCCATTTTATTAATAAAAATATTAACATGCCAGATC
65 TAGTGAACCATGACATTCTTGGG-AGTAACCCATTTTATTAATAAAAATATTAATATTCCAGATC
* * *
549412 ACAACATGTTTCTTAGTGACCCGTGA
129 GCAACATGTTTCTTAGTGAACCATGA
* * * * *
549438 CATTTTTGGGCGCAATCAATTATATTAATAAAAATGTTAACATTTCCATATCACAACCTATTTCT
1 CATTTTTGGGCGCAACCCATTTTATTAATAAAAATATTAACA-TTCCATATCGCAACCTATTTCT
* * * *
549503 TAGTGAATCATGACATTATTGGGAGTAACCCATTTTATTAATAAAAATATTAATATTCTAGATTG
65 TAGTGAACCATGACATTCTTGGGAGTAACCCATTTTATTAATAAAAATATTAATATTCCAGATCG
*
549568 CAACATGTTTCTTGGTGAACCATGA
130 CAACATGTTTCTTAGTGAACCATGA
* * *
549593 TATTTTTGGGC-TAACCCATTTTATTAAT-AAAATATTAACATTCCATATCGCAACCTATTTCCT
1 CATTTTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCTT
*
549656 AATGAACCATGACATT
66 AGTGAACCATGACATT
549672 TTTAGGTGCA
Statistics
Matches: 332, Mismatches: 51, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
152 35 0.11
153 12 0.04
154 178 0.54
155 107 0.32
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (154 bp):
CATTTTTGGGCGCAACCCATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCTT
AGTGAACCATGACATTCTTGGGAGTAACCCATTTTATTAATAAAAATATTAATATTCCAGATCGC
AACATGTTTCTTAGTGAACCATGA
Found at i:549947 original size:78 final size:79
Alignment explanation
Indices: 549796--549959 Score: 197
Period size: 78 Copynumber: 2.1 Consensus size: 79
549786 GCATAACCCA
* * * * * * * *
549796 TTTTATTATTAAAAATATTAAGATTTCAGATTGCAACCTATTTATTAGTGAACCATGATATTTTT
1 TTTTATTAATAAAAATATTAAGATTACAAATCGCAACCTATTTATTAGTGAACCATAACATCTGT
549861 TGGCGCAACC-TAT
66 TGGCGCAACCGTAT
* *
549874 TTTTATTAATAAAAATATTAATATTACAAATCGCAACCTATTTCTTAGTGAACCATAACA-CTGT
1 TTTTATTAATAAAAATATTAAGATTACAAATCGCAACCTATTTATTAGTGAACCATAACATCTGT
*
549938 TGGATGCAACCGTAT
66 TGG-CGCAACCGTAT
549953 TTCTTAT
1 TT-TTAT
549960 ATATATTAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
77 5 0.07
78 58 0.81
79 5 0.07
80 4 0.06
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (79 bp):
TTTTATTAATAAAAATATTAAGATTACAAATCGCAACCTATTTATTAGTGAACCATAACATCTGT
TGGCGCAACCGTAT
Found at i:549995 original size:264 final size:261
Alignment explanation
Indices: 549528--550046 Score: 713
Period size: 264 Copynumber: 2.0 Consensus size: 261
549518 TTATTGGGAG
* * * *
549528 TAACCCATTTTATTAATAAAAATATTAATATTCTAGATTGCAACATGTTTCTTGGTGAACCATGA
1 TAACCCATTTTATTAATAAAAATATTAAGATTCTAGATTGCAACATATTTATTAGTGAACCATGA
* *
549593 TATTTTTGGGCTAACCCATTTTATTAATAAAATATTAACATTCCATATCGCAACCTATTTCCTAA
66 TATTTTTGGGCTAACCCATTTTATTAATAAAATATTAACATTACAAATCGCAACCTATTTCCTAA
* * * *
549658 TGAACCATGACATTTTTAGGTGCAACCATATTTCTTATATATATTCATAACATTTTCAACTTTTA
131 TGAACCATAACACTGTTAGGTGCAACCATATTTCTTATATATATTAATAACATTTTCAACTTTTA
* * * * * **
549723 ACTTATTTTGTTATCATTGGAAAATCCAAAGTTTCATTAGTTTAAACTCTGTTAACATTTCATGC
196 ACTTATTTTCTTATCATGGGAAAATCCAAAGTTCCATCAGCTTAAACTCTAATAACATTTCATGC
549788 A
261 A
* *
549789 TAACCCATTTTATTATTAAAAATATTAAGATT-TCAGATTGCAACCTATTTATTAGTGAACCATG
1 TAACCCATTTTATTAATAAAAATATTAAGATTCT-AGATTGCAACATATTTATTAGTGAACCATG
* *
549853 ATATTTTTTGGCGC-AACCTATTTTTATTAATAAAAATATTAATATTACAAATCGCAACCTATTT
65 ATA-TTTTTGG-GCTAACCCA-TTTTATTAAT-AAAATATTAACATTACAAATCGCAACCTATTT
* * * *
549917 CTTAGTGAACCATAACACTGTT-GGATGCAACCGTATTTCTTATATATATTAATAATATTTTCAA
126 CCTAATGAACCATAACACTGTTAGG-TGCAACCATATTTCTTATATATATTAATAACATTTTCAA
*
549981 -TTTTCAACTTATTTTCTTATCATGGGAAAATCCAATGTTCCATCAGCTTAAACTCTAATAACAT
190 CTTTT-AACTTATTTTCTTATCATGGGAAAATCCAAAGTTCCATCAGCTTAAACTCTAATAACAT
550045 TT
254 TT
550047 TAGGCGCAAC
Statistics
Matches: 225, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
260 1 0.00
261 59 0.26
262 12 0.05
263 18 0.08
264 135 0.60
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (261 bp):
TAACCCATTTTATTAATAAAAATATTAAGATTCTAGATTGCAACATATTTATTAGTGAACCATGA
TATTTTTGGGCTAACCCATTTTATTAATAAAATATTAACATTACAAATCGCAACCTATTTCCTAA
TGAACCATAACACTGTTAGGTGCAACCATATTTCTTATATATATTAATAACATTTTCAACTTTTA
ACTTATTTTCTTATCATGGGAAAATCCAAAGTTCCATCAGCTTAAACTCTAATAACATTTCATGC
A
Found at i:555729 original size:19 final size:19
Alignment explanation
Indices: 555705--555748 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
555695 GAAATATTTT
*
555705 TATGAATAGTATTATACTA-
1 TATGAATAGTACTATA-TAG
555724 TATGAATAGTACTATATAG
1 TATGAATAGTACTATATAG
555743 TATGAA
1 TATGAA
555749 CAGTCCGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.39
Consensus pattern (19 bp):
