Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000004.1 Hibiscus syriacus cultivar Beakdansim tig00000010_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: 95223
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5045 original size:2 final size:2
Alignment explanation
Indices: 5038--5065 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5028 AAGATTCCAA
5038 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
5066 TACTGCTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6664 original size:17 final size:17
Alignment explanation
Indices: 6642--6699 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
6632 ACCAAAAATT
6642 AATAATAATATAATTAA
1 AATAATAATATAATTAA
6659 AATAATTACAT-TAATTAA
1 AATAA-TA-ATATAATTAA
* *
6677 AA-AATTAGATAA-TAA
1 AATAATAATATAATTAA
6692 TAATAATA
1 -AATAATA
6700 CTAACAAGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
15 4 0.12
16 6 0.18
17 10 0.30
18 11 0.33
19 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
AATAATAATATAATTAA
Found at i:6671 original size:14 final size:15
Alignment explanation
Indices: 6638--6698 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 15
6628 AAAGACCAAA
6638 AATTAATAATAATAT
1 AATTAATAATAATAT
6653 AATTAA-AATAAT-T
1 AATTAATAATAATAT
*
6666 ACATTAAT--TAA-AA
1 A-ATTAATAATAATAT
6679 AATTAGATAATAATAAT
1 AATTA-ATAATAAT-AT
6696 AAT
1 AAT
6699 ACTAACAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
12 4 0.11
13 8 0.22
14 11 0.31
15 9 0.25
17 4 0.11
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
AATTAATAATAATAT
Found at i:7311 original size:31 final size:31
Alignment explanation
Indices: 7275--7340 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
7265 AAAAATTTTG
* *
7275 TGACAGAATATGTGGACCCGTCAGAAATTTC
1 TGACAGAATAGGTGAACCCGTCAGAAATTTC
* * *
7306 TGACAGAATAGGTGAATCTGTCAGAAATTTG
1 TGACAGAATAGGTGAACCCGTCAGAAATTTC
7337 TGAC
1 TGAC
7341 GGATCCACGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (31 bp):
TGACAGAATAGGTGAACCCGTCAGAAATTTC
Found at i:7365 original size:31 final size:31
Alignment explanation
Indices: 7325--7397 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
7315 AGGTGAATCT
* * *
7325 GTCAGAAATTTGTGACGGATCCACGTATTCC
1 GTCACAAATTTGTAACGGATCCACATATTCC
* *
7356 GTCACAAATTTGTAATGGGTCCACATATTCC
1 GTCACAAATTTGTAACGGATCCACATATTCC
*
7387 ATCACAAATTT
1 GTCACAAATTT
7398 TAAAAATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (31 bp):
GTCACAAATTTGTAACGGATCCACATATTCC
Found at i:14048 original size:37 final size:37
Alignment explanation
Indices: 13998--14076 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
13988 AGGTACTCAA
13998 ATCGTCCTTGATGTCGCCCCCTTGGGCTAGCTAGACC
1 ATCGTCCTTGATGTCGCCCCCTTGGGCTAGCTAGACC
14035 ATCGTCCTTGATGTCGCCCCCTTGGGCTAGCTAGACC
1 ATCGTCCTTGATGTCGCCCCCTTGGGCTAGCTAGACC
14072 ATCGT
1 ATCGT
14077 TCCTCACCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.14, C:0.34, G:0.24, T:0.28
Consensus pattern (37 bp):
ATCGTCCTTGATGTCGCCCCCTTGGGCTAGCTAGACC
Found at i:16888 original size:6 final size:6
Alignment explanation
Indices: 16877--16915 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
16867 TAACGGTAAG
16877 CTCACC CTCACC CTCACC CTCACC CTCACC CTCACC CTC
1 CTCACC CTCACC CTCACC CTCACC CTCACC CTCACC CTC
