Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007421.1 Hibiscus syriacus cultivar Beakdansim tig00020087_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: 65586
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:879 original size:92 final size:91
Alignment explanation
Indices: 724--900 Score: 259
Period size: 92 Copynumber: 1.9 Consensus size: 91
714 AACTTCAACC
* *
724 AAAGACAAAACAAAGACAAATACTACTTTACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGC
1 AAAGACAAAACAAAGACAAATACTACTTCACAGTGTT--A-AATACACAGTTTAGCAGAATTGGA
789 AGCAACCGAATAAATTTACTTCAACCAAA
63 AGCAACCGAATAAATTTACTTCAACCAAA
*
818 AAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATA-ACAGTTTAGCAGTATTGGA
1 AAAGACAAAAC--AAAGACAAATACT-ACTTCACAGTGTTAAATACACAGTTTAGCAGAATTGGA
881 AGCAACCGAATAAATTTACT
63 AGCAACCGAATAAATTTACT
901 AAGCATCTAA
Statistics
Matches: 77, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
92 37 0.48
93 4 0.05
94 11 0.14
96 13 0.17
97 12 0.16
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (91 bp):
AAAGACAAAACAAAGACAAATACTACTTCACAGTGTTAAATACACAGTTTAGCAGAATTGGAAGC
AACCGAATAAATTTACTTCAACCAAA
Found at i:1135 original size:61 final size:61
Alignment explanation
Indices: 1067--1191 Score: 200
Period size: 61 Copynumber: 2.0 Consensus size: 61
1057 AAAGTAGACA
*
1067 CTCCACACGCCATGC-CCATCGTTATCGC-TAGAGTACCGATCTCCTCACGCAAGGCATTAAC
1 CTCCACACGCCATGCACCATCGTTATCACGT--AGTACCGATCTCCTCACGCAAGGCATTAAC
*
1128 CTCCACACGCCATGCACCATCGTTATCACGTAGTACCGATCTCCTCACGCAAGGCATTGAC
1 CTCCACACGCCATGCACCATCGTTATCACGTAGTACCGATCTCCTCACGCAAGGCATTAAC
1189 CTC
1 CTC
1192 ATCACGTAAC
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
61 47 0.78
62 12 0.20
63 1 0.02
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (61 bp):
CTCCACACGCCATGCACCATCGTTATCACGTAGTACCGATCTCCTCACGCAAGGCATTAAC
Found at i:2638 original size:19 final size:19
Alignment explanation
Indices: 2614--2650 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2604 TCTTTTGGTT
2614 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2633 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
2651 AGAGAATCGC
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:0.49, C:0.19, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2685 original size:19 final size:19
Alignment explanation
Indices: 2663--2707 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2653 AGAATCGCAA
*
2663 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
2682 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
2701 TGCGATT
1 TGCGATT
2708 CTCTTGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:3371 original size:20 final size:20
Alignment explanation
Indices: 3262--3372 Score: 98
Period size: 20 Copynumber: 5.5 Consensus size: 20
3252 CACTATGTAA
* * *
3262 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
3282 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
3302 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
* *
3323 ATCGCATTACGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
3343 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
3363 ATCGCATTGC
1 ATCGCATTGC
3373 AATTTTTTTC
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 60 0.79
21 11 0.14
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:4552 original size:23 final size:23
Alignment explanation
Indices: 4494--4546 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
4484 GATAATCTGG
4494 GAAGTACTGATACCCTAAGAGAA
1 GAAGTACTGATACCCTAAGAGAA
* *
4517 GAAGTATTGATACCCTAAGAGGA
1 GAAGTACTGATACCCTAAGAGAA
4540 GAAGTAC
1 GAAGTAC
4547 CAATACTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.19
Consensus pattern (23 bp):
GAAGTACTGATACCCTAAGAGAA
Found at i:6743 original size:2 final size:2
Alignment explanation
Indices: 6736--6770 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6726 ATATTTGGAG
6736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6771 CAAATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8821 original size:2 final size:2
Alignment explanation
Indices: 8816--8859 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
8806 TTTTTGATCC
8816 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
8858 AT
1 AT
8860 GGTTATAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13200 original size:27 final size:27
Alignment explanation
