Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005604.1 Hibiscus syriacus cultivar Beakdansim tig00013036_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: 76814
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3977 original size:76 final size:78
Alignment explanation
Indices: 3873--4023 Score: 195
Period size: 76 Copynumber: 2.0 Consensus size: 78
3863 ATATAGTAGG
*
3873 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAAT-TGATA-TTAATTTGGAA-TAAT
1 TAAACATTAAAAGAATGTAATTTAGATTACAACTC-TTTAATGT-ATATTTAATTT-GAATTAAT
3935 T-AATAAGATTTTAAA
63 TAAATAAGATTTTAAA
** * *
3950 TAAACATT-AAAGGGTGTAATTTAGATTATAAGTCTTTAATGTATATTTAATTTGAATTAATTAA
1 TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTAATGTATATTTAATTTGAATTAATTAA
4014 ATAAGATTTT
66 ATAAGATTTT
4024 TATTAATTCA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
75 12 0.18
76 34 0.52
77 19 0.29
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTAATGTATATTTAATTTGAATTAATTAA
ATAAGATTTTAAA
Found at i:11988 original size:10 final size:10
Alignment explanation
Indices: 11973--12035 Score: 74
Period size: 10 Copynumber: 6.2 Consensus size: 10
11963 TATTTTTTTC
11973 AAAAAAACAA
1 AAAAAAACAA
11983 AAAAAAACAA
1 AAAAAAACAA
**
11993 AAAAAGGC-A
1 AAAAAAACAA
*
12002 AAAAAACCAA
1 AAAAAAACAA
12012 AAAAAAACCAA
1 AAAAAAA-CAA
12023 AAAAAAACCAA
1 AAAAAAA-CAA
12034 AA
1 AA
12036 TTTCAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
9 7 0.15
10 23 0.50
11 16 0.35
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:11989 original size:11 final size:10
Alignment explanation
Indices: 11973--12035 Score: 67
Period size: 11 Copynumber: 6.3 Consensus size: 10
11963 TATTTTTTTC
11973 AAAAAAA-CA
1 AAAAAAACCA
*
11982 AAAAAAAACA
1 AAAAAAACCA
**
11992 AAAAAAGGC-
1 AAAAAAACCA
12001 AAAAAAACCAA
1 AAAAAAACC-A
12012 AAAAAAACCAA
1 AAAAAAACC-A
12023 AAAAAAACCA
1 AAAAAAACCA
12033 AAA
1 AAA
12036 TTTCAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
9 14 0.30
10 13 0.28
11 20 0.43
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAACCA
Found at i:19706 original size:32 final size:32
Alignment explanation
Indices: 19670--19777 Score: 135
Period size: 32 Copynumber: 3.4 Consensus size: 32
19660 GATTCTGTTG
*
19670 AGACCATGCCCAGCTGCAAGCTGATCCTGTCT
1 AGACCACGCCCAGCTGCAAGCTGATCCTGTCT
***
19702 AGACCATATCCAGCTGCAAGCTGATCCTGTCT
1 AGACCACGCCCAGCTGCAAGCTGATCCTGTCT
* * * *
19734 GGACCACGTCCAGCTGTAAGCTGATCTTGTCT
1 AGACCACGCCCAGCTGCAAGCTGATCCTGTCT
*
19766 AGTCCACGCCCA
1 AGACCACGCCCA
19778 ACTACCCAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.23
Consensus pattern (32 bp):
AGACCACGCCCAGCTGCAAGCTGATCCTGTCT
Found at i:25636 original size:32 final size:32
Alignment explanation
Indices: 25600--25660 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
25590 CCTGGGTCAT
*
25600 CTGATTCTATCGGGACCACGTCCAGCTACAAG
1 CTGATCCTATCGGGACCACGTCCAGCTACAAG
* * *
25632 CTGATCCTATCTGGTCCACGTCTAGCTAC
1 CTGATCCTATCGGGACCACGTCCAGCTAC
25661 CCAGGAGGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (32 bp):
CTGATCCTATCGGGACCACGTCCAGCTACAAG
Found at i:29307 original size:5 final size:5
Alignment explanation
