Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008982.1 Hibiscus syriacus cultivar Beakdansim tig00112344_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: 2253222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:382268 original size:15 final size:15
Alignment explanation
Indices: 382232--382298 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
382222 TTCCAGAAAT
**
382232 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
382247 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
382261 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
382276 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
*
382291 ATAATTCA
1 GTAATTCA
382299 TTTTCTGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
14 12 0.27
15 32 0.73
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:385368 original size:15 final size:15
Alignment explanation
Indices: 385350--385384 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
385340 GGTGCGTAAG
*
385350 GAGGAGGATATCCCT
1 GAGGAGGATAACCCT
*
385365 GAGGAGGATAACCTT
1 GAGGAGGATAACCCT
385380 GAGGA
1 GAGGA
385385 TATCCTTGTT
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:0.31, C:0.14, G:0.37, T:0.17
Consensus pattern (15 bp):
GAGGAGGATAACCCT
Found at i:385717 original size:2 final size:2
Alignment explanation
Indices: 385710--385736 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
385700 CGAGGATGAT
385710 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
385737 GGGTTTATTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:386906 original size:29 final size:30
Alignment explanation
Indices: 386847--386903 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 30
386837 ATATATCCTC
** *
386847 TTTTTTATCAAAATAAATATTTATAGTTAT
1 TTTTTTATCAAAATAAATACATAAAGTTAT
**
386877 TTTTTTATCAAAATAGGTACATAAAGT
1 TTTTTTATCAAAATAAATACATAAAGT
386904 ATTCATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (30 bp):
TTTTTTATCAAAATAAATACATAAAGTTAT
Found at i:387058 original size:28 final size:28
Alignment explanation
Indices: 386988--387061 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
386978 AAAAAGCTTG
386988 AATAGTTTAAGTA-TCTATTTTGACATAA
1 AATAGTTTAAGTACT-TATTTTGACATAA
* *
387016 AATATTTTTAGGTACTTATTTTGACCA-AA
1 AATA-GTTTAAGTACTTATTTTGA-CATAA
387045 AATAGTTTAAGTACTTA
1 AATAGTTTAAGTACTTA
387062 AATGAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 15 0.38
29 21 0.54
30 3 0.08
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (28 bp):
AATAGTTTAAGTACTTATTTTGACATAA
Found at i:390024 original size:13 final size:13
Alignment explanation
Indices: 390006--390031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
389996 TTGGACACTT
390006 ATTTTAGTATTAA
1 ATTTTAGTATTAA
390019 ATTTTAGTATTAA
1 ATTTTAGTATTAA
390032 GCCTATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATTTTAGTATTAA
Found at i:390777 original size:19 final size:19
Alignment explanation
Indices: 390755--390815 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 19
390745 CTGTTATTTG
*
390755 ATTAGTTAGGTTGTTGTTA
1 ATTAGTTAGATTGTTGTTA
*
390774 ATTAGTTAGATTGCAGTTATTA
1 ATTAGTTAGATT---GTTGTTA
390796 ATTAGTTAGATTGTTAGTTA
1 ATTAGTTAGATTGTT-GTTA
390816 GGCTTGTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 14 0.40
20 3 0.09
22 18 0.51
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (19 bp):
ATTAGTTAGATTGTTGTTA
Found at i:395738 original size:19 final size:19
Alignment explanation
Indices: 395682--395738 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 19
395672 CTATTATTTG
*
395682 ATTAGTTA-AGTTGTTGTTA
1 ATTAGTTAGA-TTGTTATTA
395701 ATTAGTTAGATTGCAGTTATTA
1 ATTAGTTAGATT---GTTATTA
395723 ATTAGTTAGATTGTTA
1 ATTAGTTAGATTGTTA
395739 GTTAGGCTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 14 0.42
20 1 0.03
22 18 0.55
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (19 bp):
ATTAGTTAGATTGTTATTA
Found at i:396848 original size:15 final size:16
Alignment explanation
Indices: 396819--396849 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
396809 AATGCCGACG
396819 AATAAAAAATGTGATT
1 AATAAAAAATGTGATT
396835 AATAAAAAAT-TGATT
1 AATAAAAAATGTGATT
396850 TCATGCCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (16 bp):
AATAAAAAATGTGATT
Found at i:405034 original size:4 final size:4
Alignment explanation
Indices: 405027--405056 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
405017 ACCAAACCTT
405027 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
405057 TAACTCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:407514 original size:18 final size:19
Alignment explanation
Indices: 407479--407515 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
407469 CACGGAATGT
407479 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
407499 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
407516 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:408466 original size:2 final size:2
Alignment explanation
Indices: 408459--408542 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
408449 ATATCTTCTT
408459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
408501 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
408543 GAATGTTATC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:417487 original size:15 final size:16
Alignment explanation
Indices: 417464--417511 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
417454 TTGTTATAAA
*
417464 TTTTGTTATAATT-TT
1 TTTTATTATAATTATT
*
417479 TTTTATTATACTTATT
1 TTTTATTATAATTATT
* *
417495 GTTTATTATGATTATT
1 TTTTATTATAATTATT
417511 T
1 T
417512 GAAAAAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTATTATAATTATT
Found at i:421496 original size:18 final size:18
Alignment explanation
Indices: 421473--421524 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
421463 TGGAAAGGCG
421473 GCGGCATCATATATGGTC
1 GCGGCATCATATATGGTC
*
421491 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGTC
*
421509 GCGGCATCATAAATGG
1 GCGGCATCATATATGG
421525 ATGTGGTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (18 bp):
GCGGCATCATATATGGTC
Found at i:423182 original size:17 final size:18
Alignment explanation
Indices: 423162--423202 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
423152 AAATTATATT
423162 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
423179 AGTAAAATGGTTAAATAA
1 AGTAAAATGATTAAATAA
*
423197 ATTAAA
1 AGTAAA
423203 TACTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:423813 original size:21 final size:21
Alignment explanation
Indices: 423787--423834 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
423777 GTTTCCAGAT
* *
423787 TCGCAACACGAATTTTGACTA
1 TCGCAACACGAACTTGGACTA
*
423808 TCGCAACGCGAACTTGGACTA
1 TCGCAACACGAACTTGGACTA
423829 TCGCAA
1 TCGCAA
423835 TGCGATTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (21 bp):
TCGCAACACGAACTTGGACTA
Found at i:423894 original size:21 final size:20
Alignment explanation
Indices: 423868--424059 Score: 131
Period size: 21 Copynumber: 9.3 Consensus size: 20
423858 GATAGTCCAA
423868 CCAAGTTCGCGTTGCGATAGT
1 CCAAGTT-GCGTTGCGATAGT
**
423889 CCAAGTTTGCGTTGCGATTTT
1 CCAAG-TTGCGTTGCGATAGT
*
423910 CCAAATT-CGTTGCGATAGT
1 CCAAGTTGCGTTGCGATAGT
* * *
423929 CGAAGTTCGTGTTGCGATTTATT
1 CCAAGTT-GCGTTGCGA--TAGT
*
423952 CCAAATT-CGTTGCGATAGT
1 CCAAGTTGCGTTGCGATAGT
* **
423971 CGAAGTTTGCGTTGCGATTTT
1 CCAAG-TTGCGTTGCGATAGT
*
423992 CCAAATT-CGTTGCGATAGT
1 CCAAGTTGCGTTGCGATAGT
* *
424011 CGAAGTTCGCGTTGCGATTTATT
1 CCAAGTT-GCGTTGCGA--TAGT
* *
424034 CCAAATT-TGTTGCGATAGT
1 CCAAGTTGCGTTGCGATAGT
*
424053 CGAAGTT
1 CCAAGTT
424060 CACGTTGTGA
Statistics
Matches: 130, Mismatches: 30, Indels: 24
0.71 0.16 0.13
Matches are distributed among these distances:
19 44 0.34
20 6 0.05
21 62 0.48
22 2 0.02
23 16 0.12
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.36
Consensus pattern (20 bp):
CCAAGTTGCGTTGCGATAGT
Found at i:423967 original size:42 final size:42