16916 TCTTTCTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.67, G:0.00, T:0.18
Consensus pattern (6 bp):
CTCACC
Found at i:25935 original size:20 final size:19
Alignment explanation
Indices: 25910--25966 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 19
25900 TTACTACAAC
25910 ATGAAACTAAATGACTATAA
1 ATGAAACTAAATG-CTATAA
*
25930 ATGAAACTAAATGCCTCTAA
1 ATGAAACTAAATG-CTATAA
25950 ATGAAACTAAATGCTAT
1 ATGAAACTAAATGCTAT
25967 GACATGGGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (19 bp):
ATGAAACTAAATGCTATAA
Found at i:25940 original size:10 final size:10
Alignment explanation
Indices: 25910--25962 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
25900 TTACTACAAC
25910 ATGAAACTAA
1 ATGAAACTAA
*
25920 ATGACTA-TAA
1 ATGA-AACTAA
25930 ATGAAACTAA
1 ATGAAACTAA
***
25940 ATGCCTCTAA
1 ATGAAACTAA
25950 ATGAAACTAA
1 ATGAAACTAA
25960 ATG
1 ATG
25963 CTATGACATG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
9 1 0.03
10 31 0.94
11 1 0.03
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (10 bp):
ATGAAACTAA
Found at i:36094 original size:15 final size:15
Alignment explanation
Indices: 36076--36104 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
36066 CTGGGCGAGT
36076 GGATGTGGGGCGGGC
1 GGATGTGGGGCGGGC
36091 GGATGTGGGGCGGG
1 GGATGTGGGGCGGG
36105 TAATGTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.10, G:0.69, T:0.14
Consensus pattern (15 bp):
GGATGTGGGGCGGGC
Found at i:36329 original size:9 final size:8
Alignment explanation
Indices: 36299--36327 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
36289 GCCCAGAGAA
36299 TTTTTATT
1 TTTTTATT
36307 TTTTTATT
1 TTTTTATT
36315 TTTTTATT
1 TTTTTATT
36323 TTTTT
1 TTTTT
36328 TACTTTACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTATT
Found at i:39000 original size:20 final size:19
Alignment explanation
Indices: 38970--39026 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
38960 ATATCAATAT
38970 TAAATAATAAAATTATTTCAA
1 TAAA-AATAAAATTATTT-AA
* * *
38991 TACAAATAAACTAATTTAA
1 TAAAAATAAAATTATTTAA
*
39010 TAAAAATTAAATTATTT
1 TAAAAATAAAATTATTT
39027 TTATATGATG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 15 0.52
20 11 0.38
21 3 0.10
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAAATAAAATTATTTAA
Found at i:43017 original size:43 final size:43
Alignment explanation
Indices: 42956--43299 Score: 351
Period size: 43 Copynumber: 8.0 Consensus size: 43
42946 TTATAAGCGT
42956 CGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATAAAAACGC
1 CGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATAAAAACGC
**** * *
42999 CGCAATAGGTGTTGATATTTAGTATTGTTTTTCAGAAAAACGT
1 CGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATAAAAACGC
43042 CGCAATAGGTGTTGATATTTAGCGGCGTTTGTT-ATAAAAACGC
1 CGCAATAGGTGTTGATATTTAGCGGCGTTT-TTCATAAAAACGC
* *
43085 CGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACGT
1 CGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATAAAAACGC
* * * * *
43128 CGCAATAGGTGTTAATATTTAGCAGCGTTTTTCAGACAAATGC
1 CGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATAAAAACGC
* * *
43171 CGCAATAGGT-TATGATGTTTAGCGGCATTTTTCGCT-AAAACGC
1 CGCAATAGGTGT-TGATATTTAGCGGCGTTTTTC-ATAAAAACGC
* * * * * *
