Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006899.1 Hibiscus syriacus cultivar Beakdansim tig00017619_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: 54813
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6857 original size:22 final size:22
Alignment explanation
Indices: 6830--6875 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
6820 TATTAATCCT
6830 AATTAAA-AAAAATTACAAAATA
1 AATTAAATAAAAATTA-AAAATA
* *
6852 AATTAAATAAATATTAAAATTA
1 AATTAAATAAAAATTAAAAATA
6874 AA
1 AA
6876 CAAAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AATTAAATAAAAATTAAAAATA
Found at i:8487 original size:37 final size:37
Alignment explanation
Indices: 8369--8475 Score: 196
Period size: 37 Copynumber: 2.9 Consensus size: 37
8359 AATGTAGGCA
*
8369 AATGTGTATTGGTTACATCTTTCGTATGTCACATAAC
1 AATGTGTATTGGTTACATCTTTCGTAAGTCACATAAC
8406 AATGTGTATTGGTTACATCTTTCGTAAGTCACATAAC
1 AATGTGTATTGGTTACATCTTTCGTAAGTCACATAAC
*
8443 AATGTGTATTGGTCACATCTTTCGTAAGTCACA
1 AATGTGTATTGGTTACATCTTTCGTAAGTCACA
8476 CAGCAACGTG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (37 bp):
AATGTGTATTGGTTACATCTTTCGTAAGTCACATAAC
Found at i:10201 original size:23 final size:24
Alignment explanation
Indices: 10175--10227 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
10165 TAATCTTTTA
*
10175 TATAATTTTATT-TTTAATATAAT
1 TATAATTTTATTATTTAAAATAAT
*
10198 TAT-ATATTATTATTTAAAATAAT
1 TATAATTTTATTATTTAAAATAAT
10221 T-TAATTT
1 TATAATTT
10228 AAAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TATAATTTTATTATTTAAAATAAT
Found at i:12377 original size:76 final size:76
Alignment explanation
Indices: 12239--12385 Score: 190
Period size: 76 Copynumber: 1.9 Consensus size: 76
12229 ACAATCAATT
* ** * *
12239 ATGTTATATACAACCTAACATTTTGGTTTCAACCTATAATATGACATTGTAGTTGTTATATGAAT
1 ATGTTATATACAACCTAACATTTTGGTTTCAACCTATAATATGAAATTACAATTCTTATATGAAT
12304 TACAACCTACA
66 TACAACCTACA
* * *
12315 ATGTTATATACAACCTAATATTTT-TTATTCAACCTATAATAAT-AAATTACAATTCTTTTATGA
1 ATGTTATATACAACCTAACATTTTGGT-TTCAACCTATAAT-ATGAAATTACAATTCTTATATGA
12378 ATTACAAC
64 ATTACAAC
12386 AAATCGTTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
75 1 0.02
76 58 0.95
77 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (76 bp):
ATGTTATATACAACCTAACATTTTGGTTTCAACCTATAATATGAAATTACAATTCTTATATGAAT
TACAACCTACA
Found at i:12712 original size:13 final size:13
Alignment explanation
Indices: 12692--12726 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
12682 AATGCGTACT
12692 ACTTTCCCTTGAC
1 ACTTTCCCTTGAC
12705 -CGTTTCCCTTGAC
1 AC-TTTCCCTTGAC
12718 ACTTTCCCT
1 ACTTTCCCT
12727 AAATATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.11, C:0.40, G:0.09, T:0.40
Consensus pattern (13 bp):
ACTTTCCCTTGAC
Found at i:17441 original size:29 final size:29
Alignment explanation
Indices: 17379--17441 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
17369 ACCAAGTTCC
* * *
17379 ACACTGTCATCGGCACCACACTAGTTTCC
1 ACACTGCCATCGGCACCACACCAGTTTCA
17408 ACACTGCCATCGGCACCACACCA-TTTCA
1 ACACTGCCATCGGCACCACACCAGTTTCA
17436 AGCACT
1 A-CACT
17442 ATATCGCTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.27, C:0.40, G:0.13, T:0.21
Consensus pattern (29 bp):
ACACTGCCATCGGCACCACACCAGTTTCA
Found at i:31594 original size:18 final size:18
Alignment explanation
Indices: 31573--31613 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
31563 CAGGAATGCA
* *
31573 AACCCTGATGATAATGAT
1 AACCCTGATAATAATGAC
