Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002914.1 Hibiscus syriacus cultivar Beakdansim tig00006024_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: 180357
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:447 original size:24 final size:24
Alignment explanation
Indices: 415--465 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
405 AACTTGGCTG
*
415 CACATAAACTCCAGTCATTGCCTA
1 CACATAAACTCCAGCCATTGCCTA
*
439 CACATAAACTCCCGCCATTGCCTA
1 CACATAAACTCCAGCCATTGCCTA
463 CAC
1 CAC
466 CTTATGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.39, G:0.08, T:0.22
Consensus pattern (24 bp):
CACATAAACTCCAGCCATTGCCTA
Found at i:11271 original size:15 final size:15
Alignment explanation
Indices: 11251--11282 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
11241 ATGTCATTGG
11251 GATTTTGACATTCTT
1 GATTTTGACATTCTT
11266 GATTTTGACATTCTT
1 GATTTTGACATTCTT
11281 GA
1 GA
11283 AAATACATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (15 bp):
GATTTTGACATTCTT
Found at i:27730 original size:3 final size:3
Alignment explanation
Indices: 27717--27785 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
27707 TATATATATT
* * *
27717 TAA TAAA TAA TAA TAA TAA TAA T-A TAT TAA TAA TAA TAT TTA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
27762 TAA TAA TAA TAA TTT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
27786 CAAATGAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:27741 original size:26 final size:26
Alignment explanation
Indices: 27710--27785 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
27700 ATATATATAT
27710 ATATATTTAATAAATAATAATAATAATA
1 ATATA-TTAAT-AATAATAATAATAATA
* *
27738 ATATATTAATAATAATATTTATAATA
1 ATATATTAATAATAATAATAATAATA
**
27764 ATA-A-TAATAATTTTAATAATAA
1 ATATATTAATAATAATAATAATAA
27786 CAAATGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
24 14 0.33
25 1 0.02
26 17 0.40
27 5 0.12
28 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATATTAATAATAATAATAATAATA
Found at i:28025 original size:76 final size:76
Alignment explanation
Indices: 27933--28366 Score: 814
Period size: 76 Copynumber: 5.7 Consensus size: 76
27923 GAGGTCTTAA
27933 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
27998 AGGCTTTTTGG
66 AGGCTTTTTGG
28009 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
28074 AGGCTTTTTTGG
66 AGGC-TTTTTGG
28086 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
28151 AGGCTTTTTGG
66 AGGCTTTTTGG
*
28162 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
28227 AGGCTTTTTGG
66 AGGCTTTTTGG
28238 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
28303 AGGATTTTTGG
66 AGGCTTTTTGG
* * *
28314 AAACATCATGCACTGCAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
28367 TGCACTGAAG
Statistics
Matches: 351, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
76 275 0.78
77 76 0.22
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:28211 original size:153 final size:152
Alignment explanation
Indices: 27933--28366 Score: 823
Period size: 153 Copynumber: 2.8 Consensus size: 152
27923 GAGGTCTTAA
27933 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
27998 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAA
28063 AAAGCTCCCGAAGGCTTTTTTGG
131 AAAGCTCCCGAAGGC-TTTTTGG
28086 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
28151 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAA
28216 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
28238 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* * *
28303 AGGATTTTTGGAAACATCATGCACTGCAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCA
28367 TGCACTGAAG
Statistics
Matches: 277, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
152 133 0.48
153 144 0.52
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (152 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:28364 original size:45 final size:45
Alignment explanation
Indices: 28298--28594 Score: 443
Period size: 45 Copynumber: 6.5 Consensus size: 45
28288 TCAAAAAGCT
* *
28298 CCCGAAGGATTTTTGGAAACATCATGCACTGCAGGGCTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
28345 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * * *
28390 CCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAA-GGCTTATAGATGA
1 CCCGAAGGTTTTGAAAACATC---ATGC-ACTGAAGGGCTTACAGATGA
*
28438 CCCGTAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
28483 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTATAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
28528 CCCGTAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
28573 CCCGTAGGTTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
28595 AAAAGCTCCC
Statistics
Matches: 230, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
44 4 0.02
45 179 0.78
47 8 0.03
48 35 0.15
49 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:28464 original size:93 final size:93
Alignment explanation
