Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008537.1 Hibiscus syriacus cultivar Beakdansim tig00111424_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: 80980
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Found at i:666 original size:27 final size:26
Alignment explanation
Indices: 616--668 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
606 TTTGAGGATT
616 ATGAAAAAAAAAATATATAAAATAAAA
1 ATGAAAAAAAAAATATAT-AAATAAAA
643 ATGAAAAAATGAAAATATAT-AATAAA
1 ATGAAAAAA--AAAATATATAAATAAA
669 TCGGGTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 15 0.62
29 9 0.38
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (26 bp):
ATGAAAAAAAAAATATATAAATAAAA
Found at i:3821 original size:23 final size:22
Alignment explanation
Indices: 3762--3828 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
3752 TATGGACATC
*
3762 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
3784 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
3806 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
3829 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:5356 original size:18 final size:18
Alignment explanation
Indices: 5311--5366 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
5301 ATTCAGCTGT
5311 TATAACTCCTGAAATTATATCA
1 TATAACTCCTG-AA--AT-TCA
*
5333 TGTAACTCCTGAAATTCA
1 TATAACTCCTGAAATTCA
5351 TATAACTCCTGAAATT
1 TATAACTCCTGAAATT
5367 AAATCATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 18 0.56
19 2 0.06
21 2 0.06
22 10 0.31
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (18 bp):
TATAACTCCTGAAATTCA
Found at i:5390 original size:22 final size:22
Alignment explanation
Indices: 5311--5390 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
5301 ATTCAGCTGT
*
5311 TATAACTCCTGAAATTATATCA
1 TATAACTCCTGAAATTAAATCA
*
5333 TGTAACTCCTGAAA-T---TCA
1 TATAACTCCTGAAATTAAATCA
5351 TATAACTCCTGAAATTAAATCA
1 TATAACTCCTGAAATTAAATCA
* *
5373 TATAACTCTTGATATTAA
1 TATAACTCCTGAAATTAA
5391 CAGCTTGTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
18 16 0.32
19 1 0.02
21 1 0.02
22 32 0.64
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36
Consensus pattern (22 bp):
TATAACTCCTGAAATTAAATCA
Found at i:7353 original size:21 final size:21
Alignment explanation
Indices: 7329--7388 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
7319 ACACCGCCAG
7329 TTCAGATGGCACCACAACCAT
1 TTCAGATGGCACCACAACCAT
* * *
7350 TTCAGATAGCACCGCAACTAT
1 TTCAGATGGCACCACAACCAT
* *
7371 TTTAGACGGCACCACAAC
1 TTCAGATGGCACCACAAC
7389 TGTTTTAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.20
Consensus pattern (21 bp):
TTCAGATGGCACCACAACCAT
Found at i:7389 original size:21 final size:21
Alignment explanation
Indices: 7336--7397 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
7326 CAGTTCAGAT
* * *
7336 GGCACCACAACCATTTCAGAT
1 GGCACCACAACTATTTTAGAC
* *
7357 AGCACCGCAACTATTTTAGAC
1 GGCACCACAACTATTTTAGAC
*
7378 GGCACCACAACTGTTTTAGA
1 GGCACCACAACTATTTTAGA
7398 AGCCACCAGC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (21 bp):
GGCACCACAACTATTTTAGAC
Found at i:7404 original size:21 final size:21
Alignment explanation
Indices: 7338--7405 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
7328 GTTCAGATGG
* *
7338 CACCACAACCATTTCAGATAG-
1 CACCACAACTATTTTAGA-AGC
* * *
7359 CACCGCAACTATTTTAGACGG
1 CACCACAACTATTTTAGAAGC
*
7380 CACCACAACTGTTTTAGAAGC
1 CACCACAACTATTTTAGAAGC
7401 CACCA
1 CACCA
7406 GCCGTATCAG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 1 0.03
21 37 0.97
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.21
Consensus pattern (21 bp):
CACCACAACTATTTTAGAAGC
Found at i:7933 original size:13 final size:13
Alignment explanation
Indices: 7900--7938 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
7890 TTATTATTTT
*
7900 TGTTTGAATTGTAA
1 TGTTTGTATT-TAA
*
7914 CGTTTGTATTTAA
1 TGTTTGTATTTAA
7927 TGTTTGTATTTA
1 TGTTTGTATTTA
