Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000743.1 Hibiscus syriacus cultivar Beakdansim tig00001433_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: 60809
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:461 original size:78 final size:76
Alignment explanation
Indices: 362--693 Score: 317
Period size: 78 Copynumber: 4.4 Consensus size: 76
352 GTTAAGATTG
* * * **
362 TTTGTCGATGTTTAT-CGGGAGTCCAGTTAGTGTCAAATACAAGA-ATGTCATAATCCTATGCTC
1 TTTGTCTATGTTT-TCCGGGAGTCCAGTGAGTGTCGAATACAAGATATGTCGCAATCC-ATGCTC
425 GAATTTTCTAAACT
64 GAATTTTCT-AACT
* **
439 TTTGTTCTATGTTTTCTGGGAGTCTGGTGAGTGTCGAATACAAGAGTATGTCGCAATACCATGCT
1 TTTG-TCTATGTTTTCCGGGAGTCCAGTGAGTGTCGAATACAAGA-TATGTCGCAAT-CCATGCT
*
504 CGAA--TTCTAAGT
63 CGAATTTTCTAACT
* ** *
516 TTT-TCTATGTTTTCCAGGAGTCCAGTG-GTGTCGAATATGAG-TATGTCGCAATCCATTCTC-A
1 TTTGTCTATGTTTTCCGGGAGTCCAGTGAGTGTCGAATACAAGATATGTCGCAATCCATGCTCGA
*
577 AATTTCTAAACAT
66 ATTTTCT-AAC-T
* * * *
590 TTCGTCTATGTTTTCCGAGAGTCCAGTGAGTGCCGAATACAAGAATATGTCGCAATCCTATGATC
1 TTTGTCTATGTTTTCCGGGAGTCCAGTGAGTGTCGAATACAAG-ATATGTCGCAATCC-ATGCTC
655 GAATTTTCTAACT
64 GAATTTTCTAACT
*
668 TTTAGTC--TGTTTT-TGGGAGTCCAGTG
1 TTT-GTCTATGTTTTCCGGGAGTCCAGTG
694 GTGCTGATAT
Statistics
Matches: 210, Mismatches: 29, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
70 2 0.01
71 7 0.03
72 15 0.07
73 2 0.01
74 15 0.07
75 42 0.20
76 22 0.10
77 17 0.08
78 52 0.25
79 10 0.05
80 24 0.11
81 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (76 bp):
TTTGTCTATGTTTTCCGGGAGTCCAGTGAGTGTCGAATACAAGATATGTCGCAATCCATGCTCGA
ATTTTCTAACT
Found at i:704 original size:150 final size:151
Alignment explanation
Indices: 429--724 Score: 352
Period size: 150 Copynumber: 2.0 Consensus size: 151
419 ATGCTCGAAT
* * * ** * *
429 TTTCTAAACTTTTGTTCTATGTTTTCTGGGAGTCTGGTGAGTGTCGAATACAAGAGTATGTCGCA
1 TTTCTAAACTTTCGTTCTATGTTTTCCGAGAGTCCAGTGAGTGCCGAATACAAGAATATGTCGCA
* * * *
494 ATACCATGCTCGAATTCTAAGTTTTTCTATGTTTTCCAGGAGTCCAGTGGTGTCGAATAT-GAGT
66 ATACCATGATCGAATTCTAACTTTTACTATGTTTTCCAGGAGTCCAGTGGTGTCGAATATGGACT
*
558 ATGTCGCAATCCATTCTCAAA
131 ATGTCGAAATCCATTCTCAAA
579 TTTCTAAACATTTCG-TCTATGTTTTCCGAGAGTCCAGTGAGTGCCGAATACAAGAATATGTCGC
1 TTTCTAAAC-TTTCGTTCTATGTTTTCCGAGAGTCCAGTGAGTGCCGAATACAAGAATATGTCGC
* * **
643 AAT-CCTATGATCGAATTTTCTAACTTTTAGTCTGTTTT-TGGGAGTCCAGTGGTG-CTG-ATAT
65 AATACC-ATGATCGAA--TTCTAACTTTTACTATGTTTTCCAGGAGTCCAGTGGTGTC-GAATAT
704 GGGACTATGTCGAAATCCATT
126 -GGACTATGTCGAAATCCATT
725 ATCCAATGCT
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
149 2 0.02
150 68 0.55
151 19 0.15
152 34 0.28
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (151 bp):
TTTCTAAACTTTCGTTCTATGTTTTCCGAGAGTCCAGTGAGTGCCGAATACAAGAATATGTCGCA
ATACCATGATCGAATTCTAACTTTTACTATGTTTTCCAGGAGTCCAGTGGTGTCGAATATGGACT
ATGTCGAAATCCATTCTCAAA
Found at i:3792 original size:18 final size:18
Alignment explanation
Indices: 3769--3822 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
3759 GAGGGATTAT
3769 TAGTGGTCTTTCGGGACA
1 TAGTGGTCTTTCGGGACA
*
3787 TAGTGGTCCTTCGGGACA
1 TAGTGGTCTTTCGGGACA
3805 TAGTGGTCTTTCGGGACA
1 TAGTGGTCTTTCGGGACA
3823 AATATTCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
TAGTGGTCTTTCGGGACA
Found at i:6569 original size:36 final size:36
Alignment explanation
Indices: 6527--6629 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
6517 AGTTGAGTAG
6527 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
6563 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
6599 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
6630 CCATCATCGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:16142 original size:17 final size:17
Alignment explanation
Indices: 16120--16178 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 17
16110 CTAATATAAA
16120 TTAAACAAAATATTTTT
1 TTAAACAAAATATTTTT
*
16137 TTAAACAACAATAAATATTT
1 TTAAACAA-AAT--ATTTTT
16157 TTAAACAAAATA-TTTT
1 TTAAACAAAATATTTTT
16173 TTAAAC
1 TTAAAC
16179 GTAAATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
