Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003835.1 Hibiscus syriacus cultivar Beakdansim tig00008221_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: 124939
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:922 original size:65 final size:65
Alignment explanation
Indices: 803--958 Score: 226
Period size: 65 Copynumber: 2.4 Consensus size: 65
793 CTAAGAGTGA
* * * * *
803 ATCGATGCATGAAGTGCATTCGATG-TTTCAAACCAGCCTGAGTGCATCGATGCATGGTCTGTAC
1 ATCGATGCATAAAATGCATTCGATGTTTTCAAACAAGCCTGAGTGCATCGATGCATGATATGTAC
* *
867 ATCGATGCATAAAATGCATTCGATGTTTTCATAA-AATCCTGAGTGCATCGATGCATGATATGTG
1 ATCGATGCATAAAATGCATTCGATGTTTTCA-AACAAGCCTGAGTGCATCGATGCATGATATGTA
931 C
65 C
932 ATCGATGCATAAAATGCATTCGATGTT
1 ATCGATGCATAAAATGCATTCGATGTT
959 CAATTTATTC
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 23 0.28
65 58 0.70
66 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (65 bp):
ATCGATGCATAAAATGCATTCGATGTTTTCAAACAAGCCTGAGTGCATCGATGCATGATATGTAC
Found at i:997 original size:65 final size:63
Alignment explanation
Indices: 803--1002 Score: 199
Period size: 65 Copynumber: 3.1 Consensus size: 63
793 CTAAGAGTGA
* * * * * * *
803 ATCGATGCATGAAGTGCATTCGATGTTTCA-AACCAGCCTGAGTGCATCGATGCATGGTCTGTAC
1 ATCGATGCATAAAATGCATTCGATGTTTCATAA-AATCATGAGTGCATCGATGCATGG-ATGTGC
* *
867 ATCGATGCATAAAATGCATTCGATGTTTTCATAAAATCCTGAGTGCATCGATGCATGATATGTGC
1 ATCGATGCATAAAATGCATTCGATG-TTTCATAAAATCATGAGTGCATCGATGCATG-GATGTGC
** *
932 ATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCAATG-GTGCATCGATGCATGGAGTGGT
1 ATCGATGCATAAAATGCATTCGATGTTTC-ATAAAATC-ATGAGTGCATCGATGCATGGA-T-GT
995 GC
62 GC
997 ATCGAT
1 ATCGAT
1003 ACACTCTTTT
Statistics
Matches: 117, Mismatches: 12, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
63 4 0.03
64 44 0.38
65 67 0.57
66 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (63 bp):
ATCGATGCATAAAATGCATTCGATGTTTCATAAAATCATGAGTGCATCGATGCATGGATGTGC
Found at i:1625 original size:2 final size:2
Alignment explanation
Indices: 1618--1642 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1608 ACCAAACCAA
1618 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 A
1643 AGTTCAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1953 original size:31 final size:31
Alignment explanation
Indices: 1887--1945 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
1877 AATTTAAGGA
*
1887 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAATGGTATTTGGACTTGAATTGAATTTAC
1918 AAAAT-GTATTTGGACTT-AATTGAATTTA
1 AAAATGGTATTTGGACTTGAATTGAATTTA
1946 TTCAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAATGGTATTTGGACTTGAATTGAATTTAC
Found at i:2037 original size:19 final size:19
Alignment explanation
Indices: 2010--2075 Score: 105
Period size: 19 Copynumber: 3.5 Consensus size: 19
2000 AATGTTTTTA
* *
2010 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
2029 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
*
2048 TGAACAGTAAATCACTATT
1 TGAACAGTAAATTACTATT
2067 TGAACAGTA
1 TGAACAGTA
2076 CCCAGAGGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:2207 original size:21 final size:21
Alignment explanation
Indices: 2181--2222 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2171 ATTTGAATAT
2181 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
2202 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
2223 CCCATTCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:11820 original size:20 final size:20
Alignment explanation
Indices: 11793--11945 Score: 252
Period size: 20 Copynumber: 7.7 Consensus size: 20
11783 TTTTCCTAAT
11793 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
11813 TTGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
11833 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
11853 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
11873 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
11893 TCGCAATTCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
11913 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
11933 TCGCAACGCGAAT
1 TCGCAATGCGAAT
11946 CTGACTATCG
Statistics
Matches: 123, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 123 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:12168 original size:22 final size:22
Alignment explanation
Indices: 12143--12208 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
12133 GGCGACATCT
12143 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
12165 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
12187 GTCTCCATCTCC-AGCGAAATCA
1 GTCCCCATCTCCGA-CGAAATCA
12209 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 1 0.03
22 39 0.98
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:12610 original size:20 final size:20
Alignment explanation
Indices: 12544--12613 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
12534 CGATTCTGTC
*
12544 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
***
12563 GTTGCGACAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
12583 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
12603 GTTGCGATTTT
1 GTTGCGATTTT
12614 AAGTTTCAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 10 0.23
20 33 0.77
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:12620 original size:20 final size:20