TATGAATAGTACTATATAG
Found at i:556418 original size:22 final size:22
Alignment explanation
Indices: 556371--556424 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
556361 ATGTGAAATT
* *
556371 TGTCCTGAAGGACCTATATATT
1 TGTCCCGAAGGACCTATATATA
* *
556393 TGTCCCGAAGGACCTCTGTATA
1 TGTCCCGAAGGACCTATATATA
556415 TGTCCCGAAG
1 TGTCCCGAAG
556425 AACCGCGTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATATATA
Found at i:563930 original size:95 final size:95
Alignment explanation
Indices: 563758--563959 Score: 341
Period size: 95 Copynumber: 2.1 Consensus size: 95
563748 ATATTATAAT
563758 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTA
* * **
563823 TGGATAAGATTCAGTTAGCCTGATAAAGGTG
65 TGGATAAAATTCAGCTAGCCTGATAAAGGCA
*
563854 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
*
563919 GGATAAAATTCAGCTAGTCTGATAAAGGCA
66 GGATAAAATTCAGCTAGCCTGATAAAGGCA
563949 ATTATAATATA
1 ATTATAATATA
563960 TATATATACA
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
95 94 0.94
96 6 0.06
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
GGATAAAATTCAGCTAGCCTGATAAAGGCA
Found at i:565628 original size:95 final size:97
Alignment explanation
Indices: 565445--565713 Score: 346
Period size: 95 Copynumber: 2.7 Consensus size: 97
565435 ATATTATAAT
* *
565445 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
* *
565510 TGGATAAGATTCAGTTAGCCTGATAAAGG-TG
66 TGGATAAAATTCAGCTAGCCTGATAAAGGATG
*
565541 ATTATA-ATATGCAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
*
565605 TGGATAAAATTCAGCTA-CTCTGATAAAGGCAATT
66 TGGATAAAATTCAGCTAGC-CTGATAAAGG--ATG
* * * * *
565639 ATAATATATATATATATACAATGATATTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGA
1 ATTATATATATACA-ATA-AA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGG
565704 CTTTATGGAT
61 CTTTATGGAT
565714 TCAGCTAGCC
Statistics
Matches: 151, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
94 1 0.01
95 80 0.53
96 6 0.04
98 6 0.04
99 5 0.03
100 3 0.02
101 2 0.01
102 1 0.01
104 47 0.31
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (97 bp):
ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
TGGATAAAATTCAGCTAGCCTGATAAAGGATG
Found at i:567083 original size:36 final size:37
Alignment explanation
Indices: 567040--567112 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 37
567030 CAAAACATAG
*
567040 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA-AAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
567076 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
567113 AACTTTGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 31 0.89
37 4 0.11
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:567193 original size:37 final size:36
Alignment explanation
Indices: 567135--567239 Score: 147
Period size: 37 Copynumber: 2.9 Consensus size: 36
567125 GTTTTCCTTG
**
567135 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTA
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCGTA
* *
567172 GAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTA
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCGTA
*
567209 AAACAAATTTTGTCTCTATTGAGACAGTTTC
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTC
567240 CCTTGAAACA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 25 0.42
37 32 0.53
38 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGTA
Found at i:567234 original size:36 final size:36
Alignment explanation
Indices: 567013--567111 Score: 96
Period size: 36 Copynumber: 2.7 Consensus size: 36
567003 GGTCGTCTTG
*
567013 CTTGAGACTATTTTACTC--AAAACATAGTTTTGTCTCT
1 CTTGAGAC-ATTTT-CTCTTAAAACA-AATTTTGTCTCT
*
567050 CTTGAGACAGTTTCTCTTGAAAA-AAATTTTGTCTCT
1 CTTGAGACATTTTCTCTT-AAAACAAATTTTGTCTCT
* * *
567086 CTTGAGACAGTTTCCCTTGAAACAAA
1 CTTGAGACATTTTCTCTTAAAACAAA
567112 AAACTTTGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
35 6 0.11
36 35 0.65
37 9 0.17
38 4 0.07
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (36 bp):
CTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCT
Found at i:567338 original size:138 final size:138
Alignment explanation
Indices: 567040--567473 Score: 701
Period size: 138 Copynumber: 3.1 Consensus size: 138
567030 CAAAACATAG
* *
567040 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAA-AAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 TTTTGTCTCTCTTGAGACATTTTCTCGT-AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
