Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000951.1 Hibiscus syriacus cultivar Beakdansim tig00001903_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: 91409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4595 original size:28 final size:27
Alignment explanation
Indices: 4529--4600 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
4519 ATTTTGACTC
* * *
4529 AAAATACTTAGGTATTTATTTGACAAA
1 AAAATACTTAAGTACTTATTTGAAAAA
*
4556 AAGATACTTTAAGTACTTATTTGATAAAA
1 AAAATAC-TTAAGTACTTATTTGA-AAAA
*
4585 AAAATGCTTAAGTACT
1 AAAATACTTAAGTACT
4601 GAAATAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 6 0.16
28 23 0.62
29 8 0.22
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (27 bp):
AAAATACTTAAGTACTTATTTGAAAAA
Found at i:13593 original size:17 final size:17
Alignment explanation
Indices: 13571--13604 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13561 CATAATATAA
13571 AATATTATAAATAATAT
1 AATATTATAAATAATAT
* *
13588 AATATTTTAAATTATAT
1 AATATTATAAATAATAT
13605 TTAATTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATTATAAATAATAT
Found at i:13810 original size:29 final size:29
Alignment explanation
Indices: 13759--13873 Score: 160
Period size: 29 Copynumber: 4.0 Consensus size: 29
13749 AGTGTTGGTC
* *
13759 GTAGGTCGTCATGC-CTTCCGGGCGACTTT
1 GTAGGTCGCCATGCAC-TCCGGGCGACCTT
* * *
13788 ATAAGTTGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
*
13817 GTAGGTCGCCATGCACTCGGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
13846 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
13874 ACCCTTGCTC
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
29 74 0.99
30 1 0.01
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.23
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:13958 original size:29 final size:29
Alignment explanation
Indices: 13911--13995 Score: 127
Period size: 29 Copynumber: 2.9 Consensus size: 29
13901 GTCCAACACA
13911 TAGGTCGTCATGCTA-TCCGGGCGACCTTG
1 TAGGTCGTCATGC-ACTCCGGGCGACCTTG
* *
13940 TAGGTCGTCATACCCTCCGGGCGACCTTG
1 TAGGTCGTCATGCACTCCGGGCGACCTTG
*
13969 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGTCATGCACTCCGGGCGACCT
13996 ACCCTCGCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.14, C:0.33, G:0.29, T:0.24
Consensus pattern (29 bp):
TAGGTCGTCATGCACTCCGGGCGACCTTG
Found at i:14037 original size:33 final size:33
Alignment explanation
Indices: 14000--14064 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
13990 CGACCTACCC
* *
14000 TCGCTCGACTGCCATCGGATTCCCTCGCATAGT
1 TCGCTCGACTACCATCGGATGCCCTCGCATAGT
** *
14033 TCGCTCGGTTACCCTCGGATGCCCTCGCATAG
1 TCGCTCGACTACCATCGGATGCCCTCGCATAG
14065 CTCGTTCGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.14, C:0.37, G:0.23, T:0.26
Consensus pattern (33 bp):
TCGCTCGACTACCATCGGATGCCCTCGCATAGT
Found at i:14082 original size:33 final size:33
Alignment explanation
Indices: 14014--14092 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
14004 TCGACTGCCA
* * *
14014 TCGGATTCCCTCGCATAGTTCGCTCGGTTACCC
1 TCGGATGCCCTCGCATAGCTCGCTCGGATACCC
* **
14047 TCGGATGCCCTCGCATAGCTCGTTCGGATGGCC
1 TCGGATGCCCTCGCATAGCTCGCTCGGATACCC
*
14080 TCGGATGCTCTCG
1 TCGGATGCCCTCG
14093 GATGACCTCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.11, C:0.34, G:0.27, T:0.28
