Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006637.1 Hibiscus syriacus cultivar Beakdansim tig00016334_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: 68812
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:2107 original size:135 final size:135
Alignment explanation
Indices: 1832--2406 Score: 687
Period size: 135 Copynumber: 4.3 Consensus size: 135
1822 AATAATAATC
** * * ** * * * * *
1832 GATTTGCTTTACTACTCTTCAGGGAGATAAAATCTTAAAGAAAAAAAATCTACTCCGCTACTCTT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTAAAAGAAGAAGAATATGCTCCGCTACTCTT
* * * * * * *
1897 TAAGG-GAGATCAGGCTTGA-TAAAATTTTGATCCACTTCGCTACTCTTCTGGGAAGATTGAATC
66 T-AGGCGAGATCAGACTCGAGAAAAATTTTGATCCACTTCGCTGCTCATCAGGAAAGATTGAATC
1960 GAACTT
130 GAACTT
* * * * *
1966 GATTTGCTCCGCTGCTCTTTAGGAAGACCAAATCTGAAAGAAGAAGAATCTGGTCCGCTACTCTT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTAAAAGAAGAAGAATATGCTCCGCTACTCTT
* * * * * *
2031 TAGGCAAGATCAGACTTGAGAAAAATTTTGATCCACTTCGTTGCTCTTCAGGGAAGATTAAATCG
66 TAGGCGAGATCAGACTCGAGAAAAATTTTGATCCACTTCGCTGCTCATCAGGAAAGATTGAATCG
2096 AACTT
131 AACTT
* * * * * **
2101 GATTTGCTTCACTTCTCTTCAGGAGGACCAAATCTAAAAGAACAAGAATATGTTTTGCTACTCTT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTAAAAGAAGAAGAATATGCTCCGCTACTCTT
*
2166 TAGGCGAGATCAGACTCGAGAAAAATTTTGATCCACTTTGCTGCTCATCAGGAAAGATTGAATCG
66 TAGGCGAGATCAGACTCGAGAAAAATTTTGATCCACTTCGCTGCTCATCAGGAAAGATTGAATCG
2231 AACTT
131 AACTT
* * * *
2236 GATTT-TTTTGCTGCTCTTCA-G-AGA--AAATCTGAAAGAAGAAGAATATGCTCTGCTACTCTT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTAAAAGAAGAAGAATATGCTCCGCTACTCTT
* * *
2296 TAGGGGAGATCAGACTCGAGAAAAATTTTGATCCACTTCGCTGCACATCAGGAAAGATTGAATCT
66 TAGGCGAGATCAGACTCGAGAAAAATTTTGATCCACTTCGCTGCTCATCAGGAAAGATTGAATCG
2361 AACTT
131 AACTT
*
2366 GATTTGCTTCGTTGCTCTTCAGGAAGACCAAATCTAAAAGA
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTAAAAGA
2407 TTGACTCCTC
Statistics
Matches: 379, Mismatches: 55, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
130 103 0.27
131 12 0.03
132 3 0.01
133 7 0.02
134 76 0.20
135 178 0.47
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (135 bp):
GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTAAAAGAAGAAGAATATGCTCCGCTACTCTT
TAGGCGAGATCAGACTCGAGAAAAATTTTGATCCACTTCGCTGCTCATCAGGAAAGATTGAATCG
AACTT
Found at i:2330 original size:265 final size:268
Alignment explanation
Indices: 1888--2406 Score: 726
Period size: 265 Copynumber: 1.9 Consensus size: 268
1878 AATCTACTCC
* * * * * *
1888 GCTACTCTTTAAGGGAGATCAGGCTTGATAAAATTTTGATCCACTTCGCTACTCTTCTGGGAAGA
1 GCTACTCTTTAAGGGAGATCAGACTCGAAAAAATTTTGATCCACTTCGCTACTCATCAGGAAAGA
* *
1953 TTGAATCGAACTTGATTTGCTCCGCTGCTCTTTAGGAAGACCAAATCTGAAAGAAGAAGAATCTG
66 TTGAATCGAACTTGATTTGCTCCGCTGCTCTTCAGGAAGA-CAAATCTGAAAGAAGAAGAATATG
* * * * *
2018 GTCCGCTACTCTTTAGGCAAGATCAGACTTGAGAAAAATTTTGATCCACTTCGTTGCTCTTCAGG
130 CTCCGCTACTCTTTAGGCAAGATCAGACTCGAGAAAAATTTTGATCCACTTCGCTGCACATCAGG
* *
2083 GAAGATTAAATCGAACTTGATTTGCTTCACTT-CTCTTCAGGAGGACCAAATCTAAAAGAACAAG
