Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006465.1 Hibiscus syriacus cultivar Beakdansim tig00015665_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: 109734
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:4508 original size:23 final size:23
Alignment explanation
Indices: 4481--4525 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4471 TTTTAATTTT
*
4481 AATTTAATTAATTATTTTTGAAA
1 AATTTAATTAATTATTATTGAAA
* *
4504 AATTTATTTATTTATTATTGAA
1 AATTTAATTAATTATTATTGAA
4526 TAAAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
AATTTAATTAATTATTATTGAAA
Found at i:9983 original size:21 final size:21
Alignment explanation
Indices: 9937--9993 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
9927 CCCTTTTGAG
* *
9937 AGGATCGATCTCTCAAGATAA
1 AGGATCGATCCCTTAAGATAA
*
9958 GGGATCGATCCCTTAGAGA-AA
1 AGGATCGATCCCTTA-AGATAA
9979 AGGATCGATCCCTTA
1 AGGATCGATCCCTTA
9994 TATGTTTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (21 bp):
AGGATCGATCCCTTAAGATAA
Found at i:11309 original size:40 final size:40
Alignment explanation
Indices: 11254--11336 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
11244 GAGGTTAGAA
* *
11254 ACTTAGTATTTGTATACTCATGGA-AGGGCCCTTAGTGAAG
1 ACTTAGTATTTGTATACTCACGGAGA-GGCCCTTAGCGAAG
*
11294 ACTTAGTATTTGTATACTCACGGCGAGGCCCTTAGCGAAG
1 ACTTAGTATTTGTATACTCACGGAGAGGCCCTTAGCGAAG
11334 ACT
1 ACT
11337 AAGGGAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (40 bp):
ACTTAGTATTTGTATACTCACGGAGAGGCCCTTAGCGAAG
Found at i:12040 original size:108 final size:110
Alignment explanation
Indices: 11880--12100 Score: 419
Period size: 108 Copynumber: 2.0 Consensus size: 110
11870 ACACTATGTA
*
11880 AATATAAAATAATATATATCAATTGCAAATTAATTTGTGAAAATTGAATCAAATAAAAGTTATAT
1 AATATAAAATAATATATATCAATGGCAAATTAATTTGTGAAAATTGAATCAAATAAAAGTTATAT
11945 ATATAATTACATAAAATCAAAGTTCATACATTACATTATGCATTT
66 ATATAATTACATAAAATCAAAGTTCATACATTACATTATGCATTT
11990 AATATAAAAT-A-ATATATCAATGGCAAATTAATTTGTGAAAATTGAATCAAATAAAAGTTATAT
1 AATATAAAATAATATATATCAATGGCAAATTAATTTGTGAAAATTGAATCAAATAAAAGTTATAT
12053 ATATAATTACATAAAATCAAAGTTCATACATTACATTATGCATTT
66 ATATAATTACATAAAATCAAAGTTCATACATTACATTATGCATTT
12098 AAT
1 AAT
12101 GTGAGTTTTA
Statistics
Matches: 110, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
108 99 0.90
109 1 0.01
110 10 0.09
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (110 bp):
AATATAAAATAATATATATCAATGGCAAATTAATTTGTGAAAATTGAATCAAATAAAAGTTATAT
ATATAATTACATAAAATCAAAGTTCATACATTACATTATGCATTT
Found at i:12438 original size:64 final size:65
Alignment explanation
Indices: 12370--12520 Score: 209
Period size: 65 Copynumber: 2.3 Consensus size: 65
12360 ATCAATTTAT
* *
12370 ATTCACCATTTAA-TTTTATTAAAAATAT-CAAACAATAATTATAATTCAA-TTAAATACTTATT
1 ATTCAACATTTAATTTTTAAT-AAAAT-TGCAAACAATAATTATAATTCAAGTTAAATACTTATT
12432 AA
64 AA
* * *
12434 ATTCAACATTTAATTTTTAATAAAATTGCAAACAATTATTATATTTCAAGTTTAATACTTATTAA
1 ATTCAACATTTAATTTTTAATAAAATTGCAAACAATAATTATAATTCAAGTTAAATACTTATTAA
*
12499 ATTCAACATTTAATTTTCAATA
1 ATTCAACATTTAATTTTTAATA
12521 CTTATGTTTC
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 36 0.46
65 41 0.53
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (65 bp):
ATTCAACATTTAATTTTTAATAAAATTGCAAACAATAATTATAATTCAAGTTAAATACTTATTAA
Found at i:12797 original size:9 final size:10
Alignment explanation
Indices: 12778--12812 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
12768 ACTAACATAT
12778 ATTTTTGTTT-
1 ATTTTT-TTTA
12788 ATTTTTTTTA
1 ATTTTTTTTA
12798 ATTTTTTTTA
1 ATTTTTTTTA
12808 ATTTT
1 ATTTT
12813 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 3 0.12
10 21 0.88
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:12862 original size:17 final size:17
Alignment explanation
Indices: 12840--12874 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12830 TATATATATA
* *
12840 TATTAAAACATTATTTT
1 TATTAAAAAACTATTTT
12857 TATTAAAAAACTATTTT
1 TATTAAAAAACTATTTT
12874 T
1 T
12875 TCCCTCCTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTAAAAAACTATTTT
Found at i:12904 original size:19 final size:19
Alignment explanation
Indices: 12882--12918 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12872 TTTTCCCTCC
* *
12882 TGCGTAATTTCCCCTTGCT
1 TGCGTAAATCCCCCTTGCT
12901 TGCGTAAATCCCCCTTGC
1 TGCGTAAATCCCCCTTGC
12919 ACAAATTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.35, G:0.16, T:0.35
Consensus pattern (19 bp):
TGCGTAAATCCCCCTTGCT
Found at i:13651 original size:36 final size:36