Indices: 28332--28612 Score: 471
Period size: 93 Copynumber: 3.1 Consensus size: 93
28322 TGCACTGCAG
* *
28332 GGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
1 GGCTTATAGATGACCCGTAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
28397 GTTTTGAAAACATCAAAAAGCTCCCGAA
66 GTTTTGAAAACATCAAAAAGCTCCCGAA
28425 GGCTTATAGATGACCCGTAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
1 GGCTTATAGATGACCCGTAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
* * *
28490 GTTTTGAAAACATC---ATGC-ACTGAA
66 GTTTTGAAAACATCAAAAAGCTCCCGAA
*
28514 GGGCTTATAGATGACCCGTAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGTA
1 -GGCTTATAGATGACCCGTAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAA
28579 GGTTTTGAAAACATCAAAAAGCTCCCGAA
65 GGTTTTGAAAACATCAAAAAGCTCCCGAA
28608 GGCTT
1 GGCTT
28613 TTTTGGAAAC
Statistics
Matches: 174, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
89 4 0.02
90 81 0.47
93 85 0.49
94 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (93 bp):
GGCTTATAGATGACCCGTAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
GTTTTGAAAACATCAAAAAGCTCCCGAA
Found at i:28715 original size:36 final size:36
Alignment explanation
Indices: 28675--28808 Score: 124
Period size: 36 Copynumber: 3.7 Consensus size: 36
28665 AGTGAAACTG
*
28675 TCTCAAGCGAGACAACTTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
* * * * * ** **
28711 TCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTG
1 TCTCAAGCGAGACAAATT-TTGTTTTAAGAAAAACAA
* *
28748 TCTCGAGCGAGACAAAGTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
* *
28784 TCTCAAGTGAGATAAATTGTTGTTT
1 TCTCAAGCGAGACAAATT-TTGTTT
28809 CGAGGGAAAA
Statistics
Matches: 71, Mismatches: 25, Indels: 3
0.72 0.25 0.03
Matches are distributed among these distances:
36 40 0.56
37 31 0.44
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
Found at i:28742 original size:73 final size:73
Alignment explanation
Indices: 28660--28802 Score: 250
Period size: 73 Copynumber: 2.0 Consensus size: 73
28650 AAAATTTATG
* **
28660 TTTCGAGTGAAACTGTCTCAAGCGAGACAACTTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
1 TTTCAAGTGAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
28725 AATTGCTA
66 AATTGCTA
*
28733 TTTCAAGTGAAACTGTCTCGAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
1 TTTCAAGTGAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
28798 AATTG
66 AATTG
28803 TTGTTTCGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (73 bp):
TTTCAAGTGAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
AATTGCTA
Found at i:29101 original size:166 final size:165
Alignment explanation
Indices: 28816--29137 Score: 531
Period size: 166 Copynumber: 1.9 Consensus size: 165
28806 TTTCGAGGGA
*
28816 AAATGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTCAG
1 AAATGTTTAATAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTCAG
** * *
28881 AAAAGATTGAATGAGAAACTTTGGAAATCGTTTTCTCATTATGTTTCAAAATAACCTGTTGATTG
66 AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTCAAAATAACATGTTGATTG
*
28946 GGTAACATGCCCCAATCTCCAGATAAGGTTGTTGG
131 GGTAACATGCCCCAATCTCAAGATAAGGTTGTTGG
28981 AAATAGTTTAATAAGTAAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT-
1 AAAT-GTTTAATAAGT-AAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
**
29045 AGAAAAGATAAAATGAGAAACTATGGAAATCG-TTTCTCATTATGTTTTTGAAATAACATGTTGA
64 AGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATG-TTTCAAAATAACATGTTGA
29109 TTGGGTAACATGCCCCAATCTCAAGATAA
128 TTGGGTAACATGCCCCAATCTCAAGATAA
29138 TGCTCATTCT
Statistics
Matches: 146, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
165 16 0.11
166 83 0.57
167 47 0.32
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (165 bp):
AAATGTTTAATAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTCAG
AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTCAAAATAACATGTTGATTG
GGTAACATGCCCCAATCTCAAGATAAGGTTGTTGG
Found at i:30154 original size:54 final size:54
Alignment explanation
Indices: 30072--30175 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
30062 TAACCGGTTC
***
30072 GTAAAACATTTGACATTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTTT
1 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTTT
**
30126 GTAAAACATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGCTCAGAT
1 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
30176 TTTTCAATCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.39
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATGTTT
Found at i:39124 original size:13 final size:13
Alignment explanation
Indices: 39108--39156 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
39098 TTAATTCTTG
39108 AATATAATAAATA
1 AATATAATAAATA
*
39121 AATAAAATAAA-A
1 AATATAATAAATA
*
39133 AATAATAATATATA
1 AAT-ATAATAAATA
*
39147 AAAATAATAA
1 AATATAATAA
39157 GTAATAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 4 0.14
13 22 0.76
14 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AATATAATAAATA