* * * * *
567104 GAAACAAAAAACTTTGAATTTGTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTT
65 GAAAC-AAAATCTTTGAATCTGTTTTCCTTTAAACAAA-TTTCGTCTCTCTTGAGACAATTTCTT
567169 TTAGAACTAAA
128 TTAGAACTAAA
*
567180 TTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTATTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
567245 AAACAAAATCTTTGAATCTGTTTTCCTTTAAACAAATTTCGTCTCTCATGAGACAATTTCTTTTA
66 AAACAAAATCTTTGAATCTGTTTTCCTTTAAACAAATTTCGTCTCTCTTGAGACAATTTCTTTTA
567310 GAACTAAA
131 GAACTAAA
*
567318 TTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
1 TTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* **
567383 AAACAAAATCTTTGAATCTGTTTTCCTTTAAACAAATTTCGTCTCTCTTGAGACATTTTCTCGTA
66 AAACAAAATCTTTGAATCTGTTTTCCTTTAAACAAATTTCGTCTCTCTTGAGACAATTTCTTTTA
*
567448 AAAC-AAA
131 GAACTAAA
567455 TTTTGTCTCTCTTGAGACA
1 TTTTGTCTCTCTTGAGACA
567474 GTTTATCCTG
Statistics
Matches: 277, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
137 22 0.08
138 161 0.58
139 33 0.12
140 61 0.22
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (138 bp):
TTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
AAACAAAATCTTTGAATCTGTTTTCCTTTAAACAAATTTCGTCTCTCTTGAGACAATTTCTTTTA
GAACTAAA
Found at i:567387 original size:36 final size:36
Alignment explanation
Indices: 567269--567389 Score: 145
Period size: 36 Copynumber: 3.3 Consensus size: 36
567259 AATCTGTTTT
* *
567269 CCTTTAAACAAATTTCGTCTCTCATGAGACAATTT-
1 CCTTTAAACAAATTTTGTCTCTCTTGAGACAATTTC
* *
567304 CTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTC
1 CCTTTA-AAC-AAATTTTGTCTCTCTTGAGACAATTTC
* * *
567342 TCGTAAAACAAATTTTGTCTCTCTTGAGACAATTTC
1 CCTTTAAACAAATTTTGTCTCTCTTGAGACAATTTC
*
567378 CCTTGAAACAAA
1 CCTTTAAACAAA
567390 ATCTTTGAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
35 5 0.07
36 38 0.54
37 26 0.37
38 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.39
Consensus pattern (36 bp):
CCTTTAAACAAATTTTGTCTCTCTTGAGACAATTTC
Found at i:567431 original size:101 final size:101
Alignment explanation
Indices: 567301--567646 Score: 426
Period size: 101 Copynumber: 3.4 Consensus size: 101
567291 CATGAGACAA
* * *
567301 TTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCT
1 TTTCCTTTA-AAC-AAATTTCGTCTCTCTTGAGACAGTTTCTCGTAAAACAAATTTTGTCTCTCT
* *
567366 TGAGACAATTTCCCTTGAAACAAAATCTTTGAATCTGT
64 TGAGACAGTTTACCTTGAAACAAAATCTTTGAATCTGT
*
567404 TTTCCTTTAAACAAATTTCGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTG
1 TTTCCTTTAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCGTAAAACAAATTTTGTCTCTCTTG
*
567469 AGACAGTTTATCC-TGAAACAAAATCTCTGAATCTGT
66 AGACAGTTTA-CCTTGAAACAAAATCTTTGAATCTGT
* * * * ** ** *
567505 TTTCCTTGAAACAAATTGT-TTCTCCCTTGAGATAGTTTCTTTTGGAACTAAAATTTGTCTCTCT
1 TTTCCTTTAAACAAATT-TCGTCTCTCTTGAGACAGTTTCTCGTAAAAC-AAATTTTGTCTCTCT
* *
567569 TGAGATAGTTTATCTTGAAACAAAATCTTTGAATCTGT
64 TGAGACAGTTTACCTTGAAACAAAATCTTTGAATCTGT
* * * * *
567607 TTTCCATTAAAAAAAATTCATCTCACTTGAGACAGTTTCT
1 TTTCCTTTAAACAAATTTCGTCTCTCTTGAGACAGTTTCT
567647 TTTGAGACAG
Statistics
Matches: 213, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
101 121 0.57
102 84 0.39
103 8 0.04
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.41
Consensus pattern (101 bp):
TTTCCTTTAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCGTAAAACAAATTTTGTCTCTCTTG
AGACAGTTTACCTTGAAACAAAATCTTTGAATCTGT
Found at i:567488 original size:36 final size:36
Alignment explanation
Indices: 567412--567490 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
567402 GTTTTCCTTT
* * *
567412 AAACAAATTTCGTCTCTCTTGAGACATTTTCTCGTA
1 AAACAAATTTCGTCTCTCTTGAGACAGTTTATCCTA
* *
567448 AAACAAATTTTGTCTCTCTTGAGACAGTTTATCCTG
1 AAACAAATTTCGTCTCTCTTGAGACAGTTTATCCTA
567484 AAACAAA
1 AAACAAA
567491 ATCTCTGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (36 bp):
AAACAAATTTCGTCTCTCTTGAGACAGTTTATCCTA
Found at i:567653 original size:15 final size:15
Alignment explanation
Indices: 567632--567666 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
567622 ATTCATCTCA
567632 CTTGAGACAGTTTCT
1 CTTGAGACAGTTTCT
*
567647 TTTGAGACAGTTTCT
1 CTTGAGACAGTTTCT
567662 CTTGA
1 CTTGA
567667 AACACAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (15 bp):
CTTGAGACAGTTTCT
Found at i:569396 original size:2 final size:2
Alignment explanation