Alignment explanation
Indices: 13604--13685 Score: 164
Period size: 36 Copynumber: 2.3 Consensus size: 36
13594 GTTTTATAAA
13604 TTGAGATTTTGGGTTTAGAATAAGGGATTTGAGTAT
1 TTGAGATTTTGGGTTTAGAATAAGGGATTTGAGTAT
13640 TTGAGATTTTGGGTTTAGAATAAGGGATTTGAGTAT
1 TTGAGATTTTGGGTTTAGAATAAGGGATTTGAGTAT
13676 TTGAGATTTT
1 TTGAGATTTT
13686 TTAAGAGACG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (36 bp):
TTGAGATTTTGGGTTTAGAATAAGGGATTTGAGTAT
Found at i:14072 original size:3 final size:3
Alignment explanation
Indices: 14066--14124 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
14056 TTAATTTTTT
* * * *
14066 TTA TTA TTT TTG TT- TTA TTA TTA TTA TTA TTA TTA ATA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14113 TTA TTA TTA TTA
1 TTA TTA TTA TTA
14125 AATAAATAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:20947 original size:10 final size:10
Alignment explanation
Indices: 20932--20977 Score: 69
Period size: 9 Copynumber: 4.8 Consensus size: 10
20922 AGAAAGAAGA
20932 AAAAAAAAGG
1 AAAAAAAAGG
20942 -AAAAAAAGG
1 AAAAAAAAGG
20951 AAAAAAAA-G
1 AAAAAAAAGG
*
20960 AAAAAAAAAG
1 AAAAAAAAGG
20970 AAAAAAAA
1 AAAAAAAA
20978 TTGAATCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:20956 original size:19 final size:19
Alignment explanation
Indices: 20932--20977 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
20922 AGAAAGAAGA
* *
20932 AAAAAAAAGGAAAAAAAGG
1 AAAAAAAAGAAAAAAAAAG
20951 AAAAAAAAGAAAAAAAAAG
1 AAAAAAAAGAAAAAAAAAG
20970 AAAAAAAA
1 AAAAAAAA
20978 TTGAATCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAAAG
Found at i:23338 original size:114 final size:114
Alignment explanation
Indices: 23137--23345 Score: 339
Period size: 114 Copynumber: 1.8 Consensus size: 114
23127 AATTTGGAAG
*
23137 AGGAGACTCAATAGCATCTCTTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCC
1 AGGAGACCCAATAGCATCTCTTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCC
*
23202 CAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAAAAATA
66 CAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCATAGTAAAAATA
* * *
23251 AGGAGACCCAATAGCATCT-TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAATC
1 AGGAGACCCAATAGCATCTCT-TGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACC
* *
23315 CCATAACCAATCATTGGAATTGAAAGGTGAA
65 CCAAAACCAATCATTGGAATTGAAAGATGAA
23346 CTACATGATT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
113 1 0.01
114 86 0.99
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (114 bp):
AGGAGACCCAATAGCATCTCTTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCC
CAAAACCAATCATTGGAATTGAAAGATGAATTTGCTCATAGTAAAAATA
Found at i:24545 original size:74 final size:75
Alignment explanation
Indices: 24446--24617 Score: 213
Period size: 74 Copynumber: 2.3 Consensus size: 75
24436 ATTAACAAGA
* * * *
24446 AGCAAATATTAGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
*
24511 TA-TT-TATC
66 CACTTGTATC
* * ** *
24519 AGCAAAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGA
1 AGC-AAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGA
*
24584 ACACTTGTATT
65 ACACTTGTATC
*
24595 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
24618 GGCCCACAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
73 3 0.04
74 54 0.64
75 21 0.25
76 6 0.07
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAA
CACTTGTATC
Found at i:26719 original size:76 final size:76
Alignment explanation
Indices: 26632--28307 Score: 3093
Period size: 76 Copynumber: 22.1 Consensus size: 76
26622 ACTATTTCCC
*
26632 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
26697 AAGCCTTCGGG
66 AAGCCTTCGGG
26708 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
26773 AAGCCTTCGGG
66 AAGCCTTCGGG
* *
26784 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
26849 AAGCCTTCGGG
66 AAGCCTTCGGG
*
26860 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
26925 AAGCCTTCGGG
66 AAGCCTTCGGG
26936 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27001 AAGCCTTCGGG
66 AAGCCTTCGGG
*
27012 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
27077 AAGCATTCGGG
66 AAGCCTTCGGG
*
27088 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27153 AAGCCTTCGGG
66 AAGCCTTCGGG
27164 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27229 AAGCCTTCGGG
66 AAGCCTTCGGG
27240 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27305 AAGCCTTCGGG
66 AAGCCTTCGGG
*
27316 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27381 AAGCCTTCGGG
66 AAGCCTTCGGG
