Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006584.1 Hibiscus syriacus cultivar Beakdansim tig00016138_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: 64054
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:2162 original size:4 final size:4
Alignment explanation
Indices: 2155--2181 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2145 ACATGCATGT
2155 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
2182 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:9337 original size:16 final size:16
Alignment explanation
Indices: 9300--9330 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9290 CTATATTCAA
9300 ATTTGTATACATTTTT
1 ATTTGTATACATTTTT
*
9316 ACTTGTATACATTTT
1 ATTTGTATACATTTT
9331 CTTTTGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.58
Consensus pattern (16 bp):
ATTTGTATACATTTTT
Found at i:10526 original size:20 final size:20
Alignment explanation
Indices: 10501--10544 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
10491 TCTTGGATAG
10501 GTGTTGTTCACCTTCTTCAA
1 GTGTTGTTCACCTTCTTCAA
10521 GTGTTGTTCACCTTCTTCAA
1 GTGTTGTTCACCTTCTTCAA
10541 GTGT
1 GTGT
10545 CTTGAAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (20 bp):
GTGTTGTTCACCTTCTTCAA
Found at i:13137 original size:22 final size:22
Alignment explanation
Indices: 13084--13137 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
13074 ATTTCCTTAG
13084 AAACATTTCATATAAAACTAAT
1 AAACATTTCATATAAAACTAAT
* *
13106 AAACAATTCATA-AAAACATCAT
1 AAACATTTCATATAAAAC-TAAT
*
13128 ATACATTTCA
1 AAACATTTCA
13138 ATTCTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.30
Consensus pattern (22 bp):
AAACATTTCATATAAAACTAAT
Found at i:13310 original size:19 final size:19
Alignment explanation
Indices: 13286--13329 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
13276 TTATACACTT
*
13286 TTTAATCCATATCAATTTG
1 TTTAATCCATATCAATTTA
** *
13305 TTTAATTTATATCCATTTA
1 TTTAATCCATATCAATTTA
13324 TTTAAT
1 TTTAAT
13330 TAGCCCAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTAATCCATATCAATTTA
Found at i:13330 original size:19 final size:19
Alignment explanation
Indices: 13294--13330 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13284 TTTTTAATCC
*
13294 ATATCAATTTGTTTAATTT
1 ATATCAATTTATTTAATTT
*
13313 ATATCCATTTATTTAATT
1 ATATCAATTTATTTAATT
13331 AGCCCAAAGT
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:0.08, G:0.03, T:0.57
Consensus pattern (19 bp):
ATATCAATTTATTTAATTT
Found at i:13451 original size:24 final size:23
Alignment explanation
Indices: 13419--13464 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
13409 TATAATTTGC
*
13419 ACCGAAGTGCCACGTAGAATATGG
1 ACCGAAGTGCCACATAG-ATATGG
13443 ACCGAAGTGCCACATAGATATG
1 ACCGAAGTGCCACATAGATATG
13465 TCCCAAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (23 bp):
ACCGAAGTGCCACATAGATATGG
Found at i:13505 original size:24 final size:24
Alignment explanation
Indices: 13478--13531 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
13468 CAAAGGGTCG
* *
13478 CGTAGAATTTGTCCCGAATGACCA
1 CGTAGAAGTTGTCCCGAAGGACCA
*
13502 CGTAG-AGTTGTCCCGAAGGACCG
1 CGTAGAAGTTGTCCCGAAGGACCA
13525 CGTAGAA
1 CGTAGAA
13532 CCCTCGACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (24 bp):
CGTAGAAGTTGTCCCGAAGGACCA
Found at i:13823 original size:27 final size:22
Alignment explanation
Indices: 13766--13808 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
13756 TGAATTTATT
*
13766 ATTTATTCACATAGAACCTATC
1 ATTTCTTCACATAGAACCTATC
