Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001252.1 Hibiscus syriacus cultivar Beakdansim tig00002456_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: 73798
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:876 original size:21 final size:21
Alignment explanation
Indices: 852--903 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
842 AGGCATCAGT
852 TGAAATCATCGCCTGAGACGG
1 TGAAATCATCGCCTGAGACGG
**
873 TGAAATCATCGCCTGAGGTGG
1 TGAAATCATCGCCTGAGACGG
*
894 TGAAGTCATC
1 TGAAATCATC
904 CATAAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (21 bp):
TGAAATCATCGCCTGAGACGG
Found at i:7968 original size:20 final size:20
Alignment explanation
Indices: 7943--7981 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7933 TTTTGCAAAT
*
7943 AATAGAATTACTCTGGAAAC
1 AATAGAATTACTCTAGAAAC
*
7963 AATAGAATTGCTCTAGAAA
1 AATAGAATTACTCTAGAAA
7982 TTCCGAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (20 bp):
AATAGAATTACTCTAGAAAC
Found at i:8919 original size:31 final size:31
Alignment explanation
Indices: 8884--8993 Score: 87
Period size: 31 Copynumber: 3.4 Consensus size: 31
8874 CAGTCCCTAC
8884 TGGTAATTCCTTGTATAGGTTCAACACCGAT
1 TGGTAATTCCTTGTATAGGTTCAACACCGAT
* * * * *
8915 TGGTAATTCCTTATCTCTGGCAGGTTTAATCGCTG-T
1 TGGTAATTCC-T-TGTAT---AGGTTCAA-CACCGAT
** *
8951 TGGTAATTCCTTGTATAGGTTCGGCACCGAC
1 TGGTAATTCCTTGTATAGGTTCAACACCGAT
8982 TGGTAATTCCTT
1 TGGTAATTCCTT
8994 ATGGACCTAA
Statistics
Matches: 59, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
30 3 0.05
31 27 0.46
32 1 0.02
33 3 0.05
34 3 0.05
35 1 0.02
36 18 0.31
37 3 0.05
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
TGGTAATTCCTTGTATAGGTTCAACACCGAT
Found at i:9904 original size:75 final size:76
Alignment explanation
Indices: 9780--9936 Score: 280
Period size: 75 Copynumber: 2.1 Consensus size: 76
9770 TAATAATATA
9780 ACGAAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACATAGTGCCGAAAGTACAC
1 ACGAAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACATAGTGCCGAAAGTACAC
*
9845 AAAGTATTGAT
66 AAAGTACTGAT
* *
9856 ACGAAATGGTAATTCAC-AACTCATTATGAATACCATGGATGCACACATAGTGCCTAAAGTACAC
1 ACGAAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACATAGTGCCGAAAGTACAC
9920 AAAGTACTGAT
66 AAAGTACTGAT
9931 ACGAAA
1 ACGAAA
9937 ATGCAACATA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 61 0.78
76 17 0.22
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (76 bp):
ACGAAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACATAGTGCCGAAAGTACAC
AAAGTACTGAT
Found at i:22490 original size:22 final size:22
Alignment explanation
Indices: 22437--22508 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
22427 AATAACTAAA
* *
22437 ATAAAGAAGATAAA-ATAAAGGG
1 ATAAAGAA-ATAAATAAAAAGAG
*
22459 AAAAATGAAATAAATAAAAAGAG
1 ATAAA-GAAATAAATAAAAAGAG
*
22482 ATAAAGAAA-ATAATAAAAAAAG
1 ATAAAGAAATA-AATAAAAAGAG
22504 ATAAA
1 ATAAA
22509 AACAAGTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
21 1 0.02
22 28 0.67
23 13 0.31
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (22 bp):
ATAAAGAAATAAATAAAAAGAG
Found at i:22492 original size:23 final size:22
Alignment explanation
