Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005611.1 Hibiscus syriacus cultivar Beakdansim tig00013048_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: 63656
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5677 original size:18 final size:17
Alignment explanation
Indices: 5656--5699 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
5646 AAGTTATTTT
5656 TTAAATAAAAGATAAGAA
1 TTAAATAAAAGA-AAGAA
*
5674 TTAAATAAAAGAAATAA
1 TTAAATAAAAGAAAGAA
*
5691 ATAAATAAA
1 TTAAATAAA
5700 TAATAGAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
TTAAATAAAAGAAAGAA
Found at i:6405 original size:73 final size:73
Alignment explanation
Indices: 6275--6432 Score: 180
Period size: 73 Copynumber: 2.2 Consensus size: 73
6265 TAGCTAAAAC
*
6275 ATCCTAAATCCTAATTAAAACACTTAAAACTATTAAACTAAAATACCTAAAATAAATATAAAATA
1 ATCCTAAA-CTTAATTAAAACACTTAAAACTATTAAACTAAAATACCTAAAATAAATATAAAATA
6340 TAAAA-ATA
65 TAAAATATA
* * *
6348 ATCCTAAACTTAATTAAAATAC-TAAAACCTATTTAAACTAAAATA-C-AAAGTTAAAATATAAT
1 ATCCTAAACTTAATTAAAACACTTAAAA-CTA-TTAAACTAAAATACCTAAA-AT-AAATATAAA
* * *
6410 GTTTAAAATATT
62 ATATAAAATATA
6422 ATCCTAAACTT
1 ATCCTAAACTT
6433 GAGTTTTATT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
71 8 0.11
72 17 0.23
73 35 0.48
74 13 0.18
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.31
Consensus pattern (73 bp):
ATCCTAAACTTAATTAAAACACTTAAAACTATTAAACTAAAATACCTAAAATAAATATAAAATAT
AAAATATA
Found at i:10235 original size:3 final size:3
Alignment explanation
Indices: 10227--10277 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
10217 ATATGTTTTG
*
10227 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TTT TAT TAT TGAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
10275 TAT
1 TAT
10278 GCCTCACTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:16240 original size:3 final size:3
Alignment explanation
Indices: 16232--16336 Score: 185
Period size: 3 Copynumber: 35.0 Consensus size: 3
16222 TTTGATATGA
16232 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
16279 TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16327 TAT TGAT TAT
1 TAT T-AT TAT
16337 GTCTCACTAA
Statistics
Matches: 98, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
3 93 0.95
4 3 0.03
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:17259 original size:32 final size:32
Alignment explanation
Indices: 17213--17310 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
17203 ATAATACAAG
* *
17213 AATAATATTGGTACTACAACAGTATTGGTACTA-
1 AATAGTATTGGTACT--AACAGTATTGCTACTAC
* *
17246 GA-AGTATTGGTACTAATAGTATTGCTACTAC
1 AATAGTATTGGTACTAACAGTATTGCTACTAC
* *
17277 AATAGTATTGGTACTAACAGTATCGATACTAC
1 AATAGTATTGGTACTAACAGTATTGCTACTAC
17309 AA
1 AA
17311 AAACAATATC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
30 14 0.25
31 1 0.02
32 39 0.71
33 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (32 bp):
AATAGTATTGGTACTAACAGTATTGCTACTAC
Found at i:17307 original size:47 final size:47
Alignment explanation
Indices: 17213--17307 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 47
17203 ATAATACAAG
* * *
17213 AATAATATTGGTACTACAACAGTATTGGTACTAGAAGTATTGGTACT
1 AATAATATTGCTACTACAACAGTATTGGTACTAGAAGTATCGATACT
* *
17260 AATAGTATTGCTACTACAATAGTATTGGTACTA-ACAGTATCGATACT
