Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005281.1 Hibiscus syriacus cultivar Beakdansim tig00011943_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: 76490
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1104 original size:16 final size:16
Alignment explanation
Indices: 1074--1121 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1064 TTGATTTTTC
* *
1074 TAAAATATAATATAAAT
1 TAAAA-ATAAAATAAAA
1091 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
1107 TAAAAATAAATATAA
1 TAAAAATAAA-ATAA
1122 TCGGATATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:3221 original size:59 final size:59
Alignment explanation
Indices: 3123--3472 Score: 542
Period size: 59 Copynumber: 5.9 Consensus size: 59
3113 TAAATTCAAT
* * * *
3123 TGGAATTTCATACAAACAGTATGATTTCCTTATCC-TTTTAGCACACAGAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTA-CCATTTTAGCACACAAAGTGCCCTATC
* *
3182 TGGAAATTCATACACTTAGTATGATTTTCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
3241 TAGAAATTCATACACATAGTATGATTTTCTTACAATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
3300 TGGAAATTCATACACATAGTATAATTTTCTTACCATTTTAGCACACAAAGTTCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
3359 TGGAAATTCATACACATAGTATGATTTCCTTACCAGTTTAGCACATAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
3418 TGGAAATTCATAGACATA-TATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
3473 TTGGTAATTC
Statistics
Matches: 269, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
58 37 0.14
59 232 0.86
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (59 bp):
TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:3782 original size:19 final size:19
Alignment explanation
Indices: 3737--3783 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3727 CAAAATATTT
*
3737 ATTATCAACTTCCTATAAC
1 ATTATCAGCTTCCTATAAC
3756 ATTATCAGCTTCCTATAAC
1 ATTATCAGCTTCCTATAAC
3775 ATTATCAGC
1 ATTATCAGC
3784 CCTAACTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (19 bp):
ATTATCAGCTTCCTATAAC
Found at i:3833 original size:21 final size:22
Alignment explanation
Indices: 3805--3862 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
3795 ATTTTCAACC
*
3805 CTTAGGTATCGATA-T-CCCTA
1 CTTAGGTATCGATACTACCCCA
*
3825 CTTATGGTATTGATACTACCCCA
1 CTTA-GGTATCGATACTACCCCA
3848 -TTAGGGTATCGATAC
1 CTTA-GGTATCGATAC
3863 CCCCTTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 9 0.29
22 14 0.45
23 4 0.13
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (22 bp):
CTTAGGTATCGATACTACCCCA
Found at i:3980 original size:95 final size:94
Alignment explanation
Indices: 3809--3984 Score: 207
Period size: 95 Copynumber: 1.9 Consensus size: 94
3799 TCAACCCTTA
* * * *
3809 GGTATCGATATCCCTACTTATGGTATTGATACTACCCCATTAGGGTATCGATACCCCCTTTATGT
1 GGTATCGATATCCCTACTTATGGTATTGATAC-ACCCAACTAGGGTAACGATACCCCCTCTATGT
3874 ATCAAGACCAAAATTAGCTTCGAAGTAACCT
65 ATCAAGACC-AAATTAGCTTCGAAGTAACCT
*
3905 GGTATCGATA-CCCT-CATTATGGTATTGATAC-CCCTAAGCTATGGTAACGATA-CCCCTCTAT
1 GGTATCGATATCCCTAC-TTATGGTATTGATACACCC-AA-CTAGGGTAACGATACCCCCTCTAT
* *
3966 GTATCGATATCCAAATTAG
63 GTATCAAGA-CCAAATTAG
3985 ATTTGAAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
93 3 0.04
94 24 0.35
95 32 0.46
96 10 0.14
