Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001809.1 Hibiscus syriacus cultivar Beakdansim tig00003660_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: 115519
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3200 original size:202 final size:201
Alignment explanation
Indices: 2677--3220 Score: 643
Period size: 202 Copynumber: 2.7 Consensus size: 201
2667 TAGAGGAACC
* * * * *
2677 ATTTATAA-CATAGCTCAAGGCGAAAAGGGCTATCTATCAAC-AAAACTTTCGAGTTTGATTCTA
1 ATTTACAATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATTCCA
* * * * *
2740 TTCAGCTCGAGGGCGTATCAACCG-TATGGTAGCAATGAGGAACTA-TTTTCCGGTTAAAGTTTA
66 TTCAGCTCGAAGGCATATCAACCGCT-TGGTAGCAGTGAGGAACTACTTTT-CGGTTGAATTTTA
* * *
2803 AACCGATGTCTTTAAGTCAAAAGAAGACCTAGGTTGGCTGTAATTTAGCAACAAAGAACTATCTC
129 AACCGAAGTCTTTAAGCCAAAAGAAGACCTAGGTTGGCTGCAATTTAGCAACAAAGAACTATCTC
2868 CCAGCTGA
194 CCAGCTGA
* * * *
2876 ATTTACAAT-GTAGCTCAAGGTGAGAAGGGCTATCTGTCGACAAAAAATTTCGAGTTCGATTCCA
1 ATTTACAATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATTCCA
* * * ** *
2940 TTCAGCTCGATGGCATATCAACCGCATGGTAGCAGTAAGGAACTACTTACCGGTTGAATTTTATA
66 TTCAGCTCGAAGGCATATCAACCGCTTGGTAGCAGTGAGGAACTACTTTTCGGTTGAATTTTAAA
* * *
3005 CCTAAGTCGTTTAAGCCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAAGAGCTATCTC
131 CCGAAGTC-TTTAAGCCAA-AAGAAGACCTAGGTTGGCTGCAATTTAGCAACAAAGAACTATCTC
*
3070 CTAGC-GTA
194 CCAGCTG-A
* * *
3078 GTTTAC-ATCATAGCTCAATGCGAGAAGGGTTATCTGTCAACAAAAACTTTCGAGTTCGATTCCA
1 ATTTACAATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATTCCA
* * * * * * *
3142 TTCATCTCAAAGGCATATCAACCGCTTAGTAGTAGCGAGGAGCTACTTTTCAGTTGAATTTTCAA
66 TTCAGCTCGAAGGCATATCAACCGCTTGGTAGCAGTGAGGAACTACTTTTCGGTTGAATTTT-AA
*
3207 ACCGAGGTCTTTAA
130 ACCGAAGTCTTTAA
3221 TCTGAGAAGA
Statistics
Matches: 288, Mismatches: 48, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
199 34 0.12
200 76 0.26
201 14 0.05
202 156 0.54
203 8 0.03
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (201 bp):
ATTTACAATCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACTTTCGAGTTCGATTCCA
TTCAGCTCGAAGGCATATCAACCGCTTGGTAGCAGTGAGGAACTACTTTTCGGTTGAATTTTAAA
CCGAAGTCTTTAAGCCAAAAGAAGACCTAGGTTGGCTGCAATTTAGCAACAAAGAACTATCTCCC
AGCTGA
Found at i:3681 original size:39 final size:37
Alignment explanation
Indices: 3628--3906 Score: 229
Period size: 37 Copynumber: 7.6 Consensus size: 37
3618 ATATACATAT
* * *
3628 AACACATATAATATATAATTTTGAGAACATTTTCGAA
1 AACATATATAATATATAATTTTGAAAACATTTTTGAA
*
3665 AACATATATATAATATATAGTTTTTGAAAACA-TTTTGAA
1 AAC--ATATATAATATATA-ATTTTGAAAACATTTTTGAA
* * * *
3704 TATATATAT-ATATATAA---T--ATA-GTTTTTGAA
1 AACATATATAATATATAATTTTGAAAACATTTTTGAA
*
3734 AACATATACATAATATATAGTTTTTGAAAACA-TTTTGAA
1 AACATAT--ATAATATATA-ATTTTGAAAACATTTTTGAA
* * *
3773 AACGTATATAATATATAGTTTCGAAAACATTTTTTG-A
1 AACATATATAATATATAATTTTGAAAACA-TTTTTGAA
**
3810 AACGCATATAATATATAATTTTGAAAACATTTTTTGAA
1 AACATATATAATATATAATTTTGAAAACA-TTTTTGAA
* * **
3848 AACGTATATAATATAT-AGTTTGAAAGTATTTTTTGAA
1 AACATATATAATATATAATTTTGAAAACA-TTTTTGAA
*
3885 AACATATATAATATATTATTTT
1 AACATATATAATATATAATTTT
3907 TTTAAAAGAA
Statistics
Matches: 198, Mismatches: 26, Indels: 35
0.76 0.10 0.14
Matches are distributed among these distances:
30 14 0.07
32 3 0.02
33 7 0.04
36 17 0.09
37 87 0.44
38 25 0.13
39 35 0.18
40 10 0.05
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (37 bp):
AACATATATAATATATAATTTTGAAAACATTTTTGAA
Found at i:3747 original size:69 final size:69
Alignment explanation
Indices: 3657--3789 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 69
3647 TTTGAGAACA
* *