43214 CGTAGTAGGTGTTGATGTTTTGC-GCGTTTTT--TCACAAACGT
1 CGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAT-AAAAACGC
* * * * *
43255 CGCAGTAGGTATTGATGTTTTGCGGCGTTTCTGC-TAAAAACGC
1 CGCAATAGGTGTTGATATTTAGCGGCGTTT-TTCATAAAAACGC
43298 CG
1 CG
43300 GTACAAGTCT
Statistics
Matches: 251, Mismatches: 40, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.00
41 26 0.10
42 15 0.06
43 205 0.82
44 4 0.02
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (43 bp):
CGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATAAAAACGC
Found at i:50620 original size:16 final size:16
Alignment explanation
Indices: 50586--50620 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
50576 GCCAACAAAT
*
50586 AAATTGAAACACCATA
1 AAATTGAAACACCACA
*
50602 AAATTGAAACACCGCA
1 AAATTGAAACACCACA
50618 AAA
1 AAA
50621 GTAGGTAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (16 bp):
AAATTGAAACACCACA
Found at i:52105 original size:38 final size:39
Alignment explanation
Indices: 52030--52109 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 39
52020 AACTATTACG
* * *
52030 GCGTTTATTACGAAAATGCCATTAACGGAGAAAACAATT
1 GCGTTTATTACGAAAAAGCCACTAAAGGAGAAAACAATT
*
52069 GCGTTTATTAC-AAAAAGCCACTAAAGGAGAATACAATT
1 GCGTTTATTACGAAAAAGCCACTAAAGGAGAAAACAATT
52107 GCG
1 GCG
52110 GCGTTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 26 0.70
39 11 0.30
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (39 bp):
GCGTTTATTACGAAAAAGCCACTAAAGGAGAAAACAATT
Found at i:52130 original size:41 final size:40
Alignment explanation
Indices: 51996--52134 Score: 128
Period size: 41 Copynumber: 3.5 Consensus size: 40
51986 GCAGCGTTTA
* *
51996 TATTA-AAAACGCCAC-AATGG-GATAAACTATTACGGCGTT
1 TATTACAAAACGCCACTAAAGGAGA-AAACAATT-CGGCGTT
* * *
52035 TATTACGAAAATGCCATTAACGGAGAAAACAATT--GCGTT
1 TATTAC-AAAACGCCACTAAAGGAGAAAACAATTCGGCGTT
* *
52074 TATTACAAAAAGCCACTAAAGGAGAATACAATTGCGGCGTT
1 TATTACAAAACGCCACTAAAGGAGAAAACAATT-CGGCGTT
52115 TATTTA-AAAACGCCACTAAA
1 TA-TTACAAAACGCCACTAAA
52135 TTACAACTCT
Statistics
Matches: 83, Mismatches: 9, Indels: 14
0.78 0.08 0.13
Matches are distributed among these distances:
38 23 0.28
39 16 0.19
41 28 0.34
42 14 0.17
43 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (40 bp):
TATTACAAAACGCCACTAAAGGAGAAAACAATTCGGCGTT
Found at i:52358 original size:137 final size:133
Alignment explanation
Indices: 52104--52408 Score: 346
Period size: 137 Copynumber: 2.3 Consensus size: 133
52094 GGAGAATACA
* * *
52104 ATTGCGGCGTTTATTTAAAAACGCCACTAAATTACAACTCTTTAGCGGCGTTTGGTAACAAACAC
1 ATTGCGGCGTTTATTAAAAAACGCCACTAAAGTACAACTCTTTAGCGGCATTTGGTAACAAACAC
*** * *
52169 CACTAAATAAAGAGTTTTTTACGGTGTTTGATTAAAAAGCGCCGCTATAAATGACAATATACAAC
66 CACTAAATAAAGAGTTTTTTACGGCAATTGATTAAAAAGCGCCGCTAGAAATGAAAATATACAAC
52234 TTT
131 TTT
* * * * *
52237 ATTGCGGTGTTTATGTAAAAAACGCCATTAAAGTACAACTCTTTAGTGGCATTTGGGGTTTAGAA
1 ATTGCGGCGTTTAT-TAAAAAACGCCACTAAAGTACAACTCTTTAGCGGCATTT--GG-TAACAA
* *
52302 ACACCACTAAATTAAGAGTATTTTT-CGGCAATTGATTTAAAAA-CGCCTCTAGAAATGAAAATA
62 ACACCACTAAATAAAGAGT-TTTTTACGGCAATTGA-TTAAAAAGCGCCGCTAGAAATGAAAATA
*
52365 TACAACCATT
125 TACAA-CTTT
* * *
52375 -TTGCGGCGTTGTTTTTAAAAACACCACTAAAGTA
1 ATTGCGGCGTT-TATTAAAAAACGCCACTAAAGTA
52409 TTATTTAACA
