Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004251.1 Hibiscus syriacus cultivar Beakdansim tig00009319_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: 67381
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1390 original size:29 final size:31
Alignment explanation
Indices: 1322--1387 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
1312 AGTTCAAAGT
* *
1322 TTGGCCACCAACCAAGATGAAATTTCTAATAAG
1 TTGGCCACCAACCAAGATGAAATTTC--ACAAC
1355 TTGGCCACCAACCAAGATGAAATTTC-CAAC
1 TTGGCCACCAACCAAGATGAAATTTCACAAC
1385 TTG
1 TTG
1388 CCAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
33 26 0.84
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCACAAC
Found at i:10974 original size:17 final size:18
Alignment explanation
Indices: 10944--10977 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10934 AAAACGATAC
10944 AACTAAAAAGATAAAAAG
1 AACTAAAAAGATAAAAAG
10962 AACTAAAAA-ATAAAAA
1 AACTAAAAAGATAAAAA
10978 CAATTCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (18 bp):
AACTAAAAAGATAAAAAG
Found at i:11184 original size:3 final size:3
Alignment explanation
Indices: 11178--11219 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
11168 CTCCTCACTC
*
11178 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TAA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
11220 GAAGTAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:18096 original size:41 final size:41
Alignment explanation
Indices: 18046--18307 Score: 276
Period size: 41 Copynumber: 6.3 Consensus size: 41
18036 ACTTTAGTTG
* * * * *
18046 TATAAAAACGCCGCTAAATAATCGTAATGTAGTGGCATTTT
1 TATACAAACGCCGCTATAGAATCGTACTTTAGTGGCATTTT
* *
18087 TATACAAACGCCGCTATAGACTCGTACTTTAGTGGAATTTT
1 TATACAAACGCCGCTATAGAATCGTACTTTAGTGGCATTTT
* * *
18128 TACACAAACGCCGCTATAGACA-CGTACTTTTGTGGCGTTTT
1 TATACAAACGCCGCTATAGA-ATCGTACTTTAGTGGCATTTT
* *
18169 AATACCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTT
1 TATA-CAAACGCCGCTATAGAATCGTACTTTAGTGGCATTTT
* * * *
18211 TACACAAACGTCGCTATAGACA-CGTACTTTTGTGGCGTTTT
1 TATACAAACGCCGCTATAGA-ATCGTACTTTAGTGGCATTTT
* * * **
18252 TACACAAACGCCTCTATAGACTCGTACTTTAGTGGTGTTTT
1 TATACAAACGCCGCTATAGAATCGTACTTTAGTGGCATTTT
*
18293 AATACCAAACGCCGC
1 TATA-CAAACGCCGC
18308 AATTGTCATA
Statistics
Matches: 184, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
41 140 0.76
42 44 0.24
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (41 bp):
TATACAAACGCCGCTATAGAATCGTACTTTAGTGGCATTTT
Found at i:18220 original size:124 final size:124
Alignment explanation
Indices: 18051--18307 Score: 379
Period size: 124 Copynumber: 2.1 Consensus size: 124
18041 AGTTGTATAA
* * *
18051 AAACGCCGCTAAATAATCGTAATGTAGTGGCATTTTTATACAAACGCCGCTATAGACTCGTACTT
1 AAACGCCGCTAAAGAATCGTAATGTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTT
*
18116 TAGTGGAATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
66 TAGTGGAATTTTTACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
* * * * *
18175 AAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAACGTCGCTATAGACACGTACTT
1 AAACGCCGCTAAAGAATCGTAATGTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTT
* ** * * *
18240 TTGTGGCGTTTTTACACAAACGCCTCTATAGACTCGTACTTTAGTGGTGTTTTAATACC
66 TAGTGGAATTTTTACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
18299 AAACGCCGC
1 AAACGCCGC
18308 AATTGTCATA
Statistics
Matches: 118, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
124 118 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (124 bp):
AAACGCCGCTAAAGAATCGTAATGTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTT
TAGTGGAATTTTTACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
Found at i:18303 original size:83 final size:82
Alignment explanation
Indices: 18077--18286 Score: 350
Period size: 83 Copynumber: 2.5 Consensus size: 82
