Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001404.1 Hibiscus syriacus cultivar Beakdansim tig00002740_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: 81551
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:895 original size:18 final size:17
Alignment explanation
Indices: 855--888 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
845 GTCGAAAAAC
855 ATAAAATATGACTTTTT
1 ATAAAATATGACTTTTT
* *
872 AAAAAATTTGACTTTTT
1 ATAAAATATGACTTTTT
889 GGTAAAAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
ATAAAATATGACTTTTT
Found at i:930 original size:29 final size:28
Alignment explanation
Indices: 888--942 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
878 TTTGACTTTT
888 TGGTAAAAGTCAAC-GTCAATGGTCAACTC
1 TGGTAAAAGTCAACAGTC-AT-GTCAACTC
*
917 TGGTCAAAGTCAACAGTCATGTCAAC
1 TGGTAAAAGTCAACAGTCATGTCAAC
943 GAGTAGGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 15 0.62
30 3 0.12
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (28 bp):
TGGTAAAAGTCAACAGTCATGTCAACTC
Found at i:1465 original size:18 final size:19
Alignment explanation
Indices: 1436--1471 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1426 TGATCGGAGC
1436 GAGGTGGGCGGTTCCAAAG
1 GAGGTGGGCGGTTCCAAAG
1455 GAGGT-GGCGGTTCCAAA
1 GAGGTGGGCGGTTCCAAA
1472 TGATGTGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.17, G:0.44, T:0.17
Consensus pattern (19 bp):
GAGGTGGGCGGTTCCAAAG
Found at i:1924 original size:28 final size:28
Alignment explanation
Indices: 1884--1945 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
1874 AAAGACTAAT
1884 ATACCCCTAAATAGATATAATTATAAAA
1 ATACCCCTAAATAGATATAATTATAAAA
*
1912 ATACCCCTAAATAGATATAATTGTAAAA
1 ATACCCCTAAATAGATATAATTATAAAA
1940 ATACCC
1 ATACCC
1946 TTATGGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (28 bp):
ATACCCCTAAATAGATATAATTATAAAA
Found at i:6215 original size:26 final size:26
Alignment explanation
Indices: 6166--6216 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
6156 ATTCTTATTT
* *
6166 TAATTTAAAAATAACACTTTAAAAAA
1 TAATTTAAAAATAACACATAAAAAAA
* *
6192 TAATTTAAAGATAACAGATAAAAAA
1 TAATTTAAAAATAACACATAAAAAA
6217 GAAATTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (26 bp):
TAATTTAAAAATAACACATAAAAAAA
Found at i:6222 original size:26 final size:26
Alignment explanation
Indices: 6167--6222 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
6157 TTCTTATTTT
** *
6167 AATTTAAAAATAACACTTTAAAAAAT
1 AATTTAAAAATAACACGATAAAAAAA
*
6193 AATTTAAAGATAACA-GATAAAAAAGA
1 AATTTAAAAATAACACGATAAAAAA-A
6219 AATT
1 AATT
6223 AAGATCTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (26 bp):
AATTTAAAAATAACACGATAAAAAAA
Found at i:7057 original size:12 final size:12
Alignment explanation
Indices: 7033--7132 Score: 88
Period size: 12 Copynumber: 8.5 Consensus size: 12
7023 TTATTTTATT
*
7033 TATATAAACTTA
1 TATATATACTTA
*
7045 TATGTATACTTA
1 TATATATACTTA
7057 TATATATA--TA
1 TATATATACTTA
7067 TATATATA-TATA
1 TATATATACT-TA
7079 TATATATA-TATA
1 TATATATACT-TA
7091 TATATATA-TATA
1 TATATATACT-TA
7103 TATATATA-TATA
1 TATATATACT-TA
7115 TATATATATCTTA
1 TATATATA-CTTA
7128 T-TATA
1 TATATA
7133 CTAGGTCCAT
Statistics