Statistics
Matches: 143, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
133 13 0.09
134 34 0.24
136 2 0.01
137 77 0.54
138 17 0.12
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (133 bp):
ATTGCGGCGTTTATTAAAAAACGCCACTAAAGTACAACTCTTTAGCGGCATTTGGTAACAAACAC
CACTAAATAAAGAGTTTTTTACGGCAATTGATTAAAAAGCGCCGCTAGAAATGAAAATATACAAC
TTT
Found at i:52536 original size:41 final size:41
Alignment explanation
Indices: 52479--52598 Score: 177
Period size: 41 Copynumber: 2.9 Consensus size: 41
52469 GTTTATACAA
* * *
52479 AAAAATGCCACTATTGATTAACACTATTGTGGTGTTTGTCT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
* *
52520 AAAAACGCCACTATTGATTAACACTATTACGGCATTTGTCT
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
* *
52561 AAAAACTCCACTATTGATTAATACTATTGCGGCGTTTG
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTG
52599 AGGAATAAAC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (41 bp):
AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTCT
Found at i:52649 original size:83 final size:82
Alignment explanation
Indices: 52486--52641 Score: 181
Period size: 82 Copynumber: 1.9 Consensus size: 82
52476 CAAAAAAATG
* * * *
52486 CCACTATTGATTAACACTATTGTGGTGTTTGTCTAAAAACGCCACTATTGATTAACACTATTACG
1 CCACTATTGATTAACACTATTGCGGCGTTTGACGAAAAACGCCACTATTGATTAACACTATTACG
*
52551 GCATTTGTCTAAAAACT
66 GCATTTGGCTAAAAACT
* * * *
52568 CCACTATTGATTAATACTATTGCGGCGTTTGAGGAATAAACGCCGCTA-T-ATGTATACTCTATT
1 CCACTATTGATTAACACTATTGCGGCGTTTGACGAA-AAACGCCACTATTGAT-TA-ACACTATT
*
52631 GCGGCATTTGG
63 ACGGCATTTGG
52642 GTTAAAACGC
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
81 2 0.03
82 33 0.54
83 26 0.43
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (82 bp):
CCACTATTGATTAACACTATTGCGGCGTTTGACGAAAAACGCCACTATTGATTAACACTATTACG
GCATTTGGCTAAAAACT
Found at i:55139 original size:22 final size:22
Alignment explanation
Indices: 55111--55162 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
55101 AAACTACCGT
55111 AAAACATGCCAAAAGGCATAAG
1 AAAACATGCCAAAAGGCATAAG
55133 AAAACATGCCAAAAGGCATAAG
1 AAAACATGCCAAAAGGCATAAG
55155 AAAACATG
1 AAAACATG
55163 TCATAAAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.56, C:0.17, G:0.17, T:0.10
Consensus pattern (22 bp):
AAAACATGCCAAAAGGCATAAG
Found at i:55568 original size:19 final size:19
Alignment explanation
Indices: 55544--55596 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
55534 GATATCAAGT
55544 CATAAGTATCAATACTTTC
1 CATAAGTATCAATACTTTC
55563 CATAAGTATCAATACTTTC
1 CATAAGTATCAATACTTTC
*
55582 CTTAAGTATCAATAC
1 CATAAGTATCAATAC
55597 CAAAAGTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (19 bp):
CATAAGTATCAATACTTTC
Found at i:56530 original size:2 final size:2
Alignment explanation
Indices: 56523--56560 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
56513 AGGTAGAATA
56523 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
56561 TCTTAACCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59145 original size:22 final size:22
Alignment explanation
Indices: 59099--59254 Score: 109
Period size: 21 Copynumber: 7.4 Consensus size: 22
59089 TTATGATAAC
59099 TTAT-TAT-TTTTTGAAAATATA
1 TTATATATATTTTT-AAAATATA
59120 -TATATATATTTTTAAAATATA
1 TTATATATATTTTTAAAATATA
* ** *
