Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000831.1 Hibiscus syriacus cultivar Beakdansim tig00001607_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: 136111
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3205 original size:21 final size:21
Alignment explanation
Indices: 3171--3235 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
3161 TTACTATAAG
*
3171 ATTTA-AAATAAAATTTTAAT
1 ATTTATAAATTAAATTTTAAT
*
3191 ATTTATAAATTAAATTTTGAT
1 ATTTATAAATTAAATTTTAAT
* *
3212 ATGTATAAAATAAA-TTTAAT
1 ATTTATAAATTAAATTTTAAT
3232 ATTT
1 ATTT
3236 TTTAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
ATTTATAAATTAAATTTTAAT
Found at i:3241 original size:21 final size:21
Alignment explanation
Indices: 3172--3245 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
3162 TACTATAAGA
3172 TTTAAAATAAAATTTTAATATT
1 TTTAAAAT-AAATTTTAATATT
* * * *
3194 TATAAATTAAATTTTGATATG
1 TTTAAAATAAATTTTAATATT
*
3215 TATAAAATAAA-TTTAATATTT
1 TTTAAAATAAATTTTAATA-TT
3236 TTTAAAATAA
1 TTTAAAATAA
3246 TTTGAAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
20 6 0.14
21 31 0.72
22 6 0.14
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
TTTAAAATAAATTTTAATATT
Found at i:14319 original size:21 final size:21
Alignment explanation
Indices: 14295--14354 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
14285 GGATTGTGAG
14295 GATGAGGTGTGTCCAGTGATT
1 GATGAGGTGTGTCCAGTGATT
*
14316 GATGAGGTGTGTCCAGTGCTT
1 GATGAGGTGTGTCCAGTGATT
14337 GATGAGGTGTGTCCAGTG
1 GATGAGGTGTGTCCAGTG
14355 TTTATTCCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.17, C:0.12, G:0.40, T:0.32
Consensus pattern (21 bp):
GATGAGGTGTGTCCAGTGATT
Found at i:14432 original size:19 final size:17
Alignment explanation
Indices: 14402--14436 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
14392 ATTTGAATGT
14402 AAAAAATGAAAATGCAA
1 AAAAAATGAAAATGCAA
14419 AAAAAATGCAAAAATGCA
1 AAAAAATG--AAAATGCA
14437 TGAAATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (17 bp):
AAAAAATGAAAATGCAA
Found at i:17747 original size:17 final size:16
Alignment explanation
Indices: 17713--17750 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
17703 GTTTAAAAAA
17713 TAAAAAATAAAAATAT
1 TAAAAAATAAAAATAT
17729 TAAATAAATAAAAGA-AT
1 TAAA-AAATAAAA-ATAT
17746 TAAAA
1 TAAAA
17751 GACAATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 14 0.70
18 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAATAAAAATAT
Found at i:18507 original size:14 final size:14
Alignment explanation
Indices: 18481--18519 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
18471 CTAAAAATTA
*
18481 AAAATAAAT-AAAT
1 AAAATTAATAAAAT
18494 AAAATTAATAAAAT
1 AAAATTAATAAAAT
18508 AAAATATAATAA
1 AAAAT-TAATAA
18520 TATATATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.35
14 9 0.39
15 6 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATTAATAAAAT
Found at i:18518 original size:10 final size:11
Alignment explanation
Indices: 18487--18696 Score: 57
Period size: 12 Copynumber: 18.6 Consensus size: 11
18477 ATTAAAAATA
18487 AATAA-ATAA-
1 AATAATATAAT
*
18496 AATTAATAAAAT
1 AA-TAATATAAT
18508 AA-AATATAAT
1 AATAATATAAT
18518 AATATATATAAT
1 AATA-ATATAAT
*
18530 ATATGATATAAT
1 A-ATAATATAAT
* *
18542 ACTATTATAAT
1 AATAATATAAT
*
18553 -AT-GTAT-AT
1 AATAATATAAT
*
18561 ATAGAATAT-AT
1 A-ATAATATAAT
*
18572 -ATATATATACT
1 AATA-ATATAAT
18583 ATATAATATAAT
1 A-ATAATATAAT
*
18595 ACT-ATACT-AT
1 AATAATA-TAAT
*
18605 -ATAAAATAAT
1 AATAATATAAT
18615 ATATAATATAAT
1 A-ATAATATAAT
*
18627 ACTATACTATATAT
1 A--ATAATATA-AT
* *
18641 ATATAACACAAT
1 A-ATAATATAAT
18653 ACTATAATATAAT
1 A--ATAATATAAT
18666 ACTATAATAT-AT
1 A--ATAATATAAT
**
18678 AATACCATAAT
1 AATAATATAAT
18689 ATATAATA
1 A-ATAATA
18697 CCATATAACA
Statistics
Matches: 151, Mismatches: 27, Indels: 43
0.68 0.12 0.19
Matches are distributed among these distances:
8 2 0.01
9 9 0.06
10 32 0.21
11 22 0.15
12 45 0.30
13 38 0.25
14 3 0.02
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (11 bp):
AATAATATAAT
Found at i:18526 original size:2 final size:2
Alignment explanation
Indices: 18511--18780 Score: 92
Period size: 2 Copynumber: 141.5 Consensus size: 2
18501 ATAAAATAAA
18511 AT AT A- AT A- AT AT AT AT A- AT AT AT GAT AT A- AT ACT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A-T AT AT AT