Indices: 569389--569415 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
569379 AATACGTTAT
569389 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
569416 GTTTTTGTTT
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:571904 original size:15 final size:15
Alignment explanation
Indices: 571867--571936 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
571857 AAAAATGATA
* * *
571867 TATATGAATATATTT
1 TATATGAAAATGTTC
571882 TATATGAAAATGTTC
1 TATATGAAAATGTTC
* *
571897 TATGTGAAAATGTGC
1 TATATGAAAATGTTC
*
571912 TA-ATGAGAATGTTC
1 TATATGAAAATGTTC
*
571926 TACATGAAAAT
1 TATATGAAAAT
571937 ATCCTATGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 11 0.24
15 34 0.76
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.39
Consensus pattern (15 bp):
TATATGAAAATGTTC
Found at i:572101 original size:23 final size:23
Alignment explanation
Indices: 572075--572178 Score: 86
Period size: 24 Copynumber: 4.4 Consensus size: 23
572065 GGTTCTATAC
*
572075 GGTCCTTCGGAACTAA-TCTATGT
1 GGTCCTTCGGAAC-AATTCTACGT
*
572098 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGAACAATTCTACGT
* * *
572121 GGTCCTTCGGGACAAATTCTATGC
1 GGTCCTTCGGAAC-AATTCTACGT
* * *
572145 GATCCTTTGGGACAAATTCTACGT
1 GGTCCTTCGGAAC-AATTCTACGT
572169 GG-CACTTCGG
1 GGTC-CTTCGG
572179 TGCAAATTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
22 2 0.03
23 32 0.47
24 34 0.50
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (23 bp):
GGTCCTTCGGAACAATTCTACGT
Found at i:572150 original size:24 final size:24
Alignment explanation
Indices: 572067--572165 Score: 112
Period size: 23 Copynumber: 4.2 Consensus size: 24
572057 GAGTCGAGGG
* * *
572067 TTCTATACGGTCCTTCGGAACTAA
1 TTCTATGCGGTCCTTCGGGACAAA
*
572091 -TCTATGTGGTCCTTCGGGAC-AA
1 TTCTATGCGGTCCTTCGGGACAAA
* *
572113 TTCTACGTGGTCCTTCGGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
* *
572137 TTCTATGCGATCCTTTGGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
572161 TTCTA
1 TTCTA
572166 CGTGGCACTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
22 2 0.03
23 36 0.55
24 27 0.42
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (24 bp):
TTCTATGCGGTCCTTCGGGACAAA
Found at i:572178 original size:48 final size:47
Alignment explanation
Indices: 572091--572191 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 47
572081 TCGGAACTAA
* *
572091 TCTATGTGGTCCTTCGGGACAATTCTACGTGGTCCTTCGG-GACAAAT
1 TCTATGCGATCCTTCGGGACAATTCTACGTGGTCCTTCGGTG-CAAAT
*
572138 TCTATGCGATCCTTTGGGACAAATTCTACGTGG-CACTTCGGTGCAAAT
1 TCTATGCGATCCTTCGGGAC-AATTCTACGTGGTC-CTTCGGTGCAAAT
*
572186 TATATG
1 TCTATG
572192 AGCAGTGGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
47 18 0.38
48 28 0.60
49 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (47 bp):
TCTATGCGATCCTTCGGGACAATTCTACGTGGTCCTTCGGTGCAAAT
Found at i:573637 original size:9 final size:9
Alignment explanation
Indices: 573573--573640 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
573563 TATTTTCTAG
573573 TATTTTATT
1 TATTTTATT
*
573582 TATTTCATT
1 TATTTTATT
* *
573591 TGCTTTTATG
1 T-ATTTTATT
* *
573601 GACTTTATT
1 TATTTTATT
573610 TATTTT-TT
1 TATTTTATT
*
573618 TATGTCT-TT
1 TAT-TTTATT
573627 TATTTTATT
1 TATTTTATT
573636 TATTT
1 TATTT
573641 CGTTTCTTTA
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
8 7 0.16
9 32 0.73
10 5 0.11
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (9 bp):
TATTTTATT
Found at i:579040 original size:72 final size:72
Alignment explanation
Indices: 578882--579128 Score: 250
Period size: 72 Copynumber: 3.4 Consensus size: 72
578872 TCTCACTTGT
* * *
578882 GATTGTTTTTCTTAAAGCATACTTTGTCTCACTTGAA-ACTATTTTACT-AGAAATAAGATTTAT
1 GATTGTTTTTCTTAAAACATACTTTGTCTCACTT-AAGACTGTTTTACTCA-AAAGAAGATTTAT
578945 TTCACTCAA
64 TTCACTCAA
* ** * * *
578954 GTTTACTTTGCTTAAAACATACTTTGTCTCACCTAAGACTGTTTTACTCAAAAGAAGATTTATTC
1 GATTGTTTTTCTTAAAACATACTTTGTCTCACTTAAGACTGTTTTACTCAAAAGAAGATTTATTT
579019 CACTCAA
66 CACTCAA
* ** * *
579026 GATTGTTTTTCTTAAAACCAGA-TTTGTCT-ATCTTGGGACCGTTTTCACTCGAAAGAAGATTTA
1 GATTGTTTTTCTTAAAA-CATACTTTGTCTCA-CTTAAGACTGTTTT-ACTCAAAAGAAGATTTA
*
579089 TTTCAGTCAA
63 TTTCACTCAA
* * * *
579099 GATTGTTTCTCTTGAAACAAAGTTTGTCTC
1 GATTGTTTTTCTTAAAACATACTTTGTCTC
579129 TCTTGAAACA
Statistics
Matches: 144, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
71 3 0.02
72 91 0.63
73 50 0.35
