Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002651.1 Hibiscus syriacus cultivar Beakdansim tig00005423_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: 108214
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1866 original size:70 final size:71
Alignment explanation
Indices: 1772--1907 Score: 211
Period size: 71 Copynumber: 1.9 Consensus size: 71
1762 GTCTCTACAG
*
1772 GTTCAGCTCGATCAAACTAGTAATTC-TTATATAGGTTCAGACCAATCGAATTGGTAATTCCTTA
1 GTTCAGCTCGATCAAACTAGTAATTCTTTATATAGGTTCAGACCAATCGAACTGGTAATTCCTTA
1836 CTGCAA
66 CTGCAA
* * * * *
1842 GTTCAGCTCGGTCAAATTGGTAATTCTTTATATAGGTTCAGACCGATCGAGCTGGTAATTCCTTA
1 GTTCAGCTCGATCAAACTAGTAATTCTTTATATAGGTTCAGACCAATCGAACTGGTAATTCCTTA
1907 C
66 C
1908 GGATCAAGAC
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
70 23 0.39
71 36 0.61
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (71 bp):
GTTCAGCTCGATCAAACTAGTAATTCTTTATATAGGTTCAGACCAATCGAACTGGTAATTCCTTA
CTGCAA
Found at i:1898 original size:35 final size:34
Alignment explanation
Indices: 1791--1902 Score: 109
Period size: 35 Copynumber: 3.2 Consensus size: 34
1781 GATCAAACTA
*
1791 GTAATTCTTATATAGGTTCAGACCAATCGAATTG
1 GTAATTCTTATATAGGTTCAGACCGATCGAATTG
** * * *
1825 GTAATTCCTTACTGCAAGTTCAG-CTCGGTCAAATTG
1 GTAATT-CTTA-TATAGGTTCAGAC-CGATCGAATTG
**
1861 GTAATTCTTTATATAGGTTCAGACCGATCGAGCTG
1 GTAATTC-TTATATAGGTTCAGACCGATCGAATTG
1896 GTAATTC
1 GTAATTC
1903 CTTACGGATC
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
34 6 0.10
35 28 0.47
36 26 0.43
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (34 bp):
GTAATTCTTATATAGGTTCAGACCGATCGAATTG
Found at i:3295 original size:2 final size:2
Alignment explanation
Indices: 3288--3349 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3278 TTAGCTCCAA
3288 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3330 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
3350 ATTTGAATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4483 original size:22 final size:22
Alignment explanation
Indices: 4455--4507 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
4445 ATTAGGAAAA
4455 TATAAAAATTAGCTCTCAATTT
1 TATAAAAATTAGCTCTCAATTT
4477 TATAAAAATTAGCTCTCAATTT
1 TATAAAAATTAGCTCTCAATTT
4499 TATAAAAAT
1 TATAAAAAT
4508 GATCGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (22 bp):
TATAAAAATTAGCTCTCAATTT
Found at i:16632 original size:17 final size:17
Alignment explanation
Indices: 16610--16662 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
16600 TGAATAAAGT
16610 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
16627 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
16644 TAGTTCATTTATTAGAC
1 TAGTTCATTAATTAAAC
16661 TA
1 TA
16663 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:20663 original size:18 final size:17
Alignment explanation
Indices: 20637--20700 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
20627 TCATTCATGC
20637 ATCTAGTTCATTGAATAA
1 ATCTAGTTCATT-AATAA
*
20655 AGT-TAGTTCATTAATTA
1 A-TCTAGTTCATTAATAA
*
20672 ATCTAGTTCATTCATCAA
1 ATCTAGTTCATTAAT-AA
20690 A-CTAGTTCATT
1 ATCTAGTTCATT
20701 TATTAGACTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 1 0.03
17 26 0.65
18 12 0.30
19 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (17 bp):
ATCTAGTTCATTAATAA
Found at i:20710 original size:17 final size:16
Alignment explanation
Indices: 20639--20710 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
20629 ATTCATGCAT
*
20639 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATTAA
*
20656 GTTAGTTCATTAATTAA
1 -CTAGTTCATTAATTAA
* *
20673 TCTAGTTCATTCATCAAA
1 -CTAGTTCATTAAT-TAA
*
20691 CTAGTTCATTTATTAGA
1 CTAGTTCATTAATTA-A
20708 CTA
1 CTA
20711 ACTCTTAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
16 1 0.02
17 32 0.73
18 11 0.25
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (16 bp):
CTAGTTCATTAATTAA
Found at i:25393 original size:19 final size:19
Alignment explanation
Indices: 25369--25412 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
25359 GATCAGACTG
*
25369 GTCAACGGGTC-AGGTTAAA
1 GTCAACGGGTCGA-GTCAAA
25388 GTCAACGGGTCGAGTCAAA
1 GTCAACGGGTCGAGTCAAA
25407 GTCAAC
1 GTCAAC
25413 AGGCCCAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (19 bp):
GTCAACGGGTCGAGTCAAA
Found at i:26544 original size:10 final size:10
Alignment explanation
Indices: 26529--26568 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
26519 CAAGATTTTG
26529 CGTTCGTTTA
1 CGTTCGTTTA
26539 CGTTCGATTATA
1 CGTTCG-TT-TA
