Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003160.1 Hibiscus syriacus cultivar Beakdansim tig00006652_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: 90057
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:8371 original size:40 final size:40
Alignment explanation
Indices: 8322--8401 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
8312 ATAGGAGTCA
* * * * *
8322 AATATTGCACTGTGGTACTGAGGTCGAGCCTTGCTCACCT
1 AATAATGCACCGTAGTACTGAGGTCGAGCCATGCCCACCT
* *
8362 AATAATGCACCGTAGTGCTGAGGTCGGGCCATGCCCACCT
1 AATAATGCACCGTAGTACTGAGGTCGAGCCATGCCCACCT
8402 TATACACTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (40 bp):
AATAATGCACCGTAGTACTGAGGTCGAGCCATGCCCACCT
Found at i:9447 original size:16 final size:16
Alignment explanation
Indices: 9426--9467 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
9416 TAACATTTTA
9426 GTAGTCACTCTTTACC
1 GTAGTCACTCTTTACC
9442 GTAGTCACTCTTTACC
1 GTAGTCACTCTTTACC
* *
9458 ATAGTAACTC
1 GTAGTCACTC
9468 CGTCACTGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (16 bp):
GTAGTCACTCTTTACC
Found at i:21502 original size:31 final size:31
Alignment explanation
Indices: 21452--21510 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
21442 ACAAATTGGC
**
21452 TACTAACATTATCGGTTTATCAA-AAATTGAT
1 TACTAACATTATCAATTTAT-AATAAATTGAT
21483 TACTAACATTATCAATTTATAATAAATT
1 TACTAACATTATCAATTTATAATAAATT
21511 AGTCACTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (31 bp):
TACTAACATTATCAATTTATAATAAATTGAT
Found at i:28674 original size:16 final size:15
Alignment explanation
Indices: 28650--28684 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
28640 GATTTCGACC
28650 ATATCATATAATGAAT
1 ATATCATATAAT-AAT
*
28666 ATATTATATAATAAT
1 ATATCATATAATAAT
28681 ATAT
1 ATAT
28685 ACATTTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (15 bp):
ATATCATATAATAAT
Found at i:29843 original size:21 final size:22
Alignment explanation
Indices: 29819--29904 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 22
29809 ATTTTATTCC
29819 TTTATTTATATATATATATT-T
1 TTTATTTATATATATATATTAT
* * * *
29840 TTTATGTATATTTTTATTTTAT
1 TTTATTTATATATATATATTAT
*
29862 TTTATTATATTTATATATATATAT
1 TTTATT-TATATATATATAT-TAT
** *
29886 ACATATATATATATATATA
1 -TTTATTTATATATATATA
29905 CATAATCATC
Statistics
Matches: 48, Mismatches: 13, Indels: 5
0.73 0.20 0.08
Matches are distributed among these distances:
21 16 0.33
22 6 0.12
23 9 0.19
24 14 0.29
25 3 0.06
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (22 bp):
TTTATTTATATATATATATTAT
Found at i:29880 original size:2 final size:2
Alignment explanation
Indices: 29867--29904 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
29857 TTTATTTTAT
* *
29867 TA TA TT TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29905 CATAATCATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31239 original size:10 final size:10
Alignment explanation
Indices: 31224--31257 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
31214 TTCATTTACC
31224 ATTTATTTTT
1 ATTTATTTTT
31234 ATTTATTTTT
1 ATTTATTTTT
* *
31244 ATCTATTTCT
1 ATTTATTTTT
31254 ATTT
1 ATTT
31258 TACTAACCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:40697 original size:11 final size:11
Alignment explanation
Indices: 40681--40708 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40671 CCTAAGTTGG
40681 AAAAAAAACAA
1 AAAAAAAACAA
40692 AAAAAAAACAA
1 AAAAAAAACAA
40703 AAAAAA
1 AAAAAA
40709 CAAAGAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:41318 original size:1 final size:1
Alignment explanation
Indices: 41312--41354 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
41302 GAGCATCTCC
* * * *
41312 AAAAAAAACAAAAAAAAACAAAAAACAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41355 CCCAGAATGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41326 original size:7 final size:7
