Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004309.1 Hibiscus syriacus cultivar Beakdansim tig00009447_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: 426183
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:238549 original size:28 final size:27
Alignment explanation
Indices: 238504--238581 Score: 108
Period size: 28 Copynumber: 3.0 Consensus size: 27
238494 AAGTTAATAT
238504 TAATATTAATTATATTAATATTAATTA
1 TAATATTAATTATATTAATATTAATTA
*
238531 TAATATATAATTATTTTAATATTAATTA
1 TAATAT-TAATTATATTAATATTAATTA
*
238559 TAA-A-TAATT-TATTAATATAAATT
1 TAATATTAATTATATTAATATTAATT
238582 TTATATGGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
24 12 0.26
25 5 0.11
27 7 0.15
28 23 0.49
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAATATTAATTATATTAATATTAATTA
Found at i:238569 original size:21 final size:22
Alignment explanation
Indices: 238448--238581 Score: 102
Period size: 21 Copynumber: 6.1 Consensus size: 22
238438 AAACTATATT
**
238448 TTAT-ATTAATATTAATTACAAA
1 TTATAATTAATATTAA-TATTAA
*
238470 TTATAAACT-ATATT-ATATTAA
1 TTAT-AATTAATATTAATATTAA
238491 -TATAAGTTAATATTAATATTAA
1 TTATAA-TTAATATTAATATTAA
238513 TTAT-ATTAATATTAAT-TATAA
1 TTATAATTAATATTAATAT-TAA
*
238534 TATATAATT-ATTTTAATATTAA
1 T-TATAATTAATATTAATATTAA
* *
238556 TTATAAATAATTTATTAATATAAA
1 TTATAATTAA--TATTAATATTAA
238580 TT
1 TT
238582 TTATATGGAT
Statistics
Matches: 91, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
19 2 0.02
20 5 0.05
21 30 0.33
22 28 0.31
23 12 0.13
24 14 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (22 bp):
TTATAATTAATATTAATATTAA
Found at i:241410 original size:25 final size:24
Alignment explanation
Indices: 241395--241440 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
241385 ACTCTAATAT
241395 TTTTAATTTGACTTAACTCAAAAC
1 TTTTAATTTGACTTAACTCAAAAC
*
241419 TTTTAATTTGACTTCA-TCAAAA
1 TTTTAATTTGACTTAACTCAAAA
241441 TTTCAGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.43
Consensus pattern (24 bp):
TTTTAATTTGACTTAACTCAAAAC
Found at i:242027 original size:100 final size:98
Alignment explanation
Indices: 241918--242096 Score: 259
Period size: 100 Copynumber: 1.8 Consensus size: 98
241908 TTCATACTAC
*
241918 AAAAAATGTATAACTTAACACACACTTACACTAGTATAAGTGAATAAAATAAAAAAAAGTGTAGA
1 AAAAAATGTAGAACTTAACACACACTTACACTAGTATAAGTGAATAAAAT--AAAAAAGTGTAGA
*
241983 ATTTAACACATACTTAGGTTTAATTGTATATAATA
64 ACTTAACACATACTTAGGTTTAATTGTATATAATA
* * * * * * *
242018 AAAAAATGTAGCACTTAACATATACTTATACTAGTGTAAGTGAATAAAATAAAAAGGTGTAGCAC
1 AAAAAATGTAGAACTTAACACACACTTACACTAGTATAAGTGAATAAAATAAAAAAGTGTAGAAC
242083 TTAACACATACTTA
66 TTAACACATACTTA
242097 CACCTGAGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
98 26 0.37
100 44 0.63
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (98 bp):
AAAAAATGTAGAACTTAACACACACTTACACTAGTATAAGTGAATAAAATAAAAAAGTGTAGAAC
TTAACACATACTTAGGTTTAATTGTATATAATA
Found at i:242079 original size:51 final size:51
Alignment explanation
Indices: 241930--242096 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 51
241920 AAAATGTATA
* * *
241930 ACTTAACACACACTTACACTAGTATAAGTGAATAAAATAAAAAAAAGTGTAGA
1 ACTTAACACATACTTATACTAGTATAAGTGAATAAAAT--AAAAAAGTGTAGC
* * * * * * *
241983 ATTTAACACATAC-T-TA--GGTTTAATTGTATATAATAAAAAAATGTAGC
1 ACTTAACACATACTTATACTAGTATAAGTGAATAAAATAAAAAAGTGTAGC
* * *
242030 ACTTAACATATACTTATACTAGTGTAAGTGAATAAAATAAAAAGGTGTAGC
1 ACTTAACACATACTTATACTAGTATAAGTGAATAAAATAAAAAAGTGTAGC
242081 ACTTAACACATACTTA
1 ACTTAACACATACTTA
242097 CACCTGAGCT
Statistics
Matches: 90, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
47 22 0.24
48 1 0.01
49 15 0.17
51 40 0.44
52 1 0.01
53 11 0.12
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (51 bp):
ACTTAACACATACTTATACTAGTATAAGTGAATAAAATAAAAAAGTGTAGC
Found at i:243723 original size:29 final size:28
Alignment explanation
Indices: 243690--243810 Score: 77
Period size: 28 Copynumber: 4.2 Consensus size: 28
243680 TTAAATTCAC
* *
243690 ATCTTAACATTAAAATATATATTATTTTT
1 ATCTTAACATTAAAATATAT-TTAATCTT
* *
243719 ATCTTAAC-TTATTAAAT-TGTTTAATTTT
1 ATCTTAACATTA--AAATATATTTAATCTT
* * *
243747 ATTTTTA-TTTAAAATATATTTTAATCTT
1 ATCTTAACATTAAAATATA-TTTAATCTT
* * *
243775 ATTTTAACATAAAAATATATCTTATTCTT
1 ATCTTAACATTAAAATATAT-TTAATCTT
*
243804 ATATTAA
1 ATCTTAA
243811 ATTTTAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
26 4 0.05
27 1 0.01
28 33 0.45
29 32 0.43
30 4 0.05
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.54
Consensus pattern (28 bp):
ATCTTAACATTAAAATATATTTAATCTT
Found at i:243921 original size:31 final size:31
Alignment explanation
Indices: 243896--243970 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 31
243886 AAAATTAGAC
* *
243896 TAAAATATATTTTTTTAAGTTAAAATAAAAG
1 TAAAATATATTTTATTAAGTTAAAATAAAAA
*
243927 TAAAATATA-TTTATTAAGTTAAGATAAAAA
1 TAAAATATATTTTATTAAGTTAAAATAAAAA
243957 TAAAATATATTTTA
1 TAAAATATATTTTA
243971 ACGTTAAGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 27 0.68
31 13 0.32
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (31 bp):
TAAAATATATTTTATTAAGTTAAAATAAAAA
Found at i:244000 original size:18 final size:18
Alignment explanation
Indices: 243974--244013 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
243964 TATTTTAACG
* *
243974 TTAAGATGTGAATTTAAT
1 TTAACATGTGAATTTAAA
243992 TTAACATGTGAATTTAAA
1 TTAACATGTGAATTTAAA
244010 TTAA
1 TTAA
244014 AATATATAAA
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:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (18 bp):
TTAACATGTGAATTTAAA
Found at i:244829 original size:29 final size:29
Alignment explanation
Indices: 244788--244853 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
244778 TAACATATAT
244788 AAAATAATAATTCTTCCTTTTGACCAAGA
1 AAAATAATAATTCTTCCTTTTGACCAAGA
244817 AAAATAATAATTCTTCCTTTTGACCAAGA
1 AAAATAATAATTCTTCCTTTTGACCAAGA
244846 AAAATAAT
1 AAAATAAT
244854 CATCTTATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (29 bp):
AAAATAATAATTCTTCCTTTTGACCAAGA
Found at i:246125 original size:23 final size:23
Alignment explanation
Indices: 246099--246144 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
246089 ATATATTGAT
246099 TTTAT-ATAAAAATAATAATTATA
1 TTTATAAT-AAAATAATAATTATA
* *
246122 TTTATAATAATATACTAATTATA
1 TTTATAATAAAATAATAATTATA
246145 ATCTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTATAATAAAATAATAATTATA
Found at i:247565 original size:13 final size:12
Alignment explanation
Indices: 247538--247571 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
247528 GATGGATTTT
247538 ATTTCTTTATCC
1 ATTTCTTTATCC
*
247550 ATTTCTATTCTCC
1 ATTTCT-TTATCC
247563 ATTTCTTTA
1 ATTTCTTTA
247572 CTTTAACAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTCTTTATCC
Found at i:258041 original size:32 final size:31
Alignment explanation
Indices: 257972--258041 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
257962 GGATGGCTTT
*
257972 GTGGCCCTAAGATCATTCTCAGGTAGGCCCT
1 GTGGCCCTAAGATCATTCTCAGGTAGGCCCC
* * *
258003 GCGGCCCTAAGATATATTCTTAGGTAGGCCCC
1 GTGGCCCTAAGAT-CATTCTCAGGTAGGCCCC
258035 GTGGCCC
1 GTGGCCC
258042 CGAACTTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 12 0.36
32 21 0.64
ACGTcount: A:0.19, C:0.30, G:0.27, T:0.24
Consensus pattern (31 bp):
GTGGCCCTAAGATCATTCTCAGGTAGGCCCC
Found at i:259663 original size:14 final size:13
Alignment explanation
Indices: 259635--259668 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
259625 ATTTATGCAC
*
259635 TATTTGTATTGGT
1 TATTTATATTGGT
259648 TATTTATATATGGT
1 TATTTATAT-TGGT
259662 TATTTAT
1 TATTTAT
259669 GTTACGGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
TATTTATATTGGT
Found at i:268794 original size:13 final size:13
Alignment explanation
Indices: 268776--268809 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
268766 TTATCTCCTC
* *
268776 TTTTCTTTCTTTG
1 TTTTCTTTCATTA
268789 TTTTCTTTCATTA
1 TTTTCTTTCATTA
268802 TTTTCTTT
1 TTTTCTTT
268810 TACAATGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTCTTTCATTA
Found at i:274871 original size:20 final size:23
Alignment explanation
Indices: 274816--274879 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 23
274806 AATTATTTTA
274816 TTATTTATTTTATTTTATTTCCTT
1 TTATTTA-TTTATTTTATTTCCTT
*
274840 TTAATTTCTTTATTTT-TTT-C-T
1 TT-ATTTATTTATTTTATTTCCTT
*
274861 TTATTTATTTATATTATTT
1 TTATTTATTTATTTTATTT
274880 TAGCTAGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 11 0.31
21 6 0.17
22 1 0.03
23 3 0.09
24 10 0.29
25 4 0.11
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (23 bp):
TTATTTATTTATTTTATTTCCTT
Found at i:276096 original size:391 final size:390
Alignment explanation
Indices: 275257--277167 Score: 2263
Period size: 390 Copynumber: 4.9 Consensus size: 390
275247 TTGAAATACT
* * * * * *
275257 ATGATGATATCTCATGAGTTCGTTCATTGAAAATGCACTTCACTTGATTCTAAATAAACCTTTTT
1 ATGATGACATCTCATGAATTCGTTCATTGAAAATGCACTTGACTTAATGCTAAATACACCTTTTT
* * * * * *
275322 GGTAAGATTTGAACACGTCGAGCAATTCCTTATATTCTTGCTCATTTTTCTTTTATTGAGTGTGC
66 GGTAAGATTTGAGCCCATCGAGCAATTCCTTATATTCTTGCTCATTTTTCTTGTCTTGAGTGTGT
** * * * *
275387 CGAACTTAGCATTTATATTCTAGAACTTAATTGTTAATACATTGTTGATACTACAATTTGAATTA
131 CGAACTTAGCATTTATATTCTAGAACTTGCTTGTGAATACA-TGTTGAGACTA-AATTTGGATTT
* * * * * * *
275452 AATGCTTTAAAATGATAATGGTACTTAGTATTTACCCTTTTTTCATACCTTCAAAATATGCCTAC
194 GATGCTTTAAAATGATAAGGGCACTTAGGATTTAACCATTTTTCATACCTTCAAAAAATGCCTAC
* *
275517 CCATTTATTTTGCCTTAGTTAGTTACTTTGAGTCATTTTCTCTTTTCTTTGTTTTACCACACTTT
259 CCATTTATTTTCCCTTAGTTAGTTACTTTGAGTCATTTTCCCTTTTCTTTGTTTTACCACACTTT
* * * *
275582 AAACCCAAACCCTTTGATTTTATCTCTATTTTACTACTTTTATCGAACCAAGAGGACAAGTTTTT
324 AAACCCAAAGCCTTTGATTTTATCTCTATTTTACTACCTTTATCAAAACAAGAGGACAAGTTTTT
275647 CC
389 CC
*
275649 ATGACGACATCTCATGAATTCGTTCATTGAAAATGCACTTTG-CTTAATGCTAAATACACCTTTT
1 ATGATGACATCTCATGAATTCGTTCATTGAAAATGCAC-TTGACTTAATGCTAAATACACCTTTT
* * * *
275713 TGGTAAGATTTGAGCCCATCGAGCAATTCCTTATATTCTTACCCATTTTTCTTCTCTTGAGTGCG
65 TGGTAAGATTTGAGCCCATCGAGCAATTCCTTATATTCTTGCTCATTTTTCTTGTCTTGAGTGTG
* * * * *
