Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003196.1 Hibiscus syriacus cultivar Beakdansim tig00006725_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: 143397
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:10012 original size:20 final size:20
Alignment explanation
Indices: 9989--10027 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
9979 AGGCATCAGC
*
9989 AATTTTCACAACACAGACTG
1 AATTTCCACAACACAGACTG
10009 AATTTCCACAACACAGACT
1 AATTTCCACAACACAGACT
10028 ATCTGAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.28, G:0.08, T:0.23
Consensus pattern (20 bp):
AATTTCCACAACACAGACTG
Found at i:12354 original size:18 final size:17
Alignment explanation
Indices: 12330--12377 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
12320 TTCTGTTAAT
12330 TTTTAAAAAATAA-TATA
1 TTTTAAAAAA-AATTATA
12347 TATTTAAAACTAAAATTATA
1 T-TTTAAAA--AAAATTATA
12367 TTTTAAAAAAA
1 TTTTAAAAAAA
12378 CACAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 4 0.15
18 7 0.26
19 9 0.33
20 7 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTTAAAAAAAATTATA
Found at i:14375 original size:16 final size:17
Alignment explanation
Indices: 14354--14387 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
14344 TAATTTTGAA
14354 AAAATAA-ATAATATTT
1 AAAATAATATAATATTT
*
14370 AAAATAATATTATATTT
1 AAAATAATATAATATTT
14387 A
1 A
14388 TAAAAACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAATATAATATTT
Found at i:18886 original size:73 final size:72
Alignment explanation
Indices: 18767--19138 Score: 537
Period size: 73 Copynumber: 5.1 Consensus size: 72
18757 TGTGGTTGTT
* * * * * *
18767 TTTGTTTATACGCCGCCTAACAGTCTTGATTCTTCGGATTTAAAAATGCGCGCGAGTGACATTGA
1 TTTGTCTATATGCAGCCTAACGGTCTTGATTCTTCAG-TTTAAAAATGCGCGCGAGCGACATTGA
18832 AGTGAGTG
65 AGTGAGTG
*
18840 TTTGTCTATATGCAGCCTAAAGGTCTTGATTCTTCAGTTTAAAAAATGCGCGCGAGCGACATTGA
1 TTTGTCTATATGCAGCCTAACGGTCTTGATTCTTCAGTTT-AAAAATGCGCGCGAGCGACATTGA
18905 AGTGAGTG
65 AGTGAGTG
* *
18913 TTTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGTTTTAAAAATGCGCGCGAGCGACATTAA
1 TTTGTCTATATGCAGCCTAACGGTCTTGATTCTTCAG-TTTAAAAATGCGCGCGAGCGACATTGA
18978 AGTGAGTG
65 AGTGAGTG
* * *
18986 TTTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGTTTTAAAAATGTGCGCGAGCGTCATTGA
1 TTTGTCTATATGCAGCCTAACGGTCTTGATTCTTCAG-TTTAAAAATGCGCGCGAGCGACATTGA
*
19051 AGTGAGGG
65 AGTGAGTG
* * * *
19059 TGTGTCTATATGCAGTCTAACGGTCTTGATTCTTCAGATTTAAAATTGTGCGCGAGCGACATTGA
1 TTTGTCTATATGCAGCCTAACGGTCTTGATTCTTCAG-TTTAAAAATGCGCGCGAGCGACATTGA
19124 AGTGAGTG
65 AGTGAGTG
*
19132 TGTGTCT
1 TTTGTCT
19139 TCACGCGCGG
Statistics
Matches: 276, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
72 3 0.01
73 270 0.98
74 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (72 bp):
TTTGTCTATATGCAGCCTAACGGTCTTGATTCTTCAGTTTAAAAATGCGCGCGAGCGACATTGAA
GTGAGTG
Found at i:19307 original size:93 final size:93
Alignment explanation
Indices: 19173--19479 Score: 332
Period size: 92 Copynumber: 3.3 Consensus size: 93
19163 ATATGCAGCC
* * * * ** * *
19173 TAACTGTCTTGATTCTTCCTAAATGG-AATCTCGCAGGCTGCATTTAAGTGAGTGTGCATCTACA
1 TAACGGTCTTGATTCCTCCTAAA-GGAAATCACACAAACTGCATTTAAGTAAGTGTGTATCTACA
*
19237 AGTGTGCGCATTTTTGTTAATATACGGCG
65 AGTGTGCACATTTTTGTTAATATACGGCG
* ***
19266 TAACGGTCTTGATTCCTCCTGAAGGAAATCACGTGAACTGCATTTAAGTAAGTGTGTATCTACAA
1 TAACGGTCTTGATTCCTCCTAAAGGAAATCACACAAACTGCATTTAAGTAAGTGTGTATCTACAA
* * *
19331 -TGTGCACGTTTTTGTCAATATACGACG
66 GTGTGCACATTTTTGTTAATATACGGCG
* * ** * *
