Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold470
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: 597437
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 5 of 6
Found at i:441299 original size:27 final size:24
Alignment explanation
Indices: 441227--441304 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 24
441217 AATTTTTTAA
*
441227 TTTATATTAGTTTTATTTTTTTTT
1 TTTATATTATTTTTATTTTTTTTT
* *
441251 TTTA-ATTTTTTTTTTTTATTTTTTT
1 TTTATA-TTATTTTTATT-TTTTTTT
*
441276 TTTATATTATTTTATCATTGTTTTTT
1 TTTATATTATTTT-T-ATTTTTTTTT
441302 TTT
1 TTT
441305 GTTTTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 1 0.02
24 12 0.28
25 17 0.40
26 11 0.26
27 2 0.05
ACGTcount: A:0.15, C:0.01, G:0.03, T:0.81
Consensus pattern (24 bp):
TTTATATTATTTTTATTTTTTTTT
Found at i:443624 original size:12 final size:13
Alignment explanation
Indices: 443607--443641 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
443597 TATTATTAAA
443607 ATATTAT-TTTAT
1 ATATTATATTTAT
443619 ATATTAATATTTAT
1 ATATT-ATATTTAT
443633 ATATTATAT
1 ATATTATAT
443642 AATTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 6 0.29
14 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTATATTTAT
Found at i:443651 original size:21 final size:19
Alignment explanation
Indices: 443591--443652 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 19
443581 ATTTCATTGT
443591 TTATTATATTATTAAAATATTA
1 TTATTATA-TATT-AAAT-TTA
443613 TT-TTATATATTAATATTTA
1 TTATTATATATTAA-ATTTA
443632 TATATTATATAATTAAATTTA
1 T-TATTATAT-ATTAAATTTA
443653 AATAAAGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 6 0.17
20 7 0.19
21 16 0.44
22 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTATATATTAAATTTA
Found at i:445086 original size:20 final size:20
Alignment explanation
Indices: 445063--445101 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
445053 TGTTAAAATT
445063 TATA-TAATACAAATTATAAA
1 TATATTAATACAAA-TATAAA
*
445083 TATATTAATATAAATATAA
1 TATATTAATACAAATATAA
445102 CAACTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATTAATACAAATATAAA
Found at i:453664 original size:1 final size:1
Alignment explanation
Indices: 453654--453714 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
453644 TGGCAATTGG
* * * ** * *
453654 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
453715 GGTGAAGATT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.89, C:0.05, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:453684 original size:29 final size:30
Alignment explanation
Indices: 453652--453710 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
453642 CATGGCAATT
* *
453652 GGAAAAAGAAAAAAACAAAACAA-AAAAAA
1 GGAAAAAGAAAAAAAAAAAAAAACAAAAAA
453681 GGAAAAAGAAAAAAAAAAAAAAACAAAAAA
1 GGAAAAAGAAAAAAAAAAAAAAACAAAAAA
453711 AAAAGGTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (30 bp):
GGAAAAAGAAAAAAAAAAAAAAACAAAAAA
Found at i:453687 original size:16 final size:16
Alignment explanation
Indices: 453655--453714 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
453645 GGCAATTGGA
453655 AAAAGAAAAAAACAAAAC
1 AAAA-AAAAAAA-AAAAC
** *
453673 AAAAAAAAGGAAAAAG
1 AAAAAAAAAAAAAAAC
453689 AAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAC
453705 AAAAAAAAAA
1 AAAAAAAAAA
453715 GGTGAAGATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
16 27 0.75
17 5 0.14
18 4 0.11
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAC
Found at i:457000 original size:32 final size:32
Alignment explanation
Indices: 456957--457035 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
456947 AGGAAATAGG
* *
456957 GTGGAATGCGCTAAAACG-CTCAGCGCATCTAAC
1 GTGGAA-GCGCTAAAACGCCT-AACGCATCCAAC
* *
456990 TTGGAAGCGCTAAAGCGCCTAACGCATCCAAC
1 GTGGAAGCGCTAAAACGCCTAACGCATCCAAC
*
457022 GTGGAAGCACTAAA
1 GTGGAAGCGCTAAA
457036 GCGACTTAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
32 32 0.82
33 7 0.18
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (32 bp):
GTGGAAGCGCTAAAACGCCTAACGCATCCAAC
Found at i:457750 original size:18 final size:18
Alignment explanation
Indices: 457711--457759 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
457701 TGTAGTCATT
*
457711 TTTATA-TTTATATTAAA
1 TTTATATTTTTTATTAAA
457728 TTTATATTTTTTATTATAA
1 TTTATATTTTTTATTA-AA
*
457747 -TTATATGTTTTAT
1 TTTATATTTTTTAT
457760 GTTTTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 20 0.71
19 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATATTTTTTATTAAA
Found at i:457855 original size:11 final size:11
Alignment explanation
Indices: 457816--457858 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
457806 AATATATTTA
457816 TATATTTATAT
1 TATATTTATAT
*
457827 TATTTTTTCATAT
1 TA-TATTT-ATAT
*
457840 CATATTTATAT
1 TATATTTATAT
457851 TATATTTA
1 TATATTTA
457859 AAATTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 13 0.50
12 8 0.31
13 5 0.19
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:457870 original size:26 final size:24
Alignment explanation
Indices: 457816--457873 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
457806 AATATATTTA
***
457816 TATATTTATATTATTTTTTCATAT
1 TATATTTATATTATTTTAAAATAT
*
457840 CATATTTATATTATATTTAAAATTAT
1 TATATTTATATTAT-TTTAAAA-TAT
457866 TATATTTA
1 TATATTTA
457874 CATATTTGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 13 0.48
25 4 0.15
26 10 0.37
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATTTATATTATTTTAAAATAT
Found at i:458684 original size:4 final size:4
Alignment explanation
Indices: 458677--458714 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
458667 TGGCTGGCAT
*
458677 AGAA AGAA AGAA AGAA AGAAA AAAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA A
458715 AGTGAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 28 0.90
5 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:458711 original size:25 final size:26
Alignment explanation
Indices: 458677--458739 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
458667 TGGCTGGCAT
458677 AGAAAGAAAG-AAAGAAAGAAAAAAA
1 AGAAAGAAAGAAAAGAAAGAAAAAAA
**
458702 AGAAAGAAAGAAAAGTGAGAAAAAAA
1 AGAAAGAAAGAAAAGAAAGAAAAAAA
458728 A-AAAGAAA-AAAA
1 AGAAAGAAAGAAAA
458740 TTTATGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
24 4 0.11
25 17 0.49
26 14 0.40
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (26 bp):
AGAAAGAAAGAAAAGAAAGAAAAAAA
Found at i:458722 original size:17 final size:17
Alignment explanation
Indices: 458679--458735 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
458669 GCTGGCATAG
458679 AAAGAAAGAAAGAAAGA
1 AAAGAAAGAAAGAAAGA
*
458696 AAAAAAAGAAAGAAAGA
1 AAAGAAAGAAAGAAAGA
** *
458713 AAAGTGAGAAA-AAAAA
1 AAAGAAAGAAAGAAAGA
458729 AAAGAAA
1 AAAGAAA
458736 AAAATTTATG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
16 9 0.27
17 24 0.73
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (17 bp):
AAAGAAAGAAAGAAAGA
Found at i:458837 original size:12 final size:12
Alignment explanation
Indices: 458813--458858 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
458803 ATATTAATAA
458813 TTTATTTA-A-T
1 TTTATTTATATT
458823 TTTATTTATATT
1 TTTATTTATATT
*
458835 TTTATATATATT
1 TTTATTTATATT
* *
458847 TGTATTTGTATT
1 TTTATTTATATT
458859 ATGTGCATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 8 0.27
11 1 0.03
12 21 0.70
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (12 bp):
