Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003007.1 Hibiscus syriacus cultivar Beakdansim tig00006231_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: 75361
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:8147 original size:20 final size:20
Alignment explanation
Indices: 8122--8291 Score: 72
Period size: 20 Copynumber: 8.7 Consensus size: 20
8112 GTTCAGCCTT
8122 GATGCATGGATGCATTGCAG
1 GATGCATGGATGCATTGCAG
* * *
8142 GATGCATCGATGCATGGCAT
1 GATGCATGGATGCATTGCAG
* * * *
8162 GATGCATCGATGTACT--AA
1 GATGCATGGATGCATTGCAG
* * *
8180 G-TGCATTCGATG--TT-TAA
1 GATGCA-TGGATGCATTGCAG
*
8197 G-TGCATGGATGCATTGCAT
1 GATGCATGGATGCATTGCAG
* *
8216 GATGCGTCGATGCATTAGTGCAG
1 GATGCATGGATGCA-T--TGCAG
*
8239 G-TGCATGGATGCACTGCAGG
1 GATGCATGGATGCATTGCA-G
* *
8259 GATGCAGGGATGCACT--AGG
1 GATGCATGGATGCATTGCA-G
8278 GATGCATGGATGCA
1 GATGCATGGATGCA
8292 CTTTGACACC
Statistics
Matches: 120, Mismatches: 19, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
16 6 0.05
17 11 0.09
18 10 0.08
19 22 0.18
20 42 0.35
21 14 0.12
22 10 0.08
23 5 0.04
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (20 bp):
GATGCATGGATGCATTGCAG
Found at i:8197 original size:17 final size:18
Alignment explanation
Indices: 8164--8202 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
8154 CATGGCATGA
8164 TGCA-TCGATGTACTAAG
1 TGCATTCGATGTACTAAG
*
8181 TGCATTCGATGT-TTAAG
1 TGCATTCGATGTACTAAG
8198 TGCAT
1 TGCAT
8203 GGATGCATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (18 bp):
TGCATTCGATGTACTAAG
Found at i:8258 original size:19 final size:21
Alignment explanation
Indices: 8240--8293 Score: 85
Period size: 19 Copynumber: 2.7 Consensus size: 21
8230 TTAGTGCAGG
8240 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
8261 TGCAGGGATGCACT--AGGGA
1 TGCATGGATGCACTGCAGGGA
8280 TGCATGGATGCACT
1 TGCATGGATGCACT
8294 TTGACACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 18 0.58
21 13 0.42
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.20
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:8393 original size:29 final size:29
Alignment explanation
Indices: 8361--8423 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
8351 GAAACCTTTT
8361 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
*
8391 AAATATTTTGTAAATTCAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
8421 AAA
1 AAA
8424 TATTTTACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:8419 original size:30 final size:29
Alignment explanation
Indices: 8372--8429 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
8362 AAACTTTGAA
8372 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAATATTTTG
8401 TAAATTCAATTCAAGTCCAAAAATATTTT
1 TAAATTCAATT-AAGTCCAAAAATATTTT
8430 ACCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAATATTTTG
Found at i:11503 original size:21 final size:21
Alignment explanation
Indices: 11473--11512 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
11463 TGTTGTATAT
11473 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTGGGGATGATTTTGG
11493 AGCCGGTTGGGGATGATTTT
1 AGCC-GTTGGGGATGATTTT
11513 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.42, T:0.35
Consensus pattern (21 bp):
AGCCGTTGGGGATGATTTTGG
Found at i:11664 original size:8 final size:7
Alignment explanation
Indices: 11612--11721 Score: 52
Period size: 8 Copynumber: 15.1 Consensus size: 7
11602 GTTGTATCCT
11612 TGATGCA
1 TGATGCA
11619 TGGATGCA
1 T-GATGCA
11627 TG--GCA
1 TGATGCA
*
11632 GGATGCA
1 TGATGCA
11639 TCGATGCA
1 T-GATGCA
11647 TG--GCA
1 TGATGCA
11652 TGATGCA
1 TGATGCA
11659 TCGATGCA
1 T-GATGCA
*
11667 CTTAGTGCA
1 -TGA-TGCA
**
11676 TTCGATGTT
1 -T-GATGCA
11685 TGAGTGCA
1 TGA-TGCA
11693 TGAATGCA
1 TG-ATGCA
11701 T--TGCA
1 TGATGCA
11706 TGATGCA
1 TGATGCA
11713 TCGATGCA
1 T-GATGCA
11721 T
1 T
11722 TAGTGCAGGT
Statistics
Matches: 79, Mismatches: 9, Indels: 29
0.68 0.08 0.25
Matches are distributed among these distances:
5 14 0.18
7 17 0.22
8 38 0.48
9 9 0.11
10 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (7 bp):
TGATGCA
Found at i:11757 original size:21 final size:21
Alignment explanation
Indices: 11731--11807 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
11721 TTAGTGCAGG
11731 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