19358 TAACGGTCTTGATTCCTCCTAAAGGGAATCACACAAACTGCATTTAGGTTTGTGTGTGTCTAAAA
1 TAACGGTCTTGATTCCTCCTAAAGGAAATCACACAAACTGCATTTAAGTAAGTGTGTATCTACAA
* * * *
19423 GTTTGCACATTTTCG-TAATATACAGTG
66 GTGTGCACATTTTTGTTAATATACGGCG
* *
19450 TAACGGTCTTGATTCCTCTTAAAGGTAATC
1 TAACGGTCTTGATTCCTCCTAAAGGAAATC
19480 GTGTGAGCGA
Statistics
Matches: 179, Mismatches: 33, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
92 116 0.65
93 63 0.35
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (93 bp):
TAACGGTCTTGATTCCTCCTAAAGGAAATCACACAAACTGCATTTAAGTAAGTGTGTATCTACAA
GTGTGCACATTTTTGTTAATATACGGCG
Found at i:24686 original size:135 final size:135
Alignment explanation
Indices: 24435--24971 Score: 799
Period size: 135 Copynumber: 4.0 Consensus size: 135
24425 CAGACATTGT
* * ** * ** *
24435 TACCAAAGCCAAGGATCATACTCCTAAAACTGCAAGTAGACCAGTTGACATTGGC-TCAAAAGTG
1 TACCAAAGCCAAGGATCATACCCCTAAAAGTGGTAGTATACCAGTTGATGTT-GCTTCAGAAGTG
* * * * * * **
24499 AGCAGCAAATCCAAAATTGAGGCTAGTGTCGACACACCCAAGTCTATTAAACCCAAGGATGGTGA
65 GGCAGCAAATCCAAAACTGAGGATGGTGTCGACACACCCAACTCAACCAAACCCAAGGATGGTGA
24564 CAATGC
130 CAATGC
*
24570 TACCAAAGCCAAGGATCATACCCCTAAAAGTGGTAGTATAACAGTTGATGTTGCTTCAGAAGTGG
1 TACCAAAGCCAAGGATCATACCCCTAAAAGTGGTAGTATACCAGTTGATGTTGCTTCAGAAGTGG
24635 GCAGCAAATCCAAAACTGAGGATGGTGTCGACACACCCAACTCAACCAAACCCAAGGATGGTGAC
66 GCAGCAAATCCAAAACTGAGGATGGTGTCGACACACCCAACTCAACCAAACCCAAGGATGGTGAC
*
24700 ATTGC
131 AATGC
* *
24705 TACCAAAGCCGAGGATCATACCCCTAAAAATGGTAGTATACCAGTTGATGTTGCTTCAGAAGTGG
1 TACCAAAGCCAAGGATCATACCCCTAAAAGTGGTAGTATACCAGTTGATGTTGCTTCAGAAGTGG
24770 GCAGCAAATCCAAAACTGAGGATGGTGTCGACACACCCAACTCAACCAAACCCAAGGATGGTGAC
66 GCAGCAAATCCAAAACTGAGGATGGTGTCGACACACCCAACTCAACCAAACCCAAGGATGGTGAC
*
24835 ATTGC
131 AATGC
*
24840 TACCAAAGCCAAGGATCATACTCCTAAAAGTGGTAGTATACCAGTTGATGTTGCTTCAGAAGTGG
1 TACCAAAGCCAAGGATCATACCCCTAAAAGTGGTAGTATACCAGTTGATGTTGCTTCAGAAGTGG
* * * * *
24905 GCAGCAAATCCAAAACTGAGGATGGCGTCAACACTCCCAAGC-CAACCAAACCCAAGGACGGCGA
66 GCAGCAAATCCAAAACTGAGGATGGTGTCGACACACCCAA-CTCAACCAAACCCAAGGATGGTGA
24969 CAA
130 CAA
24972 ACCCAAGGAT
Statistics
Matches: 370, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
134 2 0.01
135 367 0.99
136 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (135 bp):
TACCAAAGCCAAGGATCATACCCCTAAAAGTGGTAGTATACCAGTTGATGTTGCTTCAGAAGTGG
GCAGCAAATCCAAAACTGAGGATGGTGTCGACACACCCAACTCAACCAAACCCAAGGATGGTGAC
AATGC
Found at i:25174 original size:153 final size:152
Alignment explanation
Indices: 24816--25277 Score: 451
Period size: 153 Copynumber: 3.0 Consensus size: 152
24806 CCAACTCAAC
* * * *
24816 CAAACCCAAGGATGGTGACATTGCTACCAAAGCCAAGGATCATACTCCTAAAAGTGGTAGTATAC
1 CAAACCCAAGGATGGTGACAATGTTACCAAAGCCAAGGATCATAC-CCTAAAAGTGGTAGGAGAC
* ** *
24881 CAGTTGATGTTGCTTCAGAAGTGGGCAGCAAATCCAAAACTGAGGATGGCGTCAACACTCCCAAG
65 CAGTTGATGTTGCTGCAGAAGTGGGCAGCAAATCCAAAACTGAGGACAGCGTCAACACGCCCAAG
*
24946 CCAACCAAACCCAAGGACGGCGA
130 CCAACCAAACCCAAGGACGACGA
*
24969 CAAACCCAAGGATGGTGACAATGTTACCAAAGCCAAGGACCATACCTCTAAAAGTGGTAGGAGAC
1 CAAACCCAAGGATGGTGACAATGTTACCAAAGCCAAGGATCATACC-CTAAAAGTGGTAGGAGAC
* * * * * * ** * *
25034 CTGTTGATGTTGCTGCAGAATTGGGCAGGAAATCGAAAACTGAGGGCAGTGTTGACAGGCCTAAG
65 CAGTTGATGTTGCTGCAGAAGTGGGCAGCAAATCCAAAACTGAGGACAGCGTCAACACGCCCAAG
* * *
25099 TCAACCAAACCCAAGGCCGATGA
130 CCAACCAAACCCAAGGACGACGA
* * * * * * *
25122 CAAACCGAAGGATGGCGACAATGTTACCAAATCCAAGGGTAATGCCCGTAAAAGTGGTATTG-GA
1 CAAACCCAAGGATGGTGACAATGTTACCAAAGCCAAGGATCATACCC-TAAAAGTGGTA-GGAGA
* * ** * ** * * * **
25186 CCGGTTG-TCCTTGCTTTAAAAGCAGGCAGCAAAGCCAAAACTAAGGACAGTGTCGCCACGCCCA
