Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004210.1 Hibiscus syriacus cultivar Beakdansim tig00009220_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: 116747
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:5762 original size:24 final size:23
Alignment explanation
Indices: 5735--5934 Score: 100
Period size: 24 Copynumber: 8.3 Consensus size: 23
5725 TCAATCATGT
5735 TTAGTGCATTCGTGCACTCTAGTA
1 TTAGTGCATTCGTGCACTCT-GTA
* *
5759 TTAGTGCATTTGTTGCACTCCTGTT
1 TTAGTGCATTCG-TGCACT-CTGTA
* *
5784 TTAGTGCCTT-GATGCACTCCAGT-
1 TTAGTGCATTCG-TGCACT-CTGTA
* *
5807 TATAGTGTATTTGTGCACTCCTGTA
1 T-TAGTGCATTCGTGCACT-CTGTA
* *
5832 TAAGTGCATACGTGCACTCTTGTA
1 TTAGTGCATTCGTGCACTC-TGTA
* * * * * * *
5856 TTATTACTTTTGGGTACTCCTGCA
1 TTAGTGCATTCGTGCACT-CTGTA
* *
5880 TTAGTGCATCCGTGCACTCCTGAA
1 TTAGTGCATTCGTGCACT-CTGTA
* *
5904 TCAGTGCCATT-GAGCACTCATGTA
1 TTAGTG-CATTCGTGCACTC-TGTA
5928 TTAGTGC
1 TTAGTGC
5935 TAGTATGCAT
Statistics
Matches: 133, Mismatches: 34, Indels: 19
0.72 0.18 0.10
Matches are distributed among these distances:
23 4 0.03
24 104 0.78
25 23 0.17
26 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (23 bp):
TTAGTGCATTCGTGCACTCTGTA
Found at i:5800 original size:49 final size:48
Alignment explanation
Indices: 5734--5850 Score: 139
Period size: 49 Copynumber: 2.4 Consensus size: 48
5724 ATCAATCATG
*
5734 TTTAGTGCATTCGTGCACTCTAG-TATTAGTGCATTTGTTGCACTCCTGT
1 TTTAGTGCATTCGTGCACTCCAGTTA-TAGTGCATTTG-TGCACTCCTGT
* *
5783 TTTAGTGCCTT-GATGCACTCCAGTTATAGTGTATTTGTGCACTCCTGT
1 TTTAGTGCATTCG-TGCACTCCAGTTATAGTGCATTTGTGCACTCCTGT
* * *
5831 ATAAGTGCATACGTGCACTC
1 TTTAGTGCATTCGTGCACTC
5851 TTGTATTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
48 26 0.45
49 30 0.52
50 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (48 bp):
TTTAGTGCATTCGTGCACTCCAGTTATAGTGCATTTGTGCACTCCTGT
Found at i:10063 original size:21 final size:21
Alignment explanation
Indices: 10038--10099 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
10028 CCATAATAAG
10038 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACCCCTTCATA
10059 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTACCCCTTCATA
* *
10080 GGGTATCAGTACACCTTCAT
1 GGGTATCGGTACCCCTTCAT
10100 TAAATTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (21 bp):
GGGTATCGGTACCCCTTCATA
Found at i:10187 original size:35 final size:35
Alignment explanation
Indices: 10138--10207 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
10128 GTTATTGCAG
10138 CCAGTGTATAGATACACTACATA-GGTATCGGTACA
1 CCAGTGTATAGATACACT-CATAGGGTATCGGTACA
*
10173 CCAGTGTATGGATACACTCATAGGGGTATCGGTAC
1 CCAGTGTATAGATACACTCATA-GGGTATCGGTAC
10208 CCTTTTTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 4 0.12
35 17 0.53
36 11 0.34
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (35 bp):
CCAGTGTATAGATACACTCATAGGGTATCGGTACA
Found at i:10310 original size:36 final size:37
Alignment explanation
Indices: 10240--10310 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
10230 GCAGTCATAG
* *
10240 GTGTATGGATACACCTGCAGGGGGTATCGGTACACCA
1 GTGTATGGATACACCTGCAAGGGGTATCGATACACCA
10277 GTGTATGGATACA-CT-CATAGGGGTATCGATACAC
1 GTGTATGGATACACCTGCA-AGGGGTATCGATACAC
10311 ATTTGCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 2 0.06