27392 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27457 AAGCCTTCGGG
66 AAGCCTTCGGG
27468 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27533 AAGCCTTCGGG
66 AAGCCTTCGGG
*
27544 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27609 AAGCCTTCGGG
66 AAGCCTTCGGG
* *
27620 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27685 AAGCCTTCGGG
66 AAGCCTTCGGG
**
27696 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAATACTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27761 AAGCCTTCGGG
66 AAGCCTTCGGG
*
27772 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGACGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27837 AAGCCTTCGGG
66 AAGCCTTCGGG
*
27848 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
27913 AAGCCTTCGGG
66 AAGCCTTCGGG
*
27924 TCATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
27989 AAGCCTTCGTG
66 AAGCCTTCGGG
28000 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
28065 AAGCCTTCGGG
66 AAGCCTTCGGG
*
28076 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
28141 AAGCCTTCGGA
66 AAGCCTTCGGG
*
28152 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
**
28217 AAGCCTTAAGG
66 AAGCCTTCGGG
* * * *
28228 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAATCCTTTGGGATCTTTTTGATGTTTTTA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
28293 AA-CCCTCGGGG
66 AAGCCTTC-GGG
28304 TCAT
1 TCAT
28308 TCATAAGACC
Statistics
Matches: 1559, Mismatches: 40, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
75 3 0.00
76 1556 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTCGGG
Found at i:28480 original size:3 final size:3
Alignment explanation
Indices: 28474--28512 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
28464 TGTTTTTTTT
* *
28474 TTA TTA TTA TTA TTA ATA TTA GTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28513 AATAAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:28620 original size:20 final size:20
Alignment explanation
Indices: 28595--28642 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
28585 CCAAACCCTT
28595 TAGGGTTTGTAACATTCAGC
1 TAGGGTTTGTAACATTCAGC
28615 TAGGGTTTGTAACATTCAGC
1 TAGGGTTTGTAACATTCAGC
28635 TAGGGTTT
1 TAGGGTTT
28643 TCTAAACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (20 bp):
TAGGGTTTGTAACATTCAGC
Found at i:31680 original size:2 final size:2
Alignment explanation
Indices: 31673--31701 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31663 ATATTTAAAT
31673 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31702 GACATTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33709 original size:59 final size:60
Alignment explanation
Indices: 33617--33732 Score: 135
Period size: 59 Copynumber: 1.9 Consensus size: 60
33607 GCTTTTAAAT
* * * *
33617 ATTCCAATTTCATCCCAAAATTATCACTCTCATTCT-AATTAGTCCTTAAAATTTTGAAC
1 ATTCCAATTTCATCCCAAAACTATCAATATCATTCTAAATTAGTCCCTAAAATTTTGAAC
* * * * * *
33676 ATTCTAATTTCATCCCCAAACTATGAATATCATTTTAAATTGGTCCCTAAACTTTTG
1 ATTCCAATTTCATCCCAAAACTATCAATATCATTCTAAATTAGTCCCTAAAATTTTG
33733 CATCTTTAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
59 29 0.63
60 17 0.37
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (60 bp):
ATTCCAATTTCATCCCAAAACTATCAATATCATTCTAAATTAGTCCCTAAAATTTTGAAC
Found at i:34058 original size:60 final size:60
Alignment explanation
Indices: 33881--34050 Score: 206
Period size: 59 Copynumber: 2.9 Consensus size: 60
33871 ATACGTATAA
* * *
33881 TTTA-GGATTAAAATGAAATGTTCAAAAAGTTTGAGGACCAATTTATAATGAAGATTATAG
1 TTTAGGGATTAAAATGAAATG-TCTAAAAGTTTGAGGACCAATTTAAAATGAAGATCATAG
* * *
33941 TTTGGGGATGAAAATGAAATGT-TAAAAGTTTGAGGACTAA-TTAAGAATGACA-ATCATAG
1 TTTAGGGATTAAAATGAAATGTCTAAAAGTTTGAGGACCAATTTAA-AATGA-AGATCATAG
*
34000 TTTAGGGATTAAATTGAAATGTCTAAAAGTTTTG-GGACCAATTTAAAATGA
1 TTTAGGGATTAAAATGAAATGTCTAAAAG-TTTGAGGACCAATTTAAAATGA
34051 GGGTCATAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
58 3 0.03
59 46 0.49
60 22 0.23
61 23 0.24
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (60 bp):
TTTAGGGATTAAAATGAAATGTCTAAAAGTTTGAGGACCAATTTAAAATGAAGATCATAG
Found at i:37983 original size:14 final size:13
Alignment explanation
Indices: 37958--37991 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
37948 AATTATTCAA
37958 TAAATA-TATATT
1 TAAATATTATATT
37970 TAATATATTATATT
1 TAA-ATATTATATT
37984 TAAATATT
1 TAAATATT
37992 TGAAAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 8 0.40
14 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TAAATATTATATT
