Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004555.1 Hibiscus syriacus cultivar Beakdansim tig00010117_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: 67806
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:187 original size:13 final size:13
Alignment explanation
Indices: 169--211 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
159 GTCATAAATC
169 TATGACGCACATT
1 TATGACGCACATT
182 TATGA--CACATT
1 TATGACGCACATT
*
193 TATGACGCGCATT
1 TATGACGCACATT
206 TATGAC
1 TATGAC
212 ATTCATTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 11 0.41
13 16 0.59
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:292 original size:82 final size:82
Alignment explanation
Indices: 192--351 Score: 225
Period size: 82 Copynumber: 2.0 Consensus size: 82
182 TATGACACAT
* * * * *
192 TTATGACGCGCATTTATGACATT-CATTGAGCGTCATTGAAGC-CCCGTCATAAATTAAGATGAC
1 TTATGACACGCATGTATGAC-TTACATTGAGCGTCATTGAAGCACACATCATAAA-AAAGATGAC
*
255 ACACATTTGTGTGTCATAA
64 ACACATTCGTGTGTCATAA
*
274 TTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCACACATCATAAAAAAGATGACAC
1 TTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACATCATAAAAAAGATGACAC
339 ACATTCGTGTGTC
66 ACATTCGTGTGTC
352 GTGATTGTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
81 2 0.03
82 58 0.84
83 9 0.13
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (82 bp):
TTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACATCATAAAAAAGATGACAC
ACATTCGTGTGTCATAA
Found at i:5116 original size:222 final size:216
Alignment explanation
Indices: 4762--5157 Score: 530
Period size: 222 Copynumber: 1.8 Consensus size: 216
4752 ACAAAACAAT
*
4762 AAAATTTAAACTAAACTTACTAAAACCACTCAAATACAATTTAGTATGTAAATCAAAATAATAGT
1 AAAATTTAAACTAAACTTACTAAAACCACTCAAATACAATTTAATATGTAAATCAAAATAATAGT
* * * *
4827 CCAATAATTTATATTACTCAATAAAAAATAAAAATATAATTTAAACTAAACTTACCAAACTACTC
66 CAAATAATTTATATTACTAAAGAAAAAATAAAAATATAATTTAAACTAAACTTACCAAACCACTC
4892 AAATACAACTTAATATGTAAAATCAAAATAAATAGTCTAATAATTATAATTTAAATTTTAAAAAA
131 AAATACAACTTAATATGTAAAAT-AAAATAAATAGTCTAATAATTATAATTTAAATTTTAAAAAA
4957 AAATTATACTAAAAATTACACG
195 AAATTATACTAAAAATTACACG
* * * * * *
4979 AAAATTTAAATTTAACTTA-T-CAACCACTC-AATAGAGTTTAATATGTAAAATCATAATAATAG
1 AAAATTTAAACTAAACTTACTAAAACCACTCAAATACAATTTAATATGT-AAATCAAAATAATAG
*
5041 TGTAAATAATTTATATTTACAATAAAAGAAAAAATAAAACA-ATAAATTTTAAACTAAACTTACC
65 T-CAAATAATTTATA-TTAC--T-AAAGAAAAAATAAAA-ATAT-AA-TTTAAACTAAACTTACC
* * * *
5105 AAACCACTCAAATACGATTTAATCTGTAAAATAAAATAATTAGTCTAATAATT
122 AAACCACTCAAATACAACTTAATATGTAAAATAAAATAAATAGTCTAATAATT
5158 TATATTACTT
Statistics
Matches: 154, Mismatches: 16, Indels: 14
0.84 0.09 0.08
Matches are distributed among these distances:
214 14 0.09
215 23 0.15
216 12 0.08
217 21 0.14
219 1 0.01
220 15 0.10
221 23 0.15
222 45 0.29
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.32
Consensus pattern (216 bp):
AAAATTTAAACTAAACTTACTAAAACCACTCAAATACAATTTAATATGTAAATCAAAATAATAGT
