Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001832.1 Hibiscus syriacus cultivar Beakdansim tig00003705_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: 57205
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:937 original size:20 final size:20
Alignment explanation
Indices: 908--945 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
898 TTTCAAAGGG
908 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
928 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
946 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:1025 original size:65 final size:64
Alignment explanation
Indices: 908--1111 Score: 218
Period size: 65 Copynumber: 3.2 Consensus size: 64
898 TTTCAAAGGG
* * *
908 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CAATGA-ATAAATTG-AACATCGAATGCAT
1 ATGCATCGATGCA-CAAGCCATGCATCGATGCACTC-AGGATAT-AA-TGAAACATCGAATGCAT
*
970 TTT
62 TTC
**
973 ATGCATCGATGCACATA-CCATGCATCGATGCACTCAGGATATAATGAAAACATTAAATGCATTT
1 ATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGATATAATG-AAACATCGAATGCATTT
*
1037 G
64 C
* ** * *
1038 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTCC
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGATATAATGAAACATCGAATGCATTTC
1102 ATGCATCGAT
1 ATGCATCGAT
1112 CACTCTTAGT
Statistics
Matches: 120, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 2 0.02
64 47 0.39
65 71 0.59
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGATATAATGAAACATCGAATGCATTTC
Found at i:6996 original size:23 final size:23
Alignment explanation
Indices: 6924--7000 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 23
6914 CCTAACAGTG
*
6924 CATCAATGCA-TCCTTGAATGTA
1 CATCGATGCACTCCTTGAATGTA
* * *
6946 CATCGAT--ACACCATGAAGGTA
1 CATCGATGCACTCCTTGAATGTA
* *
6967 CACCGATGCACTCCTTGAATGTG
1 CATCGATGCACTCCTTGAATGTA
6990 CATCGATGCAC
1 CATCGATGCAC
7001 AAGGCCATGC
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
20 1 0.02
21 15 0.36
22 6 0.14
23 20 0.48
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (23 bp):
CATCGATGCACTCCTTGAATGTA
Found at i:9774 original size:46 final size:44
Alignment explanation
Indices: 9715--9822 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 44
9705 ATGTACATAC
* * * *
9715 CATGCATCAATGCACTTAGG-ATTTAATGAAAATATCGAATGCATTT
1 CATGCATCGATGCACTCAGGCATTT--TG-AAACATCGAATGCACTT
*
9761 GATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTT
1 CATGCATCGATGCACTCAGGC-ATTTTGAAACATCGAATGCACTT
9806 CATGCATCGATGCACTC
1 CATGCATCGATGCACTC
9823 TTAGTGCACC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
45 31 0.57
46 19 0.35
48 4 0.07
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (44 bp):
CATGCATCGATGCACTCAGGCATTTTGAAACATCGAATGCACTT
Found at i:9820 original size:17 final size:19
Alignment explanation
Indices: 9792--9840 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
9782 TATTTTGAAA
9792 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
9810 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
9829 CACCGATGCACT
1 CATCGATGCACT
9841 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:18110 original size:24 final size:24
Alignment explanation
Indices: 18082--18157 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
18072 ATGTTTTATT
*
18082 TGATTTCCAATTTGAATTATGTTC
1 TGATTTCCAATCTGAATTATGTTC
** *
18106 TGATTTCTGATCTGAATTTTGTTC
1 TGATTTCCAATCTGAATTATGTTC
** * *
18130 TGATTTCTGATCTGGATTCTGTTC
1 TGATTTCCAATCTGAATTATGTTC
18154 TGAT
1 TGAT
18158 ATATGATATG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.51
Consensus pattern (24 bp):
TGATTTCCAATCTGAATTATGTTC
