Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold63
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: 2211945
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 524 characters in sequence are not A, C, G, or T
File 2 of 16
Found at i:238674 original size:52 final size:51
Alignment explanation
Indices: 238582--238692 Score: 118
Period size: 52 Copynumber: 2.2 Consensus size: 51
238572 GTCGAATTTG
* ** * ***
238582 AATAATTTTTTTTAAATTTTAATTTATTATTTAAATTATTATTTTAAAAAAT
1 AATATTTTTTTTTAAATTTTAATTTAAAATATAAATTATTAAAAT-AAAAAT
238634 AATATTTTTTATTTAAA-TTTAATTATAAAATATAAA-TATTAAAATAAAAAT
1 AATATTTTTT-TTTAAATTTTAATT-TAAAATATAAATTATTAAAATAAAAAT
238685 AATATTTT
1 AATATTTT
238693 AATAATATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
51 14 0.28
52 22 0.44
53 14 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (51 bp):
AATATTTTTTTTTAAATTTTAATTTAAAATATAAATTATTAAAATAAAAAT
Found at i:240786 original size:21 final size:22
Alignment explanation
Indices: 240762--240804 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
240752 AAATAAAAAA
240762 AATTATTAGA-TGAAAAGTTAT
1 AATTATTAGAGTGAAAAGTTAT
* * *
240783 AATTTTTATAGTTAAAAGTTAT
1 AATTATTAGAGTGAAAAGTTAT
240805 CATGATTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (22 bp):
AATTATTAGAGTGAAAAGTTAT
Found at i:245486 original size:17 final size:19
Alignment explanation
Indices: 245464--245504 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
245454 TAGGTCAATA
*
245464 TTAAAATTTA-A-AATTTT
1 TTAAAATTTATATAATTAT
245481 TTAAAATTTATATAATTAT
1 TTAAAATTTATATAATTAT
245500 TTAAA
1 TTAAA
245505 TTGATTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 1 0.05
19 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATTTATATAATTAT
Found at i:257669 original size:20 final size:21
Alignment explanation
Indices: 257632--257671 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
257622 TATTATCAAA
* *
257632 TAATTTATTTTTACTCTAAAC
1 TAATTTATTTTAAATCTAAAC
257653 TAATTT-TTTTAAATCTAAA
1 TAATTTATTTTAAATCTAAA
257672 ATTTGCATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATTTATTTTAAATCTAAAC
Found at i:258613 original size:2 final size:2
Alignment explanation
Indices: 258606--258669 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
258596 TTACACAAAT
258606 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 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
*
258648 GA GA GA GA GA GA GA GG GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
258670 AATATGGCAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:259787 original size:69 final size:69
Alignment explanation
Indices: 259670--259876 Score: 342
Period size: 69 Copynumber: 3.0 Consensus size: 69
259660 GAAAACATTT
* * *
259670 AAACATATATATAAAATTGAGGGAGAATGCACATACCCCCAGACGCCTTCATATTAAAGTATCTA
1 AAACATATATAT--AATTGAGGGAGAATGCACATGCCCCCAGATGCCTTCATATTAAAGTATCCA
259735 CCTTTC
64 CCTTTC
259741 AAACATATATATAATTGAGGGAGAATGCACATGCCCCCAGATGCCTTCATATTAAAGTATCCACC
1 AAACATATATATAATTGAGGGAGAATGCACATGCCCCCAGATGCCTTCATATTAAAGTATCCACC
259806 TTTC
66 TTTC
* * *
259810 AAACATAAATATTATTGAGGGAGAATGCACATGCCCCCAGATGCCTTCATATTAAAGTATCGACC
1 AAACATATATATAATTGAGGGAGAATGCACATGCCCCCAGATGCCTTCATATTAAAGTATCCACC
259875 TT
66 TT
259877 CAACAAACAG
Statistics
Matches: 130, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
69 118 0.91
71 12 0.09
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (69 bp):
AAACATATATATAATTGAGGGAGAATGCACATGCCCCCAGATGCCTTCATATTAAAGTATCCACC
TTTC
Found at i:264520 original size:10 final size:10
Alignment explanation
Indices: 264505--264550 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
264495 CTATCATATT
264505 TATATTTTTA
1 TATATTTTTA
264515 TATATTTTTA
1 TATATTTTTA
* *
264525 TATATTAATAA
1 TATATT-TTTA
*
264536 TTTATTTTTA
1 TATATTTTTA
264546 TATAT
1 TATAT
264551 AAATTTTGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 22 0.76
11 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TATATTTTTA
Found at i:264602 original size:11 final size:10
Alignment explanation
Indices: 264576--264614 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
264566 TATATAATCA
*
264576 TATTATATTCA
1 TATTATATT-T
264587 TATTATATTT
1 TATTATATTT
264597 TAATTATATTT
1 T-ATTATATTT
264608 TATTATA
1 TATTATA
264615 ATAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATATTT
Found at i:264616 original size:16 final size:17
Alignment explanation
Indices: 264575--264616 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
264565 TTATATAATC
264575 ATATTAT-ATTCATATT
1 ATATTATAATTCATATT
*
264591 ATATTTTAATT-ATATT
1 ATATTATAATTCATATT
*
264607 TTATTATAAT
1 ATATTATAAT
264617 AATAATAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTATAATTCATATT
Found at i:266554 original size:24 final size:26
Alignment explanation
Indices: 266527--266574 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
266517 TTTTTATTTC
* *
266527 TATCCTATT-ATATATTTA-ATTTTT
1 TATCATATTCATATAATTATATTTTT
266551 TATCATATTCATATAATTATATTT
1 TATCATATTCATATAATTATATTT
266575 AATATTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 8 0.40
26 4 0.20
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (26 bp):
TATCATATTCATATAATTATATTTTT
Found at i:269753 original size:12 final size:13
Alignment explanation
Indices: 269738--269787 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
269728 ACTGTGCAGC
269738 CAATTTTG-AATT
1 CAATTTTGAAATT
269750 CAA-TTTGAAATAGT
1 CAATTTTGAAAT--T
*
269764 TAATTTTGAAATT
1 CAATTTTGAAATT
269777 CAA-TTTGAAAT
1 CAATTTTGAAAT
269788 AGTAAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 4 0.12
12 14 0.44
13 3 0.09
14 3 0.09
15 8 0.25
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (13 bp):
CAATTTTGAAATT
Found at i:269781 original size:27 final size:26
Alignment explanation
Indices: 269739--269790 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
269729 CTGTGCAGCC
269739 AATTTTGAATTCAATTTGAAATAGTT
1 AATTTTGAATTCAATTTGAAATAGTT
269765 AATTTTGAAATTCAATTTGAAATAGT
1 AATTTTG-AATTCAATTTGAAATAGT
269791 AAAAGTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (26 bp):
AATTTTGAATTCAATTTGAAATAGTT
Found at i:269863 original size:9 final size:9
Alignment explanation
Indices: 269849--269881 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
269839 AGAAGGCTCA
269849 AGCAGAGAC
1 AGCAGAGAC
269858 AGCAGAGAC
1 AGCAGAGAC
*
269867 AGCAGAGAT
1 AGCAGAGAC
269876 AGCAGA
1 AGCAGA
269882 AAGAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:274528 original size:12 final size:13
Alignment explanation
Indices: 274513--274562 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
274503 ACTGTGCAGC
274513 CAATTTTG-AATT
1 CAATTTTGAAATT
274525 CAA-TTTGAAATAGT
1 CAATTTTGAAAT--T
*
274539 TAATTTTGAAATT
1 CAATTTTGAAATT
274552 CAA-TTTGAAAT
1 CAATTTTGAAAT
274563 AGTAAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 4 0.12
12 14 0.44
13 3 0.09
14 3 0.09
15 8 0.25
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (13 bp):
CAATTTTGAAATT
