Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000112.1 Hibiscus syriacus cultivar Beakdansim tig00000201_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: 83815
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:12423 original size:20 final size:21
Alignment explanation
Indices: 12400--12444 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
12390 TATATCAAGG
12400 TCTTTGTT-GAAGCCATAAAA
1 TCTTTGTTCGAAGCCATAAAA
* *
12420 TCTTTTTTCGAAGCCATAAAT
1 TCTTTGTTCGAAGCCATAAAA
12441 TCTT
1 TCTT
12445 ACAATGAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (21 bp):
TCTTTGTTCGAAGCCATAAAA
Found at i:29413 original size:31 final size:30
Alignment explanation
Indices: 29361--29460 Score: 127
Period size: 30 Copynumber: 3.4 Consensus size: 30
29351 TTTAATTTTA
29361 AATTTGAC-TTAAACTTTAGATAAAATATT
1 AATTTGACATTAAACTTTAGATAAAATATT
*
29390 AATTTGACATTTAAA-TTTAAGAT-AAATATC
1 AATTTGACA-TTAAACTTT-AGATAAAATATT
29420 AATTTGACCATTAAACTTTAGATAAAATA-T
1 AATTTGA-CATTAAACTTTAGATAAAATATT
*
29450 AATTTGTCATT
1 AATTTGACATT
29461 TATCATCTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
29 12 0.19
30 31 0.50
31 19 0.31
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (30 bp):
AATTTGACATTAAACTTTAGATAAAATATT
Found at i:29514 original size:15 final size:16
Alignment explanation
Indices: 29489--29526 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
29479 ACAAGTTTTA
29489 CAAATATCAAATG-ATT
1 CAAA-ATCAAATGAATT
29505 CAAAATCAAATGAATT
1 CAAAATCAAATGAATT
29521 CAAAAT
1 CAAAAT
29527 TTCATCTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (16 bp):
CAAAATCAAATGAATT
Found at i:30210 original size:24 final size:24
Alignment explanation
Indices: 30171--30231 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
30161 ATACTTAAGG
*
30171 GGTATCGATACTACTTTACACAGA
1 GGTATCGATACCACTTTACACAGA
*
30195 GGTATCGACACCACTTTACACAGA
1 GGTATCGATACCACTTTACACAGA
30219 GGTATCGATACCA
1 GGTATCGATACCA
30232 TGAAGCATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (24 bp):
GGTATCGATACCACTTTACACAGA
Found at i:37532 original size:25 final size:25
Alignment explanation
Indices: 37494--37558 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
37484 TTATTAATCA
*
37494 CAAAA-TGTTGAGATGTTTCCACCC
1 CAAAAGTGTCGAGATGTTTCCACCC
37518 CAAAAGTGTCGAGATGTTTCCACCC
1 CAAAAGTGTCGAGATGTTTCCACCC
37543 CAAAAGTGTCGAGATG
1 CAAAAGTGTCGAGATG
37559 CCTTCACATA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 5 0.13
25 34 0.87
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.25
Consensus pattern (25 bp):
CAAAAGTGTCGAGATGTTTCCACCC
Found at i:41248 original size:2 final size:2
Alignment explanation
Indices: 41241--41295 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
41231 CCTGATATGA
41241 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
41283 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
41296 AAGGAAAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42395 original size:65 final size:65
Alignment explanation
Indices: 42235--42376 Score: 196
Period size: 65 Copynumber: 2.2 Consensus size: 65
42225 TTGTTTAGGG
* * * *****
42235 TGCATCGATGCACATGCAGTGCATCGATGCATGAATTTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
42300 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
42364 TGCATCGATGCAT
1 TGCATCGATGCAT
42377 GGTGTAGTGC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 32 0.47
65 36 0.53
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:43111 original size:22 final size:22
Alignment explanation
Indices: 43057--43128 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
43047 AGTCGAGGGT
43057 TTCATAGGTCCTTCGGGA-AAA
1 TTCATAGGTCCTTCGGGACAAA
*
43078 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
43100 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
43122 TTTCATA
1 -TTCATA
43129 TGCCACTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.38
22 23 0.51
23 5 0.11
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:44877 original size:22 final size:20
Alignment explanation
Indices: 44852--44896 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
44842 AAGGTATTGG
44852 TACCATAGTATAGAAGTATCGA
1 TACCATAGTA-AG-AGTATCGA
* *
44874 TACCATGGTAAGGGTATCGA
1 TACCATAGTAAGAGTATCGA
44894 TAC
1 TAC
44897 TATTGAGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (20 bp):
TACCATAGTAAGAGTATCGA
Found at i:45589 original size:81 final size:81
Alignment explanation
