Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002997.1 Hibiscus syriacus cultivar Beakdansim tig00006198_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: 142969
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:442 original size:137 final size:133
Alignment explanation
Indices: 200--468 Score: 452
Period size: 137 Copynumber: 2.0 Consensus size: 133
190 CATCCCATTA
* *
200 TTTTTAGAAAATGGTTATTTAATTTAATGTGTTAAGGAAAATAAAAAAAATTGCATACCCATTAT
1 TTTTTAGAAAATGATTATTTAATTTAATGTGTTAAGGAAAAAAAAAAAAATTGCATACCCATTAT
265 TTTTTAAAAATAAAATAAAATTTTATAATTATTTTAGTAAAATAATTTAA-GTATTAACGTTCTA
66 TTTTTAAAAATAAAATAAAATTTTATAATTATTTTAGT-AAATAATTTAATGTATTAACGTTCTA
329 TAGT
130 TAGT
333 TTTTTAGAAAAATGATTAAATTTAATTTAATGTGTTAAGGAAAAAAAAAAAAAATTGCATACCCA
1 TTTTTAG-AAAATGATT--ATTTAATTTAATGTGTTAAGG-AAAAAAAAAAAAATTGCATACCCA
398 TTATTTTTTAAAAAATAAAAT-AAATTTTATAATTATTTTAGTAAATAATTTAATGTATTAACGT
62 TTATTTTTT-AAAAATAAAATAAAATTTTATAATTATTTTAGTAAATAATTTAATGTATTAACGT
462 TCTATAG
126 TCTATAG
469 AATGTGCTTA
Statistics
Matches: 128, Mismatches: 2, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
133 7 0.05
134 8 0.06
136 32 0.25
137 70 0.55
138 11 0.09
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (133 bp):
TTTTTAGAAAATGATTATTTAATTTAATGTGTTAAGGAAAAAAAAAAAAATTGCATACCCATTAT
TTTTTAAAAATAAAATAAAATTTTATAATTATTTTAGTAAATAATTTAATGTATTAACGTTCTAT
AGT
Found at i:488 original size:35 final size:34
Alignment explanation
Indices: 444--518 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 34
434 TTTAGTAAAT
*
444 AATTTAATGTATTAACGTTCTATAGAATGTGCTTA
1 AATTTAATGTATTAACGTTATATAGAATGTG-TTA
* *
479 AATTTAATGTGTTAACGTTATATAGAATGTGTTT
1 AATTTAATGTATTAACGTTATATAGAATGTGTTA
513 AATTTA
1 AATTTA
519 GTAAAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 8 0.22
35 29 0.78
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (34 bp):
AATTTAATGTATTAACGTTATATAGAATGTGTTA
Found at i:7612 original size:35 final size:37
Alignment explanation
Indices: 7539--7613 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
7529 ACAACATCTT
**
7539 CATGAGGTATCGATACCGAAAGGGGTAGTATCGATAC
1 CATGAGGTATCGATACCGAAAGGCATAGTATCGATAC
7576 CATG-GGTATCGATACC-AGAAGGCAT-GTATCGATAC
1 CATGAGGTATCGATACCGA-AAGGCATAGTATCGATAC
7611 CAT
1 CAT
7614 TTTTGGACCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 14 0.40
36 17 0.49
37 4 0.11
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.23
Consensus pattern (37 bp):
CATGAGGTATCGATACCGAAAGGCATAGTATCGATAC
Found at i:8289 original size:21 final size:21
Alignment explanation
Indices: 8234--8320 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
8224 GTCGAGGGTC
* *
8234 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTTGGAACATA
**
8255 TATGTAATCCTTTGGAACATA
1 TATGTGGTCCTTTGGAACATA
* *
8276 TATGTGGTCATTTGAGACGCATA
1 TATGTGGTCCTTTG-GA-ACATA
*
8299 T-T-TGGTCCTTTGGAATATA
1 TATGTGGTCCTTTGGAACATA
8318 TAT
1 TAT
8321 ATATGGTTCT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 4 0.08
20 3 0.06
21 37 0.71
22 3 0.06
23 5 0.10
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (21 bp):
TATGTGGTCCTTTGGAACATA
Found at i:8399 original size:23 final size:23
Alignment explanation
Indices: 8372--8424 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
8362 TTTTGTATGA
*
8372 CACTTCGGTGCATTTCTACGCGG
1 CACTTCGGTGCAATTCTACGCGG
*
8395 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCAATTCTACGCGG
*
8418 CATTTCG
1 CACTTCG
8425 ATGTATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGG
Found at i:18345 original size:27 final size:27
Alignment explanation
Indices: 18285--18345 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
18275 TGGAAAGTAA
*
18285 AAAATTATAGTCTATAGATTTTGATCT
1 AAAATTATAGTATATAGATTTTGATCT
* *
18312 GATATTATATGATATATAGA-TTTGAT-T
1 AAAATTATA-G-TATATAGATTTTGATCT
18339 AAAATTA
1 AAAATTA
18346 GCATTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
27 13 0.48
28 7 0.26
29 7 0.26
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.44
Consensus pattern (27 bp):
