Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001799.1 Hibiscus syriacus cultivar Beakdansim tig00003638_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: 49250
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1457 original size:2 final size:2
Alignment explanation
Indices: 1450--1477 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1440 TTGGCAATGT
1450 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1478 AATTGTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4653 original size:2 final size:2
Alignment explanation
Indices: 4646--4678 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4636 TTTCAACATT
4646 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 T
4679 GTTTTGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5691 original size:84 final size:84
Alignment explanation
Indices: 5550--5820 Score: 497
Period size: 84 Copynumber: 3.2 Consensus size: 84
5540 AAGAAATGTT
5550 TCTAATATTTGATTAAATAATTATTTTAATTATTATCTTTTAGAATATTTTGGTCTCATTGTTTC
1 TCTAATATTTGATTAAATAATTATTTTAATTATTATCTTTTAGAATATTTTGGTCTCATTGTTTC
5615 GTTTTATGGTAAAATTATG
66 GTTTTATGGTAAAATTATG
5634 TCTAATATTTGATTAAATAATTATTTTAATTATTATCTTTTAGAATATTTTGGTCTCATTGTTTC
1 TCTAATATTTGATTAAATAATTATTTTAATTATTATCTTTTAGAATATTTTGGTCTCATTGTTTC
*
5699 GTTTTATAGTAAAATTATG
66 GTTTTATGGTAAAATTATG
* *
5718 TCTAATATTTGATTAAATAATTATTTTAATTATTATATTTTAGAATATTTTGGTCTCATTGATTC
1 TCTAATATTTGATTAAATAATTATTTTAATTATTATCTTTTAGAATATTTTGGTCTCATTGTTTC
5783 GTTTTATGGTAAAATTATG
66 GTTTTATGGTAAAATTATG
* *
5802 TTTAATGTTTGATTAAATA
1 TCTAATATTTGATTAAATA
5821 GTCACTTTAG
Statistics
Matches: 181, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 181 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.53
Consensus pattern (84 bp):
TCTAATATTTGATTAAATAATTATTTTAATTATTATCTTTTAGAATATTTTGGTCTCATTGTTTC
GTTTTATGGTAAAATTATG
Found at i:17283 original size:17 final size:17
Alignment explanation
Indices: 17261--17300 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
17251 TGCTTAAATA
17261 AAGTACACACTTGAATG
1 AAGTACACACTTGAATG
**
17278 AAGTACATGCTTGAATG
1 AAGTACACACTTGAATG
17295 AAGTAC
1 AAGTAC
17301 CATGCTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (17 bp):
AAGTACACACTTGAATG
Found at i:19637 original size:34 final size:32
Alignment explanation
Indices: 19557--19645 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
19547 TTAGTATTTT
* * *
19557 TTTAAATAGTTATTATTTTTTATATTAATATA
1 TTTATATAATTATTATTTTTTATATAAATATA
* *
19589 TTTATGTAAATATTATTTTATTAT-TAAAATAATA
1 TTTATATAATTATTATTTT-TTATAT-AAAT-ATA
19623 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTT-TTTA
19646 GAATTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 16 0.35
33 7 0.15
34 22 0.48
35 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTATATAATTATTATTTTTTATATAAATATA
Found at i:21757 original size:12 final size:13
Alignment explanation
Indices: 21724--21761 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
21714 AAATACATAA