Indices: 13162--13304 Score: 205
Period size: 27 Copynumber: 5.3 Consensus size: 27
13152 TTTGAATCAG
*
13162 ACATACGTTCATCAGGCATACATACAT
1 ACATACATTCATCAGGCATACATACAT
* *
13189 ACATTCATTCATCAGGCATACAAACAT
1 ACATACATTCATCAGGCATACATACAT
* * * *
13216 TCAAACATTCATCAGGCATGCATATAT
1 ACATACATTCATCAGGCATACATACAT
13243 ACATACATTCATCAGGCATACATACAT
1 ACATACATTCATCAGGCATACATACAT
* *
13270 TCAAACATTCATCAGGCATACATACAT
1 ACATACATTCATCAGGCATACATACAT
13297 ACATACAT
1 ACATACAT
13305 ACATACATAC
Statistics
Matches: 99, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (27 bp):
ACATACATTCATCAGGCATACATACAT
Found at i:13252 original size:54 final size:54
Alignment explanation
Indices: 13169--13304 Score: 236
Period size: 54 Copynumber: 2.5 Consensus size: 54
13159 CAGACATACG
*
13169 TTCATCAGGCATACATACATACATTCATTCATCAGGCATACAAACATTCAAACA
1 TTCATCAGGCATACATACATACATACATTCATCAGGCATACAAACATTCAAACA
* * *
13223 TTCATCAGGCATGCATATATACATACATTCATCAGGCATACATACATTCAAACA
1 TTCATCAGGCATACATACATACATACATTCATCAGGCATACAAACATTCAAACA
13277 TTCATCAGGCATACATACATACATACAT
1 TTCATCAGGCATACATACATACATACAT
13305 ACATACATAC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (54 bp):
TTCATCAGGCATACATACATACATACATTCATCAGGCATACAAACATTCAAACA
Found at i:13329 original size:68 final size:66
Alignment explanation
Indices: 13236--13363 Score: 202
Period size: 68 Copynumber: 1.9 Consensus size: 66
13226 ATCAGGCATG
* *
13236 CATATATACATACATTCATCAGGCATACATACATTCAAACATTCATCAGGCATACATACATACAT
1 CATACATACATACATTCATCAGGCATACATACATTCAAACATACATCAGGCATACATACATACAT
13301 A
66 A
**
13302 CATACATACATACATATTCATCAGGCATACATACATTCAAACATACATTGGGCATACATACA
1 CATACATACATAC--ATTCATCAGGCATACATACATTCAAACATACATCAGGCATACATACA
13364 CATAACCCAT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
66 12 0.21
68 44 0.79
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (66 bp):
CATACATACATACATTCATCAGGCATACATACATTCAAACATACATCAGGCATACATACATACAT
A
Found at i:13331 original size:29 final size:27
Alignment explanation
Indices: 13298--13363 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 27
13288 TACATACATA
*
13298 CATACATACATACATACATATTCATCAGG
1 CATACATACATACAAACATA--CATCAGG
* **
13327 CATACATACATTCAAACATACATTGGG
1 CATACATACATACAAACATACATCAGG
13354 CATACATACA
1 CATACATACA
13364 CATAACCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 15 0.45
29 18 0.55
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (27 bp):
CATACATACATACAAACATACATCAGG
Found at i:13363 original size:4 final size:4
Alignment explanation
Indices: 13178--13349 Score: 75
Period size: 4 Copynumber: 43.8 Consensus size: 4
13168 GTTCATCAGG
* * ** * * * *
13178 CATA CATA CATA CATT CATT CAT- CAGG CATA CAAA CATT CAAA CATT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
** * * * ** *
13225 CAT- CAGG CATG CATA TATA CATA CATT CAT- CAGG CATA CATA CATT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * **
13271 CAAA CATT CAT- CAGG CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
** * *
13318 TTCAT- CAGG CATA CATA CATT CAAA CATA CAT
1 --CATA CATA CATA CATA CATA CATA CATA CAT
13350 TGGGCATACA
Statistics
Matches: 126, Mismatches: 35, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
3 10 0.08
4 113 0.90
6 3 0.02
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:15459 original size:31 final size:29
Alignment explanation
Indices: 15393--15460 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 29
15383 TTTAAAATAT
15393 ATTTAATGAATATTTTATAATAATTGATA
1 ATTTAATGAATATTTTATAATAATTGATA
*
15422 ATTTTAAT-AATTATTTTATAATAGTTTGATA
1 A-TTTAATGAA-TATTTTATAATA-ATTGATA
15453 GATTTAAT
1 -ATTTAAT
15461 TATTTTGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
29 3 0.09
30 18 0.53
31 12 0.35
32 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (29 bp):
ATTTAATGAATATTTTATAATAATTGATA
Found at i:20845 original size:20 final size:20
Alignment explanation
Indices: 20820--20869 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
20810 GTAAGGGAAG
20820 TATCGATACTCACTAGGTAA
1 TATCGATACTCACTAGGTAA
*
20840 TATCGATACTCACTAGGTAG
1 TATCGATACTCACTAGGTAA
20860 TATCGATACT
1 TATCGATACT
20870 ATCAGTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (20 bp):
TATCGATACTCACTAGGTAA
Found at i:24156 original size:61 final size:61
Alignment explanation
Indices: 24051--24191 Score: 144