31591 AACCCTGATAATAATGAC
1 AACCCTGATAATAATGAC
31609 AACCC
1 AACCC
31614 AAATGAGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.22
Consensus pattern (18 bp):
AACCCTGATAATAATGAC
Found at i:32411 original size:22 final size:23
Alignment explanation
Indices: 32386--32433 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
32376 CAAATCAGGC
*
32386 TCGAGAGCCAATTCAG-TCGAGT
1 TCGAGAGCCAATTCAGAACGAGT
32408 TCGAGAGCCAATTCAGAACGAGT
1 TCGAGAGCCAATTCAGAACGAGT
32431 TCG
1 TCG
32434 GCTTAATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (23 bp):
TCGAGAGCCAATTCAGAACGAGT
Found at i:33387 original size:2 final size:2
Alignment explanation
Indices: 33380--33408 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33370 GTTCTATTTA
33380 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
33409 ATTTTGAAAA
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:33472 original size:36 final size:36
Alignment explanation
Indices: 33392--33710 Score: 358
Period size: 37 Copynumber: 8.6 Consensus size: 36
33382 ATATATATAT
* *
33392 ATATATATATATATATAATTTTGAAAACATTTTCAAAAA
1 ATATATATA-ATATATAGTTTTGAAAACATTTT--TAAA
*
33431 TATATATATAATATATAGTTTTGAAAACATTTTTAGA
1 -ATATATATAATATATAGTTTTGAAAACATTTTTAAA
33468 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTT-AAA
*
33505 ATATATATAATATATAGTTTTGAAAATATTTTTAAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTT-AAA
* * * *
33542 ACATATATGATGTATAGTTTTGAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTAAA
* * *
33578 ATATATATAATATATAATTTTGAAAACGTTTTGGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTT-TAAA
*
33615 ATATATATAATATATA-TTTTAGAAAACATTTTGAAAA
1 ATATATATAATATATAGTTTT-GAAAACATTTT-TAAA
* *
33652 CATATATATAATATA-AGATTTTGAAAATATTTTTTTTGAA
1 -ATATATATAATATATAG-TTTTGAAAACA---TTTTTAAA
33692 A-ATATATAATAT-TAGTTTT
1 ATATATATAATATATAGTTTT
33711 TATAATTTTT
Statistics
Matches: 248, Mismatches: 21, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
36 67 0.27
37 106 0.43
38 33 0.13
39 27 0.11
40 11 0.04
41 4 0.02
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTAAA
Found at i:33524 original size:73 final size:73
Alignment explanation
Indices: 33392--33710 Score: 371
Period size: 73 Copynumber: 4.3 Consensus size: 73
33382 ATATATATAT
* * *
33392 ATATATATATATATATAATTTTGAAAACATTTTCAAAAATATATATATAATATATAGTTTTGAAA
1 ATATATATA-ATATATAGTTTTGAAAACATTTT--GAAACATATATATAATATATAGTTTTGAAA
*
33457 ACATTTTTAGA
63 ACATTTTTAAA
*
33468 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA-ATATATATAATATATAGTTTTGAAAAT
1 ATATATATAATATATAGTTTTGAAAACA-TTTTGAAACATATATATAATATATAGTTTTGAAAAC
33532 ATTTTTAAAA
65 ATTTTT-AAA
* * * * *
33542 ACATATATGATGTATAGTTTTGAAAACATTTTGAAA-ATATATATAATATATAATTTTGAAAACG
1 ATATATATAATATATAGTTTTGAAAACATTTTGAAACATATATATAATATATAGTTTTGAAAACA
*
33606 TTTTGGAAA
66 TTTT-TAAA
33615 ATATATATAATATATA-TTTTAGAAAACATTTTGAAAACATATATATAATATA-AGATTTTGAAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTG-AAACATATATATAATATATAG-TTTTGAAA
* *
33678 ATATTTTTTTTGAA
63 ACA---TTTTTAAA
33692 A-ATATATAATAT-TAGTTTT
1 ATATATATAATATATAGTTTT
33711 TATAATTTTT
Statistics
Matches: 213, Mismatches: 19, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
72 4 0.02
73 97 0.46
74 34 0.16
75 43 0.20
76 28 0.13
77 3 0.01
78 4 0.02
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (73 bp):
ATATATATAATATATAGTTTTGAAAACATTTTGAAACATATATATAATATATAGTTTTGAAAACA
TTTTTAAA
Found at i:33777 original size:26 final size:27
