Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000840.1 Hibiscus syriacus cultivar Beakdansim tig00001622_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: 76801
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3780 original size:12 final size:13
Alignment explanation
Indices: 3759--3788 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3749 AAAATCGATA
3759 AAAAAGGAAAAAT
1 AAAAAGGAAAAAT
3772 AAAAA-GAAAAAT
1 AAAAAGGAAAAAT
3784 AAAAA
1 AAAAA
3789 CAGAGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (13 bp):
AAAAAGGAAAAAT
Found at i:3797 original size:17 final size:15
Alignment explanation
Indices: 3756--3814 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 15
3746 AAGAAAATCG
*
3756 ATAAAAAAG-GAAAA
1 ATAAAACAGAGAAAA
3770 AT-AAA-A-AGAAAA
1 ATAAAACAGAGAAAA
3782 ATAAAAACAGAGGAAAA
1 AT-AAAACAGA-GAAAA
*
3799 GTAAAACAGAGAAAA
1 ATAAAACAGAGAAAA
3814 A
1 A
3815 AATGGTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
14 5 0.14
15 6 0.16
16 9 0.24
17 6 0.16
ACGTcount: A:0.75, C:0.03, G:0.15, T:0.07
Consensus pattern (15 bp):
ATAAAACAGAGAAAA
Found at i:5307 original size:2 final size:2
Alignment explanation
Indices: 5300--5338 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5290 GCTTGTCAAT
5300 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5339 TATTTTTCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10903 original size:18 final size:19
Alignment explanation
Indices: 10868--10904 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
10858 CACAGAATGT
10868 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
10888 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
10905 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:15795 original size:21 final size:21
Alignment explanation
Indices: 15752--15795 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
15742 TGATGAACTA
**
15752 TGGCTTTATAATAGAGCTGCT
1 TGGCTTTATAATAGAGCACCT
* *
15773 TGGCTTTGTAATGGAGCACCT
1 TGGCTTTATAATAGAGCACCT
15794 TG
1 TG
15796 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.36
Consensus pattern (21 bp):
TGGCTTTATAATAGAGCACCT
Found at i:19499 original size:10 final size:10
Alignment explanation
Indices: 19484--19509 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19474 TATTTAATTA
19484 TTTTTTTTCT
1 TTTTTTTTCT
19494 TTTTTTTTCT
1 TTTTTTTTCT
19504 TTTTTT
1 TTTTTT
19510 CCATGTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:19693 original size:14 final size:15
Alignment explanation
Indices: 19676--19722 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
19666 CATTTTTCAA
19676 TATTTAATTTT-TTT
1 TATTTAATTTTATTT
*
19690 TATTTCATTTTATTTT
1 TATTTAATTTTA-TTT
*
19706 TATTCCAATTTTATTT
1 TATT-TAATTTTATTT
19722 T
1 T
19723 TGGTTTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.37
16 11 0.41
17 6 0.22
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTAATTTTATTT
Found at i:19705 original size:16 final size:17
Alignment explanation
Indices: 19686--19723 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
19676 TATTTAATTT
*
19686 TTTTTATTTC-ATTTTA
1 TTTTTATTCCAATTTTA
19702 TTTTTATTCCAATTTTA
1 TTTTTATTCCAATTTTA
19719 TTTTT
1 TTTTT
19724 GGTTTGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTATTCCAATTTTA
Found at i:19705 original size:17 final size:18
Alignment explanation
Indices: 19685--19723 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
19675 ATATTTAATT
*
19685 TTTTTTATTTC-ATTTTA
1 TTTTTTATTCCAATTTTA
19702 -TTTTTATTCCAATTTTA
1 TTTTTTATTCCAATTTTA
19719 TTTTT
1 TTTTT
19724 GGTTTGATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 9 0.47