Found at i:39135 original size:16 final size:15
Alignment explanation
Indices: 39111--39198 Score: 63
Period size: 16 Copynumber: 5.7 Consensus size: 15
39101 ATTCTTGAAT
*
39111 ATAATAAATAAATAAA
1 ATAAAAAAT-AATAAA
*
39127 ATAAAAAATAATAAT
1 ATAAAAAATAATAAA
39142 ATATAAAAATAATAAGTA
1 ATA-AAAAATAATAA--A
*
39160 ATAAAAAAT-TTAAA
1 ATAAAAAATAATAAA
* *
39174 AGAAAAGAATTA-AAA
1 ATAAAA-AATAATAAA
*
39189 ATTAAAAATA
1 ATAAAAAATA
39199 TGAATTTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
14 9 0.16
15 18 0.31
16 22 0.38
17 6 0.10
18 3 0.05
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
ATAAAAAATAATAAA
Found at i:39150 original size:23 final size:23
Alignment explanation
Indices: 39111--39168 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
39101 ATTCTTGAAT
39111 ATAATAAATAAATAAAATAAAAA
1 ATAATAAATAAATAAAATAAAAA
* *
39134 ATAAT-AATATATAAAAATAATAA
1 ATAATAAATAAAT-AAAATAAAAA
*
39157 GTAATAAA-AAAT
1 ATAATAAATAAAT
39169 TTAAAAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 6 0.21
23 21 0.72
24 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (23 bp):
ATAATAAATAAATAAAATAAAAA
Found at i:41826 original size:2 final size:2
Alignment explanation
Indices: 41819--41844 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41809 TAATTTTGTA
41819 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
41845 TTAATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41873 original size:29 final size:29
Alignment explanation
Indices: 41839--41918 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 29
41829 ATATATATAT
41839 ATATATTTAATAAATAATAATAATAATAATA
1 ATATA-TTAAT-AATAATAATAATAATAATA
41870 ATATATTAATAATAATATTTATAATAATAATA
1 ATATATTAATAATAATA---ATAATAATAATA
**
41902 ATA-ATTTTTAATAATAA
1 ATATATTAATAATAATAA
41919 CAAATGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
28 1 0.02
29 7 0.16
30 5 0.11
31 16 0.36
32 15 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATATTAATAATAATAATAATAATAATA
Found at i:41918 original size:3 final size:3
Alignment explanation
Indices: 41846--41906 Score: 79
Period size: 3 Copynumber: 20.3 Consensus size: 3
41836 TATATATATT
* * *
41846 TAA TAAA TAA TAA TAA TAA TAA TAA T-A TAT TAA TAA TAA TAT TTA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41891 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
41907 TTTTAATAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:42716 original size:16 final size:17
Alignment explanation
Indices: 42695--42729 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
42685 TTACTATTCA
42695 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
42711 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
42728 CG
1 CG
42730 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:49739 original size:20 final size:22
Alignment explanation
Indices: 49714--49756 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
49704 ATATTATATA
49714 ATAATA-ACAACAAA-ATAAAT
1 ATAATAGACAACAAAGATAAAT
*
49734 ATAATAGATAACAAAGATAAAT
1 ATAATAGACAACAAAGATAAAT
49756 A
1 A
49757 AAAGTTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 7 0.35
22 7 0.35
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (22 bp):
ATAATAGACAACAAAGATAAAT
Found at i:50919 original size:3 final size:3
Alignment explanation
Indices: 50911--50986 Score: 109
Period size: 3 Copynumber: 24.3 Consensus size: 3
50901 CTGCACAAAT
50911 ATA ATA ATA ATA ATTA ATTA ATA ATA AGTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA A-TA A-TA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
50959 ATA ATA ATA ATA ATAA ATA AT- ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA A
50987 AATGTTTTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.03
3 54 0.78
4 13 0.19
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:51582 original size:84 final size:84
Alignment explanation
Indices: 51494--51703 Score: 251
Period size: 84 Copynumber: 2.5 Consensus size: 84
51484 AAATTTGATT
* * * * *
51494 TGCCTCTGAGTTGAATGTAATCGAACTCGAGGGTCTTTGGTTGGCAGATAGCCCTTCTCGCCTTA
1 TGCCTCTGAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTA
* *
51559 AGCTATGCTGCAAAAGATG
66 AGCTATACTGCAAAAGATA
* * * * * *
51578 TGCCTTTGAGCTGAGCGTAGTCGAACTCTAAGGTCTTTGGTTGGTAGATAACCCTTCTAGACTTA
1 TGCCTCTGAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTA
* *
51643 AGTTATACTGCAAATGATA
66 AGCTATACTGCAAAAGATA
*
51662 TGCC-CTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGT
1 TGCCTCT-G-AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGT
51704 AGATAGCCTT
Statistics
Matches: 103, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
83 1 0.01
84 74 0.72
85 28 0.27
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (84 bp):
TGCCTCTGAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTA
AGCTATACTGCAAAAGATA
Found at i:51979 original size:106 final size:106
Alignment explanation