Alignment explanation
Indices: 12577--12620 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
12567 CGACAGTCAT
* *
12577 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
12597 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
12617 TTTC
1 TTTC
12621 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:14534 original size:20 final size:20
Alignment explanation
Indices: 14504--14595 Score: 148
Period size: 20 Copynumber: 4.6 Consensus size: 20
14494 TAGTTTACTA
*
14504 TCGCATTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCATTT
*
14524 TTGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCATTT
14544 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCATTT
*
14564 TTGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCATTT
*
14584 TCACGTTGCGAT
1 TCGCGTTGCGAT
14596 TTTAAGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATAGTCATTT
Found at i:14553 original size:40 final size:40
Alignment explanation
Indices: 14504--14595 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
14494 TAGTTTACTA
*
14504 TCGCATTGCGATAGTCATTTTTGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCATTTTTGCGTTGCGATAGTCATTT
14544 TCGCGTTGCGATAGTCATTTTTGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATAGTCATTTTTGCGTTGCGATAGTCATTT
*
14584 TCACGTTGCGAT
1 TCGCGTTGCGAT
14596 TTTAAGTTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.41
Consensus pattern (40 bp):
TCGCGTTGCGATAGTCATTTTTGCGTTGCGATAGTCATTT
Found at i:15131 original size:42 final size:42
Alignment explanation
Indices: 15072--15183 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 42
15062 GCCCGACTCA
** * *
15072 CCTATCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGGCC-CCTCCCACCGTTCAAGAGGCC
*
15114 CCTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
* * ** * *
15156 ACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CCTATCATCCCTCAAGAGGCCCCTCCCA
15184 ACATTCTAGA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 2 0.04
42 55 0.96
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.22
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
Found at i:15167 original size:21 final size:21
Alignment explanation
Indices: 15076--15180 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
15066 GACTCACCTA
*
15076 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
15098 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
15118 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
15139 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
15160 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
15181 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:16587 original size:14 final size:14
Alignment explanation
Indices: 16568--16603 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
16558 ATTGTTTAAT
16568 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
16582 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
16596 TGATTTGT
1 TGATTTGT
16604 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:16797 original size:34 final size:33
Alignment explanation
Indices: 16709--16804 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
16699 AAAACAGACT
* ** *
16709 ATCGCAACGCGGAAATGACTATCGCAATGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
16743 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
16776 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
16805 CGAAACTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:16800 original size:20 final size:19
Alignment explanation
Indices: 16742--16809 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
16732 GCAATGAGAG
16742 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
16761 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
16775 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
16795 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
16810 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:16844 original size:20 final size:19
Alignment explanation
Indices: 16815--16881 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
16805 CGAAACTAAA
*
16815 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
16835 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
16851 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
16868 TTCGCATTGCGATT
1 TTCGCATTGCGATT
16882 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 4 0.10
18 3 0.08
19 8 0.21
20 11 0.28
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:16860 original size:14 final size:14
Alignment explanation
Indices: 16841--16894 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
16831 CATTTTCGCA
16841 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
16855 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
16872 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
16888 TTGCGAT
1 TTGCGAT
16895 AGTCATTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:16876 original size:33 final size:33
Alignment explanation
Indices: 16819--16914 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
16809 ACTAAATTCG
16819 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
16853 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
16886 CGTTGCGATAGTCATTTCTGCGTTGCGAT
1 CGTTGCGATTTTCATTTC-GCATTGCGAT
