Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005982.1 Hibiscus syriacus cultivar Beakdansim tig00014059_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: 77415
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:3760 original size:37 final size:36
Alignment explanation
Indices: 3698--3816 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
3688 TCCCATTATC
* * *
3698 ATTTTTC-AACAAACATCTACAAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
3734 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
*
3770 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
3805 ATTTTTTCAAAG
1 A-TTTTTCAAAG
3817 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.45
36 14 0.18
37 28 0.37
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
Found at i:6587 original size:2 final size:2
Alignment explanation
Indices: 6582--6651 Score: 124
Period size: 2 Copynumber: 35.5 Consensus size: 2
6572 TGAAAAAAGA
*
6582 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG T-
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
6623 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
6652 ATACTCTATC
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:8011 original size:2 final size:2
Alignment explanation
Indices: 8004--8080 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
7994 ATCTCTTTAT
8004 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8081 GTGTCAGGGC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16019 original size:17 final size:18
Alignment explanation
Indices: 15976--16026 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
15966 GAAATGTTTA
15976 TGAAGGAATTGGAATCTG
1 TGAAGGAATTGGAATCTG
15994 TGAAGGAATTGGAATCTG
1 TGAAGGAATTGGAATCTG
* *
16012 T-CAGGAATTGAAATC
1 TGAAGGAATTGGAATC
16027 CAATTCCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.27
Consensus pattern (18 bp):
TGAAGGAATTGGAATCTG
Found at i:16082 original size:19 final size:19
Alignment explanation
Indices: 16058--16095 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16048 TGGCAGGAAA
16058 TTGAATTGGAATCCAATTT
1 TTGAATTGGAATCCAATTT
16077 TTGAATTGGAATCCAATTT
1 TTGAATTGGAATCCAATTT
16096 CATATTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (19 bp):
TTGAATTGGAATCCAATTT
Found at i:16795 original size:23 final size:23
Alignment explanation
Indices: 16769--16822 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
16759 GTTAAATTTC
16769 AATTCTATCCAACAAGATAATTG
1 AATTCTATCCAACAAGATAATTG
16792 AATTCTATCCAACAAGATAATTG
1 AATTCTATCCAACAAGATAATTG
16815 AATTCTAT
1 AATTCTAT
16823 TATAGAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (23 bp):
AATTCTATCCAACAAGATAATTG
Found at i:18118 original size:47 final size:47
Alignment explanation
Indices: 18064--18158 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
18054 AACTTTTGAA
18064 TTGTTTCATCTTCATCCCCTTTGGTTTGGTTCTTAAAATCATTACTT
1 TTGTTTCATCTTCATCCCCTTTGGTTTGGTTCTTAAAATCATTACTT
18111 TTGTTTCATCTTCATCCCCTTTGGTTTGGTTCTTAAAATCATTACTT
1 TTGTTTCATCTTCATCCCCTTTGGTTTGGTTCTTAAAATCATTACTT
18158 T
1 T
18159 GTATCTCTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.17, C:0.21, G:0.11, T:0.52
Consensus pattern (47 bp):
TTGTTTCATCTTCATCCCCTTTGGTTTGGTTCTTAAAATCATTACTT
Found at i:18158 original size:26 final size:26
Alignment explanation
Indices: 18082--18159 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
18072 TCTTCATCCC
18082 CTTTGGTTTGGTTCTTAAAATCATTA
1 CTTTGGTTTGGTTCTTAAAATCATTA
* ** * **
18108 CTTTTGTTT-CATCTT--CATC--CC
1 CTTTGGTTTGGTTCTTAAAATCATTA
18129 CTTTGGTTTGGTTCTTAAAATCATTA
1 CTTTGGTTTGGTTCTTAAAATCATTA
18155 CTTTG
1 CTTTG
18160 TATCTCTCTA
Statistics
Matches: 35, Mismatches: 12, Indels: 10
0.61 0.21 0.18
Matches are distributed among these distances:
21 8 0.23
22 4 0.11
23 3 0.09
24 3 0.09
25 4 0.11
26 13 0.37
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (26 bp):
CTTTGGTTTGGTTCTTAAAATCATTA
Found at i:26191 original size:16 final size:17
Alignment explanation
Indices: 26170--26211 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
26160 ATGTATAAAT
26170 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
* *
26186 AAATATTAAAATTTATT
1 AAATATTTAAATTTATA
26203 AAATATTTA
1 AAATATTTA
26212 GAGAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:26495 original size:20 final size:20
Alignment explanation
