Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005723.1 Hibiscus syriacus cultivar Beakdansim tig00013378_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: 94900
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:24187 original size:22 final size:22
Alignment explanation
Indices: 24156--24207 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
24146 CCCCACTGCA
24156 TGCA-GGCGACCTCTTCCGACG
1 TGCATGGCGACCTCTTCCGACG
*
24177 TGCATGGCGACCTCTTCCGACT
1 TGCATGGCGACCTCTTCCGACG
24199 TGCATGGCG
1 TGCATGGCG
24208 CATGCAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.13, C:0.35, G:0.29, T:0.23
Consensus pattern (22 bp):
TGCATGGCGACCTCTTCCGACG
Found at i:24271 original size:31 final size:32
Alignment explanation
Indices: 24211--24273 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
24201 CATGGCGCAT
24211 GCAAAACTTCATCCTCTCACCAACAGCTCGTA
1 GCAAAACTTCATCCTCTCACCAACAGCTCGTA
*
24243 GCAAAGCTTCATCCTCTCGA-C-ACAGCTCGTA
1 GCAAAACTTCATCCTCTC-ACCAACAGCTCGTA
24274 TAGAACACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 10 0.34
32 18 0.62
33 1 0.03
ACGTcount: A:0.29, C:0.37, G:0.13, T:0.22
Consensus pattern (32 bp):
GCAAAACTTCATCCTCTCACCAACAGCTCGTA
Found at i:24863 original size:14 final size:14
Alignment explanation
Indices: 24844--24870 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24834 CCGTTGGTAT
24844 TTGATCCATATACA
1 TTGATCCATATACA
24858 TTGATCCATATAC
1 TTGATCCATATAC
24871 GGCTAAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (14 bp):
TTGATCCATATACA
Found at i:26343 original size:14 final size:15
Alignment explanation
Indices: 26305--26345 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
26295 GTTTTTTCGG
26305 TTCGGTTCGGGTTTT
1 TTCGGTTCGGGTTTT
26320 TTAACGGTTCGGG-TTT
1 TT--CGGTTCGGGTTTT
26336 TTCGGTTCGG
1 TTCGGTTCGG
26346 TTCGGTTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.33
15 2 0.08
16 5 0.21
17 9 0.38
ACGTcount: A:0.05, C:0.15, G:0.34, T:0.46
Consensus pattern (15 bp):
TTCGGTTCGGGTTTT
Found at i:26497 original size:26 final size:27
Alignment explanation
Indices: 26468--26522 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
26458 ACCAAATCAA
*
26468 AAAAATGAAGCC-TTTAAA-CCGAACCG
1 AAAAATGAA-CCATTTAAAGCCAAACCG
*
26494 AAAACTGAACCATTTAAAGCCAAACCG
1 AAAAATGAACCATTTAAAGCCAAACCG
26521 AA
1 AA
26523 CCGAACCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 14 0.56
27 9 0.36
ACGTcount: A:0.49, C:0.24, G:0.13, T:0.15
Consensus pattern (27 bp):
AAAAATGAACCATTTAAAGCCAAACCG
Found at i:26777 original size:12 final size:12
Alignment explanation
Indices: 26749--26785 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
26739 TTTGGTAATC
26749 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
26762 CCCGCCCCGATA
1 CCCGCCCCGATA
*
26774 CCCGACCCGATA
1 CCCGCCCCGATA
26786 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:26808 original size:2 final size:2
Alignment explanation
Indices: 26801--26830 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
26791 TAAAAATAAT
26801 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26831 TAATAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26902 original size:12 final size:12
Alignment explanation
Indices: 26882--26924 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
26872 ATTTATATAT
*
26882 ATACCCGGCCCG
