Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009070.1 Hibiscus syriacus cultivar Beakdansim tig00112498_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: 2268343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:1872 original size:24 final size:24
Alignment explanation
Indices: 1838--1884 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1828 CTGAAACATC
1838 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1862 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1885 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2589 original size:20 final size:20
Alignment explanation
Indices: 2561--2928 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
2551 AAATTTCAGT
* * * *
2561 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2581 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2601 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2621 GTTGCGA-TTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2640 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2660 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2680 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2700 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2720 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2740 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
2760 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2780 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2800 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2820 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2840 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2860 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2880 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2900 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2920 GTTGCGATT
1 GTTGCGATT
2929 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 32, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
19 20 0.07
20 283 0.92
21 4 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:3438 original size:25 final size:24
Alignment explanation
Indices: 3408--3454 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3398 TTCTCAAATA
*
3408 TTAAAATAATTTTAAATATATTATT
1 TTAAAATAACTTTAAAT-TATTATT
*
3433 TTAAAATCACTTTAAATTATTA
1 TTAAAATAACTTTAAATTATTA
3455 AAAAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAAAATAACTTTAAATTATTATT
Found at i:5017 original size:2 final size:2
Alignment explanation
Indices: 5010--5034 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5000 CAAATCTCGT
5010 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
5035 GTATGTATGT
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:10976 original size:17 final size:17
Alignment explanation
Indices: 10956--11016 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
10946 TTCCTGTATC
10956 GTTCCTTTTACTGTACT
1 GTTCCTTTTACTGTACT
* *
10973 GTTCATTTTTCTGTACT
1 GTTCCTTTTACTGTACT
10990 GATT--TATTTACTGTACCT
1 G-TTCCT-TTTACTGTA-CT
11008 -TTCCTTTTA
1 GTTCCTTTTA
11017 TTACAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 3 0.08
17 28 0.78
18 5 0.14
ACGTcount: A:0.15, C:0.20, G:0.10, T:0.56
Consensus pattern (17 bp):
GTTCCTTTTACTGTACT
Found at i:10998 original size:18 final size:17
Alignment explanation
Indices: 10956--11005 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
10946 TTCCTGTATC
*
10956 GTTCCTTTTACTGTACT
1 GTTCATTTTACTGTACT
*
10973 GTTCATTTTTCTGTACT
1 GTTCATTTTACTGTACT
*
10990 GATTTA-TTTACTGTAC
1 G-TTCATTTTACTGTAC
11006 CTTTCCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 25 0.89
18 3 0.11
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.54
Consensus pattern (17 bp):
GTTCATTTTACTGTACT
Found at i:11019 original size:333 final size:330
Alignment explanation
Indices: 10416--11046 Score: 1005
Period size: 333 Copynumber: 1.9 Consensus size: 330
10406 TAATACTATA
10416 CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAGTTATTTGGTTGTTATCTAC
1 CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAGTTATTTGGTTGTTATCTAC
* * * * * **
10481 CGTCACACGACCTCCCACTGATTTACACTATGTTTATAATATTTATTGTAAAATGCATTTTTAAA
66 CGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTACTGTAAAATGAATAATTAAA
* * *
10546 CTTATACAGTTTTTTATCATATACTTACTCTTTTTACTGTACTAATCTTTTCACTATATTATTCT
131 CTTATACAGTTCTTTATCATATACTTACTATTTTTACTGTACTAATATTTTCACTATATTATTCT
**
10611 TTTTCCTATATCGTTCCTTTCACTGTACTGTTTCTTTTTCTATACTGATTTATTTACTGTTTCTT
196 TTTTCCTATATCGTTCCTTTCACTGTACTGTTTCTTTTTCTATACTGATTTATTTACTGTACCTT
* *
10676 TCCTTTTATTACACTATTTCTCTTATTGTATTATATCTTTTACTGTTATGTATCTGACGTTGTAC
261 TCCTTTTATTACAATATTTCTCTTATTATATTATATCTTTTACTGTTATGTATCTGACGTTGTAC
10741 TATTT
326 TATTT
* * *
10746 CATAAAATATATGTAACATCTATAATCAGATTTATTCTAAAACATGTTTATTTGGTTGTTGTCTA
1 CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAG-TTATTTGGTTGTTATCTA
10811 CCGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTTACTGTAAAATGTAATAATT
65 CCGCCACACGACCTCCCACTAATTTACACTATGTTTATAACA-TTTACTGTAAAATG-AATAATT
*
10876 AAACTTGTACAGTTCTTTATCATATACTTACTATTTTT-CATGTACTAATATTTTCACTATATTA
128 AAACTTATACAGTTCTTTATCATATACTTACTATTTTTAC-TGTACTAATATTTTCACTATATTA
* * *
10940 TTCTTTTTCCTGTATCGTTCCTTTTACTGTACTG-TTCATTTTTCTGTACTGATTTATTTACTGT
192 TTCTTTTTCCTATATCGTTCCTTTCACTGTACTGTTTC-TTTTTCTATACTGATTTATTTACTGT
*
11004 ACCTTTCCTTTTATTACAATATTTCTCTTATTATATTGTATCT
256 ACCTTTCCTTTTATTACAATATTTCTCTTATTATATTATATCT
11047 GATGTTGTAC
Statistics
Matches: 274, Mismatches: 22, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
330 44 0.16
331 56 0.20
332 17 0.06
333 157 0.57
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.48
Consensus pattern (330 bp):
CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAGTTATTTGGTTGTTATCTAC
CGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTACTGTAAAATGAATAATTAAA
CTTATACAGTTCTTTATCATATACTTACTATTTTTACTGTACTAATATTTTCACTATATTATTCT
TTTTCCTATATCGTTCCTTTCACTGTACTGTTTCTTTTTCTATACTGATTTATTTACTGTACCTT
TCCTTTTATTACAATATTTCTCTTATTATATTATATCTTTTACTGTTATGTATCTGACGTTGTAC
TATTT
Found at i:11272 original size:65 final size:63
Alignment explanation
Indices: 11166--11353 Score: 223
Period size: 65 Copynumber: 2.9 Consensus size: 63
11156 GACTTTTACA
* * * *
11166 ATATTCAATTATTATTTCACCTCATGCACCATAAATGTACATGATTCATATGACTGATATGTACT
1 ATATTCAATTATCATCT-ACCTCATGCACCACAAA-GTACATGAGTCATATGACTGATATGTACT
* * *
11231 ATATTCAATTATCACTCTACCTCATGTACCACAAAGATACATGAGTCATATGAGTGATTTGTACT
1 ATATTCAATTATCA-TCTACCTCATGCACCACAAAG-TACATGAGTCATATGACTGATATGTACT
* * * *
11296 GTATACAATTATCATTCCACCTCATGCACCACAAAGGTACATGAGTCATATTACTGAT
1 ATATTCAATTATCA-TCTACCTCATGCACCACAAA-GTACATGAGTCATATGACTGAT
11354 CTGCACCACA
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
64 1 0.01
65 102 0.96
66 3 0.03
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (63 bp):
ATATTCAATTATCATCTACCTCATGCACCACAAAGTACATGAGTCATATGACTGATATGTACT
Found at i:11366 original size:35 final size:34
Alignment explanation
Indices: 11320--11390 Score: 133
Period size: 35 Copynumber: 2.1 Consensus size: 34
11310 TTCCACCTCA
11320 TGCACCACAAAGGTACATGAGTCATATTACTGATC
1 TGCACCACAAAGGTACATGAGTCATATTA-TGATC
11355 TGCACCACAAAGGTACATGAGTCATATTATGATC
1 TGCACCACAAAGGTACATGAGTCATATTATGATC
11389 TG
1 TG
11391 TATTGTATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 7 0.19
35 29 0.81
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (34 bp):
TGCACCACAAAGGTACATGAGTCATATTATGATC
Found at i:11430 original size:99 final size:100
Alignment explanation
Indices: 11258--11445 Score: 288
Period size: 99 Copynumber: 1.9 Consensus size: 100
11248 TACCTCATGT
* * *
11258 ACCACAAAGATACATGAGTCATATGAGTGATTTGTACTGTATACAATTATCATTCCACCTCATGC
1 ACCACAAAGATACATGAGTCATATGAGTGATCTGTACTGTATACAATTATCACTCCACCCCATGC
*
11323 ACCACAAAGGTACATGAGTCATATTACTGATCTGC
66 ACCACAAAGGTACATGAATCATATTACTGATCTGC
* * * * *
11358 ACCACAAAGGTACATGAGTCATATTA-TGATCTGTATTGTATTCAATTATCACTCTACCCCATGC
1 ACCACAAAGATACATGAGTCATATGAGTGATCTGTACTGTATACAATTATCACTCCACCCCATGC
11422 ACCACAAAGGTACATGAATCATAT
66 ACCACAAAGGTACATGAATCATAT
11446 GAATGATATG
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
99 55 0.70
100 24 0.30
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (100 bp):
ACCACAAAGATACATGAGTCATATGAGTGATCTGTACTGTATACAATTATCACTCCACCCCATGC
ACCACAAAGGTACATGAATCATATTACTGATCTGC
Found at i:11462 original size:164 final size:165
Alignment explanation
Indices: 11190--11509 Score: 480
Period size: 164 Copynumber: 1.9 Consensus size: 165
11180 TTTCACCTCA
* * * *
11190 TGCACCATAAATGTACATGATTCATATGACTGATATGTACTATATTCAATTATCACTCTACCTCA
1 TGCACCACAAAGGTACATGAGTCATATGACTGATATGTACTATATTCAATTATCACTCTACCCCA
* * * * *
11255 TGTACCACAAAGATACATGAGTCATATGAGTGATTTGTACTGTATACAATTATCATTCCACCTCA
66 TGCACCACAAAGATACATGAATCATATGAATGATATGTACTGTATACAATTATCACTCCACCTCA
*
11320 TGCACCACAAAGGTACATGAGTCATATTACTGATC
131 TGCACCAAAAAGGTACATGAGTCATATTACTGATC
* * * *
11355 TGCACCACAAAGGTACATGAGTCATATTA-TGATCTGTATTGTATTCAATTATCACTCTACCCCA
1 TGCACCACAAAGGTACATGAGTCATATGACTGATATGTACTATATTCAATTATCACTCTACCCCA
* **
11419 TGCACCACAAAGGTACATGAATCATATGAATGATATGTACTGTATTTAATTATCACTCCACCTCA
66 TGCACCACAAAGATACATGAATCATATGAATGATATGTACTGTATACAATTATCACTCCACCTCA
11484 TGCACCAAAAAGGTACATGAGTCATA
131 TGCACCAAAAAGGTACATGAGTCATA
11510 GGAGTAATAT
Statistics
Matches: 138, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
164 113 0.82
165 25 0.18
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (165 bp):
TGCACCACAAAGGTACATGAGTCATATGACTGATATGTACTATATTCAATTATCACTCTACCCCA
TGCACCACAAAGATACATGAATCATATGAATGATATGTACTGTATACAATTATCACTCCACCTCA
TGCACCAAAAAGGTACATGAGTCATATTACTGATC
Found at i:11520 original size:65 final size:64
Alignment explanation
Indices: 11355--11509 Score: 229
Period size: 65 Copynumber: 2.4 Consensus size: 64
11345 ATTACTGATC
* * * *
11355 TGCACCACAAAGGTACATGAGTCATATTATGATCTGTATTGTATTCAATTATCACTCTACCCCA
1 TGCACCACAAAGGTACATGAGTCATATGATGATATGTACTGTATTCAATTATCACTCCACCCCA
* * *
11419 TGCACCACAAAGGTACATGAATCATATGAATGATATGTACTGTATTTAATTATCACTCCACCTCA
1 TGCACCACAAAGGTACATGAGTCATATG-ATGATATGTACTGTATTCAATTATCACTCCACCCCA
*
11484 TGCACCAAAAAGGTACATGAGTCATA
1 TGCACCACAAAGGTACATGAGTCATA
