Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002033.1 Hibiscus syriacus cultivar Beakdansim tig00004148_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: 86732
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2259 original size:15 final size:15
Alignment explanation
Indices: 2239--2269 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2229 GAACTGTTTT
2239 GACCCGATCCAACCC
1 GACCCGATCCAACCC
2254 GACCCGATCCAACCC
1 GACCCGATCCAACCC
2269 G
1 G
2270 TTGACTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.52, G:0.16, T:0.06
Consensus pattern (15 bp):
GACCCGATCCAACCC
Found at i:4985 original size:105 final size:105
Alignment explanation
Indices: 4778--4998 Score: 266
Period size: 105 Copynumber: 2.1 Consensus size: 105
4768 GATTGTCCAC
* * * * *
4778 AAGGACCACAT-ATAAATTCCTTAAGAACCATATATATATACCAAGGATCAAGAAAGTGTCTCAA
1 AAGGACCACGTAAAAAATTCCTTAAGAACCATATACATATACCAAGAACCAAGAAAGTGTCTCAA
4842 AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
66 AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
* * * *
4882 AAGGACCACGTAAAAAATTCCTTAAGAATCATATACATATGCTAAGAACCAA-ATACGTGTCTCA
1 AAGGACCACGTAAAAAATTCCTTAAGAACCATATACATATACCAAGAACCAAGA-AAGTGTCTCA
* * * * * * *
4946 AAAGACCTTATAGATGTTCCATAGGATACCTATATGTCCCG
65 AAAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
*
4987 AAGGACCGCGTA
1 AAGGACCACGTA
4999 GACCCTCGAC
Statistics
Matches: 98, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
104 11 0.11
105 87 0.89
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.23
Consensus pattern (105 bp):
AAGGACCACGTAAAAAATTCCTTAAGAACCATATACATATACCAAGAACCAAGAAAGTGTCTCAA
AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
Found at i:5197 original size:53 final size:53
Alignment explanation
Indices: 5140--5303 Score: 140
Period size: 53 Copynumber: 3.1 Consensus size: 53
5130 ACACATACAT
*
5140 GTAATCACGTAGTTCATATCAATTCTCATAGGATTTCATATTCATATAATCAC
1 GTAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCAC
* * * * * * * ** *
5193 GTAATTCACTTACG--CATAGCACATTTTCAT-GTAATTCACA--GATATCCCTTAGC
1 GTAA-TCACGTA-GTTCATACCA-ATTCTCATAGGATTTCATATTCATAT-AATCA-C
*
5246 TTAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCAC
1 GTAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCAC
5299 GTAAT
1 GTAAT
5304 TCACTTACAC
Statistics
Matches: 79, Mismatches: 22, Indels: 20
0.65 0.18 0.17
Matches are distributed among these distances:
51 5 0.06
52 15 0.19
53 39 0.49
54 15 0.19
55 5 0.06
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.37
Consensus pattern (53 bp):
GTAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCAC
Found at i:5275 original size:106 final size:106
Alignment explanation
Indices: 5141--5351 Score: 395
Period size: 106 Copynumber: 2.0 Consensus size: 106
5131 CACATACATG
*
5141 TAATCACGTAGTTCATATCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
*
5206 GCATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
66 ACATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
5247 TAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
*
5312 ACATAGCACATTTTCATGTAATTCACAGATGTCCCTTAGC
66 ACATAGCACATTTTCATGTAATTCACAGATATCCCTTAGC
5352 ATATGTCTCT
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.36
Consensus pattern (106 bp):
TAATCACGTAGTTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
ACATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
Found at i:10331 original size:105 final size:105
Alignment explanation
Indices: 10137--10346 Score: 276
Period size: 105 Copynumber: 2.0 Consensus size: 105
10127 GACCACATAT
* * *
10137 AAATTCCTTAAGAACCATATACATATACCAATGATCAAGTAAGTATCTCAAAAGACCTCATACAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTATCTCAAAAGACCTCATACAT
10202 GCTCCAAAGAATACATATACGTCCCGAAGGACCACGTAGA
66 GCTCCAAAGAATACATATACGTCCCGAAGGACCACGTAGA
* *** * * *
10242 AAATTCCTTAAGAATCATATACATATGTTAAGGACCAAATACGTGTCTCAAAAGACCTCATAGAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTATCTCAAAAGACCTCATACAT
* * * * * *
10307 GTTCCATAGGATACCTATATGTCCCGAAGGACCGCGTAGA
66 GCTCCAAAGAATACATATACGTCCCGAAGGACCACGTAGA
10347 CCCTCGACTC
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
105 89 1.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (105 bp):
AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTATCTCAAAAGACCTCATACAT
GCTCCAAAGAATACATATACGTCCCGAAGGACCACGTAGA
Found at i:10624 original size:106 final size:105
Alignment explanation
Indices: 10487--10699 Score: 363
Period size: 106 Copynumber: 2.0 Consensus size: 105
10477 CACATACATG
*
10487 TAATCACATATTCATATCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTACA
1 TAATCACATATTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTACA
*
10552 CATAGCACATTTTCATTTAATTCACAGATATCCCTTAGCT
66 CATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
* *
10592 TAATCACGTAGTTCATGCCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACATA-TTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTAC
* *
10657 ACATAGCATATTTTCATGTAATTCACAGATGTCCCTTAGCT
65 ACATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
10698 TA
1 TA
10700 TGTCTCTTGA
Statistics
Matches: 101, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
105 9 0.09
106 92 0.91
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.38
Consensus pattern (105 bp):
TAATCACATATTCATACCAATTCTCATAGGATTTCATATTCATATAATCACGTAATTCACTTACA
CATAGCACATTTTCATGTAATTCACAGATATCCCTTAGCT
Found at i:11984 original size:21 final size:22
Alignment explanation
Indices: 11928--11999 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
