Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007801.1 Hibiscus syriacus cultivar Beakdansim tig00110118_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: 951604
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:207670 original size:120 final size:122
Alignment explanation
Indices: 207522--207870 Score: 322
Period size: 120 Copynumber: 2.9 Consensus size: 122
207512 GATGACAATT
*
207522 TATCTCCTTCTGTGATGTAATCTAGCAAAAAGTTGAACAAATTCTCCTCCTTATGAACTTCTTCT
1 TATCTCCTTCTGTGATGTAATCTAGCAAAAAGTTGAACAAATTCTCCTCATTATGAACTTCTTCT
* *
207587 T-C-TTCAGATGAGTTCTTCTCATTATGAACTC-CTTCTGGAAATGTTGATGATGATA
66 TCCTTTCAGATAAGTTCTTCTCATTATGAACTCTC-TCTGGAAAAGTTGATGATGATA
* * * * *
207642 TATCTCCTTCTGTGATAG-AGT-TATGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTT
1 TATCTCCTTCTGTGAT-GTAATCTA-GCAAAAAGTTGAACAAATTCTCCTCATTATGAACTTCTT
*
207705 CTTCCTTTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAA---G-T--TG---
64 CTTCC-TTTCAGATAAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATGATGATA
* * * * * *
207756 -A--TCCATCGAGTGATG-AATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTT
1 TATCTCCTTC-TGTGATGTAA-TCTAGCAAAAAGTTGAACAAATTCTCCTCATTATGAACTTCTT
* * *
207817 CTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAAAGCTGAT
64 CTTC-CT-TTCAGATAAGTTCTTCTCATTATGAACTCT-CTCTGGAAAAGTTGAT
207871 CCATCAAGTG
Statistics
Matches: 192, Mismatches: 21, Indels: 35
0.77 0.08 0.14
Matches are distributed among these distances:
111 7 0.04
112 45 0.23
113 38 0.20
114 1 0.01
116 1 0.01
117 3 0.02
119 3 0.02
120 56 0.29
121 2 0.01
123 35 0.18
124 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (122 bp):
TATCTCCTTCTGTGATGTAATCTAGCAAAAAGTTGAACAAATTCTCCTCATTATGAACTTCTTCT
TCCTTTCAGATAAGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATGATGATA
Found at i:207871 original size:113 final size:113
Alignment explanation
Indices: 207666--209584 Score: 3305
Period size: 113 Copynumber: 17.0 Consensus size: 113
207656 ATAGAGTTAT
* * *
207666 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTT-TTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * **
207730 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * ** * *
207778 ACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
207843 ATTATGAACTCTAC-CTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
207891 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
207956 ATTATGAACTTTCTCTAGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
208004 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTACAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
208069 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
208117 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
208182 ATTATGAACTTGAC-CTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTT-TCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
208230 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
208295 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
208343 GCAAAAGGTTGAACAAGATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
208408 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
208456 GCAAAATGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
208521 ATTATGAACTTGAC-CTGGAAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTT-TCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
208569 GCAAAAGGTTGAACAAGCTCTCCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
208634 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
208682 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
208747 ATTATGAACTTTCTCTAGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
208795 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
208860 ATTATGAACTTTCTCTGGAAAAGCGGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
208908 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
208973 ATTATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
209021 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
209086 ATTATGAA-TTTGAC-CTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTT--CTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
209134 GAAAAAGGTTGAACAA-CTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
209198 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
209246 GCAAAAGGTTGAACAAGCTCTTCTCATTTTGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
209311 ATTATGAACTTTCTCTAGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
209359 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * ** * **
209424 ATTATGAACTTGAC-CTGGCAATGCTGATCCATCGGGTGATGAATTAAA
66 ATTATGAACTT-TCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * *
209472 GTAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
209537 ATTATGAACTTTCTCTTGAAATGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
209585 ATATTTGCTA
Statistics
Matches: 1716, Mismatches: 77, Indels: 27
0.94 0.04 0.01
Matches are distributed among these distances:
111 1 0.00
112 152 0.09
113 1557 0.91
114 6 0.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:210750 original size:18 final size:17
Alignment explanation
Indices: 210727--210774 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
210717 AAAATAAAAG
210727 AATAAATTGAATTTTGAA
1 AATAAATTGAATTTT-AA
* *
210745 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTAA
210761 AATAAATTGAATTT
1 AATAAATTGAATTT
210775 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.46
17 3 0.12
18 11 0.42
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (17 bp):
AATAAATTGAATTTTAA
Found at i:211153 original size:22 final size:21
Alignment explanation
Indices: 211128--211202 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 21
211118 TGACCCCCCC
211128 TTTTTTCTTTCTTCTTTTCTTT
1 TTTTTTCTTTCTT-TTTTCTTT
* *
211150 TTTTTTTTTATTTTTTTTCTTT
1 TTTTTTCTT-TCTTTTTTCTTT
*
211172 TTTTTTCCTTCTTTTTT-TTT
1 TTTTTTCTTTCTTTTTTCTTT
211192 CATTTTTTCTT
1 --TTTTTTCTT
211203 CAAGCATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.07
21 7 0.16
22 31 0.70
23 3 0.07
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTCTTTCTTTTTTCTTT
Found at i:211171 original size:34 final size:34
Alignment explanation
Indices: 211128--211199 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
211118 TGACCCCCCC
*
211128 TTTTTTCTTTCTTCTTTT-CTT-TTTTTTTTTTATT
1 TTTTTTCTTT-TT-TTTTCCTTCTTTTTTTTTCATT
211162 TTTTTTCTTTTTTTTTCCTTCTTTTTTTTTCATT
1 TTTTTTCTTTTTTTTTCCTTCTTTTTTTTTCATT
211196 TTTT
1 TTTT
211200 CTTCAAGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
32 4 0.11
33 5 0.14
34 26 0.74
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (34 bp):
TTTTTTCTTTTTTTTTCCTTCTTTTTTTTTCATT
Found at i:211183 original size:14 final size:13
Alignment explanation
Indices: 211127--211192 Score: 71
Period size: 14 Copynumber: 4.8 Consensus size: 13
211117 TTGACCCCCC
211127 CTTTTTTCTTTCTT
1 CTTTTTT-TTTCTT
211141 CTTTTCTTTTT-TT
1 CTTTT-TTTTTCTT
* *
211154 TTTTTATTTTTTTT
1 CTTTT-TTTTTCTT
211168 CTTTTTTTTTCCTT
1 CTTTTTTTTT-CTT
211182 CTTTTTTTTTC
1 CTTTTTTTTTC
211193 ATTTTTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
13 17 0.38
14 26 0.58
15 2 0.04
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (13 bp):
CTTTTTTTTTCTT
Found at i:218539 original size:15 final size:15
Alignment explanation
Indices: 218516--218547 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
218506 TGCAATGAAT
218516 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
218531 AATGCATGTATGCAA
1 AATGAATGTATGCAA
218546 AA
1 AA
218548 CGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:222496 original size:20 final size:20
Alignment explanation
Indices: 222471--222513 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
222461 TTTCCTTGAT
222471 ATTAAAAAAATAAATAAATA
1 ATTAAAAAAATAAATAAATA
* * *
222491 ATTAAAACAATTAATATATA
1 ATTAAAAAAATAAATAAATA
222511 ATT
1 ATT
222514 TATAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTAAAAAAATAAATAAATA
Found at i:223605 original size:13 final size:13
Alignment explanation
Indices: 223587--223628 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
223577 TTTGAGTTGG
* *
223587 TCTCTATTTTTTT
1 TCTCTATTCTTTC
223600 TCTCTATTCTTTC
1 TCTCTATTCTTTC
*
223613 TCTCTGTTCTTTC
1 TCTCTATTCTTTC
223626 TCT
1 TCT
223629 TGTTTGCAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.05, C:0.26, G:0.02, T:0.67
Consensus pattern (13 bp):
TCTCTATTCTTTC
Found at i:224053 original size:3 final size:3
Alignment explanation
Indices: 224036--224089 Score: 65
Period size: 3 Copynumber: 17.0 Consensus size: 3
224026 TTTGGGCCTG
224036 TAA TAA -AA TTAA TAA TAAA TAA TAA TAA TAA TAAA TAA TAA TAA TAAA
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA
224084 TAA TAA
1 TAA TAA
224090 AAAACCAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 2 0.04
3 33 0.72
4 11 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:224063 original size:13 final size:12
Alignment explanation
Indices: 224036--224093 Score: 73
Period size: 13 Copynumber: 4.7 Consensus size: 12
224026 TTTGGGCCTG
*
224036 TAATAAAATTAA
1 TAATAAAAATAA
224048 TAATAAATAATAA
1 TAATAAA-AATAA
224061 TAATAATAAATAA
1 TAATAA-AAATAA
224074 TAATAATAAATAA
1 TAATAA-AAATAA
224087 TAA-AAAA
1 TAATAAAA
224094 CCAAATGTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
11 2 0.05
12 9 0.21
13 31 0.72
14 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
TAATAAAAATAA
Found at i:224089 original size:16 final size:16
Alignment explanation
Indices: 224045--224082 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
224035 GTAATAAAAT
224045 TAATAATAAATAATAA
1 TAATAATAAATAATAA
224061 TAATAATAAATAATAA
1 TAATAATAAATAATAA
224077 TAATAA
1 TAATAA
224083 ATAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATAATAAATAATAA
Found at i:225820 original size:3 final size:3
Alignment explanation
Indices: 225812--225912 Score: 105
Period size: 3 Copynumber: 32.0 Consensus size: 3
225802 CAATTTGCTT
* *
225812 TTA TTA TTA TTA TTTA TTTA TTTA TTTA CTA TTA TTA TACA TTA TTA
1 TTA TTA TTA TTA -TTA -TTA -TTA -TTA TTA TTA TTA T-TA TTA TTA
* *
225859 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TAA ATA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
225904 TTA TTA TTA
1 TTA TTA TTA
225913 ATAAATAATT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.02
3 64 0.74
4 20 0.23
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:225844 original size:25 final size:23
Alignment explanation
Indices: 225812--225912 Score: 109
Period size: 22 Copynumber: 4.4 Consensus size: 23
225802 CAATTTGCTT
225812 TTATTATTATTATTTATTTATTTA
1 TTATTATTATTATTTA-TTATTTA
* **
225836 TTTACTATTATTATACATTA-TTA
1 -TTATTATTATTATTTATTATTTA
225859 TTATTATTATTA-TTATTATTTA
1 TTATTATTATTATTTATTATTTA
**
225881 TTATTATTA-TAAATATTATTATA
1 TTATTATTATTATTTATTATT-TA
225904 TTATTATTA
1 TTATTATTA
225913 ATAAATAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
21 6 0.09
22 30 0.45
23 14 0.21
24 3 0.05
25 13 0.20
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TTATTATTATTATTTATTATTTA
Found at i:225923 original size:14 final size:12
Alignment explanation
Indices: 225857--225919 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
225847 TATACATTAT
* *
225857 TATTATTATTAT
1 TATTATTATAAA
* *
225869 TATTATTATTTAT
1 TATTATTA-TAAA
225882 TATTATTATAAA
1 TATTATTATAAA
*
225894 TATTATTAT-AT
1 TATTATTATAAA
225905 TATTATTAATAAA
1 TATTATT-ATAAA
225918 TA
1 TA
225920 ATTACAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
11 8 0.18
12 21 0.48
13 15 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTATAAA
Found at i:225929 original size:34 final size:34
Alignment explanation
Indices: 225860--225929 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
225850 ACATTATTAT
* * * *
225860 TATTATTATTATTATTATTTATTATTATTATAAA
1 TATTATTATTATTATTATTAATAATAATTACAAA
225894 TATTATTA-TATTATTATTAATAAATAATTACAAA
1 TATTATTATTATTATTATTAAT-AATAATTACAAA
225928 TA
1 TA
225930 CATCGGAGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 12 0.39
34 19 0.61
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (34 bp):
TATTATTATTATTATTATTAATAATAATTACAAA
Found at i:227411 original size:28 final size:27
Alignment explanation
Indices: 227378--227466 Score: 79
Period size: 28 Copynumber: 3.5 Consensus size: 27
227368 TAAATACAAG
227378 TTTTATTATT-TTT-TTACTATAGTTTTAA
1 TTTTATTATTGTTTATT--TATA-TTTTAA
227406 TTTTATTTATTGTTTATTTATATTTTAA
1 TTTTA-TTATTGTTTATTTATATTTTAA
227434 TTTTA-TA-TGTTTA--TATA-TTTAA
1 TTTTATTATTGTTTATTTATATTTTAA
227456 --TTATTATTGTT
1 TTTTATTATTGTT
227467 ATTATTATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.05
21 2 0.04
22 9 0.16
23 4 0.07
25 6 0.11
26 2 0.04
28 16 0.29
29 9 0.16
30 3 0.05
31 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTTATTATTGTTTATTTATATTTTAA
Found at i:227432 original size:11 final size:12
Alignment explanation
Indices: 227407--227447 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
227397 TAGTTTTAAT
227407 TTTATTTAT-TG
1 TTTATTTATATG
227418 TTTATTTATAT-
1 TTTATTTATATG
227429 TTTAATTTTATATG
1 TTT-A-TTTATATG
227443 TTTAT
1 TTTAT
227448 ATATTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 12 0.46
12 3 0.12
13 8 0.31
14 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (12 bp):
TTTATTTATATG
Found at i:227448 original size:21 final size:22
Alignment explanation
Indices: 227412--227466 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
227402 TTAATTTTAT
227412 TTATTGTTTATTTATATTTTAATT-
1 TTATTGTTTA--TATA-TTTAATTA
227436 TTATATGTTTATATATTTAATTA
1 TTAT-TGTTTATATATTTAATTA
227459 TTATTGTT
1 TTATTGTT
227467 ATTATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.38
23 8 0.28
24 4 0.14
25 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTATTGTTTATATATTTAATTA
Found at i:227453 original size:29 final size:29
Alignment explanation
Indices: 227395--227454 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
227385 ATTTTTTTAC
* *
227395 TATAGTTTTAATTTTATTTATTGTTTATT
1 TATAGTTTTAATTTTATTTATTATATATT
227424 TATA-TTTTAATTTTATATGT-TTATATATT
1 TATAGTTTTAATTTTAT-T-TATTATATATT
227453 TA
1 TA
227455 ATTATTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 12 0.44
29 14 0.52
30 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (29 bp):
TATAGTTTTAATTTTATTTATTATATATT
Found at i:230651 original size:6 final size:6
Alignment explanation
Indices: 230636--230683 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
230626 ACATTCACTT
* * *
230636 ATTTAC ATTTGT ATTTGC ATTTGT ATTTGC ATTTGC ATCTTTGC ATTT
1 ATTTGC ATTTGC ATTTGC ATTTGC ATTTGC ATTTGC A--TTTGC ATTT
230684 TTACGTTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 29 0.83
8 6 0.17
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (6 bp):
ATTTGC
Found at i:230656 original size:12 final size:12
Alignment explanation
Indices: 230635--230670 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
230625 TACATTCACT
*
230635 TATTTACATTTG
1 TATTTGCATTTG
230647 TATTTGCATTTG
1 TATTTGCATTTG
230659 TATTTGCATTTG
1 TATTTGCATTTG
230671 CATCTTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.19, C:0.08, G:0.14, T:0.58
Consensus pattern (12 bp):
TATTTGCATTTG
Found at i:237863 original size:713 final size:713
Alignment explanation
Indices: 236498--237920 Score: 2479
Period size: 713 Copynumber: 2.0 Consensus size: 713
236488 CTCAGCAAGA
*
236498 AGTAATGTTGAACACATTTTTAAAATCTGTATCAACAAATGTTGAGGAATTTTAATAGTTATTTC
1 AGTAATGTTGAACACATTTTTAAAATCTATATCAACAAATGTTGAGGAATTTTAATAGTTATTTC
236563 AGACAGATCCATGTGGGGCATTTTGAAGGTTCACATCAGTATGAAAAACGTTGAGGAATTTTAAA
66 AGACAGATCCATGTGGGGCATTTTGAAGGTTCACATCAGTATGAAAAACGTTGAGGAATTTTAAA
* * *
236628 AGCTCACATCAACAAGAAGCAAATGCTGGGACATACTAAAAGCTCATTTCAATCAGAATCATAAA
131 AGCTCACATCAACAAGAAGCAAATGCTAGGACATACTAAAACCTCATTTCAATCAGAATCAGAAA
*
236693 TGTTGACGCATTAAGAACATTCATATCAGTAAATGTTGGGGCATGCTGAAGGCCCACATAATTAT
196 TGTTGACGCATTAAGAACATTCATATCAGTAAATGCTGGGGCATGCTGAAGGCCCACATAATTAT
*
236758 GTGTTAAAGATCATTGCTTTGAGCAAATATTTCCAATAAGACAGAAAGGAATGAAGAATGAAAAT
261 GTGTTAAAGATCATTGCTTTGAGCAAATATTTCCAATAAGAAAGAAAGGAATGAAGAATGAAAAT
* *
236823 GGTGAAACAATGACAGTGGAACTGATTATAAATAATTGTTTCGTTCATCAAGCAGTTACATCAGG
326 GGTGAAACAATGACAGTGGAACTGACTATAAATAATTGCTTCGTTCATCAAGCAGTTACATCAGG
236888 GTCCTGGTGTTGAACAAATATTTACTCAGCAAATATGGTTTCAAATACCCAATATTCTTAACCAT
391 GTCCTGGTGTTGAACAAATATTTACTCAGCAAATATGGTTTCAAATACCCAATATTCTTAACCAT
* * *
236953 GTGTCACATGACAACATGTTCTTTGTTAAGATACATCACGGTTGCATGGATAAAGATGGTCCCCA
456 GTGCCACATGACAACATGTTCTTTGTTAAGATACACCACGGTTGCATGGATAAAAATGGTCCCCA
* *
237018 GGCAGACTATTTGATCCACGGTTCAGTTCCTCAAAATCTCGGCTTTGAATTTTGTATTCTATGTT
521 GGCAGACTATTCGATCCACGGTTCAGTTCCTCAAAATCTCAGCTTTGAATTTTGTATTCTATGTT
* *
237083 TCGGTGATGATTGGACATATTTCTTTAAGATTCATTGTAGTTAGTTTCAATCATACTGTTAGGGC
586 TCGGTGATGATTGGACATATTTCTTTAAGATTCATTGCAGTTAGTTTCAATCATACTATTAGGGC
*
237148 TACAAAAATGTTTTTCACAACAGTTTTCGCTTACTTGATGACATTGAATAAAGAGGCTCAGCT
651 TACAAAAATGTTTTTCACAACAATTTTCGCTTACTTGATGACATTGAATAAAGAGGCTCAGCT
*
237211 AGTAATGTTGAACACATTTTTAAAATCTATATCAACAAATGTTGGGGAATTTTAATAGTTATTTC
1 AGTAATGTTGAACACATTTTTAAAATCTATATCAACAAATGTTGAGGAATTTTAATAGTTATTTC
* *
237276 AGACAGATCCATGT-GGGCATTTTGAAGGTTCACATCAGTATGAAAAAATGTTGAGGCATTTTAA
66 AGACAGATCCATGTGGGGCATTTTGAAGGTTCACATCAGTATG-AAAAACGTTGAGGAATTTTAA
* * * *
237340 AAGCTCACATCAACAATAAGCAAATGGTAGGACATACTGAAACCTCATTTCAATCAGAATCAGGA
130 AAGCTCACATCAACAAGAAGCAAATGCTAGGACATACTAAAACCTCATTTCAATCAGAATCAGAA
* * * *
237405 ATGTTGACGTATTAAGAACGTTCATATCAGTAAATGCTGGGGCATGCTGAAGGCCCACGTCATTA
195 ATGTTGACGCATTAAGAACATTCATATCAGTAAATGCTGGGGCATGCTGAAGGCCCACATAATTA
* *
237470 TGTGTTAAATATCATTGTTTTGAGCAAATATTTCCAATAAGAAAGAAAGGAATGAAGAATGAAAA
260 TGTGTTAAAGATCATTGCTTTGAGCAAATATTTCCAATAAGAAAGAAAGGAATGAAGAATGAAAA
* * *
237535 TGGTGAAACAGTGATAGTGGAACTGACTATACATAATTGCTTCGTTCATCAAGCAGTTACATCAG
325 TGGTGAAACAATGACAGTGGAACTGACTATAAATAATTGCTTCGTTCATCAAGCAGTTACATCAG
*
237600 GGTCCTGGTGTTGAACAAATATTTACTCAGTAAATATGGTTTCAAATACCCAATATTCTTAACCA
390 GGTCCTGGTGTTGAACAAATATTTACTCAGCAAATATGGTTTCAAATACCCAATATTCTTAACCA
* *
237665 TGTGCCACATGACAGCATGTTCTTTGTTAAGATACACCATGGTTGCATGGATAAAAATGGTCCCC
455 TGTGCCACATGACAACATGTTCTTTGTTAAGATACACCACGGTTGCATGGATAAAAATGGTCCCC
*
237730 AGGCAGACTATTCGATCCACGGTTCAGTTCCTCAAAATCTCAGCTTTGAATTTTGTATTCTGTGT
520 AGGCAGACTATTCGATCCACGGTTCAGTTCCTCAAAATCTCAGCTTTGAATTTTGTATTCTATGT
*
237795 TTCGGTGATGATTGGACATATTTCTTTAAGATTCATTGCAGTTAGTTTCAATCATACTATTGGGG
585 TTCGGTGATGATTGGACATATTTCTTTAAGATTCATTGCAGTTAGTTTCAATCATACTATTAGGG
* *
237860 CTACGAAGATGTTTTTCACAACAATTTTCGCTTACTTGATGACATTGAATAAAGAGGCTCA
650 CTACAAAAATGTTTTTCACAACAATTTTCGCTTACTTGATGACATTGAATAAAGAGGCTCA
237921 ACTTATGTTA
Statistics
Matches: 670, Mismatches: 39, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
712 28 0.04
713 642 0.96
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (713 bp):
AGTAATGTTGAACACATTTTTAAAATCTATATCAACAAATGTTGAGGAATTTTAATAGTTATTTC
AGACAGATCCATGTGGGGCATTTTGAAGGTTCACATCAGTATGAAAAACGTTGAGGAATTTTAAA
AGCTCACATCAACAAGAAGCAAATGCTAGGACATACTAAAACCTCATTTCAATCAGAATCAGAAA
TGTTGACGCATTAAGAACATTCATATCAGTAAATGCTGGGGCATGCTGAAGGCCCACATAATTAT
GTGTTAAAGATCATTGCTTTGAGCAAATATTTCCAATAAGAAAGAAAGGAATGAAGAATGAAAAT
GGTGAAACAATGACAGTGGAACTGACTATAAATAATTGCTTCGTTCATCAAGCAGTTACATCAGG
GTCCTGGTGTTGAACAAATATTTACTCAGCAAATATGGTTTCAAATACCCAATATTCTTAACCAT
GTGCCACATGACAACATGTTCTTTGTTAAGATACACCACGGTTGCATGGATAAAAATGGTCCCCA
GGCAGACTATTCGATCCACGGTTCAGTTCCTCAAAATCTCAGCTTTGAATTTTGTATTCTATGTT
