Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003466.1 Hibiscus syriacus cultivar Beakdansim tig00007330_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: 80727
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1996 original size:24 final size:24
Alignment explanation
Indices: 1969--2014 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1959 ATATAAATGA
1969 GAACATAAATAAACGAACATAAGC
1 GAACATAAATAAACGAACATAAGC
* **
1993 GAACTTAAATAAATTAACATAA
1 GAACATAAATAAACGAACATAA
2015 TGAACAGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.59, C:0.13, G:0.09, T:0.20
Consensus pattern (24 bp):
GAACATAAATAAACGAACATAAGC
Found at i:3217 original size:22 final size:22
Alignment explanation
Indices: 3192--3257 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 22
3182 TGTGTTTATG
3192 TTTGGTCTTAAATCTTACATGA
1 TTTGGTCTTAAATCTTACATGA
* **
3214 TTT-GT-ATATGT-TCTA-ATG-
1 TTTGGTCTTAAATCT-TACATGA
*
3232 TTTGGTCTCAAATCTTACATGA
1 TTTGGTCTTAAATCTTACATGA
3254 TTTG
1 TTTG
3258 TATATGTTCT
Statistics
Matches: 31, Mismatches: 7, Indels: 12
0.62 0.14 0.24
Matches are distributed among these distances:
18 3 0.10
19 6 0.19
20 9 0.29
21 6 0.19
22 7 0.23
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (22 bp):
TTTGGTCTTAAATCTTACATGA
Found at i:3235 original size:40 final size:40
Alignment explanation
Indices: 3189--3274 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
3179 ATGTGTGTTT
*
3189 ATGTTTGGTCTTAAATCTTACATGATTTGTATATGTTCTA
1 ATGTTTGGTCTCAAATCTTACATGATTTGTATATGTTCTA
3229 ATGTTTGGTCTCAAATCTTACATGATTTGTATATGTTCTA
1 ATGTTTGGTCTCAAATCTTACATGATTTGTATATGTTCTA
3269 ATGTTT
1 ATGTTT
3275 TGGAGGGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.50
Consensus pattern (40 bp):
ATGTTTGGTCTCAAATCTTACATGATTTGTATATGTTCTA
Found at i:8146 original size:22 final size:23
Alignment explanation
Indices: 8102--8156 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
8092 GCAGCCTACC
*
8102 TTTGAATTC--TAAGCAGCCCCA
1 TTTGAATTCAATAAGCAACCCCA
8123 TTTGAATTCAATAA-CAACCCCA
1 TTTGAATTCAATAAGCAACCCCA
8145 TTTGAATTCAAT
1 TTTGAATTCAAT
8157 TTTAACAGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 9 0.29
22 19 0.61
23 3 0.10
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.33
Consensus pattern (23 bp):
TTTGAATTCAATAAGCAACCCCA
Found at i:26377 original size:18 final size:18
Alignment explanation
Indices: 26346--26382 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
26336 TCATTTATCT
26346 ATTTCTCATGTACTCTTA
1 ATTTCTCATGTACTCTTA
26364 ATTTC-CATGCTACTCTTA
1 ATTTCTCATG-TACTCTTA
26382 A
1 A
26383 AAGTCTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTTCTCATGTACTCTTA
Found at i:31703 original size:31 final size:31
Alignment explanation
Indices: 31633--31854 Score: 268
Period size: 31 Copynumber: 7.1 Consensus size: 31
31623 GAGTCGAGGG
* *
31633 TTACCTATG-TCTTAAGGACATATGAACATGA
1 TTACCTATGTTCTTCAGGACATATGGACA-GA
*
31664 TTTACCTATGTTCTTCAGGACATATGGACATA
1 -TTACCTATGTTCTTCAGGACATATGGACAGA
* *
31696 TTACCTATG-TCTTTCTGGATATATGGACAGGA
1 TTACCTATGTTC-TTCAGGACATATGGACA-GA
* * *
31728 TTACCTATGATCTTCGGGATATATGGACAGA
1 TTACCTATGTTCTTCAGGACATATGGACAGA
* *
31759 TTACCTATGTTCTTCGGGACATATAGACAGA
