Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005572.1 Hibiscus syriacus cultivar Beakdansim tig00012930_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: 131483
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:821 original size:17 final size:16
Alignment explanation
Indices: 790--823 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
780 CACGTGAGGA
790 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
806 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
823 T
1 T
824 ACTGTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:2266 original size:23 final size:23
Alignment explanation
Indices: 2236--2282 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2226 CTGAACATGA
2236 GCGTTATTCTAAAGACACAACTT
1 GCGTTATTCTAAAGACACAACTT
2259 GCGTTATTCTAAAGACACAACTT
1 GCGTTATTCTAAAGACACAACTT
2282 G
1 G
2283 GGGCATCTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (23 bp):
GCGTTATTCTAAAGACACAACTT
Found at i:2703 original size:17 final size:19
Alignment explanation
Indices: 2666--2719 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 19
2656 TCCAATCAAG
*
2666 AACAAAA-AAAAAAAGCAAA
1 AACAAAAGAAAACAAG-AAA
2685 AA-ACAAAGAAAA-AAG-AA
1 AACA-AAAGAAAACAAGAAA
2702 AACAAAAGAAAACAAGAA
1 AACAAAAGAAAACAAGAA
2720 CACAAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
17 12 0.40
18 5 0.17
19 9 0.30
20 4 0.13
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (19 bp):
AACAAAAGAAAACAAGAAA
Found at i:2703 original size:18 final size:17
Alignment explanation
Indices: 2669--2740 Score: 65
Period size: 18 Copynumber: 4.1 Consensus size: 17
2659 AATCAAGAAC
2669 AAAAA-AAAAAAGCAAAA
1 AAAAAGAAAAAAG-AAAA
2686 AACAAAGAAAAAAGAAAA
1 AA-AAAGAAAAAAGAAAA
* *
2704 CAAAAGAAAACAAGAACAC
1 AAAAAGAAAA-AAGAA-AA
**
2723 AAAAATCAAAAAGAAAA
1 AAAAAGAAAAAAGAAAA
2740 A
1 A
2741 GGGACAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
17 12 0.27
18 18 0.40
19 15 0.33
ACGTcount: A:0.81, C:0.10, G:0.08, T:0.01
Consensus pattern (17 bp):
AAAAAGAAAAAAGAAAA
Found at i:4273 original size:21 final size:20
Alignment explanation
Indices: 4247--4351 Score: 71
Period size: 21 Copynumber: 5.4 Consensus size: 20
4237 TGAGATAGTT
4247 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAAC-AATTTTGTC
* *
4268 TCCCTTGAGACAGTTTAT-T-
1 TCCCTTGAAACAATTT-TGTC
*
4287 TCTCTTGAAACAAATTTTGTC
1 TCCCTTGAAAC-AATTTTGTC
* *
4308 TCTCTTGAGAC-A----GTC
1 TCCCTTGAAACAATTTTGTC
*
4323 TTCCTTGAAACGAATTTTGTC
1 TCCCTTGAAAC-AATTTTGTC
4344 TCCCTTGA
1 TCCCTTGA
4352 GACAGTTTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
15 11 0.17
17 1 0.02
19 11 0.17
20 10 0.16
21 31 0.48
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (20 bp):
TCCCTTGAAACAATTTTGTC
Found at i:4275 original size:36 final size:36
Alignment explanation
Indices: 4217--4371 Score: 177
Period size: 36 Copynumber: 4.2 Consensus size: 36
4207 TTTTTTCTTA
* * *
4217 AAACAAGATTTTATCTCGCTTGAGATAGTTTCCCTTG
1 AAACAA-ATTTTGTCTCCCTTGAGACAGTTTCCCTTG
*
4254 AAACAAATTTTGTCTCCCTTGAGACAGTTTATTTCTCTTG
1 AAACAAATTTTGTCTCCCTTGAGACAG----TTTCCCTTG
*
4294 AAACAAATTTTGTCTCTCTTGAGACAGTCTT-CCTTG
1 AAACAAATTTTGTCTCCCTTGAGACAGT-TTCCCTTG
* * *
4330 AAACGAATTTTGTCTCCCTTGAGACAGTTTCTCTCG
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
4366 AAACAA
1 AAACAA
4372 CACAATTTGC
Statistics
Matches: 101, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
35 2 0.02
36 57 0.56
37 8 0.08
40 34 0.34
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
Found at i:4309 original size:19 final size:19
Alignment explanation
Indices: 4250--4310 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
4240 GATAGTTTCC
4250 CTTGAAACAAATTTTGTCT
1 CTTGAAACAAATTTTGTCT
* * *
4269 CCCTTGAGAC-AGTTTATTTCT
1 --CTTGAAACAAATTT-TGTCT
4290 CTTGAAACAAATTTTGTCT
1 CTTGAAACAAATTTTGTCT
4309 CT
1 CT
4311 CTTGAGACAG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
19 13 0.41
20 8 0.25
21 11 0.34
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (19 bp):
CTTGAAACAAATTTTGTCT
Found at i:4329 original size:76 final size:77
Alignment explanation
Indices: 4212--4359 Score: 228
Period size: 76 Copynumber: 1.9 Consensus size: 77
4202 CAAGATTTTT
*
4212 TCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
1 TCTTAAAACAAGATTTTATCTCGCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
4277 ACAGTTTATTTC
66 ACAGTTTATTTC
* * * *
4289 TCTTGAAACAA-ATTTTGTCTCTCTTGAGACAGTCTT-CCTTGAAACGAATTTTGTCTCCCTTGA
1 TCTTAAAACAAGATTTTATCTCGCTTGAGACAGT-TTCCCTTGAAACAAATTTTGTCTCCCTTGA
4352 GACAGTTT
65 GACAGTTT
4360 CTCTCGAAAC
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
76 53 0.82
77 12 0.18
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (77 bp):
TCTTAAAACAAGATTTTATCTCGCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAG
ACAGTTTATTTC
Found at i:4379 original size:76 final size:76
Alignment explanation
Indices: 4216--4379 Score: 199
Period size: 76 Copynumber: 2.1 Consensus size: 76
4206 ATTTTTTCTT
*
4216 AAAACAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 AAAACAA-ATTTTATCTCGCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* **
4281 TTTATTTCTCTT
65 TTTATCTCTCGA
* * * *
4293 GAAACAAATTTTGTCTCTCTTGAGACAGTCTT-CCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 AAAACAAATTTTATCTCGCTTGAGACAGT-TTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
4357 -TT-TCTCTCGA
65 TTTATCTCTCGA
4367 AACAACACAATTT
1 AA-AACA-AATTT
4380 GCTCGAGAGT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
74 6 0.08
75 6 0.08
76 55 0.73
77 8 0.11
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (76 bp):
AAAACAAATTTTATCTCGCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGT
TTATCTCTCGA
Found at i:4915 original size:105 final size:104
Alignment explanation
Indices: 4787--4995 Score: 332
Period size: 104 Copynumber: 2.0 Consensus size: 104
4777 TCAACACTTA
* *
4787 AGACAACACAAGTTCAACTTCACAACGAAGGGAC-GCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTT-CC-ATTC
*
4851 CAGAGCCAATTTCAACTTCAC-AGCGAAGGATATTGGACTCG
64 CAGAACCAATTTCAACTTCACGA-CGAAGGATATTGGACTCG
*
4892 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCGTTCCA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCATTCCA
*
4957 GAACCAATTTCAACTTCACGACGGAGGATATTGGACTCG
66 GAACCAATTTCAACTTCACGACGAAGGATATTGGACTCG
4996 GAACAATACA
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
104 39 0.40
105 37 0.38
106 21 0.22
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (104 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCATTCCA
GAACCAATTTCAACTTCACGACGAAGGATATTGGACTCG
Found at i:5786 original size:35 final size:35
Alignment explanation
Indices: 5740--5811 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
5730 CCAACAAAGA
*
5740 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTAGATTAGGACTCAAATACTAGTCTAAAAT
*
5775 AGAGTTAGATTAGGGCTCAAATACTAGTCTAAAAT
1 AGAGTTAGATTAGGACTCAAATACTAGTCTAAAAT
5810 AG
1 AG
5812 GGTTTTTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTAGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:6459 original size:2 final size:2
Alignment explanation
Indices: 6452--6478 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6442 TATAAGTTAT
6452 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6479 TCATATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6720 original size:21 final size:20
Alignment explanation
Indices: 6694--6742 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
6684 CGTTACTTCA
*
6694 TTCTTTTTTCTT-GTTTATT
1 TTCTTTTTTCTTCTTTTATT
6713 TT-TTCTTTTACTTCTTTTATT
1 TTCTT-TTTT-CTTCTTTTATT
6734 TTCTTTTTT
1 TTCTTTTTT
6743 TTATCTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 3 0.12
21 12 0.48
22 2 0.08
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.80
Consensus pattern (20 bp):
TTCTTTTTTCTTCTTTTATT
Found at i:6741 original size:20 final size:19
Alignment explanation
Indices: 6694--6741 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
6684 CGTTACTTCA
*
6694 TTCTTTTTTCTTGTTTATT
1 TTCTTTTTACTTGTTTATT
* *
6713 TTTTCTTTTACTTCTTTTATT
1 TTCT-TTTTACTT-GTTTATT
6734 TTCTTTTT
1 TTCTTTTT
6742 TTTATCTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 11 0.48
21 9 0.39
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.79