TCGGTGATGATTGGACATATTTCTTTAAGATTCATTGCAGTTAGTTTCAATCATACTATTAGGGC
TACAAAAATGTTTTTCACAACAATTTTCGCTTACTTGATGACATTGAATAAAGAGGCTCAGCT
Found at i:238394 original size:54 final size:54
Alignment explanation
Indices: 238332--238472 Score: 167
Period size: 54 Copynumber: 2.6 Consensus size: 54
238322 AAATCACAGA
*
238332 AAAGGATGAATGTGTTGTCAAATGCTTTAC-AAACATCTGGCCAGAAGCCACAAG
1 AAAGGATGAATGTGTTGTCAAATGCTTTACGAAA-ATCCGGCCAGAAGCCACAAG
* * * * *
238386 AAATGATGAATGTGTTATCAAAAGCTTTACGAAAATCCGGGCAGAAGCCACGAG
1 AAAGGATGAATGTGTTGTCAAATGCTTTACGAAAATCCGGCCAGAAGCCACAAG
* * * * *
238440 AAAGGATTAATATATTGTCACATGTTTTACGAA
1 AAAGGATGAATGTGTTGTCAAATGCTTTACGAA
238473 CCAGTGATTA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 69 0.96
55 3 0.04
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (54 bp):
AAAGGATGAATGTGTTGTCAAATGCTTTACGAAAATCCGGCCAGAAGCCACAAG
Found at i:238860 original size:22 final size:22
Alignment explanation
Indices: 238835--238891 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
238825 ATATCTACAT
238835 TCTTCAAAGATGATAGATTCTA
1 TCTTCAAAGATGATAGATTCTA
*
238857 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTA
*
238879 TTTTCAAAGATGA
1 TCTTCAAAGATGA
238892 AAGCTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTA
Found at i:239615 original size:45 final size:45
Alignment explanation
Indices: 239546--239938 Score: 678
Period size: 45 Copynumber: 8.7 Consensus size: 45
239536 CTATTTCCCA
*
239546 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACATTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
239591 CATCTATAAGCCCTTCAGTACATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
239636 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
239681 CGTCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
239726 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
239771 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
239816 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
239861 CATCTGTAAGCCCTTCAGAGCATGATGTTTTCAAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
239907 CATCTGTAAGCCCTTCAGTGCATGATGATTTT
1 CATCTGTAAGCCCTTCAGTGCATGATG-TTTT
239939 GATATTTTCA
Statistics
Matches: 328, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 286 0.87
46 38 0.12
47 4 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:240074 original size:3 final size:3
Alignment explanation
Indices: 240066--240141 Score: 100
Period size: 3 Copynumber: 25.0 Consensus size: 3
240056 CAGTTTGCTT
*
240066 TTA TTA TTA TTA TTA TTA TACA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA TTA TTA
* *
240113 TTA TTA TAA ATA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
240142 ATAAATAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 57 0.89
4 5 0.08
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:240092 original size:16 final size:15
Alignment explanation
Indices: 240066--240141 Score: 82
Period size: 16 Copynumber: 5.0 Consensus size: 15
240056 CAGTTTGCTT
*
240066 TTATTATTATTATTA
1 TTATAATTATTATTA
240081 TTATACATTATTATTA
1 TTATA-ATTATTATTA
*
240097 TTATTATTTATTATTA
1 TTA-TAATTATTATTA
* * *
240113 TTATTATAAATATTA
1 TTATAATTATTATTA
240128 TTAT-ATTATTATTA
1 TTATAATTATTATTA
240142 ATAAATAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
14 8 0.16
15 16 0.31
16 25 0.49
17 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATAATTATTATTA
Found at i:240092 original size:19 final size:18
Alignment explanation
Indices: 240068--240141 Score: 100
Period size: 19 Copynumber: 4.2 Consensus size: 18
240058 GTTTGCTTTT
240068 ATTATTATTATTATTATA
1 ATTATTATTATTATTATA
240086 CATTATTATTATTATTAT-
1 -ATTATTATTATTATTATA
240104 -TTATTATTATTATTATA
1 ATTATTATTATTATTATA
* *
240121 AATATTATTA-TATTATT
1 ATTATTATTATTATTATA
240138 ATTA
1 ATTA
240142 ATAAATAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
16 16 0.32
17 9 0.18
18 8 0.16
19 17 0.34
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTATTATTATTATTATA
Found at i:240094 original size:22 final size:22
Alignment explanation
Indices: 240066--240141 Score: 100
Period size: 22 Copynumber: 3.4 Consensus size: 22
240056 CAGTTTGCTT
*
240066 TTATTATTATTATTATTATACA
1 TTATTATTATTATTATTATATA
240088 TTATTATTATTATTATT-TATTA
1 TTATTATTATTATTATTATA-TA
* *
240110 TTATTATTATAAATATTATTATA
1 TTATTATTATTATTATTA-TATA
240133 TTATTATTA
1 TTATTATTA
240142 ATAAATAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.04
22 33 0.69
23 11 0.23
24 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTATTATTATTATTATATA
Found at i:240158 original size:34 final size:37
Alignment explanation
Indices: 240087--240158 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 37
240077 ATTATTATAC
* * * *
240087 ATTATTATTATTATTATTTATTATTATTATTATAAAT
1 ATTATTATTATTATTATTTAATATAATAATTACAAAT
240124 ATTATTA-TATTATTA-TTAATA-AATAATTACAAAT
1 ATTATTATTATTATTATTTAATATAATAATTACAAAT
240158 A
1 A
240159 CATCGTAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 11 0.35
35 5 0.16
36 8 0.26
37 7 0.23
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (37 bp):
ATTATTATTATTATTATTTAATATAATAATTACAAAT
Found at i:241649 original size:17 final size:16
Alignment explanation
Indices: 241628--241679 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
241618 TTTACTATAG
241628 TTTTAATTTTATTTAT
1 TTTTAATTTTATTTAT
241644 TGTTT-ATTTATATTTAT
1 T-TTTAATTT-TATTTAT
*
241661 ATTTTAATTTTATATAT
1 -TTTTAATTTTATTTAT
241678 TT
1 TT
241680 ATATTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 7 0.23
17 19 0.61
18 5 0.16
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTAATTTTATTTAT
Found at i:241659 original size:27 final size:26
Alignment explanation
Indices: 241629--241704 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 26
241619 TTACTATAGT
* *
241629 TTTAATTTTATTTATTGTTTATTTATA
1 TTTAATTTTATTT-TTATATATTTATA
*
241656 TTTATATTTTAATTTTATATATTTATA
1 TTTA-ATTTTATTTTTATATATTTATA
241683 TTTAATTATTATTTTTAT-TATT
1 TTTAATT-TTATTTTTATATATT
241705 ATTATGTAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
26 7 0.16
27 28 0.65
28 8 0.19
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (26 bp):
TTTAATTTTATTTTTATATATTTATA
Found at i:241666 original size:13 final size:13
Alignment explanation
Indices: 241650--241700 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
241640 TTATTGTTTA
241650 TTTATATTTATAT
1 TTTATATTTATAT
241663 TTTA-ATTTTATAT
1 TTTATA-TTTATAT
241676 ATTTATATTTA-AT
1 -TTTATATTTATAT
*
241689 TATTATTTTTAT
1 T-TTATATTTAT
241701 TATTATTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
12 2 0.06
13 21 0.66
14 8 0.25
15 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATATTTATAT
Found at i:241671 original size:34 final size:31
Alignment explanation
Indices: 241623--241707 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 31
241613 CTTTTTTTAC
*
241623 TATAGTTTTAATTTTATTTATTGTTTATTTATATT
1 TATA-TTTTAATTTTATTTATT-TATATTTA-A-T
*
241658 TATATTTTAATTTTATATATTTATATTTAAT
1 TATATTTTAATTTTATTTATTTATATTTAAT
*
241689 TATTATTTTTATTATTATT
1 TA-TATTTTAATT-TTATT
241708 ATGTAGTCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
31 3 0.07
32 10 0.23
33 11 0.25
34 16 0.36
35 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (31 bp):
TATATTTTAATTTTATTTATTTATATTTAAT
Found at i:241676 original size:21 final size:21
Alignment explanation
Indices: 241647--241694 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
241637 TATTTATTGT
241647 TTATT-TATATTTATATTTTAA
1 TTATTATATATTTATA-TTTAA
241668 TT-TTATATATTTATATTTAA
1 TTATTATATATTTATATTTAA
241688 TTATTAT
1 TTATTAT
241695 TTTTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTATATATTTATATTTAA
Found at i:242093 original size:2 final size:2
Alignment explanation
Indices: 242086--242121 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
242076 AAATAAATAA
242086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
242122 TTTCTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:242810 original size:31 final size:31
Alignment explanation
Indices: 242772--242830 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
242762 AAAAAATATC
*
242772 AATTTAATTTATGACGGAACAATGATTCCGT
1 AATTTAATTTATGACGGAACAATCATTCCGT
* * *
242803 AATTTAATTTGTGATGGAATAATCATTC
1 AATTTAATTTATGACGGAACAATCATTC
242831 TGTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (31 bp):
AATTTAATTTATGACGGAACAATCATTCCGT
Found at i:243602 original size:31 final size:31
Alignment explanation
Indices: 243547--243617 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
243537 TTTGTGGACC
* *
243547 TGTCATAAATTTCTGATAGATCCACCTATTA
1 TGTCACAAATTTCTGATAGATCCACATATTA
* * * *
243578 TGTCACAAATTTGTGATGGGTCCACATGTTA
1 TGTCACAAATTTCTGATAGATCCACATATTA
*
243609 CGTCACAAA
1 TGTCACAAA
243618 AAATCATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (31 bp):
TGTCACAAATTTCTGATAGATCCACATATTA
Found at i:244742 original size:3 final size:3
Alignment explanation
Indices: 244734--244775 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
244724 TAATAAGGAC
244734 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
244776 TTTTTAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:244817 original size:15 final size:16
Alignment explanation
Indices: 244784--244819 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
244774 TTTTTTTAAA
244784 ATTAA-TGTAATTATT
1 ATTAATTGTAATTATT
244799 -TTAATTGT-ATTATT
1 ATTAATTGTAATTATT
244813 ATTAATT
1 ATTAATT
244820 TTTGGTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATTAATTGTAATTATT
Found at i:247248 original size:17 final size:17
Alignment explanation
Indices: 247221--247259 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
247211 AATTTAAAAT
*
247221 TAATT-TAAATAGTATC