1 TTACCTATGTTCTTCAGGACATATGGACAGA
*
31790 TTACCTATGTTCTTCGGGACATATGGACAGA
1 TTACCTATGTTCTTCAGGACATATGGACAGA
* * *
31821 TTACTTATGTTCTTTAGGATATATGGACAGA
1 TTACCTATGTTCTTCAGGACATATGGACAGA
31852 TTA
1 TTA
31855 TTATACGAGT
Statistics
Matches: 171, Mismatches: 15, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
30 2 0.01
31 114 0.67
32 36 0.21
33 19 0.11
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCAGGACATATGGACAGA
Found at i:31732 original size:63 final size:62
Alignment explanation
Indices: 31633--31854 Score: 270
Period size: 63 Copynumber: 3.5 Consensus size: 62
31623 GAGTCGAGGG
* * * *
31633 TTACCTATGTC-TTAAGGACATATGAACATGATTTACCTATGTTCTTCAGGACATATGGACATA
1 TTACCTATGTCTTTCAGGACATATGGACA-GA-TTACCTATGTTCTTCGGGACATATGGACAGA
* * * *
31696 TTACCTATGTCTTTCTGGATATATGGACAGGATTACCTATGATCTTCGGGATATATGGACAGA
1 TTACCTATGTCTTTCAGGACATATGGACA-GATTACCTATGTTCTTCGGGACATATGGACAGA
* *
31759 TTACCTATGT-TCTTCGGGACATATAGACAGATTACCTATGTTCTTCGGGACATATGGACAGA
1 TTACCTATGTCT-TTCAGGACATATGGACAGATTACCTATGTTCTTCGGGACATATGGACAGA
* *
31821 TTACTTATGTTCTTT-AGGATATATGGACAGATTA
1 TTACCTATG-TCTTTCAGGACATATGGACAGATTA
31855 TTATACGAGT
Statistics
Matches: 137, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
62 56 0.41
63 65 0.47
64 16 0.12
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (62 bp):
TTACCTATGTCTTTCAGGACATATGGACAGATTACCTATGTTCTTCGGGACATATGGACAGA
Found at i:32539 original size:21 final size:21
Alignment explanation
Indices: 32515--32558 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
32505 TACGGAAGTT
*
32515 ACTGTAACAGTGCATCGGTAC
1 ACTGTAACAGTGCATCGATAC
**
32536 ACTGTAGTAGTGCATCGATAC
1 ACTGTAACAGTGCATCGATAC
32557 AC
1 AC
32559 AATTTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
ACTGTAACAGTGCATCGATAC
Found at i:32622 original size:19 final size:19
Alignment explanation
Indices: 32598--32646 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
32588 CTATTCATGG
*
32598 TACTGTTCATATCGTATAA
1 TACTGTTCATACCGTATAA
*
32617 TACTGTTCATACCGTATAG
1 TACTGTTCATACCGTATAA
*
32636 TATTGTTCATA
1 TACTGTTCATA
32647 AATTGTGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (19 bp):
TACTGTTCATACCGTATAA
Found at i:33441 original size:22 final size:22
Alignment explanation
Indices: 33416--33470 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
33406 GGCATATAAA
*
33416 ATTTGTCCTGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
33438 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
33460 ATTTGTCCCGA
1 ATTTGTCCCGA
33471 GGGACCGCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (22 bp):
ATTTGTCCCGAATGACCTATGT
Found at i:33556 original size:21 final size:19
Alignment explanation
Indices: 33531--33569 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
33521 CTCATATCAC
33531 ATAACATGTGCATTATCATTT
1 ATAACA-GTGCA-TATCATTT
*
33552 ATAACAGTTCATATCATT
1 ATAACAGTGCATATCATT
33570 GCTCTTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (19 bp):
ATAACAGTGCATATCATTT
Found at i:33769 original size:2 final size:2
Alignment explanation
Indices: 33764--33797 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
33754 ACATATATTC
33764 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