AAAATTATAGTATATAGATTTTGATCT
Found at i:25932 original size:18 final size:18
Alignment explanation
Indices: 25909--25946 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
25899 TGATCTTTTA
*
25909 ATATAATATATTCTAATT
1 ATATAATATAGTCTAATT
25927 ATATAATATAGTCTAATT
1 ATATAATATAGTCTAATT
25945 AT
1 AT
25947 TTTCATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATAATATAGTCTAATT
Found at i:26098 original size:2 final size:2
Alignment explanation
Indices: 26091--26133 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
26081 CATTTTGAAA
26091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26133 A
1 A
26134 ATCCTTCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26190 original size:20 final size:20
Alignment explanation
Indices: 26147--26191 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
26137 CTTCAAAAGT
*
26147 TTAAAAATTATTATTATTAA
1 TTAAAAATTAATATTATTAA
*
26167 TTAAAAATTAAATATT-TTAG
1 TTAAAAATT-AATATTATTAA
26187 TTAAA
1 TTAAA
26192 CTCTCTTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAAAAATTAATATTATTAA
Found at i:28645 original size:14 final size:15
Alignment explanation
Indices: 28620--28649 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28610 TTAGTATCGT
28620 ACTAACATAATATAA
1 ACTAACATAATATAA
28635 ACTAA-ATAATATAA
1 ACTAACATAATATAA
28649 A
1 A
28650 AGTCTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (15 bp):
ACTAACATAATATAA
Found at i:29142 original size:30 final size:30
Alignment explanation
Indices: 29102--29164 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
29092 ATATATAACT
* * *
29102 TTTTAAAAA-TTATATTTTTGGTCCCTAAAC
1 TTTTAAAAATTTATACTTTAGGT-ACTAAAC
*
29132 TTTTACAAATTTATACTTTAGGTACTAAAC
1 TTTTAAAAATTTATACTTTAGGTACTAAAC
29162 TTT
1 TTT
29165 CAAAGCTTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (30 bp):
TTTTAAAAATTTATACTTTAGGTACTAAAC
Found at i:29239 original size:15 final size:15
Alignment explanation
Indices: 29219--29249 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29209 TACCCCAAAG
29219 TTTTTCTTTCATAAT
1 TTTTTCTTTCATAAT
*
29234 TTTTTCTTTTATAAT
1 TTTTTCTTTCATAAT
29249 T
1 T
29250 GTATTCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTCTTTCATAAT
Found at i:32071 original size:27 final size:25
Alignment explanation
Indices: 32011--32075 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
32001 ATTTAAGAGA
32011 TAAAAATATATTATTAATAAAAATAT
1 TAAAAATAT-TTATTAATAAAAATAT
*
32037 AAACAAATATTTACTTTATATAAAAAT-T
1 TAA-AAATATTTA--TTA-ATAAAAATAT
32065 TAAAAAT-TTTA
1 TAAAAATATTTA
32076 AGAGACAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 9 0.27
27 10 0.30
28 6 0.18
29 8 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAAAATATTTATTAATAAAAATAT
Found at i:32209 original size:28 final size:29
Alignment explanation
Indices: 32178--32236 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
32168 CTTTACACTC
*
32178 TTTTTTATTTTACTC-ATTAAC-TTTTAAT
1 TTTTTTA-TTTACTCAATGAACTTTTTAAT
32206 TTTTTTATTTACTCAATGAACTTTTTAAT
1 TTTTTTATTTACTCAATGAACTTTTTAAT
32235 TT
1 TT
32237 CTCCTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 7 0.25
28 12 0.43
29 9 0.32
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTTTATTTACTCAATGAACTTTTTAAT
Found at i:38394 original size:93 final size:94
Alignment explanation
Indices: 38235--38467 Score: 423
Period size: 93 Copynumber: 2.5 Consensus size: 94
38225 TCAGTTATGG
38235 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
1 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
38300 CTCAGTTATGG-AAAATAATATTGACCAT
66 CTCAGTTATGGAAAAATAATATTGACCAT
*
38328 AAAAACCAACCCCAAGTTGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
1 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
38393 CTCAGTTATGGAAAAATAATATTGACCAT
66 CTCAGTTATGGAAAAATAATATTGACCAT
* * *
38422 AAAAACCAACCCCAAGTAGACTCATCTAACTAAAGCATGGACCCAT
1 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCAT
38468 GAAAATCGTA
Statistics
Matches: 134, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
93 75 0.56
