Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009050.1 Hibiscus syriacus cultivar Beakdansim tig00112464_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: 74856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1604 original size:7 final size:7
Alignment explanation
Indices: 1594--1641 Score: 78
Period size: 7 Copynumber: 6.7 Consensus size: 7
1584 AAACAAAAAA
1594 AAAAAGG
1 AAAAAGG
*
1601 AAAAAGA
1 AAAAAGG
1608 AAAAAGG
1 AAAAAGG
1615 AAAAAGG
1 AAAAAGG
1622 AAAAAAGG
1 -AAAAAGG
1630 AAAAAGG
1 AAAAAGG
1637 AAAAA
1 AAAAA
1642 ATTGATCATG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 31 0.82
8 7 0.18
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:1612 original size:15 final size:15
Alignment explanation
Indices: 1593--1642 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
1583 AAAACAAAAA
1593 AAAAAAGGAAAAA-G
1 AAAAAAGGAAAAAGG
1607 AAAAAAGGAAAAAGG
1 AAAAAAGGAAAAAGG
1622 AAAAAAGGAAAAAGG
1 AAAAAAGGAAAAAGG
1637 AAAAAA
1 AAAAAA
1643 TTGATCATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 13 0.37
15 22 0.63
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAAAGGAAAAAGG
Found at i:6045 original size:51 final size:53
Alignment explanation
Indices: 5986--6104 Score: 163
Period size: 52 Copynumber: 2.3 Consensus size: 53
5976 AGAAAAAGAG
* *
5986 GAATGTGTTGTCAAAAG-TTTATGAACATCT-AGGCAGAAACCACATGAGAT-T
1 GAATGTGTTGTCAAAAGTTTTATGAACATCTGA-GCAGAAACCACAAGAAATAT
* *
6037 GAATGTGTTGTCAAAAGTTTTATGAGCATCTGAGCAGAAGCCACAAGAAATGAT
1 GAATGTGTTGTCAAAAGTTTTATGAACATCTGAGCAGAAACCACAAGAAAT-AT
6091 GAATGTGTTGTCAA
1 GAATGTGTTGTCAA
6105 GTGTTTTAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
51 17 0.28
52 27 0.45
53 1 0.02
54 15 0.25
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (53 bp):
GAATGTGTTGTCAAAAGTTTTATGAACATCTGAGCAGAAACCACAAGAAATAT
Found at i:8740 original size:73 final size:73
Alignment explanation
Indices: 8648--9109 Score: 786
Period size: 73 Copynumber: 6.4 Consensus size: 73
8638 CTATTTCCAA
* *
8648 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
8713 CTCAGGGT
66 CTCAGGGT
*
8721 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGT
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
8786 CTCAGGGT
66 CTCAGGGT
8794 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGC-TTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
8858 CT-AGGGT
66 CTCAGGGT
* * *
8865 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCTGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
*
8930 CTCATGGT
66 CTCAGGGT
* * * *
8938 CATCTATAAGACCTACAGTGTATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTTATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
9003 CTCAGGGT
66 CTCAGGGT
*
9011 CATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTAGGGAGCTTTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
9075 CTCAGGGT
66 CTCAGGGT
*
9083 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
9110 ATAAGACCTC
Statistics
Matches: 366, Mismatches: 21, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
71 51 0.14
72 101 0.28
73 214 0.58
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
CTCAGGGT
Found at i:8917 original size:144 final size:146
Alignment explanation
Indices: 8648--9109 Score: 786
Period size: 144 Copynumber: 3.2 Consensus size: 146
8638 CTATTTCCAA
* *
8648 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