3657 TTTTCGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAATA-TATATATATATATAA
1 TTTTCGAAAACATATACATAATATATAGTTTTTGAAAACATTTTGAAAACTATATA-ATATATAA
3721 TATAG
65 TATAG
*
3726 TTTTTGAAAACATATACATAATATATAGTTTTTGAAAACATTTTGAAAACGTATATAATATATA
1 TTTTCGAAAACATATACATAATATATAGTTTTTGAAAACATTTTGAAAAC-TATATAATATATA
3790 GTTTCGAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
69 46 0.78
70 7 0.12
71 6 0.10
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (69 bp):
TTTTCGAAAACATATACATAATATATAGTTTTTGAAAACATTTTGAAAACTATATAATATATAAT
ATAG
Found at i:3751 original size:28 final size:30
Alignment explanation
Indices: 3697--3766 Score: 99
Period size: 28 Copynumber: 2.4 Consensus size: 30
3687 TTTGAAAACA
* * *
3697 TTTTGAATATATATATATATATAATATAGT
1 TTTTGAAAACATATACATATATAATATAGT
3727 TTTTGAAAACATATACATA-AT-ATATAGT
1 TTTTGAAAACATATACATATATAATATAGT
3755 TTTTGAAAACAT
1 TTTTGAAAACAT
3767 TTTGAAAACG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 19 0.51
29 2 0.05
30 16 0.43
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (30 bp):
TTTTGAAAACATATACATATATAATATAGT
Found at i:3752 original size:43 final size:39
Alignment explanation
Indices: 3633--3738 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 39
3623 CATATAACAC
* * * * *
3633 ATATAATATATA-ATTTTGAGAACATTTTCGAAAACATAT
1 ATATAATATATAGTTTTTGAAAACATTAT-GAATATATAT
*
3672 ATATAATATATAGTTTTTGAAAACATTTTGAATATATAT
1 ATATAATATATAGTTTTTGAAAACATTATGAATATATAT
3711 ATATATATAATATAGTTTTTGAAAACAT
1 ATATA-AT-ATATAGTTTTTGAAAACAT
3739 ATACATAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
39 25 0.42
40 16 0.27
41 19 0.32
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (39 bp):
ATATAATATATAGTTTTTGAAAACATTATGAATATATAT
Found at i:3855 original size:75 final size:73
Alignment explanation
Indices: 3633--3906 Score: 233
Period size: 75 Copynumber: 3.7 Consensus size: 73
3623 CATATAACAC
* * * * *
3633 ATATAATATATAATTTTGAGAACA-TTTTCGAAAACATATATATAATATATAGTTTTTGAAAACA
1 ATATAATATAT-AGTTTGAAAACATTTTTTGAAAAC--ACATATAATATATA-ATTTTGAAAACA
3697 TTTTG--AA--T
62 TTTTGAAAACGT
* * * * * * * *
3705 ATAT-ATATATA-TAT-AATATAGTTTTTGAAAACATATACATAATATATAGTTTTTGAAAACAT
1 ATATAATATATAGTTTGAAAACATTTTTTG-AAA-ACACATATAATATATA-ATTTTGAAAACAT
3767 TTTGAAAACGT
63 TTTGAAAACGT
*
3778 ATATAATATATAGTTTCGAAAACATTTTTTG-AAACGCATATAATATATAATTTTGAAAACATTT
1 ATATAATATATAGTTT-GAAAACATTTTTTGAAAACACATATAATATATAATTTTGAAAACA--T
3842 TTTGAAAACGT
63 TTTGAAAACGT
** * *
3853 ATATAATATATAGTTTGAAAGTATTTTTTGAAAACATATATAATATATTATTTT
1 ATATAATATATAGTTTGAAAACATTTTTTGAAAACACATATAATATATAATTTT
3907 TTTAAAAGAA
Statistics
Matches: 167, Mismatches: 21, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
68 3 0.02
69 38 0.23
70 4 0.02
71 9 0.05
72 4 0.02
73 16 0.10
74 31 0.19
75 52 0.31
77 10 0.06
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (73 bp):
ATATAATATATAGTTTGAAAACATTTTTTGAAAACACATATAATATATAATTTTGAAAACATTTT
GAAAACGT
Found at i:5271 original size:31 final size:28
Alignment explanation
Indices: 5236--5301 Score: 69
Period size: 31 Copynumber: 2.2 Consensus size: 28
5226 TCAATCCATA
*
5236 AATTTTAATTTATTTTAATTTGATCCTTTTT
1 AATTTTAA-TT-TTTTAATTTGAACC-TTTT
*
5267 AATTTTTTAATTTTTTAATTTTAACCTTTT
1 AA--TTTTAATTTTTTAATTTGAACCTTTT
5297 AATTT
1 AATTT
5302 CTTTTTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
28 3 0.10
30 6 0.19
31 14 0.45
32 2 0.06
33 6 0.19
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (28 bp):
AATTTTAATTTTTTAATTTGAACCTTTT
Found at i:5275 original size:8 final size:8
Alignment explanation