Matches: 81, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.12
12 67 0.83
13 3 0.04
14 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (12 bp):
TATATATACTTA
Found at i:7062 original size:2 final size:2
Alignment explanation
Indices: 7055--7123 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
7045 TATGTATACT
7055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7097 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 T
7124 CTTATTATAC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9120 original size:17 final size:18
Alignment explanation
Indices: 9088--9133 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
9078 TTCCAAATTC
*
9088 TAGGTTTTATGTGCACAT
1 TAGGGTTTATGTGCACAT
9106 TAGGGTTTA-GTGCACAT
1 TAGGGTTTATGTGCACAT
9123 TAGGGTTTATG
1 TAGGGTTTATG
9134 GAATTGATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (18 bp):
TAGGGTTTATGTGCACAT
Found at i:11108 original size:39 final size:39
Alignment explanation
Indices: 11052--11223 Score: 200
Period size: 39 Copynumber: 4.4 Consensus size: 39
11042 ATCGATTAAA
* * *
11052 CACTTCGGTGCAAATGGTGGGCATGACCTTATGTGTATG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAG
* *
11091 CACTTTGGTGCATATGGTGGTCACGACCTTATGTGTAATG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAA-G
* * * * *
11131 CAATTCGGTTCATATGGTGGGAAAGATCTTATGTGTAAG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAG
** * *
11170 CACTTTAGTTCATATGGTGGACACGACCTTATGTGTAAG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAG
*
11209 CACTACGGTGCATAT
1 CACTTCGGTGCATAT
11224 ATAATTAACT
Statistics
Matches: 109, Mismatches: 23, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
39 77 0.71
40 32 0.29
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (39 bp):
CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAG
Found at i:11186 original size:79 final size:79
Alignment explanation
Indices: 11055--11220 Score: 226
Period size: 79 Copynumber: 2.1 Consensus size: 79
11045 GATTAAACAC
* * * * *
11055 TTCGGTGCAAATGGTGGGCATGACCTTATGTGTATGCACTTTGGTGCATATGGTGGTCACGACCT
1 TTCGGTGCAAATGGTGGGAAAGACCTTATGTGTAAGCACTTTAGTGCATATGGTGGACACGACCT
11120 TATGTGTAATGCAA
66 TATGTGTAATGCAA
* * * *
11134 TTCGGTTCATATGGTGGGAAAGATCTTATGTGTAAGCACTTTAGTTCATATGGTGGACACGACCT
1 TTCGGTGCAAATGGTGGGAAAGACCTTATGTGTAAGCACTTTAGTGCATATGGTGGACACGACCT
*
11199 TATGTGTAA-GCAC
66 TATGTGTAATGCAA
*
11212 TACGGTGCA
1 TTCGGTGCA
11221 TATATAATTA
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
78 10 0.13
79 65 0.87
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (79 bp):
TTCGGTGCAAATGGTGGGAAAGACCTTATGTGTAAGCACTTTAGTGCATATGGTGGACACGACCT
TATGTGTAATGCAA
Found at i:15128 original size:17 final size:17
Alignment explanation
Indices: 15077--15148 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
15067 AATTAAGAGT
* *
15077 TAGTATAATAAATGAAC
1 TAGTTTAATTAATGAAC
* * *
15094 TAGTTTGATGAATAAAC
1 TAGTTTAATTAATGAAC
15111 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
15128 TAACTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
15146 TAG
1 TAG
15149 ATGCATGAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
17 32 0.73
18 12 0.27
