Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002151.1 Hibiscus syriacus cultivar Beakdansim tig00004392_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: 78788
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:454 original size:8 final size:8
Alignment explanation
Indices: 420--469 Score: 73
Period size: 8 Copynumber: 6.0 Consensus size: 8
410 ACTTAAAAAG
420 ATTATTATT
1 ATTATTA-T
429 ATTATTAT
1 ATTATTAT
*
437 AATAATTAT
1 -ATTATTAT
446 ATTATTAT
1 ATTATTAT
454 ATTATTAT
1 ATTATTAT
462 ATTATTAT
1 ATTATTAT
470 TAAATAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 24 0.63
9 14 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTATTAT
Found at i:479 original size:16 final size:17
Alignment explanation
Indices: 425--483 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 17
415 AAAAGATTAT
425 TATTATTATTATAATAA
1 TATTATTATTATAATAA
*
442 T-TATATTATTATATTATTA
1 TAT-TATTATTATA--ATAA
461 TATTATTATTA-AATAA
1 TATTATTATTATAATAA
477 TATTATT
1 TATTATT
484 TATATTGCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 11 0.31
17 11 0.31
18 1 0.03
19 12 0.33
20 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATTATTATAATAA
Found at i:483 original size:3 final size:3
Alignment explanation
Indices: 420--471 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
410 ACTTAAAAAG
* *
420 ATT ATT ATT ATT ATT ATA ATA ATT A-T ATT ATT A-T ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
465 ATT ATT A
1 ATT ATT A
472 AATAATATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:2594 original size:14 final size:15
Alignment explanation
Indices: 2564--2596 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2554 TTTGTCTTAA
2564 AAAATGATTTTTCTT
1 AAAATGATTTTTCTT
*
2579 AAAATTATTTTT-TT
1 AAAATGATTTTTCTT
2593 AAAA
1 AAAA
2597 GACATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (15 bp):
AAAATGATTTTTCTT
Found at i:10201 original size:28 final size:28
Alignment explanation
Indices: 10161--10216 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
10151 ATGCTAAAAA
10161 GAAGGCTTTGCCGCTAAGTTTTAGCATG
1 GAAGGCTTTGCCGCTAAGTTTTAGCATG
10189 GAAGGCTTTGCCGCTAAGTTTTAGCATG
1 GAAGGCTTTGCCGCTAAGTTTTAGCATG
10217 CTCACACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (28 bp):
GAAGGCTTTGCCGCTAAGTTTTAGCATG
Found at i:10781 original size:13 final size:13
Alignment explanation
Indices: 10753--10804 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
10743 TTCATTTGTA
*
10753 TTAAACCCTAAACC
1 TTAAA-CCTAAGCC
10767 TTAAACCTAAGCC
1 TTAAACCTAAGCC
*
10780 TTAAACATCAAGCC
1 TTAAACCT-AAGCC
*
10794 CTAAACTCTAA
1 TTAAAC-CTAA
10805 ATCATAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 14 0.44
14 17 0.53
15 1 0.03
ACGTcount: A:0.42, C:0.31, G:0.04, T:0.23
Consensus pattern (13 bp):
TTAAACCTAAGCC
Found at i:13636 original size:17 final size:17
Alignment explanation
Indices: 13614--13677 Score: 110
Period size: 17 Copynumber: 3.8 Consensus size: 17
13604 AAATTCGAGT
13614 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
*
13631 TCGAGTTCGAGTTTGAA
1 TCGAGTTCGAGCTTGAA
*
13648 TCGAGTTCTAGCTTGAA
1 TCGAGTTCGAGCTTGAA
13665 TCGAGTTCGAGCT
1 TCGAGTTCGAGCT
13678 CAAAATCGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (17 bp):
TCGAGTTCGAGCTTGAA
Found at i:13922 original size:176 final size:177
Alignment explanation
Indices: 13724--14081 Score: 583
Period size: 176 Copynumber: 2.0 Consensus size: 177
13714 TCAATCGAGC
* *
13724 TCCTGAATTTTTTTTGAGTTCGAGCCTTTTCGAGTTCGAGTCCAGTTTCAATATTATCTTTCGAG
1 TCCTGAATTTTTTTTAAGTTCGAGCCTTTTCGAGTTCGAGTCCAGTTTCAATATTATCTTTCAAG
* *
13789 TTTGAGTCGAGCTTGAAAATTTTAAGCTCGCGAGTTTTCGAGTCGAGT-CTACATTTAAAGTTTT
66 TTCGAGTCGAGCTTGAAAATTTTAAGCTCGCGAGTTTTCGAGTCGAGTCCTACATTTAAAATTTT
*
13853 CGAGTTCGAGTCGAGCTTGGCAATACTCGAGCTCGACTCGGCTCGTT
131 CGAGTTCGAGTCGAGCTTGACAATACTCGAGCTCGACTCGGCTCGTT
* * *
13900 TCCTGATTTTTTTTTAAGTTCGAGCCTTTTTGAGTTCGAGTCGAGTTTCAATATTATCTTTCAAG
1 TCCTGAATTTTTTTTAAGTTCGAGCCTTTTCGAGTTCGAGTCCAGTTTCAATATTATCTTTCAAG
*
13965 TTCGAGTCGAGCTTGAAAATTTTAAGCTCGTGAGTTTTCGAGTCGAGTCGAGCCTACATTTAAAA
66 TTCGAGTCGAGCTTGAAAATTTTAAGCTCGCGAGTTTTCGAGTCGAGT----CCTACATTTAAAA
*
14030 TTTTCGAGTTCGAGTCGAGCTTGATAATACTCGAGCTCGACTCGGCTCGTT
127 TTTTCGAGTTCGAGTCGAGCTTGACAATACTCGAGCTCGACTCGGCTCGTT
14081 T
1 T
14082 ACACCATAGT
Statistics
Matches: 167, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
176 106 0.63
181 61 0.37
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (177 bp):
TCCTGAATTTTTTTTAAGTTCGAGCCTTTTCGAGTTCGAGTCCAGTTTCAATATTATCTTTCAAG
TTCGAGTCGAGCTTGAAAATTTTAAGCTCGCGAGTTTTCGAGTCGAGTCCTACATTTAAAATTTT
CGAGTTCGAGTCGAGCTTGACAATACTCGAGCTCGACTCGGCTCGTT
Found at i:14442 original size:12 final size:12
Alignment explanation