Consensus pattern (33 bp):
TCGGATGCCCTCGCATAGCTCGCTCGGATACCC
Found at i:14183 original size:29 final size:29
Alignment explanation
Indices: 14146--14203 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
14136 GAAATCTCTT
*
14146 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
*
14175 GTAGGTCGCCCGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
14204 CGGCCAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:25342 original size:31 final size:31
Alignment explanation
Indices: 25304--25365 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
25294 TCTAGGAAGT
25304 AAGATTCTACCTTGCCATCGCCAAACTGAGC
1 AAGATTCTACCTTGCCATCGCCAAACTGAGC
25335 AAGATTCTACCTTGCCATCGCCAAACTGAGC
1 AAGATTCTACCTTGCCATCGCCAAACTGAGC
25366 TCGATAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (31 bp):
AAGATTCTACCTTGCCATCGCCAAACTGAGC
Found at i:28968 original size:25 final size:24
Alignment explanation
Indices: 28899--28995 Score: 79
Period size: 25 Copynumber: 3.9 Consensus size: 24
28889 AGTGTTATAT
* *
28899 TATATTTTAAAAATATTAATT-AA
1 TATATTTTAAATATATAAATTAAA
* **
28922 TATATTTTAAATATCTTTATTAAAA
1 TATATTTTAAATATATAAATT-AAA
* *
28947 TATAATTTAAATATATAAATTATAT
1 TATATTTTAAATATATAAATTA-AA
28972 TATTCATTATTAAATATATAAATT
1 TA-T-ATT-TTAAATATATAAATT
28996 TTTTATTATA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
23 18 0.31
24 1 0.02
25 22 0.37
26 1 0.02
27 2 0.03
28 15 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATTTTAAATATATAAATTAAA
Found at i:29003 original size:30 final size:29
Alignment explanation
Indices: 28953--29101 Score: 106
Period size: 29 Copynumber: 5.3 Consensus size: 29
28943 AAAATATAAT
28953 TTAAATATATAAA-TTATATTAT-TCATTA
1 TTAAATATATAAATTTATATTATAT-ATTA
*
28981 TTAAATATATAAATTTTTTATTATATATTA
1 TTAAATATATAAA-TTTATATTATATATTA
*
29011 TTAAA-ATAAAAATATTATATCT-TATATTA
1 TTAAATATATAAAT-TTATAT-TATATATTA
* *
29040 TTATA-ATAT-AA-TT-GATTAT-T-TTA
1 TTAAATATATAAATTTATATTATATATTA
29063 -TATAATATTATAAATATTATATTATATTATTA
1 TTA-AATA-TATAAAT-TTATATTATA-TATTA
29095 -TAAATAT
1 TTAAATAT
29102 TAATAAATAA
Statistics
Matches: 97, Mismatches: 8, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
22 2 0.02
23 4 0.04
24 3 0.03
25 6 0.06
26 4 0.04
28 18 0.19
29 30 0.31
30 19 0.20
31 6 0.06
32 5 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (29 bp):
TTAAATATATAAATTTATATTATATATTA
Found at i:29037 original size:29 final size:29
Alignment explanation
Indices: 28965--29119 Score: 100
Period size: 29 Copynumber: 5.1 Consensus size: 29
28955 AAATATATAA
*
28965 ATTATATTAT-TCATTATTAAATATATAAAT
1 ATTATATTATAT-ATTATTAAA-ATAAAAAT
* *
28995 TTTTTATTATATATTATTAAAATAAAAAT
1 ATTATATTATATATTATTAAAATAAAAAT
* * *
29024 ATTATATCT-TATATTATTATAATATAATT
1 ATTATAT-TATATATTATTAAAATAAAAAT
* * **
29053 GATTATTTTATATAATATTATAAAT-ATTAT
1 -ATTATATTATATATTATTA-AAATAAAAAT
*
29083 ATTATATTATTATAAATATTAATAAATAAATAAT
1 ATTATATTA-TAT-ATTATT-A-AAATAAA-AAT
29117 ATT
1 ATT
29120 TTGATGAAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
29 38 0.39
30 37 0.38
31 10 0.10
32 6 0.06
33 1 0.01
34 5 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
ATTATATTATATATTATTAAAATAAAAAT
Found at i:29072 original size:15 final size:16
Alignment explanation
