Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001593.1 Hibiscus syriacus cultivar Beakdansim tig00003174_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: 58539
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:975 original size:74 final size:76
Alignment explanation
Indices: 839--989 Score: 245
Period size: 74 Copynumber: 2.0 Consensus size: 76
829 ATAAATGGTA
*
839 AAATATGAGAAAATGATTTGGAATAGTGTTTTAGACTAATGGGTAACACAGATGAATTAAGAGGG
1 AAATATGAGAAAATGATTTGGAATAATGTTTTA-ACTAATGGGTAACACAGATGAATTAAGAGGG
904 CATTTTGGTCCT
65 CATTTTGGTCCT
*
916 AAATATGAGAAAATGATTTGG-ATAATGTTTT-ACTAATGTGTAACAACAGAT-AATTAAGAGGG
1 AAATATGAGAAAATGATTTGGAATAATGTTTTAACTAATGGGTAAC-ACAGATGAATTAAGAGGG
978 CATTTTGGTCCT
65 CATTTTGGTCCT
990 TTAAGGGGGA
Statistics
Matches: 71, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
74 35 0.49
75 6 0.08
76 9 0.13
77 21 0.30
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (76 bp):
AAATATGAGAAAATGATTTGGAATAATGTTTTAACTAATGGGTAACACAGATGAATTAAGAGGGC
ATTTTGGTCCT
Found at i:1653 original size:20 final size:18
Alignment explanation
Indices: 1610--1658 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
1600 TGATGCAATT
*
1610 GGTATCGATACTAAGAGG
1 GGTATCGATACTAAGAGA
*
1628 GGTATCGATACTATGGAGAA
1 GGTATCGATACTA-AGAG-A
1648 GGTATCGATAC
1 GGTATCGATAC
1659 CATTGATTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 13 0.48
19 3 0.11
20 11 0.41
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (18 bp):
GGTATCGATACTAAGAGA
Found at i:10864 original size:12 final size:12
Alignment explanation
Indices: 10847--10871 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10837 TGACAATGTT
10847 TATATGTTATGA
1 TATATGTTATGA
10859 TATATGTTATGA
1 TATATGTTATGA
10871 T
1 T
10872 CCATGTGAAC
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TATATGTTATGA
Found at i:12251 original size:43 final size:43
Alignment explanation
Indices: 12166--12251 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
12156 GCAAAATGAA
* * *
12166 GACGCTGTTTTGAATCCTTCTGTGAAGAAACAGGCACTAGATT
1 GACGCTGTATTGAATCCTTCTGTGAAGAAACAAGCACAAGATT
*
12209 GACGCTG-ATTGAACTCCTTCTGTGAAGAATCAAGCGA-AAGATT
1 GACGCTGTATTGAA-TCCTTCTGTGAAGAAACAAGC-ACAAGATT
12252 TTCATTGATC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 5 0.14
43 31 0.84
44 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (43 bp):
GACGCTGTATTGAATCCTTCTGTGAAGAAACAAGCACAAGATT
Found at i:12324 original size:20 final size:20
Alignment explanation
Indices: 12294--12358 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
12284 AGTGAAAGGT
*
12294 TGAACAAGTTCTTCTCATTA
1 TGAACTAGTTCTTCTCATTA
*
12314 TGAACTTGTTCTTCCTCA-T-
1 TGAACTAGTTCTT-CTCATTA
* * *
12333 CGGACGAGTTCTTCTCATTA
1 TGAACTAGTTCTTCTCATTA
12353 TGAACT
1 TGAACT
12359 CTCCATTGAA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 4 0.12
19 10 0.30
20 15 0.45
21 4 0.12
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (20 bp):
TGAACTAGTTCTTCTCATTA
Found at i:12563 original size:124 final size:124
Alignment explanation
Indices: 12406--13153 Score: 993
Period size: 124 Copynumber: 6.1 Consensus size: 124
12396 GAATCAAATA
* * * *
12406 AAATGTTTATGCTAATCTATCTCCTTCTACGATAGAGTCGAGCAAAAAGTTGAACAAGTTCTTCT
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCT
* * * * * *
12471 CATTATGAACTTTTTCTTCATCTTCAGATGAGTTCTTCTCATTAGGAACTCTCTATTGG
66 CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * * *
12530 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTTGAGTAAACGGTTGAACAAATTCTTCT
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCT
* * *
12595 CATTATGAACTTTTTCTCCCTCATCGGATGAGTTATTCTCATTATGAACTCTCCATTGG
66 CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * ** ** *
12654 AAATTTTAATGCAAATCTATCTCCTTCTATGATAGAGTCGAACAAAAGGTTGAACAAGTTCTTCT
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCT
* * ** * *
12719 CATTATGTACTTATTCTTTCTCTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGG
66 CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * * *
12778 AAATATTGATGCTGATCTATCTCCTTTTGCGATAGAGTTGAGCAAAAGGTTGAA-AATGTTATTC
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAA-GTTCTTC
* * *
12842 TCATTATAAACTTCTTCTCTCTCATCAGATGATTTCTTCTCATTATGAACTCT--ATTGG
65 TCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * ** *
12900 AAATATTGATACTGATCTATCTTTTTCTGCGATAGAGTCGAGAAAAAGGTTGAACAAGTTCTTCT
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCT
*
12965 CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTTTCCATTGG
66 CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * *
13024 AAGTGTTGATGTTGATCTATCTCCTT-TGTGATAGAGTCGAGCGAAAAGGTTGAACAAGTTCTTC
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGC-AAAAGGTTGAACAAGTTCTTC
* * * *
13088 TCATTATGAACTTCTTCTCCCTTATCGGACGAGTTCTTCTCATTATGAACTCTCCA-TGA
65 TCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
13147 AAATGTT
1 AAATGTT
13154 AATCCCTCGA
Statistics
Matches: 545, Mismatches: 74, Indels: 11
0.87 0.12 0.02
Matches are distributed among these distances:
122 108 0.20
123 26 0.05
124 411 0.75
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (124 bp):
AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCT
CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
Found at i:13124 original size:370 final size:371
Alignment explanation
Indices: 12414--13144 Score: 1058
Period size: 370 Copynumber: 2.0 Consensus size: 371
12404 TAAAATGTTT
* *
12414 ATGCTAATCTATCTCCTTCTACGATAGAGTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
1 ATGCTAATCTATCTCCTTCTACGATAGAGTCGAGCAAAAAGTTGAACAAGTTATTCTCATTATAA
* * * *
12479 ACTTTTTCTTCATCTTCAGATGAGTTCTTCTCATTAGGAACTCTCTATTGGAAATGTTGATGCTG
66 ACTTCTTCTTCATCATCAGATGAGTTCTTCTCATTAGGAAC-CTCTATTGGAAATATTGATACTG
* * * *
12544 ATCTATCTCCTTCTGCGATAGAGTTGAGTAAACGGTTGAACAAATTCTTCTCATTATGAACTTTT
130 ATCTATCTCCTTCTGCGATAGAGTCGAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
* *
12609 TCTCCCTCATCGGATGAGTTATTCTCATTATGAACTCTCCATTGGAAATTTTAATGCAAATCTAT
195 TCTCCCTCATCAGATGAGTTATTCTCATTATGAACTCTCCATTGGAAATGTTAATGCAAATCTAT
* **
12674 CTCCTTCTATGATAGAGTCGAACAAAAGGTTGAACAAGTTCTTCTCATTATGTACTTATTCTTTC
260 CTCCTTCTATGATAGAGTCGAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCC
*
12739 TCTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATATTG
325 TCTTCGGACGAGTTCTTCTCATTATGAACTCTCCATTGGAAATATTG
* * * * *
12786 ATGCTGATCTATCTCCTTTTGCGATAGAGTTGAGCAAAAGGTTGAA-AATGTTATTCTCATTATA
1 ATGCTAATCTATCTCCTTCTACGATAGAGTCGAGCAAAAAGTTGAACAA-GTTATTCTCATTATA
* *
12850 AACTTCTTCTCTC-TCATCAGATGATTTCTTCTCATTATGAA-CTCTATTGGAAATATTGATACT
65 AACTTCTTCT-TCATCATCAGATGAGTTCTTCTCATTAGGAACCTCTATTGGAAATATTGATACT
** *
12913 GATCTATCTTTTTCTGCGATAGAGTCGAGAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
129 GATCTATCTCCTTCTGCGATAGAGTCGAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * * * ***
