Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001310.1 Hibiscus syriacus cultivar Beakdansim tig00002553_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: 68031
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:9512 original size:29 final size:30
Alignment explanation
Indices: 9479--9549 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
9469 ATTCTCTTAA
*
9479 TTAGTGACCAAAACATAAATTT-TGAAAGT
1 TTAGTGACCAAAACATAAATTTAAGAAAGT
* * ** *
9508 TTAGTGGCTAAATTATAAATTTAAGAAATT
1 TTAGTGACCAAAACATAAATTTAAGAAAGT
*
9538 TTAGGGACCAAA
1 TTAGTGACCAAA
9550 GTGGTAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.32
Consensus pattern (30 bp):
TTAGTGACCAAAACATAAATTTAAGAAAGT
Found at i:12709 original size:22 final size:20
Alignment explanation
Indices: 12658--12711 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
12648 GAATTAAACT
*
12658 AGTATCGATACTCTAGTATG
1 AGTATCGATACTATAGTATG
*
12678 AGTATTGATACTATGATGT-TG
1 AGTATCGATACTAT-A-GTATG
12699 AGGTATCGATACT
1 A-GTATCGATACT
12712 TGACTGAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (20 bp):
AGTATCGATACTATAGTATG
Found at i:14167 original size:5 final size:5
Alignment explanation
Indices: 14134--14211 Score: 68
Period size: 5 Copynumber: 15.0 Consensus size: 5
14124 ACGTCAATAC
* * * **
14134 TAAAA TTAAA TAAAA CAGAATA AAAAA TAAAA T-AAA TAAAA TAAAA TATTA
1 TAAAA TAAAA TAAAA TA-AA-A TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
14185 TAAATA TAAAA TAAAA TAAAAA TAAAA
1 TAAA-A TAAAA TAAAA T-AAAA TAAAA
14212 ATATTATTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
4 4 0.07
5 39 0.66
6 14 0.24
7 2 0.03
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:14173 original size:16 final size:17
Alignment explanation
Indices: 14141--14211 Score: 64
Period size: 16 Copynumber: 4.5 Consensus size: 17
14131 TACTAAAATT
*
14141 AAATAAAACAGAATA-AA
1 AAATAAAATA-AATATAA
14158 AAATAAAAT-AA-AT-A
1 AAATAAAATAAATATAA
*
14172 AAATAAAAT-ATTATAA
1 AAATAAAATAAATATAA
*
14188 ATATAAAATAAA-ATAA
1 AAATAAAATAAATATAA
14204 AAATAAAA
1 AAATAAAA
14212 ATATTATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
14 12 0.27
15 4 0.09
16 20 0.44
17 9 0.20
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (17 bp):
AAATAAAATAAATATAA
Found at i:14176 original size:31 final size:31
Alignment explanation
Indices: 14134--14211 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
14124 ACGTCAATAC
*
14134 TAAAATTAAATAAAACAGAATAAAAAATAAAA
1 TAAAATAAAATAAAACAGAAT-AAAAATAAAA
* ** *
14166 T-AAATAAAATAAAATATTATAAATATAAAA
1 TAAAATAAAATAAAACAGAATAAAAATAAAA
14196 TAAAATAAAAATAAAA
1 TAAAAT-AAAATAAAA
14212 ATATTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 10 0.26
31 19 0.49
32 10 0.26
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (31 bp):
TAAAATAAAATAAAACAGAATAAAAATAAAA
Found at i:14228 original size:31 final size:34
Alignment explanation
Indices: 14152--14218 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
14142 AATAAAACAG
*
14152 AATAAAAAATAAAATAAATAAAATAAAATATTATA
1 AATATAAAATAAAATAAA-AAAATAAAATATTATA
*
14187 AATATAAAATAAAATAAAAATA-AAAATATTAT
1 AATATAAAATAAAATAAAAAAATAAAATATTAT
14219 TTAATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 10 0.33
34 3 0.10
35 17 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (34 bp):
AATATAAAATAAAATAAAAAAATAAAATATTATA
Found at i:16044 original size:3 final size:3
Alignment explanation
Indices: 16029--16156 Score: 148
Period size: 3 Copynumber: 40.7 Consensus size: 3
16019 TTATTTATAT
* * *
16029 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAC TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
* *
