Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002128.1 Hibiscus syriacus cultivar Beakdansim tig00004357_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: 100793
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:910 original size:15 final size:15
Alignment explanation
Indices: 890--925 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
880 CTCCTCATTC
* *
890 TCATCATCTTCTTCA
1 TCATCATCGTCGTCA
905 TCATCATCGTCGTCA
1 TCATCATCGTCGTCA
920 TCATCA
1 TCATCA
926 GTAGCGGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.39
Consensus pattern (15 bp):
TCATCATCGTCGTCA
Found at i:1234 original size:21 final size:21
Alignment explanation
Indices: 1210--1249 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1200 CTTATGAAAT
*
1210 GGTTGCGGTGTCATCTGAATC
1 GGTTGCGATGTCATCTGAATC
**
1231 GGTTGTTATGTCATCTGAA
1 GGTTGCGATGTCATCTGAA
1250 ACGACGGCGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (21 bp):
GGTTGCGATGTCATCTGAATC
Found at i:8029 original size:16 final size:16
Alignment explanation
Indices: 8006--8066 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
7996 ATGATTAAGC
8006 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
*
8022 GTTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
8038 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
8054 GCTGAATGATTCA
1 GCTGAATGATTCA
8067 GAGGCTCTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:8659 original size:21 final size:21
Alignment explanation
Indices: 8618--8665 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 21
8608 GGATTTTGCA
8618 ATTTGAGTTTTGATTTTTAGGG
1 ATTTGAGTTTTGA-TTTTAGGG
8640 ATTTGAGATTTTGA-TTTAGGG
1 ATTTGAG-TTTTGATTTTAGGG
8661 ATTTG
1 ATTTG
8666 GGTATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 12 0.48
22 7 0.28
23 6 0.24
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (21 bp):
ATTTGAGTTTTGATTTTAGGG
Found at i:9075 original size:3 final size:3
Alignment explanation
Indices: 9067--9147 Score: 155
Period size: 3 Copynumber: 27.3 Consensus size: 3
9057 ACATTAAATC
9067 TTA TTA TTA TTA TTA TTA 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 TTA
9115 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9148 ACAACTACTA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13925 original size:4 final size:4
Alignment explanation
Indices: 13916--13950 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
13906 GATGGTTCTT
13916 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
13951 CTCTTTGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:18950 original size:23 final size:23
Alignment explanation
Indices: 18924--18980 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
18914 TGTGACATGT
* *
18924 TCTCTGCCTTTATTACAAGTTTA
1 TCTCTGTCTTTATGACAAGTTTA
18947 TCTCTGTCTTTATGACAAGTTTA
1 TCTCTGTCTTTATGACAAGTTTA
18970 TCTCTGTCTTT
1 TCTCTGTCTTT
18981 GTGGCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.51
Consensus pattern (23 bp):
TCTCTGTCTTTATGACAAGTTTA
Found at i:18996 original size:21 final size:23
Alignment explanation
Indices: 18908--18983 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
18898 AGAATAATTA
*
18908 TGTCTTTGTGAC-A-TGT-TCTC
1 TGTCTTTGTGACAAGTTTATCTC
* * *
18928 TGCCTTTATTACAAGTTTATCTC
1 TGTCTTTGTGACAAGTTTATCTC
*
18951 TGTCTTTATGACAAGTTTATCTC
1 TGTCTTTGTGACAAGTTTATCTC
18974 TGTCTTTGTG
1 TGTCTTTGTG
18984 GCATTTTTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
20 9 0.20
21 1 0.02
22 2 0.04
23 34 0.74
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.50
Consensus pattern (23 bp):
TGTCTTTGTGACAAGTTTATCTC
Found at i:19491 original size:29 final size:30
Alignment explanation
Indices: 19468--19523 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
19458 TACCAAGATG
* *
19468 TAAAATTT-GAAAGTTTAGTGACCAAAGTA