12978 TTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTTTCCATTGGAAGTGTTGATGTTGATCTA
194 TTCTCCCTCATCAGATGAGTTATTCTCATTATGAACTCTCCATTGGAAATGTTAATGCAAATCTA
* * *
13043 TCTCCTT-TGTGATAGAGTCGAGCGAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
259 TCTCCTTCTATGATAGAGTCGAAC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTC
13107 CCT-TATCGGACGAGTTCTTCTCATTATGAACTCTCCAT
323 CCTCT-TCGGACGAGTTCTTCTCATTATGAACTCTCCAT
13145 GAAAATGTTA
Statistics
Matches: 319, Mismatches: 36, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
369 15 0.05
370 212 0.66
371 2 0.01
372 88 0.28
373 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (371 bp):
ATGCTAATCTATCTCCTTCTACGATAGAGTCGAGCAAAAAGTTGAACAAGTTATTCTCATTATAA
ACTTCTTCTTCATCATCAGATGAGTTCTTCTCATTAGGAACCTCTATTGGAAATATTGATACTGA
TCTATCTCCTTCTGCGATAGAGTCGAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
CTCCCTCATCAGATGAGTTATTCTCATTATGAACTCTCCATTGGAAATGTTAATGCAAATCTATC
TCCTTCTATGATAGAGTCGAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCT
CTTCGGACGAGTTCTTCTCATTATGAACTCTCCATTGGAAATATTG
Found at i:13229 original size:138 final size:139
Alignment explanation
Indices: 13069--13427 Score: 499
Period size: 139 Copynumber: 2.6 Consensus size: 139
13059 GTCGAGCGAA
* *
13069 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGACGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
*
13134 GAACTCTCCA-TGAAAATGTTAATCC-CTCGAATGAGGTGTCACTGATTCAACTCCATATACGAT
66 GAACTCTCCACTGAAAATGTTAA-CCTCTCGAATGAGGTGTCACTGATTCAACTCCATATAAGAT
13197 GAATCGAGCT
130 GAATCGAGCT
* * * *
13207 AAGGTTGAATAAGTTATTCTCATTATGAACTTCTTTTTCCTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* * * * * *
13272 GAACTCTCTACTGGAAATGTTGACCTTTCGAGTGAGGTGTCGCTGATTCAACTCCATATAAGATG
66 GAACTCTCCACTGAAAATGTTAACCTCTCGAATGAGGTGTCACTGATTCAACTCCATATAAGATG
13337 AATCGAGCT
131 AATCGAGCT
* * * * *
13346 AAGATTGAACAAGTTCTTTTTATTATAAACCTT-TTCTCCCTCATCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAA-CTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTA
*
13410 TTAACTCTCCACTAGAAA
65 TGAACTCTCCACT-GAAA
13428 TGATGATCCA
Statistics
Matches: 192, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
138 70 0.36
139 116 0.60
140 6 0.03
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (139 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGAAAATGTTAACCTCTCGAATGAGGTGTCACTGATTCAACTCCATATAAGATG
AATCGAGCT
Found at i:18078 original size:45 final size:45
Alignment explanation
Indices: 18024--18349 Score: 510
Period size: 45 Copynumber: 7.2 Consensus size: 45
18014 ATTATTCATT
*
18024 ATTTCCATTTATGGCATCCTTTCATGCCTTTAACGCACCGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
18070 ATTTCATTT-TGACATCCTTTCATGCCTTTAATGAACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * *
18114 ATTTCATTTATAGTATCATTTCATGCCTTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
18159 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
18204 ATTTCATTTATGGCATCCTTTCATACCTTTAATGAACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
18249 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
18294 ATTTCATTTATGGCATCATTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
18339 ATTTCATTTAT
1 ATTTCATTTAT
18350 ATAAAAAATA
Statistics
Matches: 255, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
44 40 0.16
45 211 0.83
46 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:18154 original size:21 final size:21
Alignment explanation
