Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002297.1 Hibiscus syriacus cultivar Beakdansim tig00004676_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: 125846
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3086 original size:24 final size:25
Alignment explanation
Indices: 3059--3123 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 25
3049 TTTCTATTAT
*
3059 AATACCTGACCTGGATTGTGATC-G
1 AATACTTGACCTGGATTGTGATCTG
* *
3083 AATACTTGACCTGAATTTTGATCTG
1 AATACTTGACCTGGATTGTGATCTG
3108 -ATACTTGACCTGGATT
1 AATACTTGACCTGGATT
3124 ATGTTTTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (25 bp):
AATACTTGACCTGGATTGTGATCTG
Found at i:5016 original size:11 final size:11
Alignment explanation
Indices: 5002--5030 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
4992 GAAATTAAAC
5002 GAAAATAAAAT
1 GAAAATAAAAT
5013 G-AAATAAAAT
1 GAAAATAAAAT
5023 GAAAATAA
1 GAAAATAA
5031 CGAAATGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (11 bp):
GAAAATAAAAT
Found at i:10712 original size:14 final size:14
Alignment explanation
Indices: 10681--10719 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
10671 GTTGATTTTA
* *
10681 AAATAAAATATAAG
1 AAATTAAATAAAAG
10695 -AATTAAATAAAAG
1 AAATTAAATAAAAG
10708 AAATTAAATAAA
1 AAATTAAATAAA
10720 TAAATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (14 bp):
AAATTAAATAAAAG
Found at i:12173 original size:21 final size:20
Alignment explanation
Indices: 12122--12216 Score: 95
Period size: 21 Copynumber: 4.6 Consensus size: 20
12112 GTTTCCAGAT
*
12122 TCGCAATGCAAACTTTGACTA
1 TCGCAATGCGAAC-TTGACTA
12143 TCGCAATGCGAACTTGAACTA
1 TCGCAATGCGAACTTG-ACTA
*
12164 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TG-ACTA
* *
12184 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-ACTTGACTA
12205 TCGCAATGCGAA
1 TCGCAATGCGAA
12217 TATGTAAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
20 18 0.28
21 45 0.70
22 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAACTTGACTA
Found at i:12188 original size:20 final size:20
Alignment explanation
Indices: 12142--12235 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 20
12132 AACTTTGACT
12142 ATCGCAATGCGAACT-TG-AA
1 ATCGCAATGCGAA-TATGTAA
12161 CTATCGCAATGCGAATATGTAA
1 --ATCGCAATGCGAATATGTAA
*
12183 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
12204 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
12224 ATCGCAATGCGA
1 ATCGCAATGCGA
12236 TAGTCGAAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 25 0.39
21 27 0.42
22 5 0.08
23 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:12255 original size:21 final size:21
Alignment explanation
Indices: 12225--12368 Score: 109
Period size: 21 Copynumber: 6.9 Consensus size: 21
12215 AATATGTAAA
* *
12225 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
12246 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
12267 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* * **
12287 ATCGTATTGCGAT-TTATATA-T
1 -TCGCATTGCGATAGTCCA-AGT
12308 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
12329 TCGCGTTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAGT
12352 TCG--TTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
12369 AATCGCAACG
Statistics
Matches: 98, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
19 7 0.07
20 16 0.16
21 63 0.64
22 1 0.01
23 11 0.11
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:12256 original size:41 final size:41
Alignment explanation
Indices: 12142--12298 Score: 160
Period size: 41 Copynumber: 3.8 Consensus size: 41
12132 AACTTTGACT
* * *
12142 ATCGCAATGCGA-ACTTGAACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCG-ACTATCGCATTGCGAATATGTAA
*
12183 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGACTATCGCATTGCGAATATGTAA
* *
12224 ATCGCAATGCGATAGTCGAAGT-TCGCGTTGCG-ATA-GTCCAA
1 ATCGCAATGCGATAGTCG-ACTATCGCATTGCGAATATGT--AA
* * *
12265 GTTCGCATTGCGATAGTCGACTATCGTATTGCGA
1 -ATCGCAATGCGATAGTCGACTATCGCATTGCGA
12299 TTTATATATT
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 65 0.66
42 29 0.29
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (41 bp):
ATCGCAATGCGATAGTCGACTATCGCATTGCGAATATGTAA
Found at i:12277 original size:83 final size:84
Alignment explanation
Indices: 12184--12365 Score: 228
Period size: 83 Copynumber: 2.2 Consensus size: 84
12174 AATATGTAAA
* * *
12184 TCGCAATGCGATAGTCGACTATCGCAATGCGA-ATATGTAAATCGCAATGCGATAGTCGAAGTTC
1 TCGCATTGCGATAGTCGACTATCGCAATGCGATATATAT-AATCGCAATGCGATAGTCCAAGTTC
*
12248 GCGTTGCGA-TAGTCCAAGT
65 GCGTTGCGATTAGTCCAAAT
* * * * *
12267 TCGCATTGCGATAGTCGACTATCGTATTGCGATTTATATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCATTGCGATAGTCGACTATCGCAATGCGATATATATAATCGCAATGCGATAGTCCAAGTTCG
*
12332 CGTTGCGATTTATTCCAAAT
66 CGTTGCGA-TTAGTCCAAAT
12352 TCG--TTGCGATAGTC
1 TCGCATTGCGATAGTC
12366 CAAAATCGCA
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
83 71 0.83
84 4 0.05
85 11 0.13
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (84 bp):
TCGCATTGCGATAGTCGACTATCGCAATGCGATATATATAATCGCAATGCGATAGTCCAAGTTCG
CGTTGCGATTAGTCCAAAT
Found at i:13147 original size:21 final size:21
Alignment explanation
Indices: 13123--13302 Score: 224
Period size: 21 Copynumber: 8.6 Consensus size: 21
13113 TTTGGAATAA
*
13123 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
13144 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* *
13165 ATCGCAACGCGAACTTCGGCT
1 ATCGCAATGCGAACTTCGACT
13186 ATCGCAATGCGAACTT-GAACT
1 ATCGCAATGCGAACTTCG-ACT
*
13207 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
** *
13228 ATCGCCTTGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
13249 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
13269 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
13290 ATCGCAATGCGAA
1 ATCGCAATGCGAA
13303 TATGTAAATC
Statistics
Matches: 138, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.13
21 119 0.86
22 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:13169 original size:42 final size:42
Alignment explanation
Indices: 13123--13302 Score: 249
Period size: 42 Copynumber: 4.3 Consensus size: 42
13113 TTTGGAATAA
*
13123 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACT
* *
13165 ATCGCAACGCGAACTTCGGCTATCGCAATGCGAACTTGAACT
1 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACT
**
13207 ATCGCAACGCGAACTTCGACTATCGCCTTGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACT
* *
13249 ATCGCAATGCGAA-TAT-GTA-AATCGCAATGCGAACTTGGACT
1 ATCGCAACGCGAACT-TCG-ACTATCGCAATGCGAACTTGGACT
*
13290 ATCGCAATGCGAA
1 ATCGCAACGCGAA
13303 TATGTAAATC
Statistics
Matches: 125, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
41 34 0.27
42 91 0.73
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (42 bp):
ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACT
Found at i:13274 original size:20 final size:20
Alignment explanation
Indices: 13249--13321 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
13239 AACTTGGACT
13249 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
13269 ATCGCAATGCGAACT-TGGACT
1 ATCGCAATGCGAA-TATGTA-A
13290 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
