Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002546.1 Hibiscus syriacus cultivar Beakdansim tig00005169_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: 99178
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:317 original size:21 final size:21
Alignment explanation
Indices: 275--317 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
265 TTTTTGGGCT
* * *
275 AGGGGAATTGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
296 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
317 A
1 A
318 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:390 original size:23 final size:22
Alignment explanation
Indices: 346--390 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
336 AATCTCATAG
* *
346 GGGAATCGATTCCCCCATAGGA
1 GGGAACCGATTCCCCCAAAGGA
368 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
391 AAATTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:1489 original size:28 final size:28
Alignment explanation
Indices: 1434--1489 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1424 ATAAATATAG
* *
1434 TTATATGAAATATTATATGACTATGTGA
1 TTATATGAAATATTATACGACTAAGTGA
*
1462 TTATATGAAATGTTATACG-CGTAAGTGA
1 TTATATGAAATATTATACGAC-TAAGTGA
1490 ACCATGTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (28 bp):
TTATATGAAATATTATACGACTAAGTGA
Found at i:1790 original size:98 final size:99
Alignment explanation
Indices: 1653--1877 Score: 312
Period size: 98 Copynumber: 2.3 Consensus size: 99
1643 GTTGAGGGTC
* *
1653 TATGTGGTCTTTCGGGACATATATGTATTCTTTGAACATGTGTGAAGTCTGGTGAGACACATA-C
1 TATGTGGTCCTTC-GGACATATAT-TATTCTTTGAACATGTGTGAAGTCCGGTGAGACACATATC
* * *
1717 TGATCCTTGGCATATGTATATGATTCTTAGG-ATGA
64 TGATCCCTAGCATATGTATATGATTATTAGGAATGA
*
1752 TATGTGGTCCTTCGGACATATATTATTCTTTGGAACATGTGTGAAGTCCGGTGAGACACATATTT
1 TATGTGGTCCTTCGGACATATATTATTCTTT-GAACATGTGTGAAGTCCGGTGAGACACATATCT
*
1817 GATCCCTAGTATATGTATATGATTATTAGGAATGA
65 GATCCCTAGCATATGTATATGATTATTAGGAATGA
* *
1852 TATGTAGTCCTTATGGACAT-TATTAT
1 TATGTGGTCCTT-CGGACATATATTAT
1878 ATGGCACTAC
Statistics
Matches: 113, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
97 8 0.07
98 39 0.35
99 39 0.35
100 21 0.19
101 6 0.05
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (99 bp):
TATGTGGTCCTTCGGACATATATTATTCTTTGAACATGTGTGAAGTCCGGTGAGACACATATCTG
ATCCCTAGCATATGTATATGATTATTAGGAATGA
Found at i:1915 original size:23 final size:23
Alignment explanation
Indices: 1880--1947 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
1870 ATTATTATAT
*
1880 GGCACTACTGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* **
1903 GGCACTCCGGTGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACGC
* *
1926 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
1948 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:7858 original size:59 final size:57
Alignment explanation
Indices: 7751--7893 Score: 142
Period size: 59 Copynumber: 2.5 Consensus size: 57
7741 AAATTATAAT
* * * * * * * *
7751 TTTAAATTAATCTTTAAAATTTTGAATATTCAATTTTATCCCCAAACTATAGCTGTCTG
1 TTTAAATTAGTCATTAAACTTTTGAACATTAAATTTCATCCCCAAACTAT-GATAT-TG
* ** *
7810 TTTAAATTAGTCCTTAAACTTTTGAACATTAAATTTCATCCCTGAACTATGATATTT
1 TTTAAATTAGTCATTAAACTTTTGAACATTAAATTTCATCCCCAAACTATGATATTG
*
7867 TTTAAAATTAGTCATCAAACTTTTGAA
1 TTT-AAATTAGTCATTAAACTTTTGAA
7894 TATCCTAATG
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