Indices: 22466--22508 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
22456 GGGAAAAATG
*
22466 AAATAAATAAAAAGAGATAAAGA
1 AAAT-AATAAAAAAAGATAAAGA
22489 AAATAATAAAAAAAGATAAA
1 AAATAATAAAAAAAGATAAA
22509 AACAAGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (22 bp):
AAATAATAAAAAAAGATAAAGA
Found at i:22530 original size:4 final size:4
Alignment explanation
Indices: 22521--22666 Score: 80
Period size: 4 Copynumber: 33.2 Consensus size: 4
22511 CAAGTGAACA
* *
22521 AAAT AAAT AAAAT AAAATT AAATT AAAG AAAT AAAAA AAAT AAA- AAGAT
1 AAAT AAAT -AAAT -AAA-T AAA-T AAAT AAAT -AAAT AAAT AAAT AA-AT
* *
22570 ATAA- AAAT AAAGA AAAT AATAGT AATAT ACAT ATAAT AAAT AAAT AAAT
1 A-AAT AAAT AAA-T AAAT AA-A-T AA-AT AAAT A-AAT AAAT AAAT AAAT
* * *
22619 AAAT AAAA ACAAT AAAT AAAT AAAAGT AAAT AAAG GAAT AAAT AAAT A
1 AAAT AAAT A-AAT AAAT AAAT -AAA-T AAAT AAAT AAAT AAAT AAAT A
22667 TAAAGGGAAT
Statistics
Matches: 114, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
3 4 0.04
4 63 0.55
5 39 0.34
6 8 0.07
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:22565 original size:8 final size:8
Alignment explanation
Indices: 22459--22666 Score: 71
Period size: 8 Copynumber: 23.9 Consensus size: 8
22449 AAATAAAGGG
22459 AAAAATGAA
1 AAAAAT-AA
*
22468 ATAAATAA
1 AAAAATAA
22476 AAAGAGATAA
1 AAA-A-ATAA
22486 AGAAAAT--
1 A-AAAATAA
*
22493 AATAA-AA
1 AAAAATAA
*
22500 AAAGATAA
1 AAAAATAA
22508 AAACAAGTGAA
1 AAA-AA-T-AA
*
22519 CAAAATAA
1 AAAAATAA
22527 ATAAAATAA
1 A-AAAATAA
22536 AATTAAATTAA
1 AA--AAA-TAA
*
22547 AGAAATAAA
1 AAAAAT-AA
22556 AAAAATAA
1 AAAAATAA
* *
22564 AAAGATAT
1 AAAAATAA
22572 AAAAATAA
1 AAAAATAA
22580 AGAAAATAA
1 A-AAAATAA
*
22589 TAGTAATATACA
1 -A--AAAATA-A
* *
22601 TATAATAA
1 AAAAATAA
*
22609 ATAAATAA
1 AAAAATAA
*
22617 ATAAATAA
1 AAAAATAA
22625 AAACAATAA
1 AAA-AATAA
*
22634 ATAAATAA
1 AAAAATAA
22642 AAGTAAATAA
1 AA--AAATAA
**
22652 AGGAATAA
1 AAAAATAA
*
22660 ATAAATA
1 AAAAATA
22667 TAAAGGGAAT
Statistics
Matches: 149, Mismatches: 29, Indels: 43
0.67 0.13 0.19
Matches are distributed among these distances:
6 3 0.02
7 4 0.03
8 60 0.40
9 46 0.31
10 20 0.13
11 15 0.10
12 1 0.01
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (8 bp):
AAAAATAA
Found at i:22573 original size:10 final size:10
Alignment explanation
Indices: 22470--22576 Score: 53
Period size: 10 Copynumber: 10.9 Consensus size: 10
22460 AAAATGAAAT
22470 AAATAAAAAG
1 AAATAAAAAG
* *
22480 AGATAAAGAAA
1 AAATAAA-AAG
22491 ATAATAAAAA-
1 A-AATAAAAAG
*
22501 AAGATAAAAAC
1 AA-ATAAAAAG
* * *
22512 AAGTGAACA-
1 AAATAAAAAG
*
22521 AAATAAATA-
1 AAATAAAAAG
**
22530 AAATAAAATT
1 AAATAAAAAG
*
22540 AAAT-TAAAG
1 AAATAAAAAG
22549 AAATAAAAA-
1 AAATAAAAAG
22558 AAATAAAAAG
1 AAATAAAAAG
*
22568 ATATAAAAA
1 AAATAAAAA
22577 TAAAGAAAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
9 29 0.39
10 33 0.45
11 7 0.09
12 5 0.07
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (10 bp):
AAATAAAAAG
Found at i:22759 original size:20 final size:20
Alignment explanation
Indices: 22736--22776 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
22726 AAAATAACGT
22736 AAATAGAAAGAAA-AAAATAA
1 AAATA-AAAGAAACAAAATAA
*
22756 AAATAAAATAAACAAAATAA
1 AAATAAAAGAAACAAAATAA