8713 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
*
8778 TTTAAAGTCTCAGGGT
131 TTTAAAGCCTCAGGGT
8794 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGC-TTTTGATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
* * *
8858 CT-AGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCTGGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
*
8922 TTTAAAGCCTCATGGT
131 TTTAAAGCCTCAGGGT
* * * *
8938 CATCTATAAGACCTACAGTGTATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTTATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
*
9003 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTAGGGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
9067 TTTAAAGCCTCAGGGT
131 TTTAAAGCCTCAGGGT
*
9083 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
9110 ATAAGACCTC
Statistics
Matches: 295, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
144 119 0.40
145 98 0.33
146 78 0.26
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (146 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTAAAGC
CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
TTTAAAGCCTCAGGGT
Found at i:9023 original size:217 final size:218
Alignment explanation
Indices: 8648--9109 Score: 786
Period size: 217 Copynumber: 2.1 Consensus size: 218
8638 CTATTTCCAA
8648 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATCTTAAAGC
* *
8713 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
66 CTCAGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGAT
* *
8778 TTTAAAGTCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGC
131 TTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTAGGGAGC
8843 -TTTTGATTTTAAAGCCT-AGGGT
195 TTTTTGATTTTAAAGCCTCAGGGT
* * *
8865 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCTG-GAGCTTTTTGATTTTAAAG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTC-GAGAGCTTTTTGATCTTAAAG
* * *
8929 CCTCATGGTCATCTATAAGACCTACAGTGTATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTTA
65 CCTCAGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGA
8994 TTTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTAGGGAGC
130 TTTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTAGGGAGC
9059 TTTTTGATTTTAAAGCCTCAGGGT
195 TTTTTGATTTTAAAGCCTCAGGGT
*
9083 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
9110 ATAAGACCTC
Statistics
Matches: 229, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
216 20 0.09
217 179 0.78
218 30 0.13
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (218 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATCTTAAAGC
CTCAGGGTCATCTATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGAT
TTTAAAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTAGGGAGCT
TTTTGATTTTAAAGCCTCAGGGT
Found at i:12036 original size:29 final size:29
Alignment explanation
Indices: 11961--12041 Score: 71
Period size: 30 Copynumber: 2.8 Consensus size: 29
11951 TAATTTTTTA
*
11961 AAATTA-AATTTTGGTC-CCTAAACTTTTC
1 AAATTATAA-TTTGGTCACCTAAACTTTCC
* *
11989 AAAGTTTATACTTTAGTCACC-AAACTTTACC
1 AAA--TTATAATTTGGTCACCTAAACTTT-CC
12020 AAATTATAATTTGGTCA-CTAAA
1 AAATTATAATTTGGTCACCTAAA
12042 TAAATCCATT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
28 4 0.10
29 15 0.36
30 16 0.38
31 7 0.17
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.38
Consensus pattern (29 bp):
AAATTATAATTTGGTCACCTAAACTTTCC
Found at i:15152 original size:17 final size:17
Alignment explanation
