Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002427.1 Hibiscus syriacus cultivar Beakdansim tig00004965_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: 59058
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:2902 original size:20 final size:20
Alignment explanation
Indices: 2879--2920 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2869 TTTATTTTAA
2879 TTCTATTCAATTTAGTCGTG
1 TTCTATTCAATTTAGTCGTG
2899 TTCTATTCAATTTAGTCGTG
1 TTCTATTCAATTTAGTCGTG
2919 TT
1 TT
2921 GTGTCTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (20 bp):
TTCTATTCAATTTAGTCGTG
Found at i:3613 original size:40 final size:39
Alignment explanation
Indices: 3519--3614 Score: 104
Period size: 39 Copynumber: 2.4 Consensus size: 39
3509 TCACAAGCGT
* * * * * *
3519 CTTTGTTTGTCGCAACATGGAGATTCGAATCTAAAGTTC
1 CTTTGTTTGTCACAACACGAAGACTCGAATCTAAAATCC
3558 CTTTGATTT-TCACAACACGAAGACTCGAATCTAAAATCCC
1 CTTTG-TTTGTCACAACACGAAGACTCGAATCTAAAAT-CC
*
3598 CTTTGTTTGTTACAACA
1 CTTTGTTTGTCACAACA
3615 TGTTGATTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 31 0.66
40 16 0.34
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (39 bp):
CTTTGTTTGTCACAACACGAAGACTCGAATCTAAAATCC
Found at i:15528 original size:22 final size:22
Alignment explanation
Indices: 15513--15564 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
15503 AACACTACTG
15513 TGAACAGTAATAAACATTACCA
1 TGAACAGTAATAAACATTACCA
*
15535 TGAATAGTAATAAACATTACCA
1 TGAACAGTAATAAACATTACCA
15557 TGAACAGT
1 TGAACAGT
15565 GCTACAGTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (22 bp):
TGAACAGTAATAAACATTACCA
Found at i:16274 original size:23 final size:23
Alignment explanation
Indices: 16248--16292 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16238 ACTACGTTGC
*
16248 AATTTTAAGCGGCACTTCGGTGT
1 AATTCTAAGCGGCACTTCGGTGT
* *
16271 AATTCTACGTGGCACTTCGGTG
1 AATTCTAAGCGGCACTTCGGTG
16293 CATTTATACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (23 bp):
AATTCTAAGCGGCACTTCGGTGT
Found at i:16302 original size:23 final size:23
Alignment explanation
Indices: 16258--16302 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16248 AATTTTAAGC
* *
16258 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTCGGTGCAATTATACGT
*
16281 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
16303 AGCTATGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGT
Found at i:16947 original size:40 final size:40
Alignment explanation
Indices: 16871--16948 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
16861 TATTGTTCAT
* * * *
16871 TACTGTTCACACAGTATCGATATTATTCATACAATATTGG
1 TACTATTCACACAGTATCAATACTATTCATAAAATATTGG
*
16911 TACTATTCATACAGTA-CAATACTATTCATAAAAATATT
1 TACTATTCACACAGTATCAATACTATTCAT-AAAATATT
16949 TTTACCTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 11 0.34
40 21 0.66
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (40 bp):
TACTATTCACACAGTATCAATACTATTCATAAAATATTGG
Found at i:18142 original size:59 final size:59
Alignment explanation
Indices: 18071--18191 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
18061 GGAGGGTTGG
* *
18071 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTACGAGGGTTCAAATAAACAC
1 TTAGAGCCATATTATCGAGTTTGCCCTTACATTGCGACTACGAGGGTTCAAATAAACAC
* * * *
18130 TTAGAGCCATATTATCGAGTTTGCCCTTACATTGTGACTATGAGGGTTCGAATAGACAC
