Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004470.1 Hibiscus syriacus cultivar Beakdansim tig00009857_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: 61198
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1348 original size:21 final size:22
Alignment explanation
Indices: 1294--1348 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
1284 CCCTCTAGGG
*
1294 GTATCGATACTCATTCAAAAGAT
1 GTATCGATACACATTC-AAAGAT
*
1317 GTATC-AGTACACATTC-AAGGT
1 GTATCGA-TACACATTCAAAGAT
1338 GTATCGATACA
1 GTATCGATACA
1349 TAGCAAGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 13 0.46
22 2 0.07
23 13 0.46
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (22 bp):
GTATCGATACACATTCAAAGAT
Found at i:3595 original size:30 final size:30
Alignment explanation
Indices: 3559--3620 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
3549 AATTAATATT
3559 GTGCATCGATACGCTACAGTAACTACTACA
1 GTGCATCGATACGCTACAGTAACTACTACA
* *
3589 GTGCATCGATACGCTACGGTAACTGCTACA
1 GTGCATCGATACGCTACAGTAACTACTACA
3619 GT
1 GT
3621 AATTTTCGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (30 bp):
GTGCATCGATACGCTACAGTAACTACTACA
Found at i:4188 original size:33 final size:33
Alignment explanation
Indices: 4151--4217 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
4141 ACCGTAGTGC
*
4151 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTAGTGTCCACCA
4184 TAATCCGTATGACACATAAGGTAGTGTCCACCA
1 TAATCCGTATGACACATAAGGTAGTGTCCACCA
4217 T
1 T
4218 CTGTACTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTAGTGTCCACCA
Found at i:8783 original size:18 final size:18
Alignment explanation
Indices: 8742--8784 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
8732 AACTCCAACG
8742 TTCTTCTTTTTCTCTGTC
1 TTCTTCTTTTTCTCTGTC
*
8760 TCCTTCTTTTTCTC-GTCC
1 TTCTTCTTTTTCTCTGT-C
8778 TTCTTCT
1 TTCTTCT
8785 CGAGGTCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.00, C:0.33, G:0.05, T:0.63
Consensus pattern (18 bp):
TTCTTCTTTTTCTCTGTC
Found at i:10703 original size:23 final size:23
Alignment explanation
Indices: 10671--10715 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
10661 GAGTCGAGGG
*
10671 TTCTACGTGGTCCTTAGGGACAA
1 TTCTAAGTGGTCCTTAGGGACAA
* *
10694 TTCTAAGTGGTCGTTTGGGACA
1 TTCTAAGTGGTCCTTAGGGACA
10716 TTTATACGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (23 bp):
TTCTAAGTGGTCCTTAGGGACAA
Found at i:15667 original size:18 final size:18
Alignment explanation
Indices: 15644--15689 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
15634 TATTAGGGAA
15644 TATCGATACTCCCATGAG
1 TATCGATACTCCCATGAG
15662 TATCGATACTCCCATGAG
1 TATCGATACTCCCATGAG
15680 TATCGATACT
1 TATCGATACT
15690 AAAAGTGGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (18 bp):
TATCGATACTCCCATGAG
Found at i:17141 original size:25 final size:26
Alignment explanation
Indices: 17121--17170 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
17111 CTAATTGTAT
17121 TTAAAAA-GTTT-GGATCAAATTGCA
1 TTAAAAATGTTTGGGATCAAATTGCA
*
17145 TTAAAAATGTTTGGGCTCAAATTGCA
1 TTAAAAATGTTTGGGATCAAATTGCA
17171 CGTCAATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 4 0.17
26 12 0.52
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (26 bp):
TTAAAAATGTTTGGGATCAAATTGCA
Found at i:22395 original size:12 final size:12
Alignment explanation
Indices: 22370--22439 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
22360 ACGAAGATAT
* *
22370 CAGAAATCAAAA
1 CAGAATTCAGAA
22382 CAGAATTCAGAA
1 CAGAATTCAGAA
22394 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
22406 CAGAATCCAGAT
1 CAGAATTCAGAA
*
22418 CAGAAATCAGAA
1 CAGAATTCAGAA
22430 CAGAATTCAG
1 CAGAATTCAG
22440 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:22439 original size:48 final size:47
Alignment explanation
Indices: 22368--22476 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
22358 AAACGAAGAT
*
22368 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
22415 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