Indices: 5262--5288 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5252 AATTTGATCC
5262 TTTTTAAT
1 TTTTTAAT
5270 TTTTTAAT
1 TTTTTAAT
5278 TTTTTAAT
1 TTTTTAAT
5286 TTT
1 TTT
5289 AACCTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTAAT
Found at i:8604 original size:13 final size:14
Alignment explanation
Indices: 8546--8606 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
8536 CGACCCGCTG
*
8546 ACTCGACTGAGGCA
1 ACTCGACTGAGTCA
* *
8560 CCTCGCACTGAGTTA
1 ACTCG-ACTGAGTCA
*
8575 ACTCGACTGAGTTA
1 ACTCGACTGAGTCA
*
8589 ACTC-ACTGGGTCA
1 ACTCGACTGAGTCA
8602 ACTCG
1 ACTCG
8607 TTGACTGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.28
14 17 0.44
15 11 0.28
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.23
Consensus pattern (14 bp):
ACTCGACTGAGTCA
Found at i:8684 original size:13 final size:13
Alignment explanation
Indices: 8666--8691 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8656 ACTTTTTGCT
8666 GTTGACTTTGACC
1 GTTGACTTTGACC
8679 GTTGACTTTGACC
1 GTTGACTTTGACC
8692 AAAAAGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
GTTGACTTTGACC
Found at i:10238 original size:12 final size:12
Alignment explanation
Indices: 10221--10267 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
10211 GAATATTATA
*
10221 TCTGATTTCTGC
1 TCTGATTTCTGT
10233 TCTGATTTCTGT
1 TCTGATTTCTGT
10245 TCTGATTTCTGT
1 TCTGATTTCTGT
10257 TCTGATTTCTG
1 TCTGATTTCTG
10268 ATAATATCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.09, C:0.19, G:0.17, T:0.55
Consensus pattern (12 bp):
TCTGATTTCTGT
Found at i:10451 original size:31 final size:32
Alignment explanation
Indices: 10413--10481 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
10403 TAAGGTAACC
** *
10413 CTTGGGTA-GCCTCTACGGCCCTGAGATTTTT
1 CTTGGGTAGGCCTCTACGGCCCCAAGAATTTT
*
10444 CTTGGGTAGGCCTCTATGGCCCCAAGAATTTT
1 CTTGGGTAGGCCTCTACGGCCCCAAGAATTTT
10476 CTTGGG
1 CTTGGG
10482 CAAACTACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.14, C:0.25, G:0.28, T:0.33
Consensus pattern (32 bp):
CTTGGGTAGGCCTCTACGGCCCCAAGAATTTT
Found at i:11273 original size:20 final size:20
Alignment explanation
Indices: 11248--11302 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
11238 ATAATGTAAT
11248 AAGGGTATCGATACCTTAGG
1 AAGGGTATCGATACCTTAGG
11268 AAGGGTATCGATACCTTAGG
1 AAGGGTATCGATACCTTAGG
*
11288 GAGGGTATCGATACC
1 AAGGGTATCGATACC
11303 CCCTAAAGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (20 bp):
AAGGGTATCGATACCTTAGG
Found at i:14967 original size:21 final size:21
Alignment explanation
Indices: 14937--14976 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14927 TATCAAGGAC
* *
14937 TTTGTTGAAGCCATGAATTTT
1 TTTGTCGAAGCCATAAATTTT
14958 TTTGTCGAAGCCATAAATT
1 TTTGTCGAAGCCATAAATT
14977 CTTGTAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (21 bp):
TTTGTCGAAGCCATAAATTTT
Found at i:26336 original size:19 final size:20
Alignment explanation
Indices: 26296--26336 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
26286 ATTGTGCCAA
*
26296 GGGGAGTATTGATACTACAG
1 GGGGAGTATCGATACTACAG
26316 GGGGAGTATCGATACTA-AG
1 GGGGAGTATCGATACTACAG
26335 GG
1 GG
26337 TGACAATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.29, C:0.10, G:0.39, T:0.22
Consensus pattern (20 bp):
GGGGAGTATCGATACTACAG
Found at i:32417 original size:36 final size:36
Alignment explanation
Indices: 32312--32398 Score: 115
Period size: 36 Copynumber: 2.4 Consensus size: 36
32302 AAAGACGAAC
* * *
32312 ACTTGAAACGAAAGTG-CGATACATTC-TTCTGTTCG
1 ACTTGAAACGGAAGTGCCGATGC-TTCATTCCGTTCG
*
32347 ACTTGAATCGGAAGTGCCGATGCTTCATTCCGTTCG
1 ACTTGAAACGGAAGTGCCGATGCTTCATTCCGTTCG