36 16 0.52
37 13 0.42
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (37 bp):
GTGTATGGATACACCTGCAAGGGGTATCGATACACCA
Found at i:27359 original size:2 final size:2
Alignment explanation
Indices: 27290--27342 Score: 79
Period size: 2 Copynumber: 26.0 Consensus size: 2
27280 AATTAAAATC
*
27290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
27333 AT AC AT AT AT
1 AT AT AT AT AT
27343 TAACTCTAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 45 0.98
3 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:28278 original size:17 final size:19
Alignment explanation
Indices: 28256--28292 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
28246 TTCAATAAAT
28256 ACAATA-AATAATC-TATG
1 ACAATACAATAATCATATG
*
28273 ACAATACAATCATCATATG
1 ACAATACAATAATCATATG
28292 A
1 A
28293 TTGGTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.27
Consensus pattern (19 bp):
ACAATACAATAATCATATG
Found at i:28799 original size:32 final size:32
Alignment explanation
Indices: 28763--28881 Score: 150
Period size: 32 Copynumber: 3.7 Consensus size: 32
28753 CTAGTCAAGG
*
28763 TTGCATTCAAATAATGCACAACATAGTCAGTA
1 TTGCATTCATATAATGCACAACATAGTCAGTA
* *
28795 TTGCATTCATATAATGCACAGCAGAGTCAGTA
1 TTGCATTCATATAATGCACAACATAGTCAGTA
* *
28827 TTGCATTCATATAATGCACAGCAGT-GTCAGTG
1 TTGCATTCATATAATGCACAACA-TAGTCAGTA
* * *
28859 TTGCATTTAGATAATGTACAACA
1 TTGCATTCATATAATGCACAACA
28882 ATTATAATCA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (32 bp):
TTGCATTCATATAATGCACAACATAGTCAGTA
Found at i:30615 original size:13 final size:14
Alignment explanation
Indices: 30582--30619 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
30572 TTTTATTATA
*
30582 ATAAAAATAATTGC
1 ATAAAAATAAATGC
30596 ATAAAAATAAATG-
1 ATAAAAATAAATGC
30609 ATTAAAAATAA
1 A-TAAAAATAA
30620 CAATATGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (14 bp):
ATAAAAATAAATGC
Found at i:30759 original size:14 final size:14
Alignment explanation
Indices: 30721--30759 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
30711 CATTCAAATA
* *
30721 CTAAAAAATACTTT
1 CTAAAAATTATTTT
*
30735 CTAAAATTTATTTT
1 CTAAAAATTATTTT
30749 CTAAAAATTAT
1 CTAAAAATTAT
30760 AATTCGTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (14 bp):
CTAAAAATTATTTT
Found at i:38995 original size:28 final size:26
Alignment explanation
Indices: 38963--39025 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 26
38953 GTAACGAGCT
38963 TAACGAGCACAAGTCGAGCAACAAGTTC
1 TAACGAGCACAAGTCGAGCAA-AA-TTC
* *
38991 TAACGAGCACGAGTCGAGCAAAATTT
1 TAACGAGCACAAGTCGAGCAAAATTC
39017 TAACGAGCA
1 TAACGAGCA
39026 TCGAGTCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 11 0.33
27 2 0.06
28 20 0.61
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (26 bp):
TAACGAGCACAAGTCGAGCAAAATTC
Found at i:49350 original size:18 final size:18
Alignment explanation
Indices: 49323--49370 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
49313 ACCGGTCAAC
49323 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
49341 GGTTAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
49359 GGTCAACGGGTC
1 GGTCAACGGGTC