Alignment explanation
Indices: 423877--424095 Score: 338
Period size: 42 Copynumber: 5.3 Consensus size: 42
423867 ACCAAGTTCG
* *
423877 CGTTGCGATAGTCCAAGTTTGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
423917 CGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
423959 CGTTGCGATAGTCGAAGTTTGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
423999 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * * *
424041 TGTTGCGATAGTCGAAGTTCACGTTGTGATTTATTCAAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
424083 CGTTGCGATAGTC
1 CGTTGCGATAGTC
424096 CAAAATCGCA
Statistics
Matches: 164, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
40 63 0.38
41 6 0.04
42 95 0.58
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.37
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:423978 original size:82 final size:82
Alignment explanation
Indices: 423877--424095 Score: 357
Period size: 82 Copynumber: 2.6 Consensus size: 82
423867 ACCAAGTTCG
* *
423877 CGTTGCGATAGTCCAAGTTTGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGTGTT
1 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
423942 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
423959 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
424024 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
* ** * *
424041 TGTTGCGATAGTCGAAGTTCACGTTGTGATTTATTCAAAATTCGTTGCGATAGTC
1 CGTTGCGATAGTCGAAGTTTGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTC
424096 CAAAATCGCA
Statistics
Matches: 128, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
82 105 0.82
83 2 0.02
84 21 0.16
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.37
Consensus pattern (82 bp):
CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATT
Found at i:424634 original size:14 final size:14
Alignment explanation
Indices: 424615--424644 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
424605 GGGAATGGTA
424615 TTTAAGGCTTGGCT
1 TTTAAGGCTTGGCT
424629 TTTAAGGCTTGGCT
1 TTTAAGGCTTGGCT
424643 TT
1 TT
424645 CTCACTTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.27, T:0.47
Consensus pattern (14 bp):
TTTAAGGCTTGGCT
Found at i:424998 original size:21 final size:21
Alignment explanation
Indices: 424820--425068 Score: 194
Period size: 21 Copynumber: 12.0 Consensus size: 21
424810 CGTTGCGATT
*
424820 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
424839 TTGGAATAAATCGCAACGCGAAT
1 TTGGACT--ATCGCAACGCGAAC
*
424862 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
424881 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
424904 TTTGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
424923 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
424946 TTGGACTATCGTAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
424965 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* * *
424988 TTCGACTATCGCAA--CAAAT
1 TTGGACTATCGCAACGCGAAC
**
425007 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
425028 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
425049 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
425069 TATGTTAATC
Statistics
Matches: 180, Mismatches: 32, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
19 48 0.27
21 93 0.52
23 39 0.22
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:425053 original size:42 final size:42
Alignment explanation
Indices: 424823--425043 Score: 374
Period size: 42 Copynumber: 5.3 Consensus size: 42
424813 TGCGATTTTG
*
424823 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAATTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
424865 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
424907 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
424949 GACTATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
424991 GACTATCGCAACAAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
425031 GACTATCGCAACG
1 GACTATCGCAACG
425044 CGAACTTGGA
Statistics
Matches: 169, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 31 0.18
41 1 0.01
42 137 0.81
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:426513 original size:31 final size:31
Alignment explanation
Indices: 426456--426518 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
426446 CCCGACGAGG
* *
426456 TTAATAATTTTTGTTTATTATAATTAATATT
1 TTAAGAATTTTTGTTTATTATAATTAAAATT
* *
426487 TTAAGAATTTTATTTTTA-TATTATTAAAATT
1 TTAAGAATTTT-TGTTTATTATAATTAAAATT
426518 T
1 T
426519 ATTATTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (31 bp):
TTAAGAATTTTTGTTTATTATAATTAAAATT
Found at i:426521 original size:21 final size:22
Alignment explanation
Indices: 426473--426537 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
426463 TTTTTGTTTA
* *
426473 TTATAATTAATATT-TTAAGAATT
1 TTATTATTTATATTATTAA-AA-T
426496 TTATT-TTTATATTATTAAAAT
1 TTATTATTTATATTATTAAAAT
426517 TTATTATTTA-ATTATTAAAAT
1 TTATTATTTATATTATTAAAAT
426538 ATAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 17 0.45
22 13 0.34
23 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATTATTTATATTATTAAAAT
Found at i:426551 original size:41 final size:41
Alignment explanation
Indices: 426506--426606 Score: 109
Period size: 41 Copynumber: 2.4 Consensus size: 41
426496 TTATTTTTAT
426506 ATTATTAAAATTTATTATTT-A-ATTATTAAAATATAA-AAAAA
1 ATTA-TAAAATTTATTATTTAACATT-TT-AAATATAATAAAAA
* *
426547 ATTATAAAATATATTAATTTAACATTTTAAATATAATAAATA
1 ATTATAAAATTTATT-ATTTAACATTTTAAATATAATAAAAA
426589 ATTATAAATATATTATTA
1 ATTATAAA-AT-TTATTA
426607 CAATATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
40 10 0.20
41 16 0.31
42 15 0.29
43 6 0.12
44 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (41 bp):
ATTATAAAATTTATTATTTAACATTTTAAATATAATAAAAA
Found at i:426596 original size:19 final size:19
Alignment explanation
Indices: 426530--426600 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
426520 TTATTTAATT
*
426530 ATTA-AAATATAA-AAAAA
1 ATTATAAATATAATAAATA
* *
426547 ATTATAAAATATATTAATTTAA
1 ATTAT-AAATATAATAA-AT-A
*
426569 CATTTTAAATATAATAAATA
1 -ATTATAAATATAATAAATA
426589 ATTATAAATATA
1 ATTATAAATATA
426601 TTATTACAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
17 4 0.10
19 18 0.44
20 3 0.07
21 1 0.02
22 11 0.27
23 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTATAAATATAATAAATA
Found at i:427184 original size:2 final size:2
Alignment explanation
Indices: 427177--427202 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
427167 CAGTCTACAA
427177 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
427203 GAGAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:427437 original size:20 final size:21
Alignment explanation
Indices: 427412--427504 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
427402 TTTTCCCAAT
*
427412 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
** **
427432 TCGCAACACGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
427453 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
427473 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
427494 TCGCAATGCGA
1 TCGCAATGCGA
427505 TACTTACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:427457 original size:41 final size:41
Alignment explanation
Indices: 427412--427504 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
427402 TTTTCCCAAT
427412 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
*
427453 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
427494 TCGCAATGCGA
1 TCGCAATGCGA
427505 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
Found at i:427517 original size:41 final size:41
Alignment explanation
Indices: 427431--427565 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
427421 GAATAAGTAA
* ** *
427431 ATCGCAACACGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
427472 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
427513 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
* *
