Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001013.1 Hibiscus syriacus cultivar Beakdansim tig00002019_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: 69385
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:6990 original size:30 final size:30
Alignment explanation
Indices: 6954--7013 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
6944 ATTAACCATA
*
6954 ACTAGGTTGAATCATCTTCATAAAATTTAT
1 ACTAGGTTGAATAATCTTCATAAAATTTAT
6984 ACTAGGTTGAATAATCTTCATAAAATTTAT
1 ACTAGGTTGAATAATCTTCATAAAATTTAT
7014 GTACGTGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (30 bp):
ACTAGGTTGAATAATCTTCATAAAATTTAT
Found at i:14169 original size:14 final size:15
Alignment explanation
Indices: 14142--14170 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
14132 ATTTGATTCA
14142 AAAATTTATTAAATT
1 AAAATTTATTAAATT
14157 AAAATTT-TTAAATT
1 AAAATTTATTAAATT
14171 GAATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATTTATTAAATT
Found at i:16110 original size:30 final size:31
Alignment explanation
Indices: 16076--16141 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
16066 GTTGAACAGT
*
16076 AAATACATAAAGTTAAAGGA-CAAAAATA-AA
1 AAATACATAAACTTAAAGGAGCAAAAA-ACAA
16106 AAATACATAAACTTAAAGGAGCAAAAAACAA
1 AAATACATAAACTTAAAGGAGCAAAAAACAA
16137 AAATA
1 AAATA
16142 GAAATTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.15
Consensus pattern (31 bp):
AAATACATAAACTTAAAGGAGCAAAAAACAA
Found at i:16199 original size:30 final size:30
Alignment explanation
Indices: 16165--16229 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
16155 CCAAATAAGT
* * *
16165 AAAAACATACATTTAAGGGATTAAAATAGC
1 AAAAACATACATTTAAAGGACTAAAACAGC
* *
16195 AAAAACATATATTTAAAGGACTAAAACAGT
1 AAAAACATACATTTAAAGGACTAAAACAGC
16225 AAAAA
1 AAAAA
16230 AAGAATCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.22
Consensus pattern (30 bp):
AAAAACATACATTTAAAGGACTAAAACAGC
Found at i:17652 original size:20 final size:20
Alignment explanation
Indices: 17627--17667 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17617 ATATGATTTA
17627 AATAAAAATATA-ATAATAAT
1 AATAAAAATA-ACATAATAAT
*
17647 AATAAATATAACATAATAAT
1 AATAAAAATAACATAATAAT
17667 A
1 A
17668 TTTTTGGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAAAAATAACATAATAAT
Found at i:18054 original size:40 final size:40
Alignment explanation
Indices: 17924--18193 Score: 141
Period size: 40 Copynumber: 6.4 Consensus size: 40
17914 TTGATACAGC
* * *
17924 TCCTACGTGATGAAAGAGGTCTGGTCGGGGGATGACACGGT
1 TCCTACGTGATG-AGGAGGTCTGGTCGAGGGATGACACGAT
* * * * * *
17965 TCCTACGCGATGAGGACGACTGGTTATCTAGGGTTGACACGGCT
1 TCCTACGTGATGAGGAGGTCTGG---TCGAGGGATGACAC-GAT
* *
18009 T-CTACGTAATGAGGAGGTTTGGTCGAGGGATGACACGAT
1 TCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGAT
* * * * *
18048 TCCTACGTGATGAGGACGTCAGGCCATCTTTAGGAATGATAAC-ATTGT
1 TCCTACGTGATGAGGAGGTCTGG---TC--GAGGGATGA-CACGA---T
* * * * **
18096 TCCTACGTGATGAGGATGACTGATTATC-AGGGGTGACACGGC
1 TCCTACGTGATGAGGAGGTCTG---GTCGAGGGATGACACGAT
* * *
18138 TCCTACGTGATGAGGAGGTCTAGTCGGGGGATGACACGGT
1 TCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGAT
18178 TCCTACGTGATGAGGA
