Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000979.1 Hibiscus syriacus cultivar Beakdansim tig00001956_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: 117841
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1604 original size:21 final size:21
Alignment explanation
Indices: 1580--1627 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1570 CATGTGTATG
1580 TATTTTTAATAAAA-TTTATAT
1 TATTTTTAATAAAATTTTAT-T
* *
1601 TATTTTTCATATAATTTTATT
1 TATTTTTAATAAAATTTTATT
1622 TATTTT
1 TATTTT
1628 CCTTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTTTTAATAAAATTTTATT
Found at i:5465 original size:19 final size:20
Alignment explanation
Indices: 5431--5480 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5421 CAGAATGTTT
**
5431 AAAAGTATCGGTACTTGTA-
1 AAAAGTATCGAAACTTGTAC
* *
5450 TAAAGTATCGAAACTTTTAC
1 AAAAGTATCGAAACTTGTAC
5470 AAAAGTATCGA
1 AAAAGTATCGA
5481 TACTCTTGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
AAAAGTATCGAAACTTGTAC
Found at i:11838 original size:17 final size:17
Alignment explanation
Indices: 11795--11846 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
11785 TATACAGTAG
*
11795 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
11812 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
11827 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
11844 AAA
1 AAA
11847 TTTGTTCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:14531 original size:3 final size:3
Alignment explanation
Indices: 14512--14552 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
14502 CCTAAAGCCA
*
14512 ATC ACC ATC ATC AATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC -ATC ATC ATC ATC ATC ATC ATC ATC ATC A
14553 AATGGCCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.37, C:0.34, G:0.00, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:17256 original size:18 final size:19
Alignment explanation
Indices: 17233--17275 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
17223 AAAAAGTCAC
17233 TTTAATAAAGTTCTCTA-T
1 TTTAATAAAGTTCTCTACT
* *
17251 TTTAATAAATTTTTCTACT
1 TTTAATAAAGTTCTCTACT
17270 TTTAAT
1 TTTAAT
17276 CAAACTAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTAATAAAGTTCTCTACT
Found at i:20945 original size:20 final size:19
Alignment explanation
Indices: 20883--20958 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 19
20873 GATACTCAAA
* *
20883 AGGGTATCAATACTTGACCT
1 AGGGTATCGATA-TTGACTT
*
20903 AGTGTA-CTGATATTG-CATGT
1 AGGGTATC-GATATTGAC-T-T
20923 AGGGTATCGATACTTGACTT
1 AGGGTATCGATA-TTGACTT
20943 AGGGTATCGATATTGA
1 AGGGTATCGATATTGA
20959 GAAGGAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
18 1 0.02
19 8 0.17
20 31 0.67
21 5 0.11
22 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (19 bp):
AGGGTATCGATATTGACTT
Found at i:23362 original size:13 final size:13
Alignment explanation
Indices: 23344--23368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23334 GATCACATTT
23344 TATTTTTATTTTA
1 TATTTTTATTTTA
23357 TATTTTTATTTT
1 TATTTTTATTTT
23369 TTTATATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TATTTTTATTTTA
Found at i:23616 original size:18 final size:18
Alignment explanation
Indices: 23593--23631 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
23583 AACGCCGAGT
23593 GTCACACTCGCCGGTAGC
1 GTCACACTCGCCGGTAGC
23611 GTCACACTCGCCGGTAGC
1 GTCACACTCGCCGGTAGC
23629 GTC
1 GTC
23632 GCGTGAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.18