427554 TTCACAACGCGA
1 ATCGCAACGCGA
427566 TACTGACTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 5 0.06
41 72 0.91
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:427518 original size:20 final size:20
Alignment explanation
Indices: 427493--427586 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
427483 AATTGGGAAA
*
427493 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
427513 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
427534 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
427554 TTCACAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
427574 TTCGCAACGCGAT
1 ATCGCAACGCGAT
427587 TTACATAATC
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 42 0.70
21 12 0.20
22 3 0.05
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:427802 original size:22 final size:22
Alignment explanation
Indices: 427774--427817 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
427764 CACTCTCTCA
427774 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
427796 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
427818 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:428047 original size:19 final size:19
Alignment explanation
Indices: 428023--428073 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
428013 ATCAACCAAG
428023 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
428042 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
428061 AATCGCAACGCGA
1 AATCGCAACGCGA
428074 TTTTAGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.41, C:0.27, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGCA
Found at i:429359 original size:18 final size:18
Alignment explanation
Indices: 429338--429382 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
429328 TCCACTTCGG
* *
429338 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
429356 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
429374 GAGCCATCA
1 GAGCCATCA
429383 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:429927 original size:14 final size:14
Alignment explanation
Indices: 429908--429965 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
429898 ATGCGAAATG
429908 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
429922 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
429938 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
429954 AAAATCGCAACG
1 AAAATCGCAACG
429966 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:429950 original size:32 final size:33
Alignment explanation
Indices: 429892--429982 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
429882 GGAAATGGCT
*
429892 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
429925 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
429957 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
429983 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:429976 original size:19 final size:19
Alignment explanation
Indices: 429854--429987 Score: 92
Period size: 19 Copynumber: 7.6 Consensus size: 19
429844 TAGTTTACTT
* **
429854 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
429873 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
429893 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
429912 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
429926 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
429944 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
429958 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
429977 TCGCAATGCGA
1 TCGCAACGCGA
429988 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 35 0.38
20 17 0.18
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:430018 original size:14 final size:14
Alignment explanation
Indices: 429999--430056 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
429989 TTGTGTTTCG
429999 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
430013 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
430029 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
430045 CGTTGCGATTTT
1 CGTTGCGATTTT
430057 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:430033 original size:32 final size:33
Alignment explanation
Indices: 429994--430072 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
429984 GCGATTTGTG
429994 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
430026 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
430059 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
430073 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:430071 original size:19 final size:19
Alignment explanation
Indices: 430013--430130 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
430003 GCGATTTTGT
430013 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
430031 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
430045 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
430064 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
430084 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
430103 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
430123 TGTTGCGA
1 CGTTGCGA
430131 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:432127 original size:19 final size:19
Alignment explanation
Indices: 432103--432237 Score: 173
Period size: 19 Copynumber: 7.6 Consensus size: 19
432093 AAAACAGACT
* *
432103 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
432122 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
432141 ATCGCAATGAGAAATGAAA
1 ATCGCAATGCGAAATGAAA
432160 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
432174 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
432193 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
432212 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
432226 ATCGCAATGCGA
1 ATCGCAATGCGA
432238 TTTTCATTTC
Statistics
Matches: 104, Mismatches: 4, Indels: 18
0.83 0.03 0.14
Matches are distributed among these distances:
14 22 0.21
15 2 0.02
16 4 0.04
17 3 0.03
18 1 0.01
19 72 0.69
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:432174 original size:33 final size:33
Alignment explanation
Indices: 432137--432199 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
432127 AATGCGAAAT
432137 GAAAATCGCAATGAGAAATGAAAATCGCAACGA
1 GAAAATCGCAATGAGAAATGAAAATCGCAACGA
*
432170 GAAAATCGCAATGCGAAATGAAAATCGCAA
1 GAAAATCGCAATGAGAAATGAAAATCGCAA
432200 TGCGAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.21, T:0.13
Consensus pattern (33 bp):
GAAAATCGCAATGAGAAATGAAAATCGCAACGA
Found at i:432226 original size:33 final size:33
Alignment explanation
Indices: 432120--432237 Score: 109
Period size: 33 Copynumber: 3.4 Consensus size: 33
432110 CGCGAAATGG
*
432120 AAATCGCAATGCGAAATGAAAATCGCAATGAG-
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
*
432152 AAAT-GAAAAT-CGCAACGA-GAAAATCGCAATGCGAAATGA
1 AAATCG-CAATGCG-AA--ATGAAAATCGCAA--CG--A-GA
432191 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGA
432224 AAATCGCAATGCGA
1 AAATCGCAATGCGA
432238 TTTTCATTTC
Statistics
Matches: 70, Mismatches: 3, Indels: 25
0.71 0.03 0.26
Matches are distributed among these distances:
31 3 0.04
32 9 0.13
33 27 0.39
34 2 0.03
35 1 0.01
36 2 0.03
37 2 0.03
38 12 0.17
39 9 0.13
40 3 0.04
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (33 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGA
Found at i:432256 original size:52 final size:52
Alignment explanation
Indices: 432120--432237 Score: 227
Period size: 52 Copynumber: 2.3 Consensus size: 52
432110 CGCGAAATGG
*
432120 AAATCGCAATGCGAAATGAAAATCGCAATGAGAAATGAAAATCGCAACGAGA
1 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
432172 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
432224 AAATCGCAATGCGA
1 AAATCGCAATGCGA
432238 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
Found at i:432281 original size:20 final size:20
Alignment explanation
Indices: 432256--432307 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