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.36
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:17552 original size:17 final size:16
Alignment explanation
Indices: 17532--17606 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 16
17522 TAGTCTAATA
17532 AATGAACTAGTTTGATG
1 AATGAACTAGTTT-ATG
* *
17549 AATGAACTATTTTAATT
1 AATGAACTAGTTT-ATG
* * *
17566 ATTGAACTAACTTTATTC
1 AATGAACT-AGTTTA-TG
*
17584 AATGAACTAGATTCATG
1 AATGAACTAG-TTTATG
17601 AATGAA
1 AATGAA
17607 GTAGCTTACT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
17 30 0.67
18 15 0.33
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (16 bp):
AATGAACTAGTTTATG
Found at i:17710 original size:37 final size:37
Alignment explanation
Indices: 17669--17754 Score: 163
Period size: 37 Copynumber: 2.3 Consensus size: 37
17659 ACTAGATGCT
17669 TTAAATGCAATGCATGCTTAAATAAACAACACACTTA
1 TTAAATGCAATGCATGCTTAAATAAACAACACACTTA
17706 TTAAATGCAATGCATGCTTAAATAAACAACACACTTA
1 TTAAATGCAATGCATGCTTAAATAAACAACACACTTA
*
17743 TTAAAGGCAATG
1 TTAAATGCAATG
17755 AATGTCATGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.27
Consensus pattern (37 bp):
TTAAATGCAATGCATGCTTAAATAAACAACACACTTA
Found at i:17711 original size:20 final size:20
Alignment explanation
Indices: 17686--17747 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
17676 CAATGCATGC
17686 TTAAATAAACAACACACTTA
1 TTAAATAAACAACACACTTA
* ** **
17706 TTAAAT--GCAATGCA-TGC
1 TTAAATAAACAACACACTTA
17723 TTAAATAAACAACACACTTA
1 TTAAATAAACAACACACTTA
17743 TTAAA
1 TTAAA
17748 GGCAATGAAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
17 7 0.24
18 5 0.17
19 5 0.17
20 12 0.41
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (20 bp):
TTAAATAAACAACACACTTA
Found at i:20422 original size:31 final size:31
Alignment explanation
Indices: 20387--20459 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
20377 TAAGGGAGTA
20387 TCTTGGGGCC-TGAGAGCCTACCCAAGAAAGT
1 TCTTGGGGCCAT-AGAGCCTACCCAAGAAAGT
*
20418 TCTTGGGGCCATAGGGCCTACCCAAGAAAGT
1 TCTTGGGGCCATAGAGCCTACCCAAGAAAGT
* *
20449 TATCGGGGCCA
1 TCTTGGGGCCA
20460 CAACGCTTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.19
Consensus pattern (31 bp):
TCTTGGGGCCATAGAGCCTACCCAAGAAAGT
Found at i:22790 original size:19 final size:19
Alignment explanation
Indices: 22763--22801 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
22753 CAAATAGCCC
*
22763 CAGTTCGACTAGACCGGTT
1 CAGTCCGACTAGACCGGTT
* *
22782 CAGTCCGACTGGATCGGTT
1 CAGTCCGACTAGACCGGTT
22801 C
1 C
22802 CAAAAGCTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (19 bp):
CAGTCCGACTAGACCGGTT
Found at i:24293 original size:32 final size:30
Alignment explanation
Indices: 24253--24396 Score: 103
Period size: 33 Copynumber: 4.6 Consensus size: 30
24243 TACCACTTAT
24253 AATACCAACAAACTTAAACCATAATAATTTC
1 AATACCAACAAACTTAAA-CATAATAATTTC
* *
24284 AATATCCAACAAAGTTGAAACATTATAAATTTC
1 AATA-CCAACAAACTT-AAACATAAT-AATTTC
* * * * *
24317 AATGTCCAAAAAAATTAAAACATAA-CATTTAT
1 AAT-ACCAACAAACTT-AAACATAATAATTT-C
* * *
24349 AATACCAACAAACCTAAAAATAATAATGTC
1 AATACCAACAAACTTAAACATAATAATTTC
*
24379 AACACCCAACAAA-TTAAA
1 AATA-CCAACAAACTTAAA
