Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007439.1 Hibiscus syriacus cultivar Beakdansim tig00020291_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: 73817
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:3922 original size:10 final size:10
Alignment explanation
Indices: 3903--3931 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3893 TTTGATTCAA
3903 TTTTTT-TTT
1 TTTTTTCTTT
3912 TTTTTTCTTT
1 TTTTTTCTTT
3922 TTTTTTCTTT
1 TTTTTTCTTT
3932 CTTCAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:3922 original size:14 final size:14
Alignment explanation
Indices: 3905--3934 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3895 TGATTCAATT
*
3905 TTTTTTTTTTTTTC
1 TTTTTTTTTCTTTC
3919 TTTTTTTTTCTTTC
1 TTTTTTTTTCTTTC
3933 TT
1 TT
3935 CAAGTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTCTTTC
Found at i:6905 original size:43 final size:44
Alignment explanation
Indices: 6841--6927 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
6831 TCGTGCATCA
* * *
6841 AACAAAACTTTTACATGTAGGGGATATCTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGATAACTTTCACTCCTAACTTC
*
6885 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGATAACTTTCACTCCTAACTTC
6928 TCTAAAGCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 31 0.79
44 8 0.21
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGATAACTTTCACTCCTAACTTC
Found at i:9539 original size:18 final size:21
Alignment explanation
Indices: 9516--9555 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
9506 CCCATTTCTT
9516 AATATTAA-AA-AATA-AATA
1 AATATTAATAAGAATATAATA
9534 AATATTAATAAGAATATAATA
1 AATATTAATAAGAATATAATA
9555 A
1 A
9556 TTTTCCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 4 0.21
21 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
AATATTAATAAGAATATAATA
Found at i:9581 original size:2 final size:2
Alignment explanation
Indices: 9571--9617 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
9561 CTAAAAAATA
*
9571 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT CT 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
*
9612 TT AT AT
1 AT AT AT
9618 TTATTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9740 original size:31 final size:33
Alignment explanation
Indices: 9705--9766 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
9695 TAATATTTAA
*
9705 AAATAAATATTATTAAT-TTA-TAAAATTAATC
1 AAATAAATATTATTAATATGACTAAAATTAATC
* *
9736 AAATAATTTTTATTAATATGACTAAAATTAA
1 AAATAAATATTATTAATATGACTAAAATTAA
9767 AGAAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 15 0.58
32 2 0.08
33 9 0.35
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (33 bp):
AAATAAATATTATTAATATGACTAAAATTAATC
Found at i:10923 original size:22 final size:22
Alignment explanation
Indices: 10881--10924 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10871 AGGTTTCCTA
* *
10881 GGTGAGTCACCATAGCTATGGT
1 GGTGACTCACCATAGCGATGGT
*
10903 GGTGACTCACCATAGGGATGGT
1 GGTGACTCACCATAGCGATGGT
10925 CGTGGGCTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (22 bp):
GGTGACTCACCATAGCGATGGT
Found at i:11216 original size:3 final size:3
Alignment explanation
Indices: 11208--11277 Score: 131
Period size: 3 Copynumber: 23.0 Consensus size: 3
11198 TTTTGGGTCT
11208 ATA ATA ATA ATA ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
11254 ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
11278 TGATGATGGA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:14245 original size:46 final size:46
Alignment explanation
Indices: 14192--14321 Score: 233
Period size: 46 Copynumber: 2.8 Consensus size: 46
14182 TAAAGCGATT
14192 TGCTTTCCTTCTTGGTATTTGAGTAAACTACACAAATGGTCCTTTA
1 TGCTTTCCTTCTTGGTATTTGAGTAAACTACACAAATGGTCCTTTA
14238 TGCTTTCCTTCTTGGTATTTGAGTAAACTACACAAATGGTCCTTTA
1 TGCTTTCCTTCTTGGTATTTGAGTAAACTACACAAATGGTCCTTTA
* * *
14284 TGCTTTCCTTCTTGTTATTTGGGTAAAGTACACAAATG
1 TGCTTTCCTTCTTGGTATTTGAGTAAACTACACAAATG
14322 CTCCATTGAC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (46 bp):
TGCTTTCCTTCTTGGTATTTGAGTAAACTACACAAATGGTCCTTTA
Found at i:15090 original size:21 final size:21
