Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006789.1 Hibiscus syriacus cultivar Beakdansim tig00017207_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: 47692
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:2123 original size:105 final size:104
Alignment explanation
Indices: 1971--2203 Score: 434
Period size: 104 Copynumber: 2.2 Consensus size: 104
1961 TTCTCGTGAT
1971 GAGTTCTTCTCATTATGAACTCTT-TGGAAACGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAACGTTGATCCAAATCCTTTTGCGGTGGACTTAG-A
2035 AGAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
65 AGAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
*
2075 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAACGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
2140 GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
66 GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
2179 GAGTTCTTCTCATTATGAACT-TTCT
1 GAGTTCTTCTCATTATGAACTCTTCT
2204 CCTTTAGGAC
Statistics
Matches: 127, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
103 4 0.03
104 86 0.68
105 37 0.29
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (104 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAACGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
Found at i:2196 original size:35 final size:35
Alignment explanation
Indices: 2150--2234 Score: 170
Period size: 35 Copynumber: 2.4 Consensus size: 35
2140 GAACATGTTT
2150 TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTC
1 TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTC
2185 TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTC
1 TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTC
2220 TTCTCATTATGAACT
1 TTCTCATTATGAACT
2235 CTTCACTGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (35 bp):
TTCTCATTATGAACTTTCTCCTTTAGGACGAGTTC
Found at i:2395 original size:134 final size:135
Alignment explanation
Indices: 2183--2514 Score: 500
Period size: 134 Copynumber: 2.5 Consensus size: 135
2173 TAGGACGAGT
* * * *
2183 TCTTCTCATTATGAAC-T-TTCT-CCT-T-TAGGACGAGTTCTTCTCATTATGAACTCTTCACTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAG-TCTTCTCATTATGAACTCTCCATTG
** * * *
2243 GAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCAAAATGTTATGAATCGAGTGATAGGTCGA
65 GAAATACTGATCCCTCAAGCAAGCTGTCACTGATTCAAAATGTCATGAATCGAGTGATAGGTCGA
2308 AC-AGC
130 ACAAGC
2313 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTCTTCTCATTATGAACTCTCCATTGG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTCTTCTCATTATGAACTCTCCATTGG
* *
2378 AAATACTGATCCTTCAAGCAAGCTGTCACTGATTCAAAATGTCGTGAATCGAGTGATAGGTCGAA
66 AAATACTGATCCCTCAAGCAAGCTGTCACTGATTCAAAATGTCATGAATCGAGTGATAGGTCGAA
2443 CAAGC
131 CAAGC
2448 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAG--TTCTCATTATGAACTCTCCATTGG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTCTTCTCATTATGAACTCTCCATTGG
2511 AAAT
66 AAAT
2515 GCTGGTTCCC
Statistics
Matches: 185, Mismatches: 11, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
130 16 0.09
131 1 0.01
132 4 0.02
133 31 0.17
134 84 0.45
135 49 0.26
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (135 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTCTTCTCATTATGAACTCTCCATTGG
AAATACTGATCCCTCAAGCAAGCTGTCACTGATTCAAAATGTCATGAATCGAGTGATAGGTCGAA
CAAGC
Found at i:3404 original size:18 final size:16
Alignment explanation
Indices: 3383--3452 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 16
3373 TCCTTTTCTC
*
3383 TTTTTATTTTTTCA--
1 TTTTTTTTTTTTCATT
*
3397 TTTCTTTTTTTTCATT
1 TTTTTTTTTTTTCATT
3413 TTTCATTTTTTTTTCATT