* *
18550 A- AT AT GT AT AT AT AG A- AT AT AT AT AT AT AT ACT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
18590 AT A- AT ACT AT ACT AT AT A- AA AT A- AT AT AT A- AT AT A- AT ACT
1 AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
18630 AT ACT AT AT AT AT AT A- AC AC A- AT ACT AT A- AT AT A- AT ACT
1 AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T
* * *
18669 AT A- AT AT AT A- AT ACC AT A- AT AT AT A- AT ACC AT AT A- AC AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * * *
18708 AT AT -T AT AT ACT AT AT AA AT ACT AT AT GT -T AT AC A- AT AT ACC
1 AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T
*
18750 AT ACT AT A- AT AT AT AT AT A- AA AT A- AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18781 ACATATAATA
Statistics
Matches: 209, Mismatches: 16, Indels: 86
0.67 0.05 0.28
Matches are distributed among these distances:
1 28 0.13
2 154 0.74
3 27 0.13
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:18531 original size:5 final size:5
Alignment explanation
Indices: 18483--18627 Score: 61
Period size: 5 Copynumber: 27.8 Consensus size: 5
18473 AAAAATTAAA
* * *
18483 AATA- AATA- AATAA AAT-T AATAA AATAA AATAT AATAAT ATATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT-AT A-ATAT AATAT
* * *
18532 ATGATAT AATACT ATTAT AATAT -GTAT ATATAG AATAT -ATAT ATATAT
1 A--ATAT AATA-T AATAT AATAT AATAT A-ATAT AATAT AATAT A-ATAT
*
18580 ACTATAT AATAT AATACT -ATACT -ATAT AAAAT AATATAT AATAT AATA
1 A--ATAT AATAT AATA-T AATA-T AATAT AATAT -A-ATAT AATAT AATA
18628 CTATACTATA
Statistics
Matches: 114, Mismatches: 11, Indels: 31
0.73 0.07 0.20
Matches are distributed among these distances:
4 19 0.17
5 58 0.51
6 21 0.18
7 16 0.14
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:18531 original size:7 final size:7
Alignment explanation
Indices: 18506--18790 Score: 129
Period size: 7 Copynumber: 38.9 Consensus size: 7
18496 AATTAATAAA
*
18506 ATAAAAT
1 ATAATAT
18513 ATAATA-
1 ATAATAT
18519 AT-ATAT
1 ATAATAT
18525 ATAATAT
1 ATAATAT
*
18532 ATGATAT
1 ATAATAT
*
18539 AATACTATT
1 -ATAATA-T
18548 ATAATAT
1 ATAATAT
*
18555 GTATATAT
1 ATA-ATAT
*
18563 AGAATAT
1 ATAATAT
18570 ATATATAT
1 ATA-ATAT
*
18578 ATACTAT
1 ATAATAT
18585 AT-A-AT
1 ATAATAT
18590 ATAATACT
1 ATAATA-T
*
18598 ATACTAT
1 ATAATAT
18605 ATAA-A-
1 ATAATAT
18610 ATAATAT
1 ATAATAT
18617 AT-A-AT
1 ATAATAT
18622 ATAATACT
1 ATAATA-T
*
18630 ATACTAT
1 ATAATAT
18637 AT-ATAT
1 ATAATAT
* *
18643 ATAACACA
1 ATAATA-T
18651 ATACTATAAT
1 ATA--AT-AT
18661 ATAATACT
1 ATAATA-T
18669 ATAATAT
1 ATAATAT
*
18676 ATAATACC
1 ATAATA-T
18684 ATAATAT
1 ATAATAT
18691 ATAATACCAT
1 ATAAT---AT
*
18701 ATAACAT
1 ATAATAT
*
18708 ATATTAT
1 ATAATAT
*
18715 ATACTAT
1 ATAATAT
18722 ATAAATACT
1 AT-AATA-T
*
18731 ATATGTTAT
1 ATA--ATAT
*
18740 ACAATAT
1 ATAATAT
**
18747 ACCATACT
1 ATAATA-T
18755 ATAATAT
1 ATAATAT
*
18762 ATATATAAA
1 ATA-AT-AT
18771 ATAATAT
1 ATAATAT
*
18778 ATAACAT
1 ATAATAT
18785 ATAATA
1 ATAATA
18791 GTGTATATTA
Statistics
Matches: 211, Mismatches: 36, Indels: 62
0.68 0.12 0.20
Matches are distributed among these distances:
5 15 0.07
6 14 0.07
7 94 0.45
8 64 0.30
9 11 0.05
10 12 0.06
11 1 0.00
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:18569 original size:38 final size:37
Alignment explanation
Indices: 18519--18591 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 37
18509 AAATATAATA
*
18519 ATATATATAATATATGATATA-ATACTATTATAATATGT
1 ATATATAGAATATAT-ATATATATACTA-TATAATATGT
18557 ATATATAGAATATATATATATATACTATATAATAT
1 ATATATAGAATATATATATATATACTATATAATAT
18592 AATACTATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 13 0.39
38 20 0.61
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATATAGAATATATATATATATACTATATAATATGT
Found at i:18570 original size:20 final size:19
Alignment explanation
Indices: 18509--18790 Score: 130
Period size: 20 Copynumber: 14.5 Consensus size: 19
18499 TAATAAAATA
18509 AAATATAATA-ATATATAT
1 AAATATAATATATATATAT
18527 -AATAT-ATGATATA-ATACT
1 AAATATAAT-ATATATATA-T
* *
18545 -ATTATAATATGTATATAT
1 AAATATAATATATATATAT
18563 AGAATATATATATATATACTAT
1 A-AATATA-ATATATATA-TAT
18585 ATAATATAATACTATACTATAT
1 A-AATATAATA-TATA-TATAT
18607 AAA-ATAATATATA-ATAT
1 AAATATAATATATATATAT
*
18624 AATACTATACTATATATATAT
