Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000457.1 Hibiscus syriacus cultivar Beakdansim tig00000847_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: 84081
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:9196 original size:55 final size:55
Alignment explanation
Indices: 9128--9659 Score: 807
Period size: 55 Copynumber: 9.7 Consensus size: 55
9118 AGGTTCCCTA
* * * *
9128 CGATCGTTGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGGGCGGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
9183 CGATCGTTGAAGATTGTTCAAGTCTTATACTCTCTGAAGAAATAGGGGGGAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
9238 CGATAGTTGAAGATTGTTCGAGTCTTATACTCTCTGAGGAAATAGGGGGCGGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
9293 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGAGGGCAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * * *
9348 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGAGGCGGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
9403 CGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGACAGATG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
9458 CGATTGATGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
** *
9513 CGATCATTGAAGATTGTTCGAGTCTTATACTCTCTGACGAAATAGGGGGCAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
*
9568 CGATTGCTGAAGATTG-T-GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
*
9621 CGATTGTTAAAGATTGTTCGAGTCTTATACTCTCTGAAG
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAG
9660 GACTATGGAG
Statistics
Matches: 433, Mismatches: 42, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
53 49 0.11
54 2 0.00
55 382 0.88
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (55 bp):
CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
Found at i:18205 original size:3 final size:3
Alignment explanation
Indices: 18197--18224 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18187 AGATTACCAA
18197 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
18225 CGAATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18592 original size:15 final size:15
Alignment explanation
Indices: 18556--18596 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
18546 TAATAAATAA
18556 ACGAACATAAACGAAC
1 ACGAACAT-AACGAAC
* *
18572 ATGAACATAATGAAC
1 ACGAACATAACGAAC
18587 ACGAACATAA
1 ACGAACATAA
18597 ATGTTGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (15 bp):
ACGAACATAACGAAC
Found at i:19419 original size:24 final size:24
Alignment explanation
Indices: 19392--19439 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
19382 TAAATGAATA
*
19392 AACATAAACGAGCATAACCAAACG
1 AACATAAACGAACATAACCAAACG
*
19416 AACATAAACGAACATAACCGAACG
1 AACATAAACGAACATAACCAAACG
19440 TTCACGAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (24 bp):
AACATAAACGAACATAACCAAACG
Found at i:22219 original size:60 final size:59
Alignment explanation
Indices: 22131--22262 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 59
22121 TTTTTAAGGT
* * *
22131 AAAG-TACACAAATGTCCTCCGACTATAGGATATTGTTTTACTGAGTTCCCTAACTATTG
1 AAAGTTACA-AAATGTCCTCCGACTATAGGATATTGTTTTACTGAGTCCCCCAACTATTA
* * * ** * *
22190 AAAGTTACAAAATGATCCTCTGACTATAGGGTGTTGTTTTGTTGAGTCCCCCGATTATTA
1 AAAGTTACAAAATG-TCCTCCGACTATAGGATATTGTTTTACTGAGTCCCCCAACTATTA
22250 AAAGTTACAAAAT
1 AAAGTTACAAAAT
22263 AGTCATCTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 9 0.15
60 52 0.85
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (59 bp):
AAAGTTACAAAATGTCCTCCGACTATAGGATATTGTTTTACTGAGTCCCCCAACTATTA
Found at i:27757 original size:19 final size:19
Alignment explanation
Indices: 27733--27778 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
27723 GTGACAACTC
27733 TCATCCTCTTAAAATAATT
1 TCATCCTCTTAAAATAATT
27752 TCATCCTCTTAAAATAATT
1 TCATCCTCTTAAAATAATT
27771 TCATCCTC
1 TCATCCTC
27779 AAAATTCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (19 bp):