11918 GGGGGTATCA
*
11928 ATTCCCCTTTGAATGGGTACTG
1 ATTCCCCATTGAATGGGTACTG
* **
11950 ATTCCCCCTTGAATGGGTTTTG
1 ATTCCCCATTGAATGGGTACTG
* *
11972 ATT-CCCATTGAATCGGTACCG
1 ATTCCCCATTGAATGGGTACTG
11993 ATTCCCC
1 ATTCCCC
12000 TAGCCCAGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 16 0.39
22 25 0.61
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (22 bp):
ATTCCCCATTGAATGGGTACTG
Found at i:13267 original size:24 final size:24
Alignment explanation
Indices: 13195--13288 Score: 82
Period size: 24 Copynumber: 4.0 Consensus size: 24
13185 TCTTATTTGA
* * * * *
13195 ATTCTGTTATGATACCTAACCTAG
1 ATTCTGATATGATACATGACTTGG
* * **
13219 ATTCTGATCTGATA-TTGACACGG
1 ATTCTGATATGATACATGACTTGG
*
13242 ATTTTGATATGATACATGACTTGG
1 ATTCTGATATGATACATGACTTGG
*
13266 ATTCTGATATGATACTTGACTTG
1 ATTCTGATATGATACATGACTTG
13289 AATTATGTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 16 0.29
24 39 0.71
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACATGACTTGG
Found at i:13302 original size:24 final size:24
Alignment explanation
Indices: 13246--13295 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
13236 ACACGGATTT
* *
13246 TGATATGATACATGACTTGGATTC
1 TGATATGATACATGACTTGAATTA
*
13270 TGATATGATACTTGACTTGAATTA
1 TGATATGATACATGACTTGAATTA
13294 TG
1 TG
13296 TTTTGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATATGATACATGACTTGAATTA
Found at i:16112 original size:29 final size:29
Alignment explanation
Indices: 16079--16147 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
16069 AAAAACATTA
*
16079 ATTAAATAAAATATTAAAAAAT-TTAAAT
1 ATTAAATAAAATATAAAAAAATATTAAAT
16107 ACTTAAAT-AAAT-TAAAAAAATATTAAAT
1 A-TTAAATAAAATATAAAAAAATATTAAAT
16135 A-T-AATAAAATATA
1 ATTAAATAAAATATA
16148 CCTTAAACAG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 10 0.28
28 12 0.33
29 6 0.17
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (29 bp):
ATTAAATAAAATATAAAAAAATATTAAAT
Found at i:16142 original size:20 final size:21
Alignment explanation
Indices: 16103--16143 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
16093 TAAAAAATTT
16103 AAATACTTAAATAAATTAAAA
1 AAATACTTAAATAAATTAAAA
16124 AAATA-TTAAATATAA-TAAAA
1 AAATACTTAAATA-AATTAAAA
16144 TATACCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATACTTAAATAAATTAAAA
Found at i:16145 original size:17 final size:16
Alignment explanation
Indices: 16070--16146 Score: 57
Period size: 16 Copynumber: 4.4 Consensus size: 16
16060 ATATCTGTAA
* *
16070 AAAACATTAATTAAAT
1 AAAATATTAAATAAAT
16086 AAAATATTAAA-AAATT
1 AAAATATTAAATAAA-T
*
16102 TAAATACTTAAATAAATT
1 AAAATA-TTAAATAAA-T
16120 AAAAAAATATTAAATATAAT
1 ---AAAATATTAAATA-AAT
16140 AAAATAT
1 AAAATAT
16147 ACCTTAAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.06
16 15 0.30
17 12 0.24
18 5 0.10
20 8 0.16
21 7 0.14
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:20225 original size:2 final size:2
Alignment explanation
Indices: 20218--20242 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20208 ATAAGCAGAA
20218 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20243 AAAGGAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25649 original size:24 final size:24
Alignment explanation
Indices: 25622--25724 Score: 129
Period size: 24 Copynumber: 4.3 Consensus size: 24
25612 TTCCAGTTGA
*
25622 ACCAAAGGCGGGGGTGCTTGTAGC
1 ACCAAAGGCAGGGGTGCTTGTAGC
25646 ACCAAAGGCAGGGGTGCTTGT-GAC
1 ACCAAAGGCAGGGGTGCTTGTAG-C
*
25670 ACCAAAGGCAGGGGTGCTTG-AGGA
1 ACCAAAGGCAGGGGTGCTTGTA-GC
** *
25694 ACCAAAGGCAGAAGTGCTTGTGGC
1 ACCAAAGGCAGGGGTGCTTGTAGC
25718 ACCAAAG
1 ACCAAAG
25725 CTACCAACTG
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.01
24 67 0.97
25 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.37, T:0.15
Consensus pattern (24 bp):
ACCAAAGGCAGGGGTGCTTGTAGC
Found at i:25678 original size:48 final size:48
Alignment explanation
Indices: 25622--25724 Score: 145
Period size: 48 Copynumber: 2.1 Consensus size: 48
25612 TTCCAGTTGA
* * **
25622 ACCAAAGGCGGGGGTGCTTGTA-GCACCAAAGGCAGGGGTGCTTGTGAC
1 ACCAAAGGCAGGGGTGCTTG-AGGAACCAAAGGCAGAAGTGCTTGTGAC
*
25670 ACCAAAGGCAGGGGTGCTTGAGGAACCAAAGGCAGAAGTGCTTGTGGC
1 ACCAAAGGCAGGGGTGCTTGAGGAACCAAAGGCAGAAGTGCTTGTGAC
25718 ACCAAAG
1 ACCAAAG
25725 CTACCAACTG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
47 1 0.02
48 48 0.98
ACGTcount: A:0.28, C:0.20, G:0.37, T:0.15
Consensus pattern (48 bp):
ACCAAAGGCAGGGGTGCTTGAGGAACCAAAGGCAGAAGTGCTTGTGAC
Found at i:25890 original size:279 final size:278
Alignment explanation
Indices: 25479--26003 Score: 739
Period size: 279 Copynumber: 1.9 Consensus size: 278
25469 AGATGGGCTA
25479 GACCCAAAGCTGAATGAAGGAGTAGAAGATGCCCCAAAAGCAGGTGTGCTTGGTGCTCCAAAAGT
1 GACCCAAAGCTGAATGAAGGAGTAGAAGATGCCCCAAAAGCAGGTGTGCTTGGTGCTCCAAAAGT
* * * **
25544 GCCTCCAGTTCCAAAGATCGTGGTGTTAGGCGTACCAAATGCAATTCCACTGCTCCCAAATGCTG
66 ACCTCCAGTTCCAAAGACCGGGGCATTAGGCG-ACCAAATGCAATTCCACTGCTCCCAAATGCTG
* * * * * * *
25609 GACTTCCAGTTGAACCAAAGGCGGGGGTGCTTGTAGCACCAAAGGCAGGGGTGCTTG-TGACACC
130 GACTTCCAGTGGAACCAAAAGCAGGGGTACTTGTAGAACCAAAGGCAGGGGTGCTCGCGGA-ACC
* * *
25673 AAAGGCAGGGGTGCTTGAGGAACCAAAGGCAGAAGTGCTTGTGGCACCAAAGCTACCAACTGCAG
194 AAAGGCAGGGGTGCTCGAGGAACCAAAGGAAGAAGTGCTCGTGGCACCAAAGCTACCAACTGCAG
25738 GAGTTGACTGGCCAAATGCT
259 GAGTTGACTGGCCAAATGCT
* * * *
25758 GACCCAAAGCTGAATGATGGAGTTGAAGATGCTCCAAAAGCAGGTGTGCTTGGTGCTCCAAATGT
1 GACCCAAAGCTGAATGAAGGAGTAGAAGATGCCCCAAAAGCAGGTGTGCTTGGTGCTCCAAAAGT
* * ** *
25823 ACTTCCTGTTCCAAAGACCGGGGCATTAGAGAC-ACCAAATGCGGTTCCAGTGCTCCCAAATGCT
66 ACCTCCAGTTCCAAAGACCGGGGCATTAG-G-CGACCAAATGCAATTCCACTGCTCCCAAATGCT
