Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000966.1 Hibiscus syriacus cultivar Beakdansim tig00001928_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: 100856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4120 original size:21 final size:21
Alignment explanation
Indices: 4088--4127 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4078 AATTATCCAG
4088 TATAGAGGGTATCGGTACTCC
1 TATAGAGGGTATCGGTACTCC
4109 TATA-AGGAGTATCGGTACT
1 TATAGAGG-GTATCGGTACT
4128 ATCTTTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
TATAGAGGGTATCGGTACTCC
Found at i:13652 original size:2 final size:2
Alignment explanation
Indices: 13645--13669 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13635 TTCTTATTGA
13645 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13670 AACCACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18329 original size:2 final size:2
Alignment explanation
Indices: 18322--18369 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
18312 CATGATTTGA
18322 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
18364 AT AT AT
1 AT AT AT
18370 GATAAGATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40479 original size:43 final size:44
Alignment explanation
Indices: 40407--40496 Score: 137
Period size: 43 Copynumber: 2.0 Consensus size: 44
40397 ATGAATTCAG
*
40407 TTTTCAGTAAAAAGGGTGAGTCAACTCGTGCAAATT-GGGGACC
1 TTTTCAGTAAAAAGGGTGAGCCAACTCGTGCAAATTAGGGGACC
* *
40450 TTTTTAGTAAAAAGGGTGAGCCAAGTCGTGCAAATTGAGGGGACC
1 TTTTCAGTAAAAAGGGTGAGCCAACTCGTGCAAATT-AGGGGACC
40495 TT
1 TT
40497 AGAAGCCTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 33 0.79
45 9 0.21
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (44 bp):
TTTTCAGTAAAAAGGGTGAGCCAACTCGTGCAAATTAGGGGACC
Found at i:41010 original size:19 final size:21
Alignment explanation
Indices: 40966--41018 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
40956 AATTGTAGAA
*
40966 ACATATAATTTCAACCAAAGAT
1 ACATATAATTTGAACC-AAGAT
40988 ACATATAATTTGAACC-A-AT
1 ACATATAATTTGAACCAAGAT
41007 ACATATAATTTG
1 ACATATAATTTG
41019 TAGGCATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.47
20 1 0.03
22 15 0.50
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (21 bp):
ACATATAATTTGAACCAAGAT
Found at i:41171 original size:23 final size:21
Alignment explanation
Indices: 41140--41191 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
41130 ACGTATAATT
41140 ATAAATTAGTTAAATATTTAAAGG
1 ATAAATTAGTTAAA-A--TAAAGG
41164 -TAAATTAGTTAAAATAAAGG
1 ATAAATTAGTTAAAATAAAGG
41184 ATAAATTA
1 ATAAATTA
41192 TATCAGTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.22
21 7 0.26
22 1 0.04
23 13 0.48
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (21 bp):
ATAAATTAGTTAAAATAAAGG
Found at i:49265 original size:23 final size:23
Alignment explanation
Indices: 49232--49299 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
49222 AACCTTATAT
49232 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
49255 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
49278 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
49300 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:53751 original size:2 final size:2
Alignment explanation
Indices: 53702--53733 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53692 GTATTTGCGG
53702 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
53734 GAATAAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54250 original size:23 final size:23
Alignment explanation
Indices: 54217--54284 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
54207 AACCTTATAT
*
54217 GGCACTTCGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* *
54240 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
*
54263 GGCACTACGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
54285 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:57885 original size:30 final size:30
Alignment explanation
Indices: 57826--57928 Score: 145
Period size: 30 Copynumber: 3.4 Consensus size: 30
57816 CCCGAAGGAC
* *
57826 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
57855 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