94 59 0.44
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.21
Consensus pattern (94 bp):
AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
CTCAGTTATGGAAAAATAATATTGACCAT
Found at i:44548 original size:12 final size:12
Alignment explanation
Indices: 44531--44562 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
44521 AAAATAAGAT
44531 AAATAAATTGAA
1 AAATAAATTGAA
44543 AAATAAATTGAA
1 AAATAAATTGAA
44555 AAATAAAT
1 AAATAAAT
44563 AGAGATGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (12 bp):
AAATAAATTGAA
Found at i:52471 original size:2 final size:2
Alignment explanation
Indices: 52466--52516 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
52456 ATAAACACAC
52466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52508 AT AT AT AT A
1 AT AT AT AT A
52517 GCCATGTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60408 original size:28 final size:28
Alignment explanation
Indices: 60376--60430 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
60366 AATTTAAATC
* *
60376 TGGATAAA-GATGAGAAAATATATGGATT
1 TGGATAAACG-TGAGAAAAGATAGGGATT
60404 TGGATAAACGTGAGAAAAGATAGGGAT
1 TGGATAAACGTGAGAAAAGATAGGGAT
60431 GAGAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (28 bp):
TGGATAAACGTGAGAAAAGATAGGGATT
Found at i:62831 original size:39 final size:37
Alignment explanation
Indices: 62761--62833 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 37
62751 GGACCGATAT
**
62761 AAATAGTAGCCACGACTTTCAAAGTTGGGAAACTTGA
1 AAATAGTAGCCACGACTTTCAAAGTCAGGAAACTTGA
* *
62798 AAATCGTAGCCACAGGACTTTCAAGGTCAGGAAACT
1 AAATAGTAGCCAC--GACTTTCAAAGTCAGGAAACT
62834 ATATAAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 12 0.40
39 18 0.60
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (37 bp):
AAATAGTAGCCACGACTTTCAAAGTCAGGAAACTTGA
Found at i:67744 original size:39 final size:39
Alignment explanation
Indices: 67698--67772 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
67688 TTCATTTCCA
*
67698 ATCGATAA-AGTTTGTTCTAGAGATTCTCAACCATTTCTG
1 ATCGATAATA-TTTGTTCTAAAGATTCTCAACCATTTCTG
*
67737 ATCGATAATATTTGTTCTAAAGATTCTCAATCATTT
1 ATCGATAATATTTGTTCTAAAGATTCTCAACCATTT
67773 GACAATGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (39 bp):
ATCGATAATATTTGTTCTAAAGATTCTCAACCATTTCTG
Found at i:68457 original size:2 final size:2
Alignment explanation
Indices: 68452--68482 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68442 TATATATATT
68452 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
68483 CTTACCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:72596 original size:16 final size:17
Alignment explanation
Indices: 72575--72609 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
72565 TTACTATTCA
72575 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
72591 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
72608 CG
1 CG
72610 GTCAGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:73376 original size:15 final size:16
Alignment explanation
Indices: 73358--73390 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
73348 GTGGCAGATC
73358 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
73373 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
73389 AA
1 AA
73391 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:76946 original size:39 final size:37
Alignment explanation
Indices: 76876--76948 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 37
76866 GGACCGATAT
**
76876 AAATAGTAGCCACGACTTTCAAAGTTGGGAAACTTGA
1 AAATAGTAGCCACGACTTTCAAAGTCAGGAAACTTGA
* *
76913 AAATCGTAGCCACAGGACTTTCAAGGTCAGGAAACT
1 AAATAGTAGCCAC--GACTTTCAAAGTCAGGAAACT
76949 ATATAAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 12 0.40
39 18 0.60
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (37 bp):
AAATAGTAGCCACGACTTTCAAAGTCAGGAAACTTGA
Found at i:77260 original size:28 final size:29
Alignment explanation
Indices: 77229--77287 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
77219 CTTTACACTC
*
77229 TTTTTTATTTTACTC-ATTAAC-TTTTAAT
1 TTTTTTA-TTTACTCAATGAACTTTTTAAT