CAAATAATTTATATTACTAAAGAAAAAATAAAAATATAATTTAAACTAAACTTACCAAACCACTC
AAATACAACTTAATATGTAAAATAAAATAAATAGTCTAATAATTATAATTTAAATTTTAAAAAAA
AATTATACTAAAAATTACACG
Found at i:5157 original size:322 final size:323
Alignment explanation
Indices: 4702--5284 Score: 865
Period size: 322 Copynumber: 1.8 Consensus size: 323
4692 AAAAATTGTT
*
4702 AAATCAAAATAAATAGTCTAATTAATTTACATTTACAATAAAAACAAAAAACAAAACAATAAAAT
1 AAATCAAAATAAATAGTCTAAATAATTTACATTTACAATAAAAACAAAAAACAAAACAATAAAAT
*
4767 TTAAACTAAACTTACTAAAACCACTCAAATACAATTTAGTATGTAAATCAAAATAATAGTCCAAT
66 TTAAACTAAACTTACTAAAACCACTCAAATACAATTTAATATGTAAATCAAAATAATAGTCCAAT
4832 AATTTATATTACTCAATAAAAAATAAAA-ATATAATTTAAACTAAACTTACCAA-ACTACTCAAA
131 AATTTATATTACTCAATAAAAAATAAAATA-ATAATTTAAACTAAACTTACCAAGACTACTCAAA
*
4895 TACAACTTAATATGTAAAATCAAAATAAATAGTCTAATAATTATAATTTAAATTTTAAAA-AAAA
195 TACAACTTAATATGTAAAATCAAAATAAATA-TCTAATAATTATAA-TTAAA-TTAAAAACAAAA
4959 ATTATACTAAAAATTACACGAAAATTTAAATTTAACTTATCAACCACTCAATAGAGTTTAATATG
257 ATTATACTAAAAATTACACGAAAATTTAAATTTAACTTATCAACCACTCAATAGAGTTTAATATG
5024 TA
322 TA
* * * * * *
5026 AAATCATAAT-AATAGTGTAAATAATTTATATTTACAAT-AAAAGAAAAAATAAAACAATAAATT
1 AAATCAAAATAAATAGTCTAAATAATTTACATTTACAATAAAAACAAAAAACAAAACAATAAAAT
* * * *
5089 TTAAACTAAACTTAC-CAAACCACTCAAATACGATTTAATCTGTAAAAT-AAAATAATTAGTCTA
66 TTAAACTAAACTTACTAAAACCACTCAAATACAATTTAATATGT-AAATCAAAATAA-TAGTCCA
* * ** * ** *
5152 ATAATTTATATTACTTAATAAACAATAATCTAATAATTTAAACTACACTTACCAAGTTTTACTGA
129 ATAATTTATATTACTCAATAAAAAATAAAATAATAATTTAAACTAAACTTACCAAG-ACTACTCA
5217 AATACAACTTAATATGTAAAATCAAAATAAATATCTAATAATTATAATTAAATTAAAAACAAAAA
193 AATACAACTTAATATGTAAAATCAAAATAAATATCTAATAATTATAATTAAATTAAAAACAAAAA
5282 TTA
258 TTA
5285 CACGAAAATT
Statistics
Matches: 232, Mismatches: 21, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
321 37 0.16
322 108 0.47
323 40 0.17
324 47 0.20
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (323 bp):
AAATCAAAATAAATAGTCTAAATAATTTACATTTACAATAAAAACAAAAAACAAAACAATAAAAT
TTAAACTAAACTTACTAAAACCACTCAAATACAATTTAATATGTAAATCAAAATAATAGTCCAAT
AATTTATATTACTCAATAAAAAATAAAATAATAATTTAAACTAAACTTACCAAGACTACTCAAAT
ACAACTTAATATGTAAAATCAAAATAAATATCTAATAATTATAATTAAATTAAAAACAAAAATTA
TACTAAAAATTACACGAAAATTTAAATTTAACTTATCAACCACTCAATAGAGTTTAATATGTA
Found at i:5323 original size:102 final size:103
Alignment explanation
Indices: 4702--5380 Score: 429
Period size: 102 Copynumber: 6.4 Consensus size: 103
4692 AAAAATTGTT
* * ** **
4702 AAATCAAAATAAATAGTCTAATTAATTTACATTTACAATAAAAACAAAAAACAAAACAATAAAAT
1 AAATCAAAATAAATAGTCTAA-TAATTTATAATTA-AATAAAAAC--AAAA-ATTACACGAAAAT
* * * *
4767 TTAAACTAAACTTACTAAAACCACTCAAATACAATTTAGTATGT-
61 TTAAACTAAACTTAC-CAAACCACT-GAATACAACTTAATATGTA
* * * * * * ** *
4811 AAATCAAAAT-AATAGTCCAATAATTTAT-ATT-ACTCAATA-AAAAATAAAAATATAATTTAAA
1 AAATCAAAATAAATAGTCTAATAATTTATAATTAAATAAAAACAAAAATTACACGAAAATTTAAA
* *
4872 CTAAACTTACCAAACTACTCAAATACAACTTAATATGTA
