Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003274.1 Hibiscus syriacus cultivar Beakdansim tig00006885_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: 66043
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:6312 original size:59 final size:61
Alignment explanation
Indices: 6233--6363 Score: 187
Period size: 60 Copynumber: 2.2 Consensus size: 61
6223 CTAATTAAGG
* *
6233 GTATCG-ATCTACCTAATCTTCACAA-TTCTAATAGCATTTAATATCGATACCCATA-GGGA
1 GTATCGTA-CTACCTAATCTTCACAATTTCTAACAGCATTTAATATCGATACCCACAGGGGA
* *
6292 GTATCGTACTACCTATTCTTCATAATTTCTAACAGCATTTAATATCGATACCCACAGGGGA
1 GTATCGTACTACCTAATCTTCACAATTTCTAACAGCATTTAATATCGATACCCACAGGGGA
6353 GTATCGATACT
1 GTATCG-TACT
6364 TAGGAGTCAG
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
59 21 0.33
60 29 0.45
61 10 0.16
62 4 0.06
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (61 bp):
GTATCGTACTACCTAATCTTCACAATTTCTAACAGCATTTAATATCGATACCCACAGGGGA
Found at i:12226 original size:22 final size:21
Alignment explanation
Indices: 12186--12227 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
12176 CTATTTAATC
* *
12186 ATTTTTATTTTAATTATTTAT
1 ATTTATATTTTAATAATTTAT
12207 ATTTATATTATTAATAATTTA
1 ATTTATATT-TTAATAATTTA
12228 GGGTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTATATTTTAATAATTTAT
Found at i:12487 original size:36 final size:35
Alignment explanation
Indices: 12415--12489 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 35
12405 AATGAGATTA
12415 TTAATATTATTAAATAACATTAAATAGTAATTTATT
1 TTAATATTATTAAATAACATTAAATAG-AATTTATT
12451 TTAATTATT-TTAAATTAA-ATTAAATA-AATTCATATT
1 TTAA-TATTATTAAA-TAACATTAAATAGAATT--TATT
12487 TTA
1 TTA
12490 TTGCAACGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
34 4 0.11
36 24 0.69
37 7 0.20
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (35 bp):
TTAATATTATTAAATAACATTAAATAGAATTTATT
Found at i:23759 original size:35 final size:35
Alignment explanation
Indices: 23677--23840 Score: 199
Period size: 35 Copynumber: 4.6 Consensus size: 35
23667 TTGAATCTGA
** *
23677 CCTTCACAGGAGAGTAGTGAAGTC-ATTCGAACTC-AG
1 CCTTCACAAAAGAGTAGTGAAG-CAATGC-AA-TCAAG
23713 CCTTCACAAAAGAGTAGTGAAGCAATGCAATCAAG
1 CCTTCACAAAAGAGTAGTGAAGCAATGCAATCAAG
* * *
23748 CCTTCAGAAAAGAGTAGTGAAGTAGTGCAATCAAG
1 CCTTCACAAAAGAGTAGTGAAGCAATGCAATCAAG
*
23783 CCTTCATAAAAGAGTAGTGAAGCAATGCAAATCCAA-
1 CCTTCACAAAAGAGTAGTGAAGCAATGC-AAT-CAAG
23819 CCTTCACAAAAGAGTAGTGAAG
1 CCTTCACAAAAGAGTAGTGAAG
23841 GATCAAATCA
Statistics
Matches: 114, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
34 2 0.02
35 62 0.54
36 47 0.41
37 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.20
Consensus pattern (35 bp):
CCTTCACAAAAGAGTAGTGAAGCAATGCAATCAAG
Found at i:23764 original size:71 final size:71
Alignment explanation
Indices: 23676--23840 Score: 221
Period size: 71 Copynumber: 2.3 Consensus size: 71
23666 CTTGAATCTG
** *
23676 ACCTTCACAGGAGAGTAGTGAAGTCA-TTCGAACTC-AGCCTTCACAAAAGAGTAGTGAAGCAAT
1 ACCTTCACAAAAGAGTAGTGAAGT-AGTGC-AA-TCAAGCCTTCACAAAAGAGTAGTGAAGCAAT
23739 GC-AAT-CA
63 GCAAATCCA
* *
23746 AGCCTTCAGAAAAGAGTAGTGAAGTAGTGCAATCAAGCCTTCATAAAAGAGTAGTGAAGCAATGC
1 A-CCTTCACAAAAGAGTAGTGAAGTAGTGCAATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGC
23811 AAATCCA
65 AAATCCA
23818 ACCTTCACAAAAGAGTAGTGAAG
1 ACCTTCACAAAAGAGTAGTGAAG
23841 GATCAAATCA
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
69 2 0.02
70 33 0.39
71 46 0.55
72 3 0.04
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (71 bp):
ACCTTCACAAAAGAGTAGTGAAGTAGTGCAATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
AATCCA
Found at i:24047 original size:16 final size:16
Alignment explanation