TCATCCTCTTAAAATAATT
Found at i:29050 original size:16 final size:16
Alignment explanation
Indices: 29029--29068 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
29019 CTTTATTGAA
29029 AGGATTTAAAAATAAG
1 AGGATTTAAAAATAAG
29045 AGGATTTAAAAATAAG
1 AGGATTTAAAAATAAG
29061 AGGATTTA
1 AGGATTTA
29069 TTTGATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.28
Consensus pattern (16 bp):
AGGATTTAAAAATAAG
Found at i:29835 original size:20 final size:20
Alignment explanation
Indices: 29810--29847 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29800 ACTGATTATC
*
29810 AGTATCGATACCTAAGGGGG
1 AGTATCGATACCGAAGGGGG
29830 AGTATCGATACCGAAGGG
1 AGTATCGATACCGAAGGG
29848 AAGGTATAGA
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:0.16, G:0.34, T:0.18
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGGG
Found at i:29854 original size:20 final size:20
Alignment explanation
Indices: 29810--29861 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
29800 ACTGATTATC
* *
29810 AGTATCGATACCTAAGGGGG
1 AGTATCGATACCGAAGGGAG
29830 AGTATCGATACCGAAGGGA-
1 AGTATCGATACCGAAGGGAG
*
29849 AGGTATAGATACC
1 A-GTATCGATACC
29862 ATTTTGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGAG
Found at i:30484 original size:58 final size:58
Alignment explanation
Indices: 30388--30949 Score: 881
Period size: 58 Copynumber: 9.7 Consensus size: 58
30378 ACTAAGTATA
* * * *
30388 CAAAAAGTTAAAAAAAATCATACTAAGTGTATGCATTTCCGTATTGGGCACTACGTGTG
1 CAAAAAGTT-AAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
* * *
30447 CAAAAAGTTAAGAAATTCATACGAAGTGTATGAATTTCTGTATTTGGCACTTCGTGTG
1 CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
* * *
30505 CTAAAAGTTAAGAAATCCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTG
1 CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
* *
30563 CAAAAAGTTAAGAAATCCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTG
1 CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
*
30621 CAAGAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
1 CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
** *
30679 CAAATTGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTG
1 CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
30737 CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
1 CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
* *
30795 TAAAAAGTTAAGAAATTCGTACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
1 CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
* * * * *
30853 CAAAAAGTTAAGAAATTCATATTAAATGTATGAATTTCTGTATTGGGCACTTTGTTTG
1 CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
* * *
30911 CAATATGTTAAGAGATTCATACTAAGTGTATGAATTTCC
1 CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCC
30950 ATATGGGAAA
Statistics
Matches: 466, Mismatches: 37, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
58 457 0.98
59 9 0.02
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (58 bp):
CAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTG
Found at i:34333 original size:13 final size:13
Alignment explanation
Indices: 34315--34339 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34305 TCTAATTTCC
34315 ATATAATCATATA
1 ATATAATCATATA
34328 ATATAATCATAT
1 ATATAATCATAT
34340 GCACTCACCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAATCATATA
Found at i:42004 original size:2 final size:2
Alignment explanation
Indices: 41997--42044 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
41987 ATTCTATCTC
41997 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
42039 AT AT AT
1 AT AT AT
42045 CACTCATTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47848 original size:60 final size:60
Alignment explanation
Indices: 47781--47896 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
47771 ATGAATTTAG
* * *
47781 GGATGAAA-ATAAAATATTAAAAAGTTTGAAGACTAATTTAGAATGAGGAG-CATAGTATAA