Indices: 51785--52739 Score: 1608
Period size: 106 Copynumber: 9.0 Consensus size: 106
51775 TCCTCCGTCG
* *
51785 TGAAGTTGA-AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
51849 CTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
51890 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
51955 CTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
51996 T-AAAGTTGAGAGGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACCTACGTTG
1 TGAAA-TTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
* *
52060 CCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
52102 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
52167 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
52208 TAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
52273 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
52314 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
52379 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * * * *
52420 TGAAATTGAAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
52485 TTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
52526 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
52591 CAGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * * *
52632 TGAATATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACATGCGTTG
1 TGAA-ATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
52697 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
52739 T
1 T
52740 CGAGCAATAT
Statistics
Matches: 808, Mismatches: 38, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
105 10 0.01
106 696 0.86
107 102 0.13
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:57650 original size:3 final size:3
Alignment explanation
Indices: 57642--57724 Score: 114
Period size: 3 Copynumber: 26.3 Consensus size: 3
57632 CTGCACAAAT
57642 ATA ATA ATA ATA ATTA ATTA ATA ATA AGTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA A-TA A-TA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
57690 ATA ATA ATA ATA ATAA ATAA ATA ATA AT- ATA ATA A
1 ATA ATA ATA ATA AT-A AT-A ATA ATA ATA ATA ATA A
57725 AATGTTTTTT
Statistics
Matches: 76, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.03
3 57 0.75
4 17 0.22
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:61426 original size:59 final size:59
Alignment explanation
Indices: 61215--61402 Score: 317
Period size: 59 Copynumber: 3.2 Consensus size: 59
61205 GCTATTTAAT
*
61215 TTAC-AAATGATTCTTCGATTATAGGGTGTTA-TTTTTTTGATCTCATAACTATTGAAAG
1 TTACGAAATGATTCTTCGACTATAGGGTGTTATTTTTTTTG-TCTCATAACTATTGAAAG
* *
61273 TTACGAAATAATTCTTCGACTATAGGGTGTTATTTTTTTGGTCTCATAACTATTGAAAG
1 TTACGAAATGATTCTTCGACTATAGGGTGTTATTTTTTTTGTCTCATAACTATTGAAAG
*
61332 TTACGAAATGATTCTTCGACTATAGGATGTTATTTTTTTTGTCTCATAACTATTGAAAG
1 TTACGAAATGATTCTTCGACTATAGGGTGTTATTTTTTTTGTCTCATAACTATTGAAAG
61391 TTACGAAATGAT
1 TTACGAAATGAT
61403 CCCTGGATTA
Statistics
Matches: 122, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
58 4 0.03
59 111 0.91
60 7 0.06
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (59 bp):
TTACGAAATGATTCTTCGACTATAGGGTGTTATTTTTTTTGTCTCATAACTATTGAAAG
Found at i:62408 original size:16 final size:17
Alignment explanation
Indices: 62389--62435 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
62379 GATTATGACA
62389 TTAATAGAT-TTTAAAT
1 TTAATAGATATTTAAAT
* *
62405 TTAATATATATTTATAT
1 TTAATAGATATTTAAAT
*
62422 TT-ATATATATTTAA
1 TTAATAGATATTTAA
62436 CTGCATATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAATAGATATTTAAAT
Found at i:77322 original size:59 final size:61
Alignment explanation
Indices: 77236--77397 Score: 157
Period size: 61 Copynumber: 2.7 Consensus size: 61
77226 TCTTATATTG
* * * * *
77236 ATCCTTAAACTTTTAAATATTATAATTTCATACCTAAACTATAAC-TTTATTT-TAAATTA
1 ATCCTTAAACTTTTAAAAAATACAATTTCATACCCAAAATATAACTTTTATTTCTAAATTA
* * * * *
77295 ATCTTTAAACTTTTAAAAAATCCAATTTCATCCCCAAAATATGACTTTTTTTTCTAAATTA
1 ATCCTTAAACTTTTAAAAAATACAATTTCATACCCAAAATATAACTTTTATTTCTAAATTA
* ** ** * *
77356 GTCCTTAAACTTTTGTATCATTCAATTTCATCCCCAAAATAT
1 ATCCTTAAACTTTTAAAAAATACAATTTCATACCCAAAATAT
77398 CCAAATATGT
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
59 36 0.43
60 6 0.07
61 42 0.50
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (61 bp):
ATCCTTAAACTTTTAAAAAATACAATTTCATACCCAAAATATAACTTTTATTTCTAAATTA
Found at i:81678 original size:16 final size:15
Alignment explanation
Indices: 81659--81688 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
81649 TAATTTTATA
81659 ATTTATGTTGTTTAAT
1 ATTTATGTT-TTTAAT
81675 ATTTATGTTTTTAA
1 ATTTATGTTTTTAA
81689 GTCAGCAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (15 bp):
ATTTATGTTTTTAAT
Found at i:86276 original size:2 final size:2
Alignment explanation
Indices: 86269--86314 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
86259 GATTGAATCA
86269 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
86311 AT AT
1 AT AT