Found at i:40233 original size:18 final size:20
Alignment explanation
Indices: 40212--40260 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
40202 ACCCTCTTCT
40212 TCATCATCGTC-C-TCGCCC
1 TCATCATCGTCACTTCGCCC
*
40230 TCATCACCGTCATCTTCGCCC
1 TCATCATCGTCA-CTTCGCCC
*
40251 TCATCTTCGT
1 TCATCATCGT
40261 TTACGCCCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 10 0.40
20 1 0.04
21 14 0.56
ACGTcount: A:0.12, C:0.45, G:0.10, T:0.33
Consensus pattern (20 bp):
TCATCATCGTCACTTCGCCC
Found at i:45063 original size:89 final size:89
Alignment explanation
Indices: 44958--45136 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
44948 TAAACTTGCC
44958 GTATTTTACTTTTAATCTACTAATCTTTATTTTAATGTCAAATTTATTGTTATTGATTTTGTTCT
1 GTATTTTACTTTTAATCTACTAATCTTTATTTTAATGTCAAATTTATTGTTATTGATTTTGTTCT
*
45023 AAATACTCTCAACCATTTGATAAT
66 AAATACTATCAACCATTTGATAAT
45047 GTATTTTACTTTTAATCTACTAATCTTTATTTTAATGTCAAATTTATTGTTATTGATTTTGTTCT
1 GTATTTTACTTTTAATCTACTAATCTTTATTTTAATGTCAAATTTATTGTTATTGATTTTGTTCT
*
45112 AAATACTATCAATCATTTGATAAT
66 AAATACTATCAACCATTTGATAAT
45136 G
1 G
45137 AATGCTCAAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (89 bp):
GTATTTTACTTTTAATCTACTAATCTTTATTTTAATGTCAAATTTATTGTTATTGATTTTGTTCT
AAATACTATCAACCATTTGATAAT
Found at i:47930 original size:50 final size:50
Alignment explanation
Indices: 47871--47969 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
47861 AAAACTCATA
47871 AAATTCAACCCTATATCTATAATTTATGAAACCCTAAATCACTTTGATAC
1 AAATTCAACCCTATATCTATAATTTATGAAACCCTAAATCACTTTGATAC
*
47921 AAATTCAACCCTATATCTATAATTTATGACACCCTAAATCACTTTGATA
1 AAATTCAACCCTATATCTATAATTTATGAAACCCTAAATCACTTTGATA
47970 TAACTTTGGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (50 bp):
AAATTCAACCCTATATCTATAATTTATGAAACCCTAAATCACTTTGATAC
Found at i:49996 original size:5 final size:5
Alignment explanation
Indices: 49986--50067 Score: 83
Period size: 5 Copynumber: 15.2 Consensus size: 5
49976 AACGGTCAAC
* *
49986 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
50035 GGTCG GGTCG GGTCAAA GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG G
50068 ACCGGTCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
5 53 0.82
7 12 0.18
ACGTcount: A:0.09, C:0.21, G:0.52, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:50007 original size:22 final size:22
Alignment explanation
Indices: 49979--50067 Score: 169
Period size: 22 Copynumber: 4.0 Consensus size: 22
49969 AACGGTCAAC
49979 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
50001 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
50023 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
50045 GGTCAAAGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
50067 G
1 G
50068 ACCGGTCAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.10, C:0.21, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:50080 original size:9 final size:9
Alignment explanation
Indices: 50068--50159 Score: 69
Period size: 10 Copynumber: 9.7 Consensus size: 9
50058 GTCGGGTCGG
50068 ACCGGTCAA
1 ACCGGTCAA
* *
50077 ACCGATTCAG
1 ACCG-GTCAA
50087 ACCGGTC-A
1 ACCGGTCAA
*
50095 ACCGGTTCGA
1 ACCGG-TCAA
*
50105 ACCGGTTGAA
1 ACCGG-TCAA
50115 ACCGGTCAA
1 ACCGGTCAA
50124 ACCGGTCAGA
1 ACCGGTCA-A
*
50134 ACCGGTTGAAA
1 ACCGG-T-CAA
*
50145 ACCGGTTAA
1 ACCGGTCAA
50154 ACCGGT
1 ACCGGT
50160 TTCCAGCAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
8 5 0.07
9 27 0.40
10 28 0.41
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:50160 original size:9 final size:10
Alignment explanation
Indices: 50094--50160 Score: 61
Period size: 9 Copynumber: 6.8 Consensus size: 10
50084 CAGACCGGTC
50094 AACCGGTTCG-
1 AACCGGTT-GA
50104 AACCGGTTGA
1 AACCGGTTGA
*
50114 AACCGG-TCA
1 AACCGGTTGA
*
50123 AACCGG-TCA
1 AACCGGTTGA
50132 GAACCGGTTGAA
1 -AACCGGTTG-A
50144 AACCGGTT-A
1 AACCGGTTGA
50153 AACCGGTT
1 AACCGGTT
50161 TCCAGCAGCC
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
9 21 0.41
10 20 0.39
11 9 0.18
12 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (10 bp):
AACCGGTTGA
Found at i:57176 original size:5 final size:5
Alignment explanation
Indices: 57166--57247 Score: 83
Period size: 5 Copynumber: 15.2 Consensus size: 5
57156 AACGGTCAAC
* *
57166 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
57215 GGTCG GGTCG GGTCAAA GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG G
57248 ACCGGTCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
5 53 0.82
7 12 0.18