Indices: 29005--29087 Score: 52
Period size: 14 Copynumber: 5.4 Consensus size: 16
28995 TTTTTATTAT
29005 ATATTATTA-AA-ATA
1 ATATTATTATAATATA
* * * *
29019 AAAATATTAT-ATCTT
1 ATATTATTATAATATA
29034 ATATTATTATAATATA
1 ATATTATTATAATATA
*
29050 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
29067 ATATTA-TA-AATATT
1 ATATTATTATAATATA
29081 ATATTAT
1 ATATTAT
29088 ATTATTATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 13
0.68 0.15 0.17
Matches are distributed among these distances:
14 19 0.37
15 13 0.25
16 5 0.10
17 8 0.16
18 6 0.12
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:29083 original size:17 final size:16
Alignment explanation
Indices: 29061--29119 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
29051 TTGATTATTT
29061 TATATAATATTATAAA
1 TATATAATATTATAAA
*
29077 TAT-T-ATATTAT-AT
1 TATATAATATTATAAA
29090 TATTATAAATATTAATAAA
1 TA-TAT-AATATT-ATAAA
*
29109 TAAATAATATT
1 TATATAATATT
29120 TTGATGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
13 3 0.09
14 8 0.24
15 2 0.06
16 3 0.09
17 11 0.32
18 4 0.12
19 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATAATATTATAAA
Found at i:29084 original size:19 final size:20
Alignment explanation
Indices: 29060--29107 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
29050 ATTGATTATT
29060 TTATATAA-TATTATAAATA
1 TTATATAATTATTATAAATA
29079 TTATATTATATTATTATAAATA
1 TTATA-TA-ATTATTATAAATA
29101 TTA-ATAA
1 TTATATAA
29108 ATAAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
21 2 0.08
22 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATAATTATTATAAATA
Found at i:29344 original size:42 final size:42
Alignment explanation
Indices: 29293--29412 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 42
29283 ATGAATTACA
* *
29293 TTCCGGAAAACCAATTACGTTAAACAAACA-TAAGAAAACATT
1 TTCCGGAAAACAAATTACGTGAAACAAACACT-AGAAAACATT
*
29335 TTCCGGAAAACAAATTACGTGAAACAAACACTGGAAAACATT
1 TTCCGGAAAACAAATTACGTGAAACAAACACTAGAAAACATT
* ** *
29377 TTCCGAAAAATGAATTACGTGAAACAAACACGAGAA
1 TTCCGGAAAACAAATTACGTGAAACAAACACTAGAA
29413 TTCGGGAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 68 0.99
43 1 0.01
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.19
Consensus pattern (42 bp):
TTCCGGAAAACAAATTACGTGAAACAAACACTAGAAAACATT
Found at i:29824 original size:28 final size:28
Alignment explanation
Indices: 29792--29897 Score: 99
Period size: 28 Copynumber: 3.8 Consensus size: 28
29782 GGAAAAAATT
* * *
29792 AAATATTTTATGTACTTATTTTGACCAA
1 AAATACTTTAGGTACTTATTTTGACAAA
*
29820 AAATACTTTAGGTATTTATTTTGACAAAAA
1 AAATACTTTAGGTACTTATTTTGAC--AAA
* ** *
29850 AAATACTATAGGTACTTA-GAT-AAAAA
1 AAATACTTTAGGTACTTATTTTGACAAA
29876 AATATACTTTAGGTACTTATTT
1 AA-ATACTTTAGGTACTTATTT
29898 ATAATATAGG
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
26 5 0.08
27 15 0.24
28 23 0.37
29 1 0.02
30 18 0.29
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (28 bp):
AAATACTTTAGGTACTTATTTTGACAAA
Found at i:35377 original size:2 final size:2
Alignment explanation
Indices: 35370--35415 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
35360 CGAATAGATG
35370 AT AT AT AT 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 AT AT AT AT
35412 AT AT
1 AT AT