*
26551 TGTTCGTTTA
1 CGTTCGTTTA
26561 CGTTCGTT
1 CGTTCGTT
26569 CATTTATGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 15 0.58
11 4 0.15
12 7 0.27
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.50
Consensus pattern (10 bp):
CGTTCGTTTA
Found at i:26597 original size:10 final size:10
Alignment explanation
Indices: 26566--26599 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
26556 GTTTACGTTC
26566 GTTCATTTAT
1 GTTCATTTAT
*
26576 GCTCATTTAT
1 GTTCATTTAT
26586 GTTCATTTAT
1 GTTCATTTAT
26596 GTTC
1 GTTC
26600 GTTCATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.56
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:26605 original size:14 final size:14
Alignment explanation
Indices: 26586--26612 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26576 GCTCATTTAT
26586 GTTCATTTATGTTC
1 GTTCATTTATGTTC
26600 GTTCATTTATGTT
1 GTTCATTTATGTT
26613 TGAACAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.15, T:0.59
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:26900 original size:13 final size:13
Alignment explanation
Indices: 26884--26939 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 13
26874 GTGTTTGTGT
26884 TGTTCGTTTATTG
1 TGTTCGTTTATTG
26897 TGTTCGTTTA---
1 TGTTCGTTTATTG
* *
26907 TGTTCATTTATTA
1 TGTTCGTTTATTG
26920 TGTTCG--T-TTG
1 TGTTCGTTTATTG
26930 TGTTCGTTTA
1 TGTTCGTTTA
26940 CGTTCGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
10 17 0.50
11 1 0.03
12 1 0.03
13 15 0.44
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.61
Consensus pattern (13 bp):
TGTTCGTTTATTG
Found at i:26916 original size:10 final size:10
Alignment explanation
Indices: 26897--26960 Score: 74
Period size: 10 Copynumber: 6.1 Consensus size: 10
26887 TCGTTTATTG
26897 TGTTCGTTTA
1 TGTTCGTTTA
*
26907 TGTTCATTTATTA
1 TGTTC--GT-TTA
*
26920 TGTTCGTTTG
1 TGTTCGTTTA
26930 TGTTCGTTTA
1 TGTTCGTTTA
*
26940 CGTTCGTTTA
1 TGTTCGTTTA
26950 TGTTCGTTTA
1 TGTTCGTTTA
26960 T
1 T
26961 CATTTAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
10 35 0.78
11 1 0.02
12 1 0.02
13 8 0.18
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:26916 original size:23 final size:22
Alignment explanation
Indices: 26884--26960 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
26874 GTGTTTGTGT
26884 TGTTCGTTTATTGTGTTCGTTTA
1 TGTTCGTTTATT-TGTTCGTTTA
* *
26907 TGTTCATTTATTATGTTCGTTTG
1 TGTTCGTTTATT-TGTTCGTTTA
*
26930 TGTTCGTTTA--CGTTCGTTTA
1 TGTTCGTTTATTTGTTCGTTTA
26950 TGTTCGTTTAT
1 TGTTCGTTTAT
26961 CATTTAAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 18 0.38
23 29 0.62
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (22 bp):
TGTTCGTTTATTTGTTCGTTTA
Found at i:29603 original size:18 final size:18
Alignment explanation
Indices: 29563--29606 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
29553 ATCTATTAAG
29563 TAAAATAATAAAATATCA
1 TAAAATAATAAAATATCA
*
29581 T-AAATACTAAAAATAT-A
1 TAAAATAAT-AAAATATCA
29598 TAAAATAAT
1 TAAAATAAT
29607 TATTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAATAATAAAATATCA
Found at i:31499 original size:22 final size:19
Alignment explanation
Indices: 31472--31540 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 19
31462 GTTCAGTATT
31472 CGTCCCGAAGGACTGCTATATA
1 CGTCCCGAAGGACT-C-AT-TA
* *
31494 TGTCCCGTAGGAC-CATTA
1 CGTCCCGAAGGACTCATTA
31512 CGTCCCGAAGGA--C--TA
1 CGTCCCGAAGGACTCATTA
31527 CGTCCCGAAGGACT
1 CGTCCCGAAGGACT
31541 ACAGAACCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
15 14 0.34
17 1 0.02
18 12 0.29
19 2 0.05
20 1 0.02
22 11 0.27
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (19 bp):
CGTCCCGAAGGACTCATTA
Found at i:31530 original size:15 final size:15
Alignment explanation
Indices: 31510--31542 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
31500 GTAGGACCAT
31510 TACGTCCCGAAGGAC
1 TACGTCCCGAAGGAC
31525 TACGTCCCGAAGGAC
1 TACGTCCCGAAGGAC
31540 TAC
1 TAC
31543 AGAACCCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.15
Consensus pattern (15 bp):
TACGTCCCGAAGGAC
Found at i:38391 original size:15 final size:15
Alignment explanation
Indices: 38371--38401 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38361 GGACCATTAC
38371 CGTCCCGAAAGACTA
1 CGTCCCGAAAGACTA
*
38386 CGTCCCGAAGGACTA
1 CGTCCCGAAAGACTA
38401 C
1 C
38402 AGAACCCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (15 bp):
CGTCCCGAAAGACTA
Found at i:41157 original size:26 final size:26
Alignment explanation
Indices: 41128--41180 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