1 TTT--TTTTTTTTTCATT
*
3431 TTTTTTCTTTTTCATT
1 TTTTTTTTTTTTCATT
3447 TTTTTT
1 TTTTTT
3453 ATCTTTTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.25
16 21 0.44
18 15 0.31
ACGTcount: A:0.09, C:0.10, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTTTTCATT
Found at i:3406 original size:27 final size:27
Alignment explanation
Indices: 3397--3460 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
3387 TATTTTTTCA
3397 TTTC-TTTTTTTTCATTTTTCATTTTTT
1 TTTCATTTTTTTTC-TTTTTCATTTTTT
3424 TTTCATTTTTTTTCTTTTTCATTTTTT
1 TTTCATTTTTTTTCTTTTTCATTTTTT
3451 TTATC-TTTTT
1 TT-TCATTTTT
3461 ATTTGTTCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 24 0.69
28 11 0.31
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTCATTTTTTTTCTTTTTCATTTTTT
Found at i:3414 original size:21 final size:21
Alignment explanation
Indices: 3390--3442 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 21
3380 CTCTTTTTAT
3390 TTTTTCATTTCTTTTTTTTCA
1 TTTTTCATTTCTTTTTTTTCA
3411 TTTTTCA--T-TTTTTTTTCA
1 TTTTTCATTTCTTTTTTTTCA
3429 TTTTT--TTTCTTTTT
1 TTTTTCATTTCTTTTT
3443 CATTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 16 0.55
19 6 0.21
21 7 0.24
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTCATTTCTTTTTTTTCA
Found at i:3451 original size:28 final size:27
Alignment explanation
Indices: 3376--3482 Score: 103
Period size: 28 Copynumber: 4.0 Consensus size: 27
3366 CAAACCCTCC
* *
3376 TTTTCTCTTTTT-ATTTTTTCATTTCTT
1 TTTTTTCTTTTTCATTTTTT-TTTTCTT
3403 TTTTTTCATTTTTCA-TTTTTTTTTCATT
1 TTTTTTC-TTTTTCATTTTTTTTTTC-TT
*
3431 TTTTTTCTTTTTCATTTTTTTTATCTT
1 TTTTTTCTTTTTCATTTTTTTTTTCTT
* * * *
3458 TTTATT-TGTTCCCTTTTTTTTTTCT
1 TTTTTTCTTTTTCATTTTTTTTTTCT
3483 CAAGCATAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
26 15 0.22
27 24 0.35
28 28 0.41
29 1 0.01
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.79
Consensus pattern (27 bp):
TTTTTTCTTTTTCATTTTTTTTTTCTT
Found at i:3452 original size:11 final size:11
Alignment explanation
Indices: 3389--3436 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
3379 TCTCTTTTTA
3389 TTTTTTCATTT
1 TTTTTTCATTT
*
3400 CTTTTTT--TTC
1 -TTTTTTCATTT
*
3410 ATTTTTCATTT
1 TTTTTTCATTT
3421 TTTTTTCATTT
1 TTTTTTCATTT
3432 TTTTT
1 TTTTT
3437 CTTTTTCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
9 5 0.17
10 2 0.07
11 17 0.57
12 6 0.20
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:3457 original size:18 final size:17
Alignment explanation
Indices: 3404--3464 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
3394 TCATTTCTTT
3404 TTTTTCATTTTTCATTTT-
1 TTTTTCATTTTT--TTTTC
3422 TTTTTCA-TTTTTTTTC
1 TTTTTCATTTTTTTTTC
3438 TTTTTCATTTTTTTTATC
1 TTTTTCATTTTTTTT-TC
3456 TTTTT-ATTT
1 TTTTTCATTT
3465 GTTCCCTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.10
16 7 0.17
17 15 0.38
18 14 0.35
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTCATTTTTTTTTC
Found at i:15175 original size:24 final size:24
Alignment explanation
Indices: 15148--15193 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
15138 AATGGAACCT
15148 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
15172 TATACTTATTAAATAAATGATA
1 TATACTTATTAAATAAATGATA
15194 TAAAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:15296 original size:2 final size:2
Alignment explanation
Indices: 15289--15381 Score: 179
Period size: 2 Copynumber: 47.0 Consensus size: 2
15279 AATAATTTAA
15289 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
15331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
15372 AT AT AT AT AT
1 AT AT AT AT AT
15382 CAGCTAAGCT