Indices: 18130--18195 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
18120 TTTATAGTAT
18130 CATTTCATGCCTTTAATGCAC
1 CATTTCATGCCTTTAATGCAC
* *
18151 CATTATGCATTTCATTT-ATGGCATC
1 CATT-T-CA-TGCCTTTAAT-GCA-C
18176 C-TTTCATGCCTTTAATGCAC
1 CATTTCATGCCTTTAATGCAC
18196 TGTTATGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
20 1 0.03
21 12 0.34
22 5 0.14
23 5 0.14
24 10 0.29
25 2 0.06
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.41
Consensus pattern (21 bp):
CATTTCATGCCTTTAATGCAC
Found at i:18812 original size:20 final size:20
Alignment explanation
Indices: 18783--18832 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
18773 GTAATCCATG
18783 GTATCAATACTTTCCTTTTA
1 GTATCAATACTTTCCTTTTA
*
18803 GTATCGATACTTTCCTTTTA
1 GTATCAATACTTTCCTTTTA
18823 GTATCAATAC
1 GTATCAATAC
18833 CCCATTAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.46
Consensus pattern (20 bp):
GTATCAATACTTTCCTTTTA
Found at i:25078 original size:45 final size:45
Alignment explanation
Indices: 25020--25212 Score: 323
Period size: 45 Copynumber: 4.3 Consensus size: 45
25010 GTTATTCATT
*
25020 ATTTCCATTTATGGCATCCTTTCACGCCTTTAATGCACCGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
25066 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
25111 ATTTCGTTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGA
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
25156 ATTTCATTTATGGCATCCTTTCATGCCTTTAAAGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
25201 ATTTCATTTATG
1 ATTTCATTTATG
25213 TAATAAAAAC
Statistics
Matches: 137, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
45 133 0.97
46 4 0.03
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:29468 original size:18 final size:18
Alignment explanation
Indices: 29445--29479 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29435 GGAATAAAAC
29445 ATTTAGTTATTTTAAGAT
1 ATTTAGTTATTTTAAGAT
29463 ATTTAGTTATTTTAAGA
1 ATTTAGTTATTTTAAGA
29480 CAGTCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
ATTTAGTTATTTTAAGAT
Found at i:30886 original size:18 final size:19
Alignment explanation
Indices: 30863--30905 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
30853 TAGTAATCCT
*
30863 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGATAATCTTAC
30881 ATTCCCACTGATAATCTTAC
1 ATT-CCACTGATAATCTTAC
30901 ATTCC
1 ATTCC
30906 TTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:34425 original size:28 final size:26
Alignment explanation
Indices: 34385--34439 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 26
34375 ATTTAGTCAC
*
34385 TTTTTTATTCGAAATTATTCACTGTTT
1 TTTTTTATTCGAAATTAGTCACT-TTT
34412 TTTTATTATTCGAAATTAGTCACTTTT
1 TTTT-TTATTCGAAATTAGTCACTTTT
34439 T
1 T
34440 GGTTTATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (26 bp):
TTTTTTATTCGAAATTAGTCACTTTT
Found at i:34438 original size:25 final size:24
Alignment explanation
Indices: 34377--34439 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 24
34367 CTTTTTTAAT
34377 TTAGTCAC--TTTTTTATTCGAAA
1 TTAGTCACTTTTTTTTATTCGAAA
*
34399 TTATTCACTGTTTTTTTATTATTCGAAA
1 TTAGTCAC---TTTTTT-TTATTCGAAA
34427 TTAGTCACTTTTT
1 TTAGTCACTTTTT
34440 GGTTTATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
22 7 0.21
25 5 0.15
27 4 0.12
28 17 0.52
ACGTcount: A:0.24, C:0.13, G:0.08, T:0.56
Consensus pattern (24 bp):
TTAGTCACTTTTTTTTATTCGAAA
Found at i:42092 original size:38 final size:38
Alignment explanation