22463 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
22477 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:22474 original size:24 final size:25
Alignment explanation
Indices: 22368--22476 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
22358 AAACGAAGAT
*
22368 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
22392 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
22416 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
22440 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
22465 -TCGGAAATCAGA
1 ATCAGAAATCAGA
22477 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:24046 original size:31 final size:31
Alignment explanation
Indices: 24011--24110 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 31
24001 TTAATTGCTT
24011 TCTTAAACACTCTCTGATCTTGAAACGGTTC
1 TCTTAAACACTCTCTGATCTTGAAACGGTTC
* *
24042 TCTTAACAGACT-TCTAGTATCCTTCACAAAC---TC
1 TCTTAA-ACACTCTCT-G-AT-CTT--GAAACGGTTC
24075 T-TCT-AACACTCTCTGATCTTGAAACGGTTC
1 TCT-TAAACACTCTCTGATCTTGAAACGGTTC
24105 TCTTAA
1 TCTTAA
24111 CAGACTTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 26
0.63 0.05 0.32
Matches are distributed among these distances:
27 4 0.08
29 3 0.06
30 6 0.12
31 16 0.31
32 10 0.19
33 6 0.12
34 3 0.06
36 4 0.08
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (31 bp):
TCTTAAACACTCTCTGATCTTGAAACGGTTC
Found at i:24115 original size:63 final size:63
Alignment explanation
Indices: 24016--24138 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
24006 TGCTTTCTTA
24016 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
24079 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
24139 CCTAGGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:25070 original size:7 final size:7
Alignment explanation
Indices: 25058--25089 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
25048 TGGTCAATTC
25058 CGGTCAA
1 CGGTCAA
25065 CGGTCAA
1 CGGTCAA
25072 CGGGTCAA
1 C-GGTCAA
25080 CGGTCAA
1 CGGTCAA
25087 CGG
1 CGG
25090 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:25079 original size:8 final size:8
Alignment explanation
Indices: 25059--25149 Score: 69
Period size: 8 Copynumber: 12.5 Consensus size: 8
25049 GGTCAATTCC
25059 GGTCAAC-
1 GGTCAACG
25066 GGTCAACG
1 GGTCAACG
25074 GGTCAAC-
1 GGTCAACG
25081 GGTCAACG
1 GGTCAACG
25089 GGT---CG
1 GGTCAACG
25094 GGTCAACG
1 GGTCAACG
25102 GGT---CG
1 GGTCAACG
25107 GGTCAACG
1 GGTCAACG
**
25115 GGTCGGGTCG
1 GGTC--AACG
25125 GGTCAACG
1 GGTCAACG
25133 GGT---CG
1 GGTCAACG
25138 GGTCAACG
1 GGTCAACG
25146 GGTC
1 GGTC
25150 GGGTCGGGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
5 15 0.22
7 14 0.21
8 32 0.48
10 6 0.09
ACGTcount: A:0.18, C:0.24, G:0.43, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:25099 original size:13 final size:13
Alignment explanation
Indices: 25066--25154 Score: 106
Period size: 13 Copynumber: 6.3 Consensus size: 13
25056 TCCGGTCAAC
*
25066 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
25081 GGTCAACGGGTCG
1 GGTCAACGGGTCG
25094 GGTCAACGGGTCG
1 GGTCAACGGGTCG
25107 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
25125 GGTCAACGGGTCG
1 GGTCAACGGGTCG
25138 GGTCAACGGGTCG
1 GGTCAACGGGTCG
25151 GGTC
1 GGTC
25155 GGGTTGTGAC
Statistics
Matches: 68, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
13 43 0.63
15 12 0.18
18 13 0.19
ACGTcount: A:0.16, C:0.24, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:25125 original size:31 final size:31
Alignment explanation
Indices: 25087--25158 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
25077 CAACGGTCAA
25087 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
25118 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
25149 CGGGTCGGGT
1 CGGGTCGGGT
25159 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
Found at i:25158 original size:18 final size:18
Alignment explanation
Indices: 25100--25141 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
25090 GTCGGGTCAA
25100 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