Indices: 14427--14460 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
14417 AAGCAAATTT
*
14427 AAAATTAATATA
1 AAAATTAAAATA
*
14439 AAAATAAAAATA
1 AAAATTAAAATA
14451 AAAATTAAAA
1 AAAATTAAAA
14461 AAATAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTAAAATA
Found at i:15103 original size:20 final size:20
Alignment explanation
Indices: 15080--15123 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
15070 GCAACTCAGT
15080 TTTCAAATTCGCAACGCGAA
1 TTTCAAATTCGCAACGCGAA
*** *
15100 TTTCGTTTTCGCAACTCGAA
1 TTTCAAATTCGCAACGCGAA
15120 TTTC
1 TTTC
15124 GTAACGCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTCAAATTCGCAACGCGAA
Found at i:15124 original size:20 final size:20
Alignment explanation
Indices: 15087--15125 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
15077 AGTTTTCAAA
15087 TTCGCAACGCGAATTTCGTT
1 TTCGCAACGCGAATTTCGTT
*
15107 TTCGCAACTCGAATTTCGT
1 TTCGCAACGCGAATTTCGT
15126 AACGCTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (20 bp):
TTCGCAACGCGAATTTCGTT
Found at i:15400 original size:19 final size:20
Alignment explanation
Indices: 15335--15402 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
15325 ATTCGCAATA
* *
15335 CGAATTTGAAAACCACGTTA
1 CGAATTTAAAAACCACGTTG
15355 CGAATTTAAAAACCACGTTG
1 CGAATTTAAAAACCACGTTG
*
15375 CGAATTTAAAAACCGCGTTG
1 CGAATTTAAAAACCACGTTG
*
15395 CGATTTTA
1 CGAATTTA
15403 GAGAATCGCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (20 bp):
CGAATTTAAAAACCACGTTG
Found at i:15414 original size:21 final size:20
Alignment explanation
Indices: 15335--15422 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
15325 ATTCGCAATA
* * *
15335 CGAATTTGAAAACCACGTTA
1 CGAATTTAAAAACCGCGTTG
*
15355 CGAATTTAAAAACCACGTTG
1 CGAATTTAAAAACCGCGTTG
15375 CGAATTTAAAAACCGCGTTG
1 CGAATTTAAAAACCGCGTTG
* * *
15395 CGATTTTAGAGAATCGCGTTG
1 CGAATTTA-AAAACCGCGTTG
*
15416 CAAATTT
1 CGAATTT
15423 GTTGGTTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
20 44 0.75
21 15 0.25
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (20 bp):
CGAATTTAAAAACCGCGTTG
Found at i:19039 original size:21 final size:21
Alignment explanation
Indices: 19015--19057 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
19005 ATATTAATCA
19015 TATTAAAAATATTAT-TATTTT
1 TATTAAAAATA-TATGTATTTT
*
19036 TATTAAATATATATGTATTTT
1 TATTAAAAATATATGTATTTT
19057 T
1 T
19058 TATTCAACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TATTAAAAATATATGTATTTT
Found at i:20405 original size:22 final size:22
Alignment explanation
Indices: 20377--20422 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
20367 TCACTGGTTC
20377 AACCGGTCTGATCGGTCGAAAG
1 AACCGGTCTGATCGGTCGAAAG
20399 AACCGGTCTGATCGGTCGAAAG
1 AACCGGTCTGATCGGTCGAAAG
20421 AA
1 AA
20423 TCGGACGACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.17
Consensus pattern (22 bp):
AACCGGTCTGATCGGTCGAAAG
Found at i:20930 original size:24 final size:25
Alignment explanation
Indices: 20898--20944 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
20888 TTATTCTTTC
20898 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* * *
20922 ACTTTAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
20945 TTTTGAGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:24283 original size:2 final size:2
Alignment explanation
Indices: 24276--24311 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
24266 TATTTTTAAC
*
24276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24312 GAAGTGTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:28941 original size:14 final size:14
Alignment explanation
Indices: 28922--28973 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
28912 ATTTATATTT
28922 GTTTATGTTTGTTC
1 GTTTATGTTTGTTC
28936 GTTTATG-TTGATTC
1 GTTTATGTTTG-TTC
**
28950 GTTTATGTGCGTTC
1 GTTTATGTTTGTTC
28964 GTTTATGTTT
1 GTTTATGTTT
28974 AGCCCAATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 3 0.09
14 28 0.88
15 1 0.03
ACGTcount: A:0.10, C:0.08, G:0.23, T:0.60
Consensus pattern (14 bp):
GTTTATGTTTGTTC
Found at i:30124 original size:229 final size:226
Alignment explanation
Indices: 29719--30167 Score: 783
Period size: 229 Copynumber: 2.0 Consensus size: 226
29709 GTAAATTATC
* *
29719 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA-CTTTAGT
**
29784 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
65 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
29849 TGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
130 TGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
29914 AAACATAAATTACATAACTTTCAAAAAAGTATA
195 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
29947 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTAAATTA-TTTG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATT--ATTACTTTA
