Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005539.1 Hibiscus syriacus cultivar Beakdansim tig00012819_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: 129082
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5333 original size:27 final size:27
Alignment explanation
Indices: 5273--5333 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
5263 TTGCTATTTT
* *
5273 TTTCAAAAAAACAAAAAAAGGCAAAAA
1 TTTCAAAAAAAAAAAAAAAAGCAAAAA
*** *
5300 AGGCAAAAAAAAAAAAAAAAGCCAAAA
1 TTTCAAAAAAAAAAAAAAAAGCAAAAA
5327 TTTCAAA
1 TTTCAAA
5334 CAAATTGTAA
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.70, C:0.11, G:0.08, T:0.10
Consensus pattern (27 bp):
TTTCAAAAAAAAAAAAAAAAGCAAAAA
Found at i:18067 original size:24 final size:24
Alignment explanation
Indices: 18040--18100 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
18030 AGAAAGCAAG
18040 AAAAAAATCAGAAA-AG-AAGCACTC
1 AAAAAAA--AGAAATAGAAAGCACTC
* *
18064 AAAAAGAAGAAATTGAAAGCACTC
1 AAAAAAAAGAAATAGAAAGCACTC
18088 AAAAAAAAAGAAA
1 -AAAAAAAAGAAA
18101 GAAAAGTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 5 0.16
23 1 0.03
24 14 0.45
25 11 0.35
ACGTcount: A:0.67, C:0.11, G:0.13, T:0.08
Consensus pattern (24 bp):
AAAAAAAAGAAATAGAAAGCACTC
Found at i:18106 original size:24 final size:23
Alignment explanation
Indices: 18056--18104 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
18046 ATCAGAAAAG
*
18056 AAGCACTCAAAAAGAAGAAATTGA
1 AAGCACTCAAAAAAAAGAAA-TGA
18080 AAGCACTCAAAAAAAAAGAAA-GA
1 AAGCACTC-AAAAAAAAGAAATGA
18103 AA
1 AA
18105 AGTTGGAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 8 0.35
25 11 0.48
ACGTcount: A:0.65, C:0.12, G:0.14, T:0.08
Consensus pattern (23 bp):
AAGCACTCAAAAAAAAGAAATGA
Found at i:22808 original size:11 final size:11
Alignment explanation
Indices: 22792--22818 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
22782 TGTTTTCTCT
22792 TTTTTATTTTC
1 TTTTTATTTTC
22803 TTTTTATTTTC
1 TTTTTATTTTC
22814 TTTTT
1 TTTTT
22819 GCACTCCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTTTC
Found at i:31184 original size:22 final size:20
Alignment explanation
Indices: 31159--31198 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31149 ATGTTTGTTT
31159 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
31181 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
31199 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:31709 original size:24 final size:24
Alignment explanation
Indices: 31663--31714 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
31653 CCTTGGCACT
* * *
31663 TCAAGTGGCACAGCTTTTTGAACA
1 TCAAGTGGCACAACTGTTGGAACA
* *
31687 TCAAGTGGCATAACTGTTGGAACG
1 TCAAGTGGCACAACTGTTGGAACA
31711 TCAA
1 TCAA
31715 AGGACATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (24 bp):
TCAAGTGGCACAACTGTTGGAACA
Found at i:43320 original size:19 final size:20
Alignment explanation
Indices: 43296--43341 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
43286 CGGCCAAGAG
**
43296 CATGTATCTTCAT-TTAAAT
1 CATGTATCTTCATCAAAAAT
*
43315 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
43335 CATGTAT
1 CATGTAT
43342 TTTCTAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:43757 original size:35 final size:37
Alignment explanation
Indices: 43684--43763 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
43674 ATACTATTTC
* * *
43684 CATCCCCATAATCCATCTTCCATTATCACGCCTGTAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
43721 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
43756 CATCACCA
1 CATCACCA
43764 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.29, C:0.39, G:0.05, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:44919 original size:24 final size:24
Alignment explanation
Indices: 44899--44949 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
44889 TTTCTTTCTT
44899 TTTTCTTC-TTTTGAGTGCTTTCA
1 TTTTCTTCTTTTTGAGTGCTTTCA
44922 TTTTCTTCTTTTTGAGTGC-TT-A