59141 TTATACA-ATCATGAAAA-ATA
1 TTATATATATTTTTAAAATATA
* * *
59161 GTATATTATATTTTTGAAA-ATG
1 TTATA-TATATTTTTAAAATATA
*
59183 TTATATA-ATTTTAAAAATATA
1 TTATATATATTTTTAAAATATA
59204 -TAT-TATATATTTTAAAA-ATA
1 TTATATATAT-TTTTAAAATATA
*
59224 TTATATA-ATTTTAAAAAGTATA
1 TTATATATATTTTTAAAA-TATA
*
59246 ATATATATA
1 TTATATATA
59255 AAATATAGTT
Statistics
Matches: 104, Mismatches: 18, Indels: 24
0.71 0.12 0.16
Matches are distributed among these distances:
19 2 0.02
20 33 0.32
21 35 0.34
22 33 0.32
23 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (22 bp):
TTATATATATTTTTAAAATATA
Found at i:59157 original size:42 final size:41
Alignment explanation
Indices: 59110--59228 Score: 134
Period size: 42 Copynumber: 2.9 Consensus size: 41
59100 TATTATTTTT
59110 TGAAAATATATATATATATTTTTAAAATATATTATACAATCA
1 TGAAAATATATATATATATTTTTAAAA-ATATTATACAATCA
* * * **
59152 TGAAAA-ATAGTATATTATATTTTTGAAAATGTTATATAATTT
1 TGAAAATATA-TATA-TATATTTTTAAAAATATTATACAATCA
*
59194 TAAAAATATATAT-TATATATTTTAAAAATATTATA
1 TGAAAATATATATATATAT-TTTTAAAAATATTATA
59229 TAATTTTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
40 5 0.08
41 17 0.26
42 28 0.43
43 15 0.23
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (41 bp):
TGAAAATATATATATATATTTTTAAAAATATTATACAATCA
Found at i:59253 original size:42 final size:41
Alignment explanation
Indices: 59107--59254 Score: 174
Period size: 41 Copynumber: 3.5 Consensus size: 41
59097 ACTTATTATT
* *
59107 TTTTGAAAATATATATATATATTTTTAAAATATATTATACAA
1 TTTTAAAAATATATATATATATTTTTAAAA-ATATTATATAA
* * * *
59149 TCATGAAAAATAGTATAT-TATATTTTTGAAAATGTTATATAA
1 T-TTTAAAAATA-TATATATATATTTTTAAAAATATTATATAA
59191 TTTTAAAAATATATAT-TATATATTTTAAAAATATTATATAA
1 TTTTAAAAATATATATATATAT-TTTTAAAAATATTATATAA
59232 TTTTAAAAAGTATAATATATATA
1 TTTTAAAAA-TAT-ATATATATA
59255 AAATATAGTT
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
40 10 0.11
41 34 0.38
42 14 0.16
43 23 0.26
44 9 0.10
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (41 bp):
TTTTAAAAATATATATATATATTTTTAAAAATATTATATAA
Found at i:60028 original size:22 final size:22
Alignment explanation
Indices: 60000--60045 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
59990 CAAGCTCGAG
60000 AGACCATTTCATCCCATGTAAA
1 AGACCATTTCATCCCATGTAAA
60022 AGACCATTTCATCCCATGTAAA
1 AGACCATTTCATCCCATGTAAA
60044 AG
1 AG
60046 CAGTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (22 bp):
AGACCATTTCATCCCATGTAAA
Found at i:61719 original size:6 final size:6
Alignment explanation
Indices: 61710--61747 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
61700 AAATTTATCC
* *
61710 TTTAGA TTTAGA TTTATA TTTAGA TTTATA TTTAGA TT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TT
61748 ATCACACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (6 bp):
TTTAGA
Found at i:61730 original size:12 final size:12
Alignment explanation
Indices: 61710--61747 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
61700 AAATTTATCC
*
61710 TTTAGATTTAGA
1 TTTATATTTAGA
61722 TTTATATTTAGA
1 TTTATATTTAGA
61734 TTTATATTTAGA
1 TTTATATTTAGA
61746 TT
1 TT
61748 ATCACACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TTTATATTTAGA
Found at i:61733 original size:18 final size:19
Alignment explanation