Alignment explanation
Indices: 15064--15350 Score: 143
Period size: 21 Copynumber: 13.7 Consensus size: 21
15054 TATATTCACA
*
15064 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
*
15085 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
15106 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
* * *
15127 TTGTGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
15148 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
*
15169 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* * *
15190 TTGCAATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
* * *
15211 TTGAGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
* *
15232 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
15253 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
15274 TTGTTATTTATTCCAAGTT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
**
15295 TTGCGATAGTTGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
15316 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
15337 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
15351 AATCGCAACG
Statistics
Matches: 222, Mismatches: 30, Indels: 30
0.79 0.11 0.11
Matches are distributed among these distances:
19 33 0.15
21 156 0.70
23 33 0.15
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:15156 original size:63 final size:63
Alignment explanation
Indices: 15083--15256 Score: 203
Period size: 63 Copynumber: 2.8 Consensus size: 63
15073 TCGAAGTTCG
* **
15083 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGTGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCAATTTATTCCAAATT
* * *
15146 CGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCAATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCAATTTATTCCAAATT
* * *
15209 CGTTGAGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATTCGTTGC
1 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
15257 GATAGTCCAA
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
61 8 0.09
63 68 0.73
65 17 0.18
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (63 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCAATTTATTCCAAATT
Found at i:15164 original size:84 final size:84
Alignment explanation
Indices: 15064--15297 Score: 355
Period size: 84 Copynumber: 2.8 Consensus size: 84
15054 TATATTCACA
* *
15064 TTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTT
*
15129 GTGATTTATTCCAAATTCG
66 GAGATTTATTCCAAATTCG
15148 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTT
15213 GAGATTTATTCCAAATTCG
66 GAGATTTATTCCAAATTCG
* * * ** *
15232 TTGCGATTTATTCCAAATT--CGTTGCGATAGTCCAAGTTCGCGTTGTTATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCG
15295 TTG
64 TTG
15298 CGATAGTTGA
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
84 130 0.94
86 9 0.06
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (84 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTT
GAGATTTATTCCAAATTCG
Found at i:15193 original size:105 final size:105
Alignment explanation
Indices: 15064--15343 Score: 397
Period size: 105 Copynumber: 2.7 Consensus size: 105
15054 TATATTCACA
15064 TTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
1 TTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
*
15129 GTGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
66 GCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
* * * * *
15169 TTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATT--CGTTGAGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
15232 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
64 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
** * * *
15274 TTGTTATTTATTCCAAGTT--CGTTGCGATAGTTGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
15337 TTGCGAT
64 TTGCGAT
15344 AGTCCAAAAT
Statistics
Matches: 153, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
103 7 0.05
105 129 0.84
107 17 0.11
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (105 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
GCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
Found at i:15213 original size:42 final size:42
Alignment explanation
Indices: 15083--15350 Score: 296