1 GGATGAAACA-AAAATATTAAAAAGTTTAAAAACTAATCTAGAATG-GGAGTCATAGTATAA
* *
47841 GGATGAAACAGAAATATTTAAAAGTTTAAAAACTAATCTAGAATGGGAGTCATAGT
1 GGATGAAACAAAAATATTAAAAAGTTTAAAAACTAATCTAGAATGGGAGTCATAGT
47897 TTAGGGACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 4 0.08
60 44 0.90
61 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (60 bp):
GGATGAAACAAAAATATTAAAAAGTTTAAAAACTAATCTAGAATGGGAGTCATAGTATAA
Found at i:48324 original size:14 final size:14
Alignment explanation
Indices: 48305--48332 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48295 ATCATAACAA
48305 AATTATATAACTAT
1 AATTATATAACTAT
48319 AATTATATAACTAT
1 AATTATATAACTAT
48333 TCTTTTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:48623 original size:21 final size:21
Alignment explanation
Indices: 48599--48639 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48589 AAAACAAAAA
*
48599 TCCCGGTTTTTCCCGGTTTTT
1 TCCCGATTTTTCCCGGTTTTT
**
48620 TCCCGATTTTTTTCGGTTTT
1 TCCCGATTTTTCCCGGTTTT
48640 CAGCCGATCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.24, G:0.17, T:0.56
Consensus pattern (21 bp):
TCCCGATTTTTCCCGGTTTTT
Found at i:48633 original size:12 final size:11
Alignment explanation
Indices: 48599--48631 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
48589 AAAACAAAAA
48599 TCCCGG-TTTT
1 TCCCGGTTTTT
48609 TCCCGGTTTTT
1 TCCCGGTTTTT
*
48620 TCCCGATTTTT
1 TCCCGGTTTTT
48631 T
1 T
48632 TCGGTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.03, C:0.27, G:0.15, T:0.55
Consensus pattern (11 bp):
TCCCGGTTTTT
Found at i:58462 original size:3 final size:3
Alignment explanation
Indices: 58454--58482 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
58444 TGTCTTCTCA
58454 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
58483 TTGCATCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:60148 original size:15 final size:16
Alignment explanation
Indices: 60120--60150 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
60110 TCAATGGGAA
60120 ATGGAATAAAATCTTT
1 ATGGAATAAAATCTTT
60136 ATGGAAT-AAATCTTT
1 ATGGAATAAAATCTTT
60151 CTTTCAGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (16 bp):
ATGGAATAAAATCTTT
Found at i:60783 original size:15 final size:14
Alignment explanation
Indices: 60765--60811 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
60755 ATCATATGAA
*
60765 ATGTGATAGAGAGCT
1 ATGTGATA-AGAACT
60780 ATGTGA-AAGAACT
1 ATGTGATAAGAACT
*
60793 ATGTGATATGAA-T
1 ATGTGATAAGAACT
60806 ATGTGA
1 ATGTGA
60812 ATGTGTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 18 0.62
14 5 0.17
15 6 0.21
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (14 bp):
ATGTGATAAGAACT
Found at i:67311 original size:24 final size:24
Alignment explanation
Indices: 67284--67358 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
67274 AATGATAAAT
67284 TGGTAAAATAAGATTACGAGCTTA
1 TGGTAAAATAAGATTACGAGCTTA
* ** *
67308 TGGT--ATTAA-ATGGCAAG-TATA
1 TGGTAAAATAAGATTACGAGCT-TA
*
67329 TTGGTAAAATAAGCTTACGAGCTTA
1 -TGGTAAAATAAGATTACGAGCTTA
67354 TGGTA
1 TGGTA
67359 TTAAATGGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 12
0.63 0.16 0.21
Matches are distributed among these distances:
20 1 0.03
21 7 0.19
22 8 0.22
24 13 0.36
25 6 0.17
26 1 0.03
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (24 bp):
TGGTAAAATAAGATTACGAGCTTA
Found at i:67335 original size:46 final size:46
Alignment explanation
Indices: 67282--67461 Score: 283
Period size: 46 Copynumber: 3.9 Consensus size: 46
67272 TAAATGATAA
*
67282 ATTGGTAAAATAAGATTACGAGCTTATGGTATTAAATGGCAAGTAT
1 ATTGGTAAAATAAGATTACGAGCTTATGGTATTAAATGGTAAGTAT
*
67328 ATTGGTAAAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTAT
1 ATTGGTAAAATAAGATTACGAGCTTATGGTATTAAATGGTAAGTAT
*
67374 ATTGGTAAAATAA-ACTTACGAGCTTATGGTATTAAACGGTAAGTAT
1 ATTGGTAAAATAAGA-TTACGAGCTTATGGTATTAAATGGTAAGTAT
* * *