21724 ATATATTTAATAT
1 ATATATTTAATAT
*
21737 ATTTATTTAATAT
1 ATATATTTAATAT
21750 A-ATATTTAATAT
1 ATATATTTAATAT
21762 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:21799 original size:21 final size:22
Alignment explanation
Indices: 21775--21832 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
21765 TAGTTATAAT
*
21775 TTTTACATTATA-ATCGAAACA
1 TTTTACATAATATATCGAAACA
21796 TTTTACATAATATATCGAAACA
1 TTTTACATAATATATCGAAACA
21818 TTTTACATAATATAT
1 TTTTACATAATATAT
21833 TATTAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 11 0.31
22 24 0.69
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.41
Consensus pattern (22 bp):
TTTTACATAATATATCGAAACA
Found at i:24694 original size:21 final size:21
Alignment explanation
Indices: 24668--24742 Score: 141
Period size: 21 Copynumber: 3.6 Consensus size: 21
24658 TGGGAGTTAA
24668 CCAGTATCGATATTGTTCATC
1 CCAGTATCGATATTGTTCATC
24689 CCAGTATCGATATTGTTCATC
1 CCAGTATCGATATTGTTCATC
24710 CCAGTATCGATATTGTTCATC
1 CCAGTATCGATATTGTTCATC
*
24731 CGAGTATCGATA
1 CCAGTATCGATA
24743 CTCAAACTCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (21 bp):
CCAGTATCGATATTGTTCATC
Found at i:25856 original size:14 final size:14
Alignment explanation
Indices: 25837--25869 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
25827 AGTTAACCTT
25837 ACTCAATCGAGTTA
1 ACTCAATCGAGTTA
25851 ACTCAATCGAGTTA
1 ACTCAATCGAGTTA
25865 ACTCA
1 ACTCA
25870 CTGTATAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (14 bp):
ACTCAATCGAGTTA
Found at i:27379 original size:31 final size:31
Alignment explanation
Indices: 27264--27379 Score: 135
Period size: 31 Copynumber: 3.7 Consensus size: 31
27254 TACTCATATT
* * * *
27264 CATTAGCTGAATGCGAA-CATGACATATGATG
1 CATTATCTGAATGCAAATC-TGACATACGGTG
* *
27295 CATTATTTGAATGCAAATTTGACATACGGTG
1 CATTATCTGAATGCAAATCTGACATACGGTG
* **
27326 CATTATCTGAATGTAACCCTGACATACGGTG
1 CATTATCTGAATGCAAATCTGACATACGGTG
27357 CATTATCTGAATGCAAATCTGAC
1 CATTATCTGAATGCAAATCTGAC
27380 TAGTATCTGG
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
CATTATCTGAATGCAAATCTGACATACGGTG
Found at i:29887 original size:23 final size:22
Alignment explanation
Indices: 29837--29894 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
29827 ATTGTTAAAC
**
29837 CCTTTCATAAAAAATGTTAAGT
1 CCTTTCATAAAAAAACTTAAGT
**
29859 TTTTTCATAAAAAAACTTCAAGT
1 CCTTTCATAAAAAAACTT-AAGT
*
29882 CCTTTCATTAAAA
1 CCTTTCATAAAAA
29895 GGTTAAGTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (22 bp):
CCTTTCATAAAAAAACTTAAGT
Found at i:30713 original size:489 final size:491
Alignment explanation
Indices: 30038--31018 Score: 1601
Period size: 489 Copynumber: 2.0 Consensus size: 491
30028 CAAATCTTCA
* *
30038 ATTTTCTTCCAAATTCATTTTCAGTGATAGATAAAGACAAAATTTGTGTTCTATTGTTCACTACT
1 ATTTTCTTCCAAATTCATTTTCAGTGATAGATAAAGACAAAAATTGTGTTCTATTATTCACTACT
* * * *
30103 GTTATGCTTACTATCGTGAACTTTTGTTGTTATATATTGGGATACTGACGTCCAACGTTAATCAA
66 GTTATACTTACTATCGTAAACTTTTGTTGTTATATATTGGGAGACTAACGTCCAACGTTAATCAA
