Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008119.1 Hibiscus syriacus cultivar Beakdansim tig00110669_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: 56542
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1984 original size:21 final size:21
Alignment explanation
Indices: 1937--1993 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
1927 GGCAGTTTAA
*
1937 GGTGCTAACATGGCAATCCAC
1 GGTGCTAACATGACAATCCAC
* * * *
1958 GATGCTAGCATGACAGTCCAT
1 GGTGCTAACATGACAATCCAC
1979 GGTGCTGAA-ATGACA
1 GGTGCT-AACATGACA
1994 GTTTAGGGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (21 bp):
GGTGCTAACATGACAATCCAC
Found at i:2699 original size:2 final size:2
Alignment explanation
Indices: 2692--2720 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2682 ATATAAAATA
2692 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 A
2721 ATAAACTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3630 original size:20 final size:20
Alignment explanation
Indices: 3605--3649 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3595 AAAAAATAAA
*
3605 AAAAATGTAAAAATAAATTT
1 AAAAATGTAAAAATAAAGTT
3625 AAAAATGTAAAAATAAAGTT
1 AAAAATGTAAAAATAAAGTT
3645 AAAAA
1 AAAAA
3650 ATTACCTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
AAAAATGTAAAAATAAAGTT
Found at i:5504 original size:14 final size:15
Alignment explanation
Indices: 5480--5508 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5470 TGAAAAGTAG
5480 TTTAGATATTTAATA
1 TTTAGATATTTAATA
5495 TTTA-ATATTTAATA
1 TTTAGATATTTAATA
5509 AATTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTAGATATTTAATA
Found at i:7490 original size:2 final size:2
Alignment explanation
Indices: 7483--7524 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
7473 TCCATCAATA
7483 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
7525 GAATGATAAT
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:8229 original size:21 final size:21
Alignment explanation
Indices: 8204--8289 Score: 56
Period size: 23 Copynumber: 4.2 Consensus size: 21
8194 ATTGGATTTC
8204 TAAATTGATAATGTAGTGTTT
1 TAAATTGATAATGTAGTGTTT
* * * *
8225 TAAATTTACTTATCGTAATTTTT
1 TAAATTGA-TAAT-GTAGTGTTT
* *
8248 TAAATTCAT-A---AGTGTTC
1 TAAATTGATAATGTAGTGTTT
*
8265 TAAATTGACAATGTAGT-TTT
1 TAAATTGATAATGTAGTGTTT
8285 TAAAT
1 TAAAT
8290 CTAAAAATAT
Statistics
Matches: 48, Mismatches: 11, Indels: 13
0.67 0.15 0.18
Matches are distributed among these distances:
17 11 0.23
18 1 0.02
20 7 0.15
21 11 0.23
22 4 0.08
23 14 0.29
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.48
Consensus pattern (21 bp):
TAAATTGATAATGTAGTGTTT
Found at i:9173 original size:23 final size:22
Alignment explanation
Indices: 9127--9182 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
9117 AAATGGGAGG
9127 AAATTTAATTTTTTTAAAATAA
1 AAATTTAATTTTTTTAAAATAA
* * *
9149 AAATTTCATTTTTTTAGAATCA
1 AAATTTAATTTTTTTAAAATAA
9171 AAATCTTAATTT
1 AAAT-TTAATTT
9183 CATTTTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (22 bp):
AAATTTAATTTTTTTAAAATAA
Found at i:9352 original size:227 final size:226
Alignment explanation
Indices: 8951--9359 Score: 518
Period size: 227 Copynumber: 1.8 Consensus size: 226
8941 TCGAAATGTA
*
8951 AATTTTATTTTAGAATTTATGATTGAAATACTAATAATGATTTTTTAATTTTTTTAATAGAAACG
1 AATTTCATTTTAGAATTTATGATTGAAATACTAATAATGATTTTTTAATTTTTTTAATAGAAACG
* * *
9016 GAGGAGATAATATCAGTTATTCCTTCACATGGAAAATACCAAACTCAAACTACAAGATCATGATT
66 GAGGAGATAATATCAG-TATTCCTTCACATGAAAAATACCAAACACAAACAACAAGATCATGATT
** * * * **
9081 TTGTGGGATTAAATGATTATTCATGGAGTGGAACTCAAATGGGAGGAAATTTAATTTTTTTAAAA
130 TCCTAGAATTAAATGATCATTCATCAAGTGGAACTCAAATGGGAGGAAATTTAATTTTTTTAAAA
9146 TAAAAATTTCATTTTTTTAGAATCAAAATCTT
195 TAAAAATTTCATTTTTTTAGAATCAAAATCTT
* ** * *
9178 AATTTCATTTTAGAATTTGTGATTGAAATGTTAATAAT-TTTTTTTAATTTTTTT-ATAGAAATG
1 AATTTCATTTTAGAATTTATGATTGAAATACTAATAATGATTTTTTAATTTTTTTAATAGAAACG
* * * ** ** *
9241 GAGGAGATACTATTGACG-ATTCCTTCTCATGAAAAATATTAAACACAGGCAACAAGATCGTGAG
66 GAGGAGATAATA-TCA-GTATTCCTTCACATGAAAAATACCAAACACAAACAACAAGATCAT--G
* *
9305 ATTTCCTAGAATTAAATGATCATTCATCAAGTGGAGCTCAAATGGGAGGGAATTT
