Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004581.1 Hibiscus syriacus cultivar Beakdansim tig00010220_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: 83981
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:6827 original size:20 final size:20
Alignment explanation
Indices: 6801--6864 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
6791 ATTTTGGTGC
6801 AGAGGGAATCGATCCCCCCT
1 AGAGGGAATCGATCCCCCCT
* *
6821 TGAGGGAACCGATTCCCCCC-
1 AGAGGGAATCGA-TCCCCCCT
*
6841 ACAGGGGAATCGATACCCCCCT
1 AGA-GGGAATCGAT-CCCCCCT
6863 AG
1 AG
6865 GGTTCTGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 12 0.35
21 21 0.62
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.25, T:0.14
Consensus pattern (20 bp):
AGAGGGAATCGATCCCCCCT
Found at i:6839 original size:21 final size:20
Alignment explanation
Indices: 6802--6840 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6792 TTTTGGTGCA
*
6802 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
6822 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGA-TCCCCCC
6841 ACAGGGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:10781 original size:18 final size:18
Alignment explanation
Indices: 10758--10824 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 18
10748 ACTGAATATT
10758 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
10776 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAATGACCAC----TA
*
10798 TGTCTCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
10816 AGTCCCGAA
1 TGTCCCGAA
10825 GGACAACTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 24 0.60
22 16 0.40
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.22
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:10806 original size:22 final size:22
Alignment explanation
Indices: 10774--10837 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
10764 GAATGACCAC
10774 TATGTCCCGAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
* *
10796 TATGTCTCGAATGACCAC--TA
1 TATGTCCCGAAGGACCACTGTA
*
10816 -A-GTCCCGAAGGACAACTGTA
1 TATGTCCCGAAGGACCACTGTA
10836 TA
1 TA
10838 ACCCTCGACT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 12 0.35
19 1 0.03
20 4 0.12
21 1 0.03
22 16 0.47
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (22 bp):
TATGTCCCGAAGGACCACTGTA
Found at i:10807 original size:40 final size:40
Alignment explanation
Indices: 10758--10837 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
10748 ACTGAATATT
* *
10758 TGTCCCGAATGACCACTATGTCCCGAAGGACCACTGTATA
1 TGTCCCGAATGACCACTAAGTCCCGAAGGACAACTGTATA
*
10798 TGTCTCGAATGACCACTAAGTCCCGAAGGACAACTGTATA
1 TGTCCCGAATGACCACTAAGTCCCGAAGGACAACTGTATA
10838 ACCCTCGACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
TGTCCCGAATGACCACTAAGTCCCGAAGGACAACTGTATA
Found at i:12212 original size:48 final size:47
Alignment explanation
Indices: 12160--12250 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
12150 TTGCCCTTTA
*
12160 ATTCATTTGAAAATTACTAATATTCATTTATCCCATCTTTAACCCAAT
1 ATTCATTTG-AAATCACTAATATTCATTTATCCCATCTTTAACCCAAT
*** *
12208 ATTCATTTGCCCTCACTAATATTGATTTATCCCATCTTTAACC
1 ATTCATTTGAAATCACTAATATTCATTTATCCCATCTTTAACC
12251 TTAATATCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
47 29 0.76
48 9 0.24
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (47 bp):
ATTCATTTGAAATCACTAATATTCATTTATCCCATCTTTAACCCAAT
Found at i:13107 original size:16 final size:16
Alignment explanation
Indices: 13086--13135 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
13076 AAAGACATTG
13086 AAAATAATAAAAAAAC
1 AAAATAATAAAAAAAC
*
13102 AAAATAA-AATAAAAAT
1 AAAATAATAA-AAAAAC
*
13118 ATAAT-ATAAAAAAGAC
1 AAAATAATAAAAAA-AC
13134 AA
1 AA
13136 TAGAGAATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAATAATAAAAAAAC
Found at i:14136 original size:35 final size:35
Alignment explanation
Indices: 14088--14164 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
14078 AACACAGTCA
* *
14088 TCAATTACATTCTAAACCCCAAATTCCAAAATGCT
1 TCAATTACATTCTAAACCCAAAATTCCAAAATACT
* *
14123 TTAATTACATTCTAAACCTAAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCAAAATTCCAAAATACT
14158 TCAATTA
1 TCAATTA
14165 TACCCAACCC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.32
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCAAAATTCCAAAATACT
Found at i:15521 original size:35 final size:34
Alignment explanation
Indices: 15482--15557 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 34
15472 TTGGGCATGC
15482 AATTGAAATATTTTGGAATTAGAGGTTTAGAATGT
1 AATTGAAAT-TTTTGGAATTAGAGGTTTAGAATGT
** *
15517 AATTGTAGCTTTTTGGAATTTGAGGTTTAGAATGT
1 AATTG-AAATTTTTGGAATTAGAGGTTTAGAATGT
15552 AATTGA
1 AATTGA
15558 TGATTGTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 1 0.03
35 34 0.92
36 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.24, T:0.42
Consensus pattern (34 bp):
AATTGAAATTTTTGGAATTAGAGGTTTAGAATGT
Found at i:30394 original size:5 final size:6
Alignment explanation
Indices: 30379--30407 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30369 CTTAATCGAA
30379 AAAAAT AAAAAT AAAAAT -AAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
30408 GTAACAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:30400 original size:11 final size:12
Alignment explanation
Indices: 30379--30407 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
30369 CTTAATCGAA
30379 AAAAATAAAAAT
1 AAAAATAAAAAT
30391 AAAAAT-AAAAT
1 AAAAATAAAAAT
30402 AAAAAT
1 AAAAAT
30408 GTAACAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:31998 original size:20 final size:18
Alignment explanation
Indices: 31970--32041 Score: 60
Period size: 20 Copynumber: 3.9 Consensus size: 18
31960 AAGGGTGAAA
*
31970 AGTGTATCCATGCACTCT
1 AGTGCATCCATGCACTCT
31988 CCAGTGCATCCATGCA--CT
1 --AGTGCATCCATGCACTCT
* *
32006 -GTGCATCGATGCACCCTGT
1 AGTGCATCCATGCA--CTCT
32025 AGTGCATCCATGCACTC
1 AGTGCATCCATGCACTC
32042 AAACACCGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
15 12 0.29
18 4 0.10
19 1 0.02
20 25 0.60
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.26
Consensus pattern (18 bp):
AGTGCATCCATGCACTCT
Found at i:32213 original size:20 final size:22
Alignment explanation
Indices: 32175--32214 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
32165 TTTTAGTAGA
32175 AAAATCATCCCCAAACGGCTTC
1 AAAATCATCCCCAAACGGCTTC
32197 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
32215 ATATACGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTTC
Found at i:35196 original size:21 final size:21
Alignment explanation
Indices: 35170--35209 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35160 CAACAATTGG
35170 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
35191 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
35210 TATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:35215 original size:22 final size:21
Alignment explanation
Indices: 35170--35215 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
35160 CAACAATTGG
*
35170 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTAT
* *
35191 TAACAATTGGTATCTTTTTTAT
1 TAACAATTGATATC-ATTTTAT
35213 TAA
1 TAA
35216 ACATTTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTAT
Found at i:35464 original size:20 final size:18
Alignment explanation
Indices: 35436--35505 Score: 56
Period size: 20 Copynumber: 3.8 Consensus size: 18
35426 AGGGTGTCAA
*
35436 AGTGTATCCATGCACTCTG
1 AGTGCATCCATGCAC-CTG
*
35455 CAGTGCATCCATGTA-CT-
1 -AGTGCATCCATGCACCTG
*
35472 -GTGCATCGATGCACCTTG
1 AGTGCATCCATGCACC-TG
35490 TAGTGCATCCATGCAC
1 -AGTGCATCCATGCAC
35506 TCAAACACTG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 11 0.28
16 1 0.03
17 1 0.03
18 2 0.05
20 25 0.62
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (18 bp):
AGTGCATCCATGCACCTG
Found at i:35551 original size:20 final size:20
Alignment explanation
Indices: 35526--35563 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35516 AATGCAATTA
*
35526 GTGCATCAATGCACCCTGCT
1 GTGCATCAATACACCCTGCT
*
35546 GTGCATCCATACACCCTG
1 GTGCATCAATACACCCTG
35564 TCTGCAACGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (20 bp):
GTGCATCAATACACCCTGCT
Found at i:35946 original size:34 final size:33
Alignment explanation
Indices: 35889--35959 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
35879 TTTTATAAAG
35889 GGGAAAGGTTCTAGCTAAGCCCGT-ATAAAATCTA
1 GGGAAAGGTTCTAGCTAAGCCCGTGA-AAAA-CTA
* * *
35923 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
35956 GGGA
1 GGGA
35960 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 25 0.76
35 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
Found at i:38505 original size:35 final size:34
Alignment explanation
Indices: 38436--38531 Score: 90
Period size: 34 Copynumber: 2.8 Consensus size: 34
38426 AAATAATATT
* * *
38436 TATTTAGATTTGAATAATAAAAGGA-ATGTA-TATC
1 TATTTAAATTTAAATATTAAAA-GATAT-TATTATC
*
38470 TTTTTAATATTTTAAAT-TTAAAAGATATTATTATC
1 TATTTAA-A-TTTAAATATTAAAAGATATTATTATC
*
38505 TATTTAAATTTAGATATTAAAAGATAT
1 TATTTAAATTTAAATATTAAAAGATAT
38532 ATGGTTGGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
33 6 0.12
34 21 0.41
35 18 0.35
36 6 0.12
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (34 bp):
TATTTAAATTTAAATATTAAAAGATATTATTATC
Found at i:39836 original size:25 final size:25
Alignment explanation
Indices: 39802--39854 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
39792 GTAAATTCTT
*
39802 TTAGATAGCCACCGTTATTGAGAAA
1 TTAGATAGCCACCATTATTGAGAAA
39827 TTAGATAGCCACCATTATTGAGAAA
1 TTAGATAGCCACCATTATTGAGAAA
39852 TTA
1 TTA
39855 ACTCCTGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (25 bp):
TTAGATAGCCACCATTATTGAGAAA
Found at i:50141 original size:19 final size:20
Alignment explanation
Indices: 50103--50140 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
50093 GTATGCTCGG
50103 GGGGGAACCGATTCCCCCCA
1 GGGGGAACCGATTCCCCCCA
*
50123 GGGGGTACCGATTCCCCC
1 GGGGGAACCGATTCCCCC
50141 ACTTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.39, G:0.32, T:0.13
Consensus pattern (20 bp):
GGGGGAACCGATTCCCCCCA
Found at i:54012 original size:32 final size:32
Alignment explanation
Indices: 53967--54062 Score: 129
Period size: 32 Copynumber: 3.0 Consensus size: 32
53957 GATGCGTGGC
* * *
53967 ACACTATTATGCATTATCTGAATGTGACATTG
1 ACACTATTGTGCATTATCTGAATATGACACTG
* * *
53999 ACATTGTTGTGCATTATTTGAATATGACACTG
1 ACACTATTGTGCATTATCTGAATATGACACTG
*
54031 ACACTATTGTGCATTATCTGAATACGACACTG
1 ACACTATTGTGCATTATCTGAATATGACACTG
54063 GTAGTATCTT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (32 bp):
ACACTATTGTGCATTATCTGAATATGACACTG
Found at i:60450 original size:30 final size:30
Alignment explanation
Indices: 60414--60470 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
60404 TCGTTGGGCC
60414 GAGTTAGGTTTAATTTGGGTTGATTTCGGA
1 GAGTTAGGTTTAATTTGGGTTGATTTCGGA
60444 GAGTTAGGTTTAATTTGGGTTGATTTC
1 GAGTTAGGTTTAATTTGGGTTGATTTC
60471 AGAGCCCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.04, G:0.32, T:0.46
Consensus pattern (30 bp):
GAGTTAGGTTTAATTTGGGTTGATTTCGGA
Found at i:66615 original size:21 final size:21
Alignment explanation
Indices: 66575--66615 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
66565 ATACTTATAG
**
66575 GGGTATCGATACTTGACACTA
1 GGGTATCGATACTACACACTA
*
66596 GGGTATCGATACTACTCACT
1 GGGTATCGATACTACACACT
66616 TGGGACTGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACTACACACTA
Found at i:68852 original size:14 final size:13
Alignment explanation
Indices: 68835--68887 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
68825 AAAGAAAACA
*
68835 AATAAGATAAAGAG
1 AATAAAATAAA-AG
68849 AATAAAATAAAAAG
1 AATAAAAT-AAAAG
* *
68863 AAAAAAATAAAATA
1 AATAAAATAAAA-G
68877 AATAAAATAAA
1 AATAAAATAAA
68888 TAAATAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 4 0.12
14 26 0.79
15 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AATAAAATAAAAG
Found at i:68899 original size:9 final size:9
Alignment explanation
Indices: 68849--68891 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
68839 AGATAAAGAG
68849 AATAAAATA
1 AATAAAATA
* *
68858 AAAAGAAAAA
1 AATA-AAATA
68868 AATAAAATA
1 AATAAAATA
68877 AATAAAATA
1 AATAAAATA
68886 AATAAA
1 AATAAA
68892 TAAGATAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (9 bp):
AATAAAATA
Found at i:68959 original size:2 final size:2
Alignment explanation
Indices: 68952--69004 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
68942 AAAAAGGAAA
68952 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
68994 AT AT AT AT AT A
1 AT AT AT AT AT A
69005 CATCAAAGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:69290 original size:2 final size:2
Alignment explanation
Indices: 69285--69317 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
69275 ATAAAAAATA
69285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69318 ATAGTTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70036 original size:35 final size:35
Alignment explanation
Indices: 69990--70061 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
69980 ACTAAAAACC
69990 CTATTTTAGACTAGTATTCGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTCGAGTCCTAATCCAACT
*
70025 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTCGAGTCCTAATCCAACT
70060 CT
1 CT
70062 TCTTTTTGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTCGAGTCCTAATCCAACT
Found at i:71063 original size:95 final size:96
Alignment explanation
Indices: 70897--71275 Score: 384
Period size: 95 Copynumber: 3.8 Consensus size: 96
70887 ATTGACCCTA
* * *
70897 AAATTAGGAAATTGTTTGTTAACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCT
1 AAATTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC-
70962 CT-AGTCCAATATCCTTCGCT-ATTGGCTCTG
65 CTGAGTCCAATATCCTTCGCTAATTGGCTCTG
*
70992 AAATTGGGAGATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
1 AAATTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
*
71057 TAAGTCCAATATCCTTCGCTGTGAAGTTGAAAGTGACTCTG
66 TGAGTCCAATATCCTTCGC--T-AA-TT----G-G-CTCTG
*
71098 AAATTGGGAAATTGTTTATTGACAACCAGTCGTCCCTTCG-T-T---G-TG--CTTG-GTTGTCC
1 AAATTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
* * *
71154 CGAGTCCAACATCCTTCGATGTGAAGTTGAAATTGGCTCTG
66 TGAGTCCAATATCCTTC--------GCT--AATTGGCTCTG
* * *
71195 AAATTGGGAAATTGTTTGTTGACAACCAGCCGTTCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 AAATTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
71260 TGAGTCCAATATCCTT
66 TGAGTCCAATATCCTT
71276 TACTGTGCAG
Statistics
Matches: 237, Mismatches: 17, Indels: 49
0.78 0.06 0.16
Matches are distributed among these distances:
94 2 0.01
95 77 0.32
97 64 0.27
98 6 0.03
99 3 0.01
100 4 0.02
101 1 0.00
102 1 0.00
103 5 0.02
104 4 0.02
105 7 0.03
106 63 0.27
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (96 bp):
AAATTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCC
TGAGTCCAATATCCTTCGCTAATTGGCTCTG
Found at i:71108 original size:305 final size:295
Alignment explanation
Indices: 70687--71275 Score: 833
Period size: 298 Copynumber: 2.0 Consensus size: 295
70677 AAAATTGACC
70687 CTGAAATTAGGAAATTGTTTGTTGACAACCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCATCT
1 CTGAAATTAGGAAATTGTTTGTTGACAACCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCATCT
* * * *
70752 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGTTGACA
66 CAAGTCCAATATCCTTCGCTGTGAAGTTGAAAGTGACTATGAAATTGGGAAATTATTTATTGACA
* * *
70817 ACCAGCCGTCCCTTCGTTGTGAAGTTAAACTT-GTGGTCTCGAGTTCAATATCCTTCGATGTGAA
131 ACCAGCCGTCCCTTCGTTGT---G-----CTTGGTGGTCCCGAGTCCAACATCCTTCGATGTGAA
*
70881 GTTGAAATTGACCCTAAAATTAGGAAATTGTTTGTTAACAACCAGTCGTCCCTTCGTTGTGAAGT
188 GTTGAAATTGACCCTAAAATTAGGAAATTGTTTGTTAACAACCAGCCGTCCCTTCGTTGTGAAGT
70946 TGAACTTGTGTCGTCTCT-AGTCCAATATCCTTCGCTATTGGCT
253 TGAACTTGTGTCGTCT-TGAGTCCAATATCCTTCGCTATTGGCT
* * **
70989 CTGAAATTGGGAGATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
1 CTGAAATTAGGAAATTGTTTGTTGACAACC---CGTCCCTTCGTTGTGAAGTTGAACTTGTGTCA
* *
71054 TC-CTAAGTCCAATATCCTTCGCTGTGAAGTTGAAAGTGACTCTGAAATTGGGAAATTGTTTATT
63 TCTC-AAGTCCAATATCCTTCGCTGTGAAGTTGAAAGTGACTATGAAATTGGGAAATTATTTATT
* *
71118 GACAACCAGTCGTCCCTTCGTTGTGCTTGGTTGTCCCGAGTCCAACATCCTTCGATGTGAAGTTG
127 GACAACCAGCCGTCCCTTCGTTGTGCTTGGTGGTCCCGAGTCCAACATCCTTCGATGTGAAGTTG
* * * * * *
71183 AAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTTCCTTCGTTGTGAAGTTGAA
192 AAATTGACCCTAAAATTAGGAAATTGTTTGTTAACAACCAGCCGTCCCTTCGTTGTGAAGTTGAA
*
71248 CTTGTGTTGTCTTGAGTCCAATATCCTT
257 CTTGTGTCGTCTTGAGTCCAATATCCTT
71276 TACTGTGCAG
Statistics
Matches: 258, Mismatches: 23, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
297 4 0.02
298 115 0.45
302 29 0.11
304 1 0.00
305 109 0.42
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (295 bp):
CTGAAATTAGGAAATTGTTTGTTGACAACCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCATCT
CAAGTCCAATATCCTTCGCTGTGAAGTTGAAAGTGACTATGAAATTGGGAAATTATTTATTGACA
ACCAGCCGTCCCTTCGTTGTGCTTGGTGGTCCCGAGTCCAACATCCTTCGATGTGAAGTTGAAAT
TGACCCTAAAATTAGGAAATTGTTTGTTAACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
TGTCGTCTTGAGTCCAATATCCTTCGCTATTGGCT
Found at i:71168 original size:97 final size:98
Alignment explanation
Indices: 71045--71239 Score: 302
Period size: 97 Copynumber: 2.0 Consensus size: 98
71035 TGAAGTTGAA
* * *
71045 CTTGTGTTGTCCTAAGTCCAATATCCTTCGCTGTGAAGTTGAAAGTGACTCTGAAATTGGGAAAT
1 CTTGTGTTGTCCCAAGTCCAACATCCTTCGATGTGAAGTTGAAAGTGACTCTGAAATTGGGAAAT
*
71110 TGTTTATTGACAACCAGTCGTCCCTTCGTTGTG
66 TGTTTATTGACAACCAGCCGTCCCTTCGTTGTG
* * *
71143 CTTG-GTTGTCCCGAGTCCAACATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
1 CTTGTGTTGTCCCAAGTCCAACATCCTTCGATGTGAAGTTGAAAGTGACTCTGAAATTGGGAAAT
* *
71207 TGTTTGTTGACAACCAGCCGTTCCTTCGTTGTG
66 TGTTTATTGACAACCAGCCGTCCCTTCGTTGTG
71240 AAGTTGAACT
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
97 84 0.95
98 4 0.05
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (98 bp):
CTTGTGTTGTCCCAAGTCCAACATCCTTCGATGTGAAGTTGAAAGTGACTCTGAAATTGGGAAAT
TGTTTATTGACAACCAGCCGTCCCTTCGTTGTG
Found at i:71299 original size:203 final size:204
Alignment explanation
Indices: 70563--71296 Score: 838
Period size: 203 Copynumber: 3.6 Consensus size: 204
70553 ATCTTCCACC
* * *** * * *
70563 GTGAAGTTGAAATTGGCTCTGGAACTCAAAAATTGTTTGTTGACAGCCAACCGCCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
* * * * *
70628 GAAGTTGAGCTTGTGCTGTCTTGAGTCTAATATCCTTCGATGTAAAGTTAAAATTGACCCTGAAA
66 GAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAA
* *
70693 TTAGGAAATTGTTTGTTGACAACC---CGTCCCTTCGTTGTGAAGTTGAACTTGTGTCATCTCGA
131 TTAGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTG-ACTTG-A-GT-TGTC--C-CGA
70755 GTCCAATATCCTTCGCT
189 GTCCAATATCCTTCG-T
* *
70772 GTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
* * * *
70837 GAAGTTAAACTTGTG--GTCTCGAGTTCAATATCCTTCGATGTGAAGTTGAAATTGACCCTAAAA
66 GAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAA
* * * *
70900 TTAGGAAATTGTTTGTTAACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTCTA
131 TTAGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTG-ACTTG-A---GT-T-GTCCCGA
70965 GTCCAATATCCTTC--
189 GTCCAATATCCTTCGT
* * *
70979 -----GCT---ATTGGCTCTGAAATTGGGAGATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
* * * * *
71036 GAAGTTGAACTTGTGTTGTCCTAAGTCCAATATCCTTCGCTGTGAAGTTGAAAGTGACTCTGAAA
66 GAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAA
* * *
71101 TTGGGAAATTGTTTATTGACAACCAGTCGTCCCTTCGTTGTG-CTTG-GTTGTCCCGAGTCCAAC
131 TTAGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGACTTGAGTTGTCCCGAGTCCAAT
71164 ATCCTTCGAT
196 ATCCTTCG-T
*
71174 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTTCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
* *
71239 GAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTT-TACTGTGCAGTTGAAATTGAC
66 GAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGA-TGTGAAGTTGAAATTGAC
71297 TCTAGCTAAA
Statistics
Matches: 451, Mismatches: 54, Indels: 46
0.82 0.10 0.08
Matches are distributed among these distances:
192 18 0.04
193 1 0.00
194 2 0.00
199 67 0.15
200 2 0.00
201 79 0.18
202 2 0.00
203 102 0.23
207 65 0.14
209 68 0.15
210 39 0.09
212 3 0.01
213 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (204 bp):
GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
GAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAA
TTAGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGACTTGAGTTGTCCCGAGTCCAAT
ATCCTTCGT
Found at i:71431 original size:146 final size:146
Alignment explanation
Indices: 71167--71460 Score: 561
Period size: 146 Copynumber: 2.0 Consensus size: 146
71157 GTCCAACATC
* *
71167 CTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTTCCT
1 CTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCCGTCCCT
71232 TCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTTACTGTGCAGTTGAAATTGAC
66 TCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTTACTGTGCAGTTGAAATTGAC
*
71297 TCTAGCTAAAATCTGT
131 TCTAGCTAAAATATGT
71313 CTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCCGTCCCT
1 CTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCCGTCCCT
71378 TCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTTACTGTGCAGTTGAAATTGAC
66 TCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTTACTGTGCAGTTGAAATTGAC
71443 TCTAGCTAAAATATGT
131 TCTAGCTAAAATATGT
71459 CT
1 CT
71461 GGAATCTTGA
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
146 145 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (146 bp):
CTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCCGTCCCT
TCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTTACTGTGCAGTTGAAATTGAC
TCTAGCTAAAATATGT
Found at i:79497 original size:18 final size:16
Alignment explanation
Indices: 79458--79541 Score: 62
Period size: 17 Copynumber: 4.8 Consensus size: 16
79448 AATGTGTTAG
* *
79458 ATAAACAAGGTAAAGAA
1 ATAAATAAGATAAA-AA
79475 ATAAATAAGATAAAGAGA
1 ATAAATAAGATAAA-A-A
79493 ATAAAATAAAGGA-AAAAA
1 AT-AAAT-AA-GATAAAAA
*
79511 ATAAATAAAATAAAATAA
1 ATAAATAAGAT-AAA-AA
79529 ATAAATAAGATAA
1 ATAAATAAGATAA
79542 GGAAAAATAG
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 23 0.41
18 18 0.32
19 5 0.09
20 5 0.09
21 2 0.04
ACGTcount: A:0.71, C:0.01, G:0.11, T:0.17
Consensus pattern (16 bp):
ATAAATAAGATAAAAA
Found at i:79530 original size:14 final size:14
Alignment explanation
Indices: 79473--79533 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 14
79463 CAAGGTAAAG
*
79473 AAAT-AAATAAGAT
1 AAATAAAATAAAAT
* *
79486 AAAGAGAATAAAAT
1 AAATAAAATAAAAT
**
79500 AAAGGAAA-AAAAT
1 AAATAAAATAAAAT
79513 AAATAAAATAAAAT
1 AAATAAAATAAAAT
79527 AAATAAA
1 AAATAAA
79534 TAAGATAAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
13 14 0.36
14 25 0.64
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.16
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:79547 original size:27 final size:27
Alignment explanation
Indices: 79473--79547 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
79463 CAAGGTAAAG
*
79473 AAATAAATAAGATAAAGAGAATAAAAT
1 AAATAAATAAGATAAAGAAAATAAAAT
* * *
79500 AAAGGAAA-AAAATAAATAAAATAAAAT
1 AAA-TAAATAAGATAAAGAAAATAAAAT
*
79527 AAATAAATAAGATAAGGAAAA
1 AAATAAATAAGATAAAGAAAA
79548 ATAGTACAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.08
27 32 0.84
28 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (27 bp):
AAATAAATAAGATAAAGAAAATAAAAT
Found at i:79597 original size:2 final size:2
Alignment explanation
Indices: 79590--79621 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
79580 TTGAAAAGGA
79590 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
79622 CAAAGTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79765 original size:41 final size:39
Alignment explanation
Indices: 79700--79776 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
79690 TCATTTCACC
* *
79700 GAAAGTGGGGGGCTTTAGTCAGAAATAAGACAAAAAGAG
1 GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
*
79739 GAAAGTGGGAGAGACTTTAGTTAGAAATAAAACAAAAA
1 GAAAGTGGG-G-GACTTTAGTCAGAAATAAAACAAAAA
79777 AATGGGCCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 9 0.27
40 1 0.03
41 23 0.70
ACGTcount: A:0.48, C:0.06, G:0.29, T:0.17
Consensus pattern (39 bp):
GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
Found at i:79898 original size:2 final size:2
Alignment explanation
Indices: 79891--79942 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
79881 TAATAAAATA
79891 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
79933 AT A- AT AT AT A
1 AT AT AT AT AT A
79943 AATTAGATAG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80106 original size:2 final size:2
Alignment explanation
Indices: 80099--80161 Score: 89
Period size: 2 Copynumber: 33.5 Consensus size: 2
80089 ATATTAAGAA
80099 AT AT AT AT AT AT AT AT A- 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
*
80140 AT AT -T AT AT A- AT A- AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
80162 GTAAAAATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:80118 original size:27 final size:29
Alignment explanation
Indices: 80088--80149 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
80078 TTATAAGTAA
80088 AATAT-TA-AGAAATATATATATATATAT
1 AATATATATAGAAATATATATATATATAT
* *
80115 AATATATATATATATATATATATATATAT
1 AATATATATAGAAATATATATATATATAT
*
80144 TATATA
1 AATATA
80150 ATAATAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 5 0.17
28 2 0.07
29 23 0.77
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
AATATATATAGAAATATATATATATATAT
Found at i:80654 original size:35 final size:35
Alignment explanation
Indices: 80615--80686 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
80605 CTAAAAAACC
*
80615 CTATTTTAGACTAGT-TATTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTAT-TTAAGTCCTAATCCAACT
80650 CTATTTTAGACTAGTATTTAAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTAAGTCCTAATCCAACT
80685 CT
1 CT
80687 TCTTTTTGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTAAGTCCTAATCCAACT
Done.