*
30011 GTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
63 GTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
*
30076 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
128 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
30141 TGAAACATAAATTACATAACTTTAAAA
193 TGAAACATAAATTACATAACTTTAAAA
30168 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
228 40 0.19
229 167 0.79
231 4 0.02
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTACTTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTT
GTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:30256 original size:20 final size:19
Alignment explanation
Indices: 30233--30278 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
30223 CGATATACCA
30233 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
30253 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
30273 GGTAAA
1 GGTAAA
30279 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:30423 original size:20 final size:19
Alignment explanation
Indices: 30400--30446 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
30390 CGATATAACA
30400 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
30420 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
30440 GGTAAAA
1 GGTAAAA
30447 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:30448 original size:17 final size:18
Alignment explanation
Indices: 30404--30451 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
30394 ATAACAGGTA
30404 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
30423 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
30443 -AAAATGATA
1 AAAAATGATA
30452 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:32728 original size:21 final size:21
Alignment explanation
Indices: 32681--32745 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
32671 AAGACAATCA
* *
32681 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
32703 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
32723 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
32744 AG
1 AG
32746 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:32821 original size:33 final size:33
Alignment explanation
Indices: 32779--32844 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
32769 AAATAGATGG
*
32779 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
32812 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
32845 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:34661 original size:19 final size:19
Alignment explanation
Indices: 34637--34685 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
34627 AATGTCGAGT
34637 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
34656 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
34675 TATTTTTGTAT
1 TAATTTTGTAT
34686 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:35211 original size:199 final size:199
Alignment explanation
Indices: 34804--35976 Score: 2152
Period size: 199 Copynumber: 5.9 Consensus size: 199
34794 CAATATGGCC
* * *
34804 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
34869 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
34934 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
34998 ATTAAA
194 ATTAAA
35004 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
35069 CAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
35134 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
35199 TAAA
196 TAAA
*
35203 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
* *
35268 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
35333 AGAATATGTCTAAATAATGTGTCGACACTAATATAATTTGTGTCGATATTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
**
35398 ATGGAA
194 ATTAAA
35404 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
35469 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGATTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
35534 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
35598 TAAA
196 TAAA
35602 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
35667 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAATCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
35732 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTACCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
**
35797 GGAA
196 TAAA
35801 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
35866 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
35931 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
35977 CTAATTTAAA
Statistics
Matches: 944, Mismatches: 25, Indels: 9
0.97 0.03 0.01
Matches are distributed among these distances:
198 307 0.33
199 386 0.41
200 84 0.09
201 167 0.18
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