32383 ACTTGAAACGGAAGTG
1 ACTTGAAACGGAAGTG
32399 TTGATGTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 17 0.38
36 28 0.62
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (36 bp):
ACTTGAAACGGAAGTGCCGATGCTTCATTCCGTTCG
Found at i:32927 original size:4 final size:4
Alignment explanation
Indices: 32918--32946 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
32908 TTCAACTATG
32918 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
32947 GTACATGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:34807 original size:157 final size:159
Alignment explanation
Indices: 34561--34980 Score: 508
Period size: 158 Copynumber: 2.6 Consensus size: 159
34551 TTCATTATCC
* ** * * *
34561 CTTCAATTCCTCCTTCGTTTTAAGTCCATTTTTTTACCAAATTTTG-ACCACATGCTCATAAATC
1 CTTCAATTCATCCTTTATTTTAAGTCCA-TTTTTTACCAAA-TTTGAACAACATGCTCATATACC
* *
34625 ATC-GTAGAATACATATGT-ACTTTCAATTTCTCTTTTTTGATAA-CATTTTTTTATTTTTCAAT
64 A-CAGTAGAATACCTATGTAAC-TTCAATTTCTCTTTTTTGATAATAATTTTTTTATTTTTCAAT
*
34687 TTAGTCCATTAATTTTTCATAATTTCCTTATTT
127 TTAGTCCATCAATTTTTCATAATTTCCTTATTT
*
34720 CTTCAATTCATCCTTTATTTTAAGT-CAGTTTTTACCAAATTTGAACAACATGCTCATATACCAC
1 CTTCAATTCATCCTTTATTTTAAGTCCATTTTTTACCAAATTTGAACAACATGCTCATATACCAC
** * * * *
34784 AACAGAATACCTATATAACTTCAATTCCTCTTTTTTTATAATAATTTTTTTCTTTTTCAATTTAG
66 AGTAGAATACCTATGTAACTTCAATTTCTCTTTTTTGATAATAATTTTTTTATTTTTCAATTTAG
* *
34849 TCCCTCAATTTTTCATAATTTTCTTATTT
131 TCCATCAATTTTTCATAATTTCCTTATTT
* * * ****
34878 CTTCAATTCATCATTTATTTTAGGTCCTTTTTTTTACCAAATTTGAATTGGATGCTCATATACCA
1 CTTCAATTCATCCTTTATTTTAAGTCC-ATTTTTTACCAAATTTGAACAACATGCTCATATACCA
* *
34943 CAGTAGAATACCTATGTAACTTTAATTTATACTTTTTT
65 CAGTAGAATACCTATGTAACTTCAATTTCT-CTTTTTT
34981 TTACTAAAAA
Statistics
Matches: 222, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
156 5 0.02
157 58 0.26
158 74 0.33
159 23 0.10
160 55 0.25
161 7 0.03
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.48
Consensus pattern (159 bp):
CTTCAATTCATCCTTTATTTTAAGTCCATTTTTTACCAAATTTGAACAACATGCTCATATACCAC
AGTAGAATACCTATGTAACTTCAATTTCTCTTTTTTGATAATAATTTTTTTATTTTTCAATTTAG
TCCATCAATTTTTCATAATTTCCTTATTT
Found at i:35366 original size:21 final size:21
Alignment explanation
Indices: 35340--35392 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
35330 GTTTCCAGAT
*
35340 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
35361 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
35382 TCGCAATGCGA
1 TCGCAATGCGA
35393 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:35533 original size:42 final size:42
Alignment explanation
Indices: 35407--35833 Score: 718
Period size: 42 Copynumber: 10.3 Consensus size: 42
35397 CATATTCGCA
*
35407 TTGCGATAGTCCAAGTTCGCGTTGCGA--TTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
* *
35447 TTACAATAGTCGAAGTTCGCGTTGCGA--TTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
35487 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
35529 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
35571 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
35613 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
* *
35655 TTGCGATAGTCGAAGTTCGCGTTGCTATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
* * *
35697 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTTG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
*
35739 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
* * *
35781 TTGCTATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
35823 TTGCGATAGTC
1 TTGCGATAGTC
35834 CAAAATCGCA
Statistics
