Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006791.1 Hibiscus syriacus cultivar Beakdansim tig00017220_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: 80646
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:13910 original size:63 final size:63
Alignment explanation
Indices: 13801--13941 Score: 151
Period size: 63 Copynumber: 2.2 Consensus size: 63
13791 TATGGACCTA
* ** *
13801 ATGTGACTCTTAGGTAGGCTCTACAGCCCTGAGATCATTCTCGGGTAGGCCCT-ACGACCCTAAG
1 ATGTG-CTCTTAGGTAGGCCCTACAGCCCCAAAATCATTCTCGGGTAGGCCCTCA-GACCCTAAG
* * * *
13865 ATGTGCTCTTAGGTAGGCCCTACGGCCCCAAAATC-TATCTTGGGTAGGCTCTCAGGCCCTAAG
1 ATGTGCTCTTAGGTAGGCCCTACAGCCCCAAAATCAT-TCTCGGGTAGGCCCTCAGACCCTAAG
* *
13928 ATGTCCCCTTAGGT
1 ATGTGCTCTTAGGT
13942 TAACTCTTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
62 1 0.02
63 58 0.89
64 6 0.09
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (63 bp):
ATGTGCTCTTAGGTAGGCCCTACAGCCCCAAAATCATTCTCGGGTAGGCCCTCAGACCCTAAG
Found at i:14673 original size:35 final size:36
Alignment explanation
Indices: 14627--14705 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 36
14617 ATTTAGAAGT
*
14627 TGGTGATGATATAGGCGTGAT-ATGGTGATAGATTA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
* *
14662 TGGTGATGATATAGGCGTGATAATGGTGATGGAATG
1 TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
14698 TGGTGATG
1 TGGTGATG
14706 GATAGATTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 21 0.52
36 19 0.47
ACGTcount: A:0.27, C:0.03, G:0.38, T:0.33
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
Found at i:18461 original size:16 final size:18
Alignment explanation
Indices: 18440--18474 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
18430 AAGATGAAAG
18440 AATAAGAAA-TGAA-ATA
1 AATAAGAAAGTGAAGATA
18456 AATAAGAAAGTGAAGATA
1 AATAAGAAAGTGAAGATA
18474 A
1 A
18475 CTTACAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (18 bp):
AATAAGAAAGTGAAGATA
Found at i:19147 original size:35 final size:36
Alignment explanation
Indices: 19101--19168 Score: 129
Period size: 35 Copynumber: 1.9 Consensus size: 36
19091 ATTTAGAAGT
19101 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
19136 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
19169 AGGTGGTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 21 0.66
36 11 0.34
ACGTcount: A:0.26, C:0.04, G:0.38, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:19176 original size:36 final size:35
Alignment explanation
Indices: 19096--19179 Score: 123
Period size: 35 Copynumber: 2.4 Consensus size: 35
19086 TGGAAATTTA
*
19096 GAAGTTGGTGATGATATAGGCGTGATATGGTGATG
1 GAAGATGGTGATGATATAGGCGTGATATGGTGATG
**
19131 GACTATGGTGATGATATAGGCGTGATAATGGTGATG
1 GAAGATGGTGATGATATAGGCGTGAT-ATGGTGATG
*
19167 GAAGGTGGTGATG
1 GAAGATGGTGATG
19180 GATAGATTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 23 0.55
36 19 0.45
ACGTcount: A:0.26, C:0.04, G:0.40, T:0.30
Consensus pattern (35 bp):
GAAGATGGTGATGATATAGGCGTGATATGGTGATG
Found at i:22120 original size:35 final size:35
Alignment explanation
Indices: 22072--22142 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
22062 GATTATTAAC
*
22072 AGGAATTATGCGTGGAAGAAGAAGGGAAATAAGAA
1 AGGAATTAGGCGTGGAAGAAGAAGGGAAATAAGAA
22107 AGGAATTAGGCGTGGAAGAAGAAGGGAAATAAGAA
1 AGGAATTAGGCGTGGAAGAAGAAGGGAAATAAGAA