Found at i:18134 original size:48 final size:48
Alignment explanation
Indices: 18082--18183 Score: 114
Period size: 48 Copynumber: 2.1 Consensus size: 48
18072 ATGTTTTATT
* * * * *
18082 TGATTTCCAATTTGAATTATGTTCTGATTTCTGATCTGAATTTTGTTC
1 TGATTTCCAATCTGAATTATGTTCTGATATATGATATGAATTCTGTTC
** * * *
18130 TGATTTCTGATCTGGATTCTGTTCTGATATATGATATGAATTCTGTTT
1 TGATTTCCAATCTGAATTATGTTCTGATATATGATATGAATTCTGTTC
18178 TGATTT
1 TGATTT
18184 TTGATATCTC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.21, C:0.11, G:0.17, T:0.52
Consensus pattern (48 bp):
TGATTTCCAATCTGAATTATGTTCTGATATATGATATGAATTCTGTTC
Found at i:18164 original size:24 final size:24
Alignment explanation
Indices: 18094--18188 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
18084 ATTTCCAATT
*
18094 TGAATTATGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATC
*
18118 TGAATTTTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATC
* * * *
18142 TGGATTCTGTTCTGATATATGATA
1 TGAATTCTGTTCTGATTTCTGATC
* *
18166 TGAATTCTGTTTTGATTTTTGAT
1 TGAATTCTGTTCTGATTTCTGAT
18189 ATCTCCGTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:19602 original size:5 final size:5
Alignment explanation
Indices: 19594--19619 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19584 TTTTTTTATT
19594 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
19620 TTCTAAGTCA
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:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:20509 original size:44 final size:44
Alignment explanation
Indices: 20444--20735 Score: 199
Period size: 44 Copynumber: 6.7 Consensus size: 44
20434 TCAATTCTAT
*
20444 TTTTTTA-TCTTTATAA-TGAGACCCCTAATTTTTGTAATCTCAC
1 TTTTTTACT-TTTATAATTGAGACCCCTAATTTTTTTAATCTCAC
*
20487 TTTTTTACTTTTATAATTGAGACTCCTAATTTTTTTAATCTCAC
1 TTTTTTACTTTTATAATTGAGACCCCTAATTTTTTTAATCTCAC
* * * *
20531 -TTTTTACATTAATAATTGAGGCCCCTAACTTTTTTCAATCAT-AC
1 TTTTTTACTTTTATAATTGAGACCCCTAA-TTTTTTTAATC-TCAC
* * ** ** *
20575 -TTTTTAC-CTTATTGAGCGAGGTCCCTAATTTTTTTAATTTCTA-
1 TTTTTTACTTTTA-TAATTGAGACCCCTAATTTTTTTAATCTC-AC
* * * ** * *
20618 TTTCTAAC-TTTATAATTGAGATCTTTAATTATTTTTATTCTCAT
1 TTTTTTACTTTTATAATTGAGACCCCTAATT-TTTTTAATCTCAC
* * * * *
20662 TTTTTTACATTTATAATTGAGA-CTCTAATTTTTTAAATTTCGC
1 TTTTTTACTTTTATAATTGAGACCCCTAATTTTTTTAATCTCAC
* * **
20705 -CTTTTACTTTTATAATTTATCCCCCTAATTT
1 TTTTTTACTTTTATAATTGAGACCCCTAATTT
20736 AATCATTTCT
Statistics
Matches: 197, Mismatches: 40, Indels: 24
0.75 0.15 0.09
Matches are distributed among these distances:
42 17 0.09
43 78 0.40
44 88 0.45
45 14 0.07
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (44 bp):
TTTTTTACTTTTATAATTGAGACCCCTAATTTTTTTAATCTCAC
Found at i:31162 original size:20 final size:20
Alignment explanation
Indices: 31137--31189 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
31127 GACCAACAAA
31137 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
31157 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
31177 TTCGCAACGCGAA
1 TTCGCAACGCGAA
31190 TATGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:31201 original size:20 final size:20
Alignment explanation
Indices: 31178--31224 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
31168 GTTTCCAATT
31178 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
31198 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
31218 TCGCAAC
1 TCGCAAC
31225 ACAGAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:31243 original size:20 final size:19
Alignment explanation
Indices: 31218--31396 Score: 119
Period size: 20 Copynumber: 9.0 Consensus size: 19
31208 AATTTGTAAA