1 TTTTCTTCTTTTTGAGTGCTTTCA
44944 TTTTCT
1 TTTTCT
44950 GATTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.26
23 10 0.37
24 10 0.37
ACGTcount: A:0.08, C:0.16, G:0.12, T:0.65
Consensus pattern (24 bp):
TTTTCTTCTTTTTGAGTGCTTTCA
Found at i:44955 original size:22 final size:24
Alignment explanation
Indices: 44907--44956 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
44897 TTTTTTCTTC
**
44907 TTTTGAGTGCTTTCATTTTCTTCT
1 TTTTGAGTGCTTTCATTTTCTGAT
44931 TTTTGAGTGC-TT-ATTTTCTGAT
1 TTTTGAGTGCTTTCATTTTCTGAT
44953 TTTT
1 TTTT
44957 CTTGCTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.50
23 2 0.08
24 10 0.42
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (24 bp):
TTTTGAGTGCTTTCATTTTCTGAT
Found at i:60958 original size:23 final size:24
Alignment explanation
Indices: 60917--60968 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
60907 TTCTTTTTTC
60917 TTCTTCTTTTCGAGTGCTTTCAAT
1 TTCTTCTTTTCGAGTGCTTTCAAT
* *
60941 TTCTTCTTTT-GAGTGCTTTTATT
1 TTCTTCTTTTCGAGTGCTTTCAAT
60964 TTCTT
1 TTCTT
60969 TGTTGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.10, C:0.17, G:0.12, T:0.62
Consensus pattern (24 bp):
TTCTTCTTTTCGAGTGCTTTCAAT
Found at i:62184 original size:19 final size:20
Alignment explanation
Indices: 62160--62210 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
62150 CGGCCAAGAG
**
62160 CATGTATTTTCAT-TTAAAT
1 CATGTATTTTCATCAAAAAT
62179 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
62199 CATGTTTTTTCA
1 CATGTATTTTCA
62211 AAGGGGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:62594 original size:13 final size:11
Alignment explanation
Indices: 62572--62637 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
62562 TATCAAGCCT
62572 ATATCATCACC
1 ATATCATCACC
62583 ATAGTCCATCACC
1 ATA-T-CATCACC
*
62596 ATTATCA-CGCC
1 A-TATCATCACC
62607 TATATCATCACC
1 -ATATCATCACC
62619 ATATTCCATCACC
1 ATA-T-CATCACC
62632 ATATCA
1 ATATCA
62638 CGCCTATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:62597 original size:36 final size:36
Alignment explanation
Indices: 62550--62654 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
62540 GATACAATCT
*
62550 GTCCATCACCATTATCAAGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
62586 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
62622 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
62655 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:66628 original size:11 final size:11
Alignment explanation
Indices: 66597--66681 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
66587 ACAATCTGTC
66597 CATCACCATTAT
1 CATCACCA-TAT
*
66609 CA-CGCCTATAT
1 CATCACC-ATAT
*
66620 CATCACTATAGT
1 CATCACCATA-T
66632 CCATCACCATTAT
1 -CATCACCA-TAT
*
66645 CA-CGCCTATAT
1 CATCACC-ATAT
66656 CATCACCATATT
1 CATCACCATA-T
66668 CGATCACCATAT
1 C-ATCACCATAT
66680 CA
1 CA
66682 CGCCTATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
11 23 0.40
12 16 0.28
13 17 0.29
14 2 0.03
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:66688 original size:35 final size:36
Alignment explanation
Indices: 66594--66698 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
66584 GATACAATCT
*
66594 GTCCATCACCATTATCACGCCTATATCATCACTATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
66630 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
66666 TTCGATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
66699 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.30, C:0.34, G:0.06, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:67567 original size:33 final size:33
Alignment explanation
Indices: 67525--67593 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
67515 GTTGATGAAT
*
67525 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
67558 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
67591 GAA
1 GAA
67594 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:71479 original size:33 final size:33