11752 TGCATGGATGTACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
* *
11773 TGCATGGATGCACTACAAGGA
1 TGCATGGATGCACTGCAGGGA
11794 TGCATGGATGCACT
1 TGCATGGATGCACT
11808 TTGACACCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:12421 original size:29 final size:29
Alignment explanation
Indices: 12389--12451 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
12379 GAAACATTTT
12389 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
*
12419 AAATATTTTGTAAATTCAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
12449 AAA
1 AAA
12452 CATTTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:12447 original size:30 final size:29
Alignment explanation
Indices: 12400--12458 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
12390 AAACTTTGAA
*
12400 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
12429 TAAATTCAATTCAAGTCCAAAAACATTTTG
1 TAAATTCAATT-AAGTCCAAAAACATTTTG
12459 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:12697 original size:513 final size:513
Alignment explanation
Indices: 11730--12720 Score: 1799
Period size: 513 Copynumber: 1.9 Consensus size: 513
11720 ATTAGTGCAG
*
11730 GTGCATGGATGCACTGCAGGGATGCATGGATGTACTGCAGGGATGCATGGATGCACTACAAGGAT
1 GTGCATGGATGCACTGCAGGGATGCATCGATGTACTGCAGGGATGCATGGATGCACTACAAGGAT
11795 GCATGGATGCACTTTGACACCCTTTAGCATTTTGGCTCAAATCCGATTTTAATAGACTTTGAATT
66 GCATGGATGCACTTTGACACCCTTTAGCATTTTGGCTCAAATCCGATTTTAATAGACTTTGAATT
*
11860 ATTTTTGAAACATTTTAAAACTTTGAATAAATTCAATTAAGTCCAAAAATATTTTGTAAATTTAA
131 ATTTTTGAAACATTTTAAAACTTTGAATAAATTCAATTAAGTCCAAAAATATTTTGTAAATTCAA
***
11925 TTCAAGTCCAAAATTTTTTTGCCTTAAATTGTTATATCAAAACATAGTTCAACAATTACCTTATA
196 TTCAAGTCCAAAAACATTTTGCCTTAAATTGTTATATCAAAACATAGTTCAACAATTACCTTATA
*
11990 TTTACCTCAGATTAATAAGAAAAATCAAAATCCATAGGTTTAATGGTCTAATCAAGATAAAAACC
261 TTTACCTCAGATTAATAAAAAAAATCAAAATCCATAGGTTTAATGGTCTAATCAAGATAAAAACC
12055 CTTCCACTTTCTCATTGCGTTCACTTAAGCATAAAAACTTATAATGTTCACACTTAAGTCTCCAA
326 CTTCCACTTTCTCATTGCGTTCACTTAAGCATAAAAACTTATAATGTTCACACTTAAGTCTCCAA
12120 ACTTTCAATCTTCACCAAATTAGTCCCCAATCGAAACTGAATCAATTCTTAATTTAATCGAACTA
391 ACTTTCAATCTTCACCAAATTAGTCCCCAATCGAAACTGAATCAATTCTTAATTTAATCGAACTA
12185 ATTCTTTTCAATGGACACACATTGATGCATCGATGCACTAAGTGCATTCGATGTTTGA
456 ATTCTTTTCAATGGACACACATTGATGCATCGATGCACTAAGTGCATTCGATGTTTGA
* * * * *
12243 GTGCATGGATGCATTGCA-TGATGCATCGATGCATTAGTGCA-GG-TGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGGGATGCATCGATG---TACTGCAGGGATGCATGGATGCACTACAAG
*
12305 GATGCATGGATGCACTTTGACACCCTTTAGCATTTTGGCTCAAATCCGATTTTAATGGACTTTGA
63 GATGCATGGATGCACTTTGACACCCTTTAGCATTTTGGCTCAAATCCGATTTTAATAGACTTTGA
12370 ATTATTTTTGAAACATTTTAAAACTTTGAATAAATTCAATTAAGTCCAAAAATATTTTGTAAATT
128 ATTATTTTTGAAACATTTTAAAACTTTGAATAAATTCAATTAAGTCCAAAAATATTTTGTAAATT
12435 CAATTCAAGTCCAAAAACATTTTGCCTTAAATTGTTATATCAAAACATAGTTCAACAATTACCTT
193 CAATTCAAGTCCAAAAACATTTTGCCTTAAATTGTTATATCAAAACATAGTTCAACAATTACCTT
12500 ATATTTACCTCAGATTAATAAAAAAAATCAAAATCCATAGGTTTAATGGTCTAATCAAGATAAAA
258 ATATTTACCTCAGATTAATAAAAAAAATCAAAATCCATAGGTTTAATGGTCTAATCAAGATAAAA
*
12565 ACCCTTCCACTTTCTCCTTGCGTTCACTTAAGCATAAAAACTTATAATGTTCACACTTAAGTCTC
323 ACCCTTCCACTTTCTCATTGCGTTCACTTAAGCATAAAAACTTATAATGTTCACACTTAAGTCTC
* *
12630 CAAACTTTCAATCTTCACCAAATTAGTTCTCAATCGAAACTGAATCAATTCTTAATTTAATCGAA
388 CAAACTTTCAATCTTCACCAAATTAGTCCCCAATCGAAACTGAATCAATTCTTAATTTAATCGAA
12695 CTAATTCTTTTCAATGGACACACATT
453 CTAATTCTTTTCAATGGACACACATT
12721 CAAGGGCTTA
Statistics
Matches: 460, Mismatches: 15, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
512 11 0.02
513 441 0.96
514 2 0.00
515 6 0.01
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (513 bp):
GTGCATGGATGCACTGCAGGGATGCATCGATGTACTGCAGGGATGCATGGATGCACTACAAGGAT
GCATGGATGCACTTTGACACCCTTTAGCATTTTGGCTCAAATCCGATTTTAATAGACTTTGAATT
ATTTTTGAAACATTTTAAAACTTTGAATAAATTCAATTAAGTCCAAAAATATTTTGTAAATTCAA
TTCAAGTCCAAAAACATTTTGCCTTAAATTGTTATATCAAAACATAGTTCAACAATTACCTTATA
TTTACCTCAGATTAATAAAAAAAATCAAAATCCATAGGTTTAATGGTCTAATCAAGATAAAAACC
CTTCCACTTTCTCATTGCGTTCACTTAAGCATAAAAACTTATAATGTTCACACTTAAGTCTCCAA
ACTTTCAATCTTCACCAAATTAGTCCCCAATCGAAACTGAATCAATTCTTAATTTAATCGAACTA
ATTCTTTTCAATGGACACACATTGATGCATCGATGCACTAAGTGCATTCGATGTTTGA
Found at i:13133 original size:3 final size:3