TAAA
Found at i:36127 original size:598 final size:593
Alignment explanation
Indices: 34875--35976 Score: 1821
Period size: 598 Copynumber: 1.9 Consensus size: 593
34865 GAAAACCAAA
* *** * * *
34875 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATA
1 AGTATAA-GTAATAAGTAATCGATCAATATAACAGGTACAATTATACCGATTTTATGAGAGAATA
34940 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAA
65 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAA
35005 ACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
130 ACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
35070 AAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
195 AAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
* *
35135 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT
260 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTACCAGAATGAATG
35200 AAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAAACATCG
325 AAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAAACATCG
*
35265 AAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTAT
390 AAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
* * *
35330 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAATTTGTGTCGATATTTTTTTTCCAGAA
455 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAATTTGTGTCGATATTTTATATCAAGAA
* * * ** * * * * *
35395 TGAATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAT
520 CGAATCGAAAACAAGGT-CACCCATAAAGAGTAAACCCAAACATAAAAAGAGGCGATCCCAAAAT
35460 CATCGAACCC
584 CATCGAACCC
* *** * *
35470 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGATTTTATGAGAGA
1 ---AGTATAA-GTAATAAGTAATCGATCAATATAACAGGTACAATTATACCGATTTTATGAGAGA
35535 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTA
62 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTA
35600 AAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA
127 AAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA
* *
35665 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAATCGGTACAATTATACCGGTTTTATGAG
192 CCCAAAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
35730 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTACCAGAATGA
257 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTACCAGAATGA
* *
35795 ATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCA
322 ATGAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAAACA
*
35859 TCG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
387 TCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
*
35923 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
452 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAATTTGTGTCGATA
35977 CTAATTTAAA
Statistics
Matches: 494, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
596 112 0.23
597 25 0.05
598 357 0.72
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (593 bp):
AGTATAAGTAATAAGTAATCGATCAATATAACAGGTACAATTATACCGATTTTATGAGAGAATAT
GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAA
CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
AAAGTATAATGTAATAAGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTACCAGAATGAATGA
AAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAAACATCGA
AAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAATTTGTGTCGATATTTTATATCAAGAAC
GAATCGAAAACAAGGTCACCCATAAAGAGTAAACCCAAACATAAAAAGAGGCGATCCCAAAATCA
TCGAACCC
Found at i:37448 original size:18 final size:18
Alignment explanation
Indices: 37427--37511 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 18
37417 AGCGGTCGCA
37427 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
37445 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
37466 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
37487 GAAGATG-A--TGACGAT
1 GAAGATGAAGCTGACGAT
*
37502 GATGATGAAG
1 GAAGATGAAG
37512 ATGATGATCC
Statistics
Matches: 52, Mismatches: 7, Indels: 17
0.68 0.09 0.22
Matches are distributed among these distances:
15 12 0.23
16 1 0.02
17 1 0.02
18 12 0.23
19 1 0.02
20 1 0.02
21 17 0.33
22 1 0.02
23 1 0.02
24 5 0.10
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.20
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:37451 original size:6 final size:6
Alignment explanation
Indices: 37427--37515 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
37417 AGCGGTCGCA
* * * * * *
37427 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** *
37475 GAAGCT GGCGAT GAAGAT GATGACGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GA
37516 TGATCCAAAC
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
6 58 0.91
8 1 0.02
9 5 0.08
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:37462 original size:3 final size:3
Alignment explanation
Indices: 37442--37519 Score: 66
