Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001731.1 Hibiscus syriacus cultivar Beakdansim tig00003496_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: 68530
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8588 original size:60 final size:61
Alignment explanation
Indices: 8494--8613 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 61
8484 ACATCTGAAA
* *
8494 ATGCTAAGGAATCATCTGATGAGGCCGCATCATCCGCT-TGATTGATCATCCCGGAATCGAT
1 ATGCTAAGGAAACATCTGATGAGGCCGCATCATCC-CTATGATTGATCATCCCAGAATCGAT
* * * *
8555 ATGCTAA-GAAACATTTGATGAGGCTGCATCATCCTTATGCTTGATCATCCCAGAATCGA
1 ATGCTAAGGAAACATCTGATGAGGCCGCATCATCCCTATGATTGATCATCCCAGAATCGA
8614 CGAGAATCGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 1 0.02
60 44 0.85
61 7 0.13
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (61 bp):
ATGCTAAGGAAACATCTGATGAGGCCGCATCATCCCTATGATTGATCATCCCAGAATCGAT
Found at i:10856 original size:12 final size:14
Alignment explanation
Indices: 10822--10858 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
10812 AAAGAAAACA
*
10822 AATAAGATAAAGAG
1 AATAAAATAAAGAG
10836 AATAAAATAAAG-G
1 AATAAAATAAAGAG
10849 AA-AAAATAAA
1 AATAAAATAAA
10859 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.36
13 3 0.14
14 11 0.50
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAAAATAAAGAG
Found at i:11214 original size:24 final size:23
Alignment explanation
Indices: 11170--11215 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
11160 GATTTTTTTT
* **
11170 AAAATAATATAATAATGAATAAA
1 AAAATAAAATAATAAAAAATAAA
11193 AAAATGAAAATAATAAAAAATAA
1 AAAAT-AAAATAATAAAAAATAA
11216 TATATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAATAAAATAATAAAAAATAAA
Found at i:11369 original size:2 final size:2
Alignment explanation
Indices: 11288--11353 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
11278 ATAATTAAGA
11288 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
11330 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
11354 TAATAATAGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11574 original size:17 final size:18
Alignment explanation
Indices: 11541--11576 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11531 ATATATACGT
*
11541 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
11559 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
11576 A
1 A
11577 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:12702 original size:15 final size:15
Alignment explanation
Indices: 12684--12720 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
12674 TTCTTGCCAT
12684 TTATTTTTTTTATTA
1 TTATTTTTTTTATTA
*
12699 TTATTTTTTTTATTT
1 TTATTTTTTTTATTA
12714 TTATTTT
1 TTATTTT
12721 ACTAACTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTATTTTTTTTATTA
Found at i:12720 original size:12 final size:11
Alignment explanation
Indices: 12683--12721 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
12673 TTTCTTGCCA
12683 TTTATTTTTTT
1 TTTATTTTTTT
12694 TATTATTATTTTT
1 T-TTATT-TTTTT
*
12707 TTTATTTTTAT
1 TTTATTTTTTT
12718 TTTA
1 TTTA
12722 CTAACTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 9 0.36
12 10 0.40
13 6 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:16194 original size:11 final size:10
Alignment explanation
Indices: 16178--16216 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
16168 AACAAAAAAG
16178 AAAAGAAGCAA
1 AAAAGAA-CAA
*
16189 AAAAGAAAAA
1 AAAAGAACAA
16199 AACAAGAACAA
1 AA-AAGAACAA
16210 AAAAGAA
1 AAAAGAA
16217 AAGAAGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAGAACAA
Found at i:16197 original size:21 final size:21
Alignment explanation
Indices: 16173--16221 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
16163 TCAAGAACAA
16173 AAAAGAA-AAGAAGCAAAAAAG
1 AAAAGAACAAGAA-CAAAAAAG
*
16194 AAAAAAACAAGAACAAAAAAG
1 AAAAGAACAAGAACAAAAAAG