18067 TCGTAATGTA
* *
18077 GTGGCATTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGAATTTTTACACAAACGCCGC
1 GTGGCGTTTTTACACAAACGCCGCTATAGACTCGTACTTTAGTGGAATTTTTACACAAACGCCGC
18142 TATAGACACGTACTTTT
66 TATAGACACGTACTTTT
* *
18159 GTGGCGTTTTAATAC-CAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAACGTC
1 GTGGCGTTTT--TACACAAACGCCGCTATAGACTCGTACTTTAGTGGAATTTTTACACAAACGCC
18223 GCTATAGACACGTACTTTT
64 GCTATAGACACGTACTTTT
*
18242 GTGGCGTTTTTACACAAACGCCTCTATAGACTCGTACTTTAGTGG
1 GTGGCGTTTTTACACAAACGCCGCTATAGACTCGTACTTTAGTGG
18287 TGTTTTAATA
Statistics
Matches: 120, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
81 3 0.03
82 39 0.32
83 76 0.63
84 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (82 bp):
GTGGCGTTTTTACACAAACGCCGCTATAGACTCGTACTTTAGTGGAATTTTTACACAAACGCCGC
TATAGACACGTACTTTT
Found at i:21765 original size:43 final size:42
Alignment explanation
Indices: 21717--21954 Score: 282
Period size: 43 Copynumber: 5.6 Consensus size: 42
21707 AAGGTAATTA
* *
21717 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTT
** * *
21760 GCGGCGTTTGTGTTTAAAAATGCCGTTATAGGTCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTT
* * *
21803 GCAGCGTTTGTGTCCAAAAACGGCTCTATAGGTCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTT
* * *
21846 GCGGCGTTTGTTCTAAAAGCGCCAG-TATAGGTATG-CTCTTTT
1 GCGGCGTTTGTTCCAAAAACGCC-GCTATAGGTCTGAC-CTTTT
* *
21888 GCGGCATTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACCTTTT
21931 GCGGCGTTTGTTCCAAAAACGCCG
1 GCGGCGTTTGTTCCAAAAACGCCG
21955 TAATATATAT
Statistics
Matches: 165, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 47 0.28
43 116 0.70
44 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGGTCTGACCTTTT
Found at i:21917 original size:85 final size:85
Alignment explanation
Indices: 21717--21982 Score: 329
Period size: 85 Copynumber: 3.1 Consensus size: 85
21707 AAGGTAATTA
* * * *
21717 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGTTTAAAAATG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGT-TCTAAAAACG
*
21782 CCGTTATAGGTCTGACCTTTT
65 CCGTTATAGGTATGACCTTTT
* * * * *
21803 GCAGCGTTTGTGTCCAAAAACGGCTCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAGCGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
21868 CAG-TATAGGTATG-CTCTTTT
66 C-GTTATAGGTATGAC-CTTTT
* * *
21888 GCGGCATTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
* ** *
21953 CGTAATATATATTGACCTATT
66 CGTTATAGGTA-TGACCTTTT
21974 GCGGCGTTT
1 GCGGCGTTT
21983 TTTGTTCTCA
Statistics
Matches: 152, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
84 2 0.01
85 86 0.57
86 63 0.41
87 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (85 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
CGTTATAGGTATGACCTTTT
Found at i:21969 original size:43 final size:42
Alignment explanation
Indices: 21717--21982 Score: 225
Period size: 43 Copynumber: 6.2 Consensus size: 42
21707 AAGGTAATTA
* * * *
21717 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCG-TATAGATTTGACCTTTT
* ** * * *
21760 GCGGCGTTTGTGTTTAAAAATGCCGTTATAGGTCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCG-TATAGATTTGACCTTTT
* * * *
21803 GCAGCGTTTGTGTCCAAAAACGGCTC-TATAGGTCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAAC-GC-CGTATAGATTTGACCTTTT
* * * *
21846 GCGGCGTTTGT-TCTAAAAGCGCCAGTATAGGTATG-CTCTTTT
1 GCGGCGTTTGTATCCAAAAACGCC-GTATAGATTTGAC-CTTTT
* *
21888 GCGGCATTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCG-TATAGATTTGACCTTTT
* *
21931 GCGGCGTTTGT-TCCAAAAACGCCGTAATATATATTGACCTATT
1 GCGGCGTTTGTATCCAAAAACGCCGT-ATAGAT-TTGACCTTTT
21974 GCGGCGTTT
1 GCGGCGTTT
21983 TTTGTTCTCA
Statistics
Matches: 190, Mismatches: 23, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
40 1 0.01
41 4 0.02
42 50 0.26
43 131 0.69