67420 ATTGGTAAAATAAGCTTAAGAGCTTATGGGA-TAAATGGTAAG
1 ATTGGTAAAATAAGATTACGAGCTTATGGTATTAAATGGTAAG
67462 AGATTTTATA
Statistics
Matches: 124, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
45 10 0.08
46 114 0.92
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (46 bp):
ATTGGTAAAATAAGATTACGAGCTTATGGTATTAAATGGTAAGTAT
Found at i:75189 original size:51 final size:51
Alignment explanation
Indices: 75124--75277 Score: 290
Period size: 51 Copynumber: 3.0 Consensus size: 51
75114 GGTCTCCCTC
* *
75124 GCACACCCAGTACCCTACTCCAGTCCAGGGATATCCATCCCCACCTGCCAT
1 GCACACCCAATACCCTACTCCAGTCCAGGGATACCCATCCCCACCTGCCAT
75175 GCACACCCAATACCCTACTCCAGTCCAGGGATACCCATCCCCACCTGCCAT
1 GCACACCCAATACCCTACTCCAGTCCAGGGATACCCATCCCCACCTGCCAT
75226 GCACACCCAATACCCTACTCCAGTCCAGGGATACCCATCCCCACCTGCCAT
1 GCACACCCAATACCCTACTCCAGTCCAGGGATACCCATCCCCACCTGCCAT
75277 G
1 G
75278 TACGGAAGCA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 101 1.00
ACGTcount: A:0.25, C:0.46, G:0.13, T:0.16
Consensus pattern (51 bp):
GCACACCCAATACCCTACTCCAGTCCAGGGATACCCATCCCCACCTGCCAT
Found at i:76726 original size:181 final size:181
Alignment explanation
Indices: 76207--76867 Score: 862
Period size: 181 Copynumber: 3.7 Consensus size: 181
76197 GGTTTATGTT
* * * * *
76207 GATATTTTATAA-AACTATATCGATCCACATC-ATATAACAGATAAAAATATGACAAAATCGGTT
1 GATACTTTATAACAA-TGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTT
* * *
76270 TTGAAAAGACAAAACC-G-ATAAAGCGGCACC-AGATATATTGAAAGTGTCGATACTTTAATATA
65 CT-AAAGGACAAAACCGGTATAGAGC-G-ACCGA-ATATATTGAAAGTGTCGATACTTTAATATA
* * *
76332 AGTATCGAAACTTAGTGAATTTAAAAGAAAAGCAGTTTTAGCACCTATAAAGTGTC
126 AGTATCGAAACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTC
* * *
76388 GATACTTTATAACAATGTATCGATTCACAACGATATAACAGGTAAAAACTATAACAAAATCGGTC
1 GATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAA-TATGACAAAACCGGT-
* * * *
76453 TCTAAAGGACAAAATCGGTATAGAGTGACCG--GATATTGAAAG-GTCGATACTTTAATATAAAT
64 TCTAAAGGACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGT
* *
76515 ATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAGTGTC
129 ATCGAAACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTC
*
76568 GA-ACTTTATAACAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCGGTCT
1 GATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGT-T
76632 CTAAAGGACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTA
65 CTAAAGGACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTA
** *
76697 TCGGTACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGTGCCTATAAAGTGTC
130 TCGAAACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTC
* * *
76749 GATACTTTATAAAAATGTATTGATCCATAACGATATAACAGGTAAAAATATG--AAAACCGG-TC
1 GATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTTC
* * * * * *
76811 GAAATGA-AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
66 TAAAGGACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATA
76868 AGTACGCGTA
Statistics
Matches: 429, Mismatches: 40, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
177 46 0.11
178 50 0.12
179 43 0.10
180 87 0.20
181 104 0.24
182 62 0.14
183 28 0.07
184 4 0.01
185 5 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (181 bp):
GATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTTC
TAAAGGACAAAACCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATAAGTAT
CGAAACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTC
Found at i:78868 original size:22 final size:23
Alignment explanation
Indices: 78817--78872 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
78807 ACAATTTTGT
*
78817 TTTTTTTATATAAAATGATAATA
1 TTTTATTATATAAAATGATAATA
* *
78840 TAATTATTATATAAAATTATAA-A
1 T-TTTATTATATAAAATGATAATA
78863 TTTTATTATA
1 TTTTATTATA
78873 AATACAGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 17 0.61
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTTATTATATAAAATGATAATA
Found at i:79282 original size:21 final size:21