Indices: 41914--42333 Score: 292
Period size: 38 Copynumber: 10.7 Consensus size: 38
41904 GAAGCTTCAA
* *
41914 CTTGACTCCCTCGTGAAGAGAAGTTAATCTTTCAATGTTATT
1 CTTGACTCCCTCGTAAAGAGAAGTCAATC-TT---TGTTATT
* ** *
41956 CTTGACTTCCTCGGGAAGAGAAGTCAATCTTTATTATT
1 CTTGACTCCCTCGTAAAGAGAAGTCAATCTTTGTTATT
** * * * *
41994 CTTGACTTTCTCAT-GAGAGGAGTCAATAATTCAATGTTATT
1 CTTGACTCCCTCGTAAAGAGAAGTCAAT-CTT---TGTTATT
* * * *
42035 ATTGAC-CTCCTAGTGAAGAGAAGTCAATCTTTTTTATT
1 CTTGACTC-CCTCGTAAAGAGAAGTCAATCTTTGTTATT
* * * *
42073 CTTGA-TCCCCCCATAAAGAGGAGTTAATATTTCTTTGTTATT
1 CTTGACT-CCCTCGTAAAGAGAAG-TCA-A--TCTTTGTTATT
* *
42115 CTTGACTTCCTCATAAAGAGAAGGT-AATCTTTGTTATT
1 CTTGACTCCCTCGTAAAGAGAA-GTCAATCTTTGTTATT
* * *
42153 CCTGACTCCCTCGTGAAGAGCAGTCAATCTTTGTTATT
1 CTTGACTCCCTCGTAAAGAGAAGTCAATCTTTGTTATT
* * *
42191 CTTGATTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTA-T
1 CTTGACTCCCTCGTAAAGAGAAGTCAATC-TT---TGTTATT
* *
42232 CATTGACTTCCTCGTAAAGAGAAGTCAATCTATGTTATT
1 C-TTGACTCCCTCGTAAAGAGAAGTCAATCTTTGTTATT
* * * *
42271 CTTTACTTCCTCGTATAGAGAAGTCAATCTTTTTTATT
1 CTTGACTCCCTCGTAAAGAGAAGTCAATCTTTGTTATT
* * *
42309 CTTGACTTCCTCGTGAAGAGGAGTC
1 CTTGACTCCCTCGTAAAGAGAAGTC
42334 TGTCGACAGT
Statistics
Matches: 305, Mismatches: 52, Indels: 46
0.76 0.13 0.11
Matches are distributed among these distances:
37 13 0.04
38 165 0.54
39 7 0.02
40 2 0.01
41 22 0.07
42 94 0.31
43 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (38 bp):
CTTGACTCCCTCGTAAAGAGAAGTCAATCTTTGTTATT
Found at i:42137 original size:80 final size:79
Alignment explanation
Indices: 41914--42320 Score: 325
Period size: 80 Copynumber: 5.2 Consensus size: 79
41904 GAAGCTTCAA
* * * * *
41914 CTTGACTCCCTCGTGAAGAGAAGTTAATCTTTCAATGTTATTCTTGACTTCCTCGGGAAGAGAAG
1 CTTGACTCCCTCATAAAGAGAAGTTAAT-ATTCTATGTTATTCTTGACTTCCTCGTGAAGAGAAG
*
41979 TCAATCTTTATTATT
65 TCAATCTTTTTTATT
** * * * * * * *
41994 CTTGACTTTCTCAT-GAGAGGAGTCAATAATTCAATGTTATTATTGACCTCCTAGTGAAGAGAAG
1 CTTGACTCCCTCATAAAGAGAAGTTAAT-ATTCTATGTTATTCTTGACTTCCTCGTGAAGAGAAG
42058 TCAATCTTTTTTATT
65 TCAATCTTTTTTATT
* * * * *
42073 CTTGA-TCCCCCCATAAAGAGGAGTTAATATTTCTTTGTTATTCTTGACTTCCTCATAAAGAGAA
1 CTTGACT-CCCTCATAAAGAGAAGTTAATA-TTCTATGTTATTCTTGACTTCCTCGTGAAGAGAA
*
42137 GGT-AATCTTTGTTATT
64 -GTCAATCTTTTTTATT
* * * * * * *
42153 CCTGACTCCCTCGTGAAGAGCAG-TCA-A-TCTTTGTTATTCTTGA-TTCCCTCGTGAAGAGGAG
1 CTTGACTCCCTCATAAAGAGAAGTTAATATTCTATGTTATTCTTGACTT-CCTCGTGAAGAGAAG
42214 TCAATCTTTCAATGTTA-T
65 TCAATCTTT---T-TTATT
* * * *
42232 CATTGACTTCCTCGTAAAGAGAAG-TCA-A-TCTATGTTATTCTTTACTTCCTCGT-ATAGAGAA
1 C-TTGACTCCCTCATAAAGAGAAGTTAATATTCTATGTTATTCTTGACTTCCTCGTGA-AGAGAA
42293 GTCAATCTTTTTTATT
64 GTCAATCTTTTTTATT
*
42309 CTTGACTTCCTC
1 CTTGACTCCCTC
42321 GTGAAGAGGA
Statistics
Matches: 269, Mismatches: 43, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
75 4 0.01
76 48 0.18
77 3 0.01
78 2 0.01
79 70 0.26
80 137 0.51
81 5 0.02
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (79 bp):
CTTGACTCCCTCATAAAGAGAAGTTAATATTCTATGTTATTCTTGACTTCCTCGTGAAGAGAAGT
CAATCTTTTTTATT
Found at i:42321 original size:118 final size:117
Alignment explanation
Indices: 41916--42333 Score: 388
Period size: 118 Copynumber: 3.5 Consensus size: 117
41906 AGCTTCAACT
* * *
41916 TGACTCCCTCGTGAAGAGAAGTTAATCTTTCAATGTTATTCTTGACTTCCTCGGGAAGAGAAGTC
1 TGACTCCCTCGTGAAGAGAAGTCAATCTTT---T-TTATTCTTGA-TTCCTCGTGAAGAGGAGTC
* * * * **
41981 AATCTTT--A--TTATTCTTGACTTTCTCATGAGAGGAGTCAA--TAATTCAATGTTATTAT