1 AA-A-TATAATATATATATAT
* *
18645 -AACACAATACTATA-ATAT
1 AAATATAATA-TATATATAT
*
18663 AATACTATAATATATA-ATACC
1 AA-A-TATAATATATATATA-T
*
18684 ATAATAT-ATA-ATACCATAT
1 A-AATATAATATATA-TATAT
*
18703 AACATATATTATATACTATAT
1 AA-ATATAATATATA-TATAT
*
18724 AAATACT-ATATGT-TATA-
1 AAATA-TAATATATATATAT
*
18741 CAATATACCATACTATA-ATAT
1 AAATATA--ATA-TATATATAT
* *
18762 ATATATAAAATA-ATATAT
1 AAATATAATATATATATAT
18780 AACATATAATA
1 AA-ATATAATA
18791 GTGTATATTA
Statistics
Matches: 205, Mismatches: 24, Indels: 69
0.69 0.08 0.23
Matches are distributed among these distances:
16 3 0.01
17 20 0.10
18 37 0.18
19 35 0.17
20 49 0.24
21 40 0.20
22 19 0.09
23 2 0.01
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.38
Consensus pattern (19 bp):
AAATATAATATATATATAT
Found at i:18574 original size:15 final size:15
Alignment explanation
Indices: 18511--18805 Score: 142
Period size: 15 Copynumber: 18.7 Consensus size: 15
18501 ATAAAATAAA
18511 ATATA-ATAATATAT
1 ATATATATAATATAT
*
18525 ATAATATATGATATA-
1 AT-ATATATAATATAT
*
18540 ATACTATTATAATATGT
1 ATA-TA-TATAATATAT
*
18557 ATATATAGAATATAT
1 ATATATATAATATAT
*
18572 ATATATATACTATAT
1 ATATATATAATATAT
*
18587 A-ATATAATACTATACT
1 ATATAT-ATAATATA-T
*
18603 ATATAAAATAATATAT
1 ATAT-ATATAATATAT
18619 A-ATATAATACTATACTAT
1 ATATAT-ATA--ATA-TAT
* *
18637 ATATATATAACACAAT
1 ATATATATAATA-TAT
18653 ACTATAATATAATACTAT
1 A-TAT-ATATAATA-TAT
*
18671 A-ATATATAATACCAT
1 ATATATATAATA-TAT
*
18686 A-ATATATAATACCAT
1 ATATATATAATA-TAT
* *
18701 ATAACATATATTATAT
1 AT-ATATATAATATAT
18717 ACTATATA-AATACTAT
1 A-TATATATAATA-TAT
*
18733 ATGT-TATACA-ATAT
1 ATATATATA-ATATAT
*
18747 ACCATACTATAATATAT
1 A-TATA-TATAATATAT
*
18764 ATATAAAATAATATAT
1 ATAT-ATATAATATAT
* *
18780 A-ACATATAATAGTGT
1 ATATATATAATA-TAT
18795 ATATTATATAA
1 ATA-TATATAA
18806 AAAAATCCGG
Statistics
Matches: 222, Mismatches: 29, Indels: 57
0.72 0.09 0.19
Matches are distributed among these distances:
14 21 0.09
15 81 0.36
16 54 0.24
17 43 0.19
18 19 0.09
19 4 0.02
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (15 bp):
ATATATATAATATAT
Found at i:18779 original size:12 final size:13
Alignment explanation
Indices: 18515--18787 Score: 82
Period size: 13 Copynumber: 20.5 Consensus size: 13
18505 AATAAAATAT
*
18515 AATA-ATATATAT
1 AATATATATATAA
18527 AATATATGATAT--
1 AATATAT-ATATAA
18539 AATACTAT-TATAA
1 AATA-TATATATAA
* *
18552 TATGTATATATAGA
1 AATATATATATA-A
*
18566 ATATATATATATAT
1 A-ATATATATATAA
*
18580 ACTATATAATATAA
1 AATATAT-ATATAA
*
18594 TACTATACTATATAA
1 -AATATA-TATATAA
18609 AATA-ATATATAA
1 AATATATATATAA
* *
18621 TATA-ATACTATAC
1 AATATATA-TATAA
*
18634 TATATATATATAA
1 AATATATATATAA
* *
18647 CACA-ATACTATAA
1 AATATATA-TATAA
*
18660 TATA-ATACTATAA
1 AATATATA-TATAA
* * *
18673 TATATA-ATACCAT
1 AATATATATA-TAA
*
18686 AATATATA-ATAC
1 AATATATATATAA
* * *
18698 CATATAACATATAT
1 AATAT-ATATATAA
*
18712 TATATACTATATAA
1 AATATA-TATATAA
* *
18726 ATACTATATGTTATAC
1 A-A-TATAT-ATATAA
* *
18742 AATATACCATACTAT
1 AATATA-TATA-TAA
18757 AATATATATATAA
1 AATATATATATAA
18770 AATA-ATATATAA
1 AATATATATATAA
*
18782 CATATA
1 AATATA
18788 ATAGTGTATA
Statistics
Matches: 200, Mismatches: 35, Indels: 51
0.70 0.12 0.18
Matches are distributed among these distances:
11 3 0.01
12 45 0.22
13 69 0.34
14 40 0.20
15 33 0.17
16 10 0.05
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.38
Consensus pattern (13 bp):
AATATATATATAA
Found at i:20472 original size:24 final size:24
Alignment explanation
Indices: 20443--20503 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
20433 TATTTTAGAC
*
20443 ATATTAACTTAAAAAATATTTTTT
1 ATATTAACTTAAAAAATATATTTT
**
20467 ATATTAACTTATTAAATATATTTT
1 ATATTAACTTAAAAAATATATTTT
20491 ATTATTAACTTAA
1 A-TATTAACTTAA
20504 TTTTAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 22 0.69
25 10 0.31
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATTAACTTAAAAAATATATTTT
Found at i:20516 original size:28 final size:25
Alignment explanation
Indices: 20444--20521 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 25
20434 ATTTTAGACA
*
20444 TATTAACTTA--AAAAATATTTTTT
1 TATTAACTTATTAAAAATATTTTAT
*
20467 ATATTAACTTATTAAATATATTTTAT
1 -TATTAACTTATTAAAAATATTTTAT
20493 TATTAACTTAATTTTAAAAATATTTTAT
1 TATTAACTT-A--TTAAAAATATTTTAT
20521 T
1 T