Found at i:274556 original size:27 final size:26
Alignment explanation
Indices: 274514--274565 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
274504 CTGTGCAGCC
274514 AATTTTGAATTCAATTTGAAATAGTT
1 AATTTTGAATTCAATTTGAAATAGTT
274540 AATTTTGAAATTCAATTTGAAATAGT
1 AATTTTG-AATTCAATTTGAAATAGT
274566 AAAAGTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (26 bp):
AATTTTGAATTCAATTTGAAATAGTT
Found at i:274638 original size:9 final size:9
Alignment explanation
Indices: 274624--274656 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
274614 AGAAGGCTCA
274624 AGCAGAGAC
1 AGCAGAGAC
274633 AGCAGAGAC
1 AGCAGAGAC
*
274642 AGCAGAGAT
1 AGCAGAGAC
274651 AGCAGA
1 AGCAGA
274657 AAGAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:283082 original size:2 final size:2
Alignment explanation
Indices: 283077--283109 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
283067 ACACACACAC
283077 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
283110 ATTTTCATGC
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:286729 original size:3 final size:3
Alignment explanation
Indices: 286721--286773 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
286711 TGTTGGGGAA
*
286721 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAC
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
286769 GAT GA
1 GAT GA
286774 GAAGATTAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.02, G:0.34, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:287454 original size:5 final size:5
Alignment explanation
Indices: 287444--287474 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
287434 AGGTTCTGTC
287444 AATTT AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT AATTT A
287475 TCAACTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:287704 original size:25 final size:25
Alignment explanation
Indices: 287673--287721 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
287663 TAAATTAATA
*
287673 TATTATTTAT-AATAATAATAATTAT
1 TATTATTAATAAAT-ATAATAATTAT
287698 TATTATTAATAAATATAATAATTA
1 TATTATTAATAAATATAATAATTA
287722 ATAATTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTATTAATAAATATAATAATTAT
Found at i:287709 original size:16 final size:16
Alignment explanation
Indices: 287688--287739 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
287678 TTTATAATAA
287688 TAATAATTATTATTAT
1 TAATAATTATTATTAT
* * *
287704 TAATAAATATAATAAT
1 TAATAATTATTATTAT
287720 TAATAATT-TTATTCAT
1 TAATAATTATTATT-AT
287736 TAAT
1 TAAT
287740 TTTACCTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 3 0.10
16 26 0.90
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATAATTATTATTAT
Found at i:287715 original size:22 final size:22
Alignment explanation
Indices: 287663--287721 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
287653 GACTATTAGT
287663 TAAAT-TAATATATTATTTATAA
1 TAAATATAAT-TATTATTTATAA
287685 T-AATAATAATTATTA-TTATTAA
1 TAAAT-ATAATTATTATTTA-TAA
*
287707 TAAATATAATAATTA
1 TAAATATAATTATTA
287722 ATAATTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
21 6 0.19
22 19 0.59
23 7 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATATAATTATTATTTATAA
Found at i:287832 original size:14 final size:15
Alignment explanation
Indices: 287808--287839 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
287798 GTTGTTAGCA
287808 AAAATCTTTTATATT
1 AAAATCTTTTATATT
287823 AAAA-CTTTTATATT
1 AAAATCTTTTATATT
287837 AAA
1 AAA
287840 TGTGTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATCTTTTATATT
Found at i:288528 original size:2 final size:2
Alignment explanation
Indices: 288521--288553 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
288511 CCCAAAAATA
288521 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
288554 ATTTTGAACA
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:290066 original size:18 final size:18
Alignment explanation
Indices: 290043--290084 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
290033 GAAGGTATGG
290043 TATTTTG-TGCTTTGCTTT
1 TATTTTGTTG-TTTGCTTT
290061 TATTTTTGTTGTTTGCTTT
1 TA-TTTTGTTGTTTGCTTT
290080 TATTT
1 TATTT
290085 CTTTTGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.23
19 15 0.68
20 2 0.09
ACGTcount: A:0.07, C:0.07, G:0.14, T:0.71
Consensus pattern (18 bp):
TATTTTGTTGTTTGCTTT
Found at i:293513 original size:21 final size:20
Alignment explanation
Indices: 293472--293509 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
293462 CAATTAAATT
293472 TTTTAAAAAGATTAATTTTA
1 TTTTAAAAAGATTAATTTTA
293492 TTTTAAAAA-ATTAATTTT
1 TTTTAAAAAGATTAATTTT
293510 TTATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTAAAAAGATTAATTTTA
Found at i:293525 original size:18 final size:19
Alignment explanation
Indices: 293463--293525 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 19
293453 TTTTAATAAC
293463 AATTAAATTTT-TTA-AAAA
1 AATT-AATTTTATTATAAAA
* *
293481 GATTAATTTTATTTTAAAA
1 AATTAATTTTATTATAAAA
*
293500 AATTAATTTT-TTATATAA
1 AATTAATTTTATTATAAAA
*
293518 ATTTAATT
1 AATTAATT
293526 GGATATGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
17 6 0.16
18 18 0.49
19 13 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
AATTAATTTTATTATAAAA
Found at i:304071 original size:2 final size:2
Alignment explanation
Indices: 304058--304094 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
304048 TGAACGGAGG
* *
304058 GA GA GC GA GA GA GA GA GA GA GC GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
304095 TGGTCCCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.05, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:304079 original size:16 final size:16
Alignment explanation
Indices: 304058--304094 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
304048 TGAACGGAGG
304058 GAGAGCGAGAGAGAGA
1 GAGAGCGAGAGAGAGA
304074 GAGAGCGAGAGAGAGA
1 GAGAGCGAGAGAGAGA
304090 GAGAG
1 GAGAG
304095 TGGTCCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.51, T:0.00
Consensus pattern (16 bp):
GAGAGCGAGAGAGAGA
Found at i:304447 original size:10 final size:10
Alignment explanation
Indices: 304434--304467 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
304424 ATTTAATTTA
304434 ATTAATTTTT
1 ATTAATTTTT
304444 ATT-ATTTTT
1 ATTAATTTTT
304453 AATTAATTTTT
1 -ATTAATTTTT
304464 ATTA
1 ATTA
304468 TTTATTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 6 0.27
10 10 0.45
11 6 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTAATTTTT
Found at i:304455 original size:20 final size:20
Alignment explanation
Indices: 304430--304470 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
304420 TATAATTTAA
304430 TTTAATTAATTTTTATTATT
1 TTTAATTAATTTTTATTATT
304450 TTTAATTAATTTTTATTATT
1 TTTAATTAATTTTTATTATT
304470 T
1 T
304471 ATTTATCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTAATTAATTTTTATTATT
Found at i:304719 original size:21 final size:20
Alignment explanation
Indices: 304675--304724 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
304665 TAAATTAGAT
*
304675 TTTAAGAATTAAATTTATTTA
1 TTTAA-AATTAAATTTATTAA
* *
304696 TTTGAAATTTAATTTATTAAA