16915 AGTCAATTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 35 0.60
34 23 0.40
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:16911 original size:20 final size:20
Alignment explanation
Indices: 16886--16974 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
16876 GCGATTCTCT
16886 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCTG
* *
16906 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCTG
16926 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCTG
*
16946 TGTTGCGATAGTCATATTC-G
1 CGTTGCGATAGTCAT-TTCTG
16966 CGTTGCGAT
1 CGTTGCGAT
16975 TTCTGCGTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 59 0.95
21 3 0.05
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCTG
Found at i:16941 original size:40 final size:40
Alignment explanation
Indices: 16886--16974 Score: 153
Period size: 40 Copynumber: 2.2 Consensus size: 40
16876 GCGATTCTCT
16886 CGTTGCGATAGTCATTTCTGCGTTGCGATAGTCA-ATTCCG
1 CGTTGCGATAGTCATTTCTGCGTTGCGATAGTCATATT-CG
*
16926 CGTTGCGATAGTCATTTCTGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCTGCGTTGCGATAGTCATATTCG
16966 CGTTGCGAT
1 CGTTGCGAT
16975 TTCTGCGTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 44 0.94
41 3 0.06
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCTGCGTTGCGATAGTCATATTCG
Found at i:18149 original size:20 final size:20
Alignment explanation
Indices: 18124--18210 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
18114 AAATTCAGTA
*
18124 TTGCGATAGTCAAAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
18144 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
18164 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
18184 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
18204 TTGCGAT
1 TTGCGAT
18211 TTACATATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:18220 original size:20 final size:20
Alignment explanation
Indices: 18197--18289 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
18187 CGATAGTCAG
* *
18197 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
18217 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
18237 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
18257 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
18277 ATTCACATTGCGA
1 ATTCGCATTGCGA
18290 ATTAGGAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:18228 original size:40 final size:40
Alignment explanation
Indices: 18139--18270 Score: 108
Period size: 40 Copynumber: 3.3 Consensus size: 40
18129 ATAGTCAAAA
* * * * * *
18139 TCGCGTTGCGATAGTCAGAATCTCGTTGCGATAGT-CAGAA
1 TCGCATTGCGATAGTCAGATTCGCGTTGCGAT-TTACATAT
* *
18179 TCTCGTTGCGATAGTCAGATTCGCGTTGCGATTTACATAT
1 TCGCATTGCGATAGTCAGATTCGCGTTGCGATTTACATAT
* * *
18219 TCGCATTGCGAT--TTACGTATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATAGTCA-G-ATTCGCGTTGCGATTTACATAT
*
18259 TCGTATTGCGAT
1 TCGCATTGCGAT
18271 TTACGTATTC
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 73 0.95
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (40 bp):
TCGCATTGCGATAGTCAGATTCGCGTTGCGATTTACATAT
Found at i:18248 original size:60 final size:61
Alignment explanation
Indices: 18184--18330 Score: 156
Period size: 60 Copynumber: 2.4 Consensus size: 61
18174 CAGAATCTCG
* * * *
18184 TTGCGATAGTCAGATTCGCGTTGCGATTTACATATTCGCATTGCGATTTACG-TATTCGCA
1 TTGCGATAGTCAGATTCGCGTTGCGATTTACATATTCACATTGCGAATTACGAAAATCGCA
* ** * *
18244 TTGCGAT--TTACGTATTCGTATTGCGATTTACGTATTCACATTGCGAATTAGGAAAATCGCA
1 TTGCGATAGTCA-G-ATTCGCGTTGCGATTTACATATTCACATTGCGAATTACGAAAATCGCA
* *
18305 ATGCGATAGTCAGAATCGCGTTGCGA
1 TTGCGATAGTCAGATTCGCGTTGCGA
18331 ATCTGGAAAC
Statistics
Matches: 68, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
58 2 0.03
59 1 0.01
60 40 0.59
61 22 0.32
62 1 0.01
63 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (61 bp):
TTGCGATAGTCAGATTCGCGTTGCGATTTACATATTCACATTGCGAATTACGAAAATCGCA
Found at i:24568 original size:25 final size:28
Alignment explanation
Indices: 24513--24568 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
24503 TTTTTATTAA
*
24513 ATTTTTAATAAAATACATAGATGAGTGT
1 ATTTTTAATAAAATACATAGATGAATGT
* *
24541 ATTTTTAA-ATAATATATA-ATGAAT-T
1 ATTTTTAATAAAATACATAGATGAATGT
24566 ATT
1 ATT
24569 AAATCGATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.16
26 5 0.20
27 8 0.32
28 8 0.32
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (28 bp):
ATTTTTAATAAAATACATAGATGAATGT
Found at i:26918 original size:54 final size:54
Alignment explanation
Indices: 26854--27070 Score: 256
Period size: 54 Copynumber: 4.0 Consensus size: 54
26844 AGAAGCTCTT
*
26854 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCGCTTGTTCCTTCTTCAAAG
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
* * ** *
26908 AGAGCTGAAACAATGGCTGCTGCTGGTGTTATTCCACTTGTTACTTCTTCGAAA-
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTC-AAAG
* ** * * * * **
26962 AGAGCTGAAACAATGGTAGTTTCCAGTGTTGTTCCGCTTGTTCCTTCTTTGAAG
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
* * *
27016 AGGGCCGAAACAATGGTCGCTCCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
27070 A
1 A
27071 ACAAATTACA
Statistics
Matches: 135, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
53 2 0.01
54 130 0.96
55 3 0.02