Period size: 42 Copynumber: 6.4 Consensus size: 42
15073 TCGAAGTTCG
*
15083 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* * * * *
15125 CGTTGTGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
15165 CGCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATT
1 --CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
15209 CGTTGAGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATT
1 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
** *
15251 CGTTGCGATAGTCCAAGTTCGCGTTGTTATTTATTCCAAGTT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
**
15293 CGTTGCGATAGTTGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
15335 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
15351 AATCGCAACG
Statistics
Matches: 183, Mismatches: 31, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
40 26 0.14
42 132 0.72
44 25 0.14
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:15318 original size:84 final size:83
Alignment explanation
Indices: 15083--15350 Score: 337
Period size: 84 Copynumber: 3.2 Consensus size: 83
15073 TCGAAGTTCG
* * *
15083 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGTGATTTATTCCAAATTCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGAGA-TTATTCCAAATTCG
* *
15148 TTGCGA--TAGTCCAAGTT
65 TTGCGATTTATTCCAAATT
*
15165 CGCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGAGATTTATTCCAAATT
1 --CGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGAGA-TTATTCCAAATT
15230 CGTTGCGATTTATTCCAAATT
63 CGTTGCGATTTATTCCAAATT
** * * * *
15251 CGTTGCGATAGTCCAAGTTCGCGTTGTTATTTATTCCAAGTTCGTTGCGA-TAGTT-GAAGTTCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGAGATTA-TTCCAAATT--
15314 CGTTGCGATTTATTCCAAATT
63 CGTTGCGATTTATTCCAAATT
15335 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
15351 AATCGCAACG
Statistics
Matches: 168, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
82 6 0.04
83 2 0.01
84 151 0.90
86 9 0.05
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (83 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGAGATTATTCCAAATTCGT
TGCGATTTATTCCAAATT
Found at i:15976 original size:6 final size:6
Alignment explanation
Indices: 15960--15991 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
15950 GGTCGGGTTG
15960 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
15992 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:16149 original size:42 final size:42
Alignment explanation
Indices: 16084--16220 Score: 256
Period size: 42 Copynumber: 3.3 Consensus size: 42
16074 TGTGATTTTG
* *
16084 GACTATCGCAACGAACTTCGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
16126 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
16168 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
16210 GACTATCGCAA
1 GACTATCGCAA
16221 TGCGAACTTG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:16239 original size:42 final size:41
Alignment explanation
Indices: 16084--16247 Score: 231
Period size: 42 Copynumber: 3.9 Consensus size: 41
16074 TGTGATTTTG
*
16084 GACTATCGCAACGAACTTCGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
*
16126 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
*
16168 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTC
* *
16210 GACTATCGCAATGCGAACTTGGACT-ATCGCAATGCGAA
1 GACTATCGCAA--CGAACTTGGAATAATCGCAACGCGAA
16248 TATGTATATC
Statistics
Matches: 115, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
42 105 0.91
44 10 0.09
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (41 bp):
GACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTC
Found at i:16239 original size:84 final size:83
Alignment explanation
Indices: 16084--16328 Score: 268
Period size: 84 Copynumber: 2.9 Consensus size: 83
16074 TGTGATTTTG
* * *
16084 GACTATCGCAACGAACTTCGAATAAATCGCAACGCGAACTTCGACTATCGCAA--CGAATTTGGA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGA
*
16147 ATAAATCGCAACGCGAACT-T
66 CT--ATCGCAACGCGAA-TAT
16167 CGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGG
1 -GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGG
*
16232 ACTATCGCAATGCGAATAT