1 TTTAAAATTAAATTTATT-AA
304717 TTTAAAAT
1 TTTAAAAT
304725 ATTTATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTAAAATTAAATTTATTAA
Found at i:305266 original size:13 final size:15
Alignment explanation
Indices: 305243--305274 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
305233 TTTGTTTGGA
305243 AAAAAATATAAAA-T
1 AAAAAATATAAAAGT
305257 AAAAAA-ATAAAAGT
1 AAAAAATATAAAAGT
305271 AAAA
1 AAAA
305275 TTATGAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (15 bp):
AAAAAATATAAAAGT
Found at i:309511 original size:69 final size:68
Alignment explanation
Indices: 309430--309571 Score: 239
Period size: 69 Copynumber: 2.1 Consensus size: 68
309420 AAGTGTTTTT
* *
309430 TTTAATCTATCCATTTAATAGAAACATTTTCTTCAGTCTGAATTTCCATATAATAGCTGGCGAAA
1 TTTAATCTATCCAGTTAATAGAAACATTTTCTTCACTCTGAATTT-CATATAATAGCTGGCGAAA
*
309495 GTGA
65 GTCA
*
309499 TTTAATCTATCCAGTTAATAGAAACATTTTCTTCACTCTGAATTTCATATAATAGCTGGTGAAAG
1 TTTAATCTATCCAGTTAATAGAAACATTTTCTTCACTCTGAATTTCATATAATAGCTGGCGAAAG
309564 TCA
66 TCA
309567 TTTAA
1 TTTAA
309572 AGTTTCTAGT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
68 26 0.38
69 43 0.62
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (68 bp):
TTTAATCTATCCAGTTAATAGAAACATTTTCTTCACTCTGAATTTCATATAATAGCTGGCGAAAG
TCA
Found at i:314337 original size:7 final size:8
Alignment explanation
Indices: 314313--314339 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
314303 AGAAAATTTC
314313 TTTCCTTT
1 TTTCCTTT
314321 TTTCCTTT
1 TTTCCTTT
314329 TTTCCTTT
1 TTTCCTTT
314337 TTT
1 TTT
314340 GTTTTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTCCTTT
Found at i:318391 original size:20 final size:20
Alignment explanation
Indices: 318366--318407 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
318356 GAAGAATCGG
318366 AGAAACCTTACAACATTGCA
1 AGAAACCTTACAACATTGCA
318386 AGAAACCTTACAACATTGCA
1 AGAAACCTTACAACATTGCA
318406 AG
1 AG
318408 TAACTTCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (20 bp):
AGAAACCTTACAACATTGCA
Found at i:321672 original size:89 final size:88
Alignment explanation
Indices: 321522--321770 Score: 347
Period size: 89 Copynumber: 2.8 Consensus size: 88
321512 TGTTACAATC
* * *
321522 CATGAACTATAAGCAACTTTAATTAAACTTTTCAGAAATTTTGTTTTAGCAATTATGCTCTCATA
1 CATGAACTATAAGCAAATTTAGTTAAACTTTTCAGAAATTTTGTTTTAGCAGTTATGCTCTCATA
321587 TAATACAACCTTCTTGT-CGATTT
66 TAATACAACCTTCTT-TACGATTT
* *
321610 CATGAAATAAAAGCAAAGTTTAGTTAAACTTTTCAGAAATTTTGTTTTAGCAGTTATGCTCTCAT
1 CATGAACTATAAGCAAA-TTTAGTTAAACTTTTCAGAAATTTTGTTTTAGCAGTTATGCTCTCAT
* * * *
321675 ACAGTAAAACCTTCTTTATGATTT
65 ATAATACAACCTTCTTTACGATTT
* ** *
321699 CATTAACTATAAGCAATATTTAGTTAAGTTTTTCAGAAAATTTGTTTTAGCAGTTATGCTCTCAT
1 CATGAACTATAAGCAA-ATTTAGTTAAACTTTTCAGAAATTTTGTTTTAGCAGTTATGCTCTCAT
321764 ATAATAC
65 ATAATAC
321771 TCCAGCTAGG
Statistics
Matches: 140, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
88 15 0.11
89 124 0.89
90 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (88 bp):
CATGAACTATAAGCAAATTTAGTTAAACTTTTCAGAAATTTTGTTTTAGCAGTTATGCTCTCATA
TAATACAACCTTCTTTACGATTT
Found at i:323403 original size:23 final size:23
Alignment explanation
Indices: 323373--323420 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
323363 TGAACTGTTC
323373 TACCATGCTTCTTATCTTGGTCT
1 TACCATGCTTCTTATCTTGGTCT
323396 TACCATGCTTCTTATCTTGGTCT
1 TACCATGCTTCTTATCTTGGTCT
323419 TA
1 TA
323421 ATTAAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.48
Consensus pattern (23 bp):
TACCATGCTTCTTATCTTGGTCT
Found at i:324950 original size:2 final size:2
Alignment explanation
Indices: 324943--324978 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
324933 TTTCTTTTTG
324943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
324979 TGTTATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:325505 original size:16 final size:17
Alignment explanation
Indices: 325484--325515 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
325474 TACATTGCAA
325484 TGAACAATAT-AAATAT
1 TGAACAATATCAAATAT
325500 TGAACAATATCAAATA
1 TGAACAATATCAAATA
325516 CTTCCATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.28
Consensus pattern (17 bp):
TGAACAATATCAAATAT
Found at i:327457 original size:2 final size:2
Alignment explanation
Indices: 327452--327483 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
327442 CATCATTTGG
327452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
327484 TTTGTAGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:327858 original size:19 final size:20
Alignment explanation
Indices: 327820--327858 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
327810 CCTTTTTTTT
327820 TTAGCATGTTTAATTACGTA
1 TTAGCATGTTTAATTACGTA
327840 TTAGCATGTTTAA-TACGTA
1 TTAGCATGTTTAATTACGTA
327859 AACCAGAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (20 bp):
TTAGCATGTTTAATTACGTA
Found at i:328911 original size:23 final size:25
Alignment explanation
Indices: 328866--328912 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
328856 TTATTATTTA
328866 ATAATAATAAATAATTTAATTTAATT
1 ATAATAATAAATAATTT-ATTTAATT
*
328892 ATAA-AATATATAATTT-TTTAA
1 ATAATAATAAATAATTTATTTAA
328913 AATAAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
25 11 0.55
26 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATAATAATAAATAATTTATTTAATT
Found at i:328935 original size:26 final size:28
Alignment explanation
Indices: 328901--328957 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
328891 TATAAAATAT
328901 ATAATTTTTTAAA-ATAA-ATCAAA-TTTA
1 ATAA-TTTTTAAATATAATAT-AAATTTTA
328928 ATAA-TTTTAAATATAATATAAATTTTA
1 ATAATTTTTAAATATAATATAAATTTTA
328955 ATA
1 ATA
328958 TTAATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
25 7 0.26
26 7 0.26
27 13 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
ATAATTTTTAAATATAATATAAATTTTA
Found at i:328947 original size:44 final size:41
Alignment explanation
Indices: 328871--328987 Score: 98
Period size: 42 Copynumber: 2.8 Consensus size: 41
328861 ATTTAATAAT
*
328871 AATAAATAATTTAATTTAATTATAAAATATATAATTTTTTAA
1 AATAAATAATTTAA-TTAATTATAAAATATATAAATTTTTAA
*
328913 AATAAATCAAATTTAA-TAATTTTAAATATAATATAAA-TTTTAA
1 AATAAAT--AATTTAATTAATTATAAA-AT-ATATAAATTTTTAA
* * * *
328956 TATTAATATTTTAA-TAAATA-AAAATAATATAA
1 AATAAATAATTTAATTAATTATAAAAT-ATATAA
328988 TAAATATAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
39 9 0.14
40 3 0.05
41 10 0.16
42 16 0.25
43 13 0.20
44 13 0.20
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.44
Consensus pattern (41 bp):
AATAAATAATTTAATTAATTATAAAATATATAAATTTTTAA
Found at i:328953 original size:18 final size:18
Alignment explanation
Indices: 328930--328964 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
328920 CAAATTTAAT
328930 AATTTTAA-ATATAATATA
1 AATTTTAATAT-TAATATA
328948 AATTTTAATATTAATAT
1 AATTTTAATATTAATAT
328965 TTTAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTTTAATATTAATATA
Found at i:328956 original size:24 final size:24
Alignment explanation
Indices: 328907--328961 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