1 AATAATATTGCTACTACAACAGTATTGGTACTAGA-AGTATCGATACT
17307 A
1 A
17308 CAAAAACAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
46 1 0.02
47 41 0.98
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.34
Consensus pattern (47 bp):
AATAATATTGCTACTACAACAGTATTGGTACTAGAAGTATCGATACT
Found at i:24574 original size:18 final size:18
Alignment explanation
Indices: 24551--24591 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
24541 AACTTAAACA
24551 AATTAATAATGAAAAATT
1 AATTAATAATGAAAAATT
**
24569 AATTAATAATTTAAAATT
1 AATTAATAATGAAAAATT
24587 AATTA
1 AATTA
24592 TATTCGTTCG
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:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AATTAATAATGAAAAATT
Found at i:28369 original size:20 final size:20
Alignment explanation
Indices: 28344--28393 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
28334 AGTGAACTTG
*
28344 GTATCGATGCCAC-CCTATGA
1 GTATCGATGCCACACCTA-CA
* *
28364 GTATCGATACCTCACCTACA
1 GTATCGATGCCACACCTACA
28384 GTATCGATGC
1 GTATCGATGC
28394 TTATTTCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (20 bp):
GTATCGATGCCACACCTACA
Found at i:31327 original size:116 final size:115
Alignment explanation
Indices: 31168--31612 Score: 460
Period size: 116 Copynumber: 3.8 Consensus size: 115
31158 TAAGGAGTTC
* *
31168 GATCAACATTTTCAACGGAGAGTTCATAATGAGAAGAACTCATCCACGGATGAAGAAGAAGTTCA
1 GATCAACATTTTCAA-GG-GAGTTCATAATGAGAAGAACTCATCCACAGAGGAAGAAGAAGTTCA
* * * **
31233 CAATAAGAAGAACTTGTTCAACATTTTGCTCAAATCTATCAAAGAATAAGAAG
64 TAATAAGAAGAACTTGTTCAACATTTTGCTCAAATCCATCATAGAA-AAGGTG
* *
31286 GATCAACATTTTCAATGGAGTTCATAATGAGAAAAACTCATCCACAGAGGAAGAAGAAGTTCATA
1 GATCAACATTTTCAAGGGAGTTCATAATGAGAAGAACTCATCCACAGAGGAAGAAGAAGTTCATA
* * * * * *
31351 ATAAGAAGAACTTGTTCAACCTTATACTCAAATCCACCATATAAGGAGGTG
66 ATAAGAAGAACTTGTTCAACATTTTGCTCAAATCCATCATAGAA-AAGGTG
* * * * * * * *
31402 GTTCAACATTTTCAAGGGAATTTATAATAAGAAGAACAT-GTCTACGGAGGGAGAAGAAGTTCAT
1 GATCAACATTTTCAAGGGAGTTCATAATGAGAAGAAC-TCATCCACAGAGGAAGAAGAAGTTCAT
* * * * * *
31466 AATGAGAAGAATTTGTTCAACCTTTAGATCAACTCCATCATAGAAAGAGGTG
65 AATAAGAAGAACTTGTTCAACATTTTGCTCAAATCCATCATAGAAA-AGGTG
** *** * * *
31518 GATCAACATTATAAATATAAAGTTCATAATGAGAAGAACTCACCCAAAGAGGAAGAATAAGTTCA
1 GATCAACATT-TTCA-AGGGAGTTCATAATGAGAAGAACTCATCCACAGAGGAAGAAGAAGTTCA
* *
31583 TAATGAGAAGAACTTGTTCGACATTTTGCT
64 TAATAAGAAGAACTTGTTCAACATTTTGCT
31613 AAGATCTATC
Statistics
Matches: 265, Mismatches: 57, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
116 186 0.70
117 5 0.02
118 74 0.28
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.25
Consensus pattern (115 bp):
GATCAACATTTTCAAGGGAGTTCATAATGAGAAGAACTCATCCACAGAGGAAGAAGAAGTTCATA
ATAAGAAGAACTTGTTCAACATTTTGCTCAAATCCATCATAGAAAAGGTG
Found at i:31648 original size:234 final size:232
Alignment explanation
Indices: 31170--31607 Score: 538
Period size: 232 Copynumber: 1.9 Consensus size: 232
31160 AGGAGTTCGA
* * *
31170 TCAACATTTTCAACGGAGAGTTCATAATGAGAAGAACTCATCCACGGATGAAGAAGAAGTTCACA
1 TCAACATTTTCAA-GG-GAGTTTATAATAAGAAGAACTCATCCACGGAGGAAGAAGAAGTTCACA
* * * **
31235 ATAAGAAGAACTTGTTCAACATTTTGCTCAAATCTATCAAAGAATAAGAAGGATCAACATTTTCA
64 ATAAGAAGAACTTGTTCAACATTTAGATCAAATCCATCAAAGAATAAGAAGGATCAACATTTAAA
** * *
31300 ATGGAGTTCATAATGAGAAAAACTCATCCACAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTG
129 ATAAAGTTCATAATGAGAAAAACTCACCCAAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTG
* *
31365 TTCAACCTTATACTCAAATCCACCATATAAGGAGGTGGT
194 TTCAACATTATACTCAAATCCACCATAGAAGGAGGTGGT
* * * * *
31404 TCAACATTTTCAAGGGAATTTATAATAAGAAGAACAT-GTCTACGGAGGGAGAAGAAGTTCATAA
1 TCAACATTTTCAAGGGAGTTTATAATAAGAAGAAC-TCATCCACGGAGGAAGAAGAAGTTCACAA
* * * * * **
31468 TGAGAAGAATTTGTTCAACCTTTAGATCAACTCCATCATAGAA-AGAGGTGGATCAACATTATAA
65 TAAGAAGAACTTGTTCAACATTTAGATCAAATCCATCAAAGAATA-AGAAGGATCAACATT-TAA
* * *
31532 ATATAAAGTTCATAATGAGAAGAACTCACCCAAAGAGGAAGAATAAGTTCATAATGAGAAGAACT
128 A-ATAAAGTTCATAATGAGAAAAACTCACCCAAAGAGGAAGAAGAAGTTCATAATAAGAAGAACT
*
31597 TGTTCGACATT
192 TGTTCAACATT
31608 TTGCTAAGAT
Statistics
Matches: 171, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
231 1 0.01
232 87 0.51
233 5 0.03
234 78 0.46
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (232 bp):
TCAACATTTTCAAGGGAGTTTATAATAAGAAGAACTCATCCACGGAGGAAGAAGAAGTTCACAAT
AAGAAGAACTTGTTCAACATTTAGATCAAATCCATCAAAGAATAAGAAGGATCAACATTTAAAAT
AAAGTTCATAATGAGAAAAACTCACCCAAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
CAACATTATACTCAAATCCACCATAGAAGGAGGTGGT
Found at i:31953 original size:22 final size:24
Alignment explanation
Indices: 31923--31978 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
31913 TTTATTATCA
*
31923 TTATTTATTATTA-TTA-CATATG
1 TTATATATTATTAGTTAGCATATG
*
31945 TTATATATTA-TAGTTAGTATATG
1 TTATATATTATTAGTTAGCATATG
31968 TTA-ATATTATT
1 TTATATATTATT
31979 TTATTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 2 0.07
22 18 0.62
23 9 0.31
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (24 bp):
TTATATATTATTAGTTAGCATATG
Found at i:42746 original size:103 final size:103
Alignment explanation
Indices: 42567--42772 Score: 376
Period size: 103 Copynumber: 2.0 Consensus size: 103
42557 AGTTGCCATA
* * *
42567 TATTGGTGCATCTGCACCAGCAGCACCAGACCAGTAATGCTTACATTTTACTGTCTAGATGCCAT
1 TATTGGTGCATCTGCACCAGCAGCAACAGACCAGTAATGCTTACATATTACTATCTAGATGCCAT
42632 TAATAGCTTATTAGAACTAGGGGAACAGATCAGTTAAG
66 TAATAGCTTATTAGAACTAGGGGAACAGATCAGTTAAG
*
42670 TATTGGTGCATCTGCACCAGCAGCAACGGACCAGTAATGCTTACATATTACTATCTAGATGCCAT
1 TATTGGTGCATCTGCACCAGCAGCAACAGACCAGTAATGCTTACATATTACTATCTAGATGCCAT
42735 TAATAGCTTATTAGAACTAGGGGAACAGATCAGTTAAG
66 TAATAGCTTATTAGAACTAGGGGAACAGATCAGTTAAG
42773 CTTAGATTTC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (103 bp):
TATTGGTGCATCTGCACCAGCAGCAACAGACCAGTAATGCTTACATATTACTATCTAGATGCCAT
TAATAGCTTATTAGAACTAGGGGAACAGATCAGTTAAG
Found at i:47466 original size:12 final size:12
Alignment explanation
Indices: 47449--47506 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
47439 TAATATATAG
47449 TTTTGAAAACAT
1 TTTTGAAAACAT
47461 TTTTGAAAACAT
1 TTTTGAAAACAT
* * *
47473 ATAT-AATATATAT
1 TTTTGAA-A-ACAT
47486 TTTTGAAAACAT
1 TTTTGAAAACAT
47498 TTTTGAAAA
1 TTTTGAAAA
47507 TATATATAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.05
12 27 0.73
13 6 0.16
14 2 0.05
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:47474 original size:37 final size:36
Alignment explanation
Indices: 47398--47599 Score: 190
Period size: 37 Copynumber: 5.7 Consensus size: 36
47388 ATATATATAT
* *
47398 ATATATAATATATAGTTTTAAAAACA-TTTTGAAAGC
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAA-A