65 ACTATCGCAACGCGAATAT
*
16251 GTA-TATCGCAATGCGATAGTCGAATTTGG-A-AAATCGCAACGCGAACTTTGACTATCGCAATG
1 G-ACTAT--C---GC-A-A--CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATG
16313 CGAACTTGGACTATCG
56 CGAACTTGGACTATCG
16329 TATTGCGATT
Statistics
Matches: 142, Mismatches: 6, Indels: 20
0.85 0.04 0.12
Matches are distributed among these distances:
83 5 0.04
84 65 0.46
85 1 0.01
86 10 0.07
88 2 0.01
89 1 0.01
90 48 0.34
91 1 0.01
92 9 0.06
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (83 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGA
CTATCGCAACGCGAATAT
Found at i:16336 original size:21 final size:21
Alignment explanation
Indices: 16081--16328 Score: 161
Period size: 21 Copynumber: 11.5 Consensus size: 21
16071 CGTTGTGATT
16081 TTGGACTATCGCAA--CGAAC
1 TTGGACTATCGCAATGCGAAC
* * *
16100 TTCGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
* *
16123 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
* *
16142 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
* *
16165 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
* *
16184 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
*
16207 TTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
16228 TTGGACTATCGCAATGCGAA-
1 TTGGACTATCGCAATGCGAAC
*
16248 TATGTA-TATCGCAATGCGATAGTC
1 T-TGGACTATCGCAATGCGA-A--C
** *
16272 GAATTTGGAAAATCGCAACGCGAAC
1 ----TTGGACTATCGCAATGCGAAC
*
16297 TTTGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
16318 TTGGACTATCG
1 TTGGACTATCG
16329 TATTGCGATT
Statistics
Matches: 181, Mismatches: 26, Indels: 42
0.73 0.10 0.17
Matches are distributed among these distances:
19 23 0.13
20 14 0.08
21 98 0.54
23 29 0.16
25 1 0.01
27 4 0.02
28 12 0.07
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:16350 original size:90 final size:92
Alignment explanation
Indices: 16179--16361 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 92
16169 ACTATCGCAA
16179 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATG
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATG
**
16244 CGAATATGTATATCGCAATGCGATAGT
66 CGAATACATATATCGCAATGCGATAGT
* * *
16271 CGAATTTGG-A-AAATCGCAACGCGAACTTTGACTATCGCAATGCGAACTTGGACTATCGTATTG
1 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATG
* *
16334 CGATTTACATAT-TCGCATTGCGATAGT
66 CGA-ATACATATATCGCAATGCGATAGT
16361 C
1 C
16362 CAAGTTCGCA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
90 68 0.82
91 6 0.07
92 9 0.11
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (92 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATG
CGAATACATATATCGCAATGCGATAGT
Found at i:16395 original size:70 final size:70
Alignment explanation
Indices: 16312--16449 Score: 249
Period size: 70 Copynumber: 2.0 Consensus size: 70
16302 CTATCGCAAT
* * *
16312 GCGAACTTGGACTATCGTATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCG
1 GCGAACTTCGACTATCGCACTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCG
16377 ATAAC
66 ATAAC
16382 GCGAACTTCGACTATCGCACTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCG
1 GCGAACTTCGACTATCGCACTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCG
16447 ATA
66 ATA
16450 GTCGAAGTTC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (70 bp):
GCGAACTTCGACTATCGCACTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCG
ATAAC
Found at i:16441 original size:21 final size:21
Alignment explanation
Indices: 16415--16469 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
16405 GATTTACATA
16415 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
16436 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
16457 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
16470 TCTGGAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:17513 original size:2 final size:2
Alignment explanation
Indices: 17506--17557 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
17496 GAAACCAGTA
17506 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
17548 AT AT AT AT AT
1 AT AT AT AT AT
17558 CTTCTTTGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21955 original size:4 final size:4
Alignment explanation
