Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005215.1 Hibiscus syriacus cultivar Beakdansim tig00011805_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: 62326
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:9903 original size:44 final size:44
Alignment explanation
Indices: 9847--9990 Score: 148
Period size: 44 Copynumber: 3.3 Consensus size: 44
9837 ATGTACTATG
* *
9847 TGATCTATGTGAACA-TAAGAGA-ACACGATATAAGTTATGTGACA
1 TGATCTACGTGAACACT-AGA-ACACACGATATAAGCTATGTGACA
* * * *
9891 TGATCTACGTGAATACTTGAACATAGGATATAAGCTATGTGACA
1 TGATCTACGTGAACACTAGAACACACGATATAAGCTATGTGACA
* * * *
9935 TGATCTACGTGAATACTTGAACATAAGATATAAGCTATGTGACA
1 TGATCTACGTGAACACTAGAACACACGATATAAGCTATGTGACA
* *
9979 TAACCTACGTGA
1 TGATCTACGTGA
9991 TTACTGGTCT
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
43 1 0.01
44 87 0.98
45 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (44 bp):
TGATCTACGTGAACACTAGAACACACGATATAAGCTATGTGACA
Found at i:9914 original size:52 final size:47
Alignment explanation
Indices: 9873--9995 Score: 168
Period size: 44 Copynumber: 2.7 Consensus size: 47
9863 AAGAGAACAC
*
9873 GATATAAGTTATGTGACATGATCTACGTGAATACTTGAACAT---AG
1 GATATAAGCTATGTGACATGATCTACGTGAATACTTGAACATAAGAG
9917 GATATAAGCTATGTGACATGATCTACGTGAATACTTGAACAT-A-A-
1 GATATAAGCTATGTGACATGATCTACGTGAATACTTGAACATAAGAG
* * *
9961 GATATAAGCTATGTGACATAACCTACGTGATTACT
1 GATATAAGCTATGTGACATGATCTACGTGAATACT
9996 GGTCTAGTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
44 73 0.99
45 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (47 bp):
GATATAAGCTATGTGACATGATCTACGTGAATACTTGAACATAAGAG
Found at i:10154 original size:24 final size:24
Alignment explanation
Indices: 10096--10163 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 24
10086 GAGTCAAGGG
* *
10096 TTCTACGCGGTCCATCAGGAC-AA
1 TTCTACGCGGTCCTTCGGGACAAA
*
10119 TTCTACGTGGTCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
*
10143 TTCTACACGGT-CTTCGGGACA
1 TTCTACGCGGTCCTTCGGGACA
10164 TATATGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGACAAA
Found at i:12405 original size:12 final size:12
Alignment explanation
Indices: 12390--12419 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
12380 GCATCAAGAT
12390 AGTTTTAAGAGA
1 AGTTTTAAGAGA
12402 AGTTTTAAGAGA
1 AGTTTTAAGAGA
12414 AGTTTT
1 AGTTTT
12420 GCGTAGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (12 bp):
AGTTTTAAGAGA
Found at i:14852 original size:23 final size:23
Alignment explanation
Indices: 14826--14901 Score: 82
Period size: 24 Copynumber: 3.3 Consensus size: 23
14816 GAGTCGAGGG
*
14826 TTCTATGCGGTCCTTCGGGACAA
1 TTCTATGCGATCCTTCGGGACAA
* * **
14849 TTCTACGTGATCCTTCAAGACAAA
1 TTCTATGCGATCCTTCGGGAC-AA
*
14873 TTCTATGCGTTCCTTCGGGAC-A
1 TTCTATGCGATCCTTCGGGACAA
14895 TTCTATG
1 TTCTATG
14902 TGGCTCTTCG
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
22 8 0.19
23 16 0.38
24 18 0.43
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (23 bp):
TTCTATGCGATCCTTCGGGACAA
Found at i:21624 original size:16 final size:15
Alignment explanation
Indices: 21592--21625 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
21582 GTATTTCAAA
*
21592 AAAAAGTACCAAGAT
1 AAAAAGTACCAACAT
21607 AAAAAGTACCGAACAT
1 AAAAAGTACC-AACAT
21623 AAA
1 AAA
21626 CAATAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.62, C:0.15, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAAAGTACCAACAT
Found at i:26099 original size:24 final size:24
Alignment explanation
Indices: 26071--26155 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
