Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001732.1 Hibiscus syriacus cultivar Beakdansim tig00003497_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: 81752
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:7955 original size:65 final size:64
Alignment explanation
Indices: 7800--7955 Score: 217
Period size: 64 Copynumber: 2.4 Consensus size: 64
7790 ACACCCCATT
* **
7800 TCGAATGCATTTAGTGTACCAATGCACAGACCATGCATCGATGCACTCAGGGTTTATTGAAACA
1 TCGAATGCATTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCAGCCTTTATTGAAACA
7864 TCGAATGCATTTTA-TGTACCGATGCACAGACCATGCATCGATGCACTCCAGCCTTCT-TTGAAA
1 TCGAATGCA-TTTAGTGTACCGATGCACAGACCATGCATCGATGCACT-CAGCCTT-TATTGAAA
7927 CA
63 CA
* * *
7929 TCGAATGTAATTAGTGTACTGATGCAC
1 TCGAATGCATTTAGTGTACCGATGCAC
7956 TCCTAGTGTA
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
64 44 0.54
65 37 0.45
66 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (64 bp):
TCGAATGCATTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCAGCCTTTATTGAAACA
Found at i:13802 original size:23 final size:23
Alignment explanation
Indices: 13737--13804 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
13727 GACAGTGTAC
*
13737 CGATGCATGCCTTGAATGTGCAT
1 CGATGCATTCCTTGAATGTGCAT
* *
13760 CGATACA-T-CATGAA-GATGCA-
1 CGATGCATTCCTTGAATG-TGCAT
13780 CAGATGCATTCCTTGAATGTGCAT
1 C-GATGCATTCCTTGAATGTGCAT
13804 C
1 C
13805 AATAAACTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 11
0.68 0.10 0.22
Matches are distributed among these distances:
20 2 0.06
21 14 0.41
22 1 0.03
23 15 0.44
24 2 0.06
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
CGATGCATTCCTTGAATGTGCAT
Found at i:17646 original size:7 final size:7
Alignment explanation
Indices: 17634--17664 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
17624 CCAAGGTGAC
17634 CGAGAAA
1 CGAGAAA
17641 CGAGAAA
1 CGAGAAA
17648 CGAGAAA
1 CGAGAAA
*
17655 CGAGACA
1 CGAGAAA
17662 CGA
1 CGA
17665 AGTACGGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.52, C:0.19, G:0.29, T:0.00
Consensus pattern (7 bp):
CGAGAAA
Found at i:19701 original size:26 final size:24
Alignment explanation
Indices: 19647--19701 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
19637 GTGACAAGTG
* *
19647 TTATTTTTATAATTTTTGAAATTT
1 TTATTTTTAAAATTTTTGAAATTA
*
19671 TTATTTTTAAAATTATTTCTAAATTA
1 TTATTTTTAAAATT-TTT-GAAATTA
19697 TTATT
1 TTATT
19702 ATTATTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 13 0.50
25 3 0.12
26 10 0.38
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TTATTTTTAAAATTTTTGAAATTA
Found at i:19915 original size:28 final size:27
Alignment explanation
Indices: 19875--19959 Score: 118
Period size: 28 Copynumber: 3.1 Consensus size: 27
19865 ATGAAATCAC
*
19875 AAATTTATCGTTCGTATAACGACCTAAA
1 AAATATATCGTTCGT-TAACGACCTAAA
*
19903 AAATATATCGTTCG-TAACCACCTAAA
1 AAATATATCGTTCGTTAACGACCTAAA
*
19929 AAATATATCGTTCGTTTAACGACCCAAA
1 AAATATATCGTTCG-TTAACGACCTAAA
19957 AAA
1 AAA
19960 CATTTCTTCC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 25 0.49
28 26 0.51
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.28
Consensus pattern (27 bp):
AAATATATCGTTCGTTAACGACCTAAA
Found at i:19927 original size:26 final size:26
Alignment explanation
Indices: 19875--19943 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
19865 ATGAAATCAC
* *
19875 AAATTTATCGTTCGTATAACGACCTAAA
1 AAATATATCGTTCG--TAACCACCTAAA
19903 AAATATATCGTTCGTAACCACCTAAA