Consensus pattern (18 bp):
GTCACACTCGCCGGTAGC
Found at i:23760 original size:63 final size:64
Alignment explanation
Indices: 23661--23791 Score: 219
Period size: 63 Copynumber: 2.0 Consensus size: 64
23651 GTCTGTTAAG
* **
23661 AATCGGAAGCTACTAAACGACATGGGAGATTCATTTTCAAT-GGAAAAATCAGTAGCTACTAAT
1 AATCGGAAGCTACTAAACGACATGGGAGAGTCATTTTCAATAAAAAAAATCAGTAGCTACTAAT
23724 AATCGGAAGCTACTAAACGACATGGGAGAGTCATTTTCAATAAAAAAAAATCAGTAGCTACTAAT
1 AATCGGAAGCTACTAAACGACATGGGAGAGTCATTTTCAAT-AAAAAAAATCAGTAGCTACTAAT
23789 AAT
1 AAT
23792 TTAACCTCAC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 40 0.63
65 23 0.37
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (64 bp):
AATCGGAAGCTACTAAACGACATGGGAGAGTCATTTTCAATAAAAAAAATCAGTAGCTACTAAT
Found at i:28174 original size:24 final size:24
Alignment explanation
Indices: 28147--28194 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28137 AAAGAGATTT
28147 CTATCTTTTAACAAATACAGCGAG
1 CTATCTTTTAACAAATACAGCGAG
28171 CTATCTTTTAACAAATACAGCGAG
1 CTATCTTTTAACAAATACAGCGAG
28195 GGATGATCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (24 bp):
CTATCTTTTAACAAATACAGCGAG
Found at i:31653 original size:7 final size:6
Alignment explanation
Indices: 31623--31653 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
31613 TGTAGTTGTG
31623 AAAATT AAAATT AAAATT AAAATT CAAAATT
1 AAAATT AAAATT AAAATT AAAATT -AAAATT
31654 TTAATTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:31776 original size:18 final size:18
Alignment explanation
Indices: 31731--31781 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
31721 GATATTAAAT
*
31731 AAATATTAAATAAATCAAA
1 AAATAATAAA-AAATCAAA
*
31750 AAA-ACATAAAAAATGAAA
1 AAATA-ATAAAAAATCAAA
*
31768 AAATAATAATAAAT
1 AAATAATAAAAAAT
31782 TAAATGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 19 0.70
19 8 0.30
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
AAATAATAAAAAATCAAA
Found at i:31794 original size:22 final size:23
Alignment explanation
Indices: 31760--31804 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
31750 AAAACATAAA
31760 AAATGAAAAAATAATAATAAATT
1 AAATGAAAAAATAATAATAAATT
31783 AAATG-AAAAATAATAATAAATT
1 AAATGAAAAAATAATAATAAATT
31805 GAATAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (23 bp):
AAATGAAAAAATAATAATAAATT
Found at i:33043 original size:19 final size:19
Alignment explanation
Indices: 33019--33055 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33009 TCTATTAAAT
*
33019 TATACGATATGAGCAGTAC
1 TATACGATATGAACAGTAC
*
33038 TATACGGTATGAACAGTA
1 TATACGATATGAACAGTA
33056 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (19 bp):
TATACGATATGAACAGTAC
Found at i:33596 original size:16 final size:16
Alignment explanation
Indices: 33556--33599 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
33546 CATTTCTGTA
*
33556 TATCATATAACACATT
1 TATCATATCACACATT
33572 TATCATATCACACATT
1 TATCATATCACACATT
33588 TATCATATCACA
1 TATCATATCACA
33600 AAGAAACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (16 bp):
TATCATATCACACATT
Found at i:36317 original size:21 final size:20
Alignment explanation
Indices: 36275--36317 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
36265 ATTTCAAGGG
* *
36275 AAAATTGTCTCAAGTGAGAC
1 AAAATTGTCTCAAGGGAAAC
*
36295 AAAATTTGTTTCAAGGGAAAC
1 AAAA-TTGTCTCAAGGGAAAC
36316 AA
1 AA
36318 CCTCAAAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.26
Consensus pattern (20 bp):