1 TCCTACGTGATGAGGA
18194 TGGCAGGCCA
Statistics
Matches: 171, Mismatches: 39, Indels: 39
0.69 0.16 0.16
Matches are distributed among these distances:
39 5 0.03
40 64 0.37
41 11 0.06
42 19 0.11
43 29 0.17
44 5 0.03
45 14 0.08
46 2 0.01
48 22 0.13
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGAT
Found at i:18063 original size:83 final size:84
Alignment explanation
Indices: 17880--18065 Score: 257
Period size: 84 Copynumber: 2.2 Consensus size: 84
17870 GATAACATGG
* * * *
17880 TTCCTACGCGATGAGGATGGCTGGGTATCTAGGGTTGATACAGCTCCTACGTGATGAAAGAGGTC
1 TTCCTACGCGATGAGGACGACTGGGTATCTAGGGTTGACACAGCTCCTACGTAATGAAAGAGGTC
* *
17945 TGGTCGGGGGATGACACGG
66 TGGTCGAGGGATGACACGA
* * * * *
17964 TTCCTACGCGATGAGGACGACTGGTTATCTAGGGTTGACACGGCTTCTACGTAATG-AGGAGGTT
1 TTCCTACGCGATGAGGACGACTGGGTATCTAGGGTTGACACAGCTCCTACGTAATGAAAGAGGTC
18028 TGGTCGAGGGATGACACGA
66 TGGTCGAGGGATGACACGA
*
18047 TTCCTACGTGATGAGGACG
1 TTCCTACGCGATGAGGACG
18066 TCAGGCCATC
Statistics
Matches: 90, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
83 41 0.46
84 49 0.54
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (84 bp):
TTCCTACGCGATGAGGACGACTGGGTATCTAGGGTTGACACAGCTCCTACGTAATGAAAGAGGTC
TGGTCGAGGGATGACACGA
Found at i:18169 original size:130 final size:129
Alignment explanation
Indices: 17958--18343 Score: 522
Period size: 130 Copynumber: 2.9 Consensus size: 129
17948 TCGGGGGATG
* * * *
17958 ACACGGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGTTGACACGGCTTCTACGTAATGAGG
1 ACAC-GTTCCTACGTGATGAGGACGACTGATTATC-AGGGGTGACACGGCTTCTACGTGATGAGG
* * * *
18023 AGGTTTGGTCGAGGGATGACACGATTCCTACGTGATGAGGACGTCAGGCCATCTTTAGGAATGAT
64 AGGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGATGGCAGGCCATCTTTAGGAATGAT
18088 A
129 A
* * *
18089 ACATTGTTCCTACGTGATGAGGATGACTGATTATCAGGGGTGACACGGCTCCTACGTGATGAGGA
1 ACA-CGTTCCTACGTGATGAGGACGACTGATTATCAGGGGTGACACGGCTTCTACGTGATGAGGA
* * *
18154 GGTCTAGTCGGGGGATGACACGGTTCCTACGTGATGAGGATGGCAGGCCATCTTTAAGAATGATA
65 GGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGATGGCAGGCCATCTTTAGGAATGATA
* * *
18219 ACACGATTCCTACGTGATGAGGACGACT-AGTTATTAGGGGAGAGACACGGCTTTTACGTGATGA
1 ACACG-TTCCTACGTGATGAGGACGACTGA-TTATCA-GGG-GTGACACGGCTTCTACGTGATGA
* * *
18283 GGAGGTCTGGTCGAGGGATGACATGGTTCCTAAGTGATGAGGATGGCAGACCATCTTTAGG
62 GGAGGTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGATGGCAGGCCATCTTTAGG
18344 GATTATAGTT
Statistics
Matches: 224, Mismatches: 26, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
129 2 0.01
130 114 0.51
131 33 0.15
132 75 0.33
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (129 bp):
ACACGTTCCTACGTGATGAGGACGACTGATTATCAGGGGTGACACGGCTTCTACGTGATGAGGAG
GTCTGGTCGAGGGATGACACGGTTCCTACGTGATGAGGATGGCAGGCCATCTTTAGGAATGATA
Found at i:18437 original size:35 final size:36
Alignment explanation
Indices: 18397--18472 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 36
18387 GAGAAATTGT
18397 CTCAAAAGAGACAAAATTTGTTTCAAGGGAAACA-A
1 CTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAGA
* *****
18432 CTC-AAAGATAGGTGTTTTGTTTCAAGGGAAACAGA
1 CTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAGA
18467 CTCAAA
1 CTCAAA
