Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005081.1 Hibiscus syriacus cultivar Beakdansim tig00011410_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: 71514
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Found at i:820 original size:176 final size:180
Alignment explanation
Indices: 433--950 Score: 737
Period size: 176 Copynumber: 2.9 Consensus size: 180
423 TAAATCCGTA
433 AAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCC-GGCTTTATGAAT
1 AAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGAAT
*
497 AG-TTATGTTCAAAT-T-ACACTGC-TGGACATCTTGGCAATTC-GTG-TTGCTCCACTACTTTT
66 AGATTATGTTCAAATATGACACTGCTTGGACA-CTTGGCAATTCGGTGTTTGCTCCACTGCTTTT
*
556 GTCAGGCCAAAGACTTTGTGATGAGATGAACCGTTCAGTGATTTGTCCCTCT
130 GTCAGGCCAAAGACTTTGTGATGAGAT-AACCCTTCAGTGATTTGTCCCTCT
* *
608 AAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCG-AATCCCTAGCTTTATGAA
1 -AAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGAA
*
672 TAGATTATGTTCAAACTATGACACTACTTGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTT
65 TAGATTATGTTCAAA-TATGACACTGCTTGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTT
737 TGTCAGGCCAAAGACTTTGTGATGACG-T-ACCCTTCAGTGA-TTGTCCCTCT
129 TGTCAGGCCAAAGACTTTGTGATGA-GATAACCCTTCAGTGATTTGTCCCTCT
* *
787 -AGCTGAGCTATTCCACTAAGGC-ATTGATTATAGAGGAAAATCGAAAGCCCTGGC-TTATG-AT
1 AAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGAAT
** * *
848 AGATTACATTCAAATCATGACATTGCTCT-AACACTTGGCAATTCGGTGTTTGCTCCACTGCTTT
66 AGATTATGTTCAAAT-ATGACACTGCT-TGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTT
*
912 TGTCAGGTCAAAGAC-TTGTGATGAGATGAACCCTTCAGT
129 TGTCAGGCCAAAGACTTTGTGATGAGAT-AACCCTTCAGT
951 TAACCTGATA
Statistics
Matches: 312, Mismatches: 15, Indels: 30
0.87 0.04 0.08
Matches are distributed among these distances:
173 1 0.00
174 11 0.04
175 76 0.24
176 93 0.30
177 41 0.13
178 1 0.00
179 11 0.04
180 28 0.09
181 9 0.03
182 40 0.13
183 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (180 bp):
AAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGAAT
AGATTATGTTCAAATATGACACTGCTTGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTTTG
TCAGGCCAAAGACTTTGTGATGAGATAACCCTTCAGTGATTTGTCCCTCT
Found at i:2170 original size:35 final size:34
Alignment explanation
Indices: 2058--2170 Score: 95
Period size: 35 Copynumber: 3.2 Consensus size: 34
2048 TAGATGATTA
*
2058 TCTCACTCAAATTTGTTTTTCTTAAAACATA-CTTTG
1 TCTCACTCAAA-TT-TTTTTCTTAAAACA-AGATTTG
* * * * *
2094 TCTCACTTGAAACTGTTTTCTCGAAAA-AAGATTTA
1 TCTCAC-TCAAATTTTTTTCT-TAAAACAAGATTTG
*
2129 TTTCACTCAAGATTTTTTTCTTAAAACAAGATTTG
1 TCTCACTCAA-ATTTTTTTCTTAAAACAAGATTTG
2164 TCTCACT
1 TCTCACT
2171 TAGACCGTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
34 8 0.14
35 36 0.61
36 11 0.19
37 4 0.07
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (34 bp):
TCTCACTCAAATTTTTTTCTTAAAACAAGATTTG
Found at i:2282 original size:39 final size:39
Alignment explanation
Indices: 2223--2380 Score: 104
Period size: 39 Copynumber: 3.8 Consensus size: 39
2213 GCTTTTTTTA
* **
2223 AGAAGATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAAATTTTATCTCCCTTGAGATAGTTTCCCTCGAAAC
