Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000067.1 Hibiscus syriacus cultivar Beakdansim tig00000116_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: 74899
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7219 original size:12 final size:12
Alignment explanation
Indices: 7204--7233 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
7194 AAAAGTATGC
7204 GAAAAATAGAGA
1 GAAAAATAGAGA
*
7216 GAAAACTAGAGA
1 GAAAAATAGAGA
7228 GAAAAA
1 GAAAAA
7234 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:7363 original size:20 final size:21
Alignment explanation
Indices: 7320--7364 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
7310 AAAAACAAGC
**
7320 TAAAACATCTTAAATCCTAAT
1 TAAAACATCTTAAAAACTAAT
*
7341 TAAAACA-CTTAAAAACTATT
1 TAAAACATCTTAAAAACTAAT
7361 TAAA
1 TAAA
7365 CTAAAATACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAAACATCTTAAAAACTAAT
Found at i:7429 original size:63 final size:64
Alignment explanation
Indices: 7330--7451 Score: 203
Period size: 63 Copynumber: 1.9 Consensus size: 64
7320 TAAAACATCT
7330 TAAATCCTAATTAAAACACTTAAAAACTATTTAAACTAAAATACCTAAAA-ATAATATAATATTC
1 TAAATCCTAATTAAAACACTTAAAAACTATTTAAACTAAAATACCTAAAATA-AATATAATATTC
* *
7394 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAATAAATATAA
1 TAAATCCTAATTAAAACACTTAAAAACTATTTAAACTAAAATACCTAAAATAAATATAA
7452 AATATAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
63 36 0.65
64 19 0.35
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (64 bp):
TAAATCCTAATTAAAACACTTAAAAACTATTTAAACTAAAATACCTAAAATAAATATAATATTC
Found at i:7537 original size:77 final size:75
Alignment explanation
Indices: 7406--7552 Score: 199
Period size: 77 Copynumber: 1.9 Consensus size: 75
7396 AATCCTAATT
7406 AAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAAAATATAAAAATAATATCCT
1 AAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAAAATAT-AAAATAATATCCT
7471 ATAACTTAGTCA
65 A-AACTTAGTCA
* ** * *
7483 AAAATACTAAAATCTATTTAAACTAAAATA-C-AAAGATAAAATATAATGTTTAAAATATTATCC
1 AAAATACTAAAACCTATTTAAACTAAAATACCTAAA-AT-AAATATAAAATATAAAATAATATCC
7546 TAAACTT
64 TAAACTT
7553 GAGTTTAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
75 8 0.13
76 16 0.25
77 39 0.62
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (75 bp):
AAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAATATAAAATATAAAATAATATCCTA
AACTTAGTCA
Found at i:9156 original size:5 final size:5
Alignment explanation
Indices: 9146--9220 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
9136 TGTTCACAGA
* ** **
9146 AAAAT AAAAT AAAATT AATCAT ATGAT AAAAT AAAAT AAAAT -AAAT GGAAT
1 AAAAT AAAAT AAAA-T AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
9197 AAAAT -AAAT AAAAT GAAAAT AAAA
1 AAAAT AAAAT AAAAT -AAAAT AAAA
9221 CGAAATTGGT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
4 8 0.14
5 38 0.67
6 10 0.18
7 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:9197 original size:14 final size:14
Alignment explanation
Indices: 9147--9219 Score: 67
Period size: 14 Copynumber: 5.2 Consensus size: 14
9137 GTTCACAGAA
9147 AAATAAAATAAAAT
1 AAATAAAATAAAAT
* * * * *
9161 TAATCATATGATA-
1 AAATAAAATAAAAT
9174 AAATAAAATAAAAT
1 AAATAAAATAAAAT
**
9188 AAATGGAATAAAAT
1 AAATAAAATAAAAT
9202 AAATAAAATGAAAAT