33798 CTTTGAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35506 original size:19 final size:18
Alignment explanation
Indices: 35482--35539 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
35472 TGACGACTGA
35482 TGCTTCTGGCCGTTGAAAT
1 TGCTTCTGGCCGTTG-AAT
** *
35501 TGCTTCTGGATGTTGACT
1 TGCTTCTGGCCGTTGAAT
*
35519 TGCTTTCTGGCCGTTGGAT
1 TGC-TTCTGGCCGTTGAAT
35538 TG
1 TG
35540 GGTCAGATCC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.41
Consensus pattern (18 bp):
TGCTTCTGGCCGTTGAAT
Found at i:35727 original size:15 final size:14
Alignment explanation
Indices: 35695--35723 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35685 AAAAAAAAAC
35695 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
35709 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
35723 A
1 A
35724 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:35894 original size:37 final size:37
Alignment explanation
Indices: 35767--36078 Score: 318
Period size: 38 Copynumber: 8.8 Consensus size: 37
35757 AATACATATA
* *
35767 TTTCAAAAATATTTTTTAAACTATATA-T-TAT-A--
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
35799 TTT-AAAAAAGTTTTCAAAACTATA--TTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
35832 TTTC-AAAATG-TTTT-AAA--A-ATATTATATAAGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* * *
35863 TTTAAAAAACGTTTTTAAAACTATATATTATATAATT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
*
35900 TATTCAAAAATGTTTTTAAAACTATATATTATATAATT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAAGT
35938 TATTCAAAAATGTTTTTAAAACTATATATTATATAAGT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* * *
35976 TTT-TAAAATGATTTTAAAACTATATGTTATATATA-T
1 TTTCAAAAATGTTTTTAAAACTATATATTATATA-AGT
* * *
36012 TTTCTAAAATGTTTTAAAAACTATATGTTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
36048 TTTCAAAAATATTTTAAAAAACTATATATTA
1 TTTCAAAAATGTTTT-TAAAACTATATATTA
36079 CCCATATTTT
Statistics
Matches: 241, Mismatches: 20, Indels: 33
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.00
29 1 0.00
30 7 0.03
31 30 0.12
32 11 0.05
33 12 0.05
34 3 0.01
35 1 0.00
36 46 0.19
37 57 0.24
38 72 0.30
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
Found at i:35916 original size:38 final size:36
Alignment explanation
Indices: 35752--36137 Score: 309
Period size: 38 Copynumber: 10.7 Consensus size: 36
35742 TAATATAAAT
* * * * *
35752 TATATAATACATATATTTCAAAAATATTTTTTAAAC
1 TATATATTATATATTTTTCAAAAATGTTTTTAAAAC
* *
35788 TATATA-T-TATA--TTT-AAAAAAGTTTTCAAAAC
1 TATATATTATATATTTTTCAAAAATGTTTTTAAAAC
* *
35819 --TATATTATATAGTTTTC-AAAATG-TTTTAAAAA
1 TATATATTATATATTTTTCAAAAATGTTTTTAAAAC
* * *
35851 TAT-TA-TATA-AGTTTTAAAAAACGTTTTTAAAAC
1 TATATATTATATATTTTTCAAAAATGTTTTTAAAAC
35884 TATATATTATATAATTTATTCAAAAATGTTTTTAAAAC
1 TATATATTATAT-ATTT-TTCAAAAATGTTTTTAAAAC
35922 TATATATTATATAATTTATTCAAAAATGTTTTTAAAAC
1 TATATATTATAT-ATTT-TTCAAAAATGTTTTTAAAAC
*
35960 TATATATTATATAAGTTTTT--AAAATGATTTTAAAAC
1 TATATATTATAT-A-TTTTTCAAAAATGTTTTTAAAAC
* * *
35996 TATATGTTATATATATTTTCTAAAATGTTTTAAAAAC
1 TATATATTATATAT-TTTTCAAAAATGTTTTTAAAAC
* * * *
36033 TATATGTTATATAGTTTTCAAAAATATTTTAAAAAAC
1 TATATATTATATATTTTTCAAAAATGTTTT-TAAAAC
*
36070 TATATATTACCCATA-TTTTC-AAAATGTTTTCTTTTTTAAAAAC