57 4 0.06
58 24 0.34
59 42 0.60
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (57 bp):
TTTAAATTAGTCATTAAACTTTTGAACATTAAATTTCATCCCCAAACTATGATATTG
Found at i:12157 original size:2 final size:2
Alignment explanation
Indices: 12150--12176 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12140 TTATTATTAT
12150 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12177 TGAAATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13083 original size:17 final size:18
Alignment explanation
Indices: 13046--13086 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
13036 ATATTATGTA
*
13046 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
13064 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
13081 TTTACT
1 TTTACT
13087 AATATAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:16450 original size:246 final size:259
Alignment explanation
Indices: 15878--16467 Score: 811
Period size: 267 Copynumber: 2.3 Consensus size: 259
15868 AATATTTTTT
* * * *
15878 TATTATTTCAGGTTGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTAGGGTGAAATTTTATT
1 TATTATTTTA-GTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATT
*
15943 TT--T-G-GTCGGATCAAGTCAATTTTTTTAAGTGTGATATTCGGGTCGGGTAGAGTTCGGGTTT
65 TTGGTCGAGTCGGATCAAGT--ATTTTTTTAAGTGTGATATTCGGGTCGGGTAGAGTTCAGGTTT
* *
16004 AGGGTGAAAAATACCCGACCCGACCCGAATATATATAATTTTACCTTATATATTTAGGAATAATT
128 AGGGTGAAAAATACCCGACCCGA--CAAAAATATATAATTTTACCTTATATATTTAGGAATAATT
*
16069 ACAATAATACCCCTCTATCTATATATATATATATTTTAATTAAGTCACTGTTTTTATTGAATAAA
191 ACAATAATACCCCTC-ATCTATATATATATATATTTAAATTAAGTCACTGTTTTTATTGAATAAA
16134 AATAA
255 AATAA
**
16139 TTTTTTTATTATTTTAGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCATGTGAAAC
1 ------TATTATTTTA-GTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAAC
* *
16204 TTTATTTTGGTCGAGTCGGATC-GGT-TTTTTTTAAGTGTGATATTCGGGTCGGGCT-GGGTTCA
59 TTTATTTTGGTCGAGTCGGATCAAGTATTTTTTTAAGTGTGATATTCGGGTCGGG-TAGAGTTCA
16266 GGTTTAGGGTGAAAAATACCCGACCC-A-AAAAATATATAATTTTACCTTATATATTTAGGAATA
123 GGTTTAGGGTGAAAAATACCCGACCCGACAAAAATATATAATTTTACCTTATATATTTAGGAATA
16329 ATTACAATAATA-CCC-C-TCTATATATA-AT-T-TTTAAATTAAGTCACTGTTTTTATTGAATA
188 ATTACAATAATACCCCTCATCTATATATATATATATTTAAATTAAGTCACTGTTTTTATTGAATA
16388 AAAATAA
253 AAAATAA
*
16395 -ATT-TTTTA-TCGGGTCGGGTTTCTAATTCATATATTCGGGTCAGGTCGGGTGAAACTTTATTT
1 TATTATTTTAGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTT
16457 TGGTCGAGTCG
66 TGGTCGAGTCG
16468 TGCCTCGGAT
Statistics
Matches: 303, Mismatches: 15, Indels: 31
0.87 0.04 0.09
Matches are distributed among these distances:
246 62 0.20
248 5 0.02
249 3 0.01
256 36 0.12
257 1 0.00
258 2 0.01
259 10 0.03
261 1 0.00
262 3 0.01
263 46 0.15
266 1 0.00
267 120 0.40
268 1 0.00
269 1 0.00
270 3 0.01
271 8 0.03
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (259 bp):
TATTATTTTAGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTT
TGGTCGAGTCGGATCAAGTATTTTTTTAAGTGTGATATTCGGGTCGGGTAGAGTTCAGGTTTAGG
GTGAAAAATACCCGACCCGACAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAAT
AATACCCCTCATCTATATATATATATATTTAAATTAAGTCACTGTTTTTATTGAATAAAAATAA
Found at i:21928 original size:22 final size:23
Alignment explanation
Indices: 21897--21940 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
21887 ATGTTAGATA
*
21897 GAAAAAATAAATAA-ATAAAAAT
1 GAAAAAATAAAAAATATAAAAAT