1 AAATATATCGTTCGTAACCACCTAAA
19929 AAATATATCGTTCGT
1 AAATATATCGTTCGT
19944 TTAACGACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 26 0.67
28 13 0.33
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (26 bp):
AAATATATCGTTCGTAACCACCTAAA
Found at i:19957 original size:26 final size:26
Alignment explanation
Indices: 19875--19959 Score: 100
Period size: 26 Copynumber: 3.1 Consensus size: 26
19865 ATGAAATCAC
*
19875 AAATTTATCGTTCGTATAACGACCTAAA
1 AAATATATCGTTCGT-TAACGACC-AAA
*
19903 AAATATATCGTTCG-TAACCACCTAAA
1 AAATATATCGTTCGTTAACGACC-AAA
19929 AAATATATCGTTCGTTTAACGACCCAAA
1 AAATATATCGTTCG-TTAACGA-CCAAA
19957 AAA
1 AAA
19960 CATTTCTTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
26 25 0.49
28 24 0.47
29 2 0.04
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.28
Consensus pattern (26 bp):
AAATATATCGTTCGTTAACGACCAAA
Found at i:20105 original size:16 final size:17
Alignment explanation
Indices: 20084--20116 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20074 TAGAAATAAG
20084 ATTACTGAA-ATATTAT
1 ATTACTGAACATATTAT
*
20100 ATTACTTAACATATTAT
1 ATTACTGAACATATTAT
20117 TGGGATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTACTGAACATATTAT
Found at i:20515 original size:60 final size:60
Alignment explanation
Indices: 20433--20556 Score: 176
Period size: 60 Copynumber: 2.1 Consensus size: 60
20423 ATAATTTATA
* * * * *
20433 TGTTTATTTTTATGTACTAAGATATTGAGAGATGTACATACTTACATCGGCGTAAGTATG
1 TGTTTATGTTTAGGTACCAAGATAATGAGAGATGTACATACTTACATCGGCGTAAGCATG
* * *
20493 TGTTTATGTTTAGGTACCAAGATAATGAGAGATGTACATACTTATATTGGTGTAAGCATG
1 TGTTTATGTTTAGGTACCAAGATAATGAGAGATGTACATACTTACATCGGCGTAAGCATG
20553 TGTT
1 TGTT
20557 AATTACTACA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.40
Consensus pattern (60 bp):
TGTTTATGTTTAGGTACCAAGATAATGAGAGATGTACATACTTACATCGGCGTAAGCATG
Found at i:22662 original size:33 final size:35
Alignment explanation
Indices: 22620--22702 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 35
22610 TTATAACCTA
* *
22620 TATTTATTAT-TTATTAA-ATTAAGAATAATA-TAT
1 TATTAATTATATTAATAATATTAA-AATAATATTAT
*
22653 TATTAATTATATTAATAATTATTAAAATAATATTTT
1 TATTAATTATATTAATAA-TATTAAAATAATATTAT
*
22689 TATTAA-AATATTAA
1 TATTAATTATATTAA
22703 AAAATTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
33 9 0.21
34 6 0.14
35 14 0.33
36 13 0.31
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
TATTAATTATATTAATAATATTAAAATAATATTAT
Found at i:22702 original size:8 final size:8
Alignment explanation
Indices: 22689--22723 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
22679 ATAATATTTT
22689 TATTAAAA
1 TATTAAAA
22697 TATTAAAA
1 TATTAAAA
* *
22705 AATTATAA
1 TATTAAAA
22713 TATTAAAA
1 TATTAAAA
22721 TAT
1 TAT
22724 GAATATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATTAAAA
Found at i:22709 original size:36 final size:36
Alignment explanation
Indices: 22637--22710 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
22627 TATTTATTAA
* *
22637 ATTAAGAATAATATATTATTAATTATATTAATAATT
1 ATTAAGAATAATATATTATTAATAATATTAAAAATT
*
22673 ATTAA-AATAATATTTTTATTAA-AATATTAAAAAATT
1 ATTAAGAATAATA-TATTATTAATAATATT-AAAAATT
22709 AT
1 AT
22711 AATATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 12 0.36
36 21 0.64
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (36 bp):
ATTAAGAATAATATATTATTAATAATATTAAAAATT
Found at i:22894 original size:21 final size:21
Alignment explanation
Indices: 22817--22931 Score: 71