49371 AGGTAAACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.12, C:0.21, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:49394 original size:31 final size:31
Alignment explanation
Indices: 49334--49395 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
49324 GTCAACGGGT
* * * *
49334 CGGGTCGGGTTAACGGGTCGGGTCGGGTCAA
1 CGGGTCAGGTAAACGGGTCGGGACCGGTCAA
*
49365 CGGGTCAGGTAAACGGGTCGTGACCGGTCAA
1 CGGGTCAGGTAAACGGGTCGGGACCGGTCAA
49396 ACCGGTTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.18, C:0.21, G:0.44, T:0.18
Consensus pattern (31 bp):
CGGGTCAGGTAAACGGGTCGGGACCGGTCAA
Found at i:56473 original size:28 final size:29
Alignment explanation
Indices: 56439--56504 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
56429 CATTTTACAC
*
56439 AAATAGCACCC-TTTTAAAAAAATTACCA
1 AAATAGCACCCATTTCAAAAAAATTACCA
* ** *
56467 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCATTTCAAAAAAATTACCA
56496 AAATAGCAC
1 AAATAGCAC
56505 AAAAACTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAAAAATTACCA
Found at i:56588 original size:18 final size:18
Alignment explanation
Indices: 56546--56588 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
56536 GTCAACGGTC
* * *
56546 AACGGGCCGGGTCGGGTT
1 AACGGGTCGGGTCAGGTA
56564 AACGGGTCGGGTCAGGTA
1 AACGGGTCGGGTCAGGTA
56582 AACGGGT
1 AACGGGT
56589 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.47, T:0.16
Consensus pattern (18 bp):
AACGGGTCGGGTCAGGTA
Found at i:59247 original size:64 final size:64
Alignment explanation
Indices: 59170--59314 Score: 168
Period size: 64 Copynumber: 2.3 Consensus size: 64
59160 CACTACATTG
** * *
59170 ATGCATCGATGCAC-CCTTGAATAAATTGAATTTTGAATGCATTTTGTGCACCGATGCATAAGGC
1 ATGCATCGATGCACTCCTT-AATAAATTGAACATCGAATGCATTTAGTGCACCGATGCATAAGGC
* ** * * *
59234 ATGCATCGGTGCACTCCTTAATATTTTGAACATCGAATGCATTTAGTGTACCGATGCA-CAGACC
1 ATGCATCGATGCACTCCTTAATAAATTGAACATCGAATGCATTTAGTGCACCGATGCATAAG-GC
59298 ATGCATCGATGCACTCC
1 ATGCATCGATGCACTCC
59315 AGGCTTGTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 2 0.03
64 62 0.91
65 4 0.06
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTTAATAAATTGAACATCGAATGCATTTAGTGCACCGATGCATAAGGC
Found at i:61341 original size:21 final size:21
Alignment explanation
Indices: 61303--61343 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
61293 TAAGACTTTA
*
61303 ATTTCAAAATATAAAAATGAT
1 ATTTCAAAATAGAAAAATGAT
* *
61324 ATTTCAAAATGGACAAATGA
1 ATTTCAAAATAGAAAAATGA
61344 GAATAGTCTT
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:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (21 bp):
ATTTCAAAATAGAAAAATGAT
Found at i:65024 original size:23 final size:23
Alignment explanation
Indices: 64994--65073 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
64984 ACACTAGTTA
*
64994 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCATACCTTGAAT
* * *
65017 GTGCATCGAT--TTACCATGAAG
1 GTGCATCGATGCATACCTTGAAT
* *
65038 GTGCACCGATGCATGCCTTGAAT
1 GTGCATCGATGCATACCTTGAAT
65061 GTGCATCGATGCA
1 GTGCATCGATGCA
65074 CTCTGCTGTG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 16 0.36
23 29 0.64
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCATACCTTGAAT
Found at i:67726 original size:64 final size:64
Alignment explanation
Indices: 67655--67799 Score: 195
Period size: 64 Copynumber: 2.3 Consensus size: 64