Indices: 24026--24058 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
24016 TTATAAGTAT
24026 TATAATAATATTATTA
1 TATAATAATATTATTA
*
24042 TATAATATTATTATTA
1 TATAATAATATTATTA
24058 T
1 T
24059 TATATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAATAATATTATTA
Found at i:24077 original size:27 final size:27
Alignment explanation
Indices: 24023--24078 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
24013 TCATTATAAG
*
24023 TATTATAATAATATTATTATATAATAT
1 TATTATAATAATATTATAATATAATAT
* *
24050 TATTATTATTATATTATAAT-TAATTAT
1 TATTATAATAATATTATAATATAA-TAT
24077 TA
1 TA
24079 CAATTTTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTATAATAATATTATAATATAATAT
Found at i:26592 original size:12 final size:12
Alignment explanation
Indices: 26575--26615 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
26565 TTTGTGTGTG
26575 TATGTATGTATA
1 TATGTATGTATA
26587 TATGTATGTATA
1 TATGTATGTATA
* *
26599 TATATATATATGA
1 TATGTATGTAT-A
26612 TATG
1 TATG
26616 AGGAACACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.49
Consensus pattern (12 bp):
TATGTATGTATA
Found at i:26594 original size:16 final size:16
Alignment explanation
Indices: 26573--26615 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
26563 TATTTGTGTG
26573 TGTATGTATGTATATA
1 TGTATGTATGTATATA
*
26589 TGTATGTATATATATA
1 TGTATGTATGTATATA
*
26605 TATATGATATG
1 TGTATG-TATG
26616 AGGAACACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (16 bp):
TGTATGTATGTATATA
Found at i:30929 original size:37 final size:37
Alignment explanation
Indices: 30879--30960 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 37
30869 ATCATATTAT
30879 TTGAAAATAATAAACAAAAATAATTTGTAAACCTGAC
1 TTGAAAATAATAAACAAAAATAATTTGTAAACCTGAC
*
30916 TTGAAAATAATAAACAAAAATAATTTGTAAACCTGAT
1 TTGAAAATAATAAACAAAAATAATTTGTAAACCTGAC
30953 TTGAAAAT
1 TTGAAAAT
30961 TGAGAAAATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (37 bp):
TTGAAAATAATAAACAAAAATAATTTGTAAACCTGAC
Found at i:31709 original size:56 final size:56
Alignment explanation
Indices: 31565--32223 Score: 636
Period size: 56 Copynumber: 11.8 Consensus size: 56
31555 ATCAATAATG
* * * ** ***
31565 TTGTAATGTTTAACTTATCCAAGTTTTTACAATCAAATATCAAAGTTTAAATATTG
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGCA
* * * * *
31621 TTGTAATGTCTTAACTTATCCAAGTTATTACATTCAAAGATGGAAGTCTGAATAACG
1 TTGTAATGT-TTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGCA
* * **
31678 TTGTAATGTTTAGCTTATCCAAGTTATTACATTCACTGATGGAAGTTTAAATAGCA
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGCA
* ** * *
31734 TTGT-ATAGTTTAACTTATCCAATTTGTTACATTCAATTATGGAAGTTTGAATATCA
1 TTGTAAT-GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGCA
* * *
31790 TTGTAGA-GTTTAACTTATCCAACTTGTTACATTCACAA-ATGGAAGTTTGAATAGCG
1 TTGTA-ATGTTTAACTTATCCAAGTTGTTACATTCA-AAGATGGAAGTTTAAATAGCA
* *
31846 TTGTAGA-GTTTAACTTATCCAAGTTGTTACATTTAAAGATGGAAGTTTAAATAGAA
1 TTGTA-ATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGCA
* * * *
31902 TTGTAATGTATAACTTATCCAAG-TGTTACATTCAAAAATGAAAGTTTAAATAGTA
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGCA
* * * * * **
31957 TTGTAATTTCTTAACTTATCCAAGTTTTTACAATCAAATATGGAAGTTTGAATAGTG
1 TTGTAATGT-TTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGCA
* * * *
32014 CTATAGA-GTTTAACTTATCCAAGTTGTTACATTCAAA-ATTGAAAGTTTACATAGCA
1 TTGTA-ATGTTTAACTTATCCAAGTTGTTACATTCAAAGA-TGGAAGTTTAAATAGCA
* * * * **
32070 TTGTAATGTCTTAACATATCCAA---GTTACATTCAAAGATAGAGGTTTGAATAAAA
1 TTGTAATGT-TTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGCA
* * * ** * **
32124 TTTTAATGTTTAACTTATCCAAGTTGTTACATTAAAAAATACAAGATTAAATAGTG
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGCA
* *
32180 TTGTAAAGTCTTAACTTATCCAAGTTGTTGCATTCAAAGATGGA