Period size: 61 Copynumber: 2.3 Consensus size: 61
24041 TTTGGATGAA
* * * * * *
24051 TTTGGGAATTAAATTAAAA-GATATAAAATTTTAGGGACCAATTTA-AAATGAGATTCATAG
1 TTTGAGAATGAAATTAAAATGATAAAAAATTTTAAGGACCAATTTAGAAAT-AAAGTCATAG
* ** * *
24111 TTTGA-AGATGAAATTAAAATGTTAAAAAATTTTAAGGACTGATTTAGAACTAAAGTCGTAG
1 TTTGAGA-ATGAAATTAAAATGATAAAAAATTTTAAGGACCAATTTAGAAATAAAGTCATAG
24172 TTTGAGAATGAAATTAAAAT
1 TTTGAGAATGAAATTAAAAT
24192 ATTTAAAAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
59 1 0.02
60 15 0.23
61 46 0.70
62 4 0.06
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.33
Consensus pattern (61 bp):
TTTGAGAATGAAATTAAAATGATAAAAAATTTTAAGGACCAATTTAGAAATAAAGTCATAG
Found at i:26945 original size:16 final size:18
Alignment explanation
Indices: 26912--26946 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
26902 AATTAACCCA
26912 CCTTCTGAGCTATGTTTT
1 CCTTCTGAGCTATGTTTT
26930 CCTTCTGA-CT-TGTTTT
1 CCTTCTGAGCTATGTTTT
26946 C
1 C
26947 TGTCCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 2 0.12
18 8 0.47
ACGTcount: A:0.09, C:0.26, G:0.14, T:0.51
Consensus pattern (18 bp):
CCTTCTGAGCTATGTTTT
Found at i:34399 original size:229 final size:227
Alignment explanation
Indices: 33994--34442 Score: 772
Period size: 229 Copynumber: 2.0 Consensus size: 227
33984 GTAAATTATC
* * *
33994 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
34059 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
34124 TGTGTAAATGAAATTATTAAATTAATATTATAGTTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTG
34189 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
34222 TATCATTTTTATAAAAGTGTCTATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
34287 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* * *
34352 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATT
34417 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
34443 GCAGTTTTAA
Statistics
Matches: 208, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
228 39 0.19
229 169 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:34703 original size:20 final size:20
Alignment explanation
Indices: 34678--34715 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
34668 ATAACAGGTA
34678 AAAATGATAAAACCGGTATC
1 AAAATGATAAAACCGGTATC
34698 AAAATGATAAAACCGGTA
1 AAAATGATAAAACCGGTA
34716 AAATGATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAATGATAAAACCGGTATC
Found at i:36996 original size:21 final size:21
Alignment explanation
Indices: 36949--37013 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
36939 AAGACAATCA
* *
36949 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
36971 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
36991 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
37012 AG
1 AG
37014 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:37089 original size:33 final size:33
Alignment explanation
Indices: 37047--37112 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
37037 AAATAGATGG
*
37047 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
37080 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
37113 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:38932 original size:17 final size:19
Alignment explanation
Indices: 38893--38935 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
38883 GTAGGGTTAA
38893 TTTGTATAAGATTTATAAT
1 TTTGTATAAGATTTATAAT
*
38912 TTTGTATACGA-TTAT-AT
1 TTTGTATAAGATTTATAAT
38929 TTTGTAT
1 TTTGTAT
38936 GTGAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 4 0.17
19 10 0.43
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (19 bp):
TTTGTATAAGATTTATAAT
Found at i:39389 original size:196 final size:198
Alignment explanation
Indices: 39054--39624 Score: 1101
Period size: 199 Copynumber: 2.9 Consensus size: 198
39044 CAATATGGCC
39054 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
39119 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
39184 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
39248 -GAA
195 GGAA
39251 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCC
*
39316 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGGTTTATGAGAGA
66 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
39381 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAAT
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGAAT
39446 GGAA
