Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001387.1 Hibiscus syriacus cultivar Beakdansim tig00002707_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: 79291
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3153 original size:22 final size:21
Alignment explanation
Indices: 3128--3168 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3118 GCCCCTTTGA
3128 AGGGAAACCGATTACCCCCCAC
1 AGGGAAACCGA-TACCCCCCAC
* *
3150 AGGGGAATCGATACCCCCC
1 AGGGAAACCGATACCCCCC
3169 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.29, C:0.39, G:0.22, T:0.10
Consensus pattern (21 bp):
AGGGAAACCGATACCCCCCAC
Found at i:5437 original size:25 final size:25
Alignment explanation
Indices: 5403--5464 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
5393 AACAAAAAGG
*
5403 GGGAGAAGTGTTCAATGTTTTAAAT
1 GGGAGAAGTGTTCAATGTTTGAAAT
5428 GGGAGAAGTGTTCAATGTTTGAAAT
1 GGGAGAAGTGTTCAATGTTTGAAAT
5453 GGGAGAAGTGTT
1 GGGAGAAGTGTT
5465 AGAAGTGTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.32
Consensus pattern (25 bp):
GGGAGAAGTGTTCAATGTTTGAAAT
Found at i:5500 original size:17 final size:17
Alignment explanation
Indices: 5478--5510 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5468 AGTGTTCAAA
5478 GTTTTAAAATAGGAGAT
1 GTTTTAAAATAGGAGAT
5495 GTTTTAAAATAGGAGA
1 GTTTTAAAATAGGAGA
5511 AGTGTTAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.33
Consensus pattern (17 bp):
GTTTTAAAATAGGAGAT
Found at i:7170 original size:102 final size:101
Alignment explanation
Indices: 6968--7172 Score: 311
Period size: 102 Copynumber: 2.0 Consensus size: 101
6958 AGGGTCTATG
*
6968 TGGTCCTTCGGGACATATATTTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGA
* * *
7033 TCCCTAGTATGTTTATATGATTCTTAAGGAATGATA
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATA
* ***
7069 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTTTTGGAGACACATACTTG
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGT-GAGACACATACTTG
* *
7134 ATCCTTGGCATATGTATATGATTCTTAAGGAATGATA
65 ATCCCTAGCATATGTATATGATTCTTAAGGAATGATA
7171 TG
1 TG
7173 TGGTCCTTAT
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 45 0.48
102 48 0.52
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (101 bp):
TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGA
TCCCTAGCATATGTATATGATTCTTAAGGAATGATA
Found at i:7264 original size:23 final size:23
Alignment explanation
Indices: 7196--7256 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
7186 CATTATTATA
*
7196 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
7219 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
7242 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
7257 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:17644 original size:14 final size:14
Alignment explanation
Indices: 17622--17673 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
17612 TCGATTATAT
*
17622 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
17636 GTTCATTTA---T-
1 GTTCATTTATGTTC
*
17646 ATTCATTTATGTTC
1 GTTCATTTATGTTC
17660 GTTCATTTATGTTC
1 GTTCATTTATGTTC
17674 AAACAAAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
13 1 0.03
14 21 0.68
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:17674 original size:24 final size:24
Alignment explanation
Indices: 17609--17674 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
17599 CGTTCGTGAA
*
17609 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTC-ATT-TATGTTCATTTATGTT