Alignment explanation
Indices: 79258--79300 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
79248 AAGACAATCA
79258 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
79279 AGAGTCGAAGGGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
79300 A
1 A
79301 TATATAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.35, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:79377 original size:33 final size:33
Alignment explanation
Indices: 79335--79401 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
79325 AAATAGATGG
79335 AGTGGTGAAAGAAGATGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGATGAGGTGTTGAGGGGTGA
*
79368 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGATGAGGTGTTGAGGGGTGA
79401 A
1 A
79402 CTTAAGATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.22
Consensus pattern (33 bp):
AGTGGTGAAAGAAGATGAGGTGTTGAGGGGTGA
Found at i:81176 original size:19 final size:19
Alignment explanation
Indices: 81152--81198 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
81142 AATGTAGGGT
81152 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
81171 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
81190 TAATTTTGT
1 TAATTTTGT
81199 GTGTGAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:81742 original size:12 final size:13
Alignment explanation
Indices: 81720--81748 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
81710 TTTTGTCCAG
81720 AATGAATGCCCAA
1 AATGAATGCCCAA
81733 AATG-ATGCCCAA
1 AATGAATGCCCAA
81745 AATG
1 AATG
81749 GTGAGCGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (13 bp):
AATGAATGCCCAA
Found at i:81864 original size:213 final size:203
Alignment explanation
Indices: 81551--82456 Score: 926
Period size: 198 Copynumber: 4.5 Consensus size: 203
81541 GTAAAAAGAT
* * *
81551 GTGTCGATACATTTATAAAAAGTATCGACCCCAAAAACATTGAAA-CCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* *
81615 GGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAAATTTGTAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
81680 ATCGACACTTTTGAAATTGATGTCGATAATTTTTGTCCAGAATGAATGCCCAAAATGATGCCCAA
131 ATCGACACTTTTGAAATTGATGTCGATAATTTTTGTCCAGAA-GAATG------A--ATGCCCAA
81745 AATGGTGAGCGCATAAA
187 AATGGTGAGCGCATAAA
* *
81762 GTGTCGATACATTTATAAAAAAGTATTGATCCCAGAAACATTGAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTAT-AAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAAT
** ** * * * *
81827 AGGTAAATTTACAATGTAACCGAAATAACTTTACCGATTTTATGAGAGAATATGTCTACATAATG
65 AGGTAAATTTGTAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATG
* * * * * *
81892 --T--ACACTTATGGAATTTG-TGTTGAT-ACTGTTGTCCAGAAG---GAATGCCCAAAAGGGTG
130 TATCGACACTT-TTGAAATTGATGTCGATAATTTTTGTCCAGAAGAATGAATGCCCAAAATGGTG
*
81948 -GCACATAAA
194 AGCGCATAAA
* * * *
81957 GTGTCGATATATTTTTTAAAAGTGTCGATCCCA-AAGACATCGAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAA-ACATCGAAACCCATAATTATAATGTAAT
* * *
82021 AAGT-AATTTGTAATGTAACCGGTAT-AATATACCGGTTTTATGTGAAAAATAGGTCTACATAAT
65 AGGTAAATTTGTAATGTAACCGGTATAAATATACCGATTTTATGTG-AGAATAGGTCTACATAAT
** * * * *
82084 GTATCGACAAATTTAAAATTGGTATCGATACTTTTTGTCC---AGAATGAATGCCCAAAATGGTG
129 GTATCGACACTTTTGAAATTGATGTCGATAATTTTTGTCCAGAAGAATGAATGCCCAAAATGGTG
*
82146 AACGCATAAA
194 AGCGCATAAA
* * * *
82156 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAGACATCG-AACCCATAATTATAATATAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * *
82220 GGTAATTTTGTAA--TAACCGGTATAAAAATAGCGATTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAAATTTGTAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
* *
82283 ATCGACAC-TTT--AATT-ATGCGTCGATACA-TTTTATCC---ACAATGAATGCCCAAAACAAT
131 ATCGACACTTTTGAAATTGAT--GTCGATA-ATTTTTGTCCAGAAGAATGAATGCCC--AA-AAT
*
82340 AGTGCA-CGCATAAA
190 GGTG-AGCGCATAAA
*
82354 GTGTCGATACATTTATAAAAAG--T--ATCCCAGAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * ** *