* * *
2262 AGAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAAAC
1 AGAAAATTTTATCTCCCTTGAGATAGTTTCCCTCG-AAAC
* *
2302 ATTTCCTTTGAAATTAATTTTTTCTCTCC-TGAGATAGATTCCCTCGAAAC
1 A--------G-AA--AATTTTATCTC-CCTTGAGATAGTTTCCCTCGAAAC
*
2352 AGAAAATTTTGTCT-CCTTGAGATAGTTTC
1 AGAAAATTTTATCTCCCTTGAGATAGTTTC
2381 TCTTTAAACA
Statistics
Matches: 92, Mismatches: 13, Indels: 29
0.69 0.10 0.22
Matches are distributed among these distances:
37 2 0.02
38 11 0.12
39 38 0.41
40 5 0.05
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 5 0.05
51 23 0.25
52 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (39 bp):
AGAAAATTTTATCTCCCTTGAGATAGTTTCCCTCGAAAC
Found at i:2474 original size:105 final size:103
Alignment explanation
Indices: 2294--2608 Score: 417
Period size: 105 Copynumber: 3.1 Consensus size: 103
2284 ACAGTTTCTC
* * * * *
2294 TTGAAAACATTTCCTTTGAAATTAATTTTTTCTCTCCTGAGATAGATTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
* *
2359 TTTGTCTCCTTGAGATAGTTTCTCTTTAAACATAAACA
66 TTTGTCTCCTTGAGACAGTTTCTCTTCAAACATAAACA
* *
2397 TTGAAAACATTTCCCTTAAAATGATTTTTTTTTCTCTCTTGAGATAGTTTCCCTCAAAACAGAAA
1 TTGAAAACATTTCCCTTGAAATGA--TTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
*
2462 ATTTTGTCTCCTTGAGACAGTTTCTCTTGAAACATAAACA
64 ATTTTGTCTCCTTGAGACAGTTTCTCTTCAAACATAAACA
* * * *
2502 TTG-AAACATTTCCCTTGAAATGA-ATTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AA-
1 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
* *
2561 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCT-CCTTGAGACAGTTTCTCTTCAAACATAAACA
2600 TTGAAAACA
1 TTGAAAACA
2609 ATTTAACGAA
Statistics
Matches: 190, Mismatches: 18, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
97 7 0.04
98 33 0.17
99 5 0.03
100 1 0.01
101 28 0.15
103 21 0.11
104 19 0.10
105 76 0.40
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (103 bp):
TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCTTGAGACAGTTTCTCTTCAAACATAAACA
Found at i:2556 original size:35 final size:35
Alignment explanation
Indices: 2502--2583 Score: 112
Period size: 35 Copynumber: 2.4 Consensus size: 35
2492 AACATAAACA
* * *
2502 TTGAAACA-TTTCCCTTGAAATGAATTTATCTCGC
1 TTGAGACAGTTTCCCTTGAAACGAATTTATCTCCC
* *
2536 TTGAGATAGTTTCCCTTGAAACGAATTTGTCTCCC
1 TTGAGACAGTTTCCCTTGAAACGAATTTATCTCCC
2571 TTGAGACAGTTTC
1 TTGAGACAGTTTC
2584 TCTCCAAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 6 0.15
35 35 0.85
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (35 bp):
TTGAGACAGTTTCCCTTGAAACGAATTTATCTCCC
Found at i:2969 original size:105 final size:105
Alignment explanation
Indices: 2781--3404 Score: 851
Period size: 105 Copynumber: 6.0 Consensus size: 105
2771 ATATCGTGAC
* * * * *
2781 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA---C-G-TTGTCAACAAACAACATCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
*
2841 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2882 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTACTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
2947 ATTTCAAAGCCAATTTCAACTTCACAACGAATGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2987 ACTTCAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