13788 ATTTCTTCACATAGAACCTAT
1 ATTTCTTCACATAGAACCTAT
13809 ACTCATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (22 bp):
ATTTCTTCACATAGAACCTATC
Found at i:26257 original size:22 final size:21
Alignment explanation
Indices: 26215--26254 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
26205 GAGTTTGTTT
*
26215 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
26236 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
26255 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:29038 original size:23 final size:23
Alignment explanation
Indices: 29012--29085 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
29002 AAGTGCCACA
29012 TAGATATGTCCCGAATGACCGCG
1 TAGATATGTCCCGAATGACCGCG
* * * *
29035 TAGAATTTATCTCGAATGACCACG
1 TAG-ATATGTCCCGAATGACCGCG
* *
29059 TAGA-ATTGTCCCGAAGGACCGTG
1 TAGATA-TGTCCCGAATGACCGCG
29082 TAGA
1 TAGA
29086 ACCTCAACTT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (23 bp):
TAGATATGTCCCGAATGACCGCG
Found at i:29086 original size:23 final size:24
Alignment explanation
Indices: 29018--29086 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
29008 CACATAGATA
29018 TGTCCCGAATGACCGCGTAGAATT
1 TGTCCCGAATGACCGCGTAGAATT
* * *
29042 TATCTCGAATGACCACGTAGAA-T
1 TGTCCCGAATGACCGCGTAGAATT
* *
29065 TGTCCCGAAGGACCGTGTAGAA
1 TGTCCCGAATGACCGCGTAGAA
29087 CCTCAACTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (24 bp):
TGTCCCGAATGACCGCGTAGAATT
Found at i:29244 original size:16 final size:15
Alignment explanation
Indices: 29206--29254 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
29196 TAGACTAGCG
*
29206 CATTTTCACATAGAA
1 CATTTTCACGTAGAA
*
29221 CATTTTCACGTAGAT
1 CATTTTCACGTAGAA
*
29236 CATTTTTCACGTATAA
1 CA-TTTTCACGTAGAA
29252 CAT
1 CAT
29255 ATCACTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (15 bp):
CATTTTCACGTAGAA
Found at i:29276 original size:13 final size:14
Alignment explanation
Indices: 29242--29277 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29232 AGATCATTTT
*
29242 TCACGTATAACATA
1 TCACTTATAACATA
29256 TCACTTATAACATA
1 TCACTTATAACATA
29270 T-ACTTATA
1 TCACTTATA
29278 GTATTTCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (14 bp):
TCACTTATAACATA
Found at i:33973 original size:31 final size:30
Alignment explanation
Indices: 33904--33984 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
33894 TTGGAAAAAT
* *
33904 TTGGGGACC-ATTTTATAATTTTATGTAAG
1 TTGGGGACCTATTTAATAATTTTATGAAAG
*
33933 TTGGGGACCTATTTGATAATTTTATGAAAG
1 TTGGGGACCTATTTAATAATTTTATGAAAG
33963 TTGGGGGACCTATTTAATAATT
1 TT-GGGGACCTATTTAATAATT
33985 ATGGAAAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 9 0.19
30 20 0.43
31 18 0.38
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.42
Consensus pattern (30 bp):
TTGGGGACCTATTTAATAATTTTATGAAAG
Found at i:34082 original size:19 final size:20
Alignment explanation
Indices: 34039--34084 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
34029 TACTATGCTG
* *
34039 GAAATTAATATTAGAGTGTT
1 GAAATTGATATTAGAATGTT
*
34059 GAAATTGATGTTAGAATG-T
1 GAAATTGATATTAGAATGTT
34078 GAAATTG
1 GAAATTG
34085 GATCATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAATTGATATTAGAATGTT
Found at i:35879 original size:20 final size:20
Alignment explanation
Indices: 35854--35941 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
35844 TATACATTGG
*
35854 GTTATGAATATGAAAGTAAA
1 GTTATGAATCTGAAAGTAAA
35874 GTTATGAATCTGAAAGTAAA
1 GTTATGAATCTGAAAGTAAA
*
35894 GATATGAATCTGAAA-TAAA