77257 TTTTTTATTTACTCAATGAACTTTTTAAT
1 TTTTTTATTTACTCAATGAACTTTTTAAT
77286 TT
1 TT
77288 CTCCTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 7 0.25
28 12 0.43
29 9 0.32
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTTTATTTACTCAATGAACTTTTTAAT
Found at i:83435 original size:93 final size:94
Alignment explanation
Indices: 83276--83508 Score: 423
Period size: 93 Copynumber: 2.5 Consensus size: 94
83266 TCAGTTATGG
83276 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
1 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
83341 CTCAGTTATGG-AAAATAATATTGACCAT
66 CTCAGTTATGGAAAAATAATATTGACCAT
*
83369 AAAAACCAACTCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
1 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
83434 CTCAGTTATGGAAAAATAATATTGACCAT
66 CTCAGTTATGGAAAAATAATATTGACCAT
* * *
83463 AAAAACCAACCCCAAGTAGACTCATCTAACTAAAGCATGGACCCAT
1 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCAT
83509 GAAAATCGTA
Statistics
Matches: 134, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
93 75 0.56
94 59 0.44
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (94 bp):
AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
CTCAGTTATGGAAAAATAATATTGACCAT
Found at i:87065 original size:7 final size:7
Alignment explanation
Indices: 87053--87079 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
87043 ATAAAATCAA
87053 TGGTATC
1 TGGTATC
87060 TGGTATC
1 TGGTATC
87067 TGGTATC
1 TGGTATC
87074 TGGTAT
1 TGGTAT
87080 TTGCAGGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.30, T:0.44
Consensus pattern (7 bp):
TGGTATC
Found at i:88162 original size:23 final size:24
Alignment explanation
Indices: 88118--88164 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
88108 AGCAAGGTTT
***
88118 GTAAAATAAAAATAACTTGGAAAA
1 GTAAAATAAAAATAAAAAGGAAAA
88142 GTAAAAT-AAAATAAAAAGGAAAA
1 GTAAAATAAAAATAAAAAGGAAAA
88165 TGGAGACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.68, C:0.02, G:0.13, T:0.17
Consensus pattern (24 bp):
GTAAAATAAAAATAAAAAGGAAAA
Found at i:88566 original size:31 final size:31
Alignment explanation
Indices: 88528--88598 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
88518 AACACAACCC
88528 AATTTAGCAGTGATATGTTTGTAAAACGAAG
1 AATTTAGCAGTGATATGTTTGTAAAACGAAG
88559 AATTTAGCAGTGATATGTTTGTAAAACGAAG
1 AATTTAGCAGTGATATGTTTGTAAAACGAAG
88590 AATTTAGCA
1 AATTTAGCA
88599 ATTAGAAGGA
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:0.39, C:0.07, G:0.21, T:0.32
Consensus pattern (31 bp):
AATTTAGCAGTGATATGTTTGTAAAACGAAG
Found at i:88820 original size:2 final size:2
Alignment explanation
Indices: 88815--88839 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
88805 TATAATAAAC
88815 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
88840 GCCATTTTAC
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:92939 original size:39 final size:37
Alignment explanation
Indices: 92869--92941 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 37
92859 GGACCGATAT
**
92869 AAATAGTAGCCACGACTTTCAAAGTTGGGAAACTTGA
1 AAATAGTAGCCACGACTTTCAAAGTCAGGAAACTTGA
* *
92906 AAATCGTAGCCACAGGACTTTCAAGGTCAGGAAACT
1 AAATAGTAGCCAC--GACTTTCAAAGTCAGGAAACT
92942 ATATAAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 12 0.40
39 18 0.60
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (37 bp):
AAATAGTAGCCACGACTTTCAAAGTCAGGAAACTTGA
Found at i:98899 original size:28 final size:28
Alignment explanation
Indices: 98858--98912 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
98848 GATTTAAATC
* *
98858 TAGATAAAGATGAGAAAATATATGGATT
1 TAGATAAAGATGAGAAAAGATAGGGATT
98886 TAGATAAACG-TGAGAAAAGATAGGGAT
1 TAGATAAA-GATGAGAAAAGATAGGGAT
98913 GAGAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.24
Consensus pattern (28 bp):
TAGATAAAGATGAGAAAAGATAGGGATT
Found at i:98989 original size:12 final size:12
Alignment explanation
Indices: 98972--99003 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
98962 AAAATAAGAT
98972 AAATAAATTGAA
1 AAATAAATTGAA
98984 AAATAAATTGAA