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (94 bp):
GGTATCGATATCCCTACTTATGGTATTGATACACCCAACTAGGGTAACGATACCCCCTCTATGTA
TCAAGACCAAATTAGCTTCGAAGTAACCT
Found at i:10167 original size:59 final size:59
Alignment explanation
Indices: 10069--10415 Score: 525
Period size: 59 Copynumber: 5.9 Consensus size: 59
10059 TAAATTCAAT
* * ** ** *
10069 TGGAATTTCATACAAACGGTATGATTTCCTTATCC-TTTTAGCACACAGTGTTCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTA-CCATTTTAGCACACAAAGTGCCCTATC
* *
10128 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATA
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
** *
10187 TGGAAATTCATACACATAGTATGATTTCCTTAATATTTTAGCACACAAAGTGCCCCATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
10246 TGGAAACTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTGTC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
10305 TAGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
10364 TGGAAATTCATACACATAGTATGATTTTCTTACAATTTTAGCACACAAAGTG
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTG
10416 ACCTTTGGTA
Statistics
Matches: 262, Mismatches: 25, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
58 2 0.01
59 260 0.99
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.33
Consensus pattern (59 bp):
TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:10763 original size:21 final size:20
Alignment explanation
Indices: 10735--10817 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 20
10725 ATTTCCAGCC
10735 CTTA-GGTATCGATACCCCT
1 CTTATGGTATCGATACCCCT
10754 GCTTATGGTATCGATACCCCT
1 -CTTATGGTATCGATACCCCT
*
10775 ACTTATGGTATCAATACTACCC-
1 -CTTATGGTATCGATAC--CCCT
*
10797 CATTAGGGTATCGATACCCCT
1 C-TTATGGTATCGATACCCCT
10818 TCATGTATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
20 7 0.13
21 31 0.57
22 13 0.24
23 3 0.06
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (20 bp):
CTTATGGTATCGATACCCCT
Found at i:10905 original size:22 final size:21
Alignment explanation
Indices: 10852--10908 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
10842 TTCGAAGTAA
*
10852 CATGGTATCGATA-CCCTCAT
1 CATGGTATCGATACCCCTAAT
10872 CATGGTATCGATACCCCTAAT
1 CATGGTATCGATACCCCTAAT
*
10893 CTATGGTACCGATACC
1 C-ATGGTATCGATACC
10909 TTCTAAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.39
21 7 0.21
22 13 0.39
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (21 bp):
CATGGTATCGATACCCCTAAT
Found at i:11941 original size:21 final size:22
Alignment explanation
Indices: 11910--11969 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
11900 ATCTCAGTAG
11910 TGCTAAGGCACTTTAGTATTAA
1 TGCTAAGGCACTTTAGTATTAA
* *
11932 TGC-AATGCACTTTCA-TATTAG
1 TGCTAAGGCACTTT-AGTATTAA
11953 TGCTAAGGCACTTTAGT
1 TGCTAAGGCACTTTAGT
11970 TATTCAAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (22 bp):
TGCTAAGGCACTTTAGTATTAA
Found at i:23002 original size:19 final size:18
Alignment explanation
Indices: 22958--23002 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
22948 AGATGATATC
22958 AAACATTAAACAACTTAA
1 AAACATTAAACAACTTAA
* * *
22976 TAATATTATAACAATTTAA
1 AAACATTA-AACAACTTAA
22995 AAACATTA
1 AAACATTA
23003 CATTTGAAGT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (18 bp):
AAACATTAAACAACTTAA
Found at i:26962 original size:20 final size:19
