Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006031.1 Hibiscus syriacus cultivar Beakdansim tig00014236_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: 74676
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1462 original size:20 final size:20
Alignment explanation
Indices: 1409--1470 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1399 GATTCCCCTG
1409 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGG-ATCGGTT-CCC-TCA
** *
1432 AAGGGGAATCGGTTCCCTCA
1 TGGGGGGATCGGTTCCCTCA
*
1452 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1471 TGCACCAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 18 0.56
21 3 0.09
22 7 0.22
23 4 0.12
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGGATCGGTTCCCTCA
Found at i:4780 original size:22 final size:21
Alignment explanation
Indices: 4754--4800 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
4744 AAGGTCAAAA
*
4754 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
4776 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
4796 ATCAA
1 ATCAA
4801 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:9131 original size:58 final size:58
Alignment explanation
Indices: 9060--9176 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
9050 AACGACAACC
* * *
9060 AAAATTTTTAACCAATAAACATCAATTACTATTTAACAAAGTATGGCAGAATGGTACA
1 AAAATTTTCAACCAATAAACATCAATTACTATTTAACAAAGTATGGAAGAATGATACA
9118 AAAATTTTCAACCAATAAACATCAATTACTATTTAACAAAGTATGGAAGAATGATACA
1 AAAATTTTCAACCAATAAACATCAATTACTATTTAACAAAGTATGGAAGAATGATACA
9176 A
1 A
9177 CACCTCCCCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (58 bp):
AAAATTTTCAACCAATAAACATCAATTACTATTTAACAAAGTATGGAAGAATGATACA
Found at i:14438 original size:207 final size:207
Alignment explanation
Indices: 14083--14500 Score: 800
Period size: 207 Copynumber: 2.0 Consensus size: 207
14073 GGAGGTTAGG
14083 TTGGCTGAAATAATCACTGGTAGGGTTTCATCAACTCCCAGATAAGCATATTTCAAATGCGATGA
1 TTGGCTGAAATAATCACTGGTAGGGTTTCATCAACTCCCAGATAAGCATATTTCAAATGCGATGA
*
14148 TAAAGTTTTAAGTTCCAATTTCGGTGCATGTTGTGAAGATGACTCTTGAGACTTAACTTCATCAG
66 TAAAGTTTTAAGTTCCAATTTCGGTGCATGTTATGAAGATGACTCTTGAGACTTAACTTCATCAG
*
14213 AATCTAAAGGTTCAAACTTTATACCTGACCTATGAAGAAATCTCAATTGGTCATTTGTCTTTCCT
131 AATCTAAAGGTTCAAACTTTATACCTGACCTATAAAGAAATCTCAATTGGTCATTTGTCTTTCCT
14278 TCGCATCTTGCC
196 TCGCATCTTGCC
*
14290 TTGGCTGAAATAATCACTGGTAGGGTTTCATCAACTCCTAGATAAGCATATTTCAAATGCGATGA
1 TTGGCTGAAATAATCACTGGTAGGGTTTCATCAACTCCCAGATAAGCATATTTCAAATGCGATGA
*
14355 TAAAGTTTTAAGTTCCAATTTCGGTGCATGTTATGAAGATGACTCTTGAGACTTAACTTCATCAT
66 TAAAGTTTTAAGTTCCAATTTCGGTGCATGTTATGAAGATGACTCTTGAGACTTAACTTCATCAG
14420 AATCTAAAGGTTCAAACTTTATACCTGACCTATAAAGAAATCTCAATTGGTCATTTGTCTTTCCT
131 AATCTAAAGGTTCAAACTTTATACCTGACCTATAAAGAAATCTCAATTGGTCATTTGTCTTTCCT
14485 TCGCATCTTGCC
196 TCGCATCTTGCC
14497 TTGG
1 TTGG
14501 TATCACTTTT
Statistics
Matches: 207, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
207 207 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (207 bp):
TTGGCTGAAATAATCACTGGTAGGGTTTCATCAACTCCCAGATAAGCATATTTCAAATGCGATGA
TAAAGTTTTAAGTTCCAATTTCGGTGCATGTTATGAAGATGACTCTTGAGACTTAACTTCATCAG
AATCTAAAGGTTCAAACTTTATACCTGACCTATAAAGAAATCTCAATTGGTCATTTGTCTTTCCT
TCGCATCTTGCC
Found at i:15740 original size:21 final size:21
Alignment explanation
Indices: 15714--15768 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
15704 AGATGAACTA
15714 TGGCTTTGCAACAGTGTTACT
1 TGGCTTTGCAACAGTGTTACT
* *
15735 TGGCTTTGCAACATTGTTGCT
1 TGGCTTTGCAACAGTGTTACT
*
15756 TGGCTTTGTAACA
1 TGGCTTTGCAACA