1 TTAGAGCCATATTATCGAGTTTGCCCTTACATTGCGACTACGAGGGTTCAAATAAACAC
18189 TTA
1 TTA
18192 TCCATCTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCCTTACATTGCGACTACGAGGGTTCAAATAAACAC
Found at i:18696 original size:82 final size:82
Alignment explanation
Indices: 18559--18726 Score: 318
Period size: 82 Copynumber: 2.0 Consensus size: 82
18549 TATGCGATGT
18559 TTTCCCTTATACTTCCTGCAAACAAAGTTGGCTCTTGATCCACCTTGGCTATTTGTTTTCTCAAC
1 TTTCCCTTATACTTCCTGCAAACAAAGTTGGCTCTTGATCCACCTTGGCTATTTGTTTTCTCAAC
18624 CATTTCAAGTTGAGCTC
66 CATTTCAAGTTGAGCTC
*
18641 TTTCCCTTATACTTCCTGCAAACAAAGTTGGCTCTTGATCCACCTTGGCTATTTGTTTTCTCAGC
1 TTTCCCTTATACTTCCTGCAAACAAAGTTGGCTCTTGATCCACCTTGGCTATTTGTTTTCTCAAC
*
18706 CATTTTAAGTTGAGCTC
66 CATTTCAAGTTGAGCTC
18723 TTTC
1 TTTC
18727 AAATCTATGC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (82 bp):
TTTCCCTTATACTTCCTGCAAACAAAGTTGGCTCTTGATCCACCTTGGCTATTTGTTTTCTCAAC
CATTTCAAGTTGAGCTC
Found at i:20083 original size:21 final size:21
Alignment explanation
Indices: 20053--20108 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
20043 TCTGGGCAAA
*
20053 GTGTATCGATGCACATTCAAT
1 GTGTACCGATGCACATTCAAT
20074 GTGTACCGATGCACATTCAAT
1 GTGTACCGATGCACATTCAAT
20095 GTGTACCGATGCAC
1 GTGTACCGATGCAC
20109 TCTTTAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (21 bp):
GTGTACCGATGCACATTCAAT
Found at i:21782 original size:23 final size:23
Alignment explanation
Indices: 21752--21832 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
21742 TTTTATATGA
*
21752 CACTTCGGTGCAATTCTACACGG
1 CACTTCGGTGCAATTCTACATGG
* * *
21775 CACTTCGGTACAATTCTACGTGA
1 CACTTCGGTGCAATTCTACATGG
* * *
21798 TATTTCGGTGTAATTCTACATGG
1 CACTTCGGTGCAATTCTACATGG
21821 CACTTCGGTGCA
1 CACTTCGGTGCA
21833 TTTATACGAA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACATGG
Found at i:41265 original size:41 final size:41
Alignment explanation
Indices: 41198--41283 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
41188 ATTTCACTTA
* * *
41198 CAAATTAAATTCTAGCTAAACTAAACCCAACATGTGCAAAC
1 CAAATAAAATTCTAACTAAACAAAACCCAACATGTGCAAAC
* *
41239 CAAATAAAATTCTAACTAATCAAAACCCTACATGTGCAAAC
1 CAAATAAAATTCTAACTAAACAAAACCCAACATGTGCAAAC
41280 CAAA
1 CAAA
41284 CAAGGAAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.49, C:0.24, G:0.06, T:0.21
Consensus pattern (41 bp):
CAAATAAAATTCTAACTAAACAAAACCCAACATGTGCAAAC
Found at i:50602 original size:13 final size:13
Alignment explanation
Indices: 50559--50602 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
50549 TAGTATTATA
*
50559 AAAATTAAAATAT
1 AAAATTTAAATAT
* *
50572 AAAACTTAAATTT
1 AAAATTTAAATAT
*
50585 CAAATTTAAATAT
1 AAAATTTAAATAT
50598 AAAAT
1 AAAAT
50603 AAATATTAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAATTTAAATAT
Found at i:52683 original size:2 final size:2
Alignment explanation
Indices: 52671--52716 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
52661 CTTTTCGTCC
* * *
52671 AT AT TT AT AT AT AT AT TT AT AT TT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52712 AT AT A
1 AT AT A
52717 GTTTGTAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
AT
Found at i:52826 original size:35 final size:34
Alignment explanation
Indices: 52703--53146 Score: 366
Period size: 35 Copynumber: 12.9 Consensus size: 34
52693 TTATATATAT
*
52703 ATATATATTATATAGTTTGT-AAACGATTTTTGAAA
1 ATATATATTATATAGTTTTTAAAAC-A-TTTTGAAA