127 ATTTCCTAGAATTAAATGATCATTCATCAAGTGGAACTCAAATGGGAGGAAATTT
9360 GTTGACAAAT
Statistics
Matches: 152, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
225 53 0.35
226 17 0.11
227 82 0.54
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (226 bp):
AATTTCATTTTAGAATTTATGATTGAAATACTAATAATGATTTTTTAATTTTTTTAATAGAAACG
GAGGAGATAATATCAGTATTCCTTCACATGAAAAATACCAAACACAAACAACAAGATCATGATTT
CCTAGAATTAAATGATCATTCATCAAGTGGAACTCAAATGGGAGGAAATTTAATTTTTTTAAAAT
AAAAATTTCATTTTTTTAGAATCAAAATCTT
Found at i:10597 original size:2 final size:2
Alignment explanation
Indices: 10590--10637 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
10580 CCATCAAATA
10590 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
10632 AT AT AT
1 AT AT AT
10638 GAATGCTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12592 original size:40 final size:40
Alignment explanation
Indices: 12547--12627 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
12537 TGATAATGGT
*
12547 ATCATTGTACAATTGATAAAATATTTGTGTCGTCGCAGAA
1 ATCATTGTACAATTAATAAAATATTTGTGTCGTCGCAGAA
*
12587 ATCATTGTACAATTAATAAAATATTTGTGTTGTCGCAGAA
1 ATCATTGTACAATTAATAAAATATTTGTGTCGTCGCAGAA
12627 A
1 A
12628 AATAATCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (40 bp):
ATCATTGTACAATTAATAAAATATTTGTGTCGTCGCAGAA
Found at i:14816 original size:2 final size:2
Alignment explanation
Indices: 14804--14844 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
14794 TTTTATTCTG
*
14804 TA TA AA 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 TA T
14845 GGATCTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16496 original size:21 final size:21
Alignment explanation
Indices: 16482--16540 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
16472 GGCAGTTTAA
*
16482 GGTGCTAACATGGCAGTCTAC
1 GGTGCTAACATGACAGTCTAC
*
16503 GATGCTAACATGACAGTCTAC
1 GGTGCTAACATGACAGTCTAC
16524 GGTGCTGAA-ATGACAGT
1 GGTGCT-AACATGACAGT
16541 TTAGGGTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (21 bp):
GGTGCTAACATGACAGTCTAC
Found at i:22025 original size:2 final size:2
Alignment explanation
Indices: 22018--22053 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22008 ATCAAATAAA
22018 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
22054 GATGATATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22750 original size:21 final size:21
Alignment explanation
Indices: 22724--22809 Score: 56
Period size: 23 Copynumber: 4.2 Consensus size: 21
22714 ATTGGATTTC
22724 TAAATTGATAATGTAGTGTTT
1 TAAATTGATAATGTAGTGTTT
* * * *
22745 TAAATTTACTTATCGTAATTTTT
1 TAAATTGA-TAAT-GTAGTGTTT
* *
22768 TAAATTCAT-A---AGTGTTC
1 TAAATTGATAATGTAGTGTTT
*
22785 TAAATTGACAATGTAGT-TTT
1 TAAATTGATAATGTAGTGTTT
22805 TAAAT
1 TAAAT
22810 CTAAAAATAT
Statistics
Matches: 48, Mismatches: 11, Indels: 13
0.67 0.15 0.18
Matches are distributed among these distances:
17 11 0.23
18 1 0.02
20 7 0.15
21 11 0.23
22 4 0.08
23 14 0.29
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.48
Consensus pattern (21 bp):
TAAATTGATAATGTAGTGTTT
Found at i:23671 original size:23 final size:22
Alignment explanation
Indices: 23649--23691 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
23639 GGGAGGAAAT
23649 TTAATTTTTTTAAAATAAAAAA
1 TTAATTTTTTTAAAATAAAAAA
* * *
23671 TTCATTTTTTTAGAATCAAAA
1 TTAATTTTTTTAAAATAAAAA
23692 TCTAAATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAATTTTTTTAAAATAAAAAA
Found at i:25113 original size:2 final size:2
Alignment explanation
Indices: 25106--25159 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
25096 CCATCAAATA
25106 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
25148 AT AT AT AT AT AT
1 AT AT AT AT AT AT
25160 GAATGCTAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27092 original size:40 final size:40
Alignment explanation
Indices: 27047--27127 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
27037 TGATAATGGT
*
27047 ATCATTGTACAATTGATAAAATATTTGTGTCGTCGCAGAA
1 ATCATTGTACAATTAATAAAATATTTGTGTCGTCGCAGAA
* *
27087 ATCATTGTACAATTAATAAAATATTTGTGTTGTGGCAGAA
1 ATCATTGTACAATTAATAAAATATTTGTGTCGTCGCAGAA
27127 A
1 A