41118 TTCGATAATC
*
41128 TTAGAGTTTA-AGGTATTCTGGTTATT
1 TTAGAGTTTAGA-GTATTCTGGTCATT
* *
41154 TTAGGGTTTAGAGTATTTTGGTCATT
1 TTAGAGTTTAGAGTATTCTGGTCATT
41180 T
1 T
41181 GAATATTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.25, T:0.51
Consensus pattern (26 bp):
TTAGAGTTTAGAGTATTCTGGTCATT
Found at i:52860 original size:29 final size:29
Alignment explanation
Indices: 52703--52864 Score: 177
Period size: 29 Copynumber: 5.6 Consensus size: 29
52693 CCACATTCGA
* * * *
52703 AATTACAAAAATATCACCTTTTTAAAAAT
1 AATTACCAAAATGTCATCGTTTTAAAAAT
*
52732 AATTACCAAAATATCA-CTGTTTTAAAAAT
1 AATTACCAAAATGTCATC-GTTTTAAAAAT
* *
52761 AATTACCAAAATATCATCGTTTTACAAAT
1 AATTACCAAAATGTCATCGTTTTAAAAAT
*
52790 AATTCCCAAAATGTCATCGTTTTAAAAAT
1 AATTACCAAAATGTCATCGTTTTAAAAAT
*
52819 AATTACCAGAATGTCA-CTGTTTTTAAAAA-
1 AATTACCAAAATGTCATC-G-TTTTAAAAAT
* *
52848 AATTCCCTAAATGTCAT
1 AATTACCAAAATGTCAT
52865 TGGGTCGGGT
Statistics
Matches: 117, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
28 2 0.02
29 105 0.90
30 10 0.09
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (29 bp):
AATTACCAAAATGTCATCGTTTTAAAAAT
Found at i:57640 original size:180 final size:181
Alignment explanation
Indices: 57338--57698 Score: 715
Period size: 180 Copynumber: 2.0 Consensus size: 181
57328 GGTAATAAAG
57338 TCTCATCTTCTTACGACATTCTCCTCTGTGTCGACTACCACAATACTCACAAAGGGGCCCATAAT
1 TCTCATCTTCTTACGACATTCTCCTCTGTGTCGACTACCACAATACTCACAAAGGGGCCCATAAT
57403 AAAACGACGAGGTACCACCTCGACTGACAACTAAAGGTGAAGATATGCAGGCCTAGAACTAGTAT
66 AAAACGACGAGGTACCACCTCGACTGACAACTAAAGGTGAAGATATGCAGGCCTAGAACTAGTAT
57468 TGCTTTTC-AAGGACCTGAAGTACGAGTCTTCTTTACAGGACGTGCAGAGA
131 TGCTTTTCAAAGGACCTGAAGTACGAGTCTTCTTTACAGGACGTGCAGAGA
57518 TCTCATCTTCTTACGACATTCTCCTCTGTGTCGACTACCACAATACTCACAAAGGGGCCCATAAT
1 TCTCATCTTCTTACGACATTCTCCTCTGTGTCGACTACCACAATACTCACAAAGGGGCCCATAAT
57583 AAAACGACGAGGTACCACCTCGACTGACAACTAAAGGTGAAGATATGCAGGCCTAGAACTAGTAT
66 AAAACGACGAGGTACCACCTCGACTGACAACTAAAGGTGAAGATATGCAGGCCTAGAACTAGTAT
57648 TGCTTTTCAAAGGACCTGAAGTACGAGTCTTCTTTACAGGACGTGCAGAGA
131 TGCTTTTCAAAGGACCTGAAGTACGAGTCTTCTTTACAGGACGTGCAGAGA
57699 ACTCGTTCGG
Statistics
Matches: 180, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 138 0.77
181 42 0.23
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (181 bp):
TCTCATCTTCTTACGACATTCTCCTCTGTGTCGACTACCACAATACTCACAAAGGGGCCCATAAT
AAAACGACGAGGTACCACCTCGACTGACAACTAAAGGTGAAGATATGCAGGCCTAGAACTAGTAT
TGCTTTTCAAAGGACCTGAAGTACGAGTCTTCTTTACAGGACGTGCAGAGA
Found at i:60370 original size:57 final size:57
Alignment explanation
Indices: 60218--60405 Score: 234
Period size: 58 Copynumber: 3.3 Consensus size: 57
60208 GTCCACATTC
* * * * * * *
60218 AAAAATTACAAAAATATCACCTTTTTAAAAATAATTATCAAAATATCACCGTTTTACA
1 AAAAATTCCCAAAATATCAACTTTTTAAAAATAATTACCAGAATGTCACTGTTTTA-A
* *
60276 AATAATTCCCAAAATGTCAACTTTTTAAAAATAATTACCAGAATGTCGA-TGTTTTAA
1 AAAAATTCCCAAAATATCAACTTTTTAAAAATAATTACCAGAATGTC-ACTGTTTTAA
* * *
60333 AAAAATTCCCAAAATATCATCGTTTTAAAAATTATTACCAGAATGTCACTAGTTTTAA
1 AAAAATTCCCAAAATATCAACTTTTTAAAAATAATTACCAGAATGTCACT-GTTTTAA
60391 AAAAATTCCCAAAAT
1 AAAAATTCCCAAAAT
60406 GTCACTGGGT
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
56 1 0.01
57 44 0.39
58 67 0.59
59 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (57 bp):
AAAAATTCCCAAAATATCAACTTTTTAAAAATAATTACCAGAATGTCACTGTTTTAA
Found at i:60411 original size:29 final size:29
Alignment explanation
Indices: 60221--60412 Score: 180
Period size: 29 Copynumber: 6.7 Consensus size: 29
60211 CACATTCAAA
* *
60221 AATTACAAAAATATCACCT-TTTTAAAAAT
1 AATTACCAAAATGTCA-CTGTTTTAAAAAT
* * * *
60250 AATTATCAAAATATCACCGTTTTACAAAT
1 AATTACCAAAATGTCACTGTTTTAAAAAT
*
60279 AATTCCCAAAATGTCAACT-TTTTAAAAAT
1 AATTACCAAAATGTC-ACTGTTTTAAAAAT
*
60308 AATTACCAGAATGTCGA-TGTTTTAAAAA-
1 AATTACCAAAATGTC-ACTGTTTTAAAAAT
* *
60336 AATTCCCAAAATATCA-TCGTTTTAAAAAT
1 AATTACCAAAATGTCACT-GTTTTAAAAAT
* *
60365 TATTACCAGAATGTCACTAGTTTTAAAAA-
1 AATTACCAAAATGTCACT-GTTTTAAAAAT
*
60394 AATTCCCAAAATGTCACTG
1 AATTACCAAAATGTCACTG
60413 GGTCGGGTCG
Statistics
Matches: 134, Mismatches: 23, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
27 2 0.01
28 25 0.19
29 94 0.70
30 13 0.10
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.33
Consensus pattern (29 bp):
AATTACCAAAATGTCACTGTTTTAAAAAT
Found at i:61416 original size:23 final size:24
Alignment explanation
Indices: 61379--61424 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