67645 CACTACATTG
** * *
67655 ATGCATCGATGCAC-CCTTGAATAAATTGAATTTCGAATGCATTTTGTGTACCGATGCACA-AGG
1 ATGCATCGATGCACTCCTT-AATAAATTGAACATCGAATGCATTTAGTGTACCGATGCACAGA-C
67718 C
64 C
* **
67719 ATGCATCGGTGCACTCCTTAATATTTTGAACATCGAATGCATTTAGTGTACCGATGCACAGACC
1 ATGCATCGATGCACTCCTTAATAAATTGAACATCGAATGCATTTAGTGTACCGATGCACAGACC
67783 ATGCATCGATGCACTCC
1 ATGCATCGATGCACTCC
67800 AGGCTTGTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
64 66 0.93
65 5 0.07
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTTAATAAATTGAACATCGAATGCATTTAGTGTACCGATGCACAGACC
Found at i:67859 original size:19 final size:19
Alignment explanation
Indices: 67835--67882 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
67825 TTTTATGCAT
67835 CGATGCACTCCTAGTGTAC
1 CGATGCACTCCTAGTGTAC
67854 CGATGCACTCCTAGTGTAC
1 CGATGCACTCCTAGTGTAC
67873 CGATGCACTC
1 CGATGCACTC
67883 AATCTTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.25
Consensus pattern (19 bp):
CGATGCACTCCTAGTGTAC
Found at i:71123 original size:46 final size:46
Alignment explanation
Indices: 71071--71167 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 46
71061 GAGTCGAGGG
* * * *
71071 TTCTACGCGGTCCTTCGGGATAATTCTACGTGGTCCTTGGGGACAT
1 TTCTACGCAGTCCTTCGGGACAATACTACGTGGTCCTTCGGGACAT
*
71117 TTCTACGCAGTCCTTCGGGACAATACTATGTGGTCCTTCGGGACAT
1 TTCTACGCAGTCCTTCGGGACAATACTACGTGGTCCTTCGGGACAT
71163 TTCTA
1 TTCTA
71168 TGTGGAGCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (46 bp):
TTCTACGCAGTCCTTCGGGACAATACTACGTGGTCCTTCGGGACAT
Found at i:71168 original size:23 final size:23
Alignment explanation
Indices: 71071--71172 Score: 114
Period size: 23 Copynumber: 4.4 Consensus size: 23
71061 GAGTCGAGGG
* *
71071 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGTGGTCCTTCGGGACAA
* *
71094 TTCTACGTGGTCCTTGGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
**
71117 TTCTACGCAGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* * *
71140 TACTATGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
71163 TTCTATGTGG
1 TTCTACGTGG
71173 AGCTTCGGTG
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:71178 original size:23 final size:23
Alignment explanation
Indices: 71128--71180 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
71118 TCTACGCAGT
*
71128 CCTTCGGGACAATACTATGTGGT
1 CCTTCGGGACAATACTATGTGGA
* *
71151 CCTTCGGGACATTTCTATGTGGA
1 CCTTCGGGACAATACTATGTGGA
*
71174 GCTTCGG
1 CCTTCGG
71181 TGCAATTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (23 bp):
CCTTCGGGACAATACTATGTGGA
Found at i:75364 original size:13 final size:13
Alignment explanation
Indices: 75331--75373 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
75321 ATATAGTAAT
*
75331 AAAATAATAATGATG
1 AAAATAATAA--ATA
75346 AAAATAATAAATA
1 AAAATAATAAATA
*
75359 AAAATAGTAAATA
1 AAAATAATAAATA
75372 AA
1 AA
75374 TATATGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 16 0.62
15 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (13 bp):
AAAATAATAAATA
Found at i:77208 original size:106 final size:106
Alignment explanation
Indices: 77058--77448 Score: 436
Period size: 99 Copynumber: 3.8 Consensus size: 106
77048 TCAACCTGTT
* ** * * * *
77058 TGTGAAGTTGGAATTGTATATGGAACTGGGAAATTGTTTATTGACAACTAGTCGTCCCTTCGTTG