Alignment explanation
Indices: 33716--33778 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
33706 GTTTTTATAA
* *
33716 TTTTTATTTACGTGTTATTTATTTCTTT
1 TTTTTATTTA-GTGTTATTAATTTCTTG
33744 TTTATTATTT-GT-TTATTAATTTCGTTG
1 TTT-TTATTTAGTGTTATTAATTTC-TTG
33771 TTTTTATT
1 TTTTTATT
33779 GTTATTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 15 0.48
27 7 0.23
28 3 0.10
29 6 0.19
ACGTcount: A:0.16, C:0.05, G:0.08, T:0.71
Consensus pattern (27 bp):
TTTTTATTTAGTGTTATTAATTTCTTG
Found at i:37829 original size:18 final size:18
Alignment explanation
Indices: 37806--37957 Score: 88
Period size: 18 Copynumber: 8.4 Consensus size: 18
37796 AGACAAAACC
37806 AATAATAATAATAATAGT
1 AATAATAATAATAATAGT
37824 AATAATAATAATAAAATA-T
1 AATAATAATAAT--AATAGT
37843 AATAA-AAT-ATAA-A-T
1 AATAATAATAATAATAGT
37857 ATATAAT-ATAAATAAGTAG-
1 A-ATAATAAT-AATAA-TAGT
* * *
37876 AA-AAAAAGGAAAAATA-T
1 AATAATAA-TAATAATAGT
*
37893 AATAGTAGTAATAATAATAGC
1 AATA--A-TAATAATAATAGT
* *
37914 AATAGTAATAATAATAGC
1 AATAATAATAATAATAGT
*
37932 AATAATAAAAATAATAGT
1 AATAATAATAATAATAGT
*
37950 AACAATAA
1 AATAATAA
37958 AAAAATGAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 34
0.70 0.08 0.23
Matches are distributed among these distances:
14 3 0.03
15 8 0.08
17 12 0.11
18 57 0.54
19 8 0.08
20 11 0.10
21 6 0.06
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
AATAATAATAATAATAGT
Found at i:37962 original size:21 final size:21
Alignment explanation
Indices: 37920--37962 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
37910 TAGCAATAGT
* *
37920 AATAATAATAGCAATAATAAA
1 AATAATAATAACAATAAAAAA
*
37941 AATAATAGTAACAATAAAAAA
1 AATAATAATAACAATAAAAAA
37962 A
1 A
37963 TGAAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (21 bp):
AATAATAATAACAATAAAAAA
Found at i:37973 original size:3 final size:3
Alignment explanation
Indices: 37806--37957 Score: 73
Period size: 3 Copynumber: 50.7 Consensus size: 3
37796 AGACAAAACC
*
37806 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AA- AAT -AT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
37851 -AT AAAT ATAT AAT -AT AAAT AAGT AGAA AAA AAGG AAA AAT -AT AAT
1 AAT -AAT A-AT AAT AAT -AAT AA-T A-AT AAT AA-T AAT AAT AAT AAT
* * ** * ** *
37896 AGT AGT AAT AAT AAT AGC AAT AGT AAT AAT AAT AGC AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
37944 AAT AGT AAC AAT AA
1 AAT AAT AAT AAT AA
37958 AAAAATGAAA
Statistics
Matches: 113, Mismatches: 24, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
2 12 0.11
3 88 0.78
4 12 0.11
5 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:40106 original size:66 final size:68
Alignment explanation
Indices: 39979--40106 Score: 170
Period size: 69 Copynumber: 1.9 Consensus size: 68
39969 AAACTGGGAA
*
39979 GCCCCTTCGTCGTGAAGTTGAGCCTCAAATGGAACGATATCCTCTGTCGTGGAGTTGAAATCGTG
1 GCCCCTTCGTCGTGAAGTTGAGCCTCAAATGGAAC-ATATCCTCTGTCGTGAAGTTGAAATCGTG
40044 GATG
65 GATG
* ** * * *
40048 GCCCCTTCGTTGTGAAGTTGAGCCTTGACTTG-A-ATATCCTTTGTCGTGAAGTTGAAATC
1 GCCCCTTCGTCGTGAAGTTGAGCCTCAAATGGAACATATCCTCTGTCGTGAAGTTGAAATC
40107 CAAGTATTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 24 0.46
68 1 0.02
69 27 0.52
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (68 bp):
GCCCCTTCGTCGTGAAGTTGAGCCTCAAATGGAACATATCCTCTGTCGTGAAGTTGAAATCGTGG
ATG
Found at i:40444 original size:110 final size:110
Alignment explanation
Indices: 40251--40655 Score: 711