11510 GGAGTAATAT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
64 26 0.32
65 55 0.68
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (64 bp):
TGCACCACAAAGGTACATGAGTCATATGATGATATGTACTGTATTCAATTATCACTCCACCCCA
Found at i:13533 original size:18 final size:18
Alignment explanation
Indices: 13509--13552 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
13499 ATAATATGTT
*
13509 AACACATATACTCATG-CA
1 AACACATA-AATCATGACA
*
13527 CACACATAAATCATGACA
1 AACACATAAATCATGACA
13545 AACACATA
1 AACACATA
13553 CTTCTATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.50, C:0.27, G:0.05, T:0.18
Consensus pattern (18 bp):
AACACATAAATCATGACA
Found at i:19206 original size:132 final size:132
Alignment explanation
Indices: 18970--19365 Score: 756
Period size: 132 Copynumber: 3.0 Consensus size: 132
18960 GCCTGGTTCA
*
18970 TTTCATTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
1 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
* *
19035 AGCGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTAAGCGTTC
66 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
19100 TT
131 TT
19102 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
1 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
19167 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
66 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
19232 TT
131 TT
19234 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
1 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
*
19299 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGTGTTC
66 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
19364 TT
131 TT
19366 CTGACAATAA
Statistics
Matches: 260, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 260 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (132 bp):
TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
TT
Found at i:21067 original size:32 final size:33
Alignment explanation
Indices: 21028--21094 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
21018 TAAAAGTTAT
21028 AAAATTATCAT-TAAATTTTATCAAACTATTAC
1 AAAATTATCATATAAATTTTATCAAACTATTAC
***
21060 AAAATTATCATATTTTTTTTATCAAACTATTAC
1 AAAATTATCATATAAATTTTATCAAACTATTAC
21093 AA
1 AA
21095 TCTATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (33 bp):
AAAATTATCATATAAATTTTATCAAACTATTAC
Found at i:23039 original size:26 final size:28
Alignment explanation
Indices: 23010--23068 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
23000 GTCATGTATG
*
23010 TGAGATTGATA-T-TCAGCTCATCAAAA
1 TGAGACTGATACTCTCAGCTCATCAAAA
*
23036 TGAGACTGATACCTCTCAGGTCATCAAAA
1 TGAGACTGATA-CTCTCAGCTCATCAAAA
23065 -GAGA
1 TGAGA
23069 GAAAAATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 10 0.36
28 5 0.18
29 13 0.46
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (28 bp):
TGAGACTGATACTCTCAGCTCATCAAAA
Found at i:24063 original size:41 final size:41
Alignment explanation
Indices: 24006--24087 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
23996 CGTGTAGCGC
24006 TAGACAAGGTTGGCAAGGTTTTAACTTTTAAGTTTTAACCT
1 TAGACAAGGTTGGCAAGGTTTTAACTTTTAAGTTTTAACCT
24047 TAGACAAGGTTGGCAAGGTTTTAACTTTTAAGTTTTAACCT
1 TAGACAAGGTTGGCAAGGTTTTAACTTTTAAGTTTTAACCT
24088 CTAAGTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (41 bp):
TAGACAAGGTTGGCAAGGTTTTAACTTTTAAGTTTTAACCT
Found at i:24083 original size:14 final size:14
Alignment explanation
Indices: 24064--24105 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
24054 GGTTGGCAAG
*
24064 GTTTTAACTTTTAA
1 GTTTTAACCTTTAA
*
24078 GTTTTAACCTCTAA
1 GTTTTAACCTTTAA
24092 GTTTTAACCTTTAA
1 GTTTTAACCTTTAA
24106 TTGTAGACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
GTTTTAACCTTTAA
Found at i:30698 original size:19 final size:19
Alignment explanation
Indices: 30674--30720 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
30664 ATTCTTTAAG
30674 AGTGGATTGTGAGCTACAA
1 AGTGGATTGTGAGCTACAA
* *
30693 AGTGGATCGTGAGCTACGA
1 AGTGGATTGTGAGCTACAA
*
30712 AGTGAATTG
1 AGTGGATTG
30721 AGAAACTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTGGATTGTGAGCTACAA
Found at i:39792 original size:14 final size:14
Alignment explanation
Indices: 39773--39804 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
39763 TGGTGATGGA
39773 CTATACATGGTTAC
1 CTATACATGGTTAC
*
39787 CTATACATGGTTGC
1 CTATACATGGTTAC
39801 CTAT
1 CTAT
39805 GCTGGGTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (14 bp):
CTATACATGGTTAC
Found at i:52522 original size:2 final size:2
Alignment explanation
Indices: 52510--52539 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
52500 TAATACAATA
52510 AT AT GAT 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 AT AT A
52540 AACAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:63268 original size:16 final size:17
Alignment explanation
Indices: 63233--63272 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
63223 AAATCTAATG
* *
63233 TTTAATAAATATTGTAT
1 TTTAATTAATATTATAT
63250 TTTAATTAA-ATTATAT
1 TTTAATTAATATTATAT
63266 TTTAATT
1 TTTAATT
63273 TTTAACTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAATTAATATTATAT
Found at i:63321 original size:22 final size:23
Alignment explanation
Indices: 63249--63321 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
63239 AAATATTGTA
* *
63249 TTTTAATTAAATTATATTTTAAT
1 TTTTAACTAATTTATATTTTAAT
* *
63272 TTTTAACTAATTTATA-ATTATAC
1 TTTTAACTAATTTATATTTTA-AT
* *
63295 GTTTAA-TACTTTATATTTTAAT
1 TTTTAACTAATTTATATTTTAAT
63317 TTTTA
1 TTTTA
63322 TAAATTAATA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (23 bp):
TTTTAACTAATTTATATTTTAAT
Found at i:67081 original size:23 final size:23
Alignment explanation
Indices: 67055--67102 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
67045 ATAAAGTACA
*
67055 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
67078 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
67101 AT
1 AT
67103 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:67509 original size:21 final size:22
Alignment explanation
Indices: 67484--67535 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
67474 ACACTTTACA
*
67484 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
67507 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
67530 ATATAA
1 ATATAA
67536 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:67520 original size:23 final size:23
Alignment explanation
Indices: 67494--67556 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
67484 ATATAACCAC
67494 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
67517 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
67540 TACCTATTACATCATAT
1 TACCTATTACATTATAT
67557 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:69890 original size:198 final size:199
Alignment explanation
Indices: 69096--70268 Score: 2172
Period size: 199 Copynumber: 5.9 Consensus size: 199
69086 TTTAAATTAG
69096 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAAACCGGTAT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAAACCGGTAT
69161 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
* *
69226 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
69291 AAAAA
195 AAAAA
69296 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
69361 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
69426 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGGAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
69491 AAAA
196 AAAA
69495 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
69560 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
69625 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
69689 AAAA
196 AAAA
69693 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
69758 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
69822 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
69887 AAAA
196 AAAA
69891 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
69956 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTTGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
70021 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
70086 AAAAA
195 AAAAA
70091 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
70156 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
70220 TTGACACTTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACAC--TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
70269 GGCCATATTG
Statistics
Matches: 955, Mismatches: 12, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
197 66 0.07
198 255 0.27
199 407 0.43
200 187 0.20
202 40 0.04
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:70419 original size:19 final size:19
Alignment explanation
Indices: 70387--70433 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
70377 TTATATTCAC
70387 ATACAAAA--ATAAATCGT
1 ATACAAAATTATAAATCGT
*
70404 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
70423 ATACAAAATTA
1 ATACAAAATTA
70434 ACTCGACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 8 0.30
19 19 0.70
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:72267 original size:32 final size:33
Alignment explanation
Indices: 72206--72270 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
72196 CATCTTAATA
*
72206 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
72239 TCACCCCTCAACACCTCTA-TTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
72271 CCATCTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:72344 original size:21 final size:21
Alignment explanation
Indices: 72304--72368 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
72294 CCCCTTATGC
* *
72304 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
72325 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
72346 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
72367 CT
1 CT
72369 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:74643 original size:19 final size:18
Alignment explanation
Indices: 74590--74634 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
74580 ATCCGGTATC
74590 ATTTTACCGGTTTATCAT
1 ATTTTACCGGTTTATCAT
74608 -TTTGATACCGGTTTATCAT
1 ATTT--TACCGGTTTATCAT
74627 ATTTTACC
1 ATTTTACC
74635 TGTTATATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.12
18 4 0.17
19 14 0.58