Alignment explanation
Indices: 71437--71505 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
71427 GTTGATGAAT
*
71437 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
71470 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
71503 GAA
1 GAA
71506 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:76292 original size:36 final size:36
Alignment explanation
Indices: 76245--76349 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
76235 GATACAATCT
76245 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
76281 GTCCATCACCATTATCACGCCTATGTCATCGCCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
76317 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
76350 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:78435 original size:28 final size:28
Alignment explanation
Indices: 78401--78468 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
78391 AAAGAAAATC
* * *
78401 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAAATCAAGCACTCAAAAAGA
* *
78429 AGGAAAGAAAATCCAGCACTCAAAAAGA
1 AGAAAAGAAAATCAAGCACTCAAAAAGA
78457 AGAAAAGAAAAT
1 AGAAAAGAAAAT
78469 AAAAGAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (28 bp):
AGAAAAGAAAATCAAGCACTCAAAAAGA
Found at i:83918 original size:16 final size:16
Alignment explanation
Indices: 83897--83929 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
83887 TTCTGCCACC
83897 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
83913 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
83929 T
1 T
83930 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:89321 original size:16 final size:16
Alignment explanation
Indices: 89300--89332 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
89290 TTCTGCCACC
89300 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
*
89316 TATGTTAGAATGTAAA
1 TATGTTAGAATGCAAA
89332 T
1 T
89333 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.36
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:90975 original size:35 final size:36
Alignment explanation
Indices: 90881--90985 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
90871 GATACAATCT
*
90881 GTCCATCACCATTATCACGCCTATATCATCACCATC
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
90917 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
90953 GTCCATCTCCA-TATCACGCCTATATCATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
90986 AATCCCATTT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 22 0.34
36 43 0.66
ACGTcount: A:0.29, C:0.38, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:91430 original size:24 final size:26
Alignment explanation
Indices: 91389--91437 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
91379 GTGCTACAAC
*
91389 AACAAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAAGCAACAAGAAAAAAGAA
*
91415 AACAAAAGAG-AA-AAGAAAAAAGA
1 AACAAAAAAGCAACAAGAAAAAAGA
91438 CTCCTACATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 2 0.10
26 9 0.43
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (26 bp):
AACAAAAAAGCAACAAGAAAAAAGAA
Found at i:95523 original size:35 final size:36
Alignment explanation
Indices: 95414--95523 Score: 186
Period size: 36 Copynumber: 3.1 Consensus size: 36
95404 ACAATCTGTT
*
95414 CATCACCATTATCACGCCTATATCATCACCATCTTC
1 CATCACCATTATCACGCCTATATCATCACCATATTC
*
95450 CATCACCATTATCACGCCTATATCATCACCATAGTC
1 CATCACCATTATCACGCCTATATCATCACCATATTC
*
95486 CATCACCA-TATCACGCCTATATCATCACCAAATTC
1 CATCACCATTATCACGCCTATATCATCACCATATTC
95521 CAT
1 CAT
95524 TTTCCATTCC
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
35 28 0.40
36 42 0.60
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.28
Consensus pattern (36 bp):
CATCACCATTATCACGCCTATATCATCACCATATTC
Found at i:95684 original size:25 final size:21
Alignment explanation
Indices: 95664--95712 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 21
95654 AACTTTTCTA
95664 TCCATTTCAATTCTTTCC-TTTT