18473 GATAGGTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
34 24 0.73
35 7 0.21
36 2 0.06
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (36 bp):
CTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAGA
Found at i:18451 original size:34 final size:35
Alignment explanation
Indices: 18413--18484 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
18403 AGAGACAAAA
18413 TTTGTTTCAAGGGAAACA-ACTCAAAGATAGGTGT
1 TTTGTTTCAAGGGAAACAGACTCAAAGATAGGTGT
18447 TTTGTTTCAAGGGAAACAGACTCAAAGATAGGTGT
1 TTTGTTTCAAGGGAAACAGACTCAAAGATAGGTGT
18482 TTT
1 TTT
18485 CAAAAGAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 18 0.49
35 19 0.51
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (35 bp):
TTTGTTTCAAGGGAAACAGACTCAAAGATAGGTGT
Found at i:18494 original size:31 final size:32
Alignment explanation
Indices: 18414--18494 Score: 85
Period size: 34 Copynumber: 2.5 Consensus size: 32
18404 GAGACAAAAT
**
18414 TTGTTTCAAGGGAAACAACTCAAAGATAGGTG
1 TTGTTTCAAAAGAAACAACTCAAAGATAGGTG
**
18446 TTTTGTTTCAAGGGAAACAGACTCAAAGATAGGTG
1 --TTGTTTCAAAAGAAACA-ACTCAAAGATAGGTG
18481 -T-TTTCAAAAGAAAC
1 TTGTTTCAAAAGAAAC
18495 TATCTCGAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
31 11 0.25
32 1 0.02
34 17 0.39
35 15 0.34
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.27
Consensus pattern (32 bp):
TTGTTTCAAAAGAAACAACTCAAAGATAGGTG
Found at i:18603 original size:67 final size:64
Alignment explanation
Indices: 18447--18666 Score: 261
Period size: 67 Copynumber: 3.4 Consensus size: 64
18437 AGATAGGTGT
* * *
18447 TTTGTTTCAAGGGAAACAGACTCAAAGATAGGTGTTTTCAAAAGAAACTATCTCGAGAGACAAAA
1 TTTGTTTCAAGAGAAACAGACTCAAAGAT--TTTTTTTCAAAAGAAACTATCTCGAGAGACAAAA
*
18512 T
64 A
* *
18513 TTTGTTTCAA-ATGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTATCTCGAGAGAGACAA
1 TTTGTTTCAAGA-GAAACAGACTCAAAGATTTTTTT-TCAAAAGAAACTATCTC--GAGAGACAA
18577 AAA
62 AAA
* * *
18580 TTTGTTTCCAGAGAAAGAGACTCAAAGA-TTTTTTT-AAAAGAAACTGTCTCGAGAGAC-AAAA
1 TTTGTTTCAAGAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAACTATCTCGAGAGACAAAAA
*
18641 TTTGTTTCAAGAGAAATA-ACTCAAAG
1 TTTGTTTCAAGAGAAACAGACTCAAAG
18667 GATACTGATA
Statistics
Matches: 136, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
60 8 0.06
61 20 0.15
62 7 0.05
64 17 0.12
65 17 0.12
66 32 0.24
67 34 0.25
68 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (64 bp):
TTTGTTTCAAGAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAACTATCTCGAGAGACAAAAA
Found at i:18777 original size:32 final size:32
Alignment explanation
Indices: 18736--18805 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
18726 TTCGCATCAG
* *
18736 GATGTTGAATCCCCAAAGATGCTCCAATATTC
1 GATGTTGAATCCCCAAAGATGCCCCAACATTC
*
18768 GATGTTGAATCTCCAAAGATGCCCCAACATTC
1 GATGTTGAATCCCCAAAGATGCCCCAACATTC
18800 GATGTT
1 GATGTT
18806 TCTTACTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGATGCCCCAACATTC
Found at i:19876 original size:11 final size:12
Alignment explanation
Indices: 19851--19892 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
19841 TCTTGTCTTC
*
19851 TTTTTC-TTTGA
1 TTTTTCTTTTGT
19862 TTTTTCTTTTGTT
1 TTTTTCTTTTG-T
19875 TTTTTCTCTTTGT
