Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004780.1 Hibiscus syriacus cultivar Beakdansim tig00010781_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: 98406
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:424 original size:29 final size:28
Alignment explanation
Indices: 376--434 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
366 GACACTAAAT
376 TTTTATTATAATCATTTAATAGTTTATTA
1 TTTTATTATAATCATTTAATA-TTTATTA
* *
405 TTTTATTAT-ATTATTGTAATATTTTTTA
1 TTTTATTATAATCATT-TAATATTTATTA
433 TT
1 TT
435 ATTTTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (28 bp):
TTTTATTATAATCATTTAATATTTATTA
Found at i:2103 original size:21 final size:21
Alignment explanation
Indices: 2079--2154 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 21
2069 ATACAGTCGG
*
2079 TTCATATGCCACCATAGCCAT
1 TTCAGATGCCACCATAGCCAT
* *** *
2100 TTCAGATGACATTGTAGCCGT
1 TTCAGATGCCACCATAGCCAT
*
2121 TTC-GATGCCACCATAGTCAT
1 TTCAGATGCCACCATAGCCAT
*
2141 TTCAGATGTCACCA
1 TTCAGATGCCACCA
2155 CCGTAGGGTT
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 14 0.34
21 27 0.66
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (21 bp):
TTCAGATGCCACCATAGCCAT
Found at i:6479 original size:50 final size:50
Alignment explanation
Indices: 6423--6519 Score: 176
Period size: 50 Copynumber: 1.9 Consensus size: 50
6413 AAACCTTAAA
* *
6423 TCATAAATCTTAATTTGATAAATACATTAAAATTCCTAAAAATCATATTT
1 TCATAAATCTTAACTTGATAAATACATTAAAATTCATAAAAATCATATTT
6473 TCATAAATCTTAACTTGATAAATACATTAAAATTCATAAAAATCATA
1 TCATAAATCTTAACTTGATAAATACATTAAAATTCATAAAAATCATA
6520 AATAAATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.37
Consensus pattern (50 bp):
TCATAAATCTTAACTTGATAAATACATTAAAATTCATAAAAATCATATTT
Found at i:23762 original size:8 final size:8
Alignment explanation
Indices: 23749--23785 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
23739 AACACAACAA
23749 AAAAAATT
1 AAAAAATT
23757 AAAAAATT
1 AAAAAATT
23765 AAAAAATT
1 AAAAAATT
23773 AAAAAATT
1 AAAAAATT
23781 AAAAA
1 AAAAA
23786 TAATAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAAATT
Found at i:25274 original size:3 final size:3
Alignment explanation
Indices: 25266--25330 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
25256 TTAAATAAGA
* * *
25266 AAT AAT AAT AAT AAAT AA- AAT AAT TAC ACT AAT AAT AAAT AAT AAAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT
25313 AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT A
25331 GTATAATATA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 4 0.08
3 38 0.75
4 9 0.18
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:25284 original size:24 final size:22
Alignment explanation
Indices: 25259--25330 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 22
25249 AAAATAATTA
25259 AATAAGAAATAATAATAATAAAT
1 AATAA-AAATAATAATAATAAAT
*
25282 AA-AATAATTACACTAATAATAAAT
1 AATAA-AAATA-A-TAATAATAAAT
25306 AATAAATAATAATAATAATATAAT
1 AATAAA-AATAATAATAATA-AAT
25330 A
1 A
25331 GTATAATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 6 0.15
23 11 0.27
24 19 0.46
25 5 0.12
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (22 bp):
AATAAAAATAATAATAATAAAT
Found at i:25336 original size:13 final size:14
Alignment explanation
Indices: 25266--25374 Score: 68
Period size: 14 Copynumber: 7.6 Consensus size: 14
25256 TTAAATAAGA
25266 AATAATAATAATA-
1 AATAATAATAATAT
25279 AATAA-AATAAT-T
1 AATAATAATAATAT
25291 ACACTAATAATAA-AT
1 A-A-TAATAATAATAT
25306 AATAAATAATAATAAT
1 AAT-AATAATAAT-AT
*
25322 AAT-ATAATAGTAT
1 AATAATAATAATAT
25335 AATATATATATAAATAT
1 AATA-ATA-AT-AATAT
** *
25352 TTTAAAAAT-ATAT
1 AATAATAATAATAT
25365 AATATATAAT
1 AATA-ATAAT
25375 TTCAAAAATG
Statistics