20522 TTATTTTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 10 0.22
25 9 0.20
26 12 0.26
28 15 0.33
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTAACTTATTAAAAATATTTTAT
Found at i:20540 original size:26 final size:27
Alignment explanation
Indices: 20451--20555 Score: 83
Period size: 28 Copynumber: 3.9 Consensus size: 27
20441 ACATATTAAC
* *
20451 TTAAAAA-ATATT-TTTTATATTAACTT
1 TTAAAAATATTTTATTTTATCTTAA-TT
* *
20477 ATTAAATATATTTTATTATTAACTTAATT
1 -TTAAAAATATTTTATT-TTATCTTAATT
* *
20506 TTAAAAATATTTTATTTTATTTTCA-T
1 TTAAAAATATTTTATTTTATCTTAATT
* *
20532 TTAAAAATA-TATATTTTATGTTAA
1 TTAAAAATATTTTATTTTATCTTAA
20556 AATTTATTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
25 12 0.19
26 10 0.16
27 12 0.19
28 19 0.30
29 4 0.06
30 7 0.11
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (27 bp):
TTAAAAATATTTTATTTTATCTTAATT
Found at i:20543 original size:28 final size:29
Alignment explanation
Indices: 20454--20543 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 29
20444 TATTAACTTA
*
20454 AAAAATATTTTTTA-TATTAACTT-A-TT
1 AAAAATATATTTTATTATTAACTTAATTT
20480 --AAATATATTTTATTATTAACTTAATTT
1 AAAAATATATTTTATTATTAACTTAATTT
* ** *
20507 TAAAA-ATATTTTATT-TTATTTTCATTT
1 AAAAATATATTTTATTATTAACTTAATTT
20534 AAAAATATAT
1 AAAAATATAT
20544 ATTTTATGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
24 11 0.21
25 9 0.17
26 1 0.02
27 15 0.28
28 14 0.26
29 3 0.06
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (29 bp):
AAAAATATATTTTATTATTAACTTAATTT
Found at i:20730 original size:116 final size:116
Alignment explanation
Indices: 20526--20759 Score: 423
Period size: 116 Copynumber: 2.0 Consensus size: 116
20516 TTTATTTTAT
* * *
20526 TTTCATTTAAAAATATATATTTTATGTTAAAATTTATTTAAAAGTATGACTAAATTGAGATAATA
1 TTTCATTTAAAAATATATATTTTATGTTAAAATTTATTTAAAAGTATAACTAAATTAAGAGAATA
* *
20591 TGTAAATAACAGAGACCAAATGTGTGATTATACAAACTATCATGTCACATA
66 TGTAAATAACAAAGACCAAATGTGTGATTATACAAACTATCACGTCACATA
20642 TTTCATTTAAAAATATATATTTTATGTTAAAATTTATTTAAAAGTATAACTAAATTAAGAGAATA
1 TTTCATTTAAAAATATATATTTTATGTTAAAATTTATTTAAAAGTATAACTAAATTAAGAGAATA
20707 TGTAAATAACAAAGACCAAATGTGTGATTATACAAACTATCACGTCACATA
66 TGTAAATAACAAAGACCAAATGTGTGATTATACAAACTATCACGTCACATA
20758 TT
1 TT
20760 CTGTTAATTG
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 113 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (116 bp):
TTTCATTTAAAAATATATATTTTATGTTAAAATTTATTTAAAAGTATAACTAAATTAAGAGAATA
TGTAAATAACAAAGACCAAATGTGTGATTATACAAACTATCACGTCACATA
Found at i:21414 original size:60 final size:61
Alignment explanation
Indices: 21303--21420 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 61
21293 TCCTTAAATT
* * *
21303 TAATTTAATTTTATCCCCAAATTATGGCTCTCATTTTAAATGAATCTTTAAA-CTTTTGAA
1 TAATTTAATTTTATCCCCAAATTATGGCTCTCATTCTAAATGAAGCCTTAAACCTTTTGAA
* *
21363 TAATTTAATTTTATCCCCAAATTATGGCTCTCATTCTAAATTAGGCCTTAAACCTTTT
1 TAATTTAATTTTATCCCCAAATTATGGCTCTCATTCTAAATGAAGCCTTAAACCTTTT
21421 AAAATTCCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
60 47 0.90
61 5 0.10
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (61 bp):
TAATTTAATTTTATCCCCAAATTATGGCTCTCATTCTAAATGAAGCCTTAAACCTTTTGAA
Found at i:50441 original size:33 final size:33
Alignment explanation
Indices: 50394--50460 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
50384 TTTAATATCA
* *
50394 TGTTCGTTTATTTATTGTTCGCGAACATGTTCG
1 TGTTCGTTTATTTATTGTTCACGAACATATTCG
* *
50427 TGTTTGTTTATTTATTGTTCATGAACATATTCG
1 TGTTCGTTTATTTATTGTTCACGAACATATTCG
50460 T
1 T
50461 CTATATGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (33 bp):
TGTTCGTTTATTTATTGTTCACGAACATATTCG
Found at i:53390 original size:63 final size:62
Alignment explanation
Indices: 53310--53435 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 62
53300 CATTTTAAAT
* ** * *
53310 TAGTTCTTAAACTTTTGAATGTTCTAATTCCATCCCTAAACTATGACTCTCGTTCTAGATTAC
1 TAGTCCTTAAACTTTTGAACATTCTAATTCCAT-CCTAAACTATGACTATCGTTCTAAATTAC
* * *
53373 TAGTCCTTAAACTTTTGAACATTCTAATTTCATCCTAAACTATGATTATCTTTCTAAATTAC
1 TAGTCCTTAAACTTTTGAACATTCTAATTCCATCCTAAACTATGACTATCGTTCTAAATTAC
53435 T
1 T
53436 CCCCAAATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
62 26 0.47
63 29 0.53
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (62 bp):
TAGTCCTTAAACTTTTGAACATTCTAATTCCATCCTAAACTATGACTATCGTTCTAAATTAC