26061 CAGTCGAAAT
26071 TGCCACATAGAATTTGCACTGAAG
1 TGCCACATAGAATTTGCACTGAAG
* * *
26095 TGCCACGTAGGATATGCACTGAAG
1 TGCCACATAGAATTTGCACTGAAG
* *
26119 TGCCATATAG-ATTTGTC-CCGAAG
1 TGCCACATAGAATTTG-CACTGAAG
26142 -GACCACATAGAATT
1 TG-CCACATAGAATT
26156 GTCCCGAAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
22 1 0.02
23 16 0.32
24 33 0.66
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (24 bp):
TGCCACATAGAATTTGCACTGAAG
Found at i:26151 original size:23 final size:23
Alignment explanation
Indices: 26125--26199 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
26115 GAAGTGCCAT
*
26125 ATAGATTTGTCCCGAAGGACCAC
1 ATAGAATTGTCCCGAAGGACCAC
26148 ATAGAATTGTCCCGAAGGACCAC
1 ATAGAATTGTCCCGAAGGACCAC
* *
26171 ATAGAATTGTCCCCAAGGACAAC
1 ATAGAATTGTCCCGAAGGACCAC
*
26194 GTAGAA
1 ATAGAA
26200 CCCTCAACTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (23 bp):
ATAGAATTGTCCCGAAGGACCAC
Found at i:33075 original size:23 final size:23
Alignment explanation
Indices: 33049--33096 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
33039 CAATGAAGTG
*
33049 CCACATAGAGCTT-TCCTGAAGGA
1 CCACATAGA-ATTGTCCTGAAGGA
*
33072 CCACATTGAATTGTCCTGAAGGA
1 CCACATAGAATTGTCCTGAAGGA
33095 CC
1 CC
33097 GCGTAGAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (23 bp):
CCACATAGAATTGTCCTGAAGGA
Found at i:39577 original size:2 final size:2
Alignment explanation
Indices: 39570--39625 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
39560 AGTAAAACTT
39570 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39612 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
39626 AAGTTAGTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41531 original size:59 final size:59
Alignment explanation
Indices: 41439--42209 Score: 824
Period size: 59 Copynumber: 13.1 Consensus size: 59
41429 TTTTCCATAC
* ** *
41439 GGAAATTCATACACTTAGTATGATTTCATTCTCATTTTAGCACACTTAGTGCTCTATTT
1 GGAAATTCATACACTTAGTATGATTTCCTTCTCATTTTAGCACACAAAGTGCTCTATCT
* * ** *
41498 GGAAATTCATACATTTAGTATGATTTCCTTCTCATTATAGCACACTTAGTGCTCTGTCT
1 GGAAATTCATACACTTAGTATGATTTCCTTCTCATTTTAGCACACAAAGTGCTCTATCT
* * ** *
41557 GGAAATCCATACACTTAGTATGATTTCCTTCACATTTTAGCACACTTAGTGCTTTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTCTCATTTTAGCACACAAAGTGCTCTATCT
* * * * * *
41616 GGAAATTCATACACTTAGTATGATTTTCTTATCATTTTAGCACCCGAAGTTCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTCTCATTTTAGCACACAAAGTGCTCTATCT
* * *
41675 GGAAATTCAGAC-CTTTAATATAATTTCCTTAC-CATTTTAGCACACAAAGTGCTCTATCT
1 GGAAATTCATACAC-TTAGTATGATTTCCTT-CTCATTTTAGCACACAAAGTGCTCTATCT
* * * *
41734 AGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTCTCATTTTAGCACACAAAGTGCTCTATCT
* * * *
41793 GGAAATTCATACATTTAATATGATTTCCTTAC-CATTTTAGCACACAAAGTGTTCTATTT
1 GGAAATTCATACACTTAGTATGATTTCCTT-CTCATTTTAGCACACAAAGTGCTCTATCT
* ** * * * *
41852 GGAAATCCATACACTTAGTATGATTTGGTTATCATTTTAGCGCACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTCTCATTTTAGCACACAAAGTGCTCTATCT
* * * *
41911 GGAAATTCATACATTTAATATGATTTCTTTAC-CATTTTAGCACACAAAGTGCTCTATAT
1 GGAAATTCATACACTTAGTATGATTTCCTT-CTCATTTTAGCACACAAAGTGCTCTATCT
* * * * *
41970 GG-AATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATTT
1 GGAAATTCATACACTTAGTATGATTTCCTTCTCATTTTAGCACACAAAGTGCTCTATCT
* * * * * * * *
42028 GAAAATTCAAACATTTAATATGATTTCCTTAC-AATTTTAG-AAAAAAAATGCAT-TATCT
1 GGAAATTCATACACTTAGTATGATTTCCTT-CTCATTTTAGCACACAAAGTGC-TCTATCT
* * * * * *
42086 AGAAATCCATACACTTAATATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTCTCATTTTAGCACACAAAGTGCTCTATCT
* * *
