Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002123.1 Hibiscus syriacus cultivar Beakdansim tig00004349_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: 100069
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:7106 original size:19 final size:17
Alignment explanation
Indices: 7069--7116 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
7059 ATTTGAAATT
7069 ATTATATATTTTTAAAAA
1 ATTATAT-TTTTTAAAAA
7087 ATTTATATTTTTTATTAAAA
1 A-TTATATTTTTTA--AAAA
7107 A-TATATTTTT
1 ATTATATTTTT
7117 ATTTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 16 0.59
19 6 0.22
20 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATATTTTTTAAAAA
Found at i:7115 original size:17 final size:17
Alignment explanation
Indices: 7072--7119 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
7062 TGAAATTATT
7072 ATATATTTTTA--AAAA
1 ATATATTTTTATTAAAA
7087 ATTTATATTTTTTATTAAAA
1 A--TATA-TTTTTATTAAAA
7107 ATATATTTTTATT
1 ATATATTTTTATT
7120 TTTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 1 0.04
17 12 0.43
18 10 0.36
20 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATATTTTTATTAAAA
Found at i:7626 original size:14 final size:15
Alignment explanation
Indices: 7607--7637 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7597 AAAAGATTGA
7607 AATAAAG-AAAAATT
1 AATAAAGAAAAAATT
7621 AATAAAGAAAAAATT
1 AATAAAGAAAAAATT
7636 AA
1 AA
7638 ATGATACTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (15 bp):
AATAAAGAAAAAATT
Found at i:12469 original size:28 final size:28
Alignment explanation
Indices: 12404--12532 Score: 109
Period size: 28 Copynumber: 4.5 Consensus size: 28
12394 TGTCTTACTC
* * * *
12404 AAAATTATATTTTATATATCTTAAATTTT
1 AAAA-TATATTTTATTTTTCTTAACTTAT
* *
12433 AAAATATATTTTGTTTTTGTTTTAACTTAT
1 AAAATATATTTT-ATTTT-TCTTAACTTAT
12463 AAAATATATTTTATTTTTCTTAACTTAT
1 AAAATATATTTTATTTTTCTTAACTTAT
* * *
12491 TAAATATAATTTATTTTATTTTAA-TGTA-
1 AAAATATATTTTATTTT-TCTTAACT-TAT
12519 AAATATATATTTTA
1 AAA-ATATATTTTA
12533 GATTTATCAT
Statistics
Matches: 82, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
28 36 0.44
29 26 0.32
30 20 0.24
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (28 bp):
AAAATATATTTTATTTTTCTTAACTTAT
Found at i:12484 original size:58 final size:56
Alignment explanation
Indices: 12404--12532 Score: 136
Period size: 58 Copynumber: 2.2 Consensus size: 56
12394 TGTCTTACTC
* * * *
12404 AAAATTATATTTTATATATCTTAAATT-TTAAAATATATTTTGTTTTTGTTTTAACT-T
1 AAAAATATATTTTATATATCTTAAATTATT-AAATATAATTT-ATTTTATTTTAA-TGT
* * *
12461 ATAAAATATATTTTATTTTTCTTAACTTATTAAATATAATTTATTTTATTTTAATGT
1 A-AAAATATATTTTATATATCTTAAATTATTAAATATAATTTATTTTATTTTAATGT
12518 AAAATATATATTTTA
1 AAAA-ATATATTTTA
12533 GATTTATCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
56 4 0.07
57 23 0.38
58 32 0.52
59 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (56 bp):
AAAAATATATTTTATATATCTTAAATTATTAAATATAATTTATTTTATTTTAATGT
Found at i:12624 original size:28 final size:28
Alignment explanation
Indices: 12593--12652 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
12583 TATTTAAATA
12593 TTTATTAATAATTT-AATATAAAATATAT
1 TTTATTAATAATTTAAATA-AAAATATAT
** *
12621 TTTATTCTTATTTTAAATAAAAATATAT
1 TTTATTAATAATTTAAATAAAAATATAT
12649 TTTA
1 TTTA
12653 ATATTATCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTATTAATAATTTAAATAAAAATATAT
Found at i:12659 original size:28 final size:30
Alignment explanation
Indices: 12607--12665 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
12597 TTAATAATTT