1 TAAAGTTTAGAAAATTTAGTGACCAAAGTA
*
19497 TAAAGTTTAGAAAATTTAGAGACCAAA
1 TAAAGTTTAGAAAATTTAGTGACCAAA
19524 ATGGTAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (30 bp):
TAAAGTTTAGAAAATTTAGTGACCAAAGTA
Found at i:20765 original size:19 final size:21
Alignment explanation
Indices: 20732--20770 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
20722 TGGAAATTAA
*
20732 TGTTAGAGTGATG-AATTTGG
1 TGTTAGAATGATGAAATTTGG
20752 TGTTAGAATG-TGAAATTTG
1 TGTTAGAATGATGAAATTTG
20771 ACTATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (21 bp):
TGTTAGAATGATGAAATTTGG
Found at i:22545 original size:19 final size:19
Alignment explanation
Indices: 22521--22583 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
22511 TATGCATTAG
22521 GCTATGAA-CTTGAAAATAA
1 GCTATGAATC-TGAAAATAA
*
22540 GCTATGAATCTGAAATTAA
1 GCTATGAATCTGAAAATAA
*
22559 GTTATGAATCTG-AAATAA
1 GCTATGAATCTGAAAATAA
*
22577 GTTATGA
1 GCTATGA
22584 GTCCGGACAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
18 12 0.30
19 27 0.68
20 1 0.03
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:22579 original size:18 final size:18
Alignment explanation
Indices: 22534--22583 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
22524 ATGAACTTGA
*
22534 AAATAAGCTATGAATCTG
1 AAATAAGTTATGAATCTG
22552 AAATTAAGTTATGAATCTG
1 AAA-TAAGTTATGAATCTG
22571 AAATAAGTTATGA
1 AAATAAGTTATGA
22584 GTCCGGACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (18 bp):
AAATAAGTTATGAATCTG
Found at i:22653 original size:28 final size:25
Alignment explanation
Indices: 22621--22696 Score: 82
Period size: 25 Copynumber: 2.9 Consensus size: 25
22611 ATGAGTTCTA
22621 AAATGTGAAAGTGCAAATTATGAAAATG
1 AAATGTGAAAGTG--AA-TATGAAAATG
*
22649 AAATGTGAAAGTGAATATGAAAGTG
1 AAATGTGAAAGTGAATATGAAAATG
*
22674 AAA-GATGAAAATGAGATATGAAA
1 AAATG-TGAAAGTGA-ATATGAAA
22697 GTTTTGTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.02
25 20 0.45
26 10 0.23
28 13 0.30
ACGTcount: A:0.53, C:0.01, G:0.24, T:0.22
Consensus pattern (25 bp):
AAATGTGAAAGTGAATATGAAAATG
Found at i:22663 original size:13 final size:13
Alignment explanation
Indices: 22621--22698 Score: 77
Period size: 13 Copynumber: 5.9 Consensus size: 13
22611 ATGAGTTCTA
*
22621 AAATGTGAAAGTG
1 AAATATGAAAGTG
*
22634 CAAATTATGAAAATG
1 -AAA-TATGAAAGTG
*
22649 AAATGTGAAAGTG
1 AAATATGAAAGTG
22662 -AATATGAAAGTG
1 AAATATGAAAGTG
* *
22674 AAAGATGAAAATG
1 AAATATGAAAGTG
*
22687 AGATATGAAAGT
1 AAATATGAAAGT
22699 TTTGTATTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
12 11 0.21
13 27 0.52
14 6 0.12
15 8 0.15
ACGTcount: A:0.51, C:0.01, G:0.24, T:0.23
Consensus pattern (13 bp):
AAATATGAAAGTG
Found at i:24789 original size:13 final size:14
Alignment explanation
Indices: 24768--24799 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24758 GAATAAATGC
24768 TAAAA-ATA-TTTT
1 TAAAATATATTTTT
24780 TAAAATATATTTTT
1 TAAAATATATTTTT
24794 TAAAAT
1 TAAAAT
24800 TTGTAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.28
13 3 0.17
14 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAAATATATTTTT
Found at i:25992 original size:25 final size:23
Alignment explanation
Indices: 25957--26007 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
25947 TTTACTTAAT
*
25957 TTTTAATATTTA-CTTTTTAAACA
1 TTTTAATATTTATATTTTTAAA-A
25980 TTTTAATAAATTTATATTTTTAAAA
1 TTTTAAT--ATTTATATTTTTAAAA
26005 TTT
1 TTT
26008 AATGTTGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.29
25 9 0.38
26 8 0.33
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTAATATTTATATTTTTAAAA
Found at i:26610 original size:182 final size:184
Alignment explanation
Indices: 26387--26755 Score: 600
Period size: 182 Copynumber: 2.0 Consensus size: 184
26377 ATTAAATTTT
* * *