1 TTGTAATGT-TTAACTTATCCAAGTTGTTACATTCAAAGATGGA
32224 TAAGTTAAAA
Statistics
Matches: 502, Mismatches: 83, Indels: 35
0.81 0.13 0.06
Matches are distributed among these distances:
53 12 0.02
54 30 0.06
55 44 0.09
56 295 0.59
57 119 0.24
58 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (56 bp):
TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAGCA
Found at i:31801 original size:112 final size:112
Alignment explanation
Indices: 31565--32223 Score: 708
Period size: 112 Copynumber: 5.9 Consensus size: 112
31555 ATCAATAATG
* * * * ***
31565 TTGTAATGTTTAACTTATCCAAGTTTTTACAATCAAATATCAAAGTTTAAATATTGTTGTAATGT
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAAATGAAAGTTTAAATAGCATTGTAA-GT
* * *
31630 CTTAACTTATCCAAGTTATTACATTCAAAGATGGAAGTCTGAATAACG
65 CTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * *** *
31678 TTGTAATGTTTAGCTTATCCAAGTTATTACATTCACTGATGGAAGTTTAAATAGCATTGTATAGT
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAAATGAAAGTTTAAATAGCATTGTA-AGT
* ** *
31743 -TTAACTTATCCAATTTGTTACATTCAATTATGGAAGTTTGAATATCA
65 CTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * * *
31790 TTGTAGA-GTTTAACTTATCCAACTTGTTACATTCACAAATGGAAGTTTGAATAGCGTTGTAGAG
1 TTGTA-ATGTTTAACTTATCCAAGTTGTTACATTCAAAAATGAAAGTTTAAATAGCATTGTA-AG
* *
31854 T-TTAACTTATCCAAGTTGTTACATTTAAAGATGGAAGTTTAAATAGA-A
64 TCTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATA-ACA
* * *
31902 TTGTAATGTATAACTTATCCAAG-TGTTACATTCAAAAATGAAAGTTTAAATAGTATTGTAATTT
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAAATGAAAGTTTAAATAGCATTGTAA-GT
* * * ***
31966 CTTAACTTATCCAAGTTTTTACAATCAAATATGGAAGTTTGAATAGTG
65 CTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * *
32014 CTATAGA-GTTTAACTTATCCAAGTTGTTACATTCAAAATTGAAAGTTTACATAGCATTGTAATG
1 TTGTA-ATGTTTAACTTATCCAAGTTGTTACATTCAAAAATGAAAGTTTAAATAGCATTGTAA-G
* * * *
32078 TCTTAACATATCCAA---GTTACATTCAAAGATAGAGGTTTGAATAAAA
64 TCTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * **
32124 TTTTAATGTTTAACTTATCCAAGTTGTTACATTAAAAAAT-ACAAGATTAAATAGTGTTGTAAAG
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAAATGA-AAGTTTAAATAGCATTGT-AAG
*
32188 TCTTAACTTATCCAAGTTGTTGCATTCAAAGATGGA
64 TCTTAACTTATCCAAGTTGTTACATTCAAAGATGGA
32224 TAAGTTAAAA
Statistics
Matches: 457, Mismatches: 74, Indels: 30
0.81 0.13 0.05
Matches are distributed among these distances:
109 2 0.00
110 87 0.19
111 36 0.08
112 211 0.46
113 120 0.26
114 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (112 bp):
TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAAATGAAAGTTTAAATAGCATTGTAAGTC
TTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
Found at i:31865 original size:168 final size:166
Alignment explanation
Indices: 31565--32223 Score: 706
Period size: 168 Copynumber: 3.9 Consensus size: 166
31555 ATCAATAATG
* * * *
31565 TTGTAATGTTTAACTTATCCAAGTTTTTACAATCAAATATCAAAGTTTAAATATTGTTGTAATGT
1 TTGTAATGTTTAACTTATCCAA-TTGTTACATTCAAATATGAAAGTTTAAATA-TATTGTAATGT
* * * *
31630 CTTAACTTATCCAAGTTATTACATTCAAAGATGGAAGTCTGAATAACGTTGTA-ATGTTTAGCTT
64 CTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAGCGTTGTAGA-GTTTAACTT
* *
31694 ATCCAAGTTATTACATTCACTGATGGAAGTTTAAATAGCA
128 ATCCAAGTTGTTACATTCA-AGATGGAAGTTTAAATAGCA
* * *
31734 TTGT-ATAGTTTAACTTATCCAATTTGTTACATTCAATTATGGAAGTTTGAATATCATTGTAGA-
1 TTGTAAT-GTTTAACTTATCCAA-TTGTTACATTCAAATATGAAAGTTTAAATAT-ATTGTA-AT
*
31797 GT-TTAACTTATCCAACTTGTTACATTCACAA-ATGGAAGTTTGAATAGCGTTGTAGAGTTTAAC
62 GTCTTAACTTATCCAAGTTGTTACATTCA-AAGATGGAAGTTTGAATAGCGTTGTAGAGTTTAAC
* *
31860 TTATCCAAGTTGTTACATTTAAAGATGGAAGTTTAAATAGAA
126 TTATCCAAGTTGTTACA-TTCAAGATGGAAGTTTAAATAGCA
* * * *
31902 TTGTAATGTATAACTTATCCAAGTGTTACATTCAAAAATGAAAGTTTAAATAGTATTGTAATTTC