Matches: 75, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
12 7 0.09
13 18 0.24
14 23 0.31
15 12 0.16
16 9 0.12
17 6 0.08
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (14 bp):
AATAATAATAATAT
Found at i:25363 original size:23 final size:23
Alignment explanation
Indices: 25335--25383 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
25325 ATAATAGTAT
*
25335 AATATATATATAAAT-ATTTTAAA
1 AATATATA-ATAAATAATTTCAAA
*
25358 AATATATAATATATAATTTCAAA
1 AATATATAATAAATAATTTCAAA
25381 AAT
1 AAT
25384 GTTTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATATAATAAATAATTTCAAA
Found at i:25421 original size:27 final size:27
Alignment explanation
Indices: 25387--25454 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
25377 CAAAAATGTT
*
25387 TTTTTTTAAAATTATATAATATATATA
1 TTTTTTTAAAATTATATAATATATAAA
*
25414 TTTTTTTAAAAAACTATATAATATATAAA
1 TTTTTTT--AAAATTATATAATATATAAA
* *
25443 TGTTTTCAAAAT
1 TTTTTTTAAAAT
25455 GTTTTCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 11 0.32
29 23 0.68
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (27 bp):
TTTTTTTAAAATTATATAATATATAAA
Found at i:25426 original size:29 final size:29
Alignment explanation
Indices: 25385--25440 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
25375 TTCAAAAATG
** *
25385 TTTTTTTTTAAAATTATATAATATATATA
1 TTTTTTTAAAAAACTATATAATATATATA
25414 TTTTTTTAAAAAACTATATAATATATA
1 TTTTTTTAAAAAACTATATAATATATA
25441 AATGTTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTTTTTAAAAAACTATATAATATATATA
Found at i:25448 original size:29 final size:29
Alignment explanation
Indices: 25394--25453 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
25384 GTTTTTTTTT
* * * *
25394 AAAATTATATAATATATATATTTTTTTAA
1 AAAACTATATAATATATAAATGTTTTCAA
25423 AAAACTATATAATATATAAATGTTTTCAA
1 AAAACTATATAATATATAAATGTTTTCAA
25452 AA
1 AA
25454 TGTTTTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (29 bp):
AAAACTATATAATATATAAATGTTTTCAA
Found at i:25456 original size:11 final size:11
Alignment explanation
Indices: 25440--25464 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25430 TATAATATAT
25440 AAATGTTTTCA
1 AAATGTTTTCA
25451 AAATGTTTTCA
1 AAATGTTTTCA
25462 AAA
1 AAA
25465 CTATATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:25467 original size:38 final size:39
Alignment explanation
Indices: 25423--25552 Score: 148
Period size: 38 Copynumber: 3.4 Consensus size: 39
25413 ATTTTTTTAA
25423 AAAACTATATAATATATAAATGTTTTC-AAAATG-TTTTC
1 AAAACTATAT-ATATATAAATGTTTTCAAAAATGCTTTTC
*
25461 AAAACTATATATCATATAAA--TTTTCAAAAATGTTTTTC
1 AAAACTATATAT-ATATAAATGTTTTCAAAAATGCTTTTC
* * *
25499 AAAACTACATAT-TATATACGTTTTCAAAAATGCTTTT-
1 AAAACTATATATATATAAATGTTTTCAAAAATGCTTTTC
25536 AAATA-TATATATATATA
1 AAA-ACTATATATATATA
25553 TATATTATAC
Statistics
Matches: 81, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
36 10 0.12
37 17 0.21
38 54 0.67
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (39 bp):
AAAACTATATATATATAAATGTTTTCAAAAATGCTTTTC
Found at i:25553 original size:83 final size:80
Alignment explanation
Indices: 25466--25657 Score: 185
Period size: 81 Copynumber: 2.3 Consensus size: 80
25456 TTTTCAAAAC
25466 TATATATCATATAAATTTTCAAAAATGTTTTTCAAA-ACTACATATTATATACGTTTTCAAAAAT
1 TATATATCATATAAATTTTCAAAAATG-TTTTCAAAGACT--ATATTATATA-GTTTTCAAAAAT
* * *
25530 GCTTTT-AAATATATATATA
62 G-TTTTAAAAAAAACATATA
* * * **
25549 TATATAT-ATTATACA-TTTCCAAAATGTTTTCAAAGACTATATTATATATTTTTTTAAAATGTT
1 TATATATCA-TATAAATTTTCAAAAATGTTTTCAAAGACTATATTATATAGTTTTCAAAAATGTT
25612 TTCGAAAAAAAACATATA
65 TT--AAAAAAAACATATA
25630 TATATATCATATAATATATTTTCAAAAA
1 TATATATCATAT-A-A-ATTTTCAAAAA
25658 GCTATTCTCA
Statistics