13310 ATCGCAATGCGA
1 ATCGCAATGCGA
13322 TAGTCGAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:13357 original size:62 final size:61
Alignment explanation
Indices: 13291--13467 Score: 182
Period size: 62 Copynumber: 2.8 Consensus size: 61
13281 ACTTGGACTA
* *
13291 TCGCAATGCGAATATGT-AAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCG-ATA-GTCAAATCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGT
* * * *
13353 TCGCATTGTGATAGTCGACTATCGCATTGCGAT-TTAC-ATA-TTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTC-A-AATCGCATTGCGATAGT-CGA-AGTTCGCGTTGCGATAGTCCAAGT
* *
13415 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCGAAGTTCGTGTTGCGA
1 TCGCATTGCGATAGTC-AA-ATCGCATTGCGATAGTCGAAGTTCGCGTTGCGA
13468 ATCTGGAAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
60 2 0.02
61 3 0.03
62 63 0.67
63 26 0.28
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (61 bp):
TCGCATTGCGATAGTCAAATCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGT
Found at i:13357 original size:83 final size:83
Alignment explanation
Indices: 13286--13453 Score: 234
Period size: 83 Copynumber: 2.0 Consensus size: 83
13276 TGCGAACTTG
* *
13286 GACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTC
1 GACTATCGCAATGCG-AT-T-TACATATTCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTC
*
13348 CAAGTTCGCATTGTGATAGTC
63 CAAGTTCGCATTGCGATAGTC
* * *
13369 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAA
1 GACTATCGCAATGCGATTTACATATTCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAA
13434 GTTCGCATTGCGATAGTC
66 GTTCGCATTGCGATAGTC
13452 GA
1 GA
13454 AGTTCGTGTT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
80 2 0.03
81 2 0.03
82 3 0.04
83 69 0.91
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (83 bp):
GACTATCGCAATGCGATTTACATATTCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAA
GTTCGCATTGCGATAGTC
Found at i:13467 original size:21 final size:21
Alignment explanation
Indices: 13311--13459 Score: 180
Period size: 21 Copynumber: 7.1 Consensus size: 21
13301 AATATGTAAA
*
13311 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
13332 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
13353 TCGCATTGTGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
13373 ATCGCATTGCGAT-TTAC-ATA-T
1 -TCGCATTGCGATAGT-CGA-AGT
*
13394 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
13415 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
13436 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
13457 TCG
1 TCG
13460 TGTTGCGAAT
Statistics
Matches: 110, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
20 17 0.15
21 92 0.84
22 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:15314 original size:10 final size:10
Alignment explanation
Indices: 15298--15354 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
15288 TTACATTATT
15298 TTTTTATTGA
1 TTTTTATTGA
* *
15308 ATTTTATTCA
1 TTTTTATTGA
* *
15318 TTTTAATTCA
1 TTTTTATTGA
15328 TTTTTATTGTA
1 TTTTTATTG-A
15339 TTTTTATTGA
1 TTTTTATTGA
15349 TTTTTA
1 TTTTTA
15355 AAAAAAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
10 30 0.75
11 10 0.25
ACGTcount: A:0.23, C:0.04, G:0.05, T:0.68
Consensus pattern (10 bp):
TTTTTATTGA
Found at i:15341 original size:21 final size:20
Alignment explanation
Indices: 15309--15354 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
15299 TTTTATTGAA
15309 TTTTATTCATTTTAATTCAT
1 TTTTATTCATTTTAATTCAT
* * *
15329 TTTTATTGTATTTTTATTGAT
1 TTTTATT-CATTTTAATTCAT
15350 TTTTA
1 TTTTA
15355 AAAAAAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTATTCATTTTAATTCAT
Found at i:25868 original size:12 final size:12
Alignment explanation
Indices: 25851--25875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25841 TTATATTATT
25851 TTCGTTAAAACA
1 TTCGTTAAAACA
25863 TTCGTTAAAACA
1 TTCGTTAAAACA
25875 T
1 T
25876 ACAAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TTCGTTAAAACA
Found at i:26670 original size:51 final size:51
Alignment explanation
Indices: 26615--26718 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 51
26605 GATAAATTTT
* ** * *
26615 AATAAAAAATTATATTTTATTCGAACTCGTTACCCCGGCTTGACGAGTTCA
1 AATAAAAAAATATATTTTATTAAAACTCGTTACCCCAGCGTGACGAGTTCA
* * *
26666 AATAAAAAAATATTTTTTATTAAAACTTGTTACCTCAGCGTGACGAGTTCA
1 AATAAAAAAATATATTTTATTAAAACTCGTTACCCCAGCGTGACGAGTTCA
26717 AA
1 AA
26719 AAACACGATA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (51 bp):
AATAAAAAAATATATTTTATTAAAACTCGTTACCCCAGCGTGACGAGTTCA
Found at i:27862 original size:23 final size:23
Alignment explanation
Indices: 27831--27883 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
27821 TAAATAGATA
* *
27831 ATTTTTTAAGATTATATATTTTT
1 ATTTATTAAGATTACATATTTTT
*
27854 ATTTATTAATATTACATATTTTT
1 ATTTATTAAGATTACATATTTTT
27877 ATTTATT
1 ATTTATT
27884 GTATATAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTTATTAAGATTACATATTTTT
Found at i:28944 original size:3 final size:3
Alignment explanation
Indices: 28923--28963 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
28913 TCAGAAAGAA
28923 AAT AA- AAT AAAT AAAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28964 ATAAACATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 24 0.69
4 7 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:29069 original size:5 final size:5
Alignment explanation
Indices: 29061--29095 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
29051 ATAAAAGCAT
29061 AATAA AATAA AATAA AATAA AATAA AAT-A AATAA A
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA A
29096 GTCCAAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:32538 original size:2 final size:2
Alignment explanation
Indices: 32526--32564 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
32516 AGATTTATTG
*
32526 TA TA CA 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 T
32565 GTCTGGGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:33580 original size:201 final size:200
Alignment explanation
Indices: 33115--33595 Score: 626
Period size: 200 Copynumber: 2.4 Consensus size: 200
33105 TACCACGTGT
* * * *
33115 TTGATATGCCCTTGAGTTGAATGGAATCGAACTCGAAGGTTTTTTGTTGACAGATAGCCCTTCTC
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAAGTTTTTCGTTGACAAATAGCCCTTCTC
** * *
33180 GCCTTGAGCTATACTTAAATTTGACTGGGATGTAGTTCCTTGTGGCTAAATTGCAGCAATCCCAG
66 GCCTTGAGCTATGTTTAAATTCGACTGAGATGTAGTTCCTTGTGGCTAAATTGCAGCAATCCCAG
* * * *
33245 GTCTTCTTCTTGACTTAAAGACCTTAGTTTGAGCTTCAACCAAAAGTAGTTCCTTGCTGCTACAA
131 GTCTTCTTCTTGACTTAAAGACCTCAATTTAAACTTCAACCAAAAGTAGTTCCTTGCTGCTACAA
*
33310 TGCAG
196 TACAG
* * *
33315 TTGATATGTCATTGAGCTAAATGGAATCGAACTCGAAAGTTTTTCGTTGACAAATAGCCCTTCTC
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAAGTTTTTCGTTGACAAATAGCCCTTCTC
* *
33380 GCCTTGAGCTATGTTTAAATTCGACTGAGA-GATAGTTCCTTGTTGCTAAATTGTAGCTAATCCC
66 GCCTTGAGCTATGTTTAAATTCGACTGAGATG-TAGTTCCTTGTGGCTAAATTGCAGC-AATCCC
* * *
33444 GGGTCTTCTTCTTGACTTAAAGACCTCAATTTAAACTTCAACCAAAAAGTAG-TCTTTCTCTGCT
129 AGGTCTTCTTCTTGACTTAAAGACCTCAATTTAAACTTCAACC-AAAAGTAGTTCCTT-GCTGCT
**
33508 ACTGTACAG
192 ACAATACAG
* * * * * * * *
33517 TTGATAAGCCCTCGAGCCGAATGAAATCAAACTCGAAAG-TTCTCGTTGACATATAGGCCTTCTC