TTTATTTATATT
Found at i:459504 original size:22 final size:21
Alignment explanation
Indices: 459492--459539 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
459482 AGATGGAAAG
459492 AAAAAAAAGGAAAAGAGAAAAG
1 AAAAAAAAGG-AAAGAGAAAAG
* * *
459514 AAAGAAAAGGAGAGAGAGAAAT
1 AAAAAAAAGGAAAGAGA-AAAG
459536 AAAA
1 AAAA
459540 GGAAAAGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (21 bp):
AAAAAAAAGGAAAGAGAAAAG
Found at i:459526 original size:17 final size:17
Alignment explanation
Indices: 459490--459542 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
459480 AAAGATGGAA
*
459490 AGAAAAAAAAGGAAAA-G
1 AGAAAAGAAA-GAAAAGG
459507 AGAAAAGAAAGAAAAGG
1 AGAAAAGAAAGAAAAGG
* *
459524 AGAGAGAGAAATAAAAGG
1 AGA-AAAGAAAGAAAAGG
459542 A
1 A
459543 AAAGTTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 5 0.16
17 13 0.42
18 13 0.42
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (17 bp):
AGAAAAGAAAGAAAAGG
Found at i:459531 original size:23 final size:22
Alignment explanation
Indices: 459488--459534 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
459478 AGAAAGATGG
459488 AAAGAAAAAAAAGGAAAAGAGA
1 AAAGAAAAAAAAGGAAAAGAGA
* *
459510 AAAGAAAGAAAAGGAGAGAGAGA
1 AAAGAAAAAAAAGGA-AAAGAGA
459533 AA
1 AA
459535 TAAAAGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAAAAGGAAAAGAGA
Found at i:459540 original size:23 final size:21
Alignment explanation
Indices: 459487--459546 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
459477 GAGAAAGATG
459487 GAAAGAAAA-AAAAGGAAAAGA
1 GAAA-AAAAGAAAAGGAAAAGA
*
459508 GAAAAGAAAGAAAAGGAGAGAGA
1 GAAAA-AAAGAAAAGGA-AAAGA
459531 GAAATAAAAGGAAAAG
1 GAAA-AAAA-GAAAAG
459547 TTAATGTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 1 0.03
21 7 0.21
22 7 0.21
23 11 0.33
24 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (21 bp):
GAAAAAAAGAAAAGGAAAAGA
Found at i:460091 original size:15 final size:17
Alignment explanation
Indices: 460071--460103 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
460061 TATTTGATAG
460071 AGAAAG-AAAA-AGAAA
1 AGAAAGCAAAAGAGAAA
460086 AGAAAGCAAAAGAGAAA
1 AGAAAGCAAAAGAGAAA
460103 A
1 A
460104 AAATTATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 4 0.25
17 6 0.38
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (17 bp):
AGAAAGCAAAAGAGAAA
Found at i:460633 original size:15 final size:16
Alignment explanation
Indices: 460612--460669 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
460602 ATTTTTAAAT
460612 AAATTTTATTAATT-A
1 AAATTTTATTAATTAA
*
460627 TAATTTTATTTAATTAA
1 AAATTTTA-TTAATTAA
* *
460644 AAATTTTATAAATATCA
1 AAATTTTATTAAT-TAA
460661 AAATTTTAT
1 AAATTTTAT
460670 AAAAAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 7 0.19
16 10 0.28
17 19 0.53
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATTTTATTAATTAA
Found at i:460702 original size:30 final size:30
Alignment explanation
Indices: 460668--460727 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
460658 TCAAAATTTT
460668 ATAAAAAAATTAA-TTTATAATTA-AATTTAA
1 ATAAAAAAA-TAATTTTA-AATTATAATTTAA
460698 ATAAAAAAATAATTTTAAATTATAATTTAA
1 ATAAAAAAATAATTTTAAATTATAATTTAA
460728 CTCTATGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
ATAAAAAAATAATTTTAAATTATAATTTAA
Found at i:467616 original size:19 final size:18
Alignment explanation
Indices: 467592--467736 Score: 73
Period size: 19 Copynumber: 7.8 Consensus size: 18
467582 TTATATTAAA
467592 ATTATATAAATATATAAT
1 ATTATATAAATATATAAT
* * *
467610 ATATATAAAAAATAATTTAAA
1 AT-TAT-ATAAAT-ATATAAT
*
467631 ATTATGTAAATATATTAAT
1 ATTATATAAATATA-TAAT
*
467650 ATTTTA-AAATATATAAT
1 ATTATATAAATATATAAT
* *
467667 A-TAAATTAAA-ATATATT
1 ATTATA-TAAATATATAAT
* *
467684 ATTTTTATAAATATAAAAT
1 A-TTATATAAATATATAAT
*
467703 ACTTTTATATAAT-TATAAT
1 A-TTATATA-AATATATAAT
**
467722 AAAAATATAAATATA
1 -ATTATATAAATATA
467737 ATAAAATAAA
Statistics
Matches: 94, Mismatches: 21, Indels: 23
0.68 0.15 0.17
Matches are distributed among these distances:
16 2 0.02
17 12 0.13
18 21 0.22
19 40 0.43
20 12 0.13
21 7 0.07
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.43
Consensus pattern (18 bp):
ATTATATAAATATATAAT
Found at i:467658 original size:39 final size:40
Alignment explanation
Indices: 467573--467668 Score: 117
Period size: 39 Copynumber: 2.4 Consensus size: 40
467563 TATTGACGTA
*
467573 ATAT-AAAAATTATATTAAAATTATATAAATATATAATAT
1 ATATAAAAAATAATATTAAAATTATATAAATATATAATAT
*
467612 ATATAAAAAATAAT-TTAAAATTATGTAAATATATTAATAT
1 ATATAAAAAATAATATTAAAATTATATAAATATA-TAATAT
*
467652 -TTTAAAATATATAATAT
1 ATATAAAA-A-ATAATAT
467669 AAATTAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
39 28 0.57
40 15 0.31
41 5 0.10
42 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (40 bp):
ATATAAAAAATAATATTAAAATTATATAAATATATAATAT
Found at i:467731 original size:17 final size:17
Alignment explanation
Indices: 467709--467742 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
467699 AAATACTTTT
*
467709 ATATAATTATAATAAAA
1 ATATAAATATAATAAAA
467726 ATATAAATATAATAAAA
1 ATATAAATATAATAAAA
467743 TAAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATAAATATAATAAAA
Found at i:467931 original size:2 final size:2
Alignment explanation
Indices: 467924--467964 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
467914 TACGTGGATG
467924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
467965 CAAATTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:470159 original size:16 final size:16
Alignment explanation
Indices: 470105--470165 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
470095 ATTTGTTTTA
* *
470105 TTCGAATAATTTTACT
1 TTCGAATCATTTTAGT
**
470121 TTTAAATCATTTCGT-GT
1 TTCGAATCATTT--TAGT
470138 TT-GAATCATTTTAGT
1 TTCGAATCATTTTAGT
470153 TTCGAATCATTTT
1 TTCGAATCATTTT
470166 GATTGAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
14 1 0.03
15 4 0.11
16 27 0.75
17 3 0.08
18 1 0.03
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.52
Consensus pattern (16 bp):
TTCGAATCATTTTAGT
Found at i:470221 original size:13 final size:13
Alignment explanation
Indices: 470203--470227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
470193 AATTTCAAAT
470203 TATTTAAATTTAA
1 TATTTAAATTTAA
470216 TATTTAAATTTA
1 TATTTAAATTTA
470228 TTAAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTAAATTTAA
Found at i:471923 original size:32 final size:33
Alignment explanation
Indices: 471881--471952 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 33
471871 TTTGAATTAT
*
471881 TTTATATTATATAAATTTTAATAAGTTAATA-A
1 TTTATATTATATAAATTTTAATAAATTAATATA
* *
471913 TTTATTTTATATAAATTTTAATAAATTTATATA
1 TTTATATTATATAAATTTTAATAAATTAATATA
471946 TTTATAT
1 TTTATAT
471953 CTTATTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 28 0.80
33 7 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (33 bp):
TTTATATTATATAAATTTTAATAAATTAATATA
Found at i:475104 original size:12 final size:13
Alignment explanation
Indices: 475087--475121 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
475077 TATTATTAAA
475087 ATATTAT-TTTAT
1 ATATTATATTTAT
475099 ATATTAATATTTAT
1 ATATT-ATATTTAT
475113 ATATTATAT
1 ATATTATAT
475122 AATTAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 6 0.29
14 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTATATTTAT
Found at i:475658 original size:19 final size:20