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (72 bp):
GATTGTTTTTCTTAAAACATACTTTGTCTCACTTAAGACTGTTTTACTCAAAAGAAGATTTATTT
CACTCAA
Found at i:579100 original size:73 final size:72
Alignment explanation
Indices: 578994--579133 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 72
578984 ACCTAAGACT
* *
578994 GTTTTACTCAAAAGAAGATTTATTCCACTCAAGATTGTTTTTCTTAAAAC-CAGATTTGTCTATC
1 GTTTTACTCAAAAGAAGATTTATTCCACTCAAGATTGTTTCTCTTAAAACAAAG-TTTGTCTATC
579058 TTGGGACC
65 TTGGGACC
* * * * *
579066 GTTTTCACTCGAAAGAAGATTTATTTCAGTCAAGATTGTTTCTCTTGAAACAAAGTTTGTCTCTC
1 GTTTT-ACTCAAAAGAAGATTTATTCCACTCAAGATTGTTTCTCTTAAAACAAAGTTTGTCTATC
579131 TTG
65 TTG
579134 AAACAAATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
72 5 0.08
73 52 0.88
74 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (72 bp):
GTTTTACTCAAAAGAAGATTTATTCCACTCAAGATTGTTTCTCTTAAAACAAAGTTTGTCTATCT
TGGGACC
Found at i:579130 original size:21 final size:20
Alignment explanation
Indices: 579101--579155 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
579091 TCAGTCAAGA
*
579101 TTGTTTCTCTTGAAACAAAGT
1 TTGTCTCTCTTGAAACAAA-T
579122 TTGTCTCTCTTGAAACAAAT
1 TTGTCTCTCTTGAAACAAAT
*
579142 TTCGTCTCCCTTGA
1 TT-GTCTCTCTTGA
579156 GACATTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 3 0.10
21 28 0.90
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.42
Consensus pattern (20 bp):
TTGTCTCTCTTGAAACAAAT
Found at i:579265 original size:65 final size:65
Alignment explanation
Indices: 579182--579332 Score: 187
Period size: 65 Copynumber: 2.3 Consensus size: 65
579172 ACTAAGTTTC
*
579182 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAACATTTCCCTTGAAATGAATTT
1 GTCTCTCTTAAGACAGTTTCTCTTGAAACA-AAATCATTGAAAACATTTCCCTTGAAATGAATTT
579246 T
65 T
* * * * ** *
579247 GTCTCTCTTAAGATAGTTTCTCTTGAAACAAAATCTTTGAATATATTTCCCTTGAAACAAATTTC
1 GTCTCTCTTAAGACAGTTTCTCTTGAAACAAAATCATTGAAAACATTTCCCTTGAAATGAATTTT
* * *
579312 GTCTCCCTTGAGACATTTTCT
1 GTCTCTCTTAAGACAGTTTCT
579333 TTTGGAACTA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 3 0.04
65 70 0.96
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (65 bp):
GTCTCTCTTAAGACAGTTTCTCTTGAAACAAAATCATTGAAAACATTTCCCTTGAAATGAATTTT
Found at i:579366 original size:102 final size:102
Alignment explanation
Indices: 579228--579552 Score: 341
Period size: 102 Copynumber: 3.2 Consensus size: 102
579218 TTGAAAACAT
** * * * *
579228 TTCCCTTGAAA-TGAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACA-AAATCTTTGAATAT
1 TTCCCTTGAAACAAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAA-CATTGAAAAC
**
579291 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATT
65 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGG
** * * * * *
579329 TTCTTTTGGAACTAAGTTTTGTTTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTAAAAACA
1 TTCCCTTGAAACAAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
** * * *
579394 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGG
66 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGG
* *
579431 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTCCCTTGAAACAAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
* ** * * * * * *
579496 TTTCCCTTTAAATGAATTTTGTCACTCATGAGATAGT
66 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGG
579533 TTCCCTTGAAAC-AAATTTTG
1 TTCCCTTGAAACAAAATTTTG
579553 CTTCCCTTGA
Statistics
Matches: 191, Mismatches: 31, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
101 16 0.08
102 172 0.90
103 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (102 bp):
TTCCCTTGAAACAAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGG
Found at i:579369 original size:167 final size:166
Alignment explanation
Indices: 579130--579451 Score: 563
Period size: 167 Copynumber: 1.9 Consensus size: 166
579120 GTTTGTCTCT
579130 CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTAGAACTAAGTTTCGTCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTAGAACTAAGTTTCGTCTCTCTTGAGA
*
579195 CAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTAAGA
66 CAGTTTCTCTTGAAACATAAACATTAAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTAAGA
* *
579260 TAGTTTCTCTTGAAACAAAATCTTTGAATATATTTCC
131 TAGGTTCCCTTGAAACAAAAT-TTTGAATATATTTCC
* * *
579297 CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTGTTTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTAGAACTAAGTTTCGTCTCTCTTGAGA