16 9 0.24
17 9 0.24
18 3 0.08
19 3 0.08
20 13 0.35
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAACAAAATATTTTT
Found at i:16765 original size:4 final size:4
Alignment explanation
Indices: 16756--16848 Score: 102
Period size: 4 Copynumber: 23.8 Consensus size: 4
16746 GTTTGGAACT
* **
16756 TTTC TTTC TTTC TTTC -TTC -TTC TTTC TTTCC TTTC TCTC -TTC TCCC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC
* * *
16802 TTTC TTTA TTTA TTTC TGTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
16849 TTTGTGCTTC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
3 8 0.11
4 64 0.84
5 4 0.05
ACGTcount: A:0.02, C:0.27, G:0.01, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:20134 original size:76 final size:76
Alignment explanation
Indices: 20008--20164 Score: 287
Period size: 76 Copynumber: 2.1 Consensus size: 76
19998 CTTTAATAAA
*
20008 AACAATAGAACCAATCATAATTACAACACATTCAAGCATAGAGAGAAAAATGGAGACAATGGTCA
1 AACAATAGAACCAATCATAATTACAACACATTCAAGCATAGAGAAAAAAATGGAGACAATGGTCA
20073 CACAAAATTTC
66 CACAAAATTTC
*
20084 AACAATAGAACGAATCATAATTACAACACATTCAAGCATAGAGAAAAAAATGGAGACAATGGTCA
1 AACAATAGAACCAATCATAATTACAACACATTCAAGCATAGAGAAAAAAATGGAGACAATGGTCA
20149 CACAAAATTTC
66 CACAAAATTTC
*
20160 TACAA
1 AACAA
20165 AAATAAAAAT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (76 bp):
AACAATAGAACCAATCATAATTACAACACATTCAAGCATAGAGAAAAAAATGGAGACAATGGTCA
CACAAAATTTC
Found at i:20198 original size:67 final size:74
Alignment explanation
Indices: 20008--20199 Score: 182
Period size: 76 Copynumber: 2.6 Consensus size: 74
19998 CTTTAATAAA
* ** * * *
20008 AACAATAGAACCAATCATAATTACAACACATTCAAGCATAGAGAGAAAAATGGAGACAATGGTCA
1 AACAATAGAACGAAAAATAATTACAACACA-T-AAGCATACAAAAAAAAATGGAGACAATGGTCA
20073 CACAAAATTTC
64 CACAAAATTTC
** * *
20084 AACAATAGAACGAATCATAATTACAACACATTCAAGCATAGAGAAAAAAATGGAGACAATGGTCA
1 AACAATAGAACGAAAAATAATTACAACACA-T-AAGCATACAAAAAAAAATGGAGACAATGGTCA
20149 CACAAAATTTC
64 CACAAAATTTC
* * *
20160 TACAA-A-AA-TAAAAAT-ATTA-AACCCA-AAG-ATACAAAAAAAA
1 AACAATAGAACGAAAAATAATTACAACACATAAGCATACAAAAAAAA
20200 TAAAACATTC
Statistics
Matches: 107, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
67 10 0.09
68 3 0.03
71 5 0.05
72 4 0.04
73 4 0.04
74 2 0.02
75 1 0.01
76 78 0.73
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.18
Consensus pattern (74 bp):
AACAATAGAACGAAAAATAATTACAACACATAAGCATACAAAAAAAAATGGAGACAATGGTCACA
CAAAATTTC
Found at i:21184 original size:28 final size:29
Alignment explanation
Indices: 21138--21226 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
21128 GGAATCAAAG
* *
21138 AAAATTATAGGCTCC-AATT-TAAACATAA
1 AAAATTAAAGG-TCCTAATTATAAATATAA
*
21166 AAAATTAAAGGTCCTAATTATAAATATTA
1 AAAATTAAAGGTCCTAATTATAAATATAA
** *
21195 AAAATTGGAGGCCCTAATTATAAATATAA
1 AAAATTAAAGGTCCTAATTATAAATATAA
21224 AAA
1 AAA
21227 TTGAGAGCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.06
28 14 0.27
29 35 0.67
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.29
Consensus pattern (29 bp):
AAAATTAAAGGTCCTAATTATAAATATAA
Found at i:22234 original size:2 final size:2
Alignment explanation
Indices: 22227--22266 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
22217 TTCAATTACA
22227 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
22267 TATTCAATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22896 original size:15 final size:16
Alignment explanation
Indices: 22867--22897 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22857 AACCCCATTT
22867 AAATAAAATAATAAAA
1 AAATAAAATAATAAAA
22883 AAATAAAA-AATAAAA
1 AAATAAAATAATAAAA
22898 CCAGTTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAATAAAATAATAAAA
Found at i:29152 original size:130 final size:131
Alignment explanation
Indices: 29011--29259 Score: 401
Period size: 130 Copynumber: 1.9 Consensus size: 131
29001 TATTTATATA
* *
29011 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
29076 TTAGCACATGATCATGACACGTGTCA-TTGGTGACACGTGTTACCACCTAATTATTTATATATGC
66 TTAACACATGATCATGACACGTGTCATTTGGTGACACATGTCACCACCTAATTATTTATATATGC
29140 T
131 T
29141 ATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * * *
29206 TTAACACATGATCGTGATATGTGTTATTTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTTGGTGACACATGTCACCACCTAATTA
29260 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
130 84 0.78
131 24 0.22
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (131 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTTGGTGACACATGTCACCACCTAATTATTTATATATGC
T
Found at i:29617 original size:28 final size:27
Alignment explanation
Indices: 29586--29648 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
29576 AGTTGATACA
*
29586 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
29614 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
29642 ATATTTT
1 ATATTTT
29649 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:29751 original size:17 final size:17
Alignment explanation
Indices: 29725--29757 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29715 AATTCTTATT
29725 AAAAATAAAT-ATTCAA
1 AAAAATAAATGATTCAA
29741 AAAATATAAATGATTCA
1 AAAA-ATAAATGATTCA
29758 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAAATGATTCAA
Found at i:29902 original size:21 final size:21
Alignment explanation
Indices: 29878--29920 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
29868 TATTACCTTA
29878 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
29899 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
29920 A
1 A
29921 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:29938 original size:35 final size:35
Alignment explanation
Indices: 29889--29974 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
29879 ATTGAAGTAT
** * *
29889 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
29924 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
29959 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
29975 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:30156 original size:29 final size:29
Alignment explanation
Indices: 30104--30161 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
30094 GCAAACGGAA
* *
30104 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGTTT
30133 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT
30162 CAGAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGTTT
Found at i:35023 original size:25 final size:26
Alignment explanation
Indices: 34977--35028 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
34967 TAATAAAAAA
34977 ATATATCTAATGACAAATA-TTTAAT
1 ATATATCTAATGACAAATATTTTAAT
* *
35002 ATATTTCTAATGA-TAATAATTTTAAT
1 ATATATCTAATGACAAAT-ATTTTAAT
35028 A
1 A
35029 ACTGATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.13
25 13 0.57
26 7 0.30
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (26 bp):
ATATATCTAATGACAAATATTTTAAT
Found at i:39086 original size:18 final size:18
Alignment explanation
Indices: 39063--39135 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
39053 ACTAAATATT
39063 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
39081 TGTCCCAAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
39100 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
39119 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
39136 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 31 0.66
19 2 0.04
20 14 0.30
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:39118 original size:38 final size:38
Alignment explanation
Indices: 39062--39138 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
39052 CACTAAATAT
*
39062 TTGTCCCGAAGGACCACTATGTCCCAAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCAAAGGACCACTGA
* *
39100 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCAAAGGACCACTGA
39138 T
1 T
39139 AATCCCTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCAAAGGACCACTGA
Found at i:39782 original size:64 final size:63
Alignment explanation
Indices: 39703--39823 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 63
39693 GATGCATTCC
* * *
39703 TTAACGGGTGCATCGATGCACTACC-TGTGCATCGGTACACAAATCTCATTCGATGTTTATATT
1 TTAACGGGTGCATCGATGCACT-CCTTATGCATCGATACACAAATCGCATTCGATGTTTATATT
* * * *
39766 TTAAGCGGGTGTATCGATGCACTCCTTATGCATCGATGCACTAATGGCATTCGATGTT
1 TTAA-CGGGTGCATCGATGCACTCCTTATGCATCGATACACAAATCGCATTCGATGTT
39824 CATTTATTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 6 0.12
64 43 0.88
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (63 bp):
TTAACGGGTGCATCGATGCACTCCTTATGCATCGATACACAAATCGCATTCGATGTTTATATT
Found at i:45844 original size:3 final size:3
Alignment explanation
Indices: 45836--45882 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
45826 GAATAGGGTT
45836 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
45883 ATTGGTACAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:48161 original size:29 final size:30
Alignment explanation
Indices: 48093--48162 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 30
48083 AAAATTACAA
* **
48093 TTTAGTCTCTAAATTTTTCAAAGTTTATAC
1 TTTAGTCACTAAATTTTTCAAAACTTATAC
** *
48123 TTTAACCACTAAA-TTTTCAAAACTTATAT
1 TTTAGTCACTAAATTTTTCAAAACTTATAC
48152 TTTAGTCACTA
1 TTTAGTCACTA
48163 TACAAAATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.46
Consensus pattern (30 bp):
TTTAGTCACTAAATTTTTCAAAACTTATAC
Found at i:52158 original size:22 final size:22
Alignment explanation
Indices: 52116--52157 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52106 ATTTTATAAT
*
52116 CTCAAACGATTATTATATTTTA
1 CTCAAACGATCATTATATTTTA
*
52138 CTCAGACGATCATTA-ATTTT
1 CTCAAACGATCATTATATTTT
52158 TTAATGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (22 bp):
CTCAAACGATCATTATATTTTA
Found at i:55033 original size:11 final size:11
Alignment explanation
Indices: 55017--55054 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
55007 TGATAAAATA
55017 AAAAAAAGAAT
1 AAAAAAAGAAT
55028 AAAAAAAGAA-
1 AAAAAAAGAAT
*
55038 AAAGCAAAGAAT
1 AAA-AAAAGAAT
55050 AAAAA
1 AAAAA
55055 GGTAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.05
Consensus pattern (11 bp):
AAAAAAAGAAT
Found at i:56381 original size:2 final size:2
Alignment explanation
Indices: 56370--56464 Score: 124
Period size: 2 Copynumber: 48.5 Consensus size: 2
56360 ACATGTAAAA
56370 AT AT -T 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
* *
56411 AT AT AT AT AT AT AT GT AT AT AT AT AT -T ACT AT AT AT -T AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* *
56452 AC AT AT AA AT AT A
1 AT AT AT AT AT AT A
56465 ATGTATTTAA
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
1 3 0.04
2 78 0.94
3 2 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57262 original size:84 final size:83
Alignment explanation
Indices: 57163--58617 Score: 1191
Period size: 84 Copynumber: 17.7 Consensus size: 83
57153 CGGAGTGTAA
* * * * * *
57163 TCGAACTCGAAGGTCTTCGGTTGGCAGATAGCCCTTCTTGACTTAAGCTATACTGCAAAAGGTGT
1 TCGAACTCGAAGGTCTT-GGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * *
57228 ACCTTGGAGTTGAGCGTAT
65 GCCTTGGAGCTGAGCGTAG
* * * * * *
57247 TCGAACTTGAAGGTCTTTTGG-TGACAGATTAACCCTTCTAGCCTTGAGTTATGTTGTAAATGAT
1 TCGAACTCGAAGGTC--TTGGTTGGCAGA-TAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
* * * ** *
57311 GTGCCCTCGAAGCTGGGTATAA
63 GTG-CCTTGGAGCTGAGCGTAG
* * * * * *
57333 TCGAACTCGAAGGTC-T--TTGGTAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGTA
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
57395 CCTTAGAGCAGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * *** * * *
57413 TC-AACTTGAAGGTTTTGG-TCATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* * * *
57476 CCCTCGAAGCTGAGTGTAA
66 -CCTTGGAGCTGAGCGTAG
* * * * *
57495 TCGAACTCGAGGGTC-T--TTGGTAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
57557 CTTTGGAGCTGAGCGTAA
66 CCTTGGAGCTGAGCGTAG
* * * *
57575 TCGAACTCGAAGGTCTTTGGTTCGCAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
57640 ACCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * ** * * * *
57659 TCGAACTCGAAGGCCTT--TTGGTCACAGATAACCCTTCTAGCCTTGGGTTATGTTGTAAATAAC
1 TCGAACTCGAAGGTCTTGGTTGG---CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
* * * *
57722 GTGCCCTCGAAGCTGAGTGTAA
63 GTG-CCTTGGAGCTGAGCGTAG
* * * *
57744 TCGAACTCGAGGGTC-T--TTGGCAGATAACCTTTCTTGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
57806 CCTTGGAGATGAGCATAG
66 CCTTGGAGCTGAGCGTAG
* * ** *
57824 TCGAACTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCTACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* *
57889 GCCTTAGAGTTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * *
57908 TCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC--TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * *
57972 TGTCCTCGAAGCTGAGTGTAA
64 TG-CCTTGGAGCTGAGCGTAG
* * * * *
57993 TCAAACTCGAGGGTC-T--TTGGCAG--AA-CCTTCTCGACTTAAGCTATGCTGCAAATGATATG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
58052 TCTTGGGGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * * * * * * **
58070 TCGAACTCGAAGGTCTTTG-TGGTAGATAGCCCTTCTAGCCTTGAGATATGCTACAAAAAATGTG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
58134 CCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* ** * * * * *
58152 TCGAACTCGAAGGTCTTGGATGTTAGACAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
*
58217 CCTTGGAGCTGAGTGTAG
66 CCTTGGAGCTGAGCGTAG
** * * * *
58235 TCGAACTCGAAGGTC-T--TTAACAGATAGCCCTTCTAGACTTAAG-CATTGCTGTAAATGGTGT
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTA-TGCTGCAAATGATGT
58296 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * *
58315 TCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC--TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
58379 TGCCTTGGAGCTGAGCGTAG
64 TGCCTTGGAGCTGAGCGTAG
* * * * *
58399 TCGAACTCGAAGGTC-T--TTAGCATATAACCCTTCTCGACTTAAGCTATGATGCAAATGA--T-
1 TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
58458 CCCTGGAGCTGAGCATAG
66 CCTTGGAGCTGAGCGTAG
** * * * **
58476 TCGAACTCGAAGGTCTTTGG-TGATAGATAACCCTTATAG-CCTGAGTTATG-TTTAAATGATGT
1 TCGAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* *
58538 GCCTTGGAGCTGAACATAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * *
58557 TCAAACTCGAAGGTCTTTGGATGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATG
1 TCGAACTCGAAGGTC-TTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
58618 TTTCTTTACA
Statistics
Matches: 1083, Mismatches: 237, Indels: 102
0.76 0.17 0.07
Matches are distributed among these distances:
77 56 0.05
78 37 0.03
79 27 0.02
80 178 0.16
81 178 0.16
82 98 0.09
83 88 0.08
84 308 0.28
85 86 0.08
86 27 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAG
Found at i:57718 original size:249 final size:247
Alignment explanation
Indices: 57271--58617 Score: 1460
Period size: 249 Copynumber: 5.5 Consensus size: 247
57261 CTTTTGGTGA
* * * * * * * * ** *
57271 CAGATTAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGGGTATAATCG
1 CAGA-TAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCG
* * * *
57336 AACTCGAAGGTCTTTGGT---AGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGTACCT
64 AACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
* * * *
57398 TAGAGCAGAGCGTAGTC-AACTTGAAGG-TTTTGGTCATAGATAACCCTTCTAGCCTTGAGTTAT
129 TGGAGCTGAGCGTAGTCGAACTCGAAGGCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
57461 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
194 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * * * * * *
57515 TAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCTTTGGAGCTGAGCGTAATCGAA
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * *
57580 CTCGAAGGTCTTTGGTTCGCAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATATACCTT
66 CTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
*
57645 GGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTTGGTCACAGATAACCCTTCTAGCCTTGGGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGG-CTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
* * *
57710 GTTGTAAATAACGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
194 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * * *
57764 CAGATAACCTTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * *
57829 CTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCTACTTAAGTTATGCTGCAAATGATATGCCTT
66 CTCGAAGGTCTTT-GGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
* * *
57894 AGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
130 GGAGCTGAGCGTAGTCGAACTCGAAGG-CTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
* *
57959 GCTGTAAATGATGTGTCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGG
194 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * * *
58013 CAG--AA-CCTTCTCGACTTAAGCTATGCTGCAAATGATATGTCTTGGGGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * * * * **
58075 CTCGAAGGTCTTT-GTGGTAGATAGCCCTTCTAGCCTTGAGATATGCTACAAAAAATGTGCCTTG
66 CTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
* *** * *
58139 GAGCTGAGCGTAGTCGAACTCGAAGG-TCTTGGATGTTAGACAACCCTTCTAGCCTTGAGTTATA
131 GAGCTGAGCGTAGTCGAACTCGAAGGCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATG
* * * * **
58203 CTGTAAATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTAA
195 CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * *
58255 CAGATAGCCCTTCTAGACTTAAGC-ATTGCTGTAAATGGTGTGCCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGACTTAAGCTA-TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* * * * *
58319 ACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCT
65 ACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
* * * * * *
58384 TGGAGCTGAGCGTAGTCGAACTCGAAGG-TCTT--T-AGCATATAACCCTTCTCGACTTAAGCTA
129 TGGAGCTGAGCGTAGTCGAACTCGAAGGCTTTTGGTCA-CAGATAACCCTTCTAGCCTTGAGTTA
* * * ** * *
58445 TGATGCAAATGA--T-CCCT-GGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTG
193 TGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G-G
* * * * * ** * * *
58498 ATAGATAACCCTTATAG-CCTGAGTTATG-TTTAAATGATGTGCCTTGGAGCTGAACATAGTCAA
1 -CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* * *
58561 ACTCGAAGGTCTTTGGATGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATG
65 ACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
58618 TTTCTTTACA
Statistics
Matches: 947, Mismatches: 134, Indels: 46
0.84 0.12 0.04
Matches are distributed among these distances:
241 35 0.04
242 148 0.16
243 79 0.08
244 112 0.12
245 59 0.06
246 120 0.13
247 84 0.09
249 309 0.33
250 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (247 bp):
CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
GAGCTGAGCGTAGTCGAACTCGAAGGCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
Found at i:57769 original size:165 final size:164
Alignment explanation
Indices: 57163--58617 Score: 1227
Period size: 162 Copynumber: 8.9 Consensus size: 164
57153 CGGAGTGTAA
* * * * * * * * * * *
57163 TCGAACTCGAAGGTC-TTCGGTTGGCAGATAGCCCTTCTTGACTTAAGCTATACTGCAAAAGGTG
1 TCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* * * * *
57227 TACCTTGGAGTTGAGCGTATTCGAACTTGAAGGTCTTTTGGTGACAGATTAACCCTTCTAGCCTT
65 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-G-G-CAGA-TAACCCTTCTAGACTT
* * * * * * * ** *
57292 GAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGGGTATAA
125 AAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* * * * * * *
57333 TCGAACTCGAAGGTC-TTTGGT---AGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * * * * *
57394 ACCTTAGAGCAGAGCGTAGTC-AACTTGAAGGT-TTTGGTCATAGATAACCCTTCTAGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-C--AGATAACCCTTCTAGACTTAAG
* * * * * *
57457 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
128 CTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* * * * * **
57495 TCGAACTCGAGGGTC-TTTGGT---AGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * * *
57556 GCTTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTCGCAGATAACCCTTATCGACTTAA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G---GCAGATAACCCTTCTAGACTTAA
* * *
57621 GTTATGCTGCAAATGATATACCTTGGAGCTGAGCGTAG
127 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * * * *
57659 TCGAACTCGAAGGCCTTTTGGTCACAGATAACCCTTCTAGCCTTGGGTTATGTTGTAAATAACGT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * * * * * *
57724 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCTTTCTTGACTTAAGCT
66 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCT
* *
57789 ATGCTGCAAATGATGTGCCTTGGAGATGAGCATAG
130 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * ** *** * * *
57824 TCGAACTCGAAGGTCTTTAGTTGGTAGATAACCCTTCTCTACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * * *
57889 GCCTTAGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-G-G-CAGATAACCCTTCTAGACTTAA
* * * * * *
57954 GTTATGCTGTAAATGATGTGTCCTCGAAGCTGAGTGTAA
127 GCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* * * * * * * *
57993 TCAAACTCGAGGGTC-TTT-G-G-CAG--AA-CCTTCTCGACTTAAGCTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * * * * * *
58051 GTCTTGGGGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTGGTAGATAGCCCTTCTAGCCTTGAGA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TT-TGGCAGATAACCCTTCTAGACTTAAGC
* **
58116 TATGCTACAAAAAATGTGCCTTGGAGCTGAGCGTAG
129 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
** * *
58152 TCGAACTCGAAGGTC--TTGGATGTTAGACAACCCTTCTAGCCTTGAGTTATACTGTAAATGATG
1 TCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* ** *
58215 TGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTAACAGATAGCCCTTCTAGACTTAAGC-
65 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCT
* *
58279 ATTGCTGTAAATGGTGTGCCTTGGAGCTGAGCGTAG
130 A-TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
58315 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * *
58380 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGCATATAACCCTTCTCGACTTAAGCTA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTA
* * *
58445 TGATGCAAATGA--T-CCCTGGAGCTGAGCATAG
131 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * *
58476 TCGAACTCGAAGGTC-TTTGGTGATAGATAACCCTTATAGCC-TGAGTTATG-TTTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * * * * *
58538 GCCTTGGAGCTGAACATAGTCAAACTCGAAGGTCTTTGGATGGCAGATAGCCCTTCTCGATTTAA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TT---TGGCAGATAACCCTTCTAGACTTAA
58603 GCTATGCTGCAAATG
127 GCTATGCTGCAAATG
58618 TTTCTTTACA
Statistics
Matches: 1085, Mismatches: 166, Indels: 76
0.82 0.13 0.06
Matches are distributed among these distances:
158 44 0.04
159 39 0.04
160 59 0.05
161 35 0.03
162 232 0.21
163 84 0.08
164 167 0.15
165 222 0.20
166 54 0.05
167 2 0.00
168 71 0.07
169 57 0.05
170 19 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (164 bp):
TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTA
TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
Found at i:58029 original size:411 final size:409
Alignment explanation
Indices: 57098--58617 Score: 1599
Period size: 411 Copynumber: 3.7 Consensus size: 409
57088 ATAATTTTAT
* * * * * * * * * *
57098 TGACATATGACCCTTCTTGCCTTGAGCTATGATGTAAATTTGGTTTGCCTCTGAGCGGAGTGTAA
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA--TGATGTGCCTCGGAGCTGAGCGTAA
* * * * *
57163 TCGAACTCGAAGGTCTTCGGTTGGCAGATAGCCCTTCTTGACTTAAGCTATACTGCAAAAGGTGT
64 TCGAACTCGAAGGTC-T---TTGGCAGA-A-CCCTTCTCGACTTAAGCTATGCTGCAAATGATAT
* * *
57228 ACCTTGGAGTTGAGCGTATTCGAACTTGAAGGTCTTTTGGTGACAGATTAACCCTTCTAGCCTTG
123 ACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGA-TAACCCTTCTAGCCTTG
* * * *
57293 AGTTATGTTGTAAATGATGTGCCCTCGAAGCTGGGTATAATCGAACTCGAAGGTCTT-TGGTAGA
187 AGTTATGTTGTAAATAATGTG-CCTCGAAGCTGAGCATAATCGAACTCGAAGGTCTTGTGGCAGA
* * * * *
57357 TAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGTACCTTAGAGCA-GAGCGTAGTC-AACTT
251 TAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAG-ATGAGCGTAGTCGAACTC
* * * * *
57420 GAAGGT-TTTGGTCATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAA
315 GAAGGTCTTTAGT-ATAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCTTAG-A
* * *
57484 GCTGAGTGTAATCGAACTCGAGGGTC-TTTGG
378 GCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
* * * * ** * *
57515 T---AGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCTTTGGAGCTGAGCGTAATC
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCGGAGCTGAGCGTAATC
* *
57577 GAACTCGAAGGTCTTTGGTTCGCAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATATAC
66 GAACTCGAAGGTCTTT-G---GCAG--AACCCTTCTCGACTTAAGCTATGCTGCAAATGATATAC
* * *
57642 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTTGGTCACAGATAACCCTTCTAGCCTTGGGT
125 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
* ** *
57707 TATGTTGTAAATAACGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTT-TGGCAGATAA
190 TATGTTGTAAATAATGTG-CCTCGAAGCTGAGCATAATCGAACTCGAAGGTCTTGTGGCAGATAA
* * *
57771 CCTTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAACTCGAAG
254 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCGTAGTCGAACTCGAAG
* ** * * *
57836 GTCTTTAGTTGGTAGATAACCCTTCTCTACTTAAGTTATGCTGCAAATGATATGCCTTAGAGTTG
319 GTCTTTAG-T-ATAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTG
57901 AGCGTAGTCGAACTCGAAGGTCTTTTGG
382 AGCGTAGTCGAACTCGAAGGTCTTTTGG
* *
57929 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-CCTCGGAGCTGAGCGTAAT
* * **
57994 CAAACTCGAGGGTCTTTGGCAGAA-CCTTCTCGACTTAAGCTATGCTGCAAATGATATGTCTTGG
65 CGAACTCGAAGGTCTTTGGCAGAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATACCTTGG
* * *
58058 GGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTGGT---AGATAGCCCTTCTAGCCTTGAGATATG
130 AGCTGAGCGTAGTCGAACTCGAAGGTCTTT-TGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* ** * * * * * ** *
58120 CTACAAAAAATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGATGTTAGACAACCC
194 TTGTAAATAATGTGCCTCGAAGCTGAGCATAATCGAACTCGAAGGTCTT-G-TGGCAGATAACCC
* * * * * * * *
58185 TTCTAGCCTTGAGTTATACTGTAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTC
257 TTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCGTAGTCGAACTCGAAGGTC
* * * * *
58250 TTTA--ACAGATAGCCCTTCTAGACTTAAG-CATTGCTGTAAATGGTGTGCCTTGGAGCTGAGCG
322 TTTAGTATAGATAACCCTTCTAGACTTAAGTTA-TGCTGTAAATGATGTGCCTTAGAGCTGAGCG
58312 TAGTCGAACTCGAAGGTCTTTTGG
386 TAGTCGAACTCGAAGGTCTTTTGG
* *
58336 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCGGAGCTGAGCGTAATC
* * * *
58401 GAACTCGAAGGTCTTTAGCATATAACCCTTCTCGACTTAAGCTATGATGCAAATG--AT-CCCTG
66 GAACTCGAAGGTCTTTGGC--AGAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATACCTTG
* * *
58463 GAGCTGAGCATAGTCGAACTCGAAGGTC-TTTGGTGATAGATAACCCTTATAGCC-TGAGTTATG
129 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * * * * *
58526 TT-TAAATGATGTGCCTTGGAGCTGAACATAGTCAAACTCGAAGGTCTTTGGATGGCAGATAGCC
194 TTGTAAATAATGTGCCTCGAAGCTGAGCATAATCGAACTCGAAGGTC-TT-G-TGGCAGATAACC
*
58590 CTTCTCGATTTAAGCTATGCTGCAAATG
256 CTTCTCGACTTAAGCTATGCTGCAAATG
58618 TTTCTTTACA
Statistics
Matches: 929, Mismatches: 147, Indels: 65
0.81 0.13 0.06
Matches are distributed among these distances:
404 4 0.00
405 40 0.04
406 105 0.11
407 131 0.14
408 35 0.04
409 62 0.07
410 1 0.00
411 258 0.28
412 122 0.13
413 28 0.03
414 76 0.08
417 37 0.04
418 30 0.03
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (409 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTCGGAGCTGAGCGTAATC
GAACTCGAAGGTCTTTGGCAGAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATACCTTGGA
GCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTT
GTAAATAATGTGCCTCGAAGCTGAGCATAATCGAACTCGAAGGTCTTGTGGCAGATAACCCTTCT
CGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCGTAGTCGAACTCGAAGGTCTTTA
GTATAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTTGG
Found at i:59395 original size:26 final size:26
Alignment explanation
Indices: 59340--59397 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
59330 GAATCAAGAG
* *
59340 CTCTTTTAATGCTTTAAGAGTCATAG
1 CTCTTTTAATGCTTTAAGAGTCACAA
* *
59366 CTCTTTTAATGCTTTCAGAGTTACAA
1 CTCTTTTAATGCTTTAAGAGTCACAA
59392 CTCTTT
1 CTCTTT
59398 GAAAAATGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (26 bp):
CTCTTTTAATGCTTTAAGAGTCACAA
Done.