Indices: 45452--46322 Score: 1181
Period size: 81 Copynumber: 10.8 Consensus size: 81
45442 TGTTCTAAAA
* * * *
45452 TAAAAGATTAATGGCCTAGCCGTGCATTTGGCAGAAATGTGCCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
45517 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * ** *
45533 TAAAAGATAAATGGCCTAGCTGTCCATTTGACAGAAATGTGTCAATTATGTAAGTTACATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
45598 GATAAATACATTTGAG
66 GTTAAATACCTTTGAG
* *
45614 TAAAAGATTAATGGCCTAGCTGTGTATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
45679 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
45695 TAAAATATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
45760 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* ** *
45776 TAAAATATTAATTTCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATTCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
45841 GTTAAATATCTTTGAG
66 GTTAAATACCTTTGAG
*
45857 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTC-ATTATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
45921 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
45937 TAAAAGATTAATGGCCTACCTGTGCACTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
46002 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
46018 TAAAATATTAATAGCCTAACTGTGCATTTGGCAG-AAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
46082 TTTAAATACCTTTCAG
66 GTTAAATACCTTTGAG
* * * * * *
46098 TAAAAGATTAATGGCCTAGCTGTGCTTTTGCCAGAAATGTGTTAAATATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
46163 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* ** * ** * * * *
46179 TAAAAGACTAAAAGCATAAATGTGCCTTTGGCAGAAATGTGTCAATCAAGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
46244 GTTAAATACCTTTGGG
66 GTTAAATACCTTTGAG
* * * * * * * * *
46260 TAAAAGACTAAAT-GTCTAACGGTGCATTTGGCAGAAAGATGCCAATAATGCAAGTTGGATGAA
1 TAAAAGA-TTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
46323 GGATTAATTG
Statistics
Matches: 698, Mismatches: 89, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
80 146 0.21
81 550 0.79
82 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:46013 original size:242 final size:241
Alignment explanation
Indices: 45452--46297 Score: 1135
Period size: 242 Copynumber: 3.5 Consensus size: 241
45442 TGTTCTAAAA
* * * *
45452 TAAAAGATTAATGGCCTAGCC-GTGCATTTGGCAGAAATGTGCCAATTATGCTAGTTAGATGAAA
1 TAAAAGATTAATGGCCTA-CCTGTGCACTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* * * *
45516 GGTTAAATACCTTTGAGTAAAAGATAAATGGCCTAGCTGTCCATTTGACAGAAATGTGTCAATTA
65 GGTTAAATACCTTTGAGTAAAAGATAAATGGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATTA
* * * *
45581 TGT-AAGTTACATGAAAGGATAAATACATTTGAGTAAAAGATTAATGGCCTAGCTGTGTATTTGA
130 T-TCCAGTTAGATGAAAGGTTAAATAC-TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGA
*
45645 CAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAG
193 CAGAAAGGTGTC-ATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAG
* ** * *
45695 TAAAATATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTACCTGTGCACTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * ** *
45760 GTTAAATACCTTTGAGTAAAATATTAATTTCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTAT
66 GTTAAATACCTTTGAGTAAAAGATAAATGGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATTAT
*
45825 TCCAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCA
131 TCCAGTTAGATGAAAGGTTAAATA-CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACA
45890 GAAAGGTGTCATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAG
195 GAAAGGTGTCATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAG
* *
45937 TAAAAGATTAATGGCCTACCTGTGCACTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTACCTGTGCACTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
46002 GTTAAATACCTTTGAGTAAAATATTAATAGCCTAACTGTGCATTTGGCAG-AAGGTGTCAATTAT
66 GTTAAATACCTTTGAGTAAAAGATAAATGGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATTAT
* * * * *
46066 GCCAGTTAGATGAAAGTTTAAATACCTTTCAGTAAAAGATTAATGGCCTAGCTGTGCTTTTGCCA
131 TCCAGTTAGATGAAAGGTTAAATA-CTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACA
* * *
46131 GAAATGTGTTAAATATGTCAGTTAGATGAAAGGTTAAATACCTTTGAG
195 GAAAGGTG-TCATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAG
* ** * ** * * *
46179 TAAAAGACTAAAAGCATAAATGTGC-CTTTGGCAGAAATGTGTCAATCAAGCCAGTTAGATGAAA
1 TAAAAGATTAATGGCCTACCTGTGCAC-TTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* * *
