Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006444.1 Hibiscus syriacus cultivar Beakdansim tig00015573_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: 110116
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1991 original size:22 final size:22
Alignment explanation
Indices: 1960--2010 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1950 CCCCACTGCA
1960 TGCA-GGCGACCTCTTCCGACG
1 TGCATGGCGACCTCTTCCGACG
1981 TGCATGGCGACCTCTTCCGACG
1 TGCATGGCGACCTCTTCCGACG
2003 TGCATGGC
1 TGCATGGC
2011 ACATGCAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.14, C:0.35, G:0.29, T:0.22
Consensus pattern (22 bp):
TGCATGGCGACCTCTTCCGACG
Found at i:2068 original size:30 final size:31
Alignment explanation
Indices: 2015--2075 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
2005 CATGGCACAT
2015 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
* *
2046 GCAAAGCTTCCT-CTCTCGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
2076 TAGAACACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.23, C:0.39, G:0.15, T:0.23
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Found at i:2931 original size:268 final size:267
Alignment explanation
Indices: 2451--2988 Score: 880
Period size: 268 Copynumber: 2.0 Consensus size: 267
2441 ATCTTTCGAT
* *
2451 TATATGTTGTTCCTTTGTCGAGTCCTCCAACTATTAAAAGTTATAAAACAATCGTTTGACTATCT
1 TATATGTTGTTCCTTTGTCGAGTCCCCCAACTATTAAAAGTTACAAAACAATCGTTTGACTATCT
* *
2516 AGTATGTCACAAATTCATCATTTTTCATTAGAAATGACGACAATTTGAGTTGGATGTTTACATGT
66 AGTATGTCACAAATTCATCATTTTTCATTAAAAATGACGACAATTTGAGTTGAATGTTTACATGT
*
2581 TGATTAAGATATGATAAAATCGGATTCCATAATCTTAAAAAATTATCATATCTTAGTCAACAGAT
131 TGATTAAGATATGATAAAATCGGATTCCATAATCTTAAAAAATTATCATATCTTAATCAACAGAT
* *
2646 TTAACATCCAACTCATACTTTTGTCAAATTTCTAACGGAAAAGAACAAGTTTAAACATATATCAA
196 TTAACATCCAACTCATACTTTTGTCAAATTTCTAACGAAAAAGAACAAGCTTAAACATATATCAA
2711 AAGATTG
261 AAGATTG
* ** *
2718 TATATGTTGTTTCTTTGTTTAGTCCCCCAACTATTAAAAGTTACAAAACGATCGTTTGACTATCT
1 TATATGTTGTTCCTTTGTCGAGTCCCCCAACTATTAAAAGTTACAAAACAATCGTTTGACTATCT
*
2783 AGTATGTCACAAATTCATCA-TTTTCTATTATAAAATGACTACAATTTGAGTTGAATGTTTACAT
66 AGTATGTCACAAATTCATCATTTTTC-ATTA-AAAATGACGACAATTTGAGTTGAATGTTTACAT
* * *
2847 GTTGATTGAGATATGATAAAATCGGATTCCATAATCTTAAAAAATTATCATATCTTAATCCACAT
129 GTTGATTAAGATATGATAAAATCGGATTCCATAATCTTAAAAAATTATCATATCTTAATCAACAG
* * * *
2912 ATTTAACATTCAGCTCATACTTTTGTCAAATTTCTAACGAAAAAGAACAAGCTTGAACATATATT
194 ATTTAACATCCAACTCATACTTTTGTCAAATTTCTAACGAAAAAGAACAAGCTTAAACATATATC
2977 AAAAGATTG
259 AAAAGATTG
2986 TAT
1 TAT
2989 TTAAAATCTT
Statistics
Matches: 250, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
266 5 0.02
267 83 0.33
268 162 0.65
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (267 bp):
TATATGTTGTTCCTTTGTCGAGTCCCCCAACTATTAAAAGTTACAAAACAATCGTTTGACTATCT
AGTATGTCACAAATTCATCATTTTTCATTAAAAATGACGACAATTTGAGTTGAATGTTTACATGT
TGATTAAGATATGATAAAATCGGATTCCATAATCTTAAAAAATTATCATATCTTAATCAACAGAT
TTAACATCCAACTCATACTTTTGTCAAATTTCTAACGAAAAAGAACAAGCTTAAACATATATCAA
AAGATTG
Found at i:8878 original size:2 final size:2
Alignment explanation
Indices: 8834--8866 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
8824 TATATTTTCC
8834 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8867 AACATCATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11271 original size:15 final size:15
Alignment explanation
Indices: 11234--11286 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
11224 TAACTTTGGA
*
11234 GGCGGTGGCTATGGC
1 GGCGGTGGCTATGGT
11249 GGTC-GTGGCTATGGT
1 GG-CGGTGGCTATGGT
*
11264 GGCGGTGGCTACGGT
1 GGCGGTGGCTATGGT
*
11279 GGTGGTGG
1 GGCGGTGG
11287 TGGCTACAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 1 0.03
15 31 0.94
16 1 0.03
ACGTcount: A:0.06, C:0.15, G:0.55, T:0.25
Consensus pattern (15 bp):
GGCGGTGGCTATGGT