25118 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
25136 CGGGTC
1 CGGGTC
25142 AACGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:27254 original size:12 final size:12
Alignment explanation
Indices: 27229--27298 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
27219 ACGAAGATAT
* *
27229 CAGAAATCAAAA
1 CAGAATTCAGAA
27241 CAGAATTCAGAA
1 CAGAATTCAGAA
27253 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
27265 CAGAATCCAGAT
1 CAGAATTCAGAA
*
27277 CAGAAATCAGAA
1 CAGAATTCAGAA
27289 CAGAATTCAG
1 CAGAATTCAG
27299 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:27298 original size:48 final size:47
Alignment explanation
Indices: 27227--27335 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
27217 AAACGAAGAT
*
27227 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
27274 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
27322 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
27336 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:27333 original size:24 final size:25
Alignment explanation
Indices: 27227--27335 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
27217 AAACGAAGAT
*
27227 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
27251 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
27275 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
27299 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
27324 -TCGGAAATCAGA
1 ATCAGAAATCAGA
27336 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:28904 original size:31 final size:31
Alignment explanation
Indices: 28869--28968 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 31
28859 TTAATTGCTT
28869 TCTTAAACACTCTCTGATCTTGAAACGGTTC
1 TCTTAAACACTCTCTGATCTTGAAACGGTTC
* *
28900 TCTTAACAGACT-TCTAGTATCCTTCACAAAC---TC
1 TCTTAA-ACACTCTCT-G-AT-CTT--GAAACGGTTC
28933 T-TCT-AACACTCTCTGATCTTGAAACGGTTC
1 TCT-TAAACACTCTCTGATCTTGAAACGGTTC
28963 TCTTAA
1 TCTTAA
28969 CAGACTTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 26
0.63 0.05 0.32
Matches are distributed among these distances:
27 4 0.08
29 3 0.06
30 6 0.12
31 16 0.31
32 10 0.19
33 6 0.12
34 3 0.06
36 4 0.08
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (31 bp):
TCTTAAACACTCTCTGATCTTGAAACGGTTC
Found at i:28973 original size:63 final size:63
Alignment explanation
Indices: 28874--28996 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
28864 TGCTTTCTTA
28874 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
28937 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
28997 CCTAGGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:29927 original size:7 final size:7
Alignment explanation
Indices: 29915--29946 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
29905 TGGTCAATTC
29915 CGGTCAA
1 CGGTCAA
29922 CGGTCAA
1 CGGTCAA
29929 CGGGTCAA
1 C-GGTCAA
29937 CGGTCAA
1 CGGTCAA
29944 CGG
1 CGG
29947 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:29936 original size:8 final size:8
Alignment explanation
Indices: 29916--29975 Score: 64
Period size: 8 Copynumber: 8.5 Consensus size: 8
29906 GGTCAATTCC
29916 GGTCAAC-
1 GGTCAACG
29923 GGTCAACG
1 GGTCAACG
29931 GGTCAAC-
1 GGTCAACG
29938 GGTCAACG
1 GGTCAACG
29946 GGT---CG
1 GGTCAACG
29951 GGTCAACG
1 GGTCAACG
29959 GGT---CG
1 GGTCAACG
29964 GGTCAACG
1 GGTCAACG
29972 GGTC
1 GGTC
29976 GGGTCGGGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
5 10 0.22
7 14 0.31
8 21 0.47
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:29956 original size:13 final size:13
Alignment explanation
Indices: 29923--29980 Score: 89
Period size: 13 Copynumber: 4.3 Consensus size: 13
29913 TCCGGTCAAC
*
29923 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
29938 GGTCAACGGGTCG
1 GGTCAACGGGTCG
29951 GGTCAACGGGTCG
1 GGTCAACGGGTCG
29964 GGTCAACGGGTCG
1 GGTCAACGGGTCG
29977 GGTC
1 GGTC
29981 GGGTTGTGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
13 30 0.71
15 12 0.29