57885 CTGTCCAGAGGTCATAAAGATCCTCGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
* *
57916 CTGTCCATAGGTC
1 CTATCCAGAGGTC
57929 CCGAAGAACC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.28
30 35 0.51
31 14 0.21
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:57968 original size:31 final size:31
Alignment explanation
Indices: 57910--58041 Score: 115
Period size: 31 Copynumber: 4.2 Consensus size: 31
57900 AAAGATCCTC
* *
57910 GGTAAACTGTCCATAGGTCCCGAAGAACCCA
1 GGTAAACTGTCCATATGTCCCGAAGAACACA
* ** *
57941 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTCCCGAAGAACACA
* *
57972 GGTATAA-TGTCCATATGTCTCGAA-AGACATA
1 GGTA-AACTGTCCATATGTCCCGAAGA-ACACA
* * * *
58003 GGTAAAACTGTCTATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTCCCGAAGAACACA
58035 GGTAAAC
1 GGTAAAC
58042 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
30 1 0.01
31 56 0.68
32 24 0.29
33 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTCCCGAAGAACACA
Found at i:59348 original size:21 final size:21
Alignment explanation
Indices: 59318--59362 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
59308 ATTCTGTCGT
* *
59318 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
59339 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
59360 TTG
1 TTG
59363 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:62550 original size:30 final size:30
Alignment explanation
Indices: 62491--62593 Score: 145
Period size: 30 Copynumber: 3.4 Consensus size: 30
62481 CCCGAAGGAC
* *
62491 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
62520 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
62550 CTGTCCAGAGGTCATAAAGATCCTCGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
* *
62581 CTGTCCATAGGTC
1 CTATCCAGAGGTC
62594 CCGAAGAACC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.28
30 35 0.51
31 14 0.21
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:62699 original size:32 final size:31
Alignment explanation
Indices: 62575--62706 Score: 151
Period size: 31 Copynumber: 4.2 Consensus size: 31
62565 AAAGATCCTC
* * * **
62575 GGTAAACTGTCCATAGGTCCCGAAGAACCCA
1 GGTAAACTGTCCATATGTTCCGTAGAACATA
*
62606 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCGTAGAACATA
* *
62637 GGTATACTGTCCATATG-TCTCG-AAAGACATA
1 GGTAAACTGTCCATATGTTC-CGTAGA-ACATA
62668 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCGTAGAACATA
62700 GGTAAAC
1 GGTAAAC
62707 CCTCGACTCT
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
30 4 0.05
31 54 0.64
32 23 0.27
33 4 0.05
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:64020 original size:21 final size:21
Alignment explanation
Indices: 63990--64034 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
63980 ATTCTGTCGT
* *
63990 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
64011 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
64032 TTG
1 TTG
64035 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:66430 original size:6 final size:6
Alignment explanation
Indices: 66419--66467 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
66409 ATTAACACCT
*
66419 TTTGCA TTTGCA TTTGGCA TTTGCA TTTGCA TTTGCA TCTGCA -TTGCA
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA
66467 T
1 T
66468 GTACGTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 4 0.10
6 29 0.74
7 6 0.15
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.47
Consensus pattern (6 bp):
TTTGCA
Found at i:66443 original size:19 final size:18
Alignment explanation
Indices: 66419--66467 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
66409 ATTAACACCT
66419 TTTGCATTTGCATTTGGCA
1 TTTGCATTTGCATTT-GCA
66438 TTTGCATTTGCATTTGCA
1 TTTGCATTTGCATTTGCA
*
66456 TCTGCA-TTGCAT
1 TTTGCATTTGCAT
66468 GTACGTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 6 0.21
18 8 0.28
19 15 0.52
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.47
Consensus pattern (18 bp):
TTTGCATTTGCATTTGCA
Found at i:71102 original size:37 final size:37
Alignment explanation
Indices: 71061--71230 Score: 171
Period size: 37 Copynumber: 4.6 Consensus size: 37
71051 GGCAAAGTCA
*
