Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003564.1 Hibiscus syriacus cultivar Beakdansim tig00007526_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: 70727
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1564 original size:17 final size:18
Alignment explanation
Indices: 1528--1568 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1518 ATATTATGTA
*
1528 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
1546 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
1563 TTTACT
1 TTTACT
1569 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:3568 original size:3 final size:3
Alignment explanation
Indices: 3560--3611 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
3550 CAGGATGAAA
* *
3560 ACG ACG ACG ACG ACG ATG ACG ACG ACG ACG ATG ACG ACG ACG ACG ACG
1 ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG
3608 ACG A
1 ACG A
3612 TGGTGATGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.35, C:0.29, G:0.33, T:0.04
Consensus pattern (3 bp):
ACG
Found at i:10794 original size:16 final size:16
Alignment explanation
Indices: 10773--10826 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
10763 TTTAGAAGAA
*
10773 TTAAATATTAAATAAT
1 TTAAATATTAAATGAT
*
10789 TTAAATTTTAAATGAT
1 TTAAATATTAAATGAT
*
10805 TTAAATATTGAATGAT
1 TTAAATATTAAATGAT
10821 TTAAAT
1 TTAAAT
10827 GTTTTGTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (16 bp):
TTAAATATTAAATGAT
Found at i:10827 original size:9 final size:9
Alignment explanation
Indices: 10780--10827 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
10770 GAATTAAATA
*
10780 TTAAATAAT
1 TTAAATGAT
10789 TTAAAT--T
1 TTAAATGAT
10796 TTAAATGAT
1 TTAAATGAT
10805 TTAAAT-A-
1 TTAAATGAT
*
10812 TTGAATGAT
1 TTAAATGAT
10821 TTAAATG
1 TTAAATG
10828 TTTTGTATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 12 0.36
8 2 0.06
9 19 0.58
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (9 bp):
TTAAATGAT
Found at i:17579 original size:10 final size:10
Alignment explanation
Indices: 17560--17599 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
17550 CATTTAAATG
17560 ATAAACGAAC
1 ATAAACGAAC
*
17570 ATAAATGAAC
1 ATAAACGAAC
*
17580 GTAAACGAAC
1 ATAAACGAAC
*
17590 ACAAACGAAC
1 ATAAACGAAC
17600 GAACATAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:17586 original size:20 final size:20
Alignment explanation
Indices: 17561--17600 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17551 ATTTAAATGA
* *
17561 TAAACGAACATAAATGAACG
1 TAAACGAACACAAACGAACG
17581 TAAACGAACACAAACGAACG
1 TAAACGAACACAAACGAACG
17601 AACATAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.10
Consensus pattern (20 bp):
TAAACGAACACAAACGAACG
Found at i:17616 original size:27 final size:27
Alignment explanation
Indices: 17581--17657 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
17571 TAAATGAACG
* *
17581 TAAACGAACACAAACGAACGAACATAA
1 TAAATGAACATAAACGAACGAACATAA
* *
17608 TAAATGAACATAAACAAATGAACATAA
1 TAAATGAACATAAACGAACGAACATAA
17635 TAAATGAACATAAACGAAC-AACA
1 TAAATGAACATAAACGAACGAACA
17658 CAAACAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 4 0.09
27 40 0.91
ACGTcount: A:0.61, C:0.17, G:0.09, T:0.13
Consensus pattern (27 bp):
TAAATGAACATAAACGAACGAACATAA
Found at i:17618 original size:13 final size:13