64 CCAGTTGAT-GTTGCTGCAGAAGTGGGCAGCAAATCCAAAACTGAGGACAGCGTCAACACGCCCA
* * * *
25250 AGTCAACCAAACCCGAGGATGGCGA
128 AGCCAACCAAACCCAAGGACGACGA
25275 CAA
1 CAA
25278 TGTTACCAAA
Statistics
Matches: 252, Mismatches: 53, Indels: 8
0.81 0.17 0.03
Matches are distributed among these distances:
152 3 0.01
153 248 0.98
154 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (152 bp):
CAAACCCAAGGATGGTGACAATGTTACCAAAGCCAAGGATCATACCCTAAAAGTGGTAGGAGACC
AGTTGATGTTGCTGCAGAAGTGGGCAGCAAATCCAAAACTGAGGACAGCGTCAACACGCCCAAGC
CAACCAAACCCAAGGACGACGA
Found at i:25368 original size:135 final size:135
Alignment explanation
Indices: 25122--25388 Score: 338
Period size: 135 Copynumber: 2.0 Consensus size: 135
25112 AGGCCGATGA
* * * * *
25122 CAAACCGAAGGATGGCGACAATGTTACCAAATCCAAGGGTAATGCCCGTAAAAGTGGTATTGGAC
1 CAAACCGAAGGATGGCGACAATGTTACCAAAGCCAAGGATAATACCCCTAAAAGTGGTAGTGGAC
* * * * * * *
25187 CGGTTGTCCTTGCTTTAAAAGCAGGCAGCAAAGCCAAAACTAAGGACAGTGTCGCCACGCCCAAG
66 CAGTTGACATTGCTTCAAAAGCAGGAAGCAAAGCCAAAACTAAGGACAGTGTCGACACCCCCAAG
25252 TCAAC
131 TCAAC
* * *
25257 CAAACCCG-AGGATGGCGACAATGTTACCAAAGCCAAGGATCATACCCCTGAAAGTGTTAGTGGA
1 CAAA-CCGAAGGATGGCGACAATGTTACCAAAGCCAAGGATAATACCCCTAAAAGTGGTAGTGGA
* * * * *
25321 CCAGTTGACATTGCTTCAAAAGCGGGAAGCAAATCCGAATCTGAGGACAGTGTCGACACCCCCAA
65 CCAGTTGACATTGCTTCAAAAGCAGGAAGCAAAGCCAAAACTAAGGACAGTGTCGACACCCCCAA
25386 GTC
130 GTC
25389 TACTAATCCC
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
135 108 0.97
136 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (135 bp):
CAAACCGAAGGATGGCGACAATGTTACCAAAGCCAAGGATAATACCCCTAAAAGTGGTAGTGGAC
CAGTTGACATTGCTTCAAAAGCAGGAAGCAAAGCCAAAACTAAGGACAGTGTCGACACCCCCAAG
TCAAC
Found at i:26661 original size:45 final size:45
Alignment explanation
Indices: 26611--26708 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
26601 AACAAACGGA
* *
26611 AATCAAAAGGAATTAATCCTTTGATTTTACTTCTCACAATCCAAT
1 AATCAAAAGAAACTAATCCTTTGATTTTACTTCTCACAATCCAAT
* * * *
26656 AATCAAAATAAACTAATCGTTTGATTTTACTTTTGACAATCCAAT
1 AATCAAAAGAAACTAATCCTTTGATTTTACTTCTCACAATCCAAT
26701 AATCAAAA
1 AATCAAAA
26709 AGCTTTAGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (45 bp):
AATCAAAAGAAACTAATCCTTTGATTTTACTTCTCACAATCCAAT
Found at i:28911 original size:18 final size:19
Alignment explanation
Indices: 28870--28909 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
28860 TACCTAATTT
28870 TAAAATTTTAGAGGAAAAG
1 TAAAATTTTAGAGGAAAAG
28889 T-AAATTTTAGA-GAAAA-
1 TAAAATTTTAGAGGAAAAG
28905 TAAAA
1 TAAAA
28910 ATATAAACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.05
17 8 0.40
18 10 0.50
19 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (19 bp):
TAAAATTTTAGAGGAAAAG
Found at i:32332 original size:9 final size:10
Alignment explanation
Indices: 32306--32331 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
32296 GGGTATGTAC
32306 TTTTTTTATT
1 TTTTTTTATT
32316 TTTTTTTATT
1 TTTTTTTATT
32326 TTTTTT
1 TTTTTT
32332 AACACATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:32851 original size:18 final size:18
Alignment explanation
Indices: 32828--32864 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
32818 GAGTGCACAA
32828 CCATGCACAACCTTCTCC
1 CCATGCACAACCTTCTCC
*
32846 CCATGCACATCCTTCTCC
1 CCATGCACAACCTTCTCC
32864 C
1 C
32865 GGTGAAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.51, G:0.05, T:0.24
Consensus pattern (18 bp):
CCATGCACAACCTTCTCC
Found at i:33645 original size:15 final size:15
Alignment explanation