26387 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATACTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* *
26452 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
* * *
26516 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTGAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
* *
26571 AAATACTAAATATATTATATA-AA-ATATGGGTTAAGCCCAAACTATTTAAAACCCAATTAATAA
1 AAATACTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* *
26634 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
26699 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
26753 AAA
1 AAA
26756 CATTTAATTT
Statistics
Matches: 172, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
182 94 0.55
183 58 0.34
184 20 0.12
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (184 bp):
AAATACTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:27154 original size:25 final size:25
Alignment explanation
Indices: 27108--27159 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
27098 AATAAAAACT
* * *
27108 ATTATGATAATCATATTAATATTAA
1 ATTATAATAATAATATTAATATAAA
27133 ATTATAATAATAATTATT-ATATAAA
1 ATTATAATAATAA-TATTAATATAAA
27158 AT
1 AT
27160 ACACGTATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTATAATAATAATATTAATATAAA
Found at i:37221 original size:22 final size:21
Alignment explanation
Indices: 37180--37231 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
37170 CCTCTTCACC
37180 ATGGCAAAAACTTTCATTTTT
1 ATGGCAAAAACTTTCATTTTT
37201 ATGGCAAAAACTTTCATTTTT
1 ATGGCAAAAACTTTCATTTTT
* *
37222 GTAGCAAAAA
1 ATGGCAAAAA
37232 GGAAAAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGGCAAAAACTTTCATTTTT
Found at i:38265 original size:2 final size:2
Alignment explanation
Indices: 38258--38286 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38248 GACATTTACA
38258 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38287 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:38291 original size:2 final size:2
Alignment explanation
Indices: 38286--38316 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38276 TCTCTCTCTC
38286 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 T
38317 GCTATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40901 original size:23 final size:23
Alignment explanation
Indices: 40875--40919 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
40865 CAAATTATTT
*
40875 TTAGAATTATCTTTTGTATTTTC
1 TTAGAATTATCTTTAGTATTTTC
*
40898 TTAGGATTATCTTTAGTATTTT
1 TTAGAATTATCTTTAGTATTTT
40920 TAGGGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.60
Consensus pattern (23 bp):
TTAGAATTATCTTTAGTATTTTC
Found at i:43275 original size:2 final size:2
Alignment explanation
Indices: 43268--43295 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43258 TAAATTAGAA
43268 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
43296 TAAAGGAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55266 original size:2 final size:2
Alignment explanation
Indices: 55261--55298 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
55251 ATATATATAT
55261 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
55299 GGGGGGGGGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57973 original size:21 final size:21
Alignment explanation
Indices: 57949--57996 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
57939 TGAACGGCTT
*
57949 CTCTCCAACGCCAAAGATCCC
1 CTCTCCAACGCCAAAGATCAC
**
57970 CTCTCCCTCGCCAAAGATCAC
1 CTCTCCAACGCCAAAGATCAC
57991 CTCTCC
1 CTCTCC
57997 CTCGAGGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.50, G:0.08, T:0.19
Consensus pattern (21 bp):
CTCTCCAACGCCAAAGATCAC
Found at i:57997 original size:21 final size:21
Alignment explanation
Indices: 57957--58000 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
57947 TTCTCTCCAA
*
57957 CGCCAAAGATCCCCTCTCCCT
1 CGCCAAAGATCACCTCTCCCT
57978 CGCCAAAGATCACCTCTCCCT