Found at i:57493 original size:22 final size:21
Alignment explanation
Indices: 57465--57520 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
57455 GTACCCTTAT
57465 GGGGTATCGATACACATTCAAA
1 GGGGTATCGATACACATT-AAA
*
57487 GGGGTATCGATACACGTTAAA
1 GGGGTATCGATACACATTAAA
*
57508 GAGGTATCGATAC
1 GGGGTATCGATAC
57521 CTAGTGCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (21 bp):
GGGGTATCGATACACATTAAA
Found at i:57513 original size:21 final size:22
Alignment explanation
Indices: 57467--57520 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
57457 ACCCTTATGG
*
57467 GGTATCGATACACATTCAAAGG
1 GGTATCGATACACATTCAAAGA
*
57489 GGTATCGATACACGTT-AAAGA
1 GGTATCGATACACATTCAAAGA
57510 GGTATCGATAC
1 GGTATCGATAC
57521 CTAGTGCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (22 bp):
GGTATCGATACACATTCAAAGA
Found at i:63261 original size:20 final size:20
Alignment explanation
Indices: 63236--63289 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
63226 TAAATGACTA
*
63236 GGGGTATTGGTACCTCTAAG
1 GGGGTATCGGTACCTCTAAG
63256 GGGGTATCGGTACCTCTAAG
1 GGGGTATCGGTACCTCTAAG
*
63276 GGGGTATCAGTACC
1 GGGGTATCGGTACC
63290 CATAGGGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.19, G:0.35, T:0.26
Consensus pattern (20 bp):
GGGGTATCGGTACCTCTAAG
Found at i:63903 original size:19 final size:17
Alignment explanation
Indices: 63879--63919 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
63869 TTTAAATTAA
63879 TTTATTAGTTAAAATAACT
1 TTTATTA-TT-AAATAACT
*
63898 TTTATTATTTAATAACT
1 TTTATTATTAAATAACT
63915 TTTAT
1 TTTAT
63920 CAATTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 2 0.10
19 7 0.33
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTATTATTAAATAACT
Found at i:64028 original size:16 final size:16
Alignment explanation
Indices: 64007--64037 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63997 ATTCGAGTTT
*
64007 CTTTTGGTTTGGGTTG
1 CTTTTGGTTCGGGTTG
64023 CTTTTGGTTCGGGTT
1 CTTTTGGTTCGGGTT
64038 AATTTCAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.35, T:0.55
Consensus pattern (16 bp):
CTTTTGGTTCGGGTTG
Found at i:64420 original size:22 final size:21
Alignment explanation
Indices: 64377--64422 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
64367 ACAATACTAT
**
64377 ACAGTATGAACAGTATTATGA
1 ACAGTATGAACAGTACCATGA
*
64398 ACAGTAGTGAACAGTACCGTGA
1 ACAGTA-TGAACAGTACCATGA
64420 ACA
1 ACA
64423 AATACTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (21 bp):
ACAGTATGAACAGTACCATGA
Found at i:66926 original size:3 final size:3
Alignment explanation
Indices: 66920--66957 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
66910 GGAGGAGGAG
66920 GAA GAA GAA GAAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA G
66958 GGAGAAGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:69762 original size:17 final size:18
Alignment explanation
Indices: 69723--69762 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
69713 GCAAAATTAT
69723 TCTT-ATTAAAAAAAATG
1 TCTTGATTAAAAAAAATG
*
69740 TCTTGATTATAAAAAATG
1 TCTTGATTAAAAAAAATG
69758 T-TTGA
1 TCTTGA
69763 AGTAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (18 bp):
TCTTGATTAAAAAAAATG
Found at i:77135 original size:3 final size:3
Alignment explanation
Indices: 77127--77173 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
77117 CCATTTGTAT
* *
77127 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA AAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
77174 ATTAAAATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:77582 original size:39 final size:38
Alignment explanation
Indices: 77508--77582 Score: 87
Period size: 39 Copynumber: 1.9 Consensus size: 38
77498 TGGTTATCTA
* **
77508 GGGGTGACACAGCTCCTACGCGATGAGGAGATCTGGTC
1 GGGGTGACACAGCTCATACGCGATGAAAAGATCTGGTC
* * *
77546 GGGGATGACACGGCTCATACGTGATGAAAAGTTCTGG
1 GGGG-TGACACAGCTCATACGCGATGAAAAGATCTGG
77583 CCATCTTTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
38 4 0.13
39 26 0.87
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (38 bp):
GGGGTGACACAGCTCATACGCGATGAAAAGATCTGGTC
Found at i:77623 original size:133 final size:133
Alignment explanation
Indices: 77369--77807 Score: 541
Period size: 133 Copynumber: 3.3 Consensus size: 133
77359 GTTCGGGTCG
* *
77369 TCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACA-GTGCTCATACG