Alignment explanation
Indices: 17600--17647 Score: 78
Period size: 13 Copynumber: 3.6 Consensus size: 13
17590 ACAAACGAAC
17600 GAACATAATAAAT
1 GAACATAATAAAT
*
17613 GAACATAAACAAAT
1 GAACAT-AATAAAT
17627 GAACATAATAAAT
1 GAACATAATAAAT
17640 GAACATAA
1 GAACATAA
17648 ACGAACAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 20 0.62
14 12 0.38
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.19
Consensus pattern (13 bp):
GAACATAATAAAT
Found at i:17628 original size:14 final size:14
Alignment explanation
Indices: 17586--17649 Score: 69
Period size: 13 Copynumber: 4.7 Consensus size: 14
17576 GAACGTAAAC
* * *
17586 GAACACAAACGAAC
1 GAACATAAACAAAT
*
17600 GAACAT-AATAAAT
1 GAACATAAACAAAT
17613 GAACATAAACAAAT
1 GAACATAAACAAAT
*
17627 GAACAT-AATAAAT
1 GAACATAAACAAAT
17640 GAACATAAAC
1 GAACATAAAC
17650 GAACAACACA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
13 22 0.54
14 19 0.46
ACGTcount: A:0.61, C:0.16, G:0.09, T:0.14
Consensus pattern (14 bp):
GAACATAAACAAAT
Found at i:17948 original size:14 final size:14
Alignment explanation
Indices: 17929--17982 Score: 108
Period size: 14 Copynumber: 3.9 Consensus size: 14
17919 ACATAAATGG
17929 ACATAAATGAACGA
1 ACATAAATGAACGA
17943 ACATAAATGAACGA
1 ACATAAATGAACGA
17957 ACATAAATGAACGA
1 ACATAAATGAACGA
17971 ACATAAATGAAC
1 ACATAAATGAAC
17983 ATATAATCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.57, C:0.15, G:0.13, T:0.15
Consensus pattern (14 bp):
ACATAAATGAACGA
Found at i:26890 original size:15 final size:15
Alignment explanation
Indices: 26870--26900 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
26860 ATTTATATAA
26870 TTTAATTACCTAGAC
1 TTTAATTACCTAGAC
26885 TTTAATTACCTAGAC
1 TTTAATTACCTAGAC
26900 T
1 T
26901 ATCAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (15 bp):
TTTAATTACCTAGAC
Found at i:26993 original size:2 final size:2
Alignment explanation
Indices: 26986--27042 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
26976 GTAATTGGAT
26986 TA 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 TA
27028 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
27043 TGCCAGATAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30262 original size:18 final size:18
Alignment explanation
Indices: 30241--30277 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30231 GTTGATAATT
30241 TGTTTTTAACTCTTAGAA
1 TGTTTTTAACTCTTAGAA
30259 TGTTTTTAACTCTTAGAA
1 TGTTTTTAACTCTTAGAA
30277 T
1 T
30278 TTGTCGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (18 bp):
TGTTTTTAACTCTTAGAA
Found at i:34928 original size:389 final size:389
Alignment explanation
Indices: 34209--34988 Score: 1542
Period size: 389 Copynumber: 2.0 Consensus size: 389
34199 TGCTTCTGAT
34209 ATTTGCAGATTTACTTGTCTGCCTTCCTTGTTCTTTCACCGATTTTCTTCTTGTAGAACAGCAGC
1 ATTTGCAGATTTACTTGTCTGCCTTCCTTGTTCTTTCACCGATTTTCTTCTTGTAGAACAGCAGC
34274 TGCAACGTCATCGAAGACTAGACTGATGACATTACTATTTGTCAAGTTGATGATGAGTTAATCAT
66 TGCAACGTCATCGAAGACTAGACTGATGACATTACTATTTGTCAAGTTGATGATGAGTTAATCAT
*
34339 ATGAATCCGGTAGACTTTGAAGTAGAAGTTCAGCACGTTCTTGTTCTCCTATTTTACAGCTTAAG
131 ATGAATCCGGTAGACTTTGAAGTAGAAGTTCAACACGTTCTTGTTCTCCTATTTTACAGCTTAAG
34404 GATGTAAGCTGAGAAAATAAAGTGTTCAGTGTATTTAAGTGCTCCGTTACTGAAGTAGATTCTGG
196 GATGTAAGCTGAGAAAATAAAGTGTTCAGTGTATTTAAGTGCTCCGTTACTGAAGTAGATTCTGG