35416 TTTCGGGTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42689 original size:7 final size:7
Alignment explanation
Indices: 42677--42713 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
42667 GTCAAAGGAA
42677 GTCAACG
1 GTCAACG
42684 GTCAACG
1 GTCAACG
*
42691 GTC-ACA
1 GTCAACG
42697 GTCAACG
1 GTCAACG
42704 GTCAACG
1 GTCAACG
42711 GTC
1 GTC
42714 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:42701 original size:20 final size:20
Alignment explanation
Indices: 42676--42713 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
42666 GGTCAAAGGA
42676 AGTCAACGGTCAACGGTCAC
1 AGTCAACGGTCAACGGTCAC
42696 AGTCAACGGTCAACGGTC
1 AGTCAACGGTCAACGGTC
42714 GGGTCGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (20 bp):
AGTCAACGGTCAACGGTCAC
Found at i:42731 original size:22 final size:21
Alignment explanation
Indices: 42703--42749 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
42693 CACAGTCAAC
* *
42703 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGATCGGGTC-AGTCG
42725 GGTCAACGATCGGGTCAGTCG
1 GGTCAACGATCGGGTCAGTCG
42746 GGTC
1 GGTC
42750 GGGTCAGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (21 bp):
GGTCAACGATCGGGTCAGTCG
Found at i:42763 original size:9 final size:9
Alignment explanation
Indices: 42751--42800 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
42741 AGTCGGGTCG
*
42751 GGTCAGACC
1 GGTCAAACC
42760 GGTCAAACC
1 GGTCAAACC
*
42769 GGTTCAGACC
1 GG-TCAAACC
*
42779 GGTTCTAACC
1 GG-TCAAACC
42789 GGTCAAACC
1 GGTCAAACC
42798 GGT
1 GGT
42801 TTTCAGCCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
9 19 0.54
10 16 0.46
ACGTcount: A:0.24, C:0.30, G:0.28, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:42781 original size:10 final size:10
Alignment explanation
Indices: 42757--42801 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
42747 GTCGGGTCAG
42757 ACCGG-TCAA
1 ACCGGTTCAA
*
42766 ACCGGTTCAG
1 ACCGGTTCAA
*
42776 ACCGGTTCTA
1 ACCGGTTCAA
42786 ACCGG-TCAA
1 ACCGGTTCAA
42795 ACCGGTT
1 ACCGGTT
42802 TTCAGCCCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 13 0.43
10 17 0.57
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:42801 original size:19 final size:19
Alignment explanation
Indices: 42751--42801 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
42741 AGTCGGGTCG
42751 GGTCAGACCGG-TCAAACC
1 GGTCAGACCGGTTCAAACC
*
42769 GGTTCAGACCGGTTCTAACC
1 GG-TCAGACCGGTTCAAACC
*
42789 GGTCAAACCGGTT
1 GGTCAGACCGGTT
42802 TTCAGCCCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 19 0.66
20 8 0.28
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (19 bp):
GGTCAGACCGGTTCAAACC
Found at i:49905 original size:7 final size:7
Alignment explanation
Indices: 49893--49929 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
49883 GTCAAAGGAA
49893 GTCAACG
1 GTCAACG
49900 GTCAACG
1 GTCAACG
49907 GTC-ACG
1 GTCAACG
*
49913 GTCAACA
1 GTCAACG
49920 GTCAACG
1 GTCAACG
49927 GTC
1 GTC
49930 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:49915 original size:13 final size:14
Alignment explanation
Indices: 49892--49929 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
49882 GGTCAAAGGA
49892 AGTCAACGGTCAAC
1 AGTCAACGGTCAAC
*
49906 GGTC-ACGGTCAAC
1 AGTCAACGGTCAAC
49919 AGTCAACGGTC
1 AGTCAACGGTC