*
17635 CGTTCATTTATATTCATTTATGTT
1 CGTTCATTTATGTTCATTTATGTT
17659 CGTTCATTTATGTTCA
1 CGTTCATTTATGTTCA
17675 AACAAAGAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 29 0.78
25 3 0.08
26 5 0.14
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (24 bp):
CGTTCATTTATGTTCATTTATGTT
Found at i:31998 original size:11 final size:13
Alignment explanation
Indices: 31966--31995 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
31956 TGGCCAAAGA
31966 TGAAAAGGTATGT
1 TGAAAAGGTATGT
31979 TGAAAAGGTATG-
1 TGAAAAGGTATGT
31991 TGAAA
1 TGAAA
31996 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:35851 original size:19 final size:20
Alignment explanation
Indices: 35827--35870 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
35817 CGCATCGGCA
35827 CGCATC-GACCCGCATCA-AC
1 CGCATCGGA-CCGCATCAGAC
*
35846 CGCATCGGATCGCATCAGAC
1 CGCATCGGACCGCATCAGAC
35866 CGCAT
1 CGCAT
35871 TATGTACCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.25, C:0.41, G:0.20, T:0.14
Consensus pattern (20 bp):
CGCATCGGACCGCATCAGAC
Found at i:36222 original size:25 final size:25
Alignment explanation
Indices: 36186--36243 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
36176 CATCGACTGA
*
36186 GCCTCGCGCCTCAGAGCCTTGCACC
1 GCCTCGCTCCTCAGAGCCTTGCACC
36211 GCCTCGCTCCTCAGAGCCTTGCACC
1 GCCTCGCTCCTCAGAGCCTTGCACC
36236 GCCTCGCT
1 GCCTCGCT
36244 GAGCCTAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.10, C:0.48, G:0.22, T:0.19
Consensus pattern (25 bp):
GCCTCGCTCCTCAGAGCCTTGCACC
Found at i:36249 original size:20 final size:22
Alignment explanation
Indices: 36192--36249 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 22
36182 CTGAGCCTCG
36192 CGCCTCAGAGCCTTGCACCGCCT
1 CGCCT-AGAGCCTTGCACCGCCT
36215 CGCTCCTCAGAGCCTTGCACCGCCT
1 CG--CCT-AGAGCCTTGCACCGCCT
36240 CG-CT-GAGCCT
1 CGCCTAGAGCCT
36250 AGGTGCGCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
20 6 0.18
22 2 0.06
23 2 0.06
25 23 0.70
ACGTcount: A:0.12, C:0.47, G:0.22, T:0.19
Consensus pattern (22 bp):
CGCCTAGAGCCTTGCACCGCCT
Found at i:40301 original size:59 final size:59
Alignment explanation
Indices: 40238--40357 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 59
40228 ATATATATAT
* * * *
40238 ATATATATTTGAAGTTAACATAATAAGAAAATATAATTTTAAGTTAATAA-AAGAATAAA
1 ATATATATTTAAAGTCAACATAAGAAGAAAATATAATTTTAAGTTAA-AATAAAAATAAA
* * * *
40297 ATATATTTTTAAAGTCAAGATAAGAATAAAATATATTTTTAAGTTAAAATAAAAATAAA
1 ATATATATTTAAAGTCAACATAAGAAGAAAATATAATTTTAAGTTAAAATAAAAATAAA
40356 AT
1 AT
40358 CTATTTAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 2 0.04
59 50 0.96
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (59 bp):
ATATATATTTAAAGTCAACATAAGAAGAAAATATAATTTTAAGTTAAAATAAAAATAAA
Found at i:40362 original size:29 final size:29
Alignment explanation
Indices: 40238--40363 Score: 137
Period size: 29 Copynumber: 4.3 Consensus size: 29
40228 ATATATATAT
* * * *
40238 ATATATATTTGAAGTTAACATAATAAGAAA
1 ATATAT-TTTTAAGTTAAAATAAGAATAAA
*
40268 ATATAATTTTAAGTTAATAA-AAGAATAAA
1 ATATATTTTTAAGTTAA-AATAAGAATAAA
* *
40297 ATATATTTTTAAAGTCAAGATAAGAATAAA
1 ATATATTTTT-AAGTTAAAATAAGAATAAA
*
40327 ATATATTTTTAAGTTAAAATAAAAATAAA
1 ATATATTTTTAAGTTAAAATAAGAATAAA
*
40356 ATCTATTT
1 ATATATTT
40364 AATAAGTTGA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
29 50 0.62
30 31 0.38
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (29 bp):
ATATATTTTTAAGTTAAAATAAGAATAAA