*
25887 GGACTTCCAGTGGAACCAAAAGCAGGGGTACTTGTGGAACCAAAGGCAGGGGTGCTCGCGGAACC
129 GGACTTCCAGTGGAACCAAAAGCAGGGGTACTTGTAGAACCAAAGGCAGGGGTGCTCGCGGAACC
* * **
25952 AAAGGCAGGGGTGCTCGTGGCACCAAAGGAAGGGGTGCTCGTGGCACCAAAG
194 AAAGGCAGGGGTGCTCGAGGAACCAAAGGAAGAAGTGCTCGTGGCACCAAAG
26004 GAAGGGGTGC
Statistics
Matches: 214, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
279 210 0.98
280 3 0.01
281 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.18
Consensus pattern (278 bp):
GACCCAAAGCTGAATGAAGGAGTAGAAGATGCCCCAAAAGCAGGTGTGCTTGGTGCTCCAAAAGT
ACCTCCAGTTCCAAAGACCGGGGCATTAGGCGACCAAATGCAATTCCACTGCTCCCAAATGCTGG
ACTTCCAGTGGAACCAAAAGCAGGGGTACTTGTAGAACCAAAGGCAGGGGTGCTCGCGGAACCAA
AGGCAGGGGTGCTCGAGGAACCAAAGGAAGAAGTGCTCGTGGCACCAAAGCTACCAACTGCAGGA
GTTGACTGGCCAAATGCT
Found at i:26175 original size:24 final size:24
Alignment explanation
Indices: 25896--26167 Score: 379
Period size: 24 Copynumber: 11.3 Consensus size: 24
25886 TGGACTTCCA
* * * *
25896 GTGGAACCAAAAGCAGGGGTACTT
1 GTGGCACCAAAGGCAGGGGTGCTC
*
25920 GTGGAACCAAAGGCAGGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
* *
25944 GCGGAACCAAAGGCAGGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
*
25968 GTGGCACCAAAGGAAGGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
*
25992 GTGGCACCAAAGGAAGGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
*
26016 GTGGCACCAAAGGAAGGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
*
26040 GTGGCACCAAAGGCAGGCGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
26064 GTGGCACCAAAGGCAGGGGTGCTC
1 GTGGCACCAAAGGCAGGGGTGCTC
26088 GTGGCACCGAAA-GCAGGGGTGCTC
1 GTGGCACC-AAAGGCAGGGGTGCTC
*
26112 GTGGCACCGAAA-GCAGGGGTGCTG
1 GTGGCACC-AAAGGCAGGGGTGCTC
*
26136 GTGGCACCGAAA-GCAGGGGTGCTG
1 GTGGCACC-AAAGGCAGGGGTGCTC
26160 GTGGCACC
1 GTGGCACC
26168 GAATGCAGAC
Statistics
Matches: 236, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
24 233 0.99
25 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.41, T:0.12
Consensus pattern (24 bp):
GTGGCACCAAAGGCAGGGGTGCTC
Found at i:30418 original size:12 final size:12
Alignment explanation
Indices: 30393--30453 Score: 86
Period size: 12 Copynumber: 5.1 Consensus size: 12
30383 CAACTTATAT
* *
30393 ATACACGCACAC
1 ATACATGCATAC
30405 ATACATGCATAC
1 ATACATGCATAC
* *
30417 ATACACGCACAC
1 ATACATGCATAC
30429 ATACATGCATAC
1 ATACATGCATAC
30441 ATACATGCATAC
1 ATACATGCATAC
30453 A
1 A
30454 AAAAAAGGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.43, C:0.31, G:0.08, T:0.18
Consensus pattern (12 bp):
ATACATGCATAC
Found at i:30420 original size:24 final size:24
Alignment explanation
Indices: 30393--30445 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
30383 CAACTTATAT
30393 ATACACGCACACATACATGCATAC
1 ATACACGCACACATACATGCATAC
30417 ATACACGCACACATACATGCATAC
1 ATACACGCACACATACATGCATAC
30441 ATACA
1 ATACA
30446 TGCATACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.32, G:0.08, T:0.17
Consensus pattern (24 bp):
ATACACGCACACATACATGCATAC
Found at i:34422 original size:37 final size:37
Alignment explanation
Indices: 34388--34641 Score: 295
Period size: 37 Copynumber: 6.8 Consensus size: 37
34378 TATAAAATAT
34388 TTTTTAAAACTA-ATATTATATATA-TTTCGAAAAATG
1 TTTTTAAAACTATATATTATATATATTTTC-AAAAATG
* * *
34424 TTTTCAAAACCTATATATTATATATATATTCAAACATG
1 TTTTTAAAA-CTATATATTATATATATTTTCAAAAATG
*
34462 TTTTCT-AAAGTATATATTATATATATGTTTTCAAAAATG
1 TTTT-TAAAACTATATATTATATATA--TTTTCAAAAATG
*
34501 TTTTTAAAACTATATA-T-TATATATTTTCAAAAAAAACG
1 TTTTTAAAACTATATATTATATATATTTTC---AAAAATG
* *
34539 -TTTTAAGACTATATATTATATATATTTTCGAAAATG
1 TTTTTAAAACTATATATTATATATATTTTCAAAAATG
*
34575 TTTTCAAAACTATATATTATATATATTTTCAAAAATG
1 TTTTTAAAACTATATATTATATATATTTTCAAAAATG
* * *
34612 TTTTTAAAATTATATATTATGTATACTTTC
1 TTTTTAAAACTATATATTATATATATTTTC
34642 GAAGAGAAAA
Statistics
Matches: 186, Mismatches: 19, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
35 5 0.03
36 13 0.07
37 97 0.52
38 34 0.18
39 37 0.20
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (37 bp):
TTTTTAAAACTATATATTATATATATTTTCAAAAATG
Found at i:36025 original size:23 final size:23
Alignment explanation
Indices: 35999--36067 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 23
35989 TCATTTTAAA
35999 ATATTTTAAAAACACTTAATATT
1 ATATTTTAAAAACACTTAATATT
** *
36022 ATA-TTT--ATTCATTTTAA-A--
1 ATATTTTAAAAACA-CTTAATATT
36040 ATATTTTAAAAACACTTAATATT
1 ATATTTTAAAAACACTTAATATT
36063 ATATT
1 ATATT
36068 AATTTTTAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 8 0.24
21 8 0.24
22 3 0.09
23 8 0.24
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTTTAAAAACACTTAATATT
Found at i:36025 original size:41 final size:41
Alignment explanation
Indices: 35979--36067 Score: 178
Period size: 41 Copynumber: 2.2 Consensus size: 41
35969 TTAACAAATG
35979 TTATATTTATTCATTTTAAAATATTTTAAAAACACTTAATA
1 TTATATTTATTCATTTTAAAATATTTTAAAAACACTTAATA
36020 TTATATTTATTCATTTTAAAATATTTTAAAAACACTTAATA
1 TTATATTTATTCATTTTAAAATATTTTAAAAACACTTAATA
36061 TTATATT
1 TTATATT
36068 AATTTTTAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.51
Consensus pattern (41 bp):
TTATATTTATTCATTTTAAAATATTTTAAAAACACTTAATA
Found at i:39963 original size:43 final size:45
Alignment explanation
Indices: 39859--39964 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 45
39849 AGGATTAGAT
*
39859 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAACATTATTTTTAATTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAAC--TATGTTTAATTA
*
39909 TTATTATTTTATTAGGAATT-A-GAGTTAAAAC-ATGTTTAATTTG