Indices: 15130--15187 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 17
15120 GTCGAACAAG
15130 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
15147 TTCTTCTCCCTCTATCGGATGAC
1 TTCTTCT-CAT-TAT--GA--AC
15170 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
15187 T
1 T
15188 CTCCATTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
17 10 0.30
18 2 0.06
19 5 0.15
21 5 0.15
22 2 0.06
23 9 0.27
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.45
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:15278 original size:136 final size:128
Alignment explanation
Indices: 15090--15334 Score: 346
Period size: 136 Copynumber: 1.9 Consensus size: 128
15080 GAGGTATTGC
* * *
15090 TGATTCGAAATGTCGTGAATCAAGAAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTC
1 TGATTCGAAATGTCATGAATCAAGAAATAGGCCGAACAAGTTCTTCTCATTATGAAATTC--CTC
15155 CCTCTATCGGATGACTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATACCTTAAGCGAGG
64 CCTC-AT---ATGACTTC-T-TCATTATGAACTCTCCATTGGAAATGTTAATACCTTAAGCGAGG
15220 TGTTAT
123 TGTTAT
* **
15226 TGATTCGAAATGTCATGAATCAAGCAATAGGCCGAACAAGTTCTTCTCATTATGAAATTCCTCTG
1 TGATTCGAAATGTCATGAATCAAGAAATAGGCCGAACAAGTTCTTCTCATTATGAAATTCCTCCC
* *
15291 TCATATGAGTTCTTCATTATGAACTCTCTATTGGAAATGTTAAT
66 TCATATGACTTCTTCATTATGAACTCTCCATTGGAAATGTTAAT
15335 TGGTTTACCA
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
128 30 0.30
129 1 0.01
130 7 0.07
133 2 0.02
134 5 0.05
136 56 0.55
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (128 bp):
TGATTCGAAATGTCATGAATCAAGAAATAGGCCGAACAAGTTCTTCTCATTATGAAATTCCTCCC
TCATATGACTTCTTCATTATGAACTCTCCATTGGAAATGTTAATACCTTAAGCGAGGTGTTAT
Found at i:16371 original size:13 final size:12
Alignment explanation
Indices: 16333--16367 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
16323 TGAACCTCTC
*
16333 TTTTTCTTTTGT
1 TTTTTCTTTTCT
16345 TTTTTCCTTTTCT
1 TTTTT-CTTTTCT
16358 TTTTTCTTTT
1 TTTTTCTTTT
16368 TCTTAGGCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:27012 original size:21 final size:21
Alignment explanation
Indices: 26986--27025 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26976 CCCCCTTTGA
*
26986 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
27007 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
27026 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:32455 original size:31 final size:31
Alignment explanation
Indices: 32420--32491 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
32410 GTTCCGGAGA
* * *
32420 ACATAGGTAATCTGTCCATATGT-TCTAAATG
1 ACATAGGTAAACTATCCATATGTCTCGAAA-G
32451 ACATAGGTAAACTATCCATATGTCTCGAAAG
1 ACATAGGTAAACTATCCATATGTCTCGAAAG
32482 ACATAGGTAA
1 ACATAGGTAA
32492 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 32 0.86
32 5 0.14
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (31 bp):
ACATAGGTAAACTATCCATATGTCTCGAAAG
Found at i:34273 original size:17 final size:17
Alignment explanation
Indices: 34251--34284 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
34241 TCCAAGTCAG
34251 TAAAATAGGGCTTCTTT
1 TAAAATAGGGCTTCTTT
34268 TAAAATAGGGCTTCTTT
1 TAAAATAGGGCTTCTTT
34285 GACCCTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (17 bp):
TAAAATAGGGCTTCTTT
Found at i:36581 original size:56 final size:57
Alignment explanation
Indices: 36495--36610 Score: 207
Period size: 56 Copynumber: 2.0 Consensus size: 57
36485 ATCTGAGAAA
36495 CTTTTATGCTCTTTCTCTCTTTCCATATTCACCAACC-AGATTTTTTCTCTCAAAAG