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAAGTTTTTCGTTGACAAATAGCCCTTCTC
33581 GCCTTGAGCTATGTT
66 GCCTTGAGCTATGTT
33596 GCGAACAATT
Statistics
Matches: 243, Mismatches: 34, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
199 1 0.00
200 107 0.44
201 85 0.35
202 50 0.21
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (200 bp):
TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAAGTTTTTCGTTGACAAATAGCCCTTCTC
GCCTTGAGCTATGTTTAAATTCGACTGAGATGTAGTTCCTTGTGGCTAAATTGCAGCAATCCCAG
GTCTTCTTCTTGACTTAAAGACCTCAATTTAAACTTCAACCAAAAGTAGTTCCTTGCTGCTACAA
TACAG
Found at i:37468 original size:19 final size:21
Alignment explanation
Indices: 37427--37479 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
37417 GAACTGAAAT
*
37427 AAAAC-AAATAAAAGTTAGTA
1 AAAACAAAATAAAAGTCAGTA
37447 AAAACAAAATAAAAG-CAG-A
1 AAAACAAAATAAAAGTCAGTA
*
37466 AAAATAAAATAAAA
1 AAAACAAAATAAAA
37480 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 14 0.47
20 7 0.23
21 9 0.30
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.13
Consensus pattern (21 bp):
AAAACAAAATAAAAGTCAGTA
Found at i:37474 original size:5 final size:5
Alignment explanation
Indices: 37466--37494 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
37456 TAAAAGCAGA
37466 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
37495 AATAAAGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:38697 original size:3 final size:3
Alignment explanation
Indices: 38689--38762 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
38679 TGGGGCCTGC
38689 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38737 AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
38763 GTTTTTGTAG
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:46769 original size:13 final size:13
Alignment explanation
Indices: 46753--46783 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
46743 ATTTCGACAC
46753 TAAATTTTTTCTA
1 TAAATTTTTTCTA
46766 TAAATTTTTTCTA
1 TAAATTTTTTCTA
46779 TAAAT
1 TAAAT
46784 AAATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (13 bp):
TAAATTTTTTCTA
Found at i:49763 original size:4 final size:4
Alignment explanation
Indices: 49754--49809 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
49744 CGTTAGACAA
*** * *
49754 AAAT AAAT AAAT AAAT AAAT GTTT AAAA AAAT ATAT AAAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT
49803 -AAT AAAT
1 AAAT AAAT
49810 CAAGAGGAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
3 3 0.08
4 34 0.85
5 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:51115 original size:18 final size:16
Alignment explanation
Indices: 51092--51131 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
51082 AAAAATGTAA
51092 ATAATATATACATATTAT
1 ATAATATATAC--ATTAT
*
51110 ATAATATATGCATTAT
1 ATAATATATACATTAT
51126 ATAATA
1 ATAATA
51132 AGGGCGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
ATAATATATACATTAT
Found at i:52407 original size:98 final size:100
Alignment explanation
Indices: 52188--52754 Score: 703
Period size: 106 Copynumber: 5.5 Consensus size: 100
52178 AAATTATTTG
* * * * * * * **
52188 TTGACAACCAGCCGCCCCTTCG-CTGTGAAGTTCAGCTTGTGCTGTCTCGAGTCCAATGCCCTTC
1 TTGACAACCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
52252 GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-A
65 GCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATA
* * *
52287 TTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTAGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
52352 ATGTGAAGTTGAACTT-GCGT-TGAAATTGGGAA-A
66 CTGTGAAGTTGAAATTGGC-TCTGAAATTGGGAATA
* * *
52385 TTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGCCTTGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
52450 CTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAATTGTTTA
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AA-----TA
*
52491 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
52556 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA------TA
52597 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* * * *
52662 TTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTTTTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA------TA
52703 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
52755 GGCACGATAT
Statistics
Matches: 425, Mismatches: 31, Indels: 17
0.90 0.07 0.04
Matches are distributed among these distances:
98 90 0.21
99 79 0.19
100 3 0.01
105 2 0.00
106 251 0.59
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (100 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATA
Found at i:52669 original size:212 final size:208
Alignment explanation
Indices: 52130--52754 Score: 790
Period size: 212 Copynumber: 3.0 Consensus size: 208
52120 GTCTTGCTCT
* * * * * *
52130 GAGTCCAATATCCTCCACTGTGAAGTTGAAACTGGATTTGGAACTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-CTTGAAATTGGG-AATT-TTTGTTGACAA
* * * * * * **
52195 CCAGCCGCCCCTTCG-CTGTGAAGTTCAGCTTGTGCTGTCTCGAGTCCAATGCCCTTCGCTGTGA
63 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGA
*
52259 AGTTGAAATTGGCTCTGAAATTGGG-AA-----ATTGACAACCAGCGATCCCTTCGTCGTGAAGT
127 AGTTGAAATTGGCTCTGAAATTGGGAAATTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
52318 TGAACTTGCGTTATCTA
192 TGAACTTGCGTTGTCTG
* * *
52335 GAGTCCAATATCCTTCGATGTGAAGTTGAACTT-GCGTTGAAATTGGGAA-----ATTGACAACC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-TTGAAATTGGGAATTTTTGTTGACAACC
* * *
52394 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGCCTTGAGTCCAATATCCTTCGCTGTGAAGT
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGT
*
52459 TGAAATTAGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
130 TGAAATTGGCTCTGAAATTGGGAAATT-TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
52524 AACTTGCGTTGTCTG
194 AACTTGCGTTGTCTG
*
52539 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT-TGAAATTGGGAA-TT-TTTGTTGACAA
* *
52604 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
63 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
* * * *
52669 GTTGAAATTGGCTATGAAATTGAGAAGTTTTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
128 GTTGAAATTGGCTCTGAAATTGGGAA-ATTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
52734 TGAACTTGCGTTGTCTG
192 TGAACTTGCGTTGTCTG
52751 GAGT
1 GAGT
52755 GGCACGATAT
Statistics
Matches: 364, Mismatches: 37, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
197 83 0.23
198 2 0.01
203 2 0.01
204 87 0.24
205 42 0.12
212 146 0.40
213 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (208 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTGAAATTGGGAATTTTTGTTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
GAAATTGGCTCTGAAATTGGGAAATTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTG
Found at i:52690 original size:303 final size:300
Alignment explanation
Indices: 52129--52746 Score: 754
Period size: 303 Copynumber: 2.0 Consensus size: 300
52119 TGTCTTGCTC
* * * *
52129 TGAGTCCAATATCCTCCACTGTGAAGTTGAAACTGGATTTGGAACTGGGAAATTATTTGTTGACA
1 TGAGTCCAATATCCTCCACTGTGAAGTTGAAACTAGATCTGAAACTGGGAAATTATTTATTGACA
* * *
52194 ACCAGCCGCCCCTTCGCTGTGAAGTTCAGCTTGTGCTGTCTCGAGTCCAATGCCCTTCGCTGTGA