17 6 0.32
18 4 0.21
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTATTCCAATTTTA
Found at i:19829 original size:29 final size:29
Alignment explanation
Indices: 19797--19857 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
19787 ATTATTATTA
*
19797 TTTATCTCATA-TTTTTTCCTTTTTCCCTT
1 TTTATCTCATATTTTTTTCCTCTTT-CCTT
* **
19826 TTTATTTTTTATTTTTTTCCTCTTTCCTT
1 TTTATCTCATATTTTTTTCCTCTTTCCTT
19855 TTT
1 TTT
19858 GATTTATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (29 bp):
TTTATCTCATATTTTTTTCCTCTTTCCTT
Found at i:19844 original size:30 final size:30
Alignment explanation
Indices: 19808--19870 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
19798 TTATCTCATA
* *
19808 TTTTTTCCTTTTTCCCTTTTT-ATTTTTTAT
1 TTTTTTCCTCTTT-CCTTTTTGATTTATTAT
19838 TTTTTTCCTCTTTCCTTTTTGATTTATTAT
1 TTTTTTCCTCTTTCCTTTTTGATTTATTAT
19868 TTT
1 TTT
19871 GGTATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.75
Consensus pattern (30 bp):
TTTTTTCCTCTTTCCTTTTTGATTTATTAT
Found at i:23023 original size:27 final size:25
Alignment explanation
Indices: 22993--23044 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
22983 TAATTAAAGA
22993 AAAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAA-CAAAG-GAAAAT
23020 AAAAAGAGAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAACAAAGGAAAAT
23045 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (25 bp):
AAAAAGAGAAAAAACAAAGGAAAAT
Found at i:23025 original size:13 final size:13
Alignment explanation
Indices: 22995--23043 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
22985 ATTAAAGAAA
22995 AAAGAGAAAAAAGC
1 AAAGAGAAAAAA-C
23009 AAAGAGAAAATAA-
1 AAAGAGAAAA-AAC
23022 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
23035 AAAG-GAAAA
1 AAAGAGAAAA
23044 TTGAAGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
14 10 0.30
15 2 0.06
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:23233 original size:69 final size:69
Alignment explanation
Indices: 23115--23252 Score: 213
Period size: 69 Copynumber: 2.0 Consensus size: 69
23105 AGATTCAACT
*
23115 ATGAAATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAAATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
23180 TCAA
66 TCAA
* * * * * *
23184 ATGAGATTGATCAAGCACAATCATTTCTGAATTATTGAATCACTCCACTCGAAGATCATGGAGCA
1 ATGAAATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
23249 TCAA
66 TCAA
23253 GAGAGAGACA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (69 bp):
ATGAAATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TCAA
Found at i:24203 original size:30 final size:31
Alignment explanation
Indices: 24154--24259 Score: 133
Period size: 32 Copynumber: 3.4 Consensus size: 31
24144 AGGAACAATG
*
24154 AGGGCATCTTTGAAGATTTAACATCAAATATT
1 AGGGCATTTTTG-AGATTTAACATCAAATATT
*
24186 AGGGCATTTTT-AGATTTAACATCAAATGTT
1 AGGGCATTTTTGAGATTTAACATCAAATATT
* * *
24216 GGGGCATTTTTTGAGATTCAACATCGAATATT
1 AGGGCA-TTTTTGAGATTTAACATCAAATATT
*
24248 AGGGCATCTTTG
1 AGGGCATTTTTG
24260 GGAATTCAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
30 23 0.36
31 10 0.16
32 31 0.48
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (31 bp):
AGGGCATTTTTGAGATTTAACATCAAATATT
Found at i:24267 original size:32 final size:32
Alignment explanation
Indices: 24154--24272 Score: 127
Period size: 32 Copynumber: 3.8 Consensus size: 32
24144 AGGAACAATG
* * *
24154 AGGGCATCTTTGAAGATTTAACATCAAATATT
1 AGGGCATTTTTGGAGATTCAACATCAAATATT
* *
24186 AGGGCATTTTT--AGATTTAACATCAAATGTT
1 AGGGCATTTTTGGAGATTCAACATCAAATATT
* * *
24216 GGGGCATTTTTTGAGATTCAACATCGAATATT