195 AAAGATTAAATCGAACTTGATTTGCTTC-CTTGCTCTTCAGGAAGACCAAATCTAAAAGAACAAG
2147 AATATGTTTT
259 AATATGTTTT
* *
2157 GCTACTCTTT-AGGCGAGATCAGACTCGAGAAAAATTTTGATCCACTTTGCTGCTCATCAGGAAA
1 GCTACTCTTTAAGG-GAGATCAGACTCGA-AAAAATTTTGATCCACTTCGCTACTCATCAGGAAA
* **
2221 GATTGAATCGAACTTGATTT-TTTTGCTGCTCTTCA-G-AGA-AAATCTGAAAGAAGAAGAATAT
64 GATTGAATCGAACTTGATTTGCTCCGCTGCTCTTCAGGAAGACAAATCTGAAAGAAGAAGAATAT
* **
2282 GCTCTGCTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTTGATCCACTTCGCTGCACATCAG
129 GCTCCGCTACTCTTTAGGCAAGATCAGACTCGAGAAAAATTTTGATCCACTTCGCTGCACATCAG
* * *
2347 GAAAGATTGAATCTAACTTGATTTGCTTCGTTGCTCTTCAGGAAGACCAAATCTAAAAGA
194 GAAAGATTAAATCGAACTTGATTTGCTTCCTTGCTCTTCAGGAAGACCAAATCTAAAAGA
2407 TTGACTCCTC
Statistics
Matches: 221, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
264 2 0.01
265 130 0.59
267 3 0.01
268 4 0.02
269 33 0.15
270 49 0.22
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (268 bp):
GCTACTCTTTAAGGGAGATCAGACTCGAAAAAATTTTGATCCACTTCGCTACTCATCAGGAAAGA
TTGAATCGAACTTGATTTGCTCCGCTGCTCTTCAGGAAGACAAATCTGAAAGAAGAAGAATATGC
TCCGCTACTCTTTAGGCAAGATCAGACTCGAGAAAAATTTTGATCCACTTCGCTGCACATCAGGA
AAGATTAAATCGAACTTGATTTGCTTCCTTGCTCTTCAGGAAGACCAAATCTAAAAGAACAAGAA
TATGTTTT
Found at i:2451 original size:45 final size:45
Alignment explanation
Indices: 2402--2612 Score: 196
Period size: 45 Copynumber: 4.8 Consensus size: 45
2392 ACCAAATCTA
** *
2402 AAAGATTGACTCCTCTTTGCGAGAAAGTCAAGAAAGACAACACTG
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACTG
* *
2447 AAAGATTGACTTCC-CTTCATGAGAAAGTCAAGAAGGACGACACTG
1 AAAGATTGAC-TCCTCTTCACGAGAAAGTCAAGAAGGACAACACTG
* * *** * * *
2492 GAAGATTGATTCCTCTTCGTAAGAAAGTTAAGAAGGCCAACACTA
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACTG
* * * *
2537 AAAGATTGACTTCTCTTTACGAGAAAGTCAAGAATG---ACATTG
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACTG
** * *
2579 AAAGATTGACTTTTCTTCACGAGGAAGTTAAGAA
1 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA
2613 TAACAAAGAT
Statistics
Matches: 136, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
42 34 0.25
44 3 0.02
45 96 0.71
46 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.24
Consensus pattern (45 bp):
AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGACAACACTG
Found at i:2561 original size:90 final size:90
Alignment explanation
Indices: 2403--2570 Score: 237
Period size: 90 Copynumber: 1.9 Consensus size: 90
2393 CCAAATCTAA
* * * *
2403 AAGATTGACTCCTCTTTGCGAGAAAGTCAAGAAAGACAACACTGAAAGATTGACTTCCCTTCATG
1 AAGATTGACTCCTCTTCGCAAGAAAGTCAAGAAAGACAACACTAAAAGATTGACTTCCCTTCACG
2468 AGAAAGTCAAGAAGGACGACACTGG
66 AGAAAGTCAAGAAGGACGACACTGG
* * * * * * *
2493 AAGATTGATTCCTCTTCGTAAGAAAGTTAAGAAGGCCAACACTAAAAGATTGACTTCTCTTTACG
1 AAGATTGACTCCTCTTCGCAAGAAAGTCAAGAAAGACAACACTAAAAGATTGACTTCCCTTCACG
2558 AGAAAGTCAAGAA
66 AGAAAGTCAAGAA
2571 TGACATTGAA
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 67 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (90 bp):