71061 ATCTTAAGCCTTCACCGAAGAGTAGTAAAACAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAACAAATCC
* * *
71098 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGC-AGTCT
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAACAAATCC
* * * * *
71134 ATCCTAAGCCTTTACCGAAGAGTAATGAAATAAATTC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAACAAATCC
** * * *
71171 ATCTTAAGCCTTCACTAAATAGAAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAACAAATCC
* * * *
71208 ATTTTACGCCTTCTCGGAAGAGT
1 ATCTTAAGCCTTCACCGAAGAGT
71231 GTTGGAGCAA
Statistics
Matches: 103, Mismatches: 29, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
36 29 0.28
37 74 0.72
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAACAAATCC
Found at i:71198 original size:73 final size:73
Alignment explanation
Indices: 71056--71202 Score: 195
Period size: 73 Copynumber: 2.0 Consensus size: 73
71046 ATTGGGGCAA
* * * *
71056 AGTCAATCTTAAGCCTTCACCGAAGAGTAGTAAAACAAATCCATCTTAAGCCTTCACCGAAGAGT
1 AGTCAATCCTAAGCCTTCACCGAAGAGTAATAAAACAAATCCATCTTAAGCCTTCACCAAAGAGA
71121 AGTGAAGC
66 AGTGAAGC
* * * * * * *
71129 AGTCTATCCTAAGCCTTTACCGAAGAGTAATGAAATAAATTCATCTTAAGCCTTCACTAAATAGA
1 AGTCAATCCTAAGCCTTCACCGAAGAGTAATAAAACAAATCCATCTTAAGCCTTCACCAAAGAGA
71194 AGTGAAGC
66 AGTGAAGC
71202 A
1 A
71203 AATCCATTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (73 bp):
AGTCAATCCTAAGCCTTCACCGAAGAGTAATAAAACAAATCCATCTTAAGCCTTCACCAAAGAGA
AGTGAAGC
Found at i:71722 original size:55 final size:55
Alignment explanation
Indices: 71573--72253 Score: 682
Period size: 55 Copynumber: 12.4 Consensus size: 55
71563 TGAAGCAAAT
* * * * *
71573 GAAGATGTTCGAA-TTCTATACTCCCT-AAA-AAATAGGAAGCGAACCCATTGGCA
1 GAAGATGTTC-AAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * * * * * *
71626 -TAGATTATTCGAGTTCTATACTCCCT-AAAAAAAGAGGGAGCGAGCCCGTTTGTA
1 GAAGA-TGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
* **
71680 GAAGACGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACATGTTTGCA
1 GAAGATGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
* *
71735 GAAGACGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCTGTTTGCA
1 GAAGATGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
* *
71790 GAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
1 GAAGA-TGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * *
71846 GAAGATTATTCGAGTTCTATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTTTGCA
1 GAAGA-TGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * * *
71901 GAAGGTTATTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAGCCCGTTTACA
1 GAA-GATGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * * *
71957 GAAGACGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAACGAACCTGTTTACA
1 GAAGATGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * * * * *
72012 GAAGACGTTCAAGTTCTATACTTCCTGGAAGAAAGAGGAAGCAAACCTGTTTGTA
1 GAAGATGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * * * * *
72067 GAAGATGTTCGAGTTCCATACTCCCTG-AAGAAAGAGAGAGTGAACCCGTTTGTA
1 GAAGATGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * * * * * ***
72121 GAAGATTATTCGAGTTCCATAC-TCCTTAAAGAAAGAAGGAGTGAACGTATTTGCTA
1 GAAGA-TGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGC-A
* * * * *
72177 -AAGATTGTTCGAGTTCCATACTCCCTG-AAGAAAAAGGGAGCGAACCCGTTTTCA
1 GAAGA-TGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
*
72231 GAATATTGTTCAAG-TCTTATACT
1 GAAGA-TGTTCAAGTTC-TATACT
72254 CTCTGAAGAA
Statistics
Matches: 541, Mismatches: 73, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
52 4 0.01
53 20 0.04
54 68 0.13
55 343 0.63
56 106 0.20
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (55 bp):
GAAGATGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
Found at i:72254 original size:55 final size:54
Alignment explanation
Indices: 71573--72683 Score: 670
Period size: 55 Copynumber: 20.3 Consensus size: 54
71563 TGAAGCAAAT
* * * * * *
71573 GAAGA-TGTTCGAATTCTATACTCCCT-AAAAAATAGGAAGCGAACCC--ATTG
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTTA
* * * *
71623 GCATAGATTATTCGAGTTCTATACTCCCTAAAAAAAGAGGGAGCGAGCCCGTTTGTA
1 G-A-AGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTT-TA