Period size: 21 Copynumber: 5.4 Consensus size: 21
22807 TTAATTTCAT
*
22817 TAATAATTTATTATATATTATAA
1 TAATAATATA-TATA-ATTATAA
*
22840 -AATAAAAGTATA-ATATTA-AA
1 TAATAATA-TATATA-ATTATAA
22860 TATTATAATA-ATATAATTATAA
1 TA--ATAATATATATAATTATAA
*
22882 TAATAATATATATTATTA-AA
1 TAATAATATATATAATTATAA
* *
22902 TATTCAATAAATATAATT-TAA
1 TAAT-AATATATATAATTATAA
22923 TAATTAATA
1 TAA-TAATA
22932 GTTTTATTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
20 13 0.18
21 41 0.55
22 13 0.18
23 7 0.09
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (21 bp):
TAATAATATATATAATTATAA
Found at i:22903 original size:17 final size:17
Alignment explanation
Indices: 22849--22903 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
22839 AAATAAAAGT
*
22849 ATAATATTAAATATTATA
1 ATAATA-TAATTATTATA
*
22867 ATAATATAATTATAATA
1 ATAATATAATTATTATA
22884 ATAATATATATTATTA-A
1 ATAATATA-ATTATTATA
22901 ATA
1 ATA
22904 TTCAATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 21 0.64
18 12 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATATAATTATTATA
Found at i:22931 original size:42 final size:42
Alignment explanation
Indices: 22828--22931 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
22818 AATAATTTAT
* *
22828 TATATATTATAA-AATAAAAGTATAATATTAAATATTATAATAA
1 TATA-ATTATAATAATAATA-TATAATATTAAATATTACAATAA
*
22871 TATAATTATAATAATAATATATATTATTAAATATT-CAATAAA
1 TATAATTATAATAATAATATATAATATTAAATATTACAAT-AA
22913 TATAATT-TAATAATTAATA
1 TATAATTATAATAA-TAATA
22932 GTTTTATTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
41 9 0.16
42 36 0.65
43 10 0.18
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (42 bp):
TATAATTATAATAATAATATATAATATTAAATATTACAATAA
Found at i:30001 original size:21 final size:21
Alignment explanation
Indices: 29975--30016 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29965 GTTCTAAGAG
29975 AGCAATTCATACACTTAGCTT
1 AGCAATTCATACACTTAGCTT
29996 AGCAATTCATACACTTAGCTT
1 AGCAATTCATACACTTAGCTT
30017 CAGAGGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (21 bp):
AGCAATTCATACACTTAGCTT
Found at i:36951 original size:23 final size:24
Alignment explanation
Indices: 36925--36973 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
36915 TAAACATTTG
* * *
36925 TTTTATATTAAATTA-AAATATAT
1 TTTTATAATAAAATACAAAAATAT
36948 TTTTATAATAAAATACAAAAATAT
1 TTTTATAATAAAATACAAAAATAT
36972 TT
1 TT
36974 AAAAAATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTTATAATAAAATACAAAAATAT
Found at i:37888 original size:6 final size:6
Alignment explanation
Indices: 37879--37938 Score: 61
Period size: 6 Copynumber: 10.0 Consensus size: 6
37869 AGTGAAATTT
* * *
37879 AAATAA AAATAA AAATAA AAA-CA AAATAA ATAA-AT AAATAA AAAGCAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA A-AATAA AAATAA AAA-TAA
37927 AAATAA AAATAA
1 AAATAA AAATAA
37939 GGAAGAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 6 0.14
6 31 0.70
7 7 0.16
ACGTcount: A:0.80, C:0.03, G:0.02, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:37906 original size:23 final size:25
Alignment explanation
Indices: 37879--37938 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 25
37869 AGTGAAATTT
37879 AAATAAAAATAAAAATAAAAA-C-A
1 AAATAAAAATAAAAATAAAAAGCAA
*
37902 AAATAAATAA-ATAAATAAAAAGCAA
1 AAATAAA-AATAAAAATAAAAAGCAA
37927 AAATAAAAATAA
1 AAATAAAAATAA
37939 GGAAGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 17 0.55
24 5 0.16
25 9 0.29
ACGTcount: A:0.80, C:0.03, G:0.02, T:0.15