AAGATTGACTCCTCTTCGCAAGAAAGTCAAGAAAGACAACACTAAAAGATTGACTTCCCTTCACG
AGAAAGTCAAGAAGGACGACACTGG
Found at i:2634 original size:38 final size:38
Alignment explanation
Indices: 2537--2849 Score: 374
Period size: 38 Copynumber: 8.1 Consensus size: 38
2527 GCCAACACTA
* * *
2537 AAAGATTGACTTCTCTTTACGAGAAAGTCAAGAATGACATTG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-A--C
* *
2579 AAAGATTGACTTTTCTTCACGAGGAAGTTAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
2617 AAAGATTGACTTCTCTTCACGAGAAAGTAAAAAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
2655 AAAGATTGACTTCTCTTCATGAGGAATTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
2693 AAGGATTGACTTCTCTTCACGAAGAAATCAAAAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
2731 AAAGATTGACTTCTCTTTATGAGGAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * ** *
2769 AAAGATTTACTTCTATTCACTTGGAAGTCAAGAGTAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
2807 AAAGATTGACTTCTCTTCAAGAGGAAGTCAATAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
2845 AAAGA
1 AAAGA
2850 AAAATCAACT
Statistics
Matches: 232, Mismatches: 39, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
38 199 0.86
40 1 0.00
41 1 0.00
42 31 0.13
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:4119 original size:43 final size:44
Alignment explanation
Indices: 4066--4208 Score: 171
Period size: 44 Copynumber: 3.3 Consensus size: 44
4056 AAAAAAATGT
* * * * *
4066 CCCAACATTTATTATTTCTTGCTGATATGGGCCTTCAAAA-TGC
1 CCCAACATTCATTACTTCTGGATGATATGGACCTTCAAAAGTGC
* * ** **
4109 CCCAATATTTATTACTTCTGGATGATACAGATATTCAAAAGTGC
1 CCCAACATTCATTACTTCTGGATGATATGGACCTTCAAAAGTGC
*
4153 CCCAACATTCATTACTTCTGGATGATATGGTCCTTCAAAAGTGC
1 CCCAACATTCATTACTTCTGGATGATATGGACCTTCAAAAGTGC
4197 CCCAACATTCAT
1 CCCAACATTCAT
4209 CATTTCTTGC
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
43 31 0.37
44 52 0.63
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (44 bp):
CCCAACATTCATTACTTCTGGATGATATGGACCTTCAAAAGTGC
Found at i:4880 original size:16 final size:15
Alignment explanation
Indices: 4845--4896 Score: 70
Period size: 15 Copynumber: 3.4 Consensus size: 15
4835 TTTGATTTAA
4845 TTTATTGTAATTGCC
1 TTTATTGTAATTGCC
4860 TTTATTGTAATT-CAGC
1 TTTATTGTAATTGC--C
*
4876 TTTATTGTAGTTGCC
1 TTTATTGTAATTGCC
4891 TTTATT
1 TTTATT
4897 AGGCTAGCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 1 0.03
15 19 0.58
16 12 0.36
17 1 0.03
ACGTcount: A:0.19, C:0.12, G:0.13, T:0.56
Consensus pattern (15 bp):
TTTATTGTAATTGCC
Found at i:10311 original size:15 final size:17
Alignment explanation
Indices: 10286--10317 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10276 ACATATCATA
10286 AATCTTACCC-ACATTT
1 AATCTTACCCAACATTT
10302 AATC-TACCCAACATTT
1 AATCTTACCCAACATTT
10318 TACCCTCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (17 bp):
AATCTTACCCAACATTT
Found at i:13144 original size:3 final size:3
Alignment explanation
Indices: 13136--13183 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