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.32
Consensus pattern (54 bp):
AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
Found at i:37165 original size:16 final size:18
Alignment explanation
Indices: 37133--37172 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
37123 AAATATAATA
37133 TAAAAACTACTCAAATTC
1 TAAAAACTACTCAAATTC
*
37151 -AAAAACTA-TCGAATTC
1 TAAAAACTACTCAAATTC
37167 TAAAAA
1 TAAAAA
37173 ATTTCAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.25
Consensus pattern (18 bp):
TAAAAACTACTCAAATTC
Found at i:37205 original size:22 final size:22
Alignment explanation
Indices: 37180--37256 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
37170 AAAATTTCAA
37180 AAGCTCAATTGAAACTCGATCC
1 AAGCTCAATTGAAACTCGATCC
37202 AAGCTCAATTGAAACTCGATCC
1 AAGCTCAATTGAAACTCGATCC
* * *
37224 AAACTCAATTTTAAACTCAATCC
1 AAGCTCAA-TTGAAACTCGATCC
37247 AAGCTCAATT
1 AAGCTCAATT
37257 TTAAATTCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 31 0.62
23 19 0.38
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (22 bp):
AAGCTCAATTGAAACTCGATCC
Found at i:38916 original size:14 final size:14
Alignment explanation
Indices: 38894--38983 Score: 60
Period size: 14 Copynumber: 6.6 Consensus size: 14
38884 GGAGTAAGAG
*
38894 TTTATGGTTTAGGA
1 TTTAGGGTTTAGGA
*
38908 TTTAGGGTTTATGA
1 TTTAGGGTTTAGGA
** * *
38922 TTTATAGTTTGGGG
1 TTTAGGGTTTAGGA
* *
38936 TTT-GGGTTTGGGG
1 TTTAGGGTTTAGGA
*
38949 TTTAGAGTTTA-GA
1 TTTAGGGTTTAGGA
*
38962 GTTTAGGTTTTAGG-
1 -TTTAGGGTTTAGGA
38976 TTTAGGGT
1 TTTAGGGT
38984 GTAATCTAAC
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
13 19 0.33
14 38 0.66
15 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTAGGA
Found at i:38965 original size:34 final size:34
Alignment explanation
Indices: 38890--38983 Score: 109
Period size: 34 Copynumber: 2.7 Consensus size: 34
38880 AATCGGAGTA
*
38890 AGAGTTTATGGTTTAGGATTTAGGGTTTATGATTT
1 AGAGTTTAGGGTTTAGG-TTTAGGGTTTATGATTT
* * * *
38925 ATAGTTTGGGGTTTGGGTTTGGGGTTTA-GAGTTT
1 AGAGTTTAGGGTTTAGGTTTAGGGTTTATGA-TTT
*
38959 AGAGTTTAGGTTTTAGGTTTAGGGT
1 AGAGTTTAGGGTTTAGGTTTAGGGT
38984 GTAATCTAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
33 2 0.04
34 33 0.69
35 13 0.27
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (34 bp):
AGAGTTTAGGGTTTAGGTTTAGGGTTTATGATTT
Found at i:39702 original size:54 final size:54
Alignment explanation
Indices: 39614--39718 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 54
39604 GCACTTATTT
*
39614 TAAATTTGTCCTTATACTTTTGAATATTTCAATTTAATCCTCAAACTATGATTC
1 TAAATTAGTCCTTATACTTTTGAATATTTCAATTTAATCCTCAAACTATGATTC
* * *
39668 TAAATTAGTCCTTA-AGCTTTTGAATA-TTCTAATTTTATCCTTAATCTATGA
1 TAAATTAGTCCTTATA-CTTTTGAATATTTC-AATTTAATCCTCAAACTATGA
39719 CCCTCTTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
53 4 0.09
54 41 0.91
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (54 bp):
TAAATTAGTCCTTATACTTTTGAATATTTCAATTTAATCCTCAAACTATGATTC
Found at i:41291 original size:2 final size:2
Alignment explanation
Indices: 41284--41321 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
41274 AGTGAAATTC
41284 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
41322 TTCAGAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43036 original size:36 final size:35
Alignment explanation
Indices: 42977--43084 Score: 153
Period size: 36 Copynumber: 3.0 Consensus size: 35
42967 CACGAAATCT
* *
42977 CCTAAGAAGGAAAAAAGAACTGAAGATGACGAGCTG
1 CCTAAGAAGG-AAAAGGAACTGAAGATGAAGAGCTG
*
43013 CCTAAGAAGGAGAAAGGAGCTGAAGATGAAGAGCTG
1 CCTAAGAAGGA-AAAGGAACTGAAGATGAAGAGCTG
*
43049 CTTAAGAAGGAAAGAGGAACTGAAGATGAAGAGCTG
1 CCTAAGAAGGAAA-AGGAACTGAAGATGAAGAGCTG
43085 GGGTTAAGTA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 3 0.05
36 62 0.95
ACGTcount: A:0.44, C:0.11, G:0.32, T:0.12
Consensus pattern (35 bp):
CCTAAGAAGGAAAAGGAACTGAAGATGAAGAGCTG
Found at i:48630 original size:21 final size:21
Alignment explanation
Indices: 48606--48646 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48596 GAAGAAATAT
*
48606 TAGGAGATAAGCCTCAAAAGA
1 TAGGAGAGAAGCCTCAAAAGA
*
48627 TAGGAGAGAAGCCTCCAAAG
1 TAGGAGAGAAGCCTCAAAAG
48647 GTTTATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.27, T:0.12
Consensus pattern (21 bp):
TAGGAGAGAAGCCTCAAAAGA
Found at i:55575 original size:25 final size:26
Alignment explanation
Indices: 55529--55578 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
55519 CTTCGACTGT
55529 AGAATGGGGTATTGTCATGGCCTTGG
1 AGAATGGGGTATTGTCATGGCCTTGG
55555 AGAATGGGGTA-TGTCATGGCCTTG
1 AGAATGGGGTATTGTCATGGCCTTG
55579 AGGAGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.20, C:0.12, G:0.38, T:0.30
Consensus pattern (26 bp):
AGAATGGGGTATTGTCATGGCCTTGG
Found at i:56647 original size:15 final size:15
Alignment explanation
Indices: 56629--56659 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56619 AAATTCTAAA
56629 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
56644 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
56659 T
1 T
56660 CTATCCGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:61413 original size:3 final size:3
Alignment explanation
Indices: 61407--61477 Score: 110
Period size: 3 Copynumber: 24.0 Consensus size: 3
61397 CATTTGGTTT