Consensus pattern (25 bp):
AAATAAAAATAAAAATAAAAAGCAA
Found at i:37931 original size:48 final size:46
Alignment explanation
Indices: 37879--38020 Score: 126
Period size: 48 Copynumber: 2.9 Consensus size: 46
37869 AGTGAAATTT
*
37879 AAATAAAAATAAAAATAAAAACAAAATAAATAAATAAATAAAAAGCAA
1 AAATAAAAATAAGAATAAAAA-AAAATAAATAAATAAATAAAAA-CAA
* * * *
37927 AAATAAAAATAAGGAAGAAAAATGGAATTAAATAAATTAAA-AAACACAA
1 AAATAAAAATAA-GAATAAAAA--AAAATAAATAAA-TAAATAAAAACAA
*
37976 ACAA-AAAAATAAGAATAAAAAATACAATAAATATATAAAATAAAA
1 A-AATAAAAATAAGAATAAAAAA-A-AATAAATAAAT-AAATAAAA
38021 TGTAGTATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
47 2 0.03
48 31 0.41
49 22 0.29
50 16 0.21
51 4 0.05
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (46 bp):
AAATAAAAATAAGAATAAAAAAAAATAAATAAATAAATAAAAACAA
Found at i:38048 original size:3 final size:3
Alignment explanation
Indices: 38040--38066 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
38030 AAATAAATTA
38040 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
38067 GAAAAATATA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:38129 original size:2 final size:2
Alignment explanation
Indices: 38122--38152 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38112 TAATAAGATA
38122 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 A
38153 CGTTAGGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38545 original size:20 final size:20
Alignment explanation
Indices: 38507--38545 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38497 GCCACCGCCT
* *
38507 CGCCGACCGTCGTAGATCGG
1 CGCCGACCGCCGTACATCGG
*
38527 CGCCGACCGCCGTTCATCG
1 CGCCGACCGCCGTACATCG
38546 ACGGTGGCCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.41, G:0.31, T:0.15
Consensus pattern (20 bp):
CGCCGACCGCCGTACATCGG
Found at i:39215 original size:22 final size:22
Alignment explanation
Indices: 39181--39223 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39171 TTTATTTTAA
* *
39181 GGTTTCAGATTGGGTCGGTTCG
1 GGTTGCAGATTGGGTCAGTTCG
*
39203 GGTTGCAGCTTGGGTCAGTTC
1 GGTTGCAGATTGGGTCAGTTC
39224 AGTTGCTCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.16, G:0.40, T:0.35
Consensus pattern (22 bp):
GGTTGCAGATTGGGTCAGTTCG
Found at i:39397 original size:2 final size:2
Alignment explanation
Indices: 39387--39432 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
39377 TATATTCTCC
39387 AT AT A- AT AT AT AT AT AT AT A- AT AT AT A- AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39425 AT AT -T AT A
1 AT AT AT AT A
39433 AATCACATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 5 0.13
2 34 0.87
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39410 original size:7 final size:7
Alignment explanation
Indices: 39387--39432 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
39377 TATATTCTCC
39387 ATATAAT
1 ATATAAT
39394 ATATATAT
1 ATATA-AT
39402 ATATAAT
1 ATATAAT
39409 ATATAAT
1 ATATAAT
*
39416 ATATATT
1 ATATAAT
*
39423 ATATATT
1 ATATAAT
39430 ATA
1 ATA
39433 AATCACATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
7 30 0.81
8 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
ATATAAT
Found at i:43231 original size:29 final size:30
Alignment explanation
Indices: 43174--43238 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
43164 TTTTTTTACT
*
43174 TTATCTATTTTCTCATCATTTTTCATTT-A
1 TTATTTATTTTCTCATCATTTTTCATTTAA
*
43203 TTATTTATTTT-T-ATCATTTTATTACTTTAA
1 TTATTTATTTTCTCATCATTTT-TCA-TTTAA