Alignment explanation
Indices: 26937--26990 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
26927 ATTAAGGAAG
26937 TTCAAAGAAGAAAAGAAAAA
1 TTCAAA-AAGAAAAGAAAAA
* *
26957 TTCAAAAAAGAAAAAGAGAAT
1 TTC-AAAAAG-AAAAGAAAAA
26978 TTCAAAAAGAAAA
1 TTCAAAAAGAAAA
26991 CAAAGCCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.13
20 12 0.40
21 14 0.47
ACGTcount: A:0.69, C:0.06, G:0.13, T:0.13
Consensus pattern (19 bp):
TTCAAAAAGAAAAGAAAAA
Found at i:26973 original size:21 final size:21
Alignment explanation
Indices: 26937--26990 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
26927 ATTAAGGAAG
*
26937 TTCAAAGAAG-AAAAGAAAAA
1 TTCAAAAAAGAAAAAGAAAAA
* *
26957 TTCAAAAAAGAAAAAGAGAAT
1 TTCAAAAAAGAAAAAGAAAAA
26978 TTC-AAAAAGAAAA
1 TTCAAAAAAGAAAA
26991 CAAAGCCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.69, C:0.06, G:0.13, T:0.13
Consensus pattern (21 bp):
TTCAAAAAAGAAAAAGAAAAA
Found at i:37036 original size:2 final size:2
Alignment explanation
Indices: 37029--37072 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
37019 TTAATGGGTT
37029 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
37071 TA
1 TA
37073 GAAAATCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39866 original size:18 final size:18
Alignment explanation
Indices: 39843--39882 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
39833 TTGTTTGATC
39843 GATAATTTGGTGCCTTTA
1 GATAATTTGGTGCCTTTA
39861 GATAATTTGGTGCCTTTA
1 GATAATTTGGTGCCTTTA
39879 GATA
1 GATA
39883 CGTGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (18 bp):
GATAATTTGGTGCCTTTA
Found at i:41113 original size:43 final size:43
Alignment explanation
Indices: 41066--41373 Score: 140
Period size: 43 Copynumber: 7.2 Consensus size: 43
41056 TTTGTCACAA
* * *
41066 AAACGCCGCAATAAGTTTTGATGTTTAGCGGCATTTTCCCTAC
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGCATTTTACCTAC
* * * *
41109 AAACGCCGCAGTAGGTGTTGATATTTAGCGGCGTTTTACTTAC
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGCATTTTACCTAC
* * * * * * ** *
41152 AATCGCCGCAGTAGGTGTTGATATTTTGTGGCTTTTTTTCAAC
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGCATTTTACCTAC
* * * * * * *
41195 AAACGACACAATAGGTGATGATGTTTAGCGGCGTTTCT-CC-CC
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGCATTT-TACCTAC
** * * * * * * * * *
41237 AAACATCGCAGTAGGTTTTCAGATTAAGCGGCATTGTATCGA-
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGCATTTTACCTAC
* * * * * *
41279 AAACGACGCAATAAGGGTTGAGAATTAGCGGCGTTTTTA-TTGA-
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGC-ATTTTACCT-AC
* * ** * *
41322 AAACGCCGTAATAGGTGTTGAGCTTTAGCGGCATTTTTCATAC
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGCATTTTACCTAC
41365 AAACGCCGC
1 AAACGCCGC
41374 TAAAGTTCGG
Statistics
Matches: 195, Mismatches: 63, Indels: 14
0.72 0.23 0.05
Matches are distributed among these distances:
41 1 0.01
42 54 0.28
43 139 0.71
44 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (43 bp):
AAACGCCGCAATAAGTGTTGATATTTAGCGGCATTTTACCTAC
Found at i:41806 original size:21 final size:21
Alignment explanation
Indices: 41782--41828 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
41772 TGATATACTC
* *
41782 CTTCTCTCTATGTTGTCGCTG
1 CTTCTCTCTATGCTGCCGCTG
*