432246 TCGCATTGCG
432256 ATTTTCTCGTTGCGATAACC
1 ATTTTCTCGTTGCGATAACC
* *
432276 ATTTTCGCGTTGCGATAGCC
1 ATTTTCTCGTTGCGATAACC
432296 ATTTTCTCGTTG
1 ATTTTCTCGTTG
432308 TATAGGTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTTTCTCGTTGCGATAACC
Found at i:433671 original size:20 final size:19
Alignment explanation
Indices: 433626--433686 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
433616 TCTTTTGGTT
*
433626 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGA
* *
433645 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
433666 GAAATGACTATCACAACGA
1 GAAATGAAAATCGCAACGA
433685 GA
1 GA
433687 GAATCGCAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 4 0.12
20 27 0.82
21 2 0.06
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:433708 original size:33 final size:33
Alignment explanation
Indices: 433651--433738 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
433641 ATGAGATAAT
*
433651 GAGAATCGCAACGCGGAAATGACTATCACAACGA
1 GAGAATCGCAACGC-GAAATGACTATCACAACCA
* *
433685 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCACAACCA
*
433718 GACAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
433739 AAATCGCAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 36 0.72
34 14 0.28
ACGTcount: A:0.40, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCACAACCA
Found at i:433743 original size:19 final size:19
Alignment explanation
Indices: 433721--433810 Score: 153
Period size: 19 Copynumber: 4.7 Consensus size: 19
433711 GCGACCAGAC
433721 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
433740 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
433760 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
433779 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
433798 AATCGCAATGCGA
1 AATCGCAACGCGA
433811 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 49 0.73
20 18 0.27
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:433745 original size:33 final size:33
Alignment explanation
Indices: 433654--433749 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 33
433644 AGATAATGAG
* * *
433654 AATCGCAACGCGGAAATGACTATCACAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACCAGAC
*
433688 AATCGCAACGCGAAATGACTATCGCGACCAGAC
1 AATCGCAACGCGAAATGACTATCGCAACCAGAC
**
433721 AATCGCAACGCGAAATGAAAATCGCAACC
1 AATCGCAACGCGAAATGACTATCGCAACC
433750 GCGAAATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 44 0.80
34 11 0.20
ACGTcount: A:0.41, C:0.27, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACCAGAC
Found at i:433764 original size:39 final size:38
Alignment explanation
Indices: 433721--433810 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
433711 GCGACCAGAC
433721 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
433760 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
433798 AATCGCAATGCGA
1 AATCGCAACGCGA
433811 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:433839 original size:19 final size:19
Alignment explanation
Indices: 433806--433886 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
433796 AAAATCGCAA
**
433806 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
433825 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
433844 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
433858 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
433878 TGCGATTTT
1 TGCGATTTT
433887 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:434475 original size:41 final size:41
Alignment explanation
Indices: 434423--434500 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
434413 CGAAAGTCAG
* * *
434423 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
*
434464 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
434501 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:434497 original size:20 final size:20
Alignment explanation
Indices: 434404--434497 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
434394 CGCTATGTAA
* *
434404 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
434424 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* * *
434444 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTAAGT
*
434465 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
434485 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
434498 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:434516 original size:41 final size:41
Alignment explanation
Indices: 434423--434518 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
434413 CGAAAGTCAG
* * * ** *
434423 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
*
434464 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
434506 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
434519 TTACTTATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:440570 original size:30 final size:31
Alignment explanation
Indices: 440536--440593 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
440526 GTGATTTTAA
* *
440536 ATAAA-AATGAAAGTTTAGGTATTAAAATGG
1 ATAAACAATGAAAGTTTAGATACTAAAATGG
* *
440566 ATAAACATTGATAGTTTAGATACTAAAA
1 ATAAACAATGAAAGTTTAGATACTAAAA
440594 ACGTAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 5 0.22
31 18 0.78
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.31
Consensus pattern (31 bp):
ATAAACAATGAAAGTTTAGATACTAAAATGG
Found at i:441020 original size:20 final size:21
Alignment explanation
Indices: 440981--441029 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
440971 ACAGATAAAT
440981 ATTAAATAAAAAAGAAACTAA
1 ATTAAATAAAAAAGAAACTAA
* *
441002 ATTAAATATATAA-AAACTAA
1 ATTAAATAAAAAAGAAACTAA
*
441022 AATAAATA
1 ATTAAATA
441030 CGAATGCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (21 bp):
ATTAAATAAAAAAGAAACTAA
Found at i:447740 original size:25 final size:25
Alignment explanation
Indices: 447712--447766 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
447702 ATGGAATAAG
447712 CCTACTAGTTTTGAAGTTAGTTTCT
1 CCTACTAGTTTTGAAGTTAGTTTCT
447737 CCTACTAGTTTTGAAGTTAGTTTCT
1 CCTACTAGTTTTGAAGTTAGTTTCT
447762 CCTAC
1 CCTAC
447767 AATGTACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (25 bp):
CCTACTAGTTTTGAAGTTAGTTTCT
Found at i:449131 original size:27 final size:25
Alignment explanation
Indices: 449099--449151 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 25
449089 TTTAACATAA
*
449099 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT-AA-TAAGTTAAT
449126 AATAAAATATATTTAATAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
449151 A
1 A
449152 TATATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 10 0.40
26 2 0.08
27 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
AATAAAATATATTTAATAAGTTAAT
Found at i:453370 original size:18 final size:19
Alignment explanation
Indices: 453332--453373 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
453322 TTTCTCCGCC
*
453332 TTTTTGGTAGTTTACGATT
1 TTTTTCGTAGTTTACGATT
*
453351 TTTTTCGTAGTTTATG-TT
1 TTTTTCGTAGTTTACGATT
453369 TTTTT
1 TTTTT
453374 AGTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.12, C:0.05, G:0.17, T:0.67
Consensus pattern (19 bp):
TTTTTCGTAGTTTACGATT
Found at i:457686 original size:59 final size:59
Alignment explanation
Indices: 457596--457708 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 59
457586 TATTAGAGTT
* *
457596 ATATTATCGAATTTGTCTTTTCATTACGACTAGGAGGGTTTGATAGGACACTTAGAGCC
1 ATATTATCGAATTTGTCTTTTCATTACGACTAGGAAGGTTCGATAGGACACTTAGAGCC
* **
457655 ATATTATCGAGTTTG-CATTTTCATTGTGACTAGGAAGGTTCGATAGGACACTTA
1 ATATTATCGAATTTGTC-TTTTCATTACGACTAGGAAGGTTCGATAGGACACTTA
457709 TCCATCTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 1 0.02
59 47 0.98
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (59 bp):
ATATTATCGAATTTGTCTTTTCATTACGACTAGGAAGGTTCGATAGGACACTTAGAGCC
Found at i:459304 original size:31 final size:31
Alignment explanation
Indices: 459245--459304 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