42145 AGAAATTCATACA-TTAAATATGATTTCCTTACT-ATTTTAGCACAAAAAGTGCTCTATCT
1 GGAAATTCATACACTT-AGTATGATTTCCTT-CTCATTTTAGCACACAAAGTGCTCTATCT
42204 GGAAAT
1 GGAAAT
42210 CACCATATAT
Statistics
Matches: 591, Mismatches: 105, Indels: 32
0.81 0.14 0.04
Matches are distributed among these distances:
58 94 0.16
59 495 0.84
60 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCTTCTCATTTTAGCACACAAAGTGCTCTATCT
Found at i:41651 original size:118 final size:117
Alignment explanation
Indices: 41439--42210 Score: 996
Period size: 118 Copynumber: 6.6 Consensus size: 117
41429 TTTTCCATAC
* * * ** *
41439 GGAAATTCATACACTTAGTATGATTTCATTCTCATTTTAGCACACTTAGTGCTCTATTTGGAAAT
1 GGAAATTCATACACTTAATATGATTTCCTT-ACATTTTAGCACACAAAGTGCTCTATCTGGAAAT
* * * * ** * *
41504 TCATACATTTAGTATGATTTCCTTCTCATTATAGCACACTTAGTGCTCTGTCT
65 CCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * ** *
41557 GGAAATCCATACACTTAGTATGATTTCCTTCACATTTTAGCACACTTAGTGCTTTATCTGGAAAT
1 GGAAATTCATACACTTAATATGATTTCCTT-ACATTTTAGCACACAAAGTGCTCTATCTGGAAAT
* * * *
41622 TCATACACTTAGTATGATTTTCTTATCATTTTAGCACCCGAAGTTCCCTATCT
65 CCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * *
41675 GGAAATTCAGAC-CTTTAATATAATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTAGAAA
1 GGAAATTCATACAC-TTAATATGATTTCCTTA-CATTTTAGCACACAAAGTGCTCTATCTGGAAA
*
41739 TCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCT
64 TCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * *
41793 GGAAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGTTCTATTTGGAAAT
1 GGAAATTCATACACTTAATATGATTTCCTTA-CATTTTAGCACACAAAGTGCTCTATCTGGAAAT
** *
41858 CCATACACTTAGTATGATTTGGTTATCATTTTAGCGCACGAAGTGCCCTATCT
65 CCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * *
41911 GGAAATTCATACATTTAATATGATTTCTTTACCATTTTAGCACACAAAGTGCTCTATATGG-AAT
1 GGAAATTCATACACTTAATATGATTTCCTTA-CATTTTAGCACACAAAGTGCTCTATCTGGAAAT
*
41975 CCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATTT
65 CCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * * * * * *
42028 GAAAATTCAAACATTTAATATGATTTCCTTACAATTTTAG-AAAAAAAATGCAT-TATCTAGAAA
1 GGAAATTCATACACTTAATATGATTTCCTTAC-ATTTTAGCACACAAAGTGC-TCTATCTGGAAA
*
42091 TCCATACACTTAATATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
64 TCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* *
42145 AGAAATTCATACA-TTAAATATGATTTCCTTACTATTTTAGCACAAAAAGTGCTCTATCTGGAAA
1 GGAAATTCATACACTT-AATATGATTTCCTTAC-ATTTTAGCACACAAAGTGCTCTATCTGGAAA
42209 TC
64 TC
42211 ACCATATATA
Statistics
Matches: 583, Mismatches: 62, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
116 16 0.03
117 178 0.31
118 389 0.67
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (117 bp):
GGAAATTCATACACTTAATATGATTTCCTTACATTTTAGCACACAAAGTGCTCTATCTGGAAATC
CATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
Found at i:41741 original size:177 final size:177
Alignment explanation
Indices: 41439--42209 Score: 908
Period size: 177 Copynumber: 4.4 Consensus size: 177
41429 TTTTCCATAC
* * ** *
41439 GGAAATTCATACACTTAGTATGATTTCATTCTCATTTTAGCACACTTAGTGCTCTATTTGGAAAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATTTGGAAAT
* * ** * *
41504 TCATACATTTAGTATGATTTCCTT-CTCATTATAGCACACTTAGTGCTCTGTCTGGAAATCCATA
66 TCATACATTTAATATGATTTCCTTAC-CATTTTAGCACACAAAGTGCTCTATCTAGAAATCCATA
* ** **
41568 CACTTAGTATGATTTCCTTCA-CATTTTAGCACACTTAGTGCTTTATCT
130 CACTTAATATGATTTCCTT-ATCATTTTAGCACACAAAGTGCCCTATCT
* * * *
41616 GGAAATTCATACACTTAGTATGATTTTCTTATCATTTTAGCACCCGAAGTTCCCTATCTGGAAAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATTTGGAAAT
* * *
41681 TCAGACCTTTAATATAATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTAGAAATCCATAC
66 TCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTAGAAATCCATAC
*
41746 ACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCT
131 ACTTAATATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCT
* * * * **
41793 GGAAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGTTCTATTTGGAAAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATTTGGAAAT
* * * ** * * * * * *
41858 CCATACACTTAGTATGATTTGGTTATCATTTTAGCGCACGAAGTGCCCTATCTGGAAATTCATAC
66 TCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTAGAAATCCATAC
* * * * *
41923 ATTTAATATGATTTCTTTACCATTTTAGCACACAAAGTGCTCTATAT
131 ACTTAATATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCT
* *
41970 GG-AATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATTTGAAAAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATTTGGAAAT
* * * * *
42034 TCAAACATTTAATATGATTTCCTTACAATTTTAG-AAAAAAAATGCAT-TATCTAGAAATCCATA
66 TCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGC-TCTATCTAGAAATCCATA
*
42097 CACTTAATATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
130 CACTTAATATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCT
* * ** * *
42145 AGAAATTCATACA-TTAAATATGATTTCCTTA-CTATTTTAGCACAAAAAGTGCTCTATCTGGAA
1 GGAAATTCATACACTT-AGTATGATTTCCTTATC-ATTTTAGCACACGAAGTGCCCTATTTGGAA
42208 AT
64 AT
42210 CACCATATAT
Statistics
Matches: 498, Mismatches: 90, Indels: 13
0.83 0.15 0.02
Matches are distributed among these distances:
175 66 0.13
176 131 0.26
177 300 0.60
178 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (177 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATTTGGAAAT
TCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTAGAAATCCATAC
ACTTAATATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCT
Found at i:43303 original size:3 final size:3
Alignment explanation
Indices: 43295--43324 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43285 TACCCACGAT
43295 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
43325 TGTAGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:52579 original size:23 final size:21
Alignment explanation
Indices: 52527--52588 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
52517 TTTTGGTGCA
*
52527 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
52547 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
52568 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
52589 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:56369 original size:59 final size:59
Alignment explanation
Indices: 56299--57001 Score: 749
Period size: 59 Copynumber: 12.1 Consensus size: 59
56289 TTTTTCATAC
*
56299 GGAAATTCATACACTTAGTAAT-ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
1 GGAAATTCATACACTTAGT-ATGATTTCCTTATCATTTTAGCACACTAAGTGCTCTATCT
* * * ** *
56358 AGAAATACATACACTTAGTATGATTTCCTTCTTGTTTTAGCACAC-ATAGTGCTCTGTCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTA-AGTGCTCTATCT
* * * *
56417 AGAAATCCATACACTTAGTATGATTTCCTTCTCATTTTAGCACACTTAGTGCTCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCTCTATCT
*
56476 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCAC-CGGAAGTGCTCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAC-TAAGTGCTCTATCT
* * * * *
56535 GGAAATTCAGAC-CTTTAATATGATTTCCTTACCATTTTAACACA-TAAAGTGCTATATCT
1 GGAAATTCATACAC-TTAGTATGATTTCCTTATCATTTTAGCACACT-AAGTGCTCTATCT
* * * * * * * *
56594 GAAAATCCATAAACTTAGTATGA-TTCCCTATAATTTTAGCACACAAAGTTCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCTCTATCT
* * * * * *
