Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000883.1 Hibiscus syriacus cultivar Beakdansim tig00001717_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: 50333
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1424 original size:33 final size:33
Alignment explanation
Indices: 1378--1449 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
1368 ATTCAAGTAA
*
1378 GATTTTTTTAAAAAAATTTCA-GGATCGGGTC-G
1 GATTTTTTTAAAAAAAATTCAGGGA-CGGGTCAG
1410 GATTTTTTTAAAAAAAAATTCAGGGACGGGTCAG
1 GATTTTTTT-AAAAAAAATTCAGGGACGGGTCAG
1444 G-TTTTT
1 GATTTTT
1450 AAGTTTGATA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
32 9 0.25
33 22 0.61
34 5 0.14
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (33 bp):
GATTTTTTTAAAAAAAATTCAGGGACGGGTCAG
Found at i:1471 original size:31 final size:30
Alignment explanation
Indices: 1427--1527 Score: 136
Period size: 31 Copynumber: 3.4 Consensus size: 30
1417 TTAAAAAAAA
*
1427 ATTCAGGGACGGGTCAGGTTTTTAAGTTTGAT
1 ATTC-GGGTCGGGTC-GGTTTTTAAGTTTGAT
1459 ATTCGGGTCGGGT---TTTTTAAGTTTGAT
1 ATTCGGGTCGGGTCGGTTTTTAAGTTTGAT
*
1486 ATTCGGGTCGGGTCGGTTTTTTAAGTGTGAT
1 ATTCGGGTCGGGTCGG-TTTTTAAGTTTGAT
1517 ATTCGGGTCGG
1 ATTCGGGTCGG
1528 TTTAGGGTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
27 27 0.43
31 32 0.51
32 4 0.06
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.41
Consensus pattern (30 bp):
ATTCGGGTCGGGTCGGTTTTTAAGTTTGAT
Found at i:2091 original size:18 final size:18
Alignment explanation
Indices: 2064--2100 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2054 CCATTTCTTG
2064 ACAGAATCTAATTCCTTC
1 ACAGAATCTAATTCCTTC
*
2082 ACAGATTCTAATTCCTTC
1 ACAGAATCTAATTCCTTC
2100 A
1 A
2101 AAAACATTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (18 bp):
ACAGAATCTAATTCCTTC
Found at i:6357 original size:16 final size:17
Alignment explanation
Indices: 6330--6362 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
6320 TTGCCCTACT
6330 ACCCATCTTCTAAGTGG
1 ACCCATCTTCTAAGTGG
6347 ACCCA-CTTCTAAGTGG
1 ACCCATCTTCTAAGTGG
6363 TATAATCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (17 bp):
ACCCATCTTCTAAGTGG
Found at i:8717 original size:67 final size:66
Alignment explanation
Indices: 8619--8749 Score: 172
Period size: 67 Copynumber: 2.0 Consensus size: 66
8609 GTTTTCCTAA
* * * * **
8619 AAACAAATTTCGTCTCACTTGAGTCAGTTTCTCTTGGAACATAAACTTTTGAGATTGTTTCTCTC
1 AAACAAATTTCGTCTCACTTGAGACAATTTCTCTTGAAACATAAACCTTCAAGATTGTTTCTCTC
8684 C
66 C
* * *
8685 AAACAAAGTTTTGTCTCACTTGAGACAATTTCTTTTGAAACATAAGCCTTCAAGATTGTTTCTCT
1 AAACAAA-TTTCGTCTCACTTGAGACAATTTCTCTTGAAACATAAACCTTCAAGATTGTTTCTCT
8750 AAAAAAATCA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
66 7 0.13
67 48 0.87
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (66 bp):
AAACAAATTTCGTCTCACTTGAGACAATTTCTCTTGAAACATAAACCTTCAAGATTGTTTCTCTC
C
Found at i:8882 original size:102 final size:102
Alignment explanation
Indices: 8766--9036 Score: 375
Period size: 102 Copynumber: 2.6 Consensus size: 102
8756 ATCATCTCGT
*
8766 TTGAGACAGTTTTCCCTCGAAACACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTTA
1 TTGAGACAGTTTTCCCTCGAAACACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCA
* *
8831 CTTGAGATTGTTTTTCTAAAAATAAATTTCCTCTCAC
66 CTTGAGAGTGTTTTTCTAAAAACAAATTTCCTCTCAC
*
8868 TTGAGACAGCTTTCCCTC-ATAACACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTC
1 TTGAGACAGTTTTCCCTCGA-AACACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTC
* * ** *
8932 ACTTGAGAGTGTTTTTCTCATAACAAATTTTGTCTCGC
65 ACTTGAGAGTGTTTTTCTAAAAACAAATTTCCTCTCAC
* * * * *
8970 TTGAGA-TGATTTTCCCTTGAAACACAAATTTTGAAATTGTTTCACTCGACACAAAATTTTATCT
1 TTGAGACAG-TTTTCCCTCGAAACACAAATTTTGAAATTGTTTCACTTGAAACAAAA-TTGATCT
9034 CAC
64 CAC
9037 CTTAGATAGC
Statistics
Matches: 150, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
101 2 0.01
102 138 0.92
103 10 0.07
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (102 bp):
TTGAGACAGTTTTCCCTCGAAACACAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCA
CTTGAGAGTGTTTTTCTAAAAACAAATTTCCTCTCAC
Found at i:9878 original size:104 final size:103
Alignment explanation
Indices: 9697--9936 Score: 311
Period size: 104 Copynumber: 2.3 Consensus size: 103
9687 AGATTTTACC
* ** * *
9697 AGACTTCCTCAATGAAAAGGAACAACATCATATGAAAGCAGCCATAACTCTTCAATATGGATAAG
1 AGACTTCCTCAA-CAAAAGGAACAACATCATCCGAAAGCAGCCAAAACTCTTCAACATGGATAAG
**
9762 CAGTGTCATCTTCAACACCAAATTATCTTGA-ACTTGACT
65 CAGTGTCATCTTCAACACCAAATTATCTCCAGA-TTGACT
* * ** *
9801 CGACTTCCTCAACAAGAAGGAACAACGTCATCCGAAAGTGGCCAAAACTCTTCAACATGGATGAG
1 AGACTTCCTCAACAA-AAGGAACAACATCATCCGAAAGCAGCCAAAACTCTTCAACATGGATAAG
*
9866 CAGTGTCATCTTCAACTCCAAATTATCTCCAGATTGACT
65 CAGTGTCATCTTCAACACCAAATTATCTCCAGATTGACT
*
9905 AGATTTCCTCAACAATAAGGAACAACATCATC
1 AGACTTCCTCAACAA-AAGGAACAACATCATC
9937 TTCAGTAAAT
Statistics
Matches: 117, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
103 2 0.02
104 114 0.97
105 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (103 bp):
AGACTTCCTCAACAAAAGGAACAACATCATCCGAAAGCAGCCAAAACTCTTCAACATGGATAAGC
AGTGTCATCTTCAACACCAAATTATCTCCAGATTGACT
Found at i:12465 original size:17 final size:17
Alignment explanation
Indices: 12434--12467 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
12424 AACGCAGACC
12434 AATGTTTTTCTTTAAAA
1 AATGTTTTTCTTTAAAA
12451 AATGATTTTTC-TTAAAA
1 AATG-TTTTTCTTTAAAA
12468 TTATTTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (17 bp):
AATGTTTTTCTTTAAAA
Found at i:17323 original size:81 final size:81
Alignment explanation
Indices: 17210--18188 Score: 1571
Period size: 81 Copynumber: 12.1 Consensus size: 81
17200 ATTCCTTTGG
* * * * * * *
17210 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCGTGATTGACACTTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
17275 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
17291 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACTCGTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
17356 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
*
17372 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
17437 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