1 AAATAAATTGAA
98996 AAATAAAT
1 AAATAAAT
99004 AGAGATGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (12 bp):
AAATAAATTGAA
Found at i:106291 original size:23 final size:24
Alignment explanation
Indices: 106247--106293 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
106237 AGCAAGGTTT
***
106247 GTAAAATAAAAATAACTTGGAAAA
1 GTAAAATAAAAATAAAAAGGAAAA
106271 GTAAAAT-AAAATAAAAAGGAAAA
1 GTAAAATAAAAATAAAAAGGAAAA
106294 TGGAGACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.68, C:0.02, G:0.13, T:0.17
Consensus pattern (24 bp):
GTAAAATAAAAATAAAAAGGAAAA
Found at i:111040 original size:39 final size:37
Alignment explanation
Indices: 110970--111042 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 37
110960 GGACCGATAT
**
110970 AAATAGTAGCCACGACTTTCAAAGTTGGGAAACTTGA
1 AAATAGTAGCCACGACTTTCAAAGTCAGGAAACTTGA
* *
111007 AAATCGTAGCCACAGGACTTTCAAGGTCAGGAAACT
1 AAATAGTAGCCAC--GACTTTCAAAGTCAGGAAACT
111043 ATATAAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 12 0.40
39 18 0.60
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (37 bp):
AAATAGTAGCCACGACTTTCAAAGTCAGGAAACTTGA
Found at i:114461 original size:15 final size:15
Alignment explanation
Indices: 114441--114470 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
114431 ACACAAAATC
114441 TTTTCATCATTCGAG
1 TTTTCATCATTCGAG
114456 TTTTCATCATTCGAG
1 TTTTCATCATTCGAG
114471 GCAGATTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (15 bp):
TTTTCATCATTCGAG
Found at i:116267 original size:30 final size:30
Alignment explanation
Indices: 116231--116513 Score: 494
Period size: 30 Copynumber: 9.4 Consensus size: 30
116221 TCCGAAGGAC
*
116231 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116261 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116291 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
116321 CTATCCAGATGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
116351 CTATCCAGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116381 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
116411 CTATCCATAGGTTATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116441 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
116471 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
116501 CTATCCATAGGTC
1 CTATCCAGAGGTC
116514 CCGAAGAACC
Statistics
Matches: 241, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 241 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:116553 original size:31 final size:31
Alignment explanation
Indices: 116499--116591 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
116489 GATCCTCAGT
* *
116499 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
116530 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
116561 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
116592 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:116774 original size:4 final size:4
Alignment explanation
Indices: 116765--116790 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
116755 ATATAACCAT
116765 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
116791 TCATCCCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:116957 original size:2 final size:2
Alignment explanation
Indices: 116945--116983 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
116935 TACACAACTC
116945 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116984 TGTAACATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:121080 original size:30 final size:30
Alignment explanation
Indices: 120841--121063 Score: 428
Period size: 30 Copynumber: 7.4 Consensus size: 30
120831 TCCGAAGGAC
120841 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
120871 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
120901 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
120931 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
120961 CTATCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
120991 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
121021 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