31218 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* * *
31238 TTGCAACGCGATAGTCAAAA
1 TCGCAACACGA-AGTCAAAT
*
31258 TCGCAACACAAAGTCAAAT
1 TCGCAACACGAAGTCAAAT
*
31277 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
* * *
31297 TTGCACCACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
**
31317 TCGCAATGCGAATTTGT-AAA-
1 TCGCAACACGAA---GTCAAAT
*
31337 TCGCAACACATAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
31357 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
* **
31377 TTGCAATGCGAAAGTCAAAT
1 TCGCAACACG-AAGTCAAAT
31397 GTTTTTACGC
Statistics
Matches: 123, Mismatches: 25, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
18 2 0.02
19 24 0.20
20 88 0.72
21 7 0.06
22 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:31244 original size:40 final size:39
Alignment explanation
Indices: 31198--31376 Score: 206
Period size: 40 Copynumber: 4.5 Consensus size: 39
31188 AATATGTAAA
*
31198 TCGCAACGCGAATTTGT-AAATCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAA-TAGTCAAATCGCAACACA-AAGTCAAAT
*
31238 TTGCAACGCG-ATAGTCAAAATCGCAACACAAAGTCAAAT
1 TCGCAACGCGAATAGTC-AAATCGCAACACAAAGTCAAAT
* *
31277 TCGCAACGCG-ATAGTCAAATTTGCACCACAAAAGTCAAAT
1 TCGCAACGCGAATAGTCAAA-TCGCAACAC-AAAGTCAAAT
* *
31317 TCGCAATGCGAATTTGT-AAATCGCAACACATAAGTCAAAT
1 TCGCAACGCGAA-TAGTCAAATCGCAACACA-AAGTCAAAT
31357 TCGCAACGCG-ATAGTCAAAT
1 TCGCAACGCGAATAGTCAAAT
31377 TTGCAATGCG
Statistics
Matches: 120, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
38 9 0.08
39 38 0.32
40 66 0.55
41 4 0.03
42 3 0.03
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (39 bp):
TCGCAACGCGAATAGTCAAATCGCAACACAAAGTCAAAT
Found at i:31392 original size:40 final size:39
Alignment explanation
Indices: 31218--31396 Score: 209
Period size: 40 Copynumber: 4.5 Consensus size: 39
31208 AATTTGTAAA
* *
31218 TCGCAACACAGAAGTCAAATTTGCAACGCGATAGTCAAAA
1 TCGCAACACA-AAGTCAAATTCGCAACGCGATAGTCAAAT
31258 TCGCAACACAAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAGTCAAATTCGCAACGCGATAGTCAAAT
* * * *
31297 TTGCACCACAAAAGTCAAATTCGCAATGCGAATTTGT-AAA-
1 TCGCAACAC-AAAGTCAAATTCGCAACGCG-A-TAGTCAAAT
31337 TCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACA-AAGTCAAATTCGCAACGCGATAGTCAAAT
* **
31377 TTGCAATGCGAAAGTCAAAT
1 TCGCAACAC-AAAGTCAAAT
31397 GTTTTTACGC
Statistics
Matches: 119, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
38 3 0.03
39 39 0.33
40 69 0.58
41 5 0.04
42 3 0.03
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (39 bp):
TCGCAACACAAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:31719 original size:2 final size:2
Alignment explanation
Indices: 31712--31741 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31702 GGTAATTTCA
31712 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
31742 TAACCATTTC
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:31940 original size:20 final size:19
Alignment explanation
Indices: 31906--31957 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
31896 AATCGTAACA
31906 CGATTTTAGTTTCGCGTTG
1 CGATTTTAGTTTCGCGTTG
*
31925 CGATTTTCATTTTCGCGTTG
1 CGATTTT-AGTTTCGCGTTG
*
31945 CGAATTTAAGTTT
1 CG-ATTTTAGTTT
31958 TCAGAAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.25
20 17 0.61
21 4 0.14
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.48
Consensus pattern (19 bp):
CGATTTTAGTTTCGCGTTG
Found at i:34122 original size:21 final size:20
Alignment explanation
Indices: 34096--34180 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 20
34086 TAAGCCCGAT
34096 GCACCTATCATCATTCAAGAG
1 GCACCT-TCATCATTCAAGAG
34117 GCACCTTCTATCATTCAAGAG
1 GCACCTTC-ATCATTCAAGAG