Indices: 26470--26583 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
26460 AATTGGGAAA
*
26470 ATCGCAATGCGATACTGATT
1 ATCGCAATGCGATACTGACT
*
26490 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
26510 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
26531 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
26551 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
26571 TTCGCAACGCGAT
1 ATCGCAATGCGAT
26584 TTACATAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:26545 original size:61 final size:61
Alignment explanation
Indices: 26467--26583 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
26457 GCGAATTGGG
* * * * *
26467 AAAATCGCAATGCGATACTGA-TTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTT-TCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
26528 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATACTGACTATCGCAACGCGAT
26584 TTACATAGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 46 0.96
62 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTTTCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:27140 original size:19 final size:19
Alignment explanation
Indices: 27116--27157 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
27106 ACGAGATAAT
*
27116 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
27135 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
27154 CGCA
1 CGCA
27158 TTACGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:27175 original size:19 final size:18
Alignment explanation
Indices: 27161--27242 Score: 110
Period size: 19 Copynumber: 4.3 Consensus size: 18
27151 AATCGCATTA
27161 CGATTTATATTTCGCGTTG
1 CGATTT-TATTTCGCGTTG
27180 CGATTTTCATTTCGCGTTG
1 CGATTTT-ATTTCGCGTTG
27199 CGATTTTTATTTCGCGGTTG
1 CGA-TTTTATTTCGC-GTTG
*
27219 TGATTTTCATTTCGCGTTG
1 CGATTTT-ATTTCGCGTTG
27238 CGATT
1 CGATT
27243 GTCTGGTCGC
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.02
19 39 0.68
20 17 0.30
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (18 bp):
CGATTTTATTTCGCGTTG
Found at i:27234 original size:39 final size:38
Alignment explanation
Indices: 27161--27242 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 38
27151 AATCGCATTA
27161 CGATTTATATTTCGCGTTGCGATTTTCATTTCGCGTTG
1 CGATTTATATTTCGCGTTGCGATTTTCATTTCGCGTTG
* *
27199 CGATTTTTATTTCGCGGTTGTGATTTTCATTTCGCGTTG
1 CGATTTATATTTCGC-GTTGCGATTTTCATTTCGCGTTG
27238 CGATT
1 CGATT
27243 GTCTGGTCGC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 14 0.34
39 27 0.66
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (38 bp):
CGATTTATATTTCGCGTTGCGATTTTCATTTCGCGTTG
Found at i:27253 original size:39 final size:39
Alignment explanation
Indices: 27172--27253 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
27162 GATTTATATT
* **
27172 TCGC-GTTGCGATTTTCATTTCGCGTTGCGATTTTTATT
1 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAGG
*
27210 TCGCGGTTGTGATTTTCATTTCGCGTTGCGATTGTCT-GG
1 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATT-TCTAGG
27249 TCGCG
1 TCGCG
27254 ATAGTCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 4 0.11
39 32 0.84
40 2 0.05
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.45
Consensus pattern (39 bp):
TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAGG
Found at i:27267 original size:33 final size:33
Alignment explanation
Indices: 27225--27309 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
27215 GTTGTGATTT
* *
27225 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
27258 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
27291 TCATTTCCGCGTTGCGATT
1 TCATTT-CGCGTTGCGATT
27310 TTCATTTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 36 0.75
34 12 0.25
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:29421 original size:42 final size:42
Alignment explanation
Indices: 29361--29444 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
29351 GCCCGACTCG
* * *
29361 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
29403 CCTATCATTCCTCGAGAGTCCTCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
29445 ACTGTCAGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:30860 original size:14 final size:14
Alignment explanation
Indices: 30841--30874 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
30831 ATTGTTTAAT
30841 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
30855 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
30869 TGATTT