Found at i:12083 original size:26 final size:26
Alignment explanation
Indices: 12042--12103 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
12032 TAAGAATTTT
12042 TAAAGTTTGATTAAAATATGAGTGAGAA
1 TAAAG-TT-ATTAAAATATGAGTGAGAA
12070 TAAAGTTATTAAAATATGAGTGAGAA
1 TAAAGTTATTAAAATATGAGTGAGAA
12096 TAAAGTTA
1 TAAAGTTA
12104 AAGGATGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 27 0.79
27 2 0.06
28 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (26 bp):
TAAAGTTATTAAAATATGAGTGAGAA
Found at i:12111 original size:23 final size:24
Alignment explanation
Indices: 12052--12111 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 24
12042 TAAAGTTTGA
*
12052 TTAAAATATGAGTGAGAATAAAGTT
1 TTAAAAGATGAGTGAGAATAAAG-T
*
12077 ATTAAAATATGAGTGAGAATAAAG-
1 -TTAAAAGATGAGTGAGAATAAAGT
*
12101 TTAAAGGATGA
1 TTAAAAGATGA
12112 AATTTGTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 9 0.28
26 23 0.72
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (24 bp):
TTAAAAGATGAGTGAGAATAAAGT
Found at i:12344 original size:2 final size:2
Alignment explanation
Indices: 12339--12365 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12329 TAAAAAAAAT
12339 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 T
12366 TTAAAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19855 original size:16 final size:16
Alignment explanation
Indices: 19836--19866 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19826 AATCAAATTG
19836 AAATAAAAAAATAAAT
1 AAATAAAAAAATAAAT
*
19852 AAATAAAAATATAAA
1 AAATAAAAAAATAAA
19867 GGAAGAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAAAAAATAAAT
Found at i:21533 original size:38 final size:38
Alignment explanation
Indices: 21481--21557 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
21471 ATAAAATCAA
*
21481 TGAATAGACAATGGACTCGGGATTCT-TCTGAGACACCC
1 TGAATAGACAATGGACTCGGGATT-TGTCCGAGACACCC
**
21519 TGAATAGATTATGGACTCGGGATTTGTCCGAGACACCC
1 TGAATAGACAATGGACTCGGGATTTGTCCGAGACACCC
21557 T
1 T
21558 CACCGTCACT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 34 0.97
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (38 bp):
TGAATAGACAATGGACTCGGGATTTGTCCGAGACACCC
Found at i:24467 original size:31 final size:31
Alignment explanation
Indices: 24430--24512 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
24420 GTAAACTACC
24430 TATTTAGTCACTAAACTATAAGAATCATTTTA
1 TATTTAGTCACTAAACTATAAGAA-CATTTTA
*
24462 T-TTTAGACACTAAA-TA-AA-AACATTTTA
1 TATTTAGTCACTAAACTATAAGAACATTTTA
**
24489 TAATCAAGTCACTAAACT-TAAGAA
1 T-ATTTAGTCACTAAACTATAAGAA
24513 ATTCAATCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
27 8 0.19
28 2 0.05
29 12 0.29
30 5 0.12
31 14 0.33
32 1 0.02
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (31 bp):
TATTTAGTCACTAAACTATAAGAACATTTTA
Found at i:28853 original size:18 final size:19
Alignment explanation
Indices: 28815--28854 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
28805 TTATTAAAAT
*
28815 TAAAAAATATTTAGAATTA
1 TAAAAAATATTTAGAAGTA
*
28834 TAAAAAA-ATTTATAAGTA
1 TAAAAAATATTTAGAAGTA
28852 TAA
1 TAA
28855 CTGAAAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
TAAAAAATATTTAGAAGTA
Found at i:33524 original size:3 final size:3
Alignment explanation
Indices: 33518--33543 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33508 CTCTTCATCA
33518 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
33544 ATGTACGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:35163 original size:31 final size:31
Alignment explanation
Indices: 35093--35216 Score: 117
Period size: 31 Copynumber: 4.0 Consensus size: 31
35083 GTCGAGGGTT
* *
35093 TACCTATGTTCTACGGAATATATGGACA-TAA
1 TACCTATGTTCTAAGGAACATATGGACAGT-A
* * *
35124 TTACCTATGTATTTATGG-ACATATGGATAGTA
1 -TACCTATGT-TCTAAGGAACATATGGACAGTA
35156 TACCTATGTTCTAAGGAACATATGGACAGTA
1 TACCTATGTTCTAAGGAACATATGGACAGTA