41803 CTTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTATGCTGCCGCTG
41824 CTTCT
1 CTTCT
41829 TTCTCCGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.34, G:0.19, T:0.45
Consensus pattern (21 bp):
CTTCTCTCTATGCTGCCGCTG
Found at i:41846 original size:21 final size:21
Alignment explanation
Indices: 41830--41888 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
41820 GCTGCTTCTT
41830 TCTCCGCTTCCGTTGCTGCTC
1 TCTCCGCTTCCGTTGCTGCTC
** * *
41851 TGGCTGCTTCCGCTGCTGCTC
1 TCTCCGCTTCCGTTGCTGCTC
* *
41872 TCTCTGCTTCCCTTGCT
1 TCTCCGCTTCCGTTGCT
41889 TCATTTTCCG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.00, C:0.41, G:0.20, T:0.39
Consensus pattern (21 bp):
TCTCCGCTTCCGTTGCTGCTC
Found at i:51253 original size:41 final size:41
Alignment explanation
Indices: 51183--51349 Score: 221
Period size: 41 Copynumber: 4.1 Consensus size: 41
51173 TATAGTGGCA
* * *
51183 TTTG-CTAATAAACGCCACTATTGTTTAACACTTTTGCGGCG
1 TTTGTCTAA-AAACGCCACTATTGATTAACACTATTACGGCG
* *
51224 TTTGTCTAAAAATGCCACTATTGATTAACACTATTGCGGCG
1 TTTGTCTAAAAACGCCACTATTGATTAACACTATTACGGCG
* * *
51265 TTTGTATAAAAACGCCATTATTGATTAACACTATTACGACG
1 TTTGTCTAAAAACGCCACTATTGATTAACACTATTACGGCG
*
51306 TTTGTAC-AAAAATGCCACTATTGATTAACACTATTACGGCG
1 TTTGT-CTAAAAACGCCACTATTGATTAACACTATTACGGCG
51347 TTT
1 TTT
51350 TAGGAACAAA
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
41 108 0.96
42 4 0.04
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (41 bp):
TTTGTCTAAAAACGCCACTATTGATTAACACTATTACGGCG
Found at i:51287 original size:82 final size:82
Alignment explanation
Indices: 51192--51368 Score: 250
Period size: 82 Copynumber: 2.1 Consensus size: 82
51182 ATTTGCTAAT
* * * *
51192 AAACGCCACTATTGTTTAACACTTTTGCGGCGTTTGT-CTAAAAATGCCACTATTGATTAACACT
1 AAACGCCACTATTGATTAACACTATTACGACGTTTGTAC-AAAAATGCCACTATTGATTAACACT
*
51256 ATTGCGGCGTTTGTATAA
65 ATTACGGCGTTTGTATAA
*
51274 AAACGCCATTATTGATTAACACTATTACGACGTTTGTACAAAAATGCCACTATTGATTAACACTA
1 AAACGCCACTATTGATTAACACTATTACGACGTTTGTACAAAAATGCCACTATTGATTAACACTA
*
51339 TTACGGCGTTT-TAGGAA
66 TTACGGCGTTTGTA-TAA
51356 CAAACGCCACTAT
1 -AAACGCCACTAT
51369 ATGTGTAATA
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
81 2 0.02
82 70 0.83
83 12 0.14
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (82 bp):
AAACGCCACTATTGATTAACACTATTACGACGTTTGTACAAAAATGCCACTATTGATTAACACTA
TTACGGCGTTTGTATAA
Found at i:53444 original size:18 final size:18
Alignment explanation
Indices: 53421--53456 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53411 AAACATTCAA
53421 ACCTAGCCCCAAAACCAT
1 ACCTAGCCCCAAAACCAT
53439 ACCTAGCCCCAAAACCAT
1 ACCTAGCCCCAAAACCAT
53457 CTAGGTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.44, G:0.06, T:0.11
Consensus pattern (18 bp):
ACCTAGCCCCAAAACCAT
Found at i:53486 original size:3 final size:3
Alignment explanation
Indices: 53478--53507 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
53468 ATGTGAAAGC
*
53478 ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53508 GCTAGCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:59815 original size:32 final size:32
Alignment explanation
Indices: 59774--59834 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
59764 GACCAGATAC
*
59774 TAGTCAGGTTTGCATTCA-GATAATGCACAGCA