61407 TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
61453 TTA TTA TTA TTA AT- TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
61478 CAGGCCCAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
2 3 0.05
3 57 0.90
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:70998 original size:21 final size:21
Alignment explanation
Indices: 70972--71016 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
70962 GATTTCTGGG
* *
70972 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
70993 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
71014 CAA
1 CAA
71017 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:72703 original size:13 final size:13
Alignment explanation
Indices: 72685--72747 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
72675 TCTACGGGCA
72685 CTACGGTGCAATT
1 CTACGGTGCAATT
72698 CTACGG-GC-A--
1 CTACGGTGCAATT
72707 CTACGGTGCAATT
1 CTACGGTGCAATT
72720 CTACGG-GC-A--
1 CTACGGTGCAATT
*
72729 CTTCGGTGCAATT
1 CTACGGTGCAATT
72742 CTACGG
1 CTACGG
72748 GCACTTCGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 11 0.28
10 4 0.10
11 4 0.10
12 4 0.10
13 17 0.43
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:72768 original size:22 final size:22
Alignment explanation
Indices: 72673--72760 Score: 158
Period size: 22 Copynumber: 4.0 Consensus size: 22
72663 TATGGACATC
72673 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
72695 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
72717 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
72739 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
72761 TTTATACGAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:75886 original size:21 final size:21
Alignment explanation
Indices: 75860--75904 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
75850 GATTTCTGGG
* *
75860 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
75881 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
75902 CAA
1 CAA
75905 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:77595 original size:13 final size:13
Alignment explanation
Indices: 77577--77639 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
77567 TCTACGGGCA
77577 CTACGGTGCAATT
1 CTACGGTGCAATT
77590 CTACGG-GC-A--
1 CTACGGTGCAATT
77599 CTACGGTGCAATT
1 CTACGGTGCAATT
77612 CTACGG-GC-A--
1 CTACGGTGCAATT
*
77621 CTTCGGTGCAATT
1 CTACGGTGCAATT
77634 CTACGG
1 CTACGG
77640 GCACTTCGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
9 11 0.28
10 4 0.10
11 4 0.10
12 4 0.10
13 17 0.43
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:77660 original size:22 final size:22
Alignment explanation
Indices: 77565--77652 Score: 158
Period size: 22 Copynumber: 4.0 Consensus size: 22
77555 TATGGACATC
77565 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
77587 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
77609 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
77631 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
77653 TTTATACGAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:81610 original size:14 final size:13
Alignment explanation
Indices: 81593--81636 Score: 70
Period size: 13 Copynumber: 3.3 Consensus size: 13
81583 AGAAAAAATG
*
81593 AAAAAAGAAAAGAA
1 AAAAAAG-ATAGAA
81607 AAAAAAGATAGAA
1 AAAAAAGATAGAA
81620 AAAAAAGATAGAA
1 AAAAAAGATAGAA
81633 AAAA
1 AAAA
81637 GGGGGTCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 22 0.76
14 7 0.24
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (13 bp):
AAAAAAGATAGAA
Found at i:82031 original size:19 final size:17
Alignment explanation
Indices: 81989--82037 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
81979 TATTTTCTCT
81989 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
82005 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
*
82023 AAAATTCAACTTATT
1 -AAATTCAATTTATT
82038 CTATTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 12 0.44
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:82536 original size:114 final size:114
Alignment explanation
Indices: 82331--82667 Score: 575
Period size: 114 Copynumber: 3.0 Consensus size: 114
82321 TGCCACGTTA
* * *
82331 TCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
82396 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
*
82445 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCCGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
82510 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
82559 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* ** * * * *
82624 TTCGGTAGGAACCACAGAACCAATCATTAGAATTGAAAGATGAA
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAA
82668 CTGCATGATT
Statistics
Matches: 211, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 211 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
Found at i:83589 original size:69 final size:71
Alignment explanation
Indices: 83435--83600 Score: 214
Period size: 69 Copynumber: 2.3 Consensus size: 71
83425 AAGAAGAAGA
*
83435 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGCA
1 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG--T-AATTCATCACTCGATGGATCAGCA
*
83500 GTGCCAATT
63 GTGCCAATG
* * *
83509 AGAA-TTCATAATGAGAAGAACTTGTTCAACTTTTTG-AATTCATCATTCGATGGATCATCA-TT
