Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004544.1 Hibiscus syriacus cultivar Beakdansim tig00010079_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: 108976
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:333 original size:20 final size:20
Alignment explanation
Indices: 308--359 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
298 GGATGAATTA
308 GTATCCATATCGTAGATTGG
1 GTATCCATATCGTAGATTGG
328 GTATCCATATCGTAGATTGG
1 GTATCCATATCGTAGATTGG
348 GTATCCATATCG
1 GTATCCATATCG
360 AACGCTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (20 bp):
GTATCCATATCGTAGATTGG
Found at i:10671 original size:14 final size:14
Alignment explanation
Indices: 10662--10713 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
10652 GTGTTTAGGA
*
10662 TTTATGGTTTATGG
1 TTTAAGGTTTATGG
10676 TTTAAGGTTTATGG
1 TTTAAGGTTTATGG
* * *
10690 CTTAGGGCTTATGG
1 TTTAAGGTTTATGG
10704 TTTAAGGTTT
1 TTTAAGGTTT
10714 GGAATTTGGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.17, C:0.04, G:0.29, T:0.50
Consensus pattern (14 bp):
TTTAAGGTTTATGG
Found at i:10672 original size:7 final size:7
Alignment explanation
Indices: 10662--10713 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
10652 GTGTTTAGGA
10662 TTTATGG
1 TTTATGG
10669 TTTATGG
1 TTTATGG
*
10676 TTTAAGG
1 TTTATGG
10683 TTTATGG
1 TTTATGG
* *
10690 CTTAGGG
1 TTTATGG
*
10697 CTTATGG
1 TTTATGG
*
10704 TTTAAGG
1 TTTATGG
10711 TTT
1 TTT
10714 GGAATTTGGG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.17, C:0.04, G:0.29, T:0.50
Consensus pattern (7 bp):
TTTATGG
Found at i:10678 original size:21 final size:21
Alignment explanation
Indices: 10646--10713 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
10636 TCAGATTAAG
10646 GGTTTAGTGTTT-AGGATTTAT
1 GGTTTAGTGTTTAAGG-TTTAT
10667 GGTTTA-TGGTTTAAGGTTTAT
1 GGTTTAGT-GTTTAAGGTTTAT
* * * * *
10688 GGCTTAGGGCTTATGGTTTAA
1 GGTTTAGTGTTTAAGGTTTAT
10709 GGTTT
1 GGTTT
10714 GGAATTTGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 34 0.89
22 3 0.08
ACGTcount: A:0.18, C:0.03, G:0.31, T:0.49
Consensus pattern (21 bp):
GGTTTAGTGTTTAAGGTTTAT
Found at i:10686 original size:28 final size:28
Alignment explanation
Indices: 10646--10740 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
10636 TCAGATTAAG
*
10646 GGTTT-AGTGTTTAGGATTTATGGTTTAT
1 GGTTTAAG-GTTTAGGATTTAGGGTTTAT
* *
10674 GGTTTAAGGTTTATGG-CTTAGGGCTTAT
1 GGTTTAAGGTTTA-GGATTTAGGGTTTAT
* *
10702 GGTTTAAGGTTT-GGAATTTGGGGTTTAA
1 GGTTTAAGGTTTAGG-ATTTAGGGTTTAT
*
10730 GGTTTAGGGTT
1 GGTTTAAGGTT
10741 CATTGCAAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
26 2 0.04
28 49 0.89
29 4 0.07
ACGTcount: A:0.18, C:0.02, G:0.34, T:0.46
Consensus pattern (28 bp):
GGTTTAAGGTTTAGGATTTAGGGTTTAT
Found at i:10739 original size:14 final size:14
Alignment explanation
Indices: 10641--10740 Score: 53
Period size: 14 Copynumber: 7.1 Consensus size: 14
10631 CATAATCAGA
*
10641 TTAAGGGTTTAGTGT
1 TTAA-GGTTTAGGGT
*
10656 TT-AGGATTTATGGT
1 TTAAGG-TTTAGGGT
* *
10670 TTATGGTTTAAGGT
1 TTAAGGTTTAGGGT
* * *
10684 TTATGGCTTAGGGC
1 TTAAGGTTTAGGGT
* *
10698 TTATGGTTTAAGGT
1 TTAAGGTTTAGGGT
*
10712 TT--GGAATTTGGGGT
1 TTAAGG--TTTAGGGT
10726 TTAAGGTTTAGGGT
1 TTAAGGTTTAGGGT
10740 T
1 T
10741 CATTGCAAAG
Statistics
Matches: 66, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
12 2 0.03
13 2 0.03
14 56 0.85
15 4 0.06
16 2 0.03
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.46
Consensus pattern (14 bp):
TTAAGGTTTAGGGT
Found at i:11284 original size:16 final size:17
Alignment explanation
Indices: 11240--11278 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