46243 GGTTAAATACCTTTGGGTAAAAGACTAAAT-GTCTAACGGTGCATTTGGCAGAAAG
65 GGTTAAATACCTTTGAGTAAAAGA-TAAATGGCCTAACTGTGCATTTGGCAGAAAG
46298 ATGCCAATAA
Statistics
Matches: 543, Mismatches: 53, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
241 81 0.15
242 273 0.50
243 188 0.35
244 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (241 bp):
TAAAAGATTAATGGCCTACCTGTGCACTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAGTAAAAGATAAATGGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATTAT
TCCAGTTAGATGAAAGGTTAAATACTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAG
AAAGGTGTCATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAG
Found at i:50785 original size:81 final size:81
Alignment explanation
Indices: 50679--51875 Score: 1642
Period size: 81 Copynumber: 14.8 Consensus size: 81
50669 TGTTCTAAAA
* * *
50679 TAAATGATTAATGGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGGCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
50744 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
50760 TAAAAGATTAATGGCCTAGTTGTGCATTTGGTAGATAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
50825 ATTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
50841 TAAAAGACTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGGCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
50906 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
50922 TAAAATATTAATGGCCTAGTTGTGCATTTGGTAGATAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
50987 ATTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
51003 TAAAAGACTAATGGCCTAGCTATGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
51068 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * *
51084 TAAAAGATTAATGACATAGTTGTGCATTTGGCAGAAAGGTGTTAATAATGCTAGTTAAATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
51149 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
** * * * *
51165 TAAAAGATTAATGGTATAGTTGTGCATTTGGCATAAATGTGTCAATTATGCGAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
51230 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * ** *
51246 TTAAAGATTAATGGCCTAGATGTGCATTTGGAAGAAAGATGTCAACGATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
51311 GCTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
51327 TAAAAGATTAATGGCATAGCTATGCATTTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
51392 TTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
51408 TAAAAGATTAATGGTCTATCTATGCATTTGGCAGAAATGTGTTAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
51473 GTTAAATACCTTTGAT
66 GTTAAATACCTTTGAG
* *
51489 TAAAAGATTAATGGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
51554 GTTAAATACCTCTGAG
66 GTTAAATACCTTTGAG
* * * *
51570 TAAAAGATTAATTGCATAGCTTTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
51635 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * **
51651 TAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAATGTGTCAAATATGATAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
51716 GTTAAATACCATTGAG
66 GTTAAATACCTTTGAG
* ** * * * * * *
51732 TAAAAGACTAAAAGTCTAACTGTTCCTTTGGCAGAAAGGTGTCAATCATGCCAGTTAGACGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
51797 GTTAAATACCTTT-AGG
66 GTTAAATACCTTTGA-G
* ** * * * * * * *
51813 TAAAAGAATAAAT-GTTTAACGGTGCATTTGGCAGAAAGATGCCAATAATGCAAGTTGGATGAA
1 TAAAAG-ATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
51876 GGACTAATTA
Statistics
Matches: 987, Mismatches: 127, Indels: 4
0.88 0.11 0.00
Matches are distributed among these distances:
80 1 0.00
81 983 1.00
82 3 0.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:53424 original size:90 final size:89
Alignment explanation
Indices: 53271--53445 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 89
53261 CCTAACACAC
* * *
53271 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTCTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGATCTTTATTATTTCAAATTAATTAAATCTAT
*
53336 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
*
53361 CCTTTTATATCCAAGTTACCCTAATCATATCAGTGAT-TTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAG-GATCTTTATTATTTCAAATTAATTAAATCTA
53425 TATTTAATTAATTGAAATTAA
65 TATTTAATTAATTGAAATTAA
53446 ATATTGGGGA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
89 7 0.09
90 70 0.89
91 2 0.03
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGATCTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:54909 original size:32 final size:32
Alignment explanation