*
34469 CATACGGAGAGTGTACAATTTTCTCTTAAGGAAAATTTTATTGTGCAACGATGTGGCCTCGTATA
261 CATACGGAGAGTGTACAATTTTCTCTTAAGGAAAATTTTATTGTGCAACGATGTGGCCTCGTACA
34534 ATTTGGTGAGATGATCACATATCTCCTTAGCTGTCTTCTTTTCCTCGATGCTTGACAATACTTC
326 ATTTGGTGAGATGATCACATATCTCCTTAGCTGTCTTCTTTTCCTCGATGCTTGACAATACTTC
34598 ATTTGCAGATTTACTTGTCTGCCTTCCTTGTTCTTTCACCGATTTTCTTCTTGTAGAACAGCAGC
1 ATTTGCAGATTTACTTGTCTGCCTTCCTTGTTCTTTCACCGATTTTCTTCTTGTAGAACAGCAGC
34663 TGCAACGTCATCGAAGACTAGACTGATGACATTACTATTTGTCAAGTTGATGATGAGTTAATCAT
66 TGCAACGTCATCGAAGACTAGACTGATGACATTACTATTTGTCAAGTTGATGATGAGTTAATCAT
34728 ATGAATCCGGTAGACTTTGAAGTAGAAGTTCAACACGTTCTTGTTCTCCTATTTTACAGCTTAAG
131 ATGAATCCGGTAGACTTTGAAGTAGAAGTTCAACACGTTCTTGTTCTCCTATTTTACAGCTTAAG
34793 GATGTAAGCTGAGAAAATAAAGTGTTCAGTGTATTTAAGTGCTCCGTTACTGAAGTAGATTCTGG
196 GATGTAAGCTGAGAAAATAAAGTGTTCAGTGTATTTAAGTGCTCCGTTACTGAAGTAGATTCTGG
34858 CATACGGAGAGTGTACAATTTTCTCTTAAGGAAAATTTTATTGTGCAACGATGTGGCCTCGTACA
261 CATACGGAGAGTGTACAATTTTCTCTTAAGGAAAATTTTATTGTGCAACGATGTGGCCTCGTACA
34923 ATTTGGTGAGATGATCACATATCTCCTTAGCTGTCTTCTTTTCCTCGATGCTTGACAATACTTC
326 ATTTGGTGAGATGATCACATATCTCCTTAGCTGTCTTCTTTTCCTCGATGCTTGACAATACTTC
34987 AT
1 AT
34989 CTGCTAATGC
Statistics
Matches: 389, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
389 389 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (389 bp):
ATTTGCAGATTTACTTGTCTGCCTTCCTTGTTCTTTCACCGATTTTCTTCTTGTAGAACAGCAGC
TGCAACGTCATCGAAGACTAGACTGATGACATTACTATTTGTCAAGTTGATGATGAGTTAATCAT
ATGAATCCGGTAGACTTTGAAGTAGAAGTTCAACACGTTCTTGTTCTCCTATTTTACAGCTTAAG
GATGTAAGCTGAGAAAATAAAGTGTTCAGTGTATTTAAGTGCTCCGTTACTGAAGTAGATTCTGG
CATACGGAGAGTGTACAATTTTCTCTTAAGGAAAATTTTATTGTGCAACGATGTGGCCTCGTACA
ATTTGGTGAGATGATCACATATCTCCTTAGCTGTCTTCTTTTCCTCGATGCTTGACAATACTTC
Found at i:40150 original size:16 final size:16
Alignment explanation
Indices: 40129--40162 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
40119 ACCGATACAC
*
40129 CATGAGTGTATTGGTA
1 CATGAGTGTATCGGTA
40145 CATGAGTGTATCGGTA
1 CATGAGTGTATCGGTA
40161 CA
1 CA
40163 CTCCTAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (16 bp):
CATGAGTGTATCGGTA
Found at i:41480 original size:20 final size:20
Alignment explanation
Indices: 41424--41481 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
41414 TTACTGTTCA
*
41424 CACAGTATCGATACTATTTG
1 CACAGTATCGGTACTATTTG
* *
41444 CACAGCATAGGTACTATTTG
1 CACAGTATCGGTACTATTTG
*
41464 CACAGTATCGGTGCTATT
1 CACAGTATCGGTACTATT
41482 CATACAGTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
CACAGTATCGGTACTATTTG
Found at i:45192 original size:20 final size:20
Alignment explanation
Indices: 45167--45215 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
45157 CATAACAATG
*
45167 AAAGAAAATTAAATTTTTCA
1 AAAGAAAATTAAATTGTTCA
* *
45187 AAAGAAACTT-AATTGTTCT
1 AAAGAAAATTAAATTGTTCA
45206 AAA-AAAATTA
1 AAAGAAAATTA
45216 TCTTATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 9 0.38
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (20 bp):
AAAGAAAATTAAATTGTTCA
Found at i:48988 original size:16 final size:17
Alignment explanation
Indices: 48967--49002 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
48957 TTAACGTTAT
48967 TTTAAAATTAAATT-AA
1 TTTAAAATTAAATTGAA
*
48983 TTTAAATTTAAATTGAA
1 TTTAAAATTAAATTGAA
49000 TTT
1 TTT