86315 GATTGAATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87604 original size:14 final size:14
Alignment explanation
Indices: 87585--87619 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
87575 CGCTGGGCAT
87585 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
87599 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
87613 CCGAGGC
1 CCGAGGC
87620 TATCTGAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.40, G:0.34, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:87714 original size:29 final size:29
Alignment explanation
Indices: 87672--87805 Score: 205
Period size: 29 Copynumber: 4.6 Consensus size: 29
87662 AGAGCAGGAG
87672 GGAGTGCATGGCGACCTACAAGGTCGCCA
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
*
87701 GGAGTGCATGGCGACCCACAAGGTCGCCA
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
* * *
87730 GGAGTGCATGACGACCCACAAGGTCGCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
*
87759 GGAGTGCATGGCGACCTACAAGGTCGCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
* *
87788 GGAGGGCATGACGACCTA
1 GGAGTGCATGGCGACCTA
87806 TGCTTGGGGA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 98 1.00
ACGTcount: A:0.24, C:0.30, G:0.34, T:0.12
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAGGTCGCCA
Found at i:90278 original size:30 final size:31
Alignment explanation
Indices: 90244--90306 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
90234 TTAGATGATG
*
90244 AATTTAAATACATAAAATTTT-AGGAGAACA
1 AATTTAAATACATAAAATTTTAAGGAAAACA
*
90274 AATTTAAATGCATAAAATTTTAAGGAAAACA
1 AATTTAAATACATAAAATTTTAAGGAAAACA
90305 AA
1 AA
90307 AAATATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.29
Consensus pattern (31 bp):
AATTTAAATACATAAAATTTTAAGGAAAACA
Found at i:96515 original size:53 final size:53
Alignment explanation
Indices: 96402--96871 Score: 597
Period size: 53 Copynumber: 8.7 Consensus size: 53
96392 TGGGTTCGCT
* * * * ** *
96402 CCCTATTTCTTCAGAGGGTATAAGACTTGA-ATCATCTTCAACAAACTTGTATGCC
1 CCCTATTTCTTCAGAGAGTATAAGAC-TCACA--ATCTTCATCAATCGCGTCTGCC
*
96457 CCCTATTTCTTCAGAGAGTATAAGAAC-CATAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCACAATCTTCATCAATCGCGTCTGCC
* * * * *
96510 CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATTGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGCGTCTGCC
* *
96565 CCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCC
* * **
96618 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTACGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGCGTCTGCC
* *
96673 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCC
96726 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCC
*
96779 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCA-CGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTT-CATCAATCGCGTCTGCC
*
96834 CCCTATTTCTTCA-AGGAGTATAAGACCCACAATCTTCA
1 CCCTATTTCTTCAGA-GAGTATAAGACTCACAATCTTCA
96872 ACAAATGGGT
Statistics
Matches: 370, Mismatches: 34, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
52 4 0.01
53 197 0.53
54 2 0.01
55 163 0.44
56 4 0.01
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.30
Consensus pattern (53 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCGTCTGCC
Found at i:96908 original size:108 final size:108
Alignment explanation
Indices: 96402--96896 Score: 659
Period size: 108 Copynumber: 4.6 Consensus size: 108
96392 TGGGTTCGCT
* * * * *
96402 CCCTATTTCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACT-TGTATGCCCCCTATTT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAACGAA-TGCGTCTGCCCCCTATTT
* *
96465 CTTCAGAGAGTATAAGAACCATAATCTTCATCAATCGCGTCTGCC
64 CTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
* * * *
96510 CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGAATGCGTCTGCCCCCTATTTCT
96575 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
* *
96618 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTACGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGAATGCGTCTGCCCCCTATTTCT
*
96683 TCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCC
66 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
*
96726 CCCTATTTCTTCAGAGAGTATAAGACTC--ACAATCTTCATC-AATCGCGTCTGCCCCCTATTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGAAT-GCGTCTGCCCCCTATTTC
* *
96788 TTCAGAGAGTATAAGACTCGAACAATCTTCCA-CGATCGCGTCTGCC
65 TTCAGAGAGTATAAGAC-C-CACAATCTT-CATCAATCGCGTCTGCC
* * * *
96834 CCCTATTTCTTCA-AGGAGTATAAGAC-C-CACAATCTTCAACAAATGGGT-TCGCTCCCTATTT
1 CCCTATTTCTTCAGA-GAGTATAAGACTCGAACAATCTTCAACGAATGCGTCT-GCCCCCTATTT
96895 CT
64 CT
96897 CTAGGGAGTA
Statistics
Matches: 355, Mismatches: 22, Indels: 20
0.89 0.06 0.05
Matches are distributed among these distances:
105 2 0.01
106 45 0.13
107 6 0.02
108 297 0.84
109 5 0.01
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.30
Consensus pattern (108 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGAATGCGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