1 TTTTTCT-TTTGT
19888 TTTTT
1 TTTTT
19893 TCCTTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 6 0.22
12 4 0.15
13 13 0.48
14 4 0.15
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTGT
Found at i:19886 original size:14 final size:14
Alignment explanation
Indices: 19862--19899 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
19852 TTTTCTTTGA
19862 TTTTTCT-TTTGTT
1 TTTTTCTCTTTGTT
19875 TTTTTCTCTTTGTT
1 TTTTTCTCTTTGTT
19889 TTTTTC-CTTTG
1 TTTTTCTCTTTG
19900 CTCTTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (14 bp):
TTTTTCTCTTTGTT
Found at i:19891 original size:15 final size:13
Alignment explanation
Indices: 19862--19899 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
19852 TTTTCTTTGA
19862 TTTTTCTTTTGTT
1 TTTTTCTTTTGTT
19875 TTTTTCTCTTTGTT
1 TTTTTCT-TTTGTT
*
19889 TTTTTCCTTTG
1 TTTTTCTTTTG
19900 CTCTTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTTGTT
Found at i:19917 original size:21 final size:21
Alignment explanation
Indices: 19868--19918 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
19858 TTGATTTTTC
*
19868 TTTTGTTT--TTTTCTCTTTG
1 TTTTGTTTCCTTTGCTCTTTG
*
19887 TTTTT-TTCCTTTGCTCTTTG
1 TTTTGTTTCCTTTGCTCTTTG
19907 TTTTGTTTCCTT
1 TTTTGTTTCCTT
19919 CTGTTTCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 4 0.15
20 14 0.54
21 6 0.23
ACGTcount: A:0.00, C:0.16, G:0.10, T:0.75
Consensus pattern (21 bp):
TTTTGTTTCCTTTGCTCTTTG
Found at i:19928 original size:25 final size:24
Alignment explanation
Indices: 19877--19936 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 24
19867 CTTTTGTTTT
19877 TTTCTCTTTGTTTT-TTTCCTTTG
1 TTTCTCTTTGTTTTGTTTCCTTTG
19900 ---CTCTTTGTTTTGTTTCCTTCTG
1 TTTCTCTTTGTTTTGTTTCCTT-TG
*
19922 TTTCTCTTTGCTTTG
1 TTTCTCTTTGTTTTG
19937 ATTGGATCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 11 0.35
21 7 0.23
22 2 0.06
25 11 0.35
ACGTcount: A:0.00, C:0.20, G:0.12, T:0.68
Consensus pattern (24 bp):
TTTCTCTTTGTTTTGTTTCCTTTG
Found at i:23665 original size:30 final size:29
Alignment explanation
Indices: 23631--23715 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
23621 GTTGAACAAT
* *
23631 AAATACATAAAGTTAAAGGACCAAAATAAC
1 AAATACAGAAACTTAAAGGACCAAAA-AAC
*
23661 AAATATAGAAACTTAAAGGACCAAAAAAC
1 AAATACAGAAACTTAAAGGACCAAAAAAC
* * * * *
23690 AAAAATAGAAATTTACAGGTCCAAAA
1 AAATACAGAAACTTAAAGGACCAAAA
23716 TAGTAAAACC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 25 0.52
30 23 0.48
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (29 bp):
AAATACAGAAACTTAAAGGACCAAAAAAC
Found at i:23700 original size:29 final size:30
Alignment explanation
Indices: 23643--23717 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
23633 ATACATAAAG
*
23643 TTAAAGGACCAAAATAACAAATATAGAAAC
1 TTAAAGGACCAAAATAACAAAAATAGAAAC
*
23673 TTAAAGGACCAAAA-AACAAAAATAGAAAT
1 TTAAAGGACCAAAATAACAAAAATAGAAAC
* *
23702 TTACAGGTCCAAAATA
1 TTAAAGGACCAAAATA
23718 GTAAAACCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.59, C:0.13, G:0.11, T:0.17
Consensus pattern (30 bp):
TTAAAGGACCAAAATAACAAAAATAGAAAC
Found at i:23746 original size:30 final size:30
Alignment explanation