1 ATACCCGGCCCA
*
26894 ATTCCCGGCCCA
1 ATACCCGGCCCA
26906 ATACCCGGCCCA
1 ATACCCGGCCCA
26918 ATACCCG
1 ATACCCG
26925 TTTAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.21, C:0.49, G:0.19, T:0.12
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:28971 original size:18 final size:18
Alignment explanation
Indices: 28948--28984 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
28938 ACTATAATAG
*
28948 AAGGTGTGTTTATTTTAT
1 AAGGTGTGCTTATTTTAT
28966 AAGGTGTGCTTATTTTAT
1 AAGGTGTGCTTATTTTAT
28984 A
1 A
28985 CTTCCTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (18 bp):
AAGGTGTGCTTATTTTAT
Found at i:30110 original size:28 final size:28
Alignment explanation
Indices: 30049--30120 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
30039 TAAATATAAA
30049 AGATAAATA-AATAAATAAATTATTGTAT
1 AGATAAATATAAT-AATAAATTATTGTAT
*
30077 ATATAAGATATAATAA-AAATTATT-TATT
1 AGATAA-ATATAATAATAAATTATTGTA-T
30105 AGATAACA-ATAATAAT
1 AGATAA-ATATAATAAT
30121 TTACATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 9 0.24
28 20 0.54
29 5 0.14
30 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (28 bp):
AGATAAATATAATAATAAATTATTGTAT
Found at i:31580 original size:29 final size:29
Alignment explanation
Indices: 31504--31580 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
31494 CTTCCCAGCA
*
31504 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
*
31533 TAAGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
31562 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
31581 CCTGCTCCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.16, C:0.35, G:0.26, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:34216 original size:34 final size:33
Alignment explanation
Indices: 34162--34236 Score: 77
Period size: 34 Copynumber: 2.3 Consensus size: 33
34152 TATAATTAAA
*
34162 AAATATAAAATATAATATTATCAT-AATTATCTTT
1 AAATATAAAATATAATATTAT-ATCAATCAT-TTT
34196 AAATATATAAATACT-A-ATTATATCAATCATTTT
1 AAATATA-AAATA-TAATATTATATCAATCATTTT
34229 AAAT-TAAA
1 AAATATAAA
34237 TGTTTTTCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
31 2 0.05
32 2 0.05
33 9 0.24
34 17 0.46
35 6 0.16
36 1 0.03
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (33 bp):
AAATATAAAATATAATATTATATCAATCATTTT
Found at i:37693 original size:28 final size:29
Alignment explanation
Indices: 37640--37694 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
37630 AAGAGATTAA
* *
37640 GGTTTAAAGGTTATGAAGTTATGATTTAG
1 GGTTTAAAGGTTATCAAGTTAAGATTTAG
*
37669 GGTTT-AAGGTTATCAATTTAAGATTT
1 GGTTTAAAGGTTATCAAGTTAAGATTT
37695 TAAGTTAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.44
Consensus pattern (29 bp):
GGTTTAAAGGTTATCAAGTTAAGATTTAG
Found at i:40663 original size:19 final size:19
Alignment explanation
Indices: 40639--40688 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
40629 TAATGGGTGT
40639 ATCGATGCACTCCCTATGC
1 ATCGATGCACTCCCTATGC
40658 ATCGATGCACTCCCTATGC
1 ATCGATGCACTCCCTATGC
40677 ATCGATGCACTC
1 ATCGATGCACTC
40689 ATTTCATTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (19 bp):
ATCGATGCACTCCCTATGC
Found at i:44636 original size:21 final size:21
Alignment explanation
Indices: 44610--44659 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
44600 AAGTGGGTAT
44610 GGGAGAAGTTGAGGGACAAGA
1 GGGAGAAGTTGAGGGACAAGA