Alignment explanation
Indices: 41311--41354 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
41301 GGAGCATCTC
41311 CAAAAAA
1 CAAAAAA
*
41318 -AACAAA
1 CAAAAAA
41324 -AAAAAA
1 CAAAAAA
41330 CAAAAAA
1 CAAAAAA
41337 CAAAAAA
1 CAAAAAA
41344 CAAAAAA
1 CAAAAAA
41351 -AAAA
1 CAAAA
41355 CCCAGAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 14 0.41
7 20 0.59
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:41741 original size:105 final size:105
Alignment explanation
Indices: 41559--42020 Score: 744
Period size: 105 Copynumber: 4.4 Consensus size: 105
41549 CAGGTTTTAC
41559 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
41624 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
41664 CCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
41729 GACGAAGGGACCGCTGGTTGTCAACAAACGTTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
41769 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
41834 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* * ****
41874 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTATAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* ** ** * *
41939 GACGAAGGGGCCGCTGACTGTCAACCGACGATTTCCCAGTT
66 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATT
* * *
41980 CCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
42021 GGAACAATAT
Statistics
Matches: 335, Mismatches: 21, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
105 289 0.86
106 46 0.14
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:42506 original size:16 final size:15
Alignment explanation
Indices: 42482--42516 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
42472 GATTTCGACC
42482 ATATCATATAATGAAT
1 ATATCATATAAT-AAT
*
42498 ATATTATATAATAAT
1 ATATCATATAATAAT
42513 ATAT
1 ATAT
42517 ACATTTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (15 bp):
ATATCATATAATAAT
Found at i:43659 original size:2 final size:2
Alignment explanation
Indices: 43652--43743 Score: 75
Period size: 2 Copynumber: 48.0 Consensus size: 2
43642 TTCCTTTATT
* * * * * *
43652 TA TA TA TA TA TA TA T- TT TA TG TA TA TT TT TA T- TT TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
43691 TA T- TA TA TT TA TA TA TA TA CA TA TA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43732 TA TA TA TA TA TA
1 TA TA TA TA TA TA
43744 CATAATCATC
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
1 4 0.05
2 69 0.95
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (2 bp):
TA
Found at i:43685 original size:46 final size:48
Alignment explanation
Indices: 43605--43714 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 48
43595 GTCCCTACTA
*
43605 TTAT-TATATACTATATTTTCATTATTATTATATTTTA-TTCCTT-TAT
1 TTATATATATA-TATATTTTCATTATTATTATATTTTATTTCATTATAT
* *
43651 TTATATATATATATATTTT-ATGTA-TATTTTTATTTTATTTTATTATAT
1 TTATATATATATATATTTTCAT-TATTA-TTATATTTTATTTCATTATAT
*
43699 TTATATATATACATAT
1 TTATATATATATATAT
43715 ATACATATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
45 4 0.07
46 23 0.42
47 10 0.18
48 18 0.33
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.63
Consensus pattern (48 bp):
TTATATATATATATATTTTCATTATTATTATATTTTATTTCATTATAT
Found at i:44100 original size:27 final size:25
Alignment explanation
Indices: 44023--44110 Score: 68
Period size: 27 Copynumber: 3.3 Consensus size: 25
44013 TTTTTAGTTT
*
44023 TTTTTATTTATTACTATTATATATATC
1 TTTTTA-TTATTACCA-TATATATATC
* * * *
44050 TTTTTATTTTTCCCAATGTTTATATC
1 TTTTTATTATTACC-ATATATATATC
*
44076 TTTATTATTATTACCATCATATATATTA
1 TTT-TTATTATTACCAT-ATATATA-TC
44104 TTTTTAT
1 TTTTTAT
44111 ATTCTATATT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
26 18 0.38
27 25 0.53
28 4 0.09
ACGTcount: A:0.27, C:0.10, G:0.01, T:0.61
Consensus pattern (25 bp):