Indices: 23712--23786 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
23702 TTACAGGTCC
* * *
23712 AAAATAGTAAAACCATACATTTAAGGGATT
1 AAAATAGTAAAAACATACATTTAAAGGACT
* *
23742 AAAATAGAAAAAACATATATTTAAAGGACT
1 AAAATAGTAAAAACATACATTTAAAGGACT
*
23772 AAAACAGTAAAAACA
1 AAAATAGTAAAAACA
23787 AAATCTTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.21
Consensus pattern (30 bp):
AAAATAGTAAAAACATACATTTAAAGGACT
Found at i:24961 original size:20 final size:20
Alignment explanation
Indices: 24936--24974 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24926 GGTGCAGGTG
*
24936 GGACAGTCAGCGGCAGCAGT
1 GGACAGGCAGCGGCAGCAGT
*
24956 GGACAGGCGGCGGCAGCAG
1 GGACAGGCAGCGGCAGCAG
24975 CATGATATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.46, T:0.05
Consensus pattern (20 bp):
GGACAGGCAGCGGCAGCAGT
Found at i:25231 original size:3 final size:3
Alignment explanation
Indices: 25218--25268 Score: 84
Period size: 3 Copynumber: 16.3 Consensus size: 3
25208 GATTTAAATA
25218 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
25265 AAT A
1 AAT A
25269 TTTTTGGTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:30414 original size:2 final size:2
Alignment explanation
Indices: 30409--30474 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
30399 TGTCTGTGTG
30409 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
30451 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
30475 AAGTTATTGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30641 original size:15 final size:15
Alignment explanation
Indices: 30608--30642 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30598 TTAAATAATC
* *
30608 AATATAGAATATTAG
1 AATATAGAATATCAA
30623 AATATAGAATATCAA
1 AATATAGAATATCAA
30638 AATAT
1 AATAT
30643 CAAAATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (15 bp):
AATATAGAATATCAA
Found at i:34386 original size:133 final size:132
Alignment explanation
Indices: 34148--34411 Score: 474
Period size: 133 Copynumber: 2.0 Consensus size: 132
34138 CGCCATTCCT
*
34148 GAATTCCAATTTCCAAAACATAGCAGAACACAAAACGATGATGAACATAATTATTCCATATTCCA
1 GAATTCCAATTTCCAAAACATAGCAGAAAACAAAACGATGATGAACATAATTATTCCATATTCCA
* *
34213 TAATGCGTAAAAAGAAAGAGACTGTATGCAGAGCCGACCTGTTGTCAGTTCTTCTAAAAAATCAA
66 TAATGCATAAAAAGAAAGAGACCGTATGCAGAGCCGACCTGTTGTCAGTTCTTCT-AAAAATCAA
34278 TAA
130 TAA
*
34281 GAATTCCAATTTCCAAAACATAGCAGAAAACAAAACGATGATGAACATAATTATTCCGTATTCCA
1 GAATTCCAATTTCCAAAACATAGCAGAAAACAAAACGATGATGAACATAATTATTCCATATTCCA
*
34346 TAATGCATAAAATGAAAGAGACCGTATGCAGAGCCGACCTGTTGTCAGTTCTTCTAAAAATCAAT
66 TAATGCATAAAAAGAAAGAGACCGTATGCAGAGCCGACCTGTTGTCAGTTCTTCTAAAAATCAAT
34411 A
131 A
34412 GGTTTCCGGT
Statistics
Matches: 126, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
132 11 0.09
133 115 0.91
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (132 bp):
GAATTCCAATTTCCAAAACATAGCAGAAAACAAAACGATGATGAACATAATTATTCCATATTCCA
TAATGCATAAAAAGAAAGAGACCGTATGCAGAGCCGACCTGTTGTCAGTTCTTCTAAAAATCAAT
AA
Found at i:40028 original size:26 final size:25
Alignment explanation
Indices: 39974--40028 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
39964 AATAATAATA
*
39974 ATAATGACATTAATTAAATTCAACT