15769 AATTTCCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (21 bp):
TGGCTTTGCAACAGTGTTACT
Found at i:26970 original size:21 final size:20
Alignment explanation
Indices: 26944--27016 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 20
26934 AGTTAAGGGT
26944 TTATGTGGTCCTTCGGGATAA
1 TTATGTGGTCCTTCGGGA-AA
26965 TTATGTGG-CACTTCGGTGCAAA
1 TTATGTGGTC-CTTCGG-G-AAA
*
26987 CCTATGTGGTCCTTCGGGACAA
1 -TTATGTGGTCCTTCGGGA-AA
27009 TTATGTGG
1 TTATGTGG
27017 CGCTTTGGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.02
21 22 0.50
22 6 0.14
23 14 0.32
24 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (20 bp):
TTATGTGGTCCTTCGGGAAA
Found at i:28506 original size:16 final size:16
Alignment explanation
Indices: 28469--28506 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28459 AAAATAAAGT
28469 CATAATTGTTTTTAAA
1 CATAATTGTTTTTAAA
*
28485 CTTAATTGTTTTCTAAA
1 CATAATTGTTTT-TAAA
28502 -ATAAT
1 CATAAT
28507 GATTAGACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (16 bp):
CATAATTGTTTTTAAA
Found at i:34290 original size:2 final size:2
Alignment explanation
Indices: 34283--34311 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34273 AAGATATACT
34283 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 T
34312 CATTTTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34493 original size:22 final size:22
Alignment explanation
Indices: 34461--34502 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
34451 CTACATAGTT
*
34461 TTGCACCGAAGTGCCATATAGA
1 TTGCACAGAAGTGCCATATAGA
34483 TTGCACAGAAGTGCCATATA
1 TTGCACAGAAGTGCCATATA
34503 TTTGTCCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (22 bp):
TTGCACAGAAGTGCCATATAGA
Found at i:34641 original size:21 final size:21
Alignment explanation
Indices: 34615--34665 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
34605 CATAGAGTCT
34615 GTTCACATTCACTGGTTCAAA
1 GTTCACATTCACTGGTTCAAA
* *
34636 GTTCACATTCACTTGTTTAAA
1 GTTCACATTCACTGGTTCAAA
34657 GTTCACATT
1 GTTCACATT
34666 TTCATAACCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (21 bp):
GTTCACATTCACTGGTTCAAA
Found at i:35196 original size:22 final size:22
Alignment explanation
Indices: 35168--35241 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
35158 TACACTTTCA
35168 GTATCGATACCCTCCTCAACGG
1 GTATCGATACCCTCCTCAACGG
* *
35190 GTATCGATACTAC-CCTCTTA---
1 GTATCGATAC-CCTCCTC-AACGG
35210 GTATCGATACCCTCCTCAACGG
1 GTATCGATACCCTCCTCAACGG
35232 GTATCGATAC
1 GTATCGATAC
35242 TACCCTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 2 0.05
20 14 0.33
22 24 0.57
23 2 0.05
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.27
Consensus pattern (22 bp):
GTATCGATACCCTCCTCAACGG
Found at i:35199 original size:42 final size:41
Alignment explanation
Indices: 35128--35250 Score: 187
Period size: 42 Copynumber: 3.0 Consensus size: 41
35118 CTCAAAAATG
* * *
35128 GTATCGATACCATCC-C-ACTGGTATCGATACTACACTTTCA
1 GTATCGATACCCTCCTCAACGGGTATCGATACTACCCTTT-A
35168 GTATCGATACCCTCCTCAACGGGTATCGATACTACCCTCTTA
1 GTATCGATACCCTCCTCAACGGGTATCGATACTACCCT-TTA
35210 GTATCGATACCCTCCTCAACGGGTATCGATACTACCCTTTA
1 GTATCGATACCCTCCTCAACGGGTATCGATACTACCCTTTA
35251 AGAAATATGT
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
40 14 0.18
41 4 0.05
42 57 0.74
43 2 0.03
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (41 bp):
GTATCGATACCCTCCTCAACGGGTATCGATACTACCCTTTA
Found at i:35226 original size:20 final size:19
Alignment explanation
Indices: 35167--35228 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
35157 CTACACTTTC
35167 AGTATCGATACCCTCCTCA
1 AGTATCGATACCCTCCTCA
* *