121051 CTATCCATAGGTC
1 CTATCCAGAGGTC
121064 CCGAAGAACC
Statistics
Matches: 190, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 190 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:121103 original size:31 final size:31
Alignment explanation
Indices: 121049--121141 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
121039 GATCCTCGGT
* *
121049 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
121080 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
121111 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
121142 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:121324 original size:4 final size:4
Alignment explanation
Indices: 121315--121340 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
121305 ATATAACCAT
121315 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
121341 TCATCCCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:121507 original size:2 final size:2
Alignment explanation
Indices: 121495--121525 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
121485 TACACAACTC
121495 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
121526 TGTAACATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:123174 original size:39 final size:39
Alignment explanation
Indices: 123128--123202 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
123118 TTCATTTCCA
*
123128 ATCGATAAAGTTTGTTCTAGAGATTCTCAACCATTTCTG
1 ATCGATAAAGTTTGTTCCAGAGATTCTCAACCATTTCTG
* *
123167 ATCGATAATGTTTGTTCCAGAGATTCTCAATCATTT
1 ATCGATAAAGTTTGTTCCAGAGATTCTCAACCATTT
123203 GACAATAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (39 bp):
ATCGATAAAGTTTGTTCCAGAGATTCTCAACCATTTCTG
Found at i:126151 original size:174 final size:174
Alignment explanation
Indices: 125924--126323 Score: 764
Period size: 174 Copynumber: 2.3 Consensus size: 174
125914 GGAGGAATAG
*
125924 TTCTCAAGTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCACCGCAATTGAGGTG
1 TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCACCGCAATTGAGGTG
125989 CCATTTTTCATATCTTGAGGTTCCTGAGCCTGCAAGTTCGAATCAAAACCAGAGCATCCTTCAGA
66 CCATTTTTCATATCTTGAGGTTCCTGAGCCTGCAAGTTCGAATCAAAACCAGAGCATCCTTCAGA
*
126054 TTCCTGTTCCTCTATAGTCATATCAATAATGTCAACGGGCATGA
131 TTCCTGTTCCTCTATACTCATATCAATAATGTCAACGGGCATGA
126098 TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCACCGCAATTGAGGTG
1 TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCACCGCAATTGAGGTG
126163 CCATTTTTCATATCTTGAGGTTCCTGAGCCTGCAAGTTCGAATCAAAACCAGAGCATCCTTCAGA
66 CCATTTTTCATATCTTGAGGTTCCTGAGCCTGCAAGTTCGAATCAAAACCAGAGCATCCTTCAGA
126228 TTCCTGTTCCTCTATACTCATATCAATAATGTCAACGGGCATGA
131 TTCCTGTTCCTCTATACTCATATCAATAATGTCAACGGGCATGA
* *
126272 TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAAAATCAGAGGAAACCAC
1 TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCAC
126324 TACTTTTGTA
Statistics
Matches: 222, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 222 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (174 bp):
TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCACCGCAATTGAGGTG
CCATTTTTCATATCTTGAGGTTCCTGAGCCTGCAAGTTCGAATCAAAACCAGAGCATCCTTCAGA
TTCCTGTTCCTCTATACTCATATCAATAATGTCAACGGGCATGA
Found at i:126619 original size:141 final size:140
Alignment explanation
Indices: 126265--126621 Score: 365
Period size: 141 Copynumber: 2.5 Consensus size: 140
126255 AATGTCAACG
* * * * *
126265 GGCATGATTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAAAATCAGAGGAAACCACTACTTT
1 GGCATGCTTCTCAATT-TGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCTTT
* * * * * * * *
126330 TGTAGCATCTTTTTTTATACATTGTGAATCACAACCAGATTTCTGTTCCTCTGCACTCAAAACGC
65 TGTAGTATCATCTATTATACATTGTGAACCACAACCAGATTCCTGTTCCTCTGCACCCAAAACAC
126395 CAGTCCCAGCA
130 CAGTCCCAGCA
* * ** * * * *
126406 GGCATGCTTCTCAAGTCTGAGGTCATCCTATTACAACCATCAACCTCAGATAAAACAACTTCGTT
1 GGCATGCTTCTCAA-TTTGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCTTT
* * * * * *
126471 TGAAGTATCATCTATTATGTC-TTGTGAACCATAACCAGATTCCTGTTTCTCTGTACCCAAATCA