82415 GGT-AATTTTTCATGTAATTGGTATAAATATACCGGTTTTATG
66 GGTAAATTTGTAATGTAACCGGTATAAATATACCGATTTTATG
82457 CTTTTTGTCC
Statistics
Matches: 588, Mismatches: 79, Indels: 71
0.80 0.11 0.10
Matches are distributed among these distances:
192 15 0.03
193 37 0.06
194 68 0.12
195 73 0.12
196 47 0.08
197 47 0.08
198 98 0.17
199 53 0.09
200 1 0.00
204 1 0.00
207 1 0.00
208 12 0.02
209 12 0.02
210 7 0.01
211 17 0.03
212 26 0.04
213 73 0.12
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (203 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTTGTAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
ATCGACACTTTTGAAATTGATGTCGATAATTTTTGTCCAGAAGAATGAATGCCCAAAATGGTGAG
CGCATAAA
Found at i:82440 original size:393 final size:391
Alignment explanation
Indices: 81551--82456 Score: 1024
Period size: 393 Copynumber: 2.3 Consensus size: 391
81541 GTAAAAAGAT
*
81551 GTGTCGATACATTTATAAAAAGTATCGACCCCAAAAACATTGAAA-CCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTAT----CCC-AAAACATCGAAACCCATAATTATAATGTAATA
* * *
81615 GGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGT
61 GGTAATTTT-TAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTCTACATAATGT
** * *
81680 ATCGACACTTTTGAAATTGATGTCGATAATTTTTGTCCAGAATGAATGCCCAAAATGATGCCCAA
125 ATCGACAAATTTAAAATTGATATCGATAATTTTTGTCC--AATGAATG-----AA-GATGCCCAA
* * *
81745 AATGGTGAGCGCATAAAGTGTCGATACATTTATAAAAAAGTATTGATCCCAGAAACATTGAAACC
182 AATGGTGAACGCATAAAGTGTCGATACATTTATAAAAAAGTATCGATCCCAGAAACATCGAAACC
* ***
81810 CATAATTATAATGTAATAGGTAAATTTACAATGTAACCGAAATAACTTTACCGATTTTATGAGAG
247 CATAATTATAATATAATAGGTAAATTTACAA-GTAACCGAAATAAAAATACCGATTTTATGAGAG
* * * * *
81875 AATATGTCTACATAATGTACACTTATGGAATTTGTGTTGATACTGTTGTCCAGAAGGAATGCCCA
311 AATAGGTCTACATAATGTACACTTAT-GAATTTGCGTCGATACTGTTATCCACAAGGAATGCCCA
***
81940 AAAGGGTGGCACATAAA
375 AAACAATGGCACATAAA
* * *
81957 GTGTCGATATATTTTTTAAAAGTGTCGATCCCAAAGACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACA-TTTATAAAA-AGT--ATCCCAAA-ACATCGAAACCCATAATTATAATGTAATA
* *
82022 AGTAATTTGTAATGTAACCGGTAT-AATATACCGGTTTTATGTGAAAAATAGGTCTACATAATGT
61 GGTAATTTTTAATGTAACCGGTATAAATATACCGGTTTTATGTG-AAAATAGGTCTACATAATGT
* *
82086 ATCGACAAATTTAAAATTGGTATCGATACTTTTTGTCC-A-GAATG-A-ATGCCCAAAATGGTGA
125 ATCGACAAATTTAAAATTGATATCGATAATTTTTGTCCAATGAATGAAGATGCCCAAAATGGTGA
* * *
82147 ACGCATAAAGTGTCGATACATTT-TTAAAAAGTGTCGATCCCAGAGACATCG-AACCCATAATTA
190 ACGCATAAAGTGTCGATACATTTATAAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTA
* ** ** * *
82210 TAATATAATAGGTAATTTTGTAA-TAACCGGTATAAAAATAGCGATTTTATGTGAGAATAGGTCT
255 TAATATAATAGGTAAATTTACAAGTAACCGAAATAAAAATACCGATTTTATGAGAGAATAGGTCT
* *
82274 ACATAATGTATCGACACTT-T-AATTATGCGTCGATACATTTTATCCACAATGAATGCCCAAAAC
320 ACATAATG--T--ACACTTATGAATT-TGCGTCGATAC-TGTTATCCACAAGGAATGCCCAAAAC
82337 AATAGTGCACGCATAAA
379 AAT-G-GCA--CATAAA
*
82354 GTGTCGATACATTTATAAAAAGTATCCCAGAAACATCGAAACCCATGATTATAATGTAATAGGTA
1 GTGTCGATACATTTATAAAAAGTATCCCA-AAACATCGAAACCCATAATTATAATGTAATAGGTA
* **
82419 ATTTTTCATGTAATTGGTATAAATATACCGGTTTTATG
65 ATTTTTAATGTAACCGGTATAAATATACCGGTTTTATG
82457 CTTTTTGTCC
Statistics
Matches: 430, Mismatches: 51, Indels: 50
0.81 0.10 0.09
Matches are distributed among these distances:
390 41 0.10
391 4 0.01
392 41 0.10
393 99 0.23
394 64 0.15
395 5 0.01
396 9 0.02
397 16 0.04
402 5 0.01
403 1 0.00
405 21 0.05
406 86 0.20
407 34 0.08
408 2 0.00
410 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (391 bp):
GTGTCGATACATTTATAAAAAGTATCCCAAAACATCGAAACCCATAATTATAATGTAATAGGTAA
TTTTTAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTCTACATAATGTATCGAC
AAATTTAAAATTGATATCGATAATTTTTGTCCAATGAATGAAGATGCCCAAAATGGTGAACGCAT
AAAGTGTCGATACATTTATAAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATAT
AATAGGTAAATTTACAAGTAACCGAAATAAAAATACCGATTTTATGAGAGAATAGGTCTACATAA
TGTACACTTATGAATTTGCGTCGATACTGTTATCCACAAGGAATGCCCAAAACAATGGCACATAA
A
Done.