1 TCTAAGGGTGACAC-GCTCCTACGTGATGAGGAGATCTGGTCG-GGGATGACACG-GCTCATACG
* * *
77433 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGAC
63 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGAC
77498 TGGTTA
128 TGGTTA
* *
77504 TCTAGGGGTGACACAGCTCCTACGCGATGAGGAGATCTGGTCGGGGATGACACGGCTCATACGTG
1 TCTAAGGGTGACAC-GCTCCTACGTGATGAGGAGATCTGGTCGGGGATGACACGGCTCATACGTG
* * *
77569 ATGAAAAGTTC-TGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGATGTCTG
65 ATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGACTG
77633 GTTA
130 GTTA
* ** *
77637 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTAATCAGGGGATGACACTGCTCATACGT
1 TCTAAGGGTGACACG-CTCCTACGTGATGAGGAGATCTGGTC-GGGGATGACACGGCTCATACGT
* * ** * *
77702 GATGAAGAGTTCTTGGCCAT-TTTA--TA--GCGATAATATAGTTCCTACGTAATGAGGACGGCT
64 GATGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGACT
77762 GGTTA
129 GGTTA
* * ** *
77767 TCTAATGTTGACGTTGCTCCTACATGATGAGGAGATCTGGT
1 TCTAAGGGTGAC-ACGCTCCTACGTGATGAGGAGATCTGGT
77808 AAGCTGATGT
Statistics
Matches: 268, Mismatches: 31, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
130 64 0.24
131 1 0.00
132 2 0.01
133 89 0.33
134 66 0.25
135 46 0.17
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (133 bp):
TCTAAGGGTGACACGCTCCTACGTGATGAGGAGATCTGGTCGGGGATGACACGGCTCATACGTGA
TGAAGAGTTCTTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGACTGG
TTA
Found at i:85924 original size:30 final size:30
Alignment explanation
Indices: 85889--85951 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
85879 TTAAATTCGA
**
85889 ATGCATATTATTGGTAATGTGCTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
* * *
85919 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
85949 ATG
1 ATG
85952 AATTTACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (30 bp):
ATGCATATTATTGGTAATGCACTATAAATG
Found at i:92109 original size:3 final size:3
Alignment explanation
Indices: 92101--92149 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
92091 CCATTTGTAT
*
92101 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
92147 TAA
1 TAA
92150 ATTAAAATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:92158 original size:22 final size:22
Alignment explanation
Indices: 92101--92149 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
92091 CCATTTGTAT
92101 TAATAATAAT-AATAATAATAA
1 TAATAATAATAAATAATAATAA
*
92122 TAATAATAATAAATAATAATAG
1 TAATAATAATAAATAATAATAA
92144 TAATAA
1 TAATAA
92150 ATTAAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATAATAATAAATAATAATAA
Found at i:97648 original size:20 final size:20
Alignment explanation
Indices: 97620--97661 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
97610 GATACTGGGT
* *
97620 CCTTTAGTATCGATACTGAC
1 CCTTGAGTATCGATACTAAC
*
97640 CCTTGAGTATCGGTACTAAC
1 CCTTGAGTATCGATACTAAC
97660 CC
1 CC
97662 GTGGTACCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (20 bp):
CCTTGAGTATCGATACTAAC
Found at i:115605 original size:24 final size:20
Alignment explanation
Indices: 115564--115635 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
115554 AATTGTGTAC
* *
115564 CGATGCA-TGGAGAGTGCAT
1 CGATGCACTGTAGAATGCAT
115583 CGATGCACATGTTAAAGAATGCAT
1 CGATGCAC-TG-T--AGAATGCAT
* *
115607 CGATACACTGTAGAATGTAT
1 CGATGCACTGTAGAATGCAT
115627 CGATGCACT
1 CGATGCACT
115636 TTAATGGGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 7 0.16
20 16 0.37
21 2 0.05
22 1 0.02
23 2 0.05
24 15 0.35
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (20 bp):
CGATGCACTGTAGAATGCAT
Found at i:116569 original size:14 final size:15
Alignment explanation
Indices: 116550--116578 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
116540 AAGTGTGAAA
116550 TGATAT-AAGTTATG
1 TGATATGAAGTTATG
116564 TGATATGAAGTTATG
1 TGATATGAAGTTATG
116579 GGTATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (15 bp):
TGATATGAAGTTATG
Found at i:117052 original size:32 final size:32
Alignment explanation
Indices: 117011--117113 Score: 122
Period size: 32 Copynumber: 3.2 Consensus size: 32
117001 AGAGTCGAGG
117011 GTTACCTATGTCTTTCGAGACATATGGACAGT
1 GTTACCTATGTCTTTCGAGACATATGGACAGT
* *
117043 GTTACCTATGTCCTTCGGGACATATGGACAG-
1 GTTACCTATGTCTTTCGAGACATATGGACAGT
***
117074 GATTACCTATGTTCTAAGGA-ACATATGGACAGT