1 ATAATGACATTAATTAAATTCAACG
* *
39999 ATAATGAGCATTTATGTAAATT-AAGG
1 ATAATGA-CATTAAT-TAAATTCAACG
40025 ATAA
1 ATAA
40029 CATACATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 7 0.28
26 12 0.48
27 6 0.24
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (25 bp):
ATAATGACATTAATTAAATTCAACG
Found at i:40342 original size:24 final size:24
Alignment explanation
Indices: 40315--40390 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
40305 GTTGAAATGC
*
40315 TAAACGAACACAAATGAACGAACA
1 TAAACGAACACAAACGAACGAACA
* *
40339 TAAACGAACACACACGAACGAACG
1 TAAACGAACACAAACGAACGAACA
* * * * *
40363 CAAACGAACATAAAGGAATGAGCA
1 TAAACGAACACAAACGAACGAACA
40387 TAAA
1 TAAA
40391 ATTAATTGGG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.55, C:0.21, G:0.16, T:0.08
Consensus pattern (24 bp):
TAAACGAACACAAACGAACGAACA
Found at i:40347 original size:14 final size:14
Alignment explanation
Indices: 40317--40371 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
40307 TGAAATGCTA
*
40317 AACGAACACAAATG
1 AACGAACACAAACG
*
40331 AACGAACATAAACG
1 AACGAACACAAACG
40345 AAC--ACAC--ACG
1 AACGAACACAAACG
*
40355 AACGAACGCAAACG
1 AACGAACACAAACG
40369 AAC
1 AAC
40372 ATAAAGGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
10 6 0.18
12 6 0.18
14 21 0.64
ACGTcount: A:0.55, C:0.27, G:0.15, T:0.04
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:40543 original size:24 final size:24
Alignment explanation
Indices: 40516--40568 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
40506 AAAAATATTC
40516 ACGAATATAAATAAACAAACATAA
1 ACGAATATAAATAAACAAACATAA
* *
40540 ACGAATATAAATGAACGAACATAA
1 ACGAATATAAATAAACAAACATAA
40564 ACGAA
1 ACGAA
40569 CAGATTATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.62, C:0.13, G:0.09, T:0.15
Consensus pattern (24 bp):
ACGAATATAAATAAACAAACATAA
Found at i:40940 original size:16 final size:19
Alignment explanation
Indices: 40909--40947 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
40899 TTTTGTTCGG
40909 TTTTATCTTATAAAAT-AT
1 TTTTATCTTATAAAATAAT
40927 TTTTAT-TT-TAAAATAAT
1 TTTTATCTTATAAAATAAT
40944 TTTT
1 TTTT
40948 GAATTAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 8 0.40
18 6 0.30
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATCTTATAAAATAAT
Found at i:47493 original size:18 final size:18
Alignment explanation
Indices: 47470--47526 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
47460 ACCGGTTACA
47470 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
47488 ACCCGACCTGACCAGTTG
1 ACCCGACCCGACCCGTTG
* *
47506 ACCGGACCCGACTCGTTG
1 ACCCGACCCGACCCGTTG
47524 ACC
1 ACC
47527 GGTGTTGACC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.19, C:0.44, G:0.23, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:52342 original size:18 final size:18
Alignment explanation
Indices: 52319--52375 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
52309 ACCGGTTACA
*
52319 ACCCGACCCAACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
52337 ACCCGACCTGACCGGTTG
1 ACCCGACCCGACCCGTTG
*
52355 ACCGGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
52373 ACC
1 ACC