61369 TTCGATATTG
61379 AAAAAATATTAAAATAATTTATTTT
1 AAAAAATATTAAAATAA-TTATTTT
*
61404 AAAAAATA-T-AAATTATTATTT
1 AAAAAATATTAAAATAATTATTT
61425 ATCATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 1 0.05
25 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAAATATTAAAATAATTATTTT
Found at i:62432 original size:12 final size:13
Alignment explanation
Indices: 62410--62438 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
62400 GGCTGTCCTC
62410 TTTTCTTTTTCTG
1 TTTTCTTTTTCTG
62423 TTTT-TTTTTCTG
1 TTTTCTTTTTCTG
62435 TTTT
1 TTTT
62439 GTTTGTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTCTG
Found at i:62836 original size:3 final size:3
Alignment explanation
Indices: 62828--62933 Score: 133
Period size: 3 Copynumber: 34.7 Consensus size: 3
62818 GGCCCGTTTG
* * *
62828 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAAA TAA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA
* *
62875 TTA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
62923 TAA TAA TAA TA
1 TAA TAA TAA TA
62934 TTTAAATGAA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
2 2 0.02
3 81 0.90
4 7 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:73087 original size:32 final size:31
Alignment explanation
Indices: 73048--73119 Score: 135
Period size: 32 Copynumber: 2.3 Consensus size: 31
73038 CGAAAATATT
73048 TTATATATAATTAATATAAAATATATAAAATA
1 TTATATATAATTAATATAAAA-ATATAAAATA
73080 TTATATATAATTAATATAAAAATATAAAATA
1 TTATATATAATTAATATAAAAATATAAAATA
73111 TTATATATA
1 TTATATATA
73120 TATAATCGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 19 0.47
32 21 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TTATATATAATTAATATAAAAATATAAAATA
Found at i:73997 original size:46 final size:46
Alignment explanation
Indices: 73922--74010 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
73912 ACAACCTTGG
* * *
73922 GAAGATGGAGAACAATCAAGTAGCTGGAGAAAAATCCATGAGAGAT
1 GAAGATGGAGAACAATCAAGCAACCGGAGAAAAATCCATGAGAGAT
* *
73968 GAAGATGGAGAATAATCAAGCAACCGGAGAAGAATCCATGAGA
1 GAAGATGGAGAACAATCAAGCAACCGGAGAAAAATCCATGAGA
74011 AAGGAGGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.46, C:0.12, G:0.28, T:0.13
Consensus pattern (46 bp):
GAAGATGGAGAACAATCAAGCAACCGGAGAAAAATCCATGAGAGAT
Found at i:76766 original size:12 final size:12
Alignment explanation
Indices: 76749--76776 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
76739 TCTTCTTCTC
76749 CTCCCCGTTCAT
1 CTCCCCGTTCAT
76761 CTCCCCGTTCAT
1 CTCCCCGTTCAT
76773 CTCC
1 CTCC
76777 TCCGACTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.54, G:0.07, T:0.32
Consensus pattern (12 bp):
CTCCCCGTTCAT
Found at i:81559 original size:12 final size:12
Alignment explanation
Indices: 81539--81571 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
81529 ATAAGAGAAA
81539 TAGAGAGAAATT
1 TAGAGAGAAATT
*
81551 TATAGAGAAATT
1 TAGAGAGAAATT
81563 TAGAGAGAA
1 TAGAGAGAA
81572 TTCAGAGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
TAGAGAGAAATT
Found at i:81975 original size:12 final size:12
Alignment explanation
Indices: 81955--81984 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
81945 TCTTCTTCTC
*
81955 CTCCCCGTTCAT
1 CTCCTCGTTCAT
81967 CTCCTCGTTCAT
1 CTCCTCGTTCAT
81979 CTCCTC
1 CTCCTC
81985 CGACTGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.50, G:0.07, T:0.37
Consensus pattern (12 bp):
CTCCTCGTTCAT
Found at i:85935 original size:26 final size:24
Alignment explanation
Indices: 85906--85954 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 24
85896 TTAATATATA
85906 AAATATCATATAAACAATAGTACGAG
1 AAATATCATATAAA-AATA-TACGAG
85932 AAATATCATATAAAAATATACGA
1 AAATATCATATAAAAATATACGA
85955 ACATATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.22
25 4 0.17
26 14 0.61
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.24
Consensus pattern (24 bp):
AAATATCATATAAAAATATACGAG
Found at i:88293 original size:23 final size:23
Alignment explanation
Indices: 88259--88319 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
88249 CCGTCTGACT
*
88259 GTTGATCGATCTGACTGTTAACC
1 GTTGATCAATCTGACTGTTAACC
88282 GTTGATCAATCTGACTGTTAACC
1 GTTGATCAATCTGACTGTTAACC
* *
88305 GTTGATTAGTCTGAC
1 GTTGATCAATCTGAC
88320 CGTTGATCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (23 bp):
GTTGATCAATCTGACTGTTAACC
Found at i:92128 original size:16 final size:16
Alignment explanation
Indices: 92117--92173 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
92107 TCAAATAATA
*
92117 AAAATAAAAAATA-GT