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACTATGTTTAA-TTA
39952 TTATTATTTTATT
1 TTATTATTTTATT
39965 CATTAGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
42 7 0.13
43 15 0.28
45 10 0.19
49 1 0.02
50 20 0.38
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (45 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACTATGTTTAATTA
Found at i:41418 original size:20 final size:20
Alignment explanation
Indices: 41395--41446 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
41385 AACGCGATCC
41395 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
41415 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
41435 CCAAAATCGCAA
1 CCAGAATCGCAA
41447 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:41596 original size:20 final size:20
Alignment explanation
Indices: 41502--41870 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
41492 GATTTTCCAT
* ** *
41502 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
41522 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
41542 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
41562 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
41582 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
41602 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
41622 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
41642 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
41662 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
41682 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
41702 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
41722 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
41742 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
41762 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
41782 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
41802 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
41822 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
41842 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
41862 AATCACAAC
1 AATCGCAAC
41871 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:42579 original size:24 final size:24
Alignment explanation
Indices: 42552--42598 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42542 GAAATTGGTC
42552 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
42576 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
42599 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:42790 original size:12 final size:12
Alignment explanation
Indices: 42773--42797 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42763 ATATAATCCT
42773 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42785 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42797 G
1 G
42798 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:45100 original size:19 final size:19
Alignment explanation
Indices: 45078--45384 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
45068 CGGAAAATAC
*
45078 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45097 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
45111 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
45131 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
45145 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45164 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45183 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
45197 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45216 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45235 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45254 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
45268 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
45287 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45306 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45325 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45344 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
45358 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45377 AATCGCAA
1 AATCGCAA
45385 CGAGATAATC
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 16 0.06
17 14 0.06
18 3 0.01
19 156 0.62
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:45193 original size:52 final size:52
Alignment explanation
Indices: 45106--45384 Score: 384
Period size: 52 Copynumber: 5.2 Consensus size: 52
45096 AAATCCCAAC
45106 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
45159 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
45211 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* * *
45261 ACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
45320 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
45372 ATGAAAATCGCAA
1 ATGAAAATCGCAA
45385 CGAGATAATC
Statistics
Matches: 201, Mismatches: 14, Indels: 23
0.84 0.06 0.10
Matches are distributed among these distances:
50 7 0.03
51 7 0.03
52 125 0.62
53 17 0.08
54 1 0.00
55 2 0.01
57 28 0.14
58 7 0.03
59 7 0.03
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:45229 original size:71 final size:71
Alignment explanation
Indices: 45145--45384 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
45135 GCAACGAGAG
45145 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
45210 AATGAA
66 AATGAA
*
45216 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
*
45281 AATTAA
66 AATGAA
*
45287 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAA
45352 --CGAAA-G--
61 TGCGAAATGAA
45358 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
45385 CGAGATAATC
Statistics
Matches: 159, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
71 142 0.89