Indices: 29296--29329 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
29286 ATCAAAGATA
* *
29296 AAAAT TAAAT TAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
29330 ATTGAATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:29314 original size:16 final size:16
Alignment explanation
Indices: 29293--29346 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
29283 TATATCAAAG
*
29293 ATAAAAATTAAATTAA
1 ATAAAAATTAAATAAA
*
29309 AT-AAAATAAAATAAA
1 ATAAAAATTAAATAAA
* * *
29324 ATAAAAATTGAATGAG
1 ATAAAAATTAAATAAA
29340 ATAAAAA
1 ATAAAAA
29347 AATTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (16 bp):
ATAAAAATTAAATAAA
Found at i:30092 original size:33 final size:33
Alignment explanation
Indices: 30055--30139 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 33
30045 TTAGTTTGTG
30055 CAATAAATTAAAATGTTACTAA-GTTAGTAAT-AA
1 CAATAAATTAAAA-GTTACTAATGTTAGT-ATGAA
* *
30088 CAATAAAAATCAAAAGTTAGTAATGTTAGTATGAA
1 CAAT--AAATTAAAAGTTACTAATGTTAGTATGAA
*
30123 CAATAAAATAAAAGTTA
1 CAATAAATTAAAAGTTA
30140 GAATATTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
33 15 0.34
34 9 0.20
35 20 0.45
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (33 bp):
CAATAAATTAAAAGTTACTAATGTTAGTATGAA
Found at i:30118 original size:35 final size:32
Alignment explanation
Indices: 30055--30182 Score: 102
Period size: 32 Copynumber: 3.9 Consensus size: 32
30045 TTAGTTTGTG
* *
30055 CAATAAATTAAAATGTTACTAAGTTAGTAAT-AA
1 CAATAAAATAAAA-GTTAGTAAGTTAGT-ATGAA
30088 CAATAAAAATCAAAAGTTAGTAATGTTAGTATGAA
1 CAAT-AAAAT-AAAAGTTAGTAA-GTTAGTATGAA
* *
30123 CAATAAAATAAAAGTTAG-AATATTAAT-TCGAA
1 CAATAAAATAAAAGTTAGTAA-GTTAGTAT-GAA
* *
30155 CGATAAAATAAATGTTAG-AATGTTAGTA
1 CAATAAAATAAAAGTTAGTAA-GTTAGTA
30183 GATTAGTGAC
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
31 1 0.01
32 33 0.41
33 13 0.16
34 18 0.22
35 16 0.20
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.30
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGTAAGTTAGTATGAA
Found at i:34550 original size:5 final size:5
Alignment explanation
Indices: 34540--34590 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
34530 AATAGTTATC
34540 TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA
1 TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA TTAGA
34590 T
1 T
34591 CGGAGATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (5 bp):
TTAGA
Found at i:35263 original size:2 final size:2
Alignment explanation
Indices: 35256--35307 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
35246 ATATAGGCTG
35256 AT AT AT AT AT AT AT AT AT AT -T 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
35297 AT AT AT AT AT A
1 AT AT AT AT AT A
35308 GCTTGACATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37758 original size:31 final size:29
Alignment explanation
Indices: 37665--37942 Score: 140
Period size: 29 Copynumber: 9.4 Consensus size: 29
37655 AACACTTATT
*
37665 AAATATATTTTACTT-TTATTTTAAATTAA
1 AAATATATTTTA-TTCTTATTTTAATTTAA
* *
37694 AAATATTTTTTAATCTTATTTTAATTTAA
1 AAATATATTTTATTCTTATTTTAATTTAA
* *
37723 AAATATATTTTATTCTTATCTTAATTTTTAC
1 AAATATATTTTATTCTTATTTTAA--TTTAA