1 TAATTATAAATAATATC
247237 TAATTATAAATAATATC
1 TAATTATAAATAATATC
247254 TAATTA
1 TAATTA
247260 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:252223 original size:24 final size:24
Alignment explanation
Indices: 252178--252223 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
252168 TTAGTTTATG
* * *
252178 TTTTATATTTAAAATTATTTTAAT
1 TTTTATATATAAAAATAATTTAAT
252202 TTTTATATATAAAAATAATTTA
1 TTTTATATATAAAAATAATTTA
252224 GTTGTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATATATAAAAATAATTTAAT
Found at i:255412 original size:20 final size:20
Alignment explanation
Indices: 255366--255403 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
255356 ACACCAAATC
* *
255366 CTCTCAAATTCTCTCATAGA
1 CTCTTAAATTCTCTCACAGA
255386 CTCTTAAATTCTCTCACA
1 CTCTTAAATTCTCTCACA
255404 ACTAGTTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.03, T:0.37
Consensus pattern (20 bp):
CTCTTAAATTCTCTCACAGA
Found at i:257984 original size:14 final size:14
Alignment explanation
Indices: 257965--257992 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
257955 TTTATTTGAA
257965 TCACATATAACGCC
1 TCACATATAACGCC
257979 TCACATATAACGCC
1 TCACATATAACGCC
257993 AACGTCGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.07, T:0.21
Consensus pattern (14 bp):
TCACATATAACGCC
Found at i:260881 original size:29 final size:30
Alignment explanation
Indices: 260817--260908 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 30
260807 CAAAGATAAA
* * *
260817 AGGATTGTCGGGTGATATTTACAGGTTGAG
1 AGGATTGTTGTGTGATGTTTACAGGTTGAG
*
260847 AGGATTGTTGTGTGATGTTTTC-GGTTGAG
1 AGGATTGTTGTGTGATGTTTACAGGTTGAG
* *
260876 AGGATTGTTGTGTGAATGTTTACGGGGTGAG
1 AGGATTGTTGTGTG-ATGTTTACAGGTTGAG
260907 AG
1 AG
260909 CGTTTTATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
29 21 0.39
30 25 0.46
31 8 0.15
ACGTcount: A:0.20, C:0.04, G:0.39, T:0.37
Consensus pattern (30 bp):
AGGATTGTTGTGTGATGTTTACAGGTTGAG
Found at i:261176 original size:14 final size:14
Alignment explanation
Indices: 261157--261186 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
261147 TGTCACATCA
261157 GCGTAAGGCGCGGT
1 GCGTAAGGCGCGGT
261171 GCGTAAGGCGCGGT
1 GCGTAAGGCGCGGT
261185 GC
1 GC
261187 ATAGGCCGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.23, G:0.50, T:0.13
Consensus pattern (14 bp):
GCGTAAGGCGCGGT
Found at i:269477 original size:19 final size:18
Alignment explanation
Indices: 269435--269521 Score: 60
Period size: 19 Copynumber: 5.0 Consensus size: 18
269425 TAGTATTTTT
269435 TTAAATAGTTAT-TATTT-
1 TTAAATA-TTATATATTTA
*
269452 TT-TATATTATATATTTA
1 TTAAATATTATATATTTA
* *
269469 TGTAAATATTATTTTTTTA
1 T-TAAATATTATATATTTA
269488 TTAAA-A-TA-ATATTTA
1 TTAAATATTATATATTTA
* *
269503 TATAATTATTATTTATTTA
1 T-TAAATATTATATATTTA
269522 GAATTATTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
15 10 0.19
16 13 0.24
17 5 0.09
18 7 0.13
19 19 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTAAATATTATATATTTA
Found at i:269481 original size:34 final size:34
Alignment explanation
Indices: 269412--269520 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 34
269402 GTGGTAAGAA
* *
269412 ATTA-TTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTATTTTTTATATTA-TATATTTATATAAATA-TT
*
269445 ATTATTTTTTATATTATATATTTATGTAAATATT
1 ATTATTTTTTATATTATATATTTATATAAATATT
* * * *
269479 ATTTTTTTATTAAAATA-ATATTTATATAATTATT
1 ATTATTTT-TTATATTATATATTTATATAAATATT
269513 ATTTATTT
1 A-TTATTT
269521 AGAATTATTA
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
33 7 0.11
34 38 0.60
35 18 0.29
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
ATTATTTTTTATATTATATATTTATATAAATATT
Found at i:271317 original size:21 final size:21
Alignment explanation
Indices: 271291--271383 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
271281 TATGCCATCT
* *
271291 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
271312 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
*
271333 CCCCA-GGTTACATGCCTAGC
1 CCGCAGGGTTACATGCCTAGC
271353 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
271374 CCGCAGGGTT
1 CCGCAGGGTT
271384 TTATACCATA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 18 0.27
21 48 0.73
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:271342 original size:41 final size:41
Alignment explanation
Indices: 271297--271380 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
271287 ATCTCCGCAG
* *
271297 GGTTACATTCCGAGCCCG-CAGGGTTACATTCCTAGCCCCCA
1 GGTTACATGCCGAGCCCGCCA-GGTTACATGCCTAGCCCCCA
* *
271338 GGTTACATGCCTAGCCCGCCAGGTTACATGCCTAGCCCGCA
1 GGTTACATGCCGAGCCCGCCAGGTTACATGCCTAGCCCCCA
271379 GG
1 GG
271381 GTTTTATACC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 36 0.95
42 2 0.05
ACGTcount: A:0.19, C:0.36, G:0.25, T:0.20
Consensus pattern (41 bp):
GGTTACATGCCGAGCCCGCCAGGTTACATGCCTAGCCCCCA
Found at i:271965 original size:33 final size:34
Alignment explanation
Indices: 271906--272002 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
271896 AAATGTTTTT
*
271906 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
271940 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
271973 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
272003 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:272009 original size:34 final size:33
Alignment explanation
Indices: 271904--272009 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
271894 ATAAATGTTT
*
271904 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
271938 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
271970 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
272005 TTAAA
1 TTAAA
272010 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:272684 original size:128 final size:128
Alignment explanation
Indices: 272400--272877 Score: 842
Period size: 128 Copynumber: 3.8 Consensus size: 128
272390 TTACCTGATT
272400 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
272465 TGACG--A-AAT--AAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
272523 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
272588 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
*
272651 TAATGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
272716 TGACGATATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
272779 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
272844 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACG
272878 GCATTTGCAA
Statistics
Matches: 334, Mismatches: 14, Indels: 9
0.94 0.04 0.03
Matches are distributed among these distances:
123 69 0.21
125 1 0.00
126 3 0.01
127 1 0.00
128 259 0.78
129 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:275212 original size:207 final size:207
Alignment explanation
Indices: 274857--275271 Score: 821
Period size: 207 Copynumber: 2.0 Consensus size: 207
274847 TAAAAAATAA
274857 TCGAAACTTGATAATTCTTACATTATAATCGAAACATTTTACATAATATATTATTAATTTATAAT
1 TCGAAACTTGATAATTCTTACATTATAATCGAAACATTTTACATAATATATTATTAATTTATAAT
274922 AATAATTAAAATAAACTATTTATTATAAAACAAAATACGTGTCTGCTGAGTTGGCAAAGGCGCGT
66 AATAATTAAAATAAACTATTTATTATAAAACAAAATACGTGTCTGCTGAGTTGGCAAAGGCGCGT
274987 CCCCGGGGACGCGCCTTTCACACGTGGCATCCAACTCAGCGAAAACACGGGTAAAGCGCGTCCCC
131 CCCCGGGGACGCGCCTTTCACACGTGGCATCCAACTCAGCGAAAACACGGGTAAAGCGCGTCCCC
275052 GGGGACGCGCCT
196 GGGGACGCGCCT
275064 TCGAAACTTGATAATTCTTACATTATAATCGAAACATTTTACATAATATATTATTAATTTATAAT
1 TCGAAACTTGATAATTCTTACATTATAATCGAAACATTTTACATAATATATTATTAATTTATAAT
275129 AATAATTAAAATAAACTATTTATTATAAAACAAAATACGTGTCTGCTGAGTTGGCAAAGGCGCGT
66 AATAATTAAAATAAACTATTTATTATAAAACAAAATACGTGTCTGCTGAGTTGGCAAAGGCGCGT
*
275194 CCCCGGGGACTCGCCTTTCACACGTGGCATCCAACTCAGCGAAAACACGGGTAAAGCGCGTCCCC
131 CCCCGGGGACGCGCCTTTCACACGTGGCATCCAACTCAGCGAAAACACGGGTAAAGCGCGTCCCC
275259 GGGGACGCGCCT
196 GGGGACGCGCCT
275271 T
1 T
275272 TGCCAACTCA
Statistics
Matches: 207, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 207 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (207 bp):
TCGAAACTTGATAATTCTTACATTATAATCGAAACATTTTACATAATATATTATTAATTTATAAT
AATAATTAAAATAAACTATTTATTATAAAACAAAATACGTGTCTGCTGAGTTGGCAAAGGCGCGT
CCCCGGGGACGCGCCTTTCACACGTGGCATCCAACTCAGCGAAAACACGGGTAAAGCGCGTCCCC
GGGGACGCGCCT
Found at i:277399 original size:17 final size:17
Alignment explanation
Indices: 277373--277405 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
277363 TTACCATATT
*
277373 AAAAATCGATTTTTTTA
1 AAAAACCGATTTTTTTA
277390 AAAAACCGATTTTTTT
1 AAAAACCGATTTTTTT
277406 CAAACCGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
AAAAACCGATTTTTTTA
Found at i:277547 original size:22 final size:21
Alignment explanation
Indices: 277508--277548 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
277498 AGTGAAAAAA
**
277508 CCGGATCGATTTTTATCCGAT
1 CCGGATCGATTTAAATCCGAT
277529 CCGGATCAGATTTAAATCCG
1 CCGGATC-GATTTAAATCCG
277549 GCTATGTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (21 bp):
CCGGATCGATTTAAATCCGAT
Found at i:281416 original size:35 final size:35
Alignment explanation
Indices: 281370--281440 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
281360 TATTTACACT
281370 TTTACAAATGTAAATTGTGATTTGCTCAATGCCCA
1 TTTACAAATGTAAATTGTGATTTGCTCAATGCCCA
281405 TTTACAAATGTAAATTGTGATTTGCTCAATGCCCA
1 TTTACAAATGTAAATTGTGATTTGCTCAATGCCCA
281440 T
1 T
281441 GAATACTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (35 bp):
TTTACAAATGTAAATTGTGATTTGCTCAATGCCCA
Found at i:281789 original size:6 final size:6
Alignment explanation
Indices: 281780--281804 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
281770 TATATTCATG
281780 TTTATC TTTATC TTTATC TTTATC T
1 TTTATC TTTATC TTTATC TTTATC T
281805 CTAACTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATC
Found at i:283869 original size:20 final size:18