52376 GGTGTTGACC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:53697 original size:17 final size:18
Alignment explanation
Indices: 53675--53708 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53665 TTGAAAGGTC
*
53675 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
53692 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
53709 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:57242 original size:13 final size:13
Alignment explanation
Indices: 57221--57250 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
57211 TACCCGGCCC
57221 GACCAGTTGACCT
1 GACCAGTTGACCT
*
57234 GACCGGTTGACCT
1 GACCAGTTGACCT
57247 GACC
1 GACC
57251 CGACCCGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (13 bp):
GACCAGTTGACCT
Found at i:57255 original size:18 final size:18
Alignment explanation
Indices: 57228--57263 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57218 CCCGACCAGT
* *
57228 TGACCTGACCGGTTGACC
1 TGACCCGACCCGTTGACC
57246 TGACCCGACCCGTTGACC
1 TGACCCGACCCGTTGACC
57264 GTTGACCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.39, G:0.25, T:0.19
Consensus pattern (18 bp):
TGACCCGACCCGTTGACC
Found at i:58588 original size:17 final size:18
Alignment explanation
Indices: 58566--58599 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58556 TTGAAAGGTC
*
58566 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
58583 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
58600 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:61308 original size:22 final size:23
Alignment explanation
Indices: 61265--61308 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
61255 TTTAACTTGT
*
61265 ATTATTATATAATTGTAGAACTA
1 ATTATTATATAATTATAGAACTA
*
61288 ATTATTATA-ATTTATAGAACT
1 ATTATTATATAATTATAGAACT
61309 TCATATCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (23 bp):
ATTATTATATAATTATAGAACTA
Found at i:62112 original size:12 final size:12
Alignment explanation
Indices: 62097--62161 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
62087 AAACAAGCTT
62097 ATAAACGAGTTG
1 ATAAACGAGTTG
*
62109 ATAAATGAGCTT-
1 ATAAACGAG-TTG
* *
62121 ATAAATGAATTG
1 ATAAACGAGTTG
62133 ATAAACGAGCTT-
1 ATAAACGAG-TTG
* *
62145 ATAAAGGAGTCG
1 ATAAACGAGTTG
62157 ATAAA
1 ATAAA
62162 TGAGCTCATT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 3 0.07
12 36 0.84
13 4 0.09
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (12 bp):
ATAAACGAGTTG
Found at i:62124 original size:24 final size:24
Alignment explanation
Indices: 62092--62167 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
62082 CGAAAAAACA
62092 AGCTTATAAACGAGTTGATAAATG
1 AGCTTATAAACGAGTTGATAAATG
* * *
62116 AGCTTATAAATGAATTGATAAACG
1 AGCTTATAAACGAGTTGATAAATG
* *
62140 AGCTTATAAAGGAGTCGATAAATG
1 AGCTTATAAACGAGTTGATAAATG
62164 AGCT
1 AGCT
62168 CATTCGTGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (24 bp):
AGCTTATAAACGAGTTGATAAATG
Found at i:63062 original size:23 final size:23
Alignment explanation
Indices: 63029--63097 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
63019 ACTACAAGAT
*
63029 ATGTTCCGAAGGACCGCGTAGAA
1 ATGTCCCGAAGGACCGCGTAGAA
* *
63052 ATGTCCTGAAGGACCACGTAGAA
1 ATGTCCCGAAGGACCGCGTAGAA