20 3 0.12
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (18 bp):
ATTTTACCGGTTTATCAT
Found at i:74781 original size:20 final size:20
Alignment explanation
Indices: 74755--74800 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
74745 CACTTTTAAA
*
74755 TTTACCGTTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
74774 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
74795 TTTACC
1 TTTACC
74801 TGGTATATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:75261 original size:225 final size:225
Alignment explanation
Indices: 74864--75308 Score: 736
Period size: 225 Copynumber: 2.0 Consensus size: 225
74854 TTAAAACTGC
74864 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAG-GTTTCATGTTTTCCACCTACAATA
**
74929 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
65 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
74994 TTAGAATTTAAATTTAACAATATTAACCAAATAATTTAAT-AA-ATGTTTTCAACAGTGAAATAA
130 TTAGAATTTAAATTTAACAATATTAACAAAATAA-TTAATAAATATATTTTC-ACAGTGAAATAA
*
75057 GTATGGACACTTTTATAAAAATGATATATACTT
193 GTATGGACACTTTTATAAAAAGGATATATACTT
*
75090 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATA-GTTTCATGTTTTCCACCTACAATA
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGGTTTCATGTTTTCCACCTACAATA
*
75154 TTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
65 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
*
75219 TTAGATTTTAAATTTAACAATATTAACTAAAGATAA-TAATAAATATATTTTCACAGTGAAATAA
130 TTAGAATTTAAATTTAACAATATTAAC-AAA-ATAATTAATAAATATATTTTCACAGTGAAATAA
75283 GTATGGACACTTTTATAAAAAGGATA
193 GTATGGACACTTTTATAAAAAGGATA
75309 GATAATTTAC
Statistics
Matches: 206, Mismatches: 8, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
225 116 0.56
226 45 0.22
227 45 0.22
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (225 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGGTTTCATGTTTTCCACCTACAATAT
TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
TAGAATTTAAATTTAACAATATTAACAAAATAATTAATAAATATATTTTCACAGTGAAATAAGTA
TGGACACTTTTATAAAAAGGATATATACTT
Found at i:81386 original size:31 final size:30
Alignment explanation
Indices: 81294--81417 Score: 196
Period size: 30 Copynumber: 4.1 Consensus size: 30
81284 GAAGGACCTA
* * *
81294 TCCAGAGGTCACACAGATCC-CGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
81323 TCCATAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
81353 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
81384 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
81414 TCCA
1 TCCA
81418 TATGTTCCTT
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
29 17 0.19
30 41 0.47
31 30 0.34
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:81405 original size:61 final size:59
Alignment explanation
Indices: 81294--81417 Score: 194
Period size: 61 Copynumber: 2.1 Consensus size: 59
81284 GAAGGACCTA
* *
81294 TCCAGAGGTCACACAGATCCCGGTAACTATCCATAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTG
* *
81353 TCCAGAGGTCATAAAGATCCTCGGTAAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCC-CGGT-AACTATCCAGAGGTCATAAAGATCCTCGGTAACTG
81414 TCCA
1 TCCA
81418 TATGTTCCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
59 18 0.31
60 4 0.07
61 37 0.63
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (59 bp):
TCCAGAGGTCACAAAGATCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:81445 original size:61 final size:60
Alignment explanation
Indices: 81315--81503 Score: 168
Period size: 61 Copynumber: 3.1 Consensus size: 60
81305 CACAGATCCC
* * * * * * * *
81315 GGTAACTATCCATAGGTCATAAAGATCCTCGGTAACTGTCCAGA-GGTCATAAAGATCCTC
1 GGTAACTGTCCATAGGTCATAAAGATCCTCGGTAACTGTCCATATGTTCCT-TAGAACATA
*
81375 GGTAAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATATGTTCCTTAGAACATA
1 GGT-AACTGTCCATAGGTCATAAAGATCCTCGGTAACTGTCCATATGTTCCTTAGAACATA
** * * *
81436 GGTATACTGTCCATTTGTC-TCGAAAGA-CATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCAT--AAAGATCCTCGGT--AACTGTCCATATGTTCCTTAGAACATA
81499 GGTAA
1 GGTAA
81504 ACCCTCGACT
Statistics
Matches: 107, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
60 5 0.05
61 62 0.58
62 10 0.09
63 30 0.28
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (60 bp):
GGTAACTGTCCATAGGTCATAAAGATCCTCGGTAACTGTCCATATGTTCCTTAGAACATA
Found at i:81448 original size:31 final size:30
Alignment explanation
Indices: 81406--81503 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 30
81396 AAAGATCCTC
*
81406 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* * *
81436 GGTATACTGTCCATTTGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
81467 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
81499 GGTAA
1 GGTAA
81504 ACCCTCGACT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 6 0.11
31 24 0.44
32 24 0.44
33 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:81498 original size:32 final size:32
Alignment explanation
Indices: 81409--81504 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
81399 GATCCTCGGT
*
81409 AACTGTCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
* * *
81440 TACTGTCCATTTG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTAA
81472 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
81504 A
1 A
81505 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
30 4 0.08
31 20 0.38
32 25 0.47
33 4 0.08
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAA
Found at i:85898 original size:30 final size:30
Alignment explanation
Indices: 85842--85964 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
85832 GAATGACCTA
* * *
85842 TCCAGAGGTCACACAGATCC-CGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
85871 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
85901 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
85931 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
85961 TCCA
1 TCCA
85965 TATGTTCCTT
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:85995 original size:31 final size:30
Alignment explanation
Indices: 85953--86050 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 30
85943 AAAGATCCTC
*
85953 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
85983 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
* *
86014 GGTAAAATTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
86046 GGTAA
1 GGTAA
86051 ACCCTCGACT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.45
32 24 0.43
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:86045 original size:32 final size:32
Alignment explanation
Indices: 85956--86051 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
85946 GATCCTCGGT
*
85956 AACTGTCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
* *
85987 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTAA
*
86019 AATTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
86051 A
1 A
86052 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
30 4 0.07
31 21 0.39
32 25 0.46
33 4 0.07
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAA
Found at i:87220 original size:21 final size:21
Alignment explanation
Indices: 87194--87238 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
87184 ATTCTGTCGT
87194 TTGAATGAGTATCAG-TTCCCC
1 TTGAATGAGTA-CAGATTCCCC
* *
87215 TTGAATGGGTACCGATTCCCC
1 TTGAATGAGTACAGATTCCCC
87236 TTG
1 TTG
87239 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (21 bp):
TTGAATGAGTACAGATTCCCC
Found at i:107823 original size:21 final size:21
Alignment explanation
Indices: 107797--107849 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
107787 GTTTCCAGAT
107797 TCGCAACGCGAACATCAACTA
1 TCGCAACGCGAACATCAACTA
* **
107818 TCGCAACGCGAACTTCGTCTA
1 TCGCAACGCGAACATCAACTA
*
107839 TCGCAATGCGA
1 TCGCAACGCGA
107850 TTTTCCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACATCAACTA
Found at i:107887 original size:21 final size:19
Alignment explanation
Indices: 107853--108080 Score: 104
Period size: 21 Copynumber: 11.3 Consensus size: 19
107843 AATGCGATTT
*
107853 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
**
107872 TCCAAGTTCGCGTTGCGATTT
1 TCCAAGTT--CGTTGCGATAG
*
107893 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
107912 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
107935 TCCAAATTCGTTGC----G
1 TCCAAGTTCGTTGCGATAG
* *
107950 TCGAAGTTCTCGTTGCGATTTAT
1 TCCAAG-T-TCGTTGCGA--TAG
* * *
107973 TCTAAGTACGTTGCGTTAG
1 TCCAAGTTCGTTGCGATAG
* * *
107992 TCGAAGTTCGCGTTACGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
108015 TCCAAGTTTGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
108034 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
108057 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
108076 TCCAA
1 TCCAA
108081 AATCGCAAAG
Statistics
Matches: 155, Mismatches: 32, Indels: 44
0.67 0.14 0.19
Matches are distributed among these distances:
15 4 0.03
16 1 0.01
17 7 0.05
19 47 0.30
21 64 0.41
22 1 0.01
23 31 0.20
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:108011 original size:42 final size:42
Alignment explanation
Indices: 107845--108077 Score: 320
Period size: 42 Copynumber: 5.7 Consensus size: 42
107835 TCTATCGCAA
*
107845 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
*
107885 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
*
107925 TGCGATTTATTCCAAATTCGTTGC----GTCGAAGTTCTCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* * * *
107963 TGCGATTTATTCTAAGTACGTTGCGTTAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* * *
108005 TACGATTTATTCCAAGTTTGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
108047 TGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TGCGATTTATTCCAAATTCGTTGCGATAGTC
108078 CAAAATCGCA
Statistics
Matches: 173, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
38 33 0.19
40 45 0.26
41 2 0.01
42 93 0.54
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:108865 original size:42 final size:42
Alignment explanation
Indices: 108755--109026 Score: 341
Period size: 42 Copynumber: 6.4 Consensus size: 42
108745 CGTTGCGATT
*
108755 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGTGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
108797 TTCGACTACGACTATCGCAACAAATTTGTAATAAATCACAACGCGAAC