73 2 0.01
74 5 0.03
75 1 0.01
76 9 0.06
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAA
Found at i:45520 original size:19 final size:19
Alignment explanation
Indices: 45422--45512 Score: 129
Period size: 19 Copynumber: 5.0 Consensus size: 19
45412 ACGTATTAAA
45422 TTTCATTTCCGCATTGCGAT
1 TTTCATTT-CGCATTGCGAT
45442 TTTCATTTCGCATTGCGA-
1 TTTCATTTCGCATTGCGAT
*
45460 -TTC-TCTCG--TTGCGAT
1 TTTCATTTCGCATTGCGAT
45475 TTTCATTTCGCATTGCGAT
1 TTTCATTTCGCATTGCGAT
45494 TTTCATTTCGCATTGCGAT
1 TTTCATTTCGCATTGCGAT
45513 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.11
17 7 0.11
19 36 0.56
20 8 0.12
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.46
Consensus pattern (19 bp):
TTTCATTTCGCATTGCGAT
Found at i:47630 original size:14 final size:14
Alignment explanation
Indices: 47611--47666 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
47601 GCGAAATGAA
*
47611 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
47625 AATCGCATGCGAAATG
1 AATCGCA-ACGAAA-G
47641 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
47657 AATCGCAACG
1 AATCGCAACG
47667 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 17 0.49
15 4 0.11
16 2 0.06
17 5 0.14
18 7 0.20
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:47675 original size:33 final size:33
Alignment explanation
Indices: 47592--47683 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
47582 GCGAAACCAA
*
47592 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
47625 AATCGC-ATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
47657 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
47684 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:47681 original size:19 final size:19
Alignment explanation
Indices: 47555--47688 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
47545 TAGTTTACTT
* *
47555 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
47575 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
47594 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
47613 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
47627 TCGC-ATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
47645 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
47659 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
47678 TCGCAATGCGA
1 TCGCAACGCGA
47689 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
13 1 0.01
14 14 0.15
15 4 0.04
16 8 0.08
17 10 0.11
18 6 0.06
19 40 0.42
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:47706 original size:19 final size:19
Alignment explanation
Indices: 47684--47811 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
47674 AAAATCGCAA
47684 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
47703 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
47717 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
47735 TGCGATTAT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
47749 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
47768 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
47787 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
47807 TGCGA
1 TGCGA
47812 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 2 0.02
14 20 0.23
16 3 0.03
17 1 0.01
18 10 0.11
19 39 0.44
20 13 0.15
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:47769 original size:33 final size:32
Alignment explanation
Indices: 47684--47775 Score: 141
Period size: 32 Copynumber: 2.8 Consensus size: 32
47674 AAAATCGCAA
47684 TGCGATTTTGGTTTCGCGTTGCGATCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGAT-TTGTCGT
47717 TGCGA-TTTGGTTTCGCGTTGCGATTATGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TGTCGT
**
47749 TGCGATTTTCATTTCGCGTTGCGATTT
1 TGCGATTTTGGTTTCGCGTTGCGATTT
47776 TGGTTTCGCG
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 31 0.56
33 23 0.42
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (32 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTGTCGT
Found at i:48141 original size:93 final size:93
Alignment explanation
Indices: 47855--48601 Score: 1434
Period size: 93 Copynumber: 8.1 Consensus size: 93
47845 TTGAATGGAT
47855 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
47920 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
47948 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
48012 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
48040 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
48105 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
48133 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
48197 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
48225 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
48290 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
48318 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
48383 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
48411 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
48474 AG-TTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
48501 AAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
48565 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
48593 AAATTTACT
1 AAATTTACT
48602 AAGCAATCTA
Statistics
Matches: 646, Mismatches: 2, Indels: 12
0.98 0.00 0.02
Matches are distributed among these distances:
89 35 0.05
90 30 0.05
91 48 0.07
92 213 0.33
93 320 0.50
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:48167 original size:185 final size:186
Alignment explanation
Indices: 47855--48601 Score: 1434
Period size: 185 Copynumber: 4.0 Consensus size: 186
47845 TTGAATGGAT