328897 ATATATAATT
328907 TTTTAAAATAAATCAAATTTAATAA
1 TTTTAAAATAAATCAAATTT-ATAA
328932 TTTTAAATATAATAT-AAATTT-TAA
1 TTTTAAA-ATAA-ATCAAATTTATAA
*
328956 TATTAA
1 TTTTAA
328962 TATTTTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 8 0.30
25 7 0.26
26 10 0.37
27 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTTAAAATAAATCAAATTTATAA
Found at i:328975 original size:18 final size:18
Alignment explanation
Indices: 328954--329020 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
328944 TATAAATTTT
*
328954 AATATTAATATTTTAATA
1 AATATAAATATTTTAATA
* * *
328972 AATAAAAATAATATAATA
1 AATATAAATATTTTAATA
328990 AATATAAATATATTTAAATTA
1 AATATAAATAT-TTT-AA-TA
329011 AAT-TAAATAT
1 AATATAAATAT
329021 AATATTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 23 0.59
19 2 0.05
20 9 0.23
21 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATAAATATTTTAATA
Found at i:328999 original size:10 final size:10
Alignment explanation
Indices: 328968--329025 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
328958 TTAATATTTT
*
328968 AATAAATAAA
1 AATAAATATA
328978 AAT-AATAT-
1 AATAAATATA
328986 AATAAATATA
1 AATAAATATA
* *
328996 AATATATTTA
1 AATAAATATA
329006 AATTAAAT-TA
1 AA-TAAATATA
329016 AATATAATAT
1 AATA-AATAT
329026 TTTTAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 3 0.08
9 11 0.28
10 20 0.51
11 5 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATAAATATA
Found at i:329260 original size:4 final size:4
Alignment explanation
Indices: 329251--329277 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
329241 ACAAAATGAC
329251 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
329278 TAGGTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:329754 original size:14 final size:15
Alignment explanation
Indices: 329735--329781 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
329725 TTATATAGTT
329735 ATATAAATTTTAA-A
1 ATATAAATTTTAATA
*
329749 ATATAAATAATTTATATT
1 ATATAAAT--TTTA-ATA
329767 ATATAAATTTTAATA
1 ATATAAATTTTAATA
329782 TTTTCATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.30
15 2 0.07
16 8 0.30
17 1 0.04
18 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATAAATTTTAATA
Found at i:329928 original size:8 final size:8
Alignment explanation
Indices: 329917--330015 Score: 51
Period size: 8 Copynumber: 11.4 Consensus size: 8
329907 AATTTTATGT
329917 TATATTTA
1 TATATTTA
329925 TATATTATA
1 TATATT-TA
*
329934 TTGTATTATAA
1 -TATATT-T-A
329945 TTATATTTA
1 -TATATTTA
329954 TAATATTTGA
1 T-ATATTT-A
329964 TA-A-TTA
1 TATATTTA
329970 TATATTTTAA
1 TATA-TTT-A
*
329980 TATATTAA
1 TATATTTA
329988 TA-ATGTTAA
1 TATAT-TT-A
*
329997 AATATTTA
1 TATATTTA
330005 TATATTTA
1 TATATTTA
330013 TAT
1 TAT
330016 TAAATTATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
6 3 0.04
7 5 0.07
8 23 0.32
9 18 0.25
10 17 0.23
11 7 0.10
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (8 bp):
TATATTTA
Found at i:329984 original size:25 final size:22
Alignment explanation
Indices: 329941--329991 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
329931 ATATTGTATT
329941 ATAATTATATTTATAATATTTG
1 ATAATTATATTTATAATATTTG
* *
329963 ATAATTATATATTTTAATATATTA
1 ATAATTATAT-TTATAATAT-TTG
329987 ATAAT
1 ATAAT
329992 GTTAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.40
23 8 0.32
24 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATAATTATATTTATAATATTTG
Found at i:330029 original size:25 final size:26
Alignment explanation
Indices: 329937--330029 Score: 58
Period size: 25 Copynumber: 3.7 Consensus size: 26
329927 TATTATATTG
*
329937 TATTATAATTATA-TTTATAATATTTGA
1 TATTA-AATTATATTTTAT-ATATTTAA
329964 TAATT--A-TATATTTTAATATATTAATAA
1 T-ATTAAATTATATTTT-ATATATT--TAA
*
329991 TGTTAAA--ATA-TTTATATATTT-A
1 TATTAAATTATATTTTATATATTTAA
330013 TATTAAATTATATTTTA
1 TATTAAATTATATTTTA
330030 ATTATTTTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 22
0.68 0.04 0.28
Matches are distributed among these distances:
22 7 0.13
23 1 0.02
24 7 0.13
25 20 0.38
26 7 0.13
27 7 0.13
28 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TATTAAATTATATTTTATATATTTAA
Found at i:334141 original size:2 final size:2
Alignment explanation
Indices: 334134--334170 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
334124 CTTCAGTTTT
334134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
334171 CTTTTTATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:334699 original size:21 final size:20
Alignment explanation
Indices: 334660--334703 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
334650 TGATAGAACG
334660 AAATATAAAAAATTAAATTAT
1 AAATATAAAAAATTAAATT-T
* * *
334681 AAATATTAAAATTTTAATTT
1 AAATATAAAAAATTAAATTT
334701 AAA
1 AAA
334704 ATTTATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATATAAAAAATTAAATTT
Found at i:335903 original size:32 final size:33
Alignment explanation
Indices: 335829--335911 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
335819 ATATAATATA
* *
335829 ATATAATATAAATATATAAATATTTTTAAAATTT
1 ATATAATATAAAT-TATTAATATTATTAAAATTT
335863 ATATAATATAAATTATTAATA-TATTAAAATTT
1 ATATAATATAAATTATTAATATTATTAAAATTT
*
335895 -TATAAATATAAAATATT
1 ATAT-AATATAAATTATT
335912 TATAATATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
31 3 0.07
32 22 0.49
33 7 0.16
34 13 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATAATATAAATTATTAATATTATTAAAATTT
Found at i:335926 original size:19 final size:19
Alignment explanation
Indices: 335879--335928 Score: 70
Period size: 17 Copynumber: 2.8 Consensus size: 19
335869 TATAAATTAT
*
335879 TAATATATTAAAAT-TTTA
1 TAATATAATAAAATATTTA
335897 TAA-AT-ATAAAATATTTA
1 TAATATAATAAAATATTTA
335914 TAATATAATAAAATA
1 TAATATAATAAAATA
335929 GATAAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.21
17 9 0.32
18 5 0.18
19 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATATAATAAAATATTTA
Found at i:335945 original size:20 final size:19
Alignment explanation
Indices: 335920--335959 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
335910 TTTATAATAT
*
335920 AATAAAATAGATAAATATAA
1 AATAAAAAAGATAAAT-TAA
*
335940 AATAAAAAATATAAATTAA
1 AATAAAAAAGATAAATTAA
335959 A
1 A
335960 TTAATGTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AATAAAAAAGATAAATTAA
Found at i:335951 original size:14 final size:14
Alignment explanation
Indices: 335921--335959 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
335911 TTATAATATA
*
335921 ATAAAATAGATAAAT
1 ATAAAATA-AAAAAT
335936 ATAAAATAAAAAAT
1 ATAAAATAAAAAAT
*
335950 ATAAATTAAA
1 ATAAAATAAA
335960 TTAATGTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
ATAAAATAAAAAAT
Found at i:336295 original size:21 final size:21
Alignment explanation
Indices: 336250--336317 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
336240 TTAAGTACAA
336250 AATTTAATAATATAA-AATATATT
1 AATTTAAT-ATA-AATAAT-TATT
*
336273 AATTTAATTTAAATAATTATT
1 AATTTAATATAAATAATTATT
* *
336294 AATTTGATATAAATAATTTTT
1 AATTTAATATAAATAATTATT
336315 AAT
1 AAT