Found at i:40376 original size:29 final size:29
Alignment explanation
Indices: 40240--40390 Score: 114
Period size: 29 Copynumber: 5.2 Consensus size: 29
40230 ATATATATAT
* * * *
40240 ATATATTT-GAAGTTAACATAATAAGAAA
1 ATATATTTATAAGTTAAAATAAAAATAAA
*
40268 ATATAATTT-TAAGTTAATAA-AAGAATAAA
1 ATAT-ATTTATAAGTTAA-AATAAAAATAAA
* * * *
40297 ATATATTTTTAAAGTCAAGATAAGAATAAA
1 ATATATTTAT-AAGTTAAAATAAAAATAAA
*
40327 ATATATTTTTAAGTTAAAATAAAAATAAA
1 ATATATTTATAAGTTAAAATAAAAATAAA
* *
40356 ATCTATTTAATAAGTT-GAATAAAACA-AAA
1 ATATATTT-ATAAGTTAAAATAAAA-ATAAA
40385 ATATAT
1 ATATAT
40391 AGTTTTAAAC
Statistics
Matches: 103, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
28 8 0.08
29 62 0.60
30 33 0.32
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (29 bp):
ATATATTTATAAGTTAAAATAAAAATAAA
Found at i:44874 original size:31 final size:31
Alignment explanation
Indices: 44836--44960 Score: 171
Period size: 31 Copynumber: 4.0 Consensus size: 31
44826 AGGGTCGAGG
*
44836 GTTTACCTATGTTCTTCGGGACATATGGAAT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
44867 GTTTACCTATGTTCTTCGAGACATATGGGCT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
44898 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
44929 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
44960 G
1 G
44961 GTCATTCAGG
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:45278 original size:16 final size:17
Alignment explanation
Indices: 45233--45280 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
45223 TATATGATGT
*
45233 GTATTAATGATAAATAT
1 GTATTAATGATAAATAG
*
45250 ATGATTAAATGATAAA-AG
1 GT-ATT-AATGATAAATAG
45268 GTATTAATGATAA
1 GTATTAATGATAA
45281 TAAGATGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 8 0.31
17 4 0.15
18 5 0.19
19 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (17 bp):
GTATTAATGATAAATAG
Found at i:45289 original size:35 final size:33
Alignment explanation
Indices: 45233--45297 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
45223 TATATGATGT
*
45233 GTATTAATGATAAATATATGATTAAATGATAAAAG
1 GTATTAATGATAAATAGATGA-T-AATGATAAAAG
45268 GTATTAATGAT-AATAAGATGATAATGATAA
1 GTATTAATGATAAAT-AGATGATAATGATAA
45298 GGAAGAGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 8 0.29
34 4 0.14
35 16 0.57
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (33 bp):
GTATTAATGATAAATAGATGATAATGATAAAAG
Found at i:45308 original size:18 final size:17
Alignment explanation
Indices: 45272--45310 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
45262 TAAAAGGTAT
* *
45272 TAATGATAATAAGATGA
1 TAATGATAAGAAGAGGA
45289 TAATGATAAGGAAGAGGA
1 TAATGATAA-GAAGAGGA
45307 TAAT
1 TAAT
45311 CATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (17 bp):
TAATGATAAGAAGAGGA
Found at i:45806 original size:21 final size:21
Alignment explanation
Indices: 45780--45821 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
45770 TCGAAGTTTT
*
45780 ATGCATCGGTGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
*
45801 ATGCATTGATGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
45822 GGTTTGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
ATGCATCGATGCACTGTAGCA
Found at i:45930 original size:29 final size:30
Alignment explanation
Indices: 45859--45918 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
45849 CAATTTAAGG
*
45859 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACGTGAATTGAATTTA
45890 CAAAATGTTTTTGGACGT-AATTGAATTTA