Indices: 21946--21972 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21936 ATACGATTTT
21946 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
21973 TAATGAGAAA
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:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:27116 original size:3 final size:3
Alignment explanation
Indices: 27108--27193 Score: 118
Period size: 3 Copynumber: 28.7 Consensus size: 3
27098 TAATATAAAT
* *
27108 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** *
27156 TAA TGA TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
27194 TGGATAAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:27643 original size:113 final size:113
Alignment explanation
Indices: 27445--27992 Score: 839
Period size: 113 Copynumber: 4.8 Consensus size: 113
27435 TCTTGATGAG
27445 TTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-C
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTC
* * * *
27508 TGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
64 TGGAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
*
27558 TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
27623 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
* *
27671 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * * * *
27736 GCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
*
27784 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
27849 GAAAAGCTGATCCATCAAATGACGGATTCAAGTAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
*
27897 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
27962 GAAAAGCTGTTCCATCAAATGATGGATTCAA
66 GAAAAGCTGATCCATCAAATGATGGATTCAA
27993 ATCTTTGCTA
Statistics
Matches: 392, Mismatches: 41, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
112 1 0.00
113 390 0.99
114 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAATGATGGATTCAAGCAAAAGGTTGAACAAA
Found at i:28859 original size:82 final size:81
Alignment explanation
Indices: 28606--28950 Score: 537
Period size: 82 Copynumber: 4.2 Consensus size: 81
28596 TTTACTATGA
*
28606 GCAAATTCATCTTCCAAATTCAATGATTGTTCTATCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTAT-AAACCAGATCAGATAACTCAAAGAACACT
28671 TCCAGAAGATGCTATTG
65 TCCAGAAGATGCTATTG
* * *
28688 GCAAATTCATCTTCCAAATTCAATGCTTGGTTCTATATAATCAGATCAAATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCTATA-AACCAGATCAGATAACTCAAAGAACAC
28753 TTCCAGAAGATGCTATTG
64 TTCCAGAAGATGCTATTG
* * *
28771 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCT-ATAAACCAGATCAGATAACTCAAAGAACACT
28836 TCCAGAAGATGCTATTG
65 TCCAGAAGATGCTATTG
* * * *
28853 GTAAATTCATCTTCCAAATTCAATGAATGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCT-ATAAACCAGATCAGATAACTCAAAGAACACT
28918 TCCAGAAGATGCTATTG
65 TCCAGAAGATGCTATTG
*
28935 GTAAATTCATCTTCCA
1 GCAAATTCATCTTCCA
28951 TTTAATGTTT
Statistics
Matches: 247, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
82 169 0.68
83 78 0.32
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (81 bp):
GCAAATTCATCTTCCAAATTCAATGATTGTTCTATAAACCAGATCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATTG
Found at i:30101 original size:7 final size:6
Alignment explanation
Indices: 30072--30168 Score: 71
Period size: 6 Copynumber: 16.0 Consensus size: 6
30062 CTTGACCCCC
* *
30072 TTTCTT TTTC-T TCTCTTT TTTCTAT TTTCTA TTT-TT TTTCTTT TTTCTT
1 TTTCTT TTTCTT TTTC-TT TTTCT-T TTTCTT TTTCTT TTTC-TT TTTCTT
30121 TTT-TCT TTTCTTT TTTCTT TCTT-TCT TTTC-T TTTCTT TTT-TT TTTCTT
1 TTTCT-T TTTC-TT TTTCTT T-TTCT-T TTTCTT TTTCTT TTTCTT TTTCTT
30169 CAAGCATAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
5 19 0.26
6 29 0.39
7 25 0.34
8 1 0.01
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:30101 original size:25 final size:24
Alignment explanation
Indices: 30072--30168 Score: 103
Period size: 25 Copynumber: 4.0 Consensus size: 24
30062 CTTGACCCCC
*
30072 TTTCTTTTTCTTCTCTTTTTTCTAT
1 TTTCTTTTTCTTTTCTTTTTTCT-T
30097 TTTCTATTTT-TTTTCTTTTTTCTTT
1 TTTCT-TTTTCTTTTCTTTTTTC-TT
*
30122 TTTCTTTTCTTTTTTCTTTCTTTC-T
1 TTTCTTTT-TCTTTTCTTT-TTTCTT
30147 TTTC-TTTTCTTTT-TTTTTTCTT
1 TTTCTTTTTCTTTTCTTTTTTCTT