Alignment explanation
Indices: 283817--283890 Score: 94
Period size: 18 Copynumber: 4.0 Consensus size: 18
283807 ACTGAATATT
*
283817 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGAACCACTA
*
283835 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGAACCACT-A
* *
283854 TTGTTCTGAAGAACCACTA
1 -TGTCCCGAAGAACCACTA
283873 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGAACCACTA
283891 ATAATCCCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 33 0.67
19 2 0.04
20 14 0.29
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGAACCACTA
Found at i:284541 original size:63 final size:64
Alignment explanation
Indices: 284452--284595 Score: 150
Period size: 63 Copynumber: 2.3 Consensus size: 64
284442 ATCCCTTAAC
* * * *
284452 GGGTACATCGATGCACTAACTATGCATCGGTACA-TAAATCCCATTCGATGTTTGTATTTT-AGG
1 GGGTGCATCGATGCACTAACTATGCATCGATACACT-AATCACATTCGATGTTTGTATTTTAAAG
* * * * *
284515 GGGTGCATCGATGCAC-CACTTGTGCATCGATACACTGATGACATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTAAC-TATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAG
* *
284579 GAGTGCATCGATACACT
1 GGGTGCATCGATGCACT
284596 TCATGTGCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
62 2 0.03
63 47 0.71
64 17 0.26
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (64 bp):
GGGTGCATCGATGCACTAACTATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAG
Found at i:286081 original size:13 final size:14
Alignment explanation
Indices: 286060--286109 Score: 68
Period size: 13 Copynumber: 3.7 Consensus size: 14
286050 TTCTCCCATA
286060 TTTTATTCTT-TTC
1 TTTTATTCTTATTC
*
286073 TTTTCTTCTTATTC
1 TTTTATTCTTATTC
*
286087 TTTT-TTCTTCTTC
1 TTTTATTCTTATTC
286100 TTTTATTCTT
1 TTTTATTCTT
286110 CTTTTCTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 21 0.64
14 12 0.36
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTCTTATTC
Found at i:286086 original size:19 final size:19
Alignment explanation
Indices: 286062--286119 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
286052 CTCCCATATT
286062 TTATTCTTTTCTTTTCTTC
1 TTATTCTTTTCTTTTCTTC
286081 TTATTCTTTT-TTCTTCTTC
1 TTATTCTTTTCTT-TTCTTC
*
286100 TT-TTATTCTTCTTTTCTTC
1 TTATTCTT-TTCTTTTCTTC
286119 T
1 T
286120 CCAAGCCTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 6 0.17
19 27 0.77
20 2 0.06
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATTCTTTTCTTTTCTTC
Found at i:286094 original size:16 final size:15
Alignment explanation
Indices: 286060--286117 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 15
286050 TTCTCCCATA
*
286060 TTTTATTCTTTTC--
1 TTTTCTTCTTTTCTT
286073 TTTTCTTCTTATTCTT
1 TTTTCTTCTT-TTCTT
286089 TTTTCTTC--TTCTT
1 TTTTCTTCTTTTCTT
286102 TTATTCTTCTTTTCTT
1 TT-TTCTTCTTTTCTT
286118 CTCCAAGCCT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
13 16 0.42
14 9 0.24
16 13 0.34
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTCTTTTCTT
Found at i:286094 original size:21 final size:22
Alignment explanation
Indices: 286065--286119 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
286055 CCATATTTTA
286065 TTCTTTTCTT-TTCTTCTTATTC
1 TTCTTTTCTTCTTCTT-TTATTC
286087 TT-TTTTCTTCTTCTTTTATTC
1 TTCTTTTCTTCTTCTTTTATTC
286108 TTCTTTTCTTCT
1 TTCTTTTCTTCT
286120 CCAAGCCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (22 bp):
TTCTTTTCTTCTTCTTTTATTC
Found at i:286097 original size:3 final size:3
Alignment explanation
Indices: 286065--286119 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
286055 CCATATTTTA
* *
286065 TTC TT- TTC TT- TTC TTC TTA TTC TT- TT- TTC TTC TTC TT- TTA TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
286108 TTC TT- TTC TTC T
1 TTC TTC TTC TTC T
286120 CCAAGCCTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
2 12 0.27
3 32 0.73
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:286688 original size:22 final size:22
Alignment explanation
Indices: 286657--286711 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
286647 ACTCATAAGT
* * * *
286657 GGTATTGATACTTTGACCCTGG
1 GGTATCGATACTGTAACCCTAG
286679 GGTATCGATAC-GTAACCCTAG
1 GGTATCGATACTGTAACCCTAG
286700 GGTATCGATACT
1 GGTATCGATACT
286712 ACAAGTAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (22 bp):
GGTATCGATACTGTAACCCTAG
Found at i:289335 original size:23 final size:23
Alignment explanation
Indices: 289309--289374 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
289299 CCTTATATGA
*
289309 CACTTCGGTGCATTTCTATGCGG
1 CACTTCGGTGCATTTCTACGCGG
* * *
289332 CACTACGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGG
* * *
289355 CAATTCGGTGTATTTATACG
1 CACTTCGGTGCATTTCTACG
289375 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGG
Found at i:293780 original size:2 final size:2
Alignment explanation
Indices: 293773--293828 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
293763 GTATTTGCGG
293773 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
293815 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
293829 GTGTGTGTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:294362 original size:23 final size:23
Alignment explanation
Indices: 294336--294403 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
294326 AACCTTATAT
* *
294336 GGCACTTCGATGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
294359 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
294382 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
294404 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:296616 original size:2 final size:2
Alignment explanation
Indices: 296609--296633 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
296599 CTATACAACT
296609 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 T
296634 GAGGTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:296842 original size:2 final size:2
Alignment explanation
Indices: 296835--296906 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
296825 ATCTAACTCG
296835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
296877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
296907 GCCGTTTTGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:297385 original size:80 final size:79
Alignment explanation
Indices: 297253--297401 Score: 192
Period size: 80 Copynumber: 1.9 Consensus size: 79
297243 ATGATAAAGT
* * * *
297253 GCCCAATAATAACAAAACCGGTAAAAAAAATCATGTTTTATGTAGTGCTTTACCGGATATGTTAA
1 GCCCAATAATAACAAAACCGGTAAAAAAAATAATGTTTCATGTAATACTTTACCGGATATGTTAA
297318 CAAAACCGGTAAAAC
66 -AAAACCGGTAAAAC
* * * * *
297333 GCCCAATAATAACAAAACCGGTAGAAATAATAATGTTTCCA-GTAATATTTTACCGGTTTTGTTA
1 GCCCAATAATAACAAAACCGGTAAAAAAAATAATGTTT-CATGTAATACTTTACCGGATATGTTA
297397 AAAAA
65 AAAAA
297402 TAATAACAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
79 4 0.07
80 54 0.92
81 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (79 bp):
GCCCAATAATAACAAAACCGGTAAAAAAAATAATGTTTCATGTAATACTTTACCGGATATGTTAA
AAAACCGGTAAAAC
Found at i:299028 original size:21 final size:21
Alignment explanation
Indices: 298998--299045 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
298988 TAATTTTCAA
*
298998 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
299019 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
299040 ACATTG
1 ACATTG
299046 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:303673 original size:21 final size:21
Alignment explanation
Indices: 303649--303695 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
303639 ATTTTCAAAT
303649 ATTATTGCACCTAATATTAAC
1 ATTATTGCACCTAATATTAAC
* *
303670 ATTATTGCACCTAATTTTGAC
1 ATTATTGCACCTAATATTAAC
303691 ATTAT
1 ATTAT
303696 AATATTAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (21 bp):
ATTATTGCACCTAATATTAAC
Found at i:304801 original size:82 final size:81
Alignment explanation
Indices: 304693--304849 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
304683 AAACACCACG
* * *
304693 ACAGATTAGTACTTAAGCGGCATTTTTAAACAAATACCTCAATAAGGTTCATCTATAGTGATATT
1 ACAGATTAGTACTTAAGCAGCATTTTTAAACAAACACCGCAATAAGGTTCATCTATAGTGAT-TT
304758 TTTCAACAAACGCCGCA
65 TTTCAACAAACGCCGCA
* * * * * * *
304775 ACAGATTAGTATTTTAGCAGCGTTTTTATACAAACGCCGCAATAGGGTTCATCTATAGTGCTTTT
1 ACAGATTAGTACTTAAGCAGCATTTTTAAACAAACACCGCAATAAGGTTCATCTATAGTGATTTT
304840 TTCAACAAAC
66 TTCAACAAAC
304850 ACAGTAACAT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 13 0.20
82 52 0.80
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (81 bp):
ACAGATTAGTACTTAAGCAGCATTTTTAAACAAACACCGCAATAAGGTTCATCTATAGTGATTTT
TTCAACAAACGCCGCA
Found at i:304883 original size:82 final size:83
Alignment explanation
Indices: 304693--304872 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 83
304683 AAACACCACG
* * * * *
304693 ACAGATTAGTACTTAAGCGGC-ATTTTTAAACAAATACCTCAATAAGGTTCATCTATAGTGATAT
1 ACAGAGTAGTACTTTAGCAGCGATTTTTAAACAAACACCGCAATAAGGTTCATCTATAGTGATAT
* *
304757 TTTTCAACAAACGCCGCA
66 TTTTCAACAAACACAGCA
* * * * * *
304775 ACAGATTAGTATTTTAGCAGCG-TTTTTATACAAACGCCGCAATAGGGTTCATCTATAGTGCT-T
1 ACAGAGTAGTACTTTAGCAGCGATTTTTAAACAAACACCGCAATAAGGTTCATCTATAGTGATAT
*
304838 TTTTCAACAAACACAGTA
66 TTTTCAACAAACACAGCA
*
304856 ACATAGTAGTACTTTAG
1 ACAGAGTAGTACTTTAG
304873 TGACGATTTT
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 30 0.37
82 52 0.63
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (83 bp):
ACAGAGTAGTACTTTAGCAGCGATTTTTAAACAAACACCGCAATAAGGTTCATCTATAGTGATAT
TTTTCAACAAACACAGCA
Found at i:308475 original size:42 final size:43
Alignment explanation
Indices: 308405--308614 Score: 221
Period size: 42 Copynumber: 5.0 Consensus size: 43
308395 GTAATTAGCA
* *
308405 GCGTTTGTATCAAAAAACCCCGCTATAGATCT-AACCTTTTGCG
1 GCGTTTGT-TCCAAAAACGCCGCTATAGATCTCAACCTTTTGCG
* * * * *
308448 GCGTTTGTTCCAAAAATGTCGCTATAGATAT-GACATTTTGCG