1 AGGGCATTTTTGGAGATTCAACATCAAATATT
*
24248 AGGGCATCTTTGG-GAATTCAACATC
1 AGGGCATTTTTGGAG-ATTCAACATC
24273 CTGATGTAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
30 28 0.37
31 1 0.01
32 46 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
AGGGCATTTTTGGAGATTCAACATCAAATATT
Found at i:24975 original size:106 final size:105
Alignment explanation
Indices: 24819--25183 Score: 372
Period size: 106 Copynumber: 3.4 Consensus size: 105
24809 ACCACCTACG
* *
24819 ATTTCAACTCCA-AGACGAAGGATATCATGCCACTCGAGACAACACAAGTTCAACTCAACAACGA
1 ATTTCAACTTCACA-ACGAAGGATATTA-G--ACTCGAGACAACACAAGTTCAACTC-ACAACGA
** *
24883 AGGGACAACTGGTTGTCTACAAACAATTTCCCAATTTCAGAGCCA
61 AGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
24928 ATTTCAACTTCACAACGAAGGATATTAGACTCGAGACAACACAAGTTCAATTTCACAATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTAGACTCGAGACAACACAAGTTCAA-CTCACAACGAAGGG
* * *
24993 ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCGGAGACA
65 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * * * * * *
25034 ATTTTAACTTCACAGCGAAGGATATTGGACTTGAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTAGACTCGAGACAACACAAGTTCAAC-TCACAACGAAGGG
* * * * ** * *
25099 GCGGCTAGCTATCAACAAACAATTTCTTAGTTCCAGAGCCA
65 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* ** * * * *
25140 ATTTTAACTTCACGGCGGAGGATATTGGACTCGAAACAATACAA
1 ATTTCAACTTCACAACGAAGGATATTAGACTCGAGACAACACAA
25184 TTTACTTGGA
Statistics
Matches: 217, Mismatches: 36, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
106 190 0.88
107 2 0.01
108 1 0.00
109 23 0.11
110 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTAGACTCGAGACAACACAAGTTCAACTCACAACGAAGGGA
CGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
Found at i:25519 original size:22 final size:23
Alignment explanation
Indices: 25488--25545 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
25478 GATTGAGATA
*
25488 GTTTCTCTTGAAACG-AAATTTT
1 GTTTCCCTTGAAACGAAAATTTT
25510 GTTTCCCTTGAAA-GAAAATTTT
1 GTTTCCCTTGAAACGAAAATTTT
* *
25532 GTCTCCCTTAAAAC
1 GTTTCCCTTGAAAC
25546 ATAAACATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (23 bp):
GTTTCCCTTGAAACGAAAATTTT
Found at i:25617 original size:65 final size:65
Alignment explanation
Indices: 25535--25674 Score: 226
Period size: 65 Copynumber: 2.2 Consensus size: 65
25525 AAATTTTGTC
* *
25535 TCCCTTAAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTT
1 TCCCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTT
* * * *
25600 TCCCTTGAAACATAAACATTTAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTT
1 TCCCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTT
25665 TCCCTTGAAA
1 TCCCTTGAAA
25675 TAAAATTTTG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (65 bp):
TCCCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTT
Found at i:25619 original size:174 final size:167
Alignment explanation
Indices: 25415--25778 Score: 485
Period size: 174 Copynumber: 2.1 Consensus size: 167
25405 TTTGTCTCCC
* *
25415 TTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTGGAAATGAATTTTATCTCGA
1 TTGAGATAGTTTCCCTTGAAACATAAACATTGAAAACATTTCCCTGGAAATAAATTTTATCTCGA
* * * *
25480 TTGAGATAGTTTCTCTTGAAACGAAATTTTGTTTCCCTTGAAAGAAAATTTTGTCTCCCTTAAAA
66 TTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG--AG-AAA-GTT-TCT--CTTAAAA
25545 CATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGA
124 CATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGA
* * *
25589 TTGAGATAGTTTCCCTTGAAACATAAACATTTAAAACATTTCCCTTGAAATAAATTTTATCTCGC
1 TTGAGATAGTTTCCCTTGAAACATAAACATTGAAAACATTTCCCTGGAAATAAATTTTATCTCGA