Alignment explanation
Indices: 475635--475681 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
475625 TTGAAGCTTA
475635 TTTAATTA-T-TTATTATAT
1 TTTAATTATTATTATTATAT
*
475653 TATTAAAATATTATTATTATAT
1 T-TT-AATTATTATTATTATAT
475675 TTTAATT
1 TTTAATT
475682 TATATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
18 1 0.04
19 2 0.09
20 7 0.30
21 3 0.13
22 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAATTATTATTATTATAT
Found at i:476387 original size:21 final size:19
Alignment explanation
Indices: 476361--476408 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
476351 GAACATTAAA
476361 TTTTTAGATCAGATTATAATT
1 TTTTTA-ATC-GATTATAATT
* *
476382 TTTTTATTCTATTATAATT
1 TTTTTAATCGATTATAATT
476401 TTTTTAAT
1 TTTTTAAT
476409 TTTATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 2 0.08
21 6 0.25
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTTAATCGATTATAATT
Found at i:482098 original size:19 final size:18
Alignment explanation
Indices: 482071--482107 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
482061 CTTTTAAGTA
482071 TAATAAAAAATAAAAAAAT
1 TAAT-AAAAATAAAAAAAT
*
482090 TAATTAAAATAAAAAAAT
1 TAATAAAAATAAAAAAAT
482108 AAAATATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
TAATAAAAATAAAAAAAT
Found at i:483393 original size:35 final size:35
Alignment explanation
Indices: 483311--483382 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
483301 ATATTGGCTA
* * **
483311 TACATTAACTGTATAATGTTATGATGTATTAGTTG
1 TACATTAACTGTACAATATTATGACATATTAGTTG
483346 TACATTAACTGTACAATATTATGACATATTAGTTG
1 TACATTAACTGTACAATATTATGACATATTAGTTG
483381 TA
1 TA
483383 TGTTAGCTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (35 bp):
TACATTAACTGTACAATATTATGACATATTAGTTG
Found at i:485470 original size:35 final size:35
Alignment explanation
Indices: 485422--485512 Score: 101
Period size: 35 Copynumber: 2.6 Consensus size: 35
485412 TTAGTAATGT
* * * *
485422 TGTATTGGCTGTACATTAGCTATATAATGTTATAA
1 TGTATTAGTTGTACATTAGCTATACAATATTATAA
** *
485457 TGTATTAGTTGTACATTAATTATACAATATTATGA
1 TGTATTAGTTGTACATTAGCTATACAATATTATAA
**
485492 CATATTAGTTGTACATTAGCT
1 TGTATTAGTTGTACATTAGCT
485513 GTAGTTATTG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (35 bp):
TGTATTAGTTGTACATTAGCTATACAATATTATAA
Found at i:489638 original size:2 final size:2
Alignment explanation
Indices: 489631--489657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
489621 TCCCTCCCTT
489631 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 T
489658 TTAACTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:490168 original size:15 final size:15
Alignment explanation
Indices: 490059--490170 Score: 55
Period size: 16 Copynumber: 6.7 Consensus size: 15
490049 ACCGATCCAA
490059 TAAATTTAATTTATAT
1 TAAATTTAATTTAT-T
* **
490075 TAAATTAAATTTAAA
1 TAAATTTAATTTATT
*
490090 TAAATTT-TTTTATTT
1 TAAATTTAATTTA-TT
*
490105 GTATAGTTTTAATTTAATT
1 -TA-A-ATTTAATTT-ATT
490124 TAAATTATTAATTATATAAT
1 TAAA-T-TTAATT-TAT--T
*
490144 AAAATATTAATTTATT
1 TAAAT-TTAATTTATT
490160 TAAATTTAATT
1 TAAATTTAATT
490171 ATAAATTTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
14 4 0.05
15 12 0.16
16 19 0.26
17 3 0.04
18 16 0.22
19 14 0.19
20 5 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TAAATTTAATTTATT
Found at i:490186 original size:13 final size:13
Alignment explanation
Indices: 490156--490187 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
490146 AATATTAATT
490156 TATT-TAAATTTA
1 TATTATAAATTTA
490168 -ATTATAAATTTA
1 TATTATAAATTTA
490180 TATTATAA
1 TATTATAA
490188 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 8 0.44
13 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTATAAATTTA
Found at i:491651 original size:2 final size:2
Alignment explanation
Indices: 491644--491675 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
491634 CAAGTTTTTC
491644 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
491676 TGAAGATTAT
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:494532 original size:27 final size:27
Alignment explanation
Indices: 494481--494541 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 27
494471 CATGATAGAT
* *
494481 AAATATTTTAAAATTTATATAAATATA
1 AAATATTTTAAAATATATATAAATAAA
494508 AAATATTTT-AAATATA-ATTATAATAAA
1 AAATATTTTAAAATATATA-TA-AATAAA
494535 ATAATAT
1 A-AATAT
494542 ATACGAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 1 0.03
26 8 0.28
27 15 0.52
28 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AAATATTTTAAAATATATATAAATAAA
Found at i:494816 original size:15 final size:14
Alignment explanation
Indices: 494785--494837 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
494775 TTAATAATTT
*
494785 TAAATATAATTATA
1 TAAATATAATCATA
494799 TAAATATAATACATA
1 TAAATATAAT-CATA
494814 TAAATATTAA--ATA
1 TAAATA-TAATCATA
*
494827 TAATTATAATC
1 TAAATATAATC
494838 TAATATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 3 0.09
13 8 0.24
14 10 0.30
15 9 0.27
16 3 0.09
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATAATCATA
Found at i:494829 original size:13 final size:14
Alignment explanation
Indices: 494785--494828 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
494775 TTAATAATTT
*
494785 TAAATATAATTATA
1 TAAATATAAATATA
*
494799 TAAATATAATACATA
1 TAAATATAA-ATATA
494814 TAAATATTAAATATA
1 TAAATA-TAAATATA
494829 ATTATAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 13 0.52
16 3 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATATAAATATA
Found at i:494974 original size:22 final size:21
Alignment explanation
Indices: 494944--494991 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
494934 TTATACAGTC
*
494944 AATTAAAATT-TAATAAGTTTAA
1 AATTTAAATTCTAA-AA-TTTAA
*
494966 AATTTAAATTCTAAAATTTAT
1 AATTTAAATTCTAAAATTTAA
494987 AATTT
1 AATTT
494992 TTTTTATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 11 0.48
23 3 0.13
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AATTTAAATTCTAAAATTTAA
Found at i:494982 original size:14 final size:15
Alignment explanation
Indices: 494947--494990 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
494937 TACAGTCAAT
494947 TAAAATTTAATAAGTT-
1 TAAAATTT-ATAA-TTC
494963 TAAAATTTA-AATTC
1 TAAAATTTATAATTC
494977 TAAAATTTATAATT
1 TAAAATTTATAATT
494991 TTTTTTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.08
14 11 0.42
15 5 0.19
16 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
TAAAATTTATAATTC
Found at i:495657 original size:23 final size:23
Alignment explanation
Indices: 495606--495662 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
495596 TTTGTTAGAG
* * *
495606 TAATTTTTTTTA-AGTTAGTTAA
1 TAATTTTATTTATAGTAAATTAA
495628 T-ATTTTATTTATAGTAAATTAA
1 TAATTTTATTTATAGTAAATTAA
495650 TAATTTTATTTAT
1 TAATTTTATTTAT
495663 TATTTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.30
22 10 0.33
23 11 0.37
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (23 bp):
TAATTTTATTTATAGTAAATTAA
Found at i:496340 original size:30 final size:31
Alignment explanation
Indices: 496299--496388 Score: 112
Period size: 32 Copynumber: 2.9 Consensus size: 31
496289 TTAGATCGAT
496299 ATTAATTATAAATTTAATAA-ATTAAATATA
1 ATTAATTATAAATTTAATAATATTAAATATA
* *
496329 ATTATTTATAAATTTAATAAATATTAGATATA
1 ATTAATTATAAATTTAAT-AATATTAAATATA
*
496361 A-TAACTCATAAATTTAATAATTATTAAA