35186 ACGGGTATCGATACTAC-CCTCTT
1 A---GTATCGATAC-CCTCCTC-A
35209 AGTATCGATACCCTCCTCA
1 AGTATCGATACCCTCCTCA
35228 A
1 A
35229 CGGGTATCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
19 3 0.09
20 14 0.42
22 14 0.42
23 2 0.06
ACGTcount: A:0.26, C:0.34, G:0.13, T:0.27
Consensus pattern (19 bp):
AGTATCGATACCCTCCTCA
Found at i:36057 original size:36 final size:36
Alignment explanation
Indices: 36017--36135 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
36007 GGGATGTTAC
* * *
36017 ACAATTTTTTTAAAAACCAATTTTGTCTCGCTTGAG
1 ACAATTTTTCTAAAAACAAATTTTGTCTCACTTGAG
*
36053 ACAATTTTCTCTAAAAACAAAGTTTTTTCTCACTTGAG
1 ACAATTTT-TCTAAAAACAAA-TTTTGTCTCACTTGAG
* * *
36091 ACAATTTCTCTCAAAACAAATTTAGTCTCACTTGAG
1 ACAATTTTTCTAAAAACAAATTTTGTCTCACTTGAG
36127 AC-ATTTTTC
1 ACAATTTTTC
36136 CTTTGTGATG
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
35 6 0.08
36 24 0.33
37 21 0.29
38 21 0.29
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.39
Consensus pattern (36 bp):
ACAATTTTTCTAAAAACAAATTTTGTCTCACTTGAG
Found at i:36092 original size:38 final size:37
Alignment explanation
Indices: 36017--36135 Score: 152
Period size: 37 Copynumber: 3.2 Consensus size: 37
36007 GGGATGTTAC
* * *
36017 ACAATTTT-TTTAAAAACCAATTTTGTCTCGCTTGAG
1 ACAATTTTCTCTAAAAACAAATTTTGTCTCACTTGAG
*
36053 ACAATTTTCTCTAAAAACAAAGTTTTTTCTCACTTGAG
1 ACAATTTTCTCTAAAAACAAA-TTTTGTCTCACTTGAG
* *
36091 ACAA-TTTCTCTCAAAACAAATTTAGTCTCACTTGAG
1 ACAATTTTCTCTAAAAACAAATTTTGTCTCACTTGAG
*
36127 ACATTTTTC
1 ACAATTTTC
36136 CTTTGTGATG
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
36 25 0.35
37 29 0.40
38 18 0.25
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.39
Consensus pattern (37 bp):
ACAATTTTCTCTAAAAACAAATTTTGTCTCACTTGAG
Found at i:36763 original size:137 final size:137
Alignment explanation
Indices: 36517--37188 Score: 840
Period size: 137 Copynumber: 4.9 Consensus size: 137
36507 CTTGAAATAA
*
36517 ATTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCGTGTCATCCACTGACCAGATCT
1 ATTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* * * ** * ** * *
36582 CATCATCATGTAGGAGCCGTGTCATCCTTAGATATTCATACTTCCTCATCGTGTAAGAACTATGT
66 CCTCATCACGTAGGAGCCGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
*
36647 TATCTCT
131 TATCTCC
* * * **
36654 ATTATCCCTAAAGATTGTCAAACGTCCTCATCACGTAGGAACTATGTCATCCACCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* * * *
36719 CCTCATCACGTAGAAGCCGCATCATCCTTAGATAGCTAGACTTCCTCATCACGTAGGAACCATGT
66 CCTCATCACGTAGGAGCCGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
36784 TATCTCC
131 TATCTCC
* * **
36791 ATTATCCCTAAAGATGGTCAAACATCCTCATCACGTAAGAATTGTGTCATCCACCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* ** * * ** *
36856 CCTCATCACGTAGGAGTCGTATCATCCTTAGATAGCCAGACTTCCTCGTTGCGTAGGAACCGTGT
66 CCTCATCACGTAGGAGCCGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
36921 TATCTCC
131 TATCTCC
* * *
36928 ATTATCCCTAAAGATAGCCAGACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATATCT
1 ATTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* ** * ** **
36993 CCTCATCATGTAGGAGCTACGTCATCCTTAGATAACCAGACTTTCTCATCATATAGGAACCGCGT
66 CCTCATCACGTAGGAGCCGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
*
37058 TATCTCT
131 TATCTCC
* * * * **
37065 ATTATCCCTAAAGATGACCAGACGTCATCATCACGTAGGAACAATGTCATCCACCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* * * * *
37130 CCTCATTACGTAAGAGCAGCGTCATCTTTAGATAACCAGATTTCCTCATCACGTAGGAA
66 CCTCATCACGTAGGAGCCGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAA
37189 TTCGTGTTGT
Statistics