Matches: 370, Mismatches: 15, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
40 62 0.17
42 308 0.83
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTTTTCCAAATTCG
Found at i:35937 original size:6 final size:6
Alignment explanation
Indices: 35926--35956 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
35916 GACACGTATT
*
35926 ACCACG ACCACG ACCACG ACCACG ACTACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
35957 GACGGCGGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.35, C:0.45, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:36559 original size:21 final size:20
Alignment explanation
Indices: 36507--36602 Score: 79
Period size: 21 Copynumber: 4.7 Consensus size: 20
36497 CGTTGCGATT
* *
36507 TTGGACTATCACAA-CGAAT
1 TTGGACTATCGCAACCGAAC
*
36526 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAAC-CGAAC
* *
36549 TTCGACTATCGCAA-CGAAT
1 TTGGACTATCGCAACCGAAC
**
36568 TTGGAAAATCGCAACACGAAC
1 TTGGACTATCGCAAC-CGAAC
36589 TTGGACTATCGCAA
1 TTGGACTATCGCAA
36603 TGTGAATATG
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 21 0.36
21 29 0.49
23 9 0.15
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAACCGAAC
Found at i:36588 original size:40 final size:42
Alignment explanation
Indices: 36510--36602 Score: 145
Period size: 40 Copynumber: 2.3 Consensus size: 42
36500 TGCGATTTTG
* *
36510 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTC
*
36552 GACTATCGCAACGAATTTGG-A-AAATCGCAACACGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTC
36592 GACTATCGCAA
1 GACTATCGCAA
36603 TGTGAATATG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
40 28 0.58
41 1 0.02
42 19 0.40
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTC
Found at i:37175 original size:73 final size:74
Alignment explanation
Indices: 37098--37291 Score: 225
Period size: 73 Copynumber: 2.6 Consensus size: 74
37088 ATGGTCGAAT
* * * * * *
37098 CTTTTAAATATTAAAAAAATTGAAGATAA-GATCGAAATTTAAAATGGTT-ATATTTATGCTATA
1 CTTTTAAATATTGAAAAAGTTGAAGAAAATGATCGAAATTTAAAAT-ATTGATACTTATGCAATA
37161 ATGATTGATA
65 ATGATTGATA
* * *
37171 CTTTTAAATATTGTAAAAGTTGATA-AAAATG-TCAAAATTGAAAATATTGATACTTATGCAATA
1 CTTTTAAATATTGAAAAAGTTGA-AGAAAATGATCGAAATTTAAAATATTGATACTTATGCAATA
37234 ATGATTGATA
65 ATGATTGATA
* * * *
37244 CTTTTATATATTGAAAAAGTTGATGAAAATGATCGATAGTTAAAATAT
1 CTTTTAAATATTGAAAAAGTTGAAGAAAATGATCGAAATTTAAAATAT
37292 CGTTACATAT
Statistics
Matches: 100, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
72 2 0.02
73 84 0.84
74 14 0.14
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.38
Consensus pattern (74 bp):
CTTTTAAATATTGAAAAAGTTGAAGAAAATGATCGAAATTTAAAATATTGATACTTATGCAATAA
TGATTGATA
Found at i:38241 original size:13 final size:13
Alignment explanation
Indices: 38223--38247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38213 AAATGGGTCT
38223 TTGTTTTAGATTA
1 TTGTTTTAGATTA
38236 TTGTTTTAGATT
1 TTGTTTTAGATT
38248 TTTTTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGTTTTAGATTA
Found at i:46070 original size:2 final size:2
Alignment explanation
Indices: 46063--46108 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
46053 CACTGATTAA
46063 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
46105 AT AT
1 AT AT
46109 GTCCTCATTG
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:46714 original size:21 final size:21
Alignment explanation
Indices: 46688--46748 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
46678 ATCAGATTGT
46688 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
46709 CCAGGGGGAACAGATT-CCCC
1 CCAGGGGGTACAGATTCCCCC
