Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000597.1 Hibiscus syriacus cultivar Beakdansim tig00001154_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: 75275
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:4206 original size:14 final size:15
Alignment explanation
Indices: 4187--4221 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
4177 ATAATTAAAA
*
4187 TAAATTGTA-AAATT
1 TAAATTGCATAAATT
4201 TAAATTGCATAAATT
1 TAAATTGCATAAATT
4216 TAAATT
1 TAAATT
4222 ACTGAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (15 bp):
TAAATTGCATAAATT
Found at i:17475 original size:34 final size:34
Alignment explanation
Indices: 17369--17483 Score: 139
Period size: 33 Copynumber: 3.5 Consensus size: 34
17359 GGGAGACAAA
* * *
17369 TTTTGTTTCGAGAAAAACAATCTCAAAGG---CT
1 TTTTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
* *
17400 TTGTGTTTCAAGAGAAACATTTTCAAAGGTTT-T
1 TTTTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
* *
17433 TTTTGTTTCAAGTGAAACAATTTCAGAGGTTTCT
1 TTTTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
17467 TTTTGTTTCAAGAGAAA
1 TTTTGTTTCAAGAGAAA
17484 ATTTTGTTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
31 24 0.34
33 29 0.41
34 17 0.24
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (34 bp):
TTTTGTTTCAAGAGAAACAATTTCAAAGGTTTCT
Found at i:17500 original size:16 final size:18
Alignment explanation
Indices: 17467--17501 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17457 AGAGGTTTCT
17467 TTTTGTTTCAAGAGAAAA
1 TTTTGTTTCAAGAGAAAA
17485 TTTTGTTTCAAGA-AAAA
1 TTTTGTTTCAAGAGAAAA
17502 CATATTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (18 bp):
TTTTGTTTCAAGAGAAAA
Found at i:17959 original size:102 final size:103
Alignment explanation
Indices: 17611--18026 Score: 656
Period size: 102 Copynumber: 4.0 Consensus size: 103
17601 AAAACATATT
* *
17611 CAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAA-ATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* * *
17676 CAACGTTCATGTTTCAAGAGAAAAACTGTCTCAATGGAGA
65 CAATGTTTATGTTTCAAGAG-AAAACTGTCTCAAGGGAGA
* * *
17716 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGAGAAATGTTTTC
1 CAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
*
17781 AATGTTTATGCTTCAAGAGAAAACTGTCTCAAGGGAGA
66 AATGTTTATGTTTCAAGAGAAAACTGTCTCAAGGGAGA
* * *
17819 CAAAATTTTGTTTCAAGAGAAACAGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAGTGTTTTT
1 CAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
*
17884 AATGTTTATGTTTCAAGAG-AAACTGTCTCAAAGGAGA
66 AATGTTTATGTTTCAAGAGAAAACTGTCTCAAGGGAGA
* * *
17921 CAAAATTTTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTCATTTCAAGGGAAGTGTTTTT
1 CAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
17986 AATGTTTATGTTTCAAGAG-AAACTGTCTCAAGGGAGA
66 AATGTTTATGTTTCAAGAGAAAACTGTCTCAAGGGAGA
18023 CAAA
1 CAAA
18027 GGTGAGCACG
Statistics
Matches: 293, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
102 120 0.41
103 95 0.32
104 74 0.25
105 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (103 bp):
CAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC
AATGTTTATGTTTCAAGAGAAAACTGTCTCAAGGGAGA
Found at i:17972 original size:205 final size:206
Alignment explanation
Indices: 17611--18027 Score: 669
Period size: 205 Copynumber: 2.0 Consensus size: 206
17601 AAAACATATT
*
17611 CAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* *
17676 CAACGTTCATGTTTCAAGAGAAAAACTGTCTCAATGGAGACAAAATTTTGTTTCAAGGGAAACTG