22776 A
1 A
22777 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.12
Consensus pattern (20 bp):
AAATAAAAGAAACAAAATAA
Found at i:22762 original size:24 final size:24
Alignment explanation
Indices: 22735--22785 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
22725 AAAAATAACG
*
22735 TAAATAGAAAGAAAA-AAATAAAAA
1 TAAA-AGAAACAAAATAAATAAAAA
*
22759 TAAAATAAACAAAATAAATAAAAA
1 TAAAAGAAACAAAATAAATAAAAA
22783 TAA
1 TAA
22786 TAGTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (24 bp):
TAAAAGAAACAAAATAAATAAAAA
Found at i:22775 original size:116 final size:116
Alignment explanation
Indices: 22574--22785 Score: 254
Period size: 116 Copynumber: 1.8 Consensus size: 116
22564 AAAGATATAA
* * *
22574 AAATAAAGAAAATAATAGTAATATACATATAATAAATAAATAAATAAATAAAAACAATAAATAAA
1 AAATAAAGAAAATAATAATAATATACATATAATAAATAAATAAATAAATAAAAACAAGAAAAAAA
* ** *
22639 TAAAAGTAAATAAAGGAATAAATAAATATAAAGGGAATAAAATAAGTAATT
66 TAAAAATAAATAAAAAAATAAATAAAAATAAAGGGAATAAAATAAGTAATT
* * *
22690 AAATAAAGAATATAATAAT-A-ATGCATATAATAAAT-AA-AAATAACGTAAATAGA-AAGAAAA
1 AAATAAAGAAAATAATAATAATATACATATAATAAATAAATAAATAA-ATAAA-A-ACAAGAAAA
22750 AAATAAAAATAAAATAAACAAAATAAATAAAAATAA
63 AAATAAAAAT-AAATAAA-AAAATAAATAAAAATAA
22786 TAGTAAATAT
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
112 6 0.07
113 6 0.07
114 29 0.36
115 9 0.11
116 31 0.38
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (116 bp):
AAATAAAGAAAATAATAATAATATACATATAATAAATAAATAAATAAATAAAAACAAGAAAAAAA
TAAAAATAAATAAAAAAATAAATAAAAATAAAGGGAATAAAATAAGTAATT
Found at i:23954 original size:2 final size:2
Alignment explanation
Indices: 23947--24018 Score: 98
Period size: 2 Copynumber: 38.0 Consensus size: 2
23937 TAAAATGTGA
23947 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
* *
23989 A- AT AT AT TT A- AA AT AT AT A- AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24019 TAATTGAAGC
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
1 4 0.06
2 59 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27289 original size:2 final size:2
Alignment explanation
Indices: 27284--27353 Score: 83
Period size: 2 Copynumber: 36.5 Consensus size: 2
27274 ATTTTTTCCA
** * *
27284 AT AT AT AT AT AT AT AT AT AT -T GG A- AA AA AT -T 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
27323 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
27354 AAGAAAAACA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
1 3 0.05
2 59 0.95
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:27826 original size:21 final size:21
Alignment explanation
Indices: 27800--27858 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
27790 CCTTTATATC
*
27800 ATTAAACTTTCAATTTTGTTA
1 ATTAAACATTCAATTTTGTTA
27821 ATTAAACATTCAATTTTGTTA
1 ATTAAACATTCAATTTTGTTA
*
27842 ATTAAACATTAAATTTT
1 ATTAAACATTCAATTTT
27859 AGTTTTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.49
Consensus pattern (21 bp):
ATTAAACATTCAATTTTGTTA
Found at i:29265 original size:46 final size:45
Alignment explanation
Indices: 29186--29273 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 45
29176 TATAACAAAT
29186 ATTTCATATTCTTTTCATTCGTACATATTTCATAACTTTCATTTC
1 ATTTCATATTCTTTTCATTCGTACATATTTCATAACTTTCATTTC