275778 TCGATCTTAGCATTTGTATTCTAGAACTTGCTTGTAAATACATGTTGAGAGTAAAGATTGGATTT
130 TCGAACTTAGCATTTATATTCTAGAACTTGCTTGTGAATACATGTTGAGACTAAA-TTTGGATTT
275843 GATGCTTTAAAATGATAAGGGCACTTAGGATTTAACCATTTTTCATACCTTCAAAAAAATGCCTA
194 GATGCTTTAAAATGATAAGGGCACTTAGGATTTAACCATTTTTCATACCTTC-AAAAAATGCCTA
* * * *
275908 CCCATTTGTTTTCCCTTAGTTAGTTACTTTGAGTTATTTTCCCTTTT-TTTGTTGTAACACACTT
258 CCCATTTATTTTCCCTTAGTTAGTTACTTTGAGTCATTTTCCCTTTTCTTTGTTTTACCACACTT
* * * * * * *
275972 TCAACCCAAAGCTTTTGATTTTATCTTTATTTTACTACCTTTATCAAAATAATAGGATAAGCTTT
323 TAAACCCAAAGCCTTTGATTTTATCTCTATTTTACTACCTTTATCAAAACAAGAGGACAAGTTTT
276037 TCC
388 TCC
* *
276040 ATGATGACATCTCATTAA-TCTGTTCATTGAAAATGCACTTGACTTAATGCTAAATACACTTTTT
1 ATGATGACATCTCATGAATTC-GTTCATTGAAAATGCACTTGACTTAATGCTAAATACACCTTTT
** * * * * * * * * *
276104 TTCTAAGATTTGAGCCTATAGTGAAACTCCTTATATTCTTGCTCAATATTATTGTCTT-A-TATT
65 TGGTAAGATTTGAGCCCATCGAGCAATTCCTTATATTCTTGCTCATTTTTCTTGTCTTGAGT-GT
* * * * * * * * *
276167 ATAGAACATAGCATTTATATTATATAGCTTGCTTGTGAATACATGTAGAGACTACATTTTGAGTT
129 GTCGAACTTAGCATTTATATTCTAGAACTTGCTTGTGAATACATGTTGAGACTAAATTTGGA-TT
* * * * ** *
276232 TAATGCTTTGAAATGATAAGGGAAGTTAGGATTTAGTCATTTTTCATACCTTGAAAAAATG-CTA
193 TGATGCTTTAAAATGATAAGGGCACTTAGGATTTAACCATTTTTCATACCTTCAAAAAATGCCTA
* * * *
276296 CTCATTTATTTTCCCTTATTTAGCTACTTTGAGTCATTTTCCCTTTTCTTTGTTTTACGACACTT
258 CCCATTTATTTTCCCTTAGTTAGTTACTTTGAGTCATTTTCCCTTTTCTTTGTTTTACCACACTT
* * * * *
276361 TAAACCCAAGGCCTTAT-ATTTTATCTCTATTTTAATATCTTTATCAAGACAAGAGGACAAATTT
323 TAAACCCAAAGCCTT-TGATTTTATCTCTATTTTACTACCTTTATCAAAACAAGAGGACAAGTTT
276425 TTCC
387 TTCC
* * *
276429 ATGATGACATCTCATGAATTCGTCCATTGAAAATGCACTTGACTTAATGCTAAATACACCCTGTT
1 ATGATGACATCTCATGAATTCGTTCATTGAAAATGCACTTGACTTAATGCTAAATACACCTTTTT
* * * * * * * *
276494 CGTAATATCTGAGCCCATCGAGCAATTCCATATATTATTGCTCATTTTTATTGTCTTTAGTTTGT
66 GGTAAGATTTGAGCCCATCGAGCAATTCCTTATATTCTTGCTCATTTTTCTTGTCTTGAGTGTGT
*
276559 CAAACTTAGCATTTATATTCTAGAACTTGCTTGTGAATACATGTTGAGACTAAAGTTTGGATTTG
131 CGAACTTAGCATTTATATTCTAGAACTTGCTTGTGAATACATGTTGAGACTAAA-TTTGGATTTG
* * * * * * * * *
276624 ATGCTTTAAAATGATAAGGGTAATTAGAACTTAACCATTTTTCATACATTCAAAGAGTGACTGCC
195 ATGCTTTAAAATGATAAGGGCACTTAGGATTTAACCATTTTTCATACCTTCAAAAAATGCCTACC
* * * * *
276689 CATTTATTTTCCCTTAATCAGTTACTTTGAATCATTTTCCCTTTTCTTTATTTTACCACAC-TTC
260 CATTTATTTTCCCTTAGTTAGTTACTTTGAGTCATTTTCCCTTTTCTTTGTTTTACCACACTTTA
* * * *
276753 AACCCAAAGCCTTTAATTTTATCTTTATTTTACTACCTTTATCGATACAAGAGGACATA-TTTTT
325 AACCCAAAGCCTTTGATTTTATCTCTATTTTACTACCTTTATCAAAACAAGAGGACA-AGTTTTT
276817 CC
389 CC
*
276819 ATGATGACATCTCATGAATTCTTTCATTGAAAATGCACTTGACTTAATGCTAAATACACCTTTTT
1 ATGATGACATCTCATGAATTCGTTCATTGAAAATGCACTTGACTTAATGCTAAATACACCTTTTT
276884 --T--G---T------A---AGCAATTCCTTATATTCTTGCTCATTTTTCTTGTCTTGAGTGTGT
66 GGTAAGATTTGAGCCCATCGAGCAATTCCTTATATTCTTGCTCATTTTTCTTGTCTTGAGTGTGT
* * *
276933 CGAACTTAGAATTTATATTCTAGAAATTGCTTGTGAATACATGTTGAGACTACAATTTTTGATTT
131 CGAACTTAGCATTTATATTCTAGAACTTGCTTGTGAATACATGTTGAGACTA-AA-TTTGGATTT
* * * * * * * *
276998 GATGCTATAAAATGATAAAGGCACTTTGGATTCACCCATTTTTCATACCTTCAAAGAATGTCAAC
194 GATGCTTTAAAATGATAAGGGCACTTAGGATTTAACCATTTTTCATACCTTCAAAAAATGCCTAC
* ** ** *
277063 CAATTTATTTTCCCTTAGTTAGCCACTTTGAG-CATTTTATCTTTTCTTTGTTTTACCTCACTTT
259 CCATTTATTTTCCCTTAGTTAGTTACTTTGAGTCATTTTCCCTTTTCTTTGTTTTACCACACTTT
* *
277127 AAACCCAAAGCCTTTGATTTTATCTCTCTTTTGCTACCTTT
324 AAACCCAAAGCCTTTGATTTTATCTCTATTTTACTACCTTT
277168 TTCGAGATAA
Statistics
Matches: 1293, Mismatches: 208, Indels: 53
0.83 0.13 0.03
Matches are distributed among these distances:
374 114 0.09
375 125 0.10
377 1 0.00
383 1 0.00
388 46 0.04
389 183 0.14
390 323 0.25
391 297 0.23
392 201 0.16
393 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (390 bp):
ATGATGACATCTCATGAATTCGTTCATTGAAAATGCACTTGACTTAATGCTAAATACACCTTTTT
GGTAAGATTTGAGCCCATCGAGCAATTCCTTATATTCTTGCTCATTTTTCTTGTCTTGAGTGTGT
CGAACTTAGCATTTATATTCTAGAACTTGCTTGTGAATACATGTTGAGACTAAATTTGGATTTGA
TGCTTTAAAATGATAAGGGCACTTAGGATTTAACCATTTTTCATACCTTCAAAAAATGCCTACCC
ATTTATTTTCCCTTAGTTAGTTACTTTGAGTCATTTTCCCTTTTCTTTGTTTTACCACACTTTAA
ACCCAAAGCCTTTGATTTTATCTCTATTTTACTACCTTTATCAAAACAAGAGGACAAGTTTTTCC
Found at i:279114 original size:16 final size:14
Alignment explanation
Indices: 279088--279136 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 14
279078 TCTTCTACTT
279088 TTTTTACTTTTTTTA
1 TTTTTA-TTTTTTTA
279103 TTTTCTCATTTTTTTA
1 TTTT-T-ATTTTTTTA
*
279119 TATTTATTTTTATTA
1 TTTTTATTTTT-TTA
279134 TTT
1 TTT
279137 ATTTACTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 6 0.21
15 10 0.34
16 12 0.41
17 1 0.03
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:279674 original size:19 final size:19
Alignment explanation
Indices: 279647--279685 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
279637 ATATAAAAAA
279647 TAACAGTTAACCAAAATTT
1 TAACAGTTAACCAAAATTT
* * *
279666 TAACCGTTAATCAATATTT
1 TAACAGTTAACCAAAATTT
279685 T
1 T
279686 TAACGGTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (19 bp):
TAACAGTTAACCAAAATTT
Found at i:281801 original size:236 final size:236
Alignment explanation
Indices: 281382--281810 Score: 813
Period size: 236 Copynumber: 1.8 Consensus size: 236
281372 TGTTTCATGG
281382 TTTCTATTTTCTATTTTGGGTTCCTTTTTCGGAGGATAACACACCCATCATGTTTCTTATTTTTA
1 TTTCTATTTTCTATTTTGGGTTCCTTTTTCGGAGGATAACACACCCATCATGTTTCTTATTTTTA
*
281447 CTTCACCTTTTGAGGGCAATGTCCCCATCATGTTTATCTACGACGAAAGGTAAGGTTATGAGAAC
66 CTTCACCTTTTGAGGGAAATGTCCCCATCATGTTTATCTACGACGAAAGGTAAGGTTATGAGAAC
*
281512 TTCAATTGAGATACTTTGATGGTGAACAATTGGTCTTATTGTTGCCTGGTTTTTATGCTATTTTC
131 TTCAATTGAGATACTTTGATGGTGAACAATTGGTCTTATTGTTGCCTGGTTTTTATGCAATTTTC
281577 TATTTTATGTTTCTCTTCGAAGGGTAAAGTCCCCATCCTAA
196 TATTTTATGTTTCTCTTCGAAGGGTAAAGTCCCCATCCTAA
* *
281618 TTTCTTTTTTCTATTTTGGGTTCCTTTTTCGGAGGATAACACACCCATCATGTTTCTTATTTTTG
1 TTTCTATTTTCTATTTTGGGTTCCTTTTTCGGAGGATAACACACCCATCATGTTTCTTATTTTTA
*
281683 CTTCACCTTTTGAGGGAAATTTCCCCATCATGTTTATCTACGACGAAAGGTAAGGTTATGAGAAC
66 CTTCACCTTTTGAGGGAAATGTCCCCATCATGTTTATCTACGACGAAAGGTAAGGTTATGAGAAC
281748 TTCAATTGAGATACTTTGATGGTGAACAATTGGTCTTATTGTTGCCTGGTTTTTATGCAATTT
131 TTCAATTGAGATACTTTGATGGTGAACAATTGGTCTTATTGTTGCCTGGTTTTTATGCAATTT
281811 ATTACATCAT
Statistics
Matches: 188, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
236 188 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.42
Consensus pattern (236 bp):
TTTCTATTTTCTATTTTGGGTTCCTTTTTCGGAGGATAACACACCCATCATGTTTCTTATTTTTA
CTTCACCTTTTGAGGGAAATGTCCCCATCATGTTTATCTACGACGAAAGGTAAGGTTATGAGAAC
TTCAATTGAGATACTTTGATGGTGAACAATTGGTCTTATTGTTGCCTGGTTTTTATGCAATTTTC
TATTTTATGTTTCTCTTCGAAGGGTAAAGTCCCCATCCTAA
Found at i:284548 original size:14 final size:14
Alignment explanation
Indices: 284531--284558 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
284521 CATCTAAGTC
284531 AACCCATTGACTTT
1 AACCCATTGACTTT
284545 AACCCATTGACTTT
1 AACCCATTGACTTT
284559 TACCGTTAAC
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:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
AACCCATTGACTTT
Found at i:284576 original size:13 final size:13
Alignment explanation
Indices: 284537--284602 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
284527 AGTCAACCCA
* *
284537 TTGACTTTAACCCA
1 TTGACTTTGA-CCG
*
284551 TTGACTTTTACCG
1 TTGACTTTGACCG
*
284564 TTAACTTTGACCG
1 TTGACTTTGACCG
**
284577 TTGACTGTTGACTA
1 TTGACT-TTGACCG
284591 TTGACTTTGACC
1 TTGACTTTGACC
284603 TAAAAAGTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
13 23 0.53
14 20 0.47
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGACTTTGACCG
Found at i:286740 original size:18 final size:18
Alignment explanation
Indices: 286719--286754 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
286709 GGGGGGTTTG
286719 GTAAAAAGAAATTAAATA
1 GTAAAAAGAAATTAAATA
286737 GTAAAAAGAAATTAAATA
1 GTAAAAAGAAATTAAATA
286755 AATAAAGGAA
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:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (18 bp):
GTAAAAAGAAATTAAATA
Found at i:286765 original size:18 final size:17
Alignment explanation
Indices: 286721--286770 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
286711 GGGGTTTGGT
286721 AAAAAGAAATTAAATAG
1 AAAAAGAAATTAAATAG
286738 TAAAAAGAAATTAAATA-
1 -AAAAAGAAATTAAATAG
286755 AATAAAGGAAATTAAA
1 AA-AAA-GAAATTAAA
286771 GTATAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.07
17 3 0.10
18 25 0.83
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (17 bp):
AAAAAGAAATTAAATAG
Found at i:298112 original size:23 final size:23
Alignment explanation
Indices: 298080--298137 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
298070 CTATGCACTA
*
298080 GGTATCGATACCCCCTTTGAATG
1 GGTATCGATACCACCTTTGAATG
*
298103 GGTA-CTGATACCATCTTTGAATG
1 GGTATC-GATACCACCTTTGAATG
298126 GGTATCGATACC
1 GGTATCGATACC
298138 TCCATGAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 1 0.03
23 29 0.94
24 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
GGTATCGATACCACCTTTGAATG
Found at i:298638 original size:13 final size:13
Alignment explanation
Indices: 298620--298653 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
298610 TACACCTTGA
*
298620 TTTTCAAACATTG
1 TTTTCAAACATAG
298633 TTTTCAAACATAG
1 TTTTCAAACATAG
298646 TTTTCAAA
1 TTTTCAAA
298654 AAAATTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:299882 original size:15 final size:15
Alignment explanation
Indices: 299862--299899 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
299852 CGAGCACGTT
299862 ATCCTCCTCCTCCCG
1 ATCCTCCTCCTCCCG
299877 ATCCTCCTCCTCCCG
1 ATCCTCCTCCTCCCG
299892 ATCCTCCT
1 ATCCTCCT
299900 ATGGATTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.08, C:0.58, G:0.05, T:0.29
Consensus pattern (15 bp):
ATCCTCCTCCTCCCG
Found at i:313771 original size:19 final size:19
Alignment explanation
Indices: 313747--313863 Score: 61
Period size: 19 Copynumber: 6.5 Consensus size: 19
313737 AAATTTAGTT
313747 TTTATATTAATTACAATTC
1 TTTATATTAATTACAATTC
** *
313766 TTTATATTTTTTATAATTC
1 TTTATATTAATTACAATTC
* *