* ** * *
37754 AAATATATTTAATTAAATCCACATATTAAAATTAA
1 AAATATA-TT--TT--ATTCTTAT-TTTAATTTAA
* ** * * *
37789 AAA-A-AATACATTC-TATCTTAAATTATT
1 AAATATATTTTATTCTTATTTTAATTTA-A
37816 AAATATATTTTATT-TTAATTTTAATTTAA
1 AAATATATTTTATTCTT-ATTTTAATTTAA
* **
37845 AAATATATTTTAATCTTATTTTAGCTT-A
1 AAATATATTTTATTCTTATTTTAATTTAA
* * * * *
37873 AAATGTATTTTTATTTTTATGTTAACTTATG
1 AAATATA-TTTTATTCTTATTTTAATTTA-A
*
37904 AAATATATTTGACTT-TTATTTTAATTT-A
1 AAATATATTTTA-TTCTTATTTTAATTTAA
*
37932 AGATATATTTT
1 AAATATATTTT
37943 TAAAAGTTAA
Statistics
Matches: 186, Mismatches: 44, Indels: 39
0.69 0.16 0.14
Matches are distributed among these distances:
26 7 0.04
27 5 0.03
28 21 0.11
29 88 0.47
30 25 0.13
31 19 0.10
32 3 0.02
33 1 0.01
34 3 0.02
35 6 0.03
36 5 0.03
37 3 0.02
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTTAATTTAA
Found at i:37923 original size:59 final size:58
Alignment explanation
Indices: 37816--37944 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 58
37806 TTAAATTATT
* * * *
37816 AAATATA-TTTTATTTTAATTTTAATTTAAAAATATATTTTAATCTTATTTTAGCTTA
1 AAATATATTTTTATTTTAATGTTAACTTAAAAATATATTTGAATCTTATTTTAACTTA
* * * * * *
37873 AAATGTATTTTTATTTTTATGTTAACTTATGAAATATATTTGACTTTTATTTTAATTTA
1 AAATATATTTTTATTTTAATGTTAACTTA-AAAATATATTTGAATCTTATTTTAACTTA
*
37932 AGATATATTTTTA
1 AAATATATTTTTA
37945 AAAGTTAATA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
57 6 0.10
58 18 0.31
59 34 0.59
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.57
Consensus pattern (58 bp):
AAATATATTTTTATTTTAATGTTAACTTAAAAATATATTTGAATCTTATTTTAACTTA
Found at i:37970 original size:2 final size:2
Alignment explanation
Indices: 37963--37987 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37953 TATAAGAATA
37963 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 A
37988 AAGTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38010 original size:24 final size:24
Alignment explanation
Indices: 37983--38036 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
37973 ATATATATAT
37983 ATATAAAGTTAAAATAAGAT-TAAA
1 ATATAAAGTTAAAATAA-ATATAAA
** *
38007 ATAT-ACTTTTAAATAAATATAAA
1 ATATAAAGTTAAAATAAATATAAA
38030 ATATAAA
1 ATATAAA
38037 ATATATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 2 0.08
23 17 0.71
24 5 0.21
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (24 bp):
ATATAAAGTTAAAATAAATATAAA
Found at i:38027 original size:42 final size:41
Alignment explanation
Indices: 37943--38039 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 41
37933 GATATATTTT
* * * *
37943 TAAAAGTTAATATAAGAATAATATATATATATATATATATA
1 TAAAAGTTAAAATAAGAATAAAATATATATATAAATAAATA
* *
37984 TATAAAGTTAAAATAAGATTAAAATATACT-TTTAAATAAATA
1 TA-AAAGTTAAAATAAGAATAAAATATA-TATATAAATAAATA
38026 TAAAA-TATAAAATA
1 TAAAAGT-TAAAATA
38040 TATTTTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
40 1 0.02
41 12 0.26
42 33 0.70
43 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (41 bp):
TAAAAGTTAAAATAAGAATAAAATATATATATAAATAAATA
Found at i:38069 original size:19 final size:19
Alignment explanation
Indices: 38045--38083 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