459235 CTCAAAAAGT
*
459245 CGGGTCGGTGAAGGGTGTATATTATTCGGGA
1 CGGGTCGGTGAAGGGTGTAAATTATTCGGGA
459276 CGGGTCGGTTG-AGGGTGTAAAATT-TTCGG
1 CGGGTCGG-TGAAGGGTGT-AAATTATTCGG
459305 TCTGATCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.18, C:0.10, G:0.42, T:0.30
Consensus pattern (31 bp):
CGGGTCGGTGAAGGGTGTAAATTATTCGGGA
Found at i:461903 original size:10 final size:10
Alignment explanation
Indices: 461890--461985 Score: 51
Period size: 10 Copynumber: 9.5 Consensus size: 10
461880 ATTTTTATAT
461890 TATTAAAATA
1 TATTAAAATA
*
461900 TATTATTAAT-
1 TATTA-AAATA
461910 TATTAAAA-A
1 TATTAAAATA
*
461919 TA-TAAAAAA
1 TATTAAAATA
461928 TTATTATAAAATA
1 -TA-T-TAAAATA
461941 TATTAATTAAT-
1 TATTAA--AATA
*
461952 CATTAAAATA
1 TATTAAAATA
*
461962 TAAT-AAATA
1 TATTAAAATA
461971 -ATTATAAATA
1 TATTA-AAATA
461981 TATTA
1 TATTA
461986 TTATAAAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 25
0.67 0.07 0.26
Matches are distributed among these distances:
8 7 0.11
9 13 0.20
10 22 0.33
11 13 0.20
12 5 0.08
13 6 0.09
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
TATTAAAATA
Found at i:461918 original size:21 final size:21
Alignment explanation
Indices: 461879--461988 Score: 88
Period size: 21 Copynumber: 5.4 Consensus size: 21
461869 TAATTTTTTT
*
461879 TATTTTTATATTATT-AAAATA
1 TATTATTA-ATTATTAAAAATA
461900 TATTATTAATTATTAAAAATA
1 TATTATTAATTATTAAAAATA
**
461921 TA--AAAAATTATTATAAAATA
1 TATTATTAATTATTA-AAAATA
*
461941 TATTAATTAATCATT-AAAATA
1 TATT-ATTAATTATTAAAAATA
* * *
461962 TA--ATAAATAATTATAAATA
1 TATTATTAATTATTAAAAATA
461981 TATTATTA
1 TATTATTA
461989 TAAAATATAT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
18 8 0.11
19 16 0.23
20 14 0.20
21 26 0.37
23 7 0.10
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTATTAATTATTAAAAATA
Found at i:461943 original size:41 final size:40
Alignment explanation
Indices: 461887--461988 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 40
461877 TTTATTTTTA
*
461887 TATTATTAAAATATATTATTAATTATTAAAAATATAAAAAAT
1 TATTA-TAAAATATATTATTAATCATT-AAAATATAAAAAAT
*
461929 TATTATAAAATATATTAATTAATCATTAAAATATAATAAAT
1 TATTATAAAATATATT-ATTAATCATTAAAATATAAAAAAT
*
461970 AATTAT-AAATATATTATTA
1 TATTATAAAATATATTATTA
461989 TAAAATATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
39 4 0.07
40 9 0.16
41 29 0.52
42 14 0.25
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (40 bp):
TATTATAAAATATATTATTAATCATTAAAATATAAAAAAT
Found at i:461996 original size:15 final size:14
Alignment explanation
Indices: 461971--462002 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
461961 ATAATAAATA
461971 ATTATAAATATATT
1 ATTATAAATATATT
461985 ATTATAAAATATATT
1 ATTAT-AAATATATT
462000 ATT
1 ATT
462003 TTAATTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:464319 original size:21 final size:22
Alignment explanation
Indices: 464272--464327 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
464262 ACTTTTGTTG
* *
464272 TATAA-ATTATATTTTTATCTT
1 TATAATATTATATTTTCATATT
464293 TA-AATATTATATTTTCA-ATT
1 TATAATATTATATTTTCATATT
*
464313 TATAATATAATATTT
1 TATAATATTATATTT
464328 AAAAATGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 6 0.20
21 24 0.80
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
TATAATATTATATTTTCATATT
Found at i:465338 original size:22 final size:23
Alignment explanation
Indices: 465313--465359 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
465303 TTATTATATT
*
465313 AATAAATA-TAGATTAAAATAAA
1 AATAAATATTAAATTAAAATAAA
* *
465335 AATATATATTAAATTAAATTAAA
1 AATAAATATTAAATTAAAATAAA
465358 AA
1 AA
465360 AAAACTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
AATAAATATTAAATTAAAATAAA
Found at i:465339 original size:18 final size:18
Alignment explanation
Indices: 465316--465352 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
465306 TTATATTAAT
465316 AAATATAGATTAAAATAA
1 AAATATAGATTAAAATAA
* *
465334 AAATATATATTAAATTAA
1 AAATATAGATTAAAATAA
465352 A
1 A
465353 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
AAATATAGATTAAAATAA
Found at i:465339 original size:28 final size:27
Alignment explanation
Indices: 465307--465363 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
465297 TTATTATTAT
*
465307 TATATTAATAAATATAGATTAAAATAAAAA
1 TATA-TAATAAAT-TAAATTAAAA-AAAAA
*
465337 TATATATTAAATTAAATTAAAAAAAAA
1 TATATAATAAATTAAATTAAAAAAAAA
465364 CTAAAATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 9 0.36
29 7 0.28
30 4 0.16
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
TATATAATAAATTAAATTAAAAAAAAA
Found at i:468784 original size:38 final size:38
Alignment explanation
Indices: 468711--468793 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 38
468701 ACCATACCTG
468711 AAATTTAGTTTTATTTCACTTTAGTACCACGCCATTAA
1 AAATTTAGTTTTATTTCACTTTAGTACCACGCCATTAA
* * *
468749 AAACTTTAGTTTATATTTTATTTTAGTACC-C-CCATTCA
1 AAA-TTTAGTTT-TATTTCACTTTAGTACCACGCCATTAA
468787 AAATTTA
1 AAATTTA
468794 ATATTAAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
37 4 0.10
38 12 0.30
39 9 0.22
40 15 0.38
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.45
Consensus pattern (38 bp):
AAATTTAGTTTTATTTCACTTTAGTACCACGCCATTAA
Found at i:474176 original size:29 final size:29
Alignment explanation
Indices: 474129--474222 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
474119 TCTGTAGAGG
* *
474129 ATCCCATGCAGAACCAGGACA-AGTATATA
1 ATCCCATGCAAAATCAGGACATAG-ATATA
*
474158 ATCCCATGCAAAATTAGGACATAGATATA
1 ATCCCATGCAAAATCAGGACATAGATATA
* * * *
474187 ATCCCATGCAAAATCAGAACAAAAATAAA
1 ATCCCATGCAAAATCAGGACATAGATATA
474216 ATCCCAT
1 ATCCCAT
474223 TTAAAATGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 54 0.96
30 2 0.04
ACGTcount: A:0.47, C:0.22, G:0.12, T:0.19
Consensus pattern (29 bp):
ATCCCATGCAAAATCAGGACATAGATATA
Found at i:486949 original size:2 final size:2
Alignment explanation
Indices: 486942--486971 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
486932 TTCACTAATC
486942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
486972 GGTTTCCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:489881 original size:2 final size:2
Alignment explanation
Indices: 489874--489903 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
489864 TATTCAATTA
489874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
489904 TAAGAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:491094 original size:19 final size:20
Alignment explanation
Indices: 491070--491117 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
491060 TTGTTCGTTG
*
491070 GTATCGATA-CTAACCCTGA
1 GTATCGATACCTAACCCTCA
*
491089 GTATCGATACCTAACTCTCA
1 GTATCGATACCTAACCCTCA
491109 GTATCGATA
1 GTATCGATA
491118 TTGACTGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (20 bp):
GTATCGATACCTAACCCTCA
Found at i:493832 original size:21 final size:21
Alignment explanation
Indices: 493781--493833 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
493771 ATTATGACTA
493781 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
493802 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
493823 TCGCAATGCGA
1 TCGCAATGCGA
493834 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:493866 original size:21 final size:21
Alignment explanation
Indices: 493823--493895 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
493813 TTTTCCCAAT
* * *
493823 TCGCAATGCGAA-TAAGTAAA
1 TCGCAACGCGAATTTAGAAAA
* *
493843 TCGCAATGCGAATTTTGAAAA
1 TCGCAACGCGAATTTAGAAAA
*
493864 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAATTTAGAAAA
493885 TCGCAACGCGA
1 TCGCAACGCGA
493896 TACTGACTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 12 0.26
21 35 0.74
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAATTTAGAAAA
Found at i:493908 original size:41 final size:41
Alignment explanation
Indices: 493881--494018 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