1 AAAATAAAAAATACAT
92132 AAAATAAAAACA-ACAT
1 AAAATAAAAA-ATACAT
* *
92148 AAAATAAAAATTAGAT
1 AAAATAAAAAATACAT
92164 AAACATAAAA
1 AAA-ATAAAA
92174 TATGACTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 11 0.31
16 18 0.51
17 6 0.17
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.18
Consensus pattern (16 bp):
AAAATAAAAAATACAT
Found at i:92157 original size:22 final size:22
Alignment explanation
Indices: 92132--92175 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
92122 AAAAAATAGT
92132 AAAA-TAAAAACAACATAAAATA
1 AAAATTAAAAA-AACATAAAATA
* *
92154 AAAATTAGATAAACATAAAATA
1 AAAATTAAAAAAACATAAAATA
92176 TGACTACAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (22 bp):
AAAATTAAAAAAACATAAAATA
Found at i:93918 original size:92 final size:93
Alignment explanation
Indices: 93713--93961 Score: 259
Period size: 92 Copynumber: 2.7 Consensus size: 93
93703 TGGTCTTTCC
* * * *
93713 ACTGGAAATATTGATCCCTCGAGTGATGCATTGCTGATTCAAAATGTCGTGAATCAAGAAAAGGT
1 ACTGGAAATATTGGTCCCTCAAGTGAGGCATCGCTGATTCAAAATGTCGTGAATCAAGAAAAGGT
* *
93778 TGAACAAACTCTTCATTATGAATTCTAT
66 TGAACAAACTATTCATCATGAATTCTAT
* * * * * * **
93806 ACTGGAAATATTGGTCCCTCAAGTGAGGCGTCGTTGATTCGAAGTGTTGTGAATCGAGCCAAGGT
1 ACTGGAAATATTGGTCCCTCAAGTGAGGCATCGCTGATTCAAAATGTCGTGAATCAAGAAAAGGT
* *
93871 TGAA-AAAGTTATTC-TCATGAATTCTTT
66 TGAACAAA-CTATTCATCATGAATTCTAT
* * * ** * * *
93898 ACTGGAAATATTGGTCCCTCATGTGAGGCATCACTTATTTGAAATATTGTGAATCAAGCAAAGG
1 ACTGGAAATATTGGTCCCTCAAGTGAGGCATCGCTGATTCAAAATGTCGTGAATCAAGAAAAGG
93962 AAATATTGAT
Statistics
Matches: 129, Mismatches: 26, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
92 68 0.53
93 61 0.47
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (93 bp):
ACTGGAAATATTGGTCCCTCAAGTGAGGCATCGCTGATTCAAAATGTCGTGAATCAAGAAAAGGT
TGAACAAACTATTCATCATGAATTCTAT
Found at i:93985 original size:59 final size:59
Alignment explanation
Indices: 93901--94032 Score: 144
Period size: 59 Copynumber: 2.3 Consensus size: 59
93891 ATTCTTTACT
* *** *
93901 GGAAATATTGGTCCCTCATGTGAGGCATCACTT-ATTTGAAATATTGTGAATC-AAGCAAA
1 GGAAATATTGATCCCTCAAACGAGGCATCA-TTGATTCGAAATATTGTGAATCTAA-CAAA
* * *
93960 GGAAATATTGATCCCTCAAACGAGGCATTATTGATTCGAAGTGTTGTGAATCTAACAAA
1 GGAAATATTGATCCCTCAAACGAGGCATCATTGATTCGAAATATTGTGAATCTAACAAA
*
94019 GGAAATGTT-ATCCC
1 GGAAATATTGATCCC
94033 CTATGGTGGG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
58 7 0.11
59 53 0.85
60 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (59 bp):
GGAAATATTGATCCCTCAAACGAGGCATCATTGATTCGAAATATTGTGAATCTAACAAA
Found at i:94181 original size:39 final size:39
Alignment explanation
Indices: 94062--94356 Score: 324
Period size: 39 Copynumber: 7.5 Consensus size: 39
94052 GTTTTAAGAA
* * * *
94062 AAACAATCTCAAGTGTGAT-AAATCTTATTTTTCAAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCAAGTG
* **
94100 AAACTATCTCAAGCGAGAT-AAATCTTCTGTTTTGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCAAGTG
* *
94138 AAACTATCTCAAGTGAGATAAAATATTATGTTTCAAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCAAGTG
* * * * * *
94177 AAACTATATCAATCGAGAGGAAGATAAATCTTGTATTTCGAGTG
1 AAACTATCTCAA--GTGA-G-ATA-AAATCTTCTGTTTCAAGTG
* *
94221 AAACTATCTCAAGCGAGATAAATTCTTCTGTTTCAAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCAAGTG
* * * *
94260 AAACTATCTCAAGCGAGATAAAATTTTCCGTTTCGAGTG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCAAGTG
* *
94299 AAACTATCTCAAGTGAGATAAAATCTTCTATTTCAAGAG
1 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCAAGTG
94338 AAACTATCTCAAGTGAGAT
1 AAACTATCTCAAGTGAGAT
94357 TTTGATCCCT
Statistics
Matches: 215, Mismatches: 36, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
38 49 0.23
39 128 0.60
40 2 0.01
41 4 0.02
42 4 0.02
43 2 0.01
44 26 0.12
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (39 bp):
AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCAAGTG
Found at i:94225 original size:83 final size:82
Alignment explanation
Indices: 94062--94349 Score: 310
Period size: 83 Copynumber: 3.6 Consensus size: 82
94052 GTTTTAAGAA
* * *
94062 AAACAATCTCAAGTGTGAT-AAATCTTATTTTTCAAGTGAAAC--TATC--TC-A-AGCGAGATA
1 AAACTATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACTATATCAATCGAGAG-GAGATA
*
94120 AATCTTCTGTTTTGAGTG
65 AATCTTCTGTTTCGAGTG
*
94138 AAACTATCTCAAGTGAGATAAAATATTATGTTTCAAGTGAAACTATATCAATCGAGAGGAAGATA
1 AAACTATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACTATATCAATCGAGAGG-AGATA
* *
94203 AATCTTGTATTTCGAGTG
65 AATCTTCTGTTTCGAGTG
* * * * * *