1 CGCCAAAGATCACCTCTCCCT
57999 CG
1 CG
58001 AGGGTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.50, G:0.11, T:0.18
Consensus pattern (21 bp):
CGCCAAAGATCACCTCTCCCT
Found at i:60966 original size:35 final size:32
Alignment explanation
Indices: 60916--60988 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
60906 TATCTATTTT
* *
60916 AATATAAAATACTTTATGTATCTGTTTTGACTAAA
1 AATATAAAATACTTTAT-T-TAT-TTTTGACAAAA
* *
60951 AATATAAATTTCTTTATTTATTTTTGACAAAA
1 AATATAAAATACTTTATTTATTTTTGACAAAA
60983 AATATA
1 AATATA
60989 CTTAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 16 0.47
33 2 0.06
34 1 0.03
35 15 0.44
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (32 bp):
AATATAAAATACTTTATTTATTTTTGACAAAA
Found at i:62414 original size:3 final size:3
Alignment explanation
Indices: 62406--62433 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
62396 AATTCCTTAC
62406 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
62434 TCTTCAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:64899 original size:21 final size:21
Alignment explanation
Indices: 64875--64922 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
64865 TGAACGGCTT
*
64875 CTCTCCAACGCCAAAGATCCC
1 CTCTCCAACGCCAAAGATCAC
**
64896 CTCTCCCTCGCCAAAGATCAC
1 CTCTCCAACGCCAAAGATCAC
64917 CTCTCC
1 CTCTCC
64923 CTCGAGGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.50, G:0.08, T:0.19
Consensus pattern (21 bp):
CTCTCCAACGCCAAAGATCAC
Found at i:64923 original size:21 final size:21
Alignment explanation
Indices: 64883--64926 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
64873 TTCTCTCCAA
*
64883 CGCCAAAGATCCCCTCTCCCT
1 CGCCAAAGATCACCTCTCCCT
64904 CGCCAAAGATCACCTCTCCCT
1 CGCCAAAGATCACCTCTCCCT
64925 CG
1 CG
64927 AGGGTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.50, G:0.11, T:0.18
Consensus pattern (21 bp):
CGCCAAAGATCACCTCTCCCT
Found at i:71303 original size:19 final size:19
Alignment explanation
Indices: 71279--71315 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
71269 AAATACTATA
71279 GTATTAGAATTCAGATGTG
1 GTATTAGAATTCAGATGTG
71298 GTATTAGAATTCAGATGT
1 GTATTAGAATTCAGATGT
71316 TGTGTATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.38
Consensus pattern (19 bp):
GTATTAGAATTCAGATGTG
Found at i:75563 original size:7 final size:7
Alignment explanation
Indices: 75551--75580 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
75541 TTGGAATAGA
75551 CTTCAAC
1 CTTCAAC
75558 CTTCAAC
1 CTTCAAC
75565 CTTCAAC
1 CTTCAAC
75572 CTTCAAC
1 CTTCAAC
75579 CT
1 CT
75581 GCAATAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.43, G:0.00, T:0.30
Consensus pattern (7 bp):
CTTCAAC
Found at i:86625 original size:19 final size:20
Alignment explanation
Indices: 86594--86631 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
86584 ATAAGAGATA
86594 AATAAAAATGAAA-TAAATT
1 AATAAAAATGAAACTAAATT
86613 AATAAAAGA-GAAACTAAAT
1 AATAAAA-ATGAAACTAAAT
86632 AGTAACAGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (20 bp):
AATAAAAATGAAACTAAATT
Found at i:86694 original size:6 final size:6
Alignment explanation
Indices: 86680--86716 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
86670 AGCACGACAA
*
86680 GAAGAG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG G
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG G
86717 GAAGAGAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:86706 original size:18 final size:18
Alignment explanation
Indices: 86680--86722 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
86670 AGCACGACAA
86680 GAAGAGGAAGGGGAAGGG
1 GAAGAGGAAGGGGAAGGG
*
86698 GAAGGGGAAGGGGAAGGGG
1 GAAGAGGAAGGGGAA-GGG
86717 GAAGAG
1 GAAGAG
86723 AGAACAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (18 bp):
GAAGAGGAAGGGGAAGGG