16075 TAA TAA TAA TAA TAA TTAG TAA TAA TAA TTAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
*
16122 TAA TAA GTAA TAT TAA TTAA TAA TAA TAA TTAA TA
1 TAA TAA -TAA TAA TAA -TAA TAA TAA TAA -TAA TA
16157 TGTACAATTA
Statistics
Matches: 108, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
3 92 0.85
4 16 0.15
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:16080 original size:13 final size:11
Alignment explanation
Indices: 16024--16153 Score: 64
Period size: 10 Copynumber: 12.0 Consensus size: 11
16014 TTAGTTTATT
* *
16024 TATATTAATAA
1 TATAATAATTA
*
16035 TAGTAATAATAA
1 TA-TAATAATTA
*
16047 TAATAATAATAA
1 T-ATAATAATTA
16059 TAATAATAATTA
1 T-ATAATAATTA
16071 CTATTAATAA-TA
1 -TA-TAATAATTA
16083 -ATAATAATTA
1 TATAATAATTA
* *
16093 -GTAATAATAA
1 TATAATAATTA
16103 T-TAATAATTA
1 TATAATAATTA
16113 TAATAATAA-TA
1 T-ATAATAATTA
16124 -ATAAGTAA-TA
1 TATAA-TAATTA
16134 T-TAATTAA-TA
1 TATAA-TAATTA
16144 -ATAATAATTA
1 TATAATAATTA
16154 ATATGTACAA
Statistics
Matches: 101, Mismatches: 6, Indels: 25
0.77 0.05 0.19
Matches are distributed among these distances:
9 13 0.13
10 38 0.38
11 4 0.04
12 38 0.38
13 8 0.08
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (11 bp):
TATAATAATTA
Found at i:16105 original size:35 final size:35
Alignment explanation
Indices: 16041--16156 Score: 155
Period size: 35 Copynumber: 3.3 Consensus size: 35
16031 ATAATAGTAA
* *
16041 TAATAATAATAATAA-TAATAATAATAATTACTAT
1 TAATAATAATAATAATTAGTAATAATAATTAATAT
16075 TAATAATAATAATAATTAGTAATAATAATTAATAAT
1 TAATAATAATAATAATTAGTAATAATAATTAAT-AT
* * *
16111 T-ATAATAATAATAATAAGTAATATTAATTAATAA
1 TAATAATAATAATAATTAGTAATAATAATTAATAT
16145 TAATAATTAATA
1 TAATAA-TAATA
16157 TGTACAATTA
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
34 17 0.23
35 48 0.66
36 8 0.11
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (35 bp):
TAATAATAATAATAATTAGTAATAATAATTAATAT
Found at i:17878 original size:13 final size:11
Alignment explanation
Indices: 17862--17898 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
17852 TATTTAATTA
* *
17862 TTTTATTCTAT
1 TTTTTTTCTTT
17873 TTTTTTTCTTT
1 TTTTTTTCTTT
17884 TTTTTTTCTTT
1 TTTTTTTCTTT
17895 TTTT
1 TTTT
17899 AGGTTTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:23447 original size:21 final size:21
Alignment explanation
Indices: 23405--23447 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
23395 TTTTTGGGCT
* * *
23405 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
23426 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
23447 A
1 A
23448 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:24260 original size:149 final size:149
Alignment explanation
Indices: 23990--24293 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
23980 GGGTAGAGGG
* *
23990 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAGGTTTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* * *
24055 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
24120 TAGGGCACTACGGTGCAAT
131 TAGGGCACTACGGTGCAAT
24139 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
24204 ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
*
24269 TATGGCACTACGGTGCAAT
131 TAGGGCACTACGGTGCAAT
24288 TCTACG
1 TCTACG
24294 GGGCACTTCG
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TAGGGCACTACGGTGCAAT
Found at i:24316 original size:23 final size:23
Alignment explanation
Indices: 24272--24316 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
24262 ATCATTATAT
*
24272 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
24295 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