94221 AAACTATCTCAAGCGAGATAAATTCTTCTGTTTCAAGTGAAACTATCTCAA--GCGA-GATA-AA
1 AAACTATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACTATATCAATCGAGAGGAGATAA
* *
94282 ATTTTCCGTTTCGAGTG
66 ATCTTCTGTTTCGAGTG
* * * *
94299 AAACTATCTCAAGTGAGATAAAATCTTCTATTTCAAGAGAAACTATCTCAA
1 AAACTATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACTATATCAA
94350 GTGAGATTTT
Statistics
Matches: 182, Mismatches: 22, Indels: 14
0.83 0.10 0.06
Matches are distributed among these distances:
76 17 0.09
77 21 0.12
78 62 0.34
79 6 0.03
80 1 0.01
81 5 0.03
82 2 0.01
83 68 0.37
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (82 bp):
AAACTATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACTATATCAATCGAGAGGAGATAA
ATCTTCTGTTTCGAGTG
Found at i:94326 original size:78 final size:78
Alignment explanation
Indices: 94062--94356 Score: 360
Period size: 78 Copynumber: 3.7 Consensus size: 78
94052 GTTTTAAGAA
* * *
94062 AAACAATCTCAAGTGTGAT-AAATCTTATTTTTCAAGTGAAACTATCTCAAGCGAGAT-AAATCT
1 AAACTATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCT
*
94125 TCTGTTTTGAGTG
66 TCTGTTTCGAGTG
* * * *
94138 AAACTATCTCAAGTGAGATAAAATATTATGTTTCAAGTGAAACTATATCAATCGAGAGGAAGATA
1 AAACTATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACTATCTCAA--GCGA-G-ATA-A
* *
94203 AATCTTGTATTTCGAGTG
61 AATCTTCTGTTTCGAGTG
* * * *
94221 AAACTATCTCAAGCGAGATAAATTCTTCTGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATTT
1 AAACTATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCT
*
94286 TCCGTTTCGAGTG
66 TCTGTTTCGAGTG
* * * *
94299 AAACTATCTCAAGTGAGATAAAATCTTCTATTTCAAGAGAAACTATCTCAAGTGAGAT
1 AAACTATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACTATCTCAAGCGAGAT
94357 TTTGATCCCT
Statistics
Matches: 186, Mismatches: 26, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
76 17 0.09
77 28 0.15
78 68 0.37
79 5 0.03
80 2 0.01
81 4 0.02
83 62 0.33
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (78 bp):
AAACTATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCT
TCTGTTTCGAGTG
Found at i:94944 original size:41 final size:42
Alignment explanation
Indices: 94885--94971 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 42
94875 ACCCGAAGGT
* * *
94885 CTTATGGATGACCCGAAGGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
* *
94926 CTTATAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
94968 CTTA
1 CTTA
94972 CTGATAGCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 20 0.50
42 20 0.50
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGACTTAAGCATCATGCTCGAAAGA
Found at i:95243 original size:55 final size:56
Alignment explanation
Indices: 95049--95483 Score: 353
Period size: 52 Copynumber: 7.8 Consensus size: 56
95039 GTTTTCAGTT
** * * *
95049 ATCATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTAAAAAAATTCTTTGGAAATA
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTT-TTAAAATTCATTGAAAATC
* * * * * *
95107 ATCATCAAGAAACCCCTGAAAATCAAGTTTAGTTTC--TAAAAACTCATTTG--AGT-
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTTAAAATTCA-TTGAAAATC
*
95160 A-CATCAAGAAACCCCTAAAAATTAGGCTTATTTTCTTTTAAAATTCATTGAAAATC
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTTAAAATTCATTGAAAATC
* * * * * *
95216 ATCATAAAGAAACCCCT-GAATCAGGCTTAGTTTCTTTAAAAATTCTTTTAAAA--
1 ATCATCAAGAAACCCCTAAAATTAGGCTTAGTTTCTTTTAAAATTCATTGAAAATC
* * * *
95269 AT-ATCCAGAAACCCCTAAAAATTAGGCTTAGGTTCTTTTAAAAAATTCTTTGGAAATC
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTT--AAAATTCATTGAAAATC
* * * *
95327 ATCATCAAGAAACCCCTGAAAAGTAGGCTTTGTTTC--TAAAAACTCATTTG-AAA--
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTTAAAATTCA-TTGAAAATC
* *
95380 A-CATCAAGAAACCCCTAAAAATTAGGCATAGCTTCTTTTAAGAAATTCATTGAAAATC
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAGTTTCTTTT-A-AAATTCATTGAAAATC
* *
95438 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTTTTTTTAAAAT
1 ATCATCAAGAAACCCCT-AAAATTAGGCTTAG-TTTCTTTTAAAAT
95484 CTTTCTTTTG
Statistics
Matches: 302, Mismatches: 51, Indels: 48
0.75 0.13 0.12
Matches are distributed among these distances:
52 70 0.23
53 7 0.02
54 28 0.09
55 52 0.17
56 29 0.10
57 15 0.05
58 39 0.13
59 56 0.19
60 6 0.02
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (56 bp):
ATCATCAAGAAACCCCTAAAATTAGGCTTAGTTTCTTTTAAAATTCATTGAAAATC
Found at i:95367 original size:111 final size:111
Alignment explanation
Indices: 95051--95472 Score: 577
Period size: 111 Copynumber: 3.8 Consensus size: 111
95041 TTTCAGTTAT
* * * *