1 GTTATGAATCTGAAAGTAAA
*
35913 -TTATGAATTTG---G-AAA
1 GTTATGAATCTGAAAGTAAA
35928 GTTATGAATCTGAA
1 GTTATGAATCTGAA
35942 TATGAAAGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
15 3 0.05
16 10 0.17
18 9 0.15
19 4 0.07
20 33 0.56
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.32
Consensus pattern (20 bp):
GTTATGAATCTGAAAGTAAA
Found at i:35934 original size:34 final size:38
Alignment explanation
Indices: 35854--35941 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 38
35844 TATACATTGG
*
35854 GTTATGAATATGAAAGTAAAGTTATGAATCTGAAAGTAAA
1 GTTATGAATCTGAAAGTAAAGTTATGAATCTG--AGTAAA
* *
35894 GATATGAATCTGAAA-TAAA-TTATGAATTTG-G-AAA
1 GTTATGAATCTGAAAGTAAAGTTATGAATCTGAGTAAA
35928 GTTATGAATCTGAA
1 GTTATGAATCTGAA
35942 TATGAAAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
34 16 0.36
35 1 0.02
38 10 0.23
39 4 0.09
40 13 0.30
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.32
Consensus pattern (38 bp):
GTTATGAATCTGAAAGTAAAGTTATGAATCTGAGTAAA
Found at i:39407 original size:16 final size:16
Alignment explanation
Indices: 39386--39416 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39376 CTCGATTCAT
39386 TGCTCGTTAAGCTCAA
1 TGCTCGTTAAGCTCAA
39402 TGCTCGTTAAGCTCA
1 TGCTCGTTAAGCTCA
39417 CCGAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (16 bp):
TGCTCGTTAAGCTCAA
Found at i:45659 original size:21 final size:20
Alignment explanation
Indices: 45574--45728 Score: 104
Period size: 20 Copynumber: 7.7 Consensus size: 20
45564 AATGACCAAT
**
45574 AAATTCGCAACGCG-ATCTC
1 AAATTCGCAACGCGAAAGTC
45593 AAATTCGCAATC-C--AAGTTCC
1 AAATTCGCAA-CGCGAAAG-T-C
45613 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
*
45633 AAATTCGCAACGTGAAAGTC
1 AAATTCGCAACGCGAAAGTC
** *
45653 GAAATTCGCAACGCG-ATTTT
1 -AAATTCGCAACGCGAAAGTC
* * *
45673 AAGATTCGTAACGCGATAGTAG
1 AA-ATTCGCAACGCGAAAGT-C
**
45695 AAATTCGCAACGCGATACTTC
1 AAATTCGCAACGCGA-AAGTC
*
45716 AAAATCGCAACGC
1 AAATTCGCAACGC
45729 ATTTGTTTCT
Statistics
Matches: 107, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.01
19 15 0.14
20 46 0.43
21 39 0.36
22 6 0.06
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:45666 original size:41 final size:40
Alignment explanation
Indices: 45574--45727 Score: 141
Period size: 41 Copynumber: 3.8 Consensus size: 40
45564 AATGACCAAT
* ** *
45574 AAATTCGCAACGCGATCTCAAATTCGCAA--TCCAAGTTCC
1 AAATTCGCAACGCGATTTCAAATTCGCAACGTGAAAG-TCG
**
45613 AAATTCGCAACGCGAAAGTCAAATTCGCAACGTGAAAGTCG
1 AAATTCGCAACGCG-ATTTCAAATTCGCAACGTGAAAGTCG
* * * * *
45654 AAATTCGCAACGCGATTTTAAGATTCGTAACGCGATAGTAG
1 AAATTCGCAACGCGATTTCAA-ATTCGCAACGTGAAAGTCG
*
45695 AAATTCGCAACGCGATACTTCAAAATCGCAACG
1 AAATTCGCAACGCGAT--TTCAAATTCGCAACG
45728 CATTTGTTTC
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
39 14 0.15
40 17 0.18
41 47 0.50
42 12 0.13
43 4 0.04
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (40 bp):
AAATTCGCAACGCGATTTCAAATTCGCAACGTGAAAGTCG
Found at i:46713 original size:21 final size:21
Alignment explanation
Indices: 46663--46740 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
46653 GATTTTGGGG
46663 TATCGCGTTGCGAATCTT--A-
1 TATCGCGTTGCGAAT-TTCGAC
*
46682 AATCGCGTTGCGAATTTCGAC
1 TATCGCGTTGCGAATTTCGAC
*
46703 TATCGCATTGCGAATTTCGAC
1 TATCGCGTTGCGAATTTCGAC
* *
46724 TTTCGCGCTGCGAATTT
1 TATCGCGTTGCGAATTT
46741 GGAACCTGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.04
19 14 0.28
20 1 0.02
21 33 0.66
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.35