1 TAGTCAGGTTGGCATT-ATGATAATGCACAGCA
59806 TAGTCAGGTTGGCATTATGATAATGCACA
1 TAGTCAGGTTGGCATTATGATAATGCACA
59835 ATAGAGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (32 bp):
TAGTCAGGTTGGCATTATGATAATGCACAGCA
Found at i:61867 original size:14 final size:14
Alignment explanation
Indices: 61819--61867 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
61809 GGCATCGAAA
* *
61819 ATATTTATTACAAT
1 ATATATATTATAAT
*
61833 ATTTATATTAT-AT
1 ATATATATTATAAT
61846 AGTATATATTATAAT
1 A-TATATATTATAAT
61861 ATATATA
1 ATATATA
61868 GTTTTCGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 3 0.10
14 23 0.79
15 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
ATATATATTATAAT
Found at i:61931 original size:21 final size:22
Alignment explanation
Indices: 61875--61954 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
61865 ATAGTTTTCG
*
61875 AATATAATTTTTGAAAATATAT
1 AATATAGTTTTTGAAAATATAT
*
61897 AATATAGTTTTTGAAAATGTAT
1 AATATAGTTTTTGAAAATATAT
* *
61919 TATTTAG-TTTTGAGAACATATAT
1 AATATAGTTTTTGA-AA-ATATAT
61942 ATATATAGTTTTT
1 A-ATATAGTTTTT
61955 TAAATAGTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 6 0.13
22 27 0.57
23 5 0.11
24 5 0.11
25 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (22 bp):
AATATAGTTTTTGAAAATATAT
Found at i:61967 original size:81 final size:83
Alignment explanation
Indices: 61859--62053 Score: 195
Period size: 84 Copynumber: 2.3 Consensus size: 83
61849 ATATATTATA
** * **
61859 ATATATATAGTTTTCGAATATAATTTTT-GAAAATAT-ATA-ATATAGTTTTTGAAAATGTATTA
1 ATATATATAGTTTTTTAA-ATATTTTTTAGAAAATATAATATATATA-TTTTTGAAAACATATTA
*
61921 TTTAGTTTTGAGAA-CAT-AT
64 TATAGTTTTGA-AAGCATAAT
*
61940 ATATATATAGTTTTTTAAATAGTTTTTTTAGAACATATAATATATATATTTTTGAAAACATATTA
1 ATATATATAGTTTTTTAAATA--TTTTTTAGAAAATATAATATATATATTTTTGAAAACATATTA
* *
62005 TATGGTTTTGAAAGTATAAT
64 TATAGTTTTGAAAGCATAAT
62025 ATATATTATA-TTATTTTATAATATTTTTT
1 ATATA-TATAGTT-TTTTA-AATATTTTTT
62054 TTCTTTTTCT
Statistics
Matches: 95, Mismatches: 9, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
80 3 0.03
81 16 0.17
82 5 0.05
83 9 0.09
84 29 0.31
85 20 0.21
86 9 0.09
87 4 0.04
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (83 bp):
ATATATATAGTTTTTTAAATATTTTTTAGAAAATATAATATATATATTTTTGAAAACATATTATA
TAGTTTTGAAAGCATAAT
Found at i:62027 original size:21 final size:21
Alignment explanation
Indices: 61989--62028 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
61979 ATATATATAT
*
61989 TTTTGAAAACATATTATATGG
1 TTTTGAAAACATAATATATGG
**
62010 TTTTGAAAGTATAATATAT
1 TTTTGAAAACATAATATAT
62029 ATTATATTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (21 bp):
TTTTGAAAACATAATATATGG
Found at i:62091 original size:24 final size:25
Alignment explanation
Indices: 62058--62115 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
62048 TTTTTTTTCT
*
62058 TTTTCTTTTTTTCTT-TGTATTTAC
1 TTTTCATTTTTTCTTATGTATTTAC
* *
62082 TTTTCA-TTTTTCTTATTTTTTTAC
1 TTTTCATTTTTTCTTATGTATTTAC
*
62106 TTTTTATTTT
1 TTTTCATTTT
62116 CATTTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 8 0.29
24 17 0.61
25 3 0.11
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (25 bp):
TTTTCATTTTTTCTTATGTATTTAC
Found at i:62095 original size:23 final size:24
Alignment explanation