16215 AAAAGAA
1 AAAAGAA
16222 GCAAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (21 bp):
AAAAGAACAAGAACAAAAAAG
Found at i:16205 original size:22 final size:22
Alignment explanation
Indices: 16171--16227 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 22
16161 AATCAAGAAC
16171 AAAAAAGAAAAGAAGCAAAAAAG
1 AAAAAAGAAAAGAA-CAAAAAAG
*
16194 AAAAAA-ACAAGAACAAAAAAG
1 AAAAAAGAAAAGAACAAAAAAG
16215 AAAAGAAGCAAAA
1 AAAA-AAG-AAAA
16228 ATCAAAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 12 0.41
22 8 0.28
23 6 0.21
24 3 0.10
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAGAACAAAAAAG
Found at i:16221 original size:15 final size:15
Alignment explanation
Indices: 16165--16216 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
16155 AGATTCAATC
16165 AAGAACAAAAAAGAA
1 AAGAACAAAAAAGAA
16180 AAGAAGCAAAAAAGAA
1 AAGAA-CAAAAAAGAA
*
16196 AAAAACAAGAACAA-AA
1 AAGAACAA-AA-AAGAA
16212 AAGAA
1 AAGAA
16217 AAGAAGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 8 0.25
16 22 0.69
17 2 0.06
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (15 bp):
AAGAACAAAAAAGAA
Found at i:16234 original size:22 final size:22
Alignment explanation
Indices: 16173--16234 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
16163 TCAAGAACAA
* *
16173 AAAAGAAA-AGAAGCAAAAAAG
1 AAAAGAAACAAAAACAAAAAAG
*
16194 AAAA-AAACAAGAACAAAAAAG
1 AAAAGAAACAAAAACAAAAAAG
*
16215 AAAAGAAGCAAAAATCAAAA
1 AAAAGAAACAAAAA-CAAAA
16235 GGAAAAGGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 3 0.09
21 18 0.55
22 7 0.21
23 5 0.15
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.02
Consensus pattern (22 bp):
AAAAGAAACAAAAACAAAAAAG
Found at i:16235 original size:21 final size:19
Alignment explanation
Indices: 16171--16228 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
16161 AATCAAGAAC
16171 AAAAAAGAAAAGAAGCAAA
1 AAAAAAGAAAAGAAGCAAA
* *
16190 AAAGAAA-AAAACAAG-AAC
1 AAA-AAAGAAAAGAAGCAAA
16208 AAAAAAGAAAAGAAGCAAA
1 AAAAAAGAAAAGAAGCAAA
16227 AA
1 AA
16229 TCAAAAGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 3 0.09
18 12 0.38
19 14 0.44
20 3 0.09
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAGAAGCAAA
Found at i:16251 original size:37 final size:37
Alignment explanation
Indices: 16164--16234 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
16154 AAGATTCAAT
*
16164 CAAGAACAAAAAAGAAAAGAAGCAAAAAAGAAAAAAA
1 CAAGAACAAAAAAGAAAAGAAGCAAAAAACAAAAAAA
*
16201 CAAGAACAAAAAAGAAAAGAAGCAAAAATCAAAA
1 CAAGAACAAAAAAGAAAAGAAGCAAAAAACAAAA
16235 GGAAAAGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.76, C:0.10, G:0.13, T:0.01
Consensus pattern (37 bp):
CAAGAACAAAAAAGAAAAGAAGCAAAAAACAAAAAAA
Found at i:17312 original size:18 final size:18
Alignment explanation
Indices: 17289--17324 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17279 TCAACATCAA
*
17289 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
17307 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
17325 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:17860 original size:36 final size:37
Alignment explanation
Indices: 17813--17888 Score: 129
Period size: 36 Copynumber: 2.1 Consensus size: 37
17803 GTGCTCACCA
17813 TTGTCTCTCTTGAGACAGTTTCCCTT-GAAACAAA-CT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGGAAA-AAACCT
17849 TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAACCT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAACCT
17886 TTG
1 TTG
17889 AAATTGTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
36 29 0.76
37 9 0.24
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAACCT
Found at i:18111 original size:37 final size:37
Alignment explanation
Indices: 18020--18121 Score: 98
Period size: 37 Copynumber: 2.7 Consensus size: 37
18010 CCTTGGAACT
* * ** *
18020 AATTTTATCTCCCCGTGAGACAATTTCTTTTGGAACTA