Found at i:92373 original size:39 final size:39
Alignment explanation
Indices: 92307--92388 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
92297 GGAGGTTGTG
* *
92307 AAAGATGACCAGGGTGAAGGGGGTGATACCGAAACACCA
1 AAAGATGACCAGGGTGAAGGGGATGATACCAAAACACCA
* * * *
92346 AAAGGTGATCAGGGTGAAGTGGATGATACTAAAACACCA
1 AAAGATGACCAGGGTGAAGGGGATGATACCAAAACACCA
92385 AAAG
1 AAAG
92389 CTGAAGAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.41, C:0.15, G:0.30, T:0.13
Consensus pattern (39 bp):
AAAGATGACCAGGGTGAAGGGGATGATACCAAAACACCA
Found at i:92941 original size:6 final size:6
Alignment explanation
Indices: 92932--92957 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
92922 GTAGAGAAAA
92932 AGGCAG AGGCAG AGGCAG AGGCAG AG
1 AGGCAG AGGCAG AGGCAG AGGCAG AG
92958 CAAAAGGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGCAG
Found at i:92946 original size:30 final size:30
Alignment explanation
Indices: 92905--92968 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
92895 GTTCAAGAAT
* *
92905 CAGACGCAGAGGTAGAGGTAGAGAAAAAGG
1 CAGACGCAGAGGCAGAGGCAGAGAAAAAGG
* *
92935 CAGAGGCAGAGGCAGAGGCAGAGCAAAAGG
1 CAGACGCAGAGGCAGAGGCAGAGAAAAAGG
92965 CAGA
1 CAGA
92969 ACCTGAGGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.41, T:0.03
Consensus pattern (30 bp):
CAGACGCAGAGGCAGAGGCAGAGAAAAAGG
Found at i:92977 original size:30 final size:30
Alignment explanation
Indices: 92911--92980 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
92901 GAATCAGACG
* * **
92911 CAGAGGTAGAGGTAGAGAAAAAGGCAGAGG
1 CAGAGGCAGAGGCAGAGAAAAAGGCAGAAC
*
92941 CAGAGGCAGAGGCAGAGCAAAAGGCAGAAC
1 CAGAGGCAGAGGCAGAGAAAAAGGCAGAAC
*
92971 CTGAGGCAGA
1 CAGAGGCAGA
92981 AATAGAGGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.41, C:0.14, G:0.40, T:0.04
Consensus pattern (30 bp):
CAGAGGCAGAGGCAGAGAAAAAGGCAGAAC
Found at i:92988 original size:42 final size:42
Alignment explanation
Indices: 92942--93021 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
92932 AGGCAGAGGC
* * * *
92942 AGAGGCAGAGGCAGAGCAAAAGGCAGAACCTGAGGCAGAAAT
1 AGAGGAAGAAGCAGAACAAAAGGCAGAACCTGAAGCAGAAAT
* * *
92984 AGAGGAAGAAGTAGAACCAAAGGCAGAGCCTGAAGCAG
1 AGAGGAAGAAGCAGAACAAAAGGCAGAACCTGAAGCAG
93022 GAGCAGAGGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.44, C:0.16, G:0.35, T:0.05
Consensus pattern (42 bp):
AGAGGAAGAAGCAGAACAAAAGGCAGAACCTGAAGCAGAAAT
Found at i:93030 original size:42 final size:42
Alignment explanation
Indices: 92960--93051 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
92950 AGGCAGAGCA
* * *
92960 AAAGGCAGAACCTGAGGCAGAAATAGAGGAAGAAGTAGAACC
1 AAAGGCAGAACCTGAAGCAGAAACAGAGGAAAAAGTAGAACC
* * * * **
93002 AAAGGCAGAGCCTGAAGCAGGAGCAGAGGAAAAAGTCGAGGC
1 AAAGGCAGAACCTGAAGCAGAAACAGAGGAAAAAGTAGAACC
93044 AAAGGCAG
1 AAAGGCAG
93052 CGTCAGAGAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.45, C:0.15, G:0.35, T:0.05
Consensus pattern (42 bp):
AAAGGCAGAACCTGAAGCAGAAACAGAGGAAAAAGTAGAACC
Found at i:93133 original size:24 final size:24
Alignment explanation
Indices: 93106--93151 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
93096 ACAGAGGCAA
*
93106 AGGCAAAGGCAGAGGTAAAGGTGG
1 AGGCAAAGACAGAGGTAAAGGTGG
* *
93130 AGGCGAAGACAGAGGTCAAGGT
1 AGGCAAAGACAGAGGTAAAGGT
93152 AGAGTCTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.43, T:0.09
Consensus pattern (24 bp):
AGGCAAAGACAGAGGTAAAGGTGG
Found at i:99770 original size:31 final size:31
Alignment explanation
Indices: 99722--99780 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
99712 GGATGATGAC
99722 TCGAACAGATCGATAACGTTAGGGATCAAAA
1 TCGAACAGATCGATAACGTTAGGGATCAAAA
* *
99753 TCGAAC-GTATCGGTAACGTTCGGGATCA
1 TCGAACAG-ATCGATAACGTTAGGGATCA
99781 TGTACCCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (31 bp):
TCGAACAGATCGATAACGTTAGGGATCAAAA
Done.