1 AAATAAAAT-AAAAT
9217 AAA
1 AAA
9220 ACGAAATTGG
Statistics
Matches: 43, Mismatches: 14, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
13 8 0.19
14 27 0.63
15 8 0.19
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:20775 original size:22 final size:22
Alignment explanation
Indices: 20749--20829 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 22
20739 ATAGGGCAGA
20749 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* *
20771 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TTGAAG
*
20794 GGGAA-CAGATTCCCCC-T--AG
1 GGGAATC-GATACCCCCTTGAAG
20813 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
20830 GGGGTTCTGG
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
19 15 0.29
20 1 0.02
21 1 0.02
22 15 0.29
23 20 0.38
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.19
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:20791 original size:23 final size:23
Alignment explanation
Indices: 20749--20810 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
20739 ATAGGGCAGA
* *
20749 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
20771 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
20794 GGGAACAGATTCCCCCT
1 GGGAACCGATTCCCCCT
20811 AGGGGAATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:22961 original size:2 final size:2
Alignment explanation
Indices: 22954--22987 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22944 GCAGCTTAAG
22954 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
22988 CAATTGGCTA
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:24985 original size:63 final size:63
Alignment explanation
Indices: 24914--25034 Score: 183
Period size: 63 Copynumber: 1.9 Consensus size: 63
24904 TAAAACATCT
* *
24914 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACTTAAAA-ATAATATAATATTC
1 TAAATCCTAATAAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAACA-AATATAATATTC
*
24977 TAAATCCTAATAAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAA
1 TAAATCCTAATAAAAACACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAA
25035 AATATAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
62 5 0.09
63 47 0.89
64 1 0.02
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (63 bp):
TAAATCCTAATAAAAACACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAATATTC
Found at i:25016 original size:24 final size:24
Alignment explanation
Indices: 24989--25096 Score: 74
Period size: 25 Copynumber: 4.3 Consensus size: 24
24979 AATCCTAATA
24989 AAAATACTAAAACCTATTTAAACT
1 AAAATACTAAAACCTATTTAAACT
** * *
25013 AAAATACCTAAAACAAATATAAAAT
1 AAAATA-CTAAAACCTATTTAAACT
* * * * *
25038 ATAAAAAATAATATCCTAAAACTTAATC-
1 A-AAATACTAA-AACCT---ATTTAAACT
25066 AAAATACTAAAACCTATTTAAACT
1 AAAATACTAAAACCTATTTAAACT
25090 AAAATAC
1 AAAATAC
25097 AAAGATAAAA
Statistics
Matches: 59, Mismatches: 18, Indels: 14
0.65 0.20 0.15
Matches are distributed among these distances:
23 6 0.10
24 13 0.22
25 18 0.31
26 10 0.17
27 7 0.12
28 1 0.02
29 4 0.07
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAATACTAAAACCTATTTAAACT
Found at i:31215 original size:13 final size:13
Alignment explanation
Indices: 31199--31232 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
31189 TAACAACCTA
31199 TCACAACATCACT
1 TCACAACATCACT
*
31212 TCACAACATTACT