Consensus pattern (21 bp):
TATCGCGTTGCGAATTTCGAC
Found at i:51011 original size:4 final size:5
Alignment explanation
Indices: 50996--51074 Score: 54
Period size: 5 Copynumber: 14.8 Consensus size: 5
50986 TCCGAGTCTT
50996 TTTTA TTTTA -TTTA TTTTA TTTTATA TTTTA TTTTAA TTATTA TTATTA
1 TTTTA TTTTA TTTTA TTTTA -TTT-TA TTTTA TTTT-A TT-TTA TT-TTA
* * *
51045 GTATTA TTATA TATTA TTATTA -TTTA TTTT
1 -TTTTA TTTTA TTTTA TT-TTA TTTTA TTTT
51075 GTTTACATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
4 7 0.12
5 26 0.43
6 22 0.37
7 5 0.08
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (5 bp):
TTTTA
Found at i:51040 original size:3 final size:3
Alignment explanation
Indices: 50998--51068 Score: 64
Period size: 3 Copynumber: 24.7 Consensus size: 3
50988 CGAGTCTTTT
50998 TTA TT- TTA TTTA TT- TTA TT- TTA -TA TT- TTA TT- TTAA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
51039 TTA TTA GTA TTA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
51069 TATTTTGTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
2 12 0.21
3 37 0.65
4 8 0.14
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:55489 original size:25 final size:25
Alignment explanation
Indices: 55467--55569 Score: 81
Period size: 25 Copynumber: 4.2 Consensus size: 25
55457 AGATCAAATC
55467 AAAACAAAGAGAAAAGAAACAAAGA
1 AAAACAAAGAGAAAAGAAACAAAGA
*
55492 AAAACAAAGAGCAAAGAGAA-AAAG-
1 AAAACAAAGAGAAAAGA-AACAAAGA
* * *
55516 TAAAGAAAGA-AAAACAAA-AAAGAAA
1 AAAACAAAGAGAAAAGAAACAAAG--A
* *
55541 AAAAGCAAAGAGAAAA-AATCAAATA
1 AAAA-CAAAGAGAAAAGAAACAAAGA
55566 AAAA
1 AAAA
55570 GAACAAAAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
22 6 0.10
23 4 0.06
24 8 0.13
25 28 0.45
26 9 0.15
27 7 0.11
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.03
Consensus pattern (25 bp):
AAAACAAAGAGAAAAGAAACAAAGA
Found at i:55530 original size:34 final size:32
Alignment explanation
Indices: 55471--55533 Score: 99
Period size: 34 Copynumber: 1.9 Consensus size: 32
55461 CAAATCAAAA
55471 CAAAGAGAAAAGAAACAAAGAAAAACAAAGAG
1 CAAAGAGAAAAGAAACAAAGAAAAACAAAGAG
*
55503 CAAAGAGAAAAAGTAAAGAAAGAAAAACAAA
1 CAAAGAG-AAAAG-AAACAAAGAAAAACAAA
55534 AAAGAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 7 0.25
33 5 0.18
34 16 0.57
ACGTcount: A:0.73, C:0.08, G:0.17, T:0.02
Consensus pattern (32 bp):
CAAAGAGAAAAGAAACAAAGAAAAACAAAGAG
Found at i:55537 original size:17 final size:17
Alignment explanation
Indices: 55487--55549 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
55477 GAAAAGAAAC
*
55487 AAAGAAAAAC-AAAGAG
1 AAAGAAAAACAAAAAAG
**
55503 CAAAGAGAAAA-AGTAAAG
1 -AAAGA-AAAACAAAAAAG
55521 AAAGAAAAACAAAAAAG
1 AAAGAAAAACAAAAAAG
*
55538 AAA-AAAAGCAAA
1 AAAGAAAAACAAA
55550 GAGAAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
16 12 0.32
17 18 0.49
18 7 0.19
ACGTcount: A:0.76, C:0.06, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAGAAAAACAAAAAAG
Found at i:55544 original size:30 final size:32
Alignment explanation
Indices: 55466--55584 Score: 90
Period size: 30 Copynumber: 3.8 Consensus size: 32
55456 AAGATCAAAT
* *
55466 CAAA-ACAAAG-AGAAAAGAAACAAAGAAAAA
1 CAAAGACAAAGAAAAAAAGAAAGAAAGAAAAA
*
55496 CAAAGAGCAAAGAGAAAAAGTAAAGAAAGAAAAA
1 CAAAGA-CAAAGAAAAAAAG-AAAGAAAGAAAAA
*
55530 C-AA-A-AAAGAAAAAAAGCAAAGAGAA-AAAAT
1 CAAAGACAAAGAAAAAAAG-AAAGA-AAGAAAAA
* * *
55560 CAAATAAAAAGAACAAAAG-AAGAAA
1 CAAAGACAAAGAAAAAAAGAAAGAAA
55585 AAATAAGAAG
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
30 27 0.36
31 9 0.12
32 7 0.09