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 89 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15500 original size:45 final size:45
Alignment explanation
Indices: 15449--15541 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 45
15439 ATATATATAT
15449 ATATATATATGAACAAAAAAAATCAGTTTCCAAGACACATTAAATAA
1 ATATATATAT--ACAAAAAAAATCAGTTTCCAAGACACATTAAATAA
* *
15496 ATATATATATATACAAAAAATCAGTTTCCAAGACACATTAAATAA
1 ATATATATATACAAAAAAAATCAGTTTCCAAGACACATTAAATAA
15541 A
1 A
15542 CTAAGCTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 34 0.77
47 10 0.23
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (45 bp):
ATATATATATACAAAAAAAATCAGTTTCCAAGACACATTAAATAA
Found at i:15984 original size:45 final size:43
Alignment explanation
Indices: 15893--15992 Score: 173
Period size: 45 Copynumber: 2.3 Consensus size: 43
15883 GACAGGGGAG
*
15893 TTCCAAGACATGTTAAACAAATATATATATAACAAAAATCAGT
1 TTCCAAGACATGTTAAAAAAATATATATATAACAAAAATCAGT
15936 TTCCAAGACATGTTAAAAAATATATATATATGAACAAAAATCAGT
1 TTCCAAGACATGTTAAAAAA-ATATATATAT-AACAAAAATCAGT
15981 TTCCAAGACATG
1 TTCCAAGACATG
15993 GAATGAATGC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
43 19 0.35
44 10 0.19
45 25 0.46
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (43 bp):
TTCCAAGACATGTTAAAAAAATATATATATAACAAAAATCAGT
Found at i:17778 original size:3 final size:3
Alignment explanation
Indices: 17772--17814 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
17762 TAAATACACT
* *
17772 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17815 TTTTTTAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:18640 original size:54 final size:54
Alignment explanation
Indices: 18582--18896 Score: 372
Period size: 54 Copynumber: 5.9 Consensus size: 54
18572 GGGACCAAAT
* * *
18582 CGGTTATTCATCCTCATGGGATGAATTCCATGAAATGCAAACTTAGTGCCGAAA
1 CGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAAA
* * * *
18636 CGGTTATTCATCCACAAAGGATGAATTCCGTGAAATGTACACTTAGTACCGAAA
1 CGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAAA
* * *
18690 CAGTTATTCATCCACATAGGATGAATTCCATGAAA--AACACTTAGTGCTGAAA
1 CGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAAA
* * *
18742 CGGTTATTCATCCACATCGGATGAATT-CAGTGAAATACACACTTAGTGTCGAAA
1 CGGTTATTCATCCACATAGGATGAATTCCA-TGAAATGCACACTTAGTGCCGAAA
* * * * *
18796 TGGTTATTCATCCACATATGATGAATTCCGTGCAAT--ACACTTAGTACCGAAA
1 CGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAAA
* * * * *
18848 CGGTTATTCATCCGCATATGATGAATTTC-TAAAATGCACACTTATTGCC
1 CGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCC
18897 CATTTGGTAA
Statistics
Matches: 223, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
51 6 0.03
52 84 0.38
53 10 0.04
54 122 0.55
55 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (54 bp):
CGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAAA
Found at i:18775 original size:106 final size:106
Alignment explanation
Indices: 18584--18874 Score: 377
Period size: 106 Copynumber: 2.7 Consensus size: 106
18574 GACCAAATCG
* *
18584 GTTATTCATCCTCATGGGATGAATTCCATGAAATGCAA-ACTTAGTGCCGAAACGGTTATTCATC
1 GTTATTCATCCACATAGGATGAATTCCATGAAA---AACACTTAGTGCCGAAACGGTTATTCATC
* * **
18648 CACAAAGGATGAATTCCGTGAAATGTACACTTAGTACCGAAACA
63 CACATAGGATGAATTCAGTGAAATACACACTTAGTACCGAAACA
*
18692 GTTATTCATCCACATAGGATGAATTCCATGAAAAACACTTAGTGCTGAAACGGTTATTCATCCAC
1 GTTATTCATCCACATAGGATGAATTCCATGAAAAACACTTAGTGCCGAAACGGTTATTCATCCAC
* ** **
18757 ATCGGATGAATTCAGTGAAATACACACTTAGTGTCGAAATG
66 ATAGGATGAATTCAGTGAAATACACACTTAGTACCGAAACA
* * * * * *
18798 GTTATTCATCCACATATGATGAATTCCGTGCAATACACTTAGTACCGAAACGGTTATTCATCCGC