* * * * *
25654 TTGGGGTAGTTTCCCTTGAAATAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
66 TTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAAAGTTTCTCTTAAAACATAAAC
* * * **
25719 ATTGAAAACATTTCCTTTGAAATTAATTTTGTCTCTC
131 ATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGA
*
25756 TTAAGATAGTTTCCCTTGAAACA
1 TTGAGATAGTTTCCCTTGAAACA
25779 AAATTTTGTA
Statistics
Matches: 170, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
167 67 0.39
169 3 0.02
170 2 0.01
171 2 0.01
172 2 0.01
174 94 0.55
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (167 bp):
TTGAGATAGTTTCCCTTGAAACATAAACATTGAAAACATTTCCCTGGAAATAAATTTTATCTCGA
TTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAAAGTTTCTCTTAAAACATAAAC
ATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGA
Found at i:25674 original size:36 final size:37
Alignment explanation
Indices: 25627--25711 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
25617 ATTTAAAACA
* * **
25627 TTTCCCTTGAAAT-AAATTTTATCTCGCTTGGGGTAG
1 TTTCCCTTGAAATAAAATTTTATCTCCCTTGAGACAG
*
25663 TTTCCCTTGAAATAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAATAAAATTTTATCTCCCTTGAGACAG
*
25700 TTTCTCTTGAAA
1 TTTCCCTTGAAA
25712 CATAAACATT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 13 0.31
37 29 0.69
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAATAAAATTTTATCTCCCTTGAGACAG
Found at i:25766 original size:102 final size:102
Alignment explanation
Indices: 25562--25813 Score: 328
Period size: 102 Copynumber: 2.5 Consensus size: 102
25552 ATTGAAAACA
* * ** * *
25562 TTTCCCTTGAAAT-GAATTTTATCTCGATTGAGATAGTTTCCCTTGAAACATAAACATTTAAAAC
1 TTTCCCTTGAAATAAAATTTTGTCTCCCTTGAGAAAGTTTCCCTTGAAACATAAACATTGAAAAC
** *
25626 ATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAG
66 ATTTCCCTTGAAATAAATTTTATCTCGCTTAAGATAG
* *
25663 TTTCCCTTGAAATAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAATAAAATTTTGTCTCCCTTGAGAAAGTTTCCCTTGAAACATAAACATTGAAAAC
* * * *
25728 ATTTCCTTTGAAATTAATTTTGTCTCTCTTAAGATAG
66 ATTTCCCTTGAAATAAATTTTATCTCGCTTAAGATAG
* *
25765 TTTCCCTTGAAACAAAATTTTGTATCCCTTGA-AAATGTTTCCCTTGAAA
1 TTTCCCTTGAAATAAAATTTTGTCTCCCTTGAGAAA-GTTTCCCTTGAAA
25814 ACGTTTCCCT
Statistics
Matches: 131, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
101 15 0.11
102 116 0.89
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (102 bp):
TTTCCCTTGAAATAAAATTTTGTCTCCCTTGAGAAAGTTTCCCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATAAATTTTATCTCGCTTAAGATAG
Found at i:25809 original size:15 final size:15
Alignment explanation
Indices: 25789--25828 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
25779 AAATTTTGTA
*
25789 TCCCTTGAAAATGTT
1 TCCCTTGAAAACGTT
25804 TCCCTTGAAAACGTT
1 TCCCTTGAAAACGTT
25819 TCCCTTGAAA
1 TCCCTTGAAA
25829 CATAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (15 bp):
TCCCTTGAAAACGTT
Found at i:25916 original size:37 final size:37
Alignment explanation
Indices: 25866--25968 Score: 172
Period size: 36 Copynumber: 2.8 Consensus size: 37
25856 AAAACGAGTT
*
25866 TTGAGATAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGATAGTTTCCCTTGAAACAAAATCTTATCTCTC
* *
25903 TTGAGAAAGTTTCCCTTGAAAC-AAATTTTATCTCTC
1 TTGAGATAGTTTCCCTTGAAACAAAATCTTATCTCTC
25939 TTGAGATAGTTTCCCTTGAAACAAAATCTT
1 TTGAGATAGTTTCCCTTGAAACAAAATCTT
25969 TGAATATCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 33 0.55
37 27 0.45
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (37 bp):
TTGAGATAGTTTCCCTTGAAACAAAATCTTATCTCTC
Found at i:26044 original size:37 final size:36
Alignment explanation