66 CTAAACTTACCAAACCACT-GAATACAACTTAATATGTA
*
4911 AAATCAAAATAAATAGTCTAATAATTATAATTTAAATTTTAAAAAAAAATTATACTAAAAATTAC
1 AAATCAAAATAAATAGTCTAATAATT-T-A--T-AA--TT--AAATAAA--A-AC-AAAAATTAC
* * * * * **
4976 ACGAAAATTTAAATTTAACTTATC-AACCACTCAATAGAGTTTAATATGTA
53 ACGAAAATTTAAACTAAACTTACCAAACCACTGAATACAACTTAATATGTA
* * * * * *
5026 AAATCATAAT-AATAGTGTAAATAATTTATATTTACAATAAAAGA-AAAAATAAAACAATAAATT
1 AAATCAAAATAAATAGTCT-AATAATTTATAATTA-AATAAAA-ACAAAAATTACACGA-AAA-T
* * * *
5089 TTAAACTAAACTTACCAAACCACTCAAATACGATTTAATCTGTA
61 TTAAACTAAACTTACCAAACCACT-GAATACAACTTAATATGTA
* ** * *
5133 AAAT-AAAATAATTAGTCTAATAATTTAT-ATTACTTAATAAACAATAA-T-CTA--ATAATTTA
1 AAATCAAAATAAATAGTCTAATAATTTATAATTAAATAA-AAACAAAAATTAC-ACGAAAATTTA
* ***
5192 AACTACACTTACCAAGTTTTACTGAAATACAACTTAATATGTA
64 AACTAAACTTACCAA--ACCACTG-AATACAACTTAATATGTA
5235 AAATCAAAATAAATA-TCTAATAA-TTATAATTAAATTAAAAACAAAAATTACACGAAAATTTAA
1 AAATCAAAATAAATAGTCTAATAATTTATAATTAAA-TAAAAACAAAAATTACACGAAAATTTAA
* * *
5298 A-TAAACTTACCAAACCACTTGAATACAGCTTAATCTATA
65 ACTAAACTTACCAAACCAC-TGAATACAACTTAATATGTA
* * *
5337 AAATCAATATAAATAATCTAATTAATTTATATTTCAAATAAAAA
1 AAATCAAAATAAATAGTCTAA-TAATTTATAATT-AAATAAAAA
5381 TTAAAAATGA
Statistics
Matches: 448, Mismatches: 79, Indels: 90
0.73 0.13 0.15
Matches are distributed among these distances:
99 24 0.05
100 53 0.12
101 24 0.05
102 75 0.17
103 32 0.07
104 28 0.06
105 48 0.11
106 27 0.06
107 37 0.08
108 11 0.02
109 12 0.03
110 1 0.00
111 1 0.00
112 3 0.01
113 1 0.00
114 8 0.02
115 32 0.07
116 6 0.01
117 25 0.06
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.31
Consensus pattern (103 bp):
AAATCAAAATAAATAGTCTAATAATTTATAATTAAATAAAAACAAAAATTACACGAAAATTTAAA
CTAAACTTACCAAACCACTGAATACAACTTAATATGTA
Found at i:7463 original size:17 final size:18
Alignment explanation
Indices: 7431--7466 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
7421 ATATTTCAAC
*
7431 TAATATTAATAATATTTA
1 TAATATTAAAAATATTTA
7449 TAATA-TAAAAATATTTA
1 TAATATTAAAAATATTTA
7466 T
1 T
7467 GGGAGAACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATATTAAAAATATTTA
Found at i:7971 original size:14 final size:12
Alignment explanation
Indices: 7949--7994 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 12
7939 TCTACAAAAA
7949 TATTTTATTATAT
1 TATTTTATT-TAT
7962 TATATTTATTTAT
1 TAT-TTTATTTAT
7975 TATTATTATTTTAT
1 TATT-TTA-TTTAT
7989 TATTTT
1 TATTTT
7995 TGTAGGCCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.03
13 14 0.47
14 15 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTTATTTAT
Found at i:7975 original size:18 final size:18
Alignment explanation
Indices: 7952--7989 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
7942 ACAAAAATAT
7952 TTTATTA-TATTATATTTA
1 TTTATTATTATTAT-TTTA
7970 TTTATTATTATTATTTTA
1 TTTATTATTATTATTTTA
7988 TT
1 TT
7990 ATTTTTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTATTATTATTTTA
Found at i:8089 original size:33 final size:33