Indices: 33625--33657 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
33615 AAGAATTTGC
33625 AAGGGAAAAGGTGAA
1 AAGGGAAAAGGTGAA
*
33640 AAGGGAAAAGGTGGA
1 AAGGGAAAAGGTGAA
33655 AAG
1 AAG
33658 TGATTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.42, T:0.06
Consensus pattern (15 bp):
AAGGGAAAAGGTGAA
Found at i:34060 original size:88 final size:88
Alignment explanation
Indices: 33911--34087 Score: 336
Period size: 88 Copynumber: 2.0 Consensus size: 88
33901 ACTGAATGGA
33911 TAATATTGAGATCAAGTTGAGAAAACATCGAAAGAAATGAGATTAAAGCCCAAGAAATGAAATGC
1 TAATATTGAGATCAAGTTGAGAAAACATCGAAAGAAATGAGATTAAAGCCCAAGAAATGAAATGC
33976 TTTACGTGAAAGAAAACCTTCCC
66 TTTACGTGAAAGAAAACCTTCCC
*
33999 TAATATTGAGATCAAGTTGAGAAAACATCGAAAGAAATGAGATTAAAGCCCATGAAATGAAATGC
1 TAATATTGAGATCAAGTTGAGAAAACATCGAAAGAAATGAGATTAAAGCCCAAGAAATGAAATGC
*
34064 TTTATGTGAAAGAAAACCTTCCC
66 TTTACGTGAAAGAAAACCTTCCC
34087 T
1 T
34088 GATTTAAATG
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (88 bp):
TAATATTGAGATCAAGTTGAGAAAACATCGAAAGAAATGAGATTAAAGCCCAAGAAATGAAATGC
TTTACGTGAAAGAAAACCTTCCC
Found at i:36818 original size:8 final size:8
Alignment explanation
Indices: 36794--36824 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
36784 TTAAATAAAT
36794 AAAAATAA
1 AAAAATAA
36802 AATAAATAA
1 AA-AAATAA
36811 AAAAATAA
1 AAAAATAA
36819 AAAAAT
1 AAAAAT
36825 TCAAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:39391 original size:60 final size:61
Alignment explanation
Indices: 39313--39445 Score: 162
Period size: 61 Copynumber: 2.2 Consensus size: 61
39303 GGGTGACCAT
* * * * **
39313 TTTTGTAACTTTTAATAGTTGAGGGACTC-AACAAATTAACGTTCTATAGTCGAGGGATCA
1 TTTTGTAACTTTTAATAGTTAAGAGACTCAAACAAAATAACGTCCTATAGTCGAAAGATCA
* * *
39373 TTTTGTAACTTTTAATAGTTAAGATACTCAAATAAAATAACGTCCTATAGTTGAAAGATCA
1 TTTTGTAACTTTTAATAGTTAAGAGACTCAAACAAAATAACGTCCTATAGTCGAAAGATCA
39434 TTTGTGT-ACTTT
1 TTT-TGTAACTTT
39446 ACCTTTACTA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 26 0.42
61 33 0.53
62 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (61 bp):
TTTTGTAACTTTTAATAGTTAAGAGACTCAAACAAAATAACGTCCTATAGTCGAAAGATCA
Found at i:41712 original size:9 final size:9
Alignment explanation
Indices: 41698--41722 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41688 TTATTAACAG
41698 CACCGCCGC
1 CACCGCCGC
41707 CACCGCCGC
1 CACCGCCGC
41716 CACCGCC
1 CACCGCC
41723 ACCAGCACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.68, G:0.20, T:0.00
Consensus pattern (9 bp):
CACCGCCGC
Found at i:48036 original size:23 final size:23
Alignment explanation
Indices: 48010--48108 Score: 92
Period size: 23 Copynumber: 4.3 Consensus size: 23
48000 GAATAAGTTT
*
48010 GTTTTTTGTGTTCGTTTATGTTA
1 GTTTATTGTGTTCGTTTATGTTA
* *
48033 GTTTATTGTGTTCTTTTATATTCA
1 GTTTATTGTGTTCGTTTATGTT-A
* * *
48057 -TTTATTATGTTCGTTTGTGTTC
1 GTTTATTGTGTTCGTTTATGTTA
* * *
48079 GTTCATTTGTGTTCGTTTACGTTC
1 GTTTA-TTGTGTTCGTTTATGTTA
48103 GTTTAT
1 GTTTAT
48109 GTTCGTCTAT
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
23 40 0.67
24 20 0.33
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.62
Consensus pattern (23 bp):
GTTTATTGTGTTCGTTTATGTTA
Found at i:48087 original size:14 final size:14
Alignment explanation
Indices: 48065--48095 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
48055 CATTTATTAT
*
48065 GTTCGTTTGTGTTC
1 GTTCATTTGTGTTC
48079 GTTCATTTGTGTTC
1 GTTCATTTGTGTTC
48093 GTT
1 GTT
48096 TACGTTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.26, T:0.58
Consensus pattern (14 bp):
GTTCATTTGTGTTC