1 TTGTAATGTTTAACTTATCCAATTGTTACATTCAAATATGAAAGTTTAAATA-TATTGTAATGTC
* * * * * *
31967 TTAACTTATCCAAGTTTTTACAATCAAATATGGAAGTTTGAATAGTGCTATAGAGTTTAACTTAT
65 TTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAGCGTTGTAGAGTTTAACTTAT
* * *
32032 CCAAGTTGTTACATTCAAAATTGAAAGTTTACATAGCA
130 CCAAGTTGTTACATTCAAGA-TGGAAGTTTAAATAGCA
* * * * * *
32070 TTGTAATGTCTTAACATATCCAA--GTTACATTCAAAGAT-AGAGGTTTGAATAAAATTTTAATG
1 TTGTAATGT-TTAACTTATCCAATTGTTACATTCAAATATGA-AAGTTTAAAT-ATATTGTAATG
* * ** * * * *
32132 T-TTAACTTATCCAAGTTGTTACATTAAAAAATACAAGATTAAATAGTGTTGTAAAGTCTTAACT
63 TCTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAGCGTTGTAGAGT-TTAACT
*
32196 TATCCAAGTTGTTGCATTCAAAGATGGA
127 TATCCAAGTTGTTACATTC-AAGATGGA
32224 TAAGTTAAAA
Statistics
Matches: 416, Mismatches: 57, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
166 47 0.11
167 96 0.23
168 203 0.49
169 69 0.17
170 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (166 bp):
TTGTAATGTTTAACTTATCCAATTGTTACATTCAAATATGAAAGTTTAAATATATTGTAATGTCT
TAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAGCGTTGTAGAGTTTAACTTATC
CAAGTTGTTACATTCAAGATGGAAGTTTAAATAGCA
Found at i:37566 original size:40 final size:40
Alignment explanation
Indices: 37511--37594 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
37501 CTCTAAGTGT
37511 ATATGGTGGGCACAACCTTATGTGTAATGTACTTCGATGC
1 ATATGGTGGGCACAACCTTATGTGTAATGTACTTCGATGC
* *
37551 ATATGGTGGGCACAACTTTATGTGTAATGTACTTCGGTGC
1 ATATGGTGGGCACAACCTTATGTGTAATGTACTTCGATGC
37591 ATAT
1 ATAT
37595 ATTACTCGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (40 bp):
ATATGGTGGGCACAACCTTATGTGTAATGTACTTCGATGC
Found at i:48971 original size:19 final size:19
Alignment explanation
Indices: 48947--48991 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
48937 TCTTGAGTAC
48947 AGCCTTGAGCAACAAGTCT
1 AGCCTTGAGCAACAAGTCT
***
48966 AGCCTTGTTTAACAAGTCT
1 AGCCTTGAGCAACAAGTCT
48985 AGCCTTG
1 AGCCTTG
48992 TTTCTCACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (19 bp):
AGCCTTGAGCAACAAGTCT
Found at i:48992 original size:19 final size:19
Alignment explanation
Indices: 48957--48994 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
48947 AGCCTTGAGC
48957 AACAAGTCTAGCCTTGTTT
1 AACAAGTCTAGCCTTGTTT
48976 AACAAGTCTAGCCTTGTTT
1 AACAAGTCTAGCCTTGTTT
48995 CTCACTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (19 bp):
AACAAGTCTAGCCTTGTTT
Found at i:53236 original size:20 final size:19
Alignment explanation
Indices: 53211--53261 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 19
53201 AAAAAACTGA
53211 GTGCATCGATGCATGGTATT
1 GTGCATCGATGCATGGTA-T
53231 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
*
53250 ATGCATCGATGC
1 GTGCATCGATGC
53262 TTAAAATGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:53316 original size:20 final size:20
Alignment explanation
Indices: 53291--53328 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53281 TGAAAAATTA
53291 ATTGGTACATCGATGCATGG
1 ATTGGTACATCGATGCATGG
* *
53311 ATTGGTGCATCGGTGCAT
1 ATTGGTACATCGATGCAT
53329 CACTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGGTACATCGATGCATGG
Found at i:53328 original size:84 final size:85
Alignment explanation
Indices: 53166--53328 Score: 233
Period size: 84 Copynumber: 1.9 Consensus size: 85
53156 ACACTAAGAG
*
53166 TGCATCGATGCATAAAATGCATTCAATGTTTTGAAAAAAAACTGAGTGCATCGATGCATGGTATT
1 TGCATCGATGCATAAAATGCATTCAATGTTTTGAAAAAAAACTGAGTACATCGATGCATGGTATT
53231 GTGCATCGATGCATGGTATA
66 GTGCATCGATGCATGGTATA
* * * *
53251 TGCATCGATGCTTAAAATGCATTCGATG-TTTGAAAAATTAATTG-GTACATCGATGCATGG-AT
1 TGCATCGATGCATAAAATGCATTCAATGTTTTGAAAAA-AAACTGAGTACATCGATGCATGGTAT
*