1 TCACAACATCACT
31225 T-ACAACAT
1 TCACAACAT
31233 AGAGAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.26
Consensus pattern (13 bp):
TCACAACATCACT
Found at i:42799 original size:830 final size:831
Alignment explanation
Indices: 41585--43251 Score: 2932
Period size: 830 Copynumber: 2.0 Consensus size: 831
41575 GCCCGAGCAC
*
41585 AAATTTTTACTTGACGGAAAAGAAATGTGAATAAATAAATGTCTTTTCTTAAGTAAATATTTTGG
1 AAATTTTTACTTGACGGAAAAGAAATGTGAATAAATAAATGGCTTTTCTTAAGTAAATATTTTGG
*
41650 AGTCGCCATCCGCCTTTTGGTTTAGGTAGGTCGAATACCTAAAAATCATCTTTCAAAATAGTTTT
66 AGTCGCCATCCGCCTTTTAGTTTAGGTAGGTCGAATACCTAAAAATCATCTTTCAAAATAGTTTT
*
41715 TAATAAAATACCATTTTAAAAGAGAAATTGGTATGCATTTAACCAAAAATTCATTCTTTTTAGTA
131 TAAGAAAATACCATTTTAAAAGAGAAATTGGTATGCATTTAACCAAAAATTCATTCTTTTTAGT-
*
41780 AAAAAAGGGATTCGTGGTCGGTTACGTTTGGGGAAGGATTAGCACCCCCACAACGCCCAAAATTA
195 AAAAAAGGGATTCGTGGTCGGTTACATTTGGGGAAGGATTAGCACCCCCACAACGCCCAAAATTA
* **
41845 GTACCCATTGATTATAAATTGTCTATATTAGTGAAATTTAAGAATTCAAATATAAATTTAATTTA
260 GTACCCATTGATTAGAAATTGTCTATAAAAGTGAAATTTAAGAATTCAAATATAAATTTAATTTA
*
41910 TGATTCTATTATTCAAGATTTAATCATACAAAATTCTAAGGAAAAACATATATAAATTATTTTTA
325 TGATTCGATTATTCAAGATTTAATCATACAAAATTCTAAGGAAAAACATATATAAATTATTTTTA
* *
41975 TAAATTATAAATAAGGTATTTATTTATGTAAAAATATCAGAAAAGGACATCTAGTTACTTTAAGA
390 TAAATTATAAATAAGATATTTATTTATGTAAAAATATCAAAAAAGGACATCTAGTTACTTTAAGA
42040 CAACCCCTTTCTTAATATTAAAAAATAAATAAATATTAAAAAGAATACGATAATTTTCCCTAAAA
455 CAACCCCTTTCTTAATATTAAAAAATAAATAAATATTAAAAAGAATACGATAATTTTCCCTAAAA
*
42105 TAATAAAAATAAAGTAAATATATATATTTTTTGTTTTTATAAGCATAATATTTATTTATTTTTAA
520 TAATAAAAATAAAGTAAATATATATA-TTTTGGTTTTTATAAGCATAATATTTATTTATTTTTAA
*
42170 AATACTAGAATATGACATCTAGTTGCTTTAAGACAATCTTTTTCTTAATATTTAAAAATAAATAA
584 AATACTAGAATATGACATCTAGTTGCTTTAAGACAATCTTTTTCTTAATATTGAAAAATAAATAA
42235 ATATTATTATTTAATTAATTAGTGAAA-T-T-AAATAATATTTACAAATCTTTCATATATATATT
649 ATATTATTATTTAATTAATTAGTGAAATTATCAAATAATATTTACAAATCTTTCATATATATATT
42297 TCCATGATTAAAATAAAATAAAGATCAAATAAATAAATAATAATTAAAATACTAAATTAAATATT
714 TCCATGATTAAAATAAAATAAAGATCAAATAAATAAATAATAATTAAAATACTAAATTAAATATT
*
42362 GAAACTTAAAAGGGAATAATAAAATAAAATAATATTGCAATTAATAATGGCTA
779 GAAACTTAAAAGGGAATAATAAAATAAAATAAAATTGCAATTAATAATGGCTA
** * * *
42415 AAATTTTTACTTGGTGGAAAAGTAGTGTTAATAAATAAATGGCTTTT-TTAAAGTAAATATTTTG
1 AAATTTTTACTTGACGGAAAAGAAATGTGAATAAATAAATGGCTTTTCTT-AAGTAAATATTTTG
* *
42479 GAGTCGCCATCGGCCTTTTAGTTTAGGTAGGTCGAATACCTAAAAATCATCTTTTAAAATAGTTT
65 GAGTCGCCATCCGCCTTTTAGTTTAGGTAGGTCGAATACCTAAAAATCATCTTTCAAAATAGTTT
* **
42544 TTAAGAAAATACCATTTTAAAAGAGAATTTGGTATGTGTTTAACCAAAAATTCATTCTTTTTAGT
130 TTAAGAAAATACCATTTTAAAAGAGAAATTGGTATGCATTTAACCAAAAATTCATTCTTTTTAGT
*
42609 -AAAAAGGGATTCGTGGTCGGTTACATTTGGGGAATGATTAGCACCCCCACAACGCCCAAAATT-
195 AAAAAAGGGATTCGTGGTCGGTTACATTTGGGGAAGGATTAGCACCCCCACAACGCCCAAAATTA
*
42672 GATACCCATTGATTTAGAAATTGTCTATAAAAGTGAAATTTAAGAATTCAAATATGAATTTAATT
260 G-TACCCATTGA-TTAGAAATTGTCTATAAAAGTGAAATTTAAGAATTCAAATATAAATTTAATT
*
42737 TATGATTCGATTATTCAAGATTTAATCATAGAAAATTCTAAGGAAAAACATATATAAAATTATTT
323 TATGATTCGATTATTCAAGATTTAATCATACAAAATTCTAAGGAAAAACATATAT-AAATTATTT
*
42802 TTATAAATTATAAATAAGATATTTATTTATTTAAAAATATCAAAAAAGGACATCTAGTTACTTTA
387 TTATAAATTATAAATAAGATATTTATTTATGTAAAAATATCAAAAAAGGACATCTAGTTACTTTA