* *
29231 ATTTCCATATTCTTTTC-TT-TTATATACTTATCATAACTTTCAT
1 ATTT-CATATTCTTTTCATTCGTACATA-TT-TCATAACTTTCAT
29274 ATTTACCTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
44 5 0.13
45 8 0.21
46 25 0.66
ACGTcount: A:0.25, C:0.19, G:0.01, T:0.55
Consensus pattern (45 bp):
ATTTCATATTCTTTTCATTCGTACATATTTCATAACTTTCATTTC
Found at i:32251 original size:17 final size:19
Alignment explanation
Indices: 32229--32265 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
32219 ATTCTGATTC
*
32229 TCAAGA-AAATTATT-ATT
1 TCAAGACAAACTATTCATT
32246 TCAAGACAAACTATTCATT
1 TCAAGACAAACTATTCATT
32265 T
1 T
32266 ACAATCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (19 bp):
TCAAGACAAACTATTCATT
Found at i:33969 original size:23 final size:22
Alignment explanation
Indices: 33943--33999 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
33933 AAAAATGTGT
33943 AATAGAAAAAAGAGACTCATAAA
1 AATAGAAAAAAGAGA-TCATAAA
*
33966 AATAGAGAAAAATAGATCATAAA
1 AATAGA-AAAAAGAGATCATAAA
* *
33989 ACTAAAAAAAA
1 AATAGAAAAAA
34000 TACAAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.17
23 17 0.57
24 8 0.27
ACGTcount: A:0.68, C:0.07, G:0.11, T:0.14
Consensus pattern (22 bp):
AATAGAAAAAAGAGATCATAAA
Found at i:34000 original size:32 final size:33
Alignment explanation
Indices: 33963--34030 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
33953 AGAGACTCAT
*
33963 AAAAATA-GAGAAAAATAGATCATAAAACTAAA
1 AAAAATACAAGAAAAATAGATCATAAAACTAAA
*
33995 AAAAATACAAGAAAAATATATCATAAAACTAAA
1 AAAAATACAAGAAAAATAGATCATAAAACTAAA
34028 AAA
1 AAA
34031 TTACAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.71, C:0.07, G:0.06, T:0.16
Consensus pattern (33 bp):
AAAAATACAAGAAAAATAGATCATAAAACTAAA
Found at i:34036 original size:32 final size:32
Alignment explanation
Indices: 33971--34066 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 32
33961 ATAAAAATAG
* *
33971 AGAAAAATAGATCATAAAACTAAAAAAAATACA
1 AGAAAAATATATCATAAAACT-AAAAAATTACA
34004 AGAAAAATATATCATAAAACTAAAAAATTACA
1 AGAAAAATATATCATAAAACTAAAAAATTACA
* * *
34036 A-AAAAAAAGTGTAATAAAACTATAAAAATTA
1 AGAAAAATA-TATCATAAAACTA-AAAAATTA
34067 TAAAAAGAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
31 6 0.11
32 22 0.39
33 28 0.50
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (32 bp):
AGAAAAATATATCATAAAACTAAAAAATTACA
Found at i:34072 original size:32 final size:32
Alignment explanation
Indices: 33984--34083 Score: 105
Period size: 32 Copynumber: 3.1 Consensus size: 32
33974 AAAATAGATC
* * * *
33984 ATAAAACTAAAAAAAATACAAGAAAAATA-TATC
1 ATAAAACT-AAAAAATTACAA-AAAAAAAGTGTA
34017 ATAAAACTAAAAAATTACAAAAAAAAAGTGTA
1 ATAAAACTAAAAAATTACAAAAAAAAAGTGTA
* *
34049 ATAAAACTATAAAAATTA-TAAAAAGAAGTGTA
1 ATAAAACTA-AAAAATTACAAAAAAAAAGTGTA
34081 ATA
1 ATA
34084 GGAAAAAGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
31 6 0.10
32 37 0.63
33 16 0.27
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (32 bp):
ATAAAACTAAAAAATTACAAAAAAAAAGTGTA
Found at i:34529 original size:20 final size:20
Alignment explanation
Indices: 34504--34571 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
34494 TCTTTCATAT
*
34504 AATTTGATTCGTACAATTAA
1 AATTTGATTCATACAATTAA