ACGTcount: A:0.09, C:0.21, G:0.52, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:57187 original size:22 final size:22
Alignment explanation
Indices: 57159--57247 Score: 169
Period size: 22 Copynumber: 4.0 Consensus size: 22
57149 AACGGTCAAC
57159 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
57181 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
57203 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
57225 GGTCAAAGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
57247 G
1 G
57248 ACCGGTCAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.10, C:0.21, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:57260 original size:9 final size:9
Alignment explanation
Indices: 57248--57340 Score: 78
Period size: 9 Copynumber: 9.7 Consensus size: 9
57238 GTCGGGTCGG
57248 ACCGGTCAA
1 ACCGGTCAA
* *
57257 ACCGATTCAG
1 ACCG-GTCAA
57267 ACCGGTCAA
1 ACCGGTCAA
*
57276 ACCGGTTCGA
1 ACCGG-TCAA
*
57286 ACCGGTTGAA
1 ACCGG-TCAA
57296 ACCGGTCAA
1 ACCGGTCAA
57305 ACCGGTCAGA
1 ACCGGTCA-A
*
57315 ACCGGTTGAAA
1 ACCGG-T-CAA
*
57326 ACCGGTTAA
1 ACCGGTCAA
57335 ACCGGT
1 ACCGGT
57341 TTCCAGCAGC
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
9 31 0.45
10 30 0.43
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:57299 original size:29 final size:31
Alignment explanation
Indices: 57267--57341 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
57257 ACCGATTCAG
57267 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
57296 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
57326 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
57342 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:57319 original size:19 final size:19
Alignment explanation
Indices: 57248--57340 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 19
57238 GTCGGGTCGG
*
57248 ACCGGTCAAACCGATTCAG-
1 ACCGGTCAAACCG-GTCAGA
57267 ACCGGTCAAACCGGTTC-GA
1 ACCGGTCAAACCGG-TCAGA
*
57286 ACCGGTTGAAACCGGTCA-A
1 ACCGG-TCAAACCGGTCAGA
* *
57305 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGG-TCAGA
*
57326 ACCGGTTAAACCGGT
1 ACCGGTCAAACCGGT
57341 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.05
19 35 0.56
20 16 0.26
21 8 0.13
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTCAGA
Found at i:61335 original size:71 final size:71
Alignment explanation
Indices: 61201--61335 Score: 166
Period size: 71 Copynumber: 1.9 Consensus size: 71
61191 TTCGTGTTTA
* * * * * *
61201 TTTATTTATTTTTAAAGGTGTTCGTGTTTGGTTCGTTTTTGTTTAAATTTTCAATATCGTGTTCA
1 TTTATTTATTTTTAAAGGTGTTCGTGTTTCGTTCATTTTTATTTAAATGTTCAATAACATGTTCA
61266 TGTTCG
66 TGTTCG
* *
61272 TTTATTTATTTTTAAAGGTGTTCGTG-TTCGTTTATTTATTCATTT-AATGTTCACTAACATGTT
1 TTTATTTATTTTTAAAGGTGTTCGTGTTTCGTTCATTT-TT-ATTTAAATGTTCAATAACATGTT
61335 C
64 C
61336 GTTTATTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
70 8 0.15
71 43 0.80
72 3 0.06
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.56
Consensus pattern (71 bp):
TTTATTTATTTTTAAAGGTGTTCGTGTTTCGTTCATTTTTATTTAAATGTTCAATAACATGTTCA
TGTTCG
Found at i:64521 original size:29 final size:29
Alignment explanation
Indices: 64478--64560 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
64468 CTCACCTAAC
64478 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
64508 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
64537 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
64561 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:69285 original size:29 final size:29
Alignment explanation
Indices: 69242--69324 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
69232 CTCACCTAAC
69242 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
69272 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
69301 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
69325 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:77323 original size:82 final size:85
Alignment explanation
Indices: 77201--77382 Score: 232
Period size: 82 Copynumber: 2.2 Consensus size: 85
77191 AATACTCAGA
* * *
77201 GGGTCGGTATCGATA-CAGAGGCATTTTTAGAAAACATCGAAGTCAAATCCGGTATCAATACTCA
1 GGGTCAGTATCGATACCAGAGGCATTTTTACAAAACATCGAAGCCAAATCCGGTATCAATACTCA
77265 CGA-GAGTATCGATACCC-A-
66 -GATGAGTATCGATACCCAAG
* * * **
77283 GGGTAGAGTATCGATACCA-AGGTATTTTT-CAAAACATCGAAGCCAATTTTGGTATCAATACTC
1 GGGT-CAGTATCGATACCAGAGGCATTTTTACAAAACATCGAAGCCAAATCCGGTATCAATACTC
77346 AGATGAGTATCGATACCCAAG
65 AGATGAGTATCGATACCCAAG
77367 GGGTCAGTATCGATAC
1 GGGTCAGTATCGATAC
77383 TGTTGGCACA
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