* * *
42867 AGACAACCCCTTTCTTAATATTAAAAAATAAATAAATATTAATAAGAATACGATATTTTTTCCTA
452 AGACAACCCCTTTCTTAATATTAAAAAATAAATAAATATTAAAAAGAATACGATAATTTTCCCTA
*
42932 AAATAATAAAAATAAAGTAAATATATATATTTTGGTTTTTATAAGCATCATATTTATTTATTTTT
517 AAATAATAAAAATAAAGTAAATATATATATTTTGGTTTTTATAAGCATAATATTTATTTATTTTT
42997 AAAATACTAGAATATGACATCTAGTTGCTTTAAGACAATCTTTTTCTTAATATTGAAAAATAAAT
582 AAAATACTAGAATATGACATCTAGTTGCTTTAAGACAATCTTTTTCTTAATATTGAAAAATAAAT
43062 AAATATTATTATTTAATTAATTAGTGAAATTAATCAAATAATATTTACAAATCTTTCATATATAT
647 AAATATTATTATTTAATTAATTAGTGAAATT-ATCAAATAATATTTACAAATCTTTCATATATAT
* *
43127 ATTTTCATGATTAAAATAAAATAAAGATTAAATAAATAAATAATAATTAAAATACTAAATTAAAT
711 ATTTCCATGATTAAAATAAAATAAAGATCAAATAAATAAATAATAATTAAAATACTAAATTAAAT
43192 ATTGAAACTTAAAAGGGAATAATAAAATAAAATAAAATTGCAATTAATAATGGCTA
776 ATTGAAACTTAAAAGGGAATAATAAAATAAAATAAAATTGCAATTAATAATGGCTA
43248 AAAT
1 AAAT
43252 AAAGAAAATT
Statistics
Matches: 796, Mismatches: 33, Indels: 13
0.95 0.04 0.02
Matches are distributed among these distances:
827 1 0.00
828 71 0.09
829 230 0.29
830 341 0.43
832 1 0.00
833 152 0.19
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (831 bp):
AAATTTTTACTTGACGGAAAAGAAATGTGAATAAATAAATGGCTTTTCTTAAGTAAATATTTTGG
AGTCGCCATCCGCCTTTTAGTTTAGGTAGGTCGAATACCTAAAAATCATCTTTCAAAATAGTTTT
TAAGAAAATACCATTTTAAAAGAGAAATTGGTATGCATTTAACCAAAAATTCATTCTTTTTAGTA
AAAAAGGGATTCGTGGTCGGTTACATTTGGGGAAGGATTAGCACCCCCACAACGCCCAAAATTAG
TACCCATTGATTAGAAATTGTCTATAAAAGTGAAATTTAAGAATTCAAATATAAATTTAATTTAT
GATTCGATTATTCAAGATTTAATCATACAAAATTCTAAGGAAAAACATATATAAATTATTTTTAT
AAATTATAAATAAGATATTTATTTATGTAAAAATATCAAAAAAGGACATCTAGTTACTTTAAGAC
AACCCCTTTCTTAATATTAAAAAATAAATAAATATTAAAAAGAATACGATAATTTTCCCTAAAAT
AATAAAAATAAAGTAAATATATATATTTTGGTTTTTATAAGCATAATATTTATTTATTTTTAAAA
TACTAGAATATGACATCTAGTTGCTTTAAGACAATCTTTTTCTTAATATTGAAAAATAAATAAAT
ATTATTATTTAATTAATTAGTGAAATTATCAAATAATATTTACAAATCTTTCATATATATATTTC
CATGATTAAAATAAAATAAAGATCAAATAAATAAATAATAATTAAAATACTAAATTAAATATTGA
AACTTAAAAGGGAATAATAAAATAAAATAAAATTGCAATTAATAATGGCTA
Found at i:44298 original size:23 final size:23
Alignment explanation
Indices: 44270--44315 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
44260 GGGAACATGA
*
44270 CGGCGGAGCAGTTAGAGTAGAGG
1 CGGCGGAGCAATTAGAGTAGAGG
*
44293 CGGCGGAGCAATTGGAGTAGAGG
1 CGGCGGAGCAATTAGAGTAGAGG
44316 TAAAAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.48, T:0.13
Consensus pattern (23 bp):
CGGCGGAGCAATTAGAGTAGAGG
Found at i:45324 original size:38 final size:37
Alignment explanation
Indices: 45266--45373 Score: 128
Period size: 38 Copynumber: 2.9 Consensus size: 37
45256 TTAAAAACAT
* *
45266 TGAATAAGTTGGACTCTCCAACATTAGTCTTAGAAATC
1 TGAATAAGTTGGAATATCCAACATTAGT-TTAGAAATC
*
45304 TGAATAAGTTGGAATATCCAAAATTAGTTCTAGGAAATC
1 TGAATAAGTTGGAATATCCAACATTAGTT-TA-GAAATC
* * *
45343 -GAATAAATTGGAAAATCTAACATTAGTTTAG
1 TGAATAAGTTGGAATATCCAACATTAGTTTAG
45374 GATGATTGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
36 1 0.02
37 3 0.05
38 51 0.84
39 6 0.10
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (37 bp):
TGAATAAGTTGGAATATCCAACATTAGTTTAGAAATC
Found at i:48152 original size:14 final size:14
Alignment explanation
Indices: 48133--48160 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48123 TTTACTATGG
48133 TTAGAGTTTAGGGT