1 TATATATTA--TATATTTTTCAAAAATG------TTTTT-AAAAC
36113 TATATATTATATATATTTTCAAAAA
1 TATATATTATATAT-TTTTCAAAAA
36138 CCGTTTGCAA
Statistics
Matches: 293, Mismatches: 26, Indels: 54
0.79 0.07 0.14
Matches are distributed among these distances:
29 4 0.01
30 1 0.00
31 23 0.08
32 19 0.06
33 21 0.07
34 7 0.02
35 10 0.03
36 46 0.16
37 49 0.17
38 77 0.26
39 6 0.02
41 3 0.01
43 23 0.08
44 4 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
TATATATTATATATTTTTCAAAAATGTTTTTAAAAC
Found at i:36946 original size:165 final size:165
Alignment explanation
Indices: 36693--37512 Score: 1480
Period size: 165 Copynumber: 5.0 Consensus size: 165
36683 AGTTTTATTG
* * * * * * * * * *
36693 ACAGATAGCCCTTCTTGCATTGAGTTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAAT
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGTGTAAT
** *
36757 CGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
64 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
*
36822 GGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTC
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
36859 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
36924 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
36989 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
37024 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
37089 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
37154 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
37189 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
37254 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
37319 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
*
37354 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
37419 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
37484 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
37513 GGTGGCAGGT
Statistics
Matches: 638, Mismatches: 15, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
164 6 0.01
165 601 0.94
166 31 0.05
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (165 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
Found at i:42726 original size:2 final size:2
Alignment explanation
Indices: 42719--42759 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
42709 AATAATAATA
42719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42760 GAAAAACATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43801 original size:19 final size:18
Alignment explanation
Indices: 43777--43834 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
43767 TGACGACTGA
43777 TGCTTCTGGCCGTTGAAAT
1 TGCTTCTGGCCGTTG-AAT
** *
43796 TGCTTCTGGATGTTGACT
1 TGCTTCTGGCCGTTGAAT
*
43814 TGCTTTCTGGCCGTTGGAT
1 TGC-TTCTGGCCGTTGAAT
43833 TG
1 TG
43835 GGTCAGATCC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.41
Consensus pattern (18 bp):
TGCTTCTGGCCGTTGAAT
Found at i:44022 original size:15 final size:14
Alignment explanation
Indices: 43990--44018 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43980 AAAAAAAAAC
43990 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
44004 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
44018 A
1 A
44019 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:44208 original size:36 final size:35