1 TCCATTT--ATTCTTTCCTTTTT
95686 TCCATTTATTCTTTCC-TTTT
1 TCCATTTATTCTTTCCTTTTT
95706 TCCATTT
1 TCCATTT
95713 CATTTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 20 0.74
22 7 0.26
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (21 bp):
TCCATTTATTCTTTCCTTTTT
Found at i:95696 original size:20 final size:20
Alignment explanation
Indices: 95673--95712 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
95663 ATCCATTTCA
95673 ATTCTTTCCTTTTTCCATTT
1 ATTCTTTCCTTTTTCCATTT
95693 ATTCTTTCCTTTTTCCATTT
1 ATTCTTTCCTTTTTCCATTT
95713 CATTTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTCTTTCCTTTTTCCATTT
Found at i:98404 original size:25 final size:25
Alignment explanation
Indices: 98372--98428 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
98362 GAAAATCAGA
*
98372 AAAG-AAATTAAAGGACTCCAAAAG
1 AAAGAAAATTAAAGGACTCAAAAAG
** *
98396 AAAGAAAATTTTAGTACTCAAAAAG
1 AAAGAAAATTAAAGGACTCAAAAAG
*
98421 AAAAAAAA
1 AAAGAAAA
98429 AAGCAAAGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.63, C:0.09, G:0.12, T:0.16
Consensus pattern (25 bp):
AAAGAAAATTAAAGGACTCAAAAAG
Found at i:111778 original size:36 final size:36
Alignment explanation
Indices: 111701--111802 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
111691 ATTTATAAGT
* *
111701 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
111736 T-G-GATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
111770 TGGTGATGATATAGGCGTGATAATGG-GATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
111803 AGATTGTATC
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
33 16 0.26
34 15 0.24
35 9 0.15
36 22 0.35
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:112185 original size:19 final size:20
Alignment explanation
Indices: 112143--112185 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
112133 GAAACCCCTT
*
112143 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTAAA
112163 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
112182 TGAA
1 TGAA
112186 GATGCAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:115064 original size:15 final size:16
Alignment explanation
Indices: 115021--115054 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
115011 GTAATGAAAC
115021 AAGAATAAAGAAATGA
1 AAGAATAAAGAAATGA
115037 AAGAATAAAGAAATGA
1 AAGAATAAAGAAATGA
115053 AA
1 AA
115055 TAGTAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (16 bp):
AAGAATAAAGAAATGA
Found at i:115294 original size:22 final size:22
Alignment explanation
Indices: 115266--115311 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
115256 TGTAGGAGTC
*
115266 TTTTTC-T-TTTCTTTTTG-TT
1 TTTTTCTTCTTTCTTGTTGCTT
115285 TTTTTCTTCTTTCTTGTTGCTT
1 TTTTTCTTCTTTCTTGTTGCTT
115307 TTTTT
1 TTTTT
115312 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 9 0.39
22 7 0.30
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (22 bp):
TTTTTCTTCTTTCTTGTTGCTT
Found at i:115720 original size:13 final size:12
Alignment explanation
Indices: 115701--115786 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
115691 ATATAGGCGT
115701 GATATGGTGATG
1 GATATGGTGATG
115713 GAATATGGTGAT-
1 G-ATATGGTGATG
*
115725 GATATAGGCG-T-
1 GATAT-GGTGATG
115736 GATAATGGTGATG
1 GAT-ATGGTGATG
115749 GACTATGGTGAT-
1 GA-TATGGTGATG
*
115761 GATATAGGCG-T-
1 GATAT-GGTGATG
115772 GATAATGGTGATG
1 GAT-ATGGTGATG
115785 GA
1 GA
115787 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:115756 original size:36 final size:36
Alignment explanation
Indices: 115683--115787 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
115673 ATTTATAAGT
* *
115683 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
115718 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
115754 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
115788 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:116172 original size:19 final size:20
Alignment explanation