81 2 0.02
82 48 0.56
83 30 0.35
84 6 0.07
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (85 bp):
GGGTCAGTATCGATACCAGAGGCATTTTTACAAAACATCGAAGCCAAATCCGGTATCAATACTCA
GATGAGTATCGATACCCAAG
Found at i:79351 original size:4 final size:4
Alignment explanation
Indices: 79325--79373 Score: 71
Period size: 4 Copynumber: 12.2 Consensus size: 4
79315 ACATCTAAGT
* * *
79325 TATA TACA TAAA TATA CATA TATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
79373 T
1 T
79374 TGCAATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (4 bp):
TATA
Found at i:79351 original size:6 final size:6
Alignment explanation
Indices: 79325--79373 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
79315 ACATCTAAGT
* * *
79325 TATATA CATAAA TATACA TATATA TATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
79373 T
1 T
79374 TGCAATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:79371 original size:10 final size:10
Alignment explanation
Indices: 79325--79373 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
79315 ACATCTAAGT
*
79325 TATATACATA
1 TATATATATA
* *
79335 AATATACATA
1 TATATATATA
79345 TATATATATA
1 TATATATATA
79355 TATATATATA
1 TATATATATA
79365 TATATATAT
1 TATATATAT
79374 TGCAATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (10 bp):
TATATATATA
Found at i:82588 original size:26 final size:26
Alignment explanation
Indices: 82557--82606 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
82547 GTTCAAACTC
82557 GAATTTAATATCGTTTTCAAATTCTT
1 GAATTTAATATCGTTTTCAAATTCTT
**
82583 GAATTTAATATTTTTTTCAAATTC
1 GAATTTAATATCGTTTTCAAATTC
82607 AGTTCCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (26 bp):
GAATTTAATATCGTTTTCAAATTCTT
Found at i:84756 original size:49 final size:49
Alignment explanation
Indices: 84683--84778 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
84673 AGCATGCTAT
*
84683 ATTATAATCACTCTATATTATTTAAAAACGAAGTTATTAATTGGTTTAC
1 ATTATAATCACCCTATATTATTTAAAAACGAAGTTATTAATTGGTTTAC
*
84732 ATTATAATCACCCTATATTGTTTAAAAACGAAGTTATTAATTGGTTT
1 ATTATAATCACCCTATATTATTTAAAAACGAAGTTATTAATTGGTTT
84779 TATCTAATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (49 bp):
ATTATAATCACCCTATATTATTTAAAAACGAAGTTATTAATTGGTTTAC
Found at i:85210 original size:19 final size:19
Alignment explanation
Indices: 85186--85240 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
85176 AATGACCAAC
85186 TAAATCGCAATGCGATCGA
1 TAAATCGCAATGCGATCGA
85205 TAAATCGCAATGCGATCGA
1 TAAATCGCAATGCGATCGA
* *
85224 TAATTCGCAACGCGATC
1 TAAATCGCAATGCGATC
85241 TCCGGTATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (19 bp):
TAAATCGCAATGCGATCGA
Found at i:85294 original size:21 final size:21
Alignment explanation
Indices: 85268--85320 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
85258 GTTTCCAGAT
85268 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
85289 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
85310 TCGCAACGCGA
1 TCGCAACGCGA
85321 TTTACATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACTTGGACTA
Found at i:85354 original size:21 final size:21
Alignment explanation
Indices: 85329--85573 Score: 159
Period size: 21 Copynumber: 12.0 Consensus size: 21
85319 GATTTACATA
*
85329 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
85350 TTCGCGTTGCGATAATCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
85371 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
85392 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
85411 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
** *
85432 TT--CGTTATGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * * *
85451 TTTGCGTTGTGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
85474 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
85493 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
85514 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
85533 TTCGCGTTGTGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
85556 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
85574 AATCGCAACA
Statistics
Matches: 169, Mismatches: 43, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
19 58 0.34
21 95 0.56
23 16 0.09
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:85409 original size:40 final size:40
Alignment explanation
Indices: 85354--85570 Score: 344
Period size: 40 Copynumber: 5.3 Consensus size: 40
85344 TCCAAGTTCG
*
85354 CGTTGCGATAATCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