*
52738 ATACATATATAATATGTAGTTTTTAAAATCATTTTGAAA
1 AT--ATATAT--TATATAGTTTTTAAAA-CATTTTGAAA
52777 ATATATATAATATATAGTTTTTAAAACATTTTGAAA
1 ATATATAT--TATATAGTTTTTAAAACATTTTGAAA
* *
52813 ACTATATATTATATAGGTTTTAAAATATTTTGAAA
1 A-TATATATTATATAGTTTTTAAAACATTTTGAAA
52848 ACTATATATTATATAGTTTTTAAAACATTTTAGAAA
1 A-TATATATTATATAGTTTTTAAAACATTTT-GAAA
*
52884 ATATATAATATATAGTTTTTAAAATCATTTTGAAA
1 ATATATATTATATAGTTTTTAAAA-CATTTTGAAA
* *
52919 ACT-TATAATATATAGTTTTGAAAACATTTTTGAAA
1 A-TATATATTATATAGTTTTTAAAACA-TTTTGAAA
* * *
52954 ATTTATA-AATATATGTTTTGAAAAC----T----
1 ATATATATTATATA-GTTTTTAAAACATTTTGAAA
*
52980 -T-TATATTATATAGTTTTAAAAACATTTTGAAA
1 ATATATATTATATAGTTTTTAAAACATTTTGAAA
*
53012 ATATATA-TATATAGTTTTTTTTAAAAACTTTTTTG-AA
1 ATATATATTATATAG---TTTTT-AAAAC-ATTTTGAAA
*
53049 A-ATATATTATATAG-TTTTAAAACGTTTTGAAA
1 ATATATATTATATAGTTTTTAAAACATTTTGAAA
* * * *
53081 ATACGAATAATATATAGTTTTAAAAACATTTTGGAAT
1 ATA--TATATTATATAGTTTTTAAAACATTTT-GAAA
* *
53118 TTATATATTATAT-GTTTTTGAAAATATTT
1 ATATATATTATATAGTTTTT-AAAACATTT
53147 ATATATATAT
Statistics
Matches: 347, Mismatches: 25, Indels: 74
0.78 0.06 0.17
Matches are distributed among these distances:
24 14 0.04
25 6 0.02
28 1 0.00
30 1 0.00
31 5 0.01
32 8 0.02
33 13 0.04
34 17 0.05
35 152 0.44
36 44 0.13
37 56 0.16
38 5 0.01
39 20 0.06
40 4 0.01
41 1 0.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (34 bp):
ATATATATTATATAGTTTTTAAAACATTTTGAAA
Found at i:52977 original size:164 final size:162
Alignment explanation
Indices: 52805--53155 Score: 439
Period size: 164 Copynumber: 2.1 Consensus size: 162
52795 TTTTAAAACA
*
52805 TTTTGAAAACTATATATTATATAGGTTTT-AAAATATTTTGAAAACTATATATTATATAG-TTTT
1 TTTTGAAAACTATATATTATATA-GTTTTAAAAACATTTTGAAAA-TATATA-TATATAGTTTTT
**
52868 T-AAAACATTTTAGAAAATATATAATATATAGTTTTTAAAATCATTTTG-AAA-ACTTATAATAT
63 TAAAAACATTTTAGAAAATATAT--TATATAG-TTTTAAAA-CATTTTGAAAATACGAATAATAT
*
52930 ATAGTTTTGAAAACATTTTTGAAAATTTATA-AATATATG-
124 ATAGTTTTAAAAACA-TTTTG-AAATTTATATAATATATGT
*
52969 TTTTGAAAACTTTATATTATATAGTTTTAAAAACATTTTGAAAATATATATATATAGTTTTTTTT
1 TTTTGAAAACTATATATTATATAGTTTTAAAAACATTTTGAAAATATATATATATAG--TTTTTT
* * *
53034 AAAAACTTTTTTGAAAATATATTATATAGTTTTAAAACGTTTTGAAAATACGAATAATATATAGT
64 AAAAACATTTTAGAAAATATATTATATAGTTTTAAAACATTTTGAAAATACGAATAATATATAGT
* *
53099 TTTAAAAACATTTTGGAATTTATATATTATATGT
129 TTTAAAAACATTTTGAAATTTATATAATATATGT
*
53133 TTTTGAAAA-TATTTATATATATA
1 TTTTGAAAACTATATAT-TATATA
53156 TATAATATAG
Statistics
Matches: 165, Mismatches: 12, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
162 21 0.13
163 39 0.24
164 81 0.49
165 5 0.03
166 19 0.12
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (162 bp):
TTTTGAAAACTATATATTATATAGTTTTAAAAACATTTTGAAAATATATATATATAGTTTTTTAA
AAACATTTTAGAAAATATATTATATAGTTTTAAAACATTTTGAAAATACGAATAATATATAGTTT
TAAAAACATTTTGAAATTTATATAATATATGT
Found at i:52982 original size:24 final size:24
Alignment explanation
Indices: 52946--53002 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
52936 TTGAAAACAT
52946 TTTTGAAAA-TTTATAA-ATATATG
1 TTTTGAAAACTTTATAATATATA-G
*
52969 TTTTGAAAACTTTATATTATATAG
1 TTTTGAAAACTTTATAATATATAG
*
52993 TTTTAAAAAC
1 TTTTGAAAAC
53003 ATTTTGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 9 0.30
24 16 0.53
25 5 0.17
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (24 bp):