46729 CCAGGGGGTATCA-ATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
46749 GAGAACAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:46745 original size:20 final size:20
Alignment explanation
Indices: 46688--46748 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
46678 ATCAGATTGT
46688 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATT-CCCC
*
46709 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
46729 CCAGGGGGTATCA-ATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
46749 GAGAACAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:46771 original size:34 final size:35
Alignment explanation
Indices: 46716--46798 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 35
46706 CCCCCAGGGG
46716 GAACAGATTCCCCCCAGGGGGTATCAATTCCCCGA
1 GAACAGATTCCCCCCAGGGGGTATCAATTCCCCGA
* * *
46751 GAACAGATTCCCCCCA-GGGGTATCGATTCCCTGG
1 GAACAGATTCCCCCCAGGGGGTATCAATTCCCCGA
*
46785 GTACAGATTCCCCC
1 GAACAGATTCCCCC
46799 TGCATGGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 28 0.64
35 16 0.36
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (35 bp):
GAACAGATTCCCCCCAGGGGGTATCAATTCCCCGA
Found at i:46937 original size:21 final size:21
Alignment explanation
Indices: 46911--46952 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
46901 ATTTGAATAT
*
46911 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
46932 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
46953 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:47015 original size:21 final size:21
Alignment explanation
Indices: 46982--47021 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
46972 TTTTTGCAGA
*
46982 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
47004 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
47022 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:49646 original size:20 final size:21
Alignment explanation
Indices: 49618--49669 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
49608 ATTTGGTGAT
* *
49618 TTCCCAAGAGAAATTAGTCGC
1 TTCCCAAGAAAAATTAGTAGC
49639 TT-CCAAGAAAAATTAGTAGC
1 TTCCCAAGAAAAATTAGTAGC
49659 TTCCCAAGAAA
1 TTCCCAAGAAA
49670 TATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.23
Consensus pattern (21 bp):
TTCCCAAGAAAAATTAGTAGC
Found at i:53659 original size:74 final size:75
Alignment explanation
Indices: 53472--53673 Score: 255
Period size: 75 Copynumber: 2.7 Consensus size: 75
53462 GACCGTTGAA
* ** * *
53472 CAGGGGGGAATCGGTACC-CCTGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCT-ATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
**
53536 ACAAAAATGTT
65 ACAAAAACATT
* * *
53547 TAGGGGGGAATCGGTTCCTCCTATGGGGGAATTGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
* *
53612 CCAAACCATT
66 CAAAAACATT
* *
53622 CA-GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTG
53674 TAATTTTTGG
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
74 47 0.43
75 60 0.55
76 3 0.03
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (75 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
CAAAAACATT
Found at i:56306 original size:21 final size:21
Alignment explanation
Indices: 56280--56319 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
56270 CAGAACCCCA
*
56280 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
56301 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
56320 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:62226 original size:76 final size:76
Alignment explanation
Indices: 62122--62322 Score: 269
Period size: 76 Copynumber: 2.6 Consensus size: 76
62112 GACCGTTGAA
* ** *