* *
12607 AATATAAAATATATTTTATTCTTAT-TTTA
1 AATATAAAATATATTTTAATATTATCTTTA
12636 AATA-AAAATATATTTTAATATTATCTTTA
1 AATATAAAATATATTTTAATATTATCTTTA
12665 A
1 A
12666 CTTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (30 bp):
AATATAAAATATATTTTAATATTATCTTTA
Found at i:12854 original size:14 final size:14
Alignment explanation
Indices: 12819--12861 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
12809 ATAAAATATT
*
12819 AAATATATTTTAAGT
1 AAATATATTTTAA-A
*
12834 TAATATATTTTAAA
1 AAATATATTTTAAA
12848 AAATATATTTTAAA
1 AAATATATTTTAAA
12862 TGATGATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
AAATATATTTTAAA
Found at i:12956 original size:28 final size:29
Alignment explanation
Indices: 12897--12969 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 29
12887 TACATAAAAT
* * * *
12897 AAAATAAATTATATTAATAAGTAAGAA-G
1 AAAATAAAATATATTTATAAGTAACAACA
*
12925 AAAATAAAATATATTTATAAGTTACAACA
1 AAAATAAAATATATTTATAAGTAACAACA
*
12954 AAAATAAAAGATATTT
1 AAAATAAAATATATTT
12970 TCAAAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
28 23 0.61
29 15 0.39
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (29 bp):
AAAATAAAATATATTTATAAGTAACAACA
Found at i:15172 original size:19 final size:19
Alignment explanation
Indices: 15148--15192 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
15138 TACAATTTAG
15148 GTTATGAAATGCCCATCAT
1 GTTATGAAATGCCCATCAT
*
15167 GTTATGAAATGCCTATCAT
1 GTTATGAAATGCCCATCAT
15186 GTTATGA
1 GTTATGA
15193 TATGTAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (19 bp):
GTTATGAAATGCCCATCAT
Found at i:15543 original size:18 final size:19
Alignment explanation
Indices: 15503--15572 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
15493 TATGAACTTG
15503 AAAATAAGCTATGAATCTA
1 AAAATAAGCTATGAATCTA
15522 AAAATAAGCTATGAATCTA
1 AAAATAAGCTATGAATCTA
*
15541 AAAATAAGTTATGAATCT-
1 AAAATAAGCTATGAATCTA
*
15559 AAAATAAGTTATGA
1 AAAATAAGCTATGA
15573 GTCCGGAAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 14 0.28
19 36 0.72
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (19 bp):
AAAATAAGCTATGAATCTA
Found at i:15587 original size:37 final size:38
Alignment explanation
Indices: 15503--15593 Score: 94
Period size: 37 Copynumber: 2.4 Consensus size: 38
15493 TATGAACTTG
* * *
15503 AAAATAAGCTATGAATCTAAAAATAAGCTATGAATCTA
1 AAAACAAGTTATGAATCTAAAAATAAGCTATGAATCCA
* * * *
15541 AAAATAAGTTATGAATCT-AAAATAAGTTATGAGTCCG
1 AAAACAAGTTATGAATCTAAAAATAAGCTATGAATCCA
* *
15578 GAAACAAGTTCTGAAT
1 AAAACAAGTTATGAAT
15594 TTGAGAATGA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 28 0.62
38 17 0.38
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.27
Consensus pattern (38 bp):
AAAACAAGTTATGAATCTAAAAATAAGCTATGAATCCA
Found at i:15739 original size:18 final size:18
Alignment explanation
Indices: 15716--15780 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
15706 TTAAAAAGAA
15716 TATGATATGATTATTATG
1 TATGATATGATTATTATG
* *
15734 TATGATATTGTTTATCATGG
1 TATGATA-TGATTATTAT-G
* *
15754 CTTTGATATGACTATTATG
1 -TATGATATGATTATTATG
*
15773 TGTGATAT
1 TATGATAT
15781 TGTTTATCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
18 14 0.38
19 9 0.24
20 8 0.22
21 6 0.16
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (18 bp):
TATGATATGATTATTATG
Found at i:15770 original size:39 final size:39
Alignment explanation
Indices: 15718--15792 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
15708 AAAAAGAATA
*
15718 TGATATGATTATTATGTATGATATTGTTTATCATGGCTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