Indices: 61691--61743 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
61681 AATTAGAGCC
*
61691 TTAGACTTTAAATTTATCCT
1 TTAGA-TTTAAATTTATCAT
*
61711 TTAGATTTAGATTTAT-AT
1 TTAGATTTAAATTTATCAT
*
61729 TTAGATTTATATTTA
1 TTAGATTTAAATTTA
61744 GATTATCACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 15 0.50
19 10 0.33
20 5 0.17
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.55
Consensus pattern (19 bp):
TTAGATTTAAATTTATCAT
Found at i:62675 original size:15 final size:16
Alignment explanation
Indices: 62655--62688 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
62645 GACGACTCTT
*
62655 AACATTTCATAA-AAA
1 AACATTTCAAAAGAAA
62670 AACATTTCAAAAGAAA
1 AACATTTCAAAAGAAA
62686 AAC
1 AAC
62689 TCTAGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.21
Consensus pattern (16 bp):
AACATTTCAAAAGAAA
Found at i:67962 original size:20 final size:20
Alignment explanation
Indices: 67922--67964 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
67912 AATTTTAAAT
*
67922 ATTAAAATAAAAAAGTAATA
1 ATTAAAATAAAAAACTAATA
* *
67942 ATTAAAATACAAAACTTATA
1 ATTAAAATAAAAAACTAATA
67962 ATT
1 ATT
67965 TACTTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (20 bp):
ATTAAAATAAAAAACTAATA
Found at i:71100 original size:33 final size:33
Alignment explanation
Indices: 71055--71117 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
71045 TTTAAATAGG
71055 TTTTAGTATTTTA-ATTAAGTTTTAGGATATTATT
1 TTTTAGTATTTTATATT-AGTTTTAGG-TATTATT
*
71089 TTTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTTAGTATTTTATATTAGTTTTAGGTATT
71118 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 4 0.15
33 15 0.56
34 8 0.30
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.63
Consensus pattern (33 bp):
TTTTAGTATTTTATATTAGTTTTAGGTATTATT
Found at i:71180 original size:64 final size:63
Alignment explanation
Indices: 71098--71219 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 63
71088 TTTTTATATT
*
71098 TTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAA-TATTTTAATCAGGATTTAGAATA
1 TTATATTTGTTTTAGGTATTTTAGTTTAAATA-ATTTTAAGTATTTTAATCAGGATTTAGAATA
* * *
71161 TTATATTATTTTTTAGGTATTTTAGTTTAAATAATTTTAAGTGTTTTAATTAGGATTTA
1 TTATATT-TGTTTTAGGTATTTTAGTTTAAATAATTTTAAGTATTTTAATCAGGATTTA
71220 AGATGTTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
63 13 0.25
64 40 0.75
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (63 bp):
TTATATTTGTTTTAGGTATTTTAGTTTAAATAATTTTAAGTATTTTAATCAGGATTTAGAATA
Found at i:71917 original size:17 final size:18
Alignment explanation
Indices: 71870--71920 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
71860 CCTTCTATAT
* *
71870 TTATTACTATTAATATTTA
1 TTATTA-TATTATTTTTTA
71889 TTATTATATTATTTTTTA
1 TTATTATATTATTTTTTA
*
71907 TT-TTATTTTATTTT
1 TTATTATATTATTTT
71921 ATTTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 11 0.38
18 12 0.41
19 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTATATTATTTTTTA
Found at i:71924 original size:5 final size:5
Alignment explanation
Indices: 71889--71926 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
71879 TTAATATTTA
*
71889 TTATT ATATT ATT-TT TTATT TTATT TTATT TTATT TTA
1 TTATT TTATT -TTATT TTATT TTATT TTATT TTATT TTA