62122 CAGGGGGGAATCGGTACC-CCTGGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGG
1 CAGGGGGGAATCGGTTCCTCCT-ATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
**
62186 AACAAAAATGTT
65 AACAAAAACATT
* * *
62198 TAGGGGGGAATCGGTTCCTCCTATGGGGGGAATTGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
* * *
62263 GCCAAACCATT
66 ACAAAAACATT
*
62274 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCA
62323 ATCTGTAATT
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
76 106 0.97
77 3 0.03
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.22
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
ACAAAAACATT
Found at i:70331 original size:10 final size:11
Alignment explanation
Indices: 70312--70336 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
70302 CTTTTGTTCG
70312 AAAAGAAAAAA
1 AAAAGAAAAAA
70323 AAAAGAAAAAA
1 AAAAGAAAAAA
70334 AAA
1 AAA
70337 TAGCCCTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:74234 original size:21 final size:21
Alignment explanation
Indices: 74210--74255 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
74200 GTCTGAGTTC
74210 CCTCTTCCTCTTCCTCCTCCT
1 CCTCTTCCTCTTCCTCCTCCT
* *
74231 CCTCTTCTTCTTCTTCCTCCT
1 CCTCTTCCTCTTCCTCCTCCT
74252 CCTC
1 CCTC
74256 CAAAGATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (21 bp):
CCTCTTCCTCTTCCTCCTCCT
Found at i:74628 original size:2 final size:2
Alignment explanation
Indices: 74621--74668 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
74611 TACAGAACGA
74621 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
74663 AT AT AT
1 AT AT AT
74669 GAACAATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82445 original size:55 final size:56
Alignment explanation
Indices: 82362--82473 Score: 163
Period size: 55 Copynumber: 2.0 Consensus size: 56
82352 TACATATTCT
* *
82362 AGAAGAAGAAGAAGAAGACACGTGAATTA-CTTTTTATTTTTTAATTCTCAACTCA
1 AGAAGAAGAAGAAGAAGACACATGAATTATCTTTTTATTTTTCAATTCTCAACTCA
* * * *
82417 AGAAGAAGAAGAAGAATACACATGAATTATTTTTTTATTTTTCATTTGTCAACTCA
1 AGAAGAAGAAGAAGAAGACACATGAATTATCTTTTTATTTTTCAATTCTCAACTCA
82473 A
1 A
82474 ATTTCTCTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
55 27 0.54
56 23 0.46
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (56 bp):
AGAAGAAGAAGAAGAAGACACATGAATTATCTTTTTATTTTTCAATTCTCAACTCA
Found at i:83017 original size:21 final size:22
Alignment explanation
Indices: 82984--83028 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
82974 GACTCGATTC
*
82984 GAAAAATTGATTTTTCTTACTT
1 GAAAAATTCATTTTTCTTACTT
*
83006 GAAAAA-TCATTTTTTTTACTT
1 GAAAAATTCATTTTTCTTACTT
83027 GA
1 GA
83029 CTCGACTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (22 bp):
GAAAAATTCATTTTTCTTACTT
Found at i:85974 original size:22 final size:22
Alignment explanation
Indices: 85932--85974 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
85922 TTTTTCAATT
* *
85932 AAATTATTATTTTATTGAATAA
1 AAATTAGTATTTTATTAAATAA
85954 AAATTAGTATTTT-TATAAATA
1 AAATTAGTATTTTAT-TAAATA
85975 TATTTATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
AAATTAGTATTTTATTAAATAA
Found at i:86509 original size:18 final size:17
Alignment explanation
Indices: 86479--86519 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
86469 GGAGTTTAAG
*
86479 ACAAAATCTCAAATTCA
1 ACAAAATCTCAAACTCA
*
86496 ATAAAATACTCAAACTCA
1 ACAAAAT-CTCAAACTCA
86514 ACAAAA
1 ACAAAA
86520 AAAAATCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.20
Consensus pattern (17 bp):
ACAAAATCTCAAACTCA
Found at i:87074 original size:29 final size:30
Alignment explanation
Indices: 87019--87076 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