Found at i:48398 original size:2 final size:2
Alignment explanation
Indices: 48391--48485 Score: 156
Period size: 2 Copynumber: 48.0 Consensus size: 2
48381 AAAGAGAAGC
* *
48391 AT AT AT AT A- AA AA 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
48432 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
*
48474 AT AT AT GT AT AT
1 AT AT AT AT AT AT
48486 GTCAATTTTG
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
1 1 0.01
2 88 0.99
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53825 original size:14 final size:14
Alignment explanation
Indices: 53798--53831 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
53788 ATAAATTAGT
53798 TAAAAATTTAAAAA
1 TAAAAATTTAAAAA
53812 TAAAATATTT-AAAA
1 TAAAA-ATTTAAAAA
53826 TAAAAA
1 TAAAAA
53832 GTAAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 14 0.74
15 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAAATTTAAAAA
Found at i:61875 original size:64 final size:65
Alignment explanation
Indices: 61732--61876 Score: 206
Period size: 65 Copynumber: 2.2 Consensus size: 65
61722 TTTTTCAAAG
* * *
61732 TGATGCACCGATGCACACACCATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATT
1 TGATGCATCGATGCACACACCATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACT
* *
61797 TGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGG-TTATTTTG-AAACATCGAATGCA
1 TGATGCATCGATGCACACA-CCATGCATCGATGCACTCAGGATT-TTATGAAAACATCGAATGCA
61859 CT
64 CT
61861 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
61877 TCTTAGTGCA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
64 35 0.48
65 38 0.52
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (65 bp):
TGATGCATCGATGCACACACCATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACT
Found at i:61876 original size:17 final size:19
Alignment explanation
Indices: 61848--61896 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
61838 TATTTTGAAA
61848 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
61866 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
61885 CACCGATGCACT
1 CATCGATGCACT
61897 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:69248 original size:21 final size:21
Alignment explanation
Indices: 69206--69249 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
69196 ACTCCGGGAG
*
69206 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
69227 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
69248 CT
1 CT
69250 CCTCCTCCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:70442 original size:65 final size:64
Alignment explanation
Indices: 70370--70527 Score: 203
Period size: 65 Copynumber: 2.5 Consensus size: 64
70360 TCAAATTGAG
* * *
70370 CATTGAATGCATTTCATGCATCGATGCACACA-CCATGCATCGATGCACTGAGGAT-TTTATGAA
1 CATTGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCCATGCACTCAGGATATTT-TG-A
70433 AA
63 AA
* * *
70435 CATTGAATGCATTTGATGCATCGATGTACCAGCCATGCATCCATGCACTCTGGCTATTTTGAAA
1 CATTGAATGCATTTGATGCATCGATGCACCAGCCATGCATCCATGCACTCAGGATATTTTGAAA
* *
70499 CATCGAATGCACTTGATGCATCGATGCAC
1 CATTGAATGCATTTGATGCATCGATGCAC
70528 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
64 31 0.38
65 48 0.59
66 3 0.04
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (64 bp):
CATTGAATGCATTTGATGCATCGATGCACCAGCCATGCATCCATGCACTCAGGATATTTTGAAA
Found at i:71293 original size:21 final size:21
Alignment explanation
Indices: 71251--71293 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
71241 TTTCTGGGCT
* *
71251 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