TTTTGAAAACTTTATAATATATAG
Found at i:52987 original size:129 final size:125
Alignment explanation
Indices: 52840--53082 Score: 346
Period size: 129 Copynumber: 1.9 Consensus size: 125
52830 TTTTAAAATA
*
52840 TTTTGAAAACTATATATTATATAGTTTTTAAAACATTTTAGAAAATATATAATATATAG-TTTTT
1 TTTTGAAAACTATATATTATATAGTTTTAAAAACATTTT-GAAAATATAT-ATATATAGTTTTTT
* *
52904 AAAATC-ATTTTGAAAACTTATAATATATAGTTTTGAAAACATTTTTGAAAATTTATAAATATAT
64 AAAAACTATTTTGAAAA--TATAATATATAGTTTT-AAAAC-GTTTTGAAAATTTATAAATATAT
52968 G
125 G
*
52969 TTTTGAAAACTTTATATTATATAGTTTTAAAAACATTTTGAAAATATATATATATAGTTTTTTTT
1 TTTTGAAAACTATATATTATATAGTTTTAAAAACATTTTGAAAATATATATATATAG--TTTTTT
* *
53034 AAAAACTTTTTTGAAAATATATTATATAGTTTTAAAACGTTTTGAAAAT
64 AAAAACTATTTTGAAAATATAATATATAGTTTTAAAACGTTTTGAAAAT
53083 ACGAATAATA
Statistics
Matches: 104, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
127 18 0.17
128 15 0.14
129 52 0.50
130 10 0.10
131 9 0.09
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (125 bp):
TTTTGAAAACTATATATTATATAGTTTTAAAAACATTTTGAAAATATATATATATAGTTTTTTAA
AAACTATTTTGAAAATATAATATATAGTTTTAAAACGTTTTGAAAATTTATAAATATATG
Found at i:53009 original size:58 final size:57
Alignment explanation
Indices: 52911--53029 Score: 177
Period size: 58 Copynumber: 2.1 Consensus size: 57
52901 TTTAAAATCA
* *
52911 TTTTGAAAACTTATAATATATAGTTTTGAAAACATTTTTGAAAATTTATAAATATATG
1 TTTTGAAAACTTATAATATATAGTTTTAAAAACATTTTTGAAAATATATAAATATA-G
* *
52969 TTTTGAAAACTTTATATTATATAGTTTTAAAAACA-TTTTGAAAATATATATATATAG
1 TTTTGAAAAC-TTATAATATATAGTTTTAAAAACATTTTTGAAAATATATAAATATAG
53026 TTTT
1 TTTT
53030 TTTTAAAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
57 5 0.09
58 29 0.52
59 22 0.39
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (57 bp):
TTTTGAAAACTTATAATATATAGTTTTAAAAACATTTTTGAAAATATATAAATATAG
Found at i:53046 original size:38 final size:36
Alignment explanation
Indices: 52993--53066 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 36
52983 TATTATATAG
52993 TTTTAAAAACATTTTGAAAATATATATATATAGTTTT
1 TTTTAAAAACATTTTGAAAATATAT-TATATAGTTTT
*
53030 TTTTAAAAACTTTTTTGAAAATATATTATATAGTTTT
1 TTTTAAAAAC-ATTTTGAAAATATATTATATAGTTTT
53067 AAAACGTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 21 0.60
38 14 0.40
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (36 bp):
TTTTAAAAACATTTTGAAAATATATTATATAGTTTT
Found at i:53186 original size:12 final size:13
Alignment explanation
Indices: 53166--53227 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 13
53156 TATAATATAG
*
53166 TATTATTATTT-T
1 TATTTTTATTTAT
53178 TATTTTTATTTAT
1 TATTTTTATTTAT
*
53191 T-TATTTATTTAT
1 TATTTTTATTTAT
53203 T-TATTTTA-TTAT
1 TAT-TTTTATTTAT
*
53215 TATTATTATTTAT
1 TATTTTTATTTAT
53228 GTTTTTTTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 31 0.74
13 11 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTTTATTTAT
Found at i:53191 original size:4 final size:4
Alignment explanation
Indices: 53182--53227 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
53172 TATTTTTATT
53182 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TATTA -TTA -TTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA
53227 T
1 T
53228 GTTTTTTTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 10 0.26
4 29 0.74
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:53192 original size:16 final size:16