1 G-TTACCTATG-TCTTTCGAGACATATGGACAGT
117107 -TTACCTA
1 GTTACCTA
117114 GGCTCTTTGG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
31 8 0.13
32 50 0.82
33 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (32 bp):
GTTACCTATGTCTTTCGAGACATATGGACAGT
Found at i:117132 original size:31 final size:30
Alignment explanation
Indices: 117012--117138 Score: 110
Period size: 32 Copynumber: 4.0 Consensus size: 30
117002 GAGTCGAGGG
* *
117012 TTACCTATGTCTTTCGAGACATATGGACAGT
1 TTACCTATGTC-TTAGGGACATATGGACAGT
* *
117043 GTTACCTATGTCCTTCGGGACATATGGACAGGA
1 -TTACCTATGT-CTTAGGGACATATGGACA-GT
* *
117076 TTACCTATGTTCTAAGGAACATATGGACAGT
1 TTACCTATG-TCTTAGGGACATATGGACAGT
* * * *
117107 TTACCTAGGCTCTTTGGGACCTATGGATAGT
1 TTACCTATG-TCTTAGGGACATATGGACAGT
117138 T
1 T
117139 GTCGAGGTTC
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
31 26 0.33
32 50 0.63
33 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (30 bp):
TTACCTATGTCTTAGGGACATATGGACAGT
Found at i:120613 original size:24 final size:20
Alignment explanation
Indices: 120586--120643 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
120576 GCATGGATAG
120586 TGCATCGATGCACATGTGAAAGAA
1 TGCATCGATGCAC-TGT---AGAA
*
120610 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
120630 TGTATCGATGCACT
1 TGCATCGATGCACT
120644 TCAATGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
23 3 0.10
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:122062 original size:32 final size:32
Alignment explanation
Indices: 122021--122123 Score: 122
Period size: 32 Copynumber: 3.2 Consensus size: 32
122011 AGAGTCGAGG
122021 GTTACCTATGTCTTTCGAGACATATGGACAGT
1 GTTACCTATGTCTTTCGAGACATATGGACAGT
* *
122053 GTTACCTATGTCCTTCGGGACATATGGACAG-
1 GTTACCTATGTCTTTCGAGACATATGGACAGT
* **
122084 GATTACCTATGT-TCTAAAGAACATATGGACAGT
1 G-TTACCTATGTCTTTCGAG-ACATATGGACAGT
122117 -TTACCTA
1 GTTACCTA
122124 GGTTCTTTGG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
31 10 0.16
32 51 0.84
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (32 bp):
GTTACCTATGTCTTTCGAGACATATGGACAGT
Found at i:123513 original size:16 final size:16
Alignment explanation
Indices: 123492--123531 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
123482 GGGATATTAT
123492 TGTGTATAAAAAAGAG
1 TGTGTATAAAAAAGAG
*
123508 TGTGTATAAGAAAGAG
1 TGTGTATAAAAAAGAG
123524 TGTGTATA
1 TGTGTATA
123532 TGATAAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (16 bp):
TGTGTATAAAAAAGAG
Found at i:125661 original size:20 final size:20
Alignment explanation
Indices: 125636--125673 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
125626 CACATGTTAA
125636 AGAATGCATCGATACACTGT
1 AGAATGCATCGATACACTGT
*
125656 AGAATGTATCGATACACT
1 AGAATGCATCGATACACT
125674 TCAATGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTGT
Found at i:127114 original size:32 final size:32
Alignment explanation
Indices: 127040--127114 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 32
127030 AGAGTCGAGG
*
127040 GTTACCTATGTCTTTCGAGACATATGGACAGT
1 GTTACCTATGTCATTCGAGACATATGGACAGT
*
127072 GTTACATATGTCATTCGAGACATATGGACAG-
1 GTTACCTATGTCATTCGAGACATATGGACAGT
127103 GATTACCTATGT
1 G-TTACCTATGT
127115 TCTAAGGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (32 bp):
GTTACCTATGTCATTCGAGACATATGGACAGT
Found at i:128147 original size:26 final size:27
Alignment explanation
Indices: 128063--128152 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
128053 AATAGTTTAG
* * *
128063 TAAAAAT-GTTTAGGGGTTTCTTATGT
1 TAAAAATGGTTTAAGAGTTTCTTCTGT
*
128089 GAAAAATGGTTTAA-AGATTTCTTCTGT
1 TAAAAATGGTTTAAGAG-TTTCTTCTGT
*
128116 TGAAAATGGTTTAAGAGTTTCTTCTGT
1 TAAAAATGGTTTAAGAGTTTCTTCTGT
128143 TAAAAATGGT
1 TAAAAATGGT
128153 ATAGTATATA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
26 7 0.13
27 45 0.83
28 2 0.04
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (27 bp):
TAAAAATGGTTTAAGAGTTTCTTCTGT
Found at i:128195 original size:25 final size:25
Alignment explanation
Indices: 128159--128241 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
128149 TGGTATAGTA
* * *
128159 TATATGACTAGATTTGTTTACTAAT
1 TATATGAATAGATTTGTTAACTGAT
** *
128184 TATATGAATAGATTTGTCCACGGAT
1 TATATGAATAGATTTGTTAACTGAT
* *
128209 TATATGAATAAAATTGTTAACTGAT
1 TATATGAATAGATTTGTTAACTGAT
*
128234 TCTATGAA
1 TATATGAA