27128 AATAATCGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (40 bp):
ATCATTGTACAATTAATAAAATATTTGTGTCGTCGCAGAA
Found at i:28475 original size:29 final size:29
Alignment explanation
Indices: 28432--28514 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
28422 CTCACCTAAC
*
28432 TAAATTGATGTAAGCAGTGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
28462 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
28491 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
28515 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:33105 original size:29 final size:29
Alignment explanation
Indices: 33062--33144 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
33052 CTCACCTAAC
*
33062 TAAATTGATGTAAGCAGTGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
33092 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
33121 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
33145 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:34504 original size:2 final size:2
Alignment explanation
Indices: 34492--34528 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
34482 TTTTATTCTG
*
34492 TA TA AA 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 T
34529 TGGATCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:35134 original size:20 final size:21
Alignment explanation
Indices: 35109--35160 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
35099 TTTTCCCAAT
*
35109 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
35129 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
35150 TCGCAATGCGA
1 TCGCAATGCGA
35161 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:35173 original size:41 final size:41
Alignment explanation
Indices: 35146--35276 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
35136 GCGAATTGGG
*
35146 AAAATCGCAATGCGATACTGACTATCGCAATGCG---AT--
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* *
35182 ---ATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* * *
35220 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
35261 AAAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
35277 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
33 30 0.38
36 2 0.03
41 47 0.59
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
Found at i:35174 original size:20 final size:20
Alignment explanation
Indices: 35149--35256 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
35139 AATTGGGAAA
35149 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
35169 ATCGCAAT--G---C-GA-T
1 ATCGCAATGCGATACTGACT
*
35182 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
35202 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
35223 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
35243 TTCGCAACGCGATA
1 ATCGCAATGCGATA
35257 ATACAAAATC
Statistics
Matches: 69, Mismatches: 9, Indels: 20
0.70 0.09 0.20
Matches are distributed among these distances:
13 9 0.13
14 2 0.03
15 2 0.03
18 2 0.03
19 3 0.04
20 36 0.52
21 13 0.19
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:35186 original size:13 final size:13
Alignment explanation
Indices: 35168--35195 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35158 CGATACTGAC
35168 TATCGCAATGCGA
1 TATCGCAATGCGA
35181 TATCGCAATGCGA
1 TATCGCAATGCGA
35194 TA
1 TA
35196 CTTACTATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (13 bp):
TATCGCAATGCGA
Found at i:35191 original size:33 final size:33
Alignment explanation
Indices: 35149--35215 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
35139 AATTGGGAAA
35149 ATCGCAATGCGATACTGACTATCGCAATGCGAT
1 ATCGCAATGCGATACTGACTATCGCAATGCGAT
*
35182 ATCGCAATGCGATACTTACTATCGCAATGCGAT
1 ATCGCAATGCGATACTGACTATCGCAATGCGAT
35215 A
1 A
35216 ATACAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (33 bp):
ATCGCAATGCGATACTGACTATCGCAATGCGAT
Found at i:35228 original size:21 final size:21
Alignment explanation
Indices: 35202--35276 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
35192 GATACTTACT
*
35202 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* * *
35223 ATCGCAACGAGATACTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
*