1 ATTAA-TTATAAATTTAATAA-TATTAAA
496389 AGTTTTAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
30 17 0.33
31 6 0.12
32 28 0.55
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (31 bp):
ATTAATTATAAATTTAATAATATTAAATATA
Found at i:496354 original size:22 final size:22
Alignment explanation
Indices: 496310--496354 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
496300 TTAATTATAA
*
496310 ATTTAATAAATTAAATATAATT
1 ATTTAATAAATTAAATAAAATT
*
496332 ATTT-ATAAATTTAATAAATATT
1 ATTTAATAAATTAAATAAA-ATT
496354 A
1 A
496355 GATATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAATAAATTAAATAAAATT
Found at i:496388 original size:16 final size:16
Alignment explanation
Indices: 496301--496388 Score: 69
Period size: 16 Copynumber: 5.7 Consensus size: 16
496291 AGATCGATAT
496301 TAATTA-TAAATTTAA
1 TAATTATTAAATTTAA
*
496316 TAA--ATTAAATATAA
1 TAATTATTAAATTTAA
*
496330 TTATT-TATAAATTTAA
1 TAATTAT-TAAATTTAA
* * *
496346 TAAATATTAGATATAA
1 TAATTATTAAATTTAA
*
496362 TAACTCA-TAAATTTAA
1 TAA-TTATTAAATTTAA
496378 TAATTATTAAA
1 TAATTATTAAA
496389 AGTTTTAATT
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
13 1 0.02
14 10 0.19
15 6 0.11
16 35 0.65
17 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (16 bp):
TAATTATTAAATTTAA
Found at i:496749 original size:19 final size:19
Alignment explanation
Indices: 496725--496800 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
496715 TGAGATTCCG
*
496725 ATTTTATCTATTTATATAA
1 ATTTTATATATTTATATAA
496744 ATTTTAATATATTTATATAA
1 ATTTT-ATATATTTATATAA
* * *
496764 AATTTATATTATTTTTATATC
1 ATTTTATA-TATTTATATA-A
*
496785 ATATTATATA-TTATAT
1 ATTTTATATATTTATAT
496801 TTTAAATATT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 13 0.28
20 28 0.60
21 6 0.13
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTATATATTTATATAA
Found at i:496780 original size:22 final size:21
Alignment explanation
Indices: 496735--496804 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
496725 ATTTTATCTA
* *
496735 TTTATATAAATTT-TAATATA
1 TTTATATAAATTTATATTATT
496755 TTTATATAAAATTTATATTATT
1 TTTATAT-AAATTTATATTATT
*
496777 TTTATATCATATTATATATTATAT
1 TTTATAT-AAATT-TATATTAT-T
496801 TTTA
1 TTTA
496805 AATATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.17
21 6 0.14
22 16 0.38
23 8 0.19
24 5 0.12
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATATAAATTTATATTATT
Found at i:496811 original size:34 final size:34
Alignment explanation
Indices: 496745--496841 Score: 67
Period size: 34 Copynumber: 2.9 Consensus size: 34
496735 TTTATATAAA
* * * *
496745 TTTTA-AT-ATATTTATATAAAATTTATATTATT
1 TTTTATATCATATTTATATTATATTTAAAATATT
* *
496777 TTTATATCAT-AT-TATATATTATATTTTAAATATT
1 TTT-TAT-ATCATATTTATATTATATTTAAAATATT
* **
496811 TTTTATTTTTTATTTATATTATATTTAAAAT
1 TTTTATATCATATTTATATTATATTTAAAAT
496842 TATTACTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
32 4 0.08
33 6 0.12
34 36 0.72
35 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (34 bp):
TTTTATATCATATTTATATTATATTTAAAATATT
Found at i:499494 original size:2 final size:2
Alignment explanation
Indices: 499487--499537 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
499477 GGGAAATCTG
*
499487 GA GA GA GA GA GA GA GA GA GG 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
499529 GA GA GA GA G
1 GA GA GA GA G
499538 GAATTAGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:505546 original size:117 final size:117
Alignment explanation
Indices: 505340--505574 Score: 416
Period size: 117 Copynumber: 2.0 Consensus size: 117
505330 CGGTCATTAG
* *
505340 ATTCGACAAATCAGAGTGAGAAATCCAGGGAGAGCTCTGTTAGTCTCTCCGATAAAAGTTTTGCA
1 ATTCGACAAATCAGAGTGAGAAATCCAGGGAGAGCTCTGTTAGTCGCTCCGATAAAAGTGTTGCA
*
505405 TGCATAAAATGCAATGAAATGGGTCATACAGCTGAATATTGCTTGGTCTCTC
66 TGCATAAAATGCAATGAAACGGGTCATACAGCTGAATATTGCTTGGTCTCTC
* **
505457 ATTCGACAAATCAGAGTGAGAAATCTAGGGAGAGCTCTGTTAGTCGCTCCTCTAAAAGTGTTGCA
1 ATTCGACAAATCAGAGTGAGAAATCCAGGGAGAGCTCTGTTAGTCGCTCCGATAAAAGTGTTGCA
505522 TGCATAAAATGCAATGAAACGGGTCATACAGCTGAATATTGCTTGGTCTCTC
66 TGCATAAAATGCAATGAAACGGGTCATACAGCTGAATATTGCTTGGTCTCTC
505574 A
1 A
505575 GGCTTCTGGG
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 112 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (117 bp):
ATTCGACAAATCAGAGTGAGAAATCCAGGGAGAGCTCTGTTAGTCGCTCCGATAAAAGTGTTGCA
TGCATAAAATGCAATGAAACGGGTCATACAGCTGAATATTGCTTGGTCTCTC
Found at i:512108 original size:21 final size:21
Alignment explanation
Indices: 512084--512126 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
512074 AATTTAATTT
512084 TTTTAAAAAAAAATTTTAAAA
1 TTTTAAAAAAAAATTTTAAAA
****
512105 TTTTTTTTAAAAATTTTAAAA
1 TTTTAAAAAAAAATTTTAAAA
512126 T
1 T
512127 ACATATATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAAAAAAATTTTAAAA
Found at i:513111 original size:19 final size:19
Alignment explanation
Indices: 513075--513112 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
513065 ATTTAAAAGA
*
513075 TATTTTTTATTGATTAAAT
1 TATTTTTTATTGAATAAAT
513094 TATTTTTTA-TGAAATAAAT
1 TATTTTTTATTG-AATAAAT
513113 ACCAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TATTTTTTATTGAATAAAT
Found at i:513801 original size:17 final size:17
Alignment explanation
Indices: 513779--513812 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
513769 AAAAAATCAT
513779 TTTTAAA-TTTTATTTAA
1 TTTTAAAGTTTT-TTTAA
513796 TTTTAAAGTTTTTTTAA
1 TTTTAAAGTTTTTTTAA
513813 AAATATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTAAAGTTTTTTTAA
Found at i:514309 original size:19 final size:16
Alignment explanation
Indices: 514287--514328 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 16
514277 AATAAAGATG
514287 TTAAAATATAATATAATA
1 TTAAAATATAA-A-AATA
514305 TTTAAAATATAAAAATA
1 -TTAAAATATAAAAATA
514322 TTAAAAT
1 TTAAAAT
514329 TTATATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 1 0.04
19 11 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAATATAAAAATA
Found at i:514351 original size:20 final size:20
Alignment explanation
Indices: 514296--514351 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 20
514286 GTTAAAATAT
*
514296 AATATAATATTTAAAATATAAA
1 AATATAATATTT--TATATAAA
*
514318 AATATTAA-AATTTATATAAA
1 AATA-TAATATTTTATATAAA
*
514338 TATATAATATTTTA
1 AATATAATATTTTA
514352 AATATGATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 3 0.11
20 15 0.54
22 7 0.25
23 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATATAATATTTTATATAAA
Found at i:514446 original size:9 final size:9
Alignment explanation
Indices: 514432--514469 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
514422 TATGAATATT
514432 TTAAAAAAA
1 TTAAAAAAA
514441 TT-AAAAAA
1 TTAAAAAAA
514449 TT-AAAAAA
1 TTAAAAAAA
*
514457 TTAAAAAAT
1 TTAAAAAAA
514466 TTAA
1 TTAA
514470 TAATAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 16 0.59
9 11 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:514454 original size:7 final size:8
Alignment explanation
Indices: 514435--514466 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
514425 GAATATTTTA
514435 AAAAAATT
1 AAAAAATT
514443 AAAAAATT
1 AAAAAATT
514451 AAAAAATT
1 AAAAAATT
514459 AAAAAATT
1 AAAAAATT
514467 TAATAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAAAATT
Found at i:514804 original size:13 final size:13
Alignment explanation