Indices: 62065--62115 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
62055 TCTTTTTCTT
62065 TTTTTCTT-TGTATTTACTTTTCA
1 TTTTTCTTATGTATTTACTTTTCA
* * *
62088 TTTTTCTTATTTTTTTACTTTTTA
1 TTTTTCTTATGTATTTACTTTTCA
62112 TTTT
1 TTTT
62116 CATTTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTTTCTTATGTATTTACTTTTCA
Found at i:62118 original size:30 final size:30
Alignment explanation
Indices: 62048--62121 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
62038 TTTTATAATA
**
62048 TTTT-TTTTC-TTTTTCTTTTTTTCTTTGT
1 TTTTATTTTCATTTTTCTTTTTTTCTTACT
*
62076 ATTTACTTTTCATTTTTCTTATTTTT-TTACT
1 TTTTA-TTTTCATTTTTCTT-TTTTTCTTACT
62107 TTTTATTTTCATTTT
1 TTTTATTTTCATTTT
62122 ATTTTAGGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 3 0.08
30 15 0.39
31 15 0.39
32 5 0.13
ACGTcount: A:0.09, C:0.11, G:0.01, T:0.78
Consensus pattern (30 bp):
TTTTATTTTCATTTTTCTTTTTTTCTTACT
Found at i:64208 original size:20 final size:20
Alignment explanation
Indices: 64183--64229 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
64173 ACTACAGTAG
64183 GAAACAGACCCAACAAAAGT
1 GAAACAGACCCAACAAAAGT
*
64203 GAAACAGACCCAACAATAGT
1 GAAACAGACCCAACAAAAGT
64223 GAAACAG
1 GAAACAG
64230 TCATCCAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.23, G:0.17, T:0.06
Consensus pattern (20 bp):
GAAACAGACCCAACAAAAGT
Found at i:67942 original size:18 final size:18
Alignment explanation
Indices: 67904--67942 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
67894 GAAATAACTG
* **
67904 AGGAAAAATTTATTTTCT
1 AGGAAAAATTAATTTGAT
67922 AGGAAAAATTAATTTGAT
1 AGGAAAAATTAATTTGAT
67940 AGG
1 AGG
67943 GCCAATGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (18 bp):
AGGAAAAATTAATTTGAT
Found at i:75349 original size:14 final size:14
Alignment explanation
Indices: 75312--75349 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
75302 TTTTTATTAC
*
75312 AATATATATATTAT
1 AATATATATATGAT
75326 -ATAGTATATATGAT
1 AATA-TATATATGAT
75340 AATATATATA
1 AATATATATA
75350 GTTTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 15 0.71
15 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (14 bp):
AATATATATATGAT
Found at i:75372 original size:26 final size:26
Alignment explanation
Indices: 75343--75542 Score: 161
Period size: 26 Copynumber: 8.2 Consensus size: 26
75333 ATATGATAAT
**
75343 ATATATAGTTTTCAAAAATATATATA
1 ATATATAGTTTTTGAAAATATATATA
75369 ATATATAGTTTTTGAAAATATATATA
1 ATATATAGTTTTTGAAAATATATATA
75395 ATATATAGTTTTTG-AAA-ATATAT-
1 ATATATAGTTTTTGAAAATATATATA
*
75418 A-ATATAGTTTTTG--AA-ACATAT-
1 ATATATAGTTTTTGAAAATATATATA
75439 -TATATAG-TTTTG-AAATCATATA-A
1 ATATATAGTTTTTGAAAAT-ATATATA
75462 TATATATAGTTTTTGAAAACGTATATA-A
1 -ATATATAGTTTTTGAAAA--TATATATA
* *
75490 TATATATAATTTTTG-AAA-ACATAT-
1 -ATATATAGTTTTTGAAAATATATATA
75514 -TATATAGTTTTT-AAAAGTATA-AT-
1 ATATATAGTTTTTGAAAA-TATATATA
75537 ATATAT
1 ATATAT
75543 TATAATGTTT
Statistics
Matches: 150, Mismatches: 8, Indels: 34
0.78 0.04 0.18
Matches are distributed among these distances:
20 5 0.03
21 15 0.10
22 26 0.17
23 7 0.05
24 17 0.11
25 10 0.07
26 43 0.29
27 6 0.04
28 20 0.13
29 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (26 bp):
ATATATAGTTTTTGAAAATATATATA
Found at i:75488 original size:21 final size:21