336318 ATATAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 27 0.68
22 5 0.12
23 8 0.20
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
AATTTAATATAAATAATTATT
Found at i:336323 original size:18 final size:18
Alignment explanation
Indices: 336257--336326 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 18
336247 CAAAATTTAA
336257 TAATATA-AAATATATTAATT
1 TAATATATAAATA-ATT--TT
*
336277 TAAT-T-TAAATAATTAT
1 TAATATATAAATAATTTT
336293 TAATTTGATATAAATAATTTT
1 TAA--T-ATATAAATAATTTT
336314 TAATATATAAATA
1 TAATATATAAATA
336327 TTTATAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
16 4 0.10
18 13 0.31
19 7 0.17
20 5 0.12
21 13 0.31
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (18 bp):
TAATATATAAATAATTTT
Found at i:336566 original size:21 final size:20
Alignment explanation
Indices: 336540--336592 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
336530 ATTTATATAA
336540 ATTTTAATATATTAATAATTT
1 ATTTT-ATATATTAATAATTT
* *
336561 ATTTTATATAATTATTTATTT
1 ATTTTATAT-ATTAATAATTT
336582 A-TTTATATATT
1 ATTTTATATATT
336593 TATATTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 11 0.38
21 15 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTATATATTAATAATTT
Found at i:336572 original size:17 final size:17
Alignment explanation
Indices: 336517--336581 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
336507 AGAATATGTT
336517 TAATATATTATATATTTATA
1 TAATA-ATT-TAT-TTTATA
* * *
336537 TAA-ATTTTAATATAT-
1 TAATAATTTATTTTATA
336552 TAATAATTTATTTTATA
1 TAATAATTTATTTTATA
*
336569 TAATTATTTATTT
1 TAATAATTTATTT
336582 ATTTATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
15 3 0.08
16 13 0.36
17 14 0.39
18 2 0.06
19 1 0.03
20 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATAATTTATTTTATA
Found at i:336605 original size:20 final size:20
Alignment explanation
Indices: 336524--336605 Score: 64
Period size: 20 Copynumber: 4.1 Consensus size: 20
336514 GTTTAATATA
336524 TTATATATTTATA-TA-AATT
1 TTATATATTTATATTATAA-T
* *
336543 TTAATATATTAATAATT-TATT
1 TT-ATATATTTAT-ATTATAAT
* *
336564 TTATATAATTAT-TTATTTAT
1 TTATATATTTATATTA-TAAT
336584 TTATATATTTATATTATAAT
1 TTATATATTTATATTATAAT
336604 TT
1 TT
336606 TATTAAAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
18 2 0.04
19 2 0.04
20 35 0.73
21 7 0.15
22 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATATATTTATATTATAAT
Found at i:337790 original size:20 final size:20
Alignment explanation
Indices: 337743--337780 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
337733 ATAAAAAAAT
*
337743 TATTTTAAT-AATTTTTATA
1 TATTTAAATAAATTTTTATA
337762 TATTTAAATAAATTTTTAT
1 TATTTAAATAAATTTTTAT
337781 TTTATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTAAATAAATTTTTATA
Found at i:337906 original size:28 final size:29
Alignment explanation
Indices: 337865--337931 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
337855 TTACTTAAAT
337865 ATAAAATTAAAAATAAT-AAAATATATTTAA
1 ATAAAA-T-AAAATAATAAAAATATATTTAA
* *
337895 ATATAATAAAATAATAAAAATTTATTTAA
1 ATAAAATAAAATAATAAAAATATATTTAA
337924 ATAAAATA
1 ATAAAATA
337932 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 8 0.24
29 20 0.61
30 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (29 bp):
ATAAAATAAAATAATAAAAATATATTTAA
Found at i:337955 original size:3 final size:3
Alignment explanation
Indices: 337947--337986 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
337937 ATTTAAGAGT
* *
337947 TTA TTA TTA TTA TTA TTA TT- TTT TTT TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
337987 TTAGTTTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (3 bp):
TTA
Found at i:337980 original size:26 final size:26
Alignment explanation
Indices: 337946--338000 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
337936 AATTTAAGAG
*
337946 TTTATTATTATTATTATTA-TTTTTTT
1 TTTATTATTATTATT-TTAGTTTTGTT
337972 TTTATTATTATTATTTTAGTTTTGTT
1 TTTATTATTATTATTTTAGTTTTGTT
337998 TTT
1 TTT
338001 CAGTTCATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (26 bp):
TTTATTATTATTATTTTAGTTTTGTT
Found at i:337994 original size:20 final size:20
Alignment explanation
Indices: 337953--337994 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
337943 GAGTTTATTA
**
337953 TTATTATTATTATTTTTTTT
1 TTATTATTATTATTTTAGTT
337973 TTATTATTATTATTTTAGTT
1 TTATTATTATTATTTTAGTT
337993 TT
1 TT
337995 GTTTTTCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (20 bp):
TTATTATTATTATTTTAGTT
Found at i:338427 original size:18 final size:18
Alignment explanation
Indices: 338406--338440 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
338396 ATTGATATTT
338406 AATA-TTTTAATATTAAAA
1 AATATTTTTAAT-TTAAAA
338424 AATATTTTTAATTTAAA
1 AATATTTTTAATTTAAA
338441 TTTAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATTTTTAATTTAAAA
Found at i:338445 original size:30 final size:31
Alignment explanation
Indices: 338402--338460 Score: 79
Period size: 29 Copynumber: 1.9 Consensus size: 31
338392 TTTTATTGAT
338402 ATTTAATATTTTAA-TATTAAAAAATATTTTTA
1 ATTTAATATTTTAATTA-T-AAAAATATTTTTA
338434 ATTTAA-A-TTTAATTATAAAAATATTTT
1 ATTTAATATTTTAATTATAAAAATATTTT
338461 AATAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 11 0.42
30 6 0.23
31 3 0.12
32 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTTAATATTTTAATTATAAAAATATTTTTA
Found at i:338489 original size:47 final size:44
Alignment explanation
Indices: 338438--338528 Score: 105
Period size: 47 Copynumber: 2.0 Consensus size: 44
338428 TTTTTAATTT
*
338438 AAATTT-AATTATAAA-AATATTTTAATAATATTAAAAATAATAAAATA
1 AAATTTAAATTA-AAATAA-ATTTAAAT-AT-TTAAAAA-AATAAAATA
*
338485 AAATTTAAATTAAAATAAATTTAAATATTTTAAAAAATAAAATA
1 AAATTTAAATTAAAATAAATTTAAATATTTAAAAAAATAAAATA
338529 TTTAACGACA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
44 9 0.22
45 6 0.15
46 2 0.05
47 16 0.40
48 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (44 bp):
AAATTTAAATTAAAATAAATTTAAATATTTAAAAAAATAAAATA
Found at i:338506 original size:16 final size:17
Alignment explanation
Indices: 338478--338510 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
338468 TTAAAAATAA
338478 TAAAATAAAATTTAAAT
1 TAAAATAAAATTTAAAT
338495 TAAAAT-AAATTTAAAT
1 TAAAATAAAATTTAAAT
338511 ATTTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATAAAATTTAAAT
Found at i:340102 original size:13 final size:13
Alignment explanation
Indices: 340078--340133 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
340068 CGAGTCGAAA
340078 AAATTT-AAATTT
1 AAATTTAAAATTT
340090 AAATTTAAAATTT
1 AAATTTAAAATTT
** * *
340103 TTATATAATGATTT
1 AAATTTAA-AATTT
*
340117 AAATTTATAATTT
1 AAATTTAAAATTT
340130 AAAT
1 AAAT
340134 ATATTAAAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
12 6 0.18
13 19 0.58
14 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:342228 original size:33 final size:33
Alignment explanation
Indices: 342186--342249 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
342176 ATGGCGGTCT
342186 TTATGAGTTAATTATTTTACACTTCTTATTTCC
1 TTATGAGTTAATTATTTTACACTTCTTATTTCC
*