1 TT-G-----GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
108845 TTGGACTATCGCAACCAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
108887 TTAGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
108929 GTGGACTATCGCAACAAATTTGAAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * **
108971 TTGAACTATCGCAACGAATTTGG-A-AAATCGAAATACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
109011 TTCGACTATCGCAACG
1 TTGGACTATCGCAACG
109027 CGAACTTGAA
Statistics
Matches: 201, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
40 27 0.13
41 1 0.00
42 134 0.67
43 1 0.00
47 1 0.00
48 37 0.18
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:109030 original size:21 final size:21
Alignment explanation
Indices: 108835--109051 Score: 135
Period size: 21 Copynumber: 10.4 Consensus size: 21
108825 TAATAAATCA
108835 CAACGCGAACTTGGACTATCG
1 CAACGCGAACTTGGACTATCG
* *
108856 CAAC-C-AATTTGGAATAAATCG
1 CAACGCGAACTTGGACT--ATCG
*
108877 CAACGCGAACTTAGACTATCG
1 CAACGCGAACTTGGACTATCG
* * *
108898 CAA--CGAATTTGTAATAAATCG
1 CAACGCGAACTTGGACT--ATCG
*
108919 CAACGCGAACGTGGACTATCG
1 CAACGCGAACTTGGACTATCG
* * * *
108940 CAA--CAAATTTGAAATAAATCG
1 CAACGCGAACTTGGACT--ATCG
*
108961 CAACGCGAACTTGAACTATCG
1 CAACGCGAACTTGGACTATCG
* **
108982 CAA--CGAATTTGGAAAATCG
1 CAACGCGAACTTGGACTATCG
* ** *
109001 AAATACGAACTTCGACTATCG
1 CAACGCGAACTTGGACTATCG
*
109022 CAACGCGAACTTGAACTATCG
1 CAACGCGAACTTGGACTATCG
*
109043 CAATGCGAA
1 CAACGCGAA
109052 TATGTAAATC
Statistics
Matches: 146, Mismatches: 36, Indels: 28
0.70 0.17 0.13
Matches are distributed among these distances:
19 37 0.25
20 1 0.01
21 83 0.57
22 1 0.01
23 24 0.16
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (21 bp):
CAACGCGAACTTGGACTATCG
Found at i:109100 original size:21 final size:20
Alignment explanation
Indices: 109039--109100 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
109029 AACTTGAACT
* * *
109039 ATCGCAATGCGAATATGTAA
1 ATCGCATTGCGAATCTGGAA
109059 ATCGCATTGCGATAGTC--GAA
1 ATCGCATTGCGA-A-TCTGGAA
109079 ATTCGCATTGCGAATCTGGAA
1 A-TCGCATTGCGAATCTGGAA
109100 A
1 A
109101 CTGATTTGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 2 0.06
20 15 0.44
21 16 0.47
22 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (20 bp):
ATCGCATTGCGAATCTGGAA
Found at i:110119 original size:11 final size:11
Alignment explanation
Indices: 110105--110130 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
110095 TATATAAATT
110105 AATTATAGTAG
1 AATTATAGTAG
110116 AATTATAGTAG
1 AATTATAGTAG
110127 AATT
1 AATT
110131 CAATTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (11 bp):
AATTATAGTAG
Found at i:115419 original size:29 final size:30
Alignment explanation
Indices: 115385--115442 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
115375 TCGTTTTTTC
* *
115385 AGTTTAGTGCCTAATGTTT-ATTTCGTTAT
1 AGTTTAGTGCCCAATGTTTCATTCCGTTAT
115414 AGTTTAGTGCCCAATGTTTCATTCCGTTA
1 AGTTTAGTGCCCAATGTTTCATTCCGTTA
115443 CTCAAAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (30 bp):
AGTTTAGTGCCCAATGTTTCATTCCGTTAT
Found at i:115546 original size:25 final size:25
Alignment explanation
Indices: 115517--115564 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
115507 TGATTTTAAA
115517 AAAATTATATAAAATTTTAAAAAAT
1 AAAATTATATAAAATTTTAAAAAAT
* *
115542 AAAATTATATATATTTTTAAAAA
1 AAAATTATATAAAATTTTAAAAA
115565 GAAAACACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAATTATATAAAATTTTAAAAAAT
Found at i:116450 original size:2 final size:2
Alignment explanation
Indices: 116443--116483 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
116433 ATATTATTTC
116443 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
116484 AACGGGATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:123281 original size:258 final size:253
Alignment explanation
Indices: 122902--123399 Score: 813
Period size: 258 Copynumber: 1.9 Consensus size: 253
122892 ATTAGGTCAA
122902 ACCAACCTCCAAAAAGGTGCTAATGCTTCATGTATGAAATTACCAAAGGCAGCCCAAGACTTTAA
1 ACCAACCTCCAAAAAGGTGCTAATGCTTCATGTATGAAATTACCAAAGGCAGCCCAAGACTTTAA
*
122967 TATCGGCATGGCAATGCATAGGAGAAAGGTATTATGGGAAGTATACTATCATATAGAAATATTAA
66 TATCGGCATGGCAATGCATAGGAGAAAGGTATTATGAGAAGTATACTATCATATAGAAATATTAA
* *
123032 ACATTCAATGAAACCATATTGAGGATGATATTACAGCAGTTCATCAACTCCTGAATAATGAAACC
131 ACATTCAATGAAACCATATTGAAGATGATATTACAGCAGTTCATCAACTCCTAAATAATGAAACC
* *
123097 ATATCGAACATAAAGATATAGTCTTCAATCTAAAGAATTAGGTCAGACCTAAAGATTG
196 ATATCAAACATAAAGATATAGCCTTCAATCTAAAGAATTAGGTCAGACCTAAAGATTG
* * *
123155 ACCAATCC-CCAAAAAGGTGCTAATTCTTCGTGTATGAAATTACCAAAGGCAG-CC-AGATTTTA
1 ACCAA-CCTCCAAAAAGGTGCTAATGCTTCATGTATGAAATTACCAAAGGCAGCCCAAGACTTTA
* *
123217 ATATCGGCATGGCAAATGGCAATGCATAGGAGAAAGGTATTATGAGAAGTATACTGTTATATAGA
65 ATAT---C--GGC--ATGGCAATGCATAGGAGAAAGGTATTATGAGAAGTATACTATCATATAGA
123282 AATATTAAACATTCAATGAAACCATATTGAAGATGATATTACAGCAGTTCATCAACTCCTAAATA
123 AATATTAAACATTCAATGAAACCATATTGAAGATGATATTACAGCAGTTCATCAACTCCTAAATA
123347 ATGAAACCATATCAAACATAAAGATATAGCCTTCAATCTAAAGAATTAGGTCA
188 ATGAAACCATATCAAACATAAAGATATAGCCTTCAATCTAAAGAATTAGGTCA
123400 AACTACTTTT
Statistics
Matches: 227, Mismatches: 10, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
251 11 0.05
252 2 0.01
253 47 0.21
254 3 0.01
256 3 0.01
258 161 0.71
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (253 bp):
ACCAACCTCCAAAAAGGTGCTAATGCTTCATGTATGAAATTACCAAAGGCAGCCCAAGACTTTAA
TATCGGCATGGCAATGCATAGGAGAAAGGTATTATGAGAAGTATACTATCATATAGAAATATTAA
ACATTCAATGAAACCATATTGAAGATGATATTACAGCAGTTCATCAACTCCTAAATAATGAAACC
ATATCAAACATAAAGATATAGCCTTCAATCTAAAGAATTAGGTCAGACCTAAAGATTG
Found at i:140320 original size:16 final size:16
Alignment explanation
Indices: 140285--140318 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
140275 AAAGATATTC
*
140285 TTTCCACTGTGAGTTA
1 TTTCCACTGTCAGTTA
140301 TTTCCACTG-CAGTTA
1 TTTCCACTGTCAGTTA
140316 TTT
1 TTT
140319 TCTTTTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.47
Consensus pattern (16 bp):
TTTCCACTGTCAGTTA
Found at i:145631 original size:14 final size:14
Alignment explanation
Indices: 145612--145655 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
145602 TTTCTCTATT
145612 TTCTTCGATTACTC
1 TTCTTCGATTACTC
*
145626 TTCTTC---TA-TT
1 TTCTTCGATTACTC
145636 TTCTTCGATTACTC
1 TTCTTCGATTACTC
145650 TTCTTC
1 TTCTTC
145656 TTTCGCAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
13 2 0.08
14 13 0.54
ACGTcount: A:0.11, C:0.27, G:0.05, T:0.57
Consensus pattern (14 bp):
TTCTTCGATTACTC
Found at i:145634 original size:24 final size:24
Alignment explanation
Indices: 145606--145656 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
145596 CTCTATTTTC
145606 TCTATTTTCTTCGATTACTCTTCT
1 TCTATTTTCTTCGATTACTCTTCT
145630 TCTATTTTCTTCGATTACTCTTCT
1 TCTATTTTCTTCGATTACTCTTCT
145654 TCT
1 TCT
145657 TTCGCAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.25, G:0.04, T:0.59
Consensus pattern (24 bp):
TCTATTTTCTTCGATTACTCTTCT
Found at i:153008 original size:27 final size:27
Alignment explanation
Indices: 152978--153029 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
152968 TAGAATTAAA
*
152978 GGAACACTTATCAAAAGGTAACTTATT
1 GGAACACTTATCAAAAGCTAACTTATT
153005 GGAACACTTATCAAAAGCTAACTTA
1 GGAACACTTATCAAAAGCTAACTTA
153030 CTCAAATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (27 bp):
GGAACACTTATCAAAAGCTAACTTATT
Found at i:156216 original size:2 final size:2
Alignment explanation
Indices: 156209--156268 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
156199 TTCTATAAAT
156209 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
156251 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
156269 AGATAAACCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:162337 original size:229 final size:219
Alignment explanation
Indices: 161940--162380 Score: 713
Period size: 229 Copynumber: 2.0 Consensus size: 219
161930 GTAAATTATC
*
161940 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTATTATTAGTTAATATT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTATTATTAGTTAATATT
**
162005 GTTAAATTTAAAATCTAAATATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAA
66 GTTAAATTTAAAATCTAAATATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGTAAA
162070 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATA
131 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATA
162135 AA-TACATAACTTTCAAAAAGGTATA
195 AATTACATAACTTT-AAAAAGGTATA
*
162160 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGA
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TG-AAA-ATA--TATTA-T-TATTAG-
*
162225 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
58 TTAATATTGTTAAATTTAAAATCTAAAT-ATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
162290 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
122 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
162355 GAAACATAAATTACATAACTTTAAAA
187 GAAACATAAATTACATAACTTTAAAA
162381 GCAGTTATAA
Statistics
Matches: 204, Mismatches: 7, Indels: 12
0.91 0.03 0.05
Matches are distributed among these distances:
220 36 0.18
221 2 0.01
222 3 0.01
223 3 0.01
225 5 0.02
226 1 0.00
227 5 0.02
228 49 0.24
229 100 0.49
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (219 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTATTATTAGTTAATATT
GTTAAATTTAAAATCTAAATATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGTAAA
TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
ATTACATAACTTTAAAAAGGTATA
Found at i:162474 original size:20 final size:20
Alignment explanation
Indices: 162449--162487 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
162439 ATACCAGGTA
162449 AAAATGATAAAACCGGTAAC
1 AAAATGATAAAACCGGTAAC
162469 AAAATGATAAAACCGGTAA
1 AAAATGATAAAACCGGTAA
162488 ATTTAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATGATAAAACCGGTAAC
Found at i:162633 original size:20 final size:19
Alignment explanation
Indices: 162610--162656 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
162600 CGATATAACA
162610 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
162630 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
162650 GGTAAAA
1 GGTAAAA
162657 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:162658 original size:17 final size:19