1 CTTTTATGCTCTTTCTCTCTTTCCATATTCACCAACCAAGATTTTTTCTCTCAAAAG
*
36551 CTTTTATGCTCTTTCTCTCTTTCCATATTCACCAACCATATATTTTTTCTCTCAAAAG
1 CTTTTATGCTCTTTCTCTCTTTCCATATTCACCAACCA-AGATTTTTTCTCTCAAAAG
36609 CT
1 CT
36611 CGACCTCAGT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
56 37 0.65
58 20 0.35
ACGTcount: A:0.22, C:0.28, G:0.04, T:0.46
Consensus pattern (57 bp):
CTTTTATGCTCTTTCTCTCTTTCCATATTCACCAACCAAGATTTTTTCTCTCAAAAG
Found at i:41905 original size:29 final size:29
Alignment explanation
Indices: 41862--41917 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
41852 AAAAATTGAC
41862 TACAATCCAAGTTTGATGTTAACTTGTAT
1 TACAATCCAAGTTTGATGTTAACTTGTAT
* *
41891 TACAATCCGATTTTGATGTTAACTTGT
1 TACAATCCAAGTTTGATGTTAACTTGT
41918 TTATGGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (29 bp):
TACAATCCAAGTTTGATGTTAACTTGTAT
Found at i:41987 original size:26 final size:26
Alignment explanation
Indices: 41958--42009 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
41948 AGATCATATT
*
41958 TTATCATATCTCAGTCATCAAGTTAA
1 TTATCATATCTCAGTCAGCAAGTTAA
41984 TTATCATATCTCAGTCAGCAAGTTAA
1 TTATCATATCTCAGTCAGCAAGTTAA
42010 CATCCAGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (26 bp):
TTATCATATCTCAGTCAGCAAGTTAA
Found at i:42578 original size:6 final size:6
Alignment explanation
Indices: 42567--42592 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42557 AAACCCAAAT
42567 AGGGAA AGGGAA AGGGAA AGGGAA AG
1 AGGGAA AGGGAA AGGGAA AGGGAA AG
42593 CCACTTAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGGAA
Found at i:47015 original size:81 final size:80
Alignment explanation
Indices: 46911--47094 Score: 212
Period size: 81 Copynumber: 2.3 Consensus size: 80
46901 CTTTAGCGGT
* * * *
46911 GTTTTATACAAATGCCACTATA-GGTTCATC-AGTAGTGGCATTTTTCAACAAACGTCATGATAG
1 GTTTTATAAAAATGCCACTATAGGGTTCATCTA-TAGTGGCA-TTTTCAACAAACATCATAACAG
46974 AGTAGTACTTTAGAAGC
64 AGTAGTACTTTAGAAGC
*
46991 GTTTATATAAAAATGCCA-TAATAGGGTTCATCTATAGTGGCATTTTCAACAAACATCGTAACAG
1 GTTT-TATAAAAATGCCACT-ATAGGGTTCATCTATAGTGGCATTTTCAACAAACATCATAACAG
**
47055 AGTAGTACTTTAGTGGC
64 AGTAGTACTTTAGAAGC
* * *
47072 ATTTTTATACAAATGCCGCTATA
1 -GTTTTATAAAAATGCCACTATA
47095 AACTCATACT
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
80 5 0.06
81 62 0.70
82 20 0.23
83 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (80 bp):
GTTTTATAAAAATGCCACTATAGGGTTCATCTATAGTGGCATTTTCAACAAACATCATAACAGAG
TAGTACTTTAGAAGC
Found at i:47131 original size:40 final size:40
Alignment explanation
Indices: 47060--47199 Score: 145
Period size: 40 Copynumber: 3.4 Consensus size: 40
47050 AACAGAGTAG
* * *
47060 TACTTTAGTGGCATTTTTATACAAATGCCGCTATAAACTCA
1 TACTTTAGTGGC-GTTTTATACAAACGCCGCTATAGACTCA
* * *
47101 TACTTTAATGGCGTTTTATACAAACACCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTATACAAACGCCGCTATAGACTCA
* ** * *
47141 TATTTTAGTGATGTTTATGTTTAAAAACGCCGCTATAGACTCA
1 TACTTTAGTGGCG-TT-T-TATACAAACGCCGCTATAGACTCA
47184 TACTTTAGTGGCGTTT
1 TACTTTAGTGGCGTTT
47200 GTATTTTAAA
Statistics
Matches: 79, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
40 32 0.41
41 14 0.18
42 3 0.04
43 30 0.38
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (40 bp):
TACTTTAGTGGCGTTTTATACAAACGCCGCTATAGACTCA
Found at i:47211 original size:43 final size:42
Alignment explanation
Indices: 47087--47218 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 42
47077 TATACAAATG