56652 AGAAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTTTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCTCTATCT
** * * * *
56711 TAAAATCCATACTCTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCTCTATCT
* * * * * *
56770 GGAAATTGATACATTTAATATGATTTCCTTACCA-TTTAGCACACAAAGTGCTATATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCTCTATCT
* * * * *
56828 GGAAATCCATACACCTAGTATGATTTCCTTATCATTTTATCACA-TGAA--ACCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACT-AAGTGCTCTATCT
* *
56885 GGAAATGCATACA-TT--TATGATTTCCTTATCATTTTAGCACAC-AAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCTCTATCT
* *
56940 GGAAATTCATACA-TT--TATGATTTCCTTACCATTTTAGTACA-TAAAGTGCTCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACT-AAGTGCTCTATCT
56996 GGAAAT
1 GGAAAT
57002 CACCATACAT
Statistics
Matches: 539, Mismatches: 88, Indels: 37
0.81 0.13 0.06
Matches are distributed among these distances:
53 2 0.00
54 25 0.05
55 46 0.09
56 19 0.04
57 18 0.03
58 96 0.18
59 332 0.62
60 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCTCTATCT
Found at i:56704 original size:176 final size:175
Alignment explanation
Indices: 56299--57001 Score: 677
Period size: 176 Copynumber: 4.0 Consensus size: 175
56289 TTTTTCATAC
**
56299 GGAAATTCATACACTTAGTAAT-ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTAGAAA
1 GGAAATTCATACACTTAGT-ATGATTTCCTTATCATTTTAGCACACAAAGTGCTCTATCTAGAAA
** * *
56363 TACATACAC-TTAGTATGATTTCCTT-CTTGTTTTAGCACACATAGTGCTCTGTCT-AGAAATCC
65 TACATAC-CTTTAGTATGATTTCCTTAC-CATTTTAGCACACAAAGTGCTCTATCTGA-AAATCC
* * **
56425 ATACACTTAGTATGATTTCCTTCTCATTTTAGCACACTTAGTGCTCTATCT
127 ATACACTTAGTATGA-TTCCCT-TAATTTTAGCACACAAAGTGCTCTATCT
* *
56476 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCAC-CGGAAGTGCTCTATCTGGAAA
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAC-AAAGTGCTCTATCTAGAAA
* * * * * *
56540 TTCAGACCTTTAATATGATTTCCTTACCATTTTAACACATAAAGTGCTATATCTGAAAATCCATA
65 TACATACCTTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGAAAATCCATA
* * *
56605 AACTTAGTATGATTCCCTATAATTTTAGCACACAAAGTTCCCTATCT
130 CACTTAGTATGATTCCCT-TAATTTTAGCACACAAAGTGCTCTATCT
* * * * *
56652 AGAAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTTTATCTTA-AAA
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCTCTATC-TAGAAA
* * * * * **
56716 TCCATA-CTCTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAATTGAT
65 TACATACCT-TTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGAAAATCCAT
* * * *
56780 ACATTTAATATGATTTCCTTACCA-TTTAGCACACAAAGTGCTATATCT
129 ACACTTAGTATGATTCCCTTA--ATTTTAGCACACAAAGTGCTCTATCT
* * * * * *
56828 GGAAATCCATACACCTAGTATGATTTCCTTATCATTTTATCACATGAAA---CCCTATCTGGAAA
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACA-CAAAGTGCTCTATCTAGAAA
* * * * * *
56890 TGCATA-CATT--TATGATTTCCTTATCATTTTAGCACAC-AAGTGCCCTATCTGGAAATTCATA
65 TACATACCTTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGAAAATCCATA
* * *
56951 CA-TT--TATGATTTCCTTACCATTTTAGTACATAAAGTGCTCTATCT
130 CACTTAGTATGATTCCCTTA--ATTTTAGCACACAAAGTGCTCTATCT
56996 GGAAAT
1 GGAAAT
57002 CACCATACAT
Statistics
Matches: 449, Mismatches: 64, Indels: 35
0.82 0.12 0.06
Matches are distributed among these distances:
167 16 0.04
168 27 0.06
169 2 0.00
170 25 0.06
171 27 0.06
173 3 0.01
174 14 0.03
175 4 0.01
176 207 0.46
177 122 0.27
178 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (175 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCTCTATCTAGAAAT
ACATACCTTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATCTGAAAATCCATAC
ACTTAGTATGATTCCCTTAATTTTAGCACACAAAGTGCTCTATCT
Done.