Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003186.1 Hibiscus syriacus cultivar Beakdansim tig00006702_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: 65915
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3237 original size:29 final size:29
Alignment explanation
Indices: 3192--3261 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
3182 CCCGCAGGAC
*
3192 CTATCCAGAGGTCATAAGATCCTCGGTAA
1 CTATCCAGAGGTAATAAGATCCTCGGTAA
3221 CTATCCAGAGGTAATAAGATCCTCGGTAA
1 CTATCCAGAGGTAATAAGATCCTCGGTAA
* *
3250 CTGTCCATAGGT
1 CTATCCAGAGGT
3262 CCCAAAGAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (29 bp):
CTATCCAGAGGTAATAAGATCCTCGGTAA
Found at i:5139 original size:118 final size:119
Alignment explanation
Indices: 4989--5226 Score: 469
Period size: 119 Copynumber: 2.0 Consensus size: 119
4979 TTTAATCACC
4989 ATATTCTGAAATTTTACAATTTTGGTCACTAACCCGTATTTTGGGATGTTACA-CTACCCAGATT
1 ATATTCTGAAATTTTACAATTTTGGTCACTAACCCGTATTTTGGGATGTTACACCTACCCAGATT
5053 TTCCAGGTTTTCCACTCGAAATTTACCCAACTTTGGGCAATTTTCATCTTCTTT
66 TTCCAGGTTTTCCACTCGAAATTTACCCAACTTTGGGCAATTTTCATCTTCTTT
5107 ATATTCTGAAATTTTACAATTTTGGTCACTAACCCGTATTTTGGGATGTTACACCTACCCAGATT
1 ATATTCTGAAATTTTACAATTTTGGTCACTAACCCGTATTTTGGGATGTTACACCTACCCAGATT
5172 TTCCAGGTTTTCCACTCGAAATTTACCCAACTTTGGGCAATTTTCATCTTCTTT
66 TTCCAGGTTTTCCACTCGAAATTTACCCAACTTTGGGCAATTTTCATCTTCTTT
5226 A
1 A
5227 CCCCTACAAT
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 53 0.45
119 66 0.55
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (119 bp):
ATATTCTGAAATTTTACAATTTTGGTCACTAACCCGTATTTTGGGATGTTACACCTACCCAGATT
TTCCAGGTTTTCCACTCGAAATTTACCCAACTTTGGGCAATTTTCATCTTCTTT
Found at i:5628 original size:9 final size:9
Alignment explanation
Indices: 5614--5640 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5604 CTCTTCTAGG
5614 GGAAGAAGA
1 GGAAGAAGA
5623 GGAAGAAGA
1 GGAAGAAGA
5632 GGAAGAAGA
1 GGAAGAAGA
5641 AAGAGAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
GGAAGAAGA
Found at i:10826 original size:215 final size:206
Alignment explanation
Indices: 10457--10841 Score: 527
Period size: 215 Copynumber: 1.8 Consensus size: 206
10447 AAGCATCCGA
* * *
10457 GAAGAATAGTAGAGAAAATTTTGAACGAAATTTTCTTCCAATCTATAATCTATAAGTGTTATTTG
1 GAAGAATAGTAGAGAAAATTTTGAACGAAATTTTCTTCCAATCTATAATCTATAAGTATTATATA
* * * *
10522 AAATAAAATTATATTCGTATTCGAATAAAATATGTTTATTTCGGGAAGGTTTTTAAAATATTATC
66 AAATAAAATTATATTCGTATTCGAATAAAATATCTCTATTTCGGAAAGGTTATTAAAATATTATC
* *
10587 TTTAATATTTTGTTGCAGGTAAAAAAGAAGTGAGTAATAAATTCGAGAAGGTTTTTTTTATAACA
131 TTTAATATGTTGTTGCAAGTAAAAAAGAAGTGAGTAATAAATTCGAGAAGGTTTTTTTTATAACA
10652 TCAACTTGTCG
196 TCAACTTGTCG
* * *
10663 GAAGAATAGTAGAGAAAATTTTGAACGAAATTTTCTTTCAATCTATAATTTGTAAGTATTATGAA
1 GAAGAATAGTAGAGAAAATTTTGAACGAAATTTTCTTCCAATCTATAATCTATAAGTATTAT--A
** * *
10728 TAAAATTTTATTCGTATTCTTATTCGTATTCGAATAATATATCTCTATTTCGGAAAGGTTATTAA
64 TAAAA---TA---AAATT-ATATTCGTATTCGAATAAAATATCTCTATTTCGGAAAGGTTATTAA
* *
10793 AATATTGTTTTTAATATGTTGTTGCAAGTAAAAAAGAAGTGAGTAATAA
122 AATATTATCTTTAATATGTTGTTGCAAGTAAAAAAGAAGTGAGTAATAA
10842 CATCAACTTG
Statistics
Matches: 152, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
206 58 0.38
208 4 0.03
211 2 0.01
214 3 0.02
215 85 0.56
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.39