66 ACCAGCCGCCCCTTCGCTGTGAAGTTCAACTTGCGCTGTCTCGAGTCCAATACCCTTCGCTGTGA
52259 AGTTGAAATTGGCTCTGAAATTGGGAAATTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACT
131 AGTTGAAATTGGCTCTGAAATTGGGAAATTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACT
* *
52324 TGCGTTATCTAGAGTCCAATATCCTTCGATGTGAAGTTGAACTTGCGTTGAAATTGGGAAATTGA
196 TGCGTTATCTAGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGCGCT--AATT-GGAAATTGA
52389 CAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGCCT
258 CAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGCCT
* * * * * *
52432 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTCCACTGTGAAGTTGAAACTAGATCTGAAACTGGGAAATTATTTATTGACA
* * * * * * *
52497 ACCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGCTGTG
66 ACCAGCCGCCCCTTCGCT-GTGAAGTTCAACTTGCGCTGTCTCGAGTCCAATACCCTTCGCTGTG
* *
52561 AAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
130 AAGTTGAAATTGGCTCTGAAATTGGGAA-------ATTGACAACCAGCGATCCCTTCGTCGTGAA
* * *
52626 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG-GCTATGAAATT
188 GTTGAACTTGCGTTATCTAGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGCGC--T--AATT
* *
52690 GAGAAGTTTTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
249 G-GAA-------ATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTG
52747 TCTGGAGTGG
Statistics
Matches: 268, Mismatches: 29, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
302 1 0.00
303 135 0.50
309 1 0.00
310 78 0.29
311 10 0.04
318 43 0.16
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (300 bp):
TGAGTCCAATATCCTCCACTGTGAAGTTGAAACTAGATCTGAAACTGGGAAATTATTTATTGACA
ACCAGCCGCCCCTTCGCTGTGAAGTTCAACTTGCGCTGTCTCGAGTCCAATACCCTTCGCTGTGA
AGTTGAAATTGGCTCTGAAATTGGGAAATTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACT
TGCGTTATCTAGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGCGCTAATTGGAAATTGACAA
CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGCCT
Found at i:53615 original size:22 final size:22
Alignment explanation
Indices: 53589--53641 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
53579 TTGTGTTTGG
53589 TCAAAGGTTTGGAATTTGATGC
1 TCAAAGGTTTGGAATTTGATGC
*
53611 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGAATTTGATGC
53633 TCAAAGGTT
1 TCAAAGGTT
53642 GGATGGGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGAATTTGATGC
Found at i:54285 original size:11 final size:11
Alignment explanation
Indices: 54264--54328 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
54254 TCGTTTTGAT
54264 TTTTGTTCTTTC
1 TTTT-TTCTTTC
54276 TTTTTTCTTT-
1 TTTTTTCTTTC
*
54286 TGTTTTC-TTC
1 TTTTTTCTTTC
54296 TTTTTTGC-TTC
1 TTTTTT-CTTTC
54307 TTTTATT-TTTC
1 TTTT-TTCTTTC
54318 TTTTTTTCTTT
1 -TTTTTTCTTT
54329 TTGTTCTGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
9 2 0.04
10 11 0.24
11 19 0.42
12 13 0.29
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:54286 original size:19 final size:19
Alignment explanation
Indices: 54264--54335 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 19
54254 TCGTTTTGAT
54264 TTTTGTTCTTTCTTTTTTC
1 TTTTGTTCTTTCTTTTTTC
*
54283 TTTTGTTTTCTTCTTTTTTGC
1 TTTTGTTCT-TTCTTTTTT-C
* *
54304 TTCTTTTATTTTTCTTTTTTTC
1 TT-TTGT-TCTTTC-TTTTTTC
54326 TTTTTGTTCT
1 -TTTTGTTCT
54336 GATTGAATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 8 0.19
20 9 0.21
21 5 0.12
22 10 0.23
23 11 0.26
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.79
Consensus pattern (19 bp):
TTTTGTTCTTTCTTTTTTC
Found at i:54300 original size:14 final size:13
Alignment explanation
Indices: 54249--54333 Score: 55
Period size: 14 Copynumber: 6.2 Consensus size: 13
54239 TTTTTTGTCC
*
54249 TTTTTTCGTTTTG
1 TTTTTTCTTTTTG
* * *
54262 ATTTTTGTTCTTTC
1 TTTTTTCTT-TTTG
54276 TTTTTTC-TTTTG
1 TTTTTTCTTTTTG
54288 TTTTCTTCTTTTTTG
1 TTTT-TTC-TTTTTG
* *
54303 CTTCTTTTATTTTTCT
1 -TT-TTTTCTTTTT-G
54319 TTTTTTCTTTTTG
1 TTTTTTCTTTTTG
54332 TT
1 TT
54334 CTGATTGAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
12 7 0.13
13 12 0.22
14 17 0.31
15 12 0.22
16 4 0.07
17 2 0.04
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTCTTTTTG
Found at i:54329 original size:30 final size:31
Alignment explanation
Indices: 54273--54330 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
54263 TTTTTGTTCT
* *
54273 TTCTTTTTTCTTTTGTTTTCTTCTTTTTTGC
1 TTCTTTTATCTTTTCTTTTCTTCTTTTTTGC
*
54304 TTCTTTTAT-TTTTCTTTTTTTCTTTTT
1 TTCTTTTATCTTTTCTTTTCTTCTTTTT
54331 GTTCTGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.02, C:0.14, G:0.03, T:0.81
Consensus pattern (31 bp):
TTCTTTTATCTTTTCTTTTCTTCTTTTTTGC
Found at i:58749 original size:18 final size:16
Alignment explanation
Indices: 58726--58765 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
58716 AAAAATGTAA
58726 ATAATATATACATATTAT
1 ATAATATATAC--ATTAT
*
58744 ATAATATATGCATTAT
1 ATAATATATACATTAT
58760 ATAATA
1 ATAATA
58766 AGGGCGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
ATAATATATACATTAT
Found at i:60297 original size:17 final size:17
Alignment explanation
Indices: 60275--60307 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
60265 AAATAATTAC
60275 ATTTTTACACC-CATATT
1 ATTTTT-CACCTCATATT
60292 ATTTTTCACCTCATAT
1 ATTTTTCACCTCATAT
60308 AATTATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTTCACCTCATATT
Found at i:62231 original size:110 final size:110
Alignment explanation
Indices: 62038--62265 Score: 447
Period size: 110 Copynumber: 2.1 Consensus size: 110
62028 CCTTCACATT
62038 CATCGATCATTTCTGCATAAAGATTGATTCCATCATTCATTCCCATATCTTTATCGGCCTCACCG
1 CATCGATCATTTCTGCATAAAGATTGATTCCATCATTCATTCCCATATCTTTATCGGCCTCACCG
62103 ACCTTCAGAATGTTCTCAAGCCCCTCGAGACACACGGTCACAATC
66 ACCTTCAGAATGTTCTCAAGCCCCTCGAGACACACGGTCACAATC
62148 CATCGATCATTTCTGCATAAAGATTGATTCCATCATTCATTCCCATATCTTTATCGGCCTCACCG
1 CATCGATCATTTCTGCATAAAGATTGATTCCATCATTCATTCCCATATCTTTATCGGCCTCACCG
62213 ACCTTCAGAATGTTCTCAAGCCCCTCGAGACACACGGTCACAATC
66 ACCTTCAGAATGTTCTCAAGCCCCTCGAGACACACGGTCACAATC
*
62258 CATGGATC
1 CATCGATC
62266 TGGACAGAGT
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 117 1.00
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (110 bp):
CATCGATCATTTCTGCATAAAGATTGATTCCATCATTCATTCCCATATCTTTATCGGCCTCACCG
ACCTTCAGAATGTTCTCAAGCCCCTCGAGACACACGGTCACAATC
Found at i:62706 original size:31 final size:31
Alignment explanation
Indices: 62616--62699 Score: 141
Period size: 31 Copynumber: 2.7 Consensus size: 31
62606 TAGTAAAGTA
* *
62616 AGCCAAAAGCTCTTGTTCCCATTCATACCGG
1 AGCCAAATGCTCTTGTTCCCATTCATATCGG
62647 AGCCAAATGCTCTTGTTCCCATTCATATCGG
1 AGCCAAATGCTCTTGTTCCCATTCATATCGG
*
62678 AGCCAAATGCTCTTGGTCCCAT
1 AGCCAAATGCTCTTGTTCCCAT
62700 CAATATCTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.29
Consensus pattern (31 bp):
AGCCAAATGCTCTTGTTCCCATTCATATCGG
Found at i:67975 original size:29 final size:31
Alignment explanation
Indices: 67918--67976 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
67908 TTATGTTTCG
*
67918 ATCACTTACGTTATCTATTTATTAAATTTTA
1 ATCACTTACGTTATCGATTTATTAAATTTTA
*
67949 ATCACTTAC-TTATCGA-TTATTATATTTT
1 ATCACTTACGTTATCGATTTATTAAATTTT
67977 GGTACTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 11 0.42