13126 GTAGCCTGTA
13136 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13184 TATATTATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:13192 original size:3 final size:3
Alignment explanation
Indices: 13182--13252 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
13172 AATAATAATA
13182 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13229 ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
13253 GATGTTGGGA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21670 original size:158 final size:157
Alignment explanation
Indices: 21374--21795 Score: 526
Period size: 158 Copynumber: 2.7 Consensus size: 157
21364 AAAATGTAGA
* * *
21374 AATTGAAGTTACATAGGTATTCTATTGTAATAT-TCGAGCATGTGGTTCAAATTTGGTAAAAAAC
1 AATTAAAGTTACATAGGTATTCTATTGTGATATAT-GAGCATGTGGTTCAAATTTGGTAAAAAAA
* * * * * *
21438 GAACTTAAAATAAAGGATGAATTGTAGAAATAAGGAAATTATGAAATATTTAGGGACTAAATTGA
65 GGACTTAAAATAAAGGAAGAATTGAAAAAATAAGGAAATTATGAAAAATTGAGGGACTAAATTGA
*
21503 AAAATAAAAATTTATTATCAAAAAGGAGG
130 AAAAGAAAAATTTATTATCAAAAA-GAGG
* * *
21532 AATTTAAGTTACATAGGTATTCTATTGTGGTATATGAGCTTGTGGTTCAAATTTGGTAAAAAAAG
1 AATTAAAGTTACATAGGTATTCTATTGTGATATATGAGCATGTGGTTCAAATTTGGTAAAAAAAG
* *
21597 GACTTAAAATAAAGGAAGACTTGAAAAAATAAGGAAATTATGAAAAATTGAGGGACTAAATTGTA
66 GACTTAAAATAAAGGAAGAATTGAAAAAATAAGGAAATTATGAAAAATTGAGGGACTAAATTGAA
21662 AAAGAAAAATTTATTATCAAAAAGAGG
131 AAAGAAAAATTTATTATCAAAAAGAGG
* * * * * * *
21689 AATTGAAAG-TACATATGTAGTCTACTGTGTTTTAGGAGCATGTGGTTAAAATTTGGTAAACAAA
1 AATT-AAAGTTACATAGGTATTCTATTGTGATATATGAGCATGTGGTTCAAATTTGGTAAA-AAA
* * * * *
21753 ATAGACTTAAAAT-GATGAAGGAATTGAAAGAATAATGAAATTA
64 A-GGACTTAAAATAAAGGAA-GAATTGAAAAAATAAGGAAATTA
21796 GAGAATAAAT
Statistics
Matches: 230, Mismatches: 29, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
157 51 0.22
158 148 0.64
159 31 0.13
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.30
Consensus pattern (157 bp):
AATTAAAGTTACATAGGTATTCTATTGTGATATATGAGCATGTGGTTCAAATTTGGTAAAAAAAG
GACTTAAAATAAAGGAAGAATTGAAAAAATAAGGAAATTATGAAAAATTGAGGGACTAAATTGAA
AAAGAAAAATTTATTATCAAAAAGAGG
Found at i:22368 original size:25 final size:25
Alignment explanation
Indices: 22340--22394 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
22330 TTTCTACAAC
*
22340 CATATACAATACTTATATATTTCTT
1 CATATACAATACATATATATTTCTT
22365 CATATACAATACATATATATTTCTT
1 CATATACAATACATATATATTTCTT
*
22390 TATAT
1 CATAT
22395 TTGATATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (25 bp):
CATATACAATACATATATATTTCTT
Found at i:25342 original size:39 final size:39
Alignment explanation
Indices: 25288--25366 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
25278 TAAACCTAAT
* *
25288 AATCTCTTACTTACTTCACCCTCGGTATGTGAGCATGTA
1 AATCTCTTACTTACTTCACCCCCGATATGTGAGCATGTA
*
25327 AATCTCTTACTTACTTTACCCCCGATATGTGAGCATGTA
1 AATCTCTTACTTACTTCACCCCCGATATGTGAGCATGTA
25366 A
1 A
25367 GATTTTGTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (39 bp):
AATCTCTTACTTACTTCACCCCCGATATGTGAGCATGTA