1 GCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTTGCG
* *
308490 GCATTTGTTCCAAAAGCGCCGCTATAGATCTCAACCTTTTGCG
1 GCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTTGCG
*** * * * *
308533 GCGTTTCCCCCAAAAATGCCACTATAGATCTCGACC-TTTGCA
1 GCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTTGCG
* *
308575 GCTTTTGTTCCAAAAACGCCGCTATAGATCTGAA-CTTTTG
1 GCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTTG
308615 TAGATCTCGA
Statistics
Matches: 134, Mismatches: 31, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
41 1 0.01
42 88 0.66
43 45 0.34
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (43 bp):
GCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTTTTGCG
Found at i:308558 original size:85 final size:84
Alignment explanation
Indices: 308402--308614 Score: 259
Period size: 85 Copynumber: 2.5 Consensus size: 84
308392 AAGGTAATTA
* * * *** *
308402 GCAGCGTTTGTATCAAAAAACCCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCCAAAAATGT
1 GCAGCATTTGT-TCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTCCCCCAAAAATGC
* *
308467 CGCTATAGATAT-GACATTTT
65 CACTATAGATATCGAC-CTTT
* *
308487 GCGGCATTTGTTCCAAAAGCGCCGCTATAGATCTCAACCTTTTGCGGCGTTTCCCCCAAAAATGC
1 GCAGCATTTGTTCCAAAAACGCCGCTATAGATCT-AACCTTTTGCGGCGTTTCCCCCAAAAATGC
*
308552 CACTATAGATCTCGACCTTT
65 CACTATAGATATCGACCTTT
*
308572 GCAGCTTTTGTTCCAAAAACGCCGCTATAGATCTGAA-CTTTTG
1 GCAGCATTTGTTCCAAAAACGCCGCTATAGATCT-AACCTTTTG
308615 TAGATCTCGA
Statistics
Matches: 110, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
84 26 0.24
85 81 0.74
86 3 0.03
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (84 bp):
GCAGCATTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTCCCCCAAAAATGCC
ACTATAGATATCGACCTTT
Found at i:308620 original size:16 final size:17
Alignment explanation
Indices: 308599--308631 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
308589 AACGCCGCTA
308599 TAGATCT-GAACTTTTG
1 TAGATCTCGAACTTTTG
*
308615 TAGATCTCGACCTTTTG
1 TAGATCTCGAACTTTTG
308632 CCATGTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (17 bp):
TAGATCTCGAACTTTTG
Found at i:313311 original size:31 final size:31
Alignment explanation
Indices: 313273--313366 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
313263 ATACAGTCTT
313273 CCAACATTTAGTTCATTTACAATATGGTTCC
1 CCAACATTTAGTTCATTTACAATATGGTTCC
* *
313304 CCAACATTTAG-TCTATTTACAATATAGTCCC
1 CCAACATTTAGTTC-ATTTACAATATGGTTCC
* **
313335 CCAACATTTAGTCCATTTGTAATATGG-TCC
1 CCAACATTTAGTTCATTTACAATATGGTTCC
313365 CC
1 CC
313367 GACGTAACTA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
30 6 0.11
31 47 0.87
32 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.36
Consensus pattern (31 bp):
CCAACATTTAGTTCATTTACAATATGGTTCC
Found at i:314430 original size:31 final size:30
Alignment explanation
Indices: 314376--314446 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 30
314366 CTTTTAAAAC
* *
314376 TTGCAATATAATCCCCAACATTTAGTCTGT
1 TTGCAATATGATCCCCAACATTTAGTCCGT
*
314406 TTGCAATATGATCCCTTAACATTTAGTCCGT
1 TTGCAATATGATCCC-CAACATTTAGTCCGT
314437 TTGCAATATG
1 TTGCAATATG
314447 GTTCCCGGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 14 0.38
31 23 0.62
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (30 bp):
TTGCAATATGATCCCCAACATTTAGTCCGT
Found at i:314630 original size:5 final size:5
Alignment explanation
Indices: 314620--314645 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
314610 CGGAATTTTT
314620 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
314646 GAGTGTACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:315112 original size:2 final size:2
Alignment explanation
Indices: 315107--315139 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
315097 ATTTTTTTAT
315107 TA TA TA 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 TA TA TA T
315140 TAAAAAGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:322295 original size:64 final size:63
Alignment explanation
Indices: 322213--322417 Score: 193
Period size: 65 Copynumber: 3.2 Consensus size: 63
322203 CTAAGAGTGA
* *
322213 ATCGATGCATGAAGTGCATTCGATTTTTCAAAATAGCCTGAGTGCATCGATGCATGGATTGTGC
1 ATCGATGCATCAAATGCATTCGATTTTTCAAAATA-CCTGAGTGCATCGATGCATGGATTGTGC
* **
322277 ATCGATGCATCAAATGCATTCGATGTTTTCATTAAA-ACCTGAGTGCATCAATGCATGGAGAGTG
1 ATCGATGCATCAAATGCATTCGAT-TTTTCA--AAATACCTGAGTGCATCGATGCATGGATTGTG
322341 C
63 C
* * * * * *
322342 CTCGATGCAT-AAACTGCATTTGA-TGTTCAATTTATTCATTG-GTGCATCGATGCATGGATTGG
1 ATCGATGCATCAAA-TGCATTCGATTTTTCAA--AATAC-CTGAGTGCATCGATGCATGGATT-G
322404 TGC
61 TGC
*
322407 ATCGTTGCATC
1 ATCGATGCATC
322418 CCTTTGAAAA
Statistics
Matches: 115, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
61 1 0.01
63 6 0.05
64 42 0.37
65 62 0.54
66 1 0.01
67 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (63 bp):
ATCGATGCATCAAATGCATTCGATTTTTCAAAATACCTGAGTGCATCGATGCATGGATTGTGC
Found at i:322331 original size:65 final size:64
Alignment explanation
Indices: 322206--322368 Score: 197
Period size: 65 Copynumber: 2.5 Consensus size: 64
322196 CGGTGCACTA
* * *
322206 AGAGTGAATCGATGCATGAAGTGCATTCGAT-TTTTCAAAATAGCCTGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCAT-AAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCAATGCATGG
**
322270 ATTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAA-A-CCTGAGTGCATCAATGCAT
1 AGAGTGCATCGATGCAT-AAATGCATTCGATGTTTTCA--AAATAGCCTGAGTGCATCAATGCAT
322333 GG
63 GG
* *
322335 AGAGTGCCTCGATGCATAAACTGCATTTGATGTT
1 AGAGTGCATCGATGCATAAA-TGCATTCGATGTT
322369 CAATTTATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 29 0.34
65 52 0.61
66 1 0.01
67 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
AGAGTGCATCGATGCATAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCAATGCATGG
Found at i:322404 original size:20 final size:20
Alignment explanation
Indices: 322379--322416 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
322369 CAATTTATTC
322379 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
322399 ATTGGTGCATCGTTGCAT
1 ATTGGTGCATCGATGCAT
322417 CCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:325108 original size:21 final size:22
Alignment explanation
Indices: 325055--325115 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
325045 TGGCCTTGTG
325055 AATCGATGCACATTCAAGGCGT
1 AATCGATGCACATTCAAGGCGT
* * * *
325077 ACATCGGTGCACCTTCATGGTGT
1 A-ATCGATGCACATTCAAGGCGT
325100 -ATCGATGCACATTCAA
1 AATCGATGCACATTCAA
325116 AGGGATGCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 13 0.42
22 1 0.03
23 17 0.55
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (22 bp):
AATCGATGCACATTCAAGGCGT
Found at i:331006 original size:19 final size:19
Alignment explanation
Indices: 330982--331033 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
330972 AATAGACTGA
330982 GTGCATCGATGCATGGATT
1 GTGCATCGATGCATGGATT
*
331001 GTGCATTGATGCATGGATT
1 GTGCATCGATGCATGGATT
331020 GTGCATCGATGCAT
1 GTGCATCGATGCAT
331034 CAAATACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (19 bp):
GTGCATCGATGCATGGATT
Found at i:331072 original size:46 final size:46
Alignment explanation
Indices: 331020--331125 Score: 212
Period size: 46 Copynumber: 2.3 Consensus size: 46
331010 TGCATGGATT
331020 GTGCATCGATGCATCAAATACATTCGATGTTTTTATTAAAACCTGA
1 GTGCATCGATGCATCAAATACATTCGATGTTTTTATTAAAACCTGA
331066 GTGCATCGATGCATCAAATACATTCGATGTTTTTATTAAAACCTGA
1 GTGCATCGATGCATCAAATACATTCGATGTTTTTATTAAAACCTGA
331112 GTGCATCGATGCAT
1 GTGCATCGATGCAT
331126 GGAGAGTGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (46 bp):
GTGCATCGATGCATCAAATACATTCGATGTTTTTATTAAAACCTGA
Found at i:340502 original size:18 final size:18
Alignment explanation
Indices: 340446--340513 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
340436 GCACTCATTG
340446 ATGCATCGATGCACTCACC
1 ATGCATCGATGCACT-ACC
***
340465 AT--ATCGAATGCA-TTTT
1 ATGCATCG-ATGCACTACC
340481 ATGCATCGATGCACTACC
1 ATGCATCGATGCACTACC
*
340499 ATGCATCGATACACT
1 ATGCATCGATGCACT
340514 CAGGTTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
16 2 0.05
17 10 0.26
18 24 0.63
19 2 0.05
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (18 bp):
ATGCATCGATGCACTACC
Found at i:345852 original size:23 final size:23
Alignment explanation
Indices: 345797--345898 Score: 159
Period size: 23 Copynumber: 4.3 Consensus size: 23
345787 CATGCACAAG
*
345797 TTTTATGGACGAAACAACAACTACAAG
1 TTTTATGGACGAAACAACAACT----T
345824 TTTTATGGACGAAACAACAACTT
1 TTTTATGGACGAAACAACAACTT
345847 TTTTATGGACGAAACAACAACTT
1 TTTTATGGACGAAACAACAACTT
345870 TTTTATGGACGAAACAACAACTT
1 TTTTATGGACGAAACAACAACTT
345893 TTTTAT
1 TTTTAT
345899 TATGGAATTG
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
23 52 0.70
27 22 0.30
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (23 bp):
TTTTATGGACGAAACAACAACTT
Found at i:349241 original size:64 final size:63
Alignment explanation
Indices: 349107--349262 Score: 221
Period size: 64 Copynumber: 2.5 Consensus size: 63
349097 CACTCACCAT
*
349107 ATCGAATGCATTTTATGCATCGATGCACTACATTGCATCGATACACTCAGGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACTACATTGCATCGATACACTCAGCTTTTATGAAAAC
*
349170 ATCGAATGCATTTTATGCATCGATGCAC-AGGCCA-TGCATCGATGCACTCATGCTTGTT-TG-A
1 ATCGAATGCATTTTATGCATCGATGCACTA---CATTGCATCGATACACTCA-GCTT-TTATGAA
349231 AAC
61 AAC
349234 ATCGAATGCATTTTATGCATCGATGCACT
1 ATCGAATGCATTTTATGCATCGATGCACT
349263 CTTAGTGCAC
Statistics
Matches: 85, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
62 1 0.01
63 28 0.33
64 47 0.55
65 7 0.08
66 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACTACATTGCATCGATACACTCAGCTTTTATGAAAAC
Found at i:349277 original size:64 final size:61
Alignment explanation
Indices: 349107--349281 Score: 210
Period size: 64 Copynumber: 2.7 Consensus size: 61