33 18 0.24
34 13 0.18
ACGTcount: A:0.75, C:0.08, G:0.15, T:0.03
Consensus pattern (32 bp):
CAAAGACAAAGAAAAAAAGAAAGAAAGAAAAA
Found at i:55549 original size:43 final size:43
Alignment explanation
Indices: 55467--55587 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 43
55457 AGATCAAATC
*
55467 AAAA-CAAAGAGAAAAGAAACAAAGAAA-AACAAAGAGCAAAGAGAA
1 AAAATCAAAGA-AAAA-AAACAAA-AAAGAA-AAAAAGCAAAGAGAA
*
55512 AAAGT-AAAGAAAGAAAAACAAAAAAGAAAAAAAGCAAAGAGAA
1 AAAATCAAAGAAA-AAAAACAAAAAAGAAAAAAAGCAAAGAGAA
* *
55555 AAAATCAAATAAAAAGAACAAAAGAAGAAAAAA
1 AAAATCAAAGAAAAAAAACAAAA-AAGAAAAAA
55588 TAAGAAGAGC
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
43 30 0.45
44 26 0.39
45 10 0.15
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (43 bp):
AAAATCAAAGAAAAAAAACAAAAAAGAAAAAAAGCAAAGAGAA
Found at i:55558 original size:44 final size:42
Alignment explanation
Indices: 55467--55587 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 42
55457 AGATCAAATC
*
55467 AAAA-CAAAGAGAAAAGAAACAAAGAAA-AACAAAGAGCAAAGAGA
1 AAAATCAAAGA-AAAA-AAACAAA-AAAGAA-AAAAAGCAAAGAGA
55511 AAAAGT-AAAGAAAGAAAAACAAAAAAGAAAAAAAGCAAAGAGAA
1 AAAA-TCAAAGAAA-AAAAACAAAAAAGAAAAAAAGCAAAGAG-A
* *
55555 AAAATCAAATAAAAAGAACAAAAGAAGAAAAAA
1 AAAATCAAAGAAAAAAAACAAAA-AAGAAAAAA
55588 TAAGAAGAGC
Statistics
Matches: 67, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
43 25 0.37
44 35 0.52
45 7 0.10
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (42 bp):
AAAATCAAAGAAAAAAAACAAAAAAGAAAAAAAGCAAAGAGA
Found at i:56687 original size:31 final size:33
Alignment explanation
Indices: 56607--56673 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
56597 AGAATCAGTG
*
56607 TTGAAGTAATCAACATCGAATATTGGGGCATCT
1 TTGAAGCAATCAACATCGAATATTGGGGCATCT
*
56640 TTGAAGCAATCAACATCGAATGTTGGGGCATCT
1 TTGAAGCAATCAACATCGAATATTGGGGCATCT
56673 T
1 T
56674 GGGGATTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (33 bp):
TTGAAGCAATCAACATCGAATATTGGGGCATCT
Found at i:56879 original size:63 final size:63
Alignment explanation
Indices: 56758--56879 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 63
56748 ATCAGTATCC
* *
56758 TTTGAGTTGTTTTTCTAGAAACAAATTTTTGTCTCTCTTGAGACAATTTCTTTAGAAAAAATA
1 TTTGAGTTGTTTTTCTAGAAACAAAATTTTGTCTCTCTTGAGACAATTTCCTTAGAAAAAATA
* * * * * *
56821 TTTGAGTT-TTTTTATTTGAAATAAAATTTTGTCTCAT-TTGAGATAGTTTCCTTCGAAAA
1 TTTGAGTTGTTTTT-CTAGAAACAAAATTTTGTCTC-TCTTGAGACAATTTCCTTAGAAAA
56880 CAAATTTTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
62 5 0.10
63 43 0.88
64 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (63 bp):
TTTGAGTTGTTTTTCTAGAAACAAAATTTTGTCTCTCTTGAGACAATTTCCTTAGAAAAAATA
Found at i:57033 original size:36 final size:36
Alignment explanation
Indices: 56971--57076 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 36
56961 TTGAGATCGT
** * *
56971 TTTCTC-AAAAACAAACATTCTTTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTATCTCGCTTGAGACAA
*
57006 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTATCTCGCTTGAGACAA
* * * * *
57042 TTTCTATCAAAGCAAATTTCACCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTATCTCGCTTGAGACA
57077 TTTTTTTCTC
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
35 6 0.10
36 54 0.90
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTATCTCGCTTGAGACAA
Found at i:57347 original size:29 final size:29
Alignment explanation
Indices: 57302--57461 Score: 100
Period size: 28 Copynumber: 5.5 Consensus size: 29
57292 TATTGAGATA
*
57302 GTTTCTTTTG-AAGAAAAATCTTTGAGTC