11230 TGTTTCTGAG
11240 GGAATTGGAATTTGTGAA
1 GGAATTGGAATTTGT-AA
11258 GGAATTGGAATTTGT-A
1 GGAATTGGAATTTGTAA
11274 GGAAT
1 GGAAT
11279 CTGAATCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.29
18 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (17 bp):
GGAATTGGAATTTGTAA
Found at i:14702 original size:11 final size:11
Alignment explanation
Indices: 14686--14715 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
14676 AAATACTTTG
14686 TAAAATTATTT
1 TAAAATTATTT
14697 TAAAATTATTT
1 TAAAATTATTT
*
14708 TAAGATTA
1 TAAAATTA
14716 AAACTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:16888 original size:22 final size:23
Alignment explanation
Indices: 16835--16898 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
16825 TTGATTCCCT
16835 AAAGGAGGGAATCGGTTCCCATTC
1 AAAGG-GGGAATCGGTTCCCATTC
*
16859 AAAGGGGGAATCGGTTCCCCTTC
1 AAAGGGGGAATCGGTTCCCATTC
* *
16882 -AAGGGGGTATCGATTCC
1 AAAGGGGGAATCGGTTCC
16899 TCCTGTATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 15 0.41
23 17 0.46
24 5 0.14
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (23 bp):
AAAGGGGGAATCGGTTCCCATTC
Found at i:23823 original size:23 final size:23
Alignment explanation
Indices: 23793--23848 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
23783 TTCCCCTGTG
23793 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
23816 GGGGGAATCAGTTCCCCTTCAAG
1 GGGGGAATCGGTTCCCCTTCAAA
*
23839 GGGGGTATCG
1 GGGGGAATCG
23849 ATTTCCTCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.21
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:29119 original size:21 final size:21
Alignment explanation
Indices: 29094--29133 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29084 AAACCATTCA
29094 GGGGGAATCAGTACCCTCTTG
1 GGGGGAATCAGTACCCTCTTG
* *
29115 GGGGGAATCGGTTCCCTCT
1 GGGGGAATCAGTACCCTCT
29134 GAGCAATCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGAATCAGTACCCTCTTG
Found at i:29604 original size:31 final size:27
Alignment explanation
Indices: 29561--29632 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 27
29551 AACCCAACCC
* *
29561 GACCCGAACCCGAATTTCTTAAAAACAATCT
1 GACCCG-ACCCGAAATT-TTAAAAA-AA-AT
29592 GACCCGATCCCGAAATTTTAAAAAAAAT
1 GACCCGA-CCCGAAATTTTAAAAAAAAT
29620 GACCCGACCCGAA
1 GACCCGACCCGAA
29633 CCCAACCCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 6 0.16
28 8 0.21
29 2 0.05
30 8 0.21
31 14 0.37
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.18
Consensus pattern (27 bp):
GACCCGACCCGAAATTTTAAAAAAAAT
Found at i:32614 original size:18 final size:18
Alignment explanation
Indices: 32593--32637 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
32583 TTAAATCCGT
*
32593 ATAAGTTTAATTTTTAAA
1 ATAAGTTTAATTATTAAA
32611 ATAA-TATTAATTATTAAA
1 ATAAGT-TTAATTATTAAA
32629 A-AAGTTTAA
1 ATAAGTTTAA
32638 CATTTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
ATAAGTTTAATTATTAAA
Found at i:33584 original size:29 final size:29
Alignment explanation
Indices: 33542--33604 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
33532 ATAAACATAT
*
33542 ATTTCCTTATTGGTTCCAAACATCTACAG
1 ATTTTCTTATTGGTTCCAAACATCTACAG
33571 ATTTTCTTATTGGTTCCAAACATCTACAG
1 ATTTTCTTATTGGTTCCAAACATCTACAG
33600 ATTTT
1 ATTTT
33605 ATGTTGAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.43
Consensus pattern (29 bp):
ATTTTCTTATTGGTTCCAAACATCTACAG
Found at i:33964 original size:24 final size:24
Alignment explanation
Indices: 33937--34045 Score: 130
Period size: 24 Copynumber: 4.5 Consensus size: 24
33927 TATATAAAAA
* * *
33937 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
*
33961 ATCAAATCAGAATCCATGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* *
33985 ATCATATCAGAATCCATGTCAAGT
1 ATCAAATCAGAATCCAGGTCAAGT
* *
34009 ATCAAATCATAATCCAGGTCAAAT
1 ATCAAATCAGAATCCAGGTCAAGT
34033 ATCATAA-CAGAAT
1 ATCA-AATCAGAAT
34046 TCAAATCGGA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
24 72 0.97
25 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (24 bp):
ATCAAATCAGAATCCAGGTCAAGT
Found at i:34030 original size:48 final size:48
Alignment explanation
Indices: 33954--34045 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
33944 CATAATTCAG
* * *
33954 GTCAAGTATCAAATCAGAATCCATGTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAAATCAGAATCCAGGTCAAATATCATAACAGAATCCAT
*
34002 GTCAAGTATCAAATCATAATCCAGGTCAAATATCATAACAGAAT
1 GTCAAGTATCAAATCAGAATCCAGGTCAAATATCATAACAGAAT
34046 TCAAATCGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCAAATCAGAATCCAGGTCAAATATCATAACAGAATCCAT
Found at i:36432 original size:17 final size:18
Alignment explanation
Indices: 36412--36448 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
36402 CGGGTCAACG
36412 GGTTGGGTC-GGTC-GGTC
1 GGTT-GGTCGGGTCGGGTC
36429 GGTTGGTCGGGTCGGGTC
1 GGTTGGTCGGGTCGGGTC
36447 GG
1 GG
36449 ATCGGATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.00, C:0.16, G:0.57, T:0.27
Consensus pattern (18 bp):
GGTTGGTCGGGTCGGGTC
Found at i:36979 original size:20 final size:20
Alignment explanation
Indices: 36954--36999 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
36944 ACGACGAGTA
36954 GATCGGAGATCAAAGTCGTT
1 GATCGGAGATCAAAGTCGTT
36974 GATCGGAGATCAAAGTCGTT
1 GATCGGAGATCAAAGTCGTT
36994 GATCGG
1 GATCGG
37000 GGAGAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.24
Consensus pattern (20 bp):
GATCGGAGATCAAAGTCGTT
Found at i:43939 original size:4 final size:4
Alignment explanation
Indices: 43925--44314 Score: 750
Period size: 4 Copynumber: 98.2 Consensus size: 4
43915 CTATAACCAT
*
43925 ATAC A-AC ATAC ATAC ATTC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
43972 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44020 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44068 ATAC ATAC ATAC ATAC ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44114 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44162 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44210 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44258 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44306 ATAC ATAC A
1 ATAC ATAC A
44315 GGGGCAGATG
Statistics
Matches: 381, Mismatches: 2, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
2 2 0.01
3 3 0.01
4 376 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:44680 original size:13 final size:13
Alignment explanation
Indices: 44662--44688 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44652 TTTAAAGTCT
44662 AATGCATGTGGAC
1 AATGCATGTGGAC
44675 AATGCATGTGGAC
1 AATGCATGTGGAC
44688 A
1 A
44689 GAAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (13 bp):
AATGCATGTGGAC
Found at i:46724 original size:12 final size:12
Alignment explanation
Indices: 46707--46738 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
46697 CATCCCAAAC
46707 TCATCTTCGCCT
1 TCATCTTCGCCT
46719 TCATCTTCGCCT
1 TCATCTTCGCCT
46731 TCATCTTC
1 TCATCTTC
46739 AATCAAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.06, T:0.44
Consensus pattern (12 bp):
TCATCTTCGCCT
Found at i:50968 original size:3 final size:3
Alignment explanation
Indices: 50942--50995 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
50932 TCTATAAAAA
50942 TAT TA- TAT TA- TAT TATT TATT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT
50987 TAT T-T TAT T
1 TAT TAT TAT T
50996 TTTTATTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.13
3 34 0.72
4 7 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:51001 original size:12 final size:14
Alignment explanation
Indices: 50942--51004 Score: 71
Period size: 15 Copynumber: 4.6 Consensus size: 14
50932 TCTATAAAAA
*
50942 TATTATATTA-TAT
1 TATTATTTTATTAT
50955 TATT-TATTTATTAT
1 TATTAT-TTTATTAT
50969 TATTATTATTATTAT
1 TATTATT-TTATTAT
50984 TATTATTTTATT-T
1 TATTATTTTATTAT
50997 T-TTATTTT
1 TATTATTTT
51005 TTGTAGGCCT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
12 8 0.18
13 9 0.20
14 13 0.29
15 15 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:52506 original size:8 final size:9
Alignment explanation
Indices: 52478--52521 Score: 56
Period size: 8 Copynumber: 5.0 Consensus size: 9
52468 AATGTTCTTA
52478 ATTTTATTT
1 ATTTTATTT
*
52487 ATCTTTACTT
1 AT-TTTATTT
52497 A-TTTATTT
1 ATTTTATTT
52505 A-TTTATTT
1 ATTTTATTT
52513 ATTTTATTT
1 ATTTTATTT
52522 TTATTTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 15 0.48
9 9 0.29
10 7 0.23
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (9 bp):
ATTTTATTT
Found at i:52510 original size:12 final size:13
Alignment explanation
Indices: 52480--52560 Score: 67
Period size: 14 Copynumber: 6.0 Consensus size: 13
52470 TGTTCTTAAT
52480 TTTATTTATCTTTA
1 TTTATTTAT-TTTA
*
52494 CTTATTTA-TTTA
1 TTTATTTATTTTA
52506 TTTATTTATTTTA
1 TTTATTTATTTTA
52519 TTTTTATTTGATTTTA
1 --TTTATTT-ATTTTA
**
52535 TTCCTTT-TTTATA
1 TTTATTTATTT-TA
*
52548 TTTATATATTTTA
1 TTTATTTATTTTA
52561 CCATATAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
12 14 0.26
13 12 0.22
14 15 0.28
15 7 0.13
16 6 0.11
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:52532 original size:16 final size:15
Alignment explanation
Indices: 52480--52536 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
52470 TGTTCTTAAT
*
52480 TTTA-TTTATCTTTA
1 TTTATTTTATTTTTA
*
52494 CTTA-TTTATTTATTTA
1 TTTATTTTA-TT-TTTA
52510 TTTATTTTATTTTTA
1 TTTATTTTATTTTTA
52525 TTTGATTTTATT
1 TTT-ATTTTATT
52537 CCTTTTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 7 0.19
15 8 0.22
16 17 0.47
17 4 0.11
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTATTTTATTTTTA
Found at i:56609 original size:34 final size:34
Alignment explanation
Indices: 56566--56749 Score: 155
Period size: 34 Copynumber: 5.5 Consensus size: 34
56556 AAATTGGATT
56566 TCAACTTCACGACGAAGGATATCCAATTCAAAGC
1 TCAACTTCACGACGAAGGATATCCAATTCAAAGC
* * *
56600 TCAACTTCACGACGAAGGATATTCAAGTCAAGGC
1 TCAACTTCACGACGAAGGATATCCAATTCAAAGC
* ** * * *
56634 TCAACTTCACAACGAAGG--GGCC-ATCCACAGTT
1 TCAACTTCACGACGAAGGATATCCAATTCAAAG-C
* * ** * * *
56666 TCAACTTCACAATGAAGG--GGCC-ATCCACAGTT
1 TCAACTTCACGACGAAGGATATCCAATTCAAAG-C
56698 TCAACTTCACGACGAAGGATATCCAATTCAAAGC
1 TCAACTTCACGACGAAGGATATCCAATTCAAAGC
*
56732 TCAACTTCACGGCGAAGG
1 TCAACTTCACGACGAAGG
56750 GGGTCCCAAT
Statistics
Matches: 125, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
31 4 0.03
32 48 0.38
34 67 0.54
35 6 0.05
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (34 bp):
TCAACTTCACGACGAAGGATATCCAATTCAAAGC
Found at i:56675 original size:32 final size:32
Alignment explanation
Indices: 56634--56715 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
56624 AAGTCAAGGC
56634 TCAACTTCACAACGAAGGGGCCATCCACAGTT
1 TCAACTTCACAACGAAGGGGCCATCCACAGTT
*
56666 TCAACTTCACAATGAAGGGGCCATCCACAGTT
1 TCAACTTCACAACGAAGGGGCCATCCACAGTT
*
56698 TCAACTTCACGACGAAGG
1 TCAACTTCACAACGAAGG
56716 ATATCCAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.20
Consensus pattern (32 bp):