Alignment explanation
Indices: 162619--162661 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
162609 AGGTAAAAAT
162619 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
162639 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
162656 ATGATA
1 ATGATA
162662 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:164931 original size:21 final size:21
Alignment explanation
Indices: 164884--164948 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
164874 AAGACAATCA
* *
164884 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
164906 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
164926 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
164947 AG
1 AG
164949 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:165023 original size:32 final size:32
Alignment explanation
Indices: 164982--165042 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
164972 AAATAGATGG
*
164982 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
* *
165014 AGTGGTGAAAGAAGTTGGGGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
165043 GTGATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:166858 original size:19 final size:19
Alignment explanation
Indices: 166834--166882 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
166824 AATGTAGGGT
166834 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
166853 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
166872 T-ATTTTCGTAT
1 TAATTTT-GTAT
166883 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:167741 original size:196 final size:197
Alignment explanation
Indices: 167004--167993 Score: 1875
Period size: 197 Copynumber: 5.0 Consensus size: 197
166994 TGGCCAAAGG
167004 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
167069 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
167133 CATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
131 CATAAAGTGTCGATCCATATA-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
167198 AAT
195 AAT
167201 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
167266 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
167331 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
131 CATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
167396 TAAT
194 TAAT
167400 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
167465 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
167530 CATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
131 CATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
167595 AT
196 AT
167597 ATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
*
167661 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGAATAG-AAACAGGGTGCAC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGAATGGAAAACAGGGTGCAC
167725 CCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 CCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
167790 AAT
195 AAT
167793 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
167858 TGTCGACACT-ATATAG-TTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCA-C
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
167920 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
131 CATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
167985 TAAT
194 TAAT
167989 ATGTA
1 ATGTA
167994 GTTTAGCTTT
Statistics
Matches: 783, Mismatches: 2, Indels: 17
0.98 0.00 0.02
Matches are distributed among these distances:
194 37 0.05
195 23 0.03
196 236 0.30
197 239 0.31
198 51 0.07
199 192 0.25
200 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (197 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
CATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
AT
Found at i:168155 original size:18 final size:18
Alignment explanation
Indices: 168134--168170 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
168124 GTAATTGGAG
168134 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
168152 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
168170 T
1 T
168171 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:168178 original size:24 final size:24
Alignment explanation
Indices: 168126--168172 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
168116 TTTCATATGT
* *
168126 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
168150 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
168173 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:168460 original size:39 final size:39
Alignment explanation
Indices: 168417--168500 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
168407 TCCGATGCTC
*
168417 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
168456 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
168495 ATCAAA
1 ATCAAA
168501 TCTACAACTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:168954 original size:21 final size:23
Alignment explanation
Indices: 168908--168974 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
168898 TAATGGTAAA
168908 AATGTAATAGGTAGCGCTTATAT
1 AATGTAATAGGTAGCGCTTATAT
*
168931 AATGTAATAGGTATCG-TT-TAT
1 AATGTAATAGGTAGCGCTTATAT
* *
168952 AATGTAATAGGTAGTGGTTATAT
1 AATGTAATAGGTAGCGCTTATAT
168975 TGTAAAGTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 17 0.44
22 4 0.10
23 18 0.46
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.39
Consensus pattern (23 bp):
AATGTAATAGGTAGCGCTTATAT
Found at i:168978 original size:21 final size:21
Alignment explanation
Indices: 168910--168979 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
168900 ATGGTAAAAA
*
168910 TGTAATAGGTAGCGCTTATAT
1 TGTAATAGGTAGTGCTTATAT
* *
168931 AATGTAATAGGTA-TCGTTTATAA
1 --TGTAATAGGTAGT-GCTTATAT
*
168954 TGTAATAGGTAGTGGTTATAT
1 TGTAATAGGTAGTGCTTATAT
168975 TGTAA
1 TGTAA
168980 AGTGTCTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 22 0.55
22 1 0.03
23 17 0.43
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (21 bp):
TGTAATAGGTAGTGCTTATAT
Found at i:169375 original size:20 final size:22
Alignment explanation
Indices: 169326--169399 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
169316 AATAGGTAAA
169326 ATATGATGTAATAGGTAGCGCTT
1 ATAT-ATGTAATAGGTAGCGCTT
*
169349 ATATATGTAATAGGTATCG-TT
1 ATATATGTAATAGGTAGCGCTT
* *
169370 -TATATGTAATAGGTAGTGGTT
1 ATATATGTAATAGGTAGCGCTT
169391 ATAT-TGTAA
1 ATATATGTAA
169400 AGTGTCTATC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.35
21 9 0.20
22 17 0.37
23 4 0.09
ACGTcount: A:0.32, C:0.04, G:0.23, T:0.41
Consensus pattern (22 bp):
ATATATGTAATAGGTAGCGCTT
Found at i:169499 original size:422 final size:418
Alignment explanation
Indices: 168707--169723 Score: 1657
Period size: 422 Copynumber: 2.5 Consensus size: 418
168697 ATTATCTTGG
*
168707 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAAATC-AATATTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTAT-AAATATC-AAATAATCAAATATTTT
*
168771 TTGTGCAAATGAAATTATT-A--AAT-TTGTAGGTGAAAACATGAAACACTATTAAAAAAATTGA
64 TTGTGCAAATGAAATTATTAATTAATATTGTAGGTGGAAACATGAAACACTATTAAAAAAATTGA
* *
168832 AACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTT-TATAAAGGTATGGACACTTTCAA
129 AACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTATA-AAAAGTATGGACACTTTAAA
168896 TATAATGGTAAAAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATAATGTAATA
193 TATAATGGTAAAAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATAATGTAATA
168961 GGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGG
258 GGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGG
169026 AAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTAAGATTTTAATTTAGTAATTATAGGCGTC
323 AAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTAAGATTTTAATTTAGTAATTATAGGCGTC
169091 TAATGATTTATTTTTTACGTTACGATATAT-
388 TAATGATTTATTTTTTACGTTACGATATATA
169121 TTAATGTTGTTAAATT-AAAATTCTAAATAATATTTTATAAATATCAAATAATCAAATATTTTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAATATCAAATAATCAAATA-TTTTT
169185 TGTGCAAATGAAATTATTAATTAATATTGTAGGTGGAAA-ATGAAACACTATTAAAAAAAATTGA
65 TGTGCAAATGAAATTATTAATTAATATTGTAGGTGGAAACATGAAACACTATT-AAAAAAATTGA
169249 AACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTATAAAAAGTATGGACACTTTAAAT
129 AACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTATAAAAAGTATGGACACTTTAAAT
169314 ATAATAGGTAAAATATGATGTAATAGGTAGCGCTTATAT-ATGTAATAGGTATCGTTTAT-ATGT
194 ATAAT-GGT-AAA-A--ATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATAATGT
*
169377 AATAGGTAGTGGTTATATTGTAAAGTGTCTATCTTTTTTATAAAAAGTGTCCATACTTTTTTTCA
254 AATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT-AAAAGTGTCCATAC-TTTTTTCA
*
169442 CTGTTGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTAAGATTTTAATTTAGTAATTATA
317 CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTAAGATTTTAATTTAGTAATTATA
169507 GGCGTCTAATGATTTATTTTTTACGTTACGATATATA
382 GGCGTCTAATGATTTATTTTTTACGTTACGATATATA
*
169544 TT-A--TTATTAAATTAAAAATTCTAAATAATA-TTT-T--ATA--AAAT-ATCAAATAATTTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAATATCAAATAATCAAAT-ATTTTT
*
169599 TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAACATGAAACACTATT-CAAAAATTGA
65 TGTGCAAATGAAATTATT-AATTAATATTGTAGGTGGAAACATGAAACACTATTAAAAAAATTGA
*
169663 AACATAAATTACATAACTTTAAAAGAAGTA-CGATCCTTTTTATAAAAATTATGGACACTTT
129 AACATAAATTACATAACTTTAAAAGAAGTATCGATCC-TTTTATAAAAAGTATGGACACTTT
169724 CAACATATTA
Statistics
Matches: 573, Mismatches: 9, Indels: 42
0.92 0.01 0.07
Matches are distributed among these distances:
411 7 0.01
412 11 0.02
413 51 0.09
414 109 0.19
415 26 0.05
416 29 0.05
417 91 0.16
418 5 0.01
419 4 0.01
420 57 0.10
421 50 0.09
422 131 0.23
423 2 0.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (418 bp):
TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAATATCAAATAATCAAATATTTTTT
GTGCAAATGAAATTATTAATTAATATTGTAGGTGGAAACATGAAACACTATTAAAAAAATTGAAA
CATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTATAAAAAGTATGGACACTTTAAATAT
AATGGTAAAAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATAATGTAATAGGT
AGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAA
ACATTAATTTAAGGTTATCTTTTGAGTGAGTTTAAGATTTTAATTTAGTAATTATAGGCGTCTAA
TGATTTATTTTTTACGTTACGATATATA
Found at i:169583 original size:22 final size:22