1 GTTTCTTTTGAAACAAAAATCTTTGAGTC
* * *
57330 GTTTCTTTTGAAACAAAAAACTTCGAGTTT
1 GTTTCTTTTGAAACAAAAATCTTTGAG-TC
* ** *
57360 GCTTCTTTTGAAACAAAGTTTTGTCTCTTGAGAC
1 GTTTCTTTTGAAACAAA----AATCT-TTGAGTC
**
57394 AGTTT-TCATG----AAAAATCTTTGAGTC
1 -GTTTCTTTTGAAACAAAAATCTTTGAGTC
* *
57419 ATTT-TTTTGAAACAAAAATCTTTTAGTC
1 GTTTCTTTTGAAACAAAAATCTTTGAGTC
57447 GTTTCTTTTGAAACA
1 GTTTCTTTTGAAACA
57462 CCATCATCTT
Statistics
Matches: 97, Mismatches: 22, Indels: 25
0.67 0.15 0.17
Matches are distributed among these distances:
24 6 0.06
25 6 0.06
26 3 0.03
28 27 0.28
29 23 0.24
30 20 0.21
34 5 0.05
35 7 0.07
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (29 bp):
GTTTCTTTTGAAACAAAAATCTTTGAGTC
Found at i:58646 original size:45 final size:44
Alignment explanation
Indices: 58547--58648 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 44
58537 TGCATATGAG
* *
58547 GTGTATCGATGCACTCCTTTAAAATAAAACATCGAATGTCATTA
1 GTGTATCGATGCACCCCTTTAAAATAAAACATCGAATGACATTA
*
58591 GTGTATCGATGCACCCCTTTAAAATACAAACATCGAATGAGATTTA
1 GTGTATCGATGCACCCCTTTAAAATA-AAACATCGAATGACA-TTA
*
58637 -TGTACCGATGCA
1 GTGTATCGATGCA
58649 TAGATTATGC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
44 25 0.48
45 24 0.46
46 3 0.06
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (44 bp):
GTGTATCGATGCACCCCTTTAAAATAAAACATCGAATGACATTA
Found at i:59263 original size:18 final size:18
Alignment explanation
Indices: 59240--59313 Score: 85
Period size: 18 Copynumber: 4.0 Consensus size: 18
59230 GAGGGATTAT
*
59240 TAGTGGTCCTTCGGGACA
1 TAGTGGTTCTTCGGGACA
*
59258 TAGTGGTTCTTCGGAACAA
1 TAGTGGTTCTTCGGGAC-A
*
59277 TCAGTGGTTCTTCAGGACA
1 T-AGTGGTTCTTCGGGACA
**
59296 TAGTGGTAATTCGGGACA
1 TAGTGGTTCTTCGGGACA
59314 AATTTCAGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 29 0.62
19 4 0.09
20 14 0.30
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (18 bp):
TAGTGGTTCTTCGGGACA
Found at i:59309 original size:38 final size:38
Alignment explanation
Indices: 59241--59314 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
59231 AGGGATTATT
* **
59241 AGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACAATC
1 AGTGGTCCTTCAGGACATAGTGGTAATTCGGAACAATC
* *
59279 AGTGGTTCTTCAGGACATAGTGGTAATTCGGGACAA
1 AGTGGTCCTTCAGGACATAGTGGTAATTCGGAACAA
59315 ATTTCAGTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (38 bp):
AGTGGTCCTTCAGGACATAGTGGTAATTCGGAACAATC
Found at i:60678 original size:20 final size:20
Alignment explanation
Indices: 60643--60682 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
60633 TAAATAAATA
*
60643 TTAAAACATGATTAAAATAAG
1 TTAAAACATAATT-AAATAAG
60664 TTAAAA-ATAATTAAATAAG
1 TTAAAACATAATTAAATAAG
60683 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAAAACATAATTAAATAAG
Found at i:60747 original size:3 final size:3
Alignment explanation
Indices: 60739--60768 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
60729 TTTATGGCTA
*
60739 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
60769 TAAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:62086 original size:3 final size:3
Alignment explanation
Indices: 62078--62131 Score: 60
Period size: 3 Copynumber: 18.0 Consensus size: 3
62068 AGCCTGTTTG
62078 TAA TAA TAA T-A TAA TAA TAA TAA -AA TAA -AA TAA TAA TAAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA
62122 TAAA TAA TAA
1 T-AA TAA TAA
62132 ATGGGTAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.13
3 30 0.64
4 11 0.23
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:62094 original size:11 final size:11