313785 -TTATATT-A-TA-ATTTG
1 TTTATATTAATTACAATTC
* * **
313800 TATATTATAAATTTGAA-T-
1 TTTA-TATTAATTACAATTC
313818 TTTATATTAATT-CAAATTC
1 TTTATATTAATTAC-AATTC
* *
313837 TTTATATTATTTATAATTC
1 TTTATATTAATTACAATTC
313856 -TTATATTA
1 TTTATATTA
313864 TAAATTTTAT
Statistics
Matches: 74, Mismatches: 15, Indels: 19
0.69 0.14 0.18
Matches are distributed among these distances:
15 3 0.04
16 4 0.05
17 12 0.16
18 20 0.27
19 34 0.46
20 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTATATTAATTACAATTC
Found at i:313814 original size:15 final size:14
Alignment explanation
Indices: 313776--313814 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
313766 TTTATATTTT
313776 TTATAATTCT-TATA
1 TTATAATT-TGTATA
313790 TTATAATTTGTATA
1 TTATAATTTGTATA
313804 TTATAAATTTG
1 TTAT-AATTTG
313815 AATTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 16 0.70
15 6 0.26
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (14 bp):
TTATAATTTGTATA
Found at i:313821 original size:71 final size:70
Alignment explanation
Indices: 313746--313879 Score: 218
Period size: 71 Copynumber: 1.9 Consensus size: 70
313736 TAAATTTAGT
*
313746 TTTTATATTAATT-ACAATTCTTTATATTTTTTATAATTCTTATATTAT-AATTTGTATATTATA
1 TTTTATATTAATTCA-AATTCTTTATATTATTTATAATTCTTATATTATAAATTT-TAT-TTATA
313809 AATTTGAA
63 AATTTGAA
313817 TTTTATATTAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTTTATTTATAA
1 TTTTATATTAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTTTATTTATAA
313880 TCATTAAATT
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
70 6 0.10
71 48 0.80
72 6 0.10
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (70 bp):
TTTTATATTAATTCAAATTCTTTATATTATTTATAATTCTTATATTATAAATTTTATTTATAAAT
TTGAA
Found at i:313863 original size:37 final size:36
Alignment explanation
Indices: 313748--313863 Score: 118
Period size: 37 Copynumber: 3.2 Consensus size: 36
313738 AATTTAGTTT
*
313748 TTATATTAATTACAATTCTTTATATTTTTTATAATTC
1 TTATATTAATTA-AATTCTTTATATTATTTATAATTC
*
313785 TTATATT-A-T-AATT-TGTATATTATAAATT-TGAATT-
1 TTATATTAATTAAATTCTTTATATTAT---TTAT-AATTC
313819 TTATATTAATTCAAATTCTTTATATTATTTATAATTC
1 TTATATTAATT-AAATTCTTTATATTATTTATAATTC
313856 TTATATTA
1 TTATATTA
313864 TAAATTTTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 22
0.72 0.03 0.24
Matches are distributed among these distances:
32 8 0.12
33 4 0.06
34 8 0.12
35 8 0.12
36 8 0.12
37 16 0.25
38 4 0.06
39 9 0.14
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (36 bp):
TTATATTAATTAAATTCTTTATATTATTTATAATTC
Found at i:313877 original size:13 final size:14
Alignment explanation
Indices: 313843--313879 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
313833 ATTCTTTATA
313843 TTATTTAT-AATTC
1 TTATTTATAAATTC
313856 TTATATTATAAATT-
1 TTAT-TTATAAATTC
313870 TTATTTATAA
1 TTATTTATAA
313880 TCATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:314495 original size:23 final size:23
Alignment explanation
Indices: 314469--314536 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
314459 ATCAATGTAC
314469 CAATTCAACAAGCATCATTGCAT
1 CAATTCAACAAGCATCATTGCAT
314492 CAATTCAACAAGCATCATTGCAT
1 CAATTCAACAAGCATCATTGCAT
*
314515 CAATTCAGCAAGCATC-TTGCAT
1 CAATTCAACAAGCATCATTGCAT
314537 TAAGAAAGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 6 0.14
23 38 0.86
ACGTcount: A:0.37, C:0.26, G:0.10, T:0.26
Consensus pattern (23 bp):
CAATTCAACAAGCATCATTGCAT
Found at i:314667 original size:24 final size:24
Alignment explanation
Indices: 314623--314672 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
314613 AACCCTTACA
* * *
314623 ATTCAAACATAAAGCCTACATTGG
1 ATTCAAAAATAAAACCTACATAGG
314647 ATTCAAAAATAAGAACC-ACATAGG
1 ATTCAAAAATAA-AACCTACATAGG
314671 AT
1 AT
314673 ATTGAGAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (24 bp):
ATTCAAAAATAAAACCTACATAGG
Found at i:316661 original size:15 final size:15
Alignment explanation
Indices: 316643--316715 Score: 50
Period size: 15 Copynumber: 5.2 Consensus size: 15
316633 TCTTATACAT
316643 ATAAAATTTATATTA
1 ATAAAATTTATATTA
316658 AT-AAA-TTAT-TT-
1 ATAAAATTTATATTA
*
316669 AT--AATTAATATTA
1 ATAAAATTTATATTA
* *
316682 ATATAATTAATATTA
1 ATAAAATTTATATTA
* *
316697 ATATTAACTTATATTA
1 ATA-AAATTTATATTA
316713 ATA
1 ATA
316716 TAATATAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
10 2 0.04
11 5 0.10
12 4 0.08
13 6 0.12
14 3 0.06
15 16 0.33
16 13 0.27
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAAAATTTATATTA
Found at i:316712 original size:16 final size:16
Alignment explanation
Indices: 316670--316750 Score: 78
Period size: 15 Copynumber: 5.0 Consensus size: 16
316660 AAATTATTTA
316670 TAATTAATATTAATA-
1 TAATTAATATTAATAT
316685 TAATTAATATTAATAT
1 TAATTAATATTAATAT
316701 TAACTT-ATATTAATA-
1 TAA-TTAATATTAATAT
* * *
316716 TAATATAGTTTATAATTT
1 TAAT-TAATAT-TAATAT
316734 GTAATTAATATTAATAT
1 -TAATTAATATTAATAT
316751 AAAATATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
14 1 0.02
15 19 0.36
16 14 0.26
17 11 0.21
18 4 0.08
19 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (16 bp):
TAATTAATATTAATAT
Found at i:316758 original size:29 final size:30
Alignment explanation
Indices: 316709--316868 Score: 98
Period size: 31 Copynumber: 5.3 Consensus size: 30
316699 ATTAACTTAT
*** *
316709 ATTAATA-TAATATAGTTTATAATTTGT-A
1 ATTAATATTAATATAAAATATAATTTATAA
316737 ATTAATATTAATATAAAATATAATTTATAA
1 ATTAATATTAATATAAAATATAATTTATAA
* *
316767 AGATAATATTAATATAAACTAT-ATGTTATAA
1 A-TTAATATTAATATAAAATATAAT-TTATAA
* * * *
316798 ATTATATAGTATAGTTTATAAACTATAGTTAATATA
1 ATTA-ATA-T-TA--ATATAAAATATAATTTATA-A
* *
316834 ATTAATATTAATAT--AGTATAGTTTATAA
1 ATTAATATTAATATAAAATATAATTTATAA
316862 A-TAATAT
1 ATTAATAT
316869 ACTATATTAA
Statistics
Matches: 108, Mismatches: 13, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
27 6 0.06
28 9 0.08
29 27 0.25
30 6 0.06
31 31 0.29
32 1 0.01
33 4 0.04
34 1 0.01
35 17 0.16
36 6 0.06
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (30 bp):
ATTAATATTAATATAAAATATAATTTATAA
Found at i:316810 original size:21 final size:20
Alignment explanation
Indices: 316786--316889 Score: 66
Period size: 21 Copynumber: 4.8 Consensus size: 20
316776 TAATATAAAC
316786 TATATGTTATAAATTATATAG
1 TATA-GTTATAAATTATATAG
* *
316807 TATAGTTTATAAACTATAGTTAA
1 TATAG-TTATAAATTATA--TAG
* *
316830 TATAATTA-ATATTAATATAG
1 TATAGTTATAAATT-ATATAG
* *
316850 TATAGTTTATAAATAATATAC
1 TATAG-TTATAAATTATATAG
*
316871 TATATTAATATAAATTATA
1 TATAGT--TATAAATTATA
316890 GTTAATATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
20 8 0.13
21 30 0.48
22 19 0.30
23 6 0.10
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (20 bp):
TATAGTTATAAATTATATAG
Found at i:316816 original size:14 final size:14
Alignment explanation
Indices: 316799--316860 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
316789 ATGTTATAAA
316799 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
316813 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
316827 TAATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
316842 TAATATAGTATAGT
1 TTATATAGTATAGT
316856 TTATA
1 TTATA
316861 AATAATATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.61
15 9 0.24
16 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:316846 original size:15 final size:15
Alignment explanation
Indices: 316826--316914 Score: 65
Period size: 15 Copynumber: 5.6 Consensus size: 15
316816 TAAACTATAG
316826 TTAATATAATTAATA
1 TTAATATAATTAATA
* *
316841 TTAATATAGTATAGT-
1 TTAATATAAT-TAATA
*
316856 TTATAAATAATATACTATA
1 TTA-ATATAAT-TA--ATA
316875 TTAATATAAATT-ATA
1 TTAATAT-AATTAATA
*
316890 GTTAATATAATTAACA
1 -TTAATATAATTAATA
316906 TTAATATAA
1 TTAATATAA
316915 ACTATATAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
15 28 0.47
16 20 0.34
18 5 0.08
19 6 0.10
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:316892 original size:65 final size:66
Alignment explanation
Indices: 316676--316914 Score: 228
Period size: 65 Copynumber: 3.7 Consensus size: 66
316666 TTTATAATTA
* *
316676 ATATTAATAT-AATTAATA-TTAATATTAACTT-ATATTAATATAATATAGTTTATAATTTGTA-
1 ATATTAATATAAATT-ATAGTTAATA-TAACTTAATATTAATATAATATAGTTTATAAATTATAT
*
316737 ATT
64 ACT
* * * **
316740 AATATTAATATAAAATATAATTTATA-AAGATAATATTAATATAAACTATA-TGTTATAAATTAT
1 -ATATTAATATAAATTATAGTTAATATAACTTAATATTAATAT-AA-TATAGT-TTATAAATTAT
*
316803 ATAGT
62 ATACT
* * *
316808 ATAGTT--TATAAACTATAGTTAATATAA-TTAATATTAATATAGTATAGTTTATAAATAATATA
1 ATA-TTAATATAAATTATAGTTAATATAACTTAATATTAATATAATATAGTTTATAAATTATATA
316870 CT
65 CT
*
316872 ATATTAATATAAATTATAGTTAATATAA-TTAACATTAATATAA
1 ATATTAATATAAATTATAGTTAATATAACTTAATATTAATATAA
316915 ACTATATAGT
Statistics
Matches: 145, Mismatches: 17, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
63 2 0.01
64 24 0.17
65 58 0.40
66 38 0.26
67 19 0.13
68 4 0.03
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (66 bp):
ATATTAATATAAATTATAGTTAATATAACTTAATATTAATATAATATAGTTTATAAATTATATAC
T
Found at i:316928 original size:22 final size:22
Alignment explanation
Indices: 316903--317005 Score: 83
Period size: 22 Copynumber: 4.8 Consensus size: 22
316893 AATATAATTA
316903 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
*
316925 ACATTAATATAAACTATAGT-TT
1 ACATTAATATAAACTATA-TAGT
*
316947 ACA--AAT-TATA-TATTATAGGT
1 ACATTAATATAAACTA-TATA-GT
* *
316967 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
316989 ACACTAATATAAACTAT
1 ACATTAATATAAACTAT
317006 TGTTTATAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
18 3 0.05
19 6 0.10
20 4 0.06
21 2 0.03
22 35 0.56
23 11 0.17
24 2 0.03
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:316984 original size:21 final size:21
Alignment explanation
Indices: 316932--316984 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
316922 AGTACATTAA
* *
316932 TATAAACTATAGTTTACAAAT
1 TATAAACTATAGGTTACAAAG
* * *
316953 TATATATTATAGGTTATAAAG
1 TATAAACTATAGGTTACAAAG
316974 TATAAACTATA
1 TATAAACTATA
316985 TAGTACACTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTACAAAG
Found at i:317078 original size:24 final size:24
Alignment explanation
Indices: 317037--317088 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
317027 ATATATAGTT
*
317037 TATATAGCATATAAATAGATTGTA
1 TATATAGCATATAAATAGATTATA
* *
317061 TATATA-CATATACTATAGGTTATA
1 TATATAGCATATA-AATAGATTATA
317085 TATA
1 TATA
317089 GTTCATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (24 bp):
TATATAGCATATAAATAGATTATA
Found at i:317193 original size:18 final size:18
Alignment explanation
Indices: 317172--317401 Score: 133
Period size: 18 Copynumber: 12.9 Consensus size: 18
317162 AATACATTAA
317172 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
317190 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
***
317208 TA-ATAAACTATATA-A-
1 TATATAGTTTATATATAC
*
317223 TATATAGTTTGTATATAC
1 TATATAGTTTATATATAC
* * *
317241 CATATACTATATAGGTTATA-
1 TATATAGTTTATA---TATAC
* ** *
317261 TATACTAATGAACTATATAA
1 TATA-TAGTTTA-TATATAC
*
317281 TATATAGTTTATACATAC
1 TATATAGTTTATATATAC
* *
317299 TA-AT-G--AACTATATAG
1 TATATAGTTTA-TATATAC
317314 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
317332 TA-AT-GAATTATATATAA
1 TATATAG-TTTATATATAC
317349 TGA-ATAGTTTATATATAC
1 T-ATATAGTTTATATATAC
* *
317367 CATATAGTCTATATATA-
1 TATATAGTTTATATATAC
317384 TCATATAGTTTATATATA
1 T-ATATAGTTTATATATA
317402 GTAATAAACT
Statistics
Matches: 160, Mismatches: 33, Indels: 38
0.69 0.14 0.16
Matches are distributed among these distances:
14 1 0.01
15 9 0.06
16 13 0.08
17 26 0.16
18 84 0.52
19 10 0.06
20 7 0.04
21 8 0.05
22 2 0.01
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:317203 original size:51 final size:52
Alignment explanation
Indices: 317147--317300 Score: 145
Period size: 51 Copynumber: 2.9 Consensus size: 52
317137 CTTTCAGTTA
* *
317147 ATATATATTTATATTAATAC-AT-TAATATATAGTTTATATATACTATATAGT
1 ATATATA-TTATAATAATACTATATAATATATAGTTTATATATACTATATACT
* * *
317198 TTATATA-TACTAATAA-ACTATATAATATATAGTTTGTATATACCATATACT
1 ATATATATTA-TAATAATACTATATAATATATAGTTTATATATACTATATACT
* *
317249 ATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATACATACTA
1 ATATA---TAT-TATAATAAT--ACTATATAATATATAGTTTATATATACTA
317301 ATGAACTATA
Statistics
Matches: 82, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
49 4 0.05
50 7 0.09
51 36 0.44
54 2 0.02
55 5 0.06
56 2 0.02
58 26 0.32
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (52 bp):
ATATATATTATAATAATACTATATAATATATAGTTTATATATACTATATACT
Found at i:317227 original size:33 final size:33
Alignment explanation
Indices: 317183--317428 Score: 242
Period size: 33 Copynumber: 7.5 Consensus size: 33
317173 ATATAGTTTA
*
317183 TATATACTATATAGTTTATATATACTAATAAAC
1 TATATAATATATAGTTTATATATACTAATAAAC
*
317216 TATATAATATATAGTTTGTATATAC-------C
1 TATATAATATATAGTTTATATATACTAATAAAC
* * *
317242 -ATATACTATATAGGTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATAAAC
* *
317274 TATATAATATATAGTTTATACATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATAAAC
*
317307 TATATAGTATATAGTTTATATATACTAATGAATTA-
1 TATATAATATATAGTTTATATATACTAAT-AA--AC
* **
317342 TATATAATGA-ATAGTTTATATATACCATATAGTC
1 TATATAAT-ATATAGTTTATATATACTA-ATAAAC
*
317376 TATATATATCATATAGTTTATATATAGTAATAAAC
1 TATATA-AT-ATATAGTTTATATATACTAATAAAC
*
317411 TATATAATGTATAGTTTA
1 TATATAATATATAGTTTA
317429 GGGTTTAGGG
Statistics
Matches: 176, Mismatches: 21, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
25 21 0.12
26 1 0.01
32 1 0.01
33 88 0.50
34 9 0.05
35 37 0.21
36 19 0.11
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATAAAC
Found at i:317351 original size:14 final size:15
Alignment explanation
Indices: 317325--317353 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
317315 ATATAGTTTA
317325 TATATACTAATGAAT
1 TATATACTAATGAAT
317340 TATATA-TAATGAAT
1 TATATACTAATGAAT
317354 AGTTTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (15 bp):
TATATACTAATGAAT
Found at i:317434 original size:7 final size:7
Alignment explanation
Indices: 317424--317457 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
317414 ATAATGTATA
317424 GTTTAGG
1 GTTTAGG
317431 GTTTAGG
1 GTTTAGG
**
317438 GTTTATA
1 GTTTAGG
317445 GTTTAGG
1 GTTTAGG
317452 GTTTAG
1 GTTTAG
317458 TATTTTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:317502 original size:23 final size:23
Alignment explanation
Indices: 317465--317575 Score: 70
Period size: 23 Copynumber: 4.7 Consensus size: 23
317455 TAGTATTTTT
*
317465 ATATATAGTTCATATGTAAATTATA
1 ATATATAG-T-ATATATAAATTATA
* **
317490 CTATATAGTATATATAGTTTATA
1 ATATATAGTATATATAAATTATA
317513 ATATATAG--TATATAAA-TATAA
1 ATATATAGTATATATAAATTAT-A
317534 ACTATAATATGTAGTATATAAA-TATA
1 A-TAT-ATA-GTA-TATATAAATTATA
*
317560 A-ACTATAGTTTATATA
1 ATA-TATAGTATATATA
317576 TATAGTATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
20 3 0.04
21 8 0.11
22 9 0.13
23 23 0.33
24 6 0.09
25 8 0.11
26 2 0.03
27 11 0.16
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (23 bp):
ATATATAGTATATATAAATTATA
Found at i:317539 original size:27 final size:27
Alignment explanation
Indices: 317509--317760 Score: 117
Period size: 27 Copynumber: 9.4 Consensus size: 27
317499 ATATATAGTT
317509 TATAATATATAGTATATAAATATAAAC
1 TATAATATATAGTATATAAATATAAAC
*
317536 TATAATATGTAGTATATAAATATAAAC
1 TATAATATATAGTATATAAATATAAAC
* * * *
317563 TATAGTTTATA-TATAT-AGTATATAC
1 TATAATATATAGTATATAAATATAAAC
* *
317588 TAT-ATAAATAGTGTATATAGTTCACTAATAAAC
1 TATAATATATA--GTATATA----AAT-ATAAAC
**
317621 TAT-ATATATAGTTCATATGTAAACTAT-AGT
1 TATAATATATAG-T-ATA--TAAA-TATAAAC
317651 TCAT-ATATATAGTATATAAATATAAAC
1 T-ATAATATATAGTATATAAATATAAAC
*
317678 TAT-A-CT-T--TATATAAATAGT--A-
1 TATAATATATAGTATATAAATA-TAAAC
*
317698 TA-AA-ATATAGTATATAAATATAAAT
1 TATAATATATAGTATATAAATATAAAC
* *
317723 TATAGTATGTAGTTTATATAAATATAAA-
1 TATAATATATAG--TATATAAATATAAAC
317751 TATAA-ATATA
1 TATAATATATA
317761 AACCCTAAAC
Statistics
Matches: 174, Mismatches: 23, Indels: 56
0.69 0.09 0.22
Matches are distributed among these distances:
20 4 0.02
21 2 0.01
22 11 0.06
23 11 0.06
24 6 0.03
25 13 0.07
26 12 0.07
27 54 0.31
28 4 0.02
29 17 0.10
30 3 0.02
31 14 0.08
32 4 0.02
33 17 0.10
35 2 0.01
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (27 bp):
TATAATATATAGTATATAAATATAAAC
Found at i:317668 original size:20 final size:20
Alignment explanation
Indices: 317563--317668 Score: 62
Period size: 18 Copynumber: 5.2 Consensus size: 20
317553 AAATATAAAC
*
317563 TATAGTTTATATATATAGTA
1 TATAGTTCATATATATAGTA
* *
317583 TATA-CT-ATATAAATAGTGTA
1 TATAGTTCATATATATA--GTA
317603 TATAGTTCACTAATAAACTATA-TA
1 TATAGTTCA-T-AT--A-TATAGTA
*
317627 TATAGTTCATATGTA-A--A
1 TATAGTTCATATATATAGTA
317644 CTATAGTTCATATATATAGTA
1 -TATAGTTCATATATATAGTA
317665 TATA
1 TATA
317669 AATATAAACT
Statistics
Matches: 67, Mismatches: 6, Indels: 26
0.68 0.06 0.26
Matches are distributed among these distances:
17 1 0.01
18 23 0.34
19 4 0.06
20 15 0.22
21 2 0.03
22 3 0.04
23 2 0.03
24 13 0.19
26 1 0.01
27 3 0.04
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (20 bp):
TATAGTTCATATATATAGTA
Found at i:317677 original size:33 final size:32
Alignment explanation
Indices: 317640--317706 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
317630 AGTTCATATG
* *
317640 TAAACTATAGTTCATATATATAGTATATAAATA
1 TAAACTATACTTCATATAAATAGTATA-AAATA
*
317673 TAAACTATACTTTATATAAATAGTATAAAATA
1 TAAACTATACTTCATATAAATAGTATAAAATA
317705 TA
1 TA
317707 GTATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (32 bp):
TAAACTATACTTCATATAAATAGTATAAAATA
Found at i:317681 original size:20 final size:20
Alignment explanation
Indices: 317657--317762 Score: 79
Period size: 20 Copynumber: 5.0 Consensus size: 20
317647 TAGTTCATAT
317657 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
* *
317677 CTATACTTTATATAAATAGTATAAA
1 ATATA--GTATAT-AA-A-TATAAA
317702 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
* * **
317722 TTATAGTATGTAGTTTATATAA
1 ATATAGTATATA-AATATA-AA
*
317744 ATATA-AATATAAATATAAA
1 ATATAGTATATAAATATAAA
317763 CCCTAAACCA
Statistics
Matches: 66, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
19 2 0.03
20 24 0.36
21 9 0.14
22 13 0.20
23 7 0.11
24 1 0.02
25 10 0.15
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:317701 original size:82 final size:83
Alignment explanation
Indices: 317558--317713 Score: 185
Period size: 82 Copynumber: 1.9 Consensus size: 83
317548 TATATAAATA
* * * ** *
317558 TAAACTATAGTTTATATATATAGTATATACTATATAAATAGTGTATATAGTTCACTAATAAACTA
1 TAAACTATAGTTCATATATATAGTATATAATATATAAATACTGTATATAAATCACTAATAAAATA
317623 TA-TATATAGTTCATATG
66 TAGTATATAGTTCATATG
* *
317640 TAAACTATAGTTCATATATATAGTATATAA-ATATAAACTATACTTTATATAAAT-AGT-ATAAA
1 TAAACTATAGTTCATATATATAGTATATAATATAT-AA--ATACTGTATATAAATCACTAATAAA
317702 ATATAGTATATA
63 ATATAGTATATA
317714 AATATAAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
81 4 0.06
82 39 0.63
83 8 0.13
84 11 0.18
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.40
Consensus pattern (83 bp):
TAAACTATAGTTCATATATATAGTATATAATATATAAATACTGTATATAAATCACTAATAAAATA
TAGTATATAGTTCATATG
Found at i:317709 original size:12 final size:13
Alignment explanation
Indices: 317670--317719 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
317660 TAGTATATAA
*
317670 ATATAAACTATACT
1 ATATAAA-TATAGT
*
317684 TTATATAA-ATAGT
1 ATATA-AATATAGT
317697 ATA-AAATATAGT
1 ATATAAATATAGT
317709 ATATAAATATA
1 ATATAAATATA
317720 AATTATAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
11 2 0.07
12 9 0.30
13 13 0.43
14 4 0.13
15 2 0.07
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:317718 original size:29 final size:29
Alignment explanation
Indices: 317686--317754 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
317676 ACTATACTTT
317686 ATATAAATAGTATAAAATATAG-TATATAA
1 ATATAAATA-TATAAAATATAGTTATATAA
** *
317715 ATATAAAT-TATAGTATGTAGTTTATATAA
1 ATATAAATATATAAAATATAG-TTATATAA
317744 ATATAAATATA
1 ATATAAATATA
317755 AATATAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
29 23 0.68
30 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