Alignment explanation
Indices: 53171--53232 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
53161 TATAGTATTA
53171 TTATTTTTATTTTTAT
1 TTATTTTTATTTTTAT
*
53187 TTATTTATT-TATTTAT
1 TTATTT-TTATTTTTAT
*
53203 TTA-TTTTATTATTA-
1 TTATTTTTATTTTTAT
53217 TTATTATTTATGTTTT
1 TTATT-TTTAT-TTTT
53233 TTTGCAGGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 5 0.14
15 7 0.19
16 20 0.54
17 5 0.14
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
TTATTTTTATTTTTAT
Found at i:54506 original size:2 final size:2
Alignment explanation
Indices: 54499--54528 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54489 GATTACATTC
54499 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
54529 GTGTATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54584 original size:27 final size:26
Alignment explanation
Indices: 54554--54609 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 26
54544 TAGTTTATTA
54554 TTTTGATTT-TTGATTT-TTGATTTTAGT
1 TTTTGATTTATT-ATTTATT-ATTTTA-T
*
54581 TTTTTATTTATTATTTATTATTTTAT
1 TTTTGATTTATTATTTATTATTTTAT
54607 TTT
1 TTT
54610 GTATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.15
27 18 0.69
28 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (26 bp):
TTTTGATTTATTATTTATTATTTTAT
Found at i:54654 original size:2 final size:2
Alignment explanation
Indices: 54647--54681 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
54637 TGTTTGTTTC
54647 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54682 CTACTTACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:56855 original size:16 final size:17
Alignment explanation
Indices: 56823--56855 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56813 GAACCAGGAG
56823 TCCTTGGTCAAGATCAAA
1 TCCTTGGTC-AGATCAAA
56841 TCCTTGGTC-GATCAA
1 TCCTTGGTCAGATCAA
56856 TTGTGGCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (17 bp):
TCCTTGGTCAGATCAAA
Found at i:58753 original size:2 final size:2
Alignment explanation
Indices: 58746--58773 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58736 CACATTAAAT
58746 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
58774 CAATAAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58928 original size:92 final size:90
Alignment explanation
Indices: 58766--59009 Score: 286
Period size: 92 Copynumber: 2.7 Consensus size: 90
58756 TATATATATA
* * *
58766 TATATATACAATAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCCGGCTTTATGGATAA
1 TATATATACAATAAGCTTAAGATGTCCCTCT-AAGAAATTGGTTAAACCCCGGCTTTATGGATAA
58831 GATTCAGCTAGCCTGATAAAGGTGAT
65 GATTCAGCTAGCCTGATAAAGGTGAT
*
58857 TATAGTATACAATAAAGCTTAAGTTGT-CCTCT-AGAAATTGGTTAAACACCCCGGCTTTATGGA
1 TATA-TATACAAT-AAGCTTAAGATGTCCCTCTAAGAAATTGGTT-AA-ACCCCGGCTTTATGGA
*
58920 TAATATTCAGCTAGCCTGATAAAGGTGAT
62 TAAGATTCAGCTAGCCTGATAAAGGTGAT
* * *
58949 TATA-ATACAACGT-A--TTGAGATG-CCCTCTAGAGCAATTGGTTAAATGCCCGGCTTTATGGA
1 TATATATACAA--TAAGCTTAAGATGTCCCTCTA-AGAAATTGGTTAAA-CCCCGGCTTTATGGA
59009 T
62 T
59010 CCAGCTAGCC
Statistics
Matches: 134, Mismatches: 9, Indels: 22
0.81 0.05 0.13
Matches are distributed among these distances:
88 12 0.09
89 17 0.13
90 27 0.20
91 6 0.04
92 61 0.46
93 11 0.08
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (90 bp):
TATATATACAATAAGCTTAAGATGTCCCTCTAAGAAATTGGTTAAACCCCGGCTTTATGGATAAG
ATTCAGCTAGCCTGATAAAGGTGAT
Done.