Alignment explanation
Indices: 44062--44366 Score: 260
Period size: 38 Copynumber: 8.7 Consensus size: 35
44052 AATACATATA
* * *
44062 TTTCAAAAATATTTTTTAAACTATA-TAT-T-ATA
1 TTTCAAAAATGTTTTTAAAACTATATTATATAATT
* * *
44094 TTT-AAAAAAG-TTTTCAAACTATATTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATTATATAATT
*
44126 TTTC-AAAATG-TTTTAAAA--ATATTATATAAGT
1 TTTCAAAAATGTTTTTAAAACTATATTATATAATT
* *
44157 TTTAAAAAACGTTTTTAAAACTATATTATATAATT
1 TTTCAAAAATGTTTTTAAAACTATATTATATAATT
44192 TATTCAAAAATGTTTTTAAAACTATATATTATATAATT
1 T-TTCAAAAATGTTTTTAAAAC--TATATTATATAATT
44230 TATTCAAAAATGTTTTTAAAACTATATATTATATAAGTT
1 T-TTCAAAAATGTTTTTAAAAC--TATATTATATAA-TT
*
44269 TTT--AAAATGATTTTAAAACTATATGT-TATATATAT
1 TTTCAAAAATGTTTTTAAAACTATAT-TATATA-AT-T
* * *
44304 TTTCTAAAATGTTTTAAAAACTATATGT-TATATAGT
1 TTTCAAAAATGTTTTTAAAACTATAT-TATATA-ATT
* *
44340 TTTCAAAAATATTTTAAAAAACTATAT
1 TTTCAAAAATGTTTT-TAAAACTATAT
44367 ATTACCCATA
Statistics
Matches: 237, Mismatches: 18, Indels: 31
0.83 0.06 0.11
Matches are distributed among these distances:
30 21 0.09
31 14 0.06
32 25 0.11
33 8 0.03
34 10 0.04
35 19 0.08
36 47 0.20
37 38 0.16
38 52 0.22
39 3 0.01
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (35 bp):
TTTCAAAAATGTTTTTAAAACTATATTATATAATT
Found at i:44229 original size:38 final size:37
Alignment explanation
Indices: 44062--44370 Score: 275
Period size: 36 Copynumber: 8.8 Consensus size: 37
44052 AATACATATA
* *
44062 TTTCAAAAATATTTTTTAAACTATATA-T-TAT-A--
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
* * *
44094 TTT-AAAAAAG-TTTTCAAAC--TATATTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
*
44126 TTTC-AAAATG-TTTT-AAA--A-ATATTATATAAGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
* *
44157 TTTAAAAAACGTTTTTAAAAC--TATATTATATAATT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
44192 TATTCAAAAATGTTTTTAAAACTATATATTATATAATT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAATT
44230 TATTCAAAAATGTTTTTAAAACTATATATTATATAAGTT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAA-TT
* *
44269 TTT--AAAATGATTTTAAAACTATATGTTATAT-ATAT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAT-T
* * * *
44304 TTTCTAAAATGTTTTAAAAACTATATGTTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
* *
44340 TTTCAAAAATATTTTAAAAAACTATATATTA
1 TTTCAAAAATGTTTT-TAAAACTATATATTA
44371 CCCATATTTT
Statistics
Matches: 240, Mismatches: 17, Indels: 35
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.02
29 1 0.00
30 21 0.09
31 14 0.06
32 20 0.08
33 4 0.02
34 4 0.02
35 18 0.08
36 58 0.24
37 41 0.17
38 52 0.22
39 3 0.01
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
Found at i:46229 original size:21 final size:21
Alignment explanation
Indices: 46203--46279 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
46193 GACAATTCTG
*
46203 ATGGCACCTCAACCTTTTCAA
1 ATGGCACCACAACCTTTTCAA
* *
46224 ATGGCACCGCAACCATTTT-AT
1 ATGGCACCACAACC-TTTTCAA
*
46245 ATAGCACCACAA-CTATTTCAA
1 ATGGCACCACAACCT-TTTCAA
*
46266 ATGCCACCACAACC
1 ATGGCACCACAACC
46280 GATTCAGGCG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.02
20 4 0.09
21 35 0.78
22 5 0.11
ACGTcount: A:0.34, C:0.34, G:0.09, T:0.23