44 3 0.02
45 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTATCCAAAAACGCCGTATAGATTTGACCTTTT
Found at i:21976 original size:128 final size:129
Alignment explanation
Indices: 21717--21982 Score: 317
Period size: 128 Copynumber: 2.1 Consensus size: 129
21707 AAGGTAATTA
* * * ** *
21717 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGTTTAAAAATG
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTATGACTTTTTGCGGCATTTGTATCCAAAAACG
* * * * * *
21782 CCGTTATAGGTCTGACCTTTTGCAGCGTTTGTGTCCAAAAACGGCTCTATAGGTCTGACCTTTT
66 CCGCTATAGATCTGACCTTTTGCAGCGTTTGTGTCCAAAAACGCCTATATAGATCTGACCTATT
* *
21846 GCGGCGTTTGT-TCTAAAAGCGCCAG-TATAGGTATG-CTCTTTTGCGGCATTTGTATCCAAAAA
1 GCGGCGTTTGTATCAAAAAACGCC-GCTATAGGTATGACT-TTTTGCGGCATTTGTATCCAAAAA
* *
21908 CGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGTAATATATAT-TGACCT
64 CGCCGCTATAGATCTGACCTTTTGCAGCGTTTGTGTCCAAAAACGCC-T-ATATAGATCTGACCT
21971 ATT
127 ATT
21974 GCGGCGTTT
1 GCGGCGTTT
21983 TTTGTTCTCA
Statistics
Matches: 117, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
127 13 0.11
128 87 0.74
129 17 0.15
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (129 bp):
GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTATGACTTTTTGCGGCATTTGTATCCAAAAACG
CCGCTATAGATCTGACCTTTTGCAGCGTTTGTGTCCAAAAACGCCTATATAGATCTGACCTATT
Found at i:22209 original size:2 final size:2
Alignment explanation
Indices: 22202--22242 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
22192 TTCAAACACT
22202 TA 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 TA T
22243 TAAAAAAACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23132 original size:16 final size:16
Alignment explanation
Indices: 23113--23147 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
23103 AAGAAAATTC
23113 AGAAAAATAAAAAAAA
1 AGAAAAATAAAAAAAA
* *
23129 AGAAAGATATAAAAAA
1 AGAAAAATAAAAAAAA
23145 AGA
1 AGA
23148 CGCGTGCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (16 bp):
AGAAAAATAAAAAAAA
Found at i:26726 original size:24 final size:24
Alignment explanation
Indices: 26699--26798 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
26689 GATATCAAAA
*
26699 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
26723 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
26747 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
26771 GTTAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
26795 ATCA
1 ATCA
26799 GATAAAATAT
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:26798 original size:48 final size:48
Alignment explanation
Indices: 26692--26800 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
26682 AAACGGAGAT
* * * * *
26692 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
26740 TTTAGGAATCAGAACAGATTTCAGATCAGATGTTAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
26788 ATCAGAAATCAGA
1 ATCAGAAATCAGA
26801 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:29296 original size:7 final size:7
Alignment explanation
Indices: 29284--29314 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
29274 TGGTCAACTC
29284 CGGTCAA
1 CGGTCAA
29291 CGGTCAA
1 CGGTCAA
29298 CGGGTCAA
1 C-GGTCAA
29306 CGGTCAA
1 CGGTCAA
29313 CG
1 CG
29315 TTTCAACGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:29305 original size:8 final size:8
Alignment explanation
Indices: 29285--29339 Score: 57
Period size: 8 Copynumber: 7.5 Consensus size: 8
29275 GGTCAACTCC
29285 GGTCAAC-
1 GGTCAACG
29292 GGTCAACG
1 GGTCAACG
29300 GGTCAAC-
1 GGTCAACG
29307 GGTCAACG
1 GGTCAACG
**
29315 TTTCAACG
1 GGTCAACG
29323 GGT---CG
1 GGTCAACG
29328 GGTCAACG
1 GGTCAACG
29336 GGTC
1 GGTC
29340 GGGTCGGGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
5 5 0.13
7 14 0.36
8 20 0.51
ACGTcount: A:0.22, C:0.25, G:0.35, T:0.18
Consensus pattern (8 bp):