49003 TTCTCATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAAATTAAATTGAA
Found at i:50662 original size:23 final size:23
Alignment explanation
Indices: 50627--50673 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
50617 TAAGATATAA
50627 ATTTTTTATATTTGT-AGTTATGT
1 ATTTTTTATATTT-TAAGTTATGT
50650 ATTTTTT-TCATTTTAAGTTATGT
1 ATTTTTTAT-ATTTTAAGTTATGT
50673 A
1 A
50674 AAATGAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.64
Consensus pattern (23 bp):
ATTTTTTATATTTTAAGTTATGT
Found at i:50857 original size:19 final size:20
Alignment explanation
Indices: 50813--50857 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
50803 ATTTGTTTTT
*
50813 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
50833 ATTAAATTTTTAT-TCTCAA
1 AATAAATTTTTATCTATCAA
50852 AATAAA
1 AATAAA
50858 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:51410 original size:16 final size:16
Alignment explanation
Indices: 51380--51409 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51370 GTTAAAAGAG
51380 AAAATAAATGTAAAAC
1 AAAATAAATGTAAAAC
51396 AAAATAAA-GTAAAA
1 AAAATAAATGTAAAA
51410 AAATGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (16 bp):
AAAATAAATGTAAAAC
Found at i:51447 original size:16 final size:16
Alignment explanation
Indices: 51417--51446 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
51407 AAAAAATGGG
51417 AAAATAAAGATAAAAC
1 AAAATAAAGATAAAAC
51433 AAAAT-AAGATAAAA
1 AAAATAAAGATAAAA
51447 AAGTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (16 bp):
AAAATAAAGATAAAAC
Found at i:51537 original size:18 final size:18
Alignment explanation
Indices: 51516--51558 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
51506 ATTATTTTTA
51516 AAATAAAA-GATAAGAATT
1 AAATAAAAGGA-AAGAATT
*
51534 AAATAAAAGGAAATAATT
1 AAATAAAAGGAAAGAATT
51552 AAATAAA
1 AAATAAA
51559 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGGAAAGAATT
Found at i:51897 original size:153 final size:153
Alignment explanation
Indices: 51690--51992 Score: 561
Period size: 153 Copynumber: 2.0 Consensus size: 153
51680 AGGTCAATTT
* *
51690 TTCGTTGTCGACTCGGATTATGTTTTTTCAACAATAACTGGTTCTGATCTCAGTTTCCTCTTAGC
1 TTCGTTGTCGACTCGGATTATGTTATTTCAACAATAACTGGTTCCGATCTCAGTTTCCTCTTAGC
*
51755 AAACAATTTTGCTAATTGTGTTCTCGGAAAGTCGAATATGAATTCTCACGTTTGGGACTGAACCT
66 AAACAATTTTGCTAAGTGTGTTCTCGGAAAGTCGAATATGAATTCTCACGTTTGGGACTGAACCT
51820 TCGCTTTAGCCTTCGGCTTATTC
131 TCGCTTTAGCCTTCGGCTTATTC
51843 TTCGTTGTCGACTCGGATTATGTTATTTCAACAATAACTGGTTCCGATCTCAGTTTCCTCTTAGC
1 TTCGTTGTCGACTCGGATTATGTTATTTCAACAATAACTGGTTCCGATCTCAGTTTCCTCTTAGC
* *
51908 AAACAATTTTGCTAAGTGTGTTCTCGGAAAGTCGAATATGAATTCTCACGTTTGGGATTGAGCCT
66 AAACAATTTTGCTAAGTGTGTTCTCGGAAAGTCGAATATGAATTCTCACGTTTGGGACTGAACCT
51973 TCGCTTTAGCCTTCGGCTTA
131 TCGCTTTAGCCTTCGGCTTA
51993 AAAGAAAATA
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
153 145 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (153 bp):
TTCGTTGTCGACTCGGATTATGTTATTTCAACAATAACTGGTTCCGATCTCAGTTTCCTCTTAGC
AAACAATTTTGCTAAGTGTGTTCTCGGAAAGTCGAATATGAATTCTCACGTTTGGGACTGAACCT
TCGCTTTAGCCTTCGGCTTATTC
Found at i:52737 original size:147 final size:148
Alignment explanation
Indices: 52508--52795 Score: 389
Period size: 147 Copynumber: 2.0 Consensus size: 148
52498 GTCAACCTTG