AAAATTGTCTCAAGGGAAAC
Found at i:36468 original size:37 final size:37
Alignment explanation
Indices: 36408--36809 Score: 163
Period size: 37 Copynumber: 11.6 Consensus size: 37
36398 GAAACGTTTT
* * * *
36408 CAAAGTTTATGTTTCAAGAGAAACTATCTTAAGGGAGA
1 CAAAATTT-TGTTTCAAGGGAAACTATCTCAAGAGAGA
36446 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
*** * * *
36483 CAAAA-TTCAATTCAAGTGAAACGT-TTTC-A-A-TG-
1 CAAAATTTTGTTTCAAGGGAAAC-TATCTCAAGAGAGA
* *
36515 -----TTTATGTTTCAAGAGAAACTGTCTCAATG-GAGA
1 CAAAATTT-TGTTTCAAGGGAAACTATCTCAA-GAGAGA
* *
36548 CAAAATTTTGTTTCAAGAGAAACTATCTCAATAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
** * * *
36585 CAAAA-TTCATTTCAAGGGAAA-TGTTTTC-A-A-TG-
1 CAAAATTTTGTTTCAAGGGAAACT-ATCTCAAGAGAGA
* * * *
36617 -----TTTATATTTCAAGAGAAACTGTCTCAAGGGAGA
1 CAAAATTT-TGTTTCAAGGGAAACTATCTCAAGAGAGA
36650 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
** * * *
36687 CAAAA-TTCATTTCAAGGGAAA-TGTTTTC-A-A-TG-
1 CAAAATTTTGTTTCAAGGGAAACT-ATCTCAAGAGAGA
* * * * *
36719 -----TTTATTTTTCAAGAGAAACTGTCTTAAGGGAGA
1 CAAAATTT-TGTTTCAAGGGAAACTATCTCAAGAGAGA
*
36752 CAAAATTTTGTTTCAAGGGAAACTATCACAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
**
36789 CAAAA-TTCATTTCAAGGGAAA
1 CAAAATTTTGTTTCAAGGGAAA
36810 TGTTTTCAAT
Statistics
Matches: 268, Mismatches: 55, Indels: 84
0.66 0.14 0.21
Matches are distributed among these distances:
28 7 0.03
29 42 0.16
30 5 0.02
32 3 0.01
33 3 0.01
34 3 0.01
35 5 0.02
36 63 0.24
37 121 0.45
38 16 0.06
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
Found at i:36505 original size:102 final size:102
Alignment explanation
Indices: 36392--36870 Score: 832
Period size: 102 Copynumber: 4.7 Consensus size: 102
36382 ATTTTGTGTC
* * * *
36392 TCAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTTAAGGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
*
36457 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAAT
66 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATT
* * *
36494 TCAAGTGAAACGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAATGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
* *
36559 TTCAAGAGAAACTATCTCAATAGAGACAAAATTCATT
66 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATT
*
36596 TCAAGGGAAATGTTTTCAATGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
36661 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATT
66 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATT
* *
36698 TCAAGGGAAATGTTTTCAATGTTTATTTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
*
36763 TTCAAGGGAAACTATCACAAGAGAGACAAAATTCATT
66 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATT
36800 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
36865 TTCAAG
66 TTCAAG
36871 AGACACAAAA
Statistics
Matches: 358, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 358 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (102 bp):
TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATT
Found at i:36879 original size:87 final size:85
Alignment explanation
Indices: 36780--36956 Score: 300
Period size: 87 Copynumber: 2.1 Consensus size: 85
36770 GAAACTATCA
* * *
36780 CAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCT
1 CAAGAGACACAAAATTCATTTCAAGAGAAATGTTTACAATGTTTATGTTTCAAGAGAAACTGTCT
36845 CAAGGGAGACAAAATTTTGTTT
66 CAAGGGAGAC--AATTTTGTTT
*
36867 CAAGAGACACAAAATTCATTTCAAGAGATATGTTTACAATGTTTATGTTTCAAGAGAAACTGTCT
1 CAAGAGACACAAAATTCATTTCAAGAGAAATGTTTACAATGTTTATGTTTCAAGAGAAACTGTCT