44631 GGGAGAAGTTGAGGGACAAGA
1 GGGAGAAGTTGAGGGACAAGA
*
44652 GTGAGAAG
1 GGGAGAAG
44660 ATAAGATGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.48, T:0.10
Consensus pattern (21 bp):
GGGAGAAGTTGAGGGACAAGA
Found at i:45802 original size:2 final size:2
Alignment explanation
Indices: 45795--45829 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
45785 TTATTATACA
45795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45830 GACAATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57500 original size:2 final size:2
Alignment explanation
Indices: 57493--57527 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
57483 CAATAATACC
57493 TA TA TA TA 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 TA TA TA TA T
57528 TAATTAAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68197 original size:16 final size:16
Alignment explanation
Indices: 68176--68211 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
68166 ATCTCTAGGA
68176 TAGCGGCTTCTTGATG
1 TAGCGGCTTCTTGATG
68192 TAGCGGCTTCTTGATG
1 TAGCGGCTTCTTGATG
68208 TAGC
1 TAGC
68212 CGCTATGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (16 bp):
TAGCGGCTTCTTGATG
Found at i:74903 original size:60 final size:60
Alignment explanation
Indices: 74851--74965 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
74841 ACTATTACTA
* ** * *
74851 TCATCCTAAATTAGTCCTTAAAC-TTTTAAATATTTCAATTTCATCCCCAAACTATGACCT
1 TCATCCTAAACTAGTCCCCAAACATTTTAAACATTCCAATTTCAT-CCCAAACTATGACCT
* * *
74911 TTATTCTAAACTAGTCCCCAAACATTTTGAACATTCCAATTTCATCCCAAACTAT
1 TCATCCTAAACTAGTCCCCAAACATTTTAAACATTCCAATTTCATCCCAAACTAT
74966 ATGTATATAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 28 0.61
61 18 0.39
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (60 bp):
TCATCCTAAACTAGTCCCCAAACATTTTAAACATTCCAATTTCATCCCAAACTATGACCT
Found at i:75157 original size:60 final size:60
Alignment explanation
Indices: 75083--75242 Score: 180
Period size: 60 Copynumber: 2.7 Consensus size: 60
75073 TTACATATTT
* **
75083 GGATGAAACTGGAATATTCAAAAGTTTGGGGACCAATTT-GGAA-AGAAGGTCATAGTTTGA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAGGAAGAG-A-GTCATAGTTTGA
* * ** * *
75143 GGATGAAATTGGAATGTTCAAATGTTTAAGGATTAATTTAGGATGAGATTCATAGTTTGA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAGGAAGAGAGTCATAGTTTGA
* * *
75203 GGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA
1 GGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTA
75243 AAATGAAGTT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
60 78 0.93
61 4 0.05
62 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.32
Consensus pattern (60 bp):
GGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAGGAAGAGAGTCATAGTTTGA
Found at i:75229 original size:29 final size:29
Alignment explanation
Indices: 75136--75234 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 29
75126 AGAAGGTCAT
* * * *
75136 AGTTTGAGGATGAAATTGGAATGTTCAAA
1 AGTTTAAGGATAAAATTAGAATATTCAAA
* * * * *
75165 TGTTTAAGGATTAATTTAGGATGAGATTC-AT
1 AGTTTAAGGATAAAATTA-GA--ATATTCAAA
*
75196 AGTTTGAGGATAAAATTAGAATATTCAAA
1 AGTTTAAGGATAAAATTAGAATATTCAAA
75225 AGTTTAAGGA
1 AGTTTAAGGA
75235 CTAATTTAAA
Statistics
Matches: 51, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
28 5 0.10
29 23 0.45
30 4 0.08
31 15 0.29
32 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.34
