Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005137.1 Hibiscus syriacus cultivar Beakdansim tig00011567_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: 64471
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2128 original size:81 final size:82
Alignment explanation
Indices: 1960--2217 Score: 357
Period size: 81 Copynumber: 3.2 Consensus size: 82
1950 TTTTAGACTT
* * *
1960 CCAAATGCACATCTAGGCCATTTATC-TTTACTCAAC-GTCTTTAACCATTCACCTAACTAGC-A
1 CCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCATTCATCTAACTGGCAA
*
2022 TAATTGACA-TTGTTCTG
66 TAATTGACACAT-TTCTG
* * *
2039 CCAAATGCACAGCTAGGCCATTT-TCTTTTACTCAACGGTTTTTAACTATTCGTCTAACTGGCAA
1 CCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCATTCATCTAACTGGCAA
*
2103 AAATTGACACATTTCTG
66 TAATTGACACATTTCTG
2120 CCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCATTCATCTAACTGG-AA
1 CCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCATTCATCTAACTGGCAA
* *
2184 TACTTGACACCTTTCTG
66 TAATTGACACATTTCTG
* *
2201 CCAAATCCACAACTAGG
1 CCAAATGCACAGCTAGG
2218 ACTCAAAGGC
Statistics
Matches: 158, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
78 2 0.01
79 32 0.20
80 20 0.13
81 68 0.43
82 36 0.23
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (82 bp):
CCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCATTCATCTAACTGGCAA
TAATTGACACATTTCTG
Found at i:2262 original size:68 final size:68
Alignment explanation
Indices: 2169--2480 Score: 437
Period size: 68 Copynumber: 4.6 Consensus size: 68
2159 TCTTTAACCA
* * * * *
2169 TTCATCTAACTGGAATACTTGACACCTTTCTGCCAAATCCACAACTAGGACTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACTTAG
*
2234 CAT
66 CCT
* * * *
2237 TTCATCTAATTAGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCATTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACTTAG
2302 CCT
66 CCT
* * **
2305 TTCATCTAACTGGAATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACTTAG
*
2370 TCT
66 CCT
* * *
2373 TTCATCTAATTGGCATATTTGACACCTTTCTGTCAAATGCACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACTTAG
2438 CCT
66 CCT
* *
2441 TTCATCTAACTGGCATAATT-ACACTTTTCTGTAAAATGCA
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
2481 GTTAGGCCTT
Statistics
Matches: 217, Mismatches: 27, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
67 18 0.08
68 199 0.92
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACTTAG
CCT
Found at i:3344 original size:21 final size:21
Alignment explanation
Indices: 3318--3358 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3308 ATATCGATTA
3318 ATTGAATCAATATCGATACTG
1 ATTGAATCAATATCGATACTG
3339 ATTGAATCAATATCGATACT
1 ATTGAATCAATATCGATACT
3359 ACTCAGCTAA
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:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (21 bp):
ATTGAATCAATATCGATACTG
Found at i:5442 original size:44 final size:44
Alignment explanation
Indices: 5394--5490 Score: 176
Period size: 44 Copynumber: 2.2 Consensus size: 44
5384 TTGAAGGCAT
5394 TATAATTTAGTTAAGATTGCTTTTAAGATAACGATTCATTACAA
1 TATAATTTAGTTAAGATTGCTTTTAAGATAACGATTCATTACAA
* *
5438 TATAATTTAGTTAATATTGCTTTTATGATAACGATTCATTACAA