24317 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:31149 original size:11 final size:11
Alignment explanation
Indices: 31119--31157 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
31109 TACTAAAATT
31119 AAATAAAATAGA
1 AAATAAAATA-A
31131 ATAA-AAAATAA
1 A-AATAAAATAA
31142 AAATAAAATAA
1 AAATAAAATAA
31153 AAATA
1 AAATA
31158 TTACTATCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 14 0.56
12 7 0.28
13 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:31157 original size:17 final size:18
Alignment explanation
Indices: 31119--31155 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31109 TACTAAAATT
*
31119 AAAT-AAAATAGAATAAA
1 AAATAAAAATAAAATAAA
31136 AAATAAAAATAAAATAAA
1 AAATAAAAATAAAATAAA
31154 AA
1 AA
31156 TATTACTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (18 bp):
AAATAAAAATAAAATAAA
Found at i:33204 original size:90 final size:90
Alignment explanation
Indices: 33016--33190 Score: 289
Period size: 90 Copynumber: 2.0 Consensus size: 90
33006 TCCCGAATAT
* * * *
33016 TTAATTTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTA
1 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
33080 GGGTAACTTGAATATAAAAGGATTA
66 GGGTAACTTGAATATAAAAGGATTA
33105 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
1 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
**
33170 GGGTAACTTGGCTATAAAAGG
66 GGGTAACTTGAATATAAAAGG
33191 GTGTGTTAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
GGGTAACTTGAATATAAAAGGATTA
Found at i:34514 original size:10 final size:10
Alignment explanation
Indices: 34493--34601 Score: 64
Period size: 10 Copynumber: 11.2 Consensus size: 10
34483 ATAGTAGTAG
34493 TAATAA-TAA
1 TAATAATTAA
34502 TAATAATTAA
1 TAATAATTAA
*
34512 TAATAA-CAA
1 TAATAATTAA
* *
34521 TTATTATTAA
1 TAATAATTAA
*
34531 TGATAA-TAA
1 TAATAATTAA
* * *
34540 TACTTAGTAA
1 TAATAATTAA
34550 TAAT-ATATAA
1 TAATAAT-TAA
* *
34560 TAATAAATAT
1 TAATAATTAA
*
34570 TAATAAGTAA
1 TAATAATTAA
** *
34580 TGTTGATTAA
1 TAATAATTAA
34590 TAATAATTAA
1 TAATAATTAA
34600 TA
1 TA
34602 TGCAAAATTA
Statistics
Matches: 73, Mismatches: 22, Indels: 9
0.70 0.21 0.09
Matches are distributed among these distances:
9 19 0.26
10 53 0.73
11 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (10 bp):
TAATAATTAA
Found at i:34514 original size:13 final size:13
Alignment explanation
Indices: 34496--34601 Score: 64
Period size: 13 Copynumber: 8.4 Consensus size: 13
34486 GTAGTAGTAA
34496 TAATAATAATAAT
1 TAATAATAATAAT
*
34509 TAATAATAACAAT
1 TAATAATAATAAT
*
34522 T-AT--TATTAA-
1 TAATAATAATAAT
* *
34531 TGATAATAATACT
1 TAATAATAATAAT
*
34544 TAGTAATAAT-AT
1 TAATAATAATAAT
34556 ATAATAATAA-ATAT
1 -TAATAATAATA-AT
*
34570 TAATAAGTAAT-GT
1 TAATAA-TAATAAT
*
34583 TGATTAATAATAAT
1 T-AATAATAATAAT
34597 TAATA
1 TAATA
34602 TGCAAAATTA
Statistics
Matches: 69, Mismatches: 13, Indels: 22
0.66 0.12 0.21
Matches are distributed among these distances:
9 1 0.01
10 6 0.09
12 7 0.10
13 44 0.64
14 11 0.16
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.40
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:34514 original size:16 final size:16
Alignment explanation
Indices: 34493--34580 Score: 70
Period size: 16 Copynumber: 5.2 Consensus size: 16
34483 ATAGTAGTAG
34493 TAATAATAATAATAAT
1 TAATAATAATAATAAT
*
34509 TAATAATAACAATTATTAT
1 TAATAATAATAA-TA--AT
* *
34528 TAATGATAATAATACT
1 TAATAATAATAATAAT
*
34544 TAGTAATAATATATAA-
1 TAATAATAATA-ATAAT
* *
34560 TAATAAATATTAATAAG
1 TAAT-AATAATAATAAT
34577 TAAT
1 TAAT
34581 GTTGATTAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
16 28 0.49
17 15 0.26
18 2 0.04
19 12 0.21
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (16 bp):