17453 TATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAAACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
17518 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * **
17534 TATTTTACTCAAAGGTATTTAACATTTCATCTAACTAGCATAATTGACACATTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
17599 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
*
17615 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
*
17680 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
*
17696 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
* *
17761 ATAGCTAGGTCATTAA
66 ACAGCTAGGCCATTAA
* *
17777 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCACAATTGACACATTTCTACCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
17842 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
17858 TCTTTTACTCAAAGGTATTTAACCTTTAATCTAACTGGCATAATTGATACATTTTTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
**
17923 ACAGCTAAACCATTAA
66 ACAGCTAGGCCATTAA
* *
17939 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGTCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
* * *
18004 ACGGCTAGTCCTTTAA
66 ACAGCTAGGCCATTAA
* *
18020 TCTTTTACTGAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
18085 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
18101 TCTTTTACTCATAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTTTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
*
18166 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
*
18182 ACTTTTA
1 TCTTTTA
18189 TTTTAGAACA
Statistics
Matches: 830, Mismatches: 68, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 830 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
ACAGCTAGGCCATTAA
Found at i:18579 original size:46 final size:46
Alignment explanation
Indices: 18527--18622 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
18517 TTATTCGTTA
*
18527 ATTTCATTTATGACATCATTTCATGCCTTAATGCATCCTCTCATGC
1 ATTTCATTTATGACATCATTTCATGCCTTAATGCATCATCTCATGC
* * * *
18573 ATTTCATTTATGGCATCCTTTCATGCCTTGATGCATCATTTCATGC
1 ATTTCATTTATGACATCATTTCATGCCTTAATGCATCATCTCATGC
18619 ATTT
1 ATTT
18623 TTAGTTATGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (46 bp):
ATTTCATTTATGACATCATTTCATGCCTTAATGCATCATCTCATGC
Found at i:19147 original size:20 final size:20
Alignment explanation
Indices: 19118--19167 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
19108 ATTAACAATG
* *
19118 GTATCAATACCATCCTCATA
1 GTATCGATACCACCCTCATA
* * *
19138 GTATCGATACCCCCCTCTTG
1 GTATCGATACCACCCTCATA
19158 GTATCGATAC
1 GTATCGATAC
19168 TACTCAGTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (20 bp):
GTATCGATACCACCCTCATA
Found at i:20822 original size:2 final size:2
Alignment explanation
Indices: 20815--20848 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20805 CCTAATATCA
20815 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
20849 TAAAATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21903 original size:25 final size:21
Alignment explanation
Indices: 21875--21922 Score: 60
Period size: 25 Copynumber: 2.1 Consensus size: 21
21865 AATCTTTCTA
21875 TTTCTTCTAGCTTTCTCTGTTAGTT