* *
579362 TAGTTTCTCTTGAAACATAAACATTAAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGA
66 CAGTTTCTCTTGAAACATAAACATTAAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTAAGA
579427 TAGGTTCCCTTGAAACAAAATTTTG
131 TAGGTTCCCTTGAAACAAAATTTTG
579452 TCTCCCTTGA
Statistics
Matches: 147, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
166 4 0.03
167 143 0.97
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (166 bp):
CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTAGAACTAAGTTTCGTCTCTCTTGAGA
CAGTTTCTCTTGAAACATAAACATTAAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTAAGA
TAGGTTCCCTTGAAACAAAATTTTGAATATATTTCC
Found at i:579455 original size:37 final size:37
Alignment explanation
Indices: 579395--579480 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
579385 TTAAAAACAT
** * *
579395 TTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAGG
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGG
*
579431 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGT
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGG
*
579468 TTCTCTTGAAACA
1 TTCCCTTGAAACA
579481 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 11 0.26
37 32 0.74
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (37 bp):
TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGG
Found at i:579559 original size:21 final size:20
Alignment explanation
Indices: 579533--579583 Score: 84
Period size: 21 Copynumber: 2.5 Consensus size: 20
579523 ATGAGATAGT
579533 TTCCCTTGAAACAAATTTTG
1 TTCCCTTGAAACAAATTTTG
579553 CTTCCCTTGAAACAAATTTTG
1 -TTCCCTTGAAACAAATTTTG
579574 TCTCCCTTGA
1 T-TCCCTTGA
579584 GATAGTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.39
Consensus pattern (20 bp):
TTCCCTTGAAACAAATTTTG
Found at i:579976 original size:84 final size:85
Alignment explanation
Indices: 579840--579997 Score: 201
Period size: 84 Copynumber: 1.9 Consensus size: 85
579830 CACCAAACCC
* * * * * *
579840 TCGAGTTCGATTACACTCAGCTTCGAGGGCACAACATTTACAGCATAACTCAAGGCTAGAATGGT
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACAACATTTACAGCATAACTCAAGACAAGAAGGGC
579905 TATCTGTCACCAAAAGACCT
66 TATCTGTCACCAAAAGACCT
** * * * *
579925 TCGAGTTCGACTATGCTCAGC-TCTAAGGCACATCATTTACATCATAGCTCAAGACAAGAAGGGC
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACAACATTTACAGCATAACTCAAGACAAGAAGGGC
579989 TATCTGTCA
66 TATCTGTCA
579998 ATAAAATTGT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
84 43 0.70
85 18 0.30
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (85 bp):
TCGAGTTCGACTACACTCAGCTTCGAAGGCACAACATTTACAGCATAACTCAAGACAAGAAGGGC
TATCTGTCACCAAAAGACCT
Found at i:581294 original size:24 final size:26
Alignment explanation
Indices: 581244--581297 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
581234 CTTTTATGGA
* *
581244 ATTTATTTTTTTTATGTCTTTTATTT
1 ATTTATTTTTCTTATGTCGTTTATTT
*
581270 ATTTATTTTTCTT-T-TCGTTTCTTT
1 ATTTATTTTTCTTATGTCGTTTATTT
581294 ATTT
1 ATTT
581298 TTATTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.48
25 1 0.04
26 12 0.48
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (26 bp):
ATTTATTTTTCTTATGTCGTTTATTT
Found at i:583261 original size:14 final size:14
Alignment explanation
Indices: 583242--583275 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
583232 GCTAAGAACA
583242 ATGATGATGTGGAC
1 ATGATGATGTGGAC
583256 ATGATGATGTGGAC
1 ATGATGATGTGGAC
583270 ATGATG
1 ATGATG
583276 TTCAATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.29
Consensus pattern (14 bp):
ATGATGATGTGGAC
Found at i:586039 original size:25 final size:24
Alignment explanation
Indices: 585981--586039 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
585971 AATAAAATAA
*
585981 AAAATATAATATTAATAGTAATTTT
1 AAAATAAAATATTAATA-TAATTTT
586006 ATAAA-AAAATATTAAT-TCAATTTT
1 A-AAATAAAATATTAATAT-AATTTT
586030 CAAAATAAAA
1 -AAAATAAAA
586040 AGAAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
23 1 0.03
24 9 0.31
25 16 0.55
26 3 0.10
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (24 bp):
AAAATAAAATATTAATATAATTTT
Found at i:587233 original size:23 final size:23
Alignment explanation
Indices: 587203--587254 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
587193 AGTATTTTAT
587203 TATATTTTAAAAATATTAATTAA
1 TATATTTTAAAAATATTAATTAA
* * *