Indices: 25990--26080 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 36
25980 TCCTTTAAAC
* * * *
25990 AAATTTCGTCTCCCTTGAGACAGTTTCTTTTAGAACT
1 AAATTTTGTCTCTCTTGAGACAGATTCTTTT-GAAAT
* *
26027 AAGTTTTGTCTCTCTTGAGATAGATTCTTTTGAAAT
1 AAATTTTGTCTCTCTTGAGACAGATTCTTTTGAAAT
*
26063 AAATTTTGTCCCTCTTGA
1 AAATTTTGTCTCTCTTGA
26081 TTTAGTTTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
36 20 0.43
37 26 0.57
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (36 bp):
AAATTTTGTCTCTCTTGAGACAGATTCTTTTGAAAT
Found at i:26096 original size:36 final size:36
Alignment explanation
Indices: 25990--26097 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
25980 TCCTTTAAAC
* * *
25990 AAATTTCGTCTCC-CTTGAGACAGTTTCTTTTAGAACT
1 AAATTTTGTC-CCTCTTGAGATAGTTTCTTTT-GAAAT
* * *
26027 AAGTTTTGTCTCTCTTGAGATAGATTCTTTTGAAAT
1 AAATTTTGTCCCTCTTGAGATAGTTTCTTTTGAAAT
** *
26063 AAATTTTGTCCCTCTTGATTTAGTTTCTCTTGAAA
1 AAATTTTGTCCCTCTTGAGATAGTTTCTTTTGAAA
26098 CACAAAAAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
36 34 0.59
37 24 0.41
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (36 bp):
AAATTTTGTCCCTCTTGAGATAGTTTCTTTTGAAAT
Found at i:26145 original size:38 final size:39
Alignment explanation
Indices: 26097--26170 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
26087 TTCTCTTGAA
*
26097 ACACAAAAAAAACC-TCGAAATTGTTTATCTTGAAATAC
1 ACACAAAAAAAACCTTCGAAAATGTTTATCTTGAAATAC
* * *
26135 ACACACAAAAAACCTTTGAAAATGTTTCTCTTGAAA
1 ACACAAAAAAAACCTTCGAAAATGTTTATCTTGAAA
26171 CACCAAACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 13 0.42
39 18 0.58
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (39 bp):
ACACAAAAAAAACCTTCGAAAATGTTTATCTTGAAATAC
Found at i:26312 original size:84 final size:85
Alignment explanation
Indices: 26181--26338 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 85
26171 CACCAAACCC
* * * ** *
26181 TCGAGTTCGATTACACTCAGCTTCGAGGGCACATTATTTACAACATAACTCAAGGCTAGAAGGGT
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGAAAGAAGGGC
26246 TATCTATCACCAAAAGACCT
66 TATCTATCACCAAAAGACCT
** * *
26266 TCGAGTTCGACTATGCTCAGC-TCTAAGGCACATCATTTACAGCATAACTCAAGGAAAGAAGGGC
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGAAAGAAGGGC
26330 TATCTATCA
66 TATCTATCA
26339 ATAAAATTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
84 45 0.71
85 18 0.29
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (85 bp):
TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAACATAACTCAAGGAAAGAAGGGC
TATCTATCACCAAAAGACCT
Found at i:27442 original size:16 final size:17
Alignment explanation
Indices: 27423--27459 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
27413 ATATTTAATT
*
27423 TTTTTATTTC-ATTTTA
1 TTTTTATTCCAATTTTA
27439 TTTTTATTCCAATTTTA
1 TTTTTATTCCAATTTTA
27456 TTTT
1 TTTT
27460 GGTTTGATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTCCAATTTTA
Found at i:27442 original size:17 final size:18
Alignment explanation
Indices: 27422--27459 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
27412 AATATTTAAT
*
27422 TTTTTTATTTC-ATTTTA
1 TTTTTTATTCCAATTTTA
27439 -TTTTTATTCCAATTTTA
1 TTTTTTATTCCAATTTTA
27456 TTTT
1 TTTT
27460 GGTTTGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 9 0.50
17 6 0.33
18 3 0.17
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTATTCCAATTTTA
Found at i:31654 original size:18 final size:18
Alignment explanation
Indices: 31631--31679 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
31621 ACTGAATATT
*
31631 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
31649 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