1 TTTCTTCTA--TTT-TCT-TTAGTT
21900 TTTCTTCTATTTTCTTTAGTT
1 TTTCTTCTATTTTCTTTAGTT
21921 TT
1 TT
21923 CTGTTTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 8 0.35
22 3 0.13
23 3 0.13
25 9 0.39
ACGTcount: A:0.08, C:0.17, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTCTTCTATTTTCTTTAGTT
Found at i:26656 original size:24 final size:24
Alignment explanation
Indices: 26624--26669 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
26614 AAAAAGAAAG
26624 AAAAAAAAGGAACGTTGATGCAGA
1 AAAAAAAAGGAACGTTGATGCAGA
26648 AAAAAAAAGGAACGTTGATGCA
1 AAAAAAAAGGAACGTTGATGCA
26670 ATAAGAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.09, G:0.24, T:0.13
Consensus pattern (24 bp):
AAAAAAAAGGAACGTTGATGCAGA
Found at i:29980 original size:21 final size:21
Alignment explanation
Indices: 29954--29995 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
29944 CCAGAATGGG
*
29954 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
29975 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
29996 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:30187 original size:34 final size:33
Alignment explanation
Indices: 30107--30190 Score: 123
Period size: 34 Copynumber: 2.5 Consensus size: 33
30097 AAATCATGCA
* *
30107 GGGGGAATCTGTACCCGGGGAATCGATACCCCT
1 GGGGGAATCTGTTCCCAGGGAATCGATACCCCT
*
30140 GGAGGGAATCTGTTCCTAGGGAATCGATACCCCTT
1 GG-GGGAATCTGTTCCCAGGGAATCGATACCCC-T
30175 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
30191 TCTGGGCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
33 2 0.04
34 40 0.89
35 3 0.07
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (33 bp):
GGGGGAATCTGTTCCCAGGGAATCGATACCCCT
Found at i:31625 original size:19 final size:20
Alignment explanation
Indices: 31580--31627 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
31570 TCTAAATCCT
* *
31580 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTAATTTTGG
*
31600 CTTTCAAAATCTAATTTT-G
1 TTTTCAAAATCTAATTTTGG
31619 TTTTCAAAA
1 TTTTCAAAA
31628 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATCTAATTTTGG
Found at i:33014 original size:15 final size:15
Alignment explanation
Indices: 32994--33049 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
32984 AACCATGCAG
32994 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
33009 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
* *
33025 TAGGGGAATCTGTTCCT
1 --GGGGAATCTGTACCC
33042 GGGGAATC
1 GGGGAATC
33050 GATACCCCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.03
15 18 0.53
16 3 0.09
17 2 0.06
18 9 0.26
19 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.21
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:33033 original size:33 final size:33
Alignment explanation
Indices: 32994--33057 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
32984 AACCATGCAG
32994 GGGGAATCTGTACCCGGGGAATCGATACCCCTA
1 GGGGAATCTGTACCCGGGGAATCGATACCCCTA
* *
33027 GGGGAATCTGTTCCTGGGGAATCGATACCCC
1 GGGGAATCTGTACCCGGGGAATCGATACCCC
33058 CCCTGGGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (33 bp):
GGGGAATCTGTACCCGGGGAATCGATACCCCTA