43233 TTATTT
1 TTATTT
43239 TAAACCTCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 8 0.26
28 3 0.10
29 13 0.42
30 7 0.23
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (30 bp):
TTATTTATTTTCTCATCATTTTTCATTTAA
Found at i:58416 original size:45 final size:46
Alignment explanation
Indices: 58360--58467 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 46
58350 TGCACCAATC
58360 CATGCATCGATGCACCATGA-ATTAAATTG-AACATCGAATGCATTT
1 CATGCATCGATGCACCATGAGATTAAA-TGAAACATCGAATGCATTT
**
58405 CATGCATCGATGCA-C-TGAGGATTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACCATGA-GATTAAATG-AAACATCGAATGCATTT
*
58451 GATGCATCGATGCACCA
1 CATGCATCGATGCACCA
58468 GCCATGCATC
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
43 3 0.06
44 3 0.06
45 18 0.33
46 29 0.54
47 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (46 bp):
CATGCATCGATGCACCATGAGATTAAATGAAACATCGAATGCATTT
Found at i:58517 original size:64 final size:65
Alignment explanation
Indices: 58405--58529 Score: 191
Period size: 64 Copynumber: 1.9 Consensus size: 65
58395 GAATGCATTT
* *
58405 CATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
1 CATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTGATGCATCGATGCACCAGC
* *
58470 CATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATGCACTTGATGCATCGATGCAC
1 CATGCATCGATGCACTCAGGAT-TTTATGAAAACATCGAATGCACTTGATGCATCGATGCAC
58530 TCATAGTGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
64 31 0.56
65 21 0.38
66 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (65 bp):
CATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTGATGCATCGATGCACCAGC
Found at i:59642 original size:21 final size:21
Alignment explanation
Indices: 59608--59656 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
59598 AAAAGAATAA
59608 AAAAGTAAAATAAAGAT-AACAC
1 AAAA-TAAAATAAA-ATAAACAC
*
59630 AAAATAAATTAAAATAAACAC
1 AAAATAAAATAAAATAAACAC
59651 AAAATA
1 AAAATA
59657 TAAGGACCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.16
Consensus pattern (21 bp):
AAAATAAAATAAAATAAACAC
Found at i:65981 original size:5 final size:5
Alignment explanation
Indices: 65963--66006 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
65953 AAAAAAACAG
* *
65963 TAAAA TAAAGA TAACA TAAAA TAAAT TAAAA TAAACA TAAAA TA
1 TAAAA TAAA-A TAAAA TAAAA TAAAA TAAAA TAAA-A TAAAA TA
66007 TGAGGGCCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 24 0.73
6 9 0.27
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:65992 original size:21 final size:21
Alignment explanation
Indices: 65963--66006 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
65953 AAAAAAACAG
65963 TAAAATAAAGAT-AACATAAAA
1 TAAAATAAA-ATAAACATAAAA
*
65984 TAAATTAAAATAAACATAAAA
1 TAAAATAAAATAAACATAAAA
66005 TA
1 TA
66007 TGAGGGCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (21 bp):
TAAAATAAAATAAACATAAAA
Found at i:75870 original size:42 final size:42
Alignment explanation
Indices: 75770--75889 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
75760 AATCCTACCT
* * *
75770 GAAAGTCTTATGGATGGCCCGAAGGACTTA-TCATCCTACTC
1 GAAAGACTTATAGATGGCCCGAAGGACTTACTCATCATACTC
* * * * *
75811 GAAAGACTTATAAATGGCTCAAAGGACTTACGCATCATGCTC
1 GAAAGACTTATAGATGGCCCGAAGGACTTACTCATCATACTC
75853 GAAAGACTTACT-GATGGCCCGAAGGACTTACTCATCA
1 GAAAGACTTA-TAGATGGCCCGAAGGACTTACTCATCA
75890 AGAAACTGTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 25 0.38
42 39 0.60