*
21919 GAAAAGATAAAAAATATAAAAA
1 GAAAAAATAAAAAATATAAAAA
21941 ACAATGTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (23 bp):
GAAAAAATAAAAAATATAAAAAT
Found at i:22815 original size:23 final size:23
Alignment explanation
Indices: 22789--22848 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
22779 CATCATCCCA
22789 AAGGACCTGTCATCTGTGTCCTG
1 AAGGACCTGTCATCTGTGTCCTG
22812 AAGGACCTGTCATCTGTGTCCTG
1 AAGGACCTGTCATCTGTGTCCTG
22835 AAGGACCTGTCATC
1 AAGGACCTGTCATC
22849 CCGAAGGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (23 bp):
AAGGACCTGTCATCTGTGTCCTG
Found at i:23080 original size:22 final size:22
Alignment explanation
Indices: 23054--23130 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
23044 TATCATATCA
23054 CATATATCACGTATTACATATT
1 CATATATCACGTATTACATATT
* ** *
23076 CATATGTCATTTCA-TATCATATCA
1 CATATATCACGT-ATTA-CATAT-T
* *
23100 CATGTATCACGTATTGCATATT
1 CATATATCACGTATTACATATT
23122 CATATATCA
1 CATATATCA
23131 TTTCATATAG
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
22 19 0.47
23 12 0.30
24 9 0.22
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (22 bp):
CATATATCACGTATTACATATT
Found at i:23092 original size:46 final size:46
Alignment explanation
Indices: 23034--23138 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
23024 ATGTGTAACC
23034 ATGT-ATTTCATATCATATCACATATATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATATATCACGTATTACATATTCAT
* *
23079 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATATATCACGTATTACATATTCAT
*
23125 ATATCATTTCATAT
1 ATGTCATTTCATAT
23139 AGTCATATAG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 4 0.07
46 52 0.93
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATATATCACGTATTACATATTCAT
Found at i:25222 original size:26 final size:26
Alignment explanation
Indices: 25186--25259 Score: 114
Period size: 26 Copynumber: 2.8 Consensus size: 26
25176 TATATGAACG
25186 AAAAAAATATAAAAATAAATAGTAAT
1 AAAAAAATATAAAAATAAATAGTAAT
25212 AAAAAAATATAAAAATAAATAGTAAT
1 AAAAAAATATAAAAATAAATAGTAAT
*
25238 AATAAATAATA-AATAATAAATA
1 AA-AAA-AATATAAAAATAAATA
25260 TGTATATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
26 28 0.62
27 13 0.29
28 4 0.09
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (26 bp):
AAAAAAATATAAAAATAAATAGTAAT
Found at i:25247 original size:7 final size:7
Alignment explanation
Indices: 25190--25259 Score: 62
Period size: 7 Copynumber: 10.7 Consensus size: 7
25180 TGAACGAAAA
25190 AAAT-AT
1 AAATAAT
25196 AAA-AAT
1 AAATAAT
*
25202 AAATAGT
1 AAATAAT
25209 -AATAA-
1 AAATAAT
25214 AAA-AAT
1 AAATAAT
*
25220 ATAAAAAT
1 A-AATAAT
*
25228 AAATAGT
1 AAATAAT
25235 -AATAAT
1 AAATAAT
25241 AAATAAT
1 AAATAAT
25248 AAATAAT
1 AAATAAT
25255 AAATA
1 AAATA
25260 TGTATATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
5 2 0.04
6 20 0.38
7 26 0.50
8 4 0.08
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:25363 original size:51 final size:50
Alignment explanation
Indices: 25256--25364 Score: 125
Period size: 51 Copynumber: 2.1 Consensus size: 50
25246 ATAAATAATA
*
25256 AATATGTATATATATATATTATATTACTATTTATTTTTATATTTTTTCGTT
1 AATATATATATATATATATTATATTAC-ATTTATTTTTATATTTTTTCGTT
* *
25307 CATATATATATATATATA-TATATTA-ACTTTAGTTTTT-TATTTTATATCTTT
1 AATATATATATATATATATTATATTACA-TTTA-TTTTTATATTTT-T-TCGTT
25358 AATATAT
1 AATATAT