24397 TTTCACTGTC
Statistics
Matches: 87, Mismatches: 19, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
30 14 0.16
31 27 0.31
32 18 0.21
33 28 0.32
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (30 bp):
AATACCAACAAACTTAAACATAATAATTTC
Found at i:35235 original size:24 final size:24
Alignment explanation
Indices: 35208--35260 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
35198 TTGAAAACAT
*
35208 ATATATAATATATAGTTTTTGAAA
1 ATATATAATATATAATTTTTGAAA
35232 ATATATAATATATAATTTTTGAAA
1 ATATATAATATATAATTTTTGAAA
35256 A-ATAT
1 ATATAT
35261 TTTGAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
ATATATAATATATAATTTTTGAAA
Found at i:35244 original size:26 final size:25
Alignment explanation
Indices: 35196--35260 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 25
35186 TTCAAAAATA
35196 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAA-ATATATATAATATA-A-T
35224 TTTTG-AAAATATATA-ATATATAAT
1 TTTTGAAAAATATATATA-ATATAAT
35248 TTTTGAAAAATAT
1 TTTTGAAAAATAT
35261 TTTGAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
24 6 0.17
25 9 0.26
26 12 0.34
27 3 0.09
28 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTGAAAAATATATATAATATAAT
Found at i:35251 original size:64 final size:62
Alignment explanation
Indices: 35170--35359 Score: 235
Period size: 64 Copynumber: 3.0 Consensus size: 62
35160 GGTGCTATTT
35170 AATATAT-ATA-AT-ATTTTTCAAAAATATTTTGAAAACATATATATAATATATAGTTTTTGAA
1 AATATATAATATATAATTTTT-AAAAATATTTTGAAAA-ATATATATAATATATAGTTTTTGAA
* *
35231 AATATATAATATATAATTTTTGAAAAATATTTTG-AAAATGTACATAATATATAGTTTTTGAA
1 AATATATAATATATAATTTTT-AAAAATATTTTGAAAAATATATATAATATATAGTTTTTGAA
* * * * *
35293 AACCGATATATTATATAGTTTTTGAAAACATTTTGAAAATATATATATAATATATAGTTTTTGAA
1 AA--TATATAATATATAATTTTTAAAAATATTTTGAAAA-ATATATATAATATATAGTTTTTGAA
35358 AA
1 AA
35360 CATTTTGAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
61 7 0.06
62 28 0.25
63 15 0.13
64 37 0.33
65 25 0.22
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (62 bp):
AATATATAATATATAATTTTTAAAAATATTTTGAAAAATATATATAATATATAGTTTTTGAA
Found at i:35266 original size:36 final size:37
Alignment explanation
Indices: 35224--35294 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
35214 AATATATAGT
*
35224 TTTTGAAAA-TATATAATATATAATTTTTGAAAAATA
1 TTTTGAAAAGTACATAATATATAATTTTTGAAAAATA
*
35260 TTTTGAAAATGTACATAATATATAGTTTTTGAAAA
1 TTTTGAAAA-GTACATAATATATAATTTTTGAAAA
35295 CCGATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 9 0.29
38 22 0.71
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (37 bp):
TTTTGAAAAGTACATAATATATAATTTTTGAAAAATA
Found at i:35339 original size:37 final size:37
Alignment explanation
Indices: 35298--35402 Score: 183
Period size: 39 Copynumber: 2.8 Consensus size: 37
35288 TTGAAAACCG
35298 ATATATTATATAGTTTTTGAAAACATTTTGAAAATAT
1 ATATATTATATAGTTTTTGAAAACATTTTGAAAATAT
35335 ATATATAATATATAGTTTTTGAAAACATTTTGAAAATAT
1 ATATAT--TATATAGTTTTTGAAAACATTTTGAAAATAT
*
35374 ATACATTATATAGTTTTTGAAAACATTTT
1 ATATATTATATAGTTTTTGAAAACATTTT
35403 ATATATATTA
Statistics
Matches: 65, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
37 29 0.45
39 36 0.55