Consensus pattern (206 bp):
GAAGAATAGTAGAGAAAATTTTGAACGAAATTTTCTTCCAATCTATAATCTATAAGTATTATATA
AAATAAAATTATATTCGTATTCGAATAAAATATCTCTATTTCGGAAAGGTTATTAAAATATTATC
TTTAATATGTTGTTGCAAGTAAAAAAGAAGTGAGTAATAAATTCGAGAAGGTTTTTTTTATAACA
TCAACTTGTCG
Found at i:11024 original size:24 final size:24
Alignment explanation
Indices: 10990--11044 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
10980 GTTTGTAGTA
*
10990 GAAAAATAATATTTATTATAATGAC
1 GAAAAA-AATATTAATTATAATGAC
11015 GAAAAAAATATTAATTATAATGAC
1 GAAAAAAATATTAATTATAATGAC
11039 -AAAAAA
1 GAAAAAA
11045 TAATGACACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 6 0.21
24 17 0.59
25 6 0.21
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (24 bp):
GAAAAAAATATTAATTATAATGAC
Found at i:11789 original size:27 final size:28
Alignment explanation
Indices: 11758--11816 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
11748 AAAATTATTT
*
11758 TTTTTTATCAAAATAAATACTTAAAATA
1 TTTTTGATCAAAATAAATACTTAAAATA
* * *
11786 TTTTTGGTCAAAATAGATACTTAAATTA
1 TTTTTGATCAAAATAAATACTTAAAATA
11814 TTT
1 TTT
11817 AATTTTTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (28 bp):
TTTTTGATCAAAATAAATACTTAAAATA
Found at i:12747 original size:46 final size:46
Alignment explanation
Indices: 12689--12831 Score: 268
Period size: 46 Copynumber: 3.1 Consensus size: 46
12679 ATGATTTACT
*
12689 AAAACGACGTCGTTTCAACACAACTATTTTGATGTTCAATAAAGAC
1 AAAATGACGTCGTTTCAACACAACTATTTTGATGTTCAATAAAGAC
12735 AAAATGACGTCGTTTCAACACAACTATTTTGATGTTCAATAAAGAC
1 AAAATGACGTCGTTTCAACACAACTATTTTGATGTTCAATAAAGAC
*
12781 AAAATGACGTCGTTTCAACACAACTATTTTGATGCTCAATAAAGAC
1 AAAATGACGTCGTTTCAACACAACTATTTTGATGTTCAATAAAGAC
12827 AAAAT
1 AAAAT
12832 AACATTGTTT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 95 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.29
Consensus pattern (46 bp):
AAAATGACGTCGTTTCAACACAACTATTTTGATGTTCAATAAAGAC
Found at i:12751 original size:25 final size:25
Alignment explanation
Indices: 12723--12798 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
12713 TATTTTGATG
12723 TTCAATAAAGACAAAATGACGTCGT
1 TTCAATAAAGACAAAATGACGTCGT
* * ***
12748 TTCAACACA-ACTATTTTGA--T-G-
1 TTCAATAAAGAC-AAAATGACGTCGT
12769 TTCAATAAAGACAAAATGACGTCGT
1 TTCAATAAAGACAAAATGACGTCGT
12794 TTCAA
1 TTCAA
12799 CACAACTATT
Statistics
Matches: 35, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
21 11 0.31
22 3 0.09
23 2 0.06
24 3 0.09
25 16 0.46
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (25 bp):
TTCAATAAAGACAAAATGACGTCGT
Found at i:16903 original size:10 final size:10
Alignment explanation
Indices: 16888--16913 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
16878 TTCAACTTTC
16888 TTTCTTTCCT
1 TTTCTTTCCT
16898 TTTCTTTCCT
1 TTTCTTTCCT
16908 TTTCTT
1 TTTCTT
16914 CTTTTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTTTCCT
Found at i:19614 original size:28 final size:27
Alignment explanation
Indices: 19568--19621 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
19558 TGGAATACTA
* *
19568 TTTAACATAATTTTTTTAAATATTTAT
1 TTTAAAATAATTTTATTAAATATTTAT
19595 TTTAAAATACATTTTATTAAATATTTA
1 TTTAAAATA-ATTTTATTAAATATTTA
19622 CTATTTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTAAAATAATTTTATTAAATATTTAT
Found at i:20919 original size:17 final size:16