1 GTTATTCATCCACATAGGATGAATTCCATGAAAAACACTTAGTGCCGAAACGGTTATTCATCCAC
*
18863 ATATGATGAATT
66 ATAGGATGAATT
18875 TCTAAAATGC
Statistics
Matches: 161, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
105 2 0.01
106 128 0.80
108 31 0.19
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (106 bp):
GTTATTCATCCACATAGGATGAATTCCATGAAAAACACTTAGTGCCGAAACGGTTATTCATCCAC
ATAGGATGAATTCAGTGAAATACACACTTAGTACCGAAACA
Found at i:19353 original size:19 final size:19
Alignment explanation
Indices: 19307--19362 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
19297 TGATACCTTA
* *
19307 CCTTAGGTATCGATAGTCC
1 CCTTGGGTATCGATACTCC
19326 CCTTTGGGTATCGATACTCC
1 CC-TTGGGTATCGATACTCC
19346 CCTTGGGTATCGATACT
1 CCTTGGGTATCGATACT
19363 ATCTAGCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (19 bp):
CCTTGGGTATCGATACTCC
Found at i:23040 original size:17 final size:16
Alignment explanation
Indices: 23023--23070 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
23013 ATATATATAT
23023 TTAATTATATTTTTTA
1 TTAATTATATTTTTTA
*
23039 TTATTTACTATTTTTTA
1 TTAATTA-TATTTTTTA
23056 TT-ATTATCATTTTTT
1 TTAATTAT-ATTTTTT
23071 TCTATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 16 0.57
17 11 0.39
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (16 bp):
TTAATTATATTTTTTA
Found at i:23067 original size:16 final size:16
Alignment explanation
Indices: 23026--23070 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
23016 TATATATTTA
23026 ATTAT-ATTTTTTATT
1 ATTATCATTTTTTATT
23041 ATT-TACTATTTTTTATT
1 ATTAT-C-ATTTTTTATT
23058 ATTATCATTTTTT
1 ATTATCATTTTTT
23071 TCTATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 7 0.27
17 14 0.54
18 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTATCATTTTTTATT
Found at i:23105 original size:26 final size:26
Alignment explanation
Indices: 23042--23105 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
23032 TTTTTTATTA
23042 TTTACTATTTTTTATTATTATCATTT
1 TTTACTATTTTTTATTATTATCATTT
* *
23068 TTTTCTATTTTTTATTATTATTACTTT
1 TTTACTATTTTTTATTATTATCA-TTT
*
23095 TTTAGTATTTT
1 TTTACTATTTT
23106 ATTGTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 21 0.64
27 12 0.36
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTACTATTTTTTATTATTATCATTT
Found at i:23146 original size:25 final size:24
Alignment explanation
Indices: 23112--23164 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
23102 TTTTATTGTA
* *
23112 TTATATATATTTTTATATCATTATT
1 TTATATATATATATATAT-ATTATT
23137 TTATATATATATATATATATTATT
1 TTATATATATATATATATATTATT
23161 TTAT
1 TTAT
23165 TTATTTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTATATATATATATATATATTATT
Found at i:23254 original size:17 final size:17
Alignment explanation
Indices: 23234--23276 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
23224 TTTAACACTT
23234 TATTTATTTTTTATATA
1 TATTTATTTTTTATATA
*
23251 TATTT-TATTTTTATTTA
1 TATTTAT-TTTTTATATA
23268 T-TTTATTTT
1 TATTTATTTT
23277 ATTCAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TATTTATTTTTTATATA
Found at i:23271 original size:15 final size:15
Alignment explanation
Indices: 23232--23276 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
23222 TTTTTAACAC
23232 TTTATTTA-TTT-TT
1 TTTATTTATTTTATT
* *
23245 TATATATATTTTATT
1 TTTATTTATTTTATT
23260 TTTATTTATTTTATT
1 TTTATTTATTTTATT
23275 TT
1 TT
23277 ATTCAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 6 0.23
14 3 0.12
15 17 0.65
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTATTTATTTTATT
Found at i:23285 original size:15 final size:15