1 CAAAATGTTTTTGGACGTGAATTGAATTTA
45919 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACGTGAATTGAATTTA
Found at i:46033 original size:21 final size:21
Alignment explanation
Indices: 46008--46087 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
45998 TTCAAGATTG
* *
46008 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
46029 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
*
46047 CCC---GGGTATAGATACCCC
1 CCCAGGGGGTACAGATACCCC
46065 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
46086 CC
1 CC
46088 TGCAGGTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
15 10 0.20
18 8 0.16
21 31 0.63
ACGTcount: A:0.23, C:0.36, G:0.28, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:46054 original size:36 final size:36
Alignment explanation
Indices: 46014--46085 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
46004 ATTGCCCAGG
*
46014 GGGTATAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTATAGATACCCCCCCAGGGGGTACAGATACCCC
46050 GGGTATAGATACCCCCCCAGGGGGTACAGATACCCC
1 GGGTATAGATACCCCCCCAGGGGGTACAGATACCCC
46086 CCTGCAGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.33, G:0.28, T:0.15
Consensus pattern (36 bp):
GGGTATAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:46059 original size:15 final size:15
Alignment explanation
Indices: 46035--46064 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46025 CCCCCCCAGG
46035 GGGTACAGATACCCC
1 GGGTACAGATACCCC
*
46050 GGGTATAGATACCCC
1 GGGTACAGATACCCC
46065 CCCAGGGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.17
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:46161 original size:20 final size:21
Alignment explanation
Indices: 46121--46163 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
46111 AACAGAATGT
46121 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
46142 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
46163 C
1 C
46164 TGTTCAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:46225 original size:21 final size:21
Alignment explanation
Indices: 46199--46241 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
46189 ATTTGAATAT
*
46199 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
46220 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
46241 T
1 T
46242 CTATTCTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:46307 original size:20 final size:22
Alignment explanation
Indices: 46269--46308 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
46259 TTTGAGTATA
46269 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
46291 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
46309 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:46562 original size:34 final size:32
Alignment explanation
Indices: 46523--46592 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
46513 TTTTGTAAAG
*
46523 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
46557 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
46589 GGGA
1 GGGA
46593 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:46823 original size:20 final size:20
Alignment explanation
Indices: 46798--46837 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
46788 ACCGTTTCGG
46798 TTGTCGATTCGAGCTTCCGA
1 TTGTCGATTCGAGCTTCCGA
46818 TTGTCGATTCGAGCTTCCGA
1 TTGTCGATTCGAGCTTCCGA
46838 AAATCCTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (20 bp):
TTGTCGATTCGAGCTTCCGA
Found at i:47505 original size:20 final size:19