*
15757 TGATATGACTATTATGTGTGATATTGTTTATCATGG
1 TGATATGACTATTATGTATGATATTGTTTATCATGG
15793 TTTTTATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.49
Consensus pattern (39 bp):
TGATATGACTATTATGTATGATATTGTTTATCATGGCTT
Found at i:17275 original size:2 final size:2
Alignment explanation
Indices: 17268--17336 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
17258 TGAGTGCATA
17268 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
17310 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
17337 GTGTTTTATG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17657 original size:23 final size:23
Alignment explanation
Indices: 17623--17721 Score: 92
Period size: 23 Copynumber: 4.3 Consensus size: 23
17613 GAGTCGAGGG
17623 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
* * ** *
17646 TTCTACGGGGTCATTTAGGACAT
1 TTCTACGCGGTCCTTCGGGACAA
17669 TTCTACGCGGTCCTTCGGGACATA
1 TTCTACGCGGTCCTTCGGGACA-A
* * * * *
17693 TT-TATGTGGTACTTCGAGACAT
1 TTCTACGCGGTCCTTCGGGACAA
17715 TTCTACG
1 TTCTACG
17722 TGGCACATCA
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
22 2 0.03
23 54 0.93
24 2 0.03
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAA
Found at i:17714 original size:46 final size:46
Alignment explanation
Indices: 17623--17721 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
17613 GAGTCGAGGG
*
17623 TTCTACGCGGTCCTTCGGGACAATTCTACGGGGTCATTTAGGACAT
1 TTCTACGCGGTCCTTCGGGACAATTCTACGGGGTCACTTAGGACAT
* * *
17669 TTCTACGCGGTCCTTCGGGACATATT-TATGTGGT-ACTTCGAGACAT
1 TTCTACGCGGTCCTTCGGGACA-ATTCTACGGGGTCACTTAG-GACAT
17715 TTCTACG
1 TTCTACG
17722 TGGCACATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
45 4 0.09
46 40 0.85
47 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCGGGACAATTCTACGGGGTCACTTAGGACAT
Found at i:17724 original size:23 final size:23
Alignment explanation
Indices: 17623--17753 Score: 88
Period size: 23 Copynumber: 5.7 Consensus size: 23
17613 GAGTCGAGGG
* *
17623 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGCGGTACTTCGGGACAT
* **
17646 TTCTACGGGGT-CATTTAGGACAT
1 TTCTACGCGGTAC-TTCGGGACAT
*
17669 TTCTACGCGGTCCTTCGGGACAT
1 TTCTACGCGGTACTTCGGGACAT
* * *
17692 ATT-TATGTGGTACTTCGAGACAT
1 -TTCTACGCGGTACTTCGGGACAT
* * * *
17715 TTCTACGTGGCACATCAGTG-CAT
1 TTCTACGCGGTACTTC-GGGACAT
17738 ATTCTACGCGGTACTT
1 -TTCTACGCGGTACTT
17754 TGGTGCAATT
Statistics
Matches: 84, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
22 3 0.04
23 64 0.76
24 17 0.20
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTACTTCGGGACAT
Found at i:19178 original size:18 final size:17
Alignment explanation
Indices: 19143--19186 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
19133 CTCAAAATTA
*
19143 AATATTATTTTAAGTAAT
1 AATATT-TTTTAAATAAT
*
19161 TATATTTTTTACAATAAT
1 AATATTTTTTA-AATAAT
19179 AATATTTT
1 AATATTTT
19187 CACCCCATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
AATATTTTTTAAATAAT
Found at i:19312 original size:3 final size:3
Alignment explanation
Indices: 19306--19343 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19296 CTACTACTAC
19306 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
19344 AGTTTATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20038 original size:17 final size:18
Alignment explanation
Indices: 20006--20049 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
19996 AATATTTTTC
*
20006 AAAAAATATAAGAAAA-AA
1 AAAAAAT-TTAGAAAATAA
*
20024 ATAAAATTTAGAAAATAA
1 AAAAAATTTAGAAAATAA
20042 AAAAAATT