1 TGATTT
30875 ATTTAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:31148 original size:66 final size:66
Alignment explanation
Indices: 31052--31182 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
31042 ACGCGAAATT
*
31052 AAATTCGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGAGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGAGATTTTCATTTCGCATTGC
31117 A
66 A
* * *
31118 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGAGATTTTCATTTCGCATTGC
31183 GATAGTAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGAGATTTTCATTTCGCATTGC
A
Found at i:31151 original size:19 final size:19
Alignment explanation
Indices: 31127--31185 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
31117 AAAATTAGCG
31127 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
31146 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
31160 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31179 TTGCGAT
1 TTGCGAT
31186 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:31185 original size:33 final size:33
Alignment explanation
Indices: 31059--31182 Score: 178
Period size: 33 Copynumber: 3.8 Consensus size: 33
31049 ATTAAATTCG
*
31059 CGTTGCGATTTTCATTTCGCATTGCAATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
* * **
31092 CGTTGAGATTTTCATTTCGCATTGCAAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGC-AATTCTCT
*
31125 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
31158 CGTTGCGATTTTCATTTCGCATTGC
1 CGTTGCGATTTTCATTTCGCATTGC
31183 GATAGTAATT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 2 0.03
33 74 0.94
34 3 0.04
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
Found at i:33493 original size:12 final size:12
Alignment explanation
Indices: 33476--33500 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33466 TCTTCGGGAA
33476 CTTTTTCTTCTT
1 CTTTTTCTTCTT
33488 CTTTTTCTTCTT
1 CTTTTTCTTCTT
33500 C
1 C
33501 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:33709 original size:24 final size:24
Alignment explanation
Indices: 33675--33728 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
33665 CTGAAACATC
** *
33675 ATCAAAATCCGTTTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
33699 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
33723 ATCAAA
1 ATCAAA
33729 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:34809 original size:20 final size:20
Alignment explanation
Indices: 34784--34841 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
34774 ATTCATTTGA
34784 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
34804 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
34824 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
34842 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:34884 original size:14 final size:16
Alignment explanation
Indices: 34864--34937 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
34854 TGAAAATCGC
34864 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
34879 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
34896 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
34915 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
34931 -TTGCGAT
1 ATTGCGAT
34938 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:34901 original size:19 final size:19
Alignment explanation
Indices: 34860--34927 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
34850 GAAATGAAAA
34860 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
34876 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
34893 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
34912 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
34928 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:35063 original size:14 final size:14
Alignment explanation
Indices: 35044--35080 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
35034 CATCAATTAA
35044 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
35058 ACAAATCATCTTTT
1 ACAAATCAACATTT
35072 ACAAATCAA
1 ACAAATCAA
35081 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:35784 original size:20 final size:19
Alignment explanation
Indices: 35749--35815 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
35739 GAAACTTAAA
35749 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
35768 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
35788 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