ACGTcount: A:0.17, C:0.24, G:0.43, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:32069 original size:12 final size:12
Alignment explanation
Indices: 32044--32113 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
32034 ACGAAGATAT
* *
32044 CAGAAATCAAAA
1 CAGAATTCAGAA
32056 CAGAATTCAGAA
1 CAGAATTCAGAA
32068 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
32080 CAGAATCCAGAT
1 CAGAATTCAGAA
*
32092 CAGAAATCAGAA
1 CAGAATTCAGAA
32104 CAGAATTCAG
1 CAGAATTCAG
32114 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:32113 original size:48 final size:47
Alignment explanation
Indices: 32042--32150 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
32032 AAACGAAGAT
*
32042 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
32089 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
32137 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
32151 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:32148 original size:24 final size:25
Alignment explanation
Indices: 32042--32150 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
32032 AAACGAAGAT
*
32042 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
32066 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
32090 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
32114 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
32139 -TCGGAAATCAGA
1 ATCAGAAATCAGA
32151 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:33720 original size:31 final size:31
Alignment explanation
Indices: 33685--33784 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 31
33675 TTAATTGCTT
33685 TCTTAAACACTCTCTGATCTTGAAACGGTTC
1 TCTTAAACACTCTCTGATCTTGAAACGGTTC
* *
33716 TCTTAACAGACT-TCTAGTATCCTTCACAAAC---TC
1 TCTTAA-ACACTCTCT-G-AT-CTT--GAAACGGTTC
33749 T-TCT-AACACTCTCTGATCTTGAAACGGTTC
1 TCT-TAAACACTCTCTGATCTTGAAACGGTTC
33779 TCTTAA
1 TCTTAA
33785 CAGACTTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 26
0.63 0.05 0.32
Matches are distributed among these distances:
27 4 0.08
29 3 0.06
30 6 0.12
31 16 0.31
32 10 0.19
33 6 0.12
34 3 0.06
36 4 0.08
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (31 bp):
TCTTAAACACTCTCTGATCTTGAAACGGTTC
Found at i:33789 original size:63 final size:63
Alignment explanation
Indices: 33690--33812 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
33680 TGCTTTCTTA
33690 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
33753 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
33813 CCTAGGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:34742 original size:7 final size:7
Alignment explanation
Indices: 34730--34761 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
34720 TGGTCAATTC
34730 CGGTCAA
1 CGGTCAA
34737 CGGTCAA
1 CGGTCAA
34744 CGGGTCAA
1 C-GGTCAA
34752 CGGTCAA
1 CGGTCAA
34759 CGG
1 CGG
34762 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:34751 original size:8 final size:8
Alignment explanation
Indices: 34731--34821 Score: 69
Period size: 8 Copynumber: 12.5 Consensus size: 8
34721 GGTCAATTCC
34731 GGTCAAC-
1 GGTCAACG
34738 GGTCAACG
1 GGTCAACG
34746 GGTCAAC-
1 GGTCAACG
34753 GGTCAACG
1 GGTCAACG
34761 GGT---CG
1 GGTCAACG
34766 GGTCAACG
1 GGTCAACG
34774 GGT---CG
1 GGTCAACG
34779 GGTCAACG
1 GGTCAACG
**
34787 GGTCGGGTCG
1 GGTC--AACG
34797 GGTCAACG
1 GGTCAACG
34805 GGT---CG
1 GGTCAACG
34810 GGTCAACG
1 GGTCAACG
34818 GGTC
1 GGTC
34822 GGGTCGGGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
5 15 0.22
7 14 0.21
8 32 0.48
10 6 0.09
ACGTcount: A:0.18, C:0.24, G:0.43, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:34771 original size:13 final size:13
Alignment explanation
Indices: 34738--34826 Score: 106
Period size: 13 Copynumber: 6.3 Consensus size: 13
34728 TCCGGTCAAC
*
34738 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
34753 GGTCAACGGGTCG
1 GGTCAACGGGTCG
34766 GGTCAACGGGTCG
1 GGTCAACGGGTCG
34779 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
34797 GGTCAACGGGTCG
1 GGTCAACGGGTCG
34810 GGTCAACGGGTCG
1 GGTCAACGGGTCG