1 AAAAAATT
20050 CAAGGTGACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAAAATTTAGAAAATAA
Found at i:30506 original size:17 final size:18
Alignment explanation
Indices: 30484--30522 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
30474 CTGCAATGTA
30484 AAAAAAAAACAAAG-CAT
1 AAAAAAAAACAAAGACAT
* *
30501 AAAAAAGAACAAGGACAT
1 AAAAAAAAACAAAGACAT
30519 AAAA
1 AAAA
30523 GTCAGCTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.74, C:0.10, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAAAAAAACAAAGACAT
Found at i:31285 original size:17 final size:17
Alignment explanation
Indices: 31263--31298 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
31253 AAAACAGATT
31263 AGCAATAGACTGAAAAC
1 AGCAATAGACTGAAAAC
31280 AGCAATAGACTGAAAAC
1 AGCAATAGACTGAAAAC
31297 AG
1 AG
31299 AAAACTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.17, G:0.19, T:0.11
Consensus pattern (17 bp):
AGCAATAGACTGAAAAC
Found at i:31657 original size:20 final size:20
Alignment explanation
Indices: 31634--31696 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
31624 ATCTAAATTC
31634 TAAACAGATTACCTAACAAT
1 TAAACAGATTACCTAACAAT
* **
31654 TAAACATATTATAGATAAACAAT
1 TAAACAGA-T-TACCT-AACAAT
31677 TAAACAGATTACCTTAACAA
1 TAAACAGATTACC-TAACAA
31697 AATAACAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 5 0.15
23 13 0.39
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAACAGATTACCTAACAAT
Found at i:31852 original size:24 final size:27
Alignment explanation
Indices: 31791--31844 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
31781 CCAATATATA
*
31791 AACAATTAAACAAATTACATTGAAGAT
1 AACAATTAAACAAATTACAGTGAAGAT
31818 GAATCAATTAAACAAATTACAGTGAAG
1 -AA-CAATTAAACAAATTACAGTGAAG
31845 TAAATTAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (27 bp):
AACAATTAAACAAATTACAGTGAAGAT
Found at i:32227 original size:24 final size:24
Alignment explanation
Indices: 32198--32245 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
32188 TAATTGGAAT
*
32198 TTAAAAGGTTTGACTGTTGGAAGA
1 TTAAAAGGTCTGACTGTTGGAAGA
32222 TTAAAAGGTCTGACTGTTGGAAGA
1 TTAAAAGGTCTGACTGTTGGAAGA
32246 AAATCGAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.31
Consensus pattern (24 bp):
TTAAAAGGTCTGACTGTTGGAAGA
Found at i:36014 original size:2 final size:2
Alignment explanation
Indices: 36002--36049 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
35992 ATATTCTATT
* *
36002 TA TA TA T- TA TA TA T- TG TA AA TA T- 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
36041 TA TA TA TA T
1 TA TA TA TA T
36050 TAAATTTTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43307 original size:22 final size:22
Alignment explanation
Indices: 43279--43341 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
43269 GAGGGTCTAC
*
43279 GTGGTCCTTCGGGACATATACA
1 GTGGTCCTTCGGGACAAATACA
*
43301 GTGGTCCTTCGGGATAAATACA
1 GTGGTCCTTCGGGACAAATACA
43323 -TAGGTCCTTCGGGACAAAT
1 GT-GGTCCTTCGGGACAAAT
43342 TTCATATGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (22 bp):
GTGGTCCTTCGGGACAAATACA
Found at i:43647 original size:30 final size:30
Alignment explanation
Indices: 43613--43673 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
43603 TTTGATATAA
*
43613 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
43643 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
43673 C
1 C
43674 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:49758 original size:22 final size:22
Alignment explanation