Found at i:35755 original size:21 final size:21
Alignment explanation
Indices: 35730--35771 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35720 CCAGAATGGG
* *
35730 GGGAATCGGTGCCCCTTCATA
1 GGGAATCGATACCCCTTCATA
35751 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
35772 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:35923 original size:34 final size:35
Alignment explanation
Indices: 35883--35964 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 35
35873 AAACTATACA
35883 GGGGGAATCTGTACCG-GGAAAATCGATA-CCCCT-G
1 GGGGGAATCTGTACCGTGG--AATCGATACCCCCTGG
* *
35917 GGGGGAATCTGTTCCCGTGGATTCGATACCCCCTGG
1 GGGGGAATCTG-TACCGTGGAATCGATACCCCCTGG
35953 GGGGGAATCTGT
1 GGGGGAATCTGT
35965 TCCCTCTGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
34 18 0.43
35 10 0.24
36 14 0.33
ACGTcount: A:0.20, C:0.23, G:0.35, T:0.22
Consensus pattern (35 bp):
GGGGGAATCTGTACCGTGGAATCGATACCCCCTGG
Found at i:36793 original size:62 final size:63
Alignment explanation
Indices: 36703--36822 Score: 147
Period size: 62 Copynumber: 1.9 Consensus size: 63
36693 AACCTCAACA
* * *
36703 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAA-CTGGCCATA-TGTTCCTTAGAACATATGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAATATGGCCA-AGTGTTCCGTAGAACATATGTAT
* * *
36765 ACTGTCCATATGTCTCGAA-AGACATAGGTAAATATGTCCAAGTGTTCCGTAGAACATA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGTAAATATGGCCAAGTGTTCCGTAGAACATA
36823 GGTAAACCCT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
61 1 0.02
62 28 0.57
63 20 0.41
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (63 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAATATGGCCAAGTGTTCCGTAGAACATATGTAT
Found at i:38683 original size:35 final size:35
Alignment explanation
Indices: 38644--38711 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
38634 AATATAGTCC
38644 TCAA-TATCATTATAAACCCCAAATTCTAAAATAAT
1 TCAATTAT-ATTATAAACCCCAAATTCTAAAATAAT
* *
38679 TCAATTATATTTTAAACCCTAAATTCTAAAATA
1 TCAATTATATTATAAACCCCAAATTCTAAAATA
38712 CTTTAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (35 bp):
TCAATTATATTATAAACCCCAAATTCTAAAATAAT
Found at i:38788 original size:33 final size:35
Alignment explanation
Indices: 38723--38788 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
38713 TTTAATTTAA
38723 GGTTTAGAATATAATTAAAGTATTTTGAAATTTGG
1 GGTTTAGAATATAATTAAAGTATTTTGAAATTTGG
* * *
38758 GGTTTAGAATGTAA-T-AAGTGTTTTGGAATTT
1 GGTTTAGAATATAATTAAAGTATTTTGAAATTT
38789 TGAACATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 14 0.50
34 1 0.04
35 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (35 bp):
GGTTTAGAATATAATTAAAGTATTTTGAAATTTGG
Found at i:42734 original size:87 final size:87
Alignment explanation
Indices: 42617--42805 Score: 308
Period size: 87 Copynumber: 2.2 Consensus size: 87
42607 AACCAAACAC
* *
42617 GGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCACAGTAATCATATTCC
1 GGTAATATTACATTCATGCTAAACCAACCAAACACAAAATACAACATTCACAGTAATCATATTCC
42682 CT-AGTAATCTTTTATTCCCACT
66 CTGA-TAATCTTTTATTCCCACT
* *
42704 GGTAATATTACATTCATGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCCTATTCC
1 GGTAATATTACATTCATGCTAAACCAACCAAACACAAAATACAACATTCACAGTAATCATATTCC
*
42769 CTGATAATCTTTTATTTCCACT
66 CTGATAATCTTTTATTCCCACT
*
42791 TGTAATATTACATTC
1 GGTAATATTACATTC
42806 CGTGAACCAA
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 94 0.99
88 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (87 bp):
GGTAATATTACATTCATGCTAAACCAACCAAACACAAAATACAACATTCACAGTAATCATATTCC
CTGATAATCTTTTATTCCCACT
Found at i:45129 original size:135 final size:136
Alignment explanation
Indices: 44749--45129 Score: 373
Period size: 135 Copynumber: 2.8 Consensus size: 136
44739 GTTAAACAGT
* * * * *
44749 TAGGATAATAT-CCTTCCAAACAATAGAACTGGATTCGACTCTTGGCAAACGCAATTCTTTTTAA
1 TAGGATAAT-TGCCTTCCAAGCAATAGACCTGGATTAGACTCCTGGCAAACGCAATTATTTTTAA
* *
44813 ATTACTGATCGAATTAAACTTAAACAACAAAGATTAGTGTTAGCTCATTGACAAACAAAGCGTTT
65 ATTACTGATCGAATTAAA-TTAAACAACAAA-ATTA-TATTAGCTCAATGACAAACAAAGCGTTT
44878 GTAGTCTAACGA
127 GTAGTCT-AC-A
* ** * * *
44890 TTAGGATAATTGTCTTTTAAGCAATAGACCTGGTTTTGACTCCTGGCAAACGCAATTTTTTTTAA
1 -TAGGATAATTGCCTTCCAAGCAATAGACCTGGATTAGACTCCTGGCAAACGCAATTATTTTTAA
* * * * * * * *
44955 ACTATTGAGCAAATTAAA-TGAACAACAAACTTAAAATTAGCTCAGAATGACCAACAAAGCGTTT
65 ATTACTGATCGAATTAAATTAAACAACAAAATT-ATATTAGCTC--AATGACAAACAAAGCGTTT
45019 GTAGT-T-C-
127 GTAGTCTACA
* **
45026 TAGGATAATTGCCTTCCAAGGAATAGA-CTCGGATTAGACTCCCT-GCAAGTGCAATTATTTTTA
1 TAGGATAATTGCCTTCCAAGCAATAGACCT-GGATTAGACT-CCTGGCAAACGCAATTATTTTTA
45089 AATTACTGATCGAATTAAATTTAAACAACAAAATT-TATTAG
64 AATTACTGATCGAATTAAA-TTAAACAACAAAATTATATTAG
45130 TAGCTCAAAA
Statistics
Matches: 196, Mismatches: 35, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
134 2 0.01
135 67 0.34
136 3 0.02
137 12 0.06
138 1 0.01
139 9 0.05
140 12 0.06
141 23 0.12
142 67 0.34
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (136 bp):
TAGGATAATTGCCTTCCAAGCAATAGACCTGGATTAGACTCCTGGCAAACGCAATTATTTTTAAA
TTACTGATCGAATTAAATTAAACAACAAAATTATATTAGCTCAATGACAAACAAAGCGTTTGTAG
TCTACA
Found at i:45350 original size:143 final size:141
Alignment explanation
Indices: 45151--45450 Score: 365
Period size: 143 Copynumber: 2.1 Consensus size: 141
45141 GATCAGCAAA
* *
45151 CCTTCC-AGCAATAGATCCGGTCGACTCCCGGCAAACACAATTCCTTTTAAATTACTGATAGAAT
1 CCTTCCAAGCAATAGACCCGGTCGACTCCCGGCAAACACAATTCCTTTTAAATTACTGAGAGAAT
45215 TAAAATTAAAACAACAAA-TAGTAGTTAGCTCAGTAA-AACCAAAAAAGCGTTTGTAGTCCAACG
66 TAAAATTAAAACAACAAAGTAG-AGTTAGCTCAG-AATAACCAAAAAAGCGTTTGTAGTCCAACG
*
45278 GTTAGGATAATTG
129 GTTAGGAAAATTG
* * * *
45291 CCTTCCAAGCAATAGACCCGGGTTCGACTCCCGGCAAACGCAGTTCTTTTTAAATTACTGAGCGA
1 CCTTCCAAGCAATAGACCC-GG-TCGACTCCCGGCAAACACAATTCCTTTTAAATTACTGAGAGA
* * * * * * *
45356 ATTACACTTAAAACAACAAAGGTTAGAGTTAGCTCAGAATGACCAACAGAGCGTTTGTGGTTCAA
64 ATTAAAATTAAAACAACAAA-G-TAGAGTTAGCTCAGAATAACCAAAAAAGCGTTTGTAGTCCAA
*
45421 TGGTTAGGAAAATTG
127 CGGTTAGGAAAATTG
*
45436 TCTT-CAATGCAATAG
1 CCTTCCAA-GCAATAG
45451 GGTTGACTCC
Statistics
Matches: 136, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
140 6 0.04
141 11 0.08
142 2 0.01
143 55 0.40