66 CAACGTTCATGTTTCAAGAG-AAAACTGTCTCAAAGGAGACAAAATTTTGTTTCAAGAGAAACTG
* *
17741 TCTCAAGAGAGACGAAATTCATTTCAAGAGAAATGTTTTCAATGTTTATGCTTCAAGAGAAAACT
130 TCTCAAAAGAGACAAAATTCATTTCAAGAGAAATGTTTTCAATGTTTATGCTTCAAGAG-AAACT
17806 GTCTCAAGGGAGA
194 GTCTCAAGGGAGA
*
17819 CAAA-ATTTTGTTTCAAGAGAAAC-AGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAGTGTTT
1 CAAAGATTTTGTTTCAAGAGAAACTA-TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTT
* * *
17882 TTAATGTTTATGTTTCAAGAG-AAACTGTCTCAAAGGAGACAAAATTTTGTTTCAAGAGAAACTG
65 TCAACGTTCATGTTTCAAGAGAAAACTGTCTCAAAGGAGACAAAATTTTGTTTCAAGAGAAACTG
* * * *
17946 TCTCAAAAGAGACAAAATTCATTTCAAGGGAAGTGTTTTTAATGTTTATGTTTCAAGAGAAACTG
130 TCTCAAAAGAGACAAAATTCATTTCAAGAGAAATGTTTTCAATGTTTATGCTTCAAGAGAAACTG
18011 TCTCAAGGGAGA
195 TCTCAAGGGAGA
18023 CAAAG
1 CAAAG
18028 GTGAGCACGA
Statistics
Matches: 194, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
204 22 0.11
205 94 0.48
206 1 0.01
207 73 0.38
208 4 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (206 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
CAACGTTCATGTTTCAAGAGAAAACTGTCTCAAAGGAGACAAAATTTTGTTTCAAGAGAAACTGT
CTCAAAAGAGACAAAATTCATTTCAAGAGAAATGTTTTCAATGTTTATGCTTCAAGAGAAACTGT
CTCAAGGGAGA
Found at i:18928 original size:22 final size:22
Alignment explanation
Indices: 18902--18952 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
18892 TTGTGTTTTG
18902 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
18924 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
18946 TCAAAGG
1 TCAAAGG
18953 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:19591 original size:27 final size:25
Alignment explanation
Indices: 19561--19647 Score: 81
Period size: 27 Copynumber: 3.4 Consensus size: 25
19551 TTTTGTCCCC
19561 TTTTCTTTTTGATCTTTGTTCTTTCTT
1 TTTTCTTTTTG-TCTTT-TTCTTTCTT
*
19588 TTTTC-TTTTGT-TTTTT-TTCCTT
1 TTTTCTTTTTGTCTTTTTCTTTCTT
* *
19610 TTTTGTTTTTTTCTTTTTTCTTTTCTT
1 TTTTCTTTTTGTC-TTTTTC-TTTCTT
19637 TTTTCCTTTTT
1 TTTT-CTTTTT
19648 TGCTTCTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 9 0.18
23 7 0.14
24 3 0.06
25 6 0.12
26 5 0.10
27 14 0.29
28 5 0.10
ACGTcount: A:0.01, C:0.14, G:0.05, T:0.80
Consensus pattern (25 bp):
TTTTCTTTTTGTCTTTTTCTTTCTT
Found at i:19611 original size:8 final size:7
Alignment explanation
Indices: 19582--19648 Score: 68
Period size: 7 Copynumber: 9.4 Consensus size: 7
19572 ATCTTTGTTC
19582 TTTCTTT
1 TTTCTTT
19589 TTTCTTT
1 TTTCTTT
19596 TGTT-TTT
1 T-TTCTTT
19603 TTTCCTTT
1 TTT-CTTT
*
19611 TTTGTTTT
1 TTT-CTTT
19619 TTTCTTT
1 TTTCTTT
19626 TTTC--T
1 TTTCTTT
19631 TTTCTTT
1 TTTCTTT
19638 TTTCCTTT
1 TTT-CTTT
19646 TTT
1 TTT
19649 GCTTCTTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
5 5 0.10
6 2 0.04
7 23 0.45
8 21 0.41
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (7 bp):
TTTCTTT
Found at i:19648 original size:15 final size:14
Alignment explanation
Indices: 19582--19648 Score: 68
Period size: 15 Copynumber: 4.7 Consensus size: 14
19572 ATCTTTGTTC
19582 TTTCTTTTTTCTTT
1 TTTCTTTTTTCTTT
19596 TGTT-TTTTTTCCTTT
1 T-TTCTTTTTT-CTTT
*
19611 TTTGTTTTTTTCTTT
1 TTT-CTTTTTTCTTT
19626 TTTC--TTTTCTTT
1 TTTCTTTTTTCTTT
19638 TTTCCTTTTTT
1 TTT-CTTTTTT
19649 GCTTCTTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
12 11 0.24
13 1 0.02
14 9 0.20
15 18 0.40
16 6 0.13
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (14 bp):
TTTCTTTTTTCTTT
Found at i:36876 original size:3 final size:3
Alignment explanation
Indices: 36870--36922 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