Indices: 514786--514843 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
514776 ATACGATAAT
514786 TTATATATTTATA
1 TTATATATTTATA
514799 TTATAT-TTATATA
1 TTATATATT-TATA
*
514812 TT-T-TATTTTTA
1 TTATATATTTATA
*
514823 TAATAT-TTTATA
1 TTATATATTTATA
514835 TTTATATAT
1 -TTATATAT
514844 ATTTTAATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
11 5 0.14
12 11 0.31
13 18 0.51
14 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:514822 original size:15 final size:16
Alignment explanation
Indices: 514785--514849 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 16
514775 AATACGATAA
514785 TTTATATATTTATATTAT
1 TTTATATATTT-TA-TAT
514803 ATTTATATATTTTAT-T
1 -TTTATATATTTTATAT
514819 TTTATAATATTTTATAT
1 TTTAT-ATATTTTATAT
514836 TTATATATATTTTA
1 TT-TATATATTTTA
514850 ATACTTAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.12
16 10 0.23
17 12 0.28
18 5 0.12
19 11 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATATATTTTATAT
Found at i:515428 original size:20 final size:20
Alignment explanation
Indices: 515405--515465 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
515395 AATATTTGAC
515405 ATGTTTAAATTCA-AATTTTT
1 ATGTTTAAATT-ATAATTTTT
* *
515425 ATGTTTATATTTATATTTTTT
1 ATGTTTA-AATTATAATTTTT
*
515446 ATTTTTAAATTATAATTTTT
1 ATGTTTAAATTATAATTTTT
515466 TTAAAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (20 bp):
ATGTTTAAATTATAATTTTT
Found at i:515446 original size:21 final size:21
Alignment explanation
Indices: 515405--515466 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
515395 AATATTTGAC
515405 ATGTTTAAATTCA-AA-TTTTT
1 ATGTTTAAATT-ATAATTTTTT
*
515425 ATGTTTATATT-TATATTTTTT
1 ATGTTTAAATTATA-ATTTTTT
*
515446 ATTTTTAAATTATAATTTTTT
1 ATGTTTAAATTATAATTTTTT
515467 TAAAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 21 0.60
22 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (21 bp):
ATGTTTAAATTATAATTTTTT
Found at i:515605 original size:14 final size:13
Alignment explanation
Indices: 515556--515605 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
515546 TTTATTTAAA
515556 ATATTAAAATTTTT
1 ATATT-AAATTTTT
*
515570 ATATT-AATTATT
1 ATATTAAATTTTT
*
515582 ATA-TATATTTTT
1 ATATTAAATTTTT
515594 ATAATTAAATTT
1 AT-ATTAAATTT
515606 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
11 1 0.03
12 16 0.55
13 1 0.03
14 11 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATTAAATTTTT
Found at i:516262 original size:20 final size:20
Alignment explanation
Indices: 516220--516267 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
516210 TTATATCAAG
* * *
516220 ATACATGATTTATATTTATA
1 ATACATGATTAATATCTAAA
516240 ATACATGATTAATATCTAAA
1 ATACATGATTAATATCTAAA
*
516260 ATAAATGA
1 ATACATGA
516268 AAAATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (20 bp):
ATACATGATTAATATCTAAA
Found at i:516654 original size:19 final size:18
Alignment explanation
Indices: 516613--516656 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
516603 TTTGTTTTTT
516613 TTTTAAATTTTGATTTGA
1 TTTTAAATTTTGATTTGA
516631 TTTTTAAATTTTAGATTATG-
1 -TTTTAAATTTT-GATT-TGA
516651 TTTTAA
1 TTTTAA
516657 TACTTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 17 0.74
20 4 0.17
21 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (18 bp):
TTTTAAATTTTGATTTGA
Found at i:519791 original size:156 final size:156
Alignment explanation
Indices: 519507--519821 Score: 567
Period size: 156 Copynumber: 2.0 Consensus size: 156
519497 GAATCAAGGA
*
519507 ATGCTTCATTTTTTGAAGATTTATTTCCCTACAAGAGAACACAAGAAAATAAAGTTACAAAGAGA
1 ATGCTTCATTTTTTGAAGATGTATTTCCCTACAAGAGAACACAAGAAAATAAAGTTACAAAGAGA
*
519572 GCCCATGAGGACTCGAGTAGTGATCCACAAATGGCTGAGGAAGAACAAATACAACTTCGAAAGAG
66 GCCCATAAGGACTCGAGTAGTGATCCACAAATGGCTGAGGAAGAACAAATACAACTTCGAAAGAG
*
519637 TAAACGTGCTAAAGTACCGATCACTT
131 TAAACGTGCTAAAGTACCGACCACTT
519663 ATGCTTCATTTTTTGAAGATGTATTTCCCTACAAGAGAACACAAGAAAATAAAGTTACAAAGAGA
1 ATGCTTCATTTTTTGAAGATGTATTTCCCTACAAGAGAACACAAGAAAATAAAGTTACAAAGAGA
* * *
519728 GCCCATAAGGACTCGAGTAGTGTTCCACAAGTGGCTGAGGAGGAACAAATACAACTTCGAAAGAG
66 GCCCATAAGGACTCGAGTAGTGATCCACAAATGGCTGAGGAAGAACAAATACAACTTCGAAAGAG
*
519793 TAAACGTGTTAAAGTACCGACCACTT
131 TAAACGTGCTAAAGTACCGACCACTT
519819 ATG
1 ATG
519822 GTCTAGATTT
Statistics
Matches: 152, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
156 152 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (156 bp):
ATGCTTCATTTTTTGAAGATGTATTTCCCTACAAGAGAACACAAGAAAATAAAGTTACAAAGAGA
GCCCATAAGGACTCGAGTAGTGATCCACAAATGGCTGAGGAAGAACAAATACAACTTCGAAAGAG
TAAACGTGCTAAAGTACCGACCACTT
Found at i:523701 original size:39 final size:39
Alignment explanation
Indices: 523652--523729 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
523642 AAGTGAAAGT
* *
523652 AAATGTTTTTA-TGAATTGAACTATAATTTAAAAATTTTTA
1 AAATGTTTTTATTAAATTGAAAT-TAATTT-AAAATTTTTA
*
523692 AAAT-TTTTTATTAAATTTAAATTAATTTAAAATTTTTA
1 AAATGTTTTTATTAAATTGAAATTAATTTAAAATTTTTA
523730 TTATTATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 10 0.29
39 12 0.35
40 12 0.35
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (39 bp):
AAATGTTTTTATTAAATTGAAATTAATTTAAAATTTTTA
Found at i:523708 original size:29 final size:30
Alignment explanation
Indices: 523673--523741 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
523663 TGAATTGAAC
523673 TATAATTTAAAAATT-TTTAAAATTTTTTAT
1 TATAATTTAAAAATTATTTAAAA-TTTTTAT
523703 TA-AATTT--AAATTAATTTAAAATTTTTAT
1 TATAATTTAAAAATT-ATTTAAAATTTTTAT
*
523731 TATTATTTAAA
1 TATAATTTAAA
523742 TAAAATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
27 5 0.15
28 9 0.27
29 16 0.48
30 2 0.06
31 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TATAATTTAAAAATTATTTAAAATTTTTAT
Found at i:523742 original size:29 final size:29
Alignment explanation
Indices: 523688--523752 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
523678 TTTAAAAATT
*
523688 TTTAAAATTTTTTATTAAATTTAAATTAA
1 TTTAAAATTTTTTATTAAATTTAAATAAA
*
523717 TTTAAAA-TTTTTATTATTATTTAAATAAA
1 TTTAAAATTTTTTATTA-AATTTAAATAAA
*
523746 ATTAAAA
1 TTTAAAA
523753 ATTAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 9 0.28
29 23 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAAAATTTTTTATTAAATTTAAATAAA
Found at i:523751 original size:39 final size:39
Alignment explanation
Indices: 523675--523751 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
523665 AATTGAACTA
* * *
523675 TAATTTAAAAATTTTTAAAATTTTTTATTAAATTTAAAT
1 TAATTTAAAAATTTTTAAAATTTTTAAATAAAATTAAAT
**
523714 TAATTT-AAAATTTTTATTATTATTTAAATAAAATTAAA
1 TAATTTAAAAATTTTTAAAATT-TTTAAATAAAATTAAA
523752 AATTAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 13 0.41
39 19 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (39 bp):
TAATTTAAAAATTTTTAAAATTTTTAAATAAAATTAAAT
Found at i:523772 original size:9 final size:9
Alignment explanation
Indices: 523760--523843 Score: 55
Period size: 9 Copynumber: 9.1 Consensus size: 9
523750 AAAATTAAAA
523760 AAATTAATT
1 AAATTAATT
523769 AAATTAATT
1 AAATTAATT
*
523778 AAATTTAAAT
1 AAA-TTAATT
*
523788 AAAATAATTTT
1 AAATTAA--TT
* *
523799 TAATTATTT
1 AAATTAATT
523808 AAA-TAA-T
1 AAATTAATT
*
523815 AATTTAAATT
1 AAATT-AATT
* *
523825 AAATTTATC
1 AAATTAATT
523834 AAATTAATT
1 AAATTAATT
523843 A
1 A
523844 CGTAAATAAT
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 31 0.56
10 13 0.24
11 5 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (9 bp):