TCAACTTCACAACGAAGGGGCCATCCACAGTT
Found at i:62386 original size:12 final size:12
Alignment explanation
Indices: 62369--62393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62359 GTTGCATTAT
62369 CTACCACTGAAG
1 CTACCACTGAAG
62381 CTACCACTGAAG
1 CTACCACTGAAG
62393 C
1 C
62394 GGAATATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (12 bp):
CTACCACTGAAG
Found at i:66705 original size:124 final size:126
Alignment explanation
Indices: 66492--66851 Score: 498
Period size: 124 Copynumber: 2.9 Consensus size: 126
66482 CGACACCAAA
* *
66492 AACATTCATCTTTAGATTGGATTTTAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTC
1 AACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTC
* * *
66557 ACAACGAATGGGCCATCCACGGTTTCAATTTCACGACGAAGGGA-ATCGTGCTCACCAG-T
66 ACAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGATATCGTGCCCACAAGCT
* *
66616 AACATTCATCTTTAGATTGGGTTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTC
1 AACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTC
* *
66681 ACAACGAATGGGTCATCCACGGTTTCAACTTCAC-AGCGAA-AGATATCGTGCCCACAAGCT
66 ACAACGAATGGGCCATCCACGGTTTCAACTTCACGA-CGAAGGGATATCGTGCCCACAAGCT
* * * * * *
66741 -GCATCCACCTCTAGATTGGATTTCAATTTCACGACGAAGGATATCCAATTCAAGGTTCAACTTC
1 AACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTC
* * * *
66805 ACAATGAATGAGCCATCCACGATTTCAACTTCACGATGAA-GGATATC
66 ACAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGATATC
66852 CAATTCAAGG
Statistics
Matches: 209, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
123 3 0.01
124 204 0.98
125 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (126 bp):
AACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTC
ACAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAGGGATATCGTGCCCACAAGCT
Found at i:66806 original size:34 final size:34
Alignment explanation
Indices: 66762--66878 Score: 105
Period size: 34 Copynumber: 3.5 Consensus size: 34
66752 TAGATTGGAT
* *
66762 TTCAATTTCACGACGAAGGATATCCAATTCAAGG
1 TTCAACTTCACAACGAAGGATATCCAATTCAAGG
* * * * * *
66796 TTCAACTTCACAATGAATG--AGCC-ATCCACGAT
1 TTCAACTTCACAACGAAGGATATCCAATTCAAG-G
* *
66828 TTCAACTTCACGATGAAGGATATCCAATTCAAGG
1 TTCAACTTCACAACGAAGGATATCCAATTCAAGG
*
66862 CTCAACTTCACAACGAA
1 TTCAACTTCACAACGAA
66879 TGAGCCATCT
Statistics
Matches: 62, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
31 5 0.08
32 20 0.32
34 32 0.52
35 5 0.08
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (34 bp):
TTCAACTTCACAACGAAGGATATCCAATTCAAGG
Found at i:66834 original size:32 final size:32
Alignment explanation
Indices: 66796--66904 Score: 103
Period size: 32 Copynumber: 3.3 Consensus size: 32
66786 CAATTCAAGG
66796 TTCAACTTCACAATGAATGAGCCATCCACGAT
1 TTCAACTTCACAATGAATGAGCCATCCACGAT
* * * * * *
66828 TTCAACTTCACGATGAAGGATATCCAATTCAAG-G
1 TTCAACTTCACAATGAATG--AGCC-ATCCACGAT
* * *
66862 CTCAACTTCACAACGAATGAGCCATCTACGAT
1 TTCAACTTCACAATGAATGAGCCATCCACGAT
66894 TTCAACTTCAC
1 TTCAACTTCAC
66905 GACGAAGGAT
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
31 4 0.07
32 30 0.53
34 18 0.32
35 5 0.09
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.26
Consensus pattern (32 bp):
TTCAACTTCACAATGAATGAGCCATCCACGAT
Found at i:66867 original size:66 final size:66
Alignment explanation
Indices: 66759--66917 Score: 273
Period size: 66 Copynumber: 2.4 Consensus size: 66
66749 CTCTAGATTG
* * *
66759 GATTTCAATTTCACGACGAAGGATATCCAATTCAAGGTTCAACTTCACAATGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCA
66824 C
66 C
* *
66825 GATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCTA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCA
66890 C
66 C
66891 GATTTCAACTTCACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
66918 GTACCCAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 87 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (66 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCA
C
Found at i:68206 original size:328 final size:328
Alignment explanation
Indices: 67609--68268 Score: 1311
Period size: 328 Copynumber: 2.0 Consensus size: 328
67599 GTTCTCTCTC
67609 TTGGCCTTCTTTCTCTTCCTTCCATGGTTTCCACTTTCTAGTTTATAGCATCAAATGGCAATTCC
1 TTGGCCTTCTTTCTCTTCCTTCCATGGTTTCCACTTTCTAGTTTATAGCATCAAATGGCAATTCC
67674 ATTCCCACATTTAATTGGCGTTGGTCTCACGCTCTCTCGGGGGCTTAAATATCAAATCAACTTGG
66 ATTCCCACATTTAATTGGCGTTGGTCTCACGCTCTCTCGGGGGCTTAAATATCAAATCAACTTGG
67739 AGCCACTAGTGGGAAAAAAGATAGCCCTATTCCAATTTACTCTCTTCTGGTAACCTCATTTCATC
131 AGCCACTAGTGGGAAAAAAGATAGCCCTATTCCAATTTACTCTCTTCTGGTAACCTCATTTCATC
67804 GACAAGTATTAGTGCATGGCTGTCATAATCGAAGTAATCATACAAAACTCCTGGTTCTGTTAACA
196 GACAAGTATTAGTGCATGGCTGTCATAATCGAAGTAATCATACAAAACTCCTGGTTCTGTTAACA
67869 ATTACTCATCAGAAACTTGTCTTCAACCAGCTCCATCTTTCGACTCGGTTCAAAGTTGAGCATCT
261 ATTACTCATCAGAAACTTGTCTTCAACCAGCTCCATCTTTCGACTCGGTTCAAAGTTGAGCATCT
67934 TCG
326 TCG
*
67937 TTGGCCTTCTTTCTCTTCCTTCCATGGTTTCCACTTTCTAGTTTCTAGCATCAAATGGCAATTCC
1 TTGGCCTTCTTTCTCTTCCTTCCATGGTTTCCACTTTCTAGTTTATAGCATCAAATGGCAATTCC
68002 ATTCCCACATTTAATTGGCGTTGGTCTCACGCTCTCTCGGGGGCTTAAATATCAAATCAACTTGG
66 ATTCCCACATTTAATTGGCGTTGGTCTCACGCTCTCTCGGGGGCTTAAATATCAAATCAACTTGG
68067 AGCCACTAGTGGGAAAAAAGATAGCCCTATTCCAATTTACTCTCTTCTGGTAACCTCATTTCATC
131 AGCCACTAGTGGGAAAAAAGATAGCCCTATTCCAATTTACTCTCTTCTGGTAACCTCATTTCATC
68132 GACAAGTATTAGTGCATGGCTGTCATAATCGAAGTAATCATACAAAACTCCTGGTTCTGTTAACA
196 GACAAGTATTAGTGCATGGCTGTCATAATCGAAGTAATCATACAAAACTCCTGGTTCTGTTAACA
68197 ATTACTCATCAGAAACTTGTCTTCAACCAGCTCCATCTTTCGACTCGGTTCAAAGTTGAGCATCT
261 ATTACTCATCAGAAACTTGTCTTCAACCAGCTCCATCTTTCGACTCGGTTCAAAGTTGAGCATCT
68262 TCG
326 TCG
68265 TTGG
1 TTGG
68269 GCTGAAATCC
Statistics
Matches: 331, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
328 331 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (328 bp):
TTGGCCTTCTTTCTCTTCCTTCCATGGTTTCCACTTTCTAGTTTATAGCATCAAATGGCAATTCC
ATTCCCACATTTAATTGGCGTTGGTCTCACGCTCTCTCGGGGGCTTAAATATCAAATCAACTTGG
AGCCACTAGTGGGAAAAAAGATAGCCCTATTCCAATTTACTCTCTTCTGGTAACCTCATTTCATC
GACAAGTATTAGTGCATGGCTGTCATAATCGAAGTAATCATACAAAACTCCTGGTTCTGTTAACA
ATTACTCATCAGAAACTTGTCTTCAACCAGCTCCATCTTTCGACTCGGTTCAAAGTTGAGCATCT
TCG
Found at i:69274 original size:8 final size:9
Alignment explanation
Indices: 69249--69299 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
69239 GTTCTTAATG
69249 TTATTTATCT
1 TTATTTAT-T
*
69259 TTACTTA-T
1 TTATTTATT
69267 TTATTTA-T
1 TTATTTATT
69275 TTATTTTATT
1 TTA-TTTATT
69285 TTATTTTATT
1 TTA-TTTATT
69295 TTATT
1 TTATT
69300 CCTTTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
8 11 0.30
9 6 0.16
10 20 0.54
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTTATT
Found at i:69284 original size:5 final size:5
Alignment explanation
Indices: 69266--69299 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
69256 TCTTTACTTA
69266 TTTA- TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
69300 CCTTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:69306 original size:15 final size:15
Alignment explanation
Indices: 69266--69315 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
69256 TCTTTACTTA
69266 TTTATT-TA-TTTAT
1 TTTATTCTATTTTAT
*
69279 TTTATTTTATTTTAT
1 TTTATTCTATTTTAT
*
69294 TTTATTCCTTTTTTAT
1 TTTATT-CTATTTTAT
69310 ATTTAT
1 -TTTAT