Matches: 89, Mismatches: 10, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
78 4 0.04
79 10 0.11
80 10 0.11
81 28 0.31
82 16 0.18
83 12 0.13
84 1 0.01
85 8 0.09
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (80 bp):
TATATATCATATAAATTTTCAAAAATGTTTTCAAAGACTATATTATATAGTTTTCAAAAATGTTT
TAAAAAAAACATATA
Found at i:34898 original size:2 final size:2
Alignment explanation
Indices: 34849--34885 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
34839 AGATAATTAT
34849 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34886 TTTCCAGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39918 original size:24 final size:24
Alignment explanation
Indices: 39856--39929 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 24
39846 TGTTCATTTA
* *
39856 TTTAT-TGTTCACGAATATGTTCA
1 TTTATATGTTCACGAACATGTTCG
* *
39879 TTTA-ATGTTCGCGAACATGTTTG
1 TTTATATGTTCACGAACATGTTCG
*
39902 TTTATATGTTCATGAACATGTTCG
1 TTTATATGTTCACGAACATGTTCG
39926 TTTA
1 TTTA
39930 GCATTCATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
23 22 0.52
24 20 0.48
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.47
Consensus pattern (24 bp):
TTTATATGTTCACGAACATGTTCG
Found at i:39946 original size:59 final size:58
Alignment explanation
Indices: 39875--40004 Score: 206
Period size: 59 Copynumber: 2.2 Consensus size: 58
39865 CACGAATATG
* * *
39875 TTCATTTAATGTTCGCGAACATGTTTGTTTATATGTTCATGAACATGTTCGTTTAGCA
1 TTCATTTAATGTTCACGAACATGTTCGTTTATATGTTCATGAACATGTTCGTTTAACA
*
39933 TTCATTTATATGTTCACGAACATGTTCGTTTATATGTTCATGAACATGTTCGTTTAACG
1 TTCATTTA-ATGTTCACGAACATGTTCGTTTATATGTTCATGAACATGTTCGTTTAACA
*
39992 TTCATTTAGTGTT
1 TTCATTTAATGTT
40005 GTTTTAGTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 12 0.18
59 54 0.82
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (58 bp):
TTCATTTAATGTTCACGAACATGTTCGTTTATATGTTCATGAACATGTTCGTTTAACA
Found at i:39966 original size:24 final size:24
Alignment explanation
Indices: 39937--39988 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
39927 TTAGCATTCA
39937 TTTATATGTTCACGAACATGTTCG
1 TTTATATGTTCACGAACATGTTCG
*
39961 TTTATATGTTCATGAACATGTTCG
1 TTTATATGTTCACGAACATGTTCG
39985 TTTA
1 TTTA
39989 ACGTTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (24 bp):
TTTATATGTTCACGAACATGTTCG
Found at i:41837 original size:59 final size:60
Alignment explanation
Indices: 41765--41893 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
41755 AAGGGTCAAG
* * * *
41765 TATACAAATGGTCC-CCGACTATA-GGATATTGTTTTATTGAGTCTCTTGACTATTAAAAGT
1 TATA-AAATGGTCCTCAGACTATAGGGA-ATTGCTTTATTGAGTCCCTAGACTATTAAAAGT
* * * *
41825 TATAAAATGGTCCTTAGACTATAGGGAGTTGCTTTGTTGAGTCCCTAGATTATTAAAAGT
1 TATAAAATGGTCCTCAGACTATAGGGAATTGCTTTATTGAGTCCCTAGACTATTAAAAGT
*
41885 TACAAAATG
1 TATAAAATG
41894 ATCATTCGAC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
59 9 0.16
60 46 0.79
61 3 0.05
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (60 bp):
TATAAAATGGTCCTCAGACTATAGGGAATTGCTTTATTGAGTCCCTAGACTATTAAAAGT
Found at i:44696 original size:60 final size:60
Alignment explanation
Indices: 44590--44745 Score: 258
Period size: 60 Copynumber: 2.6 Consensus size: 60
44580 AGCGTAGTTA
*
44590 AAAAGCCTAATTACCGATGTAGGTAATCGTTGTTACTTAGGAAAATTTAGGTAATCGCATG
1 AAAA-CCTAATTACCGATGTAGGTAATCGTTGTTACGTAGGAAAATTTAGGTAATCGCATG
*
44651 AAAACCTAATTACCGATGTAGGTAATCGTTGTTACGTAGGGAAATTTAGGTAATCGCATG
1 AAAACCTAATTACCGATGTAGGTAATCGTTGTTACGTAGGAAAATTTAGGTAATCGCATG
* **
44711 AAAGCCTAATTACCGATGTAGGTAATATTTGTTAC
1 AAAACCTAATTACCGATGTAGGTAATCGTTGTTAC
44746 TTAGCCCAGC
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
60 86 0.96
61 4 0.04
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (60 bp):