342219 TTATGAGTTAATTGTTTTACACTTCTTATTT
1 TTATGAGTTAATTATTTTACACTTCTTATTT
342250 GGTGTAGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.56
Consensus pattern (33 bp):
TTATGAGTTAATTATTTTACACTTCTTATTTCC
Found at i:346486 original size:28 final size:29
Alignment explanation
Indices: 346454--346527 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 29
346444 AATTTAAATT
**
346454 ATTTTTTAATTAATAAAAATTTTA-TTTA
1 ATTTTTTAATTAATAAAAATTAAATTTTA
346482 A--TTTTAATT-ATAAAAA-TAAATTTTA
1 ATTTTTTAATTAATAAAAATTAAATTTTA
*
346507 ATATTTTTAAATAATAAAAAT
1 AT-TTTTTAATTAATAAAAAT
346528 CTATTGACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
24 2 0.05
25 12 0.32
26 8 0.22
28 8 0.22
29 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTTTTAATTAATAAAAATTAAATTTTA
Found at i:346520 original size:26 final size:26
Alignment explanation
Indices: 346456--346527 Score: 65
Period size: 28 Copynumber: 2.7 Consensus size: 26
346446 TTTAAATTAT
* * *
346456 TTTTTAATTAATAAAAATTTTATTTA
1 TTTTTAAATAAAAAAAATTTTATATA
*
346482 ATTTTAATTATAAAAATAAATTTTA-ATA
1 TTTTTAA--ATAAAAA-AAATTTTATATA
*
346510 TTTTTAAATAATAAAAAT
1 TTTTTAAATAAAAAAAAT
346528 CTATTGACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
25 4 0.11
26 12 0.32
28 13 0.35
29 8 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTTAAATAAAAAAAATTTTATATA
Found at i:346664 original size:38 final size:38
Alignment explanation
Indices: 346621--346759 Score: 129
Period size: 38 Copynumber: 3.6 Consensus size: 38
346611 TTGTAATAAA
* *
346621 ATTTTTGAACTCTAAATAAAATCAATAAGATAATACAT
1 ATTTTTAAACTATAAATAAAATCAATAAGATAATACAT
* ** *
346659 ATTTTTAAACTATATAAAAAACTATTCTTTAATTG-TAATA-AA
1 ATTTTTAAACTATA-AATAAA--A-TCAATAA--GATAATACAT
* *
346701 ATTTTTGAACTCTAAATAAAATCAATAAGATAATACAT
1 ATTTTTAAACTATAAATAAAATCAATAAGATAATACAT
*
346739 ATTTTTAAACTATATATAAAA
1 ATTTTTAAACTATAAATAAAA
346760 CTAAAAAATT
Statistics
Matches: 78, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
36 1 0.01
37 5 0.06
38 36 0.46
39 6 0.08
41 6 0.08
42 18 0.23
43 5 0.06
44 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.38
Consensus pattern (38 bp):
ATTTTTAAACTATAAATAAAATCAATAAGATAATACAT
Found at i:346700 original size:80 final size:80
Alignment explanation
Indices: 346603--346762 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
346593 ACTTATGAAC
346603 TTCTTTAATTGTAATAAAATTTTTGAACTCTAAATAAAATCAATAAGATAATACATATTTTTAAA
1 TTCTTTAATTGTAATAAAATTTTTGAACTCTAAATAAAATCAATAAGATAATACATATTTTTAAA
346668 CTATATAAAAAACTA
66 CTATATAAAAAACTA
346683 TTCTTTAATTGTAATAAAATTTTTGAACTCTAAATAAAATCAATAAGATAATACATATTTTTAAA
1 TTCTTTAATTGTAATAAAATTTTTGAACTCTAAATAAAATCAATAAGATAATACATATTTTTAAA
*
346748 CTATATATAAAACTA
66 CTATATAAAAAACTA
346763 AAAAATTTAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (80 bp):
TTCTTTAATTGTAATAAAATTTTTGAACTCTAAATAAAATCAATAAGATAATACATATTTTTAAA
CTATATAAAAAACTA
Found at i:347820 original size:14 final size:14
Alignment explanation
Indices: 347801--347830 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
347791 CTAGTTTATA
347801 AAAGAGAGAGAGAG
1 AAAGAGAGAGAGAG
347815 AAAGAGAGAGAGAG
1 AAAGAGAGAGAGAG
347829 AA
1 AA
347831 TTATAGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (14 bp):
AAAGAGAGAGAGAG
Found at i:349752 original size:17 final size:17
Alignment explanation
Indices: 349722--349754 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
349712 ATAAATTTAT
349722 ATTTGTATATTTATTAA
1 ATTTGTATATTTATTAA
349739 ATTT-TATATATTATTA
1 ATTTGTATAT-TTATTA
349755 TTATGGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTTGTATATTTATTAA
Found at i:350075 original size:22 final size:23
Alignment explanation
Indices: 350023--350073 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
350013 AAATATTTTC
*
350023 ATAAAATAGAAAGTCAAAAACTT
1 ATAAAATAGAAAGTAAAAAACTT
*
350046 ATAAAATAGAAAGTAAAAAATTT
1 ATAAAATAGAAAGTAAAAAACTT
350069 ATAAA
1 ATAAA
350074 TAATTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.24
Consensus pattern (23 bp):
ATAAAATAGAAAGTAAAAAACTT
Found at i:350433 original size:20 final size:19
Alignment explanation
Indices: 350410--350493 Score: 58
Period size: 20 Copynumber: 4.6 Consensus size: 19
350400 TTGATATGAG
350410 TATATAATAATTTATATATT
1 TATATAAT-ATTTATATATT
* *
350430 TATATTATATTTATTTTATT
1 TATATAATATTTA-TATATT
350450 T-TAACTAA-A-TT-TATATT
1 TAT-A-TAATATTTATATATT
350467 TA-AT-ATA-TTATATATT
1 TATATAATATTTATATATT
350483 TATATAA-ATTT
1 TATATAATATTT
350494 TAAAATATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
14 1 0.02
15 4 0.08
16 9 0.18
17 9 0.18
18 3 0.06
19 8 0.16
20 15 0.29
21 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATAATATTTATATATT
Found at i:350468 original size:16 final size:15
Alignment explanation
Indices: 350444--350493 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
350434 TTATATTTAT
350444 TTTAT-TTTAACTAAA
1 TTTATATTTAA-TAAA
*
350459 TTTATATTTAATATA
1 TTTATATTTAATAAA
350474 TTATATATTTATATAAA
1 TT-TATATTTA-ATAAA
350491 TTT
1 TTT
350494 TAAAATATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 10 0.33
16 14 0.47
17 6 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATATTTAATAAA
Found at i:359880 original size:20 final size:20
Alignment explanation
Indices: 359842--359881 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
359832 CATGAAAAAG
*
359842 ATTTTAAATATTTAAAAATA
1 ATTTTAAATATTAAAAAATA
359862 ATTTT-AATATTAAATAAATA
1 ATTTTAAATATTAAA-AAATA
359882 TTAAACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTTAAATATTAAAAAATA
Found at i:360647 original size:29 final size:29
Alignment explanation
Indices: 360586--360647 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
360576 ATATAATTAT
*
360586 TTTTAAAAAATAAGATTTAAATTTAATAT
1 TTTTAAAAAATAAGATTTAAATTTAATAA
* *
360615 TTTTAAAAATTAA-ATTTAAATATTTATAA
1 TTTTAAAAAATAAGATTTAAAT-TTAATAA
360644 TTTT
1 TTTT
360648 TTTATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTTAAAAAATAAGATTTAAATTTAATAA
Found at i:361366 original size:17 final size:17
Alignment explanation
Indices: 361345--361390 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
361335 AAAATATCGT
361345 AATTTAAAATT-TTAAA
1 AATTTAAAATTATTAAA
361361 ACATTTAAAATTATTAAA
1 A-ATTTAAAATTATTAAA
*
361379 AATTAAAAATTA
1 AATTTAAAATTA
361391 AATTTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 20 0.74
18 6 0.22
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTTAAAATTATTAAA
Found at i:369113 original size:17 final size:18
Alignment explanation
Indices: 369093--369133 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
369083 TAAAATTTTT
* *
369093 AATATAAT-TTATATTTA
1 AATATAATATTAAATATA
369110 AATAT-ATATTAAATATA
1 AATATAATATTAAATATA
369127 AATATAA
1 AATATAA
369134 AATATACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 17 0.85
18 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATAATATTAAATATA
Found at i:370686 original size:2 final size:2
Alignment explanation
Indices: 370681--370709 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
370671 GGTTTTTTGG