69316 ATATTTCACC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 6 0.19
14 2 0.06
15 11 0.35
16 7 0.23
17 5 0.16
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTCTATTTTAT
Found at i:73413 original size:2 final size:2
Alignment explanation
Indices: 73406--73447 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
73396 TATGTTTAAA
73406 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
73448 GAAAATTTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75237 original size:6 final size:6
Alignment explanation
Indices: 75221--75278 Score: 107
Period size: 6 Copynumber: 9.7 Consensus size: 6
75211 AGGCTTTCGA
*
75221 GGCTAT AGCTAT GGCTAT GGCTAT GGCTAT GGCTAT GGCTAT GGCTAT
1 GGCTAT GGCTAT GGCTAT GGCTAT GGCTAT GGCTAT GGCTAT GGCTAT
75269 GGCTAT GGCT
1 GGCTAT GGCT
75279 GTGTATTGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
GGCTAT
Found at i:76059 original size:23 final size:22
Alignment explanation
Indices: 76014--76059 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
76004 TCAAATGATT
76014 TATAAATATATTTTATAAATAA
1 TATAAATATATTTTATAAATAA
76036 TATAAATATTTATTTT-TAAATAA
1 TATAAATA--TATTTTATAAATAA
76059 T
1 T
76060 CTAAGATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATAAATATATTTTATAAATAA
Found at i:76072 original size:24 final size:24
Alignment explanation
Indices: 76014--76072 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
76004 TCAAATGATT
76014 TATAAAT-A-TATTTTATAAATAA
1 TATAAATAATTATTTTATAAATAA
*
76036 TATAAATATTTATTTT-TAAATAA
1 TATAAATAATTATTTTATAAATAA
*
76059 TCTAAGATAATTAT
1 TATAA-ATAATTAT
76073 GAGAGAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 7 0.23
23 11 0.35
24 13 0.42
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TATAAATAATTATTTTATAAATAA
Found at i:76714 original size:6 final size:6
Alignment explanation
Indices: 76703--76733 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
76693 AGGCTTTCGA
*
76703 GGCTAT GGCTAT GGCTAT GGCTAT GGATAT G
1 GGCTAT GGCTAT GGCTAT GGCTAT GGCTAT G
76734 TATTGTGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.13, G:0.35, T:0.32
Consensus pattern (6 bp):
GGCTAT
Found at i:77098 original size:5 final size:5
Alignment explanation
Indices: 77088--77113 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
77078 AATGAACTAA
77088 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
77114 CATTACATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:77356 original size:24 final size:24
Alignment explanation
Indices: 77297--77343 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
77287 TCAAATGATT
77297 TATAAATATTT-TTTTATAAATAA
1 TATAAATATTTATTTTATAAATAA
77320 TATAAATATTTATTTT-TAAATAA
1 TATAAATATTTATTTTATAAATAA
77343 T
1 T
77344 CTAAGATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TATAAATATTTATTTTATAAATAA
Found at i:77647 original size:2 final size:2
Alignment explanation
Indices: 77642--77680 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
77632 TTTTTAAATT
77642 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
77681 TTGTTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:84674 original size:2 final size:2
Alignment explanation
Indices: 84669--84693 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
84659 AAAAAATAAA
84669 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
84694 ATTTAGTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:97252 original size:60 final size:59
Alignment explanation
Indices: 97147--97263 Score: 135
Period size: 60 Copynumber: 2.0 Consensus size: 59
97137 ATTTGAAATA
* * * *** * *
97147 ATGCCTTCAAGTTCTAGGGGAGGCATTCAACTGTGAGATTCTTCGACCTTAATGTCGGG