Alignment explanation
Indices: 8047--8111 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
8037 AAAATAAATT
*
8047 AACGTATTTGAGTCTTATTGAAACACTAAAACC
1 AACGTATTTGAGTCCTATTGAAACACTAAAACC
8080 AACGTATTTGAGTCCTATTGAAACACTAAAAC
1 AACGTATTTGAGTCCTATTGAAACACTAAAAC
8112 TGAAGCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (33 bp):
AACGTATTTGAGTCCTATTGAAACACTAAAACC
Found at i:8122 original size:33 final size:33
Alignment explanation
Indices: 8047--8127 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
8037 AAAATAAATT
* *
8047 AACGTATTTGAGTCTTATTGAAACACTAAAACC
1 AACGCATTTGAGTCCTATTGAAACACTAAAACC
* *
8080 AACGTATTTGAGTCCTATTGAAACACTAAAACTG
1 AACGCATTTGAGTCCTATTGAAACACTAAAAC-C
8114 AA-GCATTTGAGTCC
1 AACGCATTTGAGTCC
8128 AAGTAGGACT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 42 0.95
34 2 0.05
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (33 bp):
AACGCATTTGAGTCCTATTGAAACACTAAAACC
Found at i:8610 original size:7 final size:7
Alignment explanation
Indices: 8606--8647 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
8596 ACATTATTTA
8606 TTATTAT
1 TTATTAT
8613 TTATTAT
1 TTATTAT
8620 TTATTTAT
1 TTA-TTAT
8628 TTA-T-T
1 TTATTAT
8633 TTATTAT
1 TTATTAT
8640 TTATTAT
1 TTATTAT
8647 T
1 T
8648 AATTTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 4 0.12
6 2 0.06
7 19 0.59
8 7 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTATTAT
Found at i:8616 original size:4 final size:4
Alignment explanation
Indices: 8599--8644 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
8589 TGATAATACA
8599 TTAT TTA- TTA- TTAT TTA- TTAT TTAT TTAT TTAT TT-T ATTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT
8644 T
1 T
8645 ATTAATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 10 0.26
4 27 0.71
5 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:8641 original size:27 final size:25
Alignment explanation
Indices: 8599--8652 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 25
8589 TGATAATACA
*
8599 TTATTTATTATTATTTATTATTTAT
1 TTATTTATTATTATTTATTATTAAT
8624 TTATTTATTTTATTATTTATTATTAAT
1 TTATTTA--TTATTATTTATTATTAAT
8651 TT
1 TT
8653 TTTTCCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 7 0.27
27 19 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (25 bp):
TTATTTATTATTATTTATTATTAAT
Found at i:13617 original size:3 final size:3
Alignment explanation
Indices: 13597--13647 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
13587 CAAAAACATT
13597 TTA TTA -TA TTA -TA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13640 TTA TTA TT
1 TTA TTA TT
13648 TTTGCAAGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.14
3 36 0.82
4 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13738 original size:33 final size:33
Alignment explanation
Indices: 13701--13765 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
13691 AAAAATAAAT
* *
13701 CAACGTATTTGAGTCTTATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