49930 GGGTCGGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (14 bp):
AGTCAACGGTCAAC
Found at i:51549 original size:15 final size:15
Alignment explanation
Indices: 51526--51555 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
51516 GTAAAACAAA
51526 AACTAATAAGTGCAG
1 AACTAATAAGTGCAG
*
51541 AACTTATAAGTGCAG
1 AACTAATAAGTGCAG
51556 GTGCAGCAGA
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:0.43, C:0.13, G:0.20, T:0.23
Consensus pattern (15 bp):
AACTAATAAGTGCAG
Found at i:51838 original size:42 final size:42
Alignment explanation
Indices: 51770--51849 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
51760 GGGTTTCAGT
* *
51770 TGGTGAATTGACTGATGTAGTATTGGATGGAGGTGGTGATGC
1 TGGTGAATTGACTGATATAGTATTGGATGGAGATGGTGATGC
* * *
51812 TGGTGCATTGATTGATATAGTCTTGGATGGAGATGGTG
1 TGGTGAATTGACTGATATAGTATTGGATGGAGATGGTG
51850 CATTGTTGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.21, C:0.05, G:0.39, T:0.35
Consensus pattern (42 bp):
TGGTGAATTGACTGATATAGTATTGGATGGAGATGGTGATGC
Found at i:61151 original size:24 final size:25
Alignment explanation
Indices: 61124--61172 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
61114 CAAATTTATC
*
61124 TTCC-AATTTGAGTAAAAAACTCTA
1 TTCCAAATTTCAGTAAAAAACTCTA
*
61148 TTCCAGAATTTCATTAAAAAACTCT
1 TTCCA-AATTTCAGTAAAAAACTCT
61173 TAATCTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
26 17 0.81
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (25 bp):
TTCCAAATTTCAGTAAAAAACTCTA
Found at i:67991 original size:18 final size:18
Alignment explanation
Indices: 67966--68021 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
67956 CACCGCATTT
67966 TCCAAAAGCAATATTTAC
1 TCCAAAAGCAATATTTAC
*
67984 TTCAAAAGCAATATTT--
1 TCCAAAAGCAATATTTAC
68000 TCCAAAAGCAATATTTAC
1 TCCAAAAGCAATATTTAC
68018 TCCA
1 TCCA
68022 TTGAAGCTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 15 0.44
18 19 0.56
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.30
Consensus pattern (18 bp):
TCCAAAAGCAATATTTAC
Found at i:68007 original size:16 final size:16
Alignment explanation
Indices: 67962--68015 Score: 81
Period size: 16 Copynumber: 3.2 Consensus size: 16
67952 TCCCCACCGC
67962 ATTTTCCAAAAGCAAT
1 ATTTTCCAAAAGCAAT
*
67978 ATTTACTTCAAAAGCAAT
1 ATTT--TCCAAAAGCAAT
67996 ATTTTCCAAAAGCAAT
1 ATTTTCCAAAAGCAAT
68012 ATTT
1 ATTT
68016 ACTCCATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 19 0.56
18 15 0.44
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTTTCCAAAAGCAAT
Found at i:74966 original size:18 final size:18
Alignment explanation
Indices: 74943--74992 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
74933 GAGATAACTT
*
74943 TTATTTTTTTATTTTGAA
1 TTATTTATTTATTTTGAA
74961 TTATTTATTTATTTTGAA
1 TTATTTATTTATTTTGAA
*
74979 TCATTTATTTATTT
1 TTATTTATTTATTT
74993 ATTTTGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (18 bp):
TTATTTATTTATTTTGAA
Found at i:74970 original size:22 final size:21
Alignment explanation
Indices: 74942--75001 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 21
74932 GGAGATAACT
*
74942 TTTATTTTTTTATTTTGAATTA
1 TTTA-TTTTTTATTTTGAATCA
74964 TTTA---TTTATTTTGAATCA
1 TTTATTTTTTATTTTGAATCA
74982 TTTATTTATTTATTTTGAAT
1 TTTATTT-TTTATTTTGAAT
75002 AAATTAGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 17 0.52