* *
47087 CCGCTATAAACTCATACTTTAATGGCGTTTTA---TACAAACA
1 CCGCTATAGACTCATACTTTAGTGGCGTTTTATTTTA-AAACA
* * ** *
47127 CCGCTATAGACTCGTATTTTAGTGATG-TTTATGTTTAAAAACG
1 CCGCTATAGACTCATACTTTAGTGGCGTTTTAT-TTT-AAAACA
47170 CCGCTATAGACTCATACTTTAGTGGCGTTTGTATTTTAAAACA
1 CCGCTATAGACTCATACTTTAGTGGCGTTT-TATTTTAAAACA
47213 CCGCTA
1 CCGCTA
47219 AAGTTTAAAG
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
39 4 0.05
40 21 0.29
43 39 0.53
44 6 0.08
45 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (42 bp):
CCGCTATAGACTCATACTTTAGTGGCGTTTTATTTTAAAACA
Found at i:58187 original size:28 final size:28
Alignment explanation
Indices: 58101--58225 Score: 96
Period size: 28 Copynumber: 4.5 Consensus size: 28
58091 ATGACTAAAC
* * * *
58101 ACCTCTGTGCTTCAATTTAGAATCTGGT
1 ACCTCTGTGCTTTAATATAAAATCTGGA
* ** *
58129 ACCTCTGTGCTTT-CTA-ATGAT-TGAGC
1 ACCTCTGTGCTTTAATATAAAATCTG-GA
* *
58155 ACCTCTGTGCTTTAATATAAGATTTGGA
1 ACCTCTGTGCTTTAATATAAAATCTGGA
* *
58183 ACCTCTGTGCTTCAATATAAAATCTGGC
1 ACCTCTGTGCTTTAATATAAAATCTGGA
58211 ACCT-TAGTGCTTTAA
1 ACCTCT-GTGCTTTAA
58226 AATTGATTGA
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
25 2 0.03
26 17 0.22
27 4 0.05
28 53 0.68
29 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (28 bp):
ACCTCTGTGCTTTAATATAAAATCTGGA
Found at i:58189 original size:82 final size:83
Alignment explanation
Indices: 58101--58277 Score: 218
Period size: 83 Copynumber: 2.1 Consensus size: 83
58091 ATGACTAAAC
* * * ** *
58101 ACCTCTGTGCTTCAATTTAGAATCTGGTACCTCT-GTGCTTTCTAA-TGATTGAGCACCTCTGTG
1 ACCTCTGTGCTTCAATATAAAATCTGGCACCT-TAGTGCTTTAAAATTGATTGAGCACCTCCGTG
* *
58164 CT-TTAATATA-AGATTTGGA
65 -TATCAATATAGAG-TATGGA
58183 ACCTCTGTGCTTCAATATAAAATCTGGCACCTTAGTGCTTTAAAATTGATTGAGCACCTCCGTGT
1 ACCTCTGTGCTTCAATATAAAATCTGGCACCTTAGTGCTTTAAAATTGATTGAGCACCTCCGTGT
*
58248 ATCAATATAGAGTATGGC
66 ATCAATATAGAGTATGGA
58266 ACCTCTGTGCTT
1 ACCTCTGTGCTT
58278 TTGATAAACG
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
81 1 0.01
82 39 0.48
83 40 0.49
84 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (83 bp):
ACCTCTGTGCTTCAATATAAAATCTGGCACCTTAGTGCTTTAAAATTGATTGAGCACCTCCGTGT
ATCAATATAGAGTATGGA
Found at i:58275 original size:83 final size:82
Alignment explanation
Indices: 58100--58277 Score: 218
Period size: 82 Copynumber: 2.2 Consensus size: 82
58090 AATGACTAAA
* * * ** *
58100 CACCTCTGTGCTTCAATTTAGAATCTGGTACCTCTGTGCTTTCTAATGATTGAGCACCTCTGTGC
1 CACCTCTGTGCTTCAATATAAAATCTGGCACCTCTGTGCTTTAAAATGATTGAGCACCTCCGTGC
* *
58165 TTTAATATAAGATTTGG
66 TTCAATATAAGATATGG
*
58182 AACCTCTGTGCTTCAATATAAAATCTGGCACCT-TAGTGCTTTAAAATTGATTGAGCACCTCCGT
1 CACCTCTGTGCTTCAATATAAAATCTGGCACCTCT-GTGCTTTAAAA-TGATTGAGCACCTCCGT
58246 G-TATCAATAT-AGAGTATGG
64 GCT-TCAATATAAGA-TATGG
58265 CACCTCTGTGCTT
1 CACCTCTGTGCTT
58278 TTGATAAACG
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
81 1 0.01
82 42 0.51
83 39 0.48
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (82 bp):
CACCTCTGTGCTTCAATATAAAATCTGGCACCTCTGTGCTTTAAAATGATTGAGCACCTCCGTGC
TTCAATATAAGATATGG
Found at i:61767 original size:29 final size:29
Alignment explanation
Indices: 61735--61809 Score: 150
Period size: 29 Copynumber: 2.6 Consensus size: 29
61725 ATAATTGACT
61735 AAAGCAATAAGTGAGGGAAATTATTGAAC
1 AAAGCAATAAGTGAGGGAAATTATTGAAC
61764 AAAGCAATAAGTGAGGGAAATTATTGAAC
1 AAAGCAATAAGTGAGGGAAATTATTGAAC
61793 AAAGCAATAAGTGAGGG
1 AAAGCAATAAGTGAGGG