Found at i:27712 original size:30 final size:31
Alignment explanation
Indices: 27654--27738 Score: 75
Period size: 31 Copynumber: 2.7 Consensus size: 31
27644 TGTAGTAAGT
* * * *
27654 ATTCTATAAGTCTTCGAAAAATTTGGGGATC-
1 ATTCTATAA-TTTTCGAAAAGTTGGGGGACCA
*
27685 ATTCTATAATTTTTGAAAAGTTGGGGGACCA
1 ATTCTATAATTTTCGAAAAGTTGGGGGACCA
* *
27716 AATC-ATTAATTTTGGAAAAGTTG
1 ATTCTA-TAATTTTCGAAAAGTTG
27739 TAGATTGTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
30 17 0.38
31 28 0.62
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.36
Consensus pattern (31 bp):
ATTCTATAATTTTCGAAAAGTTGGGGGACCA
Found at i:28999 original size:22 final size:22
Alignment explanation
Indices: 28971--29030 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
28961 ATTGGTTATC
*
28971 ATATATGATGTTTATTATGAAT
1 ATATATGATGTTTATTAGGAAT
28993 ATATATGATGTTTATTAGGAAT
1 ATATATGATGTTTATTAGGAAT
29015 ATATATGATGTTTATT
1 ATATATGATGTTTATT
29031 GCGAATGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (22 bp):
ATATATGATGTTTATTAGGAAT
Found at i:31076 original size:24 final size:24
Alignment explanation
Indices: 31016--31130 Score: 128
Period size: 24 Copynumber: 4.8 Consensus size: 24
31006 CATAAATCAG
* * * *
31016 GTCAAGAAACAGATCGGAAT-CAG
1 GTCAAGTATCAGATCAGAATCCAT
*
31039 GTCAAGTAAT-AGATCAGAATCCAA
1 GTCAAGT-ATCAGATCAGAATCCAT
*
31063 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
*
31087 GT-TAGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
31111 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
31131 TCAAATCGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
23 19 0.24
24 57 0.73
25 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:32120 original size:21 final size:21
Alignment explanation
Indices: 32089--32142 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
32079 CCAGAGTTTG
32089 AGTATCGATACTGGGATGAAC
1 AGTATCGATACTGGGATGAAC
* * *
32110 ATTATCAATACTGGGATGAGC
1 AGTATCGATACTGGGATGAAC
32131 AGTATCGATACT
1 AGTATCGATACT
32143 AATTGAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (21 bp):
AGTATCGATACTGGGATGAAC
Found at i:32319 original size:20 final size:21
Alignment explanation
Indices: 32296--32352 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
32286 ACCGAAGGAC
32296 TAGTCTCCATACTGAA-AAAT
1 TAGTCTCCATACTGAATAAAT
** *
32316 TAGTCTCTGTACCGAATAAAT
1 TAGTCTCCATACTGAATAAAT
* *
32337 GAGTATCCATACTGAA
1 TAGTCTCCATACTGAA
32353 GGCTTCGTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (21 bp):
TAGTCTCCATACTGAATAAAT
Found at i:34485 original size:21 final size:22
Alignment explanation
Indices: 34461--34501 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
34451 ATTTGGGTGT
* *
34461 TTTTCT-TCTCTTTGTGCTTTA
1 TTTTCTATCTATTTGGGCTTTA
34482 TTTTCTATCTATTTGGGCTT
1 TTTTCTATCTATTTGGGCTT
34502 ATACTAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.07, C:0.17, G:0.12, T:0.63
Consensus pattern (22 bp):
TTTTCTATCTATTTGGGCTTTA
Found at i:35344 original size:16 final size:16
Alignment explanation