Indices: 116130--116180 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
116120 GAAACCCCTT
*
116130 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTAAA
116150 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
116169 TGAAGATACATG
1 TGAAAATACATG
116181 CTCTTGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:119056 original size:16 final size:16
Alignment explanation
Indices: 119016--119049 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
119006 GTAATGAAAC
119016 AAGAATAAAGAAATGA
1 AAGAATAAAGAAATGA
119032 AAGAATAAAGAAATGA
1 AAGAATAAAGAAATGA
119048 AA
1 AA
119050 TAGTAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (16 bp):
AAGAATAAAGAAATGA
Found at i:119744 original size:36 final size:36
Alignment explanation
Indices: 119681--119775 Score: 156
Period size: 36 Copynumber: 2.7 Consensus size: 36
119671 TGGTGATAAT
*
119681 ATAGGCGTGATAA-GGTGATGGAATATGGTGACGAC
1 ATAGGCGTGATAATGGTGATGGACTATGGTGACGAC
* *
119716 ATAGGCGTGATAATGGTGATGGACTATGGTGATGAT
1 ATAGGCGTGATAATGGTGATGGACTATGGTGACGAC
119752 ATAGGCGTGATAATGGTGATGGAC
1 ATAGGCGTGATAATGGTGATGGAC
119776 AGATTGTATC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 13 0.23
36 43 0.77
ACGTcount: A:0.29, C:0.07, G:0.37, T:0.26
Consensus pattern (36 bp):
ATAGGCGTGATAATGGTGATGGACTATGGTGACGAC
Found at i:120164 original size:19 final size:20
Alignment explanation
Indices: 120117--120167 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
120107 GAAACCCCTT
**
120117 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
120137 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
120156 TGAAGATACATG
1 TGAAAATACATG
120168 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:121711 original size:48 final size:48
Alignment explanation
Indices: 121640--121743 Score: 208
Period size: 48 Copynumber: 2.2 Consensus size: 48
121630 CAAGAAACAA
121640 GTCTTTTGGGGAACCAATAGTCATGACCTTTGGTGATCCACACGACAT
1 GTCTTTTGGGGAACCAATAGTCATGACCTTTGGTGATCCACACGACAT
121688 GTCTTTTGGGGAACCAATAGTCATGACCTTTGGTGATCCACACGACAT
1 GTCTTTTGGGGAACCAATAGTCATGACCTTTGGTGATCCACACGACAT
121736 GTCTTTTG
1 GTCTTTTG
121744 AAGATCCAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (48 bp):
GTCTTTTGGGGAACCAATAGTCATGACCTTTGGTGATCCACACGACAT
Found at i:121743 original size:24 final size:24
Alignment explanation
Indices: 121668--121743 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
121658 AGTCATGACC
121668 TTTGGTGATCCACACGACATGTCT
1 TTTGGTGATCCACACGACATGTCT
* * * * * *
121692 TTTGGGGAACCA-ATAGTCATGACC
1 TTTGGTGATCCACA-CGACATGTCT
121716 TTTGGTGATCCACACGACATGTCT
1 TTTGGTGATCCACACGACATGTCT
121740 TTTG
1 TTTG
121744 AAGATCCAAC
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (24 bp):
TTTGGTGATCCACACGACATGTCT
Found at i:123863 original size:35 final size:37
Alignment explanation
Indices: 123794--123873 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
123784 ATACTATTTC
* *
123794 CATCACAATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
123831 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
123866 CATCACCA
1 CATCACCA
123874 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:124037 original size:15 final size:16
Alignment explanation
Indices: 124013--124051 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
124003 TTTGATAACT
*
124013 ATTCTATCCATTTC-A
1 ATTCTTTCCATTTCTA
124028 ATTCTTTCCATTTCTA
1 ATTCTTTCCATTTCTA
*
124044 TTTCTTTC
1 ATTCTTTC
124052 TTTATTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTCTTTCCATTTCTA
Found at i:124347 original size:14 final size:15
Alignment explanation
Indices: 124313--124359 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
124303 AATTTGGAGT
124313 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
124328 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
124342 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
124359 G
1 G
124360 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Done.