47434 ATATATAATATATAGTTTTGAAAACATTTTTGAAAA
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAA
*
47470 CATATATAATATATATTTTTGAAAACATTTTTG---A
1 -ATATATAATATATAGTTTTGAAAACATTTTTGAAAA
47504 A-A-AT-ATATATAGTTTTGAAAACA-TTTTGAAAATA
1 ATATATAATATATAGTTTTGAAAACATTTTTG-AAA-A
* ** *
47538 TATATATAAAATATATAATTTT-AAAATGTTTTTGGAAA
1 -ATATAT--AATATATAGTTTTGAAAACATTTTTGAAAA
*
47576 ATATATAAAATATA-TTTTAGAAAA
1 ATATATAATATATAGTTTT-GAAAA
47600 AAACATGTTG
Statistics
Matches: 141, Mismatches: 9, Indels: 32
0.77 0.05 0.18
Matches are distributed among these distances:
29 5 0.04
30 18 0.13
31 2 0.01
32 1 0.01
33 1 0.01
34 6 0.04
35 8 0.06
36 30 0.21
37 47 0.33
38 1 0.01
39 6 0.04
40 16 0.11
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (36 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAAAA
Found at i:47540 original size:29 final size:30
Alignment explanation
Indices: 47478--47543 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
47468 AACATATATA
*
47478 ATATATATTTTTGAAAACATTTTTGAAAAT
1 ATATATAGTTTTGAAAACATTTTTGAAAAT
47508 ATATATAGTTTTGAAAACA-TTTTGAAAAT
1 ATATATAGTTTTGAAAACATTTTTGAAAAT
47537 ATATATA
1 ATATATA
47544 TAAAATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 17 0.49
30 18 0.51
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (30 bp):
ATATATAGTTTTGAAAACATTTTTGAAAAT
Found at i:47599 original size:105 final size:103
Alignment explanation
Indices: 47405--47599 Score: 259
Period size: 105 Copynumber: 1.9 Consensus size: 103
47395 TATATATATA
* *
47405 ATATATAGTTTTAAAAACATTTTGAAAGCATATATAATATATAGTTTTGAAAACATTTTTGAAAA
1 ATATATAGTTTTAAAAACATTTTGAAAACATATATAATATATAATTTTGAAAACATTTTTGAAAA
* *
47470 CATATATAATATATATTTTTGAAAACATTTTTGAAAAT
66 CATATATAAAATATATTTTAGAAAACATTTTTGAAAAT
* * **
47508 ATATATAGTTTTGAAAACATTTTGAAAATATATATATAAAATATATAATTTT-AAAATGTTTTTG
1 ATATATAGTTTTAAAAACATTTTG-AAA-ACATATAT--AATATATAATTTTGAAAACATTTTTG
*
47572 GAAA-ATATATAAAATATATTTTAGAAAA
62 AAAACATATATAAAATATATTTTAGAAAA
47600 AAACATGTTG
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
103 23 0.29
104 3 0.04
105 28 0.35
106 13 0.16
107 12 0.15
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.42
Consensus pattern (103 bp):
ATATATAGTTTTAAAAACATTTTGAAAACATATATAATATATAATTTTGAAAACATTTTTGAAAA
CATATATAAAATATATTTTAGAAAACATTTTTGAAAAT
Found at i:48770 original size:4 final size:4
Alignment explanation
Indices: 48761--48805 Score: 65
Period size: 4 Copynumber: 11.0 Consensus size: 4
48751 TCCTTTACGT
48761 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA CTTT- TTTGA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTT-A TTTA
48806 GTATTTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.08
4 29 0.76
5 6 0.16
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:48913 original size:10 final size:10
Alignment explanation
Indices: 48898--48933 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
48888 TTATATTCGT
48898 TTTTATATTA
1 TTTTATATTA
48908 TTTTATATTA
1 TTTTATATTA
*
48918 TTTTTATTTTA
1 -TTTTATATTA
48929 TTTTA
1 TTTTA
48934 CTTTTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTATATTA
Found at i:48923 original size:21 final size:22
Alignment explanation
Indices: 48886--48933 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
48876 ATTTAACATT