34823 GGTC
1 GGTC
34827 GGGTTGTGAC
Statistics
Matches: 68, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
13 43 0.63
15 12 0.18
18 13 0.19
ACGTcount: A:0.16, C:0.24, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:34797 original size:31 final size:31
Alignment explanation
Indices: 34759--34830 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
34749 CAACGGTCAA
34759 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
34790 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
34821 CGGGTCGGGT
1 CGGGTCGGGT
34831 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
Found at i:34830 original size:18 final size:18
Alignment explanation
Indices: 34772--34813 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
34762 GTCGGGTCAA
34772 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
34790 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
34808 CGGGTC
1 CGGGTC
34814 AACGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:36919 original size:12 final size:12
Alignment explanation
Indices: 36894--36963 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
36884 ACGAAGATAT
* *
36894 CAGAAATCAAAA
1 CAGAATTCAGAA
36906 CAGAATTCAGAA
1 CAGAATTCAGAA
36918 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
36930 CAGAATCCAGAT
1 CAGAATTCAGAA
*
36942 CAGAAATCAGAA
1 CAGAATTCAGAA
36954 CAGAATTCAG
1 CAGAATTCAG
36964 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:36963 original size:48 final size:47
Alignment explanation
Indices: 36892--37000 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
36882 AAACGAAGAT
*
36892 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
36939 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
36987 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
37001 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:36998 original size:24 final size:25
Alignment explanation
Indices: 36892--37000 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
36882 AAACGAAGAT
*
36892 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
36916 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
36940 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
36964 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
36989 -TCGGAAATCAGA
1 ATCAGAAATCAGA
37001 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:38569 original size:31 final size:31
Alignment explanation
Indices: 38534--38633 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 31
38524 TTAATTGCTT
38534 TCTTAAACACTCTCTGATCTTGAAACGGTTC
1 TCTTAAACACTCTCTGATCTTGAAACGGTTC
* *
38565 TCTTAACAGACT-TCTAGTATCCTTCACAAAC---TC
1 TCTTAA-ACACTCTCT-G-AT-CTT--GAAACGGTTC
38598 T-TCT-AACACTCTCTGATCTTGAAACGGTTC
1 TCT-TAAACACTCTCTGATCTTGAAACGGTTC
38628 TCTTAA
1 TCTTAA
38634 CAGACTTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 26
0.63 0.05 0.32
Matches are distributed among these distances:
27 4 0.08
29 3 0.06
30 6 0.12
31 16 0.31
32 10 0.19
33 6 0.12
34 3 0.06
36 4 0.08
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (31 bp):
TCTTAAACACTCTCTGATCTTGAAACGGTTC
Found at i:38638 original size:63 final size:63
Alignment explanation
Indices: 38539--38661 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
38529 TGCTTTCTTA
38539 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
38602 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
38662 CCTAGGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:39600 original size:8 final size:8
Alignment explanation
Indices: 39587--39670 Score: 62
Period size: 8 Copynumber: 11.5 Consensus size: 8
39577 TCCGGTCGAC
39587 GGTCAACG
1 GGTCAACG
39595 GGTCAAC-
1 GGTCAACG
39602 GGTCAACG
1 GGTCAACG
39610 GGT---CG
1 GGTCAACG
39615 GGTCAACG
1 GGTCAACG
39623 GGT---CG
1 GGTCAACG
39628 GGTCAACG
1 GGTCAACG
**
39636 GGTCGGGTCG
1 GGTC--AACG
39646 GGTCAACG
1 GGTCAACG
39654 GGT---CG
1 GGTCAACG
39659 GGTCAACG
1 GGTCAACG
39667 GGTC
1 GGTC
39671 GGGTCGGGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 24