Alignment explanation
Indices: 13125--13187 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
13115 ATTTTTTCAT
13125 TTA TTA TTA TT- TT- TTA TTA TTA TTA TT- TTA TTA TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
* * *
13168 ATA -AA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
13188 CAGACCTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 7 0.14
3 41 0.80
4 3 0.06
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:14486 original size:20 final size:20
Alignment explanation
Indices: 14463--14506 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
14453 TACATTTTTT
14463 TATTTA-ATCCTATATTTAAA
1 TATTTATAT-CTATATTTAAA
* *
14483 TATTTATATTTATATTTTAA
1 TATTTATATCTATATTTAAA
14503 TATT
1 TATT
14507 AAGAAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTATATCTATATTTAAA
Found at i:14627 original size:2 final size:2
Alignment explanation
Indices: 14620--14650 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14610 TATAAAAAGA
14620 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 A
14651 ATTTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18770 original size:15 final size:15
Alignment explanation
Indices: 18750--18781 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18740 GATCAATACC
18750 TTTTGCATACATTCA
1 TTTTGCATACATTCA
*
18765 TTTTGCATATATTCA
1 TTTTGCATACATTCA
18780 TT
1 TT
18782 ATTCATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:25839 original size:65 final size:65
Alignment explanation
Indices: 25700--25842 Score: 150
Period size: 65 Copynumber: 2.2 Consensus size: 65
25690 AATGCTTTTT
* * * * * *
25700 GTGTACCGATGCACACTCATGCATCGATTCACTCCTGATTTTATTGAAACATCGAAATCATTTTA
1 GTGTACCGATGCACAATAATACATCGATGCACTCCTGATCTTATTGAAACATCGAAATCATATTA
* * *
25765 -CGTATCGATGCACAGATAATACATCGATGCACTCCTGGATCTT-TTGAAACATCG-AAT-GTAA
1 GTGTACCGATGCACA-ATAATACATCGATGCACTCCT-GATCTTATTGAAACATCGAAATCAT-A
25826 TTA
63 TTA
25829 GTGTACCGATGCAC
1 GTGTACCGATGCAC
25843 CCCAAGTGTA
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
63 1 0.02
64 18 0.29
65 39 0.62
66 5 0.08
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (65 bp):
GTGTACCGATGCACAATAATACATCGATGCACTCCTGATCTTATTGAAACATCGAAATCATATTA
Found at i:33033 original size:21 final size:21
Alignment explanation
Indices: 33007--33046 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32997 CCCCATTTGA
*
33007 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
33028 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
33047 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:41276 original size:44 final size:44
Alignment explanation
Indices: 41203--41308 Score: 153
Period size: 44 Copynumber: 2.4 Consensus size: 44
41193 TTTATGCGCA
* *
41203 GTGCATCGTTACACTATGATAGTGTATCGATGCATCCCTTGAAT
1 GTGCATCGATACACTATGAAAGTGTATCGATGCATCCCTTGAAT
*
41247 GTGCATCGATACACTAT-AAAG-GTTCATCGATGCATGCCTTGAAT
1 GTGCATCGATACACTATGAAAGTG-T-ATCGATGCATCCCTTGAAT
41291 GTGCATCGATACACTATG
1 GTGCATCGATACACTATG
41309 CAGTGTACCA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
42 1 0.02
43 4 0.07
44 51 0.91
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
GTGCATCGATACACTATGAAAGTGTATCGATGCATCCCTTGAAT
Found at i:41830 original size:13 final size:13
Alignment explanation
Indices: 41784--41818 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
41774 CTAAATATTG
41784 ATTTTCAAACATT
1 ATTTTCAAACATT
41797 ATTTTCAAACATT
1 ATTTTCAAACATT
41810 ATTTTCAAA
1 ATTTTCAAA
41819 AATAGTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTCAAACATT
Found at i:43572 original size:12 final size:13
Alignment explanation
Indices: 43555--43584 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
43545 ATAGTAAGGG
43555 TCAAAAATGA-TT
1 TCAAAAATGATTT
43567 TCAAAAATGATTT
1 TCAAAAATGATTT
43580 TCAAA
1 TCAAA
43585 GAAAATCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (13 bp):
TCAAAAATGATTT
Found at i:44048 original size:65 final size:63
Alignment explanation
Indices: 43938--44057 Score: 161
Period size: 65 Copynumber: 1.9 Consensus size: 63
43928 TGTTTTTTGT
* *
43938 GTACTGATGCACAGTCATGCATCGATGCACTCCTGATCTTATTGAAACATCGAAATCATTTTAC
1 GTACTGATGCACAGTAATGCATCGATGCACTCATGATCTTATTGAAACATC-AAATCATTTTAC
* * *