1 TGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTGTTGACAACTAGTCGTCCCTTCGTTG
*
77123 TGAAGTTGAACTTGTGTTGTCGCGAGTCCAATATCCTTCGC
66 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
*
77164 TGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTGTTGACAACCAGTCGTCCCTTCGTTG
1 TGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTGTTGACAACTAGTCGTCCCTTCGTTG
77229 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
66 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
* * * * *
77270 TGTGAAGTTGAAATTGGCTCTGCAATTGGG--A--A---GTTGAC-AGTCAGTCGCCCCTTCGGT
1 TGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTGTTGACAACT-AGTCGTCCCTTCGTT
* * * * *
77327 GTGAAATTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCGT
65 GTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
* * * *
77369 TGTGAAGTTGAAATTGGCTCTGAAA-TTGG-AA--A---GTTGAC-AGTCAGTCGCCCCTTCGCT
1 TGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTGTTGACAACT-AGTCGTCCCTTCGTT
*
77426 GTGAAGTTGAGCTTGTGTTGTCT
65 GTGAAGTTGAACTTGTGTTGTCT
77449 TGTGTGGATG
Statistics
Matches: 258, Mismatches: 25, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
98 4 0.02
99 127 0.49
102 1 0.00
104 1 0.00
106 125 0.48
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (106 bp):
TGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTGTTGACAACTAGTCGTCCCTTCGTTG
TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
Found at i:78660 original size:16 final size:15
Alignment explanation
Indices: 78636--78701 Score: 69
Period size: 16 Copynumber: 4.2 Consensus size: 15
78626 ACCCACCTTA
78636 TTTTCTTTTCTTTTTC
1 TTTT-TTTTCTTTTTC
*
78652 TTTTGTTTTTTTTTTC
1 TTTT-TTTTCTTTTTC
*
78668 TCTTTTTTCTTTTTTC
1 TTTTTTTTC-TTTTTC
* *
78684 CTTTTCTTCTTTTTC
1 TTTTTTTTCTTTTTC
78699 TTT
1 TTT
78702 CAATTTAGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.29
16 29 0.71
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.82
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:78661 original size:22 final size:21
Alignment explanation
Indices: 78636--78701 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
78626 ACCCACCTTA
78636 TTTTCTTTTCTTTTTCTT-TTGT
1 TTTTCTTTTCTTTTT-TTCTT-T
*
78658 TTTTTTTTTCTCTTTTTTCTTT
1 TTTTCTTTTCT-TTTTTTCTTT
*
78680 TTTCCTTTTCTTCTTTTTCTTT
1 TTTTCTTTTCTT-TTTTTCTTT
78702 CAATTTAGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.03
22 31 0.82
23 6 0.16
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTTCTTTTCTTTTTTTCTTT
Found at i:78673 original size:9 final size:8
Alignment explanation
Indices: 78646--78697 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
78636 TTTTCTTTTC
78646 TTTTTCTT
1 TTTTTCTT
78654 TTGTTT-TT
1 TT-TTTCTT
78662 TTTTTCTCT
1 TTTTTCT-T
78671 TTTTTCTT
1 TTTTTCTT
*
78679 TTTTCCTT
1 TTTTTCTT
*
78687 TTCTTCTT
1 TTTTTCTT
78695 TTT
1 TTT
78698 CTTTCAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 3 0.08
8 23 0.62
9 11 0.30
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:78688 original size:25 final size:24
Alignment explanation
Indices: 78636--78697 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
78626 ACCCACCTTA
*
78636 TTTTCTT-TTCTTTTTCTTTTGTTT
1 TTTTCTTCTT-TTTTTCTTTTGTTC
*