ATATAAATATATAAAATATAGTTATATAA
Found at i:317749 original size:6 final size:6
Alignment explanation
Indices: 317738--317762 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
317728 TATGTAGTTT
317738 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
317763 CCCTAAACCA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:317814 original size:22 final size:24
Alignment explanation
Indices: 317780--317829 Score: 86
Period size: 22 Copynumber: 2.2 Consensus size: 24
317770 CCATATGTAC
317780 TATATATATATAAACTATATAATT
1 TATATATATATAAACTATATAATT
317804 TATAT-TA-ATAAACTATATAATT
1 TATATATATATAAACTATATAATT
317826 TATA
1 TATA
317830 CAATATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 19 0.73
23 2 0.08
24 5 0.19
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
TATATATATATAAACTATATAATT
Found at i:317844 original size:22 final size:21
Alignment explanation
Indices: 317789--317852 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
317779 CTATATATAT
*
317789 ATAAACTATATAATTTATATTA
1 ATAAACTATATAATTTATA-CA
317811 ATAAACTATATAATTTATACA
1 ATAAACTATATAATTTATACA
* *
317832 ATATATTATTATAA-TTATACA
1 ATAAACTA-TATAATTTATACA
317853 TAATATATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.37
22 24 0.63
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAACTATATAATTTATACA
Found at i:317867 original size:23 final size:22
Alignment explanation
Indices: 317818--317868 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
317808 TTAATAAACT
*
317818 ATATAATTTATACAATATATTA
1 ATATAATTTATACAATATATAA
*
317840 TTATAA-TTATACATAATATATAA
1 ATATAATTTATAC--AATATATAA
317863 ATATAA
1 ATATAA
317869 ATTGTATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 6 0.25
22 5 0.21
23 13 0.54
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATAATTTATACAATATATAA
Found at i:317987 original size:27 final size:28
Alignment explanation
Indices: 317941--318001 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
317931 ATATATAAAC
* **
317941 TATATAGTATTATAGTTTATACATGGTA
1 TATATAGTATTATACTTTATACATAATA
317969 TATATAGT-TTATACTTTATACATAATA
1 TATATAGTATTATACTTTATACATAATA
317996 TATATA
1 TATATA
318002 TATAGTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (28 bp):
TATATAGTATTATACTTTATACATAATA
Found at i:318026 original size:15 final size:15
Alignment explanation
Indices: 317994--318029 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
317984 TTATACATAA
**
317994 TATATATATATAGTT
1 TATATATATATAAAT
318009 TATATATATATAAAT
1 TATATATATATAAAT
318024 TATATA
1 TATATA
318030 GTTTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TATATATATATAAAT
Found at i:318027 original size:24 final size:24
Alignment explanation
Indices: 317978--318057 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
317968 ATATATAGTT
* * *
317978 TATACTTTATACATAATATATATA
1 TATAGTTTATATATAATAAATATA
318002 TATAGTTTATATATATATAAAT-TA
1 TATAGTTTATATATA-ATAAATATA
*
318026 TATAGTTTATAT-TACATACATATA
1 TATAGTTTATATATA-ATAAATATA
318050 TATTAGTT
1 TA-TAGTT
318058 GTTTTAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.15
24 31 0.65
25 10 0.21
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (24 bp):
TATAGTTTATATATAATAAATATA
Found at i:318866 original size:216 final size:216
Alignment explanation
Indices: 318201--318876 Score: 1126
Period size: 214 Copynumber: 3.1 Consensus size: 216
318191 TTTTGTGTTG
* * *
318201 TTTATTTGTAATTTCATAATTATTCAATTTAGTCCTCTAAATTTTATTTGCACCTGAAATTGACC
1 TTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACC
*
318266 CATACTTATTACTT-TTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGTGTATAATTTAGTA
66 CATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTA
* *
318330 CTTTTTTGTATTAATTTCAACATTACAATTTAAAATTATTTCGCTTTGATCCCTCATCAATGTGT
131 CTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGT
* *
318395 GTTGTTTAATATATTTAATTT
196 GTTGTTTAATTTATTTAAATT
* *
318416 TTTATTTGTAGTTTCATATTTATTCAATTTAGTCCTCCAAATTTTATTTACATCTGAAATTGACC
1 TTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACC
* *
318481 CATATTTATTACTTATTTCCATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTA
66 CATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTA
*
318546 C--TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCACTCATCAATGTGT
131 CTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGT
*
318609 GTTGTATAATTTATTTAAATT
196 GTTGTTTAATTTATTTAAATT
* * *
318630 TTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGATC
1 TTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACC
*
318695 CATACTTATTACTTAATTCTAATTTTT-AATTGGCCCATAACTTTTTAAATGGGTATAATTTAGT
66 CATACTTATTACTTATTTCT-ATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGT
*
318759 ACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTG
130 ACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTG
318824 TGTTGTTTAATTTATTTAAATT
195 TGTTGTTTAATTTATTTAAATT
* *
318846 TTTATTTGTAATTCCATATTTGTTCAATTTA
1 TTTATTTGTAATTTCATATTTATTCAATTTA
318877 ATTCTTAAAT
Statistics
Matches: 431, Mismatches: 26, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
214 193 0.45
215 79 0.18
216 159 0.37
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.49
Consensus pattern (216 bp):
TTTATTTGTAATTTCATATTTATTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACC
CATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTA
CTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGT
GTTGTTTAATTTATTTAAATT
Found at i:320103 original size:15 final size:15
Alignment explanation
Indices: 320083--320113 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
320073 ATCAAAAATC
320083 GAATTAACGTCGCAT
1 GAATTAACGTCGCAT
*
320098 GAATTAACGTTGCAT
1 GAATTAACGTCGCAT
320113 G
1 G
320114 GGACATGCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (15 bp):
GAATTAACGTCGCAT
Found at i:320169 original size:29 final size:29
Alignment explanation
Indices: 320136--320236 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
320126 CCCAAAACAT
320136 AGGTCGCCATGTC-CTCCGGGCGACCAAGG
1 AGGTCGCCATG-CACTCCGGGCGACCAAGG
* *
320165 AGGTCACCATGCACTCCGGGTGACCAAGG
1 AGGTCGCCATGCACTCCGGGCGACCAAGG
* * *
320194 AGGTCGCCATGCACGCCAGGCGA-CATGG
1 AGGTCGCCATGCACTCCGGGCGACCAAGG
320222 TAGGTCGCCATGCAC
1 -AGGTCGCCATGCAC
320237 GCCCCGCGAC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
28 5 0.08
29 58 0.92
ACGTcount: A:0.21, C:0.33, G:0.33, T:0.14
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCGGGCGACCAAGG
Found at i:320309 original size:22 final size:22
Alignment explanation
Indices: 320263--320336 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
320253 TTTGGCCCTA
320263 CTCCCCGCTGCATGCTCG-CTG
1 CTCCCCGCTGCATGCTCGCCTG
320284 CTCCCCGCTGCATGCTCGCCTG
1 CTCCCCGCTGCATGCTCGCCTG
*
320306 CTCCCCACTGCATGCTCGCCTG
1 CTCCCCGCTGCATGCTCGCCTG
320328 CT-CCCGCTG
1 CTCCCCGCTG
320337 TTCCATGCAC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 24 0.48
22 26 0.52
ACGTcount: A:0.05, C:0.50, G:0.22, T:0.23
Consensus pattern (22 bp):
CTCCCCGCTGCATGCTCGCCTG
Found at i:320380 original size:25 final size:25
Alignment explanation
Indices: 320352--320432 Score: 116
Period size: 25 Copynumber: 3.4 Consensus size: 25
320342 TGCACCTTTA
320352 TTCGCTGCATTATTGCAGCATATTT
1 TTCGCTGCATTATTGCAGCATATTT
320377 TTCGCTGCATTATTGCAGCATATTT
1 TTCGCTGCATTATTGCAGCATATTT
*
320402 TTCGCTGC-TTCA-TGCAGCA-ATTA
1 TTCGCTGCATT-ATTGCAGCATATTT
320425 TT-GCTGCA
1 TTCGCTGCA
320433 ATCCACGAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
22 5 0.09
23 5 0.09
24 9 0.17
25 34 0.64
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (25 bp):
TTCGCTGCATTATTGCAGCATATTT
Found at i:320889 original size:30 final size:30
Alignment explanation
Indices: 320821--320926 Score: 133
Period size: 30 Copynumber: 3.5 Consensus size: 30
320811 TTTAGTTAAT
* *
320821 TAGTTTTTTAGTAGTGAA-TTATAATTAAAAAA
1 TAGTTTATTAGT--TGAAGTTAT-ATTAAAGAA
* * *
320853 TCGTTTATTAGTTTAAGTTCTATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
320883 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
320913 TAGTTTATTAGTTG
1 TAGTTTATTAGTTG
320927 TTTAAAGAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
30 52 0.80
31 3 0.05
32 10 0.15
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (30 bp):
TAGTTTATTAGTTGAAGTTATATTAAAGAA
Found at i:321007 original size:15 final size:16
Alignment explanation
Indices: 320979--321012 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
320969 GTTTGTTACT
320979 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
320995 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
321010 TTA
1 TTA
321013 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:323197 original size:60 final size:57
Alignment explanation
Indices: 323131--323643 Score: 338
Period size: 60 Copynumber: 9.2 Consensus size: 57
323121 AAACCTTAAC
323131 AAATCATTACTAAATCATTAAATATTAATAATAATTTCATTATTACTAATC---ATT
1 AAATCATTACTAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATT
* *
323185 -ACT-A-T-C-AAATCATTAAATATTATTAATAATTTCATTATTACTAATCATTATT
1 AAATCATTACTAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATT
* *
323237 AAATCATTACTATCAAATCATTAAATATTAATAATAATTCCATTATTACTAATCATTACT
1 AAATCATTAC--T-AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATT
* * * * * * * *
323297 AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATT-TAACCAAACATT
1 AAATCATTACTA-AA--TCATTA--A-ATAT-TAA-TAATA-AT--TTCATTATTACTAATCATT
*
323361 GTT
55 ATT
* ** * * * * *
323364 -CATTGTT-C-AAGTC-GTAAATCATTACT-ATCAA-ATCATTACTA--AATCA-T--T
1 AAATCATTACTAAATCATTAAAT-ATTAATAAT-AATTTCATTATTACTAATCATTATT
* *
323412 -AAT-A-T-CT-AATAATTAAATATTAATAATAAATT-ATTATTACTAATC---ATT
1 AAATCATTACTAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATT
*
323460 -ACT-A-T-C-AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATT
1 AAATCATTACTAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATT
* *
323512 AAATCATTAGTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTATT
1 AAATCATTA--CT-AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATT
* *
323572 AAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
1 AAATCATT-A-CT-AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATT
323632 AAATCATTACTA
1 AAATCATTACTA
323644 TCAAATCATT
Statistics
Matches: 363, Mismatches: 49, Indels: 91
0.72 0.10 0.18
Matches are distributed among these distances:
46 17 0.05
47 8 0.02
48 36 0.10
49 52 0.14
50 2 0.01
51 5 0.01
52 11 0.03
53 7 0.02
54 2 0.01
55 4 0.01
56 2 0.01
57 5 0.01
58 7 0.02
59 1 0.00
60 169 0.47
61 3 0.01
62 1 0.00
63 4 0.01
64 4 0.01
65 3 0.01
66 6 0.02
67 10 0.03
68 4 0.01
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (57 bp):
AAATCATTACTAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATT
Found at i:323201 original size:49 final size:46
Alignment explanation
Indices: 323132--323245 Score: 183
Period size: 49 Copynumber: 2.4 Consensus size: 46
323122 AACCTTAACA
*
323132 AATCATTACTAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTATTAAATCATTAAATATTAATAATAATTTCATTATTACT
*
323178 AATCATTACTATCAAATCATTAAATATTATTAATAATTTCATTATTACT
1 AATCATTA-T-T-AAATCATTAAATATTAATAATAATTTCATTATTACT
323227 AATCATTATTAAATCATTA
1 AATCATTATTAAATCATTA
323246 CTATCAAATC
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
46 17 0.27
47 1 0.02
48 2 0.03
49 43 0.68
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (46 bp):
AATCATTATTAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:323206 original size:21 final size:20
Alignment explanation
Indices: 323182--323266 Score: 61
Period size: 21 Copynumber: 4.2 Consensus size: 20
323172 ATTACTAATC
323182 ATTACTATCAAATCATTAAAT
1 ATTACTATC-AATCATTAAAT
* * *
323203 ATTA-T-T-AATAATTTCATT
1 ATTACTATCAATCA-TTAAAT
*
323221 ATTACTAATC-ATTATTAAAT
1 ATTACT-ATCAATCATTAAAT
323241 CATTACTATCAAATCATTAAAT
1 -ATTACTATC-AATCATTAAAT
323263 ATTA
1 ATTA
323267 ATAATAATTC
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
17 4 0.08
18 8 0.16
19 2 0.04
20 8 0.16
21 18 0.37
22 9 0.18
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTACTATCAATCATTAAAT
Found at i:323305 original size:21 final size:21
Alignment explanation
Indices: 323221--323305 Score: 54
Period size: 21 Copynumber: 4.2 Consensus size: 21
323211 TAATTTCATT
*
323221 ATTACTAATCATTATTAAATC
1 ATTACTAATCATTACTAAATC
* *
323242 ATTACT-ATCAAATCATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * *
323263 ATTAATAATAATT-C--CATT
1 ATTACTAATCATTACTAAATC
323281 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
323302 ATTA
1 ATTA
323306 TTATAATTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
17 2 0.04
18 11 0.23
19 1 0.02
20 5 0.11
21 17 0.36
22 11 0.23
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:323460 original size:48 final size:49
Alignment explanation
Indices: 323398--323509 Score: 172
Period size: 48 Copynumber: 2.3 Consensus size: 49
323388 CTATCAAATC
*
323398 ATTACTAAATCATTAATATCTAATAATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATAATTAAATATTAATAATAAATTCATT
* * *
323447 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATAATTAAATATTAATAATAAATTCATT
323496 ATTACTAATCATTA
1 ATTACTAATCATTA
323510 TTAAATCATT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 35 0.60
49 23 0.40
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATAATTAAATATTAATAATAAATTCATT
Found at i:323605 original size:120 final size:123
Alignment explanation
Indices: 323418--323720 Score: 400
Period size: 120 Copynumber: 2.4 Consensus size: 123
323408 CATTAATATC
* * * * *
323418 TAATAATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAAATCATTAAATATTAA
1 TAATAA-TAATTATTATTACTAAATCATTATTA-TAATCATTAATATCAAATCATTAAATATTAA
* *
323483 TAATAATTTCATTATTACTAATCATTATTAAATCATTAGTATCAAATCATTA-A-AAAT-
64 TAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTATATAAATA
323540 TAATAATAATTTCATTATTACT-AATCATTATTA-AATCATTAATATCAAATCATTAAATATTAA
1 TAATAATAA-TT-ATTATTACTAAATCATTATTATAATCATTAATATCAAATCATTAAATATTAA
323603 TAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTATTATTAAATCA
64 TAATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTA-TA-TAAAT-A
* * * * *
323666 TTATTATAATTATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TAATAATAATTATTATTACTAAATCATTATTATAATCATTAATATCAAATCATTA
323721 CTAAATCATC
Statistics
Matches: 159, Mismatches: 12, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
120 79 0.50
121 3 0.02
122 18 0.11
123 7 0.04
124 12 0.08
125 13 0.08
126 27 0.17
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.44
Consensus pattern (123 bp):
TAATAATAATTATTATTACTAAATCATTATTATAATCATTAATATCAAATCATTAAATATTAATA
ATAATTTCATTATTACTAATCATTACTAAATCATTACTATCAAATCATTATATAAATA
Found at i:323646 original size:60 final size:60
Alignment explanation
Indices: 323447--323654 Score: 364
Period size: 60 Copynumber: 3.5 Consensus size: 60
323437 ATAAATTATT
323447 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* * *
323506 ATTATTAAATCATTAGTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
323566 ATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
323626 ATTACTAAATCATTACTATCAAATCATTA
1 ATTACTAAATCATTACTATCAAATCATTA
323655 TTATTAAATC
Statistics
Matches: 141, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
59 5 0.04
60 136 0.96
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:323651 original size:14 final size:13
Alignment explanation
Indices: 323611--323844 Score: 155
Period size: 14 Copynumber: 17.5 Consensus size: 13
323601 AATAATAATT
323611 TCATTATTACT-AA
1 TCATTATTA-TAAA
*
323624 TCATTA--CTAAA
1 TCATTATTATAAA
*
323635 TCATTACTATCAAA
1 TCATTATTAT-AAA
323649 TCATTATTATTAAA
1 TCATTATTA-TAAA
323663 TCATTATTAT-AA
1 TCATTATTATAAA
*
323675 TTATTATTATTAAA
1 TCATTATTA-TAAA
323689 TCATTATTAT-AA
1 TCATTATTATAAA
*
323701 TGATTATTATCAAA
1 TCATTATTAT-AAA
323715 TCATTACTAAATCATCAAA
1 TCATTA-T---T-AT-AAA
*
323734 TCATTAAATATTTAAA
1 TCATT--AT-TATAAA
323750 TCATTA-T-TAAA
1 TCATTATTATAAA
323761 TCATTATTAT-AA
1 TCATTATTATAAA
* *
323773 TGATTATTACTTAA
1 TCATTATTA-TAAA
323787 TCATTATTAT-AA
1 TCATTATTATAAA
*
323799 TGATTATTATCAAA
1 TCATTATTAT-AAA
323813 TCATTATTAT-AA
1 TCATTATTATAAA
* *
323825 TAATTATTATCATA
1 TCATTATTAT-AAA
323839 TCATTA
1 TCATTA
323845 CTAAATCATC
Statistics
Matches: 182, Mismatches: 15, Indels: 47
0.75 0.06 0.19
Matches are distributed among these distances:
10 1 0.01
11 18 0.10
12 55 0.30
13 13 0.07
14 68 0.37
15 2 0.01
16 8 0.04
17 1 0.01
18 3 0.02
19 11 0.06
20 1 0.01
21 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.46
Consensus pattern (13 bp):
TCATTATTATAAA
Found at i:323686 original size:26 final size:26
Alignment explanation
Indices: 323626--323844 Score: 204
Period size: 26 Copynumber: 8.6 Consensus size: 26
323616 ATTACTAATC
* * *
323626 ATTACTAAATCATTACTATCAAATCATT
1 ATTATTAAATCATTATTAT--AATGATT
*
323654 ATTATTAAATCATTATTATAATTATT
1 ATTATTAAATCATTATTATAATGATT
323680 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
* * * *
323706 ATTATCAAATCATTACTA-AATCATCAA
1 ATTATTAAATCATTATTATAATGAT--T
* *
323733 ATCATT-AA--A-TATT-TAA--ATC
1 ATTATTAAATCATTATTATAATGATT
323752 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATGATT
323778 ATTACTT-AATCATTATTATAATGATT
1 ATTA-TTAAATCATTATTATAATGATT
* *
323804 ATTATCAAATCATTATTATAATAATT
1 ATTATTAAATCATTATTATAATGATT
* *
323830 ATTATCATATCATTA
1 ATTATTAAATCATTA
323845 CTAAATCATC
Statistics
Matches: 162, Mismatches: 17, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
19 5 0.03
20 2 0.01
21 2 0.01
22 1 0.01
23 9 0.06
24 4 0.02
25 6 0.04
26 110 0.68
27 6 0.04
28 17 0.10
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.46
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATGATT
Found at i:323805 original size:124 final size:123
Alignment explanation
Indices: 323622--323903 Score: 424
Period size: 124 Copynumber: 2.3 Consensus size: 123
323612 CATTATTACT
* * * *
323622 AATCATTACTAAATCATTACTATCAAATCATTATTATTAAATCATTATTATAATTATTATTATTA
1 AATCATTATTAAATCATTATTAT--AATCATTATTATTAAATCATTATTATAATGATTATTATCA
* *
323687 AATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTA
64 AATCATTATTATAATAATTATTATCAAATCATTACTAAATCATCAAATCATCAAATA-TTA
*
323748 AATCATTATTAAATCATTATTATAATGATTATTACTT-AATCATTATTATAATGATTATTATCAA
1 AATCATTATTAAATCATTATTATAATCATTATTA-TTAAATCATTATTATAATGATTATTATCAA
*
323812 ATCATTATTATAATAATTATTATCATATCATTACTAAATCATCAAATCATCAAATATTA
65 ATCATTATTATAATAATTATTATCAAATCATTACTAAATCATCAAATCATCAAATATTA
323871 AATTCATTATTAAATTCATTATTA-AATCATTAT
1 AA-TCATTATTAAA-TCATTATTATAATCATTAT
323904 AATGATTATT
Statistics
Matches: 144, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
123 5 0.03
124 107 0.74
125 11 0.08
126 21 0.15
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.44
Consensus pattern (123 bp):
AATCATTATTAAATCATTATTATAATCATTATTATTAAATCATTATTATAATGATTATTATCAAA
TCATTATTATAATAATTATTATCAAATCATTACTAAATCATCAAATCATCAAATATTA
Found at i:323883 original size:12 final size:12
Alignment explanation
Indices: 323866--323903 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
323856 AATCATCAAA
323866 TATTAAATTCAT
1 TATTAAATTCAT
323878 TATTAAATTCAT
1 TATTAAATTCAT
323890 TATTAAA-TCAT
1 TATTAAATTCAT
323901 TAT
1 TAT
323904 AATGATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:324119 original size:17 final size:18
Alignment explanation
Indices: 324099--324133 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
324089 TATTAGTAAA
324099 TCATTATCATT-ATAATT
1 TCATTATCATTAATAATT
*
324116 TCATTATTATTAATAATT
1 TCATTATCATTAATAATT
324134 ACTAATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (18 bp):
TCATTATCATTAATAATT
Found at i:328039 original size:21 final size:21
Alignment explanation
Indices: 328006--328054 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
327996 AATATAATAT
328006 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
328027 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
328048 ATTAACT
1 A-TAACT
328055 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:328434 original size:21 final size:21