71272 AGGGGAATTGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
71293 A
1 A
71294 CGTATATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:78045 original size:21 final size:21
Alignment explanation
Indices: 78003--78045 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
77993 TTTCTGGGCT
* *
78003 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
78024 AGGGGAATTGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
78045 A
1 A
78046 CGTATATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:78610 original size:25 final size:25
Alignment explanation
Indices: 78576--78644 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
78566 GGGTAGAGGG
* *
78576 TCTATGCGGTCATTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
78601 TCTACGCGGTCCTTCGGGACAATAT
1 TCTACGCGGTCCTTCGGGACAATAT
78626 TCTACGCGGTCCTTCGGGA
1 TCTACGCGGTCCTTCGGGA
78645 TATATATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (25 bp):
TCTACGCGGTCCTTCGGGACAATAT
Found at i:78803 original size:23 final size:23
Alignment explanation
Indices: 78759--78803 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
78749 ATTATTATAT
*
78759 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
78782 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
78804 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:80141 original size:28 final size:28
Alignment explanation
Indices: 80082--80148 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 28
80072 ATATTAAATT
*
80082 AAAAATAAAATATATTTAAAAAGTCAAGA
1 AAAAATAAAATATATTTAAAAAAT-AAGA
**
80111 AAAAGATAAAATATATTTAAAAAAT-TTA
1 AAAA-ATAAAATATATTTAAAAAATAAGA
80139 AAAAATAAAA
1 AAAAATAAAA
80149 AAAATTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.18
28 5 0.15
29 4 0.12
30 19 0.56
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (28 bp):
AAAAATAAAATATATTTAAAAAATAAGA
Found at i:80649 original size:2 final size:2
Alignment explanation
Indices: 80642--80671 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
80632 GTTTACCCTA
80642 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
80672 TTACCATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85962 original size:31 final size:31
Alignment explanation
Indices: 85926--85989 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
85916 ATGGTAAATT
*
85926 AAAAAATAATAATCTTTAATAACTAAAATAAG
1 AAAAAA-ATTAATCTTTAATAACTAAAATAAG
85958 AAAAAAATTAATCTTTAATAACTAAAATAAG
1 AAAAAAATTAATCTTTAATAACTAAAATAAG
85989 A
1 A
85990 GATTGAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.28
Consensus pattern (31 bp):
AAAAAAATTAATCTTTAATAACTAAAATAAG
Found at i:87980 original size:23 final size:22
Alignment explanation
Indices: 87937--87980 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
87927 TAATAATATA
* **
87937 TATTTATTAAAAATATTATTTT
1 TATTTAATAAAAATAGGATTTT
87959 TATTTAATAAAAATAGGGATTT
1 TATTTAATAAAAATA-GGATTT
87981 AATTGAAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
TATTTAATAAAAATAGGATTTT
Found at i:89132 original size:20 final size:21
Alignment explanation
Indices: 89102--89149 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
89092 ATGTATTGAT
*
89102 TTTTAAAAAAATATAATAAGA
1 TTTTAAAAAAATACAATAAGA
89123 TTTTAAAAAAATACAATAAGA
1 TTTTAAAAAAATACAATAAGA
89144 TTTTAA
1 TTTTAA
89150 TGTATTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (21 bp):
TTTTAAAAAAATACAATAAGA
Found at i:90658 original size:15 final size:15
Alignment explanation
Indices: 90638--90667 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