7939 CTTATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.23, C:0.03, G:0.18, T:0.56
Consensus pattern (13 bp):
TGTTTGTATTTAA
Found at i:10598 original size:23 final size:23
Alignment explanation
Indices: 10561--10665 Score: 88
Period size: 23 Copynumber: 4.6 Consensus size: 23
10551 CTACAAGGTC
*
10561 CTTC-GGACAAATCTATGTGGTT
1 CTTCGGGACAAATCTACGTGGTT
*
10583 CTTCGGGACAATTCTACGTGG-T
1 CTTCGGGACAAATCTACGTGGTT
* * *
10605 CATTCGGGACAAATTATACGCGGTG
1 C-TTCGGGACAAA-TCTACGTGGTT
* * **
10630 CTTTGGGACAAATCTATGTGGCA
1 CTTCGGGACAAATCTACGTGGTT
*
10653 CTTCGGTACAAAT
1 CTTCGGGACAAAT
10666 TATACGCAGC
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
22 6 0.09
23 41 0.63
24 17 0.26
25 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (23 bp):
CTTCGGGACAAATCTACGTGGTT
Found at i:10624 original size:24 final size:24
Alignment explanation
Indices: 10584--10671 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 24
10574 TATGTGGTTC
*
10584 TTCGGGAC-AATTCTACGTGGTCA
1 TTCGGGACAAATTATACGTGGTCA
*
10607 TTCGGGACAAATTATACGCGGTGC-
1 TTCGGGACAAATTATACGTGGT-CA
*
10631 TTTGGGACAAATCTAT--GTGG-CA
1 TTCGGGACAAAT-TATACGTGGTCA
*
10653 CTTCGGTACAAATTATACG
1 -TTCGGGACAAATTATACG
10672 CAGCACTTCG
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
21 1 0.02
22 3 0.06
23 21 0.40
24 23 0.44
25 4 0.08
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (24 bp):
TTCGGGACAAATTATACGTGGTCA
Found at i:16716 original size:24 final size:24
Alignment explanation
Indices: 16645--16730 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
16635 CTACATGGTC
* *
16645 CTTCGGAGACAAATTCTACGCGGTA
1 CTTCGGTG-CAAATTCTACGCGGCA
* * * *
16670 TTTCGAG-ACAAA-TCTATGTGGCA
1 CTTCG-GTGCAAATTCTACGCGGCA
16693 CTTCGGTGCAAATTCTACGCGGCA
1 CTTCGGTGCAAATTCTACGCGGCA
16717 CTTCGGTGCAAATT
1 CTTCGGTGCAAATT
16731 ATATGAGCAG
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
22 1 0.02
23 16 0.33
24 27 0.55
25 4 0.08
26 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (24 bp):
CTTCGGTGCAAATTCTACGCGGCA
Found at i:22086 original size:10 final size:10
Alignment explanation
Indices: 22071--22109 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
22061 AACGAACACA
22071 ATAAATGAAC
1 ATAAATGAAC
22081 ATAAATGAAC
1 ATAAATGAAC
* *
22091 GTAAACGAAC
1 ATAAATGAAC
22101 ATAAATGAA
1 ATAAATGAA
22110 AATATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:22100 original size:20 final size:20
Alignment explanation
Indices: 22072--22109 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
22062 ACGAACACAA
*
22072 TAAATGAACATAAATGAACG
1 TAAACGAACATAAATGAACG
22092 TAAACGAACATAAATGAA
1 TAAACGAACATAAATGAA
22110 AATATTTTTT
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:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (20 bp):
TAAACGAACATAAATGAACG
Found at i:22305 original size:10 final size:10
Alignment explanation
Indices: 22290--22326 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
22280 AAATGAATGC
22290 ACATAAACGA
1 ACATAAACGA
*
22300 ACATAAACAA
1 ACATAAACGA
22310 ACATAAACGA
1 ACATAAACGA
22320 ACATAAA
1 ACATAAA
22327 TTAACGAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.65, C:0.19, G:0.05, T:0.11
Consensus pattern (10 bp):
ACATAAACGA
Found at i:30425 original size:17 final size:17
Alignment explanation
Indices: 30399--30449 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
30389 TAATAGAGAC
* *
30399 TTATTTTGTTTTTTACA
1 TTATTCTGTTTTCTACA
30416 TTATTCTGTTTTCTACA
1 TTATTCTGTTTTCTACA
* *
30433 TTACTCTATTTTCTACA
1 TTATTCTGTTTTCTACA
30450 CTACCATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.61
Consensus pattern (17 bp):
TTATTCTGTTTTCTACA
Found at i:38194 original size:29 final size:29
Alignment explanation
Indices: 38141--38196 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
38131 TAAGTGTACA
* *
38141 AATCAAAGTTTCATGTTCACGTTGCACCG
1 AATCAAAGTTTCATATTCACATTGCACCG