Consensus pattern (29 bp):
AGTTTAAGGATAAAATTAGAATATTCAAA
Found at i:75489 original size:29 final size:29
Alignment explanation
Indices: 75451--75549 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 29
75441 AGAATGTCAT
*
75451 AGTTTGAGGATGAAATTGGAATGTTCAAA
1 AGTTTAAGGATGAAATTGGAATGTTCAAA
* *
75480 AGTTTAAGGACT-AATTTAGG-ATGAGATTC-AT
1 AGTTTAAGGA-TGAAATT-GGAAT--G-TTCAAA
* * *
75511 AGTTTGAGGATGAAATTAGAATATTCAAA
1 AGTTTAAGGATGAAATTGGAATGTTCAAA
75540 AGTTTAAGGA
1 AGTTTAAGGA
75550 CTAATTTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
28 3 0.06
29 25 0.47
30 5 0.09
31 17 0.32
32 3 0.06
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (29 bp):
AGTTTAAGGATGAAATTGGAATGTTCAAA
Found at i:75511 original size:60 final size:60
Alignment explanation
Indices: 75447--75579 Score: 207
Period size: 60 Copynumber: 2.2 Consensus size: 60
75437 GGAAAGAATG
* * **
75447 TCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGGATG-AGAT
1 TCATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAG-T
75507 TCATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAGT
1 TCATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAGT
75567 T-ATAGTTTGAGGA
1 TCATAGTTTGAGGA
75580 CATATGATCC
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
59 12 0.18
60 54 0.79
61 2 0.03
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.34
Consensus pattern (60 bp):
TCATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAGT
Found at i:75515 original size:31 final size:29
Alignment explanation
Indices: 75474--75557 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 29
75464 AATTGGAATG
75474 TTCAAAAGTTTAAGGACTAATTTAGGATGAGA
1 TTCAAAAGTTTAAGGACTAATTTA-GA--AGA
* * * *
75506 TTC-ATAGTTTGAGGA-TGAAATTAGAATA
1 TTCAAAAGTTTAAGGACT-AATTTAGAAGA
75534 TTCAAAAGTTTAAGGACTAATTTA
1 TTCAAAAGTTTAAGGACTAATTTA
75558 AAATGAAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
28 5 0.12
29 15 0.36
30 4 0.10
31 15 0.36
32 3 0.07
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (29 bp):
TTCAAAAGTTTAAGGACTAATTTAGAAGA
Found at i:75551 original size:315 final size:316
Alignment explanation
Indices: 74978--75610 Score: 1142
Period size: 315 Copynumber: 2.0 Consensus size: 316
74968 GTATATACTA
*
74978 ATCACATTCATTGTTAATACAATTGTTAGGCCAAGTTATATTATTATATGTTAGAAAAAAACACA
1 ATCACATTCATTGTTAATACAATTGTTAGGCCAAGTTATATCATTATATGTTAGAAAAAAACACA
* * *
75043 AAATTTAGGTTAGACTATGGTTGAAACTAATTACATATTTGGATGAAACTGGAATATTCAAAAGT
66 AAATTTAGGTTAGAATACGATTGAAACTAATTACATATTTGGATGAAACTGGAATATTCAAAAGT
*
75108 TTGGGGACCAATTTGGAAAGAAGGTCATAGTTTGAGGATGAAATTGGAATGTTCAAATGTTTAAG
131 TTGGGGACCAATTTGGAAAGAAGGTCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAG
*
75173 GATTAATTTAGGATGAGATTCATAGTTTGAGGATAAAATTAGAATATTCAAAAGTTTAAGGACTA
196 GACTAATTTAGGATGAGATTCATAGTTTGAGGATAAAATTAGAATATTCAAAAGTTTAAGGACTA
*
75238 ATTTAAAATGAAGTTATAGTTTGGGGACATATGATACAATTAACTCAATTATTTAG
261 ATTTAAAATGAAGTTATAGTTTGAGGACATATGATACAATTAACTCAATTATTTAG
*
75294 ATCACATTCATTGTTAATACAATTGTTAGGCCAAGTTATATCATTATATGTTTG-AAAAAACACA
1 ATCACATTCATTGTTAATACAATTGTTAGGCCAAGTTATATCATTATATGTTAGAAAAAAACACA
*
75358 AAATTTAGGTTAGAATACGATTGAAACTAATTACATATTTGGATTAAACTGGAATATTCAAAAGT
66 AAATTTAGGTTAGAATACGATTGAAACTAATTACATATTTGGATGAAACTGGAATATTCAAAAGT
* *