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (37 bp):
ATATATTATATAGTTTTTGAAAACATTTTGAAAATAT
Found at i:35465 original size:22 final size:22
Alignment explanation
Indices: 35440--35485 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
35430 TTATTGTAAA
35440 TTATTATTTA-TTATTTTCATTT
1 TTATT-TTTATTTATTTTCATTT
*
35462 TTATTTTTATTTATTTTCTTTT
1 TTATTTTTATTTATTTTCATTT
35484 TT
1 TT
35486 GGTCCAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (22 bp):
TTATTTTTATTTATTTTCATTT
Found at i:37797 original size:33 final size:32
Alignment explanation
Indices: 37743--37831 Score: 74
Period size: 33 Copynumber: 2.7 Consensus size: 32
37733 ATAGATAATA
* *
37743 TTAATAATATA-AGATTAAATATTTAAAATATAT
1 TTAATAATATATA-TTTTAATATTTAAAATAT-T
* * * *
37776 TTACTAATAT-TTTTTATAATATAATATAATATT
1 TTAATAATATATATTT-TAATAT-TTAAAATATT
37809 TTAATAATATATATTTTAATATT
1 TTAATAATATATATTTTAATATT
37832 ATAATAAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
32 2 0.05
33 30 0.70
34 11 0.26
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (32 bp):
TTAATAATATATATTTTAATATTTAAAATATT
Found at i:37824 original size:15 final size:15
Alignment explanation
Indices: 37796--37834 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
37786 TTTTTATAAT
37796 ATAATATAATATTTTA
1 ATAATAT-ATATTTTA
37812 ATAATATATATTTTA
1 ATAATATATATTTTA
*
37827 ATATTATA
1 ATAATATA
37835 ATAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAATATATATTTTA
Found at i:37828 original size:23 final size:23
Alignment explanation
Indices: 37770--37838 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
37760 AATATTTAAA
*
37770 ATATATTTACTAATATTTTTTATAAT
1 ATATATTT--TAATA-TTTTAATAAT
*
37796 ATA-A-TATAATATTTTAATAAT
1 ATATATTTTAATATTTTAATAAT
*
37817 ATATATTTTAATATTATAATAA
1 ATATATTTTAATATTTTAATAA
37839 AATTATTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
21 12 0.32
22 6 0.16
23 14 0.38
24 1 0.03
25 1 0.03
26 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATTTTAATATTTTAATAAT
Found at i:37831 original size:45 final size:45
Alignment explanation
Indices: 37722--37820 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
37712 ATTAATTATA
* * *
37722 AAAATATATTTA-TAGATAATATTAATAATATAAGATTAAATATTT
1 AAAATATATTTACTA-ATATTTTTTATAATATAAGATTAAATATTT
*
37767 AAAATATATTTACTAATATTTTTTATAATATAATA-T-AATATTTT
1 AAAATATATTTACTAATATTTTTTATAATATAAGATTAAATA-TTT
37811 AATAATATAT
1 AA-AATATAT
37821 ATTTTAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
43 4 0.09
44 6 0.13
45 35 0.74
46 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (45 bp):
AAAATATATTTACTAATATTTTTTATAATATAAGATTAAATATTT
Found at i:48855 original size:18 final size:17
Alignment explanation
Indices: 48815--48848 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48805 GTCGAAAAAC
48815 ATAAAATATGACTTTTT
1 ATAAAATATGACTTTTT
* *
48832 AAAAAATTTGACTTTTT
1 ATAAAATATGACTTTTT
48849 GGTAAAAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
ATAAAATATGACTTTTT
Found at i:48890 original size:29 final size:28
Alignment explanation
Indices: 48848--48902 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
48838 TTTGACTTTT