1 TATAATTTAGTTAAGATTGCTTTTAAGATAACGATTCATTACAA
5482 TATAATTTA
1 TATAATTTA
5491 TATTTTTTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.44
Consensus pattern (44 bp):
TATAATTTAGTTAAGATTGCTTTTAAGATAACGATTCATTACAA
Found at i:8472 original size:14 final size:15
Alignment explanation
Indices: 8453--8481 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
8443 TAAATTTCAA
8453 AATATTA-TAATTAT
1 AATATTATTAATTAT
8467 AATATTATTAATTAT
1 AATATTATTAATTAT
8482 TTACTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTATTAATTAT
Found at i:8655 original size:16 final size:16
Alignment explanation
Indices: 8572--8656 Score: 66
Period size: 16 Copynumber: 5.2 Consensus size: 16
8562 ATCTATTTTA
*
8572 ATTACTATATTT-ATAT
1 ATTATTATATTTAAT-T
*
8588 ATTATTGTATTTTAATT
1 ATTATTATA-TTTAATT
* *
8605 ATTTATTATACTTAATA
1 A-TTATTATATTTAATT
*
8622 ATGAATTATA-TTAATT
1 AT-TATTATATTTAATT
*
8638 ATTATTATATTTATTT
1 ATTATTATATTTAATT
8654 ATT
1 ATT
8657 CTATTCATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 6 0.11
16 23 0.42
17 17 0.31
18 9 0.16
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTATTATATTTAATT
Found at i:9760 original size:40 final size:40
Alignment explanation
Indices: 9705--9782 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
9695 TTTCCACTTC
9705 TTTATCATTTCGTAAAGCATCTCACTCGACAGAGATAATT
1 TTTATCATTTCGTAAAGCATCTCACTCGACAGAGATAATT
* * **
9745 TTTATTATTTTGTAAAGTGTCTCACTCGACAGAGATAA
1 TTTATCATTTCGTAAAGCATCTCACTCGACAGAGATAA
9783 AGGTTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (40 bp):
TTTATCATTTCGTAAAGCATCTCACTCGACAGAGATAATT
Found at i:9879 original size:16 final size:16
Alignment explanation
Indices: 9858--9912 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
9848 TTTCTTCATA
9858 TTTTTATATTTAATAT
1 TTTTTATATTTAATAT
*
9874 TTTTTATAATTAATAT
1 TTTTTATATTTAATAT
*
9890 TTTTTATATTTAATAG
1 TTTTTATATTTAATAT
9906 TTTTTAT
1 TTTTTAT
9913 TGACATCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTTATATTTAATAT
Found at i:9924 original size:32 final size:32
Alignment explanation
Indices: 9853--9927 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
9843 TTCATTTTCT
* *
9853 TCATATTTTTATATTTAATATTTTTTATAATTAA
1 TCAT-TTTTTATATTTAATAGTTTTTAT-ATGAA
9887 T-ATTTTTTATATTTAATAGTTTTTAT-TGACA
1 TCATTTTTTATATTTAATAGTTTTTATATGA-A
9918 TCATTTTTTA
1 TCATTTTTTA
9928 ATAAAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 2 0.05
31 2 0.05
32 30 0.81
33 2 0.05
34 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.63
Consensus pattern (32 bp):
TCATTTTTTATATTTAATAGTTTTTATATGAA
Found at i:9973 original size:21 final size:21
Alignment explanation
Indices: 9933--9973 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9923 TTTTAATAAA
*
9933 AAAATTTATGATATATCATTT
1 AAAATTTATGATAAATCATTT
9954 AAAATTTAT-ATAAATACATT
1 AAAATTTATGATAAAT-CATT
9974 AAATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAATTTATGATAAATCATTT
Found at i:11297 original size:30 final size:32
Alignment explanation
Indices: 11257--11331 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
11247 GGATTATTTT
*
11257 TAATACTTATTATAAAGG-TT-AATTTTTCTC