75423 TTGGGGTCCAATTTGGAAAGAATGTCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAG
131 TTGGGGACCAATTTGGAAAGAAGGTCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAG
*
75488 GACTAATTTAGGATGAGATTCATAGTTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTA
196 GACTAATTTAGGATGAGATTCATAGTTTGAGGATAAAATTAGAATATTCAAAAGTTTAAGGACTA
*
75553 ATTTAAAATGAAGTTATAGTTTGAGGACATATGATCCAATTAACTCAATTATTTAG
261 ATTTAAAATGAAGTTATAGTTTGAGGACATATGATACAATTAACTCAATTATTTAG
75609 AT
1 AT
75611 AGGTTTGACA
Statistics
Matches: 304, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
315 252 0.83
316 52 0.17
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (316 bp):
ATCACATTCATTGTTAATACAATTGTTAGGCCAAGTTATATCATTATATGTTAGAAAAAAACACA
AAATTTAGGTTAGAATACGATTGAAACTAATTACATATTTGGATGAAACTGGAATATTCAAAAGT
TTGGGGACCAATTTGGAAAGAAGGTCATAGTTTGAGGATGAAATTGGAATGTTCAAAAGTTTAAG
GACTAATTTAGGATGAGATTCATAGTTTGAGGATAAAATTAGAATATTCAAAAGTTTAAGGACTA
ATTTAAAATGAAGTTATAGTTTGAGGACATATGATACAATTAACTCAATTATTTAG
Found at i:76791 original size:13 final size:11
Alignment explanation
Indices: 76760--76802 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
76750 GACGTTATTT
76760 AAATATTTAAA
1 AAATATTTAAA
76771 ATAATATTTATCAA
1 A-AATATTTA--AA
*
76785 AAATATTAAAA
1 AAATATTTAAA
76796 AAATATT
1 AAATATT
76803 AACATTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 10 0.36
12 8 0.29
13 7 0.25
14 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATATTTAAA
Found at i:76804 original size:11 final size:12
Alignment explanation
Indices: 76760--76802 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
76750 GACGTTATTT
76760 AAATATTTAAAA
1 AAATATTTAAAA
* *
76772 TAATATTTATCAA
1 AAATATTTA-AAA
76785 AAATA-TTAAAA
1 AAATATTTAAAA
76796 AAATATT
1 AAATATT
76803 AACATTTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 7 0.28
12 12 0.48
13 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATATTTAAAA
Found at i:79245 original size:29 final size:29
Alignment explanation
Indices: 79209--79297 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 29
79199 AGTGTTGACC
*
79209 GTAGGTCGCCATGTC-CTCCGGGCGACCTT
1 GTAGGTCGCCATG-CACGCCGGGCGACCTT
* * *
79238 GTAGGTCGCCATGCACGCCAGGCGACATG
1 GTAGGTCGCCATGCACGCCGGGCGACCTT
*
79267 GTAGGTCGCCATGCACGCTGGGCGACCTT
1 GTAGGTCGCCATGCACGCCGGGCGACCTT
79296 GT
1 GT
79298 CCTACGCCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 1 0.02
29 50 0.98
ACGTcount: A:0.15, C:0.31, G:0.34, T:0.20
Consensus pattern (29 bp):
GTAGGTCGCCATGCACGCCGGGCGACCTT
Found at i:79376 original size:22 final size:22
Alignment explanation
Indices: 79349--79394 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
79339 TGCATGCAAA
79349 CGACCTCTTCCGACGTGCATGG
1 CGACCTCTTCCGACGTGCATGG
79371 CGACCTCTTCCGACGTGCATGG
1 CGACCTCTTCCGACGTGCATGG
79393 CG
1 CG
79395 CATGCAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.37, G:0.28, T:0.22
Consensus pattern (22 bp):
CGACCTCTTCCGACGTGCATGG
Found at i:79433 original size:31 final size:31
Alignment explanation
Indices: 79398--79459 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
79388 CATGGCGCAT
* *
79398 GCAAAGCTTCATTCTCTCGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
*
79429 GCAAAGCTTCATCCTCTCACTACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
79460 TAGAACACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Done.