* ** * *
35187 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGT
35217 TGCCGAGGAT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
30 5 0.06
31 47 0.61
32 19 0.25
33 6 0.08
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:35253 original size:30 final size:30
Alignment explanation
Indices: 35203--35275 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
35193 GGTTCTTCGG
* * * *
35203 GACCTATGGACAGTTGCCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCCTTAT
* *
35233 GACCTCTGGATAGTTACCGAGGTTCCTTGT
1 GACCTCTGGATAGTTACCGAGGATCCTTAT
35263 GACCTCTGGATAG
1 GACCTCTGGATAG
35276 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCCTTAT
Found at i:38153 original size:3 final size:3
Alignment explanation
Indices: 38139--38173 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
38129 AGAGATATTC
*
38139 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
38174 ATGTATAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:38754 original size:23 final size:22
Alignment explanation
Indices: 38706--38754 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
38696 CCAGAATGTC
38706 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
38727 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
38750 AAGGA
1 AAGGA
38755 AAAATGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:39792 original size:31 final size:31
Alignment explanation
Indices: 39722--39845 Score: 135
Period size: 31 Copynumber: 4.0 Consensus size: 31
39712 GTCGAGGGTT
* *
39722 TACCTATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTTCGGGACATATGGACAGT-A
*
39753 TTACCTATG-TCTTTCGGGACATATGGATAGTA
1 -TACCTATGTTC-TTCGGGACATATGGACAGTA
** *
39785 TACCTATGTTCTAAGGAACATATGGACAGTA
1 TACCTATGTTCTTCGGGACATATGGACAGTA
* *
39816 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTTCGGGACATATGGACAGT
39846 TGCCGAGGAT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
31 51 0.66
32 25 0.32
33 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTTCGGGACATATGGACAGTA
Found at i:39882 original size:30 final size:30
Alignment explanation
Indices: 39832--39904 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
39822 GGTTCTTCGG
* * * *
39832 GACCTATGGACAGTTGCCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCCTTAT
* *
39862 GACCTCTGGATAGTTACCGAGGTTCCTTGT
1 GACCTCTGGATAGTTACCGAGGATCCTTAT
39892 GACCTCTGGATAG
1 GACCTCTGGATAG
39905 GTCATTCGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCCTTAT
Found at i:46728 original size:2 final size:2
Alignment explanation
Indices: 46723--46756 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46713 ATATATGTTA
46723 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
46757 GAATATCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46762 original size:10 final size:9
Alignment explanation
Indices: 46721--46762 Score: 52
Period size: 8 Copynumber: 4.7 Consensus size: 9
46711 GAATATATGT
46721 TAATATATA
1 TAATATATA
46730 T-ATATATA
1 TAATATATA
46738 T-ATATATA
1 TAATATATA
46746 TATATATATA
1 TA-ATATATA
46756 TGAATAT
1 T-AATAT
46763 CAATGACTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.53
9 1 0.03
10 12 0.40
11 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (9 bp):
TAATATATA
Found at i:50703 original size:3 final size:3
Alignment explanation
Indices: 50695--50723 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
50685 TTGGGTTTTA
50695 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
50724 CAAATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:50869 original size:16 final size:17
Alignment explanation
Indices: 50846--50885 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
50836 GGTGTACAAA
50846 TCCGGGTACCCGG-ATT
1 TCCGGGTACCCGGAATT
* *
50862 TTCGGGTACCTGGAATT
1 TCCGGGTACCCGGAATT
50879 TCCGGGT
1 TCCGGGT