370681 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
370710 TTCTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:376403 original size:27 final size:27
Alignment explanation
Indices: 376353--376405 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
376343 ACAGGAACAT
* *
376353 AAATATTATATCAATATTTTTAATATA
1 AAATATTATATCAATAATTATAATATA
376380 AAATATTATAT-ATATAATTATAATAT
1 AAATATTATATCA-ATAATTATAATAT
376406 TATAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATATTATATCAATAATTATAATATA
Found at i:376423 original size:14 final size:14
Alignment explanation
Indices: 376373--376430 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
376363 TCAATATTTT
376373 TAATATAAAATAT-
1 TAATATAAAATATA
*
376386 TATATATATAATTATAA
1 TA-ATATA-AAATAT-A
*
376403 TATTATAAAATATA
1 TAATATAAAATATA
*
376417 TAATATAACATATA
1 TAATATAAAATATA
376431 AAAATAGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
13 2 0.06
14 18 0.50
15 10 0.28
16 4 0.11
17 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATATAAAATATA
Found at i:376533 original size:23 final size:22
Alignment explanation
Indices: 376466--376570 Score: 60
Period size: 23 Copynumber: 4.8 Consensus size: 22
376456 ACATATATAT
* *
376466 ATATATATATAAATAAT-TAAA
1 ATATATATATTAATTATATAAA
*
376487 AT-T-TAT-TTAA-AATATAAA
1 ATATATATATTAATTATATAAA
376505 ATTATATATATTAATTATATCAAA
1 A-TATATATATTAATTATAT-AAA
* *
376529 ATATAAATTATT-ATTATGTTAAA
1 ATATATA-TATTAATTAT-ATAAA
*
376552 ATAAATATAATATAATTAT
1 ATATATAT-AT-TAATTAT
376571 GTGTCTATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
17 3 0.05
18 8 0.12
19 4 0.06
20 2 0.03
21 5 0.08
22 5 0.08
23 24 0.36
24 10 0.15
25 5 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (22 bp):
ATATATATATTAATTATATAAA
Found at i:379968 original size:2 final size:2
Alignment explanation
Indices: 379961--379988 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
379951 TAATACGCAC
379961 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
379989 ACCTACCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:381153 original size:15 final size:15
Alignment explanation
Indices: 381108--381155 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
381098 TTAATGTAAA
381108 TAAAATATTTATAATT
1 TAAAATATTTA-AATT
*
381124 ATAAATTATTT-AATT
1 -TAAAATATTTAAATT
*
381139 TAAAAAATTTAAATT
1 TAAAATATTTAAATT
381154 TA
1 TA
381156 TTTTGATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 8 0.30
15 10 0.37
17 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATATTTAAATT
Found at i:381319 original size:6 final size:6
Alignment explanation
Indices: 381302--381346 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
381292 ATTTTATTAT
* ** *
381302 AATTTA AGTTTA AATTTA AATAAA AATTTA AATTTA AAATTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT
381347 ATGATAATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:381337 original size:24 final size:24
Alignment explanation
Indices: 381302--381347 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
381292 ATTTTATTAT
* *
381302 AATTTAAGTTTAAATTTAAATAAA
1 AATTTAAATTTAAAATTAAATAAA
381326 AATTTAAATTTAAAATTAAATA
1 AATTTAAATTTAAAATTAAATA
381348 TGATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
AATTTAAATTTAAAATTAAATAAA
Found at i:381725 original size:27 final size:30
Alignment explanation
Indices: 381680--381738 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 30
381670 GTTATAGAAT
*
381680 TTTTATAATATTATAATTAATTTTAAAATA
1 TTTTATAATATTATAATTAATGTTAAAATA
*
381710 TTTTAT-AT-TTAT-ATTAATGTTAATATA
1 TTTTATAATATTATAATTAATGTTAAAATA
381737 TT
1 TT
381739 AATAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 15 0.56
28 4 0.15
29 2 0.07
30 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTTATAATATTATAATTAATGTTAAAATA
Found at i:381746 original size:27 final size:26
Alignment explanation
Indices: 381682--381753 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
381672 TATAGAATTT
*
381682 TTATAATATTATAATTAATTTTAAAATA
1 TTATAAT-TTAT-ATTAATGTTAAAATA
* *
381710 TTTTATATTTATATTAATGTTAATATA
1 TTATA-ATTTATATTAATGTTAAAATA
*
381737 TTAATAATTTATTTTAA
1 TT-ATAATTTATATTAA
381754 AATATTTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 25 0.68
28 10 0.27
29 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TTATAATTTATATTAATGTTAAAATA
Found at i:381769 original size:21 final size:21
Alignment explanation
Indices: 381714--381771 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
381704 AAAATATTTT
* * *
381714 ATATTTATAT-TAATGTTAAT
1 ATATTTATATATTATTTTAAA
*
381734 ATATTAATA-ATTTATTTTAAA
1 ATATTTATATA-TTATTTTAAA
381755 ATATTTATATATTATTT
1 ATATTTATATATTATTT
381772 ATATATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
20 8 0.27
21 21 0.70
22 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATTTATATATTATTTTAAA
Found at i:381782 original size:13 final size:11
Alignment explanation
Indices: 381756--381795 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
381746 TATTTTAAAA
381756 TATTTATATAT
1 TATTTATATAT
381767 TATTTATATA-
1 TATTTATATAT
381777 T-TTTAT-TAT
1 TATTTATATAT
381786 TATATTATAT
1 TAT-TTATAT
381796 CTAATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
8 2 0.08
9 6 0.24
10 2 0.08
11 14 0.56
12 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTATATAT
Found at i:382141 original size:21 final size:21
Alignment explanation
Indices: 382120--382177 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
382110 TTTTTATATA
382120 AAAAAGTT-TAAAT-TTAAAAT
1 AAAAA-TTATAAATATTAAAAT
382140 AAAAATTATAAATATTAAAAT
1 AAAAATTATAAATATTAAAAT
* *
382161 TAAAATT-TTAATATTAA
1 AAAAATTATAAATATTAA
382178 TTTTATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 19 0.56
21 13 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAATTATAAATATTAAAAT
Found at i:382318 original size:22 final size:22
Alignment explanation
Indices: 382293--382336 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
382283 AAATTATTAT
382293 TTTTATATAATTATTATTTAAA
1 TTTTATATAATTATTATTTAAA
382315 TTTTATATAATTATTATTTAAA
1 TTTTATATAATTATTATTTAAA
382337 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTATATAATTATTATTTAAA
Found at i:382505 original size:17 final size:16
Alignment explanation
Indices: 382475--382517 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
382465 ATATATTTAT
382475 TAAAAT-TT-TAAATA
1 TAAAATATTATAAATA
382489 TAAATATATTATAAATA
1 TAAA-ATATTATAAATA
382506 TAAAATATTATA
1 TAAAATATTATA
382518 TTAATAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.15
15 2 0.08
16 10 0.38
17 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATATTATAAATA
Found at i:382523 original size:18 final size:17
Alignment explanation
Indices: 382483--382517 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
382473 ATTAAAATTT
382483 TAAATATAAATATATTA
1 TAAATATAAATATATTA
382500 TAAATATAAA-ATATTA
1 TAAATATAAATATATTA
382516 TA
1 TA
382518 TTAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATATAAATATATTA
Found at i:382545 original size:44 final size:43