Alignment explanation
Indices: 75395--75529 Score: 87
Period size: 22 Copynumber: 5.9 Consensus size: 21
75385 AATATATATA
*
75395 ATATATAGTTTTTGAAAATAT
1 ATATATAGTTTTTGAAAACAT
75416 ATAATATAGTTTTTG-AAACAT
1 AT-ATATAGTTTTTGAAAACAT
*
75437 ATTATATAG-TTTTGAAATCATATAAT
1 A-TATATAGTTTTTG-AA--A-A-CAT
75463 ATATATAGTTTTTGAAAACGTATATAAT
1 ATATATAGTTTTTGAAAAC-------AT
*
75491 ATATATAATTTTTGAAAACAT
1 ATATATAGTTTTTGAAAACAT
75512 ATTATATAGTTTTT-AAAA
1 A-TATATAGTTTTTGAAAA
75530 GTATAATATA
Statistics
Matches: 92, Mismatches: 5, Indels: 34
0.70 0.04 0.26
Matches are distributed among these distances:
20 5 0.05
21 21 0.23
22 26 0.28
23 1 0.01
24 1 0.01
25 10 0.11
26 8 0.09
28 20 0.22
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (21 bp):
ATATATAGTTTTTGAAAACAT
Found at i:75558 original size:96 final size:94
Alignment explanation
Indices: 75343--75545 Score: 241
Period size: 96 Copynumber: 2.1 Consensus size: 94
75333 ATATGATAAT
* * * *
75343 ATATATAGTTTTCAAA-AATATATATAATATATAGTTTTTGAAAATATATATAATATATAGTTTT
1 ATATATAGTTATGAAATCATATA-AT-ATATATAGTTTTTGAAAATATATATAATATATAATTTT
* *
75407 TGAAAATATATAATATAGTTTTTGAAACATA
64 TGAAAACATATAATATAGTTTTTAAAACATA
* *
75438 TTATATAGTTTTGAAATCATATAATATATATAGTTTTTGAAAACGTATATA-ATATATATAATTT
1 ATATATAGTTATGAAATCATATAATATATATAGTTTTTGAAAA--TATATATA-ATATATAATTT
* *
75502 TTGAAAACATATTATATAGTTTTTAAAAGTATA
63 TTGAAAACATATAATATAGTTTTTAAAA-CATA
75535 ATATATA-TTAT
1 ATATATAGTTAT
75546 AATGTTTTAT
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
94 18 0.19
95 17 0.18
96 49 0.53
97 9 0.10
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (94 bp):
ATATATAGTTATGAAATCATATAATATATATAGTTTTTGAAAATATATATAATATATAATTTTTG
AAAACATATAATATAGTTTTTAAAACATA
Found at i:75597 original size:17 final size:17
Alignment explanation
Indices: 75577--75637 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
75567 TATTTTCTCT
75577 TTTTTATTTTTA-TTTA
1 TTTTTATTTTTATTTTA
*
75593 CTTTTCATTTTTATTTTA
1 -TTTTTATTTTTATTTTA
*
75611 TTTTTATTTACT-TTTTA
1 TTTTTATTT-TTATTTTA
*
75628 TCTTTATTTT
1 TTTTTATTTT
75638 AGTTCCAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
17 32 0.86
18 5 0.14
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTATTTTTATTTTA
Found at i:75604 original size:7 final size:6
Alignment explanation
Indices: 75558--75637 Score: 53
Period size: 6 Copynumber: 13.5 Consensus size: 6
75548 TGTTTTATAA
* * *
75558 TTTTAT TATTAT TTTCTCTT TTTTAT TTTTA- -TTTACT TTTCAT TTTTA-
1 TTTTAT TTTTAT TTT-T-AT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT
*
75606 TTTTAT TTTTA- -TTTACT TTTTAT CTTTAT TTT
1 TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTT
75638 AGTTCCAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
4 8 0.14
5 5 0.09
6 31 0.54
7 9 0.16
8 4 0.07
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:75609 original size:28 final size:28
Alignment explanation
Indices: 75578--75638 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
75568 ATTTTCTCTT
*
75578 TTTTATTTTTATTTACTTTTCATTTTTA
1 TTTTATTTTTATTTACTTTTCATCTTTA
*
75606 TTTTATTTTTATTTACTTTTTATCTTTA
1 TTTTATTTTTATTTACTTTTCATCTTTA
75634 TTTTA
1 TTTTA
75639 GTTCCAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTTATTTTTATTTACTTTTCATCTTTA
Done.