3052 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3092 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC-ACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
3156 ATCTCA-AGCCAATTTCAACTTCAACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTC-ACAACGAAGGATATTGG
* * *
3196 ACTCCAGACAACGCAAGTTCAACTCCACGACGAA-GGACCACTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
3256 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
3295 ACTCGAGATAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * *
3360 GGTTCCAGAGCCAATTTCAACTTCACGACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3401 ACTC
1 ACTC
3405 GGAACAATGC
Statistics
Matches: 469, Mismatches: 39, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
99 48 0.10
100 31 0.07
101 38 0.08
102 4 0.01
103 34 0.07
104 76 0.16
105 192 0.41
106 46 0.10
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:4032 original size:37 final size:37
Alignment explanation
Indices: 3939--4042 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
3929 ATATTTTCTC
3939 CTACTAGGATTCAAACTCCT-AAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3975 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
4012 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
4043 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
36 18 0.32
37 39 0.68
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:4426 original size:17 final size:17
Alignment explanation
Indices: 4391--4428 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4381 TTATGATATT
*
4391 TTATTCATTTATTTTTA
1 TTATTCATTTATTTATA
4408 TTATTCATGTTA-TTATA
1 TTATTCAT-TTATTTATA
4425 TTAT
1 TTAT
4429 ATGTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (17 bp):
TTATTCATTTATTTATA
Found at i:4987 original size:39 final size:39
Alignment explanation
Indices: 4909--5012 Score: 106
Period size: 39 Copynumber: 2.6 Consensus size: 39
4899 TACTTTGATA
4909 TATATATATATATTTATATTT-TTTTTTTTCAAATATTAC-
1 TATATATAT-TATTTAT-TTTATTTTTTTTCAAATATTACT
** *
4948 TATATATAATTA-TTATTTTACTTTTTTTTCTTATCTTACT
1 TATATAT-ATTATTTATTTTA-TTTTTTTTCAAATATTACT
* *
4988 TATTTATTTTATTTATTTTATTTTT
1 TATATATATTATTTATTTTATTTTT
5013 CCCTTGTATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
37 3 0.05
38 4 0.07
39 32 0.58
40 16 0.29
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (39 bp):
TATATATATTATTTATTTTATTTTTTTTCAAATATTACT
Found at i:9296 original size:67 final size:67
Alignment explanation
Indices: 9187--9317 Score: 208
Period size: 67 Copynumber: 2.0 Consensus size: 67
9177 ACTTAAAGAT
* * * *
9187 TGATTTTTGGATGATATTTGCCCCACTATGACAATTTTATTTGGTGTTGGATGACGCTTGAATGA
1 TGATTTTTGGATAATATTTGCCACACCATGACAATTTGATTTGGTGTTGGATGACGCTTGAATGA
9252 TA
66 TA
**
9254 TGATTTTTGGATAATATTTGCCACACCATGATTATTTGATTTGGTGTTGGATGACGCTTGAATG
1 TGATTTTTGGATAATATTTGCCACACCATGACAATTTGATTTGGTGTTGGATGACGCTTGAATG
9318 GTACTTTGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.24, C:0.11, G:0.23, T:0.42
Consensus pattern (67 bp):
TGATTTTTGGATAATATTTGCCACACCATGACAATTTGATTTGGTGTTGGATGACGCTTGAATGA
TA