25365 TTTTTTTTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
48 1 0.02
49 10 0.20
50 13 0.26
51 26 0.52
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.59
Consensus pattern (50 bp):
AATATATATATATATATATTATATTACATTTATTTTTATATTTTTTCGTT
Found at i:25410 original size:22 final size:22
Alignment explanation
Indices: 25346--25411 Score: 60
Period size: 24 Copynumber: 2.9 Consensus size: 22
25336 TAGTTTTTTA
* * *
25346 TTTTATATCTTTAATATATTTTT
1 TTTTATTTTTTTAAT-TATTCTT
* *
25369 TTTTCATTTTTTCGACTTATTCTT
1 TTTT-ATTTTTT-TAATTATTCTT
25393 TTTTATTTTTTTAATTATT
1 TTTTATTTTTTTAATTATT
25412 TTACAATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
22 6 0.18
23 11 0.32
24 15 0.44
25 2 0.06
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATTTTTTTAATTATTCTT
Found at i:25423 original size:24 final size:24
Alignment explanation
Indices: 25396--25462 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
25386 TATTCTTTTT
*
25396 TATTTTTTTAATTATTTTACAATA
1 TATTTATTTAATTATTTTACAATA
* * * *
25420 TATTTGTTTAATTTTTTTATAATT
1 TATTTATTTAATTATTTTACAATA
*
25444 TATATTATTTATTTATTTT
1 TAT-TTATTTAATTATTTT
25463 TTAGTTATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 23 0.66
25 12 0.34
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (24 bp):
TATTTATTTAATTATTTTACAATA
Found at i:25465 original size:20 final size:21
Alignment explanation
Indices: 25442--25497 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
25432 TTTTTTATAA
*
25442 TTTA-TATTATTTATTTATTT
1 TTTATTATTATTTATTCATTT
25462 TTTAGTTATTATTCTTATTCATTT
1 TTTA-TTATTA-T-TTATTCATTT
*
25486 ATTATTATTATT
1 TTTATTATTATT
25498 ATTATTCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 4 0.13
21 1 0.03
22 6 0.20
23 7 0.23
24 12 0.40
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTATTATTATTTATTCATTT
Found at i:25499 original size:20 final size:19
Alignment explanation
Indices: 25436--25503 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
25426 TTTAATTTTT
*
25436 TTATAATTTA-TATTATTTA
1 TTATTATTTATTATTA-TTA
* *
25455 TTTATTTTTTAGTTATTATTC
1 -TTATTATTTA-TTATTATTA
25476 TTATTCATTTATTATTATTA
1 TTATT-ATTTATTATTATTA
25496 TTATTATT
1 TTATTATT
25504 CTAACATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.08
20 26 0.65
21 6 0.15
22 5 0.12
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (19 bp):
TTATTATTTATTATTATTA
Found at i:40700 original size:2 final size:2
Alignment explanation
Indices: 40693--40739 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
40683 TATCATTGGA
40693 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
40735 AT AT A
1 AT AT A
40740 ATTTGATTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50605 original size:16 final size:16
Alignment explanation
Indices: 50580--50618 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
50570 TGTGATTTCT
*
50580 ATTTTTTTAT-CTATC
1 ATTTTTTTATGCTATA
50595 ATTTTTATTATGCTATA
1 ATTTTT-TTATGCTATA
50612 ATTTTTT
1 ATTTTTT
50619 GTTGTGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 5 0.24
17 10 0.48
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTTTTTATGCTATA
Found at i:56659 original size:14 final size:14
Alignment explanation
Indices: 56640--56669 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56630 TCGTATCAAA
56640 TTTATTATACTTAT
1 TTTATTATACTTAT
56654 TTTATTATACTTAT
1 TTTATTATACTTAT