78660 TTTTTTTCTCTTTTTTCTTTT-TTCC
1 TTTTCTTCT-TTTTTTCTTTTGTT-C
78685 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
78698 CTTTCAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
24 12 0.38
25 19 0.59
26 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (24 bp):
TTTTCTTCTTTTTTTCTTTTGTTC
Found at i:78774 original size:67 final size:70
Alignment explanation
Indices: 78670--78802 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 70
78660 TTTTTTTCTC
* * * * *
78670 TTTTTTCTTTTTTCCTTTTCTTCTTTTTCTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTA
1 TTTTTTCCTTTTTCCTTTTCTTCTTTTTCTTTCAATTTAGGACGCCATCTCAGGTTTTCACCCTA
78735 AATGA
66 AATGA
*
78740 TTTTTTCCTTTTT-C-TTT-TTCTTTGTT-TTTCAATTTAGGACGCCATCTCAGGTTTTCATCCT
1 TTTTTTCCTTTTTCCTTTTCTTCTTT-TTCTTTCAATTTAGGACGCCATCTCAGGTTTTCACCCT
78801 AA
65 AA
78803 GCGAAGTACT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
67 38 0.68
68 5 0.09
69 1 0.02
70 12 0.21
ACGTcount: A:0.13, C:0.22, G:0.11, T:0.55
Consensus pattern (70 bp):
TTTTTTCCTTTTTCCTTTTCTTCTTTTTCTTTCAATTTAGGACGCCATCTCAGGTTTTCACCCTA
AATGA
Found at i:85651 original size:568 final size:568
Alignment explanation
Indices: 84575--85713 Score: 1857
Period size: 568 Copynumber: 2.0 Consensus size: 568
84565 TTTGCTAGAA
* * * * *
84575 TTGTAGGTGTTGACATTGTTGATCTCGCGGTCCTTGTTCTTCATGGGAGGATTTCTATTAGAGTC
1 TTGTAGGTGTTGACATTGTTGATCCCACGATCCTTGTTCTTCACGGGAGGATTTCTAATAGAGTC
* * *
84640 ACCTCCTTTAATCTTTCCTTGTTTTATGGCCAGTTCAACCATTTCACCAGCCATGACTAAATCTT
66 ACCTCCTTCAATCTTTCCTTGTTTTATGGCCAGTTCAACCATCTCACCAGCCATGACTAAATCTG
* * * *
84705 AGAAACTTCCCGACGTGATTGCCAACAAAATCCTGAAGTAAAGTTCCTTCAGGGTTTGTACAAAC
131 AGAAACTTCCCGACGTGATTGCCAACAAAATCCTAAAGTAAAGTGCCTTCAGGGTTTATAAAAAC
* * * *
84770 AACTTTCTAATTTCCTTTTCATCCAAGGGTGGATGAACTTGCATAGATAAATCCCTCCATCTCTG
196 AACTTTCTAATTTCCTTTTAATCCAAGGGTGAATGAACTTGCACAAATAAATCCCTCCATCTCTG
* * *
84835 TGCGTACTATCAGAAACTTTCGTTATTCTTCTTTTCCAAGCTCTGCAGCATAACTCGGTCTGGTC
261 TGCGTACTATCAGAAACTTTCGTTATGCTTATTTTCCAAGCTCTGCAGCATAACTCGGTCTAGTC
84900 TCATATCATTGATATATTTGTACTGCTCTAAGAAAGACTTGGCTAAGTCTTTCCACATCTTGATA
326 TCATATCATTGATATATTTGTACTGCTCTAAGAAAGACTTGGCTAAGTCTTTCCACATCTTGATA
* * *
84965 TGAGTTCGGCTGAGCTGGTTGTACCACCGGATAGCTGAACCGGGCAGGTTCTCCTGAAAGCAGTG
391 TGAGTTCGGCTGAGCTGGTTGTACCACAGGATAGCTGAACCGGACAGGCTCTCCTGAAAGCAGTG
* *
85030 GATTAAGAGTTGGTCATTTCCCCCGTACCCTGTCATCTTCCAACAGAACATAGTGATATGGGCTG
456 GATTAAGAATTGGTCATTTCCCCCGTACCCTGTCATCTTCCAACAGAACATAGTGATATGGGCTA
85095 AAGGGCAGTTGTTCCCGTCGAACTTCTCAAACTCAGAAACCTTAAATT
521 AAGGGCAGTTGTTCCCGTCGAACTTCTCAAACTCAGAAACCTTAAATT
*
85143 TTGTAGGTGTTGACATTGTTGATCCCACGATCCTTGTTCTTCACGGGAGGCTTTCTAATAGAGTC
1 TTGTAGGTGTTGACATTGTTGATCCCACGATCCTTGTTCTTCACGGGAGGATTTCTAATAGAGTC
* *
85208 ACCTCCTTCAATCTTTCTTTGTTTTATGGCCAGTTCAATCATCTCACCAGCCATGACTAAATCTG
66 ACCTCCTTCAATCTTTCCTTGTTTTATGGCCAGTTCAACCATCTCACCAGCCATGACTAAATCTG
* * * *
85273 AGAAACTTCCCGACGTGATTG-CTACCAAATGCTCAAAGTAAGGTGCCTTCAGGGTTTATAAAAA
131 AGAAACTTCCCGACGTGATTGCCAACAAAATCCT-AAAGTAAAGTGCCTTCAGGGTTTATAAAAA
* *
85337 CAACTTTCTAATTTCCTTTTAATCCAAGGGTTAATGAACTTGCACAAATAAATCCCTTCATCTCT
195 CAACTTTCTAATTTCCTTTTAATCCAAGGGTGAATGAACTTGCACAAATAAATCCCTCCATCTCT