95051 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTC-TTAAAAAAATTCTTTGGAAATAATCATCAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
* * **
95115 GAAACCCCTGAAAATCAAGTTTAGTTTCTAAAAACTCATTTGAGTA
66 GAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAA
* *
95161 CATCAAGAAACCCCTAAAAATTAGGCTTATTTTCTTTT--AAAATTCATTGAAAATCATCATAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
* * *
95224 GAAACCCCTG--AATCAGGCTTAGTTTCTTTAAAAATTCTTTTAAAAA
66 GAAACCCCTGAAAATCAGGCTTAGTTTC--TAAAAACTCATTTGAAAA
* * * * *
95270 TATCCAGAAACCCCTAAAAATTAGGCTTAGGTTCTTTTAAAAAATTCTTTGGAAATCATCATCAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
*
95335 GAAACCCCTGAAAAGT-AGGCTTTGTTTCTAAAAACTCATTTGAAAA
66 GAAACCCCTGAAAA-TCAGGCTTAGTTTCTAAAAACTCATTTGAAAA
* * *
95381 CATCAAGAAACCCCTAAAAATTAGGCATAGCTTCTTTTAAGAAATTCATTGAAAATCATCATCAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
95446 GAAACCCCTGAAAATCAGGCTTAGTTT
66 GAAACCCCTGAAAATCAGGCTTAGTTT
95473 TTTTTTAAAA
Statistics
Matches: 271, Mismatches: 32, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
107 14 0.05
109 78 0.29
110 34 0.13
111 131 0.48
113 13 0.05
114 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (111 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTTAAAAAATTCATTGAAAATCATCATCAA
GAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAA
Found at i:100179 original size:16 final size:16
Alignment explanation
Indices: 100160--100202 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
100150 TAAAAAGTAG
100160 TAAAATAAAAACAACA
1 TAAAATAAAAACAACA
* *
100176 TAAAATAAAAATAAGA
1 TAAAATAAAAACAACA
100192 TAAACATAAAA
1 TAAA-ATAAAA
100203 TATGAAGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
TAAAATAAAAACAACA
Found at i:100186 original size:22 final size:22
Alignment explanation
Indices: 100161--100204 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
100151 AAAAAGTAGT
100161 AAAATAA-AAACAACATAAAATA
1 AAAATAAGAAA-AACATAAAATA
*
100183 AAAATAAGATAAACATAAAATA
1 AAAATAAGAAAAACATAAAATA
100205 TGAAGACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAATAAGAAAAACATAAAATA
Found at i:101047 original size:18 final size:20
Alignment explanation
Indices: 101017--101053 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
101007 CAAAGATGAT
101017 TCGAAACAGAAAA-AAATAC
1 TCGAAACAGAAAATAAATAC
101036 TCGAAA-AGAAAATAAATA
1 TCGAAACAGAAAATAAATA
101054 AACCTTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.65, C:0.11, G:0.11, T:0.14
Consensus pattern (20 bp):
TCGAAACAGAAAATAAATAC
Found at i:104265 original size:538 final size:538
Alignment explanation
Indices: 103146--104330 Score: 1930
Period size: 538 Copynumber: 2.2 Consensus size: 538
103136 TGCGTTCACC
** * *
103146 TTTTGTCATTTATAGACC-GTTTTATCATATTTTTACATGTTATATTATTAT-GATCGATACA-T
1 TTTTGTCATTTCGAGACCGGTTTTGTCATA-TTTTACATGTTATATTGTTATGGATCGATACATT
*
103208 TT-TAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTATTAATTCCAAAAGTGTCGAT
65 TTATAAAGTATTGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAG-GTCGAT
* *
103271 ACTTAAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTATCTGTTTTGTCATTTCGAG
129 ACTTAAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAG
*
103336 ACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
194 ACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
* *
103401 CACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAATTA
259 CACGTTATTGGCGCTATAACTTATTCTCTTTTAAATTCCAAAAG-GTCGATACTTATAATAATTA
* *
103466 TCGACACTTTCAACATAACCGGTAGCGCTTTACCTATTTTGTCATTTCGAGACCGGTTTTGTCAT
323 TCGACAATTTCAACATAACCGATAGCGCTTTACCTATTTTGTCATTTCGAGACCGGTTTTGTCAT
*
103531 ATTATTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGC
388 ATTATTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGC
*
103596 TATAACTTCTTCTCTTTTAAATTTCAAAGTGTCGATACTTATAATAAATTATCGACACTTTCAAC
453 TATAACTTCTTCTCTTTTAAATTCCAAAGTGTCGATACTTATAATAAATTATCGACACTTTCAAC
103661 ATAACCGGTAGCGCTTTACCT
518 ATAACCGGTAGCGCTTTACCT
*
103682 GTTTGTCATTTCGAGACCGGTTTTGTCATATTTTACATG-TATATTGTTATGGATCGATACATTT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTACATGTTATATTGTTATGGATCGATACATTT
* * * *
103746 TATAAATTATTGACACGTTATTGGCGCTATAACTTATTCTCTTATTAATTCCAAAA-GTCGATGC
66 TATAAAGTATTGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGGTCGATAC
103810 TTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGA
131 TTA-AATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGA
* *
103875 CCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAATTATCGAC
195 CCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGAC
103940 ACGTTATTGGCGCTATAACTTATTCTCTTATT-AATTCCAAAA-GTCGATACTTATAATAAATTA
260 ACGTTATTGGCGCTATAACTTATTCTCTT-TTAAATTCCAAAAGGTCGATACTTATAAT-AATTA
* * *
104003 TCGACAATTTCAACATAACCGATAGCGCTTTATCTGTTTTGTCATTTCGAGACTGGTTTTGTCAT
323 TCGACAATTTCAACATAACCGATAGCGCTTTACCTATTTTGTCATTTCGAGACCGGTTTTGTCAT
*
104068 ATTTTTACATGTTAT-TTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGC
388 ATTATTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGC
104132 TATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGATA-TGTATAATAAATTATCGACACTTTCA
453 TATAACTTCTTCTCTTTTAAATTCC-AAAGTGTCGATACT-TATAATAAATTATCGACACTTTCA
104195 ACATAACCGGTAGCGCTTTACCT
516 ACATAACCGGTAGCGCTTTACCT
*
104218 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTACCTGTTATATTGTTATGGATCGATACATT
1 -TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTACATGTTATATTGTTATGGATCGATACA-T
* *
104283 TTTATAAAGTATTGACACTTTA-TGACGATATAACTTCTTCTCTT-TTAA
64 TTTATAAAGTATTGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAA
104331 AAAGGTAAAA
Statistics
Matches: 604, Mismatches: 32, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
535 28 0.05
536 163 0.27
537 142 0.24
538 227 0.38
539 44 0.07
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (538 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTACATGTTATATTGTTATGGATCGATACATTT
TATAAAGTATTGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGGTCGATAC
TTAAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGAC
CGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACA
CGTTATTGGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGGTCGATACTTATAATAATTATCG
ACAATTTCAACATAACCGATAGCGCTTTACCTATTTTGTCATTTCGAGACCGGTTTTGTCATATT
ATTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGCTAT
AACTTCTTCTCTTTTAAATTCCAAAGTGTCGATACTTATAATAAATTATCGACACTTTCAACATA
ACCGGTAGCGCTTTACCT
Found at i:104331 original size:180 final size:182
Alignment explanation
Indices: 103146--104331 Score: 1900
Period size: 180 Copynumber: 6.6 Consensus size: 182
103136 TGCGTTCACC
** * *
103146 TTTTGTCATTTATAGACC-GTTTTATCATATTTTTACATGTTATATTATTAT-GATCGATACA--
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
103207 TTT-TAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTATT-AATTCCAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
* *
103269 ATACTTA-AATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTATCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
103321 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
103386 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
103451 TACTTATAAT-AATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTA
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
103502 TTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
103567 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTTC-AAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
103631 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
103683 -TTTGTCATTTCGAGACCGGTTTTGTCATA-TTTTACATG-TATATTGTTATGGATCGATACA-T
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* * * *
103744 TTTATAAATTATTGACACGTTATTGGCGCTATAACTTATTCTCTTATT-AATTCCAAAA--GTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
*
103806 ATGCTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
103859 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* * *
103924 TTTATAAATTATCGACACGTTATTGGCGCTATAACTTATTCTCTTATT-AATTCCAAAA--GTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
* * *
103986 ATACTTATAATAAATTATCGACAATTTCAACATAACCGATAGCGCTTTATCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
104039 TTTTGTCATTTCGAGACTGGTTTTGTCATATTTTTACATGTTAT-TTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
104103 TTTATAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
104167 TA-TGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTA
131 TACT-TATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
104219 TTTTGTCATTTCGAGACCGGTTTTGTCATA-TTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* * *
104283 TTTATAAAGTATTGACACTTTA-TGACGATATAACTTCTTCTCTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
104332 AAGGTAAAAT
Statistics
Matches: 951, Mismatches: 39, Indels: 37
0.93 0.04 0.04
Matches are distributed among these distances:
175 16 0.02
176 85 0.09
177 88 0.09
178 54 0.06
179 108 0.11
180 371 0.39
181 226 0.24
182 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Done.