Period size: 3 Copynumber: 26.0 Consensus size: 3
37432 TGAAGCTGAC
* * * * * ** *
37442 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
37490 GAT GAT GAC GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
37520 CCAAACAAGT
Statistics
Matches: 56, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:37477 original size:42 final size:42
Alignment explanation
Indices: 37430--37518 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
37420 GGTCGCAGAA
* *
37430 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGAAGAC
* * *
37472 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGAAGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGAAGAC
37514 GATGA
1 GATGA
37519 TCCAAACAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGAAGAC
Found at i:37514 original size:18 final size:18
Alignment explanation
Indices: 37427--37519 Score: 69
Period size: 18 Copynumber: 5.0 Consensus size: 18
37417 AGCGGTCGCA
* *
37427 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
37445 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
37463 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
**
37481 GGCGATGAAGATGATGACGAT
1 GAAGATGAAGATGAT---GAT
*
37502 GATGATGAAGATGATGAT
1 GAAGATGAAGATGATGAT
37520 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
18 44 0.75
21 15 0.25
ACGTcount: A:0.37, C:0.08, G:0.34, T:0.22
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:39294 original size:184 final size:184
Alignment explanation
Indices: 38985--39328 Score: 589
Period size: 184 Copynumber: 1.9 Consensus size: 184
38975 CTTTCAACAT
* *
38985 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
* *
39050 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
*
39115 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACCATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
** * * *
39169 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
*
39234 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
39299 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACCATTTAAAAAAGTGTCG
39329 GTAATTTGAA
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
184 149 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (184 bp):
ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
AATGTGTCGATACCATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:41827 original size:25 final size:25
Alignment explanation
Indices: 41793--41857 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
41783 TTATCATTAA
41793 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
41818 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
41843 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
41858 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:42175 original size:23 final size:23
Alignment explanation
Indices: 42144--42207 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
42134 ATAGGTAAAC
*
42144 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
42167 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
42190 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
42208 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:42214 original size:23 final size:23
Alignment explanation
Indices: 42144--42216 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
42134 ATAGGTAAAC
* **
42144 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
42167 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
42190 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
42213 ATAT
1 ATAT
42217 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:42517 original size:25 final size:25
Alignment explanation
Indices: 42483--42533 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
42473 ACAACAAATC
*
42483 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
42508 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
42533 A
1 A
42534 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:42849 original size:18 final size:18
Alignment explanation
Indices: 42828--42864 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42818 GTAATTGGAG
42828 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
42846 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
42864 T
1 T
42865 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:42872 original size:24 final size:24
Alignment explanation
Indices: 42820--42866 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42810 TTTCATATGT
* *
42820 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
42844 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
42867 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:43164 original size:39 final size:39
Alignment explanation
Indices: 43121--43207 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