38170 AATCAAAGTTCTCATATT-ACATTGCAC
1 AATCAAAGTT-TCATATTCACATTGCAC
38197 ATTGGATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (29 bp):
AATCAAAGTTTCATATTCACATTGCACCG
Found at i:40864 original size:17 final size:18
Alignment explanation
Indices: 40828--40865 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40818 AAATAATCAC
* *
40828 AGAAAAAGAGAGAAAGAA
1 AGAAAAACAGAGAAACAA
40846 AGAAAAACAGA-AAACAA
1 AGAAAAACAGAGAAACAA
40863 AGA
1 AGA
40866 CAGACTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (18 bp):
AGAAAAACAGAGAAACAA
Found at i:47309 original size:30 final size:30
Alignment explanation
Indices: 47274--47333 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
47264 TATGTAAAAA
*
47274 TATATATCTTTTAAAA-TAATTTTAACAAAT
1 TATATAT-TTATAAAATTAATTTTAACAAAT
47304 TATATATTTATAAAATTAATTTTAACAAAT
1 TATATATTTATAAAATTAATTTTAACAAAT
47334 GAATATAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
TATATATTTATAAAATTAATTTTAACAAAT
Found at i:47333 original size:14 final size:14
Alignment explanation
Indices: 47290--47333 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
47280 TCTTTTAAAA
47290 TAATTTTAACAAAT
1 TAATTTTAACAAAT
47304 TATATATTTATA-AAAT
1 TA-AT-TTTA-ACAAAT
47320 TAATTTTAACAAAT
1 TAATTTTAACAAAT
47334 GAATATAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.04
14 10 0.38
15 4 0.15
16 10 0.38
17 1 0.04
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATTTTAACAAAT
Found at i:47364 original size:39 final size:39
Alignment explanation
Indices: 47320--47398 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
47310 TTTATAAAAT
*
47320 TAATTTTAACAAATGAATATAAGTAGAATGGTAAATGAA
1 TAATTTTAACAAATGAATATAACTAGAATGGTAAATGAA
47359 TAATTTTAACAAATGAATATAACTAGAATGGTAAATGAA
1 TAATTTTAACAAATGAATATAACTAGAATGGTAAATGAA
47398 T
1 T
47399 TATATATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.32
Consensus pattern (39 bp):
TAATTTTAACAAATGAATATAACTAGAATGGTAAATGAA
Found at i:61232 original size:17 final size:16
Alignment explanation
Indices: 61208--61240 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
61198 AAGGGAATGA
61208 CAGTAGGGGAAGAATC
1 CAGTAGGGGAAGAATC
61224 CAGTAAGGGGAAGAATC
1 CAGT-AGGGGAAGAATC
61241 TAATTAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.39, C:0.12, G:0.36, T:0.12
Consensus pattern (16 bp):
CAGTAGGGGAAGAATC
Found at i:62605 original size:2 final size:2
Alignment explanation
Indices: 62598--62633 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
62588 TCCCATGCAT
*
62598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62634 ATAATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63164 original size:3 final size:3
Alignment explanation
Indices: 63156--63180 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
63146 TCCAGTTAGG
63156 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
63181 TGCTAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:66040 original size:20 final size:20
Alignment explanation
Indices: 66017--66068 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
66007 CTTTTACAAG
66017 AGTATCGATACTCTTAGGCT
1 AGTATCGATACTCTTAGGCT
66037 AGTATCGATACTCTTAGGCT
1 AGTATCGATACTCTTAGGCT
66057 AGTATCGATACT
1 AGTATCGATACT
66069 TTCATTCTGT
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:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
AGTATCGATACTCTTAGGCT
Found at i:70077 original size:19 final size:20
Alignment explanation
Indices: 70053--70097 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
70043 AAAGTACTGA
70053 AAAATA-AAGAGAC-AAAAAT
1 AAAATATAAGA-ACAAAAAAT
*
70072 AAAATATTAGAACAAAAAAT
1 AAAATATAAGAACAAAAAAT
70092 AAAATA
1 AAAATA
70098 CAATAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (20 bp):
AAAATATAAGAACAAAAAAT
Found at i:70103 original size:77 final size:77
Alignment explanation
Indices: 70004--70162 Score: 255
Period size: 77 Copynumber: 2.1 Consensus size: 77