Alignment explanation
Indices: 328409--328479 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
328399 ACGTTGCAAT
328409 CATGCAGCTATGGATGCAACG
1 CATGCAGCTATGGATGCAACG
* *
328430 CATGCAGCTACGGATGC-AGG
1 CATGCAGCTATGGATGCAACG
* *
328450 AATCTCCCAGCTATGGATGCAACG
1 CA--T-GCAGCTATGGATGCAACG
328474 CATGCA
1 CATGCA
328480 TGAGTGATAG
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.08
21 18 0.47
22 2 0.05
23 12 0.32
24 3 0.08
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (21 bp):
CATGCAGCTATGGATGCAACG
Found at i:328558 original size:17 final size:17
Alignment explanation
Indices: 328536--328569 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
328526 ATGGATGCAT
328536 GATGAGGGATAGGGTTA
1 GATGAGGGATAGGGTTA
328553 GATGAGGGATAGGGTTA
1 GATGAGGGATAGGGTTA
328570 AAGTTTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (17 bp):
GATGAGGGATAGGGTTA
Found at i:328738 original size:29 final size:29
Alignment explanation
Indices: 328705--328859 Score: 123
Period size: 29 Copynumber: 5.3 Consensus size: 29
328695 GCAGCTCCCG
328705 CTCCTTGGTC-TCCCCGAGTGCATGGCGAC
1 CTCCTTGGTCGT-CCCGAGTGCATGGCGAC
*** *
328734 CTCCTTGGTCGTTGGGCGTGCATGGCGAC
1 CTCCTTGGTCGTCCCGAGTGCATGGCGAC
*** *
328763 CTCCTTGGTCGTTAGGCGTGCATGGCGAC
1 CTCCTTGGTCGTCCCGAGTGCATGGCGAC
* *** *
328792 CTCTTTGGTCGTTGGGCGTGCATGGCGAC
1 CTCCTTGGTCGTCCCGAGTGCATGGCGAC
* *** *
328821 CTCTTTGGTCGTTGGGCGTGCATGGCGAC
1 CTCCTTGGTCGTCCCGAGTGCATGGCGAC
*
328850 CTCTTTGGTC
1 CTCCTTGGTC
328860 ACTGTAGAAT
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
29 117 0.99
30 1 0.01
ACGTcount: A:0.08, C:0.28, G:0.34, T:0.30
Consensus pattern (29 bp):
CTCCTTGGTCGTCCCGAGTGCATGGCGAC
Found at i:328800 original size:58 final size:58
Alignment explanation
Indices: 328722--328859 Score: 249
Period size: 58 Copynumber: 2.4 Consensus size: 58
328712 GTCTCCCCGA
*
328722 GTGCATGGCGACCTCCTTGGTCGTTGGGCGTGCATGGCGACCTCCTTGGTCGTTAGGC
1 GTGCATGGCGACCTCTTTGGTCGTTGGGCGTGCATGGCGACCTCCTTGGTCGTTAGGC
* *
328780 GTGCATGGCGACCTCTTTGGTCGTTGGGCGTGCATGGCGACCTCTTTGGTCGTTGGGC
1 GTGCATGGCGACCTCTTTGGTCGTTGGGCGTGCATGGCGACCTCCTTGGTCGTTAGGC
328838 GTGCATGGCGACCTCTTTGGTC
1 GTGCATGGCGACCTCTTTGGTC
328860 ACTGTAGAAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 77 1.00
ACGTcount: A:0.08, C:0.26, G:0.36, T:0.30
Consensus pattern (58 bp):
GTGCATGGCGACCTCTTTGGTCGTTGGGCGTGCATGGCGACCTCCTTGGTCGTTAGGC
Found at i:329826 original size:3 final size:3
Alignment explanation
Indices: 329820--329918 Score: 80
Period size: 3 Copynumber: 32.3 Consensus size: 3
329810 AATAAACCAT
*
329820 ATA ATA ACA ACTA ATA ATA A-A A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
329864 ATTT ATA A-A ATA ATA TATA ATA ATA AGTAA ATA ATA GAT- ATA TTA
1 A-TA ATA ATA ATA ATA -ATA ATA ATA A-T-A ATA ATA -ATA ATA ATA
*
329909 TTA ATA ATA A
1 ATA ATA ATA A
329919 GAAAATAAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
2 8 0.10
3 60 0.74
4 11 0.14
5 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:329838 original size:13 final size:12
Alignment explanation
Indices: 329807--329864 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
329797 TCCATATAAA
*
329807 AATAATAAACCAT
1 AATAATAAA-AAT
*
329820 -ATAATAACAACT
1 AATAATAA-AAAT
329832 AATAATAAAAAAT
1 AATAAT-AAAAAT
*
329845 AATAATAATAAT
1 AATAATAAAAAT
329857 AATAATAA
1 AATAATAA
329865 TTTATAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 21 0.55
13 15 0.39
14 2 0.05
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAATAAAAAT
Found at i:329838 original size:25 final size:25
Alignment explanation
Indices: 329807--329936 Score: 77
Period size: 25 Copynumber: 5.0 Consensus size: 25
329797 TCCATATAAA
**
329807 AATAATAAACCAT-ATAATAACAACT
1 AATAATAAAAAATAATAATAACAA-T
*
329832 AATAATAAAAAATAATAATAATAAT
1 AATAATAAAAAATAATAATAACAAT
*** *
329857 AATAATAATTTATAA-AATAATATAT
1 AATAATAAAAAATAATAATAACA-AT
* * *
329882 AATAATAAGTAAATAATAGATATATTATT
1 AATAATAA-AAAATAATA-ATA-A-CAAT
329911 AATAATAAGAAAATAA-ATATAACAAT
1 AATAATAA-AAAATAATA-ATAACAAT
329937 GGAAATATTA
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
24 7 0.08
25 34 0.40
26 16 0.19
27 2 0.02
28 7 0.08
29 17 0.20
30 2 0.02
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (25 bp):
AATAATAAAAAATAATAATAACAAT
Found at i:329930 original size:51 final size:50
Alignment explanation
Indices: 329831--329932 Score: 120
Period size: 51 Copynumber: 2.1 Consensus size: 50
329821 TAATAACAAC
* *
329831 TAATAATAAAAAATAATAATAATAATAATAATAATTTATAAAATAATATA
1 TAATAATAAAAAATAATAATAATAATAATAATAATTAAGAAAATAATATA
* * *
329881 TAATAATAAGTAAATAATAGAT-ATATTATTAATAA-TAAGAAAATAA-ATA
1 TAATAATAA-AAAATAATA-ATAATAATAATAATAATTAAGAAAATAATATA
329930 TAA
1 TAA
329933 CAATGGAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
49 6 0.13
50 18 0.40
51 19 0.42
52 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (50 bp):
TAATAATAAAAAATAATAATAATAATAATAATAATTAAGAAAATAATATA
Found at i:330021 original size:19 final size:19
Alignment explanation
Indices: 329997--330033 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
329987 ACTAATGGTA
329997 ATATA-TAATAATGAATATT
1 ATATATTAATAAT-AATATT
330016 ATATATTAATAATAATAT
1 ATATATTAATAATAATAT
330034 CCTAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
ATATATTAATAATAATATT
Found at i:333245 original size:108 final size:108
Alignment explanation
Indices: 333092--333308 Score: 416
Period size: 108 Copynumber: 2.0 Consensus size: 108
333082 TGAACATGCA
333092 ACCAATTGGTCATGCAATCGATCCTAGGGTTTATGAACATGTTTGGATAGACTTGATCCACTTAG
1 ACCAATTGGTCATGCAATCGATCCTAGGGTTTATGAACATGTTTGGATAGACTTGATCCACTTAG
*
333157 AACATGTCAAAACACATATGCTACCTGCTTTATGATATCAATT
66 AACATGTCAAAACACATATGCTACCTGCTTTATGACATCAATT
333200 ACCAATTGGTCATGCAATCGATCCTAGGGTTTATGAACATGTTTGGATAGACTTGATCCACTTAG
1 ACCAATTGGTCATGCAATCGATCCTAGGGTTTATGAACATGTTTGGATAGACTTGATCCACTTAG
*
333265 AACATGTCAACACACATATGCTACCTGCTTTATGACATCAATT
66 AACATGTCAAAACACATATGCTACCTGCTTTATGACATCAATT
333308 A
1 A
333309 AACAAATCAA
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (108 bp):
ACCAATTGGTCATGCAATCGATCCTAGGGTTTATGAACATGTTTGGATAGACTTGATCCACTTAG
AACATGTCAAAACACATATGCTACCTGCTTTATGACATCAATT
Found at i:336108 original size:47 final size:48
Alignment explanation
Indices: 336016--336282 Score: 178
Period size: 48 Copynumber: 5.6 Consensus size: 48
336006 GGAGTTCATA
* * **
336016 AATCATCAACTTTCCTAGATTT-ATCCCTCATGAA-GAGACTTTGGAATG
1 AATCATCATCTTTCC-AGATTTGAT-CTTCATGAAGGAGACAGTGGAATG
* *
336064 AATCATCATC-TTCCAAGATTTGATCTTCAT-AAGGAGATAGTGGAATA
1 AATCATCATCTTTCC-AGATTTGATCTTCATGAAGGAGACAGTGGAATG
* ** * ***
336111 AATCATCGA-CATTCCTAGATTCAATCTTCATGAAGG-GACAGTAGAGCA
1 AATCATC-ATCTTTCC-AGATTTGATCTTCATGAAGGAGACAGTGGAATG
* * * *
336159 AATCAACATCTTTCCAAATTCGATCTTCAT-AAAGAGACAGTGG-A-G
1 AATCATCATCTTTCCAGATTTGATCTTCATGAAGGAGACAGTGGAATG
* * * *
336204 CAAGTCATCAACTTTTCCATATTT-ATCCTTCATGAA-GAGATAGTGGAAAG
1 -AA-TCATCATC-TTTCCAGATTTGAT-CTTCATGAAGGAGACAGTGGAATG
*
336254 AATCTTCATCTTTCCAGATTTGATCTTCA
1 AATCATCATCTTTCCAGATTTGATCTTCA
336283 CAAGAGAAAC
Statistics
Matches: 174, Mismatches: 30, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
46 7 0.04
47 77 0.44
48 80 0.46
49 9 0.05
50 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (48 bp):
AATCATCATCTTTCCAGATTTGATCTTCATGAAGGAGACAGTGGAATG
Found at i:336235 original size:95 final size:94
Alignment explanation
Indices: 336136--336314 Score: 216
Period size: 95 Copynumber: 1.9 Consensus size: 94
336126 TAGATTCAAT
* * * *
336136 CTTCATGAAGGGACAGTAGAGCA-AATCAACATCTTTCCAAATTCGATCTTCATAAAGAGACAGT
1 CTTCATGAAGAGACAGTAGA-AAGAATCAACATCTTTCCAAATTCGATCTTCA-AAAGAGAAACT
* *
336200 GGAGCAAGTCATCAACTTTTCCATATTTATC
64 AGAGCAAGTCATCAACGTTTCCATATTTATC
* * ** * * *
336231 CTTCATGAAGAGATAGTGGAAAGAATCTTCATCTTTCCAGATTTGATCTTCACAAGAGAAACTAG
1 CTTCATGAAGAGACAGTAGAAAGAATCAACATCTTTCCAAATTCGATCTTCAAAAGAGAAACTAG
336296 AGCAAGTCATCAACGTTTC
66 AGCAAGTCATCAACGTTTC
336315 TAGATCCATC
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
94 28 0.40
95 42 0.60
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (94 bp):
CTTCATGAAGAGACAGTAGAAAGAATCAACATCTTTCCAAATTCGATCTTCAAAAGAGAAACTAG
AGCAAGTCATCAACGTTTCCATATTTATC
Found at i:336886 original size:67 final size:66
Alignment explanation
Indices: 336754--336883 Score: 206
Period size: 66 Copynumber: 1.9 Consensus size: 66
336744 TCAAATAGGC
*
336754 ATTATGGTCTTGTGAAGACTCCAAAGCTCCATATCCAACAGATTCAACATTCACTTTAAAAAATG
1 ATTATGGTCTTGTGAAGACTCAAAAGCTCCATATCCAACAGATTCAACATTCACTTTAAAAAATG
336819 T
66 T
* * *
336820 ATTATGGTCTTGTGATGAGTCAAAAGCTCCATGTCCTAACAGATTCAACATTCACTTATAAAAA
1 ATTATGGTCTTGTGAAGACTCAAAAGCTCCATATCC-AACAGATTCAACATTCACTT-TAAAAA
336884 TGTTGGGGGC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 32 0.55
67 20 0.34
68 6 0.10
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (66 bp):
ATTATGGTCTTGTGAAGACTCAAAAGCTCCATATCCAACAGATTCAACATTCACTTTAAAAAATG
T
Found at i:340795 original size:2 final size:2
Alignment explanation
Indices: 340790--340814 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
340780 TTTTTTAAGA
340790 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
340815 AAAGGTTGAA
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:343231 original size:31 final size:31
Alignment explanation
Indices: 343196--343257 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
343186 TATGATGGAA
343196 GTATGATTTAATTTTATATCAATTGAATTAT
1 GTATGATTTAATTTTATATCAATTGAATTAT
343227 GTATGATTTAATTTTATATCAATTGAATTAT
1 GTATGATTTAATTTTATATCAATTGAATTAT
343258 CAATTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (31 bp):
GTATGATTTAATTTTATATCAATTGAATTAT
Found at i:343274 original size:15 final size:16
Alignment explanation
Indices: 343254--343287 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
343244 ATCAATTGAA
*
343254 TTATC-AATTTTATTT
1 TTATCAAATTTTATAT
343269 TTATCAAATTTTATAT
1 TTATCAAATTTTATAT
343285 TTA
1 TTA
343288 AGTTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATCAAATTTTATAT
Found at i:344348 original size:18 final size:17
Alignment explanation
Indices: 344325--344367 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
344315 ATGTTTATAG
*
344325 TTATCAATCATTTTTCAA
1 TTATCAAT-ATTTTACAA
*
344343 TTATCAGATGTTTTACAA
1 TTATCA-ATATTTTACAA
344361 TTATCAA
1 TTATCAA
344368 ACGTAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 19 0.86
19 2 0.09
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.47
Consensus pattern (17 bp):
TTATCAATATTTTACAA
Found at i:360264 original size:18 final size:16
Alignment explanation
Indices: 360241--360298 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 16
360231 CTTTCATGTC
360241 TTTTTTTCTTTCGAACAG
1 TTTTTTT-TTTCGAAC-G
360259 TTTTTTTTTTCGAACTG
1 TTTTTTTTTTCGAAC-G
360276 CTATTTTTTTTTC-AACG
1 -T-TTTTTTTTTCGAACG
360293 TTTTTT
1 TTTTTT
360299 GTGATGGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 5 0.14
16 1 0.03
17 10 0.27
18 11 0.30
19 10 0.27
ACGTcount: A:0.14, C:0.14, G:0.09, T:0.64
Consensus pattern (16 bp):
TTTTTTTTTTCGAACG
Found at i:362492 original size:13 final size:13
Alignment explanation
Indices: 362474--362499 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
362464 CCTAGTCGAA
362474 AAAAATAAAAATT
1 AAAAATAAAAATT
362487 AAAAATAAAAATT
1 AAAAATAAAAATT
362500 TAACGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATAAAAATT
Found at i:374311 original size:16 final size:16
Alignment explanation
Indices: 374290--374330 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
374280 TCGGCGATGA
374290 GGAGAAAATATTTAAG
1 GGAGAAAATATTTAAG
374306 GGAGAAAATATTTAAG
1 GGAGAAAATATTTAAG
*
374322 GGAAAAAAT
1 GGAGAAAAT
374331 TGAAGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (16 bp):
GGAGAAAATATTTAAG
Found at i:379122 original size:20 final size:21
Alignment explanation
Indices: 379084--379122 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
379074 CATCAAAGTC
*
379084 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCATGAAATCT
379105 TTTGTCGAAGCCAT-AAAT
1 TTTGTCGAAGCCATGAAAT
379123 TCCTGCATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (21 bp):
TTTGTCGAAGCCATGAAATCT
Found at i:380762 original size:16 final size:16
Alignment explanation
Indices: 380737--380774 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
380727 AAAATATTAT
380737 AAAGTATGGTTGTA-GA
1 AAAGTATGGTTG-AGGA
*
380753 AAAGTTTGGTTGAGGA
1 AAAGTATGGTTGAGGA
380769 AAAGTA
1 AAAGTA
380775 AATATGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (16 bp):
AAAGTATGGTTGAGGA
Found at i:384197 original size:19 final size:19
Alignment explanation
Indices: 384173--384220 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
384163 GTCAGACCAG
* *
384173 TCAACGGGTCTGGTTAAAA
1 TCAACGGGTCAGATTAAAA
*
384192 TCAACGGGTCAGATTAAAG
1 TCAACGGGTCAGATTAAAA
384211 TCAACGGGTC
1 TCAACGGGTC
384221 GGGTCGGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (19 bp):
TCAACGGGTCAGATTAAAA
Found at i:384257 original size:20 final size:20
Alignment explanation
Indices: 384224--384272 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
384214 ACGGGTCGGG
384224 TCGGGTC-AGTTTGACACGAT
1 TCGGGTCAAG-TTGACACGAT
* * *
384244 TCGTGTCAAGTTGACTCGGT
1 TCGGGTCAAGTTGACACGAT
384264 TCGGGTCAA
1 TCGGGTCAA
384273 ATAAACCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (20 bp):
TCGGGTCAAGTTGACACGAT
Found at i:386066 original size:38 final size:38
Alignment explanation
Indices: 386023--386099 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
386013 ATATAAAAGT
* * *
386023 AAGAATCTAATTGTATGATTGAAAACAGTAATAAATAA
1 AAGAATCTAATTGTAAGATTAAAAACAATAATAAATAA
*
386061 AAGAATCTAATTGTAAGATTAAAAATAATAATAAATAA
1 AAGAATCTAATTGTAAGATTAAAAACAATAATAAATAA
386099 A
1 A
386100 GTTTACTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.57, C:0.04, G:0.10, T:0.29
Consensus pattern (38 bp):
AAGAATCTAATTGTAAGATTAAAAACAATAATAAATAA
Found at i:387682 original size:27 final size:27
Alignment explanation
Indices: 387652--387717 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
387642 TTTTTTTACC
387652 TCAATGTTCATACCATCATATCATACT
1 TCAATGTTCATACCATCATATCATACT
387679 TCAATGTTCATACCATCATATCATACT
1 TCAATGTTCATACCATCATATCATACT
387706 TCAATGTTCATA
1 TCAATGTTCATA
387718 TAATGCAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (27 bp):
TCAATGTTCATACCATCATATCATACT
Found at i:387691 original size:14 final size:14
Alignment explanation
Indices: 387672--387717 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
387662 TACCATCATA
387672 TCATACTTCAATGT
1 TCATACTTCAATGT
* *
387686 TCATACCATC-AT-A
1 TCATA-CTTCAATGT
387699 TCATACTTCAATGT
1 TCATACTTCAATGT
387713 TCATA
1 TCATA
387718 TAATGCAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
12 3 0.12
13 7 0.28
14 12 0.48
15 3 0.12
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (14 bp):
TCATACTTCAATGT
Found at i:388306 original size:12 final size:13
Alignment explanation
Indices: 388275--388300 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
388265 ACATTCATAT
388275 ATACACTTTCAAA
1 ATACACTTTCAAA
388288 ATACACTTTCAAA
1 ATACACTTTCAAA
388301 TCCACTATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
ATACACTTTCAAA
Found at i:389559 original size:19 final size:19
Alignment explanation
Indices: 389524--389561 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
389514 ATTATATTAC
389524 TATTAAAAATAATATTTAA
1 TATTAAAAATAATATTTAA
*
389543 TATTATAAA-AATCATTTAA
1 TATTAAAAATAAT-ATTTAA
389562 ACACTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTAAAAATAATATTTAA
Found at i:390129 original size:27 final size:27
Alignment explanation
Indices: 390072--390141 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
390062 GGCTTTGTGG
* *
390072 ACATTTTTGAACACAATGACACTTTAT
1 ACATTTTAGAACACAATGACACTTTAA
* *
390099 ACATTTTAGGACACAATGAC-TTTTCAA
1 ACATTTTAGAACACAATGACACTTT-AA
*
390126 ACATTTTAGCACACAA
1 ACATTTTAGAACACAA
390142 GAAAGTTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 3 0.08
27 34 0.92
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (27 bp):
ACATTTTAGAACACAATGACACTTTAA
Found at i:392348 original size:18 final size:17
Alignment explanation
Indices: 392316--392361 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
392306 AATTAATGGA
392316 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
392333 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
392351 GAATAAAAAAA
1 G--TAAAAAAA
392362 ATGTGTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 6 0.24
18 11 0.44
19 3 0.12
20 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:392496 original size:16 final size:17
Alignment explanation
Indices: 392462--392523 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
392452 TGATATTAAG
392462 AAAA-AAAATAATAGAA
1 AAAATAAAATAATAGAA
392478 AAAATAAAATAA-AGTAA
1 AAAATAAAATAATAG-AA
* *
392495 AAATATAATATATATATAA
1 AAA-ATAAAATA-ATAGAA
392514 ATAAATAAAA
1 A-AAATAAAA
392524 ACAAAAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 6 0.16
17 12 0.32
18 7 0.19
19 9 0.24
20 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAATAAAATAATAGAA
Found at i:392548 original size:32 final size:36
Alignment explanation
Indices: 392518--392591 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
392508 ATATAAATAA
392518 ATAAAAA-CA-AAAATAGAATATTAAGAAAATATAT
1 ATAAAAAGCATAAAATAGAATATTAAGAAAATATAT
* * *
392552 ATAAAAATGTATAAAATATAATATTAAGAAAAAATAT
1 ATAAAAA-GCATAAAATAGAATATTAAGAAAATATAT
392589 ATA
1 ATA
392592 CATAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 7 0.21
36 1 0.03
37 26 0.76
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.27
Consensus pattern (36 bp):
ATAAAAAGCATAAAATAGAATATTAAGAAAATATAT
Found at i:392676 original size:19 final size:18
Alignment explanation
Indices: 392640--392689 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
392630 ATATATATAT
* *
392640 ATATATATAATGATATAA
1 ATATATATAATAAAATAA
392658 GATATATATAATAAAATAA
1 -ATATATATAATAAAATAA
*
392677 AAATAATATAATA
1 ATAT-ATATAATA
392690 TAAAAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 3 0.11
19 24 0.89
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (18 bp):
ATATATATAATAAAATAA
Found at i:392692 original size:16 final size:16
Alignment explanation
Indices: 392665--392748 Score: 56
Period size: 16 Copynumber: 5.5 Consensus size: 16
392655 TAAGATATAT
392665 ATAATA-AA-ATAAAA
1 ATAATATAATATAAAA
392679 ATAATATAATATAAAA
1 ATAATATAATATAAAA
* * *
392695 A-AAGAGGAATATAGTAA
1 ATAATA-TAATATA-AAA
*
392712 ATAA-ATAA-ATAAAT
1 ATAATATAATATAAAA
392726 A-AATATAAT-TAAAA
1 ATAATATAATATAAAA
392740 ATATATATA
1 ATA-ATATA
392749 TAGGGGACGA
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
13 2 0.04
14 17 0.31
15 9 0.17
16 20 0.37
17 4 0.07
18 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
ATAATATAATATAAAA
Found at i:394023 original size:33 final size:34
Alignment explanation
Indices: 393953--394035 Score: 150
Period size: 34 Copynumber: 2.5 Consensus size: 34
393943 CGAGGGTTTG
*
393953 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
393987 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
394020 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
394036 TGTATTCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 22 0.46
34 26 0.54
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (34 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
Found at i:394044 original size:34 final size:33
Alignment explanation
Indices: 393953--394046 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 33
393943 CGAGGGTTTG
393953 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTT
1 GTGTTTCAAGAGAAAC-TTTTCAAAGGTTTTTTT
*
393987 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTT
1 GTGTTTCAAGAGAAAC-TTTTCAAAGGTTTTTTT
394020 GTGTTTCAAGAGAAACTGTATTCAAAG
1 GTGTTTCAAGAGAAACT-T-TTCAAAG
394047 ATTGAAGTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
33 23 0.41
34 33 0.59
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (33 bp):
GTGTTTCAAGAGAAACTTTTCAAAGGTTTTTTT
Done.