Alignment explanation
Indices: 382459--382546 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
382449 TCTATTTTTT
* *
382459 AATATAATATATTTATTAAAATTTTAAATATAAATATATTATA
1 AATATAAAATATTTATTAAAATTTTAAATATAAATAAATTATA
* *
382502 AATATAAAATATTATATTAATAATTTTTAA-ATAATTAAATTATA
1 AATATAAAATATT-TATTAA-AATTTTAAATATAAATAAATTATA
382546 A
1 A
382547 TTATTATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
43 12 0.31
44 19 0.49
45 8 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (43 bp):
AATATAAAATATTTATTAAAATTTTAAATATAAATAAATTATA
Found at i:386370 original size:12 final size:11
Alignment explanation
Indices: 386345--386405 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
386335 TAATTTGGTT
*
386345 ATTTTAATTTA
1 ATTTTAAATTA
386356 ATTTTAAAATTA
1 ATTTT-AAATTA
*
386368 ATTGATTTAATT-
1 ATT--TTAAATTA
*
386380 ATTTTAATTTA
1 ATTTTAAATTA
386391 ATTTTAAAATTA
1 ATTTT-AAATTA
386403 ATT
1 ATT
386406 GATTAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
10 5 0.12
11 10 0.25
12 19 0.47
13 4 0.10
14 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:386383 original size:35 final size:35
Alignment explanation
Indices: 386343--386409 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
386333 TTTAATTTGG
386343 TTATTTTAATTTAATTTTAAAATTAATTGATTTAA
1 TTATTTTAATTTAATTTTAAAATTAATTGATTTAA
386378 TTATTTTAATTTAATTTTAAAATTAATTGATT
1 TTATTTTAATTTAATTTTAAAATTAATTGATT
386410 AAAAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (35 bp):
TTATTTTAATTTAATTTTAAAATTAATTGATTTAA
Found at i:404367 original size:44 final size:45
Alignment explanation
Indices: 404299--404393 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 45
404289 AGTTGCTAGA
* *
404299 ATATTTAAAAAAAGGTTTACATATACATA-TATATATATATATAT
1 ATATGTAAAAAAAGGTTCACATATACATACTATATATATATATAT
404343 ATATGTAAAACAAA-GTTCACATATACATACCTATATATATATATAT
1 ATATGTAAAA-AAAGGTTCACATATACATA-CTATATATATATATAT
404389 ATATG
1 ATATG
404394 ATAATCTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 23 0.50
45 3 0.07
46 20 0.43
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (45 bp):
ATATGTAAAAAAAGGTTCACATATACATACTATATATATATATAT
Found at i:411775 original size:33 final size:34
Alignment explanation
Indices: 411735--411812 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
411725 TAAATAATAA
* * *
411735 ATGTAATA-ATAATATATTATTATGTT-AAAATTT
1 ATGTAATATAAAAT-TATTAATATATTAAAAATTT
411768 ATGTAATATAAAATTATTAATATATTAAAAATTT
1 ATGTAATATAAAATTATTAATATATTAAAAATTT
*
411802 ATATATATATA
1 ATGTA-ATATA
411813 TATAATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 18 0.47
34 15 0.39
35 5 0.13
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (34 bp):
ATGTAATATAAAATTATTAATATATTAAAAATTT
Found at i:411790 original size:14 final size:16
Alignment explanation
Indices: 411760--411791 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
411750 ATTATTATGT
411760 TAAAATTTATGTAATA
1 TAAAATTTATGTAATA
411776 TAAAA-TTAT-TAATA
1 TAAAATTTATGTAATA
411790 TA
1 TA
411792 TTAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TAAAATTTATGTAATA
Found at i:412085 original size:27 final size:29
Alignment explanation
Indices: 412054--412121 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
412044 CAAGCTCATT
*
412054 TATATTAATTATTT-ATAAAATT-TAATA
1 TATATTAATTATTTAATAAAATTATAAAA
412081 TATA-TAATTTATTTGAATAAAATTATAAAA
1 TATATTAA-TTATTT-AATAAAATTATAAAA
*
412111 TAAATTAATTA
1 TATATTAATTA
412122 AATAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 3 0.09
27 10 0.29
29 8 0.24
30 10 0.29
31 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
TATATTAATTATTTAATAAAATTATAAAA
Found at i:413241 original size:20 final size:20
Alignment explanation
Indices: 413216--413258 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
413206 AATACCGAAC
413216 ATAAGTGCTTAAAAGAGAAA
1 ATAAGTGCTTAAAAGAGAAA
413236 ATAAGTGCTTAAAAGAGAAA
1 ATAAGTGCTTAAAAGAGAAA
413256 ATA
1 ATA
413259 GAGAGTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.19, T:0.21
Consensus pattern (20 bp):
ATAAGTGCTTAAAAGAGAAA
Found at i:417690 original size:31 final size:32
Alignment explanation
Indices: 417647--417731 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 32
417637 CAACACCCCT
417647 ATTTATGA-AATATATATATATATATT-TTAAA
1 ATTTAT-ATAATATATATATATATATTATTAAA
* *
417678 ATTTATATAATATAAAT-TAT-TAATTATTTAA
1 ATTTATATAATATATATATATAT-ATTATTAAA
*
417709 ATTTATATAA-ATATA-AAATATAT
1 ATTTATATAATATATATATATATAT
417732 GATATATAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
29 1 0.02
30 15 0.33
31 29 0.64
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (32 bp):
ATTTATATAATATATATATATATATTATTAAA
Found at i:417693 original size:16 final size:16
Alignment explanation
Indices: 417674--417740 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
417664 ATATATATTT
417674 TAAAATTTATATAATA
1 TAAAATTTATATAATA
417690 T-AAA-TTAT-TAATTA
1 TAAAATTTATATAA-TA
*
417704 TTTAAATTTATATAAATA
1 -TAAAATTTATAT-AATA
*
417722 TAAAATATATGAT-ATA
1 TAAAATTTAT-ATAATA
417738 TAA
1 TAA
417741 GAAATATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
13 3 0.07
14 6 0.14
15 4 0.10
16 10 0.24
17 12 0.29
18 5 0.12
19 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:427691 original size:18 final size:17
Alignment explanation
Indices: 427668--427702 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
427658 GGCTTGGTTG
427668 CCTCAGGATCATCTATCT
1 CCTCAGGATCATC-ATCT
*
427686 CCTCAGGCTCATCATCT
1 CCTCAGGATCATCATCT
427703 AACCATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.37, G:0.11, T:0.31
Consensus pattern (17 bp):
CCTCAGGATCATCATCT
Found at i:429942 original size:16 final size:17
Alignment explanation
Indices: 429915--429946 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
429905 CACCAACATT
429915 TAAAATATAATATAATG
1 TAAAATATAATATAATG
429932 TAAAA-ATAATATAAT
1 TAAAATATAATATAAT
429947 ATTATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
TAAAATATAATATAATG
Found at i:431267 original size:2 final size:2
Alignment explanation
Indices: 431256--431295 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
431246 TTTAGACTTC
* *
431256 TA TA -A TA TA TA TA TT TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
431296 TGTCTTTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:431436 original size:2 final size:2
Alignment explanation
Indices: 431429--431476 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
431419 TGACCTGGTT
431429 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
431471 T- TA TA T
1 TA TA TA T
431477 TTGTATTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:431518 original size:28 final size:28
Alignment explanation
Indices: 431481--431535 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
431471 TTATATTTGT
*
431481 ATTATTTTATATA-AATTTTAAAATATTA
1 ATTATGTTATATATAA-TTTAAAATATTA
*
431509 ATTATGTTATATATAATTTAATATATT
1 ATTATGTTATATATAATTTAAAATATT
431536 TATGTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTATGTTATATATAATTTAAAATATTA
Done.