** * * *
85402 GTGCGTGTTGTCGGAAACTTTCGTTATGCTTATTTTCTAAGCTCTGCAGCATAACTCGGTCTAGT
260 GTGCGTACTATCAGAAACTTTCGTTATGCTTATTTTCCAAGCTCTGCAGCATAACTCGGTCTAGT
* *
85467 CTCATATCATTGATATGTTTGTACTGCTCTAAGAAAGACTTGGCTAAGTCTTTCCACGTCTTGAT
325 CTCATATCATTGATATATTTGTACTGCTCTAAGAAAGACTTGGCTAAGTCTTTCCACATCTTGAT
*
85532 ATGAGTTCGGCTGAGCTGGTTGTACCACAGGATAGTTGAACCGGACAGGCTCTCCTGAAAGCAGT
390 ATGAGTTCGGCTGAGCTGGTTGTACCACAGGATAGCTGAACCGGACAGGCTCTCCTGAAAGCAGT
* *
85597 GGATTAAGAATTGGTCATTTCCCCCGTACCCTGTCATCTTCCGACATAACATAGTGATATGGGCT
455 GGATTAAGAATTGGTCATTTCCCCCGTACCCTGTCATCTTCCAACAGAACATAGTGATATGGGCT
* *
85662 AAAGGGCAGTTGTTCTCGTCGAACTTCTCAAACTCAGGAACCTTAAATT
520 AAAGGGCAGTTGTTCCCGTCGAACTTCTCAAACTCAGAAACCTTAAATT
85711 TTG
1 TTG
85714 GTGGAAGCAC
Statistics
Matches: 525, Mismatches: 45, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
567 9 0.02
568 516 0.98
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (568 bp):
TTGTAGGTGTTGACATTGTTGATCCCACGATCCTTGTTCTTCACGGGAGGATTTCTAATAGAGTC
ACCTCCTTCAATCTTTCCTTGTTTTATGGCCAGTTCAACCATCTCACCAGCCATGACTAAATCTG
AGAAACTTCCCGACGTGATTGCCAACAAAATCCTAAAGTAAAGTGCCTTCAGGGTTTATAAAAAC
AACTTTCTAATTTCCTTTTAATCCAAGGGTGAATGAACTTGCACAAATAAATCCCTCCATCTCTG
TGCGTACTATCAGAAACTTTCGTTATGCTTATTTTCCAAGCTCTGCAGCATAACTCGGTCTAGTC
TCATATCATTGATATATTTGTACTGCTCTAAGAAAGACTTGGCTAAGTCTTTCCACATCTTGATA
TGAGTTCGGCTGAGCTGGTTGTACCACAGGATAGCTGAACCGGACAGGCTCTCCTGAAAGCAGTG
GATTAAGAATTGGTCATTTCCCCCGTACCCTGTCATCTTCCAACAGAACATAGTGATATGGGCTA
AAGGGCAGTTGTTCCCGTCGAACTTCTCAAACTCAGAAACCTTAAATT
Found at i:89917 original size:13 final size:13
Alignment explanation
Indices: 89884--89926 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
89874 ATATAGTAAT
*
89884 AAAATAATAATGATG
1 AAAATAATAA--ATA
89899 AAAATAATAAATA
1 AAAATAATAAATA
*
89912 AAAATAGTAAATA
1 AAAATAATAAATA
89925 AA
1 AA
89927 TATATGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 16 0.62
15 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (13 bp):
AAAATAATAAATA
Found at i:91189 original size:2 final size:2
Alignment explanation
Indices: 91182--91264 Score: 123
Period size: 2 Copynumber: 42.0 Consensus size: 2
91172 ATAAGTATTC
91182 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
* * * *
91224 AT AT AT AT AT AT AT AT AT -T AA AT AA AC AT AA 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
91265 TATGAAAATG
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:91361 original size:33 final size:33
Alignment explanation
Indices: 91298--91361 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
91288 ATCGTGTGTT
* ** *
91298 CACAATAGGTTTGATATTTATTGGCGTTTTTCC
1 CACAATAGGTTCGATATTTAGCGGCATTTTTCC
*
91331 CACAATAGGTTCGCTATTTAGCGGCATTTTT
1 CACAATAGGTTCGATATTTAGCGGCATTTTT
91362 AGTCGCAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (33 bp):
CACAATAGGTTCGATATTTAGCGGCATTTTTCC
Found at i:91828 original size:21 final size:21
Alignment explanation
Indices: 91804--91844 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
91794 GAAATGTTGC
91804 TTCTCTCGCTGCTATCTCTGT
1 TTCTCTCGCTGCTATCTCTGT
* *
91825 TTCTCTCGTTGCTCTCTCTG
1 TTCTCTCGCTGCTATCTCTG
91845 CTAATCTCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.34, G:0.15, T:0.49
Consensus pattern (21 bp):
TTCTCTCGCTGCTATCTCTGT