43 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (42 bp):
GAAAGACTTATAGATGGCCCGAAGGACTTACTCATCATACTC
Found at i:75929 original size:261 final size:258
Alignment explanation
Indices: 75439--76172 Score: 921
Period size: 261 Copynumber: 2.8 Consensus size: 258
75429 TTGATTCCTA
* * * * *
75439 GAGTGAGGTGTTGTTGATTCAACTCTATATGTGATTAATCAAGTACCAGAAATTTTGAAAACATT
1 GAGTGAGGTGTTGTTGATT--ACTCCATATGTGATTAATCGAGTACCAAAAATGTTGAAAACATC
* * * * * * *
75504 TTGCCCGAATGT-TTATGGATAGCCCGAAGGTCTTATCATCTTGCTCTAAAAAGTTATAAATGGC
64 TT-ACCGAAAGTCTTATGGATGGCCCGAAGGTCTTATCATCTTACTCGAAAGACTTATAAATGG-
* *
75568 CCGAAA-GACTTACGCGTCATGCTCAAAAGACTTACTGATGGCCCAAAGGACTTACTCATCAAGA
127 CC-AAAGGACTTACGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTCATCAAGA
* * *
75632 AACCCTTGAAAATCATGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTATATATTATGTTGGTC
191 AACCCTTGAAAATCAAGCTTAGTTTCTTAATTGTCATC-AGGAACCCCTACATATTATGTTGGTC
75697 CCTC
255 CCTC
* * * * *
75701 GAGTGAGGTATTGCTGATTACTCCATATGTGATTAATCGAGTACCATAAATGTTGAAAAAATCCT
1 GAGTGAGGTGTTGTTGATTACTCCATATGTGATTAATCGAGTACCAAAAATGTTGAAAACATCTT
* *
75766 ACCTGAAAGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTCGAAAGACTTATAAATGGCTC
66 ACC-GAAAGTCTTATGGATGGCCCGAAGGTCTTATCATCTTACTCGAAAGACTTATAAATGGC-C
*
75831 AAAGGACTTACGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAAC
129 AAAGGACTTACGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTCATCAAGAAAC
** *
75896 TGTTGAAAATCAAGCTTAGTTTCTTAATTGTCATCAGGAACCCCTACATATTATGTTGGTCCTTC
194 CCTTGAAAATCAAGCTTAGTTTCTTAATTGTCATCAGGAACCCCTACATATTATGTTGGTCCCTC
* * *
75961 GAGT---GTGTTGTTCA--ACTCCATATGTGATTAATCGAGCACGAAAAATGTTGAAAACATCTT
1 GAGTGAGGTGTTGTTGATTACTCCATATGTGATTAATCGAGTACCAAAAATGTTGAAAACATCTT
* * * **
76021 GTCCGAAGGTCTTAT-GATGGCTCGAAGGTCTTATCAT-TTAGCTCGAAAGACTTATAAATATCC
66 -ACCGAAAGTCTTATGGATGGCCCGAAGGTCTTATCATCTTA-CTCGAAAGACTTATAAATGGCC
* * * * *
76084 GAAGGACTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTCATTAATAAAA
129 AAAGGACTTACGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTCATCAAGAAAC
*
76149 CCATGAAAAT-AGAGCTTAGTTTCT
194 CCTTGAAAATCA-AGCTTAGTTTCT
76173 CATAAAAATT
Statistics
Matches: 414, Mismatches: 51, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
252 1 0.00
253 81 0.20
254 39 0.09
255 51 0.12
256 2 0.00
257 7 0.02
259 2 0.00
260 80 0.19
261 134 0.32
262 17 0.04
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (258 bp):
GAGTGAGGTGTTGTTGATTACTCCATATGTGATTAATCGAGTACCAAAAATGTTGAAAACATCTT
ACCGAAAGTCTTATGGATGGCCCGAAGGTCTTATCATCTTACTCGAAAGACTTATAAATGGCCAA
AGGACTTACGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTCATCAAGAAACCC
TTGAAAATCAAGCTTAGTTTCTTAATTGTCATCAGGAACCCCTACATATTATGTTGGTCCCTC
Found at i:76066 original size:21 final size:19
Alignment explanation
Indices: 76024--76067 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
76014 ACATCTTGTC
* *
76024 CGAAGGTCTTATGATGGCT
1 CGAAGGTCTTATCATAGCT
76043 CGAAGGTCTTATCATTTAGCT
1 CGAAGGTCTTATCA--TAGCT
76064 CGAA
1 CGAA
76068 AGACTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
21 8 0.38
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (19 bp):
CGAAGGTCTTATCATAGCT
Found at i:76256 original size:57 final size:58
Alignment explanation
Indices: 76154--76266 Score: 149
Period size: 57 Copynumber: 2.0 Consensus size: 58
76144 TAAAACCATG
**
76154 AAAATAGAGCTTAGTTTCTCATAAAAATTCATTGAAAATTGTCATCAAGAAACCCCTA
1 AAAATAGAGCTTAGTTTCTCATAAAAATTCATTGAAAATAATCATCAAGAAACCCCTA