35807 ATCGCAACG
1 ATCGCAACG
35816 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:35863 original size:19 final size:19
Alignment explanation
Indices: 35841--35922 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
35831 GAAACACAAA
35841 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
35860 TCGCTTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
35876 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
35892 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
35911 TCGCATTGCGAT
1 TCGCATTGCGAT
35923 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 9 0.17
16 8 0.15
18 9 0.17
19 28 0.52
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:35929 original size:19 final size:19
Alignment explanation
Indices: 35877--35961 Score: 82
Period size: 19 Copynumber: 4.4 Consensus size: 19
35867 GCGATTTTGT
*
35877 CGTTGCGAT-TTCATTTCG
1 CGTTGCGATAGTCATTTCG
**
35895 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
35914 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
35934 CGTTACGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
35954 TGTTGCGA
1 CGTTGCGA
35962 AAGTAAACTA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
18 9 0.16
19 22 0.40
20 21 0.38
21 3 0.05
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:36469 original size:18 final size:18
Alignment explanation
Indices: 36443--36487 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
36433 GTCGATCAGA
*
36443 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
36461 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
36479 TGATGGCTC
1 TGATGGCTC
36488 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:37832 original size:20 final size:20
Alignment explanation
Indices: 37807--37849 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
37797 AATAGTTTCT
37807 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
37827 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
37847 GAA
1 GAA
37850 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:38154 original size:22 final size:22
Alignment explanation
Indices: 38127--38170 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
38117 GATGGAGATA
38127 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
38149 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
38171 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:38383 original size:20 final size:20
Alignment explanation
Indices: 38358--38410 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
38348 GATTATGTAT
*
38358 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
38378 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
38398 TATCTCGTTGCGA
1 TATCGCGTTGCGA
38411 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:38465 original size:20 final size:20
Alignment explanation
Indices: 38421--38513 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
38411 TTTTTTATTA
* **
38421 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
38442 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
38462 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
* *
38483 TAGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
38503 TCGCATTGCGA
1 TCGCATTGCGA
38514 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:38466 original size:41 final size:41
Alignment explanation
Indices: 38403--38513 Score: 179
Period size: 41 Copynumber: 2.7 Consensus size: 41
38393 GTAAGTATCT
* *
38403 CGTTGCGATTT-TTTATTATCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTA-T-TCGCATTGCGATTTTCCCAATTAG
38445 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTAG
1 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTAG
38486 CGTTGCGATTTACTTATTCGCATTGCGA
1 CGTTGCGATTTACTTATTCGCATTGCGA
38514 ATTGGGAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 51 0.77
42 12 0.18
43 3 0.05
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (41 bp):
CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTAG
Found at i:38850 original size:7 final size:7
Alignment explanation
Indices: 38838--38862 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38828 AGAAGTTGTC
38838 TTTTGAG
1 TTTTGAG
38845 TTTTGAG
1 TTTTGAG
38852 TTTTGAG
1 TTTTGAG
38859 TTTT
1 TTTT
38863 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (7 bp):
TTTTGAG
Found at i:43649 original size:33 final size:33
Alignment explanation