35243 TTCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
*
35264 ATCGCAATGCGAT
1 ATCGCAACGCGAT
35277 TTTCAAAGCG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 24 0.59
22 2 0.05
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:35472 original size:22 final size:22
Alignment explanation
Indices: 35444--35487 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
35434 CACTCTCTCA
35444 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
35466 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
35488 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:35775 original size:20 final size:20
Alignment explanation
Indices: 35731--35794 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
35721 GCGATTTTAG
* *
35731 TTTCGCGTTGCAATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
35751 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
35771 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
35791 TTTC
1 TTTC
35795 AGAAACTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:35985 original size:25 final size:24
Alignment explanation
Indices: 35931--35985 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
35921 TGTTTATTAT
* *
35931 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
35955 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
35981 TGTTT
1 TGTTT
35986 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:37215 original size:21 final size:21
Alignment explanation
Indices: 37200--37259 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
37190 AGCAGTTTAA
* *
37200 GGTGCTAACATGGCAGTCCAC
1 GGTGCTAACATGACAGTTCAC
*
37221 GATGCTAACATGACAGTTCAC
1 GGTGCTAACATGACAGTTCAC
37242 GGTGCTGAA-ATGACAGTT
1 GGTGCT-AACATGACAGTT
37260 TAGGGTGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (21 bp):
GGTGCTAACATGACAGTTCAC
Found at i:37723 original size:15 final size:14
Alignment explanation
Indices: 37685--37726 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
37675 CTCTATTCAT
37685 TTTTTTAAATT-T-
1 TTTTTTAAATTATA
*
37697 TTTTTAAAATTATA
1 TTTTTTAAATTATA
37711 TTATTTTAAATTATA
1 TT-TTTTAAATTATA
37726 T
1 T
37727 ATATATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.40
13 1 0.04
14 2 0.08
15 12 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTAAATTATA
Found at i:37971 original size:2 final size:2
Alignment explanation
Indices: 37966--38006 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
37956 ATAAAAAAAA
37966 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
38007 ATAAACTGAG
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:42737 original size:2 final size:2
Alignment explanation
Indices: 42730--42779 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
42720 CCATCAAATA
42730 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
42772 AT AT AT AT
1 AT AT AT AT
42780 GAATGATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44425 original size:23 final size:22
Alignment explanation
Indices: 44379--44426 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
44369 AAATGGGAGG
44379 AAATTTAATTTTTTTAAAATAA
1 AAATTTAATTTTTTTAAAATAA
* * *
44401 AAATTTCATTTTTTTAGAATCA
1 AAATTTAATTTTTTTAAAATAA
44423 AAAT
1 AAAT
44427 CAAAATTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (22 bp):
AAATTTAATTTTTTTAAAATAA
Found at i:45946 original size:23 final size:22
Alignment explanation
Indices: 45908--45964 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
45898 AAATGGGAGG
45908 AAATTTAATTTTTTTAAAATAA
1 AAATTTAATTTTTTTAAAATAA
* * *
45930 AAATTTCATTTTTTTTAGAATCA
1 AAATTT-AATTTTTTTAAAATAA
45953 AAATCTTAATTT
1 AAAT-TTAATTT
45965 CATTTTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 6 0.21
23 21 0.72
24 2 0.07
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
AAATTTAATTTTTTTAAAATAA
Found at i:47368 original size:2 final size:2
Alignment explanation
Indices: 47361--47426 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
47351 CCATCAAATA
*
47361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47403 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
47427 GAATGCTAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Done.