Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008899.1 Hibiscus syriacus cultivar Beakdansim tig00112172_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: 49919
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:971 original size:112 final size:109
Alignment explanation
Indices: 774--1095 Score: 430
Period size: 112 Copynumber: 2.9 Consensus size: 109
764 CACCACGGAA
* * * *
774 ATTGAATCGGGGCAGAATTATTCCGCTTACTCTAAAAGGAAAATCAAATCTTGGAAAAGTGAGAC
1 ATTGAATCGGGGCAGATTTATTCCGCTTACTCTAAAGGGAATATCAAATCTT-GAAAAGAGAGAC
839 ATGTTCCGCTTACTCTGAAGGGAAATCAGATCTGTGGGAGTTTATCC
65 ATGTT-CGCTTACTCTGAAGGGAAATCAGATCTG-GGGAGTTTATCC
*
886 ATTGAATCGGGGAAGATTTATTCCGCTTACTCTAAAGGGAATATCAAATCTTAGAAAAGAGAGAC
1 ATTGAATCGGGGCAGATTTATTCCGCTTACTCTAAAGGGAATATCAAATCTT-GAAAAGAGAGAC
951 ATGTTCTGCTTACTCTGAAGGGAAAATCAGATCTGGGGAGTTTATCC
65 ATGTTC-GCTTACTCTGAAGGG-AAATCAGATCTGGGGAGTTTATCC
* * * * * * *
998 ATTGAATCGGGCCAGATTTGTTCCGATTACTCTGAAGAGAATATCAAATCTTGAAAAAAAAGACC
1 ATTGAATCGGGGCAGATTTATTCCGCTTACTCTAAAGGGAATATCAAATCTTGAAAAGAGAGA-C
* *
1063 TAT-TTCACTTACTCTGAAGGGAATATCAAATCT
65 -ATGTTCGCTTACTCTGAAGGGAA-ATCAGATCT
1096 TGGAAAAGAG
Statistics
Matches: 189, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
110 2 0.01
111 32 0.17
112 141 0.75
113 14 0.07
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (109 bp):
ATTGAATCGGGGCAGATTTATTCCGCTTACTCTAAAGGGAATATCAAATCTTGAAAAGAGAGACA
TGTTCGCTTACTCTGAAGGGAAATCAGATCTGGGGAGTTTATCC
Found at i:1130 original size:48 final size:47
Alignment explanation
Indices: 1024--1143 Score: 134
Period size: 48 Copynumber: 2.5 Consensus size: 47
1014 TTTGTTCCGA
* *
1024 TTACTCTGAAGAGAATATCAAATCTTGAAAAAAAAGACCTATTTCAC
1 TTACTCTGAAGGGAATATCAAATCTTGAAAAAAAAGACATATTTCAC
* * * *
1071 TTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTAT-GC
1 TTACTCTGAAGGGAATATCAAATCTT-GAAAAAAAAGACATATT-TCAC
* * *
1119 TTACTCCGAAGGGAAAATCAGATCT
1 TTACTCTGAAGGGAATATCAAATCT
1144 GAGGGAGTTG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
47 25 0.40
48 36 0.58
49 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (47 bp):
TTACTCTGAAGGGAATATCAAATCTTGAAAAAAAAGACATATTTCAC
Found at i:1246 original size:112 final size:113
Alignment explanation
Indices: 1070--1322 Score: 339
Period size: 112 Copynumber: 2.2 Consensus size: 113
1060 ACCTATTTCA
* * *
1070 CTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTATGCTTACTCCGAAGGGAAA
1 CTTACTCCGAAGAGAATATCAAATCTTGGAAAAGAGAGACATGTTACGCTTACTCCGAAGGGAAA
1135 ATCAGATCTGAGGGAGTTGATCCATTGAATCGGGGTATACTTTTTTTG
66 ATCAGATCTGAGGGAGTTGATCCATTGAATCGGGGTATACTTTTTTTG
* * ** *
1183 CTTACTCCGAAGAGAATATCAAAT-TTGGAAAAGAGAGACTTGTTCCGCTTACTTTGAATGGAAA
1 CTTACTCCGAAGAGAATATCAAATCTTGGAAAAGAGAGACATGTTACGCTTACTCCGAAGGGAAA
* * * * **
1247 ATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCG
66 ATCAGATCTGAGGGAGTTGATCCATTGAATCGGGGTATACTTTTTTTG
**
1295 CTTACTCTAAAG-GTAATATCAAATCTTG
1 CTTACTCCGAAGAG-AATATCAAATCTTG
1323 AAGGAGATGG
Statistics
Matches: 122, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
111 1 0.01
112 96 0.79
113 25 0.20
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (113 bp):
CTTACTCCGAAGAGAATATCAAATCTTGGAAAAGAGAGACATGTTACGCTTACTCCGAAGGGAAA
ATCAGATCTGAGGGAGTTGATCCATTGAATCGGGGTATACTTTTTTTG
Found at i:1302 original size:272 final size:271
Alignment explanation
Indices: 799--1324 Score: 761
Period size: 272 Copynumber: 1.9 Consensus size: 271
789 AATTATTCCG
* * *
799 CTTACTCTAAAAGGAAAATCAAATCTTGGAAAAGTGAGACATGTTCCGCTTACTCTGAAGGGAAA
1 CTTACTCTAAAAGGAAAATCAAATCTTGGAAAAGAGAGACATGTTACGCTTACTCCGAAGGGAAA
* * * *
864 TCAGATCTGTGGGAGTTTATCCATTGAATCGGGGAAGATTTATTCCGCTTACTCTAAAGGGAATA
66 TCAGATCTGAGGGAGTTGATCCATTGAATCGGGGAAGATTTATTCCGCTTACTCCAAAGAGAATA
* *
929 TCAAATCTTAGAAAAGAGAGACATGTTCTGCTTACTCTGAAGGGAAAATCAGATCTGGGGAGTTT
131 TCAAATCTTAGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTGGGGAGTTG
* *
994 ATCCATTGAATCGGGCCAGATTTGTTCCGATTACTCTGAAGAG-AATATCAAATCTTGAAAAAAA
196 ATCCATTGAATCGGGCCAGACTTGTTCCGATTACTCTAAAG-GTAATATCAAATCTTGAAAAAAA
1058 AGACCTATTTCA
260 AGACCTATTTCA
* * * *
1070 CTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTATGCTTACTCCGAAGGGAAA
1 CTTACTCTAAAAGGAAAATCAAATCTTGGAAAAGAGAGACATGTTACGCTTACTCCGAAGGG-AA
* * ** *
1135 ATCAGATCTGAGGGAGTTGATCCATTGAATCGGGGTATACTTT-TTTTGCTTACTCCGAAGAGAA
65 ATCAGATCTGAGGGAGTTGATCCATTGAATCGGGGAAGA-TTTATTCCGCTTACTCCAAAGAGAA
* * * *
1199 TATCAAAT-TTGGAAAAGAGAGACTTGTTCCGCTTACTTTGAATGGAAAATCAGATCTGGGGGAG
129 TATCAAATCTTAGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAAAATCAGATCT-GGGGAG
* *
1263 TTGATCCATTGAATCGGGGCAGACTTGTTCCGCTTACTCTAAAGGTAATATCAAATCTTGAA
193 TTGATCCATTGAATCGGGCCAGACTTGTTCCGATTACTCTAAAGGTAATATCAAATCTTGAA
1325 GGAGATGGAT
Statistics
Matches: 225, Mismatches: 26, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
271 100 0.44
272 122 0.54
273 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (271 bp):
CTTACTCTAAAAGGAAAATCAAATCTTGGAAAAGAGAGACATGTTACGCTTACTCCGAAGGGAAA
TCAGATCTGAGGGAGTTGATCCATTGAATCGGGGAAGATTTATTCCGCTTACTCCAAAGAGAATA
TCAAATCTTAGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTGGGGAGTTG
ATCCATTGAATCGGGCCAGACTTGTTCCGATTACTCTAAAGGTAATATCAAATCTTGAAAAAAAA
GACCTATTTCA
Found at i:1581 original size:136 final size:134
Alignment explanation
Indices: 1270--1657 Score: 394
Period size: 136 Copynumber: 2.9 Consensus size: 134
1260 GAGTTGATCC
* * *
1270 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTAAAGGTAATATCAAATCTT-G-AAGGAGATGG
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTAAAGG-AAAATCAAAACTTGGAAAAGAGA--G
* * * *
1333 ATCTGTTATGCTTA-TCTTGAAGGGAATATCAGATCTGGGAGGA-TACGTGATTCATTCCTCTGT
63 ACCTGTTACGCTTACT-TTGAAGGGAATATCAGATCT-GGAGGAGT---TGATCCATTCCGCTGT
**
1396 TCTTCAGGGAAG
123 TCCCCAGGGAAG
* ** * *
1408 TTTGAATCAAGGTAGACTTGTTCCGCTGT-CACT-AAGGAAAATCAAAACTTGGAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCT-TACTCTAAAGGAAAATCAAAACTTGGAAAAGAGAGAC
* * * *
1471 CTCTTCCCCTTACTTTGAAGGGAATATCAGATCTGGAGGAGGTTGATCCATTTCGCTG-TCACCC
65 CTGTTACGCTTACTTTGAAGGGAATATCAGATCTGGAGGA-GTTGATCCATTCCGCTGTTC-CCC
1535 AGGGAAG
128 AGGGAAG
* *
1542 ATTGAATCGGGGCAGACTTGTTCTGCTTACTCTGAAAGGAAAATCAAAACTTGGAAAAGTGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCT-AAAGGAAAATCAAAACTTGGAAAAGAGAGAC
* * * * *
1607 CTGTTTCGCTTACTCTGAAGGGAAAATCAGATCTGGGGGAGTTTATCCATT
65 CTGTTACGCTTACTTTGAAGGGAATATCAGATCTGGAGGAGTTGATCCATT
1658 GAATCAGGGT
Statistics
Matches: 208, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
133 3 0.01
134 45 0.22
135 16 0.08
136 104 0.50
137 7 0.03
138 32 0.15
139 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (134 bp):
ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTAAAGGAAAATCAAAACTTGGAAAAGAGAGACC
TGTTACGCTTACTTTGAAGGGAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTTCCCCAGG
GAAG
Found at i:1740 original size:113 final size:113
Alignment explanation
Indices: 1542--2315 Score: 986
Period size: 113 Copynumber: 6.9 Consensus size: 113
1532 CCCAGGGAAG
* * * *
1542 ATTGAATCGGGGCAGACTTGTTCTGCTTACTCTGAAAGGAAAATCAAAACTTGGAAAAGTGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATCTTGGAAAAGAGAGAC
* * * *
1607 CTGTTTCGCTTACTCTGAAGGGAAAATCAGATCTGGGGGAGTTTATCC
66 ATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGGAGTTGATCC
* * * *
1655 ATTGAATCAGGGTAGATTTGTTCCGCTTACTCTGAAAGGAATAACAAATCTTGGAAAAGAGAGAT
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATCTTGGAAAAGAGAGA-
*
1720 C-TGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGGAGTTAATCC
65 CATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGGAGTTGATCC
* * * * *
1768 AATGAATTGGGGCAGACTTGTTCCTCTTACTCTGAAGGGAATATCAAATCTTGAAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATCTTGGAAAAGAGAGAC
*
1833 ATGTTCCGCTTACTCTGAAGGGAAAATC-GAATTTAGGGGAGTTGATCC
66 ATGTTCCGCTTACTCTGAAGGGAAAATCAG-ATCTAGGGGAGTTGATCC
* * * *
1881 ATTAAATCGGGGTAGATTTATTCCGCTTACTCT-AAAGGGAATATCAAATCTTGGAAAAGAGAGA
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAA-GGAATATCAAATCTTGGAAAAGAGAGA
1945 CATGTTCCGCTTACT-TAGAAGGGAAAATCAGATCT-GAGGGAGTTGA-CC
65 CATGTTCCGCTTACTCT-GAAGGGAAAATCAGATCTAG-GGGAGTTGATCC
* * *
1993 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTCGAAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATCTTGGAAAAGAGAGAC
* * * * *
2058 TTGTTCTGCTTACTCTGAAGGGAAAATCAGTTATAGGGGAGTTGGTCC
66 ATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGGAGTTGATCC
* * * ** * *
2106 ATTGAATCGGGGTATATTTGTTTTGTTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATCTTGGAAAAGAGAGAC
* * * *
2171 ATGTTCTGCTTACTCTAAAAGGAAAATCAGATAT-GGGGCAGTTGATCC
66 ATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGG-AGTTGATCC
* * **
2219 ATTGAATCGAGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATATTCTAAAAGAGAGAC
1 ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATCTTGGAAAAGAGAGAC
* ** * *
2284 TTGTTCATCTTATTCTGAAGGGAATATCAGAT
66 ATGTTCCGCTTACTCTGAAGGGAAAATCAGAT
2316 TTTTCAAAAA
Statistics
Matches: 574, Mismatches: 75, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
112 103 0.18
113 469 0.82
114 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (113 bp):
ATTGAATCGGGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATCTTGGAAAAGAGAGAC
ATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTAGGGGAGTTGATCC
Found at i:2166 original size:338 final size:338
Alignment explanation
Indices: 1546--2315 Score: 1021
Period size: 338 Copynumber: 2.3 Consensus size: 338
1536 GGGAAGATTG
* * * * *
1546 AATCGGGGCAGACTTGTTCTGCTTACTCTGAAAGGAAAATCAAAACTTGGAAAAGTGAGACCTGT
1 AATCGGGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATCTTGGAAAAGAGAGACATGT
* * * * *
1611 TTCGCTTACTCTGAAGGGAAAATCAGATCTGGGGGAGTTTATCCATTGAATCAGGGTAGATTTGT
66 TCCGCTTACT-TGAAGGGAAAATCAGATCTGAGGGAGTTGATCCATTGAATCAGGGCAGACTTGT
* *
1676 TCCGCTTACTCTGAAAGGAATAACAAATCTTGGAAAAGAGAGATCTGTTCCGCTTACTCTGAAGG
130 TCCGCTTACTCTGAAAGGAATAACAAATCTCGAAAAAGAGAGATCTGTTCCGCTTACTCTGAAGG
* *
1741 GAAAATCAGATCTAGGGGAGTTAATCCAATGAATTGGGGCAGACTTGTTCCTCTTACTCTGAAGG
195 GAAAATCAGATATAGGGGAGTTAATCCAATGAATCGGGGCAGACTTGTTCCTCTTACTCTGAAGG
* * *
1806 GAATATCAAATCTTGAAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAAAATC-GAATTTAGG
260 GAATATCAAATCTTGAAAAAGAGAGACATGTTCCGCTTACTCTAAAAGGAAAATCAG-ATAT-GG
1870 GG-AGTTGATCCATTA
323 GGCAGTTGATCCATTA
* * *
1885 AATCGGGGTAGATTTATTCCGCTTACTCT-AAAGGGAATATCAAATCTTGGAAAAGAGAGACATG
1 AATCGGGGCAGACTTGTTCCGCTTACTCTGAAA-GGAATATCAAATCTTGGAAAAGAGAGACATG
*
1949 TTCCGCTTACTTAGAAGGGAAAATCAGATCTGAGGGAGTTGA-CCATTGAATCGGGGCAGACTTG
65 TTCCGCTTACTT-GAAGGGAAAATCAGATCTGAGGGAGTTGATCCATTGAATCAGGGCAGACTTG
* * *
2013 TTCCGCTTACTCTGAAGGGAATATCAAATCTCGAAAAAGAGAGA-CTTGTTCTGCTTACTCTGAA
129 TTCCGCTTACTCTGAAAGGAATAACAAATCTCGAAAAAGAGAGATC-TGTTCCGCTTACTCTGAA
* ** * * * * * *
2077 GGGAAAATCAGTTATAGGGGAGTTGGTCCATTGAATCGGGGTATATTTGTT-TTGTTTACTCTGA
193 GGGAAAATCAGATATAGGGGAGTTAATCCAATGAATCGGGGCAGACTTGTTCCT-CTTACTCTGA
* *
2141 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCTGCTTACTCTAAAAGGAAAATCAGATATG
257 AGGGAATATCAAATCTTGAAAAAGAGAGACATGTTCCGCTTACTCTAAAAGGAAAATCAGATATG
*
2206 GGGCAGTTGATCCATTG
322 GGGCAGTTGATCCATTA
* * ** *
2223 AATCGAGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATATTCTAAAAGAGAGACTTGT
1 AATCGGGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATCTTGGAAAAGAGAGACATGT
** * *
2288 TCATCTTATTCTGAAGGGAATATCAGAT
66 TCCGCTTACT-TGAAGGGAAAATCAGAT
2316 TTTTCAAAAA
Statistics
Matches: 375, Mismatches: 48, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
337 6 0.02
338 275 0.73
339 94 0.25
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (338 bp):
AATCGGGGCAGACTTGTTCCGCTTACTCTGAAAGGAATATCAAATCTTGGAAAAGAGAGACATGT
TCCGCTTACTTGAAGGGAAAATCAGATCTGAGGGAGTTGATCCATTGAATCAGGGCAGACTTGTT
CCGCTTACTCTGAAAGGAATAACAAATCTCGAAAAAGAGAGATCTGTTCCGCTTACTCTGAAGGG
AAAATCAGATATAGGGGAGTTAATCCAATGAATCGGGGCAGACTTGTTCCTCTTACTCTGAAGGG
AATATCAAATCTTGAAAAAGAGAGACATGTTCCGCTTACTCTAAAAGGAAAATCAGATATGGGGC
AGTTGATCCATTA
Found at i:9120 original size:15 final size:15
Alignment explanation
Indices: 9087--9123 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
9077 TGAGACCTTA
**
9087 CCCGCCCCGCATCTT
1 CCCGCCCCGCATCCG
9102 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
9117 CCCGCCC
1 CCCGCCC
9124 AGTTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.68, G:0.16, T:0.11
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:9302 original size:28 final size:28
Alignment explanation
Indices: 9262--9327 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
9252 TAATTTTTTT
**
9262 TCTTTCAAACCTCTCCTTACTGTGCCGA
1 TCTTTCAAACCTCTCCTTACTGCACCGA
9290 TCTTTCAAACCTCTCCTTACTGCACCGA
1 TCTTTCAAACCTCTCCTTACTGCACCGA
9318 TCTTTCAAAC
1 TCTTTCAAAC
9328 ATCTGGTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.21, C:0.36, G:0.08, T:0.35
Consensus pattern (28 bp):
TCTTTCAAACCTCTCCTTACTGCACCGA
Found at i:13513 original size:3 final size:3
Alignment explanation
Indices: 13507--13538 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
13497 CATCATCATC
13507 ATT ATT ATT ATT ATT ATT ATT ATT ATT GATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT A
13539 ATTAGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:13699 original size:3 final size:3
Alignment explanation
Indices: 13691--13720 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
13681 TTTGTGCAAC
13691 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13721 GAAAACATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:16397 original size:26 final size:25
Alignment explanation
Indices: 16368--16431 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 25
16358 ATATTATCAA
16368 ATATAATAATATATTAGATAACGTTT
1 ATATAATAATATATTAG-TAACGTTT
* * *
16394 ATATAAT-GTA-ATAAGTAATGTTT
1 ATATAATAATATATTAGTAACGTTT
*
16417 ATATAATAAAATATT
1 ATATAATAATATATT
16432 TTTAATTACT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
23 14 0.47
24 5 0.17
25 4 0.13
26 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (25 bp):
ATATAATAATATATTAGTAACGTTT
Found at i:16558 original size:23 final size:23
Alignment explanation
Indices: 16532--16581 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
16522 ATCAAGCACA
* *
16532 ATAACATATTA-GATAGTGCTTAT
1 ATAACATAATATG-TAGCGCTTAT
*
16555 ATAACGTAATATGTAGCGCTTAT
1 ATAACATAATATGTAGCGCTTAT
16578 ATAA
1 ATAA
16582 TAAAATAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (23 bp):
ATAACATAATATGTAGCGCTTAT
Found at i:16716 original size:23 final size:23
Alignment explanation
Indices: 16690--16749 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
16680 ATCAAGCACA
*
16690 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
16713 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
16736 ATAATAAAATAGGT
1 ATAACATAATAGGT
16750 TAATTACTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:16875 original size:23 final size:24
Alignment explanation
Indices: 16849--16894 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
16839 TCAAGCATAA
*
16849 TAACATATTAGGTAGCGC-TTATG
1 TAACATAATAGGTAGCGCATTATG
* *
16872 TAACGTAATAGGTTGCGCATTAT
1 TAACATAATAGGTAGCGCATTAT
16895 TAAAGTTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (24 bp):
TAACATAATAGGTAGCGCATTATG
Found at i:16882 original size:158 final size:157
Alignment explanation
Indices: 16372--16894 Score: 771
Period size: 158 Copynumber: 3.3 Consensus size: 157
16362 TATCAAATAT
* * * * * ** * **
16372 AATAATATATTAGATAACGTTTATATAATGTAATAAGTAATGTTTATATAATAAAATATTTTTAA
1 AATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATA-GGTTAA
*
16437 TTACTTAATTTGTTATTACAACATATTAGGTAAACGCCTAAAATGTTACTAATGATAACATAACC
65 TTACTTAATTTGTTATTACAACATATTAGGTAAACTCCTAAAATGTTAC-AATGATAACATAACC
16502 GGTTAATTACTAGAAACATTATCAAGCAC
129 GGTTAATTACTAGAAACATTATCAAGCAC
* *
16531 AATAACATATTAGATAGTGCTTATATAACGTAATATGTAGCGCTTATATAATAAAATAGGTTAAT
1 AATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
*
16596 TACTTAATTTGTTATTACAACATATTAGGTAAA-TGCCTAAAATGTTAACAAGGATAACATAACC
66 TACTTAATTTGTTATTACAACATATTAGGTAAACT-CCTAAAATGTT-ACAATGATAACATAACC
16660 GGTTAATTACTAGAAACATTATCAAGCAC
129 GGTTAATTACTAGAAACATTATCAAGCAC
*
16689 AATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
1 AATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
* *
16754 TACTTAATTTGTTATTACAACATATTAGGTAAACTCCTAAAATATTGTCAATGATAACATAACCG
66 TACTTAATTTGTTATTACAACATATTAGGTAAACTCCTAAAATGTT-ACAATGATAACATAACCG
* *
16819 ATTAATTA-TAGGAAACATTATCAAGCAT
130 GTTAATTACTA-GAAACATTATCAAGCAC
* * *
16847 AATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTTGCGCATTAT
1 AATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGC-TTAT
16895 TAAAGTTGAT
Statistics
Matches: 335, Mismatches: 24, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
157 2 0.01
158 277 0.83
159 56 0.17
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (157 bp):
AATAACATATTAGATAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
TACTTAATTTGTTATTACAACATATTAGGTAAACTCCTAAAATGTTACAATGATAACATAACCGG
TTAATTACTAGAAACATTATCAAGCAC
Found at i:17114 original size:74 final size:73
Alignment explanation
Indices: 17008--17253 Score: 309
Period size: 74 Copynumber: 3.4 Consensus size: 73
16998 AAAATTTAAA
* * * *
17008 CTACCTATTACATTAAAATACTTACAGGTTTTTTTAAGGTTGTTAATAATGTAAATGGTAAAAAA
1 CTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAATGTAAATGGT-AAAAA
17073 AAATAGGCG
65 AAATAGGCG
* * * *
17082 TTACCTATTACATTAAAATACCTACCGATTTTTTGAAGGTTGCTAATATTGTAAACGGT-AAAAA
1 CTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAATGTAAATGGTAAAAAA
17146 AATA-GCG
66 AATAGGCG
** *
17153 CTATATATTACATTAAAATACCTACC-AGTTTTTTTGAAGGTTGCTAATAATATAAATGGTAAAA
1 CTACCTATTACATTAAAATACCTACCGA-TTTTTTT-AAGGTTGCTAATAATGTAAATGGTAAAA
* *
17217 AAAATTGGCA
64 AAAATAGGCG
* *
17227 CTACCTATTACATTAAACTACATACCG
1 CTACCTATTACATTAAAATACCTACCG
17254 GATATGTAGA
Statistics
Matches: 146, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.01
71 32 0.22
72 30 0.21
73 8 0.05
74 75 0.51
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (73 bp):
CTACCTATTACATTAAAATACCTACCGATTTTTTTAAGGTTGCTAATAATGTAAATGGTAAAAAA
AATAGGCG
Found at i:17531 original size:112 final size:112
Alignment explanation
Indices: 17334--17686 Score: 539
Period size: 112 Copynumber: 3.2 Consensus size: 112
17324 TAGCGCCTAT
* * *
17334 AAAGTATCGATACTTTATAAAAATGTATCGATACATAACAATATAACAGGAAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
*
17399 ATCAGTTTCATTATGACAAAACTGGTAAAGAGCTACCGAATATGTTA
66 ATCAGTTTCATTATGACAAAACTGGTAAAGAGCTACCGAATATGTTG
* ** * *
17446 AAAGTATCGATACTTTTTGTACATGTATCGATACTTTACAATATAACAGGTAAAAATATGAAAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* *
17511 ATCAGTTTCATTATGACAAAACCGGTAAAGAGTTACC-ATATATGTTG
66 ATCAGTTTCATTATGACAAAACTGGTAAAGAGCTACCGA-ATATGTTG
* * *
17558 AAAGTGTCGATACTTTATAAAAATGTATCAATACTTTACAATATAACAAGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
*
17623 A-CTAGTTTCATTATGACAAAACTGGTAAAGAGCTACCGGATATGTTG
66 ATC-AGTTTCATTATGACAAAACTGGTAAAGAGCTACCGAATATGTTG
17670 AAAGTATCGATACTTTA
1 AAAGTATCGATACTTTA
17687 CAATATAACA
Statistics
Matches: 215, Mismatches: 23, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
111 2 0.01
112 213 0.99
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (112 bp):
AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
ATCAGTTTCATTATGACAAAACTGGTAAAGAGCTACCGAATATGTTG
Found at i:17757 original size:90 final size:91
Alignment explanation
Indices: 17582--17776 Score: 320
Period size: 90 Copynumber: 2.2 Consensus size: 91
17572 TTATAAAAAT
* * *
17582 GTATCAATACTTTACAATATAACAAGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACTG
1 GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCG
* *
17647 GTAAAGAGCTACCGGATATGTTGAAA
66 GTAAAGAACTACCAGATATGTTGAAA
*
17673 GTATCGATACTTTACAATATAACACGTAAAAATATGAC-AAACCAGTTTCATTATGACAAAACCG
1 GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCG
17737 GTAAAGAACTACCAGATATGTTGAAA
66 GTAAAGAACTACCAGATATGTTGAAA
*
17763 GTAACGATACTTTA
1 GTATCGATACTTTA
17777 TAAAATGTAT
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 61 0.63
91 36 0.37
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (91 bp):
GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCG
GTAAAGAACTACCAGATATGTTGAAA
Found at i:17812 original size:110 final size:111
Alignment explanation
Indices: 17673--17886 Score: 349
Period size: 111 Copynumber: 1.9 Consensus size: 111
17663 TATGTTGAAA
* *
17673 GTATCGATACTTTACAATATAACACGTAAAAATATGAC-AAACCAGTTTCATTATGACAAAACCG
1 GTATCGATACTTTACAATATAAAACGTAAAAATATGACAAAACCAATTTCATTATGACAAAACCG
*
17737 GTAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTATAAAAT
66 ATAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTATAAAAT
* * *
17783 GTATCGATACTTTACAATATAAAAGGTAAAAATATGACAAAATCAATTTCATTTTGACAAAACCG
1 GTATCGATACTTTACAATATAAAACGTAAAAATATGACAAAACCAATTTCATTATGACAAAACCG
* *
17848 ATAAAGAGCTACCAGATATGTTGAAAGTATCGATACTTT
66 ATAAAGAACTACCAGATATGTTGAAAGTAACGATACTTT
17887 TTGTATATGT
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 36 0.38
111 59 0.62
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (111 bp):
GTATCGATACTTTACAATATAAAACGTAAAAATATGACAAAACCAATTTCATTATGACAAAACCG
ATAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTATAAAAT
Found at i:17843 original size:201 final size:203
Alignment explanation
Indices: 17470--17886 Score: 662
Period size: 201 Copynumber: 2.1 Consensus size: 203
17460 TTTTGTACAT
* *
17470 GTATCGATACTTTACAATATAACAGGTAAAAATATGAAAAAATCAGTTTCATTATGACAAAACCG
1 GTATCGATACTTTACAATATAACACGTAAAAATATGAAAAAACCAGTTTCATTATGACAAAACCG
** * **
17535 GTAAAGAGTTACCATATATGTTGAAAGTGTCGATACTTTATAAAAATGTATCAATACTTTACAAT
66 GTAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTATAAAAATGTATCAATACTTTACAAT
* * * *
17600 ATAACAAGTAAAAATATGACAAAACTAGTTTCATTATGACAAAACTGGTAAAGAGCTACCGGATA
131 ATAACAAGTAAAAATATGACAAAACTAATTTCATTATGACAAAACCGATAAAGAGCTACCAGATA
17665 TGTTGAAA
196 TGTTGAAA
*
17673 GTATCGATACTTTACAATATAACACGTAAAAATATG-ACAAACCAGTTTCATTATGACAAAACCG
1 GTATCGATACTTTACAATATAACACGTAAAAATATGAAAAAACCAGTTTCATTATGACAAAACCG
*
17737 GTAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTAT-AAAATGTATCGATACTTTACAAT
66 GTAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTATAAAAATGTATCAATACTTTACAAT
*
17801 ATAA-AAGGTAAAAATATGACAAAA-TCAATTTCATTTTGACAAAACCGATAAAGAGCTACCAGA
131 ATAACAA-GTAAAAATATGACAAAACT-AATTTCATTATGACAAAACCGATAAAGAGCTACCAGA
17864 TATGTTGAAA
194 TATGTTGAAA
17874 GTATCGATACTTT
1 GTATCGATACTTT
17887 TTGTATATGT
Statistics
Matches: 198, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
200 3 0.02
201 98 0.49
202 62 0.31
203 35 0.18
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (203 bp):
GTATCGATACTTTACAATATAACACGTAAAAATATGAAAAAACCAGTTTCATTATGACAAAACCG
GTAAAGAACTACCAGATATGTTGAAAGTAACGATACTTTATAAAAATGTATCAATACTTTACAAT
ATAACAAGTAAAAATATGACAAAACTAATTTCATTATGACAAAACCGATAAAGAGCTACCAGATA
TGTTGAAA
Found at i:18495 original size:7 final size:7
Alignment explanation
Indices: 18479--18508 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
18469 TTTTAAATCA
*
18479 ATAAAAT
1 ATAAATT
18486 ATAAATT
1 ATAAATT
18493 ATAAATT
1 ATAAATT
18500 ATAAATT
1 ATAAATT
18507 AT
1 AT
18509 TTGAGTTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAAATT
Found at i:18719 original size:18 final size:19
Alignment explanation
Indices: 18635--18716 Score: 69
Period size: 18 Copynumber: 4.2 Consensus size: 19
18625 AGTTTAAAAA
18635 TGATTGTAATATGTT-CGTT
1 TGATTGTAATATGTTAC-TT
* *
18654 TGATATATTTATAGTGTTACTT
1 TGAT-T-GTAATA-TGTTACTT
* **
18676 TAATTGTAATAT-TTGTTT
1 TGATTGTAATATGTTACTT
18694 TGATTGTAATATGTTACTT
1 TGATTGTAATATGTTACTT
18713 TGAT
1 TGAT
18717 GTATTTGTGA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
18 15 0.31
19 13 0.27
20 5 0.10
21 5 0.10
22 9 0.19
23 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.55
Consensus pattern (19 bp):
TGATTGTAATATGTTACTT
Found at i:23673 original size:25 final size:24
Alignment explanation
Indices: 23635--23682 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
23625 TGAAAATAAA
*
23635 ATAAAAATTGCATAACATACATAC
1 ATAAAAATTACATAACATACATAC
*
23659 ATAAAAATGTACATACCATACATA
1 ATAAAAAT-TACATAACATACATA
23683 AAGTAGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (24 bp):
ATAAAAATTACATAACATACATAC
Found at i:25797 original size:55 final size:55
Alignment explanation
Indices: 25735--26238 Score: 450
Period size: 55 Copynumber: 9.3 Consensus size: 55
25725 GACTTGGATC
* * *
25735 ATCTTCAACAAACTTGTCTGCCCCCTATTTCTTCAGAGAGTATAGGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACA
* * * *
25790 ATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACA
* * *
25845 ATCTTCAACAAAT-GGGT-TCGTTCCCTATTTC-TCTAGGGAGTAT-GGAACTCGAACA
1 ATCTTCAAC-AATCGTGTCT-GCTCCCTATTTCTTC-AGAGAGTATAGG-ACTCGAACA
* * * * * *
25900 TCTCTTC-A-GA-CGGGT-TCGCTCCTTCTTTCTTTA-AGGAGTAT-GGAACTCGAAC-
1 -ATCTTCAACAATCGTGTCT-GCTCCCTATTTCTTCAGA-GAGTATAGG-ACTCGAACA
* * * * *
25952 ATCTTCAAC--T-GGGT-TCGCTCCCTCTTTC-TCTAGGGAGTAT-GGAACTTGAAGA
1 ATCTTCAACAATCGTGTCT-GCTCCCTATTTCTTC-AGAGAGTATAGG-ACTCGAACA
* * * *
26004 ATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACA
* * * *
26059 ATCTTCATCAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCCAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACA
* * * *
26114 ATCTTCAACAGTCGTGTCTGCTCCCTATTTATGCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACA
* * *
26169 ATTTTCAACAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTAT-GAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAG-GACTCGAACA
26224 ATCTTCAACAATCGT
1 ATCTTCAACAATCGT
26239 TGGGAAACCT
Statistics
Matches: 381, Mismatches: 47, Indels: 42
0.81 0.10 0.09
Matches are distributed among these distances:
50 1 0.00
51 38 0.10
52 9 0.02
53 34 0.09
54 6 0.02
55 282 0.74
56 11 0.03
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (55 bp):
ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACA
Found at i:25978 original size:51 final size:51
Alignment explanation
Indices: 25836--25997 Score: 209
Period size: 51 Copynumber: 3.1 Consensus size: 51
25826 AGAGTATAAG
* *
25836 ACTCGAACAATCTTCAACAAATGGGTTCGTTCCCTATTTCTCTAGGGAGTATGGA
1 ACTCGAAC-ATCTTCAAC---TGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
25891 ACTCGAACATCTCTTCAGAC-GGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
1 ACTCGAACA--TCTTCA-ACTGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
25944 ACTCGAACATCTTCAACTGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCAACTGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
25995 ACT
1 ACT
25998 TGAAGAATCT
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
50 2 0.02
51 39 0.41
53 37 0.39
54 1 0.01
55 8 0.08
56 6 0.06
57 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (51 bp):
ACTCGAACATCTTCAACTGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
Found at i:27234 original size:9 final size:8
Alignment explanation
Indices: 27220--27266 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
27210 TGAACCCTTC
*
27220 TTTTTCCA
1 TTTTTTCA
27228 TTTTTTCA
1 TTTTTTCA
27236 TTTTTT--
1 TTTTTTCA
27242 TTTTTT--
1 TTTTTTCA
27248 TTTTTT-A
1 TTTTTTCA
27255 TTTTTTCA
1 TTTTTTCA
27263 TTTT
1 TTTT
27267 CATTTTCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
6 12 0.33
7 6 0.17
8 18 0.50
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTCA
Found at i:27237 original size:8 final size:7
Alignment explanation
Indices: 27227--27293 Score: 56
Period size: 6 Copynumber: 10.0 Consensus size: 7
27217 TTCTTTTTCC
27227 ATTTTTT
1 ATTTTTT
27234 CATTTTTT
1 -ATTTTTT
27242 -TTTTTT
1 ATTTTTT
27248 -TTTTTT
1 ATTTTTT
27254 ATTTTTT
1 ATTTTTT
*
27261 CA-TTTTC
1 -ATTTTTT
27268 ATTTTCTT
1 ATTTT-TT
27276 -TTTTTT
1 ATTTTTT
27282 -TTTTTT
1 ATTTTTT
27288 -TTTTTT
1 ATTTTTT
27294 TTCTTCAAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
6 27 0.51
7 17 0.32
8 9 0.17
ACGTcount: A:0.07, C:0.06, G:0.00, T:0.87
Consensus pattern (7 bp):
ATTTTTT
Found at i:27240 original size:1 final size:1
Alignment explanation
Indices: 27236--27295 Score: 66
Period size: 1 Copynumber: 60.0 Consensus size: 1
27226 CATTTTTTCA
* ** ** *
27236 TTTTTTTTTTTTTTTTTTATTTTTTCATTTTCATTTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27296 CTTCAAGCAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.05, C:0.05, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:27250 original size:27 final size:29
Alignment explanation
Indices: 27220--27281 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 29
27210 TGAACCCTTC
27220 TTTTTCCATTTTTTCATTTT-TTTT-TTT
1 TTTTTCCATTTTTTCATTTTATTTTCTTT
**
27247 TTTTTTTATTTTTTCATTTTCATTTTCTTT
1 TTTTTCCATTTTTTCATTTT-ATTTTCTTT
27277 TTTTT
1 TTTTT
27282 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 18 0.60
29 4 0.13
30 8 0.27
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTTTCCATTTTTTCATTTTATTTTCTTT
Found at i:27272 original size:33 final size:34
Alignment explanation
Indices: 27230--27294 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
27220 TTTTTCCATT
27230 TTTTCATTTT-TTTTTTTTTTTTTTATTTTTTCA
1 TTTTCATTTTCTTTTTTTTTTTTTTATTTTTTCA
*
27263 TTTTCATTTTCTTTTTTTTTTTTTTTTTTTTT
1 TTTTCATTTTCTTTTTTTTTTTTTTATTTTTT
27295 TCTTCAAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 10 0.33
34 20 0.67
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (34 bp):
TTTTCATTTTCTTTTTTTTTTTTTTATTTTTTCA
Found at i:27285 original size:27 final size:27
Alignment explanation
Indices: 27227--27298 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
27217 TTCTTTTTCC
* *
27227 ATTTTTTCATTTTTTTTTTTTTTTTTT
1 ATTTTTTCATTTTATTTTCTTTTTTTT
27254 ATTTTTTCATTTTCATTTTCTTTTTTTT
1 ATTTTTTCATTTT-ATTTTCTTTTTTTT
27282 -TTTTTT--TTTT-TTTTCTT
1 ATTTTTTCATTTTATTTTCTT
27299 CAAGCAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.17
25 4 0.10
27 19 0.45
28 12 0.29
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (27 bp):
ATTTTTTCATTTTATTTTCTTTTTTTT
Found at i:39092 original size:25 final size:24
Alignment explanation
Indices: 39054--39101 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
39044 TGAAAATAAA
*
39054 ATAAAAATTGCATAACATACATAC
1 ATAAAAATTACATAACATACATAC
*
39078 ATAAAAATGTACATACCATACATA
1 ATAAAAAT-TACATAACATACATA
39102 AAGTAGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (24 bp):
ATAAAAATTACATAACATACATAC
Found at i:45593 original size:2 final size:2
Alignment explanation
Indices: 45586--45634 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
45576 ATATTTTGAT
45586 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45628 TA TA TA T
1 TA TA TA T
45635 TATTAATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46035 original size:11 final size:11
Alignment explanation
Indices: 46009--46045 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
45999 TTTCAATATC
46009 TATATTA-TTA
1 TATATTATTTA
46019 -ATATTATTTA
1 TATATTATTTA
46029 TATATTATTTA
1 TATATTATTTA
46040 T-TATTA
1 TATATTA
46046 CTATTACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 6 0.24
10 8 0.32
11 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTATTTA
Found at i:47231 original size:13 final size:14
Alignment explanation
Indices: 47207--47235 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
47197 TCGTTCTAAT
47207 TTATTACAATTTTA
1 TTATTACAATTTTA
47221 TTATT-CAATTTTA
1 TTATTACAATTTTA
47234 TT
1 TT
47236 TTATTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTACAATTTTA
Found at i:47518 original size:21 final size:20
Alignment explanation
Indices: 47494--47548 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
47484 TTAGGTTTAG
*
47494 TTTTTTTAATTTCATGTTGTT
1 TTTTTTTAATTTCAT-TTATT
*
47515 TTTTTTTTATTT-ATTTATT
1 TTTTTTTAATTTCATTTATT
47534 TATTGTTTTAATTTC
1 T-TT-TTTTAATTTC
47549 TAAATCAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 5 0.18
20 4 0.14
21 19 0.68
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTTTTAATTTCATTTATT
Done.