Alignment explanation
Indices: 20897--20928 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
20887 TCAGGACATG
20897 TATTTTAATAATAATAT
1 TATTTTAATAA-AATAT
20914 TATTTTAATAAAATA
1 TATTTTAATAAAATA
20929 ATACCACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTTAATAAAATAT
Found at i:21775 original size:12 final size:12
Alignment explanation
Indices: 21758--21791 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
21748 AATAAAAAAA
21758 TATTATATTTTC
1 TATTATATTTTC
21770 TATTATATTTTC
1 TATTATATTTTC
*
21782 GATTATATTT
1 TATTATATTT
21792 ATCTCACCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (12 bp):
TATTATATTTTC
Found at i:22268 original size:29 final size:29
Alignment explanation
Indices: 22232--22294 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
22222 TATTTAAAGT
**
22232 TATTTTTTTGTCAAAATA-ATTACTTAAAA
1 TATTTTTTAATCAAAATAGA-TACTTAAAA
*
22261 TATTTTTTAATCAAAATAGATACTTAAAT
1 TATTTTTTAATCAAAATAGATACTTAAAA
22290 TATTT
1 TATTT
22295 AATTTTTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.49
Consensus pattern (29 bp):
TATTTTTTAATCAAAATAGATACTTAAAA
Found at i:22957 original size:14 final size:14
Alignment explanation
Indices: 22940--22967 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22930 AAATAATAAC
22940 ATTTGAATATTAAT
1 ATTTGAATATTAAT
22954 ATTTGAATATTAAT
1 ATTTGAATATTAAT
22968 TATAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTTGAATATTAAT
Found at i:30230 original size:19 final size:20
Alignment explanation
Indices: 30208--30251 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
30198 AAAAGTATCA
*
30208 AAACTATTG-AAAAGTTTAG
1 AAACTATAGTAAAAGTTTAG
*
30227 AAACTATAGTAAAAGTTTTG
1 AAACTATAGTAAAAGTTTAG
30247 AAACT
1 AAACT
30252 CCTAAGGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.32
Consensus pattern (20 bp):
AAACTATAGTAAAAGTTTAG
Found at i:33680 original size:40 final size:42
Alignment explanation
Indices: 33630--33835 Score: 181
Period size: 40 Copynumber: 4.8 Consensus size: 42
33620 TATCTGAGGT
33630 TGACACGGCTCATACGTGATGAAGAGTTCTGG-TC-AGGAGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGATCGAGGAGA
*
33670 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTGGGGACGGGCGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGG--ATC-----GA--GGAGA
* * * * * *
33721 TAACACGGTTCCTACGTGATGAGGACG-TCTGGTTATCTAGG-GG
1 TGACACGGCTCATACGTGATGAAGA-GTTCTGG--ATCGAGGAGA
*
33764 TGACACGGCTCATGCGTGATGAAGAGTTCTGG-TC-AGGAGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGATCGAGGAGA
*
33804 TGACACGACTCATACGTGATGAAGAGTTCTGG
1 TGACACGGCTCATACGTGATGAAGAGTTCTGG
33836 CCATCTTTAG
Statistics
Matches: 135, Mismatches: 17, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
39 3 0.02
40 65 0.48
42 1 0.01
43 28 0.21
44 2 0.01
46 1 0.01
49 1 0.01
51 33 0.24
52 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (42 bp):
TGACACGGCTCATACGTGATGAAGAGTTCTGGATCGAGGAGA
Found at i:33768 original size:134 final size:134
Alignment explanation
Indices: 33402--33842 Score: 466
Period size: 134 Copynumber: 3.3 Consensus size: 134
33392 TGCTGAAGAC
* * * * * * *
33402 GACACTGCTCATCCGCGATGACA-AGTTCTTGGTCATCTTTAGG-TGGAGGATAACACGGTTCCA
1 GACACGGCTCATACGTGATGA-AGAGTTC-TGGCCATCTTGAGGAAGGACGATAACACGGTTCCA
* * * * * ** **