13734 CAACGTATTTGAGTCCTATTAAAACACTAAAA
1 CAACGTATTTGAGTCCTATTAAAACACTAAAA
13766 TCGAAGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTAAAACACTAAAAC
Found at i:13777 original size:33 final size:33
Alignment explanation
Indices: 13701--13780 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
13691 AAAAATAAAT
* * *
13701 CAACGTATTTGAGTCTTATTGAAACACTAAAAC
1 CAACGCATTTGAGTCCTATTAAAACACTAAAAC
*
13734 CAACGTATTTGAGTCCTATTAAAACACTAAAATC
1 CAACGCATTTGAGTCCTATTAAAACACTAAAA-C
*
13768 GAA-GCATTTGAGT
1 CAACGCATTTGAGT
13781 ACAAGTAGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 39 0.93
34 3 0.07
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (33 bp):
CAACGCATTTGAGTCCTATTAAAACACTAAAAC
Found at i:14250 original size:7 final size:7
Alignment explanation
Indices: 14238--14273 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
14228 ATGATAATAC
14238 ATTATTT
1 ATTATTT
14245 ATTATTT
1 ATTATTT
14252 ATTTATTTT
1 A-TTA-TTT
14261 ATTATTT
1 ATTATTT
14268 ATTATT
1 ATTATT
14274 AATTTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 17 0.63
8 6 0.22
9 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTATTT
Found at i:14265 original size:23 final size:22
Alignment explanation
Indices: 14238--14282 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
14228 ATGATAATAC
*
14238 ATTATTTATTATTTATTTATTTT
1 ATTATTTATTATTAATTT-TTTT
14261 ATTATTTATTATTAATTTTTTT
1 ATTATTTATTATTAATTTTTTT
14283 CCTTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
ATTATTTATTATTAATTTTTTT
Found at i:15802 original size:3 final size:3
Alignment explanation
Indices: 15796--15828 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
15786 AATTTAAAAT
15796 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15829 ATTATTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:15941 original size:16 final size:16
Alignment explanation
Indices: 15908--15954 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
15898 GTAAACTAAA
*
15908 TTCGGATTGCTTTT-GG
1 TTCGGATT-ATTTTCGG
15924 TTCGGATTATTTTCGG
1 TTCGGATTATTTTCGG
15940 TTC-GAGTTATTTTCG
1 TTCGGA-TTATTTTCG
15955 ATTTTGGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 6 0.21
16 22 0.79
ACGTcount: A:0.11, C:0.13, G:0.26, T:0.51
Consensus pattern (16 bp):
TTCGGATTATTTTCGG
Found at i:16809 original size:30 final size:30
Alignment explanation
Indices: 16775--16835 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
16765 ACAATATAAT
16775 AGCTAATTAAGTATATAAACTCAAAATCCA
1 AGCTAATTAAGTATATAAACTCAAAATCCA
*
16805 AGCTAATTAGGTATATAAACTCAAAATCCA
1 AGCTAATTAAGTATATAAACTCAAAATCCA
16835 A
1 A
16836 AAGACAGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.26
Consensus pattern (30 bp):
AGCTAATTAAGTATATAAACTCAAAATCCA
Found at i:22534 original size:57 final size:57
Alignment explanation
Indices: 22446--22556 Score: 170
Period size: 57 Copynumber: 1.9 Consensus size: 57