Alignment explanation
Indices: 62078--62131 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
62068 AGCCTGTTTG
62078 TAATAATAATA
1 TAATAATAATA
62089 TAATAATAATA
1 TAATAATAATA
*
62100 AAATAA-AATAA
1 TAATAATAAT-A
62111 TAATAAATAA-A
1 TAAT-AATAATA
62122 TAAATAATAA
1 T-AATAATAA
62132 ATGGGTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 3 0.08
11 27 0.73
12 5 0.14
13 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAATAATAATA
Found at i:62110 original size:19 final size:19
Alignment explanation
Indices: 62082--62131 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
62072 TGTTTGTAAT
*
62082 AATAATATAATAAT-AATAA
1 AATAAAATAATAATAAAT-A
62101 AATAAAATAATAATAAATA
1 AATAAAATAATAATAAATA
62120 AAT-AAATAATAA
1 AATAAAATAATAA
62132 ATGGGTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.31
19 17 0.59
20 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATAAAATAATAATAAATA
Found at i:62652 original size:123 final size:122
Alignment explanation
Indices: 62348--62776 Score: 396
Period size: 113 Copynumber: 3.6 Consensus size: 122
62338 GTAATCTAGC
*
62348 AAAGGTTGAACAAGCTATTCTCATTGTGAA---CTTCTTC-TTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
* * * *
62409 GTGAAC-TCCTTCTGGAAATGCTGATGATGATATCTCCTTCTGTGATAGTCATGCAA
66 ATGAACTTCCTTCTGGAAAAGCTGATGATGATATATCCTTCTATGATAGTCATGCAA
* * *
62465 AAA-GTCGAACAAGCTCTT-TCATTATGAACTTCTTCTTCTTTCTTCAAATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
* * *
62528 ATGAACTTTC-TCTGGAAAAGTTGATGCTGATATATCTCTTCTATGATAGAGTCATG-AA
66 ATGAACTTCCTTCTGGAAAAGCTGATGATGATATATC-CTTCTATGAT--AGTCATGCAA
** * * *
62586 AAAGGTTGAACAAAATTTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTATTCTTATT
1 AAAGGTTGAACAAGCTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
* * ** ** * * **
62651 ATGAAC-T-CTACCTGG-CAA--T-AT--TGATCCATCAAAT-GATGA-ATTCAAAC-A
66 ATGAACTTCCT-TCTGGAAAAGCTGATGATGATATATC-CTTCTATGATAGTCATGCAA
** * *
62699 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
62764 ATGAACTT-CTTCT
66 ATGAACTTCCTTCT
62777 TCCTTCTTCA
Statistics
Matches: 263, Mismatches: 35, Indels: 32
0.80 0.11 0.10
Matches are distributed among these distances:
113 73 0.28
114 3 0.01
115 9 0.03
116 17 0.06
117 11 0.04
118 7 0.03
119 52 0.20
120 12 0.05
121 6 0.02
122 21 0.08
123 52 0.20
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (122 bp):
AAAGGTTGAACAAGCTATTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCCTTCTGGAAAAGCTGATGATGATATATCCTTCTATGATAGTCATGCAA
Found at i:62757 original size:40 final size:40
Alignment explanation
Indices: 62713--62810 Score: 196
Period size: 40 Copynumber: 2.5 Consensus size: 40
62703 GTTGAACAAA
62713 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
62753 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
62793 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
62811 CTAACTGGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.18, C:0.24, G:0.09, T:0.48
Consensus pattern (40 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:62897 original size:111 final size:113
Alignment explanation
Indices: 62751--63275 Score: 701
Period size: 111 Copynumber: 4.8 Consensus size: 113
62741 TCTTCAGATG
62751 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
* *
62816 TGGTAAAGTTGATCCA-CGAGTGATGAATTTAAGCAAAAAG-TGAACA
66 TGGTAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACA
62862 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