Found at i:96908 original size:161 final size:161
Alignment explanation
Indices: 96378--96896 Score: 658
Period size: 161 Copynumber: 3.2 Consensus size: 161
96368 GAATTCAATA
* * * *
96378 AATCTTCAGAAAAATGGGT-TCGCTCCCTATTTCTTCAGAGGGTATAAGACTTGA-ATCATCTTC
1 AATCTTCA-ACAAATGGGTCT-GCCCCCTATTTCTTCAGAGAGTATAAGAC-TCACA--ATCTTC
* * ** * * *
96441 AACAAACTTGTATGCCCCCTATTTCTTCAGAGAGTATAAGAAC-C--ATAATCTT-CATCAATCG
61 ATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCCA-CGATCG
*
96502 CGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
124 CGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CAC
* * * * * *
96542 GATCTTCAACGATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAA
1 AATCTTCAACAAATGGGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAA
* **
96607 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTACGTCTGC
66 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGC
96672 CCCCTATTTCTTCAGAGAGTATAAGACCCAC
131 CCCCTATTTCTTCAGAGAGTATAAGACCCAC
* * *
96703 AATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAA
1 AATCTTCAACAAATGGGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAA
96768 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGC
66 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGC
96833 CCCCTATTTCTTCA-AGGAGTATAAGACCCAC
131 CCCCTATTTCTTCAGA-GAGTATAAGACCCAC
*
96864 AATCTTCAACAAATGGGT-TCGCTCCCTATTTCT
1 AATCTTCAACAAATGGGTCT-GCCCCCTATTTCT
96897 CTAGGGAGTA
Statistics
Matches: 313, Mismatches: 34, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
160 4 0.01
161 221 0.71
162 2 0.01
163 77 0.25
164 9 0.03
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (161 bp):
AATCTTCAACAAATGGGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAA
TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGC
CCCCTATTTCTTCAGAGAGTATAAGACCCAC
Found at i:96970 original size:161 final size:159
Alignment explanation
Indices: 96633--97113 Score: 397
Period size: 161 Copynumber: 3.0 Consensus size: 159
96623 TTTCTTCAGA
* **
96633 GAGTATAAGACTCGAACAATCTTCAACGATTACGTCTGCCCCCTATTTCTTC-AGAGAGTATAAG
1 GAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGCCCCCTATTTCTTCAAG-GAGTATAAG
* * * * *
96697 ACCCACAATCTTCATCAATTGCG-TCTGCCCCCTATTTCTTCAGAGAGTATA-AGAC-T-CACAA
65 ACCCACAATCTTCA-CAAATGGGTTC-GCTCCCTATTTCTT-AGGGAGTATAGA-ACTTGAAC-A
* * * * * *
96758 TCTTCATCAATCGCG-TCTGCCCCCTATTTC-TTCAG
125 TC-TCTTCAAACGGGTTC-GCTCCCTCTTTCTTTAAG
96793 AGAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGCCCCCTATTTCTTCAAGGAGTATAAG
1 -GAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGCCCCCTATTTCTTCAAGGAGTATAAG
96858 ACCCACAATCTTCAACAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTTGAACATCT
65 ACCCACAATCTTC-ACAAATGGGTTCGCTCCCTATTTCT-TAGGGAGTATAGAACTTGAACATCT
* *
96923 CTTCAAACGGGTTCGCTCCTTCCTTCTTTAAG
128 CTTCAAACGGGTTCGCTCCCTCTTTCTTTAAG
* * * * * *
96955 GAGTAT-AGAACTCGAAC-ATCTT-CA--AACGGGT-TCGCTCCTTCTTTCTTTAAGGAGTAT-A
1 GAGTATAAG-ACTCGAACAATCTTCCACGATCGCGTCT-GCCCCCTATTTCTTCAAGGAGTATAA
* * * * * *
97013 GAACTCGA-ACATC-TC-CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACA
64 G-AC-CCACA-ATCTTCACAAATGGGTTCGCTCCCTATTTC-TTAGGGAGTATAGAACTTGAACA
* * *
97075 --TCTTCAAATGGGTTTGCTCCCTCTTTCTTTAGG
125 TCTCTTCAAACGGGTTCGCTCCCTCTTTCTTTAAG
97108 GAGTAT
1 GAGTAT
97114 GGAACTCGAA
Statistics
Matches: 272, Mismatches: 33, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
153 34 0.12
155 40 0.15
156 4 0.01
157 30 0.11
158 5 0.02
159 2 0.01
160 7 0.03
161 131 0.48
162 17 0.06
163 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (159 bp):
GAGTATAAGACTCGAACAATCTTCCACGATCGCGTCTGCCCCCTATTTCTTCAAGGAGTATAAGA
CCCACAATCTTCACAAATGGGTTCGCTCCCTATTTCTTAGGGAGTATAGAACTTGAACATCTCTT
CAAACGGGTTCGCTCCCTCTTTCTTTAAG
Found at i:96994 original size:51 final size:51
Alignment explanation
Indices: 96873--97324 Score: 548
Period size: 51 Copynumber: 8.8 Consensus size: 51
96863 CAATCTTCAA
* * * * *
96873 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTTGAACATCTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACA--TCTT
* *
96926 CAAACGGGTTCGCTCCTTCCTTCTTTAAGGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACATCTT
* *
96977 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTC
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACATCTT
*
97028 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACATCTT
* * * *
97079 CAAATGGGTTTGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACA--TCTT
* * * * * *
97132 C--ACGGGTTCGCTCATTCCTTCTCTAGGGGGTATGGAACTCGGACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACATCTT
* * * * *
97181 TAAACGGGTTCGCTCATTCTTTCTTTAAGGAGTATAGAACTCGCATATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACATCTT
* * * * *
97232 CACACGGGTTCGCTCCTTCCTTCTCTAGGGAGTATGGAACTCGGACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACATCTT
* * * *