36932 CAAGGGAGACAATTTTGTTT
66 CAAGGGAGACAATTTTGTTT
36952 CAAGA
1 CAAGA
36957 AAAACAATCT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
85 15 0.17
87 71 0.83
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (85 bp):
CAAGAGACACAAAATTCATTTCAAGAGAAATGTTTACAATGTTTATGTTTCAAGAGAAACTGTCT
CAAGGGAGACAATTTTGTTT
Found at i:36915 original size:102 final size:101
Alignment explanation
Indices: 36392--36966 Score: 741
Period size: 102 Copynumber: 5.8 Consensus size: 101
36382 ATTTTGTGTC
* * * *
36392 TCAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTTAAGGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
* * * *
36457 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAAT
66 TTCAAGAGAAACAATCTCAACAGAGACAAAATT-ATT
* * *
36494 TCAAGTGAAACGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAATGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
* *
36559 TTCAAGAGAAACTATCTCAATAGAGACAAAATTCATT
66 TTCAAGAGAAACAATCTCAACAGAGACAAAATT-ATT
*
36596 TCAAGGGAAATGTTTTCAATGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
* * *
36661 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATT
66 TTCAAGAGAAACAATCTCAACAGAGACAAAATT-ATT
* *
36698 TCAAGGGAAATGTTTTCAATGTTTATTTTTCAAGAGAAACTGTCTTAAGGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
* * * *
36763 TTCAAGGGAAACTATCACAAGAGAGACAAAATTCATT
66 TTCAAGAGAAACAATCTCAACAGAGACAAAATT-ATT
36800 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
* *
36865 TTCAAGAG-----A---C-AC----A-AAATTCATT
66 TTCAAGAGAAACAATCTCAACAGAGACAAAATTATT
* * *
36887 TCAAGAGATATGTTTACAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC--AATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
*
36950 TTCAAGAAAAACAATCT
66 TTCAAGAGAAACAATCT
36967 TGAGTGAAAT
Statistics
Matches: 438, Mismatches: 27, Indels: 25
0.89 0.06 0.05
Matches are distributed among these distances:
85 15 0.03
87 55 0.13
88 4 0.01
89 1 0.00
90 1 0.00
93 1 0.00
94 1 0.00
97 1 0.00
102 359 0.82
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (101 bp):
TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT
TTCAAGAGAAACAATCTCAACAGAGACAAAATTATT
Found at i:39085 original size:26 final size:26
Alignment explanation
Indices: 39049--39100 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
39039 CTCAGACACA
39049 CAAATTTCTGTTTCGAGAATGTCCTT
1 CAAATTTCTGTTTCGAGAATGTCCTT
39075 CAAATTTCTGTTTCGAGAATGTCCTT
1 CAAATTTCTGTTTCGAGAATGTCCTT
39101 ACTTTCATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (26 bp):
CAAATTTCTGTTTCGAGAATGTCCTT
Found at i:40915 original size:11 final size:11
Alignment explanation
Indices: 40899--40923 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40889 TGGATAAAAG
40899 ATATTAAATAA
1 ATATTAAATAA
40910 ATATTAAATAA
1 ATATTAAATAA
40921 ATA
1 ATA
40924 AATAAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATTAAATAA
Found at i:43660 original size:23 final size:22
Alignment explanation
Indices: 43619--43662 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
43609 AATAAATGGA
43619 AATAATATGAAAATAAAATAAC
1 AATAATATGAAAATAAAATAAC
* *
43641 AATAATATTGGAAATGAAATAA
1 AATAATA-TGAAAATAAAATAA
43663 AAACAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (22 bp):
AATAATATGAAAATAAAATAAC
Found at i:45939 original size:17 final size:17
Alignment explanation
Indices: 45917--45957 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
45907 ATTTTGTGTC
*
45917 TTTGTTCAGTTTTGTAT