33465 CTCTG-TAGGGGATGACTGGTTATCTGA-GTTGACACGGTTTCCACT-C-TGCTGGGGAAATCTG
64 CTCTGAT-GAGGACGACTGGTTATCTGAGGGTGACACGG-CT-CA-TACGTGATGAAGAGTTCTG
* *
33526 GTCGGGGGAT
125 GTCAGGAGAT
* * * *
33536 GACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAATGATGATAACACGGTTCCAC
1 GACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTTGAGGAAGGACGATAACACGGTTCCAC
* *
33601 TCTGATGGGGACGACTGGTTATCTGAGGTTGACACGGCTCATACGTGATGAAGAGTTCTGGTCAG
65 TCTGATGAGGACGACTGGTTATCTGAGGGTGACACGGCTCATACGTGATGAAGAGTTCTGGTCAG
33666 GAGAT
130 GAGAT
* * *
33671 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTGGGGACGGGCGATAACACGGTTCCTAC
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTGAGGAAGGACGATAACACGGTTCC-AC
* * *
33736 -GTGATGAGGACGTCTGGTTATCT-AGGGGTGACACGGCTCATGCGTGATGAAGAGTTCTGGTCA
65 TCTGATGAGGACGACTGGTTATCTGA-GGGTGACACGGCTCATACGTGATGAAGAGTTCTGGTCA
33799 GGAGAT
129 GGAGAT
*
33805 GACACGACTCATACGTGATGAAGAGTTCTGGCCATCTT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTT
33843 TAGGGATAAT
Statistics
Matches: 271, Mismatches: 28, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
133 3 0.01
134 168 0.62
135 89 0.33
136 11 0.04
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.27
Consensus pattern (134 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTGAGGAAGGACGATAACACGGTTCCACT
CTGATGAGGACGACTGGTTATCTGAGGGTGACACGGCTCATACGTGATGAAGAGTTCTGGTCAGG
AGAT
Found at i:33892 original size:28 final size:28
Alignment explanation
Indices: 33854--34021 Score: 192
Period size: 28 Copynumber: 6.0 Consensus size: 28
33844 AGGGATAATG
* * *
33854 GTTTCATGAGAAACCGATTCAAAGATAA
1 GTTTCAAGAGAAACAGACTCAAAGATAA
*
33882 GTTTCAAGAGAAACTGACTCAAAGATAA
1 GTTTCAAGAGAAACAGACTCAAAGATAA
* *
33910 ATTTCAAGAGAAACCGACTCAAAGATAA
1 GTTTCAAGAGAAACAGACTCAAAGATAA
* **
33938 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAGAGAAACAGACTCAAAGATAA
* * * **
33966 GTTTCAGGAAAAACAAACTCAAAGATTT
1 GTTTCAAGAGAAACAGACTCAAAGATAA
* *
33994 GTTTCAAGAAAAACTGACTCAAAGATAA
1 GTTTCAAGAGAAACAGACTCAAAGATAA
34022 TGTGTTTTAA
Statistics
Matches: 121, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 121 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (28 bp):
GTTTCAAGAGAAACAGACTCAAAGATAA
Found at i:34679 original size:106 final size:105
Alignment explanation
Indices: 34523--34869 Score: 509
Period size: 106 Copynumber: 3.3 Consensus size: 105
34513 ATTCTGAGGG
* * *
34523 AAAATGTCTCAAGTGAGACGAAATTTGTTTTGAAATAAACAACAATCTCAAGTGAGATTAATTTT
1 AAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTCAAGTGAGATTAATTTT
34588 GTTTCAAGTGAAGCAAATTCAAAATTTGTTTCTCAAAGGAA
66 GTTTCAAGTGAAGCAAATTCAAAATTTG-TTCTCAAAGGAA
* *
34629 AAAATGTCCCAAGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTCAAATGAGATTAATTTT
1 AAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTCAAGTGAGATTAATTTT
* *
34694 ATTTCAAGTGAAGCAAATTCAAAATTTG-TATCAAAGGAA
66 GTTTCAAGTGAAGCAAATTCAAAATTTGTTCTCAAAGGAA
* * *** * * *
34733 AAAATATCTCAAGCGAGACGAAGTTTGTTTTTTTGAGATATAACAATCTCAAGTGAGATTACTTT
1 AAAATGTCTCAAGCGAGACGAAATTTG-TTTTAAAAGAAACAACAATCTCAAGTGAGATTAATTT
*
34798 TGTTTCAAGTGAAACAAATTCAAAATTTGTATCTCAAAGG-A
65 TGTTTCAAGTGAAGCAAATTCAAAATTTGT-TCTCAAAGGAA
34839 AAAATGTCTCAAGCGAGACGAAATTTGTTTT
1 AAAATGTCTCAAGCGAGACGAAATTTGTTTT
34870 GAAATAAATT
Statistics
Matches: 216, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