1 TAATATTTATTATAAAGGATTCAATTTTTCTC
*** *
11287 TAATATTTATTATTGTGGATTCAATTTTTTTC
1 TAATATTTATTATAAAGGATTCAATTTTTCTC
*
11319 TAATATTTGTTAT
1 TAATATTTATTAT
11332 TAGGGGCCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 14 0.38
31 2 0.05
32 21 0.57
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.56
Consensus pattern (32 bp):
TAATATTTATTATAAAGGATTCAATTTTTCTC
Found at i:12235 original size:42 final size:43
Alignment explanation
Indices: 12167--12523 Score: 306
Period size: 43 Copynumber: 8.3 Consensus size: 43
12157 GGGCTTAAAC
* *
12167 TATAAAAGT-AAAA-TTATGATTGAAAAAATTAGGGATCTCAAT
1 TATAAAAGTAAAAAGTGA-GATTGAAAAAATTAGGGACCTCAAT
* *
12209 TATAAAAGTAAAAAGTGAGATT-AAAAAATTAGGGGCCTCGAT
1 TATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGACCTCAAT
* * *
12251 T-TTAAAGTTAAAAAGTGAGATTAAAAAAATTAGTGG-CCTAAAT
1 TATAAAAG-TAAAAAGTGAGATTGAAAAAATTAG-GGACCTCAAT
* * *
12294 TATATAAGTAAAAAATGAGATTGAAAAAAATTAGTGG-CTTCAAT
1 TATAAAAGTAAAAAGTGAGATTG-AAAAAATTAG-GGACCTCAAT
* * * *
12338 TATAAATGTAAAAAGTGAGATTGAAAAAATCA-GGAACTTAAT
1 TATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGACCTCAAT
* * * * **
12380 TATAAAGGTACAAAGTGTGATTGAAAAACTTA-GGATAATCAAT
1 TATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGA-CCTCAAT
* * *
12423 TATAAAGGTAAAAAAATGGGATTGAAAAAATTAAGGGA-CTCAAT
1 TATAAAAGT-AAAAAGTGAGATTGAAAAAATT-AGGGACCTCAAT
* *
12467 TAT-AAAGATAAAAAGTAAGATT-ACAAAAATTAGAGACCTCAAT
1 TATAAAAG-TAAAAAGTGAGATTGA-AAAAATTAGGGACCTCAAT
12510 TATAAATA-TAAAAA
1 TATAAA-AGTAAAAA
12524 TTAAATTAAA
Statistics
Matches: 261, Mismatches: 37, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
41 7 0.03
42 80 0.31
43 94 0.36
44 75 0.29
45 2 0.01
46 3 0.01
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (43 bp):
TATAAAAGTAAAAAGTGAGATTGAAAAAATTAGGGACCTCAAT
Found at i:12322 original size:129 final size:129
Alignment explanation
Indices: 12184--12541 Score: 354
Period size: 129 Copynumber: 2.8 Consensus size: 129
12174 GTAAAATTAT
** *
12184 GATTGAAAAAATTAGGGATCTCAATTATAAAAGTAAAAAGTGAGATTAAAAAATTAGGGGCCTCG
1 GATTGAAAAAATTAGGGATCTCAATTATAAAAGTAAAAAGTGAGATTAAAAAATTAGGGAACTCA
* * **
12249 ATTTTAAAGTTAAAAAGTGAGATTAAAAAAATTAGTG-GCCTAAATTATATAA-GT-AAAAAATG
66 ATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAG-GAGAATAAATTATA-AAGGTAAAAAAATG
12311 A
129 A
* * *
12312 GATTGAAAAAAATTAGTGGCT-TCAATTATAAATGTAAAAAGTGAGATTGAAAAAATCA-GGAAC
1 GATTG-AAAAAATTAG-GGATCTCAATTATAAAAGTAAAAAGTGAGATT-AAAAAATTAGGGAAC
* * * * * * *
12375 TTAATTATAAAGGTACAAAGTGTGATTGAAAAACTTAGGATAATCAATTATAAAGGTAAAAAAAT
63 TCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGAGAATAAATTATAAAGGTAAAAAAAT
*
12440 GG
128 GA
* * *
12442 GATTGAAAAAATTAAGGGA-CTCAATTAT-AAAGATAAAAAGTAAGATTACAAAAATTAGAGACC
1 GATTGAAAAAATT-AGGGATCTCAATTATAAAAG-TAAAAAGTGAGATTA-AAAAATTAGGGAAC
** * *
12505 TCAATTATAAATATAAAAA-TTAAATTAAATAAAATTA
63 TCAATTATAAAGGTAAAAAGTGAGATTAAA-AAAATTA
12542 AAAGGTTAAA
Statistics
Matches: 185, Mismatches: 33, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
128 12 0.06
129 123 0.66
130 50 0.27
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (129 bp):
GATTGAAAAAATTAGGGATCTCAATTATAAAAGTAAAAAGTGAGATTAAAAAATTAGGGAACTCA
ATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGAGAATAAATTATAAAGGTAAAAAAATGA
Found at i:12365 original size:87 final size:82
Alignment explanation
Indices: 12184--12523 Score: 322
Period size: 87 Copynumber: 4.0 Consensus size: 82
12174 GTAAAATTAT
*
12184 GATTGAAAAAATTAGGGATCTCAATTATAAAAGTAAAAAGTGAGATTAAAAAATTAGGGGCCTCG
1 GATTGAAAAAATTAGGGA-CTCAATTAT-AAAGTAAAAAGTGAGATTAAAAAATTA-GGGCCTCA
*
12249 ATTTTAAA-GTTAAAAAGTGA
63 ATTATAAATG-TAAAAAGTGA
* * * * *
12269 GATTAAAAAAATTAGTGGCCTAAATTATATAAGTAAAAAATGAGATTGAAAAAAATTAGTGGCTT
1 GATTGAAAAAATTAG-GGACTCAATTATA-AAGTAAAAAGTGAGATT--AAAAAATTAG-GGCCT
12334 CAATTATAAATGTAAAAAGTGA
61 CAATTATAAATGTAAAAAGTGA
* * * * * * ***
12356 GATTGAAAAAATCAGGAACTTAATTATAAAGGTACAAAGTGTGATTGAAAAACTTAGGATAATCA
1 GATTGAAAAAATTAGGGACTCAATTATAAA-GTAAAAAGTGAGATT-AAAAAATTAGG-GCCTCA
* * *
12421 ATTATAAAGGTAAAAAAATGG
63 ATTATAAATGT-AAAAAGTGA
* *
12442 GATTGAAAAAATTAAGGGACTCAATTATAAAGATAAAAAGTAAGATTACAAAAATTAGAGACCTC
1 GATTGAAAAAATT-AGGGACTCAATTATAAAG-TAAAAAGTGAGATTA-AAAAATTAG-GGCCTC
*
12507 AATTATAAATATAAAAA
62 AATTATAAATGTAAAAA
12524 TTAAATTAAA
Statistics
Matches: 207, Mismatches: 35, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
84 2 0.01
85 62 0.30
86 51 0.25
87 90 0.43
88 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (82 bp):
GATTGAAAAAATTAGGGACTCAATTATAAAGTAAAAAGTGAGATTAAAAAATTAGGGCCTCAATT
ATAAATGTAAAAAGTGA
Found at i:12537 original size:22 final size:25
Alignment explanation
Indices: 12511--12562 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
12501 GACCTCAATT
12511 ATAAATA-TAAAA-ATTAAATTA-A
1 ATAAATATTAAAAGATTAAATTATA
*
12533 ATAAA-ATTAAAAGGTTAAATTATA
1 ATAAATATTAAAAGATTAAATTATA
12557 A-AAATA
1 ATAAATA
12563 AATAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
22 10 0.40
23 11 0.44
24 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (25 bp):
ATAAATATTAAAAGATTAAATTATA
Found at i:13069 original size:17 final size:20
Alignment explanation
Indices: 13033--13073 Score: 61
Period size: 17 Copynumber: 2.2 Consensus size: 20
13023 AACTCGAACA
13033 TATTGAAACTAATAAAAAGT
1 TATTGAAACTAATAAAAAGT
13053 TATT-AAAC-AAT-AAAAGT
1 TATTGAAACTAATAAAAAGT
13070 TATT
1 TATT
13074 TTCAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
18 3 0.14
19 4 0.19
20 4 0.19
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (20 bp):
TATTGAAACTAATAAAAAGT
Found at i:20159 original size:51 final size:53
Alignment explanation
Indices: 20086--20193 Score: 193
Period size: 51 Copynumber: 2.1 Consensus size: 53
20076 CCATCGACAC
20086 TTAGTTTTGTACATCCAGGTACACTCAACTAC-AGGAAGAAAAAAATATTTAG
1 TTAGTTTTGTACATCCAGGTACACTCAACTACAAGGAAGAAAAAAATATTTAG
*
20138 TTAG-TTTGTACATCCAGGTACACTCAACTACAAGGAAGAAGAAAATATTTAG
1 TTAGTTTTGTACATCCAGGTACACTCAACTACAAGGAAGAAAAAAATATTTAG
20190 TTAG
1 TTAG
20194 CTTACAAAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
51 27 0.50
52 27 0.50
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (53 bp):
TTAGTTTTGTACATCCAGGTACACTCAACTACAAGGAAGAAAAAAATATTTAG
Found at i:28704 original size:95 final size:95
Alignment explanation
Indices: 28541--28715 Score: 305
Period size: 95 Copynumber: 1.8 Consensus size: 95
28531 CAAGTGTTGC
* * *
28541 TTAAAATATATAATTATTTAAAAAATTCAAATTTTAAGATGGGTACGTGTGGATCCTGGATTGAC
1 TTAAAATATATAATTATTCAAAAAATTCAAATTTTAAGATGGGTACATGTCGATCCTGGATTGAC
28606 TATTTCCAGAAACGGACATAAGTACAACTA
66 TATTTCCAGAAACGGACATAAGTACAACTA
* *
28636 TTAAAATATATAATTATTCAAAAATTTTAAATTTTAAGATGGGTACATGTCGATCCTGGATTGAC
1 TTAAAATATATAATTATTCAAAAAATTCAAATTTTAAGATGGGTACATGTCGATCCTGGATTGAC
28701 TATTTCCAGAAACGG
66 TATTTCCAGAAACGG
28716 GCCATTGGTC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 75 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (95 bp):
TTAAAATATATAATTATTCAAAAAATTCAAATTTTAAGATGGGTACATGTCGATCCTGGATTGAC
TATTTCCAGAAACGGACATAAGTACAACTA
Found at i:32657 original size:19 final size:21
Alignment explanation
Indices: 32633--32671 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
32623 TGTACTTACC
32633 AATA-TTA-ATAAAAAATATT
1 AATATTTATATAAAAAATATT
*
32652 AATATTTATATTAAAAATAT
1 AATATTTATATAAAAAATAT
32672 ACGAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATTTATATAAAAAATATT
Found at i:34181 original size:23 final size:23
Alignment explanation
Indices: 34153--34218 Score: 123
Period size: 23 Copynumber: 2.9 Consensus size: 23
34143 TGTACTTTGA
34153 TGCTGAATCATTCAACACTGTTT
1 TGCTGAATCATTCAACACTGTTT
34176 TGCTGAATCATTCAACACTGTTT
1 TGCTGAATCATTCAACACTGTTT
*
34199 TGCTGAATCAGTCAACACTG
1 TGCTGAATCATTCAACACTG
34219 AATCATTCAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (23 bp):
TGCTGAATCATTCAACACTGTTT
Found at i:34233 original size:38 final size:38
Alignment explanation
Indices: 34178--34263 Score: 154
Period size: 38 Copynumber: 2.3 Consensus size: 38
34168 CACTGTTTTG
34178 CTGAATCATTCAACACTGTTTTGCTGAATCAGTCAACA
1 CTGAATCATTCAACACTGTTTTGCTGAATCAGTCAACA
* *
34216 CTGAATCATTCAGCACTGTTTTGCTGAATCAGTCATCA
1 CTGAATCATTCAACACTGTTTTGCTGAATCAGTCAACA
34254 CTGAATCATT
1 CTGAATCATT
34264 TAGAGGTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (38 bp):
CTGAATCATTCAACACTGTTTTGCTGAATCAGTCAACA
Found at i:39666 original size:33 final size:33
Alignment explanation
Indices: 39629--39696 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
39619 TATCTTATTA
39629 AGAGATAAGAGTCAT-GGAATATCTAAACTACTT
1 AGAGATAAGAGTCATAGG-ATATCTAAACTACTT
**
39662 AGAGATAAGAGTTGTAGGATATCTAAACTACTT
1 AGAGATAAGAGTCATAGGATATCTAAACTACTT
39695 AG
1 AG
39697 TTATTAACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (33 bp):
AGAGATAAGAGTCATAGGATATCTAAACTACTT
Found at i:49021 original size:24 final size:24
Alignment explanation
Indices: 48994--49074 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
48984 ACACTTAACA
48994 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
49018 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
49040 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
49062 GTGCATCGATGCA
1 GTGCATCGATGCA
49075 CAGGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:50643 original size:21 final size:21
Alignment explanation
Indices: 50601--50644 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
50591 ACCCTGAGAG
*
50601 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
50622 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
50643 CT
1 CT
50645 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:51847 original size:45 final size:46
Alignment explanation
Indices: 51788--51879 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 46
51778 TCAAACATCG
* * *
51788 AATGTATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTC
1 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
51833 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
1 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
51879 A
1 A
51880 GGTTTTTCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (46 bp):
AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
Found at i:51896 original size:46 final size:45
Alignment explanation
Indices: 51801--51902 Score: 107
Period size: 46 Copynumber: 2.2 Consensus size: 45
51791 GTATTTTATG
* * * **
51801 CATCGATGCACATACCATGCATCGATGCACTCAATGCATTTGATG
1 CATCGATGCACAGACCATGCATCGATGCACTCAAGGCATTTAAAA
**
51846 CATCGATGCACAAGACCATGCATCGATGCACTC-AGGTTTTTCAAAA
1 CATCGATGCAC-AGACCATGCATCGATGCACTCAAGGCATTT-AAAA
51892 CATCGAATGCA
1 CATCG-ATGCA
51903 TTTTATGCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
45 16 0.34
46 26 0.55
47 5 0.11
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (45 bp):
CATCGATGCACAGACCATGCATCGATGCACTCAAGGCATTTAAAA
Found at i:55359 original size:45 final size:45
Alignment explanation
Indices: 55293--55383 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 45
55283 TCAAACATCG
*
55293 AATGCATTTATGCATCGATGCAC-ATACCATGCATCGATGCACTC
1 AATGCATTTATGCATCGATGCACAAGACCATGCATCGATGCACTC
55337 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
1 AATGCATTT-ATGCATCGATGCACAAGACCATGCATCGATGCACTC
55383 A
1 A
55384 GGTTTTCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 9 0.20
45 14 0.32
46 21 0.48
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (45 bp):
AATGCATTTATGCATCGATGCACAAGACCATGCATCGATGCACTC
Found at i:58024 original size:66 final size:66
Alignment explanation
Indices: 57913--58046 Score: 196
Period size: 66 Copynumber: 2.0 Consensus size: 66
57903 TTGTTAGGGG
* * *
57913 TTAAGAAGGGTTTTAAAACACTTCATAAGGCTAGAAATATCTAAAAAATGGATTAGAACCATCTA
1 TTAAGAAGGGTTTTAAAACACTTCACAAGACTAGAAATATATAAAAAATGGATTAGAACCATCTA
57978 A
66 A
* * * * *
57979 TTAAGGAGGGTTTTAAAATACTTCACAAGATTATAAATATATAAAAAATGGATTGGAACCATCTA
1 TTAAGAAGGGTTTTAAAACACTTCACAAGACTAGAAATATATAAAAAATGGATTAGAACCATCTA
58044 A
66 A
58045 TT
1 TT
58047 TCTTAAACCC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (66 bp):
TTAAGAAGGGTTTTAAAACACTTCACAAGACTAGAAATATATAAAAAATGGATTAGAACCATCTA
A
Found at i:58794 original size:13 final size:13
Alignment explanation
Indices: 58776--58818 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
58766 TTGAAGATGA
58776 ATGAAGAAAAGAG
1 ATGAAGAAAAGAG
58789 ATGAAGAAAAGAG
1 ATGAAGAAAAGAG
*
58802 ATAAAGAAGAAGAG
1 ATGAAGAA-AAGAG
58816 ATG
1 ATG
58819 GGGAATAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 20 0.74
14 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.09
Consensus pattern (13 bp):
ATGAAGAAAAGAG
Done.