50886 CGACGATTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.12, C:0.25, G:0.33, T:0.30
Consensus pattern (17 bp):
TCCGGGTACCCGGAATT
Found at i:51120 original size:16 final size:15
Alignment explanation
Indices: 51094--51129 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
51084 CAAAATACAA
51094 AATATAATAATTCAT
1 AATATAATAATTCAT
51109 AATATAAATAATTCAT
1 AATAT-AATAATTCAT
*
51125 TATAT
1 AATAT
51130 TTTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAATAATTCAT
Found at i:54193 original size:31 final size:28
Alignment explanation
Indices: 54141--54214 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
54131 CTTTTTTAAA
* *
54141 TTATATTTTTGGTACCTAAACTTATACAAAAT
1 TTATA-TTTTAGT-CCTAAACTT-T-CAAAAC
54173 TTATATTTTAGTCCTCAAACTTTCAAAAC
1 TTATATTTTAGTCCT-AAACTTTCAAAAC
*
54202 TTACATTTTAGTC
1 TTATATTTTAGTC
54215 ACTAGTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 17 0.45
30 4 0.11
31 12 0.32
32 5 0.13
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (28 bp):
TTATATTTTAGTCCTAAACTTTCAAAAC
Found at i:54910 original size:27 final size:27
Alignment explanation
Indices: 54872--54924 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
54862 ACGTGCAACC
54872 GTTTTAATATAC-GATTAAGGAAATATA
1 GTTTTAATATACAG-TTAAGGAAATATA
54899 GTTTTAATATACAGTTAAGGAAATAT
1 GTTTTAATATACAGTTAAGGAAATAT
54925 GCTATTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (27 bp):
GTTTTAATATACAGTTAAGGAAATATA
Found at i:55137 original size:21 final size:21
Alignment explanation
Indices: 55112--55156 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
55102 AGAAATATTA
*
55112 AAAAATATTAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
*
55133 AAAAATAATAATATTTTAGAT
1 AAAAATAATAATATTTTAAAT
55154 AAA
1 AAA
55157 TTTTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:55185 original size:21 final size:22
Alignment explanation
Indices: 55107--55187 Score: 59
Period size: 21 Copynumber: 3.9 Consensus size: 22
55097 TTACTAGAAA
55107 TATTAA-AAAATATTAAT-ATTT
1 TATTAATAAAATA-TAATAATTT
*
55128 TA--AATAAAA-ATAATAATAT
1 TATTAATAAAATATAATAATTT
* *
55147 T-TTAGATAAATTTTTAATAATTT
1 TATTA-ATAAA-ATATAATAATTT
55170 TATTAA-AAAATATAATAA
1 TATTAATAAAATATAATAA
55188 CAAAATTGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
18 4 0.09
19 7 0.15
20 5 0.11
21 14 0.30
22 3 0.07
23 10 0.22
24 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (22 bp):
TATTAATAAAATATAATAATTT
Found at i:59189 original size:20 final size:20
Alignment explanation
Indices: 59159--59205 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
59149 ATTGCTCGAT
59159 TCTTG-CCTGATTATGGAAC
1 TCTTGTCCTGATTATGGAAC
59178 TCTTGTCCTGATTATGGAAC
1 TCTTGTCCTGATTATGGAAC
59198 TCTTGTCC
1 TCTTGTCC
59206 ATTGGCAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (20 bp):
TCTTGTCCTGATTATGGAAC
Found at i:62826 original size:16 final size:17
Alignment explanation
Indices: 62796--62828 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
62786 TATGTTTCTG
62796 AAAATTGATTCTAAAAA
1 AAAATTGATTCTAAAAA
*
62813 AAAATT-ATTTTAAAAA
1 AAAATTGATTCTAAAAA
62829 TTCTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATTGATTCTAAAAA
Found at i:73173 original size:21 final size:21
Alignment explanation
Indices: 73126--73173 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
73116 TATTTTTCAA
*
73126 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
73147 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
73168 ACATTG
1 ACATTG
73174 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:77810 original size:21 final size:21
Alignment explanation
Indices: 77785--77831 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
77775 TATTTTTCAA
77785 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
*
77806 ACATTATTGCACTTAATTTTG
1 ACATTATTGCACCTAATTTTG
77827 ACATT
1 ACATT