47855 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
47920 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
47984 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
48040 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
48105 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
48170 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
*
48225 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
48290 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
48355 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
48411 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
48474 AG-TTAGCAGAATTGGCAGCAACCGAACAAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
48537 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
48593 AAATTTACT
1 AAATTTACT
48602 AAGCAATCTA
Statistics
Matches: 558, Mismatches: 2, Indels: 7
0.98 0.00 0.01
Matches are distributed among these distances:
182 97 0.17
183 28 0.05
184 24 0.04
185 313 0.56
186 96 0.17
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:48352 original size:278 final size:278
Alignment explanation
Indices: 47855--48601 Score: 1439
Period size: 278 Copynumber: 2.7 Consensus size: 278
47845 TTGAATGGAT
47855 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
47920 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
47984 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
48049 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
195 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
48114 GAATTGGCAGCAACCGAAC
260 GAATTGGCAGCAACCGAAC
48133 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
48198 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
*
48263 ATTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
48328 TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
48393 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
48411 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATA-TTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
48475 G-TTAGCAGAATTGGCAGCAACCGAACAAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
*
48538 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
48602 AAGCAATCTA
Statistics
Matches: 465, Mismatches: 3, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
275 96 0.21
276 28 0.06
277 111 0.24
278 230 0.49
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (278 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
AATTGGCAGCAACCGAAC
Found at i:50323 original size:14 final size:14
Alignment explanation
Indices: 50304--50393 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
50294 TTGAAATGAA
50304 AATCGCAACGAGAG
1 AATCGCAACGAGAG
50318 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
50335 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
50351 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
50370 AATCGCAACGAGAG
1 AATCGCAACGAGAG
50384 AATCGCAACG
1 AATCGCAACG
50394 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:50341 original size:33 final size:33
Alignment explanation
Indices: 50296--50410 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
50286 TCTTTTGGTT
50296 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
50329 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
50362 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
50395 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
50411 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:50342 original size:19 final size:18
Alignment explanation
Indices: 50303--50415 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
50293 GTTGAAATGA
50303 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
50318 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
50335 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
50351 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
50368 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
50384 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
50401 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
50416 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:50446 original size:14 final size:14
Alignment explanation
Indices: 50427--50481 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
50417 TTTGGTTTCG
50427 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
50441 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
50460 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
50474 CGTTGCGA
1 CGTTGCGA
50482 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:50459 original size:33 final size:33
Alignment explanation
Indices: 50411--50481 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
50401 AAAATCGCAA
**
50411 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
50444 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
50477 TGCGA
1 TGCGA
50482 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:50489 original size:33 final size:33
Alignment explanation
Indices: 50422--50503 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
50412 GCGATTTTGG
***
50422 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
50455 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
50488 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
50504 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:50508 original size:20 final size:20
Alignment explanation
Indices: 50434--50522 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
50424 TCGCGTTGCG
50434 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
50454 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