61 AATATTTCAATGTTATTCTTGACTTCCTCAT-A-AAGAG--AAGGTAA-TCTATGTTATTCC
* * * * * *
42037 TGAC-CTCCTAGTGAAGAGAAGTCAATCTTTTTTATTCTTGATCCCCCCATAAAGAGGAGTTAAT
1 TGACTC-CCTCGTGAAGAGAAGTCAATCTTTTTTATTCTTGAT-TCCTCGTGAAGAGGAGTCAAT
** *
42101 ATTTCTTTGTTATTCTTGACTTCCTCATAAAGAGAAGGTAATCTTTGTTATTCC
64 ATTTCAATGTTATTCTTGACTTCCTCATAAAGAGAAGGTAATCTATGTTATTCC
* * *
42155 TGACTCCCTCGTGAAGAGCAGTCAATCTTTGTTATTCTTGATTCCCTCGTGAAGAGGAGTCAATC
1 TGACTCCCTCGTGAAGAGAAGTCAATCTTTTTTATTCTTGATT-CCTCGTGAAGAGGAGTCAATA
* *
42220 TTTCAATGTTA-TCATTGACTTCCTCGTAAAGAGAA-GTCAATCTATGTTATTCT
65 TTTCAATGTTATTC-TTGACTTCCTCATAAAGAGAAGGT-AATCTATGTTATTCC
* *
42273 TTACTTCCTCGT-ATAGAGAAGTCAATCTTTTTTATTCTTGACTTCCTCGTGAAGAGGAGTC
1 TGACTCCCTCGTGA-AGAGAAGTCAATCTTTTTTATTCTTGA-TTCCTCGTGAAGAGGAGTC
42334 TGTCGACAGT
Statistics
Matches: 248, Mismatches: 35, Indels: 31
0.79 0.11 0.10
Matches are distributed among these distances:
116 1 0.00
117 34 0.14
118 157 0.63
119 10 0.04
120 2 0.01
121 44 0.18
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (117 bp):
TGACTCCCTCGTGAAGAGAAGTCAATCTTTTTTATTCTTGATTCCTCGTGAAGAGGAGTCAATAT
TTCAATGTTATTCTTGACTTCCTCATAAAGAGAAGGTAATCTATGTTATTCC
Found at i:43552 original size:2 final size:2
Alignment explanation
Indices: 43545--43590 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
43535 TCATTGCTGC
43545 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
43587 AT AT
1 AT AT
43591 TAGGATAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46742 original size:21 final size:21
Alignment explanation
Indices: 46716--46757 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
46706 CCAGAATGGG
*
46716 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
46737 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
46758 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:47002 original size:31 final size:31
Alignment explanation
Indices: 46975--47035 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
46965 AAATTTTGAA
*
46975 TAAATTCAATT-AAGTCTAAAAA-CATTTTTG
1 TAAATTCAATTCAAGTCCAAAAACCA-TTTTG
47005 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
47036 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.39
31 15 0.54
32 2 0.07
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:47009 original size:30 final size:32
Alignment explanation
Indices: 46975--47034 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
46965 AAATTTTGAA
*
46975 TAAATTCAATT-AAGTCTAAAAA-CATTTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTTG
47005 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
47035 GCCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 11 0.41
31 10 0.37
32 6 0.22
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.37
Consensus pattern (32 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTTG
Found at i:56012 original size:36 final size:36
Alignment explanation
Indices: 55952--56035 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 36
55942 CAAGTTAATA
* *
55952 AGCCTTCAC-AAATAGTAGTGAAGCAATGCAAA-TC
1 AGCCTTCACAAAAGAGTAGCGAAGCAATGCAAATTC
55986 GAGCCTTCACAAAAGAGTAGCGAAGCAATGCAAATTC
1 -AGCCTTCACAAAAGAGTAGCGAAGCAATGCAAATTC
56023 AGCCTTCACAAAA
1 AGCCTTCACAAAA
56036 AAAAGAGTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
35 9 0.20
36 34 0.76
37 2 0.04
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.18
Consensus pattern (36 bp):
AGCCTTCACAAAAGAGTAGCGAAGCAATGCAAATTC
Done.