30169 CAAGCATAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
21 4 0.06
22 4 0.06
23 5 0.08
24 6 0.09
25 28 0.44
26 13 0.20
27 4 0.06
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTCTTTTTCTTTTCTTTTTTCTT
Found at i:30110 original size:30 final size:27
Alignment explanation
Indices: 30071--30169 Score: 96
Period size: 30 Copynumber: 3.5 Consensus size: 27
30061 CCTTGACCCC
*
30071 CTTTCTTTTTCTTCTCTTTTTTCTATTTT
1 CTTTTTTTTTCTTCTCTTTTTTC--TTTT
*
30100 CTATTTTTTTTCTTTTTTCTTTTTTCTTTT
1 CT-TTTTTTTTC--TTCTCTTTTTTCTTTT
30130 CTTTTTTCTTTCTT-TC--TTTTCTTTT
1 CTTTTTT-TTTCTTCTCTTTTTTCTTTT
30155 CTTTTTTTTTTCTTC
1 C-TTTTTTTTTCTTC
30170 AAGCATAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
25 16 0.26
26 6 0.10
27 2 0.03
28 2 0.03
29 7 0.11
30 18 0.29
32 11 0.18
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (27 bp):
CTTTTTTTTTCTTCTCTTTTTTCTTTT
Found at i:30133 original size:44 final size:44
Alignment explanation
Indices: 30072--30165 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
30062 CTTGACCCCC
*
30072 TTTC-TTTTTCTTCTCTTTTTTCTAT-TTTCTATTTTTTTTCTTT
1 TTTCTTTTTTCTTCTCTTTTTTCTATCTTTCT-TTTCTTTTCTTT
* *
30115 TTTCTTTTTTCTTTTCTTTTTTCTTTCTTTCTTTTCTTTTCTTT
1 TTTCTTTTTTCTTCTCTTTTTTCTATCTTTCTTTTCTTTTCTTT
30159 TTT-TTTT
1 TTTCTTTT
30166 CTTCAAGCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
43 8 0.17
44 33 0.72
45 5 0.11
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (44 bp):
TTTCTTTTTTCTTCTCTTTTTTCTATCTTTCTTTTCTTTTCTTT
Found at i:40806 original size:17 final size:17
Alignment explanation
Indices: 40766--40807 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
40756 ATACTTGCAA
*
40766 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATC
40784 ATAAAAATAATAAATA-C
1 ATAAAAAT-ATAAATATC
40801 ATAAAAA
1 ATAAAAA
40808 ATTTGAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATATAAATATC
Found at i:50521 original size:16 final size:17
Alignment explanation
Indices: 50483--50518 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
50473 ATCTCATATT
50483 AATAAAAATATAAAATAA
1 AATAAAAATAT-AAATAA
*
50501 AATAAAAATATAATTAA
1 AATAAAAATATAAATAA
50518 A
1 A
50519 TAAGTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AATAAAAATATAAATAA
Found at i:54614 original size:36 final size:35
Alignment explanation
Indices: 54573--54644 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
54563 AATCTATTTG
* *
54573 ACCAGTGAAAAATGTTCATATTGATAGATAGAAGAA
1 ACCAGTGAAAAATGTTCACATTAATAGATAG-AGAA
** *
54609 ACCAGTGAAATTTTTTCACATTAATAGATAGAGAA
1 ACCAGTGAAAAATGTTCACATTAATAGATAGAGAA
54644 A
1 A
54645 AAACTAGGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.28
Consensus pattern (35 bp):
ACCAGTGAAAAATGTTCACATTAATAGATAGAGAA
Found at i:62372 original size:149 final size:149
Alignment explanation
Indices: 62111--62395 Score: 392
Period size: 149 Copynumber: 1.9 Consensus size: 149
62101 AGTAGCGTCA
* *
62111 AGAGGGAGTCTACCTACCAAGTAGACAAGCCAGACATCTGCCTACTGAGGTAACAAGTTGGACTC
1 AGAGGGAGTCTACCTACCAAGGAGACAAGCCAAACATCTGCCTACTGAGGTAACAAGTTGGACTC
* * ** *
62176 GAGACGATTCGACTCTGAAGCCAACAGTTGAAGATCACGAACCAGCTCGAAGGATTTCTGGAAGT
66 GAGACGATTCGAATCCGAAGCCAACAGTTGAAGATCACGAACCAGCTCGAAAAATTTCTGAAAGT
62241 AGGAGAGGAAGTAGGAGCT
131 AGGAGAGGAAGTAGGAGCT
* * * * * * **
62260 AGAGGGAGTCTATCTACCAAGGAGACGATCCAAACATTTTCTTGTTGAGGTAACAAGTTGGACTC
1 AGAGGGAGTCTACCTACCAAGGAGACAAGCCAAACATCTGCCTACTGAGGTAACAAGTTGGACTC
* * *
62325 GAGATGATTC-AATGCCGAAGCCAACAGTTGAAGATCGCGAACTAGCTCGAAAAATTTCTGAAAG
66 GAGACGATTCGAAT-CCGAAGCCAACAGTTGAAGATCACGAACCAGCTCGAAAAATTTCTGAAAG
62389 TAGGAGA
130 TAGGAGA
62396 TAAAGTAGAA
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
148 2 0.02
149 115 0.98
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (149 bp):
AGAGGGAGTCTACCTACCAAGGAGACAAGCCAAACATCTGCCTACTGAGGTAACAAGTTGGACTC
GAGACGATTCGAATCCGAAGCCAACAGTTGAAGATCACGAACCAGCTCGAAAAATTTCTGAAAGT
AGGAGAGGAAGTAGGAGCT
Found at i:63278 original size:49 final size:49
Alignment explanation
Indices: 63216--63314 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
63206 TTCCCAATCT
*
63216 AATCTTCCCAACAAAGTTCAAAATTCTAGAATTCGAAAAGTATAATGGG