44002 GTACTGATGCACAGATAATGTATTGATGCACTCATGGCTCTT-TTGAAACATCAAAT
1 GTACTGATGCACAG-TAATGCATCGATGCACTCAT-GATCTTATTGAAACATCAAAT
44058 GTAATTAGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
64 18 0.37
65 26 0.53
66 5 0.10
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (63 bp):
GTACTGATGCACAGTAATGCATCGATGCACTCATGATCTTATTGAAACATCAAATCATTTTAC
Found at i:45281 original size:20 final size:20
Alignment explanation
Indices: 45258--45309 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
45248 ATTATGCTTG
*
45258 AAGAAGAAA-AAAGGAAAGAA
1 AAGAA-AAAGAAAGAAAAGAA
45278 AAGAAAAAGAAAGAAAAGAAA
1 AAGAAAAAGAAAGAAAAG-AA
45299 ATAGAAAAAGA
1 A-AGAAAAAGA
45310 GGGTCAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 13 0.46
21 3 0.11
22 9 0.32
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AAGAAAAAGAAAGAAAAGAA
Found at i:45284 original size:15 final size:15
Alignment explanation
Indices: 45265--45305 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 15
45255 TTGAAGAAGA
45265 AAAAAGGAAAGAAAAG
1 AAAAA-GAAAGAAAAG
45281 AAAAAGAAAGAAAAG
1 AAAAAGAAAGAAAAG
45296 AAAATAGAAA
1 AAAA-AGAAA
45306 AAGAGGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAGAAAAG
Found at i:45693 original size:21 final size:22
Alignment explanation
Indices: 45653--45693 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
45643 ATTTATTAAT
45653 AAATTCCAAGTTTATCTTTTCG
1 AAATTCCAAGTTTATCTTTTCG
45675 AAATT-CAA-TTTATTCTTTT
1 AAATTCCAAGTTTA-TCTTTT
45694 ATAAACATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (22 bp):
AAATTCCAAGTTTATCTTTTCG
Found at i:45978 original size:17 final size:17
Alignment explanation
Indices: 45942--45975 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45932 CCAAGTAAAG
*
45942 AGCAAAGATTAAATTCC
1 AGCAAAGATAAAATTCC
45959 AGCAAAGATAAAGATTC
1 AGCAAAGATAAA-ATTC
45976 AGCGAAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (17 bp):
AGCAAAGATAAAATTCC
Found at i:46239 original size:20 final size:20
Alignment explanation
Indices: 46177--46240 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 20
46167 GCCAGATAGA
*
46177 GTTCATAACGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * *
46197 ATCTGAGAATGAAGAAGAA---
1 GT-TCATAATG-AGAAGAACTT
46216 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
46236 GTTCA
1 GTTCA
46241 ACCTTTTGCT
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
17 7 0.22
18 6 0.19
19 1 0.03
20 6 0.19
21 5 0.16
22 7 0.22
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:46380 original size:123 final size:123
Alignment explanation
Indices: 46158--46608 Score: 651
Period size: 123 Copynumber: 3.7 Consensus size: 123
46148 CACTCGATGG
* *
46158 ACCAACATTGCCAGATAGAGTTCATAACGAGAAGAACTTATCTG-AGAATGAAGAAGAAGTTCAT
1 ACCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG-ATGAAGAAGAAGTTCAT
46222 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAAC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAAC
* * *
46281 ACCAACATTGCCAAATAGAGTTCATAATGAGAATAACTCATATG-AGAATGAAGAAGAAGTTCAT
1 ACCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG-ATGAAGAAGAAGTTCAT
* * * * * *
46345 AATGAGAAGAACTTGTTCAATCTTTTGCTCAACTCTATCACGGAATGAGATAAATCAGC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAAC
* * * *
46404 ACCAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGATAAAGAAGAAGTTCATA
1 ACCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATA
** *
46469 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAAC
* * * *
46527 ATCAACATTTCCAGATAGAGTTCAAAAT--G-AGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ACCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATA
46589 ATGAGAAGAACTTGTTCAAC
66 ATGAGAAGAACTTGTTCAAC
46609 TTTGCCTTAA
Statistics
Matches: 291, Mismatches: 36, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
120 48 0.16
121 1 0.00
123 240 0.82
124 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (123 bp):
ACCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAAC
Found at i:47020 original size:14 final size:14
Alignment explanation
Indices: 47001--47041 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
46991 ATTTTTTTCA
47001 TTTATTATTATTAT
1 TTTATTATTATTAT
*
47015 TTTATTAGTATTAT
1 TTTATTATTATTAT
47029 TATTA-TATTATTA
1 T-TTATTATTATTA