AAATTAATT
Found at i:526136 original size:17 final size:19
Alignment explanation
Indices: 526114--526155 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
526104 TAAAAAATAG
526114 TTTTTAAGT-AATAATTA-
1 TTTTTAAGTAAATAATTAC
526131 TTTTT-AGTAAATAATTAC
1 TTTTTAAGTAAATAATTAC
526149 TTTTTAA
1 TTTTTAA
526156 AAATAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
18 5 0.23
19 1 0.05
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTTAAGTAAATAATTAC
Found at i:526159 original size:17 final size:17
Alignment explanation
Indices: 526123--526161 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
526113 GTTTTTAAGT
*
526123 AATAATTATTTTTAGTA
1 AATAATTATTTTTAGAA
526140 AATAATTACTTTTTA-AA
1 AATAATTA-TTTTTAGAA
526157 AATAA
1 AATAA
526162 CAAAAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
AATAATTATTTTTAGAA
Found at i:526301 original size:5 final size:5
Alignment explanation
Indices: 526288--526330 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
526278 TTATAATAGT
* * * *
526288 ATTAG ATTAA ATTAA AATAA AATAA AATAA ATTAA ATTAA ATT
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATT
526331 TAAGAAGGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (5 bp):
ATTAA
Found at i:527249 original size:56 final size:57
Alignment explanation
Indices: 527163--527277 Score: 214
Period size: 56 Copynumber: 2.0 Consensus size: 57
527153 ATTTTGGGTA
527163 TGTAAACTGATCAGAATCTGTTTGACTAAAATC-TCTGTATCGGATGTTATCTGATG
1 TGTAAACTGATCAGAATCTGTTTGACTAAAATCTTCTGTATCGGATGTTATCTGATG
527219 TGTAAACTGATCAGAATCTGTTTGACTAAAATCTTTCTGTATCGGATGTTATCTGATG
1 TGTAAACTGATCAGAATCTGTTTGACTAAAATC-TTCTGTATCGGATGTTATCTGATG
527277 T
1 T
527278 TTTTGATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
56 33 0.58
58 24 0.42
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (57 bp):
TGTAAACTGATCAGAATCTGTTTGACTAAAATCTTCTGTATCGGATGTTATCTGATG
Found at i:528873 original size:15 final size:17
Alignment explanation
Indices: 528848--528880 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
528838 TATTTTTAAA
528848 AATATTTATATT-ATGT
1 AATATTTATATTAATGT
528864 AATA-TTATATTAATGT
1 AATATTTATATTAATGT
528880 A
1 A
528881 TTAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
AATATTTATATTAATGT
Found at i:528927 original size:2 final size:2
Alignment explanation
Indices: 528920--528956 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
528910 TTATGAATTG
528920 AT AT AT AT AT AT AT AT CAT 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
528957 TAACAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:530966 original size:13 final size:13
Alignment explanation
Indices: 530948--530984 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
530938 TTAAAATTTT
530948 ATTTTTATAATTA
1 ATTTTTATAATTA
530961 ATTTTTAT-A-T-
1 ATTTTTATAATTA
530971 ATTTTTATAATTA
1 ATTTTTATAATTA
530984 A
1 A
530985 ATAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 2 0.10
13 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTTTATAATTA
Found at i:530995 original size:23 final size:23
Alignment explanation
Indices: 530947--530995 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
530937 ATTAAAATTT
** *
530947 TATTTTTATAATTAATTTTTATA
1 TATTTTTATAATTAATAATTACA
530970 TATTTTTATAATTAAATAATT-CA
1 TATTTTTATAATT-AATAATTACA
530993 TAT
1 TAT
530996 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTTATAATTAATAATTACA
Found at i:531235 original size:29 final size:29
Alignment explanation
Indices: 531202--531261 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
531192 AAGTGCCCCT
* *
531202 TTTAACTCCAATAATTGTATTTTGATGGC
1 TTTAACTCCAATAATTGTACTTTGATCGC
531231 TTTAACTCCAATAATTGTACTTTGATCGC
1 TTTAACTCCAATAATTGTACTTTGATCGC
531260 TT
1 TT
531262 CTCAGCCGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.45
Consensus pattern (29 bp):
TTTAACTCCAATAATTGTACTTTGATCGC
Found at i:531419 original size:22 final size:21
Alignment explanation
Indices: 531369--531419 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
531359 TAAATAGGAT
**
531369 ATTTTATTGAAAATTTATTTG
1 ATTTTATTGAAAATTTATTAA
531390 ATTATTATTGAAAAAATTT-TTAA
1 ATT-TTATTG--AAAATTTATTAA
531413 ATTTTAT
1 ATTTTAT
531420 AAATAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 3 0.12
22 10 0.40
23 5 0.20
24 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTTTATTGAAAATTTATTAA
Found at i:532003 original size:21 final size:21
Alignment explanation
Indices: 531965--532004 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
531955 ATTTAAAAGC
*
531965 TATTTTATATTAATATTTATA
1 TATTTTAAATTAATATTTATA
531986 TATTTTAAAATTAA-ATTTA
1 TATTTT-AAATTAATATTTA
532005 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTAAATTAATATTTATA
Found at i:533461 original size:15 final size:15
Alignment explanation
Indices: 533433--533476 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
533423 TTATATTTTT
533433 ATAA-TTAAATTTAAA
1 ATAATTTAAA-TTAAA
*
533448 ATAATTTAAATTAAG
1 ATAATTTAAATTAAA
*
533463 TTAATTTAAATTAA
1 ATAATTTAAATTAA
533477 TAAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATAATTTAAATTAAA
Found at i:534764 original size:22 final size:22
Alignment explanation
Indices: 534724--534765 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
534714 ATATAAAATT
*
534724 TATTTTTATTTTAATATTTATA
1 TATTTTTATATTAATATTTATA
534746 TATTTTTATAATTAA-ATTTA
1 TATTTTTAT-ATTAATATTTA
534766 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTATATTAATATTTATA
Found at i:536214 original size:25 final size:25
Alignment explanation
Indices: 536186--536248 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
536176 TAATAATTAT
536186 TTTTAAATTATTAT-ATCTATATAAA
1 TTTTAAATTATTATAATC-ATATAAA
*
536211 TTTTATATT-TTAATAATCATATAAA
1 TTTTAAATTATT-ATAATCATATAAA
536236 -TTTAAATATATTA
1 TTTTAAAT-TATTA
536249 ATATATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
24 8 0.25
25 19 0.59
26 5 0.16
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTAAATTATTATAATCATATAAA
Found at i:536287 original size:22 final size:22
Alignment explanation
Indices: 536236--536295 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
536226 ATCATATAAA
* *
536236 TTTAAATATATTAATATATTTAT
1 TTTAATTATATT-TTATATTTAT
**
536259 CAT-ATTATATTTTATATTTAT
1 TTTAATTATATTTTATATTTAT
*
536280 TTTAATTATTTTTTAT
1 TTTAATTATATTTTAT
536296 TATATATTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 10 0.34
22 18 0.62
23 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTAATTATATTTTATATTTAT
Found at i:539405 original size:19 final size:19
Alignment explanation
Indices: 539381--539435 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
539371 TCACTACAAA
539381 ATATTTTTTAATATTTAAT
1 ATATTTTTTAATATTTAAT
* *
539400 ATA-TTTTAAATAATATAAT
1 ATATTTTTTAAT-ATTTAAT
*
539419 AAATTTTTTAA-ATTTAA
1 ATATTTTTTAATATTTAA
539436 CATGTTAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 12 0.41
19 11 0.38
20 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTTTTAATATTTAAT
Found at i:540077 original size:21 final size:21
Alignment explanation
Indices: 540053--540099 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
540043 ATATAGATAT
*
540053 AATATAAAATAATTAAAATAA
1 AATATAAAATAAATAAAATAA
* *
540074 AATATAATATAAATATAATAA
1 AATATAAAATAAATAAAATAA
*
540095 GATAT
1 AATAT