53313 TGGTGCATCGGTGCAT
65 T-GTGCATCGATGCAT
53329 CACTTTGAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
83 3 0.04
84 37 0.53
85 30 0.43
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (85 bp):
TGCATCGATGCATAAAATGCATTCAATGTTTTGAAAAAAAACTGAGTACATCGATGCATGGTATT
GTGCATCGATGCATGGTATA
Found at i:55433 original size:21 final size:20
Alignment explanation
Indices: 55385--55448 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
55375 GTTATACGCA
*
55385 GTCCTTCGGACATATATGT-
1 GTCCTTCGGACATCTATGTG
*
55404 GTTCTTCGGACAATCTATGTG
1 GTCCTTCGGAC-ATCTATGTG
55425 GTCCTTCGGGACATCTATGTG
1 GTCCTTC-GGACATCTATGTG
55446 GTC
1 GTC
55449 TATCAGGGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 10 0.26
20 7 0.18
21 18 0.46
22 4 0.10
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (20 bp):
GTCCTTCGGACATCTATGTG
Found at i:56467 original size:55 final size:56
Alignment explanation
Indices: 56395--56608 Score: 227
Period size: 56 Copynumber: 3.8 Consensus size: 56
56385 CGAAGTAAGA
* * *
56395 GTTTAACATATCCAAGTTGTTACATTTAAAGATGGAAGTTTGGATAGTG-TATAGAT
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAGTGTTATA-AT
* * * *
56451 -TTTAACTTATCGAAGTTGTTGCATTCAAAAATGGAAGTTTGAATAATGTTATAAT
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAGTGTTATAAT
** * * *
56506 GTTTAACTTGCCCAAGTTGTTACATTCAAAGACT-GAAGCTTGTATAGTGTTGTAAT
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGA-TGGAAGTTTGAATAGTGTTATAAT
* ** * * *
56562 GTTTAACTTGTCCAAGTTAATCCATTAAAAGATGGAATTTTGAATAG
1 GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAG
56609 CATTAAAATG
Statistics
Matches: 130, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
55 44 0.34
56 85 0.65
57 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.38
Consensus pattern (56 bp):
GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAGTGTTATAAT
Found at i:56554 original size:111 final size:112
Alignment explanation
Indices: 56406--56607 Score: 259
Period size: 111 Copynumber: 1.8 Consensus size: 112
56396 TTTAACATAT
* * * *
56406 CCAAGTTGTTACATTTAAAGATGGAAGTTTGGATAGTG-TATAGAT-TTTAACTTATCGAAGTTG
1 CCAAGTTGTTACATTCAAAGATGGAAGCTTGGATAGTGTTATA-ATGTTTAACTTATCCAAGTTA
* *
56469 TTGCATTCAAAA-ATGGAAGTTTGAATAATGTTATAATGTTTAACTTGC
65 ATCCATT-AAAAGATGGAAGTTTGAATAATGTTATAATGTTTAACTTGC
* * *
56517 CCAAGTTGTTACATTCAAAGACT-GAAGCTTGTATAGTGTTGTAATGTTTAACTTGTCCAAGTTA
1 CCAAGTTGTTACATTCAAAGA-TGGAAGCTTGGATAGTGTTATAATGTTTAACTTATCCAAGTTA
*
56581 ATCCATTAAAAGATGGAATTTTGAATA
65 ATCCATTAAAAGATGGAAGTTTGAATA
56608 GCATTAAAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
111 39 0.51
112 38 0.49
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.38
Consensus pattern (112 bp):
CCAAGTTGTTACATTCAAAGATGGAAGCTTGGATAGTGTTATAATGTTTAACTTATCCAAGTTAA
TCCATTAAAAGATGGAAGTTTGAATAATGTTATAATGTTTAACTTGC
Found at i:56774 original size:149 final size:149
Alignment explanation
Indices: 56476--56762 Score: 362
Period size: 149 Copynumber: 1.9 Consensus size: 149
56466 TTGTTGCATT
* * * *
56476 CAAAAATGGAAGTTTGAATAATGTTATAATGTTTAACTTGCCCAAGTTGTTACATTCAAAGACTG
1 CAAAAATGAAAGTTTGAATAATGTTATAAAGTTTAACTTACCCAAGTTGATACATTCAAAGACTG
* ** * * *
56541 AAGCTTGTATAGTGTTGTAATGTTTAACTTGTCCAAGTTAATCCATTAAAAGATGGAATTTTGAA
66 AAACTTGTATAGCATTGTAATGTTTAACTTATCCAAATTAATACATTAAAAGATGGAATTTTGAA
*
56606 TAGCATTAAAATGGCTTAA
131 TAACATTAAAATGGCTTAA
* * *
56625 CAAATATGAAAGTTTGAATAATGTTGTAAAGTTTAACTTATCCAAGTTGATACATTCAAAGA-TG
1 CAAAAATGAAAGTTTGAATAATGTTATAAAGTTTAACTTACCCAAGTTGATACATTCAAAGACT-
* ** * *
56689 GAAATTTGTATAGCATTGTAATGTCTTAACTTATCCAAATTTTTACATTCAAATATGGAAGTTTT
65 GAAACTTGTATAGCATTGTAATGT-TTAACTTATCCAAATTAATACATTAAAAGATGGAA-TTTT
56754 -AATAACATT
128 GAATAACATT