1 ATGCCTTCAAGTTCAAGGGAAGACATTCAACTACCAGATTCTTCGAACTAAATGTCGGG
* *
97206 ATGCCTTCAAGTTCAAAGGGAAGACATTCAACTACCAGCTTGTTCGAACTAAATGTCG
1 ATGCCTTCAAGTTC-AAGGGAAGACATTCAACTACCAGATTCTTCGAACTAAATGTCG
97264 ACATTGTGGA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 14 0.30
60 33 0.70
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (59 bp):
ATGCCTTCAAGTTCAAGGGAAGACATTCAACTACCAGATTCTTCGAACTAAATGTCGGG
Found at i:99666 original size:16 final size:17
Alignment explanation
Indices: 99632--99665 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
99622 ATACAATTCG
99632 AACATTTAAATAATAAA
1 AACATTTAAATAATAAA
99649 AACA-TTAAAT-ATAAA
1 AACATTTAAATAATAAA
99664 AA
1 AA
99666 ATATTGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 6 0.35
17 4 0.24
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
AACATTTAAATAATAAA
Found at i:100023 original size:21 final size:21
Alignment explanation
Indices: 99999--100042 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
99989 CAGTTGAAAT
*
99999 TTTTGAAAAAGGATTGATCCC
1 TTTTGAAAAAGGATCGATCCC
**
100020 TTTTGTTAAAGGATCGATCCC
1 TTTTGAAAAAGGATCGATCCC
100041 TT
1 TT
100043 GTGTTTTAAA
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:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (21 bp):
TTTTGAAAAAGGATCGATCCC
Found at i:100047 original size:21 final size:21
Alignment explanation
Indices: 100006--100047 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
99996 AATTTTTGAA
* *
100006 AAAGGATTGATCCCTTTTGTT
1 AAAGGATCGATCCCTTGTGTT
100027 AAAGGATCGATCCCTTGTGTT
1 AAAGGATCGATCCCTTGTGTT
100048 TTAAATGTTG
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:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (21 bp):
AAAGGATCGATCCCTTGTGTT
Found at i:101867 original size:23 final size:23
Alignment explanation
Indices: 101837--101934 Score: 119
Period size: 23 Copynumber: 4.3 Consensus size: 23
101827 TCAAGAGTTC
**
101837 TATGTGGTCCTTTGGGACAAAAT
1 TATGTGGTCCTTCAGGACAAAAT
*
101860 TATGTGGTCCTTTAGGACAAAAT
1 TATGTGGTCCTTCAGGACAAAAT
* *
101883 TATGTGGTCCTTCAAGACAAAACC
1 TATGTGGTCCTTCAGGACAAAA-T
*
101907 TATGTGGTCCTTCGGGAC--AAT
1 TATGTGGTCCTTCAGGACAAAAT
101928 TATGTGG
1 TATGTGG
101935 CACTTCGGTG
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.10
22 2 0.03
23 42 0.63
24 16 0.24
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (23 bp):
TATGTGGTCCTTCAGGACAAAAT
Found at i:103187 original size:21 final size:21
Alignment explanation
Indices: 103154--103195 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
103144 GGGGTCATAA
*
103154 AACCCTGCGGTGGTGGCATCT
1 AACCCAGCGGTGGTGGCATCT
*
103175 AACCCAGCTGTGGTGGCATCT
1 AACCCAGCGGTGGTGGCATCT
103196 GAAATGGTCG
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:0.17, C:0.29, G:0.31, T:0.24
Consensus pattern (21 bp):
AACCCAGCGGTGGTGGCATCT
Found at i:103231 original size:21 final size:21
Alignment explanation
Indices: 103181--103242 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
103171 ATCTAACCCA
* *
103181 GCTGTGGTGGCATCTGAAATG
1 GCTGTGGTGCCATCTGAAACG
* **
103202 G-TCGCGGTGTAATCTGAAACG
1 GCT-GTGGTGCCATCTGAAACG
103223 GCTGTGGTGCCATCTGAAAC
1 GCTGTGGTGCCATCTGAAAC
103243 TATTGCGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (21 bp):
GCTGTGGTGCCATCTGAAACG
Found at i:106720 original size:21 final size:21
Alignment explanation
Indices: 106694--106733 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
106684 CAAAAATTGG
106694 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
106715 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
106734 CATTAAGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Done.