61810 GTAAGCTTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.48, C:0.07, G:0.27, T:0.19
Consensus pattern (29 bp):
AAAGCAATAAGTGAGGGAAATTATTGAAC
Found at i:65656 original size:46 final size:46
Alignment explanation
Indices: 65546--65700 Score: 225
Period size: 46 Copynumber: 3.5 Consensus size: 46
65536 TTTATTGGTT
*
65546 ATTAAATGGTAAG--TA-T-GT-AAATAAGCTTACGAGATTATGGA
1 ATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
* *
65587 A-T-AATGGCAAATATATTGGTAAAATAAGCTTACGAGCTTATGGA
1 ATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
*
65631 ATTAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGA
1 ATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
65677 ATTAAATGGTAAGTATATTGGTAA
1 ATTAAATGGTAAGTATATTGGTAA
65701 CATCATTTTA
Statistics
Matches: 101, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
39 7 0.07
40 1 0.01
41 3 0.03
42 1 0.01
43 2 0.02
44 23 0.23
45 1 0.01
46 63 0.62
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (46 bp):
ATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
Found at i:68330 original size:21 final size:20
Alignment explanation
Indices: 68305--68343 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
68295 TTATGATAAA
68305 CTATCA-AAGTATGAGTTTTGG
1 CTATCAGAAGT-TGA-TTTTGG
68326 CTATCAGAAGTTGATTTT
1 CTATCAGAAGTTGATTTT
68344 CTTAGTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
CTATCAGAAGTTGATTTTGG
Found at i:68435 original size:4 final size:5
Alignment explanation
Indices: 68382--68447 Score: 64
Period size: 5 Copynumber: 12.8 Consensus size: 5
68372 TAAGAGCTAA
* *
68382 AAAAG AATA- AAAAG AAAAG AAAACG AAGAAG AAAA- AAAAC AAATAG
1 AAAAG AAAAG AAAAG AAAAG AAAA-G AA-AAG AAAAG AAAAG AAA-AG
68428 AGAAAG AAAAG AAAAG AAAA
1 A-AAAG AAAAG AAAAG AAAA
68448 AGAGAAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
4 7 0.13
5 30 0.58
6 11 0.21
7 4 0.08
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:68439 original size:26 final size:25
Alignment explanation
Indices: 68382--68455 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
68372 TAAGAGCTAA
* *
68382 AAAAGAATAAAAAGAAAAGAAAACG
1 AAAAGAAAAAAAACAAAAGAAAACG
68407 AAGAAGAAAAAAAACAAATAGAGAAA-G
1 AA-AAGAAAAAAAACAAA-AGA-AAACG
* *
68434 AAAAGAAAAGAAA-AAGAGAAAA
1 AAAAGAAAAAAAACAAAAGAAAA
68456 AAATTCACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
23 3 0.07
24 3 0.07
25 4 0.10
26 23 0.55
27 6 0.14
28 3 0.07
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (25 bp):
AAAAGAAAAAAAACAAAAGAAAACG
Found at i:68458 original size:16 final size:15
Alignment explanation
Indices: 68381--68458 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 15
68371 ATAAGAGCTA
*
68381 AAAAAGAATAAAAAG
1 AAAAAGAAAAAAAAG
68396 -AAAAGAAAACGAAGAAG
1 AAAAAGAAAA--AA-AAG
*
68413 AAAAA-AAACAAATAG
1 AAAAAGAAA-AAAAAG
*
68428 AGAAAGAAAAGAAAAG
1 AAAAAGAAAA-AAAAG
68444 AAAAAGAGAAAAAAA
1 AAAAAGA-AAAAAAA
68459 TTCACTTGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
14 8 0.16
15 7 0.14
16 21 0.42
17 9 0.18
18 5 0.10
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:72567 original size:93 final size:90
Alignment explanation
Indices: 72375--72602 Score: 352
Period size: 93 Copynumber: 2.5 Consensus size: 90
72365 GTAAGTATGC
* *
72375 AAATAAGCTTACGAGCTTATGGAA-T-AATGGCAAGTATATTGGTAAGATAAGCTTACGAGCATA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCATA
72438 TGGAATAATGGCAAGTATATTGGTA
66 TGGAATAATGGCAAGTATATTGGTA