* * * ** *
71680 GAAGA-CGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACATGTTTGCA
1 GAAGATTGTTCGAGTTCTATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTTT-TA
* * * * *
71735 GAAGA-CGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCTGTTTGCA
1 GAAGATTGTTCGAGTTCTATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTTT-TA
* * *
71790 GAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
1 GAAGATTGTTCGAGTTCTATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTTT-TA
* *
71846 GAAGATTATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGCA
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTT-TA
* * * * * *
71901 GAAGGTTATTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAGCCCGTTTACA
1 GAAGATTGTTCGAGTTCTATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTTT-TA
* * * * * *
71957 GAAGA-CGTTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAACGAACCTGTTTACA
1 GAAGATTGTTCGAGTTCTATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTTT-TA
* * * * * *
72012 GAAGA-CGTTCAAGTTCTATACTTCCTGGAAGAAAGAGGAAGCAAACCTGTTTGTA
1 GAAGATTGTTCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTTT-TA
* * *
72067 GAAGA-TGTTCGAGTTCCATACTCCCTGAAGAAAGAGAGAGTGAACCCGTTTGTA
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTT-TA
* * * * * * ***
72121 GAAGATTATTCGAGTTCCATACTCCTTAAAGAAAGAAGGAGTGAACGTATTTGCTA
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTT--TA
* *
72177 -AAGATTGTTCGAGTTCCATACTCCCTGAAGAAAAAGGGAGCGAACCCGTTTTCA
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTT-A
* * * * * * *
72231 GAATATTGTTCAAG-TCTTATACTCTCTGAAGAAATAAGGAAC-AGACACGATTGTT-
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGCGA-ACCCG-TT-TTA
* * * *
72286 GAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGA-CCAGACACGATTGTT-
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGCGA-ACCCG-TT-TTA
* * *
72341 GAAGATTGTTCGAG-TCTTATACTCTCTGAA-AAATAGGGAGC-AGACACGATTATT-
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGCGA-ACCCG-TT-TTA
* * * * * * *
72395 GAAGATTGTTCAAG-TCTCATACTCTCTGAAGAAATATGGAGCAAACACGATATT-
1 GAAGATTGTTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TTTTA
* * * *
72449 GAAGATTGTTCGAG-TCTCATACTCTCTGAAAAAATAGGGAGC-AGACACGATTGTT-
1 GAAGATTGTTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCGA-ACCCG-TT-TTA
** * *
72504 GAAGATTGTTCGAG-TCTCATACTCTTTGAAGAAATAGGGAGC-AGACACGATTATT-
1 GAAGATTGTTCGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCGA-ACCCG-TT-TTA
* ** * *
72559 GAAGATTATTCGAG-TCTTATACTCTATGAAGAAATAGGGAGCAGAA-ACGATTGTT-
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGC-GAACCCG-TT-TTA
* ** *
72614 GAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATTGGGAGC-AGACACGATTGTT-
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAGAAAGAGGGAGCGA-ACCCG-TT-TTA
72669 GAAGATTGTTCGAGT
1 GAAGATTGTTCGAGT
72684 CATACCCTAA
Statistics
Matches: 935, Mismatches: 94, Indels: 58
0.86 0.09 0.05
Matches are distributed among these distances:
50 1 0.00
51 1 0.00
52 3 0.00
53 23 0.02
54 164 0.18
55 626 0.67
56 112 0.12
57 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (54 bp):
GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTTA
Found at i:72536 original size:273 final size:268
Alignment explanation
Indices: 72177--72791 Score: 789
Period size: 273 Copynumber: 2.3 Consensus size: 268
72167 GTATTTGCTA
* * *
72177 AAGATTGTTCGAGT-TCCATACTCCCTGAAGAAAA-AGGGAGC-GAACCCGTTTTCAGAATATTG
1 AAGATTGTTCGAGTCT-CATACTCTCTGAA-AAAATAGGGAGCAG-ACACGTTTT-AGAAGATTG
* * *
72239 TTCAAGTCTTATACTCTCTGAAGAAATAAGGAACAGACACGATTGTTGAAGATTGTTCGAGTCTT
62 TTCAAGTCTCATACTCTCTGAAGAAATAAGGAACAGACACGATTATTGAAGATTATTCGAGTCTT
* *
72304 ATACTCTCTGAAGAAATAGGGACCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTG
127 ATACTCTATGAAGAAATAGGGACCAGAAACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTG
72369 AA-AAATAGGGAGCAGACACGATTATTGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATATG
192 AAGAAATAGGGAGCAGACACGATTATTGAAGATTGTTCAAG--TCATAC-C-CT-AA-AAATA-G
*
72433 G-AGCAAACACGAT-ATTG
250 GAAGCAAACACGATGATCG
72450 AAGATTGTTCGAGTCTCATACTCTCTGAAAAAATAGGGAGCAGACACGATTGTT-GAAGATTGTT