Alignment explanation
Indices: 169558--169599 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
169548 TATTAAATTA
169558 AAAAT-TCTAAATAATATTTTAT
1 AAAATATC-AAATAATATTTTAT
*
169580 AAAATATCAAATAATTTTTT
1 AAAATATCAAATAATATTTT
169600 GTGCAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATATCAAATAATATTTTAT
Found at i:171666 original size:21 final size:21
Alignment explanation
Indices: 171642--171690 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
171632 AAGGGCTAAG
*
171642 ACCTTTTGATGAAAGGATTTA
1 ACCTTTTGATGAAAGGACTTA
* *
171663 ACCTTTCGATTAAAGGACTTA
1 ACCTTTTGATGAAAGGACTTA
171684 ACCTTTT
1 ACCTTTT
171691 TGAAATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (21 bp):
ACCTTTTGATGAAAGGACTTA
Found at i:173632 original size:23 final size:23
Alignment explanation
Indices: 173606--173670 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
173596 TATTTGATTT
173606 TAAATTTAATATTAATTTTTAAA
1 TAAATTTAATATTAATTTTTAAA
* *
173629 TAAATTAAATATTAATTTTTTAA
1 TAAATTTAATATTAATTTTTAAA
173652 T--ATTATATATATTAATTTT
1 TAAATT-TA-ATATTAATTTT
173671 AATATTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 3 0.08
22 1 0.03
23 33 0.89
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAAATTTAATATTAATTTTTAAA
Found at i:173680 original size:35 final size:36
Alignment explanation
Indices: 173636--173714 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 36
173626 AAATAAATTA
173636 AATATTAATTTTTT-AAT-ATTATATATATTAA-TTTT
1 AATATTAATTTTTTAAATAATTA-A-ATATTAATTTTT
173671 AATATTAATTTTTTAAATAAATTAAATATTAATTTTT
1 AATATTAATTTTTTAAAT-AATTAAATATTAATTTTT
173708 AATATTA
1 AATATTA
173715 TATTATAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 14 0.35
36 10 0.25
37 12 0.30
38 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
AATATTAATTTTTTAAATAATTAAATATTAATTTTT
Found at i:173730 original size:58 final size:60
Alignment explanation
Indices: 173605--173737 Score: 206
Period size: 58 Copynumber: 2.3 Consensus size: 60
173595 ATATTTGATT
173605 TTAA-ATTTAATATTAA-TTTTTAAATAAATTAAATATTAATTTTTTAATATTATATATA
1 TTAATATTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATATA
173663 TTAAT-TTTAATATTAATTTTTTAAATAAATTAAATATTAA-TTTTTAATATTATAT-TA
1 TTAATATTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATATA
*
173720 -TAGATATTTAATTTTAAT
1 TTA-ATATTTAATATTAAT
173738 CATATAAATT
Statistics
Matches: 70, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
56 2 0.03
57 4 0.06
58 41 0.59
59 23 0.33
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (60 bp):
TTAATATTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATATA
Found at i:174042 original size:21 final size:22
Alignment explanation
Indices: 174018--174067 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
174008 AATATTTTCT
*
174018 AAAAATAT-CATATA-ATTATAA
1 AAAAATATGAATATATATT-TAA
174039 AAAAATTATGAATATATATTTAA
1 AAAAA-TATGAATATATATTTAA
174062 AAAAAT
1 AAAAAT
174068 TAAAAGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.20
22 4 0.16
23 13 0.52
24 3 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAATATGAATATATATTTAA
Found at i:174282 original size:31 final size:31
Alignment explanation
Indices: 174247--174306 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
174237 TAGTTGTATG
* *
174247 AATTATTTAAATTTCAATATTGTAAAACTAA
1 AATTATTTAAATATCAATATTGCAAAACTAA
*
174278 AATTATTTAAATATCAGTATTGCAAAACT
1 AATTATTTAAATATCAATATTGCAAAACT
174307 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATATCAATATTGCAAAACTAA
Found at i:182863 original size:14 final size:14
Alignment explanation
Indices: 182844--182873 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
182834 TTTAGATTTT
*
182844 TTAAAATTACATTA
1 TTAAAAATACATTA
182858 TTAAAAATACATTA
1 TTAAAAATACATTA
182872 TT
1 TT
182874 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:183026 original size:7 final size:7
Alignment explanation
Indices: 183014--183064 Score: 84
Period size: 7 Copynumber: 7.3 Consensus size: 7
183004 ATTTGTAATT
183014 AACCCTA
1 AACCCTA
183021 AACCCTA
1 AACCCTA
*
183028 AAACCTA
1 AACCCTA
*
183035 AACCATA
1 AACCCTA
183042 AACCCTA
1 AACCCTA
183049 AACCCTA
1 AACCCTA
183056 AACCCTA
1 AACCCTA
183063 AA
1 AA
183065 TCCGATTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.49, C:0.37, G:0.00, T:0.14
Consensus pattern (7 bp):
AACCCTA
Found at i:185569 original size:12 final size:12
Alignment explanation
Indices: 185552--185616 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
185542 AATACCTGTC
185552 GAGCTCAGAATT
1 GAGCTCAGAATT
*
185564 GAGCTCAAAATT
1 GAGCTCAGAATT
* *
185576 GAGCT-TGAATC
1 GAGCTCAGAATT
* *
185587 GAGCTCAAAACT
1 GAGCTCAGAATT
* *
185599 GAGCT-TGAATC
1 GAGCTCAGAATT
185610 GAGCTCA
1 GAGCTCA
185617 AAACAGAGCT
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
11 15 0.39
12 23 0.61
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (12 bp):
GAGCTCAGAATT
Found at i:185590 original size:23 final size:23
Alignment explanation
Indices: 185559--185637 Score: 131
Period size: 23 Copynumber: 3.4 Consensus size: 23
185549 GTCGAGCTCA
* *
185559 GAATTGAGCTCAAAATTGAGCTT
1 GAATCGAGCTCAAAACTGAGCTT
185582 GAATCGAGCTCAAAACTGAGCTT
1 GAATCGAGCTCAAAACTGAGCTT
*
185605 GAATCGAGCTCAAAACAGAGCTT
1 GAATCGAGCTCAAAACTGAGCTT
185628 GAATCGAGCT
1 GAATCGAGCT
185638 TTAATCGAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (23 bp):
GAATCGAGCTCAAAACTGAGCTT
Found at i:185638 original size:11 final size:11
Alignment explanation
Indices: 185576--185646 Score: 61
Period size: 11 Copynumber: 6.3 Consensus size: 11
185566 GCTCAAAATT
185576 GAGCTTGAATC
1 GAGCTTGAATC
** *
185587 GAGCTCAAAAC
1 GAGCTTGAATC
185598 TGAGCTTGAATC
1 -GAGCTTGAATC
** *
185610 GAGCTCAAAAC
1 GAGCTTGAATC
185621 AGAGCTTGAATC
1 -GAGCTTGAATC
*
185633 GAGCTTTAATC
1 GAGCTTGAATC
185644 GAG
1 GAG
185647 TTCGAGCTTC
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
11 29 0.64
12 16 0.36
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (11 bp):
GAGCTTGAATC
Found at i:205781 original size:24 final size:25
Alignment explanation
Indices: 205737--205784 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
205727 GAAAAAAATT
*
205737 AAAAATTCTATAGATTCAAAAATAA
1 AAAAATTCGATAGATTCAAAAATAA
205762 AAAAATTCGA-AG-TTCTAAAAATA
1 AAAAATTCGATAGATTC-AAAAATA
205785 TTTTTTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 9 0.43
25 9 0.43
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.27
Consensus pattern (25 bp):
AAAAATTCGATAGATTCAAAAATAA
Found at i:207072 original size:19 final size:18
Alignment explanation
Indices: 207025--207132 Score: 58
Period size: 19 Copynumber: 5.5 Consensus size: 18
207015 TTAACTTGGT
*
207025 TTTTAAACTTTTAATTTTA
1 TTTTAAA-TTATAATTTTA
*
207044 TCTTTTAATTATAATTCTTA
1 T-TTTAAATTATAATT-TTA
207064 TTTTAAA-T-TAATCTTTAAA
1 TTTTAAATTATAAT-TTT--A
*
207083 TTTTTCAATATTCTAATTTTA
1 -TTTT-AA-ATTATAATTTTA
* *
207104 TCTTTAAACTATGATTTTTA
1 T-TTTAAATTAT-AATTTTA
207124 TTTTAAATT
1 TTTTAAATT
207133 GATCCTCAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
17 6 0.09
18 2 0.03
19 24 0.34
20 23 0.33
21 6 0.09
22 1 0.01
23 4 0.06
24 4 0.06
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.59
Consensus pattern (18 bp):
TTTTAAATTATAATTTTA
Found at i:207103 original size:60 final size:59
Alignment explanation
Indices: 207024--207160 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 59
207014 TTTAACTTGG
* * * *
207024 TTTTTAAACT-TTTAATTTTATCTTTTAATTATAATTCTTATTTTAAATTAATCTTTAAA
1 TTTTTAAA-TATTTAATTTTATCTTTAAACTATAATTCTTATTTTAAATTAATCCTCAAA
* * * * *
207083 TTTTTCAATATTCTAATTTTATCTTTAAACTATGATTTTTATTTTAAATTGATCCTCAAT
1 TTTTTAAATATT-TAATTTTATCTTTAAACTATAATTCTTATTTTAAATTAATCCTCAAA
207143 TTTTTAAATATTTAATTT
1 TTTTTAAATATTTAATTT
207161 CATCCTTATA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
58 1 0.02
59 15 0.23
60 50 0.76
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.58
Consensus pattern (59 bp):
TTTTTAAATATTTAATTTTATCTTTAAACTATAATTCTTATTTTAAATTAATCCTCAAA
Found at i:207387 original size:42 final size:42
Alignment explanation
Indices: 207317--207430 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
207307 GACGAAAAGT
207317 CGGGCTGGAGAAGAGGGCACCGGAGTGCAGCGGATGATCAGC
1 CGGGCTGGAGAAGAGGGCACCGGAGTGCAGCGGATGATCAGC
* ** * * ** * *
207359 CGGGATGGAGAAGAGGTTATCGGGGTGCAGTTGATTATCAGT
1 CGGGCTGGAGAAGAGGGCACCGGAGTGCAGCGGATGATCAGC
** *
207401 CGGGCTGGAGAAGAGGAAACTGGAGTGCAG
1 CGGGCTGGAGAAGAGGGCACCGGAGTGCAG
207431 AGGACTATCG
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.25, C:0.15, G:0.44, T:0.16
Consensus pattern (42 bp):
CGGGCTGGAGAAGAGGGCACCGGAGTGCAGCGGATGATCAGC
Found at i:208903 original size:60 final size:59
Alignment explanation
Indices: 208773--208954 Score: 197
Period size: 60 Copynumber: 3.1 Consensus size: 59
208763 AGGTGTGATG
* * * * * * * *
208773 GTTTGAGATGAAATTGAAATGTTTAGAAGTTTGTGAACCAA-TTAGAATGATAGTCATA
1 GTTTGAGATGAAATTGAAATATTTAAAAGTTTGAGGACTAATTTAGAATAAGAGTTATA
* * *
208831 ATTTGAGAATGAAATTGGAATATTTAAAAGTTTGAGGACTAATTTAGAACAAGAGTTATA
1 GTTTGAG-ATGAAATTGAAATATTTAAAAGTTTGAGGACTAATTTAGAATAAGAGTTATA
* * *
208891 GTTTGAGTATGAAATTAAAATATTTAAAAGTTT-AGGCACTAATTTAGAATAAGGGTTGTA
1 GTTTGAG-ATGAAATTGAAATATTTAAAAGTTTGAGG-ACTAATTTAGAATAAGAGTTATA
208951 GTTT
1 GTTT
208955 AAGGATGTGT
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
58 6 0.06
59 31 0.30
60 66 0.64
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.36
Consensus pattern (59 bp):
GTTTGAGATGAAATTGAAATATTTAAAAGTTTGAGGACTAATTTAGAATAAGAGTTATA
Found at i:213605 original size:23 final size:23
Alignment explanation
Indices: 213570--213622 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
213560 TGTTTATAAG
*
213570 ATTTT-TTTTTCTTTTAGTGTTA
1 ATTTTGTTATTCTTTTAGTGTTA
* *
213592 ATTTTGTTATTCTTTTATTTTTA
1 ATTTTGTTATTCTTTTAGTGTTA
*
213615 TTTTTGTT
1 ATTTTGTT
213623 GAATAAGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.13, C:0.04, G:0.08, T:0.75
Consensus pattern (23 bp):
ATTTTGTTATTCTTTTAGTGTTA
Found at i:214760 original size:15 final size:14
Alignment explanation
Indices: 214721--214760 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
214711 TATTAATAAT
214721 AATTAAATAA-A-A