56763 GTAATGTTTA
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
148 1 0.01
149 75 0.65
150 36 0.31
151 4 0.03
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (149 bp):
CAAAAATGAAAGTTTGAATAATGTTATAAAGTTTAACTTACCCAAGTTGATACATTCAAAGACTG
AAACTTGTATAGCATTGTAATGTTTAACTTATCCAAATTAATACATTAAAAGATGGAATTTTGAA
TAACATTAAAATGGCTTAA
Found at i:56798 original size:56 final size:56
Alignment explanation
Indices: 56625--57131 Score: 502
Period size: 56 Copynumber: 9.2 Consensus size: 56
56615 AATGGCTTAA
* ** * *
56625 CAAATATGAAAGTTTGAATAATGTTGTAAAGTTTAACTTATCCAAGTTGATACATT
1 CAAATATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * * * * *
56681 CAAAGATGGAAATTTGTATAGCATTGTAATGTCTTAACTTATCCAAATTTTTACATT
1 CAAATATGGAAGTTTGAATAACATTGTAATGT-TTAACTTATCCAAGTTGTTACATT
* *
56738 CAAATATGGAAGTTTTAATAACATTGTAATGTTTAACTTATCCCAGTTGTTACATT
1 CAAATATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * ***
56794 CAAATATGAAAGTTTAAATAGTGTTGTAGAT-TTTAACTTATCCAAGTTGTTACATT
1 CAAATATGGAAGTTTGAATAACATTGTA-ATGTTTAACTTATCCAAGTTGTTACATT
* * * * *
56850 AAAATATGTAAGTTTGAATAGCATTATAGA-GTTTAACTTATCTAAGTTGTTACATT
1 CAAATATGGAAGTTTGAATAACATTGTA-ATGTTTAACTTATCCAAGTTGTTACATT
* * *
56906 CAAAGATGGAAGTTTGAATAAAATT-TAAATGTTTAACTTATCCAAGTTGTTACAAT
1 CAAATATGGAAGTTTGAATAACATTGT-AATGTTTAACTTATCCAAGTTGTTACATT
* * * * *
56962 CAAATATGAAAGTTT---T-A-A---TAGTGTGTAACTTATCTAAGTTGTTGCATT
1 CAAATATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * * *
57010 CAAATATGGAAG-TTGAATAATATTGTAATGTTTTACTTATCCAATTTATTACATT
1 CAAATATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * * *
57065 CAAATATGGAAATTTGAA-AAGAATTATAGA-GTTTAACTTATCCAAGTTGTTACTTT
1 CAAATATGGAAGTTTGAATAA-CATTGTA-ATGTTTAACTTATCCAAGTTGTTACATT
*
57121 CAAAAATGGAA
1 CAAATATGGAA
57132 CAACTTGGAT
Statistics
Matches: 373, Mismatches: 62, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
47 2 0.01
48 35 0.09
49 1 0.00
50 1 0.00
51 2 0.01
52 2 0.01
53 1 0.00
55 38 0.10
56 240 0.64
57 51 0.14
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.39
Consensus pattern (56 bp):
CAAATATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCAAGTTGTTACATT
Found at i:56868 original size:262 final size:261
Alignment explanation
Indices: 56389--56875 Score: 626
Period size: 262 Copynumber: 1.9 Consensus size: 261
56379 ATCTTACGAA
* * * *
56389 GTAAGAGTTTAACATATCCAAGTTGTTACATTTAAAGATGGAAGTTTGGATAGTGTATAGATTTT
1 GTAAGAGTTTAACATATCCAAGTTGATACATTCAAAGATGGAAATTTGGATAGTGTATAGATCTT
* * * **
56454 AACTTATCGAAGTTGTTGCATTCAAAAATGGAAGTTTGAATAATGTTATAATGTTTAACTTGCCC
66 AACTTATCCAAATTGTTACATTCAAAAATGGAAGTTTGAATAACATTATAATGTTTAACTTGCCC
** * *
56519 AAGTTGTTACATTCAAAGACTGAAGCTTGTATAGTGTTGTAATGTTTAACTTGTCCAAGTTAATC
131 AAGTTGTTACATTCAAAGACTGAAGCTTAAATAGTGTTGTAATGTTTAACTTATCCAAGTTAATA
*
56584 CATTAAAAGATGGAATTTTGAATAGCATTAAAATGGCTTAACAAATATGAAAGTTTGAATAATGT
196 CATTAAAAGATGGAAGTTTGAATAGCATTAAAATGGCTTAACAAATATGAAAGTTTGAATAATGT
56649 T
261 T
* *
56650 GTAA-AGTTTAACTTATCCAAGTTGATACATTCAAAGATGGAAATTTGTATAGCATTGTA-ATG-
1 GTAAGAGTTTAACATATCCAAGTTGATACATTCAAAGATGGAAATTTGGATAG---TGTATA-GA
* * * *
56712 TCTTAACTTATCCAAATTTTTACATTCAAATATGGAAGTTTTAATAACATTGTAATGTTTAACTT
62 TCTTAACTTATCCAAATTGTTACATTCAAAAATGGAAGTTTGAATAACATTATAATGTTTAACTT
* * *
56777 ATCCC-AGTTGTTACATTCAAATA-TGAAAGTTTAAATAGTGTTGTAGAT-TTTAACTTATCCAA
127 -GCCCAAGTTGTTACATTCAAAGACTG-AAGCTTAAATAGTGTTGTA-ATGTTTAACTTATCCAA
** * *
56839 GTTGTTACATTAAAATATGTAAGTTTGAATAGCATTA
189 GTTAATACATTAAAAGATGGAAGTTTGAATAGCATTA
56876 TAGAGTTTAA
Statistics
Matches: 192, Mismatches: 27, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
260 43 0.22
261 6 0.03
262 133 0.69
263 10 0.05
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (261 bp):