144 5 0.04
145 54 0.40
146 3 0.02
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (141 bp):
CCTTCCAAGCAATAGACCCGGTCGACTCCCGGCAAACACAATTCCTTTTAAATTACTGAGAGAAT
TAAAATTAAAACAACAAAGTAGAGTTAGCTCAGAATAACCAAAAAAGCGTTTGTAGTCCAACGGT
TAGGAAAATTG
Found at i:48214 original size:143 final size:140
Alignment explanation
Indices: 47960--48379 Score: 454
Period size: 143 Copynumber: 2.9 Consensus size: 140
47950 ATAATATGTG
* * * *
47960 CTATTATATTAAAATAC-TACCGATTTTTTTAAGGTTACTAATGATGTAAACGGTAAAAAAATAG
1 CTATTATATTAAAATACATACCGA-TTTTTTAAAGTT-GTTATAATGTAAACGGTAAAAAAATAG
* *
48024 GCGCTACCTATTACATTAAAATACCTACTGGGGTTTTTTAAGGTTGCTAATAATGTAAAGTAAAA
64 ACGCTACCTATTA-ATT-AAATACCTA-T-CGGTTTTTTAAGGTTGCTAATAATGTAAAGTAAAA
48089 AAAAAATAGACGCTAC
125 AAAAAATAGACGCTAC
*
48105 CTATTATATT-AACTACATACCGATTTTTTAAAGTTGTTATAATGTAAACGGTAAAACAAATAGA
1 CTATTATATTAAAATACATACCGATTTTTTAAAGTTGTTATAATGTAAACGGTAAAA-AAATAGA
* * * * *
48169 CCCTACTTATTAGATTAAATACCTATTGGTTTGTTTAAAGATTGCTAATAATGTAAA-TGATAAA
65 CGCTACCTATTA-ATTAAATACCTATCGGTTT-TTT-AAGGTTGCTAATAATGTAAAGT-AAAAA
* * *
48233 ATAAATAGGCGTTAC
126 AAAAATAGACGCTAC
* * * ** *
48248 CTATTACATTAAAATACATACCGGTTTTTTTTAACATGTTAATAATCTAAACGGTAAAAAAATA-
1 CTATTATATTAAAATACATACC-GATTTTTTAAAGTTGTT-ATAATGTAAACGGTAAAAAAATAG
*
48312 AGCGCTACCTATT-ATTAAATACCTATCGGTTTTTTTTAAGGTTGCTAATAATGTAACGGTAAAA
64 A-CGCTACCTATTAATTAAATACCTATCGG--TTTTTTAAGGTTGCTAATAATGTAA-AGTAAAA
48376 AAAA
125 AAAA
48380 TAGTGATACT
Statistics
Matches: 233, Mismatches: 29, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
141 5 0.02
142 5 0.02
143 104 0.45
144 55 0.24
145 47 0.20
146 17 0.07
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (140 bp):
CTATTATATTAAAATACATACCGATTTTTTAAAGTTGTTATAATGTAAACGGTAAAAAAATAGAC
GCTACCTATTAATTAAATACCTATCGGTTTTTTAAGGTTGCTAATAATGTAAAGTAAAAAAAAAA
TAGACGCTAC
Found at i:48379 original size:70 final size:71
Alignment explanation
Indices: 47960--48381 Score: 353
Period size: 73 Copynumber: 5.9 Consensus size: 71
47950 ATAATATGTG
* * * *
47960 CTATTATATTAAAATA-CTACCGATTTTTTTAAGGTTACTAATGATGTAAACGGT-AAAAAAATA
1 CTATTA-ATT-AAATACCTACGGTTTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATA
*
48023 GGCGCTAC
64 AGCGCTAC
** *
48031 CTATTACATTAAAATACCTACTGGGGTTTTTTAAGGTTGCTAATAATGTAAA--GTAAAAAAAAA
1 CTATTA-ATT-AAATACCTAC-GGTTTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAAT
48094 ATAGACGCTAC
63 A-AG-CGCTAC
* * * * * * *
48105 CTATTATATTAACTACATACCG-ATTTTTTAAAGTTG-TTATAATGTAAACGGTAAAACAAAT-A
1 CTATTA-ATTAAATACCTACGGTTTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAA
*
48167 GACCCTAC
65 G-CGCTAC
* * * * * * * *
48175 TTATTAGATTAAATACCTATTGGTTTGTTTAAAGATTGCTAATAATGTAAATGATAAAATAAATA
1 CTATTA-ATTAAATACCTA-CGGTTTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATA
* *
48240 GGCGTTAC
64 AGCGCTAC
* ** * *
48248 CTATTACATTAAAATACATACCGGTTTTTTTTAA-CATGTTAATAATCTAAACGGT-AAAAAAAT
1 CTATTA-ATT-AAATACCTA-CGGTTTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAAT
48311 AAGCGCTAC
63 AAGCGCTAC
48320 CTATT-ATTAAATACCTATCGGTTTTTTTTAAGGTTGCTAATAATGT-AACGGTAAAAAAAATA