* *
34524 AATTTGATAT-TTAGTCATTTAA
1 AATTTGAT-TCATA--CAATTAA
*
34546 GTATTTGATTCATACAATTAA
1 -AATTTGATTCATACAATTAA
34567 AATTT
1 AATTT
34572 AAAGATTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
20 14 0.38
21 7 0.19
22 7 0.19
23 9 0.24
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (20 bp):
AATTTGATTCATACAATTAA
Found at i:42980 original size:49 final size:47
Alignment explanation
Indices: 42924--43054 Score: 147
Period size: 47 Copynumber: 2.7 Consensus size: 47
42914 CACTATTCCT
* * * * *
42924 CATCTAACCTGCATTAGTGGCACCTTTCTACC-AAAAGTACACTGTTAG
1 CATCTAACTTGCATTAATGACACCTTTCTGCCAAAAAG--CACAGTTAG
* ** *
42972 ACATCTAACTTGAATTAATGTTACCTTTTTGCCAAAAAGCACAGTTAG
1 -CATCTAACTTGCATTAATGACACCTTTCTGCCAAAAAGCACAGTTAG
43020 CATCTAACTTGCATTAATGACACCTTTCTGCCAAA
1 CATCTAACTTGCATTAATGACACCTTTCTGCCAAA
43055 TGCACAGCTA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 31 0.45
48 8 0.12
49 25 0.36
50 5 0.07
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.31
Consensus pattern (47 bp):
CATCTAACTTGCATTAATGACACCTTTCTGCCAAAAAGCACAGTTAG
Found at i:43240 original size:54 final size:54
Alignment explanation
Indices: 43158--43650 Score: 681
Period size: 54 Copynumber: 9.1 Consensus size: 54
43148 ACTCTATAGT
** * * * * *
43158 TTGCACACGTAGTGCCAATACTATAATTCA-CAACTTATTATGAATTACGT-GG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* *
43210 ATTTGCAAACACAGTGCCATTACGAAAATTCATAAACTTATTATGAATTTCTTAGG
1 --TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
43266 TTGCACACACAGTG-CAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* * *
43319 TTGCACACACAATGCCAATAC-ATAACTTCATAAACTTATTATTAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAGG
* * * *
43373 TTGCGCACATAGAGCCAATACAAAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* *
43427 TTGCATACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* *
43481 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGGATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* * *
43535 TTTCACACACAGTGCCAATACGAAAATTCATAACCTTATCATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* * *
43589 TTGCACACACAGTGTCAATACGGAAATTCATAAA-TGTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACT-TATTATGAATTTCTTAGG
43643 TTGCACAC
1 TTGCACAC
43651 GTAGTTCCAT
Statistics
Matches: 392, Mismatches: 41, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
53 53 0.14
54 319 0.81
55 18 0.05
56 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (54 bp):
TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
Found at i:53087 original size:2 final size:2
Alignment explanation
Indices: 53080--53110 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53070 CCATAAAAGC
53080 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
53111 CTTTCTAACA
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
Found at i:54970 original size:46 final size:46
Alignment explanation
Indices: 54901--54988 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
54891 ACCACTATTT
* * *
54901 ATTTTCATTTGTGGCATCATTTCATGCCAATTATGCATTGTTATAC
1 ATTTTCATTTATGGAATCATTTCATGCCAACTATGCATTGTTATAC
*
54947 ATTTTCATTTATGGAATCCTTTCATGCCAACTATGCATTGTT
1 ATTTTCATTTATGGAATCATTTCATGCCAACTATGCATTGTT