Indices: 35323--35370 Score: 87
Period size: 16 Copynumber: 2.9 Consensus size: 16
35313 ATATACTAAG
35323 ATTTAGTTAGTTTTAA
1 ATTTAGTTAGTTTTAA
35339 ATTTAGTTAGTTTTAA
1 ATTTAGTTAGTTTTAA
35355 ATTTAGTTAGCTTTTA
1 ATTTAGTTAG-TTTTA
35371 GAATACCTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 26 0.84
17 5 0.16
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.56
Consensus pattern (16 bp):
ATTTAGTTAGTTTTAA
Found at i:39244 original size:35 final size:35
Alignment explanation
Indices: 39185--39375 Score: 190
Period size: 35 Copynumber: 5.5 Consensus size: 35
39175 GGACATGATG
* * *
39185 TTTCACT--AAGAGATGCTTCTAAAAGTTGTGTCT
1 TTTCACTCCAAGAGGTGCTTCCAAAAGTCGTGTCT
*
39218 TTTCACTCCAACAGGTGCTTCCAAAAGTCGTGTCT
1 TTTCACTCCAAGAGGTGCTTCCAAAAGTCGTGTCT
* * * * *
39253 TTTTAGTCCAAGAGGTCCTTCCAAAATTCATGTCT
1 TTTCACTCCAAGAGGTGCTTCCAAAAGTCGTGTCT
* * * *
39288 TTTCACTCCAAGAGGTGCCTCTAAATGTCAG-GTTT
1 TTTCACTCCAAGAGGTGCTTCCAAAAGTC-GTGTCT
* * * *
39323 TTTCACTACAATAGGTGATTCCAAAAGTCGTGTAT
1 TTTCACTCCAAGAGGTGCTTCCAAAAGTCGTGTCT
*
39358 TATCACTCCAAGAGGTGC
1 TTTCACTCCAAGAGGTGC
39376 CTCTGGAGGT
Statistics
Matches: 124, Mismatches: 30, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
33 7 0.06
34 1 0.01
35 116 0.94
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (35 bp):
TTTCACTCCAAGAGGTGCTTCCAAAAGTCGTGTCT
Found at i:56967 original size:21 final size:20
Alignment explanation
Indices: 56941--56996 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
56931 TGTCCAATAT
*
56941 AGGATCGATCCCTTGTGAAAA
1 AGGATCGATCCCTT-TAAAAA
*
56962 AGGATCGATCTCTTTAAAAA
1 AGGATCGATCCCTTTAAAAA
* *
56982 AAGATCGATACCTTT
1 AGGATCGATCCCTTT
56997 TTTATTAAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (20 bp):
AGGATCGATCCCTTTAAAAA
Found at i:58144 original size:20 final size:20
Alignment explanation
Indices: 58119--58168 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
58109 TGAAAAGATT
*
58119 TAATAAAATAAAATAGA-TAA
1 TAATAAAATAAAA-AGAGAAA
58139 TAAT-AAATAAAAAGAGAAA
1 TAATAAAATAAAAAGAGAAA
58158 TAATAAAATAA
1 TAATAAAATAA
58169 TAAATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 14 0.52
20 10 0.37
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (20 bp):
TAATAAAATAAAAAGAGAAA
Found at i:60452 original size:5 final size:5
Alignment explanation
Indices: 60430--60526 Score: 52
Period size: 5 Copynumber: 18.8 Consensus size: 5
60420 GTTCAGAGAA
* * * * ****
60430 AAAAT AAAAT TAATT AAAAT AAAAT -AAAT ATAAT GAAAAT AAAGT TTGCT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT
* * *
60480 AAAAAT AAAAT AAAAAT AAAACA AAAAT AAAAT GAAAG AAAAT AAAA
1 -AAAAT AAAAT -AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAA
60527 AATAGAATGA
Statistics
Matches: 66, Mismatches: 21, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
4 4 0.06
5 48 0.73
6 14 0.21
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:60455 original size:20 final size:20
Alignment explanation
Indices: 60430--60472 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