77832 GCAATATTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (21 bp):
ACATTATTGCACCTAATTTTG
Found at i:89814 original size:60 final size:60
Alignment explanation
Indices: 89643--89827 Score: 155
Period size: 60 Copynumber: 3.1 Consensus size: 60
89633 GACCATACAC
* * * * * * *
89643 CCCTAAACTATGACTCTCATTTTATATT-AGTTCTTAAGCTTTTGAATATCCTAATATCAG
1 CCCTAAACTATGACTCTAATTCTATATTGAGCTCCTAAACTTTTGAATATCCAAAT-TCAT
* * * * * *
89703 CCCTAAAGTATGA--CTAATTCTAAATTGATCTCC-AAATTTTTAAACACTCCAAATTCAT
1 CCCTAAACTATGACTCTAATTCTATATTGAGCTCCTAAACTTTTGAATA-TCCAAATTCAT
* * * *
89761 CCCTAAACTATGACTCTTATTCTATATTGA-CCCCTAAACTTTTGAATATTCCAATTTTAT
1 CCCTAAACTATGACTCTAATTCTATATTGAGCTCCTAAACTTTTGAATA-TCCAAATTCAT
89821 CCCTAAA
1 CCCTAAA
89828 TTTTTGAATG
Statistics
Matches: 97, Mismatches: 23, Indels: 10
0.75 0.18 0.08
Matches are distributed among these distances:
58 34 0.35
59 12 0.12
60 51 0.53
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (60 bp):
CCCTAAACTATGACTCTAATTCTATATTGAGCTCCTAAACTTTTGAATATCCAAATTCAT
Found at i:95693 original size:35 final size:34
Alignment explanation
Indices: 95608--95694 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
95598 AAAATAATTT
* *
95608 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGA
* *
95642 TAAATGATAACCAAATTACAATAACTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGA
95680 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
95695 ACTGGGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGA
Found at i:103154 original size:18 final size:18
Alignment explanation
Indices: 103131--103202 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 18
103121 ACTGAATATT
103131 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
*
103149 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAAGACCACT-A
**
103168 T-TATTCG-AAGAACCACTA
1 TGT-CCCGAAAG-ACCACTA
103186 TGTCCCGAAAGACCACT
1 TGTCCCGAAAGACCACT
103203 GTATATGTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
18 29 0.67
19 14 0.33
ACGTcount: A:0.32, C:0.31, G:0.18, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:103323 original size:21 final size:21
Alignment explanation
Indices: 103275--103324 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
103265 GTACCAAAGC
103275 ACCACATATATGTTCCACAGA
1 ACCACATATATGTTCCACAGA
** *
103296 ATTACATATATGTTCCGA-AGG
1 ACCACATATATGTTCC-ACAGA
103317 ACCACATA
1 ACCACATA
103325 GAACCCTCGA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (21 bp):
ACCACATATATGTTCCACAGA
Found at i:105961 original size:9 final size:9
Alignment explanation
Indices: 105931--105982 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 9
105921 ATCTGCAAAA
105931 AAATTAAAT
1 AAATTAAAT
*
105940 -AAGTAAA-
1 AAATTAAAT
*
105947 ATATTAAAT
1 AAATTAAAT
105956 AAATTAAAT
1 AAATTAAAT
*
105965 -ACTTAAAT
1 AAATTAAAT
105973 AAATTAAAT
1 AAATTAAAT
105982 A
1 A
105983 TAAAATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 18 0.53
9 16 0.47
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:105963 original size:17 final size:16
Alignment explanation
Indices: 105933--105989 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
105923 CTGCAAAAAA
* *
105933 ATTAAATAAGTAAAAT
1 ATTAAATAAATTAAAT
105949 ATTAAATAAATTAAAT
1 ATTAAATAAATTAAAT
105965 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
*
105982 ATAAAATA
1 ATTAAATA
105990 TTAAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:106041 original size:10 final size:10
Alignment explanation
Indices: 106028--106067 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
106018 AGAGATTATA
*
106028 AGAGTATTTG
1 AGAGAATTTG
*
106038 AGAGAAGTTG
1 AGAGAATTTG
*
106048 AGAGAAATTG
1 AGAGAATTTG
106058 AGAGAATTTG
1 AGAGAATTTG
106068 GTGTGACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.28
Consensus pattern (10 bp):
AGAGAATTTG
Done.