Alignment explanation
Indices: 47472--47519 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
47462 AATGATTTTC
*
47472 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAAC-AAAATGAAA
47491 TTTTGAAAGACAAAATGAAA
1 TTTTGAAA-ACAAAATGAAA
47511 TTTTGAAAA
1 TTTTGAAAA
47520 AGGATTTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (19 bp):
TTTTGAAAACAAAATGAAA
Found at i:48803 original size:34 final size:30
Alignment explanation
Indices: 48765--48833 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
48755 TTGATATAAC
*
48765 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACGT-AATTG
48799 AATTT-ACAAAATGTTTTTGGACGTAATTG
1 AATTTAACAAAATGTTTTTGGACGTAATTG
48828 AATTTA
1 AATTTA
48834 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACGTAATTG
Found at i:48845 original size:29 final size:30
Alignment explanation
Indices: 48774--48833 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
48764 CAATTTAAGG
*
48774 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACGTGAATTGAATTTA
48805 CAAAATGTTTTTGGACGT-AATTGAATTTA
1 CAAAATGTTTTTGGACGTGAATTGAATTTA
48834 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACGTGAATTGAATTTA
Found at i:48948 original size:21 final size:21
Alignment explanation
Indices: 48923--49001 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
48913 TTCAAGATTA
* *
48923 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
48944 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
48962 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
48980 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
49001 C
1 C
49002 ATGCAGGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
21 31 0.62
ACGTcount: A:0.23, C:0.37, G:0.28, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:48969 original size:36 final size:36
Alignment explanation
Indices: 48929--49000 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
48919 ATTACCCAGG
* *
48929 GGGTATAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
48965 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
49001 CATGCAGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.35, G:0.28, T:0.14
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:48970 original size:15 final size:15
Alignment explanation
Indices: 48950--48979 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
48940 CCCCCCCAGG
48950 GGGTACAGATACCCC
1 GGGTACAGATACCCC
48965 GGGTACAGATACCCC
1 GGGTACAGATACCCC
48980 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:49076 original size:20 final size:21
Alignment explanation
Indices: 49036--49079 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
49026 AACAGAATGT
49036 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
49057 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
49078 CC
1 CC
49080 TGTTCAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.45, G:0.27, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:49141 original size:21 final size:21
Alignment explanation
Indices: 49115--49157 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
49105 ATTTGAATAT
*
49115 TATGAAGGGGTATCGACTCCC
1 TATGAAGGGGTACCGACTCCC
*
49136 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGACTCCC
49157 T
1 T
49158 CTATTATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGACTCCC
Found at i:49223 original size:20 final size:22
Alignment explanation
Indices: 49185--49224 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