Consensus pattern (19 bp):
TTCTTTTTACTTGTTTATT
Found at i:8771 original size:111 final size:111
Alignment explanation
Indices: 8632--8964 Score: 612
Period size: 111 Copynumber: 3.0 Consensus size: 111
8622 ATTACAAAAA
* *
8632 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTATTATTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
8697 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
8743 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
8808 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
8854 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
8919 AATTAAAGCGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
8965 ATGGTTTCCA
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:9103 original size:12 final size:10
Alignment explanation
Indices: 9090--9130 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
9080 CTTAAAAAGA
*
9090 GAGAGTATTT
1 GAGAGAATTT
9100 GAGAGAAATTT
1 GAGAG-AATTT
9111 -AGAGAATTT
1 GAGAGAATTT
9120 GAGAGAATTT
1 GAGAGAATTT
9130 G
1 G
9131 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:9377 original size:50 final size:50
Alignment explanation
Indices: 9252--9377 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 50
9242 AGATACGTAG
*
9252 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCACCAAATAACC
1 GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGGCACCAAATAACC
** * ** * ** * *
9302 GTATGTCGGGGGGCAGGGGGAGCGCTATACCCACGTGGTGCCAAATCAGC
1 GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGGCACCAAATAACC
* *
9352 GTATAACGCGGTTCAGAGGGCGCGCT
1 GTATAACGCGGATCAGGGGGCGCGCT
9378 TTACTGCTAC
Statistics
Matches: 59, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.22, C:0.26, G:0.36, T:0.16
Consensus pattern (50 bp):
GTATAACGCGGATCAGGGGGCGCGCTATACCCACGTGGCACCAAATAACC
Found at i:17128 original size:71 final size:71
Alignment explanation
Indices: 17020--17243 Score: 315
Period size: 71 Copynumber: 3.1 Consensus size: 71
17010 AATTACTCTC
* *
17020 TTAATTAGTAGTAGTGATCAATGGATGAATG-CTAATGTGAGTTGTGAGTCATAGTCAGAATTAG
1 TTAATTAGTAATAGTGATCAATGGATGAATGTC-AATGTGAGTTGTGAGTCATAGTCAGAGTTAG
17084 TTGTTTA
65 TTGTTTA
* *
17091 TTAATTAGTAATTGTGATCAATGGATGAATGTCAATGTGAGTTGTGAGTCATAGTCAGAGTTAAT
1 TTAATTAGTAATAGTGATCAATGGATGAATGTCAATGTGAGTTGTGAGTCATAGTCAGAGTTAGT
17156 TGTTTA
66 TGTTTA
* * *
17162 TTAATTAGTAACAGTGATCAATGGATGAATGTTAATGTTAATGTGAGTTGTGAGCCATAGTCAGA
1 TTAATTAGTAATAGTGATCAAT-G--G-ATG--AATGTCAATGTGAGTTGTGAGTCATAGTCAGA
17227 GTTAGTTGTTTA
60 GTTAGTTGTTTA
17239 TTAAT
1 TTAAT
17244 GGGTTTGTTG
Statistics
Matches: 137, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
71 85 0.62
72 2 0.01
74 1 0.01
75 3 0.02
77 46 0.34
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (71 bp):
TTAATTAGTAATAGTGATCAATGGATGAATGTCAATGTGAGTTGTGAGTCATAGTCAGAGTTAGT
TGTTTA
Found at i:18044 original size:70 final size:71
Alignment explanation
Indices: 17911--18046 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 71
17901 TATTTTTCAA
* * **** *
17911 TTTTAAAAAAATGAAAAATGAGAAGGCTGCAAAGTATTAATATTTTTCCACAAATATCGATACTT
1 TTTTAAAAAAATGAAAAATGAGAAGGATGCAAAGTATTAAAAAAAATCCACAAATATCAATACTT
17976 TTAAAT
66 TTAAAT
17982 TTTTAAAAAAACATG-AAAATGAGAAGGATGCAAAGT-TTAAAAAAAAT-CACAAATATCAATAC
1 TTTT-AAAAAA-ATGAAAAATGAGAAGGATGCAAAGTATTAAAAAAAATCCACAAATATCAATAC
18044 TTT
64 TTT
18047 CGAATTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
70 17 0.30
71 10 0.18
72 26 0.46
73 3 0.05
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (71 bp):
TTTTAAAAAAATGAAAAATGAGAAGGATGCAAAGTATTAAAAAAAATCCACAAATATCAATACTT
TTAAAT
Found at i:18270 original size:20 final size:19
Alignment explanation
Indices: 18222--18452 Score: 141
Period size: 20 Copynumber: 11.7 Consensus size: 19
18212 TGCGATTTTC
18222 CAAATTCGCAACACGAA-T
1 CAAATTCGCAACACGAAGT
18240 CTGTAAA-TCGCAACACAGAAGT
1 C---AAATTCGCAACAC-GAAGT
18262 CAAATTCGCAA-AGCGATAGT
1 CAAATTCGCAACA-CGA-AGT
* *
18282 CAAATCCGCAACACAAAAGT
1 CAAATTCGCAACAC-GAAGT
* *
18302 TAAATTCGCAACACAAAAGT
1 CAAATTCGCAACAC-GAAGT
18322 CAAATTCGCAA-AGCGATAGT
1 CAAATTCGCAACA-CGA-AGT
*
18342 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACACGA-AGT
**
18362 CAAATTCGCAACAAAAAAGT
1 CAAATTCGCAAC-ACGAAGT
* * *
18382 CAAATTTGCAAC-TGAATTT
1 CAAATTCGCAACACGAA-GT
**
18401 CAAATTCGCAACTA-GATTTT
1 CAAATTCGCAAC-ACGA-AGT
* *
18421 CGAATTCGCAACACGAATT
1 CAAATTCGCAACACGAAGT
* *
18440 TAATTTCGCAACA
1 CAAATTCGCAACA
18453 AGTTTTAGTT
Statistics
Matches: 173, Mismatches: 21, Indels: 37
0.75 0.09 0.16
Matches are distributed among these distances:
18 3 0.02
19 33 0.19
20 126 0.73
21 9 0.05
22 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.22
Consensus pattern (19 bp):
CAAATTCGCAACACGAAGT
Found at i:18311 original size:60 final size:60
Alignment explanation
Indices: 18243--18392 Score: 221
Period size: 60 Copynumber: 2.5 Consensus size: 60
18233 CACGAATCTG
*
18243 TAAA-TCGCAACACAGAAGTCAAATTCGCAAAGCGATAGTCAAATCCGCAACACAAAAGT
1 TAAATTCGCAACACAAAAGTCAAATTCGCAAAGCGATAGTCAAATCCGCAACACAAAAGT
* * * *
18302 TAAATTCGCAACACAAAAGTCAAATTCGCAAAGCGATAGTCAAATTCGCAACGCGATAGT
1 TAAATTCGCAACACAAAAGTCAAATTCGCAAAGCGATAGTCAAATCCGCAACACAAAAGT
* * *
18362 CAAATTCGCAACAAAAAAGTCAAATTTGCAA
1 TAAATTCGCAACACAAAAGTCAAATTCGCAA
18393 CTGAATTTCA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 4 0.05
60 78 0.95
ACGTcount: A:0.45, C:0.22, G:0.15, T:0.18
Consensus pattern (60 bp):
TAAATTCGCAACACAAAAGTCAAATTCGCAAAGCGATAGTCAAATCCGCAACACAAAAGT
Found at i:18393 original size:40 final size:40
Alignment explanation
Indices: 18222--18393 Score: 179
Period size: 40 Copynumber: 4.3 Consensus size: 40
18212 TGCGATTTTC
* * *
18222 CAAATTCGCAACACGAATCTGT-AAA-TCGCAACACAGAAGT
1 CAAATTCGCAACGCG-AT-AGTCAAATTCGCAACACAAAAGT
* *
18262 CAAATTCGCAAAGCGATAGTCAAATCCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
* * * * * *
18302 TAAATTCGCAACACAAAAGTCAAATTCGCAA-AGCGATAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACA-CAAAAGT
*
18342 CAAATTCGCAACGCGATAGTCAAATTCGCAACAAAAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
*
18382 CAAATTTGCAAC
1 CAAATTCGCAAC
18394 TGAATTTCAA
Statistics
Matches: 107, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
38 2 0.02
39 6 0.06
40 98 0.92
41 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGT
Found at i:18452 original size:19 final size:18
Alignment explanation
Indices: 18425--18471 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
18415 GATTTTCGAA
18425 TTCGCAACACGAATTTAAT
1 TTCGCAACACG-ATTTAAT
* * *
18444 TTCGCAACAAGTTTTAGT
1 TTCGCAACACGATTTAAT
18462 TTCGCAACAC
1 TTCGCAACAC
18472 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (18 bp):
TTCGCAACACGATTTAAT
Found at i:19261 original size:12 final size:12
Alignment explanation
Indices: 19240--19273 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
19230 ACCACATTTC
*
19240 CAATACCAAACA
1 CAATATCAAACA
19252 CAATATCAAACA
1 CAATATCAAACA
19264 CAATATCAAA
1 CAATATCAAA
19274 ACCCACAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:19430 original size:24 final size:24
Alignment explanation
Indices: 19403--19476 Score: 130
Period size: 24 Copynumber: 3.1 Consensus size: 24
19393 TCGAAATTTA
19403 ATCTTGGTCAATACTCGGACTTTG
1 ATCTTGGTCAATACTCGGACTTTG
*
19427 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGTCAATACTCGGACTTTG
*
19451 ATCTTGGTCAATACTCGGATTTTG
1 ATCTTGGTCAATACTCGGACTTTG
19475 AT
1 AT
19477 GATGTGATGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
ATCTTGGTCAATACTCGGACTTTG
Found at i:21747 original size:18 final size:18
Alignment explanation
Indices: 21724--21759 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21714 AAGCAAAAGG
21724 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
21742 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
21760 CAACCGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:22156 original size:20 final size:20
Alignment explanation
Indices: 22133--22178 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
22123 TCGCAATGCA
*
22133 AATTTGACTTTCGCGTTGTG
1 AATTTGACTTTCGCGTTGCG
22153 AATTTGACTTTCGCGTTGCG
1 AATTTGACTTTCGCGTTGCG
22173 AATTTG
1 AATTTG
22179 TACCTTCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.43
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTGCG
Found at i:22314 original size:66 final size:65
Alignment explanation
Indices: 22232--22407 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
22222 AATTTAAAAC
22232 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATT
22297 A
65 A
* *
22298 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
22362 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
22408 ATGTACCCCA
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 16 0.16
65 25 0.25
66 34 0.34
68 4 0.04
69 16 0.16
70 6 0.06
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:23776 original size:21 final size:21
Alignment explanation
Indices: 23752--23850 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
23742 ACAGGCGAGA
*
23752 CCTCTTGAATGATGACAGGGG
1 CCTCTTGAATGATGAGAGGGG
* * *
23773 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAGAGGGG
*
23794 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAATGATGAGAGGGG
* *
23815 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAATGATGA-GAGGGG
*
23836 CCTATTGAATGATGA
1 CCTCTTGAATGATGA
23851 TAGGTGTATT
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.03
21 57 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.24
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGGG
Found at i:23848 original size:42 final size:42
Alignment explanation
Indices: 23756--23850 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
23746 GCGAGACCTC
* * * * *
23756 TTGAATGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCTTC
1 TTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCTA
*
23798 TTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCGCCTA
1 TT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCTA
23840 TTGAATGATGA
1 TTGAATGATGA
23851 TAGGTGTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 43 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.24
Consensus pattern (42 bp):
TTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCTA
Found at i:26034 original size:19 final size:20
Alignment explanation
Indices: 25979--26038 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
25969 CTTAAATTCC
25979 CAACGCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
25999 CAACGCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
26019 CAACGC-AAAACT-AAAATCG
1 CAACGCGAAAA-TGAAAATCG
26038 C
1 C
26039 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
19 12 0.31
20 27 0.69
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (20 bp):
CAACGCGAAAATGAAAATCG
Found at i:26614 original size:20 final size:20
Alignment explanation
Indices: 26589--26640 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
26579 TGTGTTTCGC
*
26589 GTTGCGAATTTGATTTTTGT
1 GTTGCGAATTTGACTTTTGT
26609 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
26629 GTTTCGAATTTG
1 GTTGCGAATTTG
26641 GCTATCGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.08, G:0.25, T:0.52
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:27154 original size:20 final size:19
Alignment explanation
Indices: 27115--27156 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
27105 TTTCTTTGAT
27115 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
27134 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
27154 ATT
1 ATT
27157 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:28944 original size:123 final size:121
Alignment explanation
Indices: 28805--29550 Score: 741
Period size: 113 Copynumber: 6.3 Consensus size: 121
28795 GAACAAATTC
* * *
28805 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTATGGAAATGCTGATACTGATCTAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAT--TGAT-CTGATCTAT
* *
28870 CTCATTCTGTGATAGAATTAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACATCT
63 CTCATTCTGTGATAGAATTAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
* *
28928 TCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAATTGATGCTGATCTATC
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG-GAAATTGAT-CTGATCTATC
* * * ** *
28993 TCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAGCTTCT
64 TCATTCTGTGATAGAATTAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
*
29051 TCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATGCTGATTTAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA--TTGAT-CTGATCTAT
* * * * * *
29115 CTCCTTCTGGGATAGAGTCGAA-CAAAAGGTTTAACAAGCTCTTCTTATTATGAACTTCT
63 CTCATTCTGTGATAGAAT-TAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
* * * *
29174 TCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAA-TG-T-TGATCCATC-
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAATTGATCTGATCTATCT
* * *
29234 GA----ATGAT-GAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
65 CATTCTGTGATAGAATT-AAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
* *
29287 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA-AG-T-TGATCCA--TC
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATTGATCTGATCTATCTC
** * *
29347 A---AATGAT-GAATTCAAGCGAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCT
66 ATTCTGTGATAGAATT-AAGC-AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
* * * *
29400 TCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA-AG-T-TGATCCATC-G
1 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATTGATCTGATCTATCTC
* *
29461 A----ATGAT-GAATTCAAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCT
66 ATTCTGTGATAGAATT-AAGC-AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
* *
29513 TATTTAC-TCTTCAGATGAGTTCTTCTCATTATGAACTT
1 T-CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
29551 GAACTGGTAA
Statistics
Matches: 558, Mismatches: 49, Indels: 42
0.86 0.08 0.06
Matches are distributed among these distances:
112 8 0.01
113 271 0.49
114 8 0.01
118 7 0.01
120 1 0.00
121 5 0.01
122 66 0.12
123 149 0.27
124 41 0.07
125 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (121 bp):
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATTGATCTGATCTATCTC
ATTCTGTGATAGAATTAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
Found at i:30066 original size:22 final size:22
Alignment explanation
Indices: 29988--30064 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
29978 GATAAAGCTT
*
29988 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
30010 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
30032 TCATCTTTGAAGAGAGAA-CTTA
1 TCATCTTTGAAAAGAGAATC-TA
30054 TCATCTTTGAA
1 TCATCTTTGAA
30065 GAATGTAGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:30506 original size:54 final size:54
Alignment explanation
Indices: 30424--30589 Score: 269
Period size: 54 Copynumber: 3.1 Consensus size: 54
30414 AGAATAGCAG
** * *
30424 GTTCGTAAAACATTTGACGGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
*
30478 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTAGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
* *
30532 GTTCGTAAAACATTTGACAACATATTCATCCTTTCCTGTGATTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
30586 GTTC
1 GTTC
30590 TCAATCATTG
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
Found at i:38697 original size:14 final size:14
Alignment explanation
Indices: 38663--38716 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
38653 TTGTGCAATA
* *
38663 CAAATGCAAAGATG
1 CAAATGTAAATATG
38677 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
38692 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
38706 TAAATGTAAAT
1 CAAATGTAAAT
38717 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:42314 original size:21 final size:20
Alignment explanation
Indices: 42271--42338 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
42261 TTACAATCGC
*
42271 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
*
42291 GTTGCGGATTTGACTTTTTGT
1 GTTGCGAATTTGAC-TTTTGT
42312 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
42332 GTTGCGA
1 GTTGCGA
42339 TTTACAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 26 0.59
21 18 0.41
ACGTcount: A:0.15, C:0.10, G:0.28, T:0.47
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:42355 original size:20 final size:20
Alignment explanation
Indices: 42332--42378 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
42322 TGACTTTTGT
42332 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