104 34 0.16
105 61 0.28
106 113 0.52
107 8 0.04
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (105 bp):
AAAATGTCTCAAGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTCAAGTGAGATTAATTTT
GTTTCAAGTGAAGCAAATTCAAAATTTGTTCTCAAAGGAA
Found at i:34810 original size:105 final size:105
Alignment explanation
Indices: 34466--34869 Score: 494
Period size: 106 Copynumber: 3.8 Consensus size: 105
34456 TTTGAAAATA
* ** * ** ** *
34466 TCAAGTGATATTAATTTTGTTTCAAGT-ACAATAACTTTGAAATTTGTATTCTGAGG-GAAAATG
1 TCAAGTGAGATTAATTTTGTTTCAAGTGA-AGCAAATTCAAAATTTGTA-TCAAAGGAAAAAATG
* * *
34529 TCTCAAGTGAGACGAAATTTG-TTTTGAAATAAACAACAATC
64 TCTCAAGCGAGACGAAATTTGTTTTTAAAAGAAACAACAATC
*
34570 TCAAGTGAGATTAATTTTGTTTCAAGTGAAGCAAATTCAAAATTTGTTTCTCAAAGGAAAAAATG
1 TCAAGTGAGATTAATTTTGTTTCAAGTGAAGCAAATTCAAAATTTG--TATCAAAGGAAAAAATG
*
34635 TCCCAAGCGAGACGAAATTTG-TTTTAAAAGAAACAACAATC
64 TCTCAAGCGAGACGAAATTTGTTTTTAAAAGAAACAACAATC
* * *
34676 TCAAATGAGATTAATTTTATTTCAAGTGAAGCAAATTCAAAATTTGTATCAAAGGAAAAAATATC
1 TCAAGTGAGATTAATTTTGTTTCAAGTGAAGCAAATTCAAAATTTGTATCAAAGGAAAAAATGTC
* *** * *
34741 TCAAGCGAGACGAAGTTTGTTTTTTTGAGATATAACAATC
66 TCAAGCGAGACGAAATTTGTTTTTAAAAGAAACAACAATC
* *
34781 TCAAGTGAGATTACTTTTGTTTCAAGTGAAACAAATTCAAAATTTGTATCTCAAAGG-AAAAATG
1 TCAAGTGAGATTAATTTTGTTTCAAGTGAAGCAAATTCAAAATTTGTA--TCAAAGGAAAAAATG
34845 TCTCAAGCGAGACGAAATTTGTTTT
64 TCTCAAGCGAGACGAAATTTGTTTT
34870 GAAATAAATT
Statistics
Matches: 262, Mismatches: 31, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
104 72 0.27
105 65 0.25
106 118 0.45
107 7 0.03
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (105 bp):
TCAAGTGAGATTAATTTTGTTTCAAGTGAAGCAAATTCAAAATTTGTATCAAAGGAAAAAATGTC
TCAAGCGAGACGAAATTTGTTTTTAAAAGAAACAACAATC
Found at i:34934 original size:35 final size:35
Alignment explanation
Indices: 34847--34946 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 35
34837 GAAAAATGTC
* ** * * *
34847 TCAAGCGAGACGAAATTTGTTTTGAAATAAATTGTC
1 TCAAGCGAGACAAAATTTGTTTTTCAA-GAACTGTA
* *
34883 TTAAGTGAGACAAAATTTGTTTTTCAAGAACTGTA
1 TCAAGCGAGACAAAATTTGTTTTTCAAGAACTGTA
*
34918 TCAAGCGAGACAAAATTT-TGTTTCAAGAA
1 TCAAGCGAGACAAAATTTGTTTTTCAAGAA
34947 AACAACATCA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
34 10 0.19
35 21 0.40
36 22 0.42
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (35 bp):
TCAAGCGAGACAAAATTTGTTTTTCAAGAACTGTA
Found at i:35268 original size:16 final size:16
Alignment explanation
Indices: 35247--35291 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
35237 CTCATGTAAC
35247 ATGTATGTATGTTTTG
1 ATGTATGTATGTTTTG
*
35263 ATGTATGTATGTATTG
1 ATGTATGTATGTTTTG
35279 ATGTATGTATGTT
1 ATGTATGTATGTT
35292 GATCTGTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.53
Consensus pattern (16 bp):
ATGTATGTATGTTTTG
Found at i:45439 original size:21 final size:22
Alignment explanation
Indices: 45413--45453 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
45403 TTTATTATAA
45413 TTTAGTT-ATTTAACTTTGTAT
1 TTTAGTTAATTTAACTTTGTAT
*
45434 TTTAGTTAATTTAATTTTGT
1 TTTAGTTAATTTAACTTTGT
45454 GACTATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (22 bp):
TTTAGTTAATTTAACTTTGTAT
Found at i:60040 original size:12 final size:12
Alignment explanation
Indices: 60005--60052 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