90628 GCTAAAATGA
90638 AACAAATAGTAAAGG
1 AACAAATAGTAAAGG
90653 AACAAATAGTAAAGG
1 AACAAATAGTAAAGG
90668 TTAGATGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.13
Consensus pattern (15 bp):
AACAAATAGTAAAGG
Found at i:100359 original size:31 final size:30
Alignment explanation
Indices: 100259--100361 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 30
100249 AAGTAAAAAG
* *
100259 AGTACCAATGTGAGAAAATTTTCCAAGTTAA
1 AGTACCAATTTGAGAAAAGTTTCCAAGTT-A
* *
100290 AGTACCAATTTGAGACAAAG---CAAAGTTC
1 AGTACCAATTTGAGA-AAAGTTTCCAAGTTA
* *
100318 AGATATCAATTTGAGAAAAGTTTCCAAGTTT
1 AG-TACCAATTTGAGAAAAGTTTCCAAGTTA
100349 AGTTACCAATTTG
1 AG-TACCAATTTG
100362 TATAGGCATA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
28 6 0.10
29 18 0.31
31 31 0.53
32 3 0.05
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (30 bp):
AGTACCAATTTGAGAAAAGTTTCCAAGTTA
Found at i:101847 original size:14 final size:14
Alignment explanation
Indices: 101828--101855 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
101818 TCAGTATTTG
101828 GGGTTTAAAGTTTA
1 GGGTTTAAAGTTTA
101842 GGGTTTAAAGTTTA
1 GGGTTTAAAGTTTA
101856 TCTAATTGTT
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:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (14 bp):
GGGTTTAAAGTTTA
Found at i:110598 original size:27 final size:27
Alignment explanation
Indices: 110560--110616 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
110550 ATATCCAATG
110560 TTGAGAACCCAATCCAATGCATGAATT
1 TTGAGAACCCAATCCAATGCATGAATT
110587 TTGAGAACCCAATCCAATGCATGAATT
1 TTGAGAACCCAATCCAATGCATGAATT
110614 TTG
1 TTG
110617 CACGAGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (27 bp):
TTGAGAACCCAATCCAATGCATGAATT
Found at i:116456 original size:2 final size:2
Alignment explanation
Indices: 116449--116474 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
116439 AAACAGGAAA
116449 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
116475 TCTTAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128836 original size:27 final size:25
Alignment explanation
Indices: 128785--128836 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
128775 TTAAACTAAG
128785 AAAATTAAAGGTTAAAATATTATTTT
1 AAAATTAAAGGTTAAAATA-TATTTT
128811 AAAATTAAAAGGTCTTAAAATA-ATTT
1 AAAATT-AAAGG--TTAAAATATATTT
128837 AACCAACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
26 6 0.26
27 9 0.39
29 8 0.35
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (25 bp):
AAAATTAAAGGTTAAAATATATTTT
Found at i:130056 original size:21 final size:21
Alignment explanation
Indices: 130026--130089 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
130016 CAGAAATGTT
*
130026 AAAA-AATAATATTTTATGTA
1 AAAATAATAATATTTTATATA
*
130046 AAAATAATAATATTTTAAATA
1 AAAATAATAATATTTTATATA
*
130067 AAAATAATCATATTTTATATA
1 AAAATAATAATATTTTATATA
130088 AA
1 AA
130090 TTTTTATCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 4 0.10
21 35 0.90
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAATAATAATATTTTATATA
Found at i:131511 original size:3 final size:3
Alignment explanation
Indices: 131503--131527 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
131493 GAATAGAGTT
131503 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
131528 CGTCGTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:131984 original size:16 final size:16
Alignment explanation
Indices: 131965--132001 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
131955 TGATTTGATA
*
131965 TGATATTTACCTGACT