43111 TCCGATGCTC
*
43121 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
43160 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
43199 ATCAAAATC
1 ATCAAAATC
43208 TCATAAGTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:43568 original size:23 final size:23
Alignment explanation
Indices: 43537--43599 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
43527 ATAGGTAAAC
*
43537 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
43560 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
43583 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
43600 ATGGTTATAT
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:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:43607 original size:23 final size:23
Alignment explanation
Indices: 43537--43609 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
43527 ATAGGTAAAC
* * **
43537 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
43560 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
43583 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
43606 ATAT
1 ATAT
43610 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:45088 original size:27 final size:27
Alignment explanation
Indices: 45045--45097 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
45035 CTATCGTTAC
*
45045 TTTCAAGCAATAGCTCGCCAACATAAA
1 TTTCAAGCAATAGCTCGACAACATAAA
* *
45072 TTTCAAGC-ATTGACTCGACGACATAA
1 TTTCAAGCAATAG-CTCGACAACATAA
45098 TGTAAACGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (27 bp):
TTTCAAGCAATAGCTCGACAACATAAA
Found at i:45361 original size:60 final size:60
Alignment explanation
Indices: 45254--45384 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
45244 AGGTGATCAC
* *
45254 TTTGTAATTTTTAATAGTCATGTGACTCAACAAAGCATTACTCTATAGTCAATGGACCA-T
1 TTTGTAACTTTTAATAGTCATGTGACTCAAAAAAGCA-TACTCTATAGTCAATGGACCATT
* * *
45314 TTTGTAACTTTTAATAGTCATAG-GACTCAAAAAAGCA-ACATGTTATAGTCAGTGGACTATT
1 TTTGTAACTTTTAATAGTCAT-GTGACTCAAAAAAGCATAC-T-CTATAGTCAATGGACCATT
45375 TTTGT-ACTTT
1 TTTGTAACTTT
45385 ACCATATTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
58 2 0.03
59 1 0.02
60 52 0.84
61 7 0.11
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (60 bp):
TTTGTAACTTTTAATAGTCATGTGACTCAAAAAAGCATACTCTATAGTCAATGGACCATT
Found at i:48282 original size:2 final size:2
Alignment explanation
Indices: 48277--48302 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48267 ATTTTTTTTA
48277 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
48303 TAATAGACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49070 original size:50 final size:50
Alignment explanation
Indices: 48997--49092 Score: 183
Period size: 50 Copynumber: 1.9 Consensus size: 50
48987 ACTAAGCTCA
*
48997 CACCTAGGTCTCAGTGGAGTGTCATGACTTTCAGTAGCAAGGATGGACCT
1 CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGGACCT
49047 CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGG
1 CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGG
49093 TCCGGGTGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (50 bp):
CACCTAGGTCTCAGTGGAGTGTCATGACTTCCAGTAGCAAGGATGGACCT
Found at i:58218 original size:2 final size:2
Alignment explanation
Indices: 58211--58260 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
58201 CTACTATAAA
58211 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58253 AT AT AT AT
1 AT AT AT AT
58261 CTAATAGCAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58291 original size:20 final size:19
Alignment explanation
Indices: 58262--58300 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
58252 TATATATATC
*
58262 TAATAGCACTATAGATAAA
1 TAATAGCACTATAAATAAA
58281 TAATAAGCACTATAAATAAA
1 TAAT-AGCACTATAAATAAA
58301 ATAAGGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (19 bp):
TAATAGCACTATAAATAAA
Found at i:58792 original size:16 final size:18
Alignment explanation
Indices: 58760--58793 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
58750 TATTAATGTA
58760 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
58778 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
58794 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:59489 original size:128 final size:126
Alignment explanation
Indices: 59261--59518 Score: 399
Period size: 128 Copynumber: 2.0 Consensus size: 126
59251 AATTTTCTTC
* *
59261 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAAAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAAAT
** * *
59326 CCTGGTTAAATGATTAATTTATTTAATTTTATTTAATTTAGGACCAAATTGATAGCATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTATATTTAATTTAGGACCAAATTGAT--CATATAAA
* * * *
59389 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAAAT
*