47042 ATAATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 21 0.88
15 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:47026 original size:20 final size:20
Alignment explanation
Indices: 47003--47041 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
46993 TTTTTTCATT
*
47003 TATTATTATTATTTTATTAG
1 TATTATTATTATATTATTAG
47023 TATTATTATTATATTATTA
1 TATTATTATTATATTATTA
47042 ATAATAAATA
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:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
TATTATTATTATATTATTAG
Found at i:47028 original size:17 final size:17
Alignment explanation
Indices: 47006--47038 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46996 TTTCATTTAT
*
47006 TATTATTATTTTATTAG
1 TATTATTATTATATTAG
47023 TATTATTATTATATTA
1 TATTATTATTATATTA
47039 TTAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTATTATTATATTAG
Found at i:47061 original size:3 final size:3
Alignment explanation
Indices: 47002--47041 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
46992 TTTTTTTCAT
*
47002 TTA TTA TTA TTA TT- TTA TTA GTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47042 ATAATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:48495 original size:2 final size:2
Alignment explanation
Indices: 48488--48528 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
48478 TATAAAAAGA
48488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48529 CTTTAATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49145 original size:2 final size:2
Alignment explanation
Indices: 49138--49170 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
49128 AATTGAGTGT
*
49138 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49171 TAAACCGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:49254 original size:18 final size:19
Alignment explanation
Indices: 49213--49254 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
49203 AATCAATTCA
* *
49213 TATTTTTTTTTTTAAACTT
1 TATTTATTTTTTCAAACTT
*
49232 AATTTATTTTTTCAAA-TT
1 TATTTATTTTTTCAAACTT
49250 TATTT
1 TATTT
49255 TTATAATTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTATTTTTTCAAACTT
Found at i:49311 original size:20 final size:21
Alignment explanation
Indices: 49286--49325 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
49276 CATAAAATCG
49286 ATTTTTAAAATTTA-ATTAAT
1 ATTTTTAAAATTTATATTAAT
**
49306 ATTTTTCTAATTTATATTAA
1 ATTTTTAAAATTTATATTAA
49326 AATTAAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTAAAATTTATATTAAT
Found at i:58100 original size:14 final size:14
Alignment explanation
Indices: 58081--58107 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58071 AAAATCCATT
58081 TTAAATTTATTATA
1 TTAAATTTATTATA
58095 TTAAATTTATTAT
1 TTAAATTTATTAT
58108 GATTTAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAATTTATTATA
Found at i:58471 original size:18 final size:19
Alignment explanation
Indices: 58448--58489 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
58438 ATCTCTTAAA
*
58448 ATTTTAAAATTAA-TATGT
1 ATTTTAAAAATAATTATGT
58466 ATTTTAAAAATAATTATGT
1 ATTTTAAAAATAATTATGT
58485 ATTTT
1 ATTTT
58490 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
ATTTTAAAAATAATTATGT
Found at i:62600 original size:22 final size:22
Alignment explanation
Indices: 62575--62616 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
62565 ATATTTACTA
62575 ATATTTCTAATAATATAATATT
1 ATATTTCTAATAATATAATATT
* *
62597 ATATTTTTAATATTATAATA
1 ATATTTCTAATAATATAATA
62617 AAATTATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTTCTAATAATATAATATT
Found at i:62987 original size:89 final size:89
Alignment explanation
Indices: 62816--62987 Score: 190
Period size: 91 Copynumber: 1.9 Consensus size: 89
62806 TAATGATATT
* * * * * *
62816 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATA
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
*
62881 TAATTTATAATATTTTTATTTCAA
66 TAATTTATAATAATTTTATTTCAA
* *
62905 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTTAAT-AATAAAT
1 TAAAATATA-CAA-ATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
*
62969 AA-ATTATTT-TAA-AATTTTA
62 AATATAATTTATAATAATTTTA
62988 AAATTAATAA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
89 15 0.22
90 5 0.07
91 19 0.28
92 14 0.20
93 16 0.23