*
34138 GCCCCTCTCA-CAGTTCAAGAG
1 GCACCT-TCATCA-TTCAAGAG
* *
34159 GCCCCTGTCATCGTTCAAGAG
1 GCACCT-TCATCATTCAAGAG
34180 G
1 G
34181 TCCCACCCAC
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.07
21 50 0.88
22 3 0.05
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.24
Consensus pattern (20 bp):
GCACCTTCATCATTCAAGAG
Found at i:34176 original size:42 final size:42
Alignment explanation
Indices: 34109--34200 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
34099 CCTATCATCA
* *
34109 TTCAAGAGGCACCTTCTATCATTCAAGAGGCCCCTCTCACAG
1 TTCAAGAGGCACCTTCTATCATTCAAGAGGCCCCACCCACAG
* * * *
34151 TTCAAGAGGCCCCTGTC-ATCGTTCAAGAGGTCCCACCCACCG
1 TTCAAGAGGCACCT-TCTATCATTCAAGAGGCCCCACCCACAG
34193 TTCAAGAG
1 TTCAAGAG
34201 CCCAATTCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCACCTTCTATCATTCAAGAGGCCCCACCCACAG
Found at i:35646 original size:14 final size:14
Alignment explanation
Indices: 35600--35636 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
35590 TTTTGATTAA
35600 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
35614 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
35628 TTGATTTGT
1 TTGATTTGT
35637 TTAATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:35787 original size:20 final size:20
Alignment explanation
Indices: 35762--35813 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
35752 GTTGAAGGTA
35762 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
35782 CAAATTTGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
35802 CAAATTCGCAAC
1 CAAATTCGCAAC
35814 ACGATTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.17
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:36084 original size:38 final size:38
Alignment explanation
Indices: 36025--36110 Score: 127
Period size: 38 Copynumber: 2.2 Consensus size: 38
36015 TCAAGTTGTA
*
36025 GATTTTGATTTCCTTTCGCTTGGCACCATATGAGATTTG
1 GATTTTGA-TTCCTTTCGCTTGGCACCAAATGAGATTTG
* * *
36064 GATTTTGATTCCTTTTGCTTGGCACCAAATGGGCTTTG
1 GATTTTGATTCCTTTCGCTTGGCACCAAATGAGATTTG
36102 GATTTTGAT
1 GATTTTGAT
36111 GAGCATCAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 35 0.81
39 8 0.19
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.44
Consensus pattern (38 bp):
GATTTTGATTCCTTTCGCTTGGCACCAAATGAGATTTG
Found at i:36445 original size:19 final size:19
Alignment explanation
Indices: 36421--36458 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
36411 CGAAATTTAT
36421 ATTGAAATTCAAACTCAAA
1 ATTGAAATTCAAACTCAAA
* *
36440 ATTGAAATTTAAATTCAAA
1 ATTGAAATTCAAACTCAAA
36459 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTGAAATTCAAACTCAAA
Found at i:36875 original size:11 final size:12
Alignment explanation
Indices: 36842--36879 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 12
36832 AACATTATTT
36842 TTCCAAATAATG
1 TTCCAAATAATG
36854 TTCCCATAATAATG
1 TT-CCA-AATAATG
36868 TT-CAAATAATG
1 TTCCAAATAATG
36879 T
1 T
36880 ACAACGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 8 0.33
12 4 0.17
13 3 0.12
14 9 0.38
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (12 bp):
TTCCAAATAATG
Found at i:41526 original size:11 final size:13
Alignment explanation
Indices: 41494--41523 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
41484 TGGCCAAAGA
41494 TGAAAAGGTATGT
1 TGAAAAGGTATGT
41507 TGAAAAGGTATG-
1 TGAAAAGGTATGT
41519 TGAAA
1 TGAAA
41524 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:47522 original size:14 final size:15
Alignment explanation
Indices: 47497--47525 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
47487 CATGATATGA
47497 AAATGCAAAATGAAG
1 AAATGCAAAATGAAG