* *
72463 AGATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTTGGTAAAATAAGCTTACGAGCTT
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATA-TTGGTAAAATAAGCTTACGAGCAT
*
72528 ATGGAATTAAATGGTAAGTATATTGGTA
65 ATGGAA-T-AATGGCAAGTATATTGGTA
* *
72556 AAATAAGCTTACAAGCTTATGGAATTAAATGATAAGTATATTGGTAA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTAA
72603 CATGATTTTA
Statistics
Matches: 127, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
88 23 0.18
89 1 0.01
90 12 0.09
91 28 0.22
92 8 0.06
93 55 0.43
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.31
Consensus pattern (90 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCATA
TGGAATAATGGCAAGTATATTGGTA
Found at i:72573 original size:46 final size:46
Alignment explanation
Indices: 72375--72602 Score: 356
Period size: 44 Copynumber: 5.0 Consensus size: 46
72365 GTAAGTATGC
*
72375 AAATAAGCTTACGAGCTTATGGAA-T-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
* * *
72419 AGATAAGCTTACGAGCATATGGAA-T-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
*
72463 AGATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATA-TTGGTA
72510 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
* *
72556 AAATAAGCTTACAAGCTTATGGAATTAAATGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
72602 A
1 A
72603 CATGATTTTA
Statistics
Matches: 174, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
44 65 0.37
45 1 0.01
46 63 0.36
47 45 0.26
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
Found at i:73001 original size:22 final size:22
Alignment explanation
Indices: 72976--73022 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
72966 TTCCAGAATG
*
72976 CTACAAGGGTATCGATACCCT-A
1 CTAC-AGGGTACCGATACCCTCA
*
72998 CTACAGTGTACCGATACCCTCA
1 CTACAGGGTACCGATACCCTCA
73020 CTA
1 CTA
73023 TTCACTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (22 bp):
CTACAGGGTACCGATACCCTCA
Found at i:74435 original size:17 final size:18
Alignment explanation
Indices: 74403--74441 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
74393 GAATTCAATT
*
74403 TAAAGATTACATTTAATA
1 TAAACATTACATTTAATA
*
74421 TAAACATTA-ATTTAATT
1 TAAACATTACATTTAATA
74438 TAAA
1 TAAA
74442 AATAAACTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAACATTACATTTAATA
Found at i:74772 original size:27 final size:27
Alignment explanation
Indices: 74742--74823 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
74732 ACTTTAACTT
*
74742 TCTTATCTTCTTCCTCTTCTTTCTTTC
1 TCTTTTCTTCTTCCTCTTCTTTCTTTC
** * *
74769 TCTTTTC-TCTTATTTCTTCCTCCTTTC
1 TCTTTTCTTCTT-CCTCTTCTTTCTTTC
74796 TCTTCTTTCTTCTTCC-CTTCTTTCTTTC
1 TC-T-TTTCTTCTTCCTCTTCTTTCTTTC
74824 ACTCCCGGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
26 4 0.10
27 19 0.45
28 11 0.26
29 4 0.10
30 4 0.10
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (27 bp):
TCTTTTCTTCTTCCTCTTCTTTCTTTC
Found at i:74784 original size:20 final size:20
Alignment explanation
Indices: 74755--74823 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
74745 TATCTTCTTC
* *
74755 CTCTTCTTTCTTTCTCTTTT
1 CTCTTCTTTCTTCCTCCTTT
*
74775 CTCTTATTTCTTCCTCCTTT
1 CTCTTCTTTCTTCCTCCTTT
* *
74795 CTCTTCTTTCTTCTTCCCTT
1 CTCTTCTTTCTTCCTCCTTT
74815 CT-TTCTTTC
1 CTCTTCTTTC
74824 ACTCCCGGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 7 0.16
20 36 0.84
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (20 bp):
CTCTTCTTTCTTCCTCCTTT
Done.