* *
63075 TTGTCCCGAATGACCGCGTAGAA
1 ATGTCCCGAAGGACCGCGTAGAA
63098 CCCTCGACTC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (23 bp):
ATGTCCCGAAGGACCGCGTAGAA
Found at i:63192 original size:14 final size:14
Alignment explanation
Indices: 63173--63236 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
63163 TTTACGCATT
63173 TCACATAGCTTATA
1 TCACATAGCTTATA
**
63187 TCACATAGACAAATAA
1 TCACATAG-CTTAT-A
* * *
63203 TCACATAGATCATG
1 TCACATAGCTTATA
63217 TCACATAGCTTATA
1 TCACATAGCTTATA
63231 TCACAT
1 TCACAT
63237 TTTTCATATA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
14 25 0.64
15 5 0.13
16 9 0.23
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.30
Consensus pattern (14 bp):
TCACATAGCTTATA
Found at i:63226 original size:44 final size:46
Alignment explanation
Indices: 63173--63283 Score: 136
Period size: 46 Copynumber: 2.5 Consensus size: 46
63163 TTTACGCATT
*
63173 TCACATAGCTTATATCACA-TAGACAAATAATCACATAGATC-ATG
1 TCACATAGCTTATATCACATTAGACAAATAATCACATAGATCAATA
*** * * *
63217 TCACATAGCTTATATCACATTTTTCATATAATCACGTAGTTCAATA
1 TCACATAGCTTATATCACATTAGACAAATAATCACATAGATCAATA
*
63263 TCACATAGCTTATATCTCATT
1 TCACATAGCTTATATCACATT
63284 TTCATATAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 19 0.33
45 16 0.28
46 22 0.39
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (46 bp):
TCACATAGCTTATATCACATTAGACAAATAATCACATAGATCAATA
Found at i:66418 original size:2 final size:2
Alignment explanation
Indices: 66411--66443 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
66401 GTTTCAGTAA
66411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66444 CTGAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66713 original size:19 final size:20
Alignment explanation
Indices: 66691--66732 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
66681 CTAAAATTTT
*
66691 AAAAAAATCTT-AAAAAATA
1 AAAAAAATATTAAAAAAATA
* *
66710 AAAATATTATTAAAAAAATA
1 AAAAAAATATTAAAAAAATA
66730 AAA
1 AAA
66733 CCCGCGTGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAAATATTAAAAAAATA
Found at i:68134 original size:19 final size:19
Alignment explanation
Indices: 68064--68134 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 19
68054 ATACTCCTAT
68064 ATATATTATTTTTTAGATTAA
1 ATATATTATTTTTTA-A-TAA
*
68085 AT-TCTTATTTTTATTGAATAA
1 ATATATTA-TTTT-TT-AATAA
* *
68106 AAATAATATTTTTTAATAA
1 ATATATTATTTTTTAATAA
68125 ATATATTATT
1 ATATATTATT
68135 GCGGTTCGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 13 0.32
20 6 0.15
21 14 0.35
22 6 0.15
23 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (19 bp):
ATATATTATTTTTTAATAA
Found at i:68922 original size:21 final size:22
Alignment explanation
Indices: 68868--68922 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
68858 AAAGTGGTTA
*
68868 GTAAGAGGAAAATATTTTTCCG
1 GTAAGAGGAAAATATTTTTCAG
*
68890 GTCAATA-G-AAATATTTTTCAG
1 GT-AAGAGGAAAATATTTTTCAG
68911 GTAA-AGGAAAAT
1 GTAAGAGGAAAAT
68923 GACTTGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 1 0.04
20 3 0.11
21 18 0.64
22 3 0.11
23 3 0.11
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (22 bp):
GTAAGAGGAAAATATTTTTCAG
Done.