540100 GTAAAAGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AATATAAAATAAATAAAATAA
Found at i:540093 original size:16 final size:16
Alignment explanation
Indices: 540038--540093 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
540028 GTGATAAGAT
540038 TATATATATAGATAT-AA
1 TATA-ATATA-ATATAAA
*
540055 TATAAAATAAT-TAAAA
1 TATAATATAATAT-AAA
*
540071 TAAAATATAATATAAA
1 TATAATATAATATAAA
540087 TATAATA
1 TATAATA
540094 AGATATGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
14 1 0.03
15 2 0.06
16 24 0.75
17 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TATAATATAATATAAA
Found at i:540144 original size:8 final size:8
Alignment explanation
Indices: 540131--540165 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
540121 TAATATAAAT
540131 TATTAATA
1 TATTAATA
540139 TATTAATA
1 TATTAATA
540147 TATATAATA
1 TAT-TAATA
540156 TATTAA-A
1 TATTAATA
540163 TAT
1 TAT
540166 AATTATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.15
8 14 0.54
9 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
TATTAATA
Found at i:540151 original size:25 final size:26
Alignment explanation
Indices: 540123--540184 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
540113 AATTTATGTA
540123 ATATAAAT-TATT-AATAT-ATTAAT-
1 ATATAAATATATTAAATATAATT-ATG
540146 ATATATAATATATTAAATATAATTATG
1 ATATA-AATATATTAAATATAATTATG
*
540173 ATATAAAAATAT
1 ATATAAATATAT
540185 ACCAATCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 5 0.15
24 3 0.09
25 4 0.12
26 13 0.39
27 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
ATATAAATATATTAAATATAATTATG
Found at i:540176 original size:18 final size:17
Alignment explanation
Indices: 540134--540166 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
540124 TATAAATTAT
540134 TAATATATTAATATATA
1 TAATATATTAATATATA
540151 TAATATATTAA-ATATA
1 TAATATATTAATATATA
540167 ATTATGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATATTAATATATA
Found at i:540888 original size:30 final size:30
Alignment explanation
Indices: 540854--540920 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
540844 ATCAAATAAA
* *
540854 CCCTTAACTTTTAATTTTTACCTAAACAAG
1 CCCTTAACTTTTAATTTATACATAAACAAG
*
540884 CCCTTAACTTTTAATTTATATATAAACAAG
1 CCCTTAACTTTTAATTTATACATAAACAAG
*
540914 CTCTTAA
1 CCCTTAA
540921 ATTAATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (30 bp):
CCCTTAACTTTTAATTTATACATAAACAAG
Found at i:543513 original size:20 final size:21
Alignment explanation
Indices: 543470--543516 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
543460 TAGCCTGTAG
*
543470 TTCTTCTATTTCTCCCCCAAT
1 TTCTTCTAGTTCTCCCCCAAT
*
543491 TTCTTCTAGTTCT-CCCTAAT
1 TTCTTCTAGTTCTCCCCCAAT
543511 TTCTTC
1 TTCTTC
543517 AAATCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.13, C:0.34, G:0.02, T:0.51
Consensus pattern (21 bp):
TTCTTCTAGTTCTCCCCCAAT
Found at i:544441 original size:2 final size:2
Alignment explanation
Indices: 544434--544469 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
544424 AGACTGTTAA
544434 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
544470 GAGTTCAATG
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:548917 original size:2 final size:2
Alignment explanation
Indices: 548910--548946 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
548900 CTTTAAAAGA
548910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
548947 AATTCAAAAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:551259 original size:22 final size:22
Alignment explanation
Indices: 551214--551264 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
551204 TGATATTTAA
*
551214 TAATTA-AAAATTATTTAAATT
1 TAATTATAAAATTATATAAATT
551235 TAATTATAAAA-TATATAAATAT
1 TAATTATAAAATTATATAAAT-T
*
551257 TAAGTATA
1 TAATTATA
551265 TTGTTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAATTATAAAATTATATAAATT
Found at i:551757 original size:29 final size:30
Alignment explanation
Indices: 551672--551757 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
551662 ATTATTATTC
*
551672 AAAATTAAATTTAATATTTTAAATA-TAAAA
1 AAAATTAATTTTAATA-TTTAAATATTAAAA
*
551702 AAAATTAATTTTATTATTTAAAATATTAAAA
1 AAAATTAATTTTAATATTT-AAATATTAAAA
* *
551733 AATA-TATTTTTAATATTTAAATATT
1 AAAATTAATTTTAATATTTAAATATT
551758 TTTATGATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
29 10 0.20
30 31 0.63
31 8 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
AAAATTAATTTTAATATTTAAATATTAAAA
Found at i:556075 original size:32 final size:32
Alignment explanation
Indices: 556034--556132 Score: 198
Period size: 32 Copynumber: 3.1 Consensus size: 32
556024 CTATCGAGTC
556034 TGTTTTCTTTATATCCAAGTTCTGCCTTGTAA
1 TGTTTTCTTTATATCCAAGTTCTGCCTTGTAA
556066 TGTTTTCTTTATATCCAAGTTCTGCCTTGTAA
1 TGTTTTCTTTATATCCAAGTTCTGCCTTGTAA
556098 TGTTTTCTTTATATCCAAGTTCTGCCTTGTAA
1 TGTTTTCTTTATATCCAAGTTCTGCCTTGTAA
556130 TGT
1 TGT
556133 CTTTGTTGCT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (32 bp):
TGTTTTCTTTATATCCAAGTTCTGCCTTGTAA
Found at i:559073 original size:4 final size:4
Alignment explanation
Indices: 559064--559099 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
559054 AATATAAGTA
*
559064 TATT TATT TATT TATT TATT TATTT TGTT TATT TAT
1 TATT TATT TATT TATT TATT TA-TT TATT TATT TAT
559100 AAAATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.90
5 3 0.10
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:559401 original size:24 final size:24
Alignment explanation
Indices: 559374--559419 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
559364 TTTATATGTT
559374 TCAAGTTTCAATTATTT-ATAAAGG
1 TCAAGTTTCAATT-TTTCATAAAGG
* *
559398 TCAATTTTTAATTTTTCATAAA
1 TCAAGTTTCAATTTTTCATAAA
559420 TATTTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.48
Consensus pattern (24 bp):
TCAAGTTTCAATTTTTCATAAAGG
Found at i:559823 original size:86 final size:85
Alignment explanation
Indices: 559726--559882 Score: 197
Period size: 85 Copynumber: 1.8 Consensus size: 85
559716 TTTTTTTATA
* * * * * * * *
559726 TGTTATTTTCATGTCGTATTTTAATTCATCTCATATTTTGTATTATTTATTATCGTAATTCAATT
1 TGTTATGTTCATATCATATCTTAATTCATCGCATA-TTTGTATAATTTATTATAGTAACTCAATT
*
559791 TAAAAAATTTTTGTGTATTTG
65 CAAAAAATTTTTGTGTATTTG
* * *
559812 TGTTATGTTCATATCATATCTTAATTCATGGCGTATTTGTATAATTTGTTATAGTAACTCAATTC
1 TGTTATGTTCATATCATATCTTAATTCATCGCATATTTGTATAATTTATTATAGTAACTCAATTC
559877 AAAAAA
66 AAAAAA
559883 AATTTTACAT
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
85 31 0.53
86 28 0.47
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (85 bp):
TGTTATGTTCATATCATATCTTAATTCATCGCATATTTGTATAATTTATTATAGTAACTCAATTC
AAAAAATTTTTGTGTATTTG
Found at i:559883 original size:86 final size:86
Alignment explanation
Indices: 559726--559888 Score: 193
Period size: 86 Copynumber: 1.9 Consensus size: 86
559716 TTTTTTTATA
* * * * * * * *
559726 TGTTATTTTCATGTCGTATTTTAATTCATCTCATATTTTGTATTATTTATTATCGTAATTCAATT
1 TGTTATGTTCATATCATATCTTAATTCATCGCATATTTTGTATAATTTATTATAGTAACTCAATT
* *
559791 TAAAAAATTTTTGTGTATTTG
66 AAAAAAAATTTTGTGTATTTG
* * *
559812 TGTTATGTTCATATCATATCTTAATTCATGGCGTA-TTTGTATAATTTGTTATAGTAACTCAATT
1 TGTTATGTTCATATCATATCTTAATTCATCGCATATTTTGTATAATTTATTATAGTAACTCAATT
559876 CAAAAAAAATTTT
66 -AAAAAAAATTTT
559889 ACATATTCAT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
85 25 0.40
86 38 0.60
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (86 bp):