TAATAATAATAATAAT
Found at i:34596 original size:3 final size:3
Alignment explanation
Indices: 34477--34580 Score: 64
Period size: 3 Copynumber: 32.7 Consensus size: 3
34467 TATTTTATTT
* * * *
34477 ATA ATA ATA GTA GTA GTA ATA ATA ATA ATA ATTA ATA ATA ACA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A-TA
* * * * * *
34524 TTA TTA ATG ATA ATA ATA CTTA GTA ATA ATA TATA ATA ATAA ATA TTA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA ATA AT-A ATA ATA
34572 ATA AGTA AT
1 ATA A-TA AT
34581 GTTGATTAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
3 67 0.82
4 15 0.18
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:43586 original size:61 final size:64
Alignment explanation
Indices: 43498--43642 Score: 217
Period size: 61 Copynumber: 2.3 Consensus size: 64
43488 CTGCACTAAG
* *
43498 CTTACACTCTAGTGCTAATCCGGATATGGCACATAAGGTTGTG-TATACCACCTACAC-TAG-GT
1 CTTACACTCTAGTGCTAATCCGGATATGACACATAAGGTTGTGCCAT-CCACCTACACTTAGTGT
43560 -TTACACTCTAGTGCTAATCCGGATATGACACATAAGGTTGTGCCATCCACCTACACTTAGTGT
1 CTTACACTCTAGTGCTAATCCGGATATGACACATAAGGTTGTGCCATCCACCTACACTTAGTGT
*
43623 CCTTACACACTAGTGCTAAT
1 -CTTACACTCTAGTGCTAAT
43643 ATAAACCTGC
Statistics
Matches: 75, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
61 51 0.68
62 5 0.07
63 2 0.03
65 17 0.23
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (64 bp):
CTTACACTCTAGTGCTAATCCGGATATGACACATAAGGTTGTGCCATCCACCTACACTTAGTGT
Found at i:47135 original size:37 final size:37
Alignment explanation
Indices: 47085--47189 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 37
47075 TGTTCGGGTT
*
47085 GGGTTGGATTTTTTAAGTGTGATATTCGGGT-TGAGTC
1 GGGTTGGATTTTTTAAGTGTGATATTCGGGTCGGA-TC
*
47122 GGGTTGGGTTTTTTAAGTGTGATATTCGGGTCGGATC
1 GGGTTGGATTTTTTAAGTGTGATATTCGGGTCGGATC
*
47159 -GG--GGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GGGTTGGATTTTTTAAGTGTGATATTCGGGTCGG
47190 GTCATGTTTG
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
34 28 0.44
36 2 0.03
37 32 0.50
38 2 0.03
ACGTcount: A:0.14, C:0.07, G:0.37, T:0.42
Consensus pattern (37 bp):
GGGTTGGATTTTTTAAGTGTGATATTCGGGTCGGATC
Found at i:47173 original size:34 final size:37
Alignment explanation
Indices: 47093--47189 Score: 139
Period size: 34 Copynumber: 2.7 Consensus size: 37
47083 TTGGGTTGGA
*
47093 TTTTTTAAGTGTGATATTCGGGT-TGAGTCGGGTTGGG
1 TTTTTTAAGTGTGATATTCGGGTCGGAGTCGGG-TGGG
*
47130 TTTTTTAAGTGTGATATTCGGGTCGGA-TC-GG-GGT
1 TTTTTTAAGTGTGATATTCGGGTCGGAGTCGGGTGGG
47164 TTTTTTAAGTGTGATATTCGGGTCGG
1 TTTTTTAAGTGTGATATTCGGGTCGG
47190 GTCATGTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
34 28 0.49
36 2 0.04
37 25 0.44
38 2 0.04
ACGTcount: A:0.14, C:0.07, G:0.35, T:0.43
Consensus pattern (37 bp):
TTTTTTAAGTGTGATATTCGGGTCGGAGTCGGGTGGG
Found at i:47794 original size:17 final size:18
Alignment explanation
Indices: 47772--47818 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
47762 TATGGAATTG
47772 GATTCCAATTCC-TAACA
1 GATTCCAATTCCTTAACA
*
47789 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTAACA
47807 GATTCCAATTCC
1 GATTCCAATTCC
47819 CTCATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.30, C:0.32, G:0.06, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTAACA
Found at i:60030 original size:21 final size:21
Alignment explanation
Indices: 60006--60045 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59996 TCTCTGCAAT
*
60006 ATTTTATAGCTTCAGCAAAAG
1 ATTTTATAGCTTCAACAAAAG
*
60027 ATTTTATGGCTTCAACAAA
1 ATTTTATAGCTTCAACAAA
60046 GGCCTTGTTG
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:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (21 bp):
ATTTTATAGCTTCAACAAAAG
Done.