Indices: 49730--49813 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 22
49720 TTTTGGTGCA
* *
49730 GAGGGAATCGATTCCCCCCCCT
1 GAGGGAACCGATTCCCCCCACT
**
49752 GAGGGAACCGATT-CCCCCTTT
1 GAGGGAACCGATTCCCCCCACT
*
49773 GAATGGGAACCGATTCCCCCCACA
1 G-A-GGGAACCGATTCCCCCCACT
* *
49797 G-GGGAATCGATACCCCC
1 GAGGGAACCGATTCCCCC
49814 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 21 0.41
22 13 0.25
23 11 0.22
24 6 0.12
ACGTcount: A:0.23, C:0.37, G:0.24, T:0.17
Consensus pattern (22 bp):
GAGGGAACCGATTCCCCCCACT
Found at i:52258 original size:30 final size:30
Alignment explanation
Indices: 52224--52284 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
52214 TTCGATATAA
*
52224 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
52254 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
52284 C
1 C
52285 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:53407 original size:16 final size:17
Alignment explanation
Indices: 53377--53409 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
53367 AGATAAGAAA
53377 TATGAATGATAATAGAG
1 TATGAATGATAATAGAG
*
53394 TATGAAT-ATGATAGAG
1 TATGAATGATAATAGAG
53410 ATCATGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (17 bp):
TATGAATGATAATAGAG
Found at i:53843 original size:21 final size:22
Alignment explanation
Indices: 53801--53845 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
53791 TGTAGCAGTA
*
53801 CTGTAGCAGGGGAATCGGTACC
1 CTGTAGCAGGGGAATCGATACC
*
53823 CTGTAGCA-GGGTATCGATACC
1 CTGTAGCAGGGGAATCGATACC
53844 CT
1 CT
53846 ATCTGTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.22
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGATACC
Found at i:55553 original size:27 final size:23
Alignment explanation
Indices: 55482--55532 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
55472 CCACTAGGGG
55482 CTATGAGATTTATCCCGAAGGAT
1 CTATGAGATTTATCCCGAAGGAT
55505 CTATGAGATTTATCCCGAAGGAT
1 CTATGAGATTTATCCCGAAGGAT
55528 CTATG
1 CTATG
55533 TACTGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (23 bp):
CTATGAGATTTATCCCGAAGGAT
Found at i:61585 original size:23 final size:23
Alignment explanation
Indices: 61542--61594 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
61532 TGTTTGTTTG
** *
61542 TTTATTTTTATTTGTTTTATTTC
1 TTTATTTTTATTTGTAATATTAC
61565 TTTATTTTTAATTT-TAATATTAC
1 TTTATTTTT-ATTTGTAATATTAC
61588 TTT-TTTT
1 TTTATTTT
61595 AGGACAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 18 0.69
24 4 0.15
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTATTTTTATTTGTAATATTAC
Found at i:62763 original size:11 final size:11
Alignment explanation
Indices: 62744--62775 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
62734 GTGAAAAAGT
62744 GAAAA-AAAAA
1 GAAAAGAAAAA
62754 GAAAAGAAAAA
1 GAAAAGAAAAA
62765 GAAAAGAAAAA
1 GAAAAGAAAAA
62776 AAGAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:65027 original size:21 final size:21
Alignment explanation
Indices: 65001--65102 Score: 161
Period size: 21 Copynumber: 4.9 Consensus size: 21
64991 AGGGTGTCAA
65001 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACTCCTGC
65022 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACTCCTGC
65043 AGTGCATCCATGCAC-CCTTGC
1 AGTGCATCCATGCACTCC-TGC
* *
65064 AGTGCATCAATGCACCCCTGC
1 AGTGCATCCATGCACTCCTGC
*
65085 AGTGCATCCATGTACTCC
1 AGTGCATCCATGCACTCC
65103 ATTTCGAATG
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 71 0.95
22 2 0.03
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACTCCTGC
Found at i:65147 original size:20 final size:20