1 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTAATTCATCACTCGATGGATCAGCAGTG
*
83571 TCAA-G
66 CCAATG
83576 AGAAAGTTCATAATGAGAAGAACTT
1 AG-AAGTTCATAATGAGAAGAACTT
83601 ATCTGAAGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
67 2 0.02
68 6 0.07
69 40 0.48
73 32 0.38
74 4 0.05
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (71 bp):
AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTAATTCATCACTCGATGGATCAGCAGTG
CCAATG
Found at i:83705 original size:182 final size:180
Alignment explanation
Indices: 83369--83712 Score: 526
Period size: 182 Copynumber: 1.9 Consensus size: 180
83359 GATTTAAATC
* *
83369 CATCATTCAATGGAGCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 CATCATTCAATGGAGCAACATTTCAAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
* *
83434 AAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAGC
66 AAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGATGGATCAAC
*
83499 AGTGCCAATTAGAATTCATAATGAGAAGAACTTGTTCAACTTTTTGAATT
131 AGTGCCAAGTAGAATTCATAATGAGAAGAACTTGTTCAACTTTTTGAATT
* * * *
83549 CATCATTCGATGGATCATCATTTCAAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
1 CATCATTCAATGGAGCAACATTTCAAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GA
* * * *
83614 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCA
64 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGATGGATCA
* * *
83679 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACT
129 ACAGTGCCAAGTAGAATTCATAATGAGAAGAACT
83713 CGTCATCTGA
Statistics
Matches: 146, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
180 24 0.16
181 31 0.21
182 91 0.62
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (180 bp):
CATCATTCAATGGAGCAACATTTCAAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
AAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGATGGATCAAC
AGTGCCAAGTAGAATTCATAATGAGAAGAACTTGTTCAACTTTTTGAATT
Found at i:83870 original size:115 final size:115
Alignment explanation
Indices: 83509--84003 Score: 502
Period size: 123 Copynumber: 4.3 Consensus size: 115
83499 AGTGCCAATT
* *
83509 AGAA-TTCATAATGAGAAGAACTTGTTC-AA--CTT-TTTGAATTCATCATTCGATGGATCATC-
1 AGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTTGTTTGAATTCATCATTCGATGGATCATCA
* *
83568 A--TTTCAAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGA
66 ACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAA-GAAGA
** * * *
83617 AGAAGTTCATAATGAGAAGAGCTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGG---ATCA
1 AGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTTGTTTGAATTCATCATTCGATGGATCATCA
* * * *
83679 ACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG-
66 ACTTTTCCAGAG-AAAGTTCATAATAAGAAGAACT--T-ATCTGAAGAAGAAGA
83731 A-AA-TTCATAATGAGAAGAATTTGTTCAAATTTTTGTTTGAATTCATCATTCGATGGATCATCA
1 AGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTTGTTTGAATTCATCATTCGATGGATCATCA
83794 ACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGA
66 ACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGA
* ** ** * **
83844 AGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTTTGCAT-AACTTTATCACAGCAGGAGATATA
1 AGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTTGTTTGAA-TTCATCA-TTC----G--AT-
** *
83908 TCATCATCAACTTTTCCA-AAAGAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGA
57 GGATCATCAACTTTTCCAGAGA-AAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGA
* *
83967 AGAAGTTCATAAGGAGGAGAATTTGTTCAAATTTTTG
1 AGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTTG
84004 CTAGATTACA
Statistics
Matches: 325, Mismatches: 33, Indels: 43
0.81 0.08 0.11
Matches are distributed among these distances:
108 4 0.01
109 22 0.07
110 4 0.01
111 1 0.00
112 65 0.20
113 49 0.15
114 5 0.02
115 73 0.22
116 12 0.04
120 1 0.00
122 4 0.01
123 85 0.26
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (115 bp):
AGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTTGTTTGAATTCATCATTCGATGGATCATCA
ACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGA
Found at i:84017 original size:123 final size:123
Alignment explanation
Indices: 83787--84028 Score: 364
Period size: 123 Copynumber: 2.0 Consensus size: 123
83777 CATTCGATGG
*
83787 ATCATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTC
1 ATCATCAACTTTTCCAAAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTC
* * * * *
83852 ATAATGAGAAGAGTTTGTTCAACCTTTTGCATAACTTTATCACAGCAGGAGATATATC
66 ATAAGGAGAAGAATTTGTTCAAACTTTTGCATAACTTCATCACAGAAGGAGATATATC
83910 ATCATCAACTTTTCCAAA-AGAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGTT
1 ATCATCAACTTTTCCAAAGA-AAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGTT
* *
83974 CATAAGGAGGAGAATTTGTTCAAATTTTTGC-TAGA-TTACATCACAGAAGGAGATA
65 CATAAGGAGAAGAATTTGTTCAAACTTTTGCATA-ACTT-CATCACAGAAGGAGATA
84029 AATTGTCATC
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
122 5 0.05
123 103 0.95
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (123 bp):
ATCATCAACTTTTCCAAAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTC
ATAAGGAGAAGAATTTGTTCAAACTTTTGCATAACTTCATCACAGAAGGAGATATATC
Found at i:84225 original size:3 final size:3
Alignment explanation
Indices: 84219--84279 Score: 81
Period size: 3 Copynumber: 20.0 Consensus size: 3
84209 ATTTGGTTTT