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (89 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
TAATTTATAATAATTTTATTTCAA
Found at i:63008 original size:22 final size:22
Alignment explanation
Indices: 62965--63024 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
62955 TTTTAATAAT
* * *
62965 AAATAAATTATTTTAAAATTTTA
1 AAATAAATAATATT-AAGTTTTA
*
62988 AAATTAATAATATTAAGTTTTA
1 AAATAAATAATATTAAGTTTTA
**
63010 TGATAAATAATATTA
1 AAATAAATAATATTA
63025 TTTATTGTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (22 bp):
AAATAAATAATATTAAGTTTTA
Found at i:63202 original size:14 final size:14
Alignment explanation
Indices: 63155--63201 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
63145 AATATAATTT
*
63155 ATTTTACGGAAAAT
1 ATTTTACGGAAAAC
63169 ATTTTACGGAAAAC
1 ATTTTACGGAAAAC
*
63183 ATTTTCCGGAAAAC
1 ATTTTACGGAAAAC
63197 ATTTT
1 ATTTT
63202 CAGTGAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (14 bp):
ATTTTACGGAAAAC
Found at i:63211 original size:14 final size:14
Alignment explanation
Indices: 63162--63209 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
63152 TTTATTTTAC
*
63162 GGAAAATATTTT-A
1 GGAAAACATTTTCA
*
63175 CGGAAAACATTTTCC
1 -GGAAAACATTTTCA
63190 GGAAAACATTTTCA
1 GGAAAACATTTTCA
63204 GTGAAA
1 G-GAAA
63210 CAAACGGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 25 0.86
15 4 0.14
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (14 bp):
GGAAAACATTTTCA
Found at i:63351 original size:18 final size:18
Alignment explanation
Indices: 63325--63369 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
63315 TCACGAAATG
*
63325 TAAGATTACCGGTGGTAA
1 TAAGATTACCGGTGGGAA
*
63343 TAGGATTACCGGTGGGAA
1 TAAGATTACCGGTGGGAA
63361 TAAGATTAC
1 TAAGATTAC
63370 TGGGAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (18 bp):
TAAGATTACCGGTGGGAA
Found at i:68215 original size:46 final size:46
Alignment explanation
Indices: 68149--68236 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
68139 CGTGTTTTGA
* *
68149 TGATGATGTTTAAGTAGCTGAAGCCGAATGAGAATTGGAGAAATGT
1 TGATGATGTTCAAGAAGCTGAAGCCGAATGAGAATTGGAGAAATGT
*
68195 TGATGATGTTCAGGAAGCTGAAGCCGAATGAGAATTGGAGAA
1 TGATGATGTTCAAGAAGCTGAAGCCGAATGAGAATTGGAGAA
68237 CTATTGAAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.35, C:0.08, G:0.32, T:0.25
Consensus pattern (46 bp):
TGATGATGTTCAAGAAGCTGAAGCCGAATGAGAATTGGAGAAATGT
Found at i:68311 original size:4 final size:4
Alignment explanation
Indices: 68292--68765 Score: 109
Period size: 4 Copynumber: 118.2 Consensus size: 4
68282 TGAATCCTCA
68292 GAGG GAGG G-GG AGAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG
1 GAGG GAGG GAGG -GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG
* *
68340 G-GG AGAGG GA-- GAGG GAGG GA-G AAGG AGAGTG AGAGA GAGG GAGAG
1 GAGG -GAGG GAGG GAGG GAGG GAGG GAGG -GAG-G -GAGG GAGG GAG-G
* * * * * * *
68385 AAAG G-GG GAGA GA-G G-GG GAGA AAGA GAGA GAGCG GAGAG GAGAG AGATGG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG-G GAG-G GAG-G -GA-GG
* * * * * * *
68435 G-GA GAGA GAGA GAGG G-GG AGAGA GAGT GTGG GAGAG AGAGA GAGG G-GG
1 GAGG GAGG GAGG GAGG GAGG -GAGG GAGG GAGG GAG-G -GAGG GAGG GAGG
* * * * * * *
68483 GAGA GAGA GAGG TG-GA AAGA GAGA GAGG GA-- GAGG GAGAG AAAGG GA--
1 GAGG GAGG GAGG -GAGG GAGG GAGG GAGG GAGG GAGG GAG-G -GAGG GAGG
* * * *
68529 GAGG GAGG GAGGG GAGA GAGA GAGA GAGG GAAGG AGAGG G-GA GAGG GAGG
1 GAGG GAGG GA-GG GAGG GAGG GAGG GAGG G-AGG -GAGG GAGG GAGG GAGG
* * * * *
68579 GAGA GAGA GAGA TA-G G-GG GAGG GAGG GAGG GAGG GAGAG AGAGA GAGG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG-G -GAGG GAGG
* * * * * * * *
68627 GAGG GAGG GAGG GAGA AAGA GAGA GATG GAGG GAGA GATGG GAGAAA GAGA
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GA-GG GAG--G GAGG
* * * *
68678 GAGG GA-- GAGG GAGA GAGA GAGAG GAGA GAGG GGGG GAGG GAGG GA--
1 GAGG GAGG GAGG GAGG GAGG GAG-G GAGG GAGG GAGG GAGG GAGG GAGG
* *
68723 GAGG GAGA GAGG GA-G G-GG GAGG GAGG GAGAG G-GA GAGG GAGG G
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG-G GAGG GAGG GAGG G
68766 GGAGAGTTAC
Statistics
Matches: 358, Mismatches: 62, Indels: 100
0.69 0.12 0.19
Matches are distributed among these distances:
2 10 0.03
3 27 0.08
4 258 0.72
5 42 0.12
6 20 0.06