1 TTTGTTAAGTTTTGTAT
45934 TTTGTTAAGTTTTGTAT
1 TTTGTTAAGTTTTGTAT
45951 TTTGTTA
1 TTTGTTA
45958 TGCTATGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.15, C:0.02, G:0.17, T:0.66
Consensus pattern (17 bp):
TTTGTTAAGTTTTGTAT
Found at i:54280 original size:22 final size:22
Alignment explanation
Indices: 54252--54299 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
54242 ATTGTCGAGT
*
54252 AAAATCACGGCAATGAAAGGAG
1 AAAATCACGACAATGAAAGGAG
*
54274 AAAATCACGACAATGAAGGGAG
1 AAAATCACGACAATGAAAGGAG
54296 AAAA
1 AAAA
54300 AAGTGAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.25, T:0.08
Consensus pattern (22 bp):
AAAATCACGACAATGAAAGGAG
Found at i:62060 original size:18 final size:19
Alignment explanation
Indices: 62037--62073 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
62027 CTATAATATT
62037 TTAAAAC-GATTTTGAATA
1 TTAAAACTGATTTTGAATA
*
62055 TTAAAACTGATTTTTAATA
1 TTAAAACTGATTTTGAATA
62074 AATTTAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (19 bp):
TTAAAACTGATTTTGAATA
Found at i:65823 original size:32 final size:32
Alignment explanation
Indices: 65749--65851 Score: 92
Period size: 32 Copynumber: 3.4 Consensus size: 32
65739 TATATCATTC
* * *
65749 AAGATAATTATATGTTATATATCACATCA-TT
1 AAGATAATGATATGATATATATCACATCACCT
* *
65780 CAAGATAATGATATG-----TGTCACGTCACCT
1 -AAGATAATGATATGATATATATCACATCACCT
*
65808 AAGATAATGATATGATATATATCATATCACCT
1 AAGATAATGATATGATATATATCACATCACCT
*
65840 AAGGTAATGATA
1 AAGATAATGATA
65852 AGGAAATAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
27 22 0.39
28 1 0.02
32 34 0.60
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.34
Consensus pattern (32 bp):
AAGATAATGATATGATATATATCACATCACCT
Found at i:71860 original size:43 final size:43
Alignment explanation
Indices: 71795--72015 Score: 184
Period size: 43 Copynumber: 5.2 Consensus size: 43
71785 TTACAACATA
* *
71795 TAGCGGCGTTT--C-AACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGTTTGGCAAACAAACGCCGCAATAGGTGTTGATATT
* *
71835 TAGCGGTGTTTGGCAGAA-AGACGCCGCAATAGGTGTTGATATT
1 TAGCGGCGTTTGGCA-AACAAACGCCGCAATAGGTGTTGATATT
* * *
71878 TAACGGCATTTGGCAAACAAACGCCGCAATAGGTGTTGATGTT
1 TAGCGGCGTTTGGCAAACAAACGCCGCAATAGGTGTTGATATT
* ** * * *
71921 TAGCGGCGTTT-TCTTCACAAACGCCGCAGTAGATGTTGATTTT
1 TAGCGGCGTTTGGC-AAACAAACGCCGCAATAGGTGTTGATATT
* * ** ** *
71964 TACCGACGTTTTTCCTACAAACGCCGCAGA-AGATGTTGATATT
1 TAGCGGCGTTTGGCAAACAAACGCCGCA-ATAGGTGTTGATATT
*
72007 TAGTGGCGT
1 TAGCGGCGT
72016 GATAAAAATG
Statistics
Matches: 147, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
40 10 0.07
42 4 0.03
43 129 0.88
44 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTGGCAAACAAACGCCGCAATAGGTGTTGATATT
Found at i:72501 original size:21 final size:21
Alignment explanation
Indices: 72477--72532 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
72467 GTAACTACTT
72477 CTCTCTCTGCTTCCGCTGCTG
1 CTCTCTCTGCTTCCGCTGCTG
** *
72498 CTCTAGCTGCTTCTGCTGCTG
1 CTCTCTCTGCTTCCGCTGCTG
72519 CTCTCTCTGCTTCC
1 CTCTCTCTGCTTCC
72533 CTTGCTTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.02, C:0.41, G:0.18, T:0.39
Consensus pattern (21 bp):
CTCTCTCTGCTTCCGCTGCTG
Found at i:73532 original size:28 final size:28
Alignment explanation
Indices: 73500--73583 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 28
73490 GTGCACCGTA
73500 AGTATAAATTAGTATTGAATTTATATAG
1 AGTATAAATTAGTATTGAATTTATATAG
** *
73528 AGTATCTATTA-TAATGACA-TTAT-T--
1 AGTATAAATTAGTATTGA-ATTTATATAG