38035 AAATATATTT
38045 TTTAATGTTA-AGATGTGAA
1 TTTAATGTTATA-ATGTGAA
*
38064 TTTAATTTTATAATGTGAA
1 TTTAATGTTATAATGTGAA
38083 T
1 T
38084 CTAAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (19 bp):
TTTAATGTTATAATGTGAA
Found at i:45485 original size:26 final size:26
Alignment explanation
Indices: 45456--45507 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
45446 CAAAATAAAA
*
45456 TAGTATAGTA-AAATTATTTCAGTTTT
1 TAGTATAGTAGAAA-TATTTCACTTTT
*
45482 TAGTTTAGTAGAAATATTTCACTTTT
1 TAGTATAGTAGAAATATTTCACTTTT
45508 GAAGAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.50
Consensus pattern (26 bp):
TAGTATAGTAGAAATATTTCACTTTT
Found at i:57769 original size:27 final size:27
Alignment explanation
Indices: 57739--57794 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
57729 ATCTGAATGT
57739 TAGAATAAAGCTAGGGATTTGTGATTA
1 TAGAATAAAGCTAGGGATTTGTGATTA
57766 TAGAATAAAGCTAGGGATTTGTGATTA
1 TAGAATAAAGCTAGGGATTTGTGATTA
57793 TA
1 TA
57795 ATAAAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.34
Consensus pattern (27 bp):
TAGAATAAAGCTAGGGATTTGTGATTA
Found at i:58140 original size:37 final size:38
Alignment explanation
Indices: 58085--58170 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
58075 GTACCGTTGC
** * * *
58085 CATCCCCGTAACCTGTAATTTTAGGAATTGTCGTTTTT
1 CATCCCCGTCCCCCGTAATTTCAAGAATTGTCGTTTTT
58123 CAT-CCCGTCCCCCGTAATTTCAAGAATTGTCGTTTTT
1 CATCCCCGTCCCCCGTAATTTCAAGAATTGTCGTTTTT
58160 CATCCCCGTCC
1 CATCCCCGTCC
58171 TCGTATCCGT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 32 0.76
38 10 0.24
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (38 bp):
CATCCCCGTCCCCCGTAATTTCAAGAATTGTCGTTTTT
Found at i:59948 original size:108 final size:108
Alignment explanation
Indices: 59759--59980 Score: 417
Period size: 108 Copynumber: 2.1 Consensus size: 108
59749 GTTCCTCTTC
59759 ACTTACCATTGATTTTGGCCATTGTTACCTTTCTGAACTTTTTGATCATTAGTTCTTTGAAAACA
1 ACTTACCATTGATTTTGGCCATTGTTACCTTTCTGAACTTTTTGATCATTAGTTCTTTGAAAACA
* *
59824 ATACAAGCTCAATCGGCTTTGATTCTTGATAGCGGGATGACAT
66 AGACAAGCTCAATCGGCTTTGATTCTTGATAGCCGGATGACAT
59867 ACTTACCATTGATTTTGGCCATTGTTACCTTTCTGAACTTTTTGATCATTAGTTCTTTGAAAACA
1 ACTTACCATTGATTTTGGCCATTGTTACCTTTCTGAACTTTTTGATCATTAGTTCTTTGAAAACA
*
59932 AGACAAGCTCATTCGGCTTTGATTCTTGATAGCCGGATGACAT
66 AGACAAGCTCAATCGGCTTTGATTCTTGATAGCCGGATGACAT
59975 ACTTAC
1 ACTTAC
59981 AGAACCTCTA
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 111 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (108 bp):
ACTTACCATTGATTTTGGCCATTGTTACCTTTCTGAACTTTTTGATCATTAGTTCTTTGAAAACA
AGACAAGCTCAATCGGCTTTGATTCTTGATAGCCGGATGACAT
Found at i:70304 original size:42 final size:42
Alignment explanation
Indices: 70235--70536 Score: 317
Period size: 42 Copynumber: 7.3 Consensus size: 42
70225 AATTGTGCCA
* * * * *
70235 TTTATTACAAAAACATCGGTAAGGTGCATGACTATAGCGACG
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* * * * *
70277 TTTATTACAAAAGCGCTGCTAAAGTGCATGATTATTGCGGTG
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* * *
70319 TTTATTACAAAAATACCGCTAAAGTGCATGATTATTGCAGCG
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* *