60420 GTTCAGAGAA
*
60430 AAAATAAA-ATTAATTAAAAT
1 AAAATAAATA-TAATGAAAAT
60450 AAAATAAATATAATGAAAAT
1 AAAATAAATATAATGAAAAT
60470 AAA
1 AAA
60473 GTTTGCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAATAAATATAATGAAAAT
Found at i:60495 original size:11 final size:11
Alignment explanation
Indices: 60479--60527 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
60469 TAAAGTTTGC
60479 TAAAAATAAAA
1 TAAAAATAAAA
60490 TAAAAATAAAA
1 TAAAAATAAAA
*
60501 CAAAAATAAAA
1 TAAAAATAAAA
* *
60512 T-GAAAGAAAA
1 TAAAAATAAAA
60522 TAAAAA
1 TAAAAA
60528 ATAGAATGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 8 0.25
11 24 0.75
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:60527 original size:22 final size:23
Alignment explanation
Indices: 60480--60538 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
60470 AAAGTTTGCT
60480 AAAAATAAAAT-AAAAATAAAAC
1 AAAAATAAAATGAAAAATAAAAC
*
60502 AAAAATAAAATGAAAGAA-AATA-
1 AAAAATAAAATGAAA-AATAAAAC
*
60524 AAAAATAGAATGAAA
1 AAAAATAAAATGAAA
60539 TGGTTTGTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 25 0.76
23 6 0.18
24 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.14
Consensus pattern (23 bp):
AAAAATAAAATGAAAAATAAAAC
Found at i:60528 original size:17 final size:17
Alignment explanation
Indices: 60481--60530 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
60471 AAGTTTGCTA
*
60481 AAAATAAAAT-AAAAAT
1 AAAACAAAATAAAAAAT
*
60497 AAAACAAAA-ATAAAAT
1 AAAACAAAATAAAAAAT
* *
60513 GAAAGAAAATAAAAAAT
1 AAAACAAAATAAAAAAT
60530 A
1 A
60531 GAATGAAATG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (17 bp):
AAAACAAAATAAAAAAT
Found at i:66791 original size:18 final size:19
Alignment explanation
Indices: 66770--66878 Score: 67
Period size: 18 Copynumber: 6.0 Consensus size: 19
66760 AAAATATATC
66770 CTAAAA-CTAATTAAAATA
1 CTAAAACCTAATTAAAATA
*
66788 CTAAAACCTATTTAAAATA
1 CTAAAACCTAATTAAAATA
66807 --AAATACCTAA--AACAA-A
1 CTAAA-ACCTAATTAA-AATA
*
66823 CATAAAA--T-ATAAAAATA
1 C-TAAAACCTAATTAAAATA
*
66840 TCCTAAAACTTAA-TAAAATA
1 --CTAAAACCTAATTAAAATA
*
66860 CTAAAACCTATTTAAAATA
1 CTAAAACCTAATTAAAATA
66879 AAATACCTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 29
0.68 0.05 0.28
Matches are distributed among these distances:
15 1 0.01
16 6 0.08
17 8 0.11
18 26 0.37
19 22 0.31
20 7 0.10
21 1 0.01
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.27
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:66804 original size:19 final size:18
Alignment explanation
Indices: 66770--66806 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
66760 AAAATATATC
66770 CTAAAACTAATTAAAATA
1 CTAAAACTAATTAAAATA
*
66788 CTAAAACCTATTTAAAATA
1 CTAAAA-CTAATTAAAATA
66807 AAATACCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (18 bp):
CTAAAACTAATTAAAATA
Found at i:66809 original size:24 final size:25
Alignment explanation
Indices: 66781--66907 Score: 92
Period size: 24 Copynumber: 5.3 Consensus size: 25