GGTCAACG
Found at i:29323 original size:15 final size:15
Alignment explanation
Indices: 29285--29314 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29275 GGTCAACTCC
29285 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
29300 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
29315 TTTCAACGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:29335 original size:13 final size:13
Alignment explanation
Indices: 29317--29344 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29307 GGTCAACGTT
29317 TCAACGGGTCGGG
1 TCAACGGGTCGGG
29330 TCAACGGGTCGGG
1 TCAACGGGTCGGG
29343 TC
1 TC
29345 GGGTCAACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:29344 original size:18 final size:18
Alignment explanation
Indices: 29321--29397 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
29311 AACGTTTCAA
*
29321 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
29339 CGGGTCGGGTCAA-----
1 CGGGTCGGGTAAACGGGT
*
29352 CAGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
29370 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
29388 CGGGTCGGGT
1 CGGGTCGGGT
29398 TGTGACCGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
13 11 0.22
18 40 0.78
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:29358 original size:31 final size:31
Alignment explanation
Indices: 29317--29393 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
29307 GGTCAACGTT
29317 TCAACGGGTCGGGTCAACGGGTCGGGTCGGG
1 TCAACGGGTCGGGTCAACGGGTCGGGTCGGG
* *
29348 TCAACAGGTCGGGTAAACGGGTCGGGTCGGG
1 TCAACGGGTCGGGTCAACGGGTCGGGTCGGG
*
29379 TAAACGGGTCGGGTC
1 TCAACGGGTCGGGTC
29394 GGGTTGTGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (31 bp):
TCAACGGGTCGGGTCAACGGGTCGGGTCGGG
Found at i:29392 original size:13 final size:13
Alignment explanation
Indices: 29339--29374 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
29329 GTCAACGGGT
*
29339 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
29352 CAGGTCGGGTAAA
1 CGGGTCGGGTAAA
29365 CGGGTCGGGT
1 CGGGTCGGGT
29375 CGGGTAAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.47, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:31739 original size:6 final size:6
Alignment explanation
Indices: 31728--31764 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
31718 ATTATATAAC
31728 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA A
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA A
31765 GGAGTCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTATA
Found at i:33928 original size:18 final size:20
Alignment explanation
Indices: 33905--33950 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
33895 ATTTTGGTAC
*
33905 CGATACTCATTGG-AG-TAT
1 CGATACTCAGTGGAAGATAT
33923 CGATAC-CAGTGGAAGAATAT
1 CGATACTCAGTGGAAG-ATAT
33943 CGATACTC
1 CGATACTC
33951 TCCATCAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 5 0.22
18 8 0.35
20 9 0.39
21 1 0.04
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (20 bp):
CGATACTCAGTGGAAGATAT
Found at i:34391 original size:22 final size:21
Alignment explanation
Indices: 34344--34408 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
34334 TGAAACCTTC
* **
34344 GTATCAGTGCGAATACACCTTT
1 GTATCAGTGCTAAGGCA-CTTT
* *
34366 GTATCAGTGTTGAGGCACTTT
1 GTATCAGTGCTAAGGCACTTT
*
34387 AGTATTAGTGCTAAGGCACTTT
1 -GTATCAGTGCTAAGGCACTTT
34409 TGTGATTACG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
GTATCAGTGCTAAGGCACTTT
Found at i:35637 original size:21 final size:21
Alignment explanation
Indices: 35593--35645 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
35583 AATATAAATT
* *
35593 GTGTATCGATGCACTACTATA
1 GTGTACCGATGCACTACTACA
**
35614 GTGTACCGATGCACTGTTACA
1 GTGTACCGATGCACTACTACA
35635 GTGTACCGATG
1 GTGTACCGATG
35646 TATTGCTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGTACCGATGCACTACTACA
Found at i:36409 original size:31 final size:31
Alignment explanation
Indices: 36374--36451 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
36364 CCATTGATTT
* *
36374 CGAAGAACCTAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAACCCATATGTCC
* *
36405 CGAAGAACATAGGTAAATAGCCCATATGTCC
1 CGAAGAACATAGGTAAACAACCCATATGTCC
36436 CGAAGAACATAGGTAA
1 CGAAGAACATAGGTAA
36452 CCCTCGACAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAACCCATATGTCC
Found at i:39808 original size:54 final size:54
Alignment explanation
Indices: 39732--40242 Score: 749
Period size: 54 Copynumber: 9.4 Consensus size: 54
39722 ATGTATATGC
* * *
39732 TGTGAATTACCGCATCGACACTATGTGTGCAACCTAAGTAATTCATAATGAGTT
1 TGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTT
*
39786 TGTGAATTACCGTATTGGCACTATGTGTGTAACCTAAGTAATTCATAATGAGTT
1 TGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTT
*
39840 TGTGAATTACCGTATTGGCACTATGTGTGCAACTTAAGTAATTCATAATGAGTT
1 TGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTT
* * *
39894 TGTGAATTATCGTATTGCCACTATGTGTGCAACCTAAGTAATTTATAATGAGTT
1 TGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTT
* * * *
39948 TGTGAATTACCGTACTAGTACTATATGTGCAACCTAAGTAATTCATAATGAGTT
1 TGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTT
* *
40002 TGTGAATTACCGTATCGGCACTATGTGTGTAACCTAAGTAATTCATAATGAGTT
1 TGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTT
** *
40056 TGTGAATTACCGTATCAGCACTATGTGTGCAATCTAAGTAATTCATAATGAGTT
1 TGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTT
* *
40110 TGTGAATTACCATTATCT-GCACTATGTATGCAACCTACA-TAATTC-TCAATGAGTT
1 TGTGAATTACC-GTAT-TGGCACTATGTGTGCAACCTA-AGTAATTCAT-AATGAGTT
* * *
40165 TGTGAATTACCGTATTGGCACTATGTGTGCAACCTACGTAATTCACAATGAGGT
1 TGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTT
**
40219 TGTGAATTACCGTATCAGCACTAT
1 TGTGAATTACCGTATTGGCACTAT
40243 ATGTACAAAA
Statistics
Matches: 413, Mismatches: 37, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.00
54 366 0.89
55 45 0.11
56 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (54 bp):
TGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTT
Found at i:46353 original size:20 final size:20
Alignment explanation
Indices: 46330--46382 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
46320 ACTCTGGTGT
46330 AGGTATCGATACCAAGAGAA
1 AGGTATCGATACCAAGAGAA
*
46350 AGGTATCGATACCAAGAGGA
1 AGGTATCGATACCAAGAGAA
46370 AGGTATCGATACC
1 AGGTATCGATACC
46383 GTAATCAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (20 bp):
AGGTATCGATACCAAGAGAA
Found at i:46873 original size:54 final size:54
Alignment explanation
Indices: 46810--47309 Score: 608
Period size: 54 Copynumber: 9.3 Consensus size: 54
46800 ACCACATCAG
* *
46810 CACTGTGTGTGCAACCTAAGTAATTCATAATAAGTTTGTGAATTACCGTATTGA
1 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACCGTATTGA
** **
46864 CACTATGTGTTAAACCTAAGTAATTCATAATGAGTTTGTGAATTATTGTATTGGA
1 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACCGTATT-GA
* * * * * * *
46919 -ACTATGTGTACAACTTAAATAATTCATAATGTGTCTGTGAATTATCGTATTGG
1 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACCGTATTGA
* * *
46972 CACTATGCGTCCAACCTAAGTAATTCATAATGAGTTTATGAATTACCGTATTTG-
1 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACCGTA-TTGA
* *
47026 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTATCGTATTGG
1 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACCGTATTGA
* * * *
47080 CACTATATGTGCAAACTAAGTAATTCATAATGAGTTTGTGAATTACCATATCGA
1 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACCGTATTGA
* * * * **
47134 CACCATGTGTACAACCTATGTAATTCATAATAAGTTTGTGAATTACCGTATCAA
1 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACCGTATTGA
* * * *
47188 CACTATATGTGCAACCTACGTAATTCACAATGAGTTTGTGAATTACCGTATTGG