493871 GCGAATTTGG
493881 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * ** * *
493922 AAAATCGCAACGCGATACTGACTTTCACAACTAGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * * *
493962 AATTTCGCAACGCAATACTGACTTTCGCAATGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
494003 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
494019 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:493909 original size:20 final size:20
Alignment explanation
Indices: 493884--493991 Score: 92
Period size: 20 Copynumber: 5.3 Consensus size: 20
493874 AATTTGGAAA
493884 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
493904 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
493925 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * ** * *
493945 TTCACAACTAGATACTTAAT
1 ATCGCAACGCGATACTGACT
* *
493965 TTCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
*
493985 TTCGCAA
1 ATCGCAA
493992 TGAGATAATA
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
19 2 0.03
20 50 0.72
21 15 0.22
22 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:493930 original size:21 final size:22
Alignment explanation
Indices: 493860--493943 Score: 79
Period size: 21 Copynumber: 4.0 Consensus size: 22
493850 GCGAATTTTG
* *
493860 AAAATCGCAACGCGA-ATTTG-G
1 AAAATCGCAACGCGATA-ATGAC
*
493881 AAAATCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATAATGAC
*
493903 --TATCGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATAATGAC
*
493922 AAAATCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATAATGAC
493944 TTTCACAACT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
19 2 0.04
20 15 0.29
21 32 0.62
22 3 0.06
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (22 bp):
AAAATCGCAACGCGATAATGAC
Found at i:494213 original size:22 final size:22
Alignment explanation
Indices: 494185--494228 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
494175 CACTCTCTCA
494185 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
494207 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
494229 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:495895 original size:18 final size:18
Alignment explanation
Indices: 495869--495916 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
495859 TCCACTTCGG
495869 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
495887 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
495905 GAGCCATCACCT
1 GAGCCATCACCT
495917 GATCGACCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:496494 original size:20 final size:19
Alignment explanation
Indices: 496471--496557 Score: 67
Period size: 19 Copynumber: 4.8 Consensus size: 19
496461 CGCAACAAGA
*
496471 AAATGATTATCGCAACGCGG
1 AAATGAATATCGCAACGC-G
** *
496491 AAATGGCTATCGCAATGCG
1 AAATGAATATCGCAACGCG
*
496510 AAATGAAAATCGCAA--CG
1 AAATGAATATCGCAACGCG
*
496527 ACA--AA-ATCGCAACGCG
1 AAATGAATATCGCAACGCG
*
496543 AAATGAAAATCGCAA
1 AAATGAATATCGCAA
496558 TGCAATTTGT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
14 7 0.13
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 20 0.37
20 15 0.28
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.15
Consensus pattern (19 bp):
AAATGAATATCGCAACGCG
Found at i:496521 original size:19 final size:19
Alignment explanation
Indices: 496499--496560 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
496489 GGAAATGGCT
496499 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
496518 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
496532 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
496551 ATCGCAATGC
1 ATCGCAATGC
496561 AATTTGTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:496634 original size:20 final size:20
Alignment explanation
Indices: 496588--496674 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
496578 GCGATTTTGT
**
496588 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
496607 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
496627 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
496647 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
496667 CGTTGCGA
1 CGTTGCGA
496675 AAGTAAGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 13 0.22
20 47 0.78
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:496685 original size:20 final size:19
Alignment explanation
Indices: 496601--496700 Score: 83
Period size: 20 Copynumber: 5.1 Consensus size: 19
496591 TGCGATTTTC
* * **
496601 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGAAAGTA
* *
496620 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
*
496640 ATTTCCGCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
496661 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
496680 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
496700 A
1 A
496701 ACTATTCTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
19 5 0.07
20 63 0.89
21 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:496692 original size:40 final size:40
Alignment explanation
Indices: 496601--496694 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
496591 TGCGATTTTC
* * *
496601 ATTT-CGCATTGCGATAGCCATTTCCGCGTTGCGATAGTC
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
* *
496640 ATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
*
496680 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
496695 AAGTAAACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.09
40 40 0.85
41 3 0.06
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (40 bp):
ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
Found at i:497075 original size:21 final size:20
Alignment explanation
Indices: 497049--497117 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
497039 CTGTCATCCC
497049 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
497070 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
497091 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
497111 TCAAGAG
1 TCAAGAG
497118 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:497129 original size:41 final size:42
Alignment explanation
Indices: 497039--497129 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
497029 CCCGACTCAC
* *
497039 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
497081 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
497122 CTGTCATC
1 CTGTCATC
497130 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:498569 original size:14 final size:14
Alignment explanation
Indices: 498535--498573 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
498525 TTGATTGTTT
498535 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
498549 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
498563 TGTTGATTTGT
1 AATTGATTTGT
498574 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:498769 original size:20 final size:20
Alignment explanation
Indices: 498752--498801 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
498742 TGATTTTCTA
498752 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
498772 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
498792 GTTGCGATAG
1 GTTGCGATAG
498802 TCAAATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.16, C:0.22, G:0.28, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:499024 original size:20 final size:20
Alignment explanation
Indices: 499008--499124 Score: 137
Period size: 20 Copynumber: 5.8 Consensus size: 20
498998 ATTGCGATTT
499008 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCTCGTTGCGAAAG
499028 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCTCGTTGCGAAAG
* *
499048 TCAGAATCGCGTTGCGGAAG
1 TCAGAATCTCGTTGCGAAAG
* *
499068 TCAGAAT-TGCATTACGAAAG
1 TCAGAATCT-CGTTGCGAAAG
* * *
499088 TCAGTATCGCATTGCGAAAG
1 TCAGAATCTCGTTGCGAAAG
* *
499108 TCAGTATCGCGTTGCGA
1 TCAGAATCTCGTTGCGA
499125 TTTTCAAAGT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (20 bp):
TCAGAATCTCGTTGCGAAAG
Found at i:499897 original size:24 final size:24