* * * * *
30168 ATCACCAATGAGAGGACAAATCTATCTTAAGGGAACTATTTATTCAGGCCTCAATAAAATTCTTC
131 AGCACCAAGGAGAGGAAAAATCTATCTTAAGGAAACTATTTATACAGGCCTCAATAAAATTCTTC
30233 TTTTTATTCAATTTTATCCGATTACAGGTTTTATTTAATTTTTA-CTTTTAATCTA-TTTTCGGT
196 TTTTTATTCAATTTTATCCGATTACAGGTTTTATTTAA-TTTTACCTTTTAATCTATTTTTCGGT
30296 GTCTTTTCTTACGTTACTACTACAACTTTATTATTGCTACGATATTATTATTATTGTTATCATTA
260 GTCTTTTCTTACGTTACTACTACAACTTTATTATTGCTACGATATTATTATTATTGTTATCATTA
* * *
30361 GATTATCCTTACTACAGCCTTAAATTAATTTTACTACAATCTTAAGGTAAATTCC-TTTTTATTG
325 GATTATCCTTACTACAACCTTAAATCAATTTTACTACAATCTTAAGATAAATTCCTTTTTTATTG
30425 TAGTTCAATCTAAACTCAAACAGATTACTATGGTAGTATATTTAGGTTAATTTATATTTTTATTT
390 TAGTTCAATCTAAACTCAAACAGATTACTATGGTAGTATATTTAGGTTAATTTATATTTTTATTT
* * *
30490 CGTATTATATATATTTATTTCAGTTTTGATTTTGATT
455 CATATTATATATATTTATTTCAGTTTTAATTTCGATT
* *
30527 ATTTTCTTCCAAATTCATTTTCGGTGATAGATAAAGACAAAAATTGTGTT-TGATTATTCTCTAC
1 ATTTTCTTCCAAATTCATTTTCAGTGATAGATAAAGACAAAAATTGTGTTCT-ATTATTCACTAC
* * * * * *
30591 TGTTGTACTTACTATCTTAAACTTTTGTTGTTGTATCTTGGGAGACTAATGTCCAACGTTACTCA
65 TGTTATACTTACTATCGTAAACTTTTGTTGTTATATATTGGGAGACTAACGTCCAACGTTAATCA
* *
30656 AAGCACCAAGGAGAGGAAAAATCTATCTTAAGTAAACTATTTATACATGCCTCAATAAAATTCTT
130 AAGCACCAAGGAGAGGAAAAATCTATCTTAAGGAAACTATTTATACAGGCCTCAATAAAATTCTT
* *
30721 CTTTTTATTCAATTTTATCCGATTATAGGTTTTATTTAATTTTACCTTTTAATCTATTTTTTGGT
195 CTTTTTATTCAATTTTATCCGATTACAGGTTTTATTTAATTTTACCTTTTAATCTATTTTTCGGT
* *
30786 GTCTTTTGTTACGTTACTACTACAACTTTATTATTGCTACGATATTATTATTATTTTTATCATTA
260 GTCTTTTCTTACGTTACTACTACAACTTTATTATTGCTACGATATTATTATTATTGTTATCATTA
*
30851 GATTATCCTTACTACAACCTTAAATCAATTTTACTACAATCTTAAGATATATTCCTTTTTTATTG
325 GATTATCCTTACTACAACCTTAAATCAATTTTACTACAATCTTAAGATAAATTCCTTTTTTATTG
* *
30916 TAGTTTAATTTAAACTCAAACAGATTACTATGGTAGTATATTTAGGTTAATTTATATTTTTATTT
390 TAGTTCAATCTAAACTCAAACAGATTACTATGGTAGTATATTTAGGTTAATTTATATTTTTATTT
*
30981 CATATTATATATATTTATTTCTGTTTTAATTTCGATT
455 CATATTATATATATTTATTTCAGTTTTAATTTCGATT
31018 A
1 A
31019 CAAAAATATT
Statistics
Matches: 453, Mismatches: 35, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
488 6 0.01
489 220 0.49
490 121 0.27
491 106 0.23
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (491 bp):
ATTTTCTTCCAAATTCATTTTCAGTGATAGATAAAGACAAAAATTGTGTTCTATTATTCACTACT
GTTATACTTACTATCGTAAACTTTTGTTGTTATATATTGGGAGACTAACGTCCAACGTTAATCAA
AGCACCAAGGAGAGGAAAAATCTATCTTAAGGAAACTATTTATACAGGCCTCAATAAAATTCTTC
TTTTTATTCAATTTTATCCGATTACAGGTTTTATTTAATTTTACCTTTTAATCTATTTTTCGGTG
TCTTTTCTTACGTTACTACTACAACTTTATTATTGCTACGATATTATTATTATTGTTATCATTAG
ATTATCCTTACTACAACCTTAAATCAATTTTACTACAATCTTAAGATAAATTCCTTTTTTATTGT
AGTTCAATCTAAACTCAAACAGATTACTATGGTAGTATATTTAGGTTAATTTATATTTTTATTTC
ATATTATATATATTTATTTCAGTTTTAATTTCGATT
Found at i:33303 original size:21 final size:21
Alignment explanation
Indices: 33279--33336 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
33269 GATGAAGTTG
33279 AAAA-TATATTAA-AATAAATAA
1 AAAATTATA-TAATAAT-AATAA
33300 AAAATTATATAATAATAAT-A