49175 TTTTAGTATA
49185 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
49207 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
49225 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:49478 original size:34 final size:32
Alignment explanation
Indices: 49439--49508 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
49429 TTTTGTAAAG
*
49439 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
49473 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
49505 GGGA
1 GGGA
49509 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:55124 original size:20 final size:20
Alignment explanation
Indices: 55101--55149 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
55091 GTCAGTATCG
*
55101 ATATTGTTCTTTAAGTACCA
1 ATATTGTTCTTCAAGTACCA
55121 ATATTGTTCTTCAAGTACCA
1 ATATTGTTCTTCAAGTACCA
55141 ATATTGTTC
1 ATATTGTTC
55150 ATGCAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (20 bp):
ATATTGTTCTTCAAGTACCA
Found at i:58955 original size:24 final size:24
Alignment explanation
Indices: 58909--58958 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
58899 TAGCTCGTAT
***
58909 AAATTGCACCGAAGTGTTGCATAG
1 AAATTGCACCGAAGTGCCACATAG
*
58933 AAATTGCATCGAAGTGCCACATAG
1 AAATTGCACCGAAGTGCCACATAG
58957 AA
1 AA
58959 TGTCCCAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCCACATAG
Found at i:59012 original size:23 final size:22
Alignment explanation
Indices: 58949--59016 Score: 93
Period size: 21 Copynumber: 3.1 Consensus size: 22
58939 CATCGAAGTG
*
58949 CCACATAGAATGTCCCAAAGGA
1 CCACATAGAATGTCCCGAAGGA
* *
58971 CCACATA-TATATCCCGAAGGA
1 CCACATAGAATGTCCCGAAGGA
58992 CCACATAGAATTGTCCCGAAGGA
1 CCACATAGAA-TGTCCCGAAGGA
59015 CC
1 CC
59017 GCGTAGAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.46
22 8 0.21
23 13 0.33
ACGTcount: A:0.37, C:0.29, G:0.18, T:0.16
Consensus pattern (22 bp):
CCACATAGAATGTCCCGAAGGA
Found at i:63700 original size:16 final size:16
Alignment explanation
Indices: 63679--63719 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
63669 AAATGTCTAC
63679 GGTCTTGTGTCATGGA
1 GGTCTTGTGTCATGGA
*
63695 GGTCTTATGTCATGGA
1 GGTCTTGTGTCATGGA
63711 GGTCATTGT
1 GGTC-TTGT
63720 ACATGTGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.15, C:0.12, G:0.34, T:0.39
Consensus pattern (16 bp):
GGTCTTGTGTCATGGA
Found at i:64353 original size:25 final size:25
Alignment explanation
Indices: 64315--64368 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
64305 GTATTTCGTT
* *
64315 AGATGAAATAAGTGTGTTGTGTAAG
1 AGATGAAAGAAGTGTGTTGTGTAAA
*
64340 AGATGAAAGGAGTGTGTTGTGTAAA
1 AGATGAAAGAAGTGTGTTGTGTAAA
64365 AGAT
1 AGAT
64369 TGAACATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (25 bp):
AGATGAAAGAAGTGTGTTGTGTAAA
Found at i:64564 original size:61 final size:61
Alignment explanation
Indices: 64459--64583 Score: 171
Period size: 61 Copynumber: 2.0 Consensus size: 61
64449 TCACATCAAC
** *
64459 TCAGATAAAATGAAAAATTTTAGAGAGTTAGAGAATCTATACTATTCATGTCATTTGCTTT
1 TCAGATAAAATGAAAAATTTTAGAGAGACAGAGAATCTACACTATTCATGTCATTTGCTTT
* * * *
64520 TCAGATAAACTTAAAAATTTTAGAGAGACATAG-ATGTTACACTATTCATGTCATTTGCTTT
1 TCAGATAAAATGAAAAATTTTAGAGAGACAGAGAAT-CTACACTATTCATGTCATTTGCTTT
64581 TCA
1 TCA
64584 TTGACATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 2 0.04
61 54 0.96
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38
Consensus pattern (61 bp):
TCAGATAAAATGAAAAATTTTAGAGAGACAGAGAATCTACACTATTCATGTCATTTGCTTT