*
73552 A-CATAAATTAGTATTGAATTTATATAG
1 AGTATAAATTAGTATTGAATTTATATAG
73579 AGTAT
1 AGTAT
73584 CTATTATAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
23 7 0.17
24 10 0.24
25 1 0.02
26 1 0.02
27 10 0.24
28 12 0.29
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.43
Consensus pattern (28 bp):
AGTATAAATTAGTATTGAATTTATATAG
Found at i:73563 original size:51 final size:51
Alignment explanation
Indices: 73503--73604 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
73493 CACCGTAAGT
73503 ATAAATTAGTATTGAATTTATATAGAGTATCTATTATAATGACATTATTAC
1 ATAAATTAGTATTGAATTTATATAGAGTATCTATTATAATGACATTATTAC
73554 ATAAATTAGTATTGAATTTATATAGAGTATCTATTATAATGACATTATTAC
1 ATAAATTAGTATTGAATTTATATAGAGTATCTATTATAATGACATTATTAC
73605 CTTAACAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (51 bp):
ATAAATTAGTATTGAATTTATATAGAGTATCTATTATAATGACATTATTAC
Found at i:82463 original size:82 final size:83
Alignment explanation
Indices: 82377--82535 Score: 189
Period size: 83 Copynumber: 1.9 Consensus size: 83
82367 TAATATTGCG
* * * * *
82377 GCGTTTA-TCAAAAAATGCCGTACCATTAAT-ACTCAATAGCGGCGTTTG-TACAAAAACGTCGC
1 GCGTTTATTCAAAAAACGCC--ACAATAAATAACTCAATACCGGCGTTTGTTACAAAAACGCCGC
82439 TAAATGACTACTCTTTTACA
64 TAAATGACTACTCTTTTACA
* * * *
82459 GCGTTTATTGATAAAACGCCACAATAAATAACTCTATACCGGCGTTTGTTCCAAAAACGCCGCTA
1 GCGTTTATTCAAAAAACGCCACAATAAATAACTCAATACCGGCGTTTGTTACAAAAACGCCGCTA
*
82524 AATTACTACTCT
66 AATGACTACTCT
82536 ATTGCGACAT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
81 7 0.11
82 23 0.36
83 34 0.53
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (83 bp):
GCGTTTATTCAAAAAACGCCACAATAAATAACTCAATACCGGCGTTTGTTACAAAAACGCCGCTA
AATGACTACTCTTTTACA
Found at i:84125 original size:57 final size:57
Alignment explanation
Indices: 84057--84171 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
84047 ATATGAAATA
84057 AAACCACTTAAAAAAATTAGGTCCAAGTCTAAC-GTAAAGATGTGCATATGGATAATG
1 AAACCACTTAAAAAAATTAGGTCCAAGTCT-ACTGTAAAGATGTGCATATGGATAATG
* *
84114 AAACCAGTTAAAAAAATTAGGTCCAAGTCTACTGTAAAGATGTGTATATGGATAATG
1 AAACCACTTAAAAAAATTAGGTCCAAGTCTACTGTAAAGATGTGCATATGGATAATG
84171 A
1 A
84172 GCTATGCTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
56 2 0.04
57 53 0.96
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.26
Consensus pattern (57 bp):
AAACCACTTAAAAAAATTAGGTCCAAGTCTACTGTAAAGATGTGCATATGGATAATG
Found at i:85283 original size:22 final size:22
Alignment explanation
Indices: 85204--85271 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
85194 TATTCAATTA
*
85204 AAGCCTTACTGCTAACAAACTC
1 AAGCCTTAATGCTAACAAACTC
85226 AAGCCTTAATGCTAACAAACTC
1 AAGCCTTAATGCTAACAAACTC
85248 AAGCCTTAATGCTAACAAACTC
1 AAGCCTTAATGCTAACAAACTC
85270 AA
1 AA
85272 CCCTAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.22
Consensus pattern (22 bp):
AAGCCTTAATGCTAACAAACTC
Found at i:89748 original size:21 final size:21
Alignment explanation
Indices: 89722--89761 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
89712 CAGAACCCCA
89722 GGGGGGTATCGATTCCCCTGT
1 GGGGGGTATCGATTCCCCTGT
*
89743 GGGGGGTATCGGTTCCCCT
1 GGGGGGTATCGATTCCCCT
89762 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.25, G:0.40, T:0.28
Consensus pattern (21 bp):
GGGGGGTATCGATTCCCCTGT
Found at i:89797 original size:21 final size:21
Alignment explanation
Indices: 89742--89805 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
89732 GATTCCCCTG
*