1 TGATATTTACCTAACT
131981 TGATATTTACCTAACT
1 TGATATTTACCTAACT
131997 T-ATAT
1 TGATAT
132002 ATATCATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (16 bp):
TGATATTTACCTAACT
Found at i:135313 original size:84 final size:80
Alignment explanation
Indices: 135176--135335 Score: 268
Period size: 84 Copynumber: 1.9 Consensus size: 80
135166 ATATAAATGA
135176 CTGTCCCTTTTTCCAATATATGGGTAAGGGGAGGTAAGATAGTAGGCTACCCCCAACACCA-AGT
1 CTGTCCCTTTTTCCAATATATGGGTAAGGGGAGGTAAGATAGTAGGCTACCCCCAACACCAGA-T
135240 TGAGAGCAGCTTATGG
65 TGAGAGCAGCTTATGG
135256 CTGTCCCTTTTTCCCATATATATGGGGTAAGGGGGAGGTAAGATAGTAGGCTACCCCCAACACCA
1 CTGTCCCTTTTT-CCA-ATATAT-GGGTAA-GGGGAGGTAAGATAGTAGGCTACCCCCAACACCA
135321 GATTGAGAGCAGCTT
62 GATTGAGAGCAGCTT
135336 CCGTAAGAGA
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
80 12 0.16
81 3 0.04
82 6 0.08
83 6 0.08
84 47 0.63
85 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
CTGTCCCTTTTTCCAATATATGGGTAAGGGGAGGTAAGATAGTAGGCTACCCCCAACACCAGATT
GAGAGCAGCTTATGG
Found at i:140765 original size:19 final size:19
Alignment explanation
Indices: 140741--140824 Score: 105
Period size: 19 Copynumber: 4.2 Consensus size: 19
140731 GCGATTTTGA
*
140741 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
140760 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
140781 AAAAGTGTTGTTGCGATAGTG
1 AAAA-TG-TGTTGCGATAGTG
*
140802 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
140821 AAAA
1 AAAA
140825 ATCCAAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
19 33 0.58
20 1 0.02
21 11 0.19
22 2 0.04
23 10 0.18
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:140796 original size:42 final size:41
Alignment explanation
Indices: 140736--140815 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 41
140726 GCAACGCGAT
* *
140736 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
*
140777 TTTGAAAAGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAATG-TGTTGCGATAGTGAAAAAGTGTTGCGA
140816 TAGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 10 0.29
42 25 0.71
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:140916 original size:49 final size:51
Alignment explanation
Indices: 140859--140961 Score: 156
Period size: 55 Copynumber: 2.0 Consensus size: 51
140849 TATTCATTCA
140859 CGTGGAGTTTGAAAC-TAAAGAA-TTGCGATAGTGTAAAAGATTCTCAAGC
1 CGTGGAGTTTGAAACATAAAGAAGTTGCGATAGTGTAAAAGATTCTCAAGC
140908 CGTGGAGTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAG
1 CGTGGAGTTTGAAAC-ATAAAGAA---GTTGCGATAGTGTAAAAGATTCTCAAG
140962 TGTTGGCAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
49 15 0.31
51 7 0.15
55 26 0.54
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (51 bp):
CGTGGAGTTTGAAACATAAAGAAGTTGCGATAGTGTAAAAGATTCTCAAGC
Found at i:141242 original size:29 final size:29
Alignment explanation
Indices: 141178--141249 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
141168 ACCACCAATC
141178 GTTGCGAACTTGGACTATCGCAAAATCGT
1 GTTGCGAACTTGGACTATCGCAAAATCGT
***
141207 AACGCGAACTTGGACTATCGCAAAATCGT
1 GTTGCGAACTTGGACTATCGCAAAATCGT
*
141236 GTTGCGAATTTGGA
1 GTTGCGAACTTGGA
141250 AACTGATTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (29 bp):
GTTGCGAACTTGGACTATCGCAAAATCGT
Found at i:142499 original size:2 final size:2
Alignment explanation
Indices: 142492--142524 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
142482 ATACTTTATT
142492 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
142525 AGATTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.