Indices: 54844--54910 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
54834 CCCTCCTAGA
* ** *
54844 CAGCTTGCAGCTAGGCGTGGTCTTGACATAAT
1 CAGCTTGCAGCTAGGCATGGTCCCGACAGAAT
*
54876 CAGCTTGCAGCTGGGCATGGTCCCGACAGAAT
1 CAGCTTGCAGCTAGGCATGGTCCCGACAGAAT
54908 CAG
1 CAG
54911 GCGAATCAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.22
Consensus pattern (32 bp):
CAGCTTGCAGCTAGGCATGGTCCCGACAGAAT
Found at i:55221 original size:20 final size:20
Alignment explanation
Indices: 55192--55230 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55182 TTTCCACCAC
*
55192 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
55212 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
55231 TATGATCCCT
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:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:57352 original size:31 final size:30
Alignment explanation
Indices: 57317--57404 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
57307 AAATTGATAT
* * *
57317 TTTATTTAAAGTTTAAGGGTTGAATTAGTA
1 TTTATCTAAAGTTTAAGGATTAAATTAGTA
*
57347 CTTTATCAAAAGTTTAAGGATTAAATTAGTA
1 -TTTATCTAAAGTTTAAGGATTAAATTAGTA
* *
57378 TTTATCTAAACTTTTGAGG-TTAAATTA
1 TTTATCTAAA-GTTTAAGGATTAAATTA
57405 AAAAGTAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 17 0.35
31 32 0.65
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (30 bp):
TTTATCTAAAGTTTAAGGATTAAATTAGTA
Found at i:59009 original size:24 final size:25
Alignment explanation
Indices: 58982--59028 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
58972 TATTAACTAC
*
58982 AATATTATATATATA-TATATTTAT
1 AATATGATATATATATTATATTTAT
* *
59006 AATATGATTTATCTATTATATTT
1 AATATGATATATATATTATATTT
59029 TTATTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
AATATGATATATATATTATATTTAT
Found at i:63615 original size:16 final size:17
Alignment explanation
Indices: 63589--63625 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
63579 ATGGGATGAA
63589 AAAAATAGTAA-TATTGT
1 AAAAATAGTAATTATT-T
63606 AAAAAT-GTAATTATTT
1 AAAAATAGTAATTATTT
63622 AAAA
1 AAAA
63626 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (17 bp):
AAAAATAGTAATTATTT
Found at i:68168 original size:12 final size:12
Alignment explanation
Indices: 68117--68175 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
68107 ACAGCGTGAG
*
68117 TTTTGTTTGTTTG
1 TTTTGTTT-TTTT
* *
68130 TTTGGTTTTTGTC
1 TTTTGTTTTT-TT
*
68143 TTTTGTTTTGTT
1 TTTTGTTTTTTT
68155 TTTTGTTTTTTT
1 TTTTGTTTTTTT
68167 TTTT-TTTTT
1 TTTTGTTTTT
68176 GCTTAACTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 5 0.13
12 18 0.46
13 16 0.41
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:68170 original size:19 final size:19
Alignment explanation
Indices: 68117--68175 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
68107 ACAGCGTGAG
* * *
68117 TTTTGTTTGTTTGTTTGGT
1 TTTTGTTTTTTTTTTTGTT
* *
68136 TTTTGTCTTTTGTTTTGTT
1 TTTTGTTTTTTTTTTTGTT
68155 TTTTGTTTTTTTTTTT-TT
1 TTTTGTTTTTTTTTTTGTT
68173 TTT
1 TTT
68176 GCTTAACTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
18 5 0.15
19 28 0.85
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (19 bp):
TTTTGTTTTTTTTTTTGTT
Found at i:70305 original size:15 final size:15
Alignment explanation
Indices: 70285--70315 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
70275 TTGAAGAATA
70285 GAACATGAAAATGTT
1 GAACATGAAAATGTT
*
70300 GAACATGGAAATGTT
1 GAACATGAAAATGTT
70315 G
1 G
70316 TAAGATATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (15 bp):
GAACATGAAAATGTT
Found at i:75230 original size:13 final size:13
Alignment explanation
Indices: 75212--75253 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
75202 CTTTTACATA
75212 AAAAATCATCAAT
1 AAAAATCATCAAT
*
75225 AAAAATGAT--A-
1 AAAAATCATCAAT
75235 AAAAATCATCAAT
1 AAAAATCATCAAT
75248 AAAAAT
1 AAAAAT
75254 GACATCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 8 0.33
11 1 0.04
12 1 0.04
13 14 0.58
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (13 bp):
AAAAATCATCAAT
Found at i:75235 original size:23 final size:23
Alignment explanation
Indices: 75209--75255 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
75199 AATCTTTTAC
75209 ATAAAAAATCATCAATAAAAATG
1 ATAAAAAATCATCAATAAAAATG
75232 ATAAAAAATCATCAATAAAAATG
1 ATAAAAAATCATCAATAAAAATG
75255 A
1 A
75256 CATCTTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.66, C:0.09, G:0.04, T:0.21
Consensus pattern (23 bp):
ATAAAAAATCATCAATAAAAATG
Done.