587226 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAAAATATTAATTAA
*
587249 AATATT
1 TATATT
587255 ATTAGATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAA
Found at i:588753 original size:31 final size:31
Alignment explanation
Indices: 588718--588795 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
588708 TTCAACGTCA
* * *
588718 AAGTGACCAAAATTTAATAAAACAATAACGT
1 AAGTGACCAAAACTTAAGAAAACAATAACAT
**
588749 AAGTGACCAAAACTTAAGAAAATGATAACAT
1 AAGTGACCAAAACTTAAGAAAACAATAACAT
* *
588780 AAGTAACCAAGACTTA
1 AAGTGACCAAAACTTA
588796 TGTTTTTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.21
Consensus pattern (31 bp):
AAGTGACCAAAACTTAAGAAAACAATAACAT
Found at i:593523 original size:20 final size:20
Alignment explanation
Indices: 593494--593531 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
593484 AAGAAAATTA
593494 ATCCCCAACGACTCCAAAAC
1 ATCCCCAACGACTCCAAAAC
* *
593514 ATCCCGAACGGCTCCAAA
1 ATCCCCAACGACTCCAAA
593532 CTCATTCCAA
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:0.37, C:0.42, G:0.11, T:0.11
Consensus pattern (20 bp):
ATCCCCAACGACTCCAAAAC
Found at i:593612 original size:49 final size:49
Alignment explanation
Indices: 593547--593646 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
593537 TCCAACATAA
593547 AAAAAACAAGTTGAAGACACTTGAAGAAGGTTACAACACCTATCCAAGC
1 AAAAAACAAGTTGAAGACACTTGAAGAAGGTTACAACACCTATCCAAGC
*
593596 AAAAAACAAGTTGAAGACACTTGAAGAAGGTTGCAACACCTATCCAAGC
1 AAAAAACAAGTTGAAGACACTTGAAGAAGGTTACAACACCTATCCAAGC
593645 AA
1 AA
593647 TCCACATCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.16
Consensus pattern (49 bp):
AAAAAACAAGTTGAAGACACTTGAAGAAGGTTACAACACCTATCCAAGC
Found at i:594843 original size:15 final size:15
Alignment explanation
Indices: 594823--594854 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
594813 ATGTAACATT
594823 CAGAGCTAATTCATA
1 CAGAGCTAATTCATA
594838 CAGAGCTAATTCATA
1 CAGAGCTAATTCATA
594853 CA
1 CA
594855 AAGCCTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (15 bp):
CAGAGCTAATTCATA
Found at i:599239 original size:21 final size:21
Alignment explanation
Indices: 599187--599261 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
599177 CAGTTTCCAG
* * * *
599187 ATTCGCAACGCGATTATGACT
1 ATTCGCAATGCGATTTTCACA
599208 A-TCGCAATGCGATTTT-ACA
1 ATTCGCAATGCGATTTTCACA
* *
599227 ATTTCGCATTGCGATTTTCTCA
1 A-TTCGCAATGCGATTTTCACA
599249 ATTCGCAATGCGA
1 ATTCGCAATGCGA
599262 ATAAGTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 13 0.29
21 26 0.58
22 3 0.07
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCACA
Found at i:599276 original size:20 final size:21
Alignment explanation
Indices: 599251--599302 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
599241 TTTTCTCAAT
*
599251 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
599271 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
599292 TCGCAATGCGA
1 TCGCAATGCGA
599303 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:599364 original size:41 final size:42
Alignment explanation
Indices: 599288--599400 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 42
599278 GCGAATTTGG
* *
599288 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
* *
599329 AAAATCGCAACGCGATACTGATTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
** *
599371 --TTTCGCAACGCGATTCTGACTTTCGCAACG
1 AAAATCGCAACGCGATACTGACTTTCGCAACG
599401 AGATTCTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 26 0.41
41 35 0.56
42 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
Found at i:599409 original size:20 final size:20
Alignment explanation
Indices: 599292--599400 Score: 130
Period size: 20 Copynumber: 5.4 Consensus size: 20
599282 ATTTGGAAAA
* *
599292 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* **
599312 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
*
599333 TCGCAACGCGATACTGATTT
1 TCGCAACGCGATACTGACTT
599353 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
599373 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
599393 TCGCAACG
1 TCGCAACG
599401 AGATTCTGAA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
19 2 0.03
20 59 0.77
21 15 0.19
22 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:599657 original size:20 final size:20
Alignment explanation
Indices: 599632--599727 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
599622 CAACGGGGAA
*