54989 CTTCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (46 bp):
ATTTTCATTTATGGAATCATTTCATGCCAACTATGCATTGTTATAC
Found at i:55399 original size:54 final size:54
Alignment explanation
Indices: 55342--55928 Score: 780
Period size: 54 Copynumber: 10.8 Consensus size: 54
55332 CATACGAAAA
* * * *
55342 TTCATAAACTTATTATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTA
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTG
* * * * *
55396 TTCATCAACATATGATGAAGTCCGTGGGTTACACTCATAGTGCTGAAACGATTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTG
* * * *
55450 TTCATCAACTTATGATTAATTCAGTGGGTTGCACACATAGTGCCGAAACTGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTG
* * *
55504 TTCATCAACATATGATGAATTCCATGGGTTGCACACACATAGTGCTGAAACGCTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTG--CACACATAGTGCCGAAACGGTTG
* * * * *
55560 TTCATCAACATATGATGAATTTCGTGGGTTACACATATAGTGCCAAAACAGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTG
* * *
55614 TTCATCAACATATGATGAATTTCGTGGGTTACACACATAGTGTCGAAACGGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTG
* *
55668 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGTCAAAACGGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTG
* **
55722 TTAATCAACATATGATGAATTATGTGGGTTGCACACATAGTGCCGAAACGGGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCGAAAC-GGTTG
* * * *
55777 TTCATTAAAATATGATGAATTCTGTGGGTTGCACACATAATG-CGAAAACGGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCG-AAACGGTTG
* * * *
55831 TTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTCGGAACGGTTG
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTG
* *
55885 TTCATCAACATATGATGAATTCCGTGAGTTGCACATATAGTGCC
1 TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCC
55929 ATTTGGTAAT
Statistics
Matches: 468, Mismatches: 60, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
54 372 0.79
55 48 0.10
56 48 0.10
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTG
Found at i:55630 original size:218 final size:217
Alignment explanation
Indices: 55342--55929 Score: 806
Period size: 218 Copynumber: 2.7 Consensus size: 217
55332 CATACGAAAA
* * * * *
55342 TTCATAAACTTATTATGAATTCCGTGGGTTGCACACATAGTGCCGAAACGGTTATTCATCAACAT
1 TTCATAAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACAT
* * * * *
55407 ATGATGAAGTCCGTGGGTTACACTCATAGTG-CTGAAACGATTGTTCATCAACTTATGATTAATT
66 ATGATGAATTCCGTGGGTTACACACATAGTGTC-GAAACGGTTGTTCATCAACATATGATGAATT
* * * * *
55471 CAGTGGGTTGCACACATAGTGCCGAAACTGTTGTTCATCAACATATGATGAATTCCATGGGTTGC
130 CCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTAATCAACATATGATGAATTACATGGGTTG-
*
55536 ACACACATAGTGCTGAAAC-GCTTG
194 -CACACATAGTGCCGAAACGGCTTG
* * * *
55560 TTCATCAACATATGATGAATTTCGTGGGTTACACATATAGTGCCAAAACAGTTGTTCATCAACAT
1 TTCATAAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACAT
*
55625 ATGATGAATTTCGTGGGTTACACACATAGTGTCGAAACGGTTGTTCATCAACATATGATGAATTC
66 ATGATGAATTCCGTGGGTTACACACATAGTGTCGAAACGGTTGTTCATCAACATATGATGAATTC
* **
55690 CGTGGGTTGCACACATAGTGTCAAAACGGTTGTTAATCAACATATGATGAATTATGTGGGTTGCA
131 CGTGGGTTGCACACATAGTGCCAAAACGGTTGTTAATCAACATATGATGAATTACATGGGTTGCA
*
55755 CACATAGTGCCGAAACGGGTTG