1 AATTTTATCT-CCCTTGAGACAGTTTCTTTTAAAACAA
* * *
18058 AGTTTTGTCTCTCTTGAGACAGTTT-TTCTTAAAACAA
1 AATTTTATCTCCCTTGAGACAGTTTCTT-TTAAAACAA
*
18095 AATTTTATCTCCCTTGAGACCGTTTCT
1 AATTTTATCTCCCTTGAGACAGTTTCT
18122 CATGAAACAG
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
36 2 0.04
37 39 0.78
38 9 0.18
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.42
Consensus pattern (37 bp):
AATTTTATCTCCCTTGAGACAGTTTCTTTTAAAACAA
Found at i:18130 original size:37 final size:37
Alignment explanation
Indices: 18060--18130 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
18050 TGGAACTAAG
* * * *
18060 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTATCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
18097 TTTTATCTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTTATCTCCCTTGAGACAGTTTCTCATAAAACA
18131 GCAGATATCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (37 bp):
TTTTATCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:18858 original size:113 final size:110
Alignment explanation
Indices: 18723--18945 Score: 308
Period size: 110 Copynumber: 2.0 Consensus size: 110
18713 GCCATCAGCG
*
18723 ATTTCAACTCCACGACGGAGGAT-ATCGTGTCACTCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTCCACGACGAAGGATAAT-G-G--ACTCGAGACAACACAAGTTCAACTTCACAACGA
18787 AAGGACGACTGGTTGTCAACAAACCACTTTTT-AGTTTCATTCAGAGTCA
62 AAGGACGACTGGTTGTCAACAAACCA-TTTTTCAGTTTCATTCAGAGTCA
* * *
18836 ATTTCAACTTCAC-AGCGAAGGATAATGGACTCGAGGCAACACAAGTTCAACTTCACAACGAATG
1 ATTTCAACTCCACGA-CGAAGGATAATGGACTCGAGACAACACAAGTTCAACTTCACAACGAAAG
* **
18900 GATGGGTGGTTGTCAACAAACCATTTTTCAGTTTCATTCAGAGTCA
65 GACGACTGGTTGTCAACAAACCATTTTTCAGTTTCATTCAGAGTCA
18946 CAACGAAGGG
Statistics
Matches: 100, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
109 5 0.05
110 71 0.71
112 2 0.02
113 20 0.20
114 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (110 bp):
ATTTCAACTCCACGACGAAGGATAATGGACTCGAGACAACACAAGTTCAACTTCACAACGAAAGG
ACGACTGGTTGTCAACAAACCATTTTTCAGTTTCATTCAGAGTCA
Found at i:19048 original size:162 final size:160
Alignment explanation
Indices: 18778--19094 Score: 431
Period size: 162 Copynumber: 2.0 Consensus size: 160
18768 AAGTTCAACT
* * ** *
18778 TCACAACGAAAGGACGACTGGTTGTCAACAAACCACTTTTTAGTTTCATTCAGAGTCAATTTCAA
1 TCACAACGAAAGGACGACTGGTTGTCAACAAAACAATTTCCAG-TT-ATTCAGAGCCAATTTCAA
* * * * * * *
18843 CTTCACAGCGAAGGATAATGGACTCGAGGCAACACAAGTTCAACTTCACAACGAATGGATGGGTG
64 CTTCACAGCAAAGGATAATGAACTCAAGACAACACAAGTTCAACTTCAC-A--AAGGGACGGCTG
*
18908 GTTGTCAACAAACCATTTTTCAGTTTCATTCAGAG
126 GTTGTCAACAAACCACTTTTCAGTTTCATTCAGAG
*
18943 TCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCCCAG-T-TTCAGAGCCAATTTCAAC
1 TCACAACGAAAGGACGACTGGTTGTCAACAAAACAATTT-CCAGTTATTCAGAGCCAATTTCAAC
*
19006 TTCACAGCAAAGGATATTGAACTCAAGACAACACAAGTTCAACTTCACAAAGGGACGGCTGGTTG
65 TTCACAGCAAAGGATAATGAACTCAAGACAACACAAGTTCAACTTCACAAAGGGACGGCTGGTTG
19071 TCAACAAACCACTTTTCAGTTTCA
130 TCAACAAACCACTTTTCAGTTTCA
19095 GAGTCAATTT
Statistics
Matches: 136, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
159 36 0.26
161 1 0.01
162 60 0.44
164 1 0.01
165 36 0.26
166 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (160 bp):
TCACAACGAAAGGACGACTGGTTGTCAACAAAACAATTTCCAGTTATTCAGAGCCAATTTCAACT
TCACAGCAAAGGATAATGAACTCAAGACAACACAAGTTCAACTTCACAAAGGGACGGCTGGTTGT
CAACAAACCACTTTTCAGTTTCATTCAGAG
Found at i:19219 original size:106 final size:106
Alignment explanation
Indices: 18943--19451 Score: 731
Period size: 106 Copynumber: 4.8 Consensus size: 106
18933 TCATTCAGAG
*
18943 TCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCCCAGTTTCAGAGCCAATTTCAACTT
1 TCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCCCAGTTTCAGAGCCAATTTCAACTT
* *
19008 CACAGCAAAGGATATTGAACTCAAGACAACACAAGTTCAACT
65 CACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* * *