22142 A
1 A
22143 AGTGAGAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.35, T:0.13
Consensus pattern (35 bp):
AGGAATTAGGCGTGGAAGAAGAAGGGAAATAAGAA
Found at i:22155 original size:32 final size:34
Alignment explanation
Indices: 22084--22155 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
22074 GAATTATGCG
* **
22084 TGGAAGAAGAAGGGAAATAAGAAAGGAATTAGGCG
1 TGGAAGAAGAAGGGAAATAAGAAA-GAATGAGGAA
*
22119 TGGAAGAAGAAGGGAAATAAGAAA-AGTGA-GAA
1 TGGAAGAAGAAGGGAAATAAGAAAGAATGAGGAA
22151 TGGAA
1 TGGAA
22156 AATGAGAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 6 0.18
33 3 0.09
35 24 0.73
ACGTcount: A:0.51, C:0.01, G:0.36, T:0.11
Consensus pattern (34 bp):
TGGAAGAAGAAGGGAAATAAGAAAGAATGAGGAA
Found at i:24926 original size:13 final size:13
Alignment explanation
Indices: 24908--24934 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24898 ATTGCTTCGG
24908 AATTATGGTCAAT
1 AATTATGGTCAAT
24921 AATTATGGTCAAT
1 AATTATGGTCAAT
24934 A
1 A
24935 CTGACGTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
AATTATGGTCAAT
Found at i:26535 original size:31 final size:29
Alignment explanation
Indices: 26489--26561 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
26479 TTTTTATTGG
*
26489 ATTTAAAAATCAAATTAAAATTTTATATAA
1 ATTT-AAAATTAAATTAAAATTTTATATAA
* * *
26519 AGTTTAAGAATTAAATTGATATTTTATTTAA
1 A-TTTAA-AATTAAATTAAAATTTTATATAA
26550 ATTTAAAATTAA
1 ATTTAAAATTAA
26562 TCACTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 6 0.16
30 8 0.22
31 23 0.62
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (29 bp):
ATTTAAAATTAAATTAAAATTTTATATAA
Found at i:26704 original size:2 final size:2
Alignment explanation
Indices: 26637--26691 Score: 85
Period size: 2 Copynumber: 27.0 Consensus size: 2
26627 CACATCAATA
26637 AT AT AT AT GAT CA- 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
26680 AT AT AT AT AT AT
1 AT AT AT AT AT AT
26692 TTTAAAAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
1 1 0.02
2 46 0.92
3 3 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27512 original size:236 final size:235
Alignment explanation
Indices: 27102--27556 Score: 711
Period size: 235 Copynumber: 1.9 Consensus size: 235
27092 GTCAGGTCGA
*
27102 TTTTTTTAAGTGTGATATTCGGGTCGGGTCAAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGA
1 TTTTTTTAAGTGTGATATTCGGGTCGGG---AGTTCGGGTTTAGGGTGAAAAAGACCCGACCCGA
*
27167 AAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATT
63 AAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATT
* *
27232 TTTTTTCAATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTT
128 TTTTTTCAATTAAGTCAATGTTTTTATTAAATAAAAATA-TTTTTTTATTATTTCGGGTCAGGTT
27297 GGGTCGGATTTCTAATTCATATATTTGGGTCGAGTCGGGTCGGG
192 GGGTCGGATTTCTAATTCATATATTTGGGTCGAGTCGGGTCGGG
*
27341 TTTTTTTAAGTGTGATATTTGGGTC-GG-G-TCGGGTTTAGGGTGAAAAACCGGACCCGACCCGA
1 TTTTTTTAAGTGTGATATTCGGGTCGGGAGTTCGGGTTTAGGGTGAAAAA---GACCCGACCCGA
27403 AAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAA-T
63 AAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATT
* * * * *
27467 TTTTTTCAATTATGTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTATTTTGTGTCATGTT
128 TTTTTTCAATTAAGTCAATGTTTTTATTAAATAAAAAT-ATTTTTTTATTATTTCGGGTCAGGTT
*
27532 GGGTCGGTTTTCTAATTCATATATT
192 GGGTCGGATTTCTAATTCATATATT
27557 GAATAAAAAT
Statistics