196 CACATAGTGCCGAAACGGCTTG
* *
55777 TTCATTAAA-ATATGATGAA-TTCTGTGGGTTGCACACATAATGCGAAAACGGTTGTTCATCAAC
1 TTCA-TAAACATATGATGAATTTC-GTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAAC
* * * *
55840 ATATGATGAATTCTGTGGGTTGCACACTTAGTGTCGGAACGGTTGTTCATCAACATATGATGAAT
64 ATATGATGAATTCCGTGGGTTACACACATAGTGTCGAAACGGTTGTTCATCAACATATGATGAAT
* *
55905 TCCGTGAGTTGCACATATAGTGCCA
129 TCCGTGGGTTGCACACATAGTGCCA
55930 TTTGGTAATC
Statistics
Matches: 327, Mismatches: 39, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
216 20 0.06
217 135 0.41
218 171 0.52
219 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (217 bp):
TTCATAAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCAAAACGGTTGTTCATCAACAT
ATGATGAATTCCGTGGGTTACACACATAGTGTCGAAACGGTTGTTCATCAACATATGATGAATTC
CGTGGGTTGCACACATAGTGCCAAAACGGTTGTTAATCAACATATGATGAATTACATGGGTTGCA
CACATAGTGCCGAAACGGCTTG
Found at i:56138 original size:18 final size:18
Alignment explanation
Indices: 56115--56150 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
56105 TCGATCTACT
56115 CAAGCATCCATTAAAGAC
1 CAAGCATCCATTAAAGAC
56133 CAAGCATCCATTAAAGAC
1 CAAGCATCCATTAAAGAC
56151 ACGTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.17
Consensus pattern (18 bp):
CAAGCATCCATTAAAGAC
Found at i:56312 original size:22 final size:22
Alignment explanation
Indices: 56286--56363 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
56276 TACCCCTACC
*
56286 ATGGTATCGATACTTCTATACT
1 ATGGTACCGATACTTCTATACT
*
56308 ATGGTACCGATACCTT-TCT-CT
1 ATGGTACCGATA-CTTCTATACT
* * *
56329 CA--GTATCGATACTACTACACT
1 -ATGGTACCGATACTTCTATACT
56350 ATGGTACCGATACT
1 ATGGTACCGATACT
56364 CCCTTTTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
19 2 0.05
20 10 0.23
21 4 0.09
22 24 0.56
23 3 0.07
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (22 bp):
ATGGTACCGATACTTCTATACT
Found at i:58615 original size:47 final size:49
Alignment explanation
Indices: 58501--58627 Score: 186
Period size: 47 Copynumber: 2.6 Consensus size: 49
58491 TGTTCCTCAT
* * * *
58501 TAACTTGCATTAATGGCACCTTTCAACCAAAAGTGCACTGTTAGGCATC
1 TAACTTGCATTAATGGCACCTTTCTACCAAAAGAGCACAGTTAGACATC
*
58550 TAACTTGCATTAATGGCACCTTTCTGCCAAAA-AGCACAGTTA-ACATC
1 TAACTTGCATTAATGGCACCTTTCTACCAAAAGAGCACAGTTAGACATC
*
58597 TAACTTGCATTAATGGCACCTTTCTTCCAAA
1 TAACTTGCATTAATGGCACCTTTCTACCAAA
58628 TGCACAGCTA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
47 34 0.47
48 8 0.11
49 30 0.42
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.30
Consensus pattern (49 bp):
TAACTTGCATTAATGGCACCTTTCTACCAAAAGAGCACAGTTAGACATC
Found at i:59339 original size:54 final size:54
Alignment explanation
Indices: 58729--59331 Score: 874
Period size: 54 Copynumber: 11.2 Consensus size: 54
58719 ACTCTATAGT
** * ** * * *
58729 TTGCACACGTAGTGCAAATACGGTAATTCA-CAACTTATTATGAATTAT-GTGGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATT-TCTTAGG
* * *
58782 TTTACACACACAATGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGG
1 -TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
*
58837 TTGCACACACAGTTCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
*
58891 TTGCACACACAATGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* * *
58945 TTGCACACACAATGCTAATACAAAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* *
58999 TTGCATACACAGTGCCAATACGGAAATGT-ATAAACTTATTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAAT-TCATAAACTTATTATGAATTTCTTAGG
59053 TTGCACACACAGTGCCAATACGAAAATGT-ATAAACTTATTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAAT-TCATAAACTTATTATGAATTTCTTAGG
* *
59107 TTGCACACACAGTGTCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* *
59161 TTACACACACAGTGCCAATAC-AGAAATTCATAAACTTACTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAGG
* * *
59215 TTTCACACATAGTGCCAATACAAAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* *
59269 TTGCACCCACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
*
59323 TTGTACACA
1 TTGCACACA
59332 TTGTGCCATT
Statistics
Matches: 503, Mismatches: 40, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
53 1 0.00
54 482 0.96
55 20 0.04
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.33
Consensus pattern (54 bp):
TTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
Found at i:59729 original size:19 final size:19
Alignment explanation
Indices: 59702--59749 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
59692 CTATATTATG
59702 GTATCGATACTCCCTTTTA
1 GTATCGATACTCCCTTTTA
*
59721 GTATTGATACTCCCTTTTA
1 GTATCGATACTCCCTTTTA
59740 GTATCGATAC
1 GTATCGATAC
59750 CATTTCTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (19 bp):
GTATCGATACTCCCTTTTA
Found at i:61010 original size:21 final size:23
Alignment explanation
Indices: 60984--61030 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
60974 TTGGCATGAG
60984 TTTATTG-TGGATGATTA-TATT
1 TTTATTGATGGATGATTAGTATT
*
61005 TTTATTGAATGGATGGTTAGTATT
1 TTTATTG-ATGGATGATTAGTATT
61029 TT
1 TT
61031 CCATGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
23 9 0.41
24 6 0.27
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.55
Consensus pattern (23 bp):
TTTATTGATGGATGATTAGTATT
Found at i:67493 original size:20 final size:20
Alignment explanation
Indices: 67465--67502 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
67455 ATTTTGTAAA
*
67465 AAATTATCCCCAATGGCTCC
1 AAATCATCCCCAATGGCTCC
67485 AAATCATCCCCAATGGCT
1 AAATCATCCCCAATGGCT
67503 AGAAACATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.11, T:0.24
Consensus pattern (20 bp):
AAATCATCCCCAATGGCTCC
Found at i:71465 original size:15 final size:15
Alignment explanation
Indices: 71445--71485 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
71435 CATCCTTAAA
71445 AATAATTTATTACTT
1 AATAATTTATTACTT
71460 AATAATTTATTACTT
1 AATAATTTATTACTT
71475 AATAATTTATT
1 AATAATTTATT
71486 TAAATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
AATAATTTATTACTT
Found at i:71480 original size:18 final size:18
Alignment explanation
Indices: 71439--71480 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 18
71429 TGCTAACATC
*
71439 CTTAAAAATAATTTATTA
1 CTTAATAATAATTTATTA
71457 C-T--TAATAATTTATTA
1 CTTAATAATAATTTATTA
71472 CTTAATAAT
1 CTTAATAAT
71481 TTATTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
15 13 0.65
16 1 0.05
17 1 0.05
18 5 0.25
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (18 bp):
CTTAATAATAATTTATTA
Done.