19050 TCAC-A--AAGGGACGGCTGGTTGTCAACAAACCACTTT-TCAGTTTCAGAGTCAATTTCAACTT
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCCCAGTTTCAGAGCCAATTTCAACTT
*
19111 CACAGCGAAGGCTATTGGACTCAAGACAACACAAGTTCAACT
65 CACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* * * *
19153 TTACAACGAAGGGACGGCTGGTTGTCAGCAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGAGCCAATTTCAACTTC
* *
19218 ACAGCGAAGGATATTGGACTCAAGACGACACAAGTTCAAAT
66 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* *
19259 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGAGCCAATTTCAACTTC
* * *
19324 ACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACT
66 ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* * * ** *
19365 TCACAGCGAAGGGGCGGCCGACTGTCAACAAACAATTTCCTAGTTTCAGAGCCAATTTCAACTTC
1 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGAGCCAATTTCAACTTC
*
19430 AC-GACGGAGGATATTGGACTCA
66 ACAG-CGAAGGATATTGGACTCA
19452 GAACAATACT
Statistics
Matches: 359, Mismatches: 37, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
103 68 0.19
104 26 0.07
105 6 0.02
106 255 0.71
107 4 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
Found at i:20696 original size:17 final size:18
Alignment explanation
Indices: 20670--20709 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20660 ATTATATGGA
20670 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
20686 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
20704 TATTAT
1 TATTAT
20710 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:20778 original size:2 final size:2
Alignment explanation
Indices: 20771--20799 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20761 TACTATATTT
20771 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
20800 TTCTTTAATA
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:24804 original size:14 final size:14
Alignment explanation
Indices: 24785--24816 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
24775 AGTTGTAAAG
*
24785 GTTAGTTGTTAGCT
1 GTTAGTTGTTAGAT
24799 GTTAGTTGTTAGAT
1 GTTAGTTGTTAGAT
24813 GTTA
1 GTTA
24817 TGAGTAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (14 bp):
GTTAGTTGTTAGAT
Found at i:29641 original size:15 final size:16
Alignment explanation
Indices: 29623--29653 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
29613 ACAATTTTAT
29623 TTTATAAAATT-TAAA
1 TTTATAAAATTCTAAA
29638 TTTATAAAATTCTAAA
1 TTTATAAAATTCTAAA
29654 GAAAGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTATAAAATTCTAAA
Found at i:38709 original size:21 final size:21
Alignment explanation
Indices: 38658--38709 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
38648 AAAGAAAGAA
*
38658 GAAGAAGATAGGGAATGAGTT
1 GAAGAAGATGGGGAATGAGTT
38679 GAAGAAGATGGGGAATGAGTT
1 GAAGAAGATGGGGAATGAGTT
38700 GAAGAAGATG
1 GAAGAAGATG
38710 AAGAGCCAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.40, T:0.17
Consensus pattern (21 bp):
GAAGAAGATGGGGAATGAGTT
Found at i:39408 original size:21 final size:21
Alignment explanation
Indices: 39363--39407 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
39353 AACTTTCAAG
*
39363 AAAATCACTTCTCAAGAAAGA
1 AAAATAACTTCTCAAGAAAGA
*
39384 AAAATAACTT-TCAAGAAGGA
1 AAAATAACTTCTCAAGAAAGA
39404 AAAA
1 AAAA
39408 AAAGTGGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.58, C:0.13, G:0.11, T:0.18
Consensus pattern (21 bp):
AAAATAACTTCTCAAGAAAGA
Found at i:43765 original size:12 final size:12
Alignment explanation
Indices: 43745--43814 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
43735 GATACATGAC
*
43745 CTGAATTCTGTT
1 CTGATTTCTGTT
*
43757 CTGATTTCTGAT
1 CTGATTTCTGTT
*
43769 ATGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
43781 CTAATATCTGTT
1 CTGATTTCTGTT
*
43793 CTGAATTCTGTT
1 CTGATTTCTGTT
*
43805 TTGATTTCTG
1 CTGATTTCTG
43815 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 1 0.02