** * *
52508 GTCTTCTTCTTGGTTTAAAGACCTCGGTTTGAAAATTCAACCAGAAAGTAGTTCCTCGATCCTAC
1 GTCTTCTTCTTGACTTAAAGACCTCAGTTTGAAAATTCAACCAGAAAGTAGTTCCCCGATCCTAC
* * * * * ** *
52573 TATATAGTTTATATGCCCTCGAGCTGAATGAAATCGAACTCGAAGGTTTTTGTTGACAGATAGCC
66 CATACAGTTGATATGCCCTCGAGCTGAATGAAATCGAACTCAAAAGTTTTCATTGACAGATAGCA
52638 CTTCTCGCCTTGAGCTAT
131 CTTCTCGCCTTGAGCTAT
* ** * *
52656 GTCTTCTTCTTGACTTAAAGACCTCAGTTT-AAACTTCAACTGGAAAGTAGTTCCCCGTTGCTAC
1 GTCTTCTTCTTGACTTAAAGACCTCAGTTTGAAAATTCAACCAGAAAGTAGTTCCCCGATCCTAC
* * *
52720 CATGCAGTTGATGTGCCCTCGAGCTGAATGAAATCGAACTCAAAAGTTTTCATTGATAGATAGCA
66 CATACAGTTGATATGCCCTCGAGCTGAATGAAATCGAACTCAAAAGTTTTCATTGACAGATAGCA
52785 CTTCTCGCCTT
131 CTTCTCGCCTT
52796 CAGTTATACT
Statistics
Matches: 120, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
147 93 0.77
148 27 0.22
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (148 bp):
GTCTTCTTCTTGACTTAAAGACCTCAGTTTGAAAATTCAACCAGAAAGTAGTTCCCCGATCCTAC
CATACAGTTGATATGCCCTCGAGCTGAATGAAATCGAACTCAAAAGTTTTCATTGACAGATAGCA
CTTCTCGCCTTGAGCTAT
Found at i:56191 original size:48 final size:48
Alignment explanation
Indices: 56103--56198 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 48
56093 ATAGTCAAAA
* * * * *
56103 TGATCTTGAAACAAATGGTGAAGGAGAAAATCCAGTAGGGTCCAGTTC
1 TGATCATGAAACAAATAGTGAAGGAGAAAATCAAGCAGGGTCAAGTTC
* *
56151 TGATCATGAAACAAATAGTGAAGGAGCTAGA-CAAGCAGGGTCAAGTTC
1 TGATCATGAAACAAATAGTGAAGGAG-AAAATCAAGCAGGGTCAAGTTC
56199 CACCATTGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 38 0.95
49 2 0.05
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.21
Consensus pattern (48 bp):
TGATCATGAAACAAATAGTGAAGGAGAAAATCAAGCAGGGTCAAGTTC
Found at i:58782 original size:46 final size:46
Alignment explanation
Indices: 58711--58802 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
58701 TATTCGTTTT
* *
58711 TCAAATCCATTAGAGTGAATGGTTTAGAAGGTTTCCATATGGCATA
1 TCAAATCCATTAGAGTAAATGGTTTAGAAGGCTTCCATATGGCATA
* *
58757 TCAAATCCATTATAGTAAATTGTTTAGAAGGCTTCCATATGGCATA
1 TCAAATCCATTAGAGTAAATGGTTTAGAAGGCTTCCATATGGCATA
58803 CGCCTTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (46 bp):
TCAAATCCATTAGAGTAAATGGTTTAGAAGGCTTCCATATGGCATA
Found at i:60090 original size:13 final size:13
Alignment explanation
Indices: 60072--60098 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60062 CTTAAGGACT
60072 TCTTCACTCAACG
1 TCTTCACTCAACG
60085 TCTTCACTCAACG
1 TCTTCACTCAACG
60098 T
1 T
60099 GTAAACCGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.37, G:0.07, T:0.33
Consensus pattern (13 bp):
TCTTCACTCAACG
Found at i:63470 original size:19 final size:19
Alignment explanation
Indices: 63446--63483 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
63436 GCGATTTTAA
*
63446 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGAGAGTT
63465 AAAATGTGTTGCGAGAGTT
1 AAAATGTGTTGCGAGAGTT
63484 TGAAAAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (19 bp):
AAAATGTGTTGCGAGAGTT
Found at i:63520 original size:19 final size:19
Alignment explanation
Indices: 63496--63532 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
63486 AAAAACGTGT
63496 TGTTGCAATAGTGAAAAAA
1 TGTTGCAATAGTGAAAAAA
*
63515 TGTTGCGATAGTGAAAAA
1 TGTTGCAATAGTGAAAAA
63533 CCCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.27
Consensus pattern (19 bp):
TGTTGCAATAGTGAAAAAA
Done.