195 GGAA
39450 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCC
39515 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
66 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
39580 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
39625 CTAATTTAAA
Statistics
Matches: 369, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
196 139 0.38
197 35 0.09
198 18 0.05
199 177 0.48
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCC
AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATG
GAA
Found at i:41104 original size:6 final size:6
Alignment explanation
Indices: 41080--41159 Score: 61
Period size: 6 Copynumber: 13.3 Consensus size: 6
41070 AGCGGTCGCA
* * * * **
41080 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GAAGCT GGCGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * *
41128 GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
41160 TGATCCAAAC
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:41111 original size:24 final size:24
Alignment explanation
Indices: 41083--41129 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
41073 GGTCGCAGAA
41083 GATGAAGCTGACGATGAAGATGAC
1 GATGAAGCTGACGATGAAGATGAC
*
41107 GATGAAGCTGGCGATGAAGATGA
1 GATGAAGCTGACGATGAAGATGA
41130 TGACGATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.17
Consensus pattern (24 bp):
GATGAAGCTGACGATGAAGATGAC
Found at i:41140 original size:3 final size:3
Alignment explanation
Indices: 41119--41163 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
41109 TGAAGCTGGC
* * *
41119 GAT GAA GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
41164 CCAAACAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.38, C:0.02, G:0.33, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:41163 original size:12 final size:12
Alignment explanation
Indices: 41083--41159 Score: 73
Period size: 12 Copynumber: 6.4 Consensus size: 12
41073 GGTCGCAGAA
*
41083 GATGAAGCTGAC
1 GATGAAGATGAC
41095 GATGAAGATGAC
1 GATGAAGATGAC
* *
41107 GATGAAGCTGGC
1 GATGAAGATGAC
*
41119 GATGAAGATGAT
1 GATGAAGATGAC
* * *
41131 GACGATGATGAT
1 GATGAAGATGAC
* *
41143 GATGATGATGAA
1 GATGAAGATGAC
41155 GATGA
1 GATGA
41160 TGATCCAAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 55 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:42971 original size:182 final size:183
Alignment explanation
Indices: 42629--43335 Score: 1310
Period size: 182 Copynumber: 3.9 Consensus size: 183
42619 CTTTCAACAT
** * * *
42629 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
42694 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
42759 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
42812 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
42877 GGTCTACAACCTATATCAACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
42941 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
42994 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
43059 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
43124 AATGTGTCGATACGA-TTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
43176 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
43241 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
43306 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
43336 GTAATTTTAA
Statistics
Matches: 511, Mismatches: 11, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
182 359 0.70
183 152 0.30
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:43301 original size:365 final size:365
Alignment explanation
Indices: 42629--43335 Score: 1317
Period size: 365 Copynumber: 1.9 Consensus size: 365
42619 CTTTCAACAT
*
42629 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
42694 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
42759 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
*
42824 TAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCT
196 TAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
*
42889 ATATCAACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATAC
261 ATATCAACACTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC
*
42954 GATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
326 CATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
** * *
42994 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
43059 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