42352 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
42372 GTTGCGA
1 GTTGCGA
42379 ATTTGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:42392 original size:21 final size:21
Alignment explanation
Indices: 42368--42525 Score: 65
Period size: 21 Copynumber: 7.8 Consensus size: 21
42358 ATTTACAGAT
42368 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
****
42389 TCGCAACACGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
*****
42410 TCGTAACACGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
** ** * *
42431 TCGCAATGCG-ATTTACATAT
1 TCGCGTTGCGAATTTGGAAAA
* * *
42451 TCGTGTTGCGAAATTGGAAAC
1 TCGCGTTGCGAATTTGGAAAA
* * **
42472 T-GGGTTGCGAAATTGG-AGT
1 TCGCGTTGCGAATTTGGAAAA
* *
42491 TCCCGTTGCGAATTT-G-AGA
1 TCGCGTTGCGAATTTGGAAAA
42510 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
42526 TTGGTCATTT
Statistics
Matches: 106, Mismatches: 28, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.18
20 37 0.35
21 50 0.47
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAAAA
Found at i:42516 original size:19 final size:19
Alignment explanation
Indices: 42475--42525 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
42465 TGGAAACTGG
* *
42475 GTTGCGAAATTGGAGTTCCC
1 GTTGCG-AATTTGAGATCCC
*
42495 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTTGAGATCCC
42514 GTTGCGAATTTG
1 GTTGCGAATTTG
42526 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (19 bp):
GTTGCGAATTTGAGATCCC
Found at i:43156 original size:101 final size:98
Alignment explanation
Indices: 42878--43169 Score: 388
Period size: 99 Copynumber: 2.9 Consensus size: 98
42868 TATCGATAAT
* * * * *
42878 GTAATAATAATTACGACTTAACTAGTTAAAATGAAATAGGCGCAACCTATTACGTTAAACTAGTT
1 GTAA-AATATTTACAACTTAACCAGTTAAAAT-AAATAGGCGCAACATATTACGTTAAACTAGCT
* *
42943 ACTAGTTTGTTTAAAGGTATAATAAAAATGTAAACA
64 AC-GGTTTGTTTAAAGGTATAATAATAATGTAAACA
* *
42979 GTAAAATATTT-CAACTTAATCAGTTAAAATAAAATACGCGCAACATATTACGTTAAACTAGCTA
1 GTAAAATATTTACAACTTAACCAGTTAAAAT-AAATAGGCGCAACATATTACGTTAAACTAGCTA
* *
43043 CCGTTTTGTTTAAAGGTATAATAATAATGTAAACG
65 -CGGTTTGTTTAAAGGTATAATAATAATGTAAACA
*
43078 GTAAAATATTTACAACTTAACCAGTTAAAAATATAATAGGTGCAACATATTACGTTAAACTAGCT
1 GTAAAATATTTACAACTTAACCAGTT-AAAATA-AATAGGCGCAACATATTACGTTAAACTAGCT
*
43143 ATCGGTTTGTTTAAAGGTATATTAATA
64 A-CGGTTTGTTTAAAGGTATAATAATA
43170 CTATAAATGG
Statistics
Matches: 169, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
99 86 0.51
100 21 0.12
101 62 0.37
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (98 bp):
GTAAAATATTTACAACTTAACCAGTTAAAATAAATAGGCGCAACATATTACGTTAAACTAGCTAC
GGTTTGTTTAAAGGTATAATAATAATGTAAACA
Found at i:44506 original size:195 final size:190
Alignment explanation
Indices: 44133--44520 Score: 706
Period size: 195 Copynumber: 2.0 Consensus size: 190
44123 ATTAATACAA
44133 ATATAATTAACTTATTTTCTTACCGTTATAATATTTTAGGCATAACATGTTACGTATTACGGTTG
1 ATATAATTAACTTATTTTCTTACCGTTATAATATTTTAGGCATAACATGTTACGTATTACGGTTG
44198 ATAATGTTTCTACTAATTAACCTAAATTATTAAAGTCAATTTTTTTGGCCTATTTTTACATACAA
66 ATAATGTTTCTACTAATTAACCTAAATTATTAAAGTCAATTTTTTTGGCCTATTTTTACATACAA
*
44263 CGATAACATTTCCGGTATTACCATTATTCTTAACACAAATAACATTTCAGTTGAAAAACAT
131 CGATAACATTTCCGGTATTACCATTATTATTAACACAAATAACATTTCAGTTG-AAAACAT
44324 ATATAATTAACTTATTTTCTTACCGTTTATAATATTTTAGGCATAACATGTTACGTTATTACGGT
1 ATATAATTAACTTATTTTCTTACCG-TTATAATATTTTAGGCATAACATGTTACG-TATTACGGT
44389 TGATAATGTTTCTACTAATTAACCTAAATTATTAAAGTCAATATTTTTTTGGCCTA-TTTTACAT
64 TGATAATGTTTCTACTAATTAACCTAAATTATTAAAGTC-A-ATTTTTTTGGCCTATTTTTACAT
44453 ACAACGATAACATTTCCGGTTATTACCATTATTATTAACACAAATAACATTTCAGTTGAAAACAT
127 ACAACGATAACATTTCCGG-TATTACCATTATTATTAACACAAATAACATTTCAGTTGAAAACAT
44518 ATA
1 ATA
44521 ACATTTTCGG
Statistics
Matches: 191, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
191 25 0.13
192 29 0.15
193 48 0.25
194 38 0.20
195 51 0.27
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (190 bp):
ATATAATTAACTTATTTTCTTACCGTTATAATATTTTAGGCATAACATGTTACGTATTACGGTTG
ATAATGTTTCTACTAATTAACCTAAATTATTAAAGTCAATTTTTTTGGCCTATTTTTACATACAA
CGATAACATTTCCGGTATTACCATTATTATTAACACAAATAACATTTCAGTTGAAAACAT
Found at i:45638 original size:2 final size:2
Alignment explanation
Indices: 45633--45699 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
45623 CCCGCCCGAT
*
45633 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
45675 TA TA T- TA TA TA TA T- TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
45700 TTTTATATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:45700 original size:6 final size:6
Alignment explanation
Indices: 45637--45718 Score: 64
Period size: 6 Copynumber: 14.2 Consensus size: 6
45627 CCCGATTATA
* * * * *
45637 TATATA TATATA TATATA TATATA TATATA TATATT TATATAT TATA--
1 TATATT TATATT TATATT TATATT TATATT TATATT TATAT-T TATATT
* *
45684 TATA-T TATATT TATATT TTTATA TA-ATT TATATT T
1 TATATT TATATT TATATT TATATT TATATT TATATT T
45719 TTTATATTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
4 4 0.06
5 8 0.12
6 50 0.75
7 5 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TATATT
Found at i:46051 original size:4 final size:4
Alignment explanation
Indices: 46042--46076 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
46032 TTCAACTATA
46042 TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
46077 ACATGCATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:54578 original size:80 final size:80
Alignment explanation
Indices: 54444--54739 Score: 486
Period size: 80 Copynumber: 3.7 Consensus size: 80
54434 CAGCAAAAAG
* * * *
54444 GGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAGATCCGTAGGGTTACC
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
* *
54508 TTAAGCACACAGCTAA
65 TTATGCACACAGCAAA
*
54524 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
*
54589 TATGCACACAACAAA
66 TATGCACACAGCAAA
*
54604 AGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
54669 TATGCACACAGCAAA
66 TATGCACACAGCAAA
*
54684 GGGAACCAACCTAAGGATATACCTTGGGACCTATCCAAGATATCCTTAGGTCCGTA
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTA
54740 ATGACTTACA
Statistics
Matches: 202, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
80 192 0.95
81 10 0.05
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TATGCACACAGCAAA
Found at i:56404 original size:17 final size:18
Alignment explanation
Indices: 56371--56404 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56361 TCCATTCTGT
*
56371 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
56389 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
56405 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:62177 original size:25 final size:25
Alignment explanation
Indices: 62096--62170 Score: 150
Period size: 25 Copynumber: 3.0 Consensus size: 25
62086 TCGCAGGTAA
62096 ATGGGGAGAACTTATCTCCATTGAG
1 ATGGGGAGAACTTATCTCCATTGAG
62121 ATGGGGAGAACTTATCTCCATTGAG
1 ATGGGGAGAACTTATCTCCATTGAG
62146 ATGGGGAGAACTTATCTCCATTGAG
1 ATGGGGAGAACTTATCTCCATTGAG
62171 GAAGGGACCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (25 bp):
ATGGGGAGAACTTATCTCCATTGAG
Found at i:67134 original size:230 final size:227
Alignment explanation
Indices: 66727--67176 Score: 792
Period size: 230 Copynumber: 2.0 Consensus size: 227
66717 ATAAATTATC
* * *
66727 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
66792 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
66857 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATT
66922 GAAACATAAATTACATAACTTTCAAAAAAGTATA
195 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
66956 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
67021 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
67086 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
67151 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
67177 GCAGTTATAA
Statistics
Matches: 211, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
228 4 0.02
229 66 0.31
230 141 0.67
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:67265 original size:20 final size:19
Alignment explanation
Indices: 67242--67287 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
67232 CGATATACCA
67242 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
67262 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
67282 GGTAAA
1 GGTAAA