70361 TTTA-T-CAAAAACACCGCTAAGGTGCATGACTATTGTGGCG
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* * * * *
70401 TTTACTGCAAAAACATCACTAAAGTGCATGACTATTGCGGTG
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* * **
70443 TTTATTAC-AAAACACCACTAAA-TGCATGATTATTGCGGTA
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
* * * *
70483 TTTA-TAAAAAAATACCGCTAAAGTGCATAACTATTGCGGCA
1 TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
70524 TTTATTACAAAAA
1 TTTATTACAAAAA
70537 TACTGCCTTA
Statistics
Matches: 217, Mismatches: 38, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.01
40 66 0.30
41 34 0.16
42 115 0.53
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (42 bp):
TTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCG
Found at i:70404 original size:82 final size:81
Alignment explanation
Indices: 70233--70528 Score: 279
Period size: 82 Copynumber: 3.6 Consensus size: 81
70223 ACAATTGTGC
* * * * * * * *
70233 CATTTATTACAAAAACATCGGTAAGGTGCATGACTATAGCGACGTTTATTACAAAAGCGCTGCTA
1 CATTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTA-T-CAAAAACACCGCT-
70298 AAGTGCATGATTATTGCGG
63 AAGTGCATGATTATTGCGG
** * * *
70317 TGTTTATTACAAAAATACCGCTAAAGTGCATGATTATTGCAGCGTTTATCAAAAACACCGCTAAG
1 CATTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATCAAAAACACCGCTAA-
* *
70382 GTGCATGACTATTGTGG
65 GTGCATGATTATTGCGG
* * * * * * * *
70399 CGTTTACTGCAAAAACATCACTAAAGTGCATGACTATTGCGGTGTTTATTACAAAACACCACTAA
1 CATTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATCA-AAAACACCGCTAA
*
70464 ATGCATGATTATTGCGG
65 GTGCATGATTATTGCGG
* * * * *
70481 TATTTA-TAAAAAAATACCGCTAAAGTGCATAACTATTGCGGCATTTAT
1 CATTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTAT
70529 TACAAAAATA
Statistics
Matches: 171, Mismatches: 39, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
81 36 0.21
82 84 0.49
83 13 0.08
84 38 0.22
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (81 bp):
CATTTATTACAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATCAAAAACACCGCTAAG
TGCATGATTATTGCGG
Found at i:71507 original size:37 final size:37
Alignment explanation
Indices: 71460--71716 Score: 261
Period size: 37 Copynumber: 6.8 Consensus size: 37
71450 AAGTTTTTGA
* *
71460 ATAT-ATATATAATATTTTGAAAA-AATTGGAAAATAT
1 ATATAATATATAAT-TTTTGAAAACATTTTGAAAATAT
**
71496 ATATAATATATAGCTTTTGAAAACATTTTGAAAACCTAT
1 ATATAATATATAATTTTTGAAAACATTTTGAAAA--TAT
**
71535 ATATATATAATATATAGTTTTTG-AAATTTTTTGAAAATAT
1 ATATA-AT-ATATA-A-TTTTTGAAAACATTTTGAAAATAT
*
71575 ATATAATATATAGTTTTTGAAAACATTTTGAAAAAAATAT
1 ATATAATATATAATTTTTGAAAACATTTTG---AAAATAT
*
71615 ATATAATATATAATTTTTGAAAACATTTTGAAAACAT
1 ATATAATATATAATTTTTGAAAACATTTTGAAAATAT
* * **
71652 ATATAATATATAGTTTTCGAAAACATTTTGAAAACGT
1 ATATAATATATAATTTTTGAAAACATTTTGAAAATAT
* *
71689 ATATATTATATAGA-TTTTGAAAAGATTT
1 ATATAATATATA-ATTTTTGAAAACATTT
71717 AAATGTATTT
Statistics
Matches: 188, Mismatches: 20, Indels: 25
0.81 0.09 0.11
Matches are distributed among these distances:
36 19 0.10
37 86 0.46
38 5 0.03
39 10 0.05
40 46 0.24
41 5 0.03
42 12 0.06
43 5 0.03
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (37 bp):