43124 AATGTGTCGATACGA-TTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
43188 TAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
196 TAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
*
43253 ATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA
261 ATATCAACACTTT-TAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA
43318 CCATTTAAAAAAGTGTCG
325 CCATTTAAAAAAGTGTCG
43336 GTAATTTTAA
Statistics
Matches: 332, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
364 125 0.38
365 207 0.62
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (365 bp):
ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
TAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
ATATCAACACTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC
CATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:45835 original size:25 final size:25
Alignment explanation
Indices: 45801--45860 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
45791 TTATCATTAA
45801 ATTTAGGTATGCACAATAACTACAT
1 ATTTAGGTATGCACAATAACTACAT
*****
45826 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGCACAATAACTACAT
45851 ATTTAGGTAT
1 ATTTAGGTAT
45861 ATACATCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGCACAATAACTACAT
Found at i:46193 original size:22 final size:22
Alignment explanation
Indices: 46148--46193 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
46138 ATTACATAAC
*
46148 TTTTAAAAAAAGTATCGATCCT
1 TTTTAAAAAAAGTATCGAACCT
*
46170 TTTTATAAAAAGTAT-GAACACT
1 TTTTAAAAAAAGTATCGAAC-CT
46192 TT
1 TT
46194 CAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTTAAAAAAAGTATCGAACCT
Found at i:46242 original size:23 final size:23
Alignment explanation
Indices: 46211--46274 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
46201 ATAGGTAAAC
*
46211 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* * **
46234 ATATAATGTAATAGATATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
46257 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
46275 TGGTTATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:46281 original size:23 final size:23
Alignment explanation
Indices: 46211--46283 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
46201 ATAGGTAAAC
* **
46211 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
* *
46234 ATATAATGTAATAGATA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
46257 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
46280 ATAT
1 ATAT
46284 TGTAAAGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:46581 original size:25 final size:25
Alignment explanation
Indices: 46547--46597 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
46537 ACAACAAATC
*
46547 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
46572 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
46597 A
1 A
46598 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:47006 original size:18 final size:18
Alignment explanation
Indices: 46985--47021 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46975 GTAATTGGAG
46985 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
47003 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
47021 T
1 T
47022 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:47029 original size:24 final size:24
Alignment explanation
Indices: 46977--47023 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
46967 TTTCATATGT
* *
46977 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
47001 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
47024 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:47323 original size:39 final size:39
Alignment explanation
Indices: 47280--47366 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
47270 TCCGATGCTC
*
47280 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
47319 ATCAAAATCCAAATCTCATATGATGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
47358 ATCAAAATC
1 ATCAAAATC
47367 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:47840 original size:23 final size:23
Alignment explanation
Indices: 47770--47842 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
47760 ATAGGTAAAC
* * *
47770 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTCGTT
*
47793 ATATAATGTAATAGATA-TCGTTT
1 ATATAATGTAATAGGTAGTCG-TT
*
47816 ATATAATGTAATAGGTAGTAGTT
1 ATATAATGTAATAGGTAGTCGTT
47839 ATAT