TTTTTATTATTACCATATATATATC
Found at i:45688 original size:3 final size:3
Alignment explanation
Indices: 45676--45712 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
45666 ACCCCAACGT
45676 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
45713 GAGTATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:46151 original size:21 final size:20
Alignment explanation
Indices: 46125--46164 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
46115 AAAAAAAATT
46125 GAGTTATTCAAACTACTATTC
1 GAGTTATTCAAACT-CTATTC
46146 GAGTTATTCAAACTCTATT
1 GAGTTATTCAAACTCTATT
46165 TTATAACTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (20 bp):
GAGTTATTCAAACTCTATTC
Found at i:49322 original size:2 final size:2
Alignment explanation
Indices: 49315--49340 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49305 GGATTGAAGT
49315 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
49341 AAGTGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55251 original size:14 final size:14
Alignment explanation
Indices: 55232--55258 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55222 ATATTAAATA
55232 ATAATTATAATTAT
1 ATAATTATAATTAT
55246 ATAATTATAATTA
1 ATAATTATAATTA
55259 AAAAATAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAATTATAATTAT
Found at i:59646 original size:20 final size:20
Alignment explanation
Indices: 59588--59646 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
59578 ACTTACACCA
* *
59588 AAAAAATCTGGTTTCCAACC
1 AAAAAACCTGGATTCCAACC
** *
59608 TCAAAACCT-GAGTTGCAACC
1 AAAAAACCTGGA-TTCCAACC
59628 AAAAAACCTGGATTCCAAC
1 AAAAAACCTGGATTCCAAC
59647 ATAAAATATG
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (20 bp):
AAAAAACCTGGATTCCAACC
Found at i:64595 original size:30 final size:30
Alignment explanation
Indices: 64554--64697 Score: 135
Period size: 30 Copynumber: 4.7 Consensus size: 30
64544 TTACCATATA
*
64554 CACTAAGTGTCCTTACACACCACAGTGTTG
1 CACTAAGTGTCCTTACACACCACAGTATTG
* * * *
64584 CACTGAGTGTCCTTACACGCTACAATATTG
1 CACTAAGTGTCCTTACACACCACAGTATTG
* * * * *
64614 TACTAATTGTCCTTAAACACTATAGTATTG
1 CACTAAGTGTCCTTACACACCACAGTATTG
* * *
64644 TACTAAGTTTCCTTACACACCACAGTACCATATA
1 CACTAAGTGTCCTTACACACCACAGT---AT-TG
64678 CACTAAGTGTCCTTACACAC
1 CACTAAGTGTCCTTACACAC
64698 TATAGTGCTA
Statistics
Matches: 90, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
30 69 0.77
33 2 0.02
34 19 0.21
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (30 bp):
CACTAAGTGTCCTTACACACCACAGTATTG
Found at i:71157 original size:23 final size:23
Alignment explanation
Indices: 71102--71159 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
71092 TAGTCAGCGA
* *
71102 ATGATGTGGCAGCTGACATGTTG
1 ATGATGTGGTAGCTGACATGGTG
* *
71125 ATGATGTGGTAGCTTACGTGGTG
1 ATGATGTGGTAGCTGACATGGTG
71148 ATGATGTGGTAG
1 ATGATGTGGTAG
71160 GTGATGTGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.09, G:0.38, T:0.33
Consensus pattern (23 bp):
ATGATGTGGTAGCTGACATGGTG
Found at i:72927 original size:2 final size:2
Alignment explanation
Indices: 72920--72954 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
72910 TTTCAAATAC
72920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
72955 AAATAATAAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:77825 original size:2 final size:2
Alignment explanation
Indices: 77818--77844 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
77808 TACGATTTAA
77818 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
77845 CAAATGAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78030 original size:22 final size:22
Alignment explanation
Indices: 77994--78064 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
77984 ATGCACATAG
77994 TCGGATTT-AATATGATTCGGA
1 TCGGATTTAAATATGATTCGGA
78015 TCGGATTTAAATATGATTCGGA
1 TCGGATTTAAATATGATTCGGA