ATATAATATATAATTTTTGAAAACATTTTGAAAATAT
Found at i:71576 original size:79 final size:78
Alignment explanation
Indices: 71460--71700 Score: 321
Period size: 79 Copynumber: 3.1 Consensus size: 78
71450 AAGTTTTTGA
* *
71460 ATAT-ATATATAATATTTTGAAAA-AATTGGAAAATATATATAATATATAGCTTTTGAAAACATT
1 ATATAATATATAAT-TTTTGAAAACATTTTGAAAATATATATAATATATAG-TTTTGAAAACATT
71523 TTGAAAACCTATATAT
64 TTGAAAA-CTATATAT
* **
71539 ATATAATATATAGTTTTTG-AAATTTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTT
1 ATATAATATATAATTTTTGAAAACATTTTGAAAATATATATAATATATAG-TTTTGAAAACATTT
*
71603 TGAAAA--AAATAT
65 TGAAAACTATATAT
*
71615 ATATAATATATAATTTTTGAAAACATTTTGAAAACATATATAATATATAGTTTTCGAAAACATTT
1 ATATAATATATAATTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTT-GAAAACATTT
71680 TGAAAACGTATATATT
65 TGAAAAC-TATATA-T
71696 ATATA
1 ATATA
71701 GATTTTGAAA
Statistics
Matches: 143, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
76 27 0.19
77 43 0.30
78 3 0.02
79 52 0.36
80 12 0.08
81 6 0.04
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.41
Consensus pattern (78 bp):
ATATAATATATAATTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATTTT
GAAAACTATATAT
Found at i:71739 original size:5 final size:5
Alignment explanation
Indices: 71729--71788 Score: 56
Period size: 5 Copynumber: 12.6 Consensus size: 5
71719 ATGTATTTTA
* * *
71729 TATAT TATAT TGTACA TATAT TATAT TATAT TATA- -GTAT TATAT TATA-
1 TATAT TATAT TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT
71777 TATAT TAT-T TAT
1 TATAT TATAT TAT
71789 TATGGTTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
3 2 0.04
4 8 0.18
5 32 0.71
6 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:71754 original size:23 final size:24
Alignment explanation
Indices: 71727--71781 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
71717 AAATGTATTT
71727 TATATATTATATTGTACATATATTATA
1 TATATATTATA--GTA-ATATATTATA
*
71754 T-TATATTATAGTATTATATTATA
1 TATATATTATAGTAATATATTATA
71777 TATAT
1 TATAT
71782 TATTTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 10 0.38
24 6 0.23
26 9 0.35
27 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (24 bp):
TATATATTATAGTAATATATTATA
Found at i:71769 original size:34 final size:33
Alignment explanation
Indices: 71726--71791 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
71716 TAAATGTATT
*
71726 TTATATATTATATTGTACATA-TATTATATTATA
1 TTATATATTATATTATACATATTATT-TATTATA
*
71759 TTATAGTATTATATTATATATATTATTTATTAT
1 TTATA-TATTATATTATACATATTATTTATTAT
71792 GGTTTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 5 0.17
34 20 0.69
35 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (33 bp):
TTATATATTATATTATACATATTATTTATTATA
Found at i:71788 original size:13 final size:14
Alignment explanation
Indices: 71745--71788 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
71735 ATATTGTACA
71745 TATATTATATTATAT
1 TATA-TATATTATAT
*
71760 TATA-GTATTATAT
1 TATATATATTATAT
71773 TATATATATTAT-T
1 TATATATATTATAT
71786 TAT
1 TAT
71789 TATGGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 16 0.62
14 6 0.23
15 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TATATATATTATAT
Done.