Found at i:64659 original size:82 final size:82
Alignment explanation
Indices: 64520--64893 Score: 500
Period size: 82 Copynumber: 4.6 Consensus size: 82
64510 CATTTGCTTT
* * * *
64520 TCAGATAAACTTAAAAATTTTAGAGAGACATAG-ATGTTACACTATTCATGTCATTTGCTTTTCA
1 TCAGATAAACTTAAAAATTTTAGAGAGTCAGAGAAT-CTACACTATTCACGTCATTTGCTTTTCA
64584 TTGACATTTCACATCAAC
65 TTGACATTTCACATCAAC
* * * * * *
64602 TCAGATAAAATGAAAATTTTTAGAGAGTCAGAGAGTCTATACTATTCACGTCCTTTGCTTTTCAT
1 TCAGATAAACTTAAAAATTTTAGAGAGTCAGAGAATCTACACTATTCACGTCATTTGCTTTTCAT
* *
64667 TGACATTTCATATTAAC
66 TGACATTTCACATCAAC
* * *
64684 TCAGATAAACTTAAAAAATTTATAGAGTCAGAGAATCTACACTATTCACGTCATTTACTTTTCAT
1 TCAGATAAACTTAAAAATTTTAGAGAGTCAGAGAATCTACACTATTCACGTCATTTGCTTTTCAT
64749 TGACATTTCACATCAAC
66 TGACATTTCACATCAAC
* * * * *
64766 TAAGATAAACTTGAAAATTTTAGAGAGTCAAAGAATCTATACTATTCACGTCCTTTGCTTTTCAT
1 TCAGATAAACTTAAAAATTTTAGAGAGTCAGAGAATCTACACTATTCACGTCATTTGCTTTTCAT
*
64831 TGACATTTCACATTAAC
66 TGACATTTCACATCAAC
* * * *
64848 TCAGAT-AAGTTAAAATTTTTAGAGAGTCAGAAAATCTACATTATTC
1 TCAGATAAACTTAAAAATTTTAGAGAGTCAGAGAATCTACACTATTC
64894 TACCAAAATA
Statistics
Matches: 251, Mismatches: 40, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
81 33 0.13
82 217 0.86
83 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (82 bp):
TCAGATAAACTTAAAAATTTTAGAGAGTCAGAGAATCTACACTATTCACGTCATTTGCTTTTCAT
TGACATTTCACATCAAC
Found at i:64791 original size:164 final size:164
Alignment explanation
Indices: 64520--64893 Score: 565
Period size: 164 Copynumber: 2.3 Consensus size: 164
64510 CATTTGCTTT
* * * * *
64520 TCAGATAAACTTAAAAATTTTAGAGAGACATAG-ATGTTACACTATTCATGTCATTTGCTTTTCA
1 TCAGATAAACTTAAAAATTTTAGAGAGTCAGAGAAT-CTACACTATTCACGTCATTTACTTTTCA
* * *
64584 TTGACATTTCACATCAACTCAGATAAAATGAAAATTTTTAGAGAGTCAGAGAGTCTATACTATTC
65 TTGACATTTCACATCAACTAAGATAAAATGAAAATTTTTAGAGAGTCAAAGAATCTATACTATTC
*
64649 ACGTCCTTTGCTTTTCATTGACATTTCATATTAAC
130 ACGTCCTTTGCTTTTCATTGACATTTCACATTAAC
* *
64684 TCAGATAAACTTAAAAAATTTATAGAGTCAGAGAATCTACACTATTCACGTCATTTACTTTTCAT
1 TCAGATAAACTTAAAAATTTTAGAGAGTCAGAGAATCTACACTATTCACGTCATTTACTTTTCAT
*
64749 TGACATTTCACATCAACTAAGATAAACTTGAAAA-TTTTAGAGAGTCAAAGAATCTATACTATTC
66 TGACATTTCACATCAACTAAGATAAA-ATGAAAATTTTTAGAGAGTCAAAGAATCTATACTATTC
64813 ACGTCCTTTGCTTTTCATTGACATTTCACATTAAC
130 ACGTCCTTTGCTTTTCATTGACATTTCACATTAAC
* * * *
64848 TCAGAT-AAGTTAAAATTTTTAGAGAGTCAGAAAATCTACATTATTC
1 TCAGATAAACTTAAAAATTTTAGAGAGTCAGAGAATCTACACTATTC
64894 TACCAAAATA
Statistics
Matches: 190, Mismatches: 18, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
163 34 0.18
164 148 0.78
165 8 0.04
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (164 bp):
TCAGATAAACTTAAAAATTTTAGAGAGTCAGAGAATCTACACTATTCACGTCATTTACTTTTCAT
TGACATTTCACATCAACTAAGATAAAATGAAAATTTTTAGAGAGTCAAAGAATCTATACTATTCA
CGTCCTTTGCTTTTCATTGACATTTCACATTAAC
Found at i:71787 original size:35 final size:35
Alignment explanation
Indices: 71733--71895 Score: 159
Period size: 35 Copynumber: 4.7 Consensus size: 35
71723 AATGACTGTA
* * *
71733 ACTGATGTGCATTATCTGAATACAACTCAAGACTC
1 ACTGTTGTGCATTATCTGAATGCAACTCATGACTC
* * *
71768 AATGTTGTGCATTAACTGAATGCGACT-ATTGACTC
1 ACTGTTGTGCATTATCTGAATGCAACTCA-TGACTC
*
71803 ACT-TCTGTGCATTATCTGAATGCACCTCATGACTC
1 ACTGT-TGTGCATTATCTGAATGCAACTCATGACTC
* * **
71838 ACTGTTGTGTACTATCTGAATGTGACTCATGACTC
1 ACTGTTGTGCATTATCTGAATGCAACTCATGACTC
** * *
71873 ACTACTGTGAATTATATGAATGC
1 ACTGTTGTGCATTATCTGAATGC