85394 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
** * *
85434 CGTTATGATAGTCGAAGTTTGCGTTGTGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
85476 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
*
85516 CGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
85558 CGTTGCGATAGTC
1 CGTTGCGATAGTC
85571 CAAAATCGCA
Statistics
Matches: 163, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
40 101 0.62
41 6 0.04
42 56 0.34
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:85471 original size:82 final size:82
Alignment explanation
Indices: 85354--85570 Score: 366
Period size: 82 Copynumber: 2.7 Consensus size: 82
85344 TCCAAGTTCG
* * *
85354 CGTTGCGATAATCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTACGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
85417 TTGCGATTTTCCAAATT
66 TTGCGATTTTCCAAATT
* *
85434 CGTTATGATAGTCGAAGTTTGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTACGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
85499 TTGCGATTTTCCAAATT
66 TTGCGATTTTCCAAATT
*
85516 CGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTC
1 CGTTACGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTC
85571 CAAAATCGCA
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
80 24 0.19
81 2 0.02
82 101 0.80
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (82 bp):
CGTTACGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
TTGCGATTTTCCAAATT
Found at i:86169 original size:6 final size:6
Alignment explanation
Indices: 86160--86190 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
86150 CGCCGCCGTC
*
86160 TCGTGG TCGTGG TCGTGG TCGTTG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
86191 AATACGTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.16, G:0.45, T:0.39
Consensus pattern (6 bp):
TCGTGG
Found at i:86350 original size:2 final size:2
Alignment explanation
Indices: 86343--86375 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
86333 CTTCTTCTTT
86343 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
86376 GAAAATGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:86839 original size:3 final size:3
Alignment explanation
Indices: 86831--86890 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
86821 GCTTGGCCTG
86831 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
86879 TAA TAA TAA TAA
1 TAA TAA TAA TAA
86891 ATCCGAACAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:88526 original size:138 final size:138
Alignment explanation
Indices: 88278--88546 Score: 375
Period size: 138 Copynumber: 1.9 Consensus size: 138
88268 CAAGCTCTGT
** *
88278 AAGAGAAGCCAAATGGTTGAGGCAAGGTAGTTCAACCAAACTTATACAGTAATTGCACTTAAGTG
1 AAGAGAAGCCAAATGGTTGAGGCAAGGTAGTTCAACCAAACTTATACACCAATTGCACTAAAGTG
* * *
88343 ATTTAAGGTTGATGGCTCCTGATAGATTAGGGATCTCCACTAGACTCTTGCAATAAGAAAGGTCA
66 ATTTAAGATTGATGGCTCCTGATAGATTAGGGATCTCCACAAGACTCTTGCAACAAGAAAGGTCA
88408 AGGCTTTC
131 AGGCTTTC
* * *
88416 AAGAGATA-CCAACTGGTTGAGGGAAGGTAGTTCAACCAAACTT-TCACACCCATTGCAGC-AAA
1 AAGAGA-AGCCAAATGGTTGAGGCAAGGTAGTTCAACCAAACTTAT-ACACCAATTGCA-CTAAA
* *
88478 G-GCTTTGAAGATTGATGGCTCCTGATAGATTAGGGATCTCCACAAGACTCTTGCAACCAGAAAG
63 GTGATTT-AAGATTGATGGCTCCTGATAGATTAGGGATCTCCACAAGACTCTTGCAACAAGAAAG
88542 GTCAA
127 GTCAA
88547 TTGACCTTAA
Statistics
Matches: 116, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
137 5 0.04
138 109 0.94
139 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (138 bp):
AAGAGAAGCCAAATGGTTGAGGCAAGGTAGTTCAACCAAACTTATACACCAATTGCACTAAAGTG
ATTTAAGATTGATGGCTCCTGATAGATTAGGGATCTCCACAAGACTCTTGCAACAAGAAAGGTCA
AGGCTTTC
Found at i:89137 original size:30 final size:30
Alignment explanation
Indices: 89103--89286 Score: 257
Period size: 30 Copynumber: 6.1 Consensus size: 30
89093 TGTTATACCC
89103 TAAAACATTGGTCATTATATGTATAATAAG
1 TAAAACATTGGTCATTATATGTATAATAAG
89133 TAAAACATTGGTCATTATATGTATAATAAG
1 TAAAACATTGGTCATTATATGTATAATAAG
* ** **
89163 TAAAAC-TTGAGTAGATTCCATGT-T-ATACCC
1 TAAAACATTG-GT-CATTATATGTATAATA-AG
89193 TAAAACATTGGTCATTATATGTATAATAAG
1 TAAAACATTGGTCATTATATGTATAATAAG
89223 TAAAACATTGGTCATTATATGTATAATAAG
1 TAAAACATTGGTCATTATATGTATAATAAG
* *
89253 TAAAACATTGATCATTATATGTATAGTAAG
1 TAAAACATTGGTCATTATATGTATAATAAG
89283 TAAA
1 TAAA
89287 TAAATATTTT
Statistics
Matches: 136, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
29 13 0.10
30 110 0.81
31 13 0.10
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (30 bp):
TAAAACATTGGTCATTATATGTATAATAAG
Found at i:89224 original size:90 final size:90