50467 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
50487 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
50507 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
50523 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:50644 original size:33 final size:33
Alignment explanation
Indices: 50602--50672 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
50592 AATACTAACT
*
50602 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
50635 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
50668 TGAAA
1 TGAAA
50673 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:50906 original size:22 final size:22
Alignment explanation
Indices: 50854--50908 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
50844 TGGTTGTGAG
**
50854 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
50876 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
50898 GGATTTCTTCG
1 GGATTTCTTCG
50909 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:51079 original size:20 final size:20
Alignment explanation
Indices: 51054--51246 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
51044 CTTTAAATAT
51054 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
51074 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
51096 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
51115 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* * **
51135 CACATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
51155 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
51175 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
51195 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
51215 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
51235 CGCGTTGCGATT
1 CGCGTTGCGATT
51247 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:51241 original size:60 final size:60
Alignment explanation
Indices: 51054--51246 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
51044 CTTTAAATAT
**
51054 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * * *** *
51115 CGCGTTGCGATATACGGATACACATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
51175 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
51235 CGCGTTGCGATT
1 CGCGTTGCGATT
51247 ATGGAAAATC
Statistics
Matches: 109, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 82 0.75
61 27 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:51327 original size:20 final size:20
Alignment explanation
Indices: 51302--51353 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
51292 AAGAATCGCG
*
51302 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
51322 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
51342 TTGCGATTCTGG
1 TTGCGATTCTGG
51354 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:55385 original size:2 final size:2
Alignment explanation
Indices: 55378--55402 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55368 AAATCTTTAA
55378 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
55403 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55680 original size:62 final size:62
Alignment explanation
Indices: 55608--55727 Score: 181
Period size: 62 Copynumber: 1.9 Consensus size: 62
55598 CATCATTATT
*
55608 ACTAACATAAAAATAAATATAATGATGATAACACATT-TATAA-TTAATTTTATCATAATCAAC
1 ACTAACATAAAAATAAATATAATGATGATAACACATTAT-TAACTT-ACTTTATCATAATCAAC
* *
55670 ACTAATATAAAAATAAATATAATGATGATAATACATTATTAACTTACTTTATCATAAT
1 ACTAACATAAAAATAAATATAATGATGATAACACATTATTAACTTACTTTATCATAAT
55728 TGAAACACAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
62 50 0.94
63 3 0.06
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (62 bp):
ACTAACATAAAAATAAATATAATGATGATAACACATTATTAACTTACTTTATCATAATCAAC
Found at i:55750 original size:62 final size:62
Alignment explanation
Indices: 55608--55741 Score: 175
Period size: 62 Copynumber: 2.1 Consensus size: 62
55598 CATCATTATT
* *
55608 ACTAACATAAAAATAAATATAATGATGATAACACATTTATAATTAATTTTATCATAATCAAC
1 ACTAACATAAAAATAAATATAATGATGATAACACATTTATAATTAACTTTATCATAATAAAC
* *
55670 ACTAATATAAAAATAAATATAATGATGATAATACA-TTATTAACTT-ACTTTATCATAATTGAAA
1 ACTAACATAAAAATAAATATAATGATGATAACACATTTA-TAA-TTAACTTTATCATAA-T-AAA
55733 C
62 C
55734 AC-AACATA
1 ACTAACATA
55742 TACAAAATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
61 3 0.05
62 47 0.75
63 8 0.13
64 5 0.08
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (62 bp):
ACTAACATAAAAATAAATATAATGATGATAACACATTTATAATTAACTTTATCATAATAAAC
Found at i:57067 original size:4 final size:4
Alignment explanation
Indices: 57058--57082 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
57048 TTGTCAGTTT
57058 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
57083 TATTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:58109 original size:58 final size:58
Alignment explanation
Indices: 58026--58135 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 58
58016 CTTAAATTTA
* * * * * *
58026 TAAATATTTTTATTTTATCCTTAAACTATG-CTTATCATTTTAAATTATTCCCAAACTT
1 TAAACATTTTAATTTCATCCTTAAACTATGACAT-TCATTCTAAATTAGTCCCAAACTT
*
58084 TAAACATTTTAATTTCATCGTTAAACTATGACATTCATTCTAAATTAGTCCC
1 TAAACATTTTAATTTCATCCTTAAACTATGACATTCATTCTAAATTAGTCCC
58136 CAAAAATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 42 0.95
59 2 0.05
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (58 bp):
TAAACATTTTAATTTCATCCTTAAACTATGACATTCATTCTAAATTAGTCCCAAACTT
Found at i:61470 original size:38 final size:38
Alignment explanation
Indices: 61415--61512 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 38
61405 TATAAGATAT
* * * * *