87009 AGCAGAGTTC
*
87019 GAAAAATTATTTTTTGGGTTCTAAATTTAAA
1 GAAAAATTATTTTTGGGGTTC-AAATTTAAA
87050 GAAAAATTA-TTTTGGGGTGTC-AATTTA
1 GAAAAATTATTTTTGGGGT-TCAAATTTA
87077 GAAATTGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 6 0.24
30 8 0.32
31 11 0.44
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.43
Consensus pattern (30 bp):
GAAAAATTATTTTTGGGGTTCAAATTTAAA
Found at i:88401 original size:21 final size:21
Alignment explanation
Indices: 88356--88412 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
88346 CTTTTCCTCG
* *
88356 AGGGATCAATCCTTT-TTCAA
1 AGGGATCGATCCTTTGGTCAA
*
88376 TGGGATCGATCCTTTGGTCAA
1 AGGGATCGATCCTTTGGTCAA
88397 AGGGATCGATCCTTTG
1 AGGGATCGATCCTTTG
88413 AGCCAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (21 bp):
AGGGATCGATCCTTTGGTCAA
Found at i:90820 original size:20 final size:19
Alignment explanation
Indices: 90783--90831 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
90773 TCTAAATCAT
*
90783 TTTTGAAAAGTCCATTTTG
1 TTTTCAAAAGTCCATTTTG
90802 ATTTTCAAAA-TCCATTTTTG
1 -TTTTCAAAAGTCCA-TTTTG
*
90822 CTTTCAAAAG
1 TTTTCAAAAG
90832 AAAATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (19 bp):
TTTTCAAAAGTCCATTTTG
Found at i:92202 original size:21 final size:21
Alignment explanation
Indices: 92155--92211 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
92145 TTGTTGTCCT
92155 AGGGATCAATCCTTT-TTCAA
1 AGGGATCAATCCTTTGTTCAA
* *
92175 GGGGATCTATCCTTTGGTT-AA
1 AGGGATCAATCCTTT-GTTCAA
**
92196 AGGGATCGGTCCTTTG
1 AGGGATCAATCCTTTG
92212 AGCTAGAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 14 0.47
21 14 0.47
22 2 0.07
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (21 bp):
AGGGATCAATCCTTTGTTCAA
Found at i:99679 original size:28 final size:28
Alignment explanation
Indices: 99643--99740 Score: 72
Period size: 31 Copynumber: 3.4 Consensus size: 28
99633 TTGAGAATGG
*
99643 ATTTGGAATGTTCAAAGTTTAGGGACTA
1 ATTTAGAATGTTCAAAGTTTAGGGACTA
* * *
99671 ATTTAGAATGGGAGTCATAGTTTAAGGA-TGA
1 ATTTAGAAT--G-TTCAAAGTTTAGGGACT-A
* * * *
99702 AATTAAAATGTTCAAAAGTTAAGAGACTA
1 ATTTAGAATGTTC-AAAGTTTAGGGACTA
99731 ATTTAGAATG
1 ATTTAGAATG
99741 GAAGTCATAA
Statistics
Matches: 51, Mismatches: 13, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
28 10 0.20
29 18 0.35
30 3 0.06
31 20 0.39
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (28 bp):
ATTTAGAATGTTCAAAGTTTAGGGACTA
Found at i:99688 original size:59 final size:60
Alignment explanation
Indices: 99615--99756 Score: 160
Period size: 60 Copynumber: 2.4 Consensus size: 60
99605 TGGATCAATA
* * * * * ** * *
99615 TAGAATGAGTGTCATATTTTGAGAATGGATTTGGAATGTTC-AAAGTTTAGGGACTAATT
1 TAGAATGGGAGTCATAATTTGAGAATGAAATTAAAATGTTCAAAAGTTAAGAGACTAATT
* * *
99674 TAGAATGGGAGTCATAGTTTAAGGATGAAATTAAAATGTTCAAAAGTTAAGAGACTAATT
1 TAGAATGGGAGTCATAATTTGAGAATGAAATTAAAATGTTCAAAAGTTAAGAGACTAATT
*
99734 TAGAATGGAAGTCATAATTTGAG
1 TAGAATGGGAGTCATAATTTGAG
99757 GACTTATAAT
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 32 0.47
60 36 0.53
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (60 bp):
TAGAATGGGAGTCATAATTTGAGAATGAAATTAAAATGTTCAAAAGTTAAGAGACTAATT
Found at i:114617 original size:23 final size:23
Alignment explanation
Indices: 114590--114635 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
114580 AAAAACCAAG
*
114590 ATAAACT-TAAATATACCATTAAA
1 ATAAACTCTAAACAT-CCATTAAA
*
114613 ATAAAGTCTAAACATCCATTAAA
1 ATAAACTCTAAACATCCATTAAA
114636 CCAACCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.28
Consensus pattern (23 bp):
ATAAACTCTAAACATCCATTAAA
Done.