71927 ATATATCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 2 0.07
5 26 0.90
6 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:71924 original size:15 final size:15
Alignment explanation
Indices: 71883--71926 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
71873 TTACTATTAA
* *
71883 TATTTATTATTATAT
1 TATTTTTTATTTTAT
71898 TATTTTTTATTTTAT
1 TATTTTTTATTTTAT
71913 T-TTATTTTATTTTA
1 TATT-TTTTATTTTA
71927 ATATATCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 2 0.08
15 24 0.92
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TATTTTTTATTTTAT
Found at i:73744 original size:18 final size:18
Alignment explanation
Indices: 73721--73792 Score: 135
Period size: 18 Copynumber: 4.0 Consensus size: 18
73711 CATGCAATGT
*
73721 GTGACTTAAGAGCTTCAA
1 GTGACTTAGGAGCTTCAA
73739 GTGACTTAGGAGCTTCAA
1 GTGACTTAGGAGCTTCAA
73757 GTGACTTAGGAGCTTCAA
1 GTGACTTAGGAGCTTCAA
73775 GTGACTTAGGAGCTTCAA
1 GTGACTTAGGAGCTTCAA
73793 TTAATGTTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (18 bp):
GTGACTTAGGAGCTTCAA
Found at i:76973 original size:16 final size:16
Alignment explanation
Indices: 76948--76984 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
76938 AAAAAACTAA
*
76948 AGAATTTCACGATAGT
1 AGAATATCACGATAGT
76964 AGAATATCACGATAGT
1 AGAATATCACGATAGT
76980 AGAAT
1 AGAAT
76985 TTCTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (16 bp):
AGAATATCACGATAGT
Found at i:77315 original size:11 final size:11
Alignment explanation
Indices: 77296--77360 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 11
77286 AGGCAACCCA
*
77296 TTTCGTTTTAT
1 TTTCATTTTAT
77307 TTTCATTTTA-
1 TTTCATTTTAT
*
77317 TTT-ATTTCA-
1 TTTCATTTTAT
*
77326 TTCCA-TTTAT
1 TTTCATTTTAT
* *
77336 TTTAATTTTAA
1 TTTCATTTTAT
77347 TTTCATTTTAT
1 TTTCATTTTAT
77358 TTT
1 TTT
77361 TCTCTAAACA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
9 10 0.24
10 7 0.17
11 25 0.60
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTCATTTTAT
Found at i:79753 original size:19 final size:18
Alignment explanation
Indices: 79702--79750 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
79692 AATCTCTTTA
79702 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
79721 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
79740 ATTTTTTATTT
1 ATTTTTTATTT
79751 TAAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:82664 original size:28 final size:28
Alignment explanation
Indices: 82605--82664 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
82595 AAATTAATTT
* *
82605 GATGTCATTGCTTACATCAATTATTTTT
1 GATGTCATTGCTTACATCAATTATGTTA
*
82633 GATGTCATTGCTTACATTAATT-TAGTTA
1 GATGTCATTGCTTACATCAATTAT-GTTA
82661 GATG
1 GATG
82665 AAAATTAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.47
Consensus pattern (28 bp):
GATGTCATTGCTTACATCAATTATGTTA
Found at i:87326 original size:29 final size:29
Alignment explanation
Indices: 87293--87349 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
87283 TAAATTAATT
87293 TGATGTCATTGCTTACATCAATTTAGTTC
1 TGATGTCATTGCTTACATCAATTTAGTTC
87322 TGATGTCATTGCTTACATCAATTTAGTT
1 TGATGTCATTGCTTACATCAATTTAGTT
87350 ATGTGACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.46
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCAATTTAGTTC
Done.