1 AATCCTCCCAACAAAGTTCAAAATTCTAGAATTCGAAAAGTATAATGGG
63265 AATCCTCCCAACAAAGTTCAAAATTCTAGAATTCGAAAAGTATAATGGG
1 AATCCTCCCAACAAAGTTCAAAATTCTAGAATTCGAAAAGTATAATGGG
63314 A
1 A
63315 CCACATGTCC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (49 bp):
AATCCTCCCAACAAAGTTCAAAATTCTAGAATTCGAAAAGTATAATGGG
Found at i:64662 original size:12 final size:12
Alignment explanation
Indices: 64641--64696 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
64631 AATATACGAT
*
64641 ATGAATAGTATC
1 ATGAACAGTATC
*
64653 GTGAACAGTA--
1 ATGAACAGTATC
* *
64663 ATGAGCAGTACC
1 ATGAACAGTATC
64675 ATGAACAGTATC
1 ATGAACAGTATC
*
64687 GTGAACAGTA
1 ATGAACAGTA
64697 ATGAGCAGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
10 8 0.23
12 27 0.77
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.23
Consensus pattern (12 bp):
ATGAACAGTATC
Found at i:64685 original size:34 final size:34
Alignment explanation
Indices: 64641--64715 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
64631 AATATACGAT
*
64641 ATGAATAGTATCGTGAACAGTAATGAGCAGTACC
1 ATGAACAGTATCGTGAACAGTAATGAGCAGTACC
64675 ATGAACAGTATCGTGAACAGTAATGAGCAGTACC
1 ATGAACAGTATCGTGAACAGTAATGAGCAGTACC
*
64709 GTGAACA
1 ATGAACA
64716 TTACTGAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (34 bp):
ATGAACAGTATCGTGAACAGTAATGAGCAGTACC
Found at i:65337 original size:22 final size:22
Alignment explanation
Indices: 65312--65372 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
65302 GGCATGTGAA
65312 ATTTGTCCCGAAAGACCTATGT
1 ATTTGTCCCGAAAGACCTATGT
* *
65334 ATTTGTCCCGAAGGACCTCTGT
1 ATTTGTCCCGAAAGACCTATGT
* * *
65356 ATATGTCTCGAATGACC
1 ATTTGTCCCGAAAGACC
65373 GCGTAGACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (22 bp):
ATTTGTCCCGAAAGACCTATGT
Found at i:70662 original size:22 final size:22
Alignment explanation
Indices: 70637--70768 Score: 237
Period size: 22 Copynumber: 6.0 Consensus size: 22
70627 AATATACGGT
*
70637 ATGAACAATATCGTGAACAGTA
1 ATGAACAATACCGTGAACAGTA
**
70659 ATGAACAATAATGTGAACAGTA
1 ATGAACAATACCGTGAACAGTA
70681 ATGAACAATACCGTGAACAGTA
1 ATGAACAATACCGTGAACAGTA
70703 ATGAACAATACCGTGAACAGTA
1 ATGAACAATACCGTGAACAGTA
70725 ATGAACAATACCGTGAACAGTA
1 ATGAACAATACCGTGAACAGTA
70747 ATGAACAATACCGTGAACAGTA
1 ATGAACAATACCGTGAACAGTA
70769 TCGAATGTCA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 106 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (22 bp):
ATGAACAATACCGTGAACAGTA
Found at i:70838 original size:20 final size:21
Alignment explanation
Indices: 70802--70842 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
70792 TTGCTTCAAG
70802 GGTATCGATACCCCTGCTACA
1 GGTATCGATACCCCTGCTACA
70823 GGTATCGATA-CCCTGCTACA
1 GGTATCGATACCCCTGCTACA
70843 ATACTGCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (21 bp):
GGTATCGATACCCCTGCTACA
Found at i:71357 original size:3 final size:3
Alignment explanation
Indices: 71344--71391 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
71334 TTCACGTTGT
* *
71344 AGA AG- AGA AGA AGA TGA AGA AGA A-A AGA AGA TGA AGA A-A AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
71389 AGA
1 AGA
71392 TGAATTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:71366 original size:17 final size:17
Alignment explanation
Indices: 71344--71395 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
71334 TTCACGTTGT
71344 AGAAGAGAAGAAGATGA
1 AGAAGAGAAGAAGATGA
*
71361 AGAAGAAAAGAAGATGA
1 AGAAGAGAAGAAGATGA
*
71378 AGAAAAGAAGAAGATGA
1 AGAAGAGAAGAAGATGA
71395 A
1 A
71396 TTGTTTGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.63, C:0.00, G:0.31, T:0.06
Consensus pattern (17 bp):
AGAAGAGAAGAAGATGA
Found at i:71371 original size:14 final size:14
Alignment explanation
Indices: 71344--71391 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
71334 TTCACGTTGT
71344 AGAAG-AGAAGAAGA
1 AGAAGAAGAA-AAGA
*
71358 TGAAGAAGAAAAGA
1 AGAAGAAGAAAAGA
*
71372 AGATGAAGAAAAGA
1 AGAAGAAGAAAAGA
71386 AGAAGA
1 AGAAGA
71392 TGAATTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 25 0.86
15 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (14 bp):
AGAAGAAGAAAAGA
Done.