1 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACCGTATTGA
* * * * * * *
47242 CACTATGTGTGTAACCTACGTAAATCACAATGAGGTTGTGAATTACTGTATCGA
1 CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACCGTATTGA
*
47296 CAATATGTGTGCAA
1 CACTATGTGTGCAA
47310 AACCATGAAA
Statistics
Matches: 384, Mismatches: 58, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
53 4 0.01
54 375 0.98
55 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (54 bp):
CACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTGAATTACCGTATTGA
Found at i:55946 original size:45 final size:45
Alignment explanation
Indices: 55880--55965 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
55870 TTTGAGAGAT
* *
55880 CTTAGGAAATAAGTTGTGTAATGCTAGTAATATCTCCAACATAGC
1 CTTAGGAAATAAGTTGGGTAATGCTAGTAATAGCTCCAACATAGC
* *
55925 CTTAGGAAATAAGTTGGGTAATGTTGGTAATAGCTCCAACA
1 CTTAGGAAATAAGTTGGGTAATGCTAGTAATAGCTCCAACA
55966 ATATGAGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (45 bp):
CTTAGGAAATAAGTTGGGTAATGCTAGTAATAGCTCCAACATAGC
Found at i:59819 original size:24 final size:23
Alignment explanation
Indices: 59775--59819 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
59765 GATATAAAAA
59775 ATATTTTTTATTAAATATTTTTG
1 ATATTTTTTATTAAATATTTTTG
*
59798 ATATATTTTTATTTAAT-TTTTT
1 ATAT-TTTTTATTAAATATTTTT
59820 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
ATATTTTTTATTAAATATTTTTG
Found at i:59977 original size:23 final size:23
Alignment explanation
Indices: 59947--59990 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
59937 GGAGGATAGT
*
59947 CTTTGTCTATAGAGTATCCAATC
1 CTTTGTCTATACAGTATCCAATC
59970 CTTTGTCTATACAGTATCCAA
1 CTTTGTCTATACAGTATCCAA
59991 CCCGGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (23 bp):
CTTTGTCTATACAGTATCCAATC
Found at i:61314 original size:65 final size:65
Alignment explanation
Indices: 61222--61349 Score: 156
Period size: 65 Copynumber: 2.0 Consensus size: 65
61212 TACTCTCTCA
* *
61222 AACGAAAGAATCACAGAATGTATTGAGGGCATCGATACCCCCT-AGCT-GGGTATCGATACCCCC
1 AACGAAAGAATCACAGAATGCATTGAGGGCACCGATA--CCCTAAG-TAGGGTATCGATACCCCC
61285 TTG
63 TTG
* *
61288 AACGAAA-AATCACAGAATGCCA-TGAGGGTACCGATACCTTAAGTAGGGTATCGATACCCCCT
1 AACGAAAGAATCACAGAATG-CATTGAGGGCACCGATACCCTAAGTAGGGTATCGATACCCCCT
61350 AAAGGAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
63 4 0.07
64 19 0.35
65 24 0.44
66 8 0.15
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (65 bp):
AACGAAAGAATCACAGAATGCATTGAGGGCACCGATACCCTAAGTAGGGTATCGATACCCCCTTG
Found at i:61913 original size:21 final size:22
Alignment explanation
Indices: 61887--61938 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
61877 GTCAAGGGGT
61887 TCATAGGTCATTCGGGACA-AC
1 TCATAGGTCATTCGGGACATAC
*
61908 TCATAGGTCCTTCGGGACATAC
1 TCATAGGTCATTCGGGACATAC
*
61930 TCACAGGTC
1 TCATAGGTC
61939 CTTTGGGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (22 bp):
TCATAGGTCATTCGGGACATAC
Found at i:61937 original size:22 final size:21
Alignment explanation
Indices: 61891--61946 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
61881 AGGGGTTCAT
* *
61891 AGGTCATTCGGGACAACTCAT
1 AGGTCCTTCGGGACAACTCAC
61912 AGGTCCTTCGGGACATACTCAC
1 AGGTCCTTCGGGACA-ACTCAC
*
61934 AGGTCCTTTGGGA
1 AGGTCCTTCGGGA
61947 TAATTTCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (21 bp):
AGGTCCTTCGGGACAACTCAC
Found at i:64326 original size:24 final size:24
Alignment explanation
Indices: 64291--64344 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
64281 GGAATCCATT
* *
64291 GGCAAATGTTATTTTTGTGATGTC
1 GGCAAATGTTATTTCTGTGATATC
*
64315 GGCAAATTTTATTTCTGTGATATC
1 GGCAAATGTTATTTCTGTGATATC
*
64339 AGCAAA
1 GGCAAA
64345 GAAGCTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (24 bp):
GGCAAATGTTATTTCTGTGATATC
Done.