0.68 0.05 0.27
Matches are distributed among these distances:
5 15 0.25
7 7 0.12
8 32 0.53
10 6 0.10
ACGTcount: A:0.17, C:0.24, G:0.44, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:39620 original size:13 final size:13
Alignment explanation
Indices: 39587--39675 Score: 106
Period size: 13 Copynumber: 6.3 Consensus size: 13
39577 TCCGGTCGAC
*
39587 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
39602 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39615 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39628 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
39646 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39659 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39672 GGTC
1 GGTC
39676 GGGTTGTGAC
Statistics
Matches: 68, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
13 43 0.63
15 12 0.18
18 13 0.19
ACGTcount: A:0.16, C:0.24, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:39646 original size:31 final size:31
Alignment explanation
Indices: 39608--39679 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
39598 CAACGGTCAA
39608 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
39639 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
39670 CGGGTCGGGT
1 CGGGTCGGGT
39680 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
Found at i:39679 original size:18 final size:18
Alignment explanation
Indices: 39621--39662 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
39611 GTCGGGTCAA
39621 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
39639 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
39657 CGGGTC
1 CGGGTC
39663 AACGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:46551 original size:41 final size:41
Alignment explanation
Indices: 46504--46617 Score: 129
Period size: 41 Copynumber: 2.8 Consensus size: 41
46494 TTCTATAAGT
* * *
46504 GATCGATCATTTTGAAAAATTATCGATCCTTTCTCCCGAGG
1 GATCGATCCTTTTGAAAAAGTATCAATCCTTTCTCCCGAGG
* * *
46545 GATCGATCCTTTTGAAAAGGTATCAATCCTTTTTCTCGAGG
1 GATCGATCCTTTTGAAAAAGTATCAATCCTTTCTCCCGAGG
* * * * *
46586 TATCAATCCTTTTGTAAAGGGATCAATCCTTT
1 GATCGATCCTTTTGAAAAAGTATCAATCCTTT
46618 GCTGGACAGA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (41 bp):
GATCGATCCTTTTGAAAAAGTATCAATCCTTTCTCCCGAGG
Found at i:46575 original size:20 final size:20
Alignment explanation
Indices: 46550--46617 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
46540 CGAGGGATCG
*
46550 ATCCTTTTGAAAAGGTATCA
1 ATCCTTTTGTAAAGGTATCA
* **
46570 ATCCTTTTTCTCGAGGTATCA
1 ATCC-TTTTGTAAAGGTATCA
*
46591 ATCCTTTTGTAAAGGGATCA
1 ATCCTTTTGTAAAGGTATCA
46611 ATCCTTT
1 ATCCTTT
46618 GCTGGACAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 23 0.59
21 16 0.41
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (20 bp):
ATCCTTTTGTAAAGGTATCA
Found at i:48955 original size:18 final size:18
Alignment explanation
Indices: 48934--49010 Score: 127
Period size: 18 Copynumber: 4.3 Consensus size: 18
48924 TCCCATAGGG
* *
48934 CCACTATATCCCGAATGA
1 CCACTATGTCCCGAAGGA
48952 CCACTATGTCCCGAAGGA
1 CCACTATGTCCCGAAGGA
48970 CCACTATGTCCCGAAGGA
1 CCACTATGTCCCGAAGGA
*
48988 CCACTATCTCCCGAAGGA
1 CCACTATGTCCCGAAGGA
49006 CCACT
1 CCACT
49011 GATAATCCCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.29, C:0.36, G:0.17, T:0.18
Consensus pattern (18 bp):
CCACTATGTCCCGAAGGA
Found at i:48963 original size:36 final size:36
Alignment explanation
Indices: 48934--49019 Score: 127
Period size: 36 Copynumber: 2.3 Consensus size: 36
48924 TCCCATAGGG
*
48934 CCACTATATCCCGAATGACCACTATGTCCCGAAGGA
1 CCACTATATCCCGAAGGACCACTATGTCCCGAAGGA
* *
48970 CCACTATGTCCCGAAGGACCACTATCTCCCGAAGGA
1 CCACTATATCCCGAAGGACCACTATGTCCCGAAGGA
49006 CCACTGATAATCCC
1 CCACT-AT-ATCCC
49020 TCGACTCTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 38 0.86
37 2 0.05
38 4 0.09
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.19
Consensus pattern (36 bp):
CCACTATATCCCGAAGGACCACTATGTCCCGAAGGA
Found at i:51856 original size:31 final size:31