59995 TAGGGTTTTG
60005 TAATATTTAATTAA
1 TAATA-TTAA-TAA
60019 TAATATTAATAA
1 TAATATTAATAA
60031 T-ATATATAATAA
1 TAATAT-TAATAA
*
60043 TAATAATAAT
1 TAATATTAAT
60053 TTTAAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 4 0.13
12 15 0.48
13 7 0.23
14 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:60324 original size:76 final size:76
Alignment explanation
Indices: 60193--60607 Score: 713
Period size: 76 Copynumber: 5.5 Consensus size: 76
60183 GATGGAAATG
* * * * * * *
60193 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGATCCGAAGGCTTTAAAAACATCATAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
60258 CCCGAAGGCTT
66 CCCGAAGGCTT
60269 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
60334 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
60345 TTTGGAAACATCATGCACTGTAGGACTTACAGATGGCCCTAAGGCTTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
60410 CCCGAAGGCTT
66 CCCGAAGGCTT
*
60421 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAATGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
60486 CCCGAAGGCTT
66 CCCGAAGGCTT
60497 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
60562 CCCAAAGGCTT
66 CCCGAAGGCTT
* *
60573 TTTGGAAACATCATGCACTGCAGGACTTAAAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
60608 TGGGAAATAG
Statistics
Matches: 323, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 323 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:60913 original size:164 final size:164
Alignment explanation
Indices: 60610--60930 Score: 511
Period size: 165 Copynumber: 2.0 Consensus size: 164
60600 TAAAGATGTG
*
60610 GGAAATAGTTTACTAAGTAAAAAACTAAGGAAATCGTTTCCTTACTTTTCAACAATTTCATTTTA
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTCCTTACTTTTCAACAATTTCATTTTA
** * *
60675 GAAAAGATTGAATGAGAAACTATGGAAATCGTTTTTCTATTATTTTCCAAAATAACATGTTGATT
66 GAAAAGATAAAATGAGAAACTATGGAAATCATTTTTCTATTATTTTCCAAAATAACATGTCGATT
*
60740 GGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
131 AGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
* *
60774 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATTGTTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCGTTTCCTTACTTTTCAACAATTTCATTTT
**
60839 AGAAAAGATAAAATGAGAAACTATGGAAATCA-TTTTCTCATTATTTT-TGAAATAACATGTCGA
65 AGAAAAGATAAAATGAGAAACTATGGAAATCATTTTTCT-ATTATTTTCCAAAATAACATGTCGA
*
60902 TTAGGTAACATGCCCCGATCTCAAGATAA
129 TTAGGTAACATGCCCCAATCTCAAGATAA
60931 TGCTCATTTT
Statistics
Matches: 144, Mismatches: 11, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
164 64 0.44
165 80 0.56
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (164 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTCCTTACTTTTCAACAATTTCATTTTA
GAAAAGATAAAATGAGAAACTATGGAAATCATTTTTCTATTATTTTCCAAAATAACATGTCGATT
AGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
Found at i:61469 original size:22 final size:22
Alignment explanation
Indices: 61444--61503 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
61434 AATAAAGCTT
*
61444 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
61466 TCATCTTTAAAAAGATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
61488 TCATCTTTGAAAAGAG
1 TCATCTTTGAAAAGAG
61504 TGTAGATGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Done.