AAAACCTAATTACCGATGTAGGTAATCGTTGTTACGTAGGAAAATTTAGGTAATCGCATG
Found at i:70192 original size:19 final size:19
Alignment explanation
Indices: 70154--70239 Score: 84
Period size: 19 Copynumber: 4.4 Consensus size: 19
70144 TTGAAAATCG
*
70154 CGTTGCGATTTTTC-ATTT
1 CGTTGCGATTTTTCAAATT
70172 CGTTGCGATTTTTCAAATT
1 CGTTGCGATTTTTCAAATT
* * **
70191 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGAT--TTTTCAAAT-T
*
70213 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTTCAAATT
70232 CGTTGCGA
1 CGTTGCGA
70240 AAATTCGTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
18 14 0.25
19 21 0.38
20 5 0.09
21 5 0.09
22 10 0.18
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTTCAAATT
Found at i:70871 original size:6 final size:6
Alignment explanation
Indices: 70856--70889 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
70846 TCTCGTCTCT
*
70856 TGGTCG TGGTCA TGGTCG TGGTCG TGGTCG TGGT
1 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGT
70890 AATACGTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.15, G:0.47, T:0.35
Consensus pattern (6 bp):
TGGTCG
Found at i:71036 original size:42 final size:41
Alignment explanation
Indices: 70982--71066 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 41
70972 ACAACGAATT
*
70982 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAAGCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * *
71024 TGGAAAAGCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAAGCGCAACGCAACTGTCAACTATCGCAACGCGAAA
71065 TG
1 TG
71067 CAACGCGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 23 0.61
42 15 0.39
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (41 bp):
TGGAAAAGCGCAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:71070 original size:21 final size:21
Alignment explanation
Indices: 71007--71070 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
70997 ACAACTGTAG
*
71007 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
71028 A-AAGCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
71048 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
71069 AC
1 AC
71071 GCGAATTTGC
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.16
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:77276 original size:20 final size:21
Alignment explanation
Indices: 77231--77276 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
77221 ACATAAATTT
*
77231 TATT-ATTAATTTTTTAAATA
1 TATTAATTAATTTTTAAAATA
*
77251 T-GTAATTAA-TTTTAAAATA
1 TATTAATTAATTTTTAAAATA
77270 TATTAAT
1 TATTAAT
77277 ATTGTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTAATTAATTTTTAAAATA
Found at i:82959 original size:23 final size:24
Alignment explanation
Indices: 82928--82981 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
82918 AAATGTCCAG
*
82928 TTTTTATTTCATTTT-AA-TATCAA
1 TTTTAATTT-ATTTTAAACTATCAA
* *
82951 TTTTAATTTTTTTTAAACTATCAG
1 TTTTAATTTATTTTAAACTATCAA
82975 TTTTAAT
1 TTTTAAT
82982 ATTTATCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 10 0.38
24 12 0.46
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTAATTTATTTTAAACTATCAA
Found at i:89095 original size:48 final size:49
Alignment explanation
Indices: 89039--89141 Score: 190
Period size: 48 Copynumber: 2.1 Consensus size: 49
89029 ATGCTCTTCT
89039 TGCTCAGGAGATAGTGAAAGGATATAGTAGG-AATCCATCTCTCCAAGA
1 TGCTCAGGAGATAGTGAAAGGATATAGTAGGAAATCCATCTCTCCAAGA
*
89087 TGCTCAGGAGATAGTGAAAGGATATGGTAGGAAATCCATCTCTCCAAGA
1 TGCTCAGGAGATAGTGAAAGGATATAGTAGGAAATCCATCTCTCCAAGA
89136 TGCTCA
1 TGCTCA
89142 ATGAAGATTG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 30 0.57
49 23 0.43
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (49 bp):
TGCTCAGGAGATAGTGAAAGGATATAGTAGGAAATCCATCTCTCCAAGA
Done.