47512 AAATG-AAAATGAAG
1 AAATGCAAAATGAAG
47526 CATATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.03, G:0.21, T:0.14
Consensus pattern (15 bp):
AAATGCAAAATGAAG
Found at i:48141 original size:9 final size:9
Alignment explanation
Indices: 48127--48151 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
48117 AAAAGTTAGT
48127 AAAATAATA
1 AAAATAATA
48136 AAAATAATA
1 AAAATAATA
48145 AAAATAA
1 AAAATAA
48152 AATTAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAATA
Found at i:56837 original size:80 final size:80
Alignment explanation
Indices: 56631--57035 Score: 432
Period size: 80 Copynumber: 5.1 Consensus size: 80
56621 TTAAGCATTT
* * * * * * *
56631 ATCTTTTACTCAAAGGGAATTAACCTTTCATTTAACTGGCATGATTGACACATTT-TTTCAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCA-CAATGACACCTTTCTGTCAAATG
*
56695 CACAGCTAGGC-ATTA
65 CACAGCTAGACAATTA
* *
56710 ATCTTTTACTC-AAGGTATTT-ACCTTTCATCTAACTGTCACGATTGACACCTTTCTGTCAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCAC-AATGACACCTTTCTGTCAAATG
*
56773 CACAGGTAGACAATTA
65 CACAGCTAGACAATTA
56789 ATCGTTTTACTC-AAGGTATTTAACCTTTCATCTAACTGGCACAATGACACCTTTCTGTCAAATG
1 ATC-TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCACAATGACACCTTTCTGTCAAATG
*
56853 CACAGCTAGGCAATTA
65 CACAGCTAGACAATTA
* * * *
56869 AACTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTATGGCAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCACAA-TGACACCTTTCTGTCAAATG
* **
56934 CACAGTTAG-GGATTA
65 CACAGCTAGACAATTA
* * * * * ** * *
56949 ATCTTGTAATCGAATGTA-TTAACCTTTCATCTAACTGACATGATTATCATC-TTCTGTCAAATG
1 ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCACAATGA-CACCTTTCTGTCAAATG
*
57012 CTCAAG-TAGACAATTA
65 CAC-AGCTAGACAATTA
57028 ATCTTTTA
1 ATCTTTTA
57036 TTTTAAAATA
Statistics
Matches: 281, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
77 28 0.10
78 41 0.15
79 65 0.23
80 102 0.36
81 45 0.16
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (80 bp):
ATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCACAATGACACCTTTCTGTCAAATGC
ACAGCTAGACAATTA
Found at i:57004 original size:159 final size:157
Alignment explanation
Indices: 56649--57035 Score: 460
Period size: 159 Copynumber: 2.4 Consensus size: 157
56639 CTCAAAGGGA
* * *
56649 ATTAACCTTTCATTTAACTGGCATGATTGACACATTTTTTCAAATGCACAGCTAGGC-ATTAATC
1 ATTAACCTTTCATCTAACTGGCATGATT-ACACATTCTGTCAAATGCACAGCTAGGCAATTAATC
* * * *
56713 TTTTACTCAAGGTATTTACCTTTCATCTAACTGTCACGATTGACACCTTTCTGTCAAATGCACAG
65 TTTTACTCAAGGTATTTACCTTTCATCTAACTGGCACAATTGACACCTTTATGGCAAATGCACAG
* *
56778 GTAGACAATTAATCGTTTTACTCAAGGT
130 GTAGACAATTAATCGTTGTAATCAAGGT
** * * *
56806 ATTTAACCTTTCATCTAACTGGCACAATGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAAA
1 A-TTAACCTTTCATCTAACTGGCATGATTACA-CATTCTGTCAAATGCACAGCTAGGCAATTAAT
*
56871 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTATGGCAAATGCA
64 CTTTTACTC-AAGGTATTT-ACCTTTCATCTAACTGGCACAATTGACACCTTTATGGCAAATGCA
* ** *
56936 CAGTTAG-GGATTAATC-TTGTAATCGAATGT
127 CAGGTAGACAATTAATCGTTGTAATC-AAGGT
* * *
56966 ATTAACCTTTCATCTAACTGACATGATTATCATC-TTCTGTCAAATGCTCAAG-TAGACAATTAA
1 ATTAACCTTTCATCTAACTGGCATGATTA-CA-CATTCTGTCAAATGCAC-AGCTAGGCAATTAA
57029 TCTTTTA
63 TCTTTTA
57036 TTTTAAAATA
Statistics
Matches: 195, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
157 4 0.02
158 45 0.23
159 74 0.38
160 26 0.13
161 46 0.24
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (157 bp):
ATTAACCTTTCATCTAACTGGCATGATTACACATTCTGTCAAATGCACAGCTAGGCAATTAATCT
TTTACTCAAGGTATTTACCTTTCATCTAACTGGCACAATTGACACCTTTATGGCAAATGCACAGG
TAGACAATTAATCGTTGTAATCAAGGT
Done.