89742 TGGGGGGTATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTT-CCC-TCA
**
89765 AAGGGGGAATCGGTTCCCTCA
1 TGGGGGGAATCGGTTCCCTCA
* *
89786 TGGGGGGGATCGATTCCCTC
1 TGGGGGGAATCGGTTCCCTC
89806 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 19 0.56
22 3 0.09
23 12 0.35
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (21 bp):
TGGGGGGAATCGGTTCCCTCA
Found at i:93649 original size:22 final size:21
Alignment explanation
Indices: 93607--93646 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
93597 GAGTTTGTTT
*
93607 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
93628 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
93647 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:100768 original size:22 final size:21
Alignment explanation
Indices: 100726--100765 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
100716 GAGTTTGTTT
*
100726 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
100747 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
100766 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:111948 original size:3 final size:3
Alignment explanation
Indices: 111940--111980 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
111930 CATTTGCTTA
111940 TAT TAT TA- TAT TAT TAT TAT TA- TAT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
111981 AATAATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:111950 original size:8 final size:8
Alignment explanation
Indices: 111937--111978 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
111927 TCTCATTTGC
111937 TTATATTA
1 TTATATTA
111945 TTATATTA
1 TTATATTA
111953 -T-TATTA
1 TTATATTA
111959 TTATATTA
1 TTATATTA
111967 -TATTATTA
1 TTA-TATTA
111975 TTAT
1 TTAT
111979 TAAATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 5 0.17
7 4 0.13
8 19 0.63
9 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATATTA
Found at i:111956 original size:11 final size:11
Alignment explanation
Indices: 111940--111978 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
111930 CATTTGCTTA
111940 TATTATTATAT
1 TATTATTATAT
111951 TATTA-T-TAT
1 TATTATTATAT
111960 TA-TATTATAT
1 TATTATTATAT
111970 TATTATTAT
1 TATTATTAT
111979 TAAATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 2 0.08
9 6 0.24
10 6 0.24
11 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATTATAT
Found at i:111965 original size:19 final size:19
Alignment explanation
Indices: 111943--111980 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
111933 TTGCTTATAT
111943 TATTATATTATTATTATTA
1 TATTATATTATTATTATTA
111962 TATTATATTATTATTATTA
1 TATTATATTATTATTATTA
111981 AATAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTATATTATTATTATTA
Found at i:116114 original size:14 final size:14
Alignment explanation
Indices: 116076--116129 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
116066 ATTTTAAATA
*
116076 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
116090 TTTTACATTTGCAT
1 ATTTACATTTGCAT
*
116104 ATTTACATTTGGAAT
1 ATTTACATTT-GCAT
*
116119 CTTTACATTTG
1 ATTTACATTTG
116130 TATTTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:116125 original size:15 final size:15
Alignment explanation
Indices: 116091--116129 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
116081 CATTTACATT
*
116091 TTTACATTT-GCATA
1 TTTACATTTGGAATA
*
116105 TTTACATTTGGAATC
1 TTTACATTTGGAATA
116120 TTTACATTTG
1 TTTACATTTG
116130 TATTTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGAATA
Done.