Alignment explanation
Indices: 499846--499899 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
499836 GTATTCGAAA
* *
499846 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
499870 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
499894 TTTGAT
1 TTTGAT
499900 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:500090 original size:12 final size:12
Alignment explanation
Indices: 500073--500097 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
500063 ATATAATCCT
500073 GAAGAAGAAAAA
1 GAAGAAGAAAAA
500085 GAAGAAGAAAAA
1 GAAGAAGAAAAA
500097 G
1 G
500098 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:502461 original size:14 final size:14
Alignment explanation
Indices: 502439--502562 Score: 59
Period size: 14 Copynumber: 7.8 Consensus size: 14
502429 AATGCGAAAT
502439 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
502453 GATAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
502471 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
502486 GAGAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
502504 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
**
502519 GGGAATCGCAAAGCGAAA
1 GAAAATCGC-AA-CG--A
502537 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
**
502552 GGGAATCGCAA
1 GAAAATCGCAA
502563 AGCGAAATGA
Statistics
Matches: 85, Mismatches: 10, Indels: 30
0.68 0.08 0.24
Matches are distributed among these distances:
14 36 0.42
15 5 0.06
16 6 0.07
17 6 0.07
18 5 0.06
19 27 0.32
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:502466 original size:33 final size:33
Alignment explanation
Indices: 502424--502583 Score: 275
Period size: 33 Copynumber: 4.8 Consensus size: 33
502414 GAAAATTACT
*
502424 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
502457 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
502490 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
502523 ATCGCAAAGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
502556 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
502584 CGAATTTAGT
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 124 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:502618 original size:19 final size:19
Alignment explanation
Indices: 502583--502645 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
502573 AAATCGCAAC
*
502583 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
502602 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
502621 GCGATTTTTA-TTTCGCATT
1 GCGA-TTTTAGTTTCGCGTT
502640 GCGATT
1 GCGATT
502646 CTCTAGTTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
18 2 0.05
19 34 0.83
20 5 0.12
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:502700 original size:33 final size:33
Alignment explanation
Indices: 502617--502709 Score: 134
Period size: 32 Copynumber: 2.8 Consensus size: 33
502607 TTTAGTTTCG
* *
502617 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
* * *
502650 AGTTGC-AATTTCATTTCGTATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
502682 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
502710 AGTAATTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 27 0.53
33 24 0.47
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTATCT
Found at i:502708 original size:19 final size:19
Alignment explanation
Indices: 502593--502709 Score: 69
Period size: 19 Copynumber: 6.7 Consensus size: 19
502583 GCGAATTTAG
*
502593 TTTCGCGTTGCGATTTT-A
1 TTTCGCATTGCGATTTTCA
* *
502611 GTTTCGCGTTGCGATTTTTA
1 -TTTCGCATTGCGATTTTCA
502631 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
* * *
502647 TCTAG--TTGC-AATTTCA
1 TTTCGCATTGCGATTTTCA
*
502663 TTTCGTATTGCGA--TT-A
1 TTTCGCATTGCGATTTTCA
*
502679 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
502696 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
502710 AGTAATTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
13 1 0.01
14 10 0.13
15 3 0.04
16 13 0.17
17 9 0.12
18 4 0.05
19 37 0.47
20 1 0.01
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:502835 original size:14 final size:15
Alignment explanation
Indices: 502816--502852 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
502806 CATCAATTAA
502816 ACAAATCAAC-TTTT
1 ACAAATCAACATTTT
502830 ACAAATC-ACATTTT
1 ACAAATCAACATTTT
502844 ACAAATCAA
1 ACAAATCAA
502853 TTAAACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACATTTT
Found at i:504722 original size:91 final size:90
Alignment explanation
Indices: 504539--504723 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
504529 ATTTCAAACT
*
504539 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
504604 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTAGCAGCAACCGAATAAATTTAC
*
504632 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTATCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
504696 GTATTAGCAGCAACCGAATAAATTTAC
64 GAATTAGCAGCAACCGAATAAATTTAC
504723 T
1 T
504724 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 40 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTAGCAGCAACCGAATAAATTTAC
Found at i:506439 original size:20 final size:19
Alignment explanation
Indices: 506412--506472 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
506402 TCTTTTGGTT
506412 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
506431 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
506452 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
506471 GA
1 GA
506473 GAGTCGCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.11
20 30 0.83
21 2 0.06
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:506481 original size:14 final size:14
Alignment explanation
Indices: 506461--506530 Score: 68
Period size: 14 Copynumber: 4.6 Consensus size: 14
506451 GGAAATGACT
506461 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
506475 GTCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
506489 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
506506 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
*
506522 ATCACAACG
1 ATCGCAACG
506531 CGAAATGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 27 0.59
16 6 0.13
17 6 0.13
19 7 0.15
ACGTcount: A:0.40, C:0.24, G:0.26, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:506510 original size:47 final size:48
Alignment explanation
Indices: 506440--506530 Score: 157
Period size: 47 Copynumber: 1.9 Consensus size: 48
506430 AGATAATGAA
* *
506440 AATCGCAACGCGGAAATGACTATCGCAACGAGAGAGTCGCAACGAGAG
1 AATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCACAACGAGAG
506488 AATCGCAACGC-GAAATGACTATCGCAACGAGAGAATCACAACG
1 AATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCACAACG
506531 CGAAATGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
47 30 0.73
48 11 0.27
ACGTcount: A:0.40, C:0.24, G:0.25, T:0.11
Consensus pattern (48 bp):
AATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCACAACGAGAG
Found at i:506516 original size:33 final size:33
Alignment explanation
Indices: 506476--506538 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
506466 AACGAGAGAG
*
506476 TCGCAACGAGAGAATCGCAACGCGAAATGACTA
1 TCGCAACGAGAGAATCACAACGCGAAATGACTA
506509 TCGCAACGAGAGAATCACAACGCGAAATGA
1 TCGCAACGAGAGAATCACAACGCGAAATGA
506539 AAAGCGCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (33 bp):
TCGCAACGAGAGAATCACAACGCGAAATGACTA
Found at i:506547 original size:33 final size:33
Alignment explanation
Indices: 506477--506547 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
506467 ACGAGAGAGT
* ** *
506477 CGCAACGAGAGAATCGCAACGCGAAATGACTAT
1 CGCAACGAGAGAATCACAACGCGAAATGAAAAG
506510 CGCAACGAGAGAATCACAACGCGAAATGAAAAG
1 CGCAACGAGAGAATCACAACGCGAAATGAAAAG
506543 CGCAA
1 CGCAA
506548 TACGATTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.08
Consensus pattern (33 bp):
CGCAACGAGAGAATCACAACGCGAAATGAAAAG
Found at i:506574 original size:19 final size:19
Alignment explanation