1 AAAATTATATAATAATAATAA
*
33320 AAAATTA-ATAGTAATAA
1 AAAATTATATAATAATAA
33337 ATATAAAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 9 0.26
20 8 0.24
21 10 0.29
22 7 0.21
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAATTATATAATAATAATAA
Found at i:33342 original size:22 final size:20
Alignment explanation
Indices: 33291--33344 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
33281 AATATATTAA
33291 AATAAATA-AAAAATTATAT
1 AATAAATATAAAAATTATAT
33310 AAT-AATAATAAAAATTAATAGT
1 AATAAAT-ATAAAAATT-ATA-T
33332 AATAAATATAAAA
1 AATAAATATAAAA
33345 GGGGGATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.10
19 4 0.13
20 7 0.23
21 3 0.10
22 10 0.33
23 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAAATATAAAAATTATAT
Found at i:33392 original size:19 final size:19
Alignment explanation
Indices: 33373--33421 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
33363 GTTGTGGTTA
33373 AAATAAA-AAATAAGAATT
1 AAATAAACAAATAAGAATT
*
33391 AAATAAACAAATAATAATT
1 AAATAAACAAATAAGAATT
33410 AAATAAACAAAT
1 AAATAAACAAAT
33422 TAAAGAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (19 bp):
AAATAAACAAATAAGAATT
Found at i:34132 original size:75 final size:76
Alignment explanation
Indices: 34065--34228 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 76
34055 AAAAAATAAT
* *
34065 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
34129 AAAATATAAAA
66 AAAATATAAAA
* *
34140 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTGAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
* * *
34204 ATAATGTTTAAA
66 AAAAT-ATAAAA
*
34216 ATATTATCCTAAA
1 ATAATATCCTAAA
34229 TTTGAGTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 32 0.41
76 47 0.59
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (76 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAGAT
AAAATATAAAA
Found at i:35872 original size:15 final size:15
Alignment explanation
Indices: 35852--35881 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35842 CAAATCTGTT
35852 TTTTTTTCTGCACTG
1 TTTTTTTCTGCACTG
*
35867 TTTTTTTTTGCACTG
1 TTTTTTTCTGCACTG
35882 CATTGTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.13, T:0.63
Consensus pattern (15 bp):
TTTTTTTCTGCACTG
Found at i:36133 original size:19 final size:19
Alignment explanation
Indices: 36094--36133 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
36084 AAGTTCGCTG
*
36094 AAAAAAATAAAACGAAAAT
1 AAAAAAATAAAACAAAAAT
36113 AAAAAAATAAAA-AAAATAT
1 AAAAAAATAAAACAAAA-AT
36132 AA
1 AA
36134 CGAAATGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (19 bp):
AAAAAAATAAAACAAAAAT
Found at i:41769 original size:17 final size:16
Alignment explanation
Indices: 41747--41792 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
41737 GTTGTGGTTA
41747 AAATAAAAAATATAATT
1 AAATAAAAAATATAA-T
*
41764 AAATAAATAATATAAT
1 AAATAAAAAATATAAT
41780 AAATAAACAAATA
1 AAATAAA-AAATA
41793 AAGAGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAAAAAATATAAT
Found at i:42497 original size:74 final size:72
Alignment explanation
Indices: 42419--42557 Score: 217
Period size: 74 Copynumber: 1.9 Consensus size: 72
42409 CTAAAAAAAT
*
42419 AATAATATTCTAAATCCTAATTAAAATACTAAAA-CCTATTTAAACTAAAATACAAAGATAAAGA
1 AATAATATCCTAAA-CCTAATTAAAATACTAAAATCCTATTTAAACTAAAAT--AAAGATAAAGA
42483 TAAATATAAA
63 TAAATATAAA
* *
42493 AATAATATCCTAAACTTAATTAAAATACTAAAATCCTATTTAAACTAAAATAAAGATAAATATAA
1 AATAATATCCTAAACCTAATTAAAATACTAAAATCCTATTTAAACTAAAATAAAGATAAAGATAA
42558 TGTTTAAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
72 13 0.21
73 18 0.30
74 30 0.49
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (72 bp):
AATAATATCCTAAACCTAATTAAAATACTAAAATCCTATTTAAACTAAAATAAAGATAAAGATAA
ATATAAA
Found at i:42849 original size:34 final size:34
Alignment explanation
Indices: 42799--42865 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
42789 TAGGTTCATA
* * * *
42799 AGGAATTACTAGCTTGATCGGTGCTAAACCTATG
1 AGGAATTACCAACTTGATCAGAGCTAAACCTATG
*
42833 AGGAATTACCAACTTGATCAGAGCTGAACCTAT
1 AGGAATTACCAACTTGATCAGAGCTAAACCTAT
42866 AGAGACTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (34 bp):
AGGAATTACCAACTTGATCAGAGCTAAACCTATG
Found at i:43469 original size:38 final size:35
Alignment explanation
Indices: 43425--43498 Score: 121
Period size: 38 Copynumber: 2.0 Consensus size: 35
43415 TATTGACCTT
43425 AAATTAATTAAATTGCTTAAATTGCATATGCATATTCG
1 AAATTAATTAAATTGC-TAAATTGCATAT--ATATTCG
43463 AAATTAATTAAATTGCTAAATTGCATATATATTCG
1 AAATTAATTAAATTGCTAAATTGCATATATATTCG
43498 A
1 A
43499 TTTTATAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 8 0.22
37 12 0.33
38 16 0.44
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (35 bp):
AAATTAATTAAATTGCTAAATTGCATATATATTCG
Found at i:43761 original size:20 final size:20
Alignment explanation
Indices: 43738--43777 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
43728 GTTCGATCTA
*
43738 AGTTGACTCAAACCGATTCT
1 AGTTAACTCAAACCGATTCT
* *
43758 AGTTAACTCGAATCGATTCT
1 AGTTAACTCAAACCGATTCT
43778 GGAATGTTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (20 bp):
AGTTAACTCAAACCGATTCT
Found at i:45817 original size:24 final size:24
Alignment explanation
Indices: 45786--45831 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
45776 TTTGTTTTAT
45786 TTTGAACTTATTTTAATTTTATCA
1 TTTGAACTTATTTTAATTTTATCA
45810 TTTGAACTTATTTTAATTTTAT
1 TTTGAACTTATTTTAATTTTAT
45832 TATTAGTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTGAACTTATTTTAATTTTATCA
Found at i:47057 original size:22 final size:22
Alignment explanation
Indices: 47027--47087 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
47017 TCAAGTCTTA
47027 TCATAAAAAAATGTTACA-CCCTT
1 TCAT-AAAAAATGTTA-AGCCCTT
* * *
47050 TCATAAAAAAAGTTAAGTCTTT
1 TCATAAAAAATGTTAAGCCCTT
*
47072 TCATGAAAAATGTTAA
1 TCATAAAAAATGTTAA
47088 ACCATTTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.03
22 27 0.84
23 4 0.12
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (22 bp):
TCATAAAAAATGTTAAGCCCTT
Done.