12 41 0.93
13 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:43776 original size:24 final size:24
Alignment explanation
Indices: 43746--43818 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
43736 ATACATGACC
43746 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* * * * *
43770 TGGATTCTGTTCTAATATCTGTTC
1 TGAATTCTGTTCTGATTTCTGATA
*
43794 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
43818 T
1 T
43819 CTCCGTTTAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:57605 original size:186 final size:185
Alignment explanation
Indices: 57277--57639 Score: 638
Period size: 186 Copynumber: 2.0 Consensus size: 185
57267 AAATTAAATA
57277 TTTTAATTCAAAAAAATAGTTTCTAAATAATTTAAATAATATATAATTATAAAATAAAAATTTTA
1 TTTTAATTCAAAAAAATAGTTTCTAAATAATTTAAATAATATATAATTATAAAATAAAAATTTTA
57342 TATAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
66 TATAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
* * *
57407 GGGTTTTAAATGGTTTGGGTTGAGCCCATATGTTATATATAATATATTTAATATT
131 GAGTTCTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATATT
* * *
57462 TTTTAATTTAAAAAAATAGTTTAC-AATTAATTTAAATAATATATAATTATAAAATCAAAATTTT
1 TTTTAATTCAAAAAAATAGTTT-CTAAATAATTTAAATAATATATAATTATAAAATAAAAATTTT
*
57526 ATATAAATTTTTTAATTAATTTATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
65 ATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
57591 TTGAGTTCTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATAT
129 TTGAGTTCTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATAT
57640 AAAATTTAAT
Statistics
Matches: 169, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
185 63 0.37
186 106 0.63
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (185 bp):
TTTTAATTCAAAAAAATAGTTTCTAAATAATTTAAATAATATATAATTATAAAATAAAAATTTTA
TATAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
GAGTTCTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATATT
Found at i:57773 original size:30 final size:30
Alignment explanation
Indices: 57739--57816 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
57729 AACCGTTAAC
*
57739 TAACCAAACTAATTCGGTGGCCGACCGAAT
1 TAACCGAACTAATTCGGTGGCCGACCGAAT
57769 TAACCGAACTAATTCGGTGGCCGACCGAAT
1 TAACCGAACTAATTCGGTGGCCGACCGAAT
57799 TAACCGAACTAATTCGGT
1 TAACCGAACTAATTCGGT
57817 TCAGTCAGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (30 bp):
TAACCGAACTAATTCGGTGGCCGACCGAAT
Found at i:58360 original size:94 final size:95
Alignment explanation
Indices: 58198--58402 Score: 261
Period size: 94 Copynumber: 2.2 Consensus size: 95
58188 GAATTCGTTG
* * * * *
58198 AGTAGTATCGATACCATGATGAGGGTATCGACACCAGGAATCATTGAATCTAAAATTGGTATTGA
1 AGTAGTATCGATACCATGATAAGGGTATCGACACCAGCAATCATCGAACCTAAAATTAGTATTGA
* * *
58263 TACCAGAA-GGGGTATTGGTACCATAGTAT
66 TACCAAAAGGGGGTATCGGTACCATAATAT
* * * *
58292 GGTAGTATCGATACTATGGTAAGGGTATCGATACCAAGCAA-CATCGAACCTAAAATTAGTATTG
1 AGTAGTATCGATACCATGATAAGGGTATCGACACC-AGCAATCATCGAACCTAAAATTAGTATTG
58356 ATACCAAAAGGGGGTATCGGTACCATAATAT
65 ATACCAAAAGGGGGTATCGGTACCATAATAT
* *
58387 AGAAGTATCGGTACCA
1 AGTAGTATCGATACCA
58403 AGGTAGTAGT
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
94 58 0.62
95 35 0.38
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (95 bp):
AGTAGTATCGATACCATGATAAGGGTATCGACACCAGCAATCATCGAACCTAAAATTAGTATTGA
TACCAAAAGGGGGTATCGGTACCATAATAT
Found at i:58419 original size:95 final size:94
Alignment explanation
Indices: 58247--58420 Score: 224
Period size: 95 Copynumber: 1.8 Consensus size: 94
58237 ATCATTGAAT
* * * * * * * *
58247 CTAAAATTGGTATTGATACCAGAAGGGGTATTGGTACCATAGTATGGTAGTATCGATACTATGGT
1 CTAAAATTAGTATTGATACCAAAAGGGGTATCGGTACCATAATATAGAAGTATCGATACCAAGGT
* *
58312 AAGGGTATCGATACCAAGCAACATCGAAC
66 AAGAGTAGCGATACCAAGCAACATCGAAC
*
58341 CTAAAATTAGTATTGATACCAAAAGGGGGTATCGGTACCATAATATAGAAGTATCGGTACCAAGG