71896 GACTTATTGC
Statistics
Matches: 103, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
34 2 0.02
35 99 0.96
36 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (35 bp):
ACTGTTGTGCATTATCTGAATGCAACTCATGACTC
Found at i:71857 original size:70 final size:70
Alignment explanation
Indices: 71738--71895 Score: 201
Period size: 70 Copynumber: 2.3 Consensus size: 70
71728 CTGTAACTGA
* *
71738 TGTGCATTATCTGAATACAACTCAAGACTCAATGTTGTGCATTAACTGAATGCGACT-ATTGACT
1 TGTGCATTATCTGAATGCAACTCAAGACTCAATGTTGTGCACTAACTGAATGCGACTCA-TGACT
*
71802 CACTTC
65 CACTAC
* * * * * *
71808 TGTGCATTATCTGAATGCACCTCATGACTCACTGTTGTGTACTATCTGAATGTGACTCATGACTC
1 TGTGCATTATCTGAATGCAACTCAAGACTCAATGTTGTGCACTAACTGAATGCGACTCATGACTC
71873 ACTAC
66 ACTAC
* *
71878 TGTGAATTATATGAATGC
1 TGTGCATTATCTGAATGC
71896 GACTTATTGC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
70 75 0.99
71 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (70 bp):
TGTGCATTATCTGAATGCAACTCAAGACTCAATGTTGTGCACTAACTGAATGCGACTCATGACTC
ACTAC
Found at i:78581 original size:11 final size:11
Alignment explanation
Indices: 78550--78727 Score: 85
Period size: 11 Copynumber: 14.9 Consensus size: 11
78540 TATATAAACT
78550 TATTATCATTATA
1 TATTAT-ATT-TA
78563 TCATTATATTTA
1 T-ATTATATTTA
78575 TATTATATTATA
1 TATTATATT-TA
*
78587 TAATATATTTA
1 TATTATATTTA
*
78598 TATTGTATAGTATA
1 TA-T-TATA-TTTA
*
78612 GTATTATGTTT-
1 -TATTATATTTA
* *
78623 TTTTGATTATGTA
1 TATT-A-TATTTA
*
78636 TATGCGATA-TTA
1 TAT--TATATTTA
78648 TTATTATATAATTA
1 -TATTATAT--TTA
*
78662 TATTATACTTA
1 TATTATATTTA
78673 TA-TATATATT-
1 TATTATAT-TTA
78683 TATTATATTTA
1 TATTATATTTA
* *
78694 TAGTATATATA
1 TATTATATTTA
78705 TATTATATTTA
1 TATTATATTTA
78716 TTATTATCATTT
1 -TATTAT-ATTT
78728 TTGCTTTGTT
Statistics
Matches: 127, Mismatches: 18, Indels: 40
0.69 0.10 0.22
Matches are distributed among these distances:
10 11 0.09
11 46 0.36
12 26 0.20
13 29 0.23
14 13 0.10
15 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (11 bp):
TATTATATTTA
Found at i:78598 original size:18 final size:17
Alignment explanation
Indices: 78573--78611 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
78563 TCATTATATT
78573 TATATTATATTATATAA
1 TATATTATATTATATAA
* *
78590 TATATTTATATTGTATAG
1 TATA-TTATATTATATAA
78608 TATA
1 TATA
78612 GTATTATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TATATTATATTATATAA
Found at i:78687 original size:26 final size:26
Alignment explanation
Indices: 78658--78719 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
78648 TTATTATATA
*
78658 ATTATATTATACTTATATATATATT-T
1 ATTATATTATA-GTATATATATATTAT
78684 ATTATATTTATAGTATATATATATTAT
1 ATTATA-TTATAGTATATATATATTAT
78711 ATT-TATTAT
1 ATTATATTAT
78720 TATCATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 4 0.12
26 20 0.61
27 9 0.27
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
ATTATATTATAGTATATATATATTAT
Found at i:78691 original size:9 final size:9
Alignment explanation
Indices: 78662--78719 Score: 53
Period size: 9 Copynumber: 5.7 Consensus size: 9
78652 TATATAATTA
78662 TATTATACTT
1 TATTATA-TT
78672 ATATATATATT
1 -TAT-TATATT
78683 TATTATATT
1 TATTATATT
78692 TATAGTATATAT
1 TAT--TATAT-T
78704 ATATTATATT
1 -TATTATATT
78714 TATTAT
1 TATTAT
78720 TATCATTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
9 15 0.36
10 4 0.10
11 15 0.36
12 5 0.12
13 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (9 bp):
TATTATATT
Done.