349097 CACTCACCAT
* *
349107 ATCGAATGCATTTTATGCATCGATGCACTACATTGCATCGATACACTCAGGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACT-CA-TGCATCGATGCACTCAGCTTTTATGAAAAC
*
349170 ATCGAATGCATTTTATGCATCGATGCACAGGCCATGCATCGATGCACTCATGCTTGTT-TG-AAA
1 ATCGAATGCATTTTATGCATCGATGCAC---TCATGCATCGATGCACTCA-GCTT-TTATGAAAA
349233 C
61 C
*
349234 ATCGAATGCATTTTATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 ATCGAATGCATTTTATGCATCGATGCACTC--A-TGCATCGATGCACT
349282 AAGGGTTCCA
Statistics
Matches: 99, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
61 1 0.01
63 29 0.29
64 60 0.61
65 7 0.07
66 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (61 bp):
ATCGAATGCATTTTATGCATCGATGCACTCATGCATCGATGCACTCAGCTTTTATGAAAAC
Found at i:354949 original size:598 final size:599
Alignment explanation
Indices: 353808--355608 Score: 2858
Period size: 598 Copynumber: 3.0 Consensus size: 599
353798 CAGGTGAGTG
** * ** * * *
353808 TAATGAGCTAGATAGACAAGTAATAGCTGGTTGTGATAAAACTTTCTAGTCGTGACATTATAAGT
1 TAATGAGCTACCTAGACAAATAAGGGCTGGTCGTGATAAAACTTTCTAGCCGTGACCTTATAAGT
353873 TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
66 TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
* *
353938 TGACTCCTCCAGCTAGGTTCAGCTACATGCTCACTTCTCCAGCTGAATTGAGTTTTTCTTAAGTT
131 TGACTCCTCCAACTAGGTTCAGCTACATGCTCACTTCTCCAGCTGAATTGAG-ATTTCTTAAGTT
354003 TCAATGAGCTGATTGAATCTTTGTGAGCAGACTGTGAGCTGCCATGCTTTTTCAAATAGTTTCCC
195 TCAATGAGCTGATTGAATCTTTGTGAGCAGACTGTGAGCTGCCATGCTTTTTCAAATAGTTTCCC
* *
354068 AAGCTACCATAGGATGTGTCATCCCTTAATGTACCTACATAGACACACAAACTAAGGTAAAATAA
260 AAGCTACCATAGGATGTGTCATCCCTTAATGTACCTACATAGATAAACAAACTAAGGTAAAATAA
*
354133 AGGAAATGAGATGAAATGAAACATAATACATGATGATGTGAATGTATAAGTGCTTGTGAGCTATG
325 AGGAAATTAGATGAAATGAAACATAATACATGATGATGTGAATGTATAAGTGCTTGTGAGCTATG
* * *
354198 AATTCATACCATGAGCTAAGCATATAAGGATGCAATGTTAATAAGCTAATGTATATACTTTAGGA
390 AATGCATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATACTTTAGGA
*
354263 GCTGAATTTAACATGCCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATGAATGTAA
455 GCTGAATTTAACATGTCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATGAATGTAA
* *
354328 TAAAATCATATTAAATTAATGTAAAAATCAATGCAAATTAATAATAAATTAAGTAAAGATGTGAA
520 TGAAATCATATTAAATGAATGTAAAAATCAATGCAAATTAATAATAAATTAAGTAAAGATGTGAA
354393 TTAATATCATGCAGC
585 TTAATATCATGCAGC
* * *
354408 TAATGAGCTACCTAGACATATAAGGGCTGTTCGTGATAAAACTTTCTAGCCGTGACCTTCTAAGT
1 TAATGAGCTACCTAGACAAATAAGGGCTGGTCGTGATAAAACTTTCTAGCCGTGACCTTATAAGT
354473 TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
66 TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
*
354538 TGACTCCTCCATCTAGGTTCAGCTACATGCTCACTTCTCCAGCTGAATTGAGATTTCTTAAGTCT
131 TGACTCCTCCAACTAGGTTCAGCTACATGCTCACTTCTCCAGCTGAATTGAGATTTCTTAAGT-T
* * *
354603 TC-ATGAGTTGATTGAATCTTTGTGAGCAGACTGTGAGTTGCCATACTTTTTCAAATAGTTTCCC
195 TCAATGAGCTGATTGAATCTTTGTGAGCAGACTGTGAGCTGCCATGCTTTTTCAAATAGTTTCCC
*
354667 AAGCTACCATAGGATGTGTCATCCCTTAATGTACATACATAGATAAACAAACTAAGGT-AAATAA
260 AAGCTACCATAGGATGTGTCATCCCTTAATGTACCTACATAGATAAACAAACTAAGGTAAAATAA
*
354731 AGGAAATTAGATGAAATGAAACATAATACATGATGATGTGAATGTATAAGTGCTTGTGACCTATG
325 AGGAAATTAGATGAAATGAAACATAATACATGATGATGTGAATGTATAAGTGCTTGTGAGCTATG
354796 AATGCATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATACTTTAGGA
390 AATGCATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATACTTTAGGA
354861 GCTGAATTTAACATGTCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATGAATGTAA
455 GCTGAATTTAACATGTCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATGAATGTAA
* * *
354926 TGAAATCATATTAAATGAATGTAAAAAACAATGCAAATTAATAATAAGTTAAGTAAAGATATGAA
520 TGAAATCATATTAAATGAATGTAAAAATCAATGCAAATTAATAATAAATTAAGTAAAGATGTGAA
*
354991 TTAATATCATGCAAC
585 TTAATATCATGCAGC
* *
355006 TAATGAGCTAGCTAGACAAATAAGGGTTGGTCGTGATAAAACTTTCTAGCCGTGACCTTATAAGT
1 TAATGAGCTACCTAGACAAATAAGGGCTGGTCGTGATAAAACTTTCTAGCCGTGACCTTATAAGT
* *
355071 TCTTTAGCATCACCTTCAGCTACTTTTAGCTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
66 TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
* * * *
355136 TGACTCCTCCAACTAGGTTCAGTTACATGCT-AGCTCCTCCAGCTAAATTGAGCTCTTCTTAAGT
131 TGACTCCTCCAACTAGGTTCAGCTACATGCTCA-CTTCTCCAGCTGAATTGAGAT-TTCTTAAGT
** * * * **
355200 TTCTGTGAGCTGCTTGAATCATTGTGAGCTGACTGTGAGCTGCCATGCTTTGCCAAATAGTTTCC
194 TTCAATGAGCTGATTGAATCTTTGTGAGCAGACTGTGAGCTGCCATGCTTTTTCAAATAGTTTCC
* * * * *
355265 CAGGCTACCATGGGACATGT-TC-TCCCTTTATGTCCCTACATAGATAAAAAAAACTAAGGTAAA
259 CAAGCTACCATAGG--ATGTGTCATCCCTTAATGTACCTACATAGAT-AAACAAACTAAGGTAAA
* * * * * * ** *
355328 ATGAAGGAAATTAGCTGAAATAAAATAAAATGCATTCTG-TCGTGAATGTATAAGTGTTTGTGAG
321 ATAAAGGAAATTAGATGAAATGAAACATAATACATGATGAT-GTGAATGTATAAGTGCTTGTGAG
* * * *
355392 GTATGAATGCATGCCATGAGCTAATTATATAAGGATGAAATGTTAATGAGCTAATGTATATACTT
385 CTATGAATGCATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATACTT
* *
355457 TAGGAGTTGAATTTAACATGTCATAAGCTAAATAAATAATAAATAACATGCTTCCATATTATGAA
450 TAGGAGCTGAATTTAACATGTCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATGAA
* **
355522 TGTAATGAAATCATATTAAATGAATGTAAAAATGAATGCAAAACAATAATAAATTAAGTAAAGAT
515 TGTAATGAAATCATATTAAATGAATGTAAAAATCAATGCAAATTAATAATAAATTAAGTAAAGAT
355587 GTGAATTAATATCATGCAGC
580 GTGAATTAATATCATGCAGC
355607 TA
1 TA
355609 TACTAATGAC
Statistics
Matches: 1111, Mismatches: 81, Indels: 17
0.92 0.07 0.01
Matches are distributed among these distances:
597 1 0.00
598 442 0.40
599 217 0.20
600 189 0.17
601 262 0.24
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (599 bp):
TAATGAGCTACCTAGACAAATAAGGGCTGGTCGTGATAAAACTTTCTAGCCGTGACCTTATAAGT
TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
TGACTCCTCCAACTAGGTTCAGCTACATGCTCACTTCTCCAGCTGAATTGAGATTTCTTAAGTTT
CAATGAGCTGATTGAATCTTTGTGAGCAGACTGTGAGCTGCCATGCTTTTTCAAATAGTTTCCCA
AGCTACCATAGGATGTGTCATCCCTTAATGTACCTACATAGATAAACAAACTAAGGTAAAATAAA
GGAAATTAGATGAAATGAAACATAATACATGATGATGTGAATGTATAAGTGCTTGTGAGCTATGA
ATGCATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATACTTTAGGAG
CTGAATTTAACATGTCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATGAATGTAAT
GAAATCATATTAAATGAATGTAAAAATCAATGCAAATTAATAATAAATTAAGTAAAGATGTGAAT
TAATATCATGCAGC
Found at i:355699 original size:2 final size:2
Alignment explanation
Indices: 355677--355728 Score: 68
Period size: 2 Copynumber: 25.0 Consensus size: 2
355667 TTTAAACATA
* *
355677 AT AT GT AT AC AT AT AT GAT AT AT AT GAT 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
355721 AT AT AT AT
1 AT AT AT AT
355729 CAAAGTAACC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 40 0.91
3 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:361159 original size:45 final size:45
Alignment explanation
Indices: 361087--361172 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
361077 AATATGATGA
*
361087 CAACTTCACTTGCCACGACAACATCATTAATTCTACTTGCCTTGG
1 CAACTTCACTTGCCACGACAACATCATTAACTCTACTTGCCTTGG
* * *
361132 CAACTTCACTTGCCATGGCAACGTCATTAACTCTACTTGCC
1 CAACTTCACTTGCCACGACAACATCATTAACTCTACTTGCC
361173 ACGACAACGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.26, C:0.33, G:0.12, T:0.30
Consensus pattern (45 bp):
CAACTTCACTTGCCACGACAACATCATTAACTCTACTTGCCTTGG
Found at i:361341 original size:35 final size:36
Alignment explanation
Indices: 361284--361390 Score: 164
Period size: 35 Copynumber: 3.0 Consensus size: 36
361274 TTCAATTAAT
361284 CTTCAATAAG-AAAATACCCAAATTTCTTATGAAAC
1 CTTCAATAAGAAAAATACCCAAATTTCTTATGAAAC
**
361319 CTT-AATAAGAAAAATATTCAAATTTCTTATGAAAC
1 CTTCAATAAGAAAAATACCCAAATTTCTTATGAAAC
*
361354 CTTCAATAGGAAAAAATACCCAAATTTCTTATGAAAC
1 CTTCAATAAG-AAAAATACCCAAATTTCTTATGAAAC
361391 TAATTACTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
34 6 0.09
35 29 0.45
36 5 0.08
37 24 0.38
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (36 bp):
CTTCAATAAGAAAAATACCCAAATTTCTTATGAAAC
Found at i:367424 original size:44 final size:44
Alignment explanation
Indices: 367356--367461 Score: 158
Period size: 44 Copynumber: 2.4 Consensus size: 44
367346 ATTTTGTTCT
* * * *
367356 AACTCCTTATTTGATGGAAACGAGCGAACTGGTAATGTTGATCC
1 AACTCCTTATGTGATGGAAACGAGCGAACTGATAATGCTAATCC
* *
367400 AACTCCTTATGTGATGGAATCGAGCGAAGTGATAATGCTAATCC
1 AACTCCTTATGTGATGGAAACGAGCGAACTGATAATGCTAATCC
367444 AACTCCTTATGTGATGGA
1 AACTCCTTATGTGATGGA
367462 TGTGCCAAGG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
AACTCCTTATGTGATGGAAACGAGCGAACTGATAATGCTAATCC
Found at i:370986 original size:60 final size:60
Alignment explanation
Indices: 370918--371073 Score: 172
Period size: 59 Copynumber: 2.6 Consensus size: 60
370908 TTGGATGAAG
* **
370918 TTGGGGATGAAATTAAAAGATCTAAAAGTTTAGGGACCAATTTAGAATGAGATTCATAGT
1 TTGGGGATGAAATTAAAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGAGCCATAGT
* * * *
370978 TTGGGGATGAAATTCAAATGTTC-AAAAG-TTAAGGACTAGTTTAGAATGAGAGCCATAGT
1 TTGGGGATGAAATT-AAAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGAGCCATAGT
* ** * * *
371037 GTAAGGATGAAATCAAAATATTTAAAAGTTTAAGGAC
1 TTGGGGATGAAATTAAAAGATCTAAAAGTTTAAGGAC
371074 TAAGTTACAA
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
58 4 0.05
59 41 0.53
60 27 0.35
61 6 0.08
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (60 bp):
TTGGGGATGAAATTAAAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGAGCCATAGT
Found at i:371191 original size:21 final size:22
Alignment explanation
Indices: 371148--371191 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
371138 TTTTACTTTG
*
371148 AACTACTAAAATAACTTTCCAA
1 AACTACTAAAATAACTTTACAA
* *
371170 AACTATTAAATTAA-TTTACAA
1 AACTACTAAAATAACTTTACAA
371191 A
1 A
371192 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (22 bp):
AACTACTAAAATAACTTTACAA
Found at i:372871 original size:15 final size:14
Alignment explanation