1 CTAAAATTAGTATTGATACCAAAA-GGGGTATCGGTACCATAATATAGAAGTATCGATACCAAGG
58406 T-AGTAGTAGCGATAC
65 TAAG-AGTAGCGATAC
58421 TATAGAGCCA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
94 24 0.36
95 43 0.64
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (94 bp):
CTAAAATTAGTATTGATACCAAAAGGGGTATCGGTACCATAATATAGAAGTATCGATACCAAGGT
AAGAGTAGCGATACCAAGCAACATCGAAC
Found at i:59234 original size:54 final size:54
Alignment explanation
Indices: 58744--59235 Score: 750
Period size: 54 Copynumber: 9.1 Consensus size: 54
58734 TAGGCACTCG
* * * *
58744 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTCAGCATTAT
1 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
* * *
58798 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTAGTCACTAA
1 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
* * **
58852 GTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCATTTCAACACTAA
1 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
*
58906 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAA
1 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
* *
58960 GTGTGCATTTCATGGAATTCATCCTATGTTGATGAATAACCGTTTCGGCACTAA
1 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
*
59014 GTGTGCATTTGACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
1 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
*
59068 GTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
1 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
* * **
59122 GTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAATCGTTTCAACACTAA
1 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
* * * * * *
59176 GTGTGCATTTTACGGAATTGATCCTATGTGGATGAATAACTGTTTGGGCGCTAT
1 GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
59230 GTGTGC
1 GTGTGC
59236 TAAAATGTTA
Statistics
Matches: 399, Mismatches: 39, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 399 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (54 bp):
GTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAA
Found at i:59299 original size:59 final size:59
Alignment explanation
Indices: 59219--59389 Score: 229
Period size: 59 Copynumber: 2.9 Consensus size: 59
59209 GAATAACTGT
* * *
59219 TTGGGCGCTATGTGTGCTAAAATGTTAAGAAATTCATAATAAGTGTATGAATTTCCGTA
1 TTGGGCACTATGTGTGATAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
59278 TTGGGCACTATGTGTGATAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
1 TTGGGCACTATGTGTGATAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
* * * * * * *
59337 TTAGGCACTTTATGTGCA-AAAA-GATAAGAAACTAATACTAAGGGTATGAATTT
1 TTGGGCACTATGTGTG-ATAAAATGTTAAGAAATTCATACTAAGTGTATGAATTT
59390 TCACATGGGA
Statistics
Matches: 101, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
58 27 0.27
59 73 0.72
60 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (59 bp):
TTGGGCACTATGTGTGATAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
Found at i:61273 original size:15 final size:15
Alignment explanation
Indices: 61249--61285 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
61239 CATGGGGAAA
*
61249 TGAATCCTCTCAAAT
1 TGAATTCTCTCAAAT
*
61264 TGAATTCTCTCGAAT
1 TGAATTCTCTCAAAT
61279 TGAATTC
1 TGAATTC
61286 AATCTGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (15 bp):
TGAATTCTCTCAAAT
Found at i:63122 original size:30 final size:32
Alignment explanation
Indices: 63069--63133 Score: 116
Period size: 30 Copynumber: 2.1 Consensus size: 32
63059 CATCTTTGAC
63069 TTTTAGAAGATGATAATGGTTAGGTGTCTTGG
1 TTTTAGAAGATGATAATGGTTAGGTGTCTTGG
63101 TTTT-GAAGATGATAA-GGTTAGGTGTCTTGG
1 TTTTAGAAGATGATAATGGTTAGGTGTCTTGG
63131 TTT
1 TTT
63134 AATGGTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 18 0.55
31 11 0.33
32 4 0.12
ACGTcount: A:0.23, C:0.03, G:0.31, T:0.43
Consensus pattern (32 bp):
TTTTAGAAGATGATAATGGTTAGGTGTCTTGG
Done.