Period size: 110 Copynumber: 3.7 Consensus size: 110
40241 TTGTTTCGCT
* *
40251 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAATTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
40316 TGACAGTCAATCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
40361 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
40426 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
40471 TCGAGCCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTAT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
40536 TGACAGTCAGTCGCCCATTCGCTGTGAAGTTGAGCTTGTGATGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* **
40581 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAACGAAACTGAAAAGTTACTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
40646 TGACAGTCAG
66 TGACAGTCAG
40656 CTTTTCCTTA
Statistics
Matches: 281, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 281 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:41953 original size:95 final size:98
Alignment explanation
Indices: 41736--42000 Score: 335
Period size: 95 Copynumber: 2.7 Consensus size: 98
41726 AGCTAGCTGA
* * * * *
41736 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGATGGACAGCTCAA--TATTATTGTATAAA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCT-TTATTGTATAAA
41799 TATAATTATCACCTTTATCAGTCTAGCTAAATATT
65 TATAA-TATCACCTTTATCAGTCTAGCTAAATATT
* *
41834 ATCCATAAAGTTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTAT-AGT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAAAT
* * * *
41898 AT-A-ATCATCTTTATCAGGT-TAGCTGACTCTT
66 ATAATATCACCTTTATCA-GTCTAGCTAAATATT
* * *
41929 ATCCATAAAGTCGGGGTGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTTTATAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAAAT
41994 ATAATAT
66 ATAATAT
42001 TATAATCTGG
Statistics
Matches: 145, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
95 79 0.54
96 5 0.03
97 2 0.01
98 49 0.34
99 9 0.06
100 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (98 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAAAT
ATAATATCACCTTTATCAGTCTAGCTAAATATT
Found at i:51632 original size:90 final size:88
Alignment explanation
Indices: 51459--51624 Score: 280
Period size: 90 Copynumber: 1.9 Consensus size: 88
51449 ACACACCCTT
51459 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
51524 ATTAATTGGAATTTAATAATCCTC
66 ATTAATT-GAATTAAATAATCCTC
* *
51548 TTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
51613 AATTAATT-AATT
65 AATTAATTGAATT
51625 GAAAATAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
88 4 0.05
89 29 0.39
90 41 0.55
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAATTAAATAATCCTC
Found at i:54421 original size:3 final size:3
Alignment explanation
Indices: 54413--54442 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
54403 AGACAAAACC
54413 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
54443 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:54612 original size:30 final size:32
Alignment explanation
Indices: 54573--54631 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
54563 TTAAAAAAAT
*
54573 AATAAGTAT-AAATTAAAAATAA-AATGAGCA
1 AATAAGTATAAAAATAAAAATAATAATGAGCA
*
54603 AATATGTATAAAAATAAAAATAATAATGA
1 AATAAGTATAAAAATAAAAATAATAATGA
54632 AGGGATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.32
31 12 0.48
32 5 0.20
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.25
Consensus pattern (32 bp):
AATAAGTATAAAAATAAAAATAATAATGAGCA
Done.