7 1 0.00
ACGTcount: A:0.35, C:0.00, G:0.63, T:0.02
Consensus pattern (4 bp):
GAGG
Found at i:68377 original size:2 final size:2
Alignment explanation
Indices: 68342--68707 Score: 157
Period size: 2 Copynumber: 188.5 Consensus size: 2
68332 GAGGGAGGGG
* * * * *
68342 GA GA GG GA GA GG GA GG GA GA -A G- GA GA GT GA GA GA GA GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * * * *
68382 GA GA AA GG GG GA GA GA GG GG GA GA AA GA GA GA GA GC G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * *
68423 G- GA GA GA GA TG- GG GA GA GA GA GA GA GG GG GA GA GA GA GT GT
1 GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * *
68464 GG GA GA GA GA GA GA G- GG GG GA GA GA GA GA G- GT G- GA AA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * * * *
68503 GA GA GA GG GA GA GG GA GA GA AA GG GA GA GG GA GG GA G- GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * *
68544 GA GA GA GA GA GA GG GA -A G- GA GA G- GG GA GA GG GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * * * *
68583 GA GA GA GA TA GG GG GA GG GA GG GA GG GA GG GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * * * *
68625 GG GA GG GA GG GA GG GA GA AA GA GA GA GA TG- GA GG GA GA GA TGG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -GA GA GA GA GA GA -GA
* * *
68668 GA GA AA GA GA GA GG GA GA GG GA GA GA GA GA GA G- GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
68708 GGGGGGAGGG
Statistics
Matches: 267, Mismatches: 80, Indels: 34
0.70 0.21 0.09
Matches are distributed among these distances:
1 14 0.05
2 250 0.94
3 3 0.01
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (2 bp):
GA
Found at i:68670 original size:126 final size:114
Alignment explanation
Indices: 68342--68751 Score: 269
Period size: 99 Copynumber: 3.7 Consensus size: 114
68332 GAGGGAGGGG
* * * * * *
68342 GAGAGGGAGAGGGAG-G-GAGA-AGGAGAGTGAGAGAGAGGGAGAGAAAGGG-G-GAGAGAGGGG
1 GAGAGGGAGAGGGAGAGAGAGAGAGGAGAGAGAGGGGGAGGGAGGGAGAGGGAGAGAGAGAGAGG
* * *
68402 GAGAAAGAGAGAGAGCGGAG-AGGAGAGAGATGGGGAGAGAGAGAGAGGGG-GAGAGA
66 GAG---G-GAGGGAG-GGAGAAAGAGAGAGAT--GGAG-G-GAGAGAGGGGAGAAAGA
* * * * ** *
68458 GAGTGTGG-GAGAGAGAGAGAGGGGGGAGAGAGAGAGGTGGAAAGAGAGAGAGGGAGAGGGAGAG
1 GAGAG-GGAGAGGGAGAGAGAGAGAGGAGAGAGAG-GG-GGAGGGAGGGAGAGGGAGA--GAGAG
* *
68522 AAAGGGAGAGGGAGGGAGGG-GAGAGAGAGAGA--GAGGGAAGGAGAGGGGAG--AG-
61 AGA-GG-GAGGGAGGGAGGGAGAAAGAGAGAGATGGAGGG-A-GAGAGGGGAGAAAGA
*
68574 G-GA-GG-GA--GAGAGAGAGATAGG-G-G-GA--GGGAGGGAGGGAG-GG-AGAGAGAGAGAGG
1 GAGAGGGAGAGGGAGAGAGAGAGAGGAGAGAGAGGGGGAGGGAGGGAGAGGGAGAGAGAGAGAGG
*
68627 GAGGGAGGGAGGGAGAAAGAGAGAGATGGAGGGAGAGATGGGAGAAAGA
66 GAGGGAGGGAGGGAGAAAGAGAGAGATGGAGGGAGAGAGGGGAGAAAGA
* * *
68676 GAGAGGGAGAGGGAGAGAGAGAGAGGAGAGAGGGGGGGAGGGAGGGAGAGGGAGAGAGGGAGGGG
1 GAGAGGGAGAGGGAGAGAGAGAGAGGAGAGAGAGGGGGAGGGAGGGAGAGGGAGAGAGAGAGAGG
68741 GAGGGAGGGAG
66 GAGGGAGGGAG
68752 AGGGAGAGGG
Statistics
Matches: 231, Mismatches: 29, Indels: 70
0.70 0.09 0.21
Matches are distributed among these distances:
98 13 0.06
99 22 0.10
100 8 0.03
101 7 0.03
102 4 0.02
103 4 0.02
104 11 0.05
105 3 0.01
107 13 0.06
108 3 0.01
109 2 0.01
110 2 0.01
111 11 0.05
112 13 0.06
113 6 0.03
114 22 0.10
115 1 0.00
116 12 0.05
117 7 0.03
118 14 0.06
119 10 0.04
120 1 0.00
121 13 0.06
122 11 0.05
123 6 0.03
124 1 0.00
125 6 0.03
126 2 0.01
127 3 0.01
ACGTcount: A:0.37, C:0.00, G:0.61, T:0.02
Consensus pattern (114 bp):
GAGAGGGAGAGGGAGAGAGAGAGAGGAGAGAGAGGGGGAGGGAGGGAGAGGGAGAGAGAGAGAGG
GAGGGAGGGAGGGAGAAAGAGAGAGATGGAGGGAGAGAGGGGAGAAAGA
Found at i:68764 original size:16 final size:16
Alignment explanation
Indices: 68292--68765 Score: 232
Period size: 16 Copynumber: 30.3 Consensus size: 16
68282 TGAATCCTCA
*
68292 GAGGGAGGGGGAGAGG
1 GAGGGAGAGGGAGAGG
*
68308 GAGGGAG-GGAGGGAGG
1 GAGGGAGAGG-GAGAGG
68324 GA-GG-GAGGGAG-GG
1 GAGGGAGAGGGAGAGG
*
68337 AGGGGGAGAGGGAGAGG
1 -GAGGGAGAGGGAGAGG
* *
68354 GAGGGAGAAGGAGAGT
1 GAGGGAGAGGGAGAGG
* *
68370 GAGAGAGAGGGAGAGA
1 GAGGGAGAGGGAGAGG
* *
68386 AAGGG-G-GAGAGA-G
1 GAGGGAGAGGGAGAGG
** *
68399 G-GGGAGAAAGAGAGA
1 GAGGGAGAGGGAGAGG
*
68414 GAGCGGAGA-GGAGAGA
1 GAG-GGAGAGGGAGAGG
* *
68430 GATGGG-GAGAGAGAGA
1 GA-GGGAGAGGGAGAGG
* * *
68446 GAGGGGGAGAGAGAGT
1 GAGGGAGAGGGAGAGG
*
68462 GTGGGAGAGAGAGAGAGG
1 GAGGGAGAG-G-GAGAGG