1 AATTAAATAATATA
214733 AATTAAA-AATATA
1 AATTAAATAATATA
214746 AATATAAATAATATA
1 AAT-TAAATAATATA
214761 TTTAGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.08
12 8 0.33
13 4 0.17
14 4 0.17
15 6 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTAAATAATATA
Found at i:225347 original size:24 final size:24
Alignment explanation
Indices: 225302--225349 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
225292 AACACTTTTG
*
225302 TTGAATTTCTTATTAAAGAAAATT
1 TTGAATTTCTTATTAAAAAAAATT
*
225326 TTGAATTT-TTGTTAATAAAAAATT
1 TTGAATTTCTTATTAA-AAAAAATT
225350 AATATGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (24 bp):
TTGAATTTCTTATTAAAAAAAATT
Found at i:229369 original size:44 final size:44
Alignment explanation
Indices: 229286--229369 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
229276 TTTTAATTTA
**
229286 TAATTAATATACTATATTCTTTACTTTTATATTTTTAAATAGAC
1 TAATTAATATACTATATTCTTTACTTTTATATTAGTAAATAGAC
* *
229330 TAATTAATATACTATTTTTTTTTACTTTTATA-TAGTAAAT
1 TAATTAATATACTA-TATTCTTTACTTTTATATTAGTAAAT
229370 TTTAAACAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
44 20 0.57
45 15 0.43
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (44 bp):
TAATTAATATACTATATTCTTTACTTTTATATTAGTAAATAGAC
Found at i:251908 original size:13 final size:13
Alignment explanation
Indices: 251890--251915 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
251880 CTCCTATTTC
251890 ACTGAATTTTATA
1 ACTGAATTTTATA
251903 ACTGAATTTTATA
1 ACTGAATTTTATA
251916 TATCAATTTT
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:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
ACTGAATTTTATA
Found at i:261356 original size:110 final size:111
Alignment explanation
Indices: 261107--261370 Score: 406
Period size: 111 Copynumber: 2.4 Consensus size: 111
261097 CTATTAAAGA
* *
261107 AAAAATTCGGTTAATTCGGTTCGGTTAATCGAATCAAAATTTATTTGAAAATGATTAACCGAATC
1 AAAAATTCGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATGATTAACCGAAAC
261172 GAATTAACCGATTTTTTTAAAAATTATTAAGTGAATTAATCGAAGC
66 GAATTAACCGATTTTTTTAAAAATTATTAAGTGAATTAATCGAAGC
* * * *
261218 AAAAAATCGGTTAATTCGGTTTGGTTAATCAAACCAAAATTTATTTGAAAATTATTAACCGAAAC
1 AAAAATTCGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATGATTAACCGAAAC
* *
261283 -AAGTTAACCGGTTTTTTT-TAAATTATTAAGTGAATTAATCGAAGC
66 GAA-TTAACCGATTTTTTTAAAAATTATTAAGTGAATTAATCGAAGC
* *
261328 AAAAATTTGGTTAATTCGGTTCGATTAATCGAACCGAAAATTT
1 AAAAATTCGGTTAATTCGGTTCGGTTAATCGAACC-AAAATTT
261371 TTTTAACCGA
Statistics
Matches: 138, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
110 58 0.42
111 80 0.58
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (111 bp):
AAAAATTCGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATGATTAACCGAAAC
GAATTAACCGATTTTTTTAAAAATTATTAAGTGAATTAATCGAAGC
Found at i:261921 original size:26 final size:24
Alignment explanation
Indices: 261892--261940 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
261882 ATTGACATCG
261892 AAATCTAATATTTTATATTAAAAAAT
1 AAATCTAATATTTT-T-TTAAAAAAT
*
261918 AAATTTAATATTTTTTTAAAAAA
1 AAATCTAATATTTTTTTAAAAAA
261941 AATAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 1 0.05
26 13 0.59
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATCTAATATTTTTTTAAAAAAT
Found at i:270820 original size:15 final size:14
Alignment explanation
Indices: 270794--270833 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
270784 ATTTAAAATG
270794 TATTATTATTTTAA
1 TATTATTATTTTAA
*
270808 TATTATGTATTTTAT
1 TATTAT-TATTTTAA
*
270823 TATTTTTATTT
1 TATTATTATTT
270834 ACATGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TATTATTATTTTAA
Found at i:273557 original size:42 final size:42
Alignment explanation
Indices: 273495--273884 Score: 247
Period size: 41 Copynumber: 9.5 Consensus size: 42
273485 CGCCACAAAA
273495 TAGTAACTTTAGCGGCGTTTTTATACAAAACGCCGCAACAGAG
1 TAGT-ACTTTAGCGGCGTTTTTATACAAAACGCCGCAACAGAG
* * * *
273538 TAGTATTTTAGTGGTGTTTTTATAC-AAACGCCGCAATAG-G
1 TAGTACTTTAGCGGCGTTTTTATACAAAACGCCGCAACAGAG
** * * ** *
273578 T--TCATCCATAGTGGCGTTTTT-TAAACAAACGCCGTGACATAG
1 TAGT-A-CTTTAGCGGCGTTTTTATACA-AAACGCCGCAACAGAG
* * *
273620 TAGTACTTTAGCGGCGTTTTAATA-AAAACGCCGCAATAGGG
1 TAGTACTTTAGCGGCGTTTTTATACAAAACGCCGCAACAGAG
* * * *
273661 TTCA-TA-TATTA-TGGCATTTTCA-A-TAAACGCCGCAACAGAG
1 -T-AGTACT-TTAGCGGCGTTTTTATACAAAACGCCGCAACAGAG
* *
273701 TAGTACTTTAGCGGCGTTTTTTATAC-AAACACCGCAAAAGAG
1 TAGTACTTTAGCGGCG-TTTTTATACAAAACGCCGCAACAGAG
* *
273743 TAGTACTTTAGCGGCGTTTTTATACAAAA-GCCGCTATAGA-
1 TAGTACTTTAGCGGCGTTTTTATACAAAACGCCGCAACAGAG
* * * * * * *
273783 CACATACTTTAGTGGCGTTTTTATTC-AAACGCCGCTATA-AA
1 TA-GTACTTTAGCGGCGTTTTTATACAAAACGCCGCAACAGAG
* * * * *
273824 TACGTTCTTTAGCGGCATTTTTATAC-AAACGCCGCTATAGAC
1 TA-GTACTTTAGCGGCGTTTTTATACAAAACGCCGCAACAGAG
* *
273866 TCGTACTTTAGTGGCGTTT
1 TAGTACTTTAGCGGCGTTT
273885 GTGTTTACAA
Statistics
Matches: 274, Mismatches: 51, Indels: 46
0.74 0.14 0.12
Matches are distributed among these distances:
38 2 0.01
39 9 0.03
40 38 0.14
41 141 0.51
42 75 0.27
43 8 0.03
44 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (42 bp):
TAGTACTTTAGCGGCGTTTTTATACAAAACGCCGCAACAGAG
Found at i:278735 original size:43 final size:41
Alignment explanation
Indices: 278559--278791 Score: 252
Period size: 42 Copynumber: 5.5 Consensus size: 41
278549 GGCGTTTGCA
** *
278559 TCCAAAAACGCCGCTATAGATCTGAAATTTTACGGCGTTTAT
1 TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTT-T
* *
278601 TCCAAAAACGCCGCTATAAATCTGACCTTTTGCAGCGTTTT
1 TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTT
*
278642 CTCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCG-TTT
1 -TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTT
* * * *
278683 TCATAGAAAATGCCGTTATAGATCTCGACCTATTGCGGCGTTTGT
1 TC-CA-AAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTT-T
* * *
278728 TCCGAAAAACGCCGCTATAGAGCCGACCTGTTGCGGCGTTTT
1 TCC-AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTT
**
278770 CTAAAAAAACGCCGCTATAGAT
1 -TCCAAAAACGCCGCTATAGAT
278792 TTAGACCGAT
Statistics
Matches: 161, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
40 2 0.01
41 5 0.03
42 104 0.65
43 29 0.18
44 17 0.11
45 4 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (41 bp):
TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTT
Found at i:278762 original size:86 final size:84
Alignment explanation
Indices: 278547--278831 Score: 261
Period size: 86 Copynumber: 3.3 Consensus size: 84
278537 ACGATAATTA
* * * * * * **
278547 GCGGCGTTTGCATCCAAAAACGCCGCTATAGATCTGAAATTTTACGGCGTTTAT-TCCAAAAACG
1 GCGGCGTTTTC-TCCAAAAACGCCGCTATAGAGCCGACATGTTGCGGCGTTT-TCTAAAAAAACG
* *
278611 CCGCTATAAATCTGACCTTTT
64 CCGCTATAGATCTGACCTATT
* * * * * *
278632 GCAGCGTTTTCTCCAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTTC-ATAGAAAATGC
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGAGCCGACATGTTGCGGCGTTTTCTA-AAAAAACGC
*
278696 CGTTATAGATCTCGACCTATT
65 CGCTATAGATCT-GACCTATT
*
278717 GCGGCGTTTGT-TCCGAAAAACGCCGCTATAGAGCCGACCTGTTGCGGCGTTTTCTAAAAAAACG
1 GCGGCGTTT-TCTCC-AAAAACGCCGCTATAGAGCCGACATGTTGCGGCGTTTTCTAAAAAAACG
* *
278781 CCGCTATAGATTTAGACCGATT
64 CCGCTATAGATCT-GACCTATT
* * *
278803 GCGGCATTTTTTTTCCACAAACGCCGCTA
1 GCGGC--GTTTTCTCCAAAAACGCCGCTA
278832 ACTTTAGCGA
Statistics
Matches: 167, Mismatches: 24, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
83 1 0.01
84 54 0.32
85 27 0.16
86 65 0.39
87 14 0.08
88 6 0.04
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (84 bp):
GCGGCGTTTTCTCCAAAAACGCCGCTATAGAGCCGACATGTTGCGGCGTTTTCTAAAAAAACGCC
GCTATAGATCTGACCTATT
Found at i:280330 original size:2 final size:2
Alignment explanation
Indices: 280318--280370 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
280308 TATACTTCGA
280318 AT AT A- 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
*
280359 AC AT AT -T AT AT A
1 AT AT AT AT AT AT A
280371 GATTTTTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:290546 original size:44 final size:44
Alignment explanation
Indices: 290483--290586 Score: 208
Period size: 44 Copynumber: 2.4 Consensus size: 44
290473 GGTGTTTTAG
290483 TTCCGAGTGATGTCTTACTCCAAAATAATAATAAATAAAAAAGT
1 TTCCGAGTGATGTCTTACTCCAAAATAATAATAAATAAAAAAGT
290527 TTCCGAGTGATGTCTTACTCCAAAATAATAATAAATAAAAAAGT
1 TTCCGAGTGATGTCTTACTCCAAAATAATAATAAATAAAAAAGT
290571 TTCCGAGTGATGTCTT
1 TTCCGAGTGATGTCTT
290587 GGCAGGTGAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (44 bp):
TTCCGAGTGATGTCTTACTCCAAAATAATAATAAATAAAAAAGT
Found at i:292049 original size:44 final size:43
Alignment explanation
Indices: 291970--292053 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 43
291960 CAAGAATAGT
* *
291970 TGTAATATGTTAATTTGGTGCATTTGTGAATTGTTACTTTGAA
1 TGTAATATGTTAATTTAGTGCATTTGTGAAATGTTACTTTGAA
* *
292013 TGTAATATGTTTAGTTTAGTGTATTTGTGAAATGTTACTTT
1 TGTAATATG-TTAATTTAGTGCATTTGTGAAATGTTACTTT
292054 AGAGTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 9 0.25
44 27 0.75
ACGTcount: A:0.25, C:0.04, G:0.20, T:0.51
Consensus pattern (43 bp):
TGTAATATGTTAATTTAGTGCATTTGTGAAATGTTACTTTGAA
Found at i:296804 original size:18 final size:18
Alignment explanation
Indices: 296781--296822 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
296771 TTTGCATGGA
296781 GAATCTGATTCTTTCCAG
1 GAATCTGATTCTTTCCAG
296799 GAATCTGATTCTTTCCAG
1 GAATCTGATTCTTTCCAG
296817 GAATCT
1 GAATCT
296823 AATACGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (18 bp):
GAATCTGATTCTTTCCAG
Found at i:306700 original size:90 final size:90
Alignment explanation
Indices: 306547--306726 Score: 315
Period size: 90 Copynumber: 2.0 Consensus size: 90
306537 AAAAGTCGGT
* *
306547 TTCATCTAGTTAGCGTACACAACGAGCCTTTTCTTCCTGTTCCAACCCTAGTGATTTCCGTGCAT
1 TTCATCTAGTTAGCGTACACAACAAGCCTTTTCTTCCTGTCCCAACCCTAGTGATTTCCGTGCAT
306612 TTGCAATACCTTCTGGACCTGCAGC
66 TTGCAATACCTTCTGGACCTGCAGC
* *
306637 TTCATCTAGTTAGCGTACACGACAAGCCTTTTCTTCCTGTCCCAACCCTAGTGATTTCTGTGCAT
1 TTCATCTAGTTAGCGTACACAACAAGCCTTTTCTTCCTGTCCCAACCCTAGTGATTTCCGTGCAT
*
306702 TTGCAATACCTTCTGGATCTGCAGC
66 TTGCAATACCTTCTGGACCTGCAGC
306727 AATACGAATC
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (90 bp):
TTCATCTAGTTAGCGTACACAACAAGCCTTTTCTTCCTGTCCCAACCCTAGTGATTTCCGTGCAT