59454 CCTAATTAAATGATTAATTTATTAAATTATATTTAATTTAGGACCAAATTGATTATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTATATTTAATTTAGGACCAAATTGATCATATAAA
59515 TAAT
1 TAAT
59519 AAAGACTGAA
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
126 11 0.09
128 108 0.91
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (126 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAAAT
CCTAATTAAATGATTAATTTATTAAATTATATTTAATTTAGGACCAAATTGATCATATAAA
Found at i:61460 original size:16 final size:17
Alignment explanation
Indices: 61426--61465 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
61416 TTATATGAAA
*
61426 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
61443 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
61459 TGATATG
1 TGATATG
61466 CCATATGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:62065 original size:23 final size:23
Alignment explanation
Indices: 62031--62117 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
62021 ACATATTATA
62031 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
62054 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
62077 CGGTC-CTTCGG-GACAAAATTCTACG
1 TGG-CACTACGGTG-C--AATTCTACG
62102 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
62118 ATTTATATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 2 0.04
25 16 0.31
26 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:63587 original size:30 final size:29
Alignment explanation
Indices: 63523--63638 Score: 151
Period size: 29 Copynumber: 4.0 Consensus size: 29
63513 TTTCGGTTAT
*
63523 GGTGTTATTTTCGTAATTATTTTTAAAAG
1 GGTGTTATTTTTGTAATTATTTTTAAAAG
* *
63552 TGTGTTATTTTTGTATTTATTTTTAAAAAG
1 GGTGTTATTTTTGTAATTATTTTT-AAAAG
* *
63582 GGTGTTATTTTTGTAATTAATTTTAAAAC
1 GGTGTTATTTTTGTAATTATTTTTAAAAG
* * *
63611 GGTGCTATTTTGGTAATTATTGTTAAAA
1 GGTGTTATTTTTGTAATTATTTTTAAAA
63639 AACAGTGATA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
29 49 0.65
30 26 0.35
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.53
Consensus pattern (29 bp):
GGTGTTATTTTTGTAATTATTTTTAAAAG
Found at i:63591 original size:59 final size:59
Alignment explanation
Indices: 63523--63639 Score: 164
Period size: 59 Copynumber: 2.0 Consensus size: 59
63513 TTTCGGTTAT
* * * * *
63523 GGTGTTATTTTCGTAATTATTTTTAAAA-GTGTGTTATTTTTGTATTTATTTTTAAAAAG
1 GGTGTTATTTTCGTAATTAATTTTAAAACG-GTGCTATTTTGGTAATTATTGTTAAAAAG
*
63582 GGTGTTATTTTTGTAATTAATTTTAAAACGGTGCTATTTTGGTAATTATTGTTAAAAA
1 GGTGTTATTTTCGTAATTAATTTTAAAACGGTGCTATTTTGGTAATTATTGTTAAAAA
63640 ACAGTGATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 50 0.98
60 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (59 bp):
GGTGTTATTTTCGTAATTAATTTTAAAACGGTGCTATTTTGGTAATTATTGTTAAAAAG
Found at i:63653 original size:59 final size:59
Alignment explanation
Indices: 63528--63659 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 59
63518 GTTATGGTGT
* * * * * ** *
63528 TATTTTCGTAATTATTTTTAAAAGTGTGTTATTTTTGTATTTATTTTTAAAAAGGGTGT
1 TATTTTCGTAATTAATTTTAAAAGTGTGCTATTTTGGTAATTATTTTAAAAAACAGTGA
*
63587 TATTTTTGTAATTAATTTTAAAACG-GTGCTATTTTGGTAATTATTGTTAAAAAACAGTGA
1 TATTTTCGTAATTAATTTTAAAA-GTGTGCTATTTTGGTAATTATT-TTAAAAAACAGTGA
*
63647 TATTTTGGTAATT
1 TATTTTCGTAATT
63660 GTTTAAAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 38 0.62
60 23 0.38
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (59 bp):
TATTTTCGTAATTAATTTTAAAAGTGTGCTATTTTGGTAATTATTTTAAAAAACAGTGA
Found at i:63665 original size:29 final size:31
Alignment explanation
Indices: 63606--63669 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
63596 AATTAATTTT
* * *
63606 AAAACGGTGCTATTTTGGTAATTATTGTTAA
1 AAAACAGTGATATTTTGGTAATTAGTGTTAA
63637 AAAACAGTGATATTTTGGTAATT-GT-TTAA
1 AAAACAGTGATATTTTGGTAATTAGTGTTAA
63666 AAAA
1 AAAA
63670 TGATATTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 8 0.27
30 1 0.03
31 21 0.70
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (31 bp):
AAAACAGTGATATTTTGGTAATTAGTGTTAA
Found at i:70318 original size:21 final size:20
Alignment explanation
Indices: 70290--70374 Score: 109
Period size: 21 Copynumber: 4.2 Consensus size: 20
70280 TATATATATC
*
70290 TAATAGCACTATAGATAAAA
1 TAATAGCACTATAAATAAAA
70310 TAATAAGCACTATAAATAAAA
1 TAAT-AGCACTATAAATAAAA
**
70331 TAATAAGCACTATAAATATTA
1 TAAT-AGCACTATAAATAAAA
70352 TAATAGCACTA-AGAATAAAA
1 TAATAGCACTATA-AATAAAA
70372 TAA
1 TAA
70375 AATGAAGTGA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
19 1 0.02
20 19 0.33
21 38 0.66
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (20 bp):
TAATAGCACTATAAATAAAA
Found at i:70360 original size:41 final size:41
Alignment explanation
Indices: 70290--70374 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
70280 TATATATATC
*
70290 TAATAGCACTATAGATAAAATAATAAGCACTATA-AATAAAA