*
48886 TTTTATATTCGTTTTTATATTA
1 TTTTATATTCATTTTTATATTA
*
48908 TTTTATATT-ATTTTTATTTTA
1 TTTTATATTCATTTTTATATTA
48929 TTTTA
1 TTTTA
48934 CTTTTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTATATTCATTTTTATATTA
Found at i:48926 original size:16 final size:17
Alignment explanation
Indices: 48905--48939 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
48895 CGTTTTTATA
48905 TTATTTTATATTA-TTT
1 TTATTTTATATTACTTT
*
48921 TTATTTTATTTTACTTT
1 TTATTTTATATTACTTT
48938 TT
1 TT
48940 TTTCTATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTTATATTACTTT
Found at i:48986 original size:2 final size:2
Alignment explanation
Indices: 48981--49028 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
48971 ACTTTTTTTA
48981 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
49023 AT AT AT
1 AT AT AT
49029 TTCACAATTG
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:51864 original size:30 final size:29
Alignment explanation
Indices: 51826--51888 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
51816 GGTTACGTCA
**
51826 GGGGCCATATTTTAAAC-GAACTAAATGTT
1 GGGGCCATATTGCAAACAG-ACTAAATGTT
51855 GGGGACCATATTGCAAACAGACTAAATGTT
1 GGGG-CCATATTGCAAACAGACTAAATGTT
51885 GGGG
1 GGGG
51889 GATTGTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 4 0.13
30 25 0.83
31 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.25
Consensus pattern (29 bp):
GGGGCCATATTGCAAACAGACTAAATGTT
Found at i:60390 original size:253 final size:256
Alignment explanation
Indices: 59938--60439 Score: 834
Period size: 253 Copynumber: 2.0 Consensus size: 256
59928 CACATTCGTA
* *
59938 AAATGTGACATGGGCAGTTCATACCCAAAATCATTCATTAAACTTATTAAAATATTATGAATATA
1 AAATGTGACATGGGCAATTCATACCCAAAATCATTCATAAAACTTATTAAAATATTATGAATATA
60003 ATTCTATAATCAAAACATAATTCATATCTTTGAAATAAACAAGGTGAGGTTGACTTATCGCAAGT
66 ATTCTATAATCAAAACATAATTCATATCTTTGAAATAAACAAGGTGAGGTTGACTTATCGCAAGT
*
60068 CGTCCTCGATCAAAATAATAAAATAATAAATTGCACTCACCTTTGCCTCACTACAGAACTTGTAT
131 CGTCCTCGATCAAAATAATAAAATAATAAACTGCACTCACCTTTGCCTCACTACAGAACTTGTAT
**
60133 ACGATAATCCTAGTCACGAGCTTTGTCCTTTCCTTTCAGATCGTTCGGATTGCTAGTTTCAT
196 ACGATAATCCTAGTCACGAGCTTTGTCAATT-CTTTCAGATCGTTCGGATTGCTAGTTTCAT
* * *
60195 AAATGTGTCATGGGCAATTCATACCCTAAATCATTCATAAAACTTATTAAAA-ATTATGGATATA
1 AAATGTGACATGGGCAATTCATACCCAAAATCATTCATAAAACTTATTAAAATATTATGAATATA
*
60259 ATT-TCATAATC-AAA-ATAATTCATATCTTTGAAA-AAACAAGGTGAGGTTGACTTATTGCAAG
66 ATTCT-ATAATCAAAACATAATTCATATCTTTGAAATAAACAAGGTGAGGTTGACTTATCGCAAG
* * *
60320 TTGTCCTCGATCAAAATAATAAAATAATAAACTGCATTCACCTTTGCCTCACTACAGAATTTGTA
130 TCGTCCTCGATCAAAATAATAAAATAATAAACTGCACTCACCTTTGCCTCACTACAGAACTTGTA
*
60385 TACGATAATCCTAGTCTCGAGCTTTGTCAATTCTTTCAGATCGTTCGGATTGCTA
195 TACGATAATCCTAGTCACGAGCTTTGTCAATTCTTTCAGATCGTTCGGATTGCTA
60440 ATTTATTGTA
Statistics
Matches: 231, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
252 23 0.10
253 117 0.51
254 19 0.08
255 4 0.02
256 20 0.09
257 48 0.21
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Consensus pattern (256 bp):
AAATGTGACATGGGCAATTCATACCCAAAATCATTCATAAAACTTATTAAAATATTATGAATATA
ATTCTATAATCAAAACATAATTCATATCTTTGAAATAAACAAGGTGAGGTTGACTTATCGCAAGT
CGTCCTCGATCAAAATAATAAAATAATAAACTGCACTCACCTTTGCCTCACTACAGAACTTGTAT
ACGATAATCCTAGTCACGAGCTTTGTCAATTCTTTCAGATCGTTCGGATTGCTAGTTTCAT
Done.