Alignment explanation
Indices: 23236--23286 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
23226 TAACACTTTA
23236 TTTATTTTTTATATATAT
1 TTTA-TTTTTAT-TA-AT
*
23254 TTTATTTTTATTTAT
1 TTTATTTTTATTAAT
23269 TTTA-TTTTATTCAAT
1 TTTATTTTTATT-AAT
23284 TTT
1 TTT
23287 TTATTATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 7 0.23
15 11 0.37
16 1 0.03
17 7 0.23
18 4 0.13
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTTTATTAAT
Found at i:24253 original size:2 final size:2
Alignment explanation
Indices: 24246--24292 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
24236 AGTTTCAAAC
24246 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
24288 TA TA T
1 TA TA T
24293 GATCTACGTG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24500 original size:19 final size:19
Alignment explanation
Indices: 24457--24502 Score: 71
Period size: 16 Copynumber: 2.6 Consensus size: 19
24447 TAAAGTAAAT
24457 ACTAATAATATAATAGACA
1 ACTAATAATATAATAGACA
24476 A-T--TAATATAATAGACA
1 ACTAATAATATAATAGACA
24492 ACTAATAATAT
1 ACTAATAATAT
24503 CAGTTCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 15 0.62
17 1 0.04
18 1 0.04
19 7 0.29
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (19 bp):
ACTAATAATATAATAGACA
Found at i:27300 original size:24 final size:24
Alignment explanation
Indices: 27267--27324 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
27257 ATCATGCATA
*
27267 TAAGGCACTTCATAATATTAGTGC
1 TAAGGCACTTCATAATATCAGTGC
* * * *
27291 TAAGGAACTTTATTATATCAGTTC
1 TAAGGCACTTCATAATATCAGTGC
27315 TAAGGCACTT
1 TAAGGCACTT
27325 ACGTATAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (24 bp):
TAAGGCACTTCATAATATCAGTGC
Found at i:27912 original size:5 final size:5
Alignment explanation
Indices: 27902--27996 Score: 172
Period size: 5 Copynumber: 18.6 Consensus size: 5
27892 AGTGGTATTG
27902 TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA
1 TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA
27952 TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGTGA TTGTGA TTG
1 TTGTA TTGTA TTGTA TTGTA TTGTA TTGTA TTGT-A TTGT-A TTG
27997 AAAAATGACT
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 79 0.89
6 10 0.11
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (5 bp):
TTGTA
Found at i:29418 original size:20 final size:20
Alignment explanation
Indices: 29393--29436 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
29383 AAACGACCCA
*
29393 AAACATACCAAAAGGTAGAG
1 AAACATACCAAAAGCTAGAG
*
29413 AAACATGCCAAAAGCTAGAG
1 AAACATACCAAAAGCTAGAG
29433 AAAC
1 AAAC
29437 TGTTGAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.18, G:0.18, T:0.09
Consensus pattern (20 bp):
AAACATACCAAAAGCTAGAG
Found at i:30271 original size:65 final size:65
Alignment explanation
Indices: 30135--30294 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 65
30125 TGTACTAAGA
*
30135 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGCTG
* *
30199 GTACATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGATGCATGGCT
*
30262 AT
65 -G
* *
30264 GTGCATCGATGCATGAAATGCATTTGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
30295 CAATTTATTC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 28 0.33
65 55 0.64
66 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGGCTG
Found at i:30333 original size:65 final size:63
Alignment explanation
Indices: 30135--30342 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 63
30125 TGTACTAAGA
* * *
30135 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTC-AATTAACCTGAGTGCATCGATGCATGGTTG
* * *