Matches: 463, Mismatches: 72, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
137 463 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (137 bp):
ATTATCCCTAAAGATGGCCAAACATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
CCTCATCACGTAGGAGCCGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAACCATGT
TATCTCC
Found at i:37402 original size:3 final size:3
Alignment explanation
Indices: 37394--37445 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
37384 TCTAATTAAT
37394 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
37442 TTA T
1 TTA T
37446 GGTTTACATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41064 original size:5 final size:5
Alignment explanation
Indices: 41051--41135 Score: 52
Period size: 5 Copynumber: 16.4 Consensus size: 5
41041 GTTAAAAGAG
* *
41051 AAAAT AAAAC AAAAC AAAAT AAAAT AAAAT AAAA- AAGAAGT GGGAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AA-T ---AAAAT
*
41100 AAAAT -AAA- AAAAT AAAA- AAAATGT TAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAA--T AAAAT AAAAT AA
41136 TAAATAATAG
Statistics
Matches: 65, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
4 12 0.18
5 45 0.69
7 3 0.05
8 1 0.02
9 2 0.03
10 2 0.03
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:41132 original size:21 final size:21
Alignment explanation
Indices: 41104--41160 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
41094 GAAAATAAAA
41104 TAAA-AAAATAAAAAAAAT-G
1 TAAATAAAATAAAAAAAATAG
*
41123 TTAAATAAAATAATAAATAATAG
1 -TAAATAAAATAA-AAAAAATAG
41146 T-AATAAAGATAAAAA
1 TAAATAAA-ATAAAAA
41161 GGGTTTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.12
21 16 0.50
22 11 0.34
23 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (21 bp):
TAAATAAAATAAAAAAAATAG
Found at i:41149 original size:13 final size:12
Alignment explanation
Indices: 41101--41152 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
41091 TGGGAAAATA
*
41101 AAATAAAAAAAT
1 AAATAAAATAAT
* **
41113 AAAAAAAATGTT
1 AAATAAAATAAT
41125 AAATAAAATAAT
1 AAATAAAATAAT
*
41137 AAATAATAGTAAT
1 AAATAA-AATAAT
41150 AAA
1 AAA
41153 GATAAAAAGG
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
12 23 0.74
13 8 0.26
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:41191 original size:18 final size:18
Alignment explanation
Indices: 41170--41212 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
41160 AGGGTTTTTA
41170 AAATAAAA-AATAATAATT
1 AAATAAAAGAA-AATAATT
41188 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
41206 AAATAAA
1 AAATAAA
41213 TAATCTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:42844 original size:123 final size:123
Alignment explanation
Indices: 42630--42864 Score: 292
Period size: 123 Copynumber: 1.9 Consensus size: 123
42620 ATTGTAGGTG
* * *
42630 GCTCCTTCGTTGTGAAGCTGAGCTTTAAATTGGATATCCTTCATTGTGAACTTGAAATCCAATCT
1 GCTCATTCGCTGTGAAGCTGAGCTTTAAATTGGATATCCTTCATTGTGAACTTCAAATCCAATCT
* * *
42695 TGTAAATTGAATCGCTTTGAGATTAATATATTTCGC-TGTGAAGTTGAAATTATGGATA
66 TGAAAATTGAATCGCTTCGAGATTAATATACTTC-CATGTGAAGTTGAAATTATGGATA
* * * * * * *
42753 GCTCATTCGCTGTGAAGTTGAGTTTTGAATTGGATGTCCTTCGTTGTGAAGTTCAAATCTAATCT
1 GCTCATTCGCTGTGAAGCTGAGCTTTAAATTGGATATCCTTCATTGTGAACTTCAAATCCAATCT
* * * * *
42818 TGAAAATTGCATTGGTTCGAGTTTAATATCCTTCCATGTGAAGTTGA
66 TGAAAATTGAATCGCTTCGAGATTAATATACTTCCATGTGAAGTTGA
42865 CATTGACTCT
Statistics
Matches: 93, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
122 1 0.01
123 92 0.99
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (123 bp):
GCTCATTCGCTGTGAAGCTGAGCTTTAAATTGGATATCCTTCATTGTGAACTTCAAATCCAATCT