* * *
62927 TGGTAAAGTTGATCCA-CGAGTGATGAATTTAAGCAAAAAGTTGAAAA
66 TGGTAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACA
* * * *
62974 AGTTCTTCTCATTATGAACTTCTTTTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTCGACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
* * * *
63038 TGGAAAAGTTGATCCATTGAATGATGAATTCAATCGAAAAGTTGAACA
66 TGGTAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACA
* * * *
63086 AGTTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGATGAG----TATCATTATGAACTCTACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
* * *
63147 TGGT-ATG-TGATCCATCAAATGATGAATTCAAGCGAAAAGTTGAACA
66 TGGTAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACA
*
63193 AGTTCTTCTCATTATGAA------CTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
* *
63250 TAG-AAATGTTGATCCATTGAATGATG
66 TGGTAAA-GTTGATCCATCGAATGATG
63276 GATTTGAACT
Statistics
Matches: 374, Mismatches: 30, Indels: 26
0.87 0.07 0.06
Matches are distributed among these distances:
100 13 0.03
101 3 0.01
103 4 0.01
104 16 0.04
105 15 0.04
107 54 0.14
108 2 0.01
109 20 0.05
111 152 0.41
112 84 0.22
113 11 0.03
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAC
TGGTAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACA
Found at i:62920 original size:151 final size:153
Alignment explanation
Indices: 62603--62921 Score: 509
Period size: 153 Copynumber: 2.1 Consensus size: 153
62593 GAACAAAATT
* * *
62603 TTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTATTCTTATTATGAACTCTACCTGGCA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTCTAACTGGCA
*
62668 ATATTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
66 ATATTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
62733 TTCTTCCTTCTTCAGATGAGTTC
131 TTCTTCCTTCTTCAGATGAGTTC
* *
62756 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGTA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTCTAACTGGCA
* * * * *
62821 A-AGTTGATCCA-CGAGTGATGAATTTAAGCAAAAAG-TGAACAAGTTCTTCTCATTATGAACTT
66 ATA-TTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTT
62883 CTTCTTCCTTCTTCAGATGAGTTC
130 CTTCTTCCTTCTTCAGATGAGTTC
62907 TTCTCATTATGAACT
1 TTCTCATTATGAACT
62922 CTAACTGGTA
Statistics
Matches: 154, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
151 65 0.42
152 20 0.13
153 69 0.45
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.40
Consensus pattern (153 bp):
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTCTAACTGGCA
ATATTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTC
Found at i:63248 original size:16 final size:16
Alignment explanation
Indices: 63196--63250 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
63186 TTGAACAAGT
63196 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* **
63212 TTCTTCTTCA-GATGAGT
1 -TCTTC-TCATTATGAAC
63229 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
63245 TCTTCT
1 TCTTCT
63251 AGAAATGTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 3 0.10
16 15 0.50
17 9 0.30
18 3 0.10
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.47
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:63703 original size:22 final size:22
Alignment explanation
Indices: 63678--63728 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
63668 GATAAAGCTT
* *
63678 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
* *
63700 TCATCTTTAAAAAGGGAATTTA
1 TCATCTTTAAAAAGAGAATCTA
63722 TCATCTT
1 TCATCTT
63729 GAAGAGTGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Done.