65 TGTAGTATCATCTATTAT-ACATTGTGAACCACAACCAGATTCCTGTTCCTCTGCACCCAAAACA
* *
126535 TCAGTCTCAGCA
129 CCAGTCCCAGCA
* * * * *
126547 GGTATGCTTCTCAACTTTGAAGTCATCCCATTACCCCCACCAACATCGGATGAAACCATTTCTTT
1 GGCATGCTTCTCAA-TTTGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCTTT
126612 TGTAGTATCA
65 TGTAGTATCA
126622 ATTTTTATAT
Statistics
Matches: 170, Mismatches: 44, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
141 168 0.99
142 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (140 bp):
GGCATGCTTCTCAATTTGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCTTTT
GTAGTATCATCTATTATACATTGTGAACCACAACCAGATTCCTGTTCCTCTGCACCCAAAACACC
AGTCCCAGCA
Found at i:129009 original size:77 final size:77
Alignment explanation
Indices: 128882--129028 Score: 224
Period size: 77 Copynumber: 1.9 Consensus size: 77
128872 CAGTAAAAAC
* * * *
128882 ACCAAATTTATCATCAGAAGATTAGCACATCATCCTTCCGACGCATCTAAACGA-ACATTAATCC
1 ACCAAATTTATCATCAGAAGATAAGAACACCAGCCTTCCGACGCATCTAAACGACA-ATTAATCC
128946 ATCTAAACATTAT
65 ATCTAAACATTAT
* *
128959 ACCAAATTTATCATCAGAAGATAAGAACACCAGCCTTTCGACGCATCTAAATGACAATTAATCCA
1 ACCAAATTTATCATCAGAAGATAAGAACACCAGCCTTCCGACGCATCTAAACGACAATTAATCCA
129024 TCTAA
66 TCTAA
129029 CAAAAAGTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
77 62 0.98
78 1 0.02
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (77 bp):
ACCAAATTTATCATCAGAAGATAAGAACACCAGCCTTCCGACGCATCTAAACGACAATTAATCCA
TCTAAACATTAT
Found at i:131392 original size:21 final size:22
Alignment explanation
Indices: 131363--131408 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
131353 ATAAAAGAAA
* *
131363 TTATTTAAAATATT-ATTTTTT
1 TTATCTAAAATATTAATATTTT
*
131384 TTATCTAAATTATTAATATTTT
1 TTATCTAAAATATTAATATTTT
131406 TTA
1 TTA
131409 ATATTTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATCTAAAATATTAATATTTT
Found at i:135137 original size:20 final size:21
Alignment explanation
Indices: 135112--135150 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
135102 GGGCTTTCTT
*
135112 TTGACTTG-GATTTTGGGTGG
1 TTGACTTGAGATTTAGGGTGG
135132 TTGACTTGAGATTTAGGGT
1 TTGACTTGAGATTTAGGGT
135151 TTGTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.05, G:0.36, T:0.44
Consensus pattern (21 bp):
TTGACTTGAGATTTAGGGTGG
Found at i:135243 original size:31 final size:31
Alignment explanation
Indices: 135205--135278 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
135195 ATGGAATTAT
* *
135205 ATATTAATAAAATATGTTATGTCATAACAAA
1 ATATTAATAAAATATGTCAAGTCATAACAAA
135236 ATATTAATAAAATATGTCAAGTCATAACAAA
1 ATATTAATAAAATATGTCAAGTCATAACAAA
135267 ATATTAATAAAA
1 ATATTAATAAAA
135279 AAATCATTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.32
Consensus pattern (31 bp):
ATATTAATAAAATATGTCAAGTCATAACAAA
Found at i:136570 original size:29 final size:29
Alignment explanation
Indices: 136533--136595 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
136523 AAAATCTATT
* *
136533 TTCGCCCCCTAAAATTTTATAAGTTTAAG
1 TTCGTCCCCTAAAATTTTATAAGTTTAAA
*
136562 TTCGTCCCCTAAAATTTTATTAGTTTAAA
1 TTCGTCCCCTAAAATTTTATAAGTTTAAA
136591 TTCGT
1 TTCGT
136596 TCCATAGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (29 bp):
TTCGTCCCCTAAAATTTTATAAGTTTAAA
Found at i:137336 original size:29 final size:31
Alignment explanation
Indices: 137278--137345 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
137268 AACGGTTTAG
137278 TGATATAATTGAGATAAAAATCAAAATTCAA
1 TGATATAATTGAGATAAAAATCAAAATTCAA
* * * * *
137309 TGCTATAATT-AG-TAAAACTGAAAGTTCAG
1 TGATATAATTGAGATAAAAATCAAAATTCAA
137338 TGATATAA
1 TGATATAA
137346 ACGATACAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 20 0.65
30 2 0.06
31 9 0.29
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (31 bp):
TGATATAATTGAGATAAAAATCAAAATTCAA
Found at i:139125 original size:3 final size:3
Alignment explanation
Indices: 139117--139152 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
139107 TTGTCCCAAC
139117 ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT AT
139153 GCATATCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.