Consensus pattern (21 bp):
ATGGCACCACAACCTTTTCAA
Found at i:46285 original size:21 final size:21
Alignment explanation
Indices: 46261--46314 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
46251 CCACAACTAT
*
46261 TTCAAATGCCACCACAACCGA
1 TTCAGATGCCACCACAACCGA
** * *
46282 TTCAGGCGCCACCATAACCGG
1 TTCAGATGCCACCACAACCGA
46303 TTCAGATGCCAC
1 TTCAGATGCCAC
46315 TACCTCAGGG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17
Consensus pattern (21 bp):
TTCAGATGCCACCACAACCGA
Found at i:48162 original size:38 final size:38
Alignment explanation
Indices: 48120--48196 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
48110 ATGTAAACGT
48120 AAGTTTCTGAGGAAAAAAACCCAAGAATATGTATATTC
1 AAGTTTCTGAGGAAAAAAACCCAAGAATATGTATATTC
* * * *
48158 AAGTTTCTGAGGAAAAAAGCTCAAGAATTTGTATCTTC
1 AAGTTTCTGAGGAAAAAAACCCAAGAATATGTATATTC
48196 A
1 A
48197 CCTTCAACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.29
Consensus pattern (38 bp):
AAGTTTCTGAGGAAAAAAACCCAAGAATATGTATATTC
Found at i:58942 original size:29 final size:29
Alignment explanation
Indices: 58901--58965 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
58891 TGATTTTTAG
*
58901 ATGGGATTATAT-CTTAGTCCTAATTCTGC
1 ATGGGATTATATCCCTA-TCCTAATTCTGC
* *
58930 ATGGGATTGTATCCCTATCCTGATTCTGC
1 ATGGGATTATATCCCTATCCTAATTCTGC
58959 ATGGGAT
1 ATGGGAT
58966 CTTCTACGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (29 bp):
ATGGGATTATATCCCTATCCTAATTCTGC
Found at i:61816 original size:22 final size:23
Alignment explanation
Indices: 61768--61829 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
61758 CTTAAGGAGT
*
61768 GGTCCTTCGGGACATAGTAAATA
1 GGTCCTTTGGGACATAGTAAATA
**
61791 GGTCCTTTGGGACATA-TGCATA
1 GGTCCTTTGGGACATAGTAAATA
61813 GGTCCTTCT-GGACATAG
1 GGTCCTT-TGGGACATAG
61830 ATTTCACATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (23 bp):
GGTCCTTTGGGACATAGTAAATA
Found at i:68608 original size:83 final size:84
Alignment explanation
Indices: 68495--68693 Score: 251
Period size: 85 Copynumber: 2.4 Consensus size: 84
68485 TATCTTACCG
* * *
68495 TTATTTTTTAATGATAAATAAATAAAAAACATTGCAAGAAAAAGA-ATATAATTT-AAATTTGTT
1 TTATTTTTAAATGATAAATGAATAAAAAACATAGCAA-AAAAAGATATATAATTTAAAATTT-TT
* *
68558 -TTAAAACAATCATTTTATAA
64 ATAAAAACAATCACTTTATAA
* * *
68578 TTATTTTTAAATGATAAATGAATAACAAACATAGTAAAAAAATATTATATAATTTAAAATTTTTA
1 TTATTTTTAAATGATAAATGAATAAAAAACATAGCAAAAAAAGA-TATATAATTTAAAATTTTTA
* *
68643 TAAAAATAATTACTTTATAA
65 TAAAAACAATCACTTTATAA
*
68663 TTATTTTTAAATAATAAATGAATAAAAAACA
1 TTATTTTTAAATGATAAATGAATAAAAAACA
68694 CCGTAAGAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
82 6 0.06
83 32 0.32
84 11 0.11
85 51 0.51
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.39
Consensus pattern (84 bp):
TTATTTTTAAATGATAAATGAATAAAAAACATAGCAAAAAAAGATATATAATTTAAAATTTTTAT
AAAAACAATCACTTTATAA
Found at i:78669 original size:13 final size:13
Alignment explanation
Indices: 78641--78674 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
78631 TTTTCTTTAA
78641 TTTATTTTCAATT
1 TTTATTTTCAATT
78654 TTTAGTTTTCAATT
1 TTTA-TTTTCAATT
*
78668 TTCATTT
1 TTTATTT
78675 GTTATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (13 bp):
TTTATTTTCAATT
Done.