69994 AAAATAAAAT
* * **
70004 AAACAGAAAATAAAATATAATAATTAAAGGTATAAAATTAAAGTACTGAAAAATAAAGAGACAAA
1 AAACAAAAAATAAAATACAATAATTAAAGAAATAAAATTAAAGTACTGAAAAATAAAGAGACAAA
*
70069 AATAAAATATTA
66 AATAAAAGATTA
* *
70081 GAACAAAAAATAAAATACAATAATTAAAGAAATAAAATTAAAGTACTGAAAAATAAAGAGTCAAA
1 AAACAAAAAATAAAATACAATAATTAAAGAAATAAAATTAAAGTACTGAAAAATAAAGAGACAAA
70146 AATAAAAGATTA
66 AATAAAAGATTA
70158 AAACA
1 AAACA
70163 TTAAAGCAAG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (77 bp):
AAACAAAAAATAAAATACAATAATTAAAGAAATAAAATTAAAGTACTGAAAAATAAAGAGACAAA
AATAAAAGATTA
Found at i:72336 original size:133 final size:135
Alignment explanation
Indices: 72187--72556 Score: 478
Period size: 133 Copynumber: 2.8 Consensus size: 135
72177 TTCCTTTACA
** * * *
72187 TTGAGGAAGTCTGATTGTCTGAGTTTGACACTGCTCCTTCGCTTTGAGGAGATCTGGTCAGTGGA
1 TTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCCTTTGCTTTGAGGAGATCTGGTCGGTGAA
* * * *
72252 CAACATTGTTTCTTCGTATTGAGGACATCTAGGCGTATTTGGATAATTTGGAGACAACACGTT-C
66 CAACATTGTTCCTTCGTGTTGAGGACATCTAGCCGTATTTGGATAATTTGGAGACAACACATTCC
72316 -CGTG
131 TCGTG
* * *
72320 TTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTTCTTTG-TGTTAAGGTGATCTGGTCGGTGA
1 TTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCCTTTGCT-TTGAGGAGATCTGGTCGGTGA
* * ** *
72384 ACGACATTGTTCCTTCGTGTTGAGAATGTCTAGCCGTATTTGGATAATTTGGAGACAATACATTC
65 ACAACATTGTTCCTTCGTGTTGAGGACATCTAGCCGTATTTGGATAATTTGGAGACAACACATTC
72449 CTTCGTG
130 C-TCGTG
* * * * *
72456 TTGAGG-AGTCTGATTGTCTGAGGATGATACTGCTCTTTTGCGTTGAGGAGATCTGATTGGTGAA
1 TTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCCTTTGCTTTGAGGAGATCTGGTCGGTGAA
* *
72520 CAACATTGTTCCTTCATGTTGAGGACATCTAGTCGTA
66 CAACATTGTTCCTTCGTGTTGAGGACATCTAGCCGTA
72557 CTTGACGGTT
Statistics
Matches: 201, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
132 1 0.00
133 109 0.54
134 1 0.00
135 80 0.40
136 10 0.05
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (135 bp):
TTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCCTTTGCTTTGAGGAGATCTGGTCGGTGAA
CAACATTGTTCCTTCGTGTTGAGGACATCTAGCCGTATTTGGATAATTTGGAGACAACACATTCC
TCGTG
Found at i:73067 original size:101 final size:101
Alignment explanation
Indices: 72934--73260 Score: 412
Period size: 100 Copynumber: 3.2 Consensus size: 101
72924 CAAAGAAGCC
* * * * *
72934 ATCTCAGGTGAGATAAAATTTTGTTTCGAGTGAAAGAATTTCATAATTTGTGTTTCAAGGGAAAA
1 ATCTCAAGTGAGAT-CAATTTTGTTTCAAGTGAAA-AATTTCAAAATTTGTGTTTCGAGGGAAAA
* *
72999 TTATCTCAAGCGAGACAAAATTTGTTCCGAGGAAAA-A
64 TTATCTCAAGCGAGACAAAATTTGTTTCAAGGAAAACA
*
73036 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAATAATTTTAAAATTTGTGTTTCGAGGGAAAA-
1 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAA-AATTTCAAAATTTGTGTTTCGAGGGAAAAT
** **
73100 TATCTCAAGCGAGA-TGAATTTGTTTTTAGGAAAACA
65 TATCTCAAGCGAGACAAAATTTGTTTCAAGGAAAACA
* * * *
73136 ATCTCAAGTGAGGTCAATTTTGCTTCAAGTG-AAACTTTCAAAATTTGTGTTTCGAGGGAAAGTT
1 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAAAATTTCAAAATTTGTGTTTCGAGGGAAAATT
* * *
73200 GTTTCAAGCGAGACAAAATTT-TTTCAAGAGAAAATA
66 ATCTCAAGCGAGACAAAATTTGTTTCAAG-GAAAACA
73236 ATCTCAAGTGAGATCAATTTTGTTT
1 ATCTCAAGTGAGATCAATTTTGTTT
73261 AAGAAAAACT
Statistics
Matches: 195, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
98 26 0.13
99 34 0.17
100 78 0.40
101 44 0.23
102 13 0.07
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (101 bp):
ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAAAATTTCAAAATTTGTGTTTCGAGGGAAAATT
ATCTCAAGCGAGACAAAATTTGTTTCAAGGAAAACA
Found at i:73737 original size:12 final size:12
Alignment explanation
Indices: 73720--73744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
73710 GCCTCTGCCT
73720 ATATGGAATGTA
1 ATATGGAATGTA
73732 ATATGGAATGTA
1 ATATGGAATGTA
73744 A
1 A
73745 CTAAAACCAT
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:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
ATATGGAATGTA
Done.