36860 TTTTTTTAAT
*
36870 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TATA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA
*
36917 ATA TTA
1 TTA TTA
36923 CAAAATCTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:38154 original size:15 final size:14
Alignment explanation
Indices: 38134--38193 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
38124 ATCCATTAGT
38134 TTTTAATATTATTA
1 TTTTAATATTATTA
* *
38148 CTTTTAATTTTTTTAA
1 -TTTTAATATTATT-A
*
38164 TTTTAATTATTGTTA
1 TTTTAA-TATTATTA
*
38179 TTTT-ATTTTATTA
1 TTTTAATATTATTA
38192 TT
1 TT
38194 ACGTTAGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
15 22 0.59
16 6 0.16
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTTAATATTATTA
Found at i:38268 original size:14 final size:15
Alignment explanation
Indices: 38251--38283 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38241 TATTATTAAG
38251 TTATATAA-ATATAT
1 TTATATAATATATAT
*
38265 TTATATAATATTTAT
1 TTATATAATATATAT
38280 TTAT
1 TTAT
38284 TTATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:43950 original size:24 final size:26
Alignment explanation
Indices: 43916--43963 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
43906 AAGCTTATAA
43916 AAAAATAAAATCT-TTA-TATTTTTTT
1 AAAAATAAAAT-TATTATTATTTTTTT
43941 AAAAAT-AAATTATTATTATTTTT
1 AAAAATAAAATTATTATTATTTTT
43964 AAATAACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.05
24 7 0.33
25 13 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
AAAAATAAAATTATTATTATTTTTTT
Found at i:44788 original size:16 final size:15
Alignment explanation
Indices: 44757--44785 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44747 TATATTTTAA
44757 ATTAATTTTGAAAAT
1 ATTAATTTTGAAAAT
44772 ATTAATTTTGAAAA
1 ATTAATTTTGAAAA
44786 ATAACATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (15 bp):
ATTAATTTTGAAAAT
Found at i:45040 original size:78 final size:77
Alignment explanation
Indices: 44935--45143 Score: 251
Period size: 78 Copynumber: 2.7 Consensus size: 77
44925 ACGTTATCGG
* * **
44935 TTTATAACAAATTAGTTACTCTTTGTTAATAGGCGTTAATATGGGTGATAGAAACAAATCGGTCA
1 TTTATAACAAATTGGTTACTCTCTGTTAATAACCGTTAATATGGGTGAT-GAAACAAATCGGTCA
*
45000 CTGAC-ACT-ATCAA
65 CTAACGA-TAAT-AA
* * * * * *
45013 TTTATAACAAATCGGTCACTATCTGTTAATAATCGTTAACAAGGGTGATGAAAACAAATCGGTCA
1 TTTATAACAAATTGGTTACTCTCTGTTAATAACCGTTAATATGGGTGATG-AAACAAATCGGTCA
45078 CTAACGATAATAA
65 CTAACGATAATAA
* *
45091 TTTATAACAAATTGGTTACTCTCTATTAATAACCGTTAATGTGGGTGATGAAA
1 TTTATAACAAATTGGTTACTCTCTGTTAATAACCGTTAATATGGGTGATGAAA
45144 TATTGATGTG
Statistics
Matches: 110, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
77 4 0.04
78 103 0.94
79 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (77 bp):
TTTATAACAAATTGGTTACTCTCTGTTAATAACCGTTAATATGGGTGATGAAACAAATCGGTCAC
TAACGATAATAA
Found at i:47687 original size:14 final size:13
Alignment explanation
Indices: 47655--47686 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
47645 ATAAATGACT
*
47655 AAAAATGAATTGA
1 AAAAAAGAATTGA
47668 AAAAAAGAATTGA
1 AAAAAAGAATTGA
47681 AAAAAA
1 AAAAAA
47687 ATAAACTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AAAAAAGAATTGA
Found at i:48702 original size:23 final size:22
Alignment explanation
Indices: 48647--48702 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
48637 AAATGAACAT
* *
48647 TAAACAAACATATTTGTGAATG
1 TAAACTAACATATTTGTGAACG
* *
48669 TTAACTAAACATGTTTGTGAACG
1 TAAACT-AACATATTTGTGAACG
48692 CTAAACTAACA