97283 CAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1 CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTC
97325 AAATAATCTT
Statistics
Matches: 351, Mismatches: 44, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
49 4 0.01
51 302 0.86
53 45 0.13
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (51 bp):
CAAACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACATCTT
Found at i:97866 original size:36 final size:36
Alignment explanation
Indices: 97717--97863 Score: 163
Period size: 36 Copynumber: 4.1 Consensus size: 36
97707 AAGGCTTAAA
** *
97717 ATGGATCTGCTTCACTACTT-TTTGGTGAAGACTTAAG
1 ATGGAT-TGCTTCACTA-TTCTCCGGTGAAGACTTCAG
* * *
97754 ATGGTTTGCTTCACTACTCTCTGGTGAAGACTT-ATG
1 ATGGATTGCTTCACTATTCTCCGGTGAAGACTTCA-G
* *
97790 ATGGTTTGCTTCACTATTCTCCGGTGAAGGCTTCAG
1 ATGGATTGCTTCACTATTCTCCGGTGAAGACTTCAG
* *
97826 ATTGATTGCTTCACTATTCTCCGGTGAAGGCTTCAG
1 ATGGATTGCTTCACTATTCTCCGGTGAAGACTTCAG
97862 AT
1 AT
97864 TGACTTTTCT
Statistics
Matches: 99, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
35 2 0.02
36 91 0.92
37 6 0.06
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (36 bp):
ATGGATTGCTTCACTATTCTCCGGTGAAGACTTCAG
Found at i:98859 original size:124 final size:124
Alignment explanation
Indices: 98587--98889 Score: 448
Period size: 124 Copynumber: 2.4 Consensus size: 124
98577 TCAATAATTT
* **
98587 CTTGGTCTGAATCTTTTCATCTCAACATGACGTGGGTTTGGTCTCGCCCCAACATTATCTTACAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCT-GCCCCAACATTATCTTACAC
* * * * *
98652 TGGTAAAGGCCTTCAAAATGCCCCATCACCTCAAATTGTGAGGCTCATTCTTTATGCCTC
65 TGGTAAAGGCCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
*
98712 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCATGCCCCAACATTATCTTATAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTC-TGCCCCAACATTATCTTACAC
* *
98777 TGGT-ACGGGCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
65 TGGTAAAGGCCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
* *
98836 CTTGGTCTGAATCTTGTCTTCTCAACATGATG-GGGTTCAGTCGTGCCCCAACAT
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTC-TGCCCCAACAT
98890 ATCACAACTT
Statistics
Matches: 163, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
123 21 0.13
124 78 0.48
125 63 0.39
126 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.32
Consensus pattern (124 bp):
CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCTGCCCCAACATTATCTTACACT
GGTAAAGGCCATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTC
Found at i:148026 original size:16 final size:16
Alignment explanation
Indices: 148005--148037 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
147995 CAATAAATAA
148005 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
148021 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
148037 A
1 A
148038 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:148118 original size:10 final size:10
Alignment explanation
Indices: 148103--148176 Score: 61
Period size: 10 Copynumber: 7.6 Consensus size: 10
148093 CATTTAATAA
148103 ATAAACGAAC
1 ATAAACGAAC
148113 ATAAACGAAC
1 ATAAACGAAC
148123 ----ACGAAC
1 ATAAACGAAC
148129 ATAAACGAAC
1 ATAAACGAAC
*
148139 A-AGAAC-ATAA
1 ATA-AACGA-AC
148149 ATGAACACGAAC
1 AT-AA-ACGAAC
148161 ATAAACGAAC
1 ATAAACGAAC
148171 ATAAAC
1 ATAAAC
148177 ATTGGAGACC
Statistics
Matches: 52, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
6 6 0.12
9 2 0.04
10 34 0.65
11 3 0.06
12 6 0.12
13 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:148128 original size:16 final size:16
Alignment explanation
Indices: 148107--148171 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
148097 TAATAAATAA
148107 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
148123 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
148139 AAGAACATAAATGAAC
1 ACGAACATAAACGAAC
148155 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
148171 A
1 A
148172 TAAACATTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:148177 original size:16 final size:16
Alignment explanation
Indices: 148110--148178 Score: 86
Period size: 16 Copynumber: 4.3 Consensus size: 16
148100 TAAATAAACG
*
148110 AACATAAACGAACACG
1 AACATAAACGAACACA
148126 AACATAAACGAACA-A
1 AACATAAACGAACACA
* *
148141 GAACATAAATGAACACG
1 -AACATAAACGAACACA
*
148158 AACATAAACGAACATA
1 AACATAAACGAACACA
148174 AACAT
1 AACAT
148179 TGGAGACCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.59, C:0.20, G:0.10, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:149231 original size:14 final size:14
Alignment explanation
Indices: 149214--149269 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
149204 AATGAACATA
149214 AACGAACATAACCG
1 AACGAACATAACCG
149228 AACGAACAT-A---
1 AACGAACATAACCG
149238 AACGAACATAACCG
1 AACGAACATAACCG
149252 AACGAACATAACCG
1 AACGAACATAACCG
149266 AACG
1 AACG
149270 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.27, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:149268 original size:10 final size:10