67288 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:67432 original size:20 final size:19
Alignment explanation
Indices: 67409--67455 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
67399 CGATATAACA
67409 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
67429 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
67449 GGTAAAA
1 GGTAAAA
67456 TGATATCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:67457 original size:17 final size:19
Alignment explanation
Indices: 67418--67460 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
67408 AGGTAAAAAT
67418 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
67438 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
67455 ATGATA
1 ATGATA
67461 TCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:69735 original size:21 final size:21
Alignment explanation
Indices: 69688--69752 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
69678 AAGACAATCA
* *
69688 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
69710 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
69730 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
69751 AG
1 AG
69753 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:69828 original size:33 final size:33
Alignment explanation
Indices: 69786--69851 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
69776 AAATAGATGG
*
69786 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
69819 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
69852 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:71681 original size:18 final size:19
Alignment explanation
Indices: 71643--71687 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
71633 GTAGGGTTAA
71643 TTTGTATAAGATTTATAAT
1 TTTGTATAAGATTTATAAT
*
71662 TTTGTATACGATTTAT-AT
1 TTTGTATAAGATTTATAAT
71680 TTTCGTAT
1 TTT-GTAT
71688 GTGAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTGTATAAGATTTATAAT
Found at i:72347 original size:197 final size:197
Alignment explanation
Indices: 71812--73089 Score: 2407
Period size: 198 Copynumber: 6.5 Consensus size: 197
71802 GGCCAAAAGG
71812 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
71877 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
71942 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
72007 AAT
195 AAT
72010 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
72075 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
72140 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
72205 AAT
195 AAT
72208 ATGTAATTTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
72272 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
**
72337 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATTTAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
72402 AAT
195 AAT
72405 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
72470 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
* *
72535 ATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAGATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
72600 AAT
195 AAT
72603 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
72668 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
* *
72733 TAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAACATAATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
72797 AT
196 AT
72799 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
72864 TGTCGACACTTATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
* *
72929 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAACATAATCGAACCCAAAAGTATAATGTA
131 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
72994 AT
196 AT
72996 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
73061 TGTCGACACTAATATAGTTTGTGTCGATA
66 TGTCGACACTAATATAGTTTGTGTCGATA
73090 CTAATTTAAA
Statistics
Matches: 1060, Mismatches: 15, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
196 225 0.21
197 354 0.33
198 417 0.39
199 64 0.06
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (197 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
AT
Found at i:72562 original size:395 final size:396
Alignment explanation
Indices: 71812--73089 Score: 2438
Period size: 395 Copynumber: 3.2 Consensus size: 396
71802 GGCCAAAAGG
71812 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
71877 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
71942 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
72007 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
196 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
72072 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGC
261 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGC
72137 ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
326 ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
72202 TGTAAT
391 TGTAAT
72208 ATGTAATTTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
72272 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
**
72337 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATTTAACCCAAAAGTATAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
72402 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
196 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
72467 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGC
261 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGC
* *
72532 ACCATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAGATCATCGAACCCAAAAGTATAA
326 ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
72597 TGTAAT
391 TGTAAT
72603 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
72668 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
* *
72732 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAACATAATCGAACCCAAAAGTATAATGT
131 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
72796 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
196 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
* *
72861 ATGTGTCGACACTTATATAGTTTGTGTCGATA-TTTATTTCCAGAATGAATGGAAAACAGGGTGC
261 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGC
* *
72925 ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAACATAATCGAACCCAAAAGTATAA
326 ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
72990 TGTAAT
391 TGTAAT
72996 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
73061 TGTCGACACTAATATAGTTTGTGTCGATA
66 TGTCGACACTAATATAGTTTGTGTCGATA
73090 CTAATTTAAA
Statistics
Matches: 868, Mismatches: 13, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
393 193 0.22
394 135 0.16
395 414 0.48
396 126 0.15
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (396 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATA
ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGC
ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
TGTAAT
Found at i:72971 original size:21 final size:21
Alignment explanation
Indices: 72930--72971 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
72920 GGTGCACCAT
*
72930 AAAGTGTCGATCCATATATAA
1 AAAGTGTCGATCCATACATAA
72951 AAAGTGTCGATCCCA-ACATAA
1 AAAGTGTCGAT-CCATACATAA
72972 TCGAACCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (21 bp):
AAAGTGTCGATCCATACATAA
Found at i:74568 original size:18 final size:18
Alignment explanation
Indices: 74547--74608 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
74537 AGCGGTCGCA
74547 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
74565 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
74583 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
74601 GAAGATGA
1 GAAGATGA
74609 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:74571 original size:6 final size:6
Alignment explanation
Indices: 74547--74632 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
74537 AGCGGTCGCA
* * * * * *
74547 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * *
74595 GGCGAT GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
74633 TGATCCAAAC
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:74582 original size:3 final size:3
Alignment explanation
Indices: 74562--74636 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
74552 TGAAGCTGAC
* * * * * ** *
74562 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
74610 GAC GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
74637 CCAAACAAGT