* * * *
76212 AAAATTAG-GCTTAGTTTCT-TTAAAAATTCTTTGGAGATAATCATCAAGAAACCCC
1 AAAA-TAGAGCTTAGTTTCTCATAAAAATTCATTGAAAATAATCATCAAGAAACCCC
76267 AGAAAGTCAG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 30 0.62
58 15 0.31
59 3 0.06
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31
Consensus pattern (58 bp):
AAAATAGAGCTTAGTTTCTCATAAAAATTCATTGAAAATAATCATCAAGAAACCCCTA
Found at i:76279 original size:57 final size:58
Alignment explanation
Indices: 76154--76280 Score: 143
Period size: 57 Copynumber: 2.2 Consensus size: 58
76144 TAAAACCATG
**
76154 AAAAT-AGAGCTTAGTTTCTCATAAAAATTCATTGAAAATTGTCATCAAGAAACCCCTA
1 AAAATCAG-GCTTAGTTTCTCATAAAAATTCATTGAAAATAATCATCAAGAAACCCCTA
* * * * *
76212 AAAATTAGGCTTAGTTTCT-TTAAAAATTCTTTGGAGATAATCATCAAGAAACCCC-A
1 AAAATCAGGCTTAGTTTCTCATAAAAATTCATTGAAAATAATCATCAAGAAACCCCTA
*
76268 GAAAGTCAGGCTT
1 -AAAATCAGGCTT
76281 GGTTCCTAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
56 1 0.02
57 40 0.68
58 16 0.27
59 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (58 bp):
AAAATCAGGCTTAGTTTCTCATAAAAATTCATTGAAAATAATCATCAAGAAACCCCTA
Found at i:77454 original size:173 final size:173
Alignment explanation
Indices: 77165--77507 Score: 571
Period size: 173 Copynumber: 2.0 Consensus size: 173
77155 TTAAATCTCA
* *
77165 TGATCTTAATGACATCTGGTTTAGATAATGCCCCAATGTGGGTACTCAAGGCTCTCTTCATGCCA
1 TGATCTTAATGACATCTGGTTTAGATAATGCCCCAATGTGGGTACACAAGGCTCTCTTCATGACA
* *
77230 AAATCTTAATCTCGAATAGTTTCACTCTGGTGTCACTAATCAGTAATGTTATCGAATAGAC-TGA
66 AAATCTTAATCTCGAATAGTTTCACTCTAGTGTCACTAATCAGCAATGTTATCGAATAGACAT-A
77294 GGGCTTCTCTTCACGATGCCATAACCAAATGAACACTTAAATCG
130 GGGCTTCTCTTCACGATGCCATAACCAAATGAACACTTAAATCG
* *
77338 TGATCTTAATGACATCTGGTTTAGGTAATGCCCCAATGTGGGTACACATGGCTCTCTTCATGACA
1 TGATCTTAATGACATCTGGTTTAGATAATGCCCCAATGTGGGTACACAAGGCTCTCTTCATGACA
* * *
77403 AAATCTTAATCTCGAATTGTTTTACTCTAGTGTCACTAATCAGCAATGTTATCGAATTGACATAG
66 AAATCTTAATCTCGAATAGTTTCACTCTAGTGTCACTAATCAGCAATGTTATCGAATAGACATAG
* *
77468 GGCTTCTCTTCACGATGCCATAACCAAATTAAGACTTAAA
131 GGCTTCTCTTCACGATGCCATAACCAAATGAACACTTAAA
77508 AAGTGATCAA
Statistics
Matches: 158, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
173 157 0.99
174 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (173 bp):
TGATCTTAATGACATCTGGTTTAGATAATGCCCCAATGTGGGTACACAAGGCTCTCTTCATGACA
AAATCTTAATCTCGAATAGTTTCACTCTAGTGTCACTAATCAGCAATGTTATCGAATAGACATAG
GGCTTCTCTTCACGATGCCATAACCAAATGAACACTTAAATCG
Found at i:78678 original size:23 final size:22
Alignment explanation
Indices: 78629--78689 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
78619 GTTTGATTGG
* *
78629 TTTCTTTCTTTCTTTCTTTCTCC
1 TTTCTCTCTTT-TTTTTTTCTCC
78652 TTTCTCTCTTTTTTTTTTCT-C
1 TTTCTCTCTTTTTTTTTTCTCC
*
78673 TTTTTCTCTTTTTTTTT
1 TTTCTCTCTTTTTTTTT
78690 ACTTCATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 17 0.49
22 8 0.23
23 10 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTCTCTCTTTTTTTTTTCTCC
Found at i:78704 original size:22 final size:21
Alignment explanation
Indices: 78651--78705 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
78641 TTTCTTTCTC
* *
78651 CTTTCTCTCTTTTTTTTTTCT
1 CTTTATCTCTTTTTTTTTACT
*
78672 CTTTTTCTCTTTTTTTTTACTT
1 CTTTATCTCTTTTTTTTTAC-T
78694 CATTTAT-TCTTT
1 C-TTTATCTCTTT
78706 CTTGTTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.62
22 7 0.24
23 4 0.14
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (21 bp):
CTTTATCTCTTTTTTTTTACT
Done.