1 TTAGAGTTTAGGGT
48147 TTAGAGTTTAGGGT
1 TTAGAGTTTAGGGT
48161 CTACAATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (14 bp):
TTAGAGTTTAGGGT
Found at i:48800 original size:22 final size:23
Alignment explanation
Indices: 48775--48826 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
48765 TGTCAATCCT
* * *
48775 CCTTCTAGAA-TTGCTGACTATA
1 CCTTCTAGAAGCTACTGACTAGA
*
48797 CCTTCTGGAAGCTACTGACTAGA
1 CCTTCTAGAAGCTACTGACTAGA
48820 CCTTCTA
1 CCTTCTA
48827 AAAACTGCTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (23 bp):
CCTTCTAGAAGCTACTGACTAGA
Found at i:48837 original size:23 final size:23
Alignment explanation
Indices: 48786--48837 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
48776 CTTCTAGAAT
* ** *
48786 TGCTGACTATACCTTCTGGAAGC
1 TGCTGACTAGACCTTCTAAAAAC
*
48809 TACTGACTAGACCTTCTAAAAAC
1 TGCTGACTAGACCTTCTAAAAAC
48832 TGCTGA
1 TGCTGA
48838 TGAACTGCCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (23 bp):
TGCTGACTAGACCTTCTAAAAAC
Found at i:57596 original size:6 final size:6
Alignment explanation
Indices: 57585--57619 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
57575 GATAAGATTC
57585 CCCCAG CCCCAG CCCCCAG CCCCAG CCCCAG CCCC
1 CCCCAG CCCCAG -CCCCAG CCCCAG CCCCAG CCCC
57620 CACCCCTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.14, C:0.71, G:0.14, T:0.00
Consensus pattern (6 bp):
CCCCAG
Found at i:57609 original size:19 final size:18
Alignment explanation
Indices: 57585--57625 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
57575 GATAAGATTC
57585 CCCCAGCCCCAGCCCCCA
1 CCCCAGCCCCAGCCCCCA
57603 GCCCCAGCCCCAGCCCCCA
1 -CCCCAGCCCCAGCCCCCA
57622 CCCC
1 CCCC
57626 TTTAACTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.15, C:0.73, G:0.12, T:0.00
Consensus pattern (18 bp):
CCCCAGCCCCAGCCCCCA
Found at i:57621 original size:13 final size:13
Alignment explanation
Indices: 57584--57619 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
57574 TGATAAGATT
57584 CCCCCAGCCCCAG
1 CCCCCAGCCCCAG
57597 CCCCCAGCCCCAG
1 CCCCCAGCCCCAG
57610 -CCCCAGCCCC
1 CCCCCAGCCCC
57620 CACCCCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.14, C:0.72, G:0.14, T:0.00
Consensus pattern (13 bp):
CCCCCAGCCCCAG
Found at i:61637 original size:15 final size:15
Alignment explanation
Indices: 61616--61662 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
61606 TTATATTTTA
61616 AATATTACTTA-TTAT
1 AATATTA-TTAGTTAT
*
61631 TATATTATTAGTTAT
1 AATATTATTAGTTAT
*
61646 AATATTAGTATGTTAT
1 AATATTATTA-GTTAT
61662 A
1 A
61663 TAACTTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 3 0.11
15 18 0.67
16 6 0.22
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (15 bp):
AATATTATTAGTTAT
Found at i:74592 original size:36 final size:36
Alignment explanation
Indices: 74536--74637 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 36
74526 TTATCAAGTC
* *
74536 AATCAAGCCTTCACAAAAGAGCAGTGAAGCTATACA
1 AATCCAGCCTTCACAAAAGAGCAGTGAAGCGATACA
** * *
74572 AATCCAGCCTTCACGGAAGAGTAGTGAAGCGATGCA
1 AATCCAGCCTTCACAAAAGAGCAGTGAAGCGATACA
* * * *
74608 CATCCAACCTTCACAAAAGAGTAATGAAGC
1 AATCCAGCCTTCACAAAAGAGCAGTGAAGC
74638 AAGAATAAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.17
Consensus pattern (36 bp):
AATCCAGCCTTCACAAAAGAGCAGTGAAGCGATACA
Done.