56668 TT
1 TT
56670 AAATTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTATACTTAT
Found at i:66016 original size:2 final size:2
Alignment explanation
Indices: 66009--66036 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
65999 TTCGAATGAA
66009 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
66037 TTAATTAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73290 original size:24 final size:25
Alignment explanation
Indices: 73263--73313 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
73253 AAAATTTATT
73263 TTTAT-TCTCTGAAAATTTTATAAA
1 TTTATATCTCTGAAAATTTTATAAA
*
73287 TTTATACTCTCTTAAAATTTTATAAA
1 TTTATA-TCTCTGAAAATTTTATAAA
73313 T
1 T
73314 GACTCAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.21
26 19 0.79
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTATATCTCTGAAAATTTTATAAA
Found at i:75607 original size:26 final size:26
Alignment explanation
Indices: 75578--75630 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
75568 GACAGAACAC
75578 GAGCTACTCGAGATCGACTCGATCAA
1 GAGCTACTCGAGATCGACTCGATCAA
75604 GAGCTACTCGAGATCGACTCGATCAA
1 GAGCTACTCGAGATCGACTCGATCAA
75630 G
1 G
75631 GCTCGATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (26 bp):
GAGCTACTCGAGATCGACTCGATCAA
Found at i:79040 original size:7 final size:7
Alignment explanation
Indices: 79028--79072 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
79018 AGACACGTGG
79028 TTTTGGA
1 TTTTGGA
79035 TTTTGGA
1 TTTTGGA
79042 TTTTGGA
1 TTTTGGA
79049 TTTTGGA
1 TTTTGGA
*
79056 TTTTGGG
1 TTTTGGA
79063 TTTT-GA
1 TTTTGGA
79069 TTTT
1 TTTT
79073 TTATTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.11, C:0.00, G:0.27, T:0.62
Consensus pattern (7 bp):
TTTTGGA
Found at i:80507 original size:13 final size:13
Alignment explanation
Indices: 80491--80515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
80481 TTTTCCCATT
80491 TGATTTATTATTA
1 TGATTTATTATTA
80504 TGATTTATTATT
1 TGATTTATTATT
80516 TTTATTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGATTTATTATTA
Found at i:84719 original size:32 final size:32
Alignment explanation
Indices: 84661--84745 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
84651 ACATTGGGGG
* **
84661 CATCTTT-GAAGATTCAATATAAAATATT-GGA
1 CATCTTTAG-AGATTCAACATCGAATATTGGGA
*
84692 GCATTTTTAGAGATTCAACATCGAATATTGGGA
1 -CATCTTTAGAGATTCAACATCGAATATTGGGA
* *
84725 CATCTTTGGGGATTCAACATC
1 CATCTTTAGAGATTCAACATC
84746 CTGATATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
32 40 0.91
33 4 0.09
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
CATCTTTAGAGATTCAACATCGAATATTGGGA
Found at i:85553 original size:37 final size:36
Alignment explanation
Indices: 85407--85566 Score: 178
Period size: 37 Copynumber: 4.4 Consensus size: 36
85397 TTAAATCTGT
* * *
85407 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGGCAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
85442 TTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 -TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* * * * *
85480 TTTTTATTGAAACAAATCTTATTTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
85516 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
85553 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
85567 CCATCTTTGA
Statistics
Matches: 101, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
36 36 0.36