1 TAATAGCACTATAAATAAAATAATAAGCACTA-AGAATAAAA
**
70331 TAATAAGCACTATAAATATTATAAT-AGCACTAAGAATAAAA
1 TAAT-AGCACTATAAATAAAATAATAAGCACTAAGAATAAAA
70372 TAA
1 TAA
70375 AATGAAGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 1 0.03
41 21 0.54
42 17 0.44
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (41 bp):
TAATAGCACTATAAATAAAATAATAAGCACTAAGAATAAAA
Found at i:70918 original size:29 final size:29
Alignment explanation
Indices: 70886--71019 Score: 137
Period size: 29 Copynumber: 4.6 Consensus size: 29
70876 TTCGGTTATG
70886 GTGTTATTTTCGTAATTATTTTTAAAAGT
1 GTGTTATTTTCGTAATTATTTTTAAAAGT
* * *
70915 GTGTTATTTTTGTATTTATTTTTAAAAAGG
1 GTGTTATTTTCGTAATTATTTTT-AAAAGT
* *
70945 GTGTTA-TTTCGTAATTAATTTTAAAACT
1 GTGTTATTTTCGTAATTATTTTTAAAAGT
* * *
70973 GT-TCTATTTTGGTAATTATTGTTAAAAAT
1 GTGT-TATTTTCGTAATTATTTTTAAAAGT
* *
71002 AGTGATATTTTGGTAATT
1 -GTGTTATTTTCGTAATT
71020 GTTTAAAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
27 1 0.01
28 8 0.09
29 52 0.60
30 26 0.30
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (29 bp):
GTGTTATTTTCGTAATTATTTTTAAAAGT
Found at i:70981 original size:58 final size:59
Alignment explanation
Indices: 70885--71019 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 59
70875 TTTCGGTTAT
* * * * *
70885 GGTGTTATTTTCGTAATTATTTTTAAAAGTGTGTTATTTTTGTATTTATTTTTAAAAAG
1 GGTGTTATTTTCGTAATTAATTTTAAAACTGTGTTATTTTGGTAATTATTGTTAAAAAG
*
70944 GGTGTTA-TTTCGTAATTAATTTTAAAACTGT-TCTATTTTGGTAATTATTGTTAAAAAT
1 GGTGTTATTTTCGTAATTAATTTTAAAACTGTGT-TATTTTGGTAATTATTGTTAAAAAG
* * *
71002 AGTGATATTTTGGTAATT
1 GGTGTTATTTTCGTAATT
71020 GTTTAAAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 1 0.02
58 48 0.74
59 16 0.25
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (59 bp):
GGTGTTATTTTCGTAATTAATTTTAAAACTGTGTTATTTTGGTAATTATTGTTAAAAAG
Found at i:71030 original size:30 final size:28
Alignment explanation
Indices: 70977--71039 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
70967 AAAACTGTTC
*
70977 TATTTTGGTAATTATTGTTAAAAATAGTGA
1 TATTTTGGTAATTATTG-TAAAAA-AATGA
*
71007 TATTTTGGTAATTGTT-TAAAAAAAATGA
1 TATTTTGGTAATTATTGT-AAAAAAATGA
71035 TATTT
1 TATTT
71040 CTATAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.33
29 5 0.17
30 15 0.50
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (28 bp):
TATTTTGGTAATTATTGTAAAAAAATGA
Found at i:71035 original size:28 final size:30
Alignment explanation
Indices: 70977--71039 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 30
70967 AAAACTGTTC
* * *
70977 TATTTTGGTAATTATTGTTAAAAATAGTGA
1 TATTTTGGTAATTAGTGTTAAAAAAAATGA
71007 TATTTTGGTAATT-GT-TTAAAAAAAATGA
1 TATTTTGGTAATTAGTGTTAAAAAAAATGA
71035 TATTT
1 TATTT
71040 CTATAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 16 0.53
29 1 0.03
30 13 0.43
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (30 bp):
TATTTTGGTAATTAGTGTTAAAAAAAATGA
Found at i:71046 original size:28 final size:27
Alignment explanation
Indices: 70990--71047 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
70980 TTTGGTAATT
* * *
70990 ATTGTTAAAAATAGTGATATTTTGGTA
1 ATTGTTAAAAAAAATGATATTTTGATA
71017 ATTGTTTAAAAAAAATGATATTTCT-ATA
1 ATTG-TTAAAAAAAATGATATTT-TGATA
71045 ATT
1 ATT
71048 TTTTTACTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 21 0.81
29 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (27 bp):
ATTGTTAAAAAAAATGATATTTTGATA
Found at i:72905 original size:2 final size:2
Alignment explanation
Indices: 72898--72938 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
72888 TTTGAATCTT
72898 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
72939 TTTTAAATTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77862 original size:21 final size:20
Alignment explanation
Indices: 77836--77890 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
77826 CGATCACATG
77836 TATTATTTATTTTCTTTTTTA
1 TATTATTTATTTT-TTTTTTA
* *
77857 TATTATATCTTTATTTTTTTA
1 TATTATTTATTT-TTTTTTTA
*
77878 T-TTTTTTATTTTT
1 TATTATTTATTTTT
77891 AATAAGTCTG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 7 0.25
21 18 0.64
22 1 0.04
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (20 bp):
TATTATTTATTTTTTTTTTA
Found at i:77883 original size:7 final size:8
Alignment explanation
Indices: 77838--77890 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 8
77828 ATCACATGTA
77838 TTATTTATT
1 TTATTT-TT
*
77847 TTCTTTTT
1 TTATTTTT
77855 TATATTATATCT
1 T-TATT-T-T-T
77867 TTATTTTT
1 TTATTTTT
77875 TTATTTTT
1 TTATTTTT
77883 TTATTTTT
1 TTATTTTT
77891 AATAAGTCTG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 20 0.53
9 9 0.24
10 2 0.05
11 5 0.13
12 2 0.05
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (8 bp):
TTATTTTT
Done.