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:74601 original size:36 final size:36
Alignment explanation
Indices: 74550--74628 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
74540 GGTCGCAGAA
*
74550 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
74586 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
74622 GATGAAG
1 GATGAAG
74629 ATGATGATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.20
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:74636 original size:12 final size:12
Alignment explanation
Indices: 74550--74632 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
74540 GGTCGCAGAA
*
74550 GATGAAGCTGAC
1 GATGAAGATGAC
74562 GATGAAGATGAC
1 GATGAAGATGAC
*
74574 GATGATGATGAC
1 GATGAAGATGAC
* *
74586 GATGAAGCTGGC
1 GATGAAGATGAC
*
74598 GATGAAGATGAT
1 GATGAAGATGAC
* * *
74610 GACGATGATGAT
1 GATGAAGATGAC
74622 GATGAAGATGA
1 GATGAAGATGA
74633 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:76413 original size:183 final size:183
Alignment explanation
Indices: 76105--76581 Score: 882
Period size: 183 Copynumber: 2.6 Consensus size: 183
76095 CTTTCAACAT
** * * * * *
76105 ATTATAATAAAATAGGTAAATTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
76170 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
76235 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
76288 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATATCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
76353 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
76418 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
76471 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
76536 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTT
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTT
76582 TTGTGCAAAT
Statistics
Matches: 285, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 285 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:76819 original size:18 final size:18
Alignment explanation
Indices: 76798--76834 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
76788 GTAATTGGAG
76798 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
76816 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
76834 T
1 T
76835 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:76842 original size:24 final size:24
Alignment explanation
Indices: 76790--76836 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
76780 TTTCATATGT
* *
76790 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
76814 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
76837 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:77133 original size:39 final size:39
Alignment explanation
Indices: 77090--77176 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
77080 TCCGATGCTC
*
77090 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* * *
77129 ATCAAATTTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
77168 ATCAAAATC
1 ATCAAAATC
77177 TACAACTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.20
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:77628 original size:23 final size:23
Alignment explanation
Indices: 77597--77669 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
77587 ATAGGTAAAA
*
77597 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
77620 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
77643 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
77666 ATAT
1 ATAT
77670 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:78059 original size:23 final size:23
Alignment explanation
Indices: 78028--78100 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
78018 ATAGGTAAAA
*
78028 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
78051 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
78074 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
78097 ATAT
1 ATAT
78101 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:78189 original size:431 final size:429
Alignment explanation
Indices: 77386--78439 Score: 1981
Period size: 431 Copynumber: 2.5 Consensus size: 429
77376 TTATCTTTGG
77386 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
77451 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
66 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
*
77516 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAGGTATGGACACTTTC
131 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
77581 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATA
196 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATA
77646 TAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTT
261 TAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTT
77711 TTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAA
326 TTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAA
77776 TTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATA
391 TTATAGGCGTCTAATGATTTA-TTTTTACGTTACGATATA
77816 TTTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTT
1 -TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTT
77881 TTTGTGC-AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAA
65 TTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAA
77945 TTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTT
129 TTGAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTT
78010 TCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTA
194 TCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTA
*
78075 TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCTATACTT
259 TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTT
*
78140 TTTTCACTGTTGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGT
324 TTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGT
78205 AATTATAGGCGTCTAATGATTTATTTTTACGTTACGATATA
389 AATTATAGGCGTCTAATGATTTATTTTTACGTTACGATATA
* *
78246 TT-A--TTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
*
78308 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTCAAAAAATT
66 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
* *
78373 GAAACATAAATTACATAACTTTAAAAGAAGAATCGATCCTTTTTATAAAAAGTATGAACACTTTC
131 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
78438 AA
196 AA
78440 CATATTATAA
Statistics
Matches: 613, Mismatches: 8, Indels: 9
0.97 0.01 0.01
Matches are distributed among these distances:
426 136 0.22
427 49 0.08
428 1 0.00
429 2 0.00
430 67 0.11
431 358 0.58
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (429 bp):
TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATA
TAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTT
TTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAA
TTATAGGCGTCTAATGATTTATTTTTACGTTACGATATA
Found at i:78539 original size:23 final size:23
Alignment explanation
Indices: 78513--78560 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
78503 AATTAGGTAA
*
78513 ATATAAGCACTACCTATTATATT
1 ATATAAGCACTACCTAGTATATT
* *
78536 ATATAAGCGCTACCTAGTATGTT
1 ATATAAGCACTACCTAGTATATT
78559 AT
1 AT
78561 TGTACTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (23 bp):
ATATAAGCACTACCTAGTATATT
Found at i:79357 original size:17 final size:18
Alignment explanation
Indices: 79324--79357 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
79314 TTGCTATTAG
79324 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
79342 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
79358 GACCGACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:79389 original size:10 final size:11
Alignment explanation
Indices: 79366--79390 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
79356 CGGACCGACT
79366 AAAAATCGGAA
1 AAAAATCGGAA
79377 AAAAATCGGAA
1 AAAAATCGGAA
79388 AAA
1 AAA
79391 CCCGGGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAAATCGGAA
Found at i:80097 original size:22 final size:22
Alignment explanation
Indices: 80064--80108 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
80054 GATATAAAAA
80064 AGTATTTTTTATTAAATATTTTT
1 AGTATTTTTTATTAAAT-TTTTT
*
80087 AGTA-TTTTTATTTAATTTTTT
1 AGTATTTTTTATTAAATTTTTT
80108 A
1 A
80109 AATAATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
AGTATTTTTTATTAAATTTTTT
Found at i:82322 original size:2 final size:2
Alignment explanation
Indices: 82315--82340 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