Matches: 201, Mismatches: 11, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
233 19 0.09
234 1 0.00
235 81 0.40
236 74 0.37
238 2 0.01
239 24 0.12
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (235 bp):
TTTTTTTAAGTGTGATATTCGGGTCGGGAGTTCGGGTTTAGGGTGAAAAAGACCCGACCCGAAAA
AATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTT
TTTCAATTAAGTCAATGTTTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCAGGTTGGGT
CGGATTTCTAATTCATATATTTGGGTCGAGTCGGGTCGGG
Found at i:27951 original size:18 final size:18
Alignment explanation
Indices: 27906--27970 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
27896 TATGAAATTG
*
27906 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
* *
27923 TATTGCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
27941 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
27959 GATTCCAATTCC
1 GATTCCAATTCC
27971 CTCATAAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
17 10 0.24
18 31 0.76
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:36038 original size:72 final size:71
Alignment explanation
Indices: 35870--36048 Score: 259
Period size: 72 Copynumber: 2.5 Consensus size: 71
35860 GTTTCTCAAA
* * *
35870 AGTTTCGAAACTTTCCTTGAAGTTTCAATACTTTGAGTTTCAACGGTCATATTTTTATTTCCTCT
1 AGTTTCGAAACTTTCC-TAAAGTTTCGATACTTTAAGTTTCAACGGTCATATTTTTATTTCCTCT
*
35935 TTTGAAG
65 TTCGAAG
**
35942 AGTTTCGAAACTTTTATAAGAGTTTCGATACTTTAAGTTTCAACGGTCATATTTTTATTTCCTCT
1 AGTTTCGAAACTTTCCTAA-AGTTTCGATACTTTAAGTTTCAACGGTCATATTTTTATTTCCTCT
36007 TTCGAAG
65 TTCGAAG
* *
36014 AGTTTCGAAACTTTCCTCATAGTTTCGAAACTTTA
1 AGTTTCGAAACTTTCCT-AAAGTTTCGATACTTTA
36049 TGTGCATGTA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
71 2 0.02
72 92 0.97
73 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (71 bp):
AGTTTCGAAACTTTCCTAAAGTTTCGATACTTTAAGTTTCAACGGTCATATTTTTATTTCCTCTT
TCGAAG
Found at i:45619 original size:17 final size:16
Alignment explanation
Indices: 45586--45618 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45576 GTGTGAGAGG
45586 TGAAAAAATTTAATTT
1 TGAAAAAATTTAATTT
*
45602 TGAAAAAGTTTAATTT
1 TGAAAAAATTTAATTT
45618 T
1 T
45619 TTCTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (16 bp):
TGAAAAAATTTAATTT
Found at i:45762 original size:62 final size:62
Alignment explanation
Indices: 45692--45954 Score: 499
Period size: 62 Copynumber: 4.2 Consensus size: 62
45682 TAAAAAATTT
* *
45692 AAATAATAACATTCATATATTTATAGGTAATATTTATCTATAATAATATTTAACTCGAATCC
1 AAATAATAATATTCATATATTTATAGATAATATTTATCTATAATAATATTTAACTCGAATCC
45754 AAATAATAATATTCATATATTTATAGATAATATTTATCTATAATAATATTTAACTCGAATCC
1 AAATAATAATATTCATATATTTATAGATAATATTTATCTATAATAATATTTAACTCGAATCC
45816 AAATAATAATATTCATATATTTATAGATAATATTTATCTATAATAATATTTAACTCGAATCC
1 AAATAATAATATTCATATATTTATAGATAATATTTATCTATAATAATATTTAACTCGAATCC
45878 AAATAATAATATTCATATATTTATAGATAATATTTATCTATAATAATATTTAACTCGAATCC
1 AAATAATAATATTCATATATTTATAGATAATATTTATCTATAATAATATTTAACTCGAATCC
*
45940 AAATAATAACATTCA
1 AAATAATAATATTCA
45955 GATTCAACGC
Statistics
Matches: 198, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 198 1.00
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (62 bp):
AAATAATAATATTCATATATTTATAGATAATATTTATCTATAATAATATTTAACTCGAATCC
Found at i:49125 original size:18 final size:18
Alignment explanation