48848 TGGTAAAAGTCAAC-GTCAATGGTCAACTC
1 TGGTAAAAGTCAACAGTC-AT-GTCAACTC
*
48877 TGGTCAAAGTCAACAGTCATGTCAAC
1 TGGTAAAAGTCAACAGTCATGTCAAC
48903 GAGTAGGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 15 0.62
30 3 0.12
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (28 bp):
TGGTAAAAGTCAACAGTCATGTCAACTC
Found at i:49440 original size:18 final size:18
Alignment explanation
Indices: 49397--49431 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
49387 TGATCGGAGC
49397 GAGGTGGCGGTTCCAAAG
1 GAGGTGGCGGTTCCAAAG
49415 GAGGTGGCGGTTCCAAA
1 GAGGTGGCGGTTCCAAA
49432 TGATGTGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.43, T:0.17
Consensus pattern (18 bp):
GAGGTGGCGGTTCCAAAG
Found at i:49884 original size:28 final size:28
Alignment explanation
Indices: 49844--49903 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
49834 AGACTAATAT
49844 ACCCCTAAATAGATATAATTATAAAAAA
1 ACCCCTAAATAGATATAATTATAAAAAA
* *
49872 ACCCCTAAATAGATATAATTGTAAAAAT
1 ACCCCTAAATAGATATAATTATAAAAAA
49900 ACCC
1 ACCC
49904 TTATGGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (28 bp):
ACCCCTAAATAGATATAATTATAAAAAA
Found at i:52662 original size:18 final size:17
Alignment explanation
Indices: 52622--52655 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52612 GTCGAAAAAC
52622 ATAAAATATGACTTTTT
1 ATAAAATATGACTTTTT
* *
52639 AAAAAATTTGACTTTTT
1 ATAAAATATGACTTTTT
52656 GGTAAAAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
ATAAAATATGACTTTTT
Found at i:52697 original size:29 final size:28
Alignment explanation
Indices: 52655--52709 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
52645 TTTGACTTTT
52655 TGGTAAAAGTCAAC-GTCAATGGTCAACTC
1 TGGTAAAAGTCAACAGTC-AT-GTCAACTC
*
52684 TGGTCAAAGTCAACAGTCATGTCAAC
1 TGGTAAAAGTCAACAGTCATGTCAAC
52710 GAGTAGGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 15 0.62
30 3 0.12
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (28 bp):
TGGTAAAAGTCAACAGTCATGTCAACTC
Found at i:53247 original size:18 final size:18
Alignment explanation
Indices: 53204--53238 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
53194 TGATCGGAGC
53204 GAGGTGGCGGTTCCAAAG
1 GAGGTGGCGGTTCCAAAG
53222 GAGGTGGCGGTTCCAAA
1 GAGGTGGCGGTTCCAAA
53239 TGATGTGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.43, T:0.17
Consensus pattern (18 bp):
GAGGTGGCGGTTCCAAAG
Found at i:53692 original size:28 final size:28
Alignment explanation
Indices: 53652--53711 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
53642 AGACTAATAT
53652 ACCCCTAAATAGATATAATTATAAAAAA
1 ACCCCTAAATAGATATAATTATAAAAAA
* *
53680 ACCCCTAAATAGATATAATTGTAAAAAT
1 ACCCCTAAATAGATATAATTATAAAAAA
53708 ACCC
1 ACCC
53712 TTATGGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (28 bp):
ACCCCTAAATAGATATAATTATAAAAAA
Found at i:57999 original size:26 final size:26
Alignment explanation
Indices: 57950--58000 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
57940 ATTCTTATTT
* *
57950 TAATTTAAAAATAACACTTTAAAAAA
1 TAATTTAAAAATAACACATAAAAAAA
* *
57976 TAATTTAAAGATAACAGATAAAAAA
1 TAATTTAAAAATAACACATAAAAAA
58001 GAAATTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (26 bp):
TAATTTAAAAATAACACATAAAAAAA