TGTTATGTTCATATCATATCTTAATTCATCGCATATTTTGTATAATTTATTATAGTAACTCAATT
AAAAAAAATTTTGTGTATTTG
Found at i:559981 original size:18 final size:17
Alignment explanation
Indices: 559960--560066 Score: 58
Period size: 18 Copynumber: 6.1 Consensus size: 17
559950 AAATTTTTAC
559960 ATATTAATAATTTATTTT
1 ATATT-ATAATTTATTTT
***
559978 ATA-TA-AATTTTAACGT
1 ATATTATAA-TTTATTTT
559994 AT-TTATATATTTATATTT
1 ATATTATA-ATTTAT-TTT
* *
560012 ATATTTTAATATTATATT
1 ATATTATAAT-TTATTTT
*
560030 ATATTTTAATTATATTTT
1 ATATTATAATT-TATTTT
**
560048 ATAAAATAATTTAATTTT
1 ATATTATAATTT-ATTTT
560066 A
1 A
560067 ATTTTAAATT
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
15 2 0.03
16 10 0.15
17 8 0.12
18 40 0.59
19 8 0.12
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (17 bp):
ATATTATAATTTATTTT
Found at i:559981 original size:32 final size:34
Alignment explanation
Indices: 559944--560015 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 34
559934 ATATTATAAA
*
559944 TTATATAAATTTTTACATATTAATA-ATTTAT-T
1 TTATATAAATTTTAACATATTAATATATTTATAT
* *
559976 TTATATAAATTTTAACGTATTTATATATTTATAT
1 TTATATAAATTTTAACATATTAATATATTTATAT
560010 TTATAT
1 TTATAT
560016 TTTAATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 22 0.63
33 6 0.17
34 7 0.20
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (34 bp):
TTATATAAATTTTAACATATTAATATATTTATAT
Found at i:560314 original size:5 final size:5
Alignment explanation
Indices: 560272--560331 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
560262 CTATTCTTTA
* * *
560272 AATTT ATTTT TATTT AAATTT AAATTT AAATTT GATTT AATTT AATTT
1 AATTT AATTT AATTT -AATTT -AATTT -AATTT AATTT AATTT AATTT
560320 AA--T AATTT AATT
1 AATTT AATTT AATT
560332 ATTATTTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
3 3 0.07
5 27 0.59
6 16 0.35
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:560327 original size:23 final size:23
Alignment explanation
Indices: 560268--560321 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
560258 TTTGCTATTC
* *
560268 TTTAAATTT-ATTTTTATTTAAA
1 TTTAAATTTAAATTTGATTTAAA
560290 TTTAAATTTAAATTTGATTT-AA
1 TTTAAATTTAAATTTGATTTAAA
560312 TTT-AATTTAA
1 TTTAAATTTAA
560322 TAATTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.24
22 14 0.48
23 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTAAATTTAAATTTGATTTAAA
Found at i:560345 original size:20 final size:18
Alignment explanation
Indices: 560306--560345 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
560296 TTTAAATTTG
560306 ATTTAATTTAATTTAATA
1 ATTTAATTTAATTTAATA
*
560324 ATTTAATTATTATTTAAATA
1 ATTTAATT-TAATTT-AATA
560344 AT
1 AT
560346 AAAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 5 0.26
20 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTAATTTAATTTAATA
Found at i:560690 original size:28 final size:30
Alignment explanation
Indices: 560618--560690 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 30
560608 TCCAATTAGT
560618 TTAATTTATTAATATTTATTATTAAAATTTTA
1 TTAATTTA--AATATTTATTATTAAAATTTTA
* * *
560650 TTAAATTT-TATATTTTTTA-TAATA-TTTA
1 TT-AATTTAAATATTTATTATTAAAATTTTA
560678 TTAATTTAAATAT
1 TTAATTTAAATAT
560691 AGATTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
27 5 0.14
28 10 0.29
29 4 0.11
30 9 0.26
32 2 0.06
33 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTAATTTAAATATTTATTATTAAAATTTTA
Found at i:560924 original size:6 final size:6
Alignment explanation
Indices: 560913--560972 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
560903 TTAACGTAAA
* *
560913 TTATAT TTATAT TTAAAAT TT-TA- ATATAT TTAATAAT TTATA- TTATAT
1 TTATAT TTATAT TT-ATAT TTATAT TTATAT TT-AT-AT TTATAT TTATAT
560961 TTATAT TTATAT
1 TTATAT TTATAT
560973 AATTAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
4 1 0.02
5 8 0.18
6 22 0.50
7 9 0.20
8 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
TTATAT
Found at i:560972 original size:17 final size:18
Alignment explanation
Indices: 560913--560972 Score: 70
Period size: 17 Copynumber: 3.3 Consensus size: 18
560903 TTAACGTAAA
*
560913 TTATATTTATATTTAAAAT
1 TTATA-TTATATTTAATAT
*
560932 TT-TAATATATTTAATAAT
1 TTATATTATATTTAAT-AT
560950 TTATATTATATTT-ATAT
1 TTATATTATATTTAATAT
560967 TTATAT
1 TTATAT
560973 AATTAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 17 0.47
18 8 0.22
19 11 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTATATTTAATAT
Found at i:560982 original size:17 final size:17
Alignment explanation
Indices: 560914--560982 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 17
560904 TAACGTAAAT
560914 TATATTTATAT--TTAA
1 TATATTTATATAATTAA
* *
560929 AAT-TTTAATATATTTAA
1 TATATTT-ATATAATTAA
560946 TA-ATTTATATTATATT--
1 TATATTTATA-TA-ATTAA
560962 TATATTTATATAATTAA
1 TATATTTATATAATTAA
560979 TATA
1 TATA
560983 AAACTATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
14 3 0.07
15 9 0.21
16 7 0.17
17 21 0.50
18 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTTATATAATTAA
Found at i:561179 original size:6 final size:6
Alignment explanation
Indices: 561170--561210 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
561160 AAAAAATTAA
*
561170 AAAAAG AAAAAGG AAAAAA AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAA
561211 CAAACATGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:561190 original size:19 final size:18
Alignment explanation
Indices: 561168--561210 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
561158 AAAAAAAATT
561168 AAAAAAAGAAAAAGGAAAA
1 AAAAAAAGAAAAA-GAAAA
561187 AAAAAAAGAAAAAGAAAA
1 AAAAAAAGAAAAAGAAAA
561205 AGAAAA
1 A-AAAA
561211 CAAACATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAGAAAA
Found at i:561295 original size:3 final size:3
Alignment explanation
Indices: 561287--561314 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
561277 AGTTGATAGT
561287 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
561315 ATCTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:562462 original size:18 final size:18
Alignment explanation
Indices: 562426--562471 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
562416 ACATGAATAT
* *
562426 AATAT-ATAAAAAATTAA
1 AATATAATACAAAATGAA
562443 AATATAATACAAAATGAA
1 AATATAATACAAAATGAA
*
562461 AAAATAATACA
1 AATATAATACA
562472 TGCATGACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (18 bp):
AATATAATACAAAATGAA
Found at i:563443 original size:15 final size:17
Alignment explanation
Indices: 563407--563449 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
563397 ATTATATATA
*
563407 TATATTAAAGATTTAAAT
1 TATAATAAA-ATTTAAAT
563425 TATAA-AAAATTTAAA-
1 TATAATAAAATTTAAAT
563440 TATAATAAAA
1 TATAATAAAA
563450 ATAGACATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
16 11 0.48
17 3 0.13
18 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TATAATAAAATTTAAAT
Found at i:563793 original size:27 final size:24
Alignment explanation
Indices: 563737--563798 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 24
563727 ATCCATATTG
*
563737 ATATTTAATATTTAAAAAATATATT
1 ATATTTAA-ATTTAAAAAATATATA
*
563762 TTATTTAAATTTAATTATAAATATATA
1 ATATTTAAATTTAA--A-AAATATATA
*
563789 ATATTAAAAT
1 ATATTTAAAT
563799 AAGATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 6 0.20
25 7 0.23
26 1 0.03
27 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTTAAATTTAAAAAATATATA
Done.