Found at i:9575 original size:21 final size:21
Alignment explanation
Indices: 9545--9594 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
9535 AACAAGGAAA
* *
9545 CTAATTCGATATGGTGAAGTT
1 CTAATCCGATATGGTGAACTT
9566 CTAATCCGATATGGTGAACTT
1 CTAATCCGATATGGTGAACTT
9587 CTAATCCG
1 CTAATCCG
9595 TCTTAGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (21 bp):
CTAATCCGATATGGTGAACTT
Found at i:26848 original size:41 final size:41
Alignment explanation
Indices: 26744--26848 Score: 115
Period size: 41 Copynumber: 2.6 Consensus size: 41
26734 TATCGCTTAG
* *
26744 TAAGTCATTCGGGCCATCTGTAAGCATTCCAAGCATGATGT
1 TAAGTCATTCGGGCCATCTATAAGCATTCCAAGCATGATGC
* * * *
26785 TAAGTCCTTCGGACCATTTATAAGTC-TTCCTAGCA-GAATGC
1 TAAGTCATTCGGGCCATCTATAAG-CATTCCAAGCATG-ATGC
*
26826 TAAGTCATCCGGGCCATCTATAA
1 TAAGTCATTCGGGCCATCTATAA
26849 AACCTCCGGG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
40 1 0.02
41 50 0.96
42 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (41 bp):
TAAGTCATTCGGGCCATCTATAAGCATTCCAAGCATGATGC
Found at i:28735 original size:65 final size:64
Alignment explanation
Indices: 28616--28743 Score: 161
Period size: 65 Copynumber: 2.0 Consensus size: 64
28606 TATTTTGAAT
* * * *
28616 GCATTTTGTGTACCGATGCACAGTCATGCATAGATGCACTCTTGAATTTATTGAAACATCGAAC
1 GCATTTTGTGTACCAATACACAGCCATGCATAGATGCACTCTAGAATTTATTGAAACATCGAAC
* *
28680 GCATTTTGTGTACCAATACACAGACCATGCATCGATGCACTCCTAG-CTCTT-TTGAAACATCGA
1 GCATTTTGTGTACCAATACACAG-CCATGCATAGATGCACT-CTAGAAT-TTATTGAAACATCGA
28743 A
63 A
28744 TGTAATTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
64 21 0.38
65 29 0.53
66 5 0.09
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
GCATTTTGTGTACCAATACACAGCCATGCATAGATGCACTCTAGAATTTATTGAAACATCGAAC
Found at i:28774 original size:19 final size:19
Alignment explanation
Indices: 28750--28803 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
28740 CGAATGTAAT
28750 TAGTGTACCGATGCACCCC
1 TAGTGTACCGATGCACCCC
28769 TAGTGTACCGATGCACCCC
1 TAGTGTACCGATGCACCCC
28788 TAGTGTACCGATGCAC
1 TAGTGTACCGATGCAC
28804 TAAGTCTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (19 bp):
TAGTGTACCGATGCACCCC
Found at i:42148 original size:25 final size:25
Alignment explanation
Indices: 42114--42188 Score: 150
Period size: 25 Copynumber: 3.0 Consensus size: 25
42104 TATAATGAAA
42114 ATATTGTTTGGATTGAGATGGATTC
1 ATATTGTTTGGATTGAGATGGATTC
42139 ATATTGTTTGGATTGAGATGGATTC
1 ATATTGTTTGGATTGAGATGGATTC
42164 ATATTGTTTGGATTGAGATGGATTC
1 ATATTGTTTGGATTGAGATGGATTC
42189 TCAAGGACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.24, C:0.04, G:0.28, T:0.44
Consensus pattern (25 bp):
ATATTGTTTGGATTGAGATGGATTC
Found at i:47018 original size:3 final size:3
Alignment explanation
Indices: 47010--47044 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
47000 CGCTCATCAA
47010 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
47045 CTTTGTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:48623 original size:7 final size:7
Alignment explanation
Indices: 48611--48636 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48601 TGAGTAATGC
48611 TGGTCGT