1 AAGATTGTTCGAGTCTCATACTCTCTGAAAAAATAGGGAGCAGACACG-TT-TTAGAAGATTGTT
* * * *
72514 CGAGTCTCATACTCTTTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTATTCGAGTCTTAT
64 CAAGTCTCATACTCTCTGAAGAAATAAGGAACAGACACGATTATTGAAGATTATTCGAGTCTTAT
*
72579 ACTCTATGAAGAAATAGGGAGCAGAAACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAA
129 ACTCTATGAAGAAATAGGGACCAGAAACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAA
* * * *
72644 GAAATTGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCATACCCTAAAAATAGGAAGCGAAC
194 GAAATAGGGAGCAGACACGATTATTGAAGATTGTTCAAGTCATACCCTAAAAATAGGAAGCAAAC
* *
72709 TCGTTGATCG
259 ACGATGATCG
** * * * *
72719 AAGATTAATCAAGTC-CTATACTCTCTGAAAGAATAGGGAGCAGACATGTGTTCT-GAAGATTTT
1 AAGATTGTTCGAGTCTC-ATACTCTCTGAAAAAATAGGGAGCAGACACGT-TT-TAGAAGATTGT
72782 TCAAGTCTCA
63 TCAAGTCTCA
72792 CTTACTCCGG
Statistics
Matches: 304, Mismatches: 27, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
267 2 0.01
268 17 0.06
269 65 0.21
270 2 0.01
271 1 0.00
272 10 0.03
273 166 0.55
274 39 0.13
275 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (268 bp):
AAGATTGTTCGAGTCTCATACTCTCTGAAAAAATAGGGAGCAGACACGTTTTAGAAGATTGTTCA
AGTCTCATACTCTCTGAAGAAATAAGGAACAGACACGATTATTGAAGATTATTCGAGTCTTATAC
TCTATGAAGAAATAGGGACCAGAAACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGA
AATAGGGAGCAGACACGATTATTGAAGATTGTTCAAGTCATACCCTAAAAATAGGAAGCAAACAC
GATGATCG
Found at i:72684 original size:55 final size:55
Alignment explanation
Indices: 72177--72764 Score: 729
Period size: 55 Copynumber: 10.8 Consensus size: 55
72167 GTATTTGCTA
* * * *
72177 AAGATTGTTCGAGT-TCCATACTCCCTGAAGAAAAAGGGAGC-GAACCCG-TT-TTCAG
1 AAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGTT--G
* * * *
72232 AATATTGTTCAAGTCTTATACTCTCTGAAGAAATAAGGAACAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
*
72287 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGACCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
*
72342 AAGATTGTTCGAGTCTTATACTCTCTGAA-AAATAGGGAGCAGACACGATTATTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * * * *
72396 AAGATTGTTCAAGTCTCATACTCTCTGAAGAAATATGGAGCAAACACGA-TATTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* *
72450 AAGATTGTTCGAGTCTCATACTCTCTGAAAAAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * *
72505 AAGATTGTTCGAGTCTCATACTCTTTGAAGAAATAGGGAGCAGACACGATTATTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * *
72560 AAGATTATTCGAGTCTTATACTCTATGAAGAAATAGGGAGCAGAAACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
*
72615 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATTGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * *
72670 AAGATTGTTCGAGTC--ATAC-C-CT-AA-AAATAGGAAGC-GAACTCG-TTGATCG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTG-TTG
** * *
72719 AAGATTAATCAAGTCCTATACTCTCTGAA-AGAATAGGGAGCAGACA
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACA
72765 TGTGTTCTGA
Statistics
Matches: 474, Mismatches: 44, Indels: 30
0.86 0.08 0.05
Matches are distributed among these distances:
48 4 0.01
49 27 0.06
50 2 0.00
51 6 0.01
52 2 0.00
53 6 0.01
54 103 0.22
55 317 0.67
56 5 0.01
57 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
Found at i:72967 original size:14 final size:15
Alignment explanation
Indices: 72956--73015 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 15
72946 GGTTATAAAT
72956 ATTA-TATTATAATA
1 ATTATTATTATAATA
*
72970 ATTATTATTATTATA
1 ATTATTATTATAATA
*
72985 ATCATAATTATTACAATAAA
1 AT--T-ATTATTATAAT--A
73005 ATTATTATTAT
1 ATTATTATTAT
73016 TAGTAGTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 4 0.11
15 11 0.31
17 8 0.22
18 10 0.28
20 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATTATTATAATA
Found at i:80039 original size:18 final size:16
Alignment explanation
Indices: 80008--80044 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
79998 TGCTGAGCCC
80008 TTTAAAATTTTAAATT
1 TTTAAAATTTTAAATT
80024 TTTATAAATTTATAAATT
1 TTTA-AAATTT-TAAATT
80042 TTT
1 TTT
80045 CAACGGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTAAAATTTTAAATT
Found at i:85159 original size:19 final size:19