30 6 0.23
31 9 0.35
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (31 bp):
ATCACTTACGTTATCGATTTATTAAATTTTA
Found at i:68088 original size:30 final size:31
Alignment explanation
Indices: 68054--68126 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
68044 TTTGATCCGT
* * *
68054 AAATATTAATTTGAT-CTTAAATTTTAGATG
1 AAATATTAATTTGATCCCTAAATGTTAGATA
*
68084 AAATA-TCATATTGATCCCTAAATGTTAGATA
1 AAATATTAAT-TTGATCCCTAAATGTTAGATA
68115 AAATATTAATTT
1 AAATATTAATTT
68127 AACCTTTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 3 0.09
30 10 0.29
31 19 0.54
32 3 0.09
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AAATATTAATTTGATCCCTAAATGTTAGATA
Found at i:70725 original size:29 final size:28
Alignment explanation
Indices: 70685--70739 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
70675 TTTAAAAATA
*
70685 TTTTAAAATGTTTTCAAAATTATATAGT
1 TTTTAAAATGTTTTCAAAACTATATAGT
*
70713 TTTTAAAAATGTTTTTAAAACTATATA
1 TTTT-AAAATGTTTTCAAAACTATATA
70740 TTATATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (28 bp):
TTTTAAAATGTTTTCAAAACTATATAGT
Found at i:70901 original size:37 final size:37
Alignment explanation
Indices: 70703--71068 Score: 270
Period size: 37 Copynumber: 10.1 Consensus size: 37
70693 TGTTTTCAAA
* * *
70703 ATTATA-TAGTTTTTAAAAATGTTTTTAAAACTATAT
1 ATTATATTAATTTTCAAAAATGTTTTAAAAACTATAT
* *
70739 ATTATA-T-GTTTTC-AAAATGATTTCAAAAACTATAT
1 ATTATATTAATTTTCAAAAATG-TTTTAAAAACTATAT
* *
70774 AATATATTTATGTTTTC-AAAATGTTTTTTTAAAAAC--TAT
1 ATTATA-TTA-ATTTTCAAAAATG---TTTTAAAAACTATAT
*
70813 A-TATA-T--TTTT--AAAATGTTTTAAAAACTACAT
1 ATTATATTAATTTTCAAAAATGTTTTAAAAACTATAT
*
70844 A--ACATGT-ATTTTCAAAAATGTTTTAAAAACTATAT
1 ATTATAT-TAATTTTCAAAAATGTTTTAAAAACTATAT
70879 ATTATATTAATTTTCAAAAATGTTTTTAAAAACTATAT
1 ATTATATTAATTTTCAAAAATG-TTTTAAAAACTATAT
* * * *
70917 AATATA-TATATTTTCAAATATGTTTTGAAAACCATAT
1 ATTATATTA-ATTTTCAAAAATGTTTTAAAAACTATAT
* *
70954 ATTATATTAATTTTCAAAAATGTCTTAAGAACTATAT
1 ATTATATTAATTTTCAAAAATGTTTTAAAAACTATAT
* * * *
70991 AATATATAAATGTTTTCAAACATGCTTTTCAAAA-T-TAT
1 ATTATATTAA--TTTTCAAAAATG-TTTTAAAAACTATAT
* *
71029 ATTATATATATATATT-AAAAATGTTTT-CAAACTATAT
1 ATTATAT-TA-ATTTTCAAAAATGTTTTAAAAACTATAT
71066 ATT
1 ATT
71069 GTATATATAT
Statistics
Matches: 272, Mismatches: 31, Indels: 53
0.76 0.09 0.15
Matches are distributed among these distances:
29 10 0.04
30 2 0.01
31 3 0.01
32 7 0.03
33 8 0.03
34 6 0.02
35 47 0.17
36 14 0.05
37 80 0.29
38 50 0.18
39 29 0.11
40 7 0.03
41 9 0.03
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (37 bp):
ATTATATTAATTTTCAAAAATGTTTTAAAAACTATAT
Found at i:70940 original size:75 final size:74
Alignment explanation
Indices: 70705--71076 Score: 321
Period size: 75 Copynumber: 5.1 Consensus size: 74
70695 TTTTCAAAAT
* * * *
70705 TATATAGTTTTTAAAAATGTTTTTAAAACTATATATTATA-T-GTTTTC-AAAATGATTTCAAAA
1 TATATA-TTTTCAAAAATGTTTTAAAAACTATATATTATATTAATTTTCAAAAATG-TTTTAAAA
70767 ACTATATAATA
64 ACTATATAATA
*
70778 TATTTATGTTTTC-AAAATGTTTTTTTAAAAAC--TATA-TATA-T--TTTT--AAAATGTTTTA
1 TA--TATATTTTCAAAAATG---TTTTAAAAACTATATATTATATTAATTTTCAAAAATGTTTTA
*
70834 AAAACTACAT-A-A
61 AAAACTATATAATA
* *
70846 CATGTATTTTCAAAAATGTTTTAAAAACTATATATTATATTAATTTTCAAAAATGTTTTTAAAAA
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTATATTAATTTTCAAAAATG-TTTTAAAAA
70911 CTATATAATA
65 CTATATAATA
* * * * *
70921 TATATATTTTCAAATATGTTTTGAAAACCATATATTATATTAATTTTCAAAAATGTCTTAAGAAC
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTATATTAATTTTCAAAAATGTTTTAAAAAC
70986 TATATAATA
66 TATATAATA
* * * *
70995 TATAAATGTTTTCAAACATGCTTTTCAAAA-T-TATATTATATATATATATT-AAAAATGTTTT-
1 TAT--ATATTTTCAAAAATG-TTTTAAAAACTATATATTATAT-TA-ATTTTCAAAAATGTTTTA
* * *
71056 CAAACTATATATTG
61 AAAACTATATAATA
71070 TATATAT
1 TATATAT
71077 ATATATGTAG
Statistics
Matches: 250, Mismatches: 27, Indels: 44
0.78 0.08 0.14
Matches are distributed among these distances:
64 10 0.04
66 11 0.04
67 10 0.04
68 3 0.01
69 1 0.00
70 17 0.07
71 6 0.02
72 10 0.04
73 30 0.12
74 29 0.12
75 77 0.31
76 34 0.14
77 12 0.05
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (74 bp):
TATATATTTTCAAAAATGTTTTAAAAACTATATATTATATTAATTTTCAAAAATGTTTTAAAAAC
TATATAATA
Found at i:71841 original size:165 final size:164
Alignment explanation
Indices: 71641--72584 Score: 1317
Period size: 165 Copynumber: 5.7 Consensus size: 164
71631 ACAATTTTAT
* * * * * * *
71641 TGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAACTTGATTTG-CCTCTAAGTTGAATATA
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA--TGATTTGCCCTCGAAGCTGAGTGTA
* * *
71705 ATTGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATGATGTGCC
64 ATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC
71770 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGC
129 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGC
* *
71806 TGACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG-TTATGCCCTTGAAGCTGAGTGTAA
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATT-TGCCCTCGAAGCTGAGTGTAA
* * *
71870 TCGAACT-TAAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTACAAATGATGTGCC
65 TCGAACTCGAA-GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC
* *
71934 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
129 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGC
* * * * *
71971 TCATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGTTGAGTATAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATTTGCCCTCGAAGCTGAGTGTAAT
* * *
72036 CGAACTTG-GGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
66 CGAACTCGAAGG-TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCT
* * *
72100 TGGAGCTGAGCATAGTTGAACTCAAAGGTCTTTGGT
130 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GC
* * * * * *
72136 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATTTGCCCTCGAAGCTGAGTGTAAT
** *
72201 CGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT
66 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT
72266 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGC
131 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGC
*
72300 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG-TTATGCCCTTGAAGCTGAGTGTAA
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATT-TGCCCTCGAAGCTGAGTGTAA
* * * *
72364 TTGAACT-TAAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGTTATACTGCAAATGATGTGCC
65 TCGAACTCGAA-GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC
*
72428 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
129 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGC
* *
72465 TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATTTGCCCTCGAAGCTGAGTGTAAT
* *
72530 CGAACTC-AGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
66 CGAACTCGA-AGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAAT
72585 AGTTTGTTTA
Statistics
Matches: 692, Mismatches: 72, Indels: 30
0.87 0.09 0.04
Matches are distributed among these distances:
162 2 0.00
163 7 0.01
164 246 0.36
165 432 0.62
166 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (164 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATTTGCCCTCGAAGCTGAGTGTAAT
CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT
GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGC
Found at i:72080 original size:329 final size:327
Alignment explanation
Indices: 71643--72584 Score: 1409
Period size: 329 Copynumber: 2.9 Consensus size: 327
71633 AATTTTATTG
* * * * * *
71643 ACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAACTTGATTTG-CCTCTAAGTTGAATATAAT
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA--TGATATGCCCTCGAAGTTGAGTATAAT
* * * *
71707 TGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATGATGTGCCTT
64 TGAACTTG-GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT
*
71772 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTGACAAATAACCCTTCTAGCCTTGAGTTATG
128 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * * * *
71837 CTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTT
193 CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTT
* *
71902 CTCGACTTAAGCTATACTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
258 CTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-T
*
71967 TTGGTC
322 TTGCTC
* *
71973 ATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGTTGAGTATAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGTTGAGTATAATTG
*
72038 AACTTGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTTGGGG-TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGG
* * * * * * *
72103 AGCTGAGCATAGTTGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
130 AGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GCTGACAGATAACCCTTCTAGCCTTGAGTTATGC
* * *
72168 TGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTC
194 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTC
72233 TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
259 TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
*
72298 GCTG
324 GCTC
* * * *
72302 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATTG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGTTGAGTATAATTG
* * *
72367 AACTTAAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGG
66 AACTT-GGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGG
* *
72432 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
130 AGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTGACAGATAACCCTTCTAGCCTTGAGTTATGC
72497 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTC
194 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTC
*
72562 TCGACTTAAGCTATGCTGCAAAT
259 TCGACTTAAGCTATACTGCAAAT
72585 AGTTTGTTTA
Statistics
Matches: 551, Mismatches: 56, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
328 8 0.01
329 361 0.66
330 182 0.33
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (327 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGTTGAGTATAATTG
AACTTGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGA
GCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTCTC
GACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGC
TC
Found at i:79101 original size:29 final size:28
Alignment explanation
Indices: 79061--79115 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
79051 TTTAAAAATA
*
79061 TTTTAAAATGTTTTCAAAATTATATAGT
1 TTTTAAAATGTTTTCAAAACTATATAGT
*
79089 TTTTAAAAATGTTTTTAAAACTATATA
1 TTTT-AAAATGTTTTCAAAACTATATA
79116 TTATATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (28 bp):
TTTTAAAATGTTTTCAAAACTATATAGT
Found at i:79203 original size:30 final size:29
Alignment explanation
Indices: 79058--79155 Score: 74
Period size: 29 Copynumber: 3.2 Consensus size: 29
79048 ACTTTTAAAA
* *
79058 ATATTTT-AAAATGTTTTCAAAATTATAT
1 ATATTTTCAAAATGTTTTAAAAACTATAT
* *
79086 AGT-TTTTAAAAATGTTTTTAAAACTATATATT
1 A-TATTTTCAAAATGTTTTAAAAAC--TATA-T
*
79118 ATATGTTTTCAAAATGATTTCAAAAACTATAT
1 ATA--TTTTCAAAATG-TTTTAAAAACTATAT
79150 ATATTT
1 ATATTT
79156 ATGTTTTCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
28 5 0.09
29 15 0.27
30 3 0.05
31 5 0.09
32 6 0.11
33 4 0.07
34 10 0.18
35 8 0.14
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (29 bp):
ATATTTTCAAAATGTTTTAAAAACTATAT
Found at i:79214 original size:65 final size:65
Alignment explanation
Indices: 79088--79251 Score: 174
Period size: 65 Copynumber: 2.4 Consensus size: 65
79078 AATTATATAG
* * *
79088 TTTTTAAAAATGTTTTTAAAACTATATATTATATGTTTTCAAAATGATTTCAAAAACTATAT-AT
1 TTTTCAAAAATGTTTTAAAAAC--TATA-TATA--TTTTCAAAATGATTTCAAAAACTATATAAC
*
79152 ATTTA
61 ATGTA
*
79157 TGTTTTC-AAAATGTTTTTTAAAAACTATATATATTTT-AAAATG-TTTTAAAAACTATATAACA
1 --TTTTCAAAAATG--TTTTAAAAACTATATATATTTTCAAAATGATTTCAAAAACTATATAACA
79219 TGTA
62 TGTA
79223 TTTTCAAAAATGTTTTAAAAACTATATAT
1 TTTTCAAAAATGTTTTAAAAACTATATAT
79252 TATATTAATT
Statistics
Matches: 84, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
63 17 0.20
64 5 0.06
65 20 0.24
66 11 0.13
67 4 0.05
69 4 0.05
70 10 0.12
71 4 0.05
72 9 0.11
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (65 bp):
TTTTCAAAAATGTTTTAAAAACTATATATATTTTCAAAATGATTTCAAAAACTATATAACATGTA
Found at i:79289 original size:39 final size:37
Alignment explanation
Indices: 79079--79363 Score: 250
Period size: 37 Copynumber: 8.0 Consensus size: 37
79069 TGTTTTCAAA
* * *
79079 ATTATA-TAGTTTTTAAAAATGTTTTTAAAACTATAT
1 ATTATATTAATTTTCAAAAATGTTTTAAAAACTATAT
* *
79115 ATTATA-T-GTTTTC-AAAATGATTTCAAAAACTATAT
1 ATTATATTAATTTTCAAAAATG-TTTTAAAAACTATAT
*
79150 A-TAT-TTATGTTTTC-AAAATGTTTTTTAAAAAC----T
1 ATTATATTA-ATTTTCAAAAATG--TTTTAAAAACTATAT
79183 A-TATA-T-ATTTT--AAAATGTTTTAAAAACTATAT
1 ATTATATTAATTTTCAAAAATGTTTTAAAAACTATAT
*
79215 A--ACATGT-ATTTTCAAAAATGTTTTAAAAACTATAT
1 ATTATAT-TAATTTTCAAAAATGTTTTAAAAACTATAT
79250 ATTATATTAATTTTCAAAAAATGTTTTTAAAAACTATAT
1 ATTATATTAATTTTC-AAAAATG-TTTTAAAAACTATAT
* * *
79289 AATATA-TATATTTTCAAAAATGTTTTGAAAACCATAT
1 ATTATATTA-ATTTTCAAAAATGTTTTAAAAACTATAT
* *
79326 ATTATATTAATTTTCAAAAATGTCTTAAGAACTATAT
1 ATTATATTAATTTTCAAAAATGTTTTAAAAACTATAT
79363 A
1 A
79364 AATGTCTTAA
Statistics
Matches: 212, Mismatches: 16, Indels: 41
0.79 0.06 0.15
Matches are distributed among these distances:
28 10 0.05
30 6 0.03
31 6 0.03
32 2 0.01
33 12 0.06
34 10 0.05
35 41 0.19
36 20 0.09
37 61 0.29
38 18 0.08
39 26 0.12
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (37 bp):
ATTATATTAATTTTCAAAAATGTTTTAAAAACTATAT
Found at i:79306 original size:76 final size:73
Alignment explanation
Indices: 79082--79365 Score: 272
Period size: 76 Copynumber: 4.0 Consensus size: 73
79072 TTTCAAAATT
* * * * *
79082 ATATAGTTTTTAAAAATGTTTTTAAAACTATATATTATA-T-GTTTTC-AAAATGATTTCAAAAA
1 ATATA-TTTTCAAAAATGTTTTAAAAACCATATATTATATTAATTTTCAAAAATG-TTTTAAAAA
* *
79144 CTATATATAT
64 CTATATAAAC
* *
79154 TTATGTTTTC-AAAATGTTTTTTAAAAA-C---TA-TATA-T-ATTTT--AAAATGTTTTAAAAA
1 ATATATTTTCAAAAATG--TTTTAAAAACCATATATTATATTAATTTTCAAAAATGTTTTAAAAA
79209 CTATAT-AAC
64 CTATATAAAC
* *
79218 ATGTATTTTCAAAAATGTTTTAAAAACTATATATTATATTAATTTTCAAAAAATGTTTTTAAAAA
1 ATATATTTTCAAAAATGTTTTAAAAACCATATATTATATTAATTTTC-AAAAATG-TTTTAAAAA
*
79283 CTATATAATAT
64 CTATATAA-AC
* * *
79294 ATATATTTTCAAAAATGTTTTGAAAACCATATATTATATTAATTTTCAAAAATGTCTTAAGAACT
1 ATATATTTTCAAAAATGTTTTAAAAACCATATATTATATTAATTTTCAAAAATGTTTTAAAAACT
79359 ATATAAA