84219 TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTAA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A
84267 TT- TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA
84280 CAGGCCCAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.08
3 40 0.75
4 9 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:98699 original size:21 final size:21
Alignment explanation
Indices: 98653--98708 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
98643 GATTCTGACT
98653 ATCGCATTGCGA-TTTCCCAA
1 ATCGCATTGCGATTTTCCCAA
* *
98673 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGATTTTCCCAA
*
98695 ATCGCAATGCGATT
1 ATCGCATTGCGATT
98709 ACGTAAATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 21 0.70
22 8 0.27
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (21 bp):
ATCGCATTGCGATTTTCCCAA
Found at i:99612 original size:24 final size:24
Alignment explanation
Indices: 99585--99638 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
99575 GTATTCGAAA
99585 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
99609 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
99633 TTTGAT
1 TTTGAT
99639 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:102176 original size:20 final size:19
Alignment explanation
Indices: 102148--102202 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
102138 CAATCATCTT
*
102148 AATGTCTATCGCAACGCGAA
1 AATGACTATCGCAACGCG-A
*
102168 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
102187 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
102203 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:102217 original size:33 final size:33
Alignment explanation
Indices: 102175--102301 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
102165 GAAAATGACT
102175 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
102208 ATCGCAATGCGAAATGAAAATCGCAACAAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
102241 ATCGTAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
102274 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
102302 CGAATTTAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:102231 original size:19 final size:18
Alignment explanation
Indices: 102155--102305 Score: 92
Period size: 19 Copynumber: 8.7 Consensus size: 18
102145 CTTAATGTCT
**
102155 ATCGCAACGCGAAAATGACT
1 ATCGCAA-GCG-AAATGAAA
102175 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
102194 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
102208 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
102227 ATCGCAA-C--AA-GAGA
1 ATCGCAAGCGAAATGAAA
*
102241 ATCGTAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
102260 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
102274 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
102293 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
102306 TTTAGTTTCG
Statistics
Matches: 102, Mismatches: 13, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
14 26 0.25
15 6 0.06
16 5 0.05
17 5 0.05
18 6 0.06
19 44 0.43
20 10 0.10
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:102354 original size:33 final size:33
Alignment explanation
Indices: 102311--102390 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
102301 GCGAATTTAG
* * *
102311 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
102344 TTTCGTGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
102377 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
102391 AGTCATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:102516 original size:14 final size:14
Alignment explanation
Indices: 102497--102533 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
102487 CAACAATTAA
102497 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
102511 ACAAATCATCTTTT
1 ACAAATCAACTTTT
102525 ACAAATCAA
1 ACAAATCAA
102534 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:105793 original size:20 final size:20
Alignment explanation
Indices: 105768--105830 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
105758 TTTTGGTTGA
105768 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* *
105788 AATGAAAATTGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
105807 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
105828 AAT
1 AAT
105831 CGCAACGCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:105853 original size:20 final size:20
Alignment explanation
Indices: 105767--105858 Score: 63
Period size: 20 Copynumber: 4.9 Consensus size: 20
105757 CTTTTGGTTG
105767 AAATGAAAATCGCAACG-AGA
1 AAATGAAAATCGCAACGCA-A
* * **
105787 GAATGAAAATTGCAACGCGG
1 AAATGAAAATCGCAACGCAA
**
105807 AAATGACTATCGCAACG---
1 AAATGAAAATCGCAACGCAA
*
105824 --A-GAGAATCGCAACGCAA
1 AAATGAAAATCGCAACGCAA
105841 AAATGAAAATCGCAACGC
1 AAATGAAAATCGCAACGC
105859 GACGTTGCGA
Statistics
Matches: 54, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
14 11 0.20
15 1 0.02
19 1 0.02
20 41 0.76
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.12
Consensus pattern (20 bp):
AAATGAAAATCGCAACGCAA
Found at i:105914 original size:21 final size:21
Alignment explanation
Indices: 105888--105966 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
105878 CGCGTTACGA
*
105888 TTCTCTCGTTGCTATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