Indices: 506559--506632 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 19
506549 ACGATTTTGG
506559 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
506578 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* *
506594 --TCTCGTTGCGATAGTT-A
1 TTTCGCGTTGCGAT-TTTCA
506611 TTTCCGCGTTGCGATTTTCA
1 TTT-CGCGTTGCGATTTTCA
506631 TT
1 TT
506633 CTCGAAACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.23
17 5 0.11
19 16 0.36
20 13 0.30
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:507202 original size:20 final size:20
Alignment explanation
Indices: 507150--507265 Score: 89
Period size: 20 Copynumber: 5.8 Consensus size: 20
507140 GCTATGTAAA
* *
507150 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTATGTAT
507170 TCGCATTGCGATTTATGTAT
1 TCGCATTGCGATTTATGTAT
*
507190 TCGCATTGCGATTT-TCCTAAT
1 TCGCATTGCGATTTAT-GT-AT
* *
507211 T--CATTGCGAGTTACT-TAA
1 TCGCATTGCGATTTA-TGTAT
* *
507229 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTATGTAT
*
507249 TCGCATTGCGAATTATG
1 TCGCATTGCGATTTATG
507266 AAAATCGCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
18 2 0.03
19 15 0.20
20 55 0.72
21 4 0.05
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTATGTAT
Found at i:507280 original size:21 final size:21
Alignment explanation
Indices: 507256--507311 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
507246 TATTCGCATT
*
507256 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
507277 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
507297 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
507312 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:507320 original size:21 final size:21
Alignment explanation
Indices: 507249--507321 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
507239 ATTTACGTAT
* *
507249 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
507270 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
507290 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
507311 TTGCATTGCGA
1 TCGCAATGCGA
507322 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:507338 original size:82 final size:82
Alignment explanation
Indices: 507249--507425 Score: 191
Period size: 82 Copynumber: 2.2 Consensus size: 82
507239 ATTTACGTAT
* *
507249 TCGCATTGCGAATTA-TGAAAATCGCAACGCGAA-TACGTAAATCGCAATGCG-AATTAGGAAAA
1 TCGCATTGCGAATTACT--AAATCGCAACGCGAATTACGAAAATCGCAACGCGAAATT-GGAAAA
*
507311 TTGCATTGCGATAGTCAGT-A
63 TTGCATTGCAATAGTCA-TAA
* * * ** **
507331 TCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGAAAATCGCAACGCGAAATTGGAAAATTG
1 TCGCATTGCGAATTACTAAATCGCAACGCGAATTACGAAAATCGCAACGCGAAATTGGAAAATTG
507396 CATTGCAATAGTCATAA
66 CATTGCAATAGTCATAA
*
507413 TCGCGTTGCGAAT
1 TCGCATTGCGAAT
507426 CTGGAAACTG
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
81 12 0.15
82 62 0.78
83 5 0.06
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (82 bp):
TCGCATTGCGAATTACTAAATCGCAACGCGAATTACGAAAATCGCAACGCGAAATTGGAAAATTG
CATTGCAATAGTCATAA
Found at i:514976 original size:3 final size:3
Alignment explanation
Indices: 514968--515002 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
514958 AAAACACCCA
*
514968 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC GTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
515003 TCAGCTTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:518137 original size:21 final size:21
Alignment explanation
Indices: 518111--518162 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
518101 TTTCCAGATT
518111 CGCAACGCGAACTTCGACTAC
1 CGCAACGCGAACTTCGACTAC
* *
518132 CGCAACGCGAACTTGGACTAT
1 CGCAACGCGAACTTCGACTAC
*
518153 CGCAATGCGA
1 CGCAACGCGA
518163 TTTACATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (21 bp):
CGCAACGCGAACTTCGACTAC
Found at i:518245 original size:19 final size:19
Alignment explanation
Indices: 518193--518245 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
518183 TAGTCGAAGT
518193 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCGAAGTT--CGTTGCGA
** * *
518214 TTTTCCAAATTCGTTGCGA
1 TAGTCGAAGTTCGTTGCGA
518233 TAGTCGAAGTTCG
1 TAGTCGAAGTTCG
518246 CGTTGCGATT
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
19 17 0.71
21 7 0.29
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (19 bp):
TAGTCGAAGTTCGTTGCGA
Found at i:518251 original size:21 final size:21
Alignment explanation
Indices: 518193--518254 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
518183 TAGTCGAAGT
518193 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCGAAGTTCGCGTTGCGA
** * *
518214 TTTTCCAAATT--CGTTGCGA
1 TAGTCGAAGTTCGCGTTGCGA
518233 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCGAAGTTCGCGTTGCGA
518254 T
1 T
518255 TTATTCCAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (21 bp):
TAGTCGAAGTTCGCGTTGCGA
Found at i:518446 original size:21 final size:21
Alignment explanation
Indices: 518394--518535 Score: 123
Period size: 21 Copynumber: 6.8 Consensus size: 21
518384 CGTTGCGATT
*
518394 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
518413 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* * * *
518436 TTCGCCTATCGCAATGTGAAC
1 TTGGACTATCGCAACGCGAAC
518457 TTGGACTATCGCAA--CGAA-
1 TTGGACTATCGCAACGCGAAC
*
518475 TCTGGAATAAATCGCAACGCGAAC
1 T-TGGACT--ATCGCAACGCGAAC
* *
518499 TTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAACGCGAAC
518520 TTGGACTATCGCAACG
1 TTGGACTATCGCAACG
518536 AATCCAAATT
Statistics
Matches: 97, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.01
19 14 0.14
21 65 0.67
23 16 0.16
24 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:518493 original size:63 final size:63
Alignment explanation
Indices: 518394--518539 Score: 265
Period size: 63 Copynumber: 2.3 Consensus size: 63
518384 CGTTGCGATT
* * *
518394 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGCCTATCGCAATGTGAAC
1 TTGGACTATCGCAACGAATCTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAAC
518457 TTGGACTATCGCAACGAATCTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAACGAATCTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAAC
518520 TTGGACTATCGCAACGAATC
1 TTGGACTATCGCAACGAATC
518540 CAAATTTACG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 80 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (63 bp):
TTGGACTATCGCAACGAATCTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAAC
Found at i:519910 original size:11 final size:11
Alignment explanation
Indices: 519896--519923 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
519886 ATAATTAAAT
519896 AAATAAAAGTA
1 AAATAAAAGTA
519907 AAATAAAAGTA
1 AAATAAAAGTA
519918 AAATAA
1 AAATAA
519924 GTTTTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (11 bp):
AAATAAAAGTA
Found at i:522427 original size:21 final size:21
Alignment explanation
Indices: 522401--522446 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
522391 CTTTTGAAAC
522401 TTCAACGT-ATAAAAAGATCAT
1 TTCAACGTGATAAAAAG-TCAT
* *
522422 TTCAACTTGGTAAAAAGTCAT
1 TTCAACGTGATAAAAAGTCAT
522443 TTCA
1 TTCA
522447 GGAATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (21 bp):
TTCAACGTGATAAAAAGTCAT
Found at i:538743 original size:16 final size:14
Alignment explanation
Indices: 538722--538759 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
538712 TAAAAATTAA
538722 TAATTATTTAAAAAAT
1 TAATTATTT--AAAAT
538738 TAATTA-TTAAAAT
1 TAATTATTTAAAAT
538751 TAATTATTT
1 TAATTATTT
538760 CAATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 11 0.52
14 2 0.10
15 2 0.10
16 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATTTAAAAT
Found at i:538751 original size:13 final size:13
Alignment explanation
Indices: 538733--538758 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
538723 AATTATTTAA
538733 AAAATTAATTATT
1 AAAATTAATTATT
538746 AAAATTAATTATT
1 AAAATTAATTATT
538759 TCAATATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATTAATTATT
Done.