TTGCAATACCTTCTGGACCTGCAGC
Found at i:309493 original size:20 final size:20
Alignment explanation
Indices: 309443--309495 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
309433 GATTTTCCAG
* *
309443 AATCGCAACGCGAATATAAA
1 AATCGCAACGTGAACATAAA
*
309463 AATCGCAACGTGAACATATA
1 AATCGCAACGTGAACATAAA
*
309483 AATCACAACGTGA
1 AATCGCAACGTGA
309496 TTCTGACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (20 bp):
AATCGCAACGTGAACATAAA
Found at i:309552 original size:20 final size:20
Alignment explanation
Indices: 309504--309676 Score: 177
Period size: 20 Copynumber: 8.6 Consensus size: 20
309494 GATTCTGACT
* *
309504 ATCGTAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
309525 ATCCCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
309545 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
309565 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
309585 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
309605 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
309625 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
* *
309646 ATCGTAACGCGTATCCATAA
1 ATCGCAACGCGTATCCGTAA
309666 ATCGCAACGCG
1 ATCGCAACGCG
309677 ATTTTTAAAG
Statistics
Matches: 122, Mismatches: 27, Indels: 7
0.78 0.17 0.04
Matches are distributed among these distances:
20 92 0.75
21 30 0.25
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:309575 original size:40 final size:41
Alignment explanation
Indices: 309504--309674 Score: 247
Period size: 40 Copynumber: 4.2 Consensus size: 41
309494 GATTCTGACT
* * * *
309504 ATCGTAACGAGTATCCGTAAAATCCCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
309545 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
309585 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
309625 ATCGCAACGACAATACGTAAAATCGTAACGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
309666 ATCGCAACG
1 ATCGCAACG
309675 CGATTTTTAA
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 75 0.64
41 43 0.36
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:310295 original size:21 final size:21
Alignment explanation
Indices: 310234--310326 Score: 106
Period size: 20 Copynumber: 4.6 Consensus size: 21
310224 TTCTAAACTT
*
310234 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGACGAAAATG
310254 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGACGAAAATG
**
310274 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAACGACGA-AAATG
310295 AAAATCGCAACG-CG-AAATG
1 AAAATCGCAACGACGAAAATG
*
310314 AAAATCTCAACGA
1 AAAATCGCAACGA
310327 GATAATCGCA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.25
20 30 0.48
21 17 0.27
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGACGAAAATG
Found at i:310313 original size:40 final size:40
Alignment explanation
Indices: 310234--310328 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
310224 TTCTAAACTT
310234 AAAATCGCAAC-ATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATCGCAACGA-GAAAATGAAAATCGCAACACGAAAATG
** *
310274 ACTATCGCAACGAGAGAAATGAAAATCGCAACGCG-AAATG
1 AAAATCGCAACGAGA-AAATGAAAATCGCAACACGAAAATG
*
310314 AAAATCTCAACGAGA
1 AAAATCGCAACGAGA
310329 TAATCGCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 28 0.60
41 19 0.40
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.13
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAATCGCAACACGAAAATG
Found at i:310442 original size:20 final size:20
Alignment explanation
Indices: 310380--310435 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
310370 TCGCGTTACG
310380 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
310400 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
310420 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
310436 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:312270 original size:82 final size:83
Alignment explanation
Indices: 312133--312477 Score: 370
Period size: 94 Copynumber: 3.9 Consensus size: 83
312123 TAGATTGCTT
* * *
312133 AGTAAATTTATTC-AGTTGCTGCCAATACTGCTAAACTATTTATTCTTTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGA-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
312197 TATTTGTCTTTTGGTTG-A
65 TATTTGTCTTTTGGTTGAA
312215 AGTAAATTTATTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGGTAAT
1 AGTAAATTTATTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAA-GT--T
*
312280 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
63 A---G----T-ATTTGTCTTTTGGTTGAA
* * *
312309 ATTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
312374 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 A-----------TTTGTCTTTTGGTTGAA
* * * *
312403 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTTTGAAGTTAGT
1 AGTAAATTTATTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
312468 ATTTGTCTTT
66 ATTTGTCTTT
312478 GTTTTGTCTT
Statistics
Matches: 228, Mismatches: 11, Indels: 47
0.80 0.04 0.16
Matches are distributed among these distances:
82 54 0.24
83 12 0.05
84 1 0.00
85 2 0.01
88 2 0.01
91 2 0.01
92 1 0.00
93 17 0.07
94 137 0.60
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (83 bp):
AGTAAATTTATTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTTGGTTGAA
Found at i:312359 original size:94 final size:94
Alignment explanation
Indices: 312199--312500 Score: 518
Period size: 94 Copynumber: 3.2 Consensus size: 94
312189 GAAGTTAGTA
* *
312199 TTTGTCTTTTGGTTG-AAGTAAATTTATTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
* *
312263 AACACTGTGAAGGTAATATTTGTCTTTGT
66 AACACTGTGAAGTTAGTATTTGTCTTTGT
*
312292 TTTGTCTTTTGGTTGAAATTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
312357 AACACTGTGAAGTTAGTATTTGTCTTTGT
66 AACACTGTGAAGTTAGTATTTGTCTTTGT
312386 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
* *
312451 AATACTTTGAAGTTAGTATTTGTCTTTGT
66 AACACTGTGAAGTTAGTATTTGTCTTTGT
*
312480 TTTGTCTTTTGGCTG-AAGTAA
1 TTTGTCTTTTGGTTGAAAGTAA
312501 TGCAATCCAT
Statistics
Matches: 199, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
93 21 0.11
94 178 0.89
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
AACACTGTGAAGTTAGTATTTGTCTTTGT
Found at i:312644 original size:33 final size:33
Alignment explanation
Indices: 312588--312679 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
312578 AAAAATGACT
** * *
312588 ATCGCAACTCGAAATG--AATCACAACGAGAGA
1 ATCGCAACGAGAAATGAAAATCACAACGACAAA
*
312619 ATCGTAACGAGAAATGAAAATCACAACGACAAA
1 ATCGCAACGAGAAATGAAAATCACAACGACAAA
* *
312652 ATCGCAACGTGAAATGAAAATCGCAACG
1 ATCGCAACGAGAAATGAAAATCACAACG
312680 CGAAACTATA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 13 0.25
33 38 0.75
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAAATGAAAATCACAACGACAAA
Found at i:312754 original size:20 final size:20
Alignment explanation
Indices: 312729--312775 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
312719 GATTCTCTTG
312729 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
312749 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
312769 TTGCGAT
1 TTGCGAT
312776 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:313350 original size:21 final size:21
Alignment explanation
Indices: 313259--313363 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
313249 GACTCACTTG
*
313259 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
313281 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
313301 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
313322 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
313343 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
313364 CTAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:313363 original size:42 final size:43
Alignment explanation
Indices: 313257--313364 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 43
313247 CCGACTCACT
* *
313257 TGTCATCGTTCAAGAGG--CCTCCCCTATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGGTCCCT-CCCTACCGTTCAAGAGGCCAC
* **
313299 TATCATCCCTCAAGA-GTCCCCTCCC-ACCGTTCAAGAGGCCAC
1 TGTCATCGTTCAAGAGGT-CCCTCCCTACCGTTCAAGAGGCCAC
*
313341 TGTCATCGTTGAAGAGGTCCCTCC
1 TGTCATCGTTCAAGAGGTCCCTCC
313365 TAACATTCTA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.02
42 44 0.83
43 5 0.09
44 3 0.06
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.23
Consensus pattern (43 bp):
TGTCATCGTTCAAGAGGTCCCTCCCTACCGTTCAAGAGGCCAC
Found at i:314913 original size:33 final size:33
Alignment explanation
Indices: 314867--314950 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
314857 TTGCAACGCG
** *
314867 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
*
314900 GAAATGAAAATCGCAACGAGTGAATCACAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
*
314933 GAAAATG-AAATCGTAACG
1 G-AAATGAAAATCGCAACG
314951 TCACTCGTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
33 40 0.89
34 5 0.11
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATGC
Found at i:315595 original size:20 final size:19
Alignment explanation
Indices: 315574--315851 Score: 161
Period size: 20 Copynumber: 13.9 Consensus size: 19
315564 GCGATAGTCA
315574 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
* * *
315593 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
315613 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* *
315633 GTAATCGCATTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
315653 GTAA--TCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* * *
315671 GGATACACATTGCGATTTAC
1 GAAT-CTCGTTGCGATTTAC
*
315691 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
*
315711 -AGATACGCGTTGCGATTTAC
1 GA-AT-CTCGTTGCGATTTAC
*
315731 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
315751 GGATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* *
315772 GTATTGTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* * *
315792 GGATACGCATTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* *
315813 GGATACTCGTTGCGATAGT-C
1 GAAT-CTCGTTGCGAT-TTAC
*
315833 AGAATCGCGTTGCGATTTA
1 -GAATCTCGTTGCGATTTA
315852 TATGTTCGCG
Statistics
Matches: 197, Mismatches: 41, Indels: 40
0.71 0.15 0.14
Matches are distributed among these distances:
17 1 0.01
18 15 0.08
19 6 0.03
20 132 0.67
21 40 0.20
22 3 0.02
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Done.