82305 ACAAACGCAC
82315 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
82341 GGAAGGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:84541 original size:2 final size:2
Alignment explanation
Indices: 84534--84569 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
84524 TAGATATTAC
84534 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
84570 CAAACCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91309 original size:21 final size:21
Alignment explanation
Indices: 91280--91332 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
91270 ATTCTGACTA
91280 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
91301 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
91322 TCGCAATGCGA
1 TCGCATTGCGA
91333 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:91347 original size:20 final size:20
Alignment explanation
Indices: 91322--91434 Score: 154
Period size: 20 Copynumber: 5.6 Consensus size: 20
91312 TTTTCCTAAT
91322 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
91342 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
91363 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
91383 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
91403 TCGGAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
91423 TCGCAACGCGAA
1 TCGCAATGCGAA
91435 ATCTGACTAT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 64 0.81
21 15 0.19
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:91461 original size:20 final size:21
Alignment explanation
Indices: 91422--91469 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
91412 GAATACGTAA
*
91422 ATCGCAACGCGAAATCTGACT
1 ATCGCAACGAGAAATCTGACT
*
91443 ATCGCAACGAG-ATTCTGACT
1 ATCGCAACGAGAAATCTGACT
91463 ATCGCAA
1 ATCGCAA
91470 TACTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAGAAATCTGACT
Found at i:92340 original size:24 final size:24
Alignment explanation
Indices: 92313--92366 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
92303 GTATTCGAAA
92313 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
92337 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
92361 TTTGAT
1 TTTGAT
92367 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:94800 original size:20 final size:20
Alignment explanation
Indices: 94775--94868 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
94765 TACATTCATT
94775 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
* *
94795 TGACTATCGCAGCACGGAAA
1 TGACTATCGCAACGCGGAAA
*
94815 TGACTATCGCAACGCGGAAT
1 TGACTATCGCAACGCGGAAA
94835 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
94855 TGACTATCGCAACG
1 TGACTATCGCAACG
94869 AGAGAATAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 64 0.96
21 3 0.04
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:94902 original size:33 final size:33
Alignment explanation
Indices: 94851--94935 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
94841 TCGCAACGCG
**
94851 GAAATGACTATCGCAACGAGAGAATAACAATGC
1 GAAATGAAAATCGCAACGAGAGAATAACAATGC
* * **
94884 GAAATGAAAATCGTAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATAACAATGC
94917 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
94936 TGAAATTAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 28 0.64
34 16 0.36
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATAACAATGC
Found at i:94995 original size:34 final size:34
Alignment explanation
Indices: 94950--95045 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
94940 ATTAGTTTCG
*
94950 CGTTGCAATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
94984 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
95017 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
95046 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:95170 original size:14 final size:14
Alignment explanation
Indices: 95151--95187 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
95141 CATCAATTAA
95151 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
95165 ACAAATCATCTTTT
1 ACAAATCAACATTT
95179 ACAAATCAA
1 ACAAATCAA
95188 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:96579 original size:21 final size:21
Alignment explanation
Indices: 96550--96657 Score: 101
Period size: 21 Copynumber: 5.1 Consensus size: 21
96540 GAATGTTGGG
* *
96550 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* **
96571 AGTGGCCTCTTGAACGATGGG
1 AGGGGCCTCTTGAACGATGAC
* ** *
96592 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAC
96613 AGGGGCCTCTTGAACGATAGA-
1 AGGGGCCTCTTGAACGAT-GAC
* *
96634 AGAGGCCTCTTGAATGATGAC
1 AGGGGCCTCTTGAACGATGAC
96655 AGG
1 AGG
96658 TGAGTCGGGC
Statistics
Matches: 68, Mismatches: 17, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:96644 original size:42 final size:42
Alignment explanation
Indices: 96565--96657 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
96555 CCTCTTCAAC
* * * *
96565 GATGACAGTGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATAGAAGAGGACTCTTGAGG
* * **
96607 GATGATAGGGGCCTCTTGAACGATAGAAGAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGATAGAAGAGGACTCTTGAGG
96649 GATGACAGG
1 GATGACAGG
96658 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATAGAAGAGGACTCTTGAGG
Found at i:97149 original size:20 final size:20
Alignment explanation
Indices: 97126--97194 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
97116 GAAACTTAAA
97126 ATCGCAACGCGAAAATAACT
1 ATCGCAACGCGAAAATAACT
*
97146 ATCGCAACACGAAAATAACT
1 ATCGCAACGCGAAAATAACT
*
97166 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATAACT
97186 ATCGCAACG
1 ATCGCAACG
97195 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAACT
Found at i:97258 original size:20 final size:20
Alignment explanation
Indices: 97233--97284 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
97223 CAACAACAAA
*
97233 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
97253 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
97273 ATCGCAATGCGA
1 ATCGCAATGCGA
97285 TTTTCATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:97296 original size:19 final size:20
Alignment explanation
Indices: 97250--97305 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
97240 CGCGAAAATG
* *
97250 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGATTTTC
97270 ACTATCGCAATGCGATTTTC
1 ACTATCGCAATGCGATTTTC
* *
97290 A-TTTCGCATTGCGATT
1 ACTATCGCAATGCGATT
97306 CTTTCGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (20 bp):
ACTATCGCAATGCGATTTTC
Found at i:97337 original size:20 final size:20
Alignment explanation
Indices: 97312--97488 Score: 184
Period size: 20 Copynumber: 9.5 Consensus size: 20
97302 GATTCTTTCG
**
97312 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
97332 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
97352 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
97372 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
97392 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
97406 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
97425 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
97439 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
97459 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
97479 TTGCGATAGT
1 TTGCGATAGT
97489 AAACTGTTCT
Statistics
Matches: 136, Mismatches: 7, Indels: 28
0.80 0.04 0.16
Matches are distributed among these distances:
14 14 0.10
16 12 0.09
17 6 0.04
18 5 0.04
19 7 0.05
20 92 0.68
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:97427 original size:33 final size:34
Alignment explanation
Indices: 97332--97465 Score: 144
Period size: 33 Copynumber: 3.8 Consensus size: 34
97322 CAAATTCGCA
*
97332 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 TTGCGATAGTCATTTTCGCATTGCGAT--TC--TCTCG
* * *
97370 TATTGCGATAGTCATTTTCGCATTGCGATTTTGTTG
1 --TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
**
97406 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
*
97439 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
97466 AGTCATTTTC
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
33 28 0.34
34 23 0.28
36 3 0.04
38 1 0.01
40 27 0.33
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:99428 original size:20 final size:20
Alignment explanation