30199 GTACATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAT-TAA-CCTGAGTGCATCGATGCATGGT-
30263 T-
62 TG
* * * *
30264 GTGCATCGATGCATGAAATGCATTTGATG-TTCAATTTATTCCATG-GTGCATTGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA-TTA-ACC-TGAGTGCATCGATGCATGG-T
30327 TG
62 TG
*
30329 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
30343 CACTTTGAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
63 4 0.03
64 48 0.40
65 68 0.56
66 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAATTAACCTGAGTGCATCGATGCATGGTTG
Found at i:33029 original size:23 final size:22
Alignment explanation
Indices: 32999--33080 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
32989 GCATGGCCTT
32999 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
33021 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
33043 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
33066 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
33081 TGTTAAGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 19 0.40
24 12 0.25
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:33091 original size:44 final size:44
Alignment explanation
Indices: 33003--33100 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 44
32993 GGCCTTGTGC
* *
33003 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATAGTGT
*
33047 ATCGATGCACATTCAAAGG-GATGCATCGATGCA-CTGTTA-AGTGT
1 ATCGATGCACATTC-AAGGCG-TGCATCGATGCACCT-TCATAGTGT
33091 ATCGATGCAC
1 ATCGATGCAC
33101 TAAGCACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 31 0.65
45 17 0.35
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCGTGCATCGATGCACCTTCATAGTGT
Found at i:36880 original size:22 final size:21
Alignment explanation
Indices: 36838--36877 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36828 GAGATTGCTT
*
36838 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
36859 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
36878 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:39197 original size:15 final size:16
Alignment explanation
Indices: 39177--39217 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
39167 GTTTACTTCA
*
39177 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
39192 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
39208 GAATGATTCA
1 GAATGATTCA
39218 GAGGCTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:40761 original size:16 final size:16
Alignment explanation
Indices: 40740--40776 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
40730 GCCCTTAAAG
*
40740 GCTTCTAAAGTGTTGT
1 GCTTCTAAAATGTTGT
40756 GCTTCTAAAATGTTGT
1 GCTTCTAAAATGTTGT
40772 GCTTC
1 GCTTC
40777 ATGACCACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (16 bp):
GCTTCTAAAATGTTGT
Found at i:40937 original size:30 final size:29
Alignment explanation
Indices: 40855--40940 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 29
40845 CAAAATTTGG
*
40855 TTAGTGACTAAAA-CGTAATTTTG-AAAGT
1 TTAGTGAC-AAAAGTGTAATTTTGAAAAGT
* * *
40883 TTAGTGACTAAAGTATAAACTTTGAAAAGT
1 TTAGTGACAAAAGTGT-AATTTTGAAAAGT
40913 TTAAG-GACAAAAAGTGTAATTTTGAAAA
1 TT-AGTGAC-AAAAGTGTAATTTTGAAAA
40941 ATTATATATT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
27 3 0.07
28 9 0.20
29 6 0.13
30 20 0.43
31 8 0.17
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (29 bp):
TTAGTGACAAAAGTGTAATTTTGAAAAGT
Found at i:44627 original size:61 final size:63
Alignment explanation
Indices: 44547--44703 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 63
44537 TGCACTAAGA
*
44547 GTGCATCGATGGATGAAATGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATC-ATGC-AGCT-