Alignment explanation
Indices: 85135--85172 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
85125 GTTATTTCAT
85135 AGATCCTACAGTCTTAGAA
1 AGATCCTACAGTCTTAGAA
85154 AGATCCTACAGTCTTAGAA
1 AGATCCTACAGTCTTAGAA
85173 GGATACTCTG
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:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (19 bp):
AGATCCTACAGTCTTAGAA
Found at i:89818 original size:31 final size:31
Alignment explanation
Indices: 89783--89844 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
89773 CATGGCGCAT
*
89783 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAACTTCATCCTCTCACCACAGCTCGTA
*
89814 GCAAAACTTCATCCTCTCGCCACAGCTCGTA
1 GCAAAACTTCATCCTCTCACCACAGCTCGTA
89845 TAGAACACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.23
Consensus pattern (31 bp):
GCAAAACTTCATCCTCTCACCACAGCTCGTA
Found at i:90474 original size:30 final size:30
Alignment explanation
Indices: 90400--90461 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
90390 TATAGATCGT
*
90400 CAGGTGATCTGGGCGACCAATGAAGGTCGC
1 CAGGTGGTCTGGGCGACCAATGAAGGTCGC
90430 CAGGTGGTCTGGGCGACCAATGAAGGTCGC
1 CAGGTGGTCTGGGCGACCAATGAAGGTCGC
90460 CA
1 CA
90462 TGTATGTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.24, G:0.37, T:0.16
Consensus pattern (30 bp):
CAGGTGGTCTGGGCGACCAATGAAGGTCGC
Found at i:94527 original size:6 final size:6
Alignment explanation
Indices: 94516--94540 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
94506 TTCGTTGAAA
94516 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
94541 GACGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:94547 original size:5 final size:5
Alignment explanation
Indices: 94537--94569 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
94527 GACCACGACC
94537 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
94570 GCGGCGGCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.39, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:95074 original size:6 final size:6
Alignment explanation
Indices: 95048--95089 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
95038 TCGTCGTCTC
95048 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
95090 AATACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:95220 original size:22 final size:22
Alignment explanation
Indices: 95194--95236 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
95184 AATCATAACG
95194 ACAACTGTAGACTATCGCAACA
1 ACAACTGTAGACTATCGCAACA
95216 ACAACTGTAGACTATCGCAAC
1 ACAACTGTAGACTATCGCAAC
95237 GCGAAATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.19
Consensus pattern (22 bp):
ACAACTGTAGACTATCGCAACA
Found at i:98330 original size:20 final size:20
Alignment explanation
Indices: 98300--98351 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
98290 TAGTTGAAAG
* *
98300 TCGCATTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
*
98320 TCGTGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
98340 TCGCGTTGCGAT
1 TCGCGTTGCGAT
98352 AGTCTACAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:98369 original size:21 final size:21
Alignment explanation
Indices: 98343--98383 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
98333 TTCCATTTCG
98343 CGTTGCGATAGTCTACAGTTT
1 CGTTGCGATAGTCTACAGTTT
98364 CGTTGCGATAGTCTACAGTT
1 CGTTGCGATAGTCTACAGTT
98384 GTCATGCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTTT
Found at i:98391 original size:21 final size:21
Alignment explanation
Indices: 98346--98393 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
98336 CATTTCGCGT
*
98346 TGCGATAGTCTACAGTTTCGT
1 TGCGATAGTCTACAGTTTCGA
98367 TGCGATAGTCTACAGTTGTC-A
1 TGCGATAGTCTACAGTT-TCGA
98388 TGCGAT
1 TGCGAT
98394 TTTCCAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (21 bp):
TGCGATAGTCTACAGTTTCGA
Found at i:99129 original size:22 final size:22
Alignment explanation
Indices: 99101--99153 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
99091 AATTTGGAAA
99101 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
99123 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
99145 ATCGCAACG
1 ATCGCAACG
99154 CGAAATGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Done.