61415 ATGATAGGTCCTACGGGACACATATTACATCCTTTGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
61453 ATGACAGGTCTTTCGGGACACAGATGACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
61491 ATGATAGGTCCTTCGGGACACA
1 ATGACAGGTCCTTCGGGACACA
61513 ATTTATACGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:63500 original size:2 final size:2
Alignment explanation
Indices: 63493--63525 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
63483 TATCATTGGA
63493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63526 ATAATTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63986 original size:2 final size:2
Alignment explanation
Indices: 63979--64004 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63969 TATTTGGATC
63979 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
64005 GATTAAGGCA
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:67763 original size:38 final size:38
Alignment explanation
Indices: 67707--67804 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 38
67697 TATAAGACAT
* * * *
67707 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGAG
*
67745 ATGACAGGTCTTTCGGGACACAGATGACATCCTTCGAG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGAG
* *
67783 ATGATAGGTCCTTCAGGACACA
1 ATGACAGGTCCTTCGGGACACA
67805 ATTTATACGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGAG
Found at i:70073 original size:31 final size:31
Alignment explanation
Indices: 69999--70074 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 31
69989 AAGTTTATTT
*
69999 ATTTTTTGTAATTTAAATACTTAACTTTCAA
1 ATTTTTTCTAATTTAAATACTTAACTTTCAA
** *
70030 ATTACTCCTAATTT-AATCACTCTAACTTTC-A
1 ATTTTTTCTAATTTAAAT-ACT-TAACTTTCAA
*
70061 ATTTTTTTTAATTT
1 ATTTTTTCTAATTT
70075 TAATTATATA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
30 3 0.09
31 24 0.69
32 8 0.23
ACGTcount: A:0.32, C:0.14, G:0.01, T:0.53
Consensus pattern (31 bp):
ATTTTTTCTAATTTAAATACTTAACTTTCAA
Found at i:71744 original size:13 final size:13
Alignment explanation
Indices: 71726--71750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71716 TAAATAAATA
71726 AAAATTAATAATT
1 AAAATTAATAATT
71739 AAAATTAATAAT
1 AAAATTAATAAT
71751 ATATTTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATTAATAATT
Found at i:72452 original size:60 final size:60
Alignment explanation
Indices: 72281--72453 Score: 206
Period size: 60 Copynumber: 2.9 Consensus size: 60
72271 TATGTCCCCC
* **
72281 AACTATGACCCTCATTTC-AAATTGGTCCCTAAACTTTTGAATATTCCAATGCCATCCTCA
1 AACTATGACCCT-ATTTCTAAATTAGTCCCTAAACTTTTGAATATTCCAATTTCATCCTCA
* * * * * *
72341 AACTATGACTCAAGTTCTAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCC-CTA
1 AACTATGACCCTATTTCTAAATTAGTCCCTAAACTTTTGAATATTCCAATTTCATCCTC-A
* * *
72401 AACTATGACCCTTTTTCTAGATTAGTCCCCAAACTTTTGAATATTCCAATTTC
1 AACTATGACCCTATTTCTAAATTAGTCCCTAAACTTTTGAATATTCCAATTTC
72454 TTCTCCAAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
59 5 0.05
60 88 0.95
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.37
Consensus pattern (60 bp):
AACTATGACCCTATTTCTAAATTAGTCCCTAAACTTTTGAATATTCCAATTTCATCCTCA
Found at i:76602 original size:29 final size:30
Alignment explanation
Indices: 76543--76602 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
76533 TGGGATTTTC
*
76543 TCTTTCAACTTATCACCAGAAACAAGTAAG
1 TCTTTAAACTTATCACCAGAAACAAGTAAG
* *
76573 TCTTTAAACTTATCA-TAGAAACATGTAAG
1 TCTTTAAACTTATCACCAGAAACAAGTAAG
76602 T
1 T
76603 TATAATTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (30 bp):
TCTTTAAACTTATCACCAGAAACAAGTAAG
Found at i:78152 original size:11 final size:11
Alignment explanation
Indices: 78136--78164 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
78126 ATAGCACACC
78136 CATCATCTGGT
1 CATCATCTGGT
78147 CATCATCTGGT
1 CATCATCTGGT
78158 CATCATC
1 CATCATC
78165 ATACAAGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.34
Consensus pattern (11 bp):
CATCATCTGGT
Found at i:78798 original size:34 final size:34
Alignment explanation
Indices: 78755--78824 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
78745 AAATGGAGGT
*
78755 TTGTCTACATGGTTAGTCCATTCCATGAGAATGC
1 TTGTCTACATGGTTAGCCCATTCCATGAGAATGC
78789 TTGTCTACATGGTTAGCCCATTCCATGAGAATGC
1 TTGTCTACATGGTTAGCCCATTCCATGAGAATGC
78823 TT
1 TT
78825 AAATTCAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (34 bp):
TTGTCTACATGGTTAGCCCATTCCATGAGAATGC
Found at i:81134 original size:12 final size:13
Alignment explanation
Indices: 81117--81149 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
81107 CACTAAATTT
81117 TATTTTCTCAC-A
1 TATTTTCTCACTA
81129 TATTTTACTCACTA
1 TATTTT-CTCACTA
81143 TATTTTC
1 TATTTTC
81150 AATTCTTCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 6 0.32
14 7 0.37
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTTCTCACTA
Found at i:81772 original size:17 final size:17
Alignment explanation
Indices: 81741--81773 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
81731 AAATATTATT
81741 TTATTATTTATTTTAAA
1 TTATTATTTATTTTAAA
81758 TTATT-TTTATATTTAA
1 TTATTATTTAT-TTTAA
81774 TAATAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTTAAA
Found at i:82613 original size:31 final size:31
Alignment explanation
Indices: 82578--82648 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
82568 TTAGGTTCAT
82578 AAGAAATTATCAGTCGGTGATGAACCTATAC
1 AAGAAATTATCAGTCGGTGATGAACCTATAC
82609 AAGAAATTATCAGTCGGTGATGAACCTATAC
1 AAGAAATTATCAGTCGGTGATGAACCTATAC
82640 AAGAAATTA
1 AAGAAATTA
82649 CCAGCAACGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (31 bp):
AAGAAATTATCAGTCGGTGATGAACCTATAC
Done.