Indices: 49102--49136 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49092 ATGATGAATG
*
49102 ATTTTTAAGTAAATTTTT
1 ATTTTTAACTAAATTTTT
*
49120 ATTTTTTACTAAATTTT
1 ATTTTTAACTAAATTTT
49137 CGAAAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
ATTTTTAACTAAATTTTT
Found at i:49183 original size:22 final size:22
Alignment explanation
Indices: 49158--49200 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
49148 TATTGGTAAT
*
49158 TAACATTATCAATTTATAATAC
1 TAACATTATAAATTTATAATAC
*
49180 TAACATTATAAATTTGTAATA
1 TAACATTATAAATTTATAATA
49201 AAATGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (22 bp):
TAACATTATAAATTTATAATAC
Found at i:50023 original size:21 final size:21
Alignment explanation
Indices: 49997--50047 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
49987 GTTCAGTTAA
*
49997 TTCGATCGGTCACCAAATTAG
1 TTCGATCGGCCACCAAATTAG
* *
50018 TTCGATCGACCACTAAATTAG
1 TTCGATCGGCCACCAAATTAG
50039 TTCGATCGG
1 TTCGATCGG
50048 GAGAACGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (21 bp):
TTCGATCGGCCACCAAATTAG
Found at i:64992 original size:57 final size:57
Alignment explanation
Indices: 64802--65055 Score: 273
Period size: 56 Copynumber: 4.4 Consensus size: 57
64792 TACAAAATAG
* * *
64802 GAAAATAAATTGTTAA--ATTTATTTTTGTTAAAAAGTTAGAATCATTCAAGATTCTTAA
1 GAAAATAAA-T-TTAACGATTTA-TTTTCTTACAAAGTTAGAATCATTCAAGATTCTCAA
*
64860 GAAAATAAATTTAACGATTTATTTTCTTACAAAG-TAGAATCATTCAAGATTCTCAT
1 GAAAATAAATTTAACGATTTATTTTCTTACAAAGTTAGAATCATTCAAGATTCTCAA
* *
64916 GAAAATAAATTTAACGATTTATTTTCTTACAAAGTTAAAATCATTCAAGTTTCTCAA
1 GAAAATAAATTTAACGATTTATTTTCTTACAAAGTTAGAATCATTCAAGATTCTCAA
* * ** * * *
64973 GAAAATAAATTCAATGATTTGCTTTCTTTATAAAGTTAGAATGAATGCAAGATTCT-AA
1 GAAAATAAATTTAACGATTTATTTTC-TTACAAAGTTAGAAT-CATTCAAGATTCTCAA
**
65031 CGACGAAATAAATCCAACGATTTAT
1 -GA--AAATAAATTTAACGATTTAT
65056 CCCTCCCTCT
Statistics
Matches: 168, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
56 58 0.35
57 53 0.32
58 29 0.17
59 12 0.07
61 16 0.10
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (57 bp):
GAAAATAAATTTAACGATTTATTTTCTTACAAAGTTAGAATCATTCAAGATTCTCAA
Found at i:65947 original size:35 final size:35
Alignment explanation
Indices: 65889--66022 Score: 151
Period size: 36 Copynumber: 3.8 Consensus size: 35
65879 AGATGAACAA
* * *
65889 TTGAATCGAAAATGCTGACGCTTCCTTCCATTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCATTCAC
* * * *
65924 TTGAATCGAAAGTGCCGGTGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCATTC-AC
* * *
65960 TTGAATTGAAAGTGTCGATGTTTCCTTCCATTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCATTCAC
*
65995 TTTGAATCGAAAGTGCTGATGCTTCCTT
1 -TTGAATCGAAAGTGCCGATGCTTCCTT
66023 TCGTTCTTCT
Statistics
Matches: 79, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
35 28 0.35
36 51 0.65
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCATTCAC
Found at i:68518 original size:60 final size:59
Alignment explanation
Indices: 68440--68576 Score: 211
Period size: 59 Copynumber: 2.3 Consensus size: 59
68430 ACGTCGTTGG
* *
68440 TCACTTTTGTTTCATTTTTTTAAACATATGGTCACTCGTTTCAAACTATTTAACACGTGA
1 TCACTTTTGTTTC-TTTTTTTAAACATAAGGTCACTCGTTTCAAACTAGTTAACACGTGA
* * *
68500 TCACTTTTGTTTCGTTTTTTAAACTTAAGGTCACTCGTTTCAAACTAGTTAACACGTGG
1 TCACTTTTGTTTCTTTTTTTAAACATAAGGTCACTCGTTTCAAACTAGTTAACACGTGA
*