GTAAGAGTTTAACATATCCAAGTTGATACATTCAAAGATGGAAATTTGGATAGTGTATAGATCTT
AACTTATCCAAATTGTTACATTCAAAAATGGAAGTTTGAATAACATTATAATGTTTAACTTGCCC
AAGTTGTTACATTCAAAGACTGAAGCTTAAATAGTGTTGTAATGTTTAACTTATCCAAGTTAATA
CATTAAAAGATGGAAGTTTGAATAGCATTAAAATGGCTTAACAAATATGAAAGTTTGAATAATGT
T
Found at i:56956 original size:168 final size:167
Alignment explanation
Indices: 56625--57124 Score: 592
Period size: 168 Copynumber: 3.0 Consensus size: 167
56615 AATGGCTTAA
* * * *
56625 CAAATATGAAAGTTTGAATAATGTTGTAAAGTTTAACTTATCCAAGTTGATACATTCAAAGATGG
1 CAAATATGAAAGTTTAAAT-ATGTTGTAGA-TTTAACTTATCCAAGTTGTTACATTCAAATATGG
* * * *
56690 AAATTTGTATAGCATTGTAATGTCTTAACTTATCCAAATTTTTACATTCAAATATGGAAGTTTTA
64 AAGTTTGAATAGCATTGTAATGT-TTAACTTATCCAAATTATTACATTCAAATATGGAAGTTTGA
* * *
56755 ATAACATTGT-AATGTTTAACTTATCCCAGTTGTTACATT
128 ATAAAATTATAAATGTTTAACTTATCCAAGTTGTTACATT
* *
56794 CAAATATGAAAGTTTAAATAGTGTTGTAGATTTTAACTTATCCAAGTTGTTACATTAAAATATGT
1 CAAATATGAAAGTTTAAATA-TGTTGTAGA-TTTAACTTATCCAAGTTGTTACATTCAAATATGG
* * * * *
56859 AAGTTTGAATAGCATTATAGA-GTTTAACTTATCTAAGTTGTTACATTCAAAGATGGAAGTTTGA
64 AAGTTTGAATAGCATTGTA-ATGTTTAACTTATCCAAATTATTACATTCAAATATGGAAGTTTGA
*
56923 ATAAAATT-TAAATGTTTAACTTATCCAAGTTGTTACAAT
128 ATAAAATTATAAATGTTTAACTTATCCAAGTTGTTACATT
* * *
56962 CAAATATGAAAGTTTTAATA-G-TGT-G---TAACTTATCTAAGTTGTTGCATTCAAATATGGAA
1 CAAATATGAAAGTTTAAATATGTTGTAGATTTAACTTATCCAAGTTGTTACATTCAAATATGGAA
** * * *
57021 G-TTGAATAATATTGTAATGTTTTACTTATCCAATTTATTACATTCAAATATGGAAATTTGAA-A
66 GTTTGAATAGCATTGTAATGTTTAACTTATCCAAATTATTACATTCAAATATGGAAGTTTGAATA
* *
57084 AGAATTATAGA-GTTTAACTTATCCAAGTTGTTACTTT
131 A-AATTATAAATGTTTAACTTATCCAAGTTGTTACATT
57121 CAAA
1 CAAA
57125 AATGGAACAA
Statistics
Matches: 290, Mismatches: 35, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
158 3 0.01
159 82 0.28
160 34 0.12
164 1 0.00
165 3 0.01
166 1 0.00
167 1 0.00
168 90 0.31
169 74 0.26
170 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40
Consensus pattern (167 bp):
CAAATATGAAAGTTTAAATATGTTGTAGATTTAACTTATCCAAGTTGTTACATTCAAATATGGAA
GTTTGAATAGCATTGTAATGTTTAACTTATCCAAATTATTACATTCAAATATGGAAGTTTGAATA
AAATTATAAATGTTTAACTTATCCAAGTTGTTACATT
Found at i:57068 original size:103 final size:104
Alignment explanation
Indices: 56883--57072 Score: 294
Period size: 103 Copynumber: 1.8 Consensus size: 104
56873 TTATAGAGTT
56883 TAACTTATCTAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAATTTAAATGTTTAACTTATC
1 TAACTTATCTAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAATTTAAATGTTTAACTTATC
*
56948 CAAGTTGTTACAATCAAATATGAAAGTTTTAATAGTGTG
66 CAAGTTATTACAATCAAATATGAAAGTTTTAATAGTGTG
* * * *
56987 TAACTTATCTAAGTTGTTGCATTCAAATATGGAAG-TTGAATAATATTGT-AATGTTTTACTTAT
1 TAACTTATCTAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAATT-TAAATGTTTAACTTAT
* *
57050 CCAATTTATTACATTCAAATATG
65 CCAAGTTATTACAATCAAATATG
57073 GAAATTTGAA
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
103 44 0.56
104 34 0.44
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (104 bp):
TAACTTATCTAAGTTGTTACATTCAAAGATGGAAGTTTGAATAAAATTTAAATGTTTAACTTATC
CAAGTTATTACAATCAAATATGAAAGTTTTAATAGTGTG
Found at i:57258 original size:55 final size:56
Alignment explanation
Indices: 57125--57268 Score: 184
Period size: 56 Copynumber: 2.6 Consensus size: 56
57115 TACTTTCAAA
* * * *
57125 AATGGAACAACTTGGATAATTTAAAC-TCTACAATGCTATTCAAAATTCCATATTTG
1 AATGTAACAACTTGGATAAGTTAAACAT-TACAACGCTATTCAAAATTCCATACTTG
* * *
57181 AATGTATCAACTTGGATAAGTTAAACATTACAACGTTATTCAAACTTCCAT-CTTG
1 AATGTAACAACTTGGATAAGTTAAACATTACAACGCTATTCAAAATTCCATACTTG
*
57236 AATGTAACAACTTGGATAAGTTAAGAAATTACA
1 AATGTAACAACTTGGATAAGTTAA-ACATTACA