66 ATATAAA
79366 TGTCTTAAGA
Statistics
Matches: 177, Mismatches: 19, Indels: 31
0.78 0.08 0.14
Matches are distributed among these distances:
63 9 0.05
64 8 0.05
65 20 0.11
66 6 0.03
67 11 0.06
68 6 0.03
69 1 0.01
70 11 0.06
71 4 0.02
72 11 0.06
73 7 0.04
74 30 0.17
75 8 0.05
76 45 0.25
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (73 bp):
ATATATTTTCAAAAATGTTTTAAAAACCATATATTATATTAATTTTCAAAAATGTTTTAAAAACT
ATATAAAC
Found at i:79368 original size:20 final size:20
Alignment explanation
Indices: 79343--79382 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
79333 TAATTTTCAA
79343 AAATGTCTTAAGAACTATAT
1 AAATGTCTTAAGAACTATAT
79363 AAATGTCTTAAGAACTATAT
1 AAATGTCTTAAGAACTATAT
79383 TATATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
AAATGTCTTAAGAACTATAT
Found at i:79703 original size:10 final size:10
Alignment explanation
Indices: 79688--79715 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
79678 AACAAATGGC
79688 GGAAATGAAG
1 GGAAATGAAG
79698 GGAAATGAAG
1 GGAAATGAAG
79708 GGAAATGA
1 GGAAATGA
79716 GAAAATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.39, T:0.11
Consensus pattern (10 bp):
GGAAATGAAG
Found at i:85172 original size:28 final size:26
Alignment explanation
Indices: 85108--85181 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 26
85098 GACTTTGAAA
* *
85108 ATATATAATTTTTGAAAACA-AATTAT
1 ATATATAGTTTTT-AAAATATAATTAT
85134 ATA-ATAGTTTTTAAAATATAATATAT
1 ATATATAGTTTTTAAAATATAAT-TAT
*
85160 ATTATATAGTTTTTAATATATA
1 A-TATATAGTTTTTAAAATATA
85182 TGTGTGTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 5 0.12
25 11 0.27
26 7 0.17
27 2 0.05
28 16 0.39
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (26 bp):
ATATATAGTTTTTAAAATATAATTAT
Found at i:85197 original size:22 final size:21
Alignment explanation
Indices: 85152--85211 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
85142 TTTTAAAATA
*
85152 TAATATATATTATATAGTTTT
1 TAATATATATTATATAATTTT
* *
85173 TAATATATATGTGTGTAATTTT
1 TAATATATAT-TATATAATTTT
85195 TAATATATATATATATA
1 TAATATATAT-TATATA
85212 TATTATTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 10 0.31
22 22 0.69
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TAATATATATTATATAATTTT
Found at i:90856 original size:43 final size:46
Alignment explanation
Indices: 90808--90918 Score: 156
Period size: 47 Copynumber: 2.5 Consensus size: 46
90798 GTAAGTATGC
90808 AAATAAGCTTACGAGCTTATG-AA-T-AATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGTAATTAAATGGCAAGTATATTGATA
* * * *
90851 AAATAATCTTACGAGCTTATGTAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGTAA-TTAAATGGCAAGTATATTGATA
90898 AAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
90919 GAAAAAAAGG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
43 20 0.34
44 2 0.03
46 1 0.02
47 36 0.61
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGTAATTAAATGGCAAGTATATTGATA
Found at i:92924 original size:16 final size:16
Alignment explanation
Indices: 92903--92934 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
92893 ATTGATGAAA
92903 AAGTGAAATCATCAAT
1 AAGTGAAATCATCAAT
*
92919 AAGTGATATCATCAAT
1 AAGTGAAATCATCAAT
92935 GGTTACGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (16 bp):
AAGTGAAATCATCAAT
Found at i:93787 original size:6 final size:6
Alignment explanation
Indices: 93764--93882 Score: 79
Period size: 6 Copynumber: 20.3 Consensus size: 6
93754 AATATATTAT
* *
93764 AAGAAA AAAAAA ACAGAAA AAGAAA AA-AAA ATAGAAA AAGAAA ATGAAA
1 AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA
* * * * * *
93813 ACGAAG AAG-AA AA-AAA ATGAAA ATGAGA AAG-AA AAGAAA AAGAGA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
93858 AA-AAA ATGAGAA ATGAAA AA-AAA AA
1 AAGAAA AAGA-AA AAGAAA AAGAAA AA
93883 ATATTTCACT
Statistics
Matches: 90, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
5 22 0.24
6 53 0.59
7 15 0.17
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:93789 original size:18 final size:17
Alignment explanation
Indices: 93768--93882 Score: 97
Period size: 18 Copynumber: 6.6 Consensus size: 17
93758 TATTATAAGA
93768 AAAAAAAAACAGAAAAAG
1 AAAAAAAAA-AGAAAAAG
93786 AAAAAAAAATAGAAAAAG
1 AAAAAAAAA-AGAAAAAG
* * *
93804 AAAATGAAAACGAAGAAG
1 AAAA-AAAAAAGAAAAAG
* *
93822 -AAAAAAAATGAAAATG
1 AAAAAAAAAAGAAAAAG
* *
93838 AGAAAGAAAAGAAAAAG
1 AAAAAAAAAAGAAAAAG
* * *
93855 AGAAAAAAATGAGAAATG
1 AAAAAAAAAAGA-AAAAG
93873 AAAAAAAAAA
1 AAAAAAAAAA
93883 ATATTTCACT
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
16 9 0.12
17 25 0.32
18 39 0.51
19 4 0.05
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAG
Found at i:93823 original size:36 final size:35
Alignment explanation
Indices: 93768--93870 Score: 113
Period size: 34 Copynumber: 2.9 Consensus size: 35
93758 TATTATAAGA
*
93768 AAAAAAAAACAGAAAAAGAAAAAAAAATAGAAAAAG
1 AAAAGAAAAC-GAAAAAGAAAAAAAAATAGAAAAAG
* *
93804 AAAATGAAAACGAAGAAG-AAAAAAAAT-GAAAATG
1 AAAA-GAAAACGAAAAAGAAAAAAAAATAGAAAAAG
*
93838 AGAAAGAAAA-GAAAAAGAGAAAAAAATGAGAAA
1 A-AAAGAAAACGAAAAAGAAAAAAAAAT-AGAAA
93871 TGAAAAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
33 6 0.11
34 20 0.35
35 12 0.21
36 14 0.25
37 5 0.09
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.05
Consensus pattern (35 bp):
AAAAGAAAACGAAAAAGAAAAAAAAATAGAAAAAG
Found at i:93829 original size:22 final size:23
Alignment explanation
Indices: 93799--93852 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
93789 AAAAAATAGA
93799 AAAAGAAAATGAAAACGA-AGAAG
1 AAAAGAAAATGAAAACGAGA-AAG
*
93822 AAAA-AAAATGAAAATGAGAAAG
1 AAAAGAAAATGAAAACGAGAAAG
93844 AAAAGAAAA
1 AAAAGAAAA
93853 AGAGAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.06
Consensus pattern (23 bp):
AAAAGAAAATGAAAACGAGAAAG
Found at i:93829 original size:28 final size:27
Alignment explanation
Indices: 93769--93883 Score: 100
Period size: 28 Copynumber: 4.3 Consensus size: 27
93759 ATTATAAGAA
93769 AAAAAAAACAGAAAA--AGAAA-AAAA-
1 AAAAAAAA-AGAAAATGAGAAAGAAAAG
*
93793 AATAGAAAAAGAAAATGA-AAACGAAGAAG
1 AA-AAAAAAAGAAAATGAGAAA-GAA-AAG
*
93822 AAAAAAAATGAAAATGAGAAAGAAAAG
1 AAAAAAAAAGAAAATGAGAAAGAAAAG
93849 AAAAAGAGAAA-AAAATGAGAAATGAAAA-
1 AAAAA-A-AAAGAAAATGAGAAA-GAAAAG
93877 AAAAAAA
1 AAAAAAA
93884 TATTTCACTT
Statistics
Matches: 76, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
24 8 0.11
25 8 0.11
26 2 0.03
27 11 0.14
28 35 0.46
29 12 0.16
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (27 bp):
AAAAAAAAAGAAAATGAGAAAGAAAAG
Found at i:93877 original size:17 final size:17
Alignment explanation
Indices: 93823--93880 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
93813 ACGAAGAAGA
93823 AAAAAAATGAAAATGAG
1 AAAAAAATGAAAATGAG
*
93840 AAAGAAAA-GAAAAAGAG
1 AAA-AAAATGAAAATGAG
93857 AAAAAAATGAGAAATGA-
1 AAAAAAATGA-AAATGAG
93874 AAAAAAA
1 AAAAAAA
93881 AAATATTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 4 0.11
17 23 0.64
18 9 0.25
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (17 bp):
AAAAAAATGAAAATGAG
Found at i:97228 original size:47 final size:44
Alignment explanation
Indices: 97135--97248 Score: 151
Period size: 47 Copynumber: 2.5 Consensus size: 44