105909 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
105930 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
105950 TT-TCAT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
105967 AAGTTTAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.11, C:0.19, G:0.16, T:0.53
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:106564 original size:21 final size:20
Alignment explanation
Indices: 106520--106565 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
106510 ATAGTCAGAT
*
106520 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGAAA
* *
106540 TCGCGTTGCGATTTAGGAAAA
1 TCGCATTGCGATTTACG-AAA
106561 TCGCA
1 TCGCA
106566 ACACGAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (20 bp):
TCGCATTGCGATTTACGAAA
Found at i:108224 original size:31 final size:31
Alignment explanation
Indices: 108186--108251 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
108176 AGTTACGTCG
108186 GGGACCATATT-ACAAACGGACTAAATGTTGA
1 GGGACCATATTGA-AAACGGACTAAATGTTGA
* *
108217 GGGACCATATTGAAAATGGACTAAATGTTGG
1 GGGACCATATTGAAAACGGACTAAATGTTGA
108248 GGGA
1 GGGA
108252 TTATATTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (31 bp):
GGGACCATATTGAAAACGGACTAAATGTTGA
Found at i:110325 original size:31 final size:31
Alignment explanation
Indices: 110285--110351 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
110275 TACAATATAA
110285 TCCCCCAACATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
*
110316 TCCCTCAACATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
110347 TCCCC
1 TCCCC
110352 GAAGTAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCGTTTGCAATATGG
Found at i:110958 original size:16 final size:16
Alignment explanation
Indices: 110934--110967 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
110924 TAAAAATAAA
*
110934 TTTTGTTTTATTTCTT
1 TTTTGTTTTATCTCTT
*
110950 TTTTTTTTTATCTCTT
1 TTTTGTTTTATCTCTT
110966 TT
1 TT
110968 GTAAATTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTGTTTTATCTCTT
Found at i:111037 original size:18 final size:19
Alignment explanation
Indices: 111006--111042 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
110996 TATCTATTAG
111006 ATCCTTTGAAAATTTTATA
1 ATCCTTTGAAAATTTTATA
111025 ATCCTTT-AAAATTTTATA
1 ATCCTTTGAAAATTTTATA
111043 TTCTCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (19 bp):
ATCCTTTGAAAATTTTATA
Found at i:116393 original size:72 final size:71
Alignment explanation
Indices: 116276--116418 Score: 250
Period size: 72 Copynumber: 2.0 Consensus size: 71
116266 GGTCCAACTA
* *
116276 CCAGAGGTGGTCCTAACGTATCCTCGTCTTCTTCGAGGAATTACGATCTTGACTATATCTTGTTG
1 CCAGAGGTGGTCCTAACGTATCCTCGTCGTCTTCGAGGAATTACGATATTGACTATATC-TGTTG
116341 AAGCTGC
65 AAGCTGC
*
116348 CCAGAGGTGGTCCTAACGTATCCTTGTCGTCTTCGAGGAATTACGATATTGACTATATCTGTTGA
1 CCAGAGGTGGTCCTAACGTATCCTCGTCGTCTTCGAGGAATTACGATATTGACTATATCTGTTGA
116413 AGCTGC
66 AGCTGC
116419 AGCTACAGCT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 12 0.18
72 56 0.82
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (71 bp):
CCAGAGGTGGTCCTAACGTATCCTCGTCGTCTTCGAGGAATTACGATATTGACTATATCTGTTGA
AGCTGC
Found at i:117097 original size:2 final size:2
Alignment explanation
Indices: 117084--117115 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
117074 AATGTTGCAA
*
117084 AT AT AT AA 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
117116 TGTTGCAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:119829 original size:23 final size:23
Alignment explanation
Indices: 119811--119871 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
119801 CTCATATAAA
*
119811 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
119834 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
119857 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
119872 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:120058 original size:103 final size:102
Alignment explanation
Indices: 119887--120103 Score: 380
Period size: 103 Copynumber: 2.1 Consensus size: 102
119877 TAATGTCCAT
* *
119887 AAGGACCACATATCATTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
119952 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTC-CG
* *
119990 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
120055 GACTTCATACATGTTCCAAAGAATACATATATGTCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCG
120092 AAGGACCACATA
1 AAGGACCACATA
120104 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 14 0.13
103 95 0.87
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCG
Found at i:120996 original size:21 final size:21
Alignment explanation
Indices: 120972--121016 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
120962 TTTTGTTCGT
* *
120972 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
120993 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
121014 TTG
1 TTG
121017 CCCAAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:123668 original size:19 final size:19
Alignment explanation
Indices: 123633--123670 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
123623 AATTAAATAT
*
123633 AAAAAATTAATCATTTAAA
1 AAAAAATTAAACATTTAAA
*
123652 AAAAAATTAAACCTTTAAA
1 AAAAAATTAAACATTTAAA
123671 CCACCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATTAAACATTTAAA
Done.