22 16 0.48
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTATTTTTTATTTTGAATCA
Found at i:75036 original size:22 final size:22
Alignment explanation
Indices: 74942--75037 Score: 101
Period size: 22 Copynumber: 4.5 Consensus size: 22
74932 GGAGATAACT
*
74942 TTTATTTTTTTATTTTG---AA
1 TTTATTTATTTATTTTGAATAA
*
74961 -TTATTTATTTATTTTGAATCA
1 TTTATTTATTTATTTTGAATAA
74982 TTTATTTATTTATTTTGAATAA
1 TTTATTTATTTATTTTGAATAA
* * * * *
75004 ATTAGTGATTTATTTCGATTAA
1 TTTATTTATTTATTTTGAATAA
75026 TTTATTTATTTA
1 TTTATTTATTTA
75038 ATTAAAGGGG
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
18 15 0.24
21 1 0.02
22 46 0.74
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (22 bp):
TTTATTTATTTATTTTGAATAA
Found at i:75489 original size:14 final size:13
Alignment explanation
Indices: 75472--75519 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
75462 ATTTTTATTT
75472 ATTTATTTCGAATA
1 ATTTATTTC-AATA
*
75486 ATTTATTT-TATA
1 ATTTATTTCAATA
75498 ATTTATTTCAAATA
1 ATTTATTTC-AATA
75512 ATTTATTT
1 ATTTATTT
75520 ATTTATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.37
14 19 0.63
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (13 bp):
ATTTATTTCAATA
Found at i:75531 original size:26 final size:26
Alignment explanation
Indices: 75465--75606 Score: 103
Period size: 26 Copynumber: 5.4 Consensus size: 26
75455 GGAGGTAATT
* *
75465 TTTATTTATTTATTTCGAATAATTTA
1 TTTATTTATTAATTTCAAATAATTTA
* *
75491 TTT-TATAATTTATTTCAAATAATTTA
1 TTTAT-TTATTAATTTCAAATAATTTA
** *
75517 TTTATTTATTAATTTTGAATAA--TG
1 TTTATTTATTAATTTCAAATAATTTA
*
75541 TTTATTTATTAATTTTGAATGAATAATTTA
1 TTTATTTATTAA-TTT-CA--AATAATTTA
* *
75571 TTTGTTTTATTAATTTCTAATAATTT-
1 TTT-ATTTATTAATTTCAAATAATTTA
*
75597 TTAATTTATT
1 TTTATTTATT
75607 CGTTTTATTT
Statistics
Matches: 92, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
24 13 0.14
25 10 0.11
26 40 0.43
27 9 0.10
28 5 0.05
30 7 0.08
31 8 0.09
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTATTTATTAATTTCAAATAATTTA
Found at i:80742 original size:23 final size:22
Alignment explanation
Indices: 80712--80755 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
80702 TTTTGTGCTG
80712 AAAACAAGATAAAAAATAAGATT
1 AAAACAAGATAAAAAA-AAGATT
*
80735 AAAACAAGATAAAGAAAAGAT
1 AAAACAAGATAAAAAAAAGAT
80756 AAAGGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (22 bp):
AAAACAAGATAAAAAAAAGATT
Found at i:83863 original size:2 final size:2
Alignment explanation
Indices: 83858--83896 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
83848 ATACTTGAAT
83858 TA TA 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 TA TA T
83897 TGAAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:84224 original size:3 final size:3
Alignment explanation
Indices: 84218--84244 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
84208 GTTCCAAATC
84218 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
84245 ATTTTCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:84333 original size:2 final size:2
Alignment explanation
Indices: 84328--84358 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
84318 TCTCTCTCTC
84328 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 T
84359 GCTAGTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.