37 46 0.46
38 19 0.19
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:89745 original size:18 final size:18
Alignment explanation
Indices: 89722--89785 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
89712 CAACGGTCAA
* *
89722 CGGGTCGAGTCAACATGT
1 CGGGTCGGGTCAACAGGT
*
89740 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
**
89758 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCAACAGGT
89776 CGGGTCGGGT
1 CGGGTCGGGT
89786 TGTGAACGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.12, C:0.20, G:0.47, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:90377 original size:38 final size:38
Alignment explanation
Indices: 90323--90399 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 38
90313 GGAGAAGGGA
90323 AATCTGGAAATATGAAACCTGCGCAC-GGGAGGAGCTT
1 AATCTGGAAATATGAAACCTGCGCACGGGGAGGAGCTT
90360 AATCTGGAAAATATGAAACCTGCGCACGGGGAGGAGCTT
1 AATCTGG-AAATATGAAACCTGCGCACGGGGAGGAGCTT
90399 A
1 A
90400 TAATTCATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 7 0.18
38 19 0.50
39 12 0.32
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (38 bp):
AATCTGGAAATATGAAACCTGCGCACGGGGAGGAGCTT
Found at i:93315 original size:16 final size:18
Alignment explanation
Indices: 93291--93328 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
93281 CTTTAATTTA
*
93291 TTTTCTTTAA-ATT-TTT
1 TTTTATTTAACATTGTTT
93307 TTTTATTTAACATTGTTT
1 TTTTATTTAACATTGTTT
93325 TTTT
1 TTTT
93329 CCCATTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 3 0.16
18 7 0.37
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTATTTAACATTGTTT
Found at i:96123 original size:89 final size:89
Alignment explanation
Indices: 95974--96162 Score: 303
Period size: 89 Copynumber: 2.1 Consensus size: 89
95964 AAGATGCTAT
95974 CGGTTTTGTTATTATTTTTTAACAAAACTAATAAAAATTATCAAAAACATTATTATTTCTATC-G
1 CGGTTTTGTTATTATTTTTTAACAAAACTAATAAAAATTATCAAAAACATTATTATTTCTATCAG
*
96038 TTTT-TTATTA-TTGGACACTTTTC
66 TTTTGTTATTATTTGG-CACTTTAC
96061 CGGTTTTGTTATTATTTTTTTAACAAAACTAATAAAAAATTATCAAAAACATTATTATTTCTATC
1 CGGTTTTGTTATTA-TTTTTTAACAAAACTAAT-AAAAATTATCAAAAACATTATTATTTCTATC
*
96126 ATTTTTGTTATTATTTGGCACTTTAC
64 AGTTTTGTTATTATTTGGCACTTTAC
*
96152 CGATTTTGTTA
1 CGGTTTTGTTA
96163 ATATATCCGA
Statistics
Matches: 94, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
87 14 0.15
88 18 0.19
89 31 0.33
90 4 0.04
91 23 0.24
92 4 0.04
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (89 bp):
CGGTTTTGTTATTATTTTTTAACAAAACTAATAAAAATTATCAAAAACATTATTATTTCTATCAG
TTTTGTTATTATTTGGCACTTTAC
Found at i:96264 original size:21 final size:20
Alignment explanation
Indices: 96239--96281 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
96229 AAAAATATTA
*
96239 AAAAACATTAATATTTTAAAT
1 AAAAACAATAAT-TTTTAAAT
*
96260 AAAAATAATAATTTTTAAAT
1 AAAAACAATAATTTTTAAAT
96280 AA
1 AA
96282 TTTTTACTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAACAATAATTTTTAAAT
Found at i:98151 original size:17 final size:19
Alignment explanation
Indices: 98126--98163 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
98116 CAATTGTTTT
98126 TTTTAAAGTA-AAATA-AA
1 TTTTAAAGTATAAATATAA
*
98143 TTTTGAAGTATAAATATAA
1 TTTTAAAGTATAAATATAA
98162 TT
1 TT
98164 AGCTGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 5 0.28
19 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
TTTTAAAGTATAAATATAA
Done.