1 TGGTCGT
48618 TGGTCGT
1 TGGTCGT
48625 TGGTCGT
1 TGGTCGT
48632 TGGTC
1 TGGTC
48637 TCCCATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.42, T:0.42
Consensus pattern (7 bp):
TGGTCGT
Found at i:51647 original size:12 final size:13
Alignment explanation
Indices: 51606--51654 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
51596 AGCATTGTGA
51606 ATTGTGTCTCAAG
1 ATTGTGTCTCAAG
*
51619 -TTGTCTCTCAA-
1 ATTGTGTCTCAAG
51630 AGTTGTGTCT-AAG
1 A-TTGTGTCTCAAG
*
51643 ATTGTGCCTCAA
1 ATTGTGTCTCAA
51655 CTAACCTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (13 bp):
ATTGTGTCTCAAG
Found at i:55967 original size:110 final size:110
Alignment explanation
Indices: 55772--56197 Score: 552
Period size: 110 Copynumber: 3.9 Consensus size: 110
55762 GGTGCCATTA
*
55772 ATGAAAGTTATCGATCGATGTTGTTAATGCATAACAGTGCATTTTCGACATAAAAGGTGCCACCC
1 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGTGCATTTTCGACATAAAAGGTGCCACCC
* * *
55837 ATTGTATGCATAAAACGTGAATTACCATTTCGACATACCTCATGT
66 ATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCATGT
* * * * **
55882 ATGAAAGTTATCAATCGACATTGGTAATGCATAACGGTGCATTTTCGGTATAAAAGGTGCCACCC
1 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGTGCATTTTCGACATAAAAGGTGCCACCC
* * *
55947 ATGCTATTCATAAAAGGTGAATTACAAACTT-GACATACCTCATGT
66 ATGGTATTCATAAAAGGTGAATTAC-CATTTCGACATACCTCATGT
* * * *
55992 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGAGCATTTTATG-CATAAAATGTGTCACC
1 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGTGCATTTT-CGACATAAAAGGTGCCACC
* *
56056 CATGGTTTTCATAAAAGGTGAATTACCATTTCGGCATACCTCATGT
65 CATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCATGT
* * * * * *
56102 ATTAAAGTTACCGATCGATTTTGTTTAATGCATAA-TGATGCATTTTCAACATAAAAGGTTCCAC
1 ATGAAAGTTATCGATCGATATTG-TTAATGCATAACAG-TGCATTTTCGACATAAAAGGTGCCAC
* *
56166 TCATGGTATTCATAAAAGGTGAATGACCATTT
64 CCATGGTATTCATAAAAGGTGAATTACCATTT
56198 TCGCACTTCG
Statistics
Matches: 270, Mismatches: 40, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
109 3 0.01
110 204 0.76
111 63 0.23
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (110 bp):
ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGTGCATTTTCGACATAAAAGGTGCCACCC
ATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCATGT
Found at i:60607 original size:27 final size:26
Alignment explanation
Indices: 60553--60607 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
60543 AGGTACTTGG
*
60553 ATGGAAAATTATGAAAATACTCTGAT
1 ATGGAAAATTATGAAAATACCCTGAT
*
60579 ATGGTAAAATTATGAAAATACCCTTAT
1 ATGG-AAAATTATGAAAATACCCTGAT
60606 AT
1 AT
60608 TGTAGGATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (26 bp):
ATGGAAAATTATGAAAATACCCTGAT
Found at i:67468 original size:107 final size:107
Alignment explanation
Indices: 67130--67546 Score: 447
Period size: 109 Copynumber: 3.9 Consensus size: 107
67120 AAAGCCATTA
* * * * *
67130 ATGAAAGTTATCGATTGATATTGTTAATGCATAAC-ATTGCATTTTCGAAAAAAAGGTGCCACTC
1 ATGAAAGTTATCGA-TCATATTGTTAATGCATACCGA-TGCATTTTAG-CAAAAAGGTGCCACCC
** * *
67194 ATTTTATTCATATAAGGTGAATTACC-TTTCGACATACCTCGTGT
63 ATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGC
* *
67238 ATGAAAGTTATCGATCGATATTGTTAATGCATAACAGA-GCATTTTTAGCATAAAAGGTGCCATC
1 ATGAAAGTTATCGATC-ATATTGTTAATGCAT-ACCGATGCA-TTTTAGCA-AAAAGGTGCCACC
* *
67302 AATGGTATTCATAAAAGGTGAATAACCATTTCGACATACCTCGTGC
62 CATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGC
* * *
67348 ATGAAAGTTATCGATCAATATTGTTAA-GTATACCGATGCATTTTCGGC-AAAAGGCGCCACCCA
1 ATGAAAGTTATCGATC-ATATTGTTAATGCATACCGATGCATTTT-AGCAAAAAGGTGCCACCCA
67411 TGGTATTCATAAAAGGTGAATTACCATTT-GACATA-C-C-TGC
64 TGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGC
** * * * * *
67451 ATGAAAGTTATTAATCGATATTGTTAATGCATAACGGTGCATTTTTGCATAAAAGGTTCCACTCA
1 ATGAAAGTTATCGATC-ATATTGTTAATGCATACCGATGCATTTTAGCA-AAAAGGTGCCACCCA
*
67516 TGGTATTCATAAAAAGGTGAATGACCATTTC
64 TGGTATTCAT-AAAAGGTGAATTACCATTTC
67547 AGCACTTCGG
Statistics
Matches: 264, Mismatches: 32, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
103 29 0.11
104 15 0.06
105 23 0.09
106 24 0.09
107 41 0.16
108 41 0.16
109 47 0.18
110 44 0.17
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (107 bp):
ATGAAAGTTATCGATCATATTGTTAATGCATACCGATGCATTTTAGCAAAAAGGTGCCACCCATG
GTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGC
Found at i:67533 original size:213 final size:218
Alignment explanation
Indices: 67130--67546 Score: 573
Period size: 213 Copynumber: 1.9 Consensus size: 218
67120 AAAGCCATTA
** * *
67130 ATGAAAGTTATCGATTGATATTGTTAATGCATAACATTGCATTTTCGAAAAAAAGGTGCCACTCA
1 ATGAAAGTTATCGATCAATATTGTTAATGCATAACATTGCATTTTCGAAAAAAAGGCGCCACCCA
** * * *
67195 TTTTATTCATATAAGGTGAATTACCTTTCGACATACCTCGTGTATGAAAGTTATCGATCGATATT
66 TGGTATTCATAAAAGGTGAATTACCTTTCGACATACCTCGTGCATGAAAGTTATCAATCGATATT
67260 GTTAATGCATAACAGAGCATTTTTAGCATAAAAGGTGCCATCAATGGTATTCATAAAAGGTGAAT
131 GTTAATGCATAACAGAGCATTTTTAGCATAAAAGGTGCCATCAATGGTATTCATAAAAGGTGAAT
67325 AACCATTTCGACATACCTCGTGC
196 AACCATTTCGACATACCTCGTGC
* * **
67348 ATGAAAGTTATCGATCAATATTGTTAA-GTATACCGA-TGCATTTTCG-GCAAAAGGCGCCACCC
1 ATGAAAGTTATCGATCAATATTGTTAATGCATAAC-ATTGCATTTTCGAAAAAAAGGCGCCACCC
*
67410 ATGGTATTCATAAAAGGTGAATTACCATTT-GACATA-C-C-TGCATGAAAGTTATTAATCGATA
65 ATGGTATTCATAAAAGGTGAATTACC-TTTCGACATACCTCGTGCATGAAAGTTATCAATCGATA
* * *
67471 TTGTTAATGCATAACGGTGCATTTTT-GCATAAAAGGTTCCACTC-ATGGTATTCATAAAAAGGT
129 TTGTTAATGCATAACAGAGCATTTTTAGCATAAAAGGTGCCA-TCAATGGTATTCAT-AAAAGGT
*
67534 GAATGACCATTTC
192 GAATAACCATTTC
67547 AGCACTTCGG
Statistics
Matches: 177, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
212 25 0.14
213 65 0.37
214 1 0.01
215 1 0.01
216 41 0.23
217 18 0.10
218 26 0.15
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (218 bp):
ATGAAAGTTATCGATCAATATTGTTAATGCATAACATTGCATTTTCGAAAAAAAGGCGCCACCCA
TGGTATTCATAAAAGGTGAATTACCTTTCGACATACCTCGTGCATGAAAGTTATCAATCGATATT
GTTAATGCATAACAGAGCATTTTTAGCATAAAAGGTGCCATCAATGGTATTCATAAAAGGTGAAT
AACCATTTCGACATACCTCGTGC
Found at i:69467 original size:2 final size:2
Alignment explanation
Indices: 69460--69490 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
69450 AAGATATAAA
69460 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69491 GCTTTTCTGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.