Alignment explanation
Indices: 89071--89263 Score: 377
Period size: 90 Copynumber: 2.1 Consensus size: 90
89061 AGTTTTAGAC
89071 AGTAAAACTTGAGTAGATTCCATGTTATACCCTAAAACATTGGTCATTATATGTATAATAAGTAA
1 AGTAAAACTTGAGTAGATTCCATGTTATACCCTAAAACATTGGTCATTATATGTATAATAAGTAA
89136 AACATTGGTCATTATATGTATAATA
66 AACATTGGTCATTATATGTATAATA
89161 AGTAAAACTTGAGTAGATTCCATGTTATACCCTAAAACATTGGTCATTATATGTATAATAAGTAA
1 AGTAAAACTTGAGTAGATTCCATGTTATACCCTAAAACATTGGTCATTATATGTATAATAAGTAA
89226 AACATTGGTCATTATATGTATAATA
66 AACATTGGTCATTATATGTATAATA
89251 AGTAAAACATTGA
1 AGTAAAAC-TTGA
89264 TCATTATATG
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 98 0.96
91 4 0.04
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (90 bp):
AGTAAAACTTGAGTAGATTCCATGTTATACCCTAAAACATTGGTCATTATATGTATAATAAGTAA
AACATTGGTCATTATATGTATAATA
Found at i:92573 original size:131 final size:128
Alignment explanation
Indices: 92320--92580 Score: 362
Period size: 130 Copynumber: 2.0 Consensus size: 128
92310 GACCCGTTGA
* * *
92320 CCGTTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGTCATTTTTATGTTTTTCGTCGTCCTGA
1 CCGTTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGCCATTTTTATGTTTATCGACGTCCTGA
** * * * *
92385 GTCCGATTCTGAAGTATGTTTTATGAAATTCGAACCTGAAAGCCTCGAAATTGTCAGTTAAAC
66 GTCCGATTCTGAAGTACCTTTTATCAAATTCGAACCTGAAAGCCTCCAAATTATCAGTAAAAC
**
92448 CCGTTGACTTTGACCAAAAAGTCAATTTTTTCGAAAAAGCCATATTTTATGTTTATCGACGTCCT
1 CCGTTGACTTTGACCAAAAAGTCAAAATTTTC-AAAAAGCCAT-TTTTATGTTTATCGACGTCCT
* *
92513 GAGTCCGATTCTGAAGT-CCTTTTATTCCCAATTCGAACTTGAAAGCCTCCAAATTATCAGTAAA
64 GAGTCCGATTCTGAAGTACCTTTTA-T-CAAATTCGAACCTGAAAGCCTCCAAATTATCAGTAAA
92577 AC
127 AC
92579 CC
1 CC
92581 AAACATGCAT
Statistics
Matches: 116, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
128 30 0.26
129 14 0.12
130 37 0.32
131 35 0.30
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (128 bp):
CCGTTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGCCATTTTTATGTTTATCGACGTCCTGA
GTCCGATTCTGAAGTACCTTTTATCAAATTCGAACCTGAAAGCCTCCAAATTATCAGTAAAAC
Found at i:99636 original size:32 final size:32
Alignment explanation
Indices: 99564--99683 Score: 113
Period size: 32 Copynumber: 3.8 Consensus size: 32
99554 TAGTCACTAA
* *
99564 CTTACTAACATTCTAACCTTTATTT-TATTGTT
1 CTTACTAACATACTAACTTTTATTTAT-TTGTT
* *
99596 C-GAGCTAACATACTAACTTTTATTTATTTGAT
1 CTTA-CTAACATACTAACTTTTATTTATTTGTT
* *
99628 CTTACTAACATATTAA-TTTTTTTTA-TTGTT
1 CTTACTAACATACTAACTTTTATTTATTTGTT
* *
99658 ATTACTAACTTACTAACATTTTATTT
1 CTTACTAACATACTAAC-TTTTATTT
99684 TATTGCACAA
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
30 17 0.24
31 9 0.13
32 43 0.61
33 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.52
Consensus pattern (32 bp):
CTTACTAACATACTAACTTTTATTTATTTGTT
Found at i:100416 original size:26 final size:26
Alignment explanation
Indices: 100382--100433 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
100372 TTTTTACATT
*
100382 TTTTATTTTATCTCGTTCTATTTTTA
1 TTTTATTTTATCTCATTCTATTTTTA
* * *
100408 TTTTGTTTTATTTCATTTTATTTTTA
1 TTTTATTTTATCTCATTCTATTTTTA
100434 CCTTTGGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTTATTTTATCTCATTCTATTTTTA
Found at i:103290 original size:24 final size:24
Alignment explanation
Indices: 103263--103371 Score: 128
Period size: 24 Copynumber: 4.5 Consensus size: 24
103253 TTATAATATC
*
103263 TGACCTGGATTCTGATCGGATACT
1 TGACCTGGATTTTGATCGGATACT
* *
103287 TGACCTAGATTTTGATCGAATACT
1 TGACCTGGATTTTGATCGGATACT
* * *
103311 TGACCTAGATTTTTTTATCTGATACT
1 TGACCTGGA--TTTTGATCGGATACT
*
103337 TGACCTGGATTTTGATCTGATACT
1 TGACCTGGATTTTGATCGGATACT
*
103361 TGATCTGGATT
1 TGACCTGGATT
103372 ATGTTTTGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
24 54 0.73
26 20 0.27
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TGACCTGGATTTTGATCGGATACT
Found at i:108042 original size:24 final size:24
Alignment explanation
Indices: 107934--108034 Score: 102
Period size: 24 Copynumber: 4.3 Consensus size: 24
107924 TTCTATTATA
* * *
107934 ATACCTGACTTAGATTCTGATCGG
1 ATACTTGACCTAGATTCTGATCTG
107958 ATACTTGACCTAGATTCTGATC-G
1 ATACTTGACCTAGATTCTGATCTG
* * *
107981 AATACTTGAGCTCGATT-T--TTTG
1 -ATACTTGACCTAGATTCTGATCTG
*
108003 ATACTTGACCTAGATTTTGATCTG
1 ATACTTGACCTAGATTCTGATCTG
108027 ATACTTGA
1 ATACTTGA
108035 TCTGGATTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
21 15 0.23
22 2 0.03
23 2 0.03
24 45 0.70
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (24 bp):
ATACTTGACCTAGATTCTGATCTG
Done.