Indices: 99373--99436 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
99363 ACTTTAAATT
**
99373 GCAACACGAAAATGAAAATC
1 GCAACACGAAAATGACTATC
99393 GCAACACGAAAATGACTATC
1 GCAACACGAAAATGACTATC
* **
99413 GCAACGCGAATTTGACTATC
1 GCAACACGAAAATGACTATC
99433 GCAA
1 GCAA
99437 TGCAAGAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (20 bp):
GCAACACGAAAATGACTATC
Found at i:99478 original size:33 final size:34
Alignment explanation
Indices: 99410--99482 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
99400 GAAAATGACT
* ** *
99410 ATCGCAACGCGAATTTGACTATCGCAATGCAAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
99444 ATCGCAACGCGAA-ATGAAAATCGCAACG-ACAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCA-AGA
99477 ATCGCA
1 ATCGCA
99483 TTGCGATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.59
34 13 0.38
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
Found at i:99851 original size:22 final size:22
Alignment explanation
Indices: 99807--99872 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
99797 TGACCGTGAA
* * * *
99807 TGATTTCGCCGGAGATAGAGAC
1 TGATATCGTCGGAGATGGGGAC
*
99829 TGATATCGTCGGCGATGGGGAC
1 TGATATCGTCGGAGATGGGGAC
*
99851 TGATTTCGTCGGAGATGGGGAC
1 TGATATCGTCGGAGATGGGGAC
99873 GGATGTCGCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (22 bp):
TGATATCGTCGGAGATGGGGAC
Found at i:100093 original size:20 final size:20
Alignment explanation
Indices: 100070--100267 Score: 315
Period size: 20 Copynumber: 9.8 Consensus size: 20
100060 CGATAGTCAG
* *
100070 ATTCACATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
100090 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
100110 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
100130 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
100150 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
100170 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
100190 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
100210 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
100231 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
100251 ATTCGCGTTGCGATTTA
1 ATTCGCATTGCGATTTA
100268 TTCGCATTGC
Statistics
Matches: 166, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
20 151 0.91
21 15 0.09
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:100300 original size:21 final size:21
Alignment explanation
Indices: 100276--100321 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
100266 TATTCGCATT
100276 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
100297 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
100318 GCGA
1 GCGA
100322 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:110616 original size:18 final size:20
Alignment explanation
Indices: 110579--110615 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
110569 TAAAATAATG
110579 ATTTTGTCTCTTATTCTTTT
1 ATTTTGTCTCTTATTCTTTT
110599 ATTTT-TCT-TTATT-TTTT
1 ATTTTGTCTCTTATTCTTTT
110616 TGGCATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 5 0.29
19 3 0.18
20 5 0.29
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (20 bp):
ATTTTGTCTCTTATTCTTTT
Found at i:116446 original size:60 final size:60
Alignment explanation
Indices: 116305--116456 Score: 145
Period size: 60 Copynumber: 2.5 Consensus size: 60
116295 ATTGATCTTA
* * *
116305 AAACTTTTGAATATTAT-AATTTTATCCAC-AGACTATGACTCTCCTTCTAAATTAGTCCTT
1 AAACTTTTGAATATT-TCAATTTCATCC-CTAAACTATGACTCTCCTTCTAAATTAGTCCTC
* * *
116365 AAAGTTTT-AATCA-TTCTAATTTCATCCCTAAACTATGA-TCCTCTTTCTAAATTAATTCC-C
1 AAACTTTTGAAT-ATTTC-AATTTCATCCCTAAACTATGACT-CTCCTTCTAAATT-AGTCCTC
*
116425 AAACTTTTGAATATTTCAATTTCATCTCTAAA
1 AAACTTTTGAATATTTCAATTTCATCCCTAAA
116457 TTCATCCGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
58 1 0.01
59 6 0.08
60 59 0.78
61 10 0.13
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (60 bp):
AAACTTTTGAATATTTCAATTTCATCCCTAAACTATGACTCTCCTTCTAAATTAGTCCTC
Found at i:123029 original size:24 final size:24
Alignment explanation
Indices: 123005--123092 Score: 77
Period size: 24 Copynumber: 3.5 Consensus size: 24
122995 ACAAATGAAT
*
123005 GAACACAAATGAACGAACATAAAT
1 GAACACAAATGAACGAACATAAAC
** ** *
123029 GAACGGATGTAAACGAACATAAAC
1 GAACACAAATGAACGAACATAAAC
* *
123053 GAACACAATAAACGAACAAACATAAAC
1 GAACAC---AAATGAACGAACATAAAC
123080 GAACACAAATGAA
1 GAACACAAATGAA
123093 AATAGATTTT
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
24 28 0.60
27 19 0.40
ACGTcount: A:0.58, C:0.18, G:0.14, T:0.10
Consensus pattern (24 bp):
GAACACAAATGAACGAACATAAAC
Found at i:123032 original size:14 final size:14
Alignment explanation
Indices: 122991--123092 Score: 73
Period size: 14 Copynumber: 6.9 Consensus size: 14
122981 AATGATATAT
*
122991 GAACACAAATGAAT
1 GAACACAAATGAAC
123005 GAACACAAATGAAC
1 GAACACAAATGAAC
*
123019 GAACATAAATGAAC
1 GAACACAAATGAAC
* *
123033 GGATGTAAACGAACATAAAC
1 -GA---ACAC-AA-ATGAAC
*
123053 GAACAC-AATAAAC
1 GAACACAAATGAAC
*
123066 GAACA-AACATAAAC
1 GAACACAA-ATGAAC
123080 GAACACAAATGAA
1 GAACACAAATGAA
123093 AATAGATTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
13 12 0.17
14 42 0.58
15 4 0.06
16 3 0.04
18 2 0.03
19 4 0.06
20 5 0.07
ACGTcount: A:0.58, C:0.18, G:0.14, T:0.11
Consensus pattern (14 bp):
GAACACAAATGAAC
Found at i:123065 original size:13 final size:13
Alignment explanation
Indices: 123047--123087 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
123037 GTAAACGAAC
123047 ATAAACGAACACA
1 ATAAACGAACACA
*
123060 ATAAACGAACAAA
1 ATAAACGAACACA
123073 CATAAACGAACACA
1 -ATAAACGAACACA
123087 A
1 A
123088 ATGAAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.63, C:0.22, G:0.07, T:0.07
Consensus pattern (13 bp):
ATAAACGAACACA
Found at i:123295 original size:14 final size:14
Alignment explanation
Indices: 123278--123325 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
123268 AACGTACATA
123278 AACGAACATAAATG
1 AACGAACATAAATG
*
123292 AACGAACAT--ATT
1 AACGAACATAAATG
* *
123304 ACCGAACGTAAATG
1 AACGAACATAAATG
123318 AACGAACA
1 AACGAACA
123326 AGCTCTCTGC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 9 0.35
14 17 0.65
ACGTcount: A:0.52, C:0.19, G:0.15, T:0.15
Consensus pattern (14 bp):
AACGAACATAAATG
Found at i:124600 original size:87 final size:86
Alignment explanation
Indices: 124480--124687 Score: 229
Period size: 87 Copynumber: 2.4 Consensus size: 86
124470 AAAGACTCAA
* * * * *
124480 GCTATGAATTCGTTAAGAGT-TGGAAACTCAACCTCACAAATTTATGTATTTACCAAGTCCGTCT
1 GCTATGGATTCATTAAGAGTAT--AAACTCAACCTCACAAATTGATGTATTCACCAAGTCCATCT
*** * *
124544 CACTAAGACCATTTAAGTCATGG
64 CACTAAGACCACCCAAATCACGG
* * * * * *
124567 GTTATGGATTCATTAAGGGTGTAAAACTTAACCTCATAAATTGATGTATTCATCAAGTCCATCTC
1 GCTATGGATTCATTAAGAGTAT-AAACTCAACCTCACAAATTGATGTATTCACCAAGTCCATCTC
*
124632 ACTAGGACCACCCAAATCACGG
65 ACTAAGACCACCCAAATCACGG
124654 GCTATGGATTCATTAAGAGTATAAACTCAACCTC
1 GCTATGGATTCATTAAGAGTATAAACTCAACCTC
124688 TCAAGTGTAC
Statistics
Matches: 99, Mismatches: 21, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
86 11 0.11
87 87 0.88
88 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (86 bp):
GCTATGGATTCATTAAGAGTATAAACTCAACCTCACAAATTGATGTATTCACCAAGTCCATCTCA
CTAAGACCACCCAAATCACGG
Found at i:128550 original size:18 final size:17
Alignment explanation
Indices: 128518--128554 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
128508 AAGTAATGGA
128518 CTCTGCTCTCTGCTCTG
1 CTCTGCTCTCTGCTCTG
128535 CTCTGCTCTGCTGCTCTG
1 CTCTGCTCT-CTGCTCTG
128553 CT
1 CT
128555 GGCAACTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.00, C:0.41, G:0.19, T:0.41
Consensus pattern (17 bp):
CTCTGCTCTCTGCTCTG
Found at i:128851 original size:41 final size:43
Alignment explanation
Indices: 128776--128860 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 43
128766 AAATAATTTT
128776 TAAAAAAATATTATTTAATATAAAAAATTTAAAA-T-AAATAA
1 TAAAAAAATATTATTTAATATAAAAAATTTAAAATTAAAATAA
* * *
128817 TAAAATAATATT-TTTATTAT-TAAAATTTAAAAAATTAAAATAA
1 TAAAAAAATATTATTTAATATAAAAAATTT--AAAATTAAAATAA
128860 T
1 T
128861 CACCACTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
39 7 0.19
40 7 0.19
41 15 0.41
42 1 0.03
43 7 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (43 bp):
TAAAAAAATATTATTTAATATAAAAAATTTAAAATTAAAATAA
Done.