Alignment explanation
Indices: 51770--51893 Score: 126
Period size: 31 Copynumber: 4.0 Consensus size: 31
51760 GAGTCGAGGG
51770 TATACCTATGTTCTACGGAACATATGGACAA
1 TATACCTATGTTCTACGGAACATATGGACAA
* *
51801 AATTACCTATG-TCTTTCGTG-ACATATGGACAA
1 TA-TACCTATGTTC-TACG-GAACATATGGACAA
* *
51833 TATACCTATGTTCTAAGGAACATATGGACAG
1 TATACCTATGTTCTACGGAACATATGGACAA
* * * * *
51864 TTTACCTAGGTTCTTCAGAACCTATGGACA
1 TATACCTATGTTCTACGGAACATATGGACA
51894 GTTGCCAAGG
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.01
31 48 0.63
32 26 0.34
33 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (31 bp):
TATACCTATGTTCTACGGAACATATGGACAA
Found at i:51937 original size:30 final size:30
Alignment explanation
Indices: 51883--51954 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
51873 GTTCTTCAGA
* * *
51883 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
51913 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
51943 ACCTCTGGATAG
1 ACCTCTGGATAG
51955 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:55436 original size:19 final size:19
Alignment explanation
Indices: 55412--55462 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
55402 ATGCAATTAG
55412 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
55431 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
55450 TGCATCGATGCAT
1 TGCATCGATGCAT
55463 CTAAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATAAGGCA
Found at i:56766 original size:31 final size:31
Alignment explanation
Indices: 56642--56766 Score: 146
Period size: 31 Copynumber: 4.0 Consensus size: 31
56632 GTCGAGGGTA
*
56642 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
56674 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
56705 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
56736 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
56767 GCCAAGGATC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
31 53 0.67
32 26 0.33
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:57862 original size:23 final size:23
Alignment explanation
Indices: 57836--57913 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
57826 CACCACAGCT
*
57836 CATATAATTGCACCAAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
57859 CATATAATTGCACCGAAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
57882 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
57905 TATAATAAT
1 CAT-ATAAT
57914 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:58091 original size:103 final size:103
Alignment explanation
Indices: 57920--58137 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
57910 TAATGTCCAT
* * *
57920 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCTCCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCACGGATCAAGTATGTGTCTCACCA
57985 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
58023 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCACGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCACGGATCAAGTATGTGTCTCACCA
58088 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
58126 AAGGACCACATA
1 AAGGACCACATA
58138 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCACGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:59046 original size:64 final size:63
Alignment explanation
Indices: 58913--59055 Score: 146
Period size: 64 Copynumber: 2.2 Consensus size: 63
58903 TTCCCTATCG
* * ** *
58913 GTGCATCGATGCACTACTTGTGCATCGGTGCATAAAATACATTCGATGTTTGTTTATTACTGG
1 GTGCATCGATGCACTACTTATGCATCGATGCATAAAATACATTCGATGTTTGTTTATTAAAGA
* * * *
58976 GATGCATTGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATT-TATT-TTAAAA
1 G-TGCATCGATGCACTACTTATGCATCGATGCATAAAATACATTCGATGT-TTGT-TTATT-AAA
59039 GA
62 GA
*
59041 GTGCATCAATGCACT
1 GTGCATCGATGCACT
59056 TTCTGTGCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
63 1 0.02
64 57 0.88
65 7 0.11
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (63 bp):
GTGCATCGATGCACTACTTATGCATCGATGCATAAAATACATTCGATGTTTGTTTATTAAAGA
Done.