31667 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
31680 AAATGATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:50809 original size:45 final size:45
Alignment explanation
Indices: 50729--50827 Score: 101
Period size: 45 Copynumber: 2.2 Consensus size: 45
50719 AACTGGTATA
* * *
50729 ATTGACCTATGTGATTAAATGAAATAGTGAGATAAGTTAAATATT
1 ATTGATCTATATGATTAAATGAAATAGTGAGATAAGCTAAATATT
** * ** *
50774 ATTGATCTATATGATTTCATGAGAATA-TGATATAAGCTATGTGTT
1 ATTGATCTATATGATTAAATGA-AATAGTGAGATAAGCTAAATATT
50819 ATTGATCTA
1 ATTGATCTA
50828 GGAGATTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
45 40 0.91
46 4 0.09
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.39
Consensus pattern (45 bp):
ATTGATCTATATGATTAAATGAAATAGTGAGATAAGCTAAATATT
Found at i:50913 original size:31 final size:31
Alignment explanation
Indices: 50859--50928 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
50849 TATAAGCTAG
* * * **
50859 GTGATAATGATCTATGTGCTTATATGTTTAT
1 GTGATAATGAACTACGTGATTATATGAATAT
*
50890 GTGATATTGAACTACGTGATTATATGAATAT
1 GTGATAATGAACTACGTGATTATATGAATAT
50921 GTGA-AATG
1 GTGATAATG
50929 TGAAAATGGT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.41
Consensus pattern (31 bp):
GTGATAATGAACTACGTGATTATATGAATAT
Found at i:51098 original size:23 final size:23
Alignment explanation
Indices: 51072--51159 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
51062 TTTGGGATAA
*
51072 TTCTACGTGGTCCTTCGGTACAT
1 TTCTATGTGGTCCTTCGGTACAT
* *
51095 TTCTATGCGGTCCTTCGAG-ACAA
1 TTCTATGTGGTCCTTCG-GTACAT
* * *
51118 TACTATGTGGTCTTTCGGGACAT
1 TTCTATGTGGTCCTTCGGTACAT
51141 TTCTATGTGG-CGCTTCGGT
1 TTCTATGTGGTC-CTTCGGT
51160 GCAATGTCTA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.04
23 49 0.94
24 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGTACAT
Found at i:54956 original size:2 final size:2
Alignment explanation
Indices: 54949--54988 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
54939 TAAAGCACAT
54949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54989 AAGTTACTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57090 original size:23 final size:24
Alignment explanation
Indices: 57064--57124 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
57054 TAAATCCATA
57064 TATATTAACTTAAAAAATAT-TTT
1 TATATTAACTTAAAAAATATATTT
* **
57087 TATATTGACTTATTAAATATATTT
1 TATATTAACTTAAAAAATATATTT
*
57111 TATTATTAGCTTAA
1 TA-TATTAACTTAA
57125 TTTAAAAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 17 0.57
24 5 0.17
25 8 0.27
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (24 bp):
TATATTAACTTAAAAAATATATTT
Found at i:58477 original size:20 final size:20
Alignment explanation
Indices: 58449--58505 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
58439 GTTAAAAAAT
58449 AAAAAATATTTTTTATTAAA
1 AAAAAATATTTTTTATTAAA
*
58469 AATAAATATATTATTT-TTAAA
1 AA-AAA-ATATTTTTTATTAAA
*
58490 AAAAAACACTTTTTTA
1 AAAAAATA-TTTTTTA
58506 AAAAAATCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.07
20 10 0.33
21 10 0.33
22 8 0.27
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAAATATTTTTTATTAAA
Found at i:58479 original size:22 final size:22
Alignment explanation
Indices: 58443--58495 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
58433 TTAAAAGTTA
*
58443 AAAAATAAAAAATATTTTTTATT
1 AAAAATAAAAAATATTATTT-TT
*
58466 AAAAAT-AAATATATTATTTTT
1 AAAAATAAAAAATATTATTTTT
58487 AAAAA-AAAA
1 AAAAATAAAA
58496 CACTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.37
22 11 0.41
23 6 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAATAAAAAATATTATTTTT
Done.