*
68480 G-GGGAGAGAGAGAGGTG
1 GAGGGAGAGGGAGA-G-G
68497 GAAAGAGAGAGAGGGAGAGG
1 G--AG-G-GAGAGGGAGAGG
* *
68517 GAGAGAAAGGGAGAGG
1 GAGGGAGAGGGAGAGG
*
68533 GAGGGAG-GGGAGAGA
1 GAGGGAGAGGGAGAGG
*
68548 GAGAGAGAGGGA-A-G
1 GAGGGAGAGGGAGAGG
68562 GA--GAG-GGGAGAGG
1 GAGGGAGAGGGAGAGG
* *
68575 GAGGGAGAGAGAGAGA
1 GAGGGAGAGGGAGAGG
* *
68591 TAGGGGGAGGGAGGGAGG
1 GAGGGAGAGGGA--GAGG
68609 GAGGGAGAGAGAGAGAGG
1 GAGGGAGAG-G-GAGAGG
68627 GA-GG-GA-GG-GAGG
1 GAGGGAGAGGGAGAGG
** * *
68639 GAGAAAGAGAGAGATG
1 GAGGGAGAGGGAGAGG
*
68655 GAGGGAGAGATGG-GAGA
1 GAGGGAGAG--GGAGAGG
* *
68672 AAGAGAGAGGGAGAGG
1 GAGGGAGAGGGAGAGG
*
68688 GA--GAGAGAGAGA-G
1 GAGGGAGAGGGAGAGG
* * *
68701 GAGAGAGGGGGGGAGG
1 GAGGGAGAGGGAGAGG
68717 GAGGGAGAGGGAGA--
1 GAGGGAGAGGGAGAGG
68731 GAGGGAG-GGG-GAGG
1 GAGGGAGAGGGAGAGG
68745 GAGGGAGAGGGAGAGG
1 GAGGGAGAGGGAGAGG
68761 GAGGG
1 GAGGG
68766 GGAGAGTTAC
Statistics
Matches: 351, Mismatches: 60, Indels: 94
0.70 0.12 0.19
Matches are distributed among these distances:
11 4 0.01
12 15 0.04
13 13 0.04
14 42 0.12
15 49 0.14
16 158 0.45
17 28 0.08
18 25 0.07
19 1 0.00
20 5 0.01
21 2 0.01
22 9 0.03
ACGTcount: A:0.35, C:0.00, G:0.63, T:0.02
Consensus pattern (16 bp):
GAGGGAGAGGGAGAGG
Found at i:70887 original size:26 final size:28
Alignment explanation
Indices: 70847--70963 Score: 111
Period size: 26 Copynumber: 4.2 Consensus size: 28
70837 GTTGCCATGG
70847 CCGGCGACATGGTAGGTCACCATGGAGT
1 CCGGCGACATGGTAGGTCACCATGGAGT
* *
70875 -C-TCGACATGGTAGGTCGCCATGGAGT
1 CCGGCGACATGGTAGGTCACCATGGAGT
*
70901 CCCGGCGACATGGTAGGTC-GC---GAGT
1 -CCGGCGACATGGTAGGTCACCATGGAGT
*
70926 CCGGCGACGACATGGTAGGTCGCCATGGAGT
1 CC-G-G-CGACATGGTAGGTCACCATGGAGT
70957 CCCGGCG
1 -CCGGCG
70964 CGACATGGAG
Statistics
Matches: 73, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
24 2 0.03
25 5 0.07
26 24 0.33
27 15 0.21
28 3 0.04
29 16 0.22
30 1 0.01
31 5 0.07
32 2 0.03
ACGTcount: A:0.18, C:0.27, G:0.38, T:0.17
Consensus pattern (28 bp):
CCGGCGACATGGTAGGTCACCATGGAGT
Found at i:70987 original size:19 final size:18
Alignment explanation
Indices: 70949--70990 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
70939 GGTAGGTCGC
**
70949 CATGGAGTCCCGGCGCGA
1 CATGGAGTCCCACCGCGA
70967 CATGGAGTCCCACCAGCGA
1 CATGGAGTCCCACC-GCGA
70986 CATGG
1 CATGG
70991 TAGGGGAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.21, C:0.33, G:0.33, T:0.12
Consensus pattern (18 bp):
CATGGAGTCCCACCGCGA
Found at i:71516 original size:21 final size:20
Alignment explanation
Indices: 71469--71516 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
71459 ACTAAAATCT
71469 AGTTAATTAGTTGTTAGTATA
1 AGTT-ATTAGTTGTTAGTATA
* *
71490 AATTATTAGTTTGTTAGTTTA
1 AGTTATTAG-TTGTTAGTATA
71511 AGTTAT
1 AGTTAT
71517 ATTATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (20 bp):
AGTTATTAGTTGTTAGTATA
Found at i:71919 original size:14 final size:14
Alignment explanation
Indices: 71900--71926 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
71890 AGTAATTTAT
71900 TATTTTTTGTTGTC
1 TATTTTTTGTTGTC
71914 TATTTTTTGTTGT
1 TATTTTTTGTTGT
71927 TGTGTATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
TATTTTTTGTTGTC
Found at i:71926 original size:17 final size:17
Alignment explanation
Indices: 71897--71929 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
71887 GTGAGTAATT
71897 TATTATTTTTTGTTGTC
1 TATTATTTTTTGTTGTC
71914 TATT-TTTTGTTGTTGT
1 TATTATTTT-TTGTTGT
71930 GTATGTGTAA
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:0.09, C:0.03, G:0.15, T:0.73
Consensus pattern (17 bp):
TATTATTTTTTGTTGTC
Found at i:75237 original size:59 final size:59
Alignment explanation
Indices: 75165--75346 Score: 307
Period size: 59 Copynumber: 3.1 Consensus size: 59
75155 TTTATAAGAT
*
75165 TTAGTAATGATTAGTAATGATGAAATTATTA-TAATATTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
* *
75223 TTTAGTAATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
75283 TTAGTAATGATTAGTAATAAT-AAATTATTATTAAT-TTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
75340 TTAGTAA
1 TTAGTAA
75347 GAAATTATTA
Statistics
Matches: 117, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
57 28 0.24
58 14 0.12
59 49 0.42
60 26 0.22
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
Done.