Indices: 372841--372884 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
372831 AATTTTAAAG
372841 TTTAATTTCATTTTTT
1 TTTAATTT--TTTTTT
372857 TTTGAATTTTTTTTT
1 TTT-AATTTTTTTTT
*
372872 TTTACTTTTTTTT
1 TTTAATTTTTTTT
372885 AAGTTTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 9 0.35
15 9 0.35
16 3 0.12
17 5 0.19
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.80
Consensus pattern (14 bp):
TTTAATTTTTTTTT
Found at i:373363 original size:34 final size:35
Alignment explanation
Indices: 373294--373367 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
373284 AAATCATAAC
**
373294 AAAATGATATTGTTTGGTTTAATTTTTTTTTAAAA
1 AAAATGATATTGTTTGGTTTAATTTTTTTAAAAAA
373329 AAAATGATATTGTTTGGTTTAA-TTTTTTAAAAAA
1 AAAATGATATTGTTTGGTTTAATTTTTTTAAAAAA
373363 AAAAT
1 AAAAT
373368 CCCACATGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
34 15 0.41
35 22 0.59
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (35 bp):
AAAATGATATTGTTTGGTTTAATTTTTTTAAAAAA
Found at i:376002 original size:16 final size:16
Alignment explanation
Indices: 375978--376026 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
375968 AGGTTGTTTG
*
375978 AGTTCGGGTTATTTTC
1 AGTTCGGGTTAATTTC
* **
375994 AGTTTGGGTTGCTTTC
1 AGTTCGGGTTAATTTC
*
376010 GGTTCGGGTTAATTTC
1 AGTTCGGGTTAATTTC
376026 A
1 A
376027 ATTTGGATTG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.47
Consensus pattern (16 bp):
AGTTCGGGTTAATTTC
Found at i:376048 original size:32 final size:32
Alignment explanation
Indices: 375980--376050 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
375970 GTTGTTTGAG
* * * *
375980 TTCGGGTTATTTTCAGTTTGGGTTGCTTTCGG
1 TTCGGGTTAATTTCAATTTGGATTGCTTTCGA
* **
376012 TTCGGGTTAATTTCAATTTGGATTGTTTTTTA
1 TTCGGGTTAATTTCAATTTGGATTGCTTTCGA
376044 TTCGGGT
1 TTCGGGT
376051 CAAATTAGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.11, C:0.10, G:0.27, T:0.52
Consensus pattern (32 bp):
TTCGGGTTAATTTCAATTTGGATTGCTTTCGA
Found at i:384292 original size:7 final size:7
Alignment explanation
Indices: 384280--384305 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
384270 AGATTCATTC
384280 AAAATTG
1 AAAATTG
384287 AAAATTG
1 AAAATTG
384294 AAAATTG
1 AAAATTG
384301 AAAAT
1 AAAAT
384306 GACTCACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
AAAATTG
Found at i:393739 original size:18 final size:20
Alignment explanation
Indices: 393699--393749 Score: 79
Period size: 18 Copynumber: 2.6 Consensus size: 20
393689 TGAATATTTG
393699 TCCGAAGGACCACTGATTGT
1 TCCGAAGGACCACTGATTGT
*
393719 TCCGAAGAACCACT-A-TGT
1 TCCGAAGGACCACTGATTGT
393737 TCCGAAGGACCAC
1 TCCGAAGGACCAC
393750 CGATAATCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 15 0.52
19 1 0.03
20 13 0.45
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (20 bp):
TCCGAAGGACCACTGATTGT
Found at i:394337 original size:24 final size:24
Alignment explanation
Indices: 394305--394361 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
394295 TACACCATGT
394305 ATCGATGCATCCCTTGACGGGTGC
1 ATCGATGCATCCCTTGACGGGTGC
394329 ATCGATGCATCCCTTGACGGGTGC
1 ATCGATGCATCCCTTGACGGGTGC
394353 ATCGATGCA
1 ATCGATGCA
394362 CAATCTATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (24 bp):
ATCGATGCATCCCTTGACGGGTGC
Found at i:394456 original size:64 final size:64
Alignment explanation
Indices: 394388--394508 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
394378 ACATAAATCC
* * * *
394388 CATTCGATGTTTGTATTTTAAGGGGGTGCATCGATACA-CTACTTGTGCATCGATACACTAATAA
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACACCT-CATCTGCATCGATACACTAATAA
* *
394452 CATTCGATGTTTTTATTTTAAAGGAGTGTATCGATACACCTCATCTGCATCGATACA
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACACCTCATCTGCATCGATACA
394509 ACTTGAACAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 48 0.96
65 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACACCTCATCTGCATCGATACACTAATAA
Found at i:400335 original size:2 final size:2
Alignment explanation
Indices: 400328--400352 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
400318 GTGAGGCATA
400328 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
400353 ACAATGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:400635 original size:18 final size:17
Alignment explanation
Indices: 400614--400675 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
400604 GTCCCGAAGG
400614 ACCACTATGTCCTGAAAA
1 ACCACTATGTCC-GAAAA
* *
400632 ACCATTGATTGTTCCGAAGA
1 ACCACT-A-TG-TCCGAAAA
*
400652 ACCACTATGTCCCGAAAG
1 ACCACTATGT-CCGAAAA
400670 ACCACT
1 ACCACT
400676 GATAATTCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 1 0.03
18 18 0.51
19 2 0.06
20 11 0.31
21 3 0.09
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.23
Consensus pattern (17 bp):
ACCACTATGTCCGAAAA
Found at i:400658 original size:38 final size:38
Alignment explanation
Indices: 400602--400678 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
400592 CACTAAATAT
* * *
400602 TTGTCCCGAAGGACCACTATGTCCTGAAAAACCATTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAAAACCACTGA
* *
400640 TTGTTCCGAAGAACCACTATGTCCCGAAAGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAAAACCACTGA
400678 T
1 T
400679 AATTCCTCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAAAACCACTGA
Found at i:401319 original size:64 final size:64
Alignment explanation
Indices: 401247--401386 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 64
401237 ATCCCTTGAC
* * *
401247 GGGTGCATCGATGCA-TAATCTATGCATCGGTACA-TAAATCCCATTCGATGTTTGTATTTTAAG
1 GGGTGCATCGATGCACTAAT-TATGCATCGATACACT-AATCACATTCGATGTTTGTATTTTAAA
401310 G
64 G
* * * *
401311 GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATGACATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTAATTATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAG
*
401375 GAGTGCATCGAT
1 GGGTGCATCGAT
401387 ATACCTCATG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
64 62 0.94
65 4 0.06
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (64 bp):
GGGTGCATCGATGCACTAATTATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAG
Found at i:401399 original size:64 final size:64
Alignment explanation
Indices: 401288--401409 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
401278 ACATAAATCC
* * * *
401288 CATTCGATGTTTGTATTTTAAGGGGGTGCATCGATGCACTACTTGTGCATCGATACACTAATGA
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTAATGA
* *
401352 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATATACCT-CATGTGCATCGATACAC
1 CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACA-CTACATGTGCATCGATACAC
401410 CTTGAACAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 49 0.96
65 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTAATGA
Found at i:405668 original size:16 final size:15
Alignment explanation
Indices: 405645--405732 Score: 54
Period size: 16 Copynumber: 5.5 Consensus size: 15
405635 TTTCAAATTA
405645 AAAT-TAATAACAAAT
1 AAATATAATAA-AAAT
*
405660 AAATATAATAATAAT
1 AAATATAATAAAAAT
* * *
405675 TAATA-ACAGTAATTATT
1 AAATATA-A-TAA-AAAT
405692 AAATATAATAAATAAGT
1 AAATATAATAAA-AA-T
405709 AAAATATAATAATAAAT
1 -AAATATAATAA-AAAT
405726 AAATATA
1 AAATATA
405733 GTAATTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
14 1 0.02
15 12 0.21
16 20 0.34
17 10 0.17
18 14 0.24
19 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
AAATATAATAAAAAT
Found at i:405737 original size:16 final size:16
Alignment explanation
Indices: 405645--405759 Score: 78
Period size: 17 Copynumber: 7.1 Consensus size: 16
405635 TTTCAAATTA
*
405645 AAAT-TAATAACAAAT
1 AAATATAATAATAAAT
405660 AAATATAATAAT-AAT
1 AAATATAATAATAAAT
* * *
405675 TAATA-ACAGTAATTATT
1 AAATATA-A-TAATAAAT
*
405692 AAATATAATAAATAAGT
1 AAATATAAT-AATAAAT
405709 AAAATATAATAATAAAT
1 -AAATATAATAATAAAT
*
405726 AAATATAGTAATTAAA-
1 AAATATAATAA-TAAAT
*
405742 AAGATATTAT-ATAAAT
1 AA-ATATAATAATAAAT
405758 AA
1 AA
405760 TAATTATAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 19
0.73 0.09 0.17
Matches are distributed among these distances:
14 1 0.01
15 16 0.20
16 26 0.32
17 27 0.34
18 10 0.12
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATATAATAATAAAT
Found at i:406201 original size:17 final size:16
Alignment explanation
Indices: 406177--406208 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
406167 ATTTTTAGTA
406177 TTTATTTATTTGTTTG
1 TTTATTTATTTGTTTG
406193 TTTAGTTTATTTGTTT
1 TTTA-TTTATTTGTTT
406209 TGGTATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.75
Consensus pattern (16 bp):
TTTATTTATTTGTTTG
Found at i:406726 original size:24 final size:24
Alignment explanation
Indices: 406684--406746 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
406674 TTATTTATGA
* *
406684 ATATTTATTAATATTGAAATTTA-T
1 ATATTTATT-ATTTTGAAATTAAGT
406708 ATATTTATTATTTTGGAAATTAAGT
1 ATATTTATTATTTT-GAAATTAAGT
406733 A-ATTATATTATTTT
1 ATATT-TATTATTTT
406747 ATTAATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 4 0.12
24 19 0.56
25 11 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (24 bp):
ATATTTATTATTTTGAAATTAAGT
Found at i:409321 original size:6 final size:6
Alignment explanation
Indices: 409310--409336 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
409300 TTAATTGGGA
409310 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
409337 AATTCGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:411876 original size:18 final size:18
Alignment explanation
Indices: 411855--411894 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
411845 TATTGAGATG
*
411855 GAGGATATATTTGAGGAA
1 GAGGATATATGTGAGGAA
*
411873 GAGGATATATGTGAGGTA
1 GAGGATATATGTGAGGAA
411891 GAGG
1 GAGG
411895 TTGGTGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.40, T:0.25
Consensus pattern (18 bp):
GAGGATATATGTGAGGAA
Done.