1 -TAAACTAACA
48703 AACACGAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.15
23 18 0.67
24 5 0.19
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (22 bp):
TAAACTAACATATTTGTGAACG
Found at i:48920 original size:21 final size:20
Alignment explanation
Indices: 48872--48922 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
48862 ATGTTAAAAT
48872 AATAATAAA-TTTTGATAAA
1 AATAATAAATTTTTGATAAA
** *
48891 TTTAA-AAATTATTTTATAAA
1 AATAATAAATT-TTTGATAAA
48911 AATAATAAATTT
1 AATAATAAATTT
48923 AAAGATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 12 0.50
21 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AATAATAAATTTTTGATAAA
Found at i:49645 original size:17 final size:18
Alignment explanation
Indices: 49608--49648 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
49598 ATATTATGTA
*
49608 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
49626 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
49643 TTTACT
1 TTTACT
49649 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:51351 original size:18 final size:18
Alignment explanation
Indices: 51328--51363 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51318 ACAGCAGCCA
*
51328 CCGCAGCCATTTATGATG
1 CCGCAGCCATATATGATG
51346 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
51364 TTGTTATCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:51900 original size:26 final size:24
Alignment explanation
Indices: 51829--51900 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
51819 TTATATTTGT
51829 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
51854 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
51876 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
51901 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:62136 original size:152 final size:152
Alignment explanation
Indices: 61839--62135 Score: 407
Period size: 152 Copynumber: 1.9 Consensus size: 152
61829 TTAAAATATC
* * *
61839 AGTTTCATTCATCTGCTTGATTGTTTTGGCACTAGCAACTGGTTCAAATGGTGGTCAATTTCCAT
1 AGTTTCATTCATATGCTTGATTGTTTTAGCACTAGCAACTGGTTCAAATGGTGGTCAATTCCCAT
* * **
61904 CTAATGGGGCCGAAACAGCAACGAGGCAGTATCAGGGATGAACCGAAGGGAAGTAGTTGAGACGG
66 CTAATGGGGCCAAAACAGCAACAAGGCAAAATCAGGGATGAACCGAAGGGAAGTAGTTGAGACGG
* *
61969 TTGCTGTCTAAAAAATACCCAG
131 TCGCTCTCTAAAAAATACCCAG
*
61991 AGTTTCATTCATATGCTTGATTGTTTTAGCACTAGCAACTGGTTCAAATGGTGGTGAATTCCCAT
1 AGTTTCATTCATATGCTTGATTGTTTTAGCACTAGCAACTGGTTCAAATGGTGGTCAATTCCCAT
* ** * * * * *
62056 CTAGTGGGGCCAAAATGGTAACCAAGGCAAAATCAGGGATGAATCGAGGGGAAGCT-GTTGGGCC
66 CTAATGGGGCCAAAACAGCAA-CAAGGCAAAATCAGGGATGAACCGAAGGGAAG-TAGTTGAGAC
62120 GGTCGCTCTCTAAAAA
129 GGTCGCTCTCTAAAAA
62136 TTTTAAATTC
Statistics
Matches: 125, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
152 77 0.62
153 47 0.38
154 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (152 bp):
AGTTTCATTCATATGCTTGATTGTTTTAGCACTAGCAACTGGTTCAAATGGTGGTCAATTCCCAT
CTAATGGGGCCAAAACAGCAACAAGGCAAAATCAGGGATGAACCGAAGGGAAGTAGTTGAGACGG
TCGCTCTCTAAAAAATACCCAG
Found at i:69641 original size:40 final size:40
Alignment explanation
Indices: 69581--69664 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
69571 CATATGACCA
* *
69581 ATGACTGGAGATGTGGGTGCTGACTCTCCCATTGAGCCAT
1 ATGAATGGAGATGTGAGTGCTGACTCTCCCATTGAGCCAT
69621 ATGAATGGAGATGTGAGTGCTGACTCTCCCATTGAGCCAT
1 ATGAATGGAGATGTGAGTGCTGACTCTCCCATTGAGCCAT
69661 ATGA
1 ATGA
69665 CGGATGGCTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
ATGAATGGAGATGTGAGTGCTGACTCTCCCATTGAGCCAT
Done.