68559 TCAATTTTGTTTCTTTTT
1 TCACTTTTGTTTCTTTTT
68577 AATTAAGTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 57 0.81
60 13 0.19
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (59 bp):
TCACTTTTGTTTCTTTTTTTAAACATAAGGTCACTCGTTTCAAACTAGTTAACACGTGA
Found at i:69140 original size:21 final size:21
Alignment explanation
Indices: 69116--69159 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
69106 TATCGCAAAT
*
69116 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATACTTGAAAA
*
69137 TCGCTTTGCGATACTTGAAAA
1 TCGCGTTGCGATACTTGAAAA
69158 TC
1 TC
69160 ATGTTGCGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATACTTGAAAA
Found at i:69166 original size:21 final size:22
Alignment explanation
Indices: 69120--69167 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
69110 GCAAATTCGC
* *
69120 GTTGCGATAGTTGAAAATCGCT
1 GTTGCGATACTTGAAAATCGAT
69142 -TTGCGATACTTGAAAATC-AT
1 GTTGCGATACTTGAAAATCGAT
69162 GTTGCG
1 GTTGCG
69168 CTTTTCTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (22 bp):
GTTGCGATACTTGAAAATCGAT
Found at i:69187 original size:20 final size:20
Alignment explanation
Indices: 69162--69209 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
69152 TGAAAATCAT
* *
69162 GTTGCGCTTTTCTATTTCGC
1 GTTGCGATTTTCCATTTCGC
69182 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
*
69202 CTTGCGAT
1 GTTGCGAT
69210 AGTCTACAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.08, C:0.25, G:0.21, T:0.46
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGC
Found at i:69864 original size:5 final size:5
Alignment explanation
Indices: 69854--69894 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
69844 GCTGTCCGTC
69854 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
69895 TGGTAATACG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:69883 original size:6 final size:6
Alignment explanation
Indices: 69857--69898 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
69847 GTCCGTCTCG
69857 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
69899 AATACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:71162 original size:12 final size:12
Alignment explanation
Indices: 71145--71176 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
71135 AGGAGAAGTA
71145 GAAGTTGATGAG
1 GAAGTTGATGAG
*
71157 GAAGTTGATGAT
1 GAAGTTGATGAG
71169 GAAGTTGA
1 GAAGTTGA
71177 GGAAGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (12 bp):
GAAGTTGATGAG
Found at i:72147 original size:14 final size:15
Alignment explanation
Indices: 72113--72150 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
72103 AATTTGCATT
*
72113 ATTTGGTTTATTATGC
1 ATTTTGTTTATTA-GC
72129 ATTTTGTTTATTA-C
1 ATTTTGTTTATTAGC
72143 ATTTTGTT
1 ATTTTGTT
72151 AACTAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
16 12 0.57
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.63
Consensus pattern (15 bp):
ATTTTGTTTATTAGC
Found at i:73919 original size:25 final size:21
Alignment explanation
Indices: 73855--73906 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
73845 CAAAAGATAG
* * *
73855 ATTACATAAAAAACAACTTTC
1 ATTACATTACAAACAACTTCC
73876 ATTACATTACAAACAACTTCC
1 ATTACATTACAAACAACTTCC
73897 ATTACATTAC
1 ATTACATTAC
73907 CCATAAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (21 bp):
ATTACATTACAAACAACTTCC
Done.