Alignment explanation
Indices: 149207--149254 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
149197 ATAAATGAAT
149207 GAACATAAAC
1 GAACATAAAC
149217 GAACATAACCGAAC
1 GAACAT-A---AAC
149231 GAACATAAAC
1 GAACATAAAC
*
149241 GAACATAACC
1 GAACATAAAC
149251 GAAC
1 GAAC
149255 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:149279 original size:24 final size:24
Alignment explanation
Indices: 149207--149268 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
149197 ATAAATGAAT
149207 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
149231 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
149255 GAACATAACCGAAC
1 GAACATAAACGAAC
149269 GTTCACGAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:154662 original size:5 final size:5
Alignment explanation
Indices: 154652--154677 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
154642 TAATTTTCTG
154652 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
154678 TTATCGATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:160477 original size:2 final size:2
Alignment explanation
Indices: 160470--160495 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
160460 GCTGCTTCTC
160470 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
160496 GCGCGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:164558 original size:14 final size:14
Alignment explanation
Indices: 164539--164567 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
164529 AATAAAAACT
164539 TAATTAAGATAATA
1 TAATTAAGATAATA
164553 TAATTAAGATAATA
1 TAATTAAGATAATA
164567 T
1 T
164568 TTCATTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAATTAAGATAATA
Found at i:176345 original size:32 final size:31
Alignment explanation
Indices: 176304--176427 Score: 108
Period size: 32 Copynumber: 3.9 Consensus size: 31
176294 AGTCGAGGGT
176304 TTACCTATGTTCTACGGAACATATGGACATAA
1 TTACCTATG-TCTACGGAACATATGGACATAA
* * *
176336 TTACCTATGTCTTTCGGGACATATGGACAGAA
1 TTACCTATGTC-TACGGAACATATGGACATAA
* ***
176368 TTACCTTTGTCTTTTGAGACATATGGACAGT-A
1 TTACCTATGTCTACGGA-ACATATGGACA-TAA
* *
176400 -TGCCTATGTTCTAAGGAACATATGGACA
1 TTACCTATG-TCTACGGAACATATGGACA
176428 GTTTACCTAG
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
31 22 0.29
32 53 0.71
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (31 bp):
TTACCTATGTCTACGGAACATATGGACATAA
Found at i:176455 original size:31 final size:31
Alignment explanation
Indices: 176322--176461 Score: 99
Period size: 31 Copynumber: 4.5 Consensus size: 31
176312 GTTCTACGGA
* *
176322 ACATATGGACA-TAATTACCTATG-TCTTTCGGG
1 ACATATGGACAGT--TTACCTAGGTTCTTT-GAG
* **
176354 ACATATGGACAGAATTACCTTTG-TCTTTTGAG
1 ACATATGGACAG-TTTACCTAGGTTC-TTTGAG
* * * **
176386 ACATATGGACAGTATGCCTATGTTCTAAG-G
1 ACATATGGACAGTTTACCTAGGTTCTTTGAG
176416 AACATATGGACAGTTTACCTAGGTTCTTTGAG
1 -ACATATGGACAGTTTACCTAGGTTCTTTGAG
*
176448 ACCTATGGACAGTT
1 ACATATGGACAGTT
176462 GTCGAGGTTT
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
30 1 0.01
31 45 0.52
32 38 0.44
33 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (31 bp):
ACATATGGACAGTTTACCTAGGTTCTTTGAG
Found at i:177249 original size:21 final size:21
Alignment explanation
Indices: 177223--177263 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
177213 CGAAATTTAG
* *
177223 TGCATCTATGTACTATAGCAA
1 TGCATCGATGCACTATAGCAA
*
177244 TGCATCGATGCACTGTAGCA
1 TGCATCGATGCACTATAGCA
177264 CTGTTCACGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACTATAGCAA
Found at i:178867 original size:8 final size:8
Alignment explanation
Indices: 178854--178883 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
178844 TAGGTTTGGG
178854 TTTTTTAT
1 TTTTTTAT
178862 TTTTTTAT
1 TTTTTTAT
178870 TTTTTTAT
1 TTTTTTAT
178878 TTTTTT
1 TTTTTT
178884 GGAAGTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTAT
Found at i:180186 original size:71 final size:72
Alignment explanation
Indices: 180049--180288 Score: 348
Period size: 71 Copynumber: 3.4 Consensus size: 72
180039 AGGCTTAGGA
*
180049 GATGCGGTGGATG-CTAGGCGGTTTAGGATGATAGGGCGGGTTAACAACCGGAGGC-TCGGCGTT
1 GATGCGGTGGATGTTTAGGCGGTTTAGGATGATAGGGCGGGTTAACAACCGGAGGCTTCGGCG-T
180112 TTCGGGAG
65 TTCGGGAG
180120 GATGCGGTGGATGTTTAGGCGGTTTAGGATGATAGGGCGGGTTAACAACC-GAGGCTTCGGCGTT
1 GATGCGGTGGATGTTTAGGCGGTTTAGGATGATAGGGCGGGTTAACAACCGGAGGCTTCGGCGTT
180184 TCGGGAG
66 TCGGGAG
* * * * *
180191 GATGCGGTGGATGTTTAGG-TGTTTAGGATGATATGGAGGGTTAACCACCGGAGGCTTCGGTGGT
1 GATGCGGTGGATGTTTAGGCGGTTTAGGATGATAGGGCGGGTTAACAACCGGAGGCTTCGG-CGT
180255 TT-GGGAG
65 TTCGGGAG
* *
180262 GGTGCGGTGGATGTTT-GGTGGTTTAGG
1 GATGCGGTGGATGTTTAGGCGGTTTAGG
180289 GTGAAACGGA
Statistics
Matches: 156, Mismatches: 8, Indels: 10
0.90 0.05 0.06
Matches are distributed among these distances:
70 28 0.18
71 83 0.53
72 45 0.29
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (72 bp):
GATGCGGTGGATGTTTAGGCGGTTTAGGATGATAGGGCGGGTTAACAACCGGAGGCTTCGGCGTT
TCGGGAG
Done.