97125 GTAAGTATGC
97135 AAATAAGCTTACGAGCTTAT-GAATAATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGATA
* * *
97178 AAATAAGCTTACGAACTTATGGAATTTAAATGGTAAGTAT-TATGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATAT-TGATA
97225 AAATAAGCTTACGAGCTTATGGAA
1 AAATAAGCTTACGAGCTTATGGAA
97249 AAAAAGGTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
43 19 0.31
44 3 0.05
46 2 0.03
47 38 0.61
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGATA
Found at i:103065 original size:20 final size:20
Alignment explanation
Indices: 103042--103088 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
103032 TATTGAGGAG
*
103042 TGACATCA-ATCATATCACAT
1 TGACATCATATCA-ATAACAT
* *
103062 TGACACCATATCAATAACTT
1 TGACATCATATCAATAACAT
103082 TGACATC
1 TGACATC
103089 TTAGTGGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (20 bp):
TGACATCATATCAATAACAT
Found at i:103976 original size:43 final size:44
Alignment explanation
Indices: 103890--103994 Score: 160
Period size: 43 Copynumber: 2.4 Consensus size: 44
103880 AAAATGACAT
103890 AGTACACAAAGTACTCTTGTCATAATACACAAAGTACTACTCCA
1 AGTACACAAAGTACTCTTGTCATAATACACAAAGTACTACTCCA
* * *
103934 TGTACA-AGAAGTACTCTTGT-ATAGTACACAAAGTACTGCTCCA
1 AGTACACA-AAGTACTCTTGTCATAATACACAAAGTACTACTCCA
103977 AGTACACAAAGTACTCTT
1 AGTACACAAAGTACTCTT
103995 ACGAAAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
43 37 0.67
44 18 0.33
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (44 bp):
AGTACACAAAGTACTCTTGTCATAATACACAAAGTACTACTCCA
Found at i:103982 original size:21 final size:20
Alignment explanation
Indices: 103890--103993 Score: 84
Period size: 21 Copynumber: 4.8 Consensus size: 20
103880 AAAATGACAT
*
103890 AGTACACAAAGTACTCTTGTCA
1 AGTACACAAAGTACTC-T-CCA
*
103912 TAATACACAAAGTACTACTCCA
1 -AGTACACAAAGTACT-CTCCA
* **
103934 TGTACA-AGAAGTACTCTTGTA
1 AGTACACA-AAGTACTC-TCCA
103955 TAGTACACAAAGTACTGCTCCA
1 -AGTACACAAAGTACT-CTCCA
103977 AGTACACAAAGTACTCT
1 AGTACACAAAGTACTCT
103994 TACGAAAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
20 4 0.06
21 28 0.42
22 16 0.24
23 17 0.26
24 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.26
Consensus pattern (20 bp):
AGTACACAAAGTACTCTCCA
Found at i:110949 original size:17 final size:15
Alignment explanation
Indices: 110927--110970 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
110917 CCATCCTTGC
*
110927 ACACAAAGTGCCATAGT
1 ACACAAAGT-ACA-AGT
110944 ACACAAAGCTACAAGT
1 ACACAAAG-TACAAGT
110960 ACACAAAGTAC
1 ACACAAAGTAC
110971 TCTTGCCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 3 0.12
16 11 0.44
17 10 0.40
18 1 0.04
ACGTcount: A:0.48, C:0.25, G:0.14, T:0.14
Consensus pattern (15 bp):
ACACAAAGTACAAGT
Found at i:111007 original size:21 final size:23
Alignment explanation
Indices: 110957--111062 Score: 141
Period size: 23 Copynumber: 4.8 Consensus size: 23
110947 CAAAGCTACA
110957 AGTACACAAAGTACTCTTGCCAT
1 AGTACACAAAGTACTCTTGCCAT
110980 AGTACACAAAGTACTAC-T-CCAT
1 AGTACACAAAGTACT-CTTGCCAT
*
111002 -GTACACGAAGTACTCTTGCCAT
1 AGTACACAAAGTACTCTTGCCAT
*
111024 AGTACACAAAGTACTATT-CCA-
1 AGTACACAAAGTACTCTTGCCAT
*
111045 AGTACACAAAATACTCTT
1 AGTACACAAAGTACTCTT
111063 ACGATAATGC
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.01
21 30 0.41
22 11 0.15
23 31 0.42
24 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.25
Consensus pattern (23 bp):
AGTACACAAAGTACTCTTGCCAT
Found at i:111013 original size:44 final size:43
Alignment explanation
Indices: 110935--111062 Score: 183
Period size: 44 Copynumber: 3.0 Consensus size: 43
110925 GCACACAAAG
110935 TGCCATAGTACACAAAG--CTA--CAAGTACACAAAGTACTCT
1 TGCCATAGTACACAAAGTACTATCCAAGTACACAAAGTACTCT
* *
110974 TGCCATAGTACACAAAGTACTACTCCATGTACACGAAGTACTCT
1 TGCCATAGTACACAAAGTACTA-TCCAAGTACACAAAGTACTCT
*
111018 TGCCATAGTACACAAAGTACTATTCCAAGTACACAAAATACTCT
1 TGCCATAGTACACAAAGTACTA-TCCAAGTACACAAAGTACTCT
111062 T
1 T
111063 ACGATAATGC
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
39 17 0.22
41 3 0.04
44 58 0.74
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (43 bp):
TGCCATAGTACACAAAGTACTATCCAAGTACACAAAGTACTCT
Found at i:114672 original size:45 final size:45
Alignment explanation
Indices: 114613--114763 Score: 223
Period size: 45 Copynumber: 3.4 Consensus size: 45
114603 CAAATAAGCT
* * *
114613 TGGAATAAAAGGTAAGTATATTGGTAAAATATGCTTACAAGCTTA
1 TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
114658 TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTA
1 TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
114703 TGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTCA
1 TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
114748 TAGG-ATAAATGATAAG
1 T-GGAATAAATGGTAAG
114764 AAATTTTATA
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
45 95 0.98
46 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (45 bp):
TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
Found at i:115262 original size:21 final size:22
Alignment explanation
Indices: 115226--115269 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
115216 ATTTCCAGTA
115226 TGCTACAGGGGTATCGATACCC
1 TGCTACAGGGGTATCGATACCC
*
115248 TGCTACA-GTGTATCGATACCC
1 TGCTACAGGGGTATCGATACCC
115269 T
1 T
115270 CACTGTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (22 bp):
TGCTACAGGGGTATCGATACCC
Found at i:116418 original size:2 final size:2
Alignment explanation
Indices: 116411--116478 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
116401 TATAATGTGT
116411 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
116453 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
116479 AAAAACACAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:117006 original size:2 final size:2
Alignment explanation
Indices: 116999--117031 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
116989 ACTTATTTGA
116999 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 A
117032 ATTTCAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:122774 original size:24 final size:23
Alignment explanation
Indices: 122722--122781 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 23
122712 AATCAACATA
*
122722 AGGGGTATCGGTACCTTTGGGAT
1 AGGGGTATCGGTACCTTTGGCAT
* *
122745 A--GGTATCGATACCTCTTTGCAT
1 AGGGGTATCGGTACCT-TTGGCAT
122767 AGGGGTATCGGTACC
1 AGGGGTATCGGTACC
122782 CTATGGGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 12 0.40
22 6 0.20
23 1 0.03
24 11 0.37
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (23 bp):
AGGGGTATCGGTACCTTTGGCAT
Found at i:123196 original size:55 final size:56
Alignment explanation
Indices: 123132--123242 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 56
123122 AACATTTTAG
123132 AAATTTTAAGATTTTCTTTTGAAAAAA-CATATTTGAAAAATTTACTCCCACTCCC
1 AAATTTTAAGATTTTCTTTTGAAAAAATCATATTTGAAAAATTTACTCCCACTCCC
*
123187 AAATTTTAAGATTTTCTTTTGAAAAAATCATTTTTGAAAAATTTACTCCCACTCCC
1 AAATTTTAAGATTTTCTTTTGAAAAAATCATATTTGAAAAATTTACTCCCACTCCC
123243 CCATACTATA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 27 0.50
56 27 0.50
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (56 bp):
AAATTTTAAGATTTTCTTTTGAAAAAATCATATTTGAAAAATTTACTCCCACTCCC
Done.