Found at i:95046 original size:41 final size:41
Alignment explanation
Indices: 94998--95208 Score: 246
Period size: 41 Copynumber: 5.2 Consensus size: 41
94988 AACACAAACA
*
94998 CCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAAATG
1 CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
* ** * *
95039 TCACTAAAGTACAAGTCTATAATGGTGTTTCTAT-AAAATG
1 CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
*
95079 CCACT-AAGTACAAGTATATAGCGGCGTTTGTATAAAAATG
1 CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
* * * *
95119 CCACTAAAGTACGAGTCTCTAGTGGCGTTTGTATAAAAATA
1 CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
* * * * * *
95160 CCACTAAAGTACGAGTCTTTAGCGGTGTTTTTATAGAAACG
1 CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
*
95201 CTACTAAA
1 CCACTAAA
95209 ATATTACTCT
Statistics
Matches: 143, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
39 23 0.16
40 21 0.15
41 99 0.69
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (41 bp):
CCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATG
Found at i:95154 original size:80 final size:82
Alignment explanation
Indices: 94997--95208 Score: 266
Period size: 80 Copynumber: 2.6 Consensus size: 82
94987 AAACACAAAC
* *
94997 ACCACTAAAGTACAAGTGTATAGCGGCGTTTGTATAAAAATGTCACTAAAGTACAAGTCTATAAT
1 ACCACTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAAT
*
95062 GGTGTTTCTAT-AAAAT
66 GGCGTTTCTATAAAAAT
* * * *
95078 GCCACT-AAGTACAAGTATATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTCTAGT
1 ACCACTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAAT
*
95142 GGCGTTTGTATAAAAAT
66 GGCGTTTCTATAAAAAT
* * * * * * * *
95159 ACCACTAAAGTACGAGTCTTTAGCGGTGTTTTTATAGAAACGCTACTAAA
1 ACCACTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAATGCCACTAAA
95209 ATATTACTCT
Statistics
Matches: 112, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
80 62 0.55
81 15 0.13
82 35 0.31
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (82 bp):
ACCACTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAAT
GGCGTTTCTATAAAAAT
Found at i:98786 original size:35 final size:36
Alignment explanation
Indices: 98740--98811 Score: 137
Period size: 35 Copynumber: 2.0 Consensus size: 36
98730 GCCAACCATA
98740 CAGTATTGGAATTTGATCTGGACCGACAGC-TTGTC
1 CAGTATTGGAATTTGATCTGGACCGACAGCTTTGTC
98775 CAGTATTGGAATTTGATCTGGACCGACAGCTTTGTC
1 CAGTATTGGAATTTGATCTGGACCGACAGCTTTGTC
98811 C
1 C
98812 CCTCCCCATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 30 0.83
36 6 0.17
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (36 bp):
CAGTATTGGAATTTGATCTGGACCGACAGCTTTGTC
Found at i:99188 original size:2 final size:2
Alignment explanation
Indices: 99181--99219 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
99171 GCTTGCCTCT
99181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
99220 CCTTTGTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:107375 original size:20 final size:20
Alignment explanation
Indices: 107346--107384 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
107336 AGAGCTCATA
*
107346 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
107366 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
107385 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Done.