Indices: 43612--43691 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 33
43602 TAGTTTTGGG
43612 TTTATTTCAAATTTGAGTTTT-TTTTAAAAAAAA
1 TTTATTTCAAATTTGAGTTTTCTTTT-AAAAAAA
* * *
43645 TTTATTTCAAATTTGTGTTTTCTTTTTAAAAAT
1 TTTATTTCAAATTTGAGTTTTCTTTTAAAAAAA
43678 TTTATTTCAAATTT
1 TTTATTTCAAATTT
43692 TATTTCAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 39 0.91
34 4 0.09
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (33 bp):
TTTATTTCAAATTTGAGTTTTCTTTTAAAAAAA
Found at i:43691 original size:12 final size:12
Alignment explanation
Indices: 43674--43700 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43664 TTCTTTTTAA
43674 AAATTTTATTTC
1 AAATTTTATTTC
43686 AAATTTTATTTC
1 AAATTTTATTTC
43698 AAA
1 AAA
43701 AGGCGGCGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATTTTATTTC
Found at i:51962 original size:13 final size:14
Alignment explanation
Indices: 51944--51974 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
51934 GTATCATATT
51944 TCACATA-TTCATA
1 TCACATAGTTCATA
51957 TCACATAGTTCATA
1 TCACATAGTTCATA
51971 TCAC
1 TCAC
51975 TTGCATGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (14 bp):
TCACATAGTTCATA
Found at i:59831 original size:89 final size:89
Alignment explanation
Indices: 59675--59849 Score: 289
Period size: 89 Copynumber: 2.0 Consensus size: 89
59665 ATGTCTCAAC
* * *
59675 TGATCCGTATTTTTTCATTTTAATTCTAACGAACAATATTCAATATCACGAACTGTATCTTTGCA
1 TGATCCGTATTTTGTCATTTTAATTCTAACGAACAATATTCAATATCACAAACTATATCTTTGCA
59740 GCAACGGAACCACCAGGATAAAAT
66 GCAACGGAACCACCAGGATAAAAT
* *
59764 TGATCCGTATTTTGGT-ATTTTAATTCTAACGAACAATATTCAATATCGCAAACTATATCTTTTC
1 TGATCCGTATTTT-GTCATTTTAATTCTAACGAACAATATTCAATATCACAAACTATATCTTTGC
59828 AGCAACGGAACCACCAGGATAA
65 AGCAACGGAACCACCAGGATAA
59850 CCTCAACGAA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 79 0.99
90 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (89 bp):
TGATCCGTATTTTGTCATTTTAATTCTAACGAACAATATTCAATATCACAAACTATATCTTTGCA
GCAACGGAACCACCAGGATAAAAT
Found at i:63535 original size:20 final size:19
Alignment explanation
Indices: 63508--63547 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
63498 TTTATTTTAG
* *
63508 TTTATTTTAATTTAACATA
1 TTTATTTTAAATTAAAATA
63527 TTTATTTTTAAATTAAAATA
1 TTTA-TTTTAAATTAAAATA
63547 T
1 T
63548 ATTAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATTTTAAATTAAAATA
Found at i:63552 original size:15 final size:15
Alignment explanation
Indices: 63534--63567 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
63524 ATATTTATTT
*
63534 TTAAATTAAAATATA
1 TTAAATTAAAATAAA
63549 TTAAATTAAAATAAA
1 TTAAATTAAAATAAA
63564 TTAA
1 TTAA
63568 TCCTTGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAATTAAAATAAA
Found at i:69751 original size:173 final size:173
Alignment explanation
Indices: 69359--69809 Score: 600
Period size: 173 Copynumber: 2.6 Consensus size: 173
69349 TCTACACAAA
* * * *
69359 CAGAC-TTCTGCTGCTACTAAAATTCAGAGCCATTTCAGGGGCTGGCTTTTAAGGAGAAGTTTTA
1 CAGACATT-TGCTGCAACTAAAATTCAGAGCCATTTCCGGGGTTGGCATTTAAGGAGAAGTTTTA
* * * *
69423 TGAAGCAGAAGCAGGCAATAATAAGAATTCAAAGTAATTTTCGACTACTGAAATCTTGGTGGGCC
65 TGAAGCAGAAGCAAGCAATAATAAAAATTCAAAGTAA-TTTCGACAACTGAAATCTTGGAGGGCC
* * * *
69488 TTTCAGATTGCTCAGAAGGAATTTGTCCGTAAATCTCTCCAGAAT
129 TTCCAGATTGCTCAGAAGGAATTTGCCCATAAATCTCTCCAAAAT
* * *
69533 CAGATATTTGCAGCAACTAAAATTCAGAGCCATTACCGGGGTTGGCATTTAAGGAGAAGTTTTAT
1 CAGACATTTGCTGCAACTAAAATTCAGAGCCATTTCCGGGGTTGGCATTTAAGGAGAAGTTTTAT
* * * *
69598 GAAACAGAAGCAAGCTATAATAAAAATCCAAAGTAATTTCGACAACTGAAATGTTGGAGGGCCTT
66 GAAGCAGAAGCAAGCAATAATAAAAATTCAAAGTAATTTCGACAACTGAAATCTTGGAGGGCCTT
* *
69663 CCAGGTTGCTCAGAAGGAATTTGCCCATAGAT-TCCTCCAAAAT
131 CCAGATTGCTCAGAAGGAATTTGCCCATAAATCT-CTCCAAAAT
* * * * *
69706 CAGACATTTGCTGCAACAAAAATTCAGAGTCATTTCCGTGGTTGGCAATTAAGGAGGAGTTTTAT
1 CAGACATTTGCTGCAACTAAAATTCAGAGCCATTTCCGGGGTTGGCATTTAAGGAGAAGTTTTAT
* **
69771 CAAGCAGAAGCAAGCAATAATAACCATTCAAAGTAATTT
66 GAAGCAGAAGCAAGCAATAATAAAAATTCAAAGTAATTT
69810 TAGACGGCTA
Statistics
Matches: 240, Mismatches: 35, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
172 1 0.00
173 151 0.63
174 86 0.36
175 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (173 bp):
CAGACATTTGCTGCAACTAAAATTCAGAGCCATTTCCGGGGTTGGCATTTAAGGAGAAGTTTTAT
GAAGCAGAAGCAAGCAATAATAAAAATTCAAAGTAATTTCGACAACTGAAATCTTGGAGGGCCTT
CCAGATTGCTCAGAAGGAATTTGCCCATAAATCTCTCCAAAAT
Done.