599632 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
599652 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
599672 ATTGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
**
599692 ATCAAAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
599712 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
599728 CGCAATGCGA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:599789 original size:34 final size:34
Alignment explanation
Indices: 599746--599825 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 34
599736 GAAATGAAAA
* * *
599746 TCGCATTGCGATTTTCTCGTTGCGATAGCCATTT
1 TCGCGTTGCGATTCTCTCGTTGCGATAGCCAGTT
*
599780 TCGCGTTGCGATTCTCTCGTTGCGATAGTCAGTT
1 TCGCGTTGCGATTCTCTCGTTGCGATAGCCAGTT
*
599814 TCGTGTTGCGAT
1 TCGCGTTGCGAT
599826 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (34 bp):
TCGCGTTGCGATTCTCTCGTTGCGATAGCCAGTT
Found at i:601433 original size:41 final size:42
Alignment explanation
Indices: 601379--601469 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
601369 CCTCTTCAAC
* *
601379 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
601420 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
601462 GATGACAG
1 GATGACAG
601470 ATGAGTCGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:601435 original size:21 final size:21
Alignment explanation
Indices: 601406--601466 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
601396 GAACGGTGGG
*
601406 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
601427 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
601448 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
601467 CAGATGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:601857 original size:20 final size:20
Alignment explanation
Indices: 601834--601906 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
601824 AAACTTACTT
*
601834 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
601854 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
601874 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
*
601894 TCGCAATGCGAAA
1 TCGCAACGCGAAA
601907 TGAAAATCGC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGGCTA
Found at i:601858 original size:40 final size:40
Alignment explanation
Indices: 601814--601899 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
601804 TAGTTTACTT
* * * *
601814 TCGCAACACGAAACTTACTTTCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTATCGCAACGCGAAAATGGCTA
* *
601854 TCGCAACGCGAAAATGGCTATCGCAACGCGAAAATGGCTA
1 TCGCAACACGAAAATGACTATCGCAACGCGAAAATGGCTA
601894 TCGCAA
1 TCGCAA
601900 TGCGAAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (40 bp):
TCGCAACACGAAAATGACTATCGCAACGCGAAAATGGCTA
Found at i:601915 original size:19 final size:19
Alignment explanation
Indices: 601893--601951 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
601883 GAAAATGGCT
*
601893 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATAAAA
*
601912 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATAAAA
601926 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
601945 ATCGCAA
1 ATCGCAA
601952 CGAAAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:601919 original size:39 final size:40
Alignment explanation
Indices: 601834--601920 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
601824 AAACTTACTT
* ***
601834 TCGCAACGCGGAAATGGCTATCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGGCTATCGCAACGCGAAAATGAAAA
*
601874 TCGCAACGCGAAAATGGCTATCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGGCTATCGCAACGCGAAAATGAAAA
601913 TCGCAACG
1 TCGCAACG
601921 ACAAAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 14 0.33
40 28 0.67
ACGTcount: A:0.36, C:0.24, G:0.25, T:0.15
Consensus pattern (40 bp):
TCGCAACGCGAAAATGGCTATCGCAACGCGAAAATGAAAA
Found at i:601935 original size:33 final size:33
Alignment explanation
Indices: 601893--601972 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
601883 GAAAATGGCT
* *
601893 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGAAAAA
601926 ATCGCAATGCGAAATAAAAATCGCAACGAAAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGAAAAA
*
601959 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
601973 CACAAATTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.50, C:0.21, G:0.17, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAAATCGCAACGAAAAA
Done.