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCATAAA-A-CTCAGAGTGCATCGATGCAAG-TA
44607 G
63 G
* * *
44608 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTGAGTGCATCGATGCATAGTAT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCATAAAACTCAGAGTGCATCGATGCA-AGTAG
44673 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
44704 CAATTTATTC
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
61 28 0.33
62 16 0.19
63 7 0.08
64 3 0.04
65 30 0.36
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCATAAAACTCAGAGTGCATCGATGCAAGTAG
Found at i:44742 original size:65 final size:63
Alignment explanation
Indices: 44547--44751 Score: 192
Period size: 65 Copynumber: 3.2 Consensus size: 63
44537 TGCACTAAGA
* * * *
44547 GTGCATCGATGGATGAAATGCATTCGATGTTTCAAAATAGCCA-GAGTGCATC-ATGCA-GCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-AATTAACCATGAGTGCATCGATGCATGTTG
* *
44608 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTC-TGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAT-TAAC-CATGAGTGCATCGATGCAT-GT
44671 AT-
62 -TG
*
44673 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTA-ACCATGAGTGCATCGATGCAT-G-T
44736 TG
62 TG
*
44738 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
44752 CACTTTGAAA
Statistics
Matches: 119, Mismatches: 11, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
60 1 0.01
61 29 0.24
62 14 0.12
63 8 0.07
64 19 0.16
65 47 0.39
66 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAACCATGAGTGCATCGATGCATGTTG
Found at i:44937 original size:18 final size:18
Alignment explanation
Indices: 44916--44976 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 18
44906 TTAAATCGAA
44916 TATACTTAGAAAATCATT
1 TATACTTAGAAAATCATT
*
44934 TATAAAATCTTA-AAATTCATT
1 TAT---A-CTTAGAAAATCATT
44955 TATACTTAGAAAATCATT
1 TATACTTAGAAAATCATT
44973 TATA
1 TATA
44977 AAATCTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 4 0.11
18 16 0.44
21 12 0.33
22 4 0.11
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (18 bp):
TATACTTAGAAAATCATT
Found at i:44954 original size:21 final size:21
Alignment explanation
Indices: 44925--44997 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
44915 ATATACTTAG
44925 AAAA-TCATTTATAAAATCTT
1 AAAATTCATTTATAAAATCTT
44945 AAAATTCATTTAT---A-CTT
1 AAAATTCATTTATAAAATCTT
*
44962 AGAAAATCATTTATAAAATCTT
1 A-AAATTCATTTATAAAATCTT
44984 AAAATTCATTTATA
1 AAAATTCATTTATA
44998 CTTAATTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
17 4 0.09
18 12 0.27
20 4 0.09
21 21 0.47
22 4 0.09
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (21 bp):
AAAATTCATTTATAAAATCTT
Found at i:44959 original size:39 final size:39
Alignment explanation
Indices: 44916--45001 Score: 172
Period size: 39 Copynumber: 2.2 Consensus size: 39
44906 TTAAATCGAA
44916 TATACTTAGAAAATCATTTATAAAATCTTAAAATTCATT
1 TATACTTAGAAAATCATTTATAAAATCTTAAAATTCATT
44955 TATACTTAGAAAATCATTTATAAAATCTTAAAATTCATT
1 TATACTTAGAAAATCATTTATAAAATCTTAAAATTCATT
44994 TATACTTA
1 TATACTTA
45002 ATTTGTTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.42
Consensus pattern (39 bp):
TATACTTAGAAAATCATTTATAAAATCTTAAAATTCATT
Found at i:46243 original size:31 final size:31
Alignment explanation
Indices: 46207--46265 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
46197 CTAAGAGTGC
46207 ATCGATGCATAAAATGCATTCGATGTTTCAA
1 ATCGATGCATAAAATGCATTCGATGTTTCAA
*
46238 ATCGATGCATCAAATGCATTCGATGTTT
1 ATCGATGCATAAAATGCATTCGATGTTT
46266 TCATAAAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (31 bp):
ATCGATGCATAAAATGCATTCGATGTTTCAA
Done.