Alignment explanation
Indices: 65119--65225 Score: 169
Period size: 20 Copynumber: 5.3 Consensus size: 20
65109 AATGCAATTA
65119 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
* *
65139 ATACATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
* *
65159 GTGCATCGACGCATCCTGTT
1 GTGCATCGATGCATCCTGCT
*
65179 GTGCATCGACGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
65199 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
65219 GTGCATC
1 GTGCATC
65226 CATGAACCAA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.17, C:0.31, G:0.23, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:66287 original size:22 final size:22
Alignment explanation
Indices: 66262--66304 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
66252 CTATTATGTG
66262 CTTTAGGCCCAAATGAATATGA
1 CTTTAGGCCCAAATGAATATGA
66284 CTTTAGGCCCAAATGAATATG
1 CTTTAGGCCCAAATGAATATG
66305 GAAGAATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (22 bp):
CTTTAGGCCCAAATGAATATGA
Found at i:68446 original size:21 final size:21
Alignment explanation
Indices: 68420--68495 Score: 143
Period size: 21 Copynumber: 3.6 Consensus size: 21
68410 GGTGTCAAAA
*
68420 TGCATCCATGCACCCCTTCAG
1 TGCATCCATGCACCCCTGCAG
68441 TGCATCCATGCACCCCTGCAG
1 TGCATCCATGCACCCCTGCAG
68462 TGCATCCATGCACCCCTGCAG
1 TGCATCCATGCACCCCTGCAG
68483 TGCATCCATGCAC
1 TGCATCCATGCAC
68496 TCCATTTCGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.20, C:0.42, G:0.17, T:0.21
Consensus pattern (21 bp):
TGCATCCATGCACCCCTGCAG
Found at i:71233 original size:20 final size:20
Alignment explanation
Indices: 71208--71246 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
71198 AGATTGTGCA
71208 GGGGGTA-CAGATACCCCCTG
1 GGGGGTATC-GATACCCCCTG
71228 GGGGGTATCGATACCCCCT
1 GGGGGTATCGATACCCCCT
71247 AAATGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.18, C:0.31, G:0.33, T:0.18
Consensus pattern (20 bp):
GGGGGTATCGATACCCCCTG
Found at i:71997 original size:22 final size:22
Alignment explanation
Indices: 71969--72029 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
71959 GGGTCTACGC
*
71969 GGTCCTTCGGGACATATACAGT-
1 GGTCCTTCGGGACAAATACA-TA
*
71991 GGTCCTTCAGGACAAATACATA
1 GGTCCTTCGGGACAAATACATA
*
72013 GGTCATTCGGGACAAAT
1 GGTCCTTCGGGACAAAT
72030 TTCATATGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCCTTCGGGACAAATACATA
Found at i:72369 original size:16 final size:17
Alignment explanation
Indices: 72339--72371 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
72329 AGATAAGAAA
72339 TATGAATGATAATAGAG
1 TATGAATGATAATAGAG
*
72356 TATGAAT-ATGATAGAG
1 TATGAATGATAATAGAG
72372 ATCATGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (17 bp):
TATGAATGATAATAGAG
Found at i:72804 original size:25 final size:25
Alignment explanation
Indices: 72770--72817 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
72760 GGGGAATCGT
72770 TACTGTAGCAGGTTACCGTTCATGG
1 TACTGTAGCAGGTTACCGTTCATGG
* *
72795 TACTGTAGCATGTTACTGTTCAT
1 TACTGTAGCAGGTTACCGTTCAT
72818 ACCGTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (25 bp):
TACTGTAGCAGGTTACCGTTCATGG
Found at i:81547 original size:19 final size:20
Alignment explanation
Indices: 81521--81565 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
81511 CTATTTTTTT
81521 CAAAAAAAAAAACAAAAAGC
1 CAAAAAAAAAAACAAAAAGC
81541 CAAAAAAAAAAACAAAAAGC
1 CAAAAAAAAAAACAAAAAGC
81561 CAAAA
1 CAAAA
81566 TTTCAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.80, C:0.16, G:0.04, T:0.00
Consensus pattern (20 bp):
CAAAAAAAAAAACAAAAAGC
Done.