TGAAAATTGAATCGCTTCGAGATTAATATACTTCCATGTGAAGTTGAAATTATGGATA
Found at i:50310 original size:11 final size:10
Alignment explanation
Indices: 50294--50367 Score: 58
Period size: 10 Copynumber: 6.8 Consensus size: 10
50284 ATTAAATTTC
50294 ATAAAAGAAAA
1 ATAAAA-AAAA
50305 ATAAAAAAAA
1 ATAAAAAAAA
*
50315 TATTAAAAAATA
1 -A-TAAAAAAAA
*
50327 TTAAAAGAGAAA
1 ATAAAA-A-AAA
50339 ATAAAAATAAA
1 ATAAAAA-AAA
* *
50350 ACAAAATAAA
1 ATAAAAAAAA
50360 ATAAAAAA
1 ATAAAAAA
50368 TAAGTGGAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
10 18 0.36
11 17 0.34
12 15 0.30
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (10 bp):
ATAAAAAAAA
Found at i:50366 original size:16 final size:16
Alignment explanation
Indices: 50336--50365 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50326 ATTAAAAGAG
50336 AAAATAAAAATAAAAC
1 AAAATAAAAATAAAAC
50352 AAAAT-AAAATAAAA
1 AAAATAAAAATAAAA
50366 AATAAGTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAATAAAAATAAAAC
Found at i:50369 original size:12 final size:12
Alignment explanation
Indices: 50302--50417 Score: 50
Period size: 12 Copynumber: 10.2 Consensus size: 12
50292 TCATAAAAGA
50302 AAAATAAAAAA-
1 AAAATAAAAAAT
*
50313 AATATTAAAAAAT
1 AA-AATAAAAAAT
* * *
50326 --ATTAAAAGAG
1 AAAATAAAAAAT
50336 AAAAT-AAAAAT
1 AAAATAAAAAAT
*
50347 -AAA-ACAAAAT
1 AAAATAAAAAAT
50357 AAAATAAAAAAT
1 AAAATAAAAAAT
* *
50369 -AAGTGGAAAAAT
1 AAAAT-AAAAAAT
*
50381 AAAA-ATAAAAT
1 AAAATAAAAAAT
* **
50392 AAAGTATTAAAT
1 AAAATAAAAAAT
*
50404 AAAATAATAAAT
1 AAAATAAAAAAT
50416 AA
1 AA
50418 CAGTAGTAAA
Statistics
Matches: 78, Mismatches: 17, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
10 16 0.21
11 20 0.26
12 40 0.51
13 2 0.03
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:50412 original size:25 final size:24
Alignment explanation
Indices: 50353--50427 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 24
50343 AAATAAAACA
*
50353 AAATAAAATAA-AAAAT-AAGTGGAA
1 AAATAAAATAATAAAATAAAGT--AT
50377 AAAT-AAA-AATAAAATAAAGTATT
1 AAATAAAATAATAAAATAAAGTA-T
50400 AAATAAAATAAT-AAATAACAGTAGT
1 AAATAAAATAATAAAATAA-AGTA-T
50425 AAA
1 AAA
50428 GATAAAAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
22 3 0.07
23 12 0.28
24 17 0.40
25 11 0.26
ACGTcount: A:0.69, C:0.01, G:0.08, T:0.21
Consensus pattern (24 bp):
AAATAAAATAATAAAATAAAGTAT
Found at i:50479 original size:18 final size:18
Alignment explanation
Indices: 50458--50500 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
50448 GTTGTTTTTA
50458 AAATAAAA-GATAAGAATT
1 AAATAAAAGGA-AAGAATT
*
50476 AAATAAAAGGAAATAATT
1 AAATAAAAGGAAAGAATT
50494 AAATAAA
1 AAATAAA
50501 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGGAAAGAATT
Found at i:52653 original size:22 final size:22
Alignment explanation
Indices: 52610--52653 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
52600 GAACGCGTTC
* *
52610 GGATCGTTTCAAAATTGTGATT
1 GGATCGTTTCAAAATCGCGATT
52632 GGATCGTTTCAAAATCGCGATT
1 GGATCGTTTCAAAATCGCGATT
52654 CGGTATATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (22 bp):
GGATCGTTTCAAAATCGCGATT
Found at i:68395 original size:23 final size:22
Alignment explanation
Indices: 68344--68394 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
68334 AAAATATTTC
68344 TAAAAAATGAAAATAAAAATAA
1 TAAAAAATGAAAATAAAAATAA
* *
68366 TTGAAAAATGAAAATAAAAA-CA
1 -TAAAAAATGAAAATAAAAATAA
68388 TAAAAAA
1 TAAAAAA
68395 ATGTTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.24
22 1 0.04
23 18 0.72
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (22 bp):
TAAAAAATGAAAATAAAAATAA
Done.