128242 CTTGTTCTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.41
Consensus pattern (25 bp):
TATATGAATAGATTTGTTAACTGAT
Found at i:128438 original size:19 final size:20
Alignment explanation
Indices: 128399--128444 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
128389 GGTCTAGAAA
128399 TGAATGCAATGATATTTTTT
1 TGAATGCAATGATATTTTTT
128419 TGAATGCAATGATA-TTTTT
1 TGAATGCAATGATATTTTTT
128438 TGAATGC
1 TGAATGC
128445 TTTCTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
TGAATGCAATGATATTTTTT
Found at i:129071 original size:23 final size:23
Alignment explanation
Indices: 129039--129111 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
129029 GTTTTTAGAA
*
129039 TAGGGCTACTTTAAATAATGGGT
1 TAGGGTTACTTTAAATAATGGGT
*
129062 TAGGGTTACTTTAAATAATAGGT
1 TAGGGTTACTTTAAATAATGGGT
129085 TAGGGTTACTTTAAATAATGGGT
1 TAGGGTTACTTTAAATAATGGGT
129108 TAGG
1 TAGG
129112 TTTTTTTTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (23 bp):
TAGGGTTACTTTAAATAATGGGT
Found at i:131797 original size:31 final size:32
Alignment explanation
Indices: 131735--131798 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
131725 AACAAGACCC
*
131735 ATCAATCCCACGCTTCCACCTCCATACACCAA
1 ATCAATCCCACGCTTCCACCTCCATAAACCAA
* * *
131767 ATCAATCCCTCTC-TCCACCTTCATAAACCAA
1 ATCAATCCCACGCTTCCACCTCCATAAACCAA
131798 A
1 A
131799 ACAACACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.22
Consensus pattern (32 bp):
ATCAATCCCACGCTTCCACCTCCATAAACCAA
Found at i:132944 original size:30 final size:29
Alignment explanation
Indices: 132902--132967 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
132892 TGAGTTTTTT
*
132902 ATTATTAAATTTTTAAA-AGTTATAAAATA
1 ATTATTAAAATTTTAAATA-TTATAAAATA
*
132931 ATTATTAAAATTTTAAATTATTATATAATA
1 ATTATTAAAATTTTAAA-TATTATAAAATA
132961 ATTATTA
1 ATTATTA
132968 TGATATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 16 0.48
30 16 0.48
31 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
ATTATTAAAATTTTAAATATTATAAAATA
Found at i:133082 original size:32 final size:32
Alignment explanation
Indices: 133015--133118 Score: 101
Period size: 31 Copynumber: 3.4 Consensus size: 32
133005 TGATCATTAA
** * * * *
133015 TTTGATAAAGATTAATGAT-ATTTTCTTATAG
1 TTTGATAAATTTTAATAATAATTTTATAATAT
133046 TTTGATAAATTTTAATAATAATTTTATAATAT
1 TTTGATAAATTTTAATAATAATTTTATAATAT
133078 TTTGATAAA-TTTAATAATTAA-TTTATAAT-T
1 TTTGATAAATTTTAATAA-TAATTTTATAATAT
*
133108 TTT-AAAAATTT
1 TTTGATAAATTT
133119 AATCATTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.06
30 6 0.10
31 32 0.51
32 21 0.33
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (32 bp):
TTTGATAAATTTTAATAATAATTTTATAATAT
Found at i:133118 original size:29 final size:32
Alignment explanation
Indices: 133046--133127 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 32
133036 TTTCTTATAG
*
133046 TTTGATAAATTTTAATAA-TAATTTTATAATAT
1 TTTGA-AAAATTTAATAATTAATTTTATAATAT
*
133078 TTTGATAAATTTAATAATTAA-TTTATAAT-T
1 TTTGAAAAATTTAATAATTAATTTTATAATAT
*
133108 TTT-AAAAATTTAATCATTAA
1 TTTGAAAAATTTAATAATTAA
133128 ATTGAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
29 15 0.33
30 4 0.09
31 18 0.40
32 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (32 bp):
TTTGAAAAATTTAATAATTAATTTTATAATAT
Found at i:134835 original size:18 final size:18
Alignment explanation
Indices: 134814--134858 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
134804 ATAACATGTC
* *
134814 AAAATTAAAAGAGAATAA
1 AAAATTAAAAAAAAATAA
*
134832 AAAATAAAAAAAAAATAA
1 AAAATTAAAAAAAAATAA
*
134850 AAATTTAAA
1 AAAATTAAA
134859 GGATCAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (18 bp):
AAAATTAAAAAAAAATAA
Found at i:136076 original size:38 final size:38
Alignment explanation
Indices: 135994--136103 Score: 105
Period size: 38 Copynumber: 2.9 Consensus size: 38
135984 TTTCAAAACC
* ****
135994 ATATTATACGTTTTCAAAACTGTTTTTTTTTAAACTAT
1 ATATTATACGTTTTCAAAACCGTTTTTAAAAAAACTAT
* * *
136032 AAATTATACGTTTTCGAAACCGTTTTTAAAAAAATTAT
1 ATATTATACGTTTTCAAAACCGTTTTTAAAAAAACTAT
* **
136070 ATATTATGCG-TTTCAAAACTATTTTTTAAAAAAA
1 ATATTATACGTTTTCAAAAC-CGTTTTTAAAAAAA
136104 AGCTATAT
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
37 8 0.14
38 50 0.86
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (38 bp):
ATATTATACGTTTTCAAAACCGTTTTTAAAAAAACTAT
Done.