*
78037 TCGGATTTAAATCTGA-TCTGGA
1 TCGGATTTAAATATGATTC-GGA
78059 TCGGAT
1 TCGGAT
78065 AAAAATCGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
21 10 0.21
22 37 0.79
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (22 bp):
TCGGATTTAAATATGATTCGGA
Found at i:78264 original size:19 final size:20
Alignment explanation
Indices: 78233--78276 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
78223 GTCATCCAAT
*
78233 TTTTTAAACCCCAGATCGGA
1 TTTTTAAACCCCAGACCGGA
*
78253 TTTTTAAA-CCCATACCGGA
1 TTTTTAAACCCCAGACCGGA
78272 TTTTT
1 TTTTT
78277 TTCGGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Found at i:78277 original size:20 final size:21
Alignment explanation
Indices: 78231--78277 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
78221 CGGTCATCCA
*
78231 ATTTTTTAAACCCCAGATCGG
1 ATTTTTTAAACCCCAGACCGG
*
78252 A-TTTTTAAA-CCCATACCGG
1 ATTTTTTAAACCCCAGACCGG
78271 ATTTTTT
1 ATTTTTT
78278 TCGGATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 9 0.39
20 13 0.57
21 1 0.04
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (21 bp):
ATTTTTTAAACCCCAGACCGG
Found at i:81430 original size:33 final size:33
Alignment explanation
Indices: 81375--81458 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
81365 TCTATTCGGG
* * *
81375 TCGGGTC-AGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTCGGGTTTCTTTAAATGTGATAT
81407 TCGGGTCGGGTCGGGTTTCTTTAAATGTGATAT
1 TCGGGTCGGGTCGGGTTTCTTTAAATGTGATAT
*
81440 TCGGGTCGGATTCGGGTTT
1 TCGGGTCGG-GTCGGGTTT
81459 AGAGAGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 7 0.15
33 31 0.67
34 8 0.17
ACGTcount: A:0.13, C:0.12, G:0.35, T:0.40
Consensus pattern (33 bp):
TCGGGTCGGGTCGGGTTTCTTTAAATGTGATAT
Found at i:82037 original size:16 final size:18
Alignment explanation
Indices: 82016--82062 Score: 71
Period size: 16 Copynumber: 2.7 Consensus size: 18
82006 TCAAATTCTT
82016 CAGATTCCAATTCC-T-A
1 CAGATTCCAATTCCTTCA
82032 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
*
82050 CAGATTCTAATTC
1 CAGATTCCAATTC
82063 TCTCAGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 14 0.50
17 1 0.04
18 13 0.46
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:82890 original size:24 final size:24
Alignment explanation
Indices: 82860--82912 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
82850 ATTTACCATA
82860 AAATGTTAGATATGATTGTAAAAT
1 AAATGTTAGATATGATTGTAAAAT
*
82884 AAATGTTAGATATGATTGTGAAAT
1 AAATGTTAGATATGATTGTAAAAT
82908 AAATG
1 AAATG
82913 CATAATCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (24 bp):
AAATGTTAGATATGATTGTAAAAT
Found at i:87902 original size:32 final size:32
Alignment explanation
Indices: 87845--87915 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 32
87835 CCAACTTTTC
87845 TTTCC-TTTACATTTTCATTTCCCTGATAGATT
1 TTTCCTTTTACATTTTCATTTCCCTGATAGA-T
87877 TTTCCTTTTACATTTTCATTT-CCTGATAGAT
1 TTTCCTTTTACATTTTCATTTCCCTGATAGAT
87908 TTTCCTTT
1 TTTCCTTT
87916 CTTATTACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
31 9 0.24
32 14 0.37
33 15 0.39
ACGTcount: A:0.17, C:0.21, G:0.06, T:0.56
Consensus pattern (32 bp):
TTTCCTTTTACATTTTCATTTCCCTGATAGAT
Found at i:87909 original size:18 final size:18
Alignment explanation
Indices: 87855--87916 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
87845 TTTCCTTTAC
87855 ATTTTCATTTCCCTGATAG
1 ATTTTCATTT-CCTGATAG
** *
87874 A--TT--TTTCCTTTTAC
1 ATTTTCATTTCCTGATAG
87888 ATTTTCATTTCCTGATAG
1 ATTTTCATTTCCTGATAG
*
87906 ATTTTCCTTTC
1 ATTTTCATTTC
87917 TTATTACAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 9
0.67 0.15 0.19
Matches are distributed among these distances:
14 6 0.19
15 3 0.09
16 2 0.06
17 2 0.06
18 18 0.56
19 1 0.03
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.55
Consensus pattern (18 bp):
ATTTTCATTTCCTGATAG
Done.