22436 GACGGGATAA
*
22446 CATCATTATTTGATGTAGCTAGATTAGGTGAGACTTGCACAACTACTTTCTCTCGTG
1 CATCATTATTTGATGTAGCTAGATTAGGTGAGACTTGCACAACTACTTCCTCTCGTG
* * *
22503 CATCATTATTTGATGTAG-TAAGATTAGGTGAGGCTTTCACAACTTCTTCCTCTC
1 CATCATTATTTGATGTAGCT-AGATTAGGTGAGACTTGCACAACTACTTCCTCTC
22557 CAAGATCATC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 1 0.02
57 48 0.98
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (57 bp):
CATCATTATTTGATGTAGCTAGATTAGGTGAGACTTGCACAACTACTTCCTCTCGTG
Found at i:28418 original size:39 final size:39
Alignment explanation
Indices: 28358--28467 Score: 166
Period size: 39 Copynumber: 2.8 Consensus size: 39
28348 CCTGTGGTAA
* * *
28358 GGACTTACCCTGAGCATAAAGCCAAGGAGCCTATAGTAT
1 GGACTTACCCTGAGCACAAAGCCGAGGAGCCTACAGTAT
* *
28397 GGACTTACCCTGAGTACAAAGCCGATGAGCCTACAGTAT
1 GGACTTACCCTGAGCACAAAGCCGAGGAGCCTACAGTAT
*
28436 AGACTTACCCTGAGCACAAAGCCGAGGAGCCT
1 GGACTTACCCTGAGCACAAAGCCGAGGAGCCT
28468 GCAGAAAGCG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (39 bp):
GGACTTACCCTGAGCACAAAGCCGAGGAGCCTACAGTAT
Found at i:29265 original size:18 final size:18
Alignment explanation
Indices: 29238--29282 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
29228 CAAAGTCAAA
* *
29238 GTCAACGGTCAACGGTTG
1 GTCAATGGTCAACGGTGG
*
29256 GTCAATGGTCAATGGTGG
1 GTCAATGGTCAACGGTGG
29274 GTCAATGGT
1 GTCAATGGT
29283 AAACAATCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.27
Consensus pattern (18 bp):
GTCAATGGTCAACGGTGG
Found at i:34266 original size:137 final size:136
Alignment explanation
Indices: 34025--34275 Score: 315
Period size: 137 Copynumber: 1.8 Consensus size: 136
34015 TATATGATGG
* * * * * *
34025 TTATCGATCGATTTTTTTAATGCATGTTTTGTATTTTCGTATCAGTACTATATGTACTTTCGGCA
1 TTATCGACCGATTTTTTTAATGCATATGTTGCATTTTCGTATCAGTACTATATGTACGTTCGACA
* ** *
34090 CTAGATATGCAACTATGATATTCATAAGGTGTTTTTGAATTACCATTTCTACATACATTTGTGTA
66 CTAGATATGCAACCATGATATTCATAAGAAGTTTGTGAATTACCATTTCTACATACATTTGTGTA
34155 TAAAGT
131 TAAAGT
*
34161 TTATCGACCGATTTTGTTTAATGCATATGTTGCATTTTTGTATCAGTACTATATGTACGTTCGAC
1 TTATCGACCGATTTT-TTTAATGCATATGTTGCATTTTCGTATCAGTACTATATGTACGTTCGAC
* * * * * * *
34226 ACTATATGTGTACCCATGGA-ATTTATAATAAGTTTGTGAATTTCCATTTC
65 ACTAGATATGCAACCAT-GATATTCATAAGAAGTTTGTGAATTACCATTTC
34276 GACACTTAAG
Statistics
Matches: 95, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
136 14 0.15
137 79 0.83
138 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (136 bp):
TTATCGACCGATTTTTTTAATGCATATGTTGCATTTTCGTATCAGTACTATATGTACGTTCGACA
CTAGATATGCAACCATGATATTCATAAGAAGTTTGTGAATTACCATTTCTACATACATTTGTGTA
TAAAGT
Found at i:36209 original size:14 final size:14
Alignment explanation
Indices: 36173--36201 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
36163 TTGGTTTTCA
36173 ACATAATGTGTTTG
1 ACATAATGTGTTTG
36187 ACATAATGTGTTTG
1 ACATAATGTGTTTG
36201 A
1 A
36202 TGAAATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (14 bp):
ACATAATGTGTTTG
Done.