1 ATAT
47843 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
22 1 0.02
23 39 0.93
24 2 0.05
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTCGTT
Found at i:49718 original size:2 final size:2
Alignment explanation
Indices: 49713--49741 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49703 AAAAATTCTA
49713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49742 AATTTAGATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51372 original size:36 final size:38
Alignment explanation
Indices: 51332--51409 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 38
51322 ATTTAACGAC
51332 AAATTTTGAA-CG-GATACTAAAATAAAACAAAAACTA
1 AAATTTTGAACCGAGATACTAAAATAAAACAAAAACTA
* *
51368 AAATTTTTAACTGCGAGATACTAAAATGAAACAAAAACTA
1 AAATTTTGAAC--CGAGATACTAAAATAAAACAAAAACTA
51408 AA
1 AA
51410 CTTTAGGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 9 0.25
39 2 0.06
40 25 0.69
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (38 bp):
AAATTTTGAACCGAGATACTAAAATAAAACAAAAACTA
Found at i:57622 original size:19 final size:19
Alignment explanation
Indices: 57598--57634 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57588 AATGACCAAC
*
57598 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
57617 AAATCGTAACGCGATCTC
1 AAATCGCAACGCGATCTC
57635 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:57710 original size:21 final size:20
Alignment explanation
Indices: 57660--57711 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
57650 GTTTCCAGAT
**
57660 TCGCAATGCGATTTTGACTA
1 TCGCAATGCGATTTTGAAAA
** *
57680 TCGCGTTGCGATTTTCTAAAA
1 TCGCAATGCGATTTT-GAAAA
57701 TCGCAATGCGA
1 TCGCAATGCGA
57712 ATATATAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
TCGCAATGCGATTTTGAAAA
Found at i:57813 original size:61 final size:61
Alignment explanation
Indices: 57660--57805 Score: 229
Period size: 61 Copynumber: 2.4 Consensus size: 61
57650 GTTTCCAGAT
* *
57660 TCGCAATGCGATTTTGACTATCGCGTTGCGATTTTCTAAAATCGCAATGCGAATATATAAA
1 TCGCAACGCGATTCTGACTATCGCGTTGCGATTTTCTAAAATCGCAATGCGAATATATAAA
* * * * *
57721 TCGTAACGCAATTCTGATTATCGCGTTGCGATTTTCTAAAATCGTAATGCGAATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCGTTGCGATTTTCTAAAATCGCAATGCGAATATATAAA
57782 TCGCAACGCGATTCTGACTATCGC
1 TCGCAACGCGATTCTGACTATCGC
57806 AACGCGATAA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 75 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (61 bp):
TCGCAACGCGATTCTGACTATCGCGTTGCGATTTTCTAAAATCGCAATGCGAATATATAAA
Found at i:57823 original size:61 final size:61
Alignment explanation
Indices: 57695--57830 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 61
57685 TTGCGATTTT
* * *** * *
57695 CTAAAATCGCAATGCGAATATATAAATCGTAACGCAATTCTGATTATCGCGTTGCGATTTT
1 CTAAAATCGCAATGCGAATATATAAATCGCAACGCAATTCTGACTATCGCAACGCGATATA
* * *
57756 CTAAAATCGTAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCGCAACGCGATAATA
1 CTAAAATCGCAATGCGAATATATAAATCGCAACGCAATTCTGACTATCGCAACGCGAT-ATA
*
57818 C-AAAATTGCAATG
1 CTAAAATCGCAATG
57831 TGATTTTCCA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (61 bp):
CTAAAATCGCAATGCGAATATATAAATCGCAACGCAATTCTGACTATCGCAACGCGATATA
Found at i:58286 original size:19 final size:20
Alignment explanation
Indices: 58261--58351 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 20
58251 TTTATTTTGG
58261 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
58281 -TTTTTCACTATCGTAACAACAC
1 ATTTTTCACTATCG---CAACAC
* *
58303 GTTTTTCAAACTCTCGCAACAC
1 ATTTTTC--ACTATCGCAACAC
* *
58325 A-TTTTAACTTTCGCAACAC
1 ATTTTTCACTATCGCAACAC
58344 ATTTTTCA
1 ATTTTTCA
58352 AAATCGAGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
19 26 0.44
20 5 0.08
21 4 0.07
22 12 0.20
23 6 0.10
25 6 0.10
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.37
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:58323 original size:44 final size:41
Alignment explanation
Indices: 58272--58353 Score: 101
Period size: 44 Copynumber: 1.9 Consensus size: 41
58262 TTTTTCACTA
* * *
58272 TCGCAACACTTTTTCACTATCGTAACAACACGTTTTTCAAACTC
1 TCGCAACACATTTTAACTATCG---CAACACATTTTTCAAACTC
*
58316 TCGCAACACATTTTAACTTTCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
58354 ATCGAGTTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 15 0.44
44 19 0.56
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Done.