57269 TCACCTACTT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
55 26 0.34
56 50 0.65
57 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (56 bp):
AATGTAACAACTTGGATAAGTTAAACATTACAACGCTATTCAAAATTCCATACTTG
Found at i:57422 original size:54 final size:55
Alignment explanation
Indices: 57340--57445 Score: 160
Period size: 54 Copynumber: 1.9 Consensus size: 55
57330 CGAAAATTCA
57340 ATCTTTGAATATAACAACTTGGACAAGTTAAACTCTACAA-CTATTCAAACTTCC
1 ATCTTTGAATATAACAACTTGGACAAGTTAAACTCTACAATCTATTCAAACTTCC
* * * * *
57394 ATCTTTGAATGTAACAATTTGGATAAGTTAAACTCTCCAATCTATTTAAACT
1 ATCTTTGAATATAACAACTTGGACAAGTTAAACTCTACAATCTATTCAAACT
57446 CTATATGTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 36 0.78
55 10 0.22
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (55 bp):
ATCTTTGAATATAACAACTTGGACAAGTTAAACTCTACAATCTATTCAAACTTCC
Found at i:60637 original size:46 final size:44
Alignment explanation
Indices: 60575--60690 Score: 124
Period size: 45 Copynumber: 2.5 Consensus size: 44
60565 ATAACATCCA
* * *
60575 TTCATGTTTATGATGCACCATTATGAATTTTCAATTATAGCATACT
1 TTCATGTTGATAATGCACCA-TATGAA-TTTCAACTATAGCATACT
* * *
60621 TTTATGTTGATAATGCACCCATATGCATTTCAACTATAGCATCCT
1 TTCATGTTGATAATGCA-CCATATGAATTTCAACTATAGCATACT
* *
60666 TTCATGATGAAAATGCACCCATATG
1 TTCATGTTGATAATGCA-CCATATG
60691 CATTATTATT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
45 38 0.63
46 19 0.32
47 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (44 bp):
TTCATGTTGATAATGCACCATATGAATTTCAACTATAGCATACT
Found at i:60752 original size:44 final size:45
Alignment explanation
Indices: 60614--60791 Score: 197
Period size: 45 Copynumber: 4.0 Consensus size: 45
60604 TTCAATTATA
* * * * *
60614 GCATACTTTT-ATGTTGATAATGCACCCATATGCATT-TCAACTATA
1 GCAT-CTTTTCATGTCGATAATGCACCCATATGCATTAT-TATTTTG
* *
60659 GCATCCTTTCATGAT-GAAAATGCACCCATATGCATTATTATTTTG
1 GCATCTTTTCATG-TCGATAATGCACCCATATGCATTATTATTTTG
60704 GCATCTTTTCATGTCGATAATGCACCCAT-TGCATTATTATTTTG
1 GCATCTTTTCATGTCGATAATGCACCCATATGCATTATTATTTTG
* * *
60748 GCATC-CTTCATATCGATAATGAACCCATATGC-TTATTATTTTG
1 GCATCTTTTCATGTCGATAATGCACCCATATGCATTATTATTTTG
60791 G
1 G
60792 AATTCGTTTT
Statistics
Matches: 117, Mismatches: 11, Indels: 12
0.84 0.08 0.09
Matches are distributed among these distances:
43 32 0.27
44 28 0.24
45 55 0.47
46 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (45 bp):
GCATCTTTTCATGTCGATAATGCACCCATATGCATTATTATTTTG
Found at i:60786 original size:90 final size:90
Alignment explanation
Indices: 60614--60791 Score: 224
Period size: 90 Copynumber: 2.0 Consensus size: 90
60604 TTCAATTATA
*
60614 GCATACTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGCATCCTTTCATGATGAAAA
1 GCATACTTTTATGTCGATAATGCACCCATATGCATTTCAACTATAGCATCCTTTCATGATGAAAA
*
60679 TGCACCCATATGCATTATTATTTTG
66 TGAACCCATATGCATTATTATTTTG
* * * *
60704 GCAT-CTTTTCATGTCGATAATGCACCCAT-TGCATTAT-TATTTTGGCATCC-TTCAT-ATCGA
1 GCATACTTTT-ATGTCGATAATGCACCCATATGCATT-TCAACTATAGCATCCTTTCATGAT-GA
*
60764 TAATGAACCCATATGC-TTATTATTTTG
63 AAATGAACCCATATGCATTATTATTTTG
60791 G
1 G
60792 AATTCGTTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
87 14 0.18
88 21 0.27
89 20 0.26
90 23 0.29
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (90 bp):
GCATACTTTTATGTCGATAATGCACCCATATGCATTTCAACTATAGCATCCTTTCATGATGAAAA
TGAACCCATATGCATTATTATTTTG
Found at i:61242 original size:18 final size:19
Alignment explanation
Indices: 61214--61256 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
61204 ATATCGATAC
61214 TACCATACTATGATACCGA
1 TACCATACTATGATACCGA
* *
61233 TACC-TACTATGGTATCGA
1 TACCATACTATGATACCGA
61251 TACCAT
1 TACCAT
61257 TTTTAATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (19 bp):
TACCATACTATGATACCGA
Done.