Found at i:58006 original size:26 final size:26
Alignment explanation
Indices: 57951--58006 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
57941 TTCTTATTTT
** *
57951 AATTTAAAAATAACACTTTAAAAAAT
1 AATTTAAAAATAACACGATAAAAAAA
*
57977 AATTTAAAGATAACA-GATAAAAAAGA
1 AATTTAAAAATAACACGATAAAAAA-A
58003 AATT
1 AATT
58007 AAGATCTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (26 bp):
AATTTAAAAATAACACGATAAAAAAA
Found at i:58854 original size:2 final size:2
Alignment explanation
Indices: 58847--58892 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
58837 TATGTATACT
58847 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58888 TA TA T
1 TA TA T
58893 TATTTATACT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60893 original size:17 final size:18
Alignment explanation
Indices: 60861--60906 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
60851 TTCCAAATTC
*
60861 TAGGTTTTATGTGCACAT
1 TAGGGTTTATGTGCACAT
60879 TAGGGTTTA-GTGCACAT
1 TAGGGTTTATGTGCACAT
60896 TAGGGTTTATG
1 TAGGGTTTATG
60907 GAATTGATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (18 bp):
TAGGGTTTATGTGCACAT
Found at i:62876 original size:39 final size:39
Alignment explanation
Indices: 62820--62991 Score: 191
Period size: 39 Copynumber: 4.4 Consensus size: 39
62810 ATCGATTAAA
* * *
62820 CACTTCGGTGCAAATGGTGGGCATGACCTTATGTGTATG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAG
* *
62859 CACTTTGGTGCATATGGTGGTCACGACCTTATGTGTAATG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAA-G
* * * * *
62899 CAATTCGGTTCATATGGTGGGAAGGATCTTATGTGTAAG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAG
** * *
62938 CACTTTAGTTCATATGGTGGACACGACCTTATGTGTAAG
1 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAG
* *
62977 CACTACAGTGCATAT
1 CACTTCGGTGCATAT
62992 ATAATTAACT
Statistics
Matches: 110, Mismatches: 22, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
39 78 0.71
40 32 0.29
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (39 bp):
CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAG
Found at i:62954 original size:79 final size:79
Alignment explanation
Indices: 62823--62975 Score: 225
Period size: 79 Copynumber: 1.9 Consensus size: 79
62813 GATTAAACAC
* * * * *
62823 TTCGGTGCAAATGGTGGGCATGACCTTATGTGTATGCACTTTGGTGCATATGGTGGTCACGACCT
1 TTCGGTGCAAATGGTGGGAAGGACCTTATGTGTAAGCACTTTAGTGCATATGGTGGACACGACCT
62888 TATGTGTAATGCAA
66 TATGTGTAATGCAA
* * * *
62902 TTCGGTTCATATGGTGGGAAGGATCTTATGTGTAAGCACTTTAGTTCATATGGTGGACACGACCT
1 TTCGGTGCAAATGGTGGGAAGGACCTTATGTGTAAGCACTTTAGTGCATATGGTGGACACGACCT
62967 TATGTGTAA
66 TATGTGTAA
62976 GCACTACAGT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (79 bp):
TTCGGTGCAAATGGTGGGAAGGACCTTATGTGTAAGCACTTTAGTGCATATGGTGGACACGACCT
TATGTGTAATGCAA
Found at i:66905 original size:17 final size:17
Alignment explanation
Indices: 66854--66925 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
66844 AATTAAGAGT
* *
66854 TAGTATAATAAATGAAC
1 TAGTTTAATTAATGAAC
* * *
66871 TAGTTTGATGAATAAAC
1 TAGTTTAATTAATGAAC
66888 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
66905 TAACTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
66923 TAG
1 TAG
66926 ATGCATGAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
17 32 0.73
18 12 0.27
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.36
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:69326 original size:17 final size:16
Alignment explanation
Indices: 69306--69380 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 16
69296 TAGTCTAATA
69306 AATGAACTAGTTTGATG
1 AATGAACTAGTTT-ATG
* *
69323 AATGAACTATTTTAATT
1 AATGAACTAGTTT-ATG
* * *
69340 ATTGAACTAACTTTATTC
1 AATGAACT-AGTTTA-TG
*
69358 AATGAACTAGATTCATG
1 AATGAACTAG-TTTATG
69375 AATGAA
1 AATGAA
69381 GTAGCTTACT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
17 30 0.67
18 15 0.33
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (16 bp):
AATGAACTAGTTTATG
Found at i:69484 original size:37 final size:37
Alignment explanation
Indices: 69443--69528 Score: 163
Period size: 37 Copynumber: 2.3 Consensus size: 37
69433 ACTAGATGCT
69443 TTAAATGCAATGCATGCTTAAATAAACAACACACTTA
1 TTAAATGCAATGCATGCTTAAATAAACAACACACTTA
69480 TTAAATGCAATGCATGCTTAAATAAACAACACACTTA
1 TTAAATGCAATGCATGCTTAAATAAACAACACACTTA
*
69517 TTAAAGGCAATG
1 TTAAATGCAATG
69529 AATGTCATGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.27
Consensus pattern (37 bp):
TTAAATGCAATGCATGCTTAAATAAACAACACACTTA
Found at i:69485 original size:20 final size:20
Alignment explanation
Indices: 69460--69521 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
69450 CAATGCATGC
69460 TTAAATAAACAACACACTTA
1 TTAAATAAACAACACACTTA
* ** **
69480 TTAAAT--GCAATGCA-TGC
1 TTAAATAAACAACACACTTA
69497 TTAAATAAACAACACACTTA
1 TTAAATAAACAACACACTTA
69517 TTAAA
1 TTAAA
69522 GGCAATGAAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
17 7 0.24
18 5 0.17
19 5 0.17
20 12 0.41
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (20 bp):
TTAAATAAACAACACACTTA
Found at i:72196 original size:31 final size:31
Alignment explanation
Indices: 72161--72233 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
72151 TAAGGGAGTA
72161 TCTTGGGGCC-TGAGAGCCTACCCAAGAAAGT
1 TCTTGGGGCCAT-AGAGCCTACCCAAGAAAGT
*
72192 TCTTGGGGCCATAGGGCCTACCCAAGAAAGT
1 TCTTGGGGCCATAGAGCCTACCCAAGAAAGT
* *
72223 TATCGGGGCCA
1 TCTTGGGGCCA
72234 CAACGCTTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.19
Consensus pattern (31 bp):
TCTTGGGGCCATAGAGCCTACCCAAGAAAGT
Found at i:76075 original size:32 final size:30
Alignment explanation
Indices: 76035--76178 Score: 103
Period size: 33 Copynumber: 4.6 Consensus size: 30
76025 TACCACTTAT
76035 AATACCAACAAACTTAAACCATAATAATTTC
1 AATACCAACAAACTTAAA-CATAATAATTTC
* *
76066 AATATCCAACAAAGTTGAAACATTATAAATTTC
1 AATA-CCAACAAACTT-AAACATAAT-AATTTC
* * * * *
76099 AATGTCCAAAAAAATTAAAACATAA-CATTTAT
1 AAT-ACCAACAAACTT-AAACATAATAATTT-C
* * *
76131 AATACCAACAAACCTAAAAATAATAATGTC
1 AATACCAACAAACTTAAACATAATAATTTC
*
76161 AACACCCAACAAA-TTAAA
1 AATA-CCAACAAACTTAAA
76179 TTTCACTGTC
Statistics
Matches: 87, Mismatches: 19, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
30 14 0.16
31 27 0.31
32 18 0.21
33 28 0.32
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (30 bp):
AATACCAACAAACTTAAACATAATAATTTC
Done.