1 CTATTAATTAAATACCTA-CGGTTTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATA
48382 GTGATACTAT
Statistics
Matches: 279, Mismatches: 58, Indels: 29
0.76 0.16 0.08
Matches are distributed among these distances:
69 27 0.10
70 56 0.20
71 30 0.11
72 50 0.18
73 82 0.29
74 34 0.12
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (71 bp):
CTATTAATTAAATACCTACGGTTTTTTTTAAGGTTGCTAATAATGTAAACGGTAAAAAAAATAAG
CGCTAC
Found at i:48741 original size:110 final size:111
Alignment explanation
Indices: 48500--48714 Score: 291
Period size: 110 Copynumber: 2.0 Consensus size: 111
48490 AGTATCGAAT
* *
48500 CTTTATAAAAA--TATCGATTCATAACAATATAACATGTTAAAATATGACAAAACCAGTTTCATT
1 CTTTATAAAAATGTATCGATACATAACAATATAACA-GTAAAAATATGACAAAACCAGTTTCATT
* *
48563 ATGACAAAACCAGTAAAGAGCTACCAGATATGTTGAAAGTATCATTA
65 ATAACAAAACCAATAAAGAGCTACCAGATATGTTGAAAGTATCATTA
48610 CTTTATAAAAATGTATCGATACATAACAATATAACA-TAAAAATATGACAAAAACCAGTTTCATT
1 CTTTATAAAAATGTATCGATACATAACAATATAACAGTAAAAATATGAC-AAAACCAGTTTCATT
*
48674 ATAACAAATCGGCAAT-AA-A-CTACC-GAATATGTTGAAAGTAT
65 ATAACAAAAC--CAATAAAGAGCTACCAG-ATATGTTGAAAGTAT
48715 TGATACTTTT
Statistics
Matches: 94, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
109 1 0.01
110 42 0.45
111 24 0.26
112 24 0.26
113 3 0.03
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.28
Consensus pattern (111 bp):
CTTTATAAAAATGTATCGATACATAACAATATAACAGTAAAAATATGACAAAACCAGTTTCATTA
TAACAAAACCAATAAAGAGCTACCAGATATGTTGAAAGTATCATTA
Found at i:49750 original size:47 final size:44
Alignment explanation
Indices: 49659--49804 Score: 202
Period size: 45 Copynumber: 3.2 Consensus size: 44
49649 TCTCTTACTA
49659 TTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
1 TTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
*
49703 TTAATACCATAAACTCGTAAGCTTATTTTTACCAATATACTTACCAT
1 TT-AT-CCATAAGCTCGTAAGCTTA-TTTTACCAATATACTTACCAT
* * * *
49750 TTGTTCATAAGCTCGTAAGCTTATTTTACCAATACACTTGCCAT
1 TTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
*
49794 TATTTCCATAA
1 T-TATCCATAA
49805 CCATATACCA
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
44 22 0.24
45 26 0.29
46 19 0.21
47 23 0.26
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (44 bp):
TTATCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
Found at i:49774 original size:45 final size:46
Alignment explanation
Indices: 49663--49794 Score: 196
Period size: 47 Copynumber: 2.9 Consensus size: 46
49653 TTACTATTAT
49663 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATA
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATA
* *
49709 CCATAAACTCGTAAGCTTATTTTTACCAATATACTTACCATTT-GT-
1 CCATAAGCTCGTAAGCTTA-TTTTACCAATATACTTACCATTTAATA
* * *
49754 TCATAAGCTCGTAAGCTTATTTTACCAATACACTTGCCATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATT
49795 ATTTCCATAA
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 20 0.25
45 17 0.22
46 19 0.24
47 23 0.29
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.38
Consensus pattern (46 bp):
CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATA
Done.