66771 TAAAACTAAT
*
66781 TAAAATA-CTAAAACCTATTTAAAA
1 TAAAATACCTAAAACCAATTTAAAA
* * *
66805 TAAAATACCTAAAACAAACATAAAATA
1 TAAAATACCTAAAACCAA-TTTAAA-A
66832 TAAAAATATCCTAAAA-C---TT--AA
1 T-AAAATA-CCTAAAACCAATTTAAAA
*
66853 TAAAATA-CTAAAACCTATTTAAAA
1 TAAAATACCTAAAACCAATTTAAAA
*
66877 TAAAATACCTAAAA-CAATATAAAA
1 TAAAATACCTAAAACCAATTTAAAA
*
66901 TATAATA
1 TAAAATA
66908 TTAAAATATT
Statistics
Matches: 82, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
18 6 0.07
19 1 0.01
20 6 0.07
21 2 0.02
22 3 0.04
24 31 0.38
25 14 0.17
26 4 0.05
27 2 0.02
28 6 0.07
29 7 0.09
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (25 bp):
TAAAATACCTAAAACCAATTTAAAA
Found at i:66816 original size:25 final size:25
Alignment explanation
Indices: 66781--66891 Score: 94
Period size: 24 Copynumber: 4.6 Consensus size: 25
66771 TAAAACTAAT
66781 TAAAATA-CTAAAACCTATTTAAAA
1 TAAAATACCTAAAACCTATTTAAAA
** * *
66805 TAAAATACCTAAAACAAACATAAAATA
1 TAAAATACCTAAAACCTA-TTTAAA-A
66832 TAAAAATATCCTAAAA-C---TT--AA
1 T-AAAATA-CCTAAAACCTATTTAAAA
66853 TAAAATA-CTAAAACCTATTTAAAA
1 TAAAATACCTAAAACCTATTTAAAA
66877 TAAAATACCTAAAAC
1 TAAAATACCTAAAAC
66892 AATATAAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 23
0.70 0.06 0.23
Matches are distributed among these distances:
18 6 0.09
19 1 0.01
20 6 0.09
21 2 0.03
22 3 0.04
24 17 0.25
25 15 0.22
26 4 0.06
27 2 0.03
28 6 0.09
29 7 0.10
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.25
Consensus pattern (25 bp):
TAAAATACCTAAAACCTATTTAAAA
Found at i:66847 original size:72 final size:73
Alignment explanation
Indices: 66707--66905 Score: 297
Period size: 72 Copynumber: 2.8 Consensus size: 73
66697 ATCTTAAATC
* *
66707 CTAATTAAAACACTTAAAA-CTATTT-AAATAAAATACCT-AAA-AAAGATAAAATA-AAAATAT
1 CTAATTAAAATAC-TAAAACCTATTTAAAATAAAATACCTAAAACAAACATAAAATATAAAATAT
66767 ATCCTAAAA
65 ATCCTAAAA
66776 CTAATTAAAATACTAAAACCTATTTAAAATAAAATACCTAAAACAAACATAAAATATAAAA-ATA
1 CTAATTAAAATACTAAAACCTATTTAAAATAAAATACCTAAAACAAACATAAAATATAAAATATA
66840 TCCTAAAA
66 TCCTAAAA
*
66848 CTTAA-TAAAATACTAAAACCTATTTAAAATAAAATACCTAAAAC-AATATAAAATATAA
1 C-TAATTAAAATACTAAAACCTATTTAAAATAAAATACCTAAAACAAACATAAAATATAA
66906 TATTAAAATA
Statistics
Matches: 121, Mismatches: 3, Indels: 10
0.90 0.02 0.07
Matches are distributed among these distances:
68 5 0.04
69 18 0.15
70 13 0.11
71 16 0.13
72 62 0.51
73 7 0.06
ACGTcount: A:0.61, C:0.13, G:0.01, T:0.26
Consensus pattern (73 bp):
CTAATTAAAATACTAAAACCTATTTAAAATAAAATACCTAAAACAAACATAAAATATAAAATATA
TCCTAAAA
Found at i:66855 original size:28 final size:29
Alignment explanation
Indices: 66806--66865 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
66796 TATTTAAAAT
66806 AAAATACCTAAAACAAACATAAAATA-TA
1 AAAATACCTAAAACAAACATAAAATACTA
**
66834 AAAATATCCTAAAACTTA-ATAAAATACTA
1 AAAATA-CCTAAAACAAACATAAAATACTA
66863 AAA